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add labelmap tests for bonds/angles/dihedrals/impropers

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This commit is contained in:
Axel Kohlmeyer
2022-09-04 17:51:06 -04:00
parent c7ab8e160a
commit f956530f0d
1 changed files with 115 additions and 24 deletions
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139
unittest/commands/test_labelmap.cpp
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@ -16,6 +16,7 @@
#include "atom.h" #include "atom.h"
#include "compute.h" #include "compute.h"
#include "domain.h" #include "domain.h"
#include "info.h"
#include "label_map.h" #include "label_map.h"
#include "math_const.h" #include "math_const.h"
#include "modify.h" #include "modify.h"
@ -35,13 +36,13 @@ using ::testing::ExitedWithCode;
using ::testing::StrEq; using ::testing::StrEq;
namespace LAMMPS_NS { namespace LAMMPS_NS {
class SetTest : public LAMMPSTest { class LabelMapTest : public LAMMPSTest {
protected: protected:
Atom *atom; Atom *atom;
Domain *domain; Domain *domain;
void SetUp() override void SetUp() override
{ {
testbinary = "SetTest"; testbinary = "LabelMapTest";
args = {"-log", "none", "-echo", "screen", "-nocite", "-v", "num", "1"}; args = {"-log", "none", "-echo", "screen", "-nocite", "-v", "num", "1"};
LAMMPSTest::SetUp(); LAMMPSTest::SetUp();
atom = lmp->atom; atom = lmp->atom;
@ -51,10 +52,10 @@ protected:
void TearDown() override { LAMMPSTest::TearDown(); } void TearDown() override { LAMMPSTest::TearDown(); }
}; };
TEST_F(SetTest, NoBoxAtoms) TEST_F(LabelMapTest, Atoms)
{ {
ASSERT_EQ(atom->natoms, 0); EXPECT_EQ(atom->natoms, 0);
ASSERT_EQ(domain->box_exist, 0); EXPECT_EQ(domain->box_exist, 0);
ASSERT_EQ(atom->lmap, nullptr); ASSERT_EQ(atom->lmap, nullptr);
TEST_FAILURE(".*ERROR: Labelmap command before simulation box is.*", TEST_FAILURE(".*ERROR: Labelmap command before simulation box is.*",
command("labelmap atom 3 C1");); command("labelmap atom 3 C1"););
@ -70,22 +71,23 @@ TEST_F(SetTest, NoBoxAtoms)
command("mass H1 4.0"); command("mass H1 4.0");
END_HIDE_OUTPUT(); END_HIDE_OUTPUT();
ASSERT_NE(atom->lmap, nullptr); ASSERT_NE(atom->lmap, nullptr);
ASSERT_FALSE(atom->lmap->is_complete(Atom::ATOM)); EXPECT_FALSE(atom->lmap->is_complete(Atom::ATOM));
ASSERT_DOUBLE_EQ(atom->mass[1], 1.0); EXPECT_DOUBLE_EQ(atom->mass[1], 1.0);
ASSERT_DOUBLE_EQ(atom->mass[2], 2.0); EXPECT_DOUBLE_EQ(atom->mass[2], 2.0);
ASSERT_DOUBLE_EQ(atom->mass[3], 3.0); EXPECT_DOUBLE_EQ(atom->mass[3], 3.0);
ASSERT_DOUBLE_EQ(atom->mass[4], 4.0); EXPECT_DOUBLE_EQ(atom->mass[4], 4.0);
BEGIN_HIDE_OUTPUT(); BEGIN_HIDE_OUTPUT();
command("labelmap atom 1 C1 2 N2 3 ' O#' 1 C1 4 H# 2 N3"); // second '#' starts comment command("labelmap atom 1 C1 2 N2 3 ' O#' 1 C1 4 H# 2 N3"); // second '#' starts comment
command("mass \"O#\" 10.0"); command("mass \"O#\" 10.0");
END_HIDE_OUTPUT(); END_HIDE_OUTPUT();
ASSERT_TRUE(atom->lmap->is_complete(Atom::ATOM)); EXPECT_TRUE(atom->lmap->is_complete(Atom::ATOM));
ASSERT_EQ(atom->lmap->find("C1", Atom::ATOM), 1); EXPECT_EQ(atom->lmap->find("C1", Atom::ATOM), 1);
ASSERT_EQ(atom->lmap->find("N2", Atom::ATOM), 2); EXPECT_EQ(atom->lmap->find("N2", Atom::ATOM), 2);
ASSERT_EQ(atom->lmap->find("O#", Atom::ATOM), 3); EXPECT_EQ(atom->lmap->find("O#", Atom::ATOM), 3);
ASSERT_EQ(atom->lmap->find("H", Atom::ATOM), 4); EXPECT_EQ(atom->lmap->find("H", Atom::ATOM), 4);
ASSERT_DOUBLE_EQ(atom->mass[3], 10.0); EXPECT_EQ(atom->lmap->find("X", Atom::ATOM), -1);
EXPECT_DOUBLE_EQ(atom->mass[3], 10.0);
TEST_FAILURE(".*ERROR: Labelmap atom type 0 must be within 1-4.*", TEST_FAILURE(".*ERROR: Labelmap atom type 0 must be within 1-4.*",
command("labelmap atom 0 C1");); command("labelmap atom 0 C1"););
@ -132,21 +134,110 @@ TEST_F(SetTest, NoBoxAtoms)
command("labelmap clear"); command("labelmap clear");
command("labelmap atom 3 C1 2 N2"); command("labelmap atom 3 C1 2 N2");
END_HIDE_OUTPUT(); END_HIDE_OUTPUT();
ASSERT_FALSE(atom->lmap->is_complete(Atom::ATOM)); EXPECT_FALSE(atom->lmap->is_complete(Atom::ATOM));
ASSERT_EQ(atom->lmap->find("C1", Atom::ATOM), 3); EXPECT_EQ(atom->lmap->find("C1", Atom::ATOM), 3);
ASSERT_EQ(atom->lmap->find("N2", Atom::ATOM), 2); EXPECT_EQ(atom->lmap->find("N2", Atom::ATOM), 2);
BEGIN_HIDE_OUTPUT(); BEGIN_HIDE_OUTPUT();
command("labelmap clear"); command("labelmap clear");
command("labelmap atom 1 \"C1'\" 2 'C2\"' 3 \"\"\"C1'-C2\" \"\"\" 4 \"\"\" C2\"-C1'\"\"\""); command("labelmap atom 1 \"C1'\" 2 'C2\"' 3 \"\"\"C1'-C2\" \"\"\" 4 \"\"\" C2\"-C1'\"\"\"");
END_HIDE_OUTPUT(); END_HIDE_OUTPUT();
ASSERT_TRUE(atom->lmap->is_complete(Atom::ATOM)); EXPECT_TRUE(atom->lmap->is_complete(Atom::ATOM));
ASSERT_EQ(atom->lmap->find("C1'", Atom::ATOM), 1); EXPECT_EQ(atom->lmap->find("C1'", Atom::ATOM), 1);
ASSERT_EQ(atom->lmap->find("C2\"", Atom::ATOM), 2); EXPECT_EQ(atom->lmap->find("C2\"", Atom::ATOM), 2);
ASSERT_EQ(atom->lmap->find("C1'-C2\"", Atom::ATOM), 3); EXPECT_EQ(atom->lmap->find("C1'-C2\"", Atom::ATOM), 3);
ASSERT_EQ(atom->lmap->find("C2\"-C1'", Atom::ATOM), 4); EXPECT_EQ(atom->lmap->find("C2\"-C1'", Atom::ATOM), 4);
} }
TEST_F(LabelMapTest, Topology)
{
if (!info->has_style("atom", "full")) GTEST_SKIP();
EXPECT_EQ(atom->natoms, 0);
EXPECT_EQ(atom->nbonds, 0);
EXPECT_EQ(atom->nangles, 0);
EXPECT_EQ(atom->ndihedrals, 0);
EXPECT_EQ(atom->nimpropers, 0);
EXPECT_EQ(domain->box_exist, 0);
ASSERT_EQ(atom->lmap, nullptr);
TEST_FAILURE(".*ERROR: Labelmap command before simulation box is.*",
command("labelmap atom 3 C1"););
BEGIN_HIDE_OUTPUT();
command("atom_style full");
command("region box block 0 2 0 2 0 2");
command("create_box 2 box bond/types 3 angle/types 2 dihedral/types 1 improper/types 1");
command("labelmap atom 1 C1");
END_HIDE_OUTPUT();
ASSERT_NE(atom->lmap, nullptr);
EXPECT_FALSE(atom->lmap->is_complete(Atom::ATOM));
EXPECT_FALSE(atom->lmap->is_complete(Atom::BOND));
EXPECT_FALSE(atom->lmap->is_complete(Atom::ANGLE));
EXPECT_FALSE(atom->lmap->is_complete(Atom::DIHEDRAL));
EXPECT_FALSE(atom->lmap->is_complete(Atom::IMPROPER));
BEGIN_HIDE_OUTPUT();
command("labelmap atom 2 \"N2'\"");
command("labelmap bond 1 C1-N2 2 [C1][C1] 3 N2=N2");
command("labelmap angle 1 C1-N2-C1 2 \"\"\" N2'-C1\"-N2' \"\"\"");
command("labelmap dihedral 1 'C1-N2-C1-N2'");
command("labelmap improper 1 \"C1-N2-C1-N2\"");
command("mass C1 12.0");
command("mass \"N2'\" 14.0");
command("labelmap write labelmap_topology.inc");
END_HIDE_OUTPUT();
EXPECT_TRUE(atom->lmap->is_complete(Atom::ATOM));
EXPECT_TRUE(atom->lmap->is_complete(Atom::BOND));
EXPECT_TRUE(atom->lmap->is_complete(Atom::ANGLE));
EXPECT_TRUE(atom->lmap->is_complete(Atom::DIHEDRAL));
EXPECT_TRUE(atom->lmap->is_complete(Atom::IMPROPER));
EXPECT_EQ(atom->lmap->find("C1", Atom::ATOM), 1);
EXPECT_EQ(atom->lmap->find("N2'", Atom::ATOM), 2);
EXPECT_EQ(atom->lmap->find("C1-N2", Atom::BOND), 1);
EXPECT_EQ(atom->lmap->find("[C1][C1]", Atom::BOND), 2);
EXPECT_EQ(atom->lmap->find("N2=N2", Atom::BOND), 3);
EXPECT_EQ(atom->lmap->find("C1-N2-C1", Atom::ANGLE), 1);
EXPECT_EQ(atom->lmap->find("N2'-C1\"-N2'", Atom::ANGLE), 2);
EXPECT_EQ(atom->lmap->find("C1-N2-C1-N2", Atom::DIHEDRAL), 1);
EXPECT_EQ(atom->lmap->find("C1-N2-C1-N2", Atom::IMPROPER), 1);
EXPECT_EQ(atom->lmap->find("X", Atom::ATOM), -1);
EXPECT_EQ(atom->lmap->find("N2'-C1\"-N2'", Atom::BOND), -1);
EXPECT_DOUBLE_EQ(atom->mass[1], 12.0);
EXPECT_DOUBLE_EQ(atom->mass[2], 14.0);
BEGIN_HIDE_OUTPUT();
command("labelmap clear");
command("labelmap atom 1 C1");
END_HIDE_OUTPUT();
EXPECT_NE(atom->lmap, nullptr);
EXPECT_FALSE(atom->lmap->is_complete(Atom::ATOM));
EXPECT_FALSE(atom->lmap->is_complete(Atom::BOND));
EXPECT_FALSE(atom->lmap->is_complete(Atom::ANGLE));
EXPECT_FALSE(atom->lmap->is_complete(Atom::DIHEDRAL));
EXPECT_FALSE(atom->lmap->is_complete(Atom::IMPROPER));
BEGIN_HIDE_OUTPUT();
command("include labelmap_topology.inc");
END_HIDE_OUTPUT();
EXPECT_TRUE(atom->lmap->is_complete(Atom::ATOM));
EXPECT_TRUE(atom->lmap->is_complete(Atom::BOND));
EXPECT_TRUE(atom->lmap->is_complete(Atom::ANGLE));
EXPECT_TRUE(atom->lmap->is_complete(Atom::DIHEDRAL));
EXPECT_TRUE(atom->lmap->is_complete(Atom::IMPROPER));
EXPECT_EQ(atom->lmap->find("C1", Atom::ATOM), 1);
EXPECT_EQ(atom->lmap->find("N2'", Atom::ATOM), 2);
EXPECT_EQ(atom->lmap->find("C1-N2", Atom::BOND), 1);
EXPECT_EQ(atom->lmap->find("[C1][C1]", Atom::BOND), 2);
EXPECT_EQ(atom->lmap->find("N2=N2", Atom::BOND), 3);
EXPECT_EQ(atom->lmap->find("C1-N2-C1", Atom::ANGLE), 1);
EXPECT_EQ(atom->lmap->find("N2'-C1\"-N2'", Atom::ANGLE), 2);
EXPECT_EQ(atom->lmap->find("C1-N2-C1-N2", Atom::DIHEDRAL), 1);
EXPECT_EQ(atom->lmap->find("C1-N2-C1-N2", Atom::IMPROPER), 1);
EXPECT_EQ(atom->lmap->find("X", Atom::ATOM), -1);
EXPECT_EQ(atom->lmap->find("N2'-C1\"-N2'", Atom::BOND), -1);
}
} // namespace LAMMPS_NS } // namespace LAMMPS_NS
int main(int argc, char **argv) int main(int argc, char **argv)