fix spring doc page update

doc/src/fix_spring.txt

@@ -89,11 +89,7 @@ NOTE: The center of mass of a group of atoms is calculated in
 group can straddle a periodic boundary.  See the "dump"_dump.html doc
 page for a discussion of unwrapped coordinates.  It also means that a
 spring connecting two groups or a group and the tether point can cross
-a periodic boundary and its length be calculated correctly.  One
+a periodic boundary and its length be calculated correctly.  
-exception is for rigid bodies, which should not be used with the fix
-spring command, if the rigid body will cross a periodic boundary.
-This is because image flags for rigid bodies are used in a different
-way, as explained on the "fix rigid"_fix_rigid.html doc page.
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 

src/atom_vec_atomic.cpp

@@ -51,7 +51,7 @@ void AtomVecAtomic::grow(int n)
   if (n == 0) grow_nmax();
   else nmax = n;
   atom->nmax = nmax;
-  if (nmax < 0)
+  if (nmax < 0 || nmax > MAXSMALLINT)
     error->one(FLERR,"Per-processor system is too big");
 
   tag = memory->grow(atom->tag,nmax,"atom:tag");

src/atom_vec_body.cpp

@@ -118,7 +118,7 @@ void AtomVecBody::grow(int n)
   if (n == 0) grow_nmax();
   else nmax = n;
   atom->nmax = nmax;
-  if (nmax < 0)
+  if (nmax < 0 || nmax > MAXSMALLINT)
     error->one(FLERR,"Per-processor system is too big");
 
   tag = memory->grow(atom->tag,nmax,"atom:tag");

src/atom_vec_charge.cpp

@@ -53,7 +53,7 @@ void AtomVecCharge::grow(int n)
   if (n == 0) grow_nmax();
   else nmax = n;
   atom->nmax = nmax;
-  if (nmax < 0)
+  if (nmax < 0 || nmax > MAXSMALLINT)
     error->one(FLERR,"Per-processor system is too big");
 
   tag = memory->grow(atom->tag,nmax,"atom:tag");

src/atom_vec_ellipsoid.cpp

@@ -72,7 +72,7 @@ void AtomVecEllipsoid::grow(int n)
   if (n == 0) grow_nmax();
   else nmax = n;
   atom->nmax = nmax;
-  if (nmax < 0)
+  if (nmax < 0 || nmax > MAXSMALLINT)
     error->one(FLERR,"Per-processor system is too big");
 
   tag = memory->grow(atom->tag,nmax,"atom:tag");

src/atom_vec_hybrid.cpp

@@ -144,7 +144,7 @@ void AtomVecHybrid::grow(int n)
   if (n == 0) grow_nmax();
   else nmax = n;
   atom->nmax = nmax;
-  if (nmax < 0)
+  if (nmax < 0 || nmax > MAXSMALLINT)
     error->one(FLERR,"Per-processor system is too big");
 
   // sub-styles perform all reallocation

src/atom_vec_line.cpp

@@ -83,7 +83,7 @@ void AtomVecLine::grow(int n)
   if (n == 0) grow_nmax();
   else nmax = n;
   atom->nmax = nmax;
-  if (nmax < 0)
+  if (nmax < 0 || nmax > MAXSMALLINT)
     error->one(FLERR,"Per-processor system is too big");
 
   tag = memory->grow(atom->tag,nmax,"atom:tag");

src/atom_vec_sphere.cpp

@@ -84,7 +84,7 @@ void AtomVecSphere::grow(int n)
   if (n == 0) grow_nmax();
   else nmax = n;
   atom->nmax = nmax;
-  if (nmax < 0)
+  if (nmax < 0 || nmax > MAXSMALLINT)
     error->one(FLERR,"Per-processor system is too big");
 
   tag = memory->grow(atom->tag,nmax,"atom:tag");

src/atom_vec_tri.cpp

@@ -88,7 +88,7 @@ void AtomVecTri::grow(int n)
   if (n == 0) grow_nmax();
   else nmax = n;
   atom->nmax = nmax;
-  if (nmax < 0)
+  if (nmax < 0 || nmax > MAXSMALLINT)
     error->one(FLERR,"Per-processor system is too big");
 
   tag = memory->grow(atom->tag,nmax,"atom:tag");

src/comm_brick.cpp

@@ -51,10 +51,14 @@ enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED};    // several files
 
 /* ---------------------------------------------------------------------- */
 
-CommBrick::CommBrick(LAMMPS *lmp) : Comm(lmp),
+CommBrick::CommBrick(LAMMPS *lmp) : 
-  sendnum(NULL), recvnum(NULL), sendproc(NULL), recvproc(NULL), size_forward_recv(NULL),
+  Comm(lmp),
-  size_reverse_send(NULL), size_reverse_recv(NULL), slablo(NULL), slabhi(NULL), multilo(NULL), multihi(NULL),
+  sendnum(NULL), recvnum(NULL), sendproc(NULL), recvproc(NULL), 
-  cutghostmulti(NULL), pbc_flag(NULL), pbc(NULL), firstrecv(NULL), sendlist(NULL), maxsendlist(NULL), buf_send(NULL), buf_recv(NULL)
+  size_forward_recv(NULL),
+  size_reverse_send(NULL), size_reverse_recv(NULL), 
+  slablo(NULL), slabhi(NULL), multilo(NULL), multihi(NULL),
+  cutghostmulti(NULL), pbc_flag(NULL), pbc(NULL), firstrecv(NULL), 
+  sendlist(NULL), maxsendlist(NULL), buf_send(NULL), buf_recv(NULL)
 {
   style = 0;
   layout = LAYOUT_UNIFORM;

src/domain.cpp

@@ -1102,6 +1102,40 @@ int Domain::closest_image(int i, int j)
   return closest;
 }
 
+/* ----------------------------------------------------------------------
+   return local index of atom J or any of its images that is closest to pos
+   if J is not a valid index like -1, just return it
+------------------------------------------------------------------------- */
+
+int Domain::closest_image(double *pos, int j)
+{
+  if (j < 0) return j;
+
+  int *sametag = atom->sametag;
+  double **x = atom->x;
+
+  int closest = j;
+  double delx = pos[0] - x[j][0];
+  double dely = pos[1] - x[j][1];
+  double delz = pos[2] - x[j][2];
+  double rsqmin = delx*delx + dely*dely + delz*delz;
+  double rsq;
+
+  while (sametag[j] >= 0) {
+    j = sametag[j];
+    delx = pos[0] - x[j][0];
+    dely = pos[1] - x[j][1];
+    delz = pos[2] - x[j][2];
+    rsq = delx*delx + dely*dely + delz*delz;
+    if (rsq < rsqmin) {
+      rsqmin = rsq;
+      closest = j;
+    }
+  }
+
+  return closest;
+}
+
 /* ----------------------------------------------------------------------
    find and return Xj image = periodic image of Xj that is closest to Xi
    for triclinic, add/subtract tilt factors in other dims as needed

src/domain.h

@@ -113,6 +113,7 @@ class Domain : protected Pointers {
   void minimum_image(double &, double &, double &);
   void minimum_image(double *);
   int closest_image(int, int);
+  int closest_image(double *, int);
   void closest_image(const double * const, const double * const,
                      double * const);
   void remap(double *, imageint &);

src/math_extra.h

@@ -40,6 +40,7 @@ namespace MathExtra {
   inline void sub3(const double *v1, const double *v2, double *ans);
   inline double len3(const double *v);
   inline double lensq3(const double *v);
+  inline double distsq3(const double *v1, const double *v2);
   inline double dot3(const double *v1, const double *v2);
   inline void cross3(const double *v1, const double *v2, double *ans);
 
@@ -265,6 +266,18 @@ inline double MathExtra::lensq3(const double *v)
   return v[0]*v[0] + v[1]*v[1] + v[2]*v[2];
 }
 
+/* ----------------------------------------------------------------------
+   ans = distance squared between pts v1 and v2
+------------------------------------------------------------------------- */
+
+inline double MathExtra::distsq3(const double *v1, const double *v2)
+{
+  double dx = v1[0] - v2[0];
+  double dy = v1[1] - v2[1];
+  double dz = v1[2] - v2[2];
+  return dx*dx + dy*dy + dz*dz;
+}
+
 /* ----------------------------------------------------------------------
    dot product of 2 vectors
 ------------------------------------------------------------------------- */

src/npair.cpp

@@ -149,7 +149,7 @@ void NPair::build_setup()
 ------------------------------------------------------------------------- */
 
 int NPair::exclusion(int i, int j, int itype, int jtype,
-                          int *mask, tagint *molecule) const {
+                     int *mask, tagint *molecule) const {
   int m;
 
   if (nex_type && ex_type[itype][jtype]) return 1;

src/region.cpp

@@ -28,8 +28,10 @@ using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */
 
-Region::Region(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp),
+Region::Region(LAMMPS *lmp, int narg, char **arg) : 
-  id(NULL), style(NULL), contact(NULL), list(NULL), xstr(NULL), ystr(NULL), zstr(NULL), tstr(NULL)
+  Pointers(lmp),
+  id(NULL), style(NULL), contact(NULL), list(NULL), 
+  xstr(NULL), ystr(NULL), zstr(NULL), tstr(NULL)
 {
   int n = strlen(arg[0]) + 1;
   id = new char[n];