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topology_xyz.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! **************************************************************************************************
8MODULE topology_xyz
9 USE cp_log_handling, ONLY: cp_get_default_logger,&
10 cp_logger_type
11 USE cp_output_handling, ONLY: cp_print_key_finished_output,&
12 cp_print_key_unit_nr
13 USE cp_parser_methods, ONLY: parser_get_next_line,&
14 parser_get_object,&
15 read_integer_object
16 USE cp_parser_types, ONLY: cp_parser_type,&
17 parser_create,&
18 parser_release
19 USE cp_units, ONLY: cp_unit_to_cp2k
20 USE input_section_types, ONLY: section_vals_type
21 USE kinds, ONLY: default_string_length,&
22 dp,&
23 max_line_length
24 USE memory_utilities, ONLY: reallocate
25 USE message_passing, ONLY: mp_para_env_type
26 USE periodic_table, ONLY: nelem,&
27 ptable
28 USE string_table, ONLY: id2str,&
29 s2s,&
30 str2id
31 USE topology_types, ONLY: atom_info_type,&
32 topology_parameters_type
33#include "./base/base_uses.f90"
34
35 IMPLICIT NONE
36
37 CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'topology_xyz'
38
39 PRIVATE
40 PUBLIC :: read_coordinate_xyz
41
42CONTAINS
43
44! **************************************************************************************************
45!> \brief ...
46!> \param topology ...
47!> \param para_env ...
48!> \param subsys_section ...
49!> \author Teodoro Laino
50! **************************************************************************************************
51 SUBROUTINE read_coordinate_xyz(topology, para_env, subsys_section)
52 TYPE(topology_parameters_type) :: topology
53 TYPE(mp_para_env_type), POINTER :: para_env
54 TYPE(section_vals_type), POINTER :: subsys_section
55
56 CHARACTER(len=*), PARAMETER :: routinen = 'read_coordinate_xyz'
57
58 CHARACTER(LEN=default_string_length) :: my_default_index, strtmp
59 CHARACTER(LEN=max_line_length) :: error_message
60 INTEGER :: frame, handle, ian, iw, j, natom
61 LOGICAL :: my_end
62 TYPE(atom_info_type), POINTER :: atom_info
63 TYPE(cp_logger_type), POINTER :: logger
64 TYPE(cp_parser_type) :: parser
65
66 CALL timeset(routinen, handle)
67
68 NULLIFY (logger)
69 logger => cp_get_default_logger()
70 iw = cp_print_key_unit_nr(logger, subsys_section, "PRINT%TOPOLOGY_INFO/XYZ_INFO", &
71 extension=".subsysLog")
72
73 atom_info => topology%atom_info
74
75 IF (iw > 0) THEN
76 WRITE (unit=iw, fmt="(T2,A)") &
77 "BEGIN of XYZ data read from file "//trim(topology%coord_file_name)
78 END IF
79
80 CALL parser_create(parser, topology%coord_file_name, para_env=para_env, &
81 parse_white_lines=.true.)
82
83 ! Element is assigned on the basis of the atm_name
84 topology%aa_element = .true.
85
86 natom = 0
87 frame = 0
88 CALL parser_get_next_line(parser, 1)
89 frames: DO
90 ! Atom numbers
91 CALL parser_get_object(parser, natom)
92 frame = frame + 1
93 IF (frame == 1) THEN
94 CALL reallocate(atom_info%id_molname, 1, natom)
95 CALL reallocate(atom_info%id_resname, 1, natom)
96 CALL reallocate(atom_info%resid, 1, natom)
97 CALL reallocate(atom_info%id_atmname, 1, natom)
98 CALL reallocate(atom_info%r, 1, 3, 1, natom)
99 CALL reallocate(atom_info%atm_mass, 1, natom)
100 CALL reallocate(atom_info%atm_charge, 1, natom)
101 CALL reallocate(atom_info%occup, 1, natom)
102 CALL reallocate(atom_info%beta, 1, natom)
103 CALL reallocate(atom_info%id_element, 1, natom)
104 ELSE IF (natom > SIZE(atom_info%id_atmname)) THEN
105 cpabort("Atom number differs in different frames!")
106 END IF
107 ! Dummy line
108 CALL parser_get_next_line(parser, 2)
109 DO j = 1, natom
110 ! Atom coordinates
111 READ (parser%input_line, *) strtmp, &
112 atom_info%r(1, j), &
113 atom_info%r(2, j), &
114 atom_info%r(3, j)
115 error_message = ""
116 CALL read_integer_object(strtmp, ian, error_message)
117 IF (len_trim(error_message) == 0) THEN
118 ! Integer value found: assume atomic number, check it, and load
119 ! the corresponding element symbol if valid
120 IF ((ian < 0) .OR. (ian > nelem)) THEN
121 error_message = "Invalid atomic number <"//trim(strtmp)// &
122 "> found in the xyz file <"//trim(topology%coord_file_name)//">!"
123 cpabort(trim(error_message))
124 ELSE
125 atom_info%id_atmname(j) = str2id(s2s(ptable(ian)%symbol))
126 END IF
127 ELSE
128 atom_info%id_atmname(j) = str2id(s2s(strtmp))
129 END IF
130 ! For default, set atom name to residue name to molecule name
131 WRITE (my_default_index, '(I0)') j
132 atom_info%id_molname(j) = str2id(s2s(trim(id2str(atom_info%id_atmname(j)))//trim(my_default_index)))
133 atom_info%id_resname(j) = atom_info%id_molname(j)
134 atom_info%resid(j) = 1
135 atom_info%id_element(j) = atom_info%id_atmname(j)
136 atom_info%atm_mass(j) = huge(0.0_dp)
137 atom_info%atm_charge(j) = -huge(0.0_dp)
138 IF (iw > 0) THEN
139 WRITE (unit=iw, fmt="(T2,A4,3F8.3,2X,A)") &
140 trim(id2str(atom_info%id_atmname(j))), &
141 atom_info%r(1, j), &
142 atom_info%r(2, j), &
143 atom_info%r(3, j), &
144 adjustl(trim(id2str(atom_info%id_molname(j))))
145 END IF
146 atom_info%r(1, j) = cp_unit_to_cp2k(atom_info%r(1, j), "angstrom")
147 atom_info%r(2, j) = cp_unit_to_cp2k(atom_info%r(2, j), "angstrom")
148 atom_info%r(3, j) = cp_unit_to_cp2k(atom_info%r(3, j), "angstrom")
149 ! If there's a white line or end of file exit.. otherwise read other available
150 ! snapshots
151 CALL parser_get_next_line(parser, 1, at_end=my_end)
152 my_end = my_end .OR. (len_trim(parser%input_line) == 0)
153 IF (my_end) THEN
154 IF (j /= natom) &
155 CALL cp_abort(__location__, &
156 "Number of lines in XYZ format not equal to the number of atoms."// &
157 " Error in XYZ format. Very probably the line with title is missing or is empty."// &
158 " Please check the XYZ file and rerun your job!")
159 EXIT frames
160 END IF
161 END DO
162 END DO frames
163 CALL parser_release(parser)
164
165 IF (iw > 0) THEN
166 WRITE (unit=iw, fmt="(T2,A)") &
167 "END of XYZ frame data read from file "//trim(topology%coord_file_name)
168 END IF
169
170 topology%natoms = natom
171 topology%molname_generated = .true.
172
173 CALL cp_print_key_finished_output(iw, logger, subsys_section, &
174 "PRINT%TOPOLOGY_INFO/XYZ_INFO")
175
176 CALL timestop(handle)
177
178 END SUBROUTINE read_coordinate_xyz
179
180END MODULE topology_xyz
cp_parser_methods::parser_get_object
Definition cp_parser_methods.F:54
memory_utilities::reallocate
Definition memory_utilities.F:27
cp_log_handling
various routines to log and control the output. The idea is that decisions about where to log should ...
Definition cp_log_handling.F:41
cp_log_handling::cp_get_default_logger
type(cp_logger_type) function, pointer, public cp_get_default_logger()
returns the default logger
Definition cp_log_handling.F:234
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::cp_print_key_unit_nr
integer function, public cp_print_key_unit_nr(logger, basis_section, print_key_path, extension, middle_name, local, log_filename, ignore_should_output, file_form, file_position, file_action, file_status, do_backup, on_file, is_new_file, mpi_io, fout)
...
Definition cp_output_handling.F:803
cp_output_handling::cp_print_key_finished_output
subroutine, public cp_print_key_finished_output(unit_nr, logger, basis_section, print_key_path, local, ignore_should_output, on_file, mpi_io)
should be called after you finish working with a unit obtained with cp_print_key_unit_nr,...
Definition cp_output_handling.F:1013
cp_parser_methods
Utility routines to read data from files. Kept as close as possible to the old parser because.
Definition cp_parser_methods.F:20
cp_parser_methods::read_integer_object
elemental subroutine, public read_integer_object(string, object, error_message)
Returns an integer number read from a string including products of integer numbers like iz1*iz2*iz3.
Definition cp_parser_methods.F:1374
cp_parser_methods::parser_get_next_line
subroutine, public parser_get_next_line(parser, nline, at_end)
Read the next input line and broadcast the input information. Skip (nline-1) lines and skip also all ...
Definition cp_parser_methods.F:421
cp_parser_types
Utility routines to read data from files. Kept as close as possible to the old parser because.
Definition cp_parser_types.F:21
cp_parser_types::parser_release
subroutine, public parser_release(parser)
releases the parser
Definition cp_parser_types.F:109
cp_parser_types::parser_create
subroutine, public parser_create(parser, file_name, unit_nr, para_env, end_section_label, separator_chars, comment_char, continuation_char, quote_char, section_char, parse_white_lines, initial_variables, apply_preprocessing)
Start a parser run. Initial variables allow to @SET stuff before opening the file.
Definition cp_parser_types.F:147
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_section_types
objects that represent the structure of input sections and the data contained in an input section
Definition input_section_types.F:15
kinds
Defines the basic variable types.
Definition kinds.F:23
kinds::max_line_length
integer, parameter, public max_line_length
Definition kinds.F:59
kinds::dp
integer, parameter, public dp
Definition kinds.F:34
kinds::default_string_length
integer, parameter, public default_string_length
Definition kinds.F:57
memory_utilities
Utility routines for the memory handling.
Definition memory_utilities.F:14
message_passing
Interface to the message passing library MPI.
Definition message_passing.F:23
periodic_table
Periodic Table related data definitions.
Definition periodic_table.F:28
periodic_table::ptable
type(atom), dimension(0:nelem), public ptable
Definition periodic_table.F:65
periodic_table::nelem
integer, parameter, public nelem
Definition periodic_table.F:63
string_table
generates a unique id number for a string (str2id) that can be used two compare two strings....
Definition string_table.F:22
string_table::s2s
character(len=default_string_length) function, public s2s(str)
converts a string in a string of default_string_length
Definition string_table.F:141
string_table::str2id
integer function, public str2id(str)
returns a unique id for a given string, and stores the string for later retrieval using the id.
Definition string_table.F:72
string_table::id2str
character(len=default_string_length) function, public id2str(id)
returns the string associated with a given id
Definition string_table.F:115
topology_types
Definition topology_types.F:18
topology_xyz
Definition topology_xyz.F:8
topology_xyz::read_coordinate_xyz
subroutine, public read_coordinate_xyz(topology, para_env, subsys_section)
...
Definition topology_xyz.F:52
topology
Control for reading in different topologies and coordinates.
Definition topology.F:13
cp_log_handling::cp_logger_type
type of a logger, at the moment it contains just a print level starting at which level it should be l...
Definition cp_log_handling.F:140
cp_parser_types::cp_parser_type
represent a parser
Definition cp_parser_types.F:77
input_section_types::section_vals_type
stores the values of a section
Definition input_section_types.F:126
message_passing::mp_para_env_type
stores all the informations relevant to an mpi environment
Definition message_passing.F:763
topology_types::atom_info_type
Definition topology_types.F:35
topology_types::topology_parameters_type
Definition topology_types.F:142