ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/io/RestReader.cpp
(Generate patch)

Comparing trunk/src/io/RestReader.cpp (file contents):
Revision 1389 by cli2, Mon Sep 7 16:31:51 2009 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 1
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.
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. Redistributions of source code must retain the above copyright
10 > *    notice, this list of conditions and the following disclaimer.
11 > *
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.
16 > *
17 > * This software is provided "AS IS," without a warranty of any
18 > * kind. All express or implied conditions, representations and
19 > * warranties, including any implied warranty of merchantability,
20 > * fitness for a particular purpose or non-infringement, are hereby
21 > * excluded.  The University of Notre Dame and its licensors shall not
22 > * be liable for any damages suffered by licensee as a result of
23 > * using, modifying or distributing the software or its
24 > * derivatives. In no event will the University of Notre Dame or its
25 > * licensors be liable for any lost revenue, profit or data, or for
26 > * direct, indirect, special, consequential, incidental or punitive
27 > * damages, however caused and regardless of the theory of liability,
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 "io/DumpReader.hpp"
# Line 45 | Line 45
45   #include "restraints/ObjectRestraint.hpp"
46   #include "restraints/MolecularRestraint.hpp"
47  
48 < namespace oopse {
48 > namespace OpenMD {
49        
50    void RestReader::readReferenceStructure() {
51  
# Line 216 | Line 216 | namespace oopse {
216               q[3] = tokenizer.nextTokenAsDouble();
217                
218               RealType qlen = q.length();
219 <             if (qlen < oopse::epsilon) { //check quaternion is not equal to 0
219 >             if (qlen < OpenMD::epsilon) { //check quaternion is not equal to 0
220                  
221                 sprintf(painCave.errMsg,
222                         "DumpReader Error: initial quaternion error (q0^2 + q1^2 + q2^2 + q3^2) ~ 0\n");
# Line 318 | Line 318 | namespace oopse {
318    }
319  
320    
321 < }//end namespace oopse
321 > }//end namespace OpenMD

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines