/*
* This file is part of the GROMACS molecular simulation package.
*
- * Copyright (c) 2010,2011,2012,2013,2014,2015,2016, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014,2015,2016,2017, 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.
* grpn - group number in index
*/
t_trxstatus *status;
- gmx_rmpbc_t gpbc = NULL;
+ gmx_rmpbc_t gpbc = nullptr;
matrix box; /* Box - 3x3 -each step*/
rvec *x0; /* List of Coord without PBC*/
int i, j, /* loop indices, checks etc*/
ax1 = 0, ax2 = 0, /* tangent directions */
framenr = 0, /* frame number in trajectory*/
slicex, slicey, slicez; /*slice # of x y z position */
- real ***Densslice = NULL; /* Density-slice in one frame*/
+ real ***Densslice = nullptr; /* Density-slice in one frame*/
real dscale; /*physical scaling factor*/
real t, x, y, z; /* time and coordinates*/
rvec bbww;
/*Initialize Densdevel and PBC-remove*/
gpbc = gmx_rmpbc_init(&top->idef, ePBC, top->atoms.nr);
- *Densdevel = NULL;
+ *Densdevel = nullptr;
do
{
/*Reset Densslice every nsttblock steps*/
/* The first conditional is for clang to understand that this branch is
* always taken the first time. */
- if (Densslice == NULL || framenr % nsttblock == 0)
+ if (Densslice == nullptr || framenr % nsttblock == 0)
{
snew(Densslice, *xslices);
for (i = 0; i < *xslices; i++)
real *sigma1, *sigma2;
double beginfit1[4];
double beginfit2[4];
- double *fit1 = NULL, *fit2 = NULL;
+ double *fit1 = nullptr, *fit2 = nullptr;
const double *avgfit1;
const double *avgfit2;
const real onehalf = 1.00/2.00;
- t_interf ***int1 = NULL, ***int2 = NULL; /*Interface matrices [t][x,y] - last index in row-major order*/
+ t_interf ***int1 = nullptr, ***int2 = nullptr; /*Interface matrices [t][x,y] - last index in row-major order*/
/*Create int1(t,xy) and int2(t,xy) arrays with correct number of interf_t elements*/
xysize = xslices*yslices;
snew(int1, tblocks);
/*Fit average density in z over whole trajectory to obtain tentative fit-parameters in fit1 and fit2*/
/*Fit 1st half of box*/
- do_lmfit(zslices, zDensavg, sigma1, binwidth, NULL, startpoint, splitpoint, oenv, FALSE, effnERF, beginfit1, 8, NULL);
+ do_lmfit(zslices, zDensavg, sigma1, binwidth, nullptr, startpoint, splitpoint, oenv, FALSE, effnERF, beginfit1, 8, nullptr);
/*Fit 2nd half of box*/
- do_lmfit(zslices, zDensavg, sigma2, binwidth, NULL, splitpoint, endpoint, oenv, FALSE, effnERF, beginfit2, 8, NULL);
+ do_lmfit(zslices, zDensavg, sigma2, binwidth, nullptr, splitpoint, endpoint, oenv, FALSE, effnERF, beginfit2, 8, nullptr);
/*Initialise the const arrays for storing the average fit parameters*/
avgfit1 = beginfit1;
fit2[k] = avgfit2[k];
}
/*Now fit and store in structures in row-major order int[n][i][j]*/
- do_lmfit(zslices, Densmap[n][i][j], sigma1, binwidth, NULL, startpoint, splitpoint, oenv, FALSE, effnERF, fit1, 0, NULL);
+ do_lmfit(zslices, Densmap[n][i][j], sigma1, binwidth, nullptr, startpoint, splitpoint, oenv, FALSE, effnERF, fit1, 0, nullptr);
int1[n][j+(yslices*i)]->Z = fit1[2];
int1[n][j+(yslices*i)]->t = fit1[3];
- do_lmfit(zslices, Densmap[n][i][j], sigma2, binwidth, NULL, splitpoint, endpoint, oenv, FALSE, effnERF, fit2, 0, NULL);
+ do_lmfit(zslices, Densmap[n][i][j], sigma2, binwidth, nullptr, splitpoint, endpoint, oenv, FALSE, effnERF, fit2, 0, nullptr);
int2[n][j+(yslices*i)]->Z = fit2[2];
int2[n][j+(yslices*i)]->t = fit2[3];
}
static gmx_bool b1d = FALSE;
static int nlevels = 100;
/*Densitymap - Densmap[t][x][y][z]*/
- real ****Densmap = NULL;
+ real ****Densmap = nullptr;
/* Surfaces surf[t][surf_x,surf_y]*/
t_interf ***surf1, ***surf2;
- static const char *meth[] = {NULL, "bisect", "functional", NULL};
+ static const char *meth[] = {nullptr, "bisect", "functional", nullptr};
int eMeth;
char **graphfiles, **rawfiles, **spectra; /* Filenames for xpm-surface maps, rawdata and powerspectra */
t_filenm fnm[] = {
- { efTPR, "-s", NULL, ffREAD }, /* this is for the topology */
- { efTRX, "-f", NULL, ffREAD }, /* and this for the trajectory */
- { efNDX, "-n", NULL, ffREAD}, /* this is to select groups */
+ { efTPR, "-s", nullptr, ffREAD }, /* this is for the topology */
+ { efTRX, "-f", nullptr, ffREAD }, /* and this for the trajectory */
+ { efNDX, "-n", nullptr, ffREAD}, /* this is to select groups */
{ efDAT, "-o", "Density4D", ffOPTWR}, /* This is for outputting the entire 4D densityfield in binary format */
- { efOUT, "-or", NULL, ffOPTWRMULT}, /* This is for writing out the entire information in the t_interf arrays */
+ { efOUT, "-or", nullptr, ffOPTWRMULT}, /* This is for writing out the entire information in the t_interf arrays */
{ efXPM, "-og", "interface", ffOPTWRMULT}, /* This is for writing out the interface meshes - one xpm-file per tblock*/
{ efOUT, "-Spect", "intfspect", ffOPTWRMULT}, /* This is for the trajectory averaged Fourier-spectra*/
};
/* This is the routine responsible for adding default options,
* calling the X/motif interface, etc. */
if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, NULL, &oenv))
+ NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff