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Wrote docs for extract_fix,extract_variable; fixed python so it knows about string variables; doc typo fixes; part of extract_variable unit test

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This commit is contained in:
Karl Hammond
2022-09-29 19:28:15 -05:00
parent 3ab8f6ea16
commit a7071fea78
9 changed files with 861 additions and 86 deletions
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5
unittest/fortran/CMakeLists.txt
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@ -69,6 +69,11 @@ if(CMAKE_Fortran_COMPILER)
target_link_libraries(test_fortran_extract_fix PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain)
add_test(NAME FortranExtractFix COMMAND test_fortran_extract_fix)
add_executable(test_fortran_extract_variable wrap_extract_variable.cpp test_fortran_extract_variable.f90)
target_link_libraries(test_fortran_extract_variable PRIVATE flammps lammps MPI::MPI_Fortran GTest::GTestMain)
add_test(NAME FortranExtractVariable COMMAND test_fortran_extract_variable)
else()
message(STATUS "Skipping Tests for the LAMMPS Fortran Module: no Fortran compiler")
endif()

8
unittest/fortran/atomdata.txt Normal file
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@ -0,0 +1,8 @@
3
2 1.6
1 5.2
3 -1.4
2
3 2.5
1 -1.1

9
unittest/fortran/greetings.txt Normal file
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@ -0,0 +1,9 @@
hello
god dag
hola
bonjour
guten Tag
konnichiwa
shalom
salve
goedendag

161
unittest/fortran/test_fortran_extract_variable.f90 Normal file
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@ -0,0 +1,161 @@
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' ]
CHARACTER(LEN=60), DIMENSION(4), PARAMETER :: py_input = &
[ CHARACTER(LEN=60) :: &
'python square_it input 1 v_lp return v_square here """', &
'def square_it(N) :', &
' return N*N', &
'"""' ]
CONTAINS
FUNCTION absolute_path(filename)
CHARACTER(LEN=:), ALLOCATABLE :: absolute_path
CHARACTER(LEN=*), INTENT(IN) :: filename
CHARACTER(LEN=:), ALLOCATABLE :: test_input_directory
print *, 'GOT HERE! filename is ', filename
test_input_directory = lmp%extract_variable('input_dir')
print *, ' test_input_directory is ', test_input_directory
absolute_path = test_input_directory // '/' // TRIM(filename)
END FUNCTION absolute_path
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
IMPLICIT NONE
INTEGER(c_int), INTENT(IN), VALUE :: argc
TYPE(c_ptr), VALUE :: argv
TYPE(c_ptr), DIMENSION(:), POINTER :: Fargv
INTEGER, PARAMETER :: ARG_LENGTH = 80
TYPE(c_ptr) :: f_lammps_with_C_args
CHARACTER(LEN=ARG_LENGTH), DIMENSION(argc) :: args
CHARACTER(LEN=1,KIND=c_char), DIMENSION(:), POINTER :: Cstr
INTEGER :: i, length, j
INTERFACE
FUNCTION c_strlen (str) BIND(C,name='strlen')
IMPORT :: c_ptr, c_size_t
IMPLICIT NONE
TYPE(c_ptr), INTENT(IN), VALUE :: str
INTEGER(c_size_t) :: c_strlen
END FUNCTION c_strlen
END INTERFACE
CALL C_F_POINTER(argv, Fargv, [argc])
DO i = 1, argc
args(i) = ''
length = c_strlen(Fargv(i))
CALL C_F_POINTER(Fargv(i), Cstr, [length])
FORALL (j = 1:length)
args(i)(j:j) = Cstr(j)
END FORALL
END DO
lmp = lammps(args)
f_lammps_with_C_args = lmp%handle
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
IMPLICIT NONE
CALL lmp%close()
lmp%handle = c_null_ptr
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
IMPLICIT NONE
CALL lmp%commands_list(demo_input)
CALL lmp%commands_list(cont_input)
CALL lmp%commands_list(pair_input)
CALL lmp%command('variable idx index "hello" "goodbye"')
CALL lmp%command('variable lp loop 10')
CALL lmp%command('variable lp_pad loop 10 pad')
!CALL lmp%command('variable wld world "group1" "group2" "group3"')
CALL lmp%command('variable wld world "group1"')
CALL lmp%command('variable uni universe "universe1" "universeA"')
CALL lmp%command('variable ulp uloop 2')
CALL lmp%command('variable str index "this is a string"')
CALL lmp%command('variable fmt format lp %.6G')
CALL lmp%command('variable fmt_pad format lp %0.6g')
CALL lmp%command('variable shell getenv SHELL')
! CALL lmp%command('variable greet file ' // absolute_path('greetings.txt'))
! CALL lmp%command('variable atfile atomfile ' // absolute_path('atomdata.txt')
IF ( lmp%config_has_package('PYTHON') ) THEN
CALL lmp%command('variable py python square_it')
END IF
CALL lmp%command('variable time timer')
CALL lmp%command('variable int internal 4')
CALL lmp%command("variable nat equal count(all)")
CALL lmp%command("variable ts equal step")
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
IMPLICIT NONE
INTEGER(c_int) :: f_lammps_extract_variable_index_1
CHARACTER(LEN=80) :: str
str = lmp%extract_variable("idx")
IF ( trim(str) == 'hello' ) THEN
f_lammps_extract_variable_index_1 = 1_c_int
ELSE
f_lammps_extract_variable_index_1 = 0_c_int
END IF
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
IMPLICIT NONE
INTEGER(c_int) :: f_lammps_extract_variable_index_2
CHARACTER(LEN=80) :: str
str = lmp%extract_variable("idx")
IF ( trim(str) == 'goodbye' ) THEN
f_lammps_extract_variable_index_2 = 1_c_int
ELSE
f_lammps_extract_variable_index_2 = 0_c_int
END IF
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
IMPLICIT NONE
INTEGER(c_int) :: f_lammps_extract_variable_loop
CHARACTER(LEN=80) :: loop
loop = lmp%extract_variable('lp')
READ(loop,*) f_lammps_extract_variable_loop
END FUNCTION f_lammps_extract_variable_loop

87
unittest/fortran/wrap_extract_variable.cpp Normal file
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@ -0,0 +1,87 @@
// unit tests for extracting compute data from a LAMMPS instance through the
// Fortran wrapper
#include <cstdio>
#include "lammps.h"
#include "library.h"
#include <mpi.h>
#include <string>
#include <cstdlib>
#include <cstdint>
#include "gtest/gtest.h"
#define STRINGIFY(val) XSTR(val)
#define XSTR(val) #val
// prototypes for Fortran reverse wrapper functions
extern "C" {
void *f_lammps_with_c_args(int,char**);
void f_lammps_close();
void f_lammps_setup_extract_variable();
int f_lammps_extract_variable_index_1();
int f_lammps_extract_variable_index_2();
int f_lammps_extract_variable_loop();
double f_lammps_extract_variable_loop_pad();
void f_lammps_setup_extract_variable_world();
void f_lammps_setup_extract_variable_universe();
int f_lammps_setup_extract_variable_uloop();
void f_lammps_setup_extract_variable_string();
void f_lammps_setup_extract_variable_format();
void f_lammps_setup_extract_variable_getenv();
void f_lammps_setup_extract_variable_file();
void f_lammps_setup_extract_variable_atomfile();
double f_lammps_setup_extract_variable_python();
double f_lammps_setup_extract_variable_timer();
double f_lammps_setup_extract_variable_internal();
double f_lammps_extract_variable_equal_natoms();
double f_lammps_extract_variable_equal_dt();
double f_lammps_extract_variable_vector(int);
double f_lammps_extract_variable_atom(int);
}
class LAMMPS_extract_variable : public ::testing::Test {
protected:
LAMMPS_NS::LAMMPS *lmp;
LAMMPS_extract_variable() = default;
~LAMMPS_extract_variable() override = default;
void SetUp() override
{
const char *args[] = {"LAMMPS_Fortran_test", "-l", "none",
"-echo", "screen", "-nocite", "-var",
"input_dir", STRINGIFY(TEST_INPUT_FOLDER),
"-var", "zpos", "1.5", "-var", "x", "2"};
char** argv = (char**) args;
int argc = sizeof(args) / sizeof(const char*);
::testing::internal::CaptureStdout();
std::fprintf(stderr,"THIS IS A TEST\n");
lmp = (LAMMPS_NS::LAMMPS*)f_lammps_with_c_args(argc, argv);
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0, 8).c_str(), "LAMMPS (");
}
void TearDown() override
{
::testing::internal::CaptureStdout();
f_lammps_close();
std::string output = ::testing::internal::GetCapturedStdout();
EXPECT_STREQ(output.substr(0, 16).c_str(), "Total wall time:");
lmp = nullptr;
}
};
TEST_F(LAMMPS_extract_variable, index)
{
f_lammps_setup_extract_variable();
EXPECT_EQ(f_lammps_extract_variable_index_1(), 1);
EXPECT_EQ(f_lammps_extract_variable_index_2(), 0);
lammps_command(lmp, "next idx");
EXPECT_EQ(f_lammps_extract_variable_index_1(), 0);
EXPECT_EQ(f_lammps_extract_variable_index_2(), 1);
};
TEST_F(LAMMPS_extract_variable, loop)
{
f_lammps_setup_extract_variable();
EXPECT_EQ(f_lammps_extract_variable_loop(), 1);
};