add minimal unit test for netcdf dumps

unittest/formats/CMakeLists.txt

@@ -116,6 +116,14 @@ target_link_libraries(test_dump_local PRIVATE lammps GTest::GMock)
 add_test(NAME DumpLocal COMMAND test_dump_local WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
 set_tests_properties(DumpLocal PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR}")
 
+if(PKG_NETCDF)
+  find_program(NCDUMP NAMES ncdump REQUIRED)
+  add_executable(test_dump_netcdf test_dump_netcdf.cpp)
+  target_link_libraries(test_dump_netcdf PRIVATE lammps GTest::GMock)
+  add_test(NAME DumpNetCDF COMMAND test_dump_netcdf WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
+  set_tests_properties(DumpNetCDF PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};NCDUMP_BINARY=${NCDUMP}")
+endif()
+
 if(BUILD_TOOLS)
     set_tests_properties(DumpAtom PROPERTIES ENVIRONMENT "BINARY2TXT_BINARY=$<TARGET_FILE:binary2txt>")
     set_tests_properties(DumpCustom PROPERTIES ENVIRONMENT "BINARY2TXT_BINARY=$<TARGET_FILE:binary2txt>")

unittest/formats/test_dump_netcdf.cpp

@@ -0,0 +1,158 @@
+/* ----------------------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#include "../testing/core.h"
+#include "../testing/systems/melt.h"
+#include "../testing/utils.h"
+#include "fmt/format.h"
+#include "library.h"
+#include "output.h"
+#include "thermo.h"
+#include "utils.h"
+#include "gmock/gmock.h"
+#include "gtest/gtest.h"
+
+#include <string>
+
+using ::testing::Eq;
+
+char *NCDUMP_BINARY = nullptr;
+bool verbose        = false;
+
+class DumpNetCDFTest : public MeltTest {
+    std::string dump_style = "netcdf";
+
+public:
+    void set_style(const std::string &new_style) { dump_style = new_style; }
+
+    void enable_triclinic()
+    {
+        BEGIN_HIDE_OUTPUT();
+        command("change_box all triclinic");
+        END_HIDE_OUTPUT();
+    }
+
+    std::string dump_filename(std::string ident)
+    {
+        return fmt::format("dump_{}_{}.nc", dump_style, ident);
+    }
+
+    void generate_dump(std::string dump_file, std::string fields, std::string dump_modify_options,
+                       int ntimesteps)
+    {
+        BEGIN_HIDE_OUTPUT();
+        command(fmt::format("dump id all {} 1 {} {}", dump_style, dump_file, fields));
+
+        if (!dump_modify_options.empty()) {
+            command(fmt::format("dump_modify id {}", dump_modify_options));
+        }
+
+        command(fmt::format("run {} post no", ntimesteps));
+        END_HIDE_OUTPUT();
+    }
+
+    void continue_dump(int ntimesteps)
+    {
+        BEGIN_HIDE_OUTPUT();
+        command(fmt::format("run {} pre no post no", ntimesteps));
+        END_HIDE_OUTPUT();
+    }
+
+    void close_dump()
+    {
+        BEGIN_HIDE_OUTPUT();
+        command("undump id");
+        END_HIDE_OUTPUT();
+    }
+
+    std::string convert_binary_to_text(std::string binary_file)
+    {
+        BEGIN_HIDE_OUTPUT();
+        std::string cmdline = fmt::format("{0} {1} > {1}.txt", NCDUMP_BINARY, binary_file);
+        system(cmdline.c_str());
+        END_HIDE_OUTPUT();
+        return fmt::format("{}.txt", binary_file);
+    }
+};
+
+TEST_F(DumpNetCDFTest, run0_plain)
+{
+    if (!lammps_has_style(lmp, "dump", "netcdf")) GTEST_SKIP();
+    auto dump_file = dump_filename("run0");
+    auto fields    = "id type proc procp1 mass x y z ix iy iz xu yu zu vx vy vz fx fy fz";
+    set_style("netcdf");
+    generate_dump(dump_file, fields, "", 0);
+
+    ASSERT_FILE_EXISTS(dump_file);
+    if (NCDUMP_BINARY) {
+        auto converted_file = convert_binary_to_text(dump_file);
+        auto lines          = read_lines(converted_file);
+        auto words          = utils::split_words(lines[0]);
+        ASSERT_EQ(lines.size(), 233);
+        ASSERT_THAT(words[0], Eq("netcdf"));
+        ASSERT_THAT(words[1]+".nc", Eq(dump_file));
+        words = utils::split_words(lines[3]);
+        ASSERT_THAT(words[0], Eq("atom"));
+        ASSERT_THAT(words[2], Eq("32"));
+        delete_file(converted_file);
+    }
+    delete_file(dump_file);
+}
+
+TEST_F(DumpNetCDFTest, run0_mpi)
+{
+    if (!lammps_has_style(lmp, "dump", "netcdf/mpiio")) GTEST_SKIP();
+    auto dump_file = dump_filename("run0");
+    auto fields    = "id type proc procp1 mass x y z ix iy iz xu yu zu vx vy vz fx fy fz";
+    set_style("netcdf/mpiio");
+    generate_dump(dump_file, fields, "", 0);
+
+    ASSERT_FILE_EXISTS(dump_file);
+    if (NCDUMP_BINARY) {
+        auto converted_file = convert_binary_to_text(dump_file);
+        auto lines          = read_lines(converted_file);
+        auto words          = utils::split_words(lines[0]);
+        ASSERT_EQ(lines.size(), 234);
+        ASSERT_THAT(words[0], Eq("netcdf"));
+        ASSERT_THAT(words[1]+".nc", Eq(dump_file));
+        words = utils::split_words(lines[3]);
+        ASSERT_THAT(words[0], Eq("atom"));
+        ASSERT_THAT(words[2], Eq("32"));
+        delete_file(converted_file);
+    }
+    delete_file(dump_file);
+}
+
+int main(int argc, char **argv)
+{
+    MPI_Init(&argc, &argv);
+    ::testing::InitGoogleMock(&argc, argv);
+
+    // handle arguments passed via environment variable
+    if (const char *var = getenv("TEST_ARGS")) {
+        std::vector<std::string> env = utils::split_words(var);
+        for (auto arg : env) {
+            if (arg == "-v") {
+                verbose = true;
+            }
+        }
+    }
+
+    NCDUMP_BINARY = getenv("NCDUMP_BINARY");
+
+    if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
+
+    int rv = RUN_ALL_TESTS();
+    MPI_Finalize();
+    return rv;
+}