TrajectoryAnalysisRunnerCommon::Impl::~Impl()
{
finishTrajectory();
if (fr != nullptr)
{
// There doesn't seem to be a function for freeing frame data
sfree(fr->x);
sfree(fr->v);
sfree(fr->f);
sfree(fr->index);
sfree(fr);
}
if (oenv_ != nullptr)
{
output_env_done(oenv_);
}
}
TrajectoryAnalysisRunnerCommon::Impl::~Impl()
{
if (grps_ != NULL)
{
gmx_ana_indexgrps_free(grps_);
}
finishTrajectory();
if (fr)
{
// There doesn't seem to be a function for freeing frame data
sfree(fr->x);
sfree(fr->v);
sfree(fr->f);
sfree(fr);
}
if (oenv_ != NULL)
{
output_env_done(oenv_);
}
}
int gmx_genconf(int argc, char *argv[])
{
const char *desc[] = {
"[THISMODULE] multiplies a given coordinate file by simply stacking them",
"on top of each other, like a small child playing with wooden blocks.",
"The program makes a grid of [IT]user-defined[it]",
"proportions ([TT]-nbox[tt]), ",
"and interspaces the grid point with an extra space [TT]-dist[tt].[PAR]",
"When option [TT]-rot[tt] is used the program does not check for overlap",
"between molecules on grid points. It is recommended to make the box in",
"the input file at least as big as the coordinates + ",
"van der Waals radius.[PAR]",
"If the optional trajectory file is given, conformations are not",
"generated, but read from this file and translated appropriately to",
"build the grid."
};
const char *bugs[] = {
"The program should allow for random displacement of lattice points."
};
int vol;
t_atoms *atoms; /* list with all atoms */
rvec *x, *xx, *v; /* coordinates? */
real t;
vec4 *xrot, *vrot;
int ePBC;
matrix box, boxx; /* box length matrix */
rvec shift;
int natoms; /* number of atoms in one molecule */
int nres; /* number of molecules? */
int i, j, k, l, m, ndx, nrdx, nx, ny, nz;
t_trxstatus *status;
gmx_bool bTRX;
gmx_output_env_t *oenv;
t_filenm fnm[] = {
{ efSTX, "-f", "conf", ffREAD },
{ efSTO, "-o", "out", ffWRITE },
{ efTRX, "-trj", NULL, ffOPTRD }
};
#define NFILE asize(fnm)
static rvec nrbox = {1, 1, 1};
static int seed = 0; /* seed for random number generator */
static gmx_bool bRandom = FALSE; /* False: no random rotations */
static gmx_bool bRenum = TRUE; /* renumber residues */
static rvec dist = {0, 0, 0}; /* space added between molecules ? */
static rvec max_rot = {180, 180, 180}; /* maximum rotation */
t_pargs pa[] = {
{ "-nbox", FALSE, etRVEC, {nrbox}, "Number of boxes" },
{ "-dist", FALSE, etRVEC, {dist}, "Distance between boxes" },
{ "-seed", FALSE, etINT, {&seed},
"Random generator seed (0 means generate)" },
{ "-rot", FALSE, etBOOL, {&bRandom}, "Randomly rotate conformations" },
{ "-maxrot", FALSE, etRVEC, {max_rot}, "Maximum random rotation" },
{ "-renumber", FALSE, etBOOL, {&bRenum}, "Renumber residues" }
};
if (!parse_common_args(&argc, argv, 0, NFILE, fnm, asize(pa), pa,
asize(desc), desc, asize(bugs), bugs, &oenv))
{
return 0;
}
if (seed == 0)
{
seed = static_cast<int>(gmx::makeRandomSeed());
}
gmx::DefaultRandomEngine rng(seed);
bTRX = ftp2bSet(efTRX, NFILE, fnm);
nx = (int)(nrbox[XX]+0.5);
ny = (int)(nrbox[YY]+0.5);
nz = (int)(nrbox[ZZ]+0.5);
if ((nx <= 0) || (ny <= 0) || (nz <= 0))
{
gmx_fatal(FARGS, "Number of boxes (-nbox) should be larger than zero");
}
vol = nx*ny*nz; /* calculate volume in grid points (= nr. molecules) */
t_topology *top;
snew(top, 1);
atoms = &top->atoms;
read_tps_conf(opt2fn("-f", NFILE, fnm), top, &ePBC, &x, &v, box, FALSE);
natoms = atoms->nr;
nres = atoms->nres; /* nr of residues in one element? */
/* make space for all the atoms */
add_t_atoms(atoms, natoms*(vol-1), nres*(vol-1));
srenew(x, natoms*vol); /* get space for coordinates of all atoms */
srenew(v, natoms*vol); /* velocities. not really needed? */
snew(xrot, natoms); /* get space for rotation matrix? */
snew(vrot, natoms);
if (bTRX)
{
if (!read_first_x(oenv, &status, ftp2fn(efTRX, NFILE, fnm), &t, &xx, boxx))
{
gmx_fatal(FARGS, "No atoms in trajectory %s", ftp2fn(efTRX, NFILE, fnm));
}
}
else
{
snew(xx, natoms);
for (i = 0; i < natoms; i++)
{
copy_rvec(x[i], xx[i]);
}
}
for (k = 0; (k < nz); k++) /* loop over all gridpositions */
{
shift[ZZ] = k*(dist[ZZ]+box[ZZ][ZZ]);
for (j = 0; (j < ny); j++)
{
shift[YY] = j*(dist[YY]+box[YY][YY])+k*box[ZZ][YY];
for (i = 0; (i < nx); i++)
{
shift[XX] = i*(dist[XX]+box[XX][XX])+j*box[YY][XX]+k*box[ZZ][XX];
ndx = (i*ny*nz+j*nz+k)*natoms;
nrdx = (i*ny*nz+j*nz+k)*nres;
/* Random rotation on input coords */
if (bRandom)
{
rand_rot(natoms, xx, v, xrot, vrot, &rng, max_rot);
}
for (l = 0; (l < natoms); l++)
{
for (m = 0; (m < DIM); m++)
{
if (bRandom)
{
x[ndx+l][m] = xrot[l][m];
v[ndx+l][m] = vrot[l][m];
}
else
{
x[ndx+l][m] = xx[l][m];
v[ndx+l][m] = v[l][m];
}
}
if (ePBC == epbcSCREW && i % 2 == 1)
{
/* Rotate around x axis */
for (m = YY; m <= ZZ; m++)
{
x[ndx+l][m] = box[YY][m] + box[ZZ][m] - x[ndx+l][m];
v[ndx+l][m] = -v[ndx+l][m];
}
}
for (m = 0; (m < DIM); m++)
{
x[ndx+l][m] += shift[m];
}
atoms->atom[ndx+l].resind = nrdx + atoms->atom[l].resind;
atoms->atomname[ndx+l] = atoms->atomname[l];
}
for (l = 0; (l < nres); l++)
{
atoms->resinfo[nrdx+l] = atoms->resinfo[l];
if (bRenum)
{
atoms->resinfo[nrdx+l].nr += nrdx;
}
}
if (bTRX)
{
if (!read_next_x(oenv, status, &t, xx, boxx) &&
((i+1)*(j+1)*(k+1) < vol))
{
gmx_fatal(FARGS, "Not enough frames in trajectory");
}
}
}
}
}
if (bTRX)
{
close_trj(status);
}
/* make box bigger */
for (m = 0; (m < DIM); m++)
{
box[m][m] += dist[m];
}
svmul(nx, box[XX], box[XX]);
svmul(ny, box[YY], box[YY]);
svmul(nz, box[ZZ], box[ZZ]);
if (ePBC == epbcSCREW && nx % 2 == 0)
{
/* With an even number of boxes in x we can forgot about the screw */
ePBC = epbcXYZ;
}
/*depending on how you look at it, this is either a nasty hack or the way it should work*/
if (bRenum)
{
for (i = 0; i < atoms->nres; i++)
{
atoms->resinfo[i].nr = i+1;
}
}
write_sto_conf(opt2fn("-o", NFILE, fnm), *top->name, atoms, x, v, ePBC, box);
sfree(x);
sfree(v);
sfree(xrot);
sfree(vrot);
sfree(xx);
done_top(top);
sfree(top);
done_filenms(NFILE, fnm);
output_env_done(oenv);
return 0;
}