/
fix_conp.cpp
1294 lines (1183 loc) · 36.3 KB
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fix_conp.cpp
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/* ---------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Version: Sep/22/2014
Zhenxing Wang(KU)
------------------------------------------------------------------------- */
#include "math.h"
#include "string.h"
#include "stdlib.h"
#include "stddef.h"
#include "fix_conp.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "force.h"
#include "respa.h"
#include "input.h"
#include "variable.h"
#include "memory.h"
#include "error.h"
#include "compute.h"
#include "pair.h"
#include "kspace.h"
#include "comm.h"
#include "mpi.h"
#include "math_const.h"
#include "neigh_list.h"
#include "domain.h"
#include "iostream"
#define EWALD_F 1.12837917
#define EWALD_P 0.3275911
#define A1 0.254829592
#define A2 -0.284496736
#define A3 1.421413741
#define A4 -1.453152027
#define A5 1.061405429
using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
enum{CONSTANT,EQUAL,ATOM};
extern "C" {
void dgetrf_(const int *M,const int *N,double *A,const int *lda,int *ipiv,int *info);
void dgetri_(const int *N,double *A,const int *lda,const int *ipiv,double *work,const int *lwork,int *info);
}
/* ---------------------------------------------------------------------- */
FixConp::FixConp(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 11) error->all(FLERR,"Illegal fix conp command");
maxiter = 100;
tolerance = 0.000001;
everynum = utils->numeric(FLERR,arg[3],false,lmp);
eta = utils->numeric(FLERR,arg[4],false,lmp);
molidL = utils->inumeric(FLERR,arg[5],false,lmp);
molidR = utils->inumeric(FLERR,arg[6],false,lmp);
vL = utils->numeric(FLERR,arg[7],false,lmp);
vR = utils->numeric(FLERR,arg[8],false,lmp);
if (strcmp(arg[9],"cg") == 0) {
minimizer = 0;
} else if (strcmp(arg[9],"inv") == 0) {
minimizer = 1;
} else error->all(FLERR,"Unknown minimization method");
outf = fopen(arg[10],"w");
if (narg == 12) {
outa = NULL;
a_matrix_fp = fopen(arg[11],"r");
if (a_matrix_fp == NULL) error->all(FLERR,"Cannot open A matrix file");
if (strcmp(arg[11],"org") == 0) {
a_matrix_f = 1;
} else if (strcmp(arg[11],"inv") == 0) {
a_matrix_f = 2;
} else {
error->all(FLERR,"Unknown A matrix type");
}
} else {
a_matrix_f = 0;
}
elenum = elenum_old = 0;
csk = snk = NULL;
aaa_all = NULL;
bbb_all = NULL;
tag2eleall = eleall2tag = curr_tag2eleall = ele2tag = NULL;
Btime = cgtime = Ctime = Ktime = 0;
runstage = 0; //after operation
//0:init; 1: a_cal; 2: first sin/cos cal; 3: inv only, aaa inverse
}
/* ---------------------------------------------------------------------- */
FixConp::~FixConp()
{
fclose(outf);
memory->destroy3d_offset(cs,-kmax_created);
memory->destroy3d_offset(sn,-kmax_created);
delete [] aaa_all;
delete [] bbb_all;
delete [] curr_tag2eleall;
delete [] tag2eleall;
delete [] eleall2tag;
delete [] ele2tag;
delete [] kxvecs;
delete [] kyvecs;
delete [] kzvecs;
delete [] ug;
delete [] sfacrl;
delete [] sfacim;
delete [] sfacrl_all;
delete [] sfacim_all;
}
/* ---------------------------------------------------------------------- */
int FixConp::setmask()
{
int mask = 0;
mask |= PRE_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixConp::init()
{
MPI_Comm_rank(world,&me);
}
/* ---------------------------------------------------------------------- */
void FixConp::setup(int vflag)
{
g_ewald = force->kspace->g_ewald;
slab_volfactor = force->kspace->slab_volfactor;
double accuracy = force->kspace->accuracy;
int i;
double qsqsum = 0.0;
for (i = 0; i < atom->nlocal; i++) {
qsqsum += atom->q[i]*atom->q[i];
}
double tmp,q2;
MPI_Allreduce(&qsqsum,&tmp,1,MPI_DOUBLE,MPI_SUM,world);
qsqsum = tmp;
q2 = qsqsum * force->qqrd2e / force->dielectric;
// Copied from ewald.cpp
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
double zprd_slab = zprd*slab_volfactor;
volume = xprd * yprd * zprd_slab;
unitk[0] = 2.0*MY_PI/xprd;
unitk[1] = 2.0*MY_PI/yprd;
unitk[2] = 2.0*MY_PI/zprd_slab;
bigint natoms = atom->natoms;
double err;
kxmax = 1;
kymax = 1;
kzmax = 1;
err = rms(kxmax,xprd,natoms,q2);
while (err > accuracy) {
kxmax++;
err = rms(kxmax,xprd,natoms,q2);
}
err = rms(kymax,yprd,natoms,q2);
while (err > accuracy) {
kymax++;
err = rms(kymax,yprd,natoms,q2);
}
err = rms(kzmax,zprd_slab,natoms,q2);
while (err > accuracy) {
kzmax++;
err = rms(kzmax,zprd_slab,natoms,q2);
}
kmax = MAX(kxmax,kymax);
kmax = MAX(kmax,kzmax);
kmax3d = 4*kmax*kmax*kmax + 6*kmax*kmax + 3*kmax;
kxvecs = new int[kmax3d];
kyvecs = new int[kmax3d];
kzvecs = new int[kmax3d];
ug = new double[kmax3d];
double gsqxmx = unitk[0]*unitk[0]*kxmax*kxmax;
double gsqymx = unitk[1]*unitk[1]*kymax*kymax;
double gsqzmx = unitk[2]*unitk[2]*kzmax*kzmax;
gsqmx = MAX(gsqxmx,gsqymx);
gsqmx = MAX(gsqmx,gsqzmx);
gsqmx *= 1.00001;
coeffs();
kmax_created = kmax;
//copied from ewald.cpp end
int nmax = atom->nmax;
double evscale = 0.069447;
vL *= evscale;
vR *= evscale;
memory->create3d_offset(cs,-kmax,kmax,3,nmax,"fixconp:cs");
memory->create3d_offset(sn,-kmax,kmax,3,nmax,"fixconp:sn");
sfacrl = new double[kmax3d];
sfacim = new double[kmax3d];
sfacrl_all = new double[kmax3d];
sfacim_all = new double[kmax3d];
tag2eleall = new int[natoms+1];
curr_tag2eleall = new int[natoms+1];
if (runstage == 0) {
int i;
int nlocal = atom->nlocal;
for ( i = 0; i < nlocal; i++) {
if (electrode_check(i)) ++elenum;
}
MPI_Allreduce(&elenum,&elenum_all,1,MPI_INT,MPI_SUM,world);
eleall2tag = new int[elenum_all];
aaa_all = new double[elenum_all*elenum_all];
bbb_all = new double[elenum_all];
ele2tag = new int[elenum];
for (i = 0; i < natoms+1; i++) tag2eleall[i] = -1;
for (i = 0; i < natoms+1; i++) curr_tag2eleall[i] = -1;
if (minimizer == 0) {
eleallq = new double [elenum_all];
}
if (a_matrix_f == 0) {
if (me == 0) outa = fopen("amatrix","w");
a_cal();
} else {
a_read();
}
runstage = 1;
}
}
/* ---------------------------------------------------------------------- */
void FixConp::pre_force(int vflag)
{
if(update->ntimestep % everynum == 0) {
if (strstr(update->integrate_style,"verlet")) { //not respa
Btime1 = MPI_Wtime();
b_cal();
Btime2 = MPI_Wtime();
Btime += Btime2-Btime1;
if (update->laststep == update->ntimestep) {
double Btime_all;
MPI_Reduce(&Btime,&Btime_all,1,MPI_DOUBLE,MPI_SUM,0,world);
double Ctime_all;
MPI_Reduce(&Ctime,&Ctime_all,1,MPI_DOUBLE,MPI_SUM,0,world);
double Ktime_all;
MPI_Reduce(&Ktime,&Ktime_all,1,MPI_DOUBLE,MPI_SUM,0,world);
if (me == 0) {
Btime = Btime_all/comm->nprocs;
Ctime = Ctime_all/comm->nprocs;
Ktime = Ktime_all/comm->nprocs;
fprintf(outf,"B vector calculation time = %g\n",Btime);
fprintf(outf,"Coulomb calculation time = %g\n",Ctime);
fprintf(outf,"Kspace calculation time = %g\n",Ktime);
}
}
}
equation_solve();
update_charge();
}
force_cal(vflag);
}
/* ---------------------------------------------------------------------- */
int FixConp::electrode_check(int atomid)
{
int *molid = atom->molecule;
if (molid[atomid] == molidL) return 1;
else if (molid[atomid] == molidR) return -1;
else return 0;
}
/* ----------------------------------------------------------------------*/
void FixConp::b_cal()
{
Ktime1 = MPI_Wtime();
int i,j,k;
int nmax = atom->nmax;
if (atom->nlocal > nmax) {
memory->destroy3d_offset(cs,-kmax_created);
memory->destroy3d_offset(sn,-kmax_created);
nmax = atom->nmax;
kmax_created = kmax;
}
sincos_b();
MPI_Allreduce(sfacrl,sfacrl_all,kcount,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(sfacim,sfacim_all,kcount,MPI_DOUBLE,MPI_SUM,world);
double **x = atom->x;
double *q = atom->q;
int *tag = atom->tag;
int nlocal = atom->nlocal;
int kx,ky,kz;
double cypz,sypz,exprl,expim,kspacetmp;
elenum = 0;
for (i = 0; i < nlocal; i++) {
if(electrode_check(i)) elenum++;
}
double bbb[elenum];
j = 0;
for (i = 0; i < nlocal; i++) {
if (electrode_check(i) == 1) {
bbb[j] = vL;
j++;
}
if (electrode_check(i) == -1) {
bbb[j] = vR;
j++;
}
}
for (k = 0; k < kcount; k++) {
kx = kxvecs[k];
ky = kyvecs[k];
kz = kzvecs[k];
j = 0;
for (i = 0; i < nlocal; i++) {
if (electrode_check(i)) {
cypz = cs[ky][1][i]*cs[kz][2][i] - sn[ky][1][i]*sn[kz][2][i];
sypz = sn[ky][1][i]*cs[kz][2][i] + cs[ky][1][i]*sn[kz][2][i];
exprl = cs[kx][0][i]*cypz - sn[kx][0][i]*sypz;
expim = sn[kx][0][i]*cypz + cs[kx][0][i]*sypz;
bbb[j] -= 2.0*ug[k]*(exprl*sfacrl_all[k]+expim*sfacim_all[k]);
j++;
}
}
}
//elenum_list and displs for gathering ele tag list and bbb
int nprocs = comm->nprocs;
int elenum_list[nprocs];
MPI_Allgather(&elenum,1,MPI_INT,elenum_list,1,MPI_INT,world);
int displs[nprocs];
displs[0] = 0;
int displssum = 0;
for (i = 1; i < nprocs; ++i) {
displssum += elenum_list[i-1];
displs[i] = displssum;
}
//slabcorrection and create ele tag list in current timestep
double slabcorrtmp = 0.0;
double slabcorrtmp_all = 0.0;
for (i = 0; i < nlocal; i++) {
if (electrode_check(i) == 0) {
slabcorrtmp += 4*q[i]*MY_PI*x[i][2]/volume;
}
}
MPI_Allreduce(&slabcorrtmp,&slabcorrtmp_all,1,MPI_DOUBLE,MPI_SUM,world);
j = 0;
for (i = 0; i < nlocal; i++) {
if (electrode_check(i)) {
bbb[j] -= x[i][2]*slabcorrtmp_all;
ele2tag[j] = tag[i];
j++;
}
}
Ktime2 = MPI_Wtime();
Ktime += Ktime2-Ktime1;
coul_cal(1,bbb,ele2tag);
//gather ele tag list
int ele_taglist_all[elenum_all];
int tagi;
MPI_Allgatherv(ele2tag,elenum,MPI_INT,&ele_taglist_all,elenum_list,displs,MPI_INT,world);
for (i = 0; i < elenum_all; i++) {
tagi = ele_taglist_all[i];
curr_tag2eleall[tagi] = i;
}
//gather b to bbb_all and sort in the same order as aaa_all
double bbb_buf[elenum_all];
MPI_Allgatherv(&bbb,elenum,MPI_DOUBLE,&bbb_buf,elenum_list,displs,MPI_DOUBLE,world);
int elei;
for (i = 0; i < elenum_all; i++) {
tagi = eleall2tag[i];
elei = curr_tag2eleall[tagi];
bbb_all[i] = bbb_buf[elei];
}
}
/*----------------------------------------------------------------------- */
void FixConp::equation_solve()
{
//solve equations
if (minimizer == 0) {
cgtime1 = MPI_Wtime();
cg();
cgtime2 = MPI_Wtime();
cgtime += cgtime2-cgtime1;
if (update->laststep == update->ntimestep) {
double cgtime_all;
MPI_Reduce(&cgtime,&cgtime_all,1,MPI_DOUBLE,MPI_SUM,0,world);
if (me == 0) {
cgtime = cgtime_all/comm->nprocs;
if (screen) fprintf(screen,"conjugate gradient solver time = %g\n",cgtime);
if (logfile) fprintf(logfile,"conjugate gradient solver time = %g\n",cgtime);
}
}
} else if (minimizer == 1) {
inv();
}
}
/*----------------------------------------------------------------------- */
void FixConp::a_read()
{
int i = 0;
int idx1d;
if (me == 0) {
int maxchar = 21*elenum_all+1;
char line[maxchar];
char *word;
while(fgets(line,maxchar,a_matrix_fp) != NULL) {
word = strtok(line," \t");
while(word != NULL) {
if (i < elenum_all) {
eleall2tag[i] = atoi(word);
} else {
idx1d = i-elenum_all;
aaa_all[idx1d] = atof(word);
}
word = strtok(NULL," \t");
i++;
}
}
fclose(a_matrix_fp);
}
MPI_Bcast(eleall2tag,elenum_all,MPI_INT,0,world);
MPI_Bcast(aaa_all,elenum_all*elenum_all,MPI_DOUBLE,0,world);
int tagi;
for (i = 0; i < elenum_all; i++) {
tagi = eleall2tag[i];
tag2eleall[tagi] = i;
}
}
/*----------------------------------------------------------------------- */
void FixConp::a_cal()
{
double t1,t2;
t1 = MPI_Wtime();
Ktime1 = MPI_Wtime();
if (me == 0) {
fprintf(outf,"A matrix calculating ...\n");
}
double **eleallx = NULL;
memory->create(eleallx,elenum_all,3,"fixconp:eleallx");
int nprocs = comm->nprocs;
int nlocal = atom->nlocal;
int *tag = atom->tag;
int i,j,k;
int elenum_list[nprocs];
MPI_Allgather(&elenum,1,MPI_INT,elenum_list,1,MPI_INT,world);
int displs[nprocs];
displs[0] = 0;
int displssum = 0;
for (i = 1; i < nprocs; ++i) {
displssum += elenum_list[i-1];
displs[i] = displssum;
}
j = 0;
for (i = 0; i < nlocal; i++) {
if (electrode_check(i)) {
ele2tag[j] = tag[i];
j++;
}
}
//gather tag,x and q
double **x = atom->x;
double *elexyzlist = new double[3*elenum];
double *elexyzlist_all = new double[3*elenum_all];
j = 0;
for (i = 0; i < nlocal; i++) {
if (electrode_check(i)) {
elexyzlist[j] = x[i][0];
j++;
elexyzlist[j] = x[i][1];
j++;
elexyzlist[j] = x[i][2];
j++;
}
}
MPI_Allgatherv(ele2tag,elenum,MPI_INT,eleall2tag,elenum_list,displs,MPI_INT,world);
int displs2[nprocs];
int elenum_list2[nprocs];
for (i = 0; i < nprocs; i++) {
elenum_list2[i] = elenum_list[i]*3;
displs2[i] = displs[i]*3;
}
MPI_Allgatherv(elexyzlist,elenum*3,MPI_DOUBLE,elexyzlist_all,elenum_list2,displs2,MPI_DOUBLE,world);
double *aaa = new double[elenum*elenum_all];
for (i = 0; i < elenum*elenum_all; i++) {
aaa[i] = 0.0;
}
j = 0;
for (i = 0; i < elenum_all; i++) {
if (i == 0 && me == 0) fprintf(outa," ");
if (me == 0) fprintf (outa,"%20d",eleall2tag[i]);
tag2eleall[eleall2tag[i]] = i;
eleallx[i][0] = elexyzlist_all[j];
j++;
eleallx[i][1] = elexyzlist_all[j];
j++;
eleallx[i][2] = elexyzlist_all[j];
j++;
}
if (me == 0) fprintf (outa,"\n");
memory->create(csk,kcount,elenum_all,"fixconp:csk");
memory->create(snk,kcount,elenum_all,"fixconp:snk");
sincos_a(eleallx);
delete [] elexyzlist;
delete [] elexyzlist_all;
int elealli,elei,idx1d;
double zi;
double CON_4PIoverV = MY_4PI/volume;
double CON_s2overPIS = sqrt(2.0)/MY_PIS;
double CON_2overPIS = 2.0/MY_PIS;
for (i = 0; i < nlocal; ++i) {
zi = x[i][2];
if (electrode_check(i)) {
elealli = tag2eleall[tag[i]];
for (k = 0; k < elenum; ++k) {
if (ele2tag[k] == tag[i]) {
elei = k;
break;
}
}
for (j = 0; j < elenum_all; ++j) {
idx1d = elei*elenum_all+j;
for (k = 0; k < kcount; ++k) {
aaa[idx1d] += 2.0*ug[k]*(csk[k][elealli]*csk[k][j]+snk[k][elealli]*snk[k][j]);
}
aaa[idx1d] += CON_4PIoverV*zi*eleallx[j][2];
}
idx1d = elei*elenum_all+elealli;
aaa[idx1d] += CON_s2overPIS*eta-CON_2overPIS*g_ewald; //gaussian self correction
}
}
memory->destroy(eleallx);
memory->destroy(csk);
memory->destroy(snk);
coul_cal(2,aaa,ele2tag);
int elenum_list3[nprocs];
int displs3[nprocs];
for (i = 0; i < nprocs; i++) {
elenum_list3[i] = elenum_list[i]*elenum_all;
displs3[i] = displs[i]*elenum_all;
}
MPI_Allgatherv(aaa,elenum*elenum_all,MPI_DOUBLE,aaa_all,elenum_list3,displs3,MPI_DOUBLE,world);
delete [] aaa;
aaa = NULL;
for (i = 0; i < elenum_all; ++i) {
for (j = 0; j < elenum_all; ++j) {
idx1d = i*elenum_all+j;
if (j != 0 && me == 0) fprintf(outa," ");
if (me == 0) fprintf (outa,"%20.12f",aaa_all[idx1d]);
}
if (me == 0) fprintf (outa,"\n");
}
if(me == 0) fclose(outa);
t2 = MPI_Wtime();
double tsum = t2 - t1;
double tsum_all;
MPI_Allreduce(&tsum,&tsum_all,1,MPI_DOUBLE,MPI_SUM,world);
if (me == 0) {
tsum = tsum_all/nprocs;
fprintf(outf,"A matrix calculation time = %g\n",tsum);
}
Ktime2 = MPI_Wtime();
Ktime += Ktime2-Ktime1;
}
/*--------------------------------------------------------------*/
void FixConp::sincos_a(double **eleallx)
{
int i,m,k,ic;
int kx,ky,kz;
double ***csele,***snele;
memory->create3d_offset(csele,-kmax,kmax,3,elenum_all,"fixconp:csele");
memory->create3d_offset(snele,-kmax,kmax,3,elenum_all,"fixconp:snele");
double sqk,cypz,sypz;
for (ic = 0; ic < 3; ic++) {
sqk = unitk[ic]*unitk[ic];
if (sqk <= gsqmx) {
for (i = 0; i < elenum_all; i++) {
csele[0][ic][i] = 1.0;
snele[0][ic][i] = 0.0;
csele[1][ic][i] = cos(unitk[ic]*eleallx[i][ic]);
snele[1][ic][i] = sin(unitk[ic]*eleallx[i][ic]);
csele[-1][ic][i] = csele[1][ic][i];
snele[-1][ic][i] = -snele[1][ic][i];
}
}
}
for (m = 2; m <= kmax; m++) {
for (ic = 0; ic < 3; ic++) {
sqk = m*unitk[ic] * m*unitk[ic];
if (sqk <= gsqmx) {
for (i = 0; i < elenum_all; i++) {
csele[m][ic][i] = csele[m-1][ic][i]*csele[1][ic][i] -
snele[m-1][ic][i]*snele[1][ic][i];
snele[m][ic][i] = snele[m-1][ic][i]*csele[1][ic][i] +
csele[m-1][ic][i]*snele[1][ic][i];
csele[-m][ic][i] = csele[m][ic][i];
snele[-m][ic][i] = -snele[m][ic][i];
}
}
}
}
for (k = 0; k < kcount; ++k) {
kx = kxvecs[k];
ky = kyvecs[k];
kz = kzvecs[k];
for (i = 0; i < elenum_all; ++i) {
cypz = csele[ky][1][i]*csele[kz][2][i] - snele[ky][1][i]*snele[kz][2][i];
sypz = snele[ky][1][i]*csele[kz][2][i] + csele[ky][1][i]*snele[kz][2][i];
csk[k][i] = csele[kx][0][i]*cypz - snele[kx][0][i]*sypz;
snk[k][i] = snele[kx][0][i]*cypz + csele[kx][0][i]*sypz;
}
}
memory->destroy3d_offset(csele,-kmax_created);
memory->destroy3d_offset(snele,-kmax_created);
}
/*--------------------------------------------------------------*/
void FixConp::sincos_b()
{
int i,k,l,m,n,ic;
double cstr1,sstr1,cstr2,sstr2,cstr3,sstr3,cstr4,sstr4;
double sqk,clpm,slpm;
double **x = atom->x;
double *q = atom->q;
int nlocal = atom->nlocal;
n = 0;
// (k,0,0), (0,l,0), (0,0,m)
for (ic = 0; ic < 3; ic++) {
sqk = unitk[ic]*unitk[ic];
if (sqk <= gsqmx) {
cstr1 = 0.0;
sstr1 = 0.0;
for (i = 0; i < nlocal; i++) {
cs[0][ic][i] = 1.0;
sn[0][ic][i] = 0.0;
cs[1][ic][i] = cos(unitk[ic]*x[i][ic]);
sn[1][ic][i] = sin(unitk[ic]*x[i][ic]);
cs[-1][ic][i] = cs[1][ic][i];
sn[-1][ic][i] = -sn[1][ic][i];
if (electrode_check(i) == 0) {
cstr1 += q[i]*cs[1][ic][i];
sstr1 += q[i]*sn[1][ic][i];
}
}
sfacrl[n] = cstr1;
sfacim[n++] = sstr1;
}
}
for (m = 2; m <= kmax; m++) {
for (ic = 0; ic < 3; ic++) {
sqk = m*unitk[ic] * m*unitk[ic];
if (sqk <= gsqmx) {
cstr1 = 0.0;
sstr1 = 0.0;
for (i = 0; i < nlocal; i++) {
cs[m][ic][i] = cs[m-1][ic][i]*cs[1][ic][i] -
sn[m-1][ic][i]*sn[1][ic][i];
sn[m][ic][i] = sn[m-1][ic][i]*cs[1][ic][i] +
cs[m-1][ic][i]*sn[1][ic][i];
cs[-m][ic][i] = cs[m][ic][i];
sn[-m][ic][i] = -sn[m][ic][i];
if (electrode_check(i) == 0) {
cstr1 += q[i]*cs[m][ic][i];
sstr1 += q[i]*sn[m][ic][i];
}
}
sfacrl[n] = cstr1;
sfacim[n++] = sstr1;
}
}
}
// 1 = (k,l,0), 2 = (k,-l,0)
for (k = 1; k <= kxmax; k++) {
for (l = 1; l <= kymax; l++) {
sqk = (k*unitk[0] * k*unitk[0]) + (l*unitk[1] * l*unitk[1]);
if (sqk <= gsqmx) {
cstr1 = 0.0;
sstr1 = 0.0;
cstr2 = 0.0;
sstr2 = 0.0;
for (i = 0; i < nlocal; i++) {
if (electrode_check(i) == 0) {
cstr1 += q[i]*(cs[k][0][i]*cs[l][1][i] - sn[k][0][i]*sn[l][1][i]);
sstr1 += q[i]*(sn[k][0][i]*cs[l][1][i] + cs[k][0][i]*sn[l][1][i]);
cstr2 += q[i]*(cs[k][0][i]*cs[l][1][i] + sn[k][0][i]*sn[l][1][i]);
sstr2 += q[i]*(sn[k][0][i]*cs[l][1][i] - cs[k][0][i]*sn[l][1][i]);
}
}
sfacrl[n] = cstr1;
sfacim[n++] = sstr1;
sfacrl[n] = cstr2;
sfacim[n++] = sstr2;
}
}
}
// 1 = (0,l,m), 2 = (0,l,-m)
for (l = 1; l <= kymax; l++) {
for (m = 1; m <= kzmax; m++) {
sqk = (l*unitk[1] * l*unitk[1]) + (m*unitk[2] * m*unitk[2]);
if (sqk <= gsqmx) {
cstr1 = 0.0;
sstr1 = 0.0;
cstr2 = 0.0;
sstr2 = 0.0;
for (i = 0; i < nlocal; i++) {
if (electrode_check(i) == 0) {
cstr1 += q[i]*(cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i]);
sstr1 += q[i]*(sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i]);
cstr2 += q[i]*(cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i]);
sstr2 += q[i]*(sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i]);
}
}
sfacrl[n] = cstr1;
sfacim[n++] = sstr1;
sfacrl[n] = cstr2;
sfacim[n++] = sstr2;
}
}
}
// 1 = (k,0,m), 2 = (k,0,-m)
for (k = 1; k <= kxmax; k++) {
for (m = 1; m <= kzmax; m++) {
sqk = (k*unitk[0] * k*unitk[0]) + (m*unitk[2] * m*unitk[2]);
if (sqk <= gsqmx) {
cstr1 = 0.0;
sstr1 = 0.0;
cstr2 = 0.0;
sstr2 = 0.0;
for (i = 0; i < nlocal; i++) {
if (electrode_check(i) == 0) {
cstr1 += q[i]*(cs[k][0][i]*cs[m][2][i] - sn[k][0][i]*sn[m][2][i]);
sstr1 += q[i]*(sn[k][0][i]*cs[m][2][i] + cs[k][0][i]*sn[m][2][i]);
cstr2 += q[i]*(cs[k][0][i]*cs[m][2][i] + sn[k][0][i]*sn[m][2][i]);
sstr2 += q[i]*(sn[k][0][i]*cs[m][2][i] - cs[k][0][i]*sn[m][2][i]);
}
}
sfacrl[n] = cstr1;
sfacim[n++] = sstr1;
sfacrl[n] = cstr2;
sfacim[n++] = sstr2;
}
}
}
// 1 = (k,l,m), 2 = (k,-l,m), 3 = (k,l,-m), 4 = (k,-l,-m)
for (k = 1; k <= kxmax; k++) {
for (l = 1; l <= kymax; l++) {
for (m = 1; m <= kzmax; m++) {
sqk = (k*unitk[0] * k*unitk[0]) + (l*unitk[1] * l*unitk[1]) +
(m*unitk[2] * m*unitk[2]);
if (sqk <= gsqmx) {
cstr1 = 0.0;
sstr1 = 0.0;
cstr2 = 0.0;
sstr2 = 0.0;
cstr3 = 0.0;
sstr3 = 0.0;
cstr4 = 0.0;
sstr4 = 0.0;
for (i = 0; i < nlocal; i++) {
if (electrode_check(i) == 0) {
clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i];
slpm = sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i];
cstr1 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
sstr1 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i];
slpm = -sn[l][1][i]*cs[m][2][i] + cs[l][1][i]*sn[m][2][i];
cstr2 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
sstr2 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
clpm = cs[l][1][i]*cs[m][2][i] + sn[l][1][i]*sn[m][2][i];
slpm = sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i];
cstr3 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
sstr3 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
clpm = cs[l][1][i]*cs[m][2][i] - sn[l][1][i]*sn[m][2][i];
slpm = -sn[l][1][i]*cs[m][2][i] - cs[l][1][i]*sn[m][2][i];
cstr4 += q[i]*(cs[k][0][i]*clpm - sn[k][0][i]*slpm);
sstr4 += q[i]*(sn[k][0][i]*clpm + cs[k][0][i]*slpm);
}
}
sfacrl[n] = cstr1;
sfacim[n++] = sstr1;
sfacrl[n] = cstr2;
sfacim[n++] = sstr2;
sfacrl[n] = cstr3;
sfacim[n++] = sstr3;
sfacrl[n] = cstr4;
sfacim[n++] = sstr4;
}
}
}
}
if (runstage == 1) runstage = 2;
}
/* ---------------------------------------------------------------------- */
void FixConp::cg()
{
int iter,i,j,idx1d;
double d,beta,ptap,lresnorm,resnorm,netcharge,tmp;
double res[elenum_all],p[elenum_all],ap[elenum_all];
for (i = 0; i < elenum_all; i++) eleallq[i] = 0.0;
lresnorm = 0.0;
for (i = 0; i < elenum_all; ++i) {
res[i] = bbb_all[i];
p[i] = bbb_all[i];
for (j = 0; j < elenum_all; ++j) {
idx1d= i*elenum_all+j;
tmp = aaa_all[idx1d]*eleallq[j];
res[i] -= tmp;
p[i] -= tmp;
}
lresnorm += res[i]*res[i];
}
for (iter = 1; iter < maxiter; ++iter) {
d = 0.0;
for (i = 0; i < elenum_all; ++i) {
ap[i] = 0.0;
for (j = 0; j < elenum_all; ++j) {
idx1d= i*elenum_all+j;
ap[i] += aaa_all[idx1d]*p[j];
}
}
ptap = 0.0;
for (i = 0; i < elenum_all; ++i) {
ptap += ap[i]*p[i];
}
d = lresnorm/ptap;
resnorm = 0.0;
for (i = 0; i <elenum_all; ++i) {
eleallq[i] = eleallq[i]+d*p[i];
res[i] = res[i]-d*ap[i];
resnorm += res[i]*res[i];
}
if (resnorm/elenum_all < tolerance) {
netcharge = 0.0;
for (i = 0; i < elenum_all; ++i) netcharge += eleallq[i];
if (me == 0) {
fprintf(outf,"***** Converged at iteration %d. res = %g netcharge = %g\n",
iter,resnorm,netcharge);
}
break;
}
beta = resnorm/lresnorm;
for (i = 0; i < elenum_all; ++i) {
p[i] = res[i]+beta*p[i];
}
lresnorm = resnorm;
if (me == 0) {
fprintf(outf,"Iteration %d: res = %g\n",iter,lresnorm);
}
}
}
/* ---------------------------------------------------------------------- */
void FixConp::inv()
{
int i,j,k,idx1d;
if (runstage == 2 && a_matrix_f < 2) {
int m = elenum_all;
int n = elenum_all;
int lda = elenum_all;
int *ipiv = new int[elenum_all+1];
int lwork = elenum_all*elenum_all;
double *work = new double[lwork];
int info;
int infosum;
dgetrf_(&m,&n,aaa_all,&lda,ipiv,&info);
infosum = info;
dgetri_(&n,aaa_all,&lda,ipiv,work,&lwork,&info);
infosum += info;
delete [] ipiv;
ipiv = NULL;
delete [] work;
work = NULL;
if (infosum != 0) error->all(FLERR,"Inversion failed!");
if (me == 0) {
FILE *outinva = fopen("inv_a_matrix","w");
for (i = 0; i < elenum_all; i++) {
if(i == 0) fprintf (outinva," ");
fprintf (outinva,"%12d",eleall2tag[i]);
}
fprintf (outinva,"\n");
for (k = 0; k < elenum_all*elenum_all; k++) {
if (k%elenum_all != 0) {
fprintf (outinva," ");
}
fprintf(outinva,"%20.10f",aaa_all[k]);
if ((k+1)%elenum_all == 0) {
fprintf(outinva,"\n");
}
}
fclose(outinva);
}
}
if (runstage == 2) runstage = 3;
}
/* ---------------------------------------------------------------------- */
void FixConp::update_charge()
{
int i,j,idx1d;
int elealli,tagi;
double eleallq_i;
int *tag = atom->tag;
int nall = atom->nlocal+atom->nghost;
double *q = atom->q;
double **x = atom->x;
for (i = 0; i < nall; ++i) {
if (electrode_check(i)) {
tagi = tag[i];
elealli = tag2eleall[tagi];
if (minimizer == 0) {
q[i] = eleallq[elealli];
} else if (minimizer == 1) {
eleallq_i = 0.0;
for (j = 0; j < elenum_all; j++) {
idx1d=elealli*elenum_all+j;
eleallq_i += aaa_all[idx1d]*bbb_all[j];
}
q[i] = eleallq_i;
}
}
}
}
/* ---------------------------------------------------------------------- */
void FixConp::force_cal(int vflag)
{
int i;
if (force->kspace->energy) {
double eleqsqsum = 0.0;