whitespace fixes

doc/src/Howto_body.rst

@@ -416,7 +416,7 @@ by circles of diameter 0.5, is specified as follows:
 .. parsed-literal::
 
    1 3 13
-   2 1 1 
+   2 1 1
    0 1.33333 1.33333 0 0 0
    -2 0 0
    2 0 0

doc/src/compute_mliap.rst

@@ -57,7 +57,7 @@ The compute *mliap* command must be followed by two keywords
 *model* and *descriptor* in either order.
 
 The *model* keyword is followed by a model style, currently limited to
-either *linear* or *quadratic*. 
+either *linear* or *quadratic*.
 
 The *descriptor* keyword is followed by a descriptor style, and additional arguments.
 Currently the only descriptor style is *sna*, indicating the bispectrum component

doc/src/dihedral_quadratic.rst

@@ -45,7 +45,7 @@ commands:
 :math:`\phi_0` is specified in degrees, but LAMMPS converts it to
 radians internally; hence :math:`K` is effectively energy per
 radian\^2.
-  
+
 ----------
 
 Styles with a *gpu*\ , *intel*\ , *kk*\ , *omp*\ , or *opt* suffix are

src/KIM/kim_interactions.cpp

@@ -302,40 +302,40 @@ void KimInteractions::KIM_SET_TYPE_PARAMETERS(char const *const input_line) cons
 
     if(nocomment) {
       if (strcmp(key,"pair") == 0) {
-	species1 = strtok(ptr," \t");
+        species1 = strtok(ptr," \t");
-	species2 = strtok(NULL," \t");
+        species2 = strtok(NULL," \t");
-	the_rest = strtok(NULL,"\n");
+        the_rest = strtok(NULL,"\n");
 
-	for (int type_a = 0; type_a < atom->ntypes; ++type_a) {
+        for (int type_a = 0; type_a < atom->ntypes; ++type_a) {
-	  for (int type_b = type_a; type_b < atom->ntypes; ++type_b) {
+          for (int type_b = type_a; type_b < atom->ntypes; ++type_b) {
-	    if(((strcmp(species[type_a],species1) == 0) &&
+            if(((strcmp(species[type_a],species1) == 0) &&
-		(strcmp(species[type_b],species2) == 0))
+                (strcmp(species[type_b],species2) == 0))
-	       ||
+               ||
-	       ((strcmp(species[type_b],species1) == 0) &&
+               ((strcmp(species[type_b],species1) == 0) &&
-		(strcmp(species[type_a],species2) == 0))
+                (strcmp(species[type_a],species2) == 0))
-	       ) {
+               ) {
-	      char pair_command[MAXLINE];
+              char pair_command[MAXLINE];
-	      sprintf(pair_command,"pair_coeff %i %i %s",type_a+1,type_b+1,
+              sprintf(pair_command,"pair_coeff %i %i %s",type_a+1,type_b+1,
-		      the_rest);
+                      the_rest);
-	      input->one(pair_command);
+              input->one(pair_command);
-	    }
+            }
-	  }
+          }
-	}
+        }
       }
       else if (strcmp(key,"charge") == 0) {
-	species1 = strtok(ptr," \t");
+        species1 = strtok(ptr," \t");
-	the_rest = strtok(NULL,"\n");
+        the_rest = strtok(NULL,"\n");
 
-	for (int type_a = 0; type_a < atom->ntypes; ++type_a) {
+        for (int type_a = 0; type_a < atom->ntypes; ++type_a) {
-	  if(strcmp(species[type_a],species1) == 0) {
+          if(strcmp(species[type_a],species1) == 0) {
-	    char pair_command[MAXLINE];
+            char pair_command[MAXLINE];
-	    sprintf(pair_command,"set type %i charge %s",type_a+1,the_rest);
+            sprintf(pair_command,"set type %i charge %s",type_a+1,the_rest);
-	    input->one(pair_command);
+            input->one(pair_command);
-	  }
+          }
-	}
+        }
       }
       else{
-	error->one(FLERR,"Unrecognized KEY for KIM_SET_TYPE_PARAMETERS command");
+        error->one(FLERR,"Unrecognized KEY for KIM_SET_TYPE_PARAMETERS command");
       }
     }
   }

src/MC/fix_bond_create.cpp

@@ -129,7 +129,7 @@ FixBondCreate::FixBondCreate(LAMMPS *lmp, int narg, char **arg) :
       iarg += 2;
     } else if (strcmp(arg[iarg],"aconstrain") == 0 &&
         strcmp(style,"bond/create/angle") == 0) {
-      if (iarg+3 > narg) 
+      if (iarg+3 > narg)
           error->all(FLERR,"Illegal fix bond/create/angle command");
       amin = force->numeric(FLERR,arg[iarg+1]);
       amax = force->inumeric(FLERR,arg[iarg+2]);
@@ -470,7 +470,7 @@ void FixBondCreate::post_integrate()
         partner[j] = tag[i];
         distsq[j] = rsq;
       }
-  
+
     }
   }
 

src/MC/fix_bond_create_angle.cpp

@@ -54,16 +54,16 @@ int FixBondCreateAngle::constrain(int i, int j, double amin, double amax)
   int flag = 0;
 
   // pass if both atoms have no neighbors: bond is always formed
-  
+
   if (nspecial[i][0] == 0 && nspecial[j][0] == 0) flag = 1;
 
   // pass if i has at least one neighbor and angle constraint is met
-  
+
   if (nspecial[i][0] != 0 && nspecial[j][0] == 0) {
 
     // calculate first vector between i and j
     // calculate second vector between i and its first neighbor
-    
+
     v1x = x[i][0] - x[j][0];
     v1y = x[i][1] - x[j][1];
     v1z = x[i][2] - x[j][2];
@@ -73,19 +73,19 @@ int FixBondCreateAngle::constrain(int i, int j, double amin, double amax)
 
     // calculate angle between both vectors
     // set flag if the angle constraint is met
-    
+
     angle1 = acos((v1x*v2x + v1y*v2y + v1z*v2z)/
         (sqrt(v1x*v1x + v1y*v1y + v1z*v1z)*sqrt(v2x*v2x + v2y*v2y + v2z*v2z)));
     if (amin <= angle1 && angle1 <= amax) flag = 1;
   }
 
   // pass if j has at least one neighbor and angle constraint is met
-  
+
   if (nspecial[j][0] != 0 && nspecial[i][0] == 0) {
 
     // calculate first vector between j and i
     // calculate second vector between j and its first neighbor
-    
+
     v1x = x[j][0] - x[i][0];
     v1y = x[j][1] - x[i][1];
     v1z = x[j][2] - x[i][2];
@@ -108,7 +108,7 @@ int FixBondCreateAngle::constrain(int i, int j, double amin, double amax)
     // Calculate 1st angle
     // calculate first vector between i and j
     // calculate second vector between i and its first neighbor
-    
+
     v1x = x[i][0] - x[j][0];
     v1y = x[i][1] - x[j][1];
     v1z = x[i][2] - x[j][2];
@@ -117,7 +117,7 @@ int FixBondCreateAngle::constrain(int i, int j, double amin, double amax)
     v2z = x[i][2] - x[atom->map(special[i][0])][2];
 
     // calculate angle between both vectors
-    
+
     angle1 = acos((v1x*v2x + v1y*v2y + v1z*v2z) /
         (sqrt(v1x*v1x + v1y*v1y + v1z*v1z)*sqrt(v2x*v2x + v2y*v2y + v2z*v2z)));
 

src/MLIAP/compute_mliap.cpp

@@ -35,7 +35,7 @@ using namespace LAMMPS_NS;
 enum{SCALAR,VECTOR,ARRAY};
 
 ComputeMLIAP::ComputeMLIAP(LAMMPS *lmp, int narg, char **arg) :
-  Compute(lmp, narg, arg), mliaparray(NULL), 
+  Compute(lmp, narg, arg), mliaparray(NULL),
   mliaparrayall(NULL), map(NULL)
 {
   array_flag = 1;
@@ -79,7 +79,7 @@ ComputeMLIAP::ComputeMLIAP(LAMMPS *lmp, int narg, char **arg) :
     } else if (strcmp(arg[iarg],"gradgradflag") == 0) {
       if (iarg+1 > narg) error->all(FLERR,"Illegal compute mliap command");
       gradgradflag = atoi(arg[iarg+1]);
-      if (gradgradflag != 0 && gradgradflag != 1) 
+      if (gradgradflag != 0 && gradgradflag != 1)
         error->all(FLERR,"Illegal compute mliap command");
       iarg += 2;
     } else
@@ -215,29 +215,29 @@ void ComputeMLIAP::compute_array()
   neighbor->build_one(list);
 
   data->generate_neighdata(list);
-    
+
   // compute descriptors
-  
+
   descriptor->compute_descriptors(data);
-    
+
   if (gradgradflag == 1) {
 
     // calculate double gradient w.r.t. parameters and descriptors
-    
+
     model->compute_gradgrads(data);
-    
+
     // calculate gradients of forces w.r.t. parameters
-    
+
     descriptor->compute_force_gradients(data);
-    
+
   } else if (gradgradflag == 0) {
 
     // calculate descriptor gradients
-    
+
     descriptor->compute_descriptor_gradients(data);
 
     // calculate gradients of forces w.r.t. parameters
-    
+
     model->compute_force_gradients(data);
 
   } else error->all(FLERR,"Invalid value for gradgradflag");

src/MLIAP/compute_mliap.h

@@ -40,7 +40,7 @@ class ComputeMLIAP : public Compute {
   double **mliaparray, **mliaparrayall;
   class NeighList *list;
   int *map;  // map types to [0,nelements)
-  int ndescriptors;            // number of descriptors 
+  int ndescriptors;            // number of descriptors
   int nparams;                 // number of model parameters per element
   int nelements;
   int gradgradflag;           // 1 for graddesc, 0 for gamma

src/MLIAP/mliap_data.cpp

@@ -33,14 +33,14 @@
 using namespace LAMMPS_NS;
 
 MLIAPData::MLIAPData(LAMMPS *lmp,
-                     int gradgradflag_in, int *map_in, class MLIAPModel* model_in, 
+                     int gradgradflag_in, int *map_in, class MLIAPModel* model_in,
                      class MLIAPDescriptor* descriptor_in, class PairMLIAP* pairmliap_in) :
   Pointers(lmp),
-  list(NULL), 
+  list(NULL),
-  gradforce(NULL), 
+  gradforce(NULL),
   betas(NULL), descriptors(NULL), gamma_row_index(NULL), gamma_col_index(NULL),
   gamma(NULL), egradient(NULL), model(NULL), descriptor(NULL),
-  iatoms(NULL), ielems(NULL), numneighs(NULL),  
+  iatoms(NULL), ielems(NULL), numneighs(NULL),
   jatoms(NULL), jelems(NULL), rij(NULL), graddesc(NULL)
 {
   gradgradflag = gradgradflag_in;
@@ -108,10 +108,10 @@ void MLIAPData::generate_neighdata(NeighList* list_in, int eflag_in, int vflag_i
   list = list_in;
   double **x = atom->x;
   int *type = atom->type;
-  
+
   int *numneigh = list->numneigh;
   int **firstneigh = list->firstneigh;
-  
+
   // grow nmax gradforce array if necessary
 
   if (atom->nmax > nmax) {
@@ -121,15 +121,15 @@ void MLIAPData::generate_neighdata(NeighList* list_in, int eflag_in, int vflag_i
  }
 
   // clear gradforce array
-  
+
   int ntotal = atom->nlocal + atom->nghost;
   for (int i = 0; i < ntotal; i++)
     for (int j = 0; j < size_gradforce; j++) {
       gradforce[i][j] = 0.0;
     }
-  
+
   // grow gamma arrays if necessary
-  
+
   if (gradgradflag == 1) {
     const int natomgamma = list->inum;
     if (natomgamma_max < natomgamma) {
@@ -150,20 +150,20 @@ void MLIAPData::generate_neighdata(NeighList* list_in, int eflag_in, int vflag_i
   }
 
   grow_neigharrays();
-  
+
   int ij = 0;
   for (int ii = 0; ii < list->inum; ii++) {
     const int i = list->ilist[ii];
-    
+
     const double xtmp = x[i][0];
     const double ytmp = x[i][1];
     const double ztmp = x[i][2];
     const int itype = type[i];
     const int ielem = map[itype];
-    
+
     int *jlist = firstneigh[i];
     const int jnum = numneigh[i];
-    
+
     int ninside = 0;
     for (int jj = 0; jj < jnum; jj++) {
       int j = jlist[jj];
@@ -174,7 +174,7 @@ void MLIAPData::generate_neighdata(NeighList* list_in, int eflag_in, int vflag_i
       const double rsq = delx*delx + dely*dely + delz*delz;
       int jtype = type[j];
       const int jelem = map[jtype];
-      
+
       if (rsq < descriptor->cutsq[ielem][jelem]) {
         jatoms[ij] = j;
         jelems[ij] = jelem;
@@ -202,7 +202,7 @@ void MLIAPData::grow_neigharrays()
 {
 
   // grow neighbor atom arrays if necessary
-    
+
   const int natomneigh = list->inum;
   if (natomneigh_max < natomneigh) {
     memory->grow(iatoms,natomneigh,"MLIAPData:iatoms");
@@ -215,7 +215,7 @@ void MLIAPData::grow_neigharrays()
 
   int *numneigh = list->numneigh;
   int **firstneigh = list->firstneigh;
-  
+
   int iilast = list->inum-1;
   int ilast = list->ilist[iilast];
   int upperbound = firstneigh[ilast] - firstneigh[0] + numneigh[ilast];
@@ -223,20 +223,20 @@ void MLIAPData::grow_neigharrays()
 
   double **x = atom->x;
   int *type = atom->type;
-  
+
   int nneigh = 0;
   for (int ii = 0; ii < list->inum; ii++) {
     const int i = list->ilist[ii];
-    
+
     const double xtmp = x[i][0];
     const double ytmp = x[i][1];
     const double ztmp = x[i][2];
     const int itype = type[i];
     const int ielem = map[itype];
-    
+
     int *jlist = firstneigh[i];
     const int jnum = numneigh[i];
-    
+
     int ninside = 0;
     for (int jj = 0; jj < jnum; jj++) {
       int j = jlist[jj];
@@ -251,7 +251,7 @@ void MLIAPData::grow_neigharrays()
     }
     nneigh += ninside;
   }
-  
+
   if (nneigh_max < nneigh) {
     memory->grow(jatoms,nneigh,"MLIAPData:jatoms");
     memory->grow(jelems,nneigh,"MLIAPData:jelems");
@@ -284,14 +284,14 @@ double MLIAPData::memory_usage()
   bytes += natomneigh_max*sizeof(int);               // iatoms
   bytes += natomneigh_max*sizeof(int);               // ielems
   bytes += natomneigh_max*sizeof(int);               // numneighs
-  
+
   bytes += nneigh_max*sizeof(int);                   // jatoms
   bytes += nneigh_max*sizeof(int);                   // jelems
   bytes += nneigh_max*3*sizeof(double);              // rij"
-  
+
   if (gradgradflag == 0)
     bytes += nneigh_max*ndescriptors*3*sizeof(double);// graddesc
-      
+
   return bytes;
 }
 

src/MLIAP/mliap_data.h

@@ -36,17 +36,17 @@ class MLIAPData : protected Pointers {
   double **gradforce;
   double** betas;               // betas for all atoms in list
   double** descriptors;        // descriptors for all atoms in list
-  int ndescriptors;            // number of descriptors 
+  int ndescriptors;            // number of descriptors
   int nparams;                 // number of model parameters per element
   int nelements;               // number of elements
-        
+
   // data structures for grad-grad list (gamma)
 
   int natomgamma_max;          // allocated size of gamma
   int gamma_nnz;               // number of non-zero entries in gamma
   double** gamma;              // gamma element
-  int** gamma_row_index;       // row (parameter) index 
+  int** gamma_row_index;       // row (parameter) index
-  int** gamma_col_index;       // column (descriptor) index 
+  int** gamma_col_index;       // column (descriptor) index
   double* egradient;           // energy gradient w.r.t. parameters
 
   // data structures for mliap neighbor list

src/MLIAP/mliap_model_linear.cpp

@@ -50,7 +50,7 @@ int MLIAPModelLinear::get_nparams()
    ---------------------------------------------------------------------- */
 
 void MLIAPModelLinear::compute_gradients(MLIAPData* data)
-{  
+{
   for (int ii = 0; ii < data->natoms; ii++) {
     const int i = data->iatoms[ii];
     const int ielem = data->ielems[ii];
@@ -129,14 +129,14 @@ void MLIAPModelLinear::compute_gradgrads(class MLIAPData* data)
    egradient is derivative of energy w.r.t. parameters
    ---------------------------------------------------------------------- */
 
-void MLIAPModelLinear::compute_force_gradients(class MLIAPData* data) 
+void MLIAPModelLinear::compute_force_gradients(class MLIAPData* data)
 {
 
   // zero out energy gradients
 
   for (int l = 0; l < data->nelements*data->nparams; l++)
     data->egradient[l] = 0.0;
-    
+
   int ij = 0;
   for (int ii = 0; ii < data->natoms; ii++) {
     const int i = data->iatoms[ii];
@@ -161,14 +161,14 @@ void MLIAPModelLinear::compute_force_gradients(class MLIAPData* data)
     }
 
     // gradient of energy of atom I w.r.t. parameters
-    
+
     int l = elemoffset;
     data->egradient[l++] += 1.0;
     for (int icoeff = 0; icoeff < data->ndescriptors; icoeff++)
       data->egradient[l++] += data->descriptors[ii][icoeff];
-    
+
   }
-  
+
 }
 
 /* ----------------------------------------------------------------------

src/MLIAP/mliap_model_quadratic.cpp

@@ -207,7 +207,7 @@ void MLIAPModelQuadratic::compute_force_gradients(class MLIAPData* data) {
 
   for (int l = 0; l < data->nelements*data->nparams; l++)
     data->egradient[l] = 0.0;
-    
+
   int ij = 0;
   for (int ii = 0; ii < data->natoms; ii++) {
     const int i = data->iatoms[ii];
@@ -256,14 +256,14 @@ void MLIAPModelQuadratic::compute_force_gradients(class MLIAPData* data) {
     }
 
     // gradient of energy of atom I w.r.t. parameters
-    
+
     int l = elemoffset;
     data->egradient[l++] += 1.0;
     for (int icoeff = 0; icoeff < data->ndescriptors; icoeff++)
       data->egradient[l++] += data->descriptors[ii][icoeff];
-    
+
     // quadratic contributions
-    
+
     for (int icoeff = 0; icoeff < data->ndescriptors; icoeff++) {
       double bveci = data->descriptors[ii][icoeff];
       data->egradient[l++] += 0.5*bveci*bveci;
@@ -274,5 +274,5 @@ void MLIAPModelQuadratic::compute_force_gradients(class MLIAPData* data) {
     }
 
   }
-  
+
 }

src/MLIAP/pair_mliap.cpp

@@ -66,9 +66,9 @@ PairMLIAP::~PairMLIAP()
 void PairMLIAP::compute(int eflag, int vflag)
 {
   ev_init(eflag,vflag);
-    
+
   data->generate_neighdata(list, eflag, vflag);
-    
+
   // compute descriptors, if needed
 
   if (model->nonlinearflag || eflag)

src/USER-MISC/fix_npt_cauchy.cpp

@@ -2770,10 +2770,10 @@ void FixNPTCauchy::CauchyStat_Step(double (&Fi)[3][3], double (&Fdot)[3][3],
       n=uv(jj,2);
       dsds(ii,jj) = Fi(i,m)*Fi(j,n) + Fi(i,n)*Fi(j,m) + Fi(j,m)*Fi(i,n) + Fi(j,n)*Fi(i,m);
       for(int l = 1;l <= 3;l++) {
-	for(int k = 1;k <= 3;k++) {
+        for(int k = 1;k <= 3;k++) {
-	  dsdf(ii,jj) = dsdf(ii,jj) + cauchy(k,l)*
+          dsdf(ii,jj) = dsdf(ii,jj) + cauchy(k,l)*
-	    ( Fi(i,k)*Fi(j,l)*Fi(n,m) - Fi(i,m)*Fi(j,l)*Fi(n,k) - Fi(i,k)*Fi(j,m)*Fi(n,l) );
+            ( Fi(i,k)*Fi(j,l)*Fi(n,m) - Fi(i,m)*Fi(j,l)*Fi(n,k) - Fi(i,k)*Fi(j,m)*Fi(n,l) );
-	}
+        }
       }
     }
   }