Rename basis_vec to ucell_size in the geom functions using Periodic boundary conditions

in view of adding PBC for non-orthogonal cells

modules/geom/src/vecmat3_op.cc

@@ -208,20 +208,20 @@ Real MinDistance(const Vec3List& l1, const Vec3List& l2)
   return std::sqrt(min);
 }
 
-Real MinDistanceWithPBC(const Vec3List& l1, const Vec3List& l2, Vec3& basis_vec)
+Real MinDistanceWithPBC(const Vec3List& l1, const Vec3List& l2, Vec3& ucell_size)
 { 
   // returns the minimal distance between two sets of points (Vec3List)
-  // given the periodic boundary condition along x,y,z given in the basis_vec
+  // given the periodic boundary condition along x,y,z given in the ucell_size
   if (l1.size()==0 || l2.size()==0){throw GeomException("cannot calculate minimal distance: empty Vec3List");}
   Real min=Length2(*l1.begin()-*l2.begin());
   Real d;
   Vec3 v;
   for (int i=0; i<3; i++) {
-    basis_vec[i]=std::fabs(basis_vec[i]);
+    ucell_size[i]=std::fabs(ucell_size[i]);
   }
   for (Vec3List::const_iterator p1=l1.begin(),e1=l1.end(); p1!=e1; p1++) {
     for (Vec3List::const_iterator p2=l2.begin(),e2=l2.end(); p2!=e2; p2++) {
-      d=Distance2WithPBC(*p1, *p2, basis_vec);
+      d=Distance2WithPBC(*p1, *p2, ucell_size);
       if (d<min) min=d;
     }
   }
@@ -268,22 +268,22 @@ Vec3List CalculateUnitCellVectors(const Vec3& ucell_size, const Vec3& ucell_angl
   return ucell_vec;  
 }
   
-Vec3 WrapVec3(const Vec3& v1,const Vec3& box_center,const Vec3& basis_vec){
+Vec3 WrapVec3(const Vec3& v1,const Vec3& box_center,const Vec3& ucell_size){
   Vec3 v;
   Real r;
   for (int i=0; i<3; i++) {
-    r=(v1[i]-box_center[i])/basis_vec[i];
+    r=(v1[i]-box_center[i])/ucell_size[i];
     r=(r > 0.0) ? std::floor(r + 0.5) : std::ceil(r - 0.5);
-    v[i]=v1[i]-basis_vec[i]*r;
+    v[i]=v1[i]-ucell_size[i]*r;
   }
   return v;
 }
 
-Vec3List WrapVec3List(const Vec3List& vl, const Vec3& box_center,const Vec3& basis_vec){
+Vec3List WrapVec3List(const Vec3List& vl, const Vec3& box_center,const Vec3& ucell_size){
   Vec3List vl_out;
   vl_out.reserve(vl_out.size());
   for (Vec3List::const_iterator v1=vl.begin(),e=vl.end();v1!=e ; v1++) {
-    vl_out.push_back(WrapVec3(*v1,box_center,basis_vec));
+    vl_out.push_back(WrapVec3(*v1,box_center,ucell_size));
   }
   return vl_out;
 }

modules/geom/src/vecmat3_op.hh

@@ -195,35 +195,35 @@ inline Real Distance(const Vec3& p1, const Vec3& p2)
 }
 
 
-//! return the squared distance between two points with periodic boundaries in x,y,z given in basis_vec
-inline Real Distance2WithPBC(const Vec3& v1, const Vec3& v2, const Vec3& basis_vec){
+//! return the squared distance between two points with periodic boundaries in x,y,z given in ucell_size
+inline Real Distance2WithPBC(const Vec3& v1, const Vec3& v2, const Vec3& ucell_size){
   Vec3 v;
   v=v1-v2;
   for (int i=0; i<3; i++) {
-    if (std::fabs(v[i])>basis_vec[i]/2.){ 
-      v[i]=std::fabs(v[i])-basis_vec[i]*int(std::fabs(v[i])/basis_vec[i]+0.5);
+    if (std::fabs(v[i])>ucell_size[i]/2.){ 
+      v[i]=std::fabs(v[i])-ucell_size[i]*int(std::fabs(v[i])/ucell_size[i]+0.5);
     }
   }
   return Length2(v);
 }
-//! return the distance between two points with periodic boundaries in x,y,z given in basis_vec
-inline Real DistanceWithPBC(const Vec3& v1, const Vec3& v2, const Vec3& basis_vec){
-  return sqrt(Distance2WithPBC(v1, v2, basis_vec));
+//! return the distance between two points with periodic boundaries in x,y,z given in ucell_size
+inline Real DistanceWithPBC(const Vec3& v1, const Vec3& v2, const Vec3& ucell_size){
+  return sqrt(Distance2WithPBC(v1, v2, ucell_size));
 }
 //! returns the minimal distance between the points in two Vec3List
 Real DLLEXPORT_OST_GEOM MinDistance(const Vec3List& l1, const Vec3List& l2);
 //! returns the minimal distance between the points in two Vec3List 
-//  with periodic boundaries in x,y,z given in basis_vec
-Real DLLEXPORT_OST_GEOM MinDistanceWithPBC(const Vec3List& l1, const Vec3List& l2, Vec3& basis_vec);
+//  with periodic boundaries in x,y,z given in ucell_size
+Real DLLEXPORT_OST_GEOM MinDistanceWithPBC(const Vec3List& l1, const Vec3List& l2, Vec3& ucell_size);
 //! returns the indices index1, index2 corresponding to the points in
 //! the Vec3List l1 and l2 having the minimal distance.
 std::vector<unsigned int> DLLEXPORT_OST_GEOM MinDistanceIndices(const Vec3List& l1, const Vec3List& l2);
 //! Calculates the Unit Cell Vectors from their sizes and angles (given as Vec3(gamma,beta,alpha)).
 Vec3List DLLEXPORT_OST_GEOM CalculateUnitCellVectors(const Vec3& ucell_size, const Vec3& ucell_angles);
 //!wraps a vector in a box with periodic boundaries
-Vec3 DLLEXPORT_OST_GEOM WrapVec3(const Vec3& v1,const Vec3& box_center,const Vec3& basis_vec);
+Vec3 DLLEXPORT_OST_GEOM WrapVec3(const Vec3& v1,const Vec3& box_center,const Vec3& ucell_size);
 //!wraps all the verctors in a Vec3List in a box with periodic boundaries
-Vec3List DLLEXPORT_OST_GEOM WrapVec3List(const Vec3List& vl,const Vec3& box_center,const Vec3& basis_vec);
+Vec3List DLLEXPORT_OST_GEOM WrapVec3List(const Vec3List& vl,const Vec3& box_center,const Vec3& ucell_size);
 
   
 } // ns