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44 #include "gromacs/legacyheaders/macros.h"
45 #include "gromacs/legacyheaders/copyrite.h"
49 #include "gromacs/commandline/pargs.h"
50 #include "gromacs/utility/smalloc.h"
52 int gmx_saxs(int argc, char *argv[])
54 const char *desc[] = {
55 "[THISMODULE] calculates SAXS structure factors for given index",
56 "groups based on Cromer's method.",
57 "Both topology and trajectory files are required."
60 static real start_q = 0.0, end_q = 60.0, energy = 12.0;
61 static int ngroups = 1;
64 { "-ng", FALSE, etINT, {&ngroups},
65 "Number of groups to compute SAXS" },
66 {"-startq", FALSE, etREAL, {&start_q},
67 "Starting q (1/nm) "},
68 {"-endq", FALSE, etREAL, {&end_q},
70 {"-energy", FALSE, etREAL, {&energy},
71 "Energy of the incoming X-ray (keV) "}
74 const char *fnTPS, *fnTRX, *fnNDX, *fnDAT = NULL;
78 { efTRX, "-f", NULL, ffREAD },
79 { efTPS, NULL, NULL, ffREAD },
80 { efNDX, NULL, NULL, ffOPTRD },
81 { efDAT, "-d", "sfactor", ffOPTRD },
82 { efXVG, "-sq", "sq", ffWRITE },
84 #define NFILE asize(fnm)
85 if (!parse_common_args(&argc, argv, PCA_CAN_TIME,
86 NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
91 fnTPS = ftp2fn(efTPS, NFILE, fnm);
92 fnTRX = ftp2fn(efTRX, NFILE, fnm);
93 fnDAT = ftp2fn(efDAT, NFILE, fnm);
94 fnNDX = ftp2fn_null(efNDX, NFILE, fnm);
96 do_scattering_intensity(fnTPS, fnNDX, opt2fn("-sq", NFILE, fnm),
98 start_q, end_q, energy, ngroups, oenv);
100 please_cite(stdout, "Cromer1968a");