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lammps/unittest/commands/test_groups.cpp

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
LAMMPS Development team: developers@lammps.org
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 "lammps.h"
#include "atom.h"
#include "domain.h"
#include "group.h"
#include "info.h"
#include "input.h"
#include "region.h"
#include "../testing/core.h"
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include <cstring>
#include <vector>
// whether to print verbose output (i.e. not capturing LAMMPS screen output).
bool verbose = false;
using LAMMPS_NS::utils::split_words;
namespace LAMMPS_NS {
using ::testing::ExitedWithCode;
using ::testing::StrEq;
class GroupTest : public LAMMPSTest {
protected:
Group *group;
Domain *domain;
void SetUp() override
{
testbinary = "GroupTest";
LAMMPSTest::SetUp();
group = lmp->group;
domain = lmp->domain;
}
void atomic_system()
{
BEGIN_HIDE_OUTPUT();
command("units real");
command("lattice sc 1.0 origin 0.125 0.125 0.125");
command("region box block -2 2 -2 2 -2 2");
command("create_box 8 box");
command("create_atoms 1 box");
command("mass * 1.0");
command("region left block -2.0 -1.0 INF INF INF INF");
command("region right block 0.5 2.0 INF INF INF INF");
command("region top block INF INF -2.0 -1.0 INF INF");
command("set region left type 2");
command("set region right type 3");
END_HIDE_OUTPUT();
}
void molecular_system()
{
BEGIN_HIDE_OUTPUT();
command("fix props all property/atom mol rmass q");
END_HIDE_OUTPUT();
atomic_system();
BEGIN_HIDE_OUTPUT();
command("variable molid atom floor(id/4)+1");
command("variable charge atom 2.0*sin(PI/32*id)");
command("set atom * mol v_molid");
command("set atom * charge v_charge");
command("set type 1 mass 0.5");
command("set type 2*4 mass 2.0");
END_HIDE_OUTPUT();
}
};
TEST_F(GroupTest, NoBox)
{
ASSERT_EQ(group->ngroup, 1);
TEST_FAILURE(".*ERROR: Group command before simulation box.*", command("group none empty"););
}
TEST_F(GroupTest, EmptyDelete)
{
atomic_system();
BEGIN_HIDE_OUTPUT();
command("group new1 empty");
command("group new2 empty");
command("group new2 empty");
command("group new3 empty");
command("group new4 empty");
command("group new5 empty");
command("group new6 empty");
command("fix 1 new2 nve");
command("compute 1 new3 ke");
command("dump 1 new4 atom 50 dump.melt");
command("atom_modify first new5");
END_HIDE_OUTPUT();
ASSERT_EQ(group->ngroup, 7);
TEST_FAILURE(".*ERROR: Unknown group command keyword: xxx.*", command("group new3 xxx"););
TEST_FAILURE(".*ERROR: Illegal group empty command.*", command("group new3 empty xxx"););
TEST_FAILURE(".*ERROR: Group include molecule command requires atom attribute molecule.*",
command("group new2 include molecule"););
BEGIN_HIDE_OUTPUT();
group->assign("new1 delete");
END_HIDE_OUTPUT();
ASSERT_EQ(group->ngroup, 6);
TEST_FAILURE(".*ERROR: Illegal group delete command: too many arguments.*",
command("group new2 delete xxx"););
TEST_FAILURE(".*ERROR: Cannot delete group all.*", command("group all delete"););
TEST_FAILURE(".*ERROR: Could not find group delete.*", command("group new0 delete"););
TEST_FAILURE(".*ERROR: Cannot delete group new2 currently used by fix.*",
command("group new2 delete"););
TEST_FAILURE(".*ERROR: Cannot delete group new3 currently used by compute.*",
command("group new3 delete"););
TEST_FAILURE(".*ERROR: Cannot delete group new4 currently used by dump.*",
command("group new4 delete"););
TEST_FAILURE(".*ERROR: Cannot delete group new5 currently used by atom_modify.*",
command("group new5 delete"););
}
TEST_F(GroupTest, RegionClear)
{
atomic_system();
BEGIN_HIDE_OUTPUT();
command("group one region left");
command("group two region right");
command("group three empty");
command("group four region left");
command("group four region right");
END_HIDE_OUTPUT();
ASSERT_EQ(group->count(group->find("one")), 16);
ASSERT_EQ(group->count(group->find("two")), 16);
ASSERT_EQ(group->count(group->find("three")), 0);
ASSERT_EQ(group->count(group->find("four")), 32);
ASSERT_EQ(group->count(group->find("all")), lmp->atom->natoms);
ASSERT_EQ(group->count_all(), lmp->atom->natoms);
TEST_FAILURE(".*ERROR: Illegal group region command.*",
command("group three region left xxx"););
TEST_FAILURE(".*ERROR: Region dummy for group region does not exist.*",
command("group four region dummy"););
BEGIN_HIDE_OUTPUT();
command("group one clear");
command("group two clear");
command("group three clear");
command("group four clear");
END_HIDE_OUTPUT();
ASSERT_EQ(group->count(group->find("one")), 0);
ASSERT_EQ(group->count(group->find("two")), 0);
ASSERT_EQ(group->count(group->find("three")), 0);
ASSERT_EQ(group->count(group->find("four")), 0);
BEGIN_HIDE_OUTPUT();
command("delete_atoms region box");
END_HIDE_OUTPUT();
ASSERT_EQ(group->count(group->find("all")), 0);
}
TEST_F(GroupTest, SelectRestart)
{
atomic_system();
int *flags = new int[lmp->atom->natoms];
for (int i = 0; i < lmp->atom->natoms; ++i)
flags[i] = i & 1;
BEGIN_HIDE_OUTPUT();
command("group one region left");
command("group two region right");
group->create("half", flags);
group->find_or_create("three");
group->find_or_create("one");
command("group four union one two");
command("group five subtract all half four");
command("group top region top");
command("group six intersect half top");
END_HIDE_OUTPUT();
ASSERT_EQ(group->count(group->find("one")), 16);
ASSERT_EQ(group->count(group->find("two")), 16);
ASSERT_EQ(group->count(group->find("three")), 0);
ASSERT_EQ(group->count(group->find("half")), 32);
ASSERT_EQ(group->count(group->find("four")), 32);
ASSERT_EQ(group->count(group->find("five")), 16);
ASSERT_EQ(group->count(group->find("six")), 8);
ASSERT_EQ(group->count(group->find("half"), domain->get_region_by_id("top")), 8);
ASSERT_DOUBLE_EQ(group->mass(group->find("half"), domain->get_region_by_id("top")), 8.0);
BEGIN_HIDE_OUTPUT();
command("write_restart group.restart");
command("clear");
command("read_restart group.restart");
platform::unlink("group.restart");
END_HIDE_OUTPUT();
group = lmp->group;
ASSERT_EQ(group->count(group->find("one")), 16);
ASSERT_EQ(group->count(group->find("two")), 16);
ASSERT_EQ(group->count(group->find("three")), 0);
ASSERT_EQ(group->count(group->find("half")), 32);
ASSERT_EQ(group->count(group->find("four")), 32);
ASSERT_EQ(group->count(group->find("five")), 16);
ASSERT_DOUBLE_EQ(group->mass(group->find("six")), 8.0);
BEGIN_HIDE_OUTPUT();
command("group four clear");
command("group five clear");
command("group six clear");
END_HIDE_OUTPUT();
TEST_FAILURE(".*ERROR: Group ID xxx does not exist.*",
command("group four union one two xxx"););
TEST_FAILURE(".*ERROR: Group ID xxx does not exist.*",
command("group five subtract all half xxx"););
TEST_FAILURE(".*ERROR: Group ID xxx does not exist.*",
command("group five intersect half top xxx"););
}
TEST_F(GroupTest, Molecular)
{
molecular_system();
BEGIN_HIDE_OUTPUT();
command("group one region left");
command("group two region right");
command("group half id 1:1000:2");
command("group top region top");
command("group three intersect half top");
command("group three include molecule");
END_HIDE_OUTPUT();
ASSERT_EQ(group->count(group->find("one")), 16);
ASSERT_EQ(group->count(group->find("two")), 16);
ASSERT_EQ(group->count(group->find("three")), 15);
ASSERT_DOUBLE_EQ(group->mass(group->find("half")), 40);
ASSERT_DOUBLE_EQ(group->mass(group->find("half"), domain->get_region_by_id("top")), 10);
ASSERT_NEAR(group->charge(group->find("top")), 0, 1.0e-14);
ASSERT_NEAR(group->charge(group->find("right"), domain->get_region_by_id("top")), 0, 1.0e-14);
TEST_FAILURE(".*ERROR: Unknown group include keyword xxx.*",
command("group three include xxx"););
}
TEST_F(GroupTest, Dynamic)
{
atomic_system();
BEGIN_HIDE_OUTPUT();
command("variable step atom id<=step");
command("group half id 1:1000:2");
command("group grow dynamic half var step every 1");
END_HIDE_OUTPUT();
ASSERT_EQ(group->count(group->find("grow")), 0);
BEGIN_HIDE_OUTPUT();
command("run 10 post no");
END_HIDE_OUTPUT();
ASSERT_EQ(group->count(group->find("grow")), 5);
BEGIN_HIDE_OUTPUT();
command("group grow dynamic half var step every 1");
command("run 10 post no");
END_HIDE_OUTPUT();
ASSERT_EQ(group->count(group->find("grow")), 10);
BEGIN_HIDE_OUTPUT();
command("group grow static");
command("run 10 post no");
command("group part variable step");
END_HIDE_OUTPUT();
ASSERT_EQ(group->count(group->find("grow")), 10);
ASSERT_EQ(group->count(group->find("part")), 30);
BEGIN_HIDE_OUTPUT();
command("group grow dynamic half var step every 1");
command("run 10 post no");
END_HIDE_OUTPUT();
ASSERT_EQ(group->count(group->find("grow")), 20);
TEST_FAILURE(".*ERROR: Cannot subtract dynamic groups.*",
command("group chunk subtract half grow"););
TEST_FAILURE(".*ERROR: Cannot union groups from a dynamic group.*",
command("group chunk union half grow"););
TEST_FAILURE(".*ERROR: Cannot intersect groups using a dynamic group.*",
command("group chunk intersect half grow"););
BEGIN_HIDE_OUTPUT();
command("group grow delete");
command("variable ramp equal step");
END_HIDE_OUTPUT();
ASSERT_EQ(group->ngroup, 3);
TEST_FAILURE(".*ERROR: Group dynamic cannot reference itself.*",
command("group half dynamic half region top"););
TEST_FAILURE(".*ERROR: Group dynamic parent group dummy does not exist.*",
command("group half dynamic dummy region top"););
TEST_FAILURE(".*ERROR: Variable ramp for group is invalid style.*",
command("group ramp variable ramp"););
TEST_FAILURE(".*ERROR: Variable name grow for group does not exist.*",
command("group ramp variable grow"););
}
constexpr double EPSILON = 1.0e-14;
TEST_F(GroupTest, VariableFunctions)
{
molecular_system();
BEGIN_HIDE_OUTPUT();
command("group one region left");
command("group two region right");
command("group three empty");
command("group four region top");
command("set atom 5 charge $(1.0+2.0*sin(PI/32*5))");
command("set atom 12 charge $(-1.0+2.0*sin(PI/32*12))");
command("set atom 25 charge $(2.0+2.0*sin(PI/32*25))");
command("set atom 32 charge $(-2.0+2.0*sin(PI/32*32))");
command("pair_style lj/cut 5.0");
command("pair_coeff * * 0.4 3.0");
command("pair_coeff 2 2 0.5 3.3");
command("pair_coeff 3 3 0.2 3.5");
command("run 0 post no");
END_HIDE_OUTPUT();
int one = group->find("one");
int two = group->find("two");
int three = group->find("three");
int four = group->find("four");
auto right = domain->get_region_by_id("right");
auto left = domain->get_region_by_id("left");
auto top = domain->get_region_by_id("top");
EXPECT_EQ(group->count_all(), 64);
EXPECT_EQ(group->count(one), 16);
EXPECT_EQ(group->count(two), 16);
EXPECT_EQ(group->count(three), 0);
EXPECT_EQ(group->count(four), 16);
EXPECT_EQ(group->count(0, right), 16);
EXPECT_EQ(group->count(one, top), 4);
EXPECT_EQ(group->count(two, right), 16);
EXPECT_EQ(group->count(two, left), 0);
EXPECT_DOUBLE_EQ(group->mass(0), 80.0);
EXPECT_DOUBLE_EQ(group->mass(two), 32.0);
EXPECT_DOUBLE_EQ(group->mass(three), 0.0);
EXPECT_DOUBLE_EQ(group->mass(0, right), 32.0);
EXPECT_DOUBLE_EQ(group->mass(one, top), 8.0);
EXPECT_DOUBLE_EQ(group->mass(two, right), 32.0);
EXPECT_DOUBLE_EQ(group->mass(two, left), 0.0);
EXPECT_NEAR(group->charge(0), 0.0, EPSILON);
EXPECT_NEAR(group->charge(two), -3.0, EPSILON);
EXPECT_NEAR(group->charge(four), 0.0, EPSILON);
EXPECT_NEAR(group->charge(0, right), -3.0, EPSILON);
EXPECT_NEAR(group->charge(one, top), 0.0, EPSILON);
EXPECT_NEAR(group->charge(two, right), -3.0, EPSILON);
EXPECT_NEAR(group->charge(two, left), 0.0, EPSILON);
double bounds[6];
group->bounds(0, bounds);
EXPECT_DOUBLE_EQ(bounds[0], -1.875);
EXPECT_DOUBLE_EQ(bounds[1], 1.125);
EXPECT_DOUBLE_EQ(bounds[2], -1.875);
EXPECT_DOUBLE_EQ(bounds[3], 1.125);
EXPECT_DOUBLE_EQ(bounds[4], -1.875);
EXPECT_DOUBLE_EQ(bounds[5], 1.125);
group->bounds(one, bounds);
EXPECT_DOUBLE_EQ(bounds[0], -1.875);
EXPECT_DOUBLE_EQ(bounds[1], -1.875);
EXPECT_DOUBLE_EQ(bounds[2], -1.875);
EXPECT_DOUBLE_EQ(bounds[3], 1.125);
EXPECT_DOUBLE_EQ(bounds[4], -1.875);
EXPECT_DOUBLE_EQ(bounds[5], 1.125);
group->bounds(0, bounds, right);
EXPECT_DOUBLE_EQ(bounds[0], 1.125);
EXPECT_DOUBLE_EQ(bounds[1], 1.125);
EXPECT_DOUBLE_EQ(bounds[2], -1.875);
EXPECT_DOUBLE_EQ(bounds[3], 1.125);
EXPECT_DOUBLE_EQ(bounds[4], -1.875);
EXPECT_DOUBLE_EQ(bounds[5], 1.125);
group->bounds(one, bounds, top);
EXPECT_DOUBLE_EQ(bounds[0], -1.875);
EXPECT_DOUBLE_EQ(bounds[1], -1.875);
EXPECT_DOUBLE_EQ(bounds[2], -1.875);
EXPECT_DOUBLE_EQ(bounds[3], -1.875);
EXPECT_DOUBLE_EQ(bounds[4], -1.875);
EXPECT_DOUBLE_EQ(bounds[5], 1.125);
double center[3];
group->xcm(0, 80.0, center);
EXPECT_DOUBLE_EQ(center[0], -0.375);
EXPECT_DOUBLE_EQ(center[1], -0.375);
EXPECT_DOUBLE_EQ(center[2], -0.375);
group->xcm(two, 32.0, center);
EXPECT_DOUBLE_EQ(center[0], 1.125);
EXPECT_DOUBLE_EQ(center[1], -0.375);
EXPECT_DOUBLE_EQ(center[2], -0.375);
group->xcm(three, 0.0, center);
EXPECT_DOUBLE_EQ(center[0], 0);
EXPECT_DOUBLE_EQ(center[1], 0);
EXPECT_DOUBLE_EQ(center[2], 0);
group->xcm(one, 8.0, center, top);
EXPECT_DOUBLE_EQ(center[0], -1.875);
EXPECT_DOUBLE_EQ(center[1], -1.875);
EXPECT_DOUBLE_EQ(center[2], -0.375);
group->vcm(one, 80.0, center);
EXPECT_DOUBLE_EQ(center[0], 0);
EXPECT_DOUBLE_EQ(center[1], 0);
EXPECT_DOUBLE_EQ(center[2], 0);
group->vcm(one, 8.0, center, top);
EXPECT_DOUBLE_EQ(center[0], 0);
EXPECT_DOUBLE_EQ(center[1], 0);
EXPECT_DOUBLE_EQ(center[2], 0);
group->fcm(0, center);
EXPECT_NEAR(center[0], 1.9375372195540308e-08, EPSILON);
EXPECT_NEAR(center[1], -1.0289756668946382e-07, EPSILON);
EXPECT_NEAR(center[2], -1.3366961142124989e-07, EPSILON);
group->fcm(two, center);
EXPECT_NEAR(center[0], 2.4316524016576579e-08, EPSILON);
EXPECT_NEAR(center[1], -6.0179227712175987e-08, EPSILON);
EXPECT_NEAR(center[2], -1.4393012942592875e-07, EPSILON);
group->fcm(three, center);
EXPECT_NEAR(center[0], 0, EPSILON);
EXPECT_NEAR(center[1], 0, EPSILON);
EXPECT_NEAR(center[2], 0, EPSILON);
group->fcm(one, center, top);
EXPECT_NEAR(center[0], -5.5879354476928711e-09, EPSILON);
EXPECT_NEAR(center[1], -1.6743454178680395e-08, EPSILON);
EXPECT_NEAR(center[2], 2.6166095290491853e-08, EPSILON);
EXPECT_DOUBLE_EQ(group->ke(one), 0);
EXPECT_DOUBLE_EQ(group->ke(one, top), 0);
}
} // namespace LAMMPS_NS
int main(int argc, char **argv)
{
MPI_Init(&argc, &argv);
::testing::InitGoogleMock(&argc, argv);
if (LAMMPS_NS::platform::mpi_vendor() == "Open MPI" && !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 = LAMMPS_NS::utils::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;
}
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