428 lines
16 KiB
C++
428 lines
16 KiB
C++
/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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LAMMPS Development team: developers@lammps.org
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "../testing/core.h"
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#include "atom.h"
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#include "info.h"
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#include "input.h"
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#include "lammps.h"
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#include "molecule.h"
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#include "platform.h"
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#include "gmock/gmock.h"
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#include "gtest/gtest.h"
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#include <cstdio>
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#include <mpi.h>
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#include <string>
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using namespace LAMMPS_NS;
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using testing::ContainsRegex;
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using testing::StrEq;
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using utils::split_words;
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#define test_name test_info_->name()
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static void create_molecule_files(const std::string &h2o_filename, const std::string &co2_filename)
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{
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// create molecule files
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const char h2o_file[] = "# Water molecule. SPC/E model.\n\n3 atoms\n2 bonds\n1 angles\n\n"
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"Coords\n\n1 1.12456 0.09298 1.27452\n"
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"2 1.53683 0.75606 1.89928\n3 0.49482 0.56390 0.65678\n\n"
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"Types\n\n1 1\n2 2\n3 2\n\n"
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"Charges\n\n1 -0.8472\n2 0.4236\n3 0.4236\n\n"
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"Bonds\n\n1 1 1 2\n2 1 1 3\n\n"
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"Angles\n\n1 1 2 1 3\n\n"
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"Shake Flags\n\n1 1\n2 1\n3 1\n\n"
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"Shake Atoms\n\n1 1 2 3\n2 1 2 3\n3 1 2 3\n\n"
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"Shake Bond Types\n\n1 1 1 1\n2 1 1 1\n3 1 1 1\n\n"
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"Special Bond Counts\n\n1 2 0 0\n2 1 1 0\n3 1 1 0\n\n"
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"Special Bonds\n\n1 2 3\n2 1 3\n3 1 2\n\n";
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const char co2_file[] = "# CO2 molecule file. TraPPE model.\n\n"
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"3 atoms\n2 bonds\n1 angles\n\n"
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"Coords\n\n1 0.0 0.0 0.0\n2 -1.16 0.0 0.0\n3 1.16 0.0 0.0\n\n"
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"Types\n\n1 1\n2 2\n3 2\n\n"
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"Charges\n\n1 0.7\n2 -0.35\n3 -0.35\n\n"
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"Bonds\n\n1 1 1 2\n2 1 1 3\n\n"
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"Angles\n\n1 1 2 1 3\n\n"
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"Special Bond Counts\n\n1 2 0 0\n2 1 1 0\n3 1 1 0\n\n"
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"Special Bonds\n\n1 2 3\n2 1 3\n3 1 2\n\n";
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FILE *fp = fopen(h2o_filename.c_str(), "w");
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if (fp) {
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fputs(h2o_file, fp);
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fclose(fp);
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}
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fp = fopen(co2_filename.c_str(), "w");
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if (fp) {
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fputs(co2_file, fp);
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fclose(fp);
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}
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}
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static void create_labelmap_files(const std::string &h2o_filename, const std::string &co2_filename)
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{
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// create molecule files
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const char h2o_file[] = "# Water molecule. SPC/E model.\n\n3 atoms\n2 bonds\n1 angles\n\n"
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"Coords\n\n1 1.12456 0.09298 1.27452\n"
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"2 1.53683 0.75606 1.89928\n3 0.49482 0.56390 0.65678\n\n"
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"Types\n\n1 OW\n2 HO\n3 HO\n\n"
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"Charges\n\n1 -0.8472\n2 0.4236\n3 0.4236\n\n"
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"Bonds\n\n1 OW-HO 1 2\n2 OW-HO 1 3\n\n"
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"Angles\n\n1 HO-OW-HO 2 1 3\n\n"
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"Shake Flags\n\n1 1\n2 1\n3 1\n\n"
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"Shake Atoms\n\n1 1 2 3\n2 1 2 3\n3 1 2 3\n\n"
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"Shake Bond Types\n\n1 OW-HO OW-HO HO-OW-HO\n2 OW-HO OW-HO HO-OW-HO\n3 "
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"OW-HO OW-HO HO-OW-HO\n\n"
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"Special Bond Counts\n\n1 2 0 0\n2 1 1 0\n3 1 1 0\n\n"
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"Special Bonds\n\n1 2 3\n2 1 3\n3 1 2\n\n";
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const char co2_file[] = "# CO2 molecule file. TraPPE model.\n\n"
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"3 atoms\n2 bonds\n1 angles\n\n"
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"Coords\n\n1 0.0 0.0 0.0\n2 -1.16 0.0 0.0\n3 1.16 0.0 0.0\n\n"
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"Types\n\n1 C\n2 O\n3 O\n\n"
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"Charges\n\n1 0.7\n2 -0.35\n3 -0.35\n\n"
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"Bonds\n\n1 C=O 1 2\n2 C=O 1 3\n\n"
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"Angles\n\n1 O=C=O 2 1 3\n\n"
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"Special Bond Counts\n\n1 2 0 0\n2 1 1 0\n3 1 1 0\n\n"
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"Special Bonds\n\n1 2 3\n2 1 3\n3 1 2\n\n";
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FILE *fp = fopen(h2o_filename.c_str(), "w");
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if (fp) {
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fputs(h2o_file, fp);
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fclose(fp);
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}
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fp = fopen(co2_filename.c_str(), "w");
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if (fp) {
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fputs(co2_file, fp);
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fclose(fp);
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}
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}
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// whether to print verbose output (i.e. not capturing LAMMPS screen output).
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bool verbose = false;
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class MoleculeFileTest : public LAMMPSTest {
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protected:
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static void SetUpTestSuite()
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{
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create_molecule_files("moltest.h2o.mol", "moltest.co2.mol");
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create_labelmap_files("labelmap.h2o.mol", "labelmap.co2.mol");
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}
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static void TearDownTestSuite()
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{
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platform::unlink("moltest.h2o.mol");
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platform::unlink("moltest.co2.mol");
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platform::unlink("labelmap.h2o.mol");
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platform::unlink("labelmap.co2.mol");
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}
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void SetUp() override
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{
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testbinary = "MoleculeFileTest";
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LAMMPSTest::SetUp();
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ASSERT_NE(lmp, nullptr);
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}
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void TearDown() override { LAMMPSTest::TearDown(); }
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void run_mol_cmd(const std::string &name, const std::string &args, const std::string &content)
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{
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std::string file = fmt::format("moltest_{}.mol", name);
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FILE *fp = fopen(file.c_str(), "w");
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fputs(content.c_str(), fp);
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fclose(fp);
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command(fmt::format("molecule {} {} {}", name, file, args));
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remove(file.c_str());
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}
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};
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TEST_F(MoleculeFileTest, nofile)
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{
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TEST_FAILURE(".*Cannot open molecule file nofile.mol.*", command("molecule 1 nofile.mol"););
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}
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TEST_F(MoleculeFileTest, badid)
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{
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TEST_FAILURE(".*Molecule template ID must have only "
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"alphanumeric or underscore characters.*",
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command("molecule @mol nofile.mol"););
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}
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TEST_F(MoleculeFileTest, badargs)
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{
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TEST_FAILURE(".*Illegal molecule command.*",
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run_mol_cmd(test_name, "offset 1 2 3 4",
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"Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"););
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TEST_FAILURE(
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".*Illegal molecule command.*",
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run_mol_cmd(test_name, "toff", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"););
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TEST_FAILURE(
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".*Illegal molecule command.*",
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run_mol_cmd(test_name, "boff", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"););
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TEST_FAILURE(
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".*Illegal molecule command.*",
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run_mol_cmd(test_name, "aoff", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"););
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TEST_FAILURE(
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".*Illegal molecule command.*",
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run_mol_cmd(test_name, "doff", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"););
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TEST_FAILURE(
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".*Illegal molecule command.*",
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run_mol_cmd(test_name, "ioff", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"););
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TEST_FAILURE(
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".*Illegal molecule command.*",
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run_mol_cmd(test_name, "scale", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"););
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remove("badargs.mol");
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}
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TEST_F(MoleculeFileTest, noatom)
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{
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TEST_FAILURE(".*ERROR: No atoms or invalid atom count in molecule file.*",
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run_mol_cmd(test_name, "",
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"Comment\n0 atoms\n1 bonds\n\n"
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" Coords\n\nBonds\n\n 1 1 2\n"););
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remove("noatom.mol");
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}
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TEST_F(MoleculeFileTest, empty)
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{
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TEST_FAILURE(".*ERROR: Unexpected end of molecule file.*",
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run_mol_cmd(test_name, "", "Comment\n\n"););
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remove("empty.mol");
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}
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TEST_F(MoleculeFileTest, nospecial)
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{
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TEST_FAILURE(".*ERROR: Cannot auto-generate special bonds before simulation box is defined.*",
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run_mol_cmd(test_name, "",
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"Comment\n3 atoms\n\n2 bonds\n\n"
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" Coords\n\n 1 1.0 1.0 1.0\n 2 1.0 1.0 0.0\n 3 1.0 0.0 1.0\n"
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" Bonds\n\n 1 1 1 2\n 2 1 1 3\n"););
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remove("nospecial.mol");
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}
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TEST_F(MoleculeFileTest, minimal)
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{
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BEGIN_CAPTURE_OUTPUT();
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run_mol_cmd(test_name, "", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n");
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auto output = END_CAPTURE_OUTPUT();
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ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*1 molecules.*\n"
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".*0 fragments.*\n.*1 atoms.*\n.*0 bonds.*"));
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}
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TEST_F(MoleculeFileTest, notype)
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{
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BEGIN_CAPTURE_OUTPUT();
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command("atom_style atomic");
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command("region box block 0 1 0 1 0 1");
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command("create_box 1 box");
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run_mol_cmd(test_name, "", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n");
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auto output = END_CAPTURE_OUTPUT();
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ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*1 molecules.*\n"
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".*0 fragments.*\n.*1 atoms.*\n.*0 bonds.*"));
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TEST_FAILURE(".*ERROR: Create_atoms molecule must have atom types.*",
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command("create_atoms 0 single 0.0 0.0 0.0 mol notype 542465"););
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}
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TEST_F(MoleculeFileTest, extramass)
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{
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BEGIN_CAPTURE_OUTPUT();
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command("atom_style atomic");
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command("region box block 0 1 0 1 0 1");
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command("create_box 1 box");
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run_mol_cmd(test_name, "",
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"Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"
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" Types\n\n 1 1\n Masses\n\n 1 1.0\n");
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command("create_atoms 0 single 0.0 0.0 0.0 mol extramass 73546");
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auto output = END_CAPTURE_OUTPUT();
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ASSERT_THAT(output, ContainsRegex(".*WARNING: Molecule attributes do not match "
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"system attributes.*"));
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}
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TEST_F(MoleculeFileTest, twomols)
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{
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BEGIN_CAPTURE_OUTPUT();
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run_mol_cmd(test_name, "",
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"Comment\n2 atoms\n\n"
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" Coords\n\n 1 0.0 0.0 0.0\n 2 0.0 0.0 1.0\n"
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" Molecules\n\n 1 1\n 2 2\n\n Types\n\n 1 1\n 2 2\n\n");
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auto output = END_CAPTURE_OUTPUT();
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ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*2 molecules.*\n"
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".*0 fragments.*\n.*2 atoms with max type 2.*\n.*0 bonds.*"));
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ASSERT_EQ(lmp->atom->nmolecule, 1);
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auto mols = lmp->atom->get_molecule_by_id(test_name);
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ASSERT_EQ(mols.size(), 1);
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}
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TEST_F(MoleculeFileTest, twofiles)
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{
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BEGIN_CAPTURE_OUTPUT();
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command("molecule twomols moltest.h2o.mol moltest.co2.mol offset 2 1 1 0 0");
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auto output = END_CAPTURE_OUTPUT();
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ASSERT_THAT(
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output,
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ContainsRegex(".*Read molecule template twomols:.*\n.*1 molecules.*\n"
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".*0 fragments.*\n.*3 atoms with max type 2.*\n.*2 bonds with max type 1.*\n"
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".*1 angles with max type 1.*\n.*0 dihedrals.*\n.*0 impropers.*\n"
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".*Read molecule template twomols:.*\n.*1 molecules.*\n"
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".*0 fragments.*\n.*3 atoms with max type 4.*\n.*2 bonds with max type 2.*\n"
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".*1 angles with max type 2.*\n.*0 dihedrals.*"));
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BEGIN_CAPTURE_OUTPUT();
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command("molecule h2o moltest.h2o.mol");
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command("molecule co2 moltest.co2.mol");
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output = END_CAPTURE_OUTPUT();
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ASSERT_EQ(lmp->atom->nmolecule, 4);
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auto mols = lmp->atom->get_molecule_by_id("twomols");
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ASSERT_EQ(mols.size(), 2);
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mols = lmp->atom->get_molecule_by_id("h2o");
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ASSERT_EQ(mols.size(), 1);
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mols = lmp->atom->get_molecule_by_id("co2");
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ASSERT_EQ(mols.size(), 1);
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}
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TEST_F(MoleculeFileTest, labelmap)
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{
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if (!info->has_style("atom", "full")) GTEST_SKIP();
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BEGIN_CAPTURE_OUTPUT();
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command("atom_style full");
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command("region box block 0 2 0 2 0 2");
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command("create_box 4 box bond/types 2 angle/types 2");
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command("labelmap atom 1 HO 2 OW 3 C 4 O");
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command("labelmap bond 1 OW-HO 2 C=O");
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command("labelmap angle 1 HO-OW-HO 2 O=C=O");
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command("molecule h2olabel labelmap.h2o.mol");
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auto output = END_CAPTURE_OUTPUT();
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ASSERT_THAT(
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output,
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ContainsRegex(".*Read molecule template h2olabel:.*\n.*1 molecules.*\n"
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".*0 fragments.*\n.*3 atoms with max type 2.*\n.*2 bonds with max type 1.*\n"
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".*1 angles with max type 1.*\n.*0 dihedrals.*\n.*0 impropers.*"));
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BEGIN_CAPTURE_OUTPUT();
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command("molecule co2label labelmap.co2.mol");
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output = END_CAPTURE_OUTPUT();
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ASSERT_THAT(
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output,
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ContainsRegex(".*Read molecule template co2label:.*\n.*1 molecules.*\n"
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".*0 fragments.*\n.*3 atoms with max type 4.*\n.*2 bonds with max type 2.*\n"
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".*1 angles with max type 2.*\n.*0 dihedrals.*"));
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BEGIN_CAPTURE_OUTPUT();
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command("molecule h2onum moltest.h2o.mol");
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command("molecule co2num moltest.co2.mol offset 2 1 1 0 0");
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output = END_CAPTURE_OUTPUT();
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auto mark = output.find("WARNING");
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auto first = output.substr(0, mark);
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mark = output.find("Read molecule", mark);
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auto second = output.substr(mark);
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ASSERT_THAT(
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first,
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ContainsRegex(".*Read molecule template h2onum:.*\n.*1 molecules.*\n"
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".*0 fragments.*\n.*3 atoms with max type 2.*\n.*2 bonds with max type 1.*\n"
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".*1 angles with max type 1.*\n.*0 dihedrals.*\n.*0 impropers.*\n"));
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ASSERT_THAT(
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second,
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ContainsRegex(".*Read molecule template co2num:.*\n.*1 molecules.*\n"
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".*0 fragments.*\n.*3 atoms with max type 4.*\n.*2 bonds with max type 2.*\n"
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".*1 angles with max type 2.*\n.*0 dihedrals.*"));
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ASSERT_EQ(lmp->atom->nmolecule, 4);
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auto mols = lmp->atom->get_molecule_by_id("h2onum");
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ASSERT_EQ(mols.size(), 1);
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mols = lmp->atom->get_molecule_by_id("co2num");
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ASSERT_EQ(mols.size(), 1);
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mols = lmp->atom->get_molecule_by_id("h2olabel");
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ASSERT_EQ(mols.size(), 1);
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mols = lmp->atom->get_molecule_by_id("co2label");
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ASSERT_EQ(mols.size(), 1);
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BEGIN_CAPTURE_OUTPUT();
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command("labelmap atom 1 A 2 B");
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END_CAPTURE_OUTPUT();
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TEST_FAILURE(".*ERROR: Unknown atom type OW in Types section of molecule file: 1 OW.*",
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command("molecule fail labelmap.h2o.mol"););
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}
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TEST_F(MoleculeFileTest, bonds)
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{
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if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP();
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BEGIN_CAPTURE_OUTPUT();
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command("atom_style bond");
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command("region box block 0 1 0 1 0 1");
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command("create_box 2 box bond/types 2 extra/bond/per/atom 2 "
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"extra/special/per/atom 4");
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run_mol_cmd(test_name, "",
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"Comment\n"
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"4 atoms\n"
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"2 bonds\n\n"
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" Coords\n\n"
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" 1 1.0 1.0 1.0\n"
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" 2 1.0 1.0 0.0\n"
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" 3 1.0 0.0 1.0\n"
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" 4 1.0 0.0 0.0\n"
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" Types\n\n"
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" 1 1\n"
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" 2 1\n"
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" 3 2\n"
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" 4 2\n\n"
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" Bonds\n\n"
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" 1 1 1 2\n"
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" 2 2 1 3\n\n");
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auto output = END_CAPTURE_OUTPUT();
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ASSERT_THAT(output, ContainsRegex(".*Read molecule template.*\n.*1 molecules.*\n"
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".*0 fragments.*\n.*4 atoms.*type.*2.*\n"
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".*2 bonds.*type.*2.*\n.*0 angles.*"));
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BEGIN_CAPTURE_OUTPUT();
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command("mass * 2.0");
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command("create_atoms 0 single 0.5 0.5 0.5 mol bonds 67235");
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output = END_CAPTURE_OUTPUT();
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ASSERT_THAT(output, ContainsRegex(".*Created 4 atoms.*"));
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BEGIN_HIDE_OUTPUT();
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Molecule *mol = lmp->atom->molecules[0];
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ASSERT_EQ(mol->natoms, 4);
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ASSERT_EQ(lmp->atom->natoms, 4);
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mol->compute_mass();
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mol->compute_com();
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ASSERT_DOUBLE_EQ(mol->masstotal, 8.0);
|
|
EXPECT_DOUBLE_EQ(mol->com[0], 1.0);
|
|
EXPECT_DOUBLE_EQ(mol->com[1], 0.5);
|
|
EXPECT_DOUBLE_EQ(mol->com[2], 0.5);
|
|
EXPECT_DOUBLE_EQ(mol->maxextent, sqrt(2.0));
|
|
EXPECT_EQ(mol->comatom, 1);
|
|
END_HIDE_OUTPUT();
|
|
}
|
|
|
|
int main(int argc, char **argv)
|
|
{
|
|
MPI_Init(&argc, &argv);
|
|
::testing::InitGoogleMock(&argc, argv);
|
|
|
|
// handle arguments passed via environment variable
|
|
if (const char *var = getenv("TEST_ARGS")) {
|
|
std::vector<std::string> env = split_words(var);
|
|
for (auto arg : env) {
|
|
if (arg == "-v") {
|
|
verbose = true;
|
|
}
|
|
}
|
|
}
|
|
|
|
if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
|
|
|
|
int rv = RUN_ALL_TESTS();
|
|
MPI_Finalize();
|
|
return rv;
|
|
}
|