| 1 |
/* |
| 2 |
* Copyright (c) 2005, 2009 The University of Notre Dame. All Rights Reserved. |
| 3 |
* |
| 4 |
* The University of Notre Dame grants you ("Licensee") a |
| 5 |
* non-exclusive, royalty free, license to use, modify and |
| 6 |
* redistribute this software in source and binary code form, provided |
| 7 |
* that the following conditions are met: |
| 8 |
* |
| 9 |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
* notice, this list of conditions and the following disclaimer. |
| 11 |
* |
| 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. |
| 16 |
* |
| 17 |
* This software is provided "AS IS," without a warranty of any |
| 18 |
* kind. All express or implied conditions, representations and |
| 19 |
* warranties, including any implied warranty of merchantability, |
| 20 |
* fitness for a particular purpose or non-infringement, are hereby |
| 21 |
* excluded. The University of Notre Dame and its licensors shall not |
| 22 |
* be liable for any damages suffered by licensee as a result of |
| 23 |
* using, modifying or distributing the software or its |
| 24 |
* derivatives. In no event will the University of Notre Dame or its |
| 25 |
* licensors be liable for any lost revenue, profit or data, or for |
| 26 |
* direct, indirect, special, consequential, incidental or punitive |
| 27 |
* damages, however caused and regardless of the theory of liability, |
| 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 |
/** |
| 44 |
* @file Stats.cpp |
| 45 |
* @author tlin |
| 46 |
* @date 11/04/2004 |
| 47 |
* @time 14:26am |
| 48 |
* @version 1.0 |
| 49 |
*/ |
| 50 |
|
| 51 |
#include "brains/Stats.hpp" |
| 52 |
#include "brains/Thermo.hpp" |
| 53 |
|
| 54 |
namespace OpenMD { |
| 55 |
|
| 56 |
Stats::Stats(SimInfo* info) : isInit_(false), info_(info) { |
| 57 |
|
| 58 |
if (!isInit_) { |
| 59 |
init(); |
| 60 |
isInit_ = true; |
| 61 |
} |
| 62 |
} |
| 63 |
|
| 64 |
void Stats::init() { |
| 65 |
|
| 66 |
data_.resize(Stats::ENDINDEX); |
| 67 |
|
| 68 |
StatsData time; |
| 69 |
time.units = "fs"; |
| 70 |
time.title = "Time"; |
| 71 |
time.dataType = "RealType"; |
| 72 |
time.accumulator = new Accumulator(); |
| 73 |
data_[TIME] = time; |
| 74 |
statsMap_["TIME"] = TIME; |
| 75 |
|
| 76 |
StatsData total_energy; |
| 77 |
total_energy.units = "kcal/mol"; |
| 78 |
total_energy.title = "Total Energy"; |
| 79 |
total_energy.dataType = "RealType"; |
| 80 |
total_energy.accumulator = new Accumulator(); |
| 81 |
data_[TOTAL_ENERGY] = total_energy; |
| 82 |
statsMap_["TOTAL_ENERGY"] = TOTAL_ENERGY; |
| 83 |
|
| 84 |
StatsData potential_energy; |
| 85 |
potential_energy.units = "kcal/mol"; |
| 86 |
potential_energy.title = "Potential Energy"; |
| 87 |
potential_energy.dataType = "RealType"; |
| 88 |
potential_energy.accumulator = new Accumulator(); |
| 89 |
data_[POTENTIAL_ENERGY] = potential_energy; |
| 90 |
statsMap_["POTENTIAL_ENERGY"] = POTENTIAL_ENERGY; |
| 91 |
|
| 92 |
StatsData kinetic_energy; |
| 93 |
kinetic_energy.units = "kcal/mol"; |
| 94 |
kinetic_energy.title = "Kinetic Energy"; |
| 95 |
kinetic_energy.dataType = "RealType"; |
| 96 |
kinetic_energy.accumulator = new Accumulator(); |
| 97 |
data_[KINETIC_ENERGY] = kinetic_energy; |
| 98 |
statsMap_["KINETIC_ENERGY"] = KINETIC_ENERGY; |
| 99 |
|
| 100 |
StatsData temperature; |
| 101 |
temperature.units = "K"; |
| 102 |
temperature.title = "Temperature"; |
| 103 |
temperature.dataType = "RealType"; |
| 104 |
temperature.accumulator = new Accumulator(); |
| 105 |
data_[TEMPERATURE] = temperature; |
| 106 |
statsMap_["TEMPERATURE"] = TEMPERATURE; |
| 107 |
|
| 108 |
StatsData pressure; |
| 109 |
pressure.units = "atm"; |
| 110 |
pressure.title = "Pressure"; |
| 111 |
pressure.dataType = "RealType"; |
| 112 |
pressure.accumulator = new Accumulator(); |
| 113 |
data_[PRESSURE] = pressure; |
| 114 |
statsMap_["PRESSURE"] = PRESSURE; |
| 115 |
|
| 116 |
StatsData volume; |
| 117 |
volume.units = "A^3"; |
| 118 |
volume.title = "Volume"; |
| 119 |
volume.dataType = "RealType"; |
| 120 |
volume.accumulator = new Accumulator(); |
| 121 |
data_[VOLUME] = volume; |
| 122 |
statsMap_["VOLUME"] = VOLUME; |
| 123 |
|
| 124 |
StatsData hullvolume; |
| 125 |
hullvolume.units = "A^3"; |
| 126 |
hullvolume.title = "Hull Volume"; |
| 127 |
hullvolume.dataType = "RealType"; |
| 128 |
hullvolume.accumulator = new Accumulator(); |
| 129 |
data_[HULLVOLUME] = hullvolume; |
| 130 |
statsMap_["HULLVOLUME"] = HULLVOLUME; |
| 131 |
|
| 132 |
StatsData gyrvolume; |
| 133 |
gyrvolume.units = "A^3"; |
| 134 |
gyrvolume.title = "Gyrational Volume"; |
| 135 |
gyrvolume.dataType = "RealType"; |
| 136 |
gyrvolume.accumulator = new Accumulator(); |
| 137 |
data_[GYRVOLUME] = gyrvolume; |
| 138 |
statsMap_["GYRVOLUME"] = GYRVOLUME; |
| 139 |
|
| 140 |
StatsData conserved_quantity; |
| 141 |
conserved_quantity.units = "kcal/mol"; |
| 142 |
conserved_quantity.title = "Conserved Quantity"; |
| 143 |
conserved_quantity.dataType = "RealType"; |
| 144 |
conserved_quantity.accumulator = new Accumulator(); |
| 145 |
data_[CONSERVED_QUANTITY] = conserved_quantity; |
| 146 |
statsMap_["CONSERVED_QUANTITY"] = CONSERVED_QUANTITY; |
| 147 |
|
| 148 |
StatsData translational_kinetic; |
| 149 |
translational_kinetic.units = "kcal/mol"; |
| 150 |
translational_kinetic.title = "Translational Kinetic"; |
| 151 |
translational_kinetic.dataType = "RealType"; |
| 152 |
translational_kinetic.accumulator = new Accumulator(); |
| 153 |
data_[TRANSLATIONAL_KINETIC] = translational_kinetic; |
| 154 |
statsMap_["TRANSLATIONAL_KINETIC"] = TRANSLATIONAL_KINETIC; |
| 155 |
|
| 156 |
StatsData rotational_kinetic; |
| 157 |
rotational_kinetic.units = "kcal/mol"; |
| 158 |
rotational_kinetic.title = "Rotational Kinetic"; |
| 159 |
rotational_kinetic.dataType = "RealType"; |
| 160 |
rotational_kinetic.accumulator = new Accumulator(); |
| 161 |
data_[ROTATIONAL_KINETIC] = rotational_kinetic; |
| 162 |
statsMap_["ROTATIONAL_KINETIC"] = ROTATIONAL_KINETIC; |
| 163 |
|
| 164 |
StatsData long_range_potential; |
| 165 |
long_range_potential.units = "kcal/mol"; |
| 166 |
long_range_potential.title = "Long Range Potential"; |
| 167 |
long_range_potential.dataType = "RealType"; |
| 168 |
long_range_potential.accumulator = new Accumulator(); |
| 169 |
data_[LONG_RANGE_POTENTIAL] = long_range_potential; |
| 170 |
statsMap_["LONG_RANGE_POTENTIAL"] = LONG_RANGE_POTENTIAL; |
| 171 |
|
| 172 |
StatsData vanderwaals_potential; |
| 173 |
vanderwaals_potential.units = "kcal/mol"; |
| 174 |
vanderwaals_potential.title = "van der waals Potential"; |
| 175 |
vanderwaals_potential.dataType = "RealType"; |
| 176 |
vanderwaals_potential.accumulator = new Accumulator(); |
| 177 |
data_[VANDERWAALS_POTENTIAL] = vanderwaals_potential; |
| 178 |
statsMap_["VANDERWAALS_POTENTIAL"] = VANDERWAALS_POTENTIAL; |
| 179 |
|
| 180 |
StatsData electrostatic_potential; |
| 181 |
electrostatic_potential.units = "kcal/mol"; |
| 182 |
electrostatic_potential.title = "Electrostatic Potential"; |
| 183 |
electrostatic_potential.dataType = "RealType"; |
| 184 |
electrostatic_potential.accumulator = new Accumulator(); |
| 185 |
data_[ELECTROSTATIC_POTENTIAL] = electrostatic_potential; |
| 186 |
statsMap_["ELECTROSTATIC_POTENTIAL"] = ELECTROSTATIC_POTENTIAL; |
| 187 |
|
| 188 |
StatsData metallic_potential; |
| 189 |
metallic_potential.units = "kcal/mol"; |
| 190 |
metallic_potential.title = "Metallic Potential"; |
| 191 |
metallic_potential.dataType = "RealType"; |
| 192 |
metallic_potential.accumulator = new Accumulator(); |
| 193 |
data_[METALLIC_POTENTIAL] = metallic_potential; |
| 194 |
statsMap_["METALLIC_POTENTIAL"] = METALLIC_POTENTIAL; |
| 195 |
|
| 196 |
StatsData hydrogenbonding_potential; |
| 197 |
hydrogenbonding_potential.units = "kcal/mol"; |
| 198 |
hydrogenbonding_potential.title = "Hydrogen Bonding Potential"; |
| 199 |
hydrogenbonding_potential.dataType = "RealType"; |
| 200 |
hydrogenbonding_potential.accumulator = new Accumulator(); |
| 201 |
data_[HYDROGENBONDING_POTENTIAL] = hydrogenbonding_potential; |
| 202 |
statsMap_["HYDROGENBONDING_POTENTIAL"] = HYDROGENBONDING_POTENTIAL; |
| 203 |
|
| 204 |
StatsData reciprocal_potential; |
| 205 |
reciprocal_potential.units = "kcal/mol"; |
| 206 |
reciprocal_potential.title = "Reciprocal Space Potential"; |
| 207 |
reciprocal_potential.dataType = "RealType"; |
| 208 |
reciprocal_potential.accumulator = new Accumulator(); |
| 209 |
data_[RECIPROCAL_POTENTIAL] = reciprocal_potential; |
| 210 |
statsMap_["RECIPROCAL_POTENTIAL"] = RECIPROCAL_POTENTIAL; |
| 211 |
|
| 212 |
StatsData short_range_potential; |
| 213 |
short_range_potential.units = "kcal/mol"; |
| 214 |
short_range_potential.title = "Short Range Potential"; |
| 215 |
short_range_potential.dataType = "RealType"; |
| 216 |
short_range_potential.accumulator = new Accumulator(); |
| 217 |
data_[SHORT_RANGE_POTENTIAL] = short_range_potential; |
| 218 |
statsMap_["SHORT_RANGE_POTENTIAL"] = SHORT_RANGE_POTENTIAL; |
| 219 |
|
| 220 |
StatsData bond_potential; |
| 221 |
bond_potential.units = "kcal/mol"; |
| 222 |
bond_potential.title = "Bond Potential"; |
| 223 |
bond_potential.dataType = "RealType"; |
| 224 |
bond_potential.accumulator = new Accumulator(); |
| 225 |
data_[BOND_POTENTIAL] = bond_potential; |
| 226 |
statsMap_["BOND_POTENTIAL"] = BOND_POTENTIAL; |
| 227 |
|
| 228 |
StatsData bend_potential; |
| 229 |
bend_potential.units = "kcal/mol"; |
| 230 |
bend_potential.title = "Bend Potential"; |
| 231 |
bend_potential.dataType = "RealType"; |
| 232 |
bend_potential.accumulator = new Accumulator(); |
| 233 |
data_[BEND_POTENTIAL] = bend_potential; |
| 234 |
statsMap_["BEND_POTENTIAL"] = BEND_POTENTIAL; |
| 235 |
|
| 236 |
StatsData dihedral_potential; |
| 237 |
dihedral_potential.units = "kcal/mol"; |
| 238 |
dihedral_potential.title = "Dihedral Potential"; |
| 239 |
dihedral_potential.dataType = "RealType"; |
| 240 |
dihedral_potential.accumulator = new Accumulator(); |
| 241 |
data_[DIHEDRAL_POTENTIAL] = dihedral_potential; |
| 242 |
statsMap_["DIHEDRAL_POTENTIAL"] = DIHEDRAL_POTENTIAL; |
| 243 |
|
| 244 |
StatsData inversion_potential; |
| 245 |
inversion_potential.units = "kcal/mol"; |
| 246 |
inversion_potential.title = "Inversion Potential"; |
| 247 |
inversion_potential.dataType = "RealType"; |
| 248 |
inversion_potential.accumulator = new Accumulator(); |
| 249 |
data_[INVERSION_POTENTIAL] = inversion_potential; |
| 250 |
statsMap_["INVERSION_POTENTIAL"] = INVERSION_POTENTIAL; |
| 251 |
|
| 252 |
StatsData vraw; |
| 253 |
vraw.units = "kcal/mol"; |
| 254 |
vraw.title = "Raw Potential"; |
| 255 |
vraw.dataType = "RealType"; |
| 256 |
vraw.accumulator = new Accumulator(); |
| 257 |
data_[RAW_POTENTIAL] = vraw; |
| 258 |
statsMap_["RAW_POTENTIAL"] = RAW_POTENTIAL; |
| 259 |
|
| 260 |
StatsData vrestraint; |
| 261 |
vrestraint.units = "kcal/mol"; |
| 262 |
vrestraint.title = "Restraint Potential"; |
| 263 |
vrestraint.dataType = "RealType"; |
| 264 |
vrestraint.accumulator = new Accumulator(); |
| 265 |
data_[RESTRAINT_POTENTIAL] = vrestraint; |
| 266 |
statsMap_["RESTRAINT_POTENTIAL"] = RESTRAINT_POTENTIAL; |
| 267 |
|
| 268 |
StatsData pressure_tensor; |
| 269 |
pressure_tensor.units = "amu*fs^-2*Ang^-1"; |
| 270 |
pressure_tensor.title = "Ptensor"; |
| 271 |
pressure_tensor.dataType = "Mat3x3d"; |
| 272 |
pressure_tensor.accumulator = new MatrixAccumulator(); |
| 273 |
data_[PRESSURE_TENSOR] = pressure_tensor; |
| 274 |
statsMap_["PRESSURE_TENSOR"] = PRESSURE_TENSOR; |
| 275 |
|
| 276 |
StatsData system_dipole; |
| 277 |
system_dipole.units = "C*m"; |
| 278 |
system_dipole.title = "System Dipole"; |
| 279 |
system_dipole.dataType = "Vector3d"; |
| 280 |
system_dipole.accumulator = new VectorAccumulator(); |
| 281 |
data_[SYSTEM_DIPOLE] = system_dipole; |
| 282 |
statsMap_["SYSTEM_DIPOLE"] = SYSTEM_DIPOLE; |
| 283 |
|
| 284 |
StatsData tagged_pair_distance; |
| 285 |
tagged_pair_distance.units = "Ang"; |
| 286 |
tagged_pair_distance.title = "Tagged_Pair_Distance"; |
| 287 |
tagged_pair_distance.dataType = "RealType"; |
| 288 |
tagged_pair_distance.accumulator = new Accumulator(); |
| 289 |
data_[TAGGED_PAIR_DISTANCE] = tagged_pair_distance; |
| 290 |
statsMap_["TAGGED_PAIR_DISTANCE"] = TAGGED_PAIR_DISTANCE; |
| 291 |
|
| 292 |
StatsData shadowh; |
| 293 |
shadowh.units = "kcal/mol"; |
| 294 |
shadowh.title = "Shadow Hamiltonian"; |
| 295 |
shadowh.dataType = "RealType"; |
| 296 |
shadowh.accumulator = new Accumulator(); |
| 297 |
data_[SHADOWH] = shadowh; |
| 298 |
statsMap_["SHADOWH"] = SHADOWH; |
| 299 |
|
| 300 |
StatsData helfandmoment; |
| 301 |
helfandmoment.units = "Ang*kcal/mol"; |
| 302 |
helfandmoment.title = "Thermal Helfand Moment"; |
| 303 |
helfandmoment.dataType = "Vector3d"; |
| 304 |
helfandmoment.accumulator = new VectorAccumulator(); |
| 305 |
data_[HELFANDMOMENT] = helfandmoment; |
| 306 |
statsMap_["HELFANDMOMENT"] = HELFANDMOMENT; |
| 307 |
|
| 308 |
StatsData heatflux; |
| 309 |
heatflux.units = "amu/fs^3"; |
| 310 |
heatflux.title = "Heat Flux"; |
| 311 |
heatflux.dataType = "Vector3d"; |
| 312 |
heatflux.accumulator = new VectorAccumulator(); |
| 313 |
data_[HEATFLUX] = heatflux; |
| 314 |
statsMap_["HEATFLUX"] = HEATFLUX; |
| 315 |
|
| 316 |
StatsData electronic_temperature; |
| 317 |
electronic_temperature.units = "K"; |
| 318 |
electronic_temperature.title = "Electronic Temperature"; |
| 319 |
electronic_temperature.dataType = "RealType"; |
| 320 |
electronic_temperature.accumulator = new Accumulator(); |
| 321 |
data_[ELECTRONIC_TEMPERATURE] = electronic_temperature; |
| 322 |
statsMap_["ELECTRONIC_TEMPERATURE"] = ELECTRONIC_TEMPERATURE; |
| 323 |
|
| 324 |
StatsData com; |
| 325 |
com.units = "A"; |
| 326 |
com.title = "Center of Mass"; |
| 327 |
com.dataType = "Vector3d"; |
| 328 |
com.accumulator = new VectorAccumulator(); |
| 329 |
data_[COM] = com; |
| 330 |
statsMap_["COM"] = COM; |
| 331 |
|
| 332 |
StatsData comVel; |
| 333 |
comVel.units = "A/fs"; |
| 334 |
comVel.title = "Center of Mass Velocity"; |
| 335 |
comVel.dataType = "Vector3d"; |
| 336 |
comVel.accumulator = new VectorAccumulator(); |
| 337 |
data_[COM_VELOCITY] = comVel; |
| 338 |
statsMap_["COM_VELOCITY"] = COM_VELOCITY; |
| 339 |
|
| 340 |
StatsData angMom; |
| 341 |
angMom.units = "amu A^2/fs"; |
| 342 |
angMom.title = "Angular Momentum"; |
| 343 |
angMom.dataType = "Vector3d"; |
| 344 |
angMom.accumulator = new VectorAccumulator(); |
| 345 |
data_[ANGULAR_MOMENTUM] = angMom; |
| 346 |
statsMap_["ANGULAR_MOMENTUM"] = ANGULAR_MOMENTUM; |
| 347 |
|
| 348 |
// Now, set some defaults in the mask: |
| 349 |
|
| 350 |
Globals* simParams = info_->getSimParams(); |
| 351 |
std::string statFileFormatString = simParams->getStatFileFormat(); |
| 352 |
parseStatFileFormat(statFileFormatString); |
| 353 |
|
| 354 |
// if we're doing a thermodynamic integration, we'll want the raw |
| 355 |
// potential as well as the full potential: |
| 356 |
|
| 357 |
if (simParams->getUseThermodynamicIntegration()) |
| 358 |
statsMask_.set(RAW_POTENTIAL); |
| 359 |
|
| 360 |
// if we've got restraints turned on, we'll also want a report of the |
| 361 |
// total harmonic restraints |
| 362 |
if (simParams->getUseRestraints()){ |
| 363 |
statsMask_.set(RESTRAINT_POTENTIAL); |
| 364 |
} |
| 365 |
|
| 366 |
if (simParams->havePrintPressureTensor() && |
| 367 |
simParams->getPrintPressureTensor()){ |
| 368 |
statsMask_.set(PRESSURE_TENSOR); |
| 369 |
} |
| 370 |
|
| 371 |
// Why do we have both of these? |
| 372 |
if (simParams->getAccumulateBoxDipole()) { |
| 373 |
statsMask_.set(SYSTEM_DIPOLE); |
| 374 |
} |
| 375 |
if (info_->getCalcBoxDipole()){ |
| 376 |
statsMask_.set(SYSTEM_DIPOLE); |
| 377 |
} |
| 378 |
|
| 379 |
if (simParams->havePrintHeatFlux()) { |
| 380 |
if (simParams->getPrintHeatFlux()){ |
| 381 |
statsMask_.set(HEATFLUX); |
| 382 |
} |
| 383 |
} |
| 384 |
|
| 385 |
|
| 386 |
if (simParams->haveTaggedAtomPair() && simParams->havePrintTaggedPairDistance()) { |
| 387 |
if (simParams->getPrintTaggedPairDistance()) { |
| 388 |
statsMask_.set(TAGGED_PAIR_DISTANCE); |
| 389 |
} |
| 390 |
} |
| 391 |
|
| 392 |
} |
| 393 |
|
| 394 |
void Stats::parseStatFileFormat(const std::string& format) { |
| 395 |
StringTokenizer tokenizer(format, " ,;|\t\n\r"); |
| 396 |
|
| 397 |
while(tokenizer.hasMoreTokens()) { |
| 398 |
std::string token(tokenizer.nextToken()); |
| 399 |
toUpper(token); |
| 400 |
StatsMapType::iterator i = statsMap_.find(token); |
| 401 |
if (i != statsMap_.end()) { |
| 402 |
statsMask_.set(i->second); |
| 403 |
} else { |
| 404 |
sprintf( painCave.errMsg, |
| 405 |
"Stats::parseStatFileFormat: %s is not a recognized\n" |
| 406 |
"\tstatFileFormat keyword.\n", token.c_str() ); |
| 407 |
painCave.isFatal = 0; |
| 408 |
painCave.severity = OPENMD_ERROR; |
| 409 |
simError(); |
| 410 |
} |
| 411 |
} |
| 412 |
} |
| 413 |
|
| 414 |
Stats::~Stats() { |
| 415 |
data_.clear(); |
| 416 |
statsMap_.clear(); |
| 417 |
} |
| 418 |
|
| 419 |
std::string Stats::getTitle(int index) { |
| 420 |
assert(index >=0 && index < ENDINDEX); |
| 421 |
return data_[index].title; |
| 422 |
} |
| 423 |
|
| 424 |
std::string Stats::getUnits(int index) { |
| 425 |
assert(index >=0 && index < ENDINDEX); |
| 426 |
return data_[index].units; |
| 427 |
} |
| 428 |
|
| 429 |
std::string Stats::getDataType(int index) { |
| 430 |
assert(index >=0 && index < ENDINDEX); |
| 431 |
return data_[index].dataType; |
| 432 |
} |
| 433 |
|
| 434 |
void Stats::collectStats(){ |
| 435 |
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 436 |
Thermo thermo(info_); |
| 437 |
|
| 438 |
for (unsigned int i = 0; i < statsMask_.size(); ++i) { |
| 439 |
if (statsMask_[i]) { |
| 440 |
switch (i) { |
| 441 |
case TIME: |
| 442 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getTime()); |
| 443 |
break; |
| 444 |
case KINETIC_ENERGY: |
| 445 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getKinetic()); |
| 446 |
break; |
| 447 |
case POTENTIAL_ENERGY: |
| 448 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getPotential()); |
| 449 |
break; |
| 450 |
case TOTAL_ENERGY: |
| 451 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTotalEnergy()); |
| 452 |
break; |
| 453 |
case TEMPERATURE: |
| 454 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTemperature()); |
| 455 |
break; |
| 456 |
case PRESSURE: |
| 457 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getPressure()); |
| 458 |
break; |
| 459 |
case VOLUME: |
| 460 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getVolume()); |
| 461 |
break; |
| 462 |
case CONSERVED_QUANTITY: |
| 463 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getConservedQuantity()); |
| 464 |
break; |
| 465 |
case PRESSURE_TENSOR: |
| 466 |
dynamic_cast<MatrixAccumulator *>(data_[i].accumulator)->add(thermo.getPressureTensor()); |
| 467 |
break; |
| 468 |
case SYSTEM_DIPOLE: |
| 469 |
dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getSystemDipole()); |
| 470 |
break; |
| 471 |
case HEATFLUX: |
| 472 |
dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getHeatFlux()); |
| 473 |
break; |
| 474 |
case HULLVOLUME: |
| 475 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getHullVolume()); |
| 476 |
break; |
| 477 |
case GYRVOLUME: |
| 478 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getGyrationalVolume()); |
| 479 |
break; |
| 480 |
case TRANSLATIONAL_KINETIC: |
| 481 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTranslationalKinetic()); |
| 482 |
break; |
| 483 |
case ROTATIONAL_KINETIC: |
| 484 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getRotationalKinetic()); |
| 485 |
break; |
| 486 |
case LONG_RANGE_POTENTIAL: |
| 487 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotential()); |
| 488 |
break; |
| 489 |
case VANDERWAALS_POTENTIAL: |
| 490 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[VANDERWAALS_FAMILY]); |
| 491 |
break; |
| 492 |
case ELECTROSTATIC_POTENTIAL: |
| 493 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[ELECTROSTATIC_FAMILY]); |
| 494 |
break; |
| 495 |
case METALLIC_POTENTIAL: |
| 496 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[METALLIC_FAMILY]); |
| 497 |
break; |
| 498 |
case HYDROGENBONDING_POTENTIAL: |
| 499 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getLongRangePotentials()[HYDROGENBONDING_FAMILY]); |
| 500 |
break; |
| 501 |
case RECIPROCAL_POTENTIAL: |
| 502 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getReciprocalPotential()); |
| 503 |
break; |
| 504 |
case SHORT_RANGE_POTENTIAL: |
| 505 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getShortRangePotential()); |
| 506 |
break; |
| 507 |
case BOND_POTENTIAL: |
| 508 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getBondPotential()); |
| 509 |
break; |
| 510 |
case BEND_POTENTIAL: |
| 511 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getBendPotential()); |
| 512 |
break; |
| 513 |
case DIHEDRAL_POTENTIAL: |
| 514 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getTorsionPotential()); |
| 515 |
break; |
| 516 |
case INVERSION_POTENTIAL: |
| 517 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getInversionPotential()); |
| 518 |
break; |
| 519 |
case RAW_POTENTIAL: |
| 520 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getRawPotential()); |
| 521 |
break; |
| 522 |
case RESTRAINT_POTENTIAL: |
| 523 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(snap->getRestraintPotential()); |
| 524 |
break; |
| 525 |
case TAGGED_PAIR_DISTANCE: |
| 526 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getTaggedAtomPairDistance()); |
| 527 |
break; |
| 528 |
case ELECTRONIC_TEMPERATURE: |
| 529 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getElectronicTemperature()); |
| 530 |
break; |
| 531 |
case COM: |
| 532 |
dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getCom()); |
| 533 |
break; |
| 534 |
case COM_VELOCITY: |
| 535 |
dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getComVel()); |
| 536 |
break; |
| 537 |
case ANGULAR_MOMENTUM: |
| 538 |
dynamic_cast<VectorAccumulator *>(data_[i].accumulator)->add(thermo.getAngularMomentum()); |
| 539 |
break; |
| 540 |
/* |
| 541 |
case SHADOWH: |
| 542 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getShadowHamiltionian()); |
| 543 |
break; |
| 544 |
case HELFANDMOMENT: |
| 545 |
dynamic_cast<Accumulator *>(data_[i].accumulator)->add(thermo.getHelfandMoment()); |
| 546 |
break; |
| 547 |
*/ |
| 548 |
} |
| 549 |
} |
| 550 |
} |
| 551 |
} |
| 552 |
|
| 553 |
int Stats::getIntData(int index) { |
| 554 |
assert(index >=0 && index < ENDINDEX); |
| 555 |
RealType value; |
| 556 |
dynamic_cast<Accumulator *>(data_[index].accumulator)->getLastValue(value); |
| 557 |
return (int) value; |
| 558 |
} |
| 559 |
RealType Stats::getRealData(int index) { |
| 560 |
assert(index >=0 && index < ENDINDEX); |
| 561 |
RealType value(0.0); |
| 562 |
dynamic_cast<Accumulator *>(data_[index].accumulator)->getLastValue(value); |
| 563 |
return value; |
| 564 |
} |
| 565 |
Vector3d Stats::getVectorData(int index) { |
| 566 |
assert(index >=0 && index < ENDINDEX); |
| 567 |
Vector3d value; |
| 568 |
dynamic_cast<VectorAccumulator*>(data_[index].accumulator)->getLastValue(value); |
| 569 |
return value; |
| 570 |
} |
| 571 |
Mat3x3d Stats::getMatrixData(int index) { |
| 572 |
assert(index >=0 && index < ENDINDEX); |
| 573 |
Mat3x3d value; |
| 574 |
dynamic_cast<MatrixAccumulator*>(data_[index].accumulator)->getLastValue(value); |
| 575 |
return value; |
| 576 |
} |
| 577 |
|
| 578 |
Stats::StatsBitSet Stats::getStatsMask() { |
| 579 |
return statsMask_; |
| 580 |
} |
| 581 |
Stats::StatsMapType Stats::getStatsMap() { |
| 582 |
return statsMap_; |
| 583 |
} |
| 584 |
void Stats::setStatsMask(Stats::StatsBitSet mask) { |
| 585 |
statsMask_ = mask; |
| 586 |
} |
| 587 |
|
| 588 |
} |
