src/gromacs/gmxana/gmx_sans.cpp

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  35
  36 #include "gmxpre.h"
  37
  38 #include "config.h"
  39
  40 #include <array>
  41
  42 #include "gromacs/commandline/pargs.h"
  43 #include "gromacs/fileio/confio.h"
  44 #include "gromacs/fileio/trxio.h"
  45 #include "gromacs/fileio/xvgr.h"
  46 #include "gromacs/gmxana/gmx_ana.h"
  47 #include "gromacs/gmxana/gstat.h"
  48 #include "gromacs/gmxana/nsfactor.h"
  49 #include "gromacs/math/vec.h"
  50 #include "gromacs/pbcutil/rmpbc.h"
  51 #include "gromacs/topology/index.h"
  52 #include "gromacs/topology/topology.h"
  53 #include "gromacs/utility/arraysize.h"
  54 #include "gromacs/utility/cstringutil.h"
  55 #include "gromacs/utility/fatalerror.h"
  56 #include "gromacs/utility/futil.h"
  57 #include "gromacs/utility/gmxassert.h"
  58 #include "gromacs/utility/gmxomp.h"
  59 #include "gromacs/utility/pleasecite.h"
  60 #include "gromacs/utility/smalloc.h"
  61
  62 int gmx_sans(int argc, char *argv[])
  63 {
  64     const char          *desc[] = {
  65         "[THISMODULE] computes SANS spectra using Debye formula.",
  66         "It currently uses topology file (since it need to assigne element for each atom).",
  67         "[PAR]",
  68         "Parameters:[PAR]",
  69         "[TT]-pr[tt] Computes normalized g(r) function averaged over trajectory[PAR]",
  70         "[TT]-prframe[tt] Computes normalized g(r) function for each frame[PAR]",
  71         "[TT]-sq[tt] Computes SANS intensity curve averaged over trajectory[PAR]",
  72         "[TT]-sqframe[tt] Computes SANS intensity curve for each frame[PAR]",
  73         "[TT]-startq[tt] Starting q value in nm[PAR]",
  74         "[TT]-endq[tt] Ending q value in nm[PAR]",
  75         "[TT]-qstep[tt] Stepping in q space[PAR]",
  76         "Note: When using Debye direct method computational cost increases as",
  77         "1/2 * N * (N - 1) where N is atom number in group of interest.",
  78         "[PAR]",
  79         "WARNING: If sq or pr specified this tool can produce large number of files! Up to two times larger than number of frames!"
  80     };
  81     static gmx_bool      bPBC     = TRUE;
  82     static gmx_bool      bNORM    = FALSE;
  83     static real          binwidth = 0.2, grid = 0.05; /* bins shouldn't be smaller then smallest bond (~0.1nm) length */
  84     static real          start_q  = 0.0, end_q = 2.0, q_step = 0.01;
  85     static real          mcover   = -1;
  86     static unsigned int  seed     = 0;
  87     static int           nthreads = -1;
  88
  89     static const char   *emode[]   = { nullptr, "direct", "mc", nullptr };
  90     static const char   *emethod[] = { nullptr, "debye", "fft", nullptr };
  91
  92     gmx_neutron_atomic_structurefactors_t    *gnsf;
  93     gmx_sans_t                               *gsans;
  94
  95 #define NPA asize(pa)
  96
  97     t_pargs                               pa[] = {
  98         { "-bin", FALSE, etREAL, {&binwidth},
  99           "[HIDDEN]Binwidth (nm)" },
 100         { "-mode", FALSE, etENUM, {emode},
 101           "Mode for sans spectra calculation" },
 102         { "-mcover", FALSE, etREAL, {&mcover},
 103           "Monte-Carlo coverage should be -1(default) or (0,1]"},
 104         { "-method", FALSE, etENUM, {emethod},
 105           "[HIDDEN]Method for sans spectra calculation" },
 106         { "-pbc", FALSE, etBOOL, {&bPBC},
 107           "Use periodic boundary conditions for computing distances" },
 108         { "-grid", FALSE, etREAL, {&grid},
 109           "[HIDDEN]Grid spacing (in nm) for FFTs" },
 110         {"-startq", FALSE, etREAL, {&start_q},
 111          "Starting q (1/nm) "},
 112         {"-endq", FALSE, etREAL, {&end_q},
 113          "Ending q (1/nm)"},
 114         { "-qstep", FALSE, etREAL, {&q_step},
 115           "Stepping in q (1/nm)"},
 116         { "-seed",     FALSE, etINT,  {&seed},
 117           "Random seed for Monte-Carlo"},
 118 #if GMX_OPENMP
 119         { "-nt",  FALSE, etINT, {&nthreads},
 120           "Number of threads to start"},
 121 #endif
 122     };
 123     FILE                                 *fp;
 124     const char                           *fnTPX, *fnTRX, *fnDAT = nullptr;
 125     t_trxstatus                          *status;
 126     t_topology                           *top  = nullptr;
 127     gmx_rmpbc_t                           gpbc = nullptr;
 128     gmx_bool                              bFFT = FALSE, bDEBYE = FALSE;
 129     gmx_bool                              bMC  = FALSE;
 130     int                                   ePBC = -1;
 131     matrix                                box;
 132     rvec                                 *x;
 133     int                                   natoms;
 134     real                                  t;
 135     char                                **grpname = nullptr;
 136     int                                  *index   = nullptr;
 137     int                                   isize;
 138     int                                   i;
 139     char                                 *hdr            = nullptr;
 140     char                                 *suffix         = nullptr;
 141     gmx_radial_distribution_histogram_t  *prframecurrent = nullptr, *pr = nullptr;
 142     gmx_static_structurefactor_t         *sqframecurrent = nullptr, *sq = nullptr;
 143     gmx_output_env_t                     *oenv;
 144
 145     std::array<t_filenm, 8>               filenames =
 146     { { { efTPR,  "-s",       nullptr,    ffREAD  },
 147         { efTRX,  "-f",       nullptr,    ffREAD  },
 148         { efNDX,  nullptr,    nullptr,    ffOPTRD },
 149         { efDAT,  "-d",       "nsfactor", ffOPTRD },
 150         { efXVG,  "-pr",      "pr",       ffWRITE },
 151         { efXVG,  "-sq",      "sq",       ffWRITE },
 152         { efXVG,  "-prframe", "prframe",  ffOPTWR },
 153         { efXVG,  "-sqframe", "sqframe",  ffOPTWR } } };
 154     t_filenm                             *fnm = filenames.data();
 155
 156     const auto NFILE = filenames.size();
 157
 158     nthreads = gmx_omp_get_max_threads();
 159
 160     if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT,
 161                            NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
 162     {
 163         return 0;
 164     }
 165
 166     /* check that binwidth not smaller than smallers distance */
 167     check_binwidth(binwidth);
 168     check_mcover(mcover);
 169
 170     /* setting number of omp threads globaly */
 171     gmx_omp_set_num_threads(nthreads);
 172
 173     /* Now try to parse opts for modes */
 174     GMX_RELEASE_ASSERT(emethod[0] != nullptr, "Options inconsistency; emethod[0] is NULL");
 175     switch (emethod[0][0])
 176     {
 177         case 'd':
 178             bDEBYE = TRUE;
 179             switch (emode[0][0])
 180             {
 181                 case 'd':
 182                     bMC = FALSE;
 183                     break;
 184                 case 'm':
 185                     bMC = TRUE;
 186                     break;
 187                 default:
 188                     break;
 189             }
 190             break;
 191         case 'f':
 192             bFFT = TRUE;
 193             break;
 194         default:
 195             break;
 196     }
 197
 198     if (bDEBYE)
 199     {
 200         if (bMC)
 201         {
 202             fprintf(stderr, "Using Monte Carlo Debye method to calculate spectrum\n");
 203         }
 204         else
 205         {
 206             fprintf(stderr, "Using direct Debye method to calculate spectrum\n");
 207         }
 208     }
 209     else if (bFFT)
 210     {
 211         gmx_fatal(FARGS, "FFT method not implemented!");
 212     }
 213     else
 214     {
 215         gmx_fatal(FARGS, "Unknown combination for mode and method!");
 216     }
 217
 218     /* Try to read files */
 219     fnDAT = ftp2fn(efDAT, NFILE, fnm);
 220     fnTPX = ftp2fn(efTPR, NFILE, fnm);
 221     fnTRX = ftp2fn(efTRX, NFILE, fnm);
 222
 223     gnsf = gmx_neutronstructurefactors_init(fnDAT);
 224     fprintf(stderr, "Read %d atom names from %s with neutron scattering parameters\n\n", gnsf->nratoms, fnDAT);
 225
 226     snew(top, 1);
 227     snew(grpname, 1);
 228     snew(index, 1);
 229
 230     read_tps_conf(fnTPX, top, &ePBC, &x, nullptr, box, TRUE);
 231
 232     printf("\nPlease select group for SANS spectra calculation:\n");
 233     get_index(&(top->atoms), ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, grpname);
 234
 235     gsans = gmx_sans_init(top, gnsf);
 236
 237     /* Prepare reference frame */
 238     if (bPBC)
 239     {
 240         gpbc = gmx_rmpbc_init(&top->idef, ePBC, top->atoms.nr);
 241         gmx_rmpbc(gpbc, top->atoms.nr, box, x);
 242     }
 243
 244     natoms = read_first_x(oenv, &status, fnTRX, &t, &x, box);
 245     if (natoms != top->atoms.nr)
 246     {
 247         fprintf(stderr, "\nWARNING: number of atoms in tpx (%d) and trajectory (%d) do not match\n", natoms, top->atoms.nr);
 248     }
 249
 250     do
 251     {
 252         if (bPBC)
 253         {
 254             gmx_rmpbc(gpbc, top->atoms.nr, box, x);
 255         }
 256         /* allocate memory for pr */
 257         if (pr == nullptr)
 258         {
 259             /* in case its first frame to read */
 260             snew(pr, 1);
 261         }
 262         /*  realy calc p(r) */
 263         prframecurrent = calc_radial_distribution_histogram(gsans, x, box, index, isize, binwidth, bMC, bNORM, mcover, seed);
 264         /* copy prframecurrent -> pr and summ up pr->gr[i] */
 265         /* allocate and/or resize memory for pr->gr[i] and pr->r[i] */
 266         if (pr->gr == nullptr)
 267         {
 268             /* check if we use pr->gr first time */
 269             snew(pr->gr, prframecurrent->grn);
 270             snew(pr->r, prframecurrent->grn);
 271         }
 272         else
 273         {
 274             /* resize pr->gr and pr->r if needed to preven overruns */
 275             if (prframecurrent->grn > pr->grn)
 276             {
 277                 srenew(pr->gr, prframecurrent->grn);
 278                 srenew(pr->r, prframecurrent->grn);
 279             }
 280         }
 281         pr->grn      = prframecurrent->grn;
 282         pr->binwidth = prframecurrent->binwidth;
 283         /* summ up gr and fill r */
 284         for (i = 0; i < prframecurrent->grn; i++)
 285         {
 286             pr->gr[i] += prframecurrent->gr[i];
 287             pr->r[i]   = prframecurrent->r[i];
 288         }
 289         /* normalize histo */
 290         normalize_probability(prframecurrent->grn, prframecurrent->gr);
 291         /* convert p(r) to sq */
 292         sqframecurrent = convert_histogram_to_intensity_curve(prframecurrent, start_q, end_q, q_step);
 293         /* print frame data if needed */
 294         if (opt2fn_null("-prframe", NFILE, fnm))
 295         {
 296             snew(hdr, 25);
 297             snew(suffix, GMX_PATH_MAX);
 298             /* prepare header */
 299             sprintf(hdr, "g(r), t = %f", t);
 300             /* prepare output filename */
 301             auto fnmdup = filenames;
 302             sprintf(suffix, "-t%.2f", t);
 303             add_suffix_to_output_names(fnmdup.data(), NFILE, suffix);
 304             fp = xvgropen(opt2fn_null("-prframe", NFILE, fnmdup.data()), hdr, "Distance (nm)", "Probability", oenv);
 305             for (i = 0; i < prframecurrent->grn; i++)
 306             {
 307                 fprintf(fp, "%10.6f%10.6f\n", prframecurrent->r[i], prframecurrent->gr[i]);
 308             }
 309             xvgrclose(fp);
 310             sfree(hdr);
 311             sfree(suffix);
 312         }
 313         if (opt2fn_null("-sqframe", NFILE, fnm))
 314         {
 315             snew(hdr, 25);
 316             snew(suffix, GMX_PATH_MAX);
 317             /* prepare header */
 318             sprintf(hdr, "I(q), t = %f", t);
 319             /* prepare output filename */
 320             auto fnmdup = filenames;
 321             sprintf(suffix, "-t%.2f", t);
 322             add_suffix_to_output_names(fnmdup.data(), NFILE, suffix);
 323             fp = xvgropen(opt2fn_null("-sqframe", NFILE, fnmdup.data()), hdr, "q (nm^-1)", "s(q)/s(0)", oenv);
 324             for (i = 0; i < sqframecurrent->qn; i++)
 325             {
 326                 fprintf(fp, "%10.6f%10.6f\n", sqframecurrent->q[i], sqframecurrent->s[i]);
 327             }
 328             xvgrclose(fp);
 329             sfree(hdr);
 330             sfree(suffix);
 331         }
 332         /* free pr structure */
 333         sfree(prframecurrent->gr);
 334         sfree(prframecurrent->r);
 335         sfree(prframecurrent);
 336         /* free sq structure */
 337         sfree(sqframecurrent->q);
 338         sfree(sqframecurrent->s);
 339         sfree(sqframecurrent);
 340     }
 341     while (read_next_x(oenv, status, &t, x, box));
 342     close_trx(status);
 343
 344     /* normalize histo */
 345     normalize_probability(pr->grn, pr->gr);
 346     sq = convert_histogram_to_intensity_curve(pr, start_q, end_q, q_step);
 347     /* prepare pr.xvg */
 348     fp = xvgropen(opt2fn_null("-pr", NFILE, fnm), "G(r)", "Distance (nm)", "Probability", oenv);
 349     for (i = 0; i < pr->grn; i++)
 350     {
 351         fprintf(fp, "%10.6f%10.6f\n", pr->r[i], pr->gr[i]);
 352     }
 353     xvgrclose(fp);
 354
 355     /* prepare sq.xvg */
 356     fp = xvgropen(opt2fn_null("-sq", NFILE, fnm), "I(q)", "q (nm^-1)", "s(q)/s(0)", oenv);
 357     for (i = 0; i < sq->qn; i++)
 358     {
 359         fprintf(fp, "%10.6f%10.6f\n", sq->q[i], sq->s[i]);
 360     }
 361     xvgrclose(fp);
 362     /*
 363      * Clean up memory
 364      */
 365     sfree(pr->gr);
 366     sfree(pr->r);
 367     sfree(pr);
 368     sfree(sq->q);
 369     sfree(sq->s);
 370     sfree(sq);
 371
 372     please_cite(stdout, "Garmay2012");
 373
 374     return 0;
 375 }