src/gromacs/gmxana/gmx_saxs.cpp

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