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40 #include "gromacs/commandline/pargs.h"
41 #include "gromacs/fileio/tpxio.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/legacyheaders/copyrite.h"
48 #include "gromacs/legacyheaders/macros.h"
49 #include "gromacs/legacyheaders/typedefs.h"
50 #include "gromacs/math/vec.h"
51 #include "gromacs/pbcutil/rmpbc.h"
52 #include "gromacs/topology/index.h"
53 #include "gromacs/utility/fatalerror.h"
54 #include "gromacs/utility/futil.h"
55 #include "gromacs/utility/gmxomp.h"
56 #include "gromacs/utility/smalloc.h"
58 int gmx_sans(int argc, char *argv[])
60 const char *desc[] = {
61 "[THISMODULE] computes SANS spectra using Debye formula.",
62 "It currently uses topology file (since it need to assigne element for each atom).",
65 "[TT]-pr[tt] Computes normalized g(r) function averaged over trajectory[PAR]",
66 "[TT]-prframe[tt] Computes normalized g(r) function for each frame[PAR]",
67 "[TT]-sq[tt] Computes SANS intensity curve averaged over trajectory[PAR]",
68 "[TT]-sqframe[tt] Computes SANS intensity curve for each frame[PAR]",
69 "[TT]-startq[tt] Starting q value in nm[PAR]",
70 "[TT]-endq[tt] Ending q value in nm[PAR]",
71 "[TT]-qstep[tt] Stepping in q space[PAR]",
72 "Note: When using Debye direct method computational cost increases as",
73 "1/2 * N * (N - 1) where N is atom number in group of interest.",
75 "WARNING: If sq or pr specified this tool can produce large number of files! Up to two times larger than number of frames!"
77 static gmx_bool bPBC = TRUE;
78 static gmx_bool bNORM = FALSE;
79 static real binwidth = 0.2, grid = 0.05; /* bins shouldnt be smaller then smallest bond (~0.1nm) length */
80 static real start_q = 0.0, end_q = 2.0, q_step = 0.01;
81 static real mcover = -1;
82 static unsigned int seed = 0;
83 static int nthreads = -1;
85 static const char *emode[] = { NULL, "direct", "mc", NULL };
86 static const char *emethod[] = { NULL, "debye", "fft", NULL };
88 gmx_neutron_atomic_structurefactors_t *gnsf;
94 { "-bin", FALSE, etREAL, {&binwidth},
95 "[HIDDEN]Binwidth (nm)" },
96 { "-mode", FALSE, etENUM, {emode},
97 "Mode for sans spectra calculation" },
98 { "-mcover", FALSE, etREAL, {&mcover},
99 "Monte-Carlo coverage should be -1(default) or (0,1]"},
100 { "-method", FALSE, etENUM, {emethod},
101 "[HIDDEN]Method for sans spectra calculation" },
102 { "-pbc", FALSE, etBOOL, {&bPBC},
103 "Use periodic boundary conditions for computing distances" },
104 { "-grid", FALSE, etREAL, {&grid},
105 "[HIDDEN]Grid spacing (in nm) for FFTs" },
106 {"-startq", FALSE, etREAL, {&start_q},
107 "Starting q (1/nm) "},
108 {"-endq", FALSE, etREAL, {&end_q},
110 { "-qstep", FALSE, etREAL, {&q_step},
111 "Stepping in q (1/nm)"},
112 { "-seed", FALSE, etINT, {&seed},
113 "Random seed for Monte-Carlo"},
115 { "-nt", FALSE, etINT, {&nthreads},
116 "Number of threads to start"},
120 const char *fnTPX, *fnNDX, *fnTRX, *fnDAT = NULL;
122 t_topology *top = NULL;
124 gmx_rmpbc_t gpbc = NULL;
126 gmx_bool bFFT = FALSE, bDEBYE = FALSE;
127 gmx_bool bMC = FALSE;
134 char **grpname = NULL;
135 atom_id *index = NULL;
140 t_filenm *fnmdup = NULL;
141 gmx_radial_distribution_histogram_t *prframecurrent = NULL, *pr = NULL;
142 gmx_static_structurefactor_t *sqframecurrent = NULL, *sq = NULL;
145 #define NFILE asize(fnm)
148 { efTPR, "-s", NULL, ffREAD },
149 { efTRX, "-f", NULL, ffREAD },
150 { efNDX, NULL, NULL, ffOPTRD },
151 { efDAT, "-d", "nsfactor", ffOPTRD },
152 { efXVG, "-pr", "pr", ffWRITE },
153 { efXVG, "-sq", "sq", ffWRITE },
154 { efXVG, "-prframe", "prframe", ffOPTWR },
155 { efXVG, "-sqframe", "sqframe", ffOPTWR }
158 nthreads = gmx_omp_get_max_threads();
160 if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT,
161 NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
166 /* check that binwidth not smaller than smallers distance */
167 check_binwidth(binwidth);
168 check_mcover(mcover);
170 /* setting number of omp threads globaly */
171 gmx_omp_set_num_threads(nthreads);
173 /* Now try to parse opts for modes */
174 switch (emethod[0][0])
201 fprintf(stderr, "Using Monte Carlo Debye method to calculate spectrum\n");
205 fprintf(stderr, "Using direct Debye method to calculate spectrum\n");
210 gmx_fatal(FARGS, "FFT method not implemented!");
214 gmx_fatal(FARGS, "Unknown combination for mode and method!");
217 /* Try to read files */
218 fnDAT = ftp2fn(efDAT, NFILE, fnm);
219 fnTPX = ftp2fn(efTPR, NFILE, fnm);
220 fnTRX = ftp2fn(efTRX, NFILE, fnm);
222 gnsf = gmx_neutronstructurefactors_init(fnDAT);
223 fprintf(stderr, "Read %d atom names from %s with neutron scattering parameters\n\n", gnsf->nratoms, fnDAT);
229 bTPX = read_tps_conf(fnTPX, title, top, &ePBC, &x, NULL, box, TRUE);
231 printf("\nPlease select group for SANS spectra calculation:\n");
232 get_index(&(top->atoms), ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, grpname);
234 gsans = gmx_sans_init(top, gnsf);
236 /* Prepare reference frame */
239 gpbc = gmx_rmpbc_init(&top->idef, ePBC, top->atoms.nr);
240 gmx_rmpbc(gpbc, top->atoms.nr, box, x);
243 natoms = read_first_x(oenv, &status, fnTRX, &t, &x, box);
244 if (natoms != top->atoms.nr)
246 fprintf(stderr, "\nWARNING: number of atoms in tpx (%d) and trajectory (%d) do not match\n", natoms, top->atoms.nr);
253 gmx_rmpbc(gpbc, top->atoms.nr, box, x);
255 /* allocate memory for pr */
258 /* in case its first frame to read */
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] */
267 /* check if we use pr->gr first time */
268 snew(pr->gr, prframecurrent->grn);
269 snew(pr->r, prframecurrent->grn);
273 /* resize pr->gr and pr->r if needed to preven overruns */
274 if (prframecurrent->grn > pr->grn)
276 srenew(pr->gr, prframecurrent->grn);
277 srenew(pr->r, prframecurrent->grn);
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++)
285 pr->gr[i] += prframecurrent->gr[i];
286 pr->r[i] = prframecurrent->r[i];
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))
296 snew(suffix, GMX_PATH_MAX);
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++)
306 fprintf(fp, "%10.6f%10.6f\n", prframecurrent->r[i], prframecurrent->gr[i]);
308 done_filenms(NFILE, fnmdup);
314 if (opt2fn_null("-sqframe", NFILE, fnm))
317 snew(suffix, GMX_PATH_MAX);
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++)
327 fprintf(fp, "%10.6f%10.6f\n", sqframecurrent->q[i], sqframecurrent->s[i]);
329 done_filenms(NFILE, fnmdup);
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);
344 while (read_next_x(oenv, status, &t, x, box));
347 /* normalize histo */
348 normalize_probability(pr->grn, pr->gr);
349 sq = convert_histogram_to_intensity_curve(pr, start_q, end_q, q_step);
351 fp = xvgropen(opt2fn_null("-pr", NFILE, fnm), "G(r)", "Distance (nm)", "Probability", oenv);
352 for (i = 0; i < pr->grn; i++)
354 fprintf(fp, "%10.6f%10.6f\n", pr->r[i], pr->gr[i]);
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++)
362 fprintf(fp, "%10.6f%10.6f\n", sq->q[i], sq->s[i]);
375 please_cite(stdout, "Garmay2012");