504 lines
17 KiB
C++
504 lines
17 KiB
C++
#include <stdio.h>
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#include <math.h>
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extern "C" void ScaLBL_D3Q7_Membrane_AssignLinkCoef(int *membrane, int *Map, double *Distance, double *Psi, double *coef,
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double Threshold, double MassFractionIn, double MassFractionOut, double ThresholdMassFractionIn, double ThresholdMassFractionOut,
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int memLinks, int Nx, int Ny, int Nz, int Np){
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int link,iq,ip,nq,np,nqm,npm;
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double aq, ap, membranePotential;
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//double dq, dp, dist, orientation;
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/* Interior Links */
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for (link=0; link<memLinks; link++){
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// inside //outside
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aq = MassFractionIn; ap = MassFractionOut;
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iq = membrane[2*link]; ip = membrane[2*link+1];
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nq = iq%Np; np = ip%Np;
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nqm = Map[nq]; npm = Map[np]; // strided layout
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//dq = Distance[nqm]; dp = Distance[npm];
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/* orientation for link to distance gradient*/
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//orientation = 1.0/fabs(dq - dp);
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/* membrane potential for this link */
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membranePotential = Psi[nqm] - Psi[npm];
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if (membranePotential > Threshold){
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aq = ThresholdMassFractionIn; ap = ThresholdMassFractionOut;
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}
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/* Save the mass transfer coefficients */
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//coef[2*link] = aq*orientation; coef[2*link+1] = ap*orientation;
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coef[2*link] = aq; coef[2*link+1] = ap;
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}
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}
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extern "C" void ScaLBL_D3Q7_Membrane_AssignLinkCoef_halo(
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const int Cqx, const int Cqy, int const Cqz,
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int *Map, double *Distance, double *Psi, double Threshold,
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double MassFractionIn, double MassFractionOut, double ThresholdMassFractionIn, double ThresholdMassFractionOut,
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int *d3q7_recvlist, int *d3q7_linkList, double *coef, int start, int nlinks, int count,
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const int N, const int Nx, const int Ny, const int Nz) {
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//....................................................................................
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// Unack distribution from the recv buffer
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// Distribution q matche Cqx, Cqy, Cqz
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// swap rule means that the distributions in recvbuf are OPPOSITE of q
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// dist may be even or odd distributions stored by stream layout
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//....................................................................................
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int n, idx, link, nqm, npm, i, j, k;
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double distanceLocal, distanceNonlocal;
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double psiLocal, psiNonlocal, membranePotential;
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double ap,aq; // coefficient
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/* second enforce custom rule for membrane links */
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for (link = nlinks; link < count; link++) {
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// get the index for the recv list (deal with reordering of links)
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idx = d3q7_linkList[link]; // THINK start NEEDS TO BE HERE
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// get the distribution index
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n = d3q7_recvlist[start+idx];
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// get the index in strided layout
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nqm = Map[n];
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distanceLocal = Distance[nqm];
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psiLocal = Psi[nqm];
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// Get the 3-D indices from the send process
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k = nqm/(Nx*Ny); j = (nqm-Nx*Ny*k)/Nx; i = nqm-Nx*Ny*k-Nx*j;
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// Streaming link the non-local distribution
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i -= Cqx; j -= Cqy; k -= Cqz;
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npm = k*Nx*Ny + j*Nx + i;
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distanceNonlocal = Distance[npm];
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psiNonlocal = Psi[npm];
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membranePotential = psiLocal - psiNonlocal;
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aq = MassFractionIn;
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ap = MassFractionOut;
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/* link is inside membrane */
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if (distanceLocal > 0.0){
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if (membranePotential < Threshold*(-1.0)){
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ap = MassFractionIn;
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aq = MassFractionOut;
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}
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else {
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ap = ThresholdMassFractionIn;
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aq = ThresholdMassFractionOut;
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}
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}
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else if (membranePotential > Threshold){
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aq = ThresholdMassFractionIn;
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ap = ThresholdMassFractionOut;
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}
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// update link based on mass transfer coefficients
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coef[2*(link-nlinks)] = aq;
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coef[2*(link-nlinks)+1] = ap;
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}
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}
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extern "C" void ScaLBL_D3Q7_Membrane_Unpack(int q,
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int *d3q7_recvlist, int *d3q7_linkList, int start, int nlinks, int count,
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double *recvbuf, double *dist, int N, double *coef) {
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//....................................................................................
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// Unack distribution from the recv buffer
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// Distribution q matche Cqx, Cqy, Cqz
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// swap rule means that the distributions in recvbuf are OPPOSITE of q
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// dist may be even or odd distributions stored by stream layout
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//....................................................................................
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int n, idx, link;
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double fq,fp,fqq,ap,aq; // coefficient
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/* First unpack the regular links */
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for (link = 0; link < nlinks; link++) {
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// get the index for the recv list (deal with reordering of links)
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idx = d3q7_linkList[link];
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// get the distribution index
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n = d3q7_recvlist[start+idx];
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if (!(n < 0)){
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fp = recvbuf[start + idx];
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dist[q * N + n] = fp;
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}
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//printf(" site=%i, index=%i, value = %e \n",n,idx,fp);
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}
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/* second enforce custom rule for membrane links */
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for (link = nlinks; link < count; link++) {
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// get the index for the recv list (deal with reordering of links)
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idx = d3q7_linkList[link];
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// get the distribution index
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n = d3q7_recvlist[start+idx];
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// update link based on mass transfer coefficients
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if (!(n < 0)){
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aq = coef[2*(link-nlinks)];
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ap = coef[2*(link-nlinks)+1];
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fq = dist[q * N + n];
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fp = recvbuf[start + idx];
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fqq = (1-aq)*fq+ap*fp;
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dist[q * N + n] = fqq;
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}
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//printf(" LINK: site=%i, index=%i \n", n, idx);
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}
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}
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extern "C" void ScaLBL_D3Q7_Membrane_IonTransport(int *membrane, double *coef,
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double *dist, double *Den, int memLinks, int Np){
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int link,iq,ip,nq,np;
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double aq, ap, fq, fp, fqq, fpp, Cq, Cp;
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for (link=0; link<memLinks; link++){
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// inside //outside
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aq = coef[2*link]; ap = coef[2*link+1];
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iq = membrane[2*link]; ip = membrane[2*link+1];
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nq = iq%Np; np = ip%Np;
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fq = dist[iq]; fp = dist[ip];
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fqq = (1-aq)*fq+ap*fp; fpp = (1-ap)*fp+aq*fq;
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Cq = Den[nq]; Cp = Den[np];
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Cq += fqq - fq; Cp += fpp - fp;
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Den[nq] = Cq; Den[np] = Cp;
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dist[iq] = fqq; dist[ip] = fpp;
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}
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}
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extern "C" void ScaLBL_D3Q7_AAodd_IonConcentration(int *neighborList,
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double *dist, double *Den,
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int start, int finish,
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int Np) {
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int n, nread;
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double fq, Ci;
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for (n = start; n < finish; n++) {
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// q=0
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fq = dist[n];
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Ci = fq;
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// q=1
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nread = neighborList[n];
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fq = dist[nread];
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Ci += fq;
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// q=2
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nread = neighborList[n + Np];
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fq = dist[nread];
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Ci += fq;
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// q=3
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nread = neighborList[n + 2 * Np];
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fq = dist[nread];
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Ci += fq;
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// q=4
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nread = neighborList[n + 3 * Np];
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fq = dist[nread];
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Ci += fq;
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// q=5
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nread = neighborList[n + 4 * Np];
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fq = dist[nread];
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Ci += fq;
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// q=6
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nread = neighborList[n + 5 * Np];
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fq = dist[nread];
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Ci += fq;
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Den[n] = Ci;
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}
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}
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extern "C" void ScaLBL_D3Q7_AAeven_IonConcentration(double *dist, double *Den,
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int start, int finish,
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int Np) {
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int n;
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double fq, Ci;
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for (n = start; n < finish; n++) {
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// q=0
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fq = dist[n];
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Ci = fq;
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// q=1
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fq = dist[2 * Np + n];
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Ci += fq;
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// q=2
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fq = dist[1 * Np + n];
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Ci += fq;
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// q=3
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fq = dist[4 * Np + n];
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Ci += fq;
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// q=4
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fq = dist[3 * Np + n];
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Ci += fq;
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// q=5
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fq = dist[6 * Np + n];
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Ci += fq;
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// q=6
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fq = dist[5 * Np + n];
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Ci += fq;
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Den[n] = Ci;
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}
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}
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extern "C" void ScaLBL_D3Q7_AAodd_Ion(int *neighborList, double *dist,
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double *Den, double *FluxDiffusive,
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double *FluxAdvective,
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double *FluxElectrical, double *Velocity,
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double *ElectricField, double Di, int zi,
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double rlx, double Vt, int start,
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int finish, int Np) {
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int n;
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double Ci;
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double ux, uy, uz;
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double uEPx, uEPy, uEPz; //electrochemical induced velocity
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double Ex, Ey, Ez; //electrical field
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double flux_diffusive_x, flux_diffusive_y, flux_diffusive_z;
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double f0, f1, f2, f3, f4, f5, f6;
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//double X,Y,Z,factor_x, factor_y, factor_z;
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int nr1, nr2, nr3, nr4, nr5, nr6;
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for (n = start; n < finish; n++) {
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//Load data
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Ci = Den[n];
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Ex = ElectricField[n + 0 * Np];
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Ey = ElectricField[n + 1 * Np];
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Ez = ElectricField[n + 2 * Np];
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ux = Velocity[n + 0 * Np];
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uy = Velocity[n + 1 * Np];
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uz = Velocity[n + 2 * Np];
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uEPx = zi * Di / Vt * Ex;
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uEPy = zi * Di / Vt * Ey;
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uEPz = zi * Di / Vt * Ez;
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// q=0
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f0 = dist[n];
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// q=1
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nr1 = neighborList[n]; // neighbor 2 ( > 10Np => odd part of dist)
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f1 = dist[nr1]; // reading the f1 data into register fq
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// q=2
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nr2 = neighborList[n + Np]; // neighbor 1 ( < 10Np => even part of dist)
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f2 = dist[nr2]; // reading the f2 data into register fq
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// q=3
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nr3 = neighborList[n + 2 * Np]; // neighbor 4
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f3 = dist[nr3];
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// q=4
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nr4 = neighborList[n + 3 * Np]; // neighbor 3
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f4 = dist[nr4];
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// q=5
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nr5 = neighborList[n + 4 * Np];
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f5 = dist[nr5];
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// q=6
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nr6 = neighborList[n + 5 * Np];
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f6 = dist[nr6];
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// compute diffusive flux
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//Ci = f0 + f1 + f2 + f3 + f4 + f5 + f6;
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flux_diffusive_x = (1.0 - 0.5 * rlx) * ((f1 - f2) - ux * Ci);
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flux_diffusive_y = (1.0 - 0.5 * rlx) * ((f3 - f4) - uy * Ci);
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flux_diffusive_z = (1.0 - 0.5 * rlx) * ((f5 - f6) - uz * Ci);
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FluxDiffusive[n + 0 * Np] = flux_diffusive_x;
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FluxDiffusive[n + 1 * Np] = flux_diffusive_y;
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FluxDiffusive[n + 2 * Np] = flux_diffusive_z;
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FluxAdvective[n + 0 * Np] = ux * Ci;
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FluxAdvective[n + 1 * Np] = uy * Ci;
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FluxAdvective[n + 2 * Np] = uz * Ci;
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FluxElectrical[n + 0 * Np] = uEPx * Ci;
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FluxElectrical[n + 1 * Np] = uEPy * Ci;
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FluxElectrical[n + 2 * Np] = uEPz * Ci;
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//Den[n] = Ci;
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/* use logistic function to prevent negative distributions*/
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//X = 4.0 * (ux + uEPx);
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//Y = 4.0 * (uy + uEPy);
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//Z = 4.0 * (uz + uEPz);
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//factor_x = X / sqrt(1 + X*X);
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//factor_y = Y / sqrt(1 + Y*Y);
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//factor_z = Z / sqrt(1 + Z*Z);
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// q=0
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dist[n] = f0 * (1.0 - rlx) + rlx * 0.25 * Ci;
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// q = 1
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dist[nr2] =
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f1 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 + 4.0 * (ux + uEPx));
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// f1 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 + factor_x);
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// q=2
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dist[nr1] =
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f2 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 - 4.0 * (ux + uEPx));
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// f2 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 - factor_x);
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// q = 3
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dist[nr4] =
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f3 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 + 4.0 * (uy + uEPy));
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// f3 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 + factor_y );
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// q = 4
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dist[nr3] =
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f4 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 - 4.0 * (uy + uEPy));
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// f4 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 - factor_y);
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// q = 5
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dist[nr6] =
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f5 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 + 4.0 * (uz + uEPz));
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// f5 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 + factor_z);
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// q = 6
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dist[nr5] =
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f6 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 - 4.0 * (uz + uEPz));
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// f6 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 - factor_z);
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}
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}
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extern "C" void ScaLBL_D3Q7_AAeven_Ion(
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double *dist, double *Den, double *FluxDiffusive, double *FluxAdvective,
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double *FluxElectrical, double *Velocity, double *ElectricField, double Di,
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int zi, double rlx, double Vt, int start, int finish, int Np) {
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int n;
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double Ci;
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double ux, uy, uz;
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double uEPx, uEPy, uEPz; //electrochemical induced velocity
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double Ex, Ey, Ez; //electrical field
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double flux_diffusive_x, flux_diffusive_y, flux_diffusive_z;
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double f0, f1, f2, f3, f4, f5, f6;
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//double X,Y,Z, factor_x, factor_y, factor_z;
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for (n = start; n < finish; n++) {
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//Load data
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Ci = Den[n];
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Ex = ElectricField[n + 0 * Np];
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Ey = ElectricField[n + 1 * Np];
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Ez = ElectricField[n + 2 * Np];
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ux = Velocity[n + 0 * Np];
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uy = Velocity[n + 1 * Np];
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uz = Velocity[n + 2 * Np];
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uEPx = zi * Di / Vt * Ex;
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uEPy = zi * Di / Vt * Ey;
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uEPz = zi * Di / Vt * Ez;
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f0 = dist[n];
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f1 = dist[2 * Np + n];
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f2 = dist[1 * Np + n];
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f3 = dist[4 * Np + n];
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f4 = dist[3 * Np + n];
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f5 = dist[6 * Np + n];
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f6 = dist[5 * Np + n];
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// compute diffusive flux
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//Ci = f0 + f1 + f2 + f3 + f4 + f5 + f6;
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flux_diffusive_x = (1.0 - 0.5 * rlx) * ((f1 - f2) - ux * Ci);
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flux_diffusive_y = (1.0 - 0.5 * rlx) * ((f3 - f4) - uy * Ci);
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flux_diffusive_z = (1.0 - 0.5 * rlx) * ((f5 - f6) - uz * Ci);
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FluxDiffusive[n + 0 * Np] = flux_diffusive_x;
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FluxDiffusive[n + 1 * Np] = flux_diffusive_y;
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FluxDiffusive[n + 2 * Np] = flux_diffusive_z;
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FluxAdvective[n + 0 * Np] = ux * Ci;
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FluxAdvective[n + 1 * Np] = uy * Ci;
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FluxAdvective[n + 2 * Np] = uz * Ci;
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FluxElectrical[n + 0 * Np] = uEPx * Ci;
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FluxElectrical[n + 1 * Np] = uEPy * Ci;
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FluxElectrical[n + 2 * Np] = uEPz * Ci;
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//Den[n] = Ci;
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/* use logistic function to prevent negative distributions*/
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//X = 4.0 * (ux + uEPx);
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//Y = 4.0 * (uy + uEPy);
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//Z = 4.0 * (uz + uEPz);
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//factor_x = X / sqrt(1 + X*X);
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//factor_y = Y / sqrt(1 + Y*Y);
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//factor_z = Z / sqrt(1 + Z*Z);
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// q=0
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dist[n] = f0 * (1.0 - rlx) + rlx * 0.25 * Ci;
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// q = 1
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dist[1 * Np + n] =
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f1 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 + 4.0 * (ux + uEPx));
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// f1 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 + factor_x);
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// q=2
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dist[2 * Np + n] =
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f2 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 - 4.0 * (ux + uEPx));
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// f2 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 - factor_x);
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// q = 3
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dist[3 * Np + n] =
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f3 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 + 4.0 * (uy + uEPy));
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// f3 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 + factor_y);
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|
|
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// q = 4
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dist[4 * Np + n] =
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|
f4 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 - 4.0 * (uy + uEPy));
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// f4 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 - factor_y);
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|
|
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// q = 5
|
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dist[5 * Np + n] =
|
|
f5 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 + 4.0 * (uz + uEPz));
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// f5 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 + factor_z);
|
|
|
|
// q = 6
|
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dist[6 * Np + n] =
|
|
f6 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 - 4.0 * (uz + uEPz));
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// f6 * (1.0 - rlx) + rlx * 0.125 * Ci * (1.0 - factor_z);
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}
|
|
}
|
|
|
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extern "C" void ScaLBL_D3Q7_Ion_Init(double *dist, double *Den, double DenInit,
|
|
int Np) {
|
|
int n;
|
|
for (n = 0; n < Np; n++) {
|
|
dist[0 * Np + n] = 0.25 * DenInit;
|
|
dist[1 * Np + n] = 0.125 * DenInit;
|
|
dist[2 * Np + n] = 0.125 * DenInit;
|
|
dist[3 * Np + n] = 0.125 * DenInit;
|
|
dist[4 * Np + n] = 0.125 * DenInit;
|
|
dist[5 * Np + n] = 0.125 * DenInit;
|
|
dist[6 * Np + n] = 0.125 * DenInit;
|
|
Den[n] = DenInit;
|
|
}
|
|
}
|
|
|
|
extern "C" void ScaLBL_D3Q7_Ion_Init_FromFile(double *dist, double *Den,
|
|
int Np) {
|
|
int n;
|
|
double DenInit;
|
|
for (n = 0; n < Np; n++) {
|
|
DenInit = Den[n];
|
|
dist[0 * Np + n] = 0.25 * DenInit;
|
|
dist[1 * Np + n] = 0.125 * DenInit;
|
|
dist[2 * Np + n] = 0.125 * DenInit;
|
|
dist[3 * Np + n] = 0.125 * DenInit;
|
|
dist[4 * Np + n] = 0.125 * DenInit;
|
|
dist[5 * Np + n] = 0.125 * DenInit;
|
|
dist[6 * Np + n] = 0.125 * DenInit;
|
|
}
|
|
}
|
|
|
|
extern "C" void ScaLBL_D3Q7_Ion_ChargeDensity(double *Den,
|
|
double *ChargeDensity,
|
|
double IonValence, int ion_component,
|
|
int start, int finish, int Np) {
|
|
|
|
int n;
|
|
double Ci; //ion concentration of species i
|
|
double CD; //charge density
|
|
double CD_tmp;
|
|
double F =
|
|
96485.0; //Faraday's constant; unit[C/mol]; F=e*Na, where Na is the Avogadro constant
|
|
|
|
for (n = start; n < finish; n++) {
|
|
Ci = Den[n + ion_component * Np];
|
|
CD = ChargeDensity[n];
|
|
CD_tmp = F * IonValence * Ci;
|
|
ChargeDensity[n] = CD * (ion_component > 0) + CD_tmp;
|
|
}
|
|
}
|