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Merge branch 'develop' into pod-updates

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This commit is contained in:
Axel Kohlmeyer
2022-11-30 13:47:40 -05:00
parent 5900c8a06d e76e864152
commit e1d31a5633
41 changed files with 1280 additions and 713 deletions
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8
unittest/commands/CMakeLists.txt
View File

@ -53,10 +53,10 @@ endif()
target_link_libraries(test_kim_commands PRIVATE lammps GTest::GMock)
add_test(NAME KimCommands COMMAND test_kim_commands)
add_executable(test_reset_ids test_reset_ids.cpp)
target_compile_definitions(test_reset_ids PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR})
target_link_libraries(test_reset_ids PRIVATE lammps GTest::GMock)
add_test(NAME ResetIDs COMMAND test_reset_ids)
add_executable(test_reset_atoms test_reset_atoms.cpp)
target_compile_definitions(test_reset_atoms PRIVATE -DTEST_INPUT_FOLDER=${CMAKE_CURRENT_SOURCE_DIR})
target_link_libraries(test_reset_atoms PRIVATE lammps GTest::GMock)
add_test(NAME ResetAtoms COMMAND test_reset_atoms)
if(PKG_MOLECULE)
add_executable(test_compute_global test_compute_global.cpp)

208
unittest/commands/test_reset_ids.cpp → unittest/commands/test_reset_atoms.cpp
View File

@ -17,6 +17,7 @@
#include "info.h"
#include "input.h"
#include "lammps.h"
#include "library.h"
#include "output.h"
#include "update.h"
#include "utils.h"
@ -36,11 +37,11 @@ namespace LAMMPS_NS {
#define STRINGIFY(val) XSTR(val)
#define XSTR(val) #val
class ResetIDsTest : public LAMMPSTest {
class ResetAtomsIDTest : public LAMMPSTest {
protected:
void SetUp() override
{
testbinary = "ResetIDsTest";
testbinary = "ResetAtomsIDTest";
LAMMPSTest::SetUp();
if (info->has_style("atom", "full")) {
BEGIN_HIDE_OUTPUT();
@ -51,7 +52,7 @@ protected:
}
};
TEST_F(ResetIDsTest, MolIDAll)
TEST_F(ResetAtomsIDTest, MolIDAll)
{
if (lmp->atom->natoms == 0) GTEST_SKIP();
@ -89,7 +90,7 @@ TEST_F(ResetIDsTest, MolIDAll)
// the original data file has two different molecule IDs
// for two residues of the same molecule/fragment.
BEGIN_HIDE_OUTPUT();
command("reset_mol_ids all");
command("reset_atoms mol all");
END_HIDE_OUTPUT();
ASSERT_EQ(molid[GETIDX(1)], 1);
@ -123,7 +124,7 @@ TEST_F(ResetIDsTest, MolIDAll)
ASSERT_EQ(molid[GETIDX(29)], 5);
}
TEST_F(ResetIDsTest, DeletePlusAtomID)
TEST_F(ResetAtomsIDTest, DeletePlusAtomID)
{
if (lmp->atom->natoms == 0) GTEST_SKIP();
@ -134,7 +135,7 @@ TEST_F(ResetIDsTest, DeletePlusAtomID)
command("group allwater molecule 3:6");
command("group twowater molecule 4:6:2");
command("delete_atoms group twowater compress no bond yes");
command("reset_mol_ids all");
command("reset_atoms mol all");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->atom->natoms, 23);
ASSERT_EQ(lmp->atom->map_tag_max, 26);
@ -193,7 +194,7 @@ TEST_F(ResetIDsTest, DeletePlusAtomID)
ASSERT_GE(GETIDX(26), 0);
BEGIN_HIDE_OUTPUT();
command("reset_atom_ids");
command("reset_atoms id");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->atom->map_tag_max, 23);
@ -201,7 +202,7 @@ TEST_F(ResetIDsTest, DeletePlusAtomID)
ASSERT_GE(GETIDX(i), 0);
}
TEST_F(ResetIDsTest, PartialOffset)
TEST_F(ResetAtomsIDTest, PartialOffset)
{
if (lmp->atom->natoms == 0) GTEST_SKIP();
@ -211,7 +212,7 @@ TEST_F(ResetIDsTest, PartialOffset)
BEGIN_HIDE_OUTPUT();
command("group allwater molecule 3:6");
command("group nowater subtract all allwater");
command("reset_mol_ids allwater offset 4");
command("reset_atoms mol allwater offset 4");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->atom->natoms, 29);
ASSERT_EQ(lmp->atom->map_tag_max, 29);
@ -247,7 +248,7 @@ TEST_F(ResetIDsTest, PartialOffset)
ASSERT_EQ(molid[GETIDX(29)], 8);
BEGIN_HIDE_OUTPUT();
command("reset_mol_ids nowater offset 0");
command("reset_atoms mol nowater offset 0");
END_HIDE_OUTPUT();
ASSERT_EQ(molid[GETIDX(1)], 1);
@ -281,7 +282,7 @@ TEST_F(ResetIDsTest, PartialOffset)
ASSERT_EQ(molid[GETIDX(29)], 8);
}
TEST_F(ResetIDsTest, DeleteAdd)
TEST_F(ResetAtomsIDTest, DeleteAdd)
{
if (lmp->atom->natoms == 0) GTEST_SKIP();
@ -293,7 +294,7 @@ TEST_F(ResetIDsTest, DeleteAdd)
command("group twowater molecule 4:6:2");
command("group nowater subtract all allwater");
command("delete_atoms group twowater compress no bond yes mol yes");
command("reset_mol_ids allwater");
command("reset_atoms mol allwater");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->atom->natoms, 23);
ASSERT_EQ(lmp->atom->map_tag_max, 26);
@ -352,7 +353,7 @@ TEST_F(ResetIDsTest, DeleteAdd)
ASSERT_GE(GETIDX(26), 0);
BEGIN_HIDE_OUTPUT();
command("reset_atom_ids sort yes");
command("reset_atoms id sort yes");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->atom->map_tag_max, 23);
@ -360,7 +361,7 @@ TEST_F(ResetIDsTest, DeleteAdd)
ASSERT_GE(GETIDX(i), 0);
BEGIN_HIDE_OUTPUT();
command("reset_mol_ids nowater offset 1");
command("reset_atoms mol nowater offset 1");
END_HIDE_OUTPUT();
ASSERT_EQ(molid[GETIDX(1)], 2);
@ -392,7 +393,7 @@ TEST_F(ResetIDsTest, DeleteAdd)
command("create_atoms 2 single 1.0 0.0 0.0");
command("create_atoms 3 single 2.0 0.0 0.0");
command("create_atoms 4 single 3.0 0.0 0.0");
command("reset_mol_ids all single yes");
command("reset_atoms mol all single yes");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->atom->natoms, 27);
ASSERT_EQ(lmp->atom->map_tag_max, 27);
@ -406,7 +407,7 @@ TEST_F(ResetIDsTest, DeleteAdd)
ASSERT_EQ(molid[GETIDX(27)], 7);
BEGIN_HIDE_OUTPUT();
command("reset_mol_ids all single no");
command("reset_atoms mol all single no");
END_HIDE_OUTPUT();
ASSERT_EQ(molid[GETIDX(21)], 3);
@ -418,7 +419,7 @@ TEST_F(ResetIDsTest, DeleteAdd)
ASSERT_EQ(molid[GETIDX(27)], 0);
BEGIN_HIDE_OUTPUT();
command("reset_mol_ids all compress no single yes");
command("reset_atoms mol all compress no single yes");
END_HIDE_OUTPUT();
ASSERT_EQ(molid[GETIDX(21)], 21);
@ -430,7 +431,7 @@ TEST_F(ResetIDsTest, DeleteAdd)
ASSERT_EQ(molid[GETIDX(27)], 27);
}
TEST_F(ResetIDsTest, TopologyData)
TEST_F(ResetAtomsIDTest, TopologyData)
{
if (lmp->atom->natoms == 0) GTEST_SKIP();
@ -525,7 +526,7 @@ TEST_F(ResetIDsTest, TopologyData)
ASSERT_EQ(angle_atom3[GETIDX(24)][0], 26);
BEGIN_HIDE_OUTPUT();
command("reset_atom_ids sort yes");
command("reset_atoms id sort yes");
END_HIDE_OUTPUT();
num_bond = lmp->atom->num_bond;
@ -618,63 +619,186 @@ TEST_F(ResetIDsTest, TopologyData)
ASSERT_EQ(angle_atom3[GETIDX(22)][0], 23);
}
TEST_F(ResetIDsTest, DeathTests)
TEST_F(ResetAtomsIDTest, DeathTests)
{
if (lmp->atom->natoms == 0) GTEST_SKIP();
TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", command("reset_mol_ids"););
TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*",
command("reset_mol_ids all offset 1 1"););
TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*",
command("reset_mol_ids all offset -2"););
TEST_FAILURE(".*ERROR on proc 0: Expected integer.*", command("reset_mol_ids all offset xxx"););
TEST_FAILURE(".*ERROR: Illegal reset_atoms mol command.*", command("reset_atoms mol"););
TEST_FAILURE(".*ERROR: Unknown reset_atoms mol keyword: 1.*",
command("reset_atoms mol all offset 1 1"););
TEST_FAILURE(".*ERROR: Illegal reset_atoms mol offset: -2.*",
command("reset_atoms mol all offset -2"););
TEST_FAILURE(".*ERROR on proc 0: Expected integer.*",
command("reset_mol_ids all compress yes single no offset xxx"););
TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", command("reset_mol_ids all offset"););
TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*",
command("reset_mol_ids all compress"););
command("reset_atoms mol all offset xxx"););
TEST_FAILURE(".*ERROR on proc 0: Expected integer.*",
command("reset_atoms mol all compress yes single no offset xxx"););
TEST_FAILURE(".*ERROR: Illegal reset_atoms mol offset command: missing argument.*",
command("reset_atoms mol all offset"););
TEST_FAILURE(".*ERROR: Illegal reset_atoms mol compress command: missing argument.*",
command("reset_atoms mol all compress"););
TEST_FAILURE(".*ERROR: Expected boolean parameter instead of 'xxx'.*",
command("reset_mol_ids all compress xxx"););
TEST_FAILURE(".*ERROR: Illegal reset_mol_ids command.*", command("reset_mol_ids all single"););
command("reset_atoms mol all compress xxx"););
TEST_FAILURE(".*ERROR: Illegal reset_atoms mol single command: missing argument.*",
command("reset_atoms mol all single"););
TEST_FAILURE(".*ERROR: Expected boolean parameter instead of 'xxx'.*",
command("reset_mol_ids all single xxx"););
command("reset_atoms mol all single xxx"););
TEST_FAILURE(".*ERROR: Illegal reset_atoms image command: missing argument.*",
command("reset_atoms image"););
TEST_FAILURE(".*ERROR: Unknown reset_atoms image keyword: xxx.*",
command("reset_atoms image all xxx"););
TEST_FAILURE(".*ERROR: Could not find reset_atoms image group xxx.*",
command("reset_atoms image xxx"););
}
class ResetMolIDsTest : public LAMMPSTest {
class ResetAtomsMolTest : public LAMMPSTest {
protected:
void SetUp() override
{
testbinary = "ResetIDsTest";
testbinary = "ResetAtomsMolTest";
LAMMPSTest::SetUp();
}
};
TEST_F(ResetMolIDsTest, FailBeforeBox)
TEST_F(ResetAtomsMolTest, FailBeforeBox)
{
TEST_FAILURE(".*ERROR: Reset_mol_ids command before simulation box is.*",
command("reset_mol_ids all"););
TEST_FAILURE(".*ERROR: Reset_atoms id command before simulation box is.*",
command("reset_atoms id"););
TEST_FAILURE(".*ERROR: Reset_atoms mol command before simulation box is.*",
command("reset_atoms mol all"););
TEST_FAILURE(".*ERROR: Reset_atoms image command before simulation box is.*",
command("reset_atoms image all"););
}
TEST_F(ResetMolIDsTest, FailMissingId)
TEST_F(ResetAtomsMolTest, FailMissingId)
{
BEGIN_HIDE_OUTPUT();
command("atom_modify id no");
command("region box block 0 1 0 1 0 1");
command("create_box 1 box");
END_HIDE_OUTPUT();
TEST_FAILURE(".*ERROR: Cannot use reset_mol_ids unless.*", command("reset_mol_ids all"););
TEST_FAILURE(".*ERROR: Cannot use reset_atoms mol unless.*", command("reset_atoms mol all"););
TEST_FAILURE(".*ERROR: Cannot use reset_atoms image unless.*",
command("reset_atoms image all"););
}
TEST_F(ResetMolIDsTest, FailOnlyMolecular)
TEST_F(ResetAtomsMolTest, FailOnlyMolecular)
{
BEGIN_HIDE_OUTPUT();
command("clear");
command("region box block 0 1 0 1 0 1");
command("create_box 1 box");
END_HIDE_OUTPUT();
TEST_FAILURE(".*ERROR: Can only use reset_mol_ids.*", command("reset_mol_ids all"););
TEST_FAILURE(".*ERROR: Can only use reset_atoms mol.*", command("reset_atoms mol all"););
}
class ResetAtomsImageTest : public LAMMPSTest {
protected:
void SetUp() override
{
testbinary = "ResetAtomsImageTest";
LAMMPSTest::SetUp();
if (info->has_style("atom", "full")) {
BEGIN_HIDE_OUTPUT();
command("variable input_dir index \"" STRINGIFY(TEST_INPUT_FOLDER) "\"");
command("include \"${input_dir}/in.fourmol\"");
command("create_atoms 1 single 1.0 1.0 1.0");
command("create_atoms 1 single 2.0 1.0 1.0");
command("create_atoms 1 single 1.0 2.0 1.0");
command("set atom 1*7 image 1 1 -1");
command("set atom 8*9 image 2 -1 0");
command("set atom 8*9 image 2 -1 0");
command("set atom 10 image 2 0 0");
command("set atom 11*12 image 2 0 -1");
command("set atom 13*15 image 1 0 0");
command("set atom 16*17 image 0 1 1");
command("set atom 18*19 image 0 1 0");
command("set atom 20 image 0 2 0");
command("set atom 21*23 image 20 -1 0");
command("set atom 27*28 image 1 0 0");
command("set atom 29 image 1 2 0");
command("set atom 31 image -2 0 1");
command("set atom 32 image 0 20 0");
END_HIDE_OUTPUT();
}
}
};
TEST_F(ResetAtomsImageTest, ResetAtomsImage)
{
if (lmp->atom->natoms == 0) GTEST_SKIP();
EXPECT_EQ(lmp->atom->image[GETIDX(1)], lammps_encode_image_flags(1, 1, -1));
EXPECT_EQ(lmp->atom->image[GETIDX(2)], lammps_encode_image_flags(1, 1, -1));
EXPECT_EQ(lmp->atom->image[GETIDX(3)], lammps_encode_image_flags(1, 1, -1));
EXPECT_EQ(lmp->atom->image[GETIDX(4)], lammps_encode_image_flags(1, 1, -1));
EXPECT_EQ(lmp->atom->image[GETIDX(5)], lammps_encode_image_flags(1, 1, -1));
EXPECT_EQ(lmp->atom->image[GETIDX(6)], lammps_encode_image_flags(1, 1, -1));
EXPECT_EQ(lmp->atom->image[GETIDX(7)], lammps_encode_image_flags(1, 1, -1));
EXPECT_EQ(lmp->atom->image[GETIDX(8)], lammps_encode_image_flags(2, -1, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(9)], lammps_encode_image_flags(2, -1, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(10)], lammps_encode_image_flags(2, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(11)], lammps_encode_image_flags(2, 0, -1));
EXPECT_EQ(lmp->atom->image[GETIDX(12)], lammps_encode_image_flags(2, 0, -1));
EXPECT_EQ(lmp->atom->image[GETIDX(13)], lammps_encode_image_flags(1, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(14)], lammps_encode_image_flags(1, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(15)], lammps_encode_image_flags(1, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(16)], lammps_encode_image_flags(0, 1, 1));
EXPECT_EQ(lmp->atom->image[GETIDX(17)], lammps_encode_image_flags(0, 1, 1));
EXPECT_EQ(lmp->atom->image[GETIDX(18)], lammps_encode_image_flags(0, 1, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(19)], lammps_encode_image_flags(0, 1, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(20)], lammps_encode_image_flags(0, 2, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(21)], lammps_encode_image_flags(20, -1, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(22)], lammps_encode_image_flags(20, -1, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(23)], lammps_encode_image_flags(20, -1, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(24)], lammps_encode_image_flags(0, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(25)], lammps_encode_image_flags(0, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(26)], lammps_encode_image_flags(0, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(27)], lammps_encode_image_flags(1, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(28)], lammps_encode_image_flags(1, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(29)], lammps_encode_image_flags(1, 2, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(30)], lammps_encode_image_flags(0, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(31)], lammps_encode_image_flags(-2, 0, 1));
EXPECT_EQ(lmp->atom->image[GETIDX(32)], lammps_encode_image_flags(0, 20, 0));
BEGIN_HIDE_OUTPUT();
command("group subset id 5:32");
command("reset_atoms image subset");
END_HIDE_OUTPUT();
EXPECT_EQ(lmp->atom->image[GETIDX(1)], lammps_encode_image_flags(1, 1, -1));
EXPECT_EQ(lmp->atom->image[GETIDX(2)], lammps_encode_image_flags(1, 1, -1));
EXPECT_EQ(lmp->atom->image[GETIDX(3)], lammps_encode_image_flags(1, 1, -1));
EXPECT_EQ(lmp->atom->image[GETIDX(4)], lammps_encode_image_flags(1, 1, -1));
EXPECT_EQ(lmp->atom->image[GETIDX(5)], lammps_encode_image_flags(0, 1, -1));
EXPECT_EQ(lmp->atom->image[GETIDX(6)], lammps_encode_image_flags(0, 1, -1));
EXPECT_EQ(lmp->atom->image[GETIDX(7)], lammps_encode_image_flags(0, 1, -1));
EXPECT_EQ(lmp->atom->image[GETIDX(8)], lammps_encode_image_flags(1, -1, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(9)], lammps_encode_image_flags(1, -1, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(10)], lammps_encode_image_flags(1, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(11)], lammps_encode_image_flags(1, 0, -1));
EXPECT_EQ(lmp->atom->image[GETIDX(12)], lammps_encode_image_flags(1, 0, -1));
EXPECT_EQ(lmp->atom->image[GETIDX(13)], lammps_encode_image_flags(0, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(14)], lammps_encode_image_flags(0, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(15)], lammps_encode_image_flags(0, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(16)], lammps_encode_image_flags(-1, 1, 1));
EXPECT_EQ(lmp->atom->image[GETIDX(17)], lammps_encode_image_flags(-1, 1, 1));
EXPECT_EQ(lmp->atom->image[GETIDX(18)], lammps_encode_image_flags(0, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(19)], lammps_encode_image_flags(0, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(20)], lammps_encode_image_flags(0, 1, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(21)], lammps_encode_image_flags(0, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(22)], lammps_encode_image_flags(0, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(23)], lammps_encode_image_flags(0, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(24)], lammps_encode_image_flags(0, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(25)], lammps_encode_image_flags(0, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(26)], lammps_encode_image_flags(0, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(27)], lammps_encode_image_flags(0, -1, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(28)], lammps_encode_image_flags(0, -1, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(29)], lammps_encode_image_flags(0, 1, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(30)], lammps_encode_image_flags(0, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(30)], lammps_encode_image_flags(0, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(31)], lammps_encode_image_flags(0, 0, 0));
EXPECT_EQ(lmp->atom->image[GETIDX(32)], lammps_encode_image_flags(0, 0, 0));
}
} // namespace LAMMPS_NS
int main(int argc, char **argv)