/* -*- 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 #include "pointers.h" #include #include 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 any of next 3 flags are set, else 0 int box_change_size; // 1 if box size changes, 0 if not int box_change_shape; // 1 if box shape changes, 0 if not int box_change_domain; // 1 if proc sub-domains change, 0 if not 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 int copymode; typedef Region *(*RegionCreator)(LAMMPS *,int,char**); typedef std::map RegionCreatorMap; RegionCreatorMap *region_map; Domain(class LAMMPS *); virtual ~Domain(); virtual void init(); void set_initial_box(int expandflag=1); 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 subbox_too_small_check(double); 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 *, imageint &); void remap(double *); void remap_near(double *, double *); void unmap(double *, imageint); void unmap(double *, imageint, 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 *); int inside(double *); int inside_nonperiodic(double *); void x2lamda(double *, double *, double *, double *); void bbox(double *, double *, double *, double *); void box_corners(); void subbox_corners(); void lamda_box_corners(double *, double *); // minimum image convention check // return 1 if any distance > 1/2 of box size // indicates a special neighbor is actually not in a bond, // but is a far-away image that should be treated as an unbonded neighbor // 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 private: template static Region *region_creator(LAMMPS *,int,char**); }; } #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. Inconsistent 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. W: 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. 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 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. W: Proc sub-domain size < neighbor skin, could lead to lost atoms The decomposition of the physical domain (likely due to load balancing) has led to a processor's sub-domain being smaller than the neighbor skin in one or more dimensions. Since reneighboring is triggered by atoms moving the skin distance, this may lead to lost atoms, if an atom moves all the way across a neighboring processor's sub-domain before reneighboring is triggered. 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: Unknown 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. */