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

Class MSEnergyGroupAnalysis

EnergyGroupAnalysis --+
                      |
                     MSEnergyGroupAnalysis

Material Science energy group analysis module

Instance Methods

[hide private]

__init__(self, cst, trjfile, orig_cfgfile, groups, volume=False, pressure_tensor=False, specific_heat=False)
Initialize

getVolumeTimeSeries(self)
Return volume series

getPressureTensorTimeSeries(self)
Return pressure tensor series

getEnergyTimeSeries(self)
return energy values

float

_calculate_specific_heat(self, Etot, last_n_percent)
Calculates specific heat for NVT (Cv) and NPT (Cp) ensembles.

float

_calculate_specific_heat_nve(self, Ekin, last_n_percent=100.0)
Calculates specific heat for NVE (Cv)

getSpecificHeatType(self)

getResultsForLastNPercent(self, energy, function)
Function that calculates the specific heat for the last N percent of the trajectory.

getSpecificHeat(self)

_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.

(float, float)

_processFramePressureTensor(self, line)
process lines that look like this: Pressure_Tensor(4.800000) -1138.7 39.734 300.07 116.98 -1124.3 -120.67 259.95 -65.07 -963.18

_parseHeaderLine(self, line)
Parses header line that looks like this:...

(float, float)

_processFrameVolume(self, line)
processes line that looks like this, extracts V, volume time=19.2 en=3.641e+04 E_p=-1.937e+02 E_k=7.039e+03 E_x=1.071e+02 P=5.999e+02 V=9.654+04

(float, float, float)

_processFrameSpecificHeat(self, line)
parses the header of every timestep in the energy group file time=19.2 en=3.641e+04 E_p=-1.937e+02 E_k=7.039e+03 E_x=1.071e+02 P=5.999e+02 V=9.654+04 we just want the timestep, potential and kinetic energies

_processFramePressure(self, line)

_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

Static Methods

[hide private]

int

_getStartIndex(nframes, last_n_percent)
Returns starting index of the last N percent of the frames

Class Variables

[hide private]

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

bulk_pattern = '(time)'

pressure_tensor_pattern = '(Pressure_Tensor)'

MAX_NGROUPS_SUPPORTED = 870

KCAL_TO_J = 4184.0

R_GAS_CONSTANT = 8.314472

Inherited from EnergyGroupAnalysis: floating_number_pattern

Method Details

[hide private]

init(self, cst, trjfile, orig_cfgfile, groups, volume=False, pressure_tensor=False, specific_heat=False)
(Constructor)

Initialize

Parameters:

cst (Structure) - Structure of the sys (full_system ct)
trjfile (str) - Cms filename that contains links to the trajectory
orig_cfgfile (str) - a configuration file that is outputted by an md job which contains an ORIG_CFG block
groups (EnergyGroup) - Energy group definitions for a given system
volume (bool) - bool to extract the volume of the system
pressure_tensor (bool) - bool to extract the pressure of the system
specific_heat (bool) - bool to calculate Cp or Cv for a given bulk sys

Overrides: EnergyGroupAnalysis.__init__

getEnergyTimeSeries(self)

return energy values

Overrides: EnergyGroupAnalysis.getEnergyTimeSeries

_getStartIndex(nframes, last_n_percent)
Static Method

Returns starting index of the last N percent of the frames

Parameters:

nframes (int) - total number of frames in the simulation
last_n_percent (float) - return results for N% of the trajectory

Returns: int

the start index for array analysis.

_calculate_specific_heat(self, Etot, last_n_percent)

Calculates specific heat for NVT (Cv) and NPT (Cp) ensembles.

Parameters:

E (numpy.array) - total energy
last_n_percent (float) - report results for N last percent

Returns: float

Cp or Cv for last N percent

_calculate_specific_heat_nve(self, Ekin, last_n_percent=100.0)

Calculates specific heat for NVE (Cv)

Parameters:

Ekin (numpy.array) - kinetic energy
last_n_percent (float) - report results for N last percent

Returns: float

Cv for last N percent

getResultsForLastNPercent(self, energy, function)

Function that calculates the specific heat for the last N percent of the trajectory.

Parameters:

energy (numpy.array) - numpy.array of energies, depending on ensemble
function (???) - function that calculates specific heat

_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.

_processFramePressureTensor(self, line)

process lines that look like this: Pressure_Tensor(4.800000) -1138.7 39.734 300.07 116.98 -1124.3 -120.67 259.95 -65.07 -963.18

Parameters:

line (str) - a pressure tensor line that comes from engrp file

Returns: (float, float)

a tuple of chemical time and corresponding list of nine pressure tensors

_parseHeaderLine(self, line)


Parses header line that looks like this:
     time=19.2 en=3.641e+04 E_p=-1.937e+02 E_k=7.039e+03                                     E_x=1.071e+02 P=5.999e+02 V=9.654+04
and returns a dictionary of values
@param line: a frame header str that comes from engrp file
@type  line: str
@return: a dictionary of key/values pairs
@rtype: dict

_processFrameVolume(self, line)

processes line that looks like this, extracts V, volume time=19.2 en=3.641e+04 E_p=-1.937e+02 E_k=7.039e+03 E_x=1.071e+02 P=5.999e+02 V=9.654+04

Parameters:

line (str) - a str that comes from engrp file

Returns: (float, float)

a tuple of chemical time and corresponding volume

_processFrameSpecificHeat(self, line)

parses the header of every timestep in the energy group file time=19.2 en=3.641e+04 E_p=-1.937e+02 E_k=7.039e+03 E_x=1.071e+02 P=5.999e+02 V=9.654+04 we just want the timestep, potential and kinetic energies

Parameters:

line (str) - a str that comes from engrp file

Returns: (float, float, float)

a tuple of chemical time and corresponding potential and kinetic energies

_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=False, pressure_tensor=False, specific_heat=False) (Constructor)

getEnergyTimeSeries(self)

_getStartIndex(nframes, last_n_percent) Static Method

_calculate_specific_heat(self, Etot, last_n_percent)

_calculate_specific_heat_nve(self, Ekin, last_n_percent=100.0)

getResultsForLastNPercent(self, energy, function)

_processFrameEne(self)

_processFramePressureTensor(self, line)

_parseHeaderLine(self, line)

_processFrameVolume(self, line)

_processFrameSpecificHeat(self, line)

_parseOutput(self, filename)

_calcEnergy(self)

energy_term_pattern

init(self, cst, trjfile, orig_cfgfile, groups, volume=False, pressure_tensor=False, specific_heat=False)
(Constructor)

_getStartIndex(nframes, last_n_percent)
Static Method