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51 #include "gromacs/fileio/futil.h"
52 #include "gromacs/commandline/pargs.h"
53 #include "gromacs/fileio/tpxio.h"
56 #include "gromacs/utility/smalloc.h"
61 #include "gromacs/fileio/matio.h"
66 int gmx_saxs(int argc, char *argv[])
68 const char *desc[] = {
69 "[THISMODULE] calculates SAXS structure factors for given index",
70 "groups based on Cromer's method.",
71 "Both topology and trajectory files are required."
74 static real start_q = 0.0, end_q = 60.0, energy = 12.0;
75 static int ngroups = 1;
78 { "-ng", FALSE, etINT, {&ngroups},
79 "Number of groups to compute SAXS" },
80 {"-startq", FALSE, etREAL, {&start_q},
81 "Starting q (1/nm) "},
82 {"-endq", FALSE, etREAL, {&end_q},
84 {"-energy", FALSE, etREAL, {&energy},
85 "Energy of the incoming X-ray (keV) "}
88 const char *fnTPS, *fnTRX, *fnNDX, *fnDAT = NULL;
92 { efTRX, "-f", NULL, ffREAD },
93 { efTPS, NULL, NULL, ffREAD },
94 { efNDX, NULL, NULL, ffOPTRD },
95 { efDAT, "-d", "sfactor", ffOPTRD },
96 { efXVG, "-sq", "sq", ffWRITE },
98 #define NFILE asize(fnm)
99 if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_BE_NICE,
100 NFILE, fnm, NPA, pa, asize(desc), desc, 0, NULL, &oenv))
105 fnTPS = ftp2fn(efTPS, NFILE, fnm);
106 fnTRX = ftp2fn(efTRX, NFILE, fnm);
107 fnDAT = ftp2fn(efDAT, NFILE, fnm);
108 fnNDX = ftp2fn_null(efNDX, NFILE, fnm);
110 do_scattering_intensity(fnTPS, fnNDX, opt2fn("-sq", NFILE, fnm),
112 start_q, end_q, energy, ngroups, oenv);
114 please_cite(stdout, "Cromer1968a");