real numerical_deriv(int nx,real x[],real y[],real fity[],real combined[],real dy[],
real tendInt,int nsmooth)
{
FILE *tmpfp;
int i,nbegin,i0,i1;
real fac,fx,fy,integralSmth;
nbegin = calc_nbegin(nx,x,tendInt);
if (nsmooth == 0) {
for(i=0; (i<nbegin); i++)
combined[i]=y[i];
fac = y[nbegin]/fity[nbegin];
printf("scaling fitted curve by %g\n",fac);
for(i=nbegin; (i<nx); i++)
combined[i]=fity[i]*fac;
}
else {
i0 = max(0,nbegin);
i1 = min(nx-1,nbegin+nsmooth);
printf("Making smooth transition from %d thru %d\n",i0,i1);
for(i=0; (i<i0); i++)
combined[i]=y[i];
for(i=i0; (i<=i1); i++) {
fx = (i1-i)/(real)(i1-i0);
fy = (i-i0)/(real)(i1-i0);
if (debug)
fprintf(debug,"x: %g factors for smoothing: %10g %10g\n",x[i],fx,fy);
combined[i] = fx*y[i] + fy*fity[i];
}
for(i=i1+1; (i<nx); i++)
combined[i]=fity[i];
}
tmpfp = ffopen("integral_smth.xvg","w");
integralSmth=print_and_integrate(tmpfp,nx,x[1]-x[0],combined,NULL,1);
printf("SMOOTH integral = %10.5e\n",integralSmth);
dy[0] = (combined[1]-combined[0])/(x[1]-x[0]);
for(i=1; (i<nx-1); i++) {
dy[i] = (combined[i+1]-combined[i-1])/(x[i+1]-x[i-1]);
}
dy[nx-1] = (combined[nx-1]-combined[nx-2])/(x[nx-1]-x[nx-2]);
for(i=0; (i<nx); i++)
dy[i] *= -1;
return integralSmth;
}
int gmx_dielectric(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] calculates frequency dependent dielectric constants",
"from the autocorrelation function of the total dipole moment in",
"your simulation. This ACF can be generated by [gmx-dipoles].",
"The functional forms of the available functions are:[PAR]",
"One parameter: y = [EXP]-a[SUB]1[sub] x[exp],[BR]",
"Two parameters: y = a[SUB]2[sub] [EXP]-a[SUB]1[sub] x[exp],[BR]",
"Three parameters: y = a[SUB]2[sub] [EXP]-a[SUB]1[sub] x[exp] + (1 - a[SUB]2[sub]) [EXP]-a[SUB]3[sub] x[exp].[BR]",
"Start values for the fit procedure can be given on the command line.",
"It is also possible to fix parameters at their start value, use [TT]-fix[tt]",
"with the number of the parameter you want to fix.",
"[PAR]",
"Three output files are generated, the first contains the ACF,",
"an exponential fit to it with 1, 2 or 3 parameters, and the",
"numerical derivative of the combination data/fit.",
"The second file contains the real and imaginary parts of the",
"frequency-dependent dielectric constant, the last gives a plot",
"known as the Cole-Cole plot, in which the imaginary",
"component is plotted as a function of the real component.",
"For a pure exponential relaxation (Debye relaxation) the latter",
"plot should be one half of a circle."
};
t_filenm fnm[] = {
{ efXVG, "-f", "dipcorr", ffREAD },
{ efXVG, "-d", "deriv", ffWRITE },
{ efXVG, "-o", "epsw", ffWRITE },
{ efXVG, "-c", "cole", ffWRITE }
};
#define NFILE asize(fnm)
output_env_t oenv;
int i, j, nx, ny, nxtail, eFitFn, nfitparm;
real dt, integral, fitintegral, *fitparms, fac, rffac;
double **yd;
real **y;
const char *legend[] = { "Correlation", "Std. Dev.", "Fit", "Combined", "Derivative" };
static int fix = 0, bFour = 0, bX = 1, nsmooth = 3;
static real tendInt = 5.0, tbegin = 5.0, tend = 500.0;
static real A = 0.5, tau1 = 10.0, tau2 = 1.0, eps0 = 80, epsRF = 78.5, tail = 500.0;
real lambda;
t_pargs pa[] = {
{ "-fft", FALSE, etBOOL, {&bFour},
"use fast fourier transform for correlation function" },
{ "-x1", FALSE, etBOOL, {&bX},
"use first column as [IT]x[it]-axis rather than first data set" },
{ "-eint", FALSE, etREAL, {&tendInt},
"Time to end the integration of the data and start to use the fit"},
{ "-bfit", FALSE, etREAL, {&tbegin},
"Begin time of fit" },
{ "-efit", FALSE, etREAL, {&tend},
"End time of fit" },
{ "-tail", FALSE, etREAL, {&tail},
"Length of function including data and tail from fit" },
{ "-A", FALSE, etREAL, {&A},
"Start value for fit parameter A" },
{ "-tau1", FALSE, etREAL, {&tau1},
"Start value for fit parameter [GRK]tau[grk]1" },
{ "-tau2", FALSE, etREAL, {&tau2},
"Start value for fit parameter [GRK]tau[grk]2" },
{ "-eps0", FALSE, etREAL, {&eps0},
"[GRK]epsilon[grk]0 of your liquid" },
{ "-epsRF", FALSE, etREAL, {&epsRF},
"[GRK]epsilon[grk] of the reaction field used in your simulation. A value of 0 means infinity." },
{ "-fix", FALSE, etINT, {&fix},
"Fix parameters at their start values, A (2), tau1 (1), or tau2 (4)" },
{ "-ffn", FALSE, etENUM, {s_ffn},
"Fit function" },
{ "-nsmooth", FALSE, etINT, {&nsmooth},
"Number of points for smoothing" }
};
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
please_cite(stdout, "Spoel98a");
printf("WARNING: non-polarizable models can never yield an infinite\n"
"dielectric constant that is different from 1. This is incorrect\n"
"in the reference given above (Spoel98a).\n\n");
nx = read_xvg(opt2fn("-f", NFILE, fnm), &yd, &ny);
dt = yd[0][1] - yd[0][0];
nxtail = min(tail/dt, nx);
printf("Read data set containing %d colums and %d rows\n", ny, nx);
printf("Assuming (from data) that timestep is %g, nxtail = %d\n",
dt, nxtail);
snew(y, 6);
for (i = 0; (i < ny); i++)
{
snew(y[i], max(nx, nxtail));
}
for (i = 0; (i < nx); i++)
{
y[0][i] = yd[0][i];
for (j = 1; (j < ny); j++)
{
y[j][i] = yd[j][i];
}
}
if (nxtail > nx)
{
for (i = nx; (i < nxtail); i++)
{
y[0][i] = dt*i+y[0][0];
for (j = 1; (j < ny); j++)
{
y[j][i] = 0.0;
}
}
nx = nxtail;
}
/* We have read a file WITHOUT standard deviations, so we make our own... */
if (ny == 2)
{
printf("Creating standard deviation numbers ...\n");
srenew(y, 3);
snew(y[2], nx);
fac = 1.0/((real)nx);
for (i = 0; (i < nx); i++)
{
y[2][i] = fac;
}
}
eFitFn = sffn2effn(s_ffn);
nfitparm = nfp_ffn[eFitFn];
snew(fitparms, 4);
fitparms[0] = tau1;
if (nfitparm > 1)
{
fitparms[1] = A;
}
if (nfitparm > 2)
{
fitparms[2] = tau2;
}
snew(y[3], nx);
snew(y[4], nx);
snew(y[5], nx);
integral = print_and_integrate(NULL, calc_nbegin(nx, y[0], tbegin),
dt, y[1], NULL, 1);
integral += do_lmfit(nx, y[1], y[2], dt, y[0], tbegin, tend,
oenv, TRUE, eFitFn, fitparms, fix);
for (i = 0; i < nx; i++)
{
y[3][i] = fit_function(eFitFn, fitparms, y[0][i]);
}
if (epsRF == 0)
{
/* This means infinity! */
lambda = 0;
rffac = 1;
}
else
{
lambda = (eps0 - 1.0)/(2*epsRF - 1.0);
rffac = (2*epsRF+eps0)/(2*epsRF+1);
}
printf("DATA INTEGRAL: %5.1f, tauD(old) = %5.1f ps, "
"tau_slope = %5.1f, tau_slope,D = %5.1f ps\n",
integral, integral*rffac, fitparms[0], fitparms[0]*rffac);
printf("tau_D from tau1 = %8.3g , eps(Infty) = %8.3f\n",
fitparms[0]*(1 + fitparms[1]*lambda),
1 + ((1 - fitparms[1])*(eps0 - 1))/(1 + fitparms[1]*lambda));
fitintegral = numerical_deriv(nx, y[0], y[1], y[3], y[4], y[5], tendInt, nsmooth);
printf("FIT INTEGRAL (tau_M): %5.1f, tau_D = %5.1f\n",
fitintegral, fitintegral*rffac);
/* Now we have the negative gradient of <Phi(0) Phi(t)> */
write_xvg(opt2fn("-d", NFILE, fnm), "Data", nx-1, 6, y, legend, oenv);
/* Do FFT and analysis */
do_four(opt2fn("-o", NFILE, fnm), opt2fn("-c", NFILE, fnm),
nx-1, y[0], y[5], eps0, epsRF, oenv);
do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
do_view(oenv, opt2fn("-c", NFILE, fnm), NULL);
do_view(oenv, opt2fn("-d", NFILE, fnm), "-nxy");
return 0;
}
real fit_acf(int ncorr, int fitfn, const gmx_output_env_t *oenv, gmx_bool bVerbose,
real tbeginfit, real tendfit, real dt, real c1[], real *fit)
{
double fitparm[3];
double tStart, tail_corr, sum, sumtot = 0, c_start, ct_estimate;
real *sig;
int i, j, jmax, nf_int;
gmx_bool bPrint;
bPrint = bVerbose || bDebugMode();
if (bPrint)
{
printf("COR:\n");
}
if (tendfit <= 0)
{
tendfit = ncorr*dt;
}
nf_int = std::min(ncorr, (int)(tendfit/dt));
sum = print_and_integrate(debug, nf_int, dt, c1, NULL, 1);
if (bPrint)
{
printf("COR: Correlation time (plain integral from %6.3f to %6.3f ps) = %8.5f ps\n",
0.0, dt*nf_int, sum);
printf("COR: Relaxation times are computed as fit to an exponential:\n");
printf("COR: %s\n", effnDescription(fitfn));
printf("COR: Fit to correlation function from %6.3f ps to %6.3f ps, results in a\n", tbeginfit, std::min(ncorr*dt, tendfit));
}
tStart = 0;
if (bPrint)
{
printf("COR:%11s%11s%11s%11s%11s%11s%11s\n",
"Fit from", "Integral", "Tail Value", "Sum (ps)", " a1 (ps)",
(effnNparams(fitfn) >= 2) ? " a2 ()" : "",
(effnNparams(fitfn) >= 3) ? " a3 (ps)" : "");
}
snew(sig, ncorr);
if (tbeginfit > 0)
{
jmax = 3;
}
else
{
jmax = 1;
}
for (j = 0; ((j < jmax) && (tStart < tendfit) && (tStart < ncorr*dt)); j++)
{
/* Estimate the correlation time for better fitting */
c_start = -1;
ct_estimate = 0;
for (i = 0; (i < ncorr) && (dt*i < tStart || c1[i] > 0); i++)
{
if (c_start < 0)
{
if (dt*i >= tStart)
{
c_start = c1[i];
ct_estimate = 0.5*c1[i];
}
}
else
{
ct_estimate += c1[i];
}
}
if (c_start > 0)
{
ct_estimate *= dt/c_start;
}
else
{
/* The data is strange, so we need to choose somehting */
ct_estimate = tendfit;
}
if (debug)
{
fprintf(debug, "tStart %g ct_estimate: %g\n", tStart, ct_estimate);
}
if (fitfn == effnEXPEXP)
{
fitparm[0] = 0.002*ncorr*dt;
fitparm[1] = 0.95;
fitparm[2] = 0.2*ncorr*dt;
}
else
{
/* Good initial guess, this increases the probability of convergence */
fitparm[0] = ct_estimate;
fitparm[1] = 1.0;
fitparm[2] = 1.0;
}
/* Generate more or less appropriate sigma's */
for (i = 0; i < ncorr; i++)
{
sig[i] = sqrt(ct_estimate+dt*i);
}
nf_int = std::min(ncorr, (int)((tStart+1e-4)/dt));
sum = print_and_integrate(debug, nf_int, dt, c1, NULL, 1);
tail_corr = do_lmfit(ncorr, c1, sig, dt, NULL, tStart, tendfit, oenv,
bDebugMode(), fitfn, fitparm, 0, NULL);
sumtot = sum+tail_corr;
if (fit && ((jmax == 1) || (j == 1)))
{
double mfp[3];
for (i = 0; (i < 3); i++)
{
mfp[i] = fitparm[i];
}
for (i = 0; (i < ncorr); i++)
{
fit[i] = lmcurves[fitfn](i*dt, mfp);
}
}
if (bPrint)
{
printf("COR:%11.4e%11.4e%11.4e%11.4e", tStart, sum, tail_corr, sumtot);
for (i = 0; (i < effnNparams(fitfn)); i++)
{
printf(" %11.4e", fitparm[i]);
}
printf("\n");
}
tStart += tbeginfit;
}
sfree(sig);
return sumtot;
}
void low_do_autocorr(const char *fn,const output_env_t oenv,const char *title,
int nframes,int nitem,int nout,real **c1,
real dt,unsigned long mode,int nrestart,
gmx_bool bAver,gmx_bool bNormalize,
gmx_bool bVerbose,real tbeginfit,real tendfit,
int eFitFn,int nskip)
{
FILE *fp,*gp=NULL;
int i,k,nfour;
real *csum;
real *ctmp,*fit;
real c0,sum,Ct2av,Ctav;
gmx_bool bFour = acf.bFour;
/* Check flags and parameters */
nout = get_acfnout();
if (nout == -1)
nout = acf.nout = (nframes+1)/2;
else if (nout > nframes)
nout=nframes;
if (MODE(eacCos) && MODE(eacVector))
gmx_fatal(FARGS,"Incompatible options bCos && bVector (%s, %d)",
__FILE__,__LINE__);
if ((MODE(eacP3) || MODE(eacRcross)) && bFour) {
fprintf(stderr,"Can't combine mode %lu with FFT, turning off FFT\n",mode);
bFour = FALSE;
}
if (MODE(eacNormal) && MODE(eacVector))
gmx_fatal(FARGS,"Incompatible mode bits: normal and vector (or Legendre)");
/* Print flags and parameters */
if (bVerbose) {
printf("Will calculate %s of %d thingies for %d frames\n",
title ? title : "autocorrelation",nitem,nframes);
printf("bAver = %s, bFour = %s bNormalize= %s\n",
bool_names[bAver],bool_names[bFour],bool_names[bNormalize]);
printf("mode = %lu, dt = %g, nrestart = %d\n",mode,dt,nrestart);
}
if (bFour) {
c0 = log((double)nframes)/log(2.0);
k = c0;
if (k < c0)
k++;
k++;
nfour = 1<<k;
if (debug)
fprintf(debug,"Using FFT to calculate %s, #points for FFT = %d\n",
title,nfour);
/* Allocate temp arrays */
snew(csum,nfour);
snew(ctmp,nfour);
} else {
nfour = 0; /* To keep the compiler happy */
snew(csum,nframes);
snew(ctmp,nframes);
}
/* Loop over items (e.g. molecules or dihedrals)
* In this loop the actual correlation functions are computed, but without
* normalizing them.
*/
k = max(1,pow(10,(int)(log(nitem)/log(100))));
for(i=0; i<nitem; i++) {
if (bVerbose && ((i%k==0 || i==nitem-1)))
fprintf(stderr,"\rThingie %d",i+1);
if (bFour)
do_four_core(mode,nfour,nframes,nframes,c1[i],csum,ctmp);
else
do_ac_core(nframes,nout,ctmp,c1[i],nrestart,mode);
}
if (bVerbose)
fprintf(stderr,"\n");
sfree(ctmp);
sfree(csum);
if (fn) {
snew(fit,nout);
fp=xvgropen(fn,title,"Time (ps)","C(t)",oenv);
} else {
fit = NULL;
fp = NULL;
}
if (bAver) {
if (nitem > 1)
average_acf(bVerbose,nframes,nitem,c1);
if (bNormalize)
normalize_acf(nout,c1[0]);
if (eFitFn != effnNONE) {
fit_acf(nout,eFitFn,oenv,fn!=NULL,tbeginfit,tendfit,dt,c1[0],fit);
sum = print_and_integrate(fp,nout,dt,c1[0],fit,1);
} else {
sum = print_and_integrate(fp,nout,dt,c1[0],NULL,1);
if (bVerbose)
printf("Correlation time (integral over corrfn): %g (ps)\n",sum);
}
} else {
/* Not averaging. Normalize individual ACFs */
Ctav = Ct2av = 0;
if (debug)
gp = xvgropen("ct-distr.xvg","Correlation times","item","time (ps)",oenv);
for(i=0; i<nitem; i++) {
if (bNormalize)
normalize_acf(nout,c1[i]);
if (eFitFn != effnNONE) {
fit_acf(nout,eFitFn,oenv,fn!=NULL,tbeginfit,tendfit,dt,c1[i],fit);
sum = print_and_integrate(fp,nout,dt,c1[i],fit,1);
} else {
sum = print_and_integrate(fp,nout,dt,c1[i],NULL,1);
if (debug)
fprintf(debug,
"CORRelation time (integral over corrfn %d): %g (ps)\n",
i,sum);
}
Ctav += sum;
Ct2av += sum*sum;
if (debug)
fprintf(gp,"%5d %.3f\n",i,sum);
}
if (debug)
ffclose(gp);
if (nitem > 1) {
Ctav /= nitem;
Ct2av /= nitem;
printf("Average correlation time %.3f Std. Dev. %.3f Error %.3f (ps)\n",
Ctav,sqrt((Ct2av - sqr(Ctav))),
sqrt((Ct2av - sqr(Ctav))/(nitem-1)));
}
}
if (fp)
ffclose(fp);
sfree(fit);
}
real fit_acf(int ncorr,int fitfn,const output_env_t oenv,gmx_bool bVerbose,
real tbeginfit,real tendfit,real dt,real c1[],real *fit)
{
real fitparm[3];
real tStart,tail_corr,sum,sumtot=0,ct_estimate,*sig;
int i,j,jmax,nf_int;
gmx_bool bPrint;
bPrint = bVerbose || bDebugMode();
if (bPrint) printf("COR:\n");
if (tendfit <= 0)
tendfit = ncorr*dt;
nf_int = min(ncorr,(int)(tendfit/dt));
sum = print_and_integrate(debug,nf_int,dt,c1,NULL,1);
/* Estimate the correlation time for better fitting */
ct_estimate = 0.5*c1[0];
for(i=1; (i<ncorr) && (c1[i]>0); i++)
ct_estimate += c1[i];
ct_estimate *= dt/c1[0];
if (bPrint) {
printf("COR: Correlation time (plain integral from %6.3f to %6.3f ps) = %8.5f ps\n",
0.0,dt*nf_int,sum);
printf("COR: Relaxation times are computed as fit to an exponential:\n");
printf("COR: %s\n",longs_ffn[fitfn]);
printf("COR: Fit to correlation function from %6.3f ps to %6.3f ps, results in a\n",tbeginfit,min(ncorr*dt,tendfit));
}
tStart = 0;
if (bPrint)
printf("COR:%11s%11s%11s%11s%11s%11s%11s\n",
"Fit from","Integral","Tail Value","Sum (ps)"," a1 (ps)",
(nfp_ffn[fitfn]>=2) ? " a2 ()" : "",
(nfp_ffn[fitfn]>=3) ? " a3 (ps)" : "");
if (tbeginfit > 0)
jmax = 3;
else
jmax = 1;
if (fitfn == effnEXP3) {
fitparm[0] = 0.002*ncorr*dt;
fitparm[1] = 0.95;
fitparm[2] = 0.2*ncorr*dt;
} else {
/* Good initial guess, this increases the probability of convergence */
fitparm[0] = ct_estimate;
fitparm[1] = 1.0;
fitparm[2] = 1.0;
}
/* Generate more or less appropriate sigma's */
snew(sig,ncorr);
for(i=0; i<ncorr; i++)
sig[i] = sqrt(ct_estimate+dt*i);
for(j=0; ((j<jmax) && (tStart < tendfit)); j++) {
/* Use the previous fitparm as starting values for the next fit */
nf_int = min(ncorr,(int)((tStart+1e-4)/dt));
sum = print_and_integrate(debug,nf_int,dt,c1,NULL,1);
tail_corr = do_lmfit(ncorr,c1,sig,dt,NULL,tStart,tendfit,oenv,
bDebugMode(),fitfn,fitparm,0);
sumtot = sum+tail_corr;
if (fit && ((jmax == 1) || (j == 1)))
for(i=0; (i<ncorr); i++)
fit[i] = fit_function(fitfn,fitparm,i*dt);
if (bPrint) {
printf("COR:%11.4e%11.4e%11.4e%11.4e",tStart,sum,tail_corr,sumtot);
for(i=0; (i<nfp_ffn[fitfn]); i++)
printf(" %11.4e",fitparm[i]);
printf("\n");
}
tStart += tbeginfit;
}
sfree(sig);
return sumtot;
}
static void do_rdf(char *fnNDX,char *fnTPS,char *fnTRX,
char *fnRDF,char *fnCNRDF, char *fnHQ,
bool bCM,char **rdft,bool bXY,bool bPBC,bool bNormalize,
real cutoff,real binwidth,real fade,int ng)
{
FILE *fp;
int status;
char outf1[STRLEN],outf2[STRLEN];
char title[STRLEN],gtitle[STRLEN];
int g,natoms,i,j,k,nbin,j0,j1,n,nframes;
int **count;
char **grpname;
int *isize,isize_cm=0,nrdf=0,max_i,isize0,isize_g;
atom_id **index,*index_cm=NULL;
#if (defined SIZEOF_LONG_LONG_INT) && (SIZEOF_LONG_LONG_INT >= 8)
long long int *sum;
#else
double *sum;
#endif
real t,rmax2,cut2,r,r2,invhbinw,normfac;
real segvol,spherevol,prev_spherevol,**rdf;
rvec *x,dx,*x0=NULL,*x_i1,xi;
real *inv_segvol,invvol,invvol_sum,rho;
bool *bExcl,bTop,bNonSelfExcl;
matrix box,box_pbc;
int **npairs;
atom_id ix,jx,***pairs;
t_topology *top=NULL;
int ePBC=-1;
t_block *mols=NULL;
t_blocka *excl;
t_atom *atom=NULL;
t_pbc pbc;
int *is=NULL,**coi=NULL,cur,mol,i1,res,a;
excl=NULL;
if (fnTPS) {
snew(top,1);
bTop=read_tps_conf(fnTPS,title,top,&ePBC,&x,NULL,box,TRUE);
if (bTop && !bCM)
/* get exclusions from topology */
excl = &(top->excls);
}
snew(grpname,ng+1);
snew(isize,ng+1);
snew(index,ng+1);
fprintf(stderr,"\nSelect a reference group and %d group%s\n",
ng,ng==1?"":"s");
if (fnTPS) {
get_index(&(top->atoms),fnNDX,ng+1,isize,index,grpname);
atom = top->atoms.atom;
} else {
rd_index(fnNDX,ng+1,isize,index,grpname);
}
if (rdft[0][0] != 'a') {
/* Split up all the groups in molecules or residues */
switch (rdft[0][0]) {
case 'm':
mols = &top->mols;
break;
case 'r':
atom = top->atoms.atom;
break;
default:
gmx_fatal(FARGS,"Unknown rdf option '%s'",rdft[0]);
}
snew(is,ng+1);
snew(coi,ng+1);
for(g=(bCM ? 1 : 0); g<ng+1; g++) {
snew(coi[g],isize[g]+1);
is[g] = 0;
cur = -1;
mol = 0;
for(i=0; i<isize[g]; i++) {
a = index[g][i];
if (rdft[0][0] == 'm') {
/* Check if the molecule number has changed */
i1 = mols->index[mol+1];
while(a >= i1) {
mol++;
i1 = mols->index[mol+1];
}
if (mol != cur) {
coi[g][is[g]++] = i;
cur = mol;
}
} else if (rdft[0][0] == 'r') {
/* Check if the residue number has changed */
res = atom[a].resnr;
if (res != cur) {
coi[g][is[g]++] = i;
cur = res;
}
}
}
coi[g][is[g]] = i;
srenew(coi[g],is[g]+1);
printf("Group '%s' of %d atoms consists of %d %s\n",
grpname[g],isize[g],is[g],
(rdft[0][0]=='m' ? "molecules" : "residues"));
}
} else if (bCM) {
snew(is,1);
snew(coi,1);
}
if (bCM) {
is[0] = 1;
snew(coi[0],is[0]+1);
coi[0][0] = 0;
coi[0][1] = isize[0];
isize0 = is[0];
snew(x0,isize0);
} else if (rdft[0][0] != 'a') {
isize0 = is[0];
snew(x0,isize0);
} else {
isize0 = isize[0];
}
natoms=read_first_x(&status,fnTRX,&t,&x,box);
if ( !natoms )
gmx_fatal(FARGS,"Could not read coordinates from statusfile\n");
if (fnTPS)
/* check with topology */
if ( natoms > top->atoms.nr )
gmx_fatal(FARGS,"Trajectory (%d atoms) does not match topology (%d atoms)",
natoms,top->atoms.nr);
/* check with index groups */
for (i=0; i<ng+1; i++)
for (j=0; j<isize[i]; j++)
if ( index[i][j] >= natoms )
gmx_fatal(FARGS,"Atom index (%d) in index group %s (%d atoms) larger "
"than number of atoms in trajectory (%d atoms)",
index[i][j],grpname[i],isize[i],natoms);
/* initialize some handy things */
copy_mat(box,box_pbc);
if (bXY) {
check_box_c(box);
/* Make sure the z-height does not influence the cut-off */
box_pbc[ZZ][ZZ] = 2*max(box[XX][XX],box[YY][YY]);
}
if (bPBC)
rmax2 = 0.99*0.99*max_cutoff2(bXY ? epbcXY : epbcXYZ,box_pbc);
else
rmax2 = sqr(3*max(box[XX][XX],max(box[YY][YY],box[ZZ][ZZ])));
if (debug)
fprintf(debug,"rmax2 = %g\n",rmax2);
/* We use the double amount of bins, so we can correctly
* write the rdf and rdf_cn output at i*binwidth values.
*/
nbin = (int)(sqrt(rmax2) * 2 / binwidth);
invhbinw = 2.0 / binwidth;
cut2 = sqr(cutoff);
snew(count,ng);
snew(pairs,ng);
snew(npairs,ng);
snew(bExcl,natoms);
max_i = 0;
for(g=0; g<ng; g++) {
if (isize[g+1] > max_i)
max_i = isize[g+1];
/* this is THE array */
snew(count[g],nbin+1);
/* make pairlist array for groups and exclusions */
snew(pairs[g],isize[0]);
snew(npairs[g],isize[0]);
for(i=0; i<isize[0]; i++) {
/* We can only have exclusions with atomic rdfs */
if (!(bCM || rdft[0][0] != 'a')) {
ix = index[0][i];
for(j=0; j < natoms; j++)
bExcl[j] = FALSE;
/* exclusions? */
if (excl)
for( j = excl->index[ix]; j < excl->index[ix+1]; j++)
bExcl[excl->a[j]]=TRUE;
k = 0;
snew(pairs[g][i], isize[g+1]);
bNonSelfExcl = FALSE;
for(j=0; j<isize[g+1]; j++) {
jx = index[g+1][j];
if (!bExcl[jx])
pairs[g][i][k++]=jx;
else if (ix != jx)
/* Check if we have exclusions other than self exclusions */
bNonSelfExcl = TRUE;
}
if (bNonSelfExcl) {
npairs[g][i]=k;
srenew(pairs[g][i],npairs[g][i]);
} else {
/* Save a LOT of memory and some cpu cycles */
npairs[g][i]=-1;
sfree(pairs[g][i]);
}
} else {
npairs[g][i]=-1;
}
}
}
sfree(bExcl);
snew(x_i1,max_i);
nframes = 0;
invvol_sum = 0;
do {
/* Must init pbc every step because of pressure coupling */
copy_mat(box,box_pbc);
if (bPBC) {
if (top != NULL)
rm_pbc(&top->idef,ePBC,natoms,box,x,x);
if (bXY) {
check_box_c(box);
clear_rvec(box_pbc[ZZ]);
}
set_pbc(&pbc,ePBC,box_pbc);
if (bXY)
/* Set z-size to 1 so we get the surface iso the volume */
box_pbc[ZZ][ZZ] = 1;
}
invvol = 1/det(box_pbc);
invvol_sum += invvol;
if (bCM) {
/* Calculate center of mass of the whole group */
calc_comg(is[0],coi[0],index[0],TRUE ,atom,x,x0);
} else if (rdft[0][0] != 'a') {
calc_comg(is[0],coi[0],index[0],rdft[0][6]=='m',atom,x,x0);
}
for(g=0; g<ng; g++) {
if (rdft[0][0] == 'a') {
/* Copy the indexed coordinates to a continuous array */
for(i=0; i<isize[g+1]; i++)
copy_rvec(x[index[g+1][i]],x_i1[i]);
} else {
/* Calculate the COMs/COGs and store in x_i1 */
calc_comg(is[g+1],coi[g+1],index[g+1],rdft[0][6]=='m',atom,x,x_i1);
}
for(i=0; i<isize0; i++) {
if (bCM || rdft[0][0] != 'a') {
copy_rvec(x0[i],xi);
} else {
copy_rvec(x[index[0][i]],xi);
}
if (rdft[0][0] == 'a' && npairs[g][i] >= 0) {
/* Expensive loop, because of indexing */
for(j=0; j<npairs[g][i]; j++) {
jx=pairs[g][i][j];
if (bPBC)
pbc_dx(&pbc,xi,x[jx],dx);
else
rvec_sub(xi,x[jx],dx);
if (bXY)
r2 = dx[XX]*dx[XX] + dx[YY]*dx[YY];
else
r2=iprod(dx,dx);
if (r2>cut2 && r2<=rmax2)
count[g][(int)(sqrt(r2)*invhbinw)]++;
}
} else {
/* Cheaper loop, no exclusions */
if (rdft[0][0] == 'a')
isize_g = isize[g+1];
else
isize_g = is[g+1];
for(j=0; j<isize_g; j++) {
if (bPBC)
pbc_dx(&pbc,xi,x_i1[j],dx);
else
rvec_sub(xi,x_i1[j],dx);
if (bXY)
r2 = dx[XX]*dx[XX] + dx[YY]*dx[YY];
else
r2=iprod(dx,dx);
if (r2>cut2 && r2<=rmax2)
count[g][(int)(sqrt(r2)*invhbinw)]++;
}
}
}
}
nframes++;
} while (read_next_x(status,&t,natoms,x,box));
fprintf(stderr,"\n");
close_trj(status);
sfree(x);
/* Average volume */
invvol = invvol_sum/nframes;
/* Calculate volume of sphere segments or length of circle segments */
snew(inv_segvol,(nbin+1)/2);
prev_spherevol=0;
for(i=0; (i<(nbin+1)/2); i++) {
r = (i + 0.5)*binwidth;
if (bXY) {
spherevol=M_PI*r*r;
} else {
spherevol=(4.0/3.0)*M_PI*r*r*r;
}
segvol=spherevol-prev_spherevol;
inv_segvol[i]=1.0/segvol;
prev_spherevol=spherevol;
}
snew(rdf,ng);
for(g=0; g<ng; g++) {
/* We have to normalize by dividing by the number of frames */
if (rdft[0][0] == 'a')
normfac = 1.0/(nframes*invvol*isize0*isize[g+1]);
else
normfac = 1.0/(nframes*invvol*isize0*is[g+1]);
/* Do the normalization */
nrdf = max((nbin+1)/2,1+2*fade/binwidth);
snew(rdf[g],nrdf);
for(i=0; i<(nbin+1)/2; i++) {
r = i*binwidth;
if (i == 0)
j = count[g][0];
else
j = count[g][i*2-1] + count[g][i*2];
if ((fade > 0) && (r >= fade))
rdf[g][i] = 1 + (j*inv_segvol[i]*normfac-1)*exp(-16*sqr(r/fade-1));
else {
if (bNormalize)
rdf[g][i] = j*inv_segvol[i]*normfac;
else
rdf[g][i] = j/(binwidth*isize0*nframes);
}
}
for( ; (i<nrdf); i++)
rdf[g][i] = 1.0;
}
if (rdft[0][0] == 'a') {
sprintf(gtitle,"Radial distribution");
} else {
sprintf(gtitle,"Radial distribution of %s %s",
rdft[0][0]=='m' ? "molecule" : "residue",
rdft[0][6]=='m' ? "COM" : "COG");
}
fp=xvgropen(fnRDF,gtitle,"r","");
if (ng==1) {
if (bPrintXvgrCodes())
fprintf(fp,"@ subtitle \"%s%s - %s\"\n",
grpname[0],bCM ? " COM" : "",grpname[1]);
}
else {
if (bPrintXvgrCodes())
fprintf(fp,"@ subtitle \"reference %s%s\"\n",
grpname[0],bCM ? " COM" : "");
xvgr_legend(fp,ng,grpname+1);
}
for(i=0; (i<nrdf); i++) {
fprintf(fp,"%10g",i*binwidth);
for(g=0; g<ng; g++)
fprintf(fp," %10g",rdf[g][i]);
fprintf(fp,"\n");
}
ffclose(fp);
do_view(fnRDF,NULL);
/* h(Q) function: fourier transform of rdf */
if (fnHQ) {
int nhq = 401;
real *hq,*integrand,Q;
/* Get a better number density later! */
rho = isize[1]*invvol;
snew(hq,nhq);
snew(integrand,nrdf);
for(i=0; (i<nhq); i++) {
Q = i*0.5;
integrand[0] = 0;
for(j=1; (j<nrdf); j++) {
r = j*binwidth;
integrand[j] = (Q == 0) ? 1.0 : sin(Q*r)/(Q*r);
integrand[j] *= 4.0*M_PI*rho*r*r*(rdf[0][j]-1.0);
}
hq[i] = print_and_integrate(debug,nrdf,binwidth,integrand,NULL,0);
}
fp=xvgropen(fnHQ,"h(Q)","Q(/nm)","h(Q)");
for(i=0; (i<nhq); i++)
fprintf(fp,"%10g %10g\n",i*0.5,hq[i]);
ffclose(fp);
do_view(fnHQ,NULL);
sfree(hq);
sfree(integrand);
}
if (fnCNRDF) {
normfac = 1.0/(isize0*nframes);
fp=xvgropen(fnCNRDF,"Cumulative Number RDF","r","number");
if (ng==1) {
if (bPrintXvgrCodes())
fprintf(fp,"@ subtitle \"%s-%s\"\n",grpname[0],grpname[1]);
}
else {
if (bPrintXvgrCodes())
fprintf(fp,"@ subtitle \"reference %s\"\n",grpname[0]);
xvgr_legend(fp,ng,grpname+1);
}
snew(sum,ng);
for(i=0; (i<=nbin/2); i++) {
fprintf(fp,"%10g",i*binwidth);
for(g=0; g<ng; g++) {
fprintf(fp," %10g",(real)((double)sum[g]*normfac));
if (i*2+1 < nbin)
sum[g] += count[g][i*2] + count[g][i*2+1];
}
fprintf(fp,"\n");
}
ffclose(fp);
sfree(sum);
do_view(fnCNRDF,NULL);
}
for(g=0; g<ng; g++)
sfree(rdf[g]);
sfree(rdf);
}
void low_do_autocorr(const char *fn, const gmx_output_env_t *oenv, const char *title,
int nframes, int nitem, int nout, real **c1,
real dt, unsigned long mode, int nrestart,
gmx_bool bAver, gmx_bool bNormalize,
gmx_bool bVerbose, real tbeginfit, real tendfit,
int eFitFn)
{
FILE *fp, *gp = NULL;
int i;
real *csum;
real *ctmp, *fit;
real sum, Ct2av, Ctav;
gmx_bool bFour = acf.bFour;
/* Check flags and parameters */
nout = get_acfnout();
if (nout == -1)
{
nout = acf.nout = (nframes+1)/2;
}
else if (nout > nframes)
{
nout = nframes;
}
if (MODE(eacCos) && MODE(eacVector))
{
gmx_fatal(FARGS, "Incompatible options bCos && bVector (%s, %d)",
__FILE__, __LINE__);
}
if ((MODE(eacP3) || MODE(eacRcross)) && bFour)
{
if (bVerbose)
{
fprintf(stderr, "Can't combine mode %lu with FFT, turning off FFT\n", mode);
}
bFour = FALSE;
}
if (MODE(eacNormal) && MODE(eacVector))
{
gmx_fatal(FARGS, "Incompatible mode bits: normal and vector (or Legendre)");
}
/* Print flags and parameters */
if (bVerbose)
{
printf("Will calculate %s of %d thingies for %d frames\n",
title ? title : "autocorrelation", nitem, nframes);
printf("bAver = %s, bFour = %s bNormalize= %s\n",
gmx::boolToString(bAver), gmx::boolToString(bFour),
gmx::boolToString(bNormalize));
printf("mode = %lu, dt = %g, nrestart = %d\n", mode, dt, nrestart);
}
/* Allocate temp arrays */
snew(csum, nframes);
snew(ctmp, nframes);
/* Loop over items (e.g. molecules or dihedrals)
* In this loop the actual correlation functions are computed, but without
* normalizing them.
*/
for (int i = 0; i < nitem; i++)
{
if (bVerbose && (((i % 100) == 0) || (i == nitem-1)))
{
fprintf(stderr, "\rThingie %d", i+1);
fflush(stderr);
}
if (bFour)
{
do_four_core(mode, nframes, c1[i], csum, ctmp);
}
else
{
do_ac_core(nframes, nout, ctmp, c1[i], nrestart, mode);
}
}
if (bVerbose)
{
fprintf(stderr, "\n");
}
sfree(ctmp);
sfree(csum);
if (fn)
{
snew(fit, nout);
fp = xvgropen(fn, title, "Time (ps)", "C(t)", oenv);
}
else
{
fit = NULL;
fp = NULL;
}
if (bAver)
{
if (nitem > 1)
{
average_acf(bVerbose, nframes, nitem, c1);
}
if (bNormalize)
{
normalize_acf(nout, c1[0]);
}
if (eFitFn != effnNONE)
{
fit_acf(nout, eFitFn, oenv, fn != NULL, tbeginfit, tendfit, dt, c1[0], fit);
sum = print_and_integrate(fp, nout, dt, c1[0], fit, 1);
}
else
{
sum = print_and_integrate(fp, nout, dt, c1[0], NULL, 1);
}
if (bVerbose)
{
printf("Correlation time (integral over corrfn): %g (ps)\n", sum);
}
}
else
{
/* Not averaging. Normalize individual ACFs */
Ctav = Ct2av = 0;
if (debug)
{
gp = xvgropen("ct-distr.xvg", "Correlation times", "item", "time (ps)", oenv);
}
for (i = 0; i < nitem; i++)
{
if (bNormalize)
{
normalize_acf(nout, c1[i]);
}
if (eFitFn != effnNONE)
{
fit_acf(nout, eFitFn, oenv, fn != NULL, tbeginfit, tendfit, dt, c1[i], fit);
sum = print_and_integrate(fp, nout, dt, c1[i], fit, 1);
}
else
{
sum = print_and_integrate(fp, nout, dt, c1[i], NULL, 1);
if (debug)
{
fprintf(debug,
"CORRelation time (integral over corrfn %d): %g (ps)\n",
i, sum);
}
}
Ctav += sum;
Ct2av += sum*sum;
if (debug)
{
fprintf(gp, "%5d %.3f\n", i, sum);
}
}
if (debug)
{
xvgrclose(gp);
}
if (nitem > 1)
{
Ctav /= nitem;
Ct2av /= nitem;
printf("Average correlation time %.3f Std. Dev. %.3f Error %.3f (ps)\n",
Ctav, std::sqrt((Ct2av - gmx::square(Ctav))),
std::sqrt((Ct2av - gmx::square(Ctav))/(nitem-1)));
}
}
if (fp)
{
xvgrclose(fp);
}
sfree(fit);
}