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Two small patches for cell_methods.F and particle_methods.F (#5378)

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HE Zilong 2026-06-09 19:04:29 +08:00 • committed by GitHub
parent 4cf809f41f
commit f5ef6ceffd
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2 changed files with 21 additions and 10 deletions
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24
src/cell_methods.F
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@ -895,7 +895,8 @@ CONTAINS
CHARACTER(len=*), PARAMETER :: routineN = 'read_cell_extxyz'
INTEGER :: handle, i, id1, id2, j
CHARACTER(len=default_path_length) :: raw_cell_str
INTEGER :: handle, i, id1, id2, ios, j
REAL(KIND=dp), DIMENSION(3, 3) :: hmat
TYPE(cp_parser_type) :: parser
@ -908,7 +909,13 @@ CONTAINS
id1 = INDEX(parser%input_line, "LATTICE=")
IF (id1 > 0) THEN
id2 = INDEX(parser%input_line(id1 + 9:), '"')
READ (parser%input_line(id1 + 9:id1 + id2 + 7), *) hmat(:, 1), hmat(:, 2), hmat(:, 3)
READ (parser%input_line(id1 + 9:id1 + id2 + 7), '(A)') raw_cell_str
READ (raw_cell_str, *, IOSTAT=ios) hmat(:, 1), hmat(:, 2), hmat(:, 3)
IF (ios /= 0) THEN
CALL cp_abort(__LOCATION__, "Error while parsing extended XYZ file "// &
"<"//TRIM(extxyz_file_name)//"> for cell vectors: "// &
"found <lattice=> field as <"//TRIM(raw_cell_str)//">")
END IF
DO i = 1, 3
DO j = 1, 3
cell%hmat(j, i) = cp_unit_to_cp2k(hmat(j, i), "angstrom")
@ -917,7 +924,7 @@ CONTAINS
ELSE
CALL cp_abort(__LOCATION__, &
"The field (lattice=) was not found on comment line "// &
"The field <lattice=> was not found on comment line "// &
"of XYZ file, so cell information cannot be set via "// &
"extended XYZ specification! ")
END IF
@ -955,7 +962,7 @@ CONTAINS
CHARACTER(len=*), PARAMETER :: routineN = 'read_cell_pdb'
CHARACTER(LEN=default_string_length) :: cryst
INTEGER :: handle, i
INTEGER :: handle, i, ios
INTEGER, DIMENSION(3) :: periodic
LOGICAL :: found
REAL(KIND=dp), DIMENSION(3) :: cell_angles, cell_lengths
@ -969,10 +976,15 @@ CONTAINS
CALL parser_search_string(parser, "CRYST1", ignore_case=.FALSE., found=found, &
begin_line=.TRUE., search_from_begin_of_file=.TRUE.)
IF (.NOT. found) &
CPABORT("The field (CRYST1) was not found in PDB file! ")
CPABORT("The line <CRYST1> was not found in PDB file! ")
periodic = 1
READ (parser%input_line, *) cryst, cell_lengths(:), cell_angles(:)
READ (parser%input_line, *, IOSTAT=ios) cryst, cell_lengths(:), cell_angles(:)
IF (ios /= 0) THEN
CALL cp_abort(__LOCATION__, "Error while parsing PDB file "// &
"<"//TRIM(pdb_file_name)//"> for cell lengths and angles: "// &
"found CRYST1 line as <"//TRIM(parser%input_line)//">")
END IF
DO i = 1, 3
cell_lengths(i) = cp_unit_to_cp2k(cell_lengths(i), "angstrom")
cell_angles(i) = cp_unit_to_cp2k(cell_angles(i), "deg")

7
src/particle_methods.F
View file

@ -1407,11 +1407,10 @@ CONTAINS
"_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)
! positive_range=.TRUE. makes r(1:3) in [0, cell%hmat(i,i)] and
! s(1:3) in [0, 1], so there is no need to MODULO s(1:3) by 1.0
r(1:3) = pbc(particle_set(iatom)%r(1:3), cell, positive_range=.TRUE.)
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