void do_four(const char *fn, const char *cn, int nx, real x[], real dy[],
real eps0, real epsRF, const output_env_t oenv)
{
FILE *fp, *cp;
t_complex *tmp, gw, hw, kw;
int i, nnx, nxsav;
real fac, nu, dt, *ptr, maxeps, numax;
nxsav = nx;
/*while ((dy[nx-1] == 0.0) && (nx > 0))
nx--;*/
if (nx == 0)
{
gmx_fatal(FARGS, "Empty dataset in %s, line %d!", __FILE__, __LINE__);
}
nnx = 1;
while (nnx < 2*nx)
{
nnx *= 2;
}
snew(tmp, 2*nnx);
printf("Doing FFT of %d points\n", nnx);
for (i = 0; (i < nx); i++)
{
tmp[i].re = dy[i];
}
ptr = &tmp[0].re;
four1(ptr-1, nnx, -1);
dt = x[1]-x[0];
if (epsRF == 0)
{
fac = (eps0-1)/tmp[0].re;
}
else
{
fac = ((eps0-1)/(2*epsRF+eps0))/tmp[0].re;
}
fp = xvgropen(fn, "Epsilon(\\8w\\4)", "Freq. (GHz)", "eps", oenv);
cp = xvgropen(cn, "Cole-Cole plot", "Eps'", "Eps''", oenv);
maxeps = 0;
numax = 0;
for (i = 0; (i < nxsav); i++)
{
if (epsRF == 0)
{
kw.re = 1+fac*tmp[i].re;
kw.im = 1+fac*tmp[i].im;
}
else
{
gw = rcmul(fac, tmp[i]);
hw = rcmul(2*epsRF, gw);
hw.re += 1.0;
gw.re = 1.0 - gw.re;
gw.im = -gw.im;
kw = cdiv(hw, gw);
}
kw.im *= -1;
nu = (i+1)*1000.0/(nnx*dt);
if (kw.im > maxeps)
{
maxeps = kw.im;
numax = nu;
}
fprintf(fp, "%10.5e %10.5e %10.5e\n", nu, kw.re, kw.im);
fprintf(cp, "%10.5e %10.5e\n", kw.re, kw.im);
}
printf("MAXEPS = %10.5e at frequency %10.5e GHz (tauD = %8.1f ps)\n",
maxeps, numax, 1000/(2*M_PI*numax));
ffclose(fp);
ffclose(cp);
sfree(tmp);
}
real do_ewald(t_inputrec *ir,
rvec x[], rvec f[],
real chargeA[], real chargeB[],
rvec box,
t_commrec *cr, int natoms,
matrix lrvir, real ewaldcoeff,
real lambda, real *dvdlambda,
struct gmx_ewald_tab_t *et)
{
real factor = -1.0/(4*ewaldcoeff*ewaldcoeff);
real scaleRecip = 4.0*M_PI/(box[XX]*box[YY]*box[ZZ])*ONE_4PI_EPS0/ir->epsilon_r; /* 1/(Vol*e0) */
real *charge, energy_AB[2], energy;
rvec lll;
int lowiy, lowiz, ix, iy, iz, n, q;
real tmp, cs, ss, ak, akv, mx, my, mz, m2, scale;
gmx_bool bFreeEnergy;
if (cr != NULL)
{
if (PAR(cr))
{
gmx_fatal(FARGS, "No parallel Ewald. Use PME instead.\n");
}
}
if (!et->eir) /* allocate if we need to */
{
snew(et->eir, et->kmax);
for (n = 0; n < et->kmax; n++)
{
snew(et->eir[n], natoms);
}
snew(et->tab_xy, natoms);
snew(et->tab_qxyz, natoms);
}
bFreeEnergy = (ir->efep != efepNO);
clear_mat(lrvir);
calc_lll(box, lll);
/* make tables for the structure factor parts */
tabulate_eir(natoms, x, et->kmax, et->eir, lll);
for (q = 0; q < (bFreeEnergy ? 2 : 1); q++)
{
if (!bFreeEnergy)
{
charge = chargeA;
scale = 1.0;
}
else if (q == 0)
{
charge = chargeA;
scale = 1.0 - lambda;
}
else
{
charge = chargeB;
scale = lambda;
}
lowiy = 0;
lowiz = 1;
energy_AB[q] = 0;
for (ix = 0; ix < et->nx; ix++)
{
mx = ix*lll[XX];
for (iy = lowiy; iy < et->ny; iy++)
{
my = iy*lll[YY];
if (iy >= 0)
{
for (n = 0; n < natoms; n++)
{
et->tab_xy[n] = cmul(et->eir[ix][n][XX], et->eir[iy][n][YY]);
}
}
else
{
for (n = 0; n < natoms; n++)
{
et->tab_xy[n] = conjmul(et->eir[ix][n][XX], et->eir[-iy][n][YY]);
}
}
for (iz = lowiz; iz < et->nz; iz++)
{
mz = iz*lll[ZZ];
m2 = mx*mx+my*my+mz*mz;
ak = exp(m2*factor)/m2;
akv = 2.0*ak*(1.0/m2-factor);
if (iz >= 0)
{
for (n = 0; n < natoms; n++)
{
et->tab_qxyz[n] = rcmul(charge[n], cmul(et->tab_xy[n],
et->eir[iz][n][ZZ]));
}
}
else
{
for (n = 0; n < natoms; n++)
{
et->tab_qxyz[n] = rcmul(charge[n], conjmul(et->tab_xy[n],
et->eir[-iz][n][ZZ]));
}
}
cs = ss = 0;
for (n = 0; n < natoms; n++)
{
cs += et->tab_qxyz[n].re;
ss += et->tab_qxyz[n].im;
}
energy_AB[q] += ak*(cs*cs+ss*ss);
tmp = scale*akv*(cs*cs+ss*ss);
lrvir[XX][XX] -= tmp*mx*mx;
lrvir[XX][YY] -= tmp*mx*my;
lrvir[XX][ZZ] -= tmp*mx*mz;
lrvir[YY][YY] -= tmp*my*my;
lrvir[YY][ZZ] -= tmp*my*mz;
lrvir[ZZ][ZZ] -= tmp*mz*mz;
for (n = 0; n < natoms; n++)
{
/*tmp=scale*ak*(cs*tab_qxyz[n].im-ss*tab_qxyz[n].re);*/
tmp = scale*ak*(cs*et->tab_qxyz[n].im-ss*et->tab_qxyz[n].re);
f[n][XX] += tmp*mx*2*scaleRecip;
f[n][YY] += tmp*my*2*scaleRecip;
f[n][ZZ] += tmp*mz*2*scaleRecip;
#if 0
f[n][XX] += tmp*mx;
f[n][YY] += tmp*my;
f[n][ZZ] += tmp*mz;
#endif
}
lowiz = 1-et->nz;
}
lowiy = 1-et->ny;
}
}
}
if (!bFreeEnergy)
{
energy = energy_AB[0];
}
else
{
energy = (1.0 - lambda)*energy_AB[0] + lambda*energy_AB[1];
*dvdlambda += scaleRecip*(energy_AB[1] - energy_AB[0]);
}
lrvir[XX][XX] = -0.5*scaleRecip*(lrvir[XX][XX]+energy);
lrvir[XX][YY] = -0.5*scaleRecip*(lrvir[XX][YY]);
lrvir[XX][ZZ] = -0.5*scaleRecip*(lrvir[XX][ZZ]);
lrvir[YY][YY] = -0.5*scaleRecip*(lrvir[YY][YY]+energy);
lrvir[YY][ZZ] = -0.5*scaleRecip*(lrvir[YY][ZZ]);
lrvir[ZZ][ZZ] = -0.5*scaleRecip*(lrvir[ZZ][ZZ]+energy);
lrvir[YY][XX] = lrvir[XX][YY];
lrvir[ZZ][XX] = lrvir[XX][ZZ];
lrvir[ZZ][YY] = lrvir[YY][ZZ];
energy *= scaleRecip;
return energy;
}
real do_ewald(FILE *log, bool bVerbose,
t_inputrec *ir,
rvec x[], rvec f[],
real charge[], rvec box,
t_commrec *cr, t_nsborder *nsb,
matrix lrvir, real ewaldcoeff)
{
static bool bFirst = TRUE;
static int nx,ny,nz,kmax;
static cvec **eir;
static t_complex *tab_xy,*tab_qxyz;
real factor=-1.0/(4*ewaldcoeff*ewaldcoeff);
real energy;
rvec lll;
int lowiy,lowiz,ix,iy,iz,n;
real tmp,cs,ss,ak,akv,mx,my,mz,m2;
if (bFirst) {
if (bVerbose)
fprintf(log,"Will do ordinary reciprocal space Ewald sum.\n");
if (cr != NULL) {
if (cr->nnodes > 1 || cr->nthreads>1)
fatal_error(0,"No parallel Ewald. Use PME instead.\n");
}
nx = ir->nkx+1;
ny = ir->nky+1;
nz = ir->nkz+1;
kmax = max(nx,max(ny,nz));
snew(eir,kmax);
for(n=0;n<kmax;n++)
snew(eir[n],HOMENR(nsb));
snew(tab_xy,HOMENR(nsb));
snew(tab_qxyz,HOMENR(nsb));
bFirst = FALSE;
}
clear_mat(lrvir);
calc_lll(box,lll);
/* make tables for the structure factor parts */
tabulate_eir(HOMENR(nsb),x,kmax,eir,lll);
lowiy=0;
lowiz=1;
energy=0;
for(ix=0;ix<nx;ix++) {
mx=ix*lll[XX];
for(iy=lowiy;iy<ny;iy++) {
my=iy*lll[YY];
if(iy>=0)
for(n=0;n<HOMENR(nsb);n++)
tab_xy[n]=cmul(eir[ix][n][XX],eir[iy][n][YY]);
else
for(n=0;n<HOMENR(nsb);n++)
tab_xy[n]=conjmul(eir[ix][n][XX],eir[-iy][n][YY]);
for(iz=lowiz;iz<nz;iz++) {
mz=iz*lll[ZZ];
m2=mx*mx+my*my+mz*mz;
ak=exp(m2*factor)/m2;
akv=2.0*ak*(1.0/m2-factor);
if(iz>=0)
for(n=0;n<HOMENR(nsb);n++)
tab_qxyz[n]=rcmul(charge[n],cmul(tab_xy[n],eir[iz][n][ZZ]));
else
for(n=0;n<HOMENR(nsb);n++)
tab_qxyz[n]=rcmul(charge[n],conjmul(tab_xy[n],eir[-iz][n][ZZ]));
cs=ss=0;
for(n=0;n<HOMENR(nsb);n++) {
cs+=tab_qxyz[n].re;
ss+=tab_qxyz[n].im;
}
energy+=ak*(cs*cs+ss*ss);
tmp=akv*(cs*cs+ss*ss);
lrvir[XX][XX]-=tmp*mx*mx;
lrvir[XX][YY]-=tmp*mx*my;
lrvir[XX][ZZ]-=tmp*mx*mz;
lrvir[YY][YY]-=tmp*my*my;
lrvir[YY][ZZ]-=tmp*my*mz;
lrvir[ZZ][ZZ]-=tmp*mz*mz;
for(n=0;n<HOMENR(nsb);n++) {
tmp=ak*(cs*tab_qxyz[n].im-ss*tab_qxyz[n].re);
f[n][XX]+=tmp*mx;
f[n][YY]+=tmp*my;
f[n][ZZ]+=tmp*mz;
}
lowiz=1-nz;
}
lowiy=1-ny;
}
}
tmp=4.0*M_PI/(box[XX]*box[YY]*box[ZZ])*ONE_4PI_EPS0;
for(n=0;n<HOMENR(nsb);n++) {
f[n][XX]*=2*tmp;
f[n][YY]*=2*tmp;
f[n][ZZ]*=2*tmp;
}
lrvir[XX][XX]=-0.5*tmp*(lrvir[XX][XX]+energy);
lrvir[XX][YY]=-0.5*tmp*(lrvir[XX][YY]);
lrvir[XX][ZZ]=-0.5*tmp*(lrvir[XX][ZZ]);
lrvir[YY][YY]=-0.5*tmp*(lrvir[YY][YY]+energy);
lrvir[YY][ZZ]=-0.5*tmp*(lrvir[YY][ZZ]);
lrvir[ZZ][ZZ]=-0.5*tmp*(lrvir[ZZ][ZZ]+energy);
lrvir[YY][XX]=lrvir[XX][YY];
lrvir[ZZ][XX]=lrvir[XX][ZZ];
lrvir[ZZ][YY]=lrvir[YY][ZZ];
energy*=tmp;
return energy;
}
real do_ewald(FILE *log, bool bVerbose,
t_inputrec *ir,
rvec x[], rvec f[],
real chargeA[], real chargeB[],
rvec box,
t_commrec *cr, int natoms,
matrix lrvir, real ewaldcoeff,
real lambda, real *dvdlambda)
{
static bool bFirst = TRUE;
static int nx,ny,nz,kmax;
static cvec **eir;
static t_complex *tab_xy,*tab_qxyz;
real factor=-1.0/(4*ewaldcoeff*ewaldcoeff);
real *charge,energy_AB[2],energy;
rvec lll;
int lowiy,lowiz,ix,iy,iz,n,q;
real tmp,cs,ss,ak,akv,mx,my,mz,m2,scale;
bool bFreeEnergy;
bFreeEnergy = (ir->efep != efepNO);
if (bFirst) {
if (bVerbose)
fprintf(log,"Will do ordinary reciprocal space Ewald sum.\n");
if (cr != NULL) {
if (cr->nnodes > 1 || cr->nthreads>1)
gmx_fatal(FARGS,"No parallel Ewald. Use PME instead.\n");
}
nx = ir->nkx+1;
ny = ir->nky+1;
nz = ir->nkz+1;
kmax = max(nx,max(ny,nz));
snew(eir,kmax);
for(n=0;n<kmax;n++)
snew(eir[n],natoms);
snew(tab_xy,natoms);
snew(tab_qxyz,natoms);
bFirst = FALSE;
}
clear_mat(lrvir);
calc_lll(box,lll);
/* make tables for the structure factor parts */
tabulate_eir(natoms,x,kmax,eir,lll);
for(q=0; q<(bFreeEnergy ? 2 : 1); q++) {
if (!bFreeEnergy) {
charge = chargeA;
scale = 1.0;
} else if (q==0) {
charge = chargeA;
scale = 1.0 - lambda;
} else {
charge = chargeB;
scale = lambda;
}
lowiy=0;
lowiz=1;
energy_AB[q]=0;
for(ix=0;ix<nx;ix++) {
mx=ix*lll[XX];
for(iy=lowiy;iy<ny;iy++) {
my=iy*lll[YY];
if(iy>=0)
for(n=0;n<natoms;n++)
tab_xy[n]=cmul(eir[ix][n][XX],eir[iy][n][YY]);
else
for(n=0;n<natoms;n++)
tab_xy[n]=conjmul(eir[ix][n][XX],eir[-iy][n][YY]);
for(iz=lowiz;iz<nz;iz++) {
mz=iz*lll[ZZ];
m2=mx*mx+my*my+mz*mz;
ak=exp(m2*factor)/m2;
akv=2.0*ak*(1.0/m2-factor);
if(iz>=0)
for(n=0;n<natoms;n++)
tab_qxyz[n]=rcmul(charge[n],cmul(tab_xy[n],eir[iz][n][ZZ]));
else
for(n=0;n<natoms;n++)
tab_qxyz[n]=rcmul(charge[n],conjmul(tab_xy[n],eir[-iz][n][ZZ]));
cs=ss=0;
for(n=0;n<natoms;n++) {
cs+=tab_qxyz[n].re;
ss+=tab_qxyz[n].im;
}
energy_AB[q]+=ak*(cs*cs+ss*ss);
tmp=scale*akv*(cs*cs+ss*ss);
lrvir[XX][XX]-=tmp*mx*mx;
lrvir[XX][YY]-=tmp*mx*my;
lrvir[XX][ZZ]-=tmp*mx*mz;
lrvir[YY][YY]-=tmp*my*my;
lrvir[YY][ZZ]-=tmp*my*mz;
lrvir[ZZ][ZZ]-=tmp*mz*mz;
for(n=0;n<natoms;n++) {
tmp=scale*ak*(cs*tab_qxyz[n].im-ss*tab_qxyz[n].re);
f[n][XX]+=tmp*mx;
f[n][YY]+=tmp*my;
f[n][ZZ]+=tmp*mz;
}
lowiz=1-nz;
}
lowiy=1-ny;
}
}
}
tmp=4.0*M_PI/(box[XX]*box[YY]*box[ZZ])*ONE_4PI_EPS0/ir->epsilon_r;
if (!bFreeEnergy) {
energy = energy_AB[0];
} else {
energy = (1.0 - lambda)*energy_AB[0] + lambda*energy_AB[1];
*dvdlambda += tmp*(energy_AB[1] - energy_AB[0]);
}
for(n=0;n<natoms;n++) {
f[n][XX]*=2*tmp;
f[n][YY]*=2*tmp;
f[n][ZZ]*=2*tmp;
}
lrvir[XX][XX]=-0.5*tmp*(lrvir[XX][XX]+energy);
lrvir[XX][YY]=-0.5*tmp*(lrvir[XX][YY]);
lrvir[XX][ZZ]=-0.5*tmp*(lrvir[XX][ZZ]);
lrvir[YY][YY]=-0.5*tmp*(lrvir[YY][YY]+energy);
lrvir[YY][ZZ]=-0.5*tmp*(lrvir[YY][ZZ]);
lrvir[ZZ][ZZ]=-0.5*tmp*(lrvir[ZZ][ZZ]+energy);
lrvir[YY][XX]=lrvir[XX][YY];
lrvir[ZZ][XX]=lrvir[XX][ZZ];
lrvir[ZZ][YY]=lrvir[YY][ZZ];
energy*=tmp;
return energy;
}
