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lammps/unittest/commands/test_compute_chunk.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 "../testing/core.h"
#include "info.h"
#include "lammps.h"
#include "library.h"
#include "utils.h"
#include "gmock/gmock.h"
#include "gtest/gtest.h"
#include <cstdio>
#include <mpi.h>
// whether to print verbose output (i.e. not capturing LAMMPS screen output).
bool verbose = false;
// we compare floating point numbers with 8 digits precision after the decimal point
static constexpr double EPSILON = 1.0e-8;
namespace LAMMPS_NS {
#define STRINGIFY(val) XSTR(val)
#define XSTR(val) #val
class ComputeChunkTest : public LAMMPSTest {
protected:
void SetUp() override
{
testbinary = "ComputeChunkTest";
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("group allwater molecule 3:6");
command("region half block 0.0 INF INF INF INF INF");
command("compute tags all property/atom id");
command("compute bin1d all chunk/atom bin/1d x lower 3.0 units box");
command("compute bin2d all chunk/atom bin/2d x lower 3.0 y lower 3.0 units box");
command("compute bin3d all chunk/atom bin/3d x lower 3.0 y lower 3.0 z lower 3.0 units "
"box");
command("compute binsph all chunk/atom bin/sphere 0.0 0.0 0.0 0.01 6.01 6 units box");
command("compute bincyl all chunk/atom bin/cylinder z lower 3.0 1.0 1.0 0.01 6.01 6 "
"units box");
command("compute mols all chunk/atom molecule");
command("compute types all chunk/atom type");
END_HIDE_OUTPUT();
}
}
double get_scalar(const char *id)
{
return *(double *)lammps_extract_compute(lmp, id, LMP_STYLE_GLOBAL, LMP_TYPE_SCALAR);
}
double *get_vector(const char *id)
{
return (double *)lammps_extract_compute(lmp, id, LMP_STYLE_GLOBAL, LMP_TYPE_VECTOR);
}
double **get_array(const char *id)
{
return (double **)lammps_extract_compute(lmp, id, LMP_STYLE_GLOBAL, LMP_TYPE_ARRAY);
}
double *get_peratom(const char *id)
{
return (double *)lammps_extract_compute(lmp, id, LMP_STYLE_ATOM, LMP_TYPE_VECTOR);
}
};
static constexpr int chunk1d[] = {0, 2, 3, 2, 2, 2, 3, 3, 3, 3, 3, 3, 4, 4, 3,
4, 3, 3, 3, 3, 3, 4, 4, 4, 3, 3, 3, 2, 2, 2};
static constexpr int chalf1d[] = {0, 0, 3, 0, 0, 0, 3, 3, 3, 3, 3, 3, 4, 4, 3,
4, 3, 3, 3, 3, 3, 4, 4, 4, 3, 3, 3, 0, 0, 0};
static constexpr int chunk2d[] = {0, 9, 14, 8, 9, 8, 13, 13, 13, 13, 13, 12, 18, 18, 13,
18, 12, 12, 14, 14, 14, 17, 17, 17, 14, 14, 14, 7, 7, 7};
static constexpr int chunk3d[] = {0, 43, 68, 38, 43, 38, 63, 62, 63, 63, 63, 58, 88, 88, 62,
88, 58, 59, 67, 67, 67, 82, 82, 82, 69, 69, 69, 34, 34, 34};
static constexpr int chunksph[] = {0, 3, 4, 2, 3, 2, 2, 3, 2, 2, 3, 4, 4, 5, 4,
4, 4, 4, 6, 6, 6, 6, 6, 6, 5, 5, 6, 6, 6, 5};
static constexpr int chunkcyl[] = {0, 8, 13, 8, 13, 8, 8, 7, 8, 8, 13, 18, 13, 18, 12,
13, 18, 19, 12, 7, 17, 27, 27, 27, 14, 14, 19, 29, 29, 29};
static constexpr int chunkmol[] = {0, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 3, 3, 3, 4, 4, 4, 5, 5, 5, 6, 6, 6};
static constexpr int chunktyp[] = {0, 3, 2, 1, 2, 2, 1, 4, 3, 2, 1, 2, 1, 2, 2,
2, 1, 4, 4, 2, 2, 5, 2, 2, 5, 2, 2, 5, 2, 2};
TEST_F(ComputeChunkTest, ChunkAtom)
{
if (lammps_get_natoms(lmp) == 0.0) GTEST_SKIP();
BEGIN_HIDE_OUTPUT();
command("pair_style lj/cut/coul/cut 10.0");
command("pair_coeff * * 0.01 3.0");
command("bond_style harmonic");
command("bond_coeff * 100.0 1.5");
command("dump 1 all custom 1 compute_chunk_atom.lammpstrj "
"id c_bin1d c_bin2d c_bin3d c_binsph c_bincyl c_mols c_types c_tags");
command("run 0 post no");
END_HIDE_OUTPUT();
const int natoms = lammps_get_natoms(lmp);
EXPECT_EQ(get_scalar("bin1d"), 5);
EXPECT_EQ(get_scalar("bin2d"), 25);
EXPECT_EQ(get_scalar("bin3d"), 125);
EXPECT_EQ(get_scalar("binsph"), 6);
EXPECT_EQ(get_scalar("bincyl"), 30);
EXPECT_EQ(get_scalar("mols"), 6);
EXPECT_EQ(get_scalar("types"), 5);
auto cbin1d = get_peratom("bin1d");
auto cbin2d = get_peratom("bin2d");
auto cbin3d = get_peratom("bin3d");
auto cbinsph = get_peratom("binsph");
auto cbincyl = get_peratom("bincyl");
auto cmols = get_peratom("mols");
auto ctypes = get_peratom("types");
auto tag = get_peratom("tags");
for (int i = 0; i < natoms; ++i) {
EXPECT_EQ(cbin1d[i], chunk1d[(int)tag[i]]);
EXPECT_EQ(cbin2d[i], chunk2d[(int)tag[i]]);
EXPECT_EQ(cbin3d[i], chunk3d[(int)tag[i]]);
EXPECT_EQ(cbinsph[i], chunksph[(int)tag[i]]);
EXPECT_EQ(cbincyl[i], chunkcyl[(int)tag[i]]);
EXPECT_EQ(cmols[i], chunkmol[(int)tag[i]]);
EXPECT_EQ(ctypes[i], chunktyp[(int)tag[i]]);
}
BEGIN_HIDE_OUTPUT();
command("uncompute bin1d");
command("compute bin1d all chunk/atom bin/1d x lower 0.2 units reduced region half");
command("uncompute bin3d");
command("compute bin3d all chunk/atom bin/3d x lower 3.0 y lower 3.0 z lower 3.0 "
"compress yes units box");
END_HIDE_OUTPUT();
EXPECT_EQ(get_scalar("bin1d"), 5);
EXPECT_EQ(get_scalar("bin3d"), 12);
cbin1d = get_peratom("bin1d");
tag = get_peratom("tags");
for (int i = 0; i < natoms; ++i) {
EXPECT_EQ(cbin1d[i], chalf1d[(int)tag[i]]);
}
// cleanup
platform::unlink("compute_chunk_atom.lammpstrj");
}
TEST_F(ComputeChunkTest, PropertyChunk)
{
if (lammps_get_natoms(lmp) == 0.0) GTEST_SKIP();
BEGIN_HIDE_OUTPUT();
command("pair_style lj/cut/coul/cut 10.0");
command("pair_coeff * * 0.01 3.0");
command("bond_style harmonic");
command("bond_coeff * 100.0 1.5");
command("uncompute bin3d");
command("compute bin3d all chunk/atom bin/3d x lower 3.0 y lower 3.0 z lower 3.0 "
"compress yes units box");
command("compute prop1 all property/chunk bin1d count");
command("compute prop2 all property/chunk bin2d count");
command("compute prop3 all property/chunk bin3d id count");
command("fix hist1 all ave/time 1 1 1 c_prop1 mode vector");
command("fix hist2 all ave/time 1 1 1 c_prop2 mode vector");
command("fix hist3 all ave/time 1 1 1 c_prop3[*] mode vector");
command("run 0 post no");
END_HIDE_OUTPUT();
auto cprop1 = get_vector("prop1");
EXPECT_EQ(cprop1[0], 0);
EXPECT_EQ(cprop1[1], 7);
EXPECT_EQ(cprop1[2], 16);
EXPECT_EQ(cprop1[3], 6);
EXPECT_EQ(cprop1[4], 0);
auto cprop2 = get_vector("prop2");
int nempty = 0;
int ncount = 0;
for (int i = 0; i < 25; ++i) {
if (cprop2[i] == 0)
++nempty;
else
ncount += cprop2[i];
}
EXPECT_EQ(nempty, 17);
EXPECT_EQ(ncount, 29);
auto cprop3 = get_array("prop3");
EXPECT_EQ(cprop3[0][0], 34);
EXPECT_EQ(cprop3[1][0], 38);
EXPECT_EQ(cprop3[2][0], 43);
EXPECT_EQ(cprop3[3][0], 58);
EXPECT_EQ(cprop3[4][0], 59);
EXPECT_EQ(cprop3[5][0], 62);
EXPECT_EQ(cprop3[6][0], 63);
EXPECT_EQ(cprop3[7][0], 67);
EXPECT_EQ(cprop3[8][0], 68);
EXPECT_EQ(cprop3[9][0], 69);
EXPECT_EQ(cprop3[10][0], 82);
EXPECT_EQ(cprop3[11][0], 88);
EXPECT_EQ(cprop3[0][1], 3);
EXPECT_EQ(cprop3[1][1], 2);
EXPECT_EQ(cprop3[2][1], 2);
EXPECT_EQ(cprop3[3][1], 2);
EXPECT_EQ(cprop3[4][1], 1);
EXPECT_EQ(cprop3[5][1], 2);
EXPECT_EQ(cprop3[6][1], 4);
EXPECT_EQ(cprop3[7][1], 3);
EXPECT_EQ(cprop3[8][1], 1);
EXPECT_EQ(cprop3[9][1], 3);
EXPECT_EQ(cprop3[10][1], 3);
EXPECT_EQ(cprop3[11][1], 3);
}
TEST_F(ComputeChunkTest, ChunkComputes)
{
if (lammps_get_natoms(lmp) == 0.0) GTEST_SKIP();
BEGIN_HIDE_OUTPUT();
command("pair_style lj/cut/coul/cut 10.0");
command("pair_coeff * * 0.01 3.0");
command("bond_style harmonic");
command("bond_coeff * 100.0 1.5");
command("compute ang all angmom/chunk mols");
command("compute com all com/chunk mols");
command("compute dip all dipole/chunk mols geometry");
command("compute gyr all gyration/chunk mols");
command("compute mom all inertia/chunk mols");
command("compute omg all omega/chunk mols");
command("compute tmp all temp/chunk mols com yes");
command("compute trq all torque/chunk mols");
command("compute vcm all vcm/chunk mols");
command("fix hist1 all ave/time 1 1 1 c_ang[*] c_com[*] c_dip[*] c_gyr c_mom[*] c_omg[*] "
"c_trq[*] c_vcm[*] mode vector");
command("fix hist2 all ave/time 1 1 1 c_tmp mode vector");
command("run 0 post no");
END_HIDE_OUTPUT();
auto cang = get_array("ang");
auto ccom = get_array("com");
auto cdip = get_array("dip");
auto cgyr = get_vector("gyr");
auto cmom = get_array("mom");
auto comg = get_array("omg");
auto ctmp = get_vector("tmp");
auto ctrq = get_array("trq");
auto cvcm = get_array("vcm");
EXPECT_NEAR(cang[0][0], -0.01906982, EPSILON);
EXPECT_NEAR(cang[0][1], -0.02814532, EPSILON);
EXPECT_NEAR(cang[0][2], -0.03357393, EPSILON);
EXPECT_NEAR(cang[5][0], 0.00767837, EPSILON);
EXPECT_NEAR(cang[5][1], -0.00303138, EPSILON);
EXPECT_NEAR(cang[5][2], 0.00740977, EPSILON);
EXPECT_NEAR(ccom[1][0], 2.27051374, EPSILON);
EXPECT_NEAR(ccom[1][1], -1.21038876, EPSILON);
EXPECT_NEAR(ccom[1][2], -0.58581655, EPSILON);
EXPECT_NEAR(ccom[5][0], -1.98284693, EPSILON);
EXPECT_NEAR(ccom[5][1], -4.17351226, EPSILON);
EXPECT_NEAR(ccom[5][2], 2.04850072, EPSILON);
EXPECT_NEAR(cmom[2][0], 4.28810281, EPSILON);
EXPECT_NEAR(cmom[2][1], 4.99562488, EPSILON);
EXPECT_NEAR(cmom[2][2], 5.34954800, EPSILON);
EXPECT_NEAR(cmom[5][0], 3.06867233, EPSILON);
EXPECT_NEAR(cmom[5][1], 5.24202887, EPSILON);
EXPECT_NEAR(cmom[5][2], 6.06478557, EPSILON);
EXPECT_NEAR(comg[3][0], -0.00349423, EPSILON);
EXPECT_NEAR(comg[3][1], -0.00025062, EPSILON);
EXPECT_NEAR(comg[3][2], -0.00323573, EPSILON);
EXPECT_NEAR(comg[5][0], 0.00437315, EPSILON);
EXPECT_NEAR(comg[5][1], 0.00029335, EPSILON);
EXPECT_NEAR(comg[5][2], 0.00268517, EPSILON);
EXPECT_NEAR(ctrq[4][0], -0.94086086, EPSILON);
EXPECT_NEAR(ctrq[4][1], 0.56227336, EPSILON);
EXPECT_NEAR(ctrq[4][2], 0.75139995, EPSILON);
EXPECT_NEAR(ctrq[5][0], -0.07066910, EPSILON);
EXPECT_NEAR(ctrq[5][1], -0.58556032, EPSILON);
EXPECT_NEAR(ctrq[5][2], -0.81513604, EPSILON);
EXPECT_NEAR(cvcm[0][0], -0.00011274, EPSILON);
EXPECT_NEAR(cvcm[0][1], 0.00071452, EPSILON);
EXPECT_NEAR(cvcm[0][2], -0.00017908, EPSILON);
EXPECT_NEAR(cvcm[5][0], -0.00063326, EPSILON);
EXPECT_NEAR(cvcm[5][1], 0.00007092, EPSILON);
EXPECT_NEAR(cvcm[5][2], 0.00045545, EPSILON);
EXPECT_NEAR(cdip[0][3], 0.35912150, EPSILON);
EXPECT_NEAR(cdip[1][3], 0.68453713, EPSILON);
EXPECT_NEAR(cdip[2][3], 0.50272643, EPSILON);
EXPECT_NEAR(cdip[3][3], 0.50845862, EPSILON);
EXPECT_NEAR(cdip[4][3], 0.49757365, EPSILON);
EXPECT_NEAR(cdip[5][3], 0.49105019, EPSILON);
EXPECT_NEAR(cgyr[0], 1.48351858, EPSILON);
EXPECT_NEAR(cgyr[1], 1.56649567, EPSILON);
EXPECT_NEAR(cgyr[2], 0.55196552, EPSILON);
EXPECT_NEAR(cgyr[3], 0.54573649, EPSILON);
EXPECT_NEAR(cgyr[4], 0.54793875, EPSILON);
EXPECT_NEAR(cgyr[5], 0.54708204, EPSILON);
EXPECT_NEAR(ctmp[0], 1.08268576, EPSILON);
EXPECT_NEAR(ctmp[1], 1.61905718, EPSILON);
EXPECT_NEAR(ctmp[2], 1.41991778, EPSILON);
EXPECT_NEAR(ctmp[3], 0.55484671, EPSILON);
EXPECT_NEAR(ctmp[4], -0.06062938, EPSILON);
EXPECT_NEAR(ctmp[5], -0.09219489, EPSILON);
}
TEST_F(ComputeChunkTest, ChunkTIP4PComputes)
{
if (lammps_get_natoms(lmp) == 0.0) GTEST_SKIP();
if (!info->has_style("compute", "dipole/tip4p/chunk")) GTEST_SKIP();
BEGIN_HIDE_OUTPUT();
command("pair_style tip4p/cut 5 2 5 1 0.15 10.0");
command("pair_coeff * *");
command("bond_coeff * 0.9572");
command("angle_coeff * 104.52");
command("compute dip all dipole/tip4p/chunk mols geometry");
command("fix hist1 all ave/time 1 1 1 c_dip[*] mode vector");
command("run 0 post no");
END_HIDE_OUTPUT();
auto cdip = get_array("dip");
EXPECT_NEAR(cdip[0][3], 0.35912150, EPSILON);
EXPECT_NEAR(cdip[1][3], 0.68453713, EPSILON);
EXPECT_NEAR(cdip[2][3], 0.50272643, EPSILON);
EXPECT_NEAR(cdip[3][3], 0.37828094, EPSILON);
EXPECT_NEAR(cdip[4][3], 0.37018279, EPSILON);
EXPECT_NEAR(cdip[5][3], 0.36532949, EPSILON);
}
TEST_F(ComputeChunkTest, ChunkSpreadGlobal)
{
if (lammps_get_natoms(lmp) == 0.0) GTEST_SKIP();
BEGIN_HIDE_OUTPUT();
command("pair_style lj/cut/coul/cut 10.0");
command("pair_coeff * * 0.01 3.0");
command("bond_style harmonic");
command("bond_coeff * 100.0 1.5");
command("compute gyr all gyration/chunk mols");
command("compute spr all chunk/spread/atom mols c_gyr");
command("compute glb all global/atom c_mols c_gyr");
command("variable odd atom ((id+1)%2)+1");
command("compute odd all global/atom v_odd c_gyr");
command("fix ave all ave/atom 1 1 1 c_spr c_glb c_odd");
command("run 0 post no");
END_HIDE_OUTPUT();
const int natoms = lammps_get_natoms(lmp);
auto cgyr = get_vector("gyr");
auto cspr = get_peratom("spr");
auto cglb = get_peratom("glb");
auto codd = get_peratom("odd");
auto ctag = get_peratom("tags");
for (int i = 0; i < natoms; ++i) {
EXPECT_EQ(cspr[i], cgyr[chunkmol[(int)ctag[i]] - 1]);
EXPECT_EQ(cglb[i], cgyr[chunkmol[(int)ctag[i]] - 1]);
EXPECT_EQ(codd[i], cgyr[(((int)ctag[i] + 1) % 2)]);
}
}
TEST_F(ComputeChunkTest, ChunkReduce)
{
if (lammps_get_natoms(lmp) == 0.0) GTEST_SKIP();
BEGIN_HIDE_OUTPUT();
command("pair_style lj/cut/coul/cut 10.0");
command("pair_coeff * * 0.01 3.0");
command("bond_style harmonic");
command("bond_coeff * 100.0 1.5");
command("compute prp all property/chunk mols count");
command("variable one atom 1");
command("compute red all reduce/chunk mols sum v_one");
command("fix ave all ave/time 1 1 1 c_prp c_red mode vector");
command("run 0 post no");
END_HIDE_OUTPUT();
const int nchunks = get_scalar("mols");
auto cprp = get_vector("prp");
auto cred = get_vector("red");
for (int i = 0; i < nchunks; ++i)
EXPECT_EQ(cprp[i], cred[i]);
}
} // namespace LAMMPS_NS
int main(int argc, char **argv)
{
MPI_Init(&argc, &argv);
::testing::InitGoogleMock(&argc, argv);
// 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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