apply clang-format

src/bond_hybrid.cpp

@@ -96,8 +96,7 @@ void BondHybrid::compute(int eflag, int vflag)
       bondlist[m][n][0] = bondlist_orig[i][0];
       bondlist[m][n][1] = bondlist_orig[i][1];
       bondlist[m][n][2] = bondlist_orig[i][2];
-      if (partial_flag)
+      if (partial_flag) orig_map[m][n] = i;
-        orig_map[m][n] = i;
       nbondlist[m]++;
     }
   }
@@ -381,8 +380,10 @@ void BondHybrid::init_style()
   // bond style quartic will set broken bonds to bond type 0, so we need
   // to create an entry for it in the bond type to sub-style map
 
-  if (has_quartic >= 0) map[0] = has_quartic;
+  if (has_quartic >= 0)
-  else map[0] = -1;
+    map[0] = has_quartic;
+  else
+    map[0] = -1;
 }
 
 /* ---------------------------------------------------------------------- */

src/compute_msd_chunk.cpp

@@ -124,7 +124,8 @@ void ComputeMSDChunk::compute_array()
   // first time call, allocate per-chunk arrays
   // thereafter, require nchunk remain the same
 
-  if (firstflag) msdnchunk = nchunk;
+  if (firstflag)
+    msdnchunk = nchunk;
   else if (msdnchunk != nchunk)
     error->all(FLERR, "Compute msd/chunk nchunk is not static");
 

src/create_atoms.cpp

@@ -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];
@@ -1207,7 +1208,8 @@ 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");
 
@@ -1273,31 +1275,47 @@ void CreateAtoms::add_lattice()
   } 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);
   }
@@ -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++)
+    for (int i = 0; i < 3; i++) xmol[m][i] = xnew[i];
-      xmol[m][i] = xnew[i];
   }
 }
 

src/create_box.cpp

@@ -49,11 +49,13 @@ void CreateBox::command(int narg, char **arg)
   Region *region = nullptr;
   int triclinic_general = 0;
 
-  if (strcmp(arg[1],"NULL") == 0) triclinic_general = 1;
+  if (strcmp(arg[1], "NULL") == 0)
+    triclinic_general = 1;
   else {
     region = domain->get_region_by_id(arg[1]);
     if (!region) error->all(FLERR, "Create_box region {} does not exist", arg[1]);
-    if (region->bboxflag == 0) error->all(FLERR, "Create_box region does not support a bounding box");
+    if (region->bboxflag == 0)
+      error->all(FLERR, "Create_box region does not support a bounding box");
     region->init();
   }
 
@@ -130,25 +132,33 @@ void CreateBox::command(int narg, char **arg)
     double avec[3], bvec[3], cvec[3], origin[3];
     double px, py, pz;
 
-    px = alo; py = blo; pz = clo;
+    px = alo;
+    py = blo;
+    pz = clo;
     domain->lattice->lattice2box(px, py, pz);
     origin[0] = px;
     origin[1] = py;
     origin[2] = pz;
 
-    px = ahi; py = blo; pz = clo;
+    px = ahi;
+    py = blo;
+    pz = clo;
     domain->lattice->lattice2box(px, py, pz);
     avec[0] = px - origin[0];
     avec[1] = py - origin[1];
     avec[2] = pz - origin[2];
 
-    px = alo; py = bhi; pz = clo;
+    px = alo;
+    py = bhi;
+    pz = clo;
     domain->lattice->lattice2box(px, py, pz);
     bvec[0] = px - origin[0];
     bvec[1] = py - origin[1];
     bvec[2] = pz - origin[2];
 
-    px = alo; py = blo; pz = chi;
+    px = alo;
+    py = blo;
+    pz = chi;
     domain->lattice->lattice2box(px, py, pz);
     cvec[0] = px - origin[0];
     cvec[1] = py - origin[1];

src/dihedral_write.cpp

@@ -149,8 +149,7 @@ void DihedralWrite::command(int narg, char **arg)
     FILE *coeffs;
     char line[MAXLINE] = {'\0'};
     coeffs = fopen(coeffs_file.c_str(), "r");
-    if (!coeffs)
+    if (!coeffs) error->one(FLERR, "Unable to open temporary file {}: {}", utils::getsyserror());
-      error->one(FLERR, "Unable to open temporary file {}: {}", utils::getsyserror());
     for (int i = 0; i < atom->ndihedraltypes; ++i) {
       utils::sfgets(FLERR, line, MAXLINE, coeffs, coeffs_file.c_str(), error);
       writer->input->one(fmt::format("dihedral_coeff {}", line));

src/fix_property_atom.cpp

@@ -200,9 +200,12 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
     int flag = 0;
     for (int i = 0; i < nvalue; i++)
       if (styles[i] == MOLECULE || styles[i] == CHARGE || styles[i] == RMASS ||
-      styles[i] == TEMPERATURE || styles[i] == HEATFLOW) flag = 1;
+          styles[i] == TEMPERATURE || styles[i] == HEATFLOW)
+        flag = 1;
     if (flag && comm->me == 0)
-      error->warning(FLERR, "Fix property/atom mol, charge, rmass, temperature, or heatflow w/out ghost communication");
+      error->warning(FLERR,
+                     "Fix property/atom mol, charge, rmass, temperature, or heatflow w/out ghost "
+                     "communication");
   }
 
   // store current atom style
@@ -216,7 +219,6 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
   if (border) atom->add_callback(Atom::BORDER);
 }
 
-
 /* ---------------------------------------------------------------------- */
 
 void FixPropertyAtom::post_constructor()

src/region_plane.cpp

@@ -24,8 +24,8 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-RegPlane::RegPlane(LAMMPS *lmp, int narg, char **arg) : Region(lmp, narg, arg),
+RegPlane::RegPlane(LAMMPS *lmp, int narg, char **arg) :
-    xstr(nullptr), ystr(nullptr), zstr(nullptr)
+    Region(lmp, narg, arg), xstr(nullptr), ystr(nullptr), zstr(nullptr)
 {
   xvar = yvar = zvar = 0.0;
 
@@ -203,4 +203,3 @@ void RegPlane::variable_check()
       error->all(FLERR, "Variable {} for region plane is invalid style", zstr);
   }
 }
-