Package schrodinger :: Package application :: Package desmond :: Module energygroup :: Class MSEnergyGroupAnalysis

Class MSEnergyGroupAnalysis

EnergyGroupAnalysis --+
                      |
                     MSEnergyGroupAnalysis

Material Science energy group extension

Instance Methods

[hide private]

__init__(self, cst, trjfile, orig_cfgfile, groups, volume, pressure)
Initialize

getVolumeTimeSeries(self)
Return volume series

getPressureTimeSeries(self)
Return pressure series

getEnergyTimeSeries(self)
return energy values

_processFrameEne(self)
In order to reduce the amount of memory holding all the energy groups for every frame, we will process energies for each frame as we parse the .ene file.

_parseOutput(self, filename)
Parse output from vrun to retrieve energy.

_calcEnergy(self)

Inherited from EnergyGroupAnalysis: getGroups

Inherited from EnergyGroupAnalysis (private): _cleanup, _launchVrun, _prepareCfg, _prepareCmsfile, _processLine, _sort_dict

Class Variables

[hide private]

energy_term_pattern = '(far_terms|nonbonded_elec|nonbonded_vdw...

bulk_pattern = '(time)'

pressure_pattern = '(Pressure_Tensor)'

MAX_NGROUPS_SUPPORTED = 512

Inherited from EnergyGroupAnalysis: floating_number_pattern

Method Details

[hide private]

init(self, cst, trjfile, orig_cfgfile, groups, volume, pressure)
(Constructor)

Initialize

Overrides: EnergyGroupAnalysis.__init__: (inherited documentation)

getEnergyTimeSeries(self)

return energy values

Overrides: EnergyGroupAnalysis.getEnergyTimeSeries

_processFrameEne(self)

In order to reduce the amount of memory holding all the energy groups for every frame, we will process energies for each frame as we parse the .ene file. So self.energy_series should energy pairs for one frame at a time.

_parseOutput(self, filename)

Parse output from vrun to retrieve energy.

Overrides: EnergyGroupAnalysis._parseOutput

_calcEnergy(self)

Overrides: EnergyGroupAnalysis._calcEnergy

Class Variable Details

[hide private]

energy_term_pattern

Value:

'(far_terms|nonbonded_elec|nonbonded_vdw|Total)'

Class MSEnergyGroupAnalysis

__init__(self, cst, trjfile, orig_cfgfile, groups, volume, pressure) (Constructor)

getEnergyTimeSeries(self)

_processFrameEne(self)

_parseOutput(self, filename)

_calcEnergy(self)

energy_term_pattern

init(self, cst, trjfile, orig_cfgfile, groups, volume, pressure)
(Constructor)