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topology_cif.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 Handles CIF (Crystallographic Information File) files
10!> \author Teodoro Laino [tlaino]
11!> \date 12.2008
12! **************************************************************************************************
13MODULE topology_cif
14 USE cell_methods, ONLY: cell_create,&
15 read_cell_cif,&
16 write_cell
17 USE cell_types, ONLY: cell_release,&
18 cell_type,&
19 pbc,&
20 real_to_scaled,&
21 scaled_to_real
22 USE cp_log_handling, ONLY: cp_get_default_logger,&
23 cp_logger_type,&
24 cp_to_string
25 USE cp_output_handling, ONLY: cp_print_key_finished_output,&
26 cp_print_key_unit_nr
27 USE cp_parser_methods, ONLY: parser_get_next_line,&
28 parser_get_object,&
29 parser_search_string
30 USE cp_parser_types, ONLY: cp_parser_type,&
31 parser_create,&
32 parser_release
33 USE fparser, ONLY: evalf,&
34 finalizef,&
35 initf,&
36 parsef
37 USE input_section_types, ONLY: section_get_rval,&
38 section_vals_type
39 USE kinds, ONLY: default_string_length,&
40 dp
41 USE memory_utilities, ONLY: reallocate
42 USE message_passing, ONLY: mp_para_env_type
43 USE string_table, ONLY: id2str,&
44 s2s,&
45 str2id
46 USE string_utilities, ONLY: s2a
47 USE topology_types, ONLY: atom_info_type,&
48 topology_parameters_type
49#include "./base/base_uses.f90"
50
51 IMPLICIT NONE
52
53 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'topology_cif'
54
55 PRIVATE
56 PUBLIC :: read_coordinate_cif
57
58CONTAINS
59
60! **************************************************************************************************
61!> \brief Performs the real task of reading the proper information from the CIF
62!> file
63!> \param topology ...
64!> \param para_env ...
65!> \param subsys_section ...
66!> \date 12.2008
67!> \par Format Information implemented:
68!> _chemical_name
69!> _chemical_formula_sum
70!> _cell_length_a
71!> _cell_length_b
72!> _cell_length_c
73!> _cell_angle_alpha
74!> _cell_angle_beta
75!> _cell_angle_gamma
76!> _symmetry_space_group_name_h-m
77!> _symmetry_equiv_pos_as_xyz
78!> _space_group_symop_operation_xyz
79!> _atom_site_label
80!> _atom_site_type_symbol
81!> _atom_site_fract_x
82!> _atom_site_fract_y
83!> _atom_site_fract_z
84!>
85!> \author Teodoro Laino [tlaino]
86! **************************************************************************************************
87 SUBROUTINE read_coordinate_cif(topology, para_env, subsys_section)
88 TYPE(topology_parameters_type) :: topology
89 TYPE(mp_para_env_type), POINTER :: para_env
90 TYPE(section_vals_type), POINTER :: subsys_section
91
92 CHARACTER(len=*), PARAMETER :: routinen = 'read_coordinate_cif'
93 INTEGER, PARAMETER :: nblock = 1000
94 REAL(kind=dp), PARAMETER :: threshold = 1.0e-3_dp
95
96 CHARACTER(LEN=1) :: sep
97 CHARACTER(LEN=default_string_length) :: s_tag, strtmp
98 INTEGER :: field_kind, field_label, field_symbol, field_x, field_y, field_z, handle, ii, &
99 iln0, iln1, iln2, iln3, isym, iw, jj, natom, natom_orig, newsize, num_fields
100 LOGICAL :: check, found, my_end
101 REAL(kind=dp) :: pfactor
102 REAL(kind=dp), DIMENSION(3) :: r, r1, r2, s, s_tmp
103 TYPE(atom_info_type), POINTER :: atom_info
104 TYPE(cell_type), POINTER :: cell
105 TYPE(cp_logger_type), POINTER :: logger
106 TYPE(cp_parser_type) :: parser
107
108 NULLIFY (logger)
109 logger => cp_get_default_logger()
110 iw = cp_print_key_unit_nr(logger, subsys_section, "PRINT%TOPOLOGY_INFO/CIF_INFO", &
111 extension=".subsysLog")
112 CALL timeset(routinen, handle)
113 pfactor = section_get_rval(subsys_section, "TOPOLOGY%MEMORY_PROGRESSION_FACTOR")
114
115 ! Element is assigned on the basis of the atm_name
116 topology%aa_element = .true.
117
118 atom_info => topology%atom_info
119 CALL reallocate(atom_info%id_molname, 1, nblock)
120 CALL reallocate(atom_info%id_resname, 1, nblock)
121 CALL reallocate(atom_info%resid, 1, nblock)
122 CALL reallocate(atom_info%id_atmname, 1, nblock)
123 CALL reallocate(atom_info%r, 1, 3, 1, nblock)
124 CALL reallocate(atom_info%atm_mass, 1, nblock)
125 CALL reallocate(atom_info%atm_charge, 1, nblock)
126 CALL reallocate(atom_info%occup, 1, nblock)
127 CALL reallocate(atom_info%beta, 1, nblock)
128 CALL reallocate(atom_info%id_element, 1, nblock)
129
130 IF (iw > 0) WRITE (iw, "(/,A,A)") " Reading in CIF file ", trim(topology%coord_file_name)
131
132 ! Create cell
133 NULLIFY (cell)
134 CALL cell_create(cell, tag="CELL_CIF")
135 CALL read_cell_cif(topology%coord_file_name, cell, para_env)
136 CALL write_cell(cell, subsys_section)
137
138 CALL parser_create(parser, topology%coord_file_name, &
139 para_env=para_env, apply_preprocessing=.false.)
140
141 ! Check for _chemical_name
142 CALL parser_search_string(parser, "_chemical_name", ignore_case=.false., found=found, &
143 begin_line=.false., search_from_begin_of_file=.true.)
144 IF (found) THEN
145 IF (iw > 0) WRITE (iw, '(/,A)') " CIF_INFO| _chemical_name :: "//trim(parser%input_line(parser%icol:))
146 END IF
147
148 ! Check for _chemical_formula_sum
149 CALL parser_search_string(parser, "_chemical_formula_sum", ignore_case=.false., found=found, &
150 begin_line=.false., search_from_begin_of_file=.true.)
151 IF (found) THEN
152 IF (iw > 0) WRITE (iw, '(A)') " CIF_INFO| _chemical_formula_sum :: "//trim(parser%input_line(parser%icol:))
153 END IF
154
155 ! Parse atoms info and fractional coordinates
156 num_fields = 0
157 field_label = -1; field_symbol = -1; field_x = -1; field_y = -1; field_z = -1
158 CALL parser_search_string(parser, "_atom_site_", ignore_case=.false., found=found, &
159 begin_line=.false., search_from_begin_of_file=.true.)
160 DO WHILE (index(parser%input_line, "_atom_site_") /= 0)
161 num_fields = num_fields + 1
162 IF (index(parser%input_line, "_atom_site_label") /= 0) field_label = num_fields
163 IF (index(parser%input_line, "_atom_site_type_symbol") /= 0) field_symbol = num_fields
164 IF (index(parser%input_line, "_atom_site_fract_x") /= 0) field_x = num_fields
165 IF (index(parser%input_line, "_atom_site_fract_y") /= 0) field_y = num_fields
166 IF (index(parser%input_line, "_atom_site_fract_z") /= 0) field_z = num_fields
167 CALL parser_get_next_line(parser, 1)
168 END DO
169
170 ! Check for missing fields.
171 IF (field_label < 0) cpabort("Field _atom_site_label not found in CIF file.")
172 IF (field_x < 0) cpabort("Field _atom_site_fract_x not found in CIF file.")
173 IF (field_y < 0) cpabort("Field _atom_site_fract_y not found in CIF file.")
174 IF (field_z < 0) cpabort("Field _atom_site_fract_z not found in CIF file.")
175
176 ! Read atom kind from the symbol field if it's present, otherwise fall back to the label field.
177 IF (field_symbol > 0) THEN
178 field_kind = field_symbol
179 ELSE
180 field_kind = field_label
181 END IF
182
183 ! Parse real info
184 natom = 0
185 DO WHILE ((index(parser%input_line, "loop_") == 0) .AND. (parser%input_line(1:1) /= "_"))
186 natom = natom + 1
187 ! Resize in case needed
188 IF (natom > SIZE(atom_info%id_molname)) THEN
189 newsize = int(pfactor*natom)
190 CALL reallocate(atom_info%id_molname, 1, newsize)
191 CALL reallocate(atom_info%id_resname, 1, newsize)
192 CALL reallocate(atom_info%resid, 1, newsize)
193 CALL reallocate(atom_info%id_atmname, 1, newsize)
194 CALL reallocate(atom_info%r, 1, 3, 1, newsize)
195 CALL reallocate(atom_info%atm_mass, 1, newsize)
196 CALL reallocate(atom_info%atm_charge, 1, newsize)
197 CALL reallocate(atom_info%occup, 1, newsize)
198 CALL reallocate(atom_info%beta, 1, newsize)
199 CALL reallocate(atom_info%id_element, 1, newsize)
200 END IF
201 DO ii = 1, num_fields
202 IF (ii == field_kind) THEN
203 CALL parser_get_object(parser, strtmp)
204 atom_info%id_atmname(natom) = str2id(strtmp)
205 atom_info%id_molname(natom) = str2id(s2s("MOL"//trim(adjustl(cp_to_string(natom)))))
206 atom_info%id_resname(natom) = atom_info%id_molname(natom)
207 atom_info%resid(natom) = 1
208 atom_info%id_element(natom) = atom_info%id_atmname(natom)
209 ELSE IF (ii == field_x) THEN
210 CALL cif_get_real(parser, atom_info%r(1, natom))
211 ELSE IF (ii == field_y) THEN
212 CALL cif_get_real(parser, atom_info%r(2, natom))
213 ELSE IF (ii == field_z) THEN
214 CALL cif_get_real(parser, atom_info%r(3, natom))
215 ELSE
216 CALL parser_get_object(parser, s_tag) ! Skip this field
217 END IF
218 END DO
219 s = atom_info%r(1:3, natom)
220 CALL scaled_to_real(atom_info%r(1:3, natom), s, cell)
221 CALL parser_get_next_line(parser, 1, at_end=my_end)
222 IF (my_end) EXIT
223 END DO
224 ! Preliminary check: check if atoms provided are really unique.. this is a paranoic
225 ! check since they should be REALLY unique.. anyway..
226 DO ii = 1, natom
227 r1 = atom_info%r(1:3, ii)
228 DO jj = ii + 1, natom
229 r2 = atom_info%r(1:3, jj)
230 r = pbc(r1 - r2, cell)
231 ! check = (SQRT(DOT_PRODUCT(r, r)) >= threshold)
232 check = (dot_product(r, r) >= (threshold*threshold))
233 cpassert(check)
234 END DO
235 END DO
236 ! Parse Symmetry Group and generation elements..
237 ! Check for _symmetry_space_group_name_h-m
238 CALL parser_search_string(parser, "_symmetry_space_group_name_h-m", ignore_case=.false., found=found, &
239 begin_line=.false., search_from_begin_of_file=.true.)
240 IF (found) THEN
241 IF (iw > 0) WRITE (iw, '(A)') " CIF_INFO| _symmetry_space_group_name_h-m :: "//trim(parser%input_line(parser%icol:))
242 END IF
243
244 ! Check for _symmetry_equiv_pos_as_xyz
245 ! Check for _space_group_symop_operation_xyz
246 CALL parser_search_string(parser, "_symmetry_equiv_pos_as_xyz", ignore_case=.false., found=found, &
247 begin_line=.false., search_from_begin_of_file=.true.)
248 IF (.NOT. found) THEN
249 CALL parser_search_string(parser, "_space_group_symop_operation_xyz", ignore_case=.false., found=found, &
250 begin_line=.false., search_from_begin_of_file=.true.)
251 END IF
252 IF (.NOT. found) &
253 CALL cp_warn(__location__, "The fields (_symmetry_equiv_pos_as_xyz) or "// &
254 "(_space_group_symop_operation_xyz) were not found in CIF file!")
255 IF (iw > 0) WRITE (iw, '(A,I0)') " CIF_INFO| Number of atoms before applying symmetry operations :: ", natom
256 IF (iw > 0) WRITE (iw, '(A10,1X,3F12.6)') (trim(id2str(atom_info%id_atmname(ii))), atom_info%r(1:3, ii), ii=1, natom)
257 isym = 0
258 IF (found) THEN
259 ! Apply symmetry elements and generate the whole set of atoms in the unit cell
260 CALL parser_get_next_line(parser, 1)
261 isym = 0
262 natom_orig = natom
263 DO WHILE ((index(parser%input_line, "loop_") == 0) .AND. (parser%input_line(1:1) /= "_"))
264 isym = isym + 1
265 ! find seprator ' or "
266 sep = "'"
267 IF (index(parser%input_line(1:), '"') > 0) sep = '"'
268 iln0 = index(parser%input_line(1:), sep)
269 iln1 = index(parser%input_line(iln0 + 1:), ",") + iln0
270 iln2 = index(parser%input_line(iln1 + 1:), ",") + iln1
271 IF (iln0 == 0) THEN
272 iln3 = len_trim(parser%input_line) + 1
273 ELSE
274 iln3 = index(parser%input_line(iln2 + 1:), sep) + iln2
275 END IF
276 cpassert(iln1 /= 0)
277 cpassert(iln2 /= iln1)
278 cpassert(iln3 /= iln2)
279 CALL initf(3)
280 CALL parsef(1, trim(parser%input_line(iln0 + 1:iln1 - 1)), s2a("x", "y", "z"))
281 CALL parsef(2, trim(parser%input_line(iln1 + 1:iln2 - 1)), s2a("x", "y", "z"))
282 CALL parsef(3, trim(parser%input_line(iln2 + 1:iln3 - 1)), s2a("x", "y", "z"))
283 loop_over_unique_atoms: DO ii = 1, natom_orig
284 CALL real_to_scaled(s_tmp, atom_info%r(1:3, ii), cell)
285 s(1) = evalf(1, (/s_tmp(1), s_tmp(2), s_tmp(3)/))
286 s(2) = evalf(2, (/s_tmp(1), s_tmp(2), s_tmp(3)/))
287 s(3) = evalf(3, (/s_tmp(1), s_tmp(2), s_tmp(3)/))
288 CALL scaled_to_real(r1, s, cell)
289 check = .true.
290 DO jj = 1, natom
291 r2 = atom_info%r(1:3, jj)
292 r = pbc(r1 - r2, cell)
293 ! SQRT(DOT_PRODUCT(r, r)) <= threshold
294 IF (dot_product(r, r) <= (threshold*threshold)) THEN
295 check = .false.
296 EXIT
297 END IF
298 END DO
299 ! If the atom generated is unique let's add to the atom set..
300 IF (check) THEN
301 natom = natom + 1
302 ! Resize in case needed
303 IF (natom > SIZE(atom_info%id_molname)) THEN
304 newsize = int(pfactor*natom)
305 CALL reallocate(atom_info%id_molname, 1, newsize)
306 CALL reallocate(atom_info%id_resname, 1, newsize)
307 CALL reallocate(atom_info%resid, 1, newsize)
308 CALL reallocate(atom_info%id_atmname, 1, newsize)
309 CALL reallocate(atom_info%r, 1, 3, 1, newsize)
310 CALL reallocate(atom_info%atm_mass, 1, newsize)
311 CALL reallocate(atom_info%atm_charge, 1, newsize)
312 CALL reallocate(atom_info%occup, 1, newsize)
313 CALL reallocate(atom_info%beta, 1, newsize)
314 CALL reallocate(atom_info%id_element, 1, newsize)
315 END IF
316 atom_info%id_atmname(natom) = atom_info%id_atmname(ii)
317 atom_info%id_molname(natom) = atom_info%id_molname(ii)
318 atom_info%id_resname(natom) = atom_info%id_resname(ii)
319 atom_info%id_element(natom) = atom_info%id_element(ii)
320 atom_info%resid(natom) = atom_info%resid(ii)
321 atom_info%r(1:3, natom) = r1
322 END IF
323 END DO loop_over_unique_atoms
324 CALL finalizef()
325 CALL parser_get_next_line(parser, 1, at_end=my_end)
326 IF (my_end) EXIT
327 END DO
328 END IF
329 IF (iw > 0) WRITE (iw, '(A,I0)') " CIF_INFO| Number of symmetry operations :: ", isym
330 IF (iw > 0) WRITE (iw, '(A,I0)') " CIF_INFO| Number of total atoms :: ", natom
331 IF (iw > 0) WRITE (iw, '(A10,1X,3F12.6)') (trim(id2str(atom_info%id_atmname(ii))), atom_info%r(1:3, ii), ii=1, natom)
332
333 ! Releasse local cell type and parser
334 CALL cell_release(cell)
335 CALL parser_release(parser)
336
337 ! Reallocate all structures with the exact NATOM size
338 CALL reallocate(atom_info%id_molname, 1, natom)
339 CALL reallocate(atom_info%id_resname, 1, natom)
340 CALL reallocate(atom_info%resid, 1, natom)
341 CALL reallocate(atom_info%id_atmname, 1, natom)
342 CALL reallocate(atom_info%r, 1, 3, 1, natom)
343 CALL reallocate(atom_info%atm_mass, 1, natom)
344 CALL reallocate(atom_info%atm_charge, 1, natom)
345 CALL reallocate(atom_info%occup, 1, natom)
346 CALL reallocate(atom_info%beta, 1, natom)
347 CALL reallocate(atom_info%id_element, 1, natom)
348
349 topology%natoms = natom
350 topology%molname_generated = .true.
351 CALL cp_print_key_finished_output(iw, logger, subsys_section, &
352 "PRINT%TOPOLOGY_INFO/CIF_INFO")
353 CALL timestop(handle)
354 END SUBROUTINE read_coordinate_cif
355
356! **************************************************************************************************
357!> \brief Reads REAL from the CIF file.. This wrapper is needed in order to
358!> treat properly the accuracy specified in the CIF file, i.e. 3.45(6)
359!> \param parser ...
360!> \param r ...
361!> \date 12.2008
362!> \author Teodoro Laino [tlaino]
363! **************************************************************************************************
364 SUBROUTINE cif_get_real(parser, r)
365 TYPE(cp_parser_type), INTENT(INOUT) :: parser
366 REAL(kind=dp), INTENT(OUT) :: r
367
368 CHARACTER(LEN=default_string_length) :: s_tag
369 INTEGER :: iln
370
371 CALL parser_get_object(parser, s_tag)
372 iln = len_trim(s_tag)
373 IF (index(s_tag, "(") /= 0) iln = index(s_tag, "(") - 1
374 READ (s_tag(1:iln), *) r
375 END SUBROUTINE cif_get_real
376
377END MODULE topology_cif
cell_types::pbc
Definition cell_types.F:92
cp_log_handling::cp_to_string
Definition cp_log_handling.F:90
cp_parser_methods::parser_get_object
Definition cp_parser_methods.F:54
memory_utilities::reallocate
Definition memory_utilities.F:27
string_utilities::s2a
Definition string_utilities.F:48
cell_methods
Handles all functions related to the CELL.
Definition cell_methods.F:15
cell_methods::write_cell
subroutine, public write_cell(cell, subsys_section, tag)
Write the cell parameters to the output unit.
Definition cell_methods.F:731
cell_methods::read_cell_cif
subroutine, public read_cell_cif(cif_file_name, cell, para_env)
Reads cell information from CIF file.
Definition cell_methods.F:618
cell_methods::cell_create
subroutine, public cell_create(cell, hmat, periodic, tag)
allocates and initializes a cell
Definition cell_methods.F:85
cell_types
Handles all functions related to the CELL.
Definition cell_types.F:15
cell_types::scaled_to_real
subroutine, public scaled_to_real(r, s, cell)
Transform scaled cell coordinates real coordinates. r=h*s.
Definition cell_types.F:516
cell_types::real_to_scaled
subroutine, public real_to_scaled(s, r, cell)
Transform real to scaled cell coordinates. s=h_inv*r.
Definition cell_types.F:486
cell_types::cell_release
subroutine, public cell_release(cell)
releases the given cell (see doc/ReferenceCounting.html)
Definition cell_types.F:559
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:803
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_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
fparser
This public domain function parser module is intended for applications where a set of mathematical ex...
Definition fparser.F:17
fparser::parsef
subroutine, public parsef(i, funcstr, var)
Parse ith function string FuncStr and compile it into bytecode.
Definition fparser.F:148
fparser::evalf
real(rn) function, public evalf(i, val)
...
Definition fparser.F:180
fparser::finalizef
subroutine, public finalizef()
...
Definition fparser.F:101
fparser::initf
subroutine, public initf(n)
...
Definition fparser.F:130
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_get_rval
real(kind=dp) function, public section_get_rval(section_vals, keyword_name)
...
Definition input_section_types.F:941
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
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
topology_cif
Handles CIF (Crystallographic Information File) files.
Definition topology_cif.F:13
topology_cif::read_coordinate_cif
subroutine, public read_coordinate_cif(topology, para_env, subsys_section)
Performs the real task of reading the proper information from the CIF file.
Definition topology_cif.F:88
topology_types
Definition topology_types.F:18
topology
Control for reading in different topologies and coordinates.
Definition topology.F:13
cell_types::cell_type
Type defining parameters related to the simulation cell.
Definition cell_types.F:55
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
cp_parser_types::cp_parser_type
represent a parser
Definition cp_parser_types.F:77
input_section_types::section_vals_type
stores the values of a section
Definition input_section_types.F:126
message_passing::mp_para_env_type
stores all the informations relevant to an mpi environment
Definition message_passing.F:763
topology_types::atom_info_type
Definition topology_types.F:35
topology_types::topology_parameters_type
Definition topology_types.F:142