lammps/src/domain.cpp

/* ----------------------------------------------------------------------
   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
   www.cs.sandia.gov/~sjplimp/lammps.html
   Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories

   Copyright (2003) Sandia Corporation.  Under the terms of Contract
   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
   certain rights in this software.  This software is distributed under 
   the GNU General Public License.

   See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */

#include "mpi.h"
#include "stdlib.h"
#include "string.h"
#include "stdio.h"
#include "math.h"
#include "domain.h"
#include "atom.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "region.h"
#include "lattice.h"
#include "comm.h"
#include "memory.h"
#include "error.h"

#define RegionInclude
#include "style.h"
#undef RegionInclude

#define BIG   1.0e20
#define SMALL 1.0e-4
#define DELTA 1
#define MIN(a,b) ((a) < (b) ? (a) : (b))
#define MAX(a,b) ((a) > (b) ? (a) : (b))

/* ----------------------------------------------------------------------
   default is periodic 
------------------------------------------------------------------------- */

Domain::Domain()
{
  box_exist = 0;

  nonperiodic = 0;
  xperiodic = yperiodic = zperiodic = 1;
  periodicity[0] = xperiodic;
  periodicity[1] = yperiodic;
  periodicity[2] = zperiodic;

  boundary[0][0] = boundary[0][1] = 0;
  boundary[1][0] = boundary[1][1] = 0;
  boundary[2][0] = boundary[2][1] = 0;

  boxxlo = boxylo = boxzlo = -0.5;
  boxxhi = boxyhi = boxzhi = 0.5;

  lattice = NULL;
  nregion = maxregion = 0;
  regions = NULL;
}

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

Domain::~Domain()
{
  delete lattice;
  for (int i = 0; i < nregion; i++) delete regions[i];
  memory->sfree(regions);
}

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

void Domain::init()
{
  // set box_change if box dimensions ever change
  // due to shrink-wrapping, fix nph, npt, volume/rescale, uniaxial

  box_change = 0;
  if (nonperiodic == 2) box_change = 1;
  for (int i = 0; i < modify->nfix; i++) {
    if (strcmp(modify->fix[i]->style,"nph") == 0) box_change = 1;
    if (strcmp(modify->fix[i]->style,"npt") == 0) box_change = 1;
    if (strcmp(modify->fix[i]->style,"volume/rescale") == 0) box_change = 1;
    if (strcmp(modify->fix[i]->style,"uniaxial") == 0) box_change = 1;
  }
}

/* ----------------------------------------------------------------------
   set initial global box from boxlo/hi (already set by caller)
   adjust for shrink-wrapped dims
------------------------------------------------------------------------- */

void Domain::set_initial_box()
{
  if (boundary[0][0] == 2) boxxlo -= SMALL;
  else if (boundary[0][0] == 3) minxlo = boxxlo;
  if (boundary[0][1] == 2) boxxhi += SMALL;
  else if (boundary[0][1] == 3) minxhi = boxxhi;

  if (boundary[1][0] == 2) boxylo -= SMALL;
  else if (boundary[1][0] == 3) minylo = boxylo;
  if (boundary[1][1] == 2) boxyhi += SMALL;
  else if (boundary[1][1] == 3) minyhi = boxyhi;

  if (boundary[2][0] == 2) boxzlo -= SMALL;
  else if (boundary[2][0] == 3) minzlo = boxzlo;
  if (boundary[2][1] == 2) boxzhi += SMALL;
  else if (boundary[2][1] == 3) minzhi = boxzhi;
}

/* ----------------------------------------------------------------------
   set global prd, prd_half, prd[], boxlo/hi[] from boxlo/hi
------------------------------------------------------------------------- */

void Domain::set_global_box()
{
  xprd = boxxhi - boxxlo;
  yprd = boxyhi - boxylo;
  zprd = boxzhi - boxzlo;

  xprd_half = 0.5*xprd;
  yprd_half = 0.5*yprd;
  zprd_half = 0.5*zprd;

  prd[0]   = xprd;    prd[1]   = yprd;    prd[2]   = zprd;
  boxlo[0] = boxxlo;  boxlo[1] = boxylo;  boxlo[2] = boxzlo;
  boxhi[0] = boxxhi;  boxhi[1] = boxyhi;  boxhi[2] = boxzhi;
}

/* ----------------------------------------------------------------------
   set local subxlo-subzhi, sublo/hi[] from global boxxlo-boxzhi and proc grid
   for uppermost proc, insure subhi = boxhi (in case round-off occurs)
------------------------------------------------------------------------- */

void Domain::set_local_box()
{
  subxlo = boxxlo + comm->myloc[0] * xprd / comm->procgrid[0];
  if (comm->myloc[0] < comm->procgrid[0]-1)
    subxhi = boxxlo + (comm->myloc[0]+1) * xprd / comm->procgrid[0];
  else subxhi = boxxhi;

  subylo = boxylo + comm->myloc[1] * yprd / comm->procgrid[1];
  if (comm->myloc[1] < comm->procgrid[1]-1)
    subyhi = boxylo + (comm->myloc[1]+1) * yprd / comm->procgrid[1];
  else subyhi = boxyhi;

  subzlo = boxzlo + comm->myloc[2] * zprd / comm->procgrid[2];
  if (comm->myloc[2] < comm->procgrid[2]-1)
    subzhi = boxzlo + (comm->myloc[2]+1) * zprd / comm->procgrid[2];
  else subzhi = boxzhi;

  sublo[0] = subxlo;  sublo[1] = subylo;  sublo[2] = subzlo;
  subhi[0] = subxhi;  subhi[1] = subyhi;  subhi[2] = subzhi;
}

/* ----------------------------------------------------------------------
   reset global & local boxes due to global box boundary changes
   if shrink-wrapped, determine atom extent and reset boxlo/hi
   set global & local boxes from new boxlo/hi values
------------------------------------------------------------------------- */

void Domain::reset_box()
{
  if (nonperiodic == 2) {

    // compute extent of atoms on this proc

    double extent[3][2],all[3][2];

    extent[2][0] = extent[1][0] = extent[0][0] = BIG;
    extent[2][1] = extent[1][1] = extent[0][1] = -BIG;
    
    double **x = atom->x;
    int nlocal = atom->nlocal;

    for (int i = 0; i < nlocal; i++) {
      extent[0][0] = MIN(extent[0][0],x[i][0]);
      extent[0][1] = MAX(extent[0][1],x[i][0]);
      extent[1][0] = MIN(extent[1][0],x[i][1]);
      extent[1][1] = MAX(extent[1][1],x[i][1]);
      extent[2][0] = MIN(extent[2][0],x[i][2]);
      extent[2][1] = MAX(extent[2][1],x[i][2]);
    }

    // compute extent across all procs
    // flip sign of MIN to do it in one Allreduce MAX

    extent[0][0] = -extent[0][0];
    extent[1][0] = -extent[1][0];
    extent[2][0] = -extent[2][0];

    MPI_Allreduce(extent,all,6,MPI_DOUBLE,MPI_MAX,world);

    // in shrink-wrapped dims, set box by atom extent
    
    if (xperiodic == 0) {
      if (boundary[0][0] == 2) boxxlo = -all[0][0] - SMALL;
      else if (boundary[0][0] == 3) boxxlo = MIN(-all[0][0]-SMALL,minxlo);
      if (boundary[0][1] == 2) boxxhi = all[0][1] + SMALL;
      else if (boundary[0][1] == 3) boxxhi = MAX(all[0][1]+SMALL,minxhi);
      if (boxxlo > boxxhi) error->all("Illegal simulation box");
    }
    if (yperiodic == 0) {
      if (boundary[1][0] == 2) boxylo = -all[1][0] - SMALL;
      else if (boundary[1][0] == 3) boxylo = MIN(-all[1][0]-SMALL,minylo);
      if (boundary[1][1] == 2) boxyhi = all[1][1] + SMALL;
      else if (boundary[1][1] == 3) boxyhi = MAX(all[1][1]+SMALL,minyhi);
      if (boxylo > boxyhi) error->all("Illegal simulation box");
    }
    if (zperiodic == 0) {
      if (boundary[2][0] == 2) boxzlo = -all[2][0] - SMALL;
      else if (boundary[2][0] == 3) boxzlo = MIN(-all[2][0]-SMALL,minzlo);
      if (boundary[2][1] == 2) boxzhi = all[2][1] + SMALL;
      else if (boundary[2][1] == 3) boxzhi = MAX(all[2][1]+SMALL,minzhi);
      if (boxzlo > boxzhi) error->all("Illegal simulation box");
    }
  }

  set_global_box();
  set_local_box();
}

/* ----------------------------------------------------------------------
   enforce PBC and modify box image flags for each atom
   called every reneighboring
   resulting coord must satisfy lo <= coord < hi
   MAX is important since coord - prd < lo can happen when coord = hi
   image = 10 bits for each dimension
   increment/decrement in wrap-around fashion
------------------------------------------------------------------------- */

void Domain::pbc()
{
  int i,idim,otherdims;
  int nlocal = atom->nlocal;
  double **x = atom->x;
  int *image = atom->image;

  if (xperiodic) {
    for (i = 0; i < nlocal; i++) {
      if (x[i][0] < boxxlo) {
	x[i][0] += xprd;
	idim = image[i] & 1023;
        otherdims = image[i] ^ idim;
	idim--;
	idim &= 1023;
	image[i] = otherdims | idim;
      }
      if (x[i][0] >= boxxhi) {
	x[i][0] -= xprd;
	x[i][0] = MAX(x[i][0],boxxlo);
	idim = image[i] & 1023;
	otherdims = image[i] ^ idim;
	idim++;
	idim &= 1023;
	image[i] = otherdims | idim;
      }
    }
  }

  if (yperiodic) {
    for (i = 0; i < nlocal; i++) {
      if (x[i][1] < boxylo) {
	x[i][1] += yprd;
	idim = (image[i] >> 10) & 1023;
        otherdims = image[i] ^ (idim << 10);
	idim--;
	idim &= 1023;
	image[i] = otherdims | (idim << 10);
      }
      if (x[i][1] >= boxyhi) {
	x[i][1] -= yprd;
	x[i][1] = MAX(x[i][1],boxylo);
	idim = (image[i] >> 10) & 1023;
        otherdims = image[i] ^ (idim << 10);
	idim++;
	idim &= 1023;
	image[i] = otherdims | (idim << 10);
      }
    }
  }

  if (zperiodic) {
    for (i = 0; i < nlocal; i++) {
      if (x[i][2] < boxzlo) {
	x[i][2] += zprd;
	idim = image[i] >> 20;
        otherdims = image[i] ^ (idim << 20);
	idim--;
	idim &= 1023;
	image[i] = otherdims | (idim << 20);
      }
      if (x[i][2] >= boxzhi) {
	x[i][2] -= zprd;
	x[i][2] = MAX(x[i][2],boxzlo);
	idim = image[i] >> 20;
        otherdims = image[i] ^ (idim << 20);
	idim++;
	idim &= 1023;
	image[i] = otherdims | (idim << 20);
      }
    }
  }
}

/* ----------------------------------------------------------------------
   minimum image convention
   use 1/2 of box size as test 
------------------------------------------------------------------------- */

void Domain::minimum_image(double *dx, double *dy, double *dz)
{
  if (xperiodic) {
    if (fabs(*dx) > xprd_half) {
      if (*dx < 0.0) *dx += xprd;
      else *dx -= xprd;
    }
  }
  if (yperiodic) {
    if (fabs(*dy) > yprd_half) {
      if (*dy < 0.0) *dy += yprd;
      else *dy -= yprd;
    }
  }
  if (zperiodic) {
    if (fabs(*dz) > zprd_half) {
      if (*dz < 0.0) *dz += zprd;
      else *dz -= zprd;
    }
  }
}

/* ----------------------------------------------------------------------
   minimum image convention
   use 1/2 of box size as test 
------------------------------------------------------------------------- */

void Domain::minimum_image(double *x)
{
  if (xperiodic) {
    if (fabs(x[0]) > xprd_half) {
      if (x[0] < 0.0) x[0] += xprd;
      else x[0] -= xprd;
    }
  }
  if (yperiodic) {
    if (fabs(x[1]) > yprd_half) {
      if (x[1] < 0.0) x[1] += yprd;
      else x[1] -= yprd;
    }
  }
  if (zperiodic) {
    if (fabs(x[2]) > zprd_half) {
      if (x[2] < 0.0) x[2] += zprd;
      else x[2] -= zprd;
    }
  }
}

/* ----------------------------------------------------------------------
   remap the point into the periodic box no matter how far away
   adjust image accordingly
   resulting coord must satisfy lo <= coord < hi
   MAX is important since coord - prd < lo can happen when coord = hi
   image = 10 bits for each dimension
   increment/decrement in wrap-around fashion
------------------------------------------------------------------------- */

void Domain::remap(double &x, double &y, double &z, int &image)
{
  if (xperiodic) {
    while (x < boxxlo) {
      x += xprd;
      int idim = image & 1023;
      int otherdims = image ^ idim;
      idim--;
      idim &= 1023;
      image = otherdims | idim;
    }
    while (x >= boxxhi) {
      x -= xprd;
      int idim = image & 1023;
      int otherdims = image ^ idim;
      idim++;
      idim &= 1023;
      image = otherdims | idim;
    }
    x = MAX(x,boxxlo);
  }

  if (yperiodic) {
    while (y < boxylo) {
      y += yprd;
      int idim = (image >> 10) & 1023;
      int otherdims = image ^ (idim << 10);
      idim--;
      idim &= 1023;
      image = otherdims | (idim << 10);
    }
    while (y >= boxyhi) {
      y -= yprd;
      int idim = (image >> 10) & 1023;
      int otherdims = image ^ (idim << 10);
      idim++;
      idim &= 1023;
      image = otherdims | (idim << 10);
    }
    y = MAX(y,boxylo);
  }

  if (zperiodic) {
    while (z < boxzlo) {
      z += zprd;
      int idim = image >> 20;
      int otherdims = image ^ (idim << 20);
      idim--;
      idim &= 1023;
      image = otherdims | (idim << 20);
    }
    while (z >= boxzhi) {
      z -= zprd;
      int idim = image >> 20;
      int otherdims = image ^ (idim << 20);
      idim++;
      idim &= 1023;
      image = otherdims | (idim << 20);
    }
    z = MAX(z,boxzlo);
  }
}

/* ----------------------------------------------------------------------
   unmap the point via image flags
   don't reset image flag
------------------------------------------------------------------------- */

void Domain::unmap(double &x, double &y, double &z, int image)
{
  int xbox = (image & 1023) - 512;
  int ybox = (image >> 10 & 1023) - 512;
  int zbox = (image >> 20) - 512;

  x = x + xbox*xprd;
  y = y + ybox*yprd;
  z = z + zbox*zprd;
}

/* ----------------------------------------------------------------------
   create a lattice
   delete it if style = none
------------------------------------------------------------------------- */

void Domain::set_lattice(int narg, char **arg)
{
  delete lattice;
  lattice = new Lattice(narg,arg);
  if (lattice->style == 0) {
    delete lattice;
    lattice = NULL;
  }
}

/* ----------------------------------------------------------------------
   create a new region 
------------------------------------------------------------------------- */

void Domain::add_region(int narg, char **arg)
{
  if (narg < 2) error->all("Illegal region command");

  // error checks

  for (int iregion = 0; iregion < nregion; iregion++)
    if (strcmp(arg[0],regions[iregion]->id) == 0)
      error->all("Reuse of region ID");

  // extend Region list if necessary

  if (nregion == maxregion) {
    maxregion += DELTA;
    regions = (Region **) 
      memory->srealloc(regions,maxregion*sizeof(Region *),"domain:regions");
  }

  // create the Region

  if (strcmp(arg[1],"none") == 0) error->all("Invalid region style");

#define RegionClass
#define RegionStyle(key,Class) \
  else if (strcmp(arg[1],#key) == 0) regions[nregion] = new Class(narg,arg);
#include "style.h"
#undef RegionClass

  else error->all("Invalid region style");

  nregion++;
}

/* ----------------------------------------------------------------------
   boundary settings from the input script 
------------------------------------------------------------------------- */

void Domain::set_boundary(int narg, char **arg)
{
  if (narg != 3) error->all("Illegal boundary command");

  char c;
  for (int idim = 0; idim < 3; idim++)
    for (int iside = 0; iside < 2; iside++) {
      if (iside == 0) c = arg[idim][0];
      else if (iside == 1 && strlen(arg[idim]) == 1) c = arg[idim][0];
      else c = arg[idim][1];

      if (c == 'p') boundary[idim][iside] = 0;
      else if (c == 'f') boundary[idim][iside] = 1;
      else if (c == 's') boundary[idim][iside] = 2;
      else if (c == 'm') boundary[idim][iside] = 3;
      else error->all("Illegal boundary command");
    }

  for (int idim = 0; idim < 3; idim++)
    if ((boundary[idim][0] == 0 && boundary[idim][1]) ||
	(boundary[idim][0] && boundary[idim][1] == 0))
      error->all("Both sides of boundary must be periodic");

  if (boundary[0][0] == 0) xperiodic = 1;
  else xperiodic = 0;
  if (boundary[1][0] == 0) yperiodic = 1;
  else yperiodic = 0;
  if (boundary[2][0] == 0) zperiodic = 1;
  else zperiodic = 0;

  periodicity[0] = xperiodic;
  periodicity[1] = yperiodic;
  periodicity[2] = zperiodic;

  nonperiodic = 0;
  if (xperiodic == 0 || yperiodic == 0 || zperiodic == 0) {
    nonperiodic = 1;
    if (boundary[0][0] >= 2 || boundary[0][1] >= 2 ||
	boundary[1][0] >= 2 || boundary[1][1] >= 2 ||
	boundary[2][0] >= 2 || boundary[2][1] >= 2) nonperiodic = 2;
  }
}