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Added unit test for atom_style oxdna

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This commit is contained in:
Oliver Henrich
2022-01-26 19:20:34 +00:00
parent 1f81e2afad
commit 9b6bb00d07
1 changed files with 444 additions and 0 deletions
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444
unittest/formats/test_atom_styles.cpp
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@ -4809,6 +4809,450 @@ TEST_F(AtomStyleTest, property_atom)
EXPECT_NEAR(three[GETIDX(2)], 0.5, EPSILON);
}
TEST_F(AtomStyleTest, oxdna)
{
if (!LAMMPS::is_installed_pkg("MOLECULE")) GTEST_SKIP();
if (!LAMMPS::is_installed_pkg("ASPHERE")) GTEST_SKIP();
if (!LAMMPS::is_installed_pkg("CG-DNA")) GTEST_SKIP();
BEGIN_HIDE_OUTPUT();
command("atom_style hybrid bond ellipsoid oxdna");
END_HIDE_OUTPUT();
AtomState expected;
expected.atom_style = "hybrid";
expected.molecular = Atom::MOLECULAR;
expected.tag_enable = 1;
expected.molecule_flag = 1;
expected.ellipsoid_flag = 1;
expected.rmass_flag = 1;
expected.torque_flag = 1;
expected.angmom_flag = 1;
expected.has_type = true;
expected.has_mask = true;
expected.has_image = true;
expected.has_x = true;
expected.has_v = true;
expected.has_f = true;
expected.has_bonds = true;
expected.has_nspecial = true;
expected.has_special = true;
expected.map_style = 3;
ASSERT_ATOM_STATE_EQ(lmp->atom, expected);
auto hybrid = (AtomVecHybrid *)lmp->atom->avec;
ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid"));
ASSERT_EQ(hybrid->nstyles, 3);
ASSERT_THAT(std::string(hybrid->keywords[0]), Eq("bond"));
ASSERT_THAT(std::string(hybrid->keywords[1]), Eq("ellipsoid"));
ASSERT_THAT(std::string(hybrid->keywords[2]), Eq("oxdna"));
ASSERT_NE(hybrid->styles[0], nullptr);
ASSERT_NE(hybrid->styles[1], nullptr);
ASSERT_NE(hybrid->styles[2], nullptr);
BEGIN_HIDE_OUTPUT();
command("units lj");
command("dimension 3");
command("newton on");
command("boundary p p p");
command("atom_modify sort 0 1.0");
command("neighbor 2.0 bin");
command("neigh_modify every 1 delay 0 check yes");
command("region mybox block -20 20 -20 20 -20 20");
command("create_box 4 mybox bond/types 1 extra/bond/per/atom 2 extra/special/per/atom 4");
command("create_atoms 1 single -0.33741452300167507 -0.43708835412476305 0.6450685042019271");
command("create_atoms 2 single -0.32142606102826937 -0.7137743037592722 1.1817366147004618");
command("create_atoms 3 single -0.130363628207774 -0.9147144801536078 1.62581312195109");
command("create_atoms 4 single 0.16795127962282844 -0.9808507459807022 2.0894908590909003");
command("create_atoms 1 single 0.46370423490634166 -0.7803347954883079 2.4251986815515827");
command("create_atoms 4 single -0.4462950185476711 0.09062163051035639 2.4668941268777607");
command("create_atoms 1 single -0.03377054097560965 0.20979847489755046 2.078208732038921");
command("create_atoms 2 single 0.3297325391466579 0.17657587120899895 1.7206328374934152");
command("create_atoms 3 single 0.6063699309305985 0.04682595158675571 1.2335049647817748");
command("create_atoms 4 single 0.8003979559814726 -0.364393011459011 0.9884025318908612");
command("set type 1 mass 3.1575");
command("set type 2 mass 3.1575");
command("set type 3 mass 3.1575");
command("set type 4 mass 3.1575");
command("mass 1 3.1575");
command("mass 2 3.1575");
command("mass 3 3.1575");
command("mass 4 3.1575");
command("set atom 1 shape 1.173984503142341 1.173984503142341 1.173984503142341");
command("set atom 2 shape 1.173984503142341 1.173984503142341 1.173984503142341");
command("set atom 3 shape 1.173984503142341 1.173984503142341 1.173984503142341");
command("set atom 4 shape 1.173984503142341 1.173984503142341 1.173984503142341");
command("set atom 5 shape 1.173984503142341 1.173984503142341 1.173984503142341");
command("set atom 6 shape 1.173984503142341 1.173984503142341 1.173984503142341");
command("set atom 7 shape 1.173984503142341 1.173984503142341 1.173984503142341");
command("set atom 8 shape 1.173984503142341 1.173984503142341 1.173984503142341");
command("set atom 9 shape 1.173984503142341 1.173984503142341 1.173984503142341");
command("set atom 10 shape 1.173984503142341 1.173984503142341 1.173984503142341");
command("set atom 1 quat 0.120438343611269 -0.970540441176996 0.208676441957758 16.990727782866998");
command("set atom 2 quat 0.122039415796829 -0.068232256412985 0.990177125658213 40.001729435287870");
command("set atom 3 quat 0.052760168698289 0.030943512185297 0.998127679033382 69.627682451632380");
command("set atom 4 quat -0.037622918613871 0.030623545471522 0.998822664169035 97.038820280300570");
command("set atom 5 quat 0.055056042946138 0.077631917807377 0.995460756369964 137.7813218321917");
command("set atom 6 quat 0.931128471673637 -0.355724722922553 -0.080372201291206 166.2836226291888");
command("set atom 7 quat 0.753526078198930 -0.648440397941919 0.108275111595674 200.6802564250672");
command("set atom 8 quat 0.553942138074214 -0.829580511279186 0.070315595507185 192.0355407659524");
command("set atom 9 quat -0.373540155765431 0.913070802138105 -0.163613759548524 171.0789308260751");
command("set atom 10 quat 0.027515673832457 0.998248649922676 -0.052369080773879 161.2621224558284");
command("bond_style oxdna2/fene");
command("bond_coeff * 2.0 0.25 0.7564");
command("special_bonds lj 0 1 1");
command("create_bonds single/bond 1 1 2");
command("create_bonds single/bond 1 2 3");
command("create_bonds single/bond 1 3 4");
command("create_bonds single/bond 1 4 5");
command("create_bonds single/bond 1 6 7");
command("create_bonds single/bond 1 7 8");
command("create_bonds single/bond 1 8 9");
command("create_bonds single/bond 1 9 10");
command("pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh");
command("pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32");
command("pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65");
command("pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45");
command("pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45");
command("pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45");
command("pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68");
command("pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793");
command("pair_coeff * * oxdna2/dh 0.1 0.2 0.815");
END_HIDE_OUTPUT();
ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid"));
ASSERT_NE(lmp->atom->avec, nullptr);
ASSERT_EQ(lmp->atom->natoms, 10);
ASSERT_EQ(lmp->atom->nbonds, 8);
ASSERT_EQ(lmp->atom->nbondtypes, 1);
ASSERT_EQ(lmp->atom->nellipsoids, 10);
ASSERT_EQ(lmp->atom->nlocal, 10);
ASSERT_EQ(lmp->atom->nghost, 0);
ASSERT_NE(lmp->atom->nmax, -1);
ASSERT_EQ(lmp->atom->tag_enable, 1);
ASSERT_EQ(lmp->atom->molecular, Atom::MOLECULAR);
ASSERT_EQ(lmp->atom->ntypes, 4);
ASSERT_EQ(lmp->atom->nextra_grow, 0);
ASSERT_EQ(lmp->atom->nextra_restart, 0);
ASSERT_EQ(lmp->atom->nextra_border, 0);
ASSERT_EQ(lmp->atom->nextra_grow_max, 0);
ASSERT_EQ(lmp->atom->nextra_restart_max, 0);
ASSERT_EQ(lmp->atom->nextra_border_max, 0);
ASSERT_EQ(lmp->atom->nextra_store, 0);
ASSERT_EQ(lmp->atom->extra_grow, nullptr);
ASSERT_EQ(lmp->atom->extra_restart, nullptr);
ASSERT_EQ(lmp->atom->extra_border, nullptr);
ASSERT_EQ(lmp->atom->extra, nullptr);
ASSERT_NE(lmp->atom->mass, nullptr);
ASSERT_NE(lmp->atom->rmass, nullptr);
ASSERT_EQ(lmp->atom->ellipsoid_flag, 1);
ASSERT_NE(lmp->atom->ellipsoid, nullptr);
ASSERT_NE(lmp->atom->mass_setflag, nullptr);
ASSERT_NE(lmp->atom->id5p, nullptr);
BEGIN_HIDE_OUTPUT();
command("write_data test_atom_styles.data nocoeff");
command("clear");
command("units lj");
command("dimension 3");
command("newton on");
command("boundary p p p");
command("atom_style hybrid bond ellipsoid oxdna");
command("atom_modify sort 0 1.0");
command("neighbor 2.0 bin");
command("neigh_modify every 1 delay 0 check yes");
command("read_data test_atom_styles.data");
command("set type 1 mass 3.1575");
command("set type 2 mass 3.1575");
command("set type 3 mass 3.1575");
command("set type 4 mass 3.1575");
command("mass 1 3.1575");
command("mass 2 3.1575");
command("mass 3 3.1575");
command("mass 4 3.1575");
command("bond_style oxdna2/fene");
command("bond_coeff * 2.0 0.25 0.7564");
command("special_bonds lj 0 1 1");
command("pair_style hybrid/overlay oxdna2/excv oxdna2/stk oxdna2/hbond oxdna2/xstk oxdna2/coaxstk oxdna2/dh");
command("pair_coeff * * oxdna2/excv 2.0 0.7 0.675 2.0 0.515 0.5 2.0 0.33 0.32");
command("pair_coeff * * oxdna2/stk seqdep 0.1 1.3523 2.6717 6.0 0.4 0.9 0.32 0.75 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 2.0 0.65 2.0 0.65");
command("pair_coeff * * oxdna2/hbond seqdep 0.0 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45");
command("pair_coeff 1 4 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45");
command("pair_coeff 2 3 oxdna2/hbond seqdep 1.0678 8.0 0.4 0.75 0.34 0.7 1.5 0 0.7 1.5 0 0.7 1.5 0 0.7 0.46 3.141592653589793 0.7 4.0 1.5707963267948966 0.45 4.0 1.5707963267948966 0.45");
command("pair_coeff * * oxdna2/xstk 47.5 0.575 0.675 0.495 0.655 2.25 0.791592653589793 0.58 1.7 1.0 0.68 1.7 1.0 0.68 1.5 0 0.65 1.7 0.875 0.68 1.7 0.875 0.68");
command("pair_coeff * * oxdna2/coaxstk 58.5 0.4 0.6 0.22 0.58 2.0 2.891592653589793 0.65 1.3 0 0.8 0.9 0 0.95 0.9 0 0.95 40.0 3.116592653589793");
command("pair_coeff * * oxdna2/dh 0.1 0.2 0.815");
ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid"));
ASSERT_NE(lmp->atom->avec, nullptr);
hybrid = (AtomVecHybrid *)lmp->atom->avec;
ASSERT_EQ(hybrid->nstyles, 3);
ASSERT_THAT(std::string(hybrid->keywords[0]), Eq("bond"));
ASSERT_THAT(std::string(hybrid->keywords[1]), Eq("ellipsoid"));
ASSERT_THAT(std::string(hybrid->keywords[2]), Eq("oxdna"));
ASSERT_NE(hybrid->styles[0], nullptr);
ASSERT_NE(hybrid->styles[1], nullptr);
ASSERT_NE(hybrid->styles[2], nullptr);
ASSERT_EQ(lmp->atom->natoms, 10);
ASSERT_EQ(lmp->atom->nbonds, 8);
ASSERT_EQ(lmp->atom->nbondtypes, 1);
ASSERT_EQ(lmp->atom->nellipsoids, 10);
ASSERT_EQ(lmp->atom->nlocal, 10);
ASSERT_EQ(lmp->atom->nghost, 0);
ASSERT_NE(lmp->atom->nmax, -1);
ASSERT_EQ(lmp->atom->tag_enable, 1);
ASSERT_EQ(lmp->atom->molecular, Atom::MOLECULAR);
ASSERT_EQ(lmp->atom->ntypes, 4);
ASSERT_EQ(lmp->atom->nextra_grow, 0);
ASSERT_EQ(lmp->atom->nextra_restart, 0);
ASSERT_EQ(lmp->atom->nextra_border, 0);
ASSERT_EQ(lmp->atom->nextra_grow_max, 0);
ASSERT_EQ(lmp->atom->nextra_restart_max, 0);
ASSERT_EQ(lmp->atom->nextra_border_max, 0);
ASSERT_EQ(lmp->atom->nextra_store, 0);
ASSERT_EQ(lmp->atom->extra_grow, nullptr);
ASSERT_EQ(lmp->atom->extra_restart, nullptr);
ASSERT_EQ(lmp->atom->extra_border, nullptr);
ASSERT_EQ(lmp->atom->extra, nullptr);
ASSERT_NE(lmp->atom->mass, nullptr);
ASSERT_NE(lmp->atom->rmass, nullptr);
ASSERT_EQ(lmp->atom->ellipsoid_flag, 1);
ASSERT_NE(lmp->atom->ellipsoid, nullptr);
ASSERT_NE(lmp->atom->mass_setflag, nullptr);
ASSERT_NE(lmp->atom->id5p, nullptr);
auto x = lmp->atom->x;
auto v = lmp->atom->v;
auto type = lmp->atom->type;
auto ellipsoid = lmp->atom->ellipsoid;
auto rmass = lmp->atom->rmass;
auto avec = (AtomVecEllipsoid *)hybrid->styles[1];
auto bonus = avec->bonus;
EXPECT_NEAR(x[GETIDX(1)][0], -0.33741452300167507, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][1], -0.43708835412476305, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][2], 0.6450685042019271, EPSILON);
EXPECT_NEAR(x[GETIDX(2)][0], -0.32142606102826937, EPSILON);
EXPECT_NEAR(x[GETIDX(2)][1], -0.7137743037592722, EPSILON);
EXPECT_NEAR(x[GETIDX(2)][2], 1.1817366147004618, EPSILON);
EXPECT_NEAR(x[GETIDX(3)][0], -0.130363628207774, EPSILON);
EXPECT_NEAR(x[GETIDX(3)][1], -0.9147144801536078, EPSILON);
EXPECT_NEAR(x[GETIDX(3)][2], 1.62581312195109, EPSILON);
EXPECT_NEAR(x[GETIDX(4)][0], 0.16795127962282844, EPSILON);
EXPECT_NEAR(x[GETIDX(4)][1], -0.9808507459807022, EPSILON);
EXPECT_NEAR(x[GETIDX(4)][2], 2.0894908590909003, EPSILON);
EXPECT_NEAR(x[GETIDX(5)][0], 0.46370423490634166, EPSILON);
EXPECT_NEAR(x[GETIDX(5)][1], -0.7803347954883079, EPSILON);
EXPECT_NEAR(x[GETIDX(5)][2], 2.4251986815515827, EPSILON);
EXPECT_NEAR(x[GETIDX(6)][0], -0.4462950185476711, EPSILON);
EXPECT_NEAR(x[GETIDX(6)][1], 0.09062163051035639, EPSILON);
EXPECT_NEAR(x[GETIDX(6)][2], 2.4668941268777607, EPSILON);
EXPECT_NEAR(x[GETIDX(7)][0], -0.03377054097560965, EPSILON);
EXPECT_NEAR(x[GETIDX(7)][1], 0.20979847489755046, EPSILON);
EXPECT_NEAR(x[GETIDX(7)][2], 2.078208732038921, EPSILON);
EXPECT_NEAR(x[GETIDX(8)][0], 0.3297325391466579, EPSILON);
EXPECT_NEAR(x[GETIDX(8)][1], 0.17657587120899895, EPSILON);
EXPECT_NEAR(x[GETIDX(8)][2], 1.7206328374934152, EPSILON);
EXPECT_NEAR(x[GETIDX(9)][0], 0.6063699309305985, EPSILON);
EXPECT_NEAR(x[GETIDX(9)][1], 0.04682595158675571, EPSILON);
EXPECT_NEAR(x[GETIDX(9)][2], 1.2335049647817748, EPSILON);
EXPECT_NEAR(x[GETIDX(10)][0], 0.8003979559814726, EPSILON);
EXPECT_NEAR(x[GETIDX(10)][1], -0.364393011459011, EPSILON);
EXPECT_NEAR(x[GETIDX(10)][2], 0.9884025318908612, EPSILON);
EXPECT_NEAR(v[GETIDX(1)][0], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(1)][1], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(1)][2], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(2)][0], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(2)][1], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(2)][2], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(3)][0], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(3)][1], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(3)][2], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(4)][0], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(4)][1], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(4)][2], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(5)][0], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(5)][1], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(5)][2], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(6)][0], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(6)][1], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(6)][2], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(7)][0], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(7)][1], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(7)][2], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(8)][0], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(8)][1], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(8)][2], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(9)][0], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(9)][1], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(9)][2], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(10)][0], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(10)][1], 0.0, EPSILON);
EXPECT_NEAR(v[GETIDX(10)][2], 0.0, EPSILON);
ASSERT_EQ(type[GETIDX(1)], 1);
ASSERT_EQ(type[GETIDX(2)], 2);
ASSERT_EQ(type[GETIDX(3)], 3);
ASSERT_EQ(type[GETIDX(4)], 4);
ASSERT_EQ(type[GETIDX(5)], 1);
ASSERT_EQ(type[GETIDX(6)], 4);
ASSERT_EQ(type[GETIDX(7)], 1);
ASSERT_EQ(type[GETIDX(8)], 2);
ASSERT_EQ(type[GETIDX(9)], 3);
ASSERT_EQ(type[GETIDX(10)], 4);
ASSERT_EQ(ellipsoid[GETIDX(1)], 0);
ASSERT_EQ(ellipsoid[GETIDX(2)], 1);
ASSERT_EQ(ellipsoid[GETIDX(3)], 2);
ASSERT_EQ(ellipsoid[GETIDX(4)], 3);
ASSERT_EQ(ellipsoid[GETIDX(5)], 4);
ASSERT_EQ(ellipsoid[GETIDX(6)], 5);
ASSERT_EQ(ellipsoid[GETIDX(7)], 6);
ASSERT_EQ(ellipsoid[GETIDX(8)], 7);
ASSERT_EQ(ellipsoid[GETIDX(9)], 8);
ASSERT_EQ(ellipsoid[GETIDX(10)], 9);
EXPECT_NEAR(rmass[GETIDX(1)], 3.1575, EPSILON);
EXPECT_NEAR(rmass[GETIDX(2)], 3.1575, EPSILON);
EXPECT_NEAR(rmass[GETIDX(3)], 3.1575, EPSILON);
EXPECT_NEAR(rmass[GETIDX(4)], 3.1575, EPSILON);
EXPECT_NEAR(rmass[GETIDX(5)], 3.1575, EPSILON);
EXPECT_NEAR(rmass[GETIDX(6)], 3.1575, EPSILON);
EXPECT_NEAR(rmass[GETIDX(7)], 3.1575, EPSILON);
EXPECT_NEAR(rmass[GETIDX(8)], 3.1575, EPSILON);
EXPECT_NEAR(rmass[GETIDX(9)], 3.1575, EPSILON);
EXPECT_NEAR(rmass[GETIDX(10)], 3.1575, EPSILON);
EXPECT_NEAR(bonus[0].shape[0], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[0].shape[1], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[0].shape[2], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[1].shape[0], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[1].shape[1], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[1].shape[2], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[2].shape[0], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[2].shape[1], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[2].shape[2], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[3].shape[0], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[3].shape[1], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[3].shape[2], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[4].shape[0], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[4].shape[1], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[4].shape[2], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[5].shape[0], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[5].shape[1], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[5].shape[2], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[6].shape[0], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[6].shape[1], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[6].shape[2], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[7].shape[0], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[7].shape[1], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[7].shape[2], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[8].shape[0], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[8].shape[1], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[8].shape[2], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[9].shape[0], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[9].shape[1], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[9].shape[2], 0.5869922515711705, EPSILON);
EXPECT_NEAR(bonus[0].quat[0], 0.9890278201757743, EPSILON);
EXPECT_NEAR(bonus[0].quat[1], 0.01779228232037064, EPSILON);
EXPECT_NEAR(bonus[0].quat[2], -0.14337734159225404, EPSILON);
EXPECT_NEAR(bonus[0].quat[3], 0.030827642240801516, EPSILON);
EXPECT_NEAR(bonus[1].quat[0], 0.939687458852748, EPSILON);
EXPECT_NEAR(bonus[1].quat[1], 0.04174166924055095, EPSILON);
EXPECT_NEAR(bonus[1].quat[2], -0.023337773785056866, EPSILON);
EXPECT_NEAR(bonus[1].quat[3], 0.338674565089608, EPSILON);
EXPECT_NEAR(bonus[2].quat[0], 0.8210113150655425, EPSILON);
EXPECT_NEAR(bonus[2].quat[1], 0.03012140921736572, EPSILON);
EXPECT_NEAR(bonus[2].quat[2], 0.017666019956944813, EPSILON);
EXPECT_NEAR(bonus[2].quat[3], 0.5698429897612057, EPSILON);
EXPECT_NEAR(bonus[3].quat[0], 0.6623662858285051, EPSILON);
EXPECT_NEAR(bonus[3].quat[1], -0.028186343967346823, EPSILON);
EXPECT_NEAR(bonus[3].quat[2], 0.022942552517501488, EPSILON);
EXPECT_NEAR(bonus[3].quat[3], 0.7482981175276918, EPSILON);
EXPECT_NEAR(bonus[4].quat[0], 0.3601488726765216, EPSILON);
EXPECT_NEAR(bonus[4].quat[1], 0.0513614985821682, EPSILON);
EXPECT_NEAR(bonus[4].quat[2], 0.0724224158335286, EPSILON);
EXPECT_NEAR(bonus[4].quat[3], 0.9286602067807472, EPSILON);
EXPECT_NEAR(bonus[5].quat[0], 0.11941234710084649, EPSILON);
EXPECT_NEAR(bonus[5].quat[1], 0.9244660117493703, EPSILON);
EXPECT_NEAR(bonus[5].quat[2], -0.35317942248051865, EPSILON);
EXPECT_NEAR(bonus[5].quat[3], -0.07979711784524246, EPSILON);
EXPECT_NEAR(bonus[6].quat[0], -0.17949125421205164, EPSILON);
EXPECT_NEAR(bonus[6].quat[1], 0.7412884899431119, EPSILON);
EXPECT_NEAR(bonus[6].quat[2], -0.6379094464220707, EPSILON);
EXPECT_NEAR(bonus[6].quat[3], 0.1065166771202199, EPSILON);
EXPECT_NEAR(bonus[7].quat[0], -0.10483691088405202, EPSILON);
EXPECT_NEAR(bonus[7].quat[1], 0.5508895999584645, EPSILON);
EXPECT_NEAR(bonus[7].quat[2], -0.8250090480220789, EPSILON);
EXPECT_NEAR(bonus[7].quat[3], 0.06992811634525403, EPSILON);
EXPECT_NEAR(bonus[8].quat[0], 0.07777239911646, EPSILON);
EXPECT_NEAR(bonus[8].quat[1], -0.3724087549185288, EPSILON);
EXPECT_NEAR(bonus[8].quat[2], 0.9103052384821374, EPSILON);
EXPECT_NEAR(bonus[8].quat[3], -0.1631181963720798, EPSILON);
EXPECT_NEAR(bonus[9].quat[0], 0.16279109707978262, EPSILON);
EXPECT_NEAR(bonus[9].quat[1], 0.027148630125149613, EPSILON);
EXPECT_NEAR(bonus[9].quat[2], 0.9849325709665359, EPSILON);
EXPECT_NEAR(bonus[9].quat[3], -0.0516705065113425, EPSILON);
auto num_bond = lmp->atom->num_bond;
auto bond_type = lmp->atom->bond_type;
auto bond_atom = lmp->atom->bond_atom;
auto id5p = lmp->atom->id5p;
ASSERT_EQ(num_bond[GETIDX(1)], 1);
ASSERT_EQ(num_bond[GETIDX(2)], 1);
ASSERT_EQ(num_bond[GETIDX(3)], 1);
ASSERT_EQ(num_bond[GETIDX(4)], 1);
ASSERT_EQ(num_bond[GETIDX(5)], 0);
ASSERT_EQ(num_bond[GETIDX(6)], 1);
ASSERT_EQ(num_bond[GETIDX(7)], 1);
ASSERT_EQ(num_bond[GETIDX(8)], 1);
ASSERT_EQ(num_bond[GETIDX(9)], 1);
ASSERT_EQ(num_bond[GETIDX(10)], 0);
ASSERT_EQ(bond_type[GETIDX(1)][0], 1);
ASSERT_EQ(bond_type[GETIDX(2)][0], 1);
ASSERT_EQ(bond_type[GETIDX(3)][0], 1);
ASSERT_EQ(bond_type[GETIDX(4)][0], 1);
ASSERT_EQ(bond_type[GETIDX(5)][0], 0);
ASSERT_EQ(bond_type[GETIDX(6)][0], 1);
ASSERT_EQ(bond_type[GETIDX(7)][0], 1);
ASSERT_EQ(bond_type[GETIDX(8)][0], 1);
ASSERT_EQ(bond_type[GETIDX(9)][0], 1);
ASSERT_EQ(bond_type[GETIDX(10)][0], 0);
ASSERT_EQ(bond_atom[GETIDX(1)][0], 2);
ASSERT_EQ(bond_atom[GETIDX(2)][0], 3);
ASSERT_EQ(bond_atom[GETIDX(3)][0], 4);
ASSERT_EQ(bond_atom[GETIDX(4)][0], 5);
ASSERT_EQ(bond_atom[GETIDX(5)][0], 0);
ASSERT_EQ(bond_atom[GETIDX(6)][0], 7);
ASSERT_EQ(bond_atom[GETIDX(7)][0], 8);
ASSERT_EQ(bond_atom[GETIDX(8)][0], 9);
ASSERT_EQ(bond_atom[GETIDX(9)][0], 10);
ASSERT_EQ(bond_atom[GETIDX(10)][0], 0);
ASSERT_EQ(id5p[GETIDX(1)], 2);
ASSERT_EQ(id5p[GETIDX(2)], 3);
ASSERT_EQ(id5p[GETIDX(3)], 4);
ASSERT_EQ(id5p[GETIDX(4)], 5);
ASSERT_EQ(id5p[GETIDX(5)], -1);
ASSERT_EQ(id5p[GETIDX(6)], 7);
ASSERT_EQ(id5p[GETIDX(7)], 8);
ASSERT_EQ(id5p[GETIDX(8)], 9);
ASSERT_EQ(id5p[GETIDX(9)], 10);
ASSERT_EQ(id5p[GETIDX(10)], -1);
END_HIDE_OUTPUT();
}
} // namespace LAMMPS_NS
int main(int argc, char **argv)