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/compute_reduce_region.cpp

@@ -34,7 +34,7 @@ ComputeReduceRegion::ComputeReduceRegion(LAMMPS *lmp, int narg, char **arg) :
     ComputeReduce(lmp, narg, arg)
 {
   if (input_mode == LOCAL)
-    error->all(FLERR,"Compute reduce/region cannot use local data as input");
+    error->all(FLERR, "Compute reduce/region cannot use local data as input");
 }
 
 /* ----------------------------------------------------------------------
@@ -150,7 +150,7 @@ double ComputeReduceRegion::compute_one(int m, int flag)
         one = fix_array[flag][aidxm1];
     }
 
-  // evaluate atom-style variable
+    // evaluate atom-style variable
 
   } else if (val.which == ArgInfo::VARIABLE) {
     if (atom->nmax > maxatom) {

src/create_atoms.cpp

@@ -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[0] *= domain->lattice->xlattice;
-    xone[1] *= domain->lattice->ylattice;
+      xone[1] *= domain->lattice->ylattice;
-    xone[2] *= domain->lattice->zlattice;
+      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
+    // 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
+    // new set of 8 points is no longer an orthogonal bounding box
-  // instead invoke lattice->bbox() on each of 8 points
+    // 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++)
+    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();
   }
 
@@ -77,9 +79,9 @@ void CreateBox::command(int narg, char **arg)
       domain->boxlo[2] = region->extent_zlo;
       domain->boxhi[2] = region->extent_zhi;
 
-    // region is prism
+      // region is prism
-    // seutp restricted triclinic box
+      // seutp restricted triclinic box
-    // set simulation domain from prism params
+      // set simulation domain from prism params
 
     } else {
       domain->triclinic = 1;
@@ -97,17 +99,17 @@ void CreateBox::command(int narg, char **arg)
 
     if (domain->dimension == 2) {
       if (domain->boxlo[2] >= 0.0 || domain->boxhi[2] <= 0.0)
-        error->all(FLERR,"Create_box region zlo/zhi for 2d simulation must straddle 0.0");
+        error->all(FLERR, "Create_box region zlo/zhi for 2d simulation must straddle 0.0");
     }
 
-  // setup general triclinic box (with no region)
+    // setup general triclinic box (with no region)
-  // read next box extent arguments to create ABC edge vectors + origin
+    // read next box extent arguments to create ABC edge vectors + origin
-  // define_general_triclinic() converts
+    // define_general_triclinic() converts
-  //   ABC edge vectors + origin to restricted triclinic
+    //   ABC edge vectors + origin to restricted triclinic
 
   } else if (triclinic_general) {
     if (!domain->lattice->is_general_triclinic())
-      error->all(FLERR,"Create_box for general triclinic requires triclnic/general lattice");
+      error->all(FLERR, "Create_box for general triclinic requires triclnic/general lattice");
 
     if (iarg + 6 > narg) utils::missing_cmd_args(FLERR, "create_box general triclinic", error);
 
@@ -121,42 +123,50 @@ void CreateBox::command(int narg, char **arg)
 
     if (domain->dimension == 2)
       if (clo != -0.5 || chi != 0.5)
-        error->all(FLERR,"Create_box for general triclinic requires clo = -0.5 and chi = 0.5");
+        error->all(FLERR, "Create_box for general triclinic requires clo = -0.5 and chi = 0.5");
 
     // use lattice2box() to generate origin and ABC vectors
     // origin = abc lo
     // ABC vectors = hi in one dim - origin
 
-    double avec[3],bvec[3],cvec[3],origin[3];
+    double avec[3], bvec[3], cvec[3], origin[3];
-    double px,py,pz;
+    double px, py, pz;
 
-    px = alo; py = blo; pz = clo;
+    px = alo;
-    domain->lattice->lattice2box(px,py,pz);
+    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;
-    domain->lattice->lattice2box(px,py,pz);
+    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;
-    domain->lattice->lattice2box(px,py,pz);
+    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;
-    domain->lattice->lattice2box(px,py,pz);
+    py = blo;
+    pz = chi;
+    domain->lattice->lattice2box(px, py, pz);
     cvec[0] = px - origin[0];
     cvec[1] = py - origin[1];
     cvec[2] = pz - origin[2];
 
     // define general triclinic box within Domain class
 
-    domain->define_general_triclinic(avec,bvec,cvec,origin);
+    domain->define_general_triclinic(avec, bvec, cvec, origin);
   }
 
   // if molecular, zero out topology info

src/delete_atoms.cpp

@@ -777,9 +777,9 @@ void DeleteAtoms::bondring(int nbuf, char *cbuf, void *ptr)
           bond_type[i][m] = bond_type[i][n - 1];
           bond_atom[i][m] = bond_atom[i][n - 1];
           if (n_histories > 0)
-            for (auto &ihistory: histories) {
+            for (auto &ihistory : histories) {
-              dynamic_cast<FixBondHistory *>(ihistory)->shift_history(i,m,n-1);
+              dynamic_cast<FixBondHistory *>(ihistory)->shift_history(i, m, n - 1);
-              dynamic_cast<FixBondHistory *>(ihistory)->delete_history(i,n-1);
+              dynamic_cast<FixBondHistory *>(ihistory)->delete_history(i, n - 1);
             }
           n--;
         } else

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

@@ -182,7 +182,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
   // optional args
 
   while (iarg < narg) {
-    if (strcmp(arg[iarg], "ghost") == 0) { // skip here, since handled earlier
+    if (strcmp(arg[iarg], "ghost") == 0) {    // skip here, since handled earlier
       iarg += 2;
     } else if (strcmp(arg[iarg], "writedata") == 0) {
       if (iarg + 2 > narg) error->all(FLERR, "Illegal fix property/atom command");
@@ -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);
   }
 }
-