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Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 2066 by gezelter, Thu Mar 5 15:22:54 2015 UTC

# Line 35 | Line 35
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]  Vardeman & Gezelter, in progress (2009).                        
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 ForceManager.cpp
45   * @author tlin
46   * @date 11/09/2004
46 * @time 10:39am
47   * @version 1.0
48   */
49  
50 +
51   #include "brains/ForceManager.hpp"
52   #include "primitives/Molecule.hpp"
52 #include "UseTheForce/doForces_interface.h"
53   #define __OPENMD_C
54 #include "UseTheForce/DarkSide/fInteractionMap.h"
54   #include "utils/simError.h"
55   #include "primitives/Bond.hpp"
56   #include "primitives/Bend.hpp"
57   #include "primitives/Torsion.hpp"
58   #include "primitives/Inversion.hpp"
59 + #include "nonbonded/NonBondedInteraction.hpp"
60 + #include "perturbations/UniformField.hpp"
61 + #include "perturbations/UniformGradient.hpp"
62 + #include "parallel/ForceMatrixDecomposition.hpp"
63 +
64 + #include <cstdio>
65 + #include <iostream>
66 + #include <iomanip>
67 +
68 + using namespace std;
69   namespace OpenMD {
70 +  
71 +  ForceManager::ForceManager(SimInfo * info) : info_(info),
72 +                                               initialized_(false),
73 +                                               switcher_(NULL) {
74 +    forceField_ = info_->getForceField();
75 +    interactionMan_ = new InteractionManager();
76 +    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
77 +    thermo = new Thermo(info_);
78 +  }
79  
80 <  void ForceManager::calcForces(bool needPotential, bool needStress) {
80 >  ForceManager::~ForceManager() {
81 >    perturbations_.clear();
82      
83 <    if (!info_->isFortranInitialized()) {
84 <      info_->update();
85 <    }
83 >    delete switcher_;
84 >    delete interactionMan_;
85 >    delete fDecomp_;
86 >    delete thermo;
87 >  }
88 >  
89 >  /**
90 >   * setupCutoffs
91 >   *
92 >   * Sets the values of cutoffRadius, switchingRadius, and cutoffMethod
93 >   *
94 >   * cutoffRadius : realType
95 >   *  If the cutoffRadius was explicitly set, use that value.
96 >   *  If the cutoffRadius was not explicitly set:
97 >   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
98 >   *      No electrostatic atoms?  Poll the atom types present in the
99 >   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
100 >   *      Use the maximum suggested value that was found.
101 >   *
102 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, TAYLOR_SHIFTED,
103 >   *                        SHIFTED_POTENTIAL, or EWALD_FULL)
104 >   *      If cutoffMethod was explicitly set, use that choice.
105 >   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
106 >   *
107 >   * switchingRadius : realType
108 >   *  If the cutoffMethod was set to SWITCHED:
109 >   *      If the switchingRadius was explicitly set, use that value
110 >   *          (but do a sanity check first).
111 >   *      If the switchingRadius was not explicitly set: use 0.85 *
112 >   *      cutoffRadius_
113 >   *  If the cutoffMethod was not set to SWITCHED:
114 >   *      Set switchingRadius equal to cutoffRadius for safety.
115 >   */
116 >  void ForceManager::setupCutoffs() {
117      
118 <    preCalculation();
118 >    Globals* simParams_ = info_->getSimParams();
119 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
120 >    int mdFileVersion;
121 >    rCut_ = 0.0; //Needs a value for a later max() call;  
122      
123 <    calcShortRangeInteraction();
123 >    if (simParams_->haveMDfileVersion())
124 >      mdFileVersion = simParams_->getMDfileVersion();
125 >    else
126 >      mdFileVersion = 0;
127 >  
128 >    // We need the list of simulated atom types to figure out cutoffs
129 >    // as well as long range corrections.
130  
131 <    calcLongRangeInteraction(needPotential, needStress);
131 >    set<AtomType*>::iterator i;
132 >    set<AtomType*> atomTypes_;
133 >    atomTypes_ = info_->getSimulatedAtomTypes();
134  
135 <    postCalculation(needStress);
135 >    if (simParams_->haveCutoffRadius()) {
136 >      rCut_ = simParams_->getCutoffRadius();
137 >    } else {      
138 >      if (info_->usesElectrostaticAtoms()) {
139 >        sprintf(painCave.errMsg,
140 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
141 >                "\tOpenMD will use a default value of 12.0 angstroms"
142 >                "\tfor the cutoffRadius.\n");
143 >        painCave.isFatal = 0;
144 >        painCave.severity = OPENMD_INFO;
145 >        simError();
146 >        rCut_ = 12.0;
147 >      } else {
148 >        RealType thisCut;
149 >        for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
150 >          thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
151 >          rCut_ = max(thisCut, rCut_);
152 >        }
153 >        sprintf(painCave.errMsg,
154 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
155 >                "\tOpenMD will use %lf angstroms.\n",
156 >                rCut_);
157 >        painCave.isFatal = 0;
158 >        painCave.severity = OPENMD_INFO;
159 >        simError();
160 >      }
161 >    }
162 >
163 >    fDecomp_->setCutoffRadius(rCut_);
164 >    interactionMan_->setCutoffRadius(rCut_);
165 >    rCutSq_ = rCut_ * rCut_;
166 >
167 >    map<string, CutoffMethod> stringToCutoffMethod;
168 >    stringToCutoffMethod["HARD"] = HARD;
169 >    stringToCutoffMethod["SWITCHED"] = SWITCHED;
170 >    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
171 >    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
172 >    stringToCutoffMethod["TAYLOR_SHIFTED"] = TAYLOR_SHIFTED;
173 >    stringToCutoffMethod["EWALD_FULL"] = EWALD_FULL;
174 >  
175 >    if (simParams_->haveCutoffMethod()) {
176 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
177 >      map<string, CutoffMethod>::iterator i;
178 >      i = stringToCutoffMethod.find(cutMeth);
179 >      if (i == stringToCutoffMethod.end()) {
180 >        sprintf(painCave.errMsg,
181 >                "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
182 >                "\tShould be one of: "
183 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n"
184 >                "\tSHIFTED_FORCE, or EWALD_FULL\n",
185 >                cutMeth.c_str());
186 >        painCave.isFatal = 1;
187 >        painCave.severity = OPENMD_ERROR;
188 >        simError();
189 >      } else {
190 >        cutoffMethod_ = i->second;
191 >      }
192 >    } else {
193 >      if (mdFileVersion > 1) {
194 >        sprintf(painCave.errMsg,
195 >                "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
196 >                "\tOpenMD will use SHIFTED_FORCE.\n");
197 >        painCave.isFatal = 0;
198 >        painCave.severity = OPENMD_INFO;
199 >        simError();
200 >        cutoffMethod_ = SHIFTED_FORCE;        
201 >      } else {
202 >        // handle the case where the old file version was in play
203 >        // (there should be no cutoffMethod, so we have to deduce it
204 >        // from other data).        
205 >
206 >        sprintf(painCave.errMsg,
207 >                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
208 >                "\tOpenMD found a file which does not set a cutoffMethod.\n"
209 >                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
210 >                "\tbehavior of the older (version 1) code.  To remove this\n"
211 >                "\twarning, add an explicit cutoffMethod and change the top\n"
212 >                "\tof the file so that it begins with <OpenMD version=2>\n");
213 >        painCave.isFatal = 0;
214 >        painCave.severity = OPENMD_WARNING;
215 >        simError();            
216 >                
217 >        // The old file version tethered the shifting behavior to the
218 >        // electrostaticSummationMethod keyword.
219 >        
220 >        if (simParams_->haveElectrostaticSummationMethod()) {
221 >          string myMethod = simParams_->getElectrostaticSummationMethod();
222 >          toUpper(myMethod);
223 >        
224 >          if (myMethod == "SHIFTED_POTENTIAL") {
225 >            cutoffMethod_ = SHIFTED_POTENTIAL;
226 >          } else if (myMethod == "SHIFTED_FORCE") {
227 >            cutoffMethod_ = SHIFTED_FORCE;
228 >          } else if (myMethod == "TAYLOR_SHIFTED") {
229 >            cutoffMethod_ = TAYLOR_SHIFTED;
230 >          } else if (myMethod == "EWALD_FULL") {
231 >            cutoffMethod_ = EWALD_FULL;
232 >          }
233 >        
234 >          if (simParams_->haveSwitchingRadius())
235 >            rSwitch_ = simParams_->getSwitchingRadius();
236 >
237 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE" ||
238 >              myMethod == "TAYLOR_SHIFTED" || myMethod == "EWALD_FULL") {
239 >            if (simParams_->haveSwitchingRadius()){
240 >              sprintf(painCave.errMsg,
241 >                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
242 >                      "\tA value was set for the switchingRadius\n"
243 >                      "\teven though the electrostaticSummationMethod was\n"
244 >                      "\tset to %s\n", myMethod.c_str());
245 >              painCave.severity = OPENMD_WARNING;
246 >              painCave.isFatal = 1;
247 >              simError();            
248 >            }
249 >          }
250 >          if (abs(rCut_ - rSwitch_) < 0.0001) {
251 >            if (cutoffMethod_ == SHIFTED_FORCE) {              
252 >              sprintf(painCave.errMsg,
253 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
254 >                      "\tcutoffRadius and switchingRadius are set to the\n"
255 >                      "\tsame value.  OpenMD will use shifted force\n"
256 >                      "\tpotentials instead of switching functions.\n");
257 >              painCave.isFatal = 0;
258 >              painCave.severity = OPENMD_WARNING;
259 >              simError();            
260 >            } else {
261 >              cutoffMethod_ = SHIFTED_POTENTIAL;
262 >              sprintf(painCave.errMsg,
263 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
264 >                      "\tcutoffRadius and switchingRadius are set to the\n"
265 >                      "\tsame value.  OpenMD will use shifted potentials\n"
266 >                      "\tinstead of switching functions.\n");
267 >              painCave.isFatal = 0;
268 >              painCave.severity = OPENMD_WARNING;
269 >              simError();            
270 >            }
271 >          }
272 >        }
273 >      }
274 >    }
275 >        
276 >    // create the switching function object:
277 >
278 >    switcher_ = new SwitchingFunction();
279 >  
280 >    if (cutoffMethod_ == SWITCHED) {
281 >      if (simParams_->haveSwitchingRadius()) {
282 >        rSwitch_ = simParams_->getSwitchingRadius();
283 >        if (rSwitch_ > rCut_) {        
284 >          sprintf(painCave.errMsg,
285 >                  "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
286 >                  "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
287 >          painCave.isFatal = 1;
288 >          painCave.severity = OPENMD_ERROR;
289 >          simError();
290 >        }
291 >      } else {      
292 >        rSwitch_ = 0.85 * rCut_;
293 >        sprintf(painCave.errMsg,
294 >                "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
295 >                "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
296 >                "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
297 >        painCave.isFatal = 0;
298 >        painCave.severity = OPENMD_WARNING;
299 >        simError();
300 >      }
301 >    } else {
302 >      if (mdFileVersion > 1) {
303 >        // throw an error if we define a switching radius and don't need one.
304 >        // older file versions should not do this.
305 >        if (simParams_->haveSwitchingRadius()) {
306 >          map<string, CutoffMethod>::const_iterator it;
307 >          string theMeth;
308 >          for (it = stringToCutoffMethod.begin();
309 >               it != stringToCutoffMethod.end(); ++it) {
310 >            if (it->second == cutoffMethod_) {
311 >              theMeth = it->first;
312 >              break;
313 >            }
314 >          }
315 >          sprintf(painCave.errMsg,
316 >                  "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
317 >                  "\tis not set to SWITCHED, so switchingRadius value\n"
318 >                  "\twill be ignored for this simulation\n", theMeth.c_str());
319 >          painCave.isFatal = 0;
320 >          painCave.severity = OPENMD_WARNING;
321 >          simError();
322 >        }
323 >      }
324 >      rSwitch_ = rCut_;
325 >    }
326      
327 +    // Default to cubic switching function.
328 +    sft_ = cubic;
329 +    if (simParams_->haveSwitchingFunctionType()) {
330 +      string funcType = simParams_->getSwitchingFunctionType();
331 +      toUpper(funcType);
332 +      if (funcType == "CUBIC") {
333 +        sft_ = cubic;
334 +      } else {
335 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
336 +          sft_ = fifth_order_poly;
337 +        } else {
338 +          // throw error        
339 +          sprintf( painCave.errMsg,
340 +                   "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
341 +                   "\tswitchingFunctionType must be one of: "
342 +                   "\"cubic\" or \"fifth_order_polynomial\".",
343 +                   funcType.c_str() );
344 +          painCave.isFatal = 1;
345 +          painCave.severity = OPENMD_ERROR;
346 +          simError();
347 +        }          
348 +      }
349 +    }
350 +    switcher_->setSwitchType(sft_);
351 +    switcher_->setSwitch(rSwitch_, rCut_);
352    }
353 +
354 +  void ForceManager::initialize() {
355 +
356 +    if (!info_->isTopologyDone()) {
357 +
358 +      info_->update();
359 +      interactionMan_->setSimInfo(info_);
360 +      interactionMan_->initialize();
361 +
362 +      //! We want to delay the cutoffs until after the interaction
363 +      //! manager has set up the atom-atom interactions so that we can
364 +      //! query them for suggested cutoff values
365 +      setupCutoffs();
366 +
367 +      info_->prepareTopology();      
368 +
369 +      doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
370 +      doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
371 +      if (doHeatFlux_) doParticlePot_ = true;
372 +
373 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
374 +      doSitePotential_ = info_->getSimParams()->getOutputSitePotential();
375 +  
376 +    }
377 +
378 +    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
379 +    
380 +    //! Force fields can set options on how to scale van der Waals and
381 +    //! electrostatic interactions for atoms connected via bonds, bends
382 +    //! and torsions in this case the topological distance between
383 +    //! atoms is:
384 +    //! 0 = topologically unconnected
385 +    //! 1 = bonded together
386 +    //! 2 = connected via a bend
387 +    //! 3 = connected via a torsion
388 +    
389 +    vdwScale_.reserve(4);
390 +    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
391 +
392 +    electrostaticScale_.reserve(4);
393 +    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
394 +
395 +    vdwScale_[0] = 1.0;
396 +    vdwScale_[1] = fopts.getvdw12scale();
397 +    vdwScale_[2] = fopts.getvdw13scale();
398 +    vdwScale_[3] = fopts.getvdw14scale();
399 +    
400 +    electrostaticScale_[0] = 1.0;
401 +    electrostaticScale_[1] = fopts.getelectrostatic12scale();
402 +    electrostaticScale_[2] = fopts.getelectrostatic13scale();
403 +    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
404 +    
405 +    if (info_->getSimParams()->haveUniformField()) {
406 +      UniformField* eField = new UniformField(info_);
407 +      perturbations_.push_back(eField);
408 +    }
409 +    if (info_->getSimParams()->haveUniformGradientStrength() ||
410 +        info_->getSimParams()->haveUniformGradientDirection1() ||
411 +        info_->getSimParams()->haveUniformGradientDirection2() ) {
412 +      UniformGradient* eGrad = new UniformGradient(info_);
413 +      perturbations_.push_back(eGrad);
414 +    }
415 +    
416 +    usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
417 +    
418 +    fDecomp_->distributeInitialData();
419 +    
420 +    initialized_ = true;
421 +    
422 +  }
423    
424 +  void ForceManager::calcForces() {
425 +    
426 +    if (!initialized_) initialize();
427 +    
428 +    preCalculation();  
429 +    shortRangeInteractions();
430 +    longRangeInteractions();
431 +    postCalculation();    
432 +  }
433 +  
434    void ForceManager::preCalculation() {
435      SimInfo::MoleculeIterator mi;
436      Molecule* mol;
# Line 82 | Line 438 | namespace OpenMD {
438      Atom* atom;
439      Molecule::RigidBodyIterator rbIter;
440      RigidBody* rb;
441 +    Molecule::CutoffGroupIterator ci;
442 +    CutoffGroup* cg;
443      
444 <    // forces are zeroed here, before any are accumulated.
445 <    // NOTE: do not rezero the forces in Fortran.
444 >    // forces and potentials are zeroed here, before any are
445 >    // accumulated.
446      
447 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
448 +
449 +    snap->setBondPotential(0.0);
450 +    snap->setBendPotential(0.0);
451 +    snap->setTorsionPotential(0.0);
452 +    snap->setInversionPotential(0.0);
453 +
454 +    potVec zeroPot(0.0);
455 +    snap->setLongRangePotential(zeroPot);
456 +    snap->setExcludedPotentials(zeroPot);
457 +
458 +    snap->setRestraintPotential(0.0);
459 +    snap->setRawPotential(0.0);
460 +
461      for (mol = info_->beginMolecule(mi); mol != NULL;
462           mol = info_->nextMolecule(mi)) {
463 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
463 >      for(atom = mol->beginAtom(ai); atom != NULL;
464 >          atom = mol->nextAtom(ai)) {
465          atom->zeroForcesAndTorques();
466        }
467 <          
467 >      
468        //change the positions of atoms which belong to the rigidbodies
469        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
470             rb = mol->nextRigidBody(rbIter)) {
471          rb->zeroForcesAndTorques();
472        }        
473 <          
473 >      
474 >      if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
475 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
476 >            cg = mol->nextCutoffGroup(ci)) {
477 >          //calculate the center of mass of cutoff group
478 >          cg->updateCOM();
479 >        }
480 >      }      
481      }
482      
483      // Zero out the stress tensor
484 <    tau *= 0.0;
485 <    
484 >    stressTensor *= 0.0;
485 >    // Zero out the heatFlux
486 >    fDecomp_->setHeatFlux( Vector3d(0.0) );    
487    }
488    
489 <  void ForceManager::calcShortRangeInteraction() {
489 >  void ForceManager::shortRangeInteractions() {
490      Molecule* mol;
491      RigidBody* rb;
492      Bond* bond;
# Line 135 | Line 516 | namespace OpenMD {
516  
517        for (bond = mol->beginBond(bondIter); bond != NULL;
518             bond = mol->nextBond(bondIter)) {
519 <        bond->calcForce();
519 >        bond->calcForce(doParticlePot_);
520          bondPotential += bond->getPotential();
521        }
522  
# Line 143 | Line 524 | namespace OpenMD {
524             bend = mol->nextBend(bendIter)) {
525          
526          RealType angle;
527 <        bend->calcForce(angle);
527 >        bend->calcForce(angle, doParticlePot_);
528          RealType currBendPot = bend->getPotential();          
529 +        
530          bendPotential += bend->getPotential();
531 <        std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
531 >        map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
532          if (i == bendDataSets.end()) {
533            BendDataSet dataSet;
534            dataSet.prev.angle = dataSet.curr.angle = angle;
535            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
536            dataSet.deltaV = 0.0;
537 <          bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
537 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
538 >                                                                  dataSet));
539          }else {
540            i->second.prev.angle = i->second.curr.angle;
541            i->second.prev.potential = i->second.curr.potential;
# Line 166 | Line 549 | namespace OpenMD {
549        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
550             torsion = mol->nextTorsion(torsionIter)) {
551          RealType angle;
552 <        torsion->calcForce(angle);
552 >        torsion->calcForce(angle, doParticlePot_);
553          RealType currTorsionPot = torsion->getPotential();
554          torsionPotential += torsion->getPotential();
555 <        std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
555 >        map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
556          if (i == torsionDataSets.end()) {
557            TorsionDataSet dataSet;
558            dataSet.prev.angle = dataSet.curr.angle = angle;
559            dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
560            dataSet.deltaV = 0.0;
561 <          torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
561 >          torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
562          }else {
563            i->second.prev.angle = i->second.curr.angle;
564            i->second.prev.potential = i->second.curr.potential;
# Line 185 | Line 568 | namespace OpenMD {
568                                     i->second.prev.potential);
569          }      
570        }      
571 <
571 >      
572        for (inversion = mol->beginInversion(inversionIter);
573             inversion != NULL;
574             inversion = mol->nextInversion(inversionIter)) {
575          RealType angle;
576 <        inversion->calcForce(angle);
576 >        inversion->calcForce(angle, doParticlePot_);
577          RealType currInversionPot = inversion->getPotential();
578          inversionPotential += inversion->getPotential();
579 <        std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
579 >        map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
580          if (i == inversionDataSets.end()) {
581            InversionDataSet dataSet;
582            dataSet.prev.angle = dataSet.curr.angle = angle;
583            dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
584            dataSet.deltaV = 0.0;
585 <          inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
585 >          inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
586          }else {
587            i->second.prev.angle = i->second.curr.angle;
588            i->second.prev.potential = i->second.curr.potential;
# Line 210 | Line 593 | namespace OpenMD {
593          }      
594        }      
595      }
596 <    
597 <    RealType  shortRangePotential = bondPotential + bendPotential +
598 <      torsionPotential +  inversionPotential;    
599 <    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
600 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
601 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
602 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
603 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
604 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
596 >
597 > #ifdef IS_MPI
598 >    // Collect from all nodes.  This should eventually be moved into a
599 >    // SystemDecomposition, but this is a better place than in
600 >    // Thermo to do the collection.
601 >
602 >    MPI_Allreduce(MPI_IN_PLACE, &bondPotential, 1, MPI_REALTYPE,
603 >                  MPI_SUM, MPI_COMM_WORLD);
604 >    MPI_Allreduce(MPI_IN_PLACE, &bendPotential, 1, MPI_REALTYPE,
605 >                  MPI_SUM, MPI_COMM_WORLD);
606 >    MPI_Allreduce(MPI_IN_PLACE, &torsionPotential, 1,
607 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
608 >    MPI_Allreduce(MPI_IN_PLACE, &inversionPotential, 1,
609 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
610 > #endif
611 >
612 >    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
613 >
614 >    curSnapshot->setBondPotential(bondPotential);
615 >    curSnapshot->setBendPotential(bendPotential);
616 >    curSnapshot->setTorsionPotential(torsionPotential);
617 >    curSnapshot->setInversionPotential(inversionPotential);
618      
619 +    // RealType shortRangePotential = bondPotential + bendPotential +
620 +    //   torsionPotential +  inversionPotential;    
621 +
622 +    // curSnapshot->setShortRangePotential(shortRangePotential);
623    }
624    
625 <  void ForceManager::calcLongRangeInteraction(bool needPotential,
226 <                                              bool needStress) {
227 <    Snapshot* curSnapshot;
228 <    DataStorage* config;
229 <    RealType* frc;
230 <    RealType* pos;
231 <    RealType* trq;
232 <    RealType* A;
233 <    RealType* electroFrame;
234 <    RealType* rc;
235 <    RealType* particlePot;
236 <    
237 <    //get current snapshot from SimInfo
238 <    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
239 <    
240 <    //get array pointers
241 <    config = &(curSnapshot->atomData);
242 <    frc = config->getArrayPointer(DataStorage::dslForce);
243 <    pos = config->getArrayPointer(DataStorage::dslPosition);
244 <    trq = config->getArrayPointer(DataStorage::dslTorque);
245 <    A   = config->getArrayPointer(DataStorage::dslAmat);
246 <    electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
247 <    particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
625 >  void ForceManager::longRangeInteractions() {
626  
627 +    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
628 +    DataStorage* config = &(curSnapshot->atomData);
629 +    DataStorage* cgConfig = &(curSnapshot->cgData);
630 +
631      //calculate the center of mass of cutoff group
632 +
633      SimInfo::MoleculeIterator mi;
634      Molecule* mol;
635      Molecule::CutoffGroupIterator ci;
636      CutoffGroup* cg;
254    Vector3d com;
255    std::vector<Vector3d> rcGroup;
637      
638 <    if(info_->getNCutoffGroups() > 0){
258 <      
638 >    if(info_->getNCutoffGroups() != info_->getNAtoms()){
639        for (mol = info_->beginMolecule(mi); mol != NULL;
640             mol = info_->nextMolecule(mi)) {
641          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
642              cg = mol->nextCutoffGroup(ci)) {
643 <          cg->getCOM(com);
264 <          rcGroup.push_back(com);
643 >          cg->updateCOM();
644          }
645 <      }// end for (mol)
267 <      
268 <      rc = rcGroup[0].getArrayPointer();
645 >      }      
646      } else {
647        // center of mass of the group is the same as position of the atom  
648        // if cutoff group does not exist
649 <      rc = pos;
649 >      cgConfig->position = config->position;
650 >      cgConfig->velocity = config->velocity;
651      }
652 +
653 +    fDecomp_->zeroWorkArrays();
654 +    fDecomp_->distributeData();
655      
656 <    //initialize data before passing to fortran
657 <    RealType longRangePotential[LR_POT_TYPES];
658 <    RealType lrPot = 0.0;
659 <    Vector3d totalDipole;
660 <    short int passedCalcPot = needPotential;
661 <    short int passedCalcStress = needStress;
662 <    int isError = 0;
656 >    int cg1, cg2, atom1, atom2, topoDist;
657 >    Vector3d d_grp, dag, d, gvel2, vel2;
658 >    RealType rgrpsq, rgrp, r2, r;
659 >    RealType electroMult, vdwMult;
660 >    RealType vij;
661 >    Vector3d fij, fg, f1;
662 >    bool in_switching_region;
663 >    RealType sw, dswdr, swderiv;
664 >    vector<int> atomListColumn, atomListRow;
665 >    InteractionData idat;
666 >    SelfData sdat;
667 >    RealType mf;
668 >    RealType vpair;
669 >    RealType dVdFQ1(0.0);
670 >    RealType dVdFQ2(0.0);
671 >    potVec longRangePotential(0.0);
672 >    RealType reciprocalPotential(0.0);
673 >    potVec workPot(0.0);
674 >    potVec exPot(0.0);
675 >    Vector3d eField1(0.0);
676 >    Vector3d eField2(0.0);
677 >    RealType sPot1(0.0);
678 >    RealType sPot2(0.0);
679 >    bool newAtom1;
680 >                  
681 >    vector<int>::iterator ia, jb;
682  
683 <    for (int i=0; i<LR_POT_TYPES;i++){
284 <      longRangePotential[i]=0.0; //Initialize array
285 <    }
683 >    int loopStart, loopEnd;
684      
685 <    doForceLoop(pos,
686 <                rc,
687 <                A,
688 <                electroFrame,
689 <                frc,
690 <                trq,
691 <                tau.getArrayPointer(),
692 <                longRangePotential,
693 <                particlePot,
694 <                &passedCalcPot,
695 <                &passedCalcStress,
696 <                &isError );
685 >    idat.rcut = &rCut_;
686 >    idat.vdwMult = &vdwMult;
687 >    idat.electroMult = &electroMult;
688 >    idat.pot = &workPot;
689 >    idat.excludedPot = &exPot;
690 >    sdat.pot = fDecomp_->getEmbeddingPotential();
691 >    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
692 >    idat.vpair = &vpair;
693 >    idat.dVdFQ1 = &dVdFQ1;
694 >    idat.dVdFQ2 = &dVdFQ2;
695 >    idat.eField1 = &eField1;
696 >    idat.eField2 = &eField2;
697 >    idat.sPot1 = &sPot1;
698 >    idat.sPot2 = &sPot2;
699 >    idat.f1 = &f1;
700 >    idat.sw = &sw;
701 >    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
702 >    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE ||
703 >                         cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
704 >    idat.doParticlePot = doParticlePot_;
705 >    idat.doElectricField = doElectricField_;
706 >    idat.doSitePotential = doSitePotential_;
707 >    sdat.doParticlePot = doParticlePot_;
708      
709 <    if( isError ){
710 <      sprintf( painCave.errMsg,
711 <               "Error returned from the fortran force calculation.\n" );
712 <      painCave.isFatal = 1;
713 <      simError();
709 >    loopEnd = PAIR_LOOP;
710 >    if (info_->requiresPrepair() ) {
711 >      loopStart = PREPAIR_LOOP;
712 >    } else {
713 >      loopStart = PAIR_LOOP;
714      }
715 <    for (int i=0; i<LR_POT_TYPES;i++){
307 <      lrPot += longRangePotential[i]; //Quick hack
308 <    }
715 >    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
716      
717 <    // grab the simulation box dipole moment if specified
718 <    if (info_->getCalcBoxDipole()){
719 <      getAccumulatedBoxDipole(totalDipole.getArrayPointer());
720 <      
721 <      curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
722 <      curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
723 <      curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
717 >      if (iLoop == loopStart) {
718 >        bool update_nlist = fDecomp_->checkNeighborList();
719 >        if (update_nlist) {
720 >          if (!usePeriodicBoundaryConditions_)
721 >            Mat3x3d bbox = thermo->getBoundingBox();
722 >          fDecomp_->buildNeighborList(neighborList_, point_);
723 >        }
724 >      }
725 >
726 >      for (cg1 = 0; cg1 < point_.size() - 1; cg1++) {
727 >        
728 >        atomListRow = fDecomp_->getAtomsInGroupRow(cg1);        
729 >        newAtom1 = true;
730 >        
731 >        for (int m2 = point_[cg1]; m2 < point_[cg1+1]; m2++) {
732 >
733 >          cg2 = neighborList_[m2];
734 >          
735 >          d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
736 >        
737 >          // already wrapped in the getIntergroupVector call:
738 >          // curSnapshot->wrapVector(d_grp);        
739 >          rgrpsq = d_grp.lengthSquare();
740 >          
741 >          if (rgrpsq < rCutSq_) {
742 >            if (iLoop == PAIR_LOOP) {
743 >              vij = 0.0;
744 >              fij.zero();
745 >              eField1.zero();
746 >              eField2.zero();
747 >              sPot1 = 0.0;
748 >              sPot2 = 0.0;
749 >            }
750 >            
751 >            in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
752 >                                                       rgrp);
753 >            
754 >            atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
755 >            
756 >            if (doHeatFlux_)
757 >              gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
758 >            
759 >            for (ia = atomListRow.begin();
760 >                 ia != atomListRow.end(); ++ia) {            
761 >              atom1 = (*ia);
762 >              
763 >              for (jb = atomListColumn.begin();
764 >                   jb != atomListColumn.end(); ++jb) {              
765 >                atom2 = (*jb);
766 >                
767 >                if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
768 >                  
769 >                  vpair = 0.0;
770 >                  workPot = 0.0;
771 >                  exPot = 0.0;
772 >                  f1.zero();
773 >                  dVdFQ1 = 0.0;
774 >                  dVdFQ2 = 0.0;
775 >                  
776 >                  fDecomp_->fillInteractionData(idat, atom1, atom2, newAtom1);
777 >                  
778 >                  topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
779 >                  vdwMult = vdwScale_[topoDist];
780 >                  electroMult = electrostaticScale_[topoDist];
781 >                  
782 >                  if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
783 >                    idat.d = &d_grp;
784 >                    idat.r2 = &rgrpsq;
785 >                    if (doHeatFlux_)
786 >                      vel2 = gvel2;
787 >                  } else {
788 >                    d = fDecomp_->getInteratomicVector(atom1, atom2);
789 >                    curSnapshot->wrapVector( d );
790 >                    r2 = d.lengthSquare();
791 >                    idat.d = &d;
792 >                    idat.r2 = &r2;
793 >                    if (doHeatFlux_)
794 >                      vel2 = fDecomp_->getAtomVelocityColumn(atom2);
795 >                  }
796 >                  
797 >                  r = sqrt( *(idat.r2) );
798 >                  idat.rij = &r;
799 >                  
800 >                  if (iLoop == PREPAIR_LOOP) {
801 >                    interactionMan_->doPrePair(idat);
802 >                  } else {
803 >                    interactionMan_->doPair(idat);
804 >                    fDecomp_->unpackInteractionData(idat, atom1, atom2);
805 >                    vij += vpair;
806 >                    fij += f1;
807 >                    stressTensor -= outProduct( *(idat.d), f1);
808 >                    if (doHeatFlux_)
809 >                      fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
810 >                  }
811 >                }
812 >              }
813 >            }
814 >            
815 >            if (iLoop == PAIR_LOOP) {
816 >              if (in_switching_region) {
817 >                swderiv = vij * dswdr / rgrp;
818 >                fg = swderiv * d_grp;
819 >                fij += fg;
820 >                
821 >                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
822 >                  if (!fDecomp_->skipAtomPair(atomListRow[0],
823 >                                              atomListColumn[0],
824 >                                              cg1, cg2)) {
825 >                  stressTensor -= outProduct( *(idat.d), fg);
826 >                  if (doHeatFlux_)
827 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
828 >                  }                
829 >                }
830 >                
831 >                for (ia = atomListRow.begin();
832 >                     ia != atomListRow.end(); ++ia) {            
833 >                  atom1 = (*ia);                
834 >                  mf = fDecomp_->getMassFactorRow(atom1);
835 >                  // fg is the force on atom ia due to cutoff group's
836 >                  // presence in switching region
837 >                  fg = swderiv * d_grp * mf;
838 >                  fDecomp_->addForceToAtomRow(atom1, fg);
839 >                  if (atomListRow.size() > 1) {
840 >                    if (info_->usesAtomicVirial()) {
841 >                      // find the distance between the atom
842 >                      // and the center of the cutoff group:
843 >                      dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
844 >                      stressTensor -= outProduct(dag, fg);
845 >                      if (doHeatFlux_)
846 >                        fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
847 >                    }
848 >                  }
849 >                }
850 >                for (jb = atomListColumn.begin();
851 >                     jb != atomListColumn.end(); ++jb) {              
852 >                  atom2 = (*jb);
853 >                  mf = fDecomp_->getMassFactorColumn(atom2);
854 >                  // fg is the force on atom jb due to cutoff group's
855 >                  // presence in switching region
856 >                  fg = -swderiv * d_grp * mf;
857 >                  fDecomp_->addForceToAtomColumn(atom2, fg);
858 >                  
859 >                  if (atomListColumn.size() > 1) {
860 >                    if (info_->usesAtomicVirial()) {
861 >                      // find the distance between the atom
862 >                      // and the center of the cutoff group:
863 >                      dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
864 >                      stressTensor -= outProduct(dag, fg);
865 >                      if (doHeatFlux_)
866 >                        fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
867 >                    }
868 >                  }
869 >                }
870 >              }
871 >              //if (!info_->usesAtomicVirial()) {
872 >              //  stressTensor -= outProduct(d_grp, fij);
873 >              //  if (doHeatFlux_)
874 >              //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
875 >              //}
876 >            }
877 >          }
878 >        }
879 >        newAtom1 = false;
880 >      }
881 >        
882 >      if (iLoop == PREPAIR_LOOP) {
883 >        if (info_->requiresPrepair()) {
884 >          
885 >          fDecomp_->collectIntermediateData();
886 >          
887 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
888 >            fDecomp_->fillSelfData(sdat, atom1);
889 >            interactionMan_->doPreForce(sdat);
890 >          }
891 >          
892 >          fDecomp_->distributeIntermediateData();
893 >          
894 >        }
895 >      }
896      }
897      
898 <    //store the tau and long range potential    
899 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
900 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
901 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
898 >    // collects pairwise information
899 >    fDecomp_->collectData();
900 >    if (cutoffMethod_ == EWALD_FULL) {
901 >      interactionMan_->doReciprocalSpaceSum(reciprocalPotential);
902 >
903 >      curSnapshot->setReciprocalPotential(reciprocalPotential);
904 >    }
905 >        
906 >    if (info_->requiresSelfCorrection()) {
907 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
908 >        fDecomp_->fillSelfData(sdat, atom1);
909 >        interactionMan_->doSelfCorrection(sdat);
910 >      }
911 >    }
912 >
913 >    // collects single-atom information
914 >    fDecomp_->collectSelfData();
915 >
916 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
917 >      *(fDecomp_->getPairwisePotential());
918 >
919 >    curSnapshot->setLongRangePotential(longRangePotential);
920 >    
921 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
922 >                                       *(fDecomp_->getExcludedPotential()));
923 >
924    }
925  
926 <  
927 <  void ForceManager::postCalculation(bool needStress) {
926 >  void ForceManager::postCalculation() {
927 >
928 >    vector<Perturbation*>::iterator pi;
929 >    for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
930 >      (*pi)->applyPerturbation();
931 >    }
932 >
933      SimInfo::MoleculeIterator mi;
934      Molecule* mol;
935      Molecule::RigidBodyIterator rbIter;
936      RigidBody* rb;
937      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
938 <    
938 >  
939      // collect the atomic forces onto rigid bodies
940      
941      for (mol = info_->beginMolecule(mi); mol != NULL;
942           mol = info_->nextMolecule(mi)) {
943        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
944             rb = mol->nextRigidBody(rbIter)) {
945 <        if (needStress) {          
946 <          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
341 <          tau += rbTau;
342 <        } else{
343 <          rb->calcForcesAndTorques();
344 <        }
945 >        Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
946 >        stressTensor += rbTau;
947        }
948      }
949 <
348 <    if (needStress) {
949 >    
950   #ifdef IS_MPI
951 <      Mat3x3d tmpTau(tau);
952 <      MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
352 <                    9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
951 >    MPI_Allreduce(MPI_IN_PLACE, stressTensor.getArrayPointer(), 9,
952 >                  MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
953   #endif
954 <      curSnapshot->statData.setTau(tau);
955 <    }
956 <  }
954 >    curSnapshot->setStressTensor(stressTensor);
955 >    
956 >    if (info_->getSimParams()->getUseLongRangeCorrections()) {
957 >      /*
958 >        RealType vol = curSnapshot->getVolume();
959 >        RealType Elrc(0.0);
960 >        RealType Wlrc(0.0);
961  
962 < } //end namespace OpenMD
962 >        set<AtomType*>::iterator i;
963 >        set<AtomType*>::iterator j;
964 >    
965 >        RealType n_i, n_j;
966 >        RealType rho_i, rho_j;
967 >        pair<RealType, RealType> LRI;
968 >      
969 >        for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
970 >        n_i = RealType(info_->getGlobalCountOfType(*i));
971 >        rho_i = n_i /  vol;
972 >        for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
973 >        n_j = RealType(info_->getGlobalCountOfType(*j));
974 >        rho_j = n_j / vol;
975 >          
976 >        LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
977 >
978 >        Elrc += n_i   * rho_j * LRI.first;
979 >        Wlrc -= rho_i * rho_j * LRI.second;
980 >        }
981 >        }
982 >        Elrc *= 2.0 * NumericConstant::PI;
983 >        Wlrc *= 2.0 * NumericConstant::PI;
984 >
985 >        RealType lrp = curSnapshot->getLongRangePotential();
986 >        curSnapshot->setLongRangePotential(lrp + Elrc);
987 >        stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
988 >        curSnapshot->setStressTensor(stressTensor);
989 >      */
990 >    
991 >    }
992 >  }
993 > }

Comparing trunk/src/brains/ForceManager.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 2066 by gezelter, Thu Mar 5 15:22:54 2015 UTC

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