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atom.cpp
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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 "mpi.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "limits.h"
#include "atom.h"
#include "style_atom.h"
#include "atom_vec.h"
#include "atom_vec_ellipsoid.h"
#include "comm.h"
#include "neighbor.h"
#include "force.h"
#include "modify.h"
#include "fix.h"
#include "output.h"
#include "thermo.h"
#include "update.h"
#include "domain.h"
#include "group.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define DELTA 1
#define DELTA_MEMSTR 1024
#define EPSILON 1.0e-6
#define MIN(A,B) ((A) < (B)) ? (A) : (B)
#define MAX(A,B) ((A) > (B)) ? (A) : (B)
/* ---------------------------------------------------------------------- */
Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
{
natoms = 0;
nlocal = nghost = nmax = 0;
ntypes = 0;
nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
nbonds = nangles = ndihedrals = nimpropers = 0;
bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
extra_bond_per_atom = 0;
firstgroupname = NULL;
sortfreq = 1000;
nextsort = 0;
userbinsize = 0.0;
maxbin = maxnext = 0;
binhead = NULL;
next = permute = NULL;
// initialize atom arrays
// customize by adding new array
tag = type = mask = image = NULL;
x = v = f = NULL;
molecule = NULL;
q = NULL;
mu = NULL;
omega = angmom = torque = NULL;
radius = rmass = NULL;
vfrac = s0 = NULL;
x0 = NULL;
ellipsoid = NULL;
spin = NULL;
eradius = ervel = erforce = NULL;
maxspecial = 1;
nspecial = NULL;
special = NULL;
num_bond = NULL;
bond_type = bond_atom = NULL;
num_angle = NULL;
angle_type = angle_atom1 = angle_atom2 = angle_atom3 = NULL;
num_dihedral = NULL;
dihedral_type = dihedral_atom1 = dihedral_atom2 = NULL;
dihedral_atom3 = dihedral_atom4 = NULL;
num_improper = NULL;
improper_type = improper_atom1 = improper_atom2 = NULL;
improper_atom3 = improper_atom4 = NULL;
// initialize atom style and array existence flags
// customize by adding new flag
sphere_flag = ellipsoid_flag = peri_flag = electron_flag = 0;
molecule_flag = q_flag = mu_flag = 0;
rmass_flag = radius_flag = omega_flag = torque_flag = angmom_flag = 0;
vfrac_flag = spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
// ntype-length arrays
mass = NULL;
mass_setflag = NULL;
// callback lists & extra restart info
nextra_grow = nextra_restart = 0;
extra_grow = extra_restart = NULL;
nextra_grow_max = nextra_restart_max = 0;
nextra_store = 0;
extra = NULL;
// default mapping values and hash table primes
tag_enable = 1;
map_style = 0;
map_tag_max = 0;
map_nhash = 0;
nprimes = 38;
primes = new int[nprimes];
int plist[] = {5041,10007,20011,30011,40009,50021,60013,70001,80021,
90001,100003,110017,120011,130003,140009,150001,160001,
170003,180001,190027,200003,210011,220009,230003,240007,
250007,260003,270001,280001,290011,300007,310019,320009,
330017,340007,350003,362881,3628801};
for (int i = 0; i < nprimes; i++) primes[i] = plist[i];
// default atom style = atomic
atom_style = NULL;
avec = NULL;
create_avec("atomic",0,NULL);
}
/* ---------------------------------------------------------------------- */
Atom::~Atom()
{
delete [] atom_style;
delete avec;
delete [] firstgroupname;
memory->destroy(binhead);
memory->destroy(next);
memory->destroy(permute);
// delete atom arrays
// customize by adding new array
memory->destroy(tag);
memory->destroy(type);
memory->destroy(mask);
memory->destroy(image);
memory->destroy(x);
memory->destroy(v);
memory->destroy(f);
memory->destroy(q);
memory->destroy(mu);
memory->destroy(omega);
memory->destroy(angmom);
memory->destroy(torque);
memory->destroy(radius);
memory->destroy(rmass);
memory->destroy(vfrac);
memory->destroy(s0);
memory->destroy(x0);
memory->destroy(ellipsoid);
memory->destroy(spin);
memory->destroy(eradius);
memory->destroy(ervel);
memory->destroy(erforce);
memory->destroy(molecule);
memory->destroy(nspecial);
memory->destroy(special);
memory->destroy(num_bond);
memory->destroy(bond_type);
memory->destroy(bond_atom);
memory->destroy(num_angle);
memory->destroy(angle_type);
memory->destroy(angle_atom1);
memory->destroy(angle_atom2);
memory->destroy(angle_atom3);
memory->destroy(num_dihedral);
memory->destroy(dihedral_type);
memory->destroy(dihedral_atom1);
memory->destroy(dihedral_atom2);
memory->destroy(dihedral_atom3);
memory->destroy(dihedral_atom4);
memory->destroy(num_improper);
memory->destroy(improper_type);
memory->destroy(improper_atom1);
memory->destroy(improper_atom2);
memory->destroy(improper_atom3);
memory->destroy(improper_atom4);
// delete per-type arrays
delete [] mass;
delete [] mass_setflag;
// delete extra arrays
memory->destroy(extra_grow);
memory->destroy(extra_restart);
memory->destroy(extra);
// delete mapping data structures
map_delete();
delete [] primes;
}
/* ----------------------------------------------------------------------
copy modify settings from old Atom class to current Atom class
------------------------------------------------------------------------- */
void Atom::settings(Atom *old)
{
map_style = old->map_style;
}
/* ----------------------------------------------------------------------
create an AtomVec style
called from input script, restart file, replicate
------------------------------------------------------------------------- */
void Atom::create_avec(const char *style, int narg, char **arg)
{
delete [] atom_style;
if (avec) delete avec;
// unset atom style and array existence flags
// may have been set by old avec
// customize by adding new flag
sphere_flag = ellipsoid_flag = peri_flag = electron_flag = 0;
molecule_flag = q_flag = mu_flag = 0;
rmass_flag = radius_flag = omega_flag = torque_flag = angmom_flag = 0;
vfrac_flag = spin_flag = eradius_flag = ervel_flag = erforce_flag = 0;
avec = new_avec(style,narg,arg);
int n = strlen(style) + 1;
atom_style = new char[n];
strcpy(atom_style,style);
// if molecular system, default is to have array map
molecular = avec->molecular;
if (map_style == 0 && molecular) map_style = 1;
}
/* ----------------------------------------------------------------------
generate an AtomVec class
------------------------------------------------------------------------- */
AtomVec *Atom::new_avec(const char *style, int narg, char **arg)
{
if (0) return NULL;
#define ATOM_CLASS
#define AtomStyle(key,Class) \
else if (strcmp(style,#key) == 0) return new Class(lmp,narg,arg);
#include "style_atom.h"
#undef ATOM_CLASS
else error->all("Invalid atom style");
return NULL;
}
/* ---------------------------------------------------------------------- */
void Atom::init()
{
// delete extra array since it doesn't persist past first run
if (nextra_store) {
memory->destroy(extra);
extra = NULL;
nextra_store = 0;
}
// check arrays that are atom type in length
check_mass();
// setup of firstgroup
if (firstgroupname) {
firstgroup = group->find(firstgroupname);
if (firstgroup < 0)
error->all("Could not find atom_modify first group ID");
} else firstgroup = -1;
// init AtomVec
avec->init();
}
/* ---------------------------------------------------------------------- */
void Atom::setup()
{
// setup bins for sorting
// cannot do this in init() because uses neighbor cutoff
if (sortfreq > 0) setup_sort_bins();
}
/* ----------------------------------------------------------------------
return ptr to AtomVec class if matches style or to matching hybrid sub-class
return NULL if no match
------------------------------------------------------------------------- */
AtomVec *Atom::style_match(const char *style)
{
if (strcmp(atom_style,style) == 0) return avec;
else if (strcmp(atom_style,"hybrid") == 0) {
AtomVecHybrid *avec_hybrid = (AtomVecHybrid *) avec;
for (int i = 0; i < avec_hybrid->nstyles; i++)
if (strcmp(avec_hybrid->keywords[i],style) == 0)
return avec_hybrid->styles[i];
}
return NULL;
}
/* ----------------------------------------------------------------------
modify parameters of the atom style
some options can only be invoked before simulation box is defined
first and sort options cannot be used together
------------------------------------------------------------------------- */
void Atom::modify_params(int narg, char **arg)
{
if (narg == 0) error->all("Illegal atom_modify command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"map") == 0) {
if (iarg+2 > narg) error->all("Illegal atom_modify command");
if (strcmp(arg[iarg+1],"array") == 0) map_style = 1;
else if (strcmp(arg[iarg+1],"hash") == 0) map_style = 2;
else error->all("Illegal atom_modify command");
if (domain->box_exist)
error->all("Atom_modify map command after simulation box is defined");
iarg += 2;
} else if (strcmp(arg[iarg],"first") == 0) {
if (iarg+2 > narg) error->all("Illegal atom_modify command");
if (strcmp(arg[iarg+1],"all") == 0) {
delete [] firstgroupname;
firstgroupname = NULL;
} else {
int n = strlen(arg[iarg+1]) + 1;
firstgroupname = new char[n];
strcpy(firstgroupname,arg[iarg+1]);
sortfreq = 0;
}
iarg += 2;
} else if (strcmp(arg[iarg],"sort") == 0) {
if (iarg+3 > narg) error->all("Illegal atom_modify command");
sortfreq = atoi(arg[iarg+1]);
userbinsize = atof(arg[iarg+2]);
if (sortfreq < 0 || userbinsize < 0.0)
error->all("Illegal atom_modify command");
if (sortfreq >= 0 && firstgroupname)
error->all("Atom_modify sort and first options "
"cannot be used together");
iarg += 3;
} else error->all("Illegal atom_modify command");
}
}
/* ----------------------------------------------------------------------
allocate and initialize array or hash table for global -> local map
set map_tag_max = largest atom ID (may be larger than natoms)
for array option:
array length = 1 to largest tag of any atom
set entire array to -1 as initial values
for hash option:
map_nhash = length of hash table
map_nbucket = # of hash buckets, prime larger than map_nhash
so buckets will only be filled with 0 or 1 atoms on average
------------------------------------------------------------------------- */
void Atom::map_init()
{
map_delete();
if (tag_enable == 0)
error->all("Cannot create an atom map unless atoms have IDs");
int max = 0;
for (int i = 0; i < nlocal; i++) max = MAX(max,tag[i]);
MPI_Allreduce(&max,&map_tag_max,1,MPI_INT,MPI_MAX,world);
if (map_style == 1) {
memory->create(map_array,map_tag_max+1,"atom:map_array");
for (int i = 0; i <= map_tag_max; i++) map_array[i] = -1;
} else {
// map_nhash = max of atoms/proc or total atoms, times 2, at least 1000
int nper = static_cast<int> (natoms/comm->nprocs);
map_nhash = MAX(nper,nmax);
if (map_nhash > natoms) map_nhash = static_cast<int> (natoms);
if (comm->nprocs > 1) map_nhash *= 2;
map_nhash = MAX(map_nhash,1000);
// map_nbucket = prime just larger than map_nhash
int n = map_nhash/10000;
n = MIN(n,nprimes-1);
map_nbucket = primes[n];
if (map_nbucket < map_nhash && n < nprimes-1) map_nbucket = primes[n+1];
// set all buckets to empty
// set hash to map_nhash in length
// put all hash entries in free list and point them to each other
map_bucket = new int[map_nbucket];
for (int i = 0; i < map_nbucket; i++) map_bucket[i] = -1;
map_hash = new HashElem[map_nhash];
map_nused = 0;
map_free = 0;
for (int i = 0; i < map_nhash; i++) map_hash[i].next = i+1;
map_hash[map_nhash-1].next = -1;
}
}
/* ----------------------------------------------------------------------
clear global -> local map for all of my own and ghost atoms
for hash table option:
global ID may not be in table if image atom was already cleared
------------------------------------------------------------------------- */
void Atom::map_clear()
{
if (map_style == 1) {
int nall = nlocal + nghost;
for (int i = 0; i < nall; i++) map_array[tag[i]] = -1;
} else {
int previous,global,ibucket,index;
int nall = nlocal + nghost;
for (int i = 0; i < nall; i++) {
// search for key
// if don't find it, done
previous = -1;
global = tag[i];
ibucket = global % map_nbucket;
index = map_bucket[ibucket];
while (index > -1) {
if (map_hash[index].global == global) break;
previous = index;
index = map_hash[index].next;
}
if (index == -1) continue;
// delete the hash entry and add it to free list
// special logic if entry is 1st in the bucket
if (previous == -1) map_bucket[ibucket] = map_hash[index].next;
else map_hash[previous].next = map_hash[index].next;
map_hash[index].next = map_free;
map_free = index;
map_nused--;
}
}
}
/* ----------------------------------------------------------------------
set global -> local map for all of my own and ghost atoms
loop in reverse order so that nearby images take precedence over far ones
and owned atoms take precedence over images
this enables valid lookups of bond topology atoms
for hash table option:
if hash table too small, re-init
global ID may already be in table if image atom was set
------------------------------------------------------------------------- */
void Atom::map_set()
{
if (map_style == 1) {
int nall = nlocal + nghost;
for (int i = nall-1; i >= 0 ; i--) map_array[tag[i]] = i;
} else {
int previous,global,ibucket,index;
int nall = nlocal + nghost;
if (nall > map_nhash) map_init();
for (int i = nall-1; i >= 0 ; i--) {
// search for key
// if found it, just overwrite local value with index
previous = -1;
global = tag[i];
ibucket = global % map_nbucket;
index = map_bucket[ibucket];
while (index > -1) {
if (map_hash[index].global == global) break;
previous = index;
index = map_hash[index].next;
}
if (index > -1) {
map_hash[index].local = i;
continue;
}
// take one entry from free list
// add the new global/local pair as entry at end of bucket list
// special logic if this entry is 1st in bucket
index = map_free;
map_free = map_hash[map_free].next;
if (previous == -1) map_bucket[ibucket] = index;
else map_hash[previous].next = index;
map_hash[index].global = global;
map_hash[index].local = i;
map_hash[index].next = -1;
map_nused++;
}
}
}
/* ----------------------------------------------------------------------
set global to local map for one atom
for hash table option:
global ID may already be in table if atom was already set
------------------------------------------------------------------------- */
void Atom::map_one(int global, int local)
{
if (map_style == 1) map_array[global] = local;
else {
// search for key
// if found it, just overwrite local value with index
int previous = -1;
int ibucket = global % map_nbucket;
int index = map_bucket[ibucket];
while (index > -1) {
if (map_hash[index].global == global) break;
previous = index;
index = map_hash[index].next;
}
if (index > -1) {
map_hash[index].local = local;
return;
}
// take one entry from free list
// add the new global/local pair as entry at end of bucket list
// special logic if this entry is 1st in bucket
index = map_free;
map_free = map_hash[map_free].next;
if (previous == -1) map_bucket[ibucket] = index;
else map_hash[previous].next = index;
map_hash[index].global = global;
map_hash[index].local = local;
map_hash[index].next = -1;
map_nused++;
}
}
/* ----------------------------------------------------------------------
free the array or hash table for global to local mapping
------------------------------------------------------------------------- */
void Atom::map_delete()
{
if (map_style == 1) {
if (map_tag_max) memory->destroy(map_array);
} else {
if (map_nhash) {
delete [] map_bucket;
delete [] map_hash;
}
map_nhash = 0;
}
map_tag_max = 0;
}
/* ----------------------------------------------------------------------
lookup global ID in hash table, return local index
------------------------------------------------------------------------- */
int Atom::map_find_hash(int global)
{
int local = -1;
int index = map_bucket[global % map_nbucket];
while (index > -1) {
if (map_hash[index].global == global) {
local = map_hash[index].local;
break;
}
index = map_hash[index].next;
}
return local;
}
/* ----------------------------------------------------------------------
add unique tags to any atoms with tag = 0
new tags are grouped by proc and start after max current tag
called after creating new atoms
------------------------------------------------------------------------- */
void Atom::tag_extend()
{
// maxtag_all = max tag for all atoms
int maxtag = 0;
for (int i = 0; i < nlocal; i++) maxtag = MAX(maxtag,tag[i]);
int maxtag_all;
MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_INT,MPI_MAX,world);
// notag = # of atoms I own with no tag (tag = 0)
// notag_sum = # of total atoms on procs <= me with no tag
int notag = 0;
for (int i = 0; i < nlocal; i++) if (tag[i] == 0) notag++;
int notag_sum;
MPI_Scan(&notag,&notag_sum,1,MPI_INT,MPI_SUM,world);
// itag = 1st new tag that my untagged atoms should use
int itag = maxtag_all + notag_sum - notag + 1;
for (int i = 0; i < nlocal; i++) if (tag[i] == 0) tag[i] = itag++;
}
/* ----------------------------------------------------------------------
check that atom IDs span range from 1 to Natoms
return 0 if mintag != 1 or maxtag != Natoms
return 1 if OK
doesn't actually check if all tag values are used
------------------------------------------------------------------------- */
int Atom::tag_consecutive()
{
int idmin = MAXTAGINT;
int idmax = 0;
for (int i = 0; i < nlocal; i++) {
idmin = MIN(idmin,tag[i]);
idmax = MAX(idmax,tag[i]);
}
int idminall,idmaxall;
MPI_Allreduce(&idmin,&idminall,1,MPI_INT,MPI_MIN,world);
MPI_Allreduce(&idmax,&idmaxall,1,MPI_INT,MPI_MAX,world);
if (idminall != 1 || idmaxall != static_cast<int> (natoms)) return 0;
return 1;
}
/* ----------------------------------------------------------------------
count and return words in a single line
make copy of line before using strtok so as not to change line
trim anything from '#' onward
------------------------------------------------------------------------- */
int Atom::count_words(const char *line)
{
int n = strlen(line) + 1;
char *copy;
memory->create(copy,n,"atom:copy");
strcpy(copy,line);
char *ptr;
if (ptr = strchr(copy,'#')) *ptr = '\0';
if (strtok(copy," \t\n\r\f") == NULL) {
memory->destroy(copy);
return 0;
}
n = 1;
while (strtok(NULL," \t\n\r\f")) n++;
memory->destroy(copy);
return n;
}
/* ----------------------------------------------------------------------
unpack n lines from Atom section of data file
call style-specific routine to parse line
------------------------------------------------------------------------- */
void Atom::data_atoms(int n, char *buf)
{
int m,imagedata,xptr,iptr;
double xdata[3],lamda[3],sublo[3],subhi[3];
double *coord;
char *next;
next = strchr(buf,'\n');
*next = '\0';
int nwords = count_words(buf);
*next = '\n';
if (nwords != avec->size_data_atom && nwords != avec->size_data_atom + 3)
error->all("Incorrect atom format in data file");
char **values = new char*[nwords];
// set bounds for my proc
// if periodic and I am lo/hi proc, adjust bounds by EPSILON
// insures all data atoms will be owned even with round-off
int triclinic = domain->triclinic;
if (triclinic == 0) {
sublo[0] = domain->sublo[0]; subhi[0] = domain->subhi[0];
sublo[1] = domain->sublo[1]; subhi[1] = domain->subhi[1];
sublo[2] = domain->sublo[2]; subhi[2] = domain->subhi[2];
} else {
sublo[0] = domain->sublo_lamda[0]; subhi[0] = domain->subhi_lamda[0];
sublo[1] = domain->sublo_lamda[1]; subhi[1] = domain->subhi_lamda[1];
sublo[2] = domain->sublo_lamda[2]; subhi[2] = domain->subhi_lamda[2];
}
if (domain->xperiodic) {
if (comm->myloc[0] == 0) sublo[0] -= EPSILON;
if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] += EPSILON;
}
if (domain->yperiodic) {
if (comm->myloc[1] == 0) sublo[1] -= EPSILON;
if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] += EPSILON;
}
if (domain->zperiodic) {
if (comm->myloc[2] == 0) sublo[2] -= EPSILON;
if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] += EPSILON;
}
// xptr = which word in line starts xyz coords
// iptr = which word in line starts ix,iy,iz image flags
xptr = avec->xcol_data - 1;
int imageflag = 0;
if (nwords > avec->size_data_atom) imageflag = 1;
if (imageflag) iptr = nwords - 3;
// loop over lines of atom data
// tokenize the line into values
// extract xyz coords and image flags
// remap atom into simulation box
// if atom is in my sub-domain, unpack its values
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
values[0] = strtok(buf," \t\n\r\f");
for (m = 1; m < nwords; m++)
values[m] = strtok(NULL," \t\n\r\f");
if (imageflag)
imagedata = ((atoi(values[iptr+2]) + 512 & 1023) << 20) |
((atoi(values[iptr+1]) + 512 & 1023) << 10) |
(atoi(values[iptr]) + 512 & 1023);
else imagedata = (512 << 20) | (512 << 10) | 512;
xdata[0] = atof(values[xptr]);
xdata[1] = atof(values[xptr+1]);
xdata[2] = atof(values[xptr+2]);
domain->remap(xdata,imagedata);
if (triclinic) {
domain->x2lamda(xdata,lamda);
coord = lamda;
} else coord = xdata;
if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2])
avec->data_atom(xdata,imagedata,values);
buf = next + 1;
}
delete [] values;
}
/* ----------------------------------------------------------------------
unpack n lines from Velocity section of data file
check that atom IDs are > 0 and <= map_tag_max
call style-specific routine to parse line
------------------------------------------------------------------------- */
void Atom::data_vels(int n, char *buf)
{
int j,m,tagdata;
char *next;
next = strchr(buf,'\n');
*next = '\0';
int nwords = count_words(buf);
*next = '\n';
if (nwords != avec->size_data_vel)
error->all("Incorrect velocity format in data file");
char **values = new char*[nwords];
// loop over lines of atom velocities
// tokenize the line into values
// if I own atom tag, unpack its values
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
values[0] = strtok(buf," \t\n\r\f");
for (j = 1; j < nwords; j++)
values[j] = strtok(NULL," \t\n\r\f");
tagdata = atoi(values[0]);
if (tagdata <= 0 || tagdata > map_tag_max)
error->one("Invalid atom ID in Velocities section of data file");
if ((m = map(tagdata)) >= 0) avec->data_vel(m,&values[1]);
buf = next + 1;
}
delete [] values;
}
/* ----------------------------------------------------------------------
unpack n lines from atom-style specific section of data file
check that atom IDs are > 0 and <= map_tag_max
call style-specific routine to parse line
------------------------------------------------------------------------- */
void Atom::data_bonus(int n, char *buf, AtomVec *avec_bonus)
{
int j,m,tagdata;
char *next;
next = strchr(buf,'\n');
*next = '\0';
int nwords = count_words(buf);
*next = '\n';
if (nwords != avec_bonus->size_data_bonus)
error->all("Incorrect bonus data format in data file");
char **values = new char*[nwords];
// loop over lines of bonus atom data
// tokenize the line into values
// if I own atom tag, unpack its values
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
values[0] = strtok(buf," \t\n\r\f");
for (j = 1; j < nwords; j++)
values[j] = strtok(NULL," \t\n\r\f");
tagdata = atoi(values[0]);
if (tagdata <= 0 || tagdata > map_tag_max)
error->one("Invalid atom ID in Bonus section of data file");
// ok to call child's data_atom_bonus() method thru parent avec_bonus,
// since data_bonus() was called with child ptr, and method is virtual
if ((m = map(tagdata)) >= 0) avec_bonus->data_atom_bonus(m,&values[1]);
buf = next + 1;
}
delete [] values;
}
/* ----------------------------------------------------------------------
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_bonds(int n, char *buf)
{
int m,tmp,itype,atom1,atom2;
char *next;
int newton_bond = force->newton_bond;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
sscanf(buf,"%d %d %d %d",&tmp,&itype,&atom1,&atom2);
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max)
error->one("Invalid atom ID in Bonds section of data file");
if (itype <= 0 || itype > nbondtypes)
error->one("Invalid bond type in Bonds section of data file");
if ((m = map(atom1)) >= 0) {
bond_type[m][num_bond[m]] = itype;
bond_atom[m][num_bond[m]] = atom2;
num_bond[m]++;
}
if (newton_bond == 0) {
if ((m = map(atom2)) >= 0) {
bond_type[m][num_bond[m]] = itype;
bond_atom[m][num_bond[m]] = atom1;
num_bond[m]++;
}
}
buf = next + 1;
}
}
/* ----------------------------------------------------------------------
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_angles(int n, char *buf)
{
int m,tmp,itype,atom1,atom2,atom3;
char *next;
int newton_bond = force->newton_bond;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
sscanf(buf,"%d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3);
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
atom3 <= 0 || atom3 > map_tag_max)
error->one("Invalid atom ID in Angles section of data file");
if (itype <= 0 || itype > nangletypes)
error->one("Invalid angle type in Angles section of data file");
if ((m = map(atom2)) >= 0) {
angle_type[m][num_angle[m]] = itype;
angle_atom1[m][num_angle[m]] = atom1;
angle_atom2[m][num_angle[m]] = atom2;
angle_atom3[m][num_angle[m]] = atom3;
num_angle[m]++;
}
if (newton_bond == 0) {
if ((m = map(atom1)) >= 0) {
angle_type[m][num_angle[m]] = itype;
angle_atom1[m][num_angle[m]] = atom1;
angle_atom2[m][num_angle[m]] = atom2;
angle_atom3[m][num_angle[m]] = atom3;
num_angle[m]++;
}
if ((m = map(atom3)) >= 0) {
angle_type[m][num_angle[m]] = itype;
angle_atom1[m][num_angle[m]] = atom1;
angle_atom2[m][num_angle[m]] = atom2;
angle_atom3[m][num_angle[m]] = atom3;
num_angle[m]++;
}
}
buf = next + 1;
}
}
/* ----------------------------------------------------------------------
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_dihedrals(int n, char *buf)
{
int m,tmp,itype,atom1,atom2,atom3,atom4;
char *next;
int newton_bond = force->newton_bond;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
sscanf(buf,"%d %d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
atom3 <= 0 || atom3 > map_tag_max ||
atom4 <= 0 || atom4 > map_tag_max)
error->one("Invalid atom ID in Dihedrals section of data file");
if (itype <= 0 || itype > ndihedraltypes)
error->one("Invalid dihedral type in Dihedrals section of data file");
if ((m = map(atom2)) >= 0) {
dihedral_type[m][num_dihedral[m]] = itype;
dihedral_atom1[m][num_dihedral[m]] = atom1;
dihedral_atom2[m][num_dihedral[m]] = atom2;
dihedral_atom3[m][num_dihedral[m]] = atom3;
dihedral_atom4[m][num_dihedral[m]] = atom4;
num_dihedral[m]++;
}
if (newton_bond == 0) {
if ((m = map(atom1)) >= 0) {
dihedral_type[m][num_dihedral[m]] = itype;
dihedral_atom1[m][num_dihedral[m]] = atom1;
dihedral_atom2[m][num_dihedral[m]] = atom2;
dihedral_atom3[m][num_dihedral[m]] = atom3;
dihedral_atom4[m][num_dihedral[m]] = atom4;
num_dihedral[m]++;
}
if ((m = map(atom3)) >= 0) {
dihedral_type[m][num_dihedral[m]] = itype;
dihedral_atom1[m][num_dihedral[m]] = atom1;
dihedral_atom2[m][num_dihedral[m]] = atom2;
dihedral_atom3[m][num_dihedral[m]] = atom3;
dihedral_atom4[m][num_dihedral[m]] = atom4;
num_dihedral[m]++;
}
if ((m = map(atom4)) >= 0) {
dihedral_type[m][num_dihedral[m]] = itype;
dihedral_atom1[m][num_dihedral[m]] = atom1;
dihedral_atom2[m][num_dihedral[m]] = atom2;
dihedral_atom3[m][num_dihedral[m]] = atom3;
dihedral_atom4[m][num_dihedral[m]] = atom4;
num_dihedral[m]++;
}
}
buf = next + 1;
}
}
/* ----------------------------------------------------------------------
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_impropers(int n, char *buf)
{
int m,tmp,itype,atom1,atom2,atom3,atom4;
char *next;
int newton_bond = force->newton_bond;
for (int i = 0; i < n; i++) {
next = strchr(buf,'\n');
*next = '\0';
sscanf(buf,"%d %d %d %d %d %d",&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
atom3 <= 0 || atom3 > map_tag_max ||
atom4 <= 0 || atom4 > map_tag_max)
error->one("Invalid atom ID in Impropers section of data file");
if (itype <= 0 || itype > nimpropertypes)
error->one("Invalid improper type in Impropers section of data file");
if ((m = map(atom2)) >= 0) {
improper_type[m][num_improper[m]] = itype;
improper_atom1[m][num_improper[m]] = atom1;
improper_atom2[m][num_improper[m]] = atom2;
improper_atom3[m][num_improper[m]] = atom3;
improper_atom4[m][num_improper[m]] = atom4;
num_improper[m]++;
}
if (newton_bond == 0) {
if ((m = map(atom1)) >= 0) {
improper_type[m][num_improper[m]] = itype;
improper_atom1[m][num_improper[m]] = atom1;
improper_atom2[m][num_improper[m]] = atom2;
improper_atom3[m][num_improper[m]] = atom3;
improper_atom4[m][num_improper[m]] = atom4;
num_improper[m]++;
}
if ((m = map(atom3)) >= 0) {
improper_type[m][num_improper[m]] = itype;
improper_atom1[m][num_improper[m]] = atom1;
improper_atom2[m][num_improper[m]] = atom2;
improper_atom3[m][num_improper[m]] = atom3;
improper_atom4[m][num_improper[m]] = atom4;
num_improper[m]++;
}
if ((m = map(atom4)) >= 0) {
improper_type[m][num_improper[m]] = itype;
improper_atom1[m][num_improper[m]] = atom1;
improper_atom2[m][num_improper[m]] = atom2;
improper_atom3[m][num_improper[m]] = atom3;
improper_atom4[m][num_improper[m]] = atom4;
num_improper[m]++;
}
}
buf = next + 1;
}
}
/* ----------------------------------------------------------------------
allocate arrays of length ntypes
only done after ntypes is set
------------------------------------------------------------------------- */
void Atom::allocate_type_arrays()
{
if (avec->mass_type) {
mass = new double[ntypes+1];
mass_setflag = new int[ntypes+1];
for (int itype = 1; itype <= ntypes; itype++) mass_setflag[itype] = 0;
}
}
/* ----------------------------------------------------------------------
set a mass and flag it as set
called from reading of data file
------------------------------------------------------------------------- */
void Atom::set_mass(const char *str)
{
if (mass == NULL) error->all("Cannot set mass for this atom style");
int itype;
double mass_one;
int n = sscanf(str,"%d %lg",&itype,&mass_one);
if (n != 2) error->all("Invalid mass line in data file");
if (itype < 1 || itype > ntypes) error->all("Invalid type for mass set");
mass[itype] = mass_one;
mass_setflag[itype] = 1;
if (mass[itype] <= 0.0) error->all("Invalid mass value");
}
/* ----------------------------------------------------------------------
set a mass and flag it as set
called from EAM pair routine
------------------------------------------------------------------------- */
void Atom::set_mass(int itype, double value)
{
if (mass == NULL) error->all("Cannot set mass for this atom style");
if (itype < 1 || itype > ntypes) error->all("Invalid type for mass set");
mass[itype] = value;
mass_setflag[itype] = 1;
if (mass[itype] <= 0.0) error->all("Invalid mass value");
}
/* ----------------------------------------------------------------------
set one or more masses and flag them as set
called from reading of input script
------------------------------------------------------------------------- */
void Atom::set_mass(int narg, char **arg)
{
if (mass == NULL) error->all("Cannot set mass for this atom style");
int lo,hi;
force->bounds(arg[0],ntypes,lo,hi);
if (lo < 1 || hi > ntypes) error->all("Invalid type for mass set");
for (int itype = lo; itype <= hi; itype++) {
mass[itype] = atof(arg[1]);
mass_setflag[itype] = 1;
if (mass[itype] <= 0.0) error->all("Invalid mass value");
}
}
/* ----------------------------------------------------------------------
set all masses as read in from restart file
------------------------------------------------------------------------- */
void Atom::set_mass(double *values)
{
for (int itype = 1; itype <= ntypes; itype++) {
mass[itype] = values[itype];
mass_setflag[itype] = 1;
}
}
/* ----------------------------------------------------------------------
check that all masses have been set
------------------------------------------------------------------------- */
void Atom::check_mass()
{
if (mass == NULL) return;
for (int itype = 1; itype <= ntypes; itype++)
if (mass_setflag[itype] == 0) error->all("All masses are not set");
}
/* ----------------------------------------------------------------------
check that radii of all particles of itype are the same
return 1 if true, else return 0
also return the radius value for that type
------------------------------------------------------------------------- */
int Atom::radius_consistency(int itype, double &rad)
{
double value = -1.0;
int flag = 0;
for (int i = 0; i < nlocal; i++) {
if (type[i] != itype) continue;
if (value < 0.0) value = radius[i];
else if (value != radius[i]) flag = 1;
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall) return 0;
MPI_Allreduce(&value,&rad,1,MPI_DOUBLE,MPI_MAX,world);
return 1;
}
/* ----------------------------------------------------------------------
check that shape of all particles of itype are the same
return 1 if true, else return 0
also return the 3 shape params for itype
------------------------------------------------------------------------- */
int Atom::shape_consistency(int itype,
double &shapex, double &shapey, double &shapez)
{
double zero[3] = {0.0, 0.0, 0.0};
double one[3] = {-1.0, -1.0, -1.0};
double *shape;
AtomVecEllipsoid *avec_ellipsoid =
(AtomVecEllipsoid *) style_match("ellipsoid");
AtomVecEllipsoid::Bonus *bonus = avec_ellipsoid->bonus;
int flag = 0;
for (int i = 0; i < nlocal; i++) {
if (type[i] != itype) continue;
if (ellipsoid[i] < 0) shape = zero;
else shape = bonus[ellipsoid[i]].shape;
if (one[0] < 0.0) {
one[0] = shape[0];
one[1] = shape[1];
one[2] = shape[2];
} else if (one[0] != shape[0] || one[1] != shape[1] || one[2] != shape[2])
flag = 1;
}
int flagall;
MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
if (flagall) return 0;
double oneall[3];
MPI_Allreduce(one,oneall,3,MPI_DOUBLE,MPI_MAX,world);
shapex = oneall[0];
shapey = oneall[1];
shapez = oneall[2];
return 1;
}
/* ----------------------------------------------------------------------
reorder owned atoms so those in firstgroup appear first
called by comm->exchange() if atom_modify first group is set
only owned atoms exist at this point, no ghost atoms
------------------------------------------------------------------------- */
void Atom::first_reorder()
{
// insure there is one extra atom location at end of arrays for swaps
if (nlocal == nmax) avec->grow(0);
// loop over owned atoms
// nfirst = index of first atom not in firstgroup
// when find firstgroup atom out of place, swap it with atom nfirst
int bitmask = group->bitmask[firstgroup];
nfirst = 0;
while (nfirst < nlocal && mask[nfirst] & bitmask) nfirst++;
for (int i = 0; i < nlocal; i++) {
if (mask[i] & bitmask && i > nfirst) {
avec->copy(i,nlocal,0);
avec->copy(nfirst,i,0);
avec->copy(nlocal,nfirst,0);
while (nfirst < nlocal && mask[nfirst] & bitmask) nfirst++;
}
}
}
/* ----------------------------------------------------------------------
perform spatial sort of atoms within my sub-domain
always called between comm->exchange() and comm->borders()
don't have to worry about clearing/setting atom->map since done in comm
------------------------------------------------------------------------- */
void Atom::sort()
{
int i,m,n,ix,iy,iz,ibin,empty;
// set next timestep for sorting to take place
nextsort = (update->ntimestep/sortfreq)*sortfreq + sortfreq;
// re-setup sort bins if needed
if (domain->box_change) setup_sort_bins();
if (nbins == 1) return;
// reallocate per-atom vectors if needed
if (nlocal > maxnext) {
memory->destroy(next);
memory->destroy(permute);
maxnext = atom->nmax;
memory->create(next,maxnext,"atom:next");
memory->create(permute,maxnext,"atom:permute");
}
// insure there is one extra atom location at end of arrays for swaps
if (nlocal == nmax) avec->grow(0);
// bin atoms in reverse order so linked list will be in forward order
for (i = 0; i < nbins; i++) binhead[i] = -1;
for (i = nlocal-1; i >= 0; i--) {
ix = static_cast<int> ((x[i][0]-bboxlo[0])*bininvx);
iy = static_cast<int> ((x[i][1]-bboxlo[1])*bininvy);
iz = static_cast<int> ((x[i][2]-bboxlo[2])*bininvz);
ix = MAX(ix,0);
iy = MAX(iy,0);
iz = MAX(iz,0);
ix = MIN(ix,nbinx-1);
iy = MIN(iy,nbiny-1);
iz = MIN(iz,nbinz-1);
ibin = iz*nbiny*nbinx + iy*nbinx + ix;
next[i] = binhead[ibin];
binhead[ibin] = i;
}
// permute = desired permutation of atoms
// permute[I] = J means Ith new atom will be Jth old atom
n = 0;
for (m = 0; m < nbins; m++) {
i = binhead[m];
while (i >= 0) {
permute[n++] = i;
i = next[i];
}
}
// current = current permutation, just reuse next vector
// current[I] = J means Ith current atom is Jth old atom
int *current = next;
for (i = 0; i < nlocal; i++) current[i] = i;
// reorder local atom list, when done, current = permute
// perform "in place" using copy() to extra atom location at end of list
// inner while loop processes one cycle of the permutation
// copy before inner-loop moves an atom to end of atom list
// copy after inner-loop moves atom at end of list back into list
// empty = location in atom list that is currently empty
for (i = 0; i < nlocal; i++) {
if (current[i] == permute[i]) continue;
avec->copy(i,nlocal,0);
empty = i;
while (permute[empty] != i) {
avec->copy(permute[empty],empty,0);
empty = current[empty] = permute[empty];
}
avec->copy(nlocal,empty,0);
current[empty] = permute[empty];
}
// sanity check that current = permute
//int flag = 0;
//for (i = 0; i < nlocal; i++)
// if (current[i] != permute[i]) flag = 1;
//int flagall;
//MPI_Allreduce(&flag,&flagall,1,MPI_INT,MPI_SUM,world);
//if (flagall) error->all("Atom sort did not operate correctly");
}
/* ----------------------------------------------------------------------
setup bins for spatial sorting of atoms
------------------------------------------------------------------------- */
void Atom::setup_sort_bins()
{
// binsize = user setting or 1/2 of neighbor cutoff
// neighbor cutoff can be 0.0
double binsize;
if (userbinsize > 0.0) binsize = userbinsize;
else binsize = 0.5 * neighbor->cutneighmax;
if (binsize == 0.0) error->all("Atom sorting has bin size = 0.0");
double bininv = 1.0/binsize;
// nbin xyz = local bins
// bbox lo/hi = bounding box of my sub-domain
if (domain->triclinic)
domain->bbox(domain->sublo_lamda,domain->subhi_lamda,bboxlo,bboxhi);
else {
bboxlo[0] = domain->sublo[0];
bboxlo[1] = domain->sublo[1];
bboxlo[2] = domain->sublo[2];
bboxhi[0] = domain->subhi[0];
bboxhi[1] = domain->subhi[1];
bboxhi[2] = domain->subhi[2];
}
nbinx = static_cast<int> ((bboxhi[0]-bboxlo[0]) * bininv);
nbiny = static_cast<int> ((bboxhi[1]-bboxlo[1]) * bininv);
nbinz = static_cast<int> ((bboxhi[2]-bboxlo[2]) * bininv);
if (domain->dimension == 2) nbinz = 1;
if (nbinx == 0) nbinx = 1;
if (nbiny == 0) nbiny = 1;
if (nbinz == 0) nbinz = 1;
bininvx = nbinx / (bboxhi[0]-bboxlo[0]);
bininvy = nbiny / (bboxhi[1]-bboxlo[1]);
bininvz = nbinz / (bboxhi[2]-bboxlo[2]);
if (1.0*nbinx*nbiny*nbinz > INT_MAX)
error->one("Too many atom sorting bins");
nbins = nbinx*nbiny*nbinz;
// reallocate per-bin memory if needed
if (nbins > maxbin) {
memory->destroy(binhead);
maxbin = nbins;
memory->create(binhead,maxbin,"atom:binhead");
}
}
/* ----------------------------------------------------------------------
register a callback to a fix so it can manage atom-based arrays
happens when fix is created
flag = 0 for grow, 1 for restart
------------------------------------------------------------------------- */
void Atom::add_callback(int flag)
{
int ifix;
// find the fix
// if find NULL ptr:
// it's this one, since it is being replaced and has just been deleted
// at this point in re-creation
// if don't find NULL ptr:
// i is set to nfix = new one currently being added at end of list
for (ifix = 0; ifix < modify->nfix; ifix++)
if (modify->fix[ifix] == NULL) break;
// add callback to lists, reallocating if necessary
if (flag == 0) {
if (nextra_grow == nextra_grow_max) {
nextra_grow_max += DELTA;
memory->grow(extra_grow,nextra_grow_max,"atom:extra_grow");
}
extra_grow[nextra_grow] = ifix;
nextra_grow++;
} else if (flag == 1) {
if (nextra_restart == nextra_restart_max) {
nextra_restart_max += DELTA;
memory->grow(extra_restart,nextra_restart_max,"atom:extra_restart");
}
extra_restart[nextra_restart] = ifix;
nextra_restart++;
}
}
/* ----------------------------------------------------------------------
unregister a callback to a fix
happens when fix is deleted, called by its destructor
flag = 0 for grow, 1 for restart
------------------------------------------------------------------------- */
void Atom::delete_callback(const char *id, int flag)
{
int ifix;
for (ifix = 0; ifix < modify->nfix; ifix++)
if (strcmp(id,modify->fix[ifix]->id) == 0) break;
// compact the list of callbacks
if (flag == 0) {
int match;
for (match = 0; match < nextra_grow; match++)
if (extra_grow[match] == ifix) break;
for (int i = match; i < nextra_grow-1; i++)
extra_grow[i] = extra_grow[i+1];
nextra_grow--;
} else if (flag == 1) {
int match;
for (match = 0; match < nextra_grow; match++)
if (extra_restart[match] == ifix) break;
for (int i = ifix; i < nextra_restart-1; i++)
extra_restart[i] = extra_restart[i+1];
nextra_restart--;
}
}
/* ----------------------------------------------------------------------
decrement ptrs in callback lists to fixes beyond the deleted ifix
happens after fix is deleted
------------------------------------------------------------------------- */
void Atom::update_callback(int ifix)
{
for (int i = 0; i < nextra_grow; i++)
if (extra_grow[i] > ifix) extra_grow[i]--;
for (int i = 0; i < nextra_restart; i++)
if (extra_restart[i] > ifix) extra_restart[i]--;
}
/* ----------------------------------------------------------------------
return a pointer to a named internal variable
if don't recognize name, return NULL
customize by adding names
------------------------------------------------------------------------- */
void *Atom::extract(char *name)
{
if (strcmp(name,"id") == 0) return (void *) tag;
if (strcmp(name,"type") == 0) return (void *) type;
if (strcmp(name,"x") == 0) return (void *) x;
if (strcmp(name,"v") == 0) return (void *) v;
if (strcmp(name,"f") == 0) return (void *) f;
if (strcmp(name,"mass") == 0) return (void *) mass;
if (strcmp(name,"rmass") == 0) return (void *) rmass;
return NULL;
}
/* ----------------------------------------------------------------------
return # of bytes of allocated memory
call to avec tallies per-atom vectors
add in global to local mapping storage
------------------------------------------------------------------------- */
bigint Atom::memory_usage()
{
memlength = DELTA_MEMSTR;
memory->create(memstr,memlength,"atom:memstr");
memstr[0] = '\0';
bigint bytes = avec->memory_usage();
memory->destroy(memstr);
if (map_style == 1)
bytes += memory->usage(map_array,map_tag_max+1);
else if (map_style == 2) {
bytes += map_nbucket*sizeof(int);
bytes += map_nhash*sizeof(HashElem);
}
if (maxnext) {
bytes += memory->usage(next,maxnext);
bytes += memory->usage(permute,maxnext);
}
return bytes;
}
/* ----------------------------------------------------------------------
accumulate per-atom vec names in memstr, padded by spaces
return 1 if padded str is not already in memlist, else 0
------------------------------------------------------------------------- */
int Atom::memcheck(const char *str)
{
int n = strlen(str) + 3;
char *padded = new char[n];
strcpy(padded," ");
strcat(padded,str);
strcat(padded," ");
if (strstr(memstr,padded)) {
delete [] padded;
return 0;
}
if (strlen(memstr) + n >= memlength) {
memlength += DELTA_MEMSTR;
memory->grow(memstr,memlength,"atom:memstr");
}
strcat(memstr,padded);
delete [] padded;
return 1;
}

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