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Implemented, tested, and documented gather_atoms and variants; added RST docs for lammps_scatter_atoms and lammps_gather_atoms and variants (library.cpp); checked for missing atom map in lammps_gather_atoms_subset; fixed bug in keepstuff.f90; fixed docs for extract_variable

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This commit is contained in:
Karl Hammond
2022-10-02 15:28:10 -05:00
parent 2f5e0646d9
commit c5c21bb36c
9 changed files with 796 additions and 138 deletions
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42
unittest/fortran/test_fortran_extract_atom.f90
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@ -1,26 +1,7 @@
MODULE keepatom
USE liblammps
TYPE(LAMMPS) :: lmp
CHARACTER(LEN=40), DIMENSION(3), PARAMETER :: demo_input = &
[ CHARACTER(len=40) :: &
'region box block 0 $x 0 3 0 4', &
'create_box 1 box', &
'create_atoms 1 single 1.0 1.0 ${zpos}' ]
CHARACTER(LEN=40), DIMENSION(2), PARAMETER :: cont_input = &
[ CHARACTER(len=40) :: &
'create_atoms 1 single &', &
' 0.2 0.1 0.1' ]
CHARACTER(LEN=40), DIMENSION(3), PARAMETER :: pair_input = &
[ CHARACTER(LEN=40) :: &
'pair_style lj/cut 2.5', &
'pair_coeff 1 1 1.0 1.0', &
'mass 1 2.0' ]
END MODULE keepatom
FUNCTION f_lammps_with_args() BIND(C, name="f_lammps_with_args")
USE ISO_C_BINDING, ONLY: c_ptr
USE liblammps
USE keepatom, ONLY: lmp
USE keepstuff, ONLY: lmp
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_with_args
CHARACTER(len=12), DIMENSION(12), PARAMETER :: args = &
@ -34,7 +15,7 @@ END FUNCTION f_lammps_with_args
SUBROUTINE f_lammps_close() BIND(C, name="f_lammps_close")
USE ISO_C_BINDING, ONLY: c_null_ptr
USE liblammps
USE keepatom, ONLY: lmp
USE keepstuff, ONLY: lmp
IMPLICIT NONE
CALL lmp%close()
@ -43,19 +24,18 @@ END SUBROUTINE f_lammps_close
SUBROUTINE f_lammps_setup_extract_atom () BIND(C)
USE LIBLAMMPS
USE keepatom, ONLY : lmp, demo_input, cont_input, pair_input
USE keepstuff, ONLY : lmp, big_input, cont_input, pair_input
IMPLICIT NONE
CALL lmp%commands_list(demo_input)
CALL lmp%commands_list(big_input)
CALL lmp%commands_list(cont_input)
CALL lmp%commands_list(pair_input)
! CALL lmp%command('run 0')
END SUBROUTINE f_lammps_setup_extract_atom
FUNCTION f_lammps_extract_atom_mass () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
USE LIBLAMMPS
USE keepatom, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL(C_double) :: f_lammps_extract_atom_mass
REAL(C_double), DIMENSION(:), POINTER :: mass => NULL()
@ -67,7 +47,7 @@ END FUNCTION f_lammps_extract_atom_mass
FUNCTION f_lammps_extract_atom_tag_int (i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
USE LIBLAMMPS
USE keepatom, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(C_int), INTENT(IN), VALUE :: i
INTEGER(C_int) :: f_lammps_extract_atom_tag_int
@ -80,7 +60,7 @@ END FUNCTION f_lammps_extract_atom_tag_int
FUNCTION f_lammps_extract_atom_tag_int64 (i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int64_t
USE LIBLAMMPS
USE keepatom, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(C_int64_t), INTENT(IN), VALUE :: i
INTEGER(C_int64_t) :: f_lammps_extract_atom_tag_int64
@ -93,7 +73,7 @@ END FUNCTION f_lammps_extract_atom_tag_int64
FUNCTION f_lammps_extract_atom_type(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
USE LIBLAMMPS
USE keepatom, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(C_int), INTENT(IN), VALUE :: i
INTEGER(C_int) :: f_lammps_extract_atom_type
@ -106,7 +86,7 @@ END FUNCTION f_lammps_extract_atom_type
FUNCTION f_lammps_extract_atom_mask(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
USE LIBLAMMPS
USE keepatom, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(C_int), INTENT(IN), VALUE :: i
INTEGER(C_int) :: f_lammps_extract_atom_mask
@ -119,7 +99,7 @@ END FUNCTION f_lammps_extract_atom_mask
SUBROUTINE f_lammps_extract_atom_x (i, x) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
USE LIBLAMMPS
USE keepatom, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(C_int), INTENT(IN), VALUE :: i
REAL(C_double), DIMENSION(3) :: x
@ -132,7 +112,7 @@ END SUBROUTINE f_lammps_extract_atom_x
SUBROUTINE f_lammps_extract_atom_v (i, v) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
USE LIBLAMMPS
USE keepatom, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(C_int), INTENT(IN), VALUE :: i
REAL(C_double), DIMENSION(3) :: v