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/trxio.h"
  49 #include "gromacs/fileio/xvgr.h"
  50 #include "gromacs/gmxana/gmx_ana.h"
  51 #include "gromacs/gmxana/gstat.h"
  52 #include "gromacs/math/functions.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/trajectory/trajectoryframe.h"
  59 #include "gromacs/utility/arraysize.h"
  60 #include "gromacs/utility/fatalerror.h"
  61 #include "gromacs/utility/futil.h"
  62 #include "gromacs/utility/smalloc.h"
  63
  64 static void index_atom2mol(int *n, int *index, const t_block *mols)
  65 {
  66     int nat, i, nmol, mol, j;
  67
  68     nat  = *n;
  69     i    = 0;
  70     nmol = 0;
  71     mol  = 0;
  72     while (i < nat)
  73     {
  74         while (index[i] > mols->index[mol])
  75         {
  76             mol++;
  77             if (mol >= mols->nr)
  78             {
  79                 gmx_fatal(FARGS, "Atom index out of range: %d", index[i]+1);
  80             }
  81         }
  82         for (j = mols->index[mol]; j < mols->index[mol+1]; j++)
  83         {
  84             if (i >= nat || index[i] != j)
  85             {
  86                 gmx_fatal(FARGS, "The index group does not consist of whole molecules");
  87             }
  88             i++;
  89         }
  90         index[nmol++] = mol;
  91     }
  92
  93     fprintf(stderr, "\nSplit group of %d atoms into %d molecules\n", nat, nmol);
  94
  95     *n = nmol;
  96 }
  97
  98 static void precalc(const t_topology &top, real normm[])
  99 {
 100
 101     real mtot;
 102     int  i, j, k, l;
 103
 104     for (i = 0; i < top.mols.nr; i++)
 105     {
 106         k    = top.mols.index[i];
 107         l    = top.mols.index[i+1];
 108         mtot = 0.0;
 109
 110         for (j = k; j < l; j++)
 111         {
 112             mtot += top.atoms.atom[j].m;
 113         }
 114
 115         for (j = k; j < l; j++)
 116         {
 117             normm[j] = top.atoms.atom[j].m/mtot;
 118         }
 119
 120     }
 121
 122 }
 123
 124 static void calc_spectrum(int n, real c[], real dt, const char *fn,
 125                           gmx_output_env_t *oenv, gmx_bool bRecip)
 126 {
 127     FILE     *fp;
 128     gmx_fft_t fft;
 129     int       i, status;
 130     real     *data;
 131     real      nu, omega, recip_fac;
 132
 133     snew(data, n*2);
 134     for (i = 0; (i < n); i++)
 135     {
 136         data[i] = c[i];
 137     }
 138
 139     if ((status = gmx_fft_init_1d_real(&fft, n, GMX_FFT_FLAG_NONE)) != 0)
 140     {
 141         gmx_fatal(FARGS, "Invalid fft return status %d", status);
 142     }
 143     if ((status = gmx_fft_1d_real(fft, GMX_FFT_REAL_TO_COMPLEX, data, data)) != 0)
 144     {
 145         gmx_fatal(FARGS, "Invalid fft return status %d", status);
 146     }
 147     fp = xvgropen(fn, "Vibrational Power Spectrum",
 148                   bRecip ? "\\f{12}w\\f{4} (cm\\S-1\\N)" :
 149                   "\\f{12}n\\f{4} (ps\\S-1\\N)",
 150                   "a.u.", oenv);
 151     /* This is difficult.
 152      * The length of the ACF is dt (as passed to this routine).
 153      * We pass the vacf with N time steps from 0 to dt.
 154      * That means that after FFT we have lowest frequency = 1/dt
 155      * then 1/(2 dt) etc. (this is the X-axis of the data after FFT).
 156      * To convert to 1/cm we need to have to realize that
 157      * E = hbar w = h nu = h c/lambda. We want to have reciprokal cm
 158      * on the x-axis, that is 1/lambda, so we then have
 159      * 1/lambda = nu/c. Since nu has units of 1/ps and c has gromacs units
 160      * of nm/ps, we need to multiply by 1e7.
 161      * The timestep between saving the trajectory is
 162      * 1e7 is to convert nanometer to cm
 163      */
 164     recip_fac = bRecip ? (1e7/SPEED_OF_LIGHT) : 1.0;
 165     for (i = 0; (i < n); i += 2)
 166     {
 167         nu    = i/(2*dt);
 168         omega = nu*recip_fac;
 169         /* Computing the square magnitude of a complex number, since this is a power
 170          * spectrum.
 171          */
 172         fprintf(fp, "%10g  %10g\n", omega, gmx::square(data[i])+gmx::square(data[i+1]));
 173     }
 174     xvgrclose(fp);
 175     gmx_fft_destroy(fft);
 176     sfree(data);
 177 }
 178
 179 int gmx_velacc(int argc, char *argv[])
 180 {
 181     const char     *desc[] = {
 182         "[THISMODULE] computes the velocity autocorrelation function.",
 183         "When the [TT]-m[tt] option is used, the momentum autocorrelation",
 184         "function is calculated.[PAR]",
 185         "With option [TT]-mol[tt] the velocity autocorrelation function of",
 186         "molecules is calculated. In this case the index group should consist",
 187         "of molecule numbers instead of atom numbers.[PAR]",
 188         "Be sure that your trajectory contains frames with velocity information",
 189         "(i.e. [TT]nstvout[tt] was set in your original [REF].mdp[ref] file),",
 190         "and that the time interval between data collection points is",
 191         "much shorter than the time scale of the autocorrelation."
 192     };
 193
 194     static gmx_bool bMass = FALSE, bMol = FALSE, bRecip = TRUE;
 195     t_pargs         pa[]  = {
 196         { "-m", FALSE, etBOOL, {&bMass},
 197           "Calculate the momentum autocorrelation function" },
 198         { "-recip", FALSE, etBOOL, {&bRecip},
 199           "Use cm^-1 on X-axis instead of 1/ps for spectra." },
 200         { "-mol", FALSE, etBOOL, {&bMol},
 201           "Calculate the velocity acf of molecules" }
 202     };
 203
 204     t_topology      top;
 205     int             ePBC = -1;
 206     t_trxframe      fr;
 207     matrix          box;
 208     gmx_bool        bTPS = FALSE, bTop = FALSE;
 209     int             gnx;
 210     int            *index;
 211     char           *grpname;
 212     /* t0, t1 are the beginning and end time respectively.
 213      * dt is the time step, mass is temp variable for atomic mass.
 214      */
 215     real              t0, t1, dt, mass;
 216     t_trxstatus      *status;
 217     int               counter, n_alloc, i, j, counter_dim, k, l;
 218     rvec              mv_mol;
 219     /* Array for the correlation function */
 220     real            **c1;
 221     real             *normm = NULL;
 222     gmx_output_env_t *oenv;
 223
 224 #define NHISTO 360
 225
 226     t_filenm  fnm[] = {
 227         { efTRN, "-f",    NULL,   ffREAD  },
 228         { efTPS, NULL,    NULL,   ffOPTRD },
 229         { efNDX, NULL,    NULL,   ffOPTRD },
 230         { efXVG, "-o",    "vac",  ffWRITE },
 231         { efXVG, "-os",   "spectrum", ffOPTWR }
 232     };
 233 #define NFILE asize(fnm)
 234     int       npargs;
 235     t_pargs  *ppa;
 236
 237     npargs = asize(pa);
 238     ppa    = add_acf_pargs(&npargs, pa);
 239     if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
 240                            NFILE, fnm, npargs, ppa, asize(desc), desc, 0, NULL, &oenv))
 241     {
 242         return 0;
 243     }
 244
 245     if (bMol || bMass)
 246     {
 247         bTPS = ftp2bSet(efTPS, NFILE, fnm) || !ftp2bSet(efNDX, NFILE, fnm);
 248     }
 249
 250     if (bTPS)
 251     {
 252         bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, NULL, NULL, box,
 253                              TRUE);
 254         get_index(&top.atoms, ftp2fn_null(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
 255     }
 256     else
 257     {
 258         rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &gnx, &index, &grpname);
 259     }
 260
 261     if (bMol)
 262     {
 263         if (!bTop)
 264         {
 265             gmx_fatal(FARGS, "Need a topology to determine the molecules");
 266         }
 267         snew(normm, top.atoms.nr);
 268         precalc(top, normm);
 269         index_atom2mol(&gnx, index, &top.mols);
 270     }
 271
 272     /* Correlation stuff */
 273     snew(c1, gnx);
 274     for (i = 0; (i < gnx); i++)
 275     {
 276         c1[i] = NULL;
 277     }
 278
 279     read_first_frame(oenv, &status, ftp2fn(efTRN, NFILE, fnm), &fr, TRX_NEED_V);
 280     t0 = fr.time;
 281
 282     n_alloc = 0;
 283     counter = 0;
 284     do
 285     {
 286         if (counter >= n_alloc)
 287         {
 288             n_alloc += 100;
 289             for (i = 0; i < gnx; i++)
 290             {
 291                 srenew(c1[i], DIM*n_alloc);
 292             }
 293         }
 294         counter_dim = DIM*counter;
 295         if (bMol)
 296         {
 297             for (i = 0; i < gnx; i++)
 298             {
 299                 clear_rvec(mv_mol);
 300                 k = top.mols.index[index[i]];
 301                 l = top.mols.index[index[i]+1];
 302                 for (j = k; j < l; j++)
 303                 {
 304                     if (bMass)
 305                     {
 306                         mass = top.atoms.atom[j].m;
 307                     }
 308                     else
 309                     {
 310                         mass = normm[j];
 311                     }
 312                     mv_mol[XX] += mass*fr.v[j][XX];
 313                     mv_mol[YY] += mass*fr.v[j][YY];
 314                     mv_mol[ZZ] += mass*fr.v[j][ZZ];
 315                 }
 316                 c1[i][counter_dim+XX] = mv_mol[XX];
 317                 c1[i][counter_dim+YY] = mv_mol[YY];
 318                 c1[i][counter_dim+ZZ] = mv_mol[ZZ];
 319             }
 320         }
 321         else
 322         {
 323             for (i = 0; i < gnx; i++)
 324             {
 325                 if (bMass)
 326                 {
 327                     mass = top.atoms.atom[index[i]].m;
 328                 }
 329                 else
 330                 {
 331                     mass = 1;
 332                 }
 333                 c1[i][counter_dim+XX] = mass*fr.v[index[i]][XX];
 334                 c1[i][counter_dim+YY] = mass*fr.v[index[i]][YY];
 335                 c1[i][counter_dim+ZZ] = mass*fr.v[index[i]][ZZ];
 336             }
 337         }
 338
 339         t1 = fr.time;
 340
 341         counter++;
 342     }
 343     while (read_next_frame(oenv, status, &fr));
 344
 345     close_trj(status);
 346
 347     if (counter >= 4)
 348     {
 349         /* Compute time step between frames */
 350         dt = (t1-t0)/(counter-1);
 351         do_autocorr(opt2fn("-o", NFILE, fnm), oenv,
 352                     bMass ?
 353                     "Momentum Autocorrelation Function" :
 354                     "Velocity Autocorrelation Function",
 355                     counter, gnx, c1, dt, eacVector, TRUE);
 356
 357         do_view(oenv, opt2fn("-o", NFILE, fnm), "-nxy");
 358
 359         if (opt2bSet("-os", NFILE, fnm))
 360         {
 361             calc_spectrum(counter/2, (real *) (c1[0]), (t1-t0)/2, opt2fn("-os", NFILE, fnm),
 362                           oenv, bRecip);
 363             do_view(oenv, opt2fn("-os", NFILE, fnm), "-nxy");
 364         }
 365     }
 366     else
 367     {
 368         fprintf(stderr, "Not enough frames in trajectory - no output generated.\n");
 369     }
 370
 371     return 0;
 372 }