3.1   Number of bands and Electronic temperature

The method 'SetNumberOfBands(nbands)' can be used to define the number of bands for the calculatior. nbands should be a least equal to halv the number of valence electrons.

The occupation statitstics can be set using the method SetOccupationStatistics(method).

dacapo support two methods for occupation statistics:

FermiDirac:

Fermi-Dirac occupation statistics. The temperature is controlled by the method SetElectronicTemperature(temp). Default is 0.1 eV.

MethfesselPaxton:

Currently, the Methfessel-Paxton scheme (PRB 40,3616, 1989) is implemented to 1st order.

3.2   Planewave and Density-cutoff

The method SetPlaneWaveCutoff(planewavecutoff) defines the plavewave cutoff for the calculation. The unit for planewavecutoff is eV.

The method SetDensityCutoff(densitycutoff) sets the density cutoff. By default the two cutoffs are equal, corresponding to using just one grid. For elements like Cu using ultra-soft pseudo potentials the ultra-soft pseudo-wavefunction are very soft, while the density still requires a fine grid, in this case it can be advantagous to set a larger value for densitycutoff that for planewavecutoff.

3.3   Changing file names

The following two methods can be use to change the file names used by dacapo:

SetNetCDFFile(filename):

This will set the NetCDF filename, default is 'out.nc'.

SetTxtFile(filename)

This will set the Ascii text file name, default is 'out.txt'. For information on the most inportant data in the Ascii file see dacapo Ascii file.

The method:

SetScratch(scratchdir):

will set the scratch directory used for swapfiles to scratchdir. Default for this directory is /scratch/<username> or if this is not found just /scratch.

calc.SetExecutable('dacapo_2.7.8.run')
calc.infile = '/scratch/<username>/in.nc'
calc.SetNetCDFFile('/scratch/<username>/out.nc')
calc.SetTxtFile('out.txt')

3.4   Exchange-correlation functional

You can use the method SetXCFunctional(exc) to select the exchange-correlation used for the calculation. exc is one of:

LDA:

Vosko Wilk Nusair LDA-parametrization.

PW91:

Perdew Wang 91 GGA-parametrization.

PBE:

Perdew Burke Ernzerhof GGA-parametrization.

RPBE:

Revised PBE GGA-parametrization, Hammer, Hansen and Nørskov.

The method:

GetXCFunctional

tells which of the above defined exchange-correlation functionals are currently used.

The method:

GetXCEnergies(xcname)

return the non-selfconsistent energy for the given xcname (PBE,RPBE,PW91,VWN).

3.5   Defining a spin-polarized calculation

One can use the method SetSpinPolarized(True) to tell dacapo that the calculation should be spin-polarized.

One also need to specify an initial magnetic moment for the atoms. You can do this in the construction of the atoms, by using:

>>> from ASE import Atom, ListOfAtoms
>>> atoms = ListOfAtoms([Atom('O', (0, 0, 0),magmom=1.0),
...                      Atom('O', (0, 0, 1.2),magmom=1.0)])

This can also be set using the ListOfAtoms method SetMagneticMoments((1,1)) or setting the SetMagneticMoment method on each atom.

This will define an initial total magnetic moment of 2 Bohr magneton, for the O2 molecule, this being also the self-consistent result. You could also use, SetMagneticMoments((1,-1)), this will define a 'anti-ferro' magnetic state with total magnetic moment of zero. If this case probably the end result is still the same (2 Bohr magneton) but the number of self-consistent iterations will increase.

It is also possible to constrain the magnetic moment using the method:

calc.SetSpinPolarized(spinpol=True, fixmagmom=2)

3.6   K-points

The method SetBZKPoints(kpts) can be used to define the k-points in the BZ. In general kpts are a python list of k-points defined in units of the reciprocal cell. You can however specify a 10x10x10 Monkhorst-Pack 3dimensional set simple by using SetBZKpoint((10,10,10)).

Below is a list of the special k-points sets that can be used:

MonkhorstPack:

A 3-dimensional Monkhorst-Pack special k-point set. (see H.J.Monkhorst and J.D.Pack, Physical Review B, vol. 13, page 5188, 1976. You can defined this k-points set simply using, SetBZKPoints((n1,n2,n3)). This will define a n1 by n2 by n3, Monkhorst Pack special k-point set. The size along each reciprocal vector given by n1, n2 and n3, respectively.

ChadiCohen:

A Chadi-Cohen (see Chadi and Cohen, Phys. Review B., vol 8,page 5747) 1-dimensional k-point can be defined using the ASE Utilities module ChadiCohen:

>>> from ASE.Utilities.ChadiCohen import CC6_1x1
>>> calc.SetBZKPoints(CC6_1x1)

This will define a 6 k-point 1x1 Chadi-Cohen special k-point set. In general the Chadi-Cohen sets are named CC+'<Nkpoints>'+_+'shape'. For example an 18 k point sq(3)xsq(3) is named 'CC18_sq3xsq3'.

You can use the method GetBZKPoints, to access the k-points just defined. The method GetIBZKPoints returns the symmetry reduced set of k-points.

3.7   Pseudo-potentials

For an overview of the pseudopotentials for dacapo, see the Pseudopotential Library page.

You can change or view the pseudopotentials use for an element using the methods:

GetPseudoPotential(<elementnumber>):

View the pseudopotential path for element elementnumber.

SetPseudoPotential(<elementnumber>, filename):

Set the pseudopotential filename for element elementnumber.

Note that in order to access new, generated pseudopotential files, an entry is needed in Dacapo/PseudoPotentials.py.

3.8   Charge-density mixing

The method SetChargeMixing(value) can be used to enable or disable charge density mixing.

Using SetChargeMixing(True) the program will use Pulay mixing for the density (default).

You can change the Pulay density mixing coeffficient (default 0.1) and the Pulay mixing history (default 10) using:

calc.SetNetCDFEntry("ChargeMixing",att="Pulay_DensityMixingCoeff",value=0.1)
calc.SetNetCDFEntry("ChargeMixing",att="Pulay_MixingHistory",value=10)

Using SetChargeMixing(False) correspond to running a calculation using the Harris-Foulkes functional using the input density. See also the Harris calculation example.

The method SetKerkerPreconditioning(value) can be used to set Kerker preconditioning for the density mixing. For value=True Kerker preconditiong is used, i.e. q is different from zero, see eq. 82 in Kresse/Furthmller: Comp. Mat. Sci. 6 (1996). The value of q is fix to give a damping of 20 of the lowest q vector. For value=False q is zero and mixing is linear (default).

3.9   Eigenvalue solver

The eigenvalue solver can be set using the method SetEigenvalueSolver(method). Here method is one of:

1. eigsolve: Block Davidson algorithm (Claus Bendtsen et al). This is the default method.
2. rmm-diis: Residual minimization method (RMM), using DIIS (direct inversion in the iterate subspace). The implementation follows closely the algorithm outlined in Kresse and Furthmuller, Comp. Mat. Sci, III.G/III.H

3.10   Dipole-correction

The method:

DipoleCorrection(MixingParameter=0.2,InitialValue=0.0,AdditiveDipoleField=0)

will add the interslab dipole electrostatic decoupling. Presently, this feature is only active along the third unit cell vector, so you need to choose unit cell accordingly. Corrections for higher electrostatic multipoles are not implemented presently.

The default position of the field discontinuity at the vacuum position farthest from any other atoms on both sides of the slab.

The keyword AdditiveDipoleField, will add a constant electrostatic field along third unit cell vector, corresponding to an external dipole layer. This field is added to the dipole correction field. The field discontinuity follows the position of the dynamical dipole correction.

See also the Dipole correction example and the workfunction pdf document. For more information see the dacapo netcdf manual.

A fixed external field i.e. not a field added on top the the dipole correction, can be set using the NetCDF entry ExternalDipolePotential. This can be done like:

calc.SetNetCDFEntry("ExternalDipolePotential",value=0.5)

corresponding to an external field of 0.5eV/A.

3.11   Setting non-default executable

GetJobType:

SetJobType can be used to view the current executable for dacapo.

SetJobType(executable=newexecutable):

SetJobType can be used to change the default dacapo executable dacapo.run to newexecutable.

3.12   Symmetry

SetSymmetryOff:

Do not use symmtry then reducing the k-point set.

SetSymmetryOn:

Use symmtry then reducing the k-point set.

3.13   Electrostatic decoupling

SetElectrostaticDecoupling(numberofgaussians=3,ecutoff=100):

Add electrostatic decoupling (Jan Rossmeisl). Decoupling activates the three dimensional electrostatic decoupling. Based on paper by Peter E. Bloechl: JCP 103 page7422 (1995).

3.14   Stress calculation

By default dacapo will not calculate the stress acting on the unitcell, you can use the method:

CalculateStress()

to tell dacapo to calculate the stress.

3.15   Local density of states

Dacapo can calculate the density of states projected onto atomic orbitals.

Typically one would do:

atoms = ListOfAtoms(..)

calc = Dacapo(..)
calc.CalculateAtomicDOS()

atoms.SetCalculator(calc)

energy = atoms.GetPotentialEnergy()
dos = calc.GetLDOS(atoms=[1],angularchannels=[[s]])
dos.GetPlot()

This will return a density of states projected onto the s-orbital of the first atom (atom numbers starts from 1).

The method:

CalculateAtomicDOS(energywindow=None)

tells the fortran program to calculate the local density of states projected onto atomic orbitals, using energywindow for calculating the energy resolved LDOS in a specific range (must be within the eigenvalue spectrum).

The method:

``GetLDOS(**keywords )``:

returns an instance of AtomProjectedDOSTool (see below).

Keyword for the GetDOS method:

• atoms

  List of atoms numbers (default is all atoms)

• angularchannels

  List of angular channel names. The full list of names are: 's', 'p_x', 'p_y', 'p_z','d_zz','dxx-yy', 'd_xy', 'd_xz', 'd_yz'. 'p' and 'd' can be used as shorthand for all p and all d channels respectively. (default is all d channels)

• spin

  List of spins (default all spins)

• cutoffradius

  'short' or 'infinite'. For cutoffradius = 'short' the integrals are truncated at 1 Angstrom. For cutoffradius = 'infinite' the integrals are not truncated. (default 'infinite')

The resulting DOS are added over the members of the three list (atoms,angularchannels and spin).

GetDOS returns a instance of the class AtomProjectedDOSTool (Thanks to John Kitchen for providing grace plot and band moments methods).

Methods for AtomProjectedDOSTool:

GetPlot

returns a GnuPlotAvartar for the energy resolved DOS A parent can be given too combine plot.

GetIntegratedDOS

returns the integral up to the fermi energy

GetData

returns the energy resolved DOS

GetBandMoment(moments)

returns the moments of the projected DOS. GetBandMoment(0) return the integrated DOS. GetBandMoment(1,2) returns the first and second moment of the projected DOS (center and width)

SaveData(filename)

saves the data to the filename

GetGracePlot

makes a GracePlot (if GracePlot is installed)

Multicenter orbitals
````````````````````

You add the multicenter orbitals using:

mcenters = [(0,0,0,1.0),(1,0,0,-1.0)]
calc.SetMultiCenters(mcenters)

this will define an atom1_s-atom2_s orbital.

The general form is [{(atomnr,l,m,weight)}]

You can retrieve the centers using:

centers = calc.GetMultiCenters()

This will return a list of instances of the class MultiCenterProjectedDOSTool.

This class has the same method as described above, ie. GetBandMoment, `GetCutoff, GetData, GetDescription, GetEFermi, GetGracePlot, GetIntegratedDOS, GetPlot, GetSpin`and SaveData.

You can give the following keywords to SetMultiCenters:

calc.SetMultiCenters(mcenters,
                     energywindow=(-15,5),
                     energywidth=0.2,
                     numberenergypoints=250,
                     cutoffradius=1.0)

The direction cosines for which the spherical harmonics are set up are using the next different atom in the list (cyclic) as direction pointer, so the z-direction is chosen along the direction to this next atom. At the moment the rotation matrices is only given in the text file, you can use grep 'MUL: Rmatrix' out_o2.txt to get this information.

Below is a small example, which defines a s-orbital on atom 0:

#!/usr/bin/env python

from Dacapo import Dacapo
from ASE import Atom, ListOfAtoms

atoms = ListOfAtoms([Atom('O', (2,   2, 2)  ,magmom=1.0),
                     Atom('O', (3.1, 2, 2),magmom=1.0)],
                     cell=(4, 4, 4))

calc = Dacapo(planewavecutoff=350,    # in eV
              nbands=8,              # 5 extra empty bands
              out='o2.nc',
              spinpol=True )
atoms.SetCalculator(calc)


mcenters = []
mcenters.append([(0,0,0,1.0),(1,0,0,0.0)])     # [{(atomnr,l,m,weight)}]
calc.SetMultiCenters(mcenters,energywidth=0.1)

energy = atoms.GetPotentialEnergy()

centers = calc.GetMultiCenters()
center1 = centers[0]

print 'description:'
center1.GetDescription()

print 'energy resolved dos:'
for d in center1.GetData():
    print d[0],d[1]

3.16   Changing convergence parameters

The method:

SetConvergenceParameters(**keywords)

can be used to set convergence parameters for the calculations. The following keywords are defined:

• energy:

  Absolute convergence in energy (default 1e-5)

• density:

  Convergence in density (default 0.0001)

• occupation:

  Convergence in occupation numbers (default 0.001)

SetConvergenceParameters(energy=0.00001,density=0.0001,occupation=0.001) correspond to the default settings.

The method::

GetConvergenceParameters()

can be used to retrieve the convergence parameters.

3.17   dacapo fortran program/python interface communication

The method:

StayAliveOn()

can be used for normal optimization runs.

This will prevent the dacapo fortran program to terminate and write the full netcdf output file after each call of GetPotentialEnergy. Instead it will wait for python to send new positions. This way of running the program saves IO time and reduce the NFS traffic.

Do not use this mode for NEB calculations, you will end of having 10 fortran programs in memory.

3.18   NetCDF specific methods

Note: the size of the NetCDF file is limited to 2GB. Dacapo uses classic format of NetCDF files.

Two methods are defined for general reading and writing of NetCDF entries. This provides a method for reading and writing any NetCDF variable defined in the dacapo netcdf manual, so that any settings for the dacapo fortran program, not defined by the standard sets of method from the DFT Calculator or from the extra Dacapo method described above, can be defined. The methods are listed below:

SetNetCDFEntry(variable,att=None,value=None):

Define a general netcdf entry for this calculation. If the netcdf entry is allready defined, the value are modified.

GetNetCDFEntry(variable,att=None):

Returns the value of NetCDF entry <variable> or NetCDF attribute att, if specified.

The effect of writing:

>>> calc = Dacapo()
>>> calc.SetNumberOfBands(10)

and

>>> calc = Dacapo()
>>> calc.SetNetCDFEntry('ElectronicBands',att='NumberOfBands',value=10)

is the same. Now you can get the information by either using

>>> print calc.GetNumberOfBands()

or

>>> print calc.GetNetCDFEntry('ElectronicBands',att='NumberOfBands')

5.1   reading from an old calculation

If you want to restart a calculation or read specific information from an old calculation, one have to access the information via the atoms, using:

>>> atoms = Dacapo.ReadAtoms(filename='oldfile')

Now you can get the calculator, attached to the atoms, and get the information, using:

>>> calc = atoms.GetCalculator()
>>> print calc.GetEigenvalues()

Often ASE methods take the atoms as the argument, using the GetCalculator method to access the relevant information, i.e the VTK methods for 3D plotting:

>>> from ASE.Visualization.VTK import VTKPlotWaveFunction
>>> atoms = Dacapo.ReadAtoms(filename='oldfile')
>>> VTKPlotWaveFunction(atoms)