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Comparing trunk/OOPSE-2.0/src/brains/DataStorage.cpp (file contents):
Revision 1648 by tim, Tue Oct 26 22:19:22 2004 UTC vs.
Revision 1930 by gezelter, Wed Jan 12 22:41:40 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 65 | Line 81 | int DataStorage::getSize() {
81          std::cerr << "size does not match"<< std::endl;        
82      }
83  
84 <    if (storageLayout_ & dslUnitVector && unitVector.size() != size_) {
84 >    if (storageLayout_ & dslElectroFrame && electroFrame.size() != size_) {
85          //error
86          std::cerr << "size does not match"<< std::endl;        
87      }
# Line 107 | Line 123 | void DataStorage::resize(int newSize) {
123          internalResize(angularMomentum, newSize);
124      }
125  
126 <    if (storageLayout_ & dslUnitVector) {
127 <        internalResize(unitVector, newSize);
126 >    if (storageLayout_ & dslElectroFrame) {
127 >        internalResize(electroFrame, newSize);
128      }
129      
130      if (storageLayout_ & dslZAngle) {
# Line 143 | Line 159 | void DataStorage::reserve(int size) {
159          angularMomentum.reserve(size);
160      }
161  
162 <    if (storageLayout_ & dslUnitVector) {
163 <        unitVector.reserve(size);
162 >    if (storageLayout_ & dslElectroFrame) {
163 >        electroFrame.reserve(size);
164      }
165      
166      if (storageLayout_ & dslZAngle) {
# Line 167 | Line 183 | void DataStorage::copy(int source, int num, int target
183      }
184      
185      if (storageLayout_ & dslPosition) {
186 <        interalCopy(position, source, num, target);
186 >        internalCopy(position, source, num, target);
187      }
188  
189      if (storageLayout_ & dslVelocity) {
190 <        interalCopy(velocity, source, num, target);
190 >        internalCopy(velocity, source, num, target);
191    }
192  
193      if (storageLayout_ & dslAmat) {
194 <        interalCopy(aMat, source, num, target);
194 >        internalCopy(aMat, source, num, target);
195     }
196  
197      if (storageLayout_ & dslAngularMomentum) {
198 <        interalCopy(angularMomentum, source, num, target);
198 >        internalCopy(angularMomentum, source, num, target);
199      }
200  
201 <    if (storageLayout_ & dslUnitVector) {
202 <        interalCopy(unitVector, source, num, target);
201 >    if (storageLayout_ & dslElectroFrame) {
202 >        internalCopy(electroFrame, source, num, target);
203      }
204      
205      if (storageLayout_ & dslZAngle) {
206 <        interalCopy(zAngle, source, num, target);
206 >        internalCopy(zAngle, source, num, target);
207      }
208  
209      if (storageLayout_ & dslForce) {
210 <        interalCopy(force, source, num, target);
210 >        internalCopy(force, source, num, target);
211      }
212  
213      if (storageLayout_ & dslTorque) {
214 <        interalCopy(torque, source, num, target);
214 >        internalCopy(torque, source, num, target);
215      }
216      
217  
# Line 214 | Line 230 | double* DataStorage::getArrayPointer(int whichArray) {
230  
231      switch (whichArray) {
232          case dslPosition:
233 <            return internalGetArrayPointer(torque);
233 >            return internalGetArrayPointer(position);
234              break;
235              
236          case dslVelocity:
# Line 229 | Line 245 | double* DataStorage::getArrayPointer(int whichArray) {
245              return internalGetArrayPointer(angularMomentum);
246              break;
247              
248 <        case dslUnitVector:
249 <            return internalGetArrayPointer(unitVector);
248 >        case dslElectroFrame:
249 >            return internalGetArrayPointer(electroFrame);
250              break;
251              
252          case dslZAngle:
# Line 295 | Line 311 | void DataStorage::interalCopy(std::vector<T>& v, int s
311   }
312  
313   template<typename T>
314 < void DataStorage::interalCopy(std::vector<T>& v, int source,  int num, int target) {
314 > void DataStorage::internalCopy(std::vector<T>& v, int source,  int num, int target) {
315      typename std::vector<T>::iterator first;
316      typename std::vector<T>::iterator last;
317      typename std::vector<T>::iterator result;

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