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lammps/unittest/formats/test_dump_netcdf.cpp

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/* ----------------------------------------------------------------------
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 "version.h"
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include <algorithm>
#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 header = utils::split_words(lines[0]);
ASSERT_EQ(lines.size(), 233);
ASSERT_THAT(header[0], Eq("netcdf"));
ASSERT_THAT(header[1] + ".nc", Eq(dump_file));
// check dimensions section
auto section = std::find(lines.begin(), lines.end(), "dimensions:");
for (auto line = ++section; line < lines.end(); ++line) {
auto words = utils::split_words(*line);
if ((words.size() < 1) || (words[0] == "variables:")) break;
if (words[0] == "atom") ASSERT_THAT(words[2], Eq("32"));
if (words[0] == "label") ASSERT_THAT(words[2], Eq("10"));
if (words[0] == "Voigt") ASSERT_THAT(words[2], Eq("6"));
if (words[0] == "spatial") ASSERT_THAT(words[2], Eq("3"));
}
// check variables section
section = std::find(lines.begin(), lines.end(), "variables:");
for (auto line = ++section; line < lines.end(); ++line) {
auto words = utils::split_words(*line);
if ((words.size() < 2) || (words[0] == "data:")) break;
if (words[0] == "time:units") ASSERT_THAT(words[2], Eq("lj"));
if (words[0] == "time:scale_factor") ASSERT_THAT(words[2], Eq("0.005f"));
if (words[0] == "cell_origin:units") ASSERT_THAT(words[2], Eq("lj"));
if (words[0] == "cell_angles:units") ASSERT_THAT(words[2], Eq("degree"));
if (words[1] == "id(frame,") ASSERT_THAT(words[2], Eq("atom)"));
if (words[1] == "type(frame,") ASSERT_THAT(words[2], Eq("atom)"));
if (words[1] == "proc(frame,") ASSERT_THAT(words[2], Eq("atom)"));
if (words[1] == "procp1(frame,") ASSERT_THAT(words[2], Eq("atom)"));
if (words[1] == "mass(frame,") ASSERT_THAT(words[2], Eq("atom)"));
if (words[1] == "ix(frame,") ASSERT_THAT(words[2], Eq("atom)"));
if (words[1] == "iy(frame,") ASSERT_THAT(words[2], Eq("atom)"));
if (words[1] == "iz(frame,") ASSERT_THAT(words[2], Eq("atom)"));
if (words[0] == ":Conventions") ASSERT_THAT(words[2], Eq("AMBER"));
if (words[0] == ":ConventionVersion") ASSERT_THAT(words[2], Eq("1.0"));
if (words[0] == ":program") ASSERT_THAT(words[2], Eq("LAMMPS"));
if (words[0] == ":programVersion") ASSERT_THAT(words[2], Eq(LAMMPS_VERSION));
}
// check data section
section = std::find(lines.begin(), lines.end(), "data:");
for (auto line = ++section; line < lines.end(); ++line) {
auto words = utils::split_words(*line);
if (words.size() > 0) {
if (words[0] == "spatial") ASSERT_THAT(words[2], Eq("xyz"));
if (words[0] == "cell_spatial") ASSERT_THAT(words[2], Eq("abc"));
if (words[0] == "cell_origin") {
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("0,"));
ASSERT_THAT(words[1], Eq("0,"));
ASSERT_THAT(words[2], Eq("0"));
}
if (words[0] == "cell_lengths") {
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("3.359192,"));
ASSERT_THAT(words[1], Eq("3.359192,"));
ASSERT_THAT(words[2], Eq("3.359192"));
}
if (words[0] == "cell_angles") {
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("90,"));
ASSERT_THAT(words[1], Eq("90,"));
ASSERT_THAT(words[2], Eq("90"));
}
if (words[0] == "id") {
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("1,"));
ASSERT_THAT(words[1], Eq("2,"));
ASSERT_THAT(words[2], Eq("3,"));
ASSERT_THAT(words[3], Eq("4,"));
ASSERT_THAT(words[4], Eq("5,"));
ASSERT_THAT(words[5], Eq("6,"));
ASSERT_THAT(words[6], Eq("7,"));
ASSERT_THAT(words[7], Eq("8,"));
ASSERT_THAT(words[8], Eq("9,"));
ASSERT_THAT(words[9], Eq("10,"));
}
if (words[0] == "mass") {
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("1,"));
ASSERT_THAT(words[1], Eq("1,"));
ASSERT_THAT(words[2], Eq("1,"));
ASSERT_THAT(words[3], Eq("1,"));
ASSERT_THAT(words[4], Eq("1,"));
ASSERT_THAT(words[5], Eq("1,"));
ASSERT_THAT(words[6], Eq("1,"));
ASSERT_THAT(words[7], Eq("1,"));
ASSERT_THAT(words[8], Eq("1,"));
ASSERT_THAT(words[9], Eq("1,"));
}
if (words[0] == "coordinates") {
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("0,"));
ASSERT_THAT(words[1], Eq("0,"));
ASSERT_THAT(words[2], Eq("0,"));
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("0.8397981,"));
ASSERT_THAT(words[1], Eq("0.8397981,"));
ASSERT_THAT(words[2], Eq("0,"));
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("0.8397981,"));
ASSERT_THAT(words[1], Eq("0,"));
ASSERT_THAT(words[2], Eq("0.8397981,"));
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("0,"));
ASSERT_THAT(words[1], Eq("0.8397981,"));
ASSERT_THAT(words[2], Eq("0.8397981,"));
}
if (words[0] == "ix") {
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("0,"));
ASSERT_THAT(words[1], Eq("0,"));
ASSERT_THAT(words[2], Eq("0,"));
ASSERT_THAT(words[3], Eq("0,"));
ASSERT_THAT(words[4], Eq("0,"));
ASSERT_THAT(words[5], Eq("0,"));
ASSERT_THAT(words[6], Eq("0,"));
ASSERT_THAT(words[7], Eq("0,"));
ASSERT_THAT(words[8], Eq("0,"));
ASSERT_THAT(words[9], Eq("0,"));
}
}
}
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("mpi0");
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 header = utils::split_words(lines[0]);
ASSERT_EQ(lines.size(), 234);
ASSERT_THAT(header[0], Eq("netcdf"));
ASSERT_THAT(header[1] + ".nc", Eq(dump_file));
// check dimensions section
auto section = std::find(lines.begin(), lines.end(), "dimensions:");
for (auto line = ++section; line < lines.end(); ++line) {
auto words = utils::split_words(*line);
if ((words.size() < 1) || (words[0] == "variables:")) break;
if (words[0] == "atom") ASSERT_THAT(words[2], Eq("32"));
if (words[0] == "label") ASSERT_THAT(words[2], Eq("10"));
if (words[0] == "Voigt") ASSERT_THAT(words[2], Eq("6"));
if (words[0] == "spatial") ASSERT_THAT(words[2], Eq("3"));
}
// check variables section
section = std::find(lines.begin(), lines.end(), "variables:");
for (auto line = ++section; line < lines.end(); ++line) {
auto words = utils::split_words(*line);
if ((words.size() < 2) || (words[0] == "data:")) break;
if (words[0] == "time:units") ASSERT_THAT(words[2], Eq("lj"));
if (words[0] == "time:scale_factor") ASSERT_THAT(words[2], Eq("0.005f"));
if (words[0] == "cell_origin:units") ASSERT_THAT(words[2], Eq("lj"));
if (words[0] == "cell_angles:units") ASSERT_THAT(words[2], Eq("degree"));
if (words[1] == "id(frame,") ASSERT_THAT(words[2], Eq("atom)"));
if (words[1] == "type(frame,") ASSERT_THAT(words[2], Eq("atom)"));
if (words[1] == "proc(frame,") ASSERT_THAT(words[2], Eq("atom)"));
if (words[1] == "procp1(frame,") ASSERT_THAT(words[2], Eq("atom)"));
if (words[1] == "mass(frame,") ASSERT_THAT(words[2], Eq("atom)"));
if (words[1] == "ix(frame,") ASSERT_THAT(words[2], Eq("atom)"));
if (words[1] == "iy(frame,") ASSERT_THAT(words[2], Eq("atom)"));
if (words[1] == "iz(frame,") ASSERT_THAT(words[2], Eq("atom)"));
if (words[0] == ":Conventions") ASSERT_THAT(words[2], Eq("AMBER"));
if (words[0] == ":ConventionVersion") ASSERT_THAT(words[2], Eq("1.0"));
if (words[0] == ":program") ASSERT_THAT(words[2], Eq("LAMMPS"));
if (words[0] == ":programVersion") ASSERT_THAT(words[2], Eq(LAMMPS_VERSION));
}
// check data section
section = std::find(lines.begin(), lines.end(), "data:");
for (auto line = ++section; line < lines.end(); ++line) {
auto words = utils::split_words(*line);
if (words.size() > 0) {
if (words[0] == "spatial") ASSERT_THAT(words[2], Eq("xyz"));
if (words[0] == "cell_spatial") ASSERT_THAT(words[2], Eq("abc"));
if (words[0] == "cell_origin") {
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("0,"));
ASSERT_THAT(words[1], Eq("0,"));
ASSERT_THAT(words[2], Eq("0"));
}
if (words[0] == "cell_lengths") {
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("3.359192,"));
ASSERT_THAT(words[1], Eq("3.359192,"));
ASSERT_THAT(words[2], Eq("3.359192"));
}
if (words[0] == "cell_angles") {
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("90,"));
ASSERT_THAT(words[1], Eq("90,"));
ASSERT_THAT(words[2], Eq("90"));
}
if (words[0] == "id") {
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("1,"));
ASSERT_THAT(words[1], Eq("2,"));
ASSERT_THAT(words[2], Eq("3,"));
ASSERT_THAT(words[3], Eq("4,"));
ASSERT_THAT(words[4], Eq("5,"));
ASSERT_THAT(words[5], Eq("6,"));
ASSERT_THAT(words[6], Eq("7,"));
ASSERT_THAT(words[7], Eq("8,"));
ASSERT_THAT(words[8], Eq("9,"));
ASSERT_THAT(words[9], Eq("10,"));
}
if (words[0] == "mass") {
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("1,"));
ASSERT_THAT(words[1], Eq("1,"));
ASSERT_THAT(words[2], Eq("1,"));
ASSERT_THAT(words[3], Eq("1,"));
ASSERT_THAT(words[4], Eq("1,"));
ASSERT_THAT(words[5], Eq("1,"));
ASSERT_THAT(words[6], Eq("1,"));
ASSERT_THAT(words[7], Eq("1,"));
ASSERT_THAT(words[8], Eq("1,"));
ASSERT_THAT(words[9], Eq("1,"));
}
if (words[0] == "coordinates") {
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("0,"));
ASSERT_THAT(words[1], Eq("0,"));
ASSERT_THAT(words[2], Eq("0,"));
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("0.8397981,"));
ASSERT_THAT(words[1], Eq("0.8397981,"));
ASSERT_THAT(words[2], Eq("0,"));
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("0.8397981,"));
ASSERT_THAT(words[1], Eq("0,"));
ASSERT_THAT(words[2], Eq("0.8397981,"));
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("0,"));
ASSERT_THAT(words[1], Eq("0.8397981,"));
ASSERT_THAT(words[2], Eq("0.8397981,"));
}
if (words[0] == "ix") {
++line;
words = utils::split_words(*line);
ASSERT_THAT(words[0], Eq("0,"));
ASSERT_THAT(words[1], Eq("0,"));
ASSERT_THAT(words[2], Eq("0,"));
ASSERT_THAT(words[3], Eq("0,"));
ASSERT_THAT(words[4], Eq("0,"));
ASSERT_THAT(words[5], Eq("0,"));
ASSERT_THAT(words[6], Eq("0,"));
ASSERT_THAT(words[7], Eq("0,"));
ASSERT_THAT(words[8], Eq("0,"));
ASSERT_THAT(words[9], Eq("0,"));
}
}
}
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;
}
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