| 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). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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> |
| 44 |
|
#include <fstream> |
| 45 |
|
#include <string> |
| 46 |
|
|
| 46 |
– |
#include "brains/Register.hpp" |
| 47 |
|
#include "brains/SimCreator.hpp" |
| 48 |
|
#include "brains/SimInfo.hpp" |
| 49 |
|
#include "utils/StringUtils.hpp" |
| 50 |
|
#include "utils/simError.h" |
| 51 |
|
|
| 52 |
|
#include "applications/dynamicProps/DynamicPropsCmd.h" |
| 53 |
+ |
#include "applications/dynamicProps/SelectionCorrFunc.hpp" |
| 54 |
|
#include "applications/dynamicProps/DipoleCorrFunc.hpp" |
| 55 |
|
#include "applications/dynamicProps/RCorrFunc.hpp" |
| 56 |
|
#include "applications/dynamicProps/VCorrFunc.hpp" |
| 61 |
|
#include "applications/dynamicProps/EnergyCorrFunc.hpp" |
| 62 |
|
#include "applications/dynamicProps/StressCorrFunc.hpp" |
| 63 |
|
#include "applications/dynamicProps/SystemDipoleCorrFunc.hpp" |
| 64 |
+ |
#include "applications/dynamicProps/MomentumCorrFunc.hpp" |
| 65 |
|
|
| 64 |
– |
|
| 66 |
|
using namespace OpenMD; |
| 67 |
|
|
| 68 |
|
int main(int argc, char* argv[]){ |
| 69 |
|
|
| 69 |
– |
//register force fields |
| 70 |
– |
registerForceFields(); |
| 71 |
– |
|
| 70 |
|
gengetopt_args_info args_info; |
| 71 |
|
|
| 72 |
|
//parse the command line option |
| 98 |
|
|
| 99 |
|
if (args_info.sele2_given) { |
| 100 |
|
sele2 = args_info.sele2_arg; |
| 101 |
< |
}else { |
| 101 |
> |
} else { |
| 102 |
|
char* sele2Env = getenv("SELECTION2"); |
| 103 |
|
if (sele2Env) { |
| 104 |
|
sele2 = sele2Env; |
| 114 |
|
"Amount of memory being used: %llu bytes\n", memSize); |
| 115 |
|
painCave.severity = OPENMD_INFO; |
| 116 |
|
painCave.isFatal = 0; |
| 117 |
< |
simError(); |
| 118 |
< |
|
| 117 |
> |
simError(); |
| 118 |
> |
|
| 119 |
|
//parse md file and set up the system |
| 120 |
|
SimCreator creator; |
| 121 |
|
SimInfo* info = creator.createSim(dumpFileName, false); |
| 122 |
|
|
| 125 |
– |
|
| 123 |
|
TimeCorrFunc* corrFunc; |
| 124 |
|
if(args_info.sdcorr_given){ |
| 125 |
|
corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 126 |
+ |
} else if (args_info.selecorr_given){ |
| 127 |
+ |
corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 128 |
|
} else if (args_info.dcorr_given){ |
| 129 |
|
corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 130 |
|
} else if (args_info.rcorr_given) { |
| 141 |
|
corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 142 |
|
} else if (args_info.stresscorr_given){ |
| 143 |
|
corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 144 |
+ |
} else if (args_info.momentum_given){ |
| 145 |
+ |
corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 146 |
|
} else if (args_info.lcorr_given) { |
| 147 |
|
int order; |
| 148 |
|
if (args_info.order_given) |
