src/gromacs/gmxana/gmx_velacc.cpp

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  37 #include "gmxpre.h"
  38
  39 #include <cmath>
  40 #include <cstdio>
  41 #include <cstring>
  42
  43 #include "gromacs/commandline/pargs.h"
  44 #include "gromacs/commandline/viewit.h"
  45 #include "gromacs/correlationfunctions/autocorr.h"
  46 #include "gromacs/fft/fft.h"
  47 #include "gromacs/fileio/confio.h"
  48 #include "gromacs/fileio/trx.h"
  49 #include "gromacs/fileio/trxio.h"
  50 #include "gromacs/fileio/xvgr.h"
  51 #include "gromacs/gmxana/gmx_ana.h"
  52 #include "gromacs/gmxana/gstat.h"
  53 #include "gromacs/math/units.h"
  54 #include "gromacs/math/utilities.h"
  55 #include "gromacs/math/vec.h"
  56 #include "gromacs/topology/index.h"
  57 #include "gromacs/topology/topology.h"
  58 #include "gromacs/utility/arraysize.h"
  59 #include "gromacs/utility/fatalerror.h"
  60 #include "gromacs/utility/futil.h"
  61 #include "gromacs/utility/smalloc.h"
  62
  63 static void index_atom2mol(int *n, int *index, t_block *mols)
  64 {
  65     int nat, i, nmol, mol, j;
  66
  67     nat  = *n;
  68     i    = 0;
  69     nmol = 0;
  70     mol  = 0;
  71     while (i < nat)
  72     {
  73         while (index[i] > mols->index[mol])
  74         {
  75             mol++;
  76             if (mol >= mols->nr)
  77             {
  78                 gmx_fatal(FARGS, "Atom index out of range: %d", index[i]+1);
  79             }
  80         }
  81         for (j = mols->index[mol]; j < mols->index[mol+1]; j++)
  82         {
  83             if (i >= nat || index[i] != j)
  84             {
  85                 gmx_fatal(FARGS, "The index group does not consist of whole molecules");
  86             }
  87             i++;
  88         }
  89         index[nmol++] = mol;
  90     }
  91
  92     fprintf(stderr, "\nSplit group of %d atoms into %d molecules\n", nat, nmol);
  93
  94     *n = nmol;
  95 }
  96
  97 static void precalc(t_topology top, real normm[])
  98 {
  99
 100     real mtot;
 101     int  i, j, k, l;
 102
 103     for (i = 0; i < top.mols.nr; i++)
 104     {
 105         k    = top.mols.index[i];
 106         l    = top.mols.index[i+1];
 107         mtot = 0.0;
 108
 109         for (j = k; j < l; j++)
 110         {
 111             mtot += top.atoms.atom[j].m;
 112         }
 113
 114         for (j = k; j < l; j++)
 115         {
 116             normm[j] = top.atoms.atom[j].m/mtot;
 117         }
 118
 119     }
 120
 121 }
 122
 123 static void calc_spectrum(int n, real c[], real dt, const char *fn,
 124                           gmx_output_env_t *oenv, gmx_bool bRecip)
 125 {
 126     FILE     *fp;
 127     gmx_fft_t fft;
 128     int       i, status;
 129     real     *data;
 130     real      nu, omega, recip_fac;
 131
 132     snew(data, n*2);
 133     for (i = 0; (i < n); i++)
 134     {
 135         data[i] = c[i];
 136     }
 137
 138     if ((status = gmx_fft_init_1d_real(&fft, n, GMX_FFT_FLAG_NONE)) != 0)
 139     {
 140         gmx_fatal(FARGS, "Invalid fft return status %d", status);
 141     }
 142     if ((status = gmx_fft_1d_real(fft, GMX_FFT_REAL_TO_COMPLEX, data, data)) != 0)
 143     {
 144         gmx_fatal(FARGS, "Invalid fft return status %d", status);
 145     }
 146     fp = xvgropen(fn, "Vibrational Power Spectrum",
 147                   bRecip ? "\\f{12}w\\f{4} (cm\\S-1\\N)" :
 148                   "\\f{12}n\\f{4} (ps\\S-1\\N)",
 149                   "a.u.", oenv);
 150     /* This is difficult.
 151      * The length of the ACF is dt (as passed to this routine).
 152      * We pass the vacf with N time steps from 0 to dt.
 153      * That means that after FFT we have lowest frequency = 1/dt
 154      * then 1/(2 dt) etc. (this is the X-axis of the data after FFT).
 155      * To convert to 1/cm we need to have to realize that
 156      * E = hbar w = h nu = h c/lambda. We want to have reciprokal cm
 157      * on the x-axis, that is 1/lambda, so we then have
 158      * 1/lambda = nu/c. Since nu has units of 1/ps and c has gromacs units
 159      * of nm/ps, we need to multiply by 1e7.
 160      * The timestep between saving the trajectory is
 161      * 1e7 is to convert nanometer to cm
 162      */
 163     recip_fac = bRecip ? (1e7/SPEED_OF_LIGHT) : 1.0;
 164     for (i = 0; (i < n); i += 2)
 165     {
 166         nu    = i/(2*dt);
 167         omega = nu*recip_fac;
 168         /* Computing the square magnitude of a complex number, since this is a power
 169          * spectrum.
 170          */
 171         fprintf(fp, "%10g  %10g\n", omega, sqr(data[i])+sqr(data[i+1]));
 172     }
 173     xvgrclose(fp);
 174     gmx_fft_destroy(fft);
 175     sfree(data);
 176 }
 177
 178 int gmx_velacc(int argc, char *argv[])
 179 {
 180     const char     *desc[] = {
 181         "[THISMODULE] computes the velocity autocorrelation function.",
 182         "When the [TT]-m[tt] option is used, the momentum autocorrelation",
 183         "function is calculated.[PAR]",
 184         "With option [TT]-mol[tt] the velocity autocorrelation function of",
 185         "molecules is calculated. In this case the index group should consist",
 186         "of molecule numbers instead of atom numbers.[PAR]",
 187         "Be sure that your trajectory contains frames with velocity information",
 188         "(i.e. [TT]nstvout[tt] was set in your original [REF].mdp[ref] file),",
 189         "and that the time interval between data collection points is",
 190         "much shorter than the time scale of the autocorrelation."
 191     };
 192
 193     static gmx_bool bMass = FALSE, bMol = FALSE, bRecip = TRUE;
 194     t_pargs         pa[]  = {
 195         { "-m", FALSE, etBOOL, {&bMass},
 196           "Calculate the momentum autocorrelation function" },
 197         { "-recip", FALSE, etBOOL, {&bRecip},
 198           "Use cm^-1 on X-axis instead of 1/ps for spectra." },
 199         { "-mol", FALSE, etBOOL, {&bMol},
 200           "Calculate the velocity acf of molecules" }
 201     };
 202
 203     t_topology      top;
 204     int             ePBC = -1;
 205     t_trxframe      fr;
 206     matrix          box;
 207     gmx_bool        bTPS = FALSE, bTop = FALSE;
 208     int             gnx;
 209     int            *index;
 210     char           *grpname;
 211     /* t0, t1 are the beginning and end time respectively.
 212      * dt is the time step, mass is temp variable for atomic mass.
 213      */
 214     real              t0, t1, dt, mass;
 215     t_trxstatus      *status;
 216     int               counter, n_alloc, i, j, counter_dim, k, l;
 217     rvec              mv_mol;
 218     /* Array for the correlation function */
 219     real            **c1;
 220     real             *normm = NULL;
 221     gmx_output_env_t *oenv;
 222
 223 #define NHISTO 360
 224
 225     t_filenm  fnm[] = {
 226         { efTRN, "-f",    NULL,   ffREAD  },
 227         { efTPS, NULL,    NULL,   ffOPTRD },
 228         { efNDX, NULL,    NULL,   ffOPTRD },
 229         { efXVG, "-o",    "vac",  ffWRITE },
 230         { efXVG, "-os",   "spectrum", ffOPTWR }
 231     };
 232 #define NFILE asize(fnm)
 233     int       npargs;
 234     t_pargs  *ppa;
 235
 236     npargs = asize(pa);
 237     ppa    = add_acf_pargs(&npargs, pa);
 238     if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
 239                            NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
 240     {
 241         return 0;
 242     }
 243
 244     if (bMol || bMass)
 245     {
 246         bTPS = ftp2bSet(efTPS, NFILE, fnm) || !ftp2bSet(efNDX, NFILE, fnm);
 247     }
 248
 249     if (bTPS)
 250     {
 251         bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, NULL, NULL, box,
 252                              TRUE);
 253         get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
 254     }
 255     else
 256     {
 257         rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
 258     }
 259
 260     if (bMol)
 261     {
 262         if (!bTop)
 263         {
 264             gmx_fatal(FARGS, "Need a topology to determine the molecules");
 265         }
 266         snew(normm, top.atoms.nr);
 267         precalc(top, normm);
 268         index_atom2mol(&gnx, index, &top.mols);
 269     }
 270
 271     /* Correlation stuff */
 272     snew(c1, gnx);
 273     for (i = 0; (i < gnx); i++)
 274     {
 275         c1[i] = NULL;
 276     }
 277
 278     read_first_frame(oenv, &status, ftp2fn(efTRN, NFILE, fnm), &fr, TRX_NEED_V);
 279     t0 = fr.time;
 280
 281     n_alloc = 0;
 282     counter = 0;
 283     do
 284     {
 285         if (counter >= n_alloc)
 286         {
 287             n_alloc += 100;
 288             for (i = 0; i < gnx; i++)
 289             {
 290                 srenew(c1[i], DIM*n_alloc);
 291             }
 292         }
 293         counter_dim = DIM*counter;
 294         if (bMol)
 295         {
 296             for (i = 0; i < gnx; i++)
 297             {
 298                 clear_rvec(mv_mol);
 299                 k = top.mols.index[index[i]];
 300                 l = top.mols.index[index[i]+1];
 301                 for (j = k; j < l; j++)
 302                 {
 303                     if (bMass)
 304                     {
 305                         mass = top.atoms.atom[j].m;
 306                     }
 307                     else
 308                     {
 309                         mass = normm[j];
 310                     }
 311                     mv_mol[XX] += mass*fr.v[j][XX];
 312                     mv_mol[YY] += mass*fr.v[j][YY];
 313                     mv_mol[ZZ] += mass*fr.v[j][ZZ];
 314                 }
 315                 c1[i][counter_dim+XX] = mv_mol[XX];
 316                 c1[i][counter_dim+YY] = mv_mol[YY];
 317                 c1[i][counter_dim+ZZ] = mv_mol[ZZ];
 318             }
 319         }
 320         else
 321         {
 322             for (i = 0; i < gnx; i++)
 323             {
 324                 if (bMass)
 325                 {
 326                     mass = top.atoms.atom[index[i]].m;
 327                 }
 328                 else
 329                 {
 330                     mass = 1;
 331                 }
 332                 c1[i][counter_dim+XX] = mass*fr.v[index[i]][XX];
 333                 c1[i][counter_dim+YY] = mass*fr.v[index[i]][YY];
 334                 c1[i][counter_dim+ZZ] = mass*fr.v[index[i]][ZZ];
 335             }
 336         }
 337
 338         t1 = fr.time;
 339
 340         counter++;
 341     }
 342     while (read_next_frame(oenv, status, &fr));
 343
 344     close_trj(status);
 345
 346     if (counter >= 4)
 347     {
 348         /* Compute time step between frames */
 349         dt = (t1-t0)/(counter-1);
 350         do_autocorr(opt2fn("-o", NFILE, fnm), oenv,
 351                     bMass ?
 352                     "Momentum Autocorrelation Function" :
 353                     "Velocity Autocorrelation Function",
 354                     counter, gnx, c1, dt, eacVector, TRUE);
 355
 356         do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
 357
 358         if (opt2bSet("-os", NFILE, fnm))
 359         {
 360             calc_spectrum(counter/2, (real *) (c1[0]), (t1-t0)/2, opt2fn("-os", NFILE, fnm),
 361                           oenv, bRecip);
 362             do_view(oenv, opt2fn("-os", NFILE, fnm), "-nxy");
 363         }
 364     }
 365     else
 366     {
 367         fprintf(stderr, "Not enough frames in trajectory - no output generated.\n");
 368     }
 369
 370     return 0;
 371 }