| 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 <iostream> |
| 58 |
|
#include "utils/StringUtils.hpp" |
| 59 |
|
#include "utils/simError.h" |
| 60 |
|
#include "utils/MemoryUtils.hpp" |
| 61 |
< |
using namespace oopse; |
| 61 |
> |
using namespace OpenMD; |
| 62 |
|
|
| 63 |
|
struct SDShape{ |
| 64 |
|
StuntDouble* sd; |
| 68 |
|
void writeHydroProps(std::ostream& os); |
| 69 |
|
|
| 70 |
|
int main(int argc, char* argv[]){ |
| 70 |
– |
//register force fields |
| 71 |
– |
registerForceFields(); |
| 71 |
|
registerHydrodynamicsModels(); |
| 72 |
|
|
| 73 |
|
gengetopt_args_info args_info; |
| 88 |
|
exit(1); |
| 89 |
|
} |
| 90 |
|
|
| 92 |
– |
mdFileName = dumpFileName; |
| 93 |
– |
mdFileName = mdFileName.substr(0, mdFileName.rfind(".")) + ".md"; |
| 94 |
– |
|
| 91 |
|
if (args_info.output_given){ |
| 92 |
|
prefix = args_info.output_arg; |
| 93 |
|
} else { |
| 94 |
< |
prefix = getPrefix(mdFileName); |
| 94 |
> |
prefix = getPrefix(dumpFileName); |
| 95 |
|
} |
| 96 |
|
std::string outputFilename = prefix + ".diff"; |
| 97 |
|
|
| 98 |
|
//parse md file and set up the system |
| 99 |
|
SimCreator creator; |
| 100 |
< |
SimInfo* info = creator.createSim(mdFileName, true); |
| 100 |
> |
SimInfo* info = creator.createSim(dumpFileName, true); |
| 101 |
|
|
| 102 |
|
SimInfo::MoleculeIterator mi; |
| 103 |
|
Molecule* mol; |
| 153 |
|
|
| 154 |
|
|
| 155 |
|
|
| 160 |
– |
std::ofstream outputDiff(outputFilename.c_str()); |
| 156 |
|
std::map<std::string, SDShape>::iterator si; |
| 157 |
|
for (si = uniqueStuntDoubles.begin(); si != uniqueStuntDoubles.end(); ++si) { |
| 158 |
|
HydrodynamicsModel* model; |
| 178 |
|
//if beads option is turned on, skip the calculation |
| 179 |
|
if (!args_info.beads_flag) { |
| 180 |
|
model->calcHydroProps(shape, viscosity, temperature); |
| 181 |
+ |
std::ofstream outputDiff; |
| 182 |
+ |
outputDiff.open(outputFilename.c_str()); |
| 183 |
|
model->writeHydroProps(outputDiff); |
| 184 |
+ |
outputDiff.close(); |
| 185 |
|
} |
| 186 |
|
|
| 187 |
|
delete model; |
