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input_cp2k_vib.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 builds the input structure for the VIBRATIONAL_ANALYSIS module
10 !> \par History
11 !> 01.2008 [tlaino] Teodoro Laino - University of Zurich
12 !> Creating an own module for vibrational analysis
13 !> \author [tlaino]
14 ! **************************************************************************************************
15 MODULE input_cp2k_vib
16  USE cp_output_handling, ONLY: add_last_numeric,&
17  cp_print_key_section_create,&
18  debug_print_level,&
19  low_print_level,&
20  medium_print_level,&
21  silent_print_level
22  USE cp_units, ONLY: cp_unit_to_cp2k
23  USE input_constants, ONLY: do_rep_blocked,&
24  do_rep_interleaved,&
25  ms_guess_atomic,&
26  ms_guess_bfgs,&
27  ms_guess_molden,&
28  ms_guess_restart,&
29  ms_guess_restart_vec
30  USE input_keyword_types, ONLY: keyword_create,&
31  keyword_release,&
32  keyword_type
33  USE input_section_types, ONLY: section_add_keyword,&
34  section_add_subsection,&
35  section_create,&
36  section_release,&
37  section_type
38  USE input_val_types, ONLY: integer_t,&
39  real_t
40  USE kinds, ONLY: dp
41  USE string_utilities, ONLY: s2a
42 #include "../base/base_uses.f90"
43 
44  IMPLICIT NONE
45  PRIVATE
46 
47  LOGICAL, PRIVATE, PARAMETER :: debug_this_module = .true.
48  CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'input_cp2k_vib'
49 
50  PUBLIC :: create_vib_section
51 CONTAINS
52 
53 ! **************************************************************************************************
54 !> \brief Creates the exteranal restart section
55 !> \param section the section to create
56 !> \author tlaino
57 ! **************************************************************************************************
58  SUBROUTINE create_vib_section(section)
59  TYPE(section_type), POINTER :: section
60 
61  TYPE(keyword_type), POINTER :: keyword
62  TYPE(section_type), POINTER :: subsection
63 
64  cpassert(.NOT. ASSOCIATED(section))
65  CALL section_create( &
66  section, __location__, name="VIBRATIONAL_ANALYSIS", &
67  description="Section to setup parameters to perform a Normal Modes, vibrational, or phonon analysis. "// &
68  "Vibrations are computed using finite differences, "// &
69  "which implies a very tight (e.g. 1E-8) threshold is needed for EPS_SCF to get accurate low frequencies. "// &
70  "The analysis assumes a stationary state (minimum or TS),"// &
71  " i.e. tight geometry optimization (MAX_FORCE) is needed as well.", &
72  n_keywords=1, n_subsections=0, repeats=.false.)
73  NULLIFY (keyword, subsection)
74 
75  CALL keyword_create(keyword, __location__, name="DX", &
76  description="Specify the increment to be used to construct the HESSIAN with "// &
77  "finite difference method", &
78  default_r_val=1.0e-2_dp, unit_str="bohr")
79  CALL section_add_keyword(section, keyword)
80  CALL keyword_release(keyword)
81 
82  CALL keyword_create(keyword, __location__, name="NPROC_REP", &
83  description="Specify the number of processors to be used per replica "// &
84  "environment (for parallel runs). "// &
85  "In case of mode selective calculations more than one replica will start"// &
86  " a block Davidson algorithm to track more than only one frequency", &
87  default_i_val=1)
88  CALL section_add_keyword(section, keyword)
89  CALL keyword_release(keyword)
90 
91  CALL keyword_create(keyword, __location__, name="PROC_DIST_TYPE", &
92  description="Specify the topology of the mapping of processors into replicas.", &
93  usage="PROC_DIST_TYPE (INTERLEAVED|BLOCKED)", &
94  enum_c_vals=s2a("INTERLEAVED", &
95  "BLOCKED"), &
96  enum_desc=s2a("Interleaved distribution", &
97  "Blocked distribution"), &
98  enum_i_vals=(/do_rep_interleaved, do_rep_blocked/), &
99  default_i_val=do_rep_blocked)
100  CALL section_add_keyword(section, keyword)
101  CALL keyword_release(keyword)
102 
103  CALL keyword_create(keyword, __location__, name="FULLY_PERIODIC", &
104  description="Avoids to clean rotations from the Hessian matrix.", &
105  default_l_val=.false., lone_keyword_l_val=.true.)
106  CALL section_add_keyword(section, keyword)
107  CALL keyword_release(keyword)
108 
109  CALL keyword_create(keyword, __location__, name="INTENSITIES", &
110  description="Calculation of the IR/Raman-Intensities. "// &
111  "Calculation of dipoles and/or polarizabilities have to be "// &
112  "specified explicitly in DFT/PRINT/MOMENTS and/or "// &
113  "PROPERTIES/LINRES/POLAR", &
114  default_l_val=.false., lone_keyword_l_val=.true.)
115  CALL section_add_keyword(section, keyword)
116  CALL keyword_release(keyword)
117 
118  CALL keyword_create(keyword, __location__, name="THERMOCHEMISTRY", &
119  description="Calculation of the thermochemical data. Valid for molecules in the gas phase. ", &
120  default_l_val=.false., lone_keyword_l_val=.true.)
121  CALL section_add_keyword(section, keyword)
122  CALL keyword_release(keyword)
123 
124  CALL keyword_create(keyword, __location__, name="TC_TEMPERATURE", &
125  description="Temperature for the calculation of the thermochemical data ", &
126  usage="tc_temperature 325.0", default_r_val=cp_unit_to_cp2k(value=273.150_dp, unit_str="K"), &
127  unit_str="K")
128  CALL section_add_keyword(section, keyword)
129  CALL keyword_release(keyword)
130 
131  CALL keyword_create(keyword, __location__, name="TC_PRESSURE", &
132  description="Pressure for the calculation of the thermochemical data ", &
133  default_r_val=cp_unit_to_cp2k(value=101325.0_dp, unit_str="Pa"), unit_str="Pa")
134  CALL section_add_keyword(section, keyword)
135  CALL keyword_release(keyword)
136 
137  CALL create_mode_selective_section(subsection)
138  CALL section_add_subsection(section, subsection)
139  CALL section_release(subsection)
140 
141  CALL create_print_vib_section(subsection)
142  CALL section_add_subsection(section, subsection)
143  CALL section_release(subsection)
144  END SUBROUTINE create_vib_section
145 
146 ! **************************************************************************************************
147 !> \brief Create the print section for VIB
148 !> \param section the section to create
149 !> \author Teodoro Laino [tlaino] - 10.2008
150 ! **************************************************************************************************
151  SUBROUTINE create_print_vib_section(section)
152  TYPE(section_type), POINTER :: section
153 
154  TYPE(keyword_type), POINTER :: keyword
155  TYPE(section_type), POINTER :: print_key
156 
157  cpassert(.NOT. ASSOCIATED(section))
158  CALL section_create(section, __location__, name="PRINT", &
159  description="Section controlling the print information during a vibrational "// &
160  "analysis.", n_keywords=1, n_subsections=0, repeats=.false.)
161  NULLIFY (keyword, print_key)
162 
163  CALL cp_print_key_section_create(print_key, __location__, "BANNER", &
164  description="Controls the printing of the vibrational analysis banner", &
165  print_level=low_print_level, common_iter_levels=1, &
166  filename="__STD_OUT__")
167  CALL section_add_subsection(section, print_key)
168  CALL section_release(print_key)
169 
170  CALL cp_print_key_section_create(print_key, __location__, "PROGRAM_RUN_INFO", &
171  description="Controls the printing basic info about the vibrational method", &
172  print_level=medium_print_level, add_last=add_last_numeric, filename="__STD_OUT__")
173  CALL section_add_subsection(section, print_key)
174  CALL section_release(print_key)
175 
176  CALL cp_print_key_section_create(print_key, __location__, "MOLDEN_VIB", &
177  description="Controls the printing for visualization in molden format", &
178  print_level=low_print_level, add_last=add_last_numeric, filename="VIBRATIONS")
179  CALL section_add_subsection(section, print_key)
180  CALL section_release(print_key)
181 
182  CALL cp_print_key_section_create(print_key, __location__, "ROTATIONAL_INFO", &
183  description="Controls the printing basic info during the cleaning of the "// &
184  "rotational degrees of freedom.", &
185  print_level=debug_print_level, add_last=add_last_numeric, filename="__STD_OUT__")
186  ! Print_key keywords
187  CALL keyword_create(keyword, __location__, name="COORDINATES", &
188  description="Prints atomic coordinates after rotation", &
189  default_l_val=.false., lone_keyword_l_val=.true.)
190  CALL section_add_keyword(print_key, keyword)
191  CALL keyword_release(keyword)
192  CALL section_add_subsection(section, print_key)
193  CALL section_release(print_key)
194 
195  CALL cp_print_key_section_create(print_key, __location__, "CARTESIAN_EIGS", &
196  description="Controls the printing of Cartesian "// &
197  "frequencies and eigenvectors of the Hessian used "// &
198  "for initializing ensemble for MD calculations. "// &
199  "This should always print to a file, and will not "// &
200  "effect the same frequencies and eigenvectors printed "// &
201  "in the main vibrational analysis output", &
202  print_level=low_print_level, &
203  add_last=add_last_numeric, &
204  filename="VIBRATIONS")
205  CALL keyword_create(keyword, __location__, name="BACKUP_COPIES", &
206  description="Specifies the maximum number of backup copies.", &
207  usage="BACKUP_COPIES {int}", &
208  default_i_val=1)
209  CALL section_add_keyword(print_key, keyword)
210  CALL keyword_release(keyword)
211  CALL section_add_subsection(section, print_key)
212  CALL section_release(print_key)
213 
214  CALL cp_print_key_section_create(print_key, __location__, name="NAMD_PRINT", &
215  description="Adjust cartesian eigenvalues / vectors to NewtonX format.", &
216  print_level=debug_print_level + 1, add_last=add_last_numeric, &
217  filename="FullNormalizedCartesian")
218  CALL keyword_create(keyword, __location__, name="BACKUP_COPIES", &
219  description="Specifies the maximum number of backup copies.", &
220  usage="BACKUP_COPIES {int}", &
221  default_i_val=1)
222  CALL section_add_keyword(print_key, keyword)
223  CALL keyword_release(keyword)
224  CALL section_add_subsection(section, print_key)
225  CALL section_release(print_key)
226 
227  CALL cp_print_key_section_create(print_key, __location__, "HESSIAN", &
228  description="Write the Hessian matrix from a vibrational analysis calculation "// &
229  "into a binary file.", &
230  print_level=low_print_level, add_last=add_last_numeric, filename="Hessian")
231  CALL section_add_subsection(section, print_key)
232  CALL section_release(print_key)
233 
234  END SUBROUTINE create_print_vib_section
235 
236 ! **************************************************************************************************
237 !> \brief Create the input section for MODE selective
238 !> \param section the section to create
239 !> \author fschiff
240 ! **************************************************************************************************
241  SUBROUTINE create_mode_selective_section(section)
242  TYPE(section_type), POINTER :: section
243 
244  TYPE(keyword_type), POINTER :: keyword
245  TYPE(section_type), POINTER :: print_key, subsection
246 
247  NULLIFY (keyword, subsection, print_key)
248  cpassert(.NOT. ASSOCIATED(section))
249  CALL section_create(section, __location__, name="MODE_SELECTIVE", &
250  description="All parameters needed for to run a mode selective vibrational analysis. "// &
251  "The keywords FREQUENCY, RANGE, and the subsection INVOLVED_ATOMS are mutually exclusive.", &
252  n_keywords=8, n_subsections=1, repeats=.false.)
253 
254  CALL keyword_create(keyword, __location__, name="FREQUENCY", &
255  description="value close to the expected value of the frequency to look for. "// &
256  "If the block Davidson algorithm is applied, the nrep closest frequencies are tracked. ", &
257  usage="FREQUENCY {REAL}", default_r_val=-1._dp)
258  CALL section_add_keyword(section, keyword)
259  CALL keyword_release(keyword)
260 
261  CALL keyword_create(keyword, __location__, name="RANGE", &
262  description="Track modes in a given range of frequencies. "// &
263  "No warranty that the set of frequencies is complete.", &
264  usage="RANGE {REAL} {REAL}", &
265  n_var=-1, type_of_var=real_t)
266  CALL section_add_keyword(section, keyword)
267  CALL keyword_release(keyword)
268 
269  CALL keyword_create(keyword, __location__, name="LOWEST_FREQUENCY", &
270  description="Lowest frequency mode to include when writing output. "// &
271  "Use a negative value to print imaginary frequencies. "// &
272  "Useful for visualizing the imaginary frequency along a reaction path coordinate "// &
273  "Depending on accuracy settings, the output might include spurious low frequency "// &
274  "imaginary modes which should be visually checked (see MOLDEN_VIB).", &
275  usage="LOWEST_FREQUENCY <REAL>", default_r_val=0.0_dp)
276  CALL section_add_keyword(section, keyword)
277  CALL keyword_release(keyword)
278 
279  CALL keyword_create(keyword, __location__, name="ATOMS", &
280  description="Specifies the list of atoms which should be displaced for the Initial guess", &
281  usage="ATOMS {integer} {integer} .. {integer}", &
282  n_var=-1, type_of_var=integer_t)
283  CALL section_add_keyword(section, keyword)
284  CALL keyword_release(keyword)
285 
286  CALL keyword_create(keyword, __location__, name="EPS_MAX_VAL", &
287  description="Convergence criterion for the davidson algorithm. Specifies the maximal value in the "// &
288  "residuum vectors ", &
289  usage="EPS_MAX_VAL {REAL}", default_r_val=5.0e-7_dp)
290  CALL section_add_keyword(section, keyword)
291  CALL keyword_release(keyword)
292 
293  CALL keyword_create( &
294  keyword, __location__, name="EPS_NORM", &
295  description="Convergence criterion for the davidson algorithm. Specifies the maximal value of the norm "// &
296  "of the residuum vectors ", &
297  usage="EPS_NORM {REAL}", default_r_val=2.0e-6_dp)
298  CALL section_add_keyword(section, keyword)
299  CALL keyword_release(keyword)
300 
301  CALL keyword_create( &
302  keyword, __location__, name="INITIAL_GUESS", &
303  description="The type of initial guess for the normal modes", &
304  usage="INITIAL_GUESS BFGS_HESS", &
305  default_i_val=ms_guess_atomic, &
306  enum_c_vals=s2a("BFGS_HESS", "ATOMIC", "RESTART", "RESTART_VEC", "MOLDEN_RESTART"), &
307  enum_desc=s2a("get the first displacement vector out of the BFGS approximate Hessian", &
308  "use random displacements for a set of atoms specified", &
309  "use data from MS_RESTART as initial guess", &
310  "use a vector from MS_RESTART, useful if you want to increase accurcy by changing functionals or basis", &
311  "use the .mol file of a former run, to restart a vector"// &
312  " (similar to Restart_vec, but a different file FORMAT is used)"), &
313  enum_i_vals=(/ms_guess_bfgs, ms_guess_atomic, ms_guess_restart, ms_guess_restart_vec, ms_guess_molden/))
314  CALL section_add_keyword(section, keyword)
315  CALL keyword_release(keyword)
316 
317  CALL keyword_create(keyword, __location__, name="RESTART_FILE_NAME", &
318  description="Specifies the name of the file used to create the restarted vectors", &
319  usage="RESTART_FILE_NAME {filename}", &
320  default_lc_val="")
321  CALL section_add_keyword(section, keyword)
322  CALL keyword_release(keyword)
323 
324  CALL create_involved_atoms_section(subsection)
325  CALL section_add_subsection(section, subsection)
326  CALL section_release(subsection)
327 
328  CALL section_create(subsection, __location__, name="PRINT", &
329  description="Controls the printing mode selective vibrational analysis", &
330  n_keywords=0, n_subsections=1, repeats=.true.)
331 
332  CALL cp_print_key_section_create(print_key, __location__, "MS_RESTART", &
333  description="Controls the printing of the Mode Selective Restart file.", &
334  print_level=silent_print_level, common_iter_levels=1, &
335  add_last=add_last_numeric, filename="")
336  CALL section_add_subsection(subsection, print_key)
337  CALL section_release(print_key)
338 
339  CALL section_add_subsection(section, subsection)
340  CALL section_release(subsection)
341 
342  END SUBROUTINE create_mode_selective_section
343 
344 ! **************************************************************************************************
345 !> \brief Create the input section for Ivolved_atoms keyword in mode selective
346 !> \param section the section to create
347 !> \author fschiff
348 ! **************************************************************************************************
349  SUBROUTINE create_involved_atoms_section(section)
350  TYPE(section_type), POINTER :: section
351 
352  TYPE(keyword_type), POINTER :: keyword
353 
354  NULLIFY (keyword)
355  cpassert(.NOT. ASSOCIATED(section))
356  CALL section_create( &
357  section, __location__, name="INVOLVED_ATOMS", &
358  description="All parameters needed for the tracking of modes dominated by the motion of selected atoms. "// &
359  "Warning, if many atoms are involved, only low frequency modes are detected, "// &
360  "since they are more delocalized and match the tracked eigenvector.", &
361  n_keywords=2, n_subsections=0, repeats=.false.)
362 
363  CALL keyword_create( &
364  keyword, __location__, name="RANGE", &
365  description=" Specifies the range of wavenumbers in which the modes related to the ATOMS have to be tracked."// &
366  " If not specified frequencies >400cm-1 will be used to avoid tracking of translational or rotational modes", &
367  usage="RANGE {REAL} {REAL}", &
368  n_var=-1, type_of_var=real_t)
369  CALL section_add_keyword(section, keyword)
370  CALL keyword_release(keyword)
371 
372  CALL keyword_create( &
373  keyword, __location__, name="INVOLVED_ATOMS", &
374  description="Specifies the list of atoms on which the tracked eigenvector should have the highest value "// &
375  "similar to looking for the vibration of a set of atoms", &
376  usage="INVOLVED_ATOMS {integer} {integer} .. {integer}", &
377  n_var=-1, type_of_var=integer_t)
378  CALL section_add_keyword(section, keyword)
379  CALL keyword_release(keyword)
380 
381  END SUBROUTINE create_involved_atoms_section
382 
383 END MODULE input_cp2k_vib
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::debug_print_level
integer, parameter, public debug_print_level
Definition: cp_output_handling.F:73
cp_output_handling::low_print_level
integer, parameter, public low_print_level
Definition: cp_output_handling.F:73
cp_output_handling::medium_print_level
integer, parameter, public medium_print_level
Definition: cp_output_handling.F:73
cp_output_handling::add_last_numeric
integer, parameter, public add_last_numeric
Definition: cp_output_handling.F:70
cp_output_handling::silent_print_level
integer, parameter, public silent_print_level
Definition: cp_output_handling.F:73
cp_output_handling::cp_print_key_section_create
subroutine, public cp_print_key_section_create(print_key_section, location, name, description, print_level, each_iter_names, each_iter_values, add_last, filename, common_iter_levels, citations, unit_str)
creates a print_key section
Definition: cp_output_handling.F:174
cp_units
unit conversion facility
Definition: cp_units.F:30
cp_units::cp_unit_to_cp2k
real(kind=dp) function, public cp_unit_to_cp2k(value, unit_str, defaults, power)
converts to the internal cp2k units to the given unit
Definition: cp_units.F:1150
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_rep_interleaved
integer, parameter, public do_rep_interleaved
Definition: input_constants.F:91
input_constants::do_rep_blocked
integer, parameter, public do_rep_blocked
Definition: input_constants.F:91
input_constants::ms_guess_restart
integer, parameter, public ms_guess_restart
Definition: input_constants.F:832
input_constants::ms_guess_restart_vec
integer, parameter, public ms_guess_restart_vec
Definition: input_constants.F:832
input_constants::ms_guess_molden
integer, parameter, public ms_guess_molden
Definition: input_constants.F:832
input_constants::ms_guess_atomic
integer, parameter, public ms_guess_atomic
Definition: input_constants.F:832
input_constants::ms_guess_bfgs
integer, parameter, public ms_guess_bfgs
Definition: input_constants.F:832
input_cp2k_vib
builds the input structure for the VIBRATIONAL_ANALYSIS module
Definition: input_cp2k_vib.F:15
input_cp2k_vib::create_vib_section
subroutine, public create_vib_section(section)
Creates the exteranal restart section.
Definition: input_cp2k_vib.F:59
input_keyword_types
represents keywords in an input
Definition: input_keyword_types.F:14
input_keyword_types::keyword_release
subroutine, public keyword_release(keyword)
releases the given keyword (see doc/ReferenceCounting.html)
Definition: input_keyword_types.F:426
input_keyword_types::keyword_create
subroutine, public keyword_create(keyword, location, name, description, usage, type_of_var, n_var, repeats, variants, default_val, default_l_val, default_r_val, default_lc_val, default_c_val, default_i_val, default_l_vals, default_r_vals, default_c_vals, default_i_vals, lone_keyword_val, lone_keyword_l_val, lone_keyword_r_val, lone_keyword_c_val, lone_keyword_i_val, lone_keyword_l_vals, lone_keyword_r_vals, lone_keyword_c_vals, lone_keyword_i_vals, enum_c_vals, enum_i_vals, enum, enum_strict, enum_desc, unit_str, citations, deprecation_notice, removed)
creates a keyword object
Definition: input_keyword_types.F:155
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_create
subroutine, public section_create(section, location, name, description, n_keywords, n_subsections, repeats, citations)
creates a list of keywords
Definition: input_section_types.F:156
input_section_types::section_add_keyword
subroutine, public section_add_keyword(section, keyword)
adds a keyword to the given section
Definition: input_section_types.F:504
input_section_types::section_add_subsection
subroutine, public section_add_subsection(section, subsection)
adds a subsection to the given section
Definition: input_section_types.F:560
input_section_types::section_release
recursive subroutine, public section_release(section)
releases the given keyword list (see doc/ReferenceCounting.html)
Definition: input_section_types.F:231
input_val_types
a wrapper for basic fortran types.
Definition: input_val_types.F:14
input_val_types::real_t
integer, parameter, public real_t
Definition: input_val_types.F:41
input_val_types::integer_t
integer, parameter, public integer_t
Definition: input_val_types.F:41
kinds
Defines the basic variable types.
Definition: kinds.F:23
kinds::dp
integer, parameter, public dp
Definition: kinds.F:34
string_utilities
Utilities for string manipulations.
Definition: string_utilities.F:16