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topology_psf.F
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1 !--------------------------------------------------------------------------------------------------!
2 ! CP2K: A general program to perform molecular dynamics simulations !
3 ! Copyright 2000-2024 CP2K developers group <https://cp2k.org> !
4 ! !
5 ! SPDX-License-Identifier: GPL-2.0-or-later !
6 !--------------------------------------------------------------------------------------------------!
7 
8 ! **************************************************************************************************
9 !> \brief Functionality to read in PSF topologies and convert it into local
10 !> data structures
11 !> \author ikuo
12 !> tlaino 10.2006
13 ! **************************************************************************************************
14 MODULE topology_psf
15  USE cp_log_handling, ONLY: cp_get_default_logger,&
16  cp_logger_get_default_io_unit,&
17  cp_logger_type,&
18  cp_to_string
19  USE cp_output_handling, ONLY: cp_print_key_finished_output,&
20  cp_print_key_generate_filename,&
21  cp_print_key_unit_nr
22  USE cp_parser_methods, ONLY: parser_get_next_line,&
23  parser_get_object,&
24  parser_search_string,&
25  parser_test_next_token
26  USE cp_parser_types, ONLY: cp_parser_type,&
27  parser_create,&
28  parser_release
29  USE force_fields_input, ONLY: read_chrg_section
30  USE input_constants, ONLY: do_conn_psf,&
31  do_conn_psf_u
32  USE input_section_types, ONLY: section_vals_get,&
33  section_vals_get_subs_vals,&
34  section_vals_type,&
35  section_vals_val_get
36  USE kinds, ONLY: default_string_length,&
37  dp
38  USE memory_utilities, ONLY: reallocate
39  USE message_passing, ONLY: mp_para_env_type
40  USE qmmm_ff_fist, ONLY: qmmm_ff_precond_only_qm
41  USE string_table, ONLY: id2str,&
42  s2s,&
43  str2id
44  USE string_utilities, ONLY: uppercase
45  USE topology_types, ONLY: atom_info_type,&
46  connectivity_info_type,&
47  topology_parameters_type
48  USE topology_util, ONLY: array1_list_type,&
49  reorder_structure,&
50  tag_molecule
51  USE util, ONLY: sort
52 #include "./base/base_uses.f90"
53 
54  IMPLICIT NONE
55 
56  CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'topology_psf'
57 
58  PRIVATE
59  PUBLIC :: read_topology_psf, &
60  write_topology_psf, &
61  psf_post_process, &
62  idm_psf
63 
64 CONTAINS
65 
66 ! **************************************************************************************************
67 !> \brief Read PSF topology file
68 !> Teodoro Laino - Introduced CHARMM31 EXT PSF standard format
69 !> \param filename ...
70 !> \param topology ...
71 !> \param para_env ...
72 !> \param subsys_section ...
73 !> \param psf_type ...
74 !> \par History
75 !> 04-2007 Teodoro Laino - Zurich University [tlaino]
76 !> This routine should contain only information read from the PSF format
77 !> and all post_process should be performef in the psf_post_process
78 ! **************************************************************************************************
79  SUBROUTINE read_topology_psf(filename, topology, para_env, subsys_section, psf_type)
80  CHARACTER(LEN=*), INTENT(IN) :: filename
81  TYPE(topology_parameters_type), INTENT(INOUT) :: topology
82  TYPE(mp_para_env_type), POINTER :: para_env
83  TYPE(section_vals_type), POINTER :: subsys_section
84  INTEGER, INTENT(IN) :: psf_type
85 
86  CHARACTER(len=*), PARAMETER :: routinen = 'read_topology_psf'
87 
88  CHARACTER(LEN=2*default_string_length) :: psf_format
89  CHARACTER(LEN=3) :: c_int
90  CHARACTER(LEN=default_string_length) :: dummy_field, field, label, strtmp1, &
91  strtmp2, strtmp3
92  INTEGER :: handle, i, iatom, ibond, idum, index_now, iphi, itheta, iw, natom, natom_prev, &
93  nbond, nbond_prev, nphi, nphi_prev, ntheta, ntheta_prev, output_unit
94  LOGICAL :: found
95  TYPE(atom_info_type), POINTER :: atom_info
96  TYPE(connectivity_info_type), POINTER :: conn_info
97  TYPE(cp_logger_type), POINTER :: logger
98  TYPE(cp_parser_type) :: parser
99 
100  NULLIFY (logger)
101  logger => cp_get_default_logger()
102  output_unit = cp_logger_get_default_io_unit(logger)
103  iw = cp_print_key_unit_nr(logger, subsys_section, "PRINT%TOPOLOGY_INFO/PSF_INFO", &
104  extension=".subsysLog")
105  CALL timeset(routinen, handle)
106  CALL parser_create(parser, filename, para_env=para_env)
107 
108  atom_info => topology%atom_info
109  conn_info => topology%conn_info
110  natom_prev = 0
111  IF (ASSOCIATED(atom_info%id_molname)) natom_prev = SIZE(atom_info%id_molname)
112  c_int = 'I8'
113  label = 'PSF'
114  CALL parser_search_string(parser, label, .true., found, begin_line=.true.)
115  IF (.NOT. found) THEN
116  IF (output_unit > 0) THEN
117  WRITE (output_unit, '(A)') "ERROR| Missing PSF specification line"
118  END IF
119  cpabort("")
120  END IF
121  DO WHILE (parser_test_next_token(parser) /= "EOL")
122  CALL parser_get_object(parser, field)
123  SELECT CASE (field(1:3))
124  CASE ("PSF")
125  IF (psf_type == do_conn_psf) THEN
126  ! X-PLOR PSF format "similar" to the plain CHARMM PSF format
127  psf_format = '(I8,1X,A4,I5,1X,A4,1X,A4,1X,A4,1X,2G14.6,I8)'
128  END IF
129  CASE ("EXT")
130  IF (psf_type == do_conn_psf) THEN
131  ! EXTEnded CHARMM31 format
132  psf_format = '(I10,T12,A7,T21,I8,T30,A7,T39,A6,T47,A6,T53,F10.6,T69,F8.3,T88,I1)'
133  c_int = 'I10'
134  ELSE
135  cpabort("PSF_INFO| "//field(1:3)//" :: not available for UPSF format!")
136  END IF
137  CASE DEFAULT
138  cpabort("PSF_INFO| "//field(1:3)//" :: Unimplemented keyword in CP2K PSF/UPSF format!")
139  END SELECT
140  END DO
141  IF (iw > 0) WRITE (iw, '(T2,A)') 'PSF_INFO| Parsing the NATOM section'
142  !
143  ! ATOM section
144  !
145  label = '!NATOM'
146  CALL parser_search_string(parser, label, .true., found, begin_line=.true.)
147  IF (.NOT. found) THEN
148  IF (iw > 0) WRITE (iw, '(T2,A)') 'PSF_INFO| No NATOM section '
149  natom = 0
150  ELSE
151  CALL parser_get_object(parser, natom)
152  IF (natom_prev + natom > topology%natoms) &
153  CALL cp_abort(__location__, &
154  "Number of atoms in connectivity control is larger than the "// &
155  "number of atoms in coordinate control. check coordinates and "// &
156  "connectivity. ")
157  IF (iw > 0) WRITE (iw, '(T2,A,'//trim(c_int)//')') 'PSF_INFO| NATOM = ', natom
158  !malloc the memory that we need
159  CALL reallocate(atom_info%id_molname, 1, natom_prev + natom)
160  CALL reallocate(atom_info%resid, 1, natom_prev + natom)
161  CALL reallocate(atom_info%id_resname, 1, natom_prev + natom)
162  CALL reallocate(atom_info%id_atmname, 1, natom_prev + natom)
163  CALL reallocate(atom_info%atm_charge, 1, natom_prev + natom)
164  CALL reallocate(atom_info%atm_mass, 1, natom_prev + natom)
165  !Read in the atom info
166  IF (psf_type == do_conn_psf_u) THEN
167  DO iatom = 1, natom
168  index_now = iatom + natom_prev
169  CALL parser_get_next_line(parser, 1)
170  READ (parser%input_line, fmt=*, err=9) i, &
171  strtmp1, &
172  atom_info%resid(index_now), &
173  strtmp2, &
174  dummy_field, &
175  strtmp3, &
176  atom_info%atm_charge(index_now), &
177  atom_info%atm_mass(index_now)
178  atom_info%id_molname(index_now) = str2id(s2s(strtmp1))
179  atom_info%id_resname(index_now) = str2id(s2s(strtmp2))
180  atom_info%id_atmname(index_now) = str2id(s2s(strtmp3))
181  END DO
182  ELSE
183  DO iatom = 1, natom
184  index_now = iatom + natom_prev
185  CALL parser_get_next_line(parser, 1)
186  READ (parser%input_line, fmt=psf_format) &
187  i, &
188  strtmp1, &
189  atom_info%resid(index_now), &
190  strtmp2, &
191  dummy_field, &
192  strtmp3, &
193  atom_info%atm_charge(index_now), &
194  atom_info%atm_mass(index_now), &
195  idum
196  atom_info%id_molname(index_now) = str2id(s2s(strtmp1))
197  atom_info%id_resname(index_now) = str2id(s2s(strtmp2))
198  atom_info%id_atmname(index_now) = str2id(s2s(adjustl(strtmp3)))
199  END DO
200  END IF
201  END IF
202 
203  !
204  ! BOND section
205  !
206  nbond_prev = 0
207  IF (ASSOCIATED(conn_info%bond_a)) nbond_prev = SIZE(conn_info%bond_a)
208 
209  IF (iw > 0) WRITE (iw, '(T2,A)') 'PSF_INFO| Parsing the NBOND section'
210  IF (iw > 0) WRITE (iw, '(T2,A,I8)') 'PSF_INFO| Previous number of allocated BOND: ', nbond_prev
211  label = '!NBOND'
212  CALL parser_search_string(parser, label, .true., found, begin_line=.true.)
213  IF (.NOT. found) THEN
214  IF (iw > 0) WRITE (iw, '(T2,A)') 'PSF_INFO| No NBOND section '
215  nbond = 0
216  ELSE
217  CALL parser_get_object(parser, nbond)
218  IF (iw > 0) WRITE (iw, '(T2,A,'//trim(c_int)//')') 'PSF_INFO| NBOND = ', nbond
219  !malloc the memory that we need
220  CALL reallocate(conn_info%bond_a, 1, nbond_prev + nbond)
221  CALL reallocate(conn_info%bond_b, 1, nbond_prev + nbond)
222  !Read in the bond info
223  IF (psf_type == do_conn_psf_u) THEN
224  DO ibond = 1, nbond, 4
225  CALL parser_get_next_line(parser, 1)
226  index_now = nbond_prev + ibond - 1
227  READ (parser%input_line, fmt=*, err=9) (conn_info%bond_a(index_now + i), &
228  conn_info%bond_b(index_now + i), &
229  i=1, min(4, (nbond - ibond + 1)))
230  END DO
231  ELSE
232  DO ibond = 1, nbond, 4
233  CALL parser_get_next_line(parser, 1)
234  index_now = nbond_prev + ibond - 1
235  READ (parser%input_line, fmt='(8'//trim(c_int)//')') &
236  (conn_info%bond_a(index_now + i), &
237  conn_info%bond_b(index_now + i), &
238  i=1, min(4, (nbond - ibond + 1)))
239  END DO
240  END IF
241  IF (any(conn_info%bond_a(nbond_prev + 1:) <= 0) .OR. &
242  any(conn_info%bond_a(nbond_prev + 1:) > natom) .OR. &
243  any(conn_info%bond_b(nbond_prev + 1:) <= 0) .OR. &
244  any(conn_info%bond_b(nbond_prev + 1:) > natom)) THEN
245  cpabort("topology_read, invalid bond")
246  END IF
247  conn_info%bond_a(nbond_prev + 1:) = conn_info%bond_a(nbond_prev + 1:) + natom_prev
248  conn_info%bond_b(nbond_prev + 1:) = conn_info%bond_b(nbond_prev + 1:) + natom_prev
249  END IF
250  !
251  ! THETA section
252  !
253  ntheta_prev = 0
254  IF (ASSOCIATED(conn_info%theta_a)) ntheta_prev = SIZE(conn_info%theta_a)
255 
256  IF (iw > 0) WRITE (iw, '(T2,A)') 'PSF_INFO| Parsing the NTHETA section'
257  IF (iw > 0) WRITE (iw, '(T2,A,I8)') 'PSF_INFO| Previous number of allocated THETA: ', ntheta_prev
258  label = '!NTHETA'
259  CALL parser_search_string(parser, label, .true., found, begin_line=.true.)
260  IF (.NOT. found) THEN
261  IF (iw > 0) WRITE (iw, '(T2,A)') 'PSF_INFO| No NTHETA section '
262  ntheta = 0
263  ELSE
264  CALL parser_get_object(parser, ntheta)
265  IF (iw > 0) WRITE (iw, '(T2,A,'//trim(c_int)//')') 'PSF_INFO| NTHETA = ', ntheta
266  !malloc the memory that we need
267  CALL reallocate(conn_info%theta_a, 1, ntheta_prev + ntheta)
268  CALL reallocate(conn_info%theta_b, 1, ntheta_prev + ntheta)
269  CALL reallocate(conn_info%theta_c, 1, ntheta_prev + ntheta)
270  !Read in the bend info
271  IF (psf_type == do_conn_psf_u) THEN
272  DO itheta = 1, ntheta, 3
273  CALL parser_get_next_line(parser, 1)
274  index_now = ntheta_prev + itheta - 1
275  READ (parser%input_line, fmt=*, err=9) (conn_info%theta_a(index_now + i), &
276  conn_info%theta_b(index_now + i), &
277  conn_info%theta_c(index_now + i), &
278  i=1, min(3, (ntheta - itheta + 1)))
279  END DO
280  ELSE
281  DO itheta = 1, ntheta, 3
282  CALL parser_get_next_line(parser, 1)
283  index_now = ntheta_prev + itheta - 1
284  READ (parser%input_line, fmt='(9'//trim(c_int)//')') &
285  (conn_info%theta_a(index_now + i), &
286  conn_info%theta_b(index_now + i), &
287  conn_info%theta_c(index_now + i), &
288  i=1, min(3, (ntheta - itheta + 1)))
289  END DO
290  END IF
291  conn_info%theta_a(ntheta_prev + 1:) = conn_info%theta_a(ntheta_prev + 1:) + natom_prev
292  conn_info%theta_b(ntheta_prev + 1:) = conn_info%theta_b(ntheta_prev + 1:) + natom_prev
293  conn_info%theta_c(ntheta_prev + 1:) = conn_info%theta_c(ntheta_prev + 1:) + natom_prev
294  END IF
295  !
296  ! PHI section
297  !
298  nphi_prev = 0
299  IF (ASSOCIATED(conn_info%phi_a)) nphi_prev = SIZE(conn_info%phi_a)
300 
301  IF (iw > 0) WRITE (iw, '(T2,A)') 'PSF_INFO| Parsing the NPHI section'
302  IF (iw > 0) WRITE (iw, '(T2,A,I8)') 'PSF_INFO| Previous number of allocated PHI: ', nphi_prev
303  label = '!NPHI'
304  CALL parser_search_string(parser, label, .true., found, begin_line=.true.)
305  IF (.NOT. found) THEN
306  IF (iw > 0) WRITE (iw, '(T2,A)') 'PSF_INFO| No NPHI section '
307  nphi = 0
308  ELSE
309  CALL parser_get_object(parser, nphi)
310  IF (iw > 0) WRITE (iw, '(T2,A,'//trim(c_int)//')') 'PSF_INFO| NPHI = ', nphi
311  !malloc the memory that we need
312  CALL reallocate(conn_info%phi_a, 1, nphi_prev + nphi)
313  CALL reallocate(conn_info%phi_b, 1, nphi_prev + nphi)
314  CALL reallocate(conn_info%phi_c, 1, nphi_prev + nphi)
315  CALL reallocate(conn_info%phi_d, 1, nphi_prev + nphi)
316  !Read in the torsion info
317  IF (psf_type == do_conn_psf_u) THEN
318  DO iphi = 1, nphi, 2
319  CALL parser_get_next_line(parser, 1)
320  index_now = nphi_prev + iphi - 1
321  READ (parser%input_line, fmt=*, err=9) (conn_info%phi_a(index_now + i), &
322  conn_info%phi_b(index_now + i), &
323  conn_info%phi_c(index_now + i), &
324  conn_info%phi_d(index_now + i), &
325  i=1, min(2, (nphi - iphi + 1)))
326  END DO
327  ELSE
328  DO iphi = 1, nphi, 2
329  CALL parser_get_next_line(parser, 1)
330  index_now = nphi_prev + iphi - 1
331  READ (parser%input_line, fmt='(8'//trim(c_int)//')') &
332  (conn_info%phi_a(index_now + i), &
333  conn_info%phi_b(index_now + i), &
334  conn_info%phi_c(index_now + i), &
335  conn_info%phi_d(index_now + i), &
336  i=1, min(2, (nphi - iphi + 1)))
337  END DO
338  END IF
339  conn_info%phi_a(nphi_prev + 1:) = conn_info%phi_a(nphi_prev + 1:) + natom_prev
340  conn_info%phi_b(nphi_prev + 1:) = conn_info%phi_b(nphi_prev + 1:) + natom_prev
341  conn_info%phi_c(nphi_prev + 1:) = conn_info%phi_c(nphi_prev + 1:) + natom_prev
342  conn_info%phi_d(nphi_prev + 1:) = conn_info%phi_d(nphi_prev + 1:) + natom_prev
343  END IF
344  !
345  ! IMPHI section
346  !
347  nphi_prev = 0
348  IF (ASSOCIATED(conn_info%impr_a)) nphi_prev = SIZE(conn_info%impr_a)
349 
350  IF (iw > 0) WRITE (iw, '(T2,A)') 'PSF_INFO| Parsing the NIMPHI section'
351  IF (iw > 0) WRITE (iw, '(T2,A,I8)') 'PSF_INFO| Previous number of allocated IMPHI: ', nphi_prev
352  label = '!NIMPHI'
353  CALL parser_search_string(parser, label, .true., found, begin_line=.true.)
354  IF (.NOT. found) THEN
355  IF (iw > 0) WRITE (iw, '(T2,A)') 'PSF_INFO| No NIMPHI section '
356  nphi = 0
357  ELSE
358  CALL parser_get_object(parser, nphi)
359  IF (iw > 0) WRITE (iw, '(T2,A,'//trim(c_int)//')') 'PSF_INFO| NIMPR = ', nphi
360  !malloc the memory that we need
361  CALL reallocate(conn_info%impr_a, 1, nphi_prev + nphi)
362  CALL reallocate(conn_info%impr_b, 1, nphi_prev + nphi)
363  CALL reallocate(conn_info%impr_c, 1, nphi_prev + nphi)
364  CALL reallocate(conn_info%impr_d, 1, nphi_prev + nphi)
365  !Read in the improper torsion info
366  IF (psf_type == do_conn_psf_u) THEN
367  DO iphi = 1, nphi, 2
368  CALL parser_get_next_line(parser, 1)
369  index_now = nphi_prev + iphi - 1
370  READ (parser%input_line, fmt=*, err=9) (conn_info%impr_a(index_now + i), &
371  conn_info%impr_b(index_now + i), &
372  conn_info%impr_c(index_now + i), &
373  conn_info%impr_d(index_now + i), &
374  i=1, min(2, (nphi - iphi + 1)))
375  END DO
376  ELSE
377  DO iphi = 1, nphi, 2
378  CALL parser_get_next_line(parser, 1)
379  index_now = nphi_prev + iphi - 1
380  READ (parser%input_line, fmt='(8'//trim(c_int)//')') &
381  (conn_info%impr_a(index_now + i), &
382  conn_info%impr_b(index_now + i), &
383  conn_info%impr_c(index_now + i), &
384  conn_info%impr_d(index_now + i), &
385  i=1, min(2, (nphi - iphi + 1)))
386  END DO
387  END IF
388  conn_info%impr_a(nphi_prev + 1:) = conn_info%impr_a(nphi_prev + 1:) + natom_prev
389  conn_info%impr_b(nphi_prev + 1:) = conn_info%impr_b(nphi_prev + 1:) + natom_prev
390  conn_info%impr_c(nphi_prev + 1:) = conn_info%impr_c(nphi_prev + 1:) + natom_prev
391  conn_info%impr_d(nphi_prev + 1:) = conn_info%impr_d(nphi_prev + 1:) + natom_prev
392  END IF
393 
394  CALL parser_release(parser)
395  CALL timestop(handle)
396  CALL cp_print_key_finished_output(iw, logger, subsys_section, &
397  "PRINT%TOPOLOGY_INFO/PSF_INFO")
398  RETURN
399 9 CONTINUE
400  ! Print error and exit
401  IF (output_unit > 0) THEN
402  WRITE (output_unit, '(T2,A)') &
403  "PSF_INFO| Error while reading PSF using the unformatted PSF reading option!", &
404  "PSF_INFO| Try using PSF instead of UPSF."
405  END IF
406 
407  cpabort("Error while reading PSF data!")
408 
409  END SUBROUTINE read_topology_psf
410 
411 ! **************************************************************************************************
412 !> \brief Post processing of PSF informations
413 !> \param topology ...
414 !> \param subsys_section ...
415 ! **************************************************************************************************
416  SUBROUTINE psf_post_process(topology, subsys_section)
417  TYPE(topology_parameters_type), INTENT(INOUT) :: topology
418  TYPE(section_vals_type), POINTER :: subsys_section
419 
420  CHARACTER(len=*), PARAMETER :: routinen = 'psf_post_process'
421 
422  INTEGER :: handle, i, iatom, ibond, ionfo, iw, &
423  jatom, n, natom, nbond, nonfo, nphi, &
424  ntheta
425  TYPE(array1_list_type), DIMENSION(:), POINTER :: ex_bend_list, ex_bond_list
426  TYPE(atom_info_type), POINTER :: atom_info
427  TYPE(connectivity_info_type), POINTER :: conn_info
428  TYPE(cp_logger_type), POINTER :: logger
429 
430  NULLIFY (logger)
431  logger => cp_get_default_logger()
432  iw = cp_print_key_unit_nr(logger, subsys_section, "PRINT%TOPOLOGY_INFO/PSF_INFO", &
433  extension=".subsysLog")
434  CALL timeset(routinen, handle)
435  atom_info => topology%atom_info
436  conn_info => topology%conn_info
437  !
438  ! PARA_RES structure
439  !
440  natom = 0
441  nbond = 0
442  i = 0
443  IF (ASSOCIATED(atom_info%id_molname)) natom = SIZE(atom_info%id_molname)
444  IF (ASSOCIATED(conn_info%bond_a)) nbond = SIZE(conn_info%bond_a)
445  IF (ASSOCIATED(conn_info%c_bond_a)) i = SIZE(conn_info%c_bond_a)
446  DO ibond = 1, nbond
447  iatom = conn_info%bond_a(ibond)
448  jatom = conn_info%bond_b(ibond)
449  IF (topology%para_res) THEN
450  IF ((atom_info%id_molname(iatom) /= atom_info%id_molname(jatom)) .OR. &
451  (atom_info%resid(iatom) /= atom_info%resid(jatom)) .OR. &
452  (atom_info%id_resname(iatom) /= atom_info%id_resname(jatom))) THEN
453  IF (iw > 0) WRITE (iw, '(T2,A,2I6)') "PSF_INFO| PARA_RES, bond between molecules atom ", &
454  iatom, jatom
455  i = i + 1
456  CALL reallocate(conn_info%c_bond_a, 1, i)
457  CALL reallocate(conn_info%c_bond_b, 1, i)
458  conn_info%c_bond_a(i) = iatom
459  conn_info%c_bond_b(i) = jatom
460  END IF
461  ELSE
462  IF (atom_info%id_molname(iatom) /= atom_info%id_molname(jatom)) THEN
463  cpabort("")
464  END IF
465  END IF
466  END DO
467  !
468  ! UB structure
469  !
470  ntheta = 0
471  IF (ASSOCIATED(conn_info%theta_a)) ntheta = SIZE(conn_info%theta_a)
472  CALL reallocate(conn_info%ub_a, 1, ntheta)
473  CALL reallocate(conn_info%ub_b, 1, ntheta)
474  CALL reallocate(conn_info%ub_c, 1, ntheta)
475  conn_info%ub_a(:) = conn_info%theta_a(:)
476  conn_info%ub_b(:) = conn_info%theta_b(:)
477  conn_info%ub_c(:) = conn_info%theta_c(:)
478  !
479  ! ONFO structure
480  !
481  nphi = 0
482  nonfo = 0
483  IF (ASSOCIATED(conn_info%phi_a)) nphi = SIZE(conn_info%phi_a)
484  CALL reallocate(conn_info%onfo_a, 1, nphi)
485  CALL reallocate(conn_info%onfo_b, 1, nphi)
486  conn_info%onfo_a(1:) = conn_info%phi_a(1:)
487  conn_info%onfo_b(1:) = conn_info%phi_d(1:)
488  ! Reorder bonds
489  ALLOCATE (ex_bond_list(natom))
490  DO i = 1, natom
491  ALLOCATE (ex_bond_list(i)%array1(0))
492  END DO
493  n = 0
494  IF (ASSOCIATED(conn_info%bond_a)) n = SIZE(conn_info%bond_a)
495  CALL reorder_structure(ex_bond_list, conn_info%bond_a, conn_info%bond_b, n)
496  ! Reorder bends
497  ALLOCATE (ex_bend_list(natom))
498  DO i = 1, natom
499  ALLOCATE (ex_bend_list(i)%array1(0))
500  END DO
501  n = 0
502  IF (ASSOCIATED(conn_info%theta_a)) n = SIZE(conn_info%theta_a)
503  CALL reorder_structure(ex_bend_list, conn_info%theta_a, conn_info%theta_c, n)
504  DO ionfo = 1, nphi
505  ! Check if the torsion is not shared between angles or bonds
506  IF (any(ex_bond_list(conn_info%onfo_a(ionfo))%array1 == conn_info%onfo_b(ionfo)) .OR. &
507  any(ex_bend_list(conn_info%onfo_a(ionfo))%array1 == conn_info%onfo_b(ionfo))) cycle
508  nonfo = nonfo + 1
509  conn_info%onfo_a(nonfo) = conn_info%onfo_a(ionfo)
510  conn_info%onfo_b(nonfo) = conn_info%onfo_b(ionfo)
511  END DO
512  ! deallocate bends
513  DO i = 1, natom
514  DEALLOCATE (ex_bend_list(i)%array1)
515  END DO
516  DEALLOCATE (ex_bend_list)
517  ! deallocate bonds
518  DO i = 1, natom
519  DEALLOCATE (ex_bond_list(i)%array1)
520  END DO
521  DEALLOCATE (ex_bond_list)
522  ! Get unique onfo
523  ALLOCATE (ex_bond_list(natom))
524  DO i = 1, natom
525  ALLOCATE (ex_bond_list(i)%array1(0))
526  END DO
527  n = 0
528  IF (ASSOCIATED(conn_info%onfo_a)) n = nonfo
529  CALL reorder_structure(ex_bond_list, conn_info%onfo_a, conn_info%onfo_b, n)
530  nonfo = 0
531  DO i = 1, natom
532  DO ionfo = 1, SIZE(ex_bond_list(i)%array1)
533  IF (count(ex_bond_list(i)%array1 == ex_bond_list(i)%array1(ionfo)) /= 1) THEN
534  ex_bond_list(i)%array1(ionfo) = 0
535  ELSE
536  IF (ex_bond_list(i)%array1(ionfo) <= i) cycle
537  nonfo = nonfo + 1
538  conn_info%onfo_a(nonfo) = i
539  conn_info%onfo_b(nonfo) = ex_bond_list(i)%array1(ionfo)
540  END IF
541  END DO
542  END DO
543  DO i = 1, natom
544  DEALLOCATE (ex_bond_list(i)%array1)
545  END DO
546  DEALLOCATE (ex_bond_list)
547  CALL reallocate(conn_info%onfo_a, 1, nonfo)
548  CALL reallocate(conn_info%onfo_b, 1, nonfo)
549 
550  CALL timestop(handle)
551  CALL cp_print_key_finished_output(iw, logger, subsys_section, &
552  "PRINT%TOPOLOGY_INFO/PSF_INFO")
553  END SUBROUTINE psf_post_process
554 
555 ! **************************************************************************************************
556 !> \brief Input driven modification (IDM) of PSF defined structures
557 !> \param topology ...
558 !> \param section ...
559 !> \param subsys_section ...
560 !> \author Teodoro Laino - Zurich University 04.2007
561 ! **************************************************************************************************
562  SUBROUTINE idm_psf(topology, section, subsys_section)
563  TYPE(topology_parameters_type), INTENT(INOUT) :: topology
564  TYPE(section_vals_type), POINTER :: section, subsys_section
565 
566  CHARACTER(len=*), PARAMETER :: routinen = 'idm_psf'
567 
568  INTEGER :: handle, i, iend, iend1, istart, istart1, &
569  item, iw, j, mol_id, n_rep, natom, &
570  nbond, nimpr, noe, nphi, ntheta
571  INTEGER, DIMENSION(:), POINTER :: tag_mols, tmp, wrk
572  LOGICAL :: explicit
573  TYPE(array1_list_type), DIMENSION(:), POINTER :: ex_bond_list
574  TYPE(atom_info_type), POINTER :: atom_info
575  TYPE(connectivity_info_type), POINTER :: conn_info
576  TYPE(cp_logger_type), POINTER :: logger
577  TYPE(section_vals_type), POINTER :: subsection
578 
579  NULLIFY (logger)
580  logger => cp_get_default_logger()
581  iw = cp_print_key_unit_nr(logger, subsys_section, "PRINT%TOPOLOGY_INFO/PSF_INFO", &
582  extension=".subsysLog")
583  CALL timeset(routinen, handle)
584  CALL section_vals_get(section, explicit=explicit)
585  IF (explicit) THEN
586  atom_info => topology%atom_info
587  conn_info => topology%conn_info
588  natom = 0
589  IF (ASSOCIATED(atom_info%id_molname)) natom = SIZE(atom_info%id_molname)
590  nbond = 0
591  IF (ASSOCIATED(conn_info%bond_a)) nbond = SIZE(conn_info%bond_a)
592  ntheta = 0
593  IF (ASSOCIATED(conn_info%theta_a)) ntheta = SIZE(conn_info%theta_a)
594  nphi = 0
595  IF (ASSOCIATED(conn_info%phi_a)) nphi = SIZE(conn_info%phi_a)
596  nimpr = 0
597  IF (ASSOCIATED(conn_info%impr_a)) nimpr = SIZE(conn_info%impr_a)
598  ! Any new defined bond
599  subsection => section_vals_get_subs_vals(section, "BONDS")
600  CALL section_vals_get(subsection, explicit=explicit)
601  IF (explicit) THEN
602  CALL section_vals_val_get(subsection, "_DEFAULT_KEYWORD_", n_rep_val=n_rep)
603  CALL reallocate(conn_info%bond_a, 1, n_rep + nbond)
604  CALL reallocate(conn_info%bond_b, 1, n_rep + nbond)
605  DO i = 1, n_rep
606  CALL section_vals_val_get(subsection, "_DEFAULT_KEYWORD_", i_rep_val=i, i_vals=tmp)
607  conn_info%bond_a(nbond + i) = tmp(1)
608  conn_info%bond_b(nbond + i) = tmp(2)
609  END DO
610  ! And now modify the molecule name if two molecules have been bridged
611  ALLOCATE (ex_bond_list(natom))
612  ALLOCATE (tag_mols(natom))
613  ALLOCATE (wrk(natom))
614  DO j = 1, natom
615  ALLOCATE (ex_bond_list(j)%array1(0))
616  END DO
617  CALL reorder_structure(ex_bond_list, conn_info%bond_a, conn_info%bond_b, nbond + n_rep)
618  ! Loop over atoms to possiblyt change molecule name
619  tag_mols = -1
620  mol_id = 1
621  DO i = 1, natom
622  IF (tag_mols(i) /= -1) cycle
623  CALL tag_molecule(tag_mols, ex_bond_list, i, mol_id)
624  mol_id = mol_id + 1
625  END DO
626  mol_id = mol_id - 1
627  IF (iw > 0) WRITE (iw, '(T2,A,I8)') 'PSF_INFO| Number of molecules detected after merging: ', mol_id
628  ! Now simply check about the contiguousness of molecule definition
629  CALL sort(tag_mols, natom, wrk)
630  item = tag_mols(1)
631  istart = 1
632  DO i = 2, natom
633  IF (tag_mols(i) == item) cycle
634  iend = i - 1
635  noe = iend - istart + 1
636  istart1 = minval(wrk(istart:iend))
637  iend1 = maxval(wrk(istart:iend))
638  cpassert(iend1 - istart1 + 1 == noe)
639  atom_info%id_molname(istart1:iend1) = str2id(s2s("MOL"//cp_to_string(item)))
640  item = tag_mols(i)
641  istart = i
642  END DO
643  iend = i - 1
644  noe = iend - istart + 1
645  istart1 = minval(wrk(istart:iend))
646  iend1 = maxval(wrk(istart:iend))
647  cpassert(iend1 - istart1 + 1 == noe)
648  atom_info%id_molname(istart1:iend1) = str2id(s2s("MOL"//cp_to_string(item)))
649  ! Deallocate bonds
650  DO i = 1, natom
651  DEALLOCATE (ex_bond_list(i)%array1)
652  END DO
653  DEALLOCATE (ex_bond_list)
654  DEALLOCATE (tag_mols)
655  DEALLOCATE (wrk)
656  END IF
657  ! Any new defined angle
658  subsection => section_vals_get_subs_vals(section, "ANGLES")
659  CALL section_vals_get(subsection, explicit=explicit)
660  IF (explicit) THEN
661  CALL section_vals_val_get(subsection, "_DEFAULT_KEYWORD_", n_rep_val=n_rep)
662  CALL reallocate(conn_info%theta_a, 1, n_rep + ntheta)
663  CALL reallocate(conn_info%theta_b, 1, n_rep + ntheta)
664  CALL reallocate(conn_info%theta_c, 1, n_rep + ntheta)
665  DO i = 1, n_rep
666  CALL section_vals_val_get(subsection, "_DEFAULT_KEYWORD_", i_rep_val=i, i_vals=tmp)
667  conn_info%theta_a(ntheta + i) = tmp(1)
668  conn_info%theta_b(ntheta + i) = tmp(2)
669  conn_info%theta_c(ntheta + i) = tmp(3)
670  END DO
671  END IF
672  ! Any new defined torsion
673  subsection => section_vals_get_subs_vals(section, "TORSIONS")
674  CALL section_vals_get(subsection, explicit=explicit)
675  IF (explicit) THEN
676  CALL section_vals_val_get(subsection, "_DEFAULT_KEYWORD_", n_rep_val=n_rep)
677  CALL reallocate(conn_info%phi_a, 1, n_rep + nphi)
678  CALL reallocate(conn_info%phi_b, 1, n_rep + nphi)
679  CALL reallocate(conn_info%phi_c, 1, n_rep + nphi)
680  CALL reallocate(conn_info%phi_d, 1, n_rep + nphi)
681  DO i = 1, n_rep
682  CALL section_vals_val_get(subsection, "_DEFAULT_KEYWORD_", i_rep_val=i, i_vals=tmp)
683  conn_info%phi_a(nphi + i) = tmp(1)
684  conn_info%phi_b(nphi + i) = tmp(2)
685  conn_info%phi_c(nphi + i) = tmp(3)
686  conn_info%phi_d(nphi + i) = tmp(4)
687  END DO
688  END IF
689  ! Any new defined improper
690  subsection => section_vals_get_subs_vals(section, "IMPROPERS")
691  CALL section_vals_get(subsection, explicit=explicit)
692  IF (explicit) THEN
693  CALL section_vals_val_get(subsection, "_DEFAULT_KEYWORD_", n_rep_val=n_rep)
694  CALL reallocate(conn_info%impr_a, 1, n_rep + nimpr)
695  CALL reallocate(conn_info%impr_b, 1, n_rep + nimpr)
696  CALL reallocate(conn_info%impr_c, 1, n_rep + nimpr)
697  CALL reallocate(conn_info%impr_d, 1, n_rep + nimpr)
698  DO i = 1, n_rep
699  CALL section_vals_val_get(subsection, "_DEFAULT_KEYWORD_", i_rep_val=i, i_vals=tmp)
700  conn_info%impr_a(nimpr + i) = tmp(1)
701  conn_info%impr_b(nimpr + i) = tmp(2)
702  conn_info%impr_c(nimpr + i) = tmp(3)
703  conn_info%impr_d(nimpr + i) = tmp(4)
704  END DO
705  END IF
706  END IF
707  CALL timestop(handle)
708  CALL cp_print_key_finished_output(iw, logger, subsys_section, &
709  "PRINT%TOPOLOGY_INFO/PSF_INFO")
710 
711  END SUBROUTINE idm_psf
712 
713 ! **************************************************************************************************
714 !> \brief Teodoro Laino - 01.2006
715 !> Write PSF topology file in the CHARMM31 EXT standard format
716 !> \param file_unit ...
717 !> \param topology ...
718 !> \param subsys_section ...
719 !> \param force_env_section ...
720 ! **************************************************************************************************
721  SUBROUTINE write_topology_psf(file_unit, topology, subsys_section, force_env_section)
722  INTEGER, INTENT(IN) :: file_unit
723  TYPE(topology_parameters_type), INTENT(INOUT) :: topology
724  TYPE(section_vals_type), POINTER :: subsys_section, force_env_section
725 
726  CHARACTER(len=*), PARAMETER :: routinen = 'write_topology_psf'
727 
728  CHARACTER(LEN=2*default_string_length) :: psf_format
729  CHARACTER(LEN=default_string_length) :: c_int, my_tag1, my_tag2, my_tag3, record
730  CHARACTER(LEN=default_string_length), &
731  DIMENSION(:), POINTER :: charge_atm
732  INTEGER :: handle, i, iw, j, my_index, nchg
733  LOGICAL :: explicit, ldum
734  REAL(kind=dp), DIMENSION(:), POINTER :: charge_inp, charges
735  TYPE(atom_info_type), POINTER :: atom_info
736  TYPE(connectivity_info_type), POINTER :: conn_info
737  TYPE(cp_logger_type), POINTER :: logger
738  TYPE(section_vals_type), POINTER :: print_key, tmp_section
739 
740  NULLIFY (logger)
741  logger => cp_get_default_logger()
742  print_key => section_vals_get_subs_vals(subsys_section, "TOPOLOGY%DUMP_PSF")
743  iw = cp_print_key_unit_nr(logger, subsys_section, "PRINT%TOPOLOGY_INFO/PSF_INFO", &
744  extension=".subsysLog")
745  CALL timeset(routinen, handle)
746 
747  atom_info => topology%atom_info
748  conn_info => topology%conn_info
749 
750  ! Check for charges.. (need to dump them in the PSF..)
751  ALLOCATE (charges(topology%natoms))
752  charges = atom_info%atm_charge
753  ! Collect charges from Input file..
754  NULLIFY (tmp_section)
755  tmp_section => section_vals_get_subs_vals(force_env_section, "MM%FORCEFIELD%CHARGE")
756  CALL section_vals_get(tmp_section, explicit=explicit, n_repetition=nchg)
757  IF (explicit) THEN
758  ALLOCATE (charge_atm(nchg))
759  ALLOCATE (charge_inp(nchg))
760  CALL read_chrg_section(charge_atm, charge_inp, section=tmp_section, start=0)
761  DO j = 1, topology%natoms
762  record = id2str(atom_info%id_atmname(j))
763  ldum = qmmm_ff_precond_only_qm(record)
764  CALL uppercase(record)
765  DO i = 1, nchg
766  IF (record == charge_atm(i)) THEN
767  charges(j) = charge_inp(i)
768  EXIT
769  END IF
770  END DO
771  END DO
772  DEALLOCATE (charge_atm)
773  DEALLOCATE (charge_inp)
774  END IF
775  ! fixup for topology output
776  DO j = 1, topology%natoms
777  IF (charges(j) .EQ. -huge(0.0_dp)) charges(j) = -99.0_dp
778  END DO
779  record = cp_print_key_generate_filename(logger, print_key, &
780  extension=".psf", my_local=.false.)
781  ! build the EXT format
782  c_int = "I10"
783  psf_format = '(I10,T12,A,T21,I0,T30,A,T39,A,T47,A,T53,F10.6,T69,F8.3,T88,I1)'
784  IF (iw > 0) WRITE (iw, '(T2,A)') &
785  "PSF_WRITE| Writing out PSF file with CHARMM31 EXTErnal format: ", trim(record)
786 
787  WRITE (file_unit, fmt='(A)') "PSF EXT"
788  WRITE (file_unit, fmt='(A)') ""
789  WRITE (file_unit, fmt='('//trim(c_int)//',A)') 1, " !NTITLE"
790  WRITE (file_unit, fmt='(A)') " CP2K generated DUMP of connectivity"
791  WRITE (file_unit, fmt='(A)') ""
792 
793  WRITE (file_unit, fmt='('//trim(c_int)//',A)') topology%natoms, " !NATOM"
794  my_index = 1
795  i = 1
796  my_tag1 = id2str(atom_info%id_molname(i))
797  my_tag2 = id2str(atom_info%id_resname(i))
798  my_tag3 = id2str(atom_info%id_atmname(i))
799  ldum = qmmm_ff_precond_only_qm(my_tag1)
800  ldum = qmmm_ff_precond_only_qm(my_tag2)
801  ldum = qmmm_ff_precond_only_qm(my_tag3)
802  WRITE (file_unit, fmt=psf_format) &
803  i, &
804  trim(my_tag1), &
805  my_index, &
806  trim(my_tag2), &
807  trim(my_tag3), &
808  trim(my_tag3), &
809  charges(i), &
810  atom_info%atm_mass(i), &
811  0
812  DO i = 2, topology%natoms
813  IF ((atom_info%map_mol_num(i) /= atom_info%map_mol_num(i - 1)) .OR. &
814  (atom_info%map_mol_res(i) /= atom_info%map_mol_res(i - 1))) my_index = my_index + 1
815  my_tag1 = id2str(atom_info%id_molname(i))
816  my_tag2 = id2str(atom_info%id_resname(i))
817  my_tag3 = id2str(atom_info%id_atmname(i))
818  ldum = qmmm_ff_precond_only_qm(my_tag1)
819  ldum = qmmm_ff_precond_only_qm(my_tag2)
820  ldum = qmmm_ff_precond_only_qm(my_tag3)
821  WRITE (file_unit, fmt=psf_format) &
822  i, &
823  trim(my_tag1), &
824  my_index, &
825  trim(my_tag2), &
826  trim(my_tag3), &
827  trim(my_tag3), &
828  charges(i), &
829  atom_info%atm_mass(i), &
830  0
831  END DO
832  WRITE (file_unit, fmt='(/)')
833  DEALLOCATE (charges)
834 
835  WRITE (file_unit, fmt='('//trim(c_int)//',A)') SIZE(conn_info%bond_a), " !NBOND"
836  DO i = 1, SIZE(conn_info%bond_a), 4
837  j = 0
838  DO WHILE ((j < 4) .AND. ((i + j) <= SIZE(conn_info%bond_a)))
839  WRITE (file_unit, fmt='(2('//trim(c_int)//'))', advance="NO") &
840  conn_info%bond_a(i + j), conn_info%bond_b(i + j)
841  j = j + 1
842  END DO
843  WRITE (file_unit, fmt='(/)', advance="NO")
844  END DO
845  WRITE (file_unit, fmt='(/)')
846 
847  WRITE (file_unit, fmt='('//trim(c_int)//',A)') SIZE(conn_info%theta_a), " !NTHETA"
848  DO i = 1, SIZE(conn_info%theta_a), 3
849  j = 0
850  DO WHILE ((j < 3) .AND. ((i + j) <= SIZE(conn_info%theta_a)))
851  WRITE (file_unit, fmt='(3('//trim(c_int)//'))', advance="NO") &
852  conn_info%theta_a(i + j), conn_info%theta_b(i + j), &
853  conn_info%theta_c(i + j)
854  j = j + 1
855  END DO
856  WRITE (file_unit, fmt='(/)', advance="NO")
857  END DO
858  WRITE (file_unit, fmt='(/)')
859 
860  WRITE (file_unit, fmt='('//trim(c_int)//',A)') SIZE(conn_info%phi_a), " !NPHI"
861  DO i = 1, SIZE(conn_info%phi_a), 2
862  j = 0
863  DO WHILE ((j < 2) .AND. ((i + j) <= SIZE(conn_info%phi_a)))
864  WRITE (file_unit, fmt='(4('//trim(c_int)//'))', advance="NO") &
865  conn_info%phi_a(i + j), conn_info%phi_b(i + j), &
866  conn_info%phi_c(i + j), conn_info%phi_d(i + j)
867  j = j + 1
868  END DO
869  WRITE (file_unit, fmt='(/)', advance="NO")
870  END DO
871  WRITE (file_unit, fmt='(/)')
872 
873  WRITE (file_unit, fmt='('//trim(c_int)//',A)') SIZE(conn_info%impr_a), " !NIMPHI"
874  DO i = 1, SIZE(conn_info%impr_a), 2
875  j = 0
876  DO WHILE ((j < 2) .AND. ((i + j) <= SIZE(conn_info%impr_a)))
877  WRITE (file_unit, fmt='(4('//trim(c_int)//'))', advance="NO") &
878  conn_info%impr_a(i + j), conn_info%impr_b(i + j), &
879  conn_info%impr_c(i + j), conn_info%impr_d(i + j)
880  j = j + 1
881  END DO
882  WRITE (file_unit, fmt='(/)', advance="NO")
883  END DO
884  WRITE (file_unit, fmt='(/)')
885 
886  WRITE (file_unit, fmt='('//trim(c_int)//',A)') 0, " !NDON"
887  WRITE (file_unit, fmt='(/)')
888  WRITE (file_unit, fmt='('//trim(c_int)//',A)') 0, " !NACC"
889  WRITE (file_unit, fmt='(/)')
890  WRITE (file_unit, fmt='('//trim(c_int)//',A)') 0, " !NNB"
891  WRITE (file_unit, fmt='(/)')
892 
893  CALL cp_print_key_finished_output(iw, logger, subsys_section, &
894  "PRINT%TOPOLOGY_INFO/PSF_INFO")
895  CALL timestop(handle)
896 
897  END SUBROUTINE write_topology_psf
898 
899 END MODULE topology_psf
900 
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_logger_get_default_io_unit
integer function, public cp_logger_get_default_io_unit(logger)
returns the unit nr for the ionode (-1 on all other processors) skips as well checks if the procs cal...
Definition: cp_log_handling.F:515
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:803
cp_output_handling::cp_print_key_generate_filename
character(len=default_path_length) function, public cp_print_key_generate_filename(logger, print_key, middle_name, extension, my_local)
Utility function that returns a unit number to write the print key. Might open a file with a unique f...
Definition: cp_output_handling.F:704
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:1013
cp_parser_methods
Utility routines to read data from files. Kept as close as possible to the old parser because.
Definition: cp_parser_methods.F:20
cp_parser_methods::parser_get_next_line
subroutine, public parser_get_next_line(parser, nline, at_end)
Read the next input line and broadcast the input information. Skip (nline-1) lines and skip also all ...
Definition: cp_parser_methods.F:421
cp_parser_methods::parser_test_next_token
character(len=3) function, public parser_test_next_token(parser, string_length)
Test next input object.
Definition: cp_parser_methods.F:691
cp_parser_methods::parser_search_string
subroutine, public parser_search_string(parser, string, ignore_case, found, line, begin_line, search_from_begin_of_file)
Search a string pattern in a file defined by its logical unit number "unit". A case sensitive search ...
Definition: cp_parser_methods.F:786
cp_parser_types
Utility routines to read data from files. Kept as close as possible to the old parser because.
Definition: cp_parser_types.F:21
cp_parser_types::parser_release
subroutine, public parser_release(parser)
releases the parser
Definition: cp_parser_types.F:109
cp_parser_types::parser_create
subroutine, public parser_create(parser, file_name, unit_nr, para_env, end_section_label, separator_chars, comment_char, continuation_char, quote_char, section_char, parse_white_lines, initial_variables, apply_preprocessing)
Start a parser run. Initial variables allow to @SET stuff before opening the file.
Definition: cp_parser_types.F:147
force_fields_input
Definition: force_fields_input.F:20
force_fields_input::read_chrg_section
subroutine, public read_chrg_section(charge_atm, charge, section, start)
Reads the CHARGE section.
Definition: force_fields_input.F:1842
input_constants
collects all constants needed in input so that they can be used without circular dependencies
Definition: input_constants.F:17
input_constants::do_conn_psf_u
integer, parameter, public do_conn_psf_u
Definition: input_constants.F:412
input_constants::do_conn_psf
integer, parameter, public do_conn_psf
Definition: input_constants.F:412
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_get_subs_vals
recursive type(section_vals_type) function, pointer, public section_vals_get_subs_vals(section_vals, subsection_name, i_rep_section, can_return_null)
returns the values of the requested subsection
Definition: input_section_types.F:724
input_section_types::section_vals_get
subroutine, public section_vals_get(section_vals, ref_count, n_repetition, n_subs_vals_rep, section, explicit)
returns various attributes about the section_vals
Definition: input_section_types.F:697
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:1040
kinds
Defines the basic variable types.
Definition: kinds.F:23
kinds::dp
integer, parameter, public dp
Definition: kinds.F:34
kinds::default_string_length
integer, parameter, public default_string_length
Definition: kinds.F:57
memory_utilities
Utility routines for the memory handling.
Definition: memory_utilities.F:14
message_passing
Interface to the message passing library MPI.
Definition: message_passing.F:23
qmmm_ff_fist
Definition: qmmm_ff_fist.F:11
qmmm_ff_fist::qmmm_ff_precond_only_qm
logical function, public qmmm_ff_precond_only_qm(id1, id2, id3, id4, is_link)
This function handles the atom names and modifies the "_QM_" prefix, in order to find the parameters ...
Definition: qmmm_ff_fist.F:39
string_table
generates a unique id number for a string (str2id) that can be used two compare two strings....
Definition: string_table.F:22
string_table::s2s
character(len=default_string_length) function, public s2s(str)
converts a string in a string of default_string_length
Definition: string_table.F:141
string_table::str2id
integer function, public str2id(str)
returns a unique id for a given string, and stores the string for later retrieval using the id.
Definition: string_table.F:72
string_table::id2str
character(len=default_string_length) function, public id2str(id)
returns the string associated with a given id
Definition: string_table.F:115
string_utilities
Utilities for string manipulations.
Definition: string_utilities.F:16
string_utilities::uppercase
elemental subroutine, public uppercase(string)
Convert all lower case characters in a string to upper case.
Definition: string_utilities.F:3361
topology_psf
Functionality to read in PSF topologies and convert it into local data structures.
Definition: topology_psf.F:14
topology_psf::read_topology_psf
subroutine, public read_topology_psf(filename, topology, para_env, subsys_section, psf_type)
Read PSF topology file Teodoro Laino - Introduced CHARMM31 EXT PSF standard format.
Definition: topology_psf.F:80
topology_psf::idm_psf
subroutine, public idm_psf(topology, section, subsys_section)
Input driven modification (IDM) of PSF defined structures.
Definition: topology_psf.F:563
topology_psf::write_topology_psf
subroutine, public write_topology_psf(file_unit, topology, subsys_section, force_env_section)
Teodoro Laino - 01.2006 Write PSF topology file in the CHARMM31 EXT standard format.
Definition: topology_psf.F:722
topology_psf::psf_post_process
subroutine, public psf_post_process(topology, subsys_section)
Post processing of PSF informations.
Definition: topology_psf.F:417
topology_types
Definition: topology_types.F:18
topology_util
Collection of subroutine needed for topology related things.
Definition: topology_util.F:13
topology_util::tag_molecule
recursive subroutine, public tag_molecule(icheck, bond_list, i, my_mol)
gives back a mapping of molecules.. icheck needs to be initialized with -1
Definition: topology_util.F:746
topology
Control for reading in different topologies and coordinates.
Definition: topology.F:13
util
All kind of helpful little routines.
Definition: util.F:14
topology_types::atom_info_type
Definition: topology_types.F:35
topology_types::connectivity_info_type
Definition: topology_types.F:53
topology_types::topology_parameters_type
Definition: topology_types.F:142
topology_util::array1_list_type
Definition: topology_util.F:50