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--- ase:jacapo [2018/04/27 15:26] – kimi
+++ ase:jacapo [2018/04/27 15:31] (現在) – 削除 kimi
@@ 行 1: / 行 1: @@
-ase.calculators.jacapo.jacapo	index
-/var/www/html/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, 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
-  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
-eV
- >>> 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_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
-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
-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
-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 $ert Gert^2$ $<$
-*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, &
-,24, 28, 30,32, 36, 40, 42, 44, 48, &
-,60, 64, 66, 70, 72, 80, 84, 88, 90, &
-,108,110,112,120,126,128,132,140,144,154, &
-,168,176,180,192,198,200, &
-,240,264,270,280,288,324,352,360,378,384,400,432, &
-,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
-       6 k-points 1x1
-       18-kpoints sqrt(3)*sqrt(3)
-       18-kpoints 1x1
-       54-kpoints sqrt(3)*sqrt(3)
-       54-kpoints 1x1
-       162-kpoints 1x1
-       12-kpoints 2x3
-       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>