setup a simple improper-harmonic test

This commit is contained in:
abhishandy
2020-08-08 15:58:41 -04:00
parent ffb074e812
commit a33c0081cd
3 changed files with 904 additions and 8 deletions

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@ -96,7 +96,7 @@ endforeach()
add_executable(test_angle_style test_angle_style.cpp)
target_link_libraries(test_angle_style PRIVATE lammps style_tests)
file(GLOB IMPROPER_TESTS LIST_DIRECTORIES false ${TEST_INPUT_FOLDER}/angle-*.yaml)
file(GLOB ANGLE_TESTS LIST_DIRECTORIES false ${TEST_INPUT_FOLDER}/angle-*.yaml)
foreach(TEST ${ANGLE_TESTS})
string(REGEX REPLACE "^.*angle-(.*)\.yaml" "AngleStyle:\\1" TNAME ${TEST})
add_test(NAME ${TNAME} COMMAND test_angle_style ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})

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@ -72,6 +72,8 @@ static void delete_file(const std::string &filename)
remove(filename.c_str());
};
// Clean auxilliary files generated during the test
// which are also useful for debugging failing tests
void cleanup_lammps(LAMMPS *lmp, const TestConfig &cfg)
{
delete_file(cfg.basename + ".restart");
@ -80,6 +82,82 @@ void cleanup_lammps(LAMMPS *lmp, const TestConfig &cfg)
delete lmp;
}
// Initialize LAMMPS
// with the certain arguments, test configuration and an optional flag for newton
LAMMPS *init_lammps(int argc, char **argv, const TestConfig &cfg, const bool newton = true)
{
LAMMPS *lmp;
lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD);
// check if prerequisite styles are available
Info *info = new Info(lmp);
int nfail = 0;
for (auto &prerequisite : cfg.prerequisites) {
std::string style = prerequisite.second;
// if the suffixed version of improper style is not available, don't test it
if (prerequisite.first == "improper") {
if (lmp->suffix_enable) {
style += "/";
style += lmp->suffix;
}
}
if (!info->has_style(prerequisite.first, style)) ++nfail;
}
delete info;
// abort if prerequisites are not met
if (nfail > 0) {
cleanup_lammps(lmp, cfg);
return nullptr;
}
// utility lambdas to improve readability
// execute a single-line command
auto command = [&](const std::string &line) {
lmp->input->one(line.c_str());
};
// parse and execute all commands in a file
auto parse_input_script = [&](const std::string &filename) {
lmp->input->file(filename.c_str());
};
if (newton) {
command("variable newton_bond index on");
} else {
command("variable newton_bond index off");
}
command("variable input_dir index " + INPUT_FOLDER);
for (auto &pre_command : cfg.pre_commands) {
command(pre_command);
}
std::string input_file = INPUT_FOLDER + PATH_SEP + cfg.input_file;
parse_input_script(input_file);
command("improper_style " + cfg.improper_style);
for (auto &improper_coeff : cfg.improper_coeff) {
command("improper_coeff " + improper_coeff);
}
for (auto &post_command : cfg.post_commands) {
command(post_command);
}
command("run 0 post no");
// auxilliary files for running and debugging tests
command("write_restart " + cfg.basename + ".restart");
command("write_data " + cfg.basename + ".data");
command("write_coeff " + cfg.basename + "-coeffs.in");
return lmp;
}
// Run a very short NVE simulation
void run_lammps(LAMMPS *lmp)
{
// utility lambda to improve readability
@ -88,6 +166,7 @@ void run_lammps(LAMMPS *lmp)
};
command("fix 1 all nve");
// just measure the relevant part of potential energy
command("compute pe all pe/atom improper");
command("compute sum all reduce sum c_pe");
command("thermo_style custom step temp pe press c_sum");
@ -95,14 +174,748 @@ void run_lammps(LAMMPS *lmp)
command("run 4 post no");
}
LAMMPS *init_lammps(int argc, char **argv, const TestConfig &cfg, const bool newton = true){}
// Restart LAMMPS simulation
// to test "write_restart" and "read_restart" functions of improper styles
void restart_lammps(LAMMPS *lmp, const TestConfig &cfg)
{
// utility lambda to improve readability
auto command = [&](const std::string &line) {
lmp->input->one(line.c_str());
};
void restart_lammps(LAMMPS *lmp, const TestConfig &cfg){}
command("clear");
command("read_restart " + cfg.basename + ".restart");
void data_lammps(LAMMPS *lmp, const TestConfig &cfg){}
// add the improper style if it's not defined already in the restart file
if (!lmp->force->improper) {
command("improper_style " + cfg.improper_style);
}
void generate_yaml_file(const char *outfile, const TestConfig &config){}
// add the improper coefficients if hybrid style is used
// or somehow they aren't defined already in the restart file
if ((cfg.improper_style.substr(0, 6) == "hybrid") || !lmp->force->improper->writedata) {
for (auto &improper_coeff : cfg.improper_coeff) {
command("improper_coeff " + improper_coeff);
}
}
TEST(ImproperStyle, plain){}
TEST(ImproperStyle, omp){}
TEST(ImproperStyle, single){}
for (auto &post_command : cfg.post_commands) {
command(post_command);
}
command("run 0 post no");
}
// What's the purpose?
// Reads the input structure of atoms
// sets some essential variables
void data_lammps(LAMMPS *lmp, const TestConfig &cfg)
{
// utility lambdas to improve readability
auto command = [&](const std::string &line) {
lmp->input->one(line.c_str());
};
auto parse_input_script = [&](const std::string &filename) {
lmp->input->file(filename.c_str());
};
command("clear"); // clears everything except variables, log, echo
command("variable improper_style delete");
command("variable data_file delete");
command("variable newton_bond delete");
command("variable newton_bond index on");
for (auto &pre_command : cfg.pre_commands) {
command(pre_command);
}
command("variable improper_style index '" + cfg.improper_style + "'");
command("variable data_file index " + cfg.basename + ".data");
std::string input_file = INPUT_FOLDER + PATH_SEP + cfg.input_file;
parse_input_script(input_file);
for (auto &improper_coeff : cfg.improper_coeff) {
command("improper_coeff " + improper_coeff);
}
for (auto &post_command : cfg.post_commands) {
command(post_command);
}
command("run 0 post no");
}
void generate_yaml_file(const char *outfile, const TestConfig &config)
{
// initialize system geometry
const char *args[] = {"ImproperStyle", "-log", "none", "-echo", "screen", "-nocite"};
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
LAMMPS *lmp = init_lammps(argc, argv, config);
if (!lmp) {
std::cerr << "One or more prerequisite styles are not available "
"in this LAMMPS configuration:\n";
for (auto &prerequisite : config.prerequisites) {
std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n";
}
return;
}
const int natoms = lmp->atom->natoms;
std::string block("");
YamlWriter writer(outfile);
// lammps_version
writer.emit("lammps_version", lmp->universe->version);
// date_generated
std::time_t now = time(NULL);
block = ctime(&now);
block = block.substr(0, block.find("\n") - 1);
writer.emit("date_generated", block);
// epsilon
writer.emit("epsilon", config.epsilon);
// prerequisites
block.clear();
for (auto &prerequisite : config.prerequisites) {
block += prerequisite.first + " " + prerequisite.second + "\n";
}
writer.emit_block("prerequisites", block);
// pre_commands
block.clear();
for (auto &command : config.pre_commands) {
block += command + "\n";
}
writer.emit_block("pre_commands", block);
// post_commands
block.clear();
for (auto &command : config.post_commands) {
block += command + "\n";
}
writer.emit_block("post_commands", block);
// input_file
writer.emit("input_file", config.input_file);
// improper_style
writer.emit("improper_style", config.improper_style);
// improper_coeff
block.clear();
for (auto &improper_coeff : config.improper_coeff) {
block += improper_coeff + "\n";
}
writer.emit_block("improper_coeff", block);
// equilibrium improper
// block = fmt::format("{}", lmp->atom->nimpropertypes);
// for (int i = 0; i < lmp->atom->nimpropertypes; ++i)
// block += fmt::format(" {}", lmp->force->improper->equilibrium_improper(i + 1));
// writer.emit("equilibrium", block);
// extract
block.clear();
for (auto data : config.extract)
block += fmt::format("{} {}\n", data.first, data.second);
writer.emit_block("extract", block);
// natoms
writer.emit("natoms", natoms);
// init_energy
writer.emit("init_energy", lmp->force->improper->energy);
// init_stress
auto stress = lmp->force->improper->virial;
block = fmt::format("{:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e}", stress[0],
stress[1], stress[2], stress[3], stress[4], stress[5]);
writer.emit_block("init_stress", block);
// init_forces
block.clear();
auto f = lmp->atom->f;
auto tag = lmp->atom->tag;
for (int i = 1; i <= natoms; ++i) {
const int j = lmp->atom->map(i);
block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]);
}
writer.emit_block("init_forces", block);
// do a few steps of MD
run_lammps(lmp);
// run_energy
writer.emit("run_energy", lmp->force->improper->energy);
// run_stress
stress = lmp->force->improper->virial;
block = fmt::format("{:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e} {:23.16e}", stress[0],
stress[1], stress[2], stress[3], stress[4], stress[5]);
writer.emit_block("run_stress", block);
block.clear();
f = lmp->atom->f;
tag = lmp->atom->tag;
for (int i = 1; i <= natoms; ++i) {
const int j = lmp->atom->map(i);
block += fmt::format("{:3} {:23.16e} {:23.16e} {:23.16e}\n", i, f[j][0], f[j][1], f[j][2]);
}
writer.emit_block("run_forces", block);
cleanup_lammps(lmp, config);
return;
}
TEST(ImproperStyle, plain)
{
const char *args[] = {"ImproperStyle", "-log", "none", "-echo", "screen", "-nocite"};
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
::testing::internal::CaptureStdout();
LAMMPS *lmp = init_lammps(argc, argv, test_config, true);
std::string output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output;
if (!lmp) {
std::cerr << "One or more prerequisite styles are not available "
"in this LAMMPS configuration:\n";
for (auto &prerequisite : test_config.prerequisites) {
std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n";
}
GTEST_SKIP();
}
EXPECT_THAT(output, StartsWith("LAMMPS ("));
EXPECT_THAT(output, HasSubstr("Loop time"));
// abort if running in parallel and not all atoms are local
const int nlocal = lmp->atom->nlocal;
ASSERT_EQ(lmp->atom->natoms, nlocal);
double epsilon = test_config.epsilon;
auto f = lmp->atom->f;
auto tag = lmp->atom->tag;
ErrorStats stats;
stats.reset();
const std::vector<coord_t> &f_ref = test_config.init_forces;
ASSERT_EQ(nlocal + 1, f_ref.size());
for (int i = 0; i < nlocal; ++i) {
EXPECT_FP_LE_WITH_EPS(f[i][0], f_ref[tag[i]].x, epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][1], f_ref[tag[i]].y, epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][2], f_ref[tag[i]].z, epsilon);
}
if (print_stats) std::cerr << "init_forces stats, newton on: " << stats << std::endl;
auto improper = lmp->force->improper;
auto stress = improper->virial;
stats.reset();
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.init_stress.zz, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.init_stress.xy, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.init_stress.xz, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.init_stress.yz, epsilon);
if (print_stats) std::cerr << "init_stress stats, newton on: " << stats << std::endl;
stats.reset();
EXPECT_FP_LE_WITH_EPS(improper->energy, test_config.init_energy, epsilon);
if (print_stats) std::cerr << "init_energy stats, newton on: " << stats << std::endl;
if (!verbose) ::testing::internal::CaptureStdout();
run_lammps(lmp);
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
tag = lmp->atom->tag;
stress = improper->virial;
const std::vector<coord_t> &f_run = test_config.run_forces;
ASSERT_EQ(nlocal + 1, f_run.size());
stats.reset();
for (int i = 0; i < nlocal; ++i) {
EXPECT_FP_LE_WITH_EPS(f[i][0], f_run[tag[i]].x, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][1], f_run[tag[i]].y, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][2], f_run[tag[i]].z, 10 * epsilon);
}
if (print_stats) std::cerr << "run_forces stats, newton on: " << stats << std::endl;
stress = improper->virial;
stats.reset();
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon);
if (print_stats) std::cerr << "run_stress stats, newton on: " << stats << std::endl;
stats.reset();
int id = lmp->modify->find_compute("sum");
double energy = lmp->modify->compute[id]->compute_scalar();
EXPECT_FP_LE_WITH_EPS(improper->energy, test_config.run_energy, epsilon);
EXPECT_FP_LE_WITH_EPS(improper->energy, energy, epsilon);
if (print_stats) std::cerr << "run_energy stats, newton on: " << stats << std::endl;
if (!verbose) ::testing::internal::CaptureStdout();
cleanup_lammps(lmp, test_config);
lmp = init_lammps(argc, argv, test_config, false);
if (!verbose) ::testing::internal::GetCapturedStdout();
// skip over these tests if newton bond is forced to be on
if (lmp->force->newton_bond == 0) {
f = lmp->atom->f;
tag = lmp->atom->tag;
stats.reset();
for (int i = 0; i < nlocal; ++i) {
EXPECT_FP_LE_WITH_EPS(f[i][0], f_ref[tag[i]].x, epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][1], f_ref[tag[i]].y, epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][2], f_ref[tag[i]].z, epsilon);
}
if (print_stats) std::cerr << "init_forces stats, newton off:" << stats << std::endl;
improper = lmp->force->improper;
stress = improper->virial;
stats.reset();
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, 2 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, 2 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.init_stress.zz, 2 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.init_stress.xy, 2 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.init_stress.xz, 2 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.init_stress.yz, 2 * epsilon);
if (print_stats) std::cerr << "init_stress stats, newton off:" << stats << std::endl;
stats.reset();
EXPECT_FP_LE_WITH_EPS(improper->energy, test_config.init_energy, epsilon);
if (print_stats) std::cerr << "init_energy stats, newton off:" << stats << std::endl;
if (!verbose) ::testing::internal::CaptureStdout();
run_lammps(lmp);
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
tag = lmp->atom->tag;
stress = improper->virial;
stats.reset();
for (int i = 0; i < nlocal; ++i) {
EXPECT_FP_LE_WITH_EPS(f[i][0], f_run[tag[i]].x, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][1], f_run[tag[i]].y, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][2], f_run[tag[i]].z, 10 * epsilon);
}
if (print_stats) std::cerr << "run_forces stats, newton off:" << stats << std::endl;
stress = improper->virial;
stats.reset();
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, epsilon);
if (print_stats) std::cerr << "run_stress stats, newton off:" << stats << std::endl;
stats.reset();
id = lmp->modify->find_compute("sum");
energy = lmp->modify->compute[id]->compute_scalar();
EXPECT_FP_LE_WITH_EPS(improper->energy, test_config.run_energy, epsilon);
EXPECT_FP_LE_WITH_EPS(improper->energy, energy, epsilon);
if (print_stats) std::cerr << "run_energy stats, newton off:" << stats << std::endl;
}
if (!verbose) ::testing::internal::CaptureStdout();
restart_lammps(lmp, test_config);
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
tag = lmp->atom->tag;
stats.reset();
ASSERT_EQ(nlocal + 1, f_ref.size());
for (int i = 0; i < nlocal; ++i) {
EXPECT_FP_LE_WITH_EPS(f[i][0], f_ref[tag[i]].x, epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][1], f_ref[tag[i]].y, epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][2], f_ref[tag[i]].z, epsilon);
}
if (print_stats) std::cerr << "restart_forces stats:" << stats << std::endl;
improper = lmp->force->improper;
stress = improper->virial;
stats.reset();
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.init_stress.zz, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.init_stress.xy, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.init_stress.xz, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.init_stress.yz, epsilon);
if (print_stats) std::cerr << "restart_stress stats:" << stats << std::endl;
stats.reset();
EXPECT_FP_LE_WITH_EPS(improper->energy, test_config.init_energy, epsilon);
if (print_stats) std::cerr << "restart_energy stats:" << stats << std::endl;
if (!verbose) ::testing::internal::CaptureStdout();
data_lammps(lmp, test_config);
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
tag = lmp->atom->tag;
stats.reset();
ASSERT_EQ(nlocal + 1, f_ref.size());
for (int i = 0; i < nlocal; ++i) {
EXPECT_FP_LE_WITH_EPS(f[i][0], f_ref[tag[i]].x, epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][1], f_ref[tag[i]].y, epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][2], f_ref[tag[i]].z, epsilon);
}
if (print_stats) std::cerr << "data_forces stats:" << stats << std::endl;
improper = lmp->force->improper;
stress = improper->virial;
stats.reset();
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.init_stress.zz, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.init_stress.xy, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.init_stress.xz, epsilon);
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.init_stress.yz, epsilon);
if (print_stats) std::cerr << "data_stress stats:" << stats << std::endl;
stats.reset();
EXPECT_FP_LE_WITH_EPS(improper->energy, test_config.init_energy, epsilon);
if (print_stats) std::cerr << "data_energy stats:" << stats << std::endl;
if (!verbose) ::testing::internal::CaptureStdout();
cleanup_lammps(lmp, test_config);
if (!verbose) ::testing::internal::GetCapturedStdout();
};
TEST(ImproperStyle, omp)
{
if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP();
const char *args[] = {"ImproperStyle", "-log", "none", "-echo", "screen", "-nocite",
"-pk", "omp", "4", "-sf", "omp"};
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
::testing::internal::CaptureStdout();
LAMMPS *lmp = init_lammps(argc, argv, test_config, true);
std::string output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output;
if (!lmp) {
std::cerr << "One or more prerequisite styles with /omp suffix\n"
"are not available in this LAMMPS configuration:\n";
for (auto &prerequisite : test_config.prerequisites) {
std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n";
}
GTEST_SKIP();
}
EXPECT_THAT(output, StartsWith("LAMMPS ("));
EXPECT_THAT(output, HasSubstr("Loop time"));
// abort if running in parallel and not all atoms are local
const int nlocal = lmp->atom->nlocal;
ASSERT_EQ(lmp->atom->natoms, nlocal);
// relax error a bit for USER-OMP package
double epsilon = 5.0 * test_config.epsilon;
auto f = lmp->atom->f;
auto tag = lmp->atom->tag;
const std::vector<coord_t> &f_ref = test_config.init_forces;
ErrorStats stats;
stats.reset();
for (int i = 0; i < nlocal; ++i) {
EXPECT_FP_LE_WITH_EPS(f[i][0], f_ref[tag[i]].x, epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][1], f_ref[tag[i]].y, epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][2], f_ref[tag[i]].z, epsilon);
}
if (print_stats) std::cerr << "init_forces stats, newton on: " << stats << std::endl;
auto improper = lmp->force->improper;
auto stress = improper->virial;
stats.reset();
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.init_stress.zz, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.init_stress.xy, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.init_stress.xz, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.init_stress.yz, 10 * epsilon);
if (print_stats) std::cerr << "init_stress stats, newton on: " << stats << std::endl;
stats.reset();
EXPECT_FP_LE_WITH_EPS(improper->energy, test_config.init_energy, epsilon);
if (print_stats) std::cerr << "init_energy stats, newton on: " << stats << std::endl;
if (!verbose) ::testing::internal::CaptureStdout();
run_lammps(lmp);
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
tag = lmp->atom->tag;
stress = improper->virial;
const std::vector<coord_t> &f_run = test_config.run_forces;
ASSERT_EQ(nlocal + 1, f_run.size());
stats.reset();
for (int i = 0; i < nlocal; ++i) {
EXPECT_FP_LE_WITH_EPS(f[i][0], f_run[tag[i]].x, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][1], f_run[tag[i]].y, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][2], f_run[tag[i]].z, 10 * epsilon);
}
if (print_stats) std::cerr << "run_forces stats, newton on: " << stats << std::endl;
stress = improper->virial;
stats.reset();
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, 10 * epsilon);
if (print_stats) std::cerr << "run_stress stats, newton on: " << stats << std::endl;
stats.reset();
int id = lmp->modify->find_compute("sum");
double energy = lmp->modify->compute[id]->compute_scalar();
EXPECT_FP_LE_WITH_EPS(improper->energy, test_config.run_energy, epsilon);
// TODO: this is currently broken for USER-OMP with improper style hybrid
// needs to be fixed in the main code somewhere. Not sure where, though.
if (test_config.improper_style.substr(0, 6) != "hybrid")
EXPECT_FP_LE_WITH_EPS(improper->energy, energy, epsilon);
if (print_stats) std::cerr << "run_energy stats, newton on: " << stats << std::endl;
if (!verbose) ::testing::internal::CaptureStdout();
cleanup_lammps(lmp, test_config);
lmp = init_lammps(argc, argv, test_config, false);
if (!verbose) ::testing::internal::GetCapturedStdout();
// skip over these tests if newton bond is forced to be on
if (lmp->force->newton_bond == 0) {
f = lmp->atom->f;
tag = lmp->atom->tag;
stats.reset();
for (int i = 0; i < nlocal; ++i) {
EXPECT_FP_LE_WITH_EPS(f[i][0], f_ref[tag[i]].x, epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][1], f_ref[tag[i]].y, epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][2], f_ref[tag[i]].z, epsilon);
}
if (print_stats) std::cerr << "init_forces stats, newton off:" << stats << std::endl;
improper = lmp->force->improper;
stress = improper->virial;
stats.reset();
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.init_stress.xx, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.init_stress.yy, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.init_stress.zz, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.init_stress.xy, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.init_stress.xz, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.init_stress.yz, 10 * epsilon);
if (print_stats) std::cerr << "init_stress stats, newton off:" << stats << std::endl;
stats.reset();
EXPECT_FP_LE_WITH_EPS(improper->energy, test_config.init_energy, epsilon);
if (print_stats) std::cerr << "init_energy stats, newton off:" << stats << std::endl;
if (!verbose) ::testing::internal::CaptureStdout();
run_lammps(lmp);
if (!verbose) ::testing::internal::GetCapturedStdout();
f = lmp->atom->f;
tag = lmp->atom->tag;
stats.reset();
for (int i = 0; i < nlocal; ++i) {
EXPECT_FP_LE_WITH_EPS(f[i][0], f_run[tag[i]].x, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][1], f_run[tag[i]].y, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(f[i][2], f_run[tag[i]].z, 10 * epsilon);
}
if (print_stats) std::cerr << "run_forces stats, newton off:" << stats << std::endl;
stress = improper->virial;
stats.reset();
EXPECT_FP_LE_WITH_EPS(stress[0], test_config.run_stress.xx, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[1], test_config.run_stress.yy, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[2], test_config.run_stress.zz, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[3], test_config.run_stress.xy, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[4], test_config.run_stress.xz, 10 * epsilon);
EXPECT_FP_LE_WITH_EPS(stress[5], test_config.run_stress.yz, 10 * epsilon);
if (print_stats) std::cerr << "run_stress stats, newton off:" << stats << std::endl;
stats.reset();
id = lmp->modify->find_compute("sum");
energy = lmp->modify->compute[id]->compute_scalar();
EXPECT_FP_LE_WITH_EPS(improper->energy, test_config.run_energy, epsilon);
// TODO: this is currently broken for USER-OMP with improper style hybrid
// needs to be fixed in the main code somewhere. Not sure where, though.
if (test_config.improper_style.substr(0, 6) != "hybrid")
EXPECT_FP_LE_WITH_EPS(improper->energy, energy, epsilon);
if (print_stats) std::cerr << "run_energy stats, newton off:" << stats << std::endl;
}
if (!verbose) ::testing::internal::CaptureStdout();
cleanup_lammps(lmp, test_config);
if (!verbose) ::testing::internal::GetCapturedStdout();
};
// TODO: Improper styles do not have single() routines
/*
TEST(ImproperStyle, single)
{
const char *args[] = {"ImproperStyle", "-log", "none", "-echo", "screen", "-nocite"};
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
// create a LAMMPS instance with standard settings to detect the number of atom types
if (!verbose) ::testing::internal::CaptureStdout();
LAMMPS *lmp = init_lammps(argc, argv, test_config);
if (!verbose) ::testing::internal::GetCapturedStdout();
if (!lmp) {
std::cerr << "One or more prerequisite styles are not available "
"in this LAMMPS configuration:\n";
for (auto &prerequisite : test_config.prerequisites) {
std::cerr << prerequisite.first << "_style " << prerequisite.second << "\n";
}
GTEST_SKIP();
}
// gather some information and skip if unsupported
int nimpropertypes = lmp->atom->nimpropertypes;
int molecular = lmp->atom->molecular;
if (molecular != 1) {
std::cerr << "Only simple molecular atom styles are supported\n";
if (!verbose) ::testing::internal::CaptureStdout();
cleanup_lammps(lmp, test_config);
if (!verbose) ::testing::internal::GetCapturedStdout();
GTEST_SKIP();
}
// utility lambda to improve readability
auto command = [&](const std::string &line) {
lmp->input->one(line.c_str());
};
// now start over
if (!verbose) ::testing::internal::CaptureStdout();
command("clear");
command("variable newton_bond delete");
command("variable newton_bond index on");
command("variable input_dir index " + INPUT_FOLDER);
for (auto &pre_command : test_config.pre_commands) {
command(pre_command);
}
command("atom_style molecular");
command("units ${units}");
command("boundary p p p");
command("newton ${newton_pair} ${newton_bond}");
command("special_bonds lj/coul "
"${bond_factor} ${angle_factor} ${dihedral_factor}");
command("atom_modify map array");
command("region box block -10.0 10.0 -10.0 10.0 -10.0 10.0 units box");
command(fmt::format("create_box 1 box improper/types {} "
"extra/improper/per/atom 2 extra/special/per/atom 2",
nimpropertypes));
command("pair_style zero 8.0");
command("pair_coeff * *");
command("improper_style " + test_config.improper_style);
Improper *improper = lmp->force->improper;
for (auto &improper_coeff : test_config.improper_coeff) {
command("improper_coeff " + improper_coeff);
}
// create (only) four atoms and one improper
command("mass * 1.0");
command("create_atoms 1 single 5.0 -0.75 0.4 units box");
command("create_atoms 1 single 5.5 0.25 -0.1 units box");
command("create_atoms 1 single 5.0 0.75 0.4 units box");
command("create_atoms 1 single 5.5 1.25 -0.1 units box");
command("create_bonds single/improper 1 1 2 3 4");
for (auto &post_command : test_config.post_commands) {
command(post_command);
}
command("run 0 post no");
if (!verbose) ::testing::internal::GetCapturedStdout();
int idx1 = lmp->atom->map(1);
int idx2 = lmp->atom->map(2);
int idx3 = lmp->atom->map(3);
double epsilon = test_config.epsilon;
double eangle[4], esingle[4];
// TODO: why are atoms displaced randomly?
eangle[0] = angle->energy;
esingle[0] = angle->single(1, idx1, idx2, idx3);
if (!verbose) ::testing::internal::CaptureStdout();
command("displace_atoms all random 0.5 0.5 0.5 23456");
command("run 0 post no");
if (!verbose) ::testing::internal::GetCapturedStdout();
idx1 = lmp->atom->map(1);
idx2 = lmp->atom->map(2);
idx3 = lmp->atom->map(3);
eangle[1] = angle->energy;
esingle[1] = angle->single(1, idx1, idx2, idx3);
if (!verbose) ::testing::internal::CaptureStdout();
command("displace_atoms all random 0.5 0.5 0.5 456963");
command("run 0 post no");
if (!verbose) ::testing::internal::GetCapturedStdout();
idx1 = lmp->atom->map(1);
idx2 = lmp->atom->map(2);
idx3 = lmp->atom->map(3);
eangle[2] = angle->energy;
esingle[2] = angle->single(1, idx1, idx2, idx3);
if (!verbose) ::testing::internal::CaptureStdout();
command("displace_atoms all random 0.5 0.5 0.5 9726532");
command("run 0 post no");
if (!verbose) ::testing::internal::GetCapturedStdout();
idx1 = lmp->atom->map(1);
idx2 = lmp->atom->map(2);
idx3 = lmp->atom->map(3);
eangle[3] = angle->energy;
esingle[3] = angle->single(1, idx1, idx2, idx3);
ErrorStats stats;
EXPECT_FP_LE_WITH_EPS(eangle[0], esingle[0], epsilon);
EXPECT_FP_LE_WITH_EPS(eangle[1], esingle[1], epsilon);
EXPECT_FP_LE_WITH_EPS(eangle[2], esingle[2], epsilon);
EXPECT_FP_LE_WITH_EPS(eangle[3], esingle[3], epsilon);
if (print_stats) std::cerr << "single_energy stats:" << stats << std::endl;
// int i = 0;
// for (auto &dist : test_config.equilibrium)
// EXPECT_NEAR(dist, angle->equilibrium_angle(++i), 0.00001);
if (!verbose) ::testing::internal::CaptureStdout();
cleanup_lammps(lmp, test_config);
if (!verbose) ::testing::internal::GetCapturedStdout();
}
*/

View File

@ -0,0 +1,83 @@
---
lammps_version: 30 Jun 2020
date_generated: Sun Jul 12 19:14:28 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
improper harmonic
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
improper_style: harmonic
improper_coeff: ! |
1 75.0 0.1
2 45.0 1.0
extract: ! ""
natoms: 29
init_energy: 41.530817896491
init_stress: ! |2-
8.9723357320869255e+01 -8.7188643750026529e+01 -2.5347135708427588e+00 9.2043419883119697e+01 -2.8187238090404989e+01 -1.5291148024927028e+00
init_forces: ! |2
1 4.7865489310693519e+01 7.8760925902181782e+00 -3.2694525514709809e+01
2 -1.1124882516177386e+00 -9.0075464203887741e+00 -7.2431691227364725e+00
3 -5.9057050592858884e+00 5.3263619873546183e+01 5.2353380124691370e+01
4 -1.6032230038990651e+01 -2.4560529343731371e+01 1.2891625920422349e+01
5 -4.4802331573497668e+01 -4.8300919461089343e+01 -2.3310767889219321e+01
6 4.7083124388174838e+01 -9.5212933434476135e+00 -3.2526392870546800e+01
7 -1.6208182775476303e+01 1.4458587960739102e+01 -3.5314745459502710e+00
8 -6.5664612141880827e+00 -2.5126850154274180e+01 8.2187944731423329e+01
9 -1.5504395262358301e+01 1.6121044185227817e+01 -4.2007069622477866e-01
10 9.9863759179364777e+00 4.1873540105704535e+01 -6.6085640966037388e+01
11 -2.0441876158908627e+01 -6.5186824168985984e+00 9.0023620309811072e+00
12 -1.0772126658369636e+01 -1.0807367300158273e+01 -9.6049647456797036e+00
13 2.8847886813946415e+00 7.2973241014859491e+00 -1.0414233993845645e-01
14 1.5267407478336423e+01 -9.4754911480231527e+00 -6.6307012925544306e+00
15 1.2402914209534794e+01 -6.2644630791613860e+00 1.8484576795819905e+01
16 3.8927757686513598e-01 1.0690061587911142e+01 6.1542759189377589e+00
17 1.4664194297570587e+00 -1.9971277376602155e+00 1.0776844613215855e+00
18 1.5785371874873189e-01 1.6495665212200037e+00 -6.6944747776989910e+00
19 -1.9328033033421517e+00 -2.4078805870919515e+00 2.8669575541313312e+00
20 1.7749495845934198e+00 7.5831406587194772e-01 3.8275172235676602e+00
21 3.4186149299343622e+00 4.2795410364249307e+00 -1.2789555411020601e+01
22 -6.0875600315279446e+00 -4.1504951869796436e+00 4.5212856070195588e+00
23 2.6689451015935823e+00 -1.2904584944528708e-01 8.2682698040010418e+00
24 -1.3053945393770472e+00 5.0741459325182818e+00 -3.0209518576072751e+00
25 -1.0471133765834191e+00 -3.5082261409793545e+00 5.7374874908500728e-01
26 2.3525079159604663e+00 -1.5659197915389276e+00 2.4472031085222676e+00
27 -2.8720725187343144e-01 2.3577465459556626e+00 -8.0312673032167137e-01
28 -6.2799575211499037e-01 -1.4097313073755557e+00 3.2747938980615732e-02
29 9.1520300398842180e-01 -9.4801523858010661e-01 7.7037879134105569e-01
run_energy: 29.2286477697792
run_stress: ! |2-
6.7161703985479804e+01 -7.4680138065367487e+01 7.5184340798876628e+00 5.7521437901240859e+01 -2.7304190748521741e+01 -1.4932945649428730e+01
run_forces: ! |2
1 3.6220193547187421e+01 1.1585587142479543e+01 -1.7238241972840832e+01
2 -1.7637583558698005e+00 -1.3758538851839576e+01 -1.1469071109412811e+01
3 -7.1131175159873123e+00 3.1523130842685575e+01 3.9133327910920059e+01
4 -1.1598618479874565e+01 -1.4069946914275834e+01 1.1631964860700649e+01
5 -3.5092143924598361e+01 -3.4761325046913356e+01 -2.1062123798094685e+01
6 4.3880849952881221e+01 -6.1732167988806808e+00 -2.6034788339533922e+01
7 -1.4366916728367741e+01 1.3135040103127027e+01 -3.0387136809768127e+00
8 -8.5333281419768383e+00 -2.4737111100998256e+01 6.5176870591189868e+01
9 -1.2996571868203590e+01 1.3674206710496604e+01 -6.7871105914534047e-01
10 1.1736432849972278e+01 3.5147252452549246e+01 -4.9691358934493337e+01
11 -1.9930599656448706e+01 -3.2836744898198571e+00 7.6150969595859577e+00
12 -5.8293065548538978e+00 -1.3423749355667645e+01 -5.2738511429383701e+00
13 7.7658418286980746e-01 2.0512357329017221e+00 1.8932242747136039e+00
14 1.2984672111772401e+01 -7.2763363322049823e-01 -4.8588140465034959e+00
15 7.4743142834562555e+00 -3.4640965582760748e+00 9.4855052919847029e+00
16 3.6043562512330887e+00 8.0382102532623243e+00 4.0048096667552189e+00
17 5.4695804680833793e-01 -7.5537048761027403e-01 4.0487452808954988e-01
18 -1.1709942604030477e-01 -8.9468235295761567e-01 3.5008479949198765e+00
19 9.8256914435044085e-01 1.2515894863018922e+00 -1.5372413162209382e+00
20 -8.6546971831013608e-01 -3.5690713334427648e-01 -1.9636066786989381e+00
21 6.0524643645662579e-01 7.0314728523699110e-01 -2.2349906198624576e+00
22 -1.0299517357238845e+00 -6.7850914711871291e-01 8.1029011311054200e-01
23 4.2470529926725875e-01 -2.4638138118278141e-02 1.4247005067519156e+00
24 4.1516966455944304e-01 -1.5912776575035221e+00 9.3767616296745859e-01
25 3.0070697634261156e-01 1.0957067953103508e+00 -1.8209981159009775e-01
26 -7.1587664090205461e-01 4.9557086219317126e-01 -7.5557635137736079e-01
27 -1.4554421797154906e-02 1.1056084388051551e-01 -3.5467198058544314e-02
28 -2.8257906393508312e-02 -6.6089589395261994e-02 5.7412954785297787e-04
29 4.2812328190663218e-02 -4.4471254485253520e-02 3.4893068510691336e-02
...