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modernize and reformat with clang-tidy and clang-format

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This commit is contained in:
Axel Kohlmeyer
2024-07-04 11:17:54 -04:00
parent cefe76919c
commit da2bd44b73
55 changed files with 980 additions and 971 deletions
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206
unittest/formats/test_atom_styles.cpp
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@ -553,8 +553,8 @@ TEST_F(AtomStyleTest, atomic)
ASSERT_EQ(lmp->atom->molecular, Atom::ATOMIC);
ASSERT_EQ(lmp->atom->ntypes, 2);
auto x = lmp->atom->x;
auto v = lmp->atom->v;
auto *x = lmp->atom->x;
auto *v = lmp->atom->v;
EXPECT_NEAR(x[GETIDX(1)][0], -2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][1], 2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][2], 0.1, EPSILON);
@ -642,7 +642,7 @@ TEST_F(AtomStyleTest, atomic)
command("replicate 2 2 2");
END_HIDE_OUTPUT();
ASSERT_EQ(lmp->atom->map_tag_max, 16);
x = lmp->atom->x;
x = lmp->atom->x;
EXPECT_NEAR(x[GETIDX(1)][0], -2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][1], 2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][2], 0.1, EPSILON);
@ -870,9 +870,9 @@ TEST_F(AtomStyleTest, charge)
ASSERT_EQ(lmp->atom->map_user, 1);
ASSERT_EQ(lmp->atom->map_tag_max, 4);
auto x = lmp->atom->x;
auto v = lmp->atom->v;
auto q = lmp->atom->q;
auto *x = lmp->atom->x;
auto *v = lmp->atom->v;
auto *q = lmp->atom->q;
EXPECT_NEAR(x[GETIDX(1)][0], -2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][1], 2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][2], 0.1, EPSILON);
@ -1056,10 +1056,10 @@ TEST_F(AtomStyleTest, sphere)
ASSERT_EQ(lmp->atom->map_user, 1);
ASSERT_EQ(lmp->atom->map_tag_max, 4);
auto x = lmp->atom->x;
auto v = lmp->atom->v;
auto rmass = lmp->atom->rmass;
auto omega = lmp->atom->omega;
auto *x = lmp->atom->x;
auto *v = lmp->atom->v;
auto *rmass = lmp->atom->rmass;
auto *omega = lmp->atom->omega;
EXPECT_NEAR(x[GETIDX(1)][0], -2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][1], 2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][2], 0.1, EPSILON);
@ -1243,13 +1243,13 @@ TEST_F(AtomStyleTest, ellipsoid)
ASSERT_EQ(lmp->atom->map_user, 1);
ASSERT_EQ(lmp->atom->map_tag_max, 6);
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 = dynamic_cast<AtomVecEllipsoid *>(lmp->atom->avec);
auto bonus = avec->bonus;
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 = dynamic_cast<AtomVecEllipsoid *>(lmp->atom->avec);
auto *bonus = avec->bonus;
EXPECT_NEAR(x[GETIDX(1)][0], -2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][1], 2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][2], 0.1, EPSILON);
@ -1571,13 +1571,13 @@ TEST_F(AtomStyleTest, line)
ASSERT_EQ(lmp->atom->map_user, 1);
ASSERT_EQ(lmp->atom->map_tag_max, 6);
auto x = lmp->atom->x;
auto v = lmp->atom->v;
auto type = lmp->atom->type;
auto line = lmp->atom->line;
auto rmass = lmp->atom->rmass;
auto avec = dynamic_cast<AtomVecLine *>(lmp->atom->avec);
auto bonus = avec->bonus;
auto *x = lmp->atom->x;
auto *v = lmp->atom->v;
auto *type = lmp->atom->type;
auto *line = lmp->atom->line;
auto *rmass = lmp->atom->rmass;
auto *avec = dynamic_cast<AtomVecLine *>(lmp->atom->avec);
auto *bonus = avec->bonus;
EXPECT_NEAR(x[GETIDX(1)][0], -2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][1], 2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][2], 0.0, EPSILON);
@ -1853,14 +1853,14 @@ TEST_F(AtomStyleTest, tri)
ASSERT_EQ(lmp->atom->map_user, 1);
ASSERT_EQ(lmp->atom->map_tag_max, 6);
auto x = lmp->atom->x;
auto v = lmp->atom->v;
auto type = lmp->atom->type;
auto tri = lmp->atom->tri;
auto rmass = lmp->atom->rmass;
auto radius = lmp->atom->radius;
auto avec = dynamic_cast<AtomVecTri *>(lmp->atom->avec);
auto bonus = avec->bonus;
auto *x = lmp->atom->x;
auto *v = lmp->atom->v;
auto *type = lmp->atom->type;
auto *tri = lmp->atom->tri;
auto *rmass = lmp->atom->rmass;
auto *radius = lmp->atom->radius;
auto *avec = dynamic_cast<AtomVecTri *>(lmp->atom->avec);
auto *bonus = avec->bonus;
EXPECT_NEAR(x[GETIDX(1)][0], -2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][1], 2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][2], 0.1, EPSILON);
@ -2180,7 +2180,7 @@ TEST_F(AtomStyleTest, body_nparticle)
ASSERT_ATOM_STATE_EQ(lmp->atom, expected);
auto avec = dynamic_cast<AtomVecBody *>(lmp->atom->avec);
auto *avec = dynamic_cast<AtomVecBody *>(lmp->atom->avec);
ASSERT_NE(lmp->atom->avec, nullptr);
ASSERT_NE(avec->bptr, nullptr);
ASSERT_THAT(std::string(avec->bptr->style), Eq("nparticle"));
@ -2265,14 +2265,14 @@ TEST_F(AtomStyleTest, body_nparticle)
ASSERT_NE(lmp->atom->radius, nullptr);
ASSERT_EQ(lmp->atom->mass_setflag, nullptr);
auto x = lmp->atom->x;
auto v = lmp->atom->v;
auto type = lmp->atom->type;
auto body = lmp->atom->body;
auto rmass = lmp->atom->rmass;
auto radius = lmp->atom->radius;
auto angmom = lmp->atom->angmom;
auto bonus = avec->bonus;
auto *x = lmp->atom->x;
auto *v = lmp->atom->v;
auto *type = lmp->atom->type;
auto *body = lmp->atom->body;
auto *rmass = lmp->atom->rmass;
auto *radius = lmp->atom->radius;
auto *angmom = lmp->atom->angmom;
auto *bonus = avec->bonus;
EXPECT_NEAR(x[GETIDX(1)][0], -2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][1], 2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][2], 0.1, EPSILON);
@ -2832,9 +2832,9 @@ TEST_F(AtomStyleTest, template)
ASSERT_EQ(lmp->atom->map_user, 1);
ASSERT_EQ(lmp->atom->map_tag_max, 12);
auto molecule = lmp->atom->molecule;
auto molindex = lmp->atom->molindex;
auto molatom = lmp->atom->molatom;
auto *molecule = lmp->atom->molecule;
auto *molindex = lmp->atom->molindex;
auto *molatom = lmp->atom->molatom;
ASSERT_EQ(molecule[GETIDX(1)], 1);
ASSERT_EQ(molecule[GETIDX(2)], 1);
@ -2933,9 +2933,9 @@ TEST_F(AtomStyleTest, template)
ASSERT_EQ(molatom[GETIDX(11)], -1);
ASSERT_EQ(molatom[GETIDX(12)], -1);
auto x = lmp->atom->x;
auto v = lmp->atom->v;
auto type = lmp->atom->type;
auto *x = lmp->atom->x;
auto *v = lmp->atom->v;
auto *type = lmp->atom->type;
EXPECT_NEAR(x[GETIDX(10)][0], 2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(10)][1], -2.0, EPSILON);
@ -3147,7 +3147,7 @@ TEST_F(AtomStyleTest, template_charge)
ASSERT_ATOM_STATE_EQ(lmp->atom, expected);
auto hybrid = dynamic_cast<AtomVecHybrid *>(lmp->atom->avec);
auto *hybrid = dynamic_cast<AtomVecHybrid *>(lmp->atom->avec);
ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid"));
ASSERT_EQ(hybrid->nstyles, 2);
ASSERT_THAT(std::string(hybrid->keywords[0]), Eq("template"));
@ -3247,9 +3247,9 @@ TEST_F(AtomStyleTest, template_charge)
ASSERT_EQ(lmp->atom->map_user, 1);
ASSERT_EQ(lmp->atom->map_tag_max, 12);
auto molecule = lmp->atom->molecule;
auto molindex = lmp->atom->molindex;
auto molatom = lmp->atom->molatom;
auto *molecule = lmp->atom->molecule;
auto *molindex = lmp->atom->molindex;
auto *molatom = lmp->atom->molatom;
ASSERT_EQ(molecule[GETIDX(1)], 1);
ASSERT_EQ(molecule[GETIDX(2)], 1);
@ -3348,10 +3348,10 @@ TEST_F(AtomStyleTest, template_charge)
ASSERT_EQ(molatom[GETIDX(11)], -1);
ASSERT_EQ(molatom[GETIDX(12)], -1);
auto x = lmp->atom->x;
auto v = lmp->atom->v;
auto type = lmp->atom->type;
auto q = lmp->atom->q;
auto *x = lmp->atom->x;
auto *v = lmp->atom->v;
auto *type = lmp->atom->type;
auto *q = lmp->atom->q;
EXPECT_NEAR(x[GETIDX(10)][0], 2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(10)][1], -2.0, EPSILON);
@ -3655,9 +3655,9 @@ TEST_F(AtomStyleTest, bond)
ASSERT_EQ(lmp->atom->map_user, 1);
ASSERT_EQ(lmp->atom->map_tag_max, 6);
auto num_bond = lmp->atom->num_bond;
auto bond_type = lmp->atom->bond_type;
auto bond_atom = lmp->atom->bond_atom;
auto *num_bond = lmp->atom->num_bond;
auto *bond_type = lmp->atom->bond_type;
auto *bond_atom = lmp->atom->bond_atom;
ASSERT_EQ(num_bond[GETIDX(1)], 2);
ASSERT_EQ(num_bond[GETIDX(2)], 0);
@ -3714,12 +3714,12 @@ TEST_F(AtomStyleTest, bond)
ASSERT_EQ(lmp->atom->map_user, 1);
ASSERT_EQ(lmp->atom->map_tag_max, 6);
auto x = lmp->atom->x;
auto v = lmp->atom->v;
auto type = lmp->atom->type;
num_bond = lmp->atom->num_bond;
bond_type = lmp->atom->bond_type;
bond_atom = lmp->atom->bond_atom;
auto *x = lmp->atom->x;
auto *v = lmp->atom->v;
auto *type = lmp->atom->type;
num_bond = lmp->atom->num_bond;
bond_type = lmp->atom->bond_type;
bond_atom = lmp->atom->bond_atom;
EXPECT_NEAR(x[GETIDX(1)][0], -2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][1], 2.0, EPSILON);
@ -4013,14 +4013,14 @@ TEST_F(AtomStyleTest, angle)
ASSERT_EQ(lmp->atom->map_user, 1);
ASSERT_EQ(lmp->atom->map_tag_max, 6);
auto num_bond = lmp->atom->num_bond;
auto bond_type = lmp->atom->bond_type;
auto bond_atom = lmp->atom->bond_atom;
auto num_angle = lmp->atom->num_angle;
auto angle_type = lmp->atom->angle_type;
auto angle_atom1 = lmp->atom->angle_atom1;
auto angle_atom2 = lmp->atom->angle_atom2;
auto angle_atom3 = lmp->atom->angle_atom3;
auto *num_bond = lmp->atom->num_bond;
auto *bond_type = lmp->atom->bond_type;
auto *bond_atom = lmp->atom->bond_atom;
auto *num_angle = lmp->atom->num_angle;
auto *angle_type = lmp->atom->angle_type;
auto *angle_atom1 = lmp->atom->angle_atom1;
auto *angle_atom2 = lmp->atom->angle_atom2;
auto *angle_atom3 = lmp->atom->angle_atom3;
ASSERT_EQ(num_bond[GETIDX(1)], 2);
ASSERT_EQ(num_bond[GETIDX(2)], 0);
@ -4107,9 +4107,9 @@ TEST_F(AtomStyleTest, angle)
ASSERT_EQ(lmp->atom->map_user, 1);
ASSERT_EQ(lmp->atom->map_tag_max, 6);
auto x = lmp->atom->x;
auto v = lmp->atom->v;
auto type = lmp->atom->type;
auto *x = lmp->atom->x;
auto *v = lmp->atom->v;
auto *type = lmp->atom->type;
num_bond = lmp->atom->num_bond;
bond_atom = lmp->atom->bond_atom;
num_angle = lmp->atom->num_angle;
@ -4288,7 +4288,7 @@ TEST_F(AtomStyleTest, full_ellipsoid)
ASSERT_ATOM_STATE_EQ(lmp->atom, expected);
auto hybrid = dynamic_cast<AtomVecHybrid *>(lmp->atom->avec);
auto *hybrid = dynamic_cast<AtomVecHybrid *>(lmp->atom->avec);
ASSERT_THAT(std::string(lmp->atom->atom_style), Eq("hybrid"));
ASSERT_EQ(hybrid->nstyles, 2);
ASSERT_THAT(std::string(hybrid->keywords[0]), Eq("full"));
@ -4398,15 +4398,15 @@ TEST_F(AtomStyleTest, full_ellipsoid)
ASSERT_EQ(lmp->atom->map_user, 1);
ASSERT_EQ(lmp->atom->map_tag_max, 6);
auto x = lmp->atom->x;
auto v = lmp->atom->v;
auto q = lmp->atom->q;
auto type = lmp->atom->type;
auto ellipsoid = lmp->atom->ellipsoid;
auto rmass = lmp->atom->rmass;
auto *x = lmp->atom->x;
auto *v = lmp->atom->v;
auto *q = lmp->atom->q;
auto *type = lmp->atom->type;
auto *ellipsoid = lmp->atom->ellipsoid;
auto *rmass = lmp->atom->rmass;
auto avec = dynamic_cast<AtomVecEllipsoid *>(hybrid->styles[1]);
auto bonus = avec->bonus;
auto *avec = dynamic_cast<AtomVecEllipsoid *>(hybrid->styles[1]);
auto *bonus = avec->bonus;
EXPECT_NEAR(x[GETIDX(1)][0], -2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][1], 2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][2], 0.1, EPSILON);
@ -4768,9 +4768,9 @@ TEST_F(AtomStyleTest, property_atom)
ASSERT_EQ(lmp->atom->map_user, Atom::MAP_ARRAY);
ASSERT_EQ(lmp->atom->map_tag_max, 4);
auto x = lmp->atom->x;
auto v = lmp->atom->v;
auto q = lmp->atom->q;
auto *x = lmp->atom->x;
auto *v = lmp->atom->v;
auto *q = lmp->atom->q;
EXPECT_NEAR(x[GETIDX(1)][0], -2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][1], 2.0, EPSILON);
EXPECT_NEAR(x[GETIDX(1)][2], 0.1, EPSILON);
@ -4805,10 +4805,10 @@ TEST_F(AtomStyleTest, property_atom)
ASSERT_EQ(lmp->atom->mass_setflag[1], 1);
ASSERT_EQ(lmp->atom->mass_setflag[2], 1);
auto rmass = lmp->atom->rmass;
auto one = lmp->atom->ivector[0];
auto two = lmp->atom->dvector[0];
auto three = lmp->atom->dvector[1];
auto *rmass = lmp->atom->rmass;
auto *one = lmp->atom->ivector[0];
auto *two = lmp->atom->dvector[0];
auto *three = lmp->atom->dvector[1];
EXPECT_NEAR(rmass[GETIDX(1)], 4.0, EPSILON);
EXPECT_NEAR(rmass[GETIDX(2)], 4.0, EPSILON);
@ -4939,7 +4939,7 @@ TEST_F(AtomStyleTest, oxdna)
ASSERT_ATOM_STATE_EQ(lmp->atom, expected);
auto hybrid = dynamic_cast<AtomVecHybrid *>(lmp->atom->avec);
auto *hybrid = dynamic_cast<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"));
@ -5152,14 +5152,14 @@ TEST_F(AtomStyleTest, oxdna)
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 *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 = dynamic_cast<AtomVecEllipsoid *>(hybrid->styles[1]);
auto bonus = avec->bonus;
auto *avec = dynamic_cast<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);
@ -5328,10 +5328,10 @@ TEST_F(AtomStyleTest, oxdna)
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;
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);