/* ---------------------------------------------------------------------- LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator http://lammps.sandia.gov, Sandia National Laboratories Steve Plimpton, sjplimp@sandia.gov Copyright (2003) Sandia Corporation. Under the terms of Contract DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains certain rights in this software. This software is distributed under the GNU General Public License. See the README file in the top-level LAMMPS directory. ------------------------------------------------------------------------- */ #include "atom.h" #include "fmt/format.h" #include "info.h" #include "input.h" #include "lammps.h" #include "output.h" #include "update.h" #include "utils.h" #include "gmock/gmock.h" #include "gtest/gtest.h" #include #include // whether to print verbose output (i.e. not capturing LAMMPS screen output). bool verbose = false; using LAMMPS_NS::utils::split_words; namespace LAMMPS_NS { using ::testing::MatchesRegex; #define GETIDX(i) lmp->atom->map(i) #define TEST_FAILURE(...) \ if (Info::has_exceptions()) { \ ASSERT_ANY_THROW({__VA_ARGS__}); \ } else { \ ASSERT_DEATH({__VA_ARGS__}, ""); \ } #define STRINGIFY(val) XSTR(val) #define XSTR(val) #val class ResetIDsTest : public ::testing::Test { protected: LAMMPS *lmp; void SetUp() override { const char *args[] = {"ResetIDsTest", "-log", "none", "-nocite", "-echo", "screen"}; char **argv = (char **)args; int argc = sizeof(args) / sizeof(char *); if (!verbose) ::testing::internal::CaptureStdout(); lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD); Info *info = new Info(lmp); if (info->has_style("atom", "full")) { lmp->input->one("variable input_dir index " STRINGIFY(TEST_INPUT_FOLDER)); lmp->input->one("include ${input_dir}/in.fourmol"); } if (!verbose) ::testing::internal::GetCapturedStdout(); } void TearDown() override { if (!verbose) ::testing::internal::CaptureStdout(); delete lmp; if (!verbose) ::testing::internal::GetCapturedStdout(); } }; TEST_F(ResetIDsTest, MolIDAll) { if (lmp->atom->natoms == 0) GTEST_SKIP(); auto molid = lmp->atom->molecule; ASSERT_EQ(molid[GETIDX(1)], 1); ASSERT_EQ(molid[GETIDX(2)], 1); ASSERT_EQ(molid[GETIDX(3)], 1); ASSERT_EQ(molid[GETIDX(4)], 1); ASSERT_EQ(molid[GETIDX(5)], 1); ASSERT_EQ(molid[GETIDX(6)], 1); ASSERT_EQ(molid[GETIDX(7)], 1); ASSERT_EQ(molid[GETIDX(8)], 2); ASSERT_EQ(molid[GETIDX(9)], 2); ASSERT_EQ(molid[GETIDX(10)], 2); ASSERT_EQ(molid[GETIDX(11)], 2); ASSERT_EQ(molid[GETIDX(12)], 2); ASSERT_EQ(molid[GETIDX(13)], 2); ASSERT_EQ(molid[GETIDX(14)], 2); ASSERT_EQ(molid[GETIDX(15)], 2); ASSERT_EQ(molid[GETIDX(16)], 2); ASSERT_EQ(molid[GETIDX(17)], 2); ASSERT_EQ(molid[GETIDX(18)], 3); ASSERT_EQ(molid[GETIDX(19)], 3); ASSERT_EQ(molid[GETIDX(20)], 3); ASSERT_EQ(molid[GETIDX(21)], 4); ASSERT_EQ(molid[GETIDX(22)], 4); ASSERT_EQ(molid[GETIDX(23)], 4); ASSERT_EQ(molid[GETIDX(24)], 5); ASSERT_EQ(molid[GETIDX(25)], 5); ASSERT_EQ(molid[GETIDX(26)], 5); ASSERT_EQ(molid[GETIDX(27)], 6); ASSERT_EQ(molid[GETIDX(28)], 6); ASSERT_EQ(molid[GETIDX(29)], 6); // the original data file has two different molecule IDs // for two residues of the same molecule/fragment. if (!verbose) ::testing::internal::CaptureStdout(); lmp->input->one("reset_mol_ids all"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(molid[GETIDX(1)], 1); ASSERT_EQ(molid[GETIDX(2)], 1); ASSERT_EQ(molid[GETIDX(3)], 1); ASSERT_EQ(molid[GETIDX(4)], 1); ASSERT_EQ(molid[GETIDX(5)], 1); ASSERT_EQ(molid[GETIDX(6)], 1); ASSERT_EQ(molid[GETIDX(7)], 1); ASSERT_EQ(molid[GETIDX(8)], 1); ASSERT_EQ(molid[GETIDX(9)], 1); ASSERT_EQ(molid[GETIDX(10)], 1); ASSERT_EQ(molid[GETIDX(11)], 1); ASSERT_EQ(molid[GETIDX(12)], 1); ASSERT_EQ(molid[GETIDX(13)], 1); ASSERT_EQ(molid[GETIDX(14)], 1); ASSERT_EQ(molid[GETIDX(15)], 1); ASSERT_EQ(molid[GETIDX(16)], 1); ASSERT_EQ(molid[GETIDX(17)], 1); ASSERT_EQ(molid[GETIDX(18)], 2); ASSERT_EQ(molid[GETIDX(19)], 2); ASSERT_EQ(molid[GETIDX(20)], 2); ASSERT_EQ(molid[GETIDX(21)], 3); ASSERT_EQ(molid[GETIDX(22)], 3); ASSERT_EQ(molid[GETIDX(23)], 3); ASSERT_EQ(molid[GETIDX(24)], 4); ASSERT_EQ(molid[GETIDX(25)], 4); ASSERT_EQ(molid[GETIDX(26)], 4); ASSERT_EQ(molid[GETIDX(27)], 5); ASSERT_EQ(molid[GETIDX(28)], 5); ASSERT_EQ(molid[GETIDX(29)], 5); } TEST_F(ResetIDsTest, DeletePlusAtomID) { if (lmp->atom->natoms == 0) GTEST_SKIP(); auto molid = lmp->atom->molecule; // delete two water molecules if (!verbose) ::testing::internal::CaptureStdout(); lmp->input->one("group allwater molecule 3:6"); lmp->input->one("group twowater molecule 4:6:2"); lmp->input->one("delete_atoms group twowater compress no bond yes"); lmp->input->one("reset_mol_ids all"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->atom->natoms, 23); ASSERT_EQ(lmp->atom->map_tag_max, 26); ASSERT_EQ(molid[GETIDX(1)], 1); ASSERT_EQ(molid[GETIDX(2)], 1); ASSERT_EQ(molid[GETIDX(3)], 1); ASSERT_EQ(molid[GETIDX(4)], 1); ASSERT_EQ(molid[GETIDX(5)], 1); ASSERT_EQ(molid[GETIDX(6)], 1); ASSERT_EQ(molid[GETIDX(7)], 1); ASSERT_EQ(molid[GETIDX(8)], 1); ASSERT_EQ(molid[GETIDX(9)], 1); ASSERT_EQ(molid[GETIDX(10)], 1); ASSERT_EQ(molid[GETIDX(11)], 1); ASSERT_EQ(molid[GETIDX(12)], 1); ASSERT_EQ(molid[GETIDX(13)], 1); ASSERT_EQ(molid[GETIDX(14)], 1); ASSERT_EQ(molid[GETIDX(15)], 1); ASSERT_EQ(molid[GETIDX(16)], 1); ASSERT_EQ(molid[GETIDX(17)], 1); ASSERT_EQ(molid[GETIDX(18)], 2); ASSERT_EQ(molid[GETIDX(19)], 2); ASSERT_EQ(molid[GETIDX(20)], 2); ASSERT_EQ(molid[GETIDX(24)], 3); ASSERT_EQ(molid[GETIDX(25)], 3); ASSERT_EQ(molid[GETIDX(26)], 3); // now also check and reset the atom ids ASSERT_GE(GETIDX(1), 0); ASSERT_GE(GETIDX(2), 0); ASSERT_GE(GETIDX(3), 0); ASSERT_GE(GETIDX(4), 0); ASSERT_GE(GETIDX(5), 0); ASSERT_GE(GETIDX(6), 0); ASSERT_GE(GETIDX(7), 0); ASSERT_GE(GETIDX(8), 0); ASSERT_GE(GETIDX(9), 0); ASSERT_GE(GETIDX(10), 0); ASSERT_GE(GETIDX(11), 0); ASSERT_GE(GETIDX(12), 0); ASSERT_GE(GETIDX(13), 0); ASSERT_GE(GETIDX(14), 0); ASSERT_GE(GETIDX(15), 0); ASSERT_GE(GETIDX(16), 0); ASSERT_GE(GETIDX(17), 0); ASSERT_GE(GETIDX(18), 0); ASSERT_GE(GETIDX(19), 0); ASSERT_GE(GETIDX(20), 0); ASSERT_EQ(GETIDX(21), -1); ASSERT_EQ(GETIDX(22), -1); ASSERT_EQ(GETIDX(23), -1); ASSERT_GE(GETIDX(24), 0); ASSERT_GE(GETIDX(25), 0); ASSERT_GE(GETIDX(26), 0); if (!verbose) ::testing::internal::CaptureStdout(); lmp->input->one("reset_atom_ids"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->atom->map_tag_max, 23); for (int i = 1; i <= 23; ++i) ASSERT_GE(GETIDX(i), 0); } TEST_F(ResetIDsTest, PartialOffset) { if (lmp->atom->natoms == 0) GTEST_SKIP(); auto molid = lmp->atom->molecule; // delete two water molecules if (!verbose) ::testing::internal::CaptureStdout(); lmp->input->one("group allwater molecule 3:6"); lmp->input->one("group nowater subtract all allwater"); lmp->input->one("reset_mol_ids allwater offset 4"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->atom->natoms, 29); ASSERT_EQ(lmp->atom->map_tag_max, 29); ASSERT_EQ(molid[GETIDX(1)], 1); ASSERT_EQ(molid[GETIDX(2)], 1); ASSERT_EQ(molid[GETIDX(3)], 1); ASSERT_EQ(molid[GETIDX(4)], 1); ASSERT_EQ(molid[GETIDX(5)], 1); ASSERT_EQ(molid[GETIDX(6)], 1); ASSERT_EQ(molid[GETIDX(7)], 1); ASSERT_EQ(molid[GETIDX(8)], 2); ASSERT_EQ(molid[GETIDX(9)], 2); ASSERT_EQ(molid[GETIDX(10)], 2); ASSERT_EQ(molid[GETIDX(11)], 2); ASSERT_EQ(molid[GETIDX(12)], 2); ASSERT_EQ(molid[GETIDX(13)], 2); ASSERT_EQ(molid[GETIDX(14)], 2); ASSERT_EQ(molid[GETIDX(15)], 2); ASSERT_EQ(molid[GETIDX(16)], 2); ASSERT_EQ(molid[GETIDX(17)], 2); ASSERT_EQ(molid[GETIDX(18)], 5); ASSERT_EQ(molid[GETIDX(19)], 5); ASSERT_EQ(molid[GETIDX(20)], 5); ASSERT_EQ(molid[GETIDX(21)], 6); ASSERT_EQ(molid[GETIDX(22)], 6); ASSERT_EQ(molid[GETIDX(23)], 6); ASSERT_EQ(molid[GETIDX(24)], 7); ASSERT_EQ(molid[GETIDX(25)], 7); ASSERT_EQ(molid[GETIDX(26)], 7); ASSERT_EQ(molid[GETIDX(27)], 8); ASSERT_EQ(molid[GETIDX(28)], 8); ASSERT_EQ(molid[GETIDX(29)], 8); if (!verbose) ::testing::internal::CaptureStdout(); lmp->input->one("reset_mol_ids nowater offset 0"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(molid[GETIDX(1)], 1); ASSERT_EQ(molid[GETIDX(2)], 1); ASSERT_EQ(molid[GETIDX(3)], 1); ASSERT_EQ(molid[GETIDX(4)], 1); ASSERT_EQ(molid[GETIDX(5)], 1); ASSERT_EQ(molid[GETIDX(6)], 1); ASSERT_EQ(molid[GETIDX(7)], 1); ASSERT_EQ(molid[GETIDX(8)], 1); ASSERT_EQ(molid[GETIDX(9)], 1); ASSERT_EQ(molid[GETIDX(10)], 1); ASSERT_EQ(molid[GETIDX(11)], 1); ASSERT_EQ(molid[GETIDX(12)], 1); ASSERT_EQ(molid[GETIDX(13)], 1); ASSERT_EQ(molid[GETIDX(14)], 1); ASSERT_EQ(molid[GETIDX(15)], 1); ASSERT_EQ(molid[GETIDX(16)], 1); ASSERT_EQ(molid[GETIDX(17)], 1); ASSERT_EQ(molid[GETIDX(18)], 5); ASSERT_EQ(molid[GETIDX(19)], 5); ASSERT_EQ(molid[GETIDX(20)], 5); ASSERT_EQ(molid[GETIDX(21)], 6); ASSERT_EQ(molid[GETIDX(22)], 6); ASSERT_EQ(molid[GETIDX(23)], 6); ASSERT_EQ(molid[GETIDX(24)], 7); ASSERT_EQ(molid[GETIDX(25)], 7); ASSERT_EQ(molid[GETIDX(26)], 7); ASSERT_EQ(molid[GETIDX(27)], 8); ASSERT_EQ(molid[GETIDX(28)], 8); ASSERT_EQ(molid[GETIDX(29)], 8); } TEST_F(ResetIDsTest, DeleteAdd) { if (lmp->atom->natoms == 0) GTEST_SKIP(); auto molid = lmp->atom->molecule; // delete two water molecules if (!verbose) ::testing::internal::CaptureStdout(); lmp->input->one("group allwater molecule 3:6"); lmp->input->one("group twowater molecule 4:6:2"); lmp->input->one("group nowater subtract all allwater"); lmp->input->one("delete_atoms group twowater compress no bond yes mol yes"); lmp->input->one("reset_mol_ids allwater offset auto"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->atom->natoms, 23); ASSERT_EQ(lmp->atom->map_tag_max, 26); ASSERT_EQ(molid[GETIDX(1)], 1); ASSERT_EQ(molid[GETIDX(2)], 1); ASSERT_EQ(molid[GETIDX(3)], 1); ASSERT_EQ(molid[GETIDX(4)], 1); ASSERT_EQ(molid[GETIDX(5)], 1); ASSERT_EQ(molid[GETIDX(6)], 1); ASSERT_EQ(molid[GETIDX(7)], 1); ASSERT_EQ(molid[GETIDX(8)], 2); ASSERT_EQ(molid[GETIDX(9)], 2); ASSERT_EQ(molid[GETIDX(10)], 2); ASSERT_EQ(molid[GETIDX(11)], 2); ASSERT_EQ(molid[GETIDX(12)], 2); ASSERT_EQ(molid[GETIDX(13)], 2); ASSERT_EQ(molid[GETIDX(14)], 2); ASSERT_EQ(molid[GETIDX(15)], 2); ASSERT_EQ(molid[GETIDX(16)], 2); ASSERT_EQ(molid[GETIDX(17)], 2); ASSERT_EQ(molid[GETIDX(18)], 3); ASSERT_EQ(molid[GETIDX(19)], 3); ASSERT_EQ(molid[GETIDX(20)], 3); ASSERT_EQ(molid[GETIDX(24)], 4); ASSERT_EQ(molid[GETIDX(25)], 4); ASSERT_EQ(molid[GETIDX(26)], 4); // now also check and reset the atom ids ASSERT_GE(GETIDX(1), 0); ASSERT_GE(GETIDX(2), 0); ASSERT_GE(GETIDX(3), 0); ASSERT_GE(GETIDX(4), 0); ASSERT_GE(GETIDX(5), 0); ASSERT_GE(GETIDX(6), 0); ASSERT_GE(GETIDX(7), 0); ASSERT_GE(GETIDX(8), 0); ASSERT_GE(GETIDX(9), 0); ASSERT_GE(GETIDX(10), 0); ASSERT_GE(GETIDX(11), 0); ASSERT_GE(GETIDX(12), 0); ASSERT_GE(GETIDX(13), 0); ASSERT_GE(GETIDX(14), 0); ASSERT_GE(GETIDX(15), 0); ASSERT_GE(GETIDX(16), 0); ASSERT_GE(GETIDX(17), 0); ASSERT_GE(GETIDX(18), 0); ASSERT_GE(GETIDX(19), 0); ASSERT_GE(GETIDX(20), 0); ASSERT_EQ(GETIDX(21), -1); ASSERT_EQ(GETIDX(22), -1); ASSERT_EQ(GETIDX(23), -1); ASSERT_GE(GETIDX(24), 0); ASSERT_GE(GETIDX(25), 0); ASSERT_GE(GETIDX(26), 0); if (!verbose) ::testing::internal::CaptureStdout(); lmp->input->one("reset_atom_ids sort yes"); if (!verbose) ::testing::internal::GetCapturedStdout(); ASSERT_EQ(lmp->atom->map_tag_max, 23); for (int i = 1; i <= 23; ++i) ASSERT_GE(GETIDX(i), 0); if (!verbose) ::testing::internal::CaptureStdout(); lmp->input->one("reset_mol_ids nowater offset 1"); if (!verbose) ::testing::internal::GetCapturedStdout(); EXPECT_EQ(molid[GETIDX(1)], 2); EXPECT_EQ(molid[GETIDX(2)], 2); EXPECT_EQ(molid[GETIDX(3)], 2); EXPECT_EQ(molid[GETIDX(4)], 2); EXPECT_EQ(molid[GETIDX(5)], 2); EXPECT_EQ(molid[GETIDX(6)], 2); EXPECT_EQ(molid[GETIDX(7)], 2); EXPECT_EQ(molid[GETIDX(8)], 2); EXPECT_EQ(molid[GETIDX(9)], 2); EXPECT_EQ(molid[GETIDX(10)], 2); EXPECT_EQ(molid[GETIDX(11)], 2); EXPECT_EQ(molid[GETIDX(12)], 2); EXPECT_EQ(molid[GETIDX(13)], 3); EXPECT_EQ(molid[GETIDX(14)], 3); EXPECT_EQ(molid[GETIDX(15)], 3); EXPECT_EQ(molid[GETIDX(16)], 2); EXPECT_EQ(molid[GETIDX(17)], 2); EXPECT_EQ(molid[GETIDX(18)], 2); EXPECT_EQ(molid[GETIDX(19)], 2); EXPECT_EQ(molid[GETIDX(20)], 2); EXPECT_EQ(molid[GETIDX(21)], 4); EXPECT_EQ(molid[GETIDX(22)], 4); EXPECT_EQ(molid[GETIDX(23)], 4); if (!verbose) ::testing::internal::CaptureStdout(); lmp->input->one("create_atoms 1 single 0.0 0.0 0.0"); lmp->input->one("create_atoms 2 single 1.0 0.0 0.0"); lmp->input->one("create_atoms 3 single 2.0 0.0 0.0"); lmp->input->one("create_atoms 4 single 3.0 0.0 0.0"); lmp->input->one("reset_mol_ids all"); if (!verbose) ::testing::internal::GetCapturedStdout(); EXPECT_EQ(lmp->atom->natoms, 27); EXPECT_EQ(lmp->atom->map_tag_max, 27); EXPECT_EQ(molid[GETIDX(21)], 3); EXPECT_EQ(molid[GETIDX(22)], 3); EXPECT_EQ(molid[GETIDX(23)], 3); EXPECT_EQ(molid[GETIDX(24)], 4); EXPECT_EQ(molid[GETIDX(25)], 5); EXPECT_EQ(molid[GETIDX(26)], 6); EXPECT_EQ(molid[GETIDX(27)], 7); if (!verbose) ::testing::internal::CaptureStdout(); lmp->input->one("reset_mol_ids all singlezero"); if (!verbose) ::testing::internal::GetCapturedStdout(); EXPECT_EQ(molid[GETIDX(21)], 3); EXPECT_EQ(molid[GETIDX(22)], 3); EXPECT_EQ(molid[GETIDX(23)], 3); EXPECT_EQ(molid[GETIDX(24)], 0); EXPECT_EQ(molid[GETIDX(25)], 0); EXPECT_EQ(molid[GETIDX(26)], 0); EXPECT_EQ(molid[GETIDX(27)], 0); } TEST_F(ResetIDsTest, DeathTests) { ::testing::internal::CaptureStdout(); TEST_FAILURE(lmp->input->one("reset_mol_ids");); auto mesg = ::testing::internal::GetCapturedStdout(); ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*")); ::testing::internal::CaptureStdout(); TEST_FAILURE(lmp->input->one("reset_mol_ids all offset 1 1");); mesg = ::testing::internal::GetCapturedStdout(); ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*")); ::testing::internal::CaptureStdout(); TEST_FAILURE(lmp->input->one("reset_mol_ids all offset -2");); mesg = ::testing::internal::GetCapturedStdout(); ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*")); ::testing::internal::CaptureStdout(); TEST_FAILURE(lmp->input->one("reset_mol_ids all offset xxx");); mesg = ::testing::internal::GetCapturedStdout(); ASSERT_THAT(mesg, MatchesRegex(".*ERROR on proc 0: Expected integer.*")); ::testing::internal::CaptureStdout(); TEST_FAILURE(lmp->input->one("reset_mol_ids all offset");); mesg = ::testing::internal::GetCapturedStdout(); ASSERT_THAT(mesg, MatchesRegex(".*ERROR: Illegal reset_mol_ids command.*")); } } // namespace LAMMPS_NS 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 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; }