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Generalize FINAL_CIF to FINAL_STRUCTURE with XYZ output (#5140)
This commit is contained in:
HE Zilong
GitHub
parent
92364bbe53
commit
223025a8ce
3 changed files with 261 additions and 176 deletions
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@ -144,13 +144,32 @@ CONTAINS
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CALL section_add_subsection(section, print_key)
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CALL section_release(print_key)
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CALL cp_print_key_section_create(print_key, __LOCATION__, "FINAL_CIF", &
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description="Controls the dumping of a CIF containing "// &
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"the final geometry and cell for optimization tasks. "// &
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"Currently the structure will always be dumped with "// &
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"the space group `P 1` and a single symmetry-equivalent "// &
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"position `x, y, z` for all of the atoms.", &
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CALL cp_print_key_section_create(print_key, __LOCATION__, "FINAL_STRUCTURE", &
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description="Controls the dumping of the final "// &
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"geometry and cell for optimization tasks. ", &
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print_level=low_print_level, filename="FINAL")
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CALL keyword_create(keyword, __LOCATION__, name="PRINT_CIF", &
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description="Print the final structure as CIF. Currently the "// &
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"structure will always be dumped with the space "// &
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"group `P 1` and a single symmetry-equivalent "// &
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"position `x, y, z` for all of the atoms.", &
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usage="PRINT_CIF T", default_l_val=.TRUE., &
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lone_keyword_l_val=.TRUE.)
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CALL section_add_keyword(print_key, keyword)
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CALL keyword_release(keyword)
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CALL keyword_create(keyword, __LOCATION__, name="PRINT_XYZ", &
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description="Print the final structure as XYZ. The cell "// &
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"information is available in the comment line according "// &
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"to the extended XYZ specification as the `Lattice=...` "// &
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"field, and the unit is angstrom for both the cell vectors "// &
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"and the atomic coordinates.", &
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usage="PRINT_XYZ T", default_l_val=.TRUE., &
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lone_keyword_l_val=.TRUE.)
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CALL section_add_keyword(print_key, keyword)
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CALL keyword_release(keyword)
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CALL section_add_subsection(section, print_key)
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CALL section_release(print_key)
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@ -67,7 +67,7 @@ MODULE gopt_f_methods
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write_stress_tensor_to_file, &
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write_trajectory
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USE particle_list_types, ONLY: particle_list_type
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USE particle_methods, ONLY: write_final_cif, &
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USE particle_methods, ONLY: write_final_structure, &
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write_structure_data
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USE particle_types, ONLY: particle_type
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USE qmmm_util, ONLY: apply_qmmm_translate
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@ -878,7 +878,7 @@ CONTAINS
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particle_set => particles%els
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! Passing gopt_f_type pointer gopt_env to particle_methods where
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! write_final_cif is defined causes a circular dependency, so it
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! write_final_structure is defined causes a circular dependency, so it
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! is necessary to get some flags by preprocessing...
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keep_angles = .TRUE.
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keep_symmetry = .TRUE.
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@ -905,9 +905,9 @@ CONTAINS
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constraint_label = "NONE"
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END SELECT
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END IF
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CALL write_final_cif(particle_set, cell, motion_section, conv, &
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keep_angles, keep_symmetry, keep_volume, &
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gopt_env%label, constraint_label)
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CALL write_final_structure(particle_set, cell, motion_section, conv, &
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keep_angles, keep_symmetry, keep_volume, &
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gopt_env%label, constraint_label)
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IF (conv) THEN
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it = it + 1
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@ -93,7 +93,7 @@ MODULE particle_methods
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write_structure_data, &
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get_particle_set, &
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write_particle_matrix, &
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write_final_cif
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write_final_structure
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CHARACTER(len=*), PARAMETER, PRIVATE :: moduleN = 'particle_methods'
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@ -1032,10 +1032,10 @@ CONTAINS
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END SUBROUTINE write_structure_data
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! **************************************************************************************************
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!> \brief Write the final geometry and cell information to a CIF file
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!> \brief Write the final geometry and cell information to files
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!> \param particle_set pointer to particles with atm_name, element_symbol and position
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!> \param cell pointer to cell with abc, angle_alpha, angle_beta, angle_gamma and deth
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!> \param input_section pointer to motion_section which has PRINT%FINAL_CIF
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!> \param input_section pointer to motion_section which has PRINT%FINAL_STRUCTURE
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!> \param conv flag for whether convergence is achieved or not in optimization
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!> \param keep_angles flag for whether cell optimization keeps initial angles
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!> \param keep_symmetry flag for whether cell optimization keeps initial symmetry
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@ -1056,9 +1056,9 @@ CONTAINS
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!> \author HE Zilong
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!> \version 1.0
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! **************************************************************************************************
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SUBROUTINE write_final_cif(particle_set, cell, input_section, conv, &
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keep_angles, keep_symmetry, keep_volume, &
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gopt_env_label, constraint_label)
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SUBROUTINE write_final_structure(particle_set, cell, input_section, conv, &
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keep_angles, keep_symmetry, keep_volume, &
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gopt_env_label, constraint_label)
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TYPE(particle_type), DIMENSION(:), POINTER :: particle_set
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TYPE(cell_type), INTENT(IN), POINTER :: cell
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TYPE(section_vals_type), INTENT(IN), POINTER :: input_section
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@ -1067,22 +1067,24 @@ CONTAINS
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CHARACTER(LEN=default_string_length), INTENT(IN) :: gopt_env_label
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CHARACTER(LEN=4), INTENT(IN) :: constraint_label
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CHARACTER(len=*), PARAMETER :: routineN = 'write_final_cif'
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CHARACTER(len=*), PARAMETER :: routineN = 'write_final_structure'
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CHARACTER(LEN=2) :: element_symbol
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CHARACTER(LEN=2), ALLOCATABLE :: element_list(:)
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CHARACTER(LEN=4) :: perd_str
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CHARACTER(LEN=5) :: perd_str
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CHARACTER(LEN=:), ALLOCATABLE :: formula_structural, formula_sum
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CHARACTER(LEN=default_path_length) :: record
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CHARACTER(LEN=default_string_length) :: atm_name, f_cif, f_label, f_type_symbol
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CHARACTER(LEN=default_string_length), ALLOCATABLE :: label(:), type_symbol(:)
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CHARACTER(LEN=default_path_length) :: cell_str, record
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CHARACTER(LEN=default_string_length) :: atm_name, f_cif, f_cif_label, &
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f_cif_type_symbol, f_xyz
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CHARACTER(LEN=default_string_length), ALLOCATABLE :: cif_label(:), cif_type_symbol(:), &
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xyz_label(:)
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CHARACTER(LEN=timestamp_length) :: timestamp
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INTEGER :: elem_seen, file_unit, gcd_all, handle, &
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i, iatom, ielem, natom, output_unit, &
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symmetry_id, w_label, w_type_symbol
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INTEGER :: elem_seen, file_unit, gcd_all, handle, i, iatom, ielem, natom, output_unit, &
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symmetry_id, w_cif_label, w_cif_type_symbol, w_xyz_label
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INTEGER, ALLOCATABLE :: count_list(:)
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INTEGER, DIMENSION(3) :: periodic
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LOGICAL :: dummy, elem_in_list, orthorhombic
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LOGICAL :: dummy, elem_in_list, orthorhombic, &
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write_cif, write_xyz
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REAL(KIND=dp) :: angle_alpha, angle_beta, angle_gamma, &
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deth
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REAL(KIND=dp), DIMENSION(3) :: abc, r, s
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@ -1098,44 +1100,56 @@ CONTAINS
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NULLIFY (enum, logger, symmetry_keyword, print_key, tmp_cell_section)
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logger => cp_get_default_logger()
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output_unit = cp_logger_get_default_io_unit(logger)
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print_key => section_vals_get_subs_vals(input_section, "PRINT%FINAL_CIF")
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print_key => section_vals_get_subs_vals(input_section, "PRINT%FINAL_STRUCTURE")
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! Collect cell information
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perd_str = "NONE"
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perd_str = "F F F"
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CALL get_cell(cell, alpha=angle_alpha, beta=angle_beta, gamma=angle_gamma, &
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deth=deth, orthorhombic=orthorhombic, abc=abc, periodic=periodic, &
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h=hmat, symmetry_id=symmetry_id)
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IF (SUM(periodic(1:3)) /= 0) THEN
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perd_str = ""
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IF (periodic(1) == 1) perd_str = TRIM(perd_str)//"X"
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IF (periodic(2) == 1) perd_str = TRIM(perd_str)//"Y"
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IF (periodic(3) == 1) perd_str = TRIM(perd_str)//"Z"
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END IF
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IF (periodic(1) == 1) perd_str(1:1) = "T"
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IF (periodic(2) == 1) perd_str(3:3) = "T"
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IF (periodic(3) == 1) perd_str(5:5) = "T"
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CALL create_cell_section(tmp_cell_section)
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symmetry_keyword => section_get_keyword(tmp_cell_section, "SYMMETRY")
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CALL keyword_get(symmetry_keyword, enum=enum)
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! cell_str is default_path_length which is longer
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! than default_string_length and should be enough
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WRITE (UNIT=cell_str, FMT="(9(1X,F19.10))") &
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cp_unit_from_cp2k(hmat(1, 1), "angstrom"), &
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cp_unit_from_cp2k(hmat(2, 1), "angstrom"), &
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cp_unit_from_cp2k(hmat(3, 1), "angstrom"), &
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cp_unit_from_cp2k(hmat(1, 2), "angstrom"), &
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cp_unit_from_cp2k(hmat(2, 2), "angstrom"), &
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cp_unit_from_cp2k(hmat(3, 2), "angstrom"), &
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cp_unit_from_cp2k(hmat(1, 3), "angstrom"), &
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cp_unit_from_cp2k(hmat(2, 3), "angstrom"), &
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cp_unit_from_cp2k(hmat(3, 3), "angstrom")
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! Collect atom information
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natom = SIZE(particle_set)
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ALLOCATE (element_list(nelem + 1), count_list(nelem + 1))
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count_list(:) = 0
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ALLOCATE (label(natom), type_symbol(natom))
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ALLOCATE (cif_label(natom), cif_type_symbol(natom), xyz_label(natom))
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elem_seen = 0
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w_type_symbol = 0
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w_label = 0
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w_cif_type_symbol = 0
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w_cif_label = 0
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w_xyz_label = 0
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atom_loop: DO iatom = 1, natom
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elem_in_list = .FALSE.
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CALL get_atomic_kind(atomic_kind=particle_set(iatom)%atomic_kind, &
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name=atm_name, element_symbol=element_symbol)
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type_symbol(iatom) = TRIM(atm_name)
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cif_type_symbol(iatom) = TRIM(atm_name)
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! From write_particle_coordinates above it seems possible
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! for some atoms to have empty element symbols; whatever
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! these are, do not count them in the chemical formula
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IF (LEN_TRIM(element_symbol) == 0) THEN
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dummy = qmmm_ff_precond_only_qm(id1=atm_name)
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label(iatom) = TRIM(atm_name)//TRIM(ADJUSTL(cp_to_string(iatom)))
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cif_label(iatom) = TRIM(atm_name)//TRIM(ADJUSTL(cp_to_string(iatom)))
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xyz_label(iatom) = TRIM(atm_name)
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ELSE
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label(iatom) = TRIM(element_symbol)//TRIM(ADJUSTL(cp_to_string(iatom)))
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cif_label(iatom) = TRIM(element_symbol)//TRIM(ADJUSTL(cp_to_string(iatom)))
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xyz_label(iatom) = TRIM(element_symbol)
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elem_loop: DO ielem = 1, nelem + 1
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IF (element_list(ielem) == element_symbol) THEN
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elem_in_list = .TRUE.
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@ -1149,13 +1163,15 @@ CONTAINS
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count_list(elem_seen) = 1
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END IF
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END IF
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IF (LEN_TRIM(type_symbol(iatom)) > w_type_symbol) &
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w_type_symbol = LEN_TRIM(type_symbol(iatom))
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IF (LEN_TRIM(label(iatom)) > w_label) &
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w_label = LEN_TRIM(label(iatom))
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IF (LEN_TRIM(cif_type_symbol(iatom)) > w_cif_type_symbol) &
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w_cif_type_symbol = LEN_TRIM(cif_type_symbol(iatom))
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IF (LEN_TRIM(cif_label(iatom)) > w_cif_label) &
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w_cif_label = LEN_TRIM(cif_label(iatom))
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IF (LEN_TRIM(xyz_label(iatom)) > w_xyz_label) &
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w_xyz_label = LEN_TRIM(xyz_label(iatom))
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END DO atom_loop
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! Determine the format of each line in cif considering width of type_symbol and label
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! Determine the format of each line in cif considering width of cif_type_symbol and cif_label
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! The fields are, in order:
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! _atom_site_type_symbol, _atom_site_label, _atom_site_symmetry_multiplicity,
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! _atom_site_fract_x, _atom_site_fract_y, _atom_site_fract_z, _atom_site_occupancy
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@ -1163,9 +1179,12 @@ CONTAINS
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! _atom_site_type_symbol is taken as atm_name
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! _atom_site_label is taken as element_symbol//iatom
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! _atom_site_symmetry_multiplicity and _atom_site_occupancy are always 1
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f_type_symbol = "A"//TRIM(ADJUSTL(cp_to_string(w_type_symbol + 4)))
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f_label = "A"//TRIM(ADJUSTL(cp_to_string(w_label + 4)))
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f_cif = "(T3,"//TRIM(f_type_symbol)//","//TRIM(f_label)//",I4,3F14.8,F8.2)"
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f_cif_type_symbol = "A"//TRIM(ADJUSTL(cp_to_string(w_cif_type_symbol + 4)))
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f_cif_label = "A"//TRIM(ADJUSTL(cp_to_string(w_cif_label + 4)))
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f_cif = "(T3,"//TRIM(f_cif_type_symbol)//","//TRIM(f_cif_label)//",I4,3F14.8,F8.2)"
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! Determine the format of each line in xyz
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f_xyz = "(T2,A"//TRIM(ADJUSTL(cp_to_string(w_xyz_label + 4)))//",1X,3F20.10)"
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! Determine formula_sum
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CPASSERT(elem_seen > 0)
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@ -1194,156 +1213,203 @@ CONTAINS
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END DO
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formula_structural = TRIM(ADJUSTL(formula_structural))//"'"
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! Print a message to log
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record = cp_print_key_generate_filename(logger, print_key, &
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extension=".cif", &
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my_local=.FALSE.)
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IF (output_unit > 0) THEN
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IF (conv) THEN
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WRITE (UNIT=output_unit, FMT="(/,T2,A)") &
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routineN//": Optimization converged, writing CIF file gladly:"
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ELSE
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WRITE (UNIT=output_unit, FMT="(/,T2,A)") &
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routineN//": Optimization not yet converged, writing CIF file anyway:"
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! Write XYZ
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CALL section_vals_val_get(print_key, "PRINT_XYZ", l_val=write_xyz)
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IF (write_xyz) THEN
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! Print a message to log
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record = cp_print_key_generate_filename(logger, print_key, &
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extension=".xyz", &
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my_local=.FALSE.)
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IF (output_unit > 0) THEN
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IF (conv) THEN
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WRITE (UNIT=output_unit, FMT="(/,T2,A)") &
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routineN//": Optimization converged, writing XYZ file gladly:"
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ELSE
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WRITE (UNIT=output_unit, FMT="(/,T2,A)") &
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routineN//": Optimization not yet converged, writing XYZ file anyway:"
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END IF
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WRITE (UNIT=output_unit, FMT="(T3,A)") TRIM(record)
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END IF
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! Make timestamp for the file
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CALL m_timestamp(timestamp)
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! Prepare file unit and write to it
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file_unit = cp_print_key_unit_nr(logger, input_section, "PRINT%FINAL_STRUCTURE", &
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file_status="REPLACE", extension=".xyz")
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IF (file_unit > 0) THEN
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WRITE (UNIT=file_unit, FMT="(I8)") &
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natom
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WRITE (UNIT=file_unit, FMT="(A)") &
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'Lattice="'//TRIM(ADJUSTL(cell_str))// &
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'" Properties=species:S:1:pos:R:3 pbc="'// &
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TRIM(perd_str)//'"'
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DO iatom = 1, natom
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DO i = 1, 3
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r(i) = cp_unit_from_cp2k(particle_set(iatom)%r(i), "angstrom")
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END DO
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WRITE (UNIT=file_unit, FMT=TRIM(f_xyz)) &
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xyz_label(iatom), r(1:3)
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END DO
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END IF
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WRITE (UNIT=output_unit, FMT="(T3,A)") TRIM(record)
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END IF
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! Make timestamp for the file
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CALL m_timestamp(timestamp)
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! Write CIF
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CALL section_vals_val_get(print_key, "PRINT_CIF", l_val=write_cif)
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IF (write_cif) THEN
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! Print a message to log
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record = cp_print_key_generate_filename(logger, print_key, &
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extension=".cif", &
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my_local=.FALSE.)
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IF (output_unit > 0) THEN
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IF (conv) THEN
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WRITE (UNIT=output_unit, FMT="(/,T2,A)") &
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routineN//": Optimization converged, writing CIF file gladly:"
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ELSE
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WRITE (UNIT=output_unit, FMT="(/,T2,A)") &
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routineN//": Optimization not yet converged, writing CIF file anyway:"
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END IF
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WRITE (UNIT=output_unit, FMT="(T3,A)") TRIM(record)
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END IF
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! Prepare file unit and write to it
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file_unit = cp_print_key_unit_nr(logger, input_section, "PRINT%FINAL_CIF", &
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file_status="REPLACE", extension=".cif")
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IF (file_unit > 0) THEN
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! Generic information
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WRITE (UNIT=file_unit, FMT="(A)") &
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"# CIF file created by CP2K "//TRIM(moduleN)//":"//TRIM(routineN)
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WRITE (UNIT=file_unit, FMT="(A)") &
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"data_"//TRIM(logger%iter_info%project_name)
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WRITE (UNIT=file_unit, FMT="(A,T39,A)") &
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"_audit_creation_date", timestamp(:10)
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WRITE (UNIT=file_unit, FMT="(A,/,A,/,A)") &
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"_audit_creation_method", ";", &
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TRIM(cp2k_version)//" (revision "//TRIM(compile_revision)//")"
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WRITE (UNIT=file_unit, FMT="(A,/,A,/,A,/,A)") &
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"Project name "//TRIM(logger%iter_info%project_name), &
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"submitted by "//TRIM(r_user_name)//"@"//TRIM(r_host_name), &
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"processed in "//TRIM(r_cwd), &
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"generated at "//TRIM(timestamp)
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WRITE (UNIT=file_unit, FMT="(T2,A)") &
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"- Optimization type: "//TRIM(gopt_env_label)
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IF (conv) THEN
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! Make timestamp for the file
|
||||
CALL m_timestamp(timestamp)
|
||||
|
||||
! Prepare file unit and write to it
|
||||
file_unit = cp_print_key_unit_nr(logger, input_section, "PRINT%FINAL_STRUCTURE", &
|
||||
file_status="REPLACE", extension=".cif")
|
||||
IF (file_unit > 0) THEN
|
||||
! Generic information
|
||||
WRITE (UNIT=file_unit, FMT="(A)") &
|
||||
"# CIF file created by CP2K "//TRIM(moduleN)//":"//TRIM(routineN)
|
||||
WRITE (UNIT=file_unit, FMT="(A)") &
|
||||
"data_"//TRIM(logger%iter_info%project_name)
|
||||
WRITE (UNIT=file_unit, FMT="(A,T39,A)") &
|
||||
"_audit_creation_date", timestamp(:10)
|
||||
WRITE (UNIT=file_unit, FMT="(A,/,A,/,A)") &
|
||||
"_audit_creation_method", ";", &
|
||||
TRIM(cp2k_version)//" (revision "//TRIM(compile_revision)//")"
|
||||
WRITE (UNIT=file_unit, FMT="(A,/,A,/,A,/,A)") &
|
||||
"Project name "//TRIM(logger%iter_info%project_name), &
|
||||
"submitted by "//TRIM(r_user_name)//"@"//TRIM(r_host_name), &
|
||||
"processed in "//TRIM(r_cwd), &
|
||||
"generated at "//TRIM(timestamp)
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Optimization converged: TRUE"
|
||||
ELSE
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Optimization converged: FALSE"
|
||||
END IF
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Requested initial cell symmetry: "//TRIM(enum_i2c(enum, symmetry_id))
|
||||
IF (orthorhombic) THEN
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Cell is numerically orthorhombic: TRUE"
|
||||
ELSE
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Cell is numerically orthorhombic: FALSE"
|
||||
END IF
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Periodicity of cell: "//TRIM(perd_str)
|
||||
IF (gopt_env_label == "CELL_OPT") THEN
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Cell is subject to optimization: TRUE"
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Cell has constraint on direction: "//TRIM(ADJUSTL(constraint_label))
|
||||
IF (keep_angles) THEN
|
||||
"- Optimization type: "//TRIM(gopt_env_label)
|
||||
IF (conv) THEN
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Keep angles between the cell vectors during optimization: TRUE"
|
||||
"- Optimization converged: TRUE"
|
||||
ELSE
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Keep angles between the cell vectors during optimization: FALSE"
|
||||
"- Optimization converged: FALSE"
|
||||
END IF
|
||||
IF (keep_symmetry) THEN
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Keep initial cell symmetry during optimization: TRUE"
|
||||
ELSE
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Keep initial cell symmetry during optimization: FALSE"
|
||||
END IF
|
||||
IF (keep_volume) THEN
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Keep initial cell volume during optimization: TRUE"
|
||||
ELSE
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Keep initial cell volume during optimization: FALSE"
|
||||
END IF
|
||||
ELSE
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Cell is subject to optimization: FALSE"
|
||||
END IF
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Final cell vectors A, B, C by rows [angstrom]:"
|
||||
DO i = 1, 3
|
||||
WRITE (UNIT=file_unit, FMT="(T3,3(1X,F19.10))") &
|
||||
cp_unit_from_cp2k(hmat(1, i), "angstrom"), &
|
||||
cp_unit_from_cp2k(hmat(2, i), "angstrom"), &
|
||||
cp_unit_from_cp2k(hmat(3, i), "angstrom")
|
||||
END DO
|
||||
WRITE (UNIT=file_unit, FMT="(A)") ";"
|
||||
! Data of cell and geometry
|
||||
WRITE (UNIT=file_unit, FMT="(/,A,T44,A)") &
|
||||
"_symmetry_space_group_name_H-M", "'P 1'"
|
||||
WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
|
||||
"_cell_length_a", cp_unit_from_cp2k(abc(1), "angstrom")
|
||||
WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
|
||||
"_cell_length_b", cp_unit_from_cp2k(abc(2), "angstrom")
|
||||
WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
|
||||
"_cell_length_c", cp_unit_from_cp2k(abc(3), "angstrom")
|
||||
WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
|
||||
"_cell_angle_alpha", angle_alpha
|
||||
WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
|
||||
"_cell_angle_beta", angle_beta
|
||||
WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
|
||||
"_cell_angle_gamma", angle_gamma
|
||||
WRITE (UNIT=file_unit, FMT="(A,T48,A)") &
|
||||
"_symmetry_Int_Tables_number", "1"
|
||||
WRITE (UNIT=file_unit, FMT="(A,T36,A)") &
|
||||
"_chemical_formula_structural", formula_structural
|
||||
WRITE (UNIT=file_unit, FMT="(A,T36,A)") &
|
||||
"_chemical_formula_sum", formula_sum
|
||||
WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
|
||||
"_cell_volume", cp_unit_from_cp2k(ABS(deth), "angstrom^3")
|
||||
WRITE (UNIT=file_unit, FMT="(A,T41,I8)") &
|
||||
"_cell_formula_units_Z", gcd_all
|
||||
WRITE (UNIT=file_unit, FMT="(A,/,T2,A,/,T2,A,/,T3,A)") &
|
||||
"loop_", "_symmetry_equiv_pos_site_id", &
|
||||
"_symmetry_equiv_pos_as_xyz", "1 'x, y, z'"
|
||||
WRITE (UNIT=file_unit, FMT="(A,/,T2,A,/,T2,A,/,T2,A,/,T2,A,/,T2,A,/,T2,A,/,T2,A)") &
|
||||
"loop_", "_atom_site_type_symbol", "_atom_site_label", &
|
||||
"_atom_site_symmetry_multiplicity", "_atom_site_fract_x", &
|
||||
"_atom_site_fract_y", "_atom_site_fract_z", "_atom_site_occupancy"
|
||||
DO iatom = 1, natom
|
||||
r(1:3) = pbc(particle_set(iatom)%r(1:3), cell)
|
||||
CALL real_to_scaled(s, r, cell)
|
||||
"- Requested initial cell symmetry: "//TRIM(enum_i2c(enum, symmetry_id))
|
||||
IF (orthorhombic) THEN
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Cell is numerically orthorhombic: TRUE"
|
||||
ELSE
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Cell is numerically orthorhombic: FALSE"
|
||||
END IF
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Periodicity of cell: "//TRIM(perd_str)
|
||||
IF (gopt_env_label == "CELL_OPT") THEN
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Cell is subject to optimization: TRUE"
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Cell has constraint on direction: "//TRIM(ADJUSTL(constraint_label))
|
||||
IF (keep_angles) THEN
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Keep angles between the cell vectors during optimization: TRUE"
|
||||
ELSE
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Keep angles between the cell vectors during optimization: FALSE"
|
||||
END IF
|
||||
IF (keep_symmetry) THEN
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Keep initial cell symmetry during optimization: TRUE"
|
||||
ELSE
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Keep initial cell symmetry during optimization: FALSE"
|
||||
END IF
|
||||
IF (keep_volume) THEN
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Keep initial cell volume during optimization: TRUE"
|
||||
ELSE
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Keep initial cell volume during optimization: FALSE"
|
||||
END IF
|
||||
ELSE
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Cell is subject to optimization: FALSE"
|
||||
END IF
|
||||
WRITE (UNIT=file_unit, FMT="(T2,A)") &
|
||||
"- Final cell vectors A, B, C by rows [angstrom]:"
|
||||
DO i = 1, 3
|
||||
s(i) = MODULO(s(i), 1.0_dp)
|
||||
WRITE (UNIT=file_unit, FMT="(T3,3(1X,F19.10))") &
|
||||
cp_unit_from_cp2k(hmat(1, i), "angstrom"), &
|
||||
cp_unit_from_cp2k(hmat(2, i), "angstrom"), &
|
||||
cp_unit_from_cp2k(hmat(3, i), "angstrom")
|
||||
END DO
|
||||
WRITE (UNIT=file_unit, FMT=TRIM(f_cif)) &
|
||||
type_symbol(iatom), label(iatom), 1, s(1:3), 1.0_dp
|
||||
END DO
|
||||
WRITE (UNIT=file_unit, FMT="(A)") ";"
|
||||
! Data of cell and geometry
|
||||
WRITE (UNIT=file_unit, FMT="(/,A,T44,A)") &
|
||||
"_symmetry_space_group_name_H-M", "'P 1'"
|
||||
WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
|
||||
"_cell_length_a", cp_unit_from_cp2k(abc(1), "angstrom")
|
||||
WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
|
||||
"_cell_length_b", cp_unit_from_cp2k(abc(2), "angstrom")
|
||||
WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
|
||||
"_cell_length_c", cp_unit_from_cp2k(abc(3), "angstrom")
|
||||
WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
|
||||
"_cell_angle_alpha", angle_alpha
|
||||
WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
|
||||
"_cell_angle_beta", angle_beta
|
||||
WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
|
||||
"_cell_angle_gamma", angle_gamma
|
||||
WRITE (UNIT=file_unit, FMT="(A,T48,A)") &
|
||||
"_symmetry_Int_Tables_number", "1"
|
||||
WRITE (UNIT=file_unit, FMT="(A,T36,A)") &
|
||||
"_chemical_formula_structural", formula_structural
|
||||
WRITE (UNIT=file_unit, FMT="(A,T36,A)") &
|
||||
"_chemical_formula_sum", formula_sum
|
||||
WRITE (UNIT=file_unit, FMT="(A,T31,F18.8)") &
|
||||
"_cell_volume", cp_unit_from_cp2k(ABS(deth), "angstrom^3")
|
||||
WRITE (UNIT=file_unit, FMT="(A,T41,I8)") &
|
||||
"_cell_formula_units_Z", gcd_all
|
||||
WRITE (UNIT=file_unit, FMT="(A,/,T2,A,/,T2,A,/,T3,A)") &
|
||||
"loop_", "_symmetry_equiv_pos_site_id", &
|
||||
"_symmetry_equiv_pos_as_xyz", "1 'x, y, z'"
|
||||
WRITE (UNIT=file_unit, FMT="(A,/,T2,A,/,T2,A,/,T2,A,/,T2,A,/,T2,A,/,T2,A,/,T2,A)") &
|
||||
"loop_", "_atom_site_type_symbol", "_atom_site_label", &
|
||||
"_atom_site_symmetry_multiplicity", "_atom_site_fract_x", &
|
||||
"_atom_site_fract_y", "_atom_site_fract_z", "_atom_site_occupancy"
|
||||
DO iatom = 1, natom
|
||||
r(1:3) = pbc(particle_set(iatom)%r(1:3), cell)
|
||||
CALL real_to_scaled(s, r, cell)
|
||||
DO i = 1, 3
|
||||
s(i) = MODULO(s(i), 1.0_dp)
|
||||
END DO
|
||||
WRITE (UNIT=file_unit, FMT=TRIM(f_cif)) &
|
||||
cif_type_symbol(iatom), cif_label(iatom), 1, s(1:3), 1.0_dp
|
||||
END DO
|
||||
END IF
|
||||
END IF
|
||||
|
||||
! Finish
|
||||
DEALLOCATE (element_list, count_list, formula_structural, formula_sum, label, type_symbol)
|
||||
DEALLOCATE (element_list, count_list, formula_structural, &
|
||||
formula_sum, cif_label, cif_type_symbol, &
|
||||
xyz_label)
|
||||
CALL section_release(tmp_cell_section)
|
||||
CALL cp_print_key_finished_output(file_unit, logger, input_section, &
|
||||
"PRINT%FINAL_CIF")
|
||||
"PRINT%FINAL_STRUCTURE")
|
||||
IF (output_unit > 0) &
|
||||
WRITE (UNIT=output_unit, FMT='(/,T2,A)') &
|
||||
routineN//": Done!"
|
||||
|
||||
CALL timestop(handle)
|
||||
|
||||
END SUBROUTINE write_final_cif
|
||||
END SUBROUTINE write_final_structure
|
||||
|
||||
END MODULE particle_methods
|
||||
|
|
|
|||
Loading…
Add table
Add a link
Reference in a new issue