int main(int argc,char *argv[])
{
const char *desc[] = {
"[TT]g_anadock[tt] analyses the results of an Autodock run and clusters the",
"structures together, based on distance or RMSD. The docked energy",
"and free energy estimates are analysed, and for each cluster the",
"energy statistics are printed.[PAR]",
"An alternative approach to this is to cluster the structures first",
"using [TT]g_cluster[tt] and then sort the clusters on either lowest",
"energy or average energy."
};
t_filenm fnm[] = {
{ efPDB, "-f", NULL, ffREAD },
{ efPDB, "-ox", "cluster", ffWRITE },
{ efXVG, "-od", "edocked", ffWRITE },
{ efXVG, "-of", "efree", ffWRITE },
{ efLOG, "-g", "anadock", ffWRITE }
};
output_env_t oenv;
#define NFILE asize(fnm)
static gmx_bool bFree=FALSE,bRMS=TRUE;
static real cutoff = 0.2;
t_pargs pa[] = {
{ "-free", FALSE, etBOOL, {&bFree},
"Use Free energy estimate from autodock for sorting the classes" },
{ "-rms", FALSE, etBOOL, {&bRMS},
"Cluster on RMS or distance" },
{ "-cutoff", FALSE, etREAL, {&cutoff},
"Maximum RMSD/distance for belonging to the same cluster" }
};
#define NPA asize(pa)
FILE *fp;
t_pdbfile **pdbf=NULL;
int npdbf;
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,0,NFILE,fnm,NPA,pa, asize(desc),desc,0,
NULL,&oenv);
fp = ffopen(opt2fn("-g",NFILE,fnm),"w");
please_cite(stdout,"Hetenyi2002b");
please_cite(fp,"Hetenyi2002b");
pdbf = read_em_all(opt2fn("-f",NFILE,fnm),&npdbf);
analyse_em_all(npdbf,pdbf,opt2fn("-od",NFILE,fnm),opt2fn("-of",NFILE,fnm),
oenv);
cluster_em_all(fp,npdbf,pdbf,opt2fn("-ox",NFILE,fnm),
bFree,bRMS,cutoff);
thanx(fp);
ffclose(fp);
thanx(stdout);
return 0;
}
static void luzar_correl(int nn,real *time,int nset,real **val,real temp,
bool bError,real fit_start,real smooth_tail_start)
{
const real tol = 1e-8;
real *kt;
real weight,d2;
int j;
please_cite(stdout,"Spoel2006b");
/* Compute negative derivative k(t) = -dc(t)/dt */
if (!bError) {
snew(kt,nn);
compute_derivative(nn,time,val[0],kt);
for(j=0; (j<nn); j++)
kt[j] = -kt[j];
if (debug) {
d2 = 0;
for(j=0; (j<nn); j++)
d2 += sqr(kt[j] - val[3][j]);
fprintf(debug,"RMS difference in derivatives is %g\n",sqrt(d2/nn));
}
analyse_corr(nn,time,val[0],val[2],kt,NULL,NULL,NULL,fit_start,
temp,smooth_tail_start);
sfree(kt);
}
else if (nset == 6) {
analyse_corr(nn,time,val[0],val[2],val[4],
val[1],val[3],val[5],fit_start,temp,smooth_tail_start);
}
else {
printf("Inconsistent input. I need c(t) sigma_c(t) n(t) sigma_n(t) K(t) sigma_K(t)\n");
printf("Not doing anything. Sorry.\n");
}
}
static void vdw_warning(FILE *fp)
{
if (NULL != fp)
{
fprintf(fp, "NOTE: From version 5.0 %s uses the Van der Waals radii\n",
gmx::getProgramContext().displayName());
fprintf(fp, "from the source below. This means the results may be different\n");
fprintf(fp, "compared to previous GROMACS versions.\n");
please_cite(fp, "Bondi1964a");
}
}
void calc_rffac(FILE *fplog,int eel,real eps_r,real eps_rf,real Rc,real Temp,
real zsq,matrix box,
real *kappa,real *krf,real *crf)
{
/* Compute constants for Generalized reaction field */
real k1,k2,I,vol,rmin;
if (EEL_RF(eel)) {
vol = det(box);
if (eel == eelGRF) {
/* Consistency check */
if (Temp <= 0.0)
gmx_fatal(FARGS,"Temperature is %f while using"
" Generalized Reaction Field\n",Temp);
/* Ionic strength (only needed for eelGRF */
I = 0.5*zsq/vol;
*kappa = sqrt(2*I/(EPSILON0*eps_rf*BOLTZ*Temp));
}
else {
I = 0;
*kappa = 0;
}
/* eps == 0 signals infinite dielectric */
if (eps_rf == 0) {
*krf = 1/(2*Rc*Rc*Rc);
} else {
k1 = 1 + *kappa*Rc;
k2 = eps_rf*sqr((real)(*kappa*Rc));
*krf = ((eps_rf - eps_r)*k1 + 0.5*k2)/((2*eps_rf + eps_r)*k1 + k2)/(Rc*Rc*Rc);
}
*crf = 1/Rc + *krf*Rc*Rc;
rmin = pow(*krf*2.0,-1.0/3.0);
if (fplog) {
if (eel == eelGRF) {
please_cite(fplog,"Tironi95a");
fprintf(fplog,"%s:\n"
"epsRF = %10g, I = %10g, volume = %10g, kappa = %10g\n"
"rc = %10g, krf = %10g, crf = %10g, epsfac = %10g\n",
eel_names[eel],eps_rf,I,vol,*kappa,Rc,*krf,*crf,
ONE_4PI_EPS0/eps_r);
} else {
fprintf(fplog,"%s:\n"
"epsRF = %g, rc = %g, krf = %g, crf = %g, epsfac = %g\n",
eel_names[eel],eps_rf,Rc,*krf,*crf,ONE_4PI_EPS0/eps_r);
}
fprintf(fplog,
"The electrostatics potential has its minimum at r = %g\n",
rmin);
}
}
}
int gmx_saxs(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] calculates SAXS structure factors for given index",
"groups based on Cromer's method.",
"Both topology and trajectory files are required."
};
static real start_q = 0.0, end_q = 60.0, energy = 12.0;
static int ngroups = 1;
t_pargs pa[] = {
{ "-ng", FALSE, etINT, {&ngroups},
"Number of groups to compute SAXS" },
{"-startq", FALSE, etREAL, {&start_q},
"Starting q (1/nm) "},
{"-endq", FALSE, etREAL, {&end_q},
"Ending q (1/nm)"},
{"-energy", FALSE, etREAL, {&energy},
"Energy of the incoming X-ray (keV) "}
};
#define NPA asize(pa)
const char *fnTPS, *fnTRX, *fnNDX, *fnDAT = NULL;
output_env_t oenv;
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, NULL, NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efDAT, "-d", "sfactor", ffOPTRD },
{ efXVG, "-sq", "sq", ffWRITE },
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
fnTPS = ftp2fn(efTPS, NFILE, fnm);
fnTRX = ftp2fn(efTRX, NFILE, fnm);
fnDAT = ftp2fn(efDAT, NFILE, fnm);
fnNDX = ftp2fn_null(efNDX, NFILE, fnm);
do_scattering_intensity(fnTPS, fnNDX, opt2fn("-sq", NFILE, fnm),
fnTRX, fnDAT,
start_q, end_q, energy, ngroups, oenv);
please_cite(stdout, "Cromer1968a");
return 0;
}
void do_pp2shifts(FILE *fp, int nf, int nlist, t_dlist dlist[], real **dih)
{
t_shiftdata *ca_sd, *co_sd, *ha_sd, *cb_sd;
int i, j, Phi, Psi;
real phi, psi;
real ca, co, ha, cb;
/* Read the shift files */
ca_sd = read_shifts("ca-shift.dat");
cb_sd = read_shifts("cb-shift.dat");
ha_sd = read_shifts("ha-shift.dat");
co_sd = read_shifts("co-shift.dat");
fprintf(fp, "\n *** Chemical shifts from the chemical shift index ***\n");
please_cite(fp, "Wishart98a");
fprintf(fp, "%12s %10s %10s %10s %10s\n",
"Residue", "delta Ca", "delta Ha", "delta CO", "delta Cb");
for (i = 0; (i < nlist); i++)
{
if ((has_dihedral(edPhi, &(dlist[i]))) &&
(has_dihedral(edPsi, &(dlist[i]))))
{
Phi = dlist[i].j0[edPhi];
Psi = dlist[i].j0[edPsi];
ca = cb = co = ha = 0;
for (j = 0; (j < nf); j++)
{
phi = dih[Phi][j];
psi = dih[Psi][j];
ca += interpolate(phi, psi, ca_sd);
cb += interpolate(phi, psi, cb_sd);
co += interpolate(phi, psi, co_sd);
ha += interpolate(phi, psi, ha_sd);
}
fprintf(fp, "%12s %10g %10g %10g %10g\n",
dlist[i].name, ca/nf, ha/nf, co/nf, cb/nf);
}
}
fprintf(fp, "\n");
/* Free memory */
done_shifts(ca_sd);
done_shifts(cb_sd);
done_shifts(co_sd);
done_shifts(ha_sd);
}
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_mdrun(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] is the main computational chemistry engine",
"within GROMACS. Obviously, it performs Molecular Dynamics simulations,",
"but it can also perform Stochastic Dynamics, Energy Minimization,",
"test particle insertion or (re)calculation of energies.",
"Normal mode analysis is another option. In this case [TT]mdrun[tt]",
"builds a Hessian matrix from single conformation.",
"For usual Normal Modes-like calculations, make sure that",
"the structure provided is properly energy-minimized.",
"The generated matrix can be diagonalized by [gmx-nmeig].[PAR]",
"The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
"and distributes the topology over ranks if needed.",
"[TT]mdrun[tt] produces at least four output files.",
"A single log file ([TT]-g[tt]) is written, unless the option",
"[TT]-seppot[tt] is used, in which case each rank writes a log file.",
"The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
"optionally forces.",
"The structure file ([TT]-c[tt]) contains the coordinates and",
"velocities of the last step.",
"The energy file ([TT]-e[tt]) contains energies, the temperature,",
"pressure, etc, a lot of these things are also printed in the log file.",
"Optionally coordinates can be written to a compressed trajectory file",
"([TT]-x[tt]).[PAR]",
"The option [TT]-dhdl[tt] is only used when free energy calculation is",
"turned on.[PAR]",
"A simulation can be run in parallel using two different parallelization",
"schemes: MPI parallelization and/or OpenMP thread parallelization.",
"The MPI parallelization uses multiple processes when [TT]mdrun[tt] is",
"compiled with a normal MPI library or threads when [TT]mdrun[tt] is",
"compiled with the GROMACS built-in thread-MPI library. OpenMP threads",
"are supported when [TT]mdrun[tt] is compiled with OpenMP. Full OpenMP support",
"is only available with the Verlet cut-off scheme, with the (older)",
"group scheme only PME-only ranks can use OpenMP parallelization.",
"In all cases [TT]mdrun[tt] will by default try to use all the available",
"hardware resources. With a normal MPI library only the options",
"[TT]-ntomp[tt] (with the Verlet cut-off scheme) and [TT]-ntomp_pme[tt],",
"for PME-only ranks, can be used to control the number of threads.",
"With thread-MPI there are additional options [TT]-nt[tt], which sets",
"the total number of threads, and [TT]-ntmpi[tt], which sets the number",
"of thread-MPI threads.",
"The number of OpenMP threads used by [TT]mdrun[tt] can also be set with",
"the standard environment variable, [TT]OMP_NUM_THREADS[tt].",
"The [TT]GMX_PME_NUM_THREADS[tt] environment variable can be used to specify",
"the number of threads used by the PME-only ranks.[PAR]",
"Note that combined MPI+OpenMP parallelization is in many cases",
"slower than either on its own. However, at high parallelization, using the",
"combination is often beneficial as it reduces the number of domains and/or",
"the number of MPI ranks. (Less and larger domains can improve scaling,",
"with separate PME ranks, using fewer MPI ranks reduces communication costs.)",
"OpenMP-only parallelization is typically faster than MPI-only parallelization",
"on a single CPU(-die). Since we currently don't have proper hardware",
"topology detection, [TT]mdrun[tt] compiled with thread-MPI will only",
"automatically use OpenMP-only parallelization when you use up to 4",
"threads, up to 12 threads with Intel Nehalem/Westmere, or up to 16",
"threads with Intel Sandy Bridge or newer CPUs. Otherwise MPI-only",
"parallelization is used (except with GPUs, see below).",
"[PAR]",
"To quickly test the performance of the new Verlet cut-off scheme",
"with old [TT].tpr[tt] files, either on CPUs or CPUs+GPUs, you can use",
"the [TT]-testverlet[tt] option. This should not be used for production,",
"since it can slightly modify potentials and it will remove charge groups",
"making analysis difficult, as the [TT].tpr[tt] file will still contain",
"charge groups. For production simulations it is highly recommended",
"to specify [TT]cutoff-scheme = Verlet[tt] in the [TT].mdp[tt] file.",
"[PAR]",
"With GPUs (only supported with the Verlet cut-off scheme), the number",
"of GPUs should match the number of particle-particle ranks, i.e.",
"excluding PME-only ranks. With thread-MPI, unless set on the command line, the number",
"of MPI threads will automatically be set to the number of GPUs detected.",
"To use a subset of the available GPUs, or to manually provide a mapping of",
"GPUs to PP ranks, you can use the [TT]-gpu_id[tt] option. The argument of [TT]-gpu_id[tt] is",
"a string of digits (without delimiter) representing device id-s of the GPUs to be used.",
"For example, \"[TT]02[tt]\" specifies using GPUs 0 and 2 in the first and second PP ranks per compute node",
"respectively. To select different sets of GPU-s",
"on different nodes of a compute cluster, use the [TT]GMX_GPU_ID[tt] environment",
"variable instead. The format for [TT]GMX_GPU_ID[tt] is identical to ",
"[TT]-gpu_id[tt], with the difference that an environment variable can have",
"different values on different compute nodes. Multiple MPI ranks on each node",
"can share GPUs. This is accomplished by specifying the id(s) of the GPU(s)",
"multiple times, e.g. \"[TT]0011[tt]\" for four ranks sharing two GPUs in this node.",
"This works within a single simulation, or a multi-simulation, with any form of MPI.",
"[PAR]",
"With the Verlet cut-off scheme and verlet-buffer-tolerance set,",
"the pair-list update interval nstlist can be chosen freely with",
"the option [TT]-nstlist[tt]. [TT]mdrun[tt] will then adjust",
"the pair-list cut-off to maintain accuracy, and not adjust nstlist.",
"Otherwise, by default, [TT]mdrun[tt] will try to increase the",
"value of nstlist set in the [TT].mdp[tt] file to improve the",
"performance. For CPU-only runs, nstlist might increase to 20, for",
"GPU runs up to 40. For medium to high parallelization or with",
"fast GPUs, a (user-supplied) larger nstlist value can give much",
"better performance.",
"[PAR]",
"When using PME with separate PME ranks or with a GPU, the two major",
"compute tasks, the non-bonded force calculation and the PME calculation",
"run on different compute resources. If this load is not balanced,",
"some of the resources will be idle part of time. With the Verlet",
"cut-off scheme this load is automatically balanced when the PME load",
"is too high (but not when it is too low). This is done by scaling",
"the Coulomb cut-off and PME grid spacing by the same amount. In the first",
"few hundred steps different settings are tried and the fastest is chosen",
"for the rest of the simulation. This does not affect the accuracy of",
"the results, but it does affect the decomposition of the Coulomb energy",
"into particle and mesh contributions. The auto-tuning can be turned off",
"with the option [TT]-notunepme[tt].",
"[PAR]",
"[TT]mdrun[tt] pins (sets affinity of) threads to specific cores,",
"when all (logical) cores on a compute node are used by [TT]mdrun[tt],",
"even when no multi-threading is used,",
"as this usually results in significantly better performance.",
"If the queuing systems or the OpenMP library pinned threads, we honor",
"this and don't pin again, even though the layout may be sub-optimal.",
"If you want to have [TT]mdrun[tt] override an already set thread affinity",
"or pin threads when using less cores, use [TT]-pin on[tt].",
"With SMT (simultaneous multithreading), e.g. Intel Hyper-Threading,",
"there are multiple logical cores per physical core.",
"The option [TT]-pinstride[tt] sets the stride in logical cores for",
"pinning consecutive threads. Without SMT, 1 is usually the best choice.",
"With Intel Hyper-Threading 2 is best when using half or less of the",
"logical cores, 1 otherwise. The default value of 0 do exactly that:",
"it minimizes the threads per logical core, to optimize performance.",
"If you want to run multiple [TT]mdrun[tt] jobs on the same physical node,"
"you should set [TT]-pinstride[tt] to 1 when using all logical cores.",
"When running multiple [TT]mdrun[tt] (or other) simulations on the same physical",
"node, some simulations need to start pinning from a non-zero core",
"to avoid overloading cores; with [TT]-pinoffset[tt] you can specify",
"the offset in logical cores for pinning.",
"[PAR]",
"When [TT]mdrun[tt] is started with more than 1 rank,",
"parallelization with domain decomposition is used.",
"[PAR]",
"With domain decomposition, the spatial decomposition can be set",
"with option [TT]-dd[tt]. By default [TT]mdrun[tt] selects a good decomposition.",
"The user only needs to change this when the system is very inhomogeneous.",
"Dynamic load balancing is set with the option [TT]-dlb[tt],",
"which can give a significant performance improvement,",
"especially for inhomogeneous systems. The only disadvantage of",
"dynamic load balancing is that runs are no longer binary reproducible,",
"but in most cases this is not important.",
"By default the dynamic load balancing is automatically turned on",
"when the measured performance loss due to load imbalance is 5% or more.",
"At low parallelization these are the only important options",
"for domain decomposition.",
"At high parallelization the options in the next two sections",
"could be important for increasing the performace.",
"[PAR]",
"When PME is used with domain decomposition, separate ranks can",
"be assigned to do only the PME mesh calculation;",
"this is computationally more efficient starting at about 12 ranks,",
"or even fewer when OpenMP parallelization is used.",
"The number of PME ranks is set with option [TT]-npme[tt],",
"but this cannot be more than half of the ranks.",
"By default [TT]mdrun[tt] makes a guess for the number of PME",
"ranks when the number of ranks is larger than 16. With GPUs,",
"using separate PME ranks is not selected automatically,",
"since the optimal setup depends very much on the details",
"of the hardware. In all cases, you might gain performance",
"by optimizing [TT]-npme[tt]. Performance statistics on this issue",
"are written at the end of the log file.",
"For good load balancing at high parallelization, the PME grid x and y",
"dimensions should be divisible by the number of PME ranks",
"(the simulation will run correctly also when this is not the case).",
"[PAR]",
"This section lists all options that affect the domain decomposition.",
"[PAR]",
"Option [TT]-rdd[tt] can be used to set the required maximum distance",
"for inter charge-group bonded interactions.",
"Communication for two-body bonded interactions below the non-bonded",
"cut-off distance always comes for free with the non-bonded communication.",
"Atoms beyond the non-bonded cut-off are only communicated when they have",
"missing bonded interactions; this means that the extra cost is minor",
"and nearly indepedent of the value of [TT]-rdd[tt].",
"With dynamic load balancing option [TT]-rdd[tt] also sets",
"the lower limit for the domain decomposition cell sizes.",
"By default [TT]-rdd[tt] is determined by [TT]mdrun[tt] based on",
"the initial coordinates. The chosen value will be a balance",
"between interaction range and communication cost.",
"[PAR]",
"When inter charge-group bonded interactions are beyond",
"the bonded cut-off distance, [TT]mdrun[tt] terminates with an error message.",
"For pair interactions and tabulated bonds",
"that do not generate exclusions, this check can be turned off",
"with the option [TT]-noddcheck[tt].",
"[PAR]",
"When constraints are present, option [TT]-rcon[tt] influences",
"the cell size limit as well.",
"Atoms connected by NC constraints, where NC is the LINCS order plus 1,",
"should not be beyond the smallest cell size. A error message is",
"generated when this happens and the user should change the decomposition",
"or decrease the LINCS order and increase the number of LINCS iterations.",
"By default [TT]mdrun[tt] estimates the minimum cell size required for P-LINCS",
"in a conservative fashion. For high parallelization it can be useful",
"to set the distance required for P-LINCS with the option [TT]-rcon[tt].",
"[PAR]",
"The [TT]-dds[tt] option sets the minimum allowed x, y and/or z scaling",
"of the cells with dynamic load balancing. [TT]mdrun[tt] will ensure that",
"the cells can scale down by at least this factor. This option is used",
"for the automated spatial decomposition (when not using [TT]-dd[tt])",
"as well as for determining the number of grid pulses, which in turn",
"sets the minimum allowed cell size. Under certain circumstances",
"the value of [TT]-dds[tt] might need to be adjusted to account for",
"high or low spatial inhomogeneity of the system.",
"[PAR]",
"The option [TT]-gcom[tt] can be used to only do global communication",
"every n steps.",
"This can improve performance for highly parallel simulations",
"where this global communication step becomes the bottleneck.",
"For a global thermostat and/or barostat the temperature",
"and/or pressure will also only be updated every [TT]-gcom[tt] steps.",
"By default it is set to the minimum of nstcalcenergy and nstlist.[PAR]",
"With [TT]-rerun[tt] an input trajectory can be given for which ",
"forces and energies will be (re)calculated. Neighbor searching will be",
"performed for every frame, unless [TT]nstlist[tt] is zero",
"(see the [TT].mdp[tt] file).[PAR]",
"ED (essential dynamics) sampling and/or additional flooding potentials",
"are switched on by using the [TT]-ei[tt] flag followed by an [TT].edi[tt]",
"file. The [TT].edi[tt] file can be produced with the [TT]make_edi[tt] tool",
"or by using options in the essdyn menu of the WHAT IF program.",
"[TT]mdrun[tt] produces a [TT].xvg[tt] output file that",
"contains projections of positions, velocities and forces onto selected",
"eigenvectors.[PAR]",
"When user-defined potential functions have been selected in the",
"[TT].mdp[tt] file the [TT]-table[tt] option is used to pass [TT]mdrun[tt]",
"a formatted table with potential functions. The file is read from",
"either the current directory or from the [TT]GMXLIB[tt] directory.",
"A number of pre-formatted tables are presented in the [TT]GMXLIB[tt] dir,",
"for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard-Jones potentials with",
"normal Coulomb.",
"When pair interactions are present, a separate table for pair interaction",
"functions is read using the [TT]-tablep[tt] option.[PAR]",
"When tabulated bonded functions are present in the topology,",
"interaction functions are read using the [TT]-tableb[tt] option.",
"For each different tabulated interaction type the table file name is",
"modified in a different way: before the file extension an underscore is",
"appended, then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals",
"and finally the table number of the interaction type.[PAR]",
"The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
"coordinates and forces when pulling is selected",
"in the [TT].mdp[tt] file.[PAR]",
"With [TT]-multi[tt] or [TT]-multidir[tt], multiple systems can be ",
"simulated in parallel.",
"As many input files/directories are required as the number of systems. ",
"The [TT]-multidir[tt] option takes a list of directories (one for each ",
"system) and runs in each of them, using the input/output file names, ",
"such as specified by e.g. the [TT]-s[tt] option, relative to these ",
"directories.",
"With [TT]-multi[tt], the system number is appended to the run input ",
"and each output filename, for instance [TT]topol.tpr[tt] becomes",
"[TT]topol0.tpr[tt], [TT]topol1.tpr[tt] etc.",
"The number of ranks per system is the total number of ranks",
"divided by the number of systems.",
"One use of this option is for NMR refinement: when distance",
"or orientation restraints are present these can be ensemble averaged",
"over all the systems.[PAR]",
"With [TT]-replex[tt] replica exchange is attempted every given number",
"of steps. The number of replicas is set with the [TT]-multi[tt] or ",
"[TT]-multidir[tt] option, described above.",
"All run input files should use a different coupling temperature,",
"the order of the files is not important. The random seed is set with",
"[TT]-reseed[tt]. The velocities are scaled and neighbor searching",
"is performed after every exchange.[PAR]",
"Finally some experimental algorithms can be tested when the",
"appropriate options have been given. Currently under",
"investigation are: polarizability.",
"[PAR]",
"The option [TT]-membed[tt] does what used to be g_membed, i.e. embed",
"a protein into a membrane. The data file should contain the options",
"that where passed to g_membed before. The [TT]-mn[tt] and [TT]-mp[tt]",
"both apply to this as well.",
"[PAR]",
"The option [TT]-pforce[tt] is useful when you suspect a simulation",
"crashes due to too large forces. With this option coordinates and",
"forces of atoms with a force larger than a certain value will",
"be printed to stderr.",
"[PAR]",
"Checkpoints containing the complete state of the system are written",
"at regular intervals (option [TT]-cpt[tt]) to the file [TT]-cpo[tt],",
"unless option [TT]-cpt[tt] is set to -1.",
"The previous checkpoint is backed up to [TT]state_prev.cpt[tt] to",
"make sure that a recent state of the system is always available,",
"even when the simulation is terminated while writing a checkpoint.",
"With [TT]-cpnum[tt] all checkpoint files are kept and appended",
"with the step number.",
"A simulation can be continued by reading the full state from file",
"with option [TT]-cpi[tt]. This option is intelligent in the way that",
"if no checkpoint file is found, Gromacs just assumes a normal run and",
"starts from the first step of the [TT].tpr[tt] file. By default the output",
"will be appending to the existing output files. The checkpoint file",
"contains checksums of all output files, such that you will never",
"loose data when some output files are modified, corrupt or removed.",
"There are three scenarios with [TT]-cpi[tt]:[PAR]",
"[TT]*[tt] no files with matching names are present: new output files are written[PAR]",
"[TT]*[tt] all files are present with names and checksums matching those stored",
"in the checkpoint file: files are appended[PAR]",
"[TT]*[tt] otherwise no files are modified and a fatal error is generated[PAR]",
"With [TT]-noappend[tt] new output files are opened and the simulation",
"part number is added to all output file names.",
"Note that in all cases the checkpoint file itself is not renamed",
"and will be overwritten, unless its name does not match",
"the [TT]-cpo[tt] option.",
"[PAR]",
"With checkpointing the output is appended to previously written",
"output files, unless [TT]-noappend[tt] is used or none of the previous",
"output files are present (except for the checkpoint file).",
"The integrity of the files to be appended is verified using checksums",
"which are stored in the checkpoint file. This ensures that output can",
"not be mixed up or corrupted due to file appending. When only some",
"of the previous output files are present, a fatal error is generated",
"and no old output files are modified and no new output files are opened.",
"The result with appending will be the same as from a single run.",
"The contents will be binary identical, unless you use a different number",
"of ranks or dynamic load balancing or the FFT library uses optimizations",
"through timing.",
"[PAR]",
"With option [TT]-maxh[tt] a simulation is terminated and a checkpoint",
"file is written at the first neighbor search step where the run time",
"exceeds [TT]-maxh[tt]*0.99 hours.",
"[PAR]",
"When [TT]mdrun[tt] receives a TERM signal, it will set nsteps to the current",
"step plus one. When [TT]mdrun[tt] receives an INT signal (e.g. when ctrl+C is",
"pressed), it will stop after the next neighbor search step ",
"(with nstlist=0 at the next step).",
"In both cases all the usual output will be written to file.",
"When running with MPI, a signal to one of the [TT]mdrun[tt] ranks",
"is sufficient, this signal should not be sent to mpirun or",
"the [TT]mdrun[tt] process that is the parent of the others.",
"[PAR]",
"Interactive molecular dynamics (IMD) can be activated by using at least one",
"of the three IMD switches: The [TT]-imdterm[tt] switch allows to terminate the",
"simulation from the molecular viewer (e.g. VMD). With [TT]-imdwait[tt],",
"[TT]mdrun[tt] pauses whenever no IMD client is connected. Pulling from the",
"IMD remote can be turned on by [TT]-imdpull[tt].",
"The port [TT]mdrun[tt] listens to can be altered by [TT]-imdport[tt].The",
"file pointed to by [TT]-if[tt] contains atom indices and forces if IMD",
"pulling is used."
"[PAR]",
"When [TT]mdrun[tt] is started with MPI, it does not run niced by default."
};
t_commrec *cr;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efTRN, "-o", NULL, ffWRITE },
{ efCOMPRESSED, "-x", NULL, ffOPTWR },
{ efCPT, "-cpi", NULL, ffOPTRD },
{ efCPT, "-cpo", NULL, ffOPTWR },
{ efSTO, "-c", "confout", ffWRITE },
{ efEDR, "-e", "ener", ffWRITE },
{ efLOG, "-g", "md", ffWRITE },
{ efXVG, "-dhdl", "dhdl", ffOPTWR },
{ efXVG, "-field", "field", ffOPTWR },
{ efXVG, "-table", "table", ffOPTRD },
{ efXVG, "-tabletf", "tabletf", ffOPTRD },
{ efXVG, "-tablep", "tablep", ffOPTRD },
{ efXVG, "-tableb", "table", ffOPTRD },
{ efTRX, "-rerun", "rerun", ffOPTRD },
{ efXVG, "-tpi", "tpi", ffOPTWR },
{ efXVG, "-tpid", "tpidist", ffOPTWR },
{ efEDI, "-ei", "sam", ffOPTRD },
{ efXVG, "-eo", "edsam", ffOPTWR },
{ efXVG, "-devout", "deviatie", ffOPTWR },
{ efXVG, "-runav", "runaver", ffOPTWR },
{ efXVG, "-px", "pullx", ffOPTWR },
{ efXVG, "-pf", "pullf", ffOPTWR },
{ efXVG, "-ro", "rotation", ffOPTWR },
{ efLOG, "-ra", "rotangles", ffOPTWR },
{ efLOG, "-rs", "rotslabs", ffOPTWR },
{ efLOG, "-rt", "rottorque", ffOPTWR },
{ efMTX, "-mtx", "nm", ffOPTWR },
{ efNDX, "-dn", "dipole", ffOPTWR },
{ efRND, "-multidir", NULL, ffOPTRDMULT},
{ efDAT, "-membed", "membed", ffOPTRD },
{ efTOP, "-mp", "membed", ffOPTRD },
{ efNDX, "-mn", "membed", ffOPTRD },
{ efXVG, "-if", "imdforces", ffOPTWR },
{ efXVG, "-swap", "swapions", ffOPTWR },
{ efMDP, "-at", NULL, ffOPTRD }, /* at.cfg, only for do_md */
{ efMDP, "-addtop", NULL, ffOPTRD }, /* add additional topology */
};
#define NFILE asize(fnm)
/* Command line options ! */
gmx_bool bDDBondCheck = TRUE;
gmx_bool bDDBondComm = TRUE;
gmx_bool bTunePME = TRUE;
gmx_bool bTestVerlet = FALSE;
gmx_bool bVerbose = FALSE;
gmx_bool bCompact = TRUE;
gmx_bool bSepPot = FALSE;
gmx_bool bRerunVSite = FALSE;
gmx_bool bConfout = TRUE;
gmx_bool bReproducible = FALSE;
gmx_bool bIMDwait = FALSE;
gmx_bool bIMDterm = FALSE;
gmx_bool bIMDpull = FALSE;
int npme = -1;
int nstlist = 0;
int nmultisim = 0;
int nstglobalcomm = -1;
int repl_ex_nst = 0;
int repl_ex_seed = -1;
int repl_ex_nex = 0;
int nstepout = 100;
int resetstep = -1;
gmx_int64_t nsteps = -2; /* the value -2 means that the mdp option will be used */
int imdport = 8888; /* can be almost anything, 8888 is easy to remember */
rvec realddxyz = {0, 0, 0};
const char *ddno_opt[ddnoNR+1] =
{ NULL, "interleave", "pp_pme", "cartesian", NULL };
const char *dddlb_opt[] =
{ NULL, "auto", "no", "yes", NULL };
const char *thread_aff_opt[threadaffNR+1] =
{ NULL, "auto", "on", "off", NULL };
const char *nbpu_opt[] =
{ NULL, "auto", "cpu", "gpu", "gpu_cpu", NULL };
real rdd = 0.0, rconstr = 0.0, dlb_scale = 0.8, pforce = -1;
char *ddcsx = NULL, *ddcsy = NULL, *ddcsz = NULL;
real cpt_period = 15.0, max_hours = -1;
gmx_bool bAppendFiles = TRUE;
gmx_bool bKeepAndNumCPT = FALSE;
gmx_bool bResetCountersHalfWay = FALSE;
output_env_t oenv = NULL;
const char *deviceOptions = "";
/* Non transparent initialization of a complex gmx_hw_opt_t struct.
* But unfortunately we are not allowed to call a function here,
* since declarations follow below.
*/
gmx_hw_opt_t hw_opt = {
0, 0, 0, 0, threadaffSEL, 0, 0,
{ NULL, FALSE, 0, NULL }
};
t_pargs pa[] = {
{ "-dd", FALSE, etRVEC, {&realddxyz},
"Domain decomposition grid, 0 is optimize" },
{ "-ddorder", FALSE, etENUM, {ddno_opt},
"DD rank order" },
{ "-npme", FALSE, etINT, {&npme},
"Number of separate ranks to be used for PME, -1 is guess" },
{ "-nt", FALSE, etINT, {&hw_opt.nthreads_tot},
"Total number of threads to start (0 is guess)" },
{ "-ntmpi", FALSE, etINT, {&hw_opt.nthreads_tmpi},
"Number of thread-MPI threads to start (0 is guess)" },
{ "-ntomp", FALSE, etINT, {&hw_opt.nthreads_omp},
"Number of OpenMP threads per MPI rank to start (0 is guess)" },
{ "-ntomp_pme", FALSE, etINT, {&hw_opt.nthreads_omp_pme},
"Number of OpenMP threads per MPI rank to start (0 is -ntomp)" },
{ "-pin", FALSE, etENUM, {thread_aff_opt},
"Set thread affinities" },
{ "-pinoffset", FALSE, etINT, {&hw_opt.core_pinning_offset},
"The starting logical core number for pinning to cores; used to avoid pinning threads from different mdrun instances to the same core" },
{ "-pinstride", FALSE, etINT, {&hw_opt.core_pinning_stride},
"Pinning distance in logical cores for threads, use 0 to minimize the number of threads per physical core" },
{ "-gpu_id", FALSE, etSTR, {&hw_opt.gpu_opt.gpu_id},
"List of GPU device id-s to use, specifies the per-node PP rank to GPU mapping" },
{ "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
"Check for all bonded interactions with DD" },
{ "-ddbondcomm", FALSE, etBOOL, {&bDDBondComm},
"HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
{ "-rdd", FALSE, etREAL, {&rdd},
"The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
{ "-rcon", FALSE, etREAL, {&rconstr},
"Maximum distance for P-LINCS (nm), 0 is estimate" },
{ "-dlb", FALSE, etENUM, {dddlb_opt},
"Dynamic load balancing (with DD)" },
{ "-dds", FALSE, etREAL, {&dlb_scale},
"Fraction in (0,1) by whose reciprocal the initial DD cell size will be increased in order to "
"provide a margin in which dynamic load balancing can act while preserving the minimum cell size." },
{ "-ddcsx", FALSE, etSTR, {&ddcsx},
"HIDDENA string containing a vector of the relative sizes in the x "
"direction of the corresponding DD cells. Only effective with static "
"load balancing." },
{ "-ddcsy", FALSE, etSTR, {&ddcsy},
"HIDDENA string containing a vector of the relative sizes in the y "
"direction of the corresponding DD cells. Only effective with static "
"load balancing." },
{ "-ddcsz", FALSE, etSTR, {&ddcsz},
"HIDDENA string containing a vector of the relative sizes in the z "
"direction of the corresponding DD cells. Only effective with static "
"load balancing." },
{ "-gcom", FALSE, etINT, {&nstglobalcomm},
"Global communication frequency" },
{ "-nb", FALSE, etENUM, {&nbpu_opt},
"Calculate non-bonded interactions on" },
{ "-nstlist", FALSE, etINT, {&nstlist},
"Set nstlist when using a Verlet buffer tolerance (0 is guess)" },
{ "-tunepme", FALSE, etBOOL, {&bTunePME},
"Optimize PME load between PP/PME ranks or GPU/CPU" },
{ "-testverlet", FALSE, etBOOL, {&bTestVerlet},
"Test the Verlet non-bonded scheme" },
{ "-v", FALSE, etBOOL, {&bVerbose},
"Be loud and noisy" },
{ "-compact", FALSE, etBOOL, {&bCompact},
"Write a compact log file" },
{ "-seppot", FALSE, etBOOL, {&bSepPot},
"Write separate V and dVdl terms for each interaction type and rank to the log file(s)" },
{ "-pforce", FALSE, etREAL, {&pforce},
"Print all forces larger than this (kJ/mol nm)" },
{ "-reprod", FALSE, etBOOL, {&bReproducible},
"Try to avoid optimizations that affect binary reproducibility" },
{ "-cpt", FALSE, etREAL, {&cpt_period},
"Checkpoint interval (minutes)" },
{ "-cpnum", FALSE, etBOOL, {&bKeepAndNumCPT},
"Keep and number checkpoint files" },
{ "-append", FALSE, etBOOL, {&bAppendFiles},
"Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" },
{ "-nsteps", FALSE, etINT64, {&nsteps},
"Run this number of steps, overrides .mdp file option" },
{ "-maxh", FALSE, etREAL, {&max_hours},
"Terminate after 0.99 times this time (hours)" },
{ "-multi", FALSE, etINT, {&nmultisim},
"Do multiple simulations in parallel" },
{ "-replex", FALSE, etINT, {&repl_ex_nst},
"Attempt replica exchange periodically with this period (steps)" },
{ "-nex", FALSE, etINT, {&repl_ex_nex},
"Number of random exchanges to carry out each exchange interval (N^3 is one suggestion). -nex zero or not specified gives neighbor replica exchange." },
{ "-reseed", FALSE, etINT, {&repl_ex_seed},
"Seed for replica exchange, -1 is generate a seed" },
{ "-imdport", FALSE, etINT, {&imdport},
"HIDDENIMD listening port" },
{ "-imdwait", FALSE, etBOOL, {&bIMDwait},
"HIDDENPause the simulation while no IMD client is connected" },
{ "-imdterm", FALSE, etBOOL, {&bIMDterm},
"HIDDENAllow termination of the simulation from IMD client" },
{ "-imdpull", FALSE, etBOOL, {&bIMDpull},
"HIDDENAllow pulling in the simulation from IMD client" },
{ "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
"HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
{ "-confout", FALSE, etBOOL, {&bConfout},
"HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
{ "-stepout", FALSE, etINT, {&nstepout},
"HIDDENFrequency of writing the remaining wall clock time for the run" },
{ "-resetstep", FALSE, etINT, {&resetstep},
"HIDDENReset cycle counters after these many time steps" },
{ "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
"HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
};
unsigned long Flags, PCA_Flags;
ivec ddxyz;
int dd_node_order;
gmx_bool bAddPart;
FILE *fplog, *fpmulti;
int sim_part, sim_part_fn;
const char *part_suffix = ".part";
char suffix[STRLEN];
int rc;
char **multidir = NULL;
cr = init_commrec();
PCA_Flags = (PCA_CAN_SET_DEFFNM | (MASTER(cr) ? 0 : PCA_QUIET));
/* Comment this in to do fexist calls only on master
* works not with rerun or tables at the moment
* also comment out the version of init_forcerec in md.c
* with NULL instead of opt2fn
*/
/*
if (!MASTER(cr))
{
PCA_Flags |= PCA_NOT_READ_NODE;
}
*/
if (!parse_common_args(&argc, argv, PCA_Flags, NFILE, fnm, asize(pa), pa,
asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
/* we set these early because they might be used in init_multisystem()
Note that there is the potential for npme>nnodes until the number of
threads is set later on, if there's thread parallelization. That shouldn't
lead to problems. */
dd_node_order = nenum(ddno_opt);
cr->npmenodes = npme;
hw_opt.thread_affinity = nenum(thread_aff_opt);
/* now check the -multi and -multidir option */
if (opt2bSet("-multidir", NFILE, fnm))
{
if (nmultisim > 0)
{
gmx_fatal(FARGS, "mdrun -multi and -multidir options are mutually exclusive.");
}
nmultisim = opt2fns(&multidir, "-multidir", NFILE, fnm);
}
if (repl_ex_nst != 0 && nmultisim < 2)
{
gmx_fatal(FARGS, "Need at least two replicas for replica exchange (option -multi)");
}
if (repl_ex_nex < 0)
{
gmx_fatal(FARGS, "Replica exchange number of exchanges needs to be positive");
}
if (nmultisim > 1)
{
#ifndef GMX_THREAD_MPI
gmx_bool bParFn = (multidir == NULL);
init_multisystem(cr, nmultisim, multidir, NFILE, fnm, bParFn);
#else
gmx_fatal(FARGS, "mdrun -multi is not supported with the thread library. "
"Please compile GROMACS with MPI support");
#endif
}
bAddPart = !bAppendFiles;
/* Check if there is ANY checkpoint file available */
sim_part = 1;
sim_part_fn = sim_part;
if (opt2bSet("-cpi", NFILE, fnm))
{
if (bSepPot && bAppendFiles)
{
gmx_fatal(FARGS, "Output file appending is not supported with -seppot");
}
bAppendFiles =
read_checkpoint_simulation_part(opt2fn_master("-cpi", NFILE,
fnm, cr),
&sim_part_fn, NULL, cr,
bAppendFiles, NFILE, fnm,
part_suffix, &bAddPart);
if (sim_part_fn == 0 && MULTIMASTER(cr))
{
fprintf(stdout, "No previous checkpoint file present, assuming this is a new run.\n");
}
else
{
sim_part = sim_part_fn + 1;
}
if (MULTISIM(cr) && MASTER(cr))
{
if (MULTIMASTER(cr))
{
/* Log file is not yet available, so if there's a
* problem we can only write to stderr. */
fpmulti = stderr;
}
else
{
fpmulti = NULL;
}
check_multi_int(fpmulti, cr->ms, sim_part, "simulation part", TRUE);
}
}
else
{
bAppendFiles = FALSE;
}
if (!bAppendFiles)
{
sim_part_fn = sim_part;
}
if (bAddPart)
{
/* Rename all output files (except checkpoint files) */
/* create new part name first (zero-filled) */
sprintf(suffix, "%s%04d", part_suffix, sim_part_fn);
add_suffix_to_output_names(fnm, NFILE, suffix);
if (MULTIMASTER(cr))
{
fprintf(stdout, "Checkpoint file is from part %d, new output files will be suffixed '%s'.\n", sim_part-1, suffix);
}
}
Flags = opt2bSet("-rerun", NFILE, fnm) ? MD_RERUN : 0;
Flags = Flags | (bSepPot ? MD_SEPPOT : 0);
Flags = Flags | (bDDBondCheck ? MD_DDBONDCHECK : 0);
Flags = Flags | (bDDBondComm ? MD_DDBONDCOMM : 0);
Flags = Flags | (bTunePME ? MD_TUNEPME : 0);
Flags = Flags | (bTestVerlet ? MD_TESTVERLET : 0);
Flags = Flags | (bConfout ? MD_CONFOUT : 0);
Flags = Flags | (bRerunVSite ? MD_RERUN_VSITE : 0);
Flags = Flags | (bReproducible ? MD_REPRODUCIBLE : 0);
Flags = Flags | (bAppendFiles ? MD_APPENDFILES : 0);
Flags = Flags | (opt2parg_bSet("-append", asize(pa), pa) ? MD_APPENDFILESSET : 0);
Flags = Flags | (bKeepAndNumCPT ? MD_KEEPANDNUMCPT : 0);
Flags = Flags | (sim_part > 1 ? MD_STARTFROMCPT : 0);
Flags = Flags | (bResetCountersHalfWay ? MD_RESETCOUNTERSHALFWAY : 0);
Flags = Flags | (bIMDwait ? MD_IMDWAIT : 0);
Flags = Flags | (bIMDterm ? MD_IMDTERM : 0);
Flags = Flags | (bIMDpull ? MD_IMDPULL : 0);
Flags = Flags | ((opt2bSet("-at", NFILE, fnm)) ? MD_ADAPTIVETEMPERING : 0);
Flags = Flags | ((opt2bSet("-addtop", NFILE, fnm)) ? MD_MULTOP : 0);
/* We postpone opening the log file if we are appending, so we can
first truncate the old log file and append to the correct position
there instead. */
if ((MASTER(cr) || bSepPot) && !bAppendFiles)
{
gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr,
!bSepPot, Flags & MD_APPENDFILES, &fplog);
please_cite(fplog, "Hess2008b");
please_cite(fplog, "Spoel2005a");
please_cite(fplog, "Lindahl2001a");
please_cite(fplog, "Berendsen95a");
}
else if (!MASTER(cr) && bSepPot)
{
gmx_log_open(ftp2fn(efLOG, NFILE, fnm), cr, !bSepPot, Flags, &fplog);
}
else
{
fplog = NULL;
}
ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
rc = mdrunner(&hw_opt, fplog, cr, NFILE, fnm, oenv, bVerbose, bCompact,
nstglobalcomm, ddxyz, dd_node_order, rdd, rconstr,
dddlb_opt[0], dlb_scale, ddcsx, ddcsy, ddcsz,
nbpu_opt[0], nstlist,
nsteps, nstepout, resetstep,
nmultisim, repl_ex_nst, repl_ex_nex, repl_ex_seed,
pforce, cpt_period, max_hours, deviceOptions, imdport, Flags);
/* Log file has to be closed in mdrunner if we are appending to it
(fplog not set here) */
if (MASTER(cr) && !bAppendFiles)
{
gmx_log_close(fplog);
}
return rc;
}
int gmx_sans(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] computes SANS spectra using Debye formula.",
"It currently uses topology file (since it need to assigne element for each atom).",
"[PAR]",
"Parameters:[PAR]"
"[TT]-pr[tt] Computes normalized g(r) function averaged over trajectory[PAR]",
"[TT]-prframe[tt] Computes normalized g(r) function for each frame[PAR]",
"[TT]-sq[tt] Computes SANS intensity curve averaged over trajectory[PAR]",
"[TT]-sqframe[tt] Computes SANS intensity curve for each frame[PAR]",
"[TT]-startq[tt] Starting q value in nm[PAR]",
"[TT]-endq[tt] Ending q value in nm[PAR]",
"[TT]-qstep[tt] Stepping in q space[PAR]",
"Note: When using Debye direct method computational cost increases as",
"1/2 * N * (N - 1) where N is atom number in group of interest.",
"[PAR]",
"WARNING: If sq or pr specified this tool can produce large number of files! Up to two times larger than number of frames!"
};
static gmx_bool bPBC = TRUE;
static gmx_bool bNORM = FALSE;
static real binwidth = 0.2, grid = 0.05; /* bins shouldnt be smaller then smallest bond (~0.1nm) length */
static real start_q = 0.0, end_q = 2.0, q_step = 0.01;
static real mcover = -1;
static unsigned int seed = 0;
static int nthreads = -1;
static const char *emode[] = { NULL, "direct", "mc", NULL };
static const char *emethod[] = { NULL, "debye", "fft", NULL };
gmx_neutron_atomic_structurefactors_t *gnsf;
gmx_sans_t *gsans;
#define NPA asize(pa)
t_pargs pa[] = {
{ "-bin", FALSE, etREAL, {&binwidth},
"[HIDDEN]Binwidth (nm)" },
{ "-mode", FALSE, etENUM, {emode},
"Mode for sans spectra calculation" },
{ "-mcover", FALSE, etREAL, {&mcover},
"Monte-Carlo coverage should be -1(default) or (0,1]"},
{ "-method", FALSE, etENUM, {emethod},
"[HIDDEN]Method for sans spectra calculation" },
{ "-pbc", FALSE, etBOOL, {&bPBC},
"Use periodic boundary conditions for computing distances" },
{ "-grid", FALSE, etREAL, {&grid},
"[HIDDEN]Grid spacing (in nm) for FFTs" },
{"-startq", FALSE, etREAL, {&start_q},
"Starting q (1/nm) "},
{"-endq", FALSE, etREAL, {&end_q},
"Ending q (1/nm)"},
{ "-qstep", FALSE, etREAL, {&q_step},
"Stepping in q (1/nm)"},
{ "-seed", FALSE, etINT, {&seed},
"Random seed for Monte-Carlo"},
#ifdef GMX_OPENMP
{ "-nt", FALSE, etINT, {&nthreads},
"Number of threads to start"},
#endif
};
FILE *fp;
const char *fnTPX, *fnNDX, *fnTRX, *fnDAT = NULL;
t_trxstatus *status;
t_topology *top = NULL;
t_atom *atom = NULL;
gmx_rmpbc_t gpbc = NULL;
gmx_bool bTPX;
gmx_bool bFFT = FALSE, bDEBYE = FALSE;
gmx_bool bMC = FALSE;
int ePBC = -1;
matrix box;
char title[STRLEN];
rvec *x;
int natoms;
real t;
char **grpname = NULL;
atom_id *index = NULL;
int isize;
int i, j;
char *hdr = NULL;
char *suffix = NULL;
t_filenm *fnmdup = NULL;
gmx_radial_distribution_histogram_t *prframecurrent = NULL, *pr = NULL;
gmx_static_structurefactor_t *sqframecurrent = NULL, *sq = NULL;
output_env_t oenv;
#define NFILE asize(fnm)
t_filenm fnm[] = {
{ efTPX, "-s", NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efDAT, "-d", "nsfactor", ffOPTRD },
{ efXVG, "-pr", "pr", ffWRITE },
{ efXVG, "-sq", "sq", ffWRITE },
{ efXVG, "-prframe", "prframe", ffOPTWR },
{ efXVG, "-sqframe", "sqframe", ffOPTWR }
};
nthreads = gmx_omp_get_max_threads();
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
/* check that binwidth not smaller than smallers distance */
check_binwidth(binwidth);
check_mcover(mcover);
/* setting number of omp threads globaly */
gmx_omp_set_num_threads(nthreads);
/* Now try to parse opts for modes */
switch (emethod[0][0])
{
case 'd':
bDEBYE = TRUE;
switch (emode[0][0])
{
case 'd':
bMC = FALSE;
break;
case 'm':
bMC = TRUE;
break;
default:
break;
}
break;
case 'f':
bFFT = TRUE;
break;
default:
break;
}
if (bDEBYE)
{
if (bMC)
{
fprintf(stderr, "Using Monte Carlo Debye method to calculate spectrum\n");
}
else
{
fprintf(stderr, "Using direct Debye method to calculate spectrum\n");
}
}
else if (bFFT)
{
gmx_fatal(FARGS, "FFT method not implemented!");
}
else
{
gmx_fatal(FARGS, "Unknown combination for mode and method!");
}
/* Try to read files */
fnDAT = ftp2fn(efDAT, NFILE, fnm);
fnTPX = ftp2fn(efTPX, NFILE, fnm);
fnTRX = ftp2fn(efTRX, NFILE, fnm);
gnsf = gmx_neutronstructurefactors_init(fnDAT);
fprintf(stderr, "Read %d atom names from %s with neutron scattering parameters\n\n", gnsf->nratoms, fnDAT);
snew(top, 1);
snew(grpname, 1);
snew(index, 1);
bTPX = read_tps_conf(fnTPX, title, top, &ePBC, &x, NULL, box, TRUE);
printf("\nPlease select group for SANS spectra calculation:\n");
get_index(&(top->atoms), ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, grpname);
gsans = gmx_sans_init(top, gnsf);
/* Prepare reference frame */
if (bPBC)
{
gpbc = gmx_rmpbc_init(&top->idef, ePBC, top->atoms.nr);
gmx_rmpbc(gpbc, top->atoms.nr, box, x);
}
natoms = read_first_x(oenv, &status, fnTRX, &t, &x, box);
if (natoms != top->atoms.nr)
{
fprintf(stderr, "\nWARNING: number of atoms in tpx (%d) and trajectory (%d) do not match\n", natoms, top->atoms.nr);
}
do
{
if (bPBC)
{
gmx_rmpbc(gpbc, top->atoms.nr, box, x);
}
/* allocate memory for pr */
if (pr == NULL)
{
/* in case its first frame to read */
snew(pr, 1);
}
/* realy calc p(r) */
prframecurrent = calc_radial_distribution_histogram(gsans, x, box, index, isize, binwidth, bMC, bNORM, mcover, seed);
/* copy prframecurrent -> pr and summ up pr->gr[i] */
/* allocate and/or resize memory for pr->gr[i] and pr->r[i] */
if (pr->gr == NULL)
{
/* check if we use pr->gr first time */
snew(pr->gr, prframecurrent->grn);
snew(pr->r, prframecurrent->grn);
}
else
{
/* resize pr->gr and pr->r if needed to preven overruns */
if (prframecurrent->grn > pr->grn)
{
srenew(pr->gr, prframecurrent->grn);
srenew(pr->r, prframecurrent->grn);
}
}
pr->grn = prframecurrent->grn;
pr->binwidth = prframecurrent->binwidth;
/* summ up gr and fill r */
for (i = 0; i < prframecurrent->grn; i++)
{
pr->gr[i] += prframecurrent->gr[i];
pr->r[i] = prframecurrent->r[i];
}
/* normalize histo */
normalize_probability(prframecurrent->grn, prframecurrent->gr);
/* convert p(r) to sq */
sqframecurrent = convert_histogram_to_intensity_curve(prframecurrent, start_q, end_q, q_step);
/* print frame data if needed */
if (opt2fn_null("-prframe", NFILE, fnm))
{
snew(hdr, 25);
snew(suffix, GMX_PATH_MAX);
/* prepare header */
sprintf(hdr, "g(r), t = %f", t);
/* prepare output filename */
fnmdup = dup_tfn(NFILE, fnm);
sprintf(suffix, "-t%.2f", t);
add_suffix_to_output_names(fnmdup, NFILE, suffix);
fp = xvgropen(opt2fn_null("-prframe", NFILE, fnmdup), hdr, "Distance (nm)", "Probability", oenv);
for (i = 0; i < prframecurrent->grn; i++)
{
fprintf(fp, "%10.6f%10.6f\n", prframecurrent->r[i], prframecurrent->gr[i]);
}
done_filenms(NFILE, fnmdup);
fclose(fp);
sfree(hdr);
sfree(suffix);
sfree(fnmdup);
}
if (opt2fn_null("-sqframe", NFILE, fnm))
{
snew(hdr, 25);
snew(suffix, GMX_PATH_MAX);
/* prepare header */
sprintf(hdr, "I(q), t = %f", t);
/* prepare output filename */
fnmdup = dup_tfn(NFILE, fnm);
sprintf(suffix, "-t%.2f", t);
add_suffix_to_output_names(fnmdup, NFILE, suffix);
fp = xvgropen(opt2fn_null("-sqframe", NFILE, fnmdup), hdr, "q (nm^-1)", "s(q)/s(0)", oenv);
for (i = 0; i < sqframecurrent->qn; i++)
{
fprintf(fp, "%10.6f%10.6f\n", sqframecurrent->q[i], sqframecurrent->s[i]);
}
done_filenms(NFILE, fnmdup);
fclose(fp);
sfree(hdr);
sfree(suffix);
sfree(fnmdup);
}
/* free pr structure */
sfree(prframecurrent->gr);
sfree(prframecurrent->r);
sfree(prframecurrent);
/* free sq structure */
sfree(sqframecurrent->q);
sfree(sqframecurrent->s);
sfree(sqframecurrent);
}
while (read_next_x(oenv, status, &t, x, box));
close_trj(status);
/* normalize histo */
normalize_probability(pr->grn, pr->gr);
sq = convert_histogram_to_intensity_curve(pr, start_q, end_q, q_step);
/* prepare pr.xvg */
fp = xvgropen(opt2fn_null("-pr", NFILE, fnm), "G(r)", "Distance (nm)", "Probability", oenv);
for (i = 0; i < pr->grn; i++)
{
fprintf(fp, "%10.6f%10.6f\n", pr->r[i], pr->gr[i]);
}
xvgrclose(fp);
/* prepare sq.xvg */
fp = xvgropen(opt2fn_null("-sq", NFILE, fnm), "I(q)", "q (nm^-1)", "s(q)/s(0)", oenv);
for (i = 0; i < sq->qn; i++)
{
fprintf(fp, "%10.6f%10.6f\n", sq->q[i], sq->s[i]);
}
xvgrclose(fp);
/*
* Clean up memory
*/
sfree(pr->gr);
sfree(pr->r);
sfree(pr);
sfree(sq->q);
sfree(sq->s);
sfree(sq);
please_cite(stdout, "Garmay2012");
return 0;
}
int gmx_g_angle(int argc, char *argv[])
{
static const char *desc[] = {
"[TT]g_angle[tt] computes the angle distribution for a number of angles",
"or dihedrals.[PAR]",
"With option [TT]-ov[tt], you can plot the average angle of",
"a group of angles as a function of time. With the [TT]-all[tt] option,",
"the first graph is the average and the rest are the individual angles.[PAR]",
"With the [TT]-of[tt] option, [TT]g_angle[tt] also calculates the fraction of trans",
"dihedrals (only for dihedrals) as function of time, but this is",
"probably only fun for a select few.[PAR]",
"With option [TT]-oc[tt], a dihedral correlation function is calculated.[PAR]",
"It should be noted that the index file must contain",
"atom triplets 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 principal components analysis using [TT]g_covar[tt].[PAR]",
"Option [TT]-ot[tt] plots when transitions occur between",
"dihedral rotamers of multiplicity 3 and [TT]-oh[tt]",
"records a histogram of the times between such transitions,",
"assuming the input trajectory frames are equally spaced in time."
};
static const char *opt[] = { NULL, "angle", "dihedral", "improper", "ryckaert-bellemans", NULL };
static gmx_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 or phi > 60."
},
{ "-avercorr", FALSE, etBOOL, {&bAverCorr},
"Average the correlation functions for the individual angles/dihedrals"
}
};
static const 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;
gmx_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;
output_env_t oenv;
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);
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 (bTrans && opt[0][0] != 'd')
{
fprintf(stderr, "Option -ot should only accompany -type dihedral. Disabling -ot.\n");
bTrans = FALSE;
}
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,
oenv);
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)", oenv);
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");
}
ffclose(out);
}
if (opt2bSet("-or", NFILE, fnm))
{
dump_dih_trn(nframes, nangles, dih, opt2fn("-or", NFILE, fnm), time);
}
if (bFrac)
{
sprintf(title, "Trans fraction: %s", grpname);
out = xvgropen(opt2fn("-of", NFILE, fnm),
title, "Time (ps)", "Fraction", oenv);
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];
}
ffclose(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, bRb, oenv);
}
if (bCorr)
{
/* Autocorrelation function */
if (nframes < 2)
{
fprintf(stderr, "Not enough frames for correlation function\n");
}
else
{
if (bChandler)
{
real dval, sixty = DEG2RAD*60;
gmx_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), oenv,
"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", "", oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
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);
}
ffclose(out);
do_view(oenv, opt2fn("-od", NFILE, fnm), "-nxy");
if (bAver)
{
do_view(oenv, opt2fn("-ov", NFILE, fnm), "-nxy");
}
thanx(stderr);
return 0;
}
int gmx_rms(int argc, char *argv[])
{
const char *desc[] =
{
"[THISMODULE] compares two structures by computing the root mean square",
"deviation (RMSD), the size-independent [GRK]rho[grk] similarity parameter",
"([TT]rho[tt]) or the scaled [GRK]rho[grk] ([TT]rhosc[tt]), ",
"see Maiorov & Crippen, Proteins [BB]22[bb], 273 (1995).",
"This is selected by [TT]-what[tt].[PAR]"
"Each structure from a trajectory ([TT]-f[tt]) is compared to a",
"reference structure. The reference structure",
"is taken from the structure file ([TT]-s[tt]).[PAR]",
"With option [TT]-mir[tt] also a comparison with the mirror image of",
"the reference structure is calculated.",
"This is useful as a reference for 'significant' values, see",
"Maiorov & Crippen, Proteins [BB]22[bb], 273 (1995).[PAR]",
"Option [TT]-prev[tt] produces the comparison with a previous frame",
"the specified number of frames ago.[PAR]",
"Option [TT]-m[tt] produces a matrix in [TT].xpm[tt] format of",
"comparison values of each structure in the trajectory with respect to",
"each other structure. This file can be visualized with for instance",
"[TT]xv[tt] and can be converted to postscript with [gmx-xpm2ps].[PAR]",
"Option [TT]-fit[tt] controls the least-squares fitting of",
"the structures on top of each other: complete fit (rotation and",
"translation), translation only, or no fitting at all.[PAR]",
"Option [TT]-mw[tt] controls whether mass weighting is done or not.",
"If you select the option (default) and ",
"supply a valid [TT].tpr[tt] file masses will be taken from there, ",
"otherwise the masses will be deduced from the [TT]atommass.dat[tt] file in",
"[TT]GMXLIB[tt]. This is fine for proteins, but not",
"necessarily for other molecules. A default mass of 12.011 amu (carbon)",
"is assigned to unknown atoms. You can check whether this happend by",
"turning on the [TT]-debug[tt] flag and inspecting the log file.[PAR]",
"With [TT]-f2[tt], the 'other structures' are taken from a second",
"trajectory, this generates a comparison matrix of one trajectory",
"versus the other.[PAR]",
"Option [TT]-bin[tt] does a binary dump of the comparison matrix.[PAR]",
"Option [TT]-bm[tt] produces a matrix of average bond angle deviations",
"analogously to the [TT]-m[tt] option. Only bonds between atoms in the",
"comparison group are considered."
};
static gmx_bool bPBC = TRUE, bFitAll = TRUE, bSplit = FALSE;
static gmx_bool bDeltaLog = FALSE;
static int prev = 0, freq = 1, freq2 = 1, nlevels = 80, avl = 0;
static real rmsd_user_max = -1, rmsd_user_min = -1, bond_user_max = -1,
bond_user_min = -1, delta_maxy = 0.0;
/* strings and things for selecting difference method */
enum
{
ewSel, ewRMSD, ewRho, ewRhoSc, ewNR
};
int ewhat;
const char *what[ewNR + 1] =
{ NULL, "rmsd", "rho", "rhosc", NULL };
const char *whatname[ewNR] =
{ NULL, "RMSD", "Rho", "Rho sc" };
const char *whatlabel[ewNR] =
{ NULL, "RMSD (nm)", "Rho", "Rho sc" };
const char *whatxvgname[ewNR] =
{ NULL, "RMSD", "\\8r\\4", "\\8r\\4\\ssc\\N" };
const char *whatxvglabel[ewNR] =
{ NULL, "RMSD (nm)", "\\8r\\4", "\\8r\\4\\ssc\\N" };
/* strings and things for fitting methods */
enum
{
efSel, efFit, efReset, efNone, efNR
};
int efit;
const char *fit[efNR + 1] =
{ NULL, "rot+trans", "translation", "none", NULL };
const char *fitgraphlabel[efNR + 1] =
{ NULL, "lsq fit", "translational fit", "no fit" };
static int nrms = 1;
static gmx_bool bMassWeighted = TRUE;
t_pargs pa[] =
{
{ "-what", FALSE, etENUM,
{ what }, "Structural difference measure" },
{ "-pbc", FALSE, etBOOL,
{ &bPBC }, "PBC check" },
{ "-fit", FALSE, etENUM,
{ fit }, "Fit to reference structure" },
{ "-prev", FALSE, etINT,
{ &prev }, "Compare with previous frame" },
{ "-split", FALSE, etBOOL,
{ &bSplit }, "Split graph where time is zero" },
{ "-fitall", FALSE, etBOOL,
{ &bFitAll }, "HIDDENFit all pairs of structures in matrix" },
{ "-skip", FALSE, etINT,
{ &freq }, "Only write every nr-th frame to matrix" },
{ "-skip2", FALSE, etINT,
{ &freq2 }, "Only write every nr-th frame to matrix" },
{ "-max", FALSE, etREAL,
{ &rmsd_user_max }, "Maximum level in comparison matrix" },
{ "-min", FALSE, etREAL,
{ &rmsd_user_min }, "Minimum level in comparison matrix" },
{ "-bmax", FALSE, etREAL,
{ &bond_user_max }, "Maximum level in bond angle matrix" },
{ "-bmin", FALSE, etREAL,
{ &bond_user_min }, "Minimum level in bond angle matrix" },
{ "-mw", FALSE, etBOOL,
{ &bMassWeighted }, "Use mass weighting for superposition" },
{ "-nlevels", FALSE, etINT,
{ &nlevels }, "Number of levels in the matrices" },
{ "-ng", FALSE, etINT,
{ &nrms }, "Number of groups to compute RMS between" },
{ "-dlog", FALSE, etBOOL,
{ &bDeltaLog },
"HIDDENUse a log x-axis in the delta t matrix" },
{ "-dmax", FALSE, etREAL,
{ &delta_maxy }, "HIDDENMaximum level in delta matrix" },
{ "-aver", FALSE, etINT,
{ &avl },
"HIDDENAverage over this distance in the RMSD matrix" }
};
int natoms_trx, natoms_trx2, natoms;
int i, j, k, m, teller, teller2, tel_mat, tel_mat2;
#define NFRAME 5000
int maxframe = NFRAME, maxframe2 = NFRAME;
real t, *w_rls, *w_rms, *w_rls_m = NULL, *w_rms_m = NULL;
gmx_bool bNorm, bAv, bFreq2, bFile2, bMat, bBond, bDelta, bMirror, bMass;
gmx_bool bFit, bReset;
t_topology top;
int ePBC;
t_iatom *iatom = NULL;
matrix box;
rvec *x, *xp, *xm = NULL, **mat_x = NULL, **mat_x2, *mat_x2_j = NULL, vec1,
vec2;
t_trxstatus *status;
char buf[256], buf2[256];
int ncons = 0;
FILE *fp;
real rlstot = 0, **rls, **rlsm = NULL, *time, *time2, *rlsnorm = NULL,
**rmsd_mat = NULL, **bond_mat = NULL, *axis, *axis2, *del_xaxis,
*del_yaxis, rmsd_max, rmsd_min, rmsd_avg, bond_max, bond_min, ang;
real **rmsdav_mat = NULL, av_tot, weight, weight_tot;
real **delta = NULL, delta_max, delta_scalex = 0, delta_scaley = 0,
*delta_tot;
int delta_xsize = 0, del_lev = 100, mx, my, abs_my;
gmx_bool bA1, bA2, bPrev, bTop, *bInMat = NULL;
int ifit, *irms, ibond = 0, *ind_bond1 = NULL, *ind_bond2 = NULL, n_ind_m =
0;
atom_id *ind_fit, **ind_rms, *ind_m = NULL, *rev_ind_m = NULL, *ind_rms_m =
NULL;
char *gn_fit, **gn_rms;
t_rgb rlo, rhi;
output_env_t oenv;
gmx_rmpbc_t gpbc = NULL;
t_filenm fnm[] =
{
{ efTPS, NULL, NULL, ffREAD },
{ efTRX, "-f", NULL, ffREAD },
{ efTRX, "-f2", NULL, ffOPTRD },
{ efNDX, NULL, NULL, ffOPTRD },
{ efXVG, NULL, "rmsd", ffWRITE },
{ efXVG, "-mir", "rmsdmir", ffOPTWR },
{ efXVG, "-a", "avgrp", ffOPTWR },
{ efXVG, "-dist", "rmsd-dist", ffOPTWR },
{ efXPM, "-m", "rmsd", ffOPTWR },
{ efDAT, "-bin", "rmsd", ffOPTWR },
{ efXPM, "-bm", "bond", ffOPTWR }
};
#define NFILE asize(fnm)
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW
| PCA_BE_NICE, NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL,
&oenv))
{
return 0;
}
/* parse enumerated options: */
ewhat = nenum(what);
if (ewhat == ewRho || ewhat == ewRhoSc)
{
please_cite(stdout, "Maiorov95");
}
efit = nenum(fit);
bFit = efit == efFit;
bReset = efit == efReset;
if (bFit)
{
bReset = TRUE; /* for fit, reset *must* be set */
}
else
{
bFitAll = FALSE;
}
/* mark active cmdline options */
bMirror = opt2bSet("-mir", NFILE, fnm); /* calc RMSD vs mirror of ref. */
bFile2 = opt2bSet("-f2", NFILE, fnm);
bMat = opt2bSet("-m", NFILE, fnm);
bBond = opt2bSet("-bm", NFILE, fnm);
bDelta = (delta_maxy > 0); /* calculate rmsd vs delta t matrix from *
* your RMSD matrix (hidden option */
bNorm = opt2bSet("-a", NFILE, fnm);
bFreq2 = opt2parg_bSet("-skip2", asize(pa), pa);
if (freq <= 0)
{
fprintf(stderr, "The number of frames to skip is <= 0. "
"Writing out all frames.\n\n");
freq = 1;
}
if (!bFreq2)
{
freq2 = freq;
}
else if (bFile2 && freq2 <= 0)
{
fprintf(stderr,
"The number of frames to skip in second trajectory is <= 0.\n"
" Writing out all frames.\n\n");
freq2 = 1;
}
bPrev = (prev > 0);
if (bPrev)
{
prev = abs(prev);
if (freq != 1)
{
fprintf(stderr, "WARNING: option -skip also applies to -prev\n");
}
}
if (bFile2 && !bMat && !bBond)
{
fprintf(
stderr,
"WARNING: second trajectory (-f2) useless when not calculating matrix (-m/-bm),\n"
" will not read from %s\n", opt2fn("-f2", NFILE,
fnm));
bFile2 = FALSE;
}
if (bDelta)
{
bMat = TRUE;
if (bFile2)
{
fprintf(stderr,
"WARNING: second trajectory (-f2) useless when making delta matrix,\n"
" will not read from %s\n", opt2fn("-f2",
NFILE, fnm));
bFile2 = FALSE;
}
}
bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), buf, &top, &ePBC, &xp,
NULL, box, TRUE);
snew(w_rls, top.atoms.nr);
snew(w_rms, top.atoms.nr);
if (!bTop && bBond)
{
fprintf(stderr,
"WARNING: Need a run input file for bond angle matrix,\n"
" will not calculate bond angle matrix.\n");
bBond = FALSE;
}
if (bReset)
{
fprintf(stderr, "Select group for %s fit\n", bFit ? "least squares"
: "translational");
get_index(&(top.atoms), ftp2fn_null(efNDX, NFILE, fnm), 1, &ifit,
&ind_fit, &gn_fit);
}
else
{
ifit = 0;
}
if (bReset)
{
if (bFit && ifit < 3)
{
gmx_fatal(FARGS, "Need >= 3 points to fit!\n" );
}
bMass = FALSE;
for (i = 0; i < ifit; i++)
{
if (bMassWeighted)
{
w_rls[ind_fit[i]] = top.atoms.atom[ind_fit[i]].m;
}
else
{
w_rls[ind_fit[i]] = 1;
}
bMass = bMass || (top.atoms.atom[ind_fit[i]].m != 0);
}
if (!bMass)
{
fprintf(stderr, "All masses in the fit group are 0, using masses of 1\n");
for (i = 0; i < ifit; i++)
{
w_rls[ind_fit[i]] = 1;
}
}
}
if (bMat || bBond)
{
nrms = 1;
}
snew(gn_rms, nrms);
snew(ind_rms, nrms);
snew(irms, nrms);
fprintf(stderr, "Select group%s for %s calculation\n",
(nrms > 1) ? "s" : "", whatname[ewhat]);
get_index(&(top.atoms), ftp2fn_null(efNDX, NFILE, fnm),
nrms, irms, ind_rms, gn_rms);
if (bNorm)
{
snew(rlsnorm, irms[0]);
}
snew(rls, nrms);
for (j = 0; j < nrms; j++)
{
snew(rls[j], maxframe);
}
if (bMirror)
{
snew(rlsm, nrms);
for (j = 0; j < nrms; j++)
{
snew(rlsm[j], maxframe);
}
}
snew(time, maxframe);
for (j = 0; j < nrms; j++)
{
bMass = FALSE;
for (i = 0; i < irms[j]; i++)
{
if (bMassWeighted)
{
w_rms[ind_rms[j][i]] = top.atoms.atom[ind_rms[j][i]].m;
}
else
{
w_rms[ind_rms[j][i]] = 1.0;
}
bMass = bMass || (top.atoms.atom[ind_rms[j][i]].m != 0);
}
if (!bMass)
{
fprintf(stderr, "All masses in group %d are 0, using masses of 1\n", j);
for (i = 0; i < irms[j]; i++)
{
w_rms[ind_rms[j][i]] = 1;
}
}
}
/* Prepare reference frame */
if (bPBC)
{
gpbc = gmx_rmpbc_init(&top.idef, ePBC, top.atoms.nr);
gmx_rmpbc(gpbc, top.atoms.nr, box, xp);
}
if (bReset)
{
reset_x(ifit, ind_fit, top.atoms.nr, NULL, xp, w_rls);
}
if (bMirror)
{
/* generate reference structure mirror image: */
snew(xm, top.atoms.nr);
for (i = 0; i < top.atoms.nr; i++)
{
copy_rvec(xp[i], xm[i]);
xm[i][XX] = -xm[i][XX];
}
}
if (ewhat == ewRhoSc)
{
norm_princ(&top.atoms, ifit, ind_fit, top.atoms.nr, xp);
}
/* read first frame */
natoms_trx = read_first_x(oenv, &status, opt2fn("-f", NFILE, fnm), &t, &x, box);
if (natoms_trx != top.atoms.nr)
{
fprintf(stderr,
"\nWARNING: topology has %d atoms, whereas trajectory has %d\n",
top.atoms.nr, natoms_trx);
}
natoms = min(top.atoms.nr, natoms_trx);
if (bMat || bBond || bPrev)
{
snew(mat_x, NFRAME);
if (bPrev)
{
/* With -prev we use all atoms for simplicity */
n_ind_m = natoms;
}
else
{
/* Check which atoms we need (fit/rms) */
snew(bInMat, natoms);
for (i = 0; i < ifit; i++)
{
bInMat[ind_fit[i]] = TRUE;
}
n_ind_m = ifit;
for (i = 0; i < irms[0]; i++)
{
if (!bInMat[ind_rms[0][i]])
{
bInMat[ind_rms[0][i]] = TRUE;
n_ind_m++;
}
}
}
/* Make an index of needed atoms */
snew(ind_m, n_ind_m);
snew(rev_ind_m, natoms);
j = 0;
for (i = 0; i < natoms; i++)
{
if (bPrev || bInMat[i])
{
ind_m[j] = i;
rev_ind_m[i] = j;
j++;
}
}
snew(w_rls_m, n_ind_m);
snew(ind_rms_m, irms[0]);
snew(w_rms_m, n_ind_m);
for (i = 0; i < ifit; i++)
{
w_rls_m[rev_ind_m[ind_fit[i]]] = w_rls[ind_fit[i]];
}
for (i = 0; i < irms[0]; i++)
{
ind_rms_m[i] = rev_ind_m[ind_rms[0][i]];
w_rms_m[ind_rms_m[i]] = w_rms[ind_rms[0][i]];
}
sfree(bInMat);
}
if (bBond)
{
ncons = 0;
for (k = 0; k < F_NRE; k++)
{
if (IS_CHEMBOND(k))
{
iatom = top.idef.il[k].iatoms;
ncons += top.idef.il[k].nr/3;
}
}
fprintf(stderr, "Found %d bonds in topology\n", ncons);
snew(ind_bond1, ncons);
snew(ind_bond2, ncons);
ibond = 0;
for (k = 0; k < F_NRE; k++)
{
if (IS_CHEMBOND(k))
{
iatom = top.idef.il[k].iatoms;
ncons = top.idef.il[k].nr/3;
for (i = 0; i < ncons; i++)
{
bA1 = FALSE;
bA2 = FALSE;
for (j = 0; j < irms[0]; j++)
{
if (iatom[3*i+1] == ind_rms[0][j])
{
bA1 = TRUE;
}
if (iatom[3*i+2] == ind_rms[0][j])
{
bA2 = TRUE;
}
}
if (bA1 && bA2)
{
ind_bond1[ibond] = rev_ind_m[iatom[3*i+1]];
ind_bond2[ibond] = rev_ind_m[iatom[3*i+2]];
ibond++;
}
}
}
}
fprintf(stderr, "Using %d bonds for bond angle matrix\n", ibond);
if (ibond == 0)
{
gmx_fatal(FARGS, "0 bonds found");
}
}
/* start looping over frames: */
tel_mat = 0;
teller = 0;
do
{
if (bPBC)
{
gmx_rmpbc(gpbc, natoms, box, x);
}
if (bReset)
{
reset_x(ifit, ind_fit, natoms, NULL, x, w_rls);
}
if (ewhat == ewRhoSc)
{
norm_princ(&top.atoms, ifit, ind_fit, natoms, x);
}
if (bFit)
{
/*do the least squares fit to original structure*/
do_fit(natoms, w_rls, xp, x);
}
if (teller % freq == 0)
{
/* keep frame for matrix calculation */
if (bMat || bBond || bPrev)
{
if (tel_mat >= NFRAME)
{
srenew(mat_x, tel_mat+1);
}
snew(mat_x[tel_mat], n_ind_m);
for (i = 0; i < n_ind_m; i++)
{
copy_rvec(x[ind_m[i]], mat_x[tel_mat][i]);
}
}
tel_mat++;
}
/*calculate energy of root_least_squares*/
if (bPrev)
{
j = tel_mat-prev-1;
if (j < 0)
{
j = 0;
}
for (i = 0; i < n_ind_m; i++)
{
copy_rvec(mat_x[j][i], xp[ind_m[i]]);
}
if (bReset)
{
reset_x(ifit, ind_fit, natoms, NULL, xp, w_rls);
}
if (bFit)
{
do_fit(natoms, w_rls, x, xp);
}
}
for (j = 0; (j < nrms); j++)
{
rls[j][teller] =
calc_similar_ind(ewhat != ewRMSD, irms[j], ind_rms[j], w_rms, x, xp);
}
if (bNorm)
{
for (j = 0; (j < irms[0]); j++)
{
rlsnorm[j] +=
calc_similar_ind(ewhat != ewRMSD, 1, &(ind_rms[0][j]), w_rms, x, xp);
}
}
if (bMirror)
{
if (bFit)
{
/*do the least squares fit to mirror of original structure*/
do_fit(natoms, w_rls, xm, x);
}
for (j = 0; j < nrms; j++)
{
rlsm[j][teller] =
calc_similar_ind(ewhat != ewRMSD, irms[j], ind_rms[j], w_rms, x, xm);
}
}
time[teller] = output_env_conv_time(oenv, t);
teller++;
if (teller >= maxframe)
{
maxframe += NFRAME;
srenew(time, maxframe);
for (j = 0; (j < nrms); j++)
{
srenew(rls[j], maxframe);
}
if (bMirror)
{
for (j = 0; (j < nrms); j++)
{
srenew(rlsm[j], maxframe);
}
}
}
}
while (read_next_x(oenv, status, &t, x, box));
close_trj(status);
if (bFile2)
{
snew(time2, maxframe2);
fprintf(stderr, "\nWill read second trajectory file\n");
snew(mat_x2, NFRAME);
natoms_trx2 =
read_first_x(oenv, &status, opt2fn("-f2", NFILE, fnm), &t, &x, box);
if (natoms_trx2 != natoms_trx)
{
gmx_fatal(FARGS,
"Second trajectory (%d atoms) does not match the first one"
" (%d atoms)", natoms_trx2, natoms_trx);
}
tel_mat2 = 0;
teller2 = 0;
do
{
if (bPBC)
{
gmx_rmpbc(gpbc, natoms, box, x);
}
if (bReset)
{
reset_x(ifit, ind_fit, natoms, NULL, x, w_rls);
}
if (ewhat == ewRhoSc)
{
norm_princ(&top.atoms, ifit, ind_fit, natoms, x);
}
if (bFit)
{
/*do the least squares fit to original structure*/
do_fit(natoms, w_rls, xp, x);
}
if (teller2 % freq2 == 0)
{
/* keep frame for matrix calculation */
if (bMat)
{
if (tel_mat2 >= NFRAME)
{
srenew(mat_x2, tel_mat2+1);
}
snew(mat_x2[tel_mat2], n_ind_m);
for (i = 0; i < n_ind_m; i++)
{
copy_rvec(x[ind_m[i]], mat_x2[tel_mat2][i]);
}
}
tel_mat2++;
}
time2[teller2] = output_env_conv_time(oenv, t);
teller2++;
if (teller2 >= maxframe2)
{
maxframe2 += NFRAME;
srenew(time2, maxframe2);
}
}
while (read_next_x(oenv, status, &t, x, box));
close_trj(status);
}
else
{
mat_x2 = mat_x;
time2 = time;
tel_mat2 = tel_mat;
freq2 = freq;
}
gmx_rmpbc_done(gpbc);
if (bMat || bBond)
{
/* calculate RMS matrix */
fprintf(stderr, "\n");
if (bMat)
{
fprintf(stderr, "Building %s matrix, %dx%d elements\n",
whatname[ewhat], tel_mat, tel_mat2);
snew(rmsd_mat, tel_mat);
}
if (bBond)
{
fprintf(stderr, "Building bond angle matrix, %dx%d elements\n",
tel_mat, tel_mat2);
snew(bond_mat, tel_mat);
}
snew(axis, tel_mat);
snew(axis2, tel_mat2);
rmsd_max = 0;
if (bFile2)
{
rmsd_min = 1e10;
}
else
{
rmsd_min = 0;
}
rmsd_avg = 0;
bond_max = 0;
bond_min = 1e10;
for (j = 0; j < tel_mat2; j++)
{
axis2[j] = time2[freq2*j];
}
if (bDelta)
{
if (bDeltaLog)
{
delta_scalex = 8.0/log(2.0);
delta_xsize = (int)(log(tel_mat/2)*delta_scalex+0.5)+1;
}
else
{
delta_xsize = tel_mat/2;
}
delta_scaley = 1.0/delta_maxy;
snew(delta, delta_xsize);
for (j = 0; j < delta_xsize; j++)
{
snew(delta[j], del_lev+1);
}
if (avl > 0)
{
snew(rmsdav_mat, tel_mat);
for (j = 0; j < tel_mat; j++)
{
snew(rmsdav_mat[j], tel_mat);
}
}
}
if (bFitAll)
{
snew(mat_x2_j, natoms);
}
for (i = 0; i < tel_mat; i++)
{
axis[i] = time[freq*i];
fprintf(stderr, "\r element %5d; time %5.2f ", i, axis[i]);
if (bMat)
{
snew(rmsd_mat[i], tel_mat2);
}
if (bBond)
{
snew(bond_mat[i], tel_mat2);
}
for (j = 0; j < tel_mat2; j++)
{
if (bFitAll)
{
for (k = 0; k < n_ind_m; k++)
{
copy_rvec(mat_x2[j][k], mat_x2_j[k]);
}
do_fit(n_ind_m, w_rls_m, mat_x[i], mat_x2_j);
}
else
{
mat_x2_j = mat_x2[j];
}
if (bMat)
{
if (bFile2 || (i < j))
{
rmsd_mat[i][j] =
calc_similar_ind(ewhat != ewRMSD, irms[0], ind_rms_m,
w_rms_m, mat_x[i], mat_x2_j);
if (rmsd_mat[i][j] > rmsd_max)
{
rmsd_max = rmsd_mat[i][j];
}
if (rmsd_mat[i][j] < rmsd_min)
{
rmsd_min = rmsd_mat[i][j];
}
rmsd_avg += rmsd_mat[i][j];
}
else
{
rmsd_mat[i][j] = rmsd_mat[j][i];
}
}
if (bBond)
{
if (bFile2 || (i <= j))
{
ang = 0.0;
for (m = 0; m < ibond; m++)
{
rvec_sub(mat_x[i][ind_bond1[m]], mat_x[i][ind_bond2[m]], vec1);
rvec_sub(mat_x2_j[ind_bond1[m]], mat_x2_j[ind_bond2[m]], vec2);
ang += acos(cos_angle(vec1, vec2));
}
bond_mat[i][j] = ang*180.0/(M_PI*ibond);
if (bond_mat[i][j] > bond_max)
{
bond_max = bond_mat[i][j];
}
if (bond_mat[i][j] < bond_min)
{
bond_min = bond_mat[i][j];
}
}
else
{
bond_mat[i][j] = bond_mat[j][i];
}
}
}
}
if (bFile2)
{
rmsd_avg /= tel_mat*tel_mat2;
}
else
{
rmsd_avg /= tel_mat*(tel_mat - 1)/2;
}
if (bMat && (avl > 0))
{
rmsd_max = 0.0;
rmsd_min = 0.0;
rmsd_avg = 0.0;
for (j = 0; j < tel_mat-1; j++)
{
for (i = j+1; i < tel_mat; i++)
{
av_tot = 0;
weight_tot = 0;
for (my = -avl; my <= avl; my++)
{
if ((j+my >= 0) && (j+my < tel_mat))
{
abs_my = abs(my);
for (mx = -avl; mx <= avl; mx++)
{
if ((i+mx >= 0) && (i+mx < tel_mat))
{
weight = (real)(avl+1-max(abs(mx), abs_my));
av_tot += weight*rmsd_mat[i+mx][j+my];
weight_tot += weight;
}
}
}
}
rmsdav_mat[i][j] = av_tot/weight_tot;
rmsdav_mat[j][i] = rmsdav_mat[i][j];
if (rmsdav_mat[i][j] > rmsd_max)
{
rmsd_max = rmsdav_mat[i][j];
}
}
}
rmsd_mat = rmsdav_mat;
}
if (bMat)
{
fprintf(stderr, "\n%s: Min %f, Max %f, Avg %f\n",
whatname[ewhat], rmsd_min, rmsd_max, rmsd_avg);
rlo.r = 1; rlo.g = 1; rlo.b = 1;
rhi.r = 0; rhi.g = 0; rhi.b = 0;
if (rmsd_user_max != -1)
{
rmsd_max = rmsd_user_max;
}
if (rmsd_user_min != -1)
{
rmsd_min = rmsd_user_min;
}
if ((rmsd_user_max != -1) || (rmsd_user_min != -1))
{
fprintf(stderr, "Min and Max value set to resp. %f and %f\n",
rmsd_min, rmsd_max);
}
sprintf(buf, "%s %s matrix", gn_rms[0], whatname[ewhat]);
write_xpm(opt2FILE("-m", NFILE, fnm, "w"), 0, buf, whatlabel[ewhat],
output_env_get_time_label(oenv), output_env_get_time_label(oenv), tel_mat, tel_mat2,
axis, axis2, rmsd_mat, rmsd_min, rmsd_max, rlo, rhi, &nlevels);
/* Print the distribution of RMSD values */
if (opt2bSet("-dist", NFILE, fnm))
{
low_rmsd_dist(opt2fn("-dist", NFILE, fnm), rmsd_max, tel_mat, rmsd_mat, oenv);
}
if (bDelta)
{
snew(delta_tot, delta_xsize);
for (j = 0; j < tel_mat-1; j++)
{
for (i = j+1; i < tel_mat; i++)
{
mx = i-j;
if (mx < tel_mat/2)
{
if (bDeltaLog)
{
mx = (int)(log(mx)*delta_scalex+0.5);
}
my = (int)(rmsd_mat[i][j]*delta_scaley*del_lev+0.5);
delta_tot[mx] += 1.0;
if ((rmsd_mat[i][j] >= 0) && (rmsd_mat[i][j] <= delta_maxy))
{
delta[mx][my] += 1.0;
}
}
}
}
delta_max = 0;
for (i = 0; i < delta_xsize; i++)
{
if (delta_tot[i] > 0.0)
{
delta_tot[i] = 1.0/delta_tot[i];
for (j = 0; j <= del_lev; j++)
{
delta[i][j] *= delta_tot[i];
if (delta[i][j] > delta_max)
{
delta_max = delta[i][j];
}
}
}
}
fprintf(stderr, "Maximum in delta matrix: %f\n", delta_max);
snew(del_xaxis, delta_xsize);
snew(del_yaxis, del_lev+1);
for (i = 0; i < delta_xsize; i++)
{
del_xaxis[i] = axis[i]-axis[0];
}
for (i = 0; i < del_lev+1; i++)
{
del_yaxis[i] = delta_maxy*i/del_lev;
}
sprintf(buf, "%s %s vs. delta t", gn_rms[0], whatname[ewhat]);
fp = gmx_ffopen("delta.xpm", "w");
write_xpm(fp, 0, buf, "density", output_env_get_time_label(oenv), whatlabel[ewhat],
delta_xsize, del_lev+1, del_xaxis, del_yaxis,
delta, 0.0, delta_max, rlo, rhi, &nlevels);
gmx_ffclose(fp);
}
if (opt2bSet("-bin", NFILE, fnm))
{
/* NB: File must be binary if we use fwrite */
fp = ftp2FILE(efDAT, NFILE, fnm, "wb");
for (i = 0; i < tel_mat; i++)
{
if (fwrite(rmsd_mat[i], sizeof(**rmsd_mat), tel_mat2, fp) != tel_mat2)
{
gmx_fatal(FARGS, "Error writing to output file");
}
}
gmx_ffclose(fp);
}
}
if (bBond)
{
fprintf(stderr, "\nMin. angle: %f, Max. angle: %f\n", bond_min, bond_max);
if (bond_user_max != -1)
{
bond_max = bond_user_max;
}
if (bond_user_min != -1)
{
bond_min = bond_user_min;
}
if ((bond_user_max != -1) || (bond_user_min != -1))
{
fprintf(stderr, "Bond angle Min and Max set to:\n"
"Min. angle: %f, Max. angle: %f\n", bond_min, bond_max);
}
rlo.r = 1; rlo.g = 1; rlo.b = 1;
rhi.r = 0; rhi.g = 0; rhi.b = 0;
sprintf(buf, "%s av. bond angle deviation", gn_rms[0]);
write_xpm(opt2FILE("-bm", NFILE, fnm, "w"), 0, buf, "degrees",
output_env_get_time_label(oenv), output_env_get_time_label(oenv), tel_mat, tel_mat2,
axis, axis2, bond_mat, bond_min, bond_max, rlo, rhi, &nlevels);
}
}
bAv = opt2bSet("-a", NFILE, fnm);
/* Write the RMSD's to file */
if (!bPrev)
{
sprintf(buf, "%s", whatxvgname[ewhat]);
}
else
{
sprintf(buf, "%s with frame %g %s ago", whatxvgname[ewhat],
time[prev*freq]-time[0], output_env_get_time_label(oenv));
}
fp = xvgropen(opt2fn("-o", NFILE, fnm), buf, output_env_get_xvgr_tlabel(oenv),
whatxvglabel[ewhat], oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"%s%s after %s%s%s\"\n",
(nrms == 1) ? "" : "of ", gn_rms[0], fitgraphlabel[efit],
bFit ? " to " : "", bFit ? gn_fit : "");
}
if (nrms != 1)
{
xvgr_legend(fp, nrms, (const char**)gn_rms, oenv);
}
for (i = 0; (i < teller); i++)
{
if (bSplit && i > 0 &&
abs(time[bPrev ? freq*i : i]/output_env_get_time_factor(oenv)) < 1e-5)
{
fprintf(fp, "&\n");
}
fprintf(fp, "%12.7f", time[bPrev ? freq*i : i]);
for (j = 0; (j < nrms); j++)
{
fprintf(fp, " %12.7f", rls[j][i]);
if (bAv)
{
rlstot += rls[j][i];
}
}
fprintf(fp, "\n");
}
gmx_ffclose(fp);
if (bMirror)
{
/* Write the mirror RMSD's to file */
sprintf(buf, "%s with Mirror", whatxvgname[ewhat]);
sprintf(buf2, "Mirror %s", whatxvglabel[ewhat]);
fp = xvgropen(opt2fn("-mir", NFILE, fnm), buf, output_env_get_xvgr_tlabel(oenv),
buf2, oenv);
if (nrms == 1)
{
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"of %s after lsq fit to mirror of %s\"\n",
gn_rms[0], gn_fit);
}
}
else
{
if (output_env_get_print_xvgr_codes(oenv))
{
fprintf(fp, "@ subtitle \"after lsq fit to mirror %s\"\n", gn_fit);
}
xvgr_legend(fp, nrms, (const char**)gn_rms, oenv);
}
for (i = 0; (i < teller); i++)
{
if (bSplit && i > 0 && abs(time[i]) < 1e-5)
{
fprintf(fp, "&\n");
}
fprintf(fp, "%12.7f", time[i]);
for (j = 0; (j < nrms); j++)
{
fprintf(fp, " %12.7f", rlsm[j][i]);
}
fprintf(fp, "\n");
}
gmx_ffclose(fp);
}
if (bAv)
{
sprintf(buf, "Average %s", whatxvgname[ewhat]);
sprintf(buf2, "Average %s", whatxvglabel[ewhat]);
fp = xvgropen(opt2fn("-a", NFILE, fnm), buf, "Residue", buf2, oenv);
for (j = 0; (j < nrms); j++)
{
fprintf(fp, "%10d %10g\n", j, rlstot/teller);
}
gmx_ffclose(fp);
}
if (bNorm)
{
fp = xvgropen("aver.xvg", gn_rms[0], "Residue", whatxvglabel[ewhat], oenv);
for (j = 0; (j < irms[0]); j++)
{
fprintf(fp, "%10d %10g\n", j, rlsnorm[j]/teller);
}
gmx_ffclose(fp);
}
do_view(oenv, opt2fn_null("-a", NFILE, fnm), "-graphtype bar");
do_view(oenv, opt2fn("-o", NFILE, fnm), NULL);
do_view(oenv, opt2fn_null("-mir", NFILE, fnm), NULL);
do_view(oenv, opt2fn_null("-m", NFILE, fnm), NULL);
do_view(oenv, opt2fn_null("-bm", NFILE, fnm), NULL);
do_view(oenv, opt2fn_null("-dist", NFILE, fnm), NULL);
return 0;
}
void init_pull(FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[],
gmx_mtop_t *mtop, t_commrec *cr, const output_env_t oenv, real lambda,
gmx_bool bOutFile, unsigned long Flags)
{
t_pull *pull;
t_pull_group *pgrp;
int c, g, start = 0, end = 0, m;
pull = ir->pull;
pull->ePBC = ir->ePBC;
switch (pull->ePBC)
{
case epbcNONE: pull->npbcdim = 0; break;
case epbcXY: pull->npbcdim = 2; break;
default: pull->npbcdim = 3; break;
}
if (fplog)
{
gmx_bool bAbs, bCos;
bAbs = FALSE;
for (c = 0; c < pull->ncoord; c++)
{
if (pull->group[pull->coord[c].group[0]].nat == 0 ||
pull->group[pull->coord[c].group[1]].nat == 0)
{
bAbs = TRUE;
}
}
fprintf(fplog, "\nWill apply %s COM pulling in geometry '%s'\n",
EPULLTYPE(ir->ePull), EPULLGEOM(pull->eGeom));
fprintf(fplog, "with %d pull coordinate%s and %d group%s\n",
pull->ncoord, pull->ncoord == 1 ? "" : "s",
pull->ngroup, pull->ngroup == 1 ? "" : "s");
if (bAbs)
{
fprintf(fplog, "with an absolute reference\n");
}
bCos = FALSE;
for (g = 0; g < pull->ngroup; g++)
{
if (pull->group[g].nat > 1 &&
pull->group[g].pbcatom < 0)
{
/* We are using cosine weighting */
fprintf(fplog, "Cosine weighting is used for group %d\n", g);
bCos = TRUE;
}
}
if (bCos)
{
please_cite(fplog, "Engin2010");
}
}
/* We always add the virial contribution,
* except for geometry = direction_periodic where this is impossible.
*/
pull->bVirial = (pull->eGeom != epullgDIRPBC);
if (getenv("GMX_NO_PULLVIR") != NULL)
{
if (fplog)
{
fprintf(fplog, "Found env. var., will not add the virial contribution of the COM pull forces\n");
}
pull->bVirial = FALSE;
}
if (cr && PARTDECOMP(cr))
{
pd_at_range(cr, &start, &end);
}
pull->rbuf = NULL;
pull->dbuf = NULL;
pull->dbuf_cyl = NULL;
pull->bRefAt = FALSE;
pull->cosdim = -1;
for (g = 0; g < pull->ngroup; g++)
{
pgrp = &pull->group[g];
pgrp->epgrppbc = epgrppbcNONE;
if (pgrp->nat > 0)
{
/* Determine if we need to take PBC into account for calculating
* the COM's of the pull groups.
*/
for (m = 0; m < pull->npbcdim; m++)
{
if (pull->dim[m] && pgrp->nat > 1)
{
if (pgrp->pbcatom >= 0)
{
pgrp->epgrppbc = epgrppbcREFAT;
pull->bRefAt = TRUE;
}
else
{
if (pgrp->weight)
{
gmx_fatal(FARGS, "Pull groups can not have relative weights and cosine weighting at same time");
}
pgrp->epgrppbc = epgrppbcCOS;
if (pull->cosdim >= 0 && pull->cosdim != m)
{
gmx_fatal(FARGS, "Can only use cosine weighting with pulling in one dimension (use mdp option pull_dim)");
}
pull->cosdim = m;
}
}
}
/* Set the indices */
init_pull_group_index(fplog, cr, start, end, g, pgrp, pull->dim, mtop, ir, lambda);
if (PULL_CYL(pull) && pgrp->invtm == 0)
{
gmx_fatal(FARGS, "Can not have frozen atoms in a cylinder pull group");
}
}
else
{
/* Absolute reference, set the inverse mass to zero */
pgrp->invtm = 0;
pgrp->wscale = 1;
}
}
/* if we use dynamic reference groups, do some initialising for them */
if (PULL_CYL(pull))
{
if (ir->ePull == epullCONSTRAINT && pull->ncoord > 1)
{
/* We can't easily update the single reference group with multiple
* constraints. This would require recalculating COMs.
*/
gmx_fatal(FARGS, "Constraint COM pulling supports only one coordinate with geometry=cylinder, you can use umbrella pulling with multiple coordinates");
}
for (c = 0; c < pull->ncoord; c++)
{
if (pull->group[pull->coord[c].group[0]].nat == 0)
{
gmx_fatal(FARGS, "Dynamic reference groups are not supported when using absolute reference!\n");
}
}
snew(pull->dyna, pull->ncoord);
}
/* Only do I/O when we are doing dynamics and if we are the MASTER */
pull->out_x = NULL;
pull->out_f = NULL;
if (bOutFile)
{
if (pull->nstxout > 0)
{
pull->out_x = open_pull_out(opt2fn("-px", nfile, fnm), pull, oenv, TRUE, Flags);
}
if (pull->nstfout > 0)
{
pull->out_f = open_pull_out(opt2fn("-pf", nfile, fnm), pull, oenv,
FALSE, Flags);
}
}
}
gmx_mdoutf_t init_mdoutf(FILE *fplog, int nfile, const t_filenm fnm[],
int mdrun_flags, const t_commrec *cr,
const t_inputrec *ir, gmx_mtop_t *top_global,
const gmx_output_env_t *oenv, gmx_wallcycle_t wcycle)
{
gmx_mdoutf_t of;
char filemode[3];
gmx_bool bAppendFiles, bCiteTng = FALSE;
int i;
snew(of, 1);
of->fp_trn = NULL;
of->fp_ene = NULL;
of->fp_xtc = NULL;
of->tng = NULL;
of->tng_low_prec = NULL;
of->fp_dhdl = NULL;
of->fp_field = NULL;
of->eIntegrator = ir->eI;
of->bExpanded = ir->bExpanded;
of->elamstats = ir->expandedvals->elamstats;
of->simulation_part = ir->simulation_part;
of->x_compression_precision = static_cast<int>(ir->x_compression_precision);
of->wcycle = wcycle;
if (MASTER(cr))
{
bAppendFiles = (mdrun_flags & MD_APPENDFILES);
of->bKeepAndNumCPT = (mdrun_flags & MD_KEEPANDNUMCPT);
sprintf(filemode, bAppendFiles ? "a+" : "w+");
if ((EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
#ifndef GMX_FAHCORE
&&
!(EI_DYNAMICS(ir->eI) &&
ir->nstxout == 0 &&
ir->nstvout == 0 &&
ir->nstfout == 0)
#endif
)
{
const char *filename;
filename = ftp2fn(efTRN, nfile, fnm);
switch (fn2ftp(filename))
{
case efTRR:
case efTRN:
of->fp_trn = gmx_trr_open(filename, filemode);
break;
case efTNG:
gmx_tng_open(filename, filemode[0], &of->tng);
if (filemode[0] == 'w')
{
gmx_tng_prepare_md_writing(of->tng, top_global, ir);
}
bCiteTng = TRUE;
break;
default:
gmx_incons("Invalid full precision file format");
}
}
if (EI_DYNAMICS(ir->eI) &&
ir->nstxout_compressed > 0)
{
const char *filename;
filename = ftp2fn(efCOMPRESSED, nfile, fnm);
switch (fn2ftp(filename))
{
case efXTC:
of->fp_xtc = open_xtc(filename, filemode);
break;
case efTNG:
gmx_tng_open(filename, filemode[0], &of->tng_low_prec);
if (filemode[0] == 'w')
{
gmx_tng_prepare_low_prec_writing(of->tng_low_prec, top_global, ir);
}
bCiteTng = TRUE;
break;
default:
gmx_incons("Invalid reduced precision file format");
}
}
if (EI_DYNAMICS(ir->eI) || EI_ENERGY_MINIMIZATION(ir->eI))
{
of->fp_ene = open_enx(ftp2fn(efEDR, nfile, fnm), filemode);
}
of->fn_cpt = opt2fn("-cpo", nfile, fnm);
if ((ir->efep != efepNO || ir->bSimTemp) && ir->fepvals->nstdhdl > 0 &&
(ir->fepvals->separate_dhdl_file == esepdhdlfileYES ) &&
EI_DYNAMICS(ir->eI))
{
if (bAppendFiles)
{
of->fp_dhdl = gmx_fio_fopen(opt2fn("-dhdl", nfile, fnm), filemode);
}
else
{
of->fp_dhdl = open_dhdl(opt2fn("-dhdl", nfile, fnm), ir, oenv);
}
}
if (opt2bSet("-field", nfile, fnm) &&
(ir->ex[XX].n || ir->ex[YY].n || ir->ex[ZZ].n))
{
if (bAppendFiles)
{
of->fp_field = gmx_fio_fopen(opt2fn("-field", nfile, fnm),
filemode);
}
else
{
of->fp_field = xvgropen(opt2fn("-field", nfile, fnm),
"Applied electric field", "Time (ps)",
"E (V/nm)", oenv);
}
}
/* Set up atom counts so they can be passed to actual
trajectory-writing routines later. Also, XTC writing needs
to know what (and how many) atoms might be in the XTC
groups, and how to look up later which ones they are. */
of->natoms_global = top_global->natoms;
of->groups = &top_global->groups;
of->natoms_x_compressed = 0;
for (i = 0; (i < top_global->natoms); i++)
{
if (ggrpnr(of->groups, egcCompressedX, i) == 0)
{
of->natoms_x_compressed++;
}
}
}
if (bCiteTng)
{
please_cite(fplog, "Lundborg2014");
}
return of;
}
void init_md(FILE *fplog,
t_commrec *cr,t_inputrec *ir,real *t,real *t0,
real *lambda,real *lam0,
t_nrnb *nrnb,gmx_mtop_t *mtop,
gmx_stochd_t *sd,
int nfile,t_filenm fnm[],
int *fp_trn,int *fp_xtc,int *fp_ene,char **fn_cpt,
FILE **fp_dgdl,FILE **fp_field,
t_mdebin **mdebin,
tensor force_vir,tensor shake_vir,rvec mu_tot,
bool *bNEMD,bool *bSimAnn,t_vcm **vcm, unsigned long Flags)
{
int i,j,n;
real tmpt,mod;
char filemode[2];
sprintf(filemode, (Flags & MD_APPENDFILES) ? "a" : "w");
/* Initial values */
*t = *t0 = ir->init_t;
if (ir->efep != efepNO) {
*lam0 = ir->init_lambda;
*lambda = *lam0 + ir->init_step*ir->delta_lambda;
}
else {
*lambda = *lam0 = 0.0;
}
*bSimAnn=FALSE;
for(i=0;i<ir->opts.ngtc;i++) {
/* set bSimAnn if any group is being annealed */
if(ir->opts.annealing[i]!=eannNO)
*bSimAnn = TRUE;
}
if (*bSimAnn) {
update_annealing_target_temp(&(ir->opts),ir->init_t);
}
*bNEMD = (ir->opts.ngacc > 1) || (norm(ir->opts.acc[0]) > 0);
if (sd && (ir->eI == eiBD || EI_SD(ir->eI) || ir->etc == etcVRESCALE)) {
*sd = init_stochd(fplog,ir);
}
if (vcm) {
*vcm = init_vcm(fplog,&mtop->groups,ir);
}
if (EI_DYNAMICS(ir->eI) && !(Flags & MD_APPENDFILES)) {
if (ir->etc == etcBERENDSEN) {
please_cite(fplog,"Berendsen84a");
}
if (ir->etc == etcVRESCALE) {
please_cite(fplog,"Bussi2007a");
}
}
init_nrnb(nrnb);
if (nfile != -1)
{
*fp_trn = -1;
*fp_ene = -1;
*fp_xtc = -1;
if (MASTER(cr))
{
*fp_trn = open_trn(ftp2fn(efTRN,nfile,fnm), filemode);
if (ir->nstxtcout > 0)
{
*fp_xtc = open_xtc(ftp2fn(efXTC,nfile,fnm), filemode);
}
*fp_ene = open_enx(ftp2fn(efENX,nfile,fnm), filemode);
*fn_cpt = opt2fn("-cpo",nfile,fnm);
if ((fp_dgdl != NULL) && ir->efep!=efepNO)
{
if(Flags & MD_APPENDFILES)
{
*fp_dgdl= gmx_fio_fopen(opt2fn("-dgdl",nfile,fnm),filemode);
}
else
{
*fp_dgdl = xvgropen(opt2fn("-dgdl",nfile,fnm),
"dG/d\\8l\\4","Time (ps)",
"dG/d\\8l\\4 (kJ mol\\S-1\\N [\\8l\\4]\\S-1\\N)");
}
}
if ((fp_field != NULL) && (ir->ex[XX].n || ir->ex[YY].n ||ir->ex[ZZ].n))
{
if(Flags & MD_APPENDFILES)
{
*fp_field = gmx_fio_fopen(opt2fn("-field",nfile,fnm),filemode);
}
else
{
*fp_field = xvgropen(opt2fn("-field",nfile,fnm),
"Applied electric field","Time (ps)",
"E (V/nm)");
}
}
}
*mdebin = init_mdebin( (Flags & MD_APPENDFILES) ? -1 : *fp_ene,mtop,ir);
}
/* Initiate variables */
clear_mat(force_vir);
clear_mat(shake_vir);
clear_rvec(mu_tot);
debug_gmx();
}
int gmx_dielectric(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] calculates frequency dependent dielectric constants",
"from the autocorrelation function of the total dipole moment in",
"your simulation. This ACF can be generated by [gmx-dipoles].",
"The functional forms of the available functions are:[PAR]",
"One parameter: y = [EXP]-a[SUB]1[sub] x[exp],[BR]",
"Two parameters: y = a[SUB]2[sub] [EXP]-a[SUB]1[sub] x[exp],[BR]",
"Three parameters: y = a[SUB]2[sub] [EXP]-a[SUB]1[sub] x[exp] + (1 - a[SUB]2[sub]) [EXP]-a[SUB]3[sub] x[exp].[BR]",
"Start values for the fit procedure can be given on the command line.",
"It is also possible to fix parameters at their start value, use [TT]-fix[tt]",
"with the number of the parameter you want to fix.",
"[PAR]",
"Three output files are generated, the first contains the ACF,",
"an exponential fit to it with 1, 2 or 3 parameters, and the",
"numerical derivative of the combination data/fit.",
"The second file contains the real and imaginary parts of the",
"frequency-dependent dielectric constant, the last gives a plot",
"known as the Cole-Cole plot, in which the imaginary",
"component is plotted as a function of the real component.",
"For a pure exponential relaxation (Debye relaxation) the latter",
"plot should be one half of a circle."
};
t_filenm fnm[] = {
{ efXVG, "-f", "dipcorr", ffREAD },
{ efXVG, "-d", "deriv", ffWRITE },
{ efXVG, "-o", "epsw", ffWRITE },
{ efXVG, "-c", "cole", ffWRITE }
};
#define NFILE asize(fnm)
output_env_t oenv;
int i, j, nx, ny, nxtail, eFitFn, nfitparm;
real dt, integral, fitintegral, *fitparms, fac, rffac;
double **yd;
real **y;
const char *legend[] = { "Correlation", "Std. Dev.", "Fit", "Combined", "Derivative" };
static int fix = 0, bFour = 0, bX = 1, nsmooth = 3;
static real tendInt = 5.0, tbegin = 5.0, tend = 500.0;
static real A = 0.5, tau1 = 10.0, tau2 = 1.0, eps0 = 80, epsRF = 78.5, tail = 500.0;
real lambda;
t_pargs pa[] = {
{ "-fft", FALSE, etBOOL, {&bFour},
"use fast fourier transform for correlation function" },
{ "-x1", FALSE, etBOOL, {&bX},
"use first column as [IT]x[it]-axis rather than first data set" },
{ "-eint", FALSE, etREAL, {&tendInt},
"Time to end the integration of the data and start to use the fit"},
{ "-bfit", FALSE, etREAL, {&tbegin},
"Begin time of fit" },
{ "-efit", FALSE, etREAL, {&tend},
"End time of fit" },
{ "-tail", FALSE, etREAL, {&tail},
"Length of function including data and tail from fit" },
{ "-A", FALSE, etREAL, {&A},
"Start value for fit parameter A" },
{ "-tau1", FALSE, etREAL, {&tau1},
"Start value for fit parameter [GRK]tau[grk]1" },
{ "-tau2", FALSE, etREAL, {&tau2},
"Start value for fit parameter [GRK]tau[grk]2" },
{ "-eps0", FALSE, etREAL, {&eps0},
"[GRK]epsilon[grk]0 of your liquid" },
{ "-epsRF", FALSE, etREAL, {&epsRF},
"[GRK]epsilon[grk] of the reaction field used in your simulation. A value of 0 means infinity." },
{ "-fix", FALSE, etINT, {&fix},
"Fix parameters at their start values, A (2), tau1 (1), or tau2 (4)" },
{ "-ffn", FALSE, etENUM, {s_ffn},
"Fit function" },
{ "-nsmooth", FALSE, etINT, {&nsmooth},
"Number of points for smoothing" }
};
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
please_cite(stdout, "Spoel98a");
printf("WARNING: non-polarizable models can never yield an infinite\n"
"dielectric constant that is different from 1. This is incorrect\n"
"in the reference given above (Spoel98a).\n\n");
nx = read_xvg(opt2fn("-f", NFILE, fnm), &yd, &ny);
dt = yd[0][1] - yd[0][0];
nxtail = min(tail/dt, nx);
printf("Read data set containing %d colums and %d rows\n", ny, nx);
printf("Assuming (from data) that timestep is %g, nxtail = %d\n",
dt, nxtail);
snew(y, 6);
for (i = 0; (i < ny); i++)
{
snew(y[i], max(nx, nxtail));
}
for (i = 0; (i < nx); i++)
{
y[0][i] = yd[0][i];
for (j = 1; (j < ny); j++)
{
y[j][i] = yd[j][i];
}
}
if (nxtail > nx)
{
for (i = nx; (i < nxtail); i++)
{
y[0][i] = dt*i+y[0][0];
for (j = 1; (j < ny); j++)
{
y[j][i] = 0.0;
}
}
nx = nxtail;
}
/* We have read a file WITHOUT standard deviations, so we make our own... */
if (ny == 2)
{
printf("Creating standard deviation numbers ...\n");
srenew(y, 3);
snew(y[2], nx);
fac = 1.0/((real)nx);
for (i = 0; (i < nx); i++)
{
y[2][i] = fac;
}
}
eFitFn = sffn2effn(s_ffn);
nfitparm = nfp_ffn[eFitFn];
snew(fitparms, 4);
fitparms[0] = tau1;
if (nfitparm > 1)
{
fitparms[1] = A;
}
if (nfitparm > 2)
{
fitparms[2] = tau2;
}
snew(y[3], nx);
snew(y[4], nx);
snew(y[5], nx);
integral = print_and_integrate(NULL, calc_nbegin(nx, y[0], tbegin),
dt, y[1], NULL, 1);
integral += do_lmfit(nx, y[1], y[2], dt, y[0], tbegin, tend,
oenv, TRUE, eFitFn, fitparms, fix);
for (i = 0; i < nx; i++)
{
y[3][i] = fit_function(eFitFn, fitparms, y[0][i]);
}
if (epsRF == 0)
{
/* This means infinity! */
lambda = 0;
rffac = 1;
}
else
{
lambda = (eps0 - 1.0)/(2*epsRF - 1.0);
rffac = (2*epsRF+eps0)/(2*epsRF+1);
}
printf("DATA INTEGRAL: %5.1f, tauD(old) = %5.1f ps, "
"tau_slope = %5.1f, tau_slope,D = %5.1f ps\n",
integral, integral*rffac, fitparms[0], fitparms[0]*rffac);
printf("tau_D from tau1 = %8.3g , eps(Infty) = %8.3f\n",
fitparms[0]*(1 + fitparms[1]*lambda),
1 + ((1 - fitparms[1])*(eps0 - 1))/(1 + fitparms[1]*lambda));
fitintegral = numerical_deriv(nx, y[0], y[1], y[3], y[4], y[5], tendInt, nsmooth);
printf("FIT INTEGRAL (tau_M): %5.1f, tau_D = %5.1f\n",
fitintegral, fitintegral*rffac);
/* Now we have the negative gradient of <Phi(0) Phi(t)> */
write_xvg(opt2fn("-d", NFILE, fnm), "Data", nx-1, 6, y, legend, oenv);
/* Do FFT and analysis */
do_four(opt2fn("-o", NFILE, fnm), opt2fn("-c", NFILE, fnm),
nx-1, y[0], y[5], eps0, epsRF, oenv);
do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
do_view(oenv, opt2fn("-c", NFILE, fnm), NULL);
do_view(oenv, opt2fn("-d", NFILE, fnm), "-nxy");
return 0;
}
gmx_constr_t init_constraints(FILE *fplog,
gmx_mtop_t *mtop, t_inputrec *ir,
gmx_edsam_t ed, t_state *state,
t_commrec *cr)
{
int ncon, nset, nmol, settle_type, i, natoms, mt, nflexcon;
struct gmx_constr *constr;
char *env;
t_ilist *ilist;
gmx_mtop_ilistloop_t iloop;
ncon =
gmx_mtop_ftype_count(mtop, F_CONSTR) +
gmx_mtop_ftype_count(mtop, F_CONSTRNC);
nset = gmx_mtop_ftype_count(mtop, F_SETTLE);
if (ncon+nset == 0 && ir->ePull != epullCONSTRAINT && ed == NULL)
{
return NULL;
}
snew(constr, 1);
constr->ncon_tot = ncon;
constr->nflexcon = 0;
if (ncon > 0)
{
constr->n_at2con_mt = mtop->nmoltype;
snew(constr->at2con_mt, constr->n_at2con_mt);
for (mt = 0; mt < mtop->nmoltype; mt++)
{
constr->at2con_mt[mt] = make_at2con(0, mtop->moltype[mt].atoms.nr,
mtop->moltype[mt].ilist,
mtop->ffparams.iparams,
EI_DYNAMICS(ir->eI), &nflexcon);
for (i = 0; i < mtop->nmolblock; i++)
{
if (mtop->molblock[i].type == mt)
{
constr->nflexcon += mtop->molblock[i].nmol*nflexcon;
}
}
}
if (constr->nflexcon > 0)
{
if (fplog)
{
fprintf(fplog, "There are %d flexible constraints\n",
constr->nflexcon);
if (ir->fc_stepsize == 0)
{
fprintf(fplog, "\n"
"WARNING: step size for flexible constraining = 0\n"
" All flexible constraints will be rigid.\n"
" Will try to keep all flexible constraints at their original length,\n"
" but the lengths may exhibit some drift.\n\n");
constr->nflexcon = 0;
}
}
if (constr->nflexcon > 0)
{
please_cite(fplog, "Hess2002");
}
}
if (ir->eConstrAlg == econtLINCS)
{
constr->lincsd = init_lincs(fplog, mtop,
constr->nflexcon, constr->at2con_mt,
DOMAINDECOMP(cr) && cr->dd->bInterCGcons,
ir->nLincsIter, ir->nProjOrder);
}
if (ir->eConstrAlg == econtSHAKE)
{
if (DOMAINDECOMP(cr) && cr->dd->bInterCGcons)
{
gmx_fatal(FARGS, "SHAKE is not supported with domain decomposition and constraint that cross charge group boundaries, use LINCS");
}
if (constr->nflexcon)
{
gmx_fatal(FARGS, "For this system also velocities and/or forces need to be constrained, this can not be done with SHAKE, you should select LINCS");
}
please_cite(fplog, "Ryckaert77a");
if (ir->bShakeSOR)
{
please_cite(fplog, "Barth95a");
}
constr->shaked = shake_init();
}
}
if (nset > 0)
{
please_cite(fplog, "Miyamoto92a");
constr->bInterCGsettles = inter_charge_group_settles(mtop);
/* Check that we have only one settle type */
settle_type = -1;
iloop = gmx_mtop_ilistloop_init(mtop);
while (gmx_mtop_ilistloop_next(iloop, &ilist, &nmol))
{
for (i = 0; i < ilist[F_SETTLE].nr; i += 4)
{
if (settle_type == -1)
{
settle_type = ilist[F_SETTLE].iatoms[i];
}
else if (ilist[F_SETTLE].iatoms[i] != settle_type)
{
gmx_fatal(FARGS,
"The [molecules] section of your topology specifies more than one block of\n"
"a [moleculetype] with a [settles] block. Only one such is allowed. If you\n"
"are trying to partition your solvent into different *groups* (e.g. for\n"
"freezing, T-coupling, etc.) then you are using the wrong approach. Index\n"
"files specify groups. Otherwise, you may wish to change the least-used\n"
"block of molecules with SETTLE constraints into 3 normal constraints.");
}
}
}
constr->n_at2settle_mt = mtop->nmoltype;
snew(constr->at2settle_mt, constr->n_at2settle_mt);
for (mt = 0; mt < mtop->nmoltype; mt++)
{
constr->at2settle_mt[mt] =
make_at2settle(mtop->moltype[mt].atoms.nr,
&mtop->moltype[mt].ilist[F_SETTLE]);
}
}
constr->maxwarn = 999;
env = getenv("GMX_MAXCONSTRWARN");
if (env)
{
constr->maxwarn = 0;
sscanf(env, "%d", &constr->maxwarn);
if (fplog)
{
fprintf(fplog,
"Setting the maximum number of constraint warnings to %d\n",
constr->maxwarn);
}
if (MASTER(cr))
{
fprintf(stderr,
"Setting the maximum number of constraint warnings to %d\n",
constr->maxwarn);
}
}
if (constr->maxwarn < 0 && fplog)
{
fprintf(fplog, "maxwarn < 0, will not stop on constraint errors\n");
}
constr->warncount_lincs = 0;
constr->warncount_settle = 0;
/* Initialize the essential dynamics sampling.
* Put the pointer to the ED struct in constr */
constr->ed = ed;
if (ed != NULL || state->edsamstate.nED > 0)
{
init_edsam(mtop, ir, cr, ed, state->x, state->box, &state->edsamstate);
}
constr->warn_mtop = mtop;
return constr;
}
int gmx_kinetics(int argc, char *argv[])
{
const char *desc[] = {
"[TT]g_kinetics[tt] reads two [TT].xvg[tt] files, each one containing data for N replicas.",
"The first file contains the temperature of each replica at each timestep,",
"and the second contains real values that can be interpreted as",
"an indicator for folding. If the value in the file is larger than",
"the cutoff it is taken to be unfolded and the other way around.[PAR]",
"From these data an estimate of the forward and backward rate constants",
"for folding is made at a reference temperature. In addition,",
"a theoretical melting curve and free energy as a function of temperature",
"are printed in an [TT].xvg[tt] file.[PAR]",
"The user can give a max value to be regarded as intermediate",
"([TT]-ucut[tt]), which, when given will trigger the use of an intermediate state",
"in the algorithm to be defined as those structures that have",
"cutoff < DATA < ucut. Structures with DATA values larger than ucut will",
"not be regarded as potential folders. In this case 8 parameters are optimized.[PAR]",
"The average fraction foled is printed in an [TT].xvg[tt] file together with the fit to it.",
"If an intermediate is used a further file will show the build of the intermediate and the fit to that process.[PAR]",
"The program can also be used with continuous variables (by setting",
"[TT]-nodiscrete[tt]). In this case kinetics of other processes can be",
"studied. This is very much a work in progress and hence the manual",
"(this information) is lagging behind somewhat.[PAR]",
"In order to compile this program you need access to the GNU",
"scientific library."
};
static int nreplica = 1;
static real tref = 298.15;
static real cutoff = 0.2;
static real ucut = 0.0;
static real Euf = 10;
static real Efu = 30;
static real Ei = 10;
static gmx_bool bHaveT = TRUE;
static real t0 = -1;
static real t1 = -1;
static real tb = 0;
static real te = 0;
static real tol = 1e-3;
static int maxiter = 100;
static int skip = 0;
static int nmult = 1;
static gmx_bool bBack = TRUE;
static gmx_bool bSplit = TRUE;
static gmx_bool bSum = TRUE;
static gmx_bool bDiscrete = TRUE;
t_pargs pa[] = {
{ "-time", FALSE, etBOOL, {&bHaveT},
"Expect a time in the input" },
{ "-b", FALSE, etREAL, {&tb},
"First time to read from set" },
{ "-e", FALSE, etREAL, {&te},
"Last time to read from set" },
{ "-bfit", FALSE, etREAL, {&t0},
"Time to start the fit from" },
{ "-efit", FALSE, etREAL, {&t1},
"Time to end the fit" },
{ "-T", FALSE, etREAL, {&tref},
"Reference temperature for computing rate constants" },
{ "-n", FALSE, etINT, {&nreplica},
"Read data for this number of replicas. Only necessary when files are written in xmgrace format using @type and & as delimiters." },
{ "-cut", FALSE, etREAL, {&cutoff},
"Cut-off (max) value for regarding a structure as folded" },
{ "-ucut", FALSE, etREAL, {&ucut},
"Cut-off (max) value for regarding a structure as intermediate (if not folded)" },
{ "-euf", FALSE, etREAL, {&Euf},
"Initial guess for energy of activation for folding (kJ/mol)" },
{ "-efu", FALSE, etREAL, {&Efu},
"Initial guess for energy of activation for unfolding (kJ/mol)" },
{ "-ei", FALSE, etREAL, {&Ei},
"Initial guess for energy of activation for intermediates (kJ/mol)" },
{ "-maxiter", FALSE, etINT, {&maxiter},
"Max number of iterations" },
{ "-back", FALSE, etBOOL, {&bBack},
"Take the back reaction into account" },
{ "-tol", FALSE, etREAL, {&tol},
"Absolute tolerance for convergence of the Nelder and Mead simplex algorithm" },
{ "-skip", FALSE, etINT, {&skip},
"Skip points in the output [TT].xvg[tt] file" },
{ "-split", FALSE, etBOOL, {&bSplit},
"Estimate error by splitting the number of replicas in two and refitting" },
{ "-sum", FALSE, etBOOL, {&bSum},
"Average folding before computing [GRK]chi[grk]^2" },
{ "-discrete", FALSE, etBOOL, {&bDiscrete},
"Use a discrete folding criterion (F <-> U) or a continuous one" },
{ "-mult", FALSE, etINT, {&nmult},
"Factor to multiply the data with before discretization" }
};
#define NPA asize(pa)
FILE *fp;
real dt_t, dt_d, dt_d2;
int nset_t, nset_d, nset_d2, n_t, n_d, n_d2, i;
const char *tfile, *dfile, *dfile2;
t_remd_data remd;
output_env_t oenv;
t_filenm fnm[] = {
{ efXVG, "-f", "temp", ffREAD },
{ efXVG, "-d", "data", ffREAD },
{ efXVG, "-d2", "data2", ffOPTRD },
{ efXVG, "-o", "ft_all", ffWRITE },
{ efXVG, "-o2", "it_all", ffOPTWR },
{ efXVG, "-o3", "ft_repl", ffOPTWR },
{ efXVG, "-ee", "err_est", ffOPTWR },
{ efLOG, "-g", "remd", ffWRITE },
{ efXVG, "-m", "melt", ffWRITE }
};
#define NFILE asize(fnm)
parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_BE_NICE | PCA_TIME_UNIT,
NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv);
#ifdef HAVE_LIBGSL
please_cite(stdout, "Spoel2006d");
if (cutoff < 0)
{
gmx_fatal(FARGS, "cutoff should be >= 0 (rather than %f)", cutoff);
}
tfile = opt2fn("-f", NFILE, fnm);
dfile = opt2fn("-d", NFILE, fnm);
dfile2 = opt2fn_null("-d2", NFILE, fnm);
fp = ffopen(opt2fn("-g", NFILE, fnm), "w");
remd.temp = read_xvg_time(tfile, bHaveT,
opt2parg_bSet("-b", NPA, pa), tb,
opt2parg_bSet("-e", NPA, pa), te,
nreplica, &nset_t, &n_t, &dt_t, &remd.time);
printf("Read %d sets of %d points in %s, dt = %g\n\n", nset_t, n_t, tfile, dt_t);
sfree(remd.time);
remd.data = read_xvg_time(dfile, bHaveT,
opt2parg_bSet("-b", NPA, pa), tb,
opt2parg_bSet("-e", NPA, pa), te,
nreplica, &nset_d, &n_d, &dt_d, &remd.time);
printf("Read %d sets of %d points in %s, dt = %g\n\n", nset_d, n_d, dfile, dt_d);
if ((nset_t != nset_d) || (n_t != n_d) || (dt_t != dt_d))
{
gmx_fatal(FARGS, "Files %s and %s are inconsistent. Check log file",
tfile, dfile);
}
if (dfile2)
{
remd.data2 = read_xvg_time(dfile2, bHaveT,
opt2parg_bSet("-b", NPA, pa), tb,
opt2parg_bSet("-e", NPA, pa), te,
nreplica, &nset_d2, &n_d2, &dt_d2, &remd.time);
printf("Read %d sets of %d points in %s, dt = %g\n\n",
nset_d2, n_d2, dfile2, dt_d2);
if ((nset_d2 != nset_d) || (n_d != n_d2) || (dt_d != dt_d2))
{
gmx_fatal(FARGS, "Files %s and %s are inconsistent. Check log file",
dfile, dfile2);
}
}
else
{
remd.data2 = NULL;
}
remd.nreplica = nset_d;
remd.nframe = n_d;
remd.dt = 1;
preprocess_remd(fp, &remd, cutoff, tref, ucut, bBack, Euf, Efu, Ei, t0, t1,
bSum, bDiscrete, nmult);
optimize_remd_parameters(&remd, maxiter, tol);
dump_remd_parameters(fp, &remd, opt2fn("-o", NFILE, fnm),
opt2fn_null("-o2", NFILE, fnm),
opt2fn_null("-o3", NFILE, fnm),
opt2fn_null("-ee", NFILE, fnm),
opt2fn("-m", NFILE, fnm), skip, tref, oenv);
if (bSplit)
{
printf("Splitting set of replicas in two halves\n");
for (i = 0; (i < remd.nreplica); i++)
{
remd.bMask[i] = FALSE;
}
remd.nmask = 0;
for (i = 0; (i < remd.nreplica); i += 2)
{
remd.bMask[i] = TRUE;
remd.nmask++;
}
sum_ft(&remd);
optimize_remd_parameters(&remd, maxiter, tol);
dump_remd_parameters(fp, &remd, "test1.xvg", NULL, NULL, NULL, NULL, skip, tref, oenv);
for (i = 0; (i < remd.nreplica); i++)
{
remd.bMask[i] = !remd.bMask[i];
}
remd.nmask = remd.nreplica - remd.nmask;
sum_ft(&remd);
optimize_remd_parameters(&remd, maxiter, tol);
dump_remd_parameters(fp, &remd, "test2.xvg", NULL, NULL, NULL, NULL, skip, tref, oenv);
for (i = 0; (i < remd.nreplica); i++)
{
remd.bMask[i] = FALSE;
}
remd.nmask = 0;
for (i = 0; (i < remd.nreplica/2); i++)
{
remd.bMask[i] = TRUE;
remd.nmask++;
}
sum_ft(&remd);
optimize_remd_parameters(&remd, maxiter, tol);
dump_remd_parameters(fp, &remd, "test1.xvg", NULL, NULL, NULL, NULL, skip, tref, oenv);
for (i = 0; (i < remd.nreplica); i++)
{
remd.bMask[i] = FALSE;
}
remd.nmask = 0;
for (i = remd.nreplica/2; (i < remd.nreplica); i++)
{
remd.bMask[i] = TRUE;
remd.nmask++;
}
sum_ft(&remd);
optimize_remd_parameters(&remd, maxiter, tol);
dump_remd_parameters(fp, &remd, "test1.xvg", NULL, NULL, NULL, NULL, skip, tref, oenv);
}
ffclose(fp);
view_all(oenv, NFILE, fnm);
#else
fprintf(stderr, "This program should be compiled with the GNU scientific library. Please install the library and reinstall GROMACS.\n");
#endif /*HAVE_LIBGSL*/
return 0;
}
static bool low_constrain(FILE *log,t_topology *top,t_inputrec *ir,
int step,t_mdatoms *md,int start,int homenr,
rvec *x,rvec *xprime,rvec *min_proj,matrix box,
real lambda,real *dvdlambda,t_nrnb *nrnb,
bool bCoordinates,bool bInit)
{
static int nblocks=0;
static int *sblock=NULL;
static int nsettle,settle_type;
static int *owptr;
static bool bDumpOnError = TRUE;
char buf[STRLEN];
bool bOK;
t_sortblock *sb;
t_block *blocks=&(top->blocks[ebSBLOCKS]);
t_idef *idef=&(top->idef);
t_iatom *iatom;
atom_id *inv_sblock;
int i,j,m,bnr;
int ncons,bstart,error;
bOK = TRUE;
if (bInit) {
/* Output variables, initiate them right away */
if ((ir->etc==etcBERENDSEN) || (ir->epc==epcBERENDSEN))
please_cite(log,"Berendsen84a");
#ifdef SPEC_CPU
bDumpOnError = TRUE;
#else
bDumpOnError = (getenv("NO_SHAKE_ERROR") == NULL);
#endif
/* Put the oxygen atoms in the owptr array */
nsettle=idef->il[F_SETTLE].nr/2;
if (nsettle > 0) {
snew(owptr,nsettle);
settle_type=idef->il[F_SETTLE].iatoms[0];
for (j=0; (j<idef->il[F_SETTLE].nr); j+=2) {
if (idef->il[F_SETTLE].iatoms[j] != settle_type)
fatal_error(0,"More than one settle type (%d and %d)",
settle_type,idef->il[F_SETTLE].iatoms[j]);
owptr[j/2]=idef->il[F_SETTLE].iatoms[j+1];
#ifdef DEBUG
fprintf(log,"owptr[%d]=%d\n",j/2,owptr[j/2]);
#endif
}
/* We used to free this memory, but ED sampling needs it later on
* sfree(idef->il[F_SETTLE].iatoms);
*/
please_cite(log,"Miyamoto92a");
}
ncons=idef->il[F_SHAKE].nr/3;
if (ncons > 0)
{
bstart=(idef->nodeid > 0) ? blocks->multinr[idef->nodeid-1] : 0;
nblocks=blocks->multinr[idef->nodeid] - bstart;
if (debug)
fprintf(debug,"ncons: %d, bstart: %d, nblocks: %d\n",
ncons,bstart,nblocks);
/* Calculate block number for each atom */
inv_sblock=make_invblock(blocks,md->nr);
/* Store the block number in temp array and
* sort the constraints in order of the sblock number
* and the atom numbers, really sorting a segment of the array!
*/
#ifdef DEBUGIDEF
pr_idef(stdlog,0,"Before Sort",idef);
#endif
iatom=idef->il[F_SHAKE].iatoms;
snew(sb,ncons);
for(i=0; (i<ncons); i++,iatom+=3) {
for(m=0; (m<3); m++)
sb[i].iatom[m]=iatom[m];
sb[i].blocknr=inv_sblock[iatom[1]];
}
/* Now sort the blocks */
if (debug) {
pr_sortblock(debug,"Before sorting",ncons,sb);
fprintf(debug,"Going to sort constraints\n");
}
qsort(sb,ncons,(size_t)sizeof(*sb),pcomp);
if (debug) {
fprintf(debug,"I used %d calls to pcomp\n",pcount);
pr_sortblock(debug,"After sorting",ncons,sb);
}
iatom=idef->il[F_SHAKE].iatoms;
for(i=0; (i<ncons); i++,iatom+=3)
for(m=0; (m<DIM); m++)
iatom[m]=sb[i].iatom[m];
#ifdef DEBUGIDEF
pr_idef(stdlog,0,"After Sort",idef);
#endif
j=0;
snew(sblock,nblocks+1);
bnr=-2;
for(i=0; (i<ncons); i++) {
if (sb[i].blocknr != bnr) {
bnr=sb[i].blocknr;
sblock[j++]=3*i;
}
}
/* Last block... */
sblock[j++]=3*ncons;
if (j != (nblocks+1) && log) {
fprintf(log,"bstart: %d\n",bstart);
fprintf(log,"j: %d, nblocks: %d, ncons: %d\n",
j,nblocks,ncons);
for(i=0; (i<ncons); i++)
fprintf(log,"i: %5d sb[i].blocknr: %5u\n",i,sb[i].blocknr);
for(j=0; (j<=nblocks); j++)
fprintf(log,"sblock[%3d]=%5d\n",j,(int) sblock[j]);
fatal_error(0,"DEATH HORROR: "
"top->blocks[ebSBLOCKS] does not match idef->il[F_SHAKE]");
}
sfree(sb);
sfree(inv_sblock);
}
if (idef->il[F_SHAKE].nr) {
if (ir->eConstrAlg == estLINCS || !bCoordinates) {
please_cite(stdlog,"Hess97a");
bOK = constrain_lincs(stdlog,top,ir,0,md,start,homenr,&nblocks,&sblock,
NULL,NULL,NULL,NULL,0,NULL,bCoordinates,TRUE,nrnb,
bDumpOnError);
}
else
please_cite(stdlog,"Ryckaert77a");
}
}
else {
/* !bInit */
if (nblocks > 0) {
where();
if (ir->eConstrAlg == estSHAKE)
bOK = bshakef(stdlog,homenr,md->invmass,nblocks,sblock,idef,
ir,box,x,xprime,nrnb,lambda,dvdlambda,bDumpOnError);
else if (ir->eConstrAlg == estLINCS)
bOK = constrain_lincs(stdlog,top,ir,step,md,
start,homenr,&nblocks,&sblock,
x,xprime,min_proj,box,lambda,dvdlambda,
bCoordinates,FALSE,nrnb,bDumpOnError);
if (!bOK && bDumpOnError && stdlog)
fprintf(stdlog,"Constraint error in algorithm %s at step %d\n",
eshake_names[ir->eConstrAlg],step);
}
if (nsettle > 0) {
int ow1;
real mO,mH,dOH,dHH;
ow1 = owptr[0];
mO = md->massA[ow1];
mH = md->massA[ow1+1];
dOH = top->idef.iparams[settle_type].settle.doh;
dHH = top->idef.iparams[settle_type].settle.dhh;
#ifdef USE_FORTRAN
#ifdef DOUBLE
F77_FUNC(fsettled,FSETTLED)(&nsettle,owptr,x[0],xprime[0],
&dOH,&dHH,&mO,&mH,&error);
#else
F77_FUNC(fsettle,FSETTLE)(&nsettle,owptr,x[0],xprime[0],
&dOH,&dHH,&mO,&mH,&error);
#endif
#else
csettle(stdlog,nsettle,owptr,x[0],xprime[0],dOH,dHH,mO,mH,&error);
#endif
inc_nrnb(nrnb,eNR_SETTLE,nsettle);
bOK = (error < 0);
if (!bOK && bDumpOnError && stdlog)
fprintf(stdlog,"\nt = %.3f ps: Water molecule starting at atom %d can not be "
"settled.\nCheck for bad contacts and/or reduce the timestep.",
ir->init_t+step*ir->delta_t,owptr[error]+1);
}
if (!bOK && bDumpOnError)
dump_confs(step,&(top->atoms),x,xprime,box);
}
return bOK;
}
int gmx_sas(int argc,char *argv[])
{
const char *desc[] = {
"[TT]g_sas[tt] computes hydrophobic, hydrophilic and total solvent",
"accessible surface area. See Eisenhaber F, Lijnzaad P, Argos P,",
"Sander C, & Scharf M (1995) J. Comput. Chem. 16, 273-284.",
"As a side effect, the Connolly surface can be generated as well in",
"a [TT].pdb[tt] file where the nodes are represented as atoms and the",
"vertice connecting the nearest nodes as CONECT records.",
"The program will ask for a group for the surface calculation",
"and a group for the output. The calculation group should always",
"consists of all the non-solvent atoms in the system.",
"The output group can be the whole or part of the calculation group.",
"The average and standard deviation of the area over the trajectory can be plotted",
"per residue and atom as well (options [TT]-or[tt] and [TT]-oa[tt]).",
"In combination with the latter option an [TT].itp[tt] file can be",
"generated (option [TT]-i[tt])",
"which can be used to restrain surface atoms.[PAR]",
"By default, periodic boundary conditions are taken into account,",
"this can be turned off using the [TT]-nopbc[tt] option.[PAR]",
"With the [TT]-tv[tt] option the total volume and density of the",
"molecule can be computed.",
"Please consider whether the normal probe radius is appropriate",
"in this case or whether you would rather use e.g. 0. It is good",
"to keep in mind that the results for volume and density are very",
"approximate. For example, in ice Ih, one can easily fit water molecules in the",
"pores which would yield a volume that is too low, and surface area and density",
"that are both too high."
};
output_env_t oenv;
static real solsize = 0.14;
static int ndots = 24;
static real qcut = 0.2;
static real minarea = 0.5, dgs_default=0;
static gmx_bool bSave = TRUE,bPBC=TRUE,bFindex=FALSE;
t_pargs pa[] = {
{ "-probe", FALSE, etREAL, {&solsize},
"Radius of the solvent probe (nm)" },
{ "-ndots", FALSE, etINT, {&ndots},
"Number of dots per sphere, more dots means more accuracy" },
{ "-qmax", FALSE, etREAL, {&qcut},
"The maximum charge (e, absolute value) of a hydrophobic atom" },
{ "-f_index", FALSE, etBOOL, {&bFindex},
"Determine from a group in the index file what are the hydrophobic atoms rather than from the charge" },
{ "-minarea", FALSE, etREAL, {&minarea},
"The minimum area (nm^2) to count an atom as a surface atom when writing a position restraint file (see help)" },
{ "-pbc", FALSE, etBOOL, {&bPBC},
"Take periodicity into account" },
{ "-prot", FALSE, etBOOL, {&bSave},
"Output the protein to the Connelly [TT].pdb[tt] file too" },
{ "-dgs", FALSE, etREAL, {&dgs_default},
"Default value for solvation free energy per area (kJ/mol/nm^2)" }
};
t_filenm fnm[] = {
{ efTRX, "-f", NULL, ffREAD },
{ efTPS, "-s", NULL, ffREAD },
{ efXVG, "-o", "area", ffWRITE },
{ efXVG, "-or", "resarea", ffOPTWR },
{ efXVG, "-oa", "atomarea", ffOPTWR },
{ efXVG, "-tv", "volume", ffOPTWR },
{ efPDB, "-q", "connelly", ffOPTWR },
{ efNDX, "-n", "index", ffOPTRD },
{ efITP, "-i", "surfat", ffOPTWR }
};
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL,&oenv);
if (solsize < 0) {
solsize=1e-3;
fprintf(stderr,"Probe size too small, setting it to %g\n",solsize);
}
if (ndots < 20) {
ndots = 20;
fprintf(stderr,"Ndots too small, setting it to %d\n",ndots);
}
please_cite(stderr,"Eisenhaber95");
sas_plot(NFILE,fnm,solsize,ndots,qcut,bSave,minarea,bPBC,dgs_default,bFindex,
oenv);
do_view(oenv,opt2fn("-o",NFILE,fnm),"-nxy");
do_view(oenv,opt2fn_null("-or",NFILE,fnm),"-nxy");
do_view(oenv,opt2fn_null("-oa",NFILE,fnm),"-nxy");
thanx(stderr);
return 0;
}
void sas_plot(int nfile,t_filenm fnm[],real solsize,int ndots,
real qcut,gmx_bool bSave,real minarea,gmx_bool bPBC,
real dgs_default,gmx_bool bFindex, const output_env_t oenv)
{
FILE *fp,*fp2,*fp3=NULL,*vp;
const char *flegend[] = { "Hydrophobic", "Hydrophilic",
"Total", "D Gsolv" };
const char *vlegend[] = { "Volume (nm\\S3\\N)", "Density (g/l)" };
const char *or_and_oa_legend[] = { "Average (nm\\S2\\N)", "Standard deviation (nm\\S2\\N)" };
const char *vfile;
real t;
gmx_atomprop_t aps=NULL;
gmx_rmpbc_t gpbc=NULL;
t_trxstatus *status;
int ndefault;
int i,j,ii,nfr,natoms,flag,nsurfacedots,res;
rvec *xtop,*x;
matrix topbox,box;
t_topology top;
char title[STRLEN];
int ePBC;
gmx_bool bTop;
t_atoms *atoms;
gmx_bool *bOut,*bPhobic;
gmx_bool bConnelly;
gmx_bool bResAt,bITP,bDGsol;
real *radius,*dgs_factor=NULL,*area=NULL,*surfacedots=NULL;
real at_area,*atom_area=NULL,*atom_area2=NULL;
real *res_a=NULL,*res_area=NULL,*res_area2=NULL;
real totarea,totvolume,totmass=0,density,harea,tarea,fluc2;
atom_id **index,*findex;
int *nx,nphobic,npcheck,retval;
char **grpname,*fgrpname;
real dgsolv;
bITP = opt2bSet("-i",nfile,fnm);
bResAt = opt2bSet("-or",nfile,fnm) || opt2bSet("-oa",nfile,fnm) || bITP;
bTop = read_tps_conf(ftp2fn(efTPS,nfile,fnm),title,&top,&ePBC,
&xtop,NULL,topbox,FALSE);
atoms = &(top.atoms);
if (!bTop) {
fprintf(stderr,"No tpr file, will not compute Delta G of solvation\n");
bDGsol = FALSE;
} else {
bDGsol = strcmp(*(atoms->atomtype[0]),"?") != 0;
if (!bDGsol) {
fprintf(stderr,"Warning: your tpr file is too old, will not compute "
"Delta G of solvation\n");
} else {
printf("In case you use free energy of solvation predictions:\n");
please_cite(stdout,"Eisenberg86a");
}
}
aps = gmx_atomprop_init();
if ((natoms=read_first_x(oenv,&status,ftp2fn(efTRX,nfile,fnm),
&t,&x,box))==0)
gmx_fatal(FARGS,"Could not read coordinates from statusfile\n");
if ((ePBC != epbcXYZ) || (TRICLINIC(box))) {
fprintf(stderr,"\n\nWARNING: non-rectangular boxes may give erroneous results or crashes.\n"
"Analysis based on vacuum simulations (with the possibility of evaporation)\n"
"will certainly crash the analysis.\n\n");
}
snew(nx,2);
snew(index,2);
snew(grpname,2);
fprintf(stderr,"Select a group for calculation of surface and a group for output:\n");
get_index(atoms,ftp2fn_null(efNDX,nfile,fnm),2,nx,index,grpname);
if (bFindex) {
fprintf(stderr,"Select a group of hydrophobic atoms:\n");
get_index(atoms,ftp2fn_null(efNDX,nfile,fnm),1,&nphobic,&findex,&fgrpname);
}
snew(bOut,natoms);
for(i=0; i<nx[1]; i++)
bOut[index[1][i]] = TRUE;
/* Now compute atomic readii including solvent probe size */
snew(radius,natoms);
snew(bPhobic,nx[0]);
if (bResAt) {
snew(atom_area,nx[0]);
snew(atom_area2,nx[0]);
snew(res_a,atoms->nres);
snew(res_area,atoms->nres);
snew(res_area2,atoms->nres);
}
if (bDGsol)
snew(dgs_factor,nx[0]);
/* Get a Van der Waals radius for each atom */
ndefault = 0;
for(i=0; (i<natoms); i++) {
if (!gmx_atomprop_query(aps,epropVDW,
*(atoms->resinfo[atoms->atom[i].resind].name),
*(atoms->atomname[i]),&radius[i]))
ndefault++;
/* radius[i] = calc_radius(*(top->atoms.atomname[i])); */
radius[i] += solsize;
}
if (ndefault > 0)
fprintf(stderr,"WARNING: could not find a Van der Waals radius for %d atoms\n",ndefault);
/* Determine which atom is counted as hydrophobic */
if (bFindex) {
npcheck = 0;
for(i=0; (i<nx[0]); i++) {
ii = index[0][i];
for(j=0; (j<nphobic); j++) {
if (findex[j] == ii) {
bPhobic[i] = TRUE;
if (bOut[ii])
npcheck++;
}
}
}
if (npcheck != nphobic)
gmx_fatal(FARGS,"Consistency check failed: not all %d atoms in the hydrophobic index\n"
"found in the normal index selection (%d atoms)",nphobic,npcheck);
}
else
nphobic = 0;
for(i=0; (i<nx[0]); i++) {
ii = index[0][i];
if (!bFindex) {
bPhobic[i] = fabs(atoms->atom[ii].q) <= qcut;
if (bPhobic[i] && bOut[ii])
nphobic++;
}
if (bDGsol)
if (!gmx_atomprop_query(aps,epropDGsol,
*(atoms->resinfo[atoms->atom[ii].resind].name),
*(atoms->atomtype[ii]),&(dgs_factor[i])))
dgs_factor[i] = dgs_default;
if (debug)
fprintf(debug,"Atom %5d %5s-%5s: q= %6.3f, r= %6.3f, dgsol= %6.3f, hydrophobic= %s\n",
ii+1,*(atoms->resinfo[atoms->atom[ii].resind].name),
*(atoms->atomname[ii]),
atoms->atom[ii].q,radius[ii]-solsize,dgs_factor[i],
BOOL(bPhobic[i]));
}
fprintf(stderr,"%d out of %d atoms were classified as hydrophobic\n",
nphobic,nx[1]);
fp=xvgropen(opt2fn("-o",nfile,fnm),"Solvent Accessible Surface","Time (ps)",
"Area (nm\\S2\\N)",oenv);
xvgr_legend(fp,asize(flegend) - (bDGsol ? 0 : 1),flegend,oenv);
vfile = opt2fn_null("-tv",nfile,fnm);
if (vfile) {
if (!bTop) {
gmx_fatal(FARGS,"Need a tpr file for option -tv");
}
vp=xvgropen(vfile,"Volume and Density","Time (ps)","",oenv);
xvgr_legend(vp,asize(vlegend),vlegend,oenv);
totmass = 0;
ndefault = 0;
for(i=0; (i<nx[0]); i++) {
real mm;
ii = index[0][i];
/*
if (!query_atomprop(atomprop,epropMass,
*(top->atoms.resname[top->atoms.atom[ii].resnr]),
*(top->atoms.atomname[ii]),&mm))
ndefault++;
totmass += mm;
*/
totmass += atoms->atom[ii].m;
}
if (ndefault)
fprintf(stderr,"WARNING: Using %d default masses for density calculation, which most likely are inaccurate\n",ndefault);
}
else
vp = NULL;
gmx_atomprop_destroy(aps);
if (bPBC)
gpbc = gmx_rmpbc_init(&top.idef,ePBC,natoms,box);
nfr=0;
do {
if (bPBC)
gmx_rmpbc(gpbc,natoms,box,x);
bConnelly = (nfr==0 && opt2bSet("-q",nfile,fnm));
if (bConnelly) {
if (!bTop)
gmx_fatal(FARGS,"Need a tpr file for Connelly plot");
flag = FLAG_ATOM_AREA | FLAG_DOTS;
} else {
flag = FLAG_ATOM_AREA;
}
if (vp) {
flag = flag | FLAG_VOLUME;
}
if (debug)
write_sto_conf("check.pdb","pbc check",atoms,x,NULL,ePBC,box);
retval = nsc_dclm_pbc(x,radius,nx[0],ndots,flag,&totarea,
&area,&totvolume,&surfacedots,&nsurfacedots,
index[0],ePBC,bPBC ? box : NULL);
if (retval)
gmx_fatal(FARGS,"Something wrong in nsc_dclm_pbc");
if (bConnelly)
connelly_plot(ftp2fn(efPDB,nfile,fnm),
nsurfacedots,surfacedots,x,atoms,
&(top.symtab),ePBC,box,bSave);
harea = 0;
tarea = 0;
dgsolv = 0;
if (bResAt)
for(i=0; i<atoms->nres; i++)
res_a[i] = 0;
for(i=0; (i<nx[0]); i++) {
ii = index[0][i];
if (bOut[ii]) {
at_area = area[i];
if (bResAt) {
atom_area[i] += at_area;
atom_area2[i] += sqr(at_area);
res_a[atoms->atom[ii].resind] += at_area;
}
tarea += at_area;
if (bDGsol)
dgsolv += at_area*dgs_factor[i];
if (bPhobic[i])
harea += at_area;
}
}
if (bResAt)
for(i=0; i<atoms->nres; i++) {
res_area[i] += res_a[i];
res_area2[i] += sqr(res_a[i]);
}
fprintf(fp,"%10g %10g %10g %10g",t,harea,tarea-harea,tarea);
if (bDGsol)
fprintf(fp," %10g\n",dgsolv);
else
fprintf(fp,"\n");
/* Print volume */
if (vp) {
density = totmass*AMU/(totvolume*NANO*NANO*NANO);
fprintf(vp,"%12.5e %12.5e %12.5e\n",t,totvolume,density);
}
if (area) {
sfree(area);
area = NULL;
}
if (surfacedots) {
sfree(surfacedots);
surfacedots = NULL;
}
nfr++;
} while (read_next_x(oenv,status,&t,natoms,x,box));
if (bPBC)
gmx_rmpbc_done(gpbc);
fprintf(stderr,"\n");
close_trj(status);
ffclose(fp);
if (vp)
ffclose(vp);
/* if necessary, print areas per atom to file too: */
if (bResAt) {
for(i=0; i<atoms->nres; i++) {
res_area[i] /= nfr;
res_area2[i] /= nfr;
}
for(i=0; i<nx[0]; i++) {
atom_area[i] /= nfr;
atom_area2[i] /= nfr;
}
fprintf(stderr,"Printing out areas per atom\n");
fp = xvgropen(opt2fn("-or",nfile,fnm),"Area per residue over the trajectory","Residue",
"Area (nm\\S2\\N)",oenv);
xvgr_legend(fp, asize(or_and_oa_legend),or_and_oa_legend,oenv);
fp2 = xvgropen(opt2fn("-oa",nfile,fnm),"Area per atom over the trajectory","Atom #",
"Area (nm\\S2\\N)",oenv);
xvgr_legend(fp2, asize(or_and_oa_legend),or_and_oa_legend,oenv);
if (bITP) {
fp3 = ftp2FILE(efITP,nfile,fnm,"w");
fprintf(fp3,"[ position_restraints ]\n"
"#define FCX 1000\n"
"#define FCY 1000\n"
"#define FCZ 1000\n"
"; Atom Type fx fy fz\n");
}
for(i=0; i<nx[0]; i++) {
ii = index[0][i];
res = atoms->atom[ii].resind;
if (i==nx[0]-1 || res!=atoms->atom[index[0][i+1]].resind) {
fluc2 = res_area2[res]-sqr(res_area[res]);
if (fluc2 < 0)
fluc2 = 0;
fprintf(fp,"%10d %10g %10g\n",
atoms->resinfo[res].nr,res_area[res],sqrt(fluc2));
}
fluc2 = atom_area2[i]-sqr(atom_area[i]);
if (fluc2 < 0)
fluc2 = 0;
fprintf(fp2,"%d %g %g\n",index[0][i]+1,atom_area[i],sqrt(fluc2));
if (bITP && (atom_area[i] > minarea))
fprintf(fp3,"%5d 1 FCX FCX FCZ\n",ii+1);
}
if (bITP)
ffclose(fp3);
ffclose(fp);
}
/* Be a good citizen, keep our memory free! */
sfree(x);
sfree(nx);
for(i=0;i<2;i++)
{
sfree(index[i]);
sfree(grpname[i]);
}
sfree(bOut);
sfree(radius);
sfree(bPhobic);
if(bResAt)
{
sfree(atom_area);
sfree(atom_area2);
sfree(res_a);
sfree(res_area);
sfree(res_area2);
}
if(bDGsol)
{
sfree(dgs_factor);
}
}
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;
}
void init_disres(FILE *fplog,const gmx_mtop_t *mtop,
t_inputrec *ir,const t_commrec *cr,gmx_bool bPartDecomp,
t_fcdata *fcd,t_state *state)
{
int fa,nmol,i,npair,np;
t_iparams *ip;
t_disresdata *dd;
history_t *hist;
gmx_mtop_ilistloop_t iloop;
t_ilist *il;
char *ptr;
dd = &(fcd->disres);
if (gmx_mtop_ftype_count(mtop,F_DISRES) == 0)
{
dd->nres = 0;
return;
}
if (fplog)
{
fprintf(fplog,"Initializing the distance restraints\n");
}
if (ir->eDisre == edrEnsemble)
{
gmx_fatal(FARGS,"Sorry, distance restraints with ensemble averaging over multiple molecules in one system are not functional in this version of GROMACS");
}
dd->dr_weighting = ir->eDisreWeighting;
dd->dr_fc = ir->dr_fc;
if (EI_DYNAMICS(ir->eI))
{
dd->dr_tau = ir->dr_tau;
}
else
{
dd->dr_tau = 0.0;
}
if (dd->dr_tau == 0.0)
{
dd->dr_bMixed = FALSE;
dd->ETerm = 0.0;
}
else
{
dd->dr_bMixed = ir->bDisreMixed;
dd->ETerm = exp(-(ir->delta_t/ir->dr_tau));
}
dd->ETerm1 = 1.0 - dd->ETerm;
ip = mtop->ffparams.iparams;
dd->nres = 0;
dd->npair = 0;
iloop = gmx_mtop_ilistloop_init(mtop);
while (gmx_mtop_ilistloop_next(iloop,&il,&nmol)) {
np = 0;
for(fa=0; fa<il[F_DISRES].nr; fa+=3)
{
np++;
npair = mtop->ffparams.iparams[il[F_DISRES].iatoms[fa]].disres.npair;
if (np == npair)
{
dd->nres += (ir->eDisre==edrEnsemble ? 1 : nmol)*npair;
dd->npair += nmol*npair;
np = 0;
}
}
}
if (cr && PAR(cr) && !bPartDecomp)
{
/* Temporary check, will be removed when disre is implemented with DD */
const char *notestr="NOTE: atoms involved in distance restraints should be within the longest cut-off distance, if this is not the case mdrun generates a fatal error, in that case use particle decomposition (mdrun option -pd)";
if (MASTER(cr))
fprintf(stderr,"\n%s\n\n",notestr);
if (fplog)
fprintf(fplog,"%s\n",notestr);
if (dd->dr_tau != 0 || ir->eDisre == edrEnsemble || cr->ms != NULL ||
dd->nres != dd->npair)
{
gmx_fatal(FARGS,"Time or ensemble averaged or multiple pair distance restraints do not work (yet) with domain decomposition, use particle decomposition (mdrun option -pd)");
}
if (ir->nstdisreout != 0)
{
if (fplog)
{
fprintf(fplog,"\nWARNING: Can not write distance restraint data to energy file with domain decomposition\n\n");
}
if (MASTER(cr))
{
fprintf(stderr,"\nWARNING: Can not write distance restraint data to energy file with domain decomposition\n");
}
ir->nstdisreout = 0;
}
}
snew(dd->rt,dd->npair);
if (dd->dr_tau != 0.0)
{
hist = &state->hist;
/* Set the "history lack" factor to 1 */
state->flags |= (1<<estDISRE_INITF);
hist->disre_initf = 1.0;
/* Allocate space for the r^-3 time averages */
state->flags |= (1<<estDISRE_RM3TAV);
hist->ndisrepairs = dd->npair;
snew(hist->disre_rm3tav,hist->ndisrepairs);
}
/* Allocate space for a copy of rm3tav,
* so we can call do_force without modifying the state.
*/
snew(dd->rm3tav,dd->npair);
/* Allocate Rt_6 and Rtav_6 consecutively in memory so they can be
* averaged over the processors in one call (in calc_disre_R_6)
*/
snew(dd->Rt_6,2*dd->nres);
dd->Rtav_6 = &(dd->Rt_6[dd->nres]);
ptr = getenv("GMX_DISRE_ENSEMBLE_SIZE");
if (cr && cr->ms != NULL && ptr != NULL)
{
#ifdef GMX_MPI
dd->nsystems = 0;
sscanf(ptr,"%d",&dd->nsystems);
if (fplog)
{
fprintf(fplog,"Found GMX_DISRE_ENSEMBLE_SIZE set to %d systems per ensemble\n",dd->nsystems);
}
check_multi_int(fplog,cr->ms,dd->nsystems,
"the number of systems per ensemble");
if (dd->nsystems <= 0 || cr->ms->nsim % dd->nsystems != 0)
{
gmx_fatal(FARGS,"The number of systems %d is not divisible by the number of systems per ensemble %d\n",cr->ms->nsim,dd->nsystems);
}
/* Split the inter-master communicator into different ensembles */
MPI_Comm_split(cr->ms->mpi_comm_masters,
cr->ms->sim/dd->nsystems,
cr->ms->sim,
&dd->mpi_comm_ensemble);
if (fplog)
{
fprintf(fplog,"Our ensemble consists of systems:");
for(i=0; i<dd->nsystems; i++)
{
fprintf(fplog," %d",
(cr->ms->sim/dd->nsystems)*dd->nsystems+i);
}
fprintf(fplog,"\n");
}
snew(dd->Rtl_6,dd->nres);
#endif
}
else
{
dd->nsystems = 1;
dd->Rtl_6 = dd->Rt_6;
}
if (dd->npair > 0)
{
if (fplog) {
fprintf(fplog,"There are %d distance restraints involving %d atom pairs\n",dd->nres,dd->npair);
}
if (cr && cr->ms)
{
check_multi_int(fplog,cr->ms,fcd->disres.nres,
"the number of distance restraints");
}
please_cite(fplog,"Tropp80a");
please_cite(fplog,"Torda89a");
}
}
int gmx_dyecoupl(int argc, char *argv[])
{
const char *desc[] =
{
"[THISMODULE] extracts dye dynamics from trajectory files.",
"Currently, R and kappa^2 between dyes is extracted for (F)RET",
"simulations with assumed dipolar coupling as in the Foerster equation.",
"It further allows the calculation of R(t) and kappa^2(t), R and",
"kappa^2 histograms and averages, as well as the instantaneous FRET",
"efficiency E(t) for a specified Foerster radius R_0 (switch [TT]-R0[tt]).",
"The input dyes have to be whole (see res and mol pbc options",
"in [TT]trjconv[tt]).",
"The dye transition dipole moment has to be defined by at least",
"a single atom pair, however multiple atom pairs can be provided ",
"in the index file. The distance R is calculated on the basis of",
"the COMs of the given atom pairs.",
"The [TT]-pbcdist[tt] option calculates distances to the nearest periodic",
"image instead to the distance in the box. This works however only,"
"for periodic boundaries in all 3 dimensions.",
"The [TT]-norm[tt] option (area-) normalizes the histograms."
};
static gmx_bool bPBCdist = FALSE, bNormHist = FALSE;
int histbins = 50;
gmx_output_env_t *oenv;
real R0 = -1;
t_pargs pa[] =
{
{ "-pbcdist", FALSE, etBOOL, { &bPBCdist }, "Distance R based on PBC" },
{ "-norm", FALSE, etBOOL, { &bNormHist }, "Normalize histograms" },
{ "-bins", FALSE, etINT, {&histbins}, "# of histogram bins" },
{ "-R0", FALSE, etREAL, {&R0}, "Foerster radius including kappa^2=2/3 in nm" }
};
#define NPA asize(pa)
t_filenm fnm[] =
{
{ efTRX, "-f", NULL, ffREAD },
{ efNDX, NULL, NULL, ffREAD },
{ efXVG, "-ot", "rkappa", ffOPTWR },
{ efXVG, "-oe", "insteff", ffOPTWR },
{ efDAT, "-o", "rkappa", ffOPTWR },
{ efXVG, "-rhist", "rhist", ffOPTWR },
{ efXVG, "-khist", "khist", ffOPTWR }
};
#define NFILE asize(fnm)
const char *in_trajfile, *out_xvgrkfile = NULL, *out_xvginstefffile = NULL, *out_xvgrhistfile = NULL, *out_xvgkhistfile = NULL, *out_datfile = NULL;
gmx_bool bHaveFirstFrame, bHaveNextFrame, indexOK = TRUE;
int ndon, nacc;
atom_id *donindex, *accindex;
char *grpnm;
t_trxstatus *status;
t_trxframe fr;
int flags;
int allocblock = 1000;
real histexpand = 1e-6;
rvec donvec, accvec, donpos, accpos, dist, distnorm;
int natoms;
/*we rely on PBC autodetection (...currently)*/
int ePBC = -1;
real *rvalues = NULL, *kappa2values = NULL, *rhist = NULL, *khist = NULL;
t_pbc *pbc = NULL;
int i, bin;
FILE *rkfp = NULL, *rhfp = NULL, *khfp = NULL, *datfp = NULL, *iefp = NULL;
gmx_bool bRKout, bRhistout, bKhistout, bDatout, bInstEffout, grident;
const char *rkleg[2] = { "R", "\\f{Symbol}k\\f{}\\S2\\N" };
const char *rhleg[1] = { "p(R)" };
const char *khleg[1] = { "p(\\f{Symbol}k\\f{}\\S2\\N)" };
const char *ieleg[1] = { "E\\sRET\\N(t)" };
real R, kappa2, insteff, Rs = 0., kappa2s = 0., insteffs = 0., rmax, rmin, kmin = 0., kmax = 4.,
rrange, krange, rincr, kincr, Rfrac;
int rkcount = 0, rblocksallocated = 0, kblocksallocated = 0;
if (!parse_common_args(&argc, argv, PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW | PCA_TIME_UNIT,
NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
{
return 0;
}
/* Check command line options for filenames and set bool flags when switch used*/
in_trajfile = opt2fn("-f", NFILE, fnm);
out_xvgrkfile = opt2fn("-ot", NFILE, fnm);
out_xvgrhistfile = opt2fn("-rhist", NFILE, fnm);
out_xvgkhistfile = opt2fn("-khist", NFILE, fnm);
out_xvginstefffile = opt2fn("-oe", NFILE, fnm);
out_datfile = opt2fn("-o", NFILE, fnm);
bRKout = opt2bSet("-ot", NFILE, fnm);
bRhistout = opt2bSet("-rhist", NFILE, fnm);
bKhistout = opt2bSet("-khist", NFILE, fnm);
bDatout = opt2bSet("-o", NFILE, fnm);
bInstEffout = opt2bSet("-oe", NFILE, fnm);
/* PBC warning. */
if (bPBCdist)
{
printf("Calculating distances to periodic image.\n");
printf("Be careful! This produces only valid results for PBC in all three dimensions\n");
}
if (bInstEffout && R0 <= 0.)
{
gmx_fatal(FARGS, "You have to specify R0 and R0 has to be larger than 0 nm.\n\n");
}
printf("Select group with donor atom pairs defining the transition moment\n");
get_index(NULL, ftp2fn_null(efNDX, NFILE, fnm), 1, &ndon, &donindex, &grpnm);
printf("Select group with acceptor atom pairs defining the transition moment\n");
get_index(NULL, ftp2fn_null(efNDX, NFILE, fnm), 1, &nacc, &accindex, &grpnm);
/*check if groups are identical*/
grident = TRUE;
if (ndon == nacc)
{
for (i = 0; i < nacc; i++)
{
if (accindex[i] != donindex[i])
{
grident = FALSE;
break;
}
}
}
if (grident)
{
gmx_fatal(FARGS, "Donor and acceptor group are identical. This makes no sense.");
}
printf("Reading first frame\n");
/* open trx file for reading */
flags = 0;
flags = flags | TRX_READ_X;
bHaveFirstFrame = read_first_frame(oenv, &status, in_trajfile, &fr, flags);
if (bHaveFirstFrame)
{
printf("First frame is OK\n");
natoms = fr.natoms;
if ((ndon % 2 != 0) || (nacc % 2 != 0))
{
indexOK = FALSE;
}
else
{
for (i = 0; i < ndon; i++)
{
if (donindex[i] >= natoms)
{
indexOK = FALSE;
}
}
for (i = 0; i < nacc; i++)
{
if (accindex[i] >= natoms)
{
indexOK = FALSE;
}
}
}
if (indexOK)
{
if (bDatout)
{
datfp = gmx_ffopen(out_datfile, "w");
}
if (bRKout)
{
rkfp = xvgropen(out_xvgrkfile,
"Distance and \\f{Symbol}k\\f{}\\S2\\N trajectory",
"Time (ps)", "Distance (nm) / \\f{Symbol}k\\f{}\\S2\\N",
oenv);
xvgr_legend(rkfp, 2, rkleg, oenv);
}
if (bInstEffout)
{
iefp = xvgropen(out_xvginstefffile,
"Instantaneous RET Efficiency",
"Time (ps)", "RET Efficiency",
oenv);
xvgr_legend(iefp, 1, ieleg, oenv);
}
if (bRhistout)
{
snew(rvalues, allocblock);
rblocksallocated += 1;
snew(rhist, histbins);
}
if (bKhistout)
{
snew(kappa2values, allocblock);
kblocksallocated += 1;
snew(khist, histbins);
}
do
{
clear_rvec(donvec);
clear_rvec(accvec);
clear_rvec(donpos);
clear_rvec(accpos);
for (i = 0; i < ndon / 2; i++)
{
rvec_sub(donvec, fr.x[donindex[2 * i]], donvec);
rvec_add(donvec, fr.x[donindex[2 * i + 1]], donvec);
rvec_add(donpos, fr.x[donindex[2 * i]], donpos);
rvec_add(donpos, fr.x[donindex[2 * i + 1]], donpos);
}
for (i = 0; i < nacc / 2; i++)
{
rvec_sub(accvec, fr.x[accindex[2 * i]], accvec);
rvec_add(accvec, fr.x[accindex[2 * i + 1]], accvec);
rvec_add(accpos, fr.x[accindex[2 * i]], accpos);
rvec_add(accpos, fr.x[accindex[2 * i + 1]], accpos);
}
unitv(donvec, donvec);
unitv(accvec, accvec);
svmul(1.0 / ndon, donpos, donpos);
svmul(1.0 / nacc, accpos, accpos);
if (bPBCdist)
{
set_pbc(pbc, ePBC, fr.box);
pbc_dx(pbc, donpos, accpos, dist);
}
else
{
rvec_sub(donpos, accpos, dist);
}
unitv(dist, distnorm);
R = norm(dist);
kappa2 = iprod(donvec, accvec)- 3.* (iprod(donvec, distnorm) * iprod(distnorm, accvec));
kappa2 *= kappa2;
if (R0 > 0)
{
Rfrac = R/R0;
insteff = 1/(1+(Rfrac*Rfrac*Rfrac*Rfrac*Rfrac*Rfrac)*2/3/kappa2);
insteffs += insteff;
if (bInstEffout)
{
fprintf(iefp, "%12.7f %12.7f\n", fr.time, insteff);
}
}
Rs += R;
kappa2s += kappa2;
rkcount++;
if (bRKout)
{
fprintf(rkfp, "%12.7f %12.7f %12.7f\n", fr.time, R, kappa2);
}
if (bDatout)
{
fprintf(datfp, "%12.7f %12.7f %12.7f\n", fr.time, R, kappa2);
}
if (bRhistout)
{
rvalues[rkcount-1] = R;
if (rkcount % allocblock == 0)
{
srenew(rvalues, allocblock*(rblocksallocated+1));
rblocksallocated += 1;
}
}
if (bKhistout)
{
kappa2values[rkcount-1] = kappa2;
if (rkcount % allocblock == 0)
{
srenew(kappa2values, allocblock*(kblocksallocated+1));
kblocksallocated += 1;
}
}
bHaveNextFrame = read_next_frame(oenv, status, &fr);
}
while (bHaveNextFrame);
if (bRKout)
{
xvgrclose(rkfp);
}
if (bDatout)
{
gmx_ffclose(datfp);
}
if (bInstEffout)
{
xvgrclose(iefp);
}
if (bRhistout)
{
printf("Writing R-Histogram\n");
rmin = rvalues[0];
rmax = rvalues[0];
for (i = 1; i < rkcount; i++)
{
if (rvalues[i] < rmin)
{
rmin = rvalues[i];
}
else if (rvalues[i] > rmax)
{
rmax = rvalues[i];
}
}
rmin -= histexpand;
rmax += histexpand;
rrange = rmax - rmin;
rincr = rrange / histbins;
for (i = 1; i < rkcount; i++)
{
bin = static_cast<int>((rvalues[i] - rmin) / rincr);
rhist[bin] += 1;
}
if (bNormHist)
{
for (i = 0; i < histbins; i++)
{
rhist[i] /= rkcount * rrange/histbins;
}
rhfp = xvgropen(out_xvgrhistfile, "Distance Distribution",
"R (nm)", "Normalized Probability", oenv);
}
else
{
rhfp = xvgropen(out_xvgrhistfile, "Distance Distribution",
"R (nm)", "Probability", oenv);
}
xvgr_legend(rhfp, 1, rhleg, oenv);
for (i = 0; i < histbins; i++)
{
fprintf(rhfp, "%12.7f %12.7f\n", (i + 0.5) * rincr + rmin,
rhist[i]);
}
xvgrclose(rhfp);
}
if (bKhistout)
{
printf("Writing kappa^2-Histogram\n");
krange = kmax - kmin;
kincr = krange / histbins;
for (i = 1; i < rkcount; i++)
{
bin = static_cast<int>((kappa2values[i] - kmin) / kincr);
khist[bin] += 1;
}
if (bNormHist)
{
for (i = 0; i < histbins; i++)
{
khist[i] /= rkcount * krange/histbins;
}
khfp = xvgropen(out_xvgkhistfile,
"\\f{Symbol}k\\f{}\\S2\\N Distribution",
"\\f{Symbol}k\\f{}\\S2\\N",
"Normalized Probability", oenv);
}
else
{
khfp = xvgropen(out_xvgkhistfile,
"\\f{Symbol}k\\f{}\\S2\\N Distribution",
"\\f{Symbol}k\\f{}\\S2\\N", "Probability", oenv);
}
xvgr_legend(khfp, 1, khleg, oenv);
for (i = 0; i < histbins; i++)
{
fprintf(khfp, "%12.7f %12.7f\n", (i + 0.5) * kincr + kmin,
khist[i]);
}
xvgrclose(khfp);
}
printf("\nAverages:\n");
printf("R_avg = %8.4f nm\nKappa^2 = %8.4f\n", Rs / rkcount,
kappa2s / rkcount);
if (R0 > 0)
{
printf("E_RETavg = %8.4f\n", insteffs / rkcount);
}
please_cite(stdout, "Hoefling2011");
}
else
{
gmx_fatal(FARGS, "Index file invalid, check your index file for correct pairs.\n");
}
}
else
{
gmx_fatal(FARGS, "Could not read first frame of the trajectory.\n");
}
return 0;
}
gmx_repl_ex_t init_replica_exchange(FILE *fplog,
const gmx_multisim_t *ms,
const t_state *state,
const t_inputrec *ir,
int nst,int init_seed)
{
real temp,pres;
int i,j,k;
struct gmx_repl_ex *re;
fprintf(fplog,"\nInitializing Replica Exchange\n");
if (ms == NULL || ms->nsim == 1)
{
gmx_fatal(FARGS,"Nothing to exchange with only one replica, maybe you forgot to set the -multi option of mdrun?");
}
snew(re,1);
re->repl = ms->sim;
re->nrepl = ms->nsim;
fprintf(fplog,"Repl There are %d replicas:\n",re->nrepl);
check_multi_int(fplog,ms,state->natoms,"the number of atoms");
check_multi_int(fplog,ms,ir->eI,"the integrator");
check_multi_large_int(fplog,ms,ir->init_step+ir->nsteps,"init_step+nsteps");
check_multi_large_int(fplog,ms,(ir->init_step+nst-1)/nst,
"first exchange step: init_step/-replex");
check_multi_int(fplog,ms,ir->etc,"the temperature coupling");
check_multi_int(fplog,ms,ir->opts.ngtc,
"the number of temperature coupling groups");
check_multi_int(fplog,ms,ir->epc,"the pressure coupling");
check_multi_int(fplog,ms,ir->efep,"free energy");
re->temp = ir->opts.ref_t[0];
for(i=1; (i<ir->opts.ngtc); i++)
{
if (ir->opts.ref_t[i] != re->temp)
{
fprintf(fplog,"\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
fprintf(stderr,"\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
}
}
re->type = -1;
for(i=0; i<ereNR; i++)
{
switch (i)
{
case ereTEMP:
repl_quantity(fplog,ms,re,i,re->temp);
break;
case ereLAMBDA:
if (ir->efep != efepNO)
{
repl_quantity(fplog,ms,re,i,ir->init_lambda);
}
break;
default:
gmx_incons("Unknown replica exchange quantity");
}
}
if (re->type == -1)
{
gmx_fatal(FARGS,"The properties of the %d systems are all the same, there is nothing to exchange",re->nrepl);
}
switch (re->type)
{
case ereTEMP:
please_cite(fplog,"Hukushima96a");
if (ir->epc != epcNO)
{
re->bNPT = TRUE;
fprintf(fplog,"Repl Using Constant Pressure REMD.\n");
please_cite(fplog,"Okabe2001a");
}
if (ir->etc == etcBERENDSEN)
{
gmx_fatal(FARGS,"REMD with the %s thermostat does not produce correct potential energy distributions, consider using the %s thermostat instead",
ETCOUPLTYPE(ir->etc),ETCOUPLTYPE(etcVRESCALE));
}
break;
case ereLAMBDA:
if (ir->delta_lambda != 0)
{
gmx_fatal(FARGS,"delta_lambda is not zero");
}
break;
}
if (re->bNPT)
{
snew(re->pres,re->nrepl);
if (ir->epct == epctSURFACETENSION)
{
pres = ir->ref_p[ZZ][ZZ];
}
else
{
pres = 0;
j = 0;
for(i=0; i<DIM; i++)
{
if (ir->compress[i][i] != 0)
{
pres += ir->ref_p[i][i];
j++;
}
}
pres /= j;
}
re->pres[re->repl] = pres;
gmx_sum_sim(re->nrepl,re->pres,ms);
}
snew(re->ind,re->nrepl);
/* Make an index for increasing temperature order */
for(i=0; i<re->nrepl; i++)
{
re->ind[i] = i;
}
for(i=0; i<re->nrepl; i++)
{
for(j=i+1; j<re->nrepl; j++)
{
if (re->q[re->ind[j]] < re->q[re->ind[i]])
{
k = re->ind[i];
re->ind[i] = re->ind[j];
re->ind[j] = k;
}
else if (re->q[re->ind[j]] == re->q[re->ind[i]])
{
gmx_fatal(FARGS,"Two replicas have identical %ss",erename[re->type]);
}
}
}
fprintf(fplog,"Repl ");
for(i=0; i<re->nrepl; i++)
{
fprintf(fplog," %3d ",re->ind[i]);
}
switch (re->type)
{
case ereTEMP:
fprintf(fplog,"\nRepl T");
for(i=0; i<re->nrepl; i++)
{
fprintf(fplog," %5.1f",re->q[re->ind[i]]);
}
break;
case ereLAMBDA:
fprintf(fplog,"\nRepl l");
for(i=0; i<re->nrepl; i++)
{
fprintf(fplog," %5.3f",re->q[re->ind[i]]);
}
break;
default:
gmx_incons("Unknown replica exchange quantity");
}
if (re->bNPT)
{
fprintf(fplog,"\nRepl p");
for(i=0; i<re->nrepl; i++)
{
fprintf(fplog," %5.2f",re->pres[re->ind[i]]);
}
for(i=0; i<re->nrepl; i++)
{
if ((i > 0) && (re->pres[re->ind[i]] < re->pres[re->ind[i-1]]))
{
gmx_fatal(FARGS,"The reference pressure decreases with increasing temperature");
}
}
}
fprintf(fplog,"\nRepl ");
re->nst = nst;
if (init_seed == -1)
{
if (MASTERSIM(ms))
{
re->seed = make_seed();
}
else
{
re->seed = 0;
}
gmx_sumi_sim(1,&(re->seed),ms);
}
else
{
re->seed = init_seed;
}
fprintf(fplog,"\nRepl exchange interval: %d\n",re->nst);
fprintf(fplog,"\nRepl random seed: %d\n",re->seed);
re->nattempt[0] = 0;
re->nattempt[1] = 0;
snew(re->prob_sum,re->nrepl);
snew(re->nexchange,re->nrepl);
fprintf(fplog,"Repl below: x=exchange, pr=probability\n");
return re;
}
gmx_repl_ex_t init_replica_exchange(FILE *fplog,
const gmx_multisim_t *ms,
const t_state *state,
const t_inputrec *ir,
int nst, int nex, int init_seed)
{
real temp, pres;
int i, j, k;
struct gmx_repl_ex *re;
gmx_bool bTemp;
gmx_bool bLambda = FALSE;
fprintf(fplog, "\nInitializing Replica Exchange\n");
if (ms == NULL || ms->nsim == 1)
{
gmx_fatal(FARGS, "Nothing to exchange with only one replica, maybe you forgot to set the -multi option of mdrun?");
}
if (!EI_DYNAMICS(ir->eI))
{
gmx_fatal(FARGS, "Replica exchange is only supported by dynamical simulations");
/* Note that PAR(cr) is defined by cr->nnodes > 1, which is
* distinct from MULTISIM(cr). A multi-simulation only runs
* with real MPI parallelism, but this does not imply PAR(cr)
* is true!
*
* Since we are using a dynamical integrator, the only
* decomposition is DD, so PAR(cr) and DOMAINDECOMP(cr) are
* synonymous. The only way for cr->nnodes > 1 to be true is
* if we are using DD. */
}
snew(re, 1);
re->repl = ms->sim;
re->nrepl = ms->nsim;
snew(re->q, ereENDSINGLE);
fprintf(fplog, "Repl There are %d replicas:\n", re->nrepl);
check_multi_int(fplog, ms, state->natoms, "the number of atoms", FALSE);
check_multi_int(fplog, ms, ir->eI, "the integrator", FALSE);
check_multi_int64(fplog, ms, ir->init_step+ir->nsteps, "init_step+nsteps", FALSE);
check_multi_int64(fplog, ms, (ir->init_step+nst-1)/nst,
"first exchange step: init_step/-replex", FALSE);
check_multi_int(fplog, ms, ir->etc, "the temperature coupling", FALSE);
check_multi_int(fplog, ms, ir->opts.ngtc,
"the number of temperature coupling groups", FALSE);
check_multi_int(fplog, ms, ir->epc, "the pressure coupling", FALSE);
check_multi_int(fplog, ms, ir->efep, "free energy", FALSE);
check_multi_int(fplog, ms, ir->fepvals->n_lambda, "number of lambda states", FALSE);
re->temp = ir->opts.ref_t[0];
for (i = 1; (i < ir->opts.ngtc); i++)
{
if (ir->opts.ref_t[i] != re->temp)
{
fprintf(fplog, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
fprintf(stderr, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
}
}
re->type = -1;
bTemp = repl_quantity(ms, re, ereTEMP, re->temp);
if (ir->efep != efepNO)
{
bLambda = repl_quantity(ms, re, ereLAMBDA, (real)ir->fepvals->init_fep_state);
}
if (re->type == -1) /* nothing was assigned */
{
gmx_fatal(FARGS, "The properties of the %d systems are all the same, there is nothing to exchange", re->nrepl);
}
if (bLambda && bTemp)
{
re->type = ereTL;
}
if (bTemp)
{
please_cite(fplog, "Sugita1999a");
if (ir->epc != epcNO)
{
re->bNPT = TRUE;
fprintf(fplog, "Repl Using Constant Pressure REMD.\n");
please_cite(fplog, "Okabe2001a");
}
if (ir->etc == etcBERENDSEN)
{
gmx_fatal(FARGS, "REMD with the %s thermostat does not produce correct potential energy distributions, consider using the %s thermostat instead",
ETCOUPLTYPE(ir->etc), ETCOUPLTYPE(etcVRESCALE));
}
}
if (bLambda)
{
if (ir->fepvals->delta_lambda != 0) /* check this? */
{
gmx_fatal(FARGS, "delta_lambda is not zero");
}
}
if (re->bNPT)
{
snew(re->pres, re->nrepl);
if (ir->epct == epctSURFACETENSION)
{
pres = ir->ref_p[ZZ][ZZ];
}
else
{
pres = 0;
j = 0;
for (i = 0; i < DIM; i++)
{
if (ir->compress[i][i] != 0)
{
pres += ir->ref_p[i][i];
j++;
}
}
pres /= j;
}
re->pres[re->repl] = pres;
gmx_sum_sim(re->nrepl, re->pres, ms);
}
/* Make an index for increasing replica order */
/* only makes sense if one or the other is varying, not both!
if both are varying, we trust the order the person gave. */
snew(re->ind, re->nrepl);
for (i = 0; i < re->nrepl; i++)
{
re->ind[i] = i;
}
if (re->type < ereENDSINGLE)
{
for (i = 0; i < re->nrepl; i++)
{
for (j = i+1; j < re->nrepl; j++)
{
if (re->q[re->type][re->ind[j]] < re->q[re->type][re->ind[i]])
{
k = re->ind[i];
re->ind[i] = re->ind[j];
re->ind[j] = k;
}
else if (re->q[re->type][re->ind[j]] == re->q[re->type][re->ind[i]])
{
gmx_fatal(FARGS, "Two replicas have identical %ss", erename[re->type]);
}
}
}
}
/* keep track of all the swaps, starting with the initial placement. */
snew(re->allswaps, re->nrepl);
for (i = 0; i < re->nrepl; i++)
{
re->allswaps[i] = re->ind[i];
}
switch (re->type)
{
case ereTEMP:
fprintf(fplog, "\nReplica exchange in temperature\n");
for (i = 0; i < re->nrepl; i++)
{
fprintf(fplog, " %5.1f", re->q[re->type][re->ind[i]]);
}
fprintf(fplog, "\n");
break;
case ereLAMBDA:
fprintf(fplog, "\nReplica exchange in lambda\n");
for (i = 0; i < re->nrepl; i++)
{
fprintf(fplog, " %3d", (int)re->q[re->type][re->ind[i]]);
}
fprintf(fplog, "\n");
break;
case ereTL:
fprintf(fplog, "\nReplica exchange in temperature and lambda state\n");
for (i = 0; i < re->nrepl; i++)
{
fprintf(fplog, " %5.1f", re->q[ereTEMP][re->ind[i]]);
}
fprintf(fplog, "\n");
for (i = 0; i < re->nrepl; i++)
{
fprintf(fplog, " %5d", (int)re->q[ereLAMBDA][re->ind[i]]);
}
fprintf(fplog, "\n");
break;
default:
gmx_incons("Unknown replica exchange quantity");
}
if (re->bNPT)
{
fprintf(fplog, "\nRepl p");
for (i = 0; i < re->nrepl; i++)
{
fprintf(fplog, " %5.2f", re->pres[re->ind[i]]);
}
for (i = 0; i < re->nrepl; i++)
{
if ((i > 0) && (re->pres[re->ind[i]] < re->pres[re->ind[i-1]]))
{
fprintf(fplog, "\nWARNING: The reference pressures decrease with increasing temperatures\n\n");
fprintf(stderr, "\nWARNING: The reference pressures decrease with increasing temperatures\n\n");
}
}
}
re->nst = nst;
if (init_seed == -1)
{
if (MASTERSIM(ms))
{
re->seed = (int)gmx_rng_make_seed();
}
else
{
re->seed = 0;
}
gmx_sumi_sim(1, &(re->seed), ms);
}
else
{
re->seed = init_seed;
}
fprintf(fplog, "\nReplica exchange interval: %d\n", re->nst);
fprintf(fplog, "\nReplica random seed: %d\n", re->seed);
re->rng = gmx_rng_init(re->seed);
re->nattempt[0] = 0;
re->nattempt[1] = 0;
snew(re->prob_sum, re->nrepl);
snew(re->nexchange, re->nrepl);
snew(re->nmoves, re->nrepl);
for (i = 0; i < re->nrepl; i++)
{
snew(re->nmoves[i], re->nrepl);
}
fprintf(fplog, "Replica exchange information below: x=exchange, pr=probability\n");
/* generate space for the helper functions so we don't have to snew each time */
snew(re->destinations, re->nrepl);
snew(re->incycle, re->nrepl);
snew(re->tmpswap, re->nrepl);
snew(re->cyclic, re->nrepl);
snew(re->order, re->nrepl);
for (i = 0; i < re->nrepl; i++)
{
snew(re->cyclic[i], re->nrepl);
snew(re->order[i], re->nrepl);
}
/* allocate space for the functions storing the data for the replicas */
/* not all of these arrays needed in all cases, but they don't take
up much space, since the max size is nrepl**2 */
snew(re->prob, re->nrepl);
snew(re->bEx, re->nrepl);
snew(re->beta, re->nrepl);
snew(re->Vol, re->nrepl);
snew(re->Epot, re->nrepl);
snew(re->de, re->nrepl);
for (i = 0; i < re->nrepl; i++)
{
snew(re->de[i], re->nrepl);
}
re->nex = nex;
return re;
}
gmx_lincsdata_t init_lincs(FILE *fplog,gmx_mtop_t *mtop,
int nflexcon_global,t_blocka *at2con,
gmx_bool bPLINCS,int nIter,int nProjOrder)
{
struct gmx_lincsdata *li;
int mb;
gmx_moltype_t *molt;
if (fplog)
{
fprintf(fplog,"\nInitializing%s LINear Constraint Solver\n",
bPLINCS ? " Parallel" : "");
}
snew(li,1);
li->ncg =
gmx_mtop_ftype_count(mtop,F_CONSTR) +
gmx_mtop_ftype_count(mtop,F_CONSTRNC);
li->ncg_flex = nflexcon_global;
li->ncg_triangle = 0;
for(mb=0; mb<mtop->nmolblock; mb++)
{
molt = &mtop->moltype[mtop->molblock[mb].type];
li->ncg_triangle +=
mtop->molblock[mb].nmol*
count_triangle_constraints(molt->ilist,
&at2con[mtop->molblock[mb].type]);
}
li->nIter = nIter;
li->nOrder = nProjOrder;
if (bPLINCS || li->ncg_triangle > 0)
{
please_cite(fplog,"Hess2008a");
}
else
{
please_cite(fplog,"Hess97a");
}
if (fplog)
{
fprintf(fplog,"The number of constraints is %d\n",li->ncg);
if (bPLINCS)
{
fprintf(fplog,"There are inter charge-group constraints,\n"
"will communicate selected coordinates each lincs iteration\n");
}
if (li->ncg_triangle > 0)
{
fprintf(fplog,
"%d constraints are involved in constraint triangles,\n"
"will apply an additional matrix expansion of order %d for couplings\n"
"between constraints inside triangles\n",
li->ncg_triangle,li->nOrder);
}
}
return li;
}
int gmx_pme_error(int argc,char *argv[])
{
const char *desc[] = {
"[TT]g_pme_error[tt] estimates the error of the electrostatic forces",
"if using the sPME algorithm. The flag [TT]-tune[tt] will determine",
"the splitting parameter such that the error is equally",
"distributed over the real and reciprocal space part.",
"The part of the error that stems from self interaction of the particles "
"is computationally demanding. However, a good a approximation is to",
"just use a fraction of the particles for this term which can be",
"indicated by the flag [TT]-self[tt].[PAR]",
};
real fs=0.0; /* 0 indicates: not set by the user */
real user_beta=-1.0;
real fracself=1.0;
t_inputinfo info;
t_state state; /* The state from the tpr input file */
gmx_mtop_t mtop; /* The topology from the tpr input file */
t_inputrec *ir=NULL; /* The inputrec from the tpr file */
FILE *fp=NULL;
t_commrec *cr;
unsigned long PCA_Flags;
gmx_bool bTUNE=FALSE;
gmx_bool bVerbose=FALSE;
int seed=0;
static t_filenm fnm[] = {
{ efTPX, "-s", NULL, ffREAD },
{ efOUT, "-o", "error", ffWRITE },
{ efTPX, "-so", "tuned", ffOPTWR }
};
output_env_t oenv=NULL;
t_pargs pa[] = {
{ "-beta", FALSE, etREAL, {&user_beta},
"If positive, overwrite ewald_beta from [TT].tpr[tt] file with this value" },
{ "-tune", FALSE, etBOOL, {&bTUNE},
"Tune the splitting parameter such that the error is equally distributed between real and reciprocal space" },
{ "-self", FALSE, etREAL, {&fracself},
"If between 0.0 and 1.0, determine self interaction error from just this fraction of the charged particles" },
{ "-seed", FALSE, etINT, {&seed},
"Random number seed used for Monte Carlo algorithm when [TT]-self[tt] is set to a value between 0.0 and 1.0" },
{ "-v", FALSE, etBOOL, {&bVerbose},
"Be loud and noisy" }
};
#define NFILE asize(fnm)
cr = init_par(&argc,&argv);
#ifdef GMX_LIB_MPI
MPI_Barrier(MPI_COMM_WORLD);
#endif
if (MASTER(cr))
CopyRight(stderr,argv[0]);
PCA_Flags = PCA_NOEXIT_ON_ARGS;
PCA_Flags |= (MASTER(cr) ? 0 : PCA_QUIET);
parse_common_args(&argc,argv,PCA_Flags,
NFILE,fnm,asize(pa),pa,asize(desc),desc,
0,NULL,&oenv);
if (!bTUNE)
bTUNE = opt2bSet("-so",NFILE,fnm);
info.n_entries = 1;
/* Allocate memory for the inputinfo struct: */
create_info(&info);
info.fourier_sp[0] = fs;
/* Read in the tpr file and open logfile for reading */
if (MASTER(cr))
{
snew(ir,1);
read_tpr_file(opt2fn("-s",NFILE,fnm), &info, &state, &mtop, ir, user_beta,fracself);
fp=fopen(opt2fn("-o",NFILE,fnm),"w");
}
/* Check consistency if the user provided fourierspacing */
if (fs > 0 && MASTER(cr))
{
/* Recalculate the grid dimensions using fourierspacing from user input */
info.nkx[0] = 0;
info.nky[0] = 0;
info.nkz[0] = 0;
calc_grid(stdout,state.box,info.fourier_sp[0],&(info.nkx[0]),&(info.nky[0]),&(info.nkz[0]));
if ( (ir->nkx != info.nkx[0]) || (ir->nky != info.nky[0]) || (ir->nkz != info.nkz[0]) )
gmx_fatal(FARGS, "Wrong fourierspacing %f nm, input file grid = %d x %d x %d, computed grid = %d x %d x %d",
fs,ir->nkx,ir->nky,ir->nkz,info.nkx[0],info.nky[0],info.nkz[0]);
}
/* Estimate (S)PME force error */
/* Determine the volume of the simulation box */
if (MASTER(cr))
{
info.volume = det(state.box);
calc_recipbox(state.box,info.recipbox);
info.natoms = mtop.natoms;
info.bTUNE = bTUNE;
}
if (PAR(cr))
bcast_info(&info, cr);
/* Get an error estimate of the input tpr file and do some tuning if requested */
estimate_PME_error(&info, &state, &mtop, fp, bVerbose, seed, cr);
if (MASTER(cr))
{
/* Write out optimized tpr file if requested */
if ( opt2bSet("-so",NFILE,fnm) || bTUNE )
{
ir->ewald_rtol=info.ewald_rtol[0];
write_tpx_state(opt2fn("-so",NFILE,fnm),ir,&state,&mtop);
}
please_cite(fp,"Wang2010");
fclose(fp);
}
if (gmx_parallel_env_initialized())
{
gmx_finalize();
}
return 0;
}
void init_orires(FILE *fplog,const gmx_mtop_t *mtop,
rvec xref[],
const t_inputrec *ir,
const gmx_multisim_t *ms,t_oriresdata *od,
t_state *state)
{
int i,j,d,ex,nmol,nr,*nr_ex;
double mtot;
rvec com;
gmx_mtop_ilistloop_t iloop;
t_ilist *il;
gmx_mtop_atomloop_all_t aloop;
t_atom *atom;
od->fc = ir->orires_fc;
od->nex = 0;
od->S = NULL;
od->nr = gmx_mtop_ftype_count(mtop,F_ORIRES);
if (od->nr == 0)
{
return;
}
nr_ex = NULL;
iloop = gmx_mtop_ilistloop_init(mtop);
while (gmx_mtop_ilistloop_next(iloop,&il,&nmol))
{
for(i=0; i<il[F_ORIRES].nr; i+=3)
{
ex = mtop->ffparams.iparams[il[F_ORIRES].iatoms[i]].orires.ex;
if (ex >= od->nex)
{
srenew(nr_ex,ex+1);
for(j=od->nex; j<ex+1; j++)
{
nr_ex[j] = 0;
}
od->nex = ex+1;
}
nr_ex[ex]++;
}
}
snew(od->S,od->nex);
/* When not doing time averaging, the instaneous and time averaged data
* are indentical and the pointers can point to the same memory.
*/
snew(od->Dinsl,od->nr);
if (ms)
{
snew(od->Dins,od->nr);
}
else
{
od->Dins = od->Dinsl;
}
if (ir->orires_tau == 0)
{
od->Dtav = od->Dins;
od->edt = 0.0;
od->edt1 = 1.0;
}
else
{
snew(od->Dtav,od->nr);
od->edt = exp(-ir->delta_t/ir->orires_tau);
od->edt1 = 1.0 - od->edt;
/* Extend the state with the orires history */
state->flags |= (1<<estORIRE_INITF);
state->hist.orire_initf = 1;
state->flags |= (1<<estORIRE_DTAV);
state->hist.norire_Dtav = od->nr*5;
snew(state->hist.orire_Dtav,state->hist.norire_Dtav);
}
snew(od->oinsl,od->nr);
if (ms)
{
snew(od->oins,od->nr);
}
else
{
od->oins = od->oinsl;
}
if (ir->orires_tau == 0) {
od->otav = od->oins;
}
else
{
snew(od->otav,od->nr);
}
snew(od->tmp,od->nex);
snew(od->TMP,od->nex);
for(ex=0; ex<od->nex; ex++)
{
snew(od->TMP[ex],5);
for(i=0; i<5; i++)
{
snew(od->TMP[ex][i],5);
}
}
od->nref = 0;
for(i=0; i<mtop->natoms; i++)
{
if (ggrpnr(&mtop->groups,egcORFIT,i) == 0)
{
od->nref++;
}
}
snew(od->mref,od->nref);
snew(od->xref,od->nref);
snew(od->xtmp,od->nref);
snew(od->eig,od->nex*12);
/* Determine the reference structure on the master node.
* Copy it to the other nodes after checking multi compatibility,
* so we are sure the subsystems match before copying.
*/
clear_rvec(com);
mtot = 0.0;
j = 0;
aloop = gmx_mtop_atomloop_all_init(mtop);
while(gmx_mtop_atomloop_all_next(aloop,&i,&atom))
{
if (mtop->groups.grpnr[egcORFIT] == NULL ||
mtop->groups.grpnr[egcORFIT][i] == 0)
{
/* Not correct for free-energy with changing masses */
od->mref[j] = atom->m;
if (ms==NULL || MASTERSIM(ms))
{
copy_rvec(xref[i],od->xref[j]);
for(d=0; d<DIM; d++)
{
com[d] += od->mref[j]*xref[i][d];
}
}
mtot += od->mref[j];
j++;
}
}
svmul(1.0/mtot,com,com);
if (ms==NULL || MASTERSIM(ms))
{
for(j=0; j<od->nref; j++)
{
rvec_dec(od->xref[j],com);
}
}
fprintf(fplog,"Found %d orientation experiments\n",od->nex);
for(i=0; i<od->nex; i++)
{
fprintf(fplog," experiment %d has %d restraints\n",i+1,nr_ex[i]);
}
sfree(nr_ex);
fprintf(fplog," the fit group consists of %d atoms and has total mass %g\n",
od->nref,mtot);
if (ms)
{
fprintf(fplog," the orientation restraints are ensemble averaged over %d systems\n",ms->nsim);
check_multi_int(fplog,ms,od->nr,
"the number of orientation restraints");
check_multi_int(fplog,ms,od->nref,
"the number of fit atoms for orientation restraining");
check_multi_int(fplog,ms,ir->nsteps,"nsteps");
/* Copy the reference coordinates from the master to the other nodes */
gmx_sum_sim(DIM*od->nref,od->xref[0],ms);
}
please_cite(fplog,"Hess2003");
}
int main(int argc,char *argv[])
{
const char *desc[] = {
#ifdef GMX_OPENMM
"This is an experimental release of GROMACS for accelerated",
"Molecular Dynamics simulations on GPU processors. Support is provided",
"by the OpenMM library (https://simtk.org/home/openmm).[PAR]",
"*Warning*[BR]",
"This release is targeted at developers and advanced users and",
"care should be taken before production use. The following should be",
"noted before using the program:[PAR]",
" * The current release runs only on modern nVidia GPU hardware with CUDA support.",
"Make sure that the necessary CUDA drivers and libraries for your operating system",
"are already installed. The CUDA SDK also should be installed in order to compile",
"the program from source (http://www.nvidia.com/object/cuda_home.html).[PAR]",
" * Multiple GPU cards are not supported.[PAR]",
" * Only a small subset of the GROMACS features and options are supported on the GPUs.",
"See below for a detailed list.[PAR]",
" * Consumer level GPU cards are known to often have problems with faulty memory.",
"It is recommended that a full memory check of the cards is done at least once",
"(for example, using the memtest=full option).",
"A partial memory check (for example, memtest=15) before and",
"after the simulation run would help spot",
"problems resulting from processor overheating.[PAR]",
" * The maximum size of the simulated systems depends on the available",
"GPU memory,for example, a GTX280 with 1GB memory has been tested with systems",
"of up to about 100,000 atoms.[PAR]",
" * In order to take a full advantage of the GPU platform features, many algorithms",
"have been implemented in a very different way than they are on the CPUs.",
"Therefore numercal correspondence between properties of the state of",
"simulated systems should not be expected. Moreover, the values will likely vary",
"when simulations are done on different GPU hardware.[PAR]",
" * Frequent retrieval of system state information such as",
"trajectory coordinates and energies can greatly influence the performance",
"of the program due to slow CPU<->GPU memory transfer speed.[PAR]",
" * MD algorithms are complex, and although the Gromacs code is highly tuned for them,",
"they often do not translate very well onto the streaming architetures.",
"Realistic expectations about the achievable speed-up from test with GTX280:",
"For small protein systems in implicit solvent using all-vs-all kernels the acceleration",
"can be as high as 20 times, but in most other setups involving cutoffs and PME the",
"acceleration is usually only ~4 times relative to a 3GHz CPU.[PAR]",
"Supported features:[PAR]",
" * Integrators: md/md-vv/md-vv-avek, sd/sd1 and bd.\n",
" * Long-range interactions (option coulombtype): Reaction-Field, Ewald, PME, and cut-off (for Implicit Solvent only)\n",
" * Temperature control: Supported only with the md/md-vv/md-vv-avek, sd/sd1 and bd integrators.\n",
" * Pressure control: Supported.\n",
" * Implicit solvent: Supported.\n",
"A detailed description can be found on the GROMACS website:\n",
"http://www.gromacs.org/gpu[PAR]",
/* From the original mdrun documentaion */
"The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
"and distributes the topology over nodes if needed.",
"[TT]mdrun[tt] produces at least four output files.",
"A single log file ([TT]-g[tt]) is written, unless the option",
"[TT]-seppot[tt] is used, in which case each node writes a log file.",
"The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
"optionally forces.",
"The structure file ([TT]-c[tt]) contains the coordinates and",
"velocities of the last step.",
"The energy file ([TT]-e[tt]) contains energies, the temperature,",
"pressure, etc, a lot of these things are also printed in the log file.",
"Optionally coordinates can be written to a compressed trajectory file",
"([TT]-x[tt]).[PAR]",
/* openmm specific information */
"Usage with OpenMM:[BR]",
"[TT]mdrun -device \"OpenMM:platform=Cuda,memtest=15,deviceid=0,force-device=no\"[tt][PAR]",
"Options:[PAR]",
" [TT]platform[tt] = Cuda\t\t:\tThe only available value. OpenCL support will be available in future.\n",
" [TT]memtest[tt] = 15\t\t:\tRun a partial, random GPU memory test for the given amount of seconds. A full test",
"(recommended!) can be run with \"memtest=full\". Memory testing can be disabled with \"memtest=off\".\n",
" [TT]deviceid[tt] = 0\t\t:\tSpecify the target device when multiple cards are present.",
"Only one card can be used at any given time though.\n",
" [TT]force-device[tt] = no\t\t:\tIf set to \"yes\" [TT]mdrun[tt] will be forced to execute on",
"hardware that is not officially supported. GPU acceleration can also be achieved on older",
"but Cuda capable cards, although the simulation might be too slow, and the memory limits too strict.",
#else
"The [TT]mdrun[tt] program is the main computational chemistry engine",
"within GROMACS. Obviously, it performs Molecular Dynamics simulations,",
"but it can also perform Stochastic Dynamics, Energy Minimization,",
"test particle insertion or (re)calculation of energies.",
"Normal mode analysis is another option. In this case [TT]mdrun[tt]",
"builds a Hessian matrix from single conformation.",
"For usual Normal Modes-like calculations, make sure that",
"the structure provided is properly energy-minimized.",
"The generated matrix can be diagonalized by [TT]g_nmeig[tt].[PAR]",
"The [TT]mdrun[tt] program reads the run input file ([TT]-s[tt])",
"and distributes the topology over nodes if needed.",
"[TT]mdrun[tt] produces at least four output files.",
"A single log file ([TT]-g[tt]) is written, unless the option",
"[TT]-seppot[tt] is used, in which case each node writes a log file.",
"The trajectory file ([TT]-o[tt]), contains coordinates, velocities and",
"optionally forces.",
"The structure file ([TT]-c[tt]) contains the coordinates and",
"velocities of the last step.",
"The energy file ([TT]-e[tt]) contains energies, the temperature,",
"pressure, etc, a lot of these things are also printed in the log file.",
"Optionally coordinates can be written to a compressed trajectory file",
"([TT]-x[tt]).[PAR]",
"The option [TT]-dhdl[tt] is only used when free energy calculation is",
"turned on.[PAR]",
"When [TT]mdrun[tt] is started using MPI with more than 1 node, parallelization",
"is used. By default domain decomposition is used, unless the [TT]-pd[tt]",
"option is set, which selects particle decomposition.[PAR]",
"With domain decomposition, the spatial decomposition can be set",
"with option [TT]-dd[tt]. By default [TT]mdrun[tt] selects a good decomposition.",
"The user only needs to change this when the system is very inhomogeneous.",
"Dynamic load balancing is set with the option [TT]-dlb[tt],",
"which can give a significant performance improvement,",
"especially for inhomogeneous systems. The only disadvantage of",
"dynamic load balancing is that runs are no longer binary reproducible,",
"but in most cases this is not important.",
"By default the dynamic load balancing is automatically turned on",
"when the measured performance loss due to load imbalance is 5% or more.",
"At low parallelization these are the only important options",
"for domain decomposition.",
"At high parallelization the options in the next two sections",
"could be important for increasing the performace.",
"[PAR]",
"When PME is used with domain decomposition, separate nodes can",
"be assigned to do only the PME mesh calculation;",
"this is computationally more efficient starting at about 12 nodes.",
"The number of PME nodes is set with option [TT]-npme[tt],",
"this can not be more than half of the nodes.",
"By default [TT]mdrun[tt] makes a guess for the number of PME",
"nodes when the number of nodes is larger than 11 or performance wise",
"not compatible with the PME grid x dimension.",
"But the user should optimize npme. Performance statistics on this issue",
"are written at the end of the log file.",
"For good load balancing at high parallelization, the PME grid x and y",
"dimensions should be divisible by the number of PME nodes",
"(the simulation will run correctly also when this is not the case).",
"[PAR]",
"This section lists all options that affect the domain decomposition.",
"[PAR]",
"Option [TT]-rdd[tt] can be used to set the required maximum distance",
"for inter charge-group bonded interactions.",
"Communication for two-body bonded interactions below the non-bonded",
"cut-off distance always comes for free with the non-bonded communication.",
"Atoms beyond the non-bonded cut-off are only communicated when they have",
"missing bonded interactions; this means that the extra cost is minor",
"and nearly indepedent of the value of [TT]-rdd[tt].",
"With dynamic load balancing option [TT]-rdd[tt] also sets",
"the lower limit for the domain decomposition cell sizes.",
"By default [TT]-rdd[tt] is determined by [TT]mdrun[tt] based on",
"the initial coordinates. The chosen value will be a balance",
"between interaction range and communication cost.",
"[PAR]",
"When inter charge-group bonded interactions are beyond",
"the bonded cut-off distance, [TT]mdrun[tt] terminates with an error message.",
"For pair interactions and tabulated bonds",
"that do not generate exclusions, this check can be turned off",
"with the option [TT]-noddcheck[tt].",
"[PAR]",
"When constraints are present, option [TT]-rcon[tt] influences",
"the cell size limit as well.",
"Atoms connected by NC constraints, where NC is the LINCS order plus 1,",
"should not be beyond the smallest cell size. A error message is",
"generated when this happens and the user should change the decomposition",
"or decrease the LINCS order and increase the number of LINCS iterations.",
"By default [TT]mdrun[tt] estimates the minimum cell size required for P-LINCS",
"in a conservative fashion. For high parallelization it can be useful",
"to set the distance required for P-LINCS with the option [TT]-rcon[tt].",
"[PAR]",
"The [TT]-dds[tt] option sets the minimum allowed x, y and/or z scaling",
"of the cells with dynamic load balancing. [TT]mdrun[tt] will ensure that",
"the cells can scale down by at least this factor. This option is used",
"for the automated spatial decomposition (when not using [TT]-dd[tt])",
"as well as for determining the number of grid pulses, which in turn",
"sets the minimum allowed cell size. Under certain circumstances",
"the value of [TT]-dds[tt] might need to be adjusted to account for",
"high or low spatial inhomogeneity of the system.",
"[PAR]",
"The option [TT]-gcom[tt] can be used to only do global communication",
"every n steps.",
"This can improve performance for highly parallel simulations",
"where this global communication step becomes the bottleneck.",
"For a global thermostat and/or barostat the temperature",
"and/or pressure will also only be updated every [TT]-gcom[tt] steps.",
"By default it is set to the minimum of nstcalcenergy and nstlist.[PAR]",
"With [TT]-rerun[tt] an input trajectory can be given for which ",
"forces and energies will be (re)calculated. Neighbor searching will be",
"performed for every frame, unless [TT]nstlist[tt] is zero",
"(see the [TT].mdp[tt] file).[PAR]",
"ED (essential dynamics) sampling is switched on by using the [TT]-ei[tt]",
"flag followed by an [TT].edi[tt] file.",
"The [TT].edi[tt] file can be produced using options in the essdyn",
"menu of the WHAT IF program. [TT]mdrun[tt] produces a [TT].edo[tt] file that",
"contains projections of positions, velocities and forces onto selected",
"eigenvectors.[PAR]",
"When user-defined potential functions have been selected in the",
"[TT].mdp[tt] file the [TT]-table[tt] option is used to pass [TT]mdrun[tt]",
"a formatted table with potential functions. The file is read from",
"either the current directory or from the [TT]GMXLIB[tt] directory.",
"A number of pre-formatted tables are presented in the [TT]GMXLIB[tt] dir,",
"for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard-Jones potentials with",
"normal Coulomb.",
"When pair interactions are present, a separate table for pair interaction",
"functions is read using the [TT]-tablep[tt] option.[PAR]",
"When tabulated bonded functions are present in the topology,",
"interaction functions are read using the [TT]-tableb[tt] option.",
"For each different tabulated interaction type the table file name is",
"modified in a different way: before the file extension an underscore is",
"appended, then a 'b' for bonds, an 'a' for angles or a 'd' for dihedrals",
"and finally the table number of the interaction type.[PAR]",
"The options [TT]-px[tt] and [TT]-pf[tt] are used for writing pull COM",
"coordinates and forces when pulling is selected",
"in the [TT].mdp[tt] file.[PAR]",
"With [TT]-multi[tt] or [TT]-multidir[tt], multiple systems can be ",
"simulated in parallel.",
"As many input files/directories are required as the number of systems. ",
"The [TT]-multidir[tt] option takes a list of directories (one for each ",
"system) and runs in each of them, using the input/output file names, ",
"such as specified by e.g. the [TT]-s[tt] option, relative to these ",
"directories.",
"With [TT]-multi[tt], the system number is appended to the run input ",
"and each output filename, for instance [TT]topol.tpr[tt] becomes",
"[TT]topol0.tpr[tt], [TT]topol1.tpr[tt] etc.",
"The number of nodes per system is the total number of nodes",
"divided by the number of systems.",
"One use of this option is for NMR refinement: when distance",
"or orientation restraints are present these can be ensemble averaged",
"over all the systems.[PAR]",
"With [TT]-replex[tt] replica exchange is attempted every given number",
"of steps. The number of replicas is set with the [TT]-multi[tt] or ",
"[TT]-multidir[tt] option, described above.",
"All run input files should use a different coupling temperature,",
"the order of the files is not important. The random seed is set with",
"[TT]-reseed[tt]. The velocities are scaled and neighbor searching",
"is performed after every exchange.[PAR]",
"Finally some experimental algorithms can be tested when the",
"appropriate options have been given. Currently under",
"investigation are: polarizability and X-ray bombardments.",
"[PAR]",
"The option [TT]-pforce[tt] is useful when you suspect a simulation",
"crashes due to too large forces. With this option coordinates and",
"forces of atoms with a force larger than a certain value will",
"be printed to stderr.",
"[PAR]",
"Checkpoints containing the complete state of the system are written",
"at regular intervals (option [TT]-cpt[tt]) to the file [TT]-cpo[tt],",
"unless option [TT]-cpt[tt] is set to -1.",
"The previous checkpoint is backed up to [TT]state_prev.cpt[tt] to",
"make sure that a recent state of the system is always available,",
"even when the simulation is terminated while writing a checkpoint.",
"With [TT]-cpnum[tt] all checkpoint files are kept and appended",
"with the step number.",
"A simulation can be continued by reading the full state from file",
"with option [TT]-cpi[tt]. This option is intelligent in the way that",
"if no checkpoint file is found, Gromacs just assumes a normal run and",
"starts from the first step of the [TT].tpr[tt] file. By default the output",
"will be appending to the existing output files. The checkpoint file",
"contains checksums of all output files, such that you will never",
"loose data when some output files are modified, corrupt or removed.",
"There are three scenarios with [TT]-cpi[tt]:[PAR]",
"[TT]*[tt] no files with matching names are present: new output files are written[PAR]",
"[TT]*[tt] all files are present with names and checksums matching those stored",
"in the checkpoint file: files are appended[PAR]",
"[TT]*[tt] otherwise no files are modified and a fatal error is generated[PAR]",
"With [TT]-noappend[tt] new output files are opened and the simulation",
"part number is added to all output file names.",
"Note that in all cases the checkpoint file itself is not renamed",
"and will be overwritten, unless its name does not match",
"the [TT]-cpo[tt] option.",
"[PAR]",
"With checkpointing the output is appended to previously written",
"output files, unless [TT]-noappend[tt] is used or none of the previous",
"output files are present (except for the checkpoint file).",
"The integrity of the files to be appended is verified using checksums",
"which are stored in the checkpoint file. This ensures that output can",
"not be mixed up or corrupted due to file appending. When only some",
"of the previous output files are present, a fatal error is generated",
"and no old output files are modified and no new output files are opened.",
"The result with appending will be the same as from a single run.",
"The contents will be binary identical, unless you use a different number",
"of nodes or dynamic load balancing or the FFT library uses optimizations",
"through timing.",
"[PAR]",
"With option [TT]-maxh[tt] a simulation is terminated and a checkpoint",
"file is written at the first neighbor search step where the run time",
"exceeds [TT]-maxh[tt]*0.99 hours.",
"[PAR]",
"When [TT]mdrun[tt] receives a TERM signal, it will set nsteps to the current",
"step plus one. When [TT]mdrun[tt] receives an INT signal (e.g. when ctrl+C is",
"pressed), it will stop after the next neighbor search step ",
"(with nstlist=0 at the next step).",
"In both cases all the usual output will be written to file.",
"When running with MPI, a signal to one of the [TT]mdrun[tt] processes",
"is sufficient, this signal should not be sent to mpirun or",
"the [TT]mdrun[tt] process that is the parent of the others.",
"[PAR]",
"When [TT]mdrun[tt] is started with MPI, it does not run niced by default."
#endif
};
t_commrec *cr;
t_filenm fnm[] = {
{ efTPX, NULL, NULL, ffREAD },
{ efTRN, "-o", NULL, ffWRITE },
{ efXTC, "-x", NULL, ffOPTWR },
{ efCPT, "-cpi", NULL, ffOPTRD },
{ efCPT, "-cpo", NULL, ffOPTWR },
{ efSTO, "-c", "confout", ffWRITE },
{ efEDR, "-e", "ener", ffWRITE },
{ efLOG, "-g", "md", ffWRITE },
{ efXVG, "-dhdl", "dhdl", ffOPTWR },
{ efXVG, "-field", "field", ffOPTWR },
{ efXVG, "-table", "table", ffOPTRD },
{ efXVG, "-tabletf", "tabletf", ffOPTRD },
{ efXVG, "-tablep", "tablep", ffOPTRD },
{ efXVG, "-tableb", "table", ffOPTRD },
{ efTRX, "-rerun", "rerun", ffOPTRD },
{ efXVG, "-tpi", "tpi", ffOPTWR },
{ efXVG, "-tpid", "tpidist", ffOPTWR },
{ efEDI, "-ei", "sam", ffOPTRD },
{ efEDO, "-eo", "sam", ffOPTWR },
{ efGCT, "-j", "wham", ffOPTRD },
{ efGCT, "-jo", "bam", ffOPTWR },
{ efXVG, "-ffout", "gct", ffOPTWR },
{ efXVG, "-devout", "deviatie", ffOPTWR },
{ efXVG, "-runav", "runaver", ffOPTWR },
{ efXVG, "-px", "pullx", ffOPTWR },
{ efXVG, "-pf", "pullf", ffOPTWR },
{ efXVG, "-ro", "rotation", ffOPTWR },
{ efLOG, "-ra", "rotangles",ffOPTWR },
{ efLOG, "-rs", "rotslabs", ffOPTWR },
{ efLOG, "-rt", "rottorque",ffOPTWR },
{ efMTX, "-mtx", "nm", ffOPTWR },
{ efNDX, "-dn", "dipole", ffOPTWR },
{ efRND, "-multidir",NULL, ffOPTRDMULT},
{ efGMX, "-mmcg", "mmcg", ffOPTRD },
{ efWPO, "-wpot", "wpot", ffOPTRD }
};
#define NFILE asize(fnm)
/* Command line options ! */
gmx_bool bCart = FALSE;
gmx_bool bPPPME = FALSE;
gmx_bool bPartDec = FALSE;
gmx_bool bDDBondCheck = TRUE;
gmx_bool bDDBondComm = TRUE;
gmx_bool bVerbose = FALSE;
gmx_bool bCompact = TRUE;
gmx_bool bSepPot = FALSE;
gmx_bool bRerunVSite = FALSE;
gmx_bool bIonize = FALSE;
gmx_bool bConfout = TRUE;
gmx_bool bReproducible = FALSE;
int npme=-1;
int nmultisim=0;
int nstglobalcomm=-1;
int repl_ex_nst=0;
int repl_ex_seed=-1;
int nstepout=100;
int nthreads=0; /* set to determine # of threads automatically */
int resetstep=-1;
rvec realddxyz={0,0,0};
const char *ddno_opt[ddnoNR+1] =
{ NULL, "interleave", "pp_pme", "cartesian", NULL };
const char *dddlb_opt[] =
{ NULL, "auto", "no", "yes", NULL };
real rdd=0.0,rconstr=0.0,dlb_scale=0.8,pforce=-1;
char *ddcsx=NULL,*ddcsy=NULL,*ddcsz=NULL;
real cpt_period=15.0,max_hours=-1;
gmx_bool bAppendFiles=TRUE;
gmx_bool bKeepAndNumCPT=FALSE;
gmx_bool bResetCountersHalfWay=FALSE;
output_env_t oenv=NULL;
const char *deviceOptions = "";
t_pargs pa[] = {
{ "-pd", FALSE, etBOOL,{&bPartDec},
"Use particle decompostion" },
{ "-dd", FALSE, etRVEC,{&realddxyz},
"Domain decomposition grid, 0 is optimize" },
#ifdef GMX_THREADS
{ "-nt", FALSE, etINT, {&nthreads},
"Number of threads to start (0 is guess)" },
#endif
{ "-npme", FALSE, etINT, {&npme},
"Number of separate nodes to be used for PME, -1 is guess" },
{ "-ddorder", FALSE, etENUM, {ddno_opt},
"DD node order" },
{ "-ddcheck", FALSE, etBOOL, {&bDDBondCheck},
"Check for all bonded interactions with DD" },
{ "-ddbondcomm", FALSE, etBOOL, {&bDDBondComm},
"HIDDENUse special bonded atom communication when [TT]-rdd[tt] > cut-off" },
{ "-rdd", FALSE, etREAL, {&rdd},
"The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates" },
{ "-rcon", FALSE, etREAL, {&rconstr},
"Maximum distance for P-LINCS (nm), 0 is estimate" },
{ "-dlb", FALSE, etENUM, {dddlb_opt},
"Dynamic load balancing (with DD)" },
{ "-dds", FALSE, etREAL, {&dlb_scale},
"Minimum allowed dlb scaling of the DD cell size" },
{ "-ddcsx", FALSE, etSTR, {&ddcsx},
"HIDDENThe DD cell sizes in x" },
{ "-ddcsy", FALSE, etSTR, {&ddcsy},
"HIDDENThe DD cell sizes in y" },
{ "-ddcsz", FALSE, etSTR, {&ddcsz},
"HIDDENThe DD cell sizes in z" },
{ "-gcom", FALSE, etINT,{&nstglobalcomm},
"Global communication frequency" },
{ "-v", FALSE, etBOOL,{&bVerbose},
"Be loud and noisy" },
{ "-compact", FALSE, etBOOL,{&bCompact},
"Write a compact log file" },
{ "-seppot", FALSE, etBOOL, {&bSepPot},
"Write separate V and dVdl terms for each interaction type and node to the log file(s)" },
{ "-pforce", FALSE, etREAL, {&pforce},
"Print all forces larger than this (kJ/mol nm)" },
{ "-reprod", FALSE, etBOOL,{&bReproducible},
"Try to avoid optimizations that affect binary reproducibility" },
{ "-cpt", FALSE, etREAL, {&cpt_period},
"Checkpoint interval (minutes)" },
{ "-cpnum", FALSE, etBOOL, {&bKeepAndNumCPT},
"Keep and number checkpoint files" },
{ "-append", FALSE, etBOOL, {&bAppendFiles},
"Append to previous output files when continuing from checkpoint instead of adding the simulation part number to all file names" },
{ "-maxh", FALSE, etREAL, {&max_hours},
"Terminate after 0.99 times this time (hours)" },
{ "-multi", FALSE, etINT,{&nmultisim},
"Do multiple simulations in parallel" },
{ "-replex", FALSE, etINT, {&repl_ex_nst},
"Attempt replica exchange every # steps" },
{ "-reseed", FALSE, etINT, {&repl_ex_seed},
"Seed for replica exchange, -1 is generate a seed" },
{ "-rerunvsite", FALSE, etBOOL, {&bRerunVSite},
"HIDDENRecalculate virtual site coordinates with [TT]-rerun[tt]" },
{ "-ionize", FALSE, etBOOL,{&bIonize},
"Do a simulation including the effect of an X-Ray bombardment on your system" },
{ "-confout", FALSE, etBOOL, {&bConfout},
"HIDDENWrite the last configuration with [TT]-c[tt] and force checkpointing at the last step" },
{ "-stepout", FALSE, etINT, {&nstepout},
"HIDDENFrequency of writing the remaining runtime" },
{ "-resetstep", FALSE, etINT, {&resetstep},
"HIDDENReset cycle counters after these many time steps" },
{ "-resethway", FALSE, etBOOL, {&bResetCountersHalfWay},
"HIDDENReset the cycle counters after half the number of steps or halfway [TT]-maxh[tt]" }
#ifdef GMX_OPENMM
,
{ "-device", FALSE, etSTR, {&deviceOptions},
"Device option string" }
#endif
};
gmx_edsam_t ed;
unsigned long Flags, PCA_Flags;
ivec ddxyz;
int dd_node_order;
gmx_bool bAddPart;
FILE *fplog,*fptest;
int sim_part,sim_part_fn;
const char *part_suffix=".part";
char suffix[STRLEN];
int rc;
char **multidir=NULL;
cr = init_par(&argc,&argv);
if (MASTER(cr))
CopyRight(stderr, argv[0]);
PCA_Flags = (PCA_KEEP_ARGS | PCA_NOEXIT_ON_ARGS | PCA_CAN_SET_DEFFNM
| (MASTER(cr) ? 0 : PCA_QUIET));
/* Comment this in to do fexist calls only on master
* works not with rerun or tables at the moment
* also comment out the version of init_forcerec in md.c
* with NULL instead of opt2fn
*/
/*
if (!MASTER(cr))
{
PCA_Flags |= PCA_NOT_READ_NODE;
}
*/
parse_common_args(&argc,argv,PCA_Flags, NFILE,fnm,asize(pa),pa,
asize(desc),desc,0,NULL, &oenv);
/* we set these early because they might be used in init_multisystem()
Note that there is the potential for npme>nnodes until the number of
threads is set later on, if there's thread parallelization. That shouldn't
lead to problems. */
dd_node_order = nenum(ddno_opt);
cr->npmenodes = npme;
#ifndef GMX_THREADS
nthreads=1;
#endif
/* now check the -multi and -multidir option */
if (opt2bSet("-multidir", NFILE, fnm))
{
int i;
if (nmultisim > 0)
{
gmx_fatal(FARGS, "mdrun -multi and -multidir options are mutually exclusive.");
}
nmultisim = opt2fns(&multidir, "-multidir", NFILE, fnm);
}
if (repl_ex_nst != 0 && nmultisim < 2)
gmx_fatal(FARGS,"Need at least two replicas for replica exchange (option -multi)");
if (nmultisim > 1) {
#ifndef GMX_THREADS
gmx_bool bParFn = (multidir == NULL);
init_multisystem(cr, nmultisim, multidir, NFILE, fnm, bParFn);
#else
gmx_fatal(FARGS,"mdrun -multi is not supported with the thread library.Please compile GROMACS with MPI support");
#endif
}
bAddPart = !bAppendFiles;
/* Check if there is ANY checkpoint file available */
sim_part = 1;
sim_part_fn = sim_part;
if (opt2bSet("-cpi",NFILE,fnm))
{
if (bSepPot && bAppendFiles)
{
gmx_fatal(FARGS,"Output file appending is not supported with -seppot");
}
bAppendFiles =
read_checkpoint_simulation_part(opt2fn_master("-cpi", NFILE,
fnm,cr),
&sim_part_fn,NULL,cr,
bAppendFiles,NFILE,fnm,
part_suffix,&bAddPart);
if (sim_part_fn==0 && MASTER(cr))
{
fprintf(stdout,"No previous checkpoint file present, assuming this is a new run.\n");
}
else
{
sim_part = sim_part_fn + 1;
}
if (MULTISIM(cr) && MASTER(cr))
{
check_multi_int(stdout,cr->ms,sim_part,"simulation part");
}
}
else
{
bAppendFiles = FALSE;
}
if (!bAppendFiles)
{
sim_part_fn = sim_part;
}
if (bAddPart)
{
/* Rename all output files (except checkpoint files) */
/* create new part name first (zero-filled) */
sprintf(suffix,"%s%04d",part_suffix,sim_part_fn);
add_suffix_to_output_names(fnm,NFILE,suffix);
if (MASTER(cr))
{
fprintf(stdout,"Checkpoint file is from part %d, new output files will be suffixed '%s'.\n",sim_part-1,suffix);
}
}
Flags = opt2bSet("-rerun",NFILE,fnm) ? MD_RERUN : 0;
Flags = Flags | (opt2bSet("-mmcg",NFILE,fnm) ? MD_MMCG : 0);
Flags = Flags | (bSepPot ? MD_SEPPOT : 0);
Flags = Flags | (bIonize ? MD_IONIZE : 0);
Flags = Flags | (bPartDec ? MD_PARTDEC : 0);
Flags = Flags | (bDDBondCheck ? MD_DDBONDCHECK : 0);
Flags = Flags | (bDDBondComm ? MD_DDBONDCOMM : 0);
Flags = Flags | (bConfout ? MD_CONFOUT : 0);
Flags = Flags | (bRerunVSite ? MD_RERUN_VSITE : 0);
Flags = Flags | (bReproducible ? MD_REPRODUCIBLE : 0);
Flags = Flags | (bAppendFiles ? MD_APPENDFILES : 0);
Flags = Flags | (bKeepAndNumCPT ? MD_KEEPANDNUMCPT : 0);
Flags = Flags | (sim_part>1 ? MD_STARTFROMCPT : 0);
Flags = Flags | (bResetCountersHalfWay ? MD_RESETCOUNTERSHALFWAY : 0);
Flags = Flags | (opt2bSet("-wpot",NFILE,fnm) ? MD_WALLPOT : 0);
/* We postpone opening the log file if we are appending, so we can
first truncate the old log file and append to the correct position
there instead. */
if ((MASTER(cr) || bSepPot) && !bAppendFiles)
{
gmx_log_open(ftp2fn(efLOG,NFILE,fnm),cr,!bSepPot,Flags,&fplog);
CopyRight(fplog,argv[0]);
please_cite(fplog,"Hess2008b");
please_cite(fplog,"Spoel2005a");
please_cite(fplog,"Lindahl2001a");
please_cite(fplog,"Berendsen95a");
}
else if (!MASTER(cr) && bSepPot)
{
gmx_log_open(ftp2fn(efLOG,NFILE,fnm),cr,!bSepPot,Flags,&fplog);
}
else
{
fplog = NULL;
}
ddxyz[XX] = (int)(realddxyz[XX] + 0.5);
ddxyz[YY] = (int)(realddxyz[YY] + 0.5);
ddxyz[ZZ] = (int)(realddxyz[ZZ] + 0.5);
rc = mdrunner(nthreads, fplog,cr,NFILE,fnm,oenv,bVerbose,bCompact,
nstglobalcomm, ddxyz,dd_node_order,rdd,rconstr,
dddlb_opt[0],dlb_scale,ddcsx,ddcsy,ddcsz,
nstepout,resetstep,nmultisim,repl_ex_nst,repl_ex_seed,
pforce, cpt_period,max_hours,deviceOptions,Flags);
if (gmx_parallel_env_initialized())
gmx_finalize();
if (MULTIMASTER(cr)) {
thanx(stderr);
}
/* Log file has to be closed in mdrunner if we are appending to it
(fplog not set here) */
if (MASTER(cr) && !bAppendFiles)
{
gmx_log_close(fplog);
}
return rc;
}
int gmx_nmeig(int argc, char *argv[])
{
const char *desc[] = {
"[TT]g_nmeig[tt] 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.[PAR]",
"This program can be optionally used to compute quantum corrections to heat capacity",
"and enthalpy by providing an extra file argument [TT]-qcorr[tt]. See the GROMACS",
"manual, Chapter 1, for details. The result includes subtracting a harmonic",
"degree of freedom at the given temperature.",
"The total correction is printed on the terminal screen.",
"The recommended way of getting the corrections out is:[PAR]",
"[TT]g_nmeig -s topol.tpr -f nm.mtx -first 7 -last 10000 -T 300 -qc [-constr][tt][PAR]",
"The [TT]-constr[tt] option should be used when bond constraints were used during the",
"simulation [BB]for all the covalent bonds[bb]. If this is not the case, ",
"you need to analyze the [TT]quant_corr.xvg[tt] file yourself.[PAR]",
"To make things more flexible, the program can also take virtual sites into account",
"when computing quantum corrections. When selecting [TT]-constr[tt] and",
"[TT]-qc[tt], the [TT]-begin[tt] and [TT]-end[tt] options will be set automatically as well.",
"Again, if you think you know it better, please check the [TT]eigenfreq.xvg[tt]",
"output."
};
static gmx_bool bM = TRUE, bCons = FALSE;
static int begin = 1, end = 50, maxspec = 4000;
static real T = 298.15, width = 1;
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" },
{ "-maxspec", FALSE, etINT, {&maxspec},
"Highest frequency (1/cm) to consider in the spectrum" },
{ "-T", FALSE, etREAL, {&T},
"Temperature for computing quantum heat capacity and enthalpy when using normal mode calculations to correct classical simulations" },
{ "-constr", FALSE, etBOOL, {&bCons},
"If constraints were used in the simulation but not in the normal mode analysis (this is the recommended way of doing it) you will need to set this for computing the quantum corrections." },
{ "-width", FALSE, etREAL, {&width},
"Width (sigma) of the gaussian peaks (1/cm) when generating a spectrum" }
};
FILE *out, *qc, *spec;
int status, trjout;
t_topology top;
gmx_mtop_t mtop;
int ePBC;
rvec *top_x;
matrix box;
real *eigenvalues;
real *eigenvectors;
real rdum, mass_fac, qcvtot, qutot, qcv, qu;
int natoms, ndim, nrow, ncol, count, nharm, nvsite;
char *grpname;
int i, j, k, l, d, gnx;
gmx_bool bSuck;
atom_id *index;
t_tpxheader tpx;
int version, generation;
real value, omega, nu;
real factor_gmx_to_omega2;
real factor_omega_to_wavenumber;
real *spectrum = NULL;
real wfac;
output_env_t oenv;
const char *qcleg[] = {
"Heat Capacity cV (J/mol K)",
"Enthalpy H (kJ/mol)"
};
real * full_hessian = NULL;
gmx_sparsematrix_t * sparse_hessian = NULL;
t_filenm fnm[] = {
{ efMTX, "-f", "hessian", ffREAD },
{ efTPX, NULL, NULL, ffREAD },
{ efXVG, "-of", "eigenfreq", ffWRITE },
{ efXVG, "-ol", "eigenval", ffWRITE },
{ efXVG, "-os", "spectrum", ffOPTWR },
{ efXVG, "-qc", "quant_corr", ffOPTWR },
{ efTRN, "-v", "eigenvec", ffWRITE }
};
#define NFILE asize(fnm)
parse_common_args(&argc, argv, PCA_BE_NICE,
NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
/* Read tpr file for volume and number of harmonic terms */
read_tpxheader(ftp2fn(efTPX, NFILE, fnm), &tpx, TRUE, &version, &generation);
snew(top_x, tpx.natoms);
read_tpx(ftp2fn(efTPX, NFILE, fnm), NULL, box, &natoms,
top_x, NULL, NULL, &mtop);
if (bCons)
{
nharm = get_nharm(&mtop, &nvsite);
}
else
{
nharm = 0;
nvsite = 0;
}
top = gmx_mtop_t_to_t_topology(&mtop);
bM = TRUE;
ndim = DIM*natoms;
if (opt2bSet("-qc", NFILE, fnm))
{
begin = 7+DIM*nvsite;
end = DIM*natoms;
}
if (begin < 1)
{
begin = 1;
}
if (end > ndim)
{
end = ndim;
}
printf("Using begin = %d and end = %d\n", begin, end);
/*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]",
oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
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]);
}
ffclose(out);
if (opt2bSet("-qc", NFILE, fnm))
{
qc = xvgropen(opt2fn("-qc", NFILE, fnm), "Quantum Corrections", "Eigenvector index", "", oenv);
xvgr_legend(qc, asize(qcleg), qcleg, oenv);
qcvtot = qutot = 0;
}
else
{
qc = NULL;
}
printf("Writing eigenfrequencies - negative eigenvalues will be set to zero.\n");
out = xvgropen(opt2fn("-of", NFILE, fnm),
"Eigenfrequencies", "Eigenvector index", "Wavenumber [cm\\S-1\\N]",
oenv);
if (output_env_get_print_xvgr_codes(oenv))
{
if (bM)
{
fprintf(out, "@ subtitle \"mass weighted\"\n");
}
else
{
fprintf(out, "@ subtitle \"not mass weighted\"\n");
}
}
/* Spectrum ? */
spec = NULL;
if (opt2bSet("-os", NFILE, fnm) && (maxspec > 0))
{
snew(spectrum, maxspec);
spec = xvgropen(opt2fn("-os", NFILE, fnm),
"Vibrational spectrum based on harmonic approximation",
"\\f{12}w\\f{4} (cm\\S-1\\N)",
"Intensity [Gromacs units]",
oenv);
for (i = 0; (i < maxspec); i++)
{
spectrum[i] = 0;
}
}
/* 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 = begin; (i <= end); i++)
{
value = eigenvalues[i-begin];
if (value < 0)
{
value = 0;
}
omega = sqrt(value*factor_gmx_to_omega2);
nu = 1e-12*omega/(2*M_PI);
value = omega*factor_omega_to_wavenumber;
fprintf (out, "%6d %15g\n", i, value);
if (NULL != spec)
{
wfac = eigenvalues[i-begin]/(width*sqrt(2*M_PI));
for (j = 0; (j < maxspec); j++)
{
spectrum[j] += wfac*exp(-sqr(j-value)/(2*sqr(width)));
}
}
if (NULL != qc)
{
qcv = cv_corr(nu, T);
qu = u_corr(nu, T);
if (i > end-nharm)
{
qcv += BOLTZ*KILO;
qu += BOLTZ*T;
}
fprintf (qc, "%6d %15g %15g\n", i, qcv, qu);
qcvtot += qcv;
qutot += qu;
}
}
ffclose(out);
if (NULL != spec)
{
for (j = 0; (j < maxspec); j++)
{
fprintf(spec, "%10g %10g\n", 1.0*j, spectrum[j]);
}
ffclose(spec);
}
if (NULL != qc)
{
printf("Quantum corrections for harmonic degrees of freedom\n");
printf("Use appropriate -first and -last options to get reliable results.\n");
printf("There were %d constraints and %d vsites in the simulation\n",
nharm, nvsite);
printf("Total correction to cV = %g J/mol K\n", qcvtot);
printf("Total correction to H = %g kJ/mol\n", qutot);
ffclose(qc);
please_cite(stdout, "Caleman2011b");
}
/* 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;
}
