*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018, by the GROMACS development team, led by
+ * Copyright (c) 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/smalloc.h"
#include "gromacs/utility/stringutil.h"
-static void low_print_data(FILE *fp, real time, rvec x[], int n, const int *index,
- const gmx_bool bDim[], const char *sffmt)
+static void
+low_print_data(FILE* fp, real time, rvec x[], int n, const int* index, const gmx_bool bDim[], const char* sffmt)
{
int i, ii, d;
fprintf(fp, "\n");
}
-static void average_data(rvec x[], rvec xav[], const real *mass,
- int ngrps, const int isize[], int **index)
+static void average_data(rvec x[], rvec xav[], const real* mass, int ngrps, const int isize[], int** index)
{
int g, i, ind, d;
real m;
{
for (d = 0; d < DIM; d++)
{
- xav[g][d] = sum[d]/mtot;
+ xav[g][d] = sum[d] / mtot;
}
}
else
}
}
-static void print_data(FILE *fp, real time, rvec x[], real *mass, gmx_bool bCom,
- int ngrps, int isize[], int **index, gmx_bool bDim[],
- const char *sffmt)
+static void print_data(FILE* fp,
+ real time,
+ rvec x[],
+ real* mass,
+ gmx_bool bCom,
+ int ngrps,
+ int isize[],
+ int** index,
+ gmx_bool bDim[],
+ const char* sffmt)
{
- static rvec *xav = nullptr;
+ static rvec* xav = nullptr;
if (bCom)
{
}
}
-static void write_trx_x(t_trxstatus *status, const t_trxframe *fr, real *mass, gmx_bool bCom,
- int ngrps, int isize[], int **index)
+static void write_trx_x(t_trxstatus* status,
+ const t_trxframe* fr,
+ real* mass,
+ gmx_bool bCom,
+ int ngrps,
+ int isize[],
+ int** index)
{
- static rvec *xav = nullptr;
- static t_atoms *atoms = nullptr;
+ static rvec* xav = nullptr;
+ static t_atoms* atoms = nullptr;
t_trxframe fr_av;
int i;
}
}
-static void make_legend(FILE *fp, int ngrps, int isize, int index[],
- char **name, gmx_bool bCom, gmx_bool bMol, const gmx_bool bDim[],
- const gmx_output_env_t *oenv)
+static void make_legend(FILE* fp,
+ int ngrps,
+ int isize,
+ int index[],
+ char** name,
+ gmx_bool bCom,
+ gmx_bool bMol,
+ const gmx_bool bDim[],
+ const gmx_output_env_t* oenv)
{
- char **leg;
- const char *dimtxt[] = { " X", " Y", " Z", "" };
+ char** leg;
+ const char* dimtxt[] = { " X", " Y", " Z", "" };
int n, i, j, d;
if (bCom)
n = isize;
}
- snew(leg, 4*n);
+ snew(leg, 4 * n);
j = 0;
for (i = 0; i < n; i++)
{
snew(leg[j], STRLEN);
if (bMol)
{
- sprintf(leg[j], "mol %d%s", index[i]+1, dimtxt[d]);
+ sprintf(leg[j], "mol %d%s", index[i] + 1, dimtxt[d]);
}
else if (bCom)
{
}
else
{
- sprintf(leg[j], "atom %d%s", index[i]+1, dimtxt[d]);
+ sprintf(leg[j], "atom %d%s", index[i] + 1, dimtxt[d]);
}
j++;
}
static real ekrot(rvec x[], rvec v[], const real mass[], int isize, const int index[])
{
- real TCM[5][5], L[5][5];
- double tm, m0, lxx, lxy, lxz, lyy, lyz, lzz, ekrot;
- rvec a0, ocm;
- dvec dx, b0;
- dvec xcm, vcm, acm;
- int i, j, m, n;
+ real TCM[5][5], L[5][5];
+ double tm, m0, lxx, lxy, lxz, lyy, lyz, lzz, ekrot;
+ rvec a0, ocm;
+ dvec dx, b0;
+ dvec xcm, vcm, acm;
+ int i, j, m, n;
clear_dvec(xcm);
clear_dvec(vcm);
tm = 0.0;
for (i = 0; i < isize; i++)
{
- j = index[i];
- m0 = mass[j];
+ j = index[i];
+ m0 = mass[j];
tm += m0;
cprod(x[j], v[j], a0);
for (m = 0; (m < DIM); m++)
{
- xcm[m] += m0*x[j][m]; /* c.o.m. position */
- vcm[m] += m0*v[j][m]; /* c.o.m. velocity */
- acm[m] += m0*a0[m]; /* rotational velocity around c.o.m. */
+ xcm[m] += m0 * x[j][m]; /* c.o.m. position */
+ vcm[m] += m0 * v[j][m]; /* c.o.m. velocity */
+ acm[m] += m0 * a0[m]; /* rotational velocity around c.o.m. */
}
}
dcprod(xcm, vcm, b0);
{
xcm[m] /= tm;
vcm[m] /= tm;
- acm[m] -= b0[m]/tm;
+ acm[m] -= b0[m] / tm;
}
lxx = lxy = lxz = lyy = lyz = lzz = 0.0;
{
dx[m] = x[j][m] - xcm[m];
}
- lxx += dx[XX]*dx[XX]*m0;
- lxy += dx[XX]*dx[YY]*m0;
- lxz += dx[XX]*dx[ZZ]*m0;
- lyy += dx[YY]*dx[YY]*m0;
- lyz += dx[YY]*dx[ZZ]*m0;
- lzz += dx[ZZ]*dx[ZZ]*m0;
+ lxx += dx[XX] * dx[XX] * m0;
+ lxy += dx[XX] * dx[YY] * m0;
+ lxz += dx[XX] * dx[ZZ] * m0;
+ lyy += dx[YY] * dx[YY] * m0;
+ lyz += dx[YY] * dx[ZZ] * m0;
+ lzz += dx[ZZ] * dx[ZZ] * m0;
}
- L[XX][XX] = lyy + lzz;
+ L[XX][XX] = lyy + lzz;
L[YY][XX] = -lxy;
L[ZZ][XX] = -lxz;
L[XX][YY] = -lxy;
- L[YY][YY] = lxx + lzz;
+ L[YY][YY] = lxx + lzz;
L[ZZ][YY] = -lyz;
L[XX][ZZ] = -lxz;
L[YY][ZZ] = -lyz;
- L[ZZ][ZZ] = lxx + lyy;
+ L[ZZ][ZZ] = lxx + lyy;
m_inv_gen(&L[0][0], DIM, &TCM[0][0]);
{
for (n = 0; n < DIM; n++)
{
- ocm[m] += TCM[m][n]*acm[n];
+ ocm[m] += TCM[m][n] * acm[n];
}
- ekrot += 0.5*ocm[m]*acm[m];
+ ekrot += 0.5 * ocm[m] * acm[m];
}
return ekrot;
j = index[i];
for (d = 0; d < DIM; d++)
{
- mvcom[d] += mass[j]*v[j][d];
+ mvcom[d] += mass[j] * v[j][d];
}
mtot += mass[j];
}
- return dnorm2(mvcom)/(mtot*2);
+ return dnorm2(mvcom) / (mtot * 2);
}
static real temp(rvec v[], const real mass[], int isize, const int index[])
ekin2 = 0;
for (i = 0; i < isize; i++)
{
- j = index[i];
- ekin2 += mass[j]*norm2(v[j]);
+ j = index[i];
+ ekin2 += mass[j] * norm2(v[j]);
}
- return ekin2/(3*isize*BOLTZ);
+ return ekin2 / (3 * isize * BOLTZ);
}
static void remove_jump(matrix box, int natoms, rvec xp[], rvec x[])
for (d = 0; d < DIM; d++)
{
- hbox[d] = 0.5*box[d][d];
+ hbox[d] = 0.5 * box[d][d];
}
for (i = 0; i < natoms; i++)
{
- for (m = DIM-1; m >= 0; m--)
+ for (m = DIM - 1; m >= 0; m--)
{
- while (x[i][m]-xp[i][m] <= -hbox[m])
+ while (x[i][m] - xp[i][m] <= -hbox[m])
{
for (d = 0; d <= m; d++)
{
x[i][d] += box[m][d];
}
}
- while (x[i][m]-xp[i][m] > hbox[m])
+ while (x[i][m] - xp[i][m] > hbox[m])
{
for (d = 0; d <= m; d++)
{
}
}
-static void write_pdb_bfac(const char *fname, const char *xname,
- const char *title, t_atoms *atoms, int ePBC, matrix box,
- int isize, int *index, int nfr_x, rvec *x,
- int nfr_v, rvec *sum,
- const gmx_bool bDim[], real scale_factor,
- const gmx_output_env_t *oenv)
+static void write_pdb_bfac(const char* fname,
+ const char* xname,
+ const char* title,
+ t_atoms* atoms,
+ int ePBC,
+ matrix box,
+ int isize,
+ int* index,
+ int nfr_x,
+ rvec* x,
+ int nfr_v,
+ rvec* sum,
+ const gmx_bool bDim[],
+ real scale_factor,
+ const gmx_output_env_t* oenv)
{
- FILE *fp;
- real max, len2, scale;
- int maxi;
- int i, m, onedim;
+ FILE* fp;
+ real max, len2, scale;
+ int maxi;
+ int i, m, onedim;
if ((nfr_x == 0) || (nfr_v == 0))
{
- fprintf(stderr, "No frames found for %s, will not write %s\n",
- title, fname);
+ fprintf(stderr, "No frames found for %s, will not write %s\n", title, fname);
}
else
{
onedim = -1;
}
}
- scale = 1.0/nfr_v;
+ scale = 1.0 / nfr_v;
for (i = 0; i < isize; i++)
{
svmul(scale, sum[index[i]], sum[index[i]]);
fp = xvgropen(xname, title, "Atom", "Spatial component", oenv);
for (i = 0; i < isize; i++)
{
- fprintf(fp, "%-5d %10.3f %10.3f %10.3f\n", 1+i,
- sum[index[i]][XX], sum[index[i]][YY], sum[index[i]][ZZ]);
+ fprintf(fp, "%-5d %10.3f %10.3f %10.3f\n", 1 + i, sum[index[i]][XX],
+ sum[index[i]][YY], sum[index[i]][ZZ]);
}
xvgrclose(fp);
max = 0;
}
else
{
- scale = 10.0/std::sqrt(max);
+ scale = 10.0 / std::sqrt(max);
}
}
- printf("Maximum %s is %g on atom %d %s, res. %s %d\n",
- title, std::sqrt(max), maxi+1, *(atoms->atomname[maxi]),
- *(atoms->resinfo[atoms->atom[maxi].resind].name),
+ printf("Maximum %s is %g on atom %d %s, res. %s %d\n", title, std::sqrt(max), maxi + 1,
+ *(atoms->atomname[maxi]), *(atoms->resinfo[atoms->atom[maxi].resind].name),
atoms->resinfo[atoms->atom[maxi].resind].nr);
if (atoms->pdbinfo == nullptr)
len2 += gmx::square(sum[index[i]][m]);
}
}
- atoms->pdbinfo[index[i]].bfac = std::sqrt(len2)*scale;
+ atoms->pdbinfo[index[i]].bfac = std::sqrt(len2) * scale;
}
}
else
{
for (i = 0; i < isize; i++)
{
- atoms->pdbinfo[index[i]].bfac = sum[index[i]][onedim]*scale;
+ atoms->pdbinfo[index[i]].bfac = sum[index[i]][onedim] * scale;
}
}
write_sto_conf_indexed(fname, title, atoms, x, nullptr, ePBC, box, isize, index);
}
}
-static void update_histo(int gnx, const int index[], rvec v[],
- int *nhisto, int **histo, real binwidth)
+static void update_histo(int gnx, const int index[], rvec v[], int* nhisto, int** histo, real binwidth)
{
int i, m, in, nnn;
real vn, vnmax;
vn = norm(v[index[i]]);
vnmax = std::max(vn, vnmax);
}
- vnmax *= 2;
- *nhisto = static_cast<int>(1+(vnmax/binwidth));
+ vnmax *= 2;
+ *nhisto = static_cast<int>(1 + (vnmax / binwidth));
snew(*histo, *nhisto);
}
for (i = 0; (i < gnx); i++)
{
vn = norm(v[index[i]]);
- in = static_cast<int>(vn/binwidth);
+ in = static_cast<int>(vn / binwidth);
if (in >= *nhisto)
{
- nnn = in+100;
+ nnn = in + 100;
fprintf(stderr, "Extending histogram from %d to %d\n", *nhisto, nnn);
srenew(*histo, nnn);
}
}
-static void print_histo(const char *fn, int nhisto, int histo[], real binwidth,
- const gmx_output_env_t *oenv)
+static void print_histo(const char* fn, int nhisto, int histo[], real binwidth, const gmx_output_env_t* oenv)
{
- FILE *fp;
+ FILE* fp;
int i;
- fp = xvgropen(fn, "Velocity distribution", "V (nm/ps)", "arbitrary units",
- oenv);
+ fp = xvgropen(fn, "Velocity distribution", "V (nm/ps)", "arbitrary units", oenv);
for (i = 0; (i < nhisto); i++)
{
- fprintf(fp, "%10.3e %10d\n", i*binwidth, histo[i]);
+ fprintf(fp, "%10.3e %10d\n", i * binwidth, histo[i]);
}
xvgrclose(fp);
}
-int gmx_traj(int argc, char *argv[])
+int gmx_traj(int argc, char* argv[])
{
- const char *desc[] = {
+ const char* desc[] = {
"[THISMODULE] plots coordinates, velocities, forces and/or the box.",
"With [TT]-com[tt] the coordinates, velocities and forces are",
"calculated for the center of mass of each group.",
"",
"See [gmx-trajectory] for plotting similar data for selections."
};
- static gmx_bool bMol = FALSE, bCom = FALSE, bPBC = TRUE, bNoJump = FALSE;
- static gmx_bool bX = TRUE, bY = TRUE, bZ = TRUE, bNorm = FALSE, bFP = FALSE;
- static int ngroups = 1;
- static real ctime = -1, scale = 0, binwidth = 1;
- t_pargs pa[] = {
- { "-com", FALSE, etBOOL, {&bCom},
- "Plot data for the com of each group" },
- { "-pbc", FALSE, etBOOL, {&bPBC},
- "Make molecules whole for COM" },
- { "-mol", FALSE, etBOOL, {&bMol},
+ static gmx_bool bMol = FALSE, bCom = FALSE, bPBC = TRUE, bNoJump = FALSE;
+ static gmx_bool bX = TRUE, bY = TRUE, bZ = TRUE, bNorm = FALSE, bFP = FALSE;
+ static int ngroups = 1;
+ static real ctime = -1, scale = 0, binwidth = 1;
+ t_pargs pa[] = {
+ { "-com", FALSE, etBOOL, { &bCom }, "Plot data for the com of each group" },
+ { "-pbc", FALSE, etBOOL, { &bPBC }, "Make molecules whole for COM" },
+ { "-mol",
+ FALSE,
+ etBOOL,
+ { &bMol },
"Index contains molecule numbers instead of atom numbers" },
- { "-nojump", FALSE, etBOOL, {&bNoJump},
- "Remove jumps of atoms across the box" },
- { "-x", FALSE, etBOOL, {&bX},
- "Plot X-component" },
- { "-y", FALSE, etBOOL, {&bY},
- "Plot Y-component" },
- { "-z", FALSE, etBOOL, {&bZ},
- "Plot Z-component" },
- { "-ng", FALSE, etINT, {&ngroups},
- "Number of groups to consider" },
- { "-len", FALSE, etBOOL, {&bNorm},
- "Plot vector length" },
- { "-fp", FALSE, etBOOL, {&bFP},
- "Full precision output" },
- { "-bin", FALSE, etREAL, {&binwidth},
- "Binwidth for velocity histogram (nm/ps)" },
- { "-ctime", FALSE, etREAL, {&ctime},
+ { "-nojump", FALSE, etBOOL, { &bNoJump }, "Remove jumps of atoms across the box" },
+ { "-x", FALSE, etBOOL, { &bX }, "Plot X-component" },
+ { "-y", FALSE, etBOOL, { &bY }, "Plot Y-component" },
+ { "-z", FALSE, etBOOL, { &bZ }, "Plot Z-component" },
+ { "-ng", FALSE, etINT, { &ngroups }, "Number of groups to consider" },
+ { "-len", FALSE, etBOOL, { &bNorm }, "Plot vector length" },
+ { "-fp", FALSE, etBOOL, { &bFP }, "Full precision output" },
+ { "-bin", FALSE, etREAL, { &binwidth }, "Binwidth for velocity histogram (nm/ps)" },
+ { "-ctime",
+ FALSE,
+ etREAL,
+ { &ctime },
"Use frame at this time for x in [TT]-cv[tt] and [TT]-cf[tt] instead of the average x" },
- { "-scale", FALSE, etREAL, {&scale},
+ { "-scale",
+ FALSE,
+ etREAL,
+ { &scale },
"Scale factor for [REF].pdb[ref] output, 0 is autoscale" }
};
- FILE *outx = nullptr, *outv = nullptr, *outf = nullptr, *outb = nullptr, *outt = nullptr;
- FILE *outekt = nullptr, *outekr = nullptr;
- t_topology top;
- int ePBC;
- real *mass, time;
- const char *indexfn;
- t_trxframe fr;
- int flags, nvhisto = 0, *vhisto = nullptr;
- rvec *xtop, *xp = nullptr;
- rvec *sumx = nullptr, *sumv = nullptr, *sumf = nullptr;
- matrix topbox;
- t_trxstatus *status;
- t_trxstatus *status_out = nullptr;
- gmx_rmpbc_t gpbc = nullptr;
- int i, j;
- int nr_xfr, nr_vfr, nr_ffr;
- char **grpname;
- int *isize0, *isize;
- int **index0, **index;
- int *atndx;
- t_block *mols;
- gmx_bool bTop, bOX, bOXT, bOV, bOF, bOB, bOT, bEKT, bEKR, bCV, bCF;
- gmx_bool bDim[4], bDum[4], bVD;
- char sffmt[STRLEN];
- const char *box_leg[6] = { "XX", "YY", "ZZ", "YX", "ZX", "ZY" };
- gmx_output_env_t *oenv;
-
- t_filenm fnm[] = {
- { efTRX, "-f", nullptr, ffREAD },
- { efTPS, nullptr, nullptr, ffREAD },
- { efNDX, nullptr, nullptr, ffOPTRD },
- { efXVG, "-ox", "coord", ffOPTWR },
- { efTRX, "-oxt", "coord", ffOPTWR },
- { efXVG, "-ov", "veloc", ffOPTWR },
- { efXVG, "-of", "force", ffOPTWR },
- { efXVG, "-ob", "box", ffOPTWR },
- { efXVG, "-ot", "temp", ffOPTWR },
- { efXVG, "-ekt", "ektrans", ffOPTWR },
- { efXVG, "-ekr", "ekrot", ffOPTWR },
- { efXVG, "-vd", "veldist", ffOPTWR },
- { efPDB, "-cv", "veloc", ffOPTWR },
- { efPDB, "-cf", "force", ffOPTWR },
- { efXVG, "-av", "all_veloc", ffOPTWR },
- { efXVG, "-af", "all_force", ffOPTWR }
+ FILE * outx = nullptr, *outv = nullptr, *outf = nullptr, *outb = nullptr, *outt = nullptr;
+ FILE * outekt = nullptr, *outekr = nullptr;
+ t_topology top;
+ int ePBC;
+ real * mass, time;
+ const char* indexfn;
+ t_trxframe fr;
+ int flags, nvhisto = 0, *vhisto = nullptr;
+ rvec * xtop, *xp = nullptr;
+ rvec * sumx = nullptr, *sumv = nullptr, *sumf = nullptr;
+ matrix topbox;
+ t_trxstatus* status;
+ t_trxstatus* status_out = nullptr;
+ gmx_rmpbc_t gpbc = nullptr;
+ int i, j;
+ int nr_xfr, nr_vfr, nr_ffr;
+ char** grpname;
+ int * isize0, *isize;
+ int ** index0, **index;
+ int* atndx;
+ t_block* mols;
+ gmx_bool bTop, bOX, bOXT, bOV, bOF, bOB, bOT, bEKT, bEKR, bCV, bCF;
+ gmx_bool bDim[4], bDum[4], bVD;
+ char sffmt[STRLEN];
+ const char* box_leg[6] = { "XX", "YY", "ZZ", "YX", "ZX", "ZY" };
+ gmx_output_env_t* oenv;
+
+ t_filenm fnm[] = {
+ { efTRX, "-f", nullptr, ffREAD }, { efTPS, nullptr, nullptr, ffREAD },
+ { efNDX, nullptr, nullptr, ffOPTRD }, { efXVG, "-ox", "coord", ffOPTWR },
+ { efTRX, "-oxt", "coord", ffOPTWR }, { efXVG, "-ov", "veloc", ffOPTWR },
+ { efXVG, "-of", "force", ffOPTWR }, { efXVG, "-ob", "box", ffOPTWR },
+ { efXVG, "-ot", "temp", ffOPTWR }, { efXVG, "-ekt", "ektrans", ffOPTWR },
+ { efXVG, "-ekr", "ekrot", ffOPTWR }, { efXVG, "-vd", "veldist", ffOPTWR },
+ { efPDB, "-cv", "veloc", ffOPTWR }, { efPDB, "-cf", "force", ffOPTWR },
+ { efXVG, "-av", "all_veloc", ffOPTWR }, { efXVG, "-af", "all_force", ffOPTWR }
};
#define NFILE asize(fnm)
- if (!parse_common_args(&argc, argv,
- PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
- NFILE, fnm, asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
+ if (!parse_common_args(&argc, argv, PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW, NFILE, fnm,
+ asize(pa), pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
if (bMol)
{
- fprintf(stderr, "Interpreting indexfile entries as molecules.\n"
+ fprintf(stderr,
+ "Interpreting indexfile entries as molecules.\n"
"Using center of mass.\n");
}
}
std::string sffmt6 = gmx::formatString("%s%s%s%s%s%s", sffmt, sffmt, sffmt, sffmt, sffmt, sffmt);
- bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC,
- &xtop, nullptr, topbox,
+ bTop = read_tps_conf(ftp2fn(efTPS, NFILE, fnm), &top, &ePBC, &xtop, nullptr, topbox,
bCom && (bOX || bOXT || bOV || bOT || bEKT || bEKR));
sfree(xtop);
if ((bMol || bCV || bCF) && !bTop)
{
if (index0[0][i] < 0 || index0[0][i] >= mols->nr)
{
- gmx_fatal(FARGS, "Molecule index (%d) is out of range (%d-%d)",
- index0[0][i]+1, 1, mols->nr);
+ gmx_fatal(FARGS, "Molecule index (%d) is out of range (%d-%d)", index0[0][i] + 1, 1,
+ mols->nr);
}
- isize[i] = atndx[index0[0][i]+1] - atndx[index0[0][i]];
+ isize[i] = atndx[index0[0][i] + 1] - atndx[index0[0][i]];
snew(index[i], isize[i]);
for (j = 0; j < isize[i]; j++)
{
if (bOX)
{
flags = flags | TRX_READ_X;
- outx = xvgropen(opt2fn("-ox", NFILE, fnm),
- bCom ? "Center of mass" : "Coordinate",
- label, "Coordinate (nm)", oenv);
+ outx = xvgropen(opt2fn("-ox", NFILE, fnm), bCom ? "Center of mass" : "Coordinate", label,
+ "Coordinate (nm)", oenv);
make_legend(outx, ngroups, isize0[0], index0[0], grpname, bCom, bMol, bDim, oenv);
}
if (bOXT)
if (bOV)
{
flags = flags | TRX_READ_V;
- outv = xvgropen(opt2fn("-ov", NFILE, fnm),
- bCom ? "Center of mass velocity" : "Velocity",
- label, "Velocity (nm/ps)", oenv);
+ outv = xvgropen(opt2fn("-ov", NFILE, fnm), bCom ? "Center of mass velocity" : "Velocity",
+ label, "Velocity (nm/ps)", oenv);
make_legend(outv, ngroups, isize0[0], index0[0], grpname, bCom, bMol, bDim, oenv);
}
if (bOF)
{
flags = flags | TRX_READ_F;
- outf = xvgropen(opt2fn("-of", NFILE, fnm), "Force",
- label, "Force (kJ mol\\S-1\\N nm\\S-1\\N)",
- oenv);
+ outf = xvgropen(opt2fn("-of", NFILE, fnm), "Force", label,
+ "Force (kJ mol\\S-1\\N nm\\S-1\\N)", oenv);
make_legend(outf, ngroups, isize0[0], index0[0], grpname, bCom, bMol, bDim, oenv);
}
if (bOB)
{
- outb = xvgropen(opt2fn("-ob", NFILE, fnm), "Box vector elements",
- label, "(nm)", oenv);
+ outb = xvgropen(opt2fn("-ob", NFILE, fnm), "Box vector elements", label, "(nm)", oenv);
xvgr_legend(outb, 6, box_leg, oenv);
}
bDum[ZZ] = FALSE;
bDum[DIM] = TRUE;
flags = flags | TRX_READ_V;
- outt = xvgropen(opt2fn("-ot", NFILE, fnm), "Temperature",
- label, "(K)", oenv);
+ outt = xvgropen(opt2fn("-ot", NFILE, fnm), "Temperature", label, "(K)", oenv);
make_legend(outt, ngroups, isize[0], index[0], grpname, bCom, bMol, bDum, oenv);
}
if (bEKT)
bDum[ZZ] = FALSE;
bDum[DIM] = TRUE;
flags = flags | TRX_READ_V;
- outekt = xvgropen(opt2fn("-ekt", NFILE, fnm), "Center of mass translation",
- label, "Energy (kJ mol\\S-1\\N)", oenv);
+ outekt = xvgropen(opt2fn("-ekt", NFILE, fnm), "Center of mass translation", label,
+ "Energy (kJ mol\\S-1\\N)", oenv);
make_legend(outekt, ngroups, isize[0], index[0], grpname, bCom, bMol, bDum, oenv);
}
if (bEKR)
bDum[ZZ] = FALSE;
bDum[DIM] = TRUE;
flags = flags | TRX_READ_X | TRX_READ_V;
- outekr = xvgropen(opt2fn("-ekr", NFILE, fnm), "Center of mass rotation",
- label, "Energy (kJ mol\\S-1\\N)", oenv);
+ outekr = xvgropen(opt2fn("-ekr", NFILE, fnm), "Center of mass rotation", label,
+ "Energy (kJ mol\\S-1\\N)", oenv);
make_legend(outekr, ngroups, isize[0], index[0], grpname, bCom, bMol, bDum, oenv);
}
if (bVD)
if ((bOV || bOF) && fn2ftp(ftp2fn(efTRX, NFILE, fnm)) == efXTC)
{
- gmx_fatal(FARGS, "Cannot extract velocities or forces since your input XTC file does not contain them.");
+ gmx_fatal(FARGS,
+ "Cannot extract velocities or forces since your input XTC file does not contain "
+ "them.");
}
if (bCV || bCF)
if (bOB && fr.bBox)
{
fprintf(outb, "\t%g", fr.time);
- fprintf(outb, sffmt6.c_str(),
- fr.box[XX][XX], fr.box[YY][YY], fr.box[ZZ][ZZ],
+ fprintf(outb, sffmt6.c_str(), fr.box[XX][XX], fr.box[YY][YY], fr.box[ZZ][ZZ],
fr.box[YY][XX], fr.box[ZZ][XX], fr.box[ZZ][YY]);
fprintf(outb, "\n");
}
}
fprintf(outekr, "\n");
}
- if ((bCV || bCF) && fr.bX &&
- (ctime < 0 || (fr.time >= ctime*0.999999 &&
- fr.time <= ctime*1.000001)))
+ if ((bCV || bCF) && fr.bX
+ && (ctime < 0 || (fr.time >= ctime * 0.999999 && fr.time <= ctime * 1.000001)))
{
for (i = 0; i < fr.natoms; i++)
{
nr_ffr++;
}
- }
- while (read_next_frame(oenv, status, &fr));
+ } while (read_next_frame(oenv, status, &fr));
if (gpbc != nullptr)
{
{
if (ePBC != epbcNONE && !bNoJump)
{
- fprintf(stderr, "\nWARNING: More than one frame was used for option -cv or -cf\n"
- "If atoms jump across the box you should use the -nojump or -ctime option\n\n");
+ fprintf(stderr,
+ "\nWARNING: More than one frame was used for option -cv or -cf\n"
+ "If atoms jump across the box you should use the -nojump or -ctime "
+ "option\n\n");
}
for (i = 0; i < isize[0]; i++)
{
- svmul(1.0/nr_xfr, sumx[index[0][i]], sumx[index[0][i]]);
+ svmul(1.0 / nr_xfr, sumx[index[0][i]], sumx[index[0][i]]);
}
}
else if (nr_xfr == 0)
}
if (bCV)
{
- write_pdb_bfac(opt2fn("-cv", NFILE, fnm),
- opt2fn("-av", NFILE, fnm), "average velocity", &(top.atoms),
- ePBC, topbox, isize[0], index[0], nr_xfr, sumx,
- nr_vfr, sumv, bDim, scale, oenv);
+ write_pdb_bfac(opt2fn("-cv", NFILE, fnm), opt2fn("-av", NFILE, fnm), "average velocity",
+ &(top.atoms), ePBC, topbox, isize[0], index[0], nr_xfr, sumx, nr_vfr, sumv,
+ bDim, scale, oenv);
}
if (bCF)
{
- write_pdb_bfac(opt2fn("-cf", NFILE, fnm),
- opt2fn("-af", NFILE, fnm), "average force", &(top.atoms),
- ePBC, topbox, isize[0], index[0], nr_xfr, sumx,
- nr_ffr, sumf, bDim, scale, oenv);
+ write_pdb_bfac(opt2fn("-cf", NFILE, fnm), opt2fn("-af", NFILE, fnm), "average force",
+ &(top.atoms), ePBC, topbox, isize[0], index[0], nr_xfr, sumx, nr_ffr, sumf,
+ bDim, scale, oenv);
}
/* view it */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff