void do_autocorr(const char *fn,const output_env_t oenv,const char *title,
int nframes,int nitem,real **c1,
real dt,unsigned long mode,gmx_bool bAver)
{
if (!bACFinit) {
printf("ACF data structures have not been initialised. Call add_acf_pargs\n");
}
/* Handle enumerated types */
sscanf(Leg[0],"%d",&acf.P);
acf.fitfn = sffn2effn(s_ffn);
switch (acf.P) {
case 1:
mode = mode | eacP1;
break;
case 2:
mode = mode | eacP2;
break;
case 3:
mode = mode | eacP3;
break;
default:
break;
}
low_do_autocorr(fn,oenv,title,nframes,nitem,acf.nout,c1,dt,mode,
acf.nrestart,bAver,acf.bNormalize,
bDebugMode(),acf.tbeginfit,acf.tendfit,
acf.fitfn,acf.nskip);
}
static void process_tcaf(int nframes, real dt, int nkc, real **tc, rvec *kfac,
real rho, real wt, const char *fn_trans,
const char *fn_tca, const char *fn_tc,
const char *fn_tcf, const char *fn_cub,
const char *fn_vk, const gmx_output_env_t *oenv)
{
FILE *fp, *fp_vk, *fp_cub = NULL;
int nk, ntc;
real **tcaf, **tcafc = NULL, eta, *sig;
int i, j, k, kc;
int ncorr;
double fitparms[3];
nk = kset_c[nkc];
ntc = nk*NPK;
if (fn_trans)
{
fp = xvgropen(fn_trans, "Transverse Current", "Time (ps)", "TC (nm/ps)",
oenv);
for (i = 0; i < nframes; i++)
{
fprintf(fp, "%g", i*dt);
for (j = 0; j < ntc; j++)
{
fprintf(fp, " %g", tc[j][i]);
}
fprintf(fp, "\n");
}
xvgrclose(fp);
do_view(oenv, fn_trans, "-nxy");
}
ncorr = (nframes+1)/2;
if (ncorr > static_cast<int>(5*wt/dt+0.5))
{
ncorr = static_cast<int>(5*wt/dt+0.5)+1;
}
snew(tcaf, nk);
for (k = 0; k < nk; k++)
{
snew(tcaf[k], ncorr);
}
if (fn_cub)
{
snew(tcafc, nkc);
for (k = 0; k < nkc; k++)
{
snew(tcafc[k], ncorr);
}
}
snew(sig, ncorr);
for (i = 0; i < ncorr; i++)
{
sig[i] = std::exp(0.5*i*dt/wt);
}
low_do_autocorr(fn_tca, oenv, "Transverse Current Autocorrelation Functions",
nframes, ntc, ncorr, tc, dt, eacNormal,
1, FALSE, FALSE, FALSE, 0, 0, 0);
do_view(oenv, fn_tca, "-nxy");
fp = xvgropen(fn_tc, "Transverse Current Autocorrelation Functions",
"Time (ps)", "TCAF", oenv);
for (i = 0; i < ncorr; i++)
{
kc = 0;
fprintf(fp, "%g", i*dt);
for (k = 0; k < nk; k++)
{
for (j = 0; j < NPK; j++)
{
tcaf[k][i] += tc[NPK*k+j][i];
}
if (fn_cub)
{
for (j = 0; j < NPK; j++)
{
tcafc[kc][i] += tc[NPK*k+j][i];
}
}
if (i == 0)
{
fprintf(fp, " %g", 1.0);
}
else
{
tcaf[k][i] /= tcaf[k][0];
fprintf(fp, " %g", tcaf[k][i]);
}
if (k+1 == kset_c[kc+1])
{
kc++;
}
}
fprintf(fp, "\n");
}
xvgrclose(fp);
do_view(oenv, fn_tc, "-nxy");
if (fn_cub)
{
fp_cub = xvgropen(fn_cub, "TCAFs and fits", "Time (ps)", "TCAF", oenv);
for (kc = 0; kc < nkc; kc++)
{
fprintf(fp_cub, "%g %g\n", 0.0, 1.0);
for (i = 1; i < ncorr; i++)
{
tcafc[kc][i] /= tcafc[kc][0];
fprintf(fp_cub, "%g %g\n", i*dt, tcafc[kc][i]);
}
fprintf(fp_cub, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
tcafc[kc][0] = 1.0;
}
}
fp_vk = xvgropen(fn_vk, "Fits", "k (nm\\S-1\\N)",
"\\8h\\4 (10\\S-3\\N kg m\\S-1\\N s\\S-1\\N)", oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp_vk, "@ s0 symbol 2\n");
fprintf(fp_vk, "@ s0 symbol color 1\n");
fprintf(fp_vk, "@ s0 linestyle 0\n");
if (fn_cub)
{
fprintf(fp_vk, "@ s1 symbol 3\n");
fprintf(fp_vk, "@ s1 symbol color 2\n");
}
}
fp = xvgropen(fn_tcf, "TCAF Fits", "Time (ps)", "", oenv);
for (k = 0; k < nk; k++)
{
tcaf[k][0] = 1.0;
fitparms[0] = 1;
fitparms[1] = 1;
do_lmfit(ncorr, tcaf[k], sig, dt, 0, 0, ncorr*dt,
oenv, bDebugMode(), effnVAC, fitparms, 0, NULL);
eta = 1000*fitparms[1]*rho/
(4*fitparms[0]*PICO*norm2(kfac[k])/(NANO*NANO));
fprintf(stdout, "k %6.3f tau %6.3f eta %8.5f 10^-3 kg/(m s)\n",
norm(kfac[k]), fitparms[0], eta);
fprintf(fp_vk, "%6.3f %g\n", norm(kfac[k]), eta);
for (i = 0; i < ncorr; i++)
{
fprintf(fp, "%g %g\n", i*dt, fit_function(effnVAC, fitparms, i*dt));
}
fprintf(fp, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
xvgrclose(fp);
do_view(oenv, fn_tcf, "-nxy");
if (fn_cub)
{
fprintf(stdout, "Averaged over k-vectors:\n");
fprintf(fp_vk, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
for (k = 0; k < nkc; k++)
{
tcafc[k][0] = 1.0;
fitparms[0] = 1;
fitparms[1] = 1;
do_lmfit(ncorr, tcafc[k], sig, dt, 0, 0, ncorr*dt,
oenv, bDebugMode(), effnVAC, fitparms, 0, NULL);
eta = 1000*fitparms[1]*rho/
(4*fitparms[0]*PICO*norm2(kfac[kset_c[k]])/(NANO*NANO));
fprintf(stdout,
"k %6.3f tau %6.3f Omega %6.3f eta %8.5f 10^-3 kg/(m s)\n",
norm(kfac[kset_c[k]]), fitparms[0], fitparms[1], eta);
fprintf(fp_vk, "%6.3f %g\n", norm(kfac[kset_c[k]]), eta);
for (i = 0; i < ncorr; i++)
{
fprintf(fp_cub, "%g %g\n", i*dt, fit_function(effnVAC, fitparms, i*dt));
}
fprintf(fp_cub, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
}
fprintf(fp_vk, "%s\n", output_env_get_print_xvgr_codes(oenv) ? "&" : "");
xvgrclose(fp_cub);
do_view(oenv, fn_cub, "-nxy");
}
xvgrclose(fp_vk);
do_view(oenv, fn_vk, "-nxy");
}
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_dos(int argc, char *argv[])
{
const char *desc[] = {
"[TT]g_dos[tt] computes the Density of States from a simulations.",
"In order for this to be meaningful the velocities must be saved",
"in the trajecotry with sufficiently high frequency such as to cover",
"all vibrations. For flexible systems that would be around a few fs",
"between saving. Properties based on the DoS are printed on the",
"standard output."
};
const char *bugs[] = {
"This program needs a lot of memory: total usage equals the number of atoms times 3 times number of frames times 4 (or 8 when run in double precision)."
};
FILE *fp, *fplog;
t_topology top;
int ePBC = -1;
t_trxframe fr;
matrix box;
int gnx;
char title[256];
real t0, t1, m;
t_trxstatus *status;
int nV, nframes, n_alloc, i, j, k, l, fftcode, Nmol, Natom;
double rho, dt, V2sum, Vsum, V, tmass, dostot, dos2, dosabs;
real **c1, **dos, mi, beta, bfac, *nu, *tt, stddev, c1j;
output_env_t oenv;
gmx_fft_t fft;
double cP, S, A, E, DiffCoeff, Delta, f, y, z, sigHS, Shs, Sig, DoS0, recip_fac;
double wCdiff, wSdiff, wAdiff, wEdiff;
static gmx_bool bVerbose = TRUE, bAbsolute = FALSE, bNormalize = FALSE;
static gmx_bool bRecip = FALSE, bDump = FALSE;
static real Temp = 298.15, toler = 1e-6;
t_pargs pa[] = {
{ "-v", FALSE, etBOOL, {&bVerbose},
"Be loud and noisy." },
{ "-recip", FALSE, etBOOL, {&bRecip},
"Use cm^-1 on X-axis instead of 1/ps for DoS plots." },
{ "-abs", FALSE, etBOOL, {&bAbsolute},
"Use the absolute value of the Fourier transform of the VACF as the Density of States. Default is to use the real component only" },
{ "-normdos", FALSE, etBOOL, {&bNormalize},
"Normalize the DoS such that it adds up to 3N. This is a hack that should not be necessary." },
{ "-T", FALSE, etREAL, {&Temp},
"Temperature in the simulation" },
{ "-toler", FALSE, etREAL, {&toler},
"[HIDDEN]Tolerance when computing the fluidicity using bisection algorithm" },
{ "-dump", FALSE, etBOOL, {&bDump},
"[HIDDEN]Dump the y/fy plot corresponding to Fig. 2 inLin2003a and the and the weighting functions corresponding to Fig. 1 in Berens1983a." }
};
t_filenm fnm[] = {
{ efTRN, "-f", NULL, ffREAD },
{ efTPX, "-s", NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, "-vacf", "vacf", ffWRITE },
{ efXVG, "-mvacf", "mvacf", ffWRITE },
{ efXVG, "-dos", "dos", ffWRITE },
{ efLOG, "-g", "dos", ffWRITE },
};
#define NFILE asize(fnm)
int npargs;
t_pargs *ppa;
const char *DoSlegend[] = {
"DoS(v)", "DoS(v)[Solid]", "DoS(v)[Diff]"
};
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, &oenv);
beta = 1/(Temp*BOLTZ);
if (bDump)
{
printf("Dumping reference figures. Thanks for your patience.\n");
dump_fy(oenv, toler);
dump_w(oenv, beta);
exit(0);
}
fplog = gmx_fio_fopen(ftp2fn(efLOG, NFILE, fnm), "w");
fprintf(fplog, "Doing density of states analysis based on trajectory.\n");
please_cite(fplog, "Pascal2011a");
please_cite(fplog, "Caleman2011b");
read_tps_conf(ftp2fn(efTPX, NFILE, fnm), title, &top, &ePBC, NULL, NULL, box,
TRUE);
V = det(box);
tmass = 0;
for (i = 0; (i < top.atoms.nr); i++)
{
tmass += top.atoms.atom[i].m;
}
Natom = top.atoms.nr;
Nmol = top.mols.nr;
gnx = Natom*DIM;
/* Correlation stuff */
snew(c1, gnx);
for (i = 0; (i < gnx); i++)
{
c1[i] = NULL;
}
read_first_frame(oenv, &status, ftp2fn(efTRN, NFILE, fnm), &fr, TRX_NEED_V);
t0 = fr.time;
n_alloc = 0;
nframes = 0;
Vsum = V2sum = 0;
nV = 0;
do
{
if (fr.bBox)
{
V = det(fr.box);
V2sum += V*V;
Vsum += V;
nV++;
}
if (nframes >= n_alloc)
{
n_alloc += 100;
for (i = 0; i < gnx; i++)
{
srenew(c1[i], n_alloc);
}
}
for (i = 0; i < gnx; i += DIM)
{
c1[i+XX][nframes] = fr.v[i/DIM][XX];
c1[i+YY][nframes] = fr.v[i/DIM][YY];
c1[i+ZZ][nframes] = fr.v[i/DIM][ZZ];
}
t1 = fr.time;
nframes++;
}
while (read_next_frame(oenv, status, &fr));
close_trj(status);
dt = (t1-t0)/(nframes-1);
if (nV > 0)
{
V = Vsum/nV;
}
if (bVerbose)
{
printf("Going to do %d fourier transforms of length %d. Hang on.\n",
gnx, nframes);
}
low_do_autocorr(NULL, oenv, NULL, nframes, gnx, nframes, c1, dt, eacNormal, 0, FALSE,
FALSE, FALSE, -1, -1, 0, 0);
snew(dos, DOS_NR);
for (j = 0; (j < DOS_NR); j++)
{
snew(dos[j], nframes+4);
}
if (bVerbose)
{
printf("Going to merge the ACFs into the mass-weighted and plain ACF\n");
}
for (i = 0; (i < gnx); i += DIM)
{
mi = top.atoms.atom[i/DIM].m;
for (j = 0; (j < nframes/2); j++)
{
c1j = (c1[i+XX][j] + c1[i+YY][j] + c1[i+ZZ][j]);
dos[VACF][j] += c1j/Natom;
dos[MVACF][j] += mi*c1j;
}
}
fp = xvgropen(opt2fn("-vacf", NFILE, fnm), "Velocity ACF",
"Time (ps)", "C(t)", oenv);
snew(tt, nframes/2);
for (j = 0; (j < nframes/2); j++)
{
tt[j] = j*dt;
fprintf(fp, "%10g %10g\n", tt[j], dos[VACF][j]);
}
xvgrclose(fp);
fp = xvgropen(opt2fn("-mvacf", NFILE, fnm), "Mass-weighted velocity ACF",
"Time (ps)", "C(t)", oenv);
for (j = 0; (j < nframes/2); j++)
{
fprintf(fp, "%10g %10g\n", tt[j], dos[MVACF][j]);
}
xvgrclose(fp);
if ((fftcode = gmx_fft_init_1d_real(&fft, nframes/2,
GMX_FFT_FLAG_NONE)) != 0)
{
gmx_fatal(FARGS, "gmx_fft_init_1d_real returned %d", fftcode);
}
if ((fftcode = gmx_fft_1d_real(fft, GMX_FFT_REAL_TO_COMPLEX,
(void *)dos[MVACF], (void *)dos[DOS])) != 0)
{
gmx_fatal(FARGS, "gmx_fft_1d_real returned %d", fftcode);
}
/* First compute the DoS */
/* Magic factor of 8 included now. */
bfac = 8*dt*beta/2;
dos2 = 0;
snew(nu, nframes/4);
for (j = 0; (j < nframes/4); j++)
{
nu[j] = 2*j/(t1-t0);
dos2 += sqr(dos[DOS][2*j]) + sqr(dos[DOS][2*j+1]);
if (bAbsolute)
{
dos[DOS][j] = bfac*sqrt(sqr(dos[DOS][2*j]) + sqr(dos[DOS][2*j+1]));
}
else
{
dos[DOS][j] = bfac*dos[DOS][2*j];
}
}
/* Normalize it */
dostot = evaluate_integral(nframes/4, nu, dos[DOS], NULL, nframes/4, &stddev);
if (bNormalize)
{
for (j = 0; (j < nframes/4); j++)
{
dos[DOS][j] *= 3*Natom/dostot;
}
}
/* Now analyze it */
DoS0 = dos[DOS][0];
/* Note this eqn. is incorrect in Pascal2011a! */
Delta = ((2*DoS0/(9*Natom))*sqrt(M_PI*BOLTZ*Temp*Natom/tmass)*
pow((Natom/V), 1.0/3.0)*pow(6/M_PI, 2.0/3.0));
f = calc_fluidicity(Delta, toler);
y = calc_y(f, Delta, toler);
z = calc_compress(y);
Sig = BOLTZ*(5.0/2.0+log(2*M_PI*BOLTZ*Temp/(sqr(PLANCK))*V/(f*Natom)));
Shs = Sig+calc_Shs(f, y);
rho = (tmass*AMU)/(V*NANO*NANO*NANO);
sigHS = pow(6*y*V/(M_PI*Natom), 1.0/3.0);
fprintf(fplog, "System = \"%s\"\n", title);
fprintf(fplog, "Nmol = %d\n", Nmol);
fprintf(fplog, "Natom = %d\n", Natom);
fprintf(fplog, "dt = %g ps\n", dt);
fprintf(fplog, "tmass = %g amu\n", tmass);
fprintf(fplog, "V = %g nm^3\n", V);
fprintf(fplog, "rho = %g g/l\n", rho);
fprintf(fplog, "T = %g K\n", Temp);
fprintf(fplog, "beta = %g mol/kJ\n", beta);
fprintf(fplog, "\nDoS parameters\n");
fprintf(fplog, "Delta = %g\n", Delta);
fprintf(fplog, "fluidicity = %g\n", f);
fprintf(fplog, "hard sphere packing fraction = %g\n", y);
fprintf(fplog, "hard sphere compressibility = %g\n", z);
fprintf(fplog, "ideal gas entropy = %g\n", Sig);
fprintf(fplog, "hard sphere entropy = %g\n", Shs);
fprintf(fplog, "sigma_HS = %g nm\n", sigHS);
fprintf(fplog, "DoS0 = %g\n", DoS0);
fprintf(fplog, "Dos2 = %g\n", dos2);
fprintf(fplog, "DoSTot = %g\n", dostot);
/* Now compute solid (2) and diffusive (3) components */
fp = xvgropen(opt2fn("-dos", NFILE, fnm), "Density of states",
bRecip ? "E (cm\\S-1\\N)" : "\\f{12}n\\f{4} (1/ps)",
"\\f{4}S(\\f{12}n\\f{4})", oenv);
xvgr_legend(fp, asize(DoSlegend), DoSlegend, oenv);
recip_fac = bRecip ? (1e7/SPEED_OF_LIGHT) : 1.0;
for (j = 0; (j < nframes/4); j++)
{
dos[DOS_DIFF][j] = DoS0/(1+sqr(DoS0*M_PI*nu[j]/(6*f*Natom)));
dos[DOS_SOLID][j] = dos[DOS][j]-dos[DOS_DIFF][j];
fprintf(fp, "%10g %10g %10g %10g\n",
recip_fac*nu[j],
dos[DOS][j]/recip_fac,
dos[DOS_SOLID][j]/recip_fac,
dos[DOS_DIFF][j]/recip_fac);
}
xvgrclose(fp);
/* Finally analyze the results! */
wCdiff = 0.5;
wSdiff = Shs/(3*BOLTZ); /* Is this correct? */
wEdiff = 0.5;
wAdiff = wEdiff-wSdiff;
for (j = 0; (j < nframes/4); j++)
{
dos[DOS_CP][j] = (dos[DOS_DIFF][j]*wCdiff +
dos[DOS_SOLID][j]*wCsolid(nu[j], beta));
dos[DOS_S][j] = (dos[DOS_DIFF][j]*wSdiff +
dos[DOS_SOLID][j]*wSsolid(nu[j], beta));
dos[DOS_A][j] = (dos[DOS_DIFF][j]*wAdiff +
dos[DOS_SOLID][j]*wAsolid(nu[j], beta));
dos[DOS_E][j] = (dos[DOS_DIFF][j]*wEdiff +
dos[DOS_SOLID][j]*wEsolid(nu[j], beta));
}
DiffCoeff = evaluate_integral(nframes/2, tt, dos[VACF], NULL, nframes/2, &stddev);
DiffCoeff = 1000*DiffCoeff/3.0;
fprintf(fplog, "Diffusion coefficient from VACF %g 10^-5 cm^2/s\n",
DiffCoeff);
fprintf(fplog, "Diffusion coefficient from DoS %g 10^-5 cm^2/s\n",
1000*DoS0/(12*tmass*beta));
cP = BOLTZ * evaluate_integral(nframes/4, nu, dos[DOS_CP], NULL,
nframes/4, &stddev);
fprintf(fplog, "Heat capacity %g J/mol K\n", 1000*cP/Nmol);
/*
S = BOLTZ * evaluate_integral(nframes/4,nu,dos[DOS_S],NULL,
nframes/4,&stddev);
fprintf(fplog,"Entropy %g J/mol K\n",1000*S/Nmol);
A = BOLTZ * evaluate_integral(nframes/4,nu,dos[DOS_A],NULL,
nframes/4,&stddev);
fprintf(fplog,"Helmholtz energy %g kJ/mol\n",A/Nmol);
E = BOLTZ * evaluate_integral(nframes/4,nu,dos[DOS_E],NULL,
nframes/4,&stddev);
fprintf(fplog,"Internal energy %g kJ/mol\n",E/Nmol);
*/
fprintf(fplog, "\nArrivederci!\n");
gmx_fio_fclose(fplog);
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
thanx(stderr);
return 0;
}
int gmx_dos(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] computes the Density of States from a simulations.",
"In order for this to be meaningful the velocities must be saved",
"in the trajecotry with sufficiently high frequency such as to cover",
"all vibrations. For flexible systems that would be around a few fs",
"between saving. Properties based on the DoS are printed on the",
"standard output."
"Note that the density of states is calculated from the mass-weighted",
"autocorrelation, and by default only from the square of the real",
"component rather than absolute value. This means the shape can differ",
"substantially from the plain vibrational power spectrum you can",
"calculate with gmx velacc."
};
const char *bugs[] = {
"This program needs a lot of memory: total usage equals the number of atoms times 3 times number of frames times 4 (or 8 when run in double precision)."
};
FILE *fp, *fplog;
t_topology top;
int ePBC = -1;
t_trxframe fr;
matrix box;
int gnx;
real t0, t1;
t_trxstatus *status;
int nV, nframes, n_alloc, i, j, fftcode, Nmol, Natom;
double rho, dt, Vsum, V, tmass, dostot, dos2;
real **c1, **dos, mi, beta, bfac, *nu, *tt, stddev, c1j;
gmx_output_env_t *oenv;
gmx_fft_t fft;
double cP, DiffCoeff, Delta, f, y, z, sigHS, Shs, Sig, DoS0, recip_fac;
double wCdiff, wSdiff, wAdiff, wEdiff;
int grpNatoms;
int *index;
char *grpname;
double invNormalize;
gmx_bool normalizeAutocorrelation;
static gmx_bool bVerbose = TRUE, bAbsolute = FALSE, bNormalizeDos = FALSE;
static gmx_bool bRecip = FALSE;
static real Temp = 298.15, toler = 1e-6;
t_pargs pa[] = {
{ "-v", FALSE, etBOOL, {&bVerbose},
"Be loud and noisy."
},
{ "-recip", FALSE, etBOOL, {&bRecip},
"Use cm^-1 on X-axis instead of 1/ps for DoS plots."
},
{ "-abs", FALSE, etBOOL, {&bAbsolute},
"Use the absolute value of the Fourier transform of the VACF as the Density of States. Default is to use the real component only"
},
{ "-normdos", FALSE, etBOOL, {&bNormalizeDos},
"Normalize the DoS such that it adds up to 3N. This should usually not be necessary."
},
{ "-T", FALSE, etREAL, {&Temp},
"Temperature in the simulation"
},
{ "-toler", FALSE, etREAL, {&toler},
"[HIDDEN]Tolerance when computing the fluidicity using bisection algorithm"
}
};
t_filenm fnm[] = {
{ efTRN, "-f", NULL, ffREAD },
{ efTPR, "-s", NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, "-vacf", "vacf", ffWRITE },
{ efXVG, "-mvacf", "mvacf", ffWRITE },
{ efXVG, "-dos", "dos", ffWRITE },
{ efLOG, "-g", "dos", ffWRITE },
};
#define NFILE asize(fnm)
int npargs;
t_pargs *ppa;
const char *DoSlegend[] = {
"DoS(v)", "DoS(v)[Solid]", "DoS(v)[Diff]"
};
npargs = asize(pa);
ppa = add_acf_pargs(&npargs, pa);
if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
NFILE, fnm, npargs, ppa, asize(desc), desc,
asize(bugs), bugs, &oenv))
{
return 0;
}
beta = 1/(Temp*BOLTZ);
fplog = gmx_fio_fopen(ftp2fn(efLOG, NFILE, fnm), "w");
fprintf(fplog, "Doing density of states analysis based on trajectory.\n");
please_cite(fplog, "Pascal2011a");
please_cite(fplog, "Caleman2011b");
read_tps_conf(ftp2fn(efTPR, NFILE, fnm), &top, &ePBC, NULL, NULL, box, TRUE);
/* Handle index groups */
get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &grpNatoms, &index, &grpname);
V = det(box);
tmass = 0;
for (i = 0; i < grpNatoms; i++)
{
tmass += top.atoms.atom[index[i]].m;
}
Natom = grpNatoms;
Nmol = calcMoleculesInIndexGroup(&top.mols, top.atoms.nr, index, grpNatoms);
gnx = Natom*DIM;
/* Correlation stuff */
snew(c1, gnx);
for (i = 0; (i < gnx); i++)
{
c1[i] = NULL;
}
read_first_frame(oenv, &status, ftp2fn(efTRN, NFILE, fnm), &fr, TRX_NEED_V);
t0 = fr.time;
n_alloc = 0;
nframes = 0;
Vsum = 0;
nV = 0;
do
{
if (fr.bBox)
{
V = det(fr.box);
Vsum += V;
nV++;
}
if (nframes >= n_alloc)
{
n_alloc += 100;
for (i = 0; i < gnx; i++)
{
srenew(c1[i], n_alloc);
}
}
for (i = 0; i < gnx; i += DIM)
{
c1[i+XX][nframes] = fr.v[index[i/DIM]][XX];
c1[i+YY][nframes] = fr.v[index[i/DIM]][YY];
c1[i+ZZ][nframes] = fr.v[index[i/DIM]][ZZ];
}
t1 = fr.time;
nframes++;
}
while (read_next_frame(oenv, status, &fr));
close_trj(status);
dt = (t1-t0)/(nframes-1);
if (nV > 0)
{
V = Vsum/nV;
}
if (bVerbose)
{
printf("Going to do %d fourier transforms of length %d. Hang on.\n",
gnx, nframes);
}
/* Unfortunately the -normalize program option for the autocorrelation
* function calculation is added as a hack with a static variable in the
* autocorrelation.c source. That would work if we called the normal
* do_autocorr(), but this routine overrides that by directly calling
* the low-level functionality. That unfortunately leads to ignoring the
* default value for the option (which is to normalize).
* Since the absolute value seems to be important for the subsequent
* analysis below, we detect the value directly from the option, calculate
* the autocorrelation without normalization, and then apply the
* normalization just to the autocorrelation output
* (or not, if the user asked for a non-normalized autocorrelation).
*/
normalizeAutocorrelation = opt2parg_bool("-normalize", npargs, ppa);
/* Note that we always disable normalization here, regardless of user settings */
low_do_autocorr(NULL, oenv, NULL, nframes, gnx, nframes, c1, dt, eacNormal, 0, FALSE,
FALSE, FALSE, -1, -1, 0);
snew(dos, DOS_NR);
for (j = 0; (j < DOS_NR); j++)
{
snew(dos[j], nframes+4);
}
if (bVerbose)
{
printf("Going to merge the ACFs into the mass-weighted and plain ACF\n");
}
for (i = 0; (i < gnx); i += DIM)
{
mi = top.atoms.atom[index[i/DIM]].m;
for (j = 0; (j < nframes/2); j++)
{
c1j = (c1[i+XX][j] + c1[i+YY][j] + c1[i+ZZ][j]);
dos[VACF][j] += c1j/Natom;
dos[MVACF][j] += mi*c1j;
}
}
fp = xvgropen(opt2fn("-vacf", NFILE, fnm), "Velocity autocorrelation function",
"Time (ps)", "C(t)", oenv);
snew(tt, nframes/2);
invNormalize = normalizeAutocorrelation ? 1.0/dos[VACF][0] : 1.0;
for (j = 0; (j < nframes/2); j++)
{
tt[j] = j*dt;
fprintf(fp, "%10g %10g\n", tt[j], dos[VACF][j] * invNormalize);
}
xvgrclose(fp);
fp = xvgropen(opt2fn("-mvacf", NFILE, fnm), "Mass-weighted velocity autocorrelation function",
"Time (ps)", "C(t)", oenv);
invNormalize = normalizeAutocorrelation ? 1.0/dos[VACF][0] : 1.0;
for (j = 0; (j < nframes/2); j++)
{
fprintf(fp, "%10g %10g\n", tt[j], dos[MVACF][j] * invNormalize);
}
xvgrclose(fp);
if ((fftcode = gmx_fft_init_1d_real(&fft, nframes/2,
GMX_FFT_FLAG_NONE)) != 0)
{
gmx_fatal(FARGS, "gmx_fft_init_1d_real returned %d", fftcode);
}
if ((fftcode = gmx_fft_1d_real(fft, GMX_FFT_REAL_TO_COMPLEX,
(void *)dos[MVACF], (void *)dos[DOS])) != 0)
{
gmx_fatal(FARGS, "gmx_fft_1d_real returned %d", fftcode);
}
/* First compute the DoS */
/* Magic factor of 8 included now. */
bfac = 8*dt*beta/2;
dos2 = 0;
snew(nu, nframes/4);
for (j = 0; (j < nframes/4); j++)
{
nu[j] = 2*j/(t1-t0);
dos2 += gmx::square(dos[DOS][2*j]) + gmx::square(dos[DOS][2*j+1]);
if (bAbsolute)
{
dos[DOS][j] = bfac*std::hypot(dos[DOS][2*j], dos[DOS][2*j+1]);
}
else
{
dos[DOS][j] = bfac*dos[DOS][2*j];
}
}
/* Normalize it */
dostot = evaluate_integral(nframes/4, nu, dos[DOS], NULL, nframes/4, &stddev);
if (bNormalizeDos)
{
for (j = 0; (j < nframes/4); j++)
{
dos[DOS][j] *= 3*Natom/dostot;
}
}
/* Now analyze it */
DoS0 = dos[DOS][0];
/* Note this eqn. is incorrect in Pascal2011a! */
Delta = ((2*DoS0/(9*Natom))*std::sqrt(M_PI*BOLTZ*Temp*Natom/tmass)*
std::pow((Natom/V), 1.0/3.0)*std::pow(6.0/M_PI, 2.0/3.0));
f = calc_fluidicity(Delta, toler);
y = calc_y(f, Delta, toler);
z = calc_compress(y);
Sig = BOLTZ*(5.0/2.0+std::log(2*M_PI*BOLTZ*Temp/(gmx::square(PLANCK))*V/(f*Natom)));
Shs = Sig+calc_Shs(f, y);
rho = (tmass*AMU)/(V*NANO*NANO*NANO);
sigHS = std::cbrt(6*y*V/(M_PI*Natom));
fprintf(fplog, "System = \"%s\"\n", *top.name);
fprintf(fplog, "Nmol = %d\n", Nmol);
fprintf(fplog, "Natom = %d\n", Natom);
fprintf(fplog, "dt = %g ps\n", dt);
fprintf(fplog, "tmass = %g amu\n", tmass);
fprintf(fplog, "V = %g nm^3\n", V);
fprintf(fplog, "rho = %g g/l\n", rho);
fprintf(fplog, "T = %g K\n", Temp);
fprintf(fplog, "beta = %g mol/kJ\n", beta);
fprintf(fplog, "\nDoS parameters\n");
fprintf(fplog, "Delta = %g\n", Delta);
fprintf(fplog, "fluidicity = %g\n", f);
fprintf(fplog, "hard sphere packing fraction = %g\n", y);
fprintf(fplog, "hard sphere compressibility = %g\n", z);
fprintf(fplog, "ideal gas entropy = %g\n", Sig);
fprintf(fplog, "hard sphere entropy = %g\n", Shs);
fprintf(fplog, "sigma_HS = %g nm\n", sigHS);
fprintf(fplog, "DoS0 = %g\n", DoS0);
fprintf(fplog, "Dos2 = %g\n", dos2);
fprintf(fplog, "DoSTot = %g\n", dostot);
/* Now compute solid (2) and diffusive (3) components */
fp = xvgropen(opt2fn("-dos", NFILE, fnm), "Density of states",
bRecip ? "E (cm\\S-1\\N)" : "\\f{12}n\\f{4} (1/ps)",
"\\f{4}S(\\f{12}n\\f{4})", oenv);
xvgr_legend(fp, asize(DoSlegend), DoSlegend, oenv);
recip_fac = bRecip ? (1e7/SPEED_OF_LIGHT) : 1.0;
for (j = 0; (j < nframes/4); j++)
{
dos[DOS_DIFF][j] = DoS0/(1+gmx::square(DoS0*M_PI*nu[j]/(6*f*Natom)));
dos[DOS_SOLID][j] = dos[DOS][j]-dos[DOS_DIFF][j];
fprintf(fp, "%10g %10g %10g %10g\n",
recip_fac*nu[j],
dos[DOS][j]/recip_fac,
dos[DOS_SOLID][j]/recip_fac,
dos[DOS_DIFF][j]/recip_fac);
}
xvgrclose(fp);
/* Finally analyze the results! */
wCdiff = 0.5;
wSdiff = Shs/(3*BOLTZ); /* Is this correct? */
wEdiff = 0.5;
wAdiff = wEdiff-wSdiff;
for (j = 0; (j < nframes/4); j++)
{
dos[DOS_CP][j] = (dos[DOS_DIFF][j]*wCdiff +
dos[DOS_SOLID][j]*wCsolid(nu[j], beta));
dos[DOS_S][j] = (dos[DOS_DIFF][j]*wSdiff +
dos[DOS_SOLID][j]*wSsolid(nu[j], beta));
dos[DOS_A][j] = (dos[DOS_DIFF][j]*wAdiff +
dos[DOS_SOLID][j]*wAsolid(nu[j], beta));
dos[DOS_E][j] = (dos[DOS_DIFF][j]*wEdiff +
dos[DOS_SOLID][j]*wEsolid(nu[j], beta));
}
DiffCoeff = evaluate_integral(nframes/2, tt, dos[VACF], NULL, nframes/2, &stddev);
DiffCoeff = 1000*DiffCoeff/3.0;
fprintf(fplog, "Diffusion coefficient from VACF %g 10^-5 cm^2/s\n",
DiffCoeff);
fprintf(fplog, "Diffusion coefficient from DoS %g 10^-5 cm^2/s\n",
1000*DoS0/(12*tmass*beta));
cP = BOLTZ * evaluate_integral(nframes/4, nu, dos[DOS_CP], NULL,
nframes/4, &stddev);
fprintf(fplog, "Heat capacity %g J/mol K\n", 1000*cP/Nmol);
fprintf(fplog, "\nArrivederci!\n");
gmx_fio_fclose(fplog);
do_view(oenv, ftp2fn(efXVG, NFILE, fnm), "-nxy");
return 0;
}