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delete_atoms.h
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Tue, Sep 3, 09:28

delete_atoms.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 COMMAND_CLASS
CommandStyle(delete_atoms,DeleteAtoms)
#else
#ifndef LMP_DELETE_ATOMS_H
#define LMP_DELETE_ATOMS_H
#include "pointers.h"
#include <map>
namespace LAMMPS_NS {
class DeleteAtoms : protected Pointers {
public:
DeleteAtoms(class LAMMPS *);
void command(int, char **);
private:
int *dlist;
int compress_flag,bond_flag,mol_flag;
std::map<tagint,int> *hash;
void delete_group(int, char **);
void delete_region(int, char **);
void delete_overlap(int, char **);
void delete_porosity(int, char **);
void delete_bond();
void delete_molecule();
void recount_topology();
void options(int, char **);
inline int sbmask(int j) {
return j >> SBBITS & 3;
}
// static variable for ring communication callback to access class data
// callback functions for ring communication
static DeleteAtoms *cptr;
static void bondring(int, char *);
static void molring(int, char *);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Delete_atoms command before simulation box is defined
The delete_atoms command cannot be used before a read_data,
read_restart, or create_box command.
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: Cannot use delete_atoms unless atoms have IDs
Your atoms do not have IDs, so the delete_atoms command cannot be
used.
E: Could not find delete_atoms group ID
Group ID used in the delete_atoms command does not exist.
E: Could not find delete_atoms region ID
Region ID used in the delete_atoms command does not exist.
E: Delete_atoms requires a pair style be defined
This is because atom deletion within a cutoff uses a pairwise
neighbor list.
E: Delete_atoms cutoff > max neighbor cutoff
Can only delete atoms in atom pairs that will be in neighbor list.
W: Delete_atoms cutoff > minimum neighbor cutoff
This means atom pairs for some atom types may not be in the neighbor
list and thus an atom in that pair cannot be deleted.
E: Cannot delete_atoms bond yes for non-molecular systems
Self-explanatory.
E: Cannot use delete_atoms bond yes with atom_style template
This is because the bonds for that atom style are hardwired in the
molecule template.
E: Delete_atoms mol yes requires atom attribute molecule
Cannot use this option with a non-molecular system.
*/

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