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Merge branch 'master' into relres-update

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This commit is contained in:
Axel Kohlmeyer
2021-02-28 23:20:44 -05:00
parent a7e5f1acf2 9efc83195a
commit e75f1f2f82
1094 changed files with 35622 additions and 20823 deletions
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21
unittest/force-styles/CMakeLists.txt
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@ -127,3 +127,24 @@ foreach(TEST ${FIX_TIMESTEP_TESTS})
set_tests_properties(${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()

36
unittest/force-styles/test_config_reader.cpp
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@ -57,6 +57,10 @@ 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;
consumers["run_energy"] = &TestConfigReader::run_energy;
consumers["equilibrium"] = &TestConfigReader::equilibrium;
@ -259,6 +263,38 @@ 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;
}
void TestConfigReader::improper_coeff(const yaml_event_t &event)
{
config.improper_coeff.clear();
std::stringstream data((char *)event.data.scalar.value);
std::string line;
while (std::getline(data, line, '\n')) {
config.improper_coeff.push_back(line);
}
}
void TestConfigReader::equilibrium(const yaml_event_t &event)
{
std::stringstream data((char *)event.data.scalar.value);

4
unittest/force-styles/test_config_reader.h
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@ -44,6 +44,10 @@ 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);
void init_vdwl(const yaml_event_t &event);
void init_coul(const yaml_event_t &event);

743
unittest/force-styles/test_dihedral_style.cpp Normal file
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@ -0,0 +1,743 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://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 "compute.h"
#include "dihedral.h"
#include "fmt/format.h"
#include "force.h"
#include "info.h"
#include "input.h"
#include "lammps.h"
#include "modify.h"
#include "universe.h"
#include <cctype>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <ctime>
#include <mpi.h>
#include <map>
#include <string>
#include <utility>
#include <vector>
using ::testing::HasSubstr;
using ::testing::StartsWith;
using namespace LAMMPS_NS;
static void delete_file(const std::string &filename)
{
remove(filename.c_str());
};
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;
}
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;
// this is a test for dihedral styles, so if the suffixed
// version is not available, there is no reason to test.
if (prerequisite.first == "dihedral") {
if (lmp->suffix_enable) {
style += "/";
style += lmp->suffix;
}
}
if (!info->has_style(prerequisite.first, style)) ++nfail;
}
delete info;
if (nfail > 0) {
cleanup_lammps(lmp, cfg);
return nullptr;
}
// 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());
};
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");
command("write_restart " + cfg.basename + ".restart");
command("write_data " + cfg.basename + ".data");
command("write_coeff " + cfg.basename + "-coeffs.in");
return lmp;
}
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");
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");
}
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");
if (!lmp->force->dihedral) {
command("dihedral_style " + cfg.dihedral_style);
}
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");
}
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");
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");
// special treatment for dihedral styles charmm and charmmfsw
if (cfg.dihedral_style == "charmm") {
command("variable pair_style delete");
command("variable pair_style index 'lj/charmm/coul/charmm 7.0 8.0'");
} else if (cfg.dihedral_style == "charmmfsw") {
command("variable pair_style delete");
command("variable pair_style index 'lj/charmmfsw/coul/charmmfsh 7.0 8.0'");
}
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");
}
// re-generate yaml file with current settings.
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->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(DihedralStyle, plain)
{
const char *args[] = {"DihedralStyle", "-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 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<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 = 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(DihedralStyle, omp)
{
if (!LAMMPS::is_installed_pkg("USER-OMP")) GTEST_SKIP();
const char *args[] = {"DihedralStyle", "-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 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<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 = 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();
};

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unittest/force-styles/test_improper_style.cpp Normal file
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://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 improper 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 "compute.h"
#include "fmt/format.h"
#include "force.h"
#include "improper.h"
#include "info.h"
#include "input.h"
#include "lammps.h"
#include "modify.h"
#include "universe.h"
#include <cctype>
#include <cstdio>
#include <cstdlib>
#include <cstring>
#include <ctime>
#include <mpi.h>
#include <map>
#include <string>
#include <utility>
#include <vector>
using ::testing::HasSubstr;
using ::testing::StartsWith;
using namespace LAMMPS_NS;
static void delete_file(const std::string &filename)
{
remove(filename.c_str());
};
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;
}
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;
// this is a test for improper styles, so if the suffixed
// version is not available, there is no reason to test.
if (prerequisite.first == "improper") {
if (lmp->suffix_enable) {
style += "/";
style += lmp->suffix;
}
}
if (!info->has_style(prerequisite.first, style)) ++nfail;
}
delete info;
if (nfail > 0) {
cleanup_lammps(lmp, cfg);
return nullptr;
}
// 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());
};
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");
command("write_restart " + cfg.basename + ".restart");
command("write_data " + cfg.basename + ".data");
command("write_coeff " + cfg.basename + "-coeffs.in");
return lmp;
}
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");
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");
command("thermo 2");
command("run 4 post no");
}
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");
if (!lmp->force->improper) {
command("improper_style " + cfg.improper_style);
}
if ((cfg.improper_style.substr(0, 6) == "hybrid") || !lmp->force->improper->writedata) {
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 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");
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");
}
// re-generate yaml file with current settings.
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->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);
// 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();
};

2
unittest/force-styles/tests/angle-quartic.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 24 Aug 2020
date_generated: Tue Sep 15 09:44:35 202
epsilon: 2.5e-13
epsilon: 4e-13
prerequisites: ! |
atom full
angle quartic

2
unittest/force-styles/tests/atomic-pair-reax_c_lgvdw.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 24 Aug 2020
date_generated: Tue Sep 15 09:44:25 202
epsilon: 1e-10
epsilon: 2e-10
prerequisites: ! |
pair reax/c
fix qeq/reax

13
unittest/force-styles/tests/data.fourmol
View File

@ -46,6 +46,19 @@ Angle Coeffs # zero
3 120
4 108.5
Dihedral Coeffs # zero
1
2
3
4
5
Improper Coeffs # zero
1
2
Atoms # full
10 2 1 7.0000000000000007e-02 2.0185283555536988e+00 -1.4283966846517357e+00 -9.6733527271133024e-01 0 0 0

89
unittest/force-styles/tests/dihedral-charmm.yaml Normal file
View File

@ -0,0 +1,89 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 19:32:00 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
dihedral charmm
pre_commands: ! ""
post_commands: ! |
special_bonds charmm
pair_style lj/charmm/coul/charmm 7.0 8.0
pair_coeff * * 0.1 3.0
input_file: in.fourmol
dihedral_style: charmm
dihedral_coeff: ! |
1 75.0 2 160 0.5
2 45.0 4 120 1.0
3 56.0 0 110 0.0
4 23.0 1 180 0.5
5 19.0 3 90 1.0
extract: ! ""
natoms: 29
init_energy: 1317.95984412099
init_stress: ! |2-
1.1266474992363544e+02 -1.4270359924600960e+01 -9.8394389999034431e+01 -1.4122826669412839e+02 1.1178234052730829e+02 -5.8711817976295805e+01
init_forces: ! |2
1 -9.0728070828324405e+00 -4.2409023620772402e+01 1.3161109399402682e+02
2 3.3181828946933209e+01 1.4051671303009513e+01 6.3548249417335567e+00
3 5.5350289840861464e+01 1.1131831288815475e+02 -3.9480881018342950e+02
4 -1.1844907978543657e+02 -2.8998271771801804e+01 1.2935080865553104e+02
5 -1.1583671402383914e+01 5.0372406935691121e+00 -3.9128008893243305e-02
6 1.0321597937823311e+02 2.6974953442199936e+01 1.1570366758787367e+02
7 -8.9000331915157602e+01 -2.3564688140264529e+01 3.2374751781728959e+00
8 -5.6173305934035355e+01 1.4732923726825511e+01 -6.4812947497159044e+01
9 -1.0285573098962932e+02 -4.0305092163391558e+00 3.5869756696647038e+01
10 -4.3851647747590441e+01 -1.5710005359777315e+02 1.3867075586374912e+02
11 -2.1619094578728090e+02 -3.3233741870916771e+02 1.4579886837322184e+02
12 7.1261053740020756e+01 -4.9392232887317356e+01 1.0428582135201829e+01
13 1.3045274807944942e+01 3.7064676200410256e+00 -1.7391883697148632e+01
14 2.1115231856154324e+02 4.1325149711628239e+02 -1.8182836867325446e+02
15 6.6217480580178957e+01 7.9628926680111661e+01 -9.6844899654306644e+01
16 7.8335001553658429e+01 3.3029014991818336e+01 6.4117995352193278e+00
17 1.7022736711084285e+01 -6.4494546990630354e+01 3.0252482246684398e+01
18 6.6888062606310128e-01 2.5109175640033401e+00 3.5221262532274022e+00
19 -1.0595281330291315e+00 -2.2909074264278830e+00 -7.4205308886987997e-01
20 -5.6590649610114355e-02 -1.3306687981692766e-01 -1.1723524532058045e+00
21 -1.3602839150541590e+00 -5.2316783809516321e-02 2.6862171884490484e+00
22 2.1188881771188520e-01 7.6506576725652897e-01 -9.9588370661762238e-01
23 1.7197280817140093e-01 3.2328958511427264e-01 -7.9666865784211760e-01
24 8.3440060469976285e-01 -6.3373419421074084e-01 2.0837043868722125e+00
25 -1.0278907497984688e+00 3.6727316840487179e-01 -1.2445837805673781e+00
26 -5.4322936895149698e-01 -4.6377955792927761e-01 -1.3336861388577368e+00
27 -1.3095161641895547e+00 -1.2565785999785013e+00 1.5351009379260916e-01
28 6.7218786721800217e-01 7.6800634603799567e-01 -1.7119977008252721e-01
29 1.1932647806568950e+00 6.9156748341000629e-01 4.6792179831738293e-02
run_energy: 1317.13089096787
run_stress: ! |2-
1.1432326918192217e+02 -1.5602913994604187e+01 -9.8720355187318063e+01 -1.4093459949789184e+02 1.1435885495687606e+02 -5.7664013010033671e+01
run_forces: ! |2
1 -8.6738392290797321e+00 -4.3410976862478378e+01 1.3347585412854920e+02
2 3.2238389882602903e+01 1.3927988326640385e+01 6.0326853193447016e+00
3 5.5781319921623364e+01 1.1281438896518540e+02 -3.9723915447363220e+02
4 -1.1781245729470949e+02 -2.8715133630261910e+01 1.2947327229271528e+02
5 -1.1698125655644814e+01 4.8914276366056813e+00 -1.2206916593051020e-01
6 1.0064255236909239e+02 2.4089902585533437e+01 1.1708688508535455e+02
7 -8.8938396678183068e+01 -2.4269612244372958e+01 3.4046423133252497e+00
8 -5.2440942113044144e+01 1.8663724891736056e+01 -6.5986905005646207e+01
9 -1.0273771792476782e+02 -3.4152751230288336e+00 3.5403342910779550e+01
10 -4.6264267786523504e+01 -1.5988311874558323e+02 1.3948502740217890e+02
11 -2.0740380294773800e+02 -3.1362984721556523e+02 1.3680307896600868e+02
12 7.1727029511898778e+01 -4.9953583843530197e+01 1.0566391313536254e+01
13 1.2717601183517756e+01 3.6639042127491406e+00 -1.6991918462597582e+01
14 2.0160316516219288e+02 3.9605544797472220e+02 -1.7309385003473275e+02
15 6.6950478180516200e+01 8.0016328186605023e+01 -9.7109615235144631e+01
16 7.9788925340074712e+01 3.4209121284318734e+01 6.5473927657876567e+00
17 1.6122485334835080e+01 -6.5651549116138114e+01 3.0223626886103975e+01
18 6.7123875238643738e-01 2.5225106816598521e+00 3.5235417346122380e+00
19 -1.0614663134700668e+00 -2.3016803913636772e+00 -7.2888942997786199e-01
20 -5.4056934695977041e-02 -1.3199262460437394e-01 -1.1690871662309097e+00
21 -1.3614683789342612e+00 -6.1659172840990539e-02 2.6843872547994612e+00
22 2.1301744794630889e-01 7.6998500648265933e-01 -9.9626778434974805e-01
23 1.7137646754555280e-01 3.2261162434818480e-01 -7.9603557873164577e-01
24 8.3450290990328380e-01 -6.2976630391752642e-01 2.0675159711292510e+00
25 -1.0267254825899825e+00 3.6901966109757989e-01 -1.2397266170577683e+00
26 -5.4220092253858421e-01 -4.6310693711038375e-01 -1.3315676468107509e+00
27 -1.3087239984049934e+00 -1.2556095274814956e+00 1.5425738299910141e-01
28 6.7103315457032875e-01 7.6674467322075168e-01 -1.7140189867370823e-01
29 1.1910760416184893e+00 6.8980602737225627e-01 4.4586772292204771e-02
...

89
unittest/force-styles/tests/dihedral-charmmfsw.yaml Normal file
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@ -0,0 +1,89 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 19:32:07 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
dihedral charmmfsw
pre_commands: ! ""
post_commands: ! |
special_bonds charmm
pair_style lj/charmmfsw/coul/charmmfsh 7.0 8.0
pair_coeff * * 0.1 3.0
input_file: in.fourmol
dihedral_style: charmmfsw
dihedral_coeff: ! |
1 75.0 2 160 0.5
2 45.0 4 120 1.0
3 56.0 0 110 0.0
4 23.0 1 180 0.5
5 19.0 3 90 1.0
extract: ! ""
natoms: 29
init_energy: 1317.95984412099
init_stress: ! |2-
1.1266474992363544e+02 -1.4270359924600960e+01 -9.8394389999034431e+01 -1.4122826669412839e+02 1.1178234052730829e+02 -5.8711817976295805e+01
init_forces: ! |2
1 -8.9693997732828734e+00 -4.2090832180473811e+01 1.3129896410266406e+02
2 3.2939174268614089e+01 1.3776993828220547e+01 6.6047608190284564e+00
3 5.5339891213774308e+01 1.1132435962327280e+02 -3.9478906486222957e+02
4 -1.1853376295969241e+02 -2.8731355857128989e+01 1.2940461683448865e+02
5 -1.1704542931552981e+01 5.1612910145764337e+00 1.1531982356444204e-01
6 1.0315985347478912e+02 2.7858195004320272e+01 1.1495266502109652e+02
7 -8.8909058225650583e+01 -2.3837347272152069e+01 3.9392213448182849e+00
8 -5.5853617515784052e+01 1.3539223737174332e+01 -6.3713599961688189e+01
9 -1.0311156651288640e+02 -3.6164116725708757e+00 3.5075828453521936e+01
10 -4.3826637468354527e+01 -1.5710289244173734e+02 1.3864307003008477e+02
11 -2.1622582834796196e+02 -3.3219826841101195e+02 1.4556774326995796e+02
12 7.1412702974492348e+01 -4.9974052650356612e+01 1.0723258124306223e+01
13 1.2983841333488790e+01 3.6226253549259608e+00 -1.7369216643277348e+01
14 2.1111361658245866e+02 4.1312473179030422e+02 -1.8177665169218727e+02
15 6.6205967662062449e+01 7.9562081373822039e+01 -9.6816806108613221e+01
16 7.8024062158787302e+01 3.4094331075850761e+01 5.9763314082458487e+00
17 1.7445214070241107e+01 -6.4435014330300476e+01 2.9813113022057500e+01
18 2.0800160412943211e-01 2.2891124106778022e+00 3.4660835897877700e+00
19 -8.0963080390688746e-01 -2.4045945217436877e+00 -1.8583563864926739e-01
20 -3.8753637434211785e-02 -5.5448402782730866e-01 -6.7086657947375039e-01
21 -1.3905969243613909e+00 9.2263911023596146e-01 2.4245678407761346e+00
22 1.3613731081665018e-01 8.4084293030416840e-02 -8.1025131035386821e-01
23 4.1866083933707599e-01 -5.5509350762570908e-02 -7.0997382727305158e-01
24 7.1694861345295280e-01 -2.3511767137443013e-01 8.0781359710835909e-01
25 -1.0629765873976795e+00 -1.8433966653787029e-01 -1.2964080715678894e+00
26 -3.5304755132121918e-01 -1.9129024515386733e-01 -4.7932022297094667e-01
27 -7.5085140414840501e-01 -2.1332740916449014e-01 -3.4556428061080330e-01
28 3.0509542011027740e-01 4.6221002204910822e-02 8.8498260667955922e-02
29 1.1311031171809240e+00 4.1894808967987129e-01 6.1703656720310460e-02
run_energy: 1317.13142783318
run_stress: ! |2-
1.1432271538886499e+02 -1.5603844203952541e+01 -9.8718871184912416e+01 -1.4093580634465189e+02 1.1435865928680047e+02 -5.7664143378423546e+01
run_forces: ! |2
1 -8.5717926119025947e+00 -4.3091412260618227e+01 1.3316006725249042e+02
2 3.1997674214676874e+01 1.3654655784189870e+01 6.2828676384712061e+00
3 5.5770382737530170e+01 1.1281783434187146e+02 -3.9721453377879095e+02
4 -1.1789680795379847e+02 -2.8447706749956993e+01 1.2952665428714013e+02
5 -1.1819996113850017e+01 5.0146666822935302e+00 3.2281792318776925e-02
6 1.0058447730534851e+02 2.4972369765865452e+01 1.1633752546321533e+02
7 -8.8848296871465919e+01 -2.4542246520962529e+01 4.1058609991775068e+00
8 -5.2109635323526945e+01 1.7483153474801384e+01 -6.4894524111023628e+01
9 -1.0299581329057062e+02 -3.0071901661917311e+00 3.4614355229661122e+01
10 -4.6248656852080643e+01 -1.5989736943052526e+02 1.3946110129960286e+02
11 -2.0744046131487352e+02 -3.1349391104875059e+02 1.3657355191843646e+02
12 7.1878446763226236e+01 -5.0535379590486308e+01 1.0860480569904183e+01
13 1.2656630660306188e+01 3.5801817290072018e+00 -1.6968929416398453e+01
14 2.0156828471782353e+02 3.9593474256507108e+02 -1.7304498843642651e+02
15 6.6938931982383480e+01 7.9950072669406069e+01 -9.7082424123877473e+01
16 7.9480812177410172e+01 3.5274424529763422e+01 6.1163506563185468e+00
17 1.6544041468715115e+01 -6.5589692620159624e+01 2.9781616838343403e+01
18 2.1267286099045599e-01 2.2942619216574771e+00 3.4659719272782654e+00
19 -8.1337490705231874e-01 -2.4098575977295353e+00 -1.8396289009644590e-01
20 -3.7941149699885969e-02 -5.5340608883683873e-01 -6.6993848517114352e-01
21 -1.3889998509458839e+00 9.1890355468961316e-01 2.4229472564481020e+00
22 1.3595436261854707e-01 8.5481963099478642e-02 -8.0999717836214991e-01
23 4.1797076633887387e-01 -5.5351208630107784e-02 -7.0920364554695203e-01
24 7.1594583142507817e-01 -2.3421203522820028e-01 8.0152300676926436e-01
25 -1.0620978751652836e+00 -1.8302578820695936e-01 -1.2914119694215400e+00
26 -3.5226930669430428e-01 -1.9104656198469849e-01 -4.7741349806842143e-01
27 -7.4942338430179933e-01 -2.1202918409495525e-01 -3.4599837098455843e-01
28 3.0447869914249726e-01 4.5993592160623709e-02 8.8399467006803928e-02
29 1.1288622579925440e+00 4.1709427848592429e-01 6.1770301585805341e-02
...

87
unittest/force-styles/tests/dihedral-class2.yaml Normal file
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@ -0,0 +1,87 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 18:38:38 202
epsilon: 8e-13
prerequisites: ! |
atom full
dihedral class2
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
dihedral_style: class2
dihedral_coeff: ! |
* 75.0 169 45.0 10 24.0 40.0
* mbt 75 42 31 5.2
* ebt 75 42 31 75 42 31 1.4 1.4
* at 75 42 31 75 42 31 120 50
* aat 75 120 160
* bb13 75 1.4 1.4
extract: ! ""
natoms: 29
init_energy: 3355.00747173759
init_stress: ! |2-
2.1875123407705587e+01 -7.3463171958190321e+02 7.0422332087828568e+02 -2.0890942199873339e+02 -3.6451752675970380e+02 1.3400265327626121e+02
init_forces: ! |2
1 -1.0952511200405197e+03 6.4823297173207970e+02 -4.4760954488358391e+02
2 9.0092068008499132e+02 -3.6118332267415013e+02 3.5713667026397326e+02
3 -7.7532838532500693e+02 -1.2468325260439517e+03 3.8359187812682325e+02
4 1.2904186368708332e+02 2.2136621866894416e+02 -1.4642984375119335e+02
5 5.9556699584425348e+02 1.5024609743159468e+02 2.2329142626092334e+02
6 7.3251103695180063e+02 1.1448501937143062e+03 -3.0258310893753855e+02
7 -5.6987565445561142e+02 -6.9068345660300258e+02 1.5974567786362655e+02
8 2.3172356712469091e+03 1.7621991394557467e+03 -1.0823598208966904e+02
9 -1.0665980086873585e+03 -9.7028318259088303e+02 4.0830286870801143e+02
10 -1.1831159209684265e+03 -1.2136533632807443e+03 1.0278790875590396e+03
11 -6.8651636455995185e+02 9.1292605610303031e+02 -5.0138124218536382e+02
12 9.4590221018670803e+01 -1.4167468342595586e+02 -3.9159227689650663e+02
13 1.7016834910937868e+02 3.5891736246788633e+02 8.2250630442549743e+02
14 5.6198417641541641e+02 -7.5542769524397647e+02 -2.9572420497952066e+02
15 -7.0833278096116078e+02 2.2547367398085970e+02 -6.9838585028829266e+02
16 9.0926990053407053e+02 1.5375356733249265e+02 -3.5329802202150256e+02
17 -3.2627065989453854e+02 -1.9822705102427648e+02 -1.3721383717472295e+02
18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
19 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
21 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
24 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
25 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
26 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
27 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
run_energy: 3232.22368557986
run_stress: ! |2-
3.4186200218682700e+01 -7.5351720154542477e+02 5.8894003293457865e+02 -1.4452761583493597e+02 -3.8479488337510423e+02 1.2221118941124658e+02
run_forces: ! |2
1 -1.1114877010468704e+03 6.6412899312329989e+02 -4.8306781555357099e+02
2 9.0918809418895717e+02 -3.7552925375399423e+02 3.7963210720241710e+02
3 -7.4768553265259493e+02 -1.2526329500283782e+03 3.9165439571062751e+02
4 1.1598833343613694e+02 2.0353476227252435e+02 -1.2759176729615673e+02
5 5.9446880390197896e+02 1.5266302110358913e+02 2.1506481482921635e+02
6 7.6270375928437579e+02 1.1975511187402499e+03 -3.1848407740344737e+02
7 -5.6563612620259039e+02 -6.9106367799535462e+02 1.6626389201928362e+02
8 2.2261446006370847e+03 1.6471763697379154e+03 -5.9204553180719302e+01
9 -1.0508281810786864e+03 -9.5153190588270775e+02 3.6074532374710634e+02
10 -1.1002869875539902e+03 -1.1259097891078113e+03 9.9461497198463974e+02
11 -6.8671642743708378e+02 9.0225692086600691e+02 -4.6762764620034005e+02
12 8.0194355742839932e+01 -1.4025133105503551e+02 -4.1215700309601090e+02
13 1.6121978561368979e+02 3.6583968779424583e+02 8.2543084661182979e+02
14 5.6039463771180522e+02 -7.5245341384736207e+02 -2.8267617778550414e+02
15 -6.9314762831894063e+02 2.1107046433802870e+02 -6.8684015745129102e+02
16 8.5054295795981488e+02 1.2889703114277438e+02 -3.6104879490120936e+02
17 -3.0505674418592668e+02 -1.8374604744798970e+02 -1.3470835923687093e+02
18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
...

86
unittest/force-styles/tests/dihedral-cosine_shift_exp.yaml Normal file
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@ -0,0 +1,86 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 18:38:38 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
dihedral cosine/shift/exp
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
dihedral_style: cosine/shift/exp
dihedral_coeff: ! |
1 75 160 5.1
2 45 120 2.4
3 56 110 7.5
4 23 180 5.5
5 19 90 2.1
extract: ! ""
natoms: 29
init_energy: -252.253036379603
init_stress: ! |2-
1.2648173379127915e+01 9.8987186508472114e+00 -2.2546892029975140e+01 -4.8774048841283184e+00 2.3394385854749725e+01 8.0008046681362437e+00
init_forces: ! |2
1 -2.1552264641323678e+01 9.3802303976266224e+00 -5.7580855394682011e+00
2 1.7542053448836405e+01 -9.0585245111022275e+00 8.5707996887760274e+00
3 -4.5368370292539865e+01 6.2901866813565608e+00 -1.8171838280442625e+01
4 -3.9437738551082751e+00 -4.2378540140894083e+00 3.8839120634338524e+00
5 3.0958932417316447e+01 -1.7216940826097481e+01 8.8151959108927258e-01
6 1.2935503074785331e+01 4.8389291078610510e+00 1.2199210336313424e+01
7 1.0262636687925307e+01 1.0876998682721958e+01 -1.7791589083223791e+00
8 1.8474452366832249e+01 1.9606544103980980e+01 6.2220353299406197e+00
9 1.7020916758045722e+01 1.2650017097294752e+01 -6.9250534440155018e+00
10 -6.9954140460001156e+01 -4.0784510598700408e+01 -7.4483410064839335e+00
11 9.9800939432401670e+00 -4.1410083603937675e-01 -2.2031105090375496e+00
12 6.9055058996213878e+00 2.5245282650526435e+00 1.4073615205210855e+01
13 -7.1665608596457320e-02 -1.6473434103906204e-01 -3.4575048440907352e-01
14 2.4318532883817405e+00 -3.3839834090561496e+00 -1.2032631916318084e+00
15 -8.5093986224928719e-01 2.8808607565855016e-01 -8.7054599213134165e-01
16 9.8383158994739350e+00 4.3782146730454237e+00 -1.9942921984521147e+00
17 5.3908909353600105e+00 4.4269134515255688e+00 8.6834733963048583e-01
18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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28 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
run_energy: -252.29533087732
run_stress: ! |2-
1.2679233523358512e+01 9.9049911944774891e+00 -2.2584224717836005e+01 -4.9222953229219746e+00 2.3439232765403958e+01 8.0455044326920557e+00
run_forces: ! |2
1 -2.1681260602243135e+01 9.4640446498660182e+00 -5.8153660416206314e+00
2 1.7622228873435517e+01 -9.1203004442484552e+00 8.6207493217103508e+00
3 -4.5422186497022935e+01 6.2789238657259032e+00 -1.8158223155939911e+01
4 -3.9417660078991212e+00 -4.2340583918337522e+00 3.8803641977291665e+00
5 3.1033325732076925e+01 -1.7261278784796644e+01 8.6126955781857584e-01
6 1.3057761350645071e+01 5.0037796191582586e+00 1.2206425951334531e+01
7 1.0204581390079650e+01 1.0787383771900220e+01 -1.7693012874559422e+00
8 1.8495759477703640e+01 1.9607876365921989e+01 6.2445967454739897e+00
9 1.6979375388826224e+01 1.2610145808112222e+01 -6.9025331116309552e+00
10 -6.9958416307959141e+01 -4.0778006073824884e+01 -7.4878188339111018e+00
11 9.9719586693041080e+00 -4.1438168249956409e-01 -2.1985928209527419e+00
12 6.8945633023312496e+00 2.5226410282917007e+00 1.4050126397293486e+01
13 -6.8568730429444003e-02 -1.5852707806876509e-01 -3.3190435067363921e-01
14 2.4388776536331709e+00 -3.3933646938491453e+00 -1.2019882913884326e+00
15 -8.5054571191848705e-01 2.8798818238768842e-01 -8.7036353952742662e-01
16 9.8265119994301369e+00 4.3670820826747221e+00 -1.9950230823005020e+00
17 5.3978000200065610e+00 4.4300517750824797e+00 8.6758234404118428e-01
18 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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20 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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22 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
23 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
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29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
...

86
unittest/force-styles/tests/dihedral-fourier.yaml Normal file
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@ -0,0 +1,86 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 18:38:38 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
dihedral fourier
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
dihedral_style: fourier
dihedral_coeff: ! |
1 1 75 1 120
2 2 75 1 120 42 2 140
3 3 75 1 120 42 2 140 35 1 160
4 4 75 1 120 42 2 140 35 2 160 21 2 110
5 5 75 1 120 42 2 140 35 2 160 21 2 110 10 2 20
extract: ! ""
natoms: 29
init_energy: 4237.11651056645
init_stress: ! |-
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init_forces: ! |2
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run_energy: 4233.36580637715
run_stress: ! |-
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run_forces: ! |2
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...

86
unittest/force-styles/tests/dihedral-harmonic.yaml Normal file
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@ -0,0 +1,86 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 18:38:38 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
dihedral harmonic
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
dihedral_style: harmonic
dihedral_coeff: ! |
1 75.0 +1 2
2 45.0 -1 4
3 56.0 -1 2
4 23.0 +1 1
5 19.0 -1 3
extract: ! ""
natoms: 29
init_energy: 789.17395858648
init_stress: ! |-
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init_forces: ! |2
1 -2.1511698742845866e+01 4.0249060564855860e+01 -9.0013321196300495e+01
2 -8.1931697051663761e+00 4.2308632119002461e+00 -4.0030670619001576e+00
3 9.1213724359021342e+01 -1.3766351447039605e+02 8.1969246558440773e+01
4 -4.8202572898596316e+01 -8.0465316960733553e+00 6.4757081520864901e+01
5 -6.2252471689207432e+01 2.2804485244022331e+01 -5.3285277341381354e+00
6 9.1271091191895337e+01 1.3743691097166200e+02 -3.9344000137592637e+01
7 -4.7435622518386936e+01 -5.1206081255886986e+01 8.4101355581705430e+00
8 2.2568717344776448e+02 1.6221073825524249e+02 5.7667169753528370e+01
9 -2.0794865226210746e+00 5.0314964909952629e+00 -7.5468528100469179e-01
10 -4.0476567806811568e+02 -4.7270660984257171e+02 -9.9999223894595431e+01
11 3.9909170606249432e+01 2.0810704935563001e+02 -1.3665198019985243e+02
12 6.2493704719337885e+01 7.0253447917427593e+01 1.9569964347346627e+02
13 2.9234925409867770e+01 6.7200938735330823e+01 1.4104379799580224e+02
14 7.2099736490024156e+01 -1.0032854911322366e+02 -3.5674421421421059e+01
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16 -9.2273705073611623e+01 -1.2566881299602966e+02 -6.3115663814665538e+01
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run_energy: 786.186635855008
run_stress: ! |-
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run_forces: ! |2
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8 2.2272760695742204e+02 1.5895499756012089e+02 5.7194518287049874e+01
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12 6.2351939715965052e+01 6.8740733618467218e+01 1.9368291702263934e+02
13 2.9034913938879313e+01 6.7392732937882698e+01 1.4128237950589556e+02
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...

86
unittest/force-styles/tests/dihedral-helix.yaml Normal file
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@ -0,0 +1,86 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 18:38:38 202
epsilon: 4e-13
prerequisites: ! |
atom full
dihedral helix
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
dihedral_style: helix
dihedral_coeff: ! |
1 75 60 42
2 45 20 75
3 56 10 32
4 23 80 61
5 19 90 13
extract: ! ""
natoms: 29
init_energy: 4634.43654570767
init_stress: ! |-
-8.0823732518007063e+01 9.9479187244686372e+01 -1.8655454726675949e+01 3.1101576556766464e+01 7.4461883645297817e+01 4.1747530138691431e+01
init_forces: ! |2
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2 -1.1019792518885538e+02 5.6905003129041866e+01 -5.3841150676408077e+01
3 2.3246539083975540e+02 4.0296299562627843e+02 -1.1393686865859719e+02
4 3.1568060813146815e+01 7.2317480245219112e+00 -4.1634456256848267e+01
5 6.2738188559800125e+00 -1.7156050770489149e+00 7.1235927088545736e-01
6 -1.0269680933720128e+03 -1.1690454281502080e+03 2.1661954258810474e+02
7 4.5805034065516077e+02 4.9842112368971334e+02 -8.2004595690709891e+01
8 -5.7825681205863634e+02 -3.5494272038879524e+02 -3.0370616059225443e+02
9 4.4268140801703601e+02 4.4489087402560148e+02 -2.0831276526993508e+02
10 -8.7951164139994106e+01 1.0636363540938811e+02 -5.4515993120398562e+01
11 7.1220902371740760e+02 -3.3016873225873167e+02 2.5993521030531866e+01
12 -1.7787675730154284e+01 1.3423193485792939e+02 1.6661355844612928e+02
13 -1.3886141645948561e+02 -3.1919416278193785e+02 -6.6993643041455698e+02
14 -3.7790416886453352e+02 5.2586290618778116e+02 1.8698421427449404e+02
15 4.7485173910262199e+02 -1.6076127127963423e+02 4.8579258849115138e+02
16 -2.4610027154189740e+02 1.8711434954391689e+02 3.3675371434963506e+02
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run_energy: 4604.29767615419
run_stress: ! |-
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run_forces: ! |2
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2 -1.0967028219095423e+02 5.6694684619133220e+01 -5.3333029655051035e+01
3 2.4083923292691799e+02 4.0545658790486630e+02 -1.0928376525899010e+02
4 2.9004572124849197e+01 3.3433497097463150e+00 -3.9484083494241339e+01
5 5.4495253574218356e+00 -2.3234784690594568e+00 3.6744082833339320e-01
6 -1.0416416920207600e+03 -1.1728713553808166e+03 2.1517006495886761e+02
7 4.6730984467782685e+02 5.0224210584028452e+02 -7.9280667353675966e+01
8 -5.6864896514161364e+02 -3.4977436236350320e+02 -3.0403472535369667e+02
9 4.3781190409126589e+02 4.4179927003638215e+02 -2.1089303274257958e+02
10 -8.5863568189987490e+01 1.0020124487504943e+02 -6.5522998341248922e+01
11 7.1073054117197967e+02 -3.3058374406671203e+02 3.2522201110837969e+01
12 -2.4832249967654064e+01 1.3872033356079328e+02 1.6239068437785096e+02
13 -1.4153451065060841e+02 -3.1548547899029609e+02 -6.6874565279275259e+02
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...

87
unittest/force-styles/tests/dihedral-hybrid.yaml Normal file
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@ -0,0 +1,87 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 20:43:34 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
dihedral harmonic
dihedral opls
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
dihedral_style: hybrid harmonic opls
dihedral_coeff: ! |
1 harmonic 75.0 +1 2
2 harmonic 45.0 -1 4
3 opls 56 10 32 84
4 opls 23 80 61 83
5 opls 19 90 13 15
extract: ! ""
natoms: 29
init_energy: 1501.66406241746
init_stress: ! |-
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init_forces: ! |2
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2 -1.3855214618931836e+02 7.1546812691134122e+01 -6.7694622804688365e+01
3 6.5964354373895731e+01 -2.7120798820857840e+02 5.7779867477146780e+01
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5 -3.7665970146318045e+01 1.7971807362873875e+02 4.6710944552079511e+01
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run_energy: 1495.65001965091
run_stress: ! |-
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run_forces: ! |2
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8 4.9895893276330048e+02 4.4194751828933101e+02 -1.4833194600243888e+02
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...

86
unittest/force-styles/tests/dihedral-multi_harmonic.yaml Normal file
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@ -0,0 +1,86 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 18:38:38 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
dihedral multi/harmonic
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
dihedral_style: multi/harmonic
dihedral_coeff: ! |
1 75 60 42 23 91
2 45 20 75 52 24
3 56 10 32 84 52
4 23 80 61 83 74
5 19 90 13 15 58
extract: ! ""
natoms: 29
init_energy: 2854.98573165667
init_stress: ! |2-
1.5681915450818258e+02 1.8843677355938829e+02 -3.4525592806757135e+02 1.8730498639126836e+02 3.9598161309144100e+00 -4.8403883145099769e+01
init_forces: ! |2
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2 -1.0659916463476705e+02 5.5046642545209522e+01 -5.2082847070338147e+01
3 1.5886334395918402e+02 2.5338186929832096e+02 -1.6850515833682286e+02
4 -9.5225444536502579e+01 -1.1265598934657196e+02 8.9698661383677717e+01
5 -1.2852852144878329e+02 -9.0809475595387653e+01 -5.2501247333692461e+01
6 4.9246759553241205e+01 -1.8277982378705346e+01 7.0990893782854002e+01
7 7.4663926284829870e+01 8.0704027294328569e+01 -1.3258721042376479e+01
8 -5.7664771790647706e+02 -5.3918019517298592e+02 1.5396929378643614e+02
9 2.9901970531305994e+02 2.8758255690187787e+02 -1.3756295870594514e+02
10 4.5524976502054687e+02 4.2063419413217622e+02 -1.3246733864751559e+02
11 -8.1758898081829770e+01 -1.4048792663689201e+02 1.0573752188920433e+02
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run_energy: 2849.07207400097
run_stress: ! |2-
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run_forces: ! |2
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2 -1.0625167472058520e+02 5.4933080224948007e+01 -5.1680471871853584e+01
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5 -1.2825502974007455e+02 -9.0458764515265173e+01 -5.2676495841154534e+01
6 6.3049547051303456e+01 -4.3984759358165917e+00 6.7752322411553308e+01
7 7.2063814036924853e+01 7.7736010485627787e+01 -1.2790559661004870e+01
8 -5.9873994171892593e+02 -5.6106760521575166e+02 1.6173242713877039e+02
9 3.0322958895200122e+02 2.9158961031453970e+02 -1.4193327505162301e+02
10 4.6742911058701714e+02 4.3476296748266782e+02 -1.3368162420202023e+02
11 -8.2306796650785643e+01 -1.4192288611323806e+02 1.0746321420675316e+02
12 1.3859227344215885e+01 -1.1441899351494421e+01 4.4569325586518920e+00
13 -2.7707098933678509e+00 -6.4032868562592995e+00 -1.3395365036245792e+01
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...

86
unittest/force-styles/tests/dihedral-nharmonic.yaml Normal file
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@ -0,0 +1,86 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 18:38:38 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
dihedral nharmonic
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
dihedral_style: nharmonic
dihedral_coeff: ! |
1 1 75
2 2 75 42
3 3 75 42 35
4 4 75 42 35 21
5 5 75 42 35 21 10
extract: ! ""
natoms: 29
init_energy: 2981.00073511673
init_stress: ! |2-
9.7597564011001154e+01 5.1552482481468100e+00 -1.0275281225914760e+02 1.8493829126960399e+01 -2.0812476993720594e+01 -1.8522149185389509e+01
init_forces: ! |2
1 -2.2513291756353219e+01 4.7119202966322113e+00 7.8626223248943488e+00
2 1.6503301622376316e+01 -8.5221244306678052e+00 8.0632802095482496e+00
3 1.6036976766592576e+02 1.6287909459293988e+02 -7.5360356553197050e+01
4 -5.5774232874990290e+01 -5.3058913648795475e+01 5.7643742847181294e+01
5 -5.5693897474981654e+01 -4.6866567575987339e+01 -2.5012126373852766e+01
6 -1.4807705653098827e+02 -1.7439629259562869e+02 4.3508953332564516e+01
7 5.7230190824331977e+01 6.2118378860762746e+01 -1.0214660840095114e+01
8 -4.9646451985301219e+01 -1.6916018705669373e+01 -4.3263724045252935e+01
9 5.6208167529396206e+01 5.1711293643508995e+01 -2.5287150384768847e+01
10 3.0991849000677316e+01 7.1919803329260148e+01 6.0749104476882920e+01
11 4.5844405619977813e+01 -3.2881788637711445e+01 8.7606207362048369e+00
12 1.1196936677514067e+01 -5.1163625458728184e+01 -5.6831813719102982e+01
13 -5.9988298526181154e+00 -1.3789226131337799e+01 -2.8941334177588317e+01
14 -4.7822307931026252e+01 6.6545912697330365e+01 2.3662127623898343e+01
15 4.0718083591203595e+01 -1.3785125636399199e+01 4.1656250988047944e+01
16 -2.7739760389786966e+01 -3.7464205631044081e+00 1.3938205295403176e+01
17 -5.7968737353570745e+00 -4.7603000364046579e+00 -9.3374174076756766e-01
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29 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
run_energy: 2980.50579322915
run_stress: ! |2-
9.7895434490619337e+01 5.4213709524395828e+00 -1.0331680544305857e+02 1.8675877873066675e+01 -2.0991434453341569e+01 -1.8585983190992422e+01
run_forces: ! |2
1 -2.2591052968690096e+01 4.7210385354547846e+00 7.9294392105535936e+00
2 1.6498095517116187e+01 -8.5356068598615717e+00 8.0720766878856693e+00
3 1.6108997640769729e+02 1.6342942942760337e+02 -7.5708178587991824e+01
4 -5.5915690600613786e+01 -5.3286178349242775e+01 5.7920314335763067e+01
5 -5.5815960140690187e+01 -4.6852076880395700e+01 -2.5129655662229876e+01
6 -1.4887539913047536e+02 -1.7507990917559269e+02 4.3681610088691990e+01
7 5.7525784565224839e+01 6.2341547610308091e+01 -1.0221945594991276e+01
8 -4.9834734857855565e+01 -1.7115522841200708e+01 -4.3399122618009173e+01
9 5.6179010600229461e+01 5.1726594605296690e+01 -2.5317658955721360e+01
10 3.1482397830029917e+01 7.2536730495593062e+01 6.0942772446916798e+01
11 4.5792301818163743e+01 -3.2904155663801774e+01 8.8203497710706404e+00
12 1.1154082762390011e+01 -5.1190045193979515e+01 -5.6802626362359284e+01
13 -5.9632993131627696e+00 -1.3785699614683910e+01 -2.8834090735086761e+01
14 -4.7767992294731812e+01 6.6549040073025040e+01 2.3624991066144862e+01
15 4.0707922113447012e+01 -1.3798576461581593e+01 4.1602789182915110e+01
16 -2.8021580173481375e+01 -4.1280758811589067e+00 1.3726590420250155e+01
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...

86
unittest/force-styles/tests/dihedral-opls.yaml Normal file
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@ -0,0 +1,86 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 18:38:38 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
dihedral opls
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
dihedral_style: opls
dihedral_coeff: ! |
1 75 60 42 23
2 45 20 75 52
3 56 10 32 84
4 23 80 61 83
5 19 90 13 15
extract: ! ""
natoms: 29
init_energy: 2260.68345252858
init_stress: ! |-
-3.2511829957222659e+02 -2.5747791683620072e+01 3.5086609125584744e+02 -1.7284868467618747e+02 2.1513133474621105e+02 1.2517993158427078e+02
init_forces: ! |2
1 3.8418843300789013e+02 -2.0215855127626560e+02 1.9798867612265633e+02
2 -2.9487545045054014e+02 1.5227045701458118e+02 -1.4407198258290703e+02
3 -9.8281517150962827e+01 -1.6227125420394071e+02 -6.7942361484037406e+01
4 1.0637245492200609e+02 1.3269987633301724e+02 -9.7489660444067837e+01
5 -3.7665970146318045e+01 1.7971807362873875e+02 4.6710944552079511e+01
6 1.1702706522755878e+02 8.6982608420528493e+01 3.1913126533391559e+01
7 -7.7554238578063618e+01 -8.2420107806847682e+01 1.3489747654226816e+01
8 9.1569783748212430e+00 -4.0548521525557376e+01 -1.0326672032405810e+01
9 -1.7725494652391845e+02 -1.4026459257463597e+02 7.4192724911953562e+01
10 -4.1110104786839429e+02 -2.5073752258808298e+02 -1.5153435376208625e+02
11 2.5176689706800320e+02 6.4942280703724947e+01 -1.0152404897547778e+02
12 5.0683700189254068e+01 5.3499935743815783e+01 1.5370438642303918e+02
13 -9.3214628811766573e+00 -2.1426805343932180e+01 -4.4971365899031198e+01
14 -3.2894997260227250e+01 4.5774194315657610e+01 1.6276203659637716e+01
15 2.2596508786687970e+01 -7.6500582811265403e+00 2.3117144974751533e+01
16 1.2469191655312414e+01 3.9926824651176759e+01 3.0718477775528918e+01
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run_energy: 2256.24323239172
run_stress: ! |-
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run_forces: ! |2
1 3.8221543296352581e+02 -2.0141948919000066e+02 1.9557532679638945e+02
2 -2.9287695305319323e+02 1.5117733528609159e+02 -1.4124998061827318e+02
3 -9.6968901157768613e+01 -1.6021972846441955e+02 -7.1973012575105997e+01
4 1.0455346745780875e+02 1.3193080713496886e+02 -9.4604433863044719e+01
5 -3.6711061261645170e+01 1.7985412946903816e+02 4.6622409203885653e+01
6 1.1487205026090723e+02 8.2985262131686909e+01 3.2425068981410632e+01
7 -7.6158592387354744e+01 -8.0468484105613015e+01 1.3255468327869348e+01
8 6.8336233635044792e+00 -4.1069837122711107e+01 -9.2791833285164600e+00
9 -1.7541465338683531e+02 -1.3916262246574487e+02 7.2948347484376768e+01
10 -4.1175393396497520e+02 -2.5092469444234629e+02 -1.5026151846272987e+02
11 2.5362614760259910e+02 6.5949894447338195e+01 -1.0158950310115290e+02
12 5.0514163619643369e+01 5.3693737562222708e+01 1.5397975467197989e+02
13 -9.3356957620871128e+00 -2.1480978772005329e+01 -4.5135381377713500e+01
14 -3.2924384373551227e+01 4.5813164716459632e+01 1.6248139979025197e+01
15 2.2683225187118740e+01 -7.6931274678125519e+00 2.3250324273162178e+01
16 1.0385303766648718e+01 3.7834438086310726e+01 2.9952789739539185e+01
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...

86
unittest/force-styles/tests/dihedral-quadratic.yaml Normal file
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@ -0,0 +1,86 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 18:38:38 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
dihedral quadratic
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
dihedral_style: quadratic
dihedral_coeff: ! |
1 75 80
2 45 90
3 25 100
4 35 110
5 85 120
extract: ! ""
natoms: 29
init_energy: 6216.3143470666
init_stress: ! |2-
6.9779660668723466e+01 -3.5532909094858701e+02 2.8554943027986320e+02 -4.9195840209475091e+02 7.3625341259057109e+02 -5.7010808043243844e+02
init_forces: ! |2
1 4.2330351198219410e+02 -3.2157263606983582e+02 4.8778446156448956e+02
2 -2.4731144590894337e+02 1.2770892536477226e+02 -1.2083288138468879e+02
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82
unittest/force-styles/tests/dihedral-zero.yaml Normal file
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@ -0,0 +1,82 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 18:38:39 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
dihedral zero
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
dihedral_style: zero
dihedral_coeff: ! |
*
extract: ! ""
natoms: 29
init_energy: 0
init_stress: ! |2-
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2
unittest/force-styles/tests/fix-timestep-momentum.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 24 Aug 2020
date_generated: Tue Sep 15 09:44:40 202
epsilon: 4e-14
epsilon: 5e-14
prerequisites: ! |
atom full
fix momentum

2
unittest/force-styles/tests/fix-timestep-temp_csvr.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 24 Aug 2020
date_generated: Tue Sep 15 09:44:43 202
epsilon: 2e-14
epsilon: 3e-14
prerequisites: ! |
atom full
fix temp/csvr

84
unittest/force-styles/tests/improper-class2.yaml Normal file
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@ -0,0 +1,84 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 19:35:14 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
improper class2
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
improper_style: class2
improper_coeff: ! |
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extract: ! ""
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83
unittest/force-styles/tests/improper-cossq.yaml Normal file
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@ -0,0 +1,83 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 19:38:24 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
improper cossq
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
improper_style: cossq
improper_coeff: ! |
1 75.0 120.2
2 45.0 59.5
extract: ! ""
natoms: 29
init_energy: 47.9012064519622
init_stress: ! |-
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83
unittest/force-styles/tests/improper-cvff.yaml Normal file
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@ -0,0 +1,83 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 19:35:14 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
improper cvff
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
improper_style: cvff
improper_coeff: ! |
1 75.0 -1 5
2 45.0 +1 2
extract: ! ""
natoms: 29
init_energy: 89.3326668855358
init_stress: ! |2-
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83
unittest/force-styles/tests/improper-distance.yaml Normal file
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@ -0,0 +1,83 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 19:35:14 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
improper distance
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
improper_style: distance
improper_coeff: ! |
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extract: ! ""
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83
unittest/force-styles/tests/improper-distharm.yaml Normal file
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@ -0,0 +1,83 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 19:35:14 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
improper distharm
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
improper_style: distharm
improper_coeff: ! |
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extract: ! ""
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83
unittest/force-styles/tests/improper-fourier.yaml Normal file
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@ -0,0 +1,83 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 19:35:15 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
improper fourier
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
improper_style: fourier
improper_coeff: ! |
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extract: ! ""
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83
unittest/force-styles/tests/improper-harmonic.yaml Normal file
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@ -0,0 +1,83 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 19:35:15 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
improper harmonic
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post_commands: ! ""
input_file: in.fourmol
improper_style: harmonic
improper_coeff: ! |
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84
unittest/force-styles/tests/improper-hybrid.yaml Normal file
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@ -0,0 +1,84 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 20:50:39 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
improper harmonic
improper umbrella
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
improper_style: hybrid harmonic umbrella
improper_coeff: ! |
1 umbrella 75.0 120.2
2 harmonic 45.0 59.5
extract: ! ""
natoms: 29
init_energy: 154.104984286114
init_stress: ! |2-
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run_energy: 153.944034579107
run_stress: ! |2-
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...

83
unittest/force-styles/tests/improper-inversion_harmonic.yaml Normal file
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@ -0,0 +1,83 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 19:35:15 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
improper inversion/harmonic
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
improper_style: inversion/harmonic
improper_coeff: ! |
1 75.0 0.1
2 45.0 1.0
extract: ! ""
natoms: 29
init_energy: 0.352301150271594
init_stress: ! |-
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run_stress: ! |-
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83
unittest/force-styles/tests/improper-ring.yaml Normal file
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@ -0,0 +1,83 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 19:35:15 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
improper ring
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
improper_style: ring
improper_coeff: ! |
1 75.0 120.2
2 45.0 59.5
extract: ! ""
natoms: 29
init_energy: 31535.2377170405
init_stress: ! |-
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init_forces: ! |2
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run_energy: 22428.4452488262
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83
unittest/force-styles/tests/improper-sqdistharm.yaml Normal file
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@ -0,0 +1,83 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 19:35:15 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
improper sqdistharm
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
improper_style: sqdistharm
improper_coeff: ! |
1 75.0 5.5
2 45.0 6.2
extract: ! ""
natoms: 29
init_energy: 3997.62616072489
init_stress: ! |2-
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run_stress: ! |2-
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83
unittest/force-styles/tests/improper-umbrella.yaml Normal file
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@ -0,0 +1,83 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 19:35:15 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
improper umbrella
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
improper_style: umbrella
improper_coeff: ! |
1 75.0 120.2
2 45.0 59.5
extract: ! ""
natoms: 29
init_energy: 120.517350302608
init_stress: ! |2-
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run_energy: 120.514295597906
run_stress: ! |2-
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83
unittest/force-styles/tests/improper-zero.yaml Normal file
View File

@ -0,0 +1,83 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 19:37:56 202
epsilon: 2.5e-13
prerequisites: ! |
atom full
improper zero
pre_commands: ! ""
post_commands: ! ""
input_file: in.fourmol
improper_style: zero
improper_coeff: ! |
1
2
extract: ! ""
natoms: 29
init_energy: 0
init_stress: ! |2-
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init_forces: ! |2
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run_energy: 0
run_stress: ! |2-
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run_forces: ! |2
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...

3
unittest/force-styles/tests/in.fourmol
View File

@ -28,6 +28,3 @@ dihedral_style ${dihedral_style}
improper_style ${improper_style}
read_data ${data_file}
dihedral_coeff *
improper_coeff *

2
unittest/force-styles/tests/mol-pair-tip4p_table.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 24 Aug 2020
date_generated: Tue Sep 15 09:44:20 202
epsilon: 1e-13
epsilon: 2.5e-13
prerequisites: ! |
atom full
pair tip4p/long