Updating MSM code to reflect changes allowing non-periodic boundaries.

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9247 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/KSPACE/msm.h

@@ -49,33 +49,40 @@ class MSM : public KSpace {
   int *nx_msm,*ny_msm,*nz_msm;
   int *nxlo_in,*nylo_in,*nzlo_in;
   int *nxhi_in,*nyhi_in,*nzhi_in;
-  int *nxlo_in_d,*nylo_in_d,*nzlo_in_d;
-  int *nxhi_in_d,*nyhi_in_d,*nzhi_in_d;
   int *nxlo_out,*nylo_out,*nzlo_out;
   int *nxhi_out,*nyhi_out,*nzhi_out;
   int *ngrid;
+  int *alpha,*betax,*betay,*betaz;
   int nxlo_direct,nxhi_direct,nylo_direct;
   int nyhi_direct,nzlo_direct,nzhi_direct;
   int nmax_direct;
   int nlower,nupper;
   int peratom_allocate_flag;
-  int levels,cutlevel;
+  int levels;
+  
+  MPI_Comm *world_levels;  
 
   double ****qgrid;
   double ****egrid;
-  double ****fxgrid,****fygrid,****fzgrid;
   double ****v0grid,****v1grid,****v2grid;
   double ****v3grid,****v4grid,****v5grid;
   double **g_direct;
-  double **dgx_direct,**dgy_direct,**dgz_direct;
   double **v0_direct,**v1_direct,**v2_direct;
   double **v3_direct,**v4_direct,**v5_direct;
+  double *g_direct_top;
+  double *v0_direct_top,*v1_direct_top,*v2_direct_top;
+  double *v3_direct_top,*v4_direct_top,*v5_direct_top;
 
   double **phi1d,**dphi1d;
 
+  int procgrid[3];                  // procs assigned in each dim of 3d grid
+  int myloc[3];                     // which proc I am in each dim
+  int ***procneigh_levels;          // my 6 neighboring procs, 0/1 = left/right
   class CommGrid **cg;
-  class CommGrid **cg_IK;
   class CommGrid **cg_peratom;
+  class CommGrid *cg_all;
+  class CommGrid *cg_peratom_all;
+  
   int current_level;
 
   int **part2grid;             // storage for particle -> grid mapping
@@ -84,6 +91,7 @@ class MSM : public KSpace {
   double *boxlo;
 
   void set_grid_global();
+  void set_proc_grid(int);
   void set_grid_local();
   void setup_grid();
   double estimate_cutoff(double,double);
@@ -99,21 +107,21 @@ class MSM : public KSpace {
   int factorable(int,int&,int&);
   void particle_map();
   void make_rho();
-  void grid_swap(int,double*** &);
-  void direct_ad(int);
   void direct(int);
+  void direct_top(int);
   void direct_peratom(int);
+  void direct_peratom_top(int);
   void restriction(int);
   void prolongation(int);
-  void fieldforce_ad();
   void fieldforce();
   void fieldforce_peratom();
   void compute_phis_and_dphis(const double &, const double &, const double &);
   double compute_phi(const double &);
   double compute_dphi(const double &);
   void get_g_direct();
-  void get_dg_direct();
   void get_virial_direct();
+  void get_g_direct_top(int);
+  void get_virial_direct_top(int);
 
   // grid communication
   void pack_forward(int, double *, int, int *);
@@ -147,10 +155,6 @@ E: Kspace style requires atom attribute q
 
 The atom style defined does not have these attributes.
 
-E: Cannot (yet) use nonperiodic boundaries with MSM
-
-This feature is not yet supported.
-
 E: Cannot use slab correction with MSM
 
 Slab correction can only be used with Ewald and PPPM, not MSM.
@@ -185,6 +189,11 @@ The global MSM grid is larger than OFFSET in one or more dimensions.
 OFFSET is currently set to 16384.  You likely need to decrease the
 requested accuracy.
 
+W: MSM mesh too small, increasing to 2 points in each direction
+
+The global MSM grid is too small, so the number of grid points has been
+increased
+
 E: KSpace accuracy must be > 0
 
 The kspace accuracy designated in the input must be greater than zero.

src/domain.cpp

@@ -24,6 +24,7 @@
 #include "style_region.h"
 #include "atom.h"
 #include "force.h"
+#include "kspace.h"
 #include "update.h"
 #include "modify.h"
 #include "fix.h"
@@ -399,6 +400,10 @@ void Domain::reset_box()
   set_global_box();
   set_local_box();
 
+  // if shrink-wrapped & kspace is defined (i.e. using MSM) call setup()
+  
+  if (nonperiodic == 2 && force->kspace) force->kspace->setup();
+
   // if shrink-wrapped & triclinic, re-convert to lamda coords for new box
   // re-invoke pbc() b/c x2lamda result can be outside [0,1] due to roundoff