| 1 |
< |
/* Copyright (c) 2006 The University of Notre Dame. All Rights Reserved. |
| 1 |
> |
/* Copyright (c) 2006, 2009, 2010 The University of Notre Dame. All Rights Reserved. |
| 2 |
|
* |
| 3 |
|
* The University of Notre Dame grants you ("Licensee") a |
| 4 |
|
* non-exclusive, royalty free, license to use, modify and |
| 5 |
|
* redistribute this software in source and binary code form, provided |
| 6 |
|
* 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 |
|
* 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 |
|
* |
| 43 |
|
* Created by Charles F. Vardeman II on 14 Dec 2006. |
| 44 |
|
* @author Charles F. Vardeman II |
| 45 |
< |
* @version $Id: NanoVolume.cpp,v 1.9 2009-10-22 14:19:26 gezelter Exp $ |
| 45 |
> |
* @version $Id: NanoVolume.cpp,v 1.10 2009-11-25 20:01:59 gezelter Exp $ |
| 46 |
|
* |
| 47 |
|
*/ |
| 48 |
|
|
| 49 |
|
#include "applications/staticProps/NanoVolume.hpp" |
| 50 |
|
#include "math/ConvexHull.hpp" |
| 51 |
+ |
#include "math/AlphaHull.hpp" |
| 52 |
|
#include "utils/simError.h" |
| 53 |
|
#include "io/DumpReader.hpp" |
| 54 |
|
#include "primitives/Molecule.hpp" |
| 55 |
|
#include "utils/NumericConstant.hpp" |
| 56 |
|
|
| 57 |
< |
using namespace oopse; |
| 57 |
> |
using namespace OpenMD; |
| 58 |
|
|
| 59 |
|
NanoVolume::NanoVolume(SimInfo* info, |
| 60 |
|
const std::string& filename, |
| 84 |
|
int i,j; |
| 85 |
|
|
| 86 |
|
#ifdef HAVE_QHULL |
| 87 |
< |
ConvexHull* thishull = new ConvexHull(); |
| 87 |
> |
// ConvexHull* thishull = new ConvexHull(); |
| 88 |
> |
AlphaHull* thishull = new AlphaHull(2.0); |
| 89 |
|
#endif |
| 90 |
|
|
| 91 |
|
DumpReader reader(info_, dumpFilename_); |
