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continued ork on extract_compute unit tests

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This commit is contained in:
Karl Hammond
2022-09-24 12:04:27 -05:00
parent 69627eee8d
commit 26e269aacd
4 changed files with 25 additions and 98 deletions
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6
doc/src/Fortran.rst
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@ -508,10 +508,10 @@ Procedures Bound to the lammps Derived Type
USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_int64_t
USE LIBLAMMPS
TYPE(lammps) :: lmp
INTEGER(C_int), POINTER :: nlocal
INTEGER(C_int64_t), POINTER :: ntimestep
INTEGER(C_int), POINTER :: nlocal => NULL()
INTEGER(C_int64_t), POINTER :: ntimestep => NULL()
REAL(C_double), POINTER :: dt => NULL()
CHARACTER(LEN=10) :: units
REAL(C_double), POINTER :: dt
lmp = lammps()
! other commands
nlocal = lmp%extract_global('nlocal')

10
doc/src/Library_properties.rst
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@ -16,8 +16,8 @@ This section documents the following functions:
--------------------
The library interface allows the extraction of different kinds of
information about the active simulation instance and also - in some
cases - to apply modifications to it. This enables combining of a
information about the active simulation instance and also---in some
cases---to apply modifications to it. This enables combining of a
LAMMPS simulation with other processing and simulation methods computed
by the calling code, or by another code that is coupled to LAMMPS via
the library interface. In some cases the data returned is direct
@ -25,9 +25,9 @@ reference to the original data inside LAMMPS, cast to a void pointer.
In that case the data needs to be cast to a suitable pointer for the
calling program to access it, and you may need to know the correct
dimensions and lengths. This also means you can directly change those
value(s) from the calling program, e.g. to modify atom positions. Of
course, this should be done with care. When accessing per-atom data,
please note that this data is the per-processor **local** data and is
value(s) from the calling program (e.g., to modify atom positions). Of
course, changing values should be done with care. When accessing per-atom
data, please note that these data are the per-processor **local** data and are
indexed accordingly. Per-atom data can change sizes and ordering at
every neighbor list rebuild or atom sort event as atoms migrate between
sub-domains and processors.

4
unittest/fortran/CMakeLists.txt
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@ -61,6 +61,10 @@ if(CMAKE_Fortran_COMPILER)
target_link_libraries(test_fortran_extract_atom PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain)
add_test(NAME FortranExtractAtom COMMAND test_fortran_extract_atom)
add_executable(test_fortran_extract_compute wrap_extract_compute.cpp test_fortran_extract_compute.f90)
target_link_libraries(test_fortran_extract_compute PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain)
add_test(NAME FortranExtractCompute COMMAND test_fortran_extract_compute)
else()
message(STATUS "Skipping Tests for the LAMMPS Fortran Module: no Fortran compiler")
endif()

103
unittest/fortran/test_fortran_extract_compute.f90
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@ -17,10 +17,10 @@ MODULE keepcompute
'mass 1 2.0' ]
END MODULE keepcompute
FUNCTION f_lammps_with_args() BIND(C, name="f_lammps_with_args")
FUNCTION f_lammps_with_args() BIND(C)
USE ISO_C_BINDING, ONLY: c_ptr
USE liblammps
USE keepatom, ONLY: lmp
USE keepcompute, ONLY: lmp
IMPLICIT NONE
TYPE(c_ptr) :: f_lammps_with_args
CHARACTER(len=12), DIMENSION(12), PARAMETER :: args = &
@ -31,10 +31,10 @@ FUNCTION f_lammps_with_args() BIND(C, name="f_lammps_with_args")
f_lammps_with_args = lmp%handle
END FUNCTION f_lammps_with_args
SUBROUTINE f_lammps_close() BIND(C, name="f_lammps_close")
SUBROUTINE f_lammps_close() BIND(C)
USE ISO_C_BINDING, ONLY: c_null_ptr
USE liblammps
USE keepatom, ONLY: lmp
USE keepcompute, ONLY: lmp
IMPLICIT NONE
CALL lmp%close()
@ -43,7 +43,7 @@ END SUBROUTINE f_lammps_close
SUBROUTINE f_lammps_setup_extract_compute () BIND(C)
USE LIBLAMMPS
USE keepatom, ONLY : lmp, demo_input, cont_input, pair_input
USE keepcompute, ONLY : lmp, demo_input, cont_input, pair_input
IMPLICIT NONE
CALL lmp%commands_list(demo_input)
@ -56,94 +56,17 @@ SUBROUTINE f_lammps_setup_extract_compute () BIND(C)
CALL lmp%command("compute 1 all rdf 100") ! global array
CALL lmp%command("compute pairdist all pair/local dist") ! local vector
CALL lmp%command("compute pairlocal all pair/local dist dx dy dz") ! local array
END SUBROUTINE f_lammps_setup_extract_atom
END SUBROUTINE f_lammps_setup_extract_compute
FUNCTION f_lammps_extract_atom_mass () BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double
USE LIBLAMMPS
USE keepatom, ONLY : lmp
IMPLICIT NONE
REAL(C_double) :: f_lammps_extract_atom_mass
REAL(C_double), DIMENSION(:), POINTER :: mass => NULL()
mass = lmp%extract_atom('mass')
f_lammps_extract_atom_mass = mass(1)
END FUNCTION f_lammps_extract_atom_mass
FUNCTION f_lammps_extract_atom_tag_int (i) BIND(C)
FUNCTION f_lammps_extract_compute_peratom_vector (i) BIND(C)
USE, INTRINSIC :: ISO_C_BINDING, ONLY : C_double, C_int
USE LIBLAMMPS
USE keepatom, ONLY : lmp
USE keepcompute, ONLY : lmp
IMPLICIT NONE
INTEGER(C_int), INTENT(IN), VALUE :: i
INTEGER(C_int) :: f_lammps_extract_atom_tag_int
INTEGER(C_int), DIMENSION(:), POINTER :: tag => NULL()
REAL(C_double) :: f_lammps_extract_compute_peratom_vector
REAL(C_double), DIMENSION(:), POINTER :: vector => NULL()
tag = lmp%extract_atom('id')
f_lammps_extract_atom_tag_int = tag(i)
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
IMPLICIT NONE
INTEGER(C_int64_t), INTENT(IN), VALUE :: i
INTEGER(C_int64_t) :: f_lammps_extract_atom_tag_int64
INTEGER(C_int64_t), DIMENSION(:), POINTER :: tag => NULL()
tag = lmp%extract_atom('id')
f_lammps_extract_atom_tag_int64 = tag(i)
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
IMPLICIT NONE
INTEGER(C_int), INTENT(IN), VALUE :: i
INTEGER(C_int) :: f_lammps_extract_atom_type
INTEGER(C_int), DIMENSION(:), POINTER :: atype => NULL()
atype = lmp%extract_atom('type')
f_lammps_extract_atom_type = atype(i)
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
IMPLICIT NONE
INTEGER(C_int), INTENT(IN), VALUE :: i
INTEGER(C_int) :: f_lammps_extract_atom_mask
INTEGER(C_int), DIMENSION(:), POINTER :: mask => NULL()
mask = lmp%extract_atom('mask')
f_lammps_extract_atom_mask = mask(i)
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
IMPLICIT NONE
INTEGER(C_int), INTENT(IN), VALUE :: i
REAL(C_double), DIMENSION(3) :: x
REAL(C_double), DIMENSION(:,:), POINTER :: xptr => NULL()
xptr = lmp%extract_atom('x')
x = xptr(:,i)
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
IMPLICIT NONE
INTEGER(C_int), INTENT(IN), VALUE :: i
REAL(C_double), DIMENSION(3) :: v
REAL(C_double), DIMENSION(:,:), POINTER :: vptr => NULL()
vptr = lmp%extract_atom('v')
v = vptr(:,i)
END SUBROUTINE f_lammps_extract_atom_v
vector = lmp%extract_compute('peratompe', lmp%style%atom, lmp%type%vector)
f_lammps_extract_compute_peratom_vector = vector(i)
END FUNCTION f_lammps_extract_compute_peratom_vector