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Comparing trunk/src/brains/Snapshot.cpp (file contents):
Revision 890 by gezelter, Thu Feb 16 22:05:48 2006 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 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 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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