/*!
* \param[in] out Output file.
* \param[in] sc Selection collection which should be written.
*/
void
xvgr_selcollection(FILE *out, gmx_ana_selcollection_t *sc)
{
char *buf;
char *p, *nl;
if (bPrintXvgrCodes() && sc && sc->selstr)
{
fprintf(out, "# Selections:\n");
buf = strdup(sc->selstr);
p = buf;
while (p && p[0] != 0)
{
nl = strchr(p, '\n');
if (nl)
{
*nl = 0;
}
fprintf(out, "# %s\n", p);
p = nl;
if (nl)
{
++p;
}
}
fprintf(out, "#\n");
sfree(buf);
}
}
void xvgr_line_props(FILE *out, int NrSet, int LineStyle, int LineColor)
{
if (bPrintXvgrCodes()) {
fprintf(out, "@ with g0\n");
fprintf(out, "@ s%d linestyle %d\n", NrSet, LineStyle);
fprintf(out, "@ s%d color %d\n", NrSet, LineColor);
}
}
void xvgr_world(FILE *out,real xmin,real ymin,real xmax,real ymax)
{
if (bPrintXvgrCodes())
fprintf(out,"@ world xmin %g\n"
"@ world ymin %g\n"
"@ world xmax %g\n"
"@ world ymax %g\n",xmin,ymin,xmax,ymax);
}
void analyse_ss(char *outfile, t_matrix *mat, char *ss_string)
{
FILE *fp;
t_mapping *map;
int s,f,r,*count,ss_count;
char **leg;
map=mat->map;
snew(count,mat->nmap);
snew(leg,mat->nmap+1);
leg[0]="Structure";
for(s=0; s<mat->nmap; s++)
leg[s+1]=map[s].desc;
fp=xvgropen(outfile,"Secondary Structure",
xvgr_tlabel(),"Number of Residues");
if (bPrintXvgrCodes())
fprintf(fp,"@ subtitle \"Structure = ");
for(s=0; s<strlen(ss_string); s++) {
if (s>0)
fprintf(fp," + ");
for(f=0; f<mat->nmap; f++)
if (ss_string[s]==map[f].code.c1)
fprintf(fp,"%s",map[f].desc);
}
fprintf(fp,"\"\n");
xvgr_legend(fp,mat->nmap+1,leg);
for(f=0; f<mat->nx; f++) {
ss_count=0;
for(s=0; s<mat->nmap; s++)
count[s]=0;
for(r=0; r<mat->ny; r++)
count[mat->matrix[f][r]]++;
for(s=0; s<mat->nmap; s++) {
if (strchr(ss_string,map[s].code.c1))
ss_count+=count[s];
}
fprintf(fp,"%8g %5d",mat->axis_x[f],ss_count);
for(s=0; s<mat->nmap; s++)
fprintf(fp," %5d",count[s]);
fprintf(fp,"\n");
}
fclose(fp);
sfree(leg);
sfree(count);
}
void xvgr_box(FILE *out,
int LocType,
real xmin,real ymin,real xmax,real ymax,
int LineStyle,int LineWidth,int LineColor,
int BoxFill,int BoxColor,int BoxPattern)
{
if (bPrintXvgrCodes()) {
fprintf(out,"@with box\n");
fprintf(out,"@ box on\n");
fprintf(out,"@ box loctype %s\n",LocTypeStr[LocType]);
fprintf(out,"@ box %g, %g, %g, %g\n",xmin,ymin,xmax,ymax);
fprintf(out,"@ box linestyle %d\n",LineStyle);
fprintf(out,"@ box linewidth %d\n",LineWidth);
fprintf(out,"@ box color %d\n",LineColor);
fprintf(out,"@ box fill %s\n",BoxFillStr[BoxFill]);
fprintf(out,"@ box fill color %d\n",BoxColor);
fprintf(out,"@ box fill pattern %d\n",BoxPattern);
fprintf(out,"@box def\n");
}
}
void xvgr_legend(FILE *out,int nsets,char *setname[])
{
int i;
if (bPrintXvgrCodes()) {
xvgr_view(out,0.15,0.15,0.75,0.85);
fprintf(out,"@ legend on\n");
fprintf(out,"@ legend box on\n");
fprintf(out,"@ legend loctype view\n");
fprintf(out,"@ legend %g, %g\n",0.78,0.8);
fprintf(out,"@ legend length %d\n",2);
for(i=0; (i<nsets); i++)
if (setname[i]) {
if (use_xmgr())
fprintf(out,"@ legend string %d \"%s\"\n",i,setname[i]);
else
fprintf(out,"@ s%d legend \"%s\"\n",i,setname[i]);
}
}
}
FILE *xvgropen(const char *fn,const char *title,const char *xaxis,const char *yaxis)
{
FILE *xvgr;
char pukestr[100];
time_t t;
xvgr=gmx_fio_fopen(fn,"w");
if (bPrintXvgrCodes()) {
time(&t);
fprintf(xvgr,"# This file was created %s",ctime(&t));
fprintf(xvgr,"# by the following command:\n# %s\n#\n",command_line());
fprintf(xvgr,"# %s is part of G R O M A C S:\n#\n",Program());
bromacs(pukestr,99);
fprintf(xvgr,"# %s\n#\n",pukestr);
fprintf(xvgr,"@ title \"%s\"\n",title);
fprintf(xvgr,"@ xaxis label \"%s\"\n",xaxis);
fprintf(xvgr,"@ yaxis label \"%s\"\n",yaxis);
if (use_xmgr())
fprintf(xvgr,"@TYPE nxy\n");
else
fprintf(xvgr,"@TYPE xy\n");
}
return xvgr;
}
static void estimate_error(char *eefile,int nb_min,int resol,int n,int nset,
double *av,double *sig,real **val,real dt,
bool bFitAc,bool bSingleExpFit,bool bAllowNegLTCorr)
{
FILE *fp;
int bs,prev_bs,nbs,nb;
real spacing,nbr;
int s,i,j;
double blav,var;
char **leg;
real *tbs,*ybs,rtmp,dens,*fitsig,twooe,tau1_est,tau_sig;
real fitparm[4];
real ee,a,tau1,tau2;
if (n < 4)
{
fprintf(stdout,"The number of points is smaller than 4, can not make an error estimate\n");
return;
}
fp = xvgropen(eefile,"Error estimates",
"Block size (time)","Error estimate");
if (bPrintXvgrCodes())
{
fprintf(fp,
"@ subtitle \"using block averaging, total time %g (%d points)\"\n",
(n-1)*dt,n);
}
snew(leg,2*nset);
xvgr_legend(fp,2*nset,leg);
sfree(leg);
spacing = pow(2,1.0/resol);
snew(tbs,n);
snew(ybs,n);
snew(fitsig,n);
for(s=0; s<nset; s++)
{
nbs = 0;
prev_bs = 0;
nbr = nb_min;
while (nbr <= n)
{
bs = n/(int)nbr;
if (bs != prev_bs)
{
nb = n/bs;
var = 0;
for(i=0; i<nb; i++)
{
blav=0;
for (j=0; j<bs; j++)
{
blav += val[s][bs*i+j];
}
var += sqr(av[s] - blav/bs);
}
tbs[nbs] = bs*dt;
if (sig[s] == 0)
{
ybs[nbs] = 0;
}
else
{
ybs[nbs] = var/(nb*(nb-1.0))*(n*dt)/(sig[s]*sig[s]);
}
nbs++;
}
nbr *= spacing;
nb = (int)(nbr+0.5);
prev_bs = bs;
}
if (sig[s] == 0)
{
ee = 0;
a = 1;
tau1 = 0;
tau2 = 0;
}
else
{
for(i=0; i<nbs/2; i++)
{
rtmp = tbs[i];
tbs[i] = tbs[nbs-1-i];
tbs[nbs-1-i] = rtmp;
rtmp = ybs[i];
ybs[i] = ybs[nbs-1-i];
ybs[nbs-1-i] = rtmp;
}
/* The initial slope of the normalized ybs^2 is 1.
* For a single exponential autocorrelation: ybs(tau1) = 2/e tau1
* From this we take our initial guess for tau1.
*/
twooe = 2/exp(1);
i = -1;
do
{
i++;
tau1_est = tbs[i];
} while (i < nbs - 1 &&
(ybs[i] > ybs[i+1] || ybs[i] > twooe*tau1_est));
if (ybs[0] > ybs[1])
{
fprintf(stdout,"Data set %d has strange time correlations:\n"
"the std. error using single points is larger than that of blocks of 2 points\n"
"The error estimate might be inaccurate, check the fit\n",
s+1);
/* Use the total time as tau for the fitting weights */
tau_sig = (n - 1)*dt;
}
else
{
tau_sig = tau1_est;
}
if (debug)
{
fprintf(debug,"set %d tau1 estimate %f\n",s+1,tau1_est);
}
/* Generate more or less appropriate sigma's,
* also taking the density of points into account.
*/
for(i=0; i<nbs; i++)
{
if (i == 0)
{
dens = tbs[1]/tbs[0] - 1;
}
else if (i == nbs-1)
{
dens = tbs[nbs-1]/tbs[nbs-2] - 1;
}
else
{
dens = 0.5*(tbs[i+1]/tbs[i-1] - 1);
}
fitsig[i] = sqrt((tau_sig + tbs[i])/dens);
}
if (!bSingleExpFit)
{
fitparm[0] = tau1_est;
fitparm[1] = 0.95;
/* We set the initial guess for tau2
* to halfway between tau1_est and the total time (on log scale).
*/
fitparm[2] = sqrt(tau1_est*(n-1)*dt);
do_lmfit(nbs,ybs,fitsig,0,tbs,0,dt*n,bDebugMode(),effnERREST,fitparm,0);
fitparm[3] = 1-fitparm[1];
}
if (bSingleExpFit || fitparm[0]<0 || fitparm[2]<0 || fitparm[1]<0
|| (fitparm[1]>1 && !bAllowNegLTCorr) || fitparm[2]>(n-1)*dt)
{
if (!bSingleExpFit)
{
if (fitparm[2] > (n-1)*dt)
{
fprintf(stdout,
"Warning: tau2 is longer than the length of the data (%g)\n"
" the statistics might be bad\n",
(n-1)*dt);
}
else
{
fprintf(stdout,"a fitted parameter is negative\n");
}
fprintf(stdout,"invalid fit: e.e. %g a %g tau1 %g tau2 %g\n",
sig[s]*anal_ee_inf(fitparm,n*dt),
fitparm[1],fitparm[0],fitparm[2]);
/* Do a fit with tau2 fixed at the total time.
* One could also choose any other large value for tau2.
*/
fitparm[0] = tau1_est;
fitparm[1] = 0.95;
fitparm[2] = (n-1)*dt;
fprintf(stderr,"Will fix tau2 at the total time: %g\n",fitparm[2]);
do_lmfit(nbs,ybs,fitsig,0,tbs,0,dt*n,bDebugMode(),effnERREST,fitparm,4);
fitparm[3] = 1-fitparm[1];
}
if (bSingleExpFit || fitparm[0]<0 || fitparm[1]<0
|| (fitparm[1]>1 && !bAllowNegLTCorr))
{
if (!bSingleExpFit) {
fprintf(stdout,"a fitted parameter is negative\n");
fprintf(stdout,"invalid fit: e.e. %g a %g tau1 %g tau2 %g\n",
sig[s]*anal_ee_inf(fitparm,n*dt),
fitparm[1],fitparm[0],fitparm[2]);
}
/* Do a single exponential fit */
fprintf(stderr,"Will use a single exponential fit for set %d\n",s+1);
fitparm[0] = tau1_est;
fitparm[1] = 1.0;
fitparm[2] = 0.0;
do_lmfit(nbs,ybs,fitsig,0,tbs,0,dt*n,bDebugMode(),effnERREST,fitparm,6);
fitparm[3] = 1-fitparm[1];
}
}
ee = sig[s]*anal_ee_inf(fitparm,n*dt);
a = fitparm[1];
tau1 = fitparm[0];
tau2 = fitparm[2];
}
fprintf(stdout,"Set %3d: err.est. %g a %g tau1 %g tau2 %g\n",
s+1,ee,a,tau1,tau2);
fprintf(fp,"@ legend string %d \"av %f\"\n",2*s,av[s]);
fprintf(fp,"@ legend string %d \"ee %6g\"\n",
2*s+1,sig[s]*anal_ee_inf(fitparm,n*dt));
for(i=0; i<nbs; i++)
{
fprintf(fp,"%g %g %g\n",tbs[i],sig[s]*sqrt(ybs[i]/(n*dt)),
sig[s]*sqrt(fit_function(effnERREST,fitparm,tbs[i])/(n*dt)));
}
if (bFitAc)
{
int fitlen;
real *ac,acint,ac_fit[4];
snew(ac,n);
for(i=0; i<n; i++) {
ac[i] = val[s][i] - av[s];
if (i > 0)
fitsig[i] = sqrt(i);
else
fitsig[i] = 1;
}
low_do_autocorr(NULL,NULL,n,1,-1,&ac,
dt,eacNormal,1,FALSE,TRUE,
FALSE,0,0,effnNONE,0);
fitlen = n/nb_min;
/* Integrate ACF only up to fitlen/2 to avoid integrating noise */
acint = 0.5*ac[0];
for(i=1; i<=fitlen/2; i++)
{
acint += ac[i];
}
acint *= dt;
/* Generate more or less appropriate sigma's */
for(i=0; i<=fitlen; i++)
{
fitsig[i] = sqrt(acint + dt*i);
}
ac_fit[0] = 0.5*acint;
ac_fit[1] = 0.95;
ac_fit[2] = 10*acint;
do_lmfit(n/nb_min,ac,fitsig,dt,0,0,fitlen*dt,
bDebugMode(),effnEXP3,ac_fit,0);
ac_fit[3] = 1 - ac_fit[1];
fprintf(stdout,"Set %3d: ac erest %g a %g tau1 %g tau2 %g\n",
s+1,sig[s]*anal_ee_inf(ac_fit,n*dt),
ac_fit[1],ac_fit[0],ac_fit[2]);
fprintf(fp,"&\n");
for(i=0; i<nbs; i++)
{
fprintf(fp,"%g %g\n",tbs[i],
sig[s]*sqrt(fit_function(effnERREST,ac_fit,tbs[i]))/(n*dt));
}
sfree(ac);
}
if (s < nset-1)
{
fprintf(fp,"&\n");
}
}
sfree(fitsig);
sfree(ybs);
sfree(tbs);
fclose(fp);
}
int gmx_angle(int argc,char *argv[])
{
static char *desc[] = {
"g_angle computes the angle distribution for a number of angles",
"or dihedrals. This way you can check whether your simulation",
"is correct. With option -ov you can plot the average angle of",
"a group of angles as a function of time. With the -all option",
"the first graph is the average, the rest are the individual angles.[PAR]",
"With the -of option g_angle also calculates the fraction of trans",
"dihedrals (only for dihedrals) as function of time, but this is",
"probably only fun for a selected few.[PAR]",
"With option -oc a dihedral correlation function is calculated.[PAR]",
"It should be noted that the indexfile should contain",
"atom-triples for angles or atom-quadruplets for dihedrals.",
"If this is not the case, the program will crash.[PAR]",
"With option [TT]-or[tt] a trajectory file is dumped containing cos and"
"sin of selected dihedral angles which subsequently can be used as",
"input for a PCA analysis using [TT]g_covar[tt]."
};
static char *opt[] = { NULL, "angle", "dihedral", "improper", "ryckaert-bellemans", NULL };
static bool bALL=FALSE,bChandler=FALSE,bAverCorr=FALSE,bPBC=TRUE;
static real binwidth=1;
t_pargs pa[] = {
{ "-type", FALSE, etENUM, {opt},
"Type of angle to analyse"
},
{ "-all", FALSE, etBOOL, {&bALL},
"Plot all angles separately in the averages file, in the order of appearance in the index file."
},
{ "-binwidth", FALSE, etREAL, {&binwidth},
"binwidth (degrees) for calculating the distribution"
},
{ "-periodic", FALSE, etBOOL, {&bPBC},
"Print dihedral angles modulo 360 degrees"
},
{ "-chandler", FALSE, etBOOL, {&bChandler},
"Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi < -60 || phi > 60."
},
{ "-avercorr", FALSE, etBOOL, {&bAverCorr},
"Average the correlation functions for the individual angles/dihedrals"
}
};
static char *bugs[] = {
"Counting transitions only works for dihedrals with multiplicity 3"
};
FILE *out;
real tmp,dt;
int status,isize;
atom_id *index;
char *grpname;
real maxang,Jc,S2,norm_fac,maxstat;
unsigned long mode;
int nframes,maxangstat,mult,*angstat;
int i,j,total,nangles,natoms,nat2,first,last,angind;
bool bAver,bRb,bPeriodic,
bFrac, /* calculate fraction too? */
bTrans, /* worry about transtions too? */
bCorr; /* correlation function ? */
real t,aa,aver,aver2,aversig,fraction; /* fraction trans dihedrals */
double tfrac=0;
char title[256];
real **dih=NULL; /* mega array with all dih. angles at all times*/
char buf[80];
real *time,*trans_frac,*aver_angle;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efNDX, NULL, "angle", ffREAD },
{ efXVG, "-od", "angdist", ffWRITE },
{ efXVG, "-ov", "angaver", ffOPTWR },
{ efXVG, "-of", "dihfrac", ffOPTWR },
{ efXVG, "-ot", "dihtrans", ffOPTWR },
{ efXVG, "-oh", "trhisto", ffOPTWR },
{ efXVG, "-oc", "dihcorr", ffOPTWR },
{ efTRR, "-or", NULL, ffOPTWR }
};
#define NFILE asize(fnm)
int npargs;
t_pargs *ppa;
CopyRight(stderr,argv[0]);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs,pa);
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,npargs,ppa,asize(desc),desc,asize(bugs),bugs);
mult = 4;
maxang = 360.0;
bRb = FALSE;
switch(opt[0][0]) {
case 'a':
mult = 3;
maxang = 180.0;
break;
case 'd':
break;
case 'i':
break;
case 'r':
bRb = TRUE;
break;
}
if (opt2bSet("-or",NFILE,fnm)) {
if (mult != 4)
gmx_fatal(FARGS,"Can not combine angles with trn dump");
else
please_cite(stdout,"Mu2005a");
}
/* Calculate bin size */
maxangstat=(int)(maxang/binwidth+0.5);
binwidth=maxang/maxangstat;
rd_index(ftp2fn(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
nangles=isize/mult;
if ((isize % mult) != 0)
gmx_fatal(FARGS,"number of index elements not multiple of %d, "
"these can not be %s\n",
mult,(mult==3) ? "angle triplets" : "dihedral quadruplets");
/* Check whether specific analysis has to be performed */
bCorr=opt2bSet("-oc",NFILE,fnm);
bAver=opt2bSet("-ov",NFILE,fnm);
bTrans=opt2bSet("-ot",NFILE,fnm);
bFrac=opt2bSet("-of",NFILE,fnm);
if (bChandler && !bCorr)
bCorr=TRUE;
if (bFrac && !bRb) {
fprintf(stderr,"Warning:"
" calculating fractions as defined in this program\n"
"makes sense for Ryckaert Bellemans dihs. only. Ignoring -of\n\n");
bFrac = FALSE;
}
if ( (bTrans || bFrac || bCorr) && mult==3)
gmx_fatal(FARGS,"Can only do transition, fraction or correlation\n"
"on dihedrals. Select -d\n");
/*
* We need to know the nr of frames so we can allocate memory for an array
* with all dihedral angles at all timesteps. Works for me.
*/
if (bTrans || bCorr || bALL || opt2bSet("-or",NFILE,fnm))
snew(dih,nangles);
snew(angstat,maxangstat);
read_ang_dih(ftp2fn(efTRX,NFILE,fnm),(mult == 3),
bALL || bCorr || bTrans || opt2bSet("-or",NFILE,fnm),
bRb,bPBC,maxangstat,angstat,
&nframes,&time,isize,index,&trans_frac,&aver_angle,dih);
dt=(time[nframes-1]-time[0])/(nframes-1);
if (bAver) {
sprintf(title,"Average Angle: %s",grpname);
out=xvgropen(opt2fn("-ov",NFILE,fnm),
title,"Time (ps)","Angle (degrees)");
for(i=0; (i<nframes); i++) {
fprintf(out,"%10.5f %8.3f",time[i],aver_angle[i]*RAD2DEG);
if (bALL) {
for(j=0; (j<nangles); j++)
if (bPBC) {
real dd = dih[j][i];
fprintf(out," %8.3f",atan2(sin(dd),cos(dd))*RAD2DEG);
}
else
fprintf(out," %8.3f",dih[j][i]*RAD2DEG);
}
fprintf(out,"\n");
}
fclose(out);
}
if (opt2bSet("-or",NFILE,fnm))
dump_dih_trn(nframes,nangles,dih,opt2fn("-or",NFILE,fnm),dt);
if (bFrac) {
sprintf(title,"Trans fraction: %s",grpname);
out=xvgropen(opt2fn("-of",NFILE,fnm),
title,"Time (ps)","Fraction");
tfrac = 0.0;
for(i=0; (i<nframes); i++) {
fprintf(out,"%10.5f %10.3f\n",time[i],trans_frac[i]);
tfrac += trans_frac[i];
}
fclose(out);
tfrac/=nframes;
fprintf(stderr,"Average trans fraction: %g\n",tfrac);
}
sfree(trans_frac);
if (bTrans)
ana_dih_trans(opt2fn("-ot",NFILE,fnm),opt2fn("-oh",NFILE,fnm),
dih,nframes,nangles,grpname,time[0],dt,bRb);
if (bCorr) {
/* Autocorrelation function */
if (nframes < 2)
fprintf(stderr,"Not enough frames for correlation function\n");
else {
if (bChandler) {
real dval,sixty=DEG2RAD*60;
bool bTest;
for(i=0; (i<nangles); i++)
for(j=0; (j<nframes); j++) {
dval = dih[i][j];
if (bRb)
bTest=(dval > -sixty) && (dval < sixty);
else
bTest=(dval < -sixty) || (dval > sixty);
if (bTest)
dih[i][j] = dval-tfrac;
else
dih[i][j] = -tfrac;
}
}
if (bChandler)
mode = eacNormal;
else
mode = eacCos;
do_autocorr(opt2fn("-oc",NFILE,fnm),"Dihedral Autocorrelation Function",
nframes,nangles,dih,dt,mode,bAverCorr);
}
}
/* Determine the non-zero part of the distribution */
for(first=0; (first < maxangstat-1) && (angstat[first+1] == 0); first++)
;
for(last=maxangstat-1; (last > 0) && (angstat[last-1] == 0) ; last--)
;
aver=aver2=0;
for(i=0; (i<nframes); i++) {
aver += RAD2DEG*aver_angle[i];
aver2 += sqr(RAD2DEG*aver_angle[i]);
}
aver /= (real) nframes;
aver2 /= (real) nframes;
aversig = sqrt(aver2-sqr(aver));
printf("Found points in the range from %d to %d (max %d)\n",
first,last,maxangstat);
printf(" < angle > = %g\n",aver);
printf("< angle^2 > = %g\n",aver2);
printf("Std. Dev. = %g\n",aversig);
if (mult == 3)
sprintf(title,"Angle Distribution: %s",grpname);
else {
sprintf(title,"Dihedral Distribution: %s",grpname);
calc_distribution_props(maxangstat,angstat,-180.0,0,NULL,&S2);
fprintf(stderr,"Order parameter S^2 = %g\n",S2);
}
bPeriodic=(mult==4) && (first==0) && (last==maxangstat-1);
out=xvgropen(opt2fn("-od",NFILE,fnm),title,"Degrees","");
if (bPrintXvgrCodes())
fprintf(out,"@ subtitle \"average angle: %g\\So\\N\"\n",aver);
norm_fac=1.0/(nangles*nframes*binwidth);
if (bPeriodic) {
maxstat=0;
for(i=first; (i<=last); i++)
maxstat=max(maxstat,angstat[i]*norm_fac);
fprintf(out,"@with g0\n");
fprintf(out,"@ world xmin -180\n");
fprintf(out,"@ world xmax 180\n");
fprintf(out,"@ world ymin 0\n");
fprintf(out,"@ world ymax %g\n",maxstat*1.05);
fprintf(out,"@ xaxis tick major 60\n");
fprintf(out,"@ xaxis tick minor 30\n");
fprintf(out,"@ yaxis tick major 0.005\n");
fprintf(out,"@ yaxis tick minor 0.0025\n");
}
for(i=first; (i<=last); i++)
fprintf(out,"%10g %10f\n",i*binwidth+180.0-maxang,angstat[i]*norm_fac);
if ( bPeriodic )
/* print first bin again as last one */
fprintf(out,"%10g %10f\n",180.0,angstat[0]*norm_fac);
fclose(out);
do_view(opt2fn("-od",NFILE,fnm),"-nxy");
if (bAver)
do_view(opt2fn("-ov",NFILE,fnm),"-nxy");
thanx(stderr);
return 0;
}
int gmx_bundle(int argc,char *argv[])
{
static char *desc[] = {
"g_bundle analyzes bundles of axes. The axes can be for instance",
"helix axes. The program reads two index groups and divides both",
"of them in [TT]-na[tt] parts. The centers of mass of these parts",
"define the tops and bottoms of the axes.",
"Several quantities are written to file:",
"the axis length, the distance and the z-shift of the axis mid-points",
"with respect to the average center of all axes, the total tilt,",
"the radial tilt and the lateral tilt with respect to the average axis.",
"[PAR]",
"With options [TT]-ok[tt], [TT]-okr[tt] and [TT]-okl[tt] the total,",
"radial and lateral kinks of the axes are plotted. An extra index",
"group of kink atoms is required, which is also divided into [TT]-na[tt]",
"parts. The kink angle is defined as the angle between the kink-top and",
"the bottom-kink vectors.",
"[PAR]",
"With option [TT]-oa[tt] the top, mid (or kink when [TT]-ok[tt] is set)",
"and bottom points of each axis",
"are written to a pdb file each frame. The residue numbers correspond",
"to the axis numbers. When viewing this file with [TT]rasmol[tt], use the",
"command line option [TT]-nmrpdb[tt], and type [TT]set axis true[tt] to",
"display the reference axis."
};
static int n=0;
static bool bZ=FALSE;
t_pargs pa[] = {
{ "-na", FALSE, etINT, {&n},
"Number of axes" },
{ "-z", FALSE, etBOOL, {&bZ},
"Use the Z-axis as reference iso the average axis" }
};
FILE *out,*flen,*fdist,*fz,*ftilt,*ftiltr,*ftiltl;
FILE *fkink=NULL,*fkinkr=NULL,*fkinkl=NULL;
int status,fpdb;
t_topology top;
int ePBC;
rvec *xtop;
matrix box;
t_trxframe fr;
t_atoms outatoms;
real t,comp;
int natoms;
char *grpname[MAX_ENDS],title[256],*anm="CA",*rnm="GLY";
int i,j,gnx[MAX_ENDS];
atom_id *index[MAX_ENDS];
t_bundle bun;
bool bKink;
rvec va,vb,vc,vr,vl;
#define NLEG asize(leg)
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, "-ol", "bun_len", ffWRITE },
{ efXVG, "-od", "bun_dist", ffWRITE },
{ efXVG, "-oz", "bun_z", ffWRITE },
{ efXVG, "-ot", "bun_tilt", ffWRITE },
{ efXVG, "-otr", "bun_tiltr", ffWRITE },
{ efXVG, "-otl", "bun_tiltl", ffWRITE },
{ efXVG, "-ok", "bun_kink", ffOPTWR },
{ efXVG, "-okr", "bun_kinkr", ffOPTWR },
{ efXVG, "-okl", "bun_kinkl", ffOPTWR },
{ efPDB, "-oa", "axes", ffOPTWR }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xtop,NULL,box,TRUE);
bKink = opt2bSet("-ok",NFILE,fnm) || opt2bSet("-okr",NFILE,fnm)
|| opt2bSet("-okl",NFILE,fnm);
if (bKink)
bun.nend = 3;
else
bun.nend = 2;
fprintf(stderr,"Select a group of top and a group of bottom ");
if (bKink)
fprintf(stderr,"and a group of kink ");
fprintf(stderr,"atoms\n");
get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),bun.nend,
gnx,index,grpname);
if (n<=0 || gnx[0] % n || gnx[1] % n || (bKink && gnx[2] % n))
gmx_fatal(FARGS,
"The size of one of your index groups is not a multiple of n");
bun.n = n;
snew(bun.end[0],n);
snew(bun.end[1],n);
if (bKink)
snew(bun.end[2],n);
snew(bun.mid,n);
snew(bun.dir,n);
snew(bun.len,n);
flen = xvgropen(opt2fn("-ol",NFILE,fnm),"Axis lengths",
xvgr_tlabel(),"(nm)");
fdist = xvgropen(opt2fn("-od",NFILE,fnm),"Distance of axis centers",
xvgr_tlabel(),"(nm)");
fz = xvgropen(opt2fn("-oz",NFILE,fnm),"Z-shift of axis centers",
xvgr_tlabel(),"(nm)");
ftilt = xvgropen(opt2fn("-ot",NFILE,fnm),"Axis tilts",
xvgr_tlabel(),"(degrees)");
ftiltr = xvgropen(opt2fn("-otr",NFILE,fnm),"Radial axis tilts",
xvgr_tlabel(),"(degrees)");
ftiltl = xvgropen(opt2fn("-otl",NFILE,fnm),"Lateral axis tilts",
xvgr_tlabel(),"(degrees)");
if (bKink) {
fkink = xvgropen(opt2fn("-ok",NFILE,fnm),"Kink angles",
xvgr_tlabel(),"(degrees)");
fkinkr = xvgropen(opt2fn("-okr",NFILE,fnm),"Radial kink angles",
xvgr_tlabel(),"(degrees)");
if (bPrintXvgrCodes())
fprintf(fkinkr,"@ subtitle \"+ = ) ( - = ( )\"\n");
fkinkl = xvgropen(opt2fn("-okl",NFILE,fnm),"Lateral kink angles",
xvgr_tlabel(),"(degrees)");
}
if (opt2bSet("-oa",NFILE,fnm)) {
init_t_atoms(&outatoms,3*n,FALSE);
outatoms.nr = 3*n;
for(i=0; i<3*n; i++) {
outatoms.atomname[i] = &anm;
outatoms.atom[i].resnr = i/3;
outatoms.resname[i/3] = &rnm;
}
fpdb = open_trx(opt2fn("-oa",NFILE,fnm),"w");
} else
fpdb = -1;
read_first_frame(&status,ftp2fn(efTRX,NFILE,fnm),&fr,TRX_NEED_X);
do {
rm_pbc(&top.idef,ePBC,fr.natoms,fr.box,fr.x,fr.x);
calc_axes(fr.x,top.atoms.atom,gnx,index,!bZ,&bun);
t = convert_time(fr.time);
fprintf(flen," %10g",t);
fprintf(fdist," %10g",t);
fprintf(fz," %10g",t);
fprintf(ftilt," %10g",t);
fprintf(ftiltr," %10g",t);
fprintf(ftiltl," %10g",t);
if (bKink) {
fprintf(fkink," %10g",t);
fprintf(fkinkr," %10g",t);
fprintf(fkinkl," %10g",t);
}
for(i=0; i<bun.n; i++) {
fprintf(flen," %6g",bun.len[i]);
fprintf(fdist," %6g",norm(bun.mid[i]));
fprintf(fz," %6g",bun.mid[i][ZZ]);
fprintf(ftilt," %6g",RAD2DEG*acos(bun.dir[i][ZZ]));
comp = bun.mid[i][XX]*bun.dir[i][XX]+bun.mid[i][YY]*bun.dir[i][YY];
fprintf(ftiltr," %6g",RAD2DEG*
asin(comp/sqrt(sqr(comp)+sqr(bun.dir[i][ZZ]))));
comp = bun.mid[i][YY]*bun.dir[i][XX]-bun.mid[i][XX]*bun.dir[i][YY];
fprintf(ftiltl," %6g",RAD2DEG*
asin(comp/sqrt(sqr(comp)+sqr(bun.dir[i][ZZ]))));
if (bKink) {
rvec_sub(bun.end[0][i],bun.end[2][i],va);
rvec_sub(bun.end[2][i],bun.end[1][i],vb);
unitv_no_table(va,va);
unitv_no_table(vb,vb);
fprintf(fkink," %6g",RAD2DEG*acos(iprod(va,vb)));
cprod(va,vb,vc);
copy_rvec(bun.mid[i],vr);
vr[ZZ] = 0;
unitv_no_table(vr,vr);
fprintf(fkinkr," %6g",RAD2DEG*asin(iprod(vc,vr)));
vl[XX] = vr[YY];
vl[YY] = -vr[XX];
vl[ZZ] = 0;
fprintf(fkinkl," %6g",RAD2DEG*asin(iprod(vc,vl)));
}
}
fprintf(flen,"\n");
fprintf(fdist,"\n");
fprintf(fz,"\n");
fprintf(ftilt,"\n");
fprintf(ftiltr,"\n");
fprintf(ftiltl,"\n");
if (bKink) {
fprintf(fkink,"\n");
fprintf(fkinkr,"\n");
fprintf(fkinkl,"\n");
}
if (fpdb >= 0)
dump_axes(fpdb,&fr,&outatoms,&bun);
} while(read_next_frame(status,&fr));
close_trx(status);
if (fpdb >= 0)
close_trx(fpdb);
fclose(flen);
fclose(fdist);
fclose(fz);
fclose(ftilt);
fclose(ftiltr);
fclose(ftiltl);
if (bKink) {
fclose(fkink);
fclose(fkinkr);
fclose(fkinkl);
}
thanx(stderr);
return 0;
}
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);
}
int gmx_gyrate(int argc,char *argv[])
{
const char *desc[] = {
"g_gyrate computes the radius of gyration of a group of atoms",
"and the radii of gyration about the x, y and z axes,",
"as a function of time. The atoms are explicitly mass weighted.[PAR]",
"With the [TT]-nmol[tt] option the radius of gyration will be calculated",
"for multiple molecules by splitting the analysis group in equally",
"sized parts.[PAR]",
"With the option [TT]-nz[tt] 2D radii of gyration in the x-y plane",
"of slices along the z-axis are calculated."
};
static int nmol=1,nz=0;
static bool bQ=FALSE,bRot=FALSE,bMOI=FALSE;
t_pargs pa[] = {
{ "-nmol", FALSE, etINT, {&nmol},
"The number of molecules to analyze" },
{ "-q", FALSE, etBOOL, {&bQ},
"Use absolute value of the charge of an atom as weighting factor instead of mass" },
{ "-p", FALSE, etBOOL, {&bRot},
"Calculate the radii of gyration about the principal axes." },
{ "-moi", FALSE, etBOOL, {&bMOI},
"Calculate the moments of inertia (defined by the principal axes)." },
{ "-nz", FALSE, etINT, {&nz},
"Calculate the 2D radii of gyration of # slices along the z-axis" },
};
FILE *out;
int status;
t_topology top;
int ePBC;
rvec *x,*x_s;
rvec xcm,gvec,gvec1;
matrix box,trans;
bool bACF;
real **moi_trans=NULL;
int max_moi=0,delta_moi=100;
rvec d,d1; /* eigenvalues of inertia tensor */
real t,t0,tm,gyro;
int natoms;
char *grpname,title[256];
int i,j,m,gnx,nam,mol;
atom_id *index;
char *leg[] = { "Rg", "RgX", "RgY", "RgZ" };
char *legI[] = { "Itot", "I1", "I2", "I3" };
#define NLEG asize(leg)
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, NULL, "gyrate", ffWRITE },
{ efXVG, "-acf", "moi-acf", ffOPTWR },
};
#define NFILE asize(fnm)
int npargs;
t_pargs *ppa;
CopyRight(stderr,argv[0]);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs,pa);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
NFILE,fnm,npargs,ppa,asize(desc),desc,0,NULL);
bACF = opt2bSet("-acf",NFILE,fnm);
if (bACF && nmol!=1)
gmx_fatal(FARGS,"Can only do acf with nmol=1");
bRot = bRot || bMOI || bACF;
/*
if (nz > 0)
bMOI = TRUE;
*/
if (bRot) {
printf("Will rotate system along principal axes\n");
snew(moi_trans,DIM);
}
if (bMOI) {
printf("Will print moments of inertia\n");
bQ = FALSE;
}
if (bQ)
printf("Will print radius normalised by charge\n");
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&x,NULL,box,TRUE);
get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),1,&gnx,&index,&grpname);
if (nmol > gnx || gnx % nmol != 0) {
gmx_fatal(FARGS,"The number of atoms in the group (%d) is not a multiple of nmol (%d)",gnx,nmol);
}
nam = gnx/nmol;
natoms=read_first_x(&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
snew(x_s,natoms);
j = 0;
t0 = t;
if (bQ)
out=xvgropen(ftp2fn(efXVG,NFILE,fnm),
"Radius of Charge","Time (ps)","Rg (nm)");
else if (bMOI)
out=xvgropen(ftp2fn(efXVG,NFILE,fnm),
"Moments of inertia","Time (ps)","I (a.m.u. nm\\S2\\N)");
else
out=xvgropen(ftp2fn(efXVG,NFILE,fnm),
"Radius of gyration","Time (ps)","Rg (nm)");
if (bMOI)
xvgr_legend(out,NLEG,legI);
else {
if (bRot)
if (bPrintXvgrCodes())
fprintf(out,"@ subtitle \"Axes are principal component axes\"\n");
xvgr_legend(out,NLEG,leg);
}
do {
if (nz == 0)
rm_pbc(&top.idef,ePBC,natoms,box,x,x_s);
gyro = 0;
clear_rvec(gvec);
clear_rvec(d);
for(mol=0; mol<nmol; mol++) {
tm = sub_xcm(nz==0?x_s:x,nam,index+mol*nam,top.atoms.atom,xcm,bQ);
if (nz == 0)
gyro += calc_gyro(x_s,nam,index+mol*nam,top.atoms.atom,
tm,gvec1,d1,bQ,bRot,bMOI,trans);
else
calc_gyro_z(x,box,nam,index+mol*nam,top.atoms.atom,nz,t,out);
rvec_inc(gvec,gvec1);
rvec_inc(d,d1);
}
if (nmol > 0) {
gyro /= nmol;
svmul(1.0/nmol,gvec,gvec);
svmul(1.0/nmol,d,d);
}
if (nz == 0) {
if (bRot) {
if (j >= max_moi) {
max_moi += delta_moi;
for(m=0; (m<DIM); m++)
srenew(moi_trans[m],max_moi*DIM);
}
for(m=0; (m<DIM); m++)
copy_rvec(trans[m],moi_trans[m]+DIM*j);
fprintf(out,"%10g %10g %10g %10g %10g\n",
t,gyro,d[XX],d[YY],d[ZZ]); }
else {
fprintf(out,"%10g %10g %10g %10g %10g\n",
t,gyro,gvec[XX],gvec[YY],gvec[ZZ]); }
}
j++;
} while(read_next_x(status,&t,natoms,x,box));
close_trj(status);
fclose(out);
if (bACF) {
int mode = eacVector;
do_autocorr(opt2fn("-acf",NFILE,fnm),
"Moment of inertia vector ACF",
j,3,moi_trans,(t-t0)/j,mode,FALSE);
do_view(opt2fn("-acf",NFILE,fnm),"-nxy");
}
do_view(ftp2fn(efXVG,NFILE,fnm),"-nxy");
thanx(stderr);
return 0;
}
void xvgr_view(FILE *out,real xmin,real ymin,real xmax,real ymax)
{
if (bPrintXvgrCodes())
fprintf(out,"@ view %g, %g, %g, %g\n",xmin,ymin,xmax,ymax);
}
void xvgr_subtitle(FILE *out,char *subtitle)
{
if (bPrintXvgrCodes())
fprintf(out,"@ subtitle \"%s\"\n",subtitle);
}
int gmx_sorient(int argc,char *argv[])
{
t_topology top;
int ePBC;
char title[STRLEN];
int status;
int natoms;
real t;
rvec *xtop,*x;
matrix box;
FILE *fp;
int i,j,p,sa0,sa1,sa2,n,ntot,nf,m,*hist1,*hist2,*histn,nbin1,nbin2,nrbin;
real *histi1,*histi2,invbw,invrbw;
double sum1,sum2;
int *isize,nrefgrp,nrefat;
atom_id **index;
char **grpname;
real inp,outp,two_pi,nav,normfac,rmin2,rmax2,rcut,rcut2,r2,r,mass,mtot;
real c1,c2;
char str[STRLEN];
bool bTPS;
rvec xref,dx,dxh1,dxh2,outer;
t_pbc pbc;
char *legr[] = { "<cos(\\8q\\4\\s1\\N)>",
"<3cos\\S2\\N(\\8q\\4\\s2\\N)-1>" };
char *legc[] = { "cos(\\8q\\4\\s1\\N)",
"3cos\\S2\\N(\\8q\\4\\s2\\N)-1" };
static char *desc[] = {
"g_sorient analyzes solvent orientation around solutes.",
"It calculates two angles between the vector from one or more",
"reference positions to the first atom of each solvent molecule:[BR]"
"theta1: the angle with the vector from the first atom of the solvent",
"molecule to the midpoint between atoms 2 and 3.[BR]",
"theta2: the angle with the normal of the solvent plane, defined by the",
"same three atoms, or when the option [TT]-v23[tt] is set",
"the angle with the vector between atoms 2 and 3.[BR]",
"The reference can be a set of atoms or",
"the center of mass of a set of atoms. The group of solvent atoms should",
"consist of 3 atoms per solvent molecule.",
"Only solvent molecules between [TT]-rmin[tt] and [TT]-rmax[tt] are",
"considered for [TT]-o[tt] and [TT]-no[tt] each frame.[PAR]",
"[TT]-o[tt]: distribtion of cos(theta1) for rmin<=r<=rmax.[PAR]",
"[TT]-no[tt]: distribution of cos(theta2) for rmin<=r<=rmax.[PAR]",
"[TT]-ro[tt]: <cos(theta1)> and <3cos^2(theta2)-1> as a function of the",
"distance.[PAR]",
"[TT]-co[tt]: the sum over all solvent molecules within distance r",
"of cos(theta1) and 3cos^2(theta2)-1 as a function of r.[PAR]",
"[TT]-rc[tt]: the distribution of the solvent molecules as a function of r"
};
static bool bCom = FALSE,bVec23=FALSE,bPBC = FALSE;
static real rmin=0.0,rmax=0.5,binwidth=0.02,rbinw=0.02;
t_pargs pa[] = {
{ "-com", FALSE, etBOOL, {&bCom},
"Use the center of mass as the reference postion" },
{ "-v23", FALSE, etBOOL, {&bVec23},
"Use the vector between atoms 2 and 3" },
{ "-rmin", FALSE, etREAL, {&rmin}, "Minimum distance (nm)" },
{ "-rmax", FALSE, etREAL, {&rmax}, "Maximum distance (nm)" },
{ "-cbin", FALSE, etREAL, {&binwidth}, "Binwidth for the cosine" },
{ "-rbin", FALSE, etREAL, {&rbinw}, "Binwidth for r (nm)" },
{ "-pbc", FALSE, etBOOL, {&bPBC}, "Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules." }
};
t_filenm fnm[] = {
{ efTRX, NULL, NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, NULL, "sori.xvg", ffWRITE },
{ efXVG, "-no", "snor.xvg", ffWRITE },
{ efXVG, "-ro", "sord.xvg", ffWRITE },
{ efXVG, "-co", "scum.xvg", ffWRITE },
{ efXVG, "-rc", "scount.xvg", ffWRITE }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
two_pi = 2/M_PI;
bTPS = (opt2bSet("-s",NFILE,fnm) || !opt2bSet("-n",NFILE,fnm) || bCom);
if (bTPS) {
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&xtop,NULL,box,
bCom);
}
/* get index groups */
printf("Select a group of reference particles and a solvent group:\n");
snew(grpname,2);
snew(index,2);
snew(isize,2);
if (bTPS) {
get_index(&top.atoms,ftp2fn_null(efNDX,NFILE,fnm),2,isize,index,grpname);
} else {
get_index(NULL,ftp2fn(efNDX,NFILE,fnm),2,isize,index,grpname);
}
if (bCom) {
nrefgrp = 1;
nrefat = isize[0];
} else {
nrefgrp = isize[0];
nrefat = 1;
}
if (isize[1] % 3)
gmx_fatal(FARGS,"The number of solvent atoms (%d) is not a multiple of 3",
isize[1]);
/* initialize reading trajectory: */
natoms=read_first_x(&status,ftp2fn(efTRX,NFILE,fnm),&t,&x,box);
rmin2 = sqr(rmin);
rmax2 = sqr(rmax);
rcut = 0.99*sqrt(max_cutoff2(guess_ePBC(box),box));
if (rcut == 0)
rcut = 10*rmax;
rcut2 = sqr(rcut);
invbw = 1/binwidth;
nbin1 = (int)(2*invbw + 0.5);
nbin2 = (int)(invbw + 0.5);
invrbw = 1/rbinw;
snew(hist1,nbin1+1);
snew(hist2,nbin2+1);
nrbin = rcut/rbinw;
if (nrbin == 0)
nrbin = 1;
snew(histi1,nrbin);
snew(histi2,nrbin);
snew(histn,nrbin);
ntot = 0;
nf = 0;
sum1 = 0;
sum2 = 0;
/* start analysis of trajectory */
do {
if (bTPS) {
/* make molecules whole again */
rm_pbc(&top.idef,ePBC,natoms,box,x,x);
}
set_pbc(&pbc,ePBC,box);
n = 0;
inp = 0;
outp = 0;
for(p=0; (p<nrefgrp); p++) {
if (bCom)
calc_com_pbc(nrefat,&top,x,&pbc,index[0],xref,bPBC,box);
else
copy_rvec(x[index[0][p]],xref);
for(m=0; m<isize[1]; m+=3) {
sa0 = index[1][m];
sa1 = index[1][m+1];
sa2 = index[1][m+2];
pbc_dx(&pbc,x[sa0],xref,dx);
r2 = norm2(dx);
if (r2 < rcut2) {
r = sqrt(r2);
if (!bVec23) {
/* Determine the normal to the plain */
rvec_sub(x[sa1],x[sa0],dxh1);
rvec_sub(x[sa2],x[sa0],dxh2);
rvec_inc(dxh1,dxh2);
svmul(1/r,dx,dx);
unitv(dxh1,dxh1);
inp = iprod(dx,dxh1);
cprod(dxh1,dxh2,outer);
unitv(outer,outer);
outp = iprod(dx,outer);
} else {
/* Use the vector between the 2nd and 3rd atom */
rvec_sub(x[sa2],x[sa1],dxh2);
unitv(dxh2,dxh2);
outp = iprod(dx,dxh2)/r;
}
(histi1[(int)(invrbw*r)]) += inp;
(histi2[(int)(invrbw*r)]) += 3*sqr(outp) - 1;
(histn[(int)(invrbw*r)])++;
if (r2>=rmin2 && r2<rmax2) {
(hist1[(int)(invbw*(inp + 1))])++;
(hist2[(int)(invbw*fabs(outp))])++;
sum1 += inp;
sum2 += outp;
n++;
}
}
}
}
ntot += n;
nf++;
} while (read_next_x(status,&t,natoms,x,box));
/* clean up */
sfree(x);
close_trj(status);
/* Add the bin for the exact maximum to the previous bin */
hist1[nbin1-1] += hist1[nbin1];
hist2[nbin2-1] += hist2[nbin2];
nav = (real)ntot/(nrefgrp*nf);
normfac = invbw/ntot;
fprintf(stderr, "Average nr of molecules between %g and %g nm: %.1f\n",
rmin,rmax,nav);
if (ntot > 0) {
sum1 /= ntot;
sum2 /= ntot;
fprintf(stderr,"Average cos(theta1) between %g and %g nm: %6.3f\n",
rmin,rmax,sum1);
fprintf(stderr,"Average 3cos2(theta2)-1 between %g and %g nm: %6.3f\n",
rmin,rmax,sum2);
}
sprintf(str,"Solvent orientation between %g and %g nm",rmin,rmax);
fp=xvgropen(opt2fn("-o",NFILE,fnm),
str,"cos(\\8q\\4\\s1\\N)","");
if (bPrintXvgrCodes())
fprintf(fp,"@ subtitle \"average shell size %.1f molecules\"\n",nav);
for(i=0; i<nbin1; i++) {
fprintf(fp,"%g %g\n",(i+0.5)*binwidth-1,2*normfac*hist1[i]);
}
fclose(fp);
sprintf(str,"Solvent normal orientation between %g and %g nm",rmin,rmax);
fp=xvgropen(opt2fn("-no",NFILE,fnm),
str,"cos(\\8q\\4\\s2\\N)","");
if (bPrintXvgrCodes())
fprintf(fp,"@ subtitle \"average shell size %.1f molecules\"\n",nav);
for(i=0; i<nbin2; i++) {
fprintf(fp,"%g %g\n",(i+0.5)*binwidth,normfac*hist2[i]);
}
fclose(fp);
sprintf(str,"Solvent orientation");
fp=xvgropen(opt2fn("-ro",NFILE,fnm),str,"r (nm)","");
if (bPrintXvgrCodes())
fprintf(fp,"@ subtitle \"as a function of distance\"\n");
xvgr_legend(fp,2,legr);
for(i=0; i<nrbin; i++)
fprintf(fp,"%g %g %g\n",(i+0.5)*rbinw,
histn[i] ? histi1[i]/histn[i] : 0,
histn[i] ? histi2[i]/histn[i] : 0);
fclose(fp);
sprintf(str,"Cumulative solvent orientation");
fp=xvgropen(opt2fn("-co",NFILE,fnm),str,"r (nm)","");
if (bPrintXvgrCodes())
fprintf(fp,"@ subtitle \"as a function of distance\"\n");
xvgr_legend(fp,2,legc);
normfac = 1.0/(nrefgrp*nf);
c1 = 0;
c2 = 0;
fprintf(fp,"%g %g %g\n",0.0,c1,c2);
for(i=0; i<nrbin; i++) {
c1 += histi1[i]*normfac;
c2 += histi2[i]*normfac;
fprintf(fp,"%g %g %g\n",(i+1)*rbinw,c1,c2);
}
fclose(fp);
sprintf(str,"Solvent distribution");
fp=xvgropen(opt2fn("-rc",NFILE,fnm),str,"r (nm)","molecules/nm");
if (bPrintXvgrCodes())
fprintf(fp,"@ subtitle \"as a function of distance\"\n");
normfac = 1.0/(rbinw*nf);
for(i=0; i<nrbin; i++) {
fprintf(fp,"%g %g\n",(i+0.5)*rbinw,histn[i]*normfac);
}
fclose(fp);
do_view(opt2fn("-o",NFILE,fnm),NULL);
do_view(opt2fn("-no",NFILE,fnm),NULL);
do_view(opt2fn("-ro",NFILE,fnm),"-nxy");
do_view(opt2fn("-co",NFILE,fnm),"-nxy");
thanx(stderr);
return 0;
}
int gmx_nmeig(int argc,char *argv[])
{
const char *desc[] = {
"g_nmeig calculates the eigenvectors/values of a (Hessian) matrix,",
"which can be calculated with [TT]mdrun[tt].",
"The eigenvectors are written to a trajectory file ([TT]-v[tt]).",
"The structure is written first with t=0. The eigenvectors",
"are written as frames with the eigenvector number as timestamp.",
"The eigenvectors can be analyzed with [TT]g_anaeig[tt].",
"An ensemble of structures can be generated from the eigenvectors with",
"[TT]g_nmens[tt]. When mass weighting is used, the generated eigenvectors",
"will be scaled back to plain cartesian coordinates before generating the",
"output - in this case they will no longer be exactly orthogonal in the",
"standard cartesian norm (But in the mass weighted norm they would be)."
};
static bool bM=TRUE;
static int begin=1,end=50;
t_pargs pa[] =
{
{ "-m", FALSE, etBOOL, {&bM},
"Divide elements of Hessian by product of sqrt(mass) of involved "
"atoms prior to diagonalization. This should be used for 'Normal Modes' "
"analysis" },
{ "-first", FALSE, etINT, {&begin},
"First eigenvector to write away" },
{ "-last", FALSE, etINT, {&end},
"Last eigenvector to write away" }
};
FILE *out;
int status,trjout;
t_topology top;
int ePBC;
rvec *top_x;
matrix box;
real *eigenvalues;
real *eigenvectors;
real rdum,mass_fac;
int natoms,ndim,nrow,ncol,count;
char *grpname,title[256];
int i,j,k,l,d,gnx;
bool bSuck;
atom_id *index;
real value;
real factor_gmx_to_omega2;
real factor_omega_to_wavenumber;
t_commrec *cr;
real * full_hessian = NULL;
gmx_sparsematrix_t * sparse_hessian = NULL;
t_filenm fnm[] = {
{ efMTX, "-f", "hessian", ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efXVG, "-of", "eigenfreq", ffWRITE },
{ efXVG, "-ol", "eigenval", ffWRITE },
{ efTRN, "-v", "eigenvec", ffWRITE }
};
#define NFILE asize(fnm)
cr = init_par(&argc,&argv);
if(MASTER(cr))
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_BE_NICE | (MASTER(cr) ? 0 : PCA_QUIET),
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&ePBC,&top_x,NULL,box,bM);
natoms = top.atoms.nr;
ndim = DIM*natoms;
if(begin<1)
begin = 1;
if(end>ndim)
end = ndim;
/*open Hessian matrix */
gmx_mtxio_read(ftp2fn(efMTX,NFILE,fnm),&nrow,&ncol,&full_hessian,&sparse_hessian);
/* Memory for eigenvalues and eigenvectors (begin..end) */
snew(eigenvalues,nrow);
snew(eigenvectors,nrow*(end-begin+1));
/* If the Hessian is in sparse format we can calculate max (ndim-1) eigenvectors,
* and they must start at the first one. If this is not valid we convert to full matrix
* storage, but warn the user that we might run out of memory...
*/
if((sparse_hessian != NULL) && (begin!=1 || end==ndim))
{
if(begin!=1)
{
fprintf(stderr,"Cannot use sparse Hessian with first eigenvector != 1.\n");
}
else if(end==ndim)
{
fprintf(stderr,"Cannot use sparse Hessian to calculate all eigenvectors.\n");
}
fprintf(stderr,"Will try to allocate memory and convert to full matrix representation...\n");
snew(full_hessian,nrow*ncol);
for(i=0;i<nrow*ncol;i++)
full_hessian[i] = 0;
for(i=0;i<sparse_hessian->nrow;i++)
{
for(j=0;j<sparse_hessian->ndata[i];j++)
{
k = sparse_hessian->data[i][j].col;
value = sparse_hessian->data[i][j].value;
full_hessian[i*ndim+k] = value;
full_hessian[k*ndim+i] = value;
}
}
gmx_sparsematrix_destroy(sparse_hessian);
sparse_hessian = NULL;
fprintf(stderr,"Converted sparse to full matrix storage.\n");
}
if(full_hessian != NULL)
{
/* Using full matrix storage */
nma_full_hessian(full_hessian,nrow,bM,&top,begin,end,eigenvalues,eigenvectors);
}
else
{
/* Sparse memory storage, allocate memory for eigenvectors */
snew(eigenvectors,ncol*end);
nma_sparse_hessian(sparse_hessian,bM,&top,end,eigenvalues,eigenvectors);
}
/* check the output, first 6 eigenvalues should be reasonably small */
bSuck=FALSE;
for (i=begin-1; (i<6); i++)
{
if (fabs(eigenvalues[i]) > 1.0e-3)
bSuck=TRUE;
}
if (bSuck)
{
fprintf(stderr,"\nOne of the lowest 6 eigenvalues has a non-zero value.\n");
fprintf(stderr,"This could mean that the reference structure was not\n");
fprintf(stderr,"properly energy minimized.\n");
}
/* now write the output */
fprintf (stderr,"Writing eigenvalues...\n");
out=xvgropen(opt2fn("-ol",NFILE,fnm),
"Eigenvalues","Eigenvalue index","Eigenvalue [Gromacs units]");
if (bPrintXvgrCodes()) {
if (bM)
fprintf(out,"@ subtitle \"mass weighted\"\n");
else
fprintf(out,"@ subtitle \"not mass weighted\"\n");
}
for (i=0; i<=(end-begin); i++)
fprintf (out,"%6d %15g\n",begin+i,eigenvalues[i]);
fclose(out);
fprintf(stderr,"Writing eigenfrequencies - negative eigenvalues will be set to zero.\n");
out=xvgropen(opt2fn("-of",NFILE,fnm),
"Eigenfrequencies","Eigenvector index","Wavenumber [cm\\S-1\\N]");
if (bPrintXvgrCodes()) {
if (bM)
fprintf(out,"@ subtitle \"mass weighted\"\n");
else
fprintf(out,"@ subtitle \"not mass weighted\"\n");
}
/* Gromacs units are kJ/(mol*nm*nm*amu),
* where amu is the atomic mass unit.
*
* For the eigenfrequencies we want to convert this to spectroscopic absorption
* wavenumbers given in cm^(-1), which is the frequency divided by the speed of
* light. Do this by first converting to omega^2 (units 1/s), take the square
* root, and finally divide by the speed of light (nm/ps in gromacs).
*/
factor_gmx_to_omega2 = 1.0E21/(AVOGADRO*AMU);
factor_omega_to_wavenumber = 1.0E-5/(2.0*M_PI*SPEED_OF_LIGHT);
for (i=0; i<=(end-begin); i++)
{
value = eigenvalues[i];
if(value < 0)
value = 0;
value=sqrt(value*factor_gmx_to_omega2)*factor_omega_to_wavenumber;
fprintf (out,"%6d %15g\n",begin+i,value);
}
fclose(out);
/* Writing eigenvectors. Note that if mass scaling was used, the eigenvectors
* were scaled back from mass weighted cartesian to plain cartesian in the
* nma_full_hessian() or nma_sparse_hessian() routines. Mass scaled vectors
* will not be strictly orthogonal in plain cartesian scalar products.
*/
write_eigenvectors(opt2fn("-v",NFILE,fnm),natoms,eigenvectors,FALSE,begin,end,
eWXR_NO,NULL,FALSE,top_x,bM,eigenvalues);
thanx(stderr);
return 0;
}
