forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@279 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
parent
906520c086
commit
5fdeeabba5
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#include "stdlib.h"
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#include "atom_vec_full.h"
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#include "atom.h"
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#include "domain.h"
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#include "modify.h"
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#include "fix.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define MIN(A,B) ((A) < (B)) ? (A) : (B)
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#define MAX(A,B) ((A) > (B)) ? (A) : (B)
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#define DELTA 10000
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/* ---------------------------------------------------------------------- */
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AtomVecFull::AtomVecFull(LAMMPS *lmp, int narg, char **arg) :
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AtomVec(lmp, narg, arg)
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{
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molecular = 1;
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bonds_allow = 1;
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angles_allow = 1;
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dihedrals_allow = 1;
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impropers_allow = 1;
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mass_type = 1;
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size_comm = 3;
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size_reverse = 3;
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size_border = 8;
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size_data_atom = 7;
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size_data_vel = 4;
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xcol_data = 5;
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}
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/* ----------------------------------------------------------------------
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grow atom arrays
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n = 0 grows arrays by DELTA
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n > 0 allocates arrays to size n
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------------------------------------------------------------------------- */
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void AtomVecFull::grow(int n)
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{
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if (n == 0) nmax += DELTA;
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else nmax = n;
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atom->nmax = nmax;
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tag = atom->tag = (int *)
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memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
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type = atom->type = (int *)
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memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
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mask = atom->mask = (int *)
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memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
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image = atom->image = (int *)
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memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
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x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
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v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
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f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
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q = atom->q = (double *)
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memory->srealloc(atom->q,nmax*sizeof(double),"atom:q");
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molecule = atom->molecule = (int *)
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memory->srealloc(atom->molecule,nmax*sizeof(int),"atom:molecule");
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nspecial = atom->nspecial =
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memory->grow_2d_int_array(atom->nspecial,nmax,3,"atom:nspecial");
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special = atom->special =
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memory->grow_2d_int_array(atom->special,nmax,atom->maxspecial,
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"atom:special");
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num_bond = atom->num_bond = (int *)
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memory->srealloc(atom->num_bond,nmax*sizeof(int),"atom:num_bond");
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bond_type = atom->bond_type =
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memory->grow_2d_int_array(atom->bond_type,nmax,atom->bond_per_atom,
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"atom:bond_type");
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bond_atom = atom->bond_atom =
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memory->grow_2d_int_array(atom->bond_atom,nmax,atom->bond_per_atom,
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"atom:bond_atom");
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num_angle = atom->num_angle = (int *)
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memory->srealloc(atom->num_angle,nmax*sizeof(int),"atom:num_angle");
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angle_type = atom->angle_type =
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memory->grow_2d_int_array(atom->angle_type,nmax,atom->angle_per_atom,
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"atom:angle_type");
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angle_atom1 = atom->angle_atom1 =
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memory->grow_2d_int_array(atom->angle_atom1,nmax,atom->angle_per_atom,
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"atom:angle_atom1");
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angle_atom2 = atom->angle_atom2 =
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memory->grow_2d_int_array(atom->angle_atom2,nmax,atom->angle_per_atom,
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"atom:angle_atom2");
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angle_atom3 = atom->angle_atom3 =
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memory->grow_2d_int_array(atom->angle_atom3,nmax,atom->angle_per_atom,
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"atom:angle_atom3");
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num_dihedral = atom->num_dihedral = (int *)
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memory->srealloc(atom->num_dihedral,nmax*sizeof(int),"atom:num_dihedral");
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dihedral_type = atom->dihedral_type =
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memory->grow_2d_int_array(atom->dihedral_type,nmax,atom->dihedral_per_atom,
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"atom:dihedral_type");
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dihedral_atom1 = atom->dihedral_atom1 =
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memory->grow_2d_int_array(atom->dihedral_atom1,nmax,
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atom->dihedral_per_atom,"atom:dihedral_atom1");
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dihedral_atom2 = atom->dihedral_atom2 =
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memory->grow_2d_int_array(atom->dihedral_atom2,nmax,
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atom->dihedral_per_atom,"atom:dihedral_atom2");
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dihedral_atom3 = atom->dihedral_atom3 =
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memory->grow_2d_int_array(atom->dihedral_atom3,nmax,
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atom->dihedral_per_atom,"atom:dihedral_atom3");
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dihedral_atom4 = atom->dihedral_atom4 =
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memory->grow_2d_int_array(atom->dihedral_atom4,nmax,
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atom->dihedral_per_atom,"atom:dihedral_atom4");
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num_improper = atom->num_improper = (int *)
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memory->srealloc(atom->num_improper,nmax*sizeof(int),"atom:num_improper");
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improper_type = atom->improper_type =
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memory->grow_2d_int_array(atom->improper_type,nmax,atom->improper_per_atom,
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"atom:improper_type");
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improper_atom1 = atom->improper_atom1 =
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memory->grow_2d_int_array(atom->improper_atom1,nmax,
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atom->improper_per_atom,"atom:improper_atom1");
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improper_atom2 = atom->improper_atom2 =
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memory->grow_2d_int_array(atom->improper_atom2,nmax,
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atom->improper_per_atom,"atom:improper_atom2");
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improper_atom3 = atom->improper_atom3 =
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memory->grow_2d_int_array(atom->improper_atom3,nmax,
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atom->improper_per_atom,"atom:improper_atom3");
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improper_atom4 = atom->improper_atom4 =
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memory->grow_2d_int_array(atom->improper_atom4,nmax,
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atom->improper_per_atom,"atom:improper_atom4");
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if (atom->nextra_grow)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecFull::reset_ptrs()
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{
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tag = atom->tag;
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type = atom->type;
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mask = atom->mask;
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image = atom->image;
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x = atom->x;
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v = atom->v;
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f = atom->f;
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q = atom->q;
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molecule = atom->molecule;
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nspecial = atom->nspecial;
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special = atom->special;
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num_bond = atom->num_bond;
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bond_type = atom->bond_type;
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bond_atom = atom->bond_atom;
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num_angle = atom->num_angle;
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angle_type = atom->angle_type;
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angle_atom1 = atom->angle_atom1;
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angle_atom2 = atom->angle_atom2;
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angle_atom3 = atom->angle_atom3;
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num_dihedral = atom->num_dihedral;
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dihedral_type = atom->dihedral_type;
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dihedral_atom1 = atom->dihedral_atom1;
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dihedral_atom2 = atom->dihedral_atom2;
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dihedral_atom3 = atom->dihedral_atom3;
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dihedral_atom4 = atom->dihedral_atom4;
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num_improper = atom->num_improper;
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improper_type = atom->improper_type;
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improper_atom1 = atom->improper_atom1;
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improper_atom2 = atom->improper_atom2;
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improper_atom3 = atom->improper_atom3;
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improper_atom4 = atom->improper_atom4;
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}
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/* ----------------------------------------------------------------------
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zero auxiliary data for owned atom I
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data in copy(), not including tag,type,mask,image,x,v
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------------------------------------------------------------------------- */
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void AtomVecFull::zero_owned(int i)
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{
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q[i] = 0.0;
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molecule[i] = 0;
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num_bond[i] = 0;
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num_angle[i] = 0;
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num_dihedral[i] = 0;
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num_improper[i] = 0;
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nspecial[i][0] = 0;
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nspecial[i][1] = 0;
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nspecial[i][2] = 0;
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}
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/* ----------------------------------------------------------------------
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zero auxiliary data for n ghost atoms
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data in border(), not including x,tag,type,mask
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grow() is here since zero_ghost called first in hybrid::unpack_border()
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------------------------------------------------------------------------- */
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void AtomVecFull::zero_ghost(int n, int first)
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{
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int last = first + n;
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for (int i = first; i < last; i++) {
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if (i == nmax) atom->avec->grow(0);
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q[i] = 0.0;
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molecule[i] = 0;
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}
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecFull::copy(int i, int j)
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{
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int k;
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tag[j] = tag[i];
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type[j] = type[i];
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mask[j] = mask[i];
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image[j] = image[i];
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x[j][0] = x[i][0];
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x[j][1] = x[i][1];
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x[j][2] = x[i][2];
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v[j][0] = v[i][0];
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v[j][1] = v[i][1];
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v[j][2] = v[i][2];
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q[j] = q[i];
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molecule[j] = molecule[i];
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num_bond[j] = num_bond[i];
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for (k = 0; k < num_bond[j]; k++) {
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bond_type[j][k] = bond_type[i][k];
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bond_atom[j][k] = bond_atom[i][k];
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}
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num_angle[j] = num_angle[i];
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for (k = 0; k < num_angle[j]; k++) {
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angle_type[j][k] = angle_type[i][k];
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angle_atom1[j][k] = angle_atom1[i][k];
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angle_atom2[j][k] = angle_atom2[i][k];
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angle_atom3[j][k] = angle_atom3[i][k];
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}
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num_dihedral[j] = num_dihedral[i];
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for (k = 0; k < num_dihedral[j]; k++) {
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dihedral_type[j][k] = dihedral_type[i][k];
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dihedral_atom1[j][k] = dihedral_atom1[i][k];
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dihedral_atom2[j][k] = dihedral_atom2[i][k];
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dihedral_atom3[j][k] = dihedral_atom3[i][k];
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dihedral_atom4[j][k] = dihedral_atom4[i][k];
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}
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num_improper[j] = num_improper[i];
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for (k = 0; k < num_improper[j]; k++) {
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improper_type[j][k] = improper_type[i][k];
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improper_atom1[j][k] = improper_atom1[i][k];
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improper_atom2[j][k] = improper_atom2[i][k];
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improper_atom3[j][k] = improper_atom3[i][k];
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improper_atom4[j][k] = improper_atom4[i][k];
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}
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nspecial[j][0] = nspecial[i][0];
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nspecial[j][1] = nspecial[i][1];
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nspecial[j][2] = nspecial[i][2];
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for (k = 0; k < nspecial[j][2]; k++) special[j][k] = special[i][k];
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if (atom->nextra_grow)
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for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
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modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecFull::pack_comm(int n, int *list, double *buf, int *pbc_flags)
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{
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int i,j,m;
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m = 0;
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if (pbc_flags[0] == 0) {
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0];
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buf[m++] = x[j][1];
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buf[m++] = x[j][2];
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}
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} else {
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0] + pbc_flags[1]*xprd;
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buf[m++] = x[j][1] + pbc_flags[2]*yprd;
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buf[m++] = x[j][2] + pbc_flags[3]*zprd;
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}
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecFull::unpack_comm(int n, int first, double *buf)
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{
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int i,m,last;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++) {
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x[i][0] = buf[m++];
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x[i][1] = buf[m++];
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x[i][2] = buf[m++];
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}
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecFull::pack_reverse(int n, int first, double *buf)
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{
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int i,m,last;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++) {
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buf[m++] = f[i][0];
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buf[m++] = f[i][1];
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buf[m++] = f[i][2];
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecFull::unpack_reverse(int n, int *list, double *buf)
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{
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int i,j,m;
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m = 0;
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for (i = 0; i < n; i++) {
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j = list[i];
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f[j][0] += buf[m++];
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f[j][1] += buf[m++];
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f[j][2] += buf[m++];
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}
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecFull::pack_border(int n, int *list, double *buf,
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int *pbc_flags)
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{
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int i,j,m;
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m = 0;
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if (pbc_flags[0] == 0) {
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0];
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buf[m++] = x[j][1];
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buf[m++] = x[j][2];
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buf[m++] = tag[j];
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buf[m++] = type[j];
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buf[m++] = mask[j];
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buf[m++] = q[j];
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buf[m++] = molecule[j];
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}
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} else {
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double xprd = domain->xprd;
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double yprd = domain->yprd;
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double zprd = domain->zprd;
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for (i = 0; i < n; i++) {
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j = list[i];
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buf[m++] = x[j][0] + pbc_flags[1]*xprd;
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buf[m++] = x[j][1] + pbc_flags[2]*yprd;
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buf[m++] = x[j][2] + pbc_flags[3]*zprd;
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buf[m++] = tag[j];
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buf[m++] = type[j];
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buf[m++] = mask[j];
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buf[m++] = q[j];
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buf[m++] = molecule[j];
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}
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}
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return m;
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecFull::pack_border_one(int i, double *buf)
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{
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buf[0] = q[i];
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buf[1] = molecule[i];
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return 2;
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecFull::unpack_border(int n, int first, double *buf)
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{
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int i,m,last;
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m = 0;
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last = first + n;
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for (i = first; i < last; i++) {
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if (i == nmax) grow(0);
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x[i][0] = buf[m++];
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x[i][1] = buf[m++];
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x[i][2] = buf[m++];
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tag[i] = static_cast<int> (buf[m++]);
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type[i] = static_cast<int> (buf[m++]);
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mask[i] = static_cast<int> (buf[m++]);
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q[i] = buf[m++];
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molecule[i] = static_cast<int> (buf[m++]);
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}
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}
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/* ---------------------------------------------------------------------- */
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int AtomVecFull::unpack_border_one(int i, double *buf)
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{
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q[i] = buf[0];
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molecule[i] = static_cast<int> (buf[1]);
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return 2;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
pack data for atom I for sending to another proc
|
||||
xyz must be 1st 3 values, so comm::exchange() can test on them
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int AtomVecFull::pack_exchange(int i, double *buf)
|
||||
{
|
||||
int k;
|
||||
|
||||
int m = 1;
|
||||
buf[m++] = x[i][0];
|
||||
buf[m++] = x[i][1];
|
||||
buf[m++] = x[i][2];
|
||||
buf[m++] = v[i][0];
|
||||
buf[m++] = v[i][1];
|
||||
buf[m++] = v[i][2];
|
||||
buf[m++] = tag[i];
|
||||
buf[m++] = type[i];
|
||||
buf[m++] = mask[i];
|
||||
buf[m++] = image[i];
|
||||
|
||||
buf[m++] = q[i];
|
||||
buf[m++] = molecule[i];
|
||||
|
||||
buf[m++] = num_bond[i];
|
||||
for (k = 0; k < num_bond[i]; k++) {
|
||||
buf[m++] = bond_type[i][k];
|
||||
buf[m++] = bond_atom[i][k];
|
||||
}
|
||||
|
||||
buf[m++] = num_angle[i];
|
||||
for (k = 0; k < num_angle[i]; k++) {
|
||||
buf[m++] = angle_type[i][k];
|
||||
buf[m++] = angle_atom1[i][k];
|
||||
buf[m++] = angle_atom2[i][k];
|
||||
buf[m++] = angle_atom3[i][k];
|
||||
}
|
||||
|
||||
buf[m++] = num_dihedral[i];
|
||||
for (k = 0; k < num_dihedral[i]; k++) {
|
||||
buf[m++] = dihedral_type[i][k];
|
||||
buf[m++] = dihedral_atom1[i][k];
|
||||
buf[m++] = dihedral_atom2[i][k];
|
||||
buf[m++] = dihedral_atom3[i][k];
|
||||
buf[m++] = dihedral_atom4[i][k];
|
||||
}
|
||||
|
||||
buf[m++] = num_improper[i];
|
||||
for (k = 0; k < num_improper[i]; k++) {
|
||||
buf[m++] = improper_type[i][k];
|
||||
buf[m++] = improper_atom1[i][k];
|
||||
buf[m++] = improper_atom2[i][k];
|
||||
buf[m++] = improper_atom3[i][k];
|
||||
buf[m++] = improper_atom4[i][k];
|
||||
}
|
||||
|
||||
buf[m++] = nspecial[i][0];
|
||||
buf[m++] = nspecial[i][1];
|
||||
buf[m++] = nspecial[i][2];
|
||||
for (k = 0; k < nspecial[i][2]; k++) buf[m++] = special[i][k];
|
||||
|
||||
if (atom->nextra_grow)
|
||||
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
|
||||
m += modify->fix[atom->extra_grow[iextra]]->pack_exchange(i,&buf[m]);
|
||||
|
||||
buf[0] = m;
|
||||
return m;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int AtomVecFull::unpack_exchange(double *buf)
|
||||
{
|
||||
int k;
|
||||
|
||||
int nlocal = atom->nlocal;
|
||||
if (nlocal == nmax) grow(0);
|
||||
|
||||
int m = 1;
|
||||
x[nlocal][0] = buf[m++];
|
||||
x[nlocal][1] = buf[m++];
|
||||
x[nlocal][2] = buf[m++];
|
||||
v[nlocal][0] = buf[m++];
|
||||
v[nlocal][1] = buf[m++];
|
||||
v[nlocal][2] = buf[m++];
|
||||
tag[nlocal] = static_cast<int> (buf[m++]);
|
||||
type[nlocal] = static_cast<int> (buf[m++]);
|
||||
mask[nlocal] = static_cast<int> (buf[m++]);
|
||||
image[nlocal] = static_cast<int> (buf[m++]);
|
||||
|
||||
q[nlocal] = buf[m++];
|
||||
molecule[nlocal] = static_cast<int> (buf[m++]);
|
||||
|
||||
num_bond[nlocal] = static_cast<int> (buf[m++]);
|
||||
for (k = 0; k < num_bond[nlocal]; k++) {
|
||||
bond_type[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
bond_atom[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
}
|
||||
|
||||
num_angle[nlocal] = static_cast<int> (buf[m++]);
|
||||
for (k = 0; k < num_angle[nlocal]; k++) {
|
||||
angle_type[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
angle_atom1[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
angle_atom2[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
angle_atom3[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
}
|
||||
|
||||
num_dihedral[nlocal] = static_cast<int> (buf[m++]);
|
||||
for (k = 0; k < num_dihedral[nlocal]; k++) {
|
||||
dihedral_type[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
dihedral_atom1[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
dihedral_atom2[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
dihedral_atom3[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
dihedral_atom4[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
}
|
||||
|
||||
num_improper[nlocal] = static_cast<int> (buf[m++]);
|
||||
for (k = 0; k < num_improper[nlocal]; k++) {
|
||||
improper_type[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
improper_atom1[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
improper_atom2[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
improper_atom3[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
improper_atom4[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
}
|
||||
|
||||
nspecial[nlocal][0] = static_cast<int> (buf[m++]);
|
||||
nspecial[nlocal][1] = static_cast<int> (buf[m++]);
|
||||
nspecial[nlocal][2] = static_cast<int> (buf[m++]);
|
||||
for (k = 0; k < nspecial[nlocal][2]; k++)
|
||||
special[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
|
||||
if (atom->nextra_grow)
|
||||
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
|
||||
m += modify->fix[atom->extra_grow[iextra]]->
|
||||
unpack_exchange(nlocal,&buf[m]);
|
||||
|
||||
atom->nlocal++;
|
||||
return m;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
size of restart data for all atoms owned by this proc
|
||||
include extra data stored by fixes
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int AtomVecFull::size_restart()
|
||||
{
|
||||
int i;
|
||||
|
||||
int nlocal = atom->nlocal;
|
||||
int n = 0;
|
||||
for (i = 0; i < nlocal; i++)
|
||||
n += 17 + 2*num_bond[i] + 4*num_angle[i] +
|
||||
5*num_dihedral[i] + 5*num_improper[i];
|
||||
|
||||
if (atom->nextra_restart)
|
||||
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
|
||||
for (i = 0; i < nlocal; i++)
|
||||
n += modify->fix[atom->extra_restart[iextra]]->size_restart(i);
|
||||
|
||||
return n;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
size of restart data for atom I
|
||||
do not include extra data stored by fixes, included by caller
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int AtomVecFull::size_restart_one(int i)
|
||||
{
|
||||
int n = 17 + 2*num_bond[i] + 4*num_angle[i] +
|
||||
5*num_dihedral[i] + 5*num_improper[i];
|
||||
return n;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
pack atom I's data for restart file including extra quantities
|
||||
xyz must be 1st 3 values, so that read_restart can test on them
|
||||
molecular types may be negative, but write as positive
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int AtomVecFull::pack_restart(int i, double *buf)
|
||||
{
|
||||
int k;
|
||||
|
||||
int m = 1;
|
||||
buf[m++] = x[i][0];
|
||||
buf[m++] = x[i][1];
|
||||
buf[m++] = x[i][2];
|
||||
buf[m++] = tag[i];
|
||||
buf[m++] = type[i];
|
||||
buf[m++] = mask[i];
|
||||
buf[m++] = image[i];
|
||||
buf[m++] = v[i][0];
|
||||
buf[m++] = v[i][1];
|
||||
buf[m++] = v[i][2];
|
||||
|
||||
buf[m++] = q[i];
|
||||
buf[m++] = molecule[i];
|
||||
|
||||
buf[m++] = num_bond[i];
|
||||
for (k = 0; k < num_bond[i]; k++) {
|
||||
buf[m++] = MAX(bond_type[i][k],-bond_type[i][k]);
|
||||
buf[m++] = bond_atom[i][k];
|
||||
}
|
||||
|
||||
buf[m++] = num_angle[i];
|
||||
for (k = 0; k < num_angle[i]; k++) {
|
||||
buf[m++] = MAX(angle_type[i][k],-angle_type[i][k]);
|
||||
buf[m++] = angle_atom1[i][k];
|
||||
buf[m++] = angle_atom2[i][k];
|
||||
buf[m++] = angle_atom3[i][k];
|
||||
}
|
||||
|
||||
buf[m++] = num_dihedral[i];
|
||||
for (k = 0; k < num_dihedral[i]; k++) {
|
||||
buf[m++] = MAX(dihedral_type[i][k],-dihedral_type[i][k]);
|
||||
buf[m++] = dihedral_atom1[i][k];
|
||||
buf[m++] = dihedral_atom2[i][k];
|
||||
buf[m++] = dihedral_atom3[i][k];
|
||||
buf[m++] = dihedral_atom4[i][k];
|
||||
}
|
||||
|
||||
buf[m++] = num_improper[i];
|
||||
for (k = 0; k < num_improper[i]; k++) {
|
||||
buf[m++] = MAX(improper_type[i][k],-improper_type[i][k]);
|
||||
buf[m++] = improper_atom1[i][k];
|
||||
buf[m++] = improper_atom2[i][k];
|
||||
buf[m++] = improper_atom3[i][k];
|
||||
buf[m++] = improper_atom4[i][k];
|
||||
}
|
||||
|
||||
if (atom->nextra_restart)
|
||||
for (int iextra = 0; iextra < atom->nextra_restart; iextra++)
|
||||
m += modify->fix[atom->extra_restart[iextra]]->pack_restart(i,&buf[m]);
|
||||
|
||||
buf[0] = m;
|
||||
return m;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
unpack data for one atom from restart file including extra quantities
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int AtomVecFull::unpack_restart(double *buf)
|
||||
{
|
||||
int k;
|
||||
|
||||
int nlocal = atom->nlocal;
|
||||
if (nlocal == nmax) {
|
||||
grow(0);
|
||||
if (atom->nextra_store)
|
||||
atom->extra = memory->grow_2d_double_array(atom->extra,nmax,
|
||||
atom->nextra_store,
|
||||
"atom:extra");
|
||||
}
|
||||
|
||||
int m = 1;
|
||||
x[nlocal][0] = buf[m++];
|
||||
x[nlocal][1] = buf[m++];
|
||||
x[nlocal][2] = buf[m++];
|
||||
tag[nlocal] = static_cast<int> (buf[m++]);
|
||||
type[nlocal] = static_cast<int> (buf[m++]);
|
||||
mask[nlocal] = static_cast<int> (buf[m++]);
|
||||
image[nlocal] = static_cast<int> (buf[m++]);
|
||||
v[nlocal][0] = buf[m++];
|
||||
v[nlocal][1] = buf[m++];
|
||||
v[nlocal][2] = buf[m++];
|
||||
|
||||
q[nlocal] = buf[m++];
|
||||
molecule[nlocal] = static_cast<int> (buf[m++]);
|
||||
|
||||
num_bond[nlocal] = static_cast<int> (buf[m++]);
|
||||
for (k = 0; k < num_bond[nlocal]; k++) {
|
||||
bond_type[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
bond_atom[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
}
|
||||
|
||||
num_angle[nlocal] = static_cast<int> (buf[m++]);
|
||||
for (k = 0; k < num_angle[nlocal]; k++) {
|
||||
angle_type[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
angle_atom1[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
angle_atom2[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
angle_atom3[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
}
|
||||
|
||||
num_dihedral[nlocal] = static_cast<int> (buf[m++]);
|
||||
for (k = 0; k < num_dihedral[nlocal]; k++) {
|
||||
dihedral_type[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
dihedral_atom1[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
dihedral_atom2[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
dihedral_atom3[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
dihedral_atom4[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
}
|
||||
|
||||
num_improper[nlocal] = static_cast<int> (buf[m++]);
|
||||
for (k = 0; k < num_improper[nlocal]; k++) {
|
||||
improper_type[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
improper_atom1[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
improper_atom2[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
improper_atom3[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
improper_atom4[nlocal][k] = static_cast<int> (buf[m++]);
|
||||
}
|
||||
|
||||
double **extra = atom->extra;
|
||||
if (atom->nextra_store) {
|
||||
int size = static_cast<int> (buf[0]) - m;
|
||||
for (int i = 0; i < size; i++) extra[nlocal][i] = buf[m++];
|
||||
}
|
||||
|
||||
atom->nlocal++;
|
||||
return m;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
create one atom of type itype at x0,y0,z0
|
||||
set other values to defaults
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecFull::create_atom(int itype, double x0, double y0, double z0,
|
||||
int ihybrid)
|
||||
{
|
||||
int nlocal = atom->nlocal;
|
||||
if (nlocal == nmax) grow(0);
|
||||
|
||||
tag[nlocal] = 0;
|
||||
type[nlocal] = itype;
|
||||
x[nlocal][0] = x0;
|
||||
x[nlocal][1] = y0;
|
||||
x[nlocal][2] = z0;
|
||||
mask[nlocal] = 1;
|
||||
image[nlocal] = (512 << 20) | (512 << 10) | 512;
|
||||
v[nlocal][0] = 0.0;
|
||||
v[nlocal][1] = 0.0;
|
||||
v[nlocal][2] = 0.0;
|
||||
|
||||
q[nlocal] = 0.0;
|
||||
molecule[nlocal] = 0;
|
||||
num_bond[nlocal] = 0;
|
||||
num_angle[nlocal] = 0;
|
||||
num_dihedral[nlocal] = 0;
|
||||
num_improper[nlocal] = 0;
|
||||
|
||||
atom->nlocal++;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
unpack one line from Atoms section of data file
|
||||
initialize other atom quantities
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void AtomVecFull::data_atom(double xtmp, double ytmp, double ztmp,
|
||||
int imagetmp, char **values, int ihybrid)
|
||||
{
|
||||
int nlocal = atom->nlocal;
|
||||
if (nlocal == nmax) grow(0);
|
||||
|
||||
tag[nlocal] = atoi(values[0]);
|
||||
if (tag[nlocal] <= 0)
|
||||
error->one("Invalid atom ID in Atoms section of data file");
|
||||
|
||||
molecule[nlocal] = atoi(values[1]);
|
||||
|
||||
type[nlocal] = atoi(values[2]);
|
||||
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes)
|
||||
error->one("Invalid atom type in Atoms section of data file");
|
||||
|
||||
q[nlocal] = atof(values[3]);
|
||||
|
||||
x[nlocal][0] = xtmp;
|
||||
x[nlocal][1] = ytmp;
|
||||
x[nlocal][2] = ztmp;
|
||||
|
||||
image[nlocal] = imagetmp;
|
||||
|
||||
mask[nlocal] = 1;
|
||||
v[nlocal][0] = 0.0;
|
||||
v[nlocal][1] = 0.0;
|
||||
v[nlocal][2] = 0.0;
|
||||
num_bond[nlocal] = 0;
|
||||
num_angle[nlocal] = 0;
|
||||
num_dihedral[nlocal] = 0;
|
||||
num_improper[nlocal] = 0;
|
||||
|
||||
atom->nlocal++;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
return # of bytes of allocated memory
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int AtomVecFull::memory_usage()
|
||||
{
|
||||
int bytes = 0;
|
||||
|
||||
if (atom->memcheck("tag")) bytes += nmax * sizeof(int);
|
||||
if (atom->memcheck("type")) bytes += nmax * sizeof(int);
|
||||
if (atom->memcheck("mask")) bytes += nmax * sizeof(int);
|
||||
if (atom->memcheck("image")) bytes += nmax * sizeof(int);
|
||||
if (atom->memcheck("x")) bytes += nmax*3 * sizeof(double);
|
||||
if (atom->memcheck("v")) bytes += nmax*3 * sizeof(double);
|
||||
if (atom->memcheck("f")) bytes += nmax*3 * sizeof(double);
|
||||
|
||||
if (atom->memcheck("q")) bytes += nmax * sizeof(double);
|
||||
if (atom->memcheck("molecule")) bytes += nmax * sizeof(int);
|
||||
if (atom->memcheck("nspecial")) bytes += nmax*3 * sizeof(int);
|
||||
if (atom->memcheck("special")) bytes += nmax*atom->maxspecial * sizeof(int);
|
||||
|
||||
if (atom->memcheck("num_bond")) bytes += nmax * sizeof(int);
|
||||
if (atom->memcheck("bond_type"))
|
||||
bytes += nmax*atom->bond_per_atom * sizeof(int);
|
||||
if (atom->memcheck("bond_atom"))
|
||||
bytes += nmax*atom->bond_per_atom * sizeof(int);
|
||||
|
||||
if (atom->memcheck("num_angle")) bytes += nmax * sizeof(int);
|
||||
if (atom->memcheck("angle_type"))
|
||||
bytes += nmax*atom->angle_per_atom * sizeof(int);
|
||||
if (atom->memcheck("angle_atom1"))
|
||||
bytes += nmax*atom->angle_per_atom * sizeof(int);
|
||||
if (atom->memcheck("angle_atom2"))
|
||||
bytes += nmax*atom->angle_per_atom * sizeof(int);
|
||||
if (atom->memcheck("angle_atom3"))
|
||||
bytes += nmax*atom->angle_per_atom * sizeof(int);
|
||||
|
||||
if (atom->memcheck("num_dihedral")) bytes += nmax * sizeof(int);
|
||||
if (atom->memcheck("dihedral_type"))
|
||||
bytes += nmax*atom->dihedral_per_atom * sizeof(int);
|
||||
if (atom->memcheck("dihedral_atom1"))
|
||||
bytes += nmax*atom->dihedral_per_atom * sizeof(int);
|
||||
if (atom->memcheck("dihedral_atom2"))
|
||||
bytes += nmax*atom->dihedral_per_atom * sizeof(int);
|
||||
if (atom->memcheck("dihedral_atom3"))
|
||||
bytes += nmax*atom->dihedral_per_atom * sizeof(int);
|
||||
if (atom->memcheck("dihedral_atom4"))
|
||||
bytes += nmax*atom->dihedral_per_atom * sizeof(int);
|
||||
|
||||
if (atom->memcheck("num_improper")) bytes += nmax * sizeof(int);
|
||||
if (atom->memcheck("improper_type"))
|
||||
bytes += nmax*atom->improper_per_atom * sizeof(int);
|
||||
if (atom->memcheck("improper_atom1"))
|
||||
bytes += nmax*atom->improper_per_atom * sizeof(int);
|
||||
if (atom->memcheck("improper_atom2"))
|
||||
bytes += nmax*atom->improper_per_atom * sizeof(int);
|
||||
if (atom->memcheck("improper_atom3"))
|
||||
bytes += nmax*atom->improper_per_atom * sizeof(int);
|
||||
if (atom->memcheck("improper_atom4"))
|
||||
bytes += nmax*atom->improper_per_atom * sizeof(int);
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
|
@ -0,0 +1,68 @@
|
|||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef ATOM_VEC_FULL_H
|
||||
#define ATOM_VEC_FULL_H
|
||||
|
||||
#include "atom_vec.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class AtomVecFull : public AtomVec {
|
||||
public:
|
||||
AtomVecFull(class LAMMPS *, int, char **);
|
||||
void grow(int);
|
||||
void reset_ptrs();
|
||||
void zero_owned(int);
|
||||
void zero_ghost(int, int);
|
||||
void copy(int, int);
|
||||
int pack_comm(int, int *, double *, int *);
|
||||
void unpack_comm(int, int, double *);
|
||||
int pack_reverse(int, int, double *);
|
||||
void unpack_reverse(int, int *, double *);
|
||||
int pack_border(int, int *, double *, int *);
|
||||
int pack_border_one(int, double *);
|
||||
void unpack_border(int, int, double *);
|
||||
int unpack_border_one(int, double *);
|
||||
int pack_exchange(int, double *);
|
||||
int unpack_exchange(double *);
|
||||
int size_restart();
|
||||
int size_restart_one(int);
|
||||
int pack_restart(int, double *);
|
||||
int unpack_restart(double *);
|
||||
void create_atom(int, double, double, double, int);
|
||||
void data_atom(double, double, double, int, char **, int);
|
||||
int memory_usage();
|
||||
|
||||
private:
|
||||
int *tag,*type,*mask,*image;
|
||||
double **x,**v,**f;
|
||||
double *q;
|
||||
int *molecule;
|
||||
int **nspecial,**special;
|
||||
int *num_bond;
|
||||
int **bond_type,**bond_atom;
|
||||
int *num_angle;
|
||||
int **angle_type;
|
||||
int **angle_atom1,**angle_atom2,**angle_atom3;
|
||||
int *num_dihedral;
|
||||
int **dihedral_type;
|
||||
int **dihedral_atom1,**dihedral_atom2,**dihedral_atom3,**dihedral_atom4;
|
||||
int *num_improper;
|
||||
int **improper_type;
|
||||
int **improper_atom1,**improper_atom2,**improper_atom3,**improper_atom4;
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
Loading…
Reference in New Issue