forked from lijiext/lammps
Adding molecule capability to fix GCMC.
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@9059 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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pscrozi
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c3de934966
commit
b1c7c64624
1181
src/MC/fix_gcmc.cpp
1181
src/MC/fix_gcmc.cpp
File diff suppressed because it is too large
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@ -32,48 +32,75 @@ class FixGCMC : public Fix {
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int setmask();
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void init();
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void pre_exchange();
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void attempt_move();
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void attempt_deletion();
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void attempt_insertion();
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double energy(int, double *);
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void attempt_atomic_translation();
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void attempt_atomic_deletion();
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void attempt_atomic_insertion();
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void attempt_molecule_translation();
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void attempt_molecule_rotation();
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void attempt_molecule_deletion();
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void attempt_molecule_insertion();
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double energy(int, int, int, double *);
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int pick_random_gas_atom();
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int pick_random_gas_atom_in_region();
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int pick_random_gas_molecule();
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int pick_random_gas_molecule_in_region();
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double molecule_energy(int);
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void get_rotation_matrix(double, double *);
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void get_model_molecule();
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void update_gas_atoms_list();
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double compute_vector(int);
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double memory_usage();
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void write_restart(FILE *);
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void restart(char *);
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private:
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int ntype,nevery,seed;
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int rotation_group,rotation_groupbit;
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int rotation_inversegroupbit;
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int ngcmc_type,nevery,seed;
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int ncycles,nexchanges,nmcmoves;
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int ngas; // # of gas molecules (or atoms) on all procs
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int ngas_local; // # of gas molecules (or atoms) on this proc
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int ngas_before; // # of gas molecules (or atoms) on procs < this proc
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int molflag; // 0 = atomic, 1 = molecular system
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int regionflag; // 0 = anywhere, 1 = specific region
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int iregion; // exchange/move region
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char *idregion; // exchange/move region id
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int ngas; // # of gas atoms on all procs
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int ngas_local; // # of gas atoms on this proc
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int ngas_before; // # of gas atoms on procs < this proc
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int molflag; // 0 = atomic, 1 = molecular system
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int regionflag; // 0 = anywhere in box, 1 = specific region
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int iregion; // GCMC region
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char *idregion; // GCMC region id
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double nmove_attempts;
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double nmove_successes;
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double ndel_attempts;
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double ndel_successes;
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double ninsert_attempts;
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double ninsert_successes;
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int maxmol; // largest molecule tag across all existing atoms
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int natoms_per_molecule; // number of atoms in each gas molecule
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int nmax;
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double ntranslation_attempts;
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double ntranslation_successes;
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double nrotation_attempts;
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double nrotation_successes;
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double ndeletion_attempts;
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double ndeletion_successes;
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double ninsertion_attempts;
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double ninsertion_successes;
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int gcmc_nmax;
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int max_region_attempts;
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double gas_mass;
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double reservoir_temperature;
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double chemical_potential;
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double displace;
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double max_rotation_angle;
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double beta,zz,sigma,volume;
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double xlo,xhi,ylo,yhi,zlo,zhi;
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double region_xlo,region_xhi,region_ylo,region_yhi,region_zlo,region_zhi;
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double *sublo,*subhi;
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int *local_gas_list;
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double **cutsq;
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double **atom_coord;
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double *model_atom_buf;
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tagint imagetmp;
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class Pair *pair;
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class RanPark *random_equal;
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class RanPark *random_unequal;
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class Atom *model_atom;
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void options(int, char **);
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};
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@ -100,41 +127,83 @@ E: Cannot do GCMC on atoms in atom_modify first group
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This is a restriction due to the way atoms are organized in a list to
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enable the atom_modify first command.
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W: Fix GCMC may delete atom with non-zero molecule ID
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E: Fix GCMC cannot exchange individual atoms belonging to a molecule
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This is probably an error, since you should not delete only one atom
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of a molecule. The GCMC molecule exchange feature does not yet work.
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This is an error since you should not delete only one atom of a molecule.
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The user has specified atomic (non-molecular) gas exchanges, but an atom
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belonging to a molecule could be deleted.
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E: Fix GCMC molecule command requires atom attribute molecule
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E: All mol IDs should be set for fix GCMC group atoms
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The molecule flag is on, yet not all molecule ids in the fix group have
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been set to non-zero positive values by the user. This is an error since
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all atoms in the fix GCMC group are eligible for deletion, rotation, and
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translation and therefore must have valid molecule ids.
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E: Cannot use fix GCMC in a 2d simulation
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Fix GCMC is set up to run in 3d only. No 2d simulations with fix GCMC
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are allowed.
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E: Cannot use fix GCMC with a triclinic box
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Fix GCMC is set up to run with othogonal boxes only. Simulations with
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triclinic boxes and fix GCMC are not allowed.
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E: Fix GCMC molecule command requires that atoms have molecule attributes
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Should not choose the GCMC molecule feature if no molecules are being
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simulated. The general molecule flag is off, but GCMC's molecule flag
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is on.
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E: Fix GCMC molecule feature does not yet work
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E: Fix GCMC could not find any atoms in the user-supplied template molecule
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Fix GCMC cannot (yet) be used to exchange molecules, only atoms.
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When using the molecule option with fix GCMC, the user must supply a
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template molecule in the usual LAMMPS data file with its molecule id
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specified in the fix GCMC command as the "type" of the exchanged gas.
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E: Fix GCMC incompatible with given pair_style
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Some pair_styles do not provide single-atom energies, which are needed
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by fix GCMC.
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E: Fix GCMC region does not support a bounding box
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E: Fix GCMC incorrect number of atoms per molecule
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Not all regions represent bounded volumes. You cannot use
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such a region with the fix GCMC command.
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The number of atoms in each gas molecule was not computed correctly.
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E: Fix GCMC region cannot be dynamic
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E: Illegal fix GCMC gas mass <= 0
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Only static regions can be used with fix GCMC.
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The computed mass of the designated gas molecule or atom type was less
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than or equal to zero.
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E: Deposition region extends outside simulation box
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E: Fix GCMC ran out of available molecule IDs
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Self-explanatory.
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This is a code limitation where more than MAXSMALLINT (usually around
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two billion) molecules have been created. The code needs to be
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modified to either allow molecule ID recycling or use bigger ints for
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molecule IDs. A work-around is to run shorter simulations.
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E: Region ID for fix GCMC does not exist
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W: Fix GCMC fix group should be all
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Self-explanatory.
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Fix GCMC will ignore the fix group specified by the user. User should
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set the fix group to "all". Fix GCMC will overwrite the user-specified
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fix group with a group consisting of all GCMC gas atoms.
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E: Fix GCMC region does not support a bounding box
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Not all regions represent bounded volumes. You cannot use
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such a region with the fix GCMC command.
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E: Fix GCMC region cannot be dynamic
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Only static regions can be used with fix GCMC.
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E: Fix GCMC region extends outside simulation box
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Self-explanatory.
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E: Region ID for fix GCMC does not exist
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Self-explanatory.
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*/
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