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
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192

#ifndef MATRIXDEF_H 
#define MATRIXDEF_H

/******************************************************************************
* Common definitions for Matrix and Vector classes
* This header file contains macros and inline functions needed for the matrix 
* classes.  All error checking should be defined here as a macro so that it is
* neatly disabled when ATC_PRINT_DEBUGGING is not defined
******************************************************************************/

/******************************************************************************
* Headers and namespaces used by Matrix and Vector classes
******************************************************************************/
#include <iostream>
#include <fstream>
#include <map>
#include <vector>
#include <set>
#include <cstring>
#include <string>
#include <iomanip>
#include <cmath>
#include "Utility.h"

namespace ATC_matrix {

/******************************************************************************
* Typedefs used by Matrix and Vector classes
******************************************************************************/
//* @typedef INDEX
//* @brief indexing type (default: unsigned) for matrix classes
// can switch typedef back to unsigned to be more precise, but will cause warnings everywhere
//typedef unsigned INDEX;
typedef int INDEX;
//* @typedef CLONE_TYPE
//* @brief dimension of matrix to clone
enum CLONE_TYPE { CLONE_ROW=0, CLONE_COL=1, CLONE_DIAG=2 };
//* @struct TRIPLET
//* @brief Triplet output entity
template <typename T> 
struct TRIPLET { TRIPLET<T>(int _i=0, int _j=0, T _v=T(0)) : i(_i), j(_j), v(_v) {}
                 INDEX i, j; T v; };

/******************************************************************************
* Definitions for row/column major storage
******************************************************************************/
#define COL_STORAGE  /* <--- comment out this line for row-major storage*/
#ifdef COL_STORAGE
#define DATA(i,j) _data[(i)+_nRows*(j)]
#else
#define  ROW_STORAGE
#define DATA(i,j) _data[(i)*_nCols+(j)]
#endif

/******************************************************************************
* error checking macros
*  MICK:  checks if index (i,j) is in range                       MATRIX ONLY
*  VICK:  checks if index (i) is in range                         VECTOR ONLY
*  MICM:  checks if index (i,j) is in range, displays message     MATRIX ONLY
*  VICM:  checks if index (i) is in range, displays message       VECTOR ONLY
*  SQCK:  checks if matrix is square, displays message            MATRIX ONLY
*  SSCK:  checks if a has the same size as b                      VECTOR/MATRIX
*  GCK:   generic two object check, checks if c is true           VECTOR/MATRIX
*  GCHK:  generic check, checks if c is true                      ANYTHING
******************************************************************************/
#define ERROR_FOR_BACKTRACE /**/
#define MICK(i,j)     /**/
#define VICK(i)       /**/
#define MICM(i,j,m)   /**/
#define VICM(i,m)     /**/
#define SQCK(a,m)     /**/
#define SICK(a,b,m)   /**/
#define SSCK(a,b,m)   /**/
#define GCK(a,b,c,m)  /**/
#define GCHK(c,m)     /**/

// the following two convert __LINE__ to a string
#define STRING2(x) #x
#define STRING(x) STRING2(x)
// prints file and line number for error messages
#define ERROR(x) __FILE__ ":" STRING(__LINE__) " " x

/******************************************************************************
* BLAS and LAPACK definitions
******************************************************************************/
#ifdef MKL
#include "mkl.h"
#define dgemv_  dgemv
#define dgemm_  dgemm
#define dgetrf_ dgetrf
#define dgetri_ dgetri
#define dgecon_ dgecon
#define dlange_ dlange
#define dsygvd_ dsygvd
#define dgesvd_ dgesvd
#define dgesdd_ dgesdd
#else
extern "C"
{
extern void dgemv_(char*,int*,int*,double*,const double*,int*,const double*,int *,double*,double*,int*);
extern void dgemm_(char*,char*,int*,int*,int*,double*,const double*,int*,const double*,int*,double*,double*,int*);
extern void dgetrf_(int*,int*,double*,int*,int*,int*);
extern void dgetri_(int*,double*,int*,int*,double*,int*,int*);
extern void dgecon_(char*,int*,double*,int*,double*,double*,double*,int*,int*);
extern double dlange_(char*,int*,int*,const double*,int*,double*);
extern double dsygvd_(int*,char*,char*,int*,double*,int*,double*,int*,double*,double*,int*,int*,int*,int*);
extern double dgesvd_(char*,char*,int*,int*,double*,int*,double*,double*,int*,double*,int*,double*,int*,int*);
extern double dgesdd_(char*,char*,int*,int*,double*,int*,double*,double*,int*,double*,int*,double*,int*,int*);
}
#endif

// forward declarations of matrix and vector classes
template<typename T> class Matrix;
template<typename T> class DenseMatrix;
template<typename T> class ParDenseMatrix;
template<typename T> class SparseMatrix;
template<typename T> class ParSparseMatrix;
template<typename T> class SparseVector;
template<typename T> class DiagonalMatrix;
template<typename T> class ParDiagonalMatrix;
template<typename T> class Vector;
template<typename T> class DenseVector;
template<typename T> class CloneVector;
template<typename T> class WrapMatrix;
template<typename T> class WrapVector;

//* forward declaration of operations
//@{
template<class T> DenseVector<T>  operator*(const Matrix<T> &M, const SparseVector<T> &v);
template<class T> DenseVector<T>  operator*(const SparseVector<T> &v, const Matrix<T> &M);
template<class T> SparseVector<T> operator*(const SparseMatrix<T> &M, const SparseVector<T> &v);
template<class T> SparseVector<T> operator*(const SparseVector<T> &v, const SparseMatrix<T> &M);
template<class T> DenseVector<T>  operator*(const SparseMatrix<T> &A, const Vector<T>& x);
template<class T> DenseVector<T>  operator*(const Vector<T> &A, const SparseMatrix<T>& x);
template<class T> DenseMatrix<T>  operator*(const SparseMatrix<T> &A, const Matrix<T>& D);
template<class T> SparseMatrix<T> operator*(const SparseMatrix<T> &A, const DiagonalMatrix<T>& D);
template<class T> SparseMatrix<T> operator*(const SparseMatrix<T> &A, const SparseMatrix<T> &B);
template<class T> T dot(const SparseVector<T> &a, const SparseVector<T> &b);
//@}

template<class T> CloneVector<T> column(Matrix<T> &c, INDEX i) {
  return CloneVector<T>(c, CLONE_COL, i); 
}
template<class T> CloneVector<T> row(Matrix<T> &c, INDEX i) {
  return CloneVector<T>(c, CLONE_ROW, i);
}
template<class T> CloneVector<T> diagonal(Matrix<T> &c) {
  return CloneVector<T>(c, CLONE_DIAG); 
}
template<class T> const CloneVector<T> column(const Matrix<T> &c, INDEX i) {
  return CloneVector<T>(c, CLONE_COL, i); 
}
template<class T> const CloneVector<T> row(const Matrix<T> &c, INDEX i) {
  return CloneVector<T>(c, CLONE_ROW, i); 
}
template<class T> const CloneVector<T> diagonal(const Matrix<T> &c) { 
  return CloneVector<T>(c, CLONE_DIAG); 
}
template<class T> const SparseMatrix<T> *sparse_cast(const Matrix<T> *m);
template<class T> const DiagonalMatrix<T> *diag_cast(const Matrix<T> *m);
template<class T> void copy_sparse_to_matrix(const SparseMatrix<T> *s, Matrix<T> &m);
template<typename T> DenseMatrix<T> operator*(const DiagonalMatrix<T>& A, const Matrix<T> &B);
template<typename T> DenseMatrix<T> operator*(const Matrix<T> &B, const DiagonalMatrix<T>& A);

// double precision shortcuts
typedef Matrix<double>         MATRIX;          // matrix of double
typedef Vector<double>         VECTOR;          // vector of double
typedef DenseMatrix<double>    DENS_MAT;        // dense matrix of double type
typedef ParDenseMatrix<double> PAR_DENS_MAT;    // parallel dense matrix of doubles
typedef CloneVector<double>    CLON_VEC;        // cloned vector of double type
typedef DenseVector<double>    DENS_VEC;        // dense vector of double type
typedef DiagonalMatrix<double> DIAG_MAT;        // diagonal matrix of double type
typedef ParDiagonalMatrix<double> PAR_DIAG_MAT; // diagonal matrix of double type
typedef SparseMatrix<double>   SPAR_MAT;        // sparse matrix of double type
typedef ParSparseMatrix<double> PAR_SPAR_MAT;   // parallel sparse matrix of doubles
typedef SparseVector<double>   SPAR_VEC;        // sparse matrix of double type
typedef std::vector<DenseMatrix<double> > DENS_MAT_VEC;
typedef std::vector<SparseMatrix<double> * > SPAR_MAT_VEC;

// int containers
typedef DenseMatrix<int>       INT_ARRAY; // to become vector<int> or Array2D
//typedef SparseMatrix<int>      SPAR_INT_ARRAY; // to become ?
typedef DenseVector<int>       INT_VECTOR; // to become vector<int> or Array

// forward declaration of error messages
template<typename T> void ierror(const Matrix<T> &a, const char *FILE, int LINE, INDEX i, INDEX j=0);
template<typename T> void ierror(const Matrix<T> &a, INDEX i, INDEX j, const std::string m);
template<typename T> void merror(const Matrix<T> &a, const Matrix<T> &b, const std::string m);
inline void gerror(const std::string m) { std::cout<<"Error: "<<m<<"\n"; ERROR_FOR_BACKTRACE ; exit(EXIT_FAILURE); }

} // end namespace
#endif