Line data Source code
1 : !--------------------------------------------------------------------------------------------------!
2 : ! CP2K: A general program to perform molecular dynamics simulations !
3 : ! Copyright 2000-2026 CP2K developers group <https://cp2k.org> !
4 : ! !
5 : ! SPDX-License-Identifier: GPL-2.0-or-later !
6 : !--------------------------------------------------------------------------------------------------!
7 :
8 : ! **************************************************************************************************
9 : !> \par History
10 : !> - taken out of input_cp2k_motion
11 : !> \author Ole Schuett
12 : ! **************************************************************************************************
13 : MODULE input_cp2k_motion_print
14 : USE cp_output_handling, ONLY: add_last_numeric,&
15 : cp_print_key_section_create,&
16 : high_print_level,&
17 : low_print_level,&
18 : silent_print_level
19 : USE input_constants, ONLY: dump_atomic,&
20 : dump_dcd,&
21 : dump_dcd_aligned_cell,&
22 : dump_extxyz,&
23 : dump_pdb,&
24 : dump_xmol
25 : USE input_cp2k_subsys, ONLY: create_structure_data_section
26 : USE input_keyword_types, ONLY: keyword_create,&
27 : keyword_release,&
28 : keyword_type
29 : USE input_section_types, ONLY: section_add_keyword,&
30 : section_add_subsection,&
31 : section_create,&
32 : section_release,&
33 : section_type
34 : USE string_utilities, ONLY: s2a
35 : #include "./base/base_uses.f90"
36 :
37 : IMPLICIT NONE
38 : PRIVATE
39 :
40 : LOGICAL, PRIVATE, PARAMETER :: debug_this_module = .TRUE.
41 : CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'input_cp2k_motion_print'
42 :
43 : PUBLIC :: create_motion_print_section, add_format_keyword
44 :
45 : CONTAINS
46 :
47 : ! **************************************************************************************************
48 : !> \brief creates the motion%print section
49 : !> \param section the section to be created
50 : !> \author teo
51 : ! **************************************************************************************************
52 10262 : SUBROUTINE create_motion_print_section(section)
53 : TYPE(section_type), POINTER :: section
54 :
55 : TYPE(keyword_type), POINTER :: keyword
56 : TYPE(section_type), POINTER :: print_key
57 :
58 10262 : NULLIFY (keyword, section, print_key)
59 :
60 : CALL section_create(section, __LOCATION__, name="print", &
61 : description="Controls the printing properties during an MD/Optimization run", &
62 10262 : n_keywords=1, n_subsections=1, repeats=.TRUE.)
63 :
64 : CALL keyword_create(keyword, __LOCATION__, name="MEMORY_INFO", &
65 : variants=["MEMORY"], &
66 : description="Whether overall memory usage should be sampled and printed "// &
67 : "at each MD/Optimization step.", &
68 : usage="MEMORY_INFO LOGICAL", &
69 20524 : default_l_val=.TRUE., lone_keyword_l_val=.TRUE.)
70 10262 : CALL section_add_keyword(section, keyword)
71 10262 : CALL keyword_release(keyword)
72 :
73 : CALL cp_print_key_section_create(print_key, __LOCATION__, "TRAJECTORY", &
74 : description="Controls the output of the trajectory", &
75 : print_level=low_print_level, common_iter_levels=1, &
76 10262 : filename="", unit_str="angstrom")
77 : CALL add_format_keyword(keyword, print_key, pos=.TRUE., &
78 10262 : description="Specifies the format of the output file for the trajectory.")
79 10262 : CALL section_add_subsection(section, print_key)
80 10262 : CALL section_release(print_key)
81 :
82 : CALL cp_print_key_section_create( &
83 : print_key, __LOCATION__, "SHELL_TRAJECTORY", &
84 : description="Controls the output of the trajectory of shells when the shell-model is used ", &
85 : print_level=high_print_level, common_iter_levels=1, &
86 10262 : filename="", unit_str="angstrom")
87 : CALL add_format_keyword(keyword, print_key, pos=.TRUE., &
88 10262 : description="Specifies the format of the output file for the trajectory of shells.")
89 10262 : CALL section_add_subsection(section, print_key)
90 10262 : CALL section_release(print_key)
91 :
92 : CALL cp_print_key_section_create(print_key, __LOCATION__, "CORE_TRAJECTORY", &
93 : description="Controls the output of the trajectory of cores when the shell-model is used ", &
94 : print_level=high_print_level, common_iter_levels=1, &
95 10262 : filename="", unit_str="angstrom")
96 : CALL add_format_keyword(keyword, print_key, pos=.TRUE., &
97 10262 : description="Specifies the format of the output file for the trajectory of cores.")
98 10262 : CALL section_add_subsection(section, print_key)
99 10262 : CALL section_release(print_key)
100 :
101 : CALL cp_print_key_section_create(print_key, __LOCATION__, "CELL", &
102 : description="Controls the output of the simulation cell. "// &
103 : "For later analysis of the trajectory it is recommendable that the "// &
104 : "frequency of printing is the same as the one used for the trajectory file.", &
105 : print_level=high_print_level, common_iter_levels=1, &
106 10262 : filename="")
107 10262 : CALL section_add_subsection(section, print_key)
108 10262 : CALL section_release(print_key)
109 :
110 : CALL cp_print_key_section_create(print_key, __LOCATION__, "VELOCITIES", &
111 : description="Controls the output of the atomic velocities. "// &
112 : "The default unit for the atomic velocities $v$ is bohr/au_time. "// &
113 : "The kinetic energy $K_i$ in [hartree] of an atom $i$ with mass $m_i$ in "// &
114 : "atomic mass units [amu] (or just [u]) and velocity $v_i$ can be obtained by "// &
115 : "$K_i = \frac{1}{2}f_u\,m_i\,v_i^2$ with $f_u = 1822.888$ as conversion factor "// &
116 : "from [u] to [a.u.]. $f_u$ is printed in full precision in the top of the CP2K "// &
117 : "output for print level MEDIUM or higher.", &
118 : print_level=high_print_level, common_iter_levels=1, &
119 10262 : filename="", unit_str="bohr*au_t^-1")
120 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
121 10262 : description="Specifies the format of the output file for the velocities.")
122 10262 : CALL section_add_subsection(section, print_key)
123 10262 : CALL section_release(print_key)
124 :
125 : CALL cp_print_key_section_create(print_key, __LOCATION__, "SHELL_VELOCITIES", &
126 : description="Controls the output of the velocities of shells when the shell model is used", &
127 : print_level=high_print_level, common_iter_levels=1, &
128 10262 : filename="", unit_str="bohr*au_t^-1")
129 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
130 10262 : description="Specifies the format of the output file for the velocities of shells.")
131 10262 : CALL section_add_subsection(section, print_key)
132 10262 : CALL section_release(print_key)
133 :
134 : CALL cp_print_key_section_create(print_key, __LOCATION__, "CORE_VELOCITIES", &
135 : description="controls the output of the velocities of cores when the shell model is used", &
136 : print_level=high_print_level, common_iter_levels=1, &
137 10262 : filename="", unit_str="bohr*au_t^-1")
138 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
139 10262 : description="Specifies the format of the output file for the velocities of cores.")
140 10262 : CALL section_add_subsection(section, print_key)
141 10262 : CALL section_release(print_key)
142 :
143 10262 : CALL create_structure_data_section(print_key)
144 10262 : CALL section_add_subsection(section, print_key)
145 10262 : CALL section_release(print_key)
146 :
147 : CALL cp_print_key_section_create(print_key, __LOCATION__, "FINAL_STRUCTURE", &
148 : description="Controls the dumping of the final "// &
149 : "geometry and cell for optimization tasks. ", &
150 10262 : print_level=low_print_level, filename="FINAL")
151 :
152 : CALL keyword_create(keyword, __LOCATION__, name="PRINT_CIF", &
153 : description="Print the final structure as CIF. Currently the "// &
154 : "structure will always be dumped with the space "// &
155 : "group `P 1` and a single symmetry-equivalent "// &
156 : "position `x, y, z` for all of the atoms.", &
157 : usage="PRINT_CIF T", default_l_val=.TRUE., &
158 10262 : lone_keyword_l_val=.TRUE.)
159 10262 : CALL section_add_keyword(print_key, keyword)
160 10262 : CALL keyword_release(keyword)
161 :
162 : CALL keyword_create(keyword, __LOCATION__, name="PRINT_XYZ", &
163 : description="Print the final structure as XYZ. The cell "// &
164 : "information is available in the comment line according "// &
165 : "to the extended XYZ specification as the `Lattice=...` "// &
166 : "field, and the unit is angstrom for both the cell vectors "// &
167 : "and the atomic coordinates.", &
168 : usage="PRINT_XYZ T", default_l_val=.TRUE., &
169 10262 : lone_keyword_l_val=.TRUE.)
170 10262 : CALL section_add_keyword(print_key, keyword)
171 10262 : CALL keyword_release(keyword)
172 :
173 10262 : CALL section_add_subsection(section, print_key)
174 10262 : CALL section_release(print_key)
175 :
176 : CALL cp_print_key_section_create( &
177 : print_key, __LOCATION__, "FORCE_MIXING_LABELS", &
178 : description="Controls the output of the force mixing (FORCE_EVAL&QMMM&FORCE_MIXING) labels", &
179 : print_level=high_print_level, common_iter_levels=1, &
180 10262 : filename="")
181 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
182 10262 : description="Specifies the format of the output file for the force mixing labels.")
183 10262 : CALL section_add_subsection(section, print_key)
184 10262 : CALL section_release(print_key)
185 :
186 : CALL cp_print_key_section_create(print_key, __LOCATION__, "FORCES", &
187 : description="Controls the output of the forces", &
188 : print_level=high_print_level, common_iter_levels=1, &
189 10262 : filename="", unit_str="hartree*bohr^-1")
190 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
191 10262 : description="Specifies the format of the output file for the forces.")
192 10262 : CALL section_add_subsection(section, print_key)
193 10262 : CALL section_release(print_key)
194 :
195 : CALL cp_print_key_section_create(print_key, __LOCATION__, "SHELL_FORCES", &
196 : description="Controls the output of the forces on shells when shell-model is used", &
197 : print_level=high_print_level, common_iter_levels=1, &
198 10262 : filename="", unit_str="hartree*bohr^-1")
199 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
200 10262 : description="Specifies the format of the output file for the forces on shells.")
201 10262 : CALL section_add_subsection(section, print_key)
202 10262 : CALL section_release(print_key)
203 :
204 : CALL cp_print_key_section_create(print_key, __LOCATION__, "CORE_FORCES", &
205 : description="Controls the output of the forces on cores when shell-model is used", &
206 : print_level=high_print_level, common_iter_levels=1, &
207 10262 : filename="", unit_str="hartree*bohr^-1")
208 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
209 10262 : description="Specifies the format of the output file for the forces on cores.")
210 10262 : CALL section_add_subsection(section, print_key)
211 10262 : CALL section_release(print_key)
212 :
213 : CALL cp_print_key_section_create(print_key, __LOCATION__, "MIXED_ENERGIES", &
214 : description="Controls the output of the energies of the two "// &
215 : "regular FORCE_EVALS in the MIXED method "// &
216 : "printed is step,time,Etot,E_F1,E_F2,CONS_QNT", &
217 : print_level=low_print_level, common_iter_levels=1, &
218 10262 : filename="")
219 10262 : CALL section_add_subsection(section, print_key)
220 10262 : CALL section_release(print_key)
221 :
222 : CALL cp_print_key_section_create(print_key, __LOCATION__, "STRESS", &
223 : description="Controls the output of the stress tensor", &
224 : print_level=high_print_level, common_iter_levels=1, &
225 10262 : filename="")
226 10262 : CALL section_add_subsection(section, print_key)
227 10262 : CALL section_release(print_key)
228 :
229 : CALL cp_print_key_section_create(print_key, __LOCATION__, "POLAR_MATRIX", &
230 : description="Controls the output of the polarisability tensor during an MD run", &
231 : print_level=low_print_level, common_iter_levels=1, &
232 10262 : filename="")
233 10262 : CALL section_add_subsection(section, print_key)
234 10262 : CALL section_release(print_key)
235 :
236 : CALL cp_print_key_section_create(print_key, __LOCATION__, "RESTART", &
237 : description="Controls the dumping of the restart file during runs. "// &
238 : "By default keeps a short history of three restarts. See also RESTART_HISTORY", &
239 : each_iter_names=s2a("MD"), each_iter_values=[20], &
240 : print_level=silent_print_level, common_iter_levels=1, &
241 10262 : add_last=add_last_numeric, filename="")
242 :
243 : CALL keyword_create(keyword, __LOCATION__, name="BACKUP_COPIES", &
244 : description="Specifies the maximum number of backup copies.", &
245 : usage="BACKUP_COPIES {int}", &
246 10262 : default_i_val=1)
247 10262 : CALL section_add_keyword(print_key, keyword)
248 10262 : CALL keyword_release(keyword)
249 :
250 : CALL keyword_create(keyword, __LOCATION__, name="SPLIT_RESTART_FILE", &
251 : description="If specified selected input sections, which are growing with the "// &
252 : "number of atoms in the system, are written to another restart file "// &
253 : "in binary format instead of the default restart file in human "// &
254 : "readable ASCII format. This split of the restart file may "// &
255 : "provide significant memory savings and an accelerated I/O for "// &
256 : "systems with a very large number of atoms", &
257 : usage="SPLIT_RESTART_FILE yes", &
258 : default_l_val=.FALSE., &
259 10262 : lone_keyword_l_val=.TRUE.)
260 10262 : CALL section_add_keyword(print_key, keyword)
261 10262 : CALL keyword_release(keyword)
262 :
263 10262 : CALL section_add_subsection(section, print_key)
264 10262 : CALL section_release(print_key)
265 :
266 : CALL cp_print_key_section_create(print_key, __LOCATION__, "RESTART_HISTORY", &
267 : description="Dumps unique restart files during the run keeping all of them. "// &
268 : "Most useful if recovery is needed at a later point.", &
269 : print_level=low_print_level, common_iter_levels=0, &
270 : each_iter_names=s2a("MD", "GEO_OPT", "ROT_OPT"), each_iter_values=[500, 500, 500], &
271 10262 : filename="")
272 10262 : CALL section_add_subsection(section, print_key)
273 10262 : CALL section_release(print_key)
274 :
275 : CALL cp_print_key_section_create(print_key, __LOCATION__, "TRANSLATION_VECTOR", &
276 : description="Dumps the translation vector applied along an MD (if any). Useful"// &
277 : " for postprocessing of QMMM trajectories in which the QM fragment is continuously"// &
278 : " centered in the QM box", &
279 : print_level=high_print_level, common_iter_levels=1, &
280 10262 : filename="")
281 10262 : CALL section_add_subsection(section, print_key)
282 10262 : CALL section_release(print_key)
283 :
284 10262 : END SUBROUTINE create_motion_print_section
285 :
286 : ! **************************************************************************************************
287 : !> \brief creates the FORMAT keyword
288 : !> \param keyword ...
289 : !> \param section will contain the pint section
290 : !> \param pos ...
291 : !> \param description ...
292 : !> \author Teodoro Laino 10.2008 [tlaino]
293 : ! **************************************************************************************************
294 174584 : SUBROUTINE add_format_keyword(keyword, section, pos, description)
295 : TYPE(keyword_type), POINTER :: keyword
296 : TYPE(section_type), POINTER :: section
297 : LOGICAL, INTENT(IN) :: pos
298 : CHARACTER(LEN=*), INTENT(IN) :: description
299 :
300 174584 : CPASSERT(ASSOCIATED(section))
301 174584 : CPASSERT(.NOT. ASSOCIATED(keyword))
302 :
303 174584 : IF (pos) THEN
304 :
305 : CALL keyword_create( &
306 : keyword, __LOCATION__, name="FORMAT", &
307 : description=description, usage="FORMAT (ATOMIC|DCD|PDB|XMOL|XYZ|EXTXYZ)", &
308 : default_i_val=dump_xmol, &
309 : enum_c_vals=s2a("ATOMIC", "DCD", "DCD_ALIGNED_CELL", "PDB", "XMOL", "XYZ", "EXTXYZ"), &
310 : enum_i_vals=[dump_atomic, dump_dcd, dump_dcd_aligned_cell, dump_pdb, dump_xmol, dump_xmol, dump_extxyz], &
311 : enum_desc=s2a("Write only the coordinates X,Y,Z without element symbols to a formatted file", &
312 : "Write the coordinates (no element labels) and the cell information to a binary file", &
313 : "Like DCD, but the dumped coordinates refer to an aligned cell following the common convention: "// &
314 : "the cell vector **a** is aligned with the *x* axis and the cell vector **b** lies in "// &
315 : "the *xy* plane. This allows the reconstruction of scaled coordinates from the DCD data only.", &
316 : "Write the atomic information in PDB format to a formatted file", &
317 : "Mostly known as XYZ format, provides in a formatted file: element_symbol X Y Z", &
318 : "Alias name for XMOL", &
319 : "Extended XYZ format including cell information. "// &
320 : "For details see [ASE](https://ase-lib.org/ase/io/formatoptions.html#extxyz) "// &
321 92488 : "and [OVITO](https://www.ovito.org/manual/reference/file_formats/input/xyz.html)."))
322 92488 : CALL section_add_keyword(section, keyword)
323 92488 : CALL keyword_release(keyword)
324 :
325 : CALL keyword_create(keyword, __LOCATION__, name="CHARGE_OCCUP", &
326 : variants=["CHARGE_O"], &
327 : description="Write the MM charges to the OCCUP field of the PDB file", &
328 : usage="CHARGE_OCCUP logical", &
329 184976 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
330 92488 : CALL section_add_keyword(section, keyword)
331 92488 : CALL keyword_release(keyword)
332 :
333 : CALL keyword_create(keyword, __LOCATION__, name="CHARGE_BETA", &
334 : variants=["CHARGE_B"], &
335 : description="Write the MM charges to the BETA field of the PDB file", &
336 : usage="CHARGE_BETA logical", &
337 184976 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
338 92488 : CALL section_add_keyword(section, keyword)
339 92488 : CALL keyword_release(keyword)
340 :
341 : CALL keyword_create(keyword, __LOCATION__, name="CHARGE_EXTENDED", &
342 : description="Write the MM charges to the very last field of the PDB file (starting from column 81)", &
343 : usage="CHARGE_EXTENDED logical", &
344 92488 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
345 92488 : CALL section_add_keyword(section, keyword)
346 92488 : CALL keyword_release(keyword)
347 :
348 : ELSE
349 :
350 : CALL keyword_create(keyword, __LOCATION__, name="FORMAT", &
351 : description=description, usage="FORMAT (ATOMIC|DCD|XMOL|XYZ|EXTXYZ)", &
352 : default_i_val=dump_xmol, &
353 : enum_c_vals=s2a("ATOMIC", "DCD", "XMOL", "XYZ", "EXTXYZ"), &
354 : enum_i_vals=[dump_atomic, dump_dcd, dump_xmol, dump_xmol, dump_extxyz], &
355 : enum_desc=s2a("Write only the coordinates X,Y,Z without element symbols to a formatted file", &
356 : "Write the coordinates (no element labels) and the cell information to a binary file", &
357 : "Mostly known as XYZ format, provides in a formatted file: element_symbol X Y Z", &
358 : "Alias name for XMOL", &
359 : "Extended XYZ format including cell information. "// &
360 : "For details see [ASE](https://ase-lib.org/ase/io/formatoptions.html#extxyz) "// &
361 82096 : "and [OVITO](https://www.ovito.org/manual/reference/file_formats/input/xyz.html)."))
362 82096 : CALL section_add_keyword(section, keyword)
363 82096 : CALL keyword_release(keyword)
364 :
365 : END IF
366 :
367 : CALL keyword_create(keyword, __LOCATION__, name="PRINT_ATOM_KIND", &
368 : description="Write the atom kind given in the subsys section instead of the element symbol. "// &
369 : "Only valid for the XMOL and EXTXYZ format.", &
370 : usage="PRINT_ATOM_KIND logical", &
371 174584 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
372 174584 : CALL section_add_keyword(section, keyword)
373 174584 : CALL keyword_release(keyword)
374 :
375 174584 : END SUBROUTINE add_format_keyword
376 :
377 : END MODULE input_cp2k_motion_print
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