src/gromacs/gmxana/gmx_saxs.c

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