git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@279 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp 2007-02-09 21:26:58 +00:00
parent 906520c086
commit 5fdeeabba5
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/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
#include "stdlib.h"
#include "atom_vec_full.h"
#include "atom.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
#define DELTA 10000
/* ---------------------------------------------------------------------- */
AtomVecFull::AtomVecFull(LAMMPS *lmp, int narg, char **arg) :
AtomVec(lmp, narg, arg)
{
molecular = 1;
bonds_allow = 1;
angles_allow = 1;
dihedrals_allow = 1;
impropers_allow = 1;
mass_type = 1;
size_comm = 3;
size_reverse = 3;
size_border = 8;
size_data_atom = 7;
size_data_vel = 4;
xcol_data = 5;
}
/* ----------------------------------------------------------------------
grow atom arrays
n = 0 grows arrays by DELTA
n > 0 allocates arrays to size n
------------------------------------------------------------------------- */
void AtomVecFull::grow(int n)
{
if (n == 0) nmax += DELTA;
else nmax = n;
atom->nmax = nmax;
tag = atom->tag = (int *)
memory->srealloc(atom->tag,nmax*sizeof(int),"atom:tag");
type = atom->type = (int *)
memory->srealloc(atom->type,nmax*sizeof(int),"atom:type");
mask = atom->mask = (int *)
memory->srealloc(atom->mask,nmax*sizeof(int),"atom:mask");
image = atom->image = (int *)
memory->srealloc(atom->image,nmax*sizeof(int),"atom:image");
x = atom->x = memory->grow_2d_double_array(atom->x,nmax,3,"atom:x");
v = atom->v = memory->grow_2d_double_array(atom->v,nmax,3,"atom:v");
f = atom->f = memory->grow_2d_double_array(atom->f,nmax,3,"atom:f");
q = atom->q = (double *)
memory->srealloc(atom->q,nmax*sizeof(double),"atom:q");
molecule = atom->molecule = (int *)
memory->srealloc(atom->molecule,nmax*sizeof(int),"atom:molecule");
nspecial = atom->nspecial =
memory->grow_2d_int_array(atom->nspecial,nmax,3,"atom:nspecial");
special = atom->special =
memory->grow_2d_int_array(atom->special,nmax,atom->maxspecial,
"atom:special");
num_bond = atom->num_bond = (int *)
memory->srealloc(atom->num_bond,nmax*sizeof(int),"atom:num_bond");
bond_type = atom->bond_type =
memory->grow_2d_int_array(atom->bond_type,nmax,atom->bond_per_atom,
"atom:bond_type");
bond_atom = atom->bond_atom =
memory->grow_2d_int_array(atom->bond_atom,nmax,atom->bond_per_atom,
"atom:bond_atom");
num_angle = atom->num_angle = (int *)
memory->srealloc(atom->num_angle,nmax*sizeof(int),"atom:num_angle");
angle_type = atom->angle_type =
memory->grow_2d_int_array(atom->angle_type,nmax,atom->angle_per_atom,
"atom:angle_type");
angle_atom1 = atom->angle_atom1 =
memory->grow_2d_int_array(atom->angle_atom1,nmax,atom->angle_per_atom,
"atom:angle_atom1");
angle_atom2 = atom->angle_atom2 =
memory->grow_2d_int_array(atom->angle_atom2,nmax,atom->angle_per_atom,
"atom:angle_atom2");
angle_atom3 = atom->angle_atom3 =
memory->grow_2d_int_array(atom->angle_atom3,nmax,atom->angle_per_atom,
"atom:angle_atom3");
num_dihedral = atom->num_dihedral = (int *)
memory->srealloc(atom->num_dihedral,nmax*sizeof(int),"atom:num_dihedral");
dihedral_type = atom->dihedral_type =
memory->grow_2d_int_array(atom->dihedral_type,nmax,atom->dihedral_per_atom,
"atom:dihedral_type");
dihedral_atom1 = atom->dihedral_atom1 =
memory->grow_2d_int_array(atom->dihedral_atom1,nmax,
atom->dihedral_per_atom,"atom:dihedral_atom1");
dihedral_atom2 = atom->dihedral_atom2 =
memory->grow_2d_int_array(atom->dihedral_atom2,nmax,
atom->dihedral_per_atom,"atom:dihedral_atom2");
dihedral_atom3 = atom->dihedral_atom3 =
memory->grow_2d_int_array(atom->dihedral_atom3,nmax,
atom->dihedral_per_atom,"atom:dihedral_atom3");
dihedral_atom4 = atom->dihedral_atom4 =
memory->grow_2d_int_array(atom->dihedral_atom4,nmax,
atom->dihedral_per_atom,"atom:dihedral_atom4");
num_improper = atom->num_improper = (int *)
memory->srealloc(atom->num_improper,nmax*sizeof(int),"atom:num_improper");
improper_type = atom->improper_type =
memory->grow_2d_int_array(atom->improper_type,nmax,atom->improper_per_atom,
"atom:improper_type");
improper_atom1 = atom->improper_atom1 =
memory->grow_2d_int_array(atom->improper_atom1,nmax,
atom->improper_per_atom,"atom:improper_atom1");
improper_atom2 = atom->improper_atom2 =
memory->grow_2d_int_array(atom->improper_atom2,nmax,
atom->improper_per_atom,"atom:improper_atom2");
improper_atom3 = atom->improper_atom3 =
memory->grow_2d_int_array(atom->improper_atom3,nmax,
atom->improper_per_atom,"atom:improper_atom3");
improper_atom4 = atom->improper_atom4 =
memory->grow_2d_int_array(atom->improper_atom4,nmax,
atom->improper_per_atom,"atom:improper_atom4");
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->grow_arrays(nmax);
}
/* ---------------------------------------------------------------------- */
void AtomVecFull::reset_ptrs()
{
tag = atom->tag;
type = atom->type;
mask = atom->mask;
image = atom->image;
x = atom->x;
v = atom->v;
f = atom->f;
q = atom->q;
molecule = atom->molecule;
nspecial = atom->nspecial;
special = atom->special;
num_bond = atom->num_bond;
bond_type = atom->bond_type;
bond_atom = atom->bond_atom;
num_angle = atom->num_angle;
angle_type = atom->angle_type;
angle_atom1 = atom->angle_atom1;
angle_atom2 = atom->angle_atom2;
angle_atom3 = atom->angle_atom3;
num_dihedral = atom->num_dihedral;
dihedral_type = atom->dihedral_type;
dihedral_atom1 = atom->dihedral_atom1;
dihedral_atom2 = atom->dihedral_atom2;
dihedral_atom3 = atom->dihedral_atom3;
dihedral_atom4 = atom->dihedral_atom4;
num_improper = atom->num_improper;
improper_type = atom->improper_type;
improper_atom1 = atom->improper_atom1;
improper_atom2 = atom->improper_atom2;
improper_atom3 = atom->improper_atom3;
improper_atom4 = atom->improper_atom4;
}
/* ----------------------------------------------------------------------
zero auxiliary data for owned atom I
data in copy(), not including tag,type,mask,image,x,v
------------------------------------------------------------------------- */
void AtomVecFull::zero_owned(int i)
{
q[i] = 0.0;
molecule[i] = 0;
num_bond[i] = 0;
num_angle[i] = 0;
num_dihedral[i] = 0;
num_improper[i] = 0;
nspecial[i][0] = 0;
nspecial[i][1] = 0;
nspecial[i][2] = 0;
}
/* ----------------------------------------------------------------------
zero auxiliary data for n ghost atoms
data in border(), not including x,tag,type,mask
grow() is here since zero_ghost called first in hybrid::unpack_border()
------------------------------------------------------------------------- */
void AtomVecFull::zero_ghost(int n, int first)
{
int last = first + n;
for (int i = first; i < last; i++) {
if (i == nmax) atom->avec->grow(0);
q[i] = 0.0;
molecule[i] = 0;
}
}
/* ---------------------------------------------------------------------- */
void AtomVecFull::copy(int i, int j)
{
int k;
tag[j] = tag[i];
type[j] = type[i];
mask[j] = mask[i];
image[j] = image[i];
x[j][0] = x[i][0];
x[j][1] = x[i][1];
x[j][2] = x[i][2];
v[j][0] = v[i][0];
v[j][1] = v[i][1];
v[j][2] = v[i][2];
q[j] = q[i];
molecule[j] = molecule[i];
num_bond[j] = num_bond[i];
for (k = 0; k < num_bond[j]; k++) {
bond_type[j][k] = bond_type[i][k];
bond_atom[j][k] = bond_atom[i][k];
}
num_angle[j] = num_angle[i];
for (k = 0; k < num_angle[j]; k++) {
angle_type[j][k] = angle_type[i][k];
angle_atom1[j][k] = angle_atom1[i][k];
angle_atom2[j][k] = angle_atom2[i][k];
angle_atom3[j][k] = angle_atom3[i][k];
}
num_dihedral[j] = num_dihedral[i];
for (k = 0; k < num_dihedral[j]; k++) {
dihedral_type[j][k] = dihedral_type[i][k];
dihedral_atom1[j][k] = dihedral_atom1[i][k];
dihedral_atom2[j][k] = dihedral_atom2[i][k];
dihedral_atom3[j][k] = dihedral_atom3[i][k];
dihedral_atom4[j][k] = dihedral_atom4[i][k];
}
num_improper[j] = num_improper[i];
for (k = 0; k < num_improper[j]; k++) {
improper_type[j][k] = improper_type[i][k];
improper_atom1[j][k] = improper_atom1[i][k];
improper_atom2[j][k] = improper_atom2[i][k];
improper_atom3[j][k] = improper_atom3[i][k];
improper_atom4[j][k] = improper_atom4[i][k];
}
nspecial[j][0] = nspecial[i][0];
nspecial[j][1] = nspecial[i][1];
nspecial[j][2] = nspecial[i][2];
for (k = 0; k < nspecial[j][2]; k++) special[j][k] = special[i][k];
if (atom->nextra_grow)
for (int iextra = 0; iextra < atom->nextra_grow; iextra++)
modify->fix[atom->extra_grow[iextra]]->copy_arrays(i,j);
}
/* ---------------------------------------------------------------------- */
int AtomVecFull::pack_comm(int n, int *list, double *buf, int *pbc_flags)
{
int i,j,m;
m = 0;
if (pbc_flags[0] == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
}
} else {
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + pbc_flags[1]*xprd;
buf[m++] = x[j][1] + pbc_flags[2]*yprd;
buf[m++] = x[j][2] + pbc_flags[3]*zprd;
}
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecFull::unpack_comm(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecFull::pack_reverse(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void AtomVecFull::unpack_reverse(int n, int *list, double *buf)
{
int i,j,m;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
}
}
/* ---------------------------------------------------------------------- */
int AtomVecFull::pack_border(int n, int *list, double *buf,
int *pbc_flags)
{
int i,j,m;
m = 0;
if (pbc_flags[0] == 0) {
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0];
buf[m++] = x[j][1];
buf[m++] = x[j][2];
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
buf[m++] = molecule[j];
}
} else {
double xprd = domain->xprd;
double yprd = domain->yprd;
double zprd = domain->zprd;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = x[j][0] + pbc_flags[1]*xprd;
buf[m++] = x[j][1] + pbc_flags[2]*yprd;
buf[m++] = x[j][2] + pbc_flags[3]*zprd;
buf[m++] = tag[j];
buf[m++] = type[j];
buf[m++] = mask[j];
buf[m++] = q[j];
buf[m++] = molecule[j];
}
}
return m;
}
/* ---------------------------------------------------------------------- */
int AtomVecFull::pack_border_one(int i, double *buf)
{
buf[0] = q[i];
buf[1] = molecule[i];
return 2;
}
/* ---------------------------------------------------------------------- */
void AtomVecFull::unpack_border(int n, int first, double *buf)
{
int i,m,last;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
if (i == nmax) grow(0);
x[i][0] = buf[m++];
x[i][1] = buf[m++];
x[i][2] = buf[m++];
tag[i] = static_cast<int> (buf[m++]);
type[i] = static_cast<int> (buf[m++]);
mask[i] = static_cast<int> (buf[m++]);
q[i] = buf[m++];
molecule[i] = static_cast<int> (buf[m++]);
}
}
/* ---------------------------------------------------------------------- */
int AtomVecFull::unpack_border_one(int i, double *buf)
{
q[i] = buf[0];
molecule[i] = static_cast<int> (buf[1]);
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;
}

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@ -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