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debug charge density problems on crusher

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This commit is contained in:
James E McClure 2022-04-24 15:55:23 -04:00
parent 9043751281
commit 3642a6ae9b
5 changed files with 38 additions and 11 deletions
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2
common/ScaLBL.h
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@ -301,7 +301,7 @@ extern "C" void ScaLBL_D3Q7_AAeven_Ion(double *dist, double *Den, double *FluxDi
extern "C" void ScaLBL_D3Q7_Ion_Init(double *dist, double *Den, double DenInit, int Np); extern "C" void ScaLBL_D3Q7_Ion_Init(double *dist, double *Den, double DenInit, int Np);
extern "C" void ScaLBL_D3Q7_Ion_Init_FromFile(double *dist, double *Den, int Np); extern "C" void ScaLBL_D3Q7_Ion_Init_FromFile(double *dist, double *Den, int Np);
extern "C" void ScaLBL_D3Q7_Ion_ChargeDensity(double *Den, double *ChargeDensity, int IonValence, int ion_component, int start, int finish, int Np); extern "C" void ScaLBL_D3Q7_Ion_ChargeDensity(double *Den, double *ChargeDensity, double IonValence, int ion_component, int start, int finish, int Np);
// LBM Poisson solver // LBM Poisson solver

13
cuda/Ion.cu
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@ -566,7 +566,7 @@ __global__ void dvc_ScaLBL_D3Q7_Ion_Init_FromFile(double *dist, double *Den, in
} }
} }
__global__ void dvc_ScaLBL_D3Q7_Ion_ChargeDensity(double *Den, double *ChargeDensity, int IonValence, int ion_component, int start, int finish, int Np){ __global__ void dvc_ScaLBL_D3Q7_Ion_ChargeDensity(double *Den, double *ChargeDensity, double IonValence, int ion_component, int start, int finish, int Np){
int n; int n;
double Ci;//ion concentration of species i double Ci;//ion concentration of species i
@ -579,10 +579,17 @@ __global__ void dvc_ScaLBL_D3Q7_Ion_ChargeDensity(double *Den, double *ChargeDe
//........Get 1-D index for this thread.................... //........Get 1-D index for this thread....................
n = S*blockIdx.x*blockDim.x + s*blockDim.x + threadIdx.x + start; n = S*blockIdx.x*blockDim.x + s*blockDim.x + threadIdx.x + start;
if (n<finish) { if (n<finish) {
Ci = Den[n+ion_component*Np]; Ci = Den[n+ion_component*Np];
CD = ChargeDensity[n]; CD = ChargeDensity[n];
if (ion_component == 0) CD=0.0;
CD_tmp = F*IonValence*Ci; CD_tmp = F*IonValence*Ci;
ChargeDensity[n] = CD*(ion_component>0) + CD_tmp; ChargeDensity[n] = CD + CD_tmp;
// Ci = Den[n+ion_component*Np];
// CD = ChargeDensity[n];
// CD_tmp = F*IonValence*Ci;
// ChargeDensity[n] = CD*(ion_component>0) + CD_tmp;
} }
} }
} }
@ -660,7 +667,7 @@ extern "C" void ScaLBL_D3Q7_Ion_Init_FromFile(double *dist, double *Den, int Np)
//cudaProfilerStop(); //cudaProfilerStop();
} }
extern "C" void ScaLBL_D3Q7_Ion_ChargeDensity(double *Den, double *ChargeDensity, int IonValence, int ion_component, int start, int finish, int Np){ extern "C" void ScaLBL_D3Q7_Ion_ChargeDensity(double *Den, double *ChargeDensity, double IonValence, int ion_component, int start, int finish, int Np){
//cudaProfilerStart(); //cudaProfilerStart();
dvc_ScaLBL_D3Q7_Ion_ChargeDensity<<<NBLOCKS,NTHREADS >>>(Den,ChargeDensity,IonValence,ion_component,start,finish,Np); dvc_ScaLBL_D3Q7_Ion_ChargeDensity<<<NBLOCKS,NTHREADS >>>(Den,ChargeDensity,IonValence,ion_component,start,finish,Np);

7
hip/Ion.hip
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@ -564,7 +564,7 @@ __global__ void dvc_ScaLBL_D3Q7_Ion_Init_FromFile(double *dist, double *Den, in
} }
} }
__global__ void dvc_ScaLBL_D3Q7_Ion_ChargeDensity(double *Den, double *ChargeDensity, int IonValence, int ion_component, int start, int finish, int Np){ __global__ void dvc_ScaLBL_D3Q7_Ion_ChargeDensity(double *Den, double *ChargeDensity, double IonValence, int ion_component, int start, int finish, int Np){
int n; int n;
double Ci;//ion concentration of species i double Ci;//ion concentration of species i
@ -579,8 +579,9 @@ __global__ void dvc_ScaLBL_D3Q7_Ion_ChargeDensity(double *Den, double *ChargeDe
if (n<finish) { if (n<finish) {
Ci = Den[n+ion_component*Np]; Ci = Den[n+ion_component*Np];
CD = ChargeDensity[n]; CD = ChargeDensity[n];
if (ion_component == 0) CD=0.0;
CD_tmp = F*IonValence*Ci; CD_tmp = F*IonValence*Ci;
ChargeDensity[n] = CD*(ion_component>0) + CD_tmp; ChargeDensity[n] = CD + CD_tmp;
} }
} }
} }
@ -658,7 +659,7 @@ extern "C" void ScaLBL_D3Q7_Ion_Init_FromFile(double *dist, double *Den, int Np)
//cudaProfilerStop(); //cudaProfilerStop();
} }
extern "C" void ScaLBL_D3Q7_Ion_ChargeDensity(double *Den, double *ChargeDensity, int IonValence, int ion_component, int start, int finish, int Np){ extern "C" void ScaLBL_D3Q7_Ion_ChargeDensity(double *Den, double *ChargeDensity, double IonValence, int ion_component, int start, int finish, int Np){
//cudaProfilerStart(); //cudaProfilerStart();
dvc_ScaLBL_D3Q7_Ion_ChargeDensity<<<NBLOCKS,NTHREADS >>>(Den,ChargeDensity,IonValence,ion_component,start,finish,Np); dvc_ScaLBL_D3Q7_Ion_ChargeDensity<<<NBLOCKS,NTHREADS >>>(Den,ChargeDensity,IonValence,ion_component,start,finish,Np);

26
models/IonModel.cpp
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@ -1443,17 +1443,35 @@ 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++) {
ScaLBL_D3Q7_Ion_ChargeDensity(Ci, ChargeDensity, IonValence[ic], 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_Comm->FirstInterior(), ScaLBL_Comm->FirstInterior(),
ScaLBL_Comm->LastInterior(), Np); ScaLBL_Comm->LastInterior(), Np);
ScaLBL_D3Q7_Ion_ChargeDensity(Ci, ChargeDensity, IonValence[ic], ic, 0, ScaLBL_D3Q7_Ion_ChargeDensity(Ci, ChargeDensity, Valence, ic, 0,
ScaLBL_Comm->LastExterior(), Np); ScaLBL_Comm->LastExterior(), Np);
} }
DoubleArray Charge(Nx,Ny,Nz);
ScaLBL_Comm->RegularLayout(Map, ChargeDensity, Charge);
double charge_sum=0.0;
double charge_sum_total=0.0;
for (int k=1; k<Nz-1; k++){
for (int j=1; j<Ny-1; j++){
for (int i=1; i<Nx-1; i++){
charge_sum += Charge(i,j,k);
}
}
}
printf(" Local charge value = %.8g (rank=%i)\n",charge_sum, rank);
ScaLBL_Comm->Barrier(); ScaLBL_Comm->Barrier();
comm.barrier(); comm.barrier();
if (rank==0) printf(" IonMembrane: completeted full step \n");
fflush(stdout); ScaLBL_Comm->Barrier();
comm.barrier();
//if (rank==0) printf(" IonMembrane: completeted full step \n");
//fflush(stdout);
//************************************************************************/ //************************************************************************/
//if (rank==0) printf("-------------------------------------------------------------------\n"); //if (rank==0) printf("-------------------------------------------------------------------\n");
//// Compute the walltime per timestep //// Compute the walltime per timestep

1
models/PoissonSolver.cpp
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@ -557,6 +557,7 @@ void ScaLBL_Poisson::Run(double *ChargeDensity, bool UseSlippingVelBC, int times
ScaLBL_Comm->Barrier(); comm.barrier(); ScaLBL_Comm->Barrier(); comm.barrier();
//************************************************************************/ //************************************************************************/
// Check convergence of steady-state solution // Check convergence of steady-state solution
if (timestep==2){ if (timestep==2){
//save electric potential for convergence check //save electric potential for convergence check