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Python: module ase.calculators.jacapo.jacapo

ase.calculators.jacapo.jacapo

index
/usr/local/lib/python2.7/dist-packages/ase/calculators/jacapo/jacapo.py

python module for ASE2-free and Numeric-free dacapo U{John Kitchin<mailto:jkitchin@andrew.cmu.edu>} December 25, 2008 This module supports numpy directly. * ScientificPython2.8 is required - this is the first version to use numpy by default. see https://wiki.fysik.dtu.dk/stuff/nc/ for dacapo netcdf variable documentation

Modules

ase.calculators.jacapo.changed
exceptions
glob

logging
numpy
os

pickle
subprocess
string

sys
ase.calculators.jacapo.validate

Classes

Jacapo

exceptions.Exception(exceptions.BaseException)

DacapoAbnormalTermination
DacapoAborted
DacapoDryrun
DacapoInput
DacapoRunning

class DacapoAbnormalTermination(exceptions.Exception)

Raised when text file does not end correctly

Method resolution order:: DacapoAbnormalTermination; exceptions.Exception; exceptions.BaseException; __builtin__.object

Data descriptors defined here:

__weakref__: list of weak references to the object (if defined)

Methods inherited from exceptions.Exception:

__init__(...): x.__init__(...) initializes x; see help(type(x)) for signature

Data and other attributes inherited from exceptions.Exception:

__new__ = <built-in method __new__ of type object>: T.__new__(S, ...) -> a new object with type S, a subtype of T

Methods inherited from exceptions.BaseException:

__delattr__(...): x.__delattr__('name') <==> del x.name

__getattribute__(...): x.__getattribute__('name') <==> x.name

__getitem__(...): x.__getitem__(y) <==> x[y]

__getslice__(...): x.__getslice__(i, j) <==> x[i:j] Use of negative indices is not supported.

__reduce__(...)

__repr__(...): x.__repr__() <==> repr(x)

__setattr__(...): x.__setattr__('name', value) <==> x.name = value

__setstate__(...)

__str__(...): x.__str__() <==> str(x)

__unicode__(...)

Data descriptors inherited from exceptions.BaseException:

__dict__

args

message

class DacapoAborted(exceptions.Exception)

Raised when ncfile.status = 'aborted'

Method resolution order:: DacapoAborted; exceptions.Exception; exceptions.BaseException; __builtin__.object

Data descriptors defined here:

__weakref__: list of weak references to the object (if defined)

Methods inherited from exceptions.Exception:

__init__(...): x.__init__(...) initializes x; see help(type(x)) for signature

Data and other attributes inherited from exceptions.Exception:

__new__ = <built-in method __new__ of type object>: T.__new__(S, ...) -> a new object with type S, a subtype of T

Methods inherited from exceptions.BaseException:

__delattr__(...): x.__delattr__('name') <==> del x.name

__getattribute__(...): x.__getattribute__('name') <==> x.name

__getitem__(...): x.__getitem__(y) <==> x[y]

__getslice__(...): x.__getslice__(i, j) <==> x[i:j] Use of negative indices is not supported.

__reduce__(...)

__repr__(...): x.__repr__() <==> repr(x)

__setattr__(...): x.__setattr__('name', value) <==> x.name = value

__setstate__(...)

__str__(...): x.__str__() <==> str(x)

__unicode__(...)

Data descriptors inherited from exceptions.BaseException:

__dict__

args

message

class DacapoDryrun(exceptions.Exception)

Raised when text file does not end correctly

Method resolution order:: DacapoDryrun; exceptions.Exception; exceptions.BaseException; __builtin__.object

Data descriptors defined here:

__weakref__: list of weak references to the object (if defined)

Methods inherited from exceptions.Exception:

__init__(...): x.__init__(...) initializes x; see help(type(x)) for signature

Data and other attributes inherited from exceptions.Exception:

__new__ = <built-in method __new__ of type object>: T.__new__(S, ...) -> a new object with type S, a subtype of T

Methods inherited from exceptions.BaseException:

__delattr__(...): x.__delattr__('name') <==> del x.name

__getattribute__(...): x.__getattribute__('name') <==> x.name

__getitem__(...): x.__getitem__(y) <==> x[y]

__getslice__(...): x.__getslice__(i, j) <==> x[i:j] Use of negative indices is not supported.

__reduce__(...)

__repr__(...): x.__repr__() <==> repr(x)

__setattr__(...): x.__setattr__('name', value) <==> x.name = value

__setstate__(...)

__str__(...): x.__str__() <==> str(x)

__unicode__(...)

Data descriptors inherited from exceptions.BaseException:

__dict__

args

message

class DacapoInput(exceptions.Exception)

raised for bad input variables

Method resolution order:: DacapoInput; exceptions.Exception; exceptions.BaseException; __builtin__.object

Data descriptors defined here:

__weakref__: list of weak references to the object (if defined)

Methods inherited from exceptions.Exception:

__init__(...): x.__init__(...) initializes x; see help(type(x)) for signature

Data and other attributes inherited from exceptions.Exception:

__new__ = <built-in method __new__ of type object>: T.__new__(S, ...) -> a new object with type S, a subtype of T

Methods inherited from exceptions.BaseException:

__delattr__(...): x.__delattr__('name') <==> del x.name

__getattribute__(...): x.__getattribute__('name') <==> x.name

__getitem__(...): x.__getitem__(y) <==> x[y]

__getslice__(...): x.__getslice__(i, j) <==> x[i:j] Use of negative indices is not supported.

__reduce__(...)

__repr__(...): x.__repr__() <==> repr(x)

__setattr__(...): x.__setattr__('name', value) <==> x.name = value

__setstate__(...)

__str__(...): x.__str__() <==> str(x)

__unicode__(...)

Data descriptors inherited from exceptions.BaseException:

__dict__

args

message

class DacapoRunning(exceptions.Exception)

Raised when ncfile.status = 'running'

Method resolution order:: DacapoRunning; exceptions.Exception; exceptions.BaseException; __builtin__.object

Data descriptors defined here:

__weakref__: list of weak references to the object (if defined)

Methods inherited from exceptions.Exception:

__init__(...): x.__init__(...) initializes x; see help(type(x)) for signature

Data and other attributes inherited from exceptions.Exception:

__new__ = <built-in method __new__ of type object>: T.__new__(S, ...) -> a new object with type S, a subtype of T

Methods inherited from exceptions.BaseException:

__delattr__(...): x.__delattr__('name') <==> del x.name

__getattribute__(...): x.__getattribute__('name') <==> x.name

__getitem__(...): x.__getitem__(y) <==> x[y]

__getslice__(...): x.__getslice__(i, j) <==> x[i:j] Use of negative indices is not supported.

__reduce__(...)

__repr__(...): x.__repr__() <==> repr(x)

__setattr__(...): x.__setattr__('name', value) <==> x.name = value

__setstate__(...)

__str__(...): x.__str__() <==> str(x)

__unicode__(...)

Data descriptors inherited from exceptions.BaseException:

__dict__

args

message

class Jacapo

Python interface to the Fortran DACAPO code

Methods defined here:

__del__(self): If calculator is deleted try to stop dacapo program

__init__(self, nc='out.nc', outnc=None, deletenc=False, debug=30, stay_alive=False, **kwargs): Initialize the Jacapo calculator :Parameters: nc : string output netcdf file, or input file if nc already exists outnc : string output file. by default equal to nc deletenc : Boolean determines whether the ncfile is deleted on initialization so a fresh run occurs. If True, the ncfile is deleted if it exists. debug : integer logging debug level. Valid kwargs: atoms : ASE.Atoms instance atoms is an ase.Atoms object that will be attached to this calculator. pw : integer sets planewave cutoff dw : integer sets density cutoff kpts : iterable set chadi-cohen, monkhorst-pack kpt grid, e.g. kpts = (2,2,1) or explicit list of kpts spinpol : Boolean sets whether spin-polarization is used or not. fixmagmom : float set the magnetic moment of the unit cell. only used in spin polarize calculations ft : float set the Fermi temperature used in occupation smearing xc : string set the exchange-correlation functional. one of ['PZ','VWN','PW91','PBE','RPBE','revPBE'], dipole boolean turn the dipole correction on (True) or off (False) or: dictionary of parameters to fine-tune behavior {'status':False, 'mixpar':0.2, 'initval':0.0, 'adddipfield':0.0, 'position':None} nbands : integer set the number of bands symmetry : Boolean Turn symmetry reduction on (True) or off (False) stress : Boolean Turn stress calculation on (True) or off (False) debug : level for logging could be something like logging.DEBUG or an integer 0-50. The higher the integer, the less information you see set debug level (0 = off, 10 = extreme) Modification of the nc file only occurs at calculate time if needed >>> calc = Jacapo('CO.nc') reads the calculator from CO.nc if it exists or minimally initializes CO.nc with dimensions if it does not exist. >>> calc = Jacapo('CO.nc', pw=300) reads the calculator from CO.nc or initializes it if it does not exist and changes the planewave cutoff energy to 300eV >>> atoms = Jacapo.read_atoms('CO.nc') returns the atoms in the netcdffile CO.nc, with the calculator attached to it. >>> atoms, calc = read('CO.nc')

__str__(self): pretty-print the calculator and atoms. we read everything directly from the ncfile to prevent triggering any calculations

atoms_are_equal(self, atoms): comparison of atoms to self.atoms using tolerances to account for float/double differences and float math.

attach_child(self, child)

calculate(self): run a calculation. you have to be a little careful with code in here. Use the calculation_required function to tell if a calculation is required. It is assumed here that if you call this, you mean it.

calculation_required(self, atoms=None, quantities=None): determines if a calculation is needed. return True if a calculation is needed to get up to date data. return False if no calculation is needed. quantities is here because of the ase interface.

delete_ncattdimvar(self, ncf, ncattrs=None, ncdims=None, ncvars=None): helper function to delete attributes, dimensions and variables in a netcdffile this functionality is not implemented for some reason in netcdf, so the only way to do this is to copy all the attributes, dimensions, and variables to a new file, excluding the ones you want to delete and then rename the new file. if you delete a dimension, all variables with that dimension are also deleted.

execute_external_dynamics(self, nc=None, txt=None, stoppfile='stop', stopprogram=None): Implementation of the stay alive functionality with socket communication between dacapo and python. Known limitations: It is not possible to start 2 independent Dacapo calculators from the same python process, since the python PID is used as identifier for the script[PID].py file.

execute_parent_calculation(self): Implementation of an extra level of parallelization, where one jacapo calculator spawns several dacapo.run processes. This is used for NEBs parallelized over images.

get(self, *args): get values for args. e.g. calc.get('nbands')

get_ados(self, **kwargs): attempt at maintaining backward compatibility with get_ados returning data Now when we call calc.get_ados() it will return settings, and calc.get_ados(atoms=[],...) should return data

get_ados_data(self, atoms, orbitals, cutoff, spin): get atom projected data :Parameters: atoms list of atom indices (integers) orbitals list of strings ['s','p','d'], ['px','py','pz'] ['d_zz', 'dxx-yy', 'd_xy', 'd_xz', 'd_yz'] cutoff : string cutoff radius you want the results for 'short' or 'infinite' spin : list of integers spin you want the results for [0] or [1] or [0,1] for both returns (egrid, ados) egrid has the fermi level at 0 eV

get_all_eigenvalues(self, spin=0): return all the eigenvalues at all the kpoints for a spin. :Parameters: spin : integer which spin the eigenvalues are for

get_ascii_debug(self): Return the debug settings in Dacapo

get_atoms(self): return the atoms attached to a calculator()

get_bz_k_points(self): return list of kpoints in the Brillouin zone

get_calculate_stress(self): return whether stress is calculated or not

get_cd = get_charge_density(self, spin=0)

get_charge_density(self, spin=0): return x,y,z,charge density data x,y,z are grids sampling the unit cell cd is the charge density data netcdf documentation:: ChargeDensity(number_of_spin, hardgrid_dim3, hardgrid_dim2, hardgrid_dim1) ChargeDensity:Description = "realspace charge density" ; ChargeDensity:unit = "-e/A^3" ;

get_charge_mixing(self): return charge mixing parameters

get_convergence(self): return convergence settings for Dacapo

get_debug(self): Return the python logging level

get_decoupling(self): return the electrostatic decoupling parameters

get_dipole(self): return dictionary of parameters if the DipoleCorrection was used

get_dipole_moment(self, atoms=None): return dipole moment of unit cell Defined by the vector connecting the center of electron charge density to the center of nuclear charge density. Units = eV*angstrom 1 Debye = 0.208194 eV*angstrom

get_dw(self): return the density wave cutoff

get_ef = get_fermi_level(self)

get_effective_potential(self, spin=1): returns the realspace local effective potential for the spin. the units of the potential are eV :Parameters: spin : integer specify which spin you want, 0 or 1

get_eigenvalues(self, kpt=0, spin=0): return the eigenvalues for a kpt and spin :Parameters: kpt : integer index of the IBZ kpoint spin : integer which spin the eigenvalues are for

get_electronic_minimization(self): get method and diagonalizations per band for electronic minimization algorithms

get_electronic_temperature = get_ft(self)

get_electrostatic_potential(self, spin=0): get electrostatic potential Netcdf documentation:: double ElectrostaticPotential(number_of_spin, hardgrid_dim3, hardgrid_dim2, hardgrid_dim1) ; ElectrostaticPotential: Description = "realspace local effective potential" ; unit = "eV" ;

get_ensemble_coefficients(self): returns exchange correlation ensemble coefficients

get_esp = get_electrostatic_potential(self, spin=0)

get_external_dipole(self): return the External dipole settings

get_extpot(self): return the external potential set in teh calculator

get_extracharge(self): Return the extra charge set in teh calculator

get_fermi_level(self): return Fermi level

get_fftgrid(self): return soft and hard fft grids

get_fixmagmom(self): returns the value of FixedMagneticMoment

get_forces(self, atoms=None): Calculate atomic forces

get_ft(self): return the FermiTemperature used in the calculation

get_ibz_k_points = get_ibz_kpoints(self)

get_ibz_kpoints(self): return list of kpoints in the irreducible brillouin zone

get_k_point_weights(self): return the weights on the IBZ kpoints

get_kpts(self): return the BZ kpts

get_kpts_type(self): return the kpt grid type

get_magnetic_moment(self, atoms=None): calculates the magnetic moment (Bohr-magnetons) of the supercell

get_magnetic_moments(self, atoms=None): return magnetic moments on each atom after the calculation is run

get_mdos(self): return multicentered projected dos parameters

get_mdos_data(self, spin=0, cutoffradius='infinite'): returns data from multicentered projection returns (mdos, rotmat) the rotation matrices are retrieved from the text file. I am not sure what you would do with these, but there was a note about them in the old documentation so I put the code to retrieve them here. the syntax for the return value is: rotmat[atom#][label] returns the rotation matrix for the center on the atom# for label. I do not not know what the label refers to.

get_nbands(self): return the number of bands used in the calculation

get_nc(self): return the ncfile used for output

get_ncoutput(self): returns the control variables for the ncfile

get_number_of_bands = get_nbands(self)

get_number_of_electrons = get_valence(self, atoms=None)

get_number_of_grid_points(self): return soft fft grid

get_number_of_iterations(self)

get_number_of_spins(self): if spin-polarized returns 2, if not returns 1

get_occ = get_occupation_numbers(self, kpt=0, spin=0)

get_occupation_numbers(self, kpt=0, spin=0): return occupancies of eigenstates for a kpt and spin :Parameters: kpt : integer index of the IBZ kpoint you want the occupation of spin : integer 0 or 1

get_occupationstatistics(self): return occupation statistics method

get_potential_energy(self, atoms=None, force_consistent=False): return the potential energy.

get_pseudo_wave_function(self, band=0, kpt=0, spin=0, pad=True): return the pseudo wavefunction

get_pseudopotentials(self): get pseudopotentials set for atoms attached to calculator

get_psp(self, sym=None, z=None): get the pseudopotential filename from the psp database :Parameters: sym : string the chemical symbol of the species z : integer the atomic number of the species you can only specify sym or z. Returns the pseudopotential filename, not the full path.

get_psp_nuclear_charge(self, psp): get the nuclear charge of the atom from teh psp-file. This is not the same as the atomic number, nor is it necessarily the negative of the number of valence electrons, since a psp may be an ion. this function is needed to compute centers of ion charge for the dipole moment calculation. We read in the valence ion configuration from the psp file and add up the charges in each shell.

get_psp_valence(self, psp): get the psp valence charge on an atom from the pspfile.

get_pw(self): return the planewave cutoff used

get_reciprocal_bloch_function(self, band=0, kpt=0, spin=0): return the reciprocal bloch function. Need for Jacapo Wannier class.

get_reciprocal_fft_index(self, kpt=0): return the Wave Function FFT Index

get_scratch(self): finds an appropriate scratch directory for the calculation

get_spin_polarized(self): Return True if calculate is spin-polarized or False if not

get_spinpol(self): Returns the spin polarization setting, either True or False

get_status(self): get status of calculation from ncfile. usually one of: 'new', 'aborted' 'running' 'finished' None

get_stay_alive(self): return the stay alive settings

get_stress(self, atoms=None): get stress on the atoms. you should have set up the calculation to calculate stress first. returns [sxx, syy, szz, syz, sxz, sxy]

get_symmetry(self): return the type of symmetry used

get_txt(self): return the txt file used for output

get_ucgrid(self, dims): Return X,Y,Z grids for uniform sampling of the unit cell dims = (n0,n1,n2) n0 points along unitcell vector 0 n1 points along unitcell vector 1 n2 points along unitcell vector 2

get_valence(self, atoms=None): return the total number of valence electrons for the atoms. valence electrons are read directly from the pseudopotentials. the psp filenames are stored in the ncfile. They may be just the name of the file, in which case the psp may exist in the same directory as the ncfile, or in $DACAPOPATH, or the psp may be defined by an absolute or relative path. This function deals with all these possibilities.

get_wannier_localization_matrix(self, nbands, dirG, kpoint, nextkpoint, G_I, spin): return wannier localization matrix

get_wave_function(self, band=0, kpt=0, spin=0): return the wave function. This is the pseudo wave function divided by volume.

get_wf = get_wave_function(self, band=0, kpt=0, spin=0)

get_xc(self): return the self-consistent exchange-correlation functional used returns a string

get_xc_energies(self, *functional): Get energies for different functionals self-consistent and non-self-consistent. :Parameters: functional : strings some set of 'PZ','VWN','PW91','PBE','revPBE', 'RPBE' 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: get_xcenergies() #returns all the energies get_xcenergies('PBE') # returns the PBE total energy get_xcenergies('PW91','PBE','revPBE') # returns a # list of energies in the order asked for

initial_wannier(self, initialwannier, kpointgrid, fixedstates, edf, spin): return initial wannier

initnc(self, ncfile=None): create an ncfile with minimal dimensions in it this makes sure the dimensions needed for other set functions exist when needed.

read_only_atoms(self, ncfile): read only the atoms from an existing netcdf file. Used to initialize a calculator from a ncfilename. :Parameters: ncfile : string name of file to read from. return ASE.Atoms with no calculator attached or None if no atoms found

restart(self): Restart the calculator by deleting nc dimensions that will be rewritten on the next calculation. This is sometimes required when certain dimensions change related to unitcell size changes planewave/densitywave cutoffs and kpt changes. These can cause fortran netcdf errors if the data does not match the pre-defined dimension sizes. also delete all the output from previous calculation.

set(self, **kwargs): set a parameter parameter is stored in dictionary that is processed later if a calculation is need.

set_ados(self, energywindow=(-15, 5), energywidth=0.2, npoints=250, cutoff=1.0): setup calculation of atom-projected density of states :Parameters: energywindow : (float, float) sets (emin,emax) in eV referenced to the Fermi level energywidth : float the gaussian used in smearing npoints : integer the number of points to sample the DOS at cutoff : float the cutoff radius in angstroms for the integration.

set_ascii_debug(self, level): set the debug level for Dacapo :Parameters: level : string one of 'Off', 'MediumLevel', 'HighLevel'

set_atoms(self, atoms): attach an atoms to the calculator and update the ncfile :Parameters: atoms ASE.Atoms instance

set_calculate_stress(self, stress=True): Turn on stress calculation :Parameters: stress : boolean set_calculate_stress(True) calculates stress set_calculate_stress(False) do not calculate stress

set_charge_mixing(self, method='Pulay', mixinghistory=10, mixingcoeff=0.1, precondition='No', updatecharge='Yes'): set density mixing method and parameters :Parameters: method : string 'Pulay' for Pulay mixing. only one supported now mixinghistory : integer number of iterations to mix Number of charge residual vectors stored for generating the Pulay estimate on the self-consistent charge density, see Sec. 4.2 in Kresse/Furthmuller: Comp. Mat. Sci. 6 (1996) p34ff mixingcoeff : float Mixing coefficient for Pulay charge mixing, corresponding to A in G$^1$ in Sec. 4.2 in Kresse/Furthmuller: Comp. Mat. Sci. 6 (1996) p34ff precondition : string 'Yes' or 'No' * "Yes" : Kerker preconditiong is used, i.e. q$_0$ is different from zero, see eq. 82 in Kresse/Furthmuller: Comp. Mat. Sci. 6 (1996). The value of q$_0$ is fix to give a damping of 20 of the lowest q vector. * "No" : q$_0$ is zero and mixing is linear (default). updatecharge : string 'Yes' or 'No' * "Yes" : Perform charge mixing according to ChargeMixing:Method setting * "No" : Freeze charge to initial value. This setting is useful when evaluating the Harris-Foulkes density functional

set_convergence(self, energy=1e-05, density=0.0001, occupation=0.001, maxsteps=None, maxtime=None): set convergence criteria for stopping the dacapo calculator. :Parameters: energy : float set total energy change (eV) required for stopping density : float set density change required for stopping occupation : float set occupation change required for stopping maxsteps : integer specify maximum number of steps to take maxtime : integer specify maximum number of hours to run. Autopilot not supported here.

set_debug(self, debug): set debug level for python logging debug should be an integer from 0-100 or one of the logging constants like logging.DEBUG, logging.WARN, etc...

set_decoupling(self, ngaussians=3, ecutoff=100, gausswidth=0.35): Decoupling activates the three dimensional electrostatic decoupling. Based on paper by Peter E. Bloechl: JCP 103 page7422 (1995). :Parameters: ngaussians : int The number of gaussian functions per atom used for constructing the model charge of the system ecutoff : int The cut off energy (eV) of system charge density in g-space used when mapping constructing the model change of the system, i.e. only charge density components below ECutoff enters when constructing the model change. gausswidth : float The width of the Gaussians defined by $widthofgaussian*1.5^(n-1)$ $n$=(1 to numberofgaussians)

set_dipole(self, status=True, mixpar=0.2, initval=0.0, adddipfield=0.0, position=None): turn on and set dipole correction scheme :Parameters: status : Boolean True turns dipole on. False turns Dipole off mixpar : float Mixing Parameter for the the dipole correction field during the electronic minimization process. If instabilities occur during electronic minimization, this value may be decreased. initval : float initial value to start at adddipfield : float additional dipole field to add units : V/ang External additive, constant electrostatic field along third unit cell vector, corresponding to an external dipole layer. The field discontinuity follows the position of the dynamical dipole correction, i.e. if DipoleCorrection:DipoleLayerPosition is set, the field discontinuity is at this value, otherwise it is at the vacuum position farthest from any other atoms on both sides of the slab. position : float scaled coordinates along third unit cell direction. If this attribute is set, DACAPO will position the compensation dipole layer plane in at the provided value. If this attribute is not set, DACAPO will put the compensation dipole layer plane in the vacuum position farthest from any other atoms on both sides of the slab. Do not set this to 0.0 calling set_dipole() sets all default values.

set_dw(self, dw): set the density wave cutoff energy. :Parameters: dw : integer the density wave cutoff The function checks to make sure it is not less than the planewave cutoff. Density_WaveCutoff describes the kinetic energy neccesary to represent a wavefunction associated with the total density, i.e. G-vectors for which $ert Gert^2$ $<$ 4*Density_WaveCutoff will be used to describe the total density (including augmentation charge and partial core density). If Density_WaveCutoff is equal to PlaneWaveCutoff this implies that the total density is as soft as the wavefunctions described by the kinetic energy cutoff PlaneWaveCutoff. If a value of Density_WaveCutoff is specified (must be larger than or equal to PlaneWaveCutoff) the program will run using two grids, one for representing the wavefunction density (softgrid_dim) and one representing the total density (hardgrid_dim). If the density can be reprensented on the same grid as the wavefunction density Density_WaveCutoff can be chosen equal to PlaneWaveCutoff (default).

set_electronic_minimization(self, method='eigsolve', diagsperband=2): set the eigensolver method Selector for which subroutine to use for electronic minimization Recognized options : "resmin", "eigsolve" and "rmm-diis". * "resmin" : Power method (Lennart Bengtson), can only handle k-point parallization. * "eigsolve : Block Davidson algorithm (Claus Bendtsen et al). * "rmm-diis : Residual minimization method (RMM), using DIIS (direct inversion in the iterate subspace) The implementaion follows closely the algorithm outlined in Kresse and Furthmuller, Comp. Mat. Sci, III.G/III.H :Parameters: method : string should be 'resmin', 'eigsolve' or 'rmm-diis' diagsperband : int The number of diagonalizations per band for electronic minimization algorithms (maps onto internal variable ndiapb). Applies for both ElectronicMinimization:Method = "resmin" and "eigsolve". default value = 2

set_external_dipole(self, value, position=None): Externally imposed dipole potential. This option overwrites DipoleCorrection if set. :Parameters: value : float units of volts position : float scaled coordinates along third unit cell direction. if None, the compensation dipole layer plane in the vacuum position farthest from any other atoms on both sides of the slab. Do not set to 0.0.

set_extpot(self, potgrid): add external potential of value see this link before using this https://listserv.fysik.dtu.dk/pipermail/campos/2003-August/000657.html :Parameters: potgrid : np.array with shape (nx,ny,nz) the shape must be the same as the fft soft grid the value of the potential to add you have to know both of the fft grid dimensions ahead of time! if you know what you are doing, you can set the fft_grid you want before hand with: calc.set_fftgrid((n1,n2,n3))

set_extracharge(self, val): add extra charge to unit cell :Parameters: val : float extra electrons to add or subtract from the unit cell Fixed extra charge in the unit cell (i.e. deviation from charge neutrality). This assumes a compensating, positive constant backgound charge (jellium) to forge overall charge neutrality.

set_fftgrid(self, soft=None, hard=None): sets the dimensions of the FFT grid to be used :Parameters: soft : (n1,n2,n3) integers make a n1 x n2 x n3 grid hard : (n1,n2,n3) integers make a n1 x n2 x n3 grid >>> calc.set_fftgrid(soft=[42,44,46]) sets the soft and hard grid dimensions to 42,44,46 >>> calc.set_fftgrid(soft=[42,44,46],hard=[80,84,88]) sets the soft grid dimensions to 42,44,46 and the hard grid dimensions to 80,84,88 These are the fast FFt grid numbers listed in fftdimensions.F data list_of_fft /2, 4, 6, 8, 10, 12, 14, 16, 18, 20, & 22,24, 28, 30,32, 36, 40, 42, 44, 48, & 56,60, 64, 66, 70, 72, 80, 84, 88, 90, & 96,108,110,112,120,126,128,132,140,144,154, & 160,168,176,180,192,198,200, & 216,240,264,270,280,288,324,352,360,378,384,400,432, & 450,480,540,576,640/ otherwise you will get some errors from mis-dimensioned variables. this is usually automatically set by Dacapo.

set_fixmagmom(self, fixmagmom=None): set a fixed magnetic moment for a spin polarized calculation :Parameters: fixmagmom : float the magnetic moment of the cell in Bohr magnetons

set_ft(self, ft): set the Fermi temperature for occupation smearing :Parameters: ft : float Fermi temperature in kT (eV) Electronic temperature, corresponding to gaussian occupation statistics. Device used to stabilize the convergence towards the electronic ground state. Higher values stabilizes the convergence. Values in the range 0.1-1.0 eV are recommended, depending on the complexity of the Fermi surface (low values for d-metals and narrow gap semiconducters, higher for free electron-like metals).

set_kpts(self, kpts): set the kpt grid. Parameters: kpts: (n1,n2,n3) or [k1,k2,k3,...] or one of these chadi-cohen sets: * cc6_1x1 * cc12_2x3 * cc18_sq3xsq3 * cc18_1x1 * cc54_sq3xsq3 * cc54_1x1 * cc162_sq3xsq3 * cc162_1x1 (n1,n2,n3) creates an n1 x n2 x n3 monkhorst-pack grid, [k1,k2,k3,...] creates a kpt-grid based on the kpoints defined in k1,k2,k3,... There is also a possibility to have Dacapo (fortran) create the Kpoints in chadi-cohen or monkhorst-pack form. To do this you need to set the KpointSetup.gridtype attribute, and KpointSetup. KpointSetup = [3,0,0] KpointSetup.gridtype = 'ChadiCohen' KpointSetup(1) Chadi-Cohen k-point set 1 6 k-points 1x1 2 18-kpoints sqrt(3)*sqrt(3) 3 18-kpoints 1x1 4 54-kpoints sqrt(3)*sqrt(3) 5 54-kpoints 1x1 6 162-kpoints 1x1 7 12-kpoints 2x3 8 162-kpoints 3xsqrt 3 or KpointSetup = [4,4,4] KpointSetup.gridtype = 'MonkhorstPack' we do not use this functionality.

set_mdos(self, mcenters=None, energywindow=(-15, 5), energywidth=0.2, numberenergypoints=250, cutoffradius=1.0): Setup multicentered projected DOS. mcenters a list of tuples containing (atom#,l,m,weight) (0,0,0,1.0) specifies (atom 0, l=0, m=0, weight=1.0) an s orbital on atom 0 (1,1,1,1.0) specifies (atom 1, l=1, m=1, weight=1.0) a p orbital with m = +1 on atom 0 l=0 s-orbital l=1 p-orbital l=2 d-orbital m in range of ( -l ... 0 ... +l ) 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. adapated from old MultiCenterProjectedDOS.py

set_nbands(self, nbands=None): Set the number of bands. a few unoccupied bands are recommended. :Parameters: nbands : integer the number of bands. if nbands = None the function returns with nothing done. At calculate time, if there are still no bands, they will be set by: the number of bands is calculated as $nbands=nvalence*0.65 + 4$

set_nc(self, nc='out.nc'): set filename for the netcdf and text output for this calculation :Parameters: nc : string filename for netcdf file if the ncfile attached to the calculator is changing, the old file will be copied to the new file if it doesn not exist so that all the calculator details are preserved. Otherwise, the if the ncfile does not exist, it will get initialized. the text file will have the same basename as the ncfile, but with a .txt extension.

set_ncoutput(self, wf=None, cd=None, efp=None, esp=None): set the output of large variables in the netcdf output file :Parameters: wf : string controls output of wavefunction. values can be 'Yes' or 'No' cd : string controls output of charge density. values can be 'Yes' or 'No' efp : string controls output of effective potential. values can be 'Yes' or 'No' esp : string controls output of electrostatic potential. values can be 'Yes' or 'No'

set_occupationstatistics(self, method): set the method used for smearing the occupations. :Parameters: method : string one of 'FermiDirac' or 'MethfesselPaxton' Currently, the Methfessel-Paxton scheme (PRB 40, 3616 (1989).) is implemented to 1th order (which is recommemded by most authors). 'FermiDirac' is the default

set_parent(self, parent)

set_pseudopotentials(self, pspdict): Set all the pseudopotentials from a dictionary. The dictionary should have this form:: {symbol1: path1, symbol2: path2}

set_psp(self, sym=None, z=None, psp=None): set the pseudopotential file for a species or an atomic number. :Parameters: sym : string chemical symbol of the species z : integer the atomic number of the species psp : string filename of the pseudopotential you can only set sym or z. examples:: set_psp('N',psp='pspfile') set_psp(z=6,psp='pspfile')

set_psp_database(self, xc=None): get the xc-dependent psp database :Parameters: xc : string one of 'PW91', 'PBE', 'revPBE', 'RPBE', 'PZ' not all the databases are complete, and that means some psp do not exist. note: this function is not supported fully. only pw91 is imported now. Changing the xc at this point results in loading a nearly empty database, and I have not thought about how to resolve that

set_pw(self, pw): set the planewave cutoff. :Parameters: pw : integer the planewave cutoff in eV this function checks to make sure the density wave cutoff is greater than or equal to the planewave cutoff.

set_spinpol(self, spinpol=False): set Spin polarization. :Parameters: spinpol : Boolean set_spinpol(True) spin-polarized. set_spinpol(False) no spin polarization, default Specify whether to perform a spin polarized or unpolarized calculation.

set_status(self, status): set the status flag in the netcdf file :Parameters: status : string status flag, e.g. 'new', 'finished'

set_stay_alive(self, value): set the stay alive setting

set_symmetry(self, val=False): set how symmetry is used to reduce k-points :Parameters: val : Boolean set_sym(True) Maximum symmetry is used set_sym(False) No symmetry is used This variable controls the if and how DACAPO should attempt using symmetry in the calculation. Imposing symmetry generally speeds up the calculation and reduces numerical noise to some extent. Symmetry should always be applied to the maximum extent, when ions are not moved. When relaxing ions, however, the symmetry of the equilibrium state may be lower than the initial state. Such an equilibrium state with lower symmetry is missed, if symmetry is imposed. Molecular dynamics-like algorithms for ionic propagation will generally not break the symmetry of the initial state, but some algorithms, like the BFGS may break the symmetry of the initial state. Recognized options: "Off": No symmetry will be imposed, apart from time inversion symmetry in recipical space. This is utilized to reduce the k-point sampling set for Brillouin zone integration and has no influence on the ionic forces/motion. "Maximum": DACAPO will look for symmetry in the supplied atomic structure and extract the highest possible symmetry group. During the calculation, DACAPO will impose the found spatial symmetry on ionic forces and electronic structure, i.e. the symmetry will be conserved during the calculation.

set_xc(self, xc): Set the self-consistent exchange-correlation functional :Parameters: xc : string Must be one of 'PZ', 'VWN', 'PW91', 'PBE', 'revPBE', 'RPBE' Selects which density functional to use for exchange-correlation when performing electronic minimization (the electronic energy is minimized with respect to this selected functional) Notice that the electronic energy is also evaluated non-selfconsistently by DACAPO for other exchange-correlation functionals Recognized options : * "PZ" (Perdew Zunger LDA-parametrization) * "VWN" (Vosko Wilk Nusair LDA-parametrization) * "PW91" (Perdew Wang 91 GGA-parametrization) * "PBE" (Perdew Burke Ernzerhof GGA-parametrization) * "revPBE" (revised PBE/1 GGA-parametrization) * "RPBE" (revised PBE/2 GGA-parametrization) option "PZ" is not allowed for spin polarized calculation; use "VWN" instead.

strip(self): remove all large memory nc variables not needed for anything I use very often.

update_input_parameters(self): read in all the input parameters from the netcdfile

write(self, new=False): write out everything to the ncfile : get_nc() new determines whether to delete any existing ncfile, and rewrite it.

write_input(self): write out input parameters as needed you must define a self._set_keyword function that does all the actual writing.

write_nc(self, nc=None, atoms=None): write out atoms to a netcdffile. This does not write out the calculation parameters! :Parameters: nc : string ncfilename to write to. this file will get clobbered if it already exists. atoms : ASE.Atoms atoms to write. if None use the attached atoms if no atoms are attached only the calculator is written out. the ncfile is always opened in 'a' mode. note: it is good practice to use the atoms argument to make sure that the geometry you mean gets written! Otherwise, the atoms in the calculator is used, which may be different than the external copy of the atoms.

Static methods defined here:

read_atoms(filename): read atoms and calculator from an existing netcdf file. :Parameters: filename : string name of file to read from. static method example:: >>> atoms = Jacapo.read_atoms(ncfile) >>> calc = atoms.get_calculator() this method is here for legacy purposes. I used to use it alot.

Data and other attributes defined here:

__version__ = '0.4'

default_input = {'ados': None, 'ascii_debug': 'Off', 'atoms': None, 'calculate_stress': False, 'charge_mixing': {'method': 'Pulay', 'mixingcoeff': 0.1, 'mixinghistory': 10, 'precondition': 'No', 'updatecharge': 'Yes'}, 'convergence': {'density': 0.0001, 'energy': 1e-05, 'maxsteps': None, 'maxtime': None, 'occupation': 0.001}, 'decoupling': None, 'dipole': {'adddipfield': 0.0, 'initval': 0.0, 'mixpar': 0.2, 'position': None, 'status': False}, 'dw': 350, 'electronic_minimization': {'diagsperband': 2, 'method': 'eigsolve'}, ...}

Functions
		read(ncfile) `return atoms and calculator from ncfile >>> atoms, calc = read('co.nc')`

Data
		__docformat__ = 'restructuredtext' formatstring = '%(levelname)-10s function: %(funcName)s lineno: %(lineno)-4d %(message)s' formatter = <logging.Formatter object> handler = <logging.StreamHandler object> log = <logging.Logger object>

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