membrane data structures compiling
This commit is contained in:
James McClure
@@ -275,6 +275,17 @@ Membrane::Membrane(std::shared_ptr <Domain> Dm, int *initialNeighborList, int Ns
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Membrane::~Membrane() {
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ScaLBL_FreeDeviceMemory( coefficient_x );
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ScaLBL_FreeDeviceMemory( coefficient_X );
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ScaLBL_FreeDeviceMemory( coefficient_y );
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ScaLBL_FreeDeviceMemory( coefficient_Y );
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ScaLBL_FreeDeviceMemory( coefficient_z );
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ScaLBL_FreeDeviceMemory( coefficient_Z );
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ScaLBL_FreeDeviceMemory( dvcNeighborList );
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ScaLBL_FreeDeviceMemory( dvcMembraneLinks );
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ScaLBL_FreeDeviceMemory( dvcMembraneCoef );
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ScaLBL_FreeDeviceMemory( sendbuf_x );
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ScaLBL_FreeDeviceMemory( sendbuf_X );
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ScaLBL_FreeDeviceMemory( sendbuf_y );
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@@ -525,7 +536,6 @@ int Membrane::Create(std::shared_ptr <Domain> Dm, DoubleArray &Distance, IntArra
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membraneTag = new int [mlink];
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membraneLinks = new int [2*mlink];
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membraneDist = new double [2*mlink];
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membraneCoef = new double [2*mlink];
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/* construct the membrane*/
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/* *
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@@ -707,6 +717,17 @@ int Membrane::Create(std::shared_ptr <Domain> Dm, DoubleArray &Distance, IntArra
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}
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}
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}
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/* Create device copies of data structures */
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ScaLBL_AllocateDeviceMemory((void **)&dvcNeighborList, 18*Np*sizeof(int));
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ScaLBL_AllocateDeviceMemory((void **)&dvcMembraneLinks, 2*mlink*sizeof(int));
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ScaLBL_AllocateDeviceMemory((void **)&dvcMembraneCoef, 2*mlink*sizeof(double));
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ScaLBL_AllocateDeviceMemory((void **)&dvcMembraneDistance, 2*mlink*sizeof(double));
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ScaLBL_CopyToDevice(dvcNeighborList, neighborList, 18*Np*sizeof(int));
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ScaLBL_CopyToDevice(dvcMembraneLinks, membraneLinks, 2*mlink*sizeof(int));
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ScaLBL_CopyToDevice(dvcMembraneDistance, membraneDist, 2*mlink*sizeof(double));
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/* Re-organize communication based on membrane structure*/
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//...Map recieve list for the X face: q=2,8,10,12,14 .................................
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@@ -792,7 +813,15 @@ int Membrane::Create(std::shared_ptr <Domain> Dm, DoubleArray &Distance, IntArra
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CommunicationCount = SendCount+RecvCount;
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//......................................................................................
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// Allocate membrane coefficient buffers (for d3q7 recv)
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ScaLBL_AllocateZeroCopy((void **) &coefficient_x, (recvCount_x - linkCount_x[0])*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &coefficient_X, (recvCount_X - linkCount_X[0])*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &coefficient_y, (recvCount_y - linkCount_y[0])*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &coefficient_Y, (recvCount_Y - linkCount_Y[0])*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &coefficient_z, (recvCount_z - linkCount_z[0])*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &coefficient_Z, (recvCount_Z - linkCount_Z[0])*sizeof(double));
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//......................................................................................
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return mlink;
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}
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@@ -1030,7 +1059,7 @@ void Membrane::RecvD3Q19AA(double *dist){
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Membrane_D3Q19_Unpack(15,dvcRecvDist_Z, dvcRecvLinks_Z,3*recvCount_Z,linkCount_Z[3],recvbuf_Z,dist,N);
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Membrane_D3Q19_Unpack(18,dvcRecvDist_Z, dvcRecvLinks_Z,4*recvCount_Z,linkCount_Z[4],recvbuf_Z,dist,N);
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//..................................................................................
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//...Pack the xy edge (8)................................
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//...Pack the xy edge (8)...............................
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Membrane_D3Q19_Unpack(8,dvcRecvDist_xy, dvcRecvLinks_xy,0,recvCount_xy,recvbuf_xy,dist,N);
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//...Pack the Xy edge (9)................................
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Membrane_D3Q19_Unpack(9,dvcRecvDist_Xy, dvcRecvLinks_Xy,0,recvCount_Xy,recvbuf_Xy,dist,N);
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@@ -1057,6 +1086,83 @@ void Membrane::RecvD3Q19AA(double *dist){
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//...................................................................................
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Lock=false; // unlock the communicator after communications complete
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//...................................................................................
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}
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void Membrane::SendD3Q7AA(double *dist){
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if (Lock==true){
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ERROR("Membrane Error (SendD3Q7): Membrane communicator is locked -- did you forget to match Send/Recv calls?");
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}
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else{
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Lock=true;
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}
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// assign tag of 37 to D3Q7 communication
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sendtag = recvtag = 37;
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ScaLBL_DeviceBarrier();
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// Pack the distributions
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//...Packing for x face(q=2)................................
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ScaLBL_D3Q19_Pack(2,dvcSendList_x,0,sendCount_x,sendbuf_x,dist,N);
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req1[0] = MPI_COMM_SCALBL.Isend(sendbuf_x, sendCount_x,rank_x,sendtag);
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req2[0] = MPI_COMM_SCALBL.Irecv(recvbuf_X, recvCount_X,rank_X,recvtag);
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//...Packing for X face(q=1)................................
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ScaLBL_D3Q19_Pack(1,dvcSendList_X,0,sendCount_X,sendbuf_X,dist,N);
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req1[1] = MPI_COMM_SCALBL.Isend(sendbuf_X, sendCount_X,rank_X,sendtag);
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req2[1] = MPI_COMM_SCALBL.Irecv(recvbuf_x, recvCount_x,rank_x,recvtag);
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//...Packing for y face(q=4).................................
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ScaLBL_D3Q19_Pack(4,dvcSendList_y,0,sendCount_y,sendbuf_y,dist,N);
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req1[2] = MPI_COMM_SCALBL.Isend(sendbuf_y, sendCount_y,rank_y,sendtag);
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req2[2] = MPI_COMM_SCALBL.Irecv(recvbuf_Y, recvCount_Y,rank_Y,recvtag);
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//...Packing for Y face(q=3).................................
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ScaLBL_D3Q19_Pack(3,dvcSendList_Y,0,sendCount_Y,sendbuf_Y,dist,N);
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req1[3] = MPI_COMM_SCALBL.Isend(sendbuf_Y, sendCount_Y,rank_Y,sendtag);
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req2[3] = MPI_COMM_SCALBL.Irecv(recvbuf_y, recvCount_y,rank_y,recvtag);
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//...Packing for z face(q=6)................................
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ScaLBL_D3Q19_Pack(6,dvcSendList_z,0,sendCount_z,sendbuf_z,dist,N);
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req1[4] = MPI_COMM_SCALBL.Isend(sendbuf_z, sendCount_z,rank_z,sendtag);
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req2[4] = MPI_COMM_SCALBL.Irecv(recvbuf_Z, recvCount_Z,rank_Z,recvtag);
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//...Packing for Z face(q=5)................................
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ScaLBL_D3Q19_Pack(5,dvcSendList_Z,0,sendCount_Z,sendbuf_Z,dist,N);
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req1[5] = MPI_COMM_SCALBL.Isend(sendbuf_Z, sendCount_Z,rank_Z,sendtag);
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req2[5] = MPI_COMM_SCALBL.Irecv(recvbuf_z, recvCount_z,rank_z,recvtag);
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}
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void Membrane::RecvD37AA(double *dist){
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//...................................................................................
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// Wait for completion of D3Q19 communication
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MPI_COMM_SCALBL.waitAll(6,req1);
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MPI_COMM_SCALBL.waitAll(6,req2);
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ScaLBL_DeviceBarrier();
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//...................................................................................
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// NOTE: AA Routine writes to opposite
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// Unpack the distributions on the device
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//...................................................................................
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//...Unpacking for x face(q=2)................................
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ScaLBL_D3Q7_Membrane_Unpack(2,dvcRecvDist_x, dvcRecvLinks_x,0,linkCount_x[0],recvCount_x,recvbuf_x,dist,N,coefficient_x);
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//...................................................................................
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//...Packing for X face(q=1)................................
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ScaLBL_D3Q7_Membrane_Unpack(1,dvcRecvDist_X, dvcRecvLinks_X,0,linkCount_X[0],recvCount_X,recvbuf_X,dist,N,coefficient_X);
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//...................................................................................
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//...Packing for y face(q=4).................................
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ScaLBL_D3Q7_Membrane_Unpack(4,dvcRecvDist_y, dvcRecvLinks_y,0,linkCount_y[0],recvCount_y,recvbuf_y,dist,N,coefficient_y);
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//...................................................................................
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//...Packing for Y face(q=3).................................
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ScaLBL_D3Q7_Membrane_Unpack(3,dvcRecvDist_Y, dvcRecvLinks_Y,0,linkCount_Y[0],recvCount_Y,recvbuf_Y,dist,N,coefficient_Y);
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//...................................................................................
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//...Packing for z face(q=6)................................
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ScaLBL_D3Q7_Membrane_Unpack(6,dvcRecvDist_z, dvcRecvLinks_z,0,linkCount_z[0],recvCount_z,recvbuf_z,dist,N,coefficient_z);
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//...Packing for Z face(q=5)................................
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ScaLBL_D3Q7_Membrane_Unpack(5,dvcRecvDist_Z, dvcRecvLinks_Z,0,linkCount_Z[0],recvCount_Z,recvbuf_Z,dist,N,coefficient_Z);
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//..................................................................................
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//...................................................................................
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Lock=false; // unlock the communicator after communications complete
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//...................................................................................
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}
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void Membrane::AssignCoefficients(double *dvcPsi, double *dvcDistance, double *dvcMap, std::string method){
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/* Assign mass transfer coefficients to the membrane data structure */
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}
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@@ -58,8 +58,15 @@ public:
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int *membraneLinks; // D3Q19 links that cross membrane
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int *membraneTag; // label each link in the membrane
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double *membraneDist; // distance to membrane for each linked site
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double *membraneCoef; // mass transport coefficient for the membrane
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/*
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* Device data structures
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*/
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int *dvcNeighborList;
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double *dvcMembraneLinks;
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double *dvcMembraneCoef; // mass transport coefficient for the membrane
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double *dvcMembraneDistance;
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/**
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* \brief Create a flow adaptor to operate on the LB model
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* @param ScaLBL - originating data structures
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@@ -83,6 +90,9 @@ public:
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void SendD3Q19AA(double *dist);
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void RecvD3Q19AA(double *dist);
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void SendD3Q7AA(double *dist);
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void RecvD37AA(double *dist);
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void AssignCoefficients(double *dvcPsi, double *dvcDistance, double *dvcMap, std::string method);
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//......................................................................................
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// Buffers to store data sent and recieved by this MPI process
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double *sendbuf_x, *sendbuf_y, *sendbuf_z, *sendbuf_X, *sendbuf_Y, *sendbuf_Z;
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@@ -162,5 +172,9 @@ private:
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int *dvcRecvDist_xy, *dvcRecvDist_yz, *dvcRecvDist_xz, *dvcRecvDist_Xy, *dvcRecvDist_Yz, *dvcRecvDist_xZ;
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int *dvcRecvDist_xY, *dvcRecvDist_yZ, *dvcRecvDist_Xz, *dvcRecvDist_XY, *dvcRecvDist_YZ, *dvcRecvDist_XZ;
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//......................................................................................
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// mass transfer coefficient arrays
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double *coefficient_x, *coefficient_X, *coefficient_y, *coefficient_Y, *coefficient_z, *coefficient_Z;
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//......................................................................................
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};
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#endif
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@@ -221,7 +221,9 @@ extern "C" void ScaLBL_D3Q19_AAodd_BGK(int *neighborList, double *dist, int star
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extern "C" void ScaLBL_D3Q7_Membrane_IonTransport(int *membrane, double *coef, double *dist, double *Den, int memLinks, int Np);
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extern "C" void ScaLBL_D3Q7_Membrane_Unpack(int q, int *list, int start, int count, double *recvbuf, double *dist, int N, int nlinks, double *coef);
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extern "C" void ScaLBL_D3Q7_Membrane_Unpack(int q,
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int *d3q7_recvlist, int *d3q7_linkList, int start, int nlinks, int count,
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double *recvbuf, double *dist, int N, double *coef);
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// GREYSCALE MODEL (Single-component)
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36
cpu/Ion.cpp
36
cpu/Ion.cpp
@@ -1,7 +1,13 @@
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#include <stdio.h>
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extern "C" void ScaLBL_D3Q7_Membrane_Unpack(int q, int *list, int start, int count,
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double *recvbuf, double *dist, int N, int nlinks, double *coef) {
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extern "C" void ScaLBL_D3Q7_AssignLinkCoef(){
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}
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extern "C" void ScaLBL_D3Q7_Membrane_Unpack(int q,
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int *d3q7_recvlist, int *d3q7_linkList, int start, int nlinks, int count,
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double *recvbuf, double *dist, int N, double *coef) {
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//....................................................................................
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// Unack distribution from the recv buffer
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// Distribution q matche Cqx, Cqy, Cqz
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@@ -9,16 +15,28 @@ extern "C" void ScaLBL_D3Q7_Membrane_Unpack(int q, int *list, int start, int cou
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// dist may be even or odd distributions stored by stream layout
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//....................................................................................
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int n, idx, link;
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double fq fp,fqq,ap,aq; // coefficient
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double fq,fp,fqq,ap,aq; // coefficient
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/* First unpack the regular links */
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for (link = 0; link < nlinks; link++) {
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// pick out links from the end of the list
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idx = count - nlinks + link;
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// Get the value from the list -- note that n is the index is from the send (non-local) process
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n = list[idx];
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// get the index for the recv list (deal with reordering of links)
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idx = d3q7_linkList[link];
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// get the distribution index
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n = d3q7_recvlist[start+idx];
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if (!(n < 0)){
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fp = recvbuf[start + idx];
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dist[q * N + n] = fp;
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}
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}
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/* second enforce custom rule for membrane links */
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for (link = nlinks; link < count; link++) {
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// get the index for the recv list (deal with reordering of links)
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idx = d3q7_linkList[link];
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// get the distribution index
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n = d3q7_recvlist[start+idx];
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// update link based on mass transfer coefficients
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if (!(n < 0)){
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aq = coef[2*link];
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ap = coef[2*link+1];
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aq = coef[2*(link-nlinks)];
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ap = coef[2*(link-nlinks)+1];
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fq = dist[q * N + n];
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fp = recvbuf[start + idx];
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fqq = (1-aq)*fq+ap*fp;
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