| 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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include <cstdlib> |
| 65 |
|
#include "utils/StringUtils.hpp" |
| 66 |
|
|
| 67 |
|
using namespace std; |
| 68 |
< |
using namespace oopse; |
| 68 |
> |
using namespace OpenMD; |
| 69 |
|
void createMdFile(const std::string&oldMdFileName, |
| 70 |
|
const std::string&newMdFileName, |
| 71 |
|
std::vector<int> numMol); |
| 72 |
|
|
| 73 |
|
int main(int argc, char *argv []) { |
| 74 |
|
|
| 74 |
– |
//register force fields |
| 75 |
– |
registerForceFields(); |
| 75 |
|
registerLattice(); |
| 76 |
|
|
| 77 |
|
gengetopt_args_info args_info; |
| 125 |
|
/* Build a lattice and get lattice points for this lattice constant */ |
| 126 |
|
vector<Vector3d> sites = nanoParticle.getSites(); |
| 127 |
|
vector<Vector3d> orientations = nanoParticle.getOrientations(); |
| 128 |
+ |
|
| 129 |
+ |
|
| 130 |
|
std::vector<int> vacancyTargets; |
| 131 |
|
vector<bool> isVacancy; |
| 132 |
|
|
| 171 |
|
|
| 172 |
|
|
| 173 |
|
sprintf(painCave.errMsg, "Removing %d atoms from randomly-selected\n" |
| 174 |
< |
"\tsites between %lf and %lf.", vacancyTargets.size(), |
| 174 |
> |
"\tsites between %lf and %lf.", (int) vacancyTargets.size(), |
| 175 |
|
vIR, vOR); |
| 176 |
|
painCave.isFatal = 0; |
| 177 |
|
simError(); |
| 377 |
|
mol = NewInfo->beginMolecule(mi); |
| 378 |
|
|
| 379 |
|
int l = 0; |
| 379 |
– |
int whichSite = 0; |
| 380 |
|
|
| 381 |
|
for (int i = 0; i < nComponents; i++){ |
| 382 |
|
locator = new MoLocator(NewInfo->getMoleculeStamp(i), |
| 434 |
|
delete writer; |
| 435 |
|
|
| 436 |
|
// cleanup a by calling sim error..... |
| 437 |
< |
sprintf(painCave.errMsg, "A new OOPSE MD file called \"%s\" has been " |
| 437 |
> |
sprintf(painCave.errMsg, "A new OpenMD file called \"%s\" has been " |
| 438 |
|
"generated.\n", outputFileName.c_str()); |
| 439 |
|
painCave.isFatal = 0; |
| 440 |
|
simError(); |
