Changed "exclude" keyword to "overlap"

+ added new error description to header file
+ minor fix in the doc file

doc/src/create_atoms.rst

@@ -26,7 +26,7 @@ Syntax
          region-ID = create atoms within this region, use NULL for entire simulation box
 
 * zero or more keyword/value pairs may be appended
-* keyword = *mol* or *basis* or *ratio* or *subset* or *remap* or *var* or *set* or *rotate* or *units*
+* keyword = *mol* or *basis* or *ratio* or *subset* or *remap* or *var* or *set* or *rotate* or *maxtries* or *overlap* or *units*
 
   .. parsed-literal::
 
@@ -50,8 +50,8 @@ Syntax
        *rotate* values = theta Rx Ry Rz
          theta = rotation angle for single molecule (degrees)
          Rx,Ry,Rz = rotation vector for single molecule
-       *maxtries* value = N = number of tries (for a single particle) before failure
-       *exclude* value = radius = radius of exclusion area around existing atoms
+       *maxtries* value = N = number of tries (for a single particle to be created) before failure
+       *overlap* value = radius = the minimum distance from existing atoms (to avoid overlapping/huge forces)
        *units* value = *lattice* or *box*
          *lattice* = the geometry is defined in lattice units
          *box* = the geometry is defined in simulation box units
@@ -66,7 +66,7 @@ Examples
    create_atoms 3 region regsphere basis 2 3 ratio 0.5 74637
    create_atoms 3 single 0 0 5
    create_atoms 1 box var v set x xpos set y ypos
-   create_atoms 2 random 50 12345 NULL maxtries 10 exclude 2.0
+   create_atoms 2 random 50 12345 NULL maxtries 10 overlap 2.0
 
 Description
 """""""""""
@@ -131,7 +131,7 @@ outside a geometric boundary.
 
 .. note::
 
-   Particles generated by the *random* style (without the *exclude* keyword)
+   Particles generated by the *random* style (without the *overlap* keyword)
    will typically be highly overlapped which will cause many interatomic
    potentials to compute large energies and forces. Thus you should either
    perform an :doc:`energy minimization <minimize>` or run dynamics with
@@ -151,7 +151,7 @@ solvated with a surrounding box of water molecules.
 
 In all these cases, care should be taken to insure that new atoms do
 not overlap existing atoms inappropriately, especially if molecules
-are being added. For this reason the *exclude* keyword is provided,
+are being added. For this reason the *overlap* keyword is provided,
 also the :doc:`delete_atoms <delete_atoms>` command can be used to remove
 overlapping atoms or molecules.
 
@@ -297,14 +297,14 @@ rule: if your right-hand's thumb points along *R*, then your fingers
 wrap around the axis in the direction of rotation.
 
 The *maxtries* keyword limits the number of tries to generate coordinates
-for a new particle that satisfies all requirements (region, var, exclude,
+for a new particle that satisfies all requirements (region, var, overlap,
 ...) before the command fails. This keyword is available only with the
 *random* style and the default number of tries is 1000 per particle. The
-use of this keyword is recommended when using the *exclude* keyword,
+use of this keyword is recommended when using the *overlap* keyword,
 otherwise it is usually not necessary (but can be useful). 
 
-The *exclude* keyword can be used with the *random* style (and only the
-*random* style) to prevent the newly created particles overlapping or being
+The *overlap* keyword can be used with the *random* style (and only the
+*random* style) to prevent the newly created particles from overlapping or being
 created too close to others. When the particles being created are **single
 atoms** the *radius* parameter passed with the keyword denotes the distance
 between particle locations/centers, meaning that all new atoms will be created

src/create_atoms.cpp

@@ -14,7 +14,7 @@
 
 /* ----------------------------------------------------------------------
    Contributing author (ratio and subset) : Jake Gissinger (U Colorado)
-   Contributing author (maxtries & exclude) : Eugen Rozic (IRB, Zagreb)
+   Contributing author (maxtries & overlap) : Eugen Rozic (IRB, Zagreb)
 ------------------------------------------------------------------------- */
 
 #include "create_atoms.h"
@@ -140,7 +140,7 @@ void CreateAtoms::command(int narg, char **arg)
   quatone[0] = quatone[1] = quatone[2] = quatone[3] = 0.0;
   subsetflag = NONE;
   int subsetseed;
-  excludeflag = 0;
+  overlapflag = 0;
   maxtries = DEFAULT_MAXTRIES;
 
   nbasis = domain->lattice->nbasis;
@@ -238,14 +238,14 @@ void CreateAtoms::command(int narg, char **arg)
       if (maxtries <= 0)
         error->all(FLERR,"Illegal create_atoms command");
       iarg += 2;
-    } else if (strcmp(arg[iarg],"exclude") == 0) {
+    } else if (strcmp(arg[iarg],"overlap") == 0) {
       if (style != RANDOM) error->all(FLERR,"Illegal create_atoms command: "
-          "'exclude' can only be combined with 'random' style!");
+          "'overlap' can only be combined with 'random' style!");
       if (iarg+2 > narg) error->all(FLERR,"Illegal create_atoms command");
-      exclude_radius = utils::numeric(FLERR,arg[iarg+1],false,lmp);
-      if (exclude_radius <= 0)
+      overlap_radius = utils::numeric(FLERR,arg[iarg+1],false,lmp);
+      if (overlap_radius <= 0)
         error->all(FLERR,"Illegal create_atoms command");
-      excludeflag = 1;
+      overlapflag = 1;
       iarg += 2;
     } else error->all(FLERR,"Illegal create_atoms command");
   }
@@ -273,7 +273,7 @@ void CreateAtoms::command(int narg, char **arg)
     // molecule random number generator, different for each proc
     ranmol = new RanMars(lmp, molseed+me);
 
-    // a bit of memory for tries to create molecules (if exclude/maxtries)
+    // a bit of memory for tries to create molecules (if overlap/maxtries)
     memory->create(temp_mol_coords, onemol->natoms, 3, "create_atoms:temp_mol_coords");
   }
 
@@ -673,17 +673,17 @@ void CreateAtoms::add_random()
   double lamda[3],*coord;
   double *boxlo,*boxhi;
 
-  // stuff needed for the exclude option
+  // stuff needed for the overlap option
   int nlocal = atom->nlocal;
   double **x = atom->x;
   double delx, dely, delz, distsq;
-  double excut, excutsq;
-  if (excludeflag) {
-    excut = exclude_radius;
-    // exclude option takes into account the radius of the molecule
+  double ocut, ocutsq;
+  if (overlapflag) {
+    ocut = overlap_radius;
+    // overlap option takes into account the radius of the molecule
     // but not the radius of a single atom (even if it is defined)
-    if (mode == MOLECULE) excut += onemol->molradius;
-    excutsq = excut*excut;
+    if (mode == MOLECULE) ocut += onemol->molradius;
+    ocutsq = ocut*ocut;
   }
 
   // random number generator, same for all procs
@@ -751,14 +751,14 @@ void CreateAtoms::add_random()
       if (mode == MOLECULE)
         gen_mol_coords(xone, quatone);
 
-      if (excludeflag) {
+      if (overlapflag) {
         int reject = 0;
         for (int i = 0; i < nlocal; i++){
           delx = xone[0] - x[i][0];
           dely = xone[1] - x[i][1];
           delz = xone[2] - x[i][2];
           distsq = delx*delx + dely*dely + delz*delz;
-          if (distsq < excutsq){
+          if (distsq < ocutsq){
             reject = 1;
             break;
           }

src/create_atoms.h

@@ -34,8 +34,8 @@ class CreateAtoms : public Command {
   int ntype, style, mode, nregion, nbasis, nrandom, seed;
   int remapflag;
   int maxtries;
-  int excludeflag;
-  double exclude_radius;
+  int overlapflag;
+  double overlap_radius;
   int subsetflag;
   bigint nsubset;
   double subsetfrac;
@@ -179,4 +179,8 @@ W: Specifying an 'subset' value of '0' is equivalent to no 'subset' keyword
 
 Self-explanatory.
 
+E: Exceeded max number of tries in create_atoms
+
+Self-explanatory.
+
 */