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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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67
unittest/formats/test_molecule_file.cpp
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@ -11,6 +11,7 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "atom.h"
#include "info.h"
#include "input.h"
#include "lammps.h"
@ -150,31 +151,32 @@ 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"););
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"
run_mol_cmd(test_name, "",
"Comment\n0 atoms\n1 bonds\n\n"
" Coords\n\nBonds\n\n 1 1 2\n"););
remove("noatom.mol");
}
@ -189,7 +191,8 @@ TEST_F(MoleculeFileTest, empty)
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"
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");
@ -207,7 +210,8 @@ TEST_F(MoleculeFileTest, minimal)
TEST_F(MoleculeFileTest, twomols)
{
::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"
" 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();
@ -237,7 +241,8 @@ TEST_F(MoleculeFileTest, bonds)
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"
run_mol_cmd(test_name, "",
"Comment\n"
"4 atoms\n"
"2 bonds\n\n"
" Coords\n\n"
@ -259,10 +264,26 @@ TEST_F(MoleculeFileTest, bonds)
"2 bonds.*type.*2.*0 angles.*"));
::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();
if (verbose) std::cout << output;
}
int main(int argc, char **argv)