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lammps/src/atom.cpp
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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 <math.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 "molecule.h"
#include "atom_masks.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define DELTA 1
#define DELTA_MEMSTR 1024
#define EPSILON 1.0e-6
enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
/* ---------------------------------------------------------------------- */
Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
{
natoms = 0;
nlocal = nghost = nmax = 0;
ntypes = 0;
nbondtypes = nangletypes = ndihedraltypes = nimpropertypes = 0;
nbonds = nangles = ndihedrals = nimpropers = 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 = NULL;
type = mask = NULL;
image = NULL;
x = v = f = NULL;
molecule = NULL;
molindex = molatom = NULL;
q = NULL;
mu = NULL;
omega = angmom = torque = NULL;
radius = rmass = NULL;
ellipsoid = line = tri = body = NULL;
vfrac = s0 = NULL;
x0 = NULL;
spin = NULL;
eradius = ervel = erforce = NULL;
cs = csforce = vforce = ervelforce = NULL;
etag = NULL;
rho = drho = e = de = cv = NULL;
vest = NULL;
// USER-HAdResS package
lambdaH = NULL;
gradlambdaH = NULL;
replambdaH = NULL;
moltypeH = NULL;
comH = NULL;
nmoltypesH = 0;
// USER-DPD
uCond = uMech = uChem = uCG = uCGnew = NULL;
duChem = NULL;
dpdTheta = NULL;
ssaAIR = NULL;
// USER-SMD
contact_radius = NULL;
smd_data_9 = NULL;
smd_stress = NULL;
eff_plastic_strain = NULL;
eff_plastic_strain_rate = NULL;
damage = NULL;
// molecular info
bond_per_atom = extra_bond_per_atom = 0;
num_bond = NULL;
bond_type = NULL;
bond_atom = NULL;
angle_per_atom = extra_angle_per_atom = 0;
num_angle = NULL;
angle_type = NULL;
angle_atom1 = angle_atom2 = angle_atom3 = NULL;
dihedral_per_atom = extra_dihedral_per_atom = 0;
num_dihedral = NULL;
dihedral_type = NULL;
dihedral_atom1 = dihedral_atom2 = dihedral_atom3 = dihedral_atom4 = NULL;
improper_per_atom = extra_improper_per_atom = 0;
num_improper = NULL;
improper_type = NULL;
improper_atom1 = improper_atom2 = improper_atom3 = improper_atom4 = NULL;
maxspecial = 1;
nspecial = NULL;
special = NULL;
// user-defined molecules
nmolecule = 0;
molecules = NULL;
// custom atom arrays
nivector = ndvector = 0;
ivector = NULL;
dvector = NULL;
iname = dname = NULL;
// initialize atom style and array existence flags
// customize by adding new flag
sphere_flag = peri_flag = electron_flag = 0;
wavepacket_flag = sph_flag = 0;
molecule_flag = 0;
q_flag = mu_flag = 0;
omega_flag = torque_flag = angmom_flag = 0;
radius_flag = rmass_flag = 0;
ellipsoid_flag = line_flag = tri_flag = body_flag = 0;
vfrac_flag = 0;
spin_flag = eradius_flag = ervel_flag = erforce_flag = ervelforce_flag = 0;
cs_flag = csforce_flag = vforce_flag = etag_flag = 0;
rho_flag = e_flag = cv_flag = vest_flag = 0;
dpd_flag = 0;
// USER-SMD
smd_flag = 0;
contact_radius_flag = 0;
smd_data_9_flag = 0;
smd_stress_flag = 0;
x0_flag = 0;
eff_plastic_strain_flag = 0;
eff_plastic_strain_rate_flag = 0;
damage_flag = 0;
// Peridynamic scale factor
pdscale = 1.0;
// ntype-length arrays
mass = NULL;
mass_setflag = NULL;
// callback lists & extra restart info
nextra_grow = nextra_restart = nextra_border = 0;
extra_grow = extra_restart = extra_border = NULL;
nextra_grow_max = nextra_restart_max = nextra_border_max = 0;
nextra_store = 0;
extra = NULL;
// default atom ID and mapping values
tag_enable = 1;
map_style = map_user = 0;
map_tag_max = -1;
map_maxarray = map_nhash = -1;
max_same = 0;
sametag = NULL;
map_array = NULL;
map_bucket = NULL;
map_hash = NULL;
atom_style = NULL;
avec = NULL;
datamask = ALL_MASK;
datamask_ext = ALL_MASK;
}
/* ---------------------------------------------------------------------- */
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(molecule);
memory->destroy(molindex);
memory->destroy(molatom);
memory->destroy(lambdaH);
memory->destroy(replambdaH);
memory->destroy(moltypeH);
memory->destroy(gradlambdaH);
memory->destroy(comH);
memory->destroy(q);
memory->destroy(mu);
memory->destroy(omega);
memory->destroy(angmom);
memory->destroy(torque);
memory->destroy(radius);
memory->destroy(rmass);
memory->destroy(ellipsoid);
memory->destroy(line);
memory->destroy(tri);
memory->destroy(body);
memory->destroy(vfrac);
memory->destroy(s0);
memory->destroy(x0);
memory->destroy(spin);
memory->destroy(eradius);
memory->destroy(ervel);
memory->destroy(erforce);
memory->destroy(ervelforce);
memory->destroy(cs);
memory->destroy(csforce);
memory->destroy(vforce);
memory->destroy(etag);
memory->destroy(rho);
memory->destroy(drho);
memory->destroy(e);
memory->destroy(de);
memory->destroy(cv);
memory->destroy(vest);
memory->destroy(contact_radius);
memory->destroy(smd_data_9);
memory->destroy(smd_stress);
memory->destroy(eff_plastic_strain);
memory->destroy(eff_plastic_strain_rate);
memory->destroy(damage);
memory->destroy(dpdTheta);
memory->destroy(uCond);
memory->destroy(uMech);
memory->destroy(uChem);
memory->destroy(uCG);
memory->destroy(uCGnew);
memory->destroy(duChem);
memory->destroy(ssaAIR);
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 custom atom arrays
for (int i = 0; i < nivector; i++) {
delete [] iname[i];
memory->destroy(ivector[i]);
}
for (int i = 0; i < ndvector; i++) {
delete [] dname[i];
memory->destroy(dvector[i]);
}
memory->sfree(iname);
memory->sfree(dname);
memory->sfree(ivector);
memory->sfree(dvector);
// delete user-defined molecules
for (int i = 0; i < nmolecule; i++) delete molecules[i];
memory->sfree(molecules);
// delete per-type arrays
delete [] mass;
delete [] mass_setflag;
// delete extra arrays
memory->destroy(extra_grow);
memory->destroy(extra_restart);
memory->destroy(extra_border);
memory->destroy(extra);
// delete mapping data structures
map_delete();
}
/* ----------------------------------------------------------------------
copy modify settings from old Atom class to current Atom class
------------------------------------------------------------------------- */
void Atom::settings(Atom *old)
{
tag_enable = old->tag_enable;
map_user = old->map_user;
map_style = old->map_style;
sortfreq = old->sortfreq;
userbinsize = old->userbinsize;
if (old->firstgroupname) {
int n = strlen(old->firstgroupname) + 1;
firstgroupname = new char[n];
strcpy(firstgroupname,old->firstgroupname);
}
}
/* ----------------------------------------------------------------------
create an AtomVec style
called from lammps.cpp, input script, restart file, replicate
------------------------------------------------------------------------- */
void Atom::create_avec(const char *style, int narg, char **arg, int trysuffix)
{
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 = peri_flag = electron_flag = 0;
wavepacket_flag = sph_flag = 0;
molecule_flag = 0;
q_flag = mu_flag = 0;
// USER-HAdResS
replambdaH_flag = 0;
moltypeH_flag = 0;
omega_flag = torque_flag = angmom_flag = 0;
radius_flag = rmass_flag = 0;
ellipsoid_flag = line_flag = tri_flag = body_flag = 0;
vfrac_flag = 0;
spin_flag = eradius_flag = ervel_flag = erforce_flag = ervelforce_flag = 0;
cs_flag = csforce_flag = vforce_flag = etag_flag = 0;
rho_flag = e_flag = cv_flag = vest_flag = 0;
// create instance of AtomVec
// use grow() to initialize atom-based arrays to length 1
// so that x[0][0] can always be referenced even if proc has no atoms
int sflag;
avec = new_avec(style,trysuffix,sflag);
avec->store_args(narg,arg);
avec->process_args(narg,arg);
avec->grow(1);
if (sflag) {
char estyle[256];
if (sflag == 1) sprintf(estyle,"%s/%s",style,lmp->suffix);
else sprintf(estyle,"%s/%s",style,lmp->suffix2);
int n = strlen(estyle) + 1;
atom_style = new char[n];
strcpy(atom_style,estyle);
} else {
int n = strlen(style) + 1;
atom_style = new char[n];
strcpy(atom_style,style);
}
// if molecular system:
// atom IDs must be defined
// force atom map to be created
// map style may be reset by map_init() and its call to map_style_set()
molecular = avec->molecular;
if (molecular && tag_enable == 0)
error->all(FLERR,"Atom IDs must be used for molecular systems");
if (molecular) map_style = 1;
}
/* ----------------------------------------------------------------------
generate an AtomVec class, first with suffix appended
------------------------------------------------------------------------- */
AtomVec *Atom::new_avec(const char *style, int trysuffix, int &sflag)
{
if (trysuffix && lmp->suffix_enable) {
if (lmp->suffix) {
sflag = 1;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix);
if (0) return NULL;
#define ATOM_CLASS
#define AtomStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) return new Class(lmp);
#include "style_atom.h"
#undef AtomStyle
#undef ATOM_CLASS
}
if (lmp->suffix2) {
sflag = 2;
char estyle[256];
sprintf(estyle,"%s/%s",style,lmp->suffix2);
if (0) return NULL;
#define ATOM_CLASS
#define AtomStyle(key,Class) \
else if (strcmp(estyle,#key) == 0) return new Class(lmp);
#include "style_atom.h"
#undef AtomStyle
#undef ATOM_CLASS
}
}
sflag = 0;
if (0) return NULL;
#define ATOM_CLASS
#define AtomStyle(key,Class) \
else if (strcmp(style,#key) == 0) return new Class(lmp);
#include "style_atom.h"
#undef ATOM_CLASS
else error->all(FLERR,"Unknown 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(FLERR,"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(FLERR,"Illegal atom_modify command");
int iarg = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"id") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal atom_modify command");
if (domain->box_exist)
error->all(FLERR,
"Atom_modify id command after simulation box is defined");
if (strcmp(arg[iarg+1],"yes") == 0) tag_enable = 1;
else if (strcmp(arg[iarg+1],"no") == 0) tag_enable = 0;
else error->all(FLERR,"Illegal atom_modify command");
iarg += 2;
} else if (strcmp(arg[iarg],"map") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal atom_modify command");
if (domain->box_exist)
error->all(FLERR,
"Atom_modify map command after simulation box is defined");
if (strcmp(arg[iarg+1],"array") == 0) map_user = 1;
else if (strcmp(arg[iarg+1],"hash") == 0) map_user = 2;
else error->all(FLERR,"Illegal atom_modify command");
map_style = map_user;
iarg += 2;
} else if (strcmp(arg[iarg],"first") == 0) {
if (iarg+2 > narg) error->all(FLERR,"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(FLERR,"Illegal atom_modify command");
sortfreq = force->inumeric(FLERR,arg[iarg+1]);
userbinsize = force->numeric(FLERR,arg[iarg+2]);
if (sortfreq < 0 || userbinsize < 0.0)
error->all(FLERR,"Illegal atom_modify command");
if (sortfreq >= 0 && firstgroupname)
error->all(FLERR,"Atom_modify sort and first options "
"cannot be used together");
iarg += 3;
} else error->all(FLERR,"Illegal atom_modify command");
}
}
/* ----------------------------------------------------------------------
check that atom IDs are valid
error if any atom ID < 0 or atom ID = MAXTAGINT
if any atom ID > 0, error if any atom ID == 0
if any atom ID > 0, error if tag_enable = 0
if all atom IDs = 0, tag_enable must be 0
if max atom IDs < natoms, must be duplicates
OK if max atom IDs > natoms
NOTE: not fully checking that atom IDs are unique
------------------------------------------------------------------------- */
void Atom::tag_check()
{
tagint min = MAXTAGINT;
tagint max = 0;
for (int i = 0; i < nlocal; i++) {
min = MIN(min,tag[i]);
max = MAX(max,tag[i]);
}
tagint minall,maxall;
MPI_Allreduce(&min,&minall,1,MPI_LMP_TAGINT,MPI_MIN,world);
MPI_Allreduce(&max,&maxall,1,MPI_LMP_TAGINT,MPI_MAX,world);
if (minall < 0) error->all(FLERR,"One or more Atom IDs is negative");
if (maxall >= MAXTAGINT) error->all(FLERR,"One or more atom IDs is too big");
if (maxall > 0 && minall == 0)
error->all(FLERR,"One or more atom IDs is zero");
if (maxall > 0 && tag_enable == 0)
error->all(FLERR,"Non-zero atom IDs with atom_modify id = no");
if (maxall == 0 && natoms && tag_enable)
error->all(FLERR,"All atom IDs = 0 but atom_modify id = yes");
if (tag_enable && maxall < natoms)
error->all(FLERR,"Duplicate atom IDs exist");
}
/* ----------------------------------------------------------------------
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
error if new tags will exceed MAXTAGINT
------------------------------------------------------------------------- */
void Atom::tag_extend()
{
// maxtag_all = max tag for all atoms
tagint maxtag = 0;
for (int i = 0; i < nlocal; i++) maxtag = MAX(maxtag,tag[i]);
tagint maxtag_all;
MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
// DEBUG: useful for generating 64-bit IDs even for small systems
// use only when LAMMPS is compiled with BIGBIG
//maxtag_all += 1000000000000;
// notag = # of atoms I own with no tag (tag = 0)
// notag_sum = # of total atoms on procs <= me with no tag
bigint notag = 0;
for (int i = 0; i < nlocal; i++) if (tag[i] == 0) notag++;
bigint notag_total;
MPI_Allreduce(&notag,&notag_total,1,MPI_LMP_BIGINT,MPI_SUM,world);
if (notag_total >= MAXTAGINT)
error->all(FLERR,"New atom IDs exceed maximum allowed ID");
bigint notag_sum;
MPI_Scan(&notag,&notag_sum,1,MPI_LMP_BIGINT,MPI_SUM,world);
// itag = 1st new tag that my untagged atoms should use
tagint 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 inclusive
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()
{
tagint idmin = MAXTAGINT;
tagint idmax = 0;
for (int i = 0; i < nlocal; i++) {
idmin = MIN(idmin,tag[i]);
idmax = MAX(idmax,tag[i]);
}
tagint idminall,idmaxall;
MPI_Allreduce(&idmin,&idminall,1,MPI_LMP_TAGINT,MPI_MIN,world);
MPI_Allreduce(&idmax,&idmaxall,1,MPI_LMP_TAGINT,MPI_MAX,world);
if (idminall != 1 || idmaxall != 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;
}
/* ----------------------------------------------------------------------
count and return words in a single line using provided copy buf
make copy of line before using strtok so as not to change line
trim anything from '#' onward
------------------------------------------------------------------------- */
int Atom::count_words(const char *line, char *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;
}
int n = 1;
while (strtok(NULL," \t\n\r\f")) n++;
return n;
}
/* ----------------------------------------------------------------------
deallocate molecular topology arrays
done before realloc with (possibly) new 2nd dimension set to
correctly initialized per-atom values, e.g. bond_per_atom
needs to be called whenever 2nd dimensions are changed
and these arrays are already pre-allocated,
e.g. due to grow(1) in create_avec()
------------------------------------------------------------------------- */
void Atom::deallocate_topology()
{
memory->destroy(atom->bond_type);
memory->destroy(atom->bond_atom);
atom->bond_type = NULL;
atom->bond_atom = NULL;
memory->destroy(atom->angle_type);
memory->destroy(atom->angle_atom1);
memory->destroy(atom->angle_atom2);
memory->destroy(atom->angle_atom3);
atom->angle_type = NULL;
atom->angle_atom1 = atom->angle_atom2 = atom->angle_atom3 = NULL;
memory->destroy(atom->dihedral_type);
memory->destroy(atom->dihedral_atom1);
memory->destroy(atom->dihedral_atom2);
memory->destroy(atom->dihedral_atom3);
memory->destroy(atom->dihedral_atom4);
atom->dihedral_type = NULL;
atom->dihedral_atom1 = atom->dihedral_atom2 =
atom->dihedral_atom3 = atom->dihedral_atom4 = NULL;
memory->destroy(atom->improper_type);
memory->destroy(atom->improper_atom1);
memory->destroy(atom->improper_atom2);
memory->destroy(atom->improper_atom3);
memory->destroy(atom->improper_atom4);
atom->improper_type = NULL;
atom->improper_atom1 = atom->improper_atom2 =
atom->improper_atom3 = atom->improper_atom4 = NULL;
}
/* ----------------------------------------------------------------------
unpack N lines from Atom section of data file
call style-specific routine to parse line
------------------------------------------------------------------------- */
void Atom::data_atoms(int n, char *buf, tagint id_offset, int type_offset,
int shiftflag, double *shift)
{
int m,xptr,iptr;
imageint imagedata;
double xdata[3],lamda[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(FLERR,"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;
double epsilon[3];
if (triclinic) epsilon[0] = epsilon[1] = epsilon[2] = EPSILON;
else {
epsilon[0] = domain->prd[0] * EPSILON;
epsilon[1] = domain->prd[1] * EPSILON;
epsilon[2] = domain->prd[2] * EPSILON;
}
double sublo[3],subhi[3];
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 (comm->layout != LAYOUT_TILED) {
if (domain->xperiodic) {
if (comm->myloc[0] == 0) sublo[0] -= epsilon[0];
if (comm->myloc[0] == comm->procgrid[0]-1) subhi[0] += epsilon[0];
}
if (domain->yperiodic) {
if (comm->myloc[1] == 0) sublo[1] -= epsilon[1];
if (comm->myloc[1] == comm->procgrid[1]-1) subhi[1] += epsilon[1];
}
if (domain->zperiodic) {
if (comm->myloc[2] == 0) sublo[2] -= epsilon[2];
if (comm->myloc[2] == comm->procgrid[2]-1) subhi[2] += epsilon[2];
}
} else {
if (domain->xperiodic) {
if (comm->mysplit[0][0] == 0.0) sublo[0] -= epsilon[0];
if (comm->mysplit[0][1] == 1.0) subhi[0] += epsilon[0];
}
if (domain->yperiodic) {
if (comm->mysplit[1][0] == 0.0) sublo[1] -= epsilon[1];
if (comm->mysplit[1][1] == 1.0) subhi[1] += epsilon[1];
}
if (domain->zperiodic) {
if (comm->mysplit[2][0] == 0.0) sublo[2] -= epsilon[2];
if (comm->mysplit[2][1] == 1.0) subhi[2] += epsilon[2];
}
}
// 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");
if (values[0] == NULL)
error->all(FLERR,"Incorrect atom format in data file");
for (m = 1; m < nwords; m++) {
values[m] = strtok(NULL," \t\n\r\f");
if (values[m] == NULL)
error->all(FLERR,"Incorrect atom format in data file");
}
if (imageflag)
imagedata = ((imageint) (atoi(values[iptr]) + IMGMAX) & IMGMASK) |
(((imageint) (atoi(values[iptr+1]) + IMGMAX) & IMGMASK) << IMGBITS) |
(((imageint) (atoi(values[iptr+2]) + IMGMAX) & IMGMASK) << IMG2BITS);
else imagedata = ((imageint) IMGMAX << IMG2BITS) |
((imageint) IMGMAX << IMGBITS) | IMGMAX;
xdata[0] = atof(values[xptr]);
xdata[1] = atof(values[xptr+1]);
xdata[2] = atof(values[xptr+2]);
if (shiftflag) {
xdata[0] += shift[0];
xdata[1] += shift[1];
xdata[2] += shift[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);
if (id_offset) tag[nlocal-1] += id_offset;
if (type_offset) {
type[nlocal-1] += type_offset;
if (type[nlocal-1] > ntypes)
error->one(FLERR,"Invalid atom type in Atoms section of data file");
}
}
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, tagint id_offset)
{
int j,m;
tagint tagdata;
char *next;
next = strchr(buf,'\n');
*next = '\0';
int nwords = count_words(buf);
*next = '\n';
if (nwords != avec->size_data_vel)
error->all(FLERR,"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 = ATOTAGINT(values[0]) + id_offset;
if (tagdata <= 0 || tagdata > map_tag_max)
error->one(FLERR,"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;
}
/* ----------------------------------------------------------------------
process N bonds read into buf from data files
if count is non-NULL, just count bonds per atom
else store them with atoms
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
int type_offset)
{
int m,tmp,itype;
tagint 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 " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2);
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
}
itype += type_offset;
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max)
error->one(FLERR,"Invalid atom ID in Bonds section of data file");
if (itype <= 0 || itype > nbondtypes)
error->one(FLERR,"Invalid bond type in Bonds section of data file");
if ((m = map(atom1)) >= 0) {
if (count) count[m]++;
else {
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) {
if (count) count[m]++;
else {
bond_type[m][num_bond[m]] = itype;
bond_atom[m][num_bond[m]] = atom1;
num_bond[m]++;
}
}
}
buf = next + 1;
}
}
/* ----------------------------------------------------------------------
process N angles read into buf from data files
if count is non-NULL, just count angles per atom
else store them with atoms
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
int type_offset)
{
int m,tmp,itype;
tagint 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 " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3);
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
atom3 += id_offset;
}
itype += type_offset;
if (atom1 <= 0 || atom1 > map_tag_max ||
atom2 <= 0 || atom2 > map_tag_max ||
atom3 <= 0 || atom3 > map_tag_max)
error->one(FLERR,"Invalid atom ID in Angles section of data file");
if (itype <= 0 || itype > nangletypes)
error->one(FLERR,"Invalid angle type in Angles section of data file");
if ((m = map(atom2)) >= 0) {
if (count) count[m]++;
else {
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) {
if (count) count[m]++;
else {
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) {
if (count) count[m]++;
else {
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;
}
}
/* ----------------------------------------------------------------------
process N dihedrals read into buf from data files
if count is non-NULL, just count diihedrals per atom
else store them with atoms
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
int type_offset)
{
int m,tmp,itype;
tagint 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 "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
atom3 += id_offset;
atom4 += id_offset;
}
itype += type_offset;
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(FLERR,"Invalid atom ID in Dihedrals section of data file");
if (itype <= 0 || itype > ndihedraltypes)
error->one(FLERR,
"Invalid dihedral type in Dihedrals section of data file");
if ((m = map(atom2)) >= 0) {
if (count) count[m]++;
else {
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) {
if (count) count[m]++;
else {
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) {
if (count) count[m]++;
else {
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) {
if (count) count[m]++;
else {
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;
}
}
/* ----------------------------------------------------------------------
process N impropers read into buf from data files
if count is non-NULL, just count impropers per atom
else store them with atoms
check that atom IDs are > 0 and <= map_tag_max
------------------------------------------------------------------------- */
void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
int type_offset)
{
int m,tmp,itype;
tagint 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 "
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
if (id_offset) {
atom1 += id_offset;
atom2 += id_offset;
atom3 += id_offset;
atom4 += id_offset;
}
itype += type_offset;
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(FLERR,"Invalid atom ID in Impropers section of data file");
if (itype <= 0 || itype > nimpropertypes)
error->one(FLERR,
"Invalid improper type in Impropers section of data file");
if ((m = map(atom2)) >= 0) {
if (count) count[m]++;
else {
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) {
if (count) count[m]++;
else {
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) {
if (count) count[m]++;
else {
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) {
if (count) count[m]++;
else {
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;
}
}
/* ----------------------------------------------------------------------
unpack N lines from atom-style specific bonus 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, tagint id_offset)
{
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(FLERR,"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 = ATOTAGINT(values[0]) + id_offset;
if (tagdata <= 0 || tagdata > map_tag_max)
error->one(FLERR,"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;
}
/* ----------------------------------------------------------------------
unpack N bodies from Bodies section of data file
each body spans multiple lines
check that atom IDs are > 0 and <= map_tag_max
call style-specific routine to parse line
------------------------------------------------------------------------- */
void Atom::data_bodies(int n, char *buf, AtomVecBody *avec_body,
tagint id_offset)
{
int j,m,nvalues,tagdata,ninteger,ndouble;
int maxint = 0;
int maxdouble = 0;
int *ivalues = NULL;
double *dvalues = NULL;
// loop over lines of body data
// if I own atom tag, tokenize lines into ivalues/dvalues, call data_body()
// else skip values
for (int i = 0; i < n; i++) {
if (i == 0) tagdata = ATOTAGINT(strtok(buf," \t\n\r\f")) + id_offset;
else tagdata = ATOTAGINT(strtok(NULL," \t\n\r\f")) + id_offset;
if (tagdata <= 0 || tagdata > map_tag_max)
error->one(FLERR,"Invalid atom ID in Bodies section of data file");
ninteger = force->inumeric(FLERR,strtok(NULL," \t\n\r\f"));
ndouble = force->inumeric(FLERR,strtok(NULL," \t\n\r\f"));
if ((m = map(tagdata)) >= 0) {
if (ninteger > maxint) {
delete [] ivalues;
maxint = ninteger;
ivalues = new int[maxint];
}
if (ndouble > maxdouble) {
delete [] dvalues;
maxdouble = ndouble;
dvalues = new double[maxdouble];
}
for (j = 0; j < ninteger; j++)
ivalues[j] = force->inumeric(FLERR,strtok(NULL," \t\n\r\f"));
for (j = 0; j < ndouble; j++)
dvalues[j] = force->numeric(FLERR,strtok(NULL," \t\n\r\f"));
avec_body->data_body(m,ninteger,ndouble,ivalues,dvalues);
} else {
nvalues = ninteger + ndouble; // number of values to skip
for (j = 0; j < nvalues; j++)
strtok(NULL," \t\n\r\f");
}
}
delete [] ivalues;
delete [] dvalues;
}
/* ----------------------------------------------------------------------
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
type_offset may be used when reading multiple data files
------------------------------------------------------------------------- */
void Atom::set_mass(const char *str, int type_offset)
{
if (mass == NULL) error->all(FLERR,"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(FLERR,"Invalid mass line in data file");
itype += type_offset;
if (itype < 1 || itype > ntypes)
error->all(FLERR,"Invalid type for mass set");
mass[itype] = mass_one;
mass_setflag[itype] = 1;
if (mass[itype] <= 0.0) error->all(FLERR,"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(FLERR,"Cannot set mass for this atom style");
if (itype < 1 || itype > ntypes)
error->all(FLERR,"Invalid type for mass set");
mass[itype] = value;
mass_setflag[itype] = 1;
if (mass[itype] <= 0.0) error->all(FLERR,"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(FLERR,"Cannot set mass for this atom style");
int lo,hi;
force->bounds(arg[0],ntypes,lo,hi);
if (lo < 1 || hi > ntypes) error->all(FLERR,"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(FLERR,"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(FLERR,"Not all per-type masses are 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;
}
/* ----------------------------------------------------------------------
add a new molecule template = set of molecules
------------------------------------------------------------------------- */
void Atom::add_molecule(int narg, char **arg)
{
if (narg < 1) error->all(FLERR,"Illegal molecule command");
if (find_molecule(arg[0]) >= 0)
error->all(FLERR,"Reuse of molecule template ID");
// 1st molecule in set stores nset = # of mols, others store nset = 0
// ifile = count of molecules in set
// index = argument index where next molecule starts, updated by constructor
int ifile = 1;
int index = 1;
while (1) {
molecules = (Molecule **)
memory->srealloc(molecules,(nmolecule+1)*sizeof(Molecule *),
"atom::molecules");
molecules[nmolecule] = new Molecule(lmp,narg,arg,index);
molecules[nmolecule]->nset = 0;
molecules[nmolecule-ifile+1]->nset++;
nmolecule++;
if (molecules[nmolecule-1]->last) break;
ifile++;
}
}
/* ----------------------------------------------------------------------
find first molecule in set with template ID
return -1 if does not exist
------------------------------------------------------------------------- */
int Atom::find_molecule(char *id)
{
if(id == NULL) return -1;
int imol;
for (imol = 0; imol < nmolecule; imol++)
if (strcmp(id,molecules[imol]->id) == 0) return imol;
return -1;
}
/* ----------------------------------------------------------------------
add info to current atom ilocal from molecule template onemol and its iatom
offset = atom ID preceeding IDs of atoms in this molecule
called by fixes and commands that add molecules
------------------------------------------------------------------------- */
void Atom::add_molecule_atom(Molecule *onemol, int iatom,
int ilocal, tagint offset)
{
if (onemol->qflag && q_flag) q[ilocal] = onemol->q[iatom];
if (onemol->radiusflag && radius_flag) radius[ilocal] = onemol->radius[iatom];
if (onemol->rmassflag && rmass_flag) rmass[ilocal] = onemol->rmass[iatom];
if (onemol->replambdaHflag && replambdaH_flag) replambdaH[ilocal] = onemol->replambdaH[iatom];
if (onemol->moltypeHflag && moltypeH_flag) moltypeH[ilocal] = onemol->moltypeH[iatom];
else if (rmass_flag)
rmass[ilocal] = 4.0*MY_PI/3.0 *
radius[ilocal]*radius[ilocal]*radius[ilocal];
if (onemol->bodyflag) {
body[ilocal] = 0; // as if a body read from data file
onemol->avec_body->data_body(ilocal,onemol->nibody,onemol->ndbody,
onemol->ibodyparams,onemol->dbodyparams);
onemol->avec_body->set_quat(ilocal,onemol->quat_external);
}
if (molecular != 1) return;
// add bond topology info
// for molecular atom styles, but not atom style template
if (avec->bonds_allow) {
num_bond[ilocal] = onemol->num_bond[iatom];
for (int i = 0; i < num_bond[ilocal]; i++) {
bond_type[ilocal][i] = onemol->bond_type[iatom][i];
bond_atom[ilocal][i] = onemol->bond_atom[iatom][i] + offset;
}
}
if (avec->angles_allow) {
num_angle[ilocal] = onemol->num_angle[iatom];
for (int i = 0; i < num_angle[ilocal]; i++) {
angle_type[ilocal][i] = onemol->angle_type[iatom][i];
angle_atom1[ilocal][i] = onemol->angle_atom1[iatom][i] + offset;
angle_atom2[ilocal][i] = onemol->angle_atom2[iatom][i] + offset;
angle_atom3[ilocal][i] = onemol->angle_atom3[iatom][i] + offset;
}
}
if (avec->dihedrals_allow) {
num_dihedral[ilocal] = onemol->num_dihedral[iatom];
for (int i = 0; i < num_dihedral[ilocal]; i++) {
dihedral_type[ilocal][i] = onemol->dihedral_type[iatom][i];
dihedral_atom1[ilocal][i] = onemol->dihedral_atom1[iatom][i] + offset;
dihedral_atom2[ilocal][i] = onemol->dihedral_atom2[iatom][i] + offset;
dihedral_atom3[ilocal][i] = onemol->dihedral_atom3[iatom][i] + offset;
dihedral_atom4[ilocal][i] = onemol->dihedral_atom4[iatom][i] + offset;
}
}
if (avec->impropers_allow) {
num_improper[ilocal] = onemol->num_improper[iatom];
for (int i = 0; i < num_improper[ilocal]; i++) {
improper_type[ilocal][i] = onemol->improper_type[iatom][i];
improper_atom1[ilocal][i] = onemol->improper_atom1[iatom][i] + offset;
improper_atom2[ilocal][i] = onemol->improper_atom2[iatom][i] + offset;
improper_atom3[ilocal][i] = onemol->improper_atom3[iatom][i] + offset;
improper_atom4[ilocal][i] = onemol->improper_atom4[iatom][i] + offset;
}
}
if (onemol->specialflag) {
nspecial[ilocal][0] = onemol->nspecial[iatom][0];
nspecial[ilocal][1] = onemol->nspecial[iatom][1];
int n = nspecial[ilocal][2] = onemol->nspecial[iatom][2];
for (int i = 0; i < n; i++)
special[ilocal][i] = onemol->special[iatom][i] + offset;
}
}
/* ----------------------------------------------------------------------
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(FLERR,"Atom sort did not operate correctly");
}
/* ----------------------------------------------------------------------
setup bins for spatial sorting of atoms
------------------------------------------------------------------------- */
void Atom::setup_sort_bins()
{
// binsize:
// user setting if explicitly set
// default = 1/2 of neighbor cutoff
// check if neighbor cutoff = 0.0
double binsize;
if (userbinsize > 0.0) binsize = userbinsize;
else binsize = 0.5 * neighbor->cutneighmax;
if (binsize == 0.0) error->all(FLERR,"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(FLERR,"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, 2 for border comm
------------------------------------------------------------------------- */
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++;
} else if (flag == 2) {
if (nextra_border == nextra_border_max) {
nextra_border_max += DELTA;
memory->grow(extra_border,nextra_border_max,"atom:extra_border");
}
extra_border[nextra_border] = ifix;
nextra_border++;
}
}
/* ----------------------------------------------------------------------
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)
{
if(id==NULL) return;
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_restart; match++)
if (extra_restart[match] == ifix) break;
for (int i = match; i < nextra_restart-1; i++)
extra_restart[i] = extra_restart[i+1];
nextra_restart--;
} else if (flag == 2) {
int match;
for (match = 0; match < nextra_border; match++)
if (extra_border[match] == ifix) break;
for (int i = match; i < nextra_border-1; i++)
extra_border[i] = extra_border[i+1];
nextra_border--;
}
}
/* ----------------------------------------------------------------------
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]--;
for (int i = 0; i < nextra_border; i++)
if (extra_border[i] > ifix) extra_border[i]--;
}
/* ----------------------------------------------------------------------
find custom per-atom vector with name
return index if found, and flag = 0/1 for int/double
return -1 if not found
------------------------------------------------------------------------- */
int Atom::find_custom(const char *name, int &flag)
{
if(name == NULL) return -1;
for (int i = 0; i < nivector; i++)
if (iname[i] && strcmp(iname[i],name) == 0) {
flag = 0;
return i;
}
for (int i = 0; i < ndvector; i++)
if (dname[i] && strcmp(dname[i],name) == 0) {
flag = 1;
return i;
}
return -1;
}
/* ----------------------------------------------------------------------
add a custom variable with name of type flag = 0/1 for int/double
assumes name does not already exist
return index in ivector or dvector of its location
------------------------------------------------------------------------- */
int Atom::add_custom(const char *name, int flag)
{
int index;
if (flag == 0) {
index = nivector;
nivector++;
iname = (char **) memory->srealloc(iname,nivector*sizeof(char *),
"atom:iname");
int n = strlen(name) + 1;
iname[index] = new char[n];
strcpy(iname[index],name);
ivector = (int **) memory->srealloc(ivector,nivector*sizeof(int *),
"atom:ivector");
memory->create(ivector[index],nmax,"atom:ivector");
} else {
index = ndvector;
ndvector++;
dname = (char **) memory->srealloc(dname,ndvector*sizeof(char *),
"atom:dname");
int n = strlen(name) + 1;
dname[index] = new char[n];
strcpy(dname[index],name);
dvector = (double **) memory->srealloc(dvector,ndvector*sizeof(double *),
"atom:dvector");
memory->create(dvector[index],nmax,"atom:dvector");
}
return index;
}
/* ----------------------------------------------------------------------
remove a custom variable of type flag = 0/1 for int/double at index
free memory for vector and name and set ptrs to NULL
ivector/dvector and iname/dname lists never shrink
------------------------------------------------------------------------- */
void Atom::remove_custom(int flag, int index)
{
if (flag == 0) {
memory->destroy(ivector[index]);
ivector[index] = NULL;
delete [] iname[index];
iname[index] = NULL;
} else {
memory->destroy(dvector[index]);
dvector[index] = NULL;
delete [] dname[index];
dname[index] = NULL;
}
}
/* ----------------------------------------------------------------------
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,"mass") == 0) return (void *) mass;
if (strcmp(name,"id") == 0) return (void *) tag;
if (strcmp(name,"type") == 0) return (void *) type;
if (strcmp(name,"mask") == 0) return (void *) mask;
if (strcmp(name,"image") == 0) return (void *) image;
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,"molecule") == 0) return (void *) molecule;
if (strcmp(name,"q") == 0) return (void *) q;
if (strcmp(name,"lambdaH") == 0) return (void *) lambdaH;
if (strcmp(name,"gradlambdaH") == 0) return (void *) gradlambdaH;
if (strcmp(name,"replambdaH") == 0) return (void *) replambdaH;
if (strcmp(name,"mu") == 0) return (void *) mu;
if (strcmp(name,"omega") == 0) return (void *) omega;
if (strcmp(name,"angmom") == 0) return (void *) angmom;
if (strcmp(name,"torque") == 0) return (void *) torque;
if (strcmp(name,"radius") == 0) return (void *) radius;
if (strcmp(name,"rmass") == 0) return (void *) rmass;
if (strcmp(name,"ellipsoid") == 0) return (void *) ellipsoid;
if (strcmp(name,"line") == 0) return (void *) line;
if (strcmp(name,"tri") == 0) return (void *) tri;
if (strcmp(name,"vfrac") == 0) return (void *) vfrac;
if (strcmp(name,"s0") == 0) return (void *) s0;
if (strcmp(name,"x0") == 0) return (void *) x0;
if (strcmp(name,"spin") == 0) return (void *) spin;
if (strcmp(name,"eradius") == 0) return (void *) eradius;
if (strcmp(name,"ervel") == 0) return (void *) ervel;
if (strcmp(name,"erforce") == 0) return (void *) erforce;
if (strcmp(name,"ervelforce") == 0) return (void *) ervelforce;
if (strcmp(name,"cs") == 0) return (void *) cs;
if (strcmp(name,"csforce") == 0) return (void *) csforce;
if (strcmp(name,"vforce") == 0) return (void *) vforce;
if (strcmp(name,"etag") == 0) return (void *) etag;
if (strcmp(name,"rho") == 0) return (void *) rho;
if (strcmp(name,"drho") == 0) return (void *) drho;
if (strcmp(name,"e") == 0) return (void *) e;
if (strcmp(name,"de") == 0) return (void *) de;
if (strcmp(name,"cv") == 0) return (void *) cv;
if (strcmp(name,"vest") == 0) return (void *) vest;
if (strcmp(name, "contact_radius") == 0) return (void *) contact_radius;
if (strcmp(name, "smd_data_9") == 0) return (void *) smd_data_9;
if (strcmp(name, "smd_stress") == 0) return (void *) smd_stress;
if (strcmp(name, "eff_plastic_strain") == 0)
return (void *) eff_plastic_strain;
if (strcmp(name, "eff_plastic_strain_rate") == 0)
return (void *) eff_plastic_strain_rate;
if (strcmp(name, "damage") == 0) return (void *) damage;
if (strcmp(name,"dpdTheta") == 0) return (void *) dpdTheta;
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);
bytes += max_same*sizeof(int);
if (map_style == 1 && map_tag_max >= 0)
bytes += memory->usage(map_array,map_maxarray);
else if (map_style == 2 && map_nhash >=0) {
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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