forked from lijiext/lammps
270 lines
10 KiB
C++
270 lines
10 KiB
C++
/* -*- c++ -*- ----------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifndef LMP_DOMAIN_H
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#define LMP_DOMAIN_H
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#include "math.h"
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#include "pointers.h"
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namespace LAMMPS_NS {
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class Domain : protected Pointers {
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public:
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int box_exist; // 0 = not yet created, 1 = exists
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int dimension; // 2 = 2d, 3 = 3d
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int nonperiodic; // 0 = periodic in all 3 dims
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// 1 = periodic or fixed in all 6
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// 2 = shrink-wrap in any of 6
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int xperiodic,yperiodic,zperiodic; // 0 = non-periodic, 1 = periodic
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int periodicity[3]; // xyz periodicity as array
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int boundary[3][2]; // settings for 6 boundaries
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// 0 = periodic
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// 1 = fixed non-periodic
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// 2 = shrink-wrap non-periodic
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// 3 = shrink-wrap non-per w/ min
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int triclinic; // 0 = orthog box, 1 = triclinic
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int tiltsmall; // 1 if limit tilt, else 0
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// orthogonal box
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double xprd,yprd,zprd; // global box dimensions
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double xprd_half,yprd_half,zprd_half; // half dimensions
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double prd[3]; // array form of dimensions
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double prd_half[3]; // array form of half dimensions
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// triclinic box
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// xprd,xprd_half,prd,prd_half =
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// same as if untilted
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double prd_lamda[3]; // lamda box = (1,1,1)
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double prd_half_lamda[3]; // lamda half box = (0.5,0.5,0.5)
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double boxlo[3],boxhi[3]; // orthogonal box global bounds
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// triclinic box
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// boxlo/hi = same as if untilted
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double boxlo_lamda[3],boxhi_lamda[3]; // lamda box = (0,1)
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double boxlo_bound[3],boxhi_bound[3]; // bounding box of tilted domain
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double corners[8][3]; // 8 corner points
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// orthogonal box & triclinic box
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double minxlo,minxhi; // minimum size of global box
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double minylo,minyhi; // when shrink-wrapping
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double minzlo,minzhi; // tri only possible for non-skew dims
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// orthogonal box
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double sublo[3],subhi[3]; // sub-box bounds on this proc
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// triclinic box
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// sublo/hi = undefined
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double sublo_lamda[3],subhi_lamda[3]; // bounds of subbox in lamda
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// triclinic box
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double xy,xz,yz; // 3 tilt factors
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double h[6],h_inv[6]; // shape matrix in Voigt notation
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double h_rate[6],h_ratelo[3]; // rate of box size/shape change
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int box_change; // 1 if any of next 3 flags are set, else 0
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int box_change_size; // 1 if box size changes, 0 if not
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int box_change_shape; // 1 if box shape changes, 0 if not
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int box_change_domain; // 1 if proc sub-domains change, 0 if not
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int deform_flag; // 1 if fix deform exist, else 0
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int deform_vremap; // 1 if fix deform remaps v, else 0
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int deform_groupbit; // atom group to perform v remap for
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class Lattice *lattice; // user-defined lattice
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int nregion; // # of defined Regions
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int maxregion; // max # list can hold
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class Region **regions; // list of defined Regions
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int copymode;
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Domain(class LAMMPS *);
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virtual ~Domain();
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virtual void init();
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void set_initial_box(int expandflag=1);
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virtual void set_global_box();
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virtual void set_lamda_box();
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virtual void set_local_box();
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virtual void reset_box();
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virtual void pbc();
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void image_check();
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void box_too_small_check();
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void subbox_too_small_check(double);
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void minimum_image(double &, double &, double &);
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void minimum_image(double *);
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int closest_image(int, int);
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void closest_image(const double * const, const double * const,
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double * const);
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void remap(double *, imageint &);
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void remap(double *);
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void remap_near(double *, double *);
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void unmap(double *, imageint);
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void unmap(double *, imageint, double *);
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void image_flip(int, int, int);
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void set_lattice(int, char **);
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void add_region(int, char **);
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void delete_region(int, char **);
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int find_region(char *);
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void set_boundary(int, char **, int);
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void set_box(int, char **);
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void print_box(const char *);
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void boundary_string(char *);
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virtual void lamda2x(int);
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virtual void x2lamda(int);
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virtual void lamda2x(double *, double *);
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virtual void x2lamda(double *, double *);
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int inside(double *);
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int inside_nonperiodic(double *);
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void x2lamda(double *, double *, double *, double *);
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void bbox(double *, double *, double *, double *);
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void box_corners();
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void subbox_corners();
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void lamda_box_corners(double *, double *);
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// minimum image convention check
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// return 1 if any distance > 1/2 of box size
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// indicates a special neighbor is actually not in a bond,
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// but is a far-away image that should be treated as an unbonded neighbor
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// inline since called from neighbor build inner loop
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//
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inline int minimum_image_check(double dx, double dy, double dz) {
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if (xperiodic && fabs(dx) > xprd_half) return 1;
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if (yperiodic && fabs(dy) > yprd_half) return 1;
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if (zperiodic && fabs(dz) > zprd_half) return 1;
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return 0;
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}
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protected:
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double small[3]; // fractions of box lengths
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};
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}
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#endif
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/* ERROR/WARNING messages:
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E: Box bounds are invalid
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The box boundaries specified in the read_data file are invalid. The
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lo value must be less than the hi value for all 3 dimensions.
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E: Cannot skew triclinic box in z for 2d simulation
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Self-explanatory.
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E: Triclinic box skew is too large
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The displacement in a skewed direction must be less than half the box
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length in that dimension. E.g. the xy tilt must be between -half and
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+half of the x box length. This constraint can be relaxed by using
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the box tilt command.
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W: Triclinic box skew is large
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The displacement in a skewed direction is normally required to be less
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than half the box length in that dimension. E.g. the xy tilt must be
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between -half and +half of the x box length. You have relaxed the
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constraint using the box tilt command, but the warning means that a
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LAMMPS simulation may be inefficient as a result.
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E: Illegal simulation box
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The lower bound of the simulation box is greater than the upper bound.
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E: Bond atom missing in image check
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The 2nd atom in a particular bond is missing on this processor.
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Typically this is because the pairwise cutoff is set too short or the
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bond has blown apart and an atom is too far away.
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W: Inconsistent image flags
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The image flags for a pair on bonded atoms appear to be inconsistent.
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Inconsistent means that when the coordinates of the two atoms are
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unwrapped using the image flags, the two atoms are far apart.
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Specifically they are further apart than half a periodic box length.
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Or they are more than a box length apart in a non-periodic dimension.
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This is usually due to the initial data file not having correct image
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flags for the 2 atoms in a bond that straddles a periodic boundary.
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They should be different by 1 in that case. This is a warning because
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inconsistent image flags will not cause problems for dynamics or most
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LAMMPS simulations. However they can cause problems when such atoms
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are used with the fix rigid or replicate commands.
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W: Bond atom missing in image check
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The 2nd atom in a particular bond is missing on this processor.
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Typically this is because the pairwise cutoff is set too short or the
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bond has blown apart and an atom is too far away.
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E: Bond atom missing in box size check
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The 2nd atoms needed to compute a particular bond is missing on this
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processor. Typically this is because the pairwise cutoff is set too
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short or the bond has blown apart and an atom is too far away.
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W: Bond atom missing in box size check
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The 2nd atoms needed to compute a particular bond is missing on this
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processor. Typically this is because the pairwise cutoff is set too
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short or the bond has blown apart and an atom is too far away.
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W: Bond/angle/dihedral extent > half of periodic box length
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This is a restriction because LAMMPS can be confused about which image
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of an atom in the bonded interaction is the correct one to use.
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"Extent" in this context means the maximum end-to-end length of the
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bond/angle/dihedral. LAMMPS computes this by taking the maximum bond
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length, multiplying by the number of bonds in the interaction (e.g. 3
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for a dihedral) and adding a small amount of stretch.
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W: Proc sub-domain size < neighbor skin, could lead to lost atoms
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The decomposition of the physical domain (likely due to load
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balancing) has led to a processor's sub-domain being smaller than the
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neighbor skin in one or more dimensions. Since reneighboring is
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triggered by atoms moving the skin distance, this may lead to lost
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atoms, if an atom moves all the way across a neighboring processor's
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sub-domain before reneighboring is triggered.
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E: Illegal ... command
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Self-explanatory. Check the input script syntax and compare to the
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documentation for the command. You can use -echo screen as a
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command-line option when running LAMMPS to see the offending line.
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E: Reuse of region ID
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A region ID cannot be used twice.
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E: Unknown region style
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The choice of region style is unknown.
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E: Delete region ID does not exist
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Self-explanatory.
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E: Both sides of boundary must be periodic
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Cannot specify a boundary as periodic only on the lo or hi side. Must
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be periodic on both sides.
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*/
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