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Dacapo

Package Dacapo :: Module dacapo_new :: Class Dacapo
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Class Dacapo

Collection --+    
             |    
    Simulation --+
                 |
                Dacapo

Implementation of the Dacapo DFTCalculator interface.
Method Summary
  __init__(self, calculator, atoms, out, txtout, infile, nbands, xc, kpts, spinpol, planewavecutoff, usesymm)
Dacapo(...) -> DFT Dacapo calculator.
  __del__(self)
  Calculate(self)
  CalculateAtomicDOS(self, energywindow)
  CalculateStress(self)
set NetCDF entry so stress will be calculated
  DeleteNetCDFEntry(self, variable)
  DipoleCorrection(self, MixingParameter, InitialValue, AdditiveDipoleField)
This methods helps setting up the Dipole Correction scheme See the NetCDF documentation for the details.
  GetAtomsCounter(self)
  GetAttrName(self, variable)
  GetBZKPoints(self)
Return the k-points.
  GetCartesianForces(self)
Return the forces for the current state of the ListOfAtoms.
  GetDensityArray(self, spin)
Return array of density values.
  GetEigenvalues(self, kpt, spin)
Return the eigenvalues for all bands.
  GetIBZKPoints(self)
Return k-points in the irreducible part of the Brillouin zone.
  GetIBZKPointWeights(self)
Weights of the k-points.
  GetLDOS(self, **keywords)
return an instance of AtomProjectedDOSTool From John Kitchen.
  GetListOfAtoms(self)
Return the ListOfAtoms.
  GetNetCDFEntry(self, variable, att)
return the value of NetCDF entry <variable> or the value of <variable>.<attribute> if attribute is given
  GetNumberOfBands(self)
Return the number of bands.
  GetOccupationNumbers(self, kpt, spin)
Return the occupation numbers for all bands.
  GetPlaneWaveCutoff(self)
  GetPotentialEnergy(self)
Return the energy for the current state of the ListOfAtoms.
  GetPseudoPotential(self, Z)
  GetPseudoPotentials(self)
  GetSpinPolarized(self)
Is it a spin-polarized calculation?
  GetStress(self)
Return the stress for the current state of the ListOfAtoms.
  GetWavefunction(self, band, kpt, spin)
  GetWavefunctionArray(self, band, kpt, spin)
Return array of wavefunction values.
  GetWavefunctionArrayMethod(self, wavefunction, kpoint)
a function object for calculating the real space representation of the wavefunction is returned
  GetWavefunctionArrays(self, kpt, spin)
Return array of wavefunction values for all bands.
  GetWavefunctions(self)
  GetXCEnergies(self, *functional)
This function returns the self-consistent energy and/or energies associated with various functionals.
  GetXCFunctional(self)
Return the XC-functional identifier.
  ReadAtoms(self, filename)
Start from a Dacapo NetCDF file.
  ReadListOfAtoms(self, index)
Method to read data from the NetCDF entries attached to the calculator into the ListOfAtoms attached to the calculator.
  SetAtomsCounter(self, counter)
  SetBZKPoints(self, bzkpts)
Set the scaled k-points.
  SetElectrostaticDecoupling(self, numberofgaussians, ecutoff, widthofgaussian)
Add electrostatic decoupling, Jan Rossmeisl
  SetNetCDFEntry(self, variable, value, dim, att, series)
define a general netcdf entry for this calculation.
  SetNetCDFFile(self, ncfile)
  SetNumberOfBands(self, nbands)
  SetPlaneWaveCutoff(self, cutoff)
  SetPseudoPotential(self, Z, path)
  SetPseudoPotentials(self, pseudopotentials)
  SetSpinPolarized(self, spinpol)
Is it a spin-polarized calculation?
  SetSymmetryOff(self)
  SetSymmetryOn(self)
  SetTxtFile(self, txtfile)
  SetXCFunctional(self, xc)
  StartFromCalculator(self, calculator)
Get stuff from a calculator.
  StayAliveOff(self)
  StayAliveOn(self)
  Update(self, object)
  WriteAsNetCDFFile(self, filename)
Method to create a netcdf file from the current calculator.
  WriteListOfAtoms(self)
Method to write ListOfAtoms data to a netcdffile.
    Inherited from Simulation
  __getinitargs__(self)
  __getstate__(self)
  __repr__(self)
  __setstate__(self, state)
  __str__(self)
  Execute(self, outfile, ascii, scratch, infile, stopfile, nonblocking)
Method to perform a dacapo run.
  ExecuteExternalDynamics(self, outfile, infile, ascii, scratch, stopfile, stopprogram)
Method for running dacapo as an external force calculator.
  GetExecuteMethod(self, outfile, infile, ascii, scratch, stopfile, dynamics, stopprogram)
Method for generating a function pointer to the Execute method.
  GetHSMatrix(self)
calculate Hamiltonian matrix and overlab matrix for the current set of wavefunctions
  GetJobType(self)
  GetName(self)
  GetTkManipulator(self, parent, name)
  GetwxManipulator(self, parent, name)
  reprWithName(self, name)
  RestartDacapo(self)
set a flag telling that dacapo should be restarted on next call of Calulate
  SetJobType(self, jobtype)
  UpdateFromNetCDFFile(self, filename, index)
Method to read data to attributes from a netcdf file
    Inherited from Collection
  __delattr__(self, name)
  __setattr__(self, name, value)
  ReadFromNetCDFFile(self, file, index)
Method to read all non private attributes from a netcdffile.
  WriteToNetCDFFile(self, file)
Method to write all non private attributes to a netcdffile.

Method Details

__init__(self, calculator=None, atoms=None, out='out.nc', txtout='out.txt', infile=None, nbands=None, xc=None, kpts=None, spinpol=None, planewavecutoff=None, usesymm=None)
(Constructor)

Dacapo(...) -> DFT Dacapo calculator.

The calculator can be constructed from a file, from another calculator, or from scratch giving all the necessary parameters (or a combination).

Overrides:
Dacapo.Simulation.Simulation.__init__

CalculateStress(self)

set NetCDF entry so stress will be calculated

DipoleCorrection(self, MixingParameter=0.20000000000000001, InitialValue=0.0, AdditiveDipoleField=0.0)

This methods helps setting up the Dipole Correction scheme See the NetCDF documentation for the details. From John Kitchen's DipoleCorrection class.

GetBZKPoints(self)

Return the k-points.

GetCartesianForces(self)

Return the forces for the current state of the ListOfAtoms.

GetDensityArray(self, spin=0)

Return array of density values.

GetEigenvalues(self, kpt=0, spin=0)

Return the eigenvalues for all bands.

GetIBZKPoints(self)

Return k-points in the irreducible part of the Brillouin zone.

GetIBZKPointWeights(self)

Weights of the k-points.

The sum of all weights is one.

GetLDOS(self, **keywords)

return an instance of AtomProjectedDOSTool From John Kitchen.

GetListOfAtoms(self)

Return the ListOfAtoms.

GetNetCDFEntry(self, variable, att=None)

return the value of NetCDF entry <variable> or the value of <variable>.<attribute> if attribute is given

GetNumberOfBands(self)

Return the number of bands.

GetOccupationNumbers(self, kpt=0, spin=0)

Return the occupation numbers for all bands.

These numbers fall in the range [0,1] for a spin-polarized calculation, and in the range [0,2] otherwise.

GetPotentialEnergy(self)

Return the energy for the current state of the ListOfAtoms.

GetSpinPolarized(self)

Is it a spin-polarized calculation?

GetStress(self)

Return the stress for the current state of the ListOfAtoms. If the calculation is not up-to-date or the stress has not been calculated the calculation is rerun

GetWavefunctionArray(self, band, kpt=0, spin=0)

Return array of wavefunction values.

GetWavefunctionArrayMethod(self, wavefunction, kpoint)

a function object for calculating the real space representation of the wavefunction is returned

GetWavefunctionArrays(self, kpt=0, spin=0)

Return array of wavefunction values for all bands.

GetXCEnergies(self, *functional)

This function returns the self-consistent energy and/or energies associated with various functionals. The functionals are currently PZ,VWN,PW91,PBE,revPBE, RPBE. The different energies may be useful for calculating improved adsorption energies as in B. Hammer, L.B. Hansen and J.K. Norskov, Phys. Rev. B 59,7413. Examples: GetTotalPotentialEnergy() #returns the self-consistent total energy as before. GetTotalPotentialEnergy('PBE') # returns the PBE total energy GetTotalPotentialEnergy('PW91','PBE','revPBE') # returns a list of energies in the order asked for

The function should be backwards compatible with the old GetTotalPotentialEnergy. Written with assistance from Lars Hansen and Asbjorn Christensen

John Kitchin <jkitchin@udel.edu>

GetXCFunctional(self)

Return the XC-functional identifier. 'LDA', 'PBE', ...

ReadAtoms(self, filename)

Start from a Dacapo NetCDF file.

All existing NetCDF variables <variable> will be defined through either the default DFT methods, or via the GetNetCDFEntry.

ReadListOfAtoms(self, index=None)

Method to read data from the NetCDF entries attached to the calculator into the ListOfAtoms attached to the calculator. The NetCDF entries attached to the calculator are updated.

SetBZKPoints(self, bzkpts)

Set the scaled k-points.

kpts should be an array of scaled k-points.

SetElectrostaticDecoupling(self, numberofgaussians=3, ecutoff=100, widthofgaussian=0.34999999999999998)

Add electrostatic decoupling, Jan Rossmeisl

SetNetCDFEntry(self, variable, value=None, dim=None, att=None, series=None)

define a general netcdf entry for this calculation. The entry is added as calc._<variable> = NetCDF.Entry, If the entry is allready defined, only the value are modified.

SetSpinPolarized(self, spinpol)

Is it a spin-polarized calculation?

StartFromCalculator(self, calculator)

Get stuff from a calculator.

Try to get information from a general calculator: The listofatoms, the k-points, the number of bands, whether it is a spinpolarized calculation, and the functional to use for exchange-correlation. In addition check for dacapo specific methods.

WriteAsNetCDFFile(self, filename)

Method to create a netcdf file from the current calculator.

This method asks all the attributes of the instance to write them down in the file with the given filename.

Overrides:
Dacapo.Simulation.Simulation.WriteAsNetCDFFile

WriteListOfAtoms(self)

Method to write ListOfAtoms data to a netcdffile. No writing is done, this is done by the WriteAsNetCDF method.

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Dacapo

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