Merge pull request #1279 from akohlmey/create-atoms-bounding-box

  domain->lattice->bbox(1,bboxhi[0],bboxhi[1],bboxhi[2],

                        xmin,ymin,zmin,xmax,ymax,zmax);

  // narrow down min/max further by extent of the region, if possible

  if (domain->regions[nregion]->bboxflag) {

    const double rxmin = domain->regions[nregion]->extent_xlo;

    const double rxmax = domain->regions[nregion]->extent_xhi;

    const double rymin = domain->regions[nregion]->extent_ylo;

    const double rymax = domain->regions[nregion]->extent_yhi;

    const double rzmin = domain->regions[nregion]->extent_zlo;

    const double rzmax = domain->regions[nregion]->extent_zhi;

    if (rxmin > xmin) xmin = (rxmin > xmax) ? xmax : rxmin;

    if (rxmax < xmax) xmax = (rxmax < xmin) ? xmin : rxmax;

    if (rymin > ymin) ymin = (rymin > ymax) ? ymax : rymin;

    if (rymax < ymax) ymax = (rymax < ymin) ? ymin : rymax;

    if (rzmin > zmin) zmin = (rzmin > zmax) ? zmax : rzmin;

    if (rzmax < zmax) zmax = (rzmax < zmin) ? zmin : rzmax;

  }

  // ilo:ihi,jlo:jhi,klo:khi = loop bounds for lattice overlap of my subbox

  // overlap = any part of a unit cell (face,edge,pt) in common with my subbox

  // in lattice space, subbox is a tilted box

  // convert lattice coords to box coords

  // add atom or molecule (on each basis point) if it meets all criteria

  double **basis = domain->lattice->basis;

  double x[3],lamda[3];

  double *coord;

  const double * const * const basis = domain->lattice->basis;

  // rough estimate of total time used for create atoms.

  // one inner loop takes about 25ns on a typical desktop CPU core in 2019

  double testimate = 2.5e-8/3600.0; // convert seconds to hours

  testimate *= static_cast<double>(khi-klo+1);

  testimate *= static_cast<double>(jhi-jlo+1);

  testimate *= static_cast<double>(ihi-ilo+1);

  testimate *= static_cast<double>(nbasis);

  double maxestimate = 0.0;

  MPI_Reduce(&testimate,&maxestimate,1,MPI_DOUBLE,MPI_MAX,0,world);

  if ((comm->me == 0) && (maxestimate > 0.01)) {

    if (screen) fprintf(screen,"WARNING: create_atoms will take "

                        "approx. %.2f hours to complete\n",maxestimate);

    if (logfile) fprintf(logfile,"WARNING: create_atoms will take "

                         "approx. %.2f hours to complete\n",maxestimate);

  }

  int i,j,k,m;

  for (k = klo; k <= khi; k++)

    for (j = jlo; j <= jhi; j++)

      for (i = ilo; i <= ihi; i++)

  for (k = klo; k <= khi; k++) {

    for (j = jlo; j <= jhi; j++) {

      for (i = ilo; i <= ihi; i++) {

        for (m = 0; m < nbasis; m++) {

          double *coord;

          double x[3],lamda[3];

          x[0] = i + basis[m][0];

          x[1] = j + basis[m][1];

          else add_molecule(x);

        }

      }

    }

  }

}

/* ----------------------------------------------------------------------

   add a randomly rotated molecule with its center at center