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

Comparing trunk/src/brains/Snapshot.cpp (file contents):
Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 1 | Line 1
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
# 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 < /**
43 <  * @file Snapshot.cpp
44 <  * @author tlin
45 <  * @date 11/11/2004
46 <  * @time 10:56am
47 <  * @version 1.0
48 <  */
42 > /**
43 > * @file Snapshot.cpp
44 > * @author tlin
45 > * @date 11/11/2004
46 > * @time 10:56am
47 > * @version 1.0
48 > */
49  
50   #include "brains/Snapshot.hpp"
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;
56 >  void  Snapshot::setHmat(const Mat3x3d& m) {
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  
77      for (int i = 0; i < 3; i++ ) {
78 <        for (int j = 0 ; j < 3; j++) {
79 <            if (i != j) {
80 <                if (orthoRhombic_) {
81 <                    if ( fabs(hmat_(i, j)) >= tol)
82 <                        orthoRhombic_ = 0;
83 <                }        
84 <            }
85 <        }
78 >      for (int j = 0 ; j < 3; j++) {
79 >        if (i != j) {
80 >          if (orthoRhombic_) {
81 >            if ( fabs(hmat_(i, j)) >= tol)
82 >              orthoRhombic_ = 0;
83 >          }        
84 >        }
85 >      }
86      }
87  
88      if( oldOrthoRhombic != orthoRhombic_ ){
89  
90 <        if( orthoRhombic_ ) {
91 <            sprintf( painCave.errMsg,
92 <                "OOPSE 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"
95 <                "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
96 <                "\tvariable ( currently set to %G ) smaller.\n",
97 <                orthoTolerance);
98 <            painCave.severity = OOPSE_INFO;
99 <            simError();
100 <        }
101 <        else {
102 <            sprintf( painCave.errMsg,
103 <                "OOPSE 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"
107 <                "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
108 <                "\tvariable ( currently set to %G ) larger.\n",
109 <                orthoTolerance);
110 <            painCave.severity = OOPSE_WARNING;
111 <            simError();
112 <        }
90 >      if( orthoRhombic_ ) {
91 >        sprintf( painCave.errMsg,
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 = OPENMD_INFO;
99 >        simError();
100 >      }
101 >      else {
102 >        sprintf( painCave.errMsg,
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 = OPENMD_WARNING;
111 >        simError();
112 >      }
113      }    
114  
115      //notify fortran simulation box has changed
116      setFortranBox(fortranHmat, fortranInvHmat, &orthoRhombic_);
117 < }
117 >  }
118  
119  
120 < void Snapshot::wrapVector(Vector3d& pos) {
120 >  void Snapshot::wrapVector(Vector3d& pos) {
121  
122      int i;
123      Vector3d scaled;
124  
125      if( !orthoRhombic_ ){
126  
127 <        // calc the scaled coordinates.
128 <        scaled = invHmat_* pos;
127 >      // calc the scaled coordinates.
128 >      scaled = invHmat_* pos;
129  
130 <        // wrap the scaled coordinates
131 <        for (i = 0; i < 3; ++i) {
132 <            scaled[i] -= roundMe(scaled[i]);
133 <        }
130 >      // wrap the scaled coordinates
131 >      for (i = 0; i < 3; ++i) {
132 >        scaled[i] -= roundMe(scaled[i]);
133 >      }
134  
135 <        // calc the wrapped real coordinates from the wrapped scaled coordinates
136 <        pos = hmat_ * scaled;    
135 >      // calc the wrapped real coordinates from the wrapped scaled coordinates
136 >      pos = hmat_ * scaled;    
137  
138      } else {//if it is orthoRhombic, we could improve efficiency by only caculating the diagonal element
139      
140 <        // calc the scaled coordinates.
141 <        for (i=0; i<3; i++) {
142 <            scaled[i] = pos[i] * invHmat_(i, i);
143 <        }
140 >      // calc the scaled coordinates.
141 >      for (i=0; i<3; i++) {
142 >        scaled[i] = pos[i] * invHmat_(i, i);
143 >      }
144          
145 <        // wrap the scaled coordinates
146 <        for (i = 0; i < 3; ++i) {
147 <            scaled[i] -= roundMe(scaled[i]);
148 <        }
145 >      // wrap the scaled coordinates
146 >      for (i = 0; i < 3; ++i) {
147 >        scaled[i] -= roundMe(scaled[i]);
148 >      }
149  
150 <        // calc the wrapped real coordinates from the wrapped scaled coordinates
151 <        for (i=0; i<3; i++) {
152 <            pos[i] = scaled[i] * hmat_(i, i);
153 <        }
150 >      // calc the wrapped real coordinates from the wrapped scaled coordinates
151 >      for (i=0; i<3; i++) {
152 >        pos[i] = scaled[i] * hmat_(i, i);
153 >      }
154          
155      }
156  
157 < }
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    

Diff Legend

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