lammps-sys 0.6.0

Generates bindings to LAMMPS' C interface (with optional builds from source)
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114

/* -*- 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.
------------------------------------------------------------------------- */

#ifdef FIX_CLASS

FixStyle(hyper/global,FixHyperGlobal)

#else

#ifndef LMP_FIX_HYPER_GLOBAL_H
#define LMP_FIX_HYPER_GLOBAL_H

#include "fix_hyper.h"

namespace LAMMPS_NS {

class FixHyperGlobal : public FixHyper {
 public:
  FixHyperGlobal(class LAMMPS *, int, char **);
  ~FixHyperGlobal();
  int setmask();
  void init();
  void init_list(int, class NeighList *);
  void setup_pre_neighbor();
  void setup_pre_reverse(int, int);
  void pre_neighbor();
  void pre_reverse(int, int);
  double compute_scalar();
  double compute_vector(int);
  double query(int);

  double memory_usage();

  // extra methods visible to callers

  void init_hyper();
  void build_bond_list(int);

 private:
  int me;
  double cutbond,qfactor,vmax,tequil;

  int firstflag,bcastflag,owner,nevent,nevent_atom;
  double cutbondsq,beta,dt,t_hyper,invqfactorsq;
  double outvec[5];        // same as VECLEN in *.cpp
  double maxbondlen;       // max length of any bond
  double maxdriftsq;       // max distance any atom drifts from original pos
  int nobias;              // # of steps when bias = 0, b/c bond too long
  int negstrain;           // # of steps when biased bond has negative strain

  class NeighList *list;

  // list of my owned bonds
  // persists on a proc from one event until the next

  int maxbond;                 // allocated size of blist

  struct OneBond {             // single IJ bond, atom I is owner
    int i,j;                   // current local indices of 2 bond atoms
    int iold,jold;             // local indices when bonds were formed
    double r0;                 // relaxed bond length
  };

  OneBond *blist;              // list of owned bonds
  int nblocal;                 // # of owned bonds

  // coords and IDs of owned+ghost atoms when bonds were formed
  // persists on a proc from one event until the next

  int nlocal_old;               // nlocal for old atoms
  int nall_old;                 // nlocal+nghost for old atoms
  int maxold;                   // allocated size of old atoms

  double **xold;                // coords of atoms when bonds were formed
  tagint *tagold;               // IDs of atoms when bonds were forme
  int *old2now;                 // o2n[i] = current local index of old atom I

  // MPI data struct for finding bond with max strain via Allreduce

  struct Two {
    double value;
    int proc;
  };
  Two pairme,pairall;

  // internal methods

  void grow_bond();
};

}

#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.

*/