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domain.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.
------------------------------------------------------------------------- */
#ifndef LMP_DOMAIN_H
#define LMP_DOMAIN_H
#include "math.h"
#include "pointers.h"
namespace LAMMPS_NS {
class Domain : protected Pointers {
public:
int box_exist; // 0 = not yet created, 1 = exists
int dimension; // 2 = 2d, 3 = 3d
int nonperiodic; // 0 = periodic in all 3 dims
// 1 = periodic or fixed in all 6
// 2 = shrink-wrap in any of 6
int xperiodic,yperiodic,zperiodic; // 0 = non-periodic, 1 = periodic
int periodicity[3]; // xyz periodicity as array
int boundary[3][2]; // settings for 6 boundaries
// 0 = periodic
// 1 = fixed non-periodic
// 2 = shrink-wrap non-periodic
// 3 = shrink-wrap non-per w/ min
int triclinic; // 0 = orthog box, 1 = triclinic
int tiltsmall; // 1 if limit tilt, else 0
// orthogonal box
double xprd,yprd,zprd; // global box dimensions
double xprd_half,yprd_half,zprd_half; // half dimensions
double prd[3]; // array form of dimensions
double prd_half[3]; // array form of half dimensions
// triclinic box
// xprd,xprd_half,prd,prd_half =
// same as if untilted
double prd_lamda[3]; // lamda box = (1,1,1)
double prd_half_lamda[3]; // lamda half box = (0.5,0.5,0.5)
double boxlo[3],boxhi[3]; // orthogonal box global bounds
// triclinic box
// boxlo/hi = same as if untilted
double boxlo_lamda[3],boxhi_lamda[3]; // lamda box = (0,1)
double boxlo_bound[3],boxhi_bound[3]; // bounding box of tilted domain
double corners[8][3]; // 8 corner points
// orthogonal box & triclinic box
double minxlo,minxhi; // minimum size of global box
double minylo,minyhi; // when shrink-wrapping
double minzlo,minzhi; // tri only possible for non-skew dims
// orthogonal box
double sublo[3],subhi[3]; // sub-box bounds on this proc
// triclinic box
// sublo/hi = undefined
double sublo_lamda[3],subhi_lamda[3]; // bounds of subbox in lamda
// triclinic box
double xy,xz,yz; // 3 tilt factors
double h[6],h_inv[6]; // shape matrix in Voigt notation
double h_rate[6],h_ratelo[3]; // rate of box size/shape change
int box_change; // 1 if box bounds ever change, 0 if fixed
int deform_flag; // 1 if fix deform exist, else 0
int deform_vremap; // 1 if fix deform remaps v, else 0
int deform_groupbit; // atom group to perform v remap for
class Lattice *lattice; // user-defined lattice
int nregion; // # of defined Regions
int maxregion; // max # list can hold
class Region **regions; // list of defined Regions
Domain(class LAMMPS *);
virtual ~Domain();
virtual void init();
void set_initial_box();
virtual void set_global_box();
virtual void set_lamda_box();
virtual void set_local_box();
virtual void reset_box();
virtual void pbc();
void image_check();
void box_too_small_check();
void minimum_image(double &, double &, double &);
void minimum_image(double *);
int closest_image(int, int);
void closest_image(const double * const, const double * const,
double * const);
void remap(double *, tagint &);
void remap(double *);
void remap_near(double *, double *);
void unmap(double *, tagint);
void unmap(double *, tagint, double *);
void image_flip(int, int, int);
void set_lattice(int, char **);
void add_region(int, char **);
void delete_region(int, char **);
int find_region(char *);
void set_boundary(int, char **, int);
void set_box(int, char **);
void print_box(const char *);
void boundary_string(char *);
virtual void lamda2x(int);
virtual void x2lamda(int);
virtual void lamda2x(double *, double *);
virtual void x2lamda(double *, double *);
void x2lamda(double *, double *, double *, double *);
void bbox(double *, double *, double *, double *);
void box_corners();
// minimum image convention check
// return 1 if any distance > 1/2 of box size
// inline since called from neighbor build inner loop
inline int minimum_image_check(double dx, double dy, double dz) {
if (xperiodic && fabs(dx) > xprd_half) return 1;
if (yperiodic && fabs(dy) > yprd_half) return 1;
if (zperiodic && fabs(dz) > zprd_half) return 1;
return 0;
}
protected:
double small[3]; // fractions of box lengths
};
}
#endif
/* ERROR/WARNING messages:
E: Box bounds are invalid
The box boundaries specified in the read_data file are invalid. The
lo value must be less than the hi value for all 3 dimensions.
E: Cannot skew triclinic box in z for 2d simulation
Self-explanatory.
E: Triclinic box skew is too large
The displacement in a skewed direction must be less than half the box
length in that dimension. E.g. the xy tilt must be between -half and
+half of the x box length. This constraint can be relaxed by using
the box tilt command.
W: Triclinic box skew is large
The displacement in a skewed direction is normally required to be less
than half the box length in that dimension. E.g. the xy tilt must be
between -half and +half of the x box length. You have relaxed the
constraint using the box tilt command, but the warning means that a
LAMMPS simulation may be inefficient as a result.
E: Illegal simulation box
The lower bound of the simulation box is greater than the upper bound.
E: Bond atom missing in image check
The 2nd atom in a particular bond is missing on this processor.
Typically this is because the pairwise cutoff is set too short or the
bond has blown apart and an atom is too far away.
W: Inconsistent image flags
The image flags for a pair on bonded atoms appear to be inconsistent.
Inconstent means that when the coordinates of the two atoms
are unwrapped using the image flags, the two atoms are far apart.
Specifically they are further apart than half a periodic box length.
Or they are more than a box length apart in a non-periodic dimension.
This is usually due to the initial data file not having correct
image flags for the 2 atoms in a bond that straddles a periodic
boundary. They should be different by 1 in that case.
This is a warning because inconsistent image flags will not cause
problems for dynamics or most LAMMPS simulations. However they can
cause problems when such atoms are used with the fix rigid or
replicate commands.
E: Bond atom missing in box size check
The 2nd atoms needed to compute a particular bond is missing on this
processor. Typically this is because the pairwise cutoff is set too
short or the bond has blown apart and an atom is too far away.
W: Bond/angle/dihedral extent > half of periodic box length
This is a restriction because LAMMPS can be confused about which image
of an atom in the bonded interaction is the correct one to use.
"Extent" in this context means the maximum end-to-end length of the
bond/angle/dihedral. LAMMPS computes this by taking the maximum bond
length, multiplying by the number of bonds in the interaction (e.g. 3
for a dihedral) and adding a small amount of stretch.
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: Reuse of region ID
A region ID cannot be used twice.
E: Invalid region style
The choice of region style is unknown.
E: Delete region ID does not exist
Self-explanatory.
E: Both sides of boundary must be periodic
Cannot specify a boundary as periodic only on the lo or hi side. Must
be periodic on both sides.
*/

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