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59 int gmx_sans(int argc, char *argv[])
61 const char *desc[] = {
62 "This is simple tool to compute SANS spectra using Debye formula",
63 "It currently uses topology file (since it need to assigne element for each atom)",
66 "[TT]-pr[tt] Computes normalized g(r) function averaged over trajectory[PAR]",
67 "[TT]-prframe[tt] Computes normalized g(r) function for each frame[PAR]",
68 "[TT]-sq[tt] Computes SANS intensity curve averaged over trajectory[PAR]",
69 "[TT]-sqframe[tt] Computes SANS intensity curve for each frame[PAR]",
70 "[TT]-startq[tt] Starting q value in nm[PAR]",
71 "[TT]-endq[tt] Ending q value in nm[PAR]",
72 "[TT]-qstep[tt] Stepping in q space[PAR]",
73 "Note: When using Debye direct method computational cost increases as",
74 "1/2 * N * (N - 1) where N is atom number in group of interest",
76 "WARNING: If sq or pr specified this tool can produce large number of files! Up to two times larger than number of frames!"
78 static gmx_bool bPBC = TRUE;
79 static gmx_bool bNORM = FALSE;
80 static real binwidth = 0.2, grid = 0.05; /* bins shouldnt be smaller then smallest bond (~0.1nm) length */
81 static real start_q = 0.0, end_q = 2.0, q_step = 0.01;
82 static real mcover = -1;
83 static unsigned int seed = 0;
84 static int nthreads = -1;
86 static const char *emode[] = { NULL, "direct", "mc", NULL };
87 static const char *emethod[] = { NULL, "debye", "fft", NULL };
89 gmx_neutron_atomic_structurefactors_t *gnsf;
95 { "-bin", FALSE, etREAL, {&binwidth},
96 "[HIDDEN]Binwidth (nm)" },
97 { "-mode", FALSE, etENUM, {emode},
98 "Mode for sans spectra calculation" },
99 { "-mcover", FALSE, etREAL, {&mcover},
100 "Monte-Carlo coverage should be -1(default) or (0,1]"},
101 { "-method", FALSE, etENUM, {emethod},
102 "[HIDDEN]Method for sans spectra calculation" },
103 { "-pbc", FALSE, etBOOL, {&bPBC},
104 "Use periodic boundary conditions for computing distances" },
105 { "-grid", FALSE, etREAL, {&grid},
106 "[HIDDEN]Grid spacing (in nm) for FFTs" },
107 {"-startq", FALSE, etREAL, {&start_q},
108 "Starting q (1/nm) "},
109 {"-endq", FALSE, etREAL, {&end_q},
111 { "-qstep", FALSE, etREAL, {&q_step},
112 "Stepping in q (1/nm)"},
113 { "-seed", FALSE, etINT, {&seed},
114 "Random seed for Monte-Carlo"},
116 { "-nt", FALSE, etINT, {&nthreads},
117 "Number of threads to start"},
121 const char *fnTPX, *fnNDX, *fnTRX, *fnDAT = NULL;
123 t_topology *top = NULL;
125 gmx_rmpbc_t gpbc = NULL;
127 gmx_bool bFFT = FALSE, bDEBYE = FALSE;
128 gmx_bool bMC = FALSE;
135 char **grpname = NULL;
136 atom_id *index = NULL;
141 t_filenm *fnmdup = NULL;
142 gmx_radial_distribution_histogram_t *prframecurrent = NULL, *pr = NULL;
143 gmx_static_structurefactor_t *sqframecurrent = NULL, *sq = NULL;
146 #define NFILE asize(fnm)
149 { efTPX, "-s", NULL, ffREAD },
150 { efTRX, "-f", NULL, ffREAD },
151 { efNDX, NULL, NULL, ffOPTRD },
152 { efDAT, "-d", "nsfactor", ffOPTRD },
153 { efXVG, "-pr", "pr", ffWRITE },
154 { efXVG, "-sq", "sq", ffWRITE },
155 { efXVG, "-prframe", "prframe", ffOPTWR },
156 { efXVG, "-sqframe", "sqframe", ffOPTWR }
159 nthreads = gmx_omp_get_max_threads();
161 parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
162 NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv);
164 /* check that binwidth not smaller than smallers distance */
165 check_binwidth(binwidth);
166 check_mcover(mcover);
168 /* setting number of omp threads globaly */
169 gmx_omp_set_num_threads(nthreads);
171 /* Now try to parse opts for modes */
172 switch (emethod[0][0])
199 fprintf(stderr, "Using Monte Carlo Debye method to calculate spectrum\n");
203 fprintf(stderr, "Using direct Debye method to calculate spectrum\n");
208 gmx_fatal(FARGS, "FFT method not implemented!");
212 gmx_fatal(FARGS, "Unknown combination for mode and method!");
215 /* Try to read files */
216 fnDAT = ftp2fn(efDAT, NFILE, fnm);
217 fnTPX = ftp2fn(efTPX, NFILE, fnm);
218 fnTRX = ftp2fn(efTRX, NFILE, fnm);
220 gnsf = gmx_neutronstructurefactors_init(fnDAT);
221 fprintf(stderr, "Read %d atom names from %s with neutron scattering parameters\n\n", gnsf->nratoms, fnDAT);
227 bTPX = read_tps_conf(fnTPX, title, top, &ePBC, &x, NULL, box, TRUE);
229 printf("\nPlease select group for SANS spectra calculation:\n");
230 get_index(&(top->atoms), ftp2fn_null(efNDX, NFILE, fnm), 1, &isize, &index, grpname);
232 gsans = gmx_sans_init(top, gnsf);
234 /* Prepare reference frame */
237 gpbc = gmx_rmpbc_init(&top->idef, ePBC, top->atoms.nr, box);
238 gmx_rmpbc(gpbc, top->atoms.nr, box, x);
241 natoms = read_first_x(oenv, &status, fnTRX, &t, &x, box);
242 if (natoms != top->atoms.nr)
244 fprintf(stderr, "\nWARNING: number of atoms in tpx (%d) and trajectory (%d) do not match\n", natoms, top->atoms.nr);
251 gmx_rmpbc(gpbc, top->atoms.nr, box, x);
253 /* allocate memory for pr */
256 /* in case its first frame to read */
259 /* realy calc p(r) */
260 prframecurrent = calc_radial_distribution_histogram(gsans, x, box, index, isize, binwidth, bMC, bNORM, mcover, seed);
261 /* copy prframecurrent -> pr and summ up pr->gr[i] */
262 /* allocate and/or resize memory for pr->gr[i] and pr->r[i] */
265 /* check if we use pr->gr first time */
266 snew(pr->gr, prframecurrent->grn);
267 snew(pr->r, prframecurrent->grn);
271 /* resize pr->gr and pr->r if needed to preven overruns */
272 if (prframecurrent->grn > pr->grn)
274 srenew(pr->gr, prframecurrent->grn);
275 srenew(pr->r, prframecurrent->grn);
278 pr->grn = prframecurrent->grn;
279 pr->binwidth = prframecurrent->binwidth;
280 /* summ up gr and fill r */
281 for (i = 0; i < prframecurrent->grn; i++)
283 pr->gr[i] += prframecurrent->gr[i];
284 pr->r[i] = prframecurrent->r[i];
286 /* normalize histo */
287 normalize_probability(prframecurrent->grn, prframecurrent->gr);
288 /* convert p(r) to sq */
289 sqframecurrent = convert_histogram_to_intensity_curve(prframecurrent, start_q, end_q, q_step);
290 /* print frame data if needed */
291 if (opt2fn_null("-prframe", NFILE, fnm))
294 snew(suffix, GMX_PATH_MAX);
296 sprintf(hdr, "g(r), t = %f", t);
297 /* prepare output filename */
298 fnmdup = dup_tfn(NFILE, fnm);
299 sprintf(suffix, "-t%.2f", t);
300 add_suffix_to_output_names(fnmdup, NFILE, suffix);
301 fp = xvgropen(opt2fn_null("-prframe", NFILE, fnmdup), hdr, "Distance (nm)", "Probability", oenv);
302 for (i = 0; i < prframecurrent->grn; i++)
304 fprintf(fp, "%10.6f%10.6f\n", prframecurrent->r[i], prframecurrent->gr[i]);
306 done_filenms(NFILE, fnmdup);
312 if (opt2fn_null("-sqframe", NFILE, fnm))
315 snew(suffix, GMX_PATH_MAX);
317 sprintf(hdr, "I(q), t = %f", t);
318 /* prepare output filename */
319 fnmdup = dup_tfn(NFILE, fnm);
320 sprintf(suffix, "-t%.2f", t);
321 add_suffix_to_output_names(fnmdup, NFILE, suffix);
322 fp = xvgropen(opt2fn_null("-sqframe", NFILE, fnmdup), hdr, "q (nm^-1)", "s(q)/s(0)", oenv);
323 for (i = 0; i < sqframecurrent->qn; i++)
325 fprintf(fp, "%10.6f%10.6f\n", sqframecurrent->q[i], sqframecurrent->s[i]);
327 done_filenms(NFILE, fnmdup);
333 /* free pr structure */
334 sfree(prframecurrent->gr);
335 sfree(prframecurrent->r);
336 sfree(prframecurrent);
337 /* free sq structure */
338 sfree(sqframecurrent->q);
339 sfree(sqframecurrent->s);
340 sfree(sqframecurrent);
342 while (read_next_x(oenv, status, &t, natoms, x, box));
345 /* normalize histo */
346 normalize_probability(pr->grn, pr->gr);
347 sq = convert_histogram_to_intensity_curve(pr, start_q, end_q, q_step);
349 fp = xvgropen(opt2fn_null("-pr", NFILE, fnm), "G(r)", "Distance (nm)", "Probability", oenv);
350 for (i = 0; i < pr->grn; i++)
352 fprintf(fp, "%10.6f%10.6f\n", pr->r[i], pr->gr[i]);
357 fp = xvgropen(opt2fn_null("-sq", NFILE, fnm), "I(q)", "q (nm^-1)", "s(q)/s(0)", oenv);
358 for (i = 0; i < sq->qn; i++)
360 fprintf(fp, "%10.6f%10.6f\n", sq->q[i], sq->s[i]);
373 please_cite(stdout, "Garmay2012");