/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2012,2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
* Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
* and including many others, as listed in the AUTHORS file in the
* top-level source directory and at http://www.gromacs.org.
#include "gromacs/utility/pleasecite.h"
#include "gromacs/utility/smalloc.h"
-int gmx_sans(int argc, char *argv[])
+int gmx_sans(int argc, char* argv[])
{
- const char *desc[] = {
+ const char* desc[] = {
"[THISMODULE] computes SANS spectra using Debye formula.",
"It currently uses topology file (since it need to assigne element for each atom).",
"[PAR]",
"Note: When using Debye direct method computational cost increases as",
"1/2 * N * (N - 1) where N is atom number in group of interest.",
"[PAR]",
- "WARNING: If sq or pr specified this tool can produce large number of files! Up to two times larger than number of frames!"
+ "WARNING: If sq or pr specified this tool can produce large number of files! Up to ",
+ "two times larger than number of frames!"
};
- static gmx_bool bPBC = TRUE;
- static gmx_bool bNORM = FALSE;
- static real binwidth = 0.2, grid = 0.05; /* bins shouldn't be smaller then smallest bond (~0.1nm) length */
- static real start_q = 0.0, end_q = 2.0, q_step = 0.01;
- static real mcover = -1;
- static unsigned int seed = 0;
- static int nthreads = -1;
+ static gmx_bool bPBC = TRUE;
+ static gmx_bool bNORM = FALSE;
+ static real binwidth = 0.2,
+ grid = 0.05; /* bins shouldn't be smaller then smallest bond (~0.1nm) length */
+ static real start_q = 0.0, end_q = 2.0, q_step = 0.01;
+ static real mcover = -1;
+ static unsigned int seed = 0;
+ static int nthreads = -1;
- static const char *emode[] = { nullptr, "direct", "mc", nullptr };
- static const char *emethod[] = { nullptr, "debye", "fft", nullptr };
+ static const char* emode[] = { nullptr, "direct", "mc", nullptr };
+ static const char* emethod[] = { nullptr, "debye", "fft", nullptr };
- gmx_neutron_atomic_structurefactors_t *gnsf;
- gmx_sans_t *gsans;
+ gmx_neutron_atomic_structurefactors_t* gnsf;
+ gmx_sans_t* gsans;
#define NPA asize(pa)
- t_pargs pa[] = {
- { "-bin", FALSE, etREAL, {&binwidth},
- "[HIDDEN]Binwidth (nm)" },
- { "-mode", FALSE, etENUM, {emode},
- "Mode for sans spectra calculation" },
- { "-mcover", FALSE, etREAL, {&mcover},
- "Monte-Carlo coverage should be -1(default) or (0,1]"},
- { "-method", FALSE, etENUM, {emethod},
- "[HIDDEN]Method for sans spectra calculation" },
- { "-pbc", FALSE, etBOOL, {&bPBC},
+ t_pargs pa[] = {
+ { "-bin", FALSE, etREAL, { &binwidth }, "[HIDDEN]Binwidth (nm)" },
+ { "-mode", FALSE, etENUM, { emode }, "Mode for sans spectra calculation" },
+ { "-mcover",
+ FALSE,
+ etREAL,
+ { &mcover },
+ "Monte-Carlo coverage should be -1(default) or (0,1]" },
+ { "-method", FALSE, etENUM, { emethod }, "[HIDDEN]Method for sans spectra calculation" },
+ { "-pbc",
+ FALSE,
+ etBOOL,
+ { &bPBC },
"Use periodic boundary conditions for computing distances" },
- { "-grid", FALSE, etREAL, {&grid},
- "[HIDDEN]Grid spacing (in nm) for FFTs" },
- {"-startq", FALSE, etREAL, {&start_q},
- "Starting q (1/nm) "},
- {"-endq", FALSE, etREAL, {&end_q},
- "Ending q (1/nm)"},
- { "-qstep", FALSE, etREAL, {&q_step},
- "Stepping in q (1/nm)"},
- { "-seed", FALSE, etINT, {&seed},
- "Random seed for Monte-Carlo"},
+ { "-grid", FALSE, etREAL, { &grid }, "[HIDDEN]Grid spacing (in nm) for FFTs" },
+ { "-startq", FALSE, etREAL, { &start_q }, "Starting q (1/nm) " },
+ { "-endq", FALSE, etREAL, { &end_q }, "Ending q (1/nm)" },
+ { "-qstep", FALSE, etREAL, { &q_step }, "Stepping in q (1/nm)" },
+ { "-seed", FALSE, etINT, { &seed }, "Random seed for Monte-Carlo" },
#if GMX_OPENMP
- { "-nt", FALSE, etINT, {&nthreads},
- "Number of threads to start"},
+ { "-nt", FALSE, etINT, { &nthreads }, "Number of threads to start" },
#endif
};
- FILE *fp;
- const char *fnTPX, *fnTRX, *fnDAT = nullptr;
- t_trxstatus *status;
- t_topology *top = nullptr;
- gmx_rmpbc_t gpbc = nullptr;
- gmx_bool bFFT = FALSE, bDEBYE = FALSE;
- gmx_bool bMC = FALSE;
- int ePBC = -1;
- matrix box;
- rvec *x;
- int natoms;
- real t;
- char **grpname = nullptr;
- int *index = nullptr;
- int isize;
- int i;
- char *hdr = nullptr;
- char *suffix = nullptr;
- gmx_radial_distribution_histogram_t *prframecurrent = nullptr, *pr = nullptr;
- gmx_static_structurefactor_t *sqframecurrent = nullptr, *sq = nullptr;
- gmx_output_env_t *oenv;
+ FILE* fp;
+ const char * fnTPX, *fnTRX, *fnDAT = nullptr;
+ t_trxstatus* status;
+ t_topology* top = nullptr;
+ gmx_rmpbc_t gpbc = nullptr;
+ gmx_bool bFFT = FALSE, bDEBYE = FALSE;
+ gmx_bool bMC = FALSE;
+ int ePBC = -1;
+ matrix box;
+ rvec* x;
+ int natoms;
+ real t;
+ char** grpname = nullptr;
+ int* index = nullptr;
+ int isize;
+ int i;
+ char* hdr = nullptr;
+ char* suffix = nullptr;
+ gmx_radial_distribution_histogram_t *prframecurrent = nullptr, *pr = nullptr;
+ gmx_static_structurefactor_t * sqframecurrent = nullptr, *sq = nullptr;
+ gmx_output_env_t* oenv;
- std::array<t_filenm, 8> filenames =
- { { { efTPR, "-s", nullptr, ffREAD },
- { efTRX, "-f", nullptr, ffREAD },
- { efNDX, nullptr, nullptr, ffOPTRD },
- { efDAT, "-d", "nsfactor", ffOPTRD },
- { efXVG, "-pr", "pr", ffWRITE },
- { efXVG, "-sq", "sq", ffWRITE },
- { efXVG, "-prframe", "prframe", ffOPTWR },
- { efXVG, "-sqframe", "sqframe", ffOPTWR } } };
- t_filenm *fnm = filenames.data();
+ std::array<t_filenm, 8> filenames = { { { efTPR, "-s", nullptr, ffREAD },
+ { efTRX, "-f", nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD },
+ { efDAT, "-d", "nsfactor", ffOPTRD },
+ { efXVG, "-pr", "pr", ffWRITE },
+ { efXVG, "-sq", "sq", ffWRITE },
+ { efXVG, "-prframe", "prframe", ffOPTWR },
+ { efXVG, "-sqframe", "sqframe", ffOPTWR } } };
+ t_filenm* fnm = filenames.data();
const auto NFILE = filenames.size();
nthreads = gmx_omp_get_max_threads();
- if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT, NFILE, fnm, asize(pa), pa,
+ asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
bDEBYE = TRUE;
switch (emode[0][0])
{
- case 'd':
- bMC = FALSE;
- break;
- case 'm':
- bMC = TRUE;
- break;
- default:
- break;
+ case 'd': bMC = FALSE; break;
+ case 'm': bMC = TRUE; break;
+ default: break;
}
break;
- case 'f':
- bFFT = TRUE;
- break;
- default:
- break;
+ case 'f': bFFT = TRUE; break;
+ default: break;
}
if (bDEBYE)
fnTRX = ftp2fn(efTRX, NFILE, fnm);
gnsf = gmx_neutronstructurefactors_init(fnDAT);
- fprintf(stderr, "Read %d atom names from %s with neutron scattering parameters\n\n", gnsf->nratoms, fnDAT);
+ fprintf(stderr, "Read %d atom names from %s with neutron scattering parameters\n\n",
+ gnsf->nratoms, fnDAT);
snew(top, 1);
snew(grpname, 1);
natoms = read_first_x(oenv, &status, fnTRX, &t, &x, box);
if (natoms != top->atoms.nr)
{
- fprintf(stderr, "\nWARNING: number of atoms in tpx (%d) and trajectory (%d) do not match\n", natoms, top->atoms.nr);
+ fprintf(stderr, "\nWARNING: number of atoms in tpx (%d) and trajectory (%d) do not match\n",
+ natoms, top->atoms.nr);
}
do
snew(pr, 1);
}
/* realy calc p(r) */
- prframecurrent = calc_radial_distribution_histogram(gsans, x, box, index, isize, binwidth, bMC, bNORM, mcover, seed);
+ prframecurrent = calc_radial_distribution_histogram(gsans, x, box, index, isize, binwidth,
+ bMC, bNORM, mcover, seed);
/* copy prframecurrent -> pr and summ up pr->gr[i] */
/* allocate and/or resize memory for pr->gr[i] and pr->r[i] */
if (pr->gr == nullptr)
for (i = 0; i < prframecurrent->grn; i++)
{
pr->gr[i] += prframecurrent->gr[i];
- pr->r[i] = prframecurrent->r[i];
+ pr->r[i] = prframecurrent->r[i];
}
/* normalize histo */
normalize_probability(prframecurrent->grn, prframecurrent->gr);
auto fnmdup = filenames;
sprintf(suffix, "-t%.2f", t);
add_suffix_to_output_names(fnmdup.data(), NFILE, suffix);
- fp = xvgropen(opt2fn_null("-prframe", NFILE, fnmdup.data()), hdr, "Distance (nm)", "Probability", oenv);
+ fp = xvgropen(opt2fn_null("-prframe", NFILE, fnmdup.data()), hdr, "Distance (nm)",
+ "Probability", oenv);
for (i = 0; i < prframecurrent->grn; i++)
{
fprintf(fp, "%10.6f%10.6f\n", prframecurrent->r[i], prframecurrent->gr[i]);
auto fnmdup = filenames;
sprintf(suffix, "-t%.2f", t);
add_suffix_to_output_names(fnmdup.data(), NFILE, suffix);
- fp = xvgropen(opt2fn_null("-sqframe", NFILE, fnmdup.data()), hdr, "q (nm^-1)", "s(q)/s(0)", oenv);
+ fp = xvgropen(opt2fn_null("-sqframe", NFILE, fnmdup.data()), hdr, "q (nm^-1)",
+ "s(q)/s(0)", oenv);
for (i = 0; i < sqframecurrent->qn; i++)
{
fprintf(fp, "%10.6f%10.6f\n", sqframecurrent->q[i], sqframecurrent->s[i]);
sfree(sqframecurrent->q);
sfree(sqframecurrent->s);
sfree(sqframecurrent);
- }
- while (read_next_x(oenv, status, &t, x, box));
+ } while (read_next_x(oenv, status, &t, x, box));
close_trx(status);
/* normalize histo */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff