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fix_gcmc.h
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fix_gcmc.h
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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.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(gcmc,FixGCMC)
#else
#ifndef LMP_FIX_GCMC_H
#define LMP_FIX_GCMC_H
#include <stdio.h>
#include "fix.h"
namespace LAMMPS_NS {
class FixGCMC : public Fix {
public:
FixGCMC(class LAMMPS *, int, char **);
~FixGCMC();
int setmask();
void init();
void pre_exchange();
void attempt_atomic_translation();
void attempt_atomic_deletion();
void attempt_atomic_insertion();
void attempt_molecule_translation();
void attempt_molecule_rotation();
void attempt_molecule_deletion();
void attempt_molecule_insertion();
void attempt_atomic_translation_full();
void attempt_atomic_deletion_full();
void attempt_atomic_insertion_full();
void attempt_molecule_translation_full();
void attempt_molecule_rotation_full();
void attempt_molecule_deletion_full();
void attempt_molecule_insertion_full();
double energy(int, int, tagint, double *);
double molecule_energy(tagint);
double energy_full();
int pick_random_gas_atom();
tagint pick_random_gas_molecule();
void toggle_intramolecular(int);
void update_gas_atoms_list();
double compute_vector(int);
double memory_usage();
void write_restart(FILE *);
void restart(char *);
private:
int molecule_group,molecule_group_bit;
int molecule_group_inversebit;
int exclusion_group,exclusion_group_bit;
int ngcmc_type,nevery,seed;
int ncycles,nexchanges,nmcmoves;
int ngas; // # of gas atoms on all procs
int ngas_local; // # of gas atoms on this proc
int ngas_before; // # of gas atoms on procs < this proc
int mode; // ATOM or MOLECULE
int regionflag; // 0 = anywhere in box, 1 = specific region
int iregion; // gcmc region
char *idregion; // gcmc region id
bool pressure_flag; // true if user specified reservoir pressure
bool charge_flag; // true if user specified atomic charge
bool full_flag; // true if doing full system energy calculations
int natoms_per_molecule; // number of atoms in each gas molecule
int groupbitall; // group bitmask for inserted atoms
int ngroups; // number of group-ids for inserted atoms
char** groupstrings; // list of group-ids for inserted atoms
int ngrouptypes; // number of type-based group-ids for inserted atoms
char** grouptypestrings; // list of type-based group-ids for inserted atoms
int* grouptypebits; // list of type-based group bitmasks
int* grouptypes; // list of type-based group types
double ntranslation_attempts;
double ntranslation_successes;
double nrotation_attempts;
double nrotation_successes;
double ndeletion_attempts;
double ndeletion_successes;
double ninsertion_attempts;
double ninsertion_successes;
int gcmc_nmax;
int max_region_attempts;
double gas_mass;
double reservoir_temperature;
double tfac_insert;
double chemical_potential;
double displace;
double max_rotation_angle;
double beta,zz,sigma,volume;
double pressure,fugacity_coeff,charge;
double xlo,xhi,ylo,yhi,zlo,zhi;
double region_xlo,region_xhi,region_ylo,region_yhi,region_zlo,region_zhi;
double region_volume;
double energy_stored;
double *sublo,*subhi;
int *local_gas_list;
double **cutsq;
double **atom_coord;
imageint imagezero;
double energy_intra;
class Pair *pair;
class RanPark *random_equal;
class RanPark *random_unequal;
class Atom *model_atom;
class Molecule **onemols;
int imol,nmol;
double **coords;
imageint *imageflags;
class Fix *fixshake;
int shakeflag;
char *idshake;
int triclinic; // 0 = orthog box, 1 = triclinic
class Compute *c_pe;
void options(int, char **);
};
}
#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: Fix gcmc does not (yet) work with atom_style template
Self-explanatory.
E: Fix gcmc region does not support a bounding box
Not all regions represent bounded volumes. You cannot use
such a region with the fix gcmc command.
E: Fix gcmc region cannot be dynamic
Only static regions can be used with fix gcmc.
E: Fix gcmc region extends outside simulation box
Self-explanatory.
E: Fix gcmc molecule must have coordinates
The defined molecule does not specify coordinates.
E: Fix gcmc molecule must have atom types
The defined molecule does not specify atom types.
E: Atom type must be zero in fix gcmc mol command
Self-explanatory.
E: Fix gcmc molecule has charges, but atom style does not
Self-explanatory.
E: Fix gcmc molecule template ID must be same as atom_style template ID
When using atom_style template, you cannot insert molecules that are
not in that template.
E: Fix gcmc atom has charge, but atom style does not
Self-explanatory.
E: Cannot use fix gcmc shake and not molecule
Self-explanatory.
E: Molecule template ID for fix gcmc does not exist
Self-explanatory.
W: Molecule template for fix gcmc has multiple molecules
The fix gcmc command will only create molecules of a single type,
i.e. the first molecule in the template.
E: Region ID for fix gcmc does not exist
Self-explanatory.
W: Fix gcmc using full_energy option
Fix gcmc has automatically turned on the full_energy option since it
is required for systems like the one specified by the user. User input
included one or more of the following: kspace, triclinic, a hybrid
pair style, an eam pair style, or no "single" function for the pair
style.
E: Invalid atom type in fix gcmc command
The atom type specified in the gcmc command does not exist.
E: Fix gcmc cannot exchange individual atoms belonging to a molecule
This is an error since you should not delete only one atom of a
molecule. The user has specified atomic (non-molecular) gas
exchanges, but an atom belonging to a molecule could be deleted.
E: All mol IDs should be set for fix gcmc group atoms
The molecule flag is on, yet not all molecule ids in the fix group
have been set to non-zero positive values by the user. This is an
error since all atoms in the fix gcmc group are eligible for deletion,
rotation, and translation and therefore must have valid molecule ids.
E: Fix gcmc molecule command requires that atoms have molecule attributes
Should not choose the gcmc molecule feature if no molecules are being
simulated. The general molecule flag is off, but gcmc's molecule flag
is on.
E: Fix gcmc shake fix does not exist
Self-explanatory.
E: Fix gcmc and fix shake not using same molecule template ID
Self-explanatory.
E: Fix gcmc can not currently be used with fix rigid or fix rigid/small
Self-explanatory.
E: Cannot use fix gcmc in a 2d simulation
Fix gcmc is set up to run in 3d only. No 2d simulations with fix gcmc
are allowed.
E: Could not find fix gcmc exclusion group ID
Self-explanatory.
E: Could not find fix gcmc rotation group ID
Self-explanatory.
E: Illegal fix gcmc gas mass <= 0
The computed mass of the designated gas molecule or atom type was less
than or equal to zero.
E: Cannot do GCMC on atoms in atom_modify first group
This is a restriction due to the way atoms are organized in a list to
enable the atom_modify first command.
E: Could not find specified fix gcmc group ID
Self-explanatory.
E: Fix gcmc put atom outside box
This should not normally happen. Contact the developers.
E: Fix gcmc ran out of available molecule IDs
See the setting for tagint in the src/lmptype.h file.
E: Fix gcmc ran out of available atom IDs
See the setting for tagint in the src/lmptype.h file.
E: Too many total atoms
See the setting for bigint in the src/lmptype.h file.
*/

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