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1# Copyright (C) 2008 CSC - Scientific Computing Ltd.
2"""This module defines an ASE interface to VASP.
4Developed on the basis of modules by Jussi Enkovaara and John
5Kitchin. The path of the directory containing the pseudopotential
6directories (potpaw,potpaw_GGA, potpaw_PBE, ...) should be set
7by the environmental flag $VASP_PP_PATH.
9The user should also set the environmental flag $VASP_SCRIPT pointing
10to a python script looking something like::
12 import os
13 exitcode = os.system('vasp')
15Alternatively, user can set the environmental flag $VASP_COMMAND pointing
16to the command use the launch vasp e.g. 'vasp' or 'mpirun -n 16 vasp'
18http://cms.mpi.univie.ac.at/vasp/
19"""
21import os
22import warnings
23import shutil
24from os.path import join, isfile, islink
25from typing import List, Sequence, Tuple
27import numpy as np
29import ase
30from ase.calculators.calculator import kpts2ndarray
31from ase.calculators.vasp.setups import get_default_setups
33# Parameters that can be set in INCAR. The values which are None
34# are not written and default parameters of VASP are used for them.
36float_keys = [
37 'aexx', # Fraction of exact/DFT exchange
38 'aggac', # Fraction of gradient correction to correlation
39 'aggax', # Fraction of gradient correction to exchange
40 'aldac', # Fraction of LDA correlation energy
41 'amin', #
42 'amix', #
43 'amix_mag', #
44 'bmix', # tags for mixing
45 'bmix_mag', #
46 'cshift', # Complex shift for dielectric tensor calculation (LOPTICS)
47 'deper', # relative stopping criterion for optimization of eigenvalue
48 'ebreak', # absolute stopping criterion for optimization of eigenvalues
49 # (EDIFF/N-BANDS/4)
50 'efield', # applied electrostatic field
51 'emax', # energy-range for DOSCAR file
52 'emin', #
53 'enaug', # Density cutoff
54 'encut', # Planewave cutoff
55 'encutgw', # energy cutoff for response function
56 'encutfock', # FFT grid in the HF related routines
57 'hfscreen', # attribute to change from PBE0 to HSE
58 'kspacing', # determines the number of k-points if the KPOINTS
59 # file is not present. KSPACING is the smallest
60 # allowed spacing between k-points in units of
61 # $\AA$^{-1}$.
62 'potim', # time-step for ion-motion (fs)
63 'nelect', # total number of electrons
64 'param1', # Exchange parameter
65 'param2', # Exchange parameter
66 'pomass', # mass of ions in am
67 'pstress', # add this stress to the stress tensor, and energy E = V *
68 # pstress
69 'sigma', # broadening in eV
70 'smass', # Nose mass-parameter (am)
71 'spring', # spring constant for NEB
72 'time', # special control tag
73 'weimin', # maximum weight for a band to be considered empty
74 'zab_vdw', # vdW-DF parameter
75 'zval', # ionic valence
76 # The next keywords pertain to the VTST add-ons from Graeme Henkelman's
77 # group at UT Austin
78 'jacobian', # Weight of lattice to atomic motion
79 'ddr', # (DdR) dimer separation
80 'drotmax', # (DRotMax) number of rotation steps per translation step
81 'dfnmin', # (DFNMin) rotational force below which dimer is not rotated
82 'dfnmax', # (DFNMax) rotational force below which dimer rotation stops
83 'sltol', # convergence ratio for minimum eigenvalue
84 'sdr', # finite difference for setting up Lanczos matrix and step
85 # size when translating
86 'maxmove', # Max step for translation for IOPT > 0
87 'invcurv', # Initial curvature for LBFGS (IOPT = 1)
88 'timestep', # Dynamical timestep for IOPT = 3 and IOPT = 7
89 'sdalpha', # Ratio between force and step size for IOPT = 4
90 # The next keywords pertain to IOPT = 7 (i.e. FIRE)
91 'ftimemax', # Max time step
92 'ftimedec', # Factor to dec. dt
93 'ftimeinc', # Factor to inc. dt
94 'falpha', # Parameter for velocity damping
95 'falphadec', # Factor to dec. alpha
96 'clz', # electron count for core level shift
97 'vdw_radius', # Cutoff radius for Grimme's DFT-D2 and DFT-D3 and
98 # Tkatchenko and Scheffler's DFT-TS dispersion corrections
99 'vdw_scaling', # Global scaling parameter for Grimme's DFT-D2 dispersion
100 # correction
101 'vdw_d', # Global damping parameter for Grimme's DFT-D2 and Tkatchenko
102 # and Scheffler's DFT-TS dispersion corrections
103 'vdw_cnradius', # Cutoff radius for calculating coordination number in
104 # Grimme's DFT-D3 dispersion correction
105 'vdw_s6', # Damping parameter for Grimme's DFT-D2 and DFT-D3 and
106 # Tkatchenko and Scheffler's DFT-TS dispersion corrections
107 'vdw_s8', # Damping parameter for Grimme's DFT-D3 dispersion correction
108 'vdw_sr', # Scaling parameter for Grimme's DFT-D2 and DFT-D3 and
109 # Tkatchenko and Scheffler's DFT-TS dispersion correction
110 'vdw_a1', # Damping parameter for Grimme's DFT-D3 dispersion correction
111 'vdw_a2', # Damping parameter for Grimme's DFT-D3 dispersion correction
112 'eb_k', # solvent permitivity in Vaspsol
113 'tau', # surface tension parameter in Vaspsol
114 'langevin_gamma_l', # Friction for lattice degrees of freedom
115 'pmass', # Mass for latice degrees of freedom
116 'bparam', # B parameter for nonlocal VV10 vdW functional
117 'cparam', # C parameter for nonlocal VV10 vdW functional
118 'aldax', # Fraction of LDA exchange (for hybrid calculations)
119 'tebeg', #
120 'teend', # temperature during run
121 'andersen_prob', # Probability of collision in Andersen thermostat
122 'apaco', # Distance cutoff for pair correlation function calc.
123 'auger_ecblo', # Undocumented parameter for Auger calculations
124 'auger_edens', # Density of electrons in conduction band
125 'auger_hdens', # Density of holes in valence band
126 'auger_efermi', # Fixed Fermi level for Auger calculations
127 'auger_evbhi', # Upper bound for valence band maximum
128 'auger_ewidth', # Half-width of energy window function
129 'auger_occ_fac_eeh', # Undocumented parameter for Auger calculations
130 'auger_occ_fac_ehh', # Undocumented parameter for Auger calculations
131 'auger_temp', # Temperature for Auger calculation
132 'dq', # Finite difference displacement magnitude (NMR)
133 'avgap', # Average gap (Model GW)
134 'ch_sigma', # Broadening of the core electron absorption spectrum
135 'bpotim', # Undocumented Bond-Boost parameter (GH patches)
136 'qrr', # Undocumented Bond-Boost parameter (GH patches)
137 'prr', # Undocumented Bond-Boost parameter (GH patches)
138 'rcut', # Undocumented Bond-Boost parameter (GH patches)
139 'dvmax', # Undocumented Bond-Boost parameter (GH patches)
140 'bfgsinvcurv', # Initial curvature for BFGS (GH patches)
141 'damping', # Damping parameter for LBFGS (GH patches)
142 'efirst', # Energy of first NEB image (GH patches)
143 'elast', # Energy of final NEB image (GH patches)
144 'fmagval', # Force magnitude convergence criterion (GH patches)
145 'cmbj', # Modified Becke-Johnson MetaGGA c-parameter
146 'cmbja', # Modified Becke-Johnson MetaGGA alpha-parameter
147 'cmbjb', # Modified Becke-Johnson MetaGGA beta-parameter
148 'sigma_nc_k', # Width of ion gaussians (VASPsol)
149 'sigma_k', # Width of dielectric cavidty (VASPsol)
150 'nc_k', # Cavity turn-on density (VASPsol)
151 'lambda_d_k', # Debye screening length (VASPsol)
152 'ediffsol', # Tolerance for solvation convergence (VASPsol)
153 'deg_threshold', # Degeneracy threshold
154 'omegamin', # Minimum frequency for dense freq. grid
155 'omegamax', # Maximum frequency for dense freq. grid
156 'rtime', # Undocumented parameter
157 'wplasma', # Undocumented parameter
158 'wplasmai', # Undocumented parameter
159 'dfield', # Undocumented parameter
160 'omegatl', # Maximum frequency for coarse freq. grid
161 'encutgwsoft', # Soft energy cutoff for response kernel
162 'encutlf', # Undocumented parameter
163 'scissor', # Scissor correction for GW/BSE calcs
164 'dimer_dist', # Distance between dimer images
165 'step_size', # Step size for finite difference in dimer calculation
166 'step_max', # Maximum step size for dimer calculation
167 'minrot', # Minimum rotation allowed in dimer calculation
168 'dummy_mass', # Mass of dummy atom(s?)
169 'shaketol', # Tolerance for SHAKE algorithm
170 'shaketolsoft', # Soft tolerance for SHAKE algorithm
171 'shakesca', # Scaling of each step taken in SHAKE algorithm
172 'hills_stride', # Undocumented metadynamics parameter
173 'hills_h', # Height (in eV) of gaussian bias for metadynamics
174 'hills_w', # Width of gaussian bias for metadynamics
175 'hills_k', # Force constant coupling dummy&real for metadynamics
176 'hills_m', # Mass of dummy particle for use in metadynamics
177 'hills_temperature', # Temp. of dummy particle for metadynamics
178 'hills_andersen_prob', # Probability of thermostat coll. for metadynamics
179 'hills_sqq', # Nose-hoover particle mass for metadynamics
180 'dvvdelta0', # Undocumented parameter
181 'dvvvnorm0', # Undocumented parameter
182 'dvvminpotim', # Undocumented parameter
183 'dvvmaxpotim', # Undocumented parameter
184 'efermi', # Undocumented parameter
185 'enchg', # Undocumented charge fitting parameter
186 'tau0', # Undocumented charge fitting parameter
187 'encut4o', # Cutoff energy for 4-center integrals (HF)
188 'param3', # Undocumented HF parameter
189 'model_eps0', # Undocumented HF parameter
190 'model_alpha', # Undocumented HF parameter
191 'qmaxfockae', # Undocumented HF parameter
192 'hfscreenc', # Range-separated screening length for correlations
193 'hfrcut', # Cutoff radius for HF potential kernel
194 'encutae', # Undocumented parameter for all-electron density calc.
195 'encutsubrotscf', # Undocumented subspace rotation SCF parameter
196 'enini', # Cutoff energy for wavefunctions (?)
197 'wc', # Undocumented mixing parameter
198 'enmax', # Cutoff energy for wavefunctions (?)
199 'scalee', # Undocumented parameter
200 'eref', # Reference energy
201 'epsilon', # Dielectric constant of bulk charged cells
202 'rcmix', # Mixing parameter for core density in rel. core calcs.
203 'esemicore', # Energetic lower bound for states considered "semicore"
204 'external_pressure', # Pressure for NPT calcs., equivalent to PSTRESS
205 'lj_radius', # Undocumented classical vdW parameter
206 'lj_epsilon', # Undocumented classical vdW parameter
207 'lj_sigma', # Undocumented classical vdW parameter
208 'mbd_beta', # TS MBD vdW correction damping parameter
209 'scsrad', # Cutoff radius for dipole-dipole interaction tensor in SCS
210 'hitoler', # Iterative Hirschfeld partitioning tolerance
211 'lambda', # "Spring constant" for magmom constraint calcs.
212 'kproj_threshold', # Threshold for k-point projection scheme
213 'maxpwamp', # Undocumented HF parameter
214 'vcutoff', # Undocumented parameter
215 'mdtemp', # Temperature for AIMD
216 'mdgamma', # Undocumented AIMD parameter
217 'mdalpha', # Undocumented AIMD parameter
218 'ofield_kappa', # Bias potential strength for interface pinning method
219 'ofield_q6_near', # Steinhardt-Nelson Q6 parameters for interface pinning
220 'ofield_q6_far', # Steinhardt-Nelson Q6 parameters for interface pinning
221 'ofield_a', # Target order parameter for interface pinning method
222 'pthreshold', # Don't print timings for routines faster than this value
223 'qltol', # Eigenvalue tolerance for Lanczos iteration (instanton)
224 'qdr', # Step size for building Lanczos matrix & CG (instanton)
225 'qmaxmove', # Max step size (instanton)
226 'qdt', # Timestep for quickmin minimization (instanton)
227 'qtpz', # Temperature (instanton)
228 'qftol', # Tolerance (instanton)
229 'nupdown', # fix spin moment to specified value
230]
232exp_keys = [
233 'ediff', # stopping-criterion for electronic upd.
234 'ediffg', # stopping-criterion for ionic upd.
235 'symprec', # precession in symmetry routines
236 # The next keywords pertain to the VTST add-ons from Graeme Henkelman's
237 # group at UT Austin
238 'fdstep', # Finite diference step for IOPT = 1 or 2
239]
241string_keys = [
242 'algo', # algorithm: Normal (Davidson) | Fast | Very_Fast (RMM-DIIS)
243 'gga', # xc-type: PW PB LM or 91 (LDA if not set)
244 'metagga', #
245 'prec', # Precission of calculation (Low, Normal, Accurate)
246 'system', # name of System
247 'precfock', # FFT grid in the HF related routines
248 'radeq', # Which type of radial equations to use for rel. core calcs.
249 'localized_basis', # Basis to use in CRPA
250 'proutine', # Select profiling routine
251]
253int_keys = [
254 'ialgo', # algorithm: use only 8 (CG) or 48 (RMM-DIIS)
255 'ibrion', # ionic relaxation: 0-MD 1-quasi-New 2-CG
256 'icharg', # charge: 0-WAVECAR 1-CHGCAR 2-atom 10-const
257 'idipol', # monopol/dipol and quadropole corrections
258 'images', # number of images for NEB calculation
259 'iniwav', # initial electr wf. : 0-lowe 1-rand
260 'isif', # calculate stress and what to relax
261 'ismear', # part. occupancies: -5 Blochl -4-tet -1-fermi 0-gaus >0 MP
262 'ispin', # spin-polarized calculation
263 'istart', # startjob: 0-new 1-cont 2-samecut
264 'isym', # symmetry: 0-nonsym 1-usesym 2-usePAWsym
265 'iwavpr', # prediction of wf.: 0-non 1-charg 2-wave 3-comb
266 'kpar', # k-point parallelization paramater
267 'ldauprint', # 0-silent, 1-occ. matrix written to OUTCAR, 2-1+pot. matrix
268 # written
269 'ldautype', # L(S)DA+U: 1-Liechtenstein 2-Dudarev 4-Liechtenstein(LDAU)
270 'lmaxmix', #
271 'lorbit', # create PROOUT
272 'maxmix', #
273 'ngx', # FFT mesh for wavefunctions, x
274 'ngxf', # FFT mesh for charges x
275 'ngy', # FFT mesh for wavefunctions, y
276 'ngyf', # FFT mesh for charges y
277 'ngz', # FFT mesh for wavefunctions, z
278 'ngzf', # FFT mesh for charges z
279 'nbands', # Number of bands
280 'nblk', # blocking for some BLAS calls (Sec. 6.5)
281 'nbmod', # specifies mode for partial charge calculation
282 'nelm', # nr. of electronic steps (default 60)
283 'nelmdl', # nr. of initial electronic steps
284 'nelmin',
285 'nfree', # number of steps per DOF when calculting Hessian using
286 # finite differences
287 'nkred', # define sub grid of q-points for HF with
288 # nkredx=nkredy=nkredz
289 'nkredx', # define sub grid of q-points in x direction for HF
290 'nkredy', # define sub grid of q-points in y direction for HF
291 'nkredz', # define sub grid of q-points in z direction for HF
292 'nomega', # number of frequency points
293 'nomegar', # number of frequency points on real axis
294 'npar', # parallelization over bands
295 'nsim', # evaluate NSIM bands simultaneously if using RMM-DIIS
296 'nsw', # number of steps for ionic upd.
297 'nwrite', # verbosity write-flag (how much is written)
298 'vdwgr', # extra keyword for Andris program
299 'vdwrn', # extra keyword for Andris program
300 'voskown', # use Vosko, Wilk, Nusair interpolation
301 # The next keywords pertain to the VTST add-ons from Graeme Henkelman's
302 # group at UT Austin
303 'ichain', # Flag for controlling which method is being used (0=NEB,
304 # 1=DynMat, 2=Dimer, 3=Lanczos) if ichain > 3, then both
305 # IBRION and POTIM are automatically set in the INCAR file
306 'iopt', # Controls which optimizer to use. for iopt > 0, ibrion = 3
307 # and potim = 0.0
308 'snl', # Maximum dimentionality of the Lanczos matrix
309 'lbfgsmem', # Steps saved for inverse Hessian for IOPT = 1 (LBFGS)
310 'fnmin', # Max iter. before adjusting dt and alpha for IOPT = 7 (FIRE)
311 'icorelevel', # core level shifts
312 'clnt', # species index
313 'cln', # main quantum number of excited core electron
314 'cll', # l quantum number of excited core electron
315 'ivdw', # Choose which dispersion correction method to use
316 'nbandsgw', # Number of bands for GW
317 'nbandso', # Number of occupied bands for electron-hole treatment
318 'nbandsv', # Number of virtual bands for electron-hole treatment
319 'ncore', # Number of cores per band, equal to number of cores divided
320 # by npar
321 'mdalgo', # Determines which MD method of Tomas Bucko to use
322 'nedos', # Number of grid points in DOS
323 'turbo', # Ewald, 0 = Normal, 1 = PME
324 'omegapar', # Number of groups for response function calc.
325 # (Possibly Depricated) Number of groups in real time for
326 # response function calc.
327 'taupar',
328 'ntaupar', # Number of groups in real time for response function calc.
329 'antires', # How to treat antiresonant part of response function
330 'magatom', # Index of atom at which to place magnetic field (NMR)
331 'jatom', # Index of atom at which magnetic moment is evaluated (NMR)
332 'ichibare', # chi_bare stencil size (NMR)
333 'nbas', # Undocumented Bond-Boost parameter (GH patches)
334 'rmds', # Undocumented Bond-Boost parameter (GH patches)
335 'ilbfgsmem', # Number of histories to store for LBFGS (GH patches)
336 'vcaimages', # Undocumented parameter (GH patches)
337 'ntemper', # Undocumented subspace diagonalization param. (GH patches)
338 'ncshmem', # Share memory between this many cores on each process
339 'lmaxtau', # Undocumented MetaGGA parameter (prob. max ang.mom. for tau)
340 'kinter', # Additional finer grid (?)
341 'ibse', # Type of BSE calculation
342 'nbseeig', # Number of BSE wfns to write
343 'naturalo', # Use NATURALO (?)
344 'nbandsexact', # Undocumented parameter
345 'nbandsgwlow', # Number of bands for which shifts are calculated
346 'nbandslf', # Number of bands included in local field effect calc.
347 'omegagrid', # Undocumented parameter
348 'telescope', # Undocumented parameter
349 'maxmem', # Amount of memory to allocate per core in MB
350 'nelmhf', # Number of iterations for HF part (GW)
351 'dim', # Undocumented parameter
352 'nkredlf', # Reduce k-points for local field effects
353 'nkredlfx', # Reduce k-points for local field effects in X
354 'nkredlfy', # Reduce k-points for local field effects in Y
355 'nkredlfz', # Reduce k-points for local field effects in Z
356 'lmaxmp2', # Undocumented parameter
357 'switch', # Undocumented dimer parameter
358 'findiff', # Use forward (1) or central (2) finite difference for dimer
359 'engine', # Undocumented dimer parameter
360 'restartcg', # Undocumented dimer parameter
361 'thermostat', # Deprecated parameter for selecting MD method (use MDALGO)
362 'scaling', # After how many steps velocities should be rescaled
363 'shakemaxiter', # Maximum # of iterations in SHAKE algorithm
364 'equi_regime', # Number of steps to equilibrate for
365 'hills_bin', # Update metadynamics bias after this many steps
366 'hills_maxstride', # Undocumented metadynamics parameter
367 'dvvehistory', # Undocumented parameter
368 'ipead', # Undocumented parameter
369 'ngaus', # Undocumented charge fitting parameter
370 'exxoep', # Undocumented HF parameter
371 'fourorbit', # Undocumented HF parameter
372 'model_gw', # Undocumented HF parameter
373 'hflmax', # Maximum L quantum number for HF calculation
374 'lmaxfock', # Maximum L quantum number for HF calc. (same as above)
375 'lmaxfockae', # Undocumented HF parameter
376 'nmaxfockae', # Undocumented HF parameter
377 'nblock_fock', # Undocumented HF parameter
378 'idiot', # Determines which warnings/errors to print
379 'nrmm', # Number of RMM-DIIS iterations
380 'mremove', # Undocumented mixing parameter
381 'inimix', # Undocumented mixing parameter
382 'mixpre', # Undocumented mixing parameter
383 'nelmall', # Undocumented parameter
384 'nblock', # How frequently to write data
385 'kblock', # How frequently to write data
386 'npaco', # Undocumented pair correlation function parameter
387 'lmaxpaw', # Max L quantum number for on-site charge expansion
388 'irestart', # Undocumented parameter
389 'nreboot', # Undocumented parameter
390 'nmin', # Undocumented parameter
391 'nlspline', # Undocumented parameter
392 'ispecial', # "Select undocumented and unsupported special features"
393 'rcrep', # Number of steps between printing relaxed core info
394 'rcndl', # Wait this many steps before updating core density
395 'rcstrd', # Relax core density after this many SCF steps
396 'vdw_idampf', # Select type of damping function for TS vdW
397 'i_constrained_m', # Select type of magmom. constraint to use
398 'igpar', # "G parallel" direction for Berry phase calculation
399 'nppstr', # Number of kpts in "igpar' direction for Berry phase calc.
400 'nbands_out', # Undocumented QP parameter
401 'kpts_out', # Undocumented QP parameter
402 'isp_out', # Undocumented QP parameter
403 'nomega_out', # Undocumented QP parameter
404 'maxiter_ft', # Max iterations for sloppy Remez algorithm
405 'nmaxalt', # Max sample points for alternant in Remez algorithms
406 'itmaxlsq', # Max iterations in LSQ search algorithm
407 'ndatalsq', # Number of sample points for LSQ search algorithm
408 'ncore_in_image1', # Undocumented parameter
409 'kimages', # Undocumented parameter
410 'ncores_per_band', # Undocumented parameter
411 'maxlie', # Max iterations in CRPA diagonalization routine
412 'ncrpalow', # Undocumented CRPA parameter
413 'ncrpahigh', # Undocumented CRPA parameter
414 'nwlow', # Undocumented parameter
415 'nwhigh', # Undocumented parameter
416 'nkopt', # Number of k-points to include in Optics calculation
417 'nkoffopt', # K-point "counter offset" for Optics
418 'nbvalopt', # Number of valence bands to write in OPTICS file
419 'nbconopt', # Number of conduction bands to write in OPTICS file
420 'ch_nedos', # Number dielectric function calculation grid points for XAS
421 'plevel', # No timings for routines with "level" higher than this
422 'qnl', # Lanczos matrix size (instanton)
423]
425bool_keys = [
426 'addgrid', # finer grid for augmentation charge density
427 'kgamma', # The generated kpoint grid (from KSPACING) is either
428 # centred at the $\Gamma$
429 # point (e.g. includes the $\Gamma$ point)
430 # (KGAMMA=.TRUE.)
431 'laechg', # write AECCAR0/AECCAR1/AECCAR2
432 'lasph', # non-spherical contributions to XC energy (and pot for
433 # VASP.5.X)
434 'lasync', # overlap communcation with calculations
435 'lcharg', #
436 'lcorr', # Harris-correction to forces
437 'ldau', # L(S)DA+U
438 'ldiag', # algorithm: perform sub space rotation
439 'ldipol', # potential correction mode
440 'lelf', # create ELFCAR
441 'lepsilon', # enables to calculate and to print the BEC tensors
442 'lhfcalc', # switch to turn on Hartree Fock calculations
443 'loptics', # calculate the frequency dependent dielectric matrix
444 'lpard', # evaluate partial (band and/or k-point) decomposed charge
445 # density
446 'lplane', # parallelisation over the FFT grid
447 'lscalapack', # switch off scaLAPACK
448 'lscalu', # switch of LU decomposition
449 'lsepb', # write out partial charge of each band separately?
450 'lsepk', # write out partial charge of each k-point separately?
451 'lthomas', #
452 'luse_vdw', # Invoke vdW-DF implementation by Klimes et. al
453 'lvdw', # Invoke DFT-D2 method of Grimme
454 'lvhar', # write Hartree potential to LOCPOT (vasp 5.x)
455 'lvtot', # create WAVECAR/CHGCAR/LOCPOT
456 'lwave', #
457 # The next keywords pertain to the VTST add-ons from Graeme Henkelman's
458 # group at UT Austin
459 'lclimb', # Turn on CI-NEB
460 'ltangentold', # Old central difference tangent
461 'ldneb', # Turn on modified double nudging
462 'lnebcell', # Turn on SS-NEB
463 'lglobal', # Optmize NEB globally for LBFGS (IOPT = 1)
464 'llineopt', # Use force based line minimizer for translation (IOPT = 1)
465 'lbeefens', # Switch on print of BEE energy contributions in OUTCAR
466 'lbeefbas', # Switch off print of all BEEs in OUTCAR
467 'lcalcpol', # macroscopic polarization (vasp5.2). 'lcalceps'
468 'lcalceps', # Macroscopic dielectric properties and Born effective charge
469 # tensors (vasp 5.2)
470 'lvdw', # Turns on dispersion correction
471 'lvdw_ewald', # Turns on Ewald summation for Grimme's DFT-D2 and
472 # Tkatchenko and Scheffler's DFT-TS dispersion correction
473 'lspectral', # Use the spectral method to calculate independent particle
474 # polarizability
475 'lrpa', # Include local field effects on the Hartree level only
476 'lwannier90', # Switches on the interface between VASP and WANNIER90
477 'lsorbit', # Enable spin-orbit coupling
478 'lsol', # turn on solvation for Vaspsol
479 'lautoscale', # automatically calculate inverse curvature for VTST LBFGS
480 'interactive', # Enables interactive calculation for VaspInteractive
481 'lauger', # Perform Auger calculation (Auger)
482 'lauger_eeh', # Calculate EEH processes (Auger)
483 'lauger_ehh', # Calculate EHH processes (Auger)
484 'lauger_collect', # Collect wfns before looping over k-points (Auger)
485 'lauger_dhdk', # Auto-determine E. window width from E. derivs. (Auger)
486 'lauger_jit', # Distribute wavefunctions for k1-k4 (Auger)
487 'orbitalmag', # Enable orbital magnetization (NMR)
488 'lchimag', # Use linear response for shielding tensor (NMR)
489 'lwrtcur', # Write response of current to mag. field to file (NMR)
490 'lnmr_sym_red', # Reduce symmetry for finite difference (NMR)
491 'lzora', # Use ZORA approximation in linear-response NMR (NMR)
492 'lbone', # Use B-component in AE one-center terms for LR NMR (NMR)
493 'lmagbloch', # Use Bloch summations to obtain orbital magnetization (NMR)
494 'lgauge', # Use gauge transformation for zero moment terms (NMR)
495 'lbfconst', # Use constant B-field with sawtooth vector potential (NMR)
496 'nucind', # Use nuclear independent calculation (NMR)
497 'lnicsall', # Use all grid points for 'nucind' calculation (NMR)
498 'llraug', # Use two-center corrections for induced B-field (NMR)
499 'lbbm', # Undocumented Bond-Boost parameter (GH patches)
500 'lnoncollinear', # Do non-collinear spin polarized calculation
501 'bfgsdfp', # Undocumented BFGS parameter (GH patches)
502 'linemin', # Use line minimization (GH patches)
503 'ldneborg', # Undocumented NEB parameter (GH patches)
504 'dseed', # Undocumented dimer parameter (GH patches)
505 'linteract', # Undocumented parameter (GH patches)
506 'lmpmd', # Undocumented parameter (GH patches)
507 'ltwodim', # Makes stress tensor two-dimensional (GH patches)
508 'fmagflag', # Use force magnitude as convergence criterion (GH patches)
509 'ltemper', # Use subspace diagonalization (?) (GH patches)
510 'qmflag', # Undocumented FIRE parameter (GH patches)
511 'lmixtau', # Undocumented MetaGGA parameter
512 'ljdftx', # Undocumented VASPsol parameter (VASPsol)
513 'lrhob', # Write the bound charge density (VASPsol)
514 'lrhoion', # Write the ionic charge density (VASPsol)
515 'lnabla', # Undocumented parameter
516 'linterfast', # Interpolate in K using linear response routines
517 'lvel', # Undocumented parameter
518 'lrpaforce', # Calculate RPA forces
519 'lhartree', # Use IP approx. in BSE (testing only)
520 'ladder', # Use ladder diagrams
521 'lfxc', # Use approximate ladder diagrams
522 'lrsrpa', # Undocumented parameter
523 'lsingles', # Calculate HF singles
524 'lfermigw', # Iterate Fermi level
525 'ltcte', # Undocumented parameter
526 'ltete', # Undocumented parameter
527 'ltriplet', # Undocumented parameter
528 'lfxceps', # Undocumented parameter
529 'lfxheg', # Undocumented parameter
530 'l2order', # Undocumented parameter
531 'lmp2lt', # Undocumented parameter
532 'lgwlf', # Undocumented parameter
533 'lusew', # Undocumented parameter
534 'selfenergy', # Undocumented parameter
535 'oddonlygw', # Avoid gamma point in response function calc.
536 'evenonlygw', # Avoid even points in response function calc.
537 'lspectralgw', # More accurate self-energy calculation
538 'ch_lspec', # Calculate matrix elements btw. core and conduction states
539 'fletcher_reeves', # Undocumented dimer parameter
540 'lidm_selective', # Undocumented dimer parameter
541 'lblueout', # Write output of blue-moon algorithm
542 'hills_variable_w', # Enable variable-width metadynamics bias
543 'dvvminus', # Undocumented parameter
544 'lpead', # Calculate cell-periodic orbital derivs. using finite diff.
545 'skip_edotp', # Skip updating elec. polarization during scf
546 'skip_scf', # Skip calculation w/ local field effects
547 'lchgfit', # Turn on charge fitting
548 'lgausrc', # Undocumented charge fitting parameter
549 'lstockholder', # Enable ISA charge fitting (?)
550 'lsymgrad', # Restore symmetry of gradient (HF)
551 'lhfone', # Calculate one-center terms (HF)
552 'lrscor', # Include long-range correlation (HF)
553 'lrhfcalc', # Include long-range HF (HF)
554 'lmodelhf', # Model HF calculation (HF)
555 'shiftred', # Undocumented HF parameter
556 'hfkident', # Undocumented HF parameter
557 'oddonly', # Undocumented HF parameter
558 'evenonly', # Undocumented HF parameter
559 'lfockaedft', # Undocumented HF parameter
560 'lsubrot', # Enable subspace rotation diagonalization
561 'mixfirst', # Mix before diagonalization
562 'lvcader', # Calculate derivs. w.r.t. VCA parameters
563 'lcompat', # Enable "full compatibility"
564 'lmusic', # "Joke" parameter
565 'ldownsample', # Downsample WAVECAR to fewer k-points
566 'lscaaware', # Disable ScaLAPACK for some things but not all
567 'lorbitalreal', # Undocumented parameter
568 'lmetagga', # Undocumented parameter
569 'lspiral', # Undocumented parameter
570 'lzeroz', # Undocumented parameter
571 'lmono', # Enable "monopole" corrections
572 'lrelcore', # Perform relaxed core calculation
573 'lmimicfc', # Mimic frozen-core calcs. for relaxed core calcs.
574 'lmatchrw', # Match PS partial waves at RWIGS? (otherwise PAW cutoff)
575 'ladaptelin', # Linearize core state energies to avoid divergences
576 'lonlysemicore', # Only linearize semi-core state energies
577 'gga_compat', # Enable backwards-compatible symmetrization of GGA derivs.
578 'lrelvol', # Undocumented classical vdW parameter
579 'lj_only', # Undocumented classical vdW parameter
580 'lvdwscs', # Include self-consistent screening in TS vdW correction
581 'lcfdm', # Use coupled fluctuating dipoles model for TS vdW
582 'lvdw_sametype', # Include interactions between atoms of the same type
583 'lrescaler0', # Rescale damping parameters in SCS vdW correction
584 'lscsgrad', # Calculate gradients for TS+SCS vdW correction energies
585 'lvdwexpansion', # Write 2-6 body contribs. to MBD vdW correction energy
586 'lvdw_relvolone', # Undocumented classical vdW parameter
587 'lberry', # Enable Berry-phase calculation
588 'lpade_fit', # Undocumented QP parameter
589 'lkproj', # Enable projection onto k-points
590 'l_wr_moments', # Undocumented parameter
591 'l_wr_density', # Undocumented parameter
592 'lkotani', # Undocumented parameter
593 'ldyson', # Undocumented parameter
594 'laddherm', # Undocumented parameter
595 'lcrpaplot', # Plot bands used in CRPA response func. calc.
596 'lplotdis', # Plot disentangled bands in CRPA response func. calc.
597 'ldisentangle', # Disentangle bands in CRPA
598 'lweighted', # "Weighted" CRPA approach
599 'luseorth_lcaos', # Use orthogonalized LCAOs in CRPA
600 'lfrpa', # Use full RPA in CRPA
601 'lregularize', # Regularize projectors in CRPA
602 'ldrude', # Include Drude term in CRPA
603 'ldmatrix', # Undocumented parameter
604 'lefg', # Calculate electric field gradient at atomic nuclei
605 'lhyperfine', # Enable Hyperfine calculation
606 'lwannier', # Enable Wannier interface
607 'localize', # Undocumented Wannier parameter
608 'lintpol_wpot', # Interpolate WPOT for Wannier
609 'lintpol_orb', # Interpolate orbitals for Wannier
610 'lintpol_kpath', # Interpolate bandstructure on given kpath for Wannier
611 'lintpol_kpath_orb', # Interpolate orbitals on given kpath for Wannier
612 'lread_eigenvalues', # Use Eigenvalues from EIGENVALUES.INT file
613 'lintpol_velocity', # Interpolate electron velocity for Wannier
614 'lintpol_conductivity', # Interpolate conductivity for Wannier
615 'lwannierinterpol', # Undocumented Wannier parameter
616 'wanproj', # Undocumented Wannier parameter
617 'lorbmom', # Undocumented LDA+U parameter
618 'lwannier90_run', # Undocumented WANNIER90 parameter
619 'lwrite_wanproj', # Write UWAN files for WANNIER90
620 'lwrite_unk', # Write UNK files for WANNIER90
621 'lwrite_mmn_amn', # Write MMN and AMN files for WANNIER90
622 'lread_amn', # Read AMN files instead of recomputing (WANNIER90)
623 'lrhfatm', # Undocumented HF parameter
624 'lvpot', # Calculate unscreened potential
625 'lwpot', # Calculate screened potential
626 'lwswq', # Undocumented parameter
627 'pflat', # Only print "flat" timings to OUTCAR
628 'qifcg', # Use CG instead of quickmin (instanton)
629 'qdo_ins', # Find instanton
630 'qdo_pre', # Calculate prefactor (instanton)
631 # The next keyword pertains to the periodic NBO code of JR Schmidt's group
632 # at UW-Madison (https://github.com/jrschmidt2/periodic-NBO)
633 'lnbo', # Enable NBO analysis
634]
636list_int_keys = [
637 'iband', # bands to calculate partial charge for
638 'kpuse', # k-point to calculate partial charge for
639 'ldaul', # DFT+U parameters, overruled by dict key 'ldau_luj'
640 'random_seed', # List of ints used to seed RNG for advanced MD routines
641 # (Bucko)
642 'auger_bmin_eeh', # 4 ints | Various undocumented parameters for Auger
643 'auger_bmax_eeh', # 4 ints | calculations
644 'auger_bmin_ehh', # 4 ints |
645 'auger_bmax_ehh', # 4 ints |
646 'balist', # nbas ints | Undocumented Bond-Boost parameter (GH patches)
647 'kpoint_bse', # 4 ints | Undocumented parameter
648 'nsubsys', # <=3 ints | Last atom # for each of up to 3 thermostats
649 'vdw_refstate', # ntyp ints | Undocumented classical vdW parameter
650 'vdw_mbd_size', # 3 ints | Supercell size for TS MBD vdW correction
651 'nbands_index', # nbands_out ints | Undocumented QP parameter
652 'kpts_index', # kpts_out ints | Undocumented QP parameter
653 'isp_index', # isp_out ints | Undocumented QP parameter
654 'nomega_index', # nomega_out ints | Undocumented QP parameter
655 'ntarget_states', # nbands ints | Undocumented CRPA parameter
656 'wanproj_i', # nions ints | Undocumented Wannier parameter
657 'wanproj_l', # ? ints | Undocumented Wannier parameter
658]
660list_bool_keys = [
661 'lattice_constraints', # 3 bools | Undocumented advanced MD parameter
662 'lrctype', # ntyp bools | Enable relaxed-core calc. for these atoms
663 'lvdw_onecell', # 3 bools | Enable periodicity in A, B, C vector for vdW
664]
666list_float_keys = [
667 'dipol', # center of cell for dipol
668 'eint', # energy range to calculate partial charge for
669 'ferwe', # Fixed band occupation (spin-paired)
670 'ferdo', # Fixed band occupation (spin-plarized)
671 'magmom', # initial magnetic moments
672 'ropt', # number of grid points for non-local proj in real space
673 'rwigs', # Wigner-Seitz radii
674 'ldauu', # ldau parameters, has potential to redundant w.r.t. dict
675 'ldauj', # key 'ldau_luj', but 'ldau_luj' can't be read direct from
676 # the INCAR (since it needs to know information about atomic
677 # species. In case of conflict 'ldau_luj' gets written out
678 # when a calculation is set up
679 'vdw_c6', # List of floats of C6 parameters (J nm^6 mol^-1) for each
680 # species (DFT-D2 and DFT-TS)
681 'vdw_c6au', # List of floats of C6 parameters (a.u.) for each species
682 # (DFT-TS)
683 'vdw_r0', # List of floats of R0 parameters (angstroms) for each
684 # species (DFT-D2 and DFT-TS)
685 'vdw_r0au', # List of floats of R0 parameters (a.u.) for each species
686 # (DFT-TS)
687 'vdw_alpha', # List of floats of free-atomic polarizabilities for each
688 # species (DFT-TS)
689 'langevin_gamma', # List of floats for langevin friction coefficients
690 'auger_emin_eeh', # 4 floats | Various undocumented parameters for Auger
691 'auger_emax_eeh', # 4 floats | calculations
692 'auger_emin_ehh', # 4 floats |
693 'auger_emax_ehh', # 4 floats |
694 'avecconst', # 3 floats | magnitude of magnetic moment (NMR)
695 'magdipol', # 3 floats | magnitude of magnetic dipole (NMR)
696 'bconst', # 3 floats | magnitude of constant magnetic field (NMR)
697 'magpos', # 3 floats | position for magnetic moment w/ 'nucind' (NMR)
698 'bext', # 3 floats | Undocumented (probably external magnetic field)
699 'core_c', # ntyp floats | pseudo-core charge magnitude (VASPsol)
700 'sigma_rc_k', # ntyp floats | width of pseudo-core gaussians (VASPsol)
701 'darwinr', # ntypd (?) floats | Undocumented parameter
702 'darwinv', # ntypd (?) floats | Undocumented parameter
703 'dummy_k', # ? floats | Force const. connecting dummy atoms to sys.
704 'dummy_r0', # ? floats | Minimum dist., ang., etc. for dummy atom DOFs
705 'dummy_positions', # 3 floats | Position of dummy atom(s?)
706 'psubsys', # <=3 floats | Coll. prob. for each of up to 3 thermostats
707 'tsubsys', # <=3 floats | Temp. for each of up to 3 thermostats
708 'increm', # ? floats | Undocumented advanced MD parameter
709 'value_min', # ? floats | Undocumented advanced MD parameter
710 'value_max', # ? floats | Undocumented advanced MD parameter
711 'hills_position', # ? floats | Dummy particle(s) pos. for metadynamics
712 'hills_velocity', # ? floats | Dummy particle(s) vel. for metadynamics
713 'spring_k', # ? floats | Spring constant for harmonic constraints
714 'spring_r0', # ? floats | Spring minima for harmonic constraints
715 'spring_v0', # ? floats | Initial velocity of harmonic constraints
716 'hills_wall_lower', # ? floats | Undocumented metadynamics parameter
717 'hills_wall_upper', # ? floats | Undocumented metadynamics parameter
718 'efield_pead', # 3 floats | homogeneous electric field for PEAD calc.
719 'zct', # ? floats | Undocumented charge fitting parameter
720 'rgaus', # ? floats | Undocumented charge fitting parameter
721 'hfalpha', # 10 floats | Undocumented HF parameter
722 'mcalpha', # 10 floats | Undocumented HF parameter
723 'saxis', # 3 floats | Coordinate for collinear spin calculations
724 'vca', # ? floats | Atom weight for VCA calculations
725 'stm', # 7 floats | "range for STM data"
726 'qspiral', # 3 floats | Undocumented parameter
727 'external_stress', # 6 floats | Target stress (adds w/ external_pressure)
728 'm_constr', # 3*nions floats | Local magmom assigned to each spin DOF
729 'quad_efg', # ntyp floats | Nuclear quadrupole moments
730 'ngyromag', # ntyp floats | Nuclear gyromagnetic ratios
731 'rcrhocut', # ntyp floats | Core density cutoff rad. for HF relcore calc
732 'ofield_k', # 3 floats | Undocumented parameter
733 'paripot', # ? floats | Undocumented parameter
734 'smearings', # ? floats | ismear,sigma smearing params to loop over
735 'wanproj_e', # 2 floats | Undocumented Wannier parameter
736]
738special_keys = [
739 'lreal', # non-local projectors in real space
740]
742dict_keys = [
743 'ldau_luj', # dictionary with L(S)DA+U parameters, e.g. {'Fe':{'L':2,
744 # 'U':4.0, 'J':0.9}, ...}
745]
747keys: List[str] = [
748 # 'NBLOCK' and KBLOCK inner block; outer block
749 # 'NPACO' and APACO distance and nr. of slots for P.C.
750 # 'WEIMIN, EBREAK, DEPER special control tags
751]
754class GenerateVaspInput:
755 # Parameters corresponding to 'xc' settings. This may be modified
756 # by the user in-between loading calculators.vasp submodule and
757 # instantiating the calculator object with calculators.vasp.Vasp()
758 xc_defaults = {
759 'lda': {
760 'pp': 'LDA'
761 },
762 # GGAs
763 'blyp': { # https://www.vasp.at/forum/viewtopic.php?p=17234
764 'pp': 'PBE',
765 'gga': 'B5',
766 'aldax': 1.00,
767 'aggax': 1.00,
768 'aggac': 1.00,
769 'aldac': 0.00
770 },
771 'pw91': {
772 'pp': 'PW91',
773 'gga': '91'
774 },
775 'pbe': {
776 'pp': 'PBE',
777 'gga': 'PE'
778 },
779 'pbesol': {
780 'gga': 'PS'
781 },
782 'revpbe': {
783 'gga': 'RE'
784 },
785 'rpbe': {
786 'gga': 'RP'
787 },
788 'am05': {
789 'gga': 'AM'
790 },
791 # Meta-GGAs
792 'tpss': {
793 'metagga': 'TPSS'
794 },
795 'revtpss': {
796 'metagga': 'RTPSS'
797 },
798 'm06l': {
799 'metagga': 'M06L'
800 },
801 'ms0': {
802 'metagga': 'MS0'
803 },
804 'ms1': {
805 'metagga': 'MS1'
806 },
807 'ms2': {
808 'metagga': 'MS2'
809 },
810 'scan': {
811 'metagga': 'SCAN'
812 },
813 'rscan': {
814 'metagga': 'RSCAN'
815 },
816 'r2scan': {
817 'metagga': 'R2SCAN'
818 },
819 'scan-rvv10': {
820 'metagga': 'SCAN',
821 'luse_vdw': True,
822 'bparam': 15.7
823 },
824 'mbj': {
825 # Modified Becke-Johnson
826 'metagga': 'MBJ',
827 },
828 'tb09': {
829 # Alias for MBJ
830 'metagga': 'MBJ',
831 },
832 # vdW-DFs
833 'vdw-df': {
834 'gga': 'RE',
835 'luse_vdw': True,
836 'aggac': 0.
837 },
838 'vdw-df-cx': {
839 'gga': 'CX',
840 'luse_vdw': True,
841 'aggac': 0.
842 },
843 'vdw-df-cx0p': {
844 'gga': 'CX',
845 'luse_vdw': True,
846 'aggac': 0.,
847 'lhfcalc': True,
848 'aexx': 0.2,
849 'aggax': 0.8
850 },
851 'optpbe-vdw': {
852 'gga': 'OR',
853 'luse_vdw': True,
854 'aggac': 0.0
855 },
856 'optb88-vdw': {
857 'gga': 'BO',
858 'luse_vdw': True,
859 'aggac': 0.0,
860 'param1': 1.1 / 6.0,
861 'param2': 0.22
862 },
863 'optb86b-vdw': {
864 'gga': 'MK',
865 'luse_vdw': True,
866 'aggac': 0.0,
867 'param1': 0.1234,
868 'param2': 1.0
869 },
870 'vdw-df2': {
871 'gga': 'ML',
872 'luse_vdw': True,
873 'aggac': 0.0,
874 'zab_vdw': -1.8867
875 },
876 'rev-vdw-df2': {
877 'gga': 'MK',
878 'luse_vdw': True,
879 'param1': 0.1234,
880 'param2': 0.711357,
881 'zab_vdw': -1.8867,
882 'aggac': 0.0
883 },
884 'beef-vdw': {
885 'gga': 'BF',
886 'luse_vdw': True,
887 'zab_vdw': -1.8867
888 },
889 # Hartree-Fock and hybrids
890 'hf': {
891 'lhfcalc': True,
892 'aexx': 1.0,
893 'aldac': 0.0,
894 'aggac': 0.0
895 },
896 'b3lyp': {
897 'gga': 'B3',
898 'lhfcalc': True,
899 'aexx': 0.2,
900 'aggax': 0.72,
901 'aggac': 0.81,
902 'aldac': 0.19
903 },
904 'pbe0': {
905 'gga': 'PE',
906 'lhfcalc': True
907 },
908 'hse03': {
909 'gga': 'PE',
910 'lhfcalc': True,
911 'hfscreen': 0.3
912 },
913 'hse06': {
914 'gga': 'PE',
915 'lhfcalc': True,
916 'hfscreen': 0.2
917 },
918 'hsesol': {
919 'gga': 'PS',
920 'lhfcalc': True,
921 'hfscreen': 0.2
922 },
923 # MN-VFM functionals
924 'sogga': {
925 'gga': 'SA'
926 },
927 'sogga11': {
928 'gga': 'S1'
929 },
930 'sogga11-x': {
931 'gga': 'SX',
932 'lhfcalc': True,
933 'aexx': 0.401
934 },
935 'n12': {
936 'gga': 'N2'
937 },
938 'n12-sx': {
939 'gga': 'NX',
940 'lhfcalc': True,
941 'lhfscreen': 0.2
942 },
943 'mn12l': {
944 'metagga': 'MN12L'
945 },
946 'gam': {
947 'gga': 'GA'
948 },
949 'mn15l': {
950 'metagga': 'MN15L'
951 },
952 'hle17': {
953 'metagga': 'HLE17'
954 },
955 'revm06l': {
956 'metagga': 'revM06L'
957 },
958 'm06sx': {
959 'metagga': 'M06SX',
960 'lhfcalc': True,
961 'hfscreen': 0.189,
962 'aexx': 0.335
963 }
964 }
966 # environment variable for PP paths
967 VASP_PP_PATH = 'VASP_PP_PATH'
969 def __init__(self, restart=None):
970 self.float_params = {}
971 self.exp_params = {}
972 self.string_params = {}
973 self.int_params = {}
974 self.bool_params = {}
975 self.list_bool_params = {}
976 self.list_int_params = {}
977 self.list_float_params = {}
978 self.special_params = {}
979 self.dict_params = {}
980 for key in float_keys:
981 self.float_params[key] = None
982 for key in exp_keys:
983 self.exp_params[key] = None
984 for key in string_keys:
985 self.string_params[key] = None
986 for key in int_keys:
987 self.int_params[key] = None
988 for key in bool_keys:
989 self.bool_params[key] = None
990 for key in list_bool_keys:
991 self.list_bool_params[key] = None
992 for key in list_int_keys:
993 self.list_int_params[key] = None
994 for key in list_float_keys:
995 self.list_float_params[key] = None
996 for key in special_keys:
997 self.special_params[key] = None
998 for key in dict_keys:
999 self.dict_params[key] = None
1001 # Initialize internal dictionary of input parameters which are
1002 # not regular VASP keys
1003 self.input_params = {
1004 'xc': None, # Exchange-correlation recipe (e.g. 'B3LYP')
1005 'pp': None, # Pseudopotential file (e.g. 'PW91')
1006 'setups': None, # Special setups (e.g pv, sv, ...)
1007 'txt': '-', # Where to send information
1008 'kpts': (1, 1, 1), # k-points
1009 # Option to use gamma-sampling instead of Monkhorst-Pack:
1010 'gamma': False,
1011 # number of points between points in band structures:
1012 'kpts_nintersections': None,
1013 # Option to write explicit k-points in units
1014 # of reciprocal lattice vectors:
1015 'reciprocal': False,
1016 # Switch to disable writing constraints to POSCAR
1017 'ignore_constraints': False,
1018 # Net charge for the whole system; determines nelect if not 0
1019 'charge': None,
1020 # Deprecated older parameter which works just like "charge" but
1021 # with the sign flipped
1022 'net_charge': None,
1023 # Custom key-value pairs, written to INCAR with *no* type checking
1024 'custom': {},
1025 }
1027 def set_xc_params(self, xc):
1028 """Set parameters corresponding to XC functional"""
1029 xc = xc.lower()
1030 if xc is None:
1031 pass
1032 elif xc not in self.xc_defaults:
1033 xc_allowed = ', '.join(self.xc_defaults.keys())
1034 raise ValueError('{0} is not supported for xc! Supported xc values'
1035 'are: {1}'.format(xc, xc_allowed))
1036 else:
1037 # XC defaults to PBE pseudopotentials
1038 if 'pp' not in self.xc_defaults[xc]:
1039 self.set(pp='PBE')
1040 self.set(**self.xc_defaults[xc])
1042 def set(self, **kwargs):
1044 if (('ldauu' in kwargs) and ('ldaul' in kwargs) and ('ldauj' in kwargs)
1045 and ('ldau_luj' in kwargs)):
1046 raise NotImplementedError(
1047 'You can either specify ldaul, ldauu, and ldauj OR '
1048 'ldau_luj. ldau_luj is not a VASP keyword. It is a '
1049 'dictionary that specifies L, U and J for each '
1050 'chemical species in the atoms object. '
1051 'For example for a water molecule:'
1052 '''ldau_luj={'H':{'L':2, 'U':4.0, 'J':0.9},
1053 'O':{'L':2, 'U':4.0, 'J':0.9}}''')
1055 if 'xc' in kwargs:
1056 self.set_xc_params(kwargs['xc'])
1057 for key in kwargs:
1058 if key in self.float_params:
1059 self.float_params[key] = kwargs[key]
1060 elif key in self.exp_params:
1061 self.exp_params[key] = kwargs[key]
1062 elif key in self.string_params:
1063 self.string_params[key] = kwargs[key]
1064 elif key in self.int_params:
1065 self.int_params[key] = kwargs[key]
1066 elif key in self.bool_params:
1067 self.bool_params[key] = kwargs[key]
1068 elif key in self.list_bool_params:
1069 self.list_bool_params[key] = kwargs[key]
1070 elif key in self.list_int_params:
1071 self.list_int_params[key] = kwargs[key]
1072 elif key in self.list_float_params:
1073 self.list_float_params[key] = kwargs[key]
1074 elif key in self.special_params:
1075 self.special_params[key] = kwargs[key]
1076 elif key in self.dict_params:
1077 self.dict_params[key] = kwargs[key]
1078 elif key in self.input_params:
1079 self.input_params[key] = kwargs[key]
1080 else:
1081 raise TypeError('Parameter not defined: ' + key)
1083 def check_xc(self):
1084 """Make sure the calculator has functional & pseudopotentials set up
1086 If no XC combination, GGA functional or POTCAR type is specified,
1087 default to PW91. Otherwise, try to guess the desired pseudopotentials.
1088 """
1090 p = self.input_params
1092 # There is no way to correctly guess the desired
1093 # set of pseudopotentials without 'pp' being set.
1094 # Usually, 'pp' will be set by 'xc'.
1095 if 'pp' not in p or p['pp'] is None:
1096 if self.string_params['gga'] is None:
1097 p.update({'pp': 'lda'})
1098 elif self.string_params['gga'] == '91':
1099 p.update({'pp': 'pw91'})
1100 elif self.string_params['gga'] == 'PE':
1101 p.update({'pp': 'pbe'})
1102 else:
1103 raise NotImplementedError(
1104 "Unable to guess the desired set of pseudopotential"
1105 "(POTCAR) files. Please do one of the following: \n"
1106 "1. Use the 'xc' parameter to define your XC functional."
1107 "These 'recipes' determine the pseudopotential file as "
1108 "well as setting the INCAR parameters.\n"
1109 "2. Use the 'gga' settings None (default), 'PE' or '91'; "
1110 "these correspond to LDA, PBE and PW91 respectively.\n"
1111 "3. Set the POTCAR explicitly with the 'pp' flag. The "
1112 "value should be the name of a folder on the VASP_PP_PATH"
1113 ", and the aliases 'LDA', 'PBE' and 'PW91' are also"
1114 "accepted.\n")
1116 if (p['xc'] is not None and p['xc'].lower() == 'lda'
1117 and p['pp'].lower() != 'lda'):
1118 warnings.warn("XC is set to LDA, but PP is set to "
1119 "{0}. \nThis calculation is using the {0} "
1120 "POTCAR set. \n Please check that this is "
1121 "really what you intended!"
1122 "\n".format(p['pp'].upper()))
1124 def _make_sort(
1125 self, atoms: ase.Atoms, special_setups: Sequence[int] = ()
1126 ) -> Tuple[List[int], List[int]]:
1127 symbols, _ = count_symbols(atoms, exclude=special_setups)
1129 # Create sorting list
1130 srt = [] # type: List[int]
1131 srt.extend(special_setups)
1133 for symbol in symbols:
1134 for m, atom in enumerate(atoms):
1135 if m in special_setups:
1136 continue
1137 if atom.symbol == symbol:
1138 srt.append(m)
1139 # Create the resorting list
1140 resrt = list(range(len(srt)))
1141 for n in range(len(resrt)):
1142 resrt[srt[n]] = n
1143 return srt, resrt
1145 def _build_pp_list(self,
1146 atoms,
1147 setups=None,
1148 special_setups: Sequence[int] = ()):
1149 """Build the pseudopotential lists"""
1151 p = self.input_params
1153 if setups is None:
1154 setups, special_setups = self._get_setups()
1156 symbols, _ = count_symbols(atoms, exclude=special_setups)
1158 # Potpaw folders may be identified by an alias or full name
1159 for pp_alias, pp_folder in (('lda', 'potpaw'), ('pw91', 'potpaw_GGA'),
1160 ('pbe', 'potpaw_PBE')):
1161 if p['pp'].lower() == pp_alias:
1162 break
1163 else:
1164 pp_folder = p['pp']
1166 if self.VASP_PP_PATH in os.environ:
1167 pppaths = os.environ[self.VASP_PP_PATH].split(':')
1168 else:
1169 pppaths = []
1170 ppp_list = []
1171 # Setting the pseudopotentials, first special setups and
1172 # then according to symbols
1173 for m in special_setups:
1174 if m in setups:
1175 special_setup_index = m
1176 elif str(m) in setups:
1177 special_setup_index = str(m) # type: ignore
1178 else:
1179 raise Exception("Having trouble with special setup index {0}."
1180 " Please use an int.".format(m))
1181 potcar = join(pp_folder, setups[special_setup_index], 'POTCAR')
1182 for path in pppaths:
1183 filename = join(path, potcar)
1185 if isfile(filename) or islink(filename):
1186 ppp_list.append(filename)
1187 break
1188 elif isfile(filename + '.Z') or islink(filename + '.Z'):
1189 ppp_list.append(filename + '.Z')
1190 break
1191 else:
1192 symbol = atoms.symbols[m]
1193 msg = """Looking for {}.
1194 No pseudopotential for symbol{} with setup {} """.format(
1195 potcar, symbol, setups[special_setup_index])
1196 raise RuntimeError(msg)
1198 for symbol in symbols:
1199 try:
1200 potcar = join(pp_folder, symbol + setups[symbol], 'POTCAR')
1201 except (TypeError, KeyError):
1202 potcar = join(pp_folder, symbol, 'POTCAR')
1203 for path in pppaths:
1204 filename = join(path, potcar)
1206 if isfile(filename) or islink(filename):
1207 ppp_list.append(filename)
1208 break
1209 elif isfile(filename + '.Z') or islink(filename + '.Z'):
1210 ppp_list.append(filename + '.Z')
1211 break
1212 else:
1213 msg = ("""Looking for PP for {}
1214 The pseudopotentials are expected to be in:
1215 LDA: $VASP_PP_PATH/potpaw/
1216 PBE: $VASP_PP_PATH/potpaw_PBE/
1217 PW91: $VASP_PP_PATH/potpaw_GGA/
1219 No pseudopotential for {}!""".format(potcar, symbol))
1220 raise RuntimeError(msg)
1221 return ppp_list
1223 def _get_setups(self):
1224 p = self.input_params
1226 special_setups = []
1228 # Default setup lists are available: 'minimal', 'recommended' and 'GW'
1229 # These may be provided as a string e.g.::
1230 #
1231 # calc = Vasp(setups='recommended')
1232 #
1233 # or in a dict with other specifications e.g.::
1234 #
1235 # calc = Vasp(setups={'base': 'minimal', 'Ca': '_sv', 2: 'O_s'})
1236 #
1237 # Where other keys are either atom identities or indices, and the
1238 # corresponding values are suffixes or the full name of the setup
1239 # folder, respectively.
1241 # Avoid mutating the module dictionary, so we use a copy instead
1242 # Note, it is a nested dict, so a regular copy is not enough
1243 setups_defaults = get_default_setups()
1245 # Default to minimal basis
1246 if p['setups'] is None:
1247 p['setups'] = {'base': 'minimal'}
1249 # String shortcuts are initialised to dict form
1250 elif isinstance(p['setups'], str):
1251 if p['setups'].lower() in setups_defaults.keys():
1252 p['setups'] = {'base': p['setups']}
1254 # Dict form is then queried to add defaults from setups.py.
1255 if 'base' in p['setups']:
1256 setups = setups_defaults[p['setups']['base'].lower()]
1257 else:
1258 setups = {}
1260 # Override defaults with user-defined setups
1261 if p['setups'] is not None:
1262 setups.update(p['setups'])
1264 for m in setups:
1265 try:
1266 special_setups.append(int(m))
1267 except ValueError:
1268 pass
1269 return setups, special_setups
1271 def initialize(self, atoms):
1272 """Initialize a VASP calculation
1274 Constructs the POTCAR file (does not actually write it).
1275 User should specify the PATH
1276 to the pseudopotentials in VASP_PP_PATH environment variable
1278 The pseudopotentials are expected to be in:
1279 LDA: $VASP_PP_PATH/potpaw/
1280 PBE: $VASP_PP_PATH/potpaw_PBE/
1281 PW91: $VASP_PP_PATH/potpaw_GGA/
1283 if your pseudopotentials are somewhere else, or named
1284 differently you may make symlinks at the paths above that
1285 point to the right place. Alternatively, you may pass the full
1286 name of a folder on the VASP_PP_PATH to the 'pp' parameter.
1287 """
1289 self.check_xc()
1290 self.atoms = atoms
1291 self.all_symbols = atoms.get_chemical_symbols()
1292 self.natoms = len(atoms)
1294 self.spinpol = (atoms.get_initial_magnetic_moments().any()
1295 or self.int_params['ispin'] == 2)
1297 setups, special_setups = self._get_setups()
1299 # Determine the number of atoms of each atomic species
1300 # sorted after atomic species
1301 symbols, symbolcount = count_symbols(atoms, exclude=special_setups)
1302 self.sort, self.resort = self._make_sort(atoms,
1303 special_setups=special_setups)
1305 self.atoms_sorted = atoms[self.sort]
1307 # Check if the necessary POTCAR files exists and
1308 # create a list of their paths.
1309 atomtypes = atoms.get_chemical_symbols()
1310 self.symbol_count = []
1311 for m in special_setups:
1312 self.symbol_count.append([atomtypes[m], 1])
1313 for m in symbols:
1314 self.symbol_count.append([m, symbolcount[m]])
1316 # create pseudopotential list
1317 self.ppp_list = self._build_pp_list(atoms,
1318 setups=setups,
1319 special_setups=special_setups)
1321 self.converged = None
1322 self.setups_changed = None
1324 def default_nelect_from_ppp(self):
1325 """ Get default number of electrons from ppp_list and symbol_count
1327 "Default" here means that the resulting cell would be neutral.
1328 """
1329 symbol_valences = []
1330 for filename in self.ppp_list:
1331 with open_potcar(filename=filename) as ppp_file:
1332 r = read_potcar_numbers_of_electrons(ppp_file)
1333 symbol_valences.extend(r)
1334 assert len(self.symbol_count) == len(symbol_valences)
1335 default_nelect = 0
1336 for ((symbol1, count),
1337 (symbol2, valence)) in zip(self.symbol_count, symbol_valences):
1338 assert symbol1 == symbol2
1339 default_nelect += count * valence
1340 return default_nelect
1342 def write_input(self, atoms, directory='./'):
1343 from ase.io.vasp import write_vasp
1344 write_vasp(join(directory, 'POSCAR'),
1345 self.atoms_sorted,
1346 symbol_count=self.symbol_count,
1347 ignore_constraints=self.input_params['ignore_constraints'])
1348 self.write_incar(atoms, directory=directory)
1349 self.write_potcar(directory=directory)
1350 self.write_kpoints(atoms=atoms, directory=directory)
1351 self.write_sort_file(directory=directory)
1352 self.copy_vdw_kernel(directory=directory)
1354 def copy_vdw_kernel(self, directory='./'):
1355 """Method to copy the vdw_kernel.bindat file.
1356 Set ASE_VASP_VDW environment variable to the vdw_kernel.bindat
1357 folder location. Checks if LUSE_VDW is enabled, and if no location
1358 for the vdW kernel is specified, a warning is issued."""
1360 vdw_env = 'ASE_VASP_VDW'
1361 kernel = 'vdw_kernel.bindat'
1362 dst = os.path.join(directory, kernel)
1364 # No need to copy the file again
1365 if isfile(dst):
1366 return
1368 if self.bool_params['luse_vdw']:
1369 src = None
1370 if vdw_env in os.environ:
1371 src = os.path.join(os.environ[vdw_env], kernel)
1373 if not src or not isfile(src):
1374 warnings.warn(
1375 ('vdW has been enabled, however no'
1376 ' location for the {} file'
1377 ' has been specified.'
1378 ' Set {} environment variable to'
1379 ' copy the vdW kernel.').format(kernel, vdw_env))
1380 else:
1381 shutil.copyfile(src, dst)
1383 def clean(self):
1384 """Method which cleans up after a calculation.
1386 The default files generated by Vasp will be deleted IF this
1387 method is called.
1389 """
1390 files = [
1391 'CHG', 'CHGCAR', 'POSCAR', 'INCAR', 'CONTCAR', 'DOSCAR',
1392 'EIGENVAL', 'IBZKPT', 'KPOINTS', 'OSZICAR', 'OUTCAR', 'PCDAT',
1393 'POTCAR', 'vasprun.xml', 'WAVECAR', 'XDATCAR', 'PROCAR',
1394 'ase-sort.dat', 'LOCPOT', 'AECCAR0', 'AECCAR1', 'AECCAR2'
1395 ]
1396 for f in files:
1397 try:
1398 os.remove(f)
1399 except OSError:
1400 pass
1402 def write_incar(self, atoms, directory='./', **kwargs):
1403 """Writes the INCAR file."""
1404 p = self.input_params
1405 # jrk 1/23/2015 I added this flag because this function has
1406 # two places where magmoms get written. There is some
1407 # complication when restarting that often leads to magmom
1408 # getting written twice. this flag prevents that issue.
1409 magmom_written = False
1410 incar = open(join(directory, 'INCAR'), 'w')
1411 incar.write('INCAR created by Atomic Simulation Environment\n')
1412 for key, val in self.float_params.items():
1413 if key == 'nelect':
1414 charge = p.get('charge')
1415 # Handle deprecated net_charge parameter (remove at some point)
1416 net_charge = p.get('net_charge')
1417 if net_charge is not None:
1418 warnings.warn(
1419 '`net_charge`, which is given in units of '
1420 'the *negative* elementary charge (i.e., the opposite '
1421 'of what one normally calls charge) has been '
1422 'deprecated in favor of `charge`, which is given in '
1423 'units of the positive elementary charge as usual',
1424 category=FutureWarning)
1425 if charge is not None and charge != -net_charge:
1426 raise ValueError(
1427 "can't give both net_charge and charge")
1428 charge = -net_charge
1429 # We need to determine the nelect resulting from a given net
1430 # charge in any case if it's != 0, but if nelect is
1431 # additionally given explicitly, then we need to determine it
1432 # even for net charge of 0 to check for conflicts
1433 if charge is not None and (charge != 0 or val is not None):
1434 default_nelect = self.default_nelect_from_ppp()
1435 nelect_from_charge = default_nelect - charge
1436 if val is not None and val != nelect_from_charge:
1437 raise ValueError('incompatible input parameters: '
1438 'nelect=%s, but charge=%s '
1439 '(neutral nelect is %s)' %
1440 (val, charge, default_nelect))
1441 val = nelect_from_charge
1442 if val is not None:
1443 incar.write(' %s = %5.6f\n' % (key.upper(), val))
1444 for key, val in self.exp_params.items():
1445 if val is not None:
1446 incar.write(' %s = %5.2e\n' % (key.upper(), val))
1447 for key, val in self.string_params.items():
1448 if val is not None:
1449 incar.write(' %s = %s\n' % (key.upper(), val))
1450 for key, val in self.int_params.items():
1451 if val is not None:
1452 incar.write(' %s = %d\n' % (key.upper(), val))
1453 if key == 'ichain' and val > 0:
1454 incar.write(' IBRION = 3\n POTIM = 0.0\n')
1455 for key, val in self.int_params.items():
1456 if key == 'iopt' and val is None:
1457 print('WARNING: optimization is '
1458 'set to LFBGS (IOPT = 1)')
1459 incar.write(' IOPT = 1\n')
1460 for key, val in self.exp_params.items():
1461 if key == 'ediffg' and val is None:
1462 RuntimeError('Please set EDIFFG < 0')
1464 for key, val in self.list_bool_params.items():
1465 if val is None:
1466 pass
1467 else:
1468 incar.write(' %s = ' % key.upper())
1469 [incar.write('%s ' % _to_vasp_bool(x)) for x in val]
1470 incar.write('\n')
1472 for key, val in self.list_int_params.items():
1473 if val is None:
1474 pass
1475 elif key == 'ldaul' and (self.dict_params['ldau_luj'] is not None):
1476 pass
1477 else:
1478 incar.write(' %s = ' % key.upper())
1479 [incar.write('%d ' % x) for x in val]
1480 incar.write('\n')
1482 for key, val in self.list_float_params.items():
1483 if val is None:
1484 pass
1485 elif ((key in ('ldauu', 'ldauj'))
1486 and (self.dict_params['ldau_luj'] is not None)):
1487 pass
1488 elif key == 'magmom':
1489 if not len(val) == len(atoms):
1490 msg = ('Expected length of magmom tag to be'
1491 ' {}, i.e. 1 value per atom, but got {}').format(
1492 len(atoms), len(val))
1493 raise ValueError(msg)
1495 # Check if user remembered to specify ispin
1496 # note: we do not overwrite ispin if ispin=1
1497 if not self.int_params['ispin']:
1498 self.spinpol = True
1499 incar.write(' ispin = 2\n'.upper())
1501 incar.write(' %s = ' % key.upper())
1502 magmom_written = True
1503 # Work out compact a*x b*y notation and write in this form
1504 # Assume 1 magmom per atom, ordered as our atoms object
1505 val = np.array(val)
1506 val = val[self.sort] # Order in VASP format
1508 # Compactify the magmom list to symbol order
1509 lst = [[1, val[0]]]
1510 for n in range(1, len(val)):
1511 if val[n] == val[n - 1]:
1512 lst[-1][0] += 1
1513 else:
1514 lst.append([1, val[n]])
1515 incar.write(' '.join(
1516 ['{:d}*{:.4f}'.format(mom[0], mom[1]) for mom in lst]))
1517 incar.write('\n')
1518 else:
1519 incar.write(' %s = ' % key.upper())
1520 [incar.write('%.4f ' % x) for x in val]
1521 incar.write('\n')
1523 for key, val in self.bool_params.items():
1524 if val is not None:
1525 incar.write(' %s = ' % key.upper())
1526 if val:
1527 incar.write('.TRUE.\n')
1528 else:
1529 incar.write('.FALSE.\n')
1530 for key, val in self.special_params.items():
1531 if val is not None:
1532 incar.write(' %s = ' % key.upper())
1533 if key == 'lreal':
1534 if isinstance(val, str):
1535 incar.write(val + '\n')
1536 elif isinstance(val, bool):
1537 if val:
1538 incar.write('.TRUE.\n')
1539 else:
1540 incar.write('.FALSE.\n')
1541 for key, val in self.dict_params.items():
1542 if val is not None:
1543 if key == 'ldau_luj':
1544 # User didn't turn on LDAU tag.
1545 # Only turn on if ldau is unspecified
1546 if self.bool_params['ldau'] is None:
1547 self.bool_params['ldau'] = True
1548 # At this point we have already parsed our bool params
1549 incar.write(' LDAU = .TRUE.\n')
1550 llist = ulist = jlist = ''
1551 for symbol in self.symbol_count:
1552 # default: No +U
1553 luj = val.get(symbol[0], {'L': -1, 'U': 0.0, 'J': 0.0})
1554 llist += ' %i' % luj['L']
1555 ulist += ' %.3f' % luj['U']
1556 jlist += ' %.3f' % luj['J']
1557 incar.write(' LDAUL =%s\n' % llist)
1558 incar.write(' LDAUU =%s\n' % ulist)
1559 incar.write(' LDAUJ =%s\n' % jlist)
1561 if (self.spinpol and not magmom_written
1562 # We don't want to write magmoms if they are all 0.
1563 # but we could still be doing a spinpol calculation
1564 and atoms.get_initial_magnetic_moments().any()):
1565 if not self.int_params['ispin']:
1566 incar.write(' ispin = 2\n'.upper())
1567 # Write out initial magnetic moments
1568 magmom = atoms.get_initial_magnetic_moments()[self.sort]
1569 # unpack magmom array if three components specified
1570 if magmom.ndim > 1:
1571 magmom = [item for sublist in magmom for item in sublist]
1572 list = [[1, magmom[0]]]
1573 for n in range(1, len(magmom)):
1574 if magmom[n] == magmom[n - 1]:
1575 list[-1][0] += 1
1576 else:
1577 list.append([1, magmom[n]])
1578 incar.write(' magmom = '.upper())
1579 [incar.write('%i*%.4f ' % (mom[0], mom[1])) for mom in list]
1580 incar.write('\n')
1582 # Custom key-value pairs, which receive no formatting
1583 # Use the comment "# <Custom ASE key>" to denote such
1584 # a custom key-value pair, as we cannot otherwise
1585 # reliably and easily identify such non-standard entries
1586 custom_kv_pairs = p.get('custom')
1587 for key, value in custom_kv_pairs.items():
1588 incar.write(' {} = {} # <Custom ASE key>\n'.format(
1589 key.upper(), value))
1590 incar.close()
1592 def write_kpoints(self, atoms=None, directory='./', **kwargs):
1593 """Writes the KPOINTS file."""
1595 if atoms is None:
1596 atoms = self.atoms
1598 # Don't write anything if KSPACING is being used
1599 if self.float_params['kspacing'] is not None:
1600 if self.float_params['kspacing'] > 0:
1601 return
1602 else:
1603 raise ValueError("KSPACING value {0} is not allowable. "
1604 "Please use None or a positive number."
1605 "".format(self.float_params['kspacing']))
1607 p = self.input_params
1608 with open(join(directory, 'KPOINTS'), 'w') as kpoints:
1609 kpoints.write('KPOINTS created by Atomic Simulation Environment\n')
1611 if isinstance(p['kpts'], dict):
1612 p['kpts'] = kpts2ndarray(p['kpts'], atoms=atoms)
1613 p['reciprocal'] = True
1615 shape = np.array(p['kpts']).shape
1617 # Wrap scalar in list if necessary
1618 if shape == ():
1619 p['kpts'] = [p['kpts']]
1620 shape = (1, )
1622 if len(shape) == 1:
1623 kpoints.write('0\n')
1624 if shape == (1, ):
1625 kpoints.write('Auto\n')
1626 elif p['gamma']:
1627 kpoints.write('Gamma\n')
1628 else:
1629 kpoints.write('Monkhorst-Pack\n')
1630 [kpoints.write('%i ' % kpt) for kpt in p['kpts']]
1631 kpoints.write('\n0 0 0\n')
1632 elif len(shape) == 2:
1633 kpoints.write('%i \n' % (len(p['kpts'])))
1634 if p['reciprocal']:
1635 kpoints.write('Reciprocal\n')
1636 else:
1637 kpoints.write('Cartesian\n')
1638 for n in range(len(p['kpts'])):
1639 [kpoints.write('%f ' % kpt) for kpt in p['kpts'][n]]
1640 if shape[1] == 4:
1641 kpoints.write('\n')
1642 elif shape[1] == 3:
1643 kpoints.write('1.0 \n')
1645 def write_potcar(self, suffix="", directory='./'):
1646 """Writes the POTCAR file."""
1648 with open(join(directory, 'POTCAR' + suffix), 'w') as potfile:
1649 for filename in self.ppp_list:
1650 with open_potcar(filename=filename) as ppp_file:
1651 for line in ppp_file:
1652 potfile.write(line)
1654 def write_sort_file(self, directory='./'):
1655 """Writes a sortings file.
1657 This file contains information about how the atoms are sorted in
1658 the first column and how they should be resorted in the second
1659 column. It is used for restart purposes to get sorting right
1660 when reading in an old calculation to ASE."""
1662 with open(join(directory, 'ase-sort.dat'), 'w') as fd:
1663 for n in range(len(self.sort)):
1664 fd.write('%5i %5i \n' % (self.sort[n], self.resort[n]))
1666 # The below functions are used to restart a calculation
1668 def read_incar(self, filename):
1669 """Method that imports settings from INCAR file.
1671 Typically named INCAR."""
1673 self.spinpol = False
1674 with open(filename, 'r') as fd:
1675 lines = fd.readlines()
1677 for line in lines:
1678 try:
1679 # Make multiplication, comments, and parameters easier to spot
1680 line = line.replace("*", " * ")
1681 line = line.replace("=", " = ")
1682 line = line.replace("#", "# ")
1683 data = line.split()
1684 # Skip empty and commented lines.
1685 if len(data) == 0:
1686 continue
1687 elif data[0][0] in ['#', '!']:
1688 continue
1689 key = data[0].lower()
1690 if '<Custom ASE key>' in line:
1691 # This key was added with custom key-value pair formatting.
1692 # Unconditionally add it, no type checking
1693 # Get value between "=" and the comment, e.g.
1694 # key = 1 2 3 # <Custom ASE key>
1695 # value should be '1 2 3'
1697 # Split at first occurence of "="
1698 value = line.split('=', 1)[1]
1699 # First "#" denotes beginning of comment
1700 # Add everything before comment as a string to custom dict
1701 value = value.split('#', 1)[0].strip()
1702 self.input_params['custom'][key] = value
1703 elif key in float_keys:
1704 self.float_params[key] = float(data[2])
1705 elif key in exp_keys:
1706 self.exp_params[key] = float(data[2])
1707 elif key in string_keys:
1708 self.string_params[key] = str(data[2])
1709 elif key in int_keys:
1710 if key == 'ispin':
1711 # JRK added. not sure why we would want to leave ispin
1712 # out
1713 self.int_params[key] = int(data[2])
1714 if int(data[2]) == 2:
1715 self.spinpol = True
1716 else:
1717 self.int_params[key] = int(data[2])
1718 elif key in bool_keys:
1719 if 'true' in data[2].lower():
1720 self.bool_params[key] = True
1721 elif 'false' in data[2].lower():
1722 self.bool_params[key] = False
1724 elif key in list_bool_keys:
1725 self.list_bool_params[key] = [
1726 _from_vasp_bool(x)
1727 for x in _args_without_comment(data[2:])
1728 ]
1730 elif key in list_int_keys:
1731 self.list_int_params[key] = [
1732 int(x) for x in _args_without_comment(data[2:])
1733 ]
1735 elif key in list_float_keys:
1736 if key == 'magmom':
1737 lst = []
1738 i = 2
1739 while i < len(data):
1740 if data[i] in ["#", "!"]:
1741 break
1742 if data[i] == "*":
1743 b = lst.pop()
1744 i += 1
1745 for j in range(int(b)):
1746 lst.append(float(data[i]))
1747 else:
1748 lst.append(float(data[i]))
1749 i += 1
1750 self.list_float_params['magmom'] = lst
1751 lst = np.array(lst)
1752 if self.atoms is not None:
1753 self.atoms.set_initial_magnetic_moments(
1754 lst[self.resort])
1755 else:
1756 data = _args_without_comment(data)
1757 self.list_float_params[key] = [
1758 float(x) for x in data[2:]
1759 ]
1760 # elif key in list_keys:
1761 # list = []
1762 # if key in ('dipol', 'eint', 'ferwe', 'ferdo',
1763 # 'ropt', 'rwigs',
1764 # 'ldauu', 'ldaul', 'ldauj', 'langevin_gamma'):
1765 # for a in data[2:]:
1766 # if a in ["!", "#"]:
1767 # break
1768 # list.append(float(a))
1769 # elif key in ('iband', 'kpuse', 'random_seed'):
1770 # for a in data[2:]:
1771 # if a in ["!", "#"]:
1772 # break
1773 # list.append(int(a))
1774 # self.list_params[key] = list
1775 # if key == 'magmom':
1776 # list = []
1777 # i = 2
1778 # while i < len(data):
1779 # if data[i] in ["#", "!"]:
1780 # break
1781 # if data[i] == "*":
1782 # b = list.pop()
1783 # i += 1
1784 # for j in range(int(b)):
1785 # list.append(float(data[i]))
1786 # else:
1787 # list.append(float(data[i]))
1788 # i += 1
1789 # self.list_params['magmom'] = list
1790 # list = np.array(list)
1791 # if self.atoms is not None:
1792 # self.atoms.set_initial_magnetic_moments(
1793 # list[self.resort])
1794 elif key in special_keys:
1795 if key == 'lreal':
1796 if 'true' in data[2].lower():
1797 self.special_params[key] = True
1798 elif 'false' in data[2].lower():
1799 self.special_params[key] = False
1800 else:
1801 self.special_params[key] = data[2]
1802 except KeyError:
1803 raise IOError('Keyword "%s" in INCAR is'
1804 'not known by calculator.' % key)
1805 except IndexError:
1806 raise IOError('Value missing for keyword "%s".' % key)
1808 def read_kpoints(self, filename):
1809 """Read kpoints file, typically named KPOINTS."""
1810 # If we used VASP builtin kspacing,
1811 if self.float_params['kspacing'] is not None:
1812 # Don't update kpts array
1813 return
1815 with open(filename, 'r') as fd:
1816 lines = fd.readlines()
1818 ktype = lines[2].split()[0].lower()[0]
1819 if ktype in ['g', 'm', 'a']:
1820 if ktype == 'g':
1821 self.set(gamma=True)
1822 kpts = np.array([int(lines[3].split()[i]) for i in range(3)])
1823 elif ktype == 'a':
1824 kpts = np.array([int(lines[3].split()[i]) for i in range(1)])
1825 elif ktype == 'm':
1826 kpts = np.array([int(lines[3].split()[i]) for i in range(3)])
1827 else:
1828 if ktype in ['c', 'k']:
1829 self.set(reciprocal=False)
1830 else:
1831 self.set(reciprocal=True)
1832 kpts = np.array(
1833 [list(map(float, line.split())) for line in lines[3:]])
1834 self.set(kpts=kpts)
1836 def read_potcar(self, filename):
1837 """ Read the pseudopotential XC functional from POTCAR file.
1838 """
1840 # Search for key 'LEXCH' in POTCAR
1841 xc_flag = None
1842 with open(filename, 'r') as fd:
1843 for line in fd:
1844 key = line.split()[0].upper()
1845 if key == 'LEXCH':
1846 xc_flag = line.split()[-1].upper()
1847 break
1849 if xc_flag is None:
1850 raise ValueError('LEXCH flag not found in POTCAR file.')
1852 # Values of parameter LEXCH and corresponding XC-functional
1853 xc_dict = {'PE': 'PBE', '91': 'PW91', 'CA': 'LDA'}
1855 if xc_flag not in xc_dict.keys():
1856 raise ValueError('Unknown xc-functional flag found in POTCAR,'
1857 ' LEXCH=%s' % xc_flag)
1859 self.input_params['pp'] = xc_dict[xc_flag]
1861 def todict(self):
1862 """Returns a dictionary of all parameters
1863 that can be used to construct a new calculator object"""
1864 dict_list = [
1865 'float_params', 'exp_params', 'string_params', 'int_params',
1866 'bool_params', 'list_bool_params', 'list_int_params',
1867 'list_float_params', 'special_params', 'dict_params',
1868 'input_params'
1869 ]
1870 dct = {}
1871 for item in dict_list:
1872 dct.update(getattr(self, item))
1873 dct = {key: value for key, value in dct.items() if value is not None}
1874 return dct
1877def _args_without_comment(data, marks=['!', '#']):
1878 """Check split arguments list for a comment, return data up to marker
1880 INCAR reader splits list arguments on spaces and leaves comment markers as
1881 individual items. This function returns only the data portion of the list.
1883 """
1884 comment_locs = [data.index(mark) for mark in marks if mark in data]
1885 if comment_locs == []:
1886 return data
1887 else:
1888 return data[:min(comment_locs)]
1891def _from_vasp_bool(x):
1892 """Cast vasp boolean to Python bool
1894 VASP files sometimes use T or F as shorthand for the preferred Boolean
1895 notation .TRUE. or .FALSE. As capitalisation is pretty inconsistent in
1896 practice, we allow all cases to be cast to a Python bool.
1898 """
1899 assert isinstance(x, str)
1900 if x.lower() == '.true.' or x.lower() == 't':
1901 return True
1902 elif x.lower() == '.false.' or x.lower() == 'f':
1903 return False
1904 else:
1905 raise ValueError('Value "%s" not recognized as bool' % x)
1908def _to_vasp_bool(x):
1909 """Convert Python boolean to string for VASP input
1911 In case the value was modified to a string already, appropriate strings
1912 will also be accepted and cast to a standard .TRUE. / .FALSE. format.
1914 """
1915 if isinstance(x, str):
1916 if x.lower() in ('.true.', 't'):
1917 x = True
1918 elif x.lower() in ('.false.', 'f'):
1919 x = False
1920 else:
1921 raise ValueError('"%s" not recognised as VASP Boolean')
1922 assert isinstance(x, bool)
1923 if x:
1924 return '.TRUE.'
1925 else:
1926 return '.FALSE.'
1929def open_potcar(filename):
1930 """ Open POTCAR file with transparent decompression if it's an archive (.Z)
1931 """
1932 import gzip
1933 if filename.endswith('R'):
1934 return open(filename, 'r')
1935 elif filename.endswith('.Z'):
1936 return gzip.open(filename)
1937 else:
1938 raise ValueError('Invalid POTCAR filename: "%s"' % filename)
1941def read_potcar_numbers_of_electrons(file_obj):
1942 """ Read list of tuples (atomic symbol, number of valence electrons)
1943 for each atomtype from a POTCAR file."""
1944 nelect = []
1945 lines = file_obj.readlines()
1946 for n, line in enumerate(lines):
1947 if 'TITEL' in line:
1948 symbol = line.split('=')[1].split()[1].split('_')[0].strip()
1949 valence = float(
1950 lines[n + 4].split(';')[1].split('=')[1].split()[0].strip())
1951 nelect.append((symbol, valence))
1952 return nelect
1955def count_symbols(atoms, exclude=()):
1956 """Count symbols in atoms object, excluding a set of indices
1958 Parameters:
1959 atoms: Atoms object to be grouped
1960 exclude: List of indices to be excluded from the counting
1962 Returns:
1963 Tuple of (symbols, symbolcount)
1964 symbols: The unique symbols in the included list
1965 symbolscount: Count of symbols in the included list
1967 Example:
1969 >>> from ase.build import bulk
1970 >>> atoms = bulk('NaCl', crystalstructure='rocksalt', a=4.1, cubic=True)
1971 >>> count_symbols(atoms)
1972 (['Na', 'Cl'], {'Na': 4, 'Cl': 4})
1973 >>> count_symbols(atoms, exclude=(1, 2, 3))
1974 (['Na', 'Cl'], {'Na': 3, 'Cl': 2})
1975 """
1976 symbols = []
1977 symbolcount = {}
1978 for m, symbol in enumerate(atoms.symbols):
1979 if m in exclude:
1980 continue
1981 if symbol not in symbols:
1982 symbols.append(symbol)
1983 symbolcount[symbol] = 1
1984 else:
1985 symbolcount[symbol] += 1
1986 return symbols, symbolcount