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);
}
int main(int argc,char *argv[])
{
FILE *fp;
const char *desc[] = {
"testac tests the functioning of the GROMACS acf routines"
};
static int nframes = 1024;
static int datatp = 0;
static real a=0.02*M_PI;
output_env_t oenv;
t_pargs pa[] = {
{ "-np", FALSE, etINT, &nframes,
"Number of data points" },
{ "-dtp",FALSE, etINT, &datatp,
"Which data: 0=all 0.0, 1=all 1.0, 2=cos(a t), 3=random, 4=cos(a t)+random, 5=sin(a t)/(a t)" }
};
static char *str[] = {
"all 0.0",
"all 1.0",
"cos(a t)",
"random",
"cos(a t)+random",
"sin(a t)/(a t)"
};
t_filenm fnm[] = {
{ efXVG, "-d", "acf-data", ffWRITE },
{ efXVG, "-c", "acf-corr", ffWRITE },
{ efXVG, "-comb", "acf-comb.xvg", ffWRITE }
};
#define NFILE asize(fnm)
int npargs,i,nlag;
int seed=1993;
real *data,*data2,x;
t_pargs *ppa;
CopyRight(stderr,argv[0]);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs,pa);
parse_common_args_r(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
NFILE,fnm,npargs,ppa,asize(desc),desc,0,NULL,&oenv);
snew(data,nframes);
snew(data2,nframes);
fp = xvgropen(opt2fn("-d",NFILE,fnm),"testac","x","y",oenv);
for(i=0; (i<nframes); i++) {
x = a*i;
switch (datatp) {
case 1:
data[i] = 1;
break;
case 2:
data[i] = cos(x);
break;
case 3:
data[i] = 2*rando(&seed)-1.0;
break;
case 4:
data[i] = cos(x)+2*rando(&seed)-1.0;
break;
case 5:
if (i==0)
data[i] = 1;
else
data[i] = sin(x)/(x);
default:
/* Data remains 0.0 */
break;
}
fprintf(fp,"%10g %10g\n",x,data[i]);
data2[i] = data[i];
}
ffclose(fp);
do_autocorr(opt2fn("-c",NFILE,fnm),oenv,str[datatp],
nframes,1,&data,a,eacNormal,FALSE);
nlag = get_acfnout();
fp = xvgropen(opt2fn("-comb",NFILE,fnm),"testac","x","y",oenv);
for(i=0; (i<nlag); i++) {
fprintf(fp,"%10g %10g %10g\n",a*i,data2[i],data[i]);
}
ffclose(fp);
do_view(opt2fn("-c",NFILE,fnm),"-nxy");
thanx(stderr);
return 0;
}
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);
}