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

unittest/fortran/wrap_extract_variable.cpp

@@ -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);
+};