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Merge pull request #2638 from akohlmey/parse-molecule-refactor

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Further refactor parsing of molecule files
This commit is contained in:
Axel Kohlmeyer
2021-03-08 20:04:07 -05:00
committed by GitHub
parent f17ac30875 f455869de3
commit 37afa0e6d5
7 changed files with 653 additions and 220 deletions
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4
unittest/formats/CMakeLists.txt
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@ -7,6 +7,10 @@ add_executable(test_image_flags test_image_flags.cpp)
target_link_libraries(test_image_flags PRIVATE lammps GTest::GMock GTest::GTest)
add_test(NAME ImageFlags COMMAND test_image_flags WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
add_executable(test_molecule_file test_molecule_file.cpp)
target_link_libraries(test_molecule_file PRIVATE lammps GTest::GMock GTest::GTest)
add_test(NAME MoleculeFile COMMAND test_molecule_file WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})
add_executable(test_pair_unit_convert test_pair_unit_convert.cpp)
target_link_libraries(test_pair_unit_convert PRIVATE lammps GTest::GMock GTest::GTest)
add_test(NAME PairUnitConvert COMMAND test_pair_unit_convert WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR})

313
unittest/formats/test_molecule_file.cpp Normal file
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@ -0,0 +1,313 @@
/* ----------------------------------------------------------------------
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 "info.h"
#include "input.h"
#include "lammps.h"
#include "molecule.h"
#include "utils.h"
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include <cstdio>
#include <mpi.h>
#include <string>
using namespace LAMMPS_NS;
using testing::MatchesRegex;
using testing::StrEq;
using utils::split_words;
#define test_name test_info_->name()
#if defined(OMPI_MAJOR_VERSION)
const bool have_openmpi = true;
#else
const bool have_openmpi = false;
#endif
#define TEST_FAILURE(errmsg, ...) \
if (Info::has_exceptions()) { \
::testing::internal::CaptureStdout(); \
ASSERT_ANY_THROW({__VA_ARGS__}); \
auto mesg = ::testing::internal::GetCapturedStdout(); \
ASSERT_THAT(mesg, MatchesRegex(errmsg)); \
} else { \
if (!have_openmpi) { \
::testing::internal::CaptureStdout(); \
ASSERT_DEATH({__VA_ARGS__}, ""); \
auto mesg = ::testing::internal::GetCapturedStdout(); \
ASSERT_THAT(mesg, MatchesRegex(errmsg)); \
} \
}
static void create_molecule_files()
{
// create molecule files
const char h2o_file[] = "# Water molecule. SPC/E model.\n\n3 atoms\n2 bonds\n1 angles\n\n"
"Coords\n\n1 1.12456 0.09298 1.27452\n"
"2 1.53683 0.75606 1.89928\n3 0.49482 0.56390 0.65678\n\n"
"Types\n\n1 1\n2 2\n3 2\n\n"
"Charges\n\n1 -0.8472\n2 0.4236\n3 0.4236\n\n"
"Bonds\n\n1 1 1 2\n2 1 1 3\n\n"
"Angles\n\n1 1 2 1 3\n\n"
"Shake Flags\n\n1 1\n2 1\n3 1\n\n"
"Shake Atoms\n\n1 1 2 3\n2 1 2 3\n3 1 2 3\n\n"
"Shake Bond Types\n\n1 1 1 1\n2 1 1 1\n3 1 1 1\n\n"
"Special Bond Counts\n\n1 2 0 0\n2 1 1 0\n3 1 1 0\n\n"
"Special Bonds\n\n1 2 3\n2 1 3\n3 1 2\n\n";
const char co2_file[] = "# CO2 molecule file. TraPPE model.\n\n"
"3 atoms\n2 bonds\n1 angles\n\n"
"Coords\n\n1 0.0 0.0 0.0\n2 -1.16 0.0 0.0\n3 1.16 0.0 0.0\n\n"
"Types\n\n1 1\n2 2\n3 2\n\n"
"Charges\n\n1 0.7\n2 -0.35\n3 -0.35\n\n"
"Bonds\n\n1 1 1 2\n2 1 1 3\n\n"
"Angles\n\n1 1 2 1 3\n\n"
"Special Bond Counts\n\n1 2 0 0\n2 1 1 0\n3 1 1 0\n\n"
"Special Bonds\n\n1 2 3\n2 1 3\n3 1 2\n\n";
FILE *fp = fopen("tmp.h2o.mol", "w");
if (fp) {
fputs(h2o_file, fp);
fclose(fp);
}
rename("tmp.h2o.mol", "h2o.mol");
fp = fopen("tmp.co2.mol", "w");
if (fp) {
fputs(co2_file, fp);
fclose(fp);
}
rename("tmp.co2.mol", "co2.mol");
}
// whether to print verbose output (i.e. not capturing LAMMPS screen output).
bool verbose = false;
class MoleculeFileTest : public ::testing::Test {
protected:
LAMMPS *lmp;
void SetUp() override
{
const char *args[] = {"MoleculeFileTest", "-log", "none", "-echo", "screen", "-nocite"};
char **argv = (char **)args;
int argc = sizeof(args) / sizeof(char *);
if (!verbose) ::testing::internal::CaptureStdout();
lmp = new LAMMPS(argc, argv, MPI_COMM_WORLD);
create_molecule_files();
if (!verbose) ::testing::internal::GetCapturedStdout();
ASSERT_NE(lmp, nullptr);
}
void TearDown() override
{
if (!verbose) ::testing::internal::CaptureStdout();
delete lmp;
if (!verbose) ::testing::internal::GetCapturedStdout();
remove("h2o.mol");
remove("co2.mol");
}
void run_mol_cmd(const std::string &name, const std::string &args, const std::string &content)
{
std::string file = name + ".mol";
FILE *fp = fopen(file.c_str(), "w");
fputs(content.c_str(), fp);
fclose(fp);
lmp->input->one(fmt::format("molecule {} {} {}", name, file, args));
remove(file.c_str());
}
};
TEST_F(MoleculeFileTest, nofile)
{
TEST_FAILURE(".*Cannot open molecule file nofile.mol.*",
lmp->input->one("molecule 1 nofile.mol"););
}
TEST_F(MoleculeFileTest, badid)
{
TEST_FAILURE(".*Molecule template ID must have only "
"alphanumeric or underscore characters.*",
lmp->input->one("molecule @mol nofile.mol"););
}
TEST_F(MoleculeFileTest, badargs)
{
TEST_FAILURE(".*Illegal molecule command.*",
run_mol_cmd(test_name, "offset 1 2 3 4",
"Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"););
TEST_FAILURE(
".*Illegal molecule command.*",
run_mol_cmd(test_name, "toff", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"););
TEST_FAILURE(
".*Illegal molecule command.*",
run_mol_cmd(test_name, "boff", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"););
TEST_FAILURE(
".*Illegal molecule command.*",
run_mol_cmd(test_name, "aoff", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"););
TEST_FAILURE(
".*Illegal molecule command.*",
run_mol_cmd(test_name, "doff", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"););
TEST_FAILURE(
".*Illegal molecule command.*",
run_mol_cmd(test_name, "ioff", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"););
TEST_FAILURE(
".*Illegal molecule command.*",
run_mol_cmd(test_name, "scale", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"););
remove("badargs.mol");
}
TEST_F(MoleculeFileTest, noatom)
{
TEST_FAILURE(".*ERROR: No atoms or invalid atom count in molecule file.*",
run_mol_cmd(test_name, "",
"Comment\n0 atoms\n1 bonds\n\n"
" Coords\n\nBonds\n\n 1 1 2\n"););
remove("noatom.mol");
}
TEST_F(MoleculeFileTest, empty)
{
TEST_FAILURE(".*ERROR: Unexpected end of molecule file.*",
run_mol_cmd(test_name, "", "Comment\n\n"););
remove("empty.mol");
}
TEST_F(MoleculeFileTest, nospecial)
{
TEST_FAILURE(".*ERROR: Cannot auto-generate special bonds before simulation box is defined.*",
run_mol_cmd(test_name, "",
"Comment\n3 atoms\n\n2 bonds\n\n"
" Coords\n\n 1 1.0 1.0 1.0\n 2 1.0 1.0 0.0\n 3 1.0 0.0 1.0\n"
" Bonds\n\n 1 1 1 2\n 2 1 1 3\n"););
remove("nospecial.mol");
}
TEST_F(MoleculeFileTest, minimal)
{
::testing::internal::CaptureStdout();
run_mol_cmd(test_name, "", "Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n");
auto output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output;
ASSERT_THAT(output, MatchesRegex(".*Read molecule template.*1 molecules.*1 atoms.*0 bonds.*"));
}
TEST_F(MoleculeFileTest, twomols)
{
::testing::internal::CaptureStdout();
run_mol_cmd(test_name, "",
"Comment\n2 atoms\n\n"
" Coords\n\n 1 0.0 0.0 0.0\n 2 0.0 0.0 1.0\n"
" Molecules\n\n 1 1\n 2 2\n\n Types\n\n 1 1\n 2 2\n\n");
auto output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output;
ASSERT_THAT(output, MatchesRegex(".*Read molecule template.*2 molecules.*2 atoms "
"with max type 2.*0 bonds.*"));
}
TEST_F(MoleculeFileTest, twofiles)
{
::testing::internal::CaptureStdout();
lmp->input->one("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0");
auto output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output;
ASSERT_THAT(output, MatchesRegex(".*Read molecule template twomols:.*1 molecules.*3 atoms "
"with max type 2.*2 bonds with max type 1.*"
"1 angles with max type 1.*0 dihedrals.*"
".*Read molecule template twomols:.*1 molecules.*3 atoms "
"with max type 4.*2 bonds with max type 2.*"
"1 angles with max type 2.*0 dihedrals.*"));
}
TEST_F(MoleculeFileTest, bonds)
{
::testing::internal::CaptureStdout();
lmp->input->one("atom_style bond");
lmp->input->one("region box block 0 1 0 1 0 1");
lmp->input->one("create_box 2 box bond/types 2 extra/bond/per/atom 2 "
"extra/special/per/atom 4");
run_mol_cmd(test_name, "",
"Comment\n"
"4 atoms\n"
"2 bonds\n\n"
" Coords\n\n"
" 1 1.0 1.0 1.0\n"
" 2 1.0 1.0 0.0\n"
" 3 1.0 0.0 1.0\n"
" 4 1.0 0.0 0.0\n"
" Types\n\n"
" 1 1\n"
" 2 1\n"
" 3 2\n"
" 4 2\n\n"
" Bonds\n\n"
" 1 1 1 2\n"
" 2 2 1 3\n\n");
auto output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output;
ASSERT_THAT(output, MatchesRegex(".*Read molecule template.*1 molecules.*4 atoms.*type.*2.*"
"2 bonds.*type.*2.*0 angles.*"));
::testing::internal::CaptureStdout();
lmp->input->one("mass * 2.0");
lmp->input->one("create_atoms 0 single 0.5 0.5 0.5 mol bonds 67235");
output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output;
ASSERT_THAT(output, MatchesRegex(".*Created 4 atoms.*"));
::testing::internal::CaptureStdout();
Molecule *mol = lmp->atom->molecules[0];
ASSERT_EQ(mol->natoms, 4);
ASSERT_EQ(lmp->atom->natoms, 4);
mol->compute_mass();
mol->compute_com();
ASSERT_DOUBLE_EQ(mol->masstotal, 8.0);
EXPECT_DOUBLE_EQ(mol->com[0], 1.0);
EXPECT_DOUBLE_EQ(mol->com[1], 0.5);
EXPECT_DOUBLE_EQ(mol->com[2], 0.5);
EXPECT_DOUBLE_EQ(mol->maxextent, sqrt(2));
EXPECT_EQ(mol->comatom, 1);
output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output;
}
int main(int argc, char **argv)
{
MPI_Init(&argc, &argv);
::testing::InitGoogleMock(&argc, argv);
if (have_openmpi && !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<std::string> 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;
}

55
unittest/utils/test_utils.cpp
View File

@ -287,6 +287,61 @@ TEST(Utils, signed_double_and_d_exponential)
ASSERT_FALSE(utils::is_double("-10D-22"));
}
TEST(Utils, valid_id1)
{
ASSERT_TRUE(utils::is_id("abc"));
}
TEST(Utils, valid_id2)
{
ASSERT_TRUE(utils::is_id("123"));
}
TEST(Utils, valid_id3)
{
ASSERT_TRUE(utils::is_id("abc123"));
}
TEST(Utils, valid_id4)
{
ASSERT_TRUE(utils::is_id("abc_123"));
}
TEST(Utils, valid_id5)
{
ASSERT_TRUE(utils::is_id("123_abc"));
}
TEST(Utils, valid_id6)
{
ASSERT_TRUE(utils::is_id("_123"));
}
TEST(Utils, valid_id7)
{
ASSERT_TRUE(utils::is_id("___"));
}
TEST(Utils, invalid_id1)
{
ASSERT_FALSE(utils::is_id("+abc"));
}
TEST(Utils, invalid_id2)
{
ASSERT_FALSE(utils::is_id("a[1]"));
}
TEST(Utils, invalid_id3)
{
ASSERT_FALSE(utils::is_id("b(c)"));
}
TEST(Utils, invalid_id4)
{
ASSERT_FALSE(utils::is_id("a$12"));
}
TEST(Utils, strmatch_beg)
{
ASSERT_TRUE(utils::strmatch("rigid/small/omp", "^rigid"));