membrane test works with new comm
This commit is contained in:
James McClure
@@ -78,6 +78,20 @@ Membrane::Membrane(std::shared_ptr <ScaLBL_Communicator> sComm, int *dvcNeighbor
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ScaLBL_AllocateZeroCopy((void **) &dvcRecvDist_Y, recvCount_Y*sizeof(int));
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ScaLBL_AllocateZeroCopy((void **) &dvcRecvDist_Z, recvCount_Z*sizeof(int));
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ScaLBL_AllocateZeroCopy((void **) &sendbuf_x, sendCount_x*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &sendbuf_y, sendCount_y*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &sendbuf_z, sendCount_z*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &sendbuf_X, sendCount_X*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &sendbuf_Y, sendCount_Y*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &sendbuf_Z, sendCount_Z*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &recvbuf_x, recvCount_x*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &recvbuf_y, recvCount_y*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &recvbuf_z, recvCount_z*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &recvbuf_X, recvCount_X*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &recvbuf_Y, recvCount_Y*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &recvbuf_Z, recvCount_Z*sizeof(double));
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sendCount_x=sComm->copySendList("x", dvcSendList_x);
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sendCount_y=sComm->copySendList("y", dvcSendList_y);
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sendCount_z=sComm->copySendList("z", dvcSendList_z);
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@@ -639,12 +653,12 @@ int Membrane::Create(DoubleArray &Distance, IntArray &Map){
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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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ScaLBL_AllocateZeroCopy((void **) &coefficient_x, 2*(recvCount_x )*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &coefficient_X, 2*(recvCount_X)*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &coefficient_y, 2*(recvCount_y)*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &coefficient_Y, 2*(recvCount_Y)*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &coefficient_z, 2*(recvCount_z)*sizeof(double));
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ScaLBL_AllocateZeroCopy((void **) &coefficient_Z, 2*(recvCount_Z)*sizeof(double));
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//......................................................................................
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delete [] neighborList;
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@@ -753,21 +767,21 @@ void Membrane::RecvD3Q7AA(double *dist){
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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,Np,coefficient_x);
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ScaLBL_D3Q7_Membrane_Unpack(2,dvcRecvDist_x, recvbuf_x,recvCount_x,dist,Np,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,Np,coefficient_X);
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ScaLBL_D3Q7_Membrane_Unpack(1,dvcRecvDist_X, recvbuf_X,recvCount_X,dist,Np,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,Np,coefficient_y);
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ScaLBL_D3Q7_Membrane_Unpack(4,dvcRecvDist_y, recvbuf_y,recvCount_y,dist,Np,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,Np,coefficient_Y);
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ScaLBL_D3Q7_Membrane_Unpack(3,dvcRecvDist_Y, recvbuf_Y,recvCount_Y,dist,Np,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,Np,coefficient_z);
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ScaLBL_D3Q7_Membrane_Unpack(6,dvcRecvDist_z, recvbuf_z, recvCount_z,dist,Np,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,Np,coefficient_Z);
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ScaLBL_D3Q7_Membrane_Unpack(5,dvcRecvDist_Z, recvbuf_Z,recvCount_Z,dist,Np,coefficient_Z);
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//..................................................................................
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MPI_COMM_SCALBL.barrier();
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@@ -16,15 +16,14 @@
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* \brief Unpack D3Q19 distributions after communication using links determined based on membrane location
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* @param q - index for distribution based on D3Q19 discrete velocity structure
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* @param list - list of distributions to communicate
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* @param links - list of active links based on the membrane location
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* @param start - index to start parsing the list
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* @param count - number of values to unppack
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* @param recvbuf - memory buffer where recieved values have been stored
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* @param count - number of values to unppack
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* @param dist - memory buffer to hold the distributions
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* @param N - size of the distributions (derived from Domain structure)
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*/
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extern "C" void Membrane_D3Q19_Unpack(int q, int *list, int *links, int start, int count, double *recvbuf, double *dist, int N);
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extern "C" void ScaLBL_D3Q7_Membrane_Unpack(int q,
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int *d3q7_recvlist, double *recvbuf, int count,
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double *dist, int N, double *coef);
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/**
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* \brief Set custom link rules for D3Q19 distribution based on membrane location
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@@ -233,8 +233,8 @@ extern "C" void ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(
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const int N, const int Nx, const int Ny, const int Nz);
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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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int *d3q7_recvlist, double *recvbuf, int count,
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double *dist, int N, double *coef);
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// GREYSCALE MODEL (Single-component)
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107
cpu/Ion.cpp
107
cpu/Ion.cpp
@@ -44,60 +44,59 @@ extern "C" void ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(
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// swap rule means that the distributions in recvbuf are OPPOSITE of q
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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, nqm, npm, i, j, k;
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int n, idx, link, label, nqm, npm, i, j, k;
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double distanceLocal, distanceNonlocal;
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double psiLocal, psiNonlocal, membranePotential;
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double ap,aq; // coefficient
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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]; // THINK start NEEDS TO BE HERE
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// get the distribution index
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n = d3q7_recvlist[start+idx];
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// get the index in strided layout
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nqm = Map[n];
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distanceLocal = Distance[nqm];
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psiLocal = Psi[nqm];
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// Get the 3-D indices from the send process
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k = nqm/(Nx*Ny); j = (nqm-Nx*Ny*k)/Nx; i = nqm-Nx*Ny*k-Nx*j;
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// Streaming link the non-local distribution
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i -= Cqx; j -= Cqy; k -= Cqz;
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npm = k*Nx*Ny + j*Nx + i;
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distanceNonlocal = Distance[npm];
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psiNonlocal = Psi[npm];
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for (idx = 0; idx < count; idx++) {
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n = d3q7_recvlist[idx];
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label = d3q7_linkList[idx];
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ap = 1.0; // regular streaming rule
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aq = 0.0;
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if (label == 1 && !(n < 0)){
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nqm = Map[n];
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distanceLocal = Distance[nqm];
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psiLocal = Psi[nqm];
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membranePotential = psiLocal - psiNonlocal;
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aq = MassFractionIn;
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ap = MassFractionOut;
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// Get the 3-D indices from the send process
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k = nqm/(Nx*Ny); j = (nqm-Nx*Ny*k)/Nx; i = nqm-Nx*Ny*k-Nx*j;
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// Streaming link the non-local distribution
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i -= Cqx; j -= Cqy; k -= Cqz;
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npm = k*Nx*Ny + j*Nx + i;
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distanceNonlocal = Distance[npm];
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psiNonlocal = Psi[npm];
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/* link is inside membrane */
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if (distanceLocal > 0.0){
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if (membranePotential < Threshold*(-1.0)){
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ap = MassFractionIn;
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aq = MassFractionOut;
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}
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else {
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ap = ThresholdMassFractionIn;
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aq = ThresholdMassFractionOut;
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}
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}
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else if (membranePotential > Threshold){
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aq = ThresholdMassFractionIn;
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ap = ThresholdMassFractionOut;
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}
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membranePotential = psiLocal - psiNonlocal;
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aq = MassFractionIn;
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ap = MassFractionOut;
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// update link based on mass transfer coefficients
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coef[2*(link-nlinks)] = aq;
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coef[2*(link-nlinks)+1] = ap;
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/* link is inside membrane */
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if (distanceLocal > 0.0){
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if (membranePotential < Threshold*(-1.0)){
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ap = MassFractionIn;
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aq = MassFractionOut;
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}
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else {
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ap = ThresholdMassFractionIn;
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aq = ThresholdMassFractionOut;
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}
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}
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else if (membranePotential > Threshold){
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aq = ThresholdMassFractionIn;
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ap = ThresholdMassFractionOut;
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}
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}
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coef[2*idx]=aq;
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coef[2*idx+1]=ap;
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}
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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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int *d3q7_recvlist, double *recvbuf, int count,
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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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@@ -107,34 +106,18 @@ extern "C" void ScaLBL_D3Q7_Membrane_Unpack(int q,
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int n, idx, link;
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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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// 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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//printf(" site=%i, index=%i, value = %e \n",n,idx,fp);
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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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for (idx = 0; idx < count; idx++) {
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n = d3q7_recvlist[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-nlinks)];
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ap = coef[2*(link-nlinks)+1];
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aq = coef[2*idx];
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ap = coef[2*idx+1];
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fq = dist[q * N + n];
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fp = recvbuf[start + idx];
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fp = recvbuf[idx];
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fqq = (1-aq)*fq+ap*fp;
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dist[q * N + n] = fqq;
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}
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//printf(" LINK: site=%i, index=%i \n", n, idx);
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}
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}
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