refactor work
This commit is contained in:
James McClure
@@ -1,7 +1,7 @@
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#include <analysis/morphology.h>
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// Implementation of morphological opening routine
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inline void PackID(const int *list, int count, signed char *sendbuf, signed char *ID){
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inline void PackID(int *list, int count, signed char *sendbuf, signed char *ID){
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// Fill in the phase ID values from neighboring processors
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// This packs up the values that need to be sent from one processor to another
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int idx,n;
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@@ -13,7 +13,7 @@ inline void PackID(const int *list, int count, signed char *sendbuf, signed char
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}
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//***************************************************************************************
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inline void UnpackID(const int *list, int count, signed char *recvbuf, signed char *ID){
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inline void UnpackID(int *list, int count, signed char *recvbuf, signed char *ID){
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// Fill in the phase ID values from neighboring processors
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// This unpacks the values once they have been recieved from neighbors
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int idx,n;
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@@ -58,11 +58,11 @@ double MorphOpen(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain>
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}
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}
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}
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Dm->Comm.barrier();
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MPI_Barrier(Dm->Comm);
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// total Global is the number of nodes in the pore-space
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totalGlobal = Dm->Comm.sumReduce( count );
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maxdistGlobal = Dm->Comm.sumReduce( maxdist );
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MPI_Allreduce(&count,&totalGlobal,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
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MPI_Allreduce(&maxdist,&maxdistGlobal,1,MPI_DOUBLE,MPI_MAX,Dm->Comm);
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double volume=double(nprocx*nprocy*nprocz)*double(nx-2)*double(ny-2)*double(nz-2);
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double volume_fraction=totalGlobal/volume;
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if (rank==0) printf("Volume fraction for morphological opening: %f \n",volume_fraction);
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@@ -77,44 +77,44 @@ double MorphOpen(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain>
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signed char *recvID_xy, *recvID_yz, *recvID_xz, *recvID_Xy, *recvID_Yz, *recvID_xZ;
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signed char *recvID_xY, *recvID_yZ, *recvID_Xz, *recvID_XY, *recvID_YZ, *recvID_XZ;
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// send buffers
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sendID_x = new signed char [Dm->sendCount("x")];
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sendID_y = new signed char [Dm->sendCount("y")];
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sendID_z = new signed char [Dm->sendCount("z")];
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sendID_X = new signed char [Dm->sendCount("X")];
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sendID_Y = new signed char [Dm->sendCount("Y")];
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sendID_Z = new signed char [Dm->sendCount("Z")];
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sendID_xy = new signed char [Dm->sendCount("xy")];
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sendID_yz = new signed char [Dm->sendCount("yz")];
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sendID_xz = new signed char [Dm->sendCount("xz")];
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sendID_Xy = new signed char [Dm->sendCount("Xy")];
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sendID_Yz = new signed char [Dm->sendCount("Yz")];
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sendID_xZ = new signed char [Dm->sendCount("xZ")];
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sendID_xY = new signed char [Dm->sendCount("xY")];
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sendID_yZ = new signed char [Dm->sendCount("yZ")];
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sendID_Xz = new signed char [Dm->sendCount("Xz")];
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sendID_XY = new signed char [Dm->sendCount("XY")];
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sendID_YZ = new signed char [Dm->sendCount("YZ")];
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sendID_XZ = new signed char [Dm->sendCount("XZ")];
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sendID_x = new signed char [Dm->sendCount_x];
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sendID_y = new signed char [Dm->sendCount_y];
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sendID_z = new signed char [Dm->sendCount_z];
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sendID_X = new signed char [Dm->sendCount_X];
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sendID_Y = new signed char [Dm->sendCount_Y];
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sendID_Z = new signed char [Dm->sendCount_Z];
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sendID_xy = new signed char [Dm->sendCount_xy];
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sendID_yz = new signed char [Dm->sendCount_yz];
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sendID_xz = new signed char [Dm->sendCount_xz];
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sendID_Xy = new signed char [Dm->sendCount_Xy];
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sendID_Yz = new signed char [Dm->sendCount_Yz];
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sendID_xZ = new signed char [Dm->sendCount_xZ];
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sendID_xY = new signed char [Dm->sendCount_xY];
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sendID_yZ = new signed char [Dm->sendCount_yZ];
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sendID_Xz = new signed char [Dm->sendCount_Xz];
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sendID_XY = new signed char [Dm->sendCount_XY];
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sendID_YZ = new signed char [Dm->sendCount_YZ];
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sendID_XZ = new signed char [Dm->sendCount_XZ];
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//......................................................................................
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// recv buffers
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recvID_x = new signed char [Dm->recvCount("x")];
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recvID_y = new signed char [Dm->recvCount("y")];
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recvID_z = new signed char [Dm->recvCount("z")];
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recvID_X = new signed char [Dm->recvCount("X")];
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recvID_Y = new signed char [Dm->recvCount("Y")];
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recvID_Z = new signed char [Dm->recvCount("Z")];
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recvID_xy = new signed char [Dm->recvCount("xy")];
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recvID_yz = new signed char [Dm->recvCount("yz")];
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recvID_xz = new signed char [Dm->recvCount("xz")];
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recvID_Xy = new signed char [Dm->recvCount("Xy")];
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recvID_xZ = new signed char [Dm->recvCount("xZ")];
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recvID_xY = new signed char [Dm->recvCount("xY")];
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recvID_yZ = new signed char [Dm->recvCount("yZ")];
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recvID_Yz = new signed char [Dm->recvCount("Yz")];
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recvID_Xz = new signed char [Dm->recvCount("Xz")];
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recvID_XY = new signed char [Dm->recvCount("XY")];
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recvID_YZ = new signed char [Dm->recvCount("YZ")];
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recvID_XZ = new signed char [Dm->recvCount("XZ")];
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recvID_x = new signed char [Dm->recvCount_x];
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recvID_y = new signed char [Dm->recvCount_y];
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recvID_z = new signed char [Dm->recvCount_z];
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recvID_X = new signed char [Dm->recvCount_X];
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recvID_Y = new signed char [Dm->recvCount_Y];
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recvID_Z = new signed char [Dm->recvCount_Z];
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recvID_xy = new signed char [Dm->recvCount_xy];
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recvID_yz = new signed char [Dm->recvCount_yz];
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recvID_xz = new signed char [Dm->recvCount_xz];
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recvID_Xy = new signed char [Dm->recvCount_Xy];
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recvID_xZ = new signed char [Dm->recvCount_xZ];
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recvID_xY = new signed char [Dm->recvCount_xY];
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recvID_yZ = new signed char [Dm->recvCount_yZ];
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recvID_Yz = new signed char [Dm->recvCount_Yz];
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recvID_Xz = new signed char [Dm->recvCount_Xz];
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recvID_XY = new signed char [Dm->recvCount_XY];
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recvID_YZ = new signed char [Dm->recvCount_YZ];
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recvID_XZ = new signed char [Dm->recvCount_XZ];
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//......................................................................................
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int sendtag,recvtag;
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sendtag = recvtag = 7;
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@@ -131,8 +131,9 @@ double MorphOpen(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain>
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// Increase the critical radius until the target saturation is met
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double deltaR=0.05; // amount to change the radius in voxel units
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double Rcrit_old;
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double Rcrit_old=0.0;
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double GlobalNumber = 1.f;
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int imin,jmin,kmin,imax,jmax,kmax;
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if (ErodeLabel == 1){
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@@ -182,65 +183,83 @@ double MorphOpen(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain>
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}
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}
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// Pack and send the updated ID values
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PackID(Dm->sendList("x"), Dm->sendCount("x") ,sendID_x, id);
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PackID(Dm->sendList("X"), Dm->sendCount("X") ,sendID_X, id);
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PackID(Dm->sendList("y"), Dm->sendCount("y") ,sendID_y, id);
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PackID(Dm->sendList("Y"), Dm->sendCount("Y") ,sendID_Y, id);
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PackID(Dm->sendList("z"), Dm->sendCount("z") ,sendID_z, id);
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PackID(Dm->sendList("Z"), Dm->sendCount("Z") ,sendID_Z, id);
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PackID(Dm->sendList("xy"), Dm->sendCount("xy") ,sendID_xy, id);
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PackID(Dm->sendList("Xy"), Dm->sendCount("Xy") ,sendID_Xy, id);
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PackID(Dm->sendList("xY"), Dm->sendCount("xY") ,sendID_xY, id);
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PackID(Dm->sendList("XY"), Dm->sendCount("XY") ,sendID_XY, id);
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PackID(Dm->sendList("xz"), Dm->sendCount("xz") ,sendID_xz, id);
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PackID(Dm->sendList("Xz"), Dm->sendCount("Xz") ,sendID_Xz, id);
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PackID(Dm->sendList("xZ"), Dm->sendCount("xZ") ,sendID_xZ, id);
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PackID(Dm->sendList("XZ"), Dm->sendCount("XZ") ,sendID_XZ, id);
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PackID(Dm->sendList("yz"), Dm->sendCount("yz") ,sendID_yz, id);
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PackID(Dm->sendList("Yz"), Dm->sendCount("Yz") ,sendID_Yz, id);
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PackID(Dm->sendList("yZ"), Dm->sendCount("yZ") ,sendID_yZ, id);
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PackID(Dm->sendList("YZ"), Dm->sendCount("YZ") ,sendID_YZ, id);
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PackID(Dm->sendList_x, Dm->sendCount_x ,sendID_x, id);
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PackID(Dm->sendList_X, Dm->sendCount_X ,sendID_X, id);
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PackID(Dm->sendList_y, Dm->sendCount_y ,sendID_y, id);
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PackID(Dm->sendList_Y, Dm->sendCount_Y ,sendID_Y, id);
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PackID(Dm->sendList_z, Dm->sendCount_z ,sendID_z, id);
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PackID(Dm->sendList_Z, Dm->sendCount_Z ,sendID_Z, id);
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PackID(Dm->sendList_xy, Dm->sendCount_xy ,sendID_xy, id);
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PackID(Dm->sendList_Xy, Dm->sendCount_Xy ,sendID_Xy, id);
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PackID(Dm->sendList_xY, Dm->sendCount_xY ,sendID_xY, id);
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PackID(Dm->sendList_XY, Dm->sendCount_XY ,sendID_XY, id);
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PackID(Dm->sendList_xz, Dm->sendCount_xz ,sendID_xz, id);
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PackID(Dm->sendList_Xz, Dm->sendCount_Xz ,sendID_Xz, id);
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PackID(Dm->sendList_xZ, Dm->sendCount_xZ ,sendID_xZ, id);
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PackID(Dm->sendList_XZ, Dm->sendCount_XZ ,sendID_XZ, id);
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PackID(Dm->sendList_yz, Dm->sendCount_yz ,sendID_yz, id);
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PackID(Dm->sendList_Yz, Dm->sendCount_Yz ,sendID_Yz, id);
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PackID(Dm->sendList_yZ, Dm->sendCount_yZ ,sendID_yZ, id);
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PackID(Dm->sendList_YZ, Dm->sendCount_YZ ,sendID_YZ, id);
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//......................................................................................
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Dm->Comm.sendrecv(sendID_x,Dm->sendCount("x"),Dm->rank_x(),sendtag,recvID_X,Dm->recvCount("X"),Dm->rank_X(),recvtag);
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Dm->Comm.sendrecv(sendID_X,Dm->sendCount("X"),Dm->rank_X(),sendtag,recvID_x,Dm->recvCount("x"),Dm->rank_x(),recvtag);
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Dm->Comm.sendrecv(sendID_y,Dm->sendCount("y"),Dm->rank_y(),sendtag,recvID_Y,Dm->recvCount("Y"),Dm->rank_Y(),recvtag);
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Dm->Comm.sendrecv(sendID_Y,Dm->sendCount("Y"),Dm->rank_Y(),sendtag,recvID_y,Dm->recvCount("y"),Dm->rank_y(),recvtag);
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Dm->Comm.sendrecv(sendID_z,Dm->sendCount("z"),Dm->rank_z(),sendtag,recvID_Z,Dm->recvCount("Z"),Dm->rank_Z(),recvtag);
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Dm->Comm.sendrecv(sendID_Z,Dm->sendCount("Z"),Dm->rank_Z(),sendtag,recvID_z,Dm->recvCount("z"),Dm->rank_z(),recvtag);
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Dm->Comm.sendrecv(sendID_xy,Dm->sendCount("xy"),Dm->rank_xy(),sendtag,recvID_XY,Dm->recvCount("XY"),Dm->rank_XY(),recvtag);
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Dm->Comm.sendrecv(sendID_XY,Dm->sendCount("XY"),Dm->rank_XY(),sendtag,recvID_xy,Dm->recvCount("xy"),Dm->rank_xy(),recvtag);
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Dm->Comm.sendrecv(sendID_Xy,Dm->sendCount("Xy"),Dm->rank_Xy(),sendtag,recvID_xY,Dm->recvCount("xY"),Dm->rank_xY(),recvtag);
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Dm->Comm.sendrecv(sendID_xY,Dm->sendCount("xY"),Dm->rank_xY(),sendtag,recvID_Xy,Dm->recvCount("Xy"),Dm->rank_Xy(),recvtag);
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Dm->Comm.sendrecv(sendID_xz,Dm->sendCount("xz"),Dm->rank_xz(),sendtag,recvID_XZ,Dm->recvCount("XZ"),Dm->rank_XZ(),recvtag);
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Dm->Comm.sendrecv(sendID_XZ,Dm->sendCount("XZ"),Dm->rank_XZ(),sendtag,recvID_xz,Dm->recvCount("xz"),Dm->rank_xz(),recvtag);
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Dm->Comm.sendrecv(sendID_Xz,Dm->sendCount("Xz"),Dm->rank_Xz(),sendtag,recvID_xZ,Dm->recvCount("xZ"),Dm->rank_xZ(),recvtag);
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Dm->Comm.sendrecv(sendID_xZ,Dm->sendCount("xZ"),Dm->rank_xZ(),sendtag,recvID_Xz,Dm->recvCount("Xz"),Dm->rank_Xz(),recvtag);
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Dm->Comm.sendrecv(sendID_yz,Dm->sendCount("yz"),Dm->rank_yz(),sendtag,recvID_YZ,Dm->recvCount("YZ"),Dm->rank_YZ(),recvtag);
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Dm->Comm.sendrecv(sendID_YZ,Dm->sendCount("YZ"),Dm->rank_YZ(),sendtag,recvID_yz,Dm->recvCount("yz"),Dm->rank_yz(),recvtag);
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Dm->Comm.sendrecv(sendID_Yz,Dm->sendCount("Yz"),Dm->rank_Yz(),sendtag,recvID_yZ,Dm->recvCount("yZ"),Dm->rank_yZ(),recvtag);
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Dm->Comm.sendrecv(sendID_yZ,Dm->sendCount("yZ"),Dm->rank_yZ(),sendtag,recvID_Yz,Dm->recvCount("Yz"),Dm->rank_Yz(),recvtag);
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MPI_Sendrecv(sendID_x,Dm->sendCount_x,MPI_CHAR,Dm->rank_x(),sendtag,
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recvID_X,Dm->recvCount_X,MPI_CHAR,Dm->rank_X(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_X,Dm->sendCount_X,MPI_CHAR,Dm->rank_X(),sendtag,
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recvID_x,Dm->recvCount_x,MPI_CHAR,Dm->rank_x(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_y,Dm->sendCount_y,MPI_CHAR,Dm->rank_y(),sendtag,
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recvID_Y,Dm->recvCount_Y,MPI_CHAR,Dm->rank_Y(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_Y,Dm->sendCount_Y,MPI_CHAR,Dm->rank_Y(),sendtag,
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recvID_y,Dm->recvCount_y,MPI_CHAR,Dm->rank_y(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_z,Dm->sendCount_z,MPI_CHAR,Dm->rank_z(),sendtag,
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recvID_Z,Dm->recvCount_Z,MPI_CHAR,Dm->rank_Z(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_Z,Dm->sendCount_Z,MPI_CHAR,Dm->rank_Z(),sendtag,
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recvID_z,Dm->recvCount_z,MPI_CHAR,Dm->rank_z(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_xy,Dm->sendCount_xy,MPI_CHAR,Dm->rank_xy(),sendtag,
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recvID_XY,Dm->recvCount_XY,MPI_CHAR,Dm->rank_XY(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_XY,Dm->sendCount_XY,MPI_CHAR,Dm->rank_XY(),sendtag,
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recvID_xy,Dm->recvCount_xy,MPI_CHAR,Dm->rank_xy(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_Xy,Dm->sendCount_Xy,MPI_CHAR,Dm->rank_Xy(),sendtag,
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recvID_xY,Dm->recvCount_xY,MPI_CHAR,Dm->rank_xY(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_xY,Dm->sendCount_xY,MPI_CHAR,Dm->rank_xY(),sendtag,
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recvID_Xy,Dm->recvCount_Xy,MPI_CHAR,Dm->rank_Xy(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_xz,Dm->sendCount_xz,MPI_CHAR,Dm->rank_xz(),sendtag,
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recvID_XZ,Dm->recvCount_XZ,MPI_CHAR,Dm->rank_XZ(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_XZ,Dm->sendCount_XZ,MPI_CHAR,Dm->rank_XZ(),sendtag,
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recvID_xz,Dm->recvCount_xz,MPI_CHAR,Dm->rank_xz(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_Xz,Dm->sendCount_Xz,MPI_CHAR,Dm->rank_Xz(),sendtag,
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recvID_xZ,Dm->recvCount_xZ,MPI_CHAR,Dm->rank_xZ(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_xZ,Dm->sendCount_xZ,MPI_CHAR,Dm->rank_xZ(),sendtag,
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recvID_Xz,Dm->recvCount_Xz,MPI_CHAR,Dm->rank_Xz(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_yz,Dm->sendCount_yz,MPI_CHAR,Dm->rank_yz(),sendtag,
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recvID_YZ,Dm->recvCount_YZ,MPI_CHAR,Dm->rank_YZ(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_YZ,Dm->sendCount_YZ,MPI_CHAR,Dm->rank_YZ(),sendtag,
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recvID_yz,Dm->recvCount_yz,MPI_CHAR,Dm->rank_yz(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_Yz,Dm->sendCount_Yz,MPI_CHAR,Dm->rank_Yz(),sendtag,
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recvID_yZ,Dm->recvCount_yZ,MPI_CHAR,Dm->rank_yZ(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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MPI_Sendrecv(sendID_yZ,Dm->sendCount_yZ,MPI_CHAR,Dm->rank_yZ(),sendtag,
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recvID_Yz,Dm->recvCount_Yz,MPI_CHAR,Dm->rank_Yz(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
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//......................................................................................
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UnpackID(Dm->recvList("x"), Dm->recvCount("x") ,recvID_x, id);
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UnpackID(Dm->recvList("X"), Dm->recvCount("X") ,recvID_X, id);
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UnpackID(Dm->recvList("y"), Dm->recvCount("y") ,recvID_y, id);
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UnpackID(Dm->recvList("Y"), Dm->recvCount("Y") ,recvID_Y, id);
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UnpackID(Dm->recvList("z"), Dm->recvCount("z") ,recvID_z, id);
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UnpackID(Dm->recvList("Z"), Dm->recvCount("Z") ,recvID_Z, id);
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UnpackID(Dm->recvList("xy"), Dm->recvCount("xy") ,recvID_xy, id);
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UnpackID(Dm->recvList("Xy"), Dm->recvCount("Xy") ,recvID_Xy, id);
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UnpackID(Dm->recvList("xY"), Dm->recvCount("xY") ,recvID_xY, id);
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UnpackID(Dm->recvList("XY"), Dm->recvCount("XY") ,recvID_XY, id);
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UnpackID(Dm->recvList("xz"), Dm->recvCount("xz") ,recvID_xz, id);
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UnpackID(Dm->recvList("Xz"), Dm->recvCount("Xz") ,recvID_Xz, id);
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UnpackID(Dm->recvList("xZ"), Dm->recvCount("xZ") ,recvID_xZ, id);
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UnpackID(Dm->recvList("XZ"), Dm->recvCount("XZ") ,recvID_XZ, id);
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UnpackID(Dm->recvList("yz"), Dm->recvCount("yz") ,recvID_yz, id);
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UnpackID(Dm->recvList("Yz"), Dm->recvCount("Yz") ,recvID_Yz, id);
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UnpackID(Dm->recvList("yZ"), Dm->recvCount("yZ") ,recvID_yZ, id);
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UnpackID(Dm->recvList("YZ"), Dm->recvCount("YZ") ,recvID_YZ, id);
|
||||
UnpackID(Dm->recvList_x, Dm->recvCount_x ,recvID_x, id);
|
||||
UnpackID(Dm->recvList_X, Dm->recvCount_X ,recvID_X, id);
|
||||
UnpackID(Dm->recvList_y, Dm->recvCount_y ,recvID_y, id);
|
||||
UnpackID(Dm->recvList_Y, Dm->recvCount_Y ,recvID_Y, id);
|
||||
UnpackID(Dm->recvList_z, Dm->recvCount_z ,recvID_z, id);
|
||||
UnpackID(Dm->recvList_Z, Dm->recvCount_Z ,recvID_Z, id);
|
||||
UnpackID(Dm->recvList_xy, Dm->recvCount_xy ,recvID_xy, id);
|
||||
UnpackID(Dm->recvList_Xy, Dm->recvCount_Xy ,recvID_Xy, id);
|
||||
UnpackID(Dm->recvList_xY, Dm->recvCount_xY ,recvID_xY, id);
|
||||
UnpackID(Dm->recvList_XY, Dm->recvCount_XY ,recvID_XY, id);
|
||||
UnpackID(Dm->recvList_xz, Dm->recvCount_xz ,recvID_xz, id);
|
||||
UnpackID(Dm->recvList_Xz, Dm->recvCount_Xz ,recvID_Xz, id);
|
||||
UnpackID(Dm->recvList_xZ, Dm->recvCount_xZ ,recvID_xZ, id);
|
||||
UnpackID(Dm->recvList_XZ, Dm->recvCount_XZ ,recvID_XZ, id);
|
||||
UnpackID(Dm->recvList_yz, Dm->recvCount_yz ,recvID_yz, id);
|
||||
UnpackID(Dm->recvList_Yz, Dm->recvCount_Yz ,recvID_Yz, id);
|
||||
UnpackID(Dm->recvList_yZ, Dm->recvCount_yZ ,recvID_yZ, id);
|
||||
UnpackID(Dm->recvList_YZ, Dm->recvCount_YZ ,recvID_YZ, id);
|
||||
//......................................................................................
|
||||
|
||||
//double GlobalNumber = Dm->Comm.sumReduce( LocalNumber );
|
||||
MPI_Allreduce(&LocalNumber,&GlobalNumber,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
|
||||
|
||||
count = 0.f;
|
||||
for (int k=1; k<Nz-1; k++){
|
||||
@@ -253,7 +272,7 @@ double MorphOpen(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain>
|
||||
}
|
||||
}
|
||||
}
|
||||
countGlobal = Dm->Comm.sumReduce( count );
|
||||
MPI_Allreduce(&count,&countGlobal,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
|
||||
void_fraction_new = countGlobal/totalGlobal;
|
||||
void_fraction_diff_new = abs(void_fraction_new-VoidFraction);
|
||||
/* if (rank==0){
|
||||
@@ -285,7 +304,7 @@ double morph_open()
|
||||
fillHalo<char> fillChar(Dm->Comm,Dm->rank_info,{Nx-2,Ny-2,Nz-2},{1,1,1},0,1);
|
||||
|
||||
|
||||
GlobalNumber = Dm->Comm.sumReduce( LocalNumber );
|
||||
MPI_Allreduce(&LocalNumber,&GlobalNumber,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
|
||||
|
||||
count = 0.f;
|
||||
for (int k=1; k<Nz-1; k++){
|
||||
@@ -298,7 +317,7 @@ double morph_open()
|
||||
}
|
||||
}
|
||||
}
|
||||
countGlobal = Dm->Comm.sumReduce( count );
|
||||
MPI_Allreduce(&count,&countGlobal,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
|
||||
return countGlobal;
|
||||
}
|
||||
*/
|
||||
@@ -341,11 +360,11 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
|
||||
}
|
||||
}
|
||||
|
||||
Dm->Comm.barrier();
|
||||
MPI_Barrier(Dm->Comm);
|
||||
|
||||
// total Global is the number of nodes in the pore-space
|
||||
totalGlobal = Dm->Comm.sumReduce( count );
|
||||
maxdistGlobal = Dm->Comm.sumReduce( maxdist );
|
||||
MPI_Allreduce(&count,&totalGlobal,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
|
||||
MPI_Allreduce(&maxdist,&maxdistGlobal,1,MPI_DOUBLE,MPI_MAX,Dm->Comm);
|
||||
double volume=double(nprocx*nprocy*nprocz)*double(nx-2)*double(ny-2)*double(nz-2);
|
||||
double volume_fraction=totalGlobal/volume;
|
||||
if (rank==0) printf("Volume fraction for morphological opening: %f \n",volume_fraction);
|
||||
@@ -359,44 +378,44 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
|
||||
signed char *recvID_xy, *recvID_yz, *recvID_xz, *recvID_Xy, *recvID_Yz, *recvID_xZ;
|
||||
signed char *recvID_xY, *recvID_yZ, *recvID_Xz, *recvID_XY, *recvID_YZ, *recvID_XZ;
|
||||
// send buffers
|
||||
sendID_x = new signed char [Dm->sendCount("x")];
|
||||
sendID_y = new signed char [Dm->sendCount("y")];
|
||||
sendID_z = new signed char [Dm->sendCount("z")];
|
||||
sendID_X = new signed char [Dm->sendCount("X")];
|
||||
sendID_Y = new signed char [Dm->sendCount("Y")];
|
||||
sendID_Z = new signed char [Dm->sendCount("Z")];
|
||||
sendID_xy = new signed char [Dm->sendCount("xy")];
|
||||
sendID_yz = new signed char [Dm->sendCount("yz")];
|
||||
sendID_xz = new signed char [Dm->sendCount("xz")];
|
||||
sendID_Xy = new signed char [Dm->sendCount("Xy")];
|
||||
sendID_Yz = new signed char [Dm->sendCount("Yz")];
|
||||
sendID_xZ = new signed char [Dm->sendCount("xZ")];
|
||||
sendID_xY = new signed char [Dm->sendCount("xY")];
|
||||
sendID_yZ = new signed char [Dm->sendCount("yZ")];
|
||||
sendID_Xz = new signed char [Dm->sendCount("Xz")];
|
||||
sendID_XY = new signed char [Dm->sendCount("XY")];
|
||||
sendID_YZ = new signed char [Dm->sendCount("YZ")];
|
||||
sendID_XZ = new signed char [Dm->sendCount("XZ")];
|
||||
sendID_x = new signed char [Dm->sendCount_x];
|
||||
sendID_y = new signed char [Dm->sendCount_y];
|
||||
sendID_z = new signed char [Dm->sendCount_z];
|
||||
sendID_X = new signed char [Dm->sendCount_X];
|
||||
sendID_Y = new signed char [Dm->sendCount_Y];
|
||||
sendID_Z = new signed char [Dm->sendCount_Z];
|
||||
sendID_xy = new signed char [Dm->sendCount_xy];
|
||||
sendID_yz = new signed char [Dm->sendCount_yz];
|
||||
sendID_xz = new signed char [Dm->sendCount_xz];
|
||||
sendID_Xy = new signed char [Dm->sendCount_Xy];
|
||||
sendID_Yz = new signed char [Dm->sendCount_Yz];
|
||||
sendID_xZ = new signed char [Dm->sendCount_xZ];
|
||||
sendID_xY = new signed char [Dm->sendCount_xY];
|
||||
sendID_yZ = new signed char [Dm->sendCount_yZ];
|
||||
sendID_Xz = new signed char [Dm->sendCount_Xz];
|
||||
sendID_XY = new signed char [Dm->sendCount_XY];
|
||||
sendID_YZ = new signed char [Dm->sendCount_YZ];
|
||||
sendID_XZ = new signed char [Dm->sendCount_XZ];
|
||||
//......................................................................................
|
||||
// recv buffers
|
||||
recvID_x = new signed char [Dm->recvCount("x")];
|
||||
recvID_y = new signed char [Dm->recvCount("y")];
|
||||
recvID_z = new signed char [Dm->recvCount("z")];
|
||||
recvID_X = new signed char [Dm->recvCount("X")];
|
||||
recvID_Y = new signed char [Dm->recvCount("Y")];
|
||||
recvID_Z = new signed char [Dm->recvCount("Z")];
|
||||
recvID_xy = new signed char [Dm->recvCount("xy")];
|
||||
recvID_yz = new signed char [Dm->recvCount("yz")];
|
||||
recvID_xz = new signed char [Dm->recvCount("xz")];
|
||||
recvID_Xy = new signed char [Dm->recvCount("Xy")];
|
||||
recvID_xZ = new signed char [Dm->recvCount("xZ")];
|
||||
recvID_xY = new signed char [Dm->recvCount("xY")];
|
||||
recvID_yZ = new signed char [Dm->recvCount("yZ")];
|
||||
recvID_Yz = new signed char [Dm->recvCount("Yz")];
|
||||
recvID_Xz = new signed char [Dm->recvCount("Xz")];
|
||||
recvID_XY = new signed char [Dm->recvCount("XY")];
|
||||
recvID_YZ = new signed char [Dm->recvCount("YZ")];
|
||||
recvID_XZ = new signed char [Dm->recvCount("XZ")];
|
||||
recvID_x = new signed char [Dm->recvCount_x];
|
||||
recvID_y = new signed char [Dm->recvCount_y];
|
||||
recvID_z = new signed char [Dm->recvCount_z];
|
||||
recvID_X = new signed char [Dm->recvCount_X];
|
||||
recvID_Y = new signed char [Dm->recvCount_Y];
|
||||
recvID_Z = new signed char [Dm->recvCount_Z];
|
||||
recvID_xy = new signed char [Dm->recvCount_xy];
|
||||
recvID_yz = new signed char [Dm->recvCount_yz];
|
||||
recvID_xz = new signed char [Dm->recvCount_xz];
|
||||
recvID_Xy = new signed char [Dm->recvCount_Xy];
|
||||
recvID_xZ = new signed char [Dm->recvCount_xZ];
|
||||
recvID_xY = new signed char [Dm->recvCount_xY];
|
||||
recvID_yZ = new signed char [Dm->recvCount_yZ];
|
||||
recvID_Yz = new signed char [Dm->recvCount_Yz];
|
||||
recvID_Xz = new signed char [Dm->recvCount_Xz];
|
||||
recvID_XY = new signed char [Dm->recvCount_XY];
|
||||
recvID_YZ = new signed char [Dm->recvCount_YZ];
|
||||
recvID_XZ = new signed char [Dm->recvCount_XZ];
|
||||
//......................................................................................
|
||||
int sendtag,recvtag;
|
||||
sendtag = recvtag = 7;
|
||||
@@ -415,6 +434,7 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
|
||||
double deltaR=0.05; // amount to change the radius in voxel units
|
||||
double Rcrit_old;
|
||||
|
||||
double GlobalNumber = 1.f;
|
||||
int imin,jmin,kmin,imax,jmax,kmax;
|
||||
|
||||
double Rcrit_new = maxdistGlobal;
|
||||
@@ -422,7 +442,7 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
|
||||
// Rcrit_new = strtod(argv[2],NULL);
|
||||
// if (rank==0) printf("Max. distance =%f, Initial critical radius = %f \n",maxdistGlobal,Rcrit_new);
|
||||
//}
|
||||
Dm->Comm.barrier();
|
||||
MPI_Barrier(Dm->Comm);
|
||||
|
||||
|
||||
FILE *DRAIN = fopen("morphdrain.csv","w");
|
||||
@@ -469,64 +489,82 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
|
||||
}
|
||||
}
|
||||
// Pack and send the updated ID values
|
||||
PackID(Dm->sendList("x"), Dm->sendCount("x") ,sendID_x, id);
|
||||
PackID(Dm->sendList("X"), Dm->sendCount("X") ,sendID_X, id);
|
||||
PackID(Dm->sendList("y"), Dm->sendCount("y") ,sendID_y, id);
|
||||
PackID(Dm->sendList("Y"), Dm->sendCount("Y") ,sendID_Y, id);
|
||||
PackID(Dm->sendList("z"), Dm->sendCount("z") ,sendID_z, id);
|
||||
PackID(Dm->sendList("Z"), Dm->sendCount("Z") ,sendID_Z, id);
|
||||
PackID(Dm->sendList("xy"), Dm->sendCount("xy") ,sendID_xy, id);
|
||||
PackID(Dm->sendList("Xy"), Dm->sendCount("Xy") ,sendID_Xy, id);
|
||||
PackID(Dm->sendList("xY"), Dm->sendCount("xY") ,sendID_xY, id);
|
||||
PackID(Dm->sendList("XY"), Dm->sendCount("XY") ,sendID_XY, id);
|
||||
PackID(Dm->sendList("xz"), Dm->sendCount("xz") ,sendID_xz, id);
|
||||
PackID(Dm->sendList("Xz"), Dm->sendCount("Xz") ,sendID_Xz, id);
|
||||
PackID(Dm->sendList("xZ"), Dm->sendCount("xZ") ,sendID_xZ, id);
|
||||
PackID(Dm->sendList("XZ"), Dm->sendCount("XZ") ,sendID_XZ, id);
|
||||
PackID(Dm->sendList("yz"), Dm->sendCount("yz") ,sendID_yz, id);
|
||||
PackID(Dm->sendList("Yz"), Dm->sendCount("Yz") ,sendID_Yz, id);
|
||||
PackID(Dm->sendList("yZ"), Dm->sendCount("yZ") ,sendID_yZ, id);
|
||||
PackID(Dm->sendList("YZ"), Dm->sendCount("YZ") ,sendID_YZ, id);
|
||||
PackID(Dm->sendList_x, Dm->sendCount_x ,sendID_x, id);
|
||||
PackID(Dm->sendList_X, Dm->sendCount_X ,sendID_X, id);
|
||||
PackID(Dm->sendList_y, Dm->sendCount_y ,sendID_y, id);
|
||||
PackID(Dm->sendList_Y, Dm->sendCount_Y ,sendID_Y, id);
|
||||
PackID(Dm->sendList_z, Dm->sendCount_z ,sendID_z, id);
|
||||
PackID(Dm->sendList_Z, Dm->sendCount_Z ,sendID_Z, id);
|
||||
PackID(Dm->sendList_xy, Dm->sendCount_xy ,sendID_xy, id);
|
||||
PackID(Dm->sendList_Xy, Dm->sendCount_Xy ,sendID_Xy, id);
|
||||
PackID(Dm->sendList_xY, Dm->sendCount_xY ,sendID_xY, id);
|
||||
PackID(Dm->sendList_XY, Dm->sendCount_XY ,sendID_XY, id);
|
||||
PackID(Dm->sendList_xz, Dm->sendCount_xz ,sendID_xz, id);
|
||||
PackID(Dm->sendList_Xz, Dm->sendCount_Xz ,sendID_Xz, id);
|
||||
PackID(Dm->sendList_xZ, Dm->sendCount_xZ ,sendID_xZ, id);
|
||||
PackID(Dm->sendList_XZ, Dm->sendCount_XZ ,sendID_XZ, id);
|
||||
PackID(Dm->sendList_yz, Dm->sendCount_yz ,sendID_yz, id);
|
||||
PackID(Dm->sendList_Yz, Dm->sendCount_Yz ,sendID_Yz, id);
|
||||
PackID(Dm->sendList_yZ, Dm->sendCount_yZ ,sendID_yZ, id);
|
||||
PackID(Dm->sendList_YZ, Dm->sendCount_YZ ,sendID_YZ, id);
|
||||
//......................................................................................
|
||||
Dm->Comm.sendrecv(sendID_x,Dm->sendCount("x"),Dm->rank_x(),sendtag,recvID_X,Dm->recvCount("X"),Dm->rank_X(),recvtag);
|
||||
Dm->Comm.sendrecv(sendID_X,Dm->sendCount("X"),Dm->rank_X(),sendtag,recvID_x,Dm->recvCount("x"),Dm->rank_x(),recvtag);
|
||||
Dm->Comm.sendrecv(sendID_y,Dm->sendCount("y"),Dm->rank_y(),sendtag,recvID_Y,Dm->recvCount("Y"),Dm->rank_Y(),recvtag);
|
||||
Dm->Comm.sendrecv(sendID_Y,Dm->sendCount("Y"),Dm->rank_Y(),sendtag,recvID_y,Dm->recvCount("y"),Dm->rank_y(),recvtag);
|
||||
Dm->Comm.sendrecv(sendID_z,Dm->sendCount("z"),Dm->rank_z(),sendtag,recvID_Z,Dm->recvCount("Z"),Dm->rank_Z(),recvtag);
|
||||
Dm->Comm.sendrecv(sendID_Z,Dm->sendCount("Z"),Dm->rank_Z(),sendtag,recvID_z,Dm->recvCount("z"),Dm->rank_z(),recvtag);
|
||||
Dm->Comm.sendrecv(sendID_xy,Dm->sendCount("xy"),Dm->rank_xy(),sendtag,recvID_XY,Dm->recvCount("XY"),Dm->rank_XY(),recvtag);
|
||||
Dm->Comm.sendrecv(sendID_XY,Dm->sendCount("XY"),Dm->rank_XY(),sendtag,recvID_xy,Dm->recvCount("xy"),Dm->rank_xy(),recvtag);
|
||||
Dm->Comm.sendrecv(sendID_Xy,Dm->sendCount("Xy"),Dm->rank_Xy(),sendtag,recvID_xY,Dm->recvCount("xY"),Dm->rank_xY(),recvtag);
|
||||
Dm->Comm.sendrecv(sendID_xY,Dm->sendCount("xY"),Dm->rank_xY(),sendtag,recvID_Xy,Dm->recvCount("Xy"),Dm->rank_Xy(),recvtag);
|
||||
Dm->Comm.sendrecv(sendID_xz,Dm->sendCount("xz"),Dm->rank_xz(),sendtag,recvID_XZ,Dm->recvCount("XZ"),Dm->rank_XZ(),recvtag);
|
||||
Dm->Comm.sendrecv(sendID_XZ,Dm->sendCount("XZ"),Dm->rank_XZ(),sendtag,recvID_xz,Dm->recvCount("xz"),Dm->rank_xz(),recvtag);
|
||||
Dm->Comm.sendrecv(sendID_Xz,Dm->sendCount("Xz"),Dm->rank_Xz(),sendtag,recvID_xZ,Dm->recvCount("xZ"),Dm->rank_xZ(),recvtag);
|
||||
Dm->Comm.sendrecv(sendID_xZ,Dm->sendCount("xZ"),Dm->rank_xZ(),sendtag,recvID_Xz,Dm->recvCount("Xz"),Dm->rank_Xz(),recvtag);
|
||||
Dm->Comm.sendrecv(sendID_yz,Dm->sendCount("yz"),Dm->rank_yz(),sendtag,recvID_YZ,Dm->recvCount("YZ"),Dm->rank_YZ(),recvtag);
|
||||
Dm->Comm.sendrecv(sendID_YZ,Dm->sendCount("YZ"),Dm->rank_YZ(),sendtag,recvID_yz,Dm->recvCount("yz"),Dm->rank_yz(),recvtag);
|
||||
Dm->Comm.sendrecv(sendID_Yz,Dm->sendCount("Yz"),Dm->rank_Yz(),sendtag,recvID_yZ,Dm->recvCount("yZ"),Dm->rank_yZ(),recvtag);
|
||||
Dm->Comm.sendrecv(sendID_yZ,Dm->sendCount("yZ"),Dm->rank_yZ(),sendtag,recvID_Yz,Dm->recvCount("Yz"),Dm->rank_Yz(),recvtag);
|
||||
MPI_Sendrecv(sendID_x,Dm->sendCount_x,MPI_CHAR,Dm->rank_x(),sendtag,
|
||||
recvID_X,Dm->recvCount_X,MPI_CHAR,Dm->rank_X(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
|
||||
MPI_Sendrecv(sendID_X,Dm->sendCount_X,MPI_CHAR,Dm->rank_X(),sendtag,
|
||||
recvID_x,Dm->recvCount_x,MPI_CHAR,Dm->rank_x(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
|
||||
MPI_Sendrecv(sendID_y,Dm->sendCount_y,MPI_CHAR,Dm->rank_y(),sendtag,
|
||||
recvID_Y,Dm->recvCount_Y,MPI_CHAR,Dm->rank_Y(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
|
||||
MPI_Sendrecv(sendID_Y,Dm->sendCount_Y,MPI_CHAR,Dm->rank_Y(),sendtag,
|
||||
recvID_y,Dm->recvCount_y,MPI_CHAR,Dm->rank_y(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
|
||||
MPI_Sendrecv(sendID_z,Dm->sendCount_z,MPI_CHAR,Dm->rank_z(),sendtag,
|
||||
recvID_Z,Dm->recvCount_Z,MPI_CHAR,Dm->rank_Z(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
|
||||
MPI_Sendrecv(sendID_Z,Dm->sendCount_Z,MPI_CHAR,Dm->rank_Z(),sendtag,
|
||||
recvID_z,Dm->recvCount_z,MPI_CHAR,Dm->rank_z(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
|
||||
MPI_Sendrecv(sendID_xy,Dm->sendCount_xy,MPI_CHAR,Dm->rank_xy(),sendtag,
|
||||
recvID_XY,Dm->recvCount_XY,MPI_CHAR,Dm->rank_XY(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
|
||||
MPI_Sendrecv(sendID_XY,Dm->sendCount_XY,MPI_CHAR,Dm->rank_XY(),sendtag,
|
||||
recvID_xy,Dm->recvCount_xy,MPI_CHAR,Dm->rank_xy(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
|
||||
MPI_Sendrecv(sendID_Xy,Dm->sendCount_Xy,MPI_CHAR,Dm->rank_Xy(),sendtag,
|
||||
recvID_xY,Dm->recvCount_xY,MPI_CHAR,Dm->rank_xY(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
|
||||
MPI_Sendrecv(sendID_xY,Dm->sendCount_xY,MPI_CHAR,Dm->rank_xY(),sendtag,
|
||||
recvID_Xy,Dm->recvCount_Xy,MPI_CHAR,Dm->rank_Xy(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
|
||||
MPI_Sendrecv(sendID_xz,Dm->sendCount_xz,MPI_CHAR,Dm->rank_xz(),sendtag,
|
||||
recvID_XZ,Dm->recvCount_XZ,MPI_CHAR,Dm->rank_XZ(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
|
||||
MPI_Sendrecv(sendID_XZ,Dm->sendCount_XZ,MPI_CHAR,Dm->rank_XZ(),sendtag,
|
||||
recvID_xz,Dm->recvCount_xz,MPI_CHAR,Dm->rank_xz(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
|
||||
MPI_Sendrecv(sendID_Xz,Dm->sendCount_Xz,MPI_CHAR,Dm->rank_Xz(),sendtag,
|
||||
recvID_xZ,Dm->recvCount_xZ,MPI_CHAR,Dm->rank_xZ(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
|
||||
MPI_Sendrecv(sendID_xZ,Dm->sendCount_xZ,MPI_CHAR,Dm->rank_xZ(),sendtag,
|
||||
recvID_Xz,Dm->recvCount_Xz,MPI_CHAR,Dm->rank_Xz(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
|
||||
MPI_Sendrecv(sendID_yz,Dm->sendCount_yz,MPI_CHAR,Dm->rank_yz(),sendtag,
|
||||
recvID_YZ,Dm->recvCount_YZ,MPI_CHAR,Dm->rank_YZ(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
|
||||
MPI_Sendrecv(sendID_YZ,Dm->sendCount_YZ,MPI_CHAR,Dm->rank_YZ(),sendtag,
|
||||
recvID_yz,Dm->recvCount_yz,MPI_CHAR,Dm->rank_yz(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
|
||||
MPI_Sendrecv(sendID_Yz,Dm->sendCount_Yz,MPI_CHAR,Dm->rank_Yz(),sendtag,
|
||||
recvID_yZ,Dm->recvCount_yZ,MPI_CHAR,Dm->rank_yZ(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
|
||||
MPI_Sendrecv(sendID_yZ,Dm->sendCount_yZ,MPI_CHAR,Dm->rank_yZ(),sendtag,
|
||||
recvID_Yz,Dm->recvCount_Yz,MPI_CHAR,Dm->rank_Yz(),recvtag,Dm->Comm,MPI_STATUS_IGNORE);
|
||||
//......................................................................................
|
||||
UnpackID(Dm->recvList("x"), Dm->recvCount("x") ,recvID_x, id);
|
||||
UnpackID(Dm->recvList("X"), Dm->recvCount("X") ,recvID_X, id);
|
||||
UnpackID(Dm->recvList("y"), Dm->recvCount("y") ,recvID_y, id);
|
||||
UnpackID(Dm->recvList("Y"), Dm->recvCount("Y") ,recvID_Y, id);
|
||||
UnpackID(Dm->recvList("z"), Dm->recvCount("z") ,recvID_z, id);
|
||||
UnpackID(Dm->recvList("Z"), Dm->recvCount("Z") ,recvID_Z, id);
|
||||
UnpackID(Dm->recvList("xy"), Dm->recvCount("xy") ,recvID_xy, id);
|
||||
UnpackID(Dm->recvList("Xy"), Dm->recvCount("Xy") ,recvID_Xy, id);
|
||||
UnpackID(Dm->recvList("xY"), Dm->recvCount("xY") ,recvID_xY, id);
|
||||
UnpackID(Dm->recvList("XY"), Dm->recvCount("XY") ,recvID_XY, id);
|
||||
UnpackID(Dm->recvList("xz"), Dm->recvCount("xz") ,recvID_xz, id);
|
||||
UnpackID(Dm->recvList("Xz"), Dm->recvCount("Xz") ,recvID_Xz, id);
|
||||
UnpackID(Dm->recvList("xZ"), Dm->recvCount("xZ") ,recvID_xZ, id);
|
||||
UnpackID(Dm->recvList("XZ"), Dm->recvCount("XZ") ,recvID_XZ, id);
|
||||
UnpackID(Dm->recvList("yz"), Dm->recvCount("yz") ,recvID_yz, id);
|
||||
UnpackID(Dm->recvList("Yz"), Dm->recvCount("Yz") ,recvID_Yz, id);
|
||||
UnpackID(Dm->recvList("yZ"), Dm->recvCount("yZ") ,recvID_yZ, id);
|
||||
UnpackID(Dm->recvList("YZ"), Dm->recvCount("YZ") ,recvID_YZ, id);
|
||||
UnpackID(Dm->recvList_x, Dm->recvCount_x ,recvID_x, id);
|
||||
UnpackID(Dm->recvList_X, Dm->recvCount_X ,recvID_X, id);
|
||||
UnpackID(Dm->recvList_y, Dm->recvCount_y ,recvID_y, id);
|
||||
UnpackID(Dm->recvList_Y, Dm->recvCount_Y ,recvID_Y, id);
|
||||
UnpackID(Dm->recvList_z, Dm->recvCount_z ,recvID_z, id);
|
||||
UnpackID(Dm->recvList_Z, Dm->recvCount_Z ,recvID_Z, id);
|
||||
UnpackID(Dm->recvList_xy, Dm->recvCount_xy ,recvID_xy, id);
|
||||
UnpackID(Dm->recvList_Xy, Dm->recvCount_Xy ,recvID_Xy, id);
|
||||
UnpackID(Dm->recvList_xY, Dm->recvCount_xY ,recvID_xY, id);
|
||||
UnpackID(Dm->recvList_XY, Dm->recvCount_XY ,recvID_XY, id);
|
||||
UnpackID(Dm->recvList_xz, Dm->recvCount_xz ,recvID_xz, id);
|
||||
UnpackID(Dm->recvList_Xz, Dm->recvCount_Xz ,recvID_Xz, id);
|
||||
UnpackID(Dm->recvList_xZ, Dm->recvCount_xZ ,recvID_xZ, id);
|
||||
UnpackID(Dm->recvList_XZ, Dm->recvCount_XZ ,recvID_XZ, id);
|
||||
UnpackID(Dm->recvList_yz, Dm->recvCount_yz ,recvID_yz, id);
|
||||
UnpackID(Dm->recvList_Yz, Dm->recvCount_Yz ,recvID_Yz, id);
|
||||
UnpackID(Dm->recvList_yZ, Dm->recvCount_yZ ,recvID_yZ, id);
|
||||
UnpackID(Dm->recvList_YZ, Dm->recvCount_YZ ,recvID_YZ, id);
|
||||
//......................................................................................
|
||||
// double GlobalNumber = Dm->Comm.sumReduce( LocalNumber );
|
||||
MPI_Allreduce(&LocalNumber,&GlobalNumber,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
|
||||
|
||||
for (int k=0; k<nz; k++){
|
||||
for (int j=0; j<ny; j++){
|
||||
@@ -545,7 +583,7 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
|
||||
BlobIDstruct new_index;
|
||||
double vF=0.0; double vS=0.0;
|
||||
ComputeGlobalBlobIDs(nx-2,ny-2,nz-2,Dm->rank_info,phase,SignDist,vF,vS,phase_label,Dm->Comm);
|
||||
Dm->Comm.barrier();
|
||||
MPI_Barrier(Dm->Comm);
|
||||
|
||||
for (int k=0; k<nz; k++){
|
||||
for (int j=0; j<ny; j++){
|
||||
@@ -581,7 +619,7 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
|
||||
}
|
||||
|
||||
ComputeGlobalBlobIDs(nx-2,ny-2,nz-2,Dm->rank_info,phase,SignDist,vF,vS,phase_label,Dm->Comm);
|
||||
Dm->Comm.barrier();
|
||||
MPI_Barrier(Dm->Comm);
|
||||
|
||||
for (int k=1; k<nz-1; k++){
|
||||
for (int j=1; j<ny-1; j++){
|
||||
@@ -607,7 +645,7 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
|
||||
}
|
||||
}
|
||||
}
|
||||
countGlobal = Dm->Comm.sumReduce( count );
|
||||
MPI_Allreduce(&count,&countGlobal,1,MPI_DOUBLE,MPI_SUM,Dm->Comm);
|
||||
void_fraction_new = countGlobal/totalGlobal;
|
||||
void_fraction_diff_new = abs(void_fraction_new-VoidFraction);
|
||||
if (rank==0){
|
||||
@@ -647,13 +685,13 @@ double MorphDrain(DoubleArray &SignDist, signed char *id, std::shared_ptr<Domain
|
||||
return final_void_fraction;
|
||||
}
|
||||
|
||||
double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id, std::shared_ptr<Domain> Dm, double TargetGrowth)
|
||||
double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id, std::shared_ptr<Domain> Dm, double TargetGrowth, double WallFactor)
|
||||
{
|
||||
int Nx = Dm->Nx;
|
||||
int Ny = Dm->Ny;
|
||||
int Nz = Dm->Nz;
|
||||
int rank = Dm->rank();
|
||||
|
||||
|
||||
double count=0.0;
|
||||
for (int k=1; k<Nz-1; k++){
|
||||
for (int j=1; j<Ny-1; j++){
|
||||
@@ -664,7 +702,7 @@ double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id,
|
||||
}
|
||||
}
|
||||
}
|
||||
double count_original = Dm->Comm.sumReduce( count);
|
||||
double count_original=sumReduce( Dm->Comm, count);
|
||||
|
||||
// Estimate morph_delta
|
||||
double morph_delta = 0.0;
|
||||
@@ -684,8 +722,7 @@ double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id,
|
||||
for (int j=1; j<Ny-1; j++){
|
||||
for (int i=1; i<Nx-1; i++){
|
||||
double walldist=BoundaryDist(i,j,k);
|
||||
double wallweight = 1.0 / (1+exp(-5.f*(walldist-1.f)));
|
||||
//wallweight = 1.0;
|
||||
double wallweight = WallFactor/ (1+exp(-5.f*(walldist-1.f)));
|
||||
if (fabs(wallweight*morph_delta) > MAX_DISPLACEMENT) MAX_DISPLACEMENT= fabs(wallweight*morph_delta);
|
||||
|
||||
if (Dist(i,j,k) - wallweight*morph_delta < 0.0){
|
||||
@@ -694,8 +731,8 @@ double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id,
|
||||
}
|
||||
}
|
||||
}
|
||||
count = Dm->Comm.sumReduce( count );
|
||||
MAX_DISPLACEMENT = Dm->Comm.maxReduce( MAX_DISPLACEMENT );
|
||||
count=sumReduce( Dm->Comm, count);
|
||||
MAX_DISPLACEMENT = maxReduce( Dm->Comm, MAX_DISPLACEMENT);
|
||||
GrowthEstimate = count - count_original;
|
||||
ERROR = fabs((GrowthEstimate-TargetGrowth) /TargetGrowth);
|
||||
|
||||
@@ -731,14 +768,14 @@ double MorphGrow(DoubleArray &BoundaryDist, DoubleArray &Dist, Array<char> &id,
|
||||
for (int j=1; j<Ny-1; j++){
|
||||
for (int i=1; i<Nx-1; i++){
|
||||
double walldist=BoundaryDist(i,j,k);
|
||||
double wallweight = 1.0 / (1+exp(-5.f*(walldist-1.f)));
|
||||
double wallweight = WallFactor / (1+exp(-5.f*(walldist-1.f)));
|
||||
//wallweight = 1.0;
|
||||
Dist(i,j,k) -= wallweight*morph_delta;
|
||||
if (Dist(i,j,k) < 0.0) count+=1.0;
|
||||
}
|
||||
}
|
||||
}
|
||||
count = Dm->Comm.sumReduce( count );
|
||||
count=sumReduce( Dm->Comm, count);
|
||||
|
||||
return count;
|
||||
}
|
||||
|
||||
@@ -9,7 +9,7 @@ color lattice boltzmann model
|
||||
#include <stdlib.h>
|
||||
#include <time.h>
|
||||
|
||||
ScaLBL_ColorModel::ScaLBL_ColorModel(int RANK, int NP, MPI_Comm COMM):
|
||||
ScaLBL_ColorModel::ScaLBL_ColorModel(int RANK, int NP, const Utilities::MPI& COMM):
|
||||
rank(RANK), nprocs(NP), Restart(0),timestep(0),timestepMax(0),tauA(0),tauB(0),rhoA(0),rhoB(0),alpha(0),beta(0),
|
||||
Fx(0),Fy(0),Fz(0),flux(0),din(0),dout(0),inletA(0),inletB(0),outletA(0),outletB(0),
|
||||
Nx(0),Ny(0),Nz(0),N(0),Np(0),nprocx(0),nprocy(0),nprocz(0),BoundaryCondition(0),Lx(0),Ly(0),Lz(0),comm(COMM)
|
||||
|
||||
@@ -18,7 +18,7 @@ Implementation of color lattice boltzmann model
|
||||
|
||||
class ScaLBL_ColorModel{
|
||||
public:
|
||||
ScaLBL_ColorModel(int RANK, int NP, MPI_Comm COMM);
|
||||
ScaLBL_ColorModel(int RANK, int NP, const Utilities::MPI& COMM);
|
||||
~ScaLBL_ColorModel();
|
||||
|
||||
// functions in they should be run
|
||||
|
||||
24
sample_scripts/configure_ubuntu
Executable file
24
sample_scripts/configure_ubuntu
Executable file
@@ -0,0 +1,24 @@
|
||||
#!/bin/bash
|
||||
|
||||
cmake -D CMAKE_C_COMPILER:PATH=/opt/arden/openmpi/3.1.2/bin/mpicc \
|
||||
-D CMAKE_CXX_COMPILER:PATH=/opt/arden/openmpi/3.1.2/bin/mpicxx \
|
||||
-D CMAKE_C_FLAGS="-O3 -fPIC" \
|
||||
-D CMAKE_CXX_FLAGS="-O3 -fPIC " \
|
||||
-D CMAKE_CXX_STANDARD=14 \
|
||||
-D MPI_COMPILER:BOOL=TRUE \
|
||||
-D MPIEXEC=mpirun \
|
||||
-D USE_EXT_MPI_FOR_SERIAL_TESTS:BOOL=TRUE \
|
||||
-D CMAKE_BUILD_TYPE:STRING=Release \
|
||||
-D CUDA_FLAGS="-arch sm_35" \
|
||||
-D CUDA_HOST_COMPILER="/usr/bin/gcc" \
|
||||
-D HDF5_DIRECTORY="/opt/arden/hdf5/1.8.12" \
|
||||
-D HDF5_LIB="/opt/arden/hdf5/1.8.12/lib/libhdf5.a"\
|
||||
-D USE_SILO=1 \
|
||||
-D SILO_LIB="/opt/arden/silo/4.10.2/lib/libsiloh5.a" \
|
||||
-D SILO_DIRECTORY="/opt/arden/silo/4.10.2" \
|
||||
-D USE_NETCDF=1 \
|
||||
-D NETCDF_DIRECTORY="/opt/arden/netcdf/4.6.1" \
|
||||
-D USE_CUDA=0 \
|
||||
-D USE_TIMER=0 \
|
||||
~/Programs/LBPM-WIA
|
||||
|
||||
Reference in New Issue
Block a user