| 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). |
| 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 |
|
*/ |
| 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" |
| 63 |
|
#include "applications/dynamicProps/StressCorrFunc.hpp" |
| 64 |
|
#include "applications/dynamicProps/SystemDipoleCorrFunc.hpp" |
| 65 |
|
#include "applications/dynamicProps/MomentumCorrFunc.hpp" |
| 66 |
+ |
#include "applications/dynamicProps/cOHz.hpp" |
| 67 |
|
|
| 68 |
|
using namespace OpenMD; |
| 69 |
|
|
| 76 |
|
exit(1) ; |
| 77 |
|
} |
| 78 |
|
|
| 77 |
– |
|
| 79 |
|
//get the dumpfile name and meta-data file name |
| 80 |
|
std::string dumpFileName = args_info.input_arg; |
| 81 |
|
|
| 82 |
|
std::string sele1; |
| 83 |
|
std::string sele2; |
| 84 |
< |
|
| 84 |
> |
|
| 85 |
> |
// check the first selection argument, or set it to the environment |
| 86 |
> |
// variable, or failing that, set it to "select all" |
| 87 |
> |
|
| 88 |
|
if (args_info.sele1_given) { |
| 89 |
|
sele1 = args_info.sele1_arg; |
| 90 |
< |
}else { |
| 90 |
> |
} else { |
| 91 |
|
char* sele1Env= getenv("SELECTION1"); |
| 92 |
|
if (sele1Env) { |
| 93 |
|
sele1 = sele1Env; |
| 94 |
< |
}else { |
| 95 |
< |
sprintf( painCave.errMsg, |
| 92 |
< |
"neither --sele1 option nor $SELECTION1 is set"); |
| 93 |
< |
painCave.severity = OPENMD_ERROR; |
| 94 |
< |
painCave.isFatal = 1; |
| 95 |
< |
simError(); |
| 94 |
> |
} else { |
| 95 |
> |
sele1 = "select all"; |
| 96 |
|
} |
| 97 |
|
} |
| 98 |
< |
|
| 98 |
> |
|
| 99 |
> |
// check the second selection argument, or set it to the environment |
| 100 |
> |
// variable, or failing that, set it to the first selection |
| 101 |
> |
|
| 102 |
|
if (args_info.sele2_given) { |
| 103 |
|
sele2 = args_info.sele2_arg; |
| 104 |
|
} else { |
| 105 |
|
char* sele2Env = getenv("SELECTION2"); |
| 106 |
|
if (sele2Env) { |
| 107 |
|
sele2 = sele2Env; |
| 108 |
< |
} else { |
| 108 |
> |
} else { |
| 109 |
> |
//If sele2 is not specified, then the default behavior |
| 110 |
> |
//should be what is already intended for sele1 |
| 111 |
|
sele2 = sele1; |
| 112 |
|
} |
| 113 |
|
} |
| 154 |
|
order = args_info.order_arg; |
| 155 |
|
else { |
| 156 |
|
sprintf( painCave.errMsg, |
| 157 |
< |
"--order must be set if --lcoor is set\n"); |
| 157 |
> |
"--order must be set if --lcorr is set\n"); |
| 158 |
|
painCave.severity = OPENMD_ERROR; |
| 159 |
|
painCave.isFatal = 1; |
| 160 |
|
simError(); |
| 161 |
|
} |
| 162 |
|
|
| 163 |
|
corrFunc = new LegendreCorrFunc(info, dumpFileName, sele1, sele2, order, memSize); |
| 164 |
+ |
} else if (args_info.lcorrZ_given) { |
| 165 |
+ |
int order; |
| 166 |
+ |
if (args_info.order_given) |
| 167 |
+ |
order = args_info.order_arg; |
| 168 |
+ |
else { |
| 169 |
+ |
sprintf( painCave.errMsg, |
| 170 |
+ |
"--order must be set if --lcorrZ is set\n"); |
| 171 |
+ |
painCave.severity = OPENMD_ERROR; |
| 172 |
+ |
painCave.isFatal = 1; |
| 173 |
+ |
simError(); |
| 174 |
+ |
} |
| 175 |
+ |
|
| 176 |
+ |
corrFunc = new LegendreCorrFuncZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize); |
| 177 |
+ |
|
| 178 |
+ |
} else if (args_info.cohZ_given) { |
| 179 |
+ |
int order; |
| 180 |
+ |
if (args_info.order_given) |
| 181 |
+ |
order = args_info.order_arg; |
| 182 |
+ |
else { |
| 183 |
+ |
sprintf( painCave.errMsg, |
| 184 |
+ |
"--order must be set if --cohZ is set\n"); |
| 185 |
+ |
painCave.severity = OPENMD_ERROR; |
| 186 |
+ |
painCave.isFatal = 1; |
| 187 |
+ |
simError(); |
| 188 |
+ |
} |
| 189 |
+ |
|
| 190 |
+ |
corrFunc = new COHZ(info, dumpFileName, sele1, sele2, order, args_info.nzbins_arg, memSize); |
| 191 |
+ |
|
| 192 |
|
} |
| 193 |
|
|
| 194 |
+ |
|
| 195 |
|
if (args_info.output_given) { |
| 196 |
|
corrFunc->setOutputName(args_info.output_arg); |
| 197 |
|
} |
