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root/OpenMD/trunk/src/brains/DataStorage.cpp
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Comparing trunk/src/brains/DataStorage.cpp (file contents):
Revision 155 by tim, Tue Oct 26 22:19:22 2004 UTC vs.
Revision 331 by tim, Sun Feb 13 21:18:27 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  
42   /**
# Line 33 | Line 49
49  
50   #include "brains/DataStorage.hpp"
51  
52 + namespace oopse {
53  
54   DataStorage::DataStorage() : size_(0), storageLayout_(0){
55  
# Line 65 | Line 82 | int DataStorage::getSize() {
82          std::cerr << "size does not match"<< std::endl;        
83      }
84  
85 <    if (storageLayout_ & dslUnitVector && unitVector.size() != size_) {
85 >    if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) {
86          //error
87          std::cerr << "size does not match"<< std::endl;        
88      }
# Line 107 | Line 124 | void DataStorage::resize(int newSize) {
124          internalResize(angularMomentum, newSize);
125      }
126  
127 <    if (storageLayout_ & dslUnitVector) {
128 <        internalResize(unitVector, newSize);
127 >    if (storageLayout_ & dslElectroFrame) {
128 >        internalResize(electroFrame, newSize);
129      }
130      
131      if (storageLayout_ & dslZAngle) {
# Line 143 | Line 160 | void DataStorage::reserve(int size) {
160          angularMomentum.reserve(size);
161      }
162  
163 <    if (storageLayout_ & dslUnitVector) {
164 <        unitVector.reserve(size);
163 >    if (storageLayout_ & dslElectroFrame) {
164 >        electroFrame.reserve(size);
165      }
166      
167      if (storageLayout_ & dslZAngle) {
# Line 167 | Line 184 | void DataStorage::copy(int source, int num, int target
184      }
185      
186      if (storageLayout_ & dslPosition) {
187 <        interalCopy(position, source, num, target);
187 >        internalCopy(position, source, num, target);
188      }
189  
190      if (storageLayout_ & dslVelocity) {
191 <        interalCopy(velocity, source, num, target);
191 >        internalCopy(velocity, source, num, target);
192    }
193  
194      if (storageLayout_ & dslAmat) {
195 <        interalCopy(aMat, source, num, target);
195 >        internalCopy(aMat, source, num, target);
196     }
197  
198      if (storageLayout_ & dslAngularMomentum) {
199 <        interalCopy(angularMomentum, source, num, target);
199 >        internalCopy(angularMomentum, source, num, target);
200      }
201  
202 <    if (storageLayout_ & dslUnitVector) {
203 <        interalCopy(unitVector, source, num, target);
202 >    if (storageLayout_ & dslElectroFrame) {
203 >        internalCopy(electroFrame, source, num, target);
204      }
205      
206      if (storageLayout_ & dslZAngle) {
207 <        interalCopy(zAngle, source, num, target);
207 >        internalCopy(zAngle, source, num, target);
208      }
209  
210      if (storageLayout_ & dslForce) {
211 <        interalCopy(force, source, num, target);
211 >        internalCopy(force, source, num, target);
212      }
213  
214      if (storageLayout_ & dslTorque) {
215 <        interalCopy(torque, source, num, target);
215 >        internalCopy(torque, source, num, target);
216      }
217      
218  
# Line 214 | Line 231 | double* DataStorage::getArrayPointer(int whichArray) {
231  
232      switch (whichArray) {
233          case dslPosition:
234 <            return internalGetArrayPointer(torque);
234 >            return internalGetArrayPointer(position);
235              break;
236              
237          case dslVelocity:
# Line 229 | Line 246 | double* DataStorage::getArrayPointer(int whichArray) {
246              return internalGetArrayPointer(angularMomentum);
247              break;
248              
249 <        case dslUnitVector:
250 <            return internalGetArrayPointer(unitVector);
249 >        case dslElectroFrame:
250 >            return internalGetArrayPointer(electroFrame);
251              break;
252              
253          case dslZAngle:
# Line 295 | Line 312 | template<typename T>
312   }
313  
314   template<typename T>
315 < void DataStorage::interalCopy(std::vector<T>& v, int source,  int num, int target) {
315 > void DataStorage::internalCopy(std::vector<T>& v, int source,  int num, int target) {
316      typename std::vector<T>::iterator first;
317      typename std::vector<T>::iterator last;
318      typename std::vector<T>::iterator result;
# Line 311 | Line 328 | void DataStorage::interalCopy(std::vector<T>& v, int s
328  
329      std::copy(first, last, result);
330   }
331 +
332 + int DataStorage::getBytesPerStuntDouble(int layout) {
333 +    int bytes = 0;
334 +    if (layout & dslPosition) {
335 +        bytes += sizeof(Vector3d);
336 +    }
337 +    if (layout & dslVelocity) {
338 +        bytes += sizeof(Vector3d);
339 +    }
340 +    if (layout & dslAmat) {
341 +        bytes += sizeof(Mat3x3d);    
342 +    }
343 +    if (layout & dslAngularMomentum) {
344 +        bytes += sizeof(Vector3d);
345 +    }
346 +    if (layout & dslElectroFrame) {
347 +        bytes += sizeof(Mat3x3d);
348 +    }
349 +    if (layout & dslZAngle) {
350 +        bytes += sizeof(Vector3d);
351 +    }
352 +    if (layout & dslForce) {
353 +        bytes += sizeof(Vector3d);
354 +    }
355 +    if (layout & dslTorque) {
356 +        bytes += sizeof(Vector3d);
357 +    }
358 +    return bytes;
359 + }
360 +
361 + }

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