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--- info:dacapo [2018/04/28 13:46] – [Static methods] kimi
+++ info:dacapo [2022/08/23 13:34] (現在) – 外部編集 127.0.0.1
@@ 行 3: / 行 3: @@
 [[ase:Jacapo]]
-[[http://192.168.10.213/html_old/ase.calculators.jacapo.jacapo.html|{{|Jacapo}}]]
+[[http://sstweb.ee.ous.ac.jp/html_old/ase.calculators.jacapo.jacapo.html|{{|Jacapo}}]]
 ===== functions =====
@@ 行 22: / 行 22: @@
 ==== Constractor ====
+==== Jacapo ====
 <code python>
 __init__(self, nc='out.nc', outnc=None, debug=30, stay_alive=False, **kwargs)
@@ 行 41: / 行 42: @@
 | ''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|
-  ft : float
+|''xc''|//string//|set the exchange-correlation functional. one of ['PZ','VWN','PW91','PBE','RPBE','revPBE'],|
-    set the Fermi temperature used in occupation smearing
+|''dipole''|//boolean//|turn the dipole correction on (True) or off (False)|
+| ::: |//dictionary//| dictionary of parameters to fine-tune behavior\\ <code python>
-  xc : string
+  {'status':False,
-    set the exchange-correlation functional.
+   'mixpar':0.2,
-    one of ['PZ','VWN','PW91','PBE','RPBE','revPBE'],
+   'initval':0.0,
+   'adddipfield':0.0,
-  dipole
+   'position':None}</code>|
-    boolean
+|''nbands''|//integer//|set the number of bands  |
-    turn the dipole correction on (True) or off (False)
+|''symmetry''|//Boolean//|Turn symmetry reduction on (True) or off (False) |
+|''stress''|//Boolean//|Turn stress calculation on (True) or off (False)|
-    or:
+|''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)|
-    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)
-</code>
-Methods
-<code>
-Methods defined here:
 Initialize the Jacapo calculator
 Modification of the nc file only occurs at calculate time if needed
+<code python>
 >>> calc = Jacapo('CO.nc')
+</code>
 reads the calculator from CO.nc if it exists or
 minimally initializes CO.nc with dimensions if it does not exist.
+<code python>
 >>> calc = Jacapo('CO.nc', pw=300)
+</code>
 reads the calculator from CO.nc or initializes it if
 it does not exist and changes the planewave cutoff energy to
 eV
+<code python>
  >>> atoms = Jacapo.read_atoms('CO.nc')
+</code>
 returns the atoms in the netcdffile CO.nc, with the calculator
 attached to it.
+<code python>
 >>> atoms, calc = read('CO.nc')
+</code>
+==== __str__ ====
 __str__(self)
 pretty-print the calculator and atoms.
@@ 行 107: / 行 84: @@
 we read everything directly from the ncfile to prevent
 triggering any calculations
+==== atoms_are_equal ====
 atoms_are_equal(self, atoms)
 comparison of atoms to self.atoms using tolerances to account
 for float/double differences and float math.
+==== attach_child ====
 attach_child(self, child)
+==== calculate ====
 calculate(self)
 run a calculation.
@@ 行 118: / 行 103: @@
 required. It is assumed here that if you call this, you mean
 it.
+==== calculation_required ====
 calculation_required(self, atoms=None, quantities=None)
 determines if a calculation is needed.
@@ 行 125: / 行 112: @@
 quantities is here because of the ase interface.
+==== delete_ncattdimvar ----
 delete_ncattdimvar(self, ncf, ncattrs=None, ncdims=None, ncvars=None)
 helper function to delete attributes,
@@ 行 136: / 行 124: @@
 if you delete a dimension, all variables with that dimension
 are also deleted.
+==== execute_external_dynamics ====
 execute_external_dynamics(self, nc=None, txt=None, stoppfile='stop', stopprogram=None)
 Implementation of the stay alive functionality with socket
@@ 行 142: / 行 131: @@
 from the same python process, since the python PID is used as
 identifier for the script[PID].py file.
+==== execute_parent_calculation ====
 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 ====
+<code python>
 get_ados(self, **kwargs)
+</code>
 attempt at maintaining backward compatibility with get_ados
 returning data
@@ 行 152: / 行 145: @@
 and calc.get_ados(atoms=[],...) should return data
+==== get_ados_data ====
 get_ados_data(self, atoms, orbitals, cutoff, spin)
 get atom projected data
@@ 行 176: / 行 173: @@
 returns (egrid, ados)
 egrid has the fermi level at 0 eV
+==== get_all_eigenvalues ====
 get_all_eigenvalues(self, spin=0)
 return all the eigenvalues at all the kpoints for a spin.
@@ 行 183: / 行 181: @@
   spin : integer
     which spin the eigenvalues are for
+==== get_ascii_debug ====
 get_ascii_debug(self)
 Return the debug settings in Dacapo
+==== get_atoms ====
 get_atoms(self)
 return the atoms attached to a calculator()
+==== get_bz_k_points ====
 get_bz_k_points(self)
 return list of kpoints in the Brillouin zone
+==== get_calculate_stress ====
 get_calculate_stress(self)
 return whether stress is calculated or not
+==== get_cd ====
 get_cd = get_charge_density(self, spin=0)
+==== get_charge_density ====
 get_charge_density(self, spin=0)
 return x,y,z,charge density data
@@ 行 206: / 行 210: @@
   ChargeDensity:Description = "realspace charge density" ;
           ChargeDensity:unit = "-e/A^3" ;
+=== get_charge_mixing ====
 get_charge_mixing(self)
 return charge mixing parameters
+==== get_convergence ====
 get_convergence(self)
 return convergence settings for Dacapo
+==== get_debug ====
 get_debug(self)
 Return the python logging level
+==== get_decoupling ====
 get_decoupling(self)
 return the electrostatic decoupling parameters
+==== get_dipole ====
 get_dipole(self)
 return dictionary of parameters if the DipoleCorrection was used
+==== get_dipole_moment ====
 get_dipole_moment(self, atoms=None)
 return dipole moment of unit cell
@@ 行 250: / 行 260: @@
 minimization algorithms
 get_electronic_temperature = get_ft(self)
+==== get_electrostatic_potential ====
 get_electrostatic_potential(self, spin=0)
 get electrostatic potential
@@ 行 262: / 行 273: @@
              Description = "realspace local effective potential" ;
              unit = "eV" ;
+==== get_ensemble_coefficients ====
 get_ensemble_coefficients(self)
 returns exchange correlation ensemble coefficients
+==== get_esp ====
 get_esp = get_electrostatic_potential(self, spin=0)
 get_external_dipole(self)
 return the External dipole settings
+==== get_extpot ====
 get_extpot(self)
 return the external potential set in teh calculator
+==== get_extracharge ====
 get_extracharge(self)
 Return the extra charge set in teh calculator
+==== get_fermi_level ====
 get_fermi_level(self)
 return Fermi level
+==== get_fftgrid ====
 get_fftgrid(self)
 return soft and hard fft grids
+==== get_fixmagmom ====
 get_fixmagmom(self)
 returns the value of FixedMagneticMoment
+==== get_forces  ====
 get_forces(self, atoms=None)
 Calculate atomic forces
+==== get_ft ====
 get_ft(self)
 return the FermiTemperature used in the calculation
+==== get_ibz_k_points ====
 get_ibz_k_points = get_ibz_kpoints(self)
+==== get_ibz_kpoints ====
 get_ibz_kpoints(self)
 return list of kpoints in the irreducible brillouin zone
+==== get_k_point_weights ====
 get_k_point_weights(self)
 return the weights on the IBZ kpoints
+==== get_kpts ====
 get_kpts(self)
 return the BZ kpts
+==== get_kpts_type ====
 get_kpts_type(self)
 return the kpt grid type
+==== get_magnetic_moment ====
 get_magnetic_moment(self, atoms=None)
 calculates the magnetic moment (Bohr-magnetons) of the supercell
+==== get_magnetic_moments ====
 get_magnetic_moments(self, atoms=None)
 return magnetic moments on each atom after the calculation is
 run
+==== get_mdos ====
 get_mdos(self)
 return multicentered projected dos parameters
+==== get_mdos_data====
 get_mdos_data(self, spin=0, cutoffradius='infinite')
 returns data from multicentered projection
@@ 行 310: / 行 339: @@
 center on the atom# for label. I do not not know what the
 label refers to.
+==== get_nbands ====
 get_nbands(self)
 return the number of bands used in the calculation
@@ 行 511: / 行 541: @@
   atoms
     ASE.Atoms instance
+==== set_calculate_stress ====
 set_calculate_stress(self, stress=True)
 Turn on stress calculation
@@ 行 519: / 行 550: @@
     set_calculate_stress(True) calculates stress
     set_calculate_stress(False) do not calculate stress
+==== set_charge_mixing ====
 set_charge_mixing(self, method='Pulay', mixinghistory=10, mixingcoeff=0.1, precondition='No', updatecharge='Yes')
 set density mixing method and parameters
@@ 行 559: / 行 591: @@
        This setting is useful when evaluating the Harris-Foulkes
        density functional
+==== set_convergence ====
 set_convergence(self, energy=1e-05, density=0.0001, occupation=0.001, maxsteps=None, maxtime=None)
 set convergence criteria for stopping the dacapo calculator.
@@ 行 580: / 行 613: @@
 Autopilot not supported here.
+==== set_debug ====
 set_debug(self, debug)
 set debug level for python logging
@@ 行 585: / 行 619: @@
 debug should be an integer from 0-100 or one of the logging
 constants like logging.DEBUG, logging.WARN, etc...
+==== set_decoupling ====
 set_decoupling(self, ngaussians=3, ecutoff=100, gausswidth=0.35)
 Decoupling activates the three dimensional electrostatic
@@ 行 605: / 行 640: @@
     The width of the Gaussians defined by
     $widthofgaussian*1.5^(n-1)$  $n$=(1 to numberofgaussians)
+==== set_dipole ====
 set_dipole(self, status=True, mixpar=0.2, initval=0.0, adddipfield=0.0, position=None)
 turn on and set dipole correction scheme
@@ 行 645: / 行 681: @@
 calling set_dipole() sets all default values.
+==== set_dw ====
 set_dw(self, dw)
 set the density wave cutoff energy.
@@ 行 672: / 行 709: @@
 Density_WaveCutoff can be chosen equal to PlaneWaveCutoff
 (default).
+==== set_electronic_minimization ====
 set_electronic_minimization(self, method='eigsolve', diagsperband=2)
 set the eigensolver method
@@ 行 702: / 行 740: @@
     ElectronicMinimization:Method = "resmin" and "eigsolve".
     default value = 2
+==== set_external_dipole ====
 set_external_dipole(self, value, position=None)
 Externally imposed dipole potential. This option overwrites
@@ 行 716: / 行 755: @@
     vacuum position farthest from any other atoms on both
     sides of the slab. Do not set to 0.0.
+==== set_extpot ====
 set_extpot(self, potgrid)
 add external potential of value
@@ 行 733: / 行 773: @@
 before hand with:
 calc.set_fftgrid((n1,n2,n3))
+==== set_extracharge ====
 set_extracharge(self, val)
 add extra charge to unit cell
@@ 行 745: / 行 786: @@
 constant backgound charge (jellium) to forge overall charge
 neutrality.
+==== set_fftgrid  ====
 set_fftgrid(self, soft=None, hard=None)
 sets the dimensions of the FFT grid to be used
@@ 行 777: / 行 819: @@
 this is usually automatically set by Dacapo.
+==== set_fixmagmom  ====
 set_fixmagmom(self, fixmagmom=None)
 set a fixed magnetic moment for a spin polarized calculation
@@ 行 784: / 行 827: @@
   fixmagmom : float
     the magnetic moment of the cell in Bohr magnetons
+==== set_ft  ====
 set_ft(self, ft)
 set the Fermi temperature for occupation smearing
@@ 行 799: / 行 843: @@
 for d-metals and narrow gap semiconducters, higher for free
 electron-like metals).
+==== set_kpts ====
 set_kpts(self, kpts)
 set the kpt grid.
@@ 行 882: / 行 927: @@
 the number of bands is calculated as
 $nbands=nvalence*0.65 + 4$
-set_nc(self, nc='out.nc')
+==== set_nc  ====
+=== set_nc(self, nc='out.nc') ===
 set filename for the netcdf and text output for this calculation
@@ 行 898: / 行 945: @@
 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_ncoutput ====
+=== set_ncoutput(self, wf=None, cd=None, efp=None, esp=None) ===
 set the output of large variables in the netcdf output file
@@ 行 936: / 行 985: @@
     {symbol1: path1,
      symbol2: path2}
-set_psp(self, sym=None, z=None, psp=None)
+==== set_psp ====
+=== set_psp(self, sym=None, z=None, psp=None) ===
 set the pseudopotential file for a species or an atomic number.
@@ 行 973: / 行 1025: @@
 a nearly empty database, and I have not thought about how to
 resolve that
-set_pw(self, pw)
+=== set_pw(self, pw) ===
 set the planewave cutoff.
@@ 行 983: / 行 1036: @@
 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_spinpol(self, spinpol=False) ===
 set Spin polarization.
@@ 行 994: / 行 1047: @@
 Specify whether to perform a spin polarized or unpolarized
 calculation.
-set_status(self, status)
+=== set_status(self, status) ===
 set the status flag in the netcdf file
@@ 行 1001: / 行 1055: @@
   status : string
     status flag, e.g. 'new', 'finished'
-set_stay_alive(self, value)
+=== set_stay_alive(self, value) ===
 set the stay alive setting
-set_symmetry(self, val=False)
+=== set_symmetry(self, val=False) ===
 set how symmetry is used to reduce k-points
@@ 行 1035: / 行 1091: @@
 spatial symmetry on ionic forces and electronic structure,
 i.e. the symmetry will be conserved during the calculation.
-set_xc(self, xc)
+=== set_xc(self, xc) ===
 Set the self-consistent exchange-correlation functional
@@ 行 1059: / 行 1116: @@
 option "PZ" is not allowed for spin polarized
 calculation; use "VWN" instead.
-strip(self)
+=== 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(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_input(self) ===
 write out input parameters as needed
 you must define a self._set_keyword function that does all the
 actual writing.
+==== write_nc ====
+<code python>
 write_nc(self, nc=None, atoms=None)
+</code>
 write out atoms to a netcdffile.
 This does not write out the calculation parameters!
-:Parameters:
+=== Parameters ===
+^Name^Type^Description^
+|''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.|
-  nc : string
+the ncfile is always opened in '' 'a' '' mode.
-    ncfilename to write to. this file will get clobbered
-    if it already exists.
-  atoms : ASE.Atoms
+=== note ===
-    atoms to write. if None use the attached atoms
+it is good practice to use the atoms argument to make
-    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.
-</code>
 ==== Static methods ====
 === read_atoms ===