Package schrodinger :: Package application :: Package matsci :: Module equilibrium_md

Module equilibrium_md

Equilibrium molecular dynamics classes/function shared by transport property calculations using Einstein and Green-Kubo methods.

Classes

[hide private]

EquilibriumMdBase
This is a base class for equilibrium MD subclass, and should be not be instantiated directly.

TrjBase
This is a base class for equilibrium MD subclass that uses trajectory, and should be not be instantiated directly.

MixInBlockStd
This is a base class for dividing long simulation into blocks to get standard deviation, and should be not be instantiated directly.

Functions

[hide private]

None or str

check_file_exist(path_file)
Check and find the path/file on the host

list of tuple

get_files_from_folder(folder_abs_path)
Walk through a folder, find all files inside it.

str, str, str or None

get_md_results(basename, log, log_error, opts, **kwargs)
From parsed options, setup and run md simulation.

str, str, str, str

setup_md_job(name_base, icms, md_time, md_timestep, md_emsemble, md_temperature, md_pressure, trj_interval, md_save_trj, gpu, procs, write_vel=False, md_enegry_interval=None, md_save_enegrp=False, energy_groups=[])
Write the .msj file and form the command for running the molecular dynamics simulation at a specific temperature.

options: Named tuple

trim_parser_skip_md(options, extra=[])
If md is skipped, delete any options for setting up molecular dynamics simulation.

add_parser_opts(parser, final_prop, mid_prop, extra_options=[])
Add all necessary parser arguments for setting up a MD simulation and optional arguments for certain green-kubo property calculation.

check_options(opts, parser, option_flag, min_data_point)
Validate the options.

Variables

[hide private]

__doc__ = ...

PROGRAM_NAME_DIFFUSION = 'Diffusion Coefficient'

DEFAULT_JOBNAME_DIFFUSION = 'diffusion_coefficient'

PROGRAM_NAME_VISCOSITY = 'Visosity'

DEFAULT_JOBNAME_VISCOSITY = 'viscosity'

CUBIC_SPLINE = 'cubic spline'

PICOSECOND = 1e-12

FEMTO2PICO = 0.001

NANO2PICO = 1000.0

ANGSTROM2M = 1e-10

TAU_START_PROP_KEY_BASE = 'Tau_Start_(ns)'

TAU_END_PROP_KEY_BASE = 'Tau_End_(ns)'

DIFFUSIVITY_UNIT = 'm^2/s'

DIFFUSION_UNIT_CONVERT = 1e-08

DIFFUSIVITY_PROP_KEY_BASE = 'r_matsci_Diffusion_Coefficient_%s_'

DIFFUSIVITY_PROP_KEY = 'r_matsci_Diffusion_Coefficient_%s_(m^2...

DIFFUSIVITY_TAU_START_PROP_KEY = 'r_matsci_Diffusion_Coefficie...

DIFFUSIVITY_TAU_END_PROP_KEY = 'r_matsci_Diffusion_Coefficient...

VISCOSITY_UNIT = 'Pa.s'

VISCOSITY_PROP_KEY_BASE = 'r_matsci_%s_Viscosity_%s_'

VISCOSITY_PROP_KEY = 'r_matsci_%s_Viscosity_%s_(Pa.s)'

VISCOSITY_TAU_START_PROP_KEY = 'r_matsci_%s_Viscosity_%s_Tau_S...

VISCOSITY_TAU_END_PROP_KEY = 'r_matsci_%s_Viscosity_%s_Tau_End...

TRJ_EXT = 'trj'

INPUT_FILE = '-icms'

FLAG_ATOM_SELECTION = '-sel'

FLAG_ENSEMBLE = '-md_ensemble'

NVE = 'NVE'

NVT = 'NVT'

NPT = 'NPT'

ENSEMBLE = ['NVE', 'NVT', 'NPT']

FLAG_MD_TEMP = '-md_temperature'

FLAG_MD_PRESSURE = '-md_pressure'

FLAG_MD_TIME = '-md_time'

FLAG_MD_TIMESTEP = '-md_timestep'

FLAG_MD_TRJ_INTERVAL = '-md_trj_interval'

FLAG_MD_SAVE_TRJ = '-md_save_trj'

FLAG_SKIP_MD = '-md_skip'

FLAG_TRJ_START = '-trj_start'

FLAG_TAU_START = '-tau_start'

FLAG_TAU_END = '-tau_end'

FLAG_TRJ_FOLDER = '-trj_folder'

TRJ_PROP_KEYS = ['s_m_original_cms_file', 's_chorus_trajectory...

FLAG_ENEGRP_FILE = '-enegrp_file'

FLAG_ENEGRP_INTERVAL = '-md_enegry_interval'

FLAG_MD_SAVE_ENEGRP = '-md_save_enegrp'

FLAG_GPU = '-gpu'

FLAG_BLOCK_NUM = '-block_num'

FLAG_VARIATION = '-variation'

STD_FILE_EXT = '_block_std'

MIN_TIME_NS = 0.01

MAX_TIMESTEP_FS = 100

MIN_TIMESTEP_FS = 0.01

MAX_TRJ_FRAME_START = 1000000

ARG_DEFAULTS = {'-block_num': 1, '-md_enegry_interval': 0.01, ...

ALL_MD_FLAGS = ['-md_ensemble', '-md_temperature', '-md_pressu...

MAX_TIME_NS = 100

__package__ = 'schrodinger.application.matsci'

Function Details

[hide private]

check_file_exist(path_file)

Check and find the path/file on the host

Parameters:

path_file (filename with path) - string

Returns: None or str

None if the file cannot be located

get_files_from_folder(folder_abs_path)

Walk through a folder, find all files inside it.

Parameters:

folder_abs_path (folder path) - string

Returns: list of tuple

each tuple contains: absolute path of a file, and a relative path that the file will be transferred to.

get_md_results(basename, log, log_error, opts, **kwargs)

From parsed options, setup and run md simulation.

Parameters:

basename (str) - basename for md simulation job
log (function) - log information
log_error (function) - log error information and exit
opts (Named tuple) - The parsed command line option
kwargs (dict) - extra options to control md simulation

Returns: str, str, str or None

output cms, trj folder, and enegrp_file

setup_md_job(name_base, icms, md_time, md_timestep, md_emsemble, md_temperature, md_pressure, trj_interval, md_save_trj, gpu, procs, write_vel=False, md_enegry_interval=None, md_save_enegrp=False, energy_groups=`[]`)

Write the .msj file and form the command for running the molecular dynamics simulation at a specific temperature.

Parameters:

name_base (base name for the md job) - str
icms (input cms filename) - str
md_time (md simulation time in ps) - float
md_timestep (md timestep in ps) - float
md_emsemble (md ensemble) - str
md_temperature (md temperature in K) - float
md_pressure (md pressure in bar) - float
trj_interval (time interval for trj output in ps) - float
md_save_trj (save trj folder, if True) - bool
gpu (request gpu, if True) - bool
procs (number of processors) - int
write_vel (record velocity in trj frame, if True) - bool
md_enegry_interval (time interval for energy group output) - float or None
md_save_enegrp (save the enegry_file, if True) - bool
energy_groups (list of keywords for desmond energy_groups) - list of str

Returns: str, str, str, str

cmd command to submit md, output cms, trj folder, enegrp file

trim_parser_skip_md(options, extra=`[]`)

If md is skipped, delete any options for setting up molecular dynamics simulation.

Parameters:

options (Parsed command options) - Named tuple
extra (extra flags to be deleted) - list of str

Returns: options: Named tuple

Parsed command options with no md flags

add_parser_opts(parser, final_prop, mid_prop, extra_options=`[]`)

Add all necessary parser arguments for setting up a MD simulation and optional arguments for certain green-kubo property calculation.

Parameters:

parser (argparse.ArgumentParser) - The parser for error information
final_prop (the final property needs to be calculated) - str
mid_prop (the property needs to be calculated before the final prop) - str
extra_options (extra options can be added according to these keywords) - list of str

check_options(opts, parser, option_flag, min_data_point)

Validate the options.

Parameters:

opts (Named tuple) - The parsed command line options
parser (argparser.ArgumentParser) - parser to log error information
option_flag (str) - time interval is defined by this flag
min_data_point (int) - minimum required data point

Variables Details

[hide private]

doc

Value:

"""
Equilibrium molecular dynamics classes/function shared by transport
property calculations using Einstein and Green-Kubo methods.

Copyright Schrodinger, LLC. All rights reserved.
"""

DIFFUSIVITY_PROP_KEY

Value:

'r_matsci_Diffusion_Coefficient_%s_(m^2/s)'

DIFFUSIVITY_TAU_START_PROP_KEY

Value:

'r_matsci_Diffusion_Coefficient_%s_Tau_Start_(ns)'

DIFFUSIVITY_TAU_END_PROP_KEY

Value:

'r_matsci_Diffusion_Coefficient_%s_Tau_End_(ns)'

VISCOSITY_TAU_START_PROP_KEY

Value:

'r_matsci_%s_Viscosity_%s_Tau_Start_(ns)'

VISCOSITY_TAU_END_PROP_KEY

Value:

'r_matsci_%s_Viscosity_%s_Tau_End_(ns)'

TRJ_PROP_KEYS

Value:

['s_m_original_cms_file', 's_chorus_trajectory_file']

ARG_DEFAULTS

Value:

{'-block_num': 1,
 '-md_enegry_interval': 0.01,
 '-md_pressure': 1.01325,
 '-md_temperature': 300.0,
 '-md_time': 1.0,
 '-md_timestep': 1.0,
 '-md_trj_interval': 1.0,
 '-sel': 'all',
...

ALL_MD_FLAGS

Value:

['-md_ensemble',
 '-md_temperature',
 '-md_pressure',
 '-md_time',
 '-md_timestep',
 '-md_trj_interval',
 '-md_save_trj']

Module equilibrium_md

check_file_exist(path_file)

get_files_from_folder(folder_abs_path)

get_md_results(basename, log, log_error, opts, **kwargs)

setup_md_job(name_base, icms, md_time, md_timestep, md_emsemble, md_temperature, md_pressure, trj_interval, md_save_trj, gpu, procs, write_vel=False, md_enegry_interval=None, md_save_enegrp=False, energy_groups=[])

trim_parser_skip_md(options, extra=[])

add_parser_opts(parser, final_prop, mid_prop, extra_options=[])

check_options(opts, parser, option_flag, min_data_point)

__doc__

DIFFUSIVITY_PROP_KEY

DIFFUSIVITY_TAU_START_PROP_KEY

DIFFUSIVITY_TAU_END_PROP_KEY

VISCOSITY_TAU_START_PROP_KEY

VISCOSITY_TAU_END_PROP_KEY

TRJ_PROP_KEYS

ARG_DEFAULTS

ALL_MD_FLAGS

setup_md_job(name_base, icms, md_time, md_timestep, md_emsemble, md_temperature, md_pressure, trj_interval, md_save_trj, gpu, procs, write_vel=False, md_enegry_interval=None, md_save_enegrp=False, energy_groups=`[]`)

trim_parser_skip_md(options, extra=`[]`)

add_parser_opts(parser, final_prop, mid_prop, extra_options=`[]`)

doc