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lammps/src/compute_chunk_atom.h
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compute_chunk_atom.h
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/* -*- c++ -*- ----------------------------------------------------------
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.
------------------------------------------------------------------------- */
#ifdef COMPUTE_CLASS
ComputeStyle(chunk/atom,ComputeChunkAtom)
#else
#ifndef LMP_COMPUTE_CHUNK_ATOM_H
#define LMP_COMPUTE_CHUNK_ATOM_H
#include "compute.h"
#include <map>
namespace LAMMPS_NS {
class ComputeChunkAtom : public Compute {
public:
int nchunk,ncoord,compress,idsflag,lockcount;
int computeflag; // 1 if this compute invokes other computes
double chunk_volume_scalar;
double *chunk_volume_vec;
double **coord;
int *ichunk,*chunkID;
ComputeChunkAtom(class LAMMPS *, int, char **);
~ComputeChunkAtom();
void init();
void setup();
void compute_peratom();
void set_arrays(int);
double memory_usage();
void lock(class Fix *, bigint, bigint);
void unlock(class Fix *);
int setup_chunks();
void compute_ichunk();
private:
int which,binflag;
int regionflag,nchunksetflag,nchunkflag,discard;
int limit,limitstyle,limitfirst;
int scaleflag,pbcflag;
double xscale,yscale,zscale;
int argindex;
char *cfvid;
// xyz spatial bins
int ndim;
int dim[3],originflag[3],nlayers[3];
int minflag[3],maxflag[3];
double origin[3],delta[3];
double offset[3],invdelta[3];
double minvalue[3],maxvalue[3];
// spherical spatial bins
double sorigin_user[3];
double sorigin[3];
double sradmin_user,sradmax_user;
double sradmin,sradmax,sinvrad;
int nsbin;
// cylindrical spatial bins
double corigin_user[3];
double corigin[3];
double cradmin_user,cradmax_user;
double cradmin,cradmax,cinvrad;
int cdim1,cdim2;
int ncbin,ncplane;
char *idregion;
class Region *region;
class Compute *cchunk;
class Fix *fchunk;
int vchunk;
int maxvar;
double *varatom;
char *id_fix;
class FixStore *fixstore;
class Fix *lockfix; // ptr to FixAveChunk that is locking out setups
// NULL if no lock currently in place
bigint lockstart,lockstop; // timesteps for start and stop of locking
bigint invoked_setup; // last timestep setup_chunks and nchunk calculated
bigint invoked_ichunk; // last timestep ichunk values calculated
int nmax,nmaxint;
double *chunk;
int molcheck; // one-time check if all molecule atoms in chunk
int *exclude; // 1 if atom is not assigned to any chunk
std::map<tagint,int> *hash; // store original chunks IDs before compression
// static variable for ring communication callback to access class data
// callback functions for ring communication
static ComputeChunkAtom *cptr;
static void idring(int, char *);
void assign_chunk_ids();
void compress_chunk_ids();
void check_molecules();
int setup_xyz_bins();
int setup_sphere_bins();
int setup_cylinder_bins();
void bin_volumes();
void atom2bin1d();
void atom2bin2d();
void atom2bin3d();
void atom2binsphere();
void atom2bincylinder();
void readdim(int, char **, int, int);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Region ID for compute chunk/atom does not exist
Self-explanatory.
E: Compute chunk/atom molecule for non-molecular system
Self-explanatory.
E: Compute chunk/atom without bins cannot use discard mixed
That discard option only applies to the binning styles.
E: Compute chunk/atom sphere z origin must be 0.0 for 2d
Self-explanatory.
E: Compute chunk/atom cylinder axis must be z for 2d
Self-explanatory.
E: Compute ID for compute chunk /atom does not exist
Self-explanatory.
E: Compute chunk/atom compute does not calculate per-atom values
Self-explanatory.
E: Compute chunk/atom compute does not calculate a per-atom vector
Self-explanatory.
E: Compute chunk/atom compute does not calculate a per-atom array
Self-explanatory.
E: Compute chunk/atom compute array is accessed out-of-range
The index for the array is out of bounds.
E: Fix ID for compute chunk/atom does not exist
Self-explanatory.
E: Compute chunk/atom fix does not calculate per-atom values
Self-explanatory.
E: Compute chunk/atom fix does not calculate a per-atom vector
Self-explanatory.
E: Compute chunk/atom fix does not calculate a per-atom array
Self-explanatory.
E: Compute chunk/atom fix array is accessed out-of-range
the index for the array is out of bounds.
E: Variable name for compute chunk/atom does not exist
Self-explanatory.
E: Compute chunk/atom variable is not atom-style variable
Self-explanatory.
E: Compute chunk/atom for triclinic boxes requires units reduced
Self-explanatory.
E: Compute ID for compute chunk/atom does not exist
Self-explanatory.
E: Molecule IDs too large for compute chunk/atom
The IDs must not be larger than can be stored in a 32-bit integer
since chunk IDs are 32-bit integers.
E: Compute chunk/atom ids once but nchunk is not once
You cannot assign chunks IDs to atom permanently if the number of
chunks may change.
E: Two fix ave commands using same compute chunk/atom command in incompatible ways
They are both attempting to "lock" the chunk/atom command so that the
chunk assignments persist for some number of timesteps, but are doing
it in different ways.
E: Fix used in compute chunk/atom not computed at compatible time
The chunk/atom compute cannot query the output of the fix on a timestep
it is needed.
W: One or more chunks do not contain all atoms in molecule
This may not be what you intended.
E: Invalid bin bounds in compute chunk/atom
The lo/hi values are inconsistent.
E: Compute chunk/atom bin/sphere radius is too large for periodic box
Radius cannot be bigger than 1/2 of any periodic dimention.
E: Compute chunk/atom bin/cylinder radius is too large for periodic box
Radius cannot be bigger than 1/2 of a non-axis periodic dimention.
E: Cannot use compute chunk/atom bin z for 2d model
Self-explanatory.
*/
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