schrodinger.application.matsci.permittivity module¶

Permittivity module for permittivity workflow.

schrodinger.application.matsci.permittivity.log_debug(msg)¶

Add a message to debug logger file.

Parameters: msg (str) – The message to debug logging

schrodinger.application.matsci.permittivity.elapsed_timer()¶

Handy way to print time consumption for the execution of a few python line codes.

example to print line number and time elapsed: from inspect import currentframe with elapsed_timer() as elapsed:

xxx
print(currentframe().f_lineno, elapsed())
xxx
print(currentframe().f_lineno, elapsed())

Returns: float
Return type: time elapsed in second

schrodinger.application.matsci.permittivity.path_join(paths, linux=True)¶

Wrapper around os.path.join to allow forced ‘/’ as the path separator.

Parameters: linux (bool) – Force using ‘/’ as the separator if True
Returns: The str paths
Return type: str

schrodinger.application.matsci.permittivity.permittivity_transform(tau0, beta, tau_max=20, tau_num=None, omega_range=(1000000.0, 100000000000000.0), omega_num=None, simpson_quadrature=True, angular_frequency=False)¶

Based on the parameters in the KWW equation, non-uniform grid in tau and omega are used to transform the time domain (tau) signal to frequency domain (omega).

Note: the KWW is the equation 1 and implemented transform is equation 7 in the following paper.

Further Considerations of Non Symmetrical Dielectric Relaxation Behaviour arising from a Simple Empirical Decay Function. BY G. WILLIAM AND D. C. WATT

Parameters

tau0 (float) – The tau0 in unit ps is the decay constant in KWW equation
beta (float) – The beta in KWW equation, which must be positive
tau_max (float) – Tau upper limit in tau (time) domain
tau_num (int or None) – Total number of data points in the tau (time) domain
omega_range (tuple of two floats) – Output frequency domain range
omega_num (int or None) – Total number of data points in the frequency domain
simpson_quadrature (bool) – If True, simpson rule with quadratic interpolation is used to reduce the oscillation
angular_frequency (bool) – If True, the first column is angular frequency else regular frequency

Raises

ValueError – Non-uniform fourier transform yields nan (e.g. beta is negative)
AssertionError – beta <= 0

Returns

Three columns are frequency, storage permittivity, and loss permittivity

Return type

3xn numpy.array

schrodinger.application.matsci.permittivity.get_properties_from_inputfiles(opts, input_required_properties, input_readers=None, startwith=False)¶

Get properties from the input files. If the requested doesn’t exist, a KeyError error is raised.

Parameters

opts (Named tuple) – The parsed command line options
input_required_properties (dict) – Keys are struct type and values are property keys.
input_readers (dict) – Keys are struct type and values are readers for different struct types.
startwith (bool) – If True, property keys starting with the requested string are considered matches.

Raises

KeyError – When the struct misses one required property

Returns

Requested property keys and obtained values

Return type

dict

schrodinger.application.matsci.permittivity.is_file_property(property_name)¶

Whether the property is related to a file.

Parameters: property_name (str) – A property
Returns: Whether the property should point to a file
Return type: bool

class schrodinger.application.matsci.permittivity.chdir(dirname, rm_created_dir=False, always_create=False)¶

Bases: schrodinger.utils.fileutils.chdir

Make dir, change, and exit. If this indeed creates a dir, it will remove the dir on exit with rm_created_dir=True.

__init__(dirname, rm_created_dir=False, always_create=False)¶

Parameters

dirname (str) – The directory name to make and cd to
rm_created_dir (bool) – If True and this class creates a directory, the directory will be removed on exit.
always_create (bool) – If True and the input dirname exists, creates a directory, with a different name. For example ‘my_dir’ exists, the newly created dir will be ‘my_dir.1’. If ‘my_dir.1’ exists, the newly create dir will be ‘my_dir.2’.

getNextDirname(midfix='.', zfill_width=0)¶

Get the next dirname based on the input path and current existing directories.

Parameters

path (str) – Path to a directory
midfix (str) – This string split the basename and number <root><midfix><number>
zfill_width (int) – Pad a numeric string S with zeros on the left, to fill a field of the specified width

Returns

The next dirname based on the input path and all dirs in the relevant folder.

Return type

str

schrodinger.application.matsci.permittivity.get_config(config_yaml)¶

Get the Config instance from the input yaml file.

Parameters: config_yaml (str) – The input configure yaml file
Returns: The Config instance with property processed.
Return type: Config

schrodinger.application.matsci.permittivity.get_config_from_options(options)¶

Get the Config instance from the command line options.

Parameters: options (argparse.Namespace) – Command line options
Returns: The Config instance with property processed.
Return type: Config

class schrodinger.application.matsci.permittivity.Config(config_yaml)¶

Bases: object

Class to store the config file, parse workflow, provide method to get fields.

__init__(config_yaml)¶

Parameters: config_yaml (str) – The config file

static get_file(filename=None, product_dir=None)¶

Get the permittivity config yaml from the mmshare data dir.

Parameters

filename (str) – The yaml filename
product_dir (str) – Subdir name inside the mmshare_data_dir

Returns

The full path and filename for the input yaml

Return type

str

classmethod get_file_from_options(options)¶

Return the permittivity config file based on command line inputs.

Parameters: options (argparse.Namespace) – The command parsered options
Returns: The path to a config yaml
Return type: str

load()¶

Load configure file, set the task protocols by name and type

NOTE: If no type found, name is used as the type

Note: If the task type have multiple stages and each stage has its own index field, the sequence of the stages is sorted according to the index field. task_name has higher priority than task_type type, as multiple task names can share the same task type.

setWorkflow()¶

workflow is a nested data structure of list, tuple, and dict. Itself looks like an unbalanced tree data type. list gives linear job dependency as desmond msj Tuple gives independence between each task, and all these subjobs can share parent from the same level or one level up list. Dict links additional parent jobs.

NOTE: dict is unhashable and cannot be used as the key of a dict. Each key or value is either a TASK NAME or TASK NAME (int,int,..) whose (int, int,..) defines the task id so that the same task name can be used multiple times, and the additional dependence by dict can indentify unique task. (This is not tested or may not be well implemented)

The same task name can appear several times in the workflow, which means that the same task (with the same settings) run multiple times in the workflow. However, the dict value must link to a single task ( either unique task name or with task id)

The workflow section describes the task sequence and dependence. Each string corresponds to a task name (may with task id), and each task name must have a top level section in configure file to define the settings.

The title of each task setting section describe the name and type. For example, TASK NAME (TASK TYPE): [flag1 : value1, flag2 : value2] The TASK TYPE is used to map for backend class

getTaskNames()¶

Get all the task names in the workflow block

Returns: tasknames in the workflow
Return type: set

sortStages(index_field='index')¶

Sort the stage order according to the index field.

Parameters: index_field (Use this index field to sort all the stages in a task protocol) – str of None

splitNameAndType(name_and_type)¶

Split the task section title into task name and task type. ‘task name (task type)’ or ‘task name’ alone in front of the task setting section.

Parameters: name_with_prop (str) – ‘task name (task type)’ or ‘task name’
Returns: (task name, take type) or (task name , None)
Return type: (str, str) or (str , None)

setNameToTypeMap()¶

Based on the config file, get a dict map from task name to task type. If ‘task name’ instead of ‘task name (task type)’ is found, task type is assumed to be the same as task name.

Parameters: config_yaml (str) – A configure filename with path
Returns: Map from task name to task type
Return type: dict

getTaskProtocol(task_name=None, task_type=None)¶

Get the protocol for selected task by name or type. If both provided, select by type.

Parameters

task_name (str or None) – The task name of a stage. the xxx as in the ‘xxx (task type)’ before the setting block.
task_type (str or None) – The task type of a stage. the xxx as in the ‘task type (xxx)’ before the setting block.
index_field (Use this index field to sort all the stages in a task protocol) – str of None

Returns

list of list for workflow block; list of list for desmond multiple stages; dict for regular single stage

Return type

dict, list of str, or list of list

class schrodinger.application.matsci.permittivity.ConfigWriter(options, jobname)¶

Bases: object

__init__(options, jobname)¶

Class to write out config yaml.

Parameters

options (argparse.Namespace) – Commandline options
jobname (str or False) – The jobname based on which the yaml filename is set

run()¶: Main method to drive the functionality.

loadWorkflow()¶: Load the config yaml based on commandline options, and parse the file.

loadAndUpdateTaskProtocol()¶: Update the task protocols based command line input, and set task type and driver path.

validateGpuHosts()¶

Validate GPU availability against the type of protocols. (whether desmond tasks exist)

DEPRECATED due to MATSCI-9604

checkInputfileTasktypeDriverpaths()¶

Validate whether the restart flag for input file task type driver paths is followed by properly formatted values.

DEPRECATED as MATSCI-8523 is planned as the customer facing api

write()¶: Write out the updated config yaml to disk if users don’t specific their input config yaml.

class schrodinger.application.matsci.permittivity.Protocol(protocol)¶

Bases: object

__init__(protocol)¶

The protocol for the workflow or one task.

Parameters: protocol (dict or list) – dict for workflow and regular task protocol; list for multistage desmond protocol.

class schrodinger.application.matsci.permittivity.WorkflowProtocol(protocol)¶

Bases: schrodinger.application.matsci.permittivity.Protocol

__init__(protocol)¶

The protocol for the workflow.

Parameters: protocol (dict or list) – dict for workflow and regular task protocol; list for multistage desmond protocol.

indexUnbalancedWorkflow()¶

Generate an unique tuple of integers for each task (item) in the workflow. Return the map from tuple to task name.

Returns: The map from un unique tuple to task name
Return type: dict

getItemByIndex(index)¶

Get the item in the workflow protocol of this index.

Parameters: index (tuple or list of int) – The indexes of the item
Returns: The item saved in the workflow yaml with this index
Return type: str, list, or dict

getParentTasknames(index)¶

Get the parent task names for the current task pointed by this index.

Parents can be defined via three methods: parent / child by nested list or tuple: outer is parent; inner is child parent / child by list: former is the parent; later is the child parent / child by dict: key is the child; values are parents.

These methods are equivalent in setting the job dependency.

Parameters: index (tuple, list, or generator for integers) – The index of the current item
Returns: The task names of parent jobs
Return type: list of str

getParentTasknameByIndexFromDict(index)¶

Get the parent task names of the current task indicated by the dict format. (the key and value of the item in the workflow pointed by the index are child and parents). If str instead of dict, return empty.

Parameters: index (tuple or list of int) – The indexes of the item
Raises: TypeError – when it is not a str or dict, meaning this not a leaf item in the workflow tree data struct.
Returns: The task name for this item
Return type: str

flattenWithoutDict(an_iterable_item)¶

Robust function to flatten list recursively. If a dict presents as the value, use the key of the dict. The difference between the above flatten is that this function don’t return a dict as one value in the list. Instead, it uses the dict key to represent the dict.

Parameters: an_iterable_item (list, tuple or set) – The iterable item to be flatten. (an iterable that describes the whole or part of the workflow)
Returns: The flatten items in a list ([uniterable value 1, uniterable value 2, uniterable value 3 …])
Return type: list of str values

getFirstLevelTasknames(task_stages)¶

Get the first level tasknames without dict. For example, [a, [b, [c]], {d:f}, [e]] returns [a, d]

Parameters: task_stages (list, tuple, or set) – An iterable that describes the whole or part of the workflow.
Returns: The first level tasknames
Return type: list of string

getTaskNames()¶

A set of all task name in the workflow section.

Returns: set of task names
Return type: set

getTaskName(index)¶

Get the task name of this item in the workflow.

Parameters: index (list or tuple of int) – Index of an item containing a task name.
Raises: TypeError – When it is not a str or dict, meaning this not a leaf item in the workflow tree data struct.
Returns: The task name for this item
Return type: str

class schrodinger.application.matsci.permittivity.TaskProtocol(protocol)¶

Bases: schrodinger.application.matsci.permittivity.Protocol

Wrapper for task protocol: regular driver or desmond multi-stages.

__init__(protocol)¶

The protocol for the workflow or one task.

Parameters: protocol (dict or list) – The settings for a task: dict for task protocol; list for multistage desmond protocol.

getDriverPath(driver_path=None)¶

Return the driver path of the task

Parameters: driver_path (None or str) – The driver path of the task
Returns: The driver path of the task
Return type: str or None

getPreScript(pre_script=['$SCHRODINGER', 'run'])¶

Return the shell script before regular driver. For example, $SCHRODINGER/run

Parameters: pre_script (None or list) – The shell script before regular driver
Returns: The shell script before regular driver
Return type: None or str

getFlagBlock(label='cmd_flags')¶

Get the flag block with desired label.

Parameters: label (str) – The block header label to search
Returns: The flag block for a certain task in the config yaml
Return type: None or list

getInterpFlagBlock(label='cmd_flags')¶

Get the flag block with desired label and interpret the block into dict data type.

Parameters: label (str) – The block header label to search
Returns: Keys are flags without ‘-’, and values are None for positional flag, NONE for optional ‘store_true’ or ‘store_false’ flag, ‘none’ or ‘any_value’ for regular optional ‘store’ flag
Return type: dict

getReplicaKeywords()¶

Return the replica keyword list or None.

Returns: The replica keywords
Return type: None or list
Raises: ValueError – If more than one replica setting blocks are found.

rmReplicaKeywords()¶: Remove the replica keywords from xtra flag block.

getSeed(seed_flag)¶

Return the random seed for this task.

Returns: The random seed in the config or the default value
Return type: int

getCmdFromFlagBlock()¶

Return the command list from the cmd flag block.

Returns: The command list built from the task protocol cmd flag block
Return type: None or list

interpretFlagBlock(flag_block)¶

Interpret the flag block from yaml parsed values to a dict data type.

Parameters: flag_block (list of dict and str. In .yaml, {flag: NONE} means 'store_true' or 'store_false' optional arguments; [flag] means positional arguments; {flag: 'none'; flag: 'value'} means regular optional arguments.) – a list of dict and str contains flags and values
Returns: Keys are flags without ‘-’, and values are None for positional flag, NONE for optional ‘store_true’ or ‘store_false’ flag, ‘none’ or ‘any_value’ for regular optional ‘store’ flag
Return type: dict
Raises: ValueError – if the item in cmd block is not string or dict.

update(user_input, block_label='cmd_flags')¶

This function updates the task_protocol according to a user input dict. The update happens for optional arg: store, store_true and store_false. The flag to locate the optional block must be either CMD_FLAGS or XTRA_FLAGS. The logic is to put all subdriver recognizable optional flags in CMD_FLAGS, and put other flags in XTRA_FLAGS.

In short, flags in CMD_FLAGS are passed to subjob driver directly. Flags in XTRA_FLAGS can be used to control worflow (not used in subdriver) or be reformatted and passed to subdriver in a file format depending on specific implementation.

If user_input = {‘animal’: ‘cat’}, the ‘cat’ will be used for drivers. If user_input = {‘animal’: None}, auto set: drivers with animal key use their own defaults set by the driver or config yaml. If user_input = {‘is_rainy’: True}, drivers with is_rainy key adds -is_rainy to the cmd. If user_input = {‘is_rainy’: False}, drivers with is_rainy key remove -is_rainy in the cmd. If user_input = {‘is_rainy’: None}, auto set: drivers with is_rainy key check config yaml for whether to add -is_rainy in cmd.

Current implementation doesn’t support the positional argument substitution, as this is a replacements of certain list values and positional argument are input/output filenames that are changed by updateInfileAndCommand().

Parameters

user_input (dict) – dict for regular single stage
block_label (str) – The flag block in task_protocol defined by this flag is updated (either CMD_FLAGS or XTRA_FLAGS)
user_input – {flag: value}

parserUserInput(user_input)¶

Parse the user input dict data and return a dict for values to be added and a list for values to be removed.

Parameters: user_input (dict) – The dict to be parsed
Returns: Values to be added, values to be removed
Return type: dict, list

class schrodinger.application.matsci.permittivity.StepBase(basename, config_yaml, task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Bases: object

OUTFILE_EXT = '-out.mae'¶

TERMINAL_INFILE_NUM = 1¶

DRIVER_PATH = None¶

NUM_CRU_PROP = 'i_matsci_Num_Cru'¶

REPLICA_TAG = 'Replica %s: '¶

__init__(basename, config_yaml, task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Parameters

basename (str) – The basename of this subjob
config_yaml (str) – The config yaml file contain all job config
task_name (str) – Task name of this sub job
infile (str) – The input filename
outfile (str) – The output filename
additional_infiles (list of str) – This records additional input files (e.g. the second, third, and so on)
master_logger (logging.Logger) – The logger to use for recording messages into master job -driver.log.
node_index (The node index) – tuple

log(msg, add_log_tag=True)¶

Log information to the master driver.log

Parameters

msg (str) – The info to print
add_log_tag (bool) – If True, additional tags is logged in front of the msg for the replica jobs.

setLogTag()¶: Set the log tag based on node index.

updateTaskReplicaSettings()¶: Update the task protocol due to replica.

setup(copy_infile=True, copy_additional_files=True, more_files=None)¶

Setup things before the job starts. For example, logging format, and file transfer.

Parameters

copy_infile (bool) – Copy the input files of the class to current folder
copy_additional_files (bool) – Copy the additional files of the class to current folder
more_files (None or list of str) – Use this arguments to copy customized files

copyFiles(copy_infile=True, copy_additional_files=True, more_files=None)¶

Copy files to current dir.

Parameters

copy_infile (bool) – Copy the input files of the class to current folder
copy_additional_files (bool) – Copy the additional files of the class to current folder
more_files (None or list of str) – Use this arguments to copy customized files

getDownStreamPolymerJob()¶

Search and return the down-stream polymer job

Returns: A subtask step with polymer driver in the cmd
Return type: ‘Step’ or None

getFirstMatchedfilename(filenames, exts)¶

Get the filename that ends with the first extension. If multiple filenames end with that extension return the first match.

Parameters

filenames (list of string) – list of filenames
exts (list of string) – list of extensions

Returns

The matched filename or None

Return type

string or None

static finalizeStep(job)¶

Update child job’s command with the parent job output, and set output files if not set by the subjob itself.

Parameters: job (An instance of a BaseJob subclass (such as JobControlJob or SubprocessJob)) – current job

setOutfile()¶

Set the job outfile with an existing file based on the jobcontrol job, if not set.

Raises: FileNotFoundError – Failed to set an existing outfile

outfileExist()¶

Whether the outfile exists

Returns: Whether the file exists.
Return type: bool

updateInfileAndCommand(par_outfile_with_dir)¶

Update the input file in the command and the input file attributes of a child job to the output file path of the parent job.

Parameters

child_job (an instance of a BaseJob subclass (such as JobControlJob or SubprocessJob)) – The subjob whose command will be updated.
par_outfile_with_dir (str) – The output file from the parent job that will be used as the input file of this child job.

classmethod getSeedFlag()¶

Return the flag for random seed. Should be overwritten by the subclass only when subtask reads in this flag

Returns: The flag to set the random seed (without the ‘-‘)
Return type: str or None

classmethod getForceFieldFlag()¶

Return the flag for force field. Should be overwritten by the subclass only when subtask reads in this flag

Returns: The flag to set the force field (without the ‘-‘)
Return type: str or None

classmethod optionsToTaskProtocols(options, task_name, seed=None)¶

This is the class method to generate task_protocol based on command line options and default values from config yaml. This method should be overwritten by subclass method as this one returns the protocol in the default configure yaml.

Parameters

options (argparse.Namespace) – The parsed command line options
task_name (str) – Task name of the current stage
seed (int or None) – Random seed to randomize the initial velocities

Returns

Updated task protocol

Return type

TaskProtocol

class schrodinger.application.matsci.permittivity.Step(basename, config_yaml='default_permittivity_protocols.yaml', task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Bases: schrodinger.application.matsci.permittivity.StepBase, schrodinger.application.matsci.jobutils.RobustSubmissionJob

Over write the parent class, and set subjobname, subdir, and etc.

RESOURCE = 'cpu'¶

__init__(basename, config_yaml='default_permittivity_protocols.yaml', task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Parameters

basename (str) – The base name of this subjob
config_yaml (str) – The config yaml file contain all job config
task_name (str) – Task name of this sub job
infile (str) – The input filename
outfile (str) – The output filename
additional_infiles (list of str) – This records additional input files (e.g. the second, third, and so on)
master_logger (logging.Logger) – The logger to use for recording messages into master job -driver.log.
node_index (The node index) – tuple

class schrodinger.application.matsci.permittivity.PolymerBuilder(*arg, **kwargs)¶

Bases: schrodinger.application.matsci.permittivity.Step

Class for customized polymer builder.

DRIVER_PATH = 'polymer_builder_gui_dir/polymer_builder_driver.py'¶

POLYMER_BUILDER = 'polymer_builder'¶

DEFAULT_JOBNAME = 'permittivity_polymer_builder_task'¶

FLAG_NUM_CRU = '-num_cru'¶

SEQUENCE_PROP = 's_matsci_polymer_sequence'¶

FLAG_POLYMER_CRU_NUM = '-polymer_cru_num'¶

DEFAULT_NUMBER_OF_POLYMERS = 25¶

__init__(*arg, **kwargs)¶

Parameters

basename (str) – The base name of this subjob
config_yaml (str) – The config yaml file contain all job config
task_name (str) – Task name of this sub job
infile (str) – The input filename
outfile (str) – The output filename
additional_infiles (list of str) – This records additional input files (e.g. the second, third, and so on)
master_logger (logging.Logger) – The logger to use for recording messages into master job -driver.log.
node_index (The node index) – tuple

updateTaskReplicaSettings()¶: Update the task settings due to replica.

static getTemplates(moiety_dir=None, moiety_filename=None)¶

Return the polymer template file or dir

Parameters

moiety_dir (str) – Moiety dirname inside the polymer template dir
moiety_filename (str) – Filename inside the moiety dir

Returns

A polymer template file or dir

Return type

str

classmethod optionsToTaskProtocols(options, task_name, seed=None)¶

Update the polymer driver commands based on users’ input.

Parameters

options (argparse.Namespace) – The parsed command line options
task_name (str) – Task name
seed (int or None) – Random seed to randomize the initial velocities

Returns

Updated task protocol

Return type

TaskProtocol

classmethod getForceFieldFlag()¶

Return the flag for force field. Should be overwritten by the subclass only when subtask reads in this flag

Returns: The flag to set the force field (without the ‘-‘)
Return type: str or None

class schrodinger.application.matsci.permittivity.CMSParser(basename, config_yaml='default_permittivity_protocols.yaml', task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Bases: schrodinger.application.matsci.permittivity.Step

Class to parse equilibrated cms file.

DRIVER_PATH = 'permittivity_gui_dir/permittivity_cms_parser.py'¶

CMS_PARSER = 'cms_parser'¶

ICMS = 'icms'¶

DEFAULT_JOBNAME = 'permittivity_cms_parser_task'¶

FLAG_ELECTRIC_POLAR = '-electric_polar'¶

classmethod optionsToTaskProtocols(options, task_name, seed=None)¶

Process the stages, for example, update relaxation stages, update the productions stage, and remove productions markers.

Parameters

options (argparse.Namespace) – The parsed command line options
task_name (str) – Task name
seed (int or None) – Random seed to randomize the initial velocities

Returns

Updated task protocol

Return type

TaskProtocol

updateTaskReplicaSettings()¶: Update the task settings due to replica.

class schrodinger.application.matsci.permittivity.DisorderSystemBuilder(basename, config_yaml='default_permittivity_protocols.yaml', task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Bases: schrodinger.application.matsci.permittivity.Step

Class for customized disorder system builder.

DSB_DRIVER = <module 'disordered_system_builder_driver' from '/scr/buildbot/savedbuilds/2024-3/NB/build-133/mmshare-v6.7/python/scripts/disordered_system_builder_gui_dir/disordered_system_builder_driver.py'>¶

DRIVER_PATH = 'disordered_system_builder_gui_dir/disordered_system_builder_driver.py'¶

DISORDER_SYSTEM = 'disorder_system'¶

DEFAULT_JOBNAME = 'permittivity_disorder_system_task'¶

FLAG_MOLECULES = '-molecules'¶

FLAG_COMPOSITION = '-composition'¶

FLAG_DENSITY = '-density'¶

FLAG_MONOMER_CHARGE = '-monomer_ff_q'¶

DEFAULT_DENSITY = 0.5¶

DEFAULT_NUMBER_OF_MOLECULES = 500¶

classmethod getSeedFlag()¶

Return the flag for random seed.

Returns: The flag to set the random seed (without the ‘-‘)
Return type: str

classmethod getForceFieldFlag()¶

Return the flag for force field. Should be overwritten by the subclass only when subtask reads in this flag

Returns: The flag to set the force field (without the ‘-‘)
Return type: str or None

classmethod optionsToTaskProtocols(options, task_name, seed=None)¶

Process the stages, for example, update relaxation stages, update the productions stage, and remove productions markers.

Parameters

options (argparse.Namespace) – The parsed command line options
task_name (str) – Task name
seed (int or None) – Random seed to randomize the initial velocities

Returns

Updated task protocol

Return type

TaskProtocol

updateTaskReplicaSettings()¶: Update the task protocol due to replica.

class schrodinger.application.matsci.permittivity.MultiStageMd(*arg, **kwarg)¶

Bases: schrodinger.application.matsci.permittivity.Step

Multi-stage simulations with relaxation.

BROWNIAN_DYNAMICS = 'Brownian Dynamics'¶

MOLECULAR_DYNAMICS = 'Molecular Dynamics'¶

AVERAGE_CELL = 'Average Cell'¶

MATSCI_ANALYSIS = 'Matsci Analysis'¶

SIMULATE = 'simulate'¶

CFG_FILE = 'cfg_file'¶

TIME = 'time'¶

TEMP = 'temp'¶

PRESS = 'pressure'¶

TIMESTEP = 'timestep'¶

ENSEMBLE = 'ensemble'¶

DIPOLE_INTERVAL = 'dipole_moment_dot_interval'¶

SIM_TYPE = 'sim_type'¶

TRJ_INTVL = 'trajectory.interval'¶

SEED = 'seed'¶

FLAG_TO_KEY = {'-md_ensemble': 'ensemble', '-md_press': 'pressure', '-md_temp': 'temp', '-md_time': 'time', '-md_timestep': 'timestep', '-md_trj_int': 'trajectory.interval'}¶

DESMOND_UNIT_CONVERTERS = {'-md_time': <function MultiStageMd.<lambda>>, '-md_timestep': <function MultiStageMd.<lambda>>}¶

TRJ_WRITE_VEL = 'trajectory_dot_write_velocity'¶

LAST_STAGE_DICT = {'compress': '""', 'dir': '"."'}¶

FLOAT_FIELDS = ['time', 'temp', 'pressure']¶

DUMMY_FIELDS = ['index', 'is_production', 'is_relaxation', 'use_customized_relaxation']¶

MSJSTRINGERS = {'Average Cell': <class 'schrodinger.application.matsci.desconfig.AveCellMSJStringer'>, 'Brownian Dynamics': <class 'schrodinger.application.matsci.desconfig.BrownieMSJStringer'>, 'Matsci Analysis': <class 'schrodinger.application.matsci.desconfig.MSAnalysisMSJStringer'>, 'Molecular Dynamics': <class 'schrodinger.application.matsci.desconfig.MDMSJStringer'>}¶

DEFAULT_MSJ_HEADER = 'task { task = "desmond:auto"}\n'¶

HOFMANN = 'Hofmann'¶

COMPRESSIVE = 'Compressive'¶

ADD_NEW = 'Add New...'¶

HOFMANN_PROTOCOL = 'hofmann.yaml'¶

COMPRESSIVE_PROTOCOL = 'compressive.msj'¶

RELAXATION_MAP = {'Compressive': 'relaxation_protocols/compressive.msj', 'Hofmann': 'relaxation_protocols/hofmann.yaml'}¶

OUTFILE_EXT = '-out.cms'¶

RESOURCE = 'gpu'¶

__init__(*arg, **kwarg)¶: See parent class.

setup()¶: Over write parent class method.

createMSJ()¶: Create msj for desmond.

getStages()¶

Get desmond stages from config yaml.

Returns: The MSJSTRINGERS contains desmond stage information, the orig_msj_str is for msj string provided by users.
Return type: list of desconfig.MSJStringer, str

parseMsjStr(msj_str)¶

Parse MSJ string, set task stage and customize settings.

Parameters: msj_str (str) – A string in MSJ format
Returns: Modified msj string with task stage
Return type: schrodinger.application.desmond.multisim.Msj

copyCfgFiles(msj_stages)¶

Copy the config files into the subtask dir.

Parameters: msj_stages ('schrodinger.application.desmond.multisim.parser.Msj') – The msj that may contain cfg files

updateReplicaSeed(stages, msj_stages)¶

Update the random seed in the msj so that each replica has a different value.

Parameters

stages (list of desconfig.MSJStringer) – The desmond MSJSTRINGERS contains desmond information
msj_header (schrodinger.application.desmond.multisim.Msj) – The msj header with task stage (may have other simulation stages)

modifyReplicaStages(stages)¶

Search the desmond stages for seed, and tune them based on the replica index.

Parameters: stages (list of the MSJSTRINGERS) – The desmond MSJSTRINGERS contains desmond information
Returns: Whether some seeds in the stages are modified
Return type: bool

modifyReplicaMsjHeader(msj_stages)¶

Modify the replica Msj header.

Parameters: msj_stages (schrodinger.application.desmond.multisim.Msj) – The msj header with task stage (may have other simulation stages)
Returns: Whether the msj_stages are modified
Return type: bool

modifyReplicaFirstStage(stages)¶

Modify the first desmond stages to add seed based on the replica index

Parameters: stages (list of the MSJSTRINGERS) – The desmond MSJSTRINGERS contains desmond information

classmethod optionsToStage(options)¶

Convert command line options to a stage like dict.

Parameters: options (argparse.Namespace) – The command parsered options
Returns: Key and values for a desmond stage
Return type: dict

classmethod optionsToTaskProtocols(options, task_name, seed=None)¶

Process the stages, for example, update relaxation stages, update the productions stage, and remove productions markers.

Parameters

options (argparse.Namespace) – The parsed command line options
task_name (str) – Task name
seed (int or None) – Random seed to randomize the initial velocities

Returns

Updated task protocol

Return type

TaskProtocol

classmethod getRelaxationProtocolFile(relaxation_option)¶

Return the relaxation protocol file based on the relaxation option.

Parameters: relaxation_option (str) – File with path or a protocol name
Returns: Relaxation file with path
Return type: str

classmethod getAllStages(options, task_name, time=100.0)¶

Construct the stages in general by looking at the config yaml, commandline relaxation, and productions. Note: only when stages are marked by USE_CUSTOMIZED_RELAXATION and options.relaxation_protocol is provided, the stages in the relaxation_protocol is used to overwrite the stages in options.config_yaml.

Parameters

options (argparse.Namespace) – The object holding all the cmd options
task_name (str) – The task name of the stage
time (float) – A short md threshold threshold for debug mode (simulation time longer than this is reduced to this value for fast testing)

Returns

task_protocol.protocol is a list of stages

Return type

‘TaskProtocol’

static getRelaxationStages(relaxation_file)¶

Get the relaxation stages from relaxation protocol file and return it as desmond stages.

Parameters: relaxation_file (str) – A file containing relaxation protocol
Returns: list of desmond stages
Return type: list

classmethod modifyStageSettings(task_protocol, options, seed=None)¶

Modify the stages based on command line options, including update the temperature and pressure of the first flexible stages before each production stage, pass velocity to NVE production stage.

Parameters

task_protocol ('TaskProtocol') – task_protocol.protocol is a list of stages
options (argparse.Namespace) – The parsed command line options
seed (int or None) – Random seed to randomize the initial velocities

class schrodinger.application.matsci.permittivity.MdStageModifier(task_protocol, options, seed=None)¶

Bases: object

TEMPERATURE = 'temperature'¶

RANDOMIZE_VELOCITY = 'randomize_velocity'¶

FIRST = 'first'¶

RANDOMIZE_VELOCITY_DOT_FIRST = 'randomize_velocity.first'¶

RANDOMIZE_VELOCITY_DOT_SEED = 'randomize_velocity.seed'¶

LAST_RELAX_STAGE_TRJ_INTVL = 100.0¶

OTHER_RELAX_STAGE_TRJ_INTVL = 500.0¶

__init__(task_protocol, options, seed=None)¶

Parameters

task_protocol ('TaskProtocol') – task_protocol.protocol is a list of stages
options (argparse.Namespace) – The parsed command line options
seed (int or None) – Random seed to randomize the initial velocities

run()¶: Main method to drive the functionality.

setStages()¶: Set stages. If the protocol contains only one stage and the only item in this stage list is a dict with ‘msj’ being the only key, the stage is parsed by standard msj parser. Otherwise, each stage is a list.

setRelaxAndProductionIndexes()¶: Set relaxation and production stage indexes according to markers. Note: if only relaxation stages are found, the stage right after the last relaxation is assumed to be the production stages.

setRelaxRandomVel()¶: Set the randomize velocity seed for the first relaxation stage.

static getStageIndicesByMarker(stages, marker='is_production', expected_value='yes', remove_marker=False)¶

Indexes of the stages marked with certain markers. For example, IS_PRODUCTION markers stages as production stages; IS_RELAXATION markers stages as relaxation stages; If USE_CUSTOMIZED_RELAXATION markers some stages, the first with this marker and those before this one will be replaced by customized relaxation stages defined by users.

Parameters

stages (list) – Multistages for desmond serial simulations
marker (bool) – Remove the marker flag, if True
expected_value (str) – This is expected value pointed to by the marker
remove_marker (bool) – Remove the yes production flag, if True

Returns

The indexes of all the stages marked with ‘xxx:yes’

Return type

list of int

updateProductStageTempAndPress()¶: Update the temp and press of the production stage.

updateRelaxStageTempAndPress()¶: Update the temperature and pressure settings of stages. If no NPT or NVT ahead of the NVE, randomize the NVE production velocity.

connectNVEInitialVelocity()¶: Seamlessly connect the NVE production stage to the previous stages by writing out velocities and skip the randomizing initial velocities.

duplicateRelaxStage()¶: Update and duplicate the last relaxation stage settings.

updateLastStage()¶: Update the settings of the last stage.

saveMsjStages()¶: Save the msj stages to the task protocol

updateTrjIntvel()¶: Update the trajectory output interval for the stages before the last relaxation stage.

removeCom()¶: Add remove center of mass string to relaxation and production stages.

updateDipoleInterval()¶: Update the dipole interval in production run

removeDummyFields()¶: Remove the intermediate arguments that desmond doesn’t recognize.

class schrodinger.application.matsci.permittivity.MdPostAnalysis(basename, config_yaml='default_permittivity_protocols.yaml', task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Bases: schrodinger.application.matsci.permittivity.Step

Base class to hold molecular dynamics post analysis functionality.

TEMP_PROP = 'r_matsci_Temperature(K)'¶

TEMP_STD_PROP = 'r_matsci_stdev_Temperature(K)'¶

setup(copy_ene=False, write_cms=False)¶: Over write parent class method.

addEnefileToAdditionalInfiles()¶: Add the ene file as one of the additional files.

writeCms()¶: Write out cms files to current dir and each of them has a ‘msprops.ORIGINAL_CMS_PROP’ property pointing to the original cms file path.

static autocorrelation(time_serial_data, normalize=False)¶

Calculate the auto correlation of the input numpy.array data.

Parameters

time_serial_data (n x m numpy.array) – Autocorrelation of each column of the data
normalize (bool) – If True, the auto correlation data will be normalized

Returns

Autocorrelated data (by column)

Return type

n x m numpy.array

static autocorrelationWithSum(time_serial_data, normalize=False)¶

Calculate the auto correlation of the input numpy.array data.

Parameters

time_serial_data (n x m numpy.array) – Autocorrelation of each column of the data
normalize (bool) – If True, the auto correlation data will be normalized

Returns

Autocorrelated data (by column)

Return type

n x m numpy.array

static getRelatedFile(cms_file, file_ext='.ene')¶

Get the requested file based on cms file name and file extension

Parameters

cms_file (str) – The cms file whose related file is searched.
file_ext (str) – the extension of file to search for. The file extension must include the separator as well. For example, to get ene file, file_ext must be “.ene”

Returns

Found file with correct extension

Return type

str or None

static getRelatedJobFile(input_cms, orig_cms=None, file_ext='.ene')¶

Search existing ene file and return the ene found based on the input_cms. Existing ene file may be found in current folder, in the input cms folder or in the PROP_CMS (‘s_m_original_cms_file’) folder when ene is not copied from the PROP_CMS folder to the current folder.

Parameters

input_cms (str) – INPUT_CMS defined for INPUT_TRJ searching.
orig_cms (str) – The original cms defined by users.
file_ext (str) – the extension of file to search for. The file extension must include the separator as well. For example, to get ene file, file_ext must be “.ene”

Raises

KeyError, FileNotFoundError, ValueError – when ene file cannot be found.

Return type

str, str or None

Returns

Existing ene file if found, the original cms file that the ene file sits with or None (sit with the input_cms)

class schrodinger.application.matsci.permittivity.DensityAnalysis(basename, config_yaml='default_permittivity_protocols.yaml', task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Bases: schrodinger.application.matsci.permittivity.MdPostAnalysis

Class to do post desmond density analysis.

DRIVER_PATH = 'permittivity_gui_dir/permittivity_density_driver.py'¶

DENSITY = 'density'¶

DEFAULT_JOBNAME = 'permittivity_density_task'¶

DENSITY_PROP = 'r_matsci_Density(g/cm3)'¶

DENSITY_STD_PROP = 'r_matsci_stdev_Density(g/cm3)'¶

DENSITY_REPLICA_PROP = 'r_matsci_Density_Replica_%i(g/cm3)'¶

DENSITY_STD_REPLICA_PROP = 'r_matsci_stdev_Density_Replica_%i(g/cm3)'¶

TEMP_REPLICA_PROP = 'r_matsci_Temperature_Replica_%i(K)'¶

TEMP_STD_REPLICA_PROP = 'r_matsci_stdev_Temperature_Replica_%i(K)'¶

DENSITY_REPLICA_PROP_REX = 'r_matsci_Density_Replica_(\\d)\$g/cm3\$'¶

TEMP_REPLICA_PROP_REX = 'r_matsci_Temperature_Replica_(\\d)\$K\$'¶

DENSITY_EXT = '_@_{density:.5g}(g/cm3)'¶

OUTFILE_EXT = '-out.cms'¶

setup(copy_ene=True)¶: Over write parent class method.

static finalizeStep(job)¶

Finalize this step. Can be overwritten for light weight post process.

Parameters: job (An instance of a BaseJob subclass (such as JobControlJob or SubprocessJob)) – Current job

class schrodinger.application.matsci.permittivity.MdPostTrajectoryAnalysis(basename, config_yaml='default_permittivity_protocols.yaml', task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Bases: schrodinger.application.matsci.permittivity.MdPostAnalysis

Base class to hold molecular dynamics post trajectory analysis functionality.

static getTrajectoryFromCms(input_cms, orig_cms=None)¶

Search existing trajectory and return the trajectory found based on the input_cms. Existing trajectory (desmondutils.PROP_TRJ) may be found in current folder, sitting with input cms or sitting with the original cms defined by users or pointed to by PROP_CMS (‘s_m_original_cms_file’) when trajectory is not copied from the PROP_CMS folder to the current folder.

Parameters

input_cms (str) – INPUT_CMS defined for INPUT_TRJ searching.
orig_cms (str) – The original cms defined by users.

Raises

KeyError, FileNotFoundError, ValueError – when trajectory cannot be found.

Return type

str, str or None

Returns

existing trajectory if found, whether the input trajectory sits with the original cms

classmethod registerCmsAndTrjToJob(options, job_builder, orig_cms=None)¶

Register cms file and trajectory folder to job if needed.

Parameters

options (argparse.Namespace) – The parser to get the cms options from and set the trj options for.
job_builder (launchapi.JobSpecification) – JobSpecification object

class schrodinger.application.matsci.permittivity.AveCellAnalysis(basename, config_yaml='default_permittivity_protocols.yaml', task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Bases: schrodinger.application.matsci.permittivity.MdPostTrajectoryAnalysis

Class to do post cell average analysis on desmond trajectory.

DRIVER_PATH = 'permittivity_gui_dir/permittivity_ave_cell_driver.py'¶

AVE_CELL = 'ave_cell'¶

DEFAULT_JOBNAME = 'permittivity_ave_cell_task'¶

OUTFILE_EXT = '-out.cms'¶

setup(copy_ene=True, write_cms=True)¶: Over write parent class method.

static finalizeStep(job)¶

Finalize this step. Can be overwritten for light weight post process.

Parameters: job (An instance of a BaseJob subclass (such as JobControlJob or SubprocessJob)) – current job

class schrodinger.application.matsci.permittivity.AnalyzeSimulation(*arg, **kwarg)¶

Bases: schrodinger.application.matsci.permittivity.MdPostTrajectoryAnalysis

Class to analyze trajectory from desmond simulation using analyze_simulation.py

DRIVER_PATH = 'analyze_simulation.py'¶

ANALYZE_SIMULATION = 'analyze_simulation'¶

DEFAULT_JOBNAME = 'permittivity_analyze_simulation_task'¶

OUTFILE_EXT = '-out.cms'¶

ST2_EXT = '.st2'¶

OUT_ST2_EXT = '-out.st2'¶

INPUT_ST2 = 'input_st2'¶

OUT_ST2_PROP = 's_matsci_St2_File'¶

__init__(*arg, **kwarg)¶: See parent class for documentation

setup()¶: Over write parent class method.

appendTrjInOutst2ToCmd()¶: Append the trajectory, input st2, and output st2 information to the cmd.

createInputSt2()¶: Create input st2 file based on the configure yaml.

setOutfile()¶: Set the outfile of a job.

static finalizeStep(job)¶

Finalize this step. Can be overwritten for light weight post process.

Parameters: job (An instance of a BaseJob subclass (such as JobControlJob or SubprocessJob)) – Current job

class schrodinger.application.matsci.permittivity.BaseDipoleAnalysis(basename, config_yaml='default_permittivity_protocols.yaml', task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Bases: schrodinger.application.matsci.permittivity.MdPostTrajectoryAnalysis

Class to do post dipole analysis on desmond trajectory.

FLAG_SLICE_INTVL = '-slice_intvl'¶

FLAG_NORMALIZATION = '-normalization'¶

DRIVER_PATH = 'permittivity_gui_dir/permittivity_dipole_driver.py'¶

DIPOLE = 'dipole'¶

DIPOLE_CAP = 'Dipole'¶

STATISTICS_CSV_EX = '_dp-out.csv'¶

STATISTICS_FILE_PROP = 's_matsci_Dipole_Statistics_File'¶

DEFAULT_JOBNAME = 'permittivity_dipole_task'¶

OUTFILE_EXT = '-out.cms'¶

TIME_SERIAL = 'time_serial'¶

AUTOCORRELATION = 'autocorrelation'¶

COMPLEX_PERMITTIVITY = 'complex_permittivity'¶

SUSCEPTIBILITY = 'susceptibility'¶

SUSCEPT_CAP = 'Susceptibility'¶

TIME_SERIAL_CAPITALIZE = 'Time_Serial'¶

TIME_SERIAL_FILE_PROP = 's_matsci_Dipole_Time_Serial_File'¶

AUTOCORRELATION_FILE_PROP = 's_matsci_Dipole_Autocorrelation_File'¶

MD_COMPLEX_PERMITTIVITY_FILE_PROP = 's_matsci_Md_Complex_permittivity_File'¶

COMPLEX_PERMITTIVITY_FILE_PROP = 's_matsci_Complex_permittivity_File'¶

DIPOLE_SUSCEPTIBILITY_PROP = 'r_matsci_Dipole_Susceptibility'¶

DIPOLE_SUSCEPTIBILITY_STORE_PROP = 'r_matsci_Dipole_Susceptibility_Store'¶

DIPOLE_SUSCEPTIBILITY_STD_PROP = 'r_matsci_stdev_Dipole_Susceptibility'¶

SYSTEMWIDE_DIPOLE = 'systemwide_dipole'¶

SYSTEMWIDE_DIPOLE_X_PROP = 'r_matsci_Systemwide_Dipole_X'¶

SYSTEMWIDE_DIPOLE_Y_PROP = 'r_matsci_Systemwide_Dipole_Y'¶

SYSTEMWIDE_DIPOLE_Z_PROP = 'r_matsci_Systemwide_Dipole_Z'¶

SYSTEMWIDE_DIPOLE_PROPS = ['r_matsci_Systemwide_Dipole_X', 'r_matsci_Systemwide_Dipole_Y', 'r_matsci_Systemwide_Dipole_Z']¶

SYSTEMWIDE_DIPOLE_X_STD_PROP = 'r_matsci_Systemwide_Dipole_X_SD'¶

SYSTEMWIDE_DIPOLE_Y_STD_PROP = 'r_matsci_Systemwide_Dipole_Y_SD'¶

SYSTEMWIDE_DIPOLE_Z_STD_PROP = 'r_matsci_Systemwide_Dipole_Z_SD'¶

SYSTEMWIDE_DIPOLE_STD_PROPS = ['r_matsci_Systemwide_Dipole_X_SD', 'r_matsci_Systemwide_Dipole_Y_SD', 'r_matsci_Systemwide_Dipole_Z_SD']¶

KWW = 'kww'¶

TAU = 'tau'¶

BETA = 'beta'¶

TAU_START_PROP = 'r_matsci_Permittivity_Tau_Start_(ns)'¶

TAU_END_PROP = 'r_matsci_Permittivity_Tau_End_(ns)'¶

KWW_TAU_PROP = 'r_matsci_Kww_Tau_(ps)'¶

KWW_BETA_PROP = 'r_matsci_Kww_Beta'¶

TIME_SERIAL_LABELS = ['Time (ps)', 'Dipole_x (debye)', 'Dipole_y (debye)', 'Dipole_z (debye)', '<Dipole^2> (debye^2)']¶

TAU_PS = 'Tau (ps)'¶

DIPOLE_SQ = 'Dipole^2 (debye^2)'¶

DIPOLE_SQ_MEAN = 'Dipole^2 - <Dipole>^2 (debye^2)'¶

AUTOCORRELATION_LABELS = ['Tau (ps)', 'Dipole_x^2 (debye^2)', 'Dipole_y^2 (debye^2)', 'Dipole_z^2 (debye^2)', 'Dipole^2 (debye^2)', 'Dipole^2 - <Dipole>^2 (debye^2)']¶

TAU_PS_INDEX = 0¶

DIPOLE_SQ_INDEX = 4¶

DIPOLE_SQ_MEAN_INDEX = 5¶

LABEL_MAP = {'autocorrelation': ['Tau (ps)', 'Dipole_x^2 (debye^2)', 'Dipole_y^2 (debye^2)', 'Dipole_z^2 (debye^2)', 'Dipole^2 (debye^2)', 'Dipole^2 - <Dipole>^2 (debye^2)'], 'time_serial': ['Time (ps)', 'Dipole_x (debye)', 'Dipole_y (debye)', 'Dipole_z (debye)', '<Dipole^2> (debye^2)']}¶

STD_DEV = 'Std Dev of '¶

class SysDipole(mean, sd)¶

Bases: tuple

mean¶: Alias for field number 0

sd¶: Alias for field number 1

setup(copy_ene=False, write_cms=True)¶: Over write parent class method.

static finalizeStep(job)¶

Finalize this step. Can be overwritten for light weight post process.

Parameters: job (An instance of a BaseJob subclass (such as JobControlJob or SubprocessJob)) – Current job

class schrodinger.application.matsci.permittivity.DipoleAnalysis(basename, config_yaml='default_permittivity_protocols.yaml', task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Bases: schrodinger.application.matsci.permittivity.BaseDipoleAnalysis

Class to do post dipole analysis on desmond trajectory.

FLAG_DATA_LAST_FRAC = 'data_last_frac'¶

classmethod optionsToTaskProtocols(options, task_name, seed=None)¶

Update the task protocol according to the user input.

Parameters

options (argparse.Namespace) – The parsed command line options
task_name (str) – Task name
seed (int or None) – Random seed to randomize the initial velocities

Returns

Updated task protocol

Return type

TaskProtocol

class schrodinger.application.matsci.permittivity.SusceptibilityMerge(basename, config_yaml='default_permittivity_protocols.yaml', task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Bases: schrodinger.application.matsci.permittivity.BaseDipoleAnalysis

Class to merge susceptibility.

setup(copy_ene=False, write_cms=True)¶: Over write parent class method.

udpateCmd()¶: Update the command of the subjob: trim the input cms to one single; all the cms files are parsed for original cms and the original cms filenames are provided as the base filename without cms, csv, or npz.

static finalizeStep(job)¶

Update child job’s command with the parent job output, and set output files if not set by the subjob itself.

Parameters: job (An instance of a BaseJob subclass (such as JobControlJob or SubprocessJob)) – Current job

class schrodinger.application.matsci.permittivity.ComplexPermittivity(basename, config_yaml='default_permittivity_protocols.yaml', task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Bases: schrodinger.application.matsci.permittivity.SusceptibilityMerge

Class to do post complex permittivity analysis based on dipole autocorrelation output files (npz, csv).

MAX_DIEL_LOSS_VAL_PROP = 'r_matsci_Maximum_Dielectric_Loss'¶

MAX_DIEL_LOSS_FREQ_PROP = 'r_matsci_Frequency_of_Maximum_Dielectric_Loss_(Hz)'¶

KWW_INIT_GUESSES = [[10, 0.8], [30000, 0.8]]¶

static finalizeStep(job)¶

Finalize this step. Can be overwritten for light weight post process.

Parameters: job (An instance of a BaseJob subclass (such as JobControlJob or SubprocessJob)) – Current job

class schrodinger.application.matsci.permittivity.JaguarCalculation(basename, config_yaml='default_permittivity_protocols.yaml', task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Bases: schrodinger.application.matsci.permittivity.Step

Class to do a Jaguar calculation with keywords.

OPT_ATTR = 'jaguar_options'¶

IN_EXT = '.in'¶

DRIVER_PATH = 'run'¶

DEFAULT_JOBNAME = 'permittivity_jaguar_task'¶

FLAG_PARALLEL = '-PARALLEL'¶

BASIS = 'basis'¶

IGEOPT = 'igeopt'¶

MOLCHG = 'molchg'¶

MULTIP = 'multip'¶

IUHF = 'iuhf'¶

DFTNAME = 'dftname'¶

IPOLAR = 'ipolar'¶

IFDPOL = 'ifdpol'¶

IACC_FDPOL = 'iacc_fdpol'¶

B3LYP = 'B3LYP'¶

DEF2_SVPD = 'DEF2-SVPD'¶

IACCG = 'iaccg'¶

NOFAIL = 'nofail'¶

NOPS_OPT_SWITCH = 'nops_opt_switch'¶

MAXITG = 'maxitg'¶

MAXIT = 'maxit'¶

INT_KEYWORDS = ['igeopt', 'molchg', 'multip', 'iuhf', 'ipolar']¶

KEYWORD_DEFAULTS = {'dftname': 'B3LYP', 'igeopt': 0, 'ipolar': None, 'iuhf': None, 'molchg': 0, 'multip': 1}¶

POLYMER_INT_KEYWORDS_DIFF = {'basis': 'DEF2-SVPD'}¶

FLAG_JAGUAR_OPTIONS = '-jaguar_options'¶

DEFAULT_JAGUAR_OPTIONS = {'basis': '6-31G**', 'dftname': 'B3LYP', 'igeopt': 1, 'maxit': 300, 'maxitg': 300, 'nofail': 1, 'nops_opt_switch': 10}¶

MAX_ATOM_NUM = 25000¶

setup()¶: See parent class.

customizeInputAndCommand()¶: Jaguar stage requires its own input file instead of mae. The method writes out the jaguar input file and update the command with the jaguar input file.

static finalizeStep(job)¶

Finalize this step. Can be overwritten for light weight post process.

Parameters: job (An instance of a BaseJob subclass (such as JobControlJob or SubprocessJob)) – current job
Returns: The Jaguar output data
Return type: JaguarOutput or None

classmethod optionsToTaskProtocols(options, task_name, seed=None)¶

Update the task protocol according to the user input.

Parameters

options (argparse.Namespace) – The parsed command line options
task_name (str) – Task name
seed (int or None) – Random seed to randomize the initial velocities

Returns

Updated task protocol

Return type

TaskProtocol

class schrodinger.application.matsci.permittivity.JaguarFinerCalculation(basename, config_yaml='default_permittivity_protocols.yaml', task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Bases: schrodinger.application.matsci.permittivity.JaguarCalculation

Class to do a Jaguar calculation with finer basis set and functional.

OPT_ATTR = 'jaguar_finer_options'¶

FLAG_JAGUAR_FINER_OPTIONS = '-jaguar_finer_options'¶

DEFAULT_JAGUAR_OPTIONS = {'basis': 'cc-pVTZ-pp(-f)++', 'dftname': 'B3LYP', 'igeopt': 1, 'maxit': 300, 'maxitg': 300, 'nofail': 1, 'nops_opt_switch': 10}¶

class schrodinger.application.matsci.permittivity.ElectricPolarizability(*arg, **kwargs)¶

Bases: schrodinger.application.matsci.permittivity.JaguarCalculation

Class to do jaguar calculation of electric polarizability.

OPT_ATTR = 'elec_polarizability'¶

TPP = 'tpp'¶

ELECTRIC_POLARIZABILITY = 'electric_polarizability'¶

DEFAULT_JOBNAME = 'permittivity_electric_polarizability_task'¶

FLAG_JAGUAR_OPTIONS = '-jaguar_options'¶

FLAG_ELEC_POLARIZABILITY = '-elec_polarizability'¶

DEFAULT_IPOLAR = -1¶

DEFAULT_JAGUAR_OPTIONS = {'basis': 'cc-pVTZ-pp(-f)++', 'dftname': 'B3LYP', 'maxit': 300, 'nofail': 1}¶

FDPOL_FREQ1 = 'fdpol_freq1'¶

FDPOLAR_FREQ1 = 'fdpolar_freq1'¶

PROP = 'electric_polarizability'¶

KEY = 'r_matsci_Electric_Polarizability_(bohr^3)'¶

ELECTRIC_POLARIZABILITY_PROP = 'r_matsci_Electric_Polarizability_(bohr^3)'¶

DELIM = '_@_'¶

ELECTRIC_POLARIZABILITY_FREQ_PROP = 'r_matsci_Electric_Polarizability_(bohr^3)_@_%.4eeV'¶

POLAR_ALPHA = 'polar_alpha'¶

FDPOLAR_ALPHA1 = 'fdpolar_alpha1'¶

MITERTD = 'mitertd'¶

DEFAULT_KWARGS = {'jaguar_output_attr': 'polar_alpha', 'tpp': 1}¶

FLAG_NUM_CRU = '-num_cru'¶

ELECTRIC_POLARIZABILITY_SLOPE = 'r_matsci_Electric_Polarizability_Slope_(bohr^3/monomer)'¶

ELECTRIC_POLARIZABILITY_INTERCEPT = 'r_matsci_Electric_Polarizability_Intercept_(bohr^3)'¶

ELECTRIC_POLARIZABILITY_SLOPE_FREQ = 'r_matsci_Electric_Polarizability_Slope_(bohr^3/monomer)_@_%.4eeV'¶

ELECTRIC_POLARIZABILITY_INTERCEPT_FREQ = 'r_matsci_Electric_Polarizability_Intercept_(bohr^3)_@_%.4eeV'¶

PLYM = 'plym'¶

__init__(*arg, **kwargs)¶

Parameters

basename (str) – The base name of this subjob
config_yaml (str) – The config yaml file contain all job config
task_name (str) – Task name of this sub job
infile (str) – The input filename
outfile (str) – The output filename
additional_infiles (list of str) – This records additional input files (e.g. the second, third, and so on)
master_logger (logging.Logger) – The logger to use for recording messages into master job -driver.log.
node_index (The node index) – tuple

updateTaskReplicaSettings()¶: Update the task settings due to replica.

static finalizeStep(job)¶

Finalize this step. Can be overwritten for light weight post process.

Parameters: job (An instance of a BaseJob subclass (such as JobControlJob or SubprocessJob)) – Current job

classmethod getWavAndPolar(struct)¶

Get the wavelength and polarizability.

Parameters: struct ('structure.Structure') – The input structure to search properties.
Returns: Wavelength in nm, polarizability in bohr^3
Return type: (float or None, float or None)

classmethod getWavAndProp(struct, prop)¶

Get the wavelength and wavelength-related property.

Parameters

struct ('structure.Structure') – The input structure to search properties.
prop (str) – A property key

Returns

Wavelength in nm, a wavelength related property value

Return type

(float or None, float or None)

classmethod getWavAndPolars(struct, include_ipolar=False)¶

Get the wavelength and polarizability.

Parameters

struct ('structure.Structure') – The input structure to search properties.
include_ipolar (bool) – Whether to include the ipolar result, the coupled perturbed Hartree-Fock (CPHF) equations Cao, Y.; Friesner, R. A. Molecular (hyper)polarizabilities computed by pseudospectral methods. J. Chem. Phys. 2005

Returns

Wavelength in nm, polarizability in bohr^3

Return type

list, list

classmethod getWavAndProps(struct, prop)¶

Get the wavelength and wavelength-related properties. Note property keys starting with the user requested str is considered matches.

Parameters

struct ('structure.Structure') – The input structure to search properties.
prop (str) – A property key without frequency info.

Returns

Wavelength in nm, wavelength related property values

Return type

list, list

classmethod getFreqFromPropkey(propkey)¶

Get the frequency value from the property key.

Returns: The frequency of this property
Return type: float or None

classmethod optionsToTaskProtocols(options, task_name, seed=None)¶

Update the task protocol according to the user input.

Parameters

options (argparse.Namespace) – The parsed command line options
task_name (str) – Task name
seed (int or None) – Random seed to randomize the initial velocities

Returns

Updated task protocol

Return type

TaskProtocol

classmethod getWavelengths(options)¶

Get the wavelengths based on the parsed command line options.

Parameters: options (argparse.Namespace) – The parsed command line options.
Returns: All wavelengths for calculation
Return type: list of floats and NONE

static getUserWavelengths(options, default_intvl=50)¶

Get the wavelengths from the user input limits.

Parameters

options (argparse.Namespace) – The parsed command line options
default_intvl (float) – Default wavelength interval

Returns

The wavelengths based on the user input limits

Return type

list of floats

static getAbbeWavelengths(options)¶

Get the wavelengths from the users’ request on abbe number.

Parameters: options (argparse.Namespace) – The parsed command line options
Returns: The number wavelengths in nm for abbe number
Return type: list of float

class schrodinger.application.matsci.permittivity.JaguarMerge(basename, config_yaml='default_permittivity_protocols.yaml', task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Bases: schrodinger.application.matsci.permittivity.Step

Class to merge multiple Jaguar Calculations.

DRIVER_PATH = 'permittivity_gui_dir/permittivity_merge_polarizability_driver.py'¶

JAGUAR_MERGE = 'jaguar_merge'¶

DEFAULT_JOBNAME = 'permittivity_jaguar_merge_task'¶

OUTFILE_EXT = '-out.mae'¶

CSV_OUT_EXT = '_polar-out.csv'¶

WAV_EP_FILE_PROP = 's_matsci_Electric_Polarizability_File'¶

classmethod optionsToTaskProtocols(options, task_name, seed=None)¶

Update the merge commands based on users’ input.

Parameters

options (argparse.Namespace) – The parsed command line options
task_name (str) – Task name
seed (int or None) – Random seed to randomize the initial velocities

Returns

Updated task protocol

Return type

TaskProtocol

static finalizeStep(job)¶

Finalize this step. Can be overwritten for light weight post process.

Parameters: job (an instance of a BaseJob subclass (such as JobControlJob or SubprocessJob)) – current job

class schrodinger.application.matsci.permittivity.TwoFileInput(basename, config_yaml='default_permittivity_protocols.yaml', task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Bases: schrodinger.application.matsci.permittivity.Step

Class to sort the two input files based on extension.

TERMINAL_INFILE_NUM = 2¶

setup()¶: See parent class.

udpateCmd()¶: Update the command.

class schrodinger.application.matsci.permittivity.RefractiveIndex(basename, config_yaml='default_permittivity_protocols.yaml', task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Bases: schrodinger.application.matsci.permittivity.TwoFileInput

Class to do refractive index calculation.

DRIVER_PATH = 'permittivity_gui_dir/permittivity_refractive_index_driver.py'¶

REFRACTIVE_INDEX = 'refractive_index'¶

FILE_EXT = '_ri-out.csv'¶

RI_CAP = 'Refractive_Index'¶

DEFAULT_JOBNAME = 'permittivity_refractive_index_task'¶

REFRACTIVE_INDEX_PROP = 'r_matsci_Refractive_Index'¶

DELIM = '_@_'¶

NM = 'nm'¶

MATSCI_ABBE_NUMBER = 'r_matsci_Abbe_Number'¶

ABBE_NUMBER_PROP = 'r_matsci_Abbe_Number_@_%.1fnm_%.1fnm_%.1fnm'¶

RELATIVE_PERMITTIVITY_INF_PROP = 'r_matsci_Relative_Permittivity_Inf'¶

WAV_IR_FILE_PROP = 's_matsci_Wavelength_Refractive_Index_File'¶

FLAG_ABBE_NUMBER_WAVELENGTH = '-abbe_number_wavelength'¶

FLAG_REFRACTIVE_INDEX_WAVELENGTH = '-refractive_index_wavelength'¶

AbbeNumber¶: alias of schrodinger.application.matsci.permittivity.ABBE_NUMBER

ABBE_NFREQ = 3¶

classmethod optionsToTaskProtocols(options, task_name, seed=None)¶

Update the refractive index commands based on users’ input.

Parameters

options (argparse.Namespace) – The parsed command line options
task_name (str) – Task name
seed (int or None) – Random seed to randomize the initial velocities

Returns

Updated task protocol

Return type

TaskProtocol

static finalizeStep(job)¶

Finalize this step. Can be overwritten for light weight post process.

Parameters: job (An instance of a BaseJob subclass (such as JobControlJob or SubprocessJob)) – Current job

static getRefractiveIndex(struct, density, polar)¶

Get refractive index from density, polarizability, and total_weight.

Parameters

struct ('structure.Structure') – Structure of a single molecule
density (float) – Density in g/cm^3
polar (float) – The isotropically averaged polarizability in atomic units of bohr^3

Returns

Refractive index

Return type

float

static setAbbeNum(struct, abbe_num, wavs, ext=None)¶

Set the Abbe number value with wavelength information as structural property.

Parameters

struct ('structure.Structure') – The structure to save property to
abbe_num (float) – The Abbe number value
ext (str) – The str extension for the property
wavs (list of three float) – The wavelengths at which Abbe number is calculated

classmethod getAbbeNum(struct)¶

Get Abbe number and wavelengths from a structure.

Parameters: struct ('structure.Structure') – The structure to get Abbe number and wavelengths.
Returns: Abbe number and wavelengths
Return type: collections.namedtuple

classmethod calAbbeNum(data)¶

Calculate abbe number from refractive indexes.

Parameters: data (3 x 2 array) – First column: wavelengths, second column: refractive indexes
Returns: The abbe number and wavelength info
Return type: ‘collections.namedtuple’

class schrodinger.application.matsci.permittivity.StaticPermittivity(basename, config_yaml='default_permittivity_protocols.yaml', task_name=None, infile='$infile', outfile=None, additional_infiles=None, master_logger=None, node_index=None)¶

Bases: schrodinger.application.matsci.permittivity.TwoFileInput

Class to do refractive index calculation.

OUTFILE_EXT = '-out.cms'¶

DRIVER_PATH = 'permittivity_gui_dir/permittivity_static_permittivity_driver.py'¶

STATIC = 'static'¶

STATIC_PERMITTIVITY = 'static_permittivity'¶

DEFAULT_JOBNAME = 'permittivity_static_task'¶

RELATIVE_STATIC_PERMITTIVITY_PROP = 'r_matsci_Relative_Static_Permittivity'¶

RELATIVE_STATIC_PERMITTIVITY_STORE_PROP = 'r_matsci_Relative_Static_Store_Permittivity'¶

COMPLEX_PERMITTIVITY_DATA_HEADER = 'Frequency (Hz),Eps (Real),Eps (Imaginary)'¶

setup()¶: See parent class.

static finalizeStep(job)¶

Finalize this step. Can be overwritten for light weight post process.

Parameters: job (An instance of a BaseJob subclass (such as JobControlJob or SubprocessJob)) – Current job

class schrodinger.application.matsci.permittivity.WorkflowParser(config_yaml, basename, infile_job_infos, master_logger=None)¶

Bases: object

TASK_NAME = 'task_name'¶

TASK_TYPE = 'task_type'¶

TASK_DRIVER_PATH = 'task_driver_path'¶

SPECIFIC_RESTART_LOCATOR_MAP = {'driver_path': 'task_driver_path', 'name': 'task_name', 'type': 'task_type'}¶

TASK_SUBCLASS = 'task_subclass'¶

TASK_SUBJOB = 'task_subjob'¶

TASK_REPLICA = 'task_replica'¶

REPLICA_DELIM = 'r'¶

CHILD_NODE_INDEXES = 'child_node_indexes'¶

PARENT_NODE_INDEXES = 'parent_node_indexes'¶

PROP_KEYS = ['task_replica', 'child_node_indexes', 'parent_node_indexes']¶

TASK_TYPE_TO_SUBCLASS = {'CMS Parser': <class 'schrodinger.application.matsci.permittivity.CMSParser'>, 'Complex Permittivity Protocol': <class 'schrodinger.application.matsci.permittivity.ComplexPermittivity'>, 'Disorder System Builder Protocol': <class 'schrodinger.application.matsci.permittivity.DisorderSystemBuilder'>, 'Jaguar Calculation Protocol': <class 'schrodinger.application.matsci.permittivity.JaguarCalculation'>, 'Jaguar Finer Calculation Protocol': <class 'schrodinger.application.matsci.permittivity.JaguarFinerCalculation'>, 'Jaguar Merge Protocol': <class 'schrodinger.application.matsci.permittivity.JaguarMerge'>, 'Jaguar Polarizability Protocol': <class 'schrodinger.application.matsci.permittivity.ElectricPolarizability'>, 'MD Analyze Simulation Protocol': <class 'schrodinger.application.matsci.permittivity.AnalyzeSimulation'>, 'MD Average Cell Protocol': <class 'schrodinger.application.matsci.permittivity.AveCellAnalysis'>, 'MD Density Protocol': <class 'schrodinger.application.matsci.permittivity.DensityAnalysis'>, 'MD Dipole Protocol': <class 'schrodinger.application.matsci.permittivity.DipoleAnalysis'>, 'MD Simulation Protocol': <class 'schrodinger.application.matsci.permittivity.MultiStageMd'>, 'Polymer Builder Protocol': <class 'schrodinger.application.matsci.permittivity.PolymerBuilder'>, 'Refractive Index Protocol': <class 'schrodinger.application.matsci.permittivity.RefractiveIndex'>, 'Static Permittivity Protocol': <class 'schrodinger.application.matsci.permittivity.StaticPermittivity'>, 'Susceptibility Merge Protocol': <class 'schrodinger.application.matsci.permittivity.SusceptibilityMerge'>}¶

__init__(config_yaml, basename, infile_job_infos, master_logger=None)¶

Parameters

config_yaml (str) – Config file
basename (str) – Base name
infile_job_infos (list of SimpleNamespace) – The input file information
logger (logging.Logger) – The logger to use for recording messages into master job -driver.log.

setUp()¶: Parse the workflow section in the config yaml and setup the subjobs.

initialize()¶: Initialize the class by reading workflow from config file, creating networkx, indexing the workflow task names….

addNodes()¶: Add each task name using an unique index as a node to the graph.

addEdges()¶: Add edges between nodes according to the job dependence (parent / child).

addSubclass()¶: Add task type, driver path, and subclass to each graph node.

removeNodes()¶: Remove the nodes marked with remove replica keyword.

getLeafTaskNodes()¶

Return the task node without dependents in an order that the leaf with the longest path to the root is returned first.

Returns: A list of nodes without a child.
Return type: list of nodes in networkx.Graph.nodes

getFirstLevelParentNodes(node)¶

Return the first level parent task subjob node indexes of this input node.

Parameters: node (tuple) – A node index whose parent nodes are requested
Returns: A node in the job without a child
Return type: list of nodes (dict)

getOrderedTaskSubjobDirs(node)¶

Return the task subjob dirs in the order from bottom to the top.

Parameters: node (dict as a node in networkx.Graph.nodes) – A node in the job without a child.
Returns: Key is the task name and value is the subdir of the task
Return type: OrderedDict

addSubjobs()¶: Initiate each subclass and add the initiated subclass (subjob) to the node.

getSubjobname(node_index)¶

Return the subjob name based on task name and node index.

Parameters: node_index (tuple) – The index to get job info node
Returns: Subjob name
Return type: str

setParentChildJobs(clear_first=True)¶: From the edges of the graph, save the info on the first level child jobs for each parent job and the first level parent jobs for each child job.

clearFirstLevelParentChildJobs()¶: Clear the first level child jobs and first parent job information.

removeStartingJobs()¶: Remove the subjobs that are not defined as starting tasks by task type or task driver path.

setSubjobDependence()¶: Set the job dependence between each subjob pair.

JobinfoAndNodeMatched(jinfo, node)¶

Whether the job information and task node match.

Parameters

jinfo (SimpleNamespace) – One job information for specific restart.
node (networkx.Graph.nodes) – One task node in the networkx

Returns

True if the jinfo matches the node settings

Return type

bool

updateSartupJobs()¶: Set the input files for the start-up jobs.

addReplicaNode(node, node_rindex)¶

Add the replica node to the graph and set node properties.

Parameters

node (dict) – The node in graph the replica duplicates
node_rindex (tuple) – The nodex index of the replica

getReplicaType(node)¶

Get the replica type.

Parameters: node (dict) – The node in the nextworkx graph
Returns: The replica type
Return type: str or None

setReplicaType(node, ntype)¶

Set the replica type.

Parameters

node (dict) – The node in the nextworkx graph
ntype (str) – The replica type of the node

compatibleChildNodes(node)¶

Keep compatible children nodes.

Parameters: node (The node whose children's compatibility is checked.) – dict

connectReplicaNode(node_rindex)¶

Add the edges between one replica node and the parent and child nodes of the original nodes. In addition, the mapping between original node and replica nodes is saved in each child job so that further threading process can utilize before merging.

NOTE: threading mode disconnects one single parent node.

Parameters

node (dict) – The node of the original node
node_index (tuple) – The node index of the original node
node_rindex (tuple) – The node index of the replica node
replica_type (str) – The replica

disconnectOrigNode(node, node_index)¶

Disconnect the edge and first level things between the original node and all parents and children.

Parameters

node (dict) – The original node
node_index (tuple) – The original node index

setReplica()¶: Process the replica nodes (branch, thread, and merge) and treat original nodes properly.

updateThreadingNodes()¶: Update the threading nodes so that single branching is not considered as threading.

logReplicaInfo()¶: Print all the node info including replica node for debugging.

updateReplicaNodes()¶: Update replica nodes based on replica keywords.

setBranchReplicaNode()¶

Locate branching nodes, replace then with replica nodes, properly connecting and disconnecting edges, update first level parent and child jobs upstream and downstream of the original nodes.

Returns: True if one or more branch nodes are successfully processed.
Return type: bool

getRelicaNodeIndexes(node_type='branch')¶

Get the node index of a certain type (threading or merging).

Parameters: node_type (str) – ‘threading’ is a node of single parent who is a replica node. ‘merge’ is a node marked with MERGE replica keywords
Returns: Node indexes of a certain type (threading or merging)
Return type: list of tuple
Raises: TypeError – during threading, a branching node is encountered. This may come from a improper workflow design or bug. Branch should happen before thread. Currently, only one single branching node design is implemented and tested.

setThreadingReplicaNodes()¶

Locate threading nodes (node after branching replica before merge node), replace then with a single replica node, properly connecting and disconnecting edges, update first level parent and child jobs upstream and downstream of the original nodes.

Returns: True, if successfully identify and process one single node with replica.
Return type: bool

setMergeReplicaNodes()¶

Merge the replica nodes. Multiple last replica job in different threads are the parent of one single merge job, which is the original job.

Returns: True, if successfully identify and merge into one single job.
Return type: bool

addJobsToJobDj(jdj)¶

Add leaf jobs to the JobDJ and all jobs with dependence set by setSubjobDependence() are added as well.

Parameters: jdj ('queue.JobDJ') – The JobDJ instance to register jobs.
Returns: The job queue for running commands/jobs in parallel under jobcontrol.
Return type: ‘queue.JobDJ’

draw()¶: Draw the workflow with dependence and task name as png.

classmethod getTaskSubClass(task_type, task_protocol)¶

Get task subclass if the subclass is known by this driver, or a specific task driver path is provided in the config yaml setting block.

Parameters

task_type (str) – The task type of this stage
task_protocol ('TaskProtocol') – The task protocol containing task information

Raises

TypeError – When the task_type is not supported

Returns

The corresponding task class

Return type

the class or subclass of ‘Step’

classmethod writeConfig(options, jobname)¶

Command line options is a subset of all the flags, and thus write a new configure file based on command line options and configure template.

NOTE: if a config_yaml is explicitly passed from the command line, The returned the full path of the final config file pointing to the original path from the command line.

Parameters

options (argparse.Namespace) – The parsed command line options
jobname (str or False) – The jobname based on which config yaml is generated. If False, no yaml file written out.