src/gromacs/gmxana/gmx_sans.cpp

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