/* ---------------------------------------------------------------------- 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. ------------------------------------------------------------------------- */ #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 "../testing/core.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 STRINGIFY(val) XSTR(val) #define XSTR(val) #val class ResetIDsTest : public LAMMPSTest { protected: void SetUp() override { testbinary = "ResetIDsTest"; LAMMPSTest::SetUp(); if (info->has_style("atom", "full")) { BEGIN_HIDE_OUTPUT(); command("variable input_dir index " STRINGIFY(TEST_INPUT_FOLDER)); command("include ${input_dir}/in.fourmol"); END_HIDE_OUTPUT(); } } }; 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. BEGIN_HIDE_OUTPUT(); command("reset_mol_ids all"); END_HIDE_OUTPUT(); 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 BEGIN_HIDE_OUTPUT(); command("group allwater molecule 3:6"); command("group twowater molecule 4:6:2"); command("delete_atoms group twowater compress no bond yes"); command("reset_mol_ids all"); END_HIDE_OUTPUT(); 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); BEGIN_HIDE_OUTPUT(); command("reset_atom_ids"); END_HIDE_OUTPUT(); 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 BEGIN_HIDE_OUTPUT(); command("group allwater molecule 3:6"); command("group nowater subtract all allwater"); command("reset_mol_ids allwater offset 4"); END_HIDE_OUTPUT(); 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); BEGIN_HIDE_OUTPUT(); command("reset_mol_ids nowater offset 0"); END_HIDE_OUTPUT(); 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 BEGIN_HIDE_OUTPUT(); command("group allwater molecule 3:6"); command("group twowater molecule 4:6:2"); command("group nowater subtract all allwater"); command("delete_atoms group twowater compress no bond yes mol yes"); command("reset_mol_ids allwater"); END_HIDE_OUTPUT(); 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); BEGIN_HIDE_OUTPUT(); command("reset_atom_ids sort yes"); END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->map_tag_max, 23); for (int i = 1; i <= 23; ++i) ASSERT_GE(GETIDX(i), 0); BEGIN_HIDE_OUTPUT(); command("reset_mol_ids nowater offset 1"); END_HIDE_OUTPUT(); ASSERT_EQ(molid[GETIDX(1)], 2); ASSERT_EQ(molid[GETIDX(2)], 2); ASSERT_EQ(molid[GETIDX(3)], 2); ASSERT_EQ(molid[GETIDX(4)], 2); ASSERT_EQ(molid[GETIDX(5)], 2); ASSERT_EQ(molid[GETIDX(6)], 2); ASSERT_EQ(molid[GETIDX(7)], 2); 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)], 3); ASSERT_EQ(molid[GETIDX(14)], 3); ASSERT_EQ(molid[GETIDX(15)], 3); ASSERT_EQ(molid[GETIDX(16)], 2); ASSERT_EQ(molid[GETIDX(17)], 2); ASSERT_EQ(molid[GETIDX(18)], 2); ASSERT_EQ(molid[GETIDX(19)], 2); ASSERT_EQ(molid[GETIDX(20)], 2); ASSERT_EQ(molid[GETIDX(21)], 4); ASSERT_EQ(molid[GETIDX(22)], 4); ASSERT_EQ(molid[GETIDX(23)], 4); BEGIN_HIDE_OUTPUT(); command("create_atoms 1 single 0.0 0.0 0.0"); command("create_atoms 2 single 1.0 0.0 0.0"); command("create_atoms 3 single 2.0 0.0 0.0"); command("create_atoms 4 single 3.0 0.0 0.0"); command("reset_mol_ids all single yes"); END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->natoms, 27); ASSERT_EQ(lmp->atom->map_tag_max, 27); 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)], 5); ASSERT_EQ(molid[GETIDX(26)], 6); ASSERT_EQ(molid[GETIDX(27)], 7); BEGIN_HIDE_OUTPUT(); command("reset_mol_ids all single no"); END_HIDE_OUTPUT(); ASSERT_EQ(molid[GETIDX(21)], 3); ASSERT_EQ(molid[GETIDX(22)], 3); ASSERT_EQ(molid[GETIDX(23)], 3); ASSERT_EQ(molid[GETIDX(24)], 0); ASSERT_EQ(molid[GETIDX(25)], 0); ASSERT_EQ(molid[GETIDX(26)], 0); ASSERT_EQ(molid[GETIDX(27)], 0); BEGIN_HIDE_OUTPUT(); command("reset_mol_ids all compress no single yes"); END_HIDE_OUTPUT(); ASSERT_EQ(molid[GETIDX(21)], 21); ASSERT_EQ(molid[GETIDX(22)], 21); ASSERT_EQ(molid[GETIDX(23)], 21); ASSERT_EQ(molid[GETIDX(24)], 24); ASSERT_EQ(molid[GETIDX(25)], 25); ASSERT_EQ(molid[GETIDX(26)], 26); ASSERT_EQ(molid[GETIDX(27)], 27); } TEST_F(ResetIDsTest, TopologyData) { if (lmp->atom->natoms == 0) GTEST_SKIP(); // delete two water molecules BEGIN_HIDE_OUTPUT(); command("group allwater molecule 3:6"); command("group twowater molecule 4:6:2"); command("group nowater subtract all allwater"); command("delete_atoms group twowater compress no bond yes mol yes"); END_HIDE_OUTPUT(); ASSERT_EQ(lmp->atom->natoms, 23); ASSERT_EQ(lmp->atom->map_tag_max, 26); auto num_bond = lmp->atom->num_bond; auto num_angle = lmp->atom->num_angle; auto bond_atom = lmp->atom->bond_atom; auto angle_atom1 = lmp->atom->angle_atom1; auto angle_atom2 = lmp->atom->angle_atom2; auto angle_atom3 = lmp->atom->angle_atom3; ASSERT_EQ(num_bond[GETIDX(1)], 2); ASSERT_EQ(bond_atom[GETIDX(1)][0], 2); ASSERT_EQ(bond_atom[GETIDX(1)][1], 3); ASSERT_EQ(num_bond[GETIDX(2)], 0); ASSERT_EQ(num_bond[GETIDX(3)], 3); ASSERT_EQ(bond_atom[GETIDX(3)][0], 4); ASSERT_EQ(bond_atom[GETIDX(3)][1], 5); ASSERT_EQ(bond_atom[GETIDX(3)][2], 6); ASSERT_EQ(num_bond[GETIDX(4)], 0); ASSERT_EQ(num_bond[GETIDX(5)], 0); ASSERT_EQ(num_bond[GETIDX(6)], 2); ASSERT_EQ(bond_atom[GETIDX(6)][0], 8); ASSERT_EQ(bond_atom[GETIDX(6)][1], 7); ASSERT_EQ(num_bond[GETIDX(7)], 0); ASSERT_EQ(num_bond[GETIDX(8)], 2); ASSERT_EQ(bond_atom[GETIDX(8)][0], 9); ASSERT_EQ(bond_atom[GETIDX(8)][1], 10); ASSERT_EQ(num_bond[GETIDX(9)], 0); ASSERT_EQ(num_bond[GETIDX(10)], 3); ASSERT_EQ(bond_atom[GETIDX(10)][0], 11); ASSERT_EQ(bond_atom[GETIDX(10)][1], 12); ASSERT_EQ(bond_atom[GETIDX(10)][2], 16); ASSERT_EQ(num_bond[GETIDX(11)], 0); ASSERT_EQ(num_bond[GETIDX(12)], 3); ASSERT_EQ(bond_atom[GETIDX(12)][0], 13); ASSERT_EQ(bond_atom[GETIDX(12)][1], 14); ASSERT_EQ(bond_atom[GETIDX(12)][2], 15); ASSERT_EQ(num_bond[GETIDX(13)], 0); ASSERT_EQ(num_bond[GETIDX(14)], 0); ASSERT_EQ(num_bond[GETIDX(15)], 0); ASSERT_EQ(num_bond[GETIDX(16)], 1); ASSERT_EQ(bond_atom[GETIDX(16)][0], 17); ASSERT_EQ(num_bond[GETIDX(17)], 0); ASSERT_EQ(num_bond[GETIDX(18)], 2); ASSERT_EQ(bond_atom[GETIDX(18)][0], 19); ASSERT_EQ(bond_atom[GETIDX(18)][1], 20); ASSERT_EQ(num_bond[GETIDX(19)], 0); ASSERT_EQ(num_bond[GETIDX(20)], 0); ASSERT_EQ(num_bond[GETIDX(24)], 2); ASSERT_EQ(bond_atom[GETIDX(24)][0], 25); ASSERT_EQ(bond_atom[GETIDX(24)][1], 26); ASSERT_EQ(num_bond[GETIDX(25)], 0); ASSERT_EQ(num_bond[GETIDX(26)], 0); ASSERT_EQ(num_angle[GETIDX(1)], 1); ASSERT_EQ(angle_atom1[GETIDX(1)][0], 2); ASSERT_EQ(angle_atom2[GETIDX(1)][0], 1); ASSERT_EQ(angle_atom3[GETIDX(1)][0], 3); ASSERT_EQ(num_angle[GETIDX(2)], 0); ASSERT_EQ(num_angle[GETIDX(3)], 6); ASSERT_EQ(angle_atom1[GETIDX(3)][0], 1); ASSERT_EQ(angle_atom2[GETIDX(3)][0], 3); ASSERT_EQ(angle_atom3[GETIDX(3)][0], 5); ASSERT_EQ(angle_atom1[GETIDX(3)][1], 1); ASSERT_EQ(angle_atom2[GETIDX(3)][1], 3); ASSERT_EQ(angle_atom3[GETIDX(3)][1], 4); ASSERT_EQ(angle_atom1[GETIDX(3)][2], 1); ASSERT_EQ(angle_atom2[GETIDX(3)][2], 3); ASSERT_EQ(angle_atom3[GETIDX(3)][2], 6); ASSERT_EQ(angle_atom1[GETIDX(3)][3], 4); ASSERT_EQ(angle_atom2[GETIDX(3)][3], 3); ASSERT_EQ(angle_atom3[GETIDX(3)][3], 5); ASSERT_EQ(angle_atom1[GETIDX(3)][4], 5); ASSERT_EQ(angle_atom2[GETIDX(3)][4], 3); ASSERT_EQ(angle_atom3[GETIDX(3)][4], 6); ASSERT_EQ(num_angle[GETIDX(18)], 1); ASSERT_EQ(angle_atom1[GETIDX(18)][0], 19); ASSERT_EQ(angle_atom2[GETIDX(18)][0], 18); ASSERT_EQ(angle_atom3[GETIDX(18)][0], 20); ASSERT_EQ(num_angle[GETIDX(24)], 1); ASSERT_EQ(angle_atom1[GETIDX(24)][0], 25); ASSERT_EQ(angle_atom2[GETIDX(24)][0], 24); ASSERT_EQ(angle_atom3[GETIDX(24)][0], 26); BEGIN_HIDE_OUTPUT(); command("reset_atom_ids sort yes"); END_HIDE_OUTPUT(); num_bond = lmp->atom->num_bond; num_angle = lmp->atom->num_angle; bond_atom = lmp->atom->bond_atom; angle_atom1 = lmp->atom->angle_atom1; angle_atom2 = lmp->atom->angle_atom2; angle_atom3 = lmp->atom->angle_atom3; ASSERT_EQ(num_bond[GETIDX(1)], 2); ASSERT_EQ(bond_atom[GETIDX(1)][0], 3); ASSERT_EQ(bond_atom[GETIDX(1)][1], 2); ASSERT_EQ(num_bond[GETIDX(2)], 0); ASSERT_EQ(num_bond[GETIDX(3)], 2); ASSERT_EQ(bond_atom[GETIDX(3)][0], 16); ASSERT_EQ(bond_atom[GETIDX(3)][1], 5); ASSERT_EQ(num_bond[GETIDX(4)], 0); ASSERT_EQ(num_bond[GETIDX(5)], 3); ASSERT_EQ(bond_atom[GETIDX(5)][0], 4); ASSERT_EQ(bond_atom[GETIDX(5)][1], 8); ASSERT_EQ(bond_atom[GETIDX(5)][2], 18); ASSERT_EQ(num_bond[GETIDX(6)], 0); ASSERT_EQ(num_bond[GETIDX(7)], 0); ASSERT_EQ(num_bond[GETIDX(8)], 3); ASSERT_EQ(bond_atom[GETIDX(8)][0], 9); ASSERT_EQ(bond_atom[GETIDX(8)][1], 6); ASSERT_EQ(bond_atom[GETIDX(8)][2], 7); ASSERT_EQ(num_bond[GETIDX(9)], 0); ASSERT_EQ(num_bond[GETIDX(10)], 0); ASSERT_EQ(num_bond[GETIDX(11)], 3); ASSERT_EQ(bond_atom[GETIDX(11)][0], 10); ASSERT_EQ(bond_atom[GETIDX(11)][1], 19); ASSERT_EQ(bond_atom[GETIDX(11)][2], 1); ASSERT_EQ(num_bond[GETIDX(12)], 0); ASSERT_EQ(num_bond[GETIDX(13)], 0); ASSERT_EQ(num_bond[GETIDX(14)], 2); ASSERT_EQ(bond_atom[GETIDX(14)][0], 13); ASSERT_EQ(bond_atom[GETIDX(14)][1], 15); ASSERT_EQ(num_bond[GETIDX(15)], 0); ASSERT_EQ(num_bond[GETIDX(16)], 0); ASSERT_EQ(num_bond[GETIDX(17)], 0); ASSERT_EQ(num_bond[GETIDX(18)], 1); ASSERT_EQ(bond_atom[GETIDX(18)][0], 17); ASSERT_EQ(num_bond[GETIDX(19)], 0); ASSERT_EQ(num_bond[GETIDX(20)], 2); ASSERT_EQ(bond_atom[GETIDX(20)][0], 12); ASSERT_EQ(bond_atom[GETIDX(20)][1], 11); ASSERT_EQ(num_bond[GETIDX(21)], 0); ASSERT_EQ(num_bond[GETIDX(22)], 2); ASSERT_EQ(bond_atom[GETIDX(22)][0], 21); ASSERT_EQ(bond_atom[GETIDX(22)][1], 23); ASSERT_EQ(num_bond[GETIDX(23)], 0); ASSERT_EQ(num_angle[GETIDX(1)], 3); ASSERT_EQ(angle_atom1[GETIDX(1)][0], 11); ASSERT_EQ(angle_atom2[GETIDX(1)][0], 1); ASSERT_EQ(angle_atom3[GETIDX(1)][0], 2); ASSERT_EQ(angle_atom1[GETIDX(1)][1], 11); ASSERT_EQ(angle_atom2[GETIDX(1)][1], 1); ASSERT_EQ(angle_atom3[GETIDX(1)][1], 3); ASSERT_EQ(angle_atom1[GETIDX(1)][2], 2); ASSERT_EQ(angle_atom2[GETIDX(1)][2], 1); ASSERT_EQ(angle_atom3[GETIDX(1)][2], 3); ASSERT_EQ(num_angle[GETIDX(2)], 0); ASSERT_EQ(num_angle[GETIDX(5)], 6); ASSERT_EQ(angle_atom1[GETIDX(5)][0], 3); ASSERT_EQ(angle_atom2[GETIDX(5)][0], 5); ASSERT_EQ(angle_atom3[GETIDX(5)][0], 4); ASSERT_EQ(angle_atom1[GETIDX(5)][1], 3); ASSERT_EQ(angle_atom2[GETIDX(5)][1], 5); ASSERT_EQ(angle_atom3[GETIDX(5)][1], 18); ASSERT_EQ(angle_atom1[GETIDX(5)][2], 4); ASSERT_EQ(angle_atom2[GETIDX(5)][2], 5); ASSERT_EQ(angle_atom3[GETIDX(5)][2], 8); ASSERT_EQ(angle_atom1[GETIDX(5)][3], 8); ASSERT_EQ(angle_atom2[GETIDX(5)][3], 5); ASSERT_EQ(angle_atom3[GETIDX(5)][3], 18); ASSERT_EQ(angle_atom1[GETIDX(5)][4], 3); ASSERT_EQ(angle_atom2[GETIDX(5)][4], 5); ASSERT_EQ(angle_atom3[GETIDX(5)][4], 8); ASSERT_EQ(angle_atom1[GETIDX(5)][5], 4); ASSERT_EQ(angle_atom2[GETIDX(5)][5], 5); ASSERT_EQ(angle_atom3[GETIDX(5)][5], 18); ASSERT_EQ(num_angle[GETIDX(20)], 1); ASSERT_EQ(angle_atom1[GETIDX(20)][0], 12); ASSERT_EQ(angle_atom2[GETIDX(20)][0], 20); ASSERT_EQ(angle_atom3[GETIDX(20)][0], 11); ASSERT_EQ(num_angle[GETIDX(22)], 1); ASSERT_EQ(angle_atom1[GETIDX(22)][0], 21); ASSERT_EQ(angle_atom2[GETIDX(22)][0], 22); ASSERT_EQ(angle_atom3[GETIDX(22)][0], 23); } TEST_F(ResetIDsTest, DeathTests) { if (lmp->atom->natoms == 0) GTEST_SKIP(); TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", command("reset_mol_ids");); TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", command("reset_mol_ids all offset 1 1");); TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", command("reset_mol_ids all offset -2");); TEST_FAILURE(".*ERROR on proc 0: Expected integer.*", command("reset_mol_ids all offset xxx");); TEST_FAILURE(".*ERROR on proc 0: Expected integer.*", command("reset_mol_ids all compress yes single no offset xxx");); TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", command("reset_mol_ids all offset");); TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", command("reset_mol_ids all compress");); TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", command("reset_mol_ids all compress xxx");); TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", command("reset_mol_ids all single");); TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", command("reset_mol_ids all single xxx");); } class ResetMolIDsTest : public LAMMPSTest { protected: void SetUp() override { testbinary = "ResetIDsTest"; LAMMPSTest::SetUp(); } }; TEST_F(ResetMolIDsTest, FailBeforeBox) { TEST_FAILURE(".*ERROR: Reset_mol_ids command before simulation box is.*", command("reset_mol_ids all");); } TEST_F(ResetMolIDsTest, FailMissingId) { BEGIN_HIDE_OUTPUT(); command("atom_modify id no"); command("region box block 0 1 0 1 0 1"); command("create_box 1 box"); END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Cannot use reset_mol_ids unless.*", command("reset_mol_ids all");); } TEST_F(ResetMolIDsTest, FailOnlyMolecular) { BEGIN_HIDE_OUTPUT(); command("clear"); command("region box block 0 1 0 1 0 1"); command("create_box 1 box"); END_HIDE_OUTPUT(); TEST_FAILURE(".*ERROR: Can only use reset_mol_ids.*", command("reset_mol_ids all");); } } // namespace LAMMPS_NS int main(int argc, char **argv) { MPI_Init(&argc, &argv); ::testing::InitGoogleMock(&argc, argv); if (Info::get_mpi_vendor() == "Open MPI" && !LAMMPS_NS::Info::has_exceptions()) std::cout << "Warning: using OpenMPI without exceptions. " "Death tests will be skipped\n"; // 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; }