add test function to validate updated topology data after reset_atom_ids

unittest/commands/test_reset_ids.cpp

@@ -466,6 +466,198 @@ TEST_F(ResetIDsTest, DeleteAdd)
     ASSERT_EQ(molid[GETIDX(27)], 27);
 }
 
+TEST_F(ResetIDsTest, TopologyData)
+{
+    if (lmp->atom->natoms == 0) GTEST_SKIP();
+
+    // 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");
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+    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 num_dihedral   = lmp->atom->num_dihedral;
+    auto num_improper   = lmp->atom->num_improper;
+    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);
+
+    if (!verbose) ::testing::internal::CaptureStdout();
+    lmp->input->one("reset_atom_ids sort yes");
+    if (!verbose) ::testing::internal::GetCapturedStdout();
+
+    num_bond       = lmp->atom->num_bond;
+    num_angle      = lmp->atom->num_angle;
+    num_dihedral   = lmp->atom->num_dihedral;
+    num_improper   = lmp->atom->num_improper;
+    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)
 {
     TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", lmp->input->one("reset_mol_ids"););