void visualize_box(FILE *out, int a0, int r0, matrix box, rvec gridsize)
{
int *edge;
rvec *vert, shift;
int nx, ny, nz, nbox, nat;
int i, j, x, y, z;
int rectedge[24] =
{
0, 1, 1, 3, 3, 2, 0, 2, 0, 4, 1, 5, 3, 7, 2, 6, 4, 5, 5, 7, 7, 6, 6,
4
};
a0++;
r0++;
nx = static_cast<int>(gridsize[XX] + 0.5);
ny = static_cast<int>(gridsize[YY] + 0.5);
nz = static_cast<int>(gridsize[ZZ] + 0.5);
nbox = nx * ny * nz;
if (TRICLINIC(box))
{
nat = nbox * NCUCVERT;
snew(vert, nat);
calc_compact_unitcell_vertices(ecenterDEF, box, vert);
j = 0;
for (z = 0; z < nz; z++)
{
for (y = 0; y < ny; y++)
{
for (x = 0; x < nx; x++)
{
for (i = 0; i < DIM; i++)
{
shift[i] = x * box[0][i] + y * box[1][i] + z
* box[2][i];
}
for (i = 0; i < NCUCVERT; i++)
{
rvec_add(vert[i], shift, vert[j]);
j++;
}
}
}
}
for (i = 0; i < nat; i++)
{
gmx_fprintf_pdb_atomline(out, epdbATOM, a0 + i, "C", ' ', "BOX", 'K' + i / NCUCVERT, r0 + i, ' ',
10*vert[i][XX], 10*vert[i][YY], 10*vert[i][ZZ], 1.0, 0.0, "");
}
edge = compact_unitcell_edges();
for (j = 0; j < nbox; j++)
{
for (i = 0; i < NCUCEDGE; i++)
{
fprintf(out, "CONECT%5d%5d\n", a0 + j * NCUCVERT + edge[2 * i],
a0 + j * NCUCVERT + edge[2 * i + 1]);
}
}
sfree(vert);
}
else
{
i = 0;
for (z = 0; z <= 1; z++)
{
for (y = 0; y <= 1; y++)
{
for (x = 0; x <= 1; x++)
{
gmx_fprintf_pdb_atomline(out, epdbATOM, a0 + i, "C", ' ', "BOX", 'K' + i/8, r0+i, ' ',
x * 10 * box[XX][XX], y * 10 * box[YY][YY], z * 10 * box[ZZ][ZZ], 1.0, 0.0, "");
i++;
}
}
}
for (i = 0; i < 24; i += 2)
{
fprintf(out, "CONECT%5d%5d\n", a0 + rectedge[i], a0 + rectedge[i + 1]);
}
}
}
int copy_pmegrid_to_fftgrid(struct gmx_pme_t *pme, real *pmegrid, real *fftgrid, int grid_index)
{
ivec local_fft_ndata, local_fft_offset, local_fft_size;
ivec local_pme_size;
int ix, iy, iz;
int pmeidx, fftidx;
/* Dimensions should be identical for A/B grid, so we just use A here */
gmx_parallel_3dfft_real_limits(pme->pfft_setup[grid_index],
local_fft_ndata,
local_fft_offset,
local_fft_size);
local_pme_size[0] = pme->pmegrid_nx;
local_pme_size[1] = pme->pmegrid_ny;
local_pme_size[2] = pme->pmegrid_nz;
/* The fftgrid is always 'justified' to the lower-left corner of the PME grid,
the offset is identical, and the PME grid always has more data (due to overlap)
*/
{
#ifdef DEBUG_PME
FILE *fp, *fp2;
char fn[STRLEN];
real val;
sprintf(fn, "pmegrid%d.pdb", pme->nodeid);
fp = gmx_ffopen(fn, "w");
sprintf(fn, "pmegrid%d.txt", pme->nodeid);
fp2 = gmx_ffopen(fn, "w");
#endif
for (ix = 0; ix < local_fft_ndata[XX]; ix++)
{
for (iy = 0; iy < local_fft_ndata[YY]; iy++)
{
for (iz = 0; iz < local_fft_ndata[ZZ]; iz++)
{
pmeidx = ix*(local_pme_size[YY]*local_pme_size[ZZ])+iy*(local_pme_size[ZZ])+iz;
fftidx = ix*(local_fft_size[YY]*local_fft_size[ZZ])+iy*(local_fft_size[ZZ])+iz;
fftgrid[fftidx] = pmegrid[pmeidx];
#ifdef DEBUG_PME
val = 100*pmegrid[pmeidx];
if (pmegrid[pmeidx] != 0)
{
gmx_fprintf_pdb_atomline(fp, epdbATOM, pmeidx, "CA", ' ', "GLY", ' ', pmeidx, ' ',
5.0*ix, 5.0*iy, 5.0*iz, 1.0, val, "");
}
if (pmegrid[pmeidx] != 0)
{
fprintf(fp2, "%-12s %5d %5d %5d %12.5e\n",
"qgrid",
pme->pmegrid_start_ix + ix,
pme->pmegrid_start_iy + iy,
pme->pmegrid_start_iz + iz,
pmegrid[pmeidx]);
}
#endif
}
}
}
#ifdef DEBUG_PME
gmx_ffclose(fp);
gmx_ffclose(fp2);
#endif
}
return 0;
}
void write_pdbfile_indexed(FILE *out, const char *title,
t_atoms *atoms, rvec x[],
int ePBC, matrix box, char chainid,
int model_nr, int nindex, const int index[],
gmx_conect conect, gmx_bool bTerSepChains)
{
gmx_conect_t *gc = (gmx_conect_t *)conect;
char resnm[6], nm[6];
int i, ii;
int resind, resnr;
enum PDB_record type;
unsigned char resic, ch;
char altloc;
real occup, bfac;
gmx_bool bOccup;
int chainnum, lastchainnum;
gmx_residuetype_t*rt;
const char *p_restype;
const char *p_lastrestype;
gmx_residuetype_init(&rt);
fprintf(out, "TITLE %s\n", (title && title[0]) ? title : gmx::bromacs().c_str());
if (box && ( norm2(box[XX]) || norm2(box[YY]) || norm2(box[ZZ]) ) )
{
gmx_write_pdb_box(out, ePBC, box);
}
if (atoms->pdbinfo)
{
/* Check whether any occupancies are set, in that case leave it as is,
* otherwise set them all to one
*/
bOccup = TRUE;
for (ii = 0; (ii < nindex) && bOccup; ii++)
{
i = index[ii];
bOccup = bOccup && (atoms->pdbinfo[i].occup == 0.0);
}
}
else
{
bOccup = FALSE;
}
fprintf(out, "MODEL %8d\n", model_nr > 0 ? model_nr : 1);
lastchainnum = -1;
p_restype = NULL;
for (ii = 0; ii < nindex; ii++)
{
i = index[ii];
resind = atoms->atom[i].resind;
chainnum = atoms->resinfo[resind].chainnum;
p_lastrestype = p_restype;
gmx_residuetype_get_type(rt, *atoms->resinfo[resind].name, &p_restype);
/* Add a TER record if we changed chain, and if either the previous or this chain is protein/DNA/RNA. */
if (bTerSepChains && ii > 0 && chainnum != lastchainnum)
{
/* Only add TER if the previous chain contained protein/DNA/RNA. */
if (gmx_residuetype_is_protein(rt, p_lastrestype) || gmx_residuetype_is_dna(rt, p_lastrestype) || gmx_residuetype_is_rna(rt, p_lastrestype))
{
fprintf(out, "TER\n");
}
lastchainnum = chainnum;
}
strncpy(resnm, *atoms->resinfo[resind].name, sizeof(resnm)-1);
resnm[sizeof(resnm)-1] = 0;
strncpy(nm, *atoms->atomname[i], sizeof(nm)-1);
nm[sizeof(nm)-1] = 0;
/* rename HG12 to 2HG1, etc. */
xlate_atomname_gmx2pdb(nm);
resnr = atoms->resinfo[resind].nr;
resic = atoms->resinfo[resind].ic;
if (chainid != ' ')
{
ch = chainid;
}
else
{
ch = atoms->resinfo[resind].chainid;
if (ch == 0)
{
ch = ' ';
}
}
if (resnr >= 10000)
{
resnr = resnr % 10000;
}
if (atoms->pdbinfo)
{
type = static_cast<enum PDB_record>(atoms->pdbinfo[i].type);
altloc = atoms->pdbinfo[i].altloc;
if (!isalnum(altloc))
{
altloc = ' ';
}
occup = bOccup ? 1.0 : atoms->pdbinfo[i].occup;
bfac = atoms->pdbinfo[i].bfac;
}
else
{
type = epdbATOM;
occup = 1.0;
bfac = 0.0;
altloc = ' ';
}
gmx_fprintf_pdb_atomline(out,
type,
i+1,
nm,
altloc,
resnm,
ch,
resnr,
resic,
10*x[i][XX], 10*x[i][YY], 10*x[i][ZZ],
occup,
bfac,
atoms->atom[i].elem);
if (atoms->pdbinfo && atoms->pdbinfo[i].bAnisotropic)
{
fprintf(out, "ANISOU%5d %-4.4s%4.4s%c%4d%c %7d%7d%7d%7d%7d%7d\n",
(i+1)%100000, nm, resnm, ch, resnr,
(resic == '\0') ? ' ' : resic,
atoms->pdbinfo[i].uij[0], atoms->pdbinfo[i].uij[1],
atoms->pdbinfo[i].uij[2], atoms->pdbinfo[i].uij[3],
atoms->pdbinfo[i].uij[4], atoms->pdbinfo[i].uij[5]);
}
}
fprintf(out, "TER\n");
fprintf(out, "ENDMDL\n");
if (NULL != gc)
{
/* Write conect records */
for (i = 0; (i < gc->nconect); i++)
{
fprintf(out, "CONECT%5d%5d\n", gc->conect[i].ai+1, gc->conect[i].aj+1);
}
}
gmx_residuetype_destroy(rt);
}
