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Comparing trunk/src/brains/Snapshot.cpp (file contents):
Revision 1112 by chuckv, Wed Jan 3 20:47:00 2007 UTC vs.
Revision 1401 by jmarr, Wed Jan 6 21:06:59 2010 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   /**
# Line 51 | Line 51
51   #include "utils/NumericConstant.hpp"
52   #include "utils/simError.h"
53   #include "utils/Utility.hpp"
54 < namespace oopse {
54 > #include <cstdio>
55  
56 + namespace OpenMD {
57 +
58    void  Snapshot::setHmat(const Mat3x3d& m) {
59      hmat_ = m;
60      invHmat_ = hmat_.inverse();
# Line 89 | Line 91 | namespace oopse {
91  
92        if( orthoRhombic_ ) {
93          sprintf( painCave.errMsg,
94 <                 "OOPSE is switching from the default Non-Orthorhombic\n"
94 >                 "OpenMD is switching from the default Non-Orthorhombic\n"
95                   "\tto the faster Orthorhombic periodic boundary computations.\n"
96                   "\tThis is usually a good thing, but if you want the\n"
97                   "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
98                   "\tvariable ( currently set to %G ) smaller.\n",
99                   orthoTolerance_);
100 <        painCave.severity = OOPSE_INFO;
100 >        painCave.severity = OPENMD_INFO;
101          simError();
102        }
103        else {
104          sprintf( painCave.errMsg,
105 <                 "OOPSE is switching from the faster Orthorhombic to the more\n"
105 >                 "OpenMD is switching from the faster Orthorhombic to the more\n"
106                   "\tflexible Non-Orthorhombic periodic boundary computations.\n"
107                   "\tThis is usually because the box has deformed under\n"
108                   "\tNPTf integration. If you want to live on the edge with\n"
109                   "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
110                   "\tvariable ( currently set to %G ) larger.\n",
111                   orthoTolerance_);
112 <        painCave.severity = OOPSE_WARNING;
112 >        painCave.severity = OPENMD_WARNING;
113          simError();
114        }
115      }    
# Line 159 | Line 161 | namespace oopse {
161    Vector3d Snapshot::getCOM() {
162      if( !hasCOM_ ) {
163        sprintf( painCave.errMsg, "COM was requested before COM was computed!\n");
164 <      painCave.severity = OOPSE_ERROR;
164 >      painCave.severity = OPENMD_ERROR;
165        simError();
166      }
167      return COM_;
# Line 168 | Line 170 | namespace oopse {
170    Vector3d Snapshot::getCOMvel() {
171      if( !hasCOM_ ) {
172        sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n");
173 <      painCave.severity = OOPSE_ERROR;
173 >      painCave.severity = OPENMD_ERROR;
174        simError();
175      }
176      return COMvel_;
# Line 177 | Line 179 | namespace oopse {
179    Vector3d Snapshot::getCOMw() {
180      if( !hasCOM_ ) {
181        sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n");
182 <      painCave.severity = OOPSE_ERROR;
182 >      painCave.severity = OPENMD_ERROR;
183        simError();
184      }
185      return COMw_;

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