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cleanup with help from valgrind

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This commit is contained in:
James McClure
2022-05-06 16:21:37 -04:00
parent ba6d438630
commit c424e1d984
5 changed files with 340 additions and 292 deletions
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65
common/Membrane.cpp
View File

@@ -274,6 +274,7 @@ Membrane::~Membrane() {
ScaLBL_FreeDeviceMemory( NeighborList ); ScaLBL_FreeDeviceMemory( NeighborList );
ScaLBL_FreeDeviceMemory( MembraneLinks ); ScaLBL_FreeDeviceMemory( MembraneLinks );
ScaLBL_FreeDeviceMemory( MembraneCoef ); ScaLBL_FreeDeviceMemory( MembraneCoef );
ScaLBL_FreeDeviceMemory( MembraneDistance );
ScaLBL_FreeDeviceMemory( sendbuf_x ); ScaLBL_FreeDeviceMemory( sendbuf_x );
ScaLBL_FreeDeviceMemory( sendbuf_X ); ScaLBL_FreeDeviceMemory( sendbuf_X );
@@ -730,7 +731,6 @@ int Membrane::Create(std::shared_ptr <Domain> Dm, DoubleArray &Distance, IntArra
} }
if (rank == 0) printf(" Create device data structures... \n"); if (rank == 0) printf(" Create device data structures... \n");
/* Create device copies of data structures */ /* Create device copies of data structures */
ScaLBL_AllocateDeviceMemory((void **)&MembraneLinks, 2*mlink*sizeof(int)); ScaLBL_AllocateDeviceMemory((void **)&MembraneLinks, 2*mlink*sizeof(int));
ScaLBL_AllocateDeviceMemory((void **)&MembraneCoef, 2*mlink*sizeof(double)); ScaLBL_AllocateDeviceMemory((void **)&MembraneCoef, 2*mlink*sizeof(double));
@@ -995,6 +995,7 @@ int Membrane::Create(std::shared_ptr <Domain> Dm, DoubleArray &Distance, IntArra
ScaLBL_AllocateZeroCopy((void **) &coefficient_Z, (recvCount_Z - linkCount_Z[0])*sizeof(double)); ScaLBL_AllocateZeroCopy((void **) &coefficient_Z, (recvCount_Z - linkCount_Z[0])*sizeof(double));
//...................................................................................... //......................................................................................
delete [] neighborList;
delete [] TempBuffer; delete [] TempBuffer;
return mlink; return mlink;
} }
@@ -1356,39 +1357,45 @@ void Membrane::AssignCoefficients(int *Map, double *Psi, double Threshold,
double ThresholdMassFractionOut){ double ThresholdMassFractionOut){
/* Assign mass transfer coefficients to the membrane data structure */ /* Assign mass transfer coefficients to the membrane data structure */
if (membraneLinkCount > 0)
ScaLBL_D3Q7_Membrane_AssignLinkCoef(MembraneLinks, Map, MembraneDistance, Psi, MembraneCoef,
Threshold, MassFractionIn, MassFractionOut, ThresholdMassFractionIn, ThresholdMassFractionOut,
membraneLinkCount, Nx, Ny, Nz, Np);
ScaLBL_D3Q7_Membrane_AssignLinkCoef(MembraneLinks, Map, MembraneDistance, Psi, MembraneCoef, if (linkCount_X[0] < recvCount_X)
Threshold, MassFractionIn, MassFractionOut, ThresholdMassFractionIn, ThresholdMassFractionOut, ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(-1,0,0,Map,MembraneDistance,Psi,Threshold,
membraneLinkCount, Nx, Ny, Nz, Np); MassFractionIn,MassFractionOut,ThresholdMassFractionIn,ThresholdMassFractionOut,
dvcRecvDist_X,dvcRecvLinks_X,coefficient_X,0,linkCount_X[0],recvCount_X,
Np,Nx,Ny,Nz);
ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(-1,0,0,Map,MembraneDistance,Psi,Threshold, if (linkCount_x[0] < recvCount_x)
MassFractionIn,MassFractionOut,ThresholdMassFractionIn,ThresholdMassFractionOut, ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(1,0,0,Map,MembraneDistance,Psi,Threshold,
dvcRecvDist_X,dvcRecvLinks_X,coefficient_X,0,linkCount_X[0],recvCount_X, MassFractionIn,MassFractionOut,ThresholdMassFractionIn,ThresholdMassFractionOut,
Np,Nx,Ny,Nz); dvcRecvDist_x,dvcRecvLinks_x,coefficient_x,0,linkCount_x[0],recvCount_x,
Np,Nx,Ny,Nz);
ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(1,0,0,Map,MembraneDistance,Psi,Threshold, if (linkCount_Y[0] < recvCount_Y)
MassFractionIn,MassFractionOut,ThresholdMassFractionIn,ThresholdMassFractionOut, ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(0,-1,0,Map,MembraneDistance,Psi,Threshold,
dvcRecvDist_x,dvcRecvLinks_x,coefficient_x,0,linkCount_x[0],recvCount_x, MassFractionIn,MassFractionOut,ThresholdMassFractionIn,ThresholdMassFractionOut,
Np,Nx,Ny,Nz); dvcRecvDist_Y,dvcRecvLinks_Y,coefficient_Y,0,linkCount_Y[0],recvCount_Y,
Np,Nx,Ny,Nz);
ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(0,-1,0,Map,MembraneDistance,Psi,Threshold, if (linkCount_y[0]<recvCount_y)
MassFractionIn,MassFractionOut,ThresholdMassFractionIn,ThresholdMassFractionOut, ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(0,1,0,Map,MembraneDistance,Psi,Threshold,
dvcRecvDist_Y,dvcRecvLinks_Y,coefficient_Y,0,linkCount_Y[0],recvCount_Y, MassFractionIn,MassFractionOut,ThresholdMassFractionIn,ThresholdMassFractionOut,
Np,Nx,Ny,Nz); dvcRecvDist_y,dvcRecvLinks_y,coefficient_y,0,linkCount_y[0],recvCount_y,
Np,Nx,Ny,Nz);
ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(0,1,0,Map,MembraneDistance,Psi,Threshold, if (linkCount_Z[0]<recvCount_Z)
MassFractionIn,MassFractionOut,ThresholdMassFractionIn,ThresholdMassFractionOut, ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(0,0,-1,Map,MembraneDistance,Psi,Threshold,
dvcRecvDist_y,dvcRecvLinks_y,coefficient_y,0,linkCount_y[0],recvCount_y, MassFractionIn,MassFractionOut,ThresholdMassFractionIn,ThresholdMassFractionOut,
Np,Nx,Ny,Nz); dvcRecvDist_Z,dvcRecvLinks_Z,coefficient_Z,0,linkCount_Z[0],recvCount_Z,
Np,Nx,Ny,Nz);
ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(0,0,-1,Map,MembraneDistance,Psi,Threshold, if (linkCount_z[0]<recvCount_z)
MassFractionIn,MassFractionOut,ThresholdMassFractionIn,ThresholdMassFractionOut, ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(0,0,1,Map,MembraneDistance,Psi,Threshold,
dvcRecvDist_Z,dvcRecvLinks_Z,coefficient_Z,0,linkCount_Z[0],recvCount_Z, MassFractionIn,MassFractionOut,ThresholdMassFractionIn,ThresholdMassFractionOut,
Np,Nx,Ny,Nz); dvcRecvDist_z,dvcRecvLinks_z,coefficient_z,0,linkCount_z[0],recvCount_z,
Np,Nx,Ny,Nz);
ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(0,0,1,Map,MembraneDistance,Psi,Threshold,
MassFractionIn,MassFractionOut,ThresholdMassFractionIn,ThresholdMassFractionOut,
dvcRecvDist_z,dvcRecvLinks_z,coefficient_z,0,linkCount_z[0],recvCount_z,
Np,Nx,Ny,Nz);
} }

509
common/ScaLBL.cpp
View File

@@ -1114,302 +1114,313 @@ void ScaLBL_Communicator::SetupBounceBackList(IntArray &Map, signed char *id, in
} }
} }
} }
if (local_count > 0){
int *bb_dist_tmp = new int [local_count]; int *bb_dist_tmp = new int [local_count];
int *bb_interactions_tmp = new int [local_count]; int *bb_interactions_tmp = new int [local_count];
ScaLBL_AllocateDeviceMemory((void **) &bb_dist, sizeof(int)*local_count); ScaLBL_AllocateDeviceMemory((void **) &bb_dist, sizeof(int)*local_count);
ScaLBL_AllocateDeviceMemory((void **) &bb_interactions, sizeof(int)*local_count); ScaLBL_AllocateDeviceMemory((void **) &bb_interactions, sizeof(int)*local_count);
int *fluid_boundary_tmp; int *fluid_boundary_tmp;
double *lattice_weight_tmp; double *lattice_weight_tmp;
float *lattice_cx_tmp; float *lattice_cx_tmp;
float *lattice_cy_tmp; float *lattice_cy_tmp;
float *lattice_cz_tmp; float *lattice_cz_tmp;
/* allocate memory for bounce-back sites */ /* allocate memory for bounce-back sites */
fluid_boundary_tmp = new int [local_count]; fluid_boundary_tmp = new int [local_count];
lattice_weight_tmp = new double [local_count]; lattice_weight_tmp = new double [local_count];
lattice_cx_tmp = new float [local_count]; lattice_cx_tmp = new float [local_count];
lattice_cy_tmp = new float [local_count]; lattice_cy_tmp = new float [local_count];
lattice_cz_tmp = new float [local_count]; lattice_cz_tmp = new float [local_count];
ScaLBL_AllocateDeviceMemory((void **) &fluid_boundary, sizeof(int)*local_count); ScaLBL_AllocateDeviceMemory((void **) &fluid_boundary, sizeof(int)*local_count);
ScaLBL_AllocateDeviceMemory((void **) &lattice_weight, sizeof(double)*local_count); ScaLBL_AllocateDeviceMemory((void **) &lattice_weight, sizeof(double)*local_count);
ScaLBL_AllocateDeviceMemory((void **) &lattice_cx, sizeof(float)*local_count); ScaLBL_AllocateDeviceMemory((void **) &lattice_cx, sizeof(float)*local_count);
ScaLBL_AllocateDeviceMemory((void **) &lattice_cy, sizeof(float)*local_count); ScaLBL_AllocateDeviceMemory((void **) &lattice_cy, sizeof(float)*local_count);
ScaLBL_AllocateDeviceMemory((void **) &lattice_cz, sizeof(float)*local_count); ScaLBL_AllocateDeviceMemory((void **) &lattice_cz, sizeof(float)*local_count);
local_count=0; local_count=0;
for (k=1;k<Nz-1;k++){ for (k=1;k<Nz-1;k++){
for (j=1;j<Ny-1;j++){ for (j=1;j<Ny-1;j++){
for (i=1;i<Nx-1;i++){ for (i=1;i<Nx-1;i++){
n=k*Nx*Ny+j*Nx+i; n=k*Nx*Ny+j*Nx+i;
idx=Map(i,j,k); idx=Map(i,j,k);
if (!(idx<0)){ if (!(idx<0)){
int neighbor; // cycle through the neighbors of lattice site idx int neighbor; // cycle through the neighbors of lattice site idx
neighbor=Map(i-1,j,k); neighbor=Map(i-1,j,k);
if (neighbor==-1){ if (neighbor==-1){
bb_interactions_tmp[local_count] = (i-1) + (j)*Nx + (k)*Nx*Ny; bb_interactions_tmp[local_count] = (i-1) + (j)*Nx + (k)*Nx*Ny;
//if(SlippingVelBC==true){ //if(SlippingVelBC==true){
fluid_boundary_tmp[local_count] = idx; fluid_boundary_tmp[local_count] = idx;
lattice_weight_tmp[local_count] = 1.0/18.0; lattice_weight_tmp[local_count] = 1.0/18.0;
lattice_cx_tmp[local_count] = -1.0; lattice_cx_tmp[local_count] = -1.0;
lattice_cy_tmp[local_count] = 0.0; lattice_cy_tmp[local_count] = 0.0;
lattice_cz_tmp[local_count] = 0.0; lattice_cz_tmp[local_count] = 0.0;
//} //}
bb_dist_tmp[local_count++]=idx + 2*Np; bb_dist_tmp[local_count++]=idx + 2*Np;
} }
neighbor=Map(i+1,j,k); neighbor=Map(i+1,j,k);
if (neighbor==-1){ if (neighbor==-1){
bb_interactions_tmp[local_count] = (i+1) + (j)*Nx + (k)*Nx*Ny; bb_interactions_tmp[local_count] = (i+1) + (j)*Nx + (k)*Nx*Ny;
//if(SlippingVelBC==true){ //if(SlippingVelBC==true){
fluid_boundary_tmp[local_count] = idx; fluid_boundary_tmp[local_count] = idx;
lattice_weight_tmp[local_count] = 1.0/18.0; lattice_weight_tmp[local_count] = 1.0/18.0;
lattice_cx_tmp[local_count] = 1.0; lattice_cx_tmp[local_count] = 1.0;
lattice_cy_tmp[local_count] = 0.0; lattice_cy_tmp[local_count] = 0.0;
lattice_cz_tmp[local_count] = 0.0; lattice_cz_tmp[local_count] = 0.0;
//} //}
bb_dist_tmp[local_count++] = idx + 1*Np; bb_dist_tmp[local_count++] = idx + 1*Np;
} }
neighbor=Map(i,j-1,k); neighbor=Map(i,j-1,k);
if (neighbor==-1){ if (neighbor==-1){
bb_interactions_tmp[local_count] = (i) + (j-1)*Nx + (k)*Nx*Ny; bb_interactions_tmp[local_count] = (i) + (j-1)*Nx + (k)*Nx*Ny;
//if(SlippingVelBC==true){ //if(SlippingVelBC==true){
fluid_boundary_tmp[local_count] = idx; fluid_boundary_tmp[local_count] = idx;
lattice_weight_tmp[local_count] = 1.0/18.0; lattice_weight_tmp[local_count] = 1.0/18.0;
lattice_cx_tmp[local_count] = 0.0; lattice_cx_tmp[local_count] = 0.0;
lattice_cy_tmp[local_count] = -1.0; lattice_cy_tmp[local_count] = -1.0;
lattice_cz_tmp[local_count] = 0.0; lattice_cz_tmp[local_count] = 0.0;
//} //}
bb_dist_tmp[local_count++]=idx + 4*Np; bb_dist_tmp[local_count++]=idx + 4*Np;
} }
neighbor=Map(i,j+1,k); neighbor=Map(i,j+1,k);
if (neighbor==-1){ if (neighbor==-1){
bb_interactions_tmp[local_count] = (i) + (j+1)*Nx + (k)*Nx*Ny; bb_interactions_tmp[local_count] = (i) + (j+1)*Nx + (k)*Nx*Ny;
//if(SlippingVelBC==true){ //if(SlippingVelBC==true){
fluid_boundary_tmp[local_count] = idx; fluid_boundary_tmp[local_count] = idx;
lattice_weight_tmp[local_count] = 1.0/18.0; lattice_weight_tmp[local_count] = 1.0/18.0;
lattice_cx_tmp[local_count] = 0.0; lattice_cx_tmp[local_count] = 0.0;
lattice_cy_tmp[local_count] = 1.0; lattice_cy_tmp[local_count] = 1.0;
lattice_cz_tmp[local_count] = 0.0; lattice_cz_tmp[local_count] = 0.0;
//} //}
bb_dist_tmp[local_count++]=idx + 3*Np; bb_dist_tmp[local_count++]=idx + 3*Np;
} }
neighbor=Map(i,j,k-1); neighbor=Map(i,j,k-1);
if (neighbor==-1){ if (neighbor==-1){
bb_interactions_tmp[local_count] = (i) + (j)*Nx + (k-1)*Nx*Ny; bb_interactions_tmp[local_count] = (i) + (j)*Nx + (k-1)*Nx*Ny;
//if(SlippingVelBC==true){ //if(SlippingVelBC==true){
fluid_boundary_tmp[local_count] = idx; fluid_boundary_tmp[local_count] = idx;
lattice_weight_tmp[local_count] = 1.0/18.0; lattice_weight_tmp[local_count] = 1.0/18.0;
lattice_cx_tmp[local_count] = 0.0; lattice_cx_tmp[local_count] = 0.0;
lattice_cy_tmp[local_count] = 0.0; lattice_cy_tmp[local_count] = 0.0;
lattice_cz_tmp[local_count] = -1.0; lattice_cz_tmp[local_count] = -1.0;
//} //}
bb_dist_tmp[local_count++]=idx + 6*Np; bb_dist_tmp[local_count++]=idx + 6*Np;
} }
neighbor=Map(i,j,k+1); neighbor=Map(i,j,k+1);
if (neighbor==-1){ if (neighbor==-1){
bb_interactions_tmp[local_count] = (i) + (j)*Nx + (k+1)*Nx*Ny; bb_interactions_tmp[local_count] = (i) + (j)*Nx + (k+1)*Nx*Ny;
//if(SlippingVelBC==true){ //if(SlippingVelBC==true){
fluid_boundary_tmp[local_count] = idx; fluid_boundary_tmp[local_count] = idx;
lattice_weight_tmp[local_count] = 1.0/18.0; lattice_weight_tmp[local_count] = 1.0/18.0;
lattice_cx_tmp[local_count] = 0.0; lattice_cx_tmp[local_count] = 0.0;
lattice_cy_tmp[local_count] = 0.0; lattice_cy_tmp[local_count] = 0.0;
lattice_cz_tmp[local_count] = 1.0; lattice_cz_tmp[local_count] = 1.0;
//} //}
bb_dist_tmp[local_count++]=idx + 5*Np; bb_dist_tmp[local_count++]=idx + 5*Np;
}
} }
} }
} }
} }
} n_bb_d3q7 = local_count;
n_bb_d3q7 = local_count; for (k=1;k<Nz-1;k++){
for (k=1;k<Nz-1;k++){ for (j=1;j<Ny-1;j++){
for (j=1;j<Ny-1;j++){ for (i=1;i<Nx-1;i++){
for (i=1;i<Nx-1;i++){ n=k*Nx*Ny+j*Nx+i;
n=k*Nx*Ny+j*Nx+i; idx=Map(i,j,k);
idx=Map(i,j,k); if (!(idx<0)){
if (!(idx<0)){
neighbor=Map(i-1,j-1,k); neighbor=Map(i-1,j-1,k);
if (neighbor==-1){ if (neighbor==-1){
bb_interactions_tmp[local_count] = (i-1) + (j-1)*Nx + (k)*Nx*Ny; bb_interactions_tmp[local_count] = (i-1) + (j-1)*Nx + (k)*Nx*Ny;
//if(SlippingVelBC==true){ //if(SlippingVelBC==true){
fluid_boundary_tmp[local_count] = idx; fluid_boundary_tmp[local_count] = idx;
lattice_weight_tmp[local_count] = 1.0/36.0; lattice_weight_tmp[local_count] = 1.0/36.0;
lattice_cx_tmp[local_count] = -1.0; lattice_cx_tmp[local_count] = -1.0;
lattice_cy_tmp[local_count] = -1.0; lattice_cy_tmp[local_count] = -1.0;
lattice_cz_tmp[local_count] = 0.0; lattice_cz_tmp[local_count] = 0.0;
//} //}
bb_dist_tmp[local_count++]=idx + 8*Np; bb_dist_tmp[local_count++]=idx + 8*Np;
} }
neighbor=Map(i+1,j+1,k); neighbor=Map(i+1,j+1,k);
if (neighbor==-1) { if (neighbor==-1) {
bb_interactions_tmp[local_count] = (i+1) + (j+1)*Nx + (k)*Nx*Ny; bb_interactions_tmp[local_count] = (i+1) + (j+1)*Nx + (k)*Nx*Ny;
//if(SlippingVelBC==true){ //if(SlippingVelBC==true){
fluid_boundary_tmp[local_count] = idx; fluid_boundary_tmp[local_count] = idx;
lattice_weight_tmp[local_count] = 1.0/36.0; lattice_weight_tmp[local_count] = 1.0/36.0;
lattice_cx_tmp[local_count] = 1.0; lattice_cx_tmp[local_count] = 1.0;
lattice_cy_tmp[local_count] = 1.0; lattice_cy_tmp[local_count] = 1.0;
lattice_cz_tmp[local_count] = 0.0; lattice_cz_tmp[local_count] = 0.0;
//} //}
bb_dist_tmp[local_count++]=idx + 7*Np; bb_dist_tmp[local_count++]=idx + 7*Np;
} }
neighbor=Map(i-1,j+1,k); neighbor=Map(i-1,j+1,k);
if (neighbor==-1){ if (neighbor==-1){
bb_interactions_tmp[local_count] = (i-1) + (j+1)*Nx + (k)*Nx*Ny; bb_interactions_tmp[local_count] = (i-1) + (j+1)*Nx + (k)*Nx*Ny;
//if(SlippingVelBC==true){ //if(SlippingVelBC==true){
fluid_boundary_tmp[local_count] = idx; fluid_boundary_tmp[local_count] = idx;
lattice_weight_tmp[local_count] = 1.0/36.0; lattice_weight_tmp[local_count] = 1.0/36.0;
lattice_cx_tmp[local_count] = -1.0; lattice_cx_tmp[local_count] = -1.0;
lattice_cy_tmp[local_count] = 1.0; lattice_cy_tmp[local_count] = 1.0;
lattice_cz_tmp[local_count] = 0.0; lattice_cz_tmp[local_count] = 0.0;
//} //}
bb_dist_tmp[local_count++]=idx + 10*Np; bb_dist_tmp[local_count++]=idx + 10*Np;
} }
neighbor=Map(i+1,j-1,k); neighbor=Map(i+1,j-1,k);
if (neighbor==-1){ if (neighbor==-1){
bb_interactions_tmp[local_count] = (i+1) + (j-1)*Nx + (k)*Nx*Ny; bb_interactions_tmp[local_count] = (i+1) + (j-1)*Nx + (k)*Nx*Ny;
//if(SlippingVelBC==true){ //if(SlippingVelBC==true){
fluid_boundary_tmp[local_count] = idx; fluid_boundary_tmp[local_count] = idx;
lattice_weight_tmp[local_count] = 1.0/36.0; lattice_weight_tmp[local_count] = 1.0/36.0;
lattice_cx_tmp[local_count] = 1.0; lattice_cx_tmp[local_count] = 1.0;
lattice_cy_tmp[local_count] = -1.0; lattice_cy_tmp[local_count] = -1.0;
lattice_cz_tmp[local_count] = 0.0; lattice_cz_tmp[local_count] = 0.0;
//} //}
bb_dist_tmp[local_count++]=idx + 9*Np; bb_dist_tmp[local_count++]=idx + 9*Np;
} }
neighbor=Map(i-1,j,k-1); neighbor=Map(i-1,j,k-1);
if (neighbor==-1) { if (neighbor==-1) {
bb_interactions_tmp[local_count] = (i-1) + (j)*Nx + (k-1)*Nx*Ny; bb_interactions_tmp[local_count] = (i-1) + (j)*Nx + (k-1)*Nx*Ny;
//if(SlippingVelBC==true){ //if(SlippingVelBC==true){
fluid_boundary_tmp[local_count] = idx; fluid_boundary_tmp[local_count] = idx;
lattice_weight_tmp[local_count] = 1.0/36.0; lattice_weight_tmp[local_count] = 1.0/36.0;
lattice_cx_tmp[local_count] = -1.0; lattice_cx_tmp[local_count] = -1.0;
lattice_cy_tmp[local_count] = 0.0; lattice_cy_tmp[local_count] = 0.0;
lattice_cz_tmp[local_count] = -1.0; lattice_cz_tmp[local_count] = -1.0;
//} //}
bb_dist_tmp[local_count++]=idx + 12*Np; bb_dist_tmp[local_count++]=idx + 12*Np;
} }
neighbor=Map(i+1,j,k+1); neighbor=Map(i+1,j,k+1);
if (neighbor==-1){ if (neighbor==-1){
bb_interactions_tmp[local_count] = (i+1) + (j)*Nx + (k+1)*Nx*Ny; bb_interactions_tmp[local_count] = (i+1) + (j)*Nx + (k+1)*Nx*Ny;
//if(SlippingVelBC==true){ //if(SlippingVelBC==true){
fluid_boundary_tmp[local_count] = idx; fluid_boundary_tmp[local_count] = idx;
lattice_weight_tmp[local_count] = 1.0/36.0; lattice_weight_tmp[local_count] = 1.0/36.0;
lattice_cx_tmp[local_count] = 1.0; lattice_cx_tmp[local_count] = 1.0;
lattice_cy_tmp[local_count] = 0.0; lattice_cy_tmp[local_count] = 0.0;
lattice_cz_tmp[local_count] = 1.0; lattice_cz_tmp[local_count] = 1.0;
//} //}
bb_dist_tmp[local_count++]=idx + 11*Np; bb_dist_tmp[local_count++]=idx + 11*Np;
} }
neighbor=Map(i-1,j,k+1); neighbor=Map(i-1,j,k+1);
if (neighbor==-1) { if (neighbor==-1) {
bb_interactions_tmp[local_count] = (i-1) + (j)*Nx + (k+1)*Nx*Ny; bb_interactions_tmp[local_count] = (i-1) + (j)*Nx + (k+1)*Nx*Ny;
//if(SlippingVelBC==true){ //if(SlippingVelBC==true){
fluid_boundary_tmp[local_count] = idx; fluid_boundary_tmp[local_count] = idx;
lattice_weight_tmp[local_count] = 1.0/36.0; lattice_weight_tmp[local_count] = 1.0/36.0;
lattice_cx_tmp[local_count] = -1.0; lattice_cx_tmp[local_count] = -1.0;
lattice_cy_tmp[local_count] = 0.0; lattice_cy_tmp[local_count] = 0.0;
lattice_cz_tmp[local_count] = 1.0; lattice_cz_tmp[local_count] = 1.0;
//} //}
bb_dist_tmp[local_count++]=idx + 14*Np; bb_dist_tmp[local_count++]=idx + 14*Np;
} }
neighbor=Map(i+1,j,k-1); neighbor=Map(i+1,j,k-1);
if (neighbor==-1) { if (neighbor==-1) {
bb_interactions_tmp[local_count] = (i+1) + (j)*Nx + (k-1)*Nx*Ny; bb_interactions_tmp[local_count] = (i+1) + (j)*Nx + (k-1)*Nx*Ny;
//if(SlippingVelBC==true){ //if(SlippingVelBC==true){
fluid_boundary_tmp[local_count] = idx; fluid_boundary_tmp[local_count] = idx;
lattice_weight_tmp[local_count] = 1.0/36.0; lattice_weight_tmp[local_count] = 1.0/36.0;
lattice_cx_tmp[local_count] = 1.0; lattice_cx_tmp[local_count] = 1.0;
lattice_cy_tmp[local_count] = 0.0; lattice_cy_tmp[local_count] = 0.0;
lattice_cz_tmp[local_count] = -1.0; lattice_cz_tmp[local_count] = -1.0;
//} //}
bb_dist_tmp[local_count++]=idx + 13*Np; bb_dist_tmp[local_count++]=idx + 13*Np;
} }
neighbor=Map(i,j-1,k-1); neighbor=Map(i,j-1,k-1);
if (neighbor==-1){ if (neighbor==-1){
bb_interactions_tmp[local_count] = (i) + (j-1)*Nx + (k-1)*Nx*Ny; bb_interactions_tmp[local_count] = (i) + (j-1)*Nx + (k-1)*Nx*Ny;
//if(SlippingVelBC==true){ //if(SlippingVelBC==true){
fluid_boundary_tmp[local_count] = idx; fluid_boundary_tmp[local_count] = idx;
lattice_weight_tmp[local_count] = 1.0/36.0; lattice_weight_tmp[local_count] = 1.0/36.0;
lattice_cx_tmp[local_count] = 0.0; lattice_cx_tmp[local_count] = 0.0;
lattice_cy_tmp[local_count] = -1.0; lattice_cy_tmp[local_count] = -1.0;
lattice_cz_tmp[local_count] = -1.0; lattice_cz_tmp[local_count] = -1.0;
//} //}
bb_dist_tmp[local_count++]=idx + 16*Np; bb_dist_tmp[local_count++]=idx + 16*Np;
} }
neighbor=Map(i,j+1,k+1); neighbor=Map(i,j+1,k+1);
if (neighbor==-1){ if (neighbor==-1){
bb_interactions_tmp[local_count] = (i) + (j+1)*Nx + (k+1)*Nx*Ny; bb_interactions_tmp[local_count] = (i) + (j+1)*Nx + (k+1)*Nx*Ny;
//if(SlippingVelBC==true){ //if(SlippingVelBC==true){
fluid_boundary_tmp[local_count] = idx; fluid_boundary_tmp[local_count] = idx;
lattice_weight_tmp[local_count] = 1.0/36.0; lattice_weight_tmp[local_count] = 1.0/36.0;
lattice_cx_tmp[local_count] = 0.0; lattice_cx_tmp[local_count] = 0.0;
lattice_cy_tmp[local_count] = 1.0; lattice_cy_tmp[local_count] = 1.0;
lattice_cz_tmp[local_count] = 1.0; lattice_cz_tmp[local_count] = 1.0;
//} //}
bb_dist_tmp[local_count++]=idx + 15*Np; bb_dist_tmp[local_count++]=idx + 15*Np;
} }
neighbor=Map(i,j-1,k+1); neighbor=Map(i,j-1,k+1);
if (neighbor==-1){ if (neighbor==-1){
bb_interactions_tmp[local_count] = (i) + (j-1)*Nx + (k+1)*Nx*Ny; bb_interactions_tmp[local_count] = (i) + (j-1)*Nx + (k+1)*Nx*Ny;
//if(SlippingVelBC==true){ //if(SlippingVelBC==true){
fluid_boundary_tmp[local_count] = idx; fluid_boundary_tmp[local_count] = idx;
lattice_weight_tmp[local_count] = 1.0/36.0; lattice_weight_tmp[local_count] = 1.0/36.0;
lattice_cx_tmp[local_count] = 0.0; lattice_cx_tmp[local_count] = 0.0;
lattice_cy_tmp[local_count] = -1.0; lattice_cy_tmp[local_count] = -1.0;
lattice_cz_tmp[local_count] = 1.0; lattice_cz_tmp[local_count] = 1.0;
//} //}
bb_dist_tmp[local_count++]=idx + 18*Np; bb_dist_tmp[local_count++]=idx + 18*Np;
} }
neighbor=Map(i,j+1,k-1); neighbor=Map(i,j+1,k-1);
if (neighbor==-1){ if (neighbor==-1){
bb_interactions_tmp[local_count] = (i) + (j+1)*Nx + (k-1)*Nx*Ny; bb_interactions_tmp[local_count] = (i) + (j+1)*Nx + (k-1)*Nx*Ny;
//if(SlippingVelBC==true){ //if(SlippingVelBC==true){
fluid_boundary_tmp[local_count] = idx; fluid_boundary_tmp[local_count] = idx;
lattice_weight_tmp[local_count] = 1.0/36.0; lattice_weight_tmp[local_count] = 1.0/36.0;
lattice_cx_tmp[local_count] = 0.0; lattice_cx_tmp[local_count] = 0.0;
lattice_cy_tmp[local_count] = 1.0; lattice_cy_tmp[local_count] = 1.0;
lattice_cz_tmp[local_count] = -1.0; lattice_cz_tmp[local_count] = -1.0;
//} //}
bb_dist_tmp[local_count++]=idx + 17*Np; bb_dist_tmp[local_count++]=idx + 17*Np;
}
} }
} }
} }
} }
} n_bb_d3q19 = local_count; // this gives the d3q19 distributions not part of d3q7 model
n_bb_d3q19 = local_count; // this gives the d3q19 distributions not part of d3q7 model ScaLBL_CopyToDevice(bb_dist, bb_dist_tmp, local_count*sizeof(int));
ScaLBL_CopyToDevice(bb_dist, bb_dist_tmp, local_count*sizeof(int)); ScaLBL_CopyToDevice(bb_interactions, bb_interactions_tmp, local_count*sizeof(int));
ScaLBL_CopyToDevice(bb_interactions, bb_interactions_tmp, local_count*sizeof(int)); ScaLBL_CopyToDevice(fluid_boundary, fluid_boundary_tmp, local_count*sizeof(int));
ScaLBL_CopyToDevice(fluid_boundary, fluid_boundary_tmp, local_count*sizeof(int)); ScaLBL_CopyToDevice(lattice_weight, lattice_weight_tmp, local_count*sizeof(double));
ScaLBL_CopyToDevice(lattice_weight, lattice_weight_tmp, local_count*sizeof(double)); ScaLBL_CopyToDevice(lattice_cx, lattice_cx_tmp, local_count*sizeof(float));
ScaLBL_CopyToDevice(lattice_cx, lattice_cx_tmp, local_count*sizeof(float)); ScaLBL_CopyToDevice(lattice_cy, lattice_cy_tmp, local_count*sizeof(float));
ScaLBL_CopyToDevice(lattice_cy, lattice_cy_tmp, local_count*sizeof(float)); ScaLBL_CopyToDevice(lattice_cz, lattice_cz_tmp, local_count*sizeof(float));
ScaLBL_CopyToDevice(lattice_cz, lattice_cz_tmp, local_count*sizeof(float)); ScaLBL_DeviceBarrier();
ScaLBL_DeviceBarrier();
delete [] bb_dist_tmp; delete [] bb_dist_tmp;
delete [] bb_interactions_tmp; delete [] bb_interactions_tmp;
delete [] fluid_boundary_tmp; delete [] fluid_boundary_tmp;
delete [] lattice_weight_tmp; delete [] lattice_weight_tmp;
delete [] lattice_cx_tmp; delete [] lattice_cx_tmp;
delete [] lattice_cy_tmp; delete [] lattice_cy_tmp;
delete [] lattice_cz_tmp; delete [] lattice_cz_tmp;
}
else {
bb_dist = NULL;
bb_interactions = NULL;
fluid_boundary = NULL;
lattice_weight = NULL;
lattice_cx = NULL;
lattice_cy = NULL;
lattice_cz = NULL;
}
} }
void ScaLBL_Communicator::SolidDirichletD3Q7(double *fq, double *BoundaryValue){ void ScaLBL_Communicator::SolidDirichletD3Q7(double *fq, double *BoundaryValue){

31
models/IonModel.cpp
View File

@@ -13,7 +13,20 @@ ScaLBL_IonModel::ScaLBL_IonModel(int RANK, int NP, const Utilities::MPI &COMM)
nprocy(0), nprocz(0), fluidVelx_dummy(0), fluidVely_dummy(0), nprocy(0), nprocz(0), fluidVelx_dummy(0), fluidVely_dummy(0),
fluidVelz_dummy(0), BoundaryConditionInlet(0), BoundaryConditionOutlet(0), fluidVelz_dummy(0), BoundaryConditionInlet(0), BoundaryConditionOutlet(0),
BoundaryConditionSolid(0), Lx(0), Ly(0), Lz(0), comm(COMM) {} BoundaryConditionSolid(0), Lx(0), Ly(0), Lz(0), comm(COMM) {}
ScaLBL_IonModel::~ScaLBL_IonModel() {}
ScaLBL_IonModel::~ScaLBL_IonModel() {
ScaLBL_FreeDeviceMemory(NeighborList);
ScaLBL_FreeDeviceMemory(dvcMap);
ScaLBL_FreeDeviceMemory(fq);
ScaLBL_FreeDeviceMemory(Ci);
ScaLBL_FreeDeviceMemory(ChargeDensity);
ScaLBL_FreeDeviceMemory(FluxDiffusive);
ScaLBL_FreeDeviceMemory(FluxAdvective);
ScaLBL_FreeDeviceMemory(FluxElectrical);
ScaLBL_FreeDeviceMemory(IonSolid);
ScaLBL_FreeDeviceMemory(FluidVelocityDummy);
}
void ScaLBL_IonModel::ReadParams(string filename, vector<int> &num_iter) { void ScaLBL_IonModel::ReadParams(string filename, vector<int> &num_iter) {
@@ -50,6 +63,8 @@ void ScaLBL_IonModel::ReadParams(string filename, vector<int> &num_iter) {
Ez_dummy = 0.0; //for debugging, unit [V/m] Ez_dummy = 0.0; //for debugging, unit [V/m]
//--------------------------------------------------------------------------// //--------------------------------------------------------------------------//
BoundaryConditionSolid = 0;
// Read domain parameters // Read domain parameters
if (domain_db->keyExists("voxel_length")) { //default unit: um/lu if (domain_db->keyExists("voxel_length")) { //default unit: um/lu
h = domain_db->getScalar<double>("voxel_length"); h = domain_db->getScalar<double>("voxel_length");
@@ -685,7 +700,6 @@ void ScaLBL_IonModel::SetDomain() {
} }
void ScaLBL_IonModel::SetMembrane() { void ScaLBL_IonModel::SetMembrane() {
size_t NLABELS = 0;
membrane_db = db->getDatabase("Membrane"); membrane_db = db->getDatabase("Membrane");
@@ -693,7 +707,7 @@ void ScaLBL_IonModel::SetMembrane() {
auto MembraneLabels = membrane_db->getVector<int>("MembraneLabels"); auto MembraneLabels = membrane_db->getVector<int>("MembraneLabels");
IonMembrane = std::shared_ptr<Membrane>(new Membrane(Dm, NeighborList, Np)); IonMembrane = std::shared_ptr<Membrane>(new Membrane(Dm, NeighborList, Np));
size_t NLABELS = MembraneLabels.size();
signed char LABEL = 0; signed char LABEL = 0;
double *label_count; double *label_count;
double *label_count_global; double *label_count_global;
@@ -1020,7 +1034,6 @@ void ScaLBL_IonModel::Create() {
} }
ScaLBL_CopyToDevice(dvcMap, TmpMap, sizeof(int) * Np); ScaLBL_CopyToDevice(dvcMap, TmpMap, sizeof(int) * Np);
ScaLBL_Comm->Barrier(); ScaLBL_Comm->Barrier();
delete[] TmpMap;
ScaLBL_CopyToDevice(NeighborList, neighborList, neighborSize); ScaLBL_CopyToDevice(NeighborList, neighborList, neighborSize);
comm.barrier(); comm.barrier();
@@ -1042,6 +1055,13 @@ void ScaLBL_IonModel::Create() {
ScaLBL_Comm->Barrier(); ScaLBL_Comm->Barrier();
delete[] IonSolid_host; delete[] IonSolid_host;
} }
else {
IonSolid = NULL;
}
delete[] TmpMap;
delete[] neighborList;
} }
void ScaLBL_IonModel::Initialize() { void ScaLBL_IonModel::Initialize() {
@@ -1444,6 +1464,7 @@ void ScaLBL_IonModel::RunMembrane(double *Velocity, double *ElectricField, doubl
//auto t1 = std::chrono::system_clock::now(); //auto t1 = std::chrono::system_clock::now();
for (size_t ic = 0; ic < number_ion_species; ic++) { for (size_t ic = 0; ic < number_ion_species; ic++) {
/* set the mass transfer coefficients for the membrane */ /* set the mass transfer coefficients for the membrane */
IonMembrane->AssignCoefficients(dvcMap, Psi, ThresholdVoltage[ic],MassFractionIn[ic], IonMembrane->AssignCoefficients(dvcMap, Psi, ThresholdVoltage[ic],MassFractionIn[ic],
MassFractionOut[ic],ThresholdMassFractionIn[ic],ThresholdMassFractionOut[ic]); MassFractionOut[ic],ThresholdMassFractionIn[ic],ThresholdMassFractionOut[ic]);
@@ -1525,8 +1546,6 @@ void ScaLBL_IonModel::RunMembrane(double *Velocity, double *ElectricField, doubl
//Compute charge density for Poisson equation //Compute charge density for Poisson equation
for (size_t ic = 0; ic < number_ion_species; ic++) { for (size_t ic = 0; ic < number_ion_species; ic++) {
int Valence = IonValence[ic]; int Valence = IonValence[ic];
if (rank==0) printf("compute charge density for ion %i, Valence =%i \n", ic,Valence);
ScaLBL_D3Q7_Ion_ChargeDensity(Ci, ChargeDensity, Valence, ic, ScaLBL_D3Q7_Ion_ChargeDensity(Ci, ChargeDensity, Valence, ic,
ScaLBL_Comm->FirstInterior(), ScaLBL_Comm->FirstInterior(),
ScaLBL_Comm->LastInterior(), Np); ScaLBL_Comm->LastInterior(), Np);

9
models/PoissonSolver.cpp
View File

@@ -32,6 +32,14 @@ ScaLBL_Poisson::ScaLBL_Poisson(int RANK, int NP, const Utilities::MPI& COMM):
} }
ScaLBL_Poisson::~ScaLBL_Poisson() ScaLBL_Poisson::~ScaLBL_Poisson()
{ {
ScaLBL_FreeDeviceMemory(NeighborList);
ScaLBL_FreeDeviceMemory(dvcMap);
ScaLBL_FreeDeviceMemory(Psi);
ScaLBL_FreeDeviceMemory(Psi_BCLabel);
ScaLBL_FreeDeviceMemory(ElectricField);
ScaLBL_FreeDeviceMemory(ResidualError);
ScaLBL_FreeDeviceMemory(fq);
if ( TIMELOG ) if ( TIMELOG )
fclose( TIMELOG ); fclose( TIMELOG );
} }
@@ -416,6 +424,7 @@ void ScaLBL_Poisson::Create(){
//ScaLBL_Comm->Barrier(); //ScaLBL_Comm->Barrier();
//Initialize solid boundary for electric potential //Initialize solid boundary for electric potential
// DON'T USE WITH CELLULAR SYSTEM (NO SOLID -- NEED Membrane SOLUTION)
ScaLBL_Comm->SetupBounceBackList(Map, Mask->id.data(), Np); ScaLBL_Comm->SetupBounceBackList(Map, Mask->id.data(), Np);
comm.barrier(); comm.barrier();
} }

4
tests/lbpm_nernst_planck_cell_simulator.cpp
View File

@@ -23,7 +23,9 @@ using namespace std;
int main(int argc, char **argv) int main(int argc, char **argv)
{ {
// Initialize MPI and error handlers // Initialize MPI and error handlers
Utilities::startup( argc, argv ); //Utilities::startup( argc, argv );
Utilities::startup( argc, argv, true );
Utilities::MPI comm( MPI_COMM_WORLD ); Utilities::MPI comm( MPI_COMM_WORLD );
int rank = comm.getRank(); int rank = comm.getRank();
int nprocs = comm.getSize(); int nprocs = comm.getSize();