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Comparing trunk/src/brains/Snapshot.cpp (file contents):
Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 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 > namespace OpenMD {
55  
56    void  Snapshot::setHmat(const Mat3x3d& m) {
57 –    const double orthoTolerance = NumericConstant::epsilon;
57      hmat_ = m;
58      invHmat_ = hmat_.inverse();
59      
60 +
61      //prepare fortran Hmat
62 <    double fortranHmat[9];
63 <    double fortranInvHmat[9];
62 >    RealType fortranHmat[9];
63 >    RealType fortranInvHmat[9];
64      hmat_.getArray(fortranHmat);
65      invHmat_.getArray(fortranInvHmat);
66  
67      //determine whether the box is orthoTolerance or not
68      int oldOrthoRhombic = orthoRhombic_;
69      
70 <    double smallDiag = fabs(hmat_(0, 0));
70 >    RealType smallDiag = fabs(hmat_(0, 0));
71      if(smallDiag > fabs(hmat_(1, 1))) smallDiag = fabs(hmat_(1, 1));
72      if(smallDiag > fabs(hmat_(2, 2))) smallDiag = fabs(hmat_(2, 2));    
73 <    double tol = smallDiag * orthoTolerance;
73 >    RealType tol = smallDiag * orthoTolerance_;
74  
75      orthoRhombic_ = 1;
76  
# Line 89 | Line 89 | namespace oopse {
89  
90        if( orthoRhombic_ ) {
91          sprintf( painCave.errMsg,
92 <                 "OOPSE is switching from the default Non-Orthorhombic\n"
92 >                 "OpenMD is switching from the default Non-Orthorhombic\n"
93                   "\tto the faster Orthorhombic periodic boundary computations.\n"
94 <                 "\tThis is usually a good thing, but if you wan't the\n"
94 >                 "\tThis is usually a good thing, but if you want the\n"
95                   "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
96                   "\tvariable ( currently set to %G ) smaller.\n",
97 <                 orthoTolerance);
98 <        painCave.severity = OOPSE_INFO;
97 >                 orthoTolerance_);
98 >        painCave.severity = OPENMD_INFO;
99          simError();
100        }
101        else {
102          sprintf( painCave.errMsg,
103 <                 "OOPSE is switching from the faster Orthorhombic to the more\n"
103 >                 "OpenMD is switching from the faster Orthorhombic to the more\n"
104                   "\tflexible Non-Orthorhombic periodic boundary computations.\n"
105                   "\tThis is usually because the box has deformed under\n"
106 <                 "\tNPTf integration. If you wan't to live on the edge with\n"
106 >                 "\tNPTf integration. If you want to live on the edge with\n"
107                   "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
108                   "\tvariable ( currently set to %G ) larger.\n",
109 <                 orthoTolerance);
110 <        painCave.severity = OOPSE_WARNING;
109 >                 orthoTolerance_);
110 >        painCave.severity = OPENMD_WARNING;
111          simError();
112        }
113      }    
# Line 156 | Line 156 | namespace oopse {
156  
157    }
158  
159 +  Vector3d Snapshot::getCOM() {
160 +    if( !hasCOM_ ) {
161 +      sprintf( painCave.errMsg, "COM was requested before COM was computed!\n");
162 +      painCave.severity = OPENMD_ERROR;
163 +      simError();
164 +    }
165 +    return COM_;
166 +  }
167 +  
168 +  Vector3d Snapshot::getCOMvel() {
169 +    if( !hasCOM_ ) {
170 +      sprintf( painCave.errMsg, "COMvel was requested before COM was computed!\n");
171 +      painCave.severity = OPENMD_ERROR;
172 +      simError();
173 +    }
174 +    return COMvel_;
175 +  }
176 +  
177 +  Vector3d Snapshot::getCOMw() {
178 +    if( !hasCOM_ ) {
179 +      sprintf( painCave.errMsg, "COMw was requested before COM was computed!\n");
180 +      painCave.severity = OPENMD_ERROR;
181 +      simError();
182 +    }
183 +    return COMw_;
184 +  }
185 +
186   }
187    

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