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input_cp2k_voronoi.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 function that build the dft section of the input
10!> \par History
11!> 10.2005 moved out of input_cp2k [fawzi]
12!> \author fawzi
13! **************************************************************************************************
14MODULE input_cp2k_voronoi
15 USE bibliography, ONLY: brehm2018,&
16 brehm2020,&
17 brehm2021,&
18 rycroft2009,&
19 thomas2015
20 USE cp_output_handling, ONLY: cp_print_key_section_create,&
21 debug_print_level
22 USE input_constants, ONLY: voro_radii_cov,&
23 voro_radii_unity,&
24 voro_radii_user,&
25 voro_radii_vdw
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_type
31 USE input_val_types, ONLY: integer_t,&
32 lchar_t,&
33 real_t
34 USE kinds, ONLY: dp
35 USE physcon, ONLY: bohr
36 USE string_utilities, ONLY: s2a
37#include "./base/base_uses.f90"
38
39 IMPLICIT NONE
40 PRIVATE
41
42 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'input_cp2k_voronoi'
43
44 PUBLIC :: create_print_voronoi_section
45
46CONTAINS
47
48! **************************************************************************************************
49!> \brief Create the print voronoi section
50!> \param print_key ...
51!> \author Martin Brehm
52! **************************************************************************************************
53 SUBROUTINE create_print_voronoi_section(print_key)
54 TYPE(section_type), POINTER :: print_key
55
56 TYPE(keyword_type), POINTER :: keyword
57
58 cpassert(.NOT. ASSOCIATED(print_key))
59
60 ! Voronoi Integration via LibVori
61 CALL cp_print_key_section_create(print_key, __location__, name="VORONOI", &
62 description="Controls the Voronoi integration of the total electron density"// &
63 " for the computation of electromagnetic moments, see [Thomas2015],"// &
64 " [Brehm2020], and [Brehm2021]"// &
65 " (via LibVori see <https://brehm-research.de/voronoi>).", &
66 print_level=debug_print_level + 1, filename="", &
67 citations=(/rycroft2009, thomas2015, brehm2018, brehm2020, brehm2021/))
68
69 NULLIFY (keyword)
70 CALL keyword_create(keyword, __location__, name="APPEND", &
71 description="Appends frames to already existing .voronoi file.", &
72 default_l_val=.false., lone_keyword_l_val=.true.)
73 CALL section_add_keyword(print_key, keyword)
74 CALL keyword_release(keyword)
75
76 CALL keyword_create(keyword, __location__, name="SANITY_CHECK", &
77 description="Performs a sanity check before each Voronoi integration, i.e.,"// &
78 " checks if every grid point is located in exactly one Voronoi cell.", &
79 usage="SANITY_CHECK T", default_l_val=.false., lone_keyword_l_val=.true.)
80 CALL section_add_keyword(print_key, keyword)
81 CALL keyword_release(keyword)
82
83 CALL keyword_create(keyword, __location__, name="OVERWRITE", &
84 description="Specify this keyword to overwrite any existing ""properties.emp"" file if"// &
85 " it already exists. By default, the data is appended to an existing .emp file.", &
86 usage="OVERWRITE T", default_l_val=.false., lone_keyword_l_val=.true.)
87 CALL section_add_keyword(print_key, keyword)
88 CALL keyword_release(keyword)
89
90 CALL keyword_create(keyword, __location__, name="SKIP_FIRST", &
91 description="Skips the first step of a MD run (avoids duplicate step if restarted).", &
92 usage="SKIP_FIRST T", default_l_val=.false., lone_keyword_l_val=.true.)
93 CALL section_add_keyword(print_key, keyword)
94 CALL keyword_release(keyword)
95
96 CALL keyword_create(keyword, __location__, name="VERBOSE", &
97 description="Switches on verbose screen output of the Voronoi integration.", &
98 usage="VERBOSE T", default_l_val=.false., lone_keyword_l_val=.true.)
99 CALL section_add_keyword(print_key, keyword)
100 CALL keyword_release(keyword)
101
102 CALL keyword_create(keyword, __location__, name="OUTPUT_EMP", &
103 description="Writes the resulting electromagnetic moments to a binary file ""properties.emp""."// &
104 " The file name cannot be changed.", &
105 usage="OUTPUT_EMP T", default_l_val=.false., lone_keyword_l_val=.true.)
106 CALL section_add_keyword(print_key, keyword)
107 CALL keyword_release(keyword)
108
109 CALL keyword_create(keyword, __location__, name="OUTPUT_TEXT", &
110 description="Writes the resulting electromagnetic moments to text files (*.voronoi)."// &
111 " The file name is specified via FILENAME.", &
112 usage="OUTPUT_TEXT T", default_l_val=.true., lone_keyword_l_val=.true.)
113 CALL section_add_keyword(print_key, keyword)
114 CALL keyword_release(keyword)
115
116 CALL keyword_create(keyword, __location__, name="REFINEMENT_FACTOR", &
117 description="Sets the refinement factor for the Voronoi integration.", &
118 usage="REFINEMENT 2", n_var=1, default_i_val=1, type_of_var=integer_t)
119 CALL section_add_keyword(print_key, keyword)
120 CALL keyword_release(keyword)
121
122 CALL keyword_create(keyword, __location__, name="VORONOI_RADII", &
123 description="Which atomic radii to use for the radical Voronoi tessellation.", &
124 usage="VORONOI_RADII {UNITY,VDW,COVALENT,USER}", repeats=.false., n_var=1, &
125 default_i_val=voro_radii_vdw, &
126 enum_c_vals=s2a("UNITY", "VDW", "COVALENT", "USER"), &
127 enum_desc=s2a("Use unity radii (non-radical Voronoi tessellation)", "Use VdW atom radii", &
128 "Use covalent atom radii", "Use user-specified atom radii"), &
129 enum_i_vals=(/voro_radii_unity, voro_radii_vdw, voro_radii_cov, voro_radii_user/))
130 CALL section_add_keyword(print_key, keyword)
131 CALL keyword_release(keyword)
132
133 CALL keyword_create(keyword, __location__, name="USER_RADII", &
134 description="Defines user atom radii for the radical Voronoi tessellation (one per atom).", &
135 usage="USER_RADII {real} {real} {real}", repeats=.false., &
136 unit_str="angstrom", &
137 type_of_var=real_t, n_var=-1)
138 CALL section_add_keyword(print_key, keyword)
139 CALL keyword_release(keyword)
140
141 CALL keyword_create(keyword, __location__, name="MOLECULAR_PROPERTIES", &
142 description="Calculation of molecular properties from Voronoi integration.", &
143 usage="MOLECULAR_PROPERTIES T", default_l_val=.false., lone_keyword_l_val=.true.)
144 CALL section_add_keyword(print_key, keyword)
145 CALL keyword_release(keyword)
146
147 CALL keyword_create(keyword, __location__, name="MOLPROP_FILE_NAME", &
148 description="Root of the file name where to print molecular properties."// &
149 " filename.molprop is used.", &
150 usage="MOLPROP_FILE_NAME <FILENAME>", &
151 default_lc_val="__STD_OUT__", type_of_var=lchar_t)
152 CALL section_add_keyword(print_key, keyword)
153 CALL keyword_release(keyword)
154
155 CALL keyword_create(keyword, __location__, name="JITTER", &
156 description="The Voronoi tessellation can have issues with highly symmetric structures."// &
157 " This keyword displaces all atoms pseudo-randomly by a tiny amount (see JITTER_AMPLITUDE)"// &
158 " to break symmetry. The displacement is constant over time, so that no temporal noise is"// &
159 " introduced. The displacement is not visible to other CP2k routines (FORCE_EVAL, output)."// &
160 " It is only applied internally in the library for the Voronoi tessellation.", &
161 usage="JITTER T", default_l_val=.true., lone_keyword_l_val=.true.)
162 CALL section_add_keyword(print_key, keyword)
163 CALL keyword_release(keyword)
164
165 CALL keyword_create(keyword, __location__, name="JITTER_SEED", &
166 description="Sets the random seed for the jitter. The pseudo-random number generator"// &
167 " is re-initialized for each Voronoi tessellation so that the jitter is constant over"// &
168 " simulation time (no temporal noise).", &
169 usage="JITTER_SEED 1234", n_var=1, default_i_val=0, type_of_var=integer_t)
170 CALL section_add_keyword(print_key, keyword)
171 CALL keyword_release(keyword)
172
173 CALL keyword_create(keyword, __location__, name="JITTER_AMPLITUDE", &
174 description="Sets the maximum displacement amplitude for the jitter.", &
175 usage="JITTER_AMPLITUDE 0.01", unit_str="angstrom", n_var=1, default_r_val=1.e-3_dp*bohr, &
176 type_of_var=real_t)
177 CALL section_add_keyword(print_key, keyword)
178 CALL keyword_release(keyword)
179
180 END SUBROUTINE create_print_voronoi_section
181
182END MODULE input_cp2k_voronoi
string_utilities::s2a
Definition string_utilities.F:48
bibliography
collects all references to literature in CP2K as new algorithms / method are included from literature...
Definition bibliography.F:28
bibliography::brehm2021
integer, save, public brehm2021
Definition bibliography.F:43
bibliography::brehm2020
integer, save, public brehm2020
Definition bibliography.F:43
bibliography::thomas2015
integer, save, public thomas2015
Definition bibliography.F:43
bibliography::brehm2018
integer, save, public brehm2018
Definition bibliography.F:43
bibliography::rycroft2009
integer, save, public rycroft2009
Definition bibliography.F:43
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::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
input_constants
collects all constants needed in input so that they can be used without circular dependencies
Definition input_constants.F:17
input_constants::voro_radii_user
integer, parameter, public voro_radii_user
Definition input_constants.F:637
input_constants::voro_radii_vdw
integer, parameter, public voro_radii_vdw
Definition input_constants.F:637
input_constants::voro_radii_unity
integer, parameter, public voro_radii_unity
Definition input_constants.F:637
input_constants::voro_radii_cov
integer, parameter, public voro_radii_cov
Definition input_constants.F:637
input_cp2k_voronoi
function that build the dft section of the input
Definition input_cp2k_voronoi.F:14
input_cp2k_voronoi::create_print_voronoi_section
subroutine, public create_print_voronoi_section(print_key)
Create the print voronoi section.
Definition input_cp2k_voronoi.F:54
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_add_keyword
subroutine, public section_add_keyword(section, keyword)
adds a keyword to the given section
Definition input_section_types.F:504
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::lchar_t
integer, parameter, public lchar_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
physcon
Definition of physical constants:
Definition physcon.F:68
physcon::bohr
real(kind=dp), parameter, public bohr
Definition physcon.F:147
string_utilities
Utilities for string manipulations.
Definition string_utilities.F:16
input_keyword_types::keyword_type
represent a keyword in the input
Definition input_keyword_types.F:88
input_section_types::section_type
represent a section of the input file
Definition input_section_types.F:102