src/gromacs/gmxana/gmx_rotacf.cpp

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  37 #include "gmxpre.h"
  38
  39 #include <cmath>
  40 #include <cstring>
  41
  42 #include "gromacs/commandline/pargs.h"
  43 #include "gromacs/commandline/viewit.h"
  44 #include "gromacs/correlationfunctions/autocorr.h"
  45 #include "gromacs/fileio/trxio.h"
  46 #include "gromacs/gmxana/gmx_ana.h"
  47 #include "gromacs/math/vec.h"
  48 #include "gromacs/pbcutil/rmpbc.h"
  49 #include "gromacs/topology/index.h"
  50 #include "gromacs/topology/topology.h"
  51 #include "gromacs/utility/arraysize.h"
  52 #include "gromacs/utility/fatalerror.h"
  53 #include "gromacs/utility/futil.h"
  54 #include "gromacs/utility/smalloc.h"
  55
  56 int gmx_rotacf(int argc, char *argv[])
  57 {
  58     const char       *desc[] = {
  59         "[THISMODULE] calculates the rotational correlation function",
  60         "for molecules. Atom triplets (i,j,k) must be given in the index",
  61         "file, defining two vectors ij and jk. The rotational ACF",
  62         "is calculated as the autocorrelation function of the vector",
  63         "n = ij x jk, i.e. the cross product of the two vectors.",
  64         "Since three atoms span a plane, the order of the three atoms",
  65         "does not matter. Optionally, by invoking the [TT]-d[tt] switch, you can",
  66         "calculate the rotational correlation function for linear molecules",
  67         "by specifying atom pairs (i,j) in the index file.",
  68         "[PAR]",
  69         "EXAMPLES[PAR]",
  70         "[TT]gmx rotacf -P 1 -nparm 2 -fft -n index -o rotacf-x-P1",
  71         "-fa expfit-x-P1 -beginfit 2.5 -endfit 20.0[tt][PAR]",
  72         "This will calculate the rotational correlation function using a first",
  73         "order Legendre polynomial of the angle of a vector defined by the index",
  74         "file. The correlation function will be fitted from 2.5 ps until 20.0 ps",
  75         "to a two-parameter exponential."
  76     };
  77     static gmx_bool   bVec    = FALSE, bAver = TRUE;
  78
  79     t_pargs           pa[] = {
  80         { "-d",   FALSE, etBOOL, {&bVec},
  81           "Use index doublets (vectors) for correlation function instead of triplets (planes)" },
  82         { "-aver", FALSE, etBOOL, {&bAver},
  83           "Average over molecules" }
  84     };
  85
  86     t_trxstatus      *status;
  87     int               isize;
  88     int              *index;
  89     char             *grpname;
  90     rvec             *x, *x_s;
  91     matrix            box;
  92     real            **c1;
  93     rvec              xij, xjk, n;
  94     int               i, m, teller, n_alloc, natoms, nvec, ai, aj, ak;
  95     unsigned long     mode;
  96     real              t, t0, t1, dt;
  97     gmx_rmpbc_t       gpbc = nullptr;
  98     t_topology       *top;
  99     int               ePBC;
 100     t_filenm          fnm[] = {
 101         { efTRX, "-f", nullptr,  ffREAD  },
 102         { efTPR, nullptr, nullptr,  ffREAD },
 103         { efNDX, nullptr, nullptr,  ffREAD  },
 104         { efXVG, "-o", "rotacf",  ffWRITE }
 105     };
 106 #define NFILE asize(fnm)
 107     int               npargs;
 108     t_pargs          *ppa;
 109
 110     gmx_output_env_t *oenv;
 111
 112     npargs = asize(pa);
 113     ppa    = add_acf_pargs(&npargs, pa);
 114
 115     if (!parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME,
 116                            NFILE, fnm, npargs, ppa, asize(desc), desc, 0, nullptr, &oenv))
 117     {
 118         sfree(ppa);
 119         return 0;
 120     }
 121
 122     rd_index(ftp2fn(efNDX, NFILE, fnm), 1, &isize, &index, &grpname);
 123
 124     if (bVec)
 125     {
 126         nvec = isize/2;
 127     }
 128     else
 129     {
 130         nvec = isize/3;
 131     }
 132
 133     if (((isize % 3) != 0) && !bVec)
 134     {
 135         gmx_fatal(FARGS, "number of index elements not multiple of 3, "
 136                   "these can not be atom triplets\n");
 137     }
 138     if (((isize % 2) != 0) && bVec)
 139     {
 140         gmx_fatal(FARGS, "number of index elements not multiple of 2, "
 141                   "these can not be atom doublets\n");
 142     }
 143
 144     top = read_top(ftp2fn(efTPR, NFILE, fnm), &ePBC);
 145
 146     snew(c1, nvec);
 147     for (i = 0; (i < nvec); i++)
 148     {
 149         c1[i] = nullptr;
 150     }
 151     n_alloc = 0;
 152
 153     natoms = read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &x, box);
 154     snew(x_s, natoms);
 155
 156     gpbc = gmx_rmpbc_init(&(top->idef), ePBC, natoms);
 157
 158     /* Start the loop over frames */
 159     t0      = t;
 160     teller  = 0;
 161     do
 162     {
 163         if (teller >= n_alloc)
 164         {
 165             n_alloc += 100;
 166             for (i = 0; (i < nvec); i++)
 167             {
 168                 srenew(c1[i], DIM*n_alloc);
 169             }
 170         }
 171         t1 = t;
 172
 173         /* Remove periodicity */
 174         gmx_rmpbc_copy(gpbc, natoms, box, x, x_s);
 175
 176         /* Compute crossproducts for all vectors, if triplets.
 177          * else, just get the vectors in case of doublets.
 178          */
 179         if (bVec == FALSE)
 180         {
 181             for (i = 0; (i < nvec); i++)
 182             {
 183                 ai = index[3*i];
 184                 aj = index[3*i+1];
 185                 ak = index[3*i+2];
 186                 rvec_sub(x_s[ai], x_s[aj], xij);
 187                 rvec_sub(x_s[aj], x_s[ak], xjk);
 188                 cprod(xij, xjk, n);
 189                 for (m = 0; (m < DIM); m++)
 190                 {
 191                     c1[i][DIM*teller+m] = n[m];
 192                 }
 193             }
 194         }
 195         else
 196         {
 197             for (i = 0; (i < nvec); i++)
 198             {
 199                 ai = index[2*i];
 200                 aj = index[2*i+1];
 201                 rvec_sub(x_s[ai], x_s[aj], n);
 202                 for (m = 0; (m < DIM); m++)
 203                 {
 204                     c1[i][DIM*teller+m] = n[m];
 205                 }
 206             }
 207         }
 208         /* Increment loop counter */
 209         teller++;
 210     }
 211     while (read_next_x(oenv, status, &t, x, box));
 212     close_trx(status);
 213     fprintf(stderr, "\nDone with trajectory\n");
 214
 215     gmx_rmpbc_done(gpbc);
 216
 217
 218     /* Autocorrelation function */
 219     if (teller < 2)
 220     {
 221         fprintf(stderr, "Not enough frames for correlation function\n");
 222     }
 223     else
 224     {
 225         dt = (t1 - t0)/(teller-1);
 226
 227         mode = eacVector;
 228
 229         do_autocorr(ftp2fn(efXVG, NFILE, fnm), oenv, "Rotational Correlation Function",
 230                     teller, nvec, c1, dt, mode, bAver);
 231     }
 232
 233     do_view(oenv, ftp2fn(efXVG, NFILE, fnm), nullptr);
 234
 235     return 0;
 236 }