src/gromacs/gmxana/gmx_saxs.cpp

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