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Updated unit tests to use keepstuff; whitespace fixes

This commit is contained in:
Karl Hammond 2022-10-02 21:26:42 -05:00
parent db9b59c269
commit dc5324c1db
4 changed files with 49 additions and 74 deletions
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2
doc/src/Fortran.rst
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@ -1108,7 +1108,7 @@ Procedures Bound to the lammps Derived Type
of atoms, see :f:func:`gather_atoms_subset`.
The *data* array will be ordered in groups of *count* values, sorted by atom
ID (e.g., if *name* is *x* and *count* = 3, then *data* = x[1][1], x[2][1],
ID (e.g., if *name* is *x* and *count* = 3, then *data* = x[1][1], x[2][1],
x[3][1], x[1][2], x[2][2], x[3][2], x[1][3], :math:`\dots`);
*data* must be ``ALLOCATABLE`` and will be allocated to length
(*count* :math:`\times` *natoms*), as queried by

4
src/library.cpp
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@ -2235,7 +2235,7 @@ a similar array but have non-consecutive atom IDs, see
of atoms, see :cpp:func:`lammps_gather_atoms_subset`.
The *data* array will be ordered in groups of *count* values, sorted by atom ID
(e.g., if *name* is *x* and *count* = 3, then *data* = x[0][0], x[0][1],
(e.g., if *name* is *x* and *count* = 3, then *data* = x[0][0], x[0][1],
x[0][2], x[1][0], x[1][1], x[1][2], x[2][0], :math:`\dots`);
*data* must be pre-allocated by the caller to length (*count* :math:`\times`
*natoms*), as queried by :cpp:func:`lammps_get_natoms`,
@ -2383,7 +2383,7 @@ This subroutine gathers data for all atoms and stores them in a
one-dimensional array allocated by the user. The data will be a concatenation
of chunks from each processor's owned atoms, in whatever order the atoms are
in on each processor. This process has no requirement that the atom IDs be
consecutive. If you need the ID of each atom, you can do another
consecutive. If you need the ID of each atom, you can do another
:cpp:func:`lammps_gather_atoms_concat` call with *name* set to ``id``.
If you have consecutive IDs and want the data to be in order, use
:cpp:func:`lammps_gather_atoms`; for a similar array but for a subset

39
unittest/fortran/test_fortran_extract_fix.f90
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@ -1,27 +1,7 @@
MODULE keepfix
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(3), PARAMETER :: cont_input = &
[ CHARACTER(LEN=40) :: &
'create_atoms 1 single &', &
' 0.2 0.1 0.1', &
'create_atoms 1 single 0.5 0.5 0.5' ]
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 keepfix
FUNCTION f_lammps_with_args() BIND(C)
USE ISO_C_BINDING, ONLY: C_ptr
USE liblammps
USE keepfix, ONLY: lmp
USE keepstuff, ONLY: lmp
IMPLICIT NONE
TYPE(C_ptr) :: f_lammps_with_args
CHARACTER(len=12), DIMENSION(12), PARAMETER :: args = &
@ -35,7 +15,7 @@ END FUNCTION f_lammps_with_args
SUBROUTINE f_lammps_close() BIND(C)
USE ISO_C_BINDING, ONLY: c_null_ptr
USE liblammps
USE keepfix, ONLY: lmp
USE keepstuff, ONLY: lmp
IMPLICIT NONE
CALL lmp%close()
@ -44,11 +24,12 @@ END SUBROUTINE f_lammps_close
SUBROUTINE f_lammps_setup_extract_fix () BIND(C)
USE LIBLAMMPS
USE keepfix, ONLY : lmp, demo_input, cont_input, pair_input
USE keepstuff, ONLY : lmp, big_input, cont_input, pair_input, more_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(more_input)
CALL lmp%commands_list(pair_input)
CALL lmp%command("fix state all store/state 0 z") ! per-atom vector
CALL lmp%command("fix move all move linear 0 0 0") ! for per-atom array
@ -62,7 +43,7 @@ END SUBROUTINE f_lammps_setup_extract_fix
FUNCTION f_lammps_extract_fix_global_scalar () BIND(C) RESULT(scalar)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
USE LIBLAMMPS
USE keepfix, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL(C_double) :: scalar
@ -72,7 +53,7 @@ END FUNCTION f_lammps_extract_fix_global_scalar
FUNCTION f_lammps_extract_fix_global_vector (i) BIND(C) RESULT(element)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
USE LIBLAMMPS
USE keepfix, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(C_int), INTENT(IN), VALUE :: i
REAL(C_double) :: element
@ -83,7 +64,7 @@ END FUNCTION f_lammps_extract_fix_global_vector
FUNCTION f_lammps_extract_fix_global_array (i,j) BIND(C) RESULT(element)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
USE LIBLAMMPS
USE keepfix, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(C_int), INTENT(IN), VALUE :: i, j
REAL(C_double) :: element
@ -94,7 +75,7 @@ END FUNCTION f_lammps_extract_fix_global_array
FUNCTION f_lammps_extract_fix_peratom_vector (i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
USE LIBLAMMPS
USE keepfix, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(C_int), INTENT(IN), VALUE :: i
REAL(C_double) :: f_lammps_extract_fix_peratom_vector
@ -107,7 +88,7 @@ END FUNCTION f_lammps_extract_fix_peratom_vector
FUNCTION f_lammps_extract_fix_peratom_array (i,j) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
USE LIBLAMMPS
USE keepfix, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(C_int), INTENT(IN), VALUE :: i, j
REAL(C_double) :: f_lammps_extract_fix_peratom_array

78
unittest/fortran/test_fortran_extract_variable.f90
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@ -1,26 +1,11 @@
MODULE keepvar
USE liblammps
IMPLICIT NONE
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(3), PARAMETER :: cont_input = &
[ CHARACTER(LEN=40) :: &
'create_atoms 1 single &', &
' 0.2 0.1 0.1', &
'create_atoms 1 single 0.5 0.5 0.5' ]
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' ]
CONTAINS
FUNCTION absolute_path(filename)
USE keepstuff, ONLY : lmp
CHARACTER(LEN=:), ALLOCATABLE :: absolute_path
CHARACTER(LEN=*), INTENT(IN) :: filename
CHARACTER(LEN=256) :: test_input_directory
@ -60,7 +45,7 @@ END MODULE keepvar
FUNCTION f_lammps_with_C_args(argc, argv) BIND(C)
USE ISO_C_BINDING, ONLY: c_ptr, c_char, c_int, c_size_t, C_F_POINTER
USE liblammps
USE keepvar, ONLY: lmp
USE keepstuff, ONLY: lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: argc
TYPE(c_ptr), VALUE :: argv
@ -97,7 +82,7 @@ END FUNCTION f_lammps_with_C_args
SUBROUTINE f_lammps_close() BIND(C)
USE ISO_C_BINDING, ONLY: c_null_ptr
USE liblammps
USE keepvar, ONLY: lmp
USE keepstuff, ONLY: lmp
IMPLICIT NONE
CALL lmp%close()
@ -106,7 +91,8 @@ END SUBROUTINE f_lammps_close
SUBROUTINE f_lammps_setup_extract_variable () BIND(C)
USE LIBLAMMPS
USE keepvar, ONLY : lmp, demo_input, cont_input, pair_input, absolute_path
USE keepstuff, ONLY : lmp, big_input, cont_input, more_input, pair_input
USE keepvar, ONLY : absolute_path
IMPLICIT NONE
! Had to do this one as one string because lammps_commands_list and
@ -118,8 +104,9 @@ SUBROUTINE f_lammps_setup_extract_variable () BIND(C)
// NEW_LINE(' ') // '"""'
CALL lmp%command('atom_modify map array')
CALL lmp%commands_list(demo_input)
CALL lmp%commands_list(big_input)
CALL lmp%commands_list(cont_input)
CALL lmp%commands_list(more_input)
CALL lmp%commands_list(pair_input)
CALL lmp%command('variable idx index "hello" "goodbye"')
CALL lmp%command('variable lp loop 10')
@ -153,7 +140,7 @@ END SUBROUTINE f_lammps_setup_extract_variable
FUNCTION f_lammps_extract_variable_index_1 () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
USE LIBLAMMPS
USE keepvar, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int) :: f_lammps_extract_variable_index_1
CHARACTER(LEN=80) :: str
@ -169,7 +156,7 @@ END FUNCTION f_lammps_extract_variable_index_1
FUNCTION f_lammps_extract_variable_index_2 () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
USE LIBLAMMPS
USE keepvar, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int) :: f_lammps_extract_variable_index_2
CHARACTER(LEN=80) :: str
@ -185,7 +172,7 @@ END FUNCTION f_lammps_extract_variable_index_2
FUNCTION f_lammps_extract_variable_loop () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int, C_double
USE LIBLAMMPS
USE keepvar, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int) :: f_lammps_extract_variable_loop
CHARACTER(LEN=80) :: loop
@ -197,7 +184,8 @@ END FUNCTION f_lammps_extract_variable_loop
FUNCTION f_lammps_extract_variable_loop_pad () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_ptr
USE LIBLAMMPS
USE keepvar, ONLY : lmp, f2c_string
USE keepstuff, ONLY : lmp
USE keepvar, ONLY : f2c_string
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_extract_variable_loop_pad
CHARACTER(LEN=20) :: loop
@ -209,8 +197,8 @@ END FUNCTION f_lammps_extract_variable_loop_pad
FUNCTION f_lammps_extract_variable_world () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_ptr
USE LIBLAMMPS
USE keepvar, ONLY : lmp, f2c_string
USE keepstuff, ONLY : lmp
USE keepvar, ONLY : f2c_string
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_extract_variable_world
CHARACTER(LEN=20) :: world
@ -222,8 +210,8 @@ END FUNCTION f_lammps_extract_variable_world
FUNCTION f_lammps_extract_variable_universe () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_ptr
USE LIBLAMMPS
USE keepvar, ONLY : lmp, f2c_string
USE keepstuff, ONLY : lmp
USE keepvar, ONLY : f2c_string
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_extract_variable_universe
CHARACTER(LEN=20) :: universe
@ -235,7 +223,7 @@ END FUNCTION f_lammps_extract_variable_universe
FUNCTION f_lammps_extract_variable_uloop () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int
USE LIBLAMMPS
USE keepvar, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int) :: f_lammps_extract_variable_uloop
CHARACTER(LEN=80) :: uloop
@ -247,7 +235,8 @@ END FUNCTION f_lammps_extract_variable_uloop
FUNCTION f_lammps_extract_variable_string () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_ptr
USE LIBLAMMPS
USE keepvar, ONLY : lmp, f2c_string
USE keepstuff, ONLY : lmp
USE keepvar, ONLY : f2c_string
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_extract_variable_string
CHARACTER(LEN=40) :: string
@ -259,7 +248,8 @@ END FUNCTION f_lammps_extract_variable_string
FUNCTION f_lammps_extract_variable_format () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_ptr
USE LIBLAMMPS
USE keepvar, ONLY : lmp, f2c_string
USE keepstuff, ONLY : lmp
USE keepvar, ONLY : f2c_string
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_extract_variable_format
CHARACTER(LEN=20) :: form
@ -271,7 +261,8 @@ END FUNCTION f_lammps_extract_variable_format
FUNCTION f_lammps_extract_variable_format_pad () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_ptr
USE LIBLAMMPS
USE keepvar, ONLY : lmp, f2c_string
USE keepstuff, ONLY : lmp
USE keepvar, ONLY : f2c_string
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_extract_variable_format_pad
CHARACTER(LEN=20) :: form
@ -283,7 +274,8 @@ END FUNCTION f_lammps_extract_variable_format_pad
FUNCTION f_lammps_extract_variable_getenv () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_ptr
USE LIBLAMMPS
USE keepvar, ONLY : lmp, f2c_string
USE keepstuff, ONLY : lmp
USE keepvar, ONLY : f2c_string
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_extract_variable_getenv
CHARACTER(LEN=40) :: string
@ -295,7 +287,8 @@ END FUNCTION f_lammps_extract_variable_getenv
FUNCTION f_lammps_extract_variable_file () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_ptr
USE LIBLAMMPS
USE keepvar, ONLY : lmp, f2c_string
USE keepstuff, ONLY : lmp
USE keepvar, ONLY : f2c_string
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_extract_variable_file
CHARACTER(LEN=40) :: string
@ -307,7 +300,7 @@ END FUNCTION f_lammps_extract_variable_file
FUNCTION f_lammps_extract_variable_atomfile(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int, C_double
USE LIBLAMMPS
USE keepvar, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
REAL(c_double) :: f_lammps_extract_variable_atomfile
@ -320,7 +313,7 @@ END FUNCTION f_lammps_extract_variable_atomfile
FUNCTION f_lammps_extract_variable_python(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_int, C_double
USE LIBLAMMPS
USE keepvar, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
REAL(c_double) :: f_lammps_extract_variable_python
@ -331,7 +324,7 @@ END FUNCTION f_lammps_extract_variable_python
FUNCTION f_lammps_extract_variable_timer() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
USE LIBLAMMPS
USE keepvar, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL(c_double) :: f_lammps_extract_variable_timer
@ -341,7 +334,7 @@ END FUNCTION f_lammps_extract_variable_timer
FUNCTION f_lammps_extract_variable_internal() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
USE LIBLAMMPS
USE keepvar, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL(c_double) :: f_lammps_extract_variable_internal
@ -351,7 +344,7 @@ END FUNCTION f_lammps_extract_variable_internal
FUNCTION f_lammps_extract_variable_equal() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
USE LIBLAMMPS
USE keepvar, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
REAL(c_double) :: f_lammps_extract_variable_equal
@ -361,7 +354,7 @@ END FUNCTION f_lammps_extract_variable_equal
FUNCTION f_lammps_extract_variable_atom(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
USE LIBLAMMPS
USE keepvar, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
REAL(c_double) :: f_lammps_extract_variable_atom
@ -374,7 +367,7 @@ END FUNCTION f_lammps_extract_variable_atom
FUNCTION f_lammps_extract_variable_vector(i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
USE LIBLAMMPS
USE keepvar, ONLY : lmp
USE keepstuff, ONLY : lmp
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: i
REAL(c_double) :: f_lammps_extract_variable_vector
@ -387,7 +380,8 @@ END FUNCTION f_lammps_extract_variable_vector
SUBROUTINE f_lammps_set_variable_string() BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
USE LIBLAMMPS
USE keepvar, ONLY : lmp, f2c_string
USE keepstuff, ONLY : lmp
USE keepvar, ONLY : f2c_string
IMPLICIT NONE
CHARACTER(LEN=40) :: string