work on create_atoms command

src/create_atoms.cpp

@@ -450,8 +450,8 @@ void CreateAtoms::command(int narg, char **arg)
   atom->nghost = 0;
   atom->avec->clear_bonus();
 
-  // add atoms/molecules in one of 3 ways
+  // add atoms/molecules with appropriate add() method
-
+  
   bigint natoms_previous = atom->natoms;
   int nlocal_previous = atom->nlocal;
 
@@ -1155,12 +1155,34 @@ void CreateAtoms::add_mesh(const char *filename)
   }
 }
 
+/* ----------------------------------------------------------------------
+   add many atoms to general triclinic box by looping over lattice
+------------------------------------------------------------------------- */
+
+void CreateAtoms::add_lattice_triclinic_general()
+{
+  
+  
+}
+
 /* ----------------------------------------------------------------------
    add many atoms by looping over lattice
 ------------------------------------------------------------------------- */
 
 void CreateAtoms::add_lattice()
 {
+  // add atoms on general triclinic lattice if Domain has setting for it
+  // verify lattice is valid for general triclinic
+  
+  int triclinic_general = domain->triclinic_general;
+  
+  if (triclinic_general) {
+    if (!domain->lattice->is_custom())
+      error->all(FLERR,"Create_atoms for general triclinic requires custom lattice");
+    if (domain->lattice->is_oriented())
+      error->all(FLERR,"Create_atoms for general triclinic requires lattice with default orientation");
+  }
+
   // convert 8 corners of my subdomain from box coords to lattice coords
   // for orthogonal, use corner pts of my subbox
   // for triclinic, use bounding box of my subbox
@@ -1202,17 +1224,56 @@ void CreateAtoms::add_lattice()
   xmin = ymin = zmin = BIG;
   xmax = ymax = zmax = -BIG;
 
-  // convert to lattice coordinates and set bounding box
+  // convert 8 corner points of bounding box to lattice coordinates
+  // compute new bounding box (xyz min/max) in lattice coords
+  // for orthogonal or restricted triclinic, use 8 corner points of bbox lo/hi
+  
+  if (!triclinic_general) {
+    domain->lattice->bbox(1, bboxlo[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax);
+    domain->lattice->bbox(1, bboxhi[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax);
+    domain->lattice->bbox(1, bboxlo[0], bboxhi[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax);
+    domain->lattice->bbox(1, bboxhi[0], bboxhi[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax);
+    domain->lattice->bbox(1, bboxlo[0], bboxlo[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax);
+    domain->lattice->bbox(1, bboxhi[0], bboxlo[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax);
+    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);
 
-  domain->lattice->bbox(1, bboxlo[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax);
+  // for general triclinic, convert 8 corner points of bbox to general triclinic coords
-  domain->lattice->bbox(1, bboxhi[0], bboxlo[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax);
+  // new set of 8 points is no longer an orthogonal bounding box
-  domain->lattice->bbox(1, bboxlo[0], bboxhi[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax);
+  // instead invoke lattice->bbox() on each of 8 points
-  domain->lattice->bbox(1, bboxhi[0], bboxhi[1], bboxlo[2], xmin, ymin, zmin, xmax, ymax, zmax);
-  domain->lattice->bbox(1, bboxlo[0], bboxlo[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax);
-  domain->lattice->bbox(1, bboxhi[0], bboxlo[1], bboxhi[2], xmin, ymin, zmin, xmax, ymax, zmax);
-  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);
 
+  } else if (triclinic_general) {
+    double point[3];
+
+    point[0] = bboxlo[0]; point[1] = bboxlo[1]; point[2] = bboxlo[2];
+    domain->restricted_to_general(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];
+    domain->restricted_to_general(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];
+    domain->restricted_to_general(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];
+    domain->restricted_to_general(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];
+    domain->restricted_to_general(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];
+    domain->restricted_to_general(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];
+    domain->restricted_to_general(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];
+    domain->restricted_to_general(point);
+    domain->lattice->bbox(1, point[0], point[1], point[2], xmin, ymin, zmin, xmax, ymax, zmax);
+  }
+  
   // ilo:ihi,jlo:jhi,klo:khi = loop bounds for lattice overlap of my subbox
   // overlap = any part of a unit cell (face,edge,pt) in common with my subbox
   // in lattice space, subbox is a tilted box
@@ -1233,6 +1294,8 @@ void CreateAtoms::add_lattice()
   if (ymin < 0.0) jlo--;
   if (zmin < 0.0) klo--;
 
+  printf("LOOP LATTICE bounds: %d %d: %d %d: %d %d\n",ilo,ihi,jlo,jhi,klo,khi);
+  
   // count lattice sites on each proc
 
   nlatt_overflow = 0;
@@ -1298,6 +1361,7 @@ void CreateAtoms::loop_lattice(int action)
 {
   int i, j, k, m;
 
+  int triclinic_general = domain->triclinic_general;
   const double *const *const basis = domain->lattice->basis;
 
   nlatt = 0;
@@ -1317,6 +1381,10 @@ void CreateAtoms::loop_lattice(int action)
 
           domain->lattice->lattice2box(x[0], x[1], x[2]);
 
+          // convert from general to restricted triclinic coords
+
+          if (triclinic_general) domain->general_to_restricted(x);
+          
           // if a region was specified, test if atom is in it
 
           if (style == REGION)

src/create_atoms.h

@@ -69,6 +69,7 @@ class CreateAtoms : public Command {
   void add_mesh(const char *);
   int add_bisection(const double[3][3], tagint);
   int add_quasirandom(const double[3][3], tagint);
+  void add_lattice_triclinic_general();
   void add_lattice();
   void loop_lattice(int);
   void add_molecule(double *);

src/create_box.cpp

@@ -115,8 +115,10 @@ void CreateBox::command(int narg, char **arg)
     double chi = utils::numeric(FLERR, arg[iarg + 5], false, lmp);
     iarg += 6;
 
-    // use lattice2box() to generate avec, bvec, cvec and origin
+    // use lattice2box() to generate origin and ABC vectors
-
+    // origin = abc lo
+    // ABC vector = hi in one dim - orign
+    
     double avec[3],bvec[3],cvec[3],origin[3];
     double px,py,pz;
     
@@ -144,12 +146,7 @@ void CreateBox::command(int narg, char **arg)
     cvec[1] = py - origin[1];
     cvec[2] = pz - origin[2];
 
-    printf("ORIGIN %g %g %g\n",origin[0],origin[1],origin[2]);
+    // setup general triclinic box within Domain
-    printf("AVEC %g %g %g\n",avec[0],avec[1],avec[2]);
-    printf("BVEC %g %g %g\n",bvec[0],bvec[1],bvec[2]);
-    printf("CVEC %g %g %g\n",cvec[0],cvec[1],cvec[2]);
-
-    // setup general triclinic box in Domain
     
     domain->set_general_triclinic(avec,bvec,cvec,origin);
   }

src/domain.cpp

@@ -667,7 +667,7 @@ void Domain::set_general_triclinic(double *avec_caller, double *bvec_caller,
 }
 
 /* ----------------------------------------------------------------------
-   transform one atom's coords from general triclinic to restricted triclinic
+   transform atom coords from general triclinic to restricted triclinic
 ------------------------------------------------------------------------- */
 
 void Domain::general_to_restricted(double *x)
@@ -681,7 +681,7 @@ void Domain::general_to_restricted(double *x)
 }
 
 /* ----------------------------------------------------------------------
-   transform one atom's coords from restricted triclinic to general triclinic
+   transform atom coords from restricted triclinic to general triclinic
 ------------------------------------------------------------------------- */
 
 void Domain::restricted_to_general(double *x)

src/lattice.cpp

@@ -582,8 +582,9 @@ void Lattice::cross(double *x, double *y, double *z)
 }
 
 /* ----------------------------------------------------------------------
-   convert x,y,z from lattice coords to box coords (flag = 0) or vice versa
+   convert x,y,z from lattice coords to box coords (flag = 0)
-   use new point to expand bounding box (min to max)
+   or from box coords to lattice coords (flag = 1)
+   either way, use new point to expand bounding box (min to max)
 ------------------------------------------------------------------------- */
 
 void Lattice::bbox(int flag, double x, double y, double z,