| 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. |
| 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 |
|
#include <iostream> |
| 59 |
|
#include "visitors/LipidTransVisitor.hpp" |
| 60 |
|
#include "visitors/AtomNameVisitor.hpp" |
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|
|
| 62 |
< |
using namespace oopse; |
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> |
using namespace OpenMD; |
| 63 |
|
|
| 64 |
|
int main(int argc, char* argv[]){ |
| 65 |
|
|
| 127 |
|
DefaultAtomVisitor* defaultAtomVisitor = new DefaultAtomVisitor(info); |
| 128 |
|
compositeVisitor->addVisitor(defaultAtomVisitor, 700); |
| 129 |
|
|
| 130 |
< |
//create waterType visitor |
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< |
if(args_info.watertype_flag){ |
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< |
WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor; |
| 133 |
< |
compositeVisitor->addVisitor(waterTypeVisitor, 600); |
| 130 |
> |
// if we gave the -w option, we want to skip the waters: |
| 131 |
> |
std::cerr << "-w flag was set to:" << args_info.water_given << "\n"; |
| 132 |
> |
if (!args_info.water_given) { |
| 133 |
> |
//create waterType visitor |
| 134 |
> |
if(args_info.watertype_flag){ |
| 135 |
> |
WaterTypeVisitor* waterTypeVisitor = new WaterTypeVisitor; |
| 136 |
> |
compositeVisitor->addVisitor(waterTypeVisitor, 600); |
| 137 |
> |
} |
| 138 |
|
} |
| 139 |
|
|
| 140 |
|
if (args_info.basetype_flag) { |
| 204 |
|
int nframes = dumpReader->getNFrames(); |
| 205 |
|
|
| 206 |
|
|
| 207 |
< |
std::ofstream xyzStream; |
| 204 |
< |
xyzStream .open(xyzFileName.c_str()); |
| 207 |
> |
std::ofstream xyzStream(xyzFileName.c_str()); |
| 208 |
|
|
| 206 |
– |
|
| 209 |
|
SimInfo::MoleculeIterator miter; |
| 210 |
|
Molecule::IntegrableObjectIterator iiter; |
| 211 |
|
Molecule::RigidBodyIterator rbIter; |
| 268 |
|
xyzVisitor->clear(); |
| 269 |
|
|
| 270 |
|
}//end for (int i = 0; i < nframes; i += args_info.frame_arg) |
| 271 |
< |
|
| 271 |
> |
|
| 272 |
|
xyzStream.close(); |
| 271 |
– |
|
| 273 |
|
delete prepareVisitor; |
| 274 |
|
delete compositeVisitor; |
| 275 |
|
delete info; |
| 275 |
– |
|
| 276 |
|
} |
