Merge the espresso head fork to the espresso-ffans

doc/ug/setup.tex

@@ -679,8 +679,10 @@ \section{Creating bonds when particles collide}
 \begin{essyntax}
 \variant{1} on\_collision
 \variant{2} on\_collision off
-\variant{4} on\_collision \opt{exception} bind_centers \var{d} \var{bond1}
-\variant{5} on\_collision \opt{exception} bind_at_point_of_collision \var{d} \var{bond1} \var{bond2} \var{type}
+\variant{3} on\_collision \opt{exception} bind_centers \var{d} \var{bond1}
+\variant{4} on\_collision \opt{exception} bind_at_point_of_collision \var{d} \var{bond1} \var{bond2} \var{type}
+\variant{5} on\_collision \opt{exception} glue_to_surface \var{d} \var{bond1} \var{bond2} \var{type} \var{type2} \var{type3} \var{type4} \var{d2}
+\variant{6} on\_collision \opt{exception} bind_three_particles \var{d} \var{bond1} \var{bond2} \var{res}
 \end{essyntax}
 
 With the help of the feature \feature{COLLISION_DETECTION}, bonds
@@ -728,6 +730,17 @@ \section{Creating bonds when particles collide}
   created at the point of collision (if applicable). Be sure not to
   define a short-ranged interaction for this particle type, as two
   particles will be generated in the same place.
+
+\item \lit{glue_to_surface} is used to fix a particle of type \var{type2} onto the surface of a particle of type \var{type3}.
+This is achieved by creating a virtual site (particle type \var{type}) which 
+is rigidly connected to the particle of \var{type3}. A bond of type 
+\var{bond2} is then created between the virtual site and the particle 
+of \var{type}. 
+Additionally, a bond of type \var{bond1} between the colliding 
+particles is also created. 
+After the collision, the particle of type \var{type3} is changed to type \var{type4}.
+\item \lit{bind_three_particles} allows for the creating of agglomerates which maintain their shape similarly to those create by the \lit{bind_ad_point_of_collision} method. The present approach works without virtual sites. Instead, for each two-particle collision, the surrounding is searched for a third particle. If one is found, angular bounds are placed on each of the three particles in addition to the distance based bounds between the particle centers. The id of the angular bonds is determined from the angle between the particles. Zero degrees corresponds to bond id \var{bond2}, where as 180 degrees corresponds to bond id \var{bond2} +\var{res}.
+this method das not depend on the particles' rotational degrees of freedom being integrated. Virtual sites are also not required, and the method is implemented to run on more than one cpu core.
 \end{itemize}
 
 The code can throw an exception (background error) in case two

src/core/actor/DipolarDirectSum.cpp

@@ -31,13 +31,14 @@ if (dipolarDirectSum)
 {
   forceActors.remove(dipolarDirectSum);
   energyActors.remove(dipolarDirectSum);
-  free(dipolarDirectSum);
+  delete(dipolarDirectSum);
+  dipolarDirectSum=NULL;
 
 }
 }
 
 
-DipolarDirectSum *dipolarDirectSum;
+DipolarDirectSum *dipolarDirectSum=0;
 
 #endif
 

src/core/actor/DipolarDirectSum.hpp

@@ -8,6 +8,7 @@
 #include "DipolarDirectSum_cuda.hpp"
 #include "grid.hpp" 
 #include "cuda_interface.hpp"
+#include "interaction_data.hpp"
 
 #ifndef ACTOR_DIPOLARDIRECTSUM_HPP
 #define ACTOR_DIPOLARDIRECTSUM_HPP
@@ -24,7 +25,10 @@ void DipolarDirectSum_kernel_wrapper_force(dds_float k, int n, float *pos, float
 class DipolarDirectSum : public Actor {
 public:
   DipolarDirectSum(SystemInterface &s) {
-    if(!s.requestFGpu())
+
+	k = coulomb.Dbjerrum;
+
+	if(!s.requestFGpu())
       std::cerr << "DipolarDirectSum needs access to forces on GPU!" << std::endl;
 
     if(!s.requestRGpu())

src/core/actor/DipolarDirectSum_cuda.cu

@@ -136,7 +136,7 @@ __device__ dds_float dipole_ia_energy(int id,dds_float pf, float* r1, float *r2,
   dds_float dr[3];
 dds_float _r1[3],_r2[3],_dip1[3],_dip2[3];
 
-for (int i=i=0;i<3;i++)
+for (int i=0;i<3;i++)
 {
  _r1[i]=r1[i];
  _r2[i]=r2[i];
@@ -175,7 +175,6 @@ __global__ void DipolarDirectSum_kernel_force(dds_float pf,
 
   int i = blockIdx.x * blockDim.x + threadIdx.x;
 
-
   if(i >= n)
     return;
 
@@ -215,7 +214,7 @@ __global__ void DipolarDirectSum_kernel_force(dds_float pf,
 
   for (int j=i+1;j<n;j++)
   {
-      dipole_ia_force(i,1,pos+3*i,pos+3*j,dip+3*i,dip+3*j,fi,ti,tj,1,box_l,periodic);
+      dipole_ia_force(i,pf,pos+3*i,pos+3*j,dip+3*i,dip+3*j,fi,ti,tj,1,box_l,periodic);
 //      printf("%d %d: %f %f %f\n",i,j,fi[0],fi[1],fi[2]); 
       for (int k=0;k<3;k++)
       {
@@ -285,7 +284,7 @@ __global__ void DipolarDirectSum_kernel_energy(dds_float pf,
   // Summation for particle i
   for (int j=i+1;j<n;j++)
   {
-      sum+=dipole_ia_energy(i,1,pos+3*i,pos+3*j,dip+3*i,dip+3*j,box_l,periodic);
+      sum+=dipole_ia_energy(i,pf,pos+3*i,pos+3*j,dip+3*i,dip+3*j,box_l,periodic);
   }
 
   // Save per thread result into block shared mem