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lammps/unittest/formats/test_dump_atom.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 "output.h"
#include "thermo.h"
#include "utils.h"
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include <string>
using ::testing::Eq;
char *BINARY2TXT_BINARY = nullptr;
bool verbose = false;
class DumpAtomTest : public MeltTest {
std::string dump_style = "atom";
public:
void enable_triclinic()
{
BEGIN_HIDE_OUTPUT();
command("change_box all triclinic");
END_HIDE_OUTPUT();
}
void generate_dump(std::string dump_file, std::string dump_modify_options, int ntimesteps)
{
BEGIN_HIDE_OUTPUT();
command(fmt::format("dump id all {} 1 {}", dump_style, dump_file));
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 generate_text_and_binary_dump(std::string text_file, std::string binary_file,
std::string dump_modify_options, int ntimesteps)
{
BEGIN_HIDE_OUTPUT();
command(fmt::format("dump id0 all {} 1 {}", dump_style, text_file));
command(fmt::format("dump id1 all {} 1 {}", dump_style, binary_file));
if (!dump_modify_options.empty()) {
command(fmt::format("dump_modify id0 {}", dump_modify_options));
command(fmt::format("dump_modify id1 {}", dump_modify_options));
}
command(fmt::format("run {} post no", ntimesteps));
END_HIDE_OUTPUT();
}
std::string convert_binary_to_text(std::string binary_file)
{
BEGIN_HIDE_OUTPUT();
std::string cmdline = fmt::format("{} {}", BINARY2TXT_BINARY, binary_file);
system(cmdline.c_str());
END_HIDE_OUTPUT();
return fmt::format("{}.txt", binary_file);
}
};
TEST_F(DumpAtomTest, run0)
{
auto dump_file = "dump_run0.melt";
generate_dump(dump_file, "scale yes image no", 0);
ASSERT_FILE_EXISTS(dump_file);
auto lines = read_lines(dump_file);
ASSERT_EQ(lines.size(), 41);
ASSERT_THAT(lines[4], Eq("ITEM: BOX BOUNDS pp pp pp"));
ASSERT_EQ(utils::split_words(lines[5]).size(), 2);
ASSERT_THAT(lines[8], Eq("ITEM: ATOMS id type xs ys zs"));
ASSERT_EQ(utils::split_words(lines[9]).size(), 5);
ASSERT_THAT(lines[9], Eq("1 1 0 0 0"));
delete_file(dump_file);
}
TEST_F(DumpAtomTest, format_line_run0)
{
auto dump_file = "dump_format_line_run0.melt";
generate_dump(dump_file, "format line \"%d %d %20.15g %g %g\" scale yes image no", 0);
ASSERT_FILE_EXISTS(dump_file);
auto lines = read_lines(dump_file);
ASSERT_EQ(lines.size(), 41);
ASSERT_THAT(lines[4], Eq("ITEM: BOX BOUNDS pp pp pp"));
ASSERT_EQ(utils::split_words(lines[5]).size(), 2);
ASSERT_THAT(lines[8], Eq("ITEM: ATOMS id type xs ys zs"));
ASSERT_EQ(utils::split_words(lines[9]).size(), 5);
ASSERT_THAT(lines[9], Eq("1 1 0 0 0"));
delete_file(dump_file);
}
TEST_F(DumpAtomTest, no_scale_run0)
{
auto dump_file = "dump_no_scale_run0.melt";
generate_dump(dump_file, "scale no", 0);
ASSERT_FILE_EXISTS(dump_file);
auto lines = read_lines(dump_file);
ASSERT_EQ(lines.size(), 41);
ASSERT_THAT(lines[4], Eq("ITEM: BOX BOUNDS pp pp pp"));
ASSERT_EQ(utils::split_words(lines[5]).size(), 2);
ASSERT_THAT(lines[8], Eq("ITEM: ATOMS id type x y z"));
ASSERT_EQ(utils::split_words(lines[9]).size(), 5);
delete_file(dump_file);
}
TEST_F(DumpAtomTest, no_buffer_no_scale_run0)
{
auto dump_file = "dump_no_buffer_no_scale_run0.melt";
generate_dump(dump_file, "buffer no scale no", 0);
ASSERT_FILE_EXISTS(dump_file);
auto lines = read_lines(dump_file);
ASSERT_EQ(lines.size(), 41);
ASSERT_THAT(lines[4], Eq("ITEM: BOX BOUNDS pp pp pp"));
ASSERT_EQ(utils::split_words(lines[5]).size(), 2);
ASSERT_THAT(lines[8], Eq("ITEM: ATOMS id type x y z"));
ASSERT_EQ(utils::split_words(lines[9]).size(), 5);
delete_file(dump_file);
}
TEST_F(DumpAtomTest, no_buffer_with_scale_run0)
{
auto dump_file = "dump_no_buffer_with_scale_run0.melt";
generate_dump(dump_file, "buffer no scale yes", 0);
ASSERT_FILE_EXISTS(dump_file);
auto lines = read_lines(dump_file);
ASSERT_EQ(lines.size(), 41);
ASSERT_THAT(lines[4], Eq("ITEM: BOX BOUNDS pp pp pp"));
ASSERT_EQ(utils::split_words(lines[5]).size(), 2);
ASSERT_THAT(lines[8], Eq("ITEM: ATOMS id type xs ys zs"));
ASSERT_EQ(utils::split_words(lines[9]).size(), 5);
delete_file(dump_file);
}
TEST_F(DumpAtomTest, with_image_run0)
{
auto dump_file = "dump_with_image_run0.melt";
generate_dump(dump_file, "scale no image yes", 0);
ASSERT_FILE_EXISTS(dump_file);
auto lines = read_lines(dump_file);
ASSERT_EQ(lines.size(), 41);
ASSERT_THAT(lines[8], Eq("ITEM: ATOMS id type x y z ix iy iz"));
ASSERT_EQ(utils::split_words(lines[9]).size(), 8);
delete_file(dump_file);
}
TEST_F(DumpAtomTest, with_units_run0)
{
auto dump_file = "dump_with_units_run0.melt";
generate_dump(dump_file, "scale no units yes", 0);
ASSERT_FILE_EXISTS(dump_file);
auto lines = read_lines(dump_file);
ASSERT_EQ(lines.size(), 43);
ASSERT_THAT(lines[0], Eq("ITEM: UNITS"));
ASSERT_THAT(lines[1], Eq("lj"));
ASSERT_THAT(lines[10], Eq("ITEM: ATOMS id type x y z"));
ASSERT_EQ(utils::split_words(lines[11]).size(), 5);
delete_file(dump_file);
}
TEST_F(DumpAtomTest, with_time_run0)
{
auto dump_file = "dump_with_time_run0.melt";
generate_dump(dump_file, "scale no time yes", 0);
ASSERT_FILE_EXISTS(dump_file);
auto lines = read_lines(dump_file);
ASSERT_EQ(lines.size(), 43);
ASSERT_THAT(lines[0], Eq("ITEM: TIME"));
ASSERT_THAT(lines[10], Eq("ITEM: ATOMS id type x y z"));
ASSERT_EQ(utils::split_words(lines[11]).size(), 5);
delete_file(dump_file);
}
TEST_F(DumpAtomTest, with_units_run1)
{
auto dump_file = "dump_with_units_run1.melt";
generate_dump(dump_file, "scale no units yes", 1);
ASSERT_FILE_EXISTS(dump_file);
auto lines = read_lines(dump_file);
ASSERT_EQ(lines.size(), 84);
ASSERT_THAT(lines[0], Eq("ITEM: UNITS"));
ASSERT_THAT(lines[1], Eq("lj"));
ASSERT_THAT(lines[10], Eq("ITEM: ATOMS id type x y z"));
ASSERT_EQ(utils::split_words(lines[11]).size(), 5);
delete_file(dump_file);
}
TEST_F(DumpAtomTest, no_buffer_with_scale_and_image_run0)
{
auto dump_file = "dump_no_buffer_with_scale_and_image_run0.melt";
generate_dump(dump_file, "buffer no scale yes image yes", 0);
ASSERT_FILE_EXISTS(dump_file);
auto lines = read_lines(dump_file);
ASSERT_EQ(lines.size(), 41);
ASSERT_THAT(lines[4], Eq("ITEM: BOX BOUNDS pp pp pp"));
ASSERT_EQ(utils::split_words(lines[5]).size(), 2);
ASSERT_THAT(lines[8], Eq("ITEM: ATOMS id type xs ys zs ix iy iz"));
ASSERT_EQ(utils::split_words(lines[9]).size(), 8);
delete_file(dump_file);
}
TEST_F(DumpAtomTest, triclinic_run0)
{
auto dump_file = "dump_triclinic_run0.melt";
enable_triclinic();
generate_dump(dump_file, "", 0);
ASSERT_FILE_EXISTS(dump_file);
auto lines = read_lines(dump_file);
ASSERT_EQ(lines.size(), 41);
ASSERT_THAT(lines[4], Eq("ITEM: BOX BOUNDS xy xz yz pp pp pp"));
ASSERT_EQ(utils::split_words(lines[5]).size(), 3);
ASSERT_THAT(lines[8], Eq("ITEM: ATOMS id type xs ys zs"));
ASSERT_EQ(utils::split_words(lines[9]).size(), 5);
delete_file(dump_file);
}
TEST_F(DumpAtomTest, triclinic_with_units_run0)
{
auto dump_file = "dump_triclinic_with_units_run0.melt";
enable_triclinic();
generate_dump(dump_file, "units yes", 0);
ASSERT_FILE_EXISTS(dump_file);
auto lines = read_lines(dump_file);
ASSERT_EQ(lines.size(), 43);
ASSERT_THAT(lines[0], Eq("ITEM: UNITS"));
ASSERT_THAT(lines[1], Eq("lj"));
ASSERT_THAT(lines[6], Eq("ITEM: BOX BOUNDS xy xz yz pp pp pp"));
ASSERT_EQ(utils::split_words(lines[7]).size(), 3);
ASSERT_THAT(lines[10], Eq("ITEM: ATOMS id type xs ys zs"));
ASSERT_EQ(utils::split_words(lines[11]).size(), 5);
delete_file(dump_file);
}
TEST_F(DumpAtomTest, triclinic_with_time_run0)
{
auto dump_file = "dump_triclinic_with_time_run0.melt";
enable_triclinic();
generate_dump(dump_file, "time yes", 0);
ASSERT_FILE_EXISTS(dump_file);
auto lines = read_lines(dump_file);
ASSERT_EQ(lines.size(), 43);
ASSERT_THAT(lines[0], Eq("ITEM: TIME"));
ASSERT_THAT(lines[6], Eq("ITEM: BOX BOUNDS xy xz yz pp pp pp"));
ASSERT_EQ(utils::split_words(lines[7]).size(), 3);
ASSERT_THAT(lines[10], Eq("ITEM: ATOMS id type xs ys zs"));
ASSERT_EQ(utils::split_words(lines[11]).size(), 5);
delete_file(dump_file);
}
TEST_F(DumpAtomTest, triclinic_with_image_run0)
{
auto dump_file = "dump_triclinic_with_image_run0.melt";
enable_triclinic();
generate_dump(dump_file, "image yes", 0);
ASSERT_FILE_EXISTS(dump_file);
auto lines = read_lines(dump_file);
ASSERT_EQ(lines.size(), 41);
ASSERT_THAT(lines[4], Eq("ITEM: BOX BOUNDS xy xz yz pp pp pp"));
ASSERT_EQ(utils::split_words(lines[5]).size(), 3);
ASSERT_THAT(lines[8], Eq("ITEM: ATOMS id type xs ys zs ix iy iz"));
ASSERT_EQ(utils::split_words(lines[9]).size(), 8);
delete_file(dump_file);
}
//-------------------------------------------------------------------------------------------------
// binary formats
//-------------------------------------------------------------------------------------------------
TEST_F(DumpAtomTest, binary_run0)
{
if (!BINARY2TXT_BINARY) GTEST_SKIP();
auto text_file = "dump_text_run0.melt";
auto binary_file = "dump_binary_run0.melt.bin";
generate_text_and_binary_dump(text_file, binary_file, "", 0);
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(binary_file);
auto converted_file = convert_binary_to_text(binary_file);
ASSERT_FILE_EXISTS(converted_file);
ASSERT_FILE_EQUAL(text_file, converted_file);
delete_file(text_file);
delete_file(binary_file);
delete_file(converted_file);
}
TEST_F(DumpAtomTest, binary_with_units_run0)
{
if (!BINARY2TXT_BINARY) GTEST_SKIP();
auto text_file = "dump_text_with_units_run0.melt";
auto binary_file = "dump_binary_with_units_run0.melt.bin";
generate_text_and_binary_dump(text_file, binary_file, "scale no units yes", 0);
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(binary_file);
auto converted_file = convert_binary_to_text(binary_file);
ASSERT_FILE_EXISTS(converted_file);
ASSERT_FILE_EQUAL(text_file, converted_file);
delete_file(text_file);
delete_file(binary_file);
delete_file(converted_file);
}
TEST_F(DumpAtomTest, binary_with_time_run0)
{
if (!BINARY2TXT_BINARY) GTEST_SKIP();
auto text_file = "dump_text_with_time_run0.melt";
auto binary_file = "dump_binary_with_time_run0.melt.bin";
generate_text_and_binary_dump(text_file, binary_file, "scale no time yes", 0);
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(binary_file);
auto converted_file = convert_binary_to_text(binary_file);
ASSERT_FILE_EXISTS(converted_file);
ASSERT_FILE_EQUAL(text_file, converted_file);
delete_file(text_file);
delete_file(binary_file);
delete_file(converted_file);
}
TEST_F(DumpAtomTest, binary_triclinic_run0)
{
if (!BINARY2TXT_BINARY) GTEST_SKIP();
auto text_file = "dump_text_tri_run0.melt";
auto binary_file = "dump_binary_tri_run0.melt.bin";
enable_triclinic();
generate_text_and_binary_dump(text_file, binary_file, "", 0);
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(binary_file);
auto converted_file = convert_binary_to_text(binary_file);
ASSERT_FILE_EXISTS(converted_file);
ASSERT_FILE_EQUAL(text_file, converted_file);
delete_file(text_file);
delete_file(binary_file);
delete_file(converted_file);
}
TEST_F(DumpAtomTest, binary_triclinic_with_units_run0)
{
if (!BINARY2TXT_BINARY) GTEST_SKIP();
auto text_file = "dump_text_tri_with_units_run0.melt";
auto binary_file = "dump_binary_tri_with_units_run0.melt.bin";
enable_triclinic();
generate_text_and_binary_dump(text_file, binary_file, "scale no units yes", 0);
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(binary_file);
auto converted_file = convert_binary_to_text(binary_file);
ASSERT_FILE_EXISTS(converted_file);
ASSERT_FILE_EQUAL(text_file, converted_file);
delete_file(text_file);
delete_file(binary_file);
delete_file(converted_file);
}
TEST_F(DumpAtomTest, binary_triclinic_with_time_run0)
{
if (!BINARY2TXT_BINARY) GTEST_SKIP();
auto text_file = "dump_text_tri_with_time_run0.melt";
auto binary_file = "dump_binary_tri_with_time_run0.melt.bin";
enable_triclinic();
generate_text_and_binary_dump(text_file, binary_file, "scale no time yes", 0);
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(binary_file);
auto converted_file = convert_binary_to_text(binary_file);
ASSERT_FILE_EXISTS(converted_file);
ASSERT_FILE_EQUAL(text_file, converted_file);
delete_file(text_file);
delete_file(binary_file);
delete_file(converted_file);
}
TEST_F(DumpAtomTest, binary_triclinic_with_image_run0)
{
if (!BINARY2TXT_BINARY) GTEST_SKIP();
auto text_file = "dump_text_tri_with_image_run0.melt";
auto binary_file = "dump_binary_tri_with_image_run0.melt.bin";
enable_triclinic();
generate_text_and_binary_dump(text_file, binary_file, "image yes", 0);
ASSERT_FILE_EXISTS(text_file);
ASSERT_FILE_EXISTS(binary_file);
auto converted_file = convert_binary_to_text(binary_file);
ASSERT_FILE_EXISTS(converted_file);
ASSERT_FILE_EQUAL(text_file, converted_file);
delete_file(text_file);
delete_file(binary_file);
delete_file(converted_file);
}
TEST_F(DumpAtomTest, run1plus1)
{
auto dump_file = "dump_run1plus1.melt";
generate_dump(dump_file, "", 1);
ASSERT_FILE_EXISTS(dump_file);
ASSERT_EQ(count_lines(dump_file), 82);
continue_dump(1);
ASSERT_FILE_EXISTS(dump_file);
ASSERT_EQ(count_lines(dump_file), 123);
delete_file(dump_file);
}
TEST_F(DumpAtomTest, run2)
{
auto dump_file = "dump_run2.melt";
generate_dump(dump_file, "", 2);
ASSERT_FILE_EXISTS(dump_file);
ASSERT_EQ(count_lines(dump_file), 123);
delete_file(dump_file);
}
TEST_F(DumpAtomTest, rerun)
{
auto dump_file = "dump_rerun.melt";
HIDE_OUTPUT([&] {
command("fix 1 all nve");
});
generate_dump(dump_file, "format line \"%d %d %20.15g %20.15g %20.15g\"", 1);
double pe_1, pe_2, pe_rerun;
lmp->output->thermo->evaluate_keyword("pe", &pe_1);
ASSERT_FILE_EXISTS(dump_file);
ASSERT_EQ(count_lines(dump_file), 82);
continue_dump(1);
lmp->output->thermo->evaluate_keyword("pe", &pe_2);
ASSERT_FILE_EXISTS(dump_file);
ASSERT_EQ(count_lines(dump_file), 123);
HIDE_OUTPUT([&] {
command(fmt::format("rerun {} first 1 last 1 every 1 post no dump x y z", dump_file));
});
lmp->output->thermo->evaluate_keyword("pe", &pe_rerun);
ASSERT_DOUBLE_EQ(pe_1, pe_rerun);
HIDE_OUTPUT([&] {
command(fmt::format("rerun {} first 2 last 2 every 1 post yes dump x y z", dump_file));
});
lmp->output->thermo->evaluate_keyword("pe", &pe_rerun);
ASSERT_DOUBLE_EQ(pe_2, pe_rerun);
delete_file(dump_file);
}
TEST_F(DumpAtomTest, multi_file_run1)
{
auto dump_file = "dump_run1_*.melt";
generate_dump(dump_file, "", 1);
ASSERT_FILE_EXISTS("dump_run1_0.melt");
ASSERT_FILE_EXISTS("dump_run1_1.melt");
ASSERT_EQ(count_lines("dump_run1_0.melt"), 41);
ASSERT_EQ(count_lines("dump_run1_1.melt"), 41);
delete_file("dump_run1_0.melt");
delete_file("dump_run1_1.melt");
}
TEST_F(DumpAtomTest, per_processor_file_run1)
{
auto dump_file = "dump_run1_p%.melt";
generate_dump(dump_file, "", 1);
ASSERT_FILE_EXISTS("dump_run1_p0.melt");
ASSERT_EQ(count_lines("dump_run1_p0.melt"), 82);
delete_file("dump_run1_p0.melt");
}
TEST_F(DumpAtomTest, per_processor_multi_file_run1)
{
auto dump_file = "dump_run1_p%_*.melt";
generate_dump(dump_file, "", 1);
ASSERT_FILE_EXISTS("dump_run1_p0_0.melt");
ASSERT_FILE_EXISTS("dump_run1_p0_1.melt");
ASSERT_EQ(count_lines("dump_run1_p0_0.melt"), 41);
ASSERT_EQ(count_lines("dump_run1_p0_1.melt"), 41);
delete_file("dump_run1_p0_0.melt");
delete_file("dump_run1_p0_1.melt");
}
TEST_F(DumpAtomTest, dump_modify_scale_invalid)
{
BEGIN_HIDE_OUTPUT();
command("dump id all atom 1 dump.txt");
END_HIDE_OUTPUT();
TEST_FAILURE(".*Illegal dump_modify command.*", command("dump_modify id scale true"););
}
TEST_F(DumpAtomTest, dump_modify_image_invalid)
{
BEGIN_HIDE_OUTPUT();
command("dump id all atom 1 dump.txt");
END_HIDE_OUTPUT();
TEST_FAILURE(".*Illegal dump_modify command.*", command("dump_modify id image true"););
}
TEST_F(DumpAtomTest, dump_modify_invalid)
{
BEGIN_HIDE_OUTPUT();
command("dump id all atom 1 dump.txt");
END_HIDE_OUTPUT();
TEST_FAILURE(".*Illegal dump_modify command.*", command("dump_modify id true"););
}
TEST_F(DumpAtomTest, write_dump)
{
auto reference = "dump_ref_run0.melt";
auto dump_file = "write_dump_atom_run0.melt";
BEGIN_HIDE_OUTPUT();
command(fmt::format("dump id all atom 1 {}", reference));
command("dump_modify id scale no units yes");
command("run 0");
command("write_dump all atom write_dump_atom_run*.melt modify scale no units yes");
END_HIDE_OUTPUT();
ASSERT_FILE_EXISTS(reference);
ASSERT_FILE_EXISTS(dump_file);
ASSERT_FILE_EQUAL(reference, dump_file);
delete_file(reference);
delete_file(dump_file);
}
TEST_F(DumpAtomTest, binary_write_dump)
{
if (!BINARY2TXT_BINARY) GTEST_SKIP();
auto reference = "dump_run0.melt.bin";
auto dump_file = "write_dump_atom_run0_p0.melt.bin";
BEGIN_HIDE_OUTPUT();
command(fmt::format("dump id all atom 1 {}", reference));
command("dump_modify id scale no units yes");
command("run 0");
command("write_dump all atom write_dump_atom_run*_p%.melt.bin modify scale no units yes");
END_HIDE_OUTPUT();
ASSERT_FILE_EXISTS(reference);
ASSERT_FILE_EXISTS(dump_file);
auto reference_txt = convert_binary_to_text(reference);
auto dump_file_txt = convert_binary_to_text(dump_file);
ASSERT_FILE_EXISTS(reference_txt);
ASSERT_FILE_EXISTS(dump_file_txt);
ASSERT_FILE_EQUAL(reference_txt, dump_file_txt);
delete_file(reference_txt);
delete_file(dump_file_txt);
delete_file(reference);
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;
}
}
}
BINARY2TXT_BINARY = getenv("BINARY2TXT_BINARY");
if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
int rv = RUN_ALL_TESTS();
MPI_Finalize();
return rv;
}
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