Equilibrium molecular dynamics classes/function shared by transport
property calculations using Einstein and Green-Kubo methods.
Copyright Schrodinger, LLC. All rights reserved.
None or str
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list of tuple
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str, str, str or None
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get_md_results(basename,
log,
log_error,
opts,
**kwargs)
From parsed options, setup and run md simulation. |
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str, str, str, str
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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. |
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options: Named tuple
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trim_parser_skip_md(options,
extra=[ ] )
If md is skipped, delete any options for setting up molecular
dynamics simulation. |
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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. |
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check_options(opts,
parser,
option_flag,
min_data_point)
Validate the options. |
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__doc__ = ...
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PROGRAM_NAME_DIFFUSION = ' Diffusion Coefficient '
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DEFAULT_JOBNAME_DIFFUSION = ' diffusion_coefficient '
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PROGRAM_NAME_VISCOSITY = ' Visosity '
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DEFAULT_JOBNAME_VISCOSITY = ' viscosity '
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CUBIC_SPLINE = ' cubic spline '
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PICOSECOND = 1e-12
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FEMTO2PICO = 0.001
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NANO2PICO = 1000.0
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ANGSTROM2M = 1e-10
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TAU_START_PROP_KEY_BASE = ' Tau_Start_(ns) '
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TAU_END_PROP_KEY_BASE = ' Tau_End_(ns) '
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DIFFUSIVITY_UNIT = ' m^2/s '
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DIFFUSION_UNIT_CONVERT = 1e-08
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DIFFUSIVITY_PROP_KEY_BASE = ' r_matsci_Diffusion_Coefficient_%s_ '
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DIFFUSIVITY_PROP_KEY = ' r_matsci_Diffusion_Coefficient_%s_(m^2 ...
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DIFFUSIVITY_TAU_START_PROP_KEY = ' r_matsci_Diffusion_Coefficie ...
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DIFFUSIVITY_TAU_END_PROP_KEY = ' r_matsci_Diffusion_Coefficient ...
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VISCOSITY_UNIT = ' Pa.s '
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VISCOSITY_PROP_KEY_BASE = ' r_matsci_%s_Viscosity_%s_ '
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VISCOSITY_PROP_KEY = ' r_matsci_%s_Viscosity_%s_(Pa.s) '
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VISCOSITY_TAU_START_PROP_KEY = ' r_matsci_%s_Viscosity_%s_Tau_S ...
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VISCOSITY_TAU_END_PROP_KEY = ' r_matsci_%s_Viscosity_%s_Tau_End ...
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TRJ_EXT = ' trj '
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INPUT_FILE = ' -icms '
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FLAG_ATOM_SELECTION = ' -sel '
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FLAG_ENSEMBLE = ' -md_ensemble '
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NVE = ' NVE '
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NVT = ' NVT '
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NPT = ' NPT '
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ENSEMBLE = [ ' NVE ' , ' NVT ' , ' NPT ' ]
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FLAG_MD_TEMP = ' -md_temperature '
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FLAG_MD_PRESSURE = ' -md_pressure '
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FLAG_MD_TIME = ' -md_time '
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FLAG_MD_TIMESTEP = ' -md_timestep '
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FLAG_MD_TRJ_INTERVAL = ' -md_trj_interval '
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FLAG_MD_SAVE_TRJ = ' -md_save_trj '
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FLAG_SKIP_MD = ' -md_skip '
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FLAG_TRJ_START = ' -trj_start '
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FLAG_TAU_START = ' -tau_start '
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FLAG_TAU_END = ' -tau_end '
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FLAG_TRJ_FOLDER = ' -trj_folder '
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TRJ_PROP_KEYS = [ ' s_m_original_cms_file ' , ' s_chorus_trajectory ...
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FLAG_ENEGRP_FILE = ' -enegrp_file '
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FLAG_ENEGRP_INTERVAL = ' -md_enegry_interval '
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FLAG_MD_SAVE_ENEGRP = ' -md_save_enegrp '
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FLAG_GPU = ' -gpu '
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FLAG_BLOCK_NUM = ' -block_num '
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FLAG_VARIATION = ' -variation '
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STD_FILE_EXT = ' _block_std '
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MIN_TIME_NS = 0.01
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MAX_TIMESTEP_FS = 100
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MIN_TIMESTEP_FS = 0.01
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MAX_TRJ_FRAME_START = 1000000
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ARG_DEFAULTS = { ' -block_num ' : 1, ' -md_enegry_interval ' : 0.01, ...
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ALL_MD_FLAGS = [ ' -md_ensemble ' , ' -md_temperature ' , ' -md_pressu ...
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MAX_TIME_NS = 100
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__package__ = ' schrodinger.application.matsci '
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