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 G ert^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
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