fprintf(fp, "\n 2 !NTITLE\n");
fprintf(fp, " REMARKS Energy Landscape from GROMACS\n");
fprintf(fp, " REMARKS DATE: 2004-12-21 \n");
- fprintf(fp, " %7d %7d %7d %7d %7d %7d %7d %7d %7d\n", map->Nx, map->dmin[0], map->dmax[0],
- map->Ny, map->dmin[1], map->dmax[1], map->Nz, map->dmin[2], map->dmax[2]);
- fprintf(fp, "%12.5E%12.5E%12.5E%12.5E%12.5E%12.5E\n", map->cell[0], map->cell[1], map->cell[2],
- map->cell[3], map->cell[4], map->cell[5]);
+ fprintf(fp,
+ " %7d %7d %7d %7d %7d %7d %7d %7d %7d\n",
+ map->Nx,
+ map->dmin[0],
+ map->dmax[0],
+ map->Ny,
+ map->dmin[1],
+ map->dmax[1],
+ map->Nz,
+ map->dmin[2],
+ map->dmax[2]);
+ fprintf(fp,
+ "%12.5E%12.5E%12.5E%12.5E%12.5E%12.5E\n",
+ map->cell[0],
+ map->cell[1],
+ map->cell[2],
+ map->cell[3],
+ map->cell[4],
+ map->cell[5]);
fprintf(fp, "ZYX\n");
z = map->dmin[2];
fprintf(fp,
"Minimum %d at index "
"%" PRId64 " energy %10.3f\n",
- num, min->index, min->ener);
+ num,
+ min->index,
+ min->ener);
}
static inline void add_minimum(FILE* fp, int num, const t_minimum* min, t_minimum* mm)
this_min.index = index3(ibox, i, j, k);
this_min.ener = W[this_min.index];
if (is_local_minimum_from_below(&this_min, i, 0, index3(ibox, i - 1, j, k), W)
- && is_local_minimum_from_above(&this_min, i, ibox[0] - 1,
- index3(ibox, i + 1, j, k), W)
+ && is_local_minimum_from_above(
+ &this_min, i, ibox[0] - 1, index3(ibox, i + 1, j, k), W)
&& is_local_minimum_from_below(&this_min, j, 0, index3(ibox, i, j - 1, k), W)
- && is_local_minimum_from_above(&this_min, j, ibox[1] - 1,
- index3(ibox, i, j + 1, k), W)
+ && is_local_minimum_from_above(
+ &this_min, j, ibox[1] - 1, index3(ibox, i, j + 1, k), W)
&& is_local_minimum_from_below(&this_min, k, 0, index3(ibox, i, j, k - 1), W)
- && is_local_minimum_from_above(&this_min, k, ibox[2] - 1,
- index3(ibox, i, j, k + 1), W))
+ && is_local_minimum_from_above(
+ &this_min, k, ibox[2] - 1, index3(ibox, i, j, k + 1), W))
{
add_minimum(fp, nmin, &this_min, mm);
nmin++;
int index = this_point[i];
this_point[i]--;
bMin = bMin
- && is_local_minimum_from_below(&this_min, index, 0,
- indexn(ndim, ibox, this_point), W);
+ && is_local_minimum_from_below(
+ &this_min, index, 0, indexn(ndim, ibox, this_point), W);
this_point[i] += 2;
bMin = bMin
- && is_local_minimum_from_above(&this_min, index, ibox[i] - 1,
- indexn(ndim, ibox, this_point), W);
+ && is_local_minimum_from_above(
+ &this_min, index, ibox[i] - 1, indexn(ndim, ibox, this_point), W);
this_point[i]--;
}
if (bMin)
{
if (max_eig[i] > xmax[i])
{
- gmx_warning("Your xmax[%d] value %f is smaller than the largest data point %f", i,
- xmax[i], max_eig[i]);
+ gmx_warning("Your xmax[%d] value %f is smaller than the largest data point %f",
+ i,
+ xmax[i],
+ max_eig[i]);
}
max_eig[i] = xmax[i];
}
{
if (min_eig[i] < xmin[i])
{
- gmx_warning("Your xmin[%d] value %f is larger than the smallest data point %f", i,
- xmin[i], min_eig[i]);
+ gmx_warning("Your xmin[%d] value %f is larger than the smallest data point %f",
+ i,
+ xmin[i],
+ min_eig[i]);
}
min_eig[i] = xmin[i];
}
SS[i] = &(S[i * ibox[1]]);
}
fp = gmx_ffopen(xpmP, "w");
- write_xpm(fp, flags, "Probability Distribution", "", "PC1", "PC2", ibox[0], ibox[1], axis_x,
- axis_y, PP, 0, Pmax, rlo, rhi, &nlevels);
+ write_xpm(fp,
+ flags,
+ "Probability Distribution",
+ "",
+ "PC1",
+ "PC2",
+ ibox[0],
+ ibox[1],
+ axis_x,
+ axis_y,
+ PP,
+ 0,
+ Pmax,
+ rlo,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
fp = gmx_ffopen(xpm, "w");
- write_xpm(fp, flags, "Gibbs Energy Landscape", "G (kJ/mol)", "PC1", "PC2", ibox[0], ibox[1],
- axis_x, axis_y, WW, 0, gmax, rlo, rhi, &nlevels);
+ write_xpm(fp,
+ flags,
+ "Gibbs Energy Landscape",
+ "G (kJ/mol)",
+ "PC1",
+ "PC2",
+ ibox[0],
+ ibox[1],
+ axis_x,
+ axis_y,
+ WW,
+ 0,
+ gmax,
+ rlo,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
fp = gmx_ffopen(xpm2, "w");
- write_xpm(fp, flags, "Enthalpy Landscape", "H (kJ/mol)", "PC1", "PC2", ibox[0], ibox[1],
- axis_x, axis_y, EE, emin ? *emin : Emin, emax ? *emax : Einf, rlo, rhi, &nlevels);
+ write_xpm(fp,
+ flags,
+ "Enthalpy Landscape",
+ "H (kJ/mol)",
+ "PC1",
+ "PC2",
+ ibox[0],
+ ibox[1],
+ axis_x,
+ axis_y,
+ EE,
+ emin ? *emin : Emin,
+ emax ? *emax : Einf,
+ rlo,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
fp = gmx_ffopen(xpm3, "w");
- write_xpm(fp, flags, "Entropy Landscape", "TDS (kJ/mol)", "PC1", "PC2", ibox[0], ibox[1],
- axis_x, axis_y, SS, 0, Sinf, rlo, rhi, &nlevels);
+ write_xpm(fp,
+ flags,
+ "Entropy Landscape",
+ "TDS (kJ/mol)",
+ "PC1",
+ "PC2",
+ ibox[0],
+ ibox[1],
+ axis_x,
+ axis_y,
+ SS,
+ 0,
+ Sinf,
+ rlo,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
}
else if (neig == 3)
index = index3(ibox, i, j, k);
if (P[index] > 0)
{
- fprintf(fp, "%-6s%5d %-4.4s%3.3s %4d %8.3f%8.3f%8.3f%6.2f%6.2f\n",
- "ATOM", (index + 1) % 10000, "H", "H", (index + 1) % 10000, xxx[XX],
- xxx[YY], xxx[ZZ], 1.0, W[index]);
+ fprintf(fp,
+ "%-6s%5d %-4.4s%3.3s %4d %8.3f%8.3f%8.3f%6.2f%6.2f\n",
+ "ATOM",
+ (index + 1) % 10000,
+ "H",
+ "H",
+ (index + 1) % 10000,
+ xxx[XX],
+ xxx[YY],
+ xxx[ZZ],
+ 1.0,
+ W[index]);
}
}
}
sprintf(buf, "%s", xpm);
sprintf(&buf[std::strlen(xpm) - 4], "12.xpm");
fp = gmx_ffopen(buf, "w");
- write_xpm(fp, flags, "Gibbs Energy Landscape", "W (kJ/mol)", "PC1", "PC2", ibox[0], ibox[1],
- axis_x, axis_y, WW, 0, gmax, rlo, rhi, &nlevels);
+ write_xpm(fp,
+ flags,
+ "Gibbs Energy Landscape",
+ "W (kJ/mol)",
+ "PC1",
+ "PC2",
+ ibox[0],
+ ibox[1],
+ axis_x,
+ axis_y,
+ WW,
+ 0,
+ gmax,
+ rlo,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
for (i = 0; (i < ibox[0]); i++)
{
}
sprintf(&buf[std::strlen(xpm) - 4], "13.xpm");
fp = gmx_ffopen(buf, "w");
- write_xpm(fp, flags, "SHAM Energy Landscape", "kJ/mol", "PC1", "PC3", ibox[0], ibox[2],
- axis_x, axis_z, WW, 0, gmax, rlo, rhi, &nlevels);
+ write_xpm(fp,
+ flags,
+ "SHAM Energy Landscape",
+ "kJ/mol",
+ "PC1",
+ "PC3",
+ ibox[0],
+ ibox[2],
+ axis_x,
+ axis_z,
+ WW,
+ 0,
+ gmax,
+ rlo,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
for (i = 0; (i < ibox[1]); i++)
{
}
sprintf(&buf[std::strlen(xpm) - 4], "23.xpm");
fp = gmx_ffopen(buf, "w");
- write_xpm(fp, flags, "SHAM Energy Landscape", "kJ/mol", "PC2", "PC3", ibox[1], ibox[2],
- axis_y, axis_z, WW, 0, gmax, rlo, rhi, &nlevels);
+ write_xpm(fp,
+ flags,
+ "SHAM Energy Landscape",
+ "kJ/mol",
+ "PC2",
+ "PC3",
+ ibox[1],
+ ibox[2],
+ axis_y,
+ axis_z,
+ WW,
+ 0,
+ gmax,
+ rlo,
+ rhi,
+ &nlevels);
gmx_ffclose(fp);
sfree(buf);
}
int npargs;
npargs = asize(pa);
- if (!parse_common_args(&argc, argv, PCA_CAN_VIEW, NFILE, fnm, npargs, pa, asize(desc), desc, 0,
- nullptr, &oenv))
+ if (!parse_common_args(
+ &argc, argv, PCA_CAN_VIEW, NFILE, fnm, npargs, pa, asize(desc), desc, 0, nullptr, &oenv))
{
return 0;
}
- val = read_xvg_time(opt2fn("-f", NFILE, fnm), bHaveT, opt2parg_bSet("-b", npargs, pa), tb - ttol,
- opt2parg_bSet("-e", npargs, pa), te + ttol, nsets_in, &nset, &n, &dt, &t);
+ val = read_xvg_time(opt2fn("-f", NFILE, fnm),
+ bHaveT,
+ opt2parg_bSet("-b", npargs, pa),
+ tb - ttol,
+ opt2parg_bSet("-e", npargs, pa),
+ te + ttol,
+ nsets_in,
+ &nset,
+ &n,
+ &dt,
+ &t);
printf("Read %d sets of %d points, dt = %g\n\n", nset, n, dt);
fn_ge = opt2fn_null("-ge", NFILE, fnm);
if (fn_ge || fn_ene)
{
- et_val = read_xvg_time(fn_ge ? fn_ge : fn_ene, bHaveT, opt2parg_bSet("-b", npargs, pa),
- tb - ttol, opt2parg_bSet("-e", npargs, pa), te + ttol, 1, &e_nset,
- &e_n, &e_dt, &e_t);
+ et_val = read_xvg_time(fn_ge ? fn_ge : fn_ene,
+ bHaveT,
+ opt2parg_bSet("-b", npargs, pa),
+ tb - ttol,
+ opt2parg_bSet("-e", npargs, pa),
+ te + ttol,
+ 1,
+ &e_nset,
+ &e_n,
+ &e_dt,
+ &e_t);
if (fn_ge)
{
if (e_nset != 1)
if (e_nset != 1 && e_nset != 2)
{
gmx_fatal(FARGS,
- "Can only handle one energy component or one energy and one T in %s", fn_ene);
+ "Can only handle one energy component or one energy and one T in %s",
+ fn_ene);
}
}
if (e_n != n)
{
- gmx_fatal(FARGS, "Number of energies (%d) does not match number of entries (%d) in %s",
- e_n, n, opt2fn("-f", NFILE, fnm));
+ gmx_fatal(FARGS,
+ "Number of energies (%d) does not match number of entries (%d) in %s",
+ e_n,
+ n,
+ opt2fn("-f", NFILE, fnm));
}
}
else
}
/* The number of grid points fits in a int64_t. */
- do_sham(opt2fn("-dist", NFILE, fnm), opt2fn("-bin", NFILE, fnm), opt2fn("-lp", NFILE, fnm),
- opt2fn("-ls", NFILE, fnm), opt2fn("-lsh", NFILE, fnm), opt2fn("-lss", NFILE, fnm),
- opt2fn("-ls3", NFILE, fnm), opt2fn("-g", NFILE, fnm), n, nset, val, fn_ge != nullptr,
- e_nset, et_val, Tref, pmax, gmax, opt2parg_bSet("-emin", NPA, pa) ? &emin : nullptr,
- opt2parg_bSet("-emax", NPA, pa) ? &emax : nullptr, nlevels, pmin, idim, ibox,
- opt2parg_bSet("-xmin", NPA, pa), rmin, opt2parg_bSet("-xmax", NPA, pa), rmax);
+ do_sham(opt2fn("-dist", NFILE, fnm),
+ opt2fn("-bin", NFILE, fnm),
+ opt2fn("-lp", NFILE, fnm),
+ opt2fn("-ls", NFILE, fnm),
+ opt2fn("-lsh", NFILE, fnm),
+ opt2fn("-lss", NFILE, fnm),
+ opt2fn("-ls3", NFILE, fnm),
+ opt2fn("-g", NFILE, fnm),
+ n,
+ nset,
+ val,
+ fn_ge != nullptr,
+ e_nset,
+ et_val,
+ Tref,
+ pmax,
+ gmax,
+ opt2parg_bSet("-emin", NPA, pa) ? &emin : nullptr,
+ opt2parg_bSet("-emax", NPA, pa) ? &emax : nullptr,
+ nlevels,
+ pmin,
+ idim,
+ ibox,
+ opt2parg_bSet("-xmin", NPA, pa),
+ rmin,
+ opt2parg_bSet("-xmax", NPA, pa),
+ rmax);
return 0;
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff