diff --git a/unittest/force-styles/CMakeLists.txt b/unittest/force-styles/CMakeLists.txt index 1439b06572..cc84352cd8 100644 --- a/unittest/force-styles/CMakeLists.txt +++ b/unittest/force-styles/CMakeLists.txt @@ -115,17 +115,6 @@ foreach(TEST ${KSPACE_TESTS}) set_tests_properties(${TNAME} PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};PYTHONPATH=${TEST_INPUT_FOLDER}:$ENV{PYTHONPATH}") endforeach() -# improper style tester -add_executable(test_improper_style test_improper_style.cpp) -target_link_libraries(test_improper_style PRIVATE lammps style_tests) - -file(GLOB IMPROPER_TESTS LIST_DIRECTORIES false ${TEST_INPUT_FOLDER}/improper-*.yaml) -foreach(TEST ${IMPROPER_TESTS}) - string(REGEX REPLACE "^.*improper-(.*)\.yaml" "ImproperStyle:\\1" TNAME ${TEST}) - add_test(NAME ${TNAME} COMMAND test_improper_style ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) - set_tests_properties(${TNAME} PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};PYTHONPATH=${TEST_INPUT_FOLDER}:$ENV{PYTHONPATH}") -endforeach() - # tester for timestepping fixes add_executable(test_fix_timestep test_fix_timestep.cpp) target_link_libraries(test_fix_timestep PRIVATE lammps style_tests) @@ -137,3 +126,25 @@ foreach(TEST ${FIX_TIMESTEP_TESTS}) add_test(NAME ${TNAME} COMMAND test_fix_timestep ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) set_tests_properties(${TNAME} PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};PYTHONPATH=${TEST_INPUT_FOLDER}:$ENV{PYTHONPATH}") endforeach() + +# dihedral style tester +add_executable(test_dihedral_style test_dihedral_style.cpp) +target_link_libraries(test_dihedral_style PRIVATE lammps style_tests) + +file(GLOB DIHEDRAL_TESTS LIST_DIRECTORIES false ${TEST_INPUT_FOLDER}/dihedral-*.yaml) +foreach(TEST ${DIHEDRAL_TESTS}) + string(REGEX REPLACE "^.*dihedral-(.*)\.yaml" "DihedralStyle:\\1" TNAME ${TEST}) + add_test(NAME ${TNAME} COMMAND test_dihedral_style ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + set_tests_properties(${TNAME} PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};PYTHONPATH=${TEST_INPUT_FOLDER}:$ENV{PYTHONPATH}") +endforeach() + +# improper style tester +add_executable(test_improper_style test_improper_style.cpp) +target_link_libraries(test_improper_style PRIVATE lammps style_tests) + +file(GLOB IMPROPER_TESTS LIST_DIRECTORIES false ${TEST_INPUT_FOLDER}/improper-*.yaml) +foreach(TEST ${IMPROPER_TESTS}) + string(REGEX REPLACE "^.*improper-(.*)\.yaml" "ImproperStyle:\\1" TNAME ${TEST}) + add_test(NAME ${TNAME} COMMAND test_improper_style ${TEST} WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}) + set_tests_properties(${TNAME} PROPERTIES ENVIRONMENT "LAMMPS_POTENTIALS=${LAMMPS_POTENTIALS_DIR};PYTHONPATH=${TEST_INPUT_FOLDER}:$ENV{PYTHONPATH}") +endforeach() diff --git a/unittest/force-styles/test_config_reader.cpp b/unittest/force-styles/test_config_reader.cpp index e4d5386b7e..2a639784fa 100644 --- a/unittest/force-styles/test_config_reader.cpp +++ b/unittest/force-styles/test_config_reader.cpp @@ -57,6 +57,8 @@ TestConfigReader::TestConfigReader(TestConfig &config) : YamlReader(), config(co consumers["bond_coeff"] = &TestConfigReader::bond_coeff; consumers["angle_style"] = &TestConfigReader::angle_style; consumers["angle_coeff"] = &TestConfigReader::angle_coeff; + consumers["dihedral_style"] = &TestConfigReader::dihedral_style; + consumers["dihedral_coeff"] = &TestConfigReader::dihedral_coeff; consumers["improper_style"] = &TestConfigReader::improper_style; consumers["improper_coeff"] = &TestConfigReader::improper_coeff; consumers["init_energy"] = &TestConfigReader::init_energy; @@ -261,6 +263,22 @@ void TestConfigReader::angle_coeff(const yaml_event_t &event) } } +void TestConfigReader::dihedral_style(const yaml_event_t &event) +{ + config.dihedral_style = (char *)event.data.scalar.value; +} + +void TestConfigReader::dihedral_coeff(const yaml_event_t &event) +{ + config.dihedral_coeff.clear(); + std::stringstream data((char *)event.data.scalar.value); + std::string line; + + while (std::getline(data, line, '\n')) { + config.dihedral_coeff.push_back(line); + } +} + void TestConfigReader::improper_style(const yaml_event_t &event) { config.improper_style = (char *)event.data.scalar.value; diff --git a/unittest/force-styles/test_config_reader.h b/unittest/force-styles/test_config_reader.h index 55cafbcc63..840228da3a 100644 --- a/unittest/force-styles/test_config_reader.h +++ b/unittest/force-styles/test_config_reader.h @@ -44,6 +44,8 @@ public: void bond_coeff(const yaml_event_t &event); void angle_style(const yaml_event_t &event); void angle_coeff(const yaml_event_t &event); + void dihedral_style(const yaml_event_t &event); + void dihedral_coeff(const yaml_event_t &event); void improper_style(const yaml_event_t &event); void improper_coeff(const yaml_event_t &event); void equilibrium(const yaml_event_t &event); diff --git a/unittest/force-styles/test_dihedral_style.cpp b/unittest/force-styles/test_dihedral_style.cpp new file mode 100644 index 0000000000..4c6eabb0a5 --- /dev/null +++ b/unittest/force-styles/test_dihedral_style.cpp @@ -0,0 +1,749 @@ +/* ---------------------------------------------------------------------- + LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator + http://lammps.sandia.gov, 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. +------------------------------------------------------------------------- */ + +// unit tests for dihedral styles intended for molecular systems + +#include "error_stats.h" +#include "test_config.h" +#include "test_config_reader.h" +#include "test_main.h" +#include "yaml_reader.h" +#include "yaml_writer.h" + +#include "gmock/gmock.h" +#include "gtest/gtest.h" + +#include "atom.h" +#include "dihedral.h" +#include "compute.h" +#include "fmt/format.h" +#include "force.h" +#include "info.h" +#include "input.h" +#include "lammps.h" +#include "modify.h" +#include "universe.h" + +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include + +using ::testing::HasSubstr; +using ::testing::StartsWith; + +using namespace LAMMPS_NS; + +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"); + delete_file(cfg.basename + ".data"); + delete_file(cfg.basename + "-coeffs.in"); + 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 dihedral style is not available, don't test it + if (prerequisite.first == "dihedral") { + 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("dihedral_style " + cfg.dihedral_style); + + for (auto &dihedral_coeff : cfg.dihedral_coeff) { + command("dihedral_coeff " + dihedral_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 + auto command = [&](const std::string &line) { + lmp->input->one(line.c_str()); + }; + + command("fix 1 all nve"); + // just measure the relevant part of potential energy + command("compute pe all pe/atom dihedral"); + command("compute sum all reduce sum c_pe"); + command("thermo_style custom step temp pe press c_sum"); + command("thermo 2"); + command("run 4 post no"); +} + +// Restart LAMMPS simulation +// to test "write_restart" and "read_restart" functions of dihedral 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()); + }; + + command("clear"); + command("read_restart " + cfg.basename + ".restart"); + + // add the dihedral style if it's not defined already in the restart file + if (!lmp->force->dihedral) { + command("dihedral_style " + cfg.dihedral_style); + } + + // add the dihedral coefficients if hybrid style is used + // or somehow they aren't defined already in the restart file + if ((cfg.dihedral_style.substr(0, 6) == "hybrid") || !lmp->force->dihedral->writedata) { + for (auto &dihedral_coeff : cfg.dihedral_coeff) { + command("dihedral_coeff " + dihedral_coeff); + } + } + + 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 dihedral_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 dihedral_style index '" + cfg.dihedral_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 &dihedral_coeff : cfg.dihedral_coeff) { + command("dihedral_coeff " + dihedral_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[] = {"DihedralStyle", "-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); + + // dihedral_style + writer.emit("dihedral_style", config.dihedral_style); + + // dihedral_coeff + block.clear(); + for (auto &dihedral_coeff : config.dihedral_coeff) { + block += dihedral_coeff + "\n"; + } + writer.emit_block("dihedral_coeff", 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->dihedral->energy); + + // init_stress + auto stress = lmp->force->dihedral->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->dihedral->energy); + + // run_stress + stress = lmp->force->dihedral->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 &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 dihedral = lmp->force->dihedral; + auto stress = dihedral->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(dihedral->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 = dihedral->virial; + + const std::vector &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 = dihedral->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(dihedral->energy, test_config.run_energy, epsilon); + EXPECT_FP_LE_WITH_EPS(dihedral->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; + + dihedral = lmp->force->dihedral; + stress = dihedral->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(dihedral->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 = dihedral->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 = dihedral->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(dihedral->energy, test_config.run_energy, epsilon); + EXPECT_FP_LE_WITH_EPS(dihedral->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; + + dihedral = lmp->force->dihedral; + stress = dihedral->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(dihedral->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; + + dihedral = lmp->force->dihedral; + stress = dihedral->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(dihedral->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 &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 dihedral = lmp->force->dihedral; + auto stress = dihedral->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(dihedral->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 = dihedral->virial; + + const std::vector &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 = dihedral->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(dihedral->energy, test_config.run_energy, epsilon); + // TODO: this is currently broken for USER-OMP with dihedral style hybrid + // needs to be fixed in the main code somewhere. Not sure where, though. + if (test_config.dihedral_style.substr(0, 6) != "hybrid") + EXPECT_FP_LE_WITH_EPS(dihedral->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; + + dihedral = lmp->force->dihedral; + stress = dihedral->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(dihedral->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 = dihedral->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(dihedral->energy, test_config.run_energy, epsilon); + // TODO: this is currently broken for USER-OMP with dihedral style hybrid + // needs to be fixed in the main code somewhere. Not sure where, though. + if (test_config.dihedral_style.substr(0, 6) != "hybrid") + EXPECT_FP_LE_WITH_EPS(dihedral->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(); +}; diff --git a/unittest/force-styles/test_improper_style.cpp b/unittest/force-styles/test_improper_style.cpp index 9fc5412546..bbc69af791 100644 --- a/unittest/force-styles/test_improper_style.cpp +++ b/unittest/force-styles/test_improper_style.cpp @@ -1,19 +1,3 @@ -/* -- there are 7 basic functions - - delete_file - - cleanup_lammps - - init_lammps - - run_lammps - - restart_lammps - - data_lammps - - generate_yaml_file -- move delete_file amd cleanup_lammps to a single file -- I don't understand utility lambda, but they are being reused multiple times -- add as many comments as possible, to show my understanding and document the code -- code for matching forces, energy and stress are repeated 3 times -- run_lammps looks to be same across all tests - it isn't, there's subtle difference -*/ - /* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories @@ -312,12 +296,6 @@ void generate_yaml_file(const char *outfile, const TestConfig &config) } 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)