(git:ed6f26b)
Loading...
Searching...
No Matches
molden_utils.F
Go to the documentation of this file.
1!--------------------------------------------------------------------------------------------------!
2! CP2K: A general program to perform molecular dynamics simulations !
3! Copyright 2000-2025 CP2K developers group <https://cp2k.org> !
4! !
5! SPDX-License-Identifier: GPL-2.0-or-later !
6!--------------------------------------------------------------------------------------------------!
7
8! **************************************************************************************************
9!> \brief Functions handling the MOLDEN format. Split from mode_selective.
10!> \author Teodoro Laino, 03.2009
11! **************************************************************************************************
12MODULE molden_utils
13 USE atomic_kind_types, ONLY: get_atomic_kind
14 USE basis_set_types, ONLY: get_gto_basis_set,&
15 gto_basis_set_type
16 USE cp_dbcsr_operations, ONLY: copy_dbcsr_to_fm
17 USE cp_fm_types, ONLY: cp_fm_get_info,&
18 cp_fm_get_submatrix
19 USE cp_log_handling, ONLY: cp_get_default_logger,&
20 cp_logger_type
21 USE cp_output_handling, ONLY: cp_p_file,&
22 cp_print_key_finished_output,&
23 cp_print_key_should_output,&
24 cp_print_key_unit_nr
25 USE input_constants, ONLY: gto_cartesian,&
26 gto_spherical
27 USE input_section_types, ONLY: section_vals_type,&
28 section_vals_val_get
29 USE kinds, ONLY: dp
30 USE mathconstants, ONLY: pi
31 USE orbital_pointers, ONLY: nco,&
32 nso
33 USE orbital_transformation_matrices, ONLY: orbtramat
34 USE particle_types, ONLY: particle_type
35 USE periodic_table, ONLY: get_ptable_info
36 USE physcon, ONLY: massunit
37 USE qs_kind_types, ONLY: get_qs_kind,&
38 get_qs_kind_set,&
39 qs_kind_type
40 USE qs_mo_types, ONLY: mo_set_type
41#include "./base/base_uses.f90"
42
43 IMPLICIT NONE
44
45 PRIVATE
46 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'molden_utils'
47 LOGICAL, PARAMETER :: debug_this_module = .false.
48
49 INTEGER, PARAMETER :: molden_lmax = 4
50 INTEGER, PARAMETER :: molden_ncomax = (molden_lmax + 1)*(molden_lmax + 2)/2 ! 15
51
52 PUBLIC :: write_vibrations_molden, write_mos_molden
53
54CONTAINS
55
56! **************************************************************************************************
57!> \brief Write out the MOs in molden format for visualisation
58!> \param mos the set of MOs (both spins, if UKS)
59!> \param qs_kind_set for basis set info
60!> \param particle_set particles data structure, for positions and kinds
61!> \param print_section input section containing relevant print key
62!> \author MattW, IainB
63! **************************************************************************************************
64 SUBROUTINE write_mos_molden(mos, qs_kind_set, particle_set, print_section)
65 TYPE(mo_set_type), DIMENSION(:), INTENT(IN) :: mos
66 TYPE(qs_kind_type), DIMENSION(:), POINTER :: qs_kind_set
67 TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
68 TYPE(section_vals_type), POINTER :: print_section
69
70 CHARACTER(LEN=*), PARAMETER :: routinen = 'write_mos_molden'
71 CHARACTER(LEN=molden_lmax+1), PARAMETER :: angmom = "spdfg"
72
73 CHARACTER(LEN=15) :: fmtstr1, fmtstr2
74 CHARACTER(LEN=2) :: element_symbol
75 INTEGER :: gto_kind, handle, i, iatom, icgf, icol, ikind, ipgf, irow, irow_in, iset, isgf, &
76 ishell, ispin, iw, lshell, ncgf, ncol_global, ndigits, nrow_global, nset, nsgf, z
77 INTEGER, DIMENSION(:), POINTER :: npgf, nshell
78 INTEGER, DIMENSION(:, :), POINTER :: l
79 INTEGER, DIMENSION(molden_ncomax, 0:molden_lmax) :: orbmap
80 LOGICAL :: print_warn
81 REAL(kind=dp) :: expzet, prefac
82 REAL(kind=dp), ALLOCATABLE, DIMENSION(:, :) :: cmatrix, smatrix
83 REAL(kind=dp), DIMENSION(:, :), POINTER :: zet
84 REAL(kind=dp), DIMENSION(:, :, :), POINTER :: gcc
85 TYPE(cp_logger_type), POINTER :: logger
86 TYPE(gto_basis_set_type), POINTER :: orb_basis_set
87
88 CALL timeset(routinen, handle)
89
90 logger => cp_get_default_logger()
91 IF (btest(cp_print_key_should_output(logger%iter_info, print_section, ""), cp_p_file)) THEN
92
93 iw = cp_print_key_unit_nr(logger, print_section, "", &
94 extension=".molden", file_status='REPLACE')
95
96 print_warn = .true.
97
98 CALL section_vals_val_get(print_section, "NDIGITS", i_val=ndigits)
99 ndigits = min(max(3, ndigits), 30)
100 WRITE (unit=fmtstr1, fmt='("(I6,1X,ES",I0,".",I0,")")') ndigits + 7, ndigits
101 WRITE (unit=fmtstr2, fmt='("((T51,2F",I0,".",I0,"))")') ndigits + 10, ndigits
102
103 CALL section_vals_val_get(print_section, "GTO_KIND", i_val=gto_kind)
104
105 IF (mos(1)%use_mo_coeff_b) THEN
106 ! we are using the dbcsr mo_coeff
107 ! we copy it to the fm anyway
108 DO ispin = 1, SIZE(mos)
109 IF (.NOT. ASSOCIATED(mos(ispin)%mo_coeff_b)) THEN
110 cpassert(.false.)
111 END IF
112 CALL copy_dbcsr_to_fm(mos(ispin)%mo_coeff_b, &
113 mos(ispin)%mo_coeff) !fm->dbcsr
114 END DO
115 END IF
116
117 IF (iw > 0) THEN
118 WRITE (iw, '(T2,A)') "[Molden Format]"
119 WRITE (iw, '(T2,A)') "[Atoms] AU"
120 DO i = 1, SIZE(particle_set)
121 CALL get_atomic_kind(atomic_kind=particle_set(i)%atomic_kind, &
122 element_symbol=element_symbol)
123 CALL get_ptable_info(element_symbol, number=z)
124
125 WRITE (iw, '(T2,A2,I8,I8,3X,3(F12.6,3X))') &
126 element_symbol, i, z, particle_set(i)%r(:)
127 END DO
128
129 WRITE (iw, '(T2,A)') "[GTO]"
130
131 DO i = 1, SIZE(particle_set)
132 CALL get_atomic_kind(atomic_kind=particle_set(i)%atomic_kind, kind_number=ikind, &
133 element_symbol=element_symbol)
134 CALL get_qs_kind(qs_kind_set(ikind), basis_set=orb_basis_set)
135 IF (ASSOCIATED(orb_basis_set)) THEN
136 WRITE (iw, '(T2,I8,I8)') i, 0
137 CALL get_gto_basis_set(gto_basis_set=orb_basis_set, &
138 nset=nset, &
139 npgf=npgf, &
140 nshell=nshell, &
141 l=l, &
142 zet=zet, &
143 gcc=gcc)
144
145 DO iset = 1, nset
146 DO ishell = 1, nshell(iset)
147 lshell = l(ishell, iset)
148 IF (lshell <= molden_lmax) THEN
149 WRITE (unit=iw, fmt='(T25,A2,4X,I4,4X,F4.2)') &
150 angmom(lshell + 1:lshell + 1), npgf(iset), 1.0_dp
151 ! MOLDEN expects the contraction coefficient of spherical NOT CARTESIAN NORMALISED
152 ! functions. So we undo the normalisation factors included in the gccs
153 ! Reverse engineered from basis_set_types, normalise_gcc_orb
154 prefac = 2_dp**lshell*(2/pi)**0.75_dp
155 expzet = 0.25_dp*(2*lshell + 3.0_dp)
156 WRITE (unit=iw, fmt=fmtstr2) &
157 (zet(ipgf, iset), gcc(ipgf, ishell, iset)/(prefac*zet(ipgf, iset)**expzet), &
158 ipgf=1, npgf(iset))
159 ELSE
160 IF (print_warn) THEN
161 CALL cp_warn(__location__, &
162 "MOLDEN format does not support Gaussian orbitals with l > 4.")
163 print_warn = .false.
164 END IF
165 END IF
166 END DO
167 END DO
168
169 WRITE (iw, '(A4)') " "
170
171 END IF
172
173 END DO
174
175 IF (gto_kind == gto_spherical) THEN
176 WRITE (iw, '(T2,A)') "[5D7F]"
177 WRITE (iw, '(T2,A)') "[9G]"
178 END IF
179
180 WRITE (iw, '(T2,A)') "[MO]"
181 END IF
182
183 !------------------------------------------------------------------------
184 ! convert from CP2K to MOLDEN format ordering
185 ! http://www.cmbi.ru.nl/molden/molden_format.html
186 !"The following order of D, F and G functions is expected:
187 !
188 ! 5D: D 0, D+1, D-1, D+2, D-2
189 ! 6D: xx, yy, zz, xy, xz, yz
190 !
191 ! 7F: F 0, F+1, F-1, F+2, F-2, F+3, F-3
192 ! 10F: xxx, yyy, zzz, xyy, xxy, xxz, xzz, yzz, yyz, xyz
193 !
194 ! 9G: G 0, G+1, G-1, G+2, G-2, G+3, G-3, G+4, G-4
195 ! 15G: xxxx yyyy zzzz xxxy xxxz yyyx yyyz zzzx zzzy,
196 ! xxyy xxzz yyzz xxyz yyxz zzxy
197 !"
198 ! CP2K has x in the outer (slower loop), so
199 ! xx, xy, xz, yy, yz,zz for l=2, for instance
200 !
201 ! iorb_cp2k = orbmap(iorb_molden, l), l = 0 .. 4
202 ! -----------------------------------------------------------------------
203 IF (iw > 0) THEN
204 IF (gto_kind == gto_cartesian) THEN
205 ! -----------------------------------------------------------------
206 ! Use cartesian (6D, 10F, 15G) representation.
207 ! This is only format VMD can process.
208 ! -----------------------------------------------------------------
209 orbmap = reshape((/1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, &
210 1, 2, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, &
211 1, 4, 6, 2, 3, 5, 0, 0, 0, 0, 0, 0, 0, 0, 0, &
212 1, 7, 10, 4, 2, 3, 6, 9, 8, 5, 0, 0, 0, 0, 0, &
213 1, 11, 15, 2, 3, 7, 12, 10, 14, 4, 6, 13, 5, 8, 9/), &
214 (/molden_ncomax, molden_lmax + 1/))
215 ELSE IF (gto_kind == gto_spherical) THEN
216 ! -----------------------------------------------------------------
217 ! Use spherical (5D, 7F, 9G) representation.
218 ! -----------------------------------------------------------------
219 orbmap = reshape((/1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, &
220 3, 1, 2, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, &
221 3, 4, 2, 5, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, &
222 4, 5, 3, 6, 2, 7, 1, 0, 0, 0, 0, 0, 0, 0, 0, &
223 5, 6, 4, 7, 3, 8, 2, 9, 1, 0, 0, 0, 0, 0, 0/), &
224 (/molden_ncomax, molden_lmax + 1/))
225 END IF
226 END IF
227
228 DO ispin = 1, SIZE(mos)
229 CALL cp_fm_get_info(mos(ispin)%mo_coeff, &
230 nrow_global=nrow_global, &
231 ncol_global=ncol_global)
232 ALLOCATE (smatrix(nrow_global, ncol_global))
233 CALL cp_fm_get_submatrix(mos(ispin)%mo_coeff, smatrix)
234
235 IF (iw > 0) THEN
236 IF (gto_kind == gto_cartesian) THEN
237 CALL get_qs_kind_set(qs_kind_set, ncgf=ncgf, nsgf=nsgf)
238
239 ALLOCATE (cmatrix(ncgf, ncgf))
240
241 cmatrix = 0.0_dp
242
243 ! Transform spherical MOs to Cartesian MOs
244
245 icgf = 1
246 isgf = 1
247 DO iatom = 1, SIZE(particle_set)
248 NULLIFY (orb_basis_set)
249 CALL get_atomic_kind(particle_set(iatom)%atomic_kind, kind_number=ikind)
250 CALL get_qs_kind(qs_kind_set(ikind), &
251 basis_set=orb_basis_set)
252 IF (ASSOCIATED(orb_basis_set)) THEN
253 CALL get_gto_basis_set(gto_basis_set=orb_basis_set, &
254 nset=nset, &
255 nshell=nshell, &
256 l=l)
257 DO iset = 1, nset
258 DO ishell = 1, nshell(iset)
259 lshell = l(ishell, iset)
260 CALL dgemm("T", "N", nco(lshell), mos(ispin)%nmo, nso(lshell), 1.0_dp, &
261 orbtramat(lshell)%c2s, nso(lshell), &
262 smatrix(isgf, 1), nsgf, 0.0_dp, &
263 cmatrix(icgf, 1), ncgf)
264 icgf = icgf + nco(lshell)
265 isgf = isgf + nso(lshell)
266 END DO
267 END DO
268 END IF
269 END DO ! iatom
270 END IF
271
272 DO icol = 1, mos(ispin)%nmo
273 ! index of the first basis function for the given atom, set, and shell
274 irow = 1
275
276 ! index of the first basis function in MOLDEN file.
277 ! Due to limitation of the MOLDEN format, basis functions with l > molden_lmax
278 ! cannot be exported, so we need to renumber atomic orbitals
279 irow_in = 1
280
281 WRITE (iw, '(A,ES20.10)') 'Ene=', mos(ispin)%eigenvalues(icol)
282 IF (ispin < 2) THEN
283 WRITE (iw, '(A)') 'Spin= Alpha'
284 ELSE
285 WRITE (iw, '(A)') 'Spin= Beta'
286 END IF
287 WRITE (iw, '(A,F12.7)') 'Occup=', mos(ispin)%occupation_numbers(icol)
288
289 DO iatom = 1, SIZE(particle_set)
290 NULLIFY (orb_basis_set)
291 CALL get_atomic_kind(particle_set(iatom)%atomic_kind, &
292 element_symbol=element_symbol, kind_number=ikind)
293 CALL get_qs_kind(qs_kind_set(ikind), &
294 basis_set=orb_basis_set)
295 IF (ASSOCIATED(orb_basis_set)) THEN
296 CALL get_gto_basis_set(gto_basis_set=orb_basis_set, &
297 nset=nset, &
298 nshell=nshell, &
299 l=l)
300
301 IF (gto_kind == gto_cartesian) THEN
302 ! ----------------------------------------------
303 ! Use cartesian (6D, 10F, 15G) representation.
304 ! ----------------------------------------------
305 icgf = 1
306 DO iset = 1, nset
307 DO ishell = 1, nshell(iset)
308 lshell = l(ishell, iset)
309
310 IF (lshell <= molden_lmax) THEN
311 CALL print_coeffs(iw, fmtstr1, ndigits, irow_in, orbmap(:, lshell), &
312 cmatrix(irow:irow + nco(lshell) - 1, icol))
313 irow_in = irow_in + nco(lshell)
314 END IF
315
316 irow = irow + nco(lshell)
317 END DO ! ishell
318 END DO
319
320 ELSE IF (gto_kind == gto_spherical) THEN
321 ! ----------------------------------------------
322 ! Use spherical (5D, 7F, 9G) representation.
323 ! ----------------------------------------------
324 DO iset = 1, nset
325 DO ishell = 1, nshell(iset)
326 lshell = l(ishell, iset)
327
328 IF (lshell <= molden_lmax) THEN
329 CALL print_coeffs(iw, fmtstr1, ndigits, irow_in, orbmap(:, lshell), &
330 smatrix(irow:irow + nso(lshell) - 1, icol))
331 irow_in = irow_in + nso(lshell)
332 END IF
333
334 irow = irow + nso(lshell)
335 END DO
336 END DO
337 END IF
338
339 END IF
340 END DO ! iatom
341 END DO
342 END IF
343
344 IF (ALLOCATED(cmatrix)) DEALLOCATE (cmatrix)
345 IF (ALLOCATED(smatrix)) DEALLOCATE (smatrix)
346 END DO
347
348 CALL cp_print_key_finished_output(iw, logger, print_section, "")
349
350 END IF
351
352 CALL timestop(handle)
353
354 END SUBROUTINE write_mos_molden
355
356! **************************************************************************************************
357!> \brief Output MO coefficients formatted correctly for MOLDEN, omitting those <= 1E(-digits)
358!> \param iw output file unit
359!> \param fmtstr1 format string
360!> \param ndigits number of significant digits in MO coefficients
361!> \param irow_in index of the first atomic orbital: mo_coeff(orbmap(1))
362!> \param orbmap array to map Gaussian functions from MOLDEN to CP2K ordering
363!> \param mo_coeff MO coefficients
364! **************************************************************************************************
365 SUBROUTINE print_coeffs(iw, fmtstr1, ndigits, irow_in, orbmap, mo_coeff)
366 INTEGER, INTENT(in) :: iw
367 CHARACTER(LEN=*), INTENT(in) :: fmtstr1
368 INTEGER, INTENT(in) :: ndigits, irow_in
369 INTEGER, DIMENSION(molden_ncomax), INTENT(in) :: orbmap
370 REAL(kind=dp), DIMENSION(:), INTENT(in) :: mo_coeff
371
372 INTEGER :: orbital
373
374 DO orbital = 1, molden_ncomax
375 IF (orbmap(orbital) /= 0) THEN
376 IF (abs(mo_coeff(orbmap(orbital))) >= 10.0_dp**(-ndigits)) THEN
377 WRITE (iw, fmtstr1) irow_in + orbital - 1, mo_coeff(orbmap(orbital))
378 END IF
379 END IF
380 END DO
381
382 END SUBROUTINE print_coeffs
383
384! **************************************************************************************************
385!> \brief writes the output for vibrational analysis in MOLDEN format
386!> \param input ...
387!> \param particles ...
388!> \param freq ...
389!> \param eigen_vec ...
390!> \param intensities ...
391!> \param calc_intens ...
392!> \param dump_only_positive ...
393!> \param logger ...
394!> \param list array of mobile atom indices
395!> \author Florian Schiffmann 11.2007
396! **************************************************************************************************
397 SUBROUTINE write_vibrations_molden(input, particles, freq, eigen_vec, intensities, calc_intens, &
398 dump_only_positive, logger, list)
399
400 TYPE(section_vals_type), POINTER :: input
401 TYPE(particle_type), DIMENSION(:), POINTER :: particles
402 REAL(kind=dp), DIMENSION(:) :: freq
403 REAL(kind=dp), DIMENSION(:, :) :: eigen_vec
404 REAL(kind=dp), DIMENSION(:), POINTER :: intensities
405 LOGICAL, INTENT(in) :: calc_intens, dump_only_positive
406 TYPE(cp_logger_type), POINTER :: logger
407 INTEGER, DIMENSION(:), OPTIONAL, POINTER :: list
408
409 CHARACTER(len=*), PARAMETER :: routinen = 'write_vibrations_molden'
410
411 CHARACTER(LEN=2) :: element_symbol
412 INTEGER :: handle, i, iw, j, k, l, z
413 INTEGER, ALLOCATABLE, DIMENSION(:) :: my_list
414 REAL(kind=dp) :: fint
415
416 CALL timeset(routinen, handle)
417
418 iw = cp_print_key_unit_nr(logger, input, "VIBRATIONAL_ANALYSIS%PRINT%MOLDEN_VIB", &
419 extension=".mol", file_status='REPLACE')
420
421 IF (iw .GT. 0) THEN
422 cpassert(mod(SIZE(eigen_vec, 1), 3) == 0)
423 cpassert(SIZE(freq, 1) == SIZE(eigen_vec, 2))
424 ALLOCATE (my_list(SIZE(particles)))
425 ! Either we have a list of the subset of mobile atoms,
426 ! Or the eigenvectors must span the full space (all atoms)
427 IF (PRESENT(list)) THEN
428 my_list(:) = 0
429 DO i = 1, SIZE(list)
430 my_list(list(i)) = i
431 END DO
432 ELSE
433 cpassert(SIZE(particles) == SIZE(eigen_vec, 1)/3)
434 DO i = 1, SIZE(my_list)
435 my_list(i) = i
436 END DO
437 END IF
438 WRITE (iw, '(T2,A)') "[Molden Format]"
439 WRITE (iw, '(T2,A)') "[Atoms] AU"
440 DO i = 1, SIZE(particles)
441 CALL get_atomic_kind(atomic_kind=particles(i)%atomic_kind, &
442 element_symbol=element_symbol)
443 CALL get_ptable_info(element_symbol, number=z)
444
445 WRITE (iw, '(T2,A2,I8,I8,3X,3(F12.6,3X))') &
446 element_symbol, i, z, particles(i)%r(:)
447
448 END DO
449 WRITE (iw, '(T2,A)') "[FREQ]"
450 DO i = 1, SIZE(freq, 1)
451 IF ((.NOT. dump_only_positive) .OR. (freq(i) >= 0._dp)) WRITE (iw, '(T5,F12.6)') freq(i)
452 END DO
453 WRITE (iw, '(T2,A)') "[FR-COORD]"
454 DO i = 1, SIZE(particles)
455 CALL get_atomic_kind(atomic_kind=particles(i)%atomic_kind, &
456 element_symbol=element_symbol)
457 WRITE (iw, '(T2,A2,3X,3(F12.6,3X))') &
458 element_symbol, particles(i)%r(:)
459 END DO
460 WRITE (iw, '(T2,A)') "[FR-NORM-COORD]"
461 l = 0
462 DO i = 1, SIZE(eigen_vec, 2)
463 IF ((.NOT. dump_only_positive) .OR. (freq(i) >= 0._dp)) THEN
464 l = l + 1
465 WRITE (iw, '(T2,A,1X,I6)') "vibration", l
466 DO j = 1, SIZE(particles)
467 IF (my_list(j) .NE. 0) THEN
468 k = (my_list(j) - 1)*3
469 WRITE (iw, '(T2,3(F12.6,3X))') eigen_vec(k + 1, i), eigen_vec(k + 2, i), eigen_vec(k + 3, i)
470 ELSE
471 WRITE (iw, '(T2,3(F12.6,3X))') 0.0_dp, 0.0_dp, 0.0_dp
472 END IF
473 END DO
474 END IF
475 END DO
476 IF (calc_intens) THEN
477 fint = massunit
478 ! intensity units are a.u./amu
479 WRITE (iw, '(T2,A)') "[INT]"
480 DO i = 1, SIZE(intensities)
481 IF ((.NOT. dump_only_positive) .OR. (freq(i) >= 0._dp)) WRITE (iw, '(3X,F18.6)') fint*intensities(i)**2
482 END DO
483 END IF
484 DEALLOCATE (my_list)
485 END IF
486 CALL cp_print_key_finished_output(iw, logger, input, "VIBRATIONAL_ANALYSIS%PRINT%MOLDEN_VIB")
487
488 CALL timestop(handle)
489
490 END SUBROUTINE write_vibrations_molden
491
492END MODULE molden_utils
dgemm
static void dgemm(const char transa, const char transb, const int m, const int n, const int k, const double alpha, const double *a, const int lda, const double *b, const int ldb, const double beta, double *c, const int ldc)
Convenient wrapper to hide Fortran nature of dgemm_, swapping a and b.
Definition grid_cpu_task_list.c:206
atomic_kind_types
Define the atomic kind types and their sub types.
Definition atomic_kind_types.F:23
atomic_kind_types::get_atomic_kind
subroutine, public get_atomic_kind(atomic_kind, fist_potential, element_symbol, name, mass, kind_number, natom, atom_list, rcov, rvdw, z, qeff, apol, cpol, mm_radius, shell, shell_active, damping)
Get attributes of an atomic kind.
Definition atomic_kind_types.F:138
basis_set_types
Definition basis_set_types.F:15
basis_set_types::get_gto_basis_set
subroutine, public get_gto_basis_set(gto_basis_set, name, aliases, norm_type, kind_radius, ncgf, nset, nsgf, cgf_symbol, sgf_symbol, norm_cgf, set_radius, lmax, lmin, lx, ly, lz, m, ncgf_set, npgf, nsgf_set, nshell, cphi, pgf_radius, sphi, scon, zet, first_cgf, first_sgf, l, last_cgf, last_sgf, n, gcc, maxco, maxl, maxpgf, maxsgf_set, maxshell, maxso, nco_sum, npgf_sum, nshell_sum, maxder, short_kind_radius, npgf_seg_sum)
...
Definition basis_set_types.F:624
cp_dbcsr_operations
DBCSR operations in CP2K.
Definition cp_dbcsr_operations.F:18
cp_dbcsr_operations::copy_dbcsr_to_fm
subroutine, public copy_dbcsr_to_fm(matrix, fm)
Copy a DBCSR matrix to a BLACS matrix.
Definition cp_dbcsr_operations.F:214
cp_fm_types
represent a full matrix distributed on many processors
Definition cp_fm_types.F:15
cp_fm_types::cp_fm_get_info
subroutine, public cp_fm_get_info(matrix, name, nrow_global, ncol_global, nrow_block, ncol_block, nrow_local, ncol_local, row_indices, col_indices, local_data, context, nrow_locals, ncol_locals, matrix_struct, para_env)
returns all kind of information about the full matrix
Definition cp_fm_types.F:1009
cp_fm_types::cp_fm_get_submatrix
subroutine, public cp_fm_get_submatrix(fm, target_m, start_row, start_col, n_rows, n_cols, transpose)
gets a submatrix of a full matrix op(target_m)(1:n_rows,1:n_cols) =fm(start_row:start_row+n_rows,...
Definition cp_fm_types.F:894
cp_log_handling
various routines to log and control the output. The idea is that decisions about where to log should ...
Definition cp_log_handling.F:41
cp_log_handling::cp_get_default_logger
type(cp_logger_type) function, pointer, public cp_get_default_logger()
returns the default logger
Definition cp_log_handling.F:234
cp_output_handling
routines to handle the output, The idea is to remove the decision of wheter to output and what to out...
Definition cp_output_handling.F:25
cp_output_handling::cp_print_key_unit_nr
integer function, public cp_print_key_unit_nr(logger, basis_section, print_key_path, extension, middle_name, local, log_filename, ignore_should_output, file_form, file_position, file_action, file_status, do_backup, on_file, is_new_file, mpi_io, fout)
...
Definition cp_output_handling.F:853
cp_output_handling::cp_print_key_finished_output
subroutine, public cp_print_key_finished_output(unit_nr, logger, basis_section, print_key_path, local, ignore_should_output, on_file, mpi_io)
should be called after you finish working with a unit obtained with cp_print_key_unit_nr,...
Definition cp_output_handling.F:1063
cp_output_handling::cp_p_file
integer, parameter, public cp_p_file
Definition cp_output_handling.F:103
cp_output_handling::cp_print_key_should_output
integer function, public cp_print_key_should_output(iteration_info, basis_section, print_key_path, used_print_key, first_time)
returns what should be done with the given property if btest(res,cp_p_store) then the property should...
Definition cp_output_handling.F:345
input_constants
collects all constants needed in input so that they can be used without circular dependencies
Definition input_constants.F:17
input_constants::gto_cartesian
integer, parameter, public gto_cartesian
Definition input_constants.F:1289
input_constants::gto_spherical
integer, parameter, public gto_spherical
Definition input_constants.F:1289
input_section_types
objects that represent the structure of input sections and the data contained in an input section
Definition input_section_types.F:15
input_section_types::section_vals_val_get
subroutine, public section_vals_val_get(section_vals, keyword_name, i_rep_section, i_rep_val, n_rep_val, val, l_val, i_val, r_val, c_val, l_vals, i_vals, r_vals, c_vals, explicit)
returns the requested value
Definition input_section_types.F:1047
kinds
Defines the basic variable types.
Definition kinds.F:23
kinds::dp
integer, parameter, public dp
Definition kinds.F:34
list
An array-based list which grows on demand. When the internal array is full, a new array of twice the ...
Definition list.F:24
mathconstants
Definition of mathematical constants and functions.
Definition mathconstants.F:16
mathconstants::pi
real(kind=dp), parameter, public pi
Definition mathconstants.F:110
molden_utils
Functions handling the MOLDEN format. Split from mode_selective.
Definition molden_utils.F:12
molden_utils::write_mos_molden
subroutine, public write_mos_molden(mos, qs_kind_set, particle_set, print_section)
Write out the MOs in molden format for visualisation.
Definition molden_utils.F:65
molden_utils::write_vibrations_molden
subroutine, public write_vibrations_molden(input, particles, freq, eigen_vec, intensities, calc_intens, dump_only_positive, logger, list)
writes the output for vibrational analysis in MOLDEN format
Definition molden_utils.F:399
orbital_pointers
Provides Cartesian and spherical orbital pointers and indices.
Definition orbital_pointers.F:15
orbital_pointers::nco
integer, dimension(:), allocatable, public nco
Definition orbital_pointers.F:42
orbital_pointers::nso
integer, dimension(:), allocatable, public nso
Definition orbital_pointers.F:42
orbital_transformation_matrices
Calculation of the spherical harmonics and the corresponding orbital transformation matrices.
Definition orbital_transformation_matrices.F:17
orbital_transformation_matrices::orbtramat
type(orbtramat_type), dimension(:), pointer, public orbtramat
Definition orbital_transformation_matrices.F:47
particle_types
Define the data structure for the particle information.
Definition particle_types.F:19
periodic_table
Periodic Table related data definitions.
Definition periodic_table.F:28
periodic_table::get_ptable_info
subroutine, public get_ptable_info(symbol, number, amass, ielement, covalent_radius, metallic_radius, vdw_radius, found)
Pass information about the kind given the element symbol.
Definition periodic_table.F:85
physcon
Definition of physical constants:
Definition physcon.F:68
physcon::massunit
real(kind=dp), parameter, public massunit
Definition physcon.F:141
qs_kind_types
Define the quickstep kind type and their sub types.
Definition qs_kind_types.F:23
qs_kind_types::get_qs_kind
subroutine, public get_qs_kind(qs_kind, basis_set, basis_type, ncgf, nsgf, all_potential, tnadd_potential, gth_potential, sgp_potential, upf_potential, se_parameter, dftb_parameter, xtb_parameter, dftb3_param, zatom, zeff, elec_conf, mao, lmax_dftb, alpha_core_charge, ccore_charge, core_charge, core_charge_radius, paw_proj_set, paw_atom, hard_radius, hard0_radius, max_rad_local, covalent_radius, vdw_radius, gpw_type_forced, harmonics, max_iso_not0, max_s_harm, grid_atom, ngrid_ang, ngrid_rad, lmax_rho0, dft_plus_u_atom, l_of_dft_plus_u, n_of_dft_plus_u, u_minus_j, u_of_dft_plus_u, j_of_dft_plus_u, alpha_of_dft_plus_u, beta_of_dft_plus_u, j0_of_dft_plus_u, occupation_of_dft_plus_u, dispersion, bs_occupation, magnetization, no_optimize, addel, laddel, naddel, orbitals, max_scf, eps_scf, smear, u_ramping, u_minus_j_target, eps_u_ramping, init_u_ramping_each_scf, reltmat, ghost, floating, name, element_symbol, pao_basis_size, pao_model_file, pao_potentials, pao_descriptors, nelec)
Get attributes of an atomic kind.
Definition qs_kind_types.F:454
qs_kind_types::get_qs_kind_set
subroutine, public get_qs_kind_set(qs_kind_set, all_potential_present, tnadd_potential_present, gth_potential_present, sgp_potential_present, paw_atom_present, dft_plus_u_atom_present, maxcgf, maxsgf, maxco, maxco_proj, maxgtops, maxlgto, maxlprj, maxnset, maxsgf_set, ncgf, npgf, nset, nsgf, nshell, maxpol, maxlppl, maxlppnl, maxppnl, nelectron, maxder, max_ngrid_rad, max_sph_harm, maxg_iso_not0, lmax_rho0, basis_rcut, basis_type, total_zeff_corr, npgf_seg)
Get attributes of an atomic kind set.
Definition qs_kind_types.F:880
qs_mo_types
Definition and initialisation of the mo data type.
Definition qs_mo_types.F:22
basis_set_types::gto_basis_set_type
Definition basis_set_types.F:72
cp_log_handling::cp_logger_type
type of a logger, at the moment it contains just a print level starting at which level it should be l...
Definition cp_log_handling.F:140
input_section_types::section_vals_type
stores the values of a section
Definition input_section_types.F:127
orbital
Orbital angular momentum.
Definition grid_common.h:128
particle_types::particle_type
Definition particle_types.F:35
qs_kind_types::qs_kind_type
Provides all information about a quickstep kind.
Definition qs_kind_types.F:171
qs_mo_types::mo_set_type
Definition qs_mo_types.F:46