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membrane test works with new comm

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This commit is contained in:
James McClure
2022-05-12 00:31:22 -04:00
parent 7c790e8802
commit 29e4c76561
4 changed files with 81 additions and 85 deletions
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38
common/Membrane.cpp
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@@ -78,6 +78,20 @@ Membrane::Membrane(std::shared_ptr <ScaLBL_Communicator> sComm, int *dvcNeighbor
ScaLBL_AllocateZeroCopy((void **) &dvcRecvDist_Y, recvCount_Y*sizeof(int));
ScaLBL_AllocateZeroCopy((void **) &dvcRecvDist_Z, recvCount_Z*sizeof(int));
ScaLBL_AllocateZeroCopy((void **) &sendbuf_x, sendCount_x*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &sendbuf_y, sendCount_y*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &sendbuf_z, sendCount_z*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &sendbuf_X, sendCount_X*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &sendbuf_Y, sendCount_Y*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &sendbuf_Z, sendCount_Z*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &recvbuf_x, recvCount_x*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &recvbuf_y, recvCount_y*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &recvbuf_z, recvCount_z*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &recvbuf_X, recvCount_X*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &recvbuf_Y, recvCount_Y*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &recvbuf_Z, recvCount_Z*sizeof(double));
sendCount_x=sComm->copySendList("x", dvcSendList_x);
sendCount_y=sComm->copySendList("y", dvcSendList_y);
sendCount_z=sComm->copySendList("z", dvcSendList_z);
@@ -639,12 +653,12 @@ int Membrane::Create(DoubleArray &Distance, IntArray &Map){
//......................................................................................
// Allocate membrane coefficient buffers (for d3q7 recv)
ScaLBL_AllocateZeroCopy((void **) &coefficient_x, (recvCount_x - linkCount_x[0])*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &coefficient_X, (recvCount_X - linkCount_X[0])*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &coefficient_y, (recvCount_y - linkCount_y[0])*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &coefficient_Y, (recvCount_Y - linkCount_Y[0])*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &coefficient_z, (recvCount_z - linkCount_z[0])*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &coefficient_Z, (recvCount_Z - linkCount_Z[0])*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &coefficient_x, 2*(recvCount_x )*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &coefficient_X, 2*(recvCount_X)*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &coefficient_y, 2*(recvCount_y)*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &coefficient_Y, 2*(recvCount_Y)*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &coefficient_z, 2*(recvCount_z)*sizeof(double));
ScaLBL_AllocateZeroCopy((void **) &coefficient_Z, 2*(recvCount_Z)*sizeof(double));
//......................................................................................
delete [] neighborList;
@@ -753,21 +767,21 @@ void Membrane::RecvD3Q7AA(double *dist){
// Unpack the distributions on the device
//...................................................................................
//...Unpacking for x face(q=2)................................
ScaLBL_D3Q7_Membrane_Unpack(2,dvcRecvDist_x, dvcRecvLinks_x,0,linkCount_x[0],recvCount_x,recvbuf_x,dist,Np,coefficient_x);
ScaLBL_D3Q7_Membrane_Unpack(2,dvcRecvDist_x, recvbuf_x,recvCount_x,dist,Np,coefficient_x);
//...................................................................................
//...Packing for X face(q=1)................................
ScaLBL_D3Q7_Membrane_Unpack(1,dvcRecvDist_X, dvcRecvLinks_X,0,linkCount_X[0],recvCount_X,recvbuf_X,dist,Np,coefficient_X);
ScaLBL_D3Q7_Membrane_Unpack(1,dvcRecvDist_X, recvbuf_X,recvCount_X,dist,Np,coefficient_X);
//...................................................................................
//...Packing for y face(q=4).................................
ScaLBL_D3Q7_Membrane_Unpack(4,dvcRecvDist_y, dvcRecvLinks_y,0,linkCount_y[0],recvCount_y,recvbuf_y,dist,Np,coefficient_y);
ScaLBL_D3Q7_Membrane_Unpack(4,dvcRecvDist_y, recvbuf_y,recvCount_y,dist,Np,coefficient_y);
//...................................................................................
//...Packing for Y face(q=3).................................
ScaLBL_D3Q7_Membrane_Unpack(3,dvcRecvDist_Y, dvcRecvLinks_Y,0,linkCount_Y[0],recvCount_Y,recvbuf_Y,dist,Np,coefficient_Y);
ScaLBL_D3Q7_Membrane_Unpack(3,dvcRecvDist_Y, recvbuf_Y,recvCount_Y,dist,Np,coefficient_Y);
//...................................................................................
//...Packing for z face(q=6)................................
ScaLBL_D3Q7_Membrane_Unpack(6,dvcRecvDist_z, dvcRecvLinks_z,0,linkCount_z[0],recvCount_z,recvbuf_z,dist,Np,coefficient_z);
ScaLBL_D3Q7_Membrane_Unpack(6,dvcRecvDist_z, recvbuf_z, recvCount_z,dist,Np,coefficient_z);
//...Packing for Z face(q=5)................................
ScaLBL_D3Q7_Membrane_Unpack(5,dvcRecvDist_Z, dvcRecvLinks_Z,0,linkCount_Z[0],recvCount_Z,recvbuf_Z,dist,Np,coefficient_Z);
ScaLBL_D3Q7_Membrane_Unpack(5,dvcRecvDist_Z, recvbuf_Z,recvCount_Z,dist,Np,coefficient_Z);
//..................................................................................
MPI_COMM_SCALBL.barrier();

9
common/Membrane.h
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@@ -16,15 +16,14 @@
* \brief Unpack D3Q19 distributions after communication using links determined based on membrane location
* @param q - index for distribution based on D3Q19 discrete velocity structure
* @param list - list of distributions to communicate
* @param links - list of active links based on the membrane location
* @param start - index to start parsing the list
* @param count - number of values to unppack
* @param recvbuf - memory buffer where recieved values have been stored
* @param count - number of values to unppack
* @param dist - memory buffer to hold the distributions
* @param N - size of the distributions (derived from Domain structure)
*/
extern "C" void Membrane_D3Q19_Unpack(int q, int *list, int *links, int start, int count, double *recvbuf, double *dist, int N);
extern "C" void ScaLBL_D3Q7_Membrane_Unpack(int q,
int *d3q7_recvlist, double *recvbuf, int count,
double *dist, int N, double *coef);
/**
* \brief Set custom link rules for D3Q19 distribution based on membrane location

4
common/ScaLBL.h
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@@ -233,8 +233,8 @@ extern "C" void ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(
const int N, const int Nx, const int Ny, const int Nz);
extern "C" void ScaLBL_D3Q7_Membrane_Unpack(int q,
int *d3q7_recvlist, int *d3q7_linkList, int start, int nlinks, int count,
double *recvbuf, double *dist, int N, double *coef);
int *d3q7_recvlist, double *recvbuf, int count,
double *dist, int N, double *coef);
// GREYSCALE MODEL (Single-component)

53
cpu/Ion.cpp
View File

@@ -44,18 +44,18 @@ extern "C" void ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(
// swap rule means that the distributions in recvbuf are OPPOSITE of q
// dist may be even or odd distributions stored by stream layout
//....................................................................................
int n, idx, link, nqm, npm, i, j, k;
int n, idx, link, label, nqm, npm, i, j, k;
double distanceLocal, distanceNonlocal;
double psiLocal, psiNonlocal, membranePotential;
double ap,aq; // coefficient
/* second enforce custom rule for membrane links */
for (link = nlinks; link < count; link++) {
// get the index for the recv list (deal with reordering of links)
idx = d3q7_linkList[link]; // THINK start NEEDS TO BE HERE
// get the distribution index
n = d3q7_recvlist[start+idx];
// get the index in strided layout
for (idx = 0; idx < count; idx++) {
n = d3q7_recvlist[idx];
label = d3q7_linkList[idx];
ap = 1.0; // regular streaming rule
aq = 0.0;
if (label == 1 && !(n < 0)){
nqm = Map[n];
distanceLocal = Distance[nqm];
psiLocal = Psi[nqm];
@@ -87,17 +87,16 @@ extern "C" void ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(
aq = ThresholdMassFractionIn;
ap = ThresholdMassFractionOut;
}
// update link based on mass transfer coefficients
coef[2*(link-nlinks)] = aq;
coef[2*(link-nlinks)+1] = ap;
}
coef[2*idx]=aq;
coef[2*idx+1]=ap;
}
}
extern "C" void ScaLBL_D3Q7_Membrane_Unpack(int q,
int *d3q7_recvlist, int *d3q7_linkList, int start, int nlinks, int count,
double *recvbuf, double *dist, int N, double *coef) {
int *d3q7_recvlist, double *recvbuf, int count,
double *dist, int N, double *coef) {
//....................................................................................
// Unack distribution from the recv buffer
// Distribution q matche Cqx, Cqy, Cqz
@@ -107,34 +106,18 @@ extern "C" void ScaLBL_D3Q7_Membrane_Unpack(int q,
int n, idx, link;
double fq,fp,fqq,ap,aq; // coefficient
/* First unpack the regular links */
for (link = 0; link < nlinks; link++) {
// get the index for the recv list (deal with reordering of links)
idx = d3q7_linkList[link];
// get the distribution index
n = d3q7_recvlist[start+idx];
if (!(n < 0)){
fp = recvbuf[start + idx];
dist[q * N + n] = fp;
}
//printf(" site=%i, index=%i, value = %e \n",n,idx,fp);
}
/* second enforce custom rule for membrane links */
for (link = nlinks; link < count; link++) {
// get the index for the recv list (deal with reordering of links)
idx = d3q7_linkList[link];
// get the distribution index
n = d3q7_recvlist[start+idx];
for (idx = 0; idx < count; idx++) {
n = d3q7_recvlist[idx];
// update link based on mass transfer coefficients
if (!(n < 0)){
aq = coef[2*(link-nlinks)];
ap = coef[2*(link-nlinks)+1];
aq = coef[2*idx];
ap = coef[2*idx+1];
fq = dist[q * N + n];
fp = recvbuf[start + idx];
fp = recvbuf[idx];
fqq = (1-aq)*fq+ap*fp;
dist[q * N + n] = fqq;
}
//printf(" LINK: site=%i, index=%i \n", n, idx);
}
}