ichor.hpc.submission_commands package

Submodules

ichor.hpc.submission_commands.aimall_command module

class AIMAllCommand(wfn_file_path: Path, ncores: int, naat: int, atoms: List[str] | Atoms | None = 'all', usetwoe: int = 0, encomp: int = 3, boaq: str = 'auto', iasmesh: str = 'fine', bim: str = 'auto', capture: str = 'auto', ehren: int = 0, feynman: bool = False, iasprops: bool = True, magprops: str = 'none', source: bool = False, iaswrite: bool = False, atidsprops: float = 0.001, warn: bool = True, scp: str = 'some', delmog: bool = True, skipint: bool = False, f2w: str = 'wfx', f2wonly: bool = False, mir: str = 'auto', cpconn: str = 'moderate', intveeaa: str = 'new', atlaprhocps: bool = False, wsp: bool = True, shm_lmax: int = 5, maxmem: int = 2400, verifyw: str = 'yes', saw: bool = False, autonnacps: bool = True)

Bases: SubmissionCommand

A class which is used to add AIMALL-related commands to a submission script. It is used to write the submission script line where AIMALL modules are loaded. It is also used to write out the submission script line where AIMALL is ran on a specified array of files (usually AIMALL is ran as an array job because we want to run hundreds of AIMALL tasks in parallel).

Parameters:

wfn_file – Path to a .wfn file. This is not needed when running auto-run for a whole directory.
atoms – A list of strings of atom names (e.g. C1) which aimall to integrate or an Atoms instance (from which the names will be obtained)

property arguments: List[str]

command

property data: List[str]: Returns the data needed for the AIMAll job to run successfully

modules

repr(variables: List[str]) → str: Returns a string which is written out to the submission script file in order to run AIMALL correctly (with the appropriate settings).

class ATIDSProps(value)

Bases: Enum

An enumeration.

All = 'all'

No = 'no'

Some = 0.001

class BasinIntegrationMethod(value)

Bases: Enum

An enumeration.

Auto = 'auto'

ProAIM = 'proaim'

ProMega = 'promega'

ProMega1 = 'promega1'

ProMega5 = 'promega5'

class Boaq(value)

Bases: Enum

An enumeration.

Auto = 'auto'

AutoGS2 = 'auto_gs2'

AutoGS4 = 'auto_gs4'

GS1 = 'gs1'

GS10 = 'gs10'

GS15 = 'gs15'

GS2 = 'gs2'

GS20 = 'gs20'

GS25 = 'gs25'

GS3 = 'gs3'

GS30 = 'gs30'

GS35 = 'gs35'

GS4 = 'gs4'

GS40 = 'gs40'

GS45 = 'gs45'

GS5 = 'gs5'

GS50 = 'gs50'

GS55 = 'gs55'

GS6 = 'gs6'

GS60 = 'gs60'

GS7 = 'gs7'

GS8 = 'gs8'

GS9 = 'gs9'

Leb23 = 'leb23'

Leb25 = 'leb25'

Leb27 = 'leb27'

Leb29 = 'leb29'

Leb31 = 'leb31'

Leb32 = 'leb32'

class CPConn(value)

Bases: Enum

An enumeration.

Basic = 'basic'

Complex = 'complex'

Moderate = 'moderate'

Simple = 'simple'

class Capture(value)

Bases: Enum

An enumeration.

Auto = 'auto'

Basic = 'basic'

Extended = 'extended'

class Ehren(value)

Bases: Enum

An enumeration.

No = 0

OneElectronGradient = 2

StressDivergence = 1

class Encomp(value)

Bases: Enum

An enumeration.

Four = 4

One = 1

Three = 3

Two = 2

Zero = 0

class F2W(value)

Bases: Enum

An enumeration.

WFN = 'wfn'

WFX = 'wfx'

class IASMesh(value)

Bases: Enum

An enumeration.

Fine = 'fine'

Medium = 'medium'

Sparse = 'fine'

SuperFine = 'superfine'

VeryFine = 'veryfine'

class IntVeeAA(value)

Bases: Enum

An enumeration.

New = 'new'

Old = 'old'

class MIR(value)

Bases: Enum

An enumeration.

Auto = 'auto'

Custom = 'custom'

class MagProps(value)

Bases: Enum

An enumeration.

CSGTB = 'csgtb'

GIAO = 'giao'

IGAIM = 'gaim'

NONE = 'none'

class SCP(value)

Bases: Enum

An enumeration.

No = 'false'

Some = 'some'

Yes = 'true'

class SHMMax(value)

Bases: Enum

An enumeration.

All = 5

Charge = 0

Dipole = 1

Hexadecapole = 4

NONE = -1

Octupole = 3

Quadrupole = 2

class UseTwoe(value)

Bases: Enum

An enumeration.

Always = 2

No = 0

Vee_aa = 1

class VerifyW(value)

Bases: Enum

An enumeration.

No = 'no'

Only = 'only'

Yes = 'yes'

ichor.hpc.submission_commands.amber_command module

class AmberCommand(mol2_file: Path, mdin_file: Path, system_name: str, temperature: float, ncores: int)

Bases: SubmissionCommand

todo: write docs

property command: str

property data: List[str]: Do not need a datafile for this command.

group = False

modules

repr(*args) → str

Returns a strings which is then written out to the final submission script file.

The length of variables is defined by the length of self.data

ichor.hpc.submission_commands.cp2k_command module

class CP2KCommand(cp2k_input: Path, temperature: float, ncores: int, system_name: str)

Bases: SubmissionCommand

todo: write docs

property command: str: Returns the command to be used to run CP2K. The command depends on the number of cores.

property data: List[str]: Return a list of the absolute paths of the Gaussian input file (.gjf) and the output file (.gau)

group = False

modules

repr(variables: List[str]) → str

Returns a strings which is then written out to the final submission script file.

The length of variables is defined by the length of self.data

ichor.hpc.submission_commands.dlpoly_command module

class DlpolyCommand(dlpoly_program_path: Path, dlpoly_directory: Path)

Bases: SubmissionCommand

Class used to construct a Dlpoly job. Jobs are submitted using the SubmissionScript class.

Parameters:: dlpoly_directory – Path to where the working directory for dlpoly.

property command: str: Return the command word that is used to run DL POLY. In this case, the path to the DL POLY executable is returned.

property data: List[str]

modules

repr(variables: List[str]) → str: Return a string that is used to construct DL POLY job files.

ichor.hpc.submission_commands.free_flow_python_command module

class FreeFlowPythonCommand(text: str)

Bases: PythonCommand

A class which is used for jobs that will execute python code with python -c python_code_here

Parameters:: text – Arbitrary text to get compiled with python and get executed on a compute node.

repr(variables: List[str] | None = None) → str: Returns a string which is then written into the submission script in order to run a python job.

ichor.hpc.submission_commands.gaussian_command module

class GaussianCommand(ncores: int, gjf_file: Path, gjf_output: Path | None = None)

Bases: SubmissionCommand

A class which is used to add Gaussian-related commands to a submission script. It is used to write the submission script line where Gaussian modules are loaded. It is also used to write out the submission script line where Gaussian is ran on a specified array of files (usually Gaussian is ran as an array job because we want to run hundreds of Gaussian tasks in parallel).

Parameters:

gjf_file – Path to a gjf file. This is not needed when running auto-run for a whole directory.
gjf_output – Optional path to the Gaussian job output for the gjf_file. Default is None as it is set to the gjf_file_name.gau if not specified.

command

property data: List[str]: Return a list of the absolute paths of the Gaussian input file (.gjf) and the output file (.gau). This is the data that is going to be written to the datafile.

group = True

memory_per_core

modules

repr(variables: List[str]) → str: Returns a strings which is then written out to the final submission script file. The length of variables is defined by the length of self.data

total_gaussian_memory() → str: Calculates the total memory to tell Gaussian to use Calculated as (memory_per_core - 1) * number_of_cores

ichor.hpc.submission_commands.orca_command module

class OrcaCommand(orca_input: Path, orca_output: Path | None = None)

Bases: SubmissionCommand

A class which is used to add Gaussian-related commands to a submission script. It is used to write the submission script line where Gaussian modules are loaded. It is also used to write out the submission script line where Gaussian is ran on a specified array of files (usually Gaussian is ran as an array job because we want to run hundreds of Gaussian tasks in parallel).

Parameters:

gjf_file – Path to a gjf file. This is not needed when running auto-run for a whole directory.
gjf_output – Optional path to the Gaussian job output for the gjf_file. Default is None as it is set to the gjf_file_name.gau if not specified.

command

property data: List[str]: Return a list of the absolute paths of the ORCA input file (.orcainput) and the output file (.orcaoutput). This is the data that is going to be written to the datafile.

group = True

modules

repr(variables: List[str]) → str: Returns a strings which is then written out to the final submission script file. The length of variables is defined by the length of self.data

ichor.hpc.submission_commands.python_command module

class PythonCommand(python_script: Path, args: List[str] | None = None)

Bases: SubmissionCommand

A class which is used for any jobs that are going to run Python code

Parameters:

python_script – A path object to the python script that is being ran
args – A list of arguments (strings) which need to be passed to the python script via the command line

command

property data: None

modules = ''

repr(variables: List[str] | None = None) → str: Returns a string which is then written into the submission script in order to run a python job.

exception PythonEnvironmentNotFound: Bases: Exception

ichor.hpc.submission_commands.tyche_command module

class TycheCommand(freq_param: Path, g09_input: Path)

Bases: SubmissionCommand

todo: write docs

command

property data: List[str]: Return a list of the absolute paths of the Gaussian input file (.gjf) and the output file (.gau)

group = False

modules

ncores = None

repr(variables: List[str]) → str

Returns a strings which is then written out to the final submission script file.

The length of variables is defined by the length of self.data

Module contents

class AIMAllCommand(wfn_file_path: Path, ncores: int, naat: int, atoms: List[str] | Atoms | None = 'all', usetwoe: int = 0, encomp: int = 3, boaq: str = 'auto', iasmesh: str = 'fine', bim: str = 'auto', capture: str = 'auto', ehren: int = 0, feynman: bool = False, iasprops: bool = True, magprops: str = 'none', source: bool = False, iaswrite: bool = False, atidsprops: float = 0.001, warn: bool = True, scp: str = 'some', delmog: bool = True, skipint: bool = False, f2w: str = 'wfx', f2wonly: bool = False, mir: str = 'auto', cpconn: str = 'moderate', intveeaa: str = 'new', atlaprhocps: bool = False, wsp: bool = True, shm_lmax: int = 5, maxmem: int = 2400, verifyw: str = 'yes', saw: bool = False, autonnacps: bool = True)

Bases: SubmissionCommand

A class which is used to add AIMALL-related commands to a submission script. It is used to write the submission script line where AIMALL modules are loaded. It is also used to write out the submission script line where AIMALL is ran on a specified array of files (usually AIMALL is ran as an array job because we want to run hundreds of AIMALL tasks in parallel).

Parameters:

wfn_file – Path to a .wfn file. This is not needed when running auto-run for a whole directory.
atoms – A list of strings of atom names (e.g. C1) which aimall to integrate or an Atoms instance (from which the names will be obtained)

property arguments: List[str]

command

property data: List[str]: Returns the data needed for the AIMAll job to run successfully

modules

repr(variables: List[str]) → str: Returns a string which is written out to the submission script file in order to run AIMALL correctly (with the appropriate settings).

class AmberCommand(mol2_file: Path, mdin_file: Path, system_name: str, temperature: float, ncores: int)

Bases: SubmissionCommand

todo: write docs

property command: str

property data: List[str]: Do not need a datafile for this command.

group = False

modules

repr(*args) → str

Returns a strings which is then written out to the final submission script file.

The length of variables is defined by the length of self.data

class AnacondaCommand(python_script: Path, args: List[str] | None = None)

Bases: SubmissionCommand

A class which is used for any jobs that are going to run Python code

Parameters:

python_script – A path object to the python script that is being ran
args – A list of arguments (strings) which need to be passed to the python script via the command line

command

property data: None

modules

repr(variables: List[str] | None = None) → str: Returns a string which is then written into the submission script in order to run a python job.

class CP2KCommand(cp2k_input: Path, temperature: float, ncores: int, system_name: str)

Bases: SubmissionCommand

todo: write docs

property command: str: Returns the command to be used to run CP2K. The command depends on the number of cores.

property data: List[str]: Return a list of the absolute paths of the Gaussian input file (.gjf) and the output file (.gau)

group = False

modules

repr(variables: List[str]) → str

Returns a strings which is then written out to the final submission script file.

The length of variables is defined by the length of self.data

class DlpolyCommand(dlpoly_program_path: Path, dlpoly_directory: Path)

Bases: SubmissionCommand

Class used to construct a Dlpoly job. Jobs are submitted using the SubmissionScript class.

Parameters:: dlpoly_directory – Path to where the working directory for dlpoly.

property command: str: Return the command word that is used to run DL POLY. In this case, the path to the DL POLY executable is returned.

property data: List[str]

modules

repr(variables: List[str]) → str: Return a string that is used to construct DL POLY job files.

class GaussianCommand(ncores: int, gjf_file: Path, gjf_output: Path | None = None)

Bases: SubmissionCommand

A class which is used to add Gaussian-related commands to a submission script. It is used to write the submission script line where Gaussian modules are loaded. It is also used to write out the submission script line where Gaussian is ran on a specified array of files (usually Gaussian is ran as an array job because we want to run hundreds of Gaussian tasks in parallel).

Parameters:

gjf_file – Path to a gjf file. This is not needed when running auto-run for a whole directory.
gjf_output – Optional path to the Gaussian job output for the gjf_file. Default is None as it is set to the gjf_file_name.gau if not specified.

command

property data: List[str]: Return a list of the absolute paths of the Gaussian input file (.gjf) and the output file (.gau). This is the data that is going to be written to the datafile.

group = True

memory_per_core

modules

repr(variables: List[str]) → str: Returns a strings which is then written out to the final submission script file. The length of variables is defined by the length of self.data

total_gaussian_memory() → str: Calculates the total memory to tell Gaussian to use Calculated as (memory_per_core - 1) * number_of_cores

class OrcaCommand(orca_input: Path, orca_output: Path | None = None)

Bases: SubmissionCommand

A class which is used to add Gaussian-related commands to a submission script. It is used to write the submission script line where Gaussian modules are loaded. It is also used to write out the submission script line where Gaussian is ran on a specified array of files (usually Gaussian is ran as an array job because we want to run hundreds of Gaussian tasks in parallel).

Parameters:

gjf_file – Path to a gjf file. This is not needed when running auto-run for a whole directory.
gjf_output – Optional path to the Gaussian job output for the gjf_file. Default is None as it is set to the gjf_file_name.gau if not specified.

command

property data: List[str]: Return a list of the absolute paths of the ORCA input file (.orcainput) and the output file (.orcaoutput). This is the data that is going to be written to the datafile.

group = True

modules

repr(variables: List[str]) → str: Returns a strings which is then written out to the final submission script file. The length of variables is defined by the length of self.data

class PythonCommand(python_script: Path, args: List[str] | None = None)

Bases: SubmissionCommand

A class which is used for any jobs that are going to run Python code

Parameters:

python_script – A path object to the python script that is being ran
args – A list of arguments (strings) which need to be passed to the python script via the command line

command

property data: None

modules = ''

repr(variables: List[str] | None = None) → str: Returns a string which is then written into the submission script in order to run a python job.

class TycheCommand(freq_param: Path, g09_input: Path)

Bases: SubmissionCommand

todo: write docs

command

property data: List[str]: Return a list of the absolute paths of the Gaussian input file (.gjf) and the output file (.gau)

group = False

modules

ncores = None

repr(variables: List[str]) → str

Returns a strings which is then written out to the final submission script file.

The length of variables is defined by the length of self.data