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Revision 1630 by tim, Thu Oct 21 21:31:39 2004 UTC vs.
Revision 1957 by tim, Tue Jan 25 17:45:23 2005 UTC

# Line 1 | Line 1
1 < /*
2 < * Copyright (C) 2000-2004  Object Oriented Parallel Simulation Engine (OOPSE) project
3 < *
4 < * Contact: oopse@oopse.org
5 < *
6 < * This program is free software; you can redistribute it and/or
7 < * modify it under the terms of the GNU Lesser General Public License
8 < * as published by the Free Software Foundation; either version 2.1
9 < * of the License, or (at your option) any later version.
10 < * All we ask is that proper credit is given for our work, which includes
11 < * - but is not limited to - adding the above copyright notice to the beginning
12 < * of your source code files, and to any copyright notice that you may distribute
13 < * with programs based on this work.
14 < *
15 < * This program is distributed in the hope that it will be useful,
16 < * but WITHOUT ANY WARRANTY; without even the implied warranty of
17 < * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
18 < * GNU Lesser General Public License for more details.
19 < *
20 < * You should have received a copy of the GNU Lesser General Public License
21 < * along with this program; if not, write to the Free Software
22 < * Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
1 > /*
2 > * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4 + * The University of Notre Dame grants you ("Licensee") a
5 + * non-exclusive, royalty free, license to use, modify and
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
19 + *    notice, this list of conditions and the following disclaimer.
20 + *
21 + * 3. Redistributions in binary form must reproduce the above copyright
22 + *    notice, this list of conditions and the following disclaimer in the
23 + *    documentation and/or other materials provided with the
24 + *    distribution.
25 + *
26 + * This software is provided "AS IS," without a warranty of any
27 + * kind. All express or implied conditions, representations and
28 + * warranties, including any implied warranty of merchantability,
29 + * fitness for a particular purpose or non-infringement, are hereby
30 + * excluded.  The University of Notre Dame and its licensors shall not
31 + * be liable for any damages suffered by licensee as a result of
32 + * using, modifying or distributing the software or its
33 + * derivatives. In no event will the University of Notre Dame or its
34 + * licensors be liable for any lost revenue, profit or data, or for
35 + * direct, indirect, special, consequential, incidental or punitive
36 + * damages, however caused and regardless of the theory of liability,
37 + * arising out of the use of or inability to use software, even if the
38 + * University of Notre Dame has been advised of the possibility of
39 + * such damages.
40   */
41 <
41 >
42   /**
43   * @file SquareMatrix.hpp
44   * @author Teng Lin
# Line 55 | Line 71 | namespace oopse {
71                          data_[i][j] = 0.0;
72               }
73  
74 +            /** Constructs and initializes every element of this matrix to a scalar */
75 +            SquareMatrix(Real s) : RectMatrix<Real, Dim, Dim>(s){
76 +            }
77 +
78 +            /** Constructs and initializes from an array */
79 +            SquareMatrix(Real* array) : RectMatrix<Real, Dim, Dim>(array){
80 +            }
81 +
82 +
83              /** copy constructor */
84              SquareMatrix(const RectMatrix<Real, Dim, Dim>& m) : RectMatrix<Real, Dim, Dim>(m) {
85              }
# Line 150 | Line 175 | namespace oopse {
175                  return true;
176              }        
177  
178 +            /** Return the transpose of this matrix */
179 +            SquareMatrix<Real,  Dim> transpose() const{
180 +                SquareMatrix<Real,  Dim> result;
181 +                
182 +                for (unsigned int i = 0; i < Dim; i++)
183 +                    for (unsigned int j = 0; j < Dim; j++)              
184 +                        result(j, i) = data_[i][j];
185 +
186 +                return result;
187 +            }
188 +            
189              /** @todo need implementation */
190              void diagonalize() {
191                  //jacobi(m, eigenValues, ortMat);
# Line 199 | Line 235 | namespace oopse {
235      // normalized.
236      template<typename Real, int Dim>
237      int SquareMatrix<Real, Dim>::jacobi(SquareMatrix<Real, Dim>& a, Vector<Real, Dim>& w,
238 <                                  SquareMatrix<Real, Dim>& v) {
239 <      const int n = Dim;  
240 <      int i, j, k, iq, ip, numPos;
241 <      Real tresh, theta, tau, t, sm, s, h, g, c, tmp;
242 <      Real bspace[4], zspace[4];
243 <      Real *b = bspace;
244 <      Real *z = zspace;
245 <
246 <      // only allocate memory if the matrix is large
247 <      if (n > 4)
248 <        {
249 <        b = new Real[n];
214 <        z = new Real[n];
238 >                                        SquareMatrix<Real, Dim>& v) {
239 >        const int n = Dim;  
240 >        int i, j, k, iq, ip, numPos;
241 >        Real tresh, theta, tau, t, sm, s, h, g, c, tmp;
242 >        Real bspace[4], zspace[4];
243 >        Real *b = bspace;
244 >        Real *z = zspace;
245 >
246 >        // only allocate memory if the matrix is large
247 >        if (n > 4) {
248 >            b = new Real[n];
249 >            z = new Real[n];
250          }
251  
252 <      // initialize
253 <      for (ip=0; ip<n; ip++)
254 <        {
255 <        for (iq=0; iq<n; iq++)
256 <          {
257 <          v(ip, iq) = 0.0;
223 <          }
224 <        v(ip, ip) = 1.0;
252 >        // initialize
253 >        for (ip=0; ip<n; ip++) {
254 >            for (iq=0; iq<n; iq++) {
255 >                v(ip, iq) = 0.0;
256 >            }
257 >            v(ip, ip) = 1.0;
258          }
259 <      for (ip=0; ip<n; ip++)
260 <        {
261 <        b[ip] = w[ip] = a(ip, ip);
229 <        z[ip] = 0.0;
259 >        for (ip=0; ip<n; ip++) {
260 >            b[ip] = w[ip] = a(ip, ip);
261 >            z[ip] = 0.0;
262          }
263  
264 <      // begin rotation sequence
265 <      for (i=0; i<VTK_MAX_ROTATIONS; i++)
266 <        {
267 <        sm = 0.0;
268 <        for (ip=0; ip<n-1; ip++)
269 <          {
270 <          for (iq=ip+1; iq<n; iq++)
239 <            {
240 <            sm += fabs(a(ip, iq));
264 >        // begin rotation sequence
265 >        for (i=0; i<VTK_MAX_ROTATIONS; i++) {
266 >            sm = 0.0;
267 >            for (ip=0; ip<n-1; ip++) {
268 >                for (iq=ip+1; iq<n; iq++) {
269 >                    sm += fabs(a(ip, iq));
270 >                }
271              }
272 <          }
273 <        if (sm == 0.0)
274 <          {
245 <          break;
246 <          }
272 >            if (sm == 0.0) {
273 >                break;
274 >            }
275  
276 <        if (i < 3)                                // first 3 sweeps
277 <          {
278 <          tresh = 0.2*sm/(n*n);
279 <          }
280 <        else
253 <          {
254 <          tresh = 0.0;
255 <          }
276 >            if (i < 3) {                                // first 3 sweeps
277 >                tresh = 0.2*sm/(n*n);
278 >            } else {
279 >                tresh = 0.0;
280 >            }
281  
282 <        for (ip=0; ip<n-1; ip++)
283 <          {
284 <          for (iq=ip+1; iq<n; iq++)
260 <            {
261 <            g = 100.0*fabs(a(ip, iq));
282 >            for (ip=0; ip<n-1; ip++) {
283 >                for (iq=ip+1; iq<n; iq++) {
284 >                    g = 100.0*fabs(a(ip, iq));
285  
286 <            // after 4 sweeps
287 <            if (i > 3 && (fabs(w[ip])+g) == fabs(w[ip])
288 <            && (fabs(w[iq])+g) == fabs(w[iq]))
289 <              {
290 <              a(ip, iq) = 0.0;
291 <              }
292 <            else if (fabs(a(ip, iq)) > tresh)
293 <              {
294 <              h = w[iq] - w[ip];
295 <              if ( (fabs(h)+g) == fabs(h))
296 <                {
297 <                t = (a(ip, iq)) / h;
298 <                }
299 <              else
300 <                {
301 <                theta = 0.5*h / (a(ip, iq));
302 <                t = 1.0 / (fabs(theta)+sqrt(1.0+theta*theta));
303 <                if (theta < 0.0)
304 <                  {
305 <                  t = -t;
306 <                  }
307 <                }
308 <              c = 1.0 / sqrt(1+t*t);
309 <              s = t*c;
287 <              tau = s/(1.0+c);
288 <              h = t*a(ip, iq);
289 <              z[ip] -= h;
290 <              z[iq] += h;
291 <              w[ip] -= h;
292 <              w[iq] += h;
293 <              a(ip, iq)=0.0;
286 >                    // after 4 sweeps
287 >                    if (i > 3 && (fabs(w[ip])+g) == fabs(w[ip])
288 >                        && (fabs(w[iq])+g) == fabs(w[iq])) {
289 >                        a(ip, iq) = 0.0;
290 >                    } else if (fabs(a(ip, iq)) > tresh) {
291 >                        h = w[iq] - w[ip];
292 >                        if ( (fabs(h)+g) == fabs(h)) {
293 >                            t = (a(ip, iq)) / h;
294 >                        } else {
295 >                            theta = 0.5*h / (a(ip, iq));
296 >                            t = 1.0 / (fabs(theta)+sqrt(1.0+theta*theta));
297 >                            if (theta < 0.0) {
298 >                                t = -t;
299 >                            }
300 >                        }
301 >                        c = 1.0 / sqrt(1+t*t);
302 >                        s = t*c;
303 >                        tau = s/(1.0+c);
304 >                        h = t*a(ip, iq);
305 >                        z[ip] -= h;
306 >                        z[iq] += h;
307 >                        w[ip] -= h;
308 >                        w[iq] += h;
309 >                        a(ip, iq)=0.0;
310  
311 <              // ip already shifted left by 1 unit
312 <              for (j = 0;j <= ip-1;j++)
313 <                {
314 <                VTK_ROTATE(a,j,ip,j,iq);
311 >                        // ip already shifted left by 1 unit
312 >                        for (j = 0;j <= ip-1;j++) {
313 >                            VTK_ROTATE(a,j,ip,j,iq);
314 >                        }
315 >                        // ip and iq already shifted left by 1 unit
316 >                        for (j = ip+1;j <= iq-1;j++) {
317 >                            VTK_ROTATE(a,ip,j,j,iq);
318 >                        }
319 >                        // iq already shifted left by 1 unit
320 >                        for (j=iq+1; j<n; j++) {
321 >                            VTK_ROTATE(a,ip,j,iq,j);
322 >                        }
323 >                        for (j=0; j<n; j++) {
324 >                            VTK_ROTATE(v,j,ip,j,iq);
325 >                        }
326 >                    }
327                  }
300 –              // ip and iq already shifted left by 1 unit
301 –              for (j = ip+1;j <= iq-1;j++)
302 –                {
303 –                VTK_ROTATE(a,ip,j,j,iq);
304 –                }
305 –              // iq already shifted left by 1 unit
306 –              for (j=iq+1; j<n; j++)
307 –                {
308 –                VTK_ROTATE(a,ip,j,iq,j);
309 –                }
310 –              for (j=0; j<n; j++)
311 –                {
312 –                VTK_ROTATE(v,j,ip,j,iq);
313 –                }
314 –              }
328              }
316 –          }
329  
330 <        for (ip=0; ip<n; ip++)
331 <          {
332 <          b[ip] += z[ip];
333 <          w[ip] = b[ip];
334 <          z[ip] = 0.0;
323 <          }
330 >            for (ip=0; ip<n; ip++) {
331 >                b[ip] += z[ip];
332 >                w[ip] = b[ip];
333 >                z[ip] = 0.0;
334 >            }
335          }
336  
337 <      //// this is NEVER called
338 <      if ( i >= VTK_MAX_ROTATIONS )
339 <        {
340 <           std::cout << "vtkMath::Jacobi: Error extracting eigenfunctions" << std::endl;
330 <           return 0;
337 >        //// this is NEVER called
338 >        if ( i >= VTK_MAX_ROTATIONS ) {
339 >            std::cout << "vtkMath::Jacobi: Error extracting eigenfunctions" << std::endl;
340 >            return 0;
341          }
342  
343 <      // sort eigenfunctions                 these changes do not affect accuracy
344 <      for (j=0; j<n-1; j++)                  // boundary incorrect
345 <        {
336 <        k = j;
337 <        tmp = w[k];
338 <        for (i=j+1; i<n; i++)                // boundary incorrect, shifted already
339 <          {
340 <          if (w[i] >= tmp)                   // why exchage if same?
341 <            {
342 <            k = i;
343 >        // sort eigenfunctions                 these changes do not affect accuracy
344 >        for (j=0; j<n-1; j++) {                  // boundary incorrect
345 >            k = j;
346              tmp = w[k];
347 +            for (i=j+1; i<n; i++) {                // boundary incorrect, shifted already
348 +                if (w[i] >= tmp) {                   // why exchage if same?
349 +                    k = i;
350 +                    tmp = w[k];
351 +                }
352              }
353 <          }
354 <        if (k != j)
355 <          {
356 <          w[k] = w[j];
357 <          w[j] = tmp;
358 <          for (i=0; i<n; i++)
359 <            {
360 <            tmp = v(i, j);
353 <            v(i, j) = v(i, k);
354 <            v(i, k) = tmp;
353 >            if (k != j) {
354 >                w[k] = w[j];
355 >                w[j] = tmp;
356 >                for (i=0; i<n; i++) {
357 >                    tmp = v(i, j);
358 >                    v(i, j) = v(i, k);
359 >                    v(i, k) = tmp;
360 >                }
361              }
356 –          }
362          }
363 <      // insure eigenvector consistency (i.e., Jacobi can compute vectors that
364 <      // are negative of one another (.707,.707,0) and (-.707,-.707,0). This can
365 <      // reek havoc in hyperstreamline/other stuff. We will select the most
366 <      // positive eigenvector.
367 <      int ceil_half_n = (n >> 1) + (n & 1);
368 <      for (j=0; j<n; j++)
369 <        {
370 <        for (numPos=0, i=0; i<n; i++)
371 <          {
372 <          if ( v(i, j) >= 0.0 )
368 <            {
369 <            numPos++;
363 >        // insure eigenvector consistency (i.e., Jacobi can compute vectors that
364 >        // are negative of one another (.707,.707,0) and (-.707,-.707,0). This can
365 >        // reek havoc in hyperstreamline/other stuff. We will select the most
366 >        // positive eigenvector.
367 >        int ceil_half_n = (n >> 1) + (n & 1);
368 >        for (j=0; j<n; j++) {
369 >            for (numPos=0, i=0; i<n; i++) {
370 >                if ( v(i, j) >= 0.0 ) {
371 >                    numPos++;
372 >                }
373              }
374 <          }
375 <    //    if ( numPos < ceil(double(n)/double(2.0)) )
376 <        if ( numPos < ceil_half_n)
377 <          {
378 <          for(i=0; i<n; i++)
376 <            {
377 <            v(i, j) *= -1.0;
374 >            //    if ( numPos < ceil(double(n)/double(2.0)) )
375 >            if ( numPos < ceil_half_n) {
376 >                for (i=0; i<n; i++) {
377 >                    v(i, j) *= -1.0;
378 >                }
379              }
379 –          }
380          }
381  
382 <      if (n > 4)
383 <        {
384 <        delete [] b;
385 <        delete [] z;
382 >        if (n > 4) {
383 >            delete [] b;
384 >            delete [] z;
385          }
386 <      return 1;
386 >        return 1;
387      }
388  
389  

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