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cell_methods.F
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!--------------------------------------------------------------------------------------------------!
! CP2K: A general program to perform molecular dynamics simulations !
! Copyright 2000-2021 CP2K developers group <https://cp2k.org> !
! !
! SPDX-License-Identifier: GPL-2.0-or-later !
!--------------------------------------------------------------------------------------------------!
! **************************************************************************************************
!> \brief Handles all functions related to the CELL
!> \par History
!> 11.2008 Teodoro Laino [tlaino] - deeply cleaning cell_type from units
!> 10.2014 Moved many routines to cell_types.F.
!> \author Matthias KracK (16.01.2002, based on a earlier version of CJM, JGH)
! **************************************************************************************************
MODULE cell_methods
USE cell_types, ONLY: &
cell_clone, cell_create, cell_release, cell_sym_none, cell_type, get_cell, init_cell, &
set_cell_param, use_perd_none, use_perd_x, use_perd_xy, use_perd_xyz, use_perd_xz, &
use_perd_y, use_perd_yz, use_perd_z
USE cp_log_handling, ONLY: cp_get_default_logger,&
cp_logger_type
USE cp_output_handling, ONLY: cp_print_key_finished_output,&
cp_print_key_unit_nr
USE cp_para_types, ONLY: cp_para_env_type
USE cp_parser_methods, ONLY: parser_get_next_line,&
parser_get_object,&
parser_search_string
USE cp_parser_types, ONLY: cp_parser_type,&
parser_create,&
parser_release
USE cp_units, ONLY: cp_unit_from_cp2k,&
cp_unit_to_cp2k
USE input_constants, ONLY: do_cell_cif,&
do_cell_cp2k,&
do_cell_xsc
USE input_cp2k_subsys, ONLY: create_cell_section
USE input_enumeration_types, ONLY: enum_i2c,&
enumeration_type
USE input_keyword_types, ONLY: keyword_get,&
keyword_type
USE input_section_types, ONLY: &
section_get_keyword, section_release, section_type, section_vals_get, &
section_vals_get_subs_vals, section_vals_type, section_vals_val_get, section_vals_val_set, &
section_vals_val_unset
USE kinds, ONLY: default_path_length,&
default_string_length,&
dp
USE mathconstants, ONLY: degree
USE mathlib, ONLY: angle
#include "./base/base_uses.f90"
IMPLICIT NONE
PRIVATE
CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'cell_methods'
! Public subroutines
PUBLIC :: read_cell, read_cell_cif, write_cell
CONTAINS
! **************************************************************************************************
!> \brief ...
!> \param cell ...
!> \param cell_ref ...
!> \param use_ref_cell ...
!> \param cell_section ...
!> \param check_for_ref ...
!> \param para_env ...
!> \par History
!> 03.2005 created [teo]
!> \author Teodoro Laino
! **************************************************************************************************
RECURSIVE SUBROUTINE read_cell(cell, cell_ref, use_ref_cell, cell_section, &
check_for_ref, para_env)
TYPE(cell_type), POINTER :: cell, cell_ref
LOGICAL, INTENT(OUT), OPTIONAL :: use_ref_cell
TYPE(section_vals_type), OPTIONAL, POINTER :: cell_section
LOGICAL, INTENT(IN), OPTIONAL :: check_for_ref
TYPE(cp_para_env_type), POINTER :: para_env
INTEGER :: my_per
INTEGER, DIMENSION(:), POINTER :: multiple_unit_cell
LOGICAL :: cell_read_a, cell_read_abc, cell_read_b, &
cell_read_c, cell_read_file, check, &
my_check
REAL(KIND=dp), DIMENSION(:), POINTER :: cell_angles, cell_par
TYPE(section_vals_type), POINTER :: cell_ref_section
my_check = .TRUE.
NULLIFY (cell_ref_section, cell_par, multiple_unit_cell)
IF (.NOT. ASSOCIATED(cell)) CALL cell_create(cell)
IF (.NOT. ASSOCIATED(cell_ref)) CALL cell_create(cell_ref)
IF (PRESENT(check_for_ref)) my_check = check_for_ref
cell%deth = 0.0_dp
cell%orthorhombic = .FALSE.
cell%perd(:) = 1
cell%symmetry_id = cell_sym_none
cell%hmat(:, :) = 0.0_dp
cell%h_inv(:, :) = 0.0_dp
cell_read_file = .FALSE.
cell_read_a = .FALSE.
cell_read_b = .FALSE.
cell_read_c = .FALSE.
! Trying to read cell info from file
CALL section_vals_val_get(cell_section, "CELL_FILE_NAME", explicit=cell_read_file)
IF (cell_read_file) CALL read_cell_from_external_file(cell_section, para_env)
! Trying to read cell info from the separate A, B, C vectors
! If cell information is provided through file A,B,C contain the file information..
! a print warning is shown on screen..
CALL section_vals_val_get(cell_section, "A", explicit=cell_read_a)
IF (cell_read_a) THEN
CALL section_vals_val_get(cell_section, "A", r_vals=cell_par)
cell%hmat(:, 1) = cell_par(:)
END IF
CALL section_vals_val_get(cell_section, "B", explicit=cell_read_b)
IF (cell_read_b) THEN
CALL section_vals_val_get(cell_section, "B", r_vals=cell_par)
cell%hmat(:, 2) = cell_par(:)
END IF
CALL section_vals_val_get(cell_section, "C", explicit=cell_read_c)
IF (cell_read_c) THEN
CALL section_vals_val_get(cell_section, "C", r_vals=cell_par)
cell%hmat(:, 3) = cell_par(:)
END IF
check = ((cell_read_a .EQV. cell_read_b) .AND. (cell_read_b .EQV. cell_read_c))
IF (.NOT. check) &
CALL cp_warn(__LOCATION__, &
"Cell Information provided through vectors A, B and C. Not all three "// &
"vectors were provided! Cell setup may be incomplete!")
! Very last option.. Trying to read cell info from ABC keyword
CALL section_vals_val_get(cell_section, "ABC", explicit=cell_read_abc)
IF (cell_read_abc) THEN
check = (cell_read_a .OR. cell_read_b .OR. cell_read_c)
IF (check) &
CALL cp_warn(__LOCATION__, &
"Cell Information provided through vectors A, B and C in conjunction with ABC."// &
" The definition of the ABC keyword will override the one provided by A,B and C.")
cell%hmat = 0.0_dp
CALL section_vals_val_get(cell_section, "ABC", r_vals=cell_par)
CALL section_vals_val_get(cell_section, "ALPHA_BETA_GAMMA", r_vals=cell_angles)
CALL set_cell_param(cell, cell_par, cell_angles, do_init_cell=.FALSE.)
END IF
! Multiple unit cell
CALL section_vals_val_get(cell_section, "MULTIPLE_UNIT_CELL", i_vals=multiple_unit_cell)
IF (ANY(multiple_unit_cell /= 1)) CALL set_multiple_unit_cell(cell, multiple_unit_cell)
CALL section_vals_val_get(cell_section, "PERIODIC", i_val=my_per)
SELECT CASE (my_per)
CASE (use_perd_x)
cell%perd = (/1, 0, 0/)
CASE (use_perd_y)
cell%perd = (/0, 1, 0/)
CASE (use_perd_z)
cell%perd = (/0, 0, 1/)
CASE (use_perd_xy)
cell%perd = (/1, 1, 0/)
CASE (use_perd_xz)
cell%perd = (/1, 0, 1/)
CASE (use_perd_yz)
cell%perd = (/0, 1, 1/)
CASE (use_perd_xyz)
cell%perd = (/1, 1, 1/)
CASE (use_perd_none)
cell%perd = (/0, 0, 0/)
CASE DEFAULT
CPABORT("")
END SELECT
! Load requested cell symmetry
CALL section_vals_val_get(cell_section, "SYMMETRY", i_val=cell%symmetry_id)
! Initialize cell
CALL init_cell(cell)
IF (.NOT. my_check) RETURN
cell_ref_section => section_vals_get_subs_vals(cell_section, &
"CELL_REF")
IF (parsed_cp2k_input(cell_ref_section, check_this_section=.TRUE.)) THEN
IF (PRESENT(use_ref_cell)) use_ref_cell = .TRUE.
CALL read_cell(cell_ref, cell_ref, use_ref_cell, cell_section=cell_ref_section, &
check_for_ref=.FALSE., para_env=para_env)
ELSE
CALL cell_clone(cell, cell_ref)
IF (PRESENT(use_ref_cell)) use_ref_cell = .FALSE.
END IF
END SUBROUTINE read_cell
! **************************************************************************************************
!> \brief utility function to ease the transition to the new input.
!> returns true if the new input was parsed
!> \param input_file the parsed input file
!> \param check_this_section ...
!> \return ...
!> \author fawzi
! **************************************************************************************************
FUNCTION parsed_cp2k_input(input_file, check_this_section) RESULT(res)
TYPE(section_vals_type), POINTER :: input_file
LOGICAL, INTENT(IN), OPTIONAL :: check_this_section
LOGICAL :: res
LOGICAL :: my_check
TYPE(section_vals_type), POINTER :: glob_section
my_check = .FALSE.
IF (PRESENT(check_this_section)) my_check = check_this_section
res = ASSOCIATED(input_file)
IF (res) THEN
CPASSERT(input_file%ref_count > 0)
IF (.NOT. my_check) THEN
glob_section => section_vals_get_subs_vals(input_file, "GLOBAL")
CALL section_vals_get(glob_section, explicit=res)
ELSE
CALL section_vals_get(input_file, explicit=res)
END IF
END IF
END FUNCTION parsed_cp2k_input
! **************************************************************************************************
!> \brief Setup of the multiple unit_cell
!> \param cell ...
!> \param multiple_unit_cell ...
!> \date 05.2009
!> \author Teodoro Laino [tlaino]
!> \version 1.0
! **************************************************************************************************
SUBROUTINE set_multiple_unit_cell(cell, multiple_unit_cell)
TYPE(cell_type), POINTER :: cell
INTEGER, DIMENSION(:), POINTER :: multiple_unit_cell
! Fail is one of the value is set to zero..
IF (ANY(multiple_unit_cell <= 0)) &
CALL cp_abort(__LOCATION__, &
"CELL%MULTIPLE_UNIT_CELL accepts only integer values larger than 0! "// &
"A value of 0 or negative is meaningless!")
! scale abc accordingly user request
cell%hmat(:, 1) = cell%hmat(:, 1)*multiple_unit_cell(1)
cell%hmat(:, 2) = cell%hmat(:, 2)*multiple_unit_cell(2)
cell%hmat(:, 3) = cell%hmat(:, 3)*multiple_unit_cell(3)
END SUBROUTINE set_multiple_unit_cell
! **************************************************************************************************
!> \brief Read cell information from an external file
!> \param cell_section ...
!> \param para_env ...
!> \date 02.2008
!> \author Teodoro Laino [tlaino] - University of Zurich
!> \version 1.0
! **************************************************************************************************
SUBROUTINE read_cell_from_external_file(cell_section, para_env)
TYPE(section_vals_type), POINTER :: cell_section
TYPE(cp_para_env_type), POINTER :: para_env
CHARACTER(LEN=default_path_length) :: cell_file_name
INTEGER :: i, idum, j, my_format, n_rep
LOGICAL :: explicit, my_end
REAL(KIND=dp) :: xdum
REAL(KIND=dp), DIMENSION(3, 3) :: hmat
REAL(KIND=dp), DIMENSION(:), POINTER :: cell_par
TYPE(cell_type), POINTER :: cell
TYPE(cp_parser_type), POINTER :: parser
NULLIFY (parser)
CALL section_vals_val_get(cell_section, "CELL_FILE_NAME", c_val=cell_file_name)
CALL section_vals_val_get(cell_section, "CELL_FILE_FORMAT", i_val=my_format)
SELECT CASE (my_format)
CASE (do_cell_cp2k)
CALL parser_create(parser, cell_file_name, para_env=para_env)
CALL parser_get_next_line(parser, 1)
my_end = .FALSE.
DO WHILE (.NOT. my_end)
READ (parser%input_line, *) idum, xdum, hmat(:, 1), hmat(:, 2), hmat(:, 3)
CALL parser_get_next_line(parser, 1, at_end=my_end)
END DO
CALL parser_release(parser)
! Conver to CP2K units
DO i = 1, 3
DO j = 1, 3
hmat(j, i) = cp_unit_to_cp2k(hmat(j, i), "angstrom")
END DO
END DO
CASE (do_cell_xsc)
CALL parser_create(parser, cell_file_name, para_env=para_env)
CALL parser_get_next_line(parser, 1)
READ (parser%input_line, *) idum, hmat(:, 1), hmat(:, 2), hmat(:, 3)
CALL parser_release(parser)
! Conver to CP2K units
DO i = 1, 3
DO j = 1, 3
hmat(j, i) = cp_unit_to_cp2k(hmat(j, i), "angstrom")
END DO
END DO
CASE (do_cell_cif)
NULLIFY (cell)
CALL cell_create(cell)
CALL read_cell_cif(cell_file_name, cell, para_env)
hmat = cell%hmat
CALL cell_release(cell)
END SELECT
CALL section_vals_val_unset(cell_section, "CELL_FILE_NAME")
CALL section_vals_val_unset(cell_section, "CELL_FILE_FORMAT")
! Check if the cell was already defined
explicit = .FALSE.
CALL section_vals_val_get(cell_section, "A", n_rep_val=n_rep)
explicit = explicit .OR. (n_rep == 1)
CALL section_vals_val_get(cell_section, "B", n_rep_val=n_rep)
explicit = explicit .OR. (n_rep == 1)
CALL section_vals_val_get(cell_section, "C", n_rep_val=n_rep)
explicit = explicit .OR. (n_rep == 1)
CALL section_vals_val_get(cell_section, "ABC", n_rep_val=n_rep)
explicit = explicit .OR. (n_rep == 1)
! Possibly print a warning
IF (explicit) &
CALL cp_warn(__LOCATION__, &
"Cell specification (A,B,C or ABC) provided together with the external "// &
"cell setup! Ignoring (A,B,C or ABC) and proceeding with info read from the "// &
"external file! ")
! Copy cell information in the A, B, C fields..(we may need them later on..)
ALLOCATE (cell_par(3))
cell_par = hmat(:, 1)
CALL section_vals_val_set(cell_section, "A", r_vals_ptr=cell_par)
ALLOCATE (cell_par(3))
cell_par = hmat(:, 2)
CALL section_vals_val_set(cell_section, "B", r_vals_ptr=cell_par)
ALLOCATE (cell_par(3))
cell_par = hmat(:, 3)
CALL section_vals_val_set(cell_section, "C", r_vals_ptr=cell_par)
! Unset possible keywords
CALL section_vals_val_unset(cell_section, "ABC")
CALL section_vals_val_unset(cell_section, "ALPHA_BETA_GAMMA")
END SUBROUTINE read_cell_from_external_file
! **************************************************************************************************
!> \brief Reads cell information from CIF file
!> \param cif_file_name ...
!> \param cell ...
!> \param para_env ...
!> \date 12.2008
!> \par Format Information implemented:
!> _cell_length_a
!> _cell_length_b
!> _cell_length_c
!> _cell_angle_alpha
!> _cell_angle_beta
!> _cell_angle_gamma
!>
!> \author Teodoro Laino [tlaino]
!> moved from topology_cif (1/2019 JHU)
! **************************************************************************************************
SUBROUTINE read_cell_cif(cif_file_name, cell, para_env)
CHARACTER(len=*) :: cif_file_name
TYPE(cell_type), POINTER :: cell
TYPE(cp_para_env_type), POINTER :: para_env
CHARACTER(len=*), PARAMETER :: routineN = 'read_cell_cif'
INTEGER :: handle
INTEGER, DIMENSION(3) :: periodic
LOGICAL :: found
REAL(KIND=dp), DIMENSION(3) :: cell_angles, cell_lengths
TYPE(cp_parser_type), POINTER :: parser
CALL timeset(routineN, handle)
NULLIFY (parser)
CALL parser_create(parser, cif_file_name, &
para_env=para_env, apply_preprocessing=.FALSE.)
! Parsing cell infos
periodic = 1
! Check for _cell_length_a
CALL parser_search_string(parser, "_cell_length_a", ignore_case=.FALSE., found=found, &
begin_line=.FALSE., search_from_begin_of_file=.TRUE.)
IF (.NOT. found) &
CPABORT("The field (_cell_length_a) was not found in CIF file! ")
CALL cif_get_real(parser, cell_lengths(1))
cell_lengths(1) = cp_unit_to_cp2k(cell_lengths(1), "angstrom")
! Check for _cell_length_b
CALL parser_search_string(parser, "_cell_length_b", ignore_case=.FALSE., found=found, &
begin_line=.FALSE., search_from_begin_of_file=.TRUE.)
IF (.NOT. found) &
CPABORT("The field (_cell_length_b) was not found in CIF file! ")
CALL cif_get_real(parser, cell_lengths(2))
cell_lengths(2) = cp_unit_to_cp2k(cell_lengths(2), "angstrom")
! Check for _cell_length_c
CALL parser_search_string(parser, "_cell_length_c", ignore_case=.FALSE., found=found, &
begin_line=.FALSE., search_from_begin_of_file=.TRUE.)
IF (.NOT. found) &
CPABORT("The field (_cell_length_c) was not found in CIF file! ")
CALL cif_get_real(parser, cell_lengths(3))
cell_lengths(3) = cp_unit_to_cp2k(cell_lengths(3), "angstrom")
! Check for _cell_angle_alpha
CALL parser_search_string(parser, "_cell_angle_alpha", ignore_case=.FALSE., found=found, &
begin_line=.FALSE., search_from_begin_of_file=.TRUE.)
IF (.NOT. found) &
CPABORT("The field (_cell_angle_alpha) was not found in CIF file! ")
CALL cif_get_real(parser, cell_angles(1))
cell_angles(1) = cp_unit_to_cp2k(cell_angles(1), "deg")
! Check for _cell_angle_beta
CALL parser_search_string(parser, "_cell_angle_beta", ignore_case=.FALSE., found=found, &
begin_line=.FALSE., search_from_begin_of_file=.TRUE.)
IF (.NOT. found) &
CPABORT("The field (_cell_angle_beta) was not found in CIF file! ")
CALL cif_get_real(parser, cell_angles(2))
cell_angles(2) = cp_unit_to_cp2k(cell_angles(2), "deg")
! Check for _cell_angle_gamma
CALL parser_search_string(parser, "_cell_angle_gamma", ignore_case=.FALSE., found=found, &
begin_line=.FALSE., search_from_begin_of_file=.TRUE.)
IF (.NOT. found) &
CPABORT("The field (_cell_angle_gamma) was not found in CIF file! ")
CALL cif_get_real(parser, cell_angles(3))
cell_angles(3) = cp_unit_to_cp2k(cell_angles(3), "deg")
! Create cell
CALL set_cell_param(cell, cell_lengths, cell_angles, periodic=periodic, &
do_init_cell=.TRUE.)
CALL parser_release(parser)
CALL timestop(handle)
END SUBROUTINE read_cell_cif
! **************************************************************************************************
!> \brief Reads REAL from the CIF file.. This wrapper is needed in order to
!> treat properly the accuracy specified in the CIF file, i.e. 3.45(6)
!> \param parser ...
!> \param r ...
!> \date 12.2008
!> \author Teodoro Laino [tlaino]
! **************************************************************************************************
SUBROUTINE cif_get_real(parser, r)
TYPE(cp_parser_type), POINTER :: parser
REAL(KIND=dp), INTENT(OUT) :: r
CHARACTER(LEN=default_string_length) :: s_tag
INTEGER :: iln
CALL parser_get_object(parser, s_tag)
iln = LEN_TRIM(s_tag)
IF (INDEX(s_tag, "(") /= 0) iln = INDEX(s_tag, "(") - 1
READ (s_tag(1:iln), *) r
END SUBROUTINE cif_get_real
! **************************************************************************************************
!> \brief Write the cell parameters to the output unit.
!> \param cell ...
!> \param subsys_section ...
!> \param cell_ref ...
!> \param label ...
!> \date 02.06.2000
!> \par History
!> - 11.2008 Teodoro Laino [tlaino] - rewrite and enabling user driven units
!> \author Matthias Krack
!> \version 1.0
! **************************************************************************************************
RECURSIVE SUBROUTINE write_cell(cell, subsys_section, cell_ref, label)
TYPE(cell_type), POINTER :: cell
TYPE(section_vals_type), POINTER :: subsys_section
TYPE(cell_type), OPTIONAL, POINTER :: cell_ref
CHARACTER(LEN=*), INTENT(IN), OPTIONAL :: label
CHARACTER(LEN=default_string_length) :: my_label, unit_str
INTEGER :: output_unit
REAL(KIND=dp) :: alpha, beta, gamma, val
REAL(KIND=dp), DIMENSION(3) :: abc
TYPE(cp_logger_type), POINTER :: logger
TYPE(enumeration_type), POINTER :: enum
TYPE(keyword_type), POINTER :: keyword
TYPE(section_type), POINTER :: section
NULLIFY (enum)
NULLIFY (keyword)
NULLIFY (logger)
NULLIFY (section)
logger => cp_get_default_logger()
my_label = "CELL|"
IF (PRESENT(label)) my_label = TRIM(label)
output_unit = cp_print_key_unit_nr(logger, subsys_section, "PRINT%CELL", &
extension=".Log")
CALL section_vals_val_get(subsys_section, "PRINT%CELL%UNIT", c_val=unit_str)
IF (output_unit > 0) THEN
CALL get_cell(cell=cell, abc=abc, alpha=alpha, beta=beta, gamma=gamma)
WRITE (UNIT=output_unit, FMT='( )')
val = cp_unit_from_cp2k(cell%deth, TRIM(unit_str)//"^3")
WRITE (UNIT=output_unit, FMT="(T2,A,T61,F20.6)") &
TRIM(my_label)//" Volume ["//TRIM(unit_str)//"^3]:", val
val = cp_unit_from_cp2k(1.0_dp, TRIM(unit_str))
WRITE (UNIT=output_unit, FMT="(T2,A,T30,3F10.3,3X,A6,F12.6)") &
TRIM(my_label)//" Vector a ["//TRIM(unit_str)//"]:", cell%hmat(:, 1)*val, &
"|a| = ", abc(1)*val, &
TRIM(my_label)//" Vector b ["//TRIM(unit_str)//"]:", cell%hmat(:, 2)*val, &
"|b| = ", abc(2)*val, &
TRIM(my_label)//" Vector c ["//TRIM(unit_str)//"]:", cell%hmat(:, 3)*val, &
"|c| = ", abc(3)*val
WRITE (UNIT=output_unit, FMT="(T2,A,T69,F12.6)") &
TRIM(my_label)//" Angle (b,c), alpha [degree]: ", alpha, &
TRIM(my_label)//" Angle (a,c), beta [degree]: ", beta, &
TRIM(my_label)//" Angle (a,b), gamma [degree]: ", gamma
IF (cell%symmetry_id /= cell_sym_none) THEN
CALL create_cell_section(section)
keyword => section_get_keyword(section, "SYMMETRY")
CALL keyword_get(keyword, enum=enum)
WRITE (UNIT=output_unit, FMT="(T2,A,T61,A20)") &
TRIM(my_label)//" Requested initial symmetry: ", &
ADJUSTR(TRIM(enum_i2c(enum, cell%symmetry_id)))
CALL section_release(section)
END IF
IF (cell%orthorhombic) THEN
WRITE (UNIT=output_unit, FMT="(T2,A,T78,A3)") &
TRIM(my_label)//" Numerically orthorhombic: ", "YES"
ELSE
WRITE (UNIT=output_unit, FMT="(T2,A,T78,A3)") &
TRIM(my_label)//" Numerically orthorhombic: ", " NO"
END IF
END IF
CALL cp_print_key_finished_output(output_unit, logger, subsys_section, &
"PRINT%CELL")
IF (PRESENT(cell_ref)) THEN
CALL write_cell(cell_ref, subsys_section, label="CELL_REF|")
END IF
END SUBROUTINE write_cell
END MODULE cell_methods