/*double btaunu_(double *deltam)
*/
double btaunu_(void)
{
double rtau,mBu,mHp,xHp;
struct read_param_tag param;
double eps_b=0, eps_bp=0, eps_tps=0;
if(read_prm(¶m))
{
puts("btaunu: can not read parameters.");
return 0.0;
}
/* dump_prm(¶m);
*/
mHp=param.Mhc;
mBu=5.279;
xHp=mBu*mBu/mHp/mHp;
/*Large tan beta */
/* Calculates the eps_b eps_b' ..*/
calc_eps(¶m, &eps_b, &eps_bp, &eps_tps);
rtau=(1-xHp*param.tb*param.tb/(1+eps_b*param.tb))*(1-xHp*param.tb*param.tb/(1+eps_b*param.tb));
return rtau;
}
static void do_dip(t_topology *top,int ePBC,real volume,
const char *fn,
const char *out_mtot,const char *out_eps,
const char *out_aver, const char *dipdist,
const char *cosaver, const char *fndip3d,
const char *fnadip, gmx_bool bPairs,
const char *corrtype,const char *corf,
gmx_bool bGkr, const char *gkrfn,
gmx_bool bPhi, int *nlevels, int ndegrees,
int ncos,
const char *cmap, real rcmax,
gmx_bool bQuad, const char *quadfn,
gmx_bool bMU, const char *mufn,
int *gnx, int *molindex[],
real mu_max, real mu_aver,
real epsilonRF,real temp,
int *gkatom, int skip,
gmx_bool bSlab, int nslices,
const char *axtitle, const char *slabfn,
const output_env_t oenv)
{
const char *leg_mtot[] = {
"M\\sx \\N",
"M\\sy \\N",
"M\\sz \\N",
"|M\\stot \\N|"
};
#define NLEGMTOT asize(leg_mtot)
const char *leg_eps[] = {
"epsilon",
"G\\sk",
"g\\sk"
};
#define NLEGEPS asize(leg_eps)
const char *leg_aver[] = {
"< |M|\\S2\\N >",
"< |M| >\\S2\\N",
"< |M|\\S2\\N > - < |M| >\\S2\\N",
"< |M| >\\S2\\N / < |M|\\S2\\N >"
};
#define NLEGAVER asize(leg_aver)
const char *leg_cosaver[] = {
"\\f{4}<|cos\\f{12}q\\f{4}\\sij\\N|>",
"RMSD cos",
"\\f{4}<|cos\\f{12}q\\f{4}\\siX\\N|>",
"\\f{4}<|cos\\f{12}q\\f{4}\\siY\\N|>",
"\\f{4}<|cos\\f{12}q\\f{4}\\siZ\\N|>"
};
#define NLEGCOSAVER asize(leg_cosaver)
const char *leg_adip[] = {
"<mu>",
"Std. Dev.",
"Error"
};
#define NLEGADIP asize(leg_adip)
FILE *outdd,*outmtot,*outaver,*outeps,*caver=NULL;
FILE *dip3d=NULL,*adip=NULL;
rvec *x,*dipole=NULL,mu_t,quad,*dipsp=NULL;
t_gkrbin *gkrbin = NULL;
gmx_enxnm_t *enm=NULL;
t_enxframe *fr;
int nframes=1000,nre,timecheck=0,ncolour=0;
ener_file_t fmu=NULL;
int i,j,k,n,m,natom=0,nmol,gnx_tot,teller,tel3;
t_trxstatus *status;
int *dipole_bin,ndipbin,ibin,iVol,step,idim=-1;
unsigned long mode;
char buf[STRLEN];
real rcut=0,t,t0,t1,dt,lambda,dd,rms_cos;
rvec dipaxis;
matrix box;
gmx_bool bCorr,bTotal,bCont;
double M_diff=0,epsilon,invtel,vol_aver;
double mu_ave,mu_mol,M2_ave=0,M_ave2=0,M_av[DIM],M_av2[DIM];
double M[3],M2[3],M4[3],Gk=0,g_k=0;
gmx_stats_t Mx,My,Mz,Msq,Vol,*Qlsq,mulsq,muframelsq=NULL;
ivec iMu;
real **muall=NULL;
rvec *slab_dipoles=NULL;
t_atom *atom=NULL;
t_block *mols=NULL;
gmx_rmpbc_t gpbc=NULL;
gnx_tot = gnx[0];
if (ncos > 1) {
gnx_tot += gnx[1];
}
vol_aver = 0.0;
iVol=-1;
if (bMU)
{
fmu = open_enx(mufn,"r");
do_enxnms(fmu,&nre,&enm);
/* Determine the indexes of the energy grps we need */
for (i=0; (i<nre); i++) {
if (strstr(enm[i].name,"Volume"))
iVol=i;
else if (strstr(enm[i].name,"Mu-X"))
iMu[XX]=i;
else if (strstr(enm[i].name,"Mu-Y"))
iMu[YY]=i;
else if (strstr(enm[i].name,"Mu-Z"))
iMu[ZZ]=i;
}
}
else
{
atom = top->atoms.atom;
mols = &(top->mols);
}
if ((iVol == -1) && bMU)
printf("Using Volume from topology: %g nm^3\n",volume);
/* Correlation stuff */
bCorr = (corrtype[0] != 'n');
bTotal = (corrtype[0] == 't');
if (bCorr)
{
if (bTotal)
{
snew(muall,1);
snew(muall[0],nframes*DIM);
}
else
{
snew(muall,gnx[0]);
for(i=0; (i<gnx[0]); i++)
snew(muall[i],nframes*DIM);
}
}
/* Allocate array which contains for every molecule in a frame the
* dipole moment.
*/
if (!bMU)
snew(dipole,gnx_tot);
/* Statistics */
snew(Qlsq,DIM);
for(i=0; (i<DIM); i++)
Qlsq[i] = gmx_stats_init();
mulsq = gmx_stats_init();
/* Open all the files */
outmtot = xvgropen(out_mtot,
"Total dipole moment of the simulation box vs. time",
"Time (ps)","Total Dipole Moment (Debye)",oenv);
outeps = xvgropen(out_eps,"Epsilon and Kirkwood factors",
"Time (ps)","",oenv);
outaver = xvgropen(out_aver,"Total dipole moment",
"Time (ps)","D",oenv);
if (bSlab)
{
idim = axtitle[0] - 'X';
if ((idim < 0) || (idim >= DIM))
idim = axtitle[0] - 'x';
if ((idim < 0) || (idim >= DIM))
bSlab = FALSE;
if (nslices < 2)
bSlab = FALSE;
fprintf(stderr,"axtitle = %s, nslices = %d, idim = %d\n",
axtitle,nslices,idim);
if (bSlab)
{
snew(slab_dipoles,nslices);
fprintf(stderr,"Doing slab analysis\n");
}
}
if (fnadip)
{
adip = xvgropen(fnadip, "Average molecular dipole","Dipole (D)","",oenv);
xvgr_legend(adip,NLEGADIP,leg_adip, oenv);
}
if (cosaver)
{
caver = xvgropen(cosaver,bPairs ? "Average pair orientation" :
"Average absolute dipole orientation","Time (ps)","",oenv);
xvgr_legend(caver,NLEGCOSAVER,bPairs ? leg_cosaver : &(leg_cosaver[1]),
oenv);
}
if (fndip3d)
{
snew(dipsp,gnx_tot);
/* we need a dummy file for gnuplot */
dip3d = (FILE *)ffopen("dummy.dat","w");
fprintf(dip3d,"%f %f %f", 0.0,0.0,0.0);
ffclose(dip3d);
dip3d = (FILE *)ffopen(fndip3d,"w");
fprintf(dip3d,"# This file was created by %s\n",Program());
fprintf(dip3d,"# which is part of G R O M A C S:\n");
fprintf(dip3d,"#\n");
}
/* Write legends to all the files */
xvgr_legend(outmtot,NLEGMTOT,leg_mtot,oenv);
xvgr_legend(outaver,NLEGAVER,leg_aver,oenv);
if (bMU && (mu_aver == -1))
xvgr_legend(outeps,NLEGEPS-2,leg_eps,oenv);
else
xvgr_legend(outeps,NLEGEPS,leg_eps,oenv);
snew(fr,1);
clear_rvec(mu_t);
teller = 0;
/* Read the first frame from energy or traj file */
if (bMU)
do
{
bCont = read_mu_from_enx(fmu,iVol,iMu,mu_t,&volume,&t,nre,fr);
if (bCont)
{
timecheck=check_times(t);
if (timecheck < 0)
teller++;
if ((teller % 10) == 0)
fprintf(stderr,"\r Skipping Frame %6d, time: %8.3f", teller, t);
}
else
{
printf("End of %s reached\n",mufn);
break;
}
} while (bCont && (timecheck < 0));
else
natom = read_first_x(oenv,&status,fn,&t,&x,box);
/* Calculate spacing for dipole bin (simple histogram) */
ndipbin = 1+(mu_max/0.01);
snew(dipole_bin, ndipbin);
epsilon = 0.0;
mu_ave = 0.0;
for(m=0; (m<DIM); m++)
{
M[m] = M2[m] = M4[m] = 0.0;
}
if (bGkr)
{
/* Use 0.7 iso 0.5 to account for pressure scaling */
/* rcut = 0.7*sqrt(max_cutoff2(box)); */
rcut = 0.7*sqrt(sqr(box[XX][XX])+sqr(box[YY][YY])+sqr(box[ZZ][ZZ]));
gkrbin = mk_gkrbin(rcut,rcmax,bPhi,ndegrees);
}
gpbc = gmx_rmpbc_init(&top->idef,ePBC,natom,box);
/* Start while loop over frames */
t1 = t0 = t;
teller = 0;
do
{
if (bCorr && (teller >= nframes))
{
nframes += 1000;
if (bTotal)
{
srenew(muall[0],nframes*DIM);
}
else
{
for(i=0; (i<gnx_tot); i++)
srenew(muall[i],nframes*DIM);
}
}
t1 = t;
muframelsq = gmx_stats_init();
/* Initialise */
for(m=0; (m<DIM); m++)
M_av2[m] = 0;
if (bMU)
{
/* Copy rvec into double precision local variable */
for(m=0; (m<DIM); m++)
M_av[m] = mu_t[m];
}
else
{
/* Initialise */
for(m=0; (m<DIM); m++)
M_av[m] = 0;
gmx_rmpbc(gpbc,natom,box,x);
/* Begin loop of all molecules in frame */
for(n=0; (n<ncos); n++)
{
for(i=0; (i<gnx[n]); i++)
{
int gi,ind0,ind1;
ind0 = mols->index[molindex[n][i]];
ind1 = mols->index[molindex[n][i]+1];
mol_dip(ind0,ind1,x,atom,dipole[i]);
gmx_stats_add_point(mulsq,0,norm(dipole[i]),0,0);
gmx_stats_add_point(muframelsq,0,norm(dipole[i]),0,0);
if (bSlab)
update_slab_dipoles(ind0,ind1,x,
dipole[i],idim,nslices,slab_dipoles,box);
if (bQuad)
{
mol_quad(ind0,ind1,x,atom,quad);
for(m=0; (m<DIM); m++)
gmx_stats_add_point(Qlsq[m],0,quad[m],0,0);
}
if (bCorr && !bTotal)
{
tel3=DIM*teller;
muall[i][tel3+XX] = dipole[i][XX];
muall[i][tel3+YY] = dipole[i][YY];
muall[i][tel3+ZZ] = dipole[i][ZZ];
}
mu_mol = 0.0;
for(m=0; (m<DIM); m++)
{
M_av[m] += dipole[i][m]; /* M per frame */
mu_mol += dipole[i][m]*dipole[i][m]; /* calc. mu for distribution */
}
mu_mol = sqrt(mu_mol);
mu_ave += mu_mol; /* calc. the average mu */
/* Update the dipole distribution */
ibin = (int)(ndipbin*mu_mol/mu_max + 0.5);
if (ibin < ndipbin)
dipole_bin[ibin]++;
if (fndip3d)
{
rvec2sprvec(dipole[i],dipsp[i]);
if (dipsp[i][YY] > -M_PI && dipsp[i][YY] < -0.5*M_PI) {
if (dipsp[i][ZZ] < 0.5 * M_PI)
{
ncolour = 1;
}
else
{
ncolour = 2;
}
}
else if (dipsp[i][YY] > -0.5*M_PI && dipsp[i][YY] < 0.0*M_PI)
{
if (dipsp[i][ZZ] < 0.5 * M_PI)
{
ncolour = 3;
}
else
{
ncolour = 4;
}
}else if (dipsp[i][YY] > 0.0 && dipsp[i][YY] < 0.5*M_PI) {
if (dipsp[i][ZZ] < 0.5 * M_PI) {
ncolour = 5;
} else {
ncolour = 6;
}
}
else if (dipsp[i][YY] > 0.5*M_PI && dipsp[i][YY] < M_PI)
{
if (dipsp[i][ZZ] < 0.5 * M_PI)
{
ncolour = 7;
}
else
{
ncolour = 8;
}
}
if (dip3d)
fprintf(dip3d,"set arrow %d from %f, %f, %f to %f, %f, %f lt %d # %d %d\n",
i+1,
x[ind0][XX],
x[ind0][YY],
x[ind0][ZZ],
x[ind0][XX]+dipole[i][XX]/25,
x[ind0][YY]+dipole[i][YY]/25,
x[ind0][ZZ]+dipole[i][ZZ]/25,
ncolour, ind0, i);
}
} /* End loop of all molecules in frame */
if (dip3d)
{
fprintf(dip3d,"set title \"t = %4.3f\"\n",t);
fprintf(dip3d,"set xrange [0.0:%4.2f]\n",box[XX][XX]);
fprintf(dip3d,"set yrange [0.0:%4.2f]\n",box[YY][YY]);
fprintf(dip3d,"set zrange [0.0:%4.2f]\n\n",box[ZZ][ZZ]);
fprintf(dip3d,"splot 'dummy.dat' using 1:2:3 w vec\n");
fprintf(dip3d,"pause -1 'Hit return to continue'\n");
}
}
}
/* Compute square of total dipole */
for(m=0; (m<DIM); m++)
M_av2[m] = M_av[m]*M_av[m];
if (cosaver)
{
compute_avercos(gnx_tot,dipole,&dd,dipaxis,bPairs);
rms_cos = sqrt(sqr(dipaxis[XX]-0.5)+
sqr(dipaxis[YY]-0.5)+
sqr(dipaxis[ZZ]-0.5));
if (bPairs)
fprintf(caver,"%10.3e %10.3e %10.3e %10.3e %10.3e %10.3e\n",
t,dd,rms_cos,dipaxis[XX],dipaxis[YY],dipaxis[ZZ]);
else
fprintf(caver,"%10.3e %10.3e %10.3e %10.3e %10.3e\n",
t,rms_cos,dipaxis[XX],dipaxis[YY],dipaxis[ZZ]);
}
if (bGkr)
{
do_gkr(gkrbin,ncos,gnx,molindex,mols->index,x,dipole,ePBC,box,
atom,gkatom);
}
if (bTotal)
{
tel3 = DIM*teller;
muall[0][tel3+XX] = M_av[XX];
muall[0][tel3+YY] = M_av[YY];
muall[0][tel3+ZZ] = M_av[ZZ];
}
/* Write to file the total dipole moment of the box, and its components
* for this frame.
*/
if ((skip == 0) || ((teller % skip) == 0))
fprintf(outmtot,"%10g %12.8e %12.8e %12.8e %12.8e\n",
t,M_av[XX],M_av[YY],M_av[ZZ],
sqrt(M_av2[XX]+M_av2[YY]+M_av2[ZZ]));
for(m=0; (m<DIM); m++)
{
M[m] += M_av[m];
M2[m] += M_av2[m];
M4[m] += sqr(M_av2[m]);
}
/* Increment loop counter */
teller++;
/* Calculate for output the running averages */
invtel = 1.0/teller;
M2_ave = (M2[XX]+M2[YY]+M2[ZZ])*invtel;
M_ave2 = invtel*(invtel*(M[XX]*M[XX] + M[YY]*M[YY] + M[ZZ]*M[ZZ]));
M_diff = M2_ave - M_ave2;
/* Compute volume from box in traj, else we use the one from above */
if (!bMU)
volume = det(box);
vol_aver += volume;
epsilon = calc_eps(M_diff,(vol_aver/teller),epsilonRF,temp);
/* Calculate running average for dipole */
if (mu_ave != 0)
mu_aver = (mu_ave/gnx_tot)*invtel;
if ((skip == 0) || ((teller % skip) == 0))
{
/* Write to file < |M|^2 >, |< M >|^2. And the difference between
* the two. Here M is sum mu_i. Further write the finite system
* Kirkwood G factor and epsilon.
*/
fprintf(outaver,"%10g %10.3e %10.3e %10.3e %10.3e\n",
t,M2_ave,M_ave2,M_diff,M_ave2/M2_ave);
if (fnadip)
{
real aver;
gmx_stats_get_average(muframelsq,&aver);
fprintf(adip, "%10g %f \n", t,aver);
}
/*if (dipole)
printf("%f %f\n", norm(dipole[0]), norm(dipole[1]));
*/
if (!bMU || (mu_aver != -1))
{
/* Finite system Kirkwood G-factor */
Gk = M_diff/(gnx_tot*mu_aver*mu_aver);
/* Infinite system Kirkwood G-factor */
if (epsilonRF == 0.0)
g_k = ((2*epsilon+1)*Gk/(3*epsilon));
else
g_k = ((2*epsilonRF+epsilon)*(2*epsilon+1)*
Gk/(3*epsilon*(2*epsilonRF+1)));
fprintf(outeps,"%10g %10.3e %10.3e %10.3e\n",t,epsilon,Gk,g_k);
}
else
fprintf(outeps,"%10g %12.8e\n",t,epsilon);
}
gmx_stats_done(muframelsq);
if (bMU)
bCont = read_mu_from_enx(fmu,iVol,iMu,mu_t,&volume,&t,nre,fr);
else
bCont = read_next_x(oenv,status,&t,natom,x,box);
timecheck=check_times(t);
} while (bCont && (timecheck == 0) );
gmx_rmpbc_done(gpbc);
if (!bMU)
close_trj(status);
ffclose(outmtot);
ffclose(outaver);
ffclose(outeps);
if (fnadip)
ffclose(adip);
if (cosaver)
ffclose(caver);
if (dip3d) {
fprintf(dip3d,"set xrange [0.0:%4.2f]\n",box[XX][XX]);
fprintf(dip3d,"set yrange [0.0:%4.2f]\n",box[YY][YY]);
fprintf(dip3d,"set zrange [0.0:%4.2f]\n\n",box[ZZ][ZZ]);
fprintf(dip3d,"splot 'dummy.dat' using 1:2:3 w vec\n");
fprintf(dip3d,"pause -1 'Hit return to continue'\n");
ffclose(dip3d);
}
if (bSlab) {
dump_slab_dipoles(slabfn,idim,nslices,slab_dipoles,box,teller,oenv);
sfree(slab_dipoles);
}
vol_aver /= teller;
printf("Average volume over run is %g\n",vol_aver);
if (bGkr) {
print_gkrbin(gkrfn,gkrbin,gnx[0],teller,vol_aver,oenv);
print_cmap(cmap,gkrbin,nlevels);
}
/* Autocorrelation function */
if (bCorr) {
if (teller < 2) {
printf("Not enough frames for autocorrelation\n");
}
else {
dt=(t1 - t0)/(teller-1);
printf("t0 %g, t %g, teller %d\n", t0,t,teller);
mode = eacVector;
if (bTotal)
do_autocorr(corf,oenv,"Autocorrelation Function of Total Dipole",
teller,1,muall,dt,mode,TRUE);
else
do_autocorr(corf,oenv,"Dipole Autocorrelation Function",
teller,gnx_tot,muall,dt,
mode,strcmp(corrtype,"molsep"));
}
}
if (!bMU) {
real aver,sigma,error,lsq;
gmx_stats_get_ase(mulsq,&aver,&sigma,&error);
printf("\nDipole moment (Debye)\n");
printf("---------------------\n");
printf("Average = %8.4f Std. Dev. = %8.4f Error = %8.4f\n",
aver,sigma,error);
if (bQuad) {
rvec a,s,e;
int mm;
for(m=0; (m<DIM); m++)
gmx_stats_get_ase(mulsq,&(a[m]),&(s[m]),&(e[m]));
printf("\nQuadrupole moment (Debye-Ang)\n");
printf("-----------------------------\n");
printf("Averages = %8.4f %8.4f %8.4f\n",a[XX],a[YY],a[ZZ]);
printf("Std. Dev. = %8.4f %8.4f %8.4f\n",s[XX],s[YY],s[ZZ]);
printf("Error = %8.4f %8.4f %8.4f\n",e[XX],e[YY],e[ZZ]);
}
printf("\n");
}
printf("The following averages for the complete trajectory have been calculated:\n\n");
printf(" Total < M_x > = %g Debye\n", M[XX]/teller);
printf(" Total < M_y > = %g Debye\n", M[YY]/teller);
printf(" Total < M_z > = %g Debye\n\n", M[ZZ]/teller);
printf(" Total < M_x^2 > = %g Debye^2\n", M2[XX]/teller);
printf(" Total < M_y^2 > = %g Debye^2\n", M2[YY]/teller);
printf(" Total < M_z^2 > = %g Debye^2\n\n", M2[ZZ]/teller);
printf(" Total < |M|^2 > = %g Debye^2\n", M2_ave);
printf(" Total |< M >|^2 = %g Debye^2\n\n", M_ave2);
printf(" < |M|^2 > - |< M >|^2 = %g Debye^2\n\n", M_diff);
if (!bMU || (mu_aver != -1)) {
printf("Finite system Kirkwood g factor G_k = %g\n", Gk);
printf("Infinite system Kirkwood g factor g_k = %g\n\n", g_k);
}
printf("Epsilon = %g\n", epsilon);
if (!bMU) {
/* Write to file the dipole moment distibution during the simulation.
*/
outdd=xvgropen(dipdist,"Dipole Moment Distribution","mu (Debye)","",oenv);
for(i=0; (i<ndipbin); i++)
fprintf(outdd,"%10g %10f\n",
(i*mu_max)/ndipbin,dipole_bin[i]/(double)teller);
ffclose(outdd);
sfree(dipole_bin);
}
if (bGkr)
done_gkrbin(&gkrbin);
}
