Coverage for /builds/ase/ase/ase/calculators/vasp/create_input.py : 47.71%
Hot-keys on this page
r m x p toggle line displays
j k next/prev highlighted chunk
0 (zero) top of page
1 (one) first highlighted chunk
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
34def format_kpoints(kpts, atoms, reciprocal=False, gamma=False):
35 tokens = []
36 append = tokens.append
38 append('KPOINTS created by Atomic Simulation Environment\n')
40 if isinstance(kpts, dict):
41 kpts = kpts2ndarray(kpts, atoms=atoms)
42 reciprocal = True
44 shape = np.array(kpts).shape
46 # Wrap scalar in list if necessary
47 if shape == ():
48 kpts = [kpts]
49 shape = (1, )
51 if len(shape) == 1:
52 append('0\n')
53 if shape == (1, ):
54 append('Auto\n')
55 elif gamma:
56 append('Gamma\n')
57 else:
58 append('Monkhorst-Pack\n')
59 append(' '.join(f'{kpt:d}' for kpt in kpts))
60 append('\n0 0 0\n')
61 elif len(shape) == 2:
62 append('%i \n' % (len(kpts)))
63 if reciprocal:
64 append('Reciprocal\n')
65 else:
66 append('Cartesian\n')
67 for n in range(len(kpts)):
68 [append('%f ' % kpt) for kpt in kpts[n]]
69 if shape[1] == 4:
70 append('\n')
71 elif shape[1] == 3:
72 append('1.0 \n')
73 return ''.join(tokens)
76# Parameters that can be set in INCAR. The values which are None
77# are not written and default parameters of VASP are used for them.
79float_keys = [
80 'aexx', # Fraction of exact/DFT exchange
81 'aggac', # Fraction of gradient correction to correlation
82 'aggax', # Fraction of gradient correction to exchange
83 'aldac', # Fraction of LDA correlation energy
84 'amin', #
85 'amix', #
86 'amix_mag', #
87 'bmix', # tags for mixing
88 'bmix_mag', #
89 'cshift', # Complex shift for dielectric tensor calculation (LOPTICS)
90 'deper', # relative stopping criterion for optimization of eigenvalue
91 'ebreak', # absolute stopping criterion for optimization of eigenvalues
92 # (EDIFF/N-BANDS/4)
93 'efield', # applied electrostatic field
94 'emax', # energy-range for DOSCAR file
95 'emin', #
96 'enaug', # Density cutoff
97 'encut', # Planewave cutoff
98 'encutgw', # energy cutoff for response function
99 'encutfock', # FFT grid in the HF related routines
100 'hfscreen', # attribute to change from PBE0 to HSE
101 'kspacing', # determines the number of k-points if the KPOINTS
102 # file is not present. KSPACING is the smallest
103 # allowed spacing between k-points in units of
104 # $\AA$^{-1}$.
105 'potim', # time-step for ion-motion (fs)
106 'nelect', # total number of electrons
107 'param1', # Exchange parameter
108 'param2', # Exchange parameter
109 'pomass', # mass of ions in am
110 'pstress', # add this stress to the stress tensor, and energy E = V *
111 # pstress
112 'sigma', # broadening in eV
113 'smass', # Nose mass-parameter (am)
114 'spring', # spring constant for NEB
115 'time', # special control tag
116 'weimin', # maximum weight for a band to be considered empty
117 'zab_vdw', # vdW-DF parameter
118 'zval', # ionic valence
119 # The next keywords pertain to the VTST add-ons from Graeme Henkelman's
120 # group at UT Austin
121 'jacobian', # Weight of lattice to atomic motion
122 'ddr', # (DdR) dimer separation
123 'drotmax', # (DRotMax) number of rotation steps per translation step
124 'dfnmin', # (DFNMin) rotational force below which dimer is not rotated
125 'dfnmax', # (DFNMax) rotational force below which dimer rotation stops
126 'sltol', # convergence ratio for minimum eigenvalue
127 'sdr', # finite difference for setting up Lanczos matrix and step
128 # size when translating
129 'maxmove', # Max step for translation for IOPT > 0
130 'invcurv', # Initial curvature for LBFGS (IOPT = 1)
131 'timestep', # Dynamical timestep for IOPT = 3 and IOPT = 7
132 'sdalpha', # Ratio between force and step size for IOPT = 4
133 # The next keywords pertain to IOPT = 7 (i.e. FIRE)
134 'ftimemax', # Max time step
135 'ftimedec', # Factor to dec. dt
136 'ftimeinc', # Factor to inc. dt
137 'falpha', # Parameter for velocity damping
138 'falphadec', # Factor to dec. alpha
139 'clz', # electron count for core level shift
140 'vdw_radius', # Cutoff radius for Grimme's DFT-D2 and DFT-D3 and
141 # Tkatchenko and Scheffler's DFT-TS dispersion corrections
142 'vdw_scaling', # Global scaling parameter for Grimme's DFT-D2 dispersion
143 # correction
144 'vdw_d', # Global damping parameter for Grimme's DFT-D2 and Tkatchenko
145 # and Scheffler's DFT-TS dispersion corrections
146 'vdw_cnradius', # Cutoff radius for calculating coordination number in
147 # Grimme's DFT-D3 dispersion correction
148 'vdw_s6', # Damping parameter for Grimme's DFT-D2 and DFT-D3 and
149 # Tkatchenko and Scheffler's DFT-TS dispersion corrections
150 'vdw_s8', # Damping parameter for Grimme's DFT-D3 dispersion correction
151 'vdw_sr', # Scaling parameter for Grimme's DFT-D2 and DFT-D3 and
152 # Tkatchenko and Scheffler's DFT-TS dispersion correction
153 'vdw_a1', # Damping parameter for Grimme's DFT-D3 dispersion correction
154 'vdw_a2', # Damping parameter for Grimme's DFT-D3 dispersion correction
155 'eb_k', # solvent permitivity in Vaspsol
156 'tau', # surface tension parameter in Vaspsol
157 'langevin_gamma_l', # Friction for lattice degrees of freedom
158 'pmass', # Mass for latice degrees of freedom
159 'bparam', # B parameter for nonlocal VV10 vdW functional
160 'cparam', # C parameter for nonlocal VV10 vdW functional
161 'aldax', # Fraction of LDA exchange (for hybrid calculations)
162 'tebeg', #
163 'teend', # temperature during run
164 'andersen_prob', # Probability of collision in Andersen thermostat
165 'apaco', # Distance cutoff for pair correlation function calc.
166 'auger_ecblo', # Undocumented parameter for Auger calculations
167 'auger_edens', # Density of electrons in conduction band
168 'auger_hdens', # Density of holes in valence band
169 'auger_efermi', # Fixed Fermi level for Auger calculations
170 'auger_evbhi', # Upper bound for valence band maximum
171 'auger_ewidth', # Half-width of energy window function
172 'auger_occ_fac_eeh', # Undocumented parameter for Auger calculations
173 'auger_occ_fac_ehh', # Undocumented parameter for Auger calculations
174 'auger_temp', # Temperature for Auger calculation
175 'dq', # Finite difference displacement magnitude (NMR)
176 'avgap', # Average gap (Model GW)
177 'ch_sigma', # Broadening of the core electron absorption spectrum
178 'bpotim', # Undocumented Bond-Boost parameter (GH patches)
179 'qrr', # Undocumented Bond-Boost parameter (GH patches)
180 'prr', # Undocumented Bond-Boost parameter (GH patches)
181 'rcut', # Undocumented Bond-Boost parameter (GH patches)
182 'dvmax', # Undocumented Bond-Boost parameter (GH patches)
183 'bfgsinvcurv', # Initial curvature for BFGS (GH patches)
184 'damping', # Damping parameter for LBFGS (GH patches)
185 'efirst', # Energy of first NEB image (GH patches)
186 'elast', # Energy of final NEB image (GH patches)
187 'fmagval', # Force magnitude convergence criterion (GH patches)
188 'cmbj', # Modified Becke-Johnson MetaGGA c-parameter
189 'cmbja', # Modified Becke-Johnson MetaGGA alpha-parameter
190 'cmbjb', # Modified Becke-Johnson MetaGGA beta-parameter
191 'sigma_nc_k', # Width of ion gaussians (VASPsol)
192 'sigma_k', # Width of dielectric cavidty (VASPsol)
193 'nc_k', # Cavity turn-on density (VASPsol)
194 'lambda_d_k', # Debye screening length (VASPsol)
195 'ediffsol', # Tolerance for solvation convergence (VASPsol)
196 'deg_threshold', # Degeneracy threshold
197 'omegamin', # Minimum frequency for dense freq. grid
198 'omegamax', # Maximum frequency for dense freq. grid
199 'rtime', # Undocumented parameter
200 'wplasma', # Undocumented parameter
201 'wplasmai', # Undocumented parameter
202 'dfield', # Undocumented parameter
203 'omegatl', # Maximum frequency for coarse freq. grid
204 'encutgwsoft', # Soft energy cutoff for response kernel
205 'encutlf', # Undocumented parameter
206 'scissor', # Scissor correction for GW/BSE calcs
207 'dimer_dist', # Distance between dimer images
208 'step_size', # Step size for finite difference in dimer calculation
209 'step_max', # Maximum step size for dimer calculation
210 'minrot', # Minimum rotation allowed in dimer calculation
211 'dummy_mass', # Mass of dummy atom(s?)
212 'shaketol', # Tolerance for SHAKE algorithm
213 'shaketolsoft', # Soft tolerance for SHAKE algorithm
214 'shakesca', # Scaling of each step taken in SHAKE algorithm
215 'hills_stride', # Undocumented metadynamics parameter
216 'hills_h', # Height (in eV) of gaussian bias for metadynamics
217 'hills_w', # Width of gaussian bias for metadynamics
218 'hills_k', # Force constant coupling dummy&real for metadynamics
219 'hills_m', # Mass of dummy particle for use in metadynamics
220 'hills_temperature', # Temp. of dummy particle for metadynamics
221 'hills_andersen_prob', # Probability of thermostat coll. for metadynamics
222 'hills_sqq', # Nose-hoover particle mass for metadynamics
223 'dvvdelta0', # Undocumented parameter
224 'dvvvnorm0', # Undocumented parameter
225 'dvvminpotim', # Undocumented parameter
226 'dvvmaxpotim', # Undocumented parameter
227 'efermi', # Undocumented parameter
228 'enchg', # Undocumented charge fitting parameter
229 'tau0', # Undocumented charge fitting parameter
230 'encut4o', # Cutoff energy for 4-center integrals (HF)
231 'param3', # Undocumented HF parameter
232 'model_eps0', # Undocumented HF parameter
233 'model_alpha', # Undocumented HF parameter
234 'qmaxfockae', # Undocumented HF parameter
235 'hfscreenc', # Range-separated screening length for correlations
236 'hfrcut', # Cutoff radius for HF potential kernel
237 'encutae', # Undocumented parameter for all-electron density calc.
238 'encutsubrotscf', # Undocumented subspace rotation SCF parameter
239 'enini', # Cutoff energy for wavefunctions (?)
240 'wc', # Undocumented mixing parameter
241 'enmax', # Cutoff energy for wavefunctions (?)
242 'scalee', # Undocumented parameter
243 'eref', # Reference energy
244 'epsilon', # Dielectric constant of bulk charged cells
245 'rcmix', # Mixing parameter for core density in rel. core calcs.
246 'esemicore', # Energetic lower bound for states considered "semicore"
247 'external_pressure', # Pressure for NPT calcs., equivalent to PSTRESS
248 'lj_radius', # Undocumented classical vdW parameter
249 'lj_epsilon', # Undocumented classical vdW parameter
250 'lj_sigma', # Undocumented classical vdW parameter
251 'mbd_beta', # TS MBD vdW correction damping parameter
252 'scsrad', # Cutoff radius for dipole-dipole interaction tensor in SCS
253 'hitoler', # Iterative Hirschfeld partitioning tolerance
254 'lambda', # "Spring constant" for magmom constraint calcs.
255 'kproj_threshold', # Threshold for k-point projection scheme
256 'maxpwamp', # Undocumented HF parameter
257 'vcutoff', # Undocumented parameter
258 'mdtemp', # Temperature for AIMD
259 'mdgamma', # Undocumented AIMD parameter
260 'mdalpha', # Undocumented AIMD parameter
261 'ofield_kappa', # Bias potential strength for interface pinning method
262 'ofield_q6_near', # Steinhardt-Nelson Q6 parameters for interface pinning
263 'ofield_q6_far', # Steinhardt-Nelson Q6 parameters for interface pinning
264 'ofield_a', # Target order parameter for interface pinning method
265 'pthreshold', # Don't print timings for routines faster than this value
266 'qltol', # Eigenvalue tolerance for Lanczos iteration (instanton)
267 'qdr', # Step size for building Lanczos matrix & CG (instanton)
268 'qmaxmove', # Max step size (instanton)
269 'qdt', # Timestep for quickmin minimization (instanton)
270 'qtpz', # Temperature (instanton)
271 'qftol', # Tolerance (instanton)
272 'nupdown', # fix spin moment to specified value
273]
275exp_keys = [
276 'ediff', # stopping-criterion for electronic upd.
277 'ediffg', # stopping-criterion for ionic upd.
278 'symprec', # precession in symmetry routines
279 # The next keywords pertain to the VTST add-ons from Graeme Henkelman's
280 # group at UT Austin
281 'fdstep', # Finite diference step for IOPT = 1 or 2
282]
284string_keys = [
285 'algo', # algorithm: Normal (Davidson) | Fast | Very_Fast (RMM-DIIS)
286 'gga', # xc-type: PW PB LM or 91 (LDA if not set)
287 'metagga', #
288 'prec', # Precission of calculation (Low, Normal, Accurate)
289 'system', # name of System
290 'precfock', # FFT grid in the HF related routines
291 'radeq', # Which type of radial equations to use for rel. core calcs.
292 'localized_basis', # Basis to use in CRPA
293 'proutine', # Select profiling routine
294]
296int_keys = [
297 'ialgo', # algorithm: use only 8 (CG) or 48 (RMM-DIIS)
298 'ibrion', # ionic relaxation: 0-MD 1-quasi-New 2-CG
299 'icharg', # charge: 0-WAVECAR 1-CHGCAR 2-atom 10-const
300 'idipol', # monopol/dipol and quadropole corrections
301 'images', # number of images for NEB calculation
302 'iniwav', # initial electr wf. : 0-lowe 1-rand
303 'isif', # calculate stress and what to relax
304 'ismear', # part. occupancies: -5 Blochl -4-tet -1-fermi 0-gaus >0 MP
305 'ispin', # spin-polarized calculation
306 'istart', # startjob: 0-new 1-cont 2-samecut
307 'isym', # symmetry: 0-nonsym 1-usesym 2-usePAWsym
308 'iwavpr', # prediction of wf.: 0-non 1-charg 2-wave 3-comb
309 'kpar', # k-point parallelization paramater
310 'ldauprint', # 0-silent, 1-occ. matrix written to OUTCAR, 2-1+pot. matrix
311 # written
312 'ldautype', # L(S)DA+U: 1-Liechtenstein 2-Dudarev 4-Liechtenstein(LDAU)
313 'lmaxmix', #
314 'lorbit', # create PROOUT
315 'maxmix', #
316 'ngx', # FFT mesh for wavefunctions, x
317 'ngxf', # FFT mesh for charges x
318 'ngy', # FFT mesh for wavefunctions, y
319 'ngyf', # FFT mesh for charges y
320 'ngz', # FFT mesh for wavefunctions, z
321 'ngzf', # FFT mesh for charges z
322 'nbands', # Number of bands
323 'nblk', # blocking for some BLAS calls (Sec. 6.5)
324 'nbmod', # specifies mode for partial charge calculation
325 'nelm', # nr. of electronic steps (default 60)
326 'nelmdl', # nr. of initial electronic steps
327 'nelmgw', # nr. of self-consistency cycles for GW
328 'nelmin',
329 'nfree', # number of steps per DOF when calculting Hessian using
330 # finite differences
331 'nkred', # define sub grid of q-points for HF with
332 # nkredx=nkredy=nkredz
333 'nkredx', # define sub grid of q-points in x direction for HF
334 'nkredy', # define sub grid of q-points in y direction for HF
335 'nkredz', # define sub grid of q-points in z direction for HF
336 'nomega', # number of frequency points
337 'nomegar', # number of frequency points on real axis
338 'npar', # parallelization over bands
339 'nsim', # evaluate NSIM bands simultaneously if using RMM-DIIS
340 'nsw', # number of steps for ionic upd.
341 'nwrite', # verbosity write-flag (how much is written)
342 'vdwgr', # extra keyword for Andris program
343 'vdwrn', # extra keyword for Andris program
344 'voskown', # use Vosko, Wilk, Nusair interpolation
345 # The next keywords pertain to the VTST add-ons from Graeme Henkelman's
346 # group at UT Austin
347 'ichain', # Flag for controlling which method is being used (0=NEB,
348 # 1=DynMat, 2=Dimer, 3=Lanczos) if ichain > 3, then both
349 # IBRION and POTIM are automatically set in the INCAR file
350 'iopt', # Controls which optimizer to use. for iopt > 0, ibrion = 3
351 # and potim = 0.0
352 'snl', # Maximum dimentionality of the Lanczos matrix
353 'lbfgsmem', # Steps saved for inverse Hessian for IOPT = 1 (LBFGS)
354 'fnmin', # Max iter. before adjusting dt and alpha for IOPT = 7 (FIRE)
355 'icorelevel', # core level shifts
356 'clnt', # species index
357 'cln', # main quantum number of excited core electron
358 'cll', # l quantum number of excited core electron
359 'ivdw', # Choose which dispersion correction method to use
360 'nbandsgw', # Number of bands for GW
361 'nbandso', # Number of occupied bands for electron-hole treatment
362 'nbandsv', # Number of virtual bands for electron-hole treatment
363 'ncore', # Number of cores per band, equal to number of cores divided
364 # by npar
365 'mdalgo', # Determines which MD method of Tomas Bucko to use
366 'nedos', # Number of grid points in DOS
367 'turbo', # Ewald, 0 = Normal, 1 = PME
368 'omegapar', # Number of groups for response function calc.
369 # (Possibly Depricated) Number of groups in real time for
370 # response function calc.
371 'taupar',
372 'ntaupar', # Number of groups in real time for response function calc.
373 'antires', # How to treat antiresonant part of response function
374 'magatom', # Index of atom at which to place magnetic field (NMR)
375 'jatom', # Index of atom at which magnetic moment is evaluated (NMR)
376 'ichibare', # chi_bare stencil size (NMR)
377 'nbas', # Undocumented Bond-Boost parameter (GH patches)
378 'rmds', # Undocumented Bond-Boost parameter (GH patches)
379 'ilbfgsmem', # Number of histories to store for LBFGS (GH patches)
380 'vcaimages', # Undocumented parameter (GH patches)
381 'ntemper', # Undocumented subspace diagonalization param. (GH patches)
382 'ncshmem', # Share memory between this many cores on each process
383 'lmaxtau', # Undocumented MetaGGA parameter (prob. max ang.mom. for tau)
384 'kinter', # Additional finer grid (?)
385 'ibse', # Type of BSE calculation
386 'nbseeig', # Number of BSE wfns to write
387 'naturalo', # Use NATURALO (?)
388 'nbandsexact', # Undocumented parameter
389 'nbandsgwlow', # Number of bands for which shifts are calculated
390 'nbandslf', # Number of bands included in local field effect calc.
391 'omegagrid', # Undocumented parameter
392 'telescope', # Undocumented parameter
393 'maxmem', # Amount of memory to allocate per core in MB
394 'nelmhf', # Number of iterations for HF part (GW)
395 'dim', # Undocumented parameter
396 'nkredlf', # Reduce k-points for local field effects
397 'nkredlfx', # Reduce k-points for local field effects in X
398 'nkredlfy', # Reduce k-points for local field effects in Y
399 'nkredlfz', # Reduce k-points for local field effects in Z
400 'lmaxmp2', # Undocumented parameter
401 'switch', # Undocumented dimer parameter
402 'findiff', # Use forward (1) or central (2) finite difference for dimer
403 'engine', # Undocumented dimer parameter
404 'restartcg', # Undocumented dimer parameter
405 'thermostat', # Deprecated parameter for selecting MD method (use MDALGO)
406 'scaling', # After how many steps velocities should be rescaled
407 'shakemaxiter', # Maximum # of iterations in SHAKE algorithm
408 'equi_regime', # Number of steps to equilibrate for
409 'hills_bin', # Update metadynamics bias after this many steps
410 'hills_maxstride', # Undocumented metadynamics parameter
411 'dvvehistory', # Undocumented parameter
412 'ipead', # Undocumented parameter
413 'ngaus', # Undocumented charge fitting parameter
414 'exxoep', # Undocumented HF parameter
415 'fourorbit', # Undocumented HF parameter
416 'model_gw', # Undocumented HF parameter
417 'hflmax', # Maximum L quantum number for HF calculation
418 'lmaxfock', # Maximum L quantum number for HF calc. (same as above)
419 'lmaxfockae', # Undocumented HF parameter
420 'nmaxfockae', # Undocumented HF parameter
421 'nblock_fock', # Undocumented HF parameter
422 'idiot', # Determines which warnings/errors to print
423 'nrmm', # Number of RMM-DIIS iterations
424 'mremove', # Undocumented mixing parameter
425 'inimix', # Undocumented mixing parameter
426 'mixpre', # Undocumented mixing parameter
427 'nelmall', # Undocumented parameter
428 'nblock', # How frequently to write data
429 'kblock', # How frequently to write data
430 'npaco', # Undocumented pair correlation function parameter
431 'lmaxpaw', # Max L quantum number for on-site charge expansion
432 'irestart', # Undocumented parameter
433 'nreboot', # Undocumented parameter
434 'nmin', # Undocumented parameter
435 'nlspline', # Undocumented parameter
436 'ispecial', # "Select undocumented and unsupported special features"
437 'rcrep', # Number of steps between printing relaxed core info
438 'rcndl', # Wait this many steps before updating core density
439 'rcstrd', # Relax core density after this many SCF steps
440 'vdw_idampf', # Select type of damping function for TS vdW
441 'i_constrained_m', # Select type of magmom. constraint to use
442 'igpar', # "G parallel" direction for Berry phase calculation
443 'nppstr', # Number of kpts in "igpar' direction for Berry phase calc.
444 'nbands_out', # Undocumented QP parameter
445 'kpts_out', # Undocumented QP parameter
446 'isp_out', # Undocumented QP parameter
447 'nomega_out', # Undocumented QP parameter
448 'maxiter_ft', # Max iterations for sloppy Remez algorithm
449 'nmaxalt', # Max sample points for alternant in Remez algorithms
450 'itmaxlsq', # Max iterations in LSQ search algorithm
451 'ndatalsq', # Number of sample points for LSQ search algorithm
452 'ncore_in_image1', # Undocumented parameter
453 'kimages', # Undocumented parameter
454 'ncores_per_band', # Undocumented parameter
455 'maxlie', # Max iterations in CRPA diagonalization routine
456 'ncrpalow', # Undocumented CRPA parameter
457 'ncrpahigh', # Undocumented CRPA parameter
458 'nwlow', # Undocumented parameter
459 'nwhigh', # Undocumented parameter
460 'nkopt', # Number of k-points to include in Optics calculation
461 'nkoffopt', # K-point "counter offset" for Optics
462 'nbvalopt', # Number of valence bands to write in OPTICS file
463 'nbconopt', # Number of conduction bands to write in OPTICS file
464 'ch_nedos', # Number dielectric function calculation grid points for XAS
465 'plevel', # No timings for routines with "level" higher than this
466 'qnl', # Lanczos matrix size (instanton)
467]
469bool_keys = [
470 'addgrid', # finer grid for augmentation charge density
471 'kgamma', # The generated kpoint grid (from KSPACING) is either
472 # centred at the $\Gamma$
473 # point (e.g. includes the $\Gamma$ point)
474 # (KGAMMA=.TRUE.)
475 'laechg', # write AECCAR0/AECCAR1/AECCAR2
476 'lasph', # non-spherical contributions to XC energy (and pot for
477 # VASP.5.X)
478 'lasync', # overlap communcation with calculations
479 'lcharg', #
480 'lcorr', # Harris-correction to forces
481 'ldau', # L(S)DA+U
482 'ldiag', # algorithm: perform sub space rotation
483 'ldipol', # potential correction mode
484 'lelf', # create ELFCAR
485 'lepsilon', # enables to calculate and to print the BEC tensors
486 'lhfcalc', # switch to turn on Hartree Fock calculations
487 'loptics', # calculate the frequency dependent dielectric matrix
488 'lpard', # evaluate partial (band and/or k-point) decomposed charge
489 # density
490 'lplane', # parallelisation over the FFT grid
491 'lscalapack', # switch off scaLAPACK
492 'lscalu', # switch of LU decomposition
493 'lsepb', # write out partial charge of each band separately?
494 'lsepk', # write out partial charge of each k-point separately?
495 'lthomas', #
496 'luse_vdw', # Invoke vdW-DF implementation by Klimes et. al
497 'lvdw', # Invoke DFT-D2 method of Grimme
498 'lvhar', # write Hartree potential to LOCPOT (vasp 5.x)
499 'lvtot', # create WAVECAR/CHGCAR/LOCPOT
500 'lwave', #
501 # The next keywords pertain to the VTST add-ons from Graeme Henkelman's
502 # group at UT Austin
503 'lclimb', # Turn on CI-NEB
504 'ltangentold', # Old central difference tangent
505 'ldneb', # Turn on modified double nudging
506 'lnebcell', # Turn on SS-NEB
507 'lglobal', # Optmize NEB globally for LBFGS (IOPT = 1)
508 'llineopt', # Use force based line minimizer for translation (IOPT = 1)
509 'lbeefens', # Switch on print of BEE energy contributions in OUTCAR
510 'lbeefbas', # Switch off print of all BEEs in OUTCAR
511 'lcalcpol', # macroscopic polarization (vasp5.2). 'lcalceps'
512 'lcalceps', # Macroscopic dielectric properties and Born effective charge
513 # tensors (vasp 5.2)
514 'lvdw', # Turns on dispersion correction
515 'lvdw_ewald', # Turns on Ewald summation for Grimme's DFT-D2 and
516 # Tkatchenko and Scheffler's DFT-TS dispersion correction
517 'lspectral', # Use the spectral method to calculate independent particle
518 # polarizability
519 'lrpa', # Include local field effects on the Hartree level only
520 'lwannier90', # Switches on the interface between VASP and WANNIER90
521 'lsorbit', # Enable spin-orbit coupling
522 'lsol', # turn on solvation for Vaspsol
523 'lautoscale', # automatically calculate inverse curvature for VTST LBFGS
524 'interactive', # Enables interactive calculation for VaspInteractive
525 'lauger', # Perform Auger calculation (Auger)
526 'lauger_eeh', # Calculate EEH processes (Auger)
527 'lauger_ehh', # Calculate EHH processes (Auger)
528 'lauger_collect', # Collect wfns before looping over k-points (Auger)
529 'lauger_dhdk', # Auto-determine E. window width from E. derivs. (Auger)
530 'lauger_jit', # Distribute wavefunctions for k1-k4 (Auger)
531 'orbitalmag', # Enable orbital magnetization (NMR)
532 'lchimag', # Use linear response for shielding tensor (NMR)
533 'lwrtcur', # Write response of current to mag. field to file (NMR)
534 'lnmr_sym_red', # Reduce symmetry for finite difference (NMR)
535 'lzora', # Use ZORA approximation in linear-response NMR (NMR)
536 'lbone', # Use B-component in AE one-center terms for LR NMR (NMR)
537 'lmagbloch', # Use Bloch summations to obtain orbital magnetization (NMR)
538 'lgauge', # Use gauge transformation for zero moment terms (NMR)
539 'lbfconst', # Use constant B-field with sawtooth vector potential (NMR)
540 'nucind', # Use nuclear independent calculation (NMR)
541 'lnicsall', # Use all grid points for 'nucind' calculation (NMR)
542 'llraug', # Use two-center corrections for induced B-field (NMR)
543 'lbbm', # Undocumented Bond-Boost parameter (GH patches)
544 'lnoncollinear', # Do non-collinear spin polarized calculation
545 'bfgsdfp', # Undocumented BFGS parameter (GH patches)
546 'linemin', # Use line minimization (GH patches)
547 'ldneborg', # Undocumented NEB parameter (GH patches)
548 'dseed', # Undocumented dimer parameter (GH patches)
549 'linteract', # Undocumented parameter (GH patches)
550 'lmpmd', # Undocumented parameter (GH patches)
551 'ltwodim', # Makes stress tensor two-dimensional (GH patches)
552 'fmagflag', # Use force magnitude as convergence criterion (GH patches)
553 'ltemper', # Use subspace diagonalization (?) (GH patches)
554 'qmflag', # Undocumented FIRE parameter (GH patches)
555 'lmixtau', # Undocumented MetaGGA parameter
556 'ljdftx', # Undocumented VASPsol parameter (VASPsol)
557 'lrhob', # Write the bound charge density (VASPsol)
558 'lrhoion', # Write the ionic charge density (VASPsol)
559 'lnabla', # Undocumented parameter
560 'linterfast', # Interpolate in K using linear response routines
561 'lvel', # Undocumented parameter
562 'lrpaforce', # Calculate RPA forces
563 'lhartree', # Use IP approx. in BSE (testing only)
564 'ladder', # Use ladder diagrams
565 'lfxc', # Use approximate ladder diagrams
566 'lrsrpa', # Undocumented parameter
567 'lsingles', # Calculate HF singles
568 'lfermigw', # Iterate Fermi level
569 'ltcte', # Undocumented parameter
570 'ltete', # Undocumented parameter
571 'ltriplet', # Undocumented parameter
572 'lfxceps', # Undocumented parameter
573 'lfxheg', # Undocumented parameter
574 'l2order', # Undocumented parameter
575 'lmp2lt', # Undocumented parameter
576 'lgwlf', # Undocumented parameter
577 'lusew', # Undocumented parameter
578 'selfenergy', # Undocumented parameter
579 'oddonlygw', # Avoid gamma point in response function calc.
580 'evenonlygw', # Avoid even points in response function calc.
581 'lspectralgw', # More accurate self-energy calculation
582 'ch_lspec', # Calculate matrix elements btw. core and conduction states
583 'fletcher_reeves', # Undocumented dimer parameter
584 'lidm_selective', # Undocumented dimer parameter
585 'lblueout', # Write output of blue-moon algorithm
586 'hills_variable_w', # Enable variable-width metadynamics bias
587 'dvvminus', # Undocumented parameter
588 'lpead', # Calculate cell-periodic orbital derivs. using finite diff.
589 'skip_edotp', # Skip updating elec. polarization during scf
590 'skip_scf', # Skip calculation w/ local field effects
591 'lchgfit', # Turn on charge fitting
592 'lgausrc', # Undocumented charge fitting parameter
593 'lstockholder', # Enable ISA charge fitting (?)
594 'lsymgrad', # Restore symmetry of gradient (HF)
595 'lhfone', # Calculate one-center terms (HF)
596 'lrscor', # Include long-range correlation (HF)
597 'lrhfcalc', # Include long-range HF (HF)
598 'lmodelhf', # Model HF calculation (HF)
599 'shiftred', # Undocumented HF parameter
600 'hfkident', # Undocumented HF parameter
601 'oddonly', # Undocumented HF parameter
602 'evenonly', # Undocumented HF parameter
603 'lfockaedft', # Undocumented HF parameter
604 'lsubrot', # Enable subspace rotation diagonalization
605 'mixfirst', # Mix before diagonalization
606 'lvcader', # Calculate derivs. w.r.t. VCA parameters
607 'lcompat', # Enable "full compatibility"
608 'lmusic', # "Joke" parameter
609 'ldownsample', # Downsample WAVECAR to fewer k-points
610 'lscaaware', # Disable ScaLAPACK for some things but not all
611 'lorbitalreal', # Undocumented parameter
612 'lmetagga', # Undocumented parameter
613 'lspiral', # Undocumented parameter
614 'lzeroz', # Undocumented parameter
615 'lmono', # Enable "monopole" corrections
616 'lrelcore', # Perform relaxed core calculation
617 'lmimicfc', # Mimic frozen-core calcs. for relaxed core calcs.
618 'lmatchrw', # Match PS partial waves at RWIGS? (otherwise PAW cutoff)
619 'ladaptelin', # Linearize core state energies to avoid divergences
620 'lonlysemicore', # Only linearize semi-core state energies
621 'gga_compat', # Enable backwards-compatible symmetrization of GGA derivs.
622 'lrelvol', # Undocumented classical vdW parameter
623 'lj_only', # Undocumented classical vdW parameter
624 'lvdwscs', # Include self-consistent screening in TS vdW correction
625 'lcfdm', # Use coupled fluctuating dipoles model for TS vdW
626 'lvdw_sametype', # Include interactions between atoms of the same type
627 'lrescaler0', # Rescale damping parameters in SCS vdW correction
628 'lscsgrad', # Calculate gradients for TS+SCS vdW correction energies
629 'lvdwexpansion', # Write 2-6 body contribs. to MBD vdW correction energy
630 'lvdw_relvolone', # Undocumented classical vdW parameter
631 'lberry', # Enable Berry-phase calculation
632 'lpade_fit', # Undocumented QP parameter
633 'lkproj', # Enable projection onto k-points
634 'l_wr_moments', # Undocumented parameter
635 'l_wr_density', # Undocumented parameter
636 'lkotani', # Undocumented parameter
637 'ldyson', # Undocumented parameter
638 'laddherm', # Undocumented parameter
639 'lcrpaplot', # Plot bands used in CRPA response func. calc.
640 'lplotdis', # Plot disentangled bands in CRPA response func. calc.
641 'ldisentangle', # Disentangle bands in CRPA
642 'lweighted', # "Weighted" CRPA approach
643 'luseorth_lcaos', # Use orthogonalized LCAOs in CRPA
644 'lfrpa', # Use full RPA in CRPA
645 'lregularize', # Regularize projectors in CRPA
646 'ldrude', # Include Drude term in CRPA
647 'ldmatrix', # Undocumented parameter
648 'lefg', # Calculate electric field gradient at atomic nuclei
649 'lhyperfine', # Enable Hyperfine calculation
650 'lwannier', # Enable Wannier interface
651 'localize', # Undocumented Wannier parameter
652 'lintpol_wpot', # Interpolate WPOT for Wannier
653 'lintpol_orb', # Interpolate orbitals for Wannier
654 'lintpol_kpath', # Interpolate bandstructure on given kpath for Wannier
655 'lintpol_kpath_orb', # Interpolate orbitals on given kpath for Wannier
656 'lread_eigenvalues', # Use Eigenvalues from EIGENVALUES.INT file
657 'lintpol_velocity', # Interpolate electron velocity for Wannier
658 'lintpol_conductivity', # Interpolate conductivity for Wannier
659 'lwannierinterpol', # Undocumented Wannier parameter
660 'wanproj', # Undocumented Wannier parameter
661 'lorbmom', # Undocumented LDA+U parameter
662 'lwannier90_run', # Undocumented WANNIER90 parameter
663 'lwrite_wanproj', # Write UWAN files for WANNIER90
664 'lwrite_unk', # Write UNK files for WANNIER90
665 'lwrite_mmn_amn', # Write MMN and AMN files for WANNIER90
666 'lread_amn', # Read AMN files instead of recomputing (WANNIER90)
667 'lrhfatm', # Undocumented HF parameter
668 'lvpot', # Calculate unscreened potential
669 'lwpot', # Calculate screened potential
670 'lwswq', # Undocumented parameter
671 'pflat', # Only print "flat" timings to OUTCAR
672 'qifcg', # Use CG instead of quickmin (instanton)
673 'qdo_ins', # Find instanton
674 'qdo_pre', # Calculate prefactor (instanton)
675 # The next keyword pertains to the periodic NBO code of JR Schmidt's group
676 # at UW-Madison (https://github.com/jrschmidt2/periodic-NBO)
677 'lnbo', # Enable NBO analysis
678]
680list_int_keys = [
681 'iband', # bands to calculate partial charge for
682 'kpuse', # k-point to calculate partial charge for
683 'ldaul', # DFT+U parameters, overruled by dict key 'ldau_luj'
684 'random_seed', # List of ints used to seed RNG for advanced MD routines
685 # (Bucko)
686 'auger_bmin_eeh', # 4 ints | Various undocumented parameters for Auger
687 'auger_bmax_eeh', # 4 ints | calculations
688 'auger_bmin_ehh', # 4 ints |
689 'auger_bmax_ehh', # 4 ints |
690 'balist', # nbas ints | Undocumented Bond-Boost parameter (GH patches)
691 'kpoint_bse', # 4 ints | Undocumented parameter
692 'nsubsys', # <=3 ints | Last atom # for each of up to 3 thermostats
693 'vdw_refstate', # ntyp ints | Undocumented classical vdW parameter
694 'vdw_mbd_size', # 3 ints | Supercell size for TS MBD vdW correction
695 'nbands_index', # nbands_out ints | Undocumented QP parameter
696 'kpts_index', # kpts_out ints | Undocumented QP parameter
697 'isp_index', # isp_out ints | Undocumented QP parameter
698 'nomega_index', # nomega_out ints | Undocumented QP parameter
699 'ntarget_states', # nbands ints | Undocumented CRPA parameter
700 'wanproj_i', # nions ints | Undocumented Wannier parameter
701 'wanproj_l', # ? ints | Undocumented Wannier parameter
702]
704list_bool_keys = [
705 'lattice_constraints', # 3 bools | Undocumented advanced MD parameter
706 'lrctype', # ntyp bools | Enable relaxed-core calc. for these atoms
707 'lvdw_onecell', # 3 bools | Enable periodicity in A, B, C vector for vdW
708]
710list_float_keys = [
711 'dipol', # center of cell for dipol
712 'eint', # energy range to calculate partial charge for
713 'ferwe', # Fixed band occupation (spin-paired)
714 'ferdo', # Fixed band occupation (spin-plarized)
715 'magmom', # initial magnetic moments
716 'ropt', # number of grid points for non-local proj in real space
717 'rwigs', # Wigner-Seitz radii
718 'ldauu', # ldau parameters, has potential to redundant w.r.t. dict
719 'ldauj', # key 'ldau_luj', but 'ldau_luj' can't be read direct from
720 # the INCAR (since it needs to know information about atomic
721 # species. In case of conflict 'ldau_luj' gets written out
722 # when a calculation is set up
723 'vdw_c6', # List of floats of C6 parameters (J nm^6 mol^-1) for each
724 # species (DFT-D2 and DFT-TS)
725 'vdw_c6au', # List of floats of C6 parameters (a.u.) for each species
726 # (DFT-TS)
727 'vdw_r0', # List of floats of R0 parameters (angstroms) for each
728 # species (DFT-D2 and DFT-TS)
729 'vdw_r0au', # List of floats of R0 parameters (a.u.) for each species
730 # (DFT-TS)
731 'vdw_alpha', # List of floats of free-atomic polarizabilities for each
732 # species (DFT-TS)
733 'langevin_gamma', # List of floats for langevin friction coefficients
734 'auger_emin_eeh', # 4 floats | Various undocumented parameters for Auger
735 'auger_emax_eeh', # 4 floats | calculations
736 'auger_emin_ehh', # 4 floats |
737 'auger_emax_ehh', # 4 floats |
738 'avecconst', # 3 floats | magnitude of magnetic moment (NMR)
739 'magdipol', # 3 floats | magnitude of magnetic dipole (NMR)
740 'bconst', # 3 floats | magnitude of constant magnetic field (NMR)
741 'magpos', # 3 floats | position for magnetic moment w/ 'nucind' (NMR)
742 'bext', # 3 floats | Undocumented (probably external magnetic field)
743 'core_c', # ntyp floats | pseudo-core charge magnitude (VASPsol)
744 'sigma_rc_k', # ntyp floats | width of pseudo-core gaussians (VASPsol)
745 'darwinr', # ntypd (?) floats | Undocumented parameter
746 'darwinv', # ntypd (?) floats | Undocumented parameter
747 'dummy_k', # ? floats | Force const. connecting dummy atoms to sys.
748 'dummy_r0', # ? floats | Minimum dist., ang., etc. for dummy atom DOFs
749 'dummy_positions', # 3 floats | Position of dummy atom(s?)
750 'psubsys', # <=3 floats | Coll. prob. for each of up to 3 thermostats
751 'tsubsys', # <=3 floats | Temp. for each of up to 3 thermostats
752 'increm', # ? floats | Undocumented advanced MD parameter
753 'value_min', # ? floats | Undocumented advanced MD parameter
754 'value_max', # ? floats | Undocumented advanced MD parameter
755 'hills_position', # ? floats | Dummy particle(s) pos. for metadynamics
756 'hills_velocity', # ? floats | Dummy particle(s) vel. for metadynamics
757 'spring_k', # ? floats | Spring constant for harmonic constraints
758 'spring_r0', # ? floats | Spring minima for harmonic constraints
759 'spring_v0', # ? floats | Initial velocity of harmonic constraints
760 'hills_wall_lower', # ? floats | Undocumented metadynamics parameter
761 'hills_wall_upper', # ? floats | Undocumented metadynamics parameter
762 'efield_pead', # 3 floats | homogeneous electric field for PEAD calc.
763 'zct', # ? floats | Undocumented charge fitting parameter
764 'rgaus', # ? floats | Undocumented charge fitting parameter
765 'hfalpha', # 10 floats | Undocumented HF parameter
766 'mcalpha', # 10 floats | Undocumented HF parameter
767 'saxis', # 3 floats | Coordinate for collinear spin calculations
768 'vca', # ? floats | Atom weight for VCA calculations
769 'stm', # 7 floats | "range for STM data"
770 'qspiral', # 3 floats | Undocumented parameter
771 'external_stress', # 6 floats | Target stress (adds w/ external_pressure)
772 'm_constr', # 3*nions floats | Local magmom assigned to each spin DOF
773 'quad_efg', # ntyp floats | Nuclear quadrupole moments
774 'ngyromag', # ntyp floats | Nuclear gyromagnetic ratios
775 'rcrhocut', # ntyp floats | Core density cutoff rad. for HF relcore calc
776 'ofield_k', # 3 floats | Undocumented parameter
777 'paripot', # ? floats | Undocumented parameter
778 'smearings', # ? floats | ismear,sigma smearing params to loop over
779 'wanproj_e', # 2 floats | Undocumented Wannier parameter
780]
782special_keys = [
783 'lreal', # non-local projectors in real space
784]
786dict_keys = [
787 'ldau_luj', # dictionary with L(S)DA+U parameters, e.g. {'Fe':{'L':2,
788 # 'U':4.0, 'J':0.9}, ...}
789]
791keys: List[str] = [
792 # 'NBLOCK' and KBLOCK inner block; outer block
793 # 'NPACO' and APACO distance and nr. of slots for P.C.
794 # 'WEIMIN, EBREAK, DEPER special control tags
795]
798class GenerateVaspInput:
799 # Parameters corresponding to 'xc' settings. This may be modified
800 # by the user in-between loading calculators.vasp submodule and
801 # instantiating the calculator object with calculators.vasp.Vasp()
802 xc_defaults = {
803 'lda': {
804 'pp': 'LDA'
805 },
806 # GGAs
807 'blyp': { # https://www.vasp.at/forum/viewtopic.php?p=17234
808 'pp': 'PBE',
809 'gga': 'B5',
810 'aldax': 1.00,
811 'aggax': 1.00,
812 'aggac': 1.00,
813 'aldac': 0.00
814 },
815 'pw91': {
816 'pp': 'PW91',
817 'gga': '91'
818 },
819 'pbe': {
820 'pp': 'PBE',
821 'gga': 'PE'
822 },
823 'pbesol': {
824 'gga': 'PS'
825 },
826 'revpbe': {
827 'gga': 'RE'
828 },
829 'rpbe': {
830 'gga': 'RP'
831 },
832 'am05': {
833 'gga': 'AM'
834 },
835 # Meta-GGAs
836 'tpss': {
837 'metagga': 'TPSS'
838 },
839 'revtpss': {
840 'metagga': 'RTPSS'
841 },
842 'm06l': {
843 'metagga': 'M06L'
844 },
845 'ms0': {
846 'metagga': 'MS0'
847 },
848 'ms1': {
849 'metagga': 'MS1'
850 },
851 'ms2': {
852 'metagga': 'MS2'
853 },
854 'scan': {
855 'metagga': 'SCAN'
856 },
857 'rscan': {
858 'metagga': 'RSCAN'
859 },
860 'r2scan': {
861 'metagga': 'R2SCAN'
862 },
863 'scan-rvv10': {
864 'metagga': 'SCAN',
865 'luse_vdw': True,
866 'bparam': 15.7
867 },
868 'mbj': {
869 # Modified Becke-Johnson
870 'metagga': 'MBJ',
871 },
872 'tb09': {
873 # Alias for MBJ
874 'metagga': 'MBJ',
875 },
876 # vdW-DFs
877 'vdw-df': {
878 'gga': 'RE',
879 'luse_vdw': True,
880 'aggac': 0.
881 },
882 'vdw-df-cx': {
883 'gga': 'CX',
884 'luse_vdw': True,
885 'aggac': 0.
886 },
887 'vdw-df-cx0p': {
888 'gga': 'CX',
889 'luse_vdw': True,
890 'aggac': 0.,
891 'lhfcalc': True,
892 'aexx': 0.2,
893 'aggax': 0.8
894 },
895 'optpbe-vdw': {
896 'gga': 'OR',
897 'luse_vdw': True,
898 'aggac': 0.0
899 },
900 'optb88-vdw': {
901 'gga': 'BO',
902 'luse_vdw': True,
903 'aggac': 0.0,
904 'param1': 1.1 / 6.0,
905 'param2': 0.22
906 },
907 'optb86b-vdw': {
908 'gga': 'MK',
909 'luse_vdw': True,
910 'aggac': 0.0,
911 'param1': 0.1234,
912 'param2': 1.0
913 },
914 'vdw-df2': {
915 'gga': 'ML',
916 'luse_vdw': True,
917 'aggac': 0.0,
918 'zab_vdw': -1.8867
919 },
920 'rev-vdw-df2': {
921 'gga': 'MK',
922 'luse_vdw': True,
923 'param1': 0.1234,
924 'param2': 0.711357,
925 'zab_vdw': -1.8867,
926 'aggac': 0.0
927 },
928 'beef-vdw': {
929 'gga': 'BF',
930 'luse_vdw': True,
931 'zab_vdw': -1.8867
932 },
933 # Hartree-Fock and hybrids
934 'hf': {
935 'lhfcalc': True,
936 'aexx': 1.0,
937 'aldac': 0.0,
938 'aggac': 0.0
939 },
940 'b3lyp': {
941 'gga': 'B3',
942 'lhfcalc': True,
943 'aexx': 0.2,
944 'aggax': 0.72,
945 'aggac': 0.81,
946 'aldac': 0.19
947 },
948 'pbe0': {
949 'gga': 'PE',
950 'lhfcalc': True
951 },
952 'hse03': {
953 'gga': 'PE',
954 'lhfcalc': True,
955 'hfscreen': 0.3
956 },
957 'hse06': {
958 'gga': 'PE',
959 'lhfcalc': True,
960 'hfscreen': 0.2
961 },
962 'hsesol': {
963 'gga': 'PS',
964 'lhfcalc': True,
965 'hfscreen': 0.2
966 },
967 # MN-VFM functionals
968 'sogga': {
969 'gga': 'SA'
970 },
971 'sogga11': {
972 'gga': 'S1'
973 },
974 'sogga11-x': {
975 'gga': 'SX',
976 'lhfcalc': True,
977 'aexx': 0.401
978 },
979 'n12': {
980 'gga': 'N2'
981 },
982 'n12-sx': {
983 'gga': 'NX',
984 'lhfcalc': True,
985 'lhfscreen': 0.2
986 },
987 'mn12l': {
988 'metagga': 'MN12L'
989 },
990 'gam': {
991 'gga': 'GA'
992 },
993 'mn15l': {
994 'metagga': 'MN15L'
995 },
996 'hle17': {
997 'metagga': 'HLE17'
998 },
999 'revm06l': {
1000 'metagga': 'revM06L'
1001 },
1002 'm06sx': {
1003 'metagga': 'M06SX',
1004 'lhfcalc': True,
1005 'hfscreen': 0.189,
1006 'aexx': 0.335
1007 }
1008 }
1010 # environment variable for PP paths
1011 VASP_PP_PATH = 'VASP_PP_PATH'
1013 def __init__(self, restart=None):
1014 self.float_params = {}
1015 self.exp_params = {}
1016 self.string_params = {}
1017 self.int_params = {}
1018 self.bool_params = {}
1019 self.list_bool_params = {}
1020 self.list_int_params = {}
1021 self.list_float_params = {}
1022 self.special_params = {}
1023 self.dict_params = {}
1024 for key in float_keys:
1025 self.float_params[key] = None
1026 for key in exp_keys:
1027 self.exp_params[key] = None
1028 for key in string_keys:
1029 self.string_params[key] = None
1030 for key in int_keys:
1031 self.int_params[key] = None
1032 for key in bool_keys:
1033 self.bool_params[key] = None
1034 for key in list_bool_keys:
1035 self.list_bool_params[key] = None
1036 for key in list_int_keys:
1037 self.list_int_params[key] = None
1038 for key in list_float_keys:
1039 self.list_float_params[key] = None
1040 for key in special_keys:
1041 self.special_params[key] = None
1042 for key in dict_keys:
1043 self.dict_params[key] = None
1045 # Initialize internal dictionary of input parameters which are
1046 # not regular VASP keys
1047 self.input_params = {
1048 'xc': None, # Exchange-correlation recipe (e.g. 'B3LYP')
1049 'pp': None, # Pseudopotential file (e.g. 'PW91')
1050 'setups': None, # Special setups (e.g pv, sv, ...)
1051 'txt': '-', # Where to send information
1052 'kpts': (1, 1, 1), # k-points
1053 # Option to use gamma-sampling instead of Monkhorst-Pack:
1054 'gamma': False,
1055 # number of points between points in band structures:
1056 'kpts_nintersections': None,
1057 # Option to write explicit k-points in units
1058 # of reciprocal lattice vectors:
1059 'reciprocal': False,
1060 # Switch to disable writing constraints to POSCAR
1061 'ignore_constraints': False,
1062 # Net charge for the whole system; determines nelect if not 0
1063 'charge': None,
1064 # Deprecated older parameter which works just like "charge" but
1065 # with the sign flipped
1066 'net_charge': None,
1067 # Custom key-value pairs, written to INCAR with *no* type checking
1068 'custom': {},
1069 }
1071 def set_xc_params(self, xc):
1072 """Set parameters corresponding to XC functional"""
1073 xc = xc.lower()
1074 if xc is None:
1075 pass
1076 elif xc not in self.xc_defaults:
1077 xc_allowed = ', '.join(self.xc_defaults.keys())
1078 raise ValueError('{0} is not supported for xc! Supported xc values'
1079 'are: {1}'.format(xc, xc_allowed))
1080 else:
1081 # XC defaults to PBE pseudopotentials
1082 if 'pp' not in self.xc_defaults[xc]:
1083 self.set(pp='PBE')
1084 self.set(**self.xc_defaults[xc])
1086 def set(self, **kwargs):
1088 if (('ldauu' in kwargs) and ('ldaul' in kwargs) and ('ldauj' in kwargs)
1089 and ('ldau_luj' in kwargs)):
1090 raise NotImplementedError(
1091 'You can either specify ldaul, ldauu, and ldauj OR '
1092 'ldau_luj. ldau_luj is not a VASP keyword. It is a '
1093 'dictionary that specifies L, U and J for each '
1094 'chemical species in the atoms object. '
1095 'For example for a water molecule:'
1096 '''ldau_luj={'H':{'L':2, 'U':4.0, 'J':0.9},
1097 'O':{'L':2, 'U':4.0, 'J':0.9}}''')
1099 if 'xc' in kwargs:
1100 self.set_xc_params(kwargs['xc'])
1101 for key in kwargs:
1102 if key in self.float_params:
1103 self.float_params[key] = kwargs[key]
1104 elif key in self.exp_params:
1105 self.exp_params[key] = kwargs[key]
1106 elif key in self.string_params:
1107 self.string_params[key] = kwargs[key]
1108 elif key in self.int_params:
1109 self.int_params[key] = kwargs[key]
1110 elif key in self.bool_params:
1111 self.bool_params[key] = kwargs[key]
1112 elif key in self.list_bool_params:
1113 self.list_bool_params[key] = kwargs[key]
1114 elif key in self.list_int_params:
1115 self.list_int_params[key] = kwargs[key]
1116 elif key in self.list_float_params:
1117 self.list_float_params[key] = kwargs[key]
1118 elif key in self.special_params:
1119 self.special_params[key] = kwargs[key]
1120 elif key in self.dict_params:
1121 self.dict_params[key] = kwargs[key]
1122 elif key in self.input_params:
1123 self.input_params[key] = kwargs[key]
1124 else:
1125 raise TypeError('Parameter not defined: ' + key)
1127 def check_xc(self):
1128 """Make sure the calculator has functional & pseudopotentials set up
1130 If no XC combination, GGA functional or POTCAR type is specified,
1131 default to PW91. Otherwise, try to guess the desired pseudopotentials.
1132 """
1134 p = self.input_params
1136 # There is no way to correctly guess the desired
1137 # set of pseudopotentials without 'pp' being set.
1138 # Usually, 'pp' will be set by 'xc'.
1139 if 'pp' not in p or p['pp'] is None:
1140 if self.string_params['gga'] is None:
1141 p.update({'pp': 'lda'})
1142 elif self.string_params['gga'] == '91':
1143 p.update({'pp': 'pw91'})
1144 elif self.string_params['gga'] == 'PE':
1145 p.update({'pp': 'pbe'})
1146 else:
1147 raise NotImplementedError(
1148 "Unable to guess the desired set of pseudopotential"
1149 "(POTCAR) files. Please do one of the following: \n"
1150 "1. Use the 'xc' parameter to define your XC functional."
1151 "These 'recipes' determine the pseudopotential file as "
1152 "well as setting the INCAR parameters.\n"
1153 "2. Use the 'gga' settings None (default), 'PE' or '91'; "
1154 "these correspond to LDA, PBE and PW91 respectively.\n"
1155 "3. Set the POTCAR explicitly with the 'pp' flag. The "
1156 "value should be the name of a folder on the VASP_PP_PATH"
1157 ", and the aliases 'LDA', 'PBE' and 'PW91' are also"
1158 "accepted.\n")
1160 if (p['xc'] is not None and p['xc'].lower() == 'lda'
1161 and p['pp'].lower() != 'lda'):
1162 warnings.warn("XC is set to LDA, but PP is set to "
1163 "{0}. \nThis calculation is using the {0} "
1164 "POTCAR set. \n Please check that this is "
1165 "really what you intended!"
1166 "\n".format(p['pp'].upper()))
1168 def _make_sort(
1169 self, atoms: ase.Atoms, special_setups: Sequence[int] = ()
1170 ) -> Tuple[List[int], List[int]]:
1171 symbols, _ = count_symbols(atoms, exclude=special_setups)
1173 # Create sorting list
1174 srt = [] # type: List[int]
1175 srt.extend(special_setups)
1177 for symbol in symbols:
1178 for m, atom in enumerate(atoms):
1179 if m in special_setups:
1180 continue
1181 if atom.symbol == symbol:
1182 srt.append(m)
1183 # Create the resorting list
1184 resrt = list(range(len(srt)))
1185 for n in range(len(resrt)):
1186 resrt[srt[n]] = n
1187 return srt, resrt
1189 def _build_pp_list(self,
1190 atoms,
1191 setups=None,
1192 special_setups: Sequence[int] = ()):
1193 """Build the pseudopotential lists"""
1195 p = self.input_params
1197 if setups is None:
1198 setups, special_setups = self._get_setups()
1200 symbols, _ = count_symbols(atoms, exclude=special_setups)
1202 # Potpaw folders may be identified by an alias or full name
1203 for pp_alias, pp_folder in (('lda', 'potpaw'), ('pw91', 'potpaw_GGA'),
1204 ('pbe', 'potpaw_PBE')):
1205 if p['pp'].lower() == pp_alias:
1206 break
1207 else:
1208 pp_folder = p['pp']
1210 if self.VASP_PP_PATH in os.environ:
1211 pppaths = os.environ[self.VASP_PP_PATH].split(':')
1212 else:
1213 pppaths = []
1214 ppp_list = []
1215 # Setting the pseudopotentials, first special setups and
1216 # then according to symbols
1217 for m in special_setups:
1218 if m in setups:
1219 special_setup_index = m
1220 elif str(m) in setups:
1221 special_setup_index = str(m) # type: ignore
1222 else:
1223 raise Exception("Having trouble with special setup index {0}."
1224 " Please use an int.".format(m))
1225 potcar = join(pp_folder, setups[special_setup_index], 'POTCAR')
1226 for path in pppaths:
1227 filename = join(path, potcar)
1229 if isfile(filename) or islink(filename):
1230 ppp_list.append(filename)
1231 break
1232 elif isfile(filename + '.Z') or islink(filename + '.Z'):
1233 ppp_list.append(filename + '.Z')
1234 break
1235 else:
1236 symbol = atoms.symbols[m]
1237 msg = """Looking for {}.
1238 No pseudopotential for symbol{} with setup {} """.format(
1239 potcar, symbol, setups[special_setup_index])
1240 raise RuntimeError(msg)
1242 for symbol in symbols:
1243 try:
1244 potcar = join(pp_folder, symbol + setups[symbol], 'POTCAR')
1245 except (TypeError, KeyError):
1246 potcar = join(pp_folder, symbol, 'POTCAR')
1247 for path in pppaths:
1248 filename = join(path, potcar)
1250 if isfile(filename) or islink(filename):
1251 ppp_list.append(filename)
1252 break
1253 elif isfile(filename + '.Z') or islink(filename + '.Z'):
1254 ppp_list.append(filename + '.Z')
1255 break
1256 else:
1257 msg = ("""Looking for PP for {}
1258 The pseudopotentials are expected to be in:
1259 LDA: $VASP_PP_PATH/potpaw/
1260 PBE: $VASP_PP_PATH/potpaw_PBE/
1261 PW91: $VASP_PP_PATH/potpaw_GGA/
1263 No pseudopotential for {}!""".format(potcar, symbol))
1264 raise RuntimeError(msg)
1265 return ppp_list
1267 def _get_setups(self):
1268 p = self.input_params
1270 special_setups = []
1272 # Default setup lists are available: 'minimal', 'recommended' and 'GW'
1273 # These may be provided as a string e.g.::
1274 #
1275 # calc = Vasp(setups='recommended')
1276 #
1277 # or in a dict with other specifications e.g.::
1278 #
1279 # calc = Vasp(setups={'base': 'minimal', 'Ca': '_sv', 2: 'O_s'})
1280 #
1281 # Where other keys are either atom identities or indices, and the
1282 # corresponding values are suffixes or the full name of the setup
1283 # folder, respectively.
1285 # Avoid mutating the module dictionary, so we use a copy instead
1286 # Note, it is a nested dict, so a regular copy is not enough
1287 setups_defaults = get_default_setups()
1289 # Default to minimal basis
1290 if p['setups'] is None:
1291 p['setups'] = {'base': 'minimal'}
1293 # String shortcuts are initialised to dict form
1294 elif isinstance(p['setups'], str):
1295 if p['setups'].lower() in setups_defaults.keys():
1296 p['setups'] = {'base': p['setups']}
1298 # Dict form is then queried to add defaults from setups.py.
1299 if 'base' in p['setups']:
1300 setups = setups_defaults[p['setups']['base'].lower()]
1301 else:
1302 setups = {}
1304 # Override defaults with user-defined setups
1305 if p['setups'] is not None:
1306 setups.update(p['setups'])
1308 for m in setups:
1309 try:
1310 special_setups.append(int(m))
1311 except ValueError:
1312 pass
1313 return setups, special_setups
1315 def initialize(self, atoms):
1316 """Initialize a VASP calculation
1318 Constructs the POTCAR file (does not actually write it).
1319 User should specify the PATH
1320 to the pseudopotentials in VASP_PP_PATH environment variable
1322 The pseudopotentials are expected to be in:
1323 LDA: $VASP_PP_PATH/potpaw/
1324 PBE: $VASP_PP_PATH/potpaw_PBE/
1325 PW91: $VASP_PP_PATH/potpaw_GGA/
1327 if your pseudopotentials are somewhere else, or named
1328 differently you may make symlinks at the paths above that
1329 point to the right place. Alternatively, you may pass the full
1330 name of a folder on the VASP_PP_PATH to the 'pp' parameter.
1331 """
1333 self.check_xc()
1334 self.atoms = atoms
1335 self.all_symbols = atoms.get_chemical_symbols()
1336 self.natoms = len(atoms)
1338 self.spinpol = (atoms.get_initial_magnetic_moments().any()
1339 or self.int_params['ispin'] == 2)
1341 setups, special_setups = self._get_setups()
1343 # Determine the number of atoms of each atomic species
1344 # sorted after atomic species
1345 symbols, symbolcount = count_symbols(atoms, exclude=special_setups)
1346 self.sort, self.resort = self._make_sort(atoms,
1347 special_setups=special_setups)
1349 self.atoms_sorted = atoms[self.sort]
1351 # Check if the necessary POTCAR files exists and
1352 # create a list of their paths.
1353 atomtypes = atoms.get_chemical_symbols()
1354 self.symbol_count = []
1355 for m in special_setups:
1356 self.symbol_count.append([atomtypes[m], 1])
1357 for m in symbols:
1358 self.symbol_count.append([m, symbolcount[m]])
1360 # create pseudopotential list
1361 self.ppp_list = self._build_pp_list(atoms,
1362 setups=setups,
1363 special_setups=special_setups)
1365 self.converged = None
1366 self.setups_changed = None
1368 def default_nelect_from_ppp(self):
1369 """ Get default number of electrons from ppp_list and symbol_count
1371 "Default" here means that the resulting cell would be neutral.
1372 """
1373 symbol_valences = []
1374 for filename in self.ppp_list:
1375 with open_potcar(filename=filename) as ppp_file:
1376 r = read_potcar_numbers_of_electrons(ppp_file)
1377 symbol_valences.extend(r)
1378 assert len(self.symbol_count) == len(symbol_valences)
1379 default_nelect = 0
1380 for ((symbol1, count),
1381 (symbol2, valence)) in zip(self.symbol_count, symbol_valences):
1382 assert symbol1 == symbol2
1383 default_nelect += count * valence
1384 return default_nelect
1386 def write_input(self, atoms, directory='./'):
1387 from ase.io.vasp import write_vasp
1388 write_vasp(join(directory, 'POSCAR'),
1389 self.atoms_sorted,
1390 symbol_count=self.symbol_count,
1391 ignore_constraints=self.input_params['ignore_constraints'])
1392 self.write_incar(atoms, directory=directory)
1393 self.write_potcar(directory=directory)
1394 self.write_kpoints(atoms=atoms, directory=directory)
1395 self.write_sort_file(directory=directory)
1396 self.copy_vdw_kernel(directory=directory)
1398 def copy_vdw_kernel(self, directory='./'):
1399 """Method to copy the vdw_kernel.bindat file.
1400 Set ASE_VASP_VDW environment variable to the vdw_kernel.bindat
1401 folder location. Checks if LUSE_VDW is enabled, and if no location
1402 for the vdW kernel is specified, a warning is issued."""
1404 vdw_env = 'ASE_VASP_VDW'
1405 kernel = 'vdw_kernel.bindat'
1406 dst = os.path.join(directory, kernel)
1408 # No need to copy the file again
1409 if isfile(dst):
1410 return
1412 if self.bool_params['luse_vdw']:
1413 src = None
1414 if vdw_env in os.environ:
1415 src = os.path.join(os.environ[vdw_env], kernel)
1417 if not src or not isfile(src):
1418 warnings.warn(
1419 ('vdW has been enabled, however no'
1420 ' location for the {} file'
1421 ' has been specified.'
1422 ' Set {} environment variable to'
1423 ' copy the vdW kernel.').format(kernel, vdw_env))
1424 else:
1425 shutil.copyfile(src, dst)
1427 def clean(self):
1428 """Method which cleans up after a calculation.
1430 The default files generated by Vasp will be deleted IF this
1431 method is called.
1433 """
1434 files = [
1435 'CHG', 'CHGCAR', 'POSCAR', 'INCAR', 'CONTCAR', 'DOSCAR',
1436 'EIGENVAL', 'IBZKPT', 'KPOINTS', 'OSZICAR', 'OUTCAR', 'PCDAT',
1437 'POTCAR', 'vasprun.xml', 'WAVECAR', 'XDATCAR', 'PROCAR',
1438 'ase-sort.dat', 'LOCPOT', 'AECCAR0', 'AECCAR1', 'AECCAR2'
1439 ]
1440 for f in files:
1441 try:
1442 os.remove(f)
1443 except OSError:
1444 pass
1446 def write_incar(self, atoms, directory='./', **kwargs):
1447 """Writes the INCAR file."""
1448 p = self.input_params
1449 # jrk 1/23/2015 I added this flag because this function has
1450 # two places where magmoms get written. There is some
1451 # complication when restarting that often leads to magmom
1452 # getting written twice. this flag prevents that issue.
1453 magmom_written = False
1454 incar = open(join(directory, 'INCAR'), 'w')
1455 incar.write('INCAR created by Atomic Simulation Environment\n')
1456 for key, val in self.float_params.items():
1457 if key == 'nelect':
1458 charge = p.get('charge')
1459 # Handle deprecated net_charge parameter (remove at some point)
1460 net_charge = p.get('net_charge')
1461 if net_charge is not None:
1462 warnings.warn(
1463 '`net_charge`, which is given in units of '
1464 'the *negative* elementary charge (i.e., the opposite '
1465 'of what one normally calls charge) has been '
1466 'deprecated in favor of `charge`, which is given in '
1467 'units of the positive elementary charge as usual',
1468 category=FutureWarning)
1469 if charge is not None and charge != -net_charge:
1470 raise ValueError(
1471 "can't give both net_charge and charge")
1472 charge = -net_charge
1473 # We need to determine the nelect resulting from a given net
1474 # charge in any case if it's != 0, but if nelect is
1475 # additionally given explicitly, then we need to determine it
1476 # even for net charge of 0 to check for conflicts
1477 if charge is not None and (charge != 0 or val is not None):
1478 default_nelect = self.default_nelect_from_ppp()
1479 nelect_from_charge = default_nelect - charge
1480 if val is not None and val != nelect_from_charge:
1481 raise ValueError('incompatible input parameters: '
1482 'nelect=%s, but charge=%s '
1483 '(neutral nelect is %s)' %
1484 (val, charge, default_nelect))
1485 val = nelect_from_charge
1486 if val is not None:
1487 incar.write(' %s = %5.6f\n' % (key.upper(), val))
1488 for key, val in self.exp_params.items():
1489 if val is not None:
1490 incar.write(' %s = %5.2e\n' % (key.upper(), val))
1491 for key, val in self.string_params.items():
1492 if val is not None:
1493 incar.write(' %s = %s\n' % (key.upper(), val))
1494 for key, val in self.int_params.items():
1495 if val is not None:
1496 incar.write(' %s = %d\n' % (key.upper(), val))
1497 if key == 'ichain' and val > 0:
1498 incar.write(' IBRION = 3\n POTIM = 0.0\n')
1499 for key, val in self.int_params.items():
1500 if key == 'iopt' and val is None:
1501 print('WARNING: optimization is '
1502 'set to LFBGS (IOPT = 1)')
1503 incar.write(' IOPT = 1\n')
1504 for key, val in self.exp_params.items():
1505 if key == 'ediffg' and val is None:
1506 RuntimeError('Please set EDIFFG < 0')
1508 for key, val in self.list_bool_params.items():
1509 if val is None:
1510 pass
1511 else:
1512 incar.write(' %s = ' % key.upper())
1513 [incar.write('%s ' % _to_vasp_bool(x)) for x in val]
1514 incar.write('\n')
1516 for key, val in self.list_int_params.items():
1517 if val is None:
1518 pass
1519 elif key == 'ldaul' and (self.dict_params['ldau_luj'] is not None):
1520 pass
1521 else:
1522 incar.write(' %s = ' % key.upper())
1523 [incar.write('%d ' % x) for x in val]
1524 incar.write('\n')
1526 for key, val in self.list_float_params.items():
1527 if val is None:
1528 pass
1529 elif ((key in ('ldauu', 'ldauj'))
1530 and (self.dict_params['ldau_luj'] is not None)):
1531 pass
1532 elif key == 'magmom':
1533 if not len(val) == len(atoms):
1534 msg = ('Expected length of magmom tag to be'
1535 ' {}, i.e. 1 value per atom, but got {}').format(
1536 len(atoms), len(val))
1537 raise ValueError(msg)
1539 # Check if user remembered to specify ispin
1540 # note: we do not overwrite ispin if ispin=1
1541 if not self.int_params['ispin']:
1542 self.spinpol = True
1543 incar.write(' ispin = 2\n'.upper())
1545 incar.write(' %s = ' % key.upper())
1546 magmom_written = True
1547 # Work out compact a*x b*y notation and write in this form
1548 # Assume 1 magmom per atom, ordered as our atoms object
1549 val = np.array(val)
1550 val = val[self.sort] # Order in VASP format
1552 # Compactify the magmom list to symbol order
1553 lst = [[1, val[0]]]
1554 for n in range(1, len(val)):
1555 if val[n] == val[n - 1]:
1556 lst[-1][0] += 1
1557 else:
1558 lst.append([1, val[n]])
1559 incar.write(' '.join(
1560 ['{:d}*{:.4f}'.format(mom[0], mom[1]) for mom in lst]))
1561 incar.write('\n')
1562 else:
1563 incar.write(' %s = ' % key.upper())
1564 [incar.write('%.4f ' % x) for x in val]
1565 incar.write('\n')
1567 for key, val in self.bool_params.items():
1568 if val is not None:
1569 incar.write(' %s = ' % key.upper())
1570 if val:
1571 incar.write('.TRUE.\n')
1572 else:
1573 incar.write('.FALSE.\n')
1574 for key, val in self.special_params.items():
1575 if val is not None:
1576 incar.write(' %s = ' % key.upper())
1577 if key == 'lreal':
1578 if isinstance(val, str):
1579 incar.write(val + '\n')
1580 elif isinstance(val, bool):
1581 if val:
1582 incar.write('.TRUE.\n')
1583 else:
1584 incar.write('.FALSE.\n')
1585 for key, val in self.dict_params.items():
1586 if val is not None:
1587 if key == 'ldau_luj':
1588 # User didn't turn on LDAU tag.
1589 # Only turn on if ldau is unspecified
1590 if self.bool_params['ldau'] is None:
1591 self.bool_params['ldau'] = True
1592 # At this point we have already parsed our bool params
1593 incar.write(' LDAU = .TRUE.\n')
1594 llist = ulist = jlist = ''
1595 for symbol in self.symbol_count:
1596 # default: No +U
1597 luj = val.get(symbol[0], {'L': -1, 'U': 0.0, 'J': 0.0})
1598 llist += ' %i' % luj['L']
1599 ulist += ' %.3f' % luj['U']
1600 jlist += ' %.3f' % luj['J']
1601 incar.write(' LDAUL =%s\n' % llist)
1602 incar.write(' LDAUU =%s\n' % ulist)
1603 incar.write(' LDAUJ =%s\n' % jlist)
1605 if (self.spinpol and not magmom_written
1606 # We don't want to write magmoms if they are all 0.
1607 # but we could still be doing a spinpol calculation
1608 and atoms.get_initial_magnetic_moments().any()):
1609 if not self.int_params['ispin']:
1610 incar.write(' ispin = 2\n'.upper())
1611 # Write out initial magnetic moments
1612 magmom = atoms.get_initial_magnetic_moments()[self.sort]
1613 # unpack magmom array if three components specified
1614 if magmom.ndim > 1:
1615 magmom = [item for sublist in magmom for item in sublist]
1616 list = [[1, magmom[0]]]
1617 for n in range(1, len(magmom)):
1618 if magmom[n] == magmom[n - 1]:
1619 list[-1][0] += 1
1620 else:
1621 list.append([1, magmom[n]])
1622 incar.write(' magmom = '.upper())
1623 [incar.write('%i*%.4f ' % (mom[0], mom[1])) for mom in list]
1624 incar.write('\n')
1626 # Custom key-value pairs, which receive no formatting
1627 # Use the comment "# <Custom ASE key>" to denote such
1628 # a custom key-value pair, as we cannot otherwise
1629 # reliably and easily identify such non-standard entries
1630 custom_kv_pairs = p.get('custom')
1631 for key, value in custom_kv_pairs.items():
1632 incar.write(' {} = {} # <Custom ASE key>\n'.format(
1633 key.upper(), value))
1634 incar.close()
1636 def write_kpoints(self, atoms=None, directory='./', **kwargs):
1637 """Writes the KPOINTS file."""
1639 if atoms is None:
1640 atoms = self.atoms
1642 # Don't write anything if KSPACING is being used
1643 if self.float_params['kspacing'] is not None:
1644 if self.float_params['kspacing'] > 0:
1645 return
1646 else:
1647 raise ValueError("KSPACING value {0} is not allowable. "
1648 "Please use None or a positive number."
1649 "".format(self.float_params['kspacing']))
1651 kpointstring = format_kpoints(
1652 kpts=self.input_params['kpts'],
1653 atoms=atoms,
1654 reciprocal=self.input_params['reciprocal'],
1655 gamma=self.input_params['gamma'])
1656 with open(join(directory, 'KPOINTS'), 'w') as kpoints:
1657 kpoints.write(kpointstring)
1659 def write_potcar(self, suffix="", directory='./'):
1660 """Writes the POTCAR file."""
1662 with open(join(directory, 'POTCAR' + suffix), 'w') as potfile:
1663 for filename in self.ppp_list:
1664 with open_potcar(filename=filename) as ppp_file:
1665 for line in ppp_file:
1666 potfile.write(line)
1668 def write_sort_file(self, directory='./'):
1669 """Writes a sortings file.
1671 This file contains information about how the atoms are sorted in
1672 the first column and how they should be resorted in the second
1673 column. It is used for restart purposes to get sorting right
1674 when reading in an old calculation to ASE."""
1676 with open(join(directory, 'ase-sort.dat'), 'w') as fd:
1677 for n in range(len(self.sort)):
1678 fd.write('%5i %5i \n' % (self.sort[n], self.resort[n]))
1680 # The below functions are used to restart a calculation
1682 def read_incar(self, filename):
1683 """Method that imports settings from INCAR file.
1685 Typically named INCAR."""
1687 self.spinpol = False
1688 with open(filename, 'r') as fd:
1689 lines = fd.readlines()
1691 for line in lines:
1692 try:
1693 # Make multiplication, comments, and parameters easier to spot
1694 line = line.replace("*", " * ")
1695 line = line.replace("=", " = ")
1696 line = line.replace("#", "# ")
1697 data = line.split()
1698 # Skip empty and commented lines.
1699 if len(data) == 0:
1700 continue
1701 elif data[0][0] in ['#', '!']:
1702 continue
1703 key = data[0].lower()
1704 if '<Custom ASE key>' in line:
1705 # This key was added with custom key-value pair formatting.
1706 # Unconditionally add it, no type checking
1707 # Get value between "=" and the comment, e.g.
1708 # key = 1 2 3 # <Custom ASE key>
1709 # value should be '1 2 3'
1711 # Split at first occurence of "="
1712 value = line.split('=', 1)[1]
1713 # First "#" denotes beginning of comment
1714 # Add everything before comment as a string to custom dict
1715 value = value.split('#', 1)[0].strip()
1716 self.input_params['custom'][key] = value
1717 elif key in float_keys:
1718 self.float_params[key] = float(data[2])
1719 elif key in exp_keys:
1720 self.exp_params[key] = float(data[2])
1721 elif key in string_keys:
1722 self.string_params[key] = str(data[2])
1723 elif key in int_keys:
1724 if key == 'ispin':
1725 # JRK added. not sure why we would want to leave ispin
1726 # out
1727 self.int_params[key] = int(data[2])
1728 if int(data[2]) == 2:
1729 self.spinpol = True
1730 else:
1731 self.int_params[key] = int(data[2])
1732 elif key in bool_keys:
1733 if 'true' in data[2].lower():
1734 self.bool_params[key] = True
1735 elif 'false' in data[2].lower():
1736 self.bool_params[key] = False
1738 elif key in list_bool_keys:
1739 self.list_bool_params[key] = [
1740 _from_vasp_bool(x)
1741 for x in _args_without_comment(data[2:])
1742 ]
1744 elif key in list_int_keys:
1745 self.list_int_params[key] = [
1746 int(x) for x in _args_without_comment(data[2:])
1747 ]
1749 elif key in list_float_keys:
1750 if key == 'magmom':
1751 lst = []
1752 i = 2
1753 while i < len(data):
1754 if data[i] in ["#", "!"]:
1755 break
1756 if data[i] == "*":
1757 b = lst.pop()
1758 i += 1
1759 for j in range(int(b)):
1760 lst.append(float(data[i]))
1761 else:
1762 lst.append(float(data[i]))
1763 i += 1
1764 self.list_float_params['magmom'] = lst
1765 lst = np.array(lst)
1766 if self.atoms is not None:
1767 self.atoms.set_initial_magnetic_moments(
1768 lst[self.resort])
1769 else:
1770 data = _args_without_comment(data)
1771 self.list_float_params[key] = [
1772 float(x) for x in data[2:]
1773 ]
1774 # elif key in list_keys:
1775 # list = []
1776 # if key in ('dipol', 'eint', 'ferwe', 'ferdo',
1777 # 'ropt', 'rwigs',
1778 # 'ldauu', 'ldaul', 'ldauj', 'langevin_gamma'):
1779 # for a in data[2:]:
1780 # if a in ["!", "#"]:
1781 # break
1782 # list.append(float(a))
1783 # elif key in ('iband', 'kpuse', 'random_seed'):
1784 # for a in data[2:]:
1785 # if a in ["!", "#"]:
1786 # break
1787 # list.append(int(a))
1788 # self.list_params[key] = list
1789 # if key == 'magmom':
1790 # list = []
1791 # i = 2
1792 # while i < len(data):
1793 # if data[i] in ["#", "!"]:
1794 # break
1795 # if data[i] == "*":
1796 # b = list.pop()
1797 # i += 1
1798 # for j in range(int(b)):
1799 # list.append(float(data[i]))
1800 # else:
1801 # list.append(float(data[i]))
1802 # i += 1
1803 # self.list_params['magmom'] = list
1804 # list = np.array(list)
1805 # if self.atoms is not None:
1806 # self.atoms.set_initial_magnetic_moments(
1807 # list[self.resort])
1808 elif key in special_keys:
1809 if key == 'lreal':
1810 if 'true' in data[2].lower():
1811 self.special_params[key] = True
1812 elif 'false' in data[2].lower():
1813 self.special_params[key] = False
1814 else:
1815 self.special_params[key] = data[2]
1816 except KeyError:
1817 raise IOError('Keyword "%s" in INCAR is'
1818 'not known by calculator.' % key)
1819 except IndexError:
1820 raise IOError('Value missing for keyword "%s".' % key)
1822 def read_kpoints(self, filename):
1823 """Read kpoints file, typically named KPOINTS."""
1824 # If we used VASP builtin kspacing,
1825 if self.float_params['kspacing'] is not None:
1826 # Don't update kpts array
1827 return
1829 with open(filename, 'r') as fd:
1830 lines = fd.readlines()
1832 ktype = lines[2].split()[0].lower()[0]
1833 if ktype in ['g', 'm', 'a']:
1834 if ktype == 'g':
1835 self.set(gamma=True)
1836 kpts = np.array([int(lines[3].split()[i]) for i in range(3)])
1837 elif ktype == 'a':
1838 kpts = np.array([int(lines[3].split()[i]) for i in range(1)])
1839 elif ktype == 'm':
1840 kpts = np.array([int(lines[3].split()[i]) for i in range(3)])
1841 else:
1842 if ktype in ['c', 'k']:
1843 self.set(reciprocal=False)
1844 else:
1845 self.set(reciprocal=True)
1846 kpts = np.array(
1847 [list(map(float, line.split())) for line in lines[3:]])
1848 self.set(kpts=kpts)
1850 def read_potcar(self, filename):
1851 """ Read the pseudopotential XC functional from POTCAR file.
1852 """
1854 # Search for key 'LEXCH' in POTCAR
1855 xc_flag = None
1856 with open(filename, 'r') as fd:
1857 for line in fd:
1858 key = line.split()[0].upper()
1859 if key == 'LEXCH':
1860 xc_flag = line.split()[-1].upper()
1861 break
1863 if xc_flag is None:
1864 raise ValueError('LEXCH flag not found in POTCAR file.')
1866 # Values of parameter LEXCH and corresponding XC-functional
1867 xc_dict = {'PE': 'PBE', '91': 'PW91', 'CA': 'LDA'}
1869 if xc_flag not in xc_dict.keys():
1870 raise ValueError('Unknown xc-functional flag found in POTCAR,'
1871 ' LEXCH=%s' % xc_flag)
1873 self.input_params['pp'] = xc_dict[xc_flag]
1875 def todict(self):
1876 """Returns a dictionary of all parameters
1877 that can be used to construct a new calculator object"""
1878 dict_list = [
1879 'float_params', 'exp_params', 'string_params', 'int_params',
1880 'bool_params', 'list_bool_params', 'list_int_params',
1881 'list_float_params', 'special_params', 'dict_params',
1882 'input_params'
1883 ]
1884 dct = {}
1885 for item in dict_list:
1886 dct.update(getattr(self, item))
1887 dct = {key: value for key, value in dct.items() if value is not None}
1888 return dct
1891def _args_without_comment(data, marks=['!', '#']):
1892 """Check split arguments list for a comment, return data up to marker
1894 INCAR reader splits list arguments on spaces and leaves comment markers as
1895 individual items. This function returns only the data portion of the list.
1897 """
1898 comment_locs = [data.index(mark) for mark in marks if mark in data]
1899 if comment_locs == []:
1900 return data
1901 else:
1902 return data[:min(comment_locs)]
1905def _from_vasp_bool(x):
1906 """Cast vasp boolean to Python bool
1908 VASP files sometimes use T or F as shorthand for the preferred Boolean
1909 notation .TRUE. or .FALSE. As capitalisation is pretty inconsistent in
1910 practice, we allow all cases to be cast to a Python bool.
1912 """
1913 assert isinstance(x, str)
1914 if x.lower() == '.true.' or x.lower() == 't':
1915 return True
1916 elif x.lower() == '.false.' or x.lower() == 'f':
1917 return False
1918 else:
1919 raise ValueError('Value "%s" not recognized as bool' % x)
1922def _to_vasp_bool(x):
1923 """Convert Python boolean to string for VASP input
1925 In case the value was modified to a string already, appropriate strings
1926 will also be accepted and cast to a standard .TRUE. / .FALSE. format.
1928 """
1929 if isinstance(x, str):
1930 if x.lower() in ('.true.', 't'):
1931 x = True
1932 elif x.lower() in ('.false.', 'f'):
1933 x = False
1934 else:
1935 raise ValueError('"%s" not recognised as VASP Boolean')
1936 assert isinstance(x, bool)
1937 if x:
1938 return '.TRUE.'
1939 else:
1940 return '.FALSE.'
1943def open_potcar(filename):
1944 """ Open POTCAR file with transparent decompression if it's an archive (.Z)
1945 """
1946 import gzip
1947 if filename.endswith('R'):
1948 return open(filename, 'r')
1949 elif filename.endswith('.Z'):
1950 return gzip.open(filename)
1951 else:
1952 raise ValueError('Invalid POTCAR filename: "%s"' % filename)
1955def read_potcar_numbers_of_electrons(file_obj):
1956 """ Read list of tuples (atomic symbol, number of valence electrons)
1957 for each atomtype from a POTCAR file."""
1958 nelect = []
1959 lines = file_obj.readlines()
1960 for n, line in enumerate(lines):
1961 if 'TITEL' in line:
1962 symbol = line.split('=')[1].split()[1].split('_')[0].strip()
1963 valence = float(
1964 lines[n + 4].split(';')[1].split('=')[1].split()[0].strip())
1965 nelect.append((symbol, valence))
1966 return nelect
1969def count_symbols(atoms, exclude=()):
1970 """Count symbols in atoms object, excluding a set of indices
1972 Parameters:
1973 atoms: Atoms object to be grouped
1974 exclude: List of indices to be excluded from the counting
1976 Returns:
1977 Tuple of (symbols, symbolcount)
1978 symbols: The unique symbols in the included list
1979 symbolscount: Count of symbols in the included list
1981 Example:
1983 >>> from ase.build import bulk
1984 >>> atoms = bulk('NaCl', crystalstructure='rocksalt', a=4.1, cubic=True)
1985 >>> count_symbols(atoms)
1986 (['Na', 'Cl'], {'Na': 4, 'Cl': 4})
1987 >>> count_symbols(atoms, exclude=(1, 2, 3))
1988 (['Na', 'Cl'], {'Na': 3, 'Cl': 2})
1989 """
1990 symbols = []
1991 symbolcount = {}
1992 for m, symbol in enumerate(atoms.symbols):
1993 if m in exclude:
1994 continue
1995 if symbol not in symbols:
1996 symbols.append(symbol)
1997 symbolcount[symbol] = 1
1998 else:
1999 symbolcount[symbol] += 1
2000 return symbols, symbolcount