The DUPLICATE Action

To understand how to use hsolve for network simulations, remember for a moment how hsolve examines the model it has to compute:

1. First during the SETUP action, hsolve examines the structure of the model and stores parameters that describe it.
2. Second during a RESET, hsolve stores recalculated quantitative values in its private data structures.

With the DUPLICATE action it is possible to have multiple hsolve elements share the structure between identical neurons (neurons with an identical morphology, number of channels etc. The descriptive quantitative aspects like reversal potential of channels may differ between these neurons).

To use hsolve for a population of resembling cells, you have to:

1. create and use SETUP to have hsolve examine the structure of the first cell.
2. create an hsolve element for every other cell in the population. This is not done with a regular create command, but by calling the DUPLICATE action on the solver element for the first cell, to have the new hsolve element share some of its internal data structures with the first hsolve element. The syntax for the DUPLICATE action is:

       genesis > call hsolve1 DUPLICATE hsolve2 <path>
   

   The <path> argument points to the compartments to be computed by the hsolve about to be created and is (as always) a wild card specification that will be expanded relative to the hsolve element.
3. call the RESET action on every hsolve element. This is most conveniently done with the reset command.

NOTE: Never use the -hsolve option for readcell for cells that you want to duplicate. The layout of the cells when using e.g. createmap assumes that all cells reside in neutral elements. Such commands do not take special precautions when copying hsolve elements. The net result is that you are not allowed to use the DUPLICATE action on hsolve elements created by the -hsolve option of the readcell.

Let us examine an example:

    genesis > include ht_granule_compartments.g
    genesis > granule_make_compartments
    genesis > setclock 0 0.000010
    genesis > readcell granule.p /granule
    genesis > createmap \
    genesis >         /granule /granule_cell_layer 5 1 \
    genesis >         -delta 1e-4 7.5e-5 -origin 5e-5 3.75e-5
    genesis > ce /granule_cell_layer/granule[0]
    genesis > create hsolve solver
    genesis > setmethod granule 11
    genesis > setfield solver chanmode 4 path "../[][TYPE=compartment]"
    genesis > call solver SETUP
    genesis > int i
    genesis > for (i = 1 ; i < 5 ; i = i + 1)
    genesis >         call solver DUPLICATE \
    genesis >                 /granule_cell_layer/granule[{i}]/solver \
    genesis >                 ../##[][TYPE=compartment]
    genesis > end
    genesis > reset

As already noted, we do not use the -hsolve option for readcell here. After creating a grid of cells, we manually create an hsolve element for the first cell in the grid and initialize it with SETUP after proper configuration. Then comes a small for-loop that walks over the remaining cells of the population and calls the DUPLICATE action for each cell. Note that the wild card specification that points to the compartments to be computed is - as usual - relative to the hsolve element that will do the wild card expansion, it is not relative the current working element or the original hsolve element (that was initialized with SETUP). At this point we have a correctly initialized set of hsolve elements regarding structure. Finally we still have to initialize all data structures with the computed values, that is done with the 'reset' command.

Although almost complete, there is still one caveat in this example that becomes clear if we inspect the simulation schedule:

    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=hsolver]      -action PROCESS 
    [5] Simulate    /##[CLASS=concentration]        -action PROCESS

As apparent from the simulation schedule, some compartment(s) and channel(s) are still scheduled to compute their internal state. Requesting a list of elements at the top of the element hierarchy makes all clear:

    genesis > le /
    *proto
    output                                  
    *library/
    granule/                               
    granule_cell_layer/

The original cell that was used to create the grid of cells in the population is still scheduled for simulation (indicated by the lacking asterisk '*'). Disabling it, solves the situation, only hsolve will be scheduled for computations. It is necessary to do reset again such that Genesis recomputes the simulation schedule. If the disable command is put at an appropriate place in the script, only one reset is necessary of course.

    genesis > disable /granule
    OK
    genesis > reset
    genesis > le /
    *proto
    output                                  
    *library/
    *granule/                               
    granule_cell_layer/                     
    genesis > showsched
    WORKING SIMULATION SCHEDULE
    [1] Simulate        /##[CLASS=hsolver]      -action PROCESS

NOTE: The way to setup input or output for hsolve that has been created with a DUPLICATE is not the same as for hsolve elements that have been created with SETUP. Only with the findsolvefield command you will be able to access computed fields. Messages created before the DUPLICATE action are ignored. (also take a look at the exercises for networks)