Prep

AmberSimPrep

Bases: SimPrep

Prepares files for Amber molecular dynamics simulations.

This class implements the SimPrep abstract base class to provide a concrete workflow for preparing input files, run scripts, and other necessary files specifically for running molecular dynamics simulations using the Amber simulation package. It handles tasks such as setting up Amber-specific file paths, generating input files in the Amber format, constructing the command to execute Amber's pmemd engine, and managing multi-stage simulations.

get_stage_input_lines(simlify_config)

Prepares the lines for a single Amber simulation stage's input file (.in file).

This class method renders the content of the Amber input file based on the engine.inputs attribute of the provided SimlifyConfig object. The engine.inputs is expected to be an object with a render method that generates the input file content as a list of strings.

PARAMETER	DESCRIPTION
simlify_config	The Simlify configuration object containing the input parameters for the current Amber simulation stage, typically defined within the engine.inputs attribute. TYPE: SimlifyConfig

RETURNS	DESCRIPTION
list[str]	list[str]: A list of strings, where each string represents a line in the Amber input file (.in file). The lines do not include the newline character (\n) at the end.

get_stage_run_command(simlify_config)

Prepares the bash command to run a single Amber simulation stage using the pmemd engine.

This class method constructs the command-line invocation of Amber's pmemd engine based on the provided SimlifyConfig. It handles different computational platforms, including serial and MPI execution. If the use_scratch option is enabled in the configuration, it also adds commands to check if the simulation has already been completed and to move the output files from the scratch directory to the designated output directory.

PARAMETER	DESCRIPTION
simlify_config	The Simlify configuration object containing options and parameters for the current Amber simulation stage, such as the input file paths, output directory, and computational platform. TYPE: SimlifyConfig

RETURNS	DESCRIPTION
list[str]	A list of strings, where each string represents a line in the bash script that constitutes the command to run the Amber simulation stage.

RAISES	DESCRIPTION
ValueError	If simlify_config.label is None, as it is used to construct file paths.

Notes

This method relies on the simlify_config object having been preprocessed by the prepare_sim_config method.

Uses the following attributes from simlify_config:

• label: Unique label for this simulation stage.
• run.use_scratch: Boolean indicating whether to use a scratch directory.
• run.dir_work: Path to the main working directory.
• run.dir_output: Path to the final output directory.
• engine.cli: An object representing the Amber command-line interface, with attributes like compute_platform, mdin, mdout, restrt, and mdcrd.
• temp['cpu_cores']: The number of CPU cores to use for MPI simulations.

prepare(simlify_config)

Runs all necessary steps to prepare the Amber simulations based on the provided configuration.

This class method orchestrates the complete preparation process for Amber simulations. It handles both single-stage and multi-stage simulations as defined in the simlify_config. For multi-stage simulations, it iterates through the configured stages, updating the simlify_config with the parameters for each stage. For each stage, it calls prepare_sim_config to preprocess the configuration and then prepare_stage to generate the input files and run commands. Finally, if the write flag in the configuration is True, it writes the accumulated bash commands to the run script file specified in the configuration.

PARAMETER	DESCRIPTION
simlify_config	The Simlify configuration object containing all the necessary options and parameters for the Amber simulation workflow, including settings for single or multiple stages. TYPE: SimlifyConfig

Notes

This method assumes that the simlify_config object is properly initialized with all the required parameters for the Amber simulation.

prepare_sim_config(simlify_config)

Preprocesses and validates the simulation configuration specifically for Amber simulations.

This static method performs Amber-specific preprocessing and validation of the SimlifyConfig object. It sets up various Amber-specific file paths based on the configuration, such as the paths for the input file (.in), output file (.out), restart file (.rst), trajectory file (.nc), and MD info file (.mdinfo). It also checks for the existence of the working directory and creates it if necessary. For MPI-based simulations, it calculates the total number of CPU cores based on the SLURM configuration.

PARAMETER	DESCRIPTION
simlify_config	The Simlify configuration object containing options and TYPE: SimlifyConfig

RETURNS	DESCRIPTION
SimlifyConfig	The modified Simlify configuration object with Amber-specific settings and paths.

RAISES	DESCRIPTION
ValueError	If simlify_config.label is None, as it is used to construct file paths.

prepare_stage(simlify_config, run_commands=None, write=True)

Writes the input file for a single Amber simulation stage and builds the bash commands to run it.

This class method orchestrates the preparation of a single stage in the Amber simulation workflow. It first retrieves the input file lines using get_stage_input_lines. If the write flag is True, it writes these lines to an Amber input file (.in) in the designated input directory. It then retrieves the bash commands to run this stage using get_stage_run_command and appends them to the cumulative list of run_commands. This method also handles the splitting of long simulations into multiple shorter segments if specified in the configuration.

PARAMETER	DESCRIPTION
simlify_config	The Simlify configuration object containing options and parameters for the current Amber simulation stage. TYPE: SimlifyConfig
run_commands	A list of bash commands accumulated from previous stages. The commands for the current stage will be appended to this list. Defaults to None, in which case a new list is initialized. TYPE: list[str] | None DEFAULT: None
write	A boolean flag indicating whether to write the Amber input file (.in) to disk. Defaults to True. TYPE: bool DEFAULT: True

RETURNS	DESCRIPTION
tuple[list[str], list[str]]	A tuple containing two lists: - The lines of the Amber input file generated for this stage. - The updated list of bash commands, including the command(s) for this stage.

RAISES	DESCRIPTION
ValueError	If simlify_config.label is None, as it is used to construct file paths.

Notes

This method relies on the simlify_config object having been preprocessed by the prepare_sim_config method.