| 1 |
/* |
| 2 |
* Copyright (c) 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, 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 "config.h" |
| 44 |
#include <cmath> |
| 45 |
|
| 46 |
#include "restraints/RestraintForceManager.hpp" |
| 47 |
#include "restraints/MolecularRestraint.hpp" |
| 48 |
#include "restraints/ObjectRestraint.hpp" |
| 49 |
#include "io/RestReader.hpp" |
| 50 |
#include "utils/simError.h" |
| 51 |
#include "utils/PhysicalConstants.hpp" |
| 52 |
#include "utils/StringUtils.hpp" |
| 53 |
#include "selection/SelectionEvaluator.hpp" |
| 54 |
#include "selection/SelectionManager.hpp" |
| 55 |
#ifdef IS_MPI |
| 56 |
#include <mpi.h> |
| 57 |
#endif |
| 58 |
|
| 59 |
|
| 60 |
namespace OpenMD { |
| 61 |
|
| 62 |
RestraintForceManager::RestraintForceManager(SimInfo* info): ForceManager(info) { |
| 63 |
|
| 64 |
// order of affairs: |
| 65 |
// |
| 66 |
// 1) create restraints from the restraintStamps found in the MD |
| 67 |
// file. |
| 68 |
// |
| 69 |
// 2) Create RestraintReader to parse the input files for the ideal |
| 70 |
// structures. This reader will set reference structures, and will |
| 71 |
// calculate molecular centers of mass, etc. |
| 72 |
// |
| 73 |
// 3) sit around and wait for calcForces to be called. When it comes, |
| 74 |
// call the normal force manager calcForces, then loop through the |
| 75 |
// restrained objects and do their restraint forces. |
| 76 |
|
| 77 |
currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 78 |
Globals* simParam = info_->getSimParams(); |
| 79 |
|
| 80 |
if (simParam->haveStatusTime()){ |
| 81 |
restTime_ = simParam->getStatusTime(); |
| 82 |
} else { |
| 83 |
sprintf(painCave.errMsg, |
| 84 |
"Restraint warning: If you use restraints without setting\n" |
| 85 |
"\tstatusTime, no restraint data will be written to the rest\n" |
| 86 |
"\tfile.\n"); |
| 87 |
painCave.isFatal = 0; |
| 88 |
simError(); |
| 89 |
restTime_ = simParam->getRunTime(); |
| 90 |
} |
| 91 |
|
| 92 |
int nRestraintStamps = simParam->getNRestraintStamps(); |
| 93 |
std::vector<RestraintStamp*> stamp = simParam->getRestraintStamps(); |
| 94 |
|
| 95 |
std::vector<int> stuntDoubleIndex; |
| 96 |
|
| 97 |
for (int i = 0; i < nRestraintStamps; i++){ |
| 98 |
|
| 99 |
std::string myType = toUpperCopy(stamp[i]->getType()); |
| 100 |
|
| 101 |
if (myType.compare("MOLECULAR")==0){ |
| 102 |
|
| 103 |
int molIndex; |
| 104 |
std::vector<Vector3d> ref; |
| 105 |
Vector3d refCom; |
| 106 |
|
| 107 |
if (!stamp[i]->haveMolIndex()) { |
| 108 |
sprintf(painCave.errMsg, |
| 109 |
"Restraint Error: A molecular restraint was specified\n" |
| 110 |
"\twithout providing a value for molIndex.\n"); |
| 111 |
painCave.isFatal = 1; |
| 112 |
simError(); |
| 113 |
} else { |
| 114 |
molIndex = stamp[i]->getMolIndex(); |
| 115 |
} |
| 116 |
|
| 117 |
if (molIndex < 0) { |
| 118 |
sprintf(painCave.errMsg, |
| 119 |
"Restraint Error: A molecular restraint was specified\n" |
| 120 |
"\twith a molIndex that was less than 0\n"); |
| 121 |
painCave.isFatal = 1; |
| 122 |
simError(); |
| 123 |
} |
| 124 |
if (molIndex >= info_->getNGlobalMolecules()) { |
| 125 |
sprintf(painCave.errMsg, |
| 126 |
"Restraint Error: A molecular restraint was specified with\n" |
| 127 |
"\ta molIndex that was greater than the total number of molecules\n"); |
| 128 |
painCave.isFatal = 1; |
| 129 |
simError(); |
| 130 |
} |
| 131 |
|
| 132 |
Molecule* mol = info_->getMoleculeByGlobalIndex(molIndex); |
| 133 |
|
| 134 |
if (mol == NULL) { |
| 135 |
#ifdef IS_MPI |
| 136 |
// getMoleculeByGlobalIndex returns a NULL in parallel if |
| 137 |
// this proc doesn't have the molecule. Do a quick check to |
| 138 |
// make sure another processor is supposed to have it. |
| 139 |
|
| 140 |
int myrank = MPI::COMM_WORLD.Get_rank(); |
| 141 |
if (info_->getMolToProc(molIndex) == myrank) { |
| 142 |
|
| 143 |
// If we were supposed to have it but got a null, then freak out. |
| 144 |
#endif |
| 145 |
|
| 146 |
sprintf(painCave.errMsg, |
| 147 |
"Restraint Error: A molecular restraint was specified, but\n" |
| 148 |
"\tno molecule was found with global index %d.\n", |
| 149 |
molIndex); |
| 150 |
painCave.isFatal = 1; |
| 151 |
simError(); |
| 152 |
|
| 153 |
#ifdef IS_MPI |
| 154 |
} |
| 155 |
#endif |
| 156 |
} |
| 157 |
|
| 158 |
|
| 159 |
#ifdef IS_MPI |
| 160 |
// only handle this molecular restraint if this processor owns the |
| 161 |
// molecule |
| 162 |
int myrank = MPI::COMM_WORLD.Get_rank(); |
| 163 |
if (info_->getMolToProc(molIndex) == myrank) { |
| 164 |
|
| 165 |
#endif |
| 166 |
|
| 167 |
MolecularRestraint* rest = new MolecularRestraint(); |
| 168 |
|
| 169 |
std::string restPre("mol_"); |
| 170 |
std::stringstream restName; |
| 171 |
restName << restPre << molIndex; |
| 172 |
rest->setRestraintName(restName.str()); |
| 173 |
|
| 174 |
if (stamp[i]->haveDisplacementSpringConstant()) { |
| 175 |
rest->setDisplacementForceConstant(stamp[i]->getDisplacementSpringConstant()); |
| 176 |
} |
| 177 |
if (stamp[i]->haveTwistSpringConstant()) { |
| 178 |
rest->setTwistForceConstant(stamp[i]->getTwistSpringConstant()); |
| 179 |
} |
| 180 |
if (stamp[i]->haveSwingXSpringConstant()) { |
| 181 |
rest->setSwingXForceConstant(stamp[i]->getSwingXSpringConstant()); |
| 182 |
} |
| 183 |
if (stamp[i]->haveSwingYSpringConstant()) { |
| 184 |
rest->setSwingYForceConstant(stamp[i]->getSwingYSpringConstant()); |
| 185 |
} |
| 186 |
if (stamp[i]->haveRestrainedTwistAngle()) { |
| 187 |
rest->setRestrainedTwistAngle(stamp[i]->getRestrainedTwistAngle() * M_PI/180.0); |
| 188 |
} |
| 189 |
if (stamp[i]->haveRestrainedSwingYAngle()) { |
| 190 |
rest->setRestrainedSwingYAngle(stamp[i]->getRestrainedSwingYAngle() * M_PI/180.0); |
| 191 |
} |
| 192 |
if (stamp[i]->haveRestrainedSwingXAngle()) { |
| 193 |
rest->setRestrainedSwingXAngle(stamp[i]->getRestrainedSwingXAngle() * M_PI/180.0); |
| 194 |
} |
| 195 |
if (stamp[i]->havePrint()) { |
| 196 |
rest->setPrintRestraint(stamp[i]->getPrint()); |
| 197 |
} |
| 198 |
|
| 199 |
restraints_.push_back(rest); |
| 200 |
mol->addProperty(new RestraintData("Restraint", rest)); |
| 201 |
restrainedMols_.push_back(mol); |
| 202 |
#ifdef IS_MPI |
| 203 |
} |
| 204 |
#endif |
| 205 |
} else if (myType.compare("OBJECT") == 0) { |
| 206 |
|
| 207 |
std::string objectSelection; |
| 208 |
|
| 209 |
if (!stamp[i]->haveObjectSelection()) { |
| 210 |
sprintf(painCave.errMsg, |
| 211 |
"Restraint Error: An object restraint was specified\n" |
| 212 |
"\twithout providing a selection script in the\n" |
| 213 |
"\tobjectSelection variable.\n"); |
| 214 |
painCave.isFatal = 1; |
| 215 |
simError(); |
| 216 |
} else { |
| 217 |
objectSelection = stamp[i]->getObjectSelection(); |
| 218 |
} |
| 219 |
|
| 220 |
SelectionEvaluator evaluator(info); |
| 221 |
SelectionManager seleMan(info); |
| 222 |
|
| 223 |
evaluator.loadScriptString(objectSelection); |
| 224 |
seleMan.setSelectionSet(evaluator.evaluate()); |
| 225 |
int selectionCount = seleMan.getSelectionCount(); |
| 226 |
|
| 227 |
sprintf(painCave.errMsg, |
| 228 |
"Restraint Info: The specified restraint objectSelection,\n" |
| 229 |
"\t\t%s\n" |
| 230 |
"\twill result in %d integrable objects being\n" |
| 231 |
"\trestrained.\n", objectSelection.c_str(), selectionCount); |
| 232 |
painCave.isFatal = 0; |
| 233 |
simError(); |
| 234 |
|
| 235 |
int selei; |
| 236 |
StuntDouble* sd; |
| 237 |
|
| 238 |
for (sd = seleMan.beginSelected(selei); sd != NULL; |
| 239 |
sd = seleMan.nextSelected(selei)) { |
| 240 |
stuntDoubleIndex.push_back(sd->getGlobalIntegrableObjectIndex()); |
| 241 |
|
| 242 |
ObjectRestraint* rest = new ObjectRestraint(); |
| 243 |
|
| 244 |
if (stamp[i]->haveDisplacementSpringConstant()) { |
| 245 |
rest->setDisplacementForceConstant(stamp[i]->getDisplacementSpringConstant()); |
| 246 |
} |
| 247 |
if (stamp[i]->haveTwistSpringConstant()) { |
| 248 |
rest->setTwistForceConstant(stamp[i]->getTwistSpringConstant()); |
| 249 |
} |
| 250 |
if (stamp[i]->haveSwingXSpringConstant()) { |
| 251 |
rest->setSwingXForceConstant(stamp[i]->getSwingXSpringConstant()); |
| 252 |
} |
| 253 |
if (stamp[i]->haveSwingYSpringConstant()) { |
| 254 |
rest->setSwingYForceConstant(stamp[i]->getSwingYSpringConstant()); |
| 255 |
} |
| 256 |
if (stamp[i]->haveRestrainedTwistAngle()) { |
| 257 |
rest->setRestrainedTwistAngle(stamp[i]->getRestrainedTwistAngle()); |
| 258 |
} |
| 259 |
if (stamp[i]->haveRestrainedSwingXAngle()) { |
| 260 |
rest->setRestrainedSwingXAngle(stamp[i]->getRestrainedSwingXAngle()); |
| 261 |
} |
| 262 |
if (stamp[i]->haveRestrainedSwingYAngle()) { |
| 263 |
rest->setRestrainedSwingYAngle(stamp[i]->getRestrainedSwingYAngle()); |
| 264 |
} |
| 265 |
if (stamp[i]->havePrint()) { |
| 266 |
rest->setPrintRestraint(stamp[i]->getPrint()); |
| 267 |
} |
| 268 |
|
| 269 |
restraints_.push_back(rest); |
| 270 |
sd->addProperty(new RestraintData("Restraint", rest)); |
| 271 |
restrainedObjs_.push_back(sd); |
| 272 |
} |
| 273 |
|
| 274 |
} |
| 275 |
} |
| 276 |
|
| 277 |
// ThermodynamicIntegration subclasses RestraintForceManager, and there |
| 278 |
// are times when it won't use restraints at all, so only open the |
| 279 |
// restraint file if we are actually using restraints: |
| 280 |
|
| 281 |
if (simParam->getUseRestraints()) { |
| 282 |
std::string refFile = simParam->getRestraint_file(); |
| 283 |
RestReader* rr = new RestReader(info, refFile, stuntDoubleIndex); |
| 284 |
rr->readReferenceStructure(); |
| 285 |
} |
| 286 |
|
| 287 |
restOutput_ = getPrefix(info_->getFinalConfigFileName()) + ".rest"; |
| 288 |
restOut = new RestWriter(info_, restOutput_.c_str(), restraints_); |
| 289 |
if(!restOut){ |
| 290 |
sprintf(painCave.errMsg, "Restraint error: Failed to create RestWriter\n"); |
| 291 |
painCave.isFatal = 1; |
| 292 |
simError(); |
| 293 |
} |
| 294 |
|
| 295 |
// todo: figure out the scale factor. Right now, just scale them all to 1 |
| 296 |
std::vector<Restraint*>::const_iterator resti; |
| 297 |
for(resti=restraints_.begin(); resti != restraints_.end(); ++resti){ |
| 298 |
(*resti)->setScaleFactor(1.0); |
| 299 |
} |
| 300 |
} |
| 301 |
|
| 302 |
RestraintForceManager::~RestraintForceManager(){ |
| 303 |
if (restOut) |
| 304 |
delete restOut; |
| 305 |
} |
| 306 |
|
| 307 |
void RestraintForceManager::init() { |
| 308 |
currRestTime_ = currSnapshot_->getTime(); |
| 309 |
} |
| 310 |
|
| 311 |
void RestraintForceManager::calcForces(){ |
| 312 |
|
| 313 |
ForceManager::calcForces(); |
| 314 |
RealType restPot_local, restPot; |
| 315 |
|
| 316 |
restPot_local = doRestraints(1.0); |
| 317 |
|
| 318 |
#ifdef IS_MPI |
| 319 |
MPI::COMM_WORLD.Allreduce(&restPot_local, &restPot, 1, |
| 320 |
MPI::REALTYPE, MPI::SUM); |
| 321 |
#else |
| 322 |
restPot = restPot_local; |
| 323 |
#endif |
| 324 |
currSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 325 |
RealType pot = currSnapshot_->getLongRangePotential(); |
| 326 |
pot += restPot; |
| 327 |
currSnapshot_->setLongRangePotential(pot); |
| 328 |
currSnapshot_->setRestraintPotential(restPot); |
| 329 |
|
| 330 |
//write out forces and current positions of restrained molecules |
| 331 |
if (currSnapshot_->getTime() >= currRestTime_){ |
| 332 |
restOut->writeRest(restInfo_); |
| 333 |
currRestTime_ += restTime_; |
| 334 |
} |
| 335 |
} |
| 336 |
|
| 337 |
RealType RestraintForceManager::doRestraints(RealType scalingFactor){ |
| 338 |
std::vector<Molecule*>::const_iterator rm; |
| 339 |
GenericData* data; |
| 340 |
Molecule::IntegrableObjectIterator ioi; |
| 341 |
MolecularRestraint* mRest; |
| 342 |
StuntDouble* sd; |
| 343 |
|
| 344 |
std::vector<StuntDouble*>::const_iterator ro; |
| 345 |
ObjectRestraint* oRest; |
| 346 |
|
| 347 |
std::map<int, Restraint::RealPair> restInfo; |
| 348 |
|
| 349 |
unscaledPotential_ = 0.0; |
| 350 |
|
| 351 |
restInfo_.clear(); |
| 352 |
|
| 353 |
for(rm=restrainedMols_.begin(); rm != restrainedMols_.end(); ++rm){ |
| 354 |
|
| 355 |
// make sure this molecule (*rm) has a generic data for restraints: |
| 356 |
data = (*rm)->getPropertyByName("Restraint"); |
| 357 |
if (data != NULL) { |
| 358 |
// make sure we can reinterpret the generic data as restraint data: |
| 359 |
RestraintData* restData= dynamic_cast<RestraintData*>(data); |
| 360 |
if (restData != NULL) { |
| 361 |
// make sure we can reinterpet the restraint data as a pointer to |
| 362 |
// an MolecularRestraint: |
| 363 |
mRest = dynamic_cast<MolecularRestraint*>(restData->getData()); |
| 364 |
if (mRest == NULL) { |
| 365 |
sprintf( painCave.errMsg, |
| 366 |
"Can not cast RestraintData to MolecularRestraint\n"); |
| 367 |
painCave.severity = OPENMD_ERROR; |
| 368 |
painCave.isFatal = 1; |
| 369 |
simError(); |
| 370 |
} |
| 371 |
} else { |
| 372 |
sprintf( painCave.errMsg, |
| 373 |
"Can not cast GenericData to RestraintData\n"); |
| 374 |
painCave.severity = OPENMD_ERROR; |
| 375 |
painCave.isFatal = 1; |
| 376 |
simError(); |
| 377 |
} |
| 378 |
} else { |
| 379 |
sprintf( painCave.errMsg, "Can not find Restraint for RestrainedObject\n"); |
| 380 |
painCave.severity = OPENMD_ERROR; |
| 381 |
painCave.isFatal = 1; |
| 382 |
simError(); |
| 383 |
} |
| 384 |
|
| 385 |
// phew. At this point, we should have the pointer to the |
| 386 |
// correct MolecularRestraint in the variable mRest. |
| 387 |
|
| 388 |
Vector3d molCom = (*rm)->getCom(); |
| 389 |
|
| 390 |
std::vector<Vector3d> struc; |
| 391 |
std::vector<Vector3d> forces; |
| 392 |
|
| 393 |
for(sd = (*rm)->beginIntegrableObject(ioi); sd != NULL; |
| 394 |
sd = (*rm)->nextIntegrableObject(ioi)) { |
| 395 |
struc.push_back(sd->getPos()); |
| 396 |
} |
| 397 |
|
| 398 |
mRest->setScaleFactor(scalingFactor); |
| 399 |
mRest->calcForce(struc, molCom); |
| 400 |
forces = mRest->getRestraintForces(); |
| 401 |
int index = 0; |
| 402 |
|
| 403 |
for(sd = (*rm)->beginIntegrableObject(ioi); sd != NULL; |
| 404 |
sd = (*rm)->nextIntegrableObject(ioi)) { |
| 405 |
sd->addFrc(forces[index]); |
| 406 |
struc.push_back(sd->getPos()); |
| 407 |
index++; |
| 408 |
} |
| 409 |
|
| 410 |
unscaledPotential_ += mRest->getUnscaledPotential(); |
| 411 |
|
| 412 |
restInfo = mRest->getRestraintInfo(); |
| 413 |
|
| 414 |
// only collect data on restraints that we're going to print: |
| 415 |
if (mRest->getPrintRestraint()) |
| 416 |
restInfo_.push_back(restInfo); |
| 417 |
} |
| 418 |
|
| 419 |
for(ro=restrainedObjs_.begin(); ro != restrainedObjs_.end(); ++ro){ |
| 420 |
// make sure this object (*ro) has a generic data for restraints: |
| 421 |
data = (*ro)->getPropertyByName("Restraint"); |
| 422 |
if (data != NULL) { |
| 423 |
// make sure we can reinterpret the generic data as restraint data: |
| 424 |
RestraintData* restData= dynamic_cast<RestraintData*>(data); |
| 425 |
if (restData != NULL) { |
| 426 |
// make sure we can reinterpet the restraint data as a pointer to |
| 427 |
// an ObjectRestraint: |
| 428 |
oRest = dynamic_cast<ObjectRestraint*>(restData->getData()); |
| 429 |
if (oRest == NULL) { |
| 430 |
sprintf( painCave.errMsg, |
| 431 |
"Can not cast RestraintData to ObjectRestraint\n"); |
| 432 |
painCave.severity = OPENMD_ERROR; |
| 433 |
painCave.isFatal = 1; |
| 434 |
simError(); |
| 435 |
} |
| 436 |
} else { |
| 437 |
sprintf( painCave.errMsg, |
| 438 |
"Can not cast GenericData to RestraintData\n"); |
| 439 |
painCave.severity = OPENMD_ERROR; |
| 440 |
painCave.isFatal = 1; |
| 441 |
simError(); |
| 442 |
} |
| 443 |
} else { |
| 444 |
sprintf( painCave.errMsg, "Can not find Restraint for RestrainedObject\n"); |
| 445 |
painCave.severity = OPENMD_ERROR; |
| 446 |
painCave.isFatal = 1; |
| 447 |
simError(); |
| 448 |
} |
| 449 |
|
| 450 |
// phew. At this point, we should have the pointer to the |
| 451 |
// correct Object restraint in the variable oRest. |
| 452 |
|
| 453 |
oRest->setScaleFactor(scalingFactor); |
| 454 |
|
| 455 |
Vector3d pos = (*ro)->getPos(); |
| 456 |
|
| 457 |
if ( (*ro)->isDirectional() ) { |
| 458 |
|
| 459 |
// directional objects may have orientational restraints as well |
| 460 |
// as positional, so get the rotation matrix first: |
| 461 |
|
| 462 |
RotMat3x3d A = (*ro)->getA(); |
| 463 |
oRest->calcForce(pos, A); |
| 464 |
(*ro)->addFrc(oRest->getRestraintForce()); |
| 465 |
(*ro)->addTrq(oRest->getRestraintTorque()); |
| 466 |
} else { |
| 467 |
|
| 468 |
// plain vanilla positional restraints: |
| 469 |
|
| 470 |
oRest->calcForce(pos); |
| 471 |
(*ro)->addFrc(oRest->getRestraintForce()); |
| 472 |
} |
| 473 |
|
| 474 |
unscaledPotential_ += oRest->getUnscaledPotential(); |
| 475 |
|
| 476 |
restInfo = oRest->getRestraintInfo(); |
| 477 |
|
| 478 |
// only collect data on restraints that we're going to print: |
| 479 |
if (oRest->getPrintRestraint()) |
| 480 |
restInfo_.push_back(restInfo); |
| 481 |
} |
| 482 |
|
| 483 |
return unscaledPotential_ * scalingFactor; |
| 484 |
} |
| 485 |
} |
