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25. GENESIS Command Reference

25.1 abort

Routine Name:   abort

Description:    Cleanly interrupts simulation in progress.

Usage:          abort

Example:        abort

Notes:          
See also: stop , step

25.2 abs

 Routine Name: abs

Description:    Returns absolute value of number.

Usage:          positive-number = abs any-number

                positive-number         returned as absolute value of
                                        any_number

                any-number              number (float or int) for which to
                                        compute absolute value

Example:        genesis >  echo { abs -22 }
                22

                genesis >  int x
                genesis >  float y
                genesis >  y = -33.333
                genesis >  echo { abs {y} }
                33.333000183
                genesis >  x = {abs {y}}
                genesis >  echo {x}
                33

Notes:          

25.3 acos

Routine Name:   acos

Description:    Returns angle (in radians) corresponding to given cosine.

Usage:          angle-in-radians = {acos cosine}

Example:        genesis >  echo { acos 1 }
                0

                genesis >  float degrees_per_radian = 360 / (2 * 3.1415926)
                genesis >  echo {{ acos 0.707} * degrees_per_radian}
                45.00865245

Notes:          
See also: cos

25.4 addaction

Routine Name:   addaction

Description:    Adds a named action to the action table used by element types.

Usage:          addaction name action_func
                addaction name id-number

Example:        addaction  NEWACTION  10
                addaction  K_squid_hh K_squid_hh_SET
                (see Scripts/tutorials/hhchan_K.g)

Notes:          Each object in a simulation is capable of performing one or
                more "actions".  An action can be described as an operation
                that an object performs on its data. Actions are defined
                within compiled functions which are attached to each object.
                (You can display a list of actions which an object can perform
                and the function(s) which perform using the showobject
                routine.)  For instance, objects of type compartment can
                perform the actions:

                RESTORE2  SAVE2  SET  CHECK  RESET  PROCESS  INIT  

                (The actions are actually performed by an underlying C
                function associated with the compartment element type.)

                You use the addaction routine to add the named action to the
                action table.  Actions are passed to the handler routines
                associated with each type of GENESIS object.  The handler is
                expected to perform the necessary actions when a given action
                type is passed to it by the simulator.

                For the most part this routine will only be used when adding
                new object types which require use of additional (non-default)
                actions already known to GENESIS.

                You use the addaction routine to define new actions to be used
                by elements.  There are a number of predefined actions 
                which are typically used by objects. PROCESS is one of them.
                New actions can be added in any object. Use the 'addaction'
                routine in the object definition script to inform the
                simulator of the new action. The case number assigned to new
                actions is relatively arbitrary as long as it does not
                conflict with the case numbers of other actions defined in the
                object.  (you should get a compiler error if there is a
                conflict). 

                When used as a GENESIS command, addaction is primarily used
                in the construction of extended objects.  It is also used as
                a library intialization command during the compilation of
                GENESIS libraries.
See also: object , Extended Objects, Defining New Objects and Commands ( NewObjects )

25.5 addalias

Routine Name:   addalias

Description:    Associates alternative name with existing GENESIS command.

Usage:          addalias alias-name command-name

Example:        addalias set setfield

Notes:          You may put a number of addalias statements in a file and
                use an include statement in the .simrc file to include the
                file when GENESIS is started.
See also: addescape

25.6 addclass

Command Name:   addclass

Description:    Adds a new class to list of currently recognized GENESIS
                element classes.

                Adds a new class tag to a given element.

Usage:          addclass [element] class-name

Example:        addclass /sine device

Notes:          The addclass routine adds a class tag to a given element
                identifying it as belonging to the given class.  Omitting
                the element defines a class name without assigning any
                element to the class.  (This is a deprecated usage which
                may not be supported in future releases).

                Objects can be grouped into named classes.  This
                grouping can be used to facilitate the specification of
                operations to be performed on functionally related
                elements.  See scheduling (e.g., the addtask
                routine, and Schedules) for an example of class use.

                Classes are simply used for grouping of related
                elements and do not alter the element functionality in
                any way.  Classes in GENESIS don't carry the full
                connotations of classes within a true object-oriented
                programming environment.  They are simply convenient
                ways of creating named groupings to which objects can be
                assigned.
See also: listclasses, deleteclass , showobject , Extended

25.7 addescape

Routine Name:   addescape

Description:    Adds an escape-key macro binding.

Usage:          addescape esc_sequence command-string [-execute] [-id string]

                esc_sequence            actual keystrokes (or representation)
                                        to associate with escape action

                command-string          string to insert in place when escape
                                        sequence is issued (should be in
                                        quotation marks if it contains blank
                                        spaces)

                -execute                flag to have command-string executed
                                        when escape sequence is called
                                        (this puts the field EXEC in the
                                        listescape table; if -exec is left
                                        out, default is REPLACE, i.e., insert
                                        command-string, unexecuted, in command
                                        line at point escape sequence is
                                        issued)

                -id string              label for this escape sequence, used
                                        typically to identify the escape
                                        sequence in user-understandable
                                        language

Example:        genesis >  addescape [15~ "/xproto" -id "F5"
                genesis >  le <F5>

                [line changes to:]

                genesis >  le /xproto
                /draw

                [associate command string 'echo "I am not a duck"' with key
                stroke sequence escape-a:]

                genesis >  addescape a "echo I am not a duck" -execute
                genesis >  <escape-a>
                I am not a duck

                [from escapelist.g file, included in startup:]

                addescape [A     <^P>                        -id "up arrow"
                addescape [B     <^N>                        -id "down arrow"
                addescape [C     <^F>                        -id "right arrow"
                addescape [D     <^H>                        -id "left arrow"
                addescape [1~    "execute movebol"   -exec   -id Find
                addescape [2~    <^I>                        -id "Insert Here"
                addescape [3~    <^D>                        -id Remove
                addescape [11~   stop                -exec   -id F1
                addescape [17~   "status -process"   -exec   -id F6
                addescape [18~   status              -exec   -id F7
                addescape [28~   "commands | more"   -exec   -id Help
                addescape [29~   step<CR>                    -id Do

Notes:          You use the addescape routine to create escape-key macros for
                commonly used command lines.  Here, the key is the key you
                will depress after the escape key, and command-string is the
                string which will be substituted into the SLI interpreter when
                the the escape sequence occurs.  (When the key is preceded by
                escape -- ctrl [ -- during keyboard input, the command-string
                is substituted.)

                A standard set of escape-key macros is specified during
                startup through the file escapelist.g.
See also: listescape

25.8 addfield

Routine Name:   addfield

Description:    Add an extended (user-defined) field to an element.

Usage:          addfield [element] field-name [-indirect element field]
                        [-description text]

                field-name      name of the new field to be added to element

                -indirect       make the field-name an alias for the a field
                                in another element

                -description    add a descriptive text string

Example:        addfield /cell/soma area -d "Area of the compartment"

Notes:          If you have a compartment, /soma, with a hh_channel
                /soma/hh_Na, then

                    addfield /soma Gk -indirect hh_Na Gk

                will add a field to /soma called Gk which is an alias for
                /soma/hh_na Gk.  Note that the path in the -indirect option
                is relative to the element to which you are adding the
                field.  The indirect element path can also be an absolute
                path.
See also: deletefield

25.9 addforwmsg

Routine Name:   addforwmsg

Description:    Forwards an incoming message to one element to another
                element.

Usage:          addforwmsg source-element message-number destination-element

                source-element  element from which the message will be
                                forwarded
        
                msg-number      number (index)  of message in message list
                                (messages are numbered from 0 up)

                destination-element
                                element to which the message will be forwarded

Notes:          The destination element must accept messages of the same
                name and with the same number of data slots as the message
                being forwarded.
See also: deleteforwmsg , showmsg , Extended

25.10 addglobal

Routine Name:   addglobal

Description:    Declares a global variable of the specified type, allowing the
                name of the global variable to be held in a string variable.

Usage:          addglobal type name [value]
                type must be one of int, float or str.

Example:

                genesis > str name = "foo"
                genesis > addglobal float {name} 5.55
                genesis > listglobals
                float           foo = 5.55
                str             name = "foo"
                (plus many others)

Notes:

Often it is useful to use a string variable name to hold the name of a
global variable.  For example, one may want to pass the name of a global
variable to a function that declares a global variable, or that sets or
returns its value.  However, normal GENESIS syntax for declarations and
assignments does not permit a variable name to be specified by a string
variable.   The routines addglobal, getglobal, and setglobal are designed
to overcome this limitation.

Note that if addglobal is used within a function definition, the declared
variable will nevertheless be global, and not local to the function.
See also: Variables , setglobal , getglobal , listglobals

25.11 addmsg

Routine Name:   addmsg

Description:    Establishes message links between two elements.

Usage:          addmsg source-element dest-delement msg-type [msg-fields]

Example:        addmsg  /cell/dend /cell/soma      RAXIAL Ra previous_state
                addmsg  /cell/soma /cell/dend      AXIAL  previous_state
                addmsg  /cell/soma /graphs/Vmgraph PLOT   Vm *voltage *red

Notes:          addmsg sets up communication links to pass information
                between elements.  Messages flow along message links created
                by the addmsg routine each time a simulation timestep is
                executed.

                For example, an asymmetric compartment connected to another
                asymmetric compartment needs to send both its axial
                resistance, Ra, and its membrane potential at the previous
                simulation step to the second compartment.  In order to update
                its state, it needs to receive the second compartment's
                previous membrane potential.
See also: deletemsg , showmsg , getmsg , gen3dmsg, dd3dmsg

25.12 addmsgdef

Routine Name:   addmsgdef

Description:    Adds a new message type allowing messages of that type
                to be added to the element.

Usage:          addmsgdef element message-name [message-arguments...]
                 -type message-type

                element         element for which to add the message
                                definition
        
                message-name    name of the message (the convention is
                                to use all upper case)

                messages-arguments
                                zero or more names for the data slots
                                of the message

                -type           option to set the message type number
                                explicitly
                                
Notes:          It is normally unnecessary use the -type option as
                addmsgdef assigns an unused message type number
                automatically. -type should be necessary only for
                specifying active messages.
See also: deletemsgdef , showobject , Extended

25.13 addobject

Routine Name:   addobject

Description:    Adds a new object to GENESIS defined by the fields, message,
                actions and class tags of the given element.  The element
                is removed and used as a prototype for initial field values
                of new elements created from the new object.

Usage:          addobject object-name element -author author-info
                 -description descriptive-text ...

                object-name     the new name for the object

                element         element from which to create the new object
        
                -author         Information about the author of the object

                -description    A description of the object; multiple
                                arguments to -description may be given
                                resulting in multiple lines of descriptive
                                text

Notes:          The object name must not be the same as an existing
                object.  Currently, there is no corresponding
                deleteobject command.
See also: listobjects , showobject , Extended

25.14 addtask

Routine Name:   addtask

Description:    Adds a simulation event to the simulation schedule.

Usage:          addtask function [arguments...]

                function        a compiled C function to be executed at each
                                step in the simulation phase according to its
                                order in the schedule table (almost always,
                                this fucntion will be "Simulate")

                arguments       arguments for the specified function

                [practically speaking this means:]

                addtask Simulate path -action action-name

                path            path specification of elements affected
                                (typically a wildcard path designation
                                with a CLASS-conditioned selection to
                                identify all elements of a specific type)

                action-name     action to perform on specified elements
                                (usually INIT or PROCESS; must be a valid
                                action, as determined by listactions)

Example:

        addtask  Simulate /##[CLASS=myclass]  -action PROCESS
        addtask  myfunction  myargs

        from startup/schedule.g:]

        deletetasks
        addtask Simulate /##[CLASS=buffer]      -action INIT
        addtask Simulate /##[CLASS=segment]     -action INIT
        addtask Simulate /##[CLASS=device]      -action INIT
        addtask Simulate /##[CLASS=buffer]      -action PROCESS
        addtask Simulate /##[CLASS=projection]  -action PROCESS
        addtask Simulate /##[CLASS=spiking]     -action PROCESS
        addtask Simulate /##[CLASS=gate] -action PROCESS
        addtask Simulate /##[CLASS=segment][CLASS!=membrane][CLASS!=gate]\
            [CLASS!=concentration][CLASS!=concbuffer] -action PROCESS
        addtask Simulate /##[CLASS=membrane]    -action PROCESS
        addtask Simulate /##[CLASS=hsolver]     -action PROCESS
        addtask Simulate /##[CLASS=concentration]       -action PROCESS
        addtask Simulate /##[CLASS=concbuffer]  -action PROCESS
        addtask Simulate /##[CLASS=device]      -action PROCESS
        addtask Simulate /##[CLASS=output]      -action PROCESS
        resched

Notes:          GENESIS provides a default simulation schedule that handles
                most simulation configurations (see above), but for your
                simulation you may need to specify a different order in which
                the simulator should process elements in the simulation.  You
                use addtask to enter simulation events to the simulation
                schedule.  

                You must be careful to avoid multiple references to elements
                with the same action. For instance, given a model containing
                the six elements /test[1-6], the following schedule would be
                an invalid specification since it would cause test[1] to be
                invoked twice on each simulation step.

                  addtask Simulate  /test[1]    -action PROCESS
                  addtask Simulate  /test[1-6]  -action PROCESS

                With broad path specifications, it is easy to accidentally
                include multiple reference. However, you can check for these
                occurrences by running the check routine.  In the above case,
                calling check after entering the above specifications would
                generate the following message:

                  ** Error - '/test[1]' multiply invoked
                    with action 'PROCESS'. Check task [2]

                Task [2] refers to the second addtask command. This
                command was responsible for the conflict.

                Alternately, not scheduling all enabled elements (see enable)
                for simulation is detected as an error by the check routine.
                For instance, given the model of six elements used above, you
                might define a schedule with one addtask call as follows:

                  addtask Simulate  /test[1-5]  -action PROCESS

                Running check would produce the following message:

                  * Warning - '/test[6]' is not scheduled for simulation.

                A valid schedule for this set of elements might be:

                    addtask Simulate  /test[1]  -action PROCESS
                    addtask Simulate  /test[2-6]  -action PROCESS

                or

                    addtask Simulate  /test[1-6]  -action PROCESS

See also:       <href id="Schedules">, <href id="resched">,
<href id="deletetasks">, <href id="showsched">, <href id="check">

25.15 argc

Routine Name:   argc

Description:    Returns argument count (number of arguments passed to a
                function).

Usage:          int-value = {argc}

Example:        if ({argc} > 3)
                        echo usage:  foo a b c
                        return
                end

Notes:          
See also: argc , argv , getarg , printargs

25.16 arglist

Routine Name:   arglist

Description:    Converts list of items into an argument list.

Usage:          arglist string

Example:
                genesis >  str s ="a b c d"
                genesis >  echo { getarg {arglist {s}} -arg 3}
                c

                str s
                str thingys = "foo bar baz"
                foreach s ({arglist {thingys}})
                    echo {s}
                end

Notes:          In each of these examples, a single string consisting of
                items separated by spaces has been converted into a list.
See also: argc , argv , getarg , printargs

25.17 argv

Routine Name:   argv

Description:    An array of strings containing the arguments passed to
                a function.

Usage:          argv position-number

Example:        

function echoargs
    int i
    echo "Number of arguments = "{argc}
    for(i=1;i<= {argc};i=i+1)
        echo {argv {i}}
    end
end

genesis > echoargs foo 5 1.23
Number of arguments = 3
foo
5
1.23

Notes:          As with C, indices of argv should start with 1.
See also: argc , arglist , getarg , printargs

25.18 asciidata

Routine Name:   asciidata

Description:  
    Converts a FMT1 formatted binary file (as produced by the
    disk_out object, for example) to ASCII.  Output is to stdout.

Usage: 
    asciidata file-name -time t -cell cell -gain g -old -xy -skip n -header
    One of options -cell, -time or -header must be given.

Example: (using the horiz_disk file from Scripts/orient_tut)

genesis > asciidata horiz_disk -header
FMT1
start time           = 0.000000e+00
time step            = 1.000000e-05
cellnum              = 25
data type            = 4
data size            = 4

genesis  > asciidata horiz_disk -cell 24 | more
-7.006086e-02
-7.012120e-02
.
.
-7.597300e-02
-7.596859e-02
//(provides Vm at each time step; adding -xy option gives t and Vm)

genesis > asciidata horiz_disk -time 1.e-4 -xy
0       -0.0706427
1       -0.0706427
2       -0.0706427
.
.
23      -0.0706427
24      -0.0706427
//(cell number and Vm for each of the 25 cells)
See also: disk_out

25.19 asin

Routine Name:   asin

Description:    Returns angle (in radians) corresponding to given sine.

Usage:          angle-in-radians = {asin sine}

Example:        genesis > echo {{ asin 0.5 }*(180/3.1415926)}
                30.00000135

Notes:          
See also: sin

25.20 atan

Routine Name:   atan

Description:    Returns angle (in radians) corresponding to given tangent.

Usage:          angle-in-radians = {atan tangent}

Example:        genesis >  echo { atan 0.876 }

Notes:          
See also: tan

25.21 call

Routine Name:   call

Description:    Allows an element to execute the function associated with the
                named action.

Usage:          call path action [args...] -parent -virtual

-parent         call the action on the element using the parent object
                of the current object context as the new object
                context

-virtual        call the action on the element using the element's
                object as the object context during the action.

Example:        call /form/graph RESET
                call /form/graph/plot ADDPTS {x} {y}

Notes:          The call routine allows the user to send an action to an
                element's handler routine (outside of the simulation cycle).

                An action executes in the context of a specific object which
                is either the element's object or some base object for the
                element.  The object context determines what fields,
                actions, messages and classes are known and accessibility of
                fields during execution of the action function.  Without any
                other options to call, the object context during the call is
                the element's object or the current object context if the
                element is already executing an action.  The -parent and
                -virtual options modify this.  These options are to be used
                when an action is called within the function definition of
                an action to be added with the addaction command.  They have
                no affect when used outside an action function.
See also: addaction , Extended

25.22 callfunc

Routine Name:   callfunc 

Description:    Allows you to call a function whose name is stored in a
                string variable.

Usage:          callfunc funcname ...

Example:        genesis  > str foo = "echo"
                genesis  > callfunc {foo} a b c
                a b c

Notes:          

See also:       

25.23 cd

Routine Name:   cd

Description:    Changes current working operating system directory.

Usage:          cd directory

Example:        genesis >  cd /usr/genesis/Scripts/neuron

Notes:          This is a GENESIS implementation of the operating system
                command cd, to assure that any change you make in the working
                directory is known to GENESIS.  (If you just issued a normal
                cd command directly, via "sh cd" for instance, the
                change in the current working directory would last only as
                long as the subshell created to enact the command, and future
                actions in GENESIS would not recognize a change.  The GENESIS
                implementation of cd fixes this.)
See also: sh

25.24 ce

Routine Name:   ce

Description:    Changes the current working element.

Usage:          ce element-path

                element-path    complete or relative pathname of element to
                                make current working element; can also be
                                operating-system style hierarchy
                                abbreviations, such as . (current),
                                .. (element above current)

Example:        ce /
                ce /proto
                ce output
                ce ..

                genesis >  create compartment foo
                genesis >  ce ^
                genesis >  pwe
                /foo
        
Notes:          All GENESIS elements exist in a hierarchy.  The root element
                lives at the top of the tree (designated by /) and child
                elements are created beneath the root.  You use the ce routine
                to move about the tree (much as you can use the "cd" command
                to move about the operating system file system).

                If the element-path specified in a ce call starts with a /
                then the path is assumed to be an absolute path from the root
                of the element hierarchy.  If the first character of the path
                specified is not a / then the path is assumed to be relative
                to the current working element.
See also: pwe , le , pushe , pope , stack

25.25 cellsheet

Routine Name:   cellsheet

Description:    Copies prototype cells into a 3-D sheet specified by
                coordinates in a file.

Usage:          cellsheet prototype dest filename [-orient][-curve]
                        [-randomise x y z] [-twirl theta]

                prototype       existing cell to copy to create cells in the
                                sheet (prototype is not changed by the
                                routine; all operations are done on the
                                copies)

                destination     element to become parent of all cells in sheet

                filename        file defining position and orientation of
                                cells (ascii file with 3 numbers for each
                                coordinate (cartesian only), followed by 3
                                coordinates for the normal vector to the
                                surface of the sheet at that point; this
                                vector does not have to be normalised; each
                                set of 6 numbers should be on different lines)

                -orient         reorients the cell to be normal to the local
                                region of the sheet

                -curve          distorts copies of prototype cell to follow
                                curvature of sheet of cells; the lengths (and
                                electrical properties) of the cell are not
                                changed (this option assumes that length of
                                each compartment is less than the radius of
                                curvature of the surface; also, the sampling
                                density over the cell sheet should be high
                                enough that the spacing between the points is
                                smaller than the length of each compartment;
                                does not attempt to curve compartments where
                                the angle of rotation would be less than 10
                                degrees, or more than 60)

                -randomise x y z
                                randomises the coordinates of copied cells by
                                the specified factors in x, y and z before the
                                orienting/positioning/curving steps
                                (randomisation involves finding length of each
                                compartment in each direction, scaling it by a
                                random number within the range of the
                                specified factor, and adding it to the
                                original; e.g., a factor of 1 would permit a
                                change of up to the original length of the
                                compartment; the electrical properties and
                                channel conductances in each compartment are
                                scaled according to the total length change)

                -twirl theta    rotates the finally positioned cell about its
                                normal by a random angle from 0 to theta
                                degrees

Example:

include protodefs.g // copied from Scripts/tutorials
readcell cell.p /library/cell  // use cell.p from Scripts/tutorials

plane planepoints 400e-6 400e-6 100e-6 100e-6 -normal
egg eggpoints 400e-6 400e-6 400e-6 100e-6 -normal

create neutral /planenet
create neutral /eggnet

rotcoord /library/cell {-3.1415927/2} -y  // point dendrite up along z-axis

cellsheet  /library/cell /planenet planepoints -orient
cellsheet  /library/cell /eggnet eggpoints -orient

showfield /planenet/cell[]/dend x y z

Notes:          Creates a sheet of cells by copying from a prototype, and
                placing them at 3-D positions specified by an ascii file. A
                number of options permit the cells to be oriented, conformed
                to the curvature of the surface, randomised, and rotated, in
                order to make the geometry more natural. 

                In the example above, the prototype cell had the apical
                dendrite pointing along the x-axis, so rotcoord was used to
                rotate it 90 degrees about the y-axis to point outward along
                the z-axis.  Then, cellsheet was used, first on a file
                containing points in a plane, and then on a file containing
                points distributed over the surface of an ovoid.  In both
                cases, the orient option was used to point the dendrite along
                the outward normal to the surface.

25.26 check

Routine Name:   check

Description:    Checks various aspects of simulation to catch specification
                errors.

Usage:          check

Example:        check

                genesis >  setfield /soma Rm -5000 Cm 0
                genesis >  check
                ** Error - Compartment : Invalid Rm. '/soma'
                ** Error - Compartment : Invalid Cm. '/soma'

Notes:          The check routine sends the CHECK action to the handlers for
                all enabled elements.  The CHECK action should verify the
                consistency and well being of the element and report any
                problems with it to the user.  (Each element which supports
                self-checking will be invoked with the CHECK action and report
                any problems.)

                In the example above, the CHECK action of the compartment
                checks to be sure that the Rm and Cm fields are set to
                positive values, and running a check prints an error message.
See also: addtask , setclock , enable , reset

25.27 chr

Routine Name:   chr

Description:    Returns ASCII character specified by number code.

Usage:          character = {chr ASCII-number}

Example:        genesis >  echo { chr 64 }
                @
                genesis > echo {chr 65}
                A
                genesis > echo {chr 97}
                a

Notes:          

25.28 clearerrors

Routine Name:   clearerrors

Description:    Resets error count to 0.

Usage:          clearerrors

Example:        clearerrors

Notes:          When the number of errors reaches its maximum value (default:
                10 syntax errors or 20 warnings) the current action is
                interrupted, the simulator goes back to the command line, and
                the errors are reset.  The clearerrors routine can be used to
                reset the error count before this occurs, allowing a
                simulation to continue running despite errors.
See also: maxerrors , maxwarnings

25.29 closefile

Routine Name:   closefile

Description:    Closes an ASCII file opened with the openfile routine.

Usage:          closefile filename

Example:        openfile myfile w
                writefile myfile 10 20 30
                closefile myfile

Notes:          When you open a file using openfile, you work on a copy of
                the file.  The closefile routine writes your changes back
                into the actual file and eliminates it from the list of open
                files.  (Closefile is automatically called for all opened
                files when you exit from GENESIS).
See also: openfile , listfiles , writefile

25.30 convert

Converting GENESIS 1.4 Scripts to GENESIS 2.0

What Does Convert Do?

GENESIS 2.0 includes a major revision of command format and command
option naming, script language syntax changes and changes in various
GENESIS features.  The convert program converts GENESIS 1.4 compatible
scripts to use GENESIS 2.0 syntax, commands and features.  Some
features have changed dramatically enough that an automatic conversion
to the new features is not feasible.  In these cases, convert generates
script code for compatibility libraries which support the GENESIS 1.4
features.

Some scripts can be converted and run successfully without any manual
changes to the converted scripts.  In most cases, however, some changes
to the converted scripts will be necessary.

The Conversion Process

Below is the process through which a GENESIS 1.4 script is converted
to run under GENESIS 2.0.

        1 - Use the convert program to convert scripts from 1.4 to
            2.0 syntax.

        2 - Fix any known problem areas (See, Convert Problem Areas).

        3 - Try the script out and fix any remaining problems.

Using the Convert Program

The easiest way to use convert is to create a new directory for the new
scripts, cd to the new directory and convert the files from the old
directory.  A simple shell procedure may be used to convert an entire
directory.  For example, if your 1.4 script files are in the directory
../oldscript, then the following shell commands will convert the entire
directory placing the converted scripts in the current working
directory:

  csh:
        foreach script (../oldscript/*.g)
            convert $script
        end

  sh:
        for script in (../oldscript/*.g)
            convert $script
        end

Global Script Variables

In order for convert to handle certain script expressions involving
global script variables, it must know what globals exist for a given
set of scripts.  (This is not a problem for a self contained script
where global variables are defined and used within the script.)
Often a single script file is devoted to defining and initializing
global variables and constants for a given set of scripts.

The -constants option of the convert program gives a list of script
files which define the global variables for the script set.  For
example, if the file constants.g contains global variable definitions
which are used througout a set of scripts in the ../oldscripts
directory then the following csh code would convert the scripts:

        foreach script (../oldscripts/*.g)
            convert $script -constants ../oldscripts/constants,g
        end

The -constants option will allow one or more scripts to be given.

Compatibility Libraries

Two areas of major change in GENESIS 2.0 are the Xodus GUI and support
for network modeling (e.g. GENESIS 1.4 connections).  Support for use
of these facilities in GENESIS 2.0 is provided by compatibility
libraries.

While the compatibility libraries allow faster conversion of GENESIS
1.4 scripts for use under GENESIS 2.0, these libraries will not be
aggresively supported and should be viewed as a transitional step in
converting scripts to GENESIS 2.0 facilities.  Those areas of your
scripts which use these libraries should eventually be recoded to use
the new GENESIS 2.0 features.  Assistance for recoding of these
features may be found in the new GENESIS 2.0 Reference Manual (not
available at this time).

The X1compat Library

Compatibility for GENESIS 1.4 features of Xodus is provided as a set of
scripts using GENESIS 2.0 extended objects to implement the old Xodus
objects and script functions to implement old Xodus commands.  To load
the X1compat library, include Scripts/X1compat in your SIMPATH and
include X1compat from your .simrc or your main simulation script.
Convert will not add an include statement for X1compat to your
scripts.

X1compat defines a set of old Xodus compatible objects which are named
using the prefix "x1" in place of the normal "x" prefix for Xodus
objects (e.g. xform becomes x1form, etc).  Convert will automatically
transform create statements from Xodus objects in 1.4 scripts to use
the X1compat objects.  Some support for field naming of old Xodus
objects is included in the new Xodus objects, which may allow direct
use of the new Xodus objects.  The -noX1compat convert option causes
convert not to perform the translation to X1compat objects.  This is
likely to be useful for only those scripts which use the basic Xodus
widgets (i.e. xform, xlabel, xbutton, xtoggle and xdialog).  Uses of
xdraw or xgraph are likely to require use of X1compat.

Convert and the X1compat library cannot address various issues of
layout of widgets on a form.  See, Convert Problem Areas, for more
information.

The Connection Compatibility Library

While GENESIS 1.4 connections are not a standard part of GENESIS 2.0, a
compatibility library may be compiled into GENESIS 2.0 which supports
the old connection feature.  (See, src/Makefile or Usermake for
instructions on including the library.) The library defines the
connection related objects (e.g. axon, synapses, etc) and the
connection related commands (e.g. region_connect, expweight,
radialdelay, etc) as well as connection specific commands which support
set/get/show of connections (e.g. setconn, getconn and showconn).
Access to connection fields is not supported by the GENESIS 2.0
setfield, getfield and showfield commands.

Convert will change connection related script statements as needed to
use the Connection Compatibility Library.  In particular, it will
convert uses of set, get and show on connections to use setconn, et
al.  In some cases, convert will be unable to convert these statements
(See, Convert Problem Areas).

Converting User Libraries

Objects and commands defined in user libraries (for the most part) will
not need to change to run under GENESIS 2.0.  To compile your libraries
and create a new GENESIS you will need to replace and update your
Usermake, Libmake(s), liblist and perhaps the library startup script.

Copy the Usermake and liblist files from the GENESIS 2.0 installation
directory to your local GENESIS directory renaming Usermake to
Makefile.  Add your user libraries to the Makefile and liblist files.

In each user library you must copy the Libmake from the GENESIS 2.0
installation directory into the library directory renaming it
Makefile.  Add your library specific information and files to the
Makefile.

The convert program cannot be used to convert startup scripts.  The
only changes you should need to make are to modify any GENESIS 1.4
script language features which change in 2.0 and to remove any
non-startup commands from the script.  (Startup commands are object,
addfunc, hashfunc, newclass and addaction.) Since a startup script is
usually straight line code and the typical commands in a 1.4 startup
script are the above named commands, there are normally no changes
required.  There are, however, some GENESIS 2.0 features you may want
to take advantage of in your startup scripts.  See the new GENESIS
Reference Manual section on library startup scripts for details.

Convert Problem Areas

There are a number of areas in which convert will be unable to
transform script statements or where the converted code will perform in
a less than optimal manner.  Each problem area described below must be
found and fixed manually.

Script Callbacks

Commands used as callbacks to script commands or functions are not
translated by convert.  As such, script callbacks like the following
would fail:

        create xbutton echoButton -script "echo -n this is a test"
        create xdialog vmDialog -script "set /mycompt Vm <v>"

The echoButton will result in a usage error when pressed and the
vmDialog will fail because the set command no longer exists.

Command Options in Script Variables

A command option which is passed to a command through a script variable
or as the result of a command or script function will not be
translated.  For example, if leoptions is a script string variable
holding the value "-R" (a recursive listing), then the following code
will not be converted:

        le {leoptions}

The code which sets leoptions must be found and changed.

Command Arguments That Look Like Options

All GENESIS 2.0 commands check for valid command options and complain
when an unkown option is given.  As a result, code like

        echo -notAnOption

will result in a usage error.  This will also be the case if a script
variable value looks like an option, e.g.

        str echoOption = "-notAnOption"
        echo {echoOption} // Usage error!

The usage statement can be avoided by placing whitespace before the
value, e.g.

        echo " -notAnOption"
        echo " "{echoOption}

Set/Get/Show Connections in Script Variables

Commands like

        set anElm:0 weight 10

will be correctly translated to use the setconn command.  However, code
like

        str connelm = "anElm:0"
        set {connelm} weight 10

will be translated to a setfield command.  Convert behaves similarly
with translating the get and show commands.

Script Variable/Command Name Conflicts

With all the command name changes in GENESIS 2.0, it is possible that a
script variable in a GENESIS 1.4 script may coinside with a new GENESIS
2.0 command name.  In this case, you may receive a syntax error or
unexpected result as the script variable will take precedence over the
command name.  This is may be particularly likely with the el command.

(The convert program may be updated at some future point to rename
 script variables which clash with GENESIS 2.0 command names.)

Setting Integration Methods

GENESIS 2.0 removes some of the previously existing integration methods
and renumbers some of the remaining methods.  Convert will handle the
renumbering as long as a number is given directly to the setmethod
command.  If this is not the case, convert will issue a warning and the
command will be left unaltered.  You must change the integration
numbering manually.  See setmethod.txt (or type "help setmethod" in
GENESIS) for the new numbering.

Sizing of Xodus Forms

XODUS 1 made use of an unsupported feature of MIT X11 which allowed
forms to automatically adjust their height to accomodate all the
widgets which they contain, even if the form was made too short.
Although this did not work under Openwindows, it allowed users of MIT
X11 to be somewhat sloppy in the sizing of forms when writing scripts.
This feature no longer exists in XODUS, so forms which are incorrectly
sized may not show all the widgets which they contain.  The most
convenient way to detemine the proper hgeom for the form is to properly
resize it with the mouse and then inspect the hgeom field for the value
to use in your script.

Apart from the preceeding issue, forms previously large enough to
encompass a given set of widgets may not be large enough under GENESIS
2.0, as the border widths of XODUS object have increased.

Positioning and Sizing of Widgets

Scripts which explicitly set the dimensions of a widget based on the
expected dimensional requirements of a 1.4 widget may cause text or
graphics within the widget to be clipped under 2.0.  This is due to the
additional requirements of the Motif style borders.

Likewise, widgets which are positioned using absolute coordinates on
the form based on expected default dimensions of other widgets on the
form may overlap other widgets on the form.

The only widget layouts used under GENESIS 1.4 which are likely to work
well under 2.0 are those using relative positioning.  Even if this is
the case, the form size may need to be changed (See Sizing of XODUS
Forms above).

25.31 copy

Routine Name:   copy

Description:    Copies an element (and its children, if any) from one portion
                of the element tree to another.

Usage:          copy src-element dest-element -repeat # -autoindex

                src-element     element to copy (if this element has
                                subelements, they too are copied)
                
                dst-element     location into which to copy src-element (if
                                dst-element already exists, src-element is
                                copied beneath it with original name; if
                                dst-element does not exist, copy of
                                src-element is given that name as new name)

                -repeat         is followed by an integer specifying how
                                many duplicates of src-element to make

                -autoindex      automatically assigns the first free element
                                index to the newly created element.

Example:        copy /cell1 /cell2

                // create 5 cells, cell[0-4]
                copy /library/protocell /cell[0] -repeat 5

Notes:          This routine copies an element and its children, without
                changing the original.

                Simulation messages and connections between elements within
                the copied subtree will be copied, but messages and
                connections to elements outside of the copied subtree will not
                be copied.

                After it has copied the object, the copy routine issues the
                COPY action for that element type, if any.
See also: create , createmap , move

25.32 cos

Routine Name:   cos

Description:    Returns cosine for given angle (specified in radians).

Usage:          cosine = {cos angle-in-radians}

Example:        float x
                x = {cos {3.14159/4}}

Notes:          
See also: acos

25.33 countchar

Routine Name:   countchar

Description:    Counts occurrences of specified character in string.

Usage:          number-of-occurrences = {countchar string char}

                number-of-occurrences   returned as integer indicating how
                                        many occurences of char were found
                                        in string

Example:        genesis >  echo {countchar "abcbdb" b}
                3

Notes:          

25.34 countelementlist

Routine Name:   countelementlist

Description:    Returns the number of elements in an element list.

Usage:          countelementlist path [-listname listname]

                path         path specification, which may include
                             wildcards such as [] or #  (note,
                             however, that operating-system style
                             use of * is not supported)

                listname     The listname argument tells it to look for the
                             field <listname> on the element in <path> and
                             treat that as an element list.

Example:

                genesis > echo {el /#}
                /proto /output /cell /control /data

                genesis > echo {countelementlist /#}
                5

                genesis > echo {countelementlist /##}
                19

Notes:
See also: el , Tree

25.35 cpu

Routine Name:   cpu

Description:    Displays current cumulative cpu usage for user and system time.

Usage:          cpu

Example:        genesis >  cpu
                user time used          = 3 sec  510000 usec
                system time used        = 1 sec  180000 usec

Notes:          This routine calls the getrusage operating system command to
                display user/system usage statistics.
See also: showstat

25.36 create

Routine Name:   create

Description:    Creates new element of specified element type.

Usage:          create element-type name -autoindex [object-specific-options]

                element-type    type of element; must be one of the valid
                                element types (objects) compiled into the
                                genesis executable, or an extended object
                                created with the GENESIS scripting language.

                name            element or path name where new element is to
                                be attached in the GENESIS element hierarchy;
                                if single name is given (i.e., no path
                                separators "/"), element is created on the
                                current working element [also can be indexed;
                                see below]

                -autoindex      automatically assigns the first free element
                                index to the newly created element.

                [options]       some elements can be created with additional
                                options which are specific to the object type
                                (see individual object documentation for
                                options)

Example:        create neutral /cell
                create compartment /cell/soma
                create xgraph voltage_plot

Notes:          The create routine is used to create new elements in the
                GENESIS element tree.  It generates an element of type
                "element-type" and places it in the element tree with the
                assigned name.

                The additional options which can be specified for the create
                routine depend on the element-type being created.  For
                example, elements which represent graphical widgets contain
                data fields for screen information such as the position and
                dimensions of the graphical object. This information may
                also be specified as an option in the creation of an element.

                    create compartment soma[0]
                    create compartment soma[1]
                    create compartment soma[10]
                    create compartment soma -autoindex

                In the example above, he name field of each element will be
                "soma" but the index fields will have values 0-2 and 10.
                The "-autoindex" option in the last statement creates the
                element with index 2.  Note that soma and soma[0] are
                equivalent i.e. the absence of an index implies an index of
                0 (the default).  Also note that the index is an arbitrary
                value and does not need to follow any order.
See also: listobjects , showobject , le

25.37 createmap

Routine Name:   createmap

Description:    Copies an element multiple times to form a two-dimensional
                array.

Usage:          createmap source dest Nx Ny -delta dx dy -origin x y -object

                source          path to the element that will be copied

                dest            pathname of the parent of the array of copies

                Nx,Ny           number of elements in the x and y dimensions
                                of resulting array

                dx,dy           distance between adjacent elements in the
                                array in x and y dimensions, in world or
                                actual coordinates (default: 1,1)

                x,y             position of first element of array (i.e.,
                                corner of array, in world coordinates
                                (default: 0,0)

                -object         indicates that the source is the name of
                                an object, rather than the path to an element

Example:        createmap /prototypes/cell /map 10 10
                createmap mycell  /network 3 5 -delta 0.1 0.2 -object

                [from /usr/genesis/Scripts/orient_tut/retina.g:]

                genesis > createmap /library/rec /retina/recplane \
                    {REC_NX}   {REC_NY} \
                    -delta  {REC_SEPX} {REC_SEPY}   \
                    -origin {-REC_NX * REC_SEPX / 2} {-REC_NY * REC_SEPY / 2}
                genesis > le /retina/recplane
                rec[0-99]/

Notes:          The createmap routine creates a two-dimensional array of the
                specified source element by making copies of the source
                element and assigning the copies x,y coordinates within the
                specified bounds.  The resulting array is placed under the
                specified destination path.  As with the copy command, the
                entire tree of child elements and messages is copied along
                with the source element.  When the "-object" option is
                used, the source is the name of a GENESIS object, instead of
                the path to an element tree.  This is most useful when a
                prototype cell is created as an extended object composed from
                a combination of basic objects with added fields and default
                values.

                The resulting array coordinates can be used by routines such
                as planarconnect, planarweight, and planardelay to assign
                connections, synaptic weights and propagation delays for
                simulation-oriented elements.  The coordinates can also be
                used to display the cells in a draw widget.
See also: copy , planarconnect , planarweight , planardelay , Extended

25.38 debug

Routine Name:   debug

Description:    Sets (or displays) the debug level used by some routines.

Usage:          debug [level]

                level           integer indicating debug level to use:
                                 0 = disable debug (nothing printed)
                                 1 = intermediate debug
                                 2 = intermediate debug
                                 3 = full Debug (print everything)

Example:        genesis >  debug
                debug level 0
                genesis >  debug 2
                debug level 2

Notes:          Sets the debug level used by some routines to report status
                information.  Increasing the level typically increases the
                amount of information produced. If no argument is given the
                current debug level is displayed.
See also: silent

25.39 delete

Routine Name:   delete

Description:    Deletes an element and all of its children.

Usage:          delete  element

Example:        delete /neuron

Notes:          The delete routine is used to delete elements from the GENESIS
                element hierarchy.  Deleting an element which has children
                attached to it will also delete all of the child elements.

                In the course of deleting the object, the delete routine also
                issues the DELETE action for the object before it is
                eliminated.

                When deleting interpol_structs that share tables between them
                (e.g. tabchannel, tab2Dchannel, or tabcurrent), or the cells
                or compartments containing them, you must call TABDELETE
                first, in order to deallocate the memory for the tables.
                Finally, you have to give the "reclaim" command for the memory
                to actually be freed.  Note that the tables are shared among
                all copies of the interpol_struct that are created by copy or
                readcell from a prototype.  Therefore, you shouldn't call
                TABDELETE unless you plan to delete all copies of the
                interpol_struct.
See also: create , reclaim

25.40 deleteaction

Routine Name:   deleteaction

Description:    Deletes an action from an element added by a previous
                addaction command

Usage:          deleteaction element action-name

                element         element to delete the action from
        
                action-name     name of the action to delete

Notes:          An object's built in actions are permanent and may
                not be deleted using deleteaction.
See also: addaction , listactions, Extended

25.41 deleteall

Routine Name:   deleteall

Description:    Deletes all existing elements.  [not recommended]

Usage:          deleteall -force

                -f              flag to force deletions

Example:        genesis > deleteall
                
                *** WARNING ***
                This function removes all elements from the simulation.
                If you really want to do this use 'deleteall -force'.

                usage: deleteall -force

                genesis > deleteall -f
                Simulator cleaned out.

Notes:          If no flags are specified, deleteall displays a warning
                message.

                The deleteall routine can be used to return the simulator to
                a startup state by deleting all existing elements, including
                elements which may be provided by default at startup.  If
                this is done, running the simulation scripts again could
                produce different results.

                If you really need to delete all the elements in your GENESIS
                session, you might as well quit exit from GENESIS completely
                and start again -- deleteall just deletes all the elements
                and might not reset other parameters to appropriate values.

                In general, you should not use the deleteall routine.
See also: delete

25.42 deleteclass

Routine Name:   deleteclass

Description:    Delete a class tag from an element which was previously
                added using addclass.

Usage:          deleteclass element class-name

                element         element from which to delete the class

                class-name      name of the class to delete
        
Notes:          Deleteclass will not delete classes defined for the
                built in objects.
See also: addclass , listclasses, Extended

25.43 deletefield

Routine Name:   deletefield

Description:    Deletes an extended field which has been added to an element.

Usage:          deletefield [element] field-name

Example:        genesis > addfield /soma area
                OK
                genesis > deletefield /soma area
                OK
                genesis > deletefield /soma inject
                deletefield: Cannot delete permanent field 'inject' on element '/soma'

Notes:          Only added extended field may be deleted with deletefield.
See also: addfield

25.44 deleteforwmsg

Routine Name:   deleteforwmsg

Description:    Deletes a forwarded message previously forwarded using
                addforwmsg.

Usage:          deleteforwmsg source-element message-number destination-element

                source-element  element from which the message was
                                forwarded
        
                msg-number      number (index)  of message in message list
                                (messages are numbered from 0 up)

                destination-element
                                element to which the message was forwarded

Notes:          The destination element must accept messages of the same
                name and with the same number of data slots as the message
                being forwarded.
See also: addforwmsg , showmsg , Extended

25.45 deletemsg

Routine Name:   deletemsg

Description:    Deletes a message link between two elements.

Usage:          deletemsg element msg-number -incoming -outgoing
                        -find srcelem type

                element         element receiving or sending the message

                msg-number      index of message in element message list
                                (index can be obtained with 'showmsg'
                                routine, or, in a script, with 'getmsg' used
                                with the -find option)

                srcelem         element sending the message

                type            message type (PLOT, AXIAL, VOLTAGE, etc.)

                -incoming       message to be deleted is incoming

                -outgoing       message to be deleted is outgoing

                -find           delete the first message (lowest index)
                                matching the srcelem and type

Example:        deletemsg /cell/soma 2 -incoming

                deletemsg /data/voltage -in 0 -find /cell/soma PLOT

Notes:          The deletemsg routine is used to remove messages added using
                the addmsg routine.  Deleting earlier messages will change
                the message numbers of the remaining messages.  If
                msg-number is not known for the desired message, it may be
                found by using getmsg with the -find option.

                When the -find option of deletemsg is used, the msg-number
                argument is required, but ignored, and the message must be
                an incoming one. (The -incoming and -outcoming options are
                ignored, if specified.)
See also: addmsg , showmsg , getmsg

25.46 deletemsgdef

Routine Name:   deletemsgdef

Description:    Deletes a message definition previously added to an element
                using addmsgdef.

Usage:          deletemsgdef element msg-name

                element         element from which to remove the message
                                definition
        
                msg-name        name of the message type to delete

Notes:          Deletemsgdef will not delete permanent message definitions
                defined by the built in objects.
See also: addmsgdef , showobject , Extended

25.47 deletetasks

Routine Name:   deletetasks

Description:    Removes all simulation events from the simulation schedule.

Usage:          deletetasks

Example:        deletetasks

Notes:          deletetasks removes from the simulation schedule table any
                functions currently scheduled for execution during simulation.
                This allows you to construct a new schedule using a sequence
                of addtask calls.
See also: Schedules , addtask , resched , showsched

25.48 disable

Routine Name:   disable

Description:    Disables an element and its children from participating in a
                simulation.

Usage:          disable  element

Example:        disable /prototypes/mitral_cell

Notes:          The specified elements are still accessible to basic
                operations such as setfield and showfield, but they will not
                participate in the simulation or be updated during the run of
                the simulation (i.e., when you use the step routine).

                You should run reset or resched after you disable an element
                to be sure that the simulation properly takes into account the
                disabling of the element.  (The resched command may be used to
                recompute the simulation schedule in order to remove the
                disabled element without resetting the simulation.  It is not
                a good idea to call resched frequently, especially for large
                simulations, as it does quite a bit of work.)

                The disable command cannot be used with script_out elements.
                If you need to disable a script_out element, it will be best
                to use a more versatile extended object, instead.  (See
                Extended.txt.)
See also: enable , step , reset

25.49 echo

Routine Name:   echo

Description:    Prints out its arguments to the console.

Usage:          echo [arguments] [-nonewline] [-format format-string]

                arguments       strings, or expressions enclosed in braces

                -nonewline      do not include carriage return at end of line

                format-string   a string of the form "%[flag][width]s", where
                                "width" is the minimum number of characters
                                to be output.  If the output width is less
                                than this, it is padded with blanks.  "flag"
                                is as in C; "0" means pad with zeroes, "-"
                                means left justify.  (to construct mixed
                                formats, use multiple echo commands with
                                -nonewline to place them on a single line)

Example:        
                genesis >  int five = 5
                genesis >  echo five
                five
                genesis > echo { five }
                5

                genesis > echo "Give me" -n; echo space! -f %20s
                Give me              space!

Notes:          The echo routine is used to print output to the command
                interpreter window.  If echo is followed by a string (or a
                quoted string) that string will be printed.  If echo is
                followed by a string enclosed in curly brackets, then the
                value assigned the variable named by the string will be
                printed.

25.50 egg

Routine Name:   egg

Description:    Generates coordinates for points on the surface of an ovoid.

Usage:          egg  filename  x  y  z  d  -normal

                filename        name for file into which to put generated
                                coordinates

                x, y, z         dimensions of the egg

                d               approximate distance between points

                -normal         "normal"; if selected, generates an
                                additional set of 3 coordinates per line,
                                to define the normal to the surface.  This
                                format is used by the cellsheet routine.

Example:        egg eggpoints 400e-6 400e-6 400e-6 100e-6 -normal

Notes:          Generates coordinates for points on the surface of an ovoid,
                (an egg) and puts them into a file, with an option for
                generating the normals at each point.  This is useful for
                generating layers of cells on an ovoid.  It tries to get
                fairly even spacing.  The coordinates are dumped into the
                file specified by filename with one set of coordinates per
                line.
See also: plane , cellsheet

25.51 el

Routine Name:   el

Description:    Returns list of elements matching wildcard specification.

Usage:          list-of-elements = el path [-listname listname]

                list-of-elements        returned as a text 

                path                    path specification, which may include
                                        wildcards such as [] or #  (note,
                                        however, that operating-system style
                                        use of * is not supported)

Example:        genesis >  echo {el /#}
                /proto /output  /net

                genesis >  echo {el /net/neuron[]}
                /net/neuron /net/neuron[1] /net/neuron[2] /net/neuron[3]
                
                genesis >  str name
                genesis >  foreach name ({el /# })
                ?  echo {name}
                ?  end
                /proto
                /output
                /net

Notes:          In GENESIS 1, this was EL or element_list.  getelementlist
                is an alias for el in GENESIS 2.

                The listname argument tells it to look for the field
                <listname> on the element in <path> and treat that
                as an element list.

25.52 enable

Routine Name:   enable

Description:    Enables previously disabled elements to participate in a
                simulation.

Usage:          enable  element

Example:        enable /neuron

Notes:          The enable routine is used to enable an element which has been
                disabled using the disable routine.

                You should run reset or resched after you enable a previously
                disabled element to be sure that the simulation state properly
                takes into account the newly enabled element.
See also: disable , step , reset

25.53 enddump

Routine name:   enddump

Description:    Cleans up at the end of a dumpfile. Normally
                generated by default in a dumpfile. Doesn't do much of
                anything outside a dumpfile.

Usage:          enddump

Example:        Here is a little dumpfile using initdump that recreates a
                simple 2-compartment model, and ignores the orphan element
                /x/y/z.

                ============================================================
                //genesis

                initdump -version 3 -ignoreorphans 1
                simobjdump neutral
                simobjdump compartment activation Vm previous_state \
                        Im Em Rm Cm Ra inject dia len initVm
                simundump neutral /x/y/z 0
                simundump neutral /a 0
                simundump compartment /a/compt 0 0 0.6632976405 0.6632942696 \
                        -0.3333315551 0 1 1 1 1 0 0 0
                simundump neutral /b 0
                simundump compartment /b/compt 0 0 0.3299660931 0.3299627243 \
                        0.3333349228 0 1 1 1 0 0 0 0
                addmsg /b/compt /a/compt RAXIAL Ra Vm 
                addmsg /a/compt /b/compt AXIAL Vm 
                enddump
                // End of dump

                ============================================================
Notes:          
See also: initdump , simdump , simobjdump , simundump

25.54 eof

Routine Name:   eof

Description:    Tests whether at end of currently opened file.

Usage:          eof-flag = {eof filename}

                eof-flag        returned as 1 if at end of file;
                                returned as 0 if not at end of file

                filename        name of open file to test

Example:
                str line
                openfile TestFile r
                line = {readfile TestFile -linemode}
                while (!{eof TestFile})
                    // process line from the file
                    echo {line}
                    line = {readfile TestFile -linemode}
                end

Notes:          The file must be currently open.
See also: openfile , listfiles , readfile

25.55 exists

Routine Name:   exists

Description:    Tests for existence of specified element or field.

Usage:          exists-flag = {exists element [field]}

                exists-flag     returned as 1 if element (or element field)
                                exists; returned as 0 otherwise

                element         name or full pathname of element to test

                field           element field to test existence of
                                (does not check whether field is nonempty)

Example:        if ({exists /cell/dendrite})
                        delete /cell/dendrite
                end

                genesis > create compartment soma
                genesis > echo {exists soma}
                1
                genesis > echo {exists bogus}
                0
                genesis > echo {exists soma len}
                1
                genesis > echo {exists soma bogusfield}
                0

Notes:          

25.56 exit

Routine Name:   exit

Description:    Exits from GENESIS, terminating any simulation in progress.

Usage:          exit

Notes:          You can also use "quit", which is identical to "exit".

25.57 exp

Routine Name:   exp

Description:    Returns "e" raised to specified power.

Usage:          number = {exp power}

Example:        genesis >  echo { exp 1 }
                2.718281746

Notes:          
See also: log , pow

25.58 file2tab

Routine Name:   file2tab

Description:    Utility function for loading a file into an interpol struct
                of an element

Usage:          file2tab filename element table -table2 table -table3 table
                -xy xdivs -skiplines number -calc_mode mode -autofill table

Arguments:      filename: name of ascii file to load into table.  Entries
                          must be separated by spaces, tabs or line breaks.
                          Line breaks in input file are ignored. In other
                          words, any number of numeric entries per line are
                          allowed, and all are used.

                element:  path of element containing the table
                table:    name of interpol_struct within the element.

Options:        -table2 table
                This option allows one to specify an additional table to load
                the file into. Entries are loaded alternately into the first
                table and table2. Note that table2 must be on the same
                element as table. If there are an odd number of entries in
                the file, the last one is not used.

                -table3 table
                This allows a third table. This option is similar to table2.

                -xy xdivs
                Uses xy mode for the table entries. Assumes that the points
                are stored in the file as x,y pairs. Uses the xdivs argument
                to set the table size, then figures out xmin, xmax
                and sets the table limits and dx accordingly. Uses dx 
                between all points and fills up table using linear
                interpolation if the x,y pairs in the file are not evenly
                spaced. Assumes x is monotonically increasing, behavior
                in other situations is undefined.

                -skiplines number
                Skips "number" lines at the start of the file. Useful
                for reading in 'xplot' files into a table, since these
                files usually have headers.

                -calc_mode mode
                'mode' is an integer representing one of the legal
                interpolation modes (0 = no interpolation, 1 = linear
                interpolation, 2 = fixed, see interpol doc).

                -autofill table
                table is the name of an interpol_struct in which we wish
                to place successive integers. Useful for displaying plots
                from a single series of numbers in a file:

                file2tab yvalue_file /form/graph/plot ypts -autofill xpts

                will load the numbers in yvalue_file into ypts, and put
                successive integers into xpts.

Example:        This simple example illustrates loading an xplot file into
                a table using different options to file2tab. In the first
                case we end up with the x and y values alternating. In
                the second case we end up with the y values only. In the 
                third case we use the xy mode to load the values into a linear
                table while preserving the x information.

                Datafile name is xplot.data:

                    /newplot
                    /plotname "testplot"
                    0 5
                    4 10
                    8 5
                    10 10

                script file:

                    //genesis

                    create table /tab1
                    file2tab xplot.data /tab1 table -skiplines 2
                    create table /tab2
                    file2tab xplot.data /tab2 table -table2 table -skiplines 2
                    create table /tab3
                    file2tab xplot.data /tab3 table -skiplines 2 -xy 50

                    showfield /tab1 *
                    showfield /tab2 *
                    showfield /tab3 *

-----------------------------------------------------------------------------

Notes:          The control fields of the interpol are set as follows:
                xdivs:  for 1 table:    (num_entries -1)
                        for 2 tables:   (int)(num_entries / 2 -1)
                        for 3 tables:   (int)(num_entries / 3 -1)
                xmin : 0
                xmax : 1
                calc_mode: defaults to 0 (lin-interp), but may be set on the
                        command line.
See also: tab2file , interpol_struct documentation ( Tables ), table

25.59 fileconnect

Routine Name:   fileconnect

Description:    Establishes synaptic connections and weights between groups
                of elements based on a file of weights. The routine
                sets up the connections by adding SPIKE messages between the 
                source and destination objects and then assigning a weight.

Usage:          fileconnect source_elements destination_elements \
                        filename -wtscale w

                source_elements  A wildcarded list of elements which are the 
                        sources of the SPIKE messages.  These must be of
                        class "spiking" and are usually spikegen or 
                        randomspike objects.

                destination_elements  A wildcarded list of elements which are
                        the destinations of the SPIKE messages.  These must  
                        be synchans or objects derived from synchan.

                filename        The name of an ascii file with weights
                        (as floats) separated by whitespace. Separation
                        can include spaces, line breaks etc.
                        The file is expected to have  weights for all possible
                        connections, i.e., :
                                src_nelements * dest_nelements
                        entries.
                                The order of entries is source-first. For
                        example, if the source_elements list has 9 entries
                        and the dest_elements list has 16, then the
                        first 9 entries will specify weights from each of
                        the sources to the first destination. The next 9
                        entries will be to the second destination, and so on.
                                Weights less than or equal to zero will not
                        form connections at all. 
                                Negative weights are often used to indicate
                        inhibitory input, so the command provides a way
                        around that: use a negative wtscale argument.
                        If a file has +ve as well as -ve weights,
                        it would be read twice: first with the paths of
                        excitatory receptor channels and a +ve wtscale,
                        then with the paths of the inhibitory ones and a
                        -ve wtscale.
                        
                -wtscale w      -- This specifies a scale factor for all
                        weights. As noted above, it can be negative to
                        select for inhibitory (negative) weights.
                
Example:        
                int nx = 5
                int ny = 5
                int destx = 5
                int desty = 5
                
                include cellproto.g
                
                createmap /proto/cell /lgn {nx} {ny}
                createmap /proto/cell /v1 {destx} {desty}
                fileconnect /lgn/##[TYPE=spikegen] /v1/cell[]/glu \
                        wts.file -wtscale 0.1
                fileconnect /lgn/##[TYPE=spikegen] /v1/cell[]/GABA \
                        wts.file -wtscale -0.1
                
        wts.file would have 5x5x5x5 entries. A centre-surround
        pattern for the above example could start like this:

                10 -1 0 0 0 
                -1 -1 0 0 0 
                0 0 0 0 0 
                0 0 0 0 0 
                0 0 0 0 0 

                -1 10 -1 0 0 
                -1 -1 -1 0 0 
                0 0 0 0 0 
                0 0 0 0 0 
                0 0 0 0 0 

                0 -1 10 -1 0 
                0 -1 -1 -1 0 
                0 0 0 0 0 
                0 0 0 0 0 
                0 0 0 0 0 

                ...
                
Notes:          The routine is somewhat inefficient for large input and output
                arrays with sparse connectivity, since it has to read
                Nsrc x Ndest entries. This is offset by the fact that
                the routine simultaneously creates synapses and sets
                their weights, thereby eliminating a scan for setting
                weights.  The main use is for setting up large
                networks based on weight files generated by other
                programs.  
See also: planarconnect , planarweight , planardelay ; chapter 18 of the Book of GENESIS has a lengthy discussion on these and related commands. A detailed example of the use of fileconnect is given in Scripts/examples/fileconnect.

25.60 findchar

Routine Name:   findchar

Description:    Returns location of specified character in a given string.

Usage:          position = {findchar string char}

                position        returned as integer indicating position of
                                first occurrence of char in string (positions
                                start with 0); returns -1 if char not found in
                                string

                string          string to search

                char            single character to locate in string (any
                                extra characters in char are ignored)

Example:        genesis >  echo {findchar abcbx b}
                1
                genesis > echo {findchar "a bcbx" b}
                2
                genesis > echo {findchar abcbx bx}
                1
                genesis > echo {findchar abcbx q}
                -1

Notes:
See also: strcat , strcmp , strncmp , strlen , substring

25.61 findsolvefield

Routine Name:   findsolvefield

Description:    Returns a string giving the array location of a particular
                element field value in the hines solver.  Used for
                input/output of values when the original element has been
                taken over by the hines solver and its fields may not be
                updated.

Usage:          findsolvefield hsolve element field

                hsolve      name of the hsolve element
                element     name of an element which was taken over by hsolve
                field       the field of the element whiich is to be accessed

Example:    // statements to create the hsolve element "/cell"
                ...
                setfield /cell chanmode 4
                call /cell SETUP
                ...
                create disk_out /output
                addmsg /cell /output OUTPUT \
                    {findsolvefield /cell /cell/soma/Na Gk}
                ...
                reset
or:
        genesis > echo {findsolvefield /cell /cell/soma/Na Gk}
        givals[108]
        genesis > echo {getfield /cell {findsolvefield /cell /cell/soma/Na Gk}}
        2.634178326e-10

Notes:          When using chanmodes 2 through 5 with the hines solver
                (hsolve), you can no longer assume that all the fields of the
                elements that are taken over by hsolve will be updated.  The
                findsolvefield function is used to access the hsolve arrays
                directly to output field values instead of having to use the
                old disabled elements.  This allows one to establish new
                messages for the output of field values after setup of the
                hsolve element.  The example above shows how to output the Gk
                field of the Na channel from the hsolve element /cell.  Note
                that the fields Gk, Ik, Ek, and Im are not available for
                chanmodes 2 and 3, and require the use of findsolvefield
                in chanmodes 4 and 5.
See also: hsolve

25.62 floatformat

Routine Name:   floatformat

Description:    Sets format for display of variables of type float.

Usage:          floatformat format-string

                format-string   "%[flag][width].[precision][type]",
                                indicating format to use in displaying
                                float-type variables. (default: "%0.10g")
                                The flag, width, precsion and type are
                                defined as in C, but only f and g type
                                formats are allowed.

Example:
                genesis >  float x = 3.12345678
                genesis >  echo { x }
                3.12345678
                genesis >  floatformat %0.5g
                genesis >  echo { x }
                3.1235
                genesis >  floatformat %10.5g
                genesis >  echo { x }
                    3.1235
                genesis > floatformat %10.5f
                genesis > echo { x }
                   3.12346

                genesis > float y = 1e-5
                genesis > floatformat %0.10g
                genesis > echo {y}
                1e-05
                genesis > floatformat %0.10f
                genesis > echo {y}
                0.0000100000

                genesis > floatformat %+10.2f  // show sign
                genesis > echo {x}
                     +3.12

                genesis > float pi = 3.14159265
                genesis > floatformat %-10.2f //left justify with width 10
                genesis > echo {x} {pi}
                3.12       3.14

                genesis > floatformat %010.2f  // "0" flag pads with zeroes
                genesis > echo {x} {pi}
                0000003.12 0000003.14

Notes:          As in C, the width is the minimum number of characters to be
                output.  If the output width is less than this, it is padded
                with blanks, unless the "0" flag is used.  For type f, the
                precision is the number of digits after the decimal point;
                for type g, it is the maximum number of significant digits.

25.63 flushfile

Routine Name:   flushfile

Description:    The contents of a file opened with ``openfile <filename> w''
                and written with ``writefile <filename>'' are flushed from
                the buffer onto disk. The file remains open for further
                writefile operations.

Usage:          flushfile file-name

Example:

        genesis > openfile test w
        genesis > writefile test 1.0 2.0 3.0
        genesis > more test
        genesis >
        genesis > flushfile test
        genesis > more test
        1.0 2.0 3.0
        genesis > writefile test 4.0 5.0 6.0
        genesis > more test
        1.0 2.0 3.0
        genesis > closefile test
        genesis > more test
        1.0 2.0 3.0
        4.0 5.0 6.0

Notes:          This command is useful when the contents of a file need to
                be checked before a simulation has terminated. (Writefile
                alone does not flush the buffer, and file contents are only
                available after closefile has been issued).
See also: openfile , writefile , closefile

25.64 gaussian

Routine Name:   gaussian

Description:    Returns a random value from a Gaussian (Normal) distribution.

Usage:          value = {gaussian mean standard-deviation}

Example:        genesis  > echo {gaussian 0 1 }
                0.5069125295
                genesis > echo {gaussian 0 100 }
                -63.29789352

Notes:          
See also: randseed , rand

25.65 gen2spk

Routine Name:   gen2spk

Description:    This program takes ascii files generated by GENESIS
                containing simulation times and membrane potentials
                (normally of the soma) and extracts the spike times
                relative to the onset of a current-clamp square-wave
                pulse.   The output will be a file which will have currents
                and spike times listed in the file.

Usage:          gen2spk datafile current-start current-duration \
                        total-duration -stepsize dt -maxaccuracy

Arguments:      datafile: the ascii input file.  The format of the input
                    file is as follows: The beginning of a trial is
                    indicated by the following two lines:

                        /newplot
                        /plotname 0.234

                    i.e. the plotname is the current value for that
                    trial (units are arbitrary but are usually in nA).
                    This format is taken from Matt Wilson's xplot
                    program, which is useful for displaying simulation
                    output.  The subsequent lines consist of time/Vm pairs
                    as follows:

                        0 -0.0770584
                        0.0002 -0.077233
                        etc.

                    which can be generated automatically by the
                    asc_file object of GENESIS.  Multiple trials can be
                    put in one file, as long as they're separated by the
                    /newplot, /plotname ... sequence described above.

                current-start: the time in the trace where current
                    injection begins.  Most simulations allow the cell to
                    reach equilibrium before injecting current (e.g.  for
                    50-100 msec or more).  All spike times will be relative
                    to the starting time of the current injection.  Units
                    are in seconds (SI units).

                current-duration: the duration of the current injection, in
                    seconds.

                total-duration: the total duration of the entire trace,
                    including the time before and after the current
                    injection.

Options:        -stepsize dt: the output time step i.e. the time between
                    samples in the output file.  This is usually much
                    larger than the simulation time step.  The default
                    value is 0.0001 (0.1 msec).

                -maxaccuracy:  the output spike times are printed with ten
                    digits of precision rather than 4 (the default).
                    Obviously this is only useful if your output step
                    size is small enough so that the accuracy will make
                    a difference (i.e. less than 0.0001).

Output:         A file with the same name as the input file but with
                .spk.sim added.  The file format is:

                CURR 0.1
                SPK  0.0010
                SPK  0.0123
                --------------------
                CURR 0.2
                SPK  0.0004
                SPK  0.0054
                SPK  0.0080
                ...

                etc.  CURR means the current value and is equal to the
                value in the /plotname line in the input file.  Each spike
                gets a SPK line; the value to the right of the SPK is the
                time in seconds when the spike occurred, relative to the
                start of the current injection.  Different currents are
                separated by a line of dashes.

Algorithm:      See the comments in the file src/param/gen2spk.c.

Notes:          This routine is used mainly for generating data for the
                spkcmp function for current injection simulations.
                However, it is not limited to this use and will extract
                spikes from any membrane potential waveform.

                The /newplot and /plotname lines must be written out
                explicitly to disk using writefile.  Make sure they are
                flushed to disk before starting the simulation so that they
                don't appear in the middle of what asc_file writes.  See
                the parameter search demos for examples of this.

                Some weird waveforms may defeat the spike-identifying
                algorithm.  Very small (low amplitude) spikes are a good
                example of this.  Be careful when using this routine in
                cases like this, and check the outputs with a visual
                display of the membrane potential waveform.

Example:            genesis>  gen2spk "Vmfile" 0.2 1.0 1.5

                In this case, the current comes on at 0.2 seconds, lasts
                for 1.0 seconds (i.e. until the simulation time is 1.2
                seconds) and the whole trace is 1.5 seconds long.
See also: Parameter Search ( Param ), spkcmp , shapematch

25.66 genesis

Routine Name:   genesis

Description:    Starts up the GENESIS program.  (operating system command)

Usage:          genesis [-usage][-nosimrc][-altsimrc filename][-notty][-nosig]
                        [-execdir dirname][-nice nice-level][-nox]
                        [-defaultcolor][-batch][script arg1 ...]

                -usage          print the usage message, listing options.
                -nosimrc        ignore the .simrc file
                -altsimrc       use 'filename' instead of the .simrc file
                -notty          do not accept terminal input
                -execdir        change to 'dirname' after starting genesis
                -nice           give genesis 'nice-level' priority
                -nox            start GENESIS without initializing XODUS
                -defaultcolor   use the display's default colormap
                -batch          run genesis in the background
                script          name of a GENESIS script to run

Example:        %  genesis -altsimrc ~/.backup_simrc

        Starting Genesis
   ==========================================================================
                                  G E N E S I S
                                      Release Version: 2.0

             Copyright 1988 - 1995, California Institute of Technology

    Some components are copyright by the originating institution and are used
    with the permission of the authors.
   ==========================================================================

        Executable:         /usr/genesis/genesis

        ----------------------- Starting XODUS 2.0 -----------------------

        Startup script:     ~/.backup_simrc
        SIMPATH=. /usr/home/jouser/mystartup
        SIMNOTES=/usr/home/jouser/.notes
        GENESIS_HELP=/usr/genesis/Doc
                
        genesis #0 >

Notes:  When starting, GENESIS looks for an initialization file, .simrc,
        first in the current working directory, and then in your home
        directory.  After installing genesis, this file is created in the
        GENESIS installation directory.  After making any appropriate edits,
        you should copy it to your home directory and insure that the
        genesis executable is in your path.

        A new GENESIS command line option -defaultcolor will cause GENESIS
        to use the display's default colormap, even if the default visual is
        readonly.  The net result is that colorscale colors will be shared
        among multiple GENESIS processes, but GENESIS will fail to allocate
        a colorscale if the default colortable is full.  This option may be
        used to avoid X protocol errors on some SGI systems where the X11
        server defaults to a TrueColor (24 bit) visual.

        To perform a GENESIS simulation in the background (for example if you
        want to login from home over a modem, start a simulation, and logout
        while the simulation continues to run), your simulation script should
        use no graphics, and write all output to files.

        Besides specifying the -nox option when starting genesis to avoid
        starting XODUS, you also need to use the -notty and -batch options.
        GENESIS will attempt to read from stdin after the .simrc and command
        line script are completed.  The -batch option causes genesis to exit
        rather than try to read stdin.  -notty will avoid doing any terminal
        setup and cleanup procedures which can also cause this type of
        behaviour.  You must specify both on the command line (i.e. neither
        option implies the other).  In addition, you need to redirect output
        (both stdout and stderr) to a file.  For example, to run a script
        ``batchtest.g'' and direct startup messages and any error messages to
        a log file (using the C shell) you would use:

            genesis -nox -batch -notty batchtest >& batch.log &

        With the Bourne shell (or bash) it would be:

            genesis -nox -batch -notty batchtest > batch.log 2>&1 &
See also: src/README, Simulations

25.67 getarg

Routine Name:   getarg

Description:    Returns specified item from an argument list.

Usage:          getarg [arguments] -count -arg #
                One of -count or -arg must be given

Example:        genesis >  echo {getarg 11 22 33 44 55 -arg 3}
                33
                genesis >  echo {getarg 11 22 33 44 55 -count}
                5
Notes:
See also: argc , argv , arglist , printargs

25.68 getclock

Routine Name:   getclock

Description:    Returns value of the time interval for the specified clock.

Usage:          clock-value = {getclock clock-number}

Example:        genesis >  echo { getclock 0 }
                5.000000e-05

Notes:          The getclock routine returns the current value of the step
                size for the specified clock (as a floating point number).
See also: showclocks , useclock , setclock

25.69 getdate

Routine Name:   getdate

Description:    Returns operating system date-time.

Usage:          str-value = getdate

Example:        genesis >  echo { getdate }
                Thu Jun 22 22:11:13 1995

Notes:          This is a GENESIS implementation of the operating system
                date command, to have the value returned by the routine rather
                than displayed directly to the user.  This allows the current
                date to be used as a data value within GENESIS.
See also: sh

25.70 getdefault

Routine Name:   getdefault

Description:    Returns the default value of an object field.

Usage:          getdefault object-name field-name

Example:        genesis > echo {getdefault compartment Rm}
                1

Notes:
See also: setdefault

25.71 getelementlist

Routine Name:   getelementlist

Description:    Returns list of elements matching wildcard specification.

Usage:          getelementlist path -listname listname

Notes:          This is an alias for el.

See also: el

25.72 getenv

Routine Name:   getenv

Description:    Returns value of operating-system environmental variable.

Usage:          str-value = {getenv environment-variable}

Example:        genesis >  echo { getenv DISPLAY }
                babel.bbb.edu:0

Notes:          This is a GENESIS implementation of the operating system
                printenv command, to have the value returned by the routine
                rather than displayed directly to the user.  (GENESIS also
                includes a version of printenv to have the value displayed
                directly to the user.)  The getenv routine allows the value of
                the particular operating system environmental variables to be
                used as a data value within GENESIS.
See also: setenv , printenv

25.73 getfield

Routine Name:   getfield

Description:    Returns value of field in data structure of specified element.

Usage:          getfield [pathname] field

                field-value = {getfield pathname field}

                pathname        path specification
                                defaults to current working element

                field           name of field in element data structure
                
Example:        echo {getfield /cell/soma Vm}
                setfield /cell/soma Rm {getfield /form/Rm_dialog value}

Notes:          The getfield routine returns the value of fields in the
                specified path.
See also: setfield , showfield , getfieldnames

25.74 getfieldnames

Routine Name:   getfieldnames

Description:    Returns names of all existing fields in specified element.

Usage:          element-fields = {getfieldnames Element}

                element-fields          returned as a single line (i.e., a
                                        string without carriage returns)
                                        listing fields of specified element

Example:        echo { getfieldnames /output }

                str name
                foreach name ( {getfieldnames soma })
                echo {name}
                end

Notes:          
See also: getfield , showfield , setfield

25.75 getglobal

Routine Name:   getglobal

Description:    Returns the value of a global variable, allowing the name of
                the global variable to be held in a string variable.

Usage:          getglobal name

Example:

                genesis >  str variable = "EREST"
                genesis >  addglobal float {variable}
                genesis >  setglobal {variable} -0.07
                genesis >  echo {variable} = {getglobal {variable}}
                EREST = -0.070000

Notes:

Often it is useful to use a string variable name to hold the name of a
global variable.  For example, one may want to pass the name of a global
variable to a function that declares a global variable, or that sets or
returns its value.  However, normal GENESIS syntax for declarations and
assignments does not permit a variable name to be specified by a string
variable.   The routines addglobal, getglobal, and setglobal are designed
to overcome this limitation.
See also: Variables , addglobal , setglobal , listglobals

25.76 getmsg

Routine Name:   getmsg

Description:    Returns information about a message into or out of element.

Usage:          getmsg element -incoming -outgoing -slot msg-number slot-number
                 -count -type msg-number -destination msg-number
                 -source msg-number -find srcelem type

                [One of -slot, -count, -type, -destination, -source or -find
                must be given]

                element         element for which to determine information
        
                msg-number      number (index)  of message in message list
                                (messages are numbered from 0 up)

                srcelem         element sending the message

                type            message type (PLOT, AXIAL, VOLTAGE, etc.)

                -incoming       look for an incoming message

                -outgoing       look for an outgoing message

                -slot           return the slot value for the given message
                                and slot numbers

                -count          return the number of messages in or out
                                of this element

                -type           return the message type for the message
                                having the index msg-number

                -destination    return the destination element for the
                                message having the index msg-number
                                
                -source         return the source element for the
                                message having the index msg-number

                -find           return the index (msg-number) of the first
                                message matching the srcelem and type

Example:        

        genesis > echo { getmsg /cell/dend1 -out -destination 0}
        /cell/soma
        
        genesis > echo { getmsg /cell/dend1 -out -source 0}
        /cell/dend1

        genesis > echo { getmsg /cell/dend1 -out -count }
        5

        genesis > echo { getmsg /cell/dend1  -in -destination 1 }
        /cell/dend1

        genesis > echo {getmsg /cell/soma -in -find /cell/dend1 RAXIAL}
        2

        genesis >  echo {getmsg /cell/soma  -in -type 2}
        RAXIAL

        genesis >  echo {getmsg /cell/soma  -in -slot 2 0}
        -0.07

Notes:          The -find option may only be used to find the index of
                an incoming message.  It returns -1 if there is no message
                from the specified source element and message type.

                The -count option may be useful if you want to loop over the
                index in order to find multiple messages which meet some
                specification.
See also: addmsg , deletemsg , showmsg

25.77 getparamGA

Routine Name:   getparamGA

Description:    gets the value of a parameter in a paramtableGA object as a
                floating-point number.

Usage:          getparamGA path table param

                path:   The location of the paramtableGA object in the
                        element hierarchy.

                table:  The parameter table to be accessed.

                param:  The location of the desired parameter in the
                        table.

Return value:   a float, representing the parameter value desired.

Example:            float val
                    val = {getparamGA /GA 10 1}

                This returns the second parameter (zero-indexed) from
                the tenth parameter table in the paramtableGA object
                called /GA.  The value is stored in the
                variable val.

Notes:          The reason for having this routine and setparamGA is that
                the parameter table array in paramtableGA objects is in an
                object-specific binary form (optimized for the genetic
                algorithm method) and thus can't be viewed or set directly
                using the showfield, getfield or setfield commands (at
                least not meaningfully).

                This routine and setparamGA are hacks; ultimately they should
                be made obsolete by overloading the SET and SHOW actions of
                the paramtableGA object.
See also: Parameter Search ( Param ), paramtableGA , setparamGA

25.78 getpath

Routine Name:   getpath

Description:    Returns subpart of full element pathname.

Usage:          head-string = {getpath name -head}
                tail-string = {getpath name -tail}

                head-string     full path leading to element, without actual
                                element name

                tail-string     only actual element name, without full path

                name            an element pathname

Example:        genesis > echo {getpath /cell/soma/Na_channel -head}
                /cell/soma/
                genesis >  echo {getpath /cell/soma/Na_channel -tail}
                Na_channel

Notes:          You use getpath to extract the parent or head of a path.
See also: el , pwe , stack

25.79 getsolvechildname

Routine Name:   getsolvechildname

Description:    Returns the name of the child stored at the index value
                inside the hines solver.

Usage:          getsolvechildname hsolve_element index

Example:
                genesis > showfield /cell/solve nchildren
                [ /cell/solve ]
                nchildren            = 2

                genesis > echo {getsolvechildname /cell/solve 1}
                /cell/soma/K_mit_tchan
                genesis > echo {getsolvechildname /cell/solve 2}
                /cell/soma/Na_mit_tchan

Notes:          Mainly used for debugging.
See also: hsolve , getsolvecompname , findsolvefield

25.80 getsolvecompname

Routine Name:   getsolvecompname

Description:    Returns the name of the compartment stored at the index value
                inside the hines solver.

Usage:          getsolvecompname hsolve_element index

Example:
                genesis > showfield /cell/solve ncompts
                [ /cell/solve ]
                ncompts              = 1

                genesis > echo {getsolvecompname /cell/solve 0}
                soma[0]

Notes:          Mainly used for debugging.
See also: hsolve , getsolvechildname , findsolvefield

25.81 getstat

Routine Name:   getstat

Description:    Returns current simulation time, step number, or memory used

Usage:          getstat -time -step -memory

Example:

genesis > echo {getstat -time}
0.1000500023

genesis > echo {getstat -step}
2001

genesis > {getstat -memory}
3704068

Notes:
See also: showstat

25.82 getsyncount

Routine Name:   getsyncount

Description:    This function is used to count SPIKE messages coming from a
                particular presynaptic element and/or synapses on a
                particular postsynaptic element.  If both the presynaptic
                and postsynaptic elements are specified this function
                returns the number of connections between the two i.e. the
                number of SPIKE messages from the presynaptic element which
                are sent to the given postsynaptic element.  This function
                is often used inside a loop to set fields in synapses
                between specific elements to particular values.

Usage:          getsyncount [presynaptic-element] [postsynaptic-element]

                presynaptic-element  The element sending SPIKE messages to
                        postsynaptic targets.

                postsynaptic-element  The synchan or derived element which 
                        receives SPIKE messages.

Example:        // Set the weights of all synapses that receive SPIKE messages 
                // from a given source to 10.0

                int i
                str dest
                int nsyn = {getsyncount /input[0]/spike}
                for (i = 0; i = {nsyn}; i = i + 1)
                    dest  = {getsyndest /input[0]/spike {i}}
                    index = {getsyndest /input[0]/spike {i} -index}
                    setfield {dest} synapse[{index}].weight 10.0
                end

Notes:          Synchans have an "nsynapses" field which holds a count of the
                number of synapses on a given element; this can be used instead
                of getsyncount when getting synapse counts for postsynaptic 
                elements.  
See also: getsynindex , getsynsrc , getsyndest , BoG chapter 18

25.83 getsyndest

Routine Name:   getsyndest

Description:    Returns a string which is the path of the postsynaptic
                element which receives the nth SPIKE message sent by the
                given presynaptic element.  Can also return the index of
                the synapse on this element.

Usage:          getsyndest presynaptic-element spikemsg-number -index

                presynaptic-element  The element sending SPIKE messages to
                        postsynaptic targets.

                spikemsg-number The number of the SPIKE message whose
                        destination we want.  This can be obtained by getmsg
                        or showmsg.

                -index This option returns the index of the synapse which
                        receives the SPIKE message on the destination
                        element.

Example:        str dest  = {getsyndest input[0]/spike 0}
                int index = {getsyndest input[0]/spike 0 -index}
                setfield {dest} synapse[{index}].weight 10.0

Notes:          getsynindex can also be used to get the index of a synapse
                if you know the names of the pre- and postsynaptic elements.
See also: getsyncount , getsynindex , getsynsrc , BoG chapter 18

25.84 getsynindex

Routine Name:   getsynindex

Description:    getsynindex is used to find the index of synapses between
                particular presynaptic and postsynaptic elements.  

Usage:          getsynindex presynaptic-element postsynaptic-element
                        [-number n]

                presynaptic-element  The element sending SPIKE messages to
                        postsynaptic targets.

                postsynaptic-element The synchan or derived element
                       receiving the SPIKE message from the presynaptic
                       element.

                -number n  If there is more than one synapse between the
                           given pre- and postsynaptic elements, this option
                           will return the index of the nth such synapse.
                           This option will rarely be necessary, since
                           usually there is at most one synapse between a
                           given presynaptic and postsynaptic element.  

Example:        int index = {getsynindex /input[0]/spike /cell/soma/Ex_channel}
                if (index >= 0)
                    setfield /cell/soma/Ex_channel synapse[{index}].weight 10.0
                end

Notes:          If the desired synapse does not exist a value of -1 is
                returned.
See also: getsyncount , getsynsrc , getsyndest , BoG chapter 18

25.85 getsynsrc

Routine Name:   getsynsrc

Description:    Returns a string which is the path of the presynaptic
                element sending the SPIKE message to the synapse of the
                postsynaptic element with the given index.

Usage:          getsynsrc postsynaptic-element index

                postsynaptic-element The synchan or derived element
                       receiving the SPIKE message from the source element.

                index  The index of the synapse on a synchan or derived element
                       whose source you want.

Example:        str src = {getsynsrc /cell/soma/Ex_chan 0}
                if (src == "input[0]/spike")
                    setfield /cell/soma/Ex_chan synapse[0].weight 10.0
                else
                    setfield /cell/soma/Ex_chan synapse[0].weight 0.0
                end

Notes:          
See also: getsyncount , getsynindex , getsyndest , BoG chapter 18

25.86 h

Routine Name:   h

Description:    Displays the contents of the command-history buffer.

Usage:          h
                h [start [end] ]

                start           number of first command to list (default: 1)

                end             number of last command to list (default:
                                number of most recently issued command)

Example:        genesis > h 1 5
                     1    echo { x }
                     2    floatformat %0.5g
                     3    echo { x }
                     4    floatformat %2.5g
                     5    echo { x }

Notes:          Every command typed into the simulator at the keyboard is
                saved into a command buffer referred to as the 'history'.
                Commands saved in the history buffer can be re-executed using
                command recall mechanisms built into the script language.  The
                h routine displays the list of all commands in the range
                specified.  Typing h without any arguments will print the
                entire history buffer.  Typing h with a range will print all
                of the commands executed in the range specified.

                The following history recall functions are also built into the
                script language:

                Command   Example   Description
                --------------------------------------------------------------
                !!        !!        Re-execute last command.
                !n        !5        Re-execute the fifth command entered.
                !string   !echo     Re-execute the last command whose first
                                    chars match the string entered.
                ctrl-P    ctrl-P    Retrieve previous command in the history
                                    buffer. Repeat ctrl-P's to scan backwards
                                    through previous commands.
                ctrl-N    ctrl-N    Scan forward, after executing ctrl-P's,
                                    to echo next command.

25.87 help

Routine Name:   help

Description:    Displays help on GENESIS topics.

Usage:          help [ topic [help-directory-list] ]

                topic                   string (typically a routine name)

                help-directory          list of directories containing
                                        ascii help files

Example:        genesis >  help CONTENTS | more
                genesis >  help synchan  | more
                genesis >  help myroutine /myhelpdirectory /basichelp

Notes:          Help searches specified help directories for documentation on
                the given topic (typically a routine name).  If no directory
                is specified then the current default help directory (the last
                help directory referenced) will be used.  If no default help
                directory exists (e.g., when help is used for the first time),
                the value of the environment variable GENESIS_HELP is used as
                the help directory (cf. setenv, getenv); this variable is
                set to the genesis/Doc directory, using the full path
                given in the default .simrc file.

                As most of these files are longer than a single screen, it is
                best to pipe the output into "more".

                If no topic is given, the genesis/Doc/README file is printed
                to the screen.   This gives further information about the
                current version of the one-line help, the GENESIS Reference
                Manual, and the hypertext documentation.

                [for help writers:]

                The Help facility allows text to be included from other files
                (use ## as first characters on a line, followed by the local
                file name; you can omit the .txt suffix).  For instance, you
                might create the following file trig.txt:

                        TRIG Routines
                        ##cos
                        ##sin
                        ##tan

                When you type "help trig" to view this file, instead of seeing
                the text "##cos" etc., the contents of the file cos.txt would
                be read in and displayed at that point in the file.

25.88 initdump

Routine name:   initdump

Description:    Initializes the simulation dumping/undumping system.  Normally
                generated by default in a dumpfile, but it can be overridden
                from the script to set various flags.

Usage:          initdump -version # -ignoreorphans # -allowmsgdup

                -version #: The version number of the dumpfile. Allows it to
                read old dumpfiles. Each dumpfile keeps its version number in
                its header. This is relevant only for reading in dumpfiles, as
                simdump always dumps using the latest version.

                -ignoreorphans #: # can be 0 or 1. Orphans are elements
                without a parent. If ignoreorphans is 1, then simundump will
                simply skip over orphan elements. Otherwise it will complain.

                -allowmsgdup: When a dumped simulation is being loaded onto
                an existing one, then some messages are likely to be duplicated.
                Normally such duplicate messages are detected and are NOT
                created. This flag disables the mechanism that protects
                dumps from duplicating msgs when the elements specified in
                the dumps overlap.

Example:        Here is a little dumpfile using initdump that recreates a
                simple 2-compartment model, and ignores the orphan element
                /x/y/z.

                ============================================================
                //genesis

                initdump -version 3 -ignoreorphans 1
                simobjdump neutral
                simobjdump compartment activation Vm previous_state \
                        Im Em Rm Cm Ra inject dia len initVm
                simundump neutral /x/y/z 0
                simundump neutral /a 0
                simundump compartment /a/compt 0 0 0.6632976405 0.6632942696 \
                        -0.3333315551 0 1 1 1 1 0 0 0
                simundump neutral /b 0
                simundump compartment /b/compt 0 0 0.3299660931 0.3299627243 \
                        0.3333349228 0 1 1 1 0 0 0 0
                addmsg /b/compt /a/compt RAXIAL Ra Vm 
                addmsg /a/compt /b/compt AXIAL Vm 
                enddump
                // End of dump

                ============================================================
        
Notes:          
See also: enddump , simdump , simobjdump , simundump

25.89 initparamBF

Routine Name:   initparamBF

Description:    Initializes a number of fields involving a single parameter
                for the paramtableBF object.

Usage:          initparamBF path param type range center label

                path:   The location of the parameter search object in
                        the element hierarchy.

                param:  The numerical index of the parameter whose ranges
                        etc. are to be set.

                type:   The type of the parameter; 0 = additive,
                        1 = multiplicative.

                range:  The range of the parameter.  For additive
                        parameters, this is a maximum offset from the
                        center value; for multiplicative parameters, it's
                        a maximum scaling factor.  In other words, for
                        additive parameters the full parameter range is
                        [center - range, center + range] while for
                        multiplicative parameters it's equal to
                        [center / range, center * range].  The range
                        value must be >= 0.

                center: The original value of the parameter, which is also
                        the center of the range to be searched over.

                label:  A string which is the name of the parameter.  This
                        is useful for identifying the parameter in a text
                        file output by the SAVEBEST or DISPLAY actions.

Return value:   int; 0 for failure and 1 for success.

Examples:           initparamBF /BF_object  0  1  2.0  1.0  "Na Gbar"

                This sets parameter 0 to be a multiplicative parameter
                (type 1) with a range of 2.0 (from 0.5 to 2.0 times the
                center value) with a center value of 1.0.  The label
                indicates that this parameter represents the maximum
                conductance of a sodium channel.  The label is just for
                reference and has no effect on the search process.

Notes:          This routine (and the other initparamXX routines) are
                shortcuts to set a number of parameter-related fields
                simultaneously.  All of these fields can also be set
                manually, but it's usually much more convenient to use
                these functions.
See also: Parameter Search ( Param ), Paramtable , paramtableBF

25.90 initparamCG

Routine Name:   initparamCG

Description:    Initializes a number of fields involving a single parameter
                for the paramtableCG object.

Usage:          initparamCG path param type range center label

                path:   The location of the parameter search object in
                        the element hierarchy.

                param:  The numerical index of the parameter whose ranges
                        etc. are to be set.

                type:   The type of the parameter; 0 = additive,
                        1 = multiplicative.

                range:  The range of the parameter.  For additive
                        parameters, this is a maximum offset from the
                        center value; for multiplicative parameters, it's
                        a maximum scaling factor.  In other words, for
                        additive parameters the full parameter range is
                        [center - range, center + range] while for
                        multiplicative parameters it's equal to
                        [center / range, center * range].  The range
                        value must be >= 0.

                center: The original value of the parameter, which is also
                        the center of the range to be searched over.

                label:  A string which is the name of the parameter.  This
                        is useful for identifying the parameter in a text
                        file output by the SAVEBEST or DISPLAY actions.

Return value:   int; 0 for failure and 1 for success.

Examples:           initparamCG /CG_object  0  1  2.0  1.0  "Na Gbar"

                This sets parameter 0 to be a multiplicative parameter
                (type 1) with a range of 2.0 (from 0.5 to 2.0 times the
                center value) with a center value of 1.0.  The label
                indicates that this parameter represents the maximum
                conductance of a sodium channel.  The label is just for
                reference and has no effect on the search process.

Notes:          This routine (and the other initparamXX routines) are
                shortcuts to set a number of parameter-related fields
                simultaneously.  All of these fields can also be set
                manually, but it's usually much more convenient to use
                these functions.
See also: Parameter Search ( Param ), Paramtable , paramtableCG

25.91 initparamGA

Routine Name:   initparamGA

Description:    Initializes a number of fields involving a single parameter
                for the paramtableGA object.

Usage:          initparamGA path param type range center label

                path:   The location of the parameter search object in
                        the element hierarchy.

                param:  The numerical index of the parameter whose ranges
                        etc. are to be set.

                type:   The type of the parameter; 0 = additive,
                        1 = multiplicative.

                range:  The range of the parameter.  For additive
                        parameters, this is a maximum offset from the
                        center value; for multiplicative parameters, it's
                        a maximum scaling factor.  In other words, for
                        additive parameters the full parameter range is
                        [center - range, center + range] while for
                        multiplicative parameters it's equal to
                        [center / range, center * range].  The range
                        value must be >= 0.

                center: The original value of the parameter, which is also
                        the center of the range to be searched over.

                label:  A string which is the name of the parameter.  This
                        is useful for identifying the parameter in a text
                        file output by the SAVEBEST or DISPLAY actions.

Return value:   int; 0 for failure and 1 for success.

Examples:           initparamGA /GA_object  0  1  2.0  1.0  "Na Gbar"

                This sets parameter 0 to be a multiplicative parameter
                (type 1) with a range of 2.0 (from 0.5 to 2.0 times the
                center value) with a center value of 1.0.  The label
                indicates that this parameter represents the maximum
                conductance of a sodium channel.  The label is just for
                reference and has no effect on the search process.

Notes:          This routine (and the other initparamXX routines) are
                shortcuts to set a number of parameter-related fields
                simultaneously.  All of these fields can also be set
                manually, but it's usually much more convenient to use
                these functions.
See also: Parameter Search ( Param ), Paramtable , paramtableGA

25.92 initparamSA

Routine Name:   initparamSA

Description:    Initializes a number of fields involving a single parameter
                for the paramtableSA object.

Usage:          initparamSA path param type range center scalemod label

                path:   The location of the parameter search object in
                        the element hierarchy.

                param:  The numerical index of the parameter whose ranges
                        etc. are to be set.

                type:   The type of the parameter; 0 = additive,
                        1 = multiplicative.

                range:  The range of the parameter.  For additive
                        parameters, this is a maximum offset from the
                        center value; for multiplicative parameters, it's
                        a maximum scaling factor.  In other words, for
                        additive parameters the full parameter range is
                        [center - range, center + range] while for
                        multiplicative parameters it's equal to
                        [center / range, center * range].  The range
                        value must be >= 0.

                center: The original value of the parameter, which is also
                        the center of the range to be searched over.

                scalemod: Modifies the range of the initial points on the
                        simplex.  See the paramtableSA doc file for more
                        details.

                label:  A string which is the name of the parameter.  This
                        is useful for identifying the parameter in a text
                        file output by the SAVEBEST or DISPLAY actions.

Return value:   int; 0 for failure and 1 for success.

Examples:           initparamSA /SA_object  0  1  2.0  1.0  1.5 "Na Gbar"

                This sets parameter 0 to be a multiplicative parameter
                (type 1) with a range of 2.0 (from 0.5 to 2.0 times the
                center value) with a center value of 1.0 and a scalemod
                value of 1.5.  The label indicates that this parameter
                represents the maximum conductance of a sodium channel.
                The label is just for reference and has no effect on the
                search process.

Notes:          This routine (and the other initparamXX routines) are
                shortcuts to set a number of parameter-related fields
                simultaneously.  All of these fields can also be set
                manually, but it's usually much more convenient to use
                these functions.
See also: Parameter Search ( Param ), Paramtable , paramtableSA

25.93 initparamSS

Routine Name:   initparamSS

Description:    Initializes a number of fields involving a single parameter
                for the paramtableSS object.

Usage:          initparamSS path param type range center label

                path:   The location of the parameter search object in
                        the element hierarchy.

                param:  The numerical index of the parameter whose ranges
                        etc. are to be set.

                type:   The type of the parameter; 0 = additive,
                        1 = multiplicative.

                range:  The range of the parameter.  For additive
                        parameters, this is a maximum offset from the
                        center value; for multiplicative parameters, it's
                        a maximum scaling factor.  In other words, for
                        additive parameters the full parameter range is
                        [center - range, center + range] while for
                        multiplicative parameters it's equal to
                        [center / range, center * range].  The range
                        value must be >= 0.

                center: The original value of the parameter, which is also
                        the center of the range to be searched over.

                label:  A string which is the name of the parameter.  This
                        is useful for identifying the parameter in a text
                        file output by the SAVEBEST or DISPLAY actions.

Return value:   int; 0 for failure and 1 for success.

Examples:           initparamSS /SS_object  0  1  2.0  1.0  "Na Gbar"

                This sets parameter 0 to be a multiplicative parameter
                (type 1) with a range of 2.0 (from 0.5 to 2.0 times the
                center value) with a center value of 1.0.  The label
                indicates that this parameter represents the maximum
                conductance of a sodium channel.  The label is just for
                reference and has no effect on the search process.

Notes:          This routine (and the other initparamXX routines) are
                shortcuts to set a number of parameter-related fields
                simultaneously.  All of these fields can also be set
                manually, but it's usually much more convenient to use
                these functions.
See also: Parameter Search ( Param ), Paramtable , paramtableSS

25.94 input

Routine Name:   input

Description:    Obtains input from the user at the GENESIS prompt.

Usage:          value = input [ prompt-string [ default-value]  ]

                value           value entered by user

                prompt-string   string to use to prompt user for input
                                (default: "?"; to use a string that includes
                                spaces, include the string in quotation marks;
                                in any case, two blank spaces are always
                                automatically shown after the prompt string)

                default-value   value to use if user responds by just pressing
                                the RETURN key (to use a string that includes
                                spaces, include the string in quotation marks)

Example:        genesis >  int x = {input "Value for x:" 3}
                (def = 3) Value for x:  666
                genesis >  echo { x }
                666

Notes:          The input routine can be used to get input from the keyboard.
                If supplied, the default-value is displayed before the
                prompt-string, in the form:
                
                    (def = <default-value>) prompt-string

25.95 isa

Routine Name:   isa

Description:    Tests to see if an element is derived from a specified object.

Usage:          isa-flag = {isa object element}

                isa-flag        returned as 1 if element is derived from
                                object; returned as 0 otherwise

                object          name of a GENESIS object (element-type)

                element         name or full pathname of element to test

Example:        if ({isa symcompartment /cell/dendrite})
                        echo "This is a symmetric compartment"
                end

                genesis > create compartment /soma
                genesis > echo {isa compartment /soma}
                1
                genesis > echo {isa symcompartment /soma}
                0

Notes:          The test will also be true if the element is created from
                an extended object that is derived from the specified
                object.
See also: Extended

25.96 le

Routine Name:   le

Description:    Displays a list of elements in the element tree.

Usage:          le [path] -recursive -type

                path            pathname of element (default: current
                                element);  path cannot include wildcards

                -r              recursively display entire tree starting
                                at given element

                -t              display object type along with element name
                                (type will be included in curly braces just
                                after element name)

Example:        genesis > le / -t
                *proto {neutral}        output {neutral}   
                cell/ {neutral}         data/ {xform}   

                genesis > le / -r
                *proto          output   
                cell/           data/   

                /cell:
                soma                                    

                /data:
                voltage/        RESET   
                RUN             QUIT   

                /data/voltage:
                x_axis          y_axis   
                title           volts   
                current                                 

Notes:          Unlike the listings produced by the analogous operating-system
                command "ls", the listings produced by the le routine show
                elements not in alphabetical order, but in the order in which
                they were created.

                In the le listings, items preceded by an asterisk (e.g.,
                *proto) will not participate in simulations (see the enable
                and disable routines for control of this).

25.97 listcommands

Routine Name:   listcommands

Description:    Displays a list of routines currently recognized by GENESIS.

Usage:          listcommands

Example:        genesis > listcommands | more

                Available commands:
                [routines are listed, one screen at a time]

Notes:          

25.98 listescape

Routine Name:   listescape

Description:    Lists available escape-key/command-sequence bindings.

Usage:          listescape

Example:        genesis >  listescape
                AVAILABLE ESCAPE KEYS
                ---------------------
                [29~       Do              REPLACE   step<CR>
                [28~       Help            EXEC      commands | more
                [18~       F7              EXEC      status
                [17~       F6              EXEC      status -process
                [11~       F1              EXEC      stop
                [3~        Remove          REPLACE   <^D>
                [2~        Insert Here     REPLACE   <^I>
                [1~        Find            EXEC      execute movebol
                [D         left arrow      REPLACE   <^H>
                [C         right arrow     REPLACE   <^F>
                [B         down arrow      REPLACE   <^N>
                [A         up arrow        REPLACE   <^P>

Notes:          The listescape routine displays a list of the current escape
                key to string bindings which have been created using the
                addescape routine (in reverse order of creation).
See also: addescape

25.99 listfiles

Routine Name:   listfiles

Description:    Lists ASCII files currently opened by openfiles routine.

Usage:          listfiles

Example:        genesis > listfiles

                OPEN ASCII FILES
                -----------------

                genesis > openfile run.g r
                genesis > listfiles

                OPEN ASCII FILES
                -----------------
                run.g                r

Notes:          
See also: openfile

25.100 listglobals

Routine Name:   listglobals

Description:    Lists currently defined GENESIS global variables and their
                current values.

Usage:          listglobals [global-symbols] -functions -variables

                -variables      only show variables (types int, float, str)
                -functions      only show functions (type function)
                                
                (Uses last switch on line; if no switches, shows both
                functions and variables.  If the name is given, it shows
                only that global-symbol.)

Example:        genesis >  listglobals
                int             B_SPLINE_FILL = 0
                int             C_SPLINE_FILL = 1
                int             LINEAR_FILL = 2

Notes:          Four datatypes are recognized in listglobals:

                        int
                        float
                        str
                        function
See also: echo , Variables , Functions

25.101 listobjects

Routine Name:   listobjects

Description:    Lists available element types.

Usage:          genesis >  listobjects

Notes:          The listobjects routine displays a list of the element types
                currently defined within GENESIS.  GENESIS comes with an
                extensive set of element types already included.
See also: showobject

25.102 log

Routine Name:   log

Description:    Returns logarithm (base "e") of number.

Usage:          log-value = {log number}

Example:        genesis >  echo { log 1 }
                0
                genesis > echo {log {exp 1}}
                0.9999999404
                genesis > echo {log 0}
                -Infinity

Notes:          To get the base 10 log of x, use {log {x}}/{log 10}.
See also: exp

25.103 logfile

Routine Name:   logfile

Description:    Activates/deactivates logging of all commands issued in
                GENESIS session.

Usage:          logfile file-name
                logfile -off

                file-name       name for file in which to save record of
                                messages typed to or displayed at the GENESIS
                                shell -- if file already exists, information
                                will be appended; if file does not exist,
                                it will be created and information entered

                -off            flag to deactivate logging

Example:        genesis >  logfile mylog
                logging to 'mylog' at Sat Jun 24 18:44:59 1995
                ...
                genesis >  logfile -off
                logging done at Sat Jun 24 19:08:08 1995

Notes:          The logfile routine is used to activate command line logging.
                All commands typed from the keyboard as well as various error
                messages reported by the simulator will be saved in the
                specified logfile.
See also: notes

25.104 max

Routine Name:   max

Description:    Returns maximum value of two numbers.

Usage:          maximum-value = {max value1 value2}

Example:        genesis > echo {max {tan 0.1} 0.1}
                0.1003346741

Notes:                          
See also: min

25.105 maxerrors

Routine Name:   maxerrors

Description:    Sets (or displays) number of errors currently allowed before
                a simulation is automatically stopped.

Usage:          maxerrors [number-of-errors]

Example:        genesis >  maxerrors
                max errors = 10
                genesis >  maxerrors 30
                max errors = 30

Notes:          By default, the maximum number of errors allowed before the
                system stops a simulation is 10.
See also: maxwarnings , clearerrors

25.106 maxwarnings

Routine Name:   maxwarnings

Description:    Sets (or displays) number of warning messages currently
                allowed before a simulation is automatically stopped.

Usage:          maxwarnings [number-of-warnings]

Example:        genesis >  maxwarnings
                max warnings = 20
                genesis > maxwarnings 40
                max warnings = 40

Notes:          By default, the maximum number of warning messages allowed
                before the system stops a simulation is 20.
See also: maxerrors , clearerrors

25.107 min

Routine Name:   min

Description:    Returns minumum value of two numbers.

Usage:          minimum-value = min {value1 value2}

Example:        genesis > float x = 33.333
                genesis > int y = {x}
                genesis > echo {min {x} {y}}
                33

Notes:          
See also: max

25.108 move

Routine Name:   move

Description:    Moves an element and its children from one portion of the tree
                to another.

Usage:          move src_element dst_element

                src_element     element to move (if this element has
                                sub-elements, they too are moved)
                
                dst_element     location into which to move src_element (if
                                dst_element already exists, src_element is
                                moved beneath it with original name; if
                                dst_element does not exist, src_element is
                                given that name as new name)

Example:        move /cell1 /cell5

                create neutral /network
                move /cell[1] /network

Notes:          In the example above, if /cell5 does not exist, /cell1 will
                be renamed to /cell5.  The second example turns /cell[1]
                into /network/cell[1].
See also: copy

25.109 msgsubstitute

Routine Name:       msgsubstitute

Description:        Allows undump of saved simulation with new message names

Usage:              msgsubstitute destobj orig_msg_type new_msg_type field1 ...

Example:            objsubstitute xplot fakeplot
                    msgsubstitute fakeplot PLOT INPUT .

                    also see Scripts/kinetikit/batch_interface.g

Notes:              msgsubstitute is used along with objsubstitute  to allow
                    you to save an object of one type using simobjdump and
                    simdump, and then use simundump to reload it as a
                    different type.  It allows for example, xgraph and xplot
                    elements to be saved as neutral and table elements, so
                    that the simulation can run in batch mode.  In the example
                    above, a real xplot object takes a PLOT message, but we
                    are using a table as fakeplot, which takes an INPUT
                    message.  Here, the "." represets the same field (the
                    data to be plotted) originally sent with the PLOT message.
See also: objsubstitute , substituteinfo , simobjdump , simdump , swapdump , simundump

25.110 notes

Routine Name:   notes

Description:    Allows user to enter text notes into a file.

Usage:          notes [file]

                file            file into which to put notes (default:
                                most recent notes file used; if first time
                                in this GENESIS session, uses file specified
                                by operating system variable SIMNOTES) -- if
                                file already exists, notes will be appended;
                                if file does not exist, it will be created and
                                notes entered

Example:        genesis >  notes
                using notes file '/myhomedirectory/.notes'
                End with '.' alone on the last line
                ->  running the first tutorial script
                -> .
                genesis >  notes squid_notes
                using notes file 'squid_notes'
                End with '.' alone on the last line
                -> We may want to look at the tutorial for ideas
                -> about the implemention of voltage clamp
                -> circuitry.
                -> .
                genesis >  more squid_notes
                +------------------------------------------------------+
                Sat Jun 24 19:14:54 1995

                We may want to look at the tutorial for ideas
                about the implemention of voltage clamp
                circuitry.
                genesis >

Notes:          You end the note by including a period (.) on a line by itself.

                The note is entered into the notes file preceded by a dashed
                line and the date and time the entry was made.
See also: logfile

25.111 objsubstitute

Routine Name:       objsubstitute

Description:        Allows undump of saved simulation with new object names

Usage:              objsubstitute orig_obj_name new_obj_name

Example:            create table fakeplot
                    // commands to add fields and actions to fakeplot
                    // to make it look like an xplot
                    ...
                    addobject fakeplot fakeplot
                    objsubstitute xplot fakeplot

                    see Scripts/kinetikit/batch_interface.g

Notes:              objsubstitute is used to allow you to save an object of
                    one type using simobjdump and simdump, and then use
                    simundump to reload it as a different type.  It allows for
                    example, xgraph and xplot elements to be saved as neutral
                    and table elements, so that the simulation can run in
                    batch mode.
See also: msgsubstitute , substituteinfo , simobjdump , simdump , swapdump , simundump

25.112 openfile

Routine Name:   openfile

Description:    Opens ASCII file for reading or writing.

Usage:          openfile filename mode

                filename        name of existing file to open for access from
                                other GENESIS file-manipulation routines

                mode            mode in which to open file:
                                r to open file for read-only access;
                                w to open file for write-only access (this
                                wipes out any content of the file; see Notes);
                                a to open file for appending to the file
                                (existing content is not erased, but
                                writefiles are allowed)

Example:        genesis >  openfile hello w
                genesis >  writefile hello 10 20
                genesis >  openfile oldfile r
                genesis >  echo { readfile oldfile }

Notes:          You can have up to 20 files opened simultaneously.

                You can read data from an opened file using the readfile
                routine, and write data to the file using the writefile
                routine (if the file was opened for writing).

                Beware: If you open a file for writing (mode w) that already
                has text in it, that text will be DELETED!
See also: closefile , listfiles , readfile , writefile

25.113 planarconnect

Routine Name:   planarconnect

Description:    Establishes synaptic connections between groups of elements
                based on the x-y positions of the elements.  This routine 
                sets up the connections by adding SPIKE messages between the 
                source and destination objects.

Usage:          planarconnect source_elements destination_elements \
                -relative \
                -sourcemask {box, ellipse} x1 y1 x2 y2 \
                -sourcehole {box, ellipse} x1 y1 x2 y2 \
                -destmask   {box, ellipse} x1 y1 x2 y2 \
                -desthole   {box, ellipse} x1 y1 x2 y2 \
                -probability p

                source_elements  A wildcarded list of elements which are the 
                        sources of the SPIKE messages.  These must be of
                        class "spiking" and are usually spikegen or 
                        randomspike objects.

                destination_elements  A wildcarded list of elements which are
                        the destinations of the SPIKE messages.  These must  
                        be synchans or objects derived from synchan.

                -relative This option means that connections will be set up
                        based on the locations of destination objects
                        relative to source objects.  If this option is not
                        selected, the absolute locations of source and
                        destination elements will be used to determine
                        whichconnections are to be set up.

                -sourcemask {box, ellipse} x1 y1 x2 y2  -- This specifies a
                        rectangular or elliptical region from which source
                        elements are to be taken.  If the "box" option is 
                        used, then x1 and y1 are the minimum x and y values
                        of the region while x2 and y2 are the maximum x and y
                        values of the region.  If the "ellipse" option is 
                        used, then the source region is an ellipse with x1
                        and y1 representing the center of the ellipse while
                        x2 and y2 represent the lengths of the principal axes
                        in the x and y directions respectively.  Note that
                        to choose a circular region x2 and y2 must be equal.
                        Note also that one or the other of {box, ellipse} 
                        MUST be chosen; leaving both of them out will generate 
                        an error.  Finally, one can choose multiple source 
                        regions by having multiple -sourcemask options.  
                        The same conventions are followed for the next three 
                        options.  

                -sourcehole {box, ellipse} x1 y1 x2 y2  -- This specifies a
                        rectangular or elliptical region NOT to include in
                        the source region(s).  You can exclude multiple 
                        regions by having multiple -sourcehole options.

                -destmask {box, ellipse} x1 y1 x2 y2  -- This specifies a 
                        rectangular or elliptical region to which SPIKE
                        messages will be sent.

                -desthole {box, ellipse} x1 y1 x2 y2  -- This specifies a
                        rectangular or elliptical region NOT to include in
                        the destination region(s). 

                -probability p  -- This option causes connections to be 
                        made with a probability p, which must be in the
                        range [0,1].  This allows probabilistically-connected
                        networks to be set up.

Example:        [From the "Orient_tut" simulation:]
                
                planarconnect /retina/recplane/rec[]/input     \
                              /V1/horiz/soma[]/exc_syn         \
                              -relative                        \
                              -sourcemask box -1 -1  1  1      \
                              -destmask   box {-V1_SEPX * 2.4} \
                                              {-V1_SEPY * 0.6} \
                                              { V1_SEPX * 2.4} \
                                              { V1_SEPY * 0.6}

Notes:          This routine calculates distance using only the x and y 
                coordinates of the element positions.  It is convenient for
                objects laid out in planar arrays but ignoring the z
                direction is somewhat unrealistic.  volumeconnect is almost 
                identical with planarconnect except that it uses the positions
                of elements in three dimensions to specify whether connections 
                are made or not.  

                The weights and delays of the connections set up by this   
                command are typically specified using the planarweight and 
                planardelay commands, although they can be set up by hand.
See also: volumeconnect , planarweight , planardelay ; chapter 18 of the Book of GENESIS (2nd ed.) has a lengthy discussion on this and related commands.

25.114 planardelay

Routine Name:   planardelay

Description:    Sets the delay fields on groups of synapses between
                specified lists of elements.  Most often used to set
                delays on groups of synapses that have been set up
                by calling the "planarconnect" command.  This function
                can assign groups of synapses to a fixed delay, can
                assign delays in proportion to the distances between
                pre- and postsynaptic elements, and can add various
                types of randomness to delay values.

Usage:          planardelay sourcepath [destination_path]  \
                -fixed delay                               \
                -radial conduction_velocity                \
                -add                                       \
                -uniform scale                             \
                -gaussian stdev maxdev                     \
                -exponential mid max                       \
                -absoluterandom

                sourcepath  A wildcarded list of elements which are the 
                        sources of the SPIKE messages connecting the
                        pre- and postsynaptic elements (i.e. the presynaptic
                        elements).  These must be of class "spiking" and are 
                        usually spikegen or randomspike objects.

                destination_path  A wildcarded list of elements which must be
                        synchans or objects derived from synchan.  If this
                        (optional) argument is given, only the delays between 
                        the given set of pre- and postsynaptic elements will
                        be set by this command.  If this argument is not
                        given, then all the synapses receiving SPIKE messages
                        from the presynaptic elements will have their delays
                        set by this command.  NOTE: this optional argument is 
                        new and is not documented in the Book of GENESIS.

                -fixed delay  -- This option sets all the synaptic delays in
                        question to be equal to "delay".

                -radial conduction_velocity  -- This option sets the synaptic 
                        delays in question to be proportional to
                        the distance between the source and destination 
                        elements according to the equation:

                        delay = radial_distance / conduction_velocity

                        Where conduction_velocity is usually measured in
                        meters/sec (SI units).  "conduction_velocity"
                        represents the conduction velocity of the 
                        (hypothetical) axon that the spikes travel down.
                        For planardelay, the distance is measured as:

                        distance = 
                          sqrt((x_src - x_dest)^2 + (y_src - y_dest)^2)

                        where x_src is the x component of the source element,
                        x_dest is the x component of the destination element,
                        and so on.  Note that the z component is not taken
                        into account, which is unrealistic.  volumedelay
                        uses the z component as well.

                -add  This option causes the computed delays to be added to 
                        the preexisting delays in the synapses instead of
                        overwriting them.  This is useful when adding small 
                        synaptic delays, among other uses.  

                The next four options are used to add random components to the
                delays established using the -fixed or -decay options.  How
                these random components are added to the delays is explained
                below.

                -uniform scale  -- This option gives a random number taken 
                        from a uniform distribution in the range 
                        {-scale, scale}.

                -gaussian stdev maxdev  -- This option gives a random number
                        taken from a gaussian distribution centered on zero,
                        with a standard deviation equal to "stdev" and with
                        a maximum value of "maxdev".  The maximum value is
                        used to limit the random component to a given range.

                -exponential mid max  -- This option gives a random number
                        taken from an exponential distribution with a 
                        minimum value of zero, a 1/e point of "mid" and a 
                        maximum value of "max".  This is mainly for backwards
                        compatibility with genesis 1.4.

                -absoluterandom  This option alters the way the random number
                        is combined with the nominal delay to give the actual
                        delay, as described below.

                Once a random component has been created for a given delay, 
                it is used to set the delay as follows.  If the 
                -absoluterandom option has not been selected the delay is set 
                to be:

                final_delay = delay + (delay * random_number)

                Whereas if the -absoluterandom option has been selected then
                we have

                final_delay = delay + random_number

                Thus the default is to have the amount of randomness as a 
                constant proportion of the delay value.

Example:        [modified from the Orient_tut simulation:]

                planardelay /retina/recplane/rec[]/input \
                            -radial {CABLE_VEL}          \
                            -gaussian 0.1 0.3

                This command will set the size of the delays of synapses 
                that are receiving their inputs from 
                /retina/recplane/rec[]/input.  It gives delays equal to the
                radial distance between elements divided by the conduction
                velocity (CABLE_VEL).  It also specifies that gaussian noise 
                be added to the delays with a mean value of 0.1 (which 
                represents 10% of the original delay, since -absoluterandom 
                has not been selected) and a maximum value of 0.3 (which is 
                30% of the original delay value).

Notes:          The "destination_path" optional argument is new and is not
                documented in the Book of GENESIS.

                This routine calculates distance using only the x and y 
                coordinates of the element positions.  It is convenient for
                objects laid out in planar arrays but ignoring the z
                direction is somewhat unrealistic.  volumedelay is identical 
                to planardelay except that it uses the positions of elements 
                in three dimensions to calculate distances and is thus more 
                realistic.

                The delays are never allowed to go negative even if a large
                negative random component is added.  Negative delays are set
                to zero.

                If the -add option is chosen, the random component modifies 
                only the delay added and not the total delay.
See also: volumedelay , planarconnect , planarweight , syndelay ; Chapter 18 of the Book of GENESIS (2nd ed.) has a lengthy discussion on this and related commands.

25.115 planardelay2

Routine Name:   planardelay2

Description:    

Description:    A faster version of planardelay, which sets the delay fields
                on groups of synapses between specified lists of elements.
                Most often used to set delays on groups of synapses that have
                been set up by calling the "planarconnect" command.  This
                function can assign groups of synapses to a fixed delay, can
                assign delays in proportion to the distances between pre- and
                postsynaptic elements, and can add various types of randomness
                to delay values.

Usage:          planardelay sourcepath destination_path   \
                -fixed delay                              \
                -radial conduction_velocity                \
                -add                                       \
                -uniform scale                             \
                -gaussian stdev maxdev                     \
                -exponential mid max                       \
                -absoluterandom

Notes:          In contrast to planardelay, which can set the delays of all
                efferent synapses from the source map when no destination is
                given, planardelay2 only sets the delays of the synapses
                from the source map to a particular destination map.  By
                requiring the destination parameter, planardelay2 achieves
                faster setup times than planardelay.  For further details of
                usage and examples, see the documentation for planardelay.
See also: planardelay , planarconnect , planarweight , planarweight2

25.116 planarweight

Routine Name:   planarweight

Description:    Sets the weight fields on groups of synapses between
                specified lists of elements.  Most often used to set
                weights on groups of synapses that have been set up
                by calling the "planarconnect" command.  This function
                can assign groups of synapses to a fixed weight, can
                assign weights in proportion to the distances between
                pre- and postsynaptic elements, and can add various
                types of randomness to weight values.

Usage:          planarweight sourcepath [destination_path] \
                -fixed weight                              \
                -decay decay_rate max_weight min_weight    \
                -uniform scale                             \
                -gaussian stdev maxdev                     \
                -exponential mid max                       \
                -absoluterandom

                sourcepath  A wildcarded list of elements which are the 
                        sources of the SPIKE messages connecting the
                        pre- and postsynaptic elements (i.e. the presynaptic
                        elements).  These must be of class "spiking" and are 
                        usually spikegen or randomspike objects.

                destination_path  A wildcarded list of elements which must be
                        synchans or objects derived from synchan.  If this
                        (optional) argument is given, only the weights between 
                        the given set of pre- and postsynaptic elements will
                        be set by this command.  If this argument is not
                        given, then all the synapses receiving SPIKE messages
                        from the presynaptic elements will have their weights
                        set by this command.  NOTE: this optional argument is 
                        new and is not documented in the Book of GENESIS.

                -fixed weight  -- This option sets all the synaptic weights in
                        question to be equal to "weight".

                -decay decay_rate max_weight min_weight  -- This option sets
                        the synaptic weights in question to be proportional to
                        the distance between the source and destination 
                        elements according to the equation:

                        weight = (max_weight - min_weight) * 
                          exp(-decay_rate * distance) + min_weight

                        For planarweight, the distance is measured as:

                        distance = 
                          sqrt((x_src - x_dest)^2 + (y_src - y_dest)^2)

                        where x_src is the x component of the source element,
                        x_dest is the x component of the destination element,
                        and so on.  Note that the z component is not taken
                        into account, which is unrealistic.  volumedelay
                        uses the z component as well.

                The next four options are used to add random components to the
                weights established using the -fixed or -decay options.  How
                these random components are added to the weights is explained
                below.

                -uniform scale  -- This option gives a random number taken 
                        from a uniform distribution in the range 
                        {-scale, scale}.

                -gaussian stdev maxdev  -- This option gives a random number
                        taken from a gaussian distribution centered on zero,
                        with a standard deviation equal to "stdev" and with
                        a maximum value of "maxdev".  The maximum value is
                        used to limit the random component to a given range.

                -exponential mid max  -- This option gives a random number
                        taken from an exponential distribution with a 
                        minimum value of zero, a 1/e point of "mid" and a 
                        maximum value of "max".  This is mainly for backwards
                        compatibility with genesis 1.4.

                -absoluterandom  This option alters the way the random number
                        is combined with the nominal weight to give the actual
                        weight, as described below.

                Once a random component has been created for a given weight, 
                it is used to set the weight as follows.  If the 
                -absoluterandom option has not been selected the weight is set 
                to be:

                final_weight = weight + (weight * random_number)

                Whereas if the -absoluterandom option has been selected then
                we have

                final_weight = weight + random_number

                Thus the default is to have the amount of randomness as a 
                constant proportion of the weight value.

Example:        [modified from the Orient_tut simulation:]

                planarweight /retina/recplane/rec[]/input \
                             -decay 0.5 10.0 0.1          \
                             -gaussian 0.1 0.3

                This command will set the size of the weights of synapses 
                that are receiving their inputs from 
                /retina/recplane/rec[]/input.  It gives exponentially decaying
                weights with a maximum size of 10.0, a minimum size of 0.1,
                and a decay rate of 0.5.  It also specifies that gaussian
                noise be added to the weights with a mean value of 0.1 
                (which represents 10% of the original weight, since 
                -absoluterandom has not been selected) and a maximum value of
                0.3 (which is 30% of the original weight value).

Notes:          The "destination_path" optional argument is new and is not
                documented in the Book of Genesis.

                This routine calculates distance using only the x and y 
                coordinates of the element positions.  It is convenient for
                objects laid out in planar arrays but ignoring the z
                direction is somewhat unrealistic.  volumeweight is identical 
                to planarweight except that it uses the positions of elements 
                in three dimensions to calculate distances and is thus more 
                realistic.

                The weights are never allowed to go negative even if a large
                negative random component is added.  Negative weights are set
                to zero.

                The options -fixed and -decay are mutually exclusive.  The 
                different random options -uniform, -gaussian, and -exponential
                are also mutually exclusive.
See also: volumeweight , planarconnect , planardelay ; Chapter 18 of the Book of GENESIS (2nd ed.) has a lengthy discussion on this and related commands.

25.117 planarweight2

Routine Name:   planarweight2

Description:    

Description:    A faster version of planarweight, which sets the weight fields
                on groups of synapses between specified lists of elements.
                Most often used to set weights on groups of synapses that have
                been set up by calling the "planarconnect" command.  This
                function can assign groups of synapses to a fixed weight, can
                assign weights in proportion to the distances between pre- and
                postsynaptic elements, and can add various types of randomness
                to weight values.

Usage:          planarweight sourcepath destination_path   \
                -fixed weight                              \
                -decay decay_rate max_weight min_weight    \
                -uniform scale                             \
                -gaussian stdev maxdev                     \
                -exponential mid max                       \
                -absoluterandom

Notes:          In contrast to planarweight, which can set the weights of all
                efferent synapses from the source map when no destination is
                given, planarweight2 only sets the weights of the synapses
                from the source map to a particular destination map.  By
                requiring the destination parameter, planarweight2 achieves
                faster setup times than planarweight.  For further details of
                usage and examples, see the documentation for planarweight.
See also: planarweight , planarconnect , planardelay , planardelay2

25.118 plane

Routine Name:   plane

Description:    Generates 3-D coordinates for a plane with specified
                dimensions and characteristics.

Usage:          plane filename x y dx dy [-center cx cy] [-jitter jx jy]
                        [-normal] [-ellipse] [-hexagonal]

                filename        name for file into which to put generated
                                coordinates

                x               x dimension of rectangular area; if -e option
                                selected, x axis of ellipsoid area

                y               y dimension of rectangular area; if -e option
                                selected, y axis of ellipsoid area

                dx              spacing in x dimension between points

                dy              spacing in y dimension between points

                -center         flag specifying that center of plane should be
                                set at coordinates (cx,cy) (default: (0,0))

                cx              x coordinate of center of plane (default: 0)

                cy              y coordinate of center of plane (default: 0)

                -jitter         flag specifying that linearly random jitter
                                should be added to offset coordinates from a
                                perfect array (jitter in x dimension will vary
                                in range -jx*dx < jitter < jx*dx; jitter in y
                                dimension will vary in range
                                -jy*dy < jitter < jy*dy)

                jx              jitter in x dimension (as fraction of dx)
                                (default: 0)

                jy              jitter in y dimension (as fraction of dy)
                                (default: 0)

                -normal         flag specifying that an additional set of 3
                                coordinates is generated per line, to define
                                the normal to the surface (this format is
                                compatible with that read by the cellsheet
                                routine)

                -ellipse        flag specifying that generated coordinates
                                should be restricted to lie in an ellipse with
                                major axes specified by x,y

                -hexagonal      (not yet implemented) flag specifying that
                                generated coordinates should lie in a
                                hexagonal (rather than rectangular) array

Example:        plane planepoints 400e-6 400e-6 100e-6 100e-6 -normal

Notes:          All of the cells in the plane have an initial z coordinate of
                0.0.  (See position for how to change this).
See also: egg , cellsheet

25.119 pope

Routine Name:   pope

Description:    Restores previously stacked ("pushed") element as current
                working element.

Usage:          pope

Example:        genesis >  pwe
                /neuron
                genesis >  pushe /somewhereelse
                /somewhereelse
                genesis >  pwe
                /somewhereelse
                genesis >  pope
                /neuron
                genesis >  pwe
                /neuron

Notes:          This routine ("pop element") is analogous to the
                operating-system shell "popd" feature for directories.
See also: pushe , stack

25.120 position

Routine Name:   position

Description:    Sets xyz coordinates of an element and all of its children.

Usage:          position element x y z

                element         element whose coordinates to specify

                x, y, z         x, y, z coordinates to give element; to
                                specify absolute coordinates, use a number;
                                to specify coordinates relative to the current
                                position, use the form Rnumber; to ignore the
                                coordinate (leave it as it is), use I

Example:        position /neuron 10 20 4.6
                position /neuron I I R5.2
                position /neuron 1.5 R1.1 I
                position /V1/horiz 0 0 {-5 * V1_SEPZ}

Notes:          This routine affects the positions of the child elements as
                well as that of the parent.

25.121 pow

Routine Name:   pow

Description:    Returns a number raised to a specified power.

Usage:          raised-value = {pow number power)

Example:        genesis >  echo { pow 10 3 }
                1000

Notes:          
See also: exp

25.122 printargs

Routine Name:   printargs

Description:    Displays its arguments with argument numbers.

Usage:          printargs(argument)

Example:        genesis > printargs "a b c d"
                argc 1 : a,b,c,d
                genesis > printargs a b c d
                argc 1 : a
                argc 2 : b
                argc 3 : c
                argc 4 : d

Notes:
See also: argc , argv , arglist , getarg

25.123 printenv

Routine Name:   printenv

Description:    Displays value of operating-system environmental variable.

Usage:          printenv environment-variable

Example:        genesis >  printenv SIMPATH
                SIMPATH=. /usr/genesis/startup

Notes:          This is a GENESIS implementation of the operating system
                command printenv, which displays the value of a particular
                operating system environmental variable.  Unlike its
                operating-system counterpart, printenv from within GENESIS
                requires that you supply a variable name (outside of GENESIS,
                printenv with no arguments displays the list of all your
                environmental variables).

                Printenv sends its output directly to the screen.  If you need
                to capture the information that printenv displays in a GENESIS
                variable, use the getenv routine instead.
See also: getenv , setenv

25.124 pushe

Routine Name:   pushe

Description:    Saves current working element on stack (for later retrieval
                using pop), with option to go to new current working element.

Usage:          pushe [path]

                path            pathname of element to make new current
                                working element (default: leave pushed
                                element as current working element)

Example:        genesis >  ce /output
                genesis >  pushe /mitral
                /mitral
                genesis >  pwe
                /mitral
                genesis >  ce /
                genesis >  pope
                /output

Notes:          This routine ("push element") is analogous to the
                operating-system shell "pushd" feature for directories.

                pushe is used to change element to a new working element while
                saving the location of the current working element on a stack.
                The pope routine can then be used to return to the element path
                stored on the stack.
See also: pope , stack

25.125 putevent

Routine Name:   putevent

Description:    Used to place events into a buffer class element

Usage:          putevent buffer time amplitude [time amplitude]

Example:        

create playback /test
putevent /test 10 10.0 20 0.0 30 30.0 40 0.0 50 50.0 60 0.0
See also: playback

25.126 pwe

Routine Name:   pwe

Description:    Displays full pathname of current working element.

Usage:          pwe

Example:        genesis >  pwe
                /neuron/test
                genesis >  ce ..
                /neuron

Notes:          The pwe routine prints the path of the current working element
                in the GENESIS element hierarchy.  (This routine is analogous
                to the operating-system command "pwd", which prints the current
                working directory.)
See also: ce

25.127 quit

Routine Name:   quit

Description:    Exits from GENESIS, terminating any simulation in progress.

Usage:          quit

Notes:          Alias for exit routine.

25.128 rand

Routine Name:   rand

Description:    Returns a random number falling in a specified range.

Usage:          number = { rand lo hi}

Example:        genesis >  echo { rand 0 1 }
                0.2742720246
                genesis >  echo { rand 0 1 }
                0.5690608621
                genesis >  echo { rand 0 100 }
                32.53029251

Notes:          
See also: randseed

25.129 randcoord

Routine Name:   randcoord

Description:    Shuffles positions of compartments in a neuron.

Usage:          randcoord element fraction [-electrical] [-channel]

                element         name of element to shuffle

                fraction        fractional amount of shift

                -electrical     flag for scaling electrical properties with
                                changes in length of compartment

                -channel        flag for scaling conductance of channels with
                                changes in length of compartment (currently,
                                only hh_channels and channelC2s are recognised)

Example:        randcoord /cell 0.1 -electrical

Notes:          Shuffles around the positions of compartments in a neuron,
                based on messages, to make the cell look more natural.  If the
                given element is not a compartment, it looks for children that
                are compartments without incoming AXIAL messages, i.e. somas.
                If the given element is a compartment, it starts the traversal
                at the compartment itself.  Having found the root elements, it
                then traverses them by their message trees, relatively
                positioning the children.
See also: relposition

25.130 randseed

Routine Name:   randseed

Description:    Initializes random-number generator with new random seed.

Usage:          randseed  [seed]

Example:        genesis > echo {randseed}
                803971369

                genesis > randseed 54321
                WARNING from init_rng: changing global seed value!
                Independence of streams is not guaranteed

Notes:          Re-seeding the random-number generator with different values
                insures that a simulation using commands or objects based on
                random numbers (e.g. rand or randomspike) produces different
                results each time that it is run.  Likewise, re-seeding with
                the same value will guarantee that your results are
                reproducible.  If no argument is given, a seed is chosen using
                the system clock, otherwise the argument is used as the seed.

                The randseed command sets the seed of both the default
                Numerical Recipes genenerator and the SPRNG generator,
                regardless of which one has been made active by the setrand
                command.  The warning message shown in the example above
                is generated by the SPRNG generator, and should not be
                a cause for concern.
See also: setrand , rand

25.131 readcell

Routine Name:   readcell

Description:    Creates a model neuron from a description in a cell parameter
                file.

Usage:          readcell filename cellname -hsolve -prand SDlen SDdia
                         -rand SDlen SDdia -split Number -lambdasplit maxl

                filename        name of the  cell descriptor file
                                (should end with extension .p)

                cellname        name of the neutral element to be at the
                                head of the tree of elements which comprise
                                the cell

                -hsolve         create cellname as an hsolve element

Example:        readcell cell.p /cell
                readcell cell.p /hcell -hsolve

        "cell.p" contains:

        *relative
        *cartesian
        *asymmetric

        *set_compt_param        RM      0.33333
        *set_compt_param        RA      0.3
        *set_compt_param        CM      0.01
        *set_compt_param     EREST_ACT  -0.07

        // For the soma, use the leakage potential (-0.07 + 0.0106) for Em
        *set_compt_param     ELEAK      -0.0594
        soma  none   30  0  0  30 Na_squid_hh 1200 K_squid_hh 360 spike 0.0

        // The dendrite has no H-H channels, so ELEAK = EREST_ACT
        *set_compt_param     ELEAK      -0.07
        dend  soma  100  0  0   2   Ex_channel 0.795775

Notes:

    The first example above will produce the element tree

        /cell/soma:
        Na_squid_hh K_squid_hh  spike

        /cell/dend:
        Ex_channel

    with the maxium channel conductances scaled by the area of the
    compartment.  Here, "/cell" will be a neutral element.  In the second
    example, "/hcell" will be an hsolve element.  This is the preferred way of
    creating a cell which is to be taken over by the Hines solver, as it
    automatically creates the hsolve element as the root of the element tree
    and sets the path for the elements to be solved.  Note that, starting with
    GENESIS version 2.2, it is necessary to provide the full path to the cell
    when using readcell to directly create an hsolve.  (e.g.  you can't use
    "readcell cell.p hcell -hsolve", even if "/" is the current working
    element.)  

    In cartesian coordinates, the format for each compartment parameter line
    in a cell parameter file is
    
        name parent x y z dia chan dens [chan dens] ...  

    For polar coordinates, it is

        name parent r theta phi dia chan dens [chan dens] ...

    Here, 'name' gives the name of the compartment, and 'parent' refers to the
    adjacent compartment to which it is connected.  'parent' may be replaced
    by '.' to refer to the compartment defined on the preceding line.  For
    asymmetric compartments, the connection to 'parent' is through the axial
    resistance (Ra) of 'name'.  The coordinates and diameter (x, y, z, dia)
    are in microns, all other units are SI (Meter, Kg, Second, Ampere).  In
    polar mode 'r' is in microns, theta and phi in degrees.  Theta is measured
    from the z-axis and phi from the x-axis in the x-y plane.  The compartment
    length, which is not stated explicitly, is calculated from the coodinates
    of the compartment and its parent.

    'chan' is the name of one of the channel prototypes under the neutral
    element '/library'.  At present, the supported channel types are
    hh_channel, tabchannel, tab2Dchannel, tabcurrent, vdep_channel, synchan,
    hebbsynchan, ddsyn, receptor2, manuelconduct, and graded.  'chan' may also
    refer to the other neural element types:  spikegen, Ca_concen, difshell,
    difbuffer, concpool, mmpump, and hillpump.  Presently, the obsolete
    channelC, channelC2, channelC3, and spike objects are also supported.

    For channels, 'dens' is the conductance density (Gbar or gmax per unit
    compartment area) in Siemens/m^2.  If a negative value is specified, the
    absolute value is taken, and it is interpreted as the maximum
    conductance in Siemens, without scaling by the compartment area.

    For spikegen elements, the 'dens' parameter is the 'thresh' field of the
    element.  For Ca_concen elements, it is the 'B' field, divided by the
    volume of the compartment.  However, if the 'thick' field of the Ca_concen
    element is non-zero, the volume is scaled using the volume of a true shell
    of thickness 'thick'.  A negative value of 'dens' is used to indicate that
    it should be taken as an absolute value of B, without scaling.

    A maximum of 30 'chan dens' pairs are allowed in a compartment
    specification.  The '*compt' option described below provides a way to
    overcome this limitation.

    Several types of options may be specified in the cell parameter file.
    These options start with a '*', and affect all lines following them,
    until canceled by the opposite command.

    COMPARTMENT COORDINATES

    *relative           coordinates are relative to parent
    *absolute           coordinates are absolute (default)
    *polar              polar coordinates
    *cartesian          cartesian coordinates (default)

    *lambda_warn        will issue warning if the electrotonic length of the
                        compartment (in terms of the space constant, lambda)
                        is outside the range 0.01-0.20.

    *lambda_warn MIN MAX    same as above, but uses the range MIN-MAX.

    *lambda_unwarn      turns off lambda warning (default)

    *double_endpoint

        allows both endpoints to be explicitly entered for all compartments.
        The syntax is:

        name parent x0 y0 z0 x y z chans dens... for cartesian mode, and
        name parent r0 t0 p0 r t p chans dens... for polar mode.

        The double endpoint mode has two main uses.  First, when one is adding
        dendrites to a spherical compartment like a soma, one wants the
        dendrite to begin at the edge of the sphere, not in the middle.  The
        double endpoint mode allows the user to attach the cylinder at any
        desired point.  While this does not matter electrically, the cell will
        be prettier when displayed with xcell.

        Second, this allows the anatomical (not electrical) attachment of
        dendrites in the middle of another compartment rather than at an
        endpoint.  This flexibility may be particularly important for modeling
        invertebrate neurons, whose large process diameters often mean that
        the distance between two branch points is just a tiny fraction of the
        electrotonic length constant.  The only caveat in using the mode for
        this purpose is that the view in xcell gives less information about
        how the model is performing electrically.  For example, if a branch is
        connected in the middle of a compartment anatomically (and thus it
        will be displayed as such in the cell viewer), one must remember that
        it is not connected electrically at that point, but (presumably) at
        the closer endpoint of that compartment.

    *double_endpoint_off    turns off double endpoint mode

    COMPARTMENT SHAPE

    *spherical          make a spherical compartment
    *cylindrical        make a cylindrical compartment (default)
    *symmetric          make symmetric compartments
    *asymmetric         make asymmetric compartments (default)

    PARAMETER VALUES

    *set_compt_param variable value

        sets one of the following internal variables used by the cell
        reader to 'value'.  'value' may be a number, or the name of a
        globally defined script variable.

        RM            specific membrane resistance in ohm*m^2
        RA            specific axial resistance in ohm*m
        CM            specific membrane capacitance in farad/m^2
        EREST_ACT     resting potential in volts (initial Em and initVm)
        ELEAK         if specified, gives an alternate value for initial Em,
                      so that Vm will be initialized to initVm (EREST_ACT)
                      on reset, instead of Em.  Otherwise, ELEAK = EREST_ACT.

    *set_global variable value    

        similar to the above, but also sets the value of global script
        variables of the same name.  However, it does not support the ELEAK
        internal variable.  If the RM, CM, RA and EREST_ACT global variables
        have not been previously declared, readcell will create them.
        'variable' may also be the name of any other previously declared
        global script variable other than the internal variables listed
        above.  In this case '*set_global' may be used to set the values of
        these script variables.

    COMPARTMENT AND CELL PROTOTYPES

    *start_cell CELL_NAME     start new cell (in separate tree)

    *append_to_cell CELL_NAME append to existing cell

    *makeproto COMP_NAME      converts new cell to prototype configuration

    *compt COMP_NAME          all following compartments will be copies of
                              COMP_NAME, including its complete subtree and
                              messages between its elements, with gmax/Gbar
                              appropriately scaled (unless 'dens' is
                              negative).  This allows you to avoid repeating
                              many long strings of channel specifications when
                              there are many compartments that have the same
                              channels with the same conductance densities.
                              It also permits compartments to contain elements
                              of types other than the ones recognized by
                              readcell.  In this case, create a prototype
                              compartment that contains the desired channels
                              or other elements linked by any necessary
                              messages, and use "*compt" in the cell parameter
                              file to make additional copies of the
                              compartment.

    These commands are illustrated in Scripts/int_methods/granule.p and
    Scripts/examples/pore/markov.

    Messages can be specified between elements in different compartment
    subtrees by creating and setting an extended field "addmsg#", where "#" is
    an integer.  This field will contain a string of the form "source
    destination message-name [values]", defining the message.  For example,
    this commonly done to allow readcell to properly set up the needed
    messages between calcium channels, Ca_concen elements, and calcium
    dependent potassium channels.  This is illustrated in
    Scripts/neurokit/prototypes/traub91chan.g.

    SPINES and BRANCHES

    There are a variety of commands used for adding dendritic spines and
    branches to compartments.  These commands affect the passive structure
    of the neuron only.

    *memb_factor MEMB_FACTOR    scales all membrane surface by this factor

    *add_spines DENDR_DIAM SPINE_DENS SPINE_SUR   

        Adds membrane surface for collapsed spines to all compartments with
        dia <= DENDR_DIAM; units: um, 1/um, um^2.

    *rand_spines DENDR_DIAM SPINE_DENS SPINE_SURF AV_LENGTH SPINE_FREQ
        spine_proto

        Like above, but a random number of spines will be attached as copies
        of the compartment(s) spine_proto. The number of spines added
        depends on SPINE_FREQ and AV_LENGTH.  On the average a compartment
        with dia <= DENDR_DIAM and len = AV_LENGTH will receive n =
        SPINE_FREQ spines.  If SPINE_FREQ >= 1.0 then all compartments with
        dia <= DENDR_DIAM will receive at least one spine.  The dendritic
        surface area is still corrected for the 'missing' spines.
        (See, for example, Scripts/purkinje/Purk2M9s.p.)

    *mrand_spines DENDR_MIN DENDR_DIAM SPINE_DENS SPINE_SURF AV_LENGTH
        SPINE_FREQ spine_proto

        Like above, but a random number of spines will be attached as copies
        of the compartment(s) spine_proto. Number of spines added depends on
        SPINE_FREQ and AV_LENGTH.  On the average a compartment with
        DENDR_MIN < dia <= DENDR_DIAM and len = AV_LENGTH will receive
        n=SPINE_FREQ spines.  If SPINE_FREQ >= 1.0 then all compartments
        with DENDR_MIN < dia <= DENDR_DIAM will receive at least one spine.
        The dendritic surface area is still corrected for the 'missing'
        spines on dendrites with dia <= DENDR_DIAM.

    *fixed_spines DENDR_DIAM SPINE_NUM SPINE_SURF SPINE_SKIP spine_proto

        Like above, but a fixed number of spines will be attached as copies
        of the compartment(s) spine_proto. Number of spines added is
        SPINE_NUM, from this command onward a spine will be added every
        SPINE_SKIP compartments (if dia <= DENDR_DIAM) The dendritic surface
        area is still corrected for the 'missing' spines.

    *mfixed_spines DENDR_MIN DENDR_DIAM SPINE_NUM SPINE_SURF SPINE_SKIP
        spine_proto

        Like above, but a fixed number of spines will be attached as copies
        of the compartment(s) spine_proto. Number of spines added is
        SPINE_NUM, from this command onward a spine will be added every
        SPINE_SKIP compartments (if DENDR_MIN < dia <= DENDR_DIAM).  The
        dendritic surface area is still corrected for the 'missing' spines.

    *rand_branches MAX_DIA RAND_FREQ NUM_ORDERS POSTFIX NUM_COMPS MIN_L
        MAX_L MIN_D MAX_D [NUM_COMPS MIN_L MAX_L MIN_D MAX_D] ...

        Adds more branches randomly at the end of dendrites.  The routine
        assumes that the .p file has a logical order, where each branch
        segment is defined in continuing lines and the first segment after a
        branchpoint is defined immediately after the segment before the
        branchpoint (if this is not the case the things might still work
        correctly by the MAX_DIA control).  The branching is binary (thus
        either 2 or 4 or 8 or ...  segments are added.  NUM_ORDERS (1-5)
        determines the number of branchpoints that are added.  For each
        branchpoint one gives the MIN_L and MAX_L (length) and MIN_D and
        MAX_D (diameter) and NUM_COMPS, the number of compartments per
        segment.  Adds smartly:  will skip thick segments if the existing
        dendritic tip is thin and will only add to 'tips' with a diameter <
        MAX_DIAM.  Frequency of addition of these branches is controlled by
        RAND_FREQ (0-1): if RAND_FREQ == 1 all tips smaller than MAX_DIAM
        will have branches appended.  The name will be the name of the
        parent + POSTFIX, indexed from 0 to 2^(NUM_ORDERS-1).  For a "full"
        addition (to a thick dendritic tip) the number of added compartments
        is 2*NUM_COMPS[1] + ... + 2*NUM_COMPS[NUM_ORDERS].
See also: writecell , compartment , Scripts/neurokit/README, Scripts/int_methods/granule.p

25.132 readfile

Routine Name:   readfile

Description:    Reads a line of data from an opened ASCII file.

Usage:          readfile filename -linemode

                -linemode       option indicating that entire line of file
                                should be returned as a single string, rather
                                than as a list of arguments (the latter is the
                                default)

                filename        name of ascii file (must be already opened
                                using r option of openfile routine)

Example:
        openfile test w
        writefile test 1.0 2.0 3.0
        writefile test 4.0 5.0 6.0
        writefile test 7.0 8.0 9.0
        closefile test
        openfile test r
        // 1st line as 3 args:
        echo {readfile test}
        // gives: 1.0 2.0 3.0
        // 2nd arg of 2nd line:
        echo {getarg {readfile test} -arg 2}
        // gives: 5.0
        // 3d line as one argument:
        echo {getarg {readfile test -l} -arg 1}
        // gives: 7.0 8.0 9.0

        // using the file Vm1 generated by the MultiCell demo
        function processline
           int step = {argv 1}
           float Vm = {argv 2}
           echo "Time step: "{step}
           echo "Membrane potential: "{Vm}
        end

        openfile Vm1 r
        processline {readfile Vm1}
        processline {readfile Vm1}
        .
        .
        closefile Vm1

Notes:          The readfile routine does not alter the file in any way.
See also: openfile , closefile , listfiles , readfile , getarg

25.133 reclaim

Routine Name:   reclaim

Description:    Reclaims memory from deleted elements

Usage:          reclaim

Example:        call Na_hh_tchan TABDELETE
                delete Na_hh_tchan
                reclaim

Notes:          Memory from deleted elements is usually freed when the
                simulator returns to the command prompt.  When running
                in batch mode in situations where many elements are being
                created and deleted, it may be necessary to use reclaim
                to free the memory from deleted elements.

                At present, elements containing interpol_structs (tables) do
                not free up the memory allocated to the tables, when they are
                deleted.  Objects that have a TABDELETE action (e.g.
                tabchannels) will deallocate this memory, if TABDELETE is
                called before the element is deleted.  Finally, you have to
                give the reclaim command for the memory to actually be freed.

                Note that the tables are shared among all tabchannels that are
                created by copy or readcell from a prototype.  Therefore, you
                shouldn't call TABDELETE unless you plan to delete all copies
                of the channel.

                Care should be taken to ensure that deleted elements
                will not be actively executing after reclaim is
                called.  This should only be a potential problem within
                an extended object action function or a widget callback
                script.  Also, it should be noted that reclaim will
                recompute the simulation schedule which could be time
                consuming.
See also: delete , Tables

25.134 relposition

Routine Name:   relposition

Description:    Positions element and its child compartments based on messages
                rather than directory-type parent-child relationships.

Usage:          relposition element dx dy dz

                element         name of element to shift

                dx dy dz        amount of shift in x, y, and z directions

Example:        (Using the traub91 simulation)

                genesis > showfield /cell/soma x y z
                [ /cell/soma ]
                x                    = -0.001324999961
                y                    = 0
                z                    = 0

                genesis > showfield /cell/soma x y z
                [ /cell/soma ]
                x                    = 0.09867500514
                y                    = 0.200000003
                z                    = 0.3000000119

                genesis > showfield /cell/apical_10 x y z
                [ /cell/apical_10 ]
                x                    = -0.001199999941
                y                    = 0
                z                    = 0

                genesis > showfield /cell/basal_8 x y z
                [ /cell/basal_8 ]
                x                    = 0.09856500477
                y                    = 0.200000003
                z                    = 0.3000000119

Notes:          Moves the element and all children by dx, dy, dz.  The child
                elements are determined from messages rather than parent-child
                relationships.  This is necessary for handling 'flat' element
                structures.  When we have a cell loaded by readcell, the
                children dendrites cannot be identified by the parent soma, so
                this command traverses the AXIAL/RAXIAL compartment messages
                to figure out the children to move.

                In the example above, the relposition command moved the soma
                and all of the basal compartments, but none of the apical
                compartments.  This is because only the basal compartments are
                children of the soma.
See also: position , randcoord

25.135 resched

Routine Name:   resched

Description:    Assigns elements for simulation according to the
                current simulation schedule. 

Usage:          resched

Example:        [from startup/schedule.g:]

                deletetasks
                ...
                addtask Simulate /##[CLASS=device]      -action PROCESS
                addtask Simulate /##[CLASS=output]      -action PROCESS
                resched

Notes:          If you have created any new objects you want included in the
                current simulation schedule, you need to run resched so that
                the new object will be made known to the simulator.  This
                applies in particular to either compiled or extended objects
                that have an INIT or PROCESS action.   (However, the reset
                command also does an implicit resched.)

                In the example, all simulation events are removed from the
                schedule, and then new simulation tasks are listed in the
                schedule.  (Only the last two are shown here.)  Finally,
                resched is called in order to reread the simulation schedule
                and schedule the listed element types for simulation.
See also: Schedules , addtask

25.136 reset

Routine Name:   reset

Description:    Resets simulation to initial conditions.

Usage:          reset

Example:        genesis > reset
                time = 0.000000 ; step = 0

Notes:          The reset routine returns the simulation state to its initial
                conditions (e.g., the simulation time is set back to 0) and
                invokes each enabled element with the RESET action in order
                for them to place themselves back in the initial condition
                state.  You should reset the simulation whenever you are
                getting ready to start a new simulation run, or after you
                adding new elements to the simulation.

                If the initial state of one element depends on the initial
                state of another element, you may need to call the RESET
                action for specific elements in the proper order -- the reset
                routine gives no control over the order in which the elements
                are RESET, and the simulator does not check for such
                dependencies.  (In most cases, you can issue two reset
                commands, instead.)

                For instance, the object which computes the Nernst equilibrium
                potential requires ionic concentrations. The initial potential
                therefore relies on the initial ionic concentrations. Thus the
                elements which compute the ionic concentrations must be reset
                before the elements which compute the concentration-dependent
                equilibrium potentials.  An example is given in nernst.txt.

                It is up to you to determine whether reset order is
                important.  Also, you should make sure that any objects you
                create document the conditions under which these
                dependencies arise.

25.137 resetsynchanbuffers

Routine Name:   resetsynchanbuffers
 
Description:    resets the size of all synchan event buffers (and event 
                buffers of objects derived from synchan) to the default
                size (specified in the nodes_per_synapse field of the
                object).
 
Usage:          resetsynchanbuffers
 
Example:        genesis > resetsynchanbuffers
                genesis >

Notes:          This command also flushes all the pending events from the
                event buffers.  This command is never necessary unless
                you're running out of memory because there were too
                many spikes generated as inputs to synchan objects 
                This might happen, for instance, if you set up a
                simulation incorrectly so that huge numbers of spikes were
                generated by mistake.  For instance, if the abs_refract field 
                of a spikegen object is set to zero and the input to the
                spikegen crosses threshold then large numbers of spikes
                will be generated.
See also: synchan

25.138 restore

Routine Name:   restore

Description:    Restores element state stored in file with save routine.

Usage:          restore file-name

Example:        restore mycell.save

Notes:          After using the save command, restore may be used to restore
                save element field values from a file.  This allows you to
                resume a long simulation at the point where you left off.
                An element must be capable of performing the RESTORE2 action
                for its fields to be restored.
See also: save

25.139 rotcoord

Routine Name:   rotcoord

Description:    Rotates coordinates of elements in 3-D space.

Usage:          rotcoord path angle [-x | -y | -z | -axis x y z] [-center]
                                    [-translatekids | -fixkids]

                path            path of element to be rotated

                angle           angle (in radians) for rotation

                -x              rotate about the x axis
                -y              rotate about the y axis
                -z              rotate about the z axis

                -axis x y z     use vector specified by x, y, z coordinates
                                as the axis of rotation

                -center x y z   offset center of rotation (default: 0,0,0)

                -translatekids  have children of selected element translated
                                parallel to the parent rather than rotated
                                (default is to rotate)

                -fixkids        prevent children of selected elements
                                from being moved

Example:        rotcoord /library/cell {-3.1415927/2} -y

Notes:          Note that the angle of rotation is in radians, clockwise
                about the specified axis.  By default, all the children of
                the selected element are rotated as well.  In the example,
                the original cell had the apical dendrite pointing along the
                x-axis.  This command will rotate it 90 degrees
                counterclockwise about the y-axis to point outward along the
                z-axis.  This is useful when using createmap or cellsheet to
                make a grid of cells having their dendrites normal to a
                surface.
See also: cellsheet

25.140 round

Routine Name:   round

Description:    Rounds decimal number to nearest integer value.

Usage:          rounded-value = {round number}

                rounded-value           returned as integer

                number                  integer or floating-point number
                                        to round

Example:        genesis > echo { round 3.333 }
                3
                genesis > echo { round 3.666 }
                4

Notes:          This routine converts any number to an integer by rounding
                to the nearest whole number.
See also: trunc

25.141 save

Routine Name:   save

Description:    Saves current field values for specified element in a file. 

Usage:          save  path  file-name  -append

                path            pathname of element for which to save
                                field values in file

                file-name               name of file in which to store field values

                -append         flag specifying that field values should
                                be appended to file (if omitted, field
                                values overwrite any existing values in file)

Example:        save /cell/## mycell.save
                reset  // (Or quit and restart genesis)
                restore mycell.save

Notes:          The save and restore commands are useful when you need to
                resume a long simulation at the point where you left off.
                However, some of the older simulation objects do not have
                the required SAVE2 action which is invoked with save.  (The
                showobject command will list the actions performed by an
                object.)  When using hsolve elements in chanmode 2 or 3, one
                must also call HSAVE and HRESTORE for the hsolve element.
See also: restore , hsolve

25.142 scaletabchan

Routine Name:   scaletabchan

Description:    Performs scaling and offsets of the tabchannel A and B tables
                for a specified gate.

Usage:          scaletabchan channel-element gate mode sx sy ox oy -duplicate

                channel-element name of a the tabcahnnel
                gate            gate to be modified; one of: X, Y, or Z
                sx              x-axis (voltage) scale factor
                sy              y-axis scale factor
                ox              x-axis (voltage) offset
                oy              y-axis offset
                mode            one of: a[lpha] b[eta] t[au] m[inf]

Example:        // double (spread out) the voltage range for the Na
                // activation alpha rate constant.
                scale_tabchan Na X alpha 2.0 1.0 0.0 0.0

                // increase the K_dr activation time constant by 20%.
                scaletabchan K_dr X tau 1.0 1.2 0.0 0.0

                // shift the Na inactivation curve (Y gate) left by 5 mV.
                scale_tabchan Na Y minf 1.0 1.0 -0.005 0.0

                // increase the K_dr activation time constant by 0.1 sec.
                scaletabchan K_dr X tau 1.0 1.0 0.0 0.1

Notes:          The tabchannel internal tables for the specified gate are
                modified to provide scalings and/or offsets to the voltage
                dependent function specified by the mode.  Here, alpha and
                beta are the Hodgkin-Huxley rate constants, tau is the time
                constant for activation or inactivation, and minf is the
                steady state activation or inactivation.  The effect of
                applying these scalings and offsets may be viewed by using the
                edit_channel menu of Neurokit.

                Note that the scale and offset is always relative to the last
                operation, and not to the original values.  One can reverse
                changes in oy and sy because they just shift and scale the
                table values.  However, ox and sx perform offsets and scaling
                of the horizontal axes by moving data in the tables.  This can
                cause data to spill out of the ends of the tables and be lost.
                Thus, large changes in the x-axis should be avoided, if you
                plan to reverse your changes.

                In a large compartmental model or large network, one may have
                many copies of a particular prototype channel.  Usually, one
                wants these to behave identically.  It is also desirable to
                minimize the amount of storage space used by the internal
                tables.  For these reasons, copies of the channel which are
                created by the copy command or by readcell use the same tables
                as the original prototype, rather than creating new copies of
                the tables.  This is true of all objects which contain tabular
                fields.  Sometimes you may want to change just the one copy of
                the channel.  In this case, use the "-duplicate" option with
                scaletabchan.
See also: tabchannel , Tables .

25.143 setclock

Routine Name:   setclock

Description:    Sets time interval (step size) associated with specified clock.

Usage:          setclock clock-number value

Example:        setclock 0 0.01     // simulation time step in msec
                setclock 1 0.05     // plotting interval can be larger

                genesis >  setclock 0 5.5
                changing clock [0] from 1 to 5.5

Notes:          The setclock routine is used to set the current value
                assigned to the time increment for one of the GENESIS
                simulator clocks.  These clocks are updated each time a step
                is performed.

                Clock number 0 is the default clock used by each element to
                determine how often it should perform a simulation step.  When
                components of a simulation run at significantly different time
                scales, it may be useful to use other clocks (specified with
                useclock) having different time intervals.
See also: showclocks , useclock , getclock

25.144 setdefault

Routine Name:   setdefault

Description:    Sets the default value of an object field.

Usage:          setdefault object-name field-name value ...

Example:        genesis > setdefault compartment Em -0.07
                genesis > create compartment /soma
                OK
                genesis > showfield /soma Em

                [ /soma ]
                Em                   = -0.0700000003
                genesis > echo {getdefault compartment Em}
                -0.0700000003

Notes:          Once you have changed the default value of an object
                field, all elements created from that object will
                have that field initialized to the new value.
See also: getdefault

25.145 setenv

Routine Name:   setenv

Description:    Set value of operating system environmental variable.

Usage:          setenv environment-variable [new-value...]

Example:        genesis > setenv SIMPATH . ~/genesis/Scripts/neurokit
                SIMPATH=. ~/genesis/Scripts/neurokit

                [also see the GENESIS default .simrc file]

Notes:          This is a GENESIS implementation of the operating system
                command setenv, which lets you set the value of a particular
                operating system environmental variable.  Unlike its
                operating-system counterpart, setenv from within GENESIS
                requires that you supply a variable name (outside of GENESIS,
                setenv with no arguments displays the list of all your
                environmental variables).

                Unlike its operating system counterpart, setenv from within
                GENESIS displays the change that you make (outside of GENESIS,
                setenv just returns you to the prompt with no acknowledgement).

                The setenv routine is used most commonly from within GENESIS
                to define the DISPLAY and SIMPATH environment variables.
                DISPLAY determines the X11 host on which the display is made
                and SIMPATH lists the path which the simulator will search
                through for script files (cf. where).
See also: printenv , getenv

25.146 setfield

Routine Name:   setfield

Description:    Sets value of field in data structure of specified element.

Usage:          setfield  [pathname] field value [field value ... ...]

                pathname        name of element; if wildcard path
                                specification, all elements referred to will
                                have their fields set to specified values
                                (default: current working element)

                field           field in element data structure to which to
                                assign new value

                value           value to assign specified field

Example:        setfield /soma initVm -70.0
                setfield /test[] x 10 y 20 // for all indexed elements test[i]
                setfield x 10           // set value for current element

                genesis >  setfield /neutral_test x 100 y 50
                genesis >  showfield /neutral_test x y 
                
                [ /neural_test ]
                x           = 100
                y           = 50

Notes:          You can define and add additional fields with the addfield
                command.  These may then be set with the setfield command
                just like the predefined fields.
See also: getfield , getfieldnames , showfield

25.147 setfieldprot

Routine Name:   setfieldprot

Description:    Set the accessibility level element fields.

Usage:          setfieldprot element -readwrite fields ... -readonly fields ...
                    -hidden fields ...

                element         element for which to change field protections
        
                -readwrite      make the following fields readwrite

                -readonly       make the following fields readonly

                -hidden         make the following fields hidden

                -debug          turn on debugging mode; all hidden fields
                                are treated as if they were readonly and
                                any field may be made readwrite

                -nodebug        turn off debugging mode

Notes:          Hidden fields are not presented by showfield and are
                not readable in any way.  The presence of hidden fields
                may be determined using the showobject command.

                NOTE: The -debug option is intended to be used when
                debugging new objects.  Hidden and readonly fields
                should not usually be changed to readwrite as these
                fields are either private fields or computed by the
                object.  Setfieldprot will give a warning if a built in
                field is being made more accessible than the protection
                defined by the built in object.  If it is necessary to
                use debug mode to run a simulation please email the
                GENESIS development group and report the problem.
See also: addfield , showobject , Extended

25.148 setglobal

Routine Name:   setglobal

Description:    Sets the value of a global variable, allowing the name of
                the global variable to be held in a string variable.

Usage:          setglobal name value

Example:

float RM, RA, CM
create xform /control
create xdialog /control/RM  -value 1.0 -script "setglobal RM <value>"
create xdialog /control/RA  -value 0.1 -script "setglobal RA <value>"
create xdialog /control/CM  -value 0.01 -script "setglobal CM <value>"
xshow /control

Notes:

Often it is useful to use a string variable name to hold the name of a
global variable.  For example, one may want to pass the name of a global
variable to a function that declares a global variable, or that sets or
returns its value.  However, normal GENESIS syntax for declarations and
assignments does not permit a variable name to be specified by a string
variable.   The routines addglobal, getglobal, and setglobal are designed
to overcome this limitation.

The example above shows another use of setglobal to assign the value of
a global variable with the "script" field of an XODUS widget.  A normal
assignment statement would not work in this case.
See also: Variables , addglobal , getglobal , listglobals

25.149 setmethod

Routine Name:   setmethod

Description:    Sets integration method for elements to use in simulation.

Usage:          setmethod [path] method

                path            path of element for which to set integration
                                method (if omitted, specified method is
                                applied to all elements in the simulation)

                method          integer identifying integration method to use:
                                 -1  Forward Euler
                                  0  Exponential Euler (default)
                                  2  2nd order Adams-Bashforth predictor
                                  3  3rd order Adams-Bashforth predictor
                                  4  4th Adams-Bashforth predictor
                                  5  5th order Adams-Bashforth predictor
                                 10  Backward Euler
                                 11  Crank-Nicholson

Example:        setmethod /cell/##[OBJECT=compartment] 2

Notes:          The method used is stored within the "object" data structure
                of the element.  For example:

                genesis > showfield /cell/soma object->method
                [ /cell/soma ]
                object->method       = 2

                The default Exponential Euler method is a good compromise
                between speed, accuracy and ease of use for network models
                and single cell models involving a few compartments.
                Multi-compartmental models result in numerically "stiff"
                equations which are best solved with one of the implicit
                (Backward Euler or Crank-Nicholson) methods.  The implicit
                methods must used in conjunction with the hsolve object,
                which takes over the computations of compartments,
                tabchannels and other selected element types.
See also: hsolve

25.150 setparamGA

Routine Name:   setparamGA

Description:    sets the value of a parameter in a paramtableGA object from
                a floating-point number.

Usage:          setparamGA path table param value

                path:   The location of the paramtableGA object in the
                        element hierarchy.

                table:  The parameter table to be accessed.

                param:  The location of the desired parameter in the
                        table.

                value:  The floating-point value of the parameter.

Return value:   a float, representing the parameter value desired.

Example:            float val = 10.0
                    setparamGA /GA_object 10 1 {val}

                This sets the second parameter (zero-indexed) from
                the tenth parameter table in the paramtableGA object
                called /GA_object to 10.0.

Notes:          The reason for having this routine and getparamGA is that
                the parameter table array in paramtableGA objects is in an
                object-specific binary form (optimized for the genetic
                algorithm method) and thus can't be viewed or set directly
                using the showfield, getfield or setfield commands (at
                least not meaningfully).

                This routine and getparamGA are hacks; ultimately they should
                be made obsolete by overloading the SET and SHOW actions of
                the paramtableGA object.
See also: Parameter Search ( Param ), paramtableGA , getparamGA

25.151 setpostscript

Routine Name:   setpostscript

Description:    Sets parameters used to generate postscript output of widgets.

Usage:          setpostscript [-maxgray maxgray] [-mingray mingray]
                        [-inverse inverse-flag] [-dpi screendpi]
                        [-filename name] [-printer]

Notes:          This is an alias for xps.
See also: xps

25.152 setprompt

Routine Name:   setprompt

Description:    Sets string to use as prompt for GENESIS shell.

Usage:          setprompt prompt-string

                prompt-string   string to use as shell prompt (default:
                                "genesis #!", where "!" is replaced by
                                command number); if you want to use a string
                                that includes blank spaces, you must include
                                the prompt in quotation marks to make the
                                string a single argument (additional
                                arguments are ignored)

Example:        genesis #13 >  setprompt tutorial
                tutorial >  setprompt "tutorial !"
                tutorial 15 >

Notes:          When starting up GENESIS the command line will appear as a
                prompt waiting for user input.

                genesis #0 > 

                The number contained in the prompt refers to the index of the
                command which is incremented for each line entered from the
                keyboard. This number can be used in conjunction with the
                'history' recall mechanism to re-execute commands based on
                their index.  [Note that GENESIS starts with 0 rather than 1.]

                The prompt string displayed in the command interpreter window
                can be set using the setprompt routine.  Specific simulations
                often wish to change the prompt to reflect the nature of the
                simulation.  
See also: h

25.153 setrand

Routine Name:   setrand

Description:    Selects Numerical Recipes or SPRNG random number generator

Usage:          setrand -nr -sprng

                -nr     Use the Numerical Recipes generator (default)
                -sprng  Use the SPRNG random number generator

Example:        genesis > setrand
                Using Numerical Recipes random number generator
                genesis > setrand -sprng
                Using SPRNG random number generator

Notes:

As of GENESIS version 2.2, SPRNG (the scalable portable random number
generator) has been incorporated into GENESIS to provide faster and higher
quality random numbers, which will be the same across all hardware platforms.
We continue to support use of the Numerical Recipes generator, which is used
by default.  In order to use the SPRNG generator, GENESIS must be compiled
with the appropriate lines uncommented in genesis/src/Makefile.  (This is done
by default, but the use of SPRNG may be disabled for some platforms on which
it refuses to compile.)  This allows you to choose among several algorithms
for random number generation.  Lagged Fibonacci is the default, as it is the
fastest and has the longest number sequence.

The setrand command is used to select between the NR or SPRNG generators.
When used with no options, setrand reports the currently used random number
generator.
See also: randseed , rand

25.154 setrandfield

Routine Name:   setrandfield

Description:    Sets an element field to a random value

Usage:                                  | [-uniform low high]
                setrandfield path field | [-gaussian mean sd]
                                        | [-exponential mid max] 

Example:        setrandfield /pyr/pyramidal[]/HH_Na_channel \
                    X_alpha_V0 -gaussian -40 3

Notes:          In the example above (from Scripts/piriform/pyramidal.g),
                setrandfield is being used to give some variation to the
                voltage dependence of the activation of Na channels used in
                all of the pyramidal cells used in the model.  In this case,
                there is a gaussian distribution about the mean of -40 mV,
                with a standard deviation of 3 mV.  Another use of the
                setrandfield comamnd would be to use it in script function to
                be executed as the command of a script_out object, or as the
                PROCESS action of an extended object, in order to randomly
                change a field at every time step.  This would be a way to
                inject a noise current into a compartment, for example.

                The -uniform option gives a a random number taken from a
                uniform distribution in the range "low" to "high".

                The -exponential option gives a random number taken from an
                exponential distribution with a minimum value of zero, a 1/e
                point of "mid" and a maximum value of "max".  Versions of
                GENESIS prior to 2.2 used a different interpretation of the
                two arguments.
See also: setfield

25.155 setsearch

Routine Name:   setsearch

Description:    This function allows the user to change which parameters
                will be varied in a parameter search and which will stay
                constant.  It allows users to perform restricted parameter
                searches, keeping certain parameters constant while others
                are searched over.

Usage:          setsearch path [param1] [param2] ... -all -not -add

                path:   The location of the parameter search object in
                        the element hierarchy.

                param1 etc.: The numerical indices of the parameters to be
                        varied.  All other parameters will be fixed by
                        default (but see below). There can be any number of
                        these arguments up to the total number of parameters.

                -all:   Causes all parameters to be searched over.  All
                        other options or parameter numbers are ignored.

                -not:   Changes the meaning of the paramX arguments; now
                        they are parameters NOT to be searched over.  All
                        other parameters are searched over.

                -add:   Searches over the listed parameters.  Also searches
                        over whatever other parameters whose search flags
                        were previously on (i.e. equal to 1).

Return value:   int; 0 for failure and 1 for success.

Examples:       // Search over parameters 0, 4, 8 only.
                setsearch /param_object 0 4 8

                // Search over all parameters except for 0, 4, and 8.
                setsearch /param_object 0 4 8 -not

                // Search over all parameters.
                setsearch /param_object -all

                // Search over parameters 0, 4, and 8 in addition to
                // whatever parameters were previously being searched over.
                setsearch /param_object 0 4 8 -add

Notes:          This routine is just a shortcut way to set the search[]
                fields of paramtable objects.  Anything this routine can do
                can also be done by manually setting these flags.  These
                flags have the following values: 0 means "don't search this
                parameter" while 1 means "do search this parameter".

Limitations:    This routine only works for the paramtable objects included
                in this library.  It will not automatically work for new
                objects written by the user without hacking
                src/param/param_utils.c
See also: Parameter Search ( Param ), Paramtable

25.156 setupNaCa

Routine Name:   setupNaCa

Description:    Allocates and fills tabcurrent tables with the values needed
                to implement the Na-Ca exchanger pump.

Usage:          setupNaCa tabcurrent-element gamma Celcius Cain Caout \
                     Nain Naout -xsize n -xrange min max -ysize n \
                     -yrange min max

                tabcurrent-element  This must have been created from a
                                    tabcurrent object.

                gamma               Parameter representing the fractional
                                    position of the energy barrier within the
                                    membrane, usually taken to be 0.38.

                Celsius             Temperature in degrees Celsius.

                Cain                Ca concentration inside the compartment.
                Caout               Ca concentration outside the cell.
                Nain                Na concentration inside the compartment.
                Naout               Na concentration outside the cell.

                -xsize xdivs        Number of divisions for the x variable
                                    of the tabcurrent I_tab and G_tab tables.

                -xrange min max     Minimum and maximum values of the x
                                    variable for the I_tab and G_tab tables.

                -ysize ydivs        Number of divisions for the y variable
                                    of the tabcurrent I_tab and G_tab tables.

                -yrange min max     Minimum and maximum values of the y
                                    variable for the I_tab and G_tab tables.
                
Example:

// Assume there is a parent compartment, and a Ca_concen element Ca_conc
create tabcurrent NaCa
setfield NaCa Gindex {VOLT_C1_INDEX}
setfield NaCa Gbar {1.4e-5*compt_area} // kCaNa = 1.4e-5 Amp/(mM^4)/m^2
setupNaCa NaCa 0.38 37 0 2.4 10 125 -xsize 100 -xrange -0.1 0.05 \
    -ysize 100 -yrange 0 0.300

addmsg .. NaCa VOLTAGE Vm
addmsg Ca_conc CONCEN1 Ca
addmsg NaCa .. CHANNEL Gk Ek

Notes:

The setupNaCa routine fills the I_tab table of a tabcurrent element with
values of

 Cain*Naout^3 * exp((gamma-1)*V*F/(R*T)) - Caout*Nain^3 *exp(gamma*V*F/(R*T))

where F is the Faraday constant (9.6487e4 coul/mol), R is the gas constant
(8.314 volts*coul/(deg K * mol)), and T = Celsius + 273.15.  The G_tab table
is filled with values of -dI_tab/dV, to give the slope conductance Gk when
it is scaled by Gbar.  The concentrations should be given in mM (millimoles
per liter =  moles/m^3).

When the tabcurrent Gbar is set to the compartment area times the constant
kNaCa, this results in the expression for the Na+ - Ca2+ exchanger pump
current given by Equation (6.11) in De Schutter E., and Smolen P., "Calcium
dynamics in large neuronal models", in Methods in neuronal modeling: From ions
to networks (2nd edition), C. Koch and I. Segev editors, pp. 211-250 (1998).

This is similar to the expression used for a similar electrogenic current in
DiFrancesco, D., and Noble, D., "A model of cardiac electrical activity
incorporating ionic pumps and concentration changes", Phil. Trans. Roy. Soc.
London Ser. B 307: 353-398 (1985).

When setting the concentration parameters, either Cain or Caout (but not both)
should be set to zero.  The one that is set to zero is expected to be
delivered to the tabcurrent element with a CONCEN1 or CONCEN2 message.  In
almost every case, this will be Cain, as it will vary much more than the Ca
concentration outside the cell.  The tabcurrent Gindex field should be set to
VOLT_C1_INDEX if the Ca concentration is delivered with a CONCEN1 message, and
VOLT_C2_INDEX if it is delivered with a CONCEN2 message.  The voltage V should
be provided by a VOLTAGE message from the compartment that contains the
tabcurrent element.

The -xsize and -ysize parameters give the number of divisions in the tables,
with the first index (corresponding to voltage) running from 0 to xdivs and
the second one (corresponding to Ca concentration) from 0 to ydivs.
See also: tabcurrent , setupghk

25.157 setupalpha

Routine Name:   setupalpha

Description:    Sets up A and B tables of voltage-dependent gates based on
                generic equations describing the form of the alpha and beta
                rate functions.

Usage:          setupalpha channel-element gate AA AB AC AD AF BA BB BC BD BF \
                   -size n -range min max

                channel-element   This must be a tabgate or a tabchannel i.e.
                                  a voltage-dependent gate or channel with
                                  tabulated activation functions.

                gate              The name of the gate (must be X, Y, or Z).

                AA-AF             Coefficients A to F of the alpha table 
                                  (see below).

                BA-BF             Coefficients A to F of the beta table 
                                  (see below).

                -size n           Number of divisions in the table 
                                  (default = 3000).

                -range min max    Range of the table (default: min = -0.100; 
                                  max = 0.050).

                This routine makes it easy to set up the A and B tables of 
                tabulated channels or gates (tabchannel or tabgate objects) 
                when the equations describing the rate constants alpha and 
                beta are of the form:

                y(x) = (A + B * x) / (C + exp((x + D) / F))

                Many standard channels have alpha and beta parameters that can
                be cast into this form.  In these cases to set up the tables
                we can simply call setupalpha with the parameter values as
                arguments to the function.  Since there are both alpha and
                beta variables, we use the coefficients AA-AF to refer to the
                alpha variable and BA-BF to refer to the beta variable.

                setupalpha calls the TABCREATE action of the tabchannel or
                tabgate to allocate tables with n divisions (n + 1 entries)
                representing x values from min to max.  It then evalutes the
                functions at these points to fill the tables.

                tabgates have tables for the alpha and beta rate variables, so
                these alpha and beta values are used to directly fill the
                tables.  The gates of a tabchannel each have an A table that
                holds alpha values, and a B table that contains alpha + beta.
                These tables are filled with A = alpha and B = alpha + beta.

                The tables are by default set up in "no interpolation" mode, 
                which means that the process of finding the correct table
                value is simply a lookup operation.  With 3000 divisions in 
                the table (i.e. the table size is 3001) the lookup usually
                provides sufficient accuracy.  If not, you can override this 
                behavior; see the tabchannel documentation.  The range of the
                activation variable is between -0.100 and 0.050 by default.
                This is adequate for most voltage-dependent channels, but 
                can be overridden using the -range option.

Example:        from Scripts/neurokit/prototypes/traub91chan.g:

                create  tabchannel      Kdr_hip_traub91
                        setfield        ^       \
                        Ek              {EK}    \                  //      V
                        Gbar            { 150 * SOMA_A }    \      //      S
                        Ik              0       \                  //      A
                        Gk              0       \                  //      S
                        Xpower  1       \
                        Ypower  0       \
                        Zpower  0
 
                setupalpha Kdr_hip_traub91 X               \
                           {16e3 * (0.0351 + EREST_ACT)}   \  // AA
                           -16e3                           \  // AB
                           -1.0                            \  // AC
                           {-1.0 * (0.0351 + EREST_ACT) }  \  // AD
                           -0.005                          \  // AF
                           250                             \  // BA
                           0.0                             \  // BB
                           0.0                             \  // BC 
                           {-1.0 * (0.02 + EREST_ACT)}     \  // BD
                           0.04                               // BF
                
                This command sets up the X gate (activation gate) of Traub's
                delayed-rectifier potassium channel (Kdr_hip_traub91).
                SOMA_A and EREST_ACT are constants defined in the script
                file.  Note that the C value for the A table (AC) is -1; this
                can cause problems in general but does not cause any problems
                here (see below).

Notes:          For tabgate elements, which represent only a single gate, the
                 "gate" argument is ignored, but it should still be given as
                X, Y, or Z.  The setuptau command is similar to setupalpha,
                but uses the state variables tau and minf instead.

                If the alpha and beta rate constant of your channel cannot be
                described using the above equation, you must fill the tables
                with one of the other methods described in the tabchannel
                documentation, or The Book of GENESIS, Chapter 19 (2nd ed.).

                The rate equation described above has a removable singularity
                when C = -1 at the point x = -D (which is, unfortunately, a
                common case).  In this case the routine may generate
                inaccurate results due to roundoff errors.  We STRONGLY
                RECOMMEND that if you must use a C value of -1 you check the
                resulting activation curves by using Neurokit (in the "Edit
                Channel" mode) to see if they look reasonable.  If they do
                not then you will have to define the channel using a script
                function as mentioned above.  Such a function will result in
                a slower setup time for the channel but will be much more
                accurate.
See also: tabchannel , tabgate , setuptau , tweakalpha , tweaktau , Tables

25.158 setupgate

Routine Name:   setupgate

Description:    Sets up the internal tables of tabgate or table elements,
                based on a generic equation describing the values of the
                entries.

Usage:          setupgate channel-element table A B C D F -size n \
                -range min max -noalloc

                channel-element   This must be a tabgate or a table

                gate              The name of the table (must be
                                  alpha or beta for tabgates, "table" for
                                  table elements)

                A-F               Coefficients A to F of the table 
                                  equation (see below).

                -size n           Number of divisions in the table 
                                  (default = 3000).

                -range min max    Range of the table (default: min = -0.100; 
                                  max = 0.050).

                -noalloc          used to prevent allocation of the table
                                  when the table has already been allocated
                                  with a call to TABCREATE or a previous use
                                  of setupgate
                
                This routine makes it easy to set up the internal tables of
                tagate or table elements when the equations describing them
                are of the form:

                y(x) = (A + B * x) / (C + exp((x + D) / F))

                setupgate calls the TABCREATE action of the element
                to allocate tables with n divisions (n + 1 entries)
                representing x values from min to max.  It then evalutes the
                functions at these points to fill the tables.

Example:        see Scripts/neurokit/prototypes/newbulbchan.g

Notes:          The setupgate routine may not be used on tabchannels.
                The state equation described above has a removable singularity
                when C = -1 at the point x = -D.  common case).  In this case
                the routine may generate inaccurate results due to roundoff
                errors.
See also: setupalpha , setuptau , Tables

25.159 setupghk

Routine Name:   setupghk

Description:    Allocates and fills tabcurrent tables with the values needed
                to implement the Goldman-Hodgkin-Katz equation.

Usage:          setupghk tabcurrent-element charge Celcius Cain Caout \
                     -xsize n -xrange min max -ysize n -yrange min max

                tabcurrent-element  This must have been created from a
                                    tabcurrent object.

                charge              The ionic valence, z.

                Celsius             Temperature in degrees Celsius.

                Cain                Ca concentration inside the compartment.

                Caout               Ca concentration outside the cell.

                -xsize xdivs        Number of divisions for the x variable
                                    of the tabcurrent I_tab and G_tab tables.

                -xrange min max     Minimum and maximum values of the x
                                    variable for the I_tab and G_tab tables.

                -ysize ydivs        Number of divisions for the y variable
                                    of the tabcurrent I_tab and G_tab tables.

                -yrange min max     Minimum and maximum values of the y
                                    variable for the I_tab and G_tab tables.
                
Example:        create tabcurrent ghk_tab
                setfield ghk_tab Gindex {VOLT_C1_INDEX} Gbar 0.0
                setupghk ghk_tab 2 {Temp} 0 {CCaO} \
                    -xsize {tab_xfills} -xrange {tab_xmin} {tab_xmax} \
                    -ysize {tab_xfills} -yrange {tab_ymin} {tab_ymax}
                setfield ghk_tab G_tab->calc_mode {LIN_INTERP}
                setfield ghk_tab I_tab->calc_mode {LIN_INTERP}

Notes:

The setupghk routine fills the I_tab table of a tabcurrent element with
values of

 -V/(R*T)*(zF)^2(Cain - Caout*exp(-z*F*V/(R*T)))/(1 - exp(-z*F*V/(R*T)))

where z is the charge (ionic valence = 2 for calcium), F is the Faraday
constant (9.6487e4 coul/mol), R is the gas constant (8.314 volts*coul/(deg K *
mol)), and T = Celsius + 273.15.  The G_tab table is filled with values of
-dI_tab/dV, to give the slope conductance Gk when it is scaled by Gbar.  The
concentrations should be given in mM (millimoles per liter = moles/m^3).

When the tabcurrent Gbar is set to the permeability constant PCa, this results
in the expression for the non-ohmic GHK current given by Equation (6.6) in De
Schutter E., and Smolen P., "Calcium dynamics in large neuronal models", in
Methods in neuronal modeling: From ions to networks (2nd edition), C. Koch and
I. Segev editors, pp. 211-250 (1998).   The negative sign here expresses
the GENESIS convention of treating inward currents as positive.

When setting the concentration parameters, either Cain or Caout (but not both)
should be set to zero.  The one that is set to zero is expected to be
delivered to the tabcurrent element with a CONCEN1 or CONCEN2 message.  In
almost every case, this will be Cain, as it will vary much more than the Ca
concentration outside the cell.  The tabcurrent Gindex field should be set to
VOLT_C1_INDEX if the Ca concentration is delivered with a CONCEN1 message, and
VOLT_C2_INDEX if it is delivered with a CONCEN2 message.  The voltage V should
be provided by a VOLTAGE message from the compartment that contains the
tabcurrent element.  An "ADD_GBAR Gk" message may be sent to the tabcurrent
element from a calcium channel to change the calcium permeability.

The -xsize and -ysize parameters give the number of divisions in the tables,
with the first index (corresponding to voltage) running from 0 to xdivs and
the second one (corresponding to Ca concentration) from 0 to ydivs.
See also: tabcurrent , setupNaCa

25.160 setuptau

Routine Name:   setuptau

Description:    Sets up A and B tables of voltage-dependent gates based on
                generic equations describing the form of the tau (time
                constant) and minf (steady state activation) state constants.

Usage:          setuptau channel-element gate AA AB AC AD AF BA BB BC BD BF \
                   -size n -range min max

                channel-element   This must be a tabgate or a tabchannel i.e.
                                  a voltage-dependent gate or channel with
                                  tabulated activation functions.

                gate              The name of the gate (must be X, Y, or Z).

                AA-AF             Coefficients A to F of the tau table 
                                  (see below).

                BA-BF             Coefficients A to F of the minf table 
                                  (see below).

                -size n           Number of divisions in the table 
                                  (default = 3000).

                -range min max    Range of the table (default: min = -0.100; 
                                  max = 0.050).

                This routine makes it easy to set up the A and B tables of 
                tabulated channels or gates (tabchannel or tabgate objects) 
                when the equations describing the state constants tau and 
                minf are of the form:

                y(x) = (A + B * x) / (C + exp((x + D) / F))

                Many standard channels have tau and minf parameters that can
                be cast into this form.  In these cases to set up the tables
                we can simply call setuptau with the parameter values as
                arguments to the function.  Since there are both tau and minf
                variables, we use the coefficients AA-AF to refer to the tau
                variable and BA-BF to refer to the minf variable.

                setuptau calls the TABCREATE action of the tabchannel or
                tabgate to allocate tables with n divisions (n + 1 entries)
                representing x values from min to max.  It then evalutes the
                functions at these points to fill the tables.

                tabgates have tables for the alpha and beta rate variables, so
                the tau and minf values are used to calculate alpha = minf/tau
                and beta = (1 - minf)/tau, and fill these tables.  The gates of
                a tabchannel each have an A table that holds alpha values, and
                a B table that contains alpha + beta.  These tables are filled
                with A = minf/tau and B = 1/tau.

                The tables are by default set up in "no interpolation" mode, 
                which means that the process of finding the correct table
                value is simply a lookup operation.  With 3000 divisions in 
                the table (i.e. the table size is 3001) the lookup usually
                provides sufficient accuracy.  If not, you can override this 
                behavior; see the tabchannel documentation.  The range of the
                activation variable is between -0.100 and 0.050 by default.
                This is adequate for most voltage-dependent channels, but 
                can be overridden using the -range option.

Example:        see Scripts/neurokit/prototypes/newbulbchan.g

Notes:          For tabgate elements, which represent only a single gate, the
                 "gate" argument is ignored, but it should still be given as
                X, Y, or Z.  The setupalpha command is similar to setuptau,
                but uses the rate variables alpha and beta instead.

                If the tau and minf state constant of your channel cannot be
                described using the above equation, you must fill the tables
                with one of the other methods described in the tabchannel
                documentation, or The Book of GENESIS, Chapter 19 (2nd ed.).

                The state equation described above has a removable singularity
                when C = -1 at the point x = -D (which is, unfortunately, a
                common case).  In this case the routine may generate
                inaccurate results due to roundoff errors.  We STRONGLY
                RECOMMEND that if you must use a C value of -1 you check the
                resulting activation curves by using Neurokit (in the "Edit
                Channel" mode) to see if they look reasonable.  If they do
                not then you will have to define the channel using a script
                function as mentioned above.  Such a function will result in
                a slower setup time for the channel but will be much more
                accurate.
See also: tabchannel , tabgate , setupalpha , tweakalpha , tweaktau , Tables

25.161 sh

Routine Name:   sh

Description:    Issues operating system command from GENESIS shell.

Usage:          sh command

Example:        genesis > echo hello there
                hello there
                genesis > sh echo hello there
                hello there
                genesis > echo $DISPLAY
                ** Error - parse error
                genesis > sh echo $DISPLAY
                ** Error - parse error
                genesis > sh "echo $DISPLAY"
                babel.bbb.edu:0
                genesis >

Notes:          You can issue most operating system commands just by typing
                them at the GENESIS prompt (if the GENESIS interpreter does
                not recognize them as GENESIS commands, it automatically
                passes them on to the operating system for evaluation).
                However, if you have a GENESIS routine with the same name as
                an operating system command, you need to use the sh routine to
                send the command directly to the operating system.

See also:

25.162 shapematch

Routine Name:   shapematch

Description:    This function compares two waveforms generated by GENESIS
                and returns a number which represents how similar the
                waveforms are to each other.

Usage:          shapematch reference-file simulation-file
                    -start start-time -stepsize dt
                    -absdev -alternate

Arguments:      reference-file:  reference data file of outputs vs. time
                simulation-file: simulation data file of outputs vs. time

                The reference data is what you want the parameter search
                to match; the simulation data is what the simulation
                produces.

Options:        -start start-time:  The time at which waveform comparison
                    starts.  If no value is given, start at time = 0.

                -stepsize dt: The time step of the samples in the files.
                    Default = 0.0001 sec.

                -absdev: Uses the mean of absolute differences of samples
                    instead of the root-mean-squared differences to
                    calculate the match value.

                -alternate: Uses an alternate algorithm which can deal with
                    waveforms having spikes and waveforms using
                    different time points.  The alternative algorithm
                    is considerably slower than the default algorithm,
                    and has not been thoroughly debugged.

Return value:   Returns a nonnegative floating-point number representing the
                goodness of the match, with 0 representing a perfect match.
                The more different the waveforms are, the larger the value.
                The value represents the root of the mean of the squared
                differences in the waveforms at corresponding time points,
                unless the -absdev option is chosen (see above).  A huge
                positive value is returned on an error.  In the event of an
                error, a massive penalty value (1.0e6) is returned.

Example:        float match
                match = {shapematch "refdata" "simdata" -stepsize 0.00005}

Notes:          The default algorithm requires both waveforms to be defined
                on the same time points.  It should not be used for
                comparing waveforms with spikes.

                The alternate algorithm compares interspike intervals only,
                ignoring spikes.  To do this it will transform the time
                base of corresponding ISIs so that they match.  This is
                reasonable if the ISIs are similar, but if they are very
                different the results will not be very meaningful.  The
                alternate algorithm should probably be used in conjunction
                with spkcmp to compare the spike times as well.

                The -absdev option will not work for the alternate
                algorithm; it uses mean squared deviations only.

                The alternate algorithm has not been as well tested as the
                default algorithm and we cannot guarantee that it will
                function correctly.  It was stolen from Upi Bhalla's
                shapematch routine.
See also: Parameter Search ( Param ) gen2spk , spkcmp

25.163 showclocks

Routine Name:   showclocks

Description:    Displays currently defined clocks and their assigned values.

Usage:          showclocks

Example:        genesis > showclocks

                ACTIVE CLOCKS
                -------------
                [0] : 0.001
                [1] : 0.005

Notes:          Clock number 0 is the global simulation clock.  The default
                step size is 1.0 in whatever units you are using.
See also: useclock , setclock , getclock

25.164 showcommand

Routine Name:   showcommand

Description:    Displays name of C function invoked by a GENESIS routine.

Usage:          showcommand routine-name

Example:        genesis >  showcommand el
                'el' ==> 'do_construct_list'

Notes:          This command is useful when you are looking in the GENESIS
                source code for the function which implements a particular
                command.

See also:

25.165 showfield

Routine Name:   showfield

Description:    Displays value of field in data structure of specified element.

Usage:          showfield [pathname] [field] ... -all -basic -describe

                pathname        name of existing element; if wildcard path
                                specification, all elements referred to will
                                have their specified fields displayed
                                (default: current working element)

                field           field in element data structure for which to
                                display value; some special options for field:
                                 -basic displays basic information;
                                 -all displays basic info and all fields;
                                 -describe displays a description of the
                                    object from which the element was created;
                                 *  displays all fields;
                                 ** displays an extended listing of the element
                                    contents, including a description of the
                                    object from which the element was created

Example:        //showfield membrane potential, axial resistance
                showfield /cell/soma Vm Ra

                // show values of all soma fields
                showfield /cell/soma -a

                genesis >  showfield /neutral_test basic
                [ /neutral_test ]
                flags      = 0
                NOT FUNCTIONAL
                Clock [ 0 ] = 1.000000e+00
                0 incoming messages
                0 outgoing messages
                -----------------------------------------------------

Notes:          When a field is specified, the showfield routine is similar
                to getfield, but it displays its values rather than returning
                them.

                When the -describe option is given instead of a field name,
                the showfield routine is similar to the showobject routine.
See also: setfield , getfield , getfieldnames , showobject

25.166 showmsg

Routine Name:   showmsg

Description:    Displays list of incoming and outgoing messages of an element.

Usage:          showmsg  element

Example:        genesis > showmsg /cell/soma

                INCOMING MESSAGES
                MSG 0 from '/cell/soma/Na_squid_hh' type [0] 'CHANNEL' 
                        < Gk = 2.99968e-10 > < Ek = 0.045 >
                MSG 1 from '/cell/soma/K_squid_hh' type [0] 'CHANNEL'
                         < Gk = 1.03666e-08 > < Ek = -0.082 >

                OUTGOING MESSAGES
                MSG 0 to '/cell/soma/Na_squid_hh' type [0] 'VOLTAGE'
                        < Vm = -0.07 >
                MSG 1 to '/cell/soma/K_squid_hh' type [0] 'VOLTAGE'
                        < Vm = -0.07 >
                MSG 2 to '/data/voltage' type [0] 'PLOT' < data = -0.07 >
                        < name = volts > < color = red >

Notes:          showmsg is usually used interactively, when debugging or
                trying to understand a simulation, as it prints detailed
                information to the screen.  Use getmsg within a simulation
                script to return specific information.
See also: addmsg , deletemsg , getmsg

25.167 showobject

Routine Name:   showobject

Description:    Displays description of specified element type.

Usage:          showobject object-type

Example:        genesis > showobject compartment

                object               = compartment
                datatype             = compartment_type
                function             = Compartment()
                class                = [ membrane ] [ segment ] 
                size                 = 124 bytes
                author               = M.Wilson Caltech 6/88

                VALID ACTIONS
                        RESTORE2  SAVE2  SET  CHECK  RESET  PROCESS  INIT  

                VALID MESSAGES
                        [6] EREST                : Em 
                        [3] INJECT               : inject 
                        [2] AXIAL                : Vm 
                        [1] RAXIAL               : Ra Vm 
                        [0] CHANNEL              : Gk Ek 

                FIELDS
                  (ro)       name            compartment 
                  (ro)       index           0          
                  (ro)       object          &1688896   
                  (hidden)   flags                      
                  (hidden)   nextfields                 
                  (hidden)   extfields                  
                             x               0          
                             y               0          
                             z               0          
                  (hidden)   nmsgin                     
                  (hidden)   msgin                      
                  (hidden)   nmsgout                    
                  (hidden)   msgout                     
                  (hidden)   compositeobject            
                  (hidden)   componentof                
                  (hidden)   parent                     
                  (hidden)   child                      
                  (hidden)   next                       
                             activation      0          
                             Vm              0          
                             previous_state  0          
                             Im              0          
                             Em              0          
                             Rm              0          
                             Cm              0          
                             Ra              0          
                             inject          0          
                             dia             0          
                             len             0          
                             initVm          0          

                DESCRIPTION
                        Axially asymmetric compartment. Ra is located on
                one side of the compartment. This is slightly more
                computationally efficient than the symmetric
                counterpart.
                genesis >

Notes:          This routine returns many pieces of information about the
                object type, including the class, size, author, valid actions
                and messages, and data fields with the default values which
                are assigned when the object is instantiated as an element.
                If the field is not readable and writeable, the field is
                labeled (ro) if it is protected as read-only, and (hidden) if 
                it and its contents are hidden to the user.
See also: showfield , setfieldprot

25.168 showsched

Routine Name:   showsched

Description:    Displays current working simulation schedule.

Usage:          showsched

Example:        genesis > showsched

                WORKING SIMULATION SCHEDULE

                [1] Simulate  /##[CLASS=segment]      -action INIT
                [2] Simulate  /##[CLASS=segment][CLASS!=membrane][CLASS!=gate]
                    [CLASS!=concentration][CLASS!=concbuffer] -action PROCESS
                [3] Simulate    /##[CLASS=membrane]     -action PROCESS
                [4] Simulate    /##[CLASS=output]       -action PROCESS

Notes:          
See also: Schedules , addtask

25.169 showstat

Routine Name:   showstat

Description:    Reports statistics about current simulation time
                or memory use

Usage:          showstat [-process] [-element [element-name]]

                -process    prints statistics of time and memory used
                -element    prints simulation status of all elements,
                            or the specified element

Example:

genesis > showstat
current simulation time = 0.100050 ; step = 2001; dt = 5.000000e-05

genesis > showstat -process
process status:  0:0.79  user  0:0.09  sys   0:39 real    3.70 Mbytes

genesis > showstat -element /cell/soma
'/cell/soma' element count:
         2 hh_channel             384 bytes (  0.00 Mbytes)
         2 messages                96 bytes (  0.00 Mbytes)
----------------------------------------------------------
         4                        480 bytes (  0.00 Mbytes)

total memory usage : 3032324 bytes   (   3.03 Mbytes )

genesis > showstat -element
'/' element count:
         3 neutral                228 bytes (  0.00 Mbytes)
         5 messages               316 bytes (  0.00 Mbytes)
         1 compartment            144 bytes (  0.00 Mbytes)
         2 hh_channel             384 bytes (  0.00 Mbytes)
         2 xform                  272 bytes (  0.00 Mbytes)
         2 xlabel                 224 bytes (  0.00 Mbytes)
         3 xbutton                420 bytes (  0.00 Mbytes)
         1 xdialog                124 bytes (  0.00 Mbytes)
         1 xgraph                 188 bytes (  0.00 Mbytes)
         2 xaxis                  416 bytes (  0.00 Mbytes)
         1 xshape                 168 bytes (  0.00 Mbytes)
         1 xplot                  204 bytes (  0.00 Mbytes)
----------------------------------------------------------
        24                       3088 bytes (  0.00 Mbytes)

total memory usage : 3032324 bytes   (   3.03 Mbytes )

Notes:          
See also: getstat

25.170 silent

Routine Name:   silent

Description:    Sets and returns flag which supresses certain information
                displays to console.

Usage:          silence-status = silent [silent-flag]

                silent-flag     1 to suppress informative displays; 0 to
                                allow informative displays; 2 suppresses
                                startup messages.

Example:        genesis >  echo { silent }
                0
                genesis >  silent 1
                echo { silent }
                1

Notes:          Note that in the example above, the prompt is supressed after
                the silent flag is set to 1.  Various routines use the
                status of the silent flag to decide whether to print out
                certain informative messages.
                For
                example, the routines related to element stack (pushe, pope,
                stack) normally display the working element they deal with;
                if silent is > 0, these routines will not echo that
                information.  Within any SLI control structure, the flag
                behaves as if it were one greater.  For example, if the
                "step" command is used within a script function, the usual
                message reporting the number of steps and cpu time is
                supressed unless the flag is set to -1.
See also: debug

25.171 simdump

Routine name:   simdump

Description:    Dumps an entire simulation to a GENESIS script file.
                Should generally be invoked after calling the 
                'simobjdump' function to specify object fields.

                One of a family of functions for dumping and restoring
                simulations in their entirety, and merging overlapping
                simulations. The output of these functions is an ascii file
                readable by the GENESIS script interpreter.  However, this
                ascii file uses 'simundump' to restore field values, which is
                efficient but not very human-friendly.

                Since the output of simdump is GENESIS script file, one
                can dump various parts of a simulation into different files,
                and read them back in separately, or read them into a different
                simulation, and so on.

                Simdump files do quasi-intelligent 'merging' of files with
                existing simulations. If an element is already there, it
                will content itself with updating the field values and
                adding missing messages. By default it will avoid duplicating
                existing messages. It also has a provision for
                ignoring orphan elements, whose parents are not defined. These
                options are activated by the initdump command.

Usage:          simdump filename -path path -tree tree -messages -all
                        
                filename: The name of the output dump file.

                -path path: specifies a wildcard path of elements to
                        be dumped. This option can be used repeatedly to put
                        several different bits of the simulation into the
                        file. The same effect could be achieved by using
                        the extended wildcard specification.

                -tree tree: A currently disabled option for getting the
                        wildcard path from an xtree.

                -messages: A currently disabled option.

                -all : Tells simdump to dump the entire simulation.

Example:        See below for an example of a simple and a complex dump of
                a simulation plus interface.
                
Notes:          In theory it should be possible to use simdump on its own,
                without invoking simobjdump or initdump. In this situation, 
                the command assumes that all fields of the objects are to
                be dumped. This is inefficient. Worse, it causes problems
                because fields can take values that should not be reloaded
                into them. Pointers are a good example. Also see below about
                what happens with Xodus.

                Simdump always saves files in 'append' mode. This means that
                if you accidently use the same filename as an existing .g file,
                the original won't be destroyed, and you can edit the file
                to extract the dumped part and the original.
                
                Xodus poses lots of problems for simdump, because Xodus
                objects do not always behave cleanly. For example,
                Xodus objects often have default field values like 'nil' 
                which are not valid when trying to reload the dumpfile. It
                is necessary to exclude the offending fields by using
                simobjdump to select well-behaved fields for the dump.
                Furthermore, there is no 'field' to determine whether an
                xform is displayed or not, so the forms won't appear until
                explicity 'shown'. There are various other annoyances, like
                things not updating when you expect them to. For this reason,
                simdump will need help if you are trying to dump an interface.

                Simdump will happily dump the entire contents of a 1-Megabyte
                xplot or table. This gives a valid, but enormous dumpfile.
                If this is not desirable, simobjdump allows one to specify
                the -noDUMP option. See simobjdump documentation.

                A few objects will dump too much information for the
                parser to handle as part of a single command. This is only
                likely to occur in very rare situations.

                The hsolver can be dumped, but its fields must be restricted
                to the path. The solver will need to be re-initialized
                when trying to restore the simulation. It is better to
                just rebuild the whole hsolver from scratch.

                In general, cell models are much more compactly specified
                by the .p files than by the simdump files. It is also much
                more user-friendly that way.

                The long-bewailed problem with re-entrant parsers means that
                the generated script file cannot be read in on a mouse-click.
                You will have to type in a command to load the script file.

Example:

This example consists of two files: a demo simulation file called "dumpdemo.g",
and a file "savefunc.g" with two versions of simulation dumping functions.
Cut out the scripts to the appropriate files. Run dumpdemo, which is a 
little compartmental model with interface. Save using the simple and complex
versions of the dumping interface. Examine the resulting dumpfiles using
your favourite editor, and then reload them to see what happens.

================ Cut here for file "dumpdemo.g" =============================

//genesis

setclock 0 0.001

include savefunc.g

create neutral /a
create compartment /a/compt
setfield ^ Ra 1 Cm 1 Rm 1

copy /a /b

addmsg /a/compt /b/compt AXIAL Vm
addmsg /b/compt /a/compt RAXIAL Ra Vm

create xform /form
create xgraph /form/graph -ymax 0.5 -xmax 5
create xplot /form/graph/plot -fg red
create xbutton /form/simple_save -script "do_simple_save"
create xbutton /form/complex_save -script "do_complex_save"
create xbutton /form/quit -script quit
xshow /form

addmsg /b/compt /form/graph/plot PLOT Vm *Vm *red

setfield /a/compt inject 1

reset

step 5 -t

============== Cut here for file savefunc.g ================================

//genesis

// This function saves only the structure of the simulation. None
// of the interface objects will be saved.
function do_simple_save
        // compartments are well-behaved, so we can get away with
        // dumping all compartment fields by default
        // Here we illustrate two ways of dumping multiple paths
        simdump simple_dump.g -path /a -path /a/## -path "/b,/b/##"
        echo "Simple dump done to file: simple_dump.g"
end

// This function saves everything about the simulation. It has
// to jump through many hoops to deal with Xodus oddness.
function do_complex_save
        str filename = "complex_dump.g"

        // Write out some general info for the dumpfile
    openfile {filename} "w"
    writefile {filename} "//genesis"
    writefile {filename} {"// Saved on " @ {getdate}}
    writefile {filename} "setclock 0 0.001"
    writefile {filename} "include savefunc.g"
        closefile {filename}

        // Specify which fields of the Xodus objects we want to save
        simobjdump xform xgeom ygeom wgeom hgeom
        simobjdump xaxis script
        simobjdump xshape script
        simobjdump xgraph xmin ymin xmax ymax xgeom ygeom wgeom hgeom
        simobjdump xplot npts
        simobjdump xbutton script
        simobjdump xdialog script value
        
        // Dump the entire simulation
        simdump {filename} -all

        // We're not done yet: we need to help the interface get back
        // to its original state.
    openfile {filename} "a"
    writefile {filename} "xshow /form"
    writefile {filename} \
        "setfield /form/graph/plot npts "{getfield /form/graph/plot npts}
    writefile {filename} "xupdate /form/graph"
        closefile {filename}

        echo "Complete dump done to file: "{filename}
end

=============================================================================
See also: initdump , simobjdump , simundump .

25.172 simobjdump

Routine name:   simobjdump

Description:    Sets up the format for dumping and reading objects to a file
                using simdump.

Usage:          simobjdump object ... -coords -default -noDUMP
                        
                object:  The name of the GENESIS object class

                ... :    The fields to be dumped for this object

                -coords: Dump the x y z coords. 

                -default: Use all the fields defined for the object. This
                        will also happen if you call simobjdump with no
                        arguments, or if you don't call simobjdump at all.
                
                -noDUMP: A few GENESIS object classes, such as tables, have
                        a DUMP action which does object-specific things.
                        noDUMP inactivates this DUMP action. For example, in
                        a table, the DUMP action would normally dump the entire
                        contents of the table. noDUMP prevents this from 
                        happening.

Example:        Here is a little dumpfile using simobjdump that recreates a
                simple 2-compartment model. In this case the simobjdump
                command was not used at all before the simdump, so the
                simdump command caused the entire set of fields for the
                relevent classes (neutrals and compartments) to be specified
                for the dumpfile.

                ============================================================
                //genesis

                initdump -version 3
                simobjdump neutral
                simobjdump compartment activation Vm previous_state \
                        Im Em Rm Cm Ra inject dia len initVm
                simundump neutral /a 0
                simundump compartment /a/compt 0 0 0.6632976405 0.6632942696 \
                        -0.3333315551 0 1 1 1 1 0 0 0
                simundump neutral /b 0
                simundump compartment /b/compt 0 0 0.3299660931 0.3299627243 \
                        0.3333349228 0 1 1 1 0 0 0 0
                addmsg /b/compt /a/compt RAXIAL Ra Vm 
                addmsg /a/compt /b/compt AXIAL Vm 
                enddump
                // End of dump

                ============================================================
                
Notes:          In theory it should be possible to use simdump on its own,
                without invoking simobjdump or initdump. In this situation, 
                the command assumes that all fields of the objects are to
                be dumped. This is inefficient. Worse, it causes problems
                because fields can take values that should not be reloaded
                into them. Pointers are a good example. Also see below about
                what happens with Xodus.

                Simdump will happily dump the entire contents of a 1-Megabyte
                xplot or table. This gives a valid, but enormous dumpfile.
                If this is not desirable, simobjdump allows one to specify
                the -noDUMP option.
See also: initdump , simdump , simundump .

25.173 simundump

Routine name:   simundump

Description:    Creates an element and assigns values to its fields.
                Simundump is not really a human-use command. It only
                occurs in dumpfiles, and is always preceeded by initdump
                and simobjdump, and followed up by enddump at the end of
                the file.

Usage:          simundump object element ... -tree tree x y z

                object: The object class to be created

                element: The path of the new element

                ... : Fields values of the element. The field names are
                specified earlier in the file by the simobjdump command.

                -tree tree: A currently disabled option for getting the
                        wildcard path from an xtree.

Example:        Here is a little dumpfile using simundump that recreates a
                simple 2-compartment model.

                ============================================================
                //genesis

                initdump -version 3
                simobjdump neutral
                simobjdump compartment activation Vm previous_state \
                        Im Em Rm Cm Ra inject dia len initVm
                simundump neutral /a 0
                simundump compartment /a/compt 0 0 0.6632976405 0.6632942696 \
                        -0.3333315551 0 1 1 1 1 0 0 0
                simundump neutral /b 0
                simundump compartment /b/compt 0 0 0.3299660931 0.3299627243 \
                        0.3333349228 0 1 1 1 0 0 0 0
                addmsg /b/compt /a/compt RAXIAL Ra Vm 
                addmsg /a/compt /b/compt AXIAL Vm 
                enddump
                // End of dump

                ============================================================
Notes:          
                Simundump does quasi-intelligent 'merging' of files with
                existing simulations. If an element is already there, it
                will content itself with updating the field values and
                adding missing messages. It won't try to add messages to
                missing elements, and won't complain: it assumes that you
                meant to leave them out. It also has a provision for
                ignoring orphan elements, whose parents are not defined. These
                options are activated by the initdump command.

                In current versions of simdump/undump, the first field argument
                to simundump is always the 'flags' field of the element (even
                if it not requested). This restores the clocks, and other
                status attributes of elements.
        
                Xodus poses lots of problems for simundump, because Xodus
                objects do not always behave cleanly. For example,
                Xodus objects often have default field values like 'nil' 
                which are not valid when trying to reload the dumpfile. It
                is necessary to exclude the offending fields by using
                simobjdump to select well-behaved fields for the dump.
                Furthermore, there is no 'field' to determine whether an
                xform is displayed or not, so the forms won't appear until
                explicity 'shown'. There are various other annoyances, like
                things not updating when you expect them to. For this reason,
                simundump will need help if you are trying to reload an
                interface.
See also: initdump , simdump , simobjdump

25.174 sin

Routine Name:   sin

Description:    Returns sine for given angle (specified in radians).

Usage:          sine = {sin angle-in-radians}

Example:        float s
                s = {sin {3.14159/4}}

Notes:          
See also: asin

25.175 spkcmp

Routine Name:   spkcmp

Description:    This function compares two spike time files, one from raw
                data and one from a GENESIS simulation; it returns a number
                which is a measure of how different the spike times are for
                the two cases.

Usage:          spkcmp reference-data simulation-data
                        -offset time
                        -pow1 p
                        -pow2 q
                        -msp  missing_spike_penalty
                        -nmp  nonmonotonicity_penalty
                        -et   end-time
                        -spk

Arguments:      reference-data:  reference data spike time file
                simulation-data: simulation data spike time file

                The reference data is what you want the parameter search to
                match; the simulation data is what the simulation produces.
                The recommended convention is to have the reference data
                spike time file end in .spk and the simulation data spike
                time file end in .spk.sim.

Options:        -offset time
                    This offsets the simulation spikes by a fixed
                    amount.  It's useful when the delay before current
                    injection is different for the experiments and the
                    simulations.  This value can be positive or negative.

                -pow1 p
                    This controls the degree to which spike mismatches
                    at the beginning of the trace are more heavily
                    weighted than those at the end.  A value of zero
                    (the default) means there is no extra weight.  p
                    must be >= 0.

                -pow2 q
                    This controls the degree to which missing spikes
                    are penalized differently according to how many
                    spikes there were in the real trace.  The idea is
                    that when the real trace has lots of spikes, each
                    missing or extra spike should not be penalized too
                    harshly, but when it has only a few it should be
                    penalized very harshly.  A value of zero (the
                    default) means all missing spikes get the same
                    penalty.  q must be >= 0.

                -msp missing_spike_penalty
                    Penalty for spikes which are in one trace but not
                    the other; default = 1.0 per spike.

                -nmp nonmonotonicity_penalty
                    Penalty for simulated traces where the interspike
                    intervals do not get larger monotonically with time.
                    This allows us to select against cells with bursting
                    behaviors.  A nonmonotonicity penalty of (say) 2.0
                    would add 2.0 for each second of nonmonotonicity; in
                    other words, if you have a nonmonotonic interspike
                    interval, the duration of that particular ISI in
                    seconds will be multiplied by 2.0. and this would be
                    added to the total penalty.  Default = 0.0 per second
                    of monotonicity per spike (i.e. no penalty).

                -et end-time
                    If used, ignore spikes beyond a certain end time.

                -spk
                    This causes the number of missing spikes to be
                    printed out instead of having a penalty added to
                    the total.

Return value:   Returns a nonnegative floating-point number representing
                the goodness of the match, with 0 representing a perfect
                match.  The units of the match are roughly in units of
                (msec error)/spike. The more different the times are, the
                larger the value.  In the event of an error, a massive
                penalty value (1.0e6) is returned.

Input spike file format:

                Spike time files should be in the following format:

                CURR  <current-value>
                SPK   <spike time>
                ----------
                etc.

                The line of dashes delimits the different current values.
                The spike times may be omitted for a given current; this
                will happen if no spikes occur at a given current.  Note
                that this assumes a fixed current input (current clamp).
                Multiple currents may be put one after another in the file.
                Typically a single file will contain spike times from
                several different current injections into a single cell
                (real or modeled).  Make sure the currents in the
                simulation spike results and in the target spike results
                (what you are trying to match) are in the same order.

Algorithm:      The algorithm is essentially an average of the absolute
                values of the differences in spike times between the real
                and simulated outputs, with corrections for spikes which
                are only present in one of the outputs.  There are several
                other parameters controlled by the options (described
                above).  The algorithm is described in detail in the file
                src/param/spkcmp.c (function compare_spikes()).

Example:        genesis > float match
                genesis > match = {spkcmp "realpyr.spk" "simpyr.spk.sim" \
                                   -pow1 1.0 -pow2 0.6 -msp 0.5 -nmp 200.0}

Notes:          This function is typically used for processing data
                generated by the gen2spk function, which outputs spike time
                files in the correct format for this function.

                This function expects that the two spike time files have
                the same values for input currents in the same order; if
                not, it exits with an error message and returns a huge
                penalty.

                The spike file format has clearly been optimized for
                current-clamp experiments, which is a limitation.

                This function has been optimized to work with typical
                outputs of pyramidal cells from piriform cortex.  It should
                work well for all regular-spiking pyramidal cells.  It may
                work well for other cell types as well (with some
                adjustment of the option values), but for cells with very
                different behavior (e.g. Purkinje cells in bursting mode)
                you may be better off writing your own custom match function.
See also: Parameter Search ( Param ), gen2spk , shapematch

25.176 sqrt

Routine Name:   sqrt

Description:    Returns square root of positive number.

Usage:          square-root = {sqrt positive-number}

Example:        genesis > echo {sqrt 2}
                1.414213538
                genesis > echo {sqrt 0}
                0
                
Notes:          

25.177 stack

Routine Name:   stack

Description:    Displays list of elements on working element stack.

Usage:          stack

Example:        genesis >  pwe
                /
                genesis >  pushe /neuron1
                /neuron1
                genesis >  pushe /neuron2
                /neuron2
                genesis >  stack
                /
                /neuron1

Notes:          The stack routine prints out the current contents of the
                element stack (the stack used to store paths pushed and 'pop'ed
                from the stack using the GENESIS pushe and pope routines).

                The stacked elements are listed in the reverse order in which
                they will be 'pop'ed (i.e., the last element listed will be
                the first 'pop'ed).
See also: pushe , pope

25.178 step

Routine Name:   step

Description:    Advances the simulation by one or more steps.

Usage:          step [steps-or-time] -time -verbose -background

                steps           number of steps to advance simulation

                time            time by which to advance simulation

                -time           interpret the first argument as time

                -verbose        use verbose mode (display status of simulation
                                at each step)

                -background     run simulation as background process, and
                                return user to GENESIS shell

Example:        step 100
                step 5 -v
                step 25.4 -t -b

                genesis >  step
                time = 1.000000 ; step = 1
                completed 1 steps in 0.000000 cpu seconds

Notes:          When run in the background, the simulation is still sensitive
                to ^C.  Generating a ^C interrupt can cause the simulation to
                abnormally terminate a step giving erroneous results.  To halt
                an simulation in progress, use the stop routine.

                Only one simulation can be started at any given time. A
                background simulation must already be running. The showjobs
                routine will display this status (as the Simulate function).
See also: stop , showstat , reset , check

25.179 stop

Routine Name:   stop

Description:    Completes current simulation step, stopping simulation.

Usage:          stop

Example:        stop

Notes:          After cleanly stopping the simulation, the routine returns you
                to the GENESIS shell.  The stop routine is NOT equivalent to
                interrupting with ^C, which leaves the simulation in an
                unknown state -- stop completes the current step in progress.
See also: step , abort

25.180 strcat

Routine Name:   strcat

Description:    Returns new string as concatenation of two strings.

Usage:          new-string = {strcat s1 s2}

Example:        genesis >  echo { strcat "bad" "dog" }
                baddog

Notes:          Unlike the C function of the same name, this routine does not
                modify the string s1.

                You can also concatenate strings using the ``@'' operator.

25.181 strcmp

Routine Name:   strcmp

Description:    Compares two strings.

Usage:          compare-flag = {strcmp s1 s2}

                compare-flag    returned as 0 if strings are identical; 1 if
                                s1 is "greater than" s2; -1 if s1 is "less
                                than" s2

Example:        genesis >  echo { strcmp "hi" "hi" }
                0
                genesis >  echo { strcmp "hi" "he"}
                1
                genesis >  echo { strcmp "hi" "ho"}
                -1

Notes:          "Greater than" means "later in the standard ASCII sequence".

                You can compare strings up to a specified character using the
                strncmp routine.
See also: strcat , strlen , substring , findchar

25.182 strlen

Routine Name:   strlen

Description:    Returns length of string in number of characters.

Usage:          length-int = {strlen string}

Example:        genesis >  echo { strlen "string" }
                6
                genesis >  echo { strlen "hi there" }
                8

Notes:          Blanks, TABs, and so forth are included in the count.
See also: strcat , strcmp , substring , findchar

25.183 strncmp

Routine Name:   strncmp

Description:    Compares two strings up to specified number of characters.

Usage:          compare-flag = {strncmp s1 s2 n}

                compare-flag    returned as 0 if strings are identical;
                                1 if s1 is "greater than" s2;
                                -1 if s1 is "less than" s2

                n               number of characters up to which to make
                                comparison

Example:        genesis >  echo { strncmp "hip" "hit" 2 }
                0
                genesis >  echo { strncmp "hip" "hit" 3 }
                -1

Notes:          The strncmp routine is like the strcmp routine, but restricted
                to a certain number of characters for comparison.

                "Greater than" means "later in the standard ASCII sequence".
See also: strcat , strlen , substring , findchar

25.184 strsub

Routine Name:   strsub

Description:    Returns a string with one substring replaced by another

Usage:          strsub string old-substring new-substring [-all]

Example:        genesis > echo {strsub "old dogs chase old cats" old young}
                young dogs chase old cats

                genesis > {strsub "old dogs chase old cats" old young -all}
                young dogs chase young cats
Notes:          

25.185 substituteinfo

Routine Name:       substituteinfo

Description:        Lists the substitutions made with the use of objsubstitute
                    and msgsubstitute

Usage:              substituteinfo

Example:            genesis > objsubstitute compartment mycompt
                    genesis > substituteinfo
                    Number of object substitutions: 1
                    0   orig=compartment        new=mycompt

                    Number of msg substitutions: 0

Notes:              objsubstitute and msgsubstitute are used to allow
                    you to save an object of one type using simobjdump and
                    simdump, and then use simundump to reload it as a
                    different type.  substituteinfo provides information
                    about these substitutions.
See also: objsubstitute , msgsubstitute , simobjdump , simdump , swapdump , simundump

25.186 substring

Routine Name:   substring

Description:    Returns part of original string as new substring.

Usage:          new-string = {substring string startindex [endindex]}

                new-string      returned as new string created

                string          original string
        
                startindex      integer indicating position of first character
                                in string to include in new string

                endindex        integer indicating position of final character
                                in string to include in new string (default:
                                final character in string)

Example:        genesis >  echo { substring "0123456789" 3 7 }
                34567
                genesis >  echo { substring "0123456789" 3 }
                3456789

Notes:          The substring routine can be useful in conjunction with other
                routines (e.g., getpath) for constructing names based on part
                of an element path name.

See also: strcat , strcmp , strncmp , strlen , findchar

25.187 swapdump

Routine name:   swapdump

Description:    Mirrors initialization data for doing simulation dumps
                using simdump.  Consider this situation: we have a dumpfile
                that we want to read in, but at the same time we have
                laboriously defined (using simobjdump) our favourite sets of
                fields for all objects. Unfortunately the dumpfile has its own
                set of simobjdumps, which will overwrite ours. So we use
                swapdump, which puts our own simobjumps into storage, while we
                read in the dumpfile.  Then we can do swapdump again to go back
                to our original set of simobjdumps.

Usage:          swapdump

Example:        Complicated model is already set up, with its own preferences
                for simobjdump. Now we want to read in a dumpfile called foo.g.

                ...
                swapdump // put original simobjdump preferences into storage
                include foo.g // read in dumpfile which has its own simobjdumps
                swapdump // restore original simobjdump preferences
                ...
                simdump bar.g -all      // Save combined model using original
                                        // simobjdump preferences.
Notes:          
See also: initdump , simdump , simobjdump , simundump

25.188 syndelay

Routine Name:   syndelay

Description:    This command is used to set or to add a small "synaptic" 
                component to the delay fields of synapses.  It is useful 
                for when cells are very close together and thus where 
                planardelay or volumedelay give unrealistically small
                delays.

Usage:          syndelay path delay                        \
                -add                                       \
                -uniform scale                             \
                -gaussian stdev maxdev                     \
                -exponential mid max                       \
                -absoluterandom

                path  A wildcarded list of elements which must be synchans or 
                        objects derived from synchan.  

                delay -- This sets all the synaptic delays in question to be
                        equal to "delay", or adds "delay" to the existing
                        delay if the -add option is selected.

                -add  This option causes the delays to be added to the 
                        preexisting delays in the synapses instead of
                        overwriting them.  

                The next four options are used to add random components to the
                delay.  How these random components are added to the delays is 
                explained below.

                -uniform scale  -- This option gives a random number taken 
                        from a uniform distribution in the range 
                        {-scale, scale}.

                -gaussian stdev maxdev  -- This option gives a random number
                        taken from a gaussian distribution centered on zero,
                        with a standard deviation equal to "stdev" and with
                        a maximum value of "maxdev".  The maximum value is
                        used to limit the random component to a given range.

                -exponential mid max  -- This option gives a random number
                        taken from an exponential distribution with a 
                        minimum value of zero, a 1/e point of "mid" and a 
                        maximum value of "max".  This is mainly for backwards
                        compatibility with genesis 1.4.

                -absoluterandom  This option alters the way the random number
                        is combined with the nominal delay to give the actual
                        delay, as described below.

                Once a random component has been created for a given delay, 
                it is used to set the delay as follows.  If the 
                -absoluterandom option has not been selected the delay is set 
                to be:

                final_delay = delay + (delay * random_number)

                Whereas if the -absoluterandom option has been selected then
                we have

                final_delay = delay + random_number

                Thus the default is to have the amount of randomness as a 
                constant proportion of the delay value.

Example:        syndelay /cell[]/apical_dend/Ex_chan 0.001 \
                            -add -gaussian 0.1 0.3 

                This command will add a small delay to the delay fields in the
                synapses in /cell[]/soma/apical_dend/Ex_chan.  The "synaptic"
                delay added will be 1 millisecond plus a random component.

Notes:          The delays are never allowed to go negative even if a large
                negative random component is added.  Negative delays are set
                to zero.

                If the -add option is chosen, the random component modifies 
                only the delay added and not the total delay.

See also: planardelay , volumeconnect , volumeweight , syndelay ; Chapter 18 of the Book of GENESIS (2nd ed.) has a lengthy discussion of this and related commands.

25.189 tab2file

Routine Name:   tab2file

Description:    Utility function for writing one or more tables of an element
                that uses interpol_structs (e.g. a table, tabchannel, xplot,
                etc.) to an ascii file.  The output file has the entries for
                the respective tables in successive positions. Various
                specialized output modes let one do on-the-fly conversions of
                the table entries.

Usage:          tab2file file-name element table -table2 table -table3 table \
                    -mode mode -nentries n -overwrite

Arguments:      filename: name of ascii file to which the table contents
                          will be written
                element:  path of element containing the table
                table:    name of interpol_struct within the element

Options:        -table2 table
                This option allows one to specify an additional table to write
                into the  file. Entries are written alternately from the first
                table and table2.  Note that table2 must be in the same
                element as table.

                -table3 table
                This allows a third table. This option is similar to table2.

                -mode mode
                mode can be y (the default), xy, alpha, beta, tau, minf, or
                index.  In modes alpha, tau, xy, or index, one table must be
                specified.  In modes beta and minf, two tables must be
                specified.

                y:  The table contents are written one to a line, without
                the x values.  If the -table2 or -table3 option is used,
                then the entry for each table is written om the same line.

                xy:  The table contents are written as one (x,y) pair per
                line.

                index: The table contents are written as one (i,y) pair per
                line, where i is the index, which runs from 0 to nentries.

                alpha: This mode, as well as beta, tau, and minf, assume that
                the element containing the tables is a tabchannel, with each
                gate having an A table containing alpha values, and a B table
                containing values of alpha + beta.  When the table specified
                is an A table, the alpha mode is the same as the xy mode,
                giving an (x,alpha) pair per line.

                beta: In this case, the A table is specified as the table, and
                the B table is used with -table2.  Then the output is one
                (x,beta) pair per line, with beta = B - A.

                tau: Like the beta mode, the A table is specified as the
                table, and the B table is used with -table2.  Then the output
                is one (x,tau) pair per line, with tau = 1/(A + B).

                minf: Like the beta mode, the A table is specified as the
                table, and the B table is used with -table2.  Then the output
                is one (x,minf) pair per line, with the steady state
                activation minf = A/B = alpha/(alpha + beta).

                -nentries n
                The parameter n, or nentries, is more properly described as
                xdivs, the number of divisions, with indices of the entries
                running from 0 to n, so the actual number of entries is n + 1.
                If the --nentries option is not used, the default is to
                calculate n from the xivs field of the interpol_struct.  Some
                objects (e.g. xplot) do not have an xdivs field of the
                interpol_struct.  In this case, n must be specified as the
                total number of entries - 1.

                -overwrite
                The default behavior is to append to the file file-name if it
                already exists.  The overwrite option is used to create a new
                file, overwriting the old one.

Example:  (using the elements created by Scripts/tutorials/newtutorial3.g)

/* create a file that looks like:
    -0.100000       0.039416
    -0.099950       0.039586
    -0.099900       0.039756
    ...
    0.049900        0.975220
    0.049950        0.975246
    0.050000        0.975272
*/
tab2file mfile /cell/soma/K_hh_tchan X_A -table2 X_B -mode minf

/* create a file that looks like:
    0       7.462942
    1       7.491676
    2       7.520512
    ...
    2998    1099.018540
    2999    1099.518456
    3000    1100.018372
*/
tab2file ifile /cell/soma/K_hh_tchan X_A -mode index

/* save an xplot (from Scripts/kinetikit/xgraphs.g) */
    function do_save_plot(file)
        str file
        str plot = {getfield /parmedit/plot elmpath}
        int x
        x = {getfield {plot} npts} // Get the actual number of points
        tab2file {file} {plot} xpts -table2 ypts -nentries {x - 1}
        xhide /parmedit/plot
    end

Notes:          Elements having TABSAVE and TABREAD actions (e.g. tabchannel,
                tab2Dchannel, and tabcurrent) can also call these actions
                instead of using tab2file and file2tab.
See also: file2tab , interpol_struct documentation ( Tables )

25.190 tan

Routine Name:   tan

Description:    Returns tangent for given angle (specified in radians).

Usage:          tangent = {tan angle-in-radians}

Example:        float t = {tan {3.14159/4}}

Notes:          
See also: atan

25.191 trunc

Routine Name:   trunc

Description:    Returns integer part of number.

Usage:          integer = {trunc number}

Example:        genesis >  echo { trunc 5.999 }
                5

Notes:          This routine converts any number to an integer by deleting
                the decimal part without any rounding.
See also: round

25.192 tweakalpha

Routine Name:   tweakalpha

Description:    Allows one to fill the A and B tables of a tabchannel
                with values of the rate constants alpha and beta, and
                then convert them to the proper values A = alpha and
                B = alpha + beta.

Usage:          tweakalpha channel-element gate
                gate    X, Y, or Z

Example:        tweakalpha K_mit_usb X

Notes:
See also: tabchannel , tweaktau

25.193 tweaktau

Routine Name:   tweaktau

Description:    Allows one to fill the A table of a tabchannel with the
                activation time constant tau, and the B table with the steady
                state activation m_inf, and then convert the tables to the
                proper values A = alpha and B = alpha + beta.

Usage:          tweaktau channel-element gate
                gate    X, Y, or Z

Example:        tweaktau Na_rat_smsnn X

Notes:
See also: tabchannel , tweakalpha

25.194 useclock

Routine Name:   useclock

Description:    Specifies which clock an element should use during simulation.

Usage:          useclock path clock-number

Example:        useclock /graphform/Vmgraph 1

Notes:          The useclock routine specifies which clock is to be used by a
                GENESIS element.  You might use it, for instance, to allow
                some elements to be updated at greater intervals than the
                basic simulation step.

See also: showclocks , setclock , getclock

25.195 version

Routine Name:   version

Description:    Returns the GENESIS version number.

Usage:          version_number = {version}

Example:
                if ({version} < 2.0)
                    echo "This simulation requires version 2.0 or later"
                    exit
                end

Notes:  

See also:       

25.196 volumeconnect

Routine Name:   volumeconnect

Description:    Establishes synaptic connections between groups of elements
                based on the x-y-z positions of the elements.  This routine 
                sets up the connections by adding SPIKE messages between the 
                source and destination objects.

Usage:          volumeconnect source_elements destination_elements \
                -relative \
                -sourcemask {box, ellipsoid} x1 y1 z1 x2 y2 z2 \
                -sourcehole {box, ellipsoid} x1 y1 z1 x2 y2 z2 \
                -destmask   {box, ellipsoid} x1 y1 z1 x2 y2 z2 \
                -desthole   {box, ellipsoid} x1 y1 z1 x2 y2 z2 \
                -probability p

                source_elements  A wildcarded list of elements which are the 
                        sources of the SPIKE messages.  These must be of
                        class "spiking" and are usually spikegen or 
                        randomspike objects.

                destination_elements  A wildcarded list of elements which are
                        the destinations of the SPIKE messages.  These must  
                        be synchans or objects derived from synchan.

                -relative This option means that connections will be set up
                        based on the locations of destination objects
                        relative to source objects.  If this option is not
                        selected, the absolute locations of source and
                        destination elements will be used to determine
                        which connections are to be set up.

                -sourcemask {box, ellipsoid} x1 y1 z1 x2 y2 z2 -- This
                        specifies a rectangular or ellipsoidal region from
                        which source elements are to be taken.  If the "box"
                        option is used, then x1, y1, and z1 are the minimum
                        x, y, and z values of the region while x2, y2, and
                        z2 are the maximum x, y, and z values of the
                        region.  If the "ellipsoid" option is used, then the
                        source region is an ellipsoid with x1, y1 and z1
                        representing the center of the ellipsoid while x2,
                        y2, and z2 represent the lengths of the principal
                        axes in the x, y, and z directions respectively.
                        Note that to choose a spherical region x2, y2, and
                        z2 must be equal.  Note also that one or the other
                        of {box, ellipsoid} MUST be chosen; leaving both of
                        them out will generate an error.  Finally, one can
                        choose multiple source regions by having multiple
                        -sourcemask options.  The same conventions are
                        followed for the next three options.  

                -sourcehole {box, ellipsoid} x1 y1 z1 x2 y2 z2  -- This 
                        specifies a rectangular or elliptical region NOT to 
                        include in the source region(s).  You can exclude 
                        multiple regions by having multiple -sourcehole 
                        options.

                -destmask {box, ellipsoid} x1 y1 z1 x2 y2 z2  -- This 
                        specifies a rectangular or elliptical region to which 
                        SPIKE messages will be sent.

                -desthole {box, ellipsoid} x1 y1 z1 x2 y2 z2  -- This 
                        specifies a rectangular or elliptical region NOT to 
                        include in the destination region(s). 

                -probability p  -- This option causes connections to be 
                        made with a probability p, which must be in the
                        range [0,1].  This allows probabilistically-connected
                        networks to be set up.

Example:        Say we want to connect the spike generating-region of a group
                of cells with excitatory synapses on the apical dendritic 
                compartments of the same group of cells, without connecting 
                any cell to itself.  We could do this:

                volumeconnect /cell[]/soma/spike                 \
                              /cell[]/apical_dend/exc_syn        \
                              -relative                          \
                              -sourcemask box -1 -1 -1  1  1  1  \
                              -sourcehole box -10e-6 -10e-6 -1   \
                                               10e-6  10e-6  1   \
                              -destmask   box -1 -1 -1  1  1  1

                Note that here we are excluding a region 10 microns square in
                the x and y direction (but essentially unlimited in the z
                direction) so that cells don't connect to themselves.  Here
                I'm assuming we're using SI units.  This could also have
                been done with planarconnect.  Note also that the usual way
                to specify "all cells in a region" is to give source or
                destination regions using -sourcemask or -destmask with
                limits far greater than the entire extent of all the
                elements in the region.

Notes:          This routine is almost identical with planarconnect except 
                that it uses the positions of elements in three dimensions 
                to specify whether connections are made or not, whereas
                planarconnect uses only the x and y dimensions.

                The weights and delays of the connections set up by this   
                command are typically specified using the volumeweight and 
                volumedelay commands, although they can be set up by hand.
See also: planarconnect , volumeweight , volumedelay ; Chapter 18 of the Book of GENESIS (2nd ed.) has a lengthy discussion on this and related commands.

25.197 volumedelay

Routine Name:   volumedelay

Description:    Sets the delay fields on groups of synapses between
                specified lists of elements.  Most often used to set
                delays on groups of synapses that have been set up
                by calling the "volumeconnect" command.  This function
                can assign groups of synapses to a fixed delay, can
                assign delays in proportion to the distances between
                pre- and postsynaptic elements, and can add various
                types of randomness to delay values.

Usage:          volumedelay sourcepath [destination_path]  \
                -fixed delay                               \
                -radial conduction_velocity                \
                -add                                       \
                -uniform scale                             \
                -gaussian stdev maxdev                     \
                -exponential mid max                       \
                -absoluterandom

                sourcepath  A wildcarded list of elements which are the 
                        sources of the SPIKE messages connecting the
                        pre- and postsynaptic elements (i.e. the presynaptic
                        elements).  These must be of class "spiking" and are 
                        usually spikegen or randomspike objects.

                destination_path  A wildcarded list of elements which must be
                        synchans or objects derived from synchan.  If this
                        (optional) argument is given, only the delays between 
                        the given set of pre- and postsynaptic elements will
                        be set by this command.  If this argument is not
                        given, then all the synapses receiving SPIKE messages
                        from the presynaptic elements will have their delays
                        set by this command.  NOTE: this optional argument is 
                        new and is not documented in the Book of Genesis.

                -fixed delay  -- This option sets all the synaptic delays in
                        question to be equal to "delay".

                -radial conduction_velocity  -- This option sets the synaptic 
                        delays in question to be proportional to
                        the distance between the source and destination 
                        elements according to the equation:

                        delay = radial_distance / conduction_velocity

                        Where conduction_velocity is usually measured in
                        meters/sec (SI units).  "conduction_velocity"
                        represents the conduction velocity of the 
                        (hypothetical) axon that the spikes travel down.
                        For volumedelay, the distance is measured as:
 
                        distance = 
                          sqrt((x_src - x_dest)^2 + 
                               (y_src - y_dest)^2 + 
                               (z_src - z_dest)^2)
 
                        where x_src is the x component of the source element,
                        x_dest is the x component of the destination element,
                        and so on. 

                -add  This option causes the computed delays to be added to 
                        the preexisting delays in the synapses instead of
                        overwriting them.  This is useful when adding small 
                        synaptic delays, among other uses.  

                The next four options are used to add random components to the
                delays established using the -fixed or -decay options.  How
                these random components are added to the delays is explained
                below.

                -uniform scale  -- This option gives a random number taken 
                        from a uniform distribution in the range 
                        {-scale, scale}.

                -gaussian stdev maxdev  -- This option gives a random number
                        taken from a gaussian distribution centered on zero,
                        with a standard deviation equal to "stdev" and with
                        a maximum value of "maxdev".  The maximum value is
                        used to limit the random component to a given range.

                -exponential mid max  -- This option gives a random number
                        taken from an exponential distribution with a 
                        minimum value of zero, a 1/e point of "mid" and a 
                        maximum value of "max".  This is mainly for backwards
                        compatibility with genesis 1.4.

                -absoluterandom  This option alters the way the random number
                        is combined with the nominal delay to give the actual
                        delay, as described below.

                Once a random component has been created for a given delay, 
                it is used to set the delay as follows.  If the 
                -absoluterandom option has not been selected the delay is set 
                to be:

                final_delay = delay + (delay * random_number)

                Whereas if the -absoluterandom option has been selected then
                we have

                final_delay = delay + random_number

                Thus the default is to have the amount of randomness as a 
                constant proportion of the delay value.

Example:        [modified from the Orient_tut simulation:]

                volumedelay /retina/recplane/rec[]/input \
                            -radial {CABLE_VEL}          \
                            -gaussian 0.1 0.3

                This command will set the size of the delays of synapses 
                that are receiving their inputs from 
                /retina/recplane/rec[]/input.  It gives delays equal to the
                radial distance between elements divided by the conduction
                velocity (CABLE_VEL).  It also specifies that gaussian noise 
                be added to the delays with a mean value of 0.1 (which 
                represents 10% of the original delay, since -absoluterandom 
                has not been selected) and a maximum value of 0.3 (which is 
                30% of the original delay value).

Notes:          The "destination_path" optional argument is new and is not
                documented in the Book of GENESIS.

                This routine calculates distance using the x, y, and z
                coordinates of the element positions and is thus more 
                realistic than planardelay, which only uses the x and y
                directions.  In general, we encourage users to use this
                function instead of planardelay, which is mainly provided
                for backwards compatibility with genesis 1.4.

                The delays are never allowed to go negative even if a large
                negative random component is added.  Negative delays are set
                to zero.

                If the -add option is chosen, the random component modifies 
                only the delay added and not the total delay.
See also: planardelay , volumeconnect , volumeweight , syndelay ; Chapter 18 of the Book of GENESIS (2nd ed.) has a lengthy discussion on this and related commands.

25.198 volumedelay2

Routine Name:   volumedelay2

Description:    

Description:    A faster version of volumedelay, which sets the delay fields
                on groups of synapses between specified lists of elements.
                Most often used to set delays on groups of synapses that have
                been set up by calling the "volumeconnect" command.  This
                function can assign groups of synapses to a fixed delay, can
                assign delays in proportion to the distances between pre- and
                postsynaptic elements, and can add various types of randomness
                to delay values.

Usage:          volumedelay sourcepath destination_path   \
                -fixed delay                              \
                -radial conduction_velocity                \
                -add                                       \
                -uniform scale                             \
                -gaussian stdev maxdev                     \
                -exponential mid max                       \
                -absoluterandom

Notes:          In contrast to volumedelay, which can set the delays of all
                efferent synapses from the source map when no destination is
                given, volumedelay2 only sets the delays of the synapses
                from the source map to a particular destination map.  By
                requiring the destination parameter, volumedelay2 achieves
                faster setup times than volumedelay.  For further details of
                usage and examples, see the documentation for volumedelay.
See also: volumedelay , volumeconnect , volumeweight , volumeweight2

25.199 volumeweight

Routine Name:   volumeweight

Description:    Sets the weight fields on groups of synapses between
                specified lists of elements.  Most often used to set
                weights on groups of synapses that have been set up
                by calling the "volumeconnect" command.  This function
                can assign groups of synapses to a fixed weight, can
                assign weights in proportion to the distances between
                pre- and postsynaptic elements, and can add various
                types of randomness to weight values.

Usage:          volumeweight sourcepath [destination_path] \
                -fixed weight                              \
                -decay decay_rate max_weight min_weight    \
                -uniform scale                             \
                -gaussian stdev maxdev                     \
                -exponential mid max                       \
                -absoluterandom

                sourcepath  A wildcarded list of elements which are the 
                        sources of the SPIKE messages connecting the
                        pre- and postsynaptic elements (i.e. the presynaptic
                        elements).  These must be of class "spiking" and are 
                        usually spikegen or randomspike objects.

                destination_path  A wildcarded list of elements which must be
                        synchans or objects derived from synchan.  If this
                        (optional) argument is given, only the weights between 
                        the given set of pre- and postsynaptic elements will
                        be set by this command.  If this argument is not
                        given, then all the synapses receiving SPIKE messages
                        from the presynaptic elements will have their weights
                        set by this command.  NOTE: this optional argument is 
                        new and is not documented in the Book of GENESIS.

                -fixed weight  -- This option sets all the synaptic weights in
                        question to be equal to "weight".

                -decay decay_rate max_weight min_weight  -- This option sets
                        the synaptic weights in question to be proportional to
                        the distance between the source and destination 
                        elements according to the equation:

                        weight = (max_weight - min_weight) * 
                          exp(-decay_rate * distance) + min_weight

                        For volumeweight, the distance is measured as:

                        distance = 
                          sqrt((x_src - x_dest)^2 + 
                               (y_src - y_dest)^2 + 
                               (z_src - z_dest)^2)

                        where x_src is the x component of the source element,
                        x_dest is the x component of the destination element,
                        and so on. 

                The next four options are used to add random components to the
                weights established using the -fixed or -decay options.  How
                these random components are added to the weights is explained
                below.

                -uniform scale  -- This option gives a random number taken 
                        from a uniform distribution in the range 
                        {-scale, scale}.

                -gaussian stdev maxdev  -- This option gives a random number
                        taken from a gaussian distribution centered on zero,
                        with a standard deviation equal to "stdev" and with
                        a maximum value of "maxdev".  The maximum value is
                        used to limit the random component to a given range.

                -exponential mid max  -- This option gives a random number
                        taken from an exponential distribution with a 
                        minimum value of zero, a 1/e point of "mid" and a 
                        maximum value of "max".  This is mainly for backwards
                        compatibility with genesis 1.4.

                -absoluterandom  This option alters the way the random number
                        is combined with the nominal weight to give the actual
                        weight, as described below.

                Once a random component has been created for a given weight, 
                it is used to set the weight as follows.  If the 
                -absoluterandom option has not been selected the weight is set 
                to be:

                final_weight = weight + (weight * random_number)

                Whereas if the -absoluterandom option has been selected then
                we have

                final_weight = weight + random_number

                Thus the default is to have the amount of randomness as a 
                constant proportion of the weight value.

Example:        [modified from the Orient_tut simulation:]

                volumeweight /retina/recplane/rec[]/input \
                             -decay 0.5 10.0 0.1          \
                             -gaussian 0.1 0.3

                This command will set the size of the weights of synapses 
                that are receiving their inputs from 
                /retina/recplane/rec[]/input.  It gives exponentially decaying
                weights with a maximum size of 10.0, a minimum size of 0.1,
                and a decay rate of 0.5.  It also specifies that gaussian
                noise be added to the weights with a mean value of 0.1 
                (which represents 10% of the original weight, since 
                -absoluterandom has not been selected) and a maximum value of
                0.3 (which is 30% of the original weight value).

Notes:          The "destination_path" optional argument is new and is not
                documented in the Book of Genesis.

                This routine calculates distance using the x, y, and z
                coordinates of the element positions and is thus more 
                realistic than planarweight, which only uses the x and y
                directions.  In general, we encourage users to use this
                function instead of planarweight, which is mainly provided
                for backwards compatibility with genesis 1.4.

                The weights are never allowed to go negative even if a large
                negative random component is added.  Negative weights are set
                to zero.

                The options -fixed and -decay are mutually exclusive.  The 
                different random options -uniform, -gaussian, and -exponential
                are also mutually exclusive.
See also: planarweight , volumeconnect , volumedelay ; Chapter 18 of the Book of GENESIS (2nd ed.) has a lengthy discussion on this and related commands.

25.200 volumeweight2

Routine Name:   volumeweight2

Description:    

Description:    A faster version of volumeweight, which sets the weight fields
                on groups of synapses between specified lists of elements.
                Most often used to set weights on groups of synapses that have
                been set up by calling the "volumeconnect" command.  This
                function can assign groups of synapses to a fixed weight, can
                assign weights in proportion to the distances between pre- and
                postsynaptic elements, and can add various types of randomness
                to weight values.

Usage:          volumeweight sourcepath destination_path   \
                -fixed weight                              \
                -decay decay_rate max_weight min_weight    \
                -uniform scale                             \
                -gaussian stdev maxdev                     \
                -exponential mid max                       \
                -absoluterandom

Notes:          In contrast to volumeweight, which can set the weights of all
                efferent synapses from the source map when no destination is
                given, volumeweight2 only sets the weights of the synapses
                from the source map to a particular destination map.  By
                requiring the destination parameter, volumeweight2 achieves
                faster setup times than volumeweight.  For further details of
                usage and examples, see the documentation for volumeweight.
See also: volumeweight , volumeconnect , volumedelay , volumedelay2

25.201 where

Routine Name:   where

Description:    Returns name of operating-system directory in which specified
                file is located.

Usage:          where filename

                filename        name of file to search for (must be actual
                                name; where does not add a .g if you do not
                                explicitly supply it, and does not accept
                                wildcarded names)

Example:        genesis >  where mysim.g
                'mysim.g' found in .

                genesis >  where fooby
                could not find 'fooby' in . /usr/genesis/startup

Notes:          The where routine searches the script path list (as specified
                in the operating system environmental variable SIMPATH) and
                reports the first instance found of the specified file.

25.202 writecell

Routine Name:   writecell

Description:    Writes parameters of neuron to a cell parameter file in a
                standard format.

Usage:          writecell filename cellname -cartesian -polar -relative
                        -absolute -syndens -syncond -author author

                filename                name to give cell descriptor file
                                        (should end with extension .p)

                cellname                name of GENESIS cell for which you
                                        want to store description

                author                  who made the cell

                default options         -cartesian -relative -syndens

Example:        writecell  newmitral.p  /mitral 

Notes:          This cell-writing routine is the counterpart of the readcell
                routine.  writecell takes a multicompartment neuron set up
                in GENESIS and writes it in the neuron descriptor format to
                a file.  Options allow you to specify whether the compartment
                coordinates are cartesion or polar, and whether they are
                given in absolute units or relative to the postion of the
                parent compartment.  The -syndens and -syncond options
                specify whether synaptic conductances are expressed as
                densities (conductance per unit area) or in absolute units.
                The format of the cell parameter file is described in the
                documentation for readcell.  The routine is capable of
                parsing GENESIS neurons which are not in the 'flat' element
                structure produced by the readcell routine.  There are
                limitations to the present version of writecell, as there
                have been new features added to readcell which have not yet
                been incorporated into writecell.  Thus, not all cell models
                can be parameterized with writecell.
See also: readcell

25.203 writefile

Routine Name:   writefile

Description:    Writes out ASCII data to currently opened file.

Usage:          writefile filename [arguments ...] [-nonewline] [-format str] 

                filename        name of file to write to (must first be opened
                                with openfile routine with w or a switch)

                -nonewline      do not append carriage return at end of line
                                (if omitted, carriage return is appended)

                -format str     use specified format string str to format each
                                argument (to construct mixed formats, use
                                multiple writefile calls with -n option to
                                place them on a single line)

                arguments       strings to be written out to file (default is
                                nothing, which effectively means a blank line
                                unless -n is selected to suppress carriage
                                return; the arguments are written out with
                                single spaces between each and are terminated
                                with a carriage return)

Example:        openfile test2 w
                // both of these write three entries per line,
                // each separated by a space
                writefile test2 1.0 2.0 3.0
                writefile test2 "4.0 5.0 6.0"

                genesis >  openfile test w
                genesis >  writefile test Vm = 10 "string   with space" {10+5}
                genesis >  writefile test  one -n
                genesis >  writefile test line
                genesis >  writefile test X Y -format "%5s"
                genesis >  writefile test 5.3 6.5 -format "(%3s)"
                genesis >  writefile test FIRST SECOND -n -format "%-10s"
                genesis >  writefile test  THIRD -format "%30s"
                genesis >  writefile test done
                genesis >  closefile test
                genesis >  more test
                Vm = 10 string   with space 15
                oneline
                    X    Y
                (5.3)(6.5)
                FIRST     SECOND                         THIRD
                done            
                genesis >

Notes:          The changes you make are made permanent when you close the
                file (using closefile), or flush the buffer with flushfile.

                There is limited formatting of output.
See also: openfile , closefile , listfiles , readfile , flushfile , floatformat

25.204 xcolorscale

Routine Name:   xcolorscale

Description:    Sets the color scale for mapping numerical values to
                color.

Usage:          xcolorscale colorscale
                colorscale:     hot, rainbow, rainbow2, redhot, or grey

Example:        xcolorscale hot

Notes:          The colorscale (which is a file in genesis/startup) applies
                to pixes which have a field mapped to color, such as the
                shapes in an xvar or xview, or the cell display in xcell.  It
                does not apply to widgets, like buttons, labels, etc.

25.205 xgetstat

Routine Name:           xgetstat

Description:            returns 0 if Xodus is not properly initialized.

Usage:                  status = {xgetstat}

Example:                echo {xgetstat}
                        1

                        if ({{xgetstat})
                                include graphics
                        end

Notes:                  It is possible to run GENESIS without XODUS by using
                        the -nox option to the genesis command line.  If a
                        simulation is to intended to be run both with and
                        without XODUS, a simulation script may use xgetstat to
                        determine if XODUS is available.
See also: genesis

25.206 xps

Routine Name:   xps

Description:    Sets parameters used to generate postscript output of widgets.

Usage:          xps [-maxgray maxgray] [-mingray mingray]
                        [-inverse inverse-flag] [-dpi screendpi]
                        [-filename name] [-printer]

                maxgray         integer between 0 and 256 (with mingray,
                                sets the range of black to white)

                mingray         integer between 0 and 256 (threshold for
                                a pixel to be black)

                inverse-flag    0 to leave image as is; 1 to reverse
                                image

                screendpi       screen resolution in dots per inch

                name            name of the file to which output will be
                                directed

                -printer        flag indicating that print commands should be
                                sent directly to printer rather than to file

Examples:       genesis > xps -inverse 0 -filename dump.ps
                genesis >  xps

                usage: xps [-maxgray maxgray(0-256)][-mingray mingray]
                [-inverse 0/1] [-dpi screendpi][-filename name][-printer]
                [-help][-usage]
                status : maxgray = 256, mingray = 0, inverse = 0, dpi = 100
                output to file 'dump.ps'

Notes:          The xgraph and xdraw widgets are able to output their contents
                to a postscript printer or file when ctrl-p is typed while the
                cursor is within the widget.  xps is used to set some relevant
                parameters.  Called with no arguments, the routine displays a
                usage message plus the current settings for output parameters
                that you can set with the routine.

                The default is to send the output to the postscript printer
                that is specified by the PRINTER environment variable.  The
                filename option may be used to specify a filename to which the
                output may be sent instead.  Use the printer option to restore
                output to the printer.  Note that this is NOT used to set the
                printer name.

                The inverse flag should normally be set to 0 for dark colors
                plotted on a light background, such as the default gray
                background provided by XODUS.  However, you will generally get
                better results by setting the bg field of the widget to
                "white".  If you make light plots on a black background, set
                inverse to 1.  The dots per inch of the display (specified
                with the dpi option) is used for setting the line width of
                plotted lines.  A larger dpi will make a narrower line.

                mingray is subtracted from the pixel value to define the pixel
                value at which the color is black.  Reducing the range
                (maxgray - mingray) increases the contrast, scaling the pixel
                value by 1/(maxgray - mingray).

                This method of producing graphical output has the advantage of
                being independent of the screen resolution.  To produce an
                exact bit-mapped replica of the image on the screen, it is
                best to use one of the screen capture utilities such as xv or
                import (from the ImageMagick package), available at the usual
                X windows archive sites.  For publication quality graphs, it
                is best to use an asc_file object to write data to a file that
                can be processed with a plotting package such as gnuplot.

                setpostscript is an alias for xps.

25.207 xsimplot

Routine Name:           xsimplot

Description:            Allows 2-D plotting of data/subsets of data from the
                        binary file on disk. At present it can deal with files
                        in the FMT1 and the Netcdf file formats.

Usage:                  xsimplot graphelm pathtofile -cell cellnum \
                        -skip skipby -overlay overlaynum \
                        -offset overlayoffset -color col -gain gainval -old

Example:                See Scripts/examples/diskiolib/diskio/simplot.g

Notes:                  xsimplot can be used to plot data or subsets of data
                        from a binary simulation file onto an xgraph.  At the
                        moment it can be reliably used to plot data from a
                        FMT1 or a netcdf file generated by genesis simulations
                        via the use of the disk_out or diskio elements. 

                        Explanation of arguments and options:
                        ____________________________________

                        The 2 mandatory arguments to xsimplot are the 

                                1. the genesis path of the xgraph element
                                on which the data is to be plotted.

                                2. the unix pathname of the binary data file.

                        -cell cellnum:
                                
                                The -cell option allows plotting of a
                                particular set of values dumped onto the file.
                                For example, if a 100 SAVE messages are sent
                                to a diskio/disk_out element and the
                                simulation stepped 100 times, by specifying a
                                cellnum anywhere from 0-99, one can plot
                                values corresponding to a particular message.
                                cellnum defaults to 0 if this option is not
                                specified.

                        -skip skipby:
                                        
                                The -skip option allows plotting of a subset
                                of values within a cell. For example, in order
                                to plot values corresponding to the 30th, 60th
                                and the 90th time step in a 100 step
                                simulation file, a skipby value of 30 will
                                plot these points joined by a discontinuous
                                straight line.  Defaults to 1 if not
                                specified.

                        -overlay overlaynum:

                                Allows successive renderings of the same plot
                                to overlay on the graph instead of overwriting
                                previous ones. Goes hand in hand with the
                                usage of the -offset option.

                        -offset overlayoffset:
                
                                Allows the same plot to be offset in the
                                y-axis by the amount equal to overlayoffset.
                                When used with the -overlay option, gives a
                                means of graphically comparing plots from 2
                                different simulation runs.

                        -color col:
                                
                                Color of plot pix - can be specified as a
                                string or an index into a colorscale.
                                Defaults to black.

                        -gain gainval:
                                Currently not implemented
                        -old:
                                A No-op. Retained for backwards compatibility
                                with GENESIS 1.4.
See also: disk_out , diskio , xgraph , xplot , xcolorscale


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