| 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). |
| 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 |
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#include <iostream> |
| 44 |
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#include <fstream> |
| 45 |
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#include <string> |
| 46 |
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|
| 46 |
– |
#include "brains/Register.hpp" |
| 47 |
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#include "brains/SimCreator.hpp" |
| 48 |
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#include "brains/SimInfo.hpp" |
| 49 |
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#include "io/DumpReader.hpp" |
| 69 |
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#include "applications/staticProps/pAngle.hpp" |
| 70 |
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#include "applications/staticProps/BondAngleDistribution.hpp" |
| 71 |
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#include "applications/staticProps/NanoVolume.hpp" |
| 72 |
+ |
#include "applications/staticProps/NanoLength.hpp" |
| 73 |
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#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H) |
| 74 |
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#include "applications/staticProps/Hxy.hpp" |
| 75 |
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#endif |
| 76 |
|
#include "applications/staticProps/RhoR.hpp" |
| 77 |
|
#include "applications/staticProps/AngleR.hpp" |
| 77 |
– |
#include "applications/staticProps/RhoAngleR.hpp" |
| 78 |
|
#include "applications/staticProps/TetrahedralityParam.hpp" |
| 79 |
< |
|
| 79 |
> |
#include "applications/staticProps/TetrahedralityParamZ.hpp" |
| 80 |
|
using namespace OpenMD; |
| 81 |
|
|
| 82 |
|
int main(int argc, char* argv[]){ |
| 83 |
|
|
| 84 |
– |
//register force fields |
| 85 |
– |
registerForceFields(); |
| 84 |
|
|
| 85 |
|
gengetopt_args_info args_info; |
| 86 |
|
|
| 93 |
|
std::string dumpFileName = args_info.input_arg; |
| 94 |
|
std::string sele1; |
| 95 |
|
std::string sele2; |
| 98 |
– |
bool userSpecifiedSelect1; |
| 99 |
– |
bool userSpecifiedSelect2; |
| 96 |
|
|
| 97 |
|
// check the first selection argument, or set it to the environment |
| 98 |
|
// variable, or failing that, set it to "select all" |
| 118 |
|
if (sele2Env) { |
| 119 |
|
sele2 = sele2Env; |
| 120 |
|
} else { |
| 121 |
< |
sele2 = "select all"; |
| 121 |
> |
//It seems likely (from previous discussions) that if sele2 is not specified, then the default behavior |
| 122 |
> |
//should not be 'select all' but rather what is already intended for sele1 |
| 123 |
> |
//JRM 8/22/12 |
| 124 |
> |
sele2 = sele1; |
| 125 |
> |
//sele2 = "select all"; |
| 126 |
|
} |
| 127 |
|
} |
| 128 |
|
|
| 233 |
|
simError(); |
| 234 |
|
} |
| 235 |
|
} else if (args_info.p2_given) { |
| 236 |
< |
analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2); |
| 236 |
> |
if (args_info.sele1_given) { |
| 237 |
> |
if (args_info.sele2_given) |
| 238 |
> |
analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2); |
| 239 |
> |
else |
| 240 |
> |
analyser = new P2OrderParameter(info, dumpFileName, sele1); |
| 241 |
> |
} else { |
| 242 |
> |
sprintf( painCave.errMsg, |
| 243 |
> |
"At least one selection script (--sele1) must be specified when calculating P2 order parameters"); |
| 244 |
> |
painCave.severity = OPENMD_ERROR; |
| 245 |
> |
painCave.isFatal = 1; |
| 246 |
> |
simError(); |
| 247 |
> |
} |
| 248 |
|
} else if (args_info.rp2_given){ |
| 249 |
|
analyser = new RippleOP(info, dumpFileName, sele1, sele2); |
| 250 |
|
} else if (args_info.bo_given){ |
| 272 |
|
painCave.isFatal = 1; |
| 273 |
|
simError(); |
| 274 |
|
} |
| 275 |
+ |
} else if (args_info.tet_param_z_given) { |
| 276 |
+ |
if (args_info.rcut_given) { |
| 277 |
+ |
analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, |
| 278 |
+ |
args_info.rcut_arg, |
| 279 |
+ |
args_info.nbins_arg); |
| 280 |
+ |
} else { |
| 281 |
+ |
sprintf( painCave.errMsg, |
| 282 |
+ |
"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters"); |
| 283 |
+ |
painCave.severity = OPENMD_ERROR; |
| 284 |
+ |
painCave.isFatal = 1; |
| 285 |
+ |
simError(); |
| 286 |
+ |
} |
| 287 |
|
} else if (args_info.bor_given){ |
| 288 |
|
if (args_info.rcut_given) { |
| 289 |
|
analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg, |
| 340 |
|
} |
| 341 |
|
} else if (args_info.hullvol_given) { |
| 342 |
|
analyser = new NanoVolume(info, dumpFileName, sele1); |
| 343 |
+ |
} else if (args_info.rodlength_given) { |
| 344 |
+ |
analyser = new NanoLength(info, dumpFileName, sele1); |
| 345 |
|
} else if (args_info.angle_r_given) { |
| 346 |
|
analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg); |
| 347 |
|
} |
| 352 |
|
if (args_info.step_given) { |
| 353 |
|
analyser->setStep(args_info.step_arg); |
| 354 |
|
} |
| 355 |
< |
|
| 355 |
> |
|
| 356 |
|
analyser->process(); |
| 357 |
|
|
| 358 |
|
delete analyser; |
