Implemented more unit tests; stuck on atomfile

fortran/lammps.f90

@@ -193,6 +193,7 @@ MODULE LIBLAMMPS
       assign_doublemat_to_lammps_fix_data
     ! Variables, too
     MODULE PROCEDURE assign_double_to_lammps_variable_data, &
+      assign_doublevec_to_lammps_variable_data, &
       assign_string_to_lammps_variable_data
   END INTERFACE
 

unittest/fortran/CMakeLists.txt

@@ -70,10 +70,10 @@ if(CMAKE_Fortran_COMPILER)
   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_compile_definitions(test_fortran_extract_variable PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR})
   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()

unittest/fortran/greetings.txt

@@ -1,8 +1,8 @@
 hello
-god dag
+god_dag
 hola
 bonjour
-guten Tag
+guten_Tag
 konnichiwa
 shalom
 salve

unittest/fortran/test_fortran_extract_variable.f90

@@ -29,18 +29,42 @@ CONTAINS
   FUNCTION absolute_path(filename)
     CHARACTER(LEN=:), ALLOCATABLE :: absolute_path
     CHARACTER(LEN=*), INTENT(IN) :: filename
-    CHARACTER(LEN=:), ALLOCATABLE :: test_input_directory
+    CHARACTER(LEN=256) :: 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)
+    absolute_path = TRIM(test_input_directory) // '/' // TRIM(filename)
   END FUNCTION absolute_path
 
+  FUNCTION f2c_string(f_string) RESULT(ptr)
+    USE, INTRINSIC :: ISO_C_BINDING, ONLY : c_char, c_ptr, c_size_t, &
+      c_null_char, C_F_POINTER
+    CHARACTER(LEN=*), INTENT(IN)           :: f_string
+    CHARACTER(LEN=1, KIND=c_char), POINTER :: c_string(:)
+    TYPE(c_ptr) :: ptr
+    INTEGER(c_size_t) :: i, n
+
+    INTERFACE
+      FUNCTION lammps_malloc(size) BIND(C, name='malloc')
+        IMPORT :: c_ptr, c_size_t
+        IMPLICIT NONE
+        INTEGER(c_size_t), VALUE :: size
+        TYPE(c_ptr) :: lammps_malloc
+      END FUNCTION lammps_malloc
+    END INTERFACE
+
+    n = LEN_TRIM(f_string)
+    ptr = lammps_malloc(n+1)
+    CALL C_F_POINTER(ptr, c_string, [1])
+    DO i=1, n
+        c_string(i) = f_string(i:i)
+    END DO
+    c_string(n+1) = c_null_char
+  END FUNCTION f2c_string
+
 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 ISO_C_BINDING, ONLY: c_ptr, c_char, c_int, c_size_t, C_F_POINTER
   USE liblammps
   USE keepvar, ONLY: lmp
   IMPLICIT NONE
@@ -87,33 +111,36 @@ SUBROUTINE f_lammps_close() BIND(C)
 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
+  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")
+  CALL lmp%command('atom_modify map array')
+  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"')
+  CALL lmp%command('variable uni universe "universe1" "universeA"')
+  CALL lmp%command('variable ulp uloop 2')
+  CALL lmp%command('variable str string "this is a string"')
+  CALL lmp%command('variable ex equal exp(v_lp)')
+  CALL lmp%command('variable fmt format ex %.6G')
+  CALL lmp%command('variable fmt_pad format ex %08.6g')
+  ! USERNAME should exist on all platforms (incl. Windows)
+  CALL lmp%command('variable username getenv USERNAME')
+  CALL lmp%command('variable greeting 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)
@@ -159,3 +186,128 @@ FUNCTION f_lammps_extract_variable_loop () BIND(C)
   loop = lmp%extract_variable('lp')
   READ(loop,*) f_lammps_extract_variable_loop
 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
+  IMPLICIT NONE
+  TYPE(c_ptr) :: f_lammps_extract_variable_loop_pad
+  CHARACTER(LEN=20) :: loop
+
+  loop = lmp%extract_variable('lp_pad')
+  f_lammps_extract_variable_loop_pad = f2c_string(loop)
+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
+
+  IMPLICIT NONE
+  TYPE(c_ptr) :: f_lammps_extract_variable_world
+  CHARACTER(LEN=20) :: world
+
+  world = lmp%extract_variable('wld')
+  f_lammps_extract_variable_world = f2c_string(world)
+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
+
+  IMPLICIT NONE
+  TYPE(c_ptr) :: f_lammps_extract_variable_universe
+  CHARACTER(LEN=20) :: universe
+
+  universe = lmp%extract_variable('uni')
+  f_lammps_extract_variable_universe = f2c_string(universe)
+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
+  IMPLICIT NONE
+  INTEGER(c_int) :: f_lammps_extract_variable_uloop
+  CHARACTER(LEN=80) :: uloop
+
+  uloop = lmp%extract_variable('ulp')
+  READ(uloop,*) f_lammps_extract_variable_uloop
+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
+
+  IMPLICIT NONE
+  TYPE(c_ptr) :: f_lammps_extract_variable_string
+  CHARACTER(LEN=20) :: string
+
+  string = lmp%extract_variable('str')
+  f_lammps_extract_variable_string = f2c_string(string)
+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
+  IMPLICIT NONE
+  TYPE(c_ptr) :: f_lammps_extract_variable_format
+  CHARACTER(LEN=20) :: form
+
+  form = lmp%extract_variable('fmt')
+  f_lammps_extract_variable_format = f2c_string(form)
+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
+  IMPLICIT NONE
+  TYPE(c_ptr) :: f_lammps_extract_variable_format_pad
+  CHARACTER(LEN=20) :: form
+
+  form = lmp%extract_variable('fmt_pad')
+  f_lammps_extract_variable_format_pad = f2c_string(form)
+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
+  IMPLICIT NONE
+  TYPE(c_ptr) :: f_lammps_extract_variable_getenv
+  CHARACTER(LEN=20) :: string
+
+  string = lmp%extract_variable('username')
+  f_lammps_extract_variable_getenv = f2c_string(string)
+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
+  IMPLICIT NONE
+  TYPE(c_ptr) :: f_lammps_extract_variable_file
+  CHARACTER(LEN=40) :: string
+
+  string = lmp%extract_variable('greeting')
+  f_lammps_extract_variable_file = f2c_string(string)
+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
+  IMPLICIT NONE
+  INTEGER(c_int), INTENT(IN), VALUE :: i
+  REAL(c_double) :: f_lammps_extract_variable_atomfile
+  REAL(c_double), DIMENSION(:), POINTER :: atom_data
+
+  atom_data = lmp%extract_variable('atfile')
+print*, 'TESTING: atom_data is', atom_data
+  f_lammps_extract_variable_atomfile = atom_data(i)
+END FUNCTION f_lammps_extract_variable_atomfile

unittest/fortran/wrap_extract_variable.cpp

@@ -1,13 +1,14 @@
 // 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 <cstdio>
 #include <cstdlib>
 #include <cstdint>
+#include <cmath>
 
 #include "gtest/gtest.h"
 
@@ -22,18 +23,19 @@ 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();
+char* f_lammps_extract_variable_loop_pad();
+char* f_lammps_extract_variable_world();
+char* f_lammps_extract_variable_universe();
+int f_lammps_extract_variable_uloop();
+char* f_lammps_extract_variable_string();
+char* f_lammps_extract_variable_format();
+char* f_lammps_extract_variable_format_pad();
+char* f_lammps_extract_variable_getenv();
+char* f_lammps_extract_variable_file();
+double f_lammps_extract_variable_atomfile(int);
+double f_lammps_extract_variable_python();
+double f_lammps_extract_variable_timer();
+double f_lammps_extract_variable_internal();
 double f_lammps_extract_variable_equal_natoms();
 double f_lammps_extract_variable_equal_dt();
 double f_lammps_extract_variable_vector(int);
@@ -55,7 +57,6 @@ protected:
         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 (");
@@ -83,5 +84,120 @@ TEST_F(LAMMPS_extract_variable, index)
 TEST_F(LAMMPS_extract_variable, loop)
 {
    f_lammps_setup_extract_variable();
-   EXPECT_EQ(f_lammps_extract_variable_loop(), 1);
+   int i;
+   for ( i = 1; i <= 10; i++ ) {
+      EXPECT_EQ(f_lammps_extract_variable_loop(), i);
+      lammps_command(lmp, "next lp");
+   }
+};
+
+TEST_F(LAMMPS_extract_variable, loop_pad)
+{
+   f_lammps_setup_extract_variable();
+   int i;
+   char str[10];
+   char* fstr;
+   for ( i = 1; i <= 10; i++ ) {
+      std::sprintf(str,"%02d",i);
+      fstr = f_lammps_extract_variable_loop_pad();
+      EXPECT_STREQ(fstr, str);
+      std::free(fstr);
+      lammps_command(lmp, "next lp_pad");
+   }
+};
+
+TEST_F(LAMMPS_extract_variable, world)
+{
+   f_lammps_setup_extract_variable();
+   char* fstr = f_lammps_extract_variable_world();
+   EXPECT_STREQ(fstr, "group1");
+   std::free(fstr);
+};
+
+TEST_F(LAMMPS_extract_variable, universe)
+{
+   f_lammps_setup_extract_variable();
+   char* fstr = f_lammps_extract_variable_universe();
+   EXPECT_STREQ(fstr, "universe1");
+   std::free(fstr);
+};
+
+TEST_F(LAMMPS_extract_variable, uloop)
+{
+   f_lammps_setup_extract_variable();
+   EXPECT_EQ(f_lammps_extract_variable_uloop(), 1);
+};
+
+TEST_F(LAMMPS_extract_variable, string)
+{
+   f_lammps_setup_extract_variable();
+   char* fstr = f_lammps_extract_variable_string();
+   EXPECT_STREQ(fstr, "this is a string");
+   std::free(fstr);
+};
+
+TEST_F(LAMMPS_extract_variable, format)
+{
+   f_lammps_setup_extract_variable();
+   int i;
+   char str[10];
+   char* fstr;
+   for ( i = 1; i <= 10; i++ ) {
+      std::sprintf(str,"%.6G",std::exp(i));
+      fstr = f_lammps_extract_variable_format();
+      EXPECT_STREQ(fstr, str);
+      std::free(fstr);
+      lammps_command(lmp, "next lp");
+   }
+};
+
+TEST_F(LAMMPS_extract_variable, format_pad)
+{
+   f_lammps_setup_extract_variable();
+   int i;
+   char str[10];
+   char* fstr;
+   for ( i = 1; i <= 10; i++ ) {
+      std::sprintf(str,"%08.6G",std::exp(i));
+      fstr = f_lammps_extract_variable_format_pad();
+      EXPECT_STREQ(fstr, str);
+      std::free(fstr);
+      lammps_command(lmp, "next lp");
+   }
+};
+
+TEST_F(LAMMPS_extract_variable, getenv)
+{
+   f_lammps_setup_extract_variable();
+   char *env = std::getenv("USERNAME");
+   char *fenv = f_lammps_extract_variable_getenv();
+   EXPECT_STREQ(fenv, env);
+   std::free(fenv);
+};
+
+TEST_F(LAMMPS_extract_variable, file)
+{
+   f_lammps_setup_extract_variable();
+   int i;
+   const char* str[9] = {"hello","god_dag","hola","bonjour","guten_Tag",
+      "konnichiwa","shalom","salve","goedendag"};
+   char* fstr;
+   for ( i = 0; i < 9; i++ ) {
+      fstr = f_lammps_extract_variable_file();
+      EXPECT_STREQ(fstr, str[i]);
+      std::free(fstr);
+      lammps_command(lmp, "next greeting");
+   }
+};
+
+TEST_F(LAMMPS_extract_variable, atomfile)
+{
+   f_lammps_setup_extract_variable();
+   EXPECT_DOUBLE_EQ(f_lammps_extract_variable_atomfile(1), 5.2);
+   EXPECT_DOUBLE_EQ(f_lammps_extract_variable_atomfile(2), 1.6);
+   EXPECT_DOUBLE_EQ(f_lammps_extract_variable_atomfile(3), -1.4);
+/*   lammps_command(lmp, "next atfile");
+   EXPECT_DOUBLE_EQ(f_lammps_extract_variable_atomfile(1), -1.1);
+   EXPECT_DOUBLE_EQ(f_lammps_extract_variable_atomfile(2), 0.0);
+   EXPECT_DOUBLE_EQ(f_lammps_extract_variable_atomfile(3), 2.5); */
 };