318 lines
13 KiB
C++
318 lines
13 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 "lammps.h"
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#include "atom.h"
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#include "compute.h"
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#include "domain.h"
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#include "info.h"
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#include "label_map.h"
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#include "math_const.h"
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#include "modify.h"
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#include "../testing/core.h"
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#include "gmock/gmock.h"
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#include "gtest/gtest.h"
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#define STRINGIFY(val) XSTR(val)
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#define XSTR(val) #val
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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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using ::testing::ContainsRegex;
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using ::testing::ExitedWithCode;
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using ::testing::StrEq;
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namespace LAMMPS_NS {
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class LabelMapTest : public LAMMPSTest {
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protected:
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Atom *atom;
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Domain *domain;
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void SetUp() override
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{
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testbinary = "LabelMapTest";
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args = {"-log", "none", "-echo", "screen", "-nocite", "-v", "num", "1"};
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LAMMPSTest::SetUp();
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atom = lmp->atom;
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domain = lmp->domain;
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}
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void TearDown() override { LAMMPSTest::TearDown(); }
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};
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TEST_F(LabelMapTest, Atoms)
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{
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EXPECT_EQ(atom->natoms, 0);
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EXPECT_EQ(domain->box_exist, 0);
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EXPECT_EQ(atom->labelmapflag, 0);
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EXPECT_EQ(atom->types_style, Atom::NUMERIC);
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ASSERT_EQ(atom->lmap, nullptr);
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TEST_FAILURE(".*ERROR: Labelmap command before simulation box is.*",
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command("labelmap atom 3 C1"););
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BEGIN_HIDE_OUTPUT();
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command("region box block 0 2 0 2 0 2");
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command("create_box 4 box");
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END_HIDE_OUTPUT();
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EXPECT_EQ(domain->box_exist, 1);
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EXPECT_EQ(atom->lmap, nullptr);
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EXPECT_EQ(atom->labelmapflag, 0);
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EXPECT_EQ(utils::expand_type(FLERR, "C1", Atom::ATOM, lmp), nullptr);
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BEGIN_HIDE_OUTPUT();
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command("labelmap atom 2 N1");
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command("labelmap atom 3 O1 4 H1");
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command("mass * 1.0");
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command("mass O1 3.0");
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command("mass N1 2.0");
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command("mass H1 4.0");
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END_HIDE_OUTPUT();
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EXPECT_EQ(atom->labelmapflag, 1);
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ASSERT_NE(atom->lmap, nullptr);
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EXPECT_FALSE(atom->lmap->is_complete(Atom::ATOM));
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EXPECT_DOUBLE_EQ(atom->mass[1], 1.0);
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EXPECT_DOUBLE_EQ(atom->mass[2], 2.0);
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EXPECT_DOUBLE_EQ(atom->mass[3], 3.0);
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EXPECT_DOUBLE_EQ(atom->mass[4], 4.0);
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BEGIN_HIDE_OUTPUT();
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command("labelmap atom 1 C1 2 N2 3 ' O#' 1 C1 4 H# 2 N3"); // second '#' starts comment
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command("mass \"O#\" 10.0");
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END_HIDE_OUTPUT();
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EXPECT_TRUE(atom->lmap->is_complete(Atom::ATOM));
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EXPECT_EQ(atom->lmap->find("C1", Atom::ATOM), 1);
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EXPECT_EQ(atom->lmap->find("N2", Atom::ATOM), 2);
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EXPECT_EQ(atom->lmap->find("O#", Atom::ATOM), 3);
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EXPECT_EQ(atom->lmap->find("H", Atom::ATOM), 4);
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EXPECT_EQ(atom->lmap->find("X", Atom::ATOM), -1);
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EXPECT_DOUBLE_EQ(atom->mass[3], 10.0);
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EXPECT_EQ(utils::expand_type(FLERR, "1", Atom::ATOM, lmp), nullptr);
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EXPECT_EQ(utils::expand_type(FLERR, "*3", Atom::ATOM, lmp), nullptr);
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EXPECT_EQ(utils::expand_type(FLERR, "1*2", Atom::ATOM, lmp), nullptr);
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EXPECT_EQ(utils::expand_type(FLERR, "*", Atom::ATOM, lmp), nullptr);
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EXPECT_EQ(utils::expand_type(FLERR, "**", Atom::ATOM, lmp), nullptr);
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EXPECT_EQ(utils::expand_type(FLERR, "1*2*", Atom::ATOM, lmp), nullptr);
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auto expanded = utils::expand_type(FLERR, "C1", Atom::ATOM, lmp);
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EXPECT_THAT(expanded, StrEq("1"));
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delete[] expanded;
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expanded = utils::expand_type(FLERR, "O#", Atom::ATOM, lmp);
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EXPECT_THAT(expanded, StrEq("3"));
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delete[] expanded;
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TEST_FAILURE(".*ERROR: Atom type string XX not found in labelmap.*",
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utils::expand_type(FLERR, "XX", Atom::ATOM, lmp););
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TEST_FAILURE(".*ERROR: Labelmap atom type 0 must be within 1-4.*",
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command("labelmap atom 0 C1"););
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TEST_FAILURE(".*ERROR: Labelmap atom type 5 must be within 1-4.*",
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command("labelmap atom 5 C1"););
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TEST_FAILURE(".*ERROR: Type label string 1C for atom type 1 is invalid.*",
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command("labelmap atom 1 1C"););
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TEST_FAILURE(".*ERROR: Type label string #C for atom type 1 is invalid.*",
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command("labelmap atom 1 '#C'"););
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TEST_FAILURE(".*ERROR: Type label string CA CB for atom type 1 is invalid.*",
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command("labelmap atom 1 ' CA CB '"););
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TEST_FAILURE(".*ERROR: Type label string \\*C for atom type 1 is invalid.*",
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command("labelmap atom 1 *C"););
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TEST_FAILURE(".*ERROR: The atom type label N2 is already in use for type 2.*",
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command("labelmap atom 1 N2"););
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TEST_FAILURE(".*ERROR: No bond types allowed with current box settings.*",
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command("labelmap bond 1 C1-C1"););
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TEST_FAILURE(".*ERROR: No angle types allowed with current box settings.*",
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command("labelmap angle 1 C1-C1-C1"););
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TEST_FAILURE(".*ERROR: No dihedral types allowed with current box settings.*",
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command("labelmap dihedral 1 C1-C1-C1-C1"););
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TEST_FAILURE(".*ERROR: No improper types allowed with current box settings.*",
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command("labelmap improper 1 C1-C1-C1-C1"););
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TEST_FAILURE(".*ERROR: Incorrect number of arguments for labelmap command.*",
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command("labelmap atom 1 C1 2"););
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TEST_FAILURE(".*ERROR: Incorrect number of arguments for labelmap command.*",
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command("labelmap atom 1 C1 atom 2 C2"););
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TEST_FAILURE(".*ERROR: Incorrect number of arguments for labelmap clear command.*",
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command("labelmap clear atom"););
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TEST_FAILURE(".*ERROR: Incorrect number of arguments for labelmap clear command.*",
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command("labelmap clear atom bond"););
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TEST_FAILURE(".*ERROR: Incorrect number of arguments for labelmap write command.*",
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command("labelmap write"););
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TEST_FAILURE(".*ERROR: Incorrect number of arguments for labelmap write command.*",
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command("labelmap write filename xxx"););
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TEST_FAILURE(".*ERROR: Illegal labelmap atom command: missing argument.*",
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command("labelmap atom 1"););
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TEST_FAILURE(".*ERROR: Illegal labelmap atom command: missing argument.*",
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command("labelmap atom"););
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BEGIN_HIDE_OUTPUT();
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command("labelmap clear");
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command("labelmap atom 3 C1 2 N2");
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END_HIDE_OUTPUT();
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EXPECT_FALSE(atom->lmap->is_complete(Atom::ATOM));
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EXPECT_EQ(atom->lmap->find("C1", Atom::ATOM), 3);
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EXPECT_EQ(atom->lmap->find("N2", Atom::ATOM), 2);
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BEGIN_HIDE_OUTPUT();
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command("labelmap clear");
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command("labelmap atom 1 \"C1'\" 2 'C2\"' 3 \"\"\"C1'-C2\" \"\"\" 4 \"\"\" C2\"-C1'\"\"\"");
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END_HIDE_OUTPUT();
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EXPECT_TRUE(atom->lmap->is_complete(Atom::ATOM));
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EXPECT_EQ(atom->lmap->find("C1'", Atom::ATOM), 1);
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EXPECT_EQ(atom->lmap->find("C2\"", Atom::ATOM), 2);
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EXPECT_EQ(atom->lmap->find("C1'-C2\"", Atom::ATOM), 3);
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EXPECT_EQ(atom->lmap->find("C2\"-C1'", Atom::ATOM), 4);
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}
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TEST_F(LabelMapTest, Topology)
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{
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if (!info->has_style("atom", "full")) GTEST_SKIP();
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EXPECT_EQ(atom->natoms, 0);
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EXPECT_EQ(atom->nbonds, 0);
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EXPECT_EQ(atom->nangles, 0);
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EXPECT_EQ(atom->ndihedrals, 0);
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EXPECT_EQ(atom->nimpropers, 0);
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EXPECT_EQ(domain->box_exist, 0);
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EXPECT_EQ(atom->labelmapflag, 0);
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ASSERT_EQ(atom->lmap, nullptr);
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TEST_FAILURE(".*ERROR: Labelmap command before simulation box is.*",
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command("labelmap atom 3 C1"););
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BEGIN_HIDE_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 2 box bond/types 3 angle/types 2 dihedral/types 1 improper/types 1");
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command("labelmap atom 1 C1");
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END_HIDE_OUTPUT();
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EXPECT_EQ(atom->labelmapflag, 1);
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ASSERT_NE(atom->lmap, nullptr);
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EXPECT_FALSE(atom->lmap->is_complete(Atom::ATOM));
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EXPECT_FALSE(atom->lmap->is_complete(Atom::BOND));
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EXPECT_FALSE(atom->lmap->is_complete(Atom::ANGLE));
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EXPECT_FALSE(atom->lmap->is_complete(Atom::DIHEDRAL));
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EXPECT_FALSE(atom->lmap->is_complete(Atom::IMPROPER));
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BEGIN_HIDE_OUTPUT();
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command("labelmap atom 2 \"N2'\"");
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command("labelmap bond 1 C1-N2 2 [C1][C1] 3 N2=N2");
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command("labelmap angle 1 C1-N2-C1 2 \"\"\" N2'-C1\"-N2' \"\"\"");
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command("labelmap dihedral 1 'C1-N2-C1-N2'");
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command("labelmap improper 1 \"C1-N2-C1-N2\"");
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command("mass C1 12.0");
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command("mass \"N2'\" 14.0");
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command("labelmap write labelmap_topology.inc");
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END_HIDE_OUTPUT();
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EXPECT_TRUE(atom->lmap->is_complete(Atom::ATOM));
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EXPECT_TRUE(atom->lmap->is_complete(Atom::BOND));
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EXPECT_TRUE(atom->lmap->is_complete(Atom::ANGLE));
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EXPECT_TRUE(atom->lmap->is_complete(Atom::DIHEDRAL));
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EXPECT_TRUE(atom->lmap->is_complete(Atom::IMPROPER));
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EXPECT_EQ(atom->lmap->find("C1", Atom::ATOM), 1);
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EXPECT_EQ(atom->lmap->find("N2'", Atom::ATOM), 2);
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EXPECT_EQ(atom->lmap->find("C1-N2", Atom::BOND), 1);
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EXPECT_EQ(atom->lmap->find("[C1][C1]", Atom::BOND), 2);
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EXPECT_EQ(atom->lmap->find("N2=N2", Atom::BOND), 3);
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EXPECT_EQ(atom->lmap->find("C1-N2-C1", Atom::ANGLE), 1);
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EXPECT_EQ(atom->lmap->find("N2'-C1\"-N2'", Atom::ANGLE), 2);
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EXPECT_EQ(atom->lmap->find("C1-N2-C1-N2", Atom::DIHEDRAL), 1);
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EXPECT_EQ(atom->lmap->find("C1-N2-C1-N2", Atom::IMPROPER), 1);
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EXPECT_EQ(atom->lmap->find("X", Atom::ATOM), -1);
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EXPECT_EQ(atom->lmap->find("N2'-C1\"-N2'", Atom::BOND), -1);
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EXPECT_DOUBLE_EQ(atom->mass[1], 12.0);
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EXPECT_DOUBLE_EQ(atom->mass[2], 14.0);
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BEGIN_HIDE_OUTPUT();
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command("labelmap clear");
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command("labelmap atom 1 C1");
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END_HIDE_OUTPUT();
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EXPECT_EQ(atom->labelmapflag, 1);
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ASSERT_NE(atom->lmap, nullptr);
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EXPECT_FALSE(atom->lmap->is_complete(Atom::ATOM));
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EXPECT_FALSE(atom->lmap->is_complete(Atom::BOND));
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EXPECT_FALSE(atom->lmap->is_complete(Atom::ANGLE));
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EXPECT_FALSE(atom->lmap->is_complete(Atom::DIHEDRAL));
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EXPECT_FALSE(atom->lmap->is_complete(Atom::IMPROPER));
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BEGIN_HIDE_OUTPUT();
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command("include labelmap_topology.inc");
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END_HIDE_OUTPUT();
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EXPECT_TRUE(atom->lmap->is_complete(Atom::ATOM));
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EXPECT_TRUE(atom->lmap->is_complete(Atom::BOND));
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EXPECT_TRUE(atom->lmap->is_complete(Atom::ANGLE));
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EXPECT_TRUE(atom->lmap->is_complete(Atom::DIHEDRAL));
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EXPECT_TRUE(atom->lmap->is_complete(Atom::IMPROPER));
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EXPECT_EQ(atom->lmap->find("C1", Atom::ATOM), 1);
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EXPECT_EQ(atom->lmap->find("N2'", Atom::ATOM), 2);
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EXPECT_EQ(atom->lmap->find("C1-N2", Atom::BOND), 1);
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EXPECT_EQ(atom->lmap->find("[C1][C1]", Atom::BOND), 2);
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EXPECT_EQ(atom->lmap->find("N2=N2", Atom::BOND), 3);
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EXPECT_EQ(atom->lmap->find("C1-N2-C1", Atom::ANGLE), 1);
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EXPECT_EQ(atom->lmap->find("N2'-C1\"-N2'", Atom::ANGLE), 2);
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EXPECT_EQ(atom->lmap->find("C1-N2-C1-N2", Atom::DIHEDRAL), 1);
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EXPECT_EQ(atom->lmap->find("C1-N2-C1-N2", Atom::IMPROPER), 1);
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EXPECT_EQ(atom->lmap->find("X", Atom::ATOM), -1);
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EXPECT_EQ(atom->lmap->find("N2'-C1\"-N2'", Atom::BOND), -1);
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platform::unlink("labelmap_topology.inc");
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auto expanded = utils::expand_type(FLERR, "N2'", Atom::ATOM, lmp);
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EXPECT_THAT(expanded, StrEq("2"));
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delete[] expanded;
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expanded = utils::expand_type(FLERR, "[C1][C1]", Atom::BOND, lmp);
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EXPECT_THAT(expanded, StrEq("2"));
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delete[] expanded;
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expanded = utils::expand_type(FLERR, "C1-N2-C1", Atom::ANGLE, lmp);
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EXPECT_THAT(expanded, StrEq("1"));
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delete[] expanded;
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expanded = utils::expand_type(FLERR, "C1-N2-C1-N2", Atom::DIHEDRAL, lmp);
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EXPECT_THAT(expanded, StrEq("1"));
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delete[] expanded;
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expanded = utils::expand_type(FLERR, "C1-N2-C1-N2", Atom::IMPROPER, lmp);
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EXPECT_THAT(expanded, StrEq("1"));
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delete[] expanded;
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TEST_FAILURE(".*ERROR: Bond type string XX not found in labelmap.*",
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utils::expand_type(FLERR, "XX", Atom::BOND, lmp););
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TEST_FAILURE(".*ERROR: Angle type string XX not found in labelmap.*",
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utils::expand_type(FLERR, "XX", Atom::ANGLE, lmp););
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TEST_FAILURE(".*ERROR: Dihedral type string XX not found in labelmap.*",
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utils::expand_type(FLERR, "XX", Atom::DIHEDRAL, lmp););
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TEST_FAILURE(".*ERROR: Improper type string XX not found in labelmap.*",
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utils::expand_type(FLERR, "XX", Atom::IMPROPER, lmp););
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}
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} // namespace LAMMPS_NS
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int main(int argc, char **argv)
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{
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MPI_Init(&argc, &argv);
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::testing::InitGoogleMock(&argc, argv);
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// handle arguments passed via environment variable
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if (const char *var = getenv("TEST_ARGS")) {
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std::vector<std::string> env = LAMMPS_NS::utils::split_words(var);
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for (auto arg : env) {
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if (arg == "-v") {
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verbose = true;
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}
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}
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}
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if ((argc > 1) && (strcmp(argv[1], "-v") == 0)) verbose = true;
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int rv = RUN_ALL_TESTS();
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MPI_Finalize();
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return rv;
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}
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