| 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, 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 "io/DumpReader.hpp" |
| 52 |
|
#include "applications/staticProps/StaticPropsCmd.h" |
| 53 |
|
#include "applications/staticProps/StaticAnalyser.hpp" |
| 54 |
|
#include "applications/staticProps/GofR.hpp" |
| 55 |
+ |
#include "applications/staticProps/GofZ.hpp" |
| 56 |
+ |
#include "applications/staticProps/GofRZ.hpp" |
| 57 |
|
#include "applications/staticProps/GofRAngle.hpp" |
| 58 |
|
#include "applications/staticProps/GofAngle2.hpp" |
| 59 |
|
#include "applications/staticProps/GofXyz.hpp" |
| 60 |
+ |
#include "applications/staticProps/TwoDGofR.hpp" |
| 61 |
|
#include "applications/staticProps/P2OrderParameter.hpp" |
| 62 |
+ |
#include "applications/staticProps/BondOrderParameter.hpp" |
| 63 |
+ |
#include "applications/staticProps/BOPofR.hpp" |
| 64 |
+ |
#include "applications/staticProps/RippleOP.hpp" |
| 65 |
+ |
#include "applications/staticProps/SCDOrderParameter.hpp" |
| 66 |
+ |
#include "applications/staticProps/DensityPlot.hpp" |
| 67 |
+ |
#include "applications/staticProps/ObjectCount.hpp" |
| 68 |
+ |
#include "applications/staticProps/RhoZ.hpp" |
| 69 |
+ |
#include "applications/staticProps/pAngle.hpp" |
| 70 |
+ |
#include "applications/staticProps/BondAngleDistribution.hpp" |
| 71 |
+ |
#include "applications/staticProps/NanoVolume.hpp" |
| 72 |
+ |
#include "applications/staticProps/NanoLength.hpp" |
| 73 |
+ |
#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H) |
| 74 |
+ |
#include "applications/staticProps/Hxy.hpp" |
| 75 |
+ |
#endif |
| 76 |
+ |
#include "applications/staticProps/RhoR.hpp" |
| 77 |
+ |
#include "applications/staticProps/AngleR.hpp" |
| 78 |
+ |
#include "applications/staticProps/TetrahedralityParam.hpp" |
| 79 |
+ |
#include "applications/staticProps/TetrahedralityParamZ.hpp" |
| 80 |
+ |
#include "applications/staticProps/RNEMDStats.hpp" |
| 81 |
|
|
| 82 |
+ |
using namespace OpenMD; |
| 83 |
|
|
| 61 |
– |
using namespace oopse; |
| 62 |
– |
|
| 84 |
|
int main(int argc, char* argv[]){ |
| 85 |
|
|
| 86 |
< |
//register force fields |
| 66 |
< |
registerForceFields(); |
| 67 |
< |
|
| 86 |
> |
|
| 87 |
|
gengetopt_args_info args_info; |
| 88 |
< |
|
| 88 |
> |
|
| 89 |
|
//parse the command line option |
| 90 |
|
if (cmdline_parser (argc, argv, &args_info) != 0) { |
| 91 |
|
exit(1) ; |
| 92 |
|
} |
| 93 |
< |
|
| 94 |
< |
|
| 76 |
< |
//get the dumpfile name and meta-data file name |
| 93 |
> |
|
| 94 |
> |
//get the dumpfile name |
| 95 |
|
std::string dumpFileName = args_info.input_arg; |
| 78 |
– |
|
| 79 |
– |
std::string mdFileName = dumpFileName.substr(0, dumpFileName.rfind(".")) + ".md"; |
| 80 |
– |
|
| 81 |
– |
|
| 96 |
|
std::string sele1; |
| 97 |
|
std::string sele2; |
| 98 |
< |
|
| 98 |
> |
|
| 99 |
> |
// check the first selection argument, or set it to the environment |
| 100 |
> |
// variable, or failing that, set it to "select all" |
| 101 |
> |
|
| 102 |
|
if (args_info.sele1_given) { |
| 103 |
|
sele1 = args_info.sele1_arg; |
| 104 |
< |
}else { |
| 105 |
< |
char* sele1Env= getenv("OOPSE_SELE1"); |
| 104 |
> |
} else { |
| 105 |
> |
char* sele1Env= getenv("SELECTION1"); |
| 106 |
|
if (sele1Env) { |
| 107 |
|
sele1 = sele1Env; |
| 108 |
< |
}else { |
| 109 |
< |
sprintf( painCave.errMsg, |
| 93 |
< |
"neither --sele1 option nor $OOPSE_SELE1 is set"); |
| 94 |
< |
painCave.severity = OOPSE_ERROR; |
| 95 |
< |
painCave.isFatal = 1; |
| 96 |
< |
simError(); |
| 108 |
> |
} else { |
| 109 |
> |
sele1 = "select all"; |
| 110 |
|
} |
| 111 |
|
} |
| 112 |
< |
|
| 112 |
> |
|
| 113 |
> |
// check the second selection argument, or set it to the environment |
| 114 |
> |
// variable, or failing that, set it to the first selection |
| 115 |
> |
|
| 116 |
|
if (args_info.sele2_given) { |
| 117 |
|
sele2 = args_info.sele2_arg; |
| 118 |
< |
}else { |
| 119 |
< |
char* sele2Env = getenv("OOPSE_SELE2"); |
| 118 |
> |
} else { |
| 119 |
> |
char* sele2Env = getenv("SELECTION2"); |
| 120 |
|
if (sele2Env) { |
| 121 |
|
sele2 = sele2Env; |
| 122 |
< |
} else { |
| 122 |
> |
} else { |
| 123 |
> |
//If sele2 is not specified, then the default behavior |
| 124 |
> |
//should be what is already intended for sele1 |
| 125 |
> |
sele2 = sele1; |
| 126 |
> |
} |
| 127 |
> |
} |
| 128 |
> |
|
| 129 |
> |
bool batchMode; |
| 130 |
> |
if (args_info.scd_given){ |
| 131 |
> |
if (args_info.sele1_given && |
| 132 |
> |
args_info.sele2_given && args_info.sele3_given) { |
| 133 |
> |
batchMode = false; |
| 134 |
> |
} else if (args_info.molname_given && |
| 135 |
> |
args_info.begin_given && args_info.end_given) { |
| 136 |
> |
if (args_info.begin_arg < 0 || |
| 137 |
> |
args_info.end_arg < 0 || args_info.begin_arg > args_info.end_arg-2) { |
| 138 |
> |
sprintf( painCave.errMsg, |
| 139 |
> |
"below conditions are not satisfied:\n" |
| 140 |
> |
"0 <= begin && 0<= end && begin <= end-2\n"); |
| 141 |
> |
painCave.severity = OPENMD_ERROR; |
| 142 |
> |
painCave.isFatal = 1; |
| 143 |
> |
simError(); |
| 144 |
> |
} |
| 145 |
> |
batchMode = true; |
| 146 |
> |
} else{ |
| 147 |
|
sprintf( painCave.errMsg, |
| 148 |
< |
"neither --sele2 option nor $OOPSE_SELE2 is set"); |
| 149 |
< |
painCave.severity = OOPSE_ERROR; |
| 148 |
> |
"either --sele1, --sele2, --sele3 are specified," |
| 149 |
> |
" or --molname, --begin, --end are specified\n"); |
| 150 |
> |
painCave.severity = OPENMD_ERROR; |
| 151 |
|
painCave.isFatal = 1; |
| 152 |
< |
simError(); |
| 152 |
> |
simError(); |
| 153 |
|
} |
| 154 |
|
} |
| 155 |
< |
|
| 155 |
> |
|
| 156 |
|
//parse md file and set up the system |
| 157 |
|
SimCreator creator; |
| 158 |
< |
SimInfo* info = creator.createSim(mdFileName); |
| 158 |
> |
SimInfo* info = creator.createSim(dumpFileName); |
| 159 |
|
|
| 160 |
< |
double maxLen; |
| 160 |
> |
RealType maxLen; |
| 161 |
> |
RealType zmaxLen; |
| 162 |
|
if (args_info.length_given) { |
| 163 |
|
maxLen = args_info.length_arg; |
| 164 |
+ |
if (args_info.zlength_given){ |
| 165 |
+ |
zmaxLen = args_info.zlength_arg; |
| 166 |
+ |
} |
| 167 |
|
} else { |
| 168 |
|
Mat3x3d hmat = info->getSnapshotManager()->getCurrentSnapshot()->getHmat(); |
| 169 |
< |
maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0; |
| 169 |
> |
maxLen = std::min(std::min(hmat(0, 0), hmat(1, 1)), hmat(2, 2)) /2.0; |
| 170 |
> |
zmaxLen = hmat(2,2); |
| 171 |
|
} |
| 172 |
< |
|
| 172 |
> |
|
| 173 |
|
StaticAnalyser* analyser; |
| 174 |
|
if (args_info.gofr_given){ |
| 175 |
< |
analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg); |
| 175 |
> |
analyser= new GofR(info, dumpFileName, sele1, sele2, maxLen, |
| 176 |
> |
args_info.nbins_arg); |
| 177 |
> |
} else if (args_info.gofz_given) { |
| 178 |
> |
analyser= new GofZ(info, dumpFileName, sele1, sele2, maxLen, |
| 179 |
> |
args_info.nbins_arg); |
| 180 |
> |
} else if (args_info.r_z_given) { |
| 181 |
> |
analyser = new GofRZ(info, dumpFileName, sele1, sele2, maxLen, zmaxLen, |
| 182 |
> |
args_info.nbins_arg, args_info.nbins_z_arg); |
| 183 |
|
} else if (args_info.r_theta_given) { |
| 184 |
< |
analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg); |
| 184 |
> |
analyser = new GofRTheta(info, dumpFileName, sele1, sele2, maxLen, |
| 185 |
> |
args_info.nbins_arg, args_info.nanglebins_arg); |
| 186 |
|
} else if (args_info.r_omega_given) { |
| 187 |
< |
analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, args_info.nrbins_arg, args_info.nanglebins_arg); |
| 187 |
> |
analyser = new GofROmega(info, dumpFileName, sele1, sele2, maxLen, |
| 188 |
> |
args_info.nbins_arg, args_info.nanglebins_arg); |
| 189 |
|
} else if (args_info.theta_omega_given) { |
| 190 |
< |
analyser = new GofAngle2(info, dumpFileName, sele1, sele2, args_info.nanglebins_arg); |
| 190 |
> |
analyser = new GofAngle2(info, dumpFileName, sele1, sele2, |
| 191 |
> |
args_info.nanglebins_arg); |
| 192 |
|
} else if (args_info.gxyz_given) { |
| 193 |
|
if (args_info.refsele_given) { |
| 194 |
< |
analyser= new GofXyz(info, dumpFileName, sele1, sele2,args_info.refsele_arg, maxLen, args_info.nrbins_arg); |
| 194 |
> |
analyser= new GofXyz(info, dumpFileName, sele1, sele2, |
| 195 |
> |
args_info.refsele_arg, maxLen, args_info.nbins_arg); |
| 196 |
|
} else { |
| 197 |
|
sprintf( painCave.errMsg, |
| 198 |
< |
"--refsele must set when --gxyz is used"); |
| 199 |
< |
painCave.severity = OOPSE_ERROR; |
| 198 |
> |
"--refsele must set when --gxyz is used"); |
| 199 |
> |
painCave.severity = OPENMD_ERROR; |
| 200 |
|
painCave.isFatal = 1; |
| 201 |
|
simError(); |
| 202 |
|
} |
| 203 |
+ |
} else if (args_info.twodgofr_given){ |
| 204 |
+ |
if (args_info.dz_given) { |
| 205 |
+ |
analyser= new TwoDGofR(info, dumpFileName, sele1, sele2, maxLen, |
| 206 |
+ |
args_info.dz_arg, args_info.nbins_arg); |
| 207 |
+ |
} else { |
| 208 |
+ |
sprintf( painCave.errMsg, |
| 209 |
+ |
"A slab width (dz) must be specified when calculating TwoDGofR"); |
| 210 |
+ |
painCave.severity = OPENMD_ERROR; |
| 211 |
+ |
painCave.isFatal = 1; |
| 212 |
+ |
simError(); |
| 213 |
+ |
} |
| 214 |
|
} else if (args_info.p2_given) { |
| 215 |
< |
analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2); |
| 216 |
< |
} |
| 215 |
> |
if (args_info.sele1_given) { |
| 216 |
> |
if (args_info.sele2_given) |
| 217 |
> |
analyser = new P2OrderParameter(info, dumpFileName, sele1, sele2); |
| 218 |
> |
else |
| 219 |
> |
if (args_info.seleoffset_given) |
| 220 |
> |
analyser = new P2OrderParameter(info, dumpFileName, sele1, |
| 221 |
> |
args_info.seleoffset_arg); |
| 222 |
> |
else |
| 223 |
> |
analyser = new P2OrderParameter(info, dumpFileName, sele1); |
| 224 |
> |
} else { |
| 225 |
> |
sprintf( painCave.errMsg, |
| 226 |
> |
"At least one selection script (--sele1) must be specified when calculating P2 order parameters"); |
| 227 |
> |
painCave.severity = OPENMD_ERROR; |
| 228 |
> |
painCave.isFatal = 1; |
| 229 |
> |
simError(); |
| 230 |
> |
} |
| 231 |
> |
} else if (args_info.rp2_given){ |
| 232 |
> |
analyser = new RippleOP(info, dumpFileName, sele1, sele2); |
| 233 |
> |
} else if (args_info.bo_given){ |
| 234 |
> |
if (args_info.rcut_given) { |
| 235 |
> |
analyser = new BondOrderParameter(info, dumpFileName, sele1, |
| 236 |
> |
args_info.rcut_arg, |
| 237 |
> |
args_info.nbins_arg); |
| 238 |
> |
} else { |
| 239 |
> |
sprintf( painCave.errMsg, |
| 240 |
> |
"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters"); |
| 241 |
> |
painCave.severity = OPENMD_ERROR; |
| 242 |
> |
painCave.isFatal = 1; |
| 243 |
> |
simError(); |
| 244 |
> |
} |
| 245 |
|
|
| 246 |
+ |
} else if (args_info.tet_param_given) { |
| 247 |
+ |
if (args_info.rcut_given) { |
| 248 |
+ |
analyser = new TetrahedralityParam(info, dumpFileName, sele1, |
| 249 |
+ |
args_info.rcut_arg, |
| 250 |
+ |
args_info.nbins_arg); |
| 251 |
+ |
} else { |
| 252 |
+ |
sprintf( painCave.errMsg, |
| 253 |
+ |
"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters"); |
| 254 |
+ |
painCave.severity = OPENMD_ERROR; |
| 255 |
+ |
painCave.isFatal = 1; |
| 256 |
+ |
simError(); |
| 257 |
+ |
} |
| 258 |
+ |
} else if (args_info.tet_param_z_given) { |
| 259 |
+ |
if (args_info.rcut_given) { |
| 260 |
+ |
analyser = new TetrahedralityParamZ(info, dumpFileName, sele1, sele2, |
| 261 |
+ |
args_info.rcut_arg, |
| 262 |
+ |
args_info.nbins_arg); |
| 263 |
+ |
} else { |
| 264 |
+ |
sprintf( painCave.errMsg, |
| 265 |
+ |
"A cutoff radius (rcut) must be specified when calculating Tetrahedrality Parameters"); |
| 266 |
+ |
painCave.severity = OPENMD_ERROR; |
| 267 |
+ |
painCave.isFatal = 1; |
| 268 |
+ |
simError(); |
| 269 |
+ |
} |
| 270 |
+ |
} else if (args_info.bor_given){ |
| 271 |
+ |
if (args_info.rcut_given) { |
| 272 |
+ |
analyser = new BOPofR(info, dumpFileName, sele1, args_info.rcut_arg, |
| 273 |
+ |
args_info.nbins_arg, maxLen); |
| 274 |
+ |
} else { |
| 275 |
+ |
sprintf( painCave.errMsg, |
| 276 |
+ |
"A cutoff radius (rcut) must be specified when calculating Bond Order Parameters"); |
| 277 |
+ |
painCave.severity = OPENMD_ERROR; |
| 278 |
+ |
painCave.isFatal = 1; |
| 279 |
+ |
simError(); |
| 280 |
+ |
} |
| 281 |
+ |
} else if (args_info.bad_given){ |
| 282 |
+ |
if (args_info.rcut_given) { |
| 283 |
+ |
analyser = new BondAngleDistribution(info, dumpFileName, sele1, |
| 284 |
+ |
args_info.rcut_arg, |
| 285 |
+ |
args_info.nbins_arg); |
| 286 |
+ |
} else { |
| 287 |
+ |
sprintf( painCave.errMsg, |
| 288 |
+ |
"A cutoff radius (rcut) must be specified when calculating Bond Angle Distributions"); |
| 289 |
+ |
painCave.severity = OPENMD_ERROR; |
| 290 |
+ |
painCave.isFatal = 1; |
| 291 |
+ |
simError(); |
| 292 |
+ |
} |
| 293 |
+ |
} else if (args_info.scd_given) { |
| 294 |
+ |
if (batchMode) { |
| 295 |
+ |
analyser = new SCDOrderParameter(info, dumpFileName, |
| 296 |
+ |
args_info.molname_arg, |
| 297 |
+ |
args_info.begin_arg, args_info.end_arg); |
| 298 |
+ |
} else{ |
| 299 |
+ |
std::string sele3 = args_info.sele3_arg; |
| 300 |
+ |
analyser = new SCDOrderParameter(info, dumpFileName, |
| 301 |
+ |
sele1, sele2, sele3); |
| 302 |
+ |
} |
| 303 |
+ |
}else if (args_info.density_given) { |
| 304 |
+ |
analyser= new DensityPlot(info, dumpFileName, sele1, sele2, maxLen, |
| 305 |
+ |
args_info.nbins_arg); |
| 306 |
+ |
} else if (args_info.count_given) { |
| 307 |
+ |
analyser = new ObjectCount(info, dumpFileName, sele1 ); |
| 308 |
+ |
} else if (args_info.slab_density_given) { |
| 309 |
+ |
analyser = new RhoZ(info, dumpFileName, sele1, args_info.nbins_arg); |
| 310 |
+ |
} else if (args_info.rnemdz_given) { |
| 311 |
+ |
analyser = new RNEMDZ(info, dumpFileName, sele1, args_info.nbins_arg); |
| 312 |
+ |
} else if (args_info.rnemdr_given) { |
| 313 |
+ |
analyser = new RNEMDR(info, dumpFileName, sele1, args_info.nbins_arg); |
| 314 |
+ |
} else if (args_info.p_angle_given) { |
| 315 |
+ |
analyser = new pAngle(info, dumpFileName, sele1, args_info.nbins_arg); |
| 316 |
+ |
#if defined(HAVE_FFTW_H) || defined(HAVE_DFFTW_H) || defined(HAVE_FFTW3_H) |
| 317 |
+ |
}else if (args_info.hxy_given) { |
| 318 |
+ |
analyser = new Hxy(info, dumpFileName, sele1, args_info.nbins_x_arg, |
| 319 |
+ |
args_info.nbins_y_arg, args_info.nbins_arg); |
| 320 |
+ |
#endif |
| 321 |
+ |
}else if (args_info.rho_r_given) { |
| 322 |
+ |
if (args_info.radius_given){ |
| 323 |
+ |
analyser = new RhoR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg,args_info.radius_arg); |
| 324 |
+ |
}else{ |
| 325 |
+ |
sprintf( painCave.errMsg, |
| 326 |
+ |
"A particle radius (radius) must be specified when calculating Rho(r)"); |
| 327 |
+ |
painCave.severity = OPENMD_ERROR; |
| 328 |
+ |
painCave.isFatal = 1; |
| 329 |
+ |
simError(); |
| 330 |
+ |
} |
| 331 |
+ |
} else if (args_info.hullvol_given) { |
| 332 |
+ |
analyser = new NanoVolume(info, dumpFileName, sele1); |
| 333 |
+ |
} else if (args_info.rodlength_given) { |
| 334 |
+ |
analyser = new NanoLength(info, dumpFileName, sele1); |
| 335 |
+ |
} else if (args_info.angle_r_given) { |
| 336 |
+ |
analyser = new AngleR(info, dumpFileName, sele1, maxLen,args_info.nbins_arg); |
| 337 |
+ |
} |
| 338 |
+ |
|
| 339 |
|
if (args_info.output_given) { |
| 340 |
|
analyser->setOutputName(args_info.output_arg); |
| 341 |
|
} |
| 342 |
|
if (args_info.step_given) { |
| 343 |
|
analyser->setStep(args_info.step_arg); |
| 344 |
|
} |
| 345 |
< |
|
| 345 |
> |
|
| 346 |
|
analyser->process(); |
| 347 |
< |
|
| 347 |
> |
|
| 348 |
|
delete analyser; |
| 349 |
|
delete info; |
| 350 |
< |
|
| 350 |
> |
|
| 351 |
|
return 0; |
| 352 |
|
} |
| 164 |
– |
|
