src/gromacs/gmxana/gmx_saxs.c

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  37
  38 #ifdef HAVE_CONFIG_H
  39 #include <config.h>
  40 #endif
  41
  42 #include <math.h>
  43
  44 #include "typedefs.h"
  45 #include "macros.h"
  46 #include "gromacs/math/vec.h"
  47 #include "pbc.h"
  48 #include "copyrite.h"
  49 #include "gromacs/utility/futil.h"
  50 #include "gromacs/commandline/pargs.h"
  51 #include "gromacs/fileio/tpxio.h"
  52 #include "index.h"
  53 #include "gromacs/utility/smalloc.h"
  54 #include "calcgrid.h"
  55 #include "nrnb.h"
  56 #include "coulomb.h"
  57 #include "gstat.h"
  58 #include "gromacs/fileio/matio.h"
  59 #include "gmx_ana.h"
  60 #include "names.h"
  61 #include "sfactor.h"
  62
  63 int gmx_saxs(int argc, char *argv[])
  64 {
  65     const char  *desc[] = {
  66         "[THISMODULE] calculates SAXS structure factors for given index",
  67         "groups based on Cromer's method.",
  68         "Both topology and trajectory files are required."
  69     };
  70
  71     static real  start_q = 0.0, end_q = 60.0, energy = 12.0;
  72     static int   ngroups = 1;
  73
  74     t_pargs      pa[] = {
  75         { "-ng",       FALSE, etINT, {&ngroups},
  76           "Number of groups to compute SAXS" },
  77         {"-startq", FALSE, etREAL, {&start_q},
  78          "Starting q (1/nm) "},
  79         {"-endq", FALSE, etREAL, {&end_q},
  80          "Ending q (1/nm)"},
  81         {"-energy", FALSE, etREAL, {&energy},
  82          "Energy of the incoming X-ray (keV) "}
  83     };
  84 #define NPA asize(pa)
  85     const char  *fnTPS, *fnTRX, *fnNDX, *fnDAT = NULL;
  86     output_env_t oenv;
  87
  88     t_filenm     fnm[] = {
  89         { efTRX, "-f",  NULL,      ffREAD },
  90         { efTPS, NULL,  NULL,      ffREAD },
  91         { efNDX, NULL,  NULL,      ffOPTRD },
  92         { efDAT, "-d",  "sfactor", ffOPTRD },
  93         { efXVG, "-sq", "sq",      ffWRITE },
  94     };
  95 #define NFILE asize(fnm)
  96     if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
  97                            NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
  98     {
  99         return 0;
 100     }
 101
 102     fnTPS = ftp2fn(efTPS, NFILE, fnm);
 103     fnTRX = ftp2fn(efTRX, NFILE, fnm);
 104     fnDAT = ftp2fn(efDAT, NFILE, fnm);
 105     fnNDX = ftp2fn_null(efNDX, NFILE, fnm);
 106
 107     do_scattering_intensity(fnTPS, fnNDX, opt2fn("-sq", NFILE, fnm),
 108                             fnTRX, fnDAT,
 109                             start_q, end_q, energy, ngroups, oenv);
 110
 111     please_cite(stdout, "Cromer1968a");
 112
 113     return 0;
 114 }