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apply clang-format

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This commit is contained in:
Axel Kohlmeyer
2024-10-05 22:25:07 -04:00
parent 6ab0b2c249
commit 719a64d9dd
9 changed files with 93 additions and 64 deletions
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61
src/create_atoms.cpp
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@ -114,7 +114,7 @@ void CreateAtoms::command(int narg, char **arg)
xone[1] = utils::numeric(FLERR, arg[3], false, lmp);
xone[2] = utils::numeric(FLERR, arg[4], false, lmp);
if (domain->dimension == 2 && xone[2] != 0.0)
error->all(FLERR,"Create_atoms single for 2d simulation requires z coord = 0.0");
error->all(FLERR, "Create_atoms single for 2d simulation requires z coord = 0.0");
iarg = 5;
} else if (strcmp(arg[1], "random") == 0) {
style = RANDOM;
@ -184,7 +184,8 @@ void CreateAtoms::command(int narg, char **arg)
if (imol == -1)
error->all(FLERR, "Molecule template ID {} for create_atoms does not exist", arg[iarg + 1]);
if ((atom->molecules[imol]->nset > 1) && (comm->me == 0))
error->warning(FLERR, "Molecule template for create_atoms has multiple molecule sets. "
error->warning(FLERR,
"Molecule template for create_atoms has multiple molecule sets. "
"Only the first set will be used.");
mode = MOLECULE;
onemol = atom->molecules[imol];
@ -371,9 +372,9 @@ void CreateAtoms::command(int narg, char **arg)
if (scaleflag) {
if (style == SINGLE) {
xone[0] *= domain->lattice->xlattice;
xone[1] *= domain->lattice->ylattice;
xone[2] *= domain->lattice->zlattice;
xone[0] *= domain->lattice->xlattice;
xone[1] *= domain->lattice->ylattice;
xone[2] *= domain->lattice->zlattice;
} else if (style == RANDOM) {
if (overlapflag) overlap *= domain->lattice->xlattice;
} else if (style == MESH) {
@ -835,7 +836,7 @@ void CreateAtoms::add_random()
}
} else {
if (comm->me == 0) get_xmol(xone);
MPI_Bcast(&xmol[0][0], onemol->natoms*3, MPI_DOUBLE, 0, world);
MPI_Bcast(&xmol[0][0], onemol->natoms * 3, MPI_DOUBLE, 0, world);
for (int i = 0; i < nlocal; i++) {
for (int j = 0; j < onemol->natoms; j++) {
@ -1207,9 +1208,10 @@ void CreateAtoms::add_lattice()
// verify lattice was defined with triclinic/general option
if (!domain->triclinic_general && domain->lattice->is_general_triclinic())
error->all(FLERR,"Create_atoms for non general triclinic box cannot use triclinic/general lattice");
error->all(FLERR,
"Create_atoms for non general triclinic box cannot use triclinic/general lattice");
if (domain->triclinic_general && !domain->lattice->is_general_triclinic())
error->all(FLERR,"Create_atoms for general triclinic box requires triclinic/general lattice");
error->all(FLERR, "Create_atoms for general triclinic box requires triclinic/general lattice");
// convert 8 corners of my subdomain from box coords to lattice coords
// for orthogonal, use corner pts of my subbox
@ -1266,38 +1268,54 @@ void CreateAtoms::add_lattice()
domain->lattice->bbox(1, bboxlo[0], bboxhi[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax);
domain->lattice->bbox(1, bboxhi[0], bboxhi[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax);
// for general triclinic, convert 8 corner points of bbox to general triclinic coords
// new set of 8 points is no longer an orthogonal bounding box
// instead invoke lattice->bbox() on each of 8 points
// for general triclinic, convert 8 corner points of bbox to general triclinic coords
// new set of 8 points is no longer an orthogonal bounding box
// instead invoke lattice->bbox() on each of 8 points
} else if (domain->triclinic_general) {
double point[3];
point[0] = bboxlo[0]; point[1] = bboxlo[1]; point[2] = bboxlo[2];
point[0] = bboxlo[0];
point[1] = bboxlo[1];
point[2] = bboxlo[2];
domain->restricted_to_general_coords(point);
domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax);
point[0] = bboxhi[0]; point[1] = bboxlo[1]; point[2] = bboxlo[2];
point[0] = bboxhi[0];
point[1] = bboxlo[1];
point[2] = bboxlo[2];
domain->restricted_to_general_coords(point);
domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax);
point[0] = bboxlo[0]; point[1] = bboxhi[1]; point[2] = bboxlo[2];
point[0] = bboxlo[0];
point[1] = bboxhi[1];
point[2] = bboxlo[2];
domain->restricted_to_general_coords(point);
domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax);
point[0] = bboxhi[0]; point[1] = bboxhi[1]; point[2] = bboxlo[2];
point[0] = bboxhi[0];
point[1] = bboxhi[1];
point[2] = bboxlo[2];
domain->restricted_to_general_coords(point);
domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax);
point[0] = bboxlo[0]; point[1] = bboxlo[1]; point[2] = bboxhi[2];
point[0] = bboxlo[0];
point[1] = bboxlo[1];
point[2] = bboxhi[2];
domain->restricted_to_general_coords(point);
domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax);
point[0] = bboxhi[0]; point[1] = bboxlo[1]; point[2] = bboxhi[2];
point[0] = bboxhi[0];
point[1] = bboxlo[1];
point[2] = bboxhi[2];
domain->restricted_to_general_coords(point);
domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax);
point[0] = bboxlo[0]; point[1] = bboxhi[1]; point[2] = bboxhi[2];
point[0] = bboxlo[0];
point[1] = bboxhi[1];
point[2] = bboxhi[2];
domain->restricted_to_general_coords(point);
domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax);
point[0] = bboxhi[0]; point[1] = bboxhi[1]; point[2] = bboxhi[2];
point[0] = bboxhi[0];
point[1] = bboxhi[1];
point[2] = bboxhi[2];
domain->restricted_to_general_coords(point);
domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax);
}
@ -1419,7 +1437,7 @@ void CreateAtoms::loop_lattice(int action)
domain->general_to_restricted_coords(x);
if (dimension == 2) {
if (fabs(x[2]) > EPS_ZCOORD)
error->all(FLERR,"Create_atoms atom z coord is non-zero for 2d simulation");
error->all(FLERR, "Create_atoms atom z coord is non-zero for 2d simulation");
x[2] = 0.0;
}
}
@ -1510,8 +1528,7 @@ void CreateAtoms::get_xmol(double *center)
for (int m = 0; m < natoms; m++) {
MathExtra::matvec(rotmat, onemol->dx[m], xnew);
MathExtra::add3(xnew, center, xnew);
for (int i = 0; i < 3; i++)
xmol[m][i] = xnew[i];
for (int i = 0; i < 3; i++) xmol[m][i] = xnew[i];
}
}