Prep
simulation.prep.SimPrep()
¶
Bases: ABC
Standardized framework for preparing files for molecular simulation runs.
get_stage_input_lines(simlify_config)
abstractmethod
classmethod
¶
Prepare input file lines for a single stage.
| PARAMETER | DESCRIPTION |
|---|---|
context |
Specifies options and parameters.
|
| RETURNS | DESCRIPTION |
|---|---|
Collection[str]
|
Input file lines for a single simulations. The lines do not end in |
get_stage_run_command(simlify_config)
abstractmethod
classmethod
¶
Prepare bash command to run a single simulation.
| PARAMETER | DESCRIPTION |
|---|---|
context |
Specifies options and parameters.
|
| RETURNS | DESCRIPTION |
|---|---|
Collection[str]
|
Bash commands in a list to run one stage of a simulation. |
Notes:
[prepare_context][simulation.amber.prep.AmberSimPrep.prepare_context]
should be ran before this.
prepare(simlify_config)
abstractmethod
classmethod
¶
Run all steps to prepare simulations.
| PARAMETER | DESCRIPTION |
|---|---|
simlify_config |
Simlify configuration.
TYPE:
|
prepare_sim_config(simlify_config)
abstractmethod
staticmethod
¶
Preprocessing and validation of a simulation context. This is unique to each simulation package and can be customized based on the context.
| PARAMETER | DESCRIPTION |
|---|---|
simlify_config |
Specifies options and parameters.
TYPE:
|
| RETURNS | DESCRIPTION |
|---|---|
SimlifyConfig
|
Bash commands in a list to run one stage of a simulation. |
prepare_slurm(file_path, simlify_config, write=True)
classmethod
¶
Prepare slurm submission script lines.
| PARAMETER | DESCRIPTION |
|---|---|
context |
Specifies options and parameters.
|
prepare_stage(simlify_config, run_commands=None, write=True)
abstractmethod
classmethod
¶
simulation.prep.cli_run_sim_slurm_prep()
¶
Command-line interface to prepare files for simulations using slurm.
simulation.prep.run_sim_slurm_prep(name_job, dir_work, path_run_write, path_slurm_write, prep_class_string, simlify_config)
¶
Prepare files for simulations using slurm.
| PARAMETER | DESCRIPTION |
|---|---|
name_job |
Unique name for this slurm job.
TYPE:
|
dir_work |
Path to local directory where we will write the simulation files.
TYPE:
|
path_run_write |
Local path to write a run script with respect to
TYPE:
|
path_slurm_write |
Local path to write a slurm submission script with respect to
TYPE:
|
prep_class_string |
Import string to a simulation preparation class. For example,
TYPE:
|
simlify_config |
Simlify configuration.
TYPE:
|