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

add single cell example

Browse Source
This commit is contained in:
James McClure
2022-03-20 15:13:53 -04:00
parent 3522d35de1
commit 4927e54707
6 changed files with 180 additions and 15 deletions
Download Patch File Download Diff File Expand all files Collapse all files

38
models/IonModel.cpp
View File

@@ -629,7 +629,7 @@ void ScaLBL_IonModel::SetMembrane() {
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) */
@@ -844,6 +844,7 @@ void ScaLBL_IonModel::Create() {
int neighborSize = 18 * (Np * sizeof(int));
//...........................................................................
ScaLBL_AllocateDeviceMemory((void **)&NeighborList, neighborSize);
ScaLBL_AllocateDeviceMemory((void **)&dvcMap, sizeof(int) * Np);
ScaLBL_AllocateDeviceMemory((void **)&fq,
number_ion_species * 7 * dist_mem_size);
ScaLBL_AllocateDeviceMemory((void **)&Ci,
@@ -860,6 +861,37 @@ void ScaLBL_IonModel::Create() {
if (rank == 0)
printf("LB Ion Solver: Setting up device map and neighbor list \n");
// copy the neighbor list
int *TmpMap;
TmpMap = new int[Np];
for (int k = 1; k < Nz - 1; k++) {
for (int j = 1; j < Ny - 1; j++) {
for (int i = 1; i < Nx - 1; i++) {
int idx = Map(i, j, k);
if (!(idx < 0))
TmpMap[idx] = k * Nx * Ny + j * Nx + i;
}
}
}
// check that TmpMap is valid
for (int idx = 0; idx < ScaLBL_Comm->LastExterior(); idx++) {
auto n = TmpMap[idx];
if (n > Nx * Ny * Nz) {
printf("Bad value! idx=%i \n", n);
TmpMap[idx] = Nx * Ny * Nz - 1;
}
}
for (int idx = ScaLBL_Comm->FirstInterior();
idx < ScaLBL_Comm->LastInterior(); idx++) {
auto n = TmpMap[idx];
if (n > Nx * Ny * Nz) {
printf("Bad value! idx=%i \n", n);
TmpMap[idx] = Nx * Ny * Nz - 1;
}
}
ScaLBL_CopyToDevice(dvcMap, TmpMap, sizeof(int) * Np);
ScaLBL_Comm->Barrier();
delete[] TmpMap;
ScaLBL_CopyToDevice(NeighborList, neighborList, neighborSize);
comm.barrier();
@@ -1263,7 +1295,9 @@ void ScaLBL_IonModel::RunMembrane(double *Velocity, double *ElectricField, doubl
//double starttime,stoptime,cputime;
//ScaLBL_Comm->Barrier(); comm.barrier();
//auto t1 = std::chrono::system_clock::now();
/* set the mass transfer coefficients for the membrane */
IonMembrane->AssignCoefficients(dvcMap, Psi, "default");
for (size_t ic = 0; ic < number_ion_species; ic++) {
timestep = 0;
while (timestep < timestepMax[ic]) {

1
models/IonModel.h
View File

@@ -90,6 +90,7 @@ public:
IntArray Map;
DoubleArray Distance;
int *NeighborList;
int *dvcMap;
double *fq;
double *Ci;
double *ChargeDensity;