| 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" |
| 57 |
|
#include "applications/dynamicProps/LegendreCorrFunc.hpp" |
| 58 |
+ |
#include "applications/dynamicProps/LegendreCorrFuncZ.hpp" |
| 59 |
|
#include "applications/dynamicProps/RadialRCorrFunc.hpp" |
| 60 |
|
#include "applications/dynamicProps/ThetaCorrFunc.hpp" |
| 61 |
|
#include "applications/dynamicProps/DirectionalRCorrFunc.hpp" |
| 62 |
|
#include "applications/dynamicProps/EnergyCorrFunc.hpp" |
| 63 |
+ |
#include "applications/dynamicProps/StressCorrFunc.hpp" |
| 64 |
+ |
#include "applications/dynamicProps/SystemDipoleCorrFunc.hpp" |
| 65 |
+ |
#include "applications/dynamicProps/MomentumCorrFunc.hpp" |
| 66 |
|
|
| 61 |
– |
|
| 67 |
|
using namespace OpenMD; |
| 68 |
|
|
| 69 |
|
int main(int argc, char* argv[]){ |
| 70 |
|
|
| 66 |
– |
//register force fields |
| 67 |
– |
registerForceFields(); |
| 68 |
– |
|
| 71 |
|
gengetopt_args_info args_info; |
| 72 |
|
|
| 73 |
|
//parse the command line option |
| 99 |
|
|
| 100 |
|
if (args_info.sele2_given) { |
| 101 |
|
sele2 = args_info.sele2_arg; |
| 102 |
< |
}else { |
| 102 |
> |
} else { |
| 103 |
|
char* sele2Env = getenv("SELECTION2"); |
| 104 |
|
if (sele2Env) { |
| 105 |
|
sele2 = sele2Env; |
| 108 |
|
} |
| 109 |
|
} |
| 110 |
|
|
| 111 |
+ |
// use the memory string to figure out how much memory we can use: |
| 112 |
+ |
char *end; |
| 113 |
+ |
long long int memSize = memparse(args_info.memory_arg, &end); |
| 114 |
+ |
sprintf( painCave.errMsg, |
| 115 |
+ |
"Amount of memory being used: %llu bytes\n", memSize); |
| 116 |
+ |
painCave.severity = OPENMD_INFO; |
| 117 |
+ |
painCave.isFatal = 0; |
| 118 |
+ |
simError(); |
| 119 |
+ |
|
| 120 |
|
//parse md file and set up the system |
| 121 |
|
SimCreator creator; |
| 122 |
|
SimInfo* info = creator.createSim(dumpFileName, false); |
| 123 |
|
|
| 113 |
– |
|
| 124 |
|
TimeCorrFunc* corrFunc; |
| 125 |
< |
if (args_info.dcorr_given){ |
| 126 |
< |
corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2); |
| 125 |
> |
if(args_info.sdcorr_given){ |
| 126 |
> |
corrFunc = new SystemDipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 127 |
> |
} else if (args_info.selecorr_given){ |
| 128 |
> |
corrFunc = new SelectionCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 129 |
> |
} else if (args_info.dcorr_given){ |
| 130 |
> |
corrFunc = new DipoleCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 131 |
|
} else if (args_info.rcorr_given) { |
| 132 |
< |
corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2); |
| 132 |
> |
corrFunc = new RCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 133 |
|
} else if (args_info.r_rcorr_given) { |
| 134 |
< |
corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2); |
| 134 |
> |
corrFunc = new RadialRCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 135 |
|
} else if (args_info.thetacorr_given) { |
| 136 |
< |
corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2); |
| 136 |
> |
corrFunc = new ThetaCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 137 |
|
} else if (args_info.drcorr_given) { |
| 138 |
< |
corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2); |
| 138 |
> |
corrFunc = new DirectionalRCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 139 |
|
} else if (args_info.vcorr_given) { |
| 140 |
< |
corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2); |
| 140 |
> |
corrFunc = new VCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 141 |
|
} else if (args_info.helfandEcorr_given){ |
| 142 |
< |
corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2); |
| 142 |
> |
corrFunc = new EnergyCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 143 |
> |
} else if (args_info.stresscorr_given){ |
| 144 |
> |
corrFunc = new StressCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 145 |
> |
} else if (args_info.momentum_given){ |
| 146 |
> |
corrFunc = new MomentumCorrFunc(info, dumpFileName, sele1, sele2, memSize); |
| 147 |
|
} else if (args_info.lcorr_given) { |
| 148 |
|
int order; |
| 149 |
|
if (args_info.order_given) |
| 150 |
|
order = args_info.order_arg; |
| 151 |
|
else { |
| 152 |
|
sprintf( painCave.errMsg, |
| 153 |
< |
"--order must be set if --lcoor is set\n"); |
| 153 |
> |
"--order must be set if --lcorr is set\n"); |
| 154 |
|
painCave.severity = OPENMD_ERROR; |
| 155 |
|
painCave.isFatal = 1; |
| 156 |
|
simError(); |
| 157 |
|
} |
| 158 |
|
|
| 159 |
< |
corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order); |
| 159 |
> |
corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize); |
| 160 |
> |
} else if (args_info.lcorrZ_given) { |
| 161 |
> |
int order; |
| 162 |
> |
if (args_info.order_given) |
| 163 |
> |
order = args_info.order_arg; |
| 164 |
> |
else { |
| 165 |
> |
sprintf( painCave.errMsg, |
| 166 |
> |
"--order must be set if --lcorrZ is set\n"); |
| 167 |
> |
painCave.severity = OPENMD_ERROR; |
| 168 |
> |
painCave.isFatal = 1; |
| 169 |
> |
simError(); |
| 170 |
> |
} |
| 171 |
> |
|
| 172 |
> |
corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize); |
| 173 |
> |
|
| 174 |
|
} |
| 175 |
|
|
| 176 |
|
if (args_info.output_given) { |
