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Comparing trunk/src/math/MatVec3.c (file contents):
Revision 564 by tim, Wed Jul 13 15:54:00 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
36 + * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37 + * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38 + * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 + * [4]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42   #include <stdio.h>
# Line 49 | Line 49
49   * length 3 vectors
50   */
51  
52 < void identityMat3(double A[3][3]) {
52 > void identityMat3(RealType A[3][3]) {
53    int i;
54    for (i = 0; i < 3; i++) {
55      A[i][0] = A[i][1] = A[i][2] = 0.0;
# Line 57 | Line 57 | void identityMat3(double A[3][3]) {
57    }
58   }
59  
60 < void swapVectors3(double v1[3], double v2[3]) {
60 > void swapVectors3(RealType v1[3], RealType v2[3]) {
61    int i;
62    for (i = 0; i < 3; i++) {
63 <    double tmp = v1[i];
63 >    RealType tmp = v1[i];
64      v1[i] = v2[i];
65      v2[i] = tmp;
66    }
67   }
68  
69 < double normalize3(double x[3]) {
70 <  double den;
69 > RealType normalize3(RealType x[3]) {
70 >  RealType den;
71    int i;
72    if ( (den = norm3(x)) != 0.0 ) {
73      for (i=0; i < 3; i++)
# Line 78 | Line 78 | double normalize3(double x[3]) {
78    return den;
79   }
80  
81 < void matMul3(double a[3][3], double b[3][3], double c[3][3]) {
82 <  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
81 > void matMul3(RealType a[3][3], RealType b[3][3], RealType c[3][3]) {
82 >  RealType r00, r01, r02, r10, r11, r12, r20, r21, r22;
83    
84    r00 = a[0][0]*b[0][0] + a[0][1]*b[1][0] + a[0][2]*b[2][0];
85    r01 = a[0][0]*b[0][1] + a[0][1]*b[1][1] + a[0][2]*b[2][1];
# Line 98 | Line 98 | void matMul3(double a[3][3], double b[3][3], double c[
98    c[2][0] = r20; c[2][1] = r21; c[2][2] = r22;
99   }
100  
101 < void matVecMul3(double m[3][3], double inVec[3], double outVec[3]) {
102 <  double a0, a1, a2;
101 > void matVecMul3(RealType m[3][3], RealType inVec[3], RealType outVec[3]) {
102 >  RealType a0, a1, a2;
103    
104    a0 = inVec[0];  a1 = inVec[1];  a2 = inVec[2];
105    
# Line 108 | Line 108 | void matVecMul3(double m[3][3], double inVec[3], doubl
108    outVec[2] = m[2][0]*a0 + m[2][1]*a1 + m[2][2]*a2;
109   }
110  
111 < double matDet3(double a[3][3]) {
111 > RealType matDet3(RealType a[3][3]) {
112    int i, j, k;
113 <  double determinant;
113 >  RealType determinant;
114    
115    determinant = 0.0;
116    
# Line 124 | Line 124 | double matDet3(double a[3][3]) {
124    return determinant;
125   }
126  
127 < void invertMat3(double a[3][3], double b[3][3]) {
127 > void invertMat3(RealType a[3][3], RealType b[3][3]) {
128    
129    int  i, j, k, l, m, n;
130 <  double determinant;
130 >  RealType determinant;
131    
132    determinant = matDet3( a );
133    
# Line 150 | Line 150 | void invertMat3(double a[3][3], double b[3][3]) {
150    }
151   }
152  
153 < void transposeMat3(double in[3][3], double out[3][3]) {
154 <  double temp[3][3];
153 > void transposeMat3(RealType in[3][3], RealType out[3][3]) {
154 >  RealType temp[3][3];
155    int i, j;
156    
157    for (i = 0; i < 3; i++) {
# Line 166 | Line 166 | void transposeMat3(double in[3][3], double out[3][3])
166    }
167   }
168  
169 < void printMat3(double A[3][3] ){
169 > void printMat3(RealType A[3][3] ){
170    
171    fprintf(stderr, "[ %g, %g, %g ]\n[ %g, %g, %g ]\n[ %g, %g, %g ]\n",          
172            A[0][0] , A[0][1] , A[0][2],
# Line 174 | Line 174 | void printMat3(double A[3][3] ){
174            A[2][0] , A[2][1] , A[2][2]) ;
175   }
176  
177 < void printMat9(double A[9] ){
177 > void printMat9(RealType A[9] ){
178    
179    fprintf(stderr, "[ %g, %g, %g ]\n[ %g, %g, %g ]\n[ %g, %g, %g ]\n",          
180            A[0], A[1], A[2],
# Line 182 | Line 182 | void printMat9(double A[9] ){
182            A[6], A[7], A[8]);
183   }
184  
185 < double matTrace3(double m[3][3]){
186 <  double trace;
185 > RealType matTrace3(RealType m[3][3]){
186 >  RealType trace;
187    trace = m[0][0] + m[1][1] + m[2][2];
188    
189    return trace;
190   }
191  
192 < void crossProduct3(double a[3],double b[3], double out[3]){
192 > void crossProduct3(RealType a[3],RealType b[3], RealType out[3]){
193    
194    out[0] = a[1] * b[2] - a[2] * b[1];
195    out[1] = a[2] * b[0] - a[0] * b[2] ;
# Line 197 | Line 197 | void crossProduct3(double a[3],double b[3], double out
197    
198   }
199  
200 < double dotProduct3(double a[3], double b[3]){
200 > RealType dotProduct3(RealType a[3], RealType b[3]){
201    return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2];
202   }
203  
# Line 207 | Line 207 | double dotProduct3(double a[3], double b[3]){
207   /* The eigenvectors are aligned optimally with the x, y, and z*/
208   /* axes respectively.*/
209  
210 < void diagonalize3x3(const double A[3][3], double w[3], double V[3][3]) {
210 > void diagonalize3x3(const RealType A[3][3], RealType w[3], RealType V[3][3]) {
211    int i,j,k,maxI;
212 <  double tmp, maxVal;
212 >  RealType tmp, maxVal;
213  
214    /* do the matrix[3][3] to **matrix conversion for Jacobi*/
215 <  double C[3][3];
216 <  double *ATemp[3],*VTemp[3];
215 >  RealType C[3][3];
216 >  RealType *ATemp[3],*VTemp[3];
217    for (i = 0; i < 3; i++)
218      {
219        C[i][0] = A[i][0];
# Line 351 | Line 351 | void diagonalize3x3(const double A[3][3], double w[3],
351   /* output eigenvalues in w; and output eigenvectors in v. Resulting*/
352   /* eigenvalues/vectors are sorted in decreasing order; eigenvectors are*/
353   /* normalized.*/
354 < int JacobiN(double **a, int n, double *w, double **v) {
354 > int JacobiN(RealType **a, int n, RealType *w, RealType **v) {
355  
356    int i, j, k, iq, ip, numPos;
357    int ceil_half_n;
358 <  double tresh, theta, tau, t, sm, s, h, g, c, tmp;
359 <  double bspace[4], zspace[4];
360 <  double *b = bspace;
361 <  double *z = zspace;
358 >  RealType tresh, theta, tau, t, sm, s, h, g, c, tmp;
359 >  RealType bspace[4], zspace[4];
360 >  RealType *b = bspace;
361 >  RealType *z = zspace;
362    
363  
364    /* only allocate memory if the matrix is large*/
365    if (n > 4)
366      {
367 <      b = (double *) calloc(n, sizeof(double));
368 <      z = (double *) calloc(n, sizeof(double));
367 >      b = (RealType *) calloc(n, sizeof(RealType));
368 >      z = (RealType *) calloc(n, sizeof(RealType));
369      }
370    
371    /* initialize*/
# Line 526 | Line 526 | int JacobiN(double **a, int n, double *w, double **v)
526                numPos++;
527              }
528          }
529 <      /*    if ( numPos < ceil(double(n)/double(2.0)) )*/
529 >      /*    if ( numPos < ceil(RealType(n)/RealType(2.0)) )*/
530        if ( numPos < ceil_half_n)
531          {
532            for(i=0; i<n; i++)

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