| 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, 24107 (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 <cmath> |
| 46 |
|
#include "restraints/ObjectRestraint.hpp" |
| 47 |
|
#include "io/RestReader.hpp" |
| 48 |
|
#include "utils/simError.h" |
| 49 |
< |
#include "utils/OOPSEConstant.hpp" |
| 49 |
> |
#include "utils/PhysicalConstants.hpp" |
| 50 |
|
#include "utils/StringUtils.hpp" |
| 51 |
|
#include "selection/SelectionEvaluator.hpp" |
| 52 |
|
#include "selection/SelectionManager.hpp" |
| 55 |
|
#endif |
| 56 |
|
|
| 57 |
|
|
| 58 |
< |
namespace oopse { |
| 58 |
> |
namespace OpenMD { |
| 59 |
|
|
| 60 |
|
RestraintForceManager::RestraintForceManager(SimInfo* info): ForceManager(info) { |
| 61 |
|
|
| 79 |
|
restTime_ = simParam->getStatusTime(); |
| 80 |
|
} else { |
| 81 |
|
sprintf(painCave.errMsg, |
| 82 |
< |
"Restraint warning: If you use restraints without setting\n", |
| 83 |
< |
"\tstatusTime, no restraint data will be written to the rest\n", |
| 82 |
> |
"Restraint warning: If you use restraints without setting\n" |
| 83 |
> |
"\tstatusTime, no restraint data will be written to the rest\n" |
| 84 |
|
"\tfile.\n"); |
| 85 |
|
painCave.isFatal = 0; |
| 86 |
|
simError(); |
| 90 |
|
int nRestraintStamps = simParam->getNRestraintStamps(); |
| 91 |
|
std::vector<RestraintStamp*> stamp = simParam->getRestraintStamps(); |
| 92 |
|
|
| 93 |
+ |
std::vector<int> stuntDoubleIndex; |
| 94 |
+ |
|
| 95 |
|
for (int i = 0; i < nRestraintStamps; i++){ |
| 96 |
|
|
| 97 |
|
std::string myType = toUpperCopy(stamp[i]->getType()); |
| 112 |
|
molIndex = stamp[i]->getMolIndex(); |
| 113 |
|
} |
| 114 |
|
|
| 115 |
< |
Molecule* mol = info_->getMoleculeByGlobalIndex(molIndex); |
| 113 |
< |
|
| 114 |
< |
if (mol == NULL) { |
| 115 |
> |
if (molIndex < 0) { |
| 116 |
|
sprintf(painCave.errMsg, |
| 117 |
< |
"Restraint Error: A molecular restraint was specified, but\n" |
| 118 |
< |
"\tno molecule was found with global index %d.\n", |
| 118 |
< |
molIndex); |
| 117 |
> |
"Restraint Error: A molecular restraint was specified\n" |
| 118 |
> |
"\twith a molIndex that was less than 0\n"); |
| 119 |
|
painCave.isFatal = 1; |
| 120 |
|
simError(); |
| 121 |
+ |
} |
| 122 |
+ |
if (molIndex >= info_->getNGlobalMolecules()) { |
| 123 |
+ |
sprintf(painCave.errMsg, |
| 124 |
+ |
"Restraint Error: A molecular restraint was specified with\n" |
| 125 |
+ |
"\ta molIndex that was greater than the total number of molecules\n"); |
| 126 |
+ |
painCave.isFatal = 1; |
| 127 |
+ |
simError(); |
| 128 |
+ |
} |
| 129 |
+ |
|
| 130 |
+ |
Molecule* mol = info_->getMoleculeByGlobalIndex(molIndex); |
| 131 |
+ |
|
| 132 |
+ |
if (mol == NULL) { |
| 133 |
+ |
#ifdef IS_MPI |
| 134 |
+ |
// getMoleculeByGlobalIndex returns a NULL in parallel if |
| 135 |
+ |
// this proc doesn't have the molecule. Do a quick check to |
| 136 |
+ |
// make sure another processor is supposed to have it. |
| 137 |
+ |
|
| 138 |
+ |
int myrank = MPI::COMM_WORLD.Get_rank(); |
| 139 |
+ |
if (info_->getMolToProc(molIndex) == myrank) { |
| 140 |
+ |
|
| 141 |
+ |
// If we were supposed to have it but got a null, then freak out. |
| 142 |
+ |
#endif |
| 143 |
+ |
|
| 144 |
+ |
sprintf(painCave.errMsg, |
| 145 |
+ |
"Restraint Error: A molecular restraint was specified, but\n" |
| 146 |
+ |
"\tno molecule was found with global index %d.\n", |
| 147 |
+ |
molIndex); |
| 148 |
+ |
painCave.isFatal = 1; |
| 149 |
+ |
simError(); |
| 150 |
+ |
|
| 151 |
+ |
#ifdef IS_MPI |
| 152 |
+ |
} |
| 153 |
+ |
#endif |
| 154 |
|
} |
| 155 |
|
|
| 156 |
+ |
|
| 157 |
+ |
#ifdef IS_MPI |
| 158 |
+ |
// only handle this molecular restraint if this processor owns the |
| 159 |
+ |
// molecule |
| 160 |
+ |
int myrank = MPI::COMM_WORLD.Get_rank(); |
| 161 |
+ |
if (info_->getMolToProc(molIndex) == myrank) { |
| 162 |
+ |
|
| 163 |
+ |
#endif |
| 164 |
+ |
|
| 165 |
|
MolecularRestraint* rest = new MolecularRestraint(); |
| 166 |
|
|
| 167 |
|
std::string restPre("mol_"); |
| 190 |
|
if (stamp[i]->haveRestrainedSwingXAngle()) { |
| 191 |
|
rest->setRestrainedSwingXAngle(stamp[i]->getRestrainedSwingXAngle() * M_PI/180.0); |
| 192 |
|
} |
| 193 |
+ |
if (stamp[i]->havePrint()) { |
| 194 |
+ |
rest->setPrintRestraint(stamp[i]->getPrint()); |
| 195 |
+ |
} |
| 196 |
|
|
| 197 |
|
restraints_.push_back(rest); |
| 198 |
|
mol->addProperty(new RestraintData("Restraint", rest)); |
| 199 |
|
restrainedMols_.push_back(mol); |
| 200 |
< |
|
| 200 |
> |
#ifdef IS_MPI |
| 201 |
> |
} |
| 202 |
> |
#endif |
| 203 |
|
} else if (myType.compare("OBJECT") == 0) { |
| 204 |
|
|
| 205 |
|
std::string objectSelection; |
| 217 |
|
|
| 218 |
|
SelectionEvaluator evaluator(info); |
| 219 |
|
SelectionManager seleMan(info); |
| 220 |
< |
|
| 220 |
> |
|
| 221 |
|
evaluator.loadScriptString(objectSelection); |
| 222 |
|
seleMan.setSelectionSet(evaluator.evaluate()); |
| 223 |
|
int selectionCount = seleMan.getSelectionCount(); |
| 235 |
|
|
| 236 |
|
for (sd = seleMan.beginSelected(selei); sd != NULL; |
| 237 |
|
sd = seleMan.nextSelected(selei)) { |
| 238 |
< |
|
| 238 |
> |
stuntDoubleIndex.push_back(sd->getGlobalIntegrableObjectIndex()); |
| 239 |
> |
|
| 240 |
|
ObjectRestraint* rest = new ObjectRestraint(); |
| 241 |
|
|
| 242 |
|
if (stamp[i]->haveDisplacementSpringConstant()) { |
| 259 |
|
} |
| 260 |
|
if (stamp[i]->haveRestrainedSwingYAngle()) { |
| 261 |
|
rest->setRestrainedSwingYAngle(stamp[i]->getRestrainedSwingYAngle()); |
| 262 |
< |
} |
| 262 |
> |
} |
| 263 |
> |
if (stamp[i]->havePrint()) { |
| 264 |
> |
rest->setPrintRestraint(stamp[i]->getPrint()); |
| 265 |
> |
} |
| 266 |
> |
|
| 267 |
|
restraints_.push_back(rest); |
| 268 |
|
sd->addProperty(new RestraintData("Restraint", rest)); |
| 269 |
|
restrainedObjs_.push_back(sd); |
| 276 |
|
// are times when it won't use restraints at all, so only open the |
| 277 |
|
// restraint file if we are actually using restraints: |
| 278 |
|
|
| 279 |
< |
if (simParam->getUseRestraints()) { |
| 279 |
> |
if (simParam->getUseRestraints()) { |
| 280 |
|
std::string refFile = simParam->getRestraint_file(); |
| 281 |
< |
RestReader* rr = new RestReader(info, refFile); |
| 230 |
< |
|
| 281 |
> |
RestReader* rr = new RestReader(info, refFile, stuntDoubleIndex); |
| 282 |
|
rr->readReferenceStructure(); |
| 283 |
|
} |
| 284 |
|
|
| 285 |
|
restOutput_ = getPrefix(info_->getFinalConfigFileName()) + ".rest"; |
| 286 |
|
restOut = new RestWriter(info_, restOutput_.c_str(), restraints_); |
| 236 |
– |
|
| 287 |
|
if(!restOut){ |
| 288 |
|
sprintf(painCave.errMsg, "Restraint error: Failed to create RestWriter\n"); |
| 289 |
|
painCave.isFatal = 1; |
| 306 |
|
currRestTime_ = currSnapshot_->getTime(); |
| 307 |
|
} |
| 308 |
|
|
| 309 |
< |
void RestraintForceManager::calcForces(bool needPotential, bool needStress){ |
| 309 |
> |
void RestraintForceManager::calcForces(){ |
| 310 |
|
|
| 311 |
< |
ForceManager::calcForces(needPotential, needStress); |
| 311 |
> |
ForceManager::calcForces(); |
| 312 |
|
RealType restPot_local, restPot; |
| 313 |
|
|
| 314 |
|
restPot_local = doRestraints(1.0); |
| 320 |
|
restPot = restPot_local; |
| 321 |
|
#endif |
| 322 |
|
currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 323 |
< |
currSnapshot_->statData[Stats::LONG_RANGE_POTENTIAL] += restPot; |
| 324 |
< |
currSnapshot_->statData[Stats::VHARM] = restPot; |
| 323 |
> |
RealType pot = currSnapshot_->getLongRangePotential(); |
| 324 |
> |
pot += restPot; |
| 325 |
> |
currSnapshot_->setLongRangePotential(pot); |
| 326 |
> |
currSnapshot_->setRestraintPotential(restPot); |
| 327 |
|
|
| 328 |
|
//write out forces and current positions of restrained molecules |
| 329 |
|
if (currSnapshot_->getTime() >= currRestTime_){ |
| 363 |
|
if (mRest == NULL) { |
| 364 |
|
sprintf( painCave.errMsg, |
| 365 |
|
"Can not cast RestraintData to MolecularRestraint\n"); |
| 366 |
< |
painCave.severity = OOPSE_ERROR; |
| 366 |
> |
painCave.severity = OPENMD_ERROR; |
| 367 |
|
painCave.isFatal = 1; |
| 368 |
|
simError(); |
| 369 |
|
} |
| 370 |
|
} else { |
| 371 |
|
sprintf( painCave.errMsg, |
| 372 |
|
"Can not cast GenericData to RestraintData\n"); |
| 373 |
< |
painCave.severity = OOPSE_ERROR; |
| 373 |
> |
painCave.severity = OPENMD_ERROR; |
| 374 |
|
painCave.isFatal = 1; |
| 375 |
|
simError(); |
| 376 |
|
} |
| 377 |
|
} else { |
| 378 |
|
sprintf( painCave.errMsg, "Can not find Restraint for RestrainedObject\n"); |
| 379 |
< |
painCave.severity = OOPSE_ERROR; |
| 379 |
> |
painCave.severity = OPENMD_ERROR; |
| 380 |
|
painCave.isFatal = 1; |
| 381 |
|
simError(); |
| 382 |
|
} |
| 390 |
|
std::vector<Vector3d> forces; |
| 391 |
|
|
| 392 |
|
for(sd = (*rm)->beginIntegrableObject(ioi); sd != NULL; |
| 393 |
< |
sd = (*rm)->nextIntegrableObject(ioi)) { |
| 393 |
> |
sd = (*rm)->nextIntegrableObject(ioi)) { |
| 394 |
|
struc.push_back(sd->getPos()); |
| 395 |
|
} |
| 396 |
|
|
| 409 |
|
unscaledPotential_ += mRest->getUnscaledPotential(); |
| 410 |
|
|
| 411 |
|
restInfo = mRest->getRestraintInfo(); |
| 412 |
< |
restInfo_.push_back(restInfo); |
| 412 |
> |
|
| 413 |
> |
// only collect data on restraints that we're going to print: |
| 414 |
> |
if (mRest->getPrintRestraint()) |
| 415 |
> |
restInfo_.push_back(restInfo); |
| 416 |
|
} |
| 417 |
|
|
| 418 |
|
for(ro=restrainedObjs_.begin(); ro != restrainedObjs_.end(); ++ro){ |
| 428 |
|
if (oRest == NULL) { |
| 429 |
|
sprintf( painCave.errMsg, |
| 430 |
|
"Can not cast RestraintData to ObjectRestraint\n"); |
| 431 |
< |
painCave.severity = OOPSE_ERROR; |
| 431 |
> |
painCave.severity = OPENMD_ERROR; |
| 432 |
|
painCave.isFatal = 1; |
| 433 |
|
simError(); |
| 434 |
|
} |
| 435 |
|
} else { |
| 436 |
|
sprintf( painCave.errMsg, |
| 437 |
|
"Can not cast GenericData to RestraintData\n"); |
| 438 |
< |
painCave.severity = OOPSE_ERROR; |
| 438 |
> |
painCave.severity = OPENMD_ERROR; |
| 439 |
|
painCave.isFatal = 1; |
| 440 |
|
simError(); |
| 441 |
|
} |
| 442 |
|
} else { |
| 443 |
|
sprintf( painCave.errMsg, "Can not find Restraint for RestrainedObject\n"); |
| 444 |
< |
painCave.severity = OOPSE_ERROR; |
| 444 |
> |
painCave.severity = OPENMD_ERROR; |
| 445 |
|
painCave.isFatal = 1; |
| 446 |
|
simError(); |
| 447 |
|
} |
| 473 |
|
unscaledPotential_ += oRest->getUnscaledPotential(); |
| 474 |
|
|
| 475 |
|
restInfo = oRest->getRestraintInfo(); |
| 476 |
< |
restInfo_.push_back(restInfo); |
| 476 |
> |
|
| 477 |
> |
// only collect data on restraints that we're going to print: |
| 478 |
> |
if (oRest->getPrintRestraint()) |
| 479 |
> |
restInfo_.push_back(restInfo); |
| 480 |
|
} |
| 481 |
|
|
| 482 |
|
return unscaledPotential_ * scalingFactor; |
