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 10390 : 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 10390 : 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 10390 : 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 20780 : default_l_val=.TRUE., lone_keyword_l_val=.TRUE.)
70 10390 : CALL section_add_keyword(section, keyword)
71 10390 : 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 10390 : filename="", unit_str="angstrom")
77 : CALL add_format_keyword(keyword, print_key, pos=.TRUE., &
78 10390 : description="Specifies the format of the output file for the trajectory.")
79 10390 : CALL section_add_subsection(section, print_key)
80 10390 : 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 10390 : filename="", unit_str="angstrom")
87 : CALL add_format_keyword(keyword, print_key, pos=.TRUE., &
88 10390 : description="Specifies the format of the output file for the trajectory of shells.")
89 10390 : CALL section_add_subsection(section, print_key)
90 10390 : 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 10390 : filename="", unit_str="angstrom")
96 : CALL add_format_keyword(keyword, print_key, pos=.TRUE., &
97 10390 : description="Specifies the format of the output file for the trajectory of cores.")
98 10390 : CALL section_add_subsection(section, print_key)
99 10390 : 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 10390 : filename="")
107 10390 : CALL section_add_subsection(section, print_key)
108 10390 : 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 10390 : filename="", unit_str="bohr*au_t^-1")
120 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
121 10390 : description="Specifies the format of the output file for the velocities.")
122 10390 : CALL section_add_subsection(section, print_key)
123 10390 : 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 10390 : filename="", unit_str="bohr*au_t^-1")
129 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
130 10390 : description="Specifies the format of the output file for the velocities of shells.")
131 10390 : CALL section_add_subsection(section, print_key)
132 10390 : 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 10390 : filename="", unit_str="bohr*au_t^-1")
138 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
139 10390 : description="Specifies the format of the output file for the velocities of cores.")
140 10390 : CALL section_add_subsection(section, print_key)
141 10390 : CALL section_release(print_key)
142 :
143 10390 : CALL create_structure_data_section(print_key)
144 10390 : CALL section_add_subsection(section, print_key)
145 10390 : 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 geometry "// &
149 : "and cell for optimization tasks. Currently CIF and XYZ "// &
150 : "formats are available, as controlled independently by "// &
151 : "PRINT_CIF and PRINT_XYZ respectively, with the same "// &
152 : "file name except for extension suffix.", &
153 10390 : print_level=low_print_level, filename="FINAL")
154 :
155 : CALL keyword_create(keyword, __LOCATION__, name="PRINT_CIF", &
156 : description="Print the final structure as CIF. Currently "// &
157 : "the structure will always be dumped with the asymmetric "// &
158 : "space group `P 1` as a triclinic system with a single "// &
159 : "symmetry-equivalent position `x, y, z` for all atoms. "// &
160 : "All fractional coordinates are in the range [0,1] and "// &
161 : "all occupancies are unity.", &
162 : usage="PRINT_CIF T", default_l_val=.TRUE., &
163 10390 : lone_keyword_l_val=.TRUE.)
164 10390 : CALL section_add_keyword(print_key, keyword)
165 10390 : CALL keyword_release(keyword)
166 :
167 : CALL keyword_create(keyword, __LOCATION__, name="PRINT_XYZ", &
168 : description="Print the final structure as XYZ. The cell "// &
169 : "information is available in the comment line according "// &
170 : "to the extended XYZ specification as the `Lattice=...` "// &
171 : "field, and the unit is angstrom for both the cell vectors "// &
172 : "and the atomic coordinates.", &
173 : usage="PRINT_XYZ T", default_l_val=.TRUE., &
174 10390 : lone_keyword_l_val=.TRUE.)
175 10390 : CALL section_add_keyword(print_key, keyword)
176 10390 : CALL keyword_release(keyword)
177 :
178 : CALL keyword_create(keyword, __LOCATION__, name="PRINT_ATOM_KIND", &
179 : description="Write the atom kind given in the subsys section instead "// &
180 : "of the element symbol in the extended XYZ file.", &
181 : usage="PRINT_ATOM_KIND {LOGICAL}", &
182 10390 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
183 10390 : CALL section_add_keyword(print_key, keyword)
184 10390 : CALL keyword_release(keyword)
185 :
186 10390 : CALL section_add_subsection(section, print_key)
187 10390 : CALL section_release(print_key)
188 :
189 : CALL cp_print_key_section_create( &
190 : print_key, __LOCATION__, "FORCE_MIXING_LABELS", &
191 : description="Controls the output of the force mixing (FORCE_EVAL&QMMM&FORCE_MIXING) labels", &
192 : print_level=high_print_level, common_iter_levels=1, &
193 10390 : filename="")
194 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
195 10390 : description="Specifies the format of the output file for the force mixing labels.")
196 10390 : CALL section_add_subsection(section, print_key)
197 10390 : CALL section_release(print_key)
198 :
199 : CALL cp_print_key_section_create(print_key, __LOCATION__, "FORCES", &
200 : description="Controls the output of the forces", &
201 : print_level=high_print_level, common_iter_levels=1, &
202 10390 : filename="", unit_str="hartree*bohr^-1")
203 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
204 10390 : description="Specifies the format of the output file for the forces.")
205 10390 : CALL section_add_subsection(section, print_key)
206 10390 : CALL section_release(print_key)
207 :
208 : CALL cp_print_key_section_create(print_key, __LOCATION__, "SHELL_FORCES", &
209 : description="Controls the output of the forces on shells when shell-model is used", &
210 : print_level=high_print_level, common_iter_levels=1, &
211 10390 : filename="", unit_str="hartree*bohr^-1")
212 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
213 10390 : description="Specifies the format of the output file for the forces on shells.")
214 10390 : CALL section_add_subsection(section, print_key)
215 10390 : CALL section_release(print_key)
216 :
217 : CALL cp_print_key_section_create(print_key, __LOCATION__, "CORE_FORCES", &
218 : description="Controls the output of the forces on cores when shell-model is used", &
219 : print_level=high_print_level, common_iter_levels=1, &
220 10390 : filename="", unit_str="hartree*bohr^-1")
221 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
222 10390 : description="Specifies the format of the output file for the forces on cores.")
223 10390 : CALL section_add_subsection(section, print_key)
224 10390 : CALL section_release(print_key)
225 :
226 : CALL cp_print_key_section_create(print_key, __LOCATION__, "MIXED_ENERGIES", &
227 : description="Controls the output of the energies of the two "// &
228 : "regular FORCE_EVALS in the MIXED method "// &
229 : "printed is step,time,Etot,E_F1,E_F2,CONS_QNT", &
230 : print_level=low_print_level, common_iter_levels=1, &
231 10390 : filename="")
232 10390 : CALL section_add_subsection(section, print_key)
233 10390 : CALL section_release(print_key)
234 :
235 : CALL cp_print_key_section_create(print_key, __LOCATION__, "STRESS", &
236 : description="Controls the output of the stress tensor", &
237 : print_level=high_print_level, common_iter_levels=1, &
238 10390 : filename="")
239 10390 : CALL section_add_subsection(section, print_key)
240 10390 : CALL section_release(print_key)
241 :
242 : CALL cp_print_key_section_create(print_key, __LOCATION__, "POLAR_MATRIX", &
243 : description="Controls the output of the polarisability tensor during an MD run", &
244 : print_level=low_print_level, common_iter_levels=1, &
245 10390 : filename="")
246 10390 : CALL section_add_subsection(section, print_key)
247 10390 : CALL section_release(print_key)
248 :
249 : CALL cp_print_key_section_create(print_key, __LOCATION__, "RESTART", &
250 : description="Controls the dumping of the restart file during runs. "// &
251 : "By default keeps a short history of three restarts. See also RESTART_HISTORY", &
252 : each_iter_names=s2a("MD"), each_iter_values=[20], &
253 : print_level=silent_print_level, common_iter_levels=1, &
254 10390 : add_last=add_last_numeric, filename="")
255 :
256 : CALL keyword_create(keyword, __LOCATION__, name="BACKUP_COPIES", &
257 : description="Specifies the maximum number of backup copies.", &
258 : usage="BACKUP_COPIES {int}", &
259 10390 : default_i_val=1)
260 10390 : CALL section_add_keyword(print_key, keyword)
261 10390 : CALL keyword_release(keyword)
262 :
263 : CALL keyword_create(keyword, __LOCATION__, name="SPLIT_RESTART_FILE", &
264 : description="If specified selected input sections, which are growing with the "// &
265 : "number of atoms in the system, are written to another restart file "// &
266 : "in binary format instead of the default restart file in human "// &
267 : "readable ASCII format. This split of the restart file may "// &
268 : "provide significant memory savings and an accelerated I/O for "// &
269 : "systems with a very large number of atoms", &
270 : usage="SPLIT_RESTART_FILE yes", &
271 : default_l_val=.FALSE., &
272 10390 : lone_keyword_l_val=.TRUE.)
273 10390 : CALL section_add_keyword(print_key, keyword)
274 10390 : CALL keyword_release(keyword)
275 :
276 10390 : CALL section_add_subsection(section, print_key)
277 10390 : CALL section_release(print_key)
278 :
279 : CALL cp_print_key_section_create(print_key, __LOCATION__, "RESTART_HISTORY", &
280 : description="Dumps unique restart files during the run keeping all of them. "// &
281 : "Most useful if recovery is needed at a later point.", &
282 : print_level=low_print_level, common_iter_levels=0, &
283 : each_iter_names=s2a("MD", "GEO_OPT", "ROT_OPT"), each_iter_values=[500, 500, 500], &
284 10390 : filename="")
285 10390 : CALL section_add_subsection(section, print_key)
286 10390 : CALL section_release(print_key)
287 :
288 : CALL cp_print_key_section_create(print_key, __LOCATION__, "TRANSLATION_VECTOR", &
289 : description="Dumps the translation vector applied along an MD (if any). Useful"// &
290 : " for postprocessing of QMMM trajectories in which the QM fragment is continuously"// &
291 : " centered in the QM box", &
292 : print_level=high_print_level, common_iter_levels=1, &
293 10390 : filename="")
294 10390 : CALL section_add_subsection(section, print_key)
295 10390 : CALL section_release(print_key)
296 :
297 10390 : END SUBROUTINE create_motion_print_section
298 :
299 : ! **************************************************************************************************
300 : !> \brief creates the FORMAT keyword
301 : !> \param keyword ...
302 : !> \param section will contain the pint section
303 : !> \param pos ...
304 : !> \param description ...
305 : !> \author Teodoro Laino 10.2008 [tlaino]
306 : ! **************************************************************************************************
307 176760 : SUBROUTINE add_format_keyword(keyword, section, pos, description)
308 : TYPE(keyword_type), POINTER :: keyword
309 : TYPE(section_type), POINTER :: section
310 : LOGICAL, INTENT(IN) :: pos
311 : CHARACTER(LEN=*), INTENT(IN) :: description
312 :
313 176760 : CPASSERT(ASSOCIATED(section))
314 176760 : CPASSERT(.NOT. ASSOCIATED(keyword))
315 :
316 176760 : IF (pos) THEN
317 :
318 : CALL keyword_create( &
319 : keyword, __LOCATION__, name="FORMAT", &
320 : description=description, usage="FORMAT (ATOMIC|DCD|PDB|XMOL|XYZ|EXTXYZ)", &
321 : default_i_val=dump_xmol, &
322 : enum_c_vals=s2a("ATOMIC", "DCD", "DCD_ALIGNED_CELL", "PDB", "XMOL", "XYZ", "EXTXYZ"), &
323 : enum_i_vals=[dump_atomic, dump_dcd, dump_dcd_aligned_cell, dump_pdb, dump_xmol, dump_xmol, dump_extxyz], &
324 : enum_desc=s2a("Write only the coordinates X,Y,Z without element symbols to a formatted file", &
325 : "Write the coordinates (no element labels) and the cell information to a binary file", &
326 : "Like DCD, but the dumped coordinates refer to an aligned cell following the common convention: "// &
327 : "the cell vector **a** is aligned with the *x* axis and the cell vector **b** lies in "// &
328 : "the *xy* plane. This allows the reconstruction of scaled coordinates from the DCD data only.", &
329 : "Write the atomic information in PDB format to a formatted file", &
330 : "Mostly known as XYZ format, provides in a formatted file: element_symbol X Y Z", &
331 : "Alias name for XMOL", &
332 : "Extended XYZ format including cell information. "// &
333 : "For details see [ASE](https://ase-lib.org/ase/io/formatoptions.html#extxyz) "// &
334 93640 : "and [OVITO](https://www.ovito.org/manual/reference/file_formats/input/xyz.html)."))
335 93640 : CALL section_add_keyword(section, keyword)
336 93640 : CALL keyword_release(keyword)
337 :
338 : CALL keyword_create(keyword, __LOCATION__, name="CHARGE_OCCUP", &
339 : variants=["CHARGE_O"], &
340 : description="Write the MM charges to the OCCUP field of the PDB file", &
341 : usage="CHARGE_OCCUP logical", &
342 187280 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
343 93640 : CALL section_add_keyword(section, keyword)
344 93640 : CALL keyword_release(keyword)
345 :
346 : CALL keyword_create(keyword, __LOCATION__, name="CHARGE_BETA", &
347 : variants=["CHARGE_B"], &
348 : description="Write the MM charges to the BETA field of the PDB file", &
349 : usage="CHARGE_BETA logical", &
350 187280 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
351 93640 : CALL section_add_keyword(section, keyword)
352 93640 : CALL keyword_release(keyword)
353 :
354 : CALL keyword_create(keyword, __LOCATION__, name="CHARGE_EXTENDED", &
355 : description="Write the MM charges to the very last field of the PDB file (starting from column 81)", &
356 : usage="CHARGE_EXTENDED logical", &
357 93640 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
358 93640 : CALL section_add_keyword(section, keyword)
359 93640 : CALL keyword_release(keyword)
360 :
361 : ELSE
362 :
363 : CALL keyword_create(keyword, __LOCATION__, name="FORMAT", &
364 : description=description, usage="FORMAT (ATOMIC|DCD|XMOL|XYZ|EXTXYZ)", &
365 : default_i_val=dump_xmol, &
366 : enum_c_vals=s2a("ATOMIC", "DCD", "XMOL", "XYZ", "EXTXYZ"), &
367 : enum_i_vals=[dump_atomic, dump_dcd, dump_xmol, dump_xmol, dump_extxyz], &
368 : enum_desc=s2a("Write only the coordinates X,Y,Z without element symbols to a formatted file", &
369 : "Write the coordinates (no element labels) and the cell information to a binary file", &
370 : "Mostly known as XYZ format, provides in a formatted file: element_symbol X Y Z", &
371 : "Alias name for XMOL", &
372 : "Extended XYZ format including cell information. "// &
373 : "For details see [ASE](https://ase-lib.org/ase/io/formatoptions.html#extxyz) "// &
374 83120 : "and [OVITO](https://www.ovito.org/manual/reference/file_formats/input/xyz.html)."))
375 83120 : CALL section_add_keyword(section, keyword)
376 83120 : CALL keyword_release(keyword)
377 :
378 : END IF
379 :
380 : CALL keyword_create(keyword, __LOCATION__, name="PRINT_ATOM_KIND", &
381 : description="Write the atom kind given in the subsys section instead of the element symbol. "// &
382 : "Only valid for the XMOL and EXTXYZ format.", &
383 : usage="PRINT_ATOM_KIND logical", &
384 176760 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
385 176760 : CALL section_add_keyword(section, keyword)
386 176760 : CALL keyword_release(keyword)
387 :
388 176760 : END SUBROUTINE add_format_keyword
389 :
390 : END MODULE input_cp2k_motion_print
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