OilfieldToolsNet/LBPM
4
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

cell simulator runs

Browse Source
This commit is contained in:
James McClure 2022-03-20 11:22:46 -04:00
parent 9e3a07d419
commit 51c88f0055
2 changed files with 17 additions and 7 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

20
common/Membrane.cpp
View File

@ -6,10 +6,9 @@
Membrane::Membrane(std::shared_ptr <Domain> Dm, int *dvcNeighborList, int Nsites) {
Np = Nsites;
int * initialNeighborList = new int[18*Np];
ScaLBL_AllocateDeviceMemory((void **)&NeighborList, 18*Np*sizeof(int));
Lock=false; // unlock the communicator
initialNeighborList = new int[18*Np];
ScaLBL_AllocateDeviceMemory((void **)&NeighborList, 18*Np*sizeof(int));
Lock=false; // unlock the communicator
//......................................................................................
// Create a separate copy of the communicator for the device
MPI_COMM_SCALBL = Dm->Comm.dup();
@ -85,7 +84,12 @@ Membrane::Membrane(std::shared_ptr <Domain> Dm, int *dvcNeighborList, int Nsites
recvCount_Xz=Dm->recvCount("Xz");
recvCount_XY=Dm->recvCount("XY");
recvCount_YZ=Dm->recvCount("YZ");
recvCount_XZ=Dm->recvCount("XZ");\
recvCount_XZ=Dm->recvCount("XZ");
if (rank == 0){
printf("**** Creating membrane data structure ****** \n");
}
printf(" Number of active lattice sites (rank = %i): %i \n",rank, Np);
/* check symmetry for send / recv counts */
if (sendCount_x != recvCount_X) printf("WARNING: rank %i send/recv mismatch (x/X)! \n",rank);
@ -407,6 +411,7 @@ int Membrane::Create(std::shared_ptr <Domain> Dm, DoubleArray &Distance, IntArra
int idx, neighbor;
double dist, locdist;
if (rank == 0) printf(" Copy initial neighborlist... \n");
int * neighborList = new int[18*Np];
/* Copy neighborList */
for (int idx=0; idx<Np; idx++){
@ -417,6 +422,7 @@ int Membrane::Create(std::shared_ptr <Domain> Dm, DoubleArray &Distance, IntArra
/* go through the neighborlist structure */
/* count & cut the links */
if (rank == 0) printf(" Cut membrane links... \n");
for (k=1;k<Nz-1;k++){
for (j=1;j<Ny-1;j++){
for (i=1;i<Nx-1;i++){
@ -556,6 +562,7 @@ int Membrane::Create(std::shared_ptr <Domain> Dm, DoubleArray &Distance, IntArra
* Sites inside the membrane (negative distance) -- store at 2*mlink
* Sites outside the membrane (positive distance) -- store at 2*mlink+1
*/
if (rank == 0) printf(" Construct membrane data structures... \n");
mlink = 0;
int localSite = 0; int neighborSite = 0;
for (k=1;k<Nz-1;k++){
@ -731,6 +738,8 @@ int Membrane::Create(std::shared_ptr <Domain> Dm, DoubleArray &Distance, IntArra
}
}
}
if (rank == 0) printf(" Create device data structures... \n");
/* Create device copies of data structures */
ScaLBL_AllocateDeviceMemory((void **)&MembraneLinks, 2*mlink*sizeof(int));
@ -742,6 +751,7 @@ int Membrane::Create(std::shared_ptr <Domain> Dm, DoubleArray &Distance, IntArra
ScaLBL_CopyToDevice(MembraneDistance, membraneDist, 2*mlink*sizeof(double));
if (rank == 0) printf(" Construct communication data structures... \n");
/* Re-organize communication based on membrane structure*/
//...Map recieve list for the X face: q=2,8,10,12,14 .................................
linkCount_X[0] = D3Q19_MapRecv(-1,0,0, Dm->recvList("X"),0,recvCount_X,dvcRecvDist_X,dvcRecvLinks_X,Distance,Map);

4
models/IonModel.cpp
View File

@ -623,12 +623,12 @@ void ScaLBL_IonModel::SetMembrane() {
label_count_global[m] = Dm->Comm.sumReduce(label_count[m]);
}
if (rank == 0) {
printf("Membrane labels: %lu \n", MembraneLabels.size());
printf(" Membrane labels: %lu \n", MembraneLabels.size());
for (size_t m=0; m<MembraneLabels.size(); m++){
LABEL = MembraneLabels[m];
double volume_fraction = double(label_count_global[m]) /
double((Nx - 2) * (Ny - 2) * (Nz - 2) * nprocs);
printf(" label=%d, volume fraction==%f\n", LABEL, volume_fraction);
printf(" label=%d, volume fraction==%f\n", LABEL, volume_fraction);
}
}
/* signed distance to the membrane ( - inside / + outside) */