name | value | description | default |
---|---|---|---|
model_file | FILENAME | input model filename | required |
max_time | REAL | time in seconds to run model for | required |
simulation_algorithm | dm ldm |
simulation algorithm to use dm = direct method ldm = logarithmic direct method |
dm |
data_file | FILENAME | file to save simulation data to | simulation.h5 |
model_format | sbml xml |
format which model is specified in | sbml |
log_type | levels reactions |
type of log to save reactions = save data on each reaction performed levels = save levels of species periodically |
reactions |
log_interval | REAL | interval (seconds) to save species level data | 1.0 |
duplicate_initial_amounts | BOOL | duplicate initial amounts of species given in templates | 0 |
seed | ULONG | random number generator seed if set to 0 use a random seed |
0 |
log_propensities | BOOL | log rule propensities for each compartment | 0 |
log_degraded | BOOL | log levels of degraded species | 0 |
log_memory | BOOL | log data to memory | 0 |
periodic_x | BOOL | use periodic boundary condition for x axis | 0 |
periodic_y | BOOL | use periodic boundary condition for y axis | 0 |
periodic_z | BOOL | use periodic boundary condition for z axis | 0 |
show_progress | BOOL | output current log interval to screen | 0 |