AZmodel_mouse_main.mdl

/*This is the main file for the mouse azmodel simulation*/

INCLUDE_FILE="parameters.mdl"  /*read parameters for the simulation*/

NOTIFICATIONS
{
DIFFUSION_CONSTANT_REPORT=OFF
ITERATION_REPORT=OFF
PROBABILITY_REPORT=OFF
VARYING_PROBABILITY_REPORT=OFF
PROGRESS_REPORT=OFF
RELEASE_EVENT_REPORT=OFF
FINAL_SUMMARY=OFF
}

ITERATIONS=iterations
TIME_STEP=time_step
TIME_STEP_MAX=maximum_time_step
EFFECTOR_GRID_DENSITY=effector_grid_density

PARTITION_X=[[-1.1 TO 1.1 STEP 0.04]]
PARTITION_Y=[[-1 TO 1 STEP 0.04]]
PARTITION_Z=[[-0.1 TO 1.2 STEP 0.02]]

/*molecules,reactions,channel release sites,and surface classes*/

INCLUDE_FILE="molecules.mdl"
INCLUDE_FILE="reactions.mdl"
INCLUDE_FILE="channel_release_site.mdl"
INCLUDE_FILE="surface_classes.mdl"

/*object template files*/

INCLUDE_FILE="./geometry/ca_binding_site_template.mdl"
INCLUDE_FILE = "./geometry/ca_Y_binding_site_template.mdl"
INCLUDE_FILE="./geometry/vesicle_template.mdl"

/*object files*/

INCLUDE_FILE="./geometry/main_membrane.mdl"
INCLUDE_FILE="./geometry/active_zone_vesicles.mdl"
INCLUDE_FILE="./geometry/endcaps.mdl"
INCLUDE_FILE="./geometry/volume_buffer.mdl"


/*create instances of the subjects in the simulation*/

INSTANTIATE presynaptic_segment OBJECT {
endcaps OBJECT endcaps {}
main_membrane OBJECT main_membrane {}
vesicles OBJECT vesicles {}
buffer OBJECT buffer {}
channel_release_site OBJECT channel_release_site {}
}

/*visual and reaction data output*/

sprintf(seed,"%04g",SEED) /*write the internal variable SEED into the variable seed*/

INCLUDE_FILE="local_directory.mdl" /*file written by control script that defines the destination of the reaction_data*/

/*for default conditions, rewrite local_directory.mdl to state locladir=/react_data */

/*INCLUDE_FILE="viz_data.mdl"*/
INCLUDE_FILE="reaction_data.mdl"

/*end of the file*/