差分

このページの2つのバージョン間の差分を表示します。

--- info:dacapo [2018/04/28 15:58] – 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 44: / 行 45: @@
 |''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)|
-|  |//dictionary//| dictionary of parameters to fine-tune behavior\\ <code python>
+| ::: |//dictionary//| dictionary of parameters to fine-tune behavior\\ <code python>
   {'status':False,
    'mixpar':0.2,
@@ 行 51: / 行 52: @@
    'position':None}</code>|
 |''nbands''|//integer//|set the number of bands  |
-|''symmetry''|//Boolean//Turn symmetry reduction 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)|
-  stress : Boolean
+|''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)|
-    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
-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 94: / 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 105: / 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 112: / 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 123: / 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 129: / 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 139: / 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 163: / 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 170: / 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 193: / 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 237: / 行 260: @@
 minimization algorithms
 get_electronic_temperature = get_ft(self)
+==== get_electrostatic_potential ====
 get_electrostatic_potential(self, spin=0)
 get electrostatic potential
@@ 行 249: / 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 297: / 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 498: / 行 541: @@
   atoms
     ASE.Atoms instance
+==== set_calculate_stress ====
 set_calculate_stress(self, stress=True)
 Turn on stress calculation
@@ 行 506: / 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 546: / 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 567: / 行 613: @@
 Autopilot not supported here.
+==== set_debug ====
 set_debug(self, debug)
 set debug level for python logging
@@ 行 572: / 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 592: / 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 632: / 行 681: @@
 calling set_dipole() sets all default values.
+==== set_dw ====
 set_dw(self, dw)
 set the density wave cutoff energy.
@@ 行 659: / 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 689: / 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 703: / 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 720: / 行 773: @@
 before hand with:
 calc.set_fftgrid((n1,n2,n3))
+==== set_extracharge ====
 set_extracharge(self, val)
 add extra charge to unit cell
@@ 行 732: / 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 764: / 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 771: / 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 786: / 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 869: / 行 927: @@
 the number of bands is calculated as
 $nbands=nvalence*0.65 + 4$
+==== set_nc  ====
 === set_nc(self, nc='out.nc') ===
@@ 行 886: / 行 945: @@
 the text file will have the same basename as the ncfile, but
 with a .txt extension.
+==== set_ncoutput ====
 === set_ncoutput(self, wf=None, cd=None, efp=None, esp=None) ===
@@ 行 925: / 行 985: @@
     {symbol1: path1,
      symbol2: path2}
+==== set_psp ====
 === set_psp(self, sym=None, z=None, psp=None) ===
@@ 行 1071: / 行 1133: @@
 you must define a self._set_keyword function that does all the
 actual writing.
 ==== write_nc ====