src/gromacs/gmxana/gmx_sans.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2012,2013,2014,2015,2016,2017, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  35
  36 #include "gmxpre.h"
  37
  38 #include "config.h"
  39
  40 #include "gromacs/commandline/pargs.h"
  41 #include "gromacs/fileio/confio.h"
  42 #include "gromacs/fileio/trxio.h"
  43 #include "gromacs/fileio/xvgr.h"
  44 #include "gromacs/gmxana/gmx_ana.h"
  45 #include "gromacs/gmxana/gstat.h"
  46 #include "gromacs/gmxana/nsfactor.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/cstringutil.h"
  53 #include "gromacs/utility/fatalerror.h"
  54 #include "gromacs/utility/futil.h"
  55 #include "gromacs/utility/gmxassert.h"
  56 #include "gromacs/utility/gmxomp.h"
  57 #include "gromacs/utility/pleasecite.h"
  58 #include "gromacs/utility/smalloc.h"
  59
  60 int gmx_sans(int argc, char *argv[])
  61 {
  62     const char          *desc[] = {
  63         "[THISMODULE] computes SANS spectra using Debye formula.",
  64         "It currently uses topology file (since it need to assigne element for each atom).",
  65         "[PAR]",
  66         "Parameters:[PAR]"
  67         "[TT]-pr[tt] Computes normalized g(r) function averaged over trajectory[PAR]",
  68         "[TT]-prframe[tt] Computes normalized g(r) function for each frame[PAR]",
  69         "[TT]-sq[tt] Computes SANS intensity curve averaged over trajectory[PAR]",
  70         "[TT]-sqframe[tt] Computes SANS intensity curve for each frame[PAR]",
  71         "[TT]-startq[tt] Starting q value in nm[PAR]",
  72         "[TT]-endq[tt] Ending q value in nm[PAR]",
  73         "[TT]-qstep[tt] Stepping in q space[PAR]",
  74         "Note: When using Debye direct method computational cost increases as",
  75         "1/2 * N * (N - 1) where N is atom number in group of interest.",
  76         "[PAR]",
  77         "WARNING: If sq or pr specified this tool can produce large number of files! Up to two times larger than number of frames!"
  78     };
  79     static gmx_bool      bPBC     = TRUE;
  80     static gmx_bool      bNORM    = FALSE;
  81     static real          binwidth = 0.2, grid = 0.05; /* bins shouldn't be smaller then smallest bond (~0.1nm) length */
  82     static real          start_q  = 0.0, end_q = 2.0, q_step = 0.01;
  83     static real          mcover   = -1;
  84     static unsigned int  seed     = 0;
  85     static int           nthreads = -1;
  86
  87     static const char   *emode[]   = { nullptr, "direct", "mc", nullptr };
  88     static const char   *emethod[] = { nullptr, "debye", "fft", nullptr };
  89
  90     gmx_neutron_atomic_structurefactors_t    *gnsf;
  91     gmx_sans_t                               *gsans;
  92
  93 #define NPA asize(pa)
  94
  95     t_pargs                               pa[] = {
  96         { "-bin", FALSE, etREAL, {&binwidth},
  97           "[HIDDEN]Binwidth (nm)" },
  98         { "-mode", FALSE, etENUM, {emode},
  99           "Mode for sans spectra calculation" },
 100         { "-mcover", FALSE, etREAL, {&mcover},
 101           "Monte-Carlo coverage should be -1(default) or (0,1]"},
 102         { "-method", FALSE, etENUM, {emethod},
 103           "[HIDDEN]Method for sans spectra calculation" },
 104         { "-pbc", FALSE, etBOOL, {&bPBC},
 105           "Use periodic boundary conditions for computing distances" },
 106         { "-grid", FALSE, etREAL, {&grid},
 107           "[HIDDEN]Grid spacing (in nm) for FFTs" },
 108         {"-startq", FALSE, etREAL, {&start_q},
 109          "Starting q (1/nm) "},
 110         {"-endq", FALSE, etREAL, {&end_q},
 111          "Ending q (1/nm)"},
 112         { "-qstep", FALSE, etREAL, {&q_step},
 113           "Stepping in q (1/nm)"},
 114         { "-seed",     FALSE, etINT,  {&seed},
 115           "Random seed for Monte-Carlo"},
 116 #if GMX_OPENMP
 117         { "-nt",  FALSE, etINT, {&nthreads},
 118           "Number of threads to start"},
 119 #endif
 120     };
 121     FILE                                 *fp;
 122     const char                           *fnTPX, *fnTRX, *fnDAT = nullptr;
 123     t_trxstatus                          *status;
 124     t_topology                           *top  = nullptr;
 125     gmx_rmpbc_t                           gpbc = nullptr;
 126     gmx_bool                              bFFT = FALSE, bDEBYE = FALSE;
 127     gmx_bool                              bMC  = FALSE;
 128     int                                   ePBC = -1;
 129     matrix                                box;
 130     rvec                                 *x;
 131     int                                   natoms;
 132     real                                  t;
 133     char                                **grpname = nullptr;
 134     int                                  *index   = nullptr;
 135     int                                   isize;
 136     int                                   i;
 137     char                                 *hdr            = nullptr;
 138     char                                 *suffix         = nullptr;
 139     t_filenm                             *fnmdup         = nullptr;
 140     gmx_radial_distribution_histogram_t  *prframecurrent = nullptr, *pr = nullptr;
 141     gmx_static_structurefactor_t         *sqframecurrent = nullptr, *sq = nullptr;
 142     gmx_output_env_t                     *oenv;
 143
 144 #define NFILE asize(fnm)
 145
 146     t_filenm   fnm[] = {
 147         { efTPR,  "-s",       nullptr,       ffREAD },
 148         { efTRX,  "-f",       nullptr,       ffREAD },
 149         { efNDX,  nullptr,       nullptr,       ffOPTRD },
 150         { efDAT,  "-d",       "nsfactor", ffOPTRD },
 151         { efXVG,  "-pr",      "pr",       ffWRITE },
 152         { efXVG,  "-sq",       "sq",      ffWRITE },
 153         { efXVG,  "-prframe", "prframe",  ffOPTWR },
 154         { efXVG,  "-sqframe", "sqframe",  ffOPTWR }
 155     };
 156
 157     nthreads = gmx_omp_get_max_threads();
 158
 159     if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT,
 160                            NFILE, fnm, asize(pa), pa, 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':
 181                     bMC = FALSE;
 182                     break;
 183                 case 'm':
 184                     bMC = TRUE;
 185                     break;
 186                 default:
 187                     break;
 188             }
 189             break;
 190         case 'f':
 191             bFFT = TRUE;
 192             break;
 193         default:
 194             break;
 195     }
 196
 197     if (bDEBYE)
 198     {
 199         if (bMC)
 200         {
 201             fprintf(stderr, "Using Monte Carlo Debye method to calculate spectrum\n");
 202         }
 203         else
 204         {
 205             fprintf(stderr, "Using direct Debye method to calculate spectrum\n");
 206         }
 207     }
 208     else if (bFFT)
 209     {
 210         gmx_fatal(FARGS, "FFT method not implemented!");
 211     }
 212     else
 213     {
 214         gmx_fatal(FARGS, "Unknown combination for mode and method!");
 215     }
 216
 217     /* Try to read files */
 218     fnDAT = ftp2fn(efDAT, NFILE, fnm);
 219     fnTPX = ftp2fn(efTPR, NFILE, fnm);
 220     fnTRX = ftp2fn(efTRX, NFILE, fnm);
 221
 222     gnsf = gmx_neutronstructurefactors_init(fnDAT);
 223     fprintf(stderr, "Read %d atom names from %s with neutron scattering parameters\n\n", gnsf->nratoms, fnDAT);
 224
 225     snew(top, 1);
 226     snew(grpname, 1);
 227     snew(index, 1);
 228
 229     read_tps_conf(fnTPX, top, &ePBC, &x, nullptr, box, TRUE);
 230
 231     printf("\nPlease select group for SANS spectra calculation:\n");
 232     get_index(&(top->atoms), ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, grpname);
 233
 234     gsans = gmx_sans_init(top, gnsf);
 235
 236     /* Prepare reference frame */
 237     if (bPBC)
 238     {
 239         gpbc = gmx_rmpbc_init(&top->idef, ePBC, top->atoms.nr);
 240         gmx_rmpbc(gpbc, top->atoms.nr, box, x);
 241     }
 242
 243     natoms = read_first_x(oenv, &status, fnTRX, &t, &x, box);
 244     if (natoms != top->atoms.nr)
 245     {
 246         fprintf(stderr, "\nWARNING: number of atoms in tpx (%d) and trajectory (%d) do not match\n", natoms, top->atoms.nr);
 247     }
 248
 249     do
 250     {
 251         if (bPBC)
 252         {
 253             gmx_rmpbc(gpbc, top->atoms.nr, box, x);
 254         }
 255         /* allocate memory for pr */
 256         if (pr == nullptr)
 257         {
 258             /* in case its first frame to read */
 259             snew(pr, 1);
 260         }
 261         /*  realy calc p(r) */
 262         prframecurrent = calc_radial_distribution_histogram(gsans, x, box, index, isize, binwidth, bMC, bNORM, mcover, seed);
 263         /* copy prframecurrent -> pr and summ up pr->gr[i] */
 264         /* allocate and/or resize memory for pr->gr[i] and pr->r[i] */
 265         if (pr->gr == nullptr)
 266         {
 267             /* check if we use pr->gr first time */
 268             snew(pr->gr, prframecurrent->grn);
 269             snew(pr->r, prframecurrent->grn);
 270         }
 271         else
 272         {
 273             /* resize pr->gr and pr->r if needed to preven overruns */
 274             if (prframecurrent->grn > pr->grn)
 275             {
 276                 srenew(pr->gr, prframecurrent->grn);
 277                 srenew(pr->r, prframecurrent->grn);
 278             }
 279         }
 280         pr->grn      = prframecurrent->grn;
 281         pr->binwidth = prframecurrent->binwidth;
 282         /* summ up gr and fill r */
 283         for (i = 0; i < prframecurrent->grn; i++)
 284         {
 285             pr->gr[i] += prframecurrent->gr[i];
 286             pr->r[i]   = prframecurrent->r[i];
 287         }
 288         /* normalize histo */
 289         normalize_probability(prframecurrent->grn, prframecurrent->gr);
 290         /* convert p(r) to sq */
 291         sqframecurrent = convert_histogram_to_intensity_curve(prframecurrent, start_q, end_q, q_step);
 292         /* print frame data if needed */
 293         if (opt2fn_null("-prframe", NFILE, fnm))
 294         {
 295             snew(hdr, 25);
 296             snew(suffix, GMX_PATH_MAX);
 297             /* prepare header */
 298             sprintf(hdr, "g(r), t = %f", t);
 299             /* prepare output filename */
 300             fnmdup = dup_tfn(NFILE, fnm);
 301             sprintf(suffix, "-t%.2f", t);
 302             add_suffix_to_output_names(fnmdup, NFILE, suffix);
 303             fp = xvgropen(opt2fn_null("-prframe", NFILE, fnmdup), hdr, "Distance (nm)", "Probability", oenv);
 304             for (i = 0; i < prframecurrent->grn; i++)
 305             {
 306                 fprintf(fp, "%10.6f%10.6f\n", prframecurrent->r[i], prframecurrent->gr[i]);
 307             }
 308             done_filenms(NFILE, fnmdup);
 309             xvgrclose(fp);
 310             sfree(hdr);
 311             sfree(suffix);
 312             sfree(fnmdup);
 313         }
 314         if (opt2fn_null("-sqframe", NFILE, fnm))
 315         {
 316             snew(hdr, 25);
 317             snew(suffix, GMX_PATH_MAX);
 318             /* prepare header */
 319             sprintf(hdr, "I(q), t = %f", t);
 320             /* prepare output filename */
 321             fnmdup = dup_tfn(NFILE, fnm);
 322             sprintf(suffix, "-t%.2f", t);
 323             add_suffix_to_output_names(fnmdup, NFILE, suffix);
 324             fp = xvgropen(opt2fn_null("-sqframe", NFILE, fnmdup), hdr, "q (nm^-1)", "s(q)/s(0)", oenv);
 325             for (i = 0; i < sqframecurrent->qn; i++)
 326             {
 327                 fprintf(fp, "%10.6f%10.6f\n", sqframecurrent->q[i], sqframecurrent->s[i]);
 328             }
 329             done_filenms(NFILE, fnmdup);
 330             xvgrclose(fp);
 331             sfree(hdr);
 332             sfree(suffix);
 333             sfree(fnmdup);
 334         }
 335         /* free pr structure */
 336         sfree(prframecurrent->gr);
 337         sfree(prframecurrent->r);
 338         sfree(prframecurrent);
 339         /* free sq structure */
 340         sfree(sqframecurrent->q);
 341         sfree(sqframecurrent->s);
 342         sfree(sqframecurrent);
 343     }
 344     while (read_next_x(oenv, status, &t, x, box));
 345     close_trx(status);
 346
 347     /* normalize histo */
 348     normalize_probability(pr->grn, pr->gr);
 349     sq = convert_histogram_to_intensity_curve(pr, start_q, end_q, q_step);
 350     /* prepare pr.xvg */
 351     fp = xvgropen(opt2fn_null("-pr", NFILE, fnm), "G(r)", "Distance (nm)", "Probability", oenv);
 352     for (i = 0; i < pr->grn; i++)
 353     {
 354         fprintf(fp, "%10.6f%10.6f\n", pr->r[i], pr->gr[i]);
 355     }
 356     xvgrclose(fp);
 357
 358     /* prepare sq.xvg */
 359     fp = xvgropen(opt2fn_null("-sq", NFILE, fnm), "I(q)", "q (nm^-1)", "s(q)/s(0)", oenv);
 360     for (i = 0; i < sq->qn; i++)
 361     {
 362         fprintf(fp, "%10.6f%10.6f\n", sq->q[i], sq->s[i]);
 363     }
 364     xvgrclose(fp);
 365     /*
 366      * Clean up memory
 367      */
 368     sfree(pr->gr);
 369     sfree(pr->r);
 370     sfree(pr);
 371     sfree(sq->q);
 372     sfree(sq->s);
 373     sfree(sq);
 374
 375     please_cite(stdout, "Garmay2012");
 376
 377     return 0;
 378 }