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 10340 : 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 10340 : 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 10340 : 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 20680 : default_l_val=.TRUE., lone_keyword_l_val=.TRUE.)
70 10340 : CALL section_add_keyword(section, keyword)
71 10340 : 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 10340 : filename="", unit_str="angstrom")
77 : CALL add_format_keyword(keyword, print_key, pos=.TRUE., &
78 10340 : description="Specifies the format of the output file for the trajectory.")
79 10340 : CALL section_add_subsection(section, print_key)
80 10340 : 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 10340 : filename="", unit_str="angstrom")
87 : CALL add_format_keyword(keyword, print_key, pos=.TRUE., &
88 10340 : description="Specifies the format of the output file for the trajectory of shells.")
89 10340 : CALL section_add_subsection(section, print_key)
90 10340 : 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 10340 : filename="", unit_str="angstrom")
96 : CALL add_format_keyword(keyword, print_key, pos=.TRUE., &
97 10340 : description="Specifies the format of the output file for the trajectory of cores.")
98 10340 : CALL section_add_subsection(section, print_key)
99 10340 : 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 10340 : filename="")
107 10340 : CALL section_add_subsection(section, print_key)
108 10340 : 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 10340 : filename="", unit_str="bohr*au_t^-1")
120 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
121 10340 : description="Specifies the format of the output file for the velocities.")
122 10340 : CALL section_add_subsection(section, print_key)
123 10340 : 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 10340 : filename="", unit_str="bohr*au_t^-1")
129 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
130 10340 : description="Specifies the format of the output file for the velocities of shells.")
131 10340 : CALL section_add_subsection(section, print_key)
132 10340 : 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 10340 : filename="", unit_str="bohr*au_t^-1")
138 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
139 10340 : description="Specifies the format of the output file for the velocities of cores.")
140 10340 : CALL section_add_subsection(section, print_key)
141 10340 : CALL section_release(print_key)
142 :
143 10340 : CALL create_structure_data_section(print_key)
144 10340 : CALL section_add_subsection(section, print_key)
145 10340 : 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 10340 : 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 10340 : lone_keyword_l_val=.TRUE.)
159 10340 : CALL section_add_keyword(print_key, keyword)
160 10340 : 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 10340 : lone_keyword_l_val=.TRUE.)
170 10340 : CALL section_add_keyword(print_key, keyword)
171 10340 : CALL keyword_release(keyword)
172 :
173 : CALL keyword_create(keyword, __LOCATION__, name="PRINT_ATOM_KIND", &
174 : description="Write the atom kind given in the subsys section instead "// &
175 : "of the element symbol in the extended XYZ file.", &
176 : usage="PRINT_ATOM_KIND {LOGICAL}", &
177 10340 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
178 10340 : CALL section_add_keyword(print_key, keyword)
179 10340 : CALL keyword_release(keyword)
180 :
181 10340 : CALL section_add_subsection(section, print_key)
182 10340 : CALL section_release(print_key)
183 :
184 : CALL cp_print_key_section_create( &
185 : print_key, __LOCATION__, "FORCE_MIXING_LABELS", &
186 : description="Controls the output of the force mixing (FORCE_EVAL&QMMM&FORCE_MIXING) labels", &
187 : print_level=high_print_level, common_iter_levels=1, &
188 10340 : filename="")
189 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
190 10340 : description="Specifies the format of the output file for the force mixing labels.")
191 10340 : CALL section_add_subsection(section, print_key)
192 10340 : CALL section_release(print_key)
193 :
194 : CALL cp_print_key_section_create(print_key, __LOCATION__, "FORCES", &
195 : description="Controls the output of the forces", &
196 : print_level=high_print_level, common_iter_levels=1, &
197 10340 : filename="", unit_str="hartree*bohr^-1")
198 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
199 10340 : description="Specifies the format of the output file for the forces.")
200 10340 : CALL section_add_subsection(section, print_key)
201 10340 : CALL section_release(print_key)
202 :
203 : CALL cp_print_key_section_create(print_key, __LOCATION__, "SHELL_FORCES", &
204 : description="Controls the output of the forces on shells when shell-model is used", &
205 : print_level=high_print_level, common_iter_levels=1, &
206 10340 : filename="", unit_str="hartree*bohr^-1")
207 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
208 10340 : description="Specifies the format of the output file for the forces on shells.")
209 10340 : CALL section_add_subsection(section, print_key)
210 10340 : CALL section_release(print_key)
211 :
212 : CALL cp_print_key_section_create(print_key, __LOCATION__, "CORE_FORCES", &
213 : description="Controls the output of the forces on cores when shell-model is used", &
214 : print_level=high_print_level, common_iter_levels=1, &
215 10340 : filename="", unit_str="hartree*bohr^-1")
216 : CALL add_format_keyword(keyword, print_key, pos=.FALSE., &
217 10340 : description="Specifies the format of the output file for the forces on cores.")
218 10340 : CALL section_add_subsection(section, print_key)
219 10340 : CALL section_release(print_key)
220 :
221 : CALL cp_print_key_section_create(print_key, __LOCATION__, "MIXED_ENERGIES", &
222 : description="Controls the output of the energies of the two "// &
223 : "regular FORCE_EVALS in the MIXED method "// &
224 : "printed is step,time,Etot,E_F1,E_F2,CONS_QNT", &
225 : print_level=low_print_level, common_iter_levels=1, &
226 10340 : filename="")
227 10340 : CALL section_add_subsection(section, print_key)
228 10340 : CALL section_release(print_key)
229 :
230 : CALL cp_print_key_section_create(print_key, __LOCATION__, "STRESS", &
231 : description="Controls the output of the stress tensor", &
232 : print_level=high_print_level, common_iter_levels=1, &
233 10340 : filename="")
234 10340 : CALL section_add_subsection(section, print_key)
235 10340 : CALL section_release(print_key)
236 :
237 : CALL cp_print_key_section_create(print_key, __LOCATION__, "POLAR_MATRIX", &
238 : description="Controls the output of the polarisability tensor during an MD run", &
239 : print_level=low_print_level, common_iter_levels=1, &
240 10340 : filename="")
241 10340 : CALL section_add_subsection(section, print_key)
242 10340 : CALL section_release(print_key)
243 :
244 : CALL cp_print_key_section_create(print_key, __LOCATION__, "RESTART", &
245 : description="Controls the dumping of the restart file during runs. "// &
246 : "By default keeps a short history of three restarts. See also RESTART_HISTORY", &
247 : each_iter_names=s2a("MD"), each_iter_values=[20], &
248 : print_level=silent_print_level, common_iter_levels=1, &
249 10340 : add_last=add_last_numeric, filename="")
250 :
251 : CALL keyword_create(keyword, __LOCATION__, name="BACKUP_COPIES", &
252 : description="Specifies the maximum number of backup copies.", &
253 : usage="BACKUP_COPIES {int}", &
254 10340 : default_i_val=1)
255 10340 : CALL section_add_keyword(print_key, keyword)
256 10340 : CALL keyword_release(keyword)
257 :
258 : CALL keyword_create(keyword, __LOCATION__, name="SPLIT_RESTART_FILE", &
259 : description="If specified selected input sections, which are growing with the "// &
260 : "number of atoms in the system, are written to another restart file "// &
261 : "in binary format instead of the default restart file in human "// &
262 : "readable ASCII format. This split of the restart file may "// &
263 : "provide significant memory savings and an accelerated I/O for "// &
264 : "systems with a very large number of atoms", &
265 : usage="SPLIT_RESTART_FILE yes", &
266 : default_l_val=.FALSE., &
267 10340 : lone_keyword_l_val=.TRUE.)
268 10340 : CALL section_add_keyword(print_key, keyword)
269 10340 : CALL keyword_release(keyword)
270 :
271 10340 : CALL section_add_subsection(section, print_key)
272 10340 : CALL section_release(print_key)
273 :
274 : CALL cp_print_key_section_create(print_key, __LOCATION__, "RESTART_HISTORY", &
275 : description="Dumps unique restart files during the run keeping all of them. "// &
276 : "Most useful if recovery is needed at a later point.", &
277 : print_level=low_print_level, common_iter_levels=0, &
278 : each_iter_names=s2a("MD", "GEO_OPT", "ROT_OPT"), each_iter_values=[500, 500, 500], &
279 10340 : filename="")
280 10340 : CALL section_add_subsection(section, print_key)
281 10340 : CALL section_release(print_key)
282 :
283 : CALL cp_print_key_section_create(print_key, __LOCATION__, "TRANSLATION_VECTOR", &
284 : description="Dumps the translation vector applied along an MD (if any). Useful"// &
285 : " for postprocessing of QMMM trajectories in which the QM fragment is continuously"// &
286 : " centered in the QM box", &
287 : print_level=high_print_level, common_iter_levels=1, &
288 10340 : filename="")
289 10340 : CALL section_add_subsection(section, print_key)
290 10340 : CALL section_release(print_key)
291 :
292 10340 : END SUBROUTINE create_motion_print_section
293 :
294 : ! **************************************************************************************************
295 : !> \brief creates the FORMAT keyword
296 : !> \param keyword ...
297 : !> \param section will contain the pint section
298 : !> \param pos ...
299 : !> \param description ...
300 : !> \author Teodoro Laino 10.2008 [tlaino]
301 : ! **************************************************************************************************
302 175910 : SUBROUTINE add_format_keyword(keyword, section, pos, description)
303 : TYPE(keyword_type), POINTER :: keyword
304 : TYPE(section_type), POINTER :: section
305 : LOGICAL, INTENT(IN) :: pos
306 : CHARACTER(LEN=*), INTENT(IN) :: description
307 :
308 175910 : CPASSERT(ASSOCIATED(section))
309 175910 : CPASSERT(.NOT. ASSOCIATED(keyword))
310 :
311 175910 : IF (pos) THEN
312 :
313 : CALL keyword_create( &
314 : keyword, __LOCATION__, name="FORMAT", &
315 : description=description, usage="FORMAT (ATOMIC|DCD|PDB|XMOL|XYZ|EXTXYZ)", &
316 : default_i_val=dump_xmol, &
317 : enum_c_vals=s2a("ATOMIC", "DCD", "DCD_ALIGNED_CELL", "PDB", "XMOL", "XYZ", "EXTXYZ"), &
318 : enum_i_vals=[dump_atomic, dump_dcd, dump_dcd_aligned_cell, dump_pdb, dump_xmol, dump_xmol, dump_extxyz], &
319 : enum_desc=s2a("Write only the coordinates X,Y,Z without element symbols to a formatted file", &
320 : "Write the coordinates (no element labels) and the cell information to a binary file", &
321 : "Like DCD, but the dumped coordinates refer to an aligned cell following the common convention: "// &
322 : "the cell vector **a** is aligned with the *x* axis and the cell vector **b** lies in "// &
323 : "the *xy* plane. This allows the reconstruction of scaled coordinates from the DCD data only.", &
324 : "Write the atomic information in PDB format to a formatted file", &
325 : "Mostly known as XYZ format, provides in a formatted file: element_symbol X Y Z", &
326 : "Alias name for XMOL", &
327 : "Extended XYZ format including cell information. "// &
328 : "For details see [ASE](https://ase-lib.org/ase/io/formatoptions.html#extxyz) "// &
329 93190 : "and [OVITO](https://www.ovito.org/manual/reference/file_formats/input/xyz.html)."))
330 93190 : CALL section_add_keyword(section, keyword)
331 93190 : CALL keyword_release(keyword)
332 :
333 : CALL keyword_create(keyword, __LOCATION__, name="CHARGE_OCCUP", &
334 : variants=["CHARGE_O"], &
335 : description="Write the MM charges to the OCCUP field of the PDB file", &
336 : usage="CHARGE_OCCUP logical", &
337 186380 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
338 93190 : CALL section_add_keyword(section, keyword)
339 93190 : CALL keyword_release(keyword)
340 :
341 : CALL keyword_create(keyword, __LOCATION__, name="CHARGE_BETA", &
342 : variants=["CHARGE_B"], &
343 : description="Write the MM charges to the BETA field of the PDB file", &
344 : usage="CHARGE_BETA logical", &
345 186380 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
346 93190 : CALL section_add_keyword(section, keyword)
347 93190 : CALL keyword_release(keyword)
348 :
349 : CALL keyword_create(keyword, __LOCATION__, name="CHARGE_EXTENDED", &
350 : description="Write the MM charges to the very last field of the PDB file (starting from column 81)", &
351 : usage="CHARGE_EXTENDED logical", &
352 93190 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
353 93190 : CALL section_add_keyword(section, keyword)
354 93190 : CALL keyword_release(keyword)
355 :
356 : ELSE
357 :
358 : CALL keyword_create(keyword, __LOCATION__, name="FORMAT", &
359 : description=description, usage="FORMAT (ATOMIC|DCD|XMOL|XYZ|EXTXYZ)", &
360 : default_i_val=dump_xmol, &
361 : enum_c_vals=s2a("ATOMIC", "DCD", "XMOL", "XYZ", "EXTXYZ"), &
362 : enum_i_vals=[dump_atomic, dump_dcd, dump_xmol, dump_xmol, dump_extxyz], &
363 : enum_desc=s2a("Write only the coordinates X,Y,Z without element symbols to a formatted file", &
364 : "Write the coordinates (no element labels) and the cell information to a binary file", &
365 : "Mostly known as XYZ format, provides in a formatted file: element_symbol X Y Z", &
366 : "Alias name for XMOL", &
367 : "Extended XYZ format including cell information. "// &
368 : "For details see [ASE](https://ase-lib.org/ase/io/formatoptions.html#extxyz) "// &
369 82720 : "and [OVITO](https://www.ovito.org/manual/reference/file_formats/input/xyz.html)."))
370 82720 : CALL section_add_keyword(section, keyword)
371 82720 : CALL keyword_release(keyword)
372 :
373 : END IF
374 :
375 : CALL keyword_create(keyword, __LOCATION__, name="PRINT_ATOM_KIND", &
376 : description="Write the atom kind given in the subsys section instead of the element symbol. "// &
377 : "Only valid for the XMOL and EXTXYZ format.", &
378 : usage="PRINT_ATOM_KIND logical", &
379 175910 : default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
380 175910 : CALL section_add_keyword(section, keyword)
381 175910 : CALL keyword_release(keyword)
382 :
383 175910 : END SUBROUTINE add_format_keyword
384 :
385 : END MODULE input_cp2k_motion_print
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