Module energygroup

Module for calculating and retriving energy components from Desmond's vrun program.

Classes

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EnergyComponent
Class for storing different energy components.

PairDict
PairDict is a special dictionary that treats pairs with the same element as equals, independent of order.

_Group

EnergyGroupAnalysis
General Energy Group analysis class.

MSEnergyGroupAnalysis
Material Science energy group analysis module

EnergyGroup
A tool to calculate group-group interaction.

MSEnergyGroup
A tool to calculate material-science related energy analyses

Functions

[hide private]

sea.Map

get_orig_cfg(desmond_cfg)
Read in the cfg file and return 'ORIG_CFG' block as an ark.map object

str

get_ensemble_type(ark_obj)
extract ensemble type from the original cfg block

float

get_target_pressure(ark_obj)
Extract target pressure type for NPT from ORIG_CFG block

float

get_temperature(ark_obj)
Extract target simulation temperature from the original cfg block Use 300K by default.

Variables

[hide private]

logger = log.get_output_logger("energygroup")

ENERGY_GROUP_PREFIX = 'i_ffio_grp_energy'

__package__ = 'schrodinger.application.desmond'

Function Details

[hide private]

get_orig_cfg(desmond_cfg)

Read in the cfg file and return 'ORIG_CFG' block as an ark.map object

Parameters:

desmond_cfg (str) - cfg filename

Returns: sea.Map

'ORIG_CFG' ark object

get_ensemble_type(ark_obj)

extract ensemble type from the original cfg block

Parameters:

ark_obj (sea.Map) - 'ORIG_CFG' block as ark object

Returns: str

ensemble type

get_target_pressure(ark_obj)

Extract target pressure type for NPT from ORIG_CFG block

Parameters:

ark_obj (sea.Map) - 'ORIG_CFG' block as ark object

Returns: float

pressure in Atm units

get_temperature(ark_obj)

Extract target simulation temperature from the original cfg block Use 300K by default.

Parameters:

ark_obj (sea.Map) - 'ORIG_CFG' block as ark object

Returns: float

temperature in Kelvin