| 5 |
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* redistribute this software in source and binary code form, provided |
| 6 |
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* that the following conditions are met: |
| 7 |
|
* |
| 8 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 9 |
< |
* publication of scientific results based in part on use of the |
| 10 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 11 |
< |
* the article in which the program was described (Matthew |
| 12 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 13 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 14 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 15 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 16 |
< |
* |
| 17 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 8 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 9 |
|
* notice, this list of conditions and the following disclaimer. |
| 10 |
|
* |
| 11 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 11 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 12 |
|
* notice, this list of conditions and the following disclaimer in the |
| 13 |
|
* documentation and/or other materials provided with the |
| 14 |
|
* distribution. |
| 28 |
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* University of Notre Dame has been advised of the possibility of |
| 29 |
|
* such damages. |
| 30 |
|
* |
| 31 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 32 |
+ |
* research, please cite the appropriate papers when you publish your |
| 33 |
+ |
* work. Good starting points are: |
| 34 |
+ |
* |
| 35 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 36 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 37 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 38 |
+ |
* [4] Vardeman & Gezelter, in progress (2009). |
| 39 |
|
* |
| 40 |
+ |
* |
| 41 |
|
* NanoVolume.cpp |
| 42 |
|
* |
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– |
* Purpose: To calculate convexhull, hull volume and radius |
| 44 |
– |
* using the CGAL library. |
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– |
* |
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|
* Created by Charles F. Vardeman II on 14 Dec 2006. |
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|
* @author Charles F. Vardeman II |
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< |
* @version $Id: NanoVolume.cpp,v 1.8 2008-10-15 18:26:01 chuckv Exp $ |
| 45 |
> |
* @version $Id: NanoVolume.cpp,v 1.10 2009-11-25 20:01:59 gezelter Exp $ |
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* |
| 47 |
|
*/ |
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|
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#include "applications/staticProps/NanoVolume.hpp" |
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#include "math/ConvexHull.hpp" |
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– |
//#include "math/AlphaShape.hpp" |
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#include "utils/simError.h" |
| 52 |
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#include "io/DumpReader.hpp" |
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#include "primitives/Molecule.hpp" |
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|
#include "utils/NumericConstant.hpp" |
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|
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< |
using namespace oopse; |
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> |
using namespace OpenMD; |
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|
| 58 |
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NanoVolume::NanoVolume(SimInfo* info, |
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const std::string& filename, |
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} |
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|
| 72 |
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void NanoVolume::process() { |
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#if defined(HAVE_CGAL) || defined(HAVE_QHULL) |
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> |
#if defined(HAVE_QHULL) |
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Molecule* mol; |
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Atom* atom; |
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RigidBody* rb; |
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#ifdef HAVE_QHULL |
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ConvexHull* thishull = new ConvexHull(); |
| 87 |
|
#endif |
| 92 |
– |
#ifdef HAVE_CGAL |
| 93 |
– |
// AlphaShape* hull = new AlphaShape(); |
| 94 |
– |
ConvexHull* thishull = new ConvexHull(); |
| 95 |
– |
#endif |
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|
|
| 89 |
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DumpReader reader(info_, dumpFilename_); |
| 90 |
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int nFrames = reader.getNFrames(); |
| 150 |
|
osq.close(); |
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*/ |
| 152 |
|
#else |
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< |
sprintf(painCave.errMsg, "NanoVolume: Neither CGAL nor qhull support was compiled in!\n"); |
| 153 |
> |
sprintf(painCave.errMsg, "NanoVolume: qhull support was not compiled in!\n"); |
| 154 |
|
painCave.isFatal = 1; |
| 155 |
|
simError(); |
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|
