comp-chem/cp2k
1
0
Fork 0
mirror of https://github.com/cp2k/cp2k.git synced 2026-07-28 22:25:32 -04:00
Code Issues Projects Releases Packages Wiki Activity Actions

Molden: Replace [Nval] with [Pseudo] and enable marking ghost atoms (#5226)

Browse source
This commit is contained in:
SY Wang 2026-05-17 23:15:38 +08:00 • committed by GitHub
parent 16ac5b65f8
commit ef9d0990c2
No known key found for this signature in database
GPG key ID: B5690EEEBB952194
3 changed files with 68 additions and 25 deletions
Download patch file Download diff file Expand all files Collapse all files

52
src/input_cp2k_print_dft.F
View file

@ -616,9 +616,16 @@ CONTAINS
default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(print_key, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="WRITE_NVAL", &
description="Controls whether the [Nval] block is written to the MOLDEN file.", &
usage="WRITE_NVAL T", &
CALL keyword_create(keyword, __LOCATION__, name="WRITE_PSEUDO", &
description="Controls whether the [Pseudo] block is written to the MOLDEN file.", &
usage="WRITE_PSEUDO T", &
default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(print_key, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="MARK_GHOST", &
description="Controls whether ghost atoms are marked in the [Atoms] block by "// &
"setting their atomic number to zero.", &
usage="MARK_GHOST T", &
default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(print_key, keyword)
CALL keyword_release(keyword)
@ -1491,9 +1498,16 @@ CONTAINS
default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(sub_print_key, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="WRITE_NVAL", &
description="Controls whether the [Nval] block is written to the MOLDEN file.", &
usage="WRITE_NVAL T", &
CALL keyword_create(keyword, __LOCATION__, name="WRITE_PSEUDO", &
description="Controls whether the [Pseudo] block is written to the MOLDEN file.", &
usage="WRITE_PSEUDO T", &
default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(sub_print_key, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="MARK_GHOST", &
description="Controls whether ghost atoms are marked in the [Atoms] block by "// &
"setting their atomic number to zero.", &
usage="MARK_GHOST T", &
default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(sub_print_key, keyword)
CALL keyword_release(keyword)
@ -1598,9 +1612,16 @@ CONTAINS
default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(sub_print_key, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="WRITE_NVAL", &
description="Controls whether the [Nval] block is written to the MOLDEN file.", &
usage="WRITE_NVAL T", &
CALL keyword_create(keyword, __LOCATION__, name="WRITE_PSEUDO", &
description="Controls whether the [Pseudo] block is written to the MOLDEN file.", &
usage="WRITE_PSEUDO T", &
default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(sub_print_key, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="MARK_GHOST", &
description="Controls whether ghost atoms are marked in the [Atoms] block by "// &
"setting their atomic number to zero.", &
usage="MARK_GHOST T", &
default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(sub_print_key, keyword)
CALL keyword_release(keyword)
@ -1743,9 +1764,16 @@ CONTAINS
default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(subsection, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="WRITE_NVAL", &
description="Controls whether the [Nval] block is written to the MOLDEN file.", &
usage="WRITE_NVAL T", &
CALL keyword_create(keyword, __LOCATION__, name="WRITE_PSEUDO", &
description="Controls whether the [Pseudo] block is written to the MOLDEN file.", &
usage="WRITE_PSEUDO T", &
default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(subsection, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="MARK_GHOST", &
description="Controls whether ghost atoms are marked in the [Atoms] block by "// &
"setting their atomic number to zero.", &
usage="MARK_GHOST T", &
default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(subsection, keyword)
CALL keyword_release(keyword)

13
src/input_cp2k_properties_dft.F
View file

@ -2081,9 +2081,16 @@ CONTAINS
default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(print_key, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="WRITE_NVAL", &
description="Controls whether the [Nval] block is written to the MOLDEN file.", &
usage="WRITE_NVAL TRUE", &
CALL keyword_create(keyword, __LOCATION__, name="WRITE_PSEUDO", &
description="Controls whether the [Pseudo] block is written to the MOLDEN file.", &
usage="WRITE_PSEUDO TRUE", &
default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(print_key, keyword)
CALL keyword_release(keyword)
CALL keyword_create(keyword, __LOCATION__, name="MARK_GHOST", &
description="Controls whether ghost atoms are marked in the [Atoms] block by "// &
"setting their atomic number to zero.", &
usage="MARK_GHOST T", &
default_l_val=.FALSE., lone_keyword_l_val=.TRUE.)
CALL section_add_keyword(print_key, keyword)
CALL keyword_release(keyword)

28
src/molden_utils.F
View file

@ -105,8 +105,9 @@ CONTAINS
INTEGER, DIMENSION(:), POINTER :: npgf, nshell
INTEGER, DIMENSION(:, :), POINTER :: l
INTEGER, DIMENSION(molden_ncomax, 0:molden_lmax) :: orbmap
LOGICAL :: do_calc_energies, print_warn, &
write_cell, write_nval
LOGICAL :: do_calc_energies, ghost_atom, &
mark_ghost, print_warn, write_cell, &
write_pseudo
REAL(KIND=dp) :: expzet, prefac, scale_factor, zeff
REAL(KIND=dp), ALLOCATABLE, DIMENSION(:, :) :: cmatrix, smatrix
REAL(KIND=dp), DIMENSION(:), POINTER :: mo_eigenvalues
@ -144,7 +145,8 @@ CONTAINS
CALL section_vals_val_get(print_section, "GTO_KIND", i_val=gto_kind)
CALL section_vals_val_get(print_section, "WRITE_CELL", l_val=write_cell)
CALL section_vals_val_get(print_section, "WRITE_NVAL", l_val=write_nval)
CALL section_vals_val_get(print_section, "WRITE_PSEUDO", l_val=write_pseudo)
CALL section_vals_val_get(print_section, "MARK_GHOST", l_val=mark_ghost)
IF (mos(1)%use_mo_coeff_b) THEN
! we are using the dbcsr mo_coeff
@ -179,19 +181,25 @@ CONTAINS
WRITE (iw, '(T2,A)') "[Atoms] AU"
END IF
DO i = 1, SIZE(particle_set)
CALL get_atomic_kind(atomic_kind=particle_set(i)%atomic_kind, &
CALL get_atomic_kind(atomic_kind=particle_set(i)%atomic_kind, kind_number=ikind, &
element_symbol=element_symbol)
CALL get_ptable_info(element_symbol, number=z)
IF (mark_ghost) THEN
CALL get_qs_kind(qs_kind_set(ikind), ghost=ghost_atom)
IF (ghost_atom) z = 0
END IF
WRITE (iw, '(T2,A2,I6,I6,3X,3(F12.6,3X))') &
element_symbol, i, z, particle_set(i)%r(:)*scale_factor
END DO
IF (write_nval) THEN
WRITE (iw, '(T2,A)') "[Nval]"
DO i = 1, SIZE(qs_kind_set)
CALL get_qs_kind(qs_kind_set(i), zeff=zeff)
WRITE (iw, '(T2,A,1X,I6)') &
TRIM(ADJUSTL(qs_kind_set(i)%element_symbol)), NINT(zeff)
IF (write_pseudo) THEN
WRITE (iw, '(T2,A)') "[Pseudo]"
DO i = 1, SIZE(particle_set)
CALL get_atomic_kind(atomic_kind=particle_set(i)%atomic_kind, kind_number=ikind, &
element_symbol=element_symbol)
CALL get_qs_kind(qs_kind_set(ikind), zeff=zeff)
WRITE (iw, '(T2,A2,I6,I6)') &
element_symbol, i, NINT(zeff)
END DO
END IF