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reformat. compute/check some molecule properties

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This commit is contained in:
Axel Kohlmeyer
2021-03-02 23:05:27 -05:00
parent c44dbc567d
commit 7b4034d07a
1 changed files with 64 additions and 43 deletions
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107
unittest/formats/test_molecule_file.cpp
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@ -11,6 +11,7 @@
See the README file in the top-level LAMMPS directory. See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
#include "atom.h"
#include "info.h" #include "info.h"
#include "input.h" #include "input.h"
#include "lammps.h" #include "lammps.h"
@ -123,13 +124,13 @@ protected:
void run_mol_cmd(const std::string &name, const std::string &args, const std::string &content) void run_mol_cmd(const std::string &name, const std::string &args, const std::string &content)
{ {
std::string file = name + ".mol"; std::string file = name + ".mol";
FILE *fp = fopen(file.c_str(), "w"); FILE *fp = fopen(file.c_str(), "w");
fputs(content.c_str(),fp); fputs(content.c_str(), fp);
fclose(fp); fclose(fp);
lmp->input->one(fmt::format("molecule {} {} {}",name,file,args)); lmp->input->one(fmt::format("molecule {} {} {}", name, file, args));
remove(file.c_str()); remove(file.c_str());
} }
}; };
TEST_F(MoleculeFileTest, nofile) TEST_F(MoleculeFileTest, nofile)
@ -148,48 +149,50 @@ TEST_F(MoleculeFileTest, badid)
TEST_F(MoleculeFileTest, badargs) TEST_F(MoleculeFileTest, badargs)
{ {
TEST_FAILURE(".*Illegal molecule command.*", TEST_FAILURE(".*Illegal molecule command.*",
run_mol_cmd(test_name,"offset 1 2 3 4", 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");); "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"); remove("badargs.mol");
} }
TEST_F(MoleculeFileTest, noatom) TEST_F(MoleculeFileTest, noatom)
{ {
TEST_FAILURE(".*ERROR: No atoms or invalid atom count in molecule file.*", TEST_FAILURE(".*ERROR: No atoms or invalid atom count in molecule file.*",
run_mol_cmd(test_name,"","Comment\n0 atoms\n1 bonds\n\n" run_mol_cmd(test_name, "",
" Coords\n\nBonds\n\n 1 1 2\n");); "Comment\n0 atoms\n1 bonds\n\n"
" Coords\n\nBonds\n\n 1 1 2\n"););
remove("noatom.mol"); remove("noatom.mol");
} }
TEST_F(MoleculeFileTest, empty) TEST_F(MoleculeFileTest, empty)
{ {
TEST_FAILURE(".*ERROR: Unexpected end of molecule file.*", TEST_FAILURE(".*ERROR: Unexpected end of molecule file.*",
run_mol_cmd(test_name,"","Comment\n\n");); run_mol_cmd(test_name, "", "Comment\n\n"););
remove("empty.mol"); remove("empty.mol");
} }
TEST_F(MoleculeFileTest, nospecial) TEST_F(MoleculeFileTest, nospecial)
{ {
TEST_FAILURE(".*ERROR: Cannot auto-generate special bonds before simulation box is defined.*", 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" 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" " 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");); " Bonds\n\n 1 1 1 2\n 2 1 1 3\n"););
remove("nospecial.mol"); remove("nospecial.mol");
@ -198,22 +201,23 @@ TEST_F(MoleculeFileTest, nospecial)
TEST_F(MoleculeFileTest, minimal) TEST_F(MoleculeFileTest, minimal)
{ {
::testing::internal::CaptureStdout(); ::testing::internal::CaptureStdout();
run_mol_cmd(test_name,"","Comment\n1 atoms\n\n Coords\n\n 1 0.0 0.0 0.0\n"); 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(); auto output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output; if (verbose) std::cout << output;
ASSERT_THAT(output,MatchesRegex(".*Read molecule template.*1 molecules.*1 atoms.*0 bonds.*")); ASSERT_THAT(output, MatchesRegex(".*Read molecule template.*1 molecules.*1 atoms.*0 bonds.*"));
} }
TEST_F(MoleculeFileTest, twomols) TEST_F(MoleculeFileTest, twomols)
{ {
::testing::internal::CaptureStdout(); ::testing::internal::CaptureStdout();
run_mol_cmd(test_name,"","Comment\n2 atoms\n\n" 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" " 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"); " 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(); auto output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output; if (verbose) std::cout << output;
ASSERT_THAT(output,MatchesRegex(".*Read molecule template.*2 molecules.*2 atoms " ASSERT_THAT(output, MatchesRegex(".*Read molecule template.*2 molecules.*2 atoms "
"with max type 2.*0 bonds.*")); "with max type 2.*0 bonds.*"));
} }
TEST_F(MoleculeFileTest, twofiles) TEST_F(MoleculeFileTest, twofiles)
@ -222,12 +226,12 @@ TEST_F(MoleculeFileTest, twofiles)
lmp->input->one("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0"); lmp->input->one("molecule twomols h2o.mol co2.mol offset 2 1 1 0 0");
auto output = ::testing::internal::GetCapturedStdout(); auto output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output; if (verbose) std::cout << output;
ASSERT_THAT(output,MatchesRegex(".*Read molecule template twomols:.*1 molecules.*3 atoms " ASSERT_THAT(output, MatchesRegex(".*Read molecule template twomols:.*1 molecules.*3 atoms "
"with max type 2.*2 bonds with max type 1.*" "with max type 2.*2 bonds with max type 1.*"
"1 angles with max type 1.*0 dihedrals.*" "1 angles with max type 1.*0 dihedrals.*"
".*Read molecule template twomols:.*1 molecules.*3 atoms " ".*Read molecule template twomols:.*1 molecules.*3 atoms "
"with max type 4.*2 bonds with max type 2.*" "with max type 4.*2 bonds with max type 2.*"
"1 angles with max type 2.*0 dihedrals.*")); "1 angles with max type 2.*0 dihedrals.*"));
} }
TEST_F(MoleculeFileTest, bonds) TEST_F(MoleculeFileTest, bonds)
@ -237,7 +241,8 @@ TEST_F(MoleculeFileTest, bonds)
lmp->input->one("region box block 0 1 0 1 0 1"); 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 " lmp->input->one("create_box 2 box bond/types 2 extra/bond/per/atom 2 "
"extra/special/per/atom 4"); "extra/special/per/atom 4");
run_mol_cmd(test_name,"","Comment\n" run_mol_cmd(test_name, "",
"Comment\n"
"4 atoms\n" "4 atoms\n"
"2 bonds\n\n" "2 bonds\n\n"
" Coords\n\n" " Coords\n\n"
@ -255,14 +260,30 @@ TEST_F(MoleculeFileTest, bonds)
" 2 2 1 3\n\n"); " 2 2 1 3\n\n");
auto output = ::testing::internal::GetCapturedStdout(); auto output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output; if (verbose) std::cout << output;
ASSERT_THAT(output,MatchesRegex(".*Read molecule template.*1 molecules.*4 atoms.*type.*2.*" ASSERT_THAT(output, MatchesRegex(".*Read molecule template.*1 molecules.*4 atoms.*type.*2.*"
"2 bonds.*type.*2.*0 angles.*")); "2 bonds.*type.*2.*0 angles.*"));
::testing::internal::CaptureStdout(); ::testing::internal::CaptureStdout();
lmp->input->one("create_atoms 0 single 0.0 0.0 0.0 mol bonds 67235"); 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(); output = ::testing::internal::GetCapturedStdout();
if (verbose) std::cout << output; if (verbose) std::cout << output;
ASSERT_THAT(output,MatchesRegex(".*Created 4 atoms.*"));
} }
int main(int argc, char **argv) int main(int argc, char **argv)