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Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 UTC vs.
Revision 1866 by gezelter, Thu Apr 25 14:32:56 2013 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/ElectricField.hpp"
61 + #include "parallel/ForceMatrixDecomposition.hpp"
62  
63 + #include <cstdio>
64 + #include <iostream>
65 + #include <iomanip>
66 +
67 + using namespace std;
68   namespace OpenMD {
69    
70 <  ForceManager::ForceManager(SimInfo * info) : info_(info),
71 <                                               NBforcesInitialized_(false) {
70 >  ForceManager::ForceManager(SimInfo * info) : info_(info) {
71 >    forceField_ = info_->getForceField();
72 >    interactionMan_ = new InteractionManager();
73 >    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
74 >    thermo = new Thermo(info_);
75    }
76 <
77 <  void ForceManager::calcForces() {
76 >
77 >  /**
78 >   * setupCutoffs
79 >   *
80 >   * Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
81 >   * and cutoffPolicy
82 >   *
83 >   * cutoffRadius : realType
84 >   *  If the cutoffRadius was explicitly set, use that value.
85 >   *  If the cutoffRadius was not explicitly set:
86 >   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
87 >   *      No electrostatic atoms?  Poll the atom types present in the
88 >   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
89 >   *      Use the maximum suggested value that was found.
90 >   *
91 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
92 >   *                        or SHIFTED_POTENTIAL)
93 >   *      If cutoffMethod was explicitly set, use that choice.
94 >   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
95 >   *
96 >   * cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
97 >   *      If cutoffPolicy was explicitly set, use that choice.
98 >   *      If cutoffPolicy was not explicitly set, use TRADITIONAL
99 >   *
100 >   * switchingRadius : realType
101 >   *  If the cutoffMethod was set to SWITCHED:
102 >   *      If the switchingRadius was explicitly set, use that value
103 >   *          (but do a sanity check first).
104 >   *      If the switchingRadius was not explicitly set: use 0.85 *
105 >   *      cutoffRadius_
106 >   *  If the cutoffMethod was not set to SWITCHED:
107 >   *      Set switchingRadius equal to cutoffRadius for safety.
108 >   */
109 >  void ForceManager::setupCutoffs() {
110      
111 <    if (!info_->isFortranInitialized()) {
112 <      info_->update();
113 <    }
111 >    Globals* simParams_ = info_->getSimParams();
112 >    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
113 >    int mdFileVersion;
114 >    rCut_ = 0.0; //Needs a value for a later max() call;  
115      
116 <    preCalculation();
117 <    
118 <    calcShortRangeInteraction();
116 >    if (simParams_->haveMDfileVersion())
117 >      mdFileVersion = simParams_->getMDfileVersion();
118 >    else
119 >      mdFileVersion = 0;
120 >  
121 >    // We need the list of simulated atom types to figure out cutoffs
122 >    // as well as long range corrections.
123  
124 <    calcLongRangeInteraction();
124 >    set<AtomType*>::iterator i;
125 >    set<AtomType*> atomTypes_;
126 >    atomTypes_ = info_->getSimulatedAtomTypes();
127  
128 <    postCalculation();
128 >    if (simParams_->haveCutoffRadius()) {
129 >      rCut_ = simParams_->getCutoffRadius();
130 >    } else {      
131 >      if (info_->usesElectrostaticAtoms()) {
132 >        sprintf(painCave.errMsg,
133 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
134 >                "\tOpenMD will use a default value of 12.0 angstroms"
135 >                "\tfor the cutoffRadius.\n");
136 >        painCave.isFatal = 0;
137 >        painCave.severity = OPENMD_INFO;
138 >        simError();
139 >        rCut_ = 12.0;
140 >      } else {
141 >        RealType thisCut;
142 >        for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
143 >          thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
144 >          rCut_ = max(thisCut, rCut_);
145 >        }
146 >        sprintf(painCave.errMsg,
147 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
148 >                "\tOpenMD will use %lf angstroms.\n",
149 >                rCut_);
150 >        painCave.isFatal = 0;
151 >        painCave.severity = OPENMD_INFO;
152 >        simError();
153 >      }
154 >    }
155 >
156 >    fDecomp_->setUserCutoff(rCut_);
157 >    interactionMan_->setCutoffRadius(rCut_);
158 >
159 >    map<string, CutoffMethod> stringToCutoffMethod;
160 >    stringToCutoffMethod["HARD"] = HARD;
161 >    stringToCutoffMethod["SWITCHED"] = SWITCHED;
162 >    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
163 >    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
164 >  
165 >    if (simParams_->haveCutoffMethod()) {
166 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
167 >      map<string, CutoffMethod>::iterator i;
168 >      i = stringToCutoffMethod.find(cutMeth);
169 >      if (i == stringToCutoffMethod.end()) {
170 >        sprintf(painCave.errMsg,
171 >                "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
172 >                "\tShould be one of: "
173 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
174 >                cutMeth.c_str());
175 >        painCave.isFatal = 1;
176 >        painCave.severity = OPENMD_ERROR;
177 >        simError();
178 >      } else {
179 >        cutoffMethod_ = i->second;
180 >      }
181 >    } else {
182 >      if (mdFileVersion > 1) {
183 >        sprintf(painCave.errMsg,
184 >                "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
185 >                "\tOpenMD will use SHIFTED_FORCE.\n");
186 >        painCave.isFatal = 0;
187 >        painCave.severity = OPENMD_INFO;
188 >        simError();
189 >        cutoffMethod_ = SHIFTED_FORCE;        
190 >      } else {
191 >        // handle the case where the old file version was in play
192 >        // (there should be no cutoffMethod, so we have to deduce it
193 >        // from other data).        
194 >
195 >        sprintf(painCave.errMsg,
196 >                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
197 >                "\tOpenMD found a file which does not set a cutoffMethod.\n"
198 >                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
199 >                "\tbehavior of the older (version 1) code.  To remove this\n"
200 >                "\twarning, add an explicit cutoffMethod and change the top\n"
201 >                "\tof the file so that it begins with <OpenMD version=2>\n");
202 >        painCave.isFatal = 0;
203 >        painCave.severity = OPENMD_WARNING;
204 >        simError();            
205 >                
206 >        // The old file version tethered the shifting behavior to the
207 >        // electrostaticSummationMethod keyword.
208 >        
209 >        if (simParams_->haveElectrostaticSummationMethod()) {
210 >          string myMethod = simParams_->getElectrostaticSummationMethod();
211 >          toUpper(myMethod);
212 >        
213 >          if (myMethod == "SHIFTED_POTENTIAL") {
214 >            cutoffMethod_ = SHIFTED_POTENTIAL;
215 >          } else if (myMethod == "SHIFTED_FORCE") {
216 >            cutoffMethod_ = SHIFTED_FORCE;
217 >          }
218 >        
219 >          if (simParams_->haveSwitchingRadius())
220 >            rSwitch_ = simParams_->getSwitchingRadius();
221 >
222 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
223 >            if (simParams_->haveSwitchingRadius()){
224 >              sprintf(painCave.errMsg,
225 >                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
226 >                      "\tA value was set for the switchingRadius\n"
227 >                      "\teven though the electrostaticSummationMethod was\n"
228 >                      "\tset to %s\n", myMethod.c_str());
229 >              painCave.severity = OPENMD_WARNING;
230 >              painCave.isFatal = 1;
231 >              simError();            
232 >            }
233 >          }
234 >          if (abs(rCut_ - rSwitch_) < 0.0001) {
235 >            if (cutoffMethod_ == SHIFTED_FORCE) {              
236 >              sprintf(painCave.errMsg,
237 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
238 >                      "\tcutoffRadius and switchingRadius are set to the\n"
239 >                      "\tsame value.  OpenMD will use shifted force\n"
240 >                      "\tpotentials instead of switching functions.\n");
241 >              painCave.isFatal = 0;
242 >              painCave.severity = OPENMD_WARNING;
243 >              simError();            
244 >            } else {
245 >              cutoffMethod_ = SHIFTED_POTENTIAL;
246 >              sprintf(painCave.errMsg,
247 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
248 >                      "\tcutoffRadius and switchingRadius are set to the\n"
249 >                      "\tsame value.  OpenMD will use shifted potentials\n"
250 >                      "\tinstead of switching functions.\n");
251 >              painCave.isFatal = 0;
252 >              painCave.severity = OPENMD_WARNING;
253 >              simError();            
254 >            }
255 >          }
256 >        }
257 >      }
258 >    }
259 >
260 >    map<string, CutoffPolicy> stringToCutoffPolicy;
261 >    stringToCutoffPolicy["MIX"] = MIX;
262 >    stringToCutoffPolicy["MAX"] = MAX;
263 >    stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
264 >
265 >    string cutPolicy;
266 >    if (forceFieldOptions_.haveCutoffPolicy()){
267 >      cutPolicy = forceFieldOptions_.getCutoffPolicy();
268 >    }else if (simParams_->haveCutoffPolicy()) {
269 >      cutPolicy = simParams_->getCutoffPolicy();
270 >    }
271 >
272 >    if (!cutPolicy.empty()){
273 >      toUpper(cutPolicy);
274 >      map<string, CutoffPolicy>::iterator i;
275 >      i = stringToCutoffPolicy.find(cutPolicy);
276 >
277 >      if (i == stringToCutoffPolicy.end()) {
278 >        sprintf(painCave.errMsg,
279 >                "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
280 >                "\tShould be one of: "
281 >                "MIX, MAX, or TRADITIONAL\n",
282 >                cutPolicy.c_str());
283 >        painCave.isFatal = 1;
284 >        painCave.severity = OPENMD_ERROR;
285 >        simError();
286 >      } else {
287 >        cutoffPolicy_ = i->second;
288 >      }
289 >    } else {
290 >      sprintf(painCave.errMsg,
291 >              "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
292 >              "\tOpenMD will use TRADITIONAL.\n");
293 >      painCave.isFatal = 0;
294 >      painCave.severity = OPENMD_INFO;
295 >      simError();
296 >      cutoffPolicy_ = TRADITIONAL;        
297 >    }
298 >
299 >    fDecomp_->setCutoffPolicy(cutoffPolicy_);
300 >        
301 >    // create the switching function object:
302 >
303 >    switcher_ = new SwitchingFunction();
304 >  
305 >    if (cutoffMethod_ == SWITCHED) {
306 >      if (simParams_->haveSwitchingRadius()) {
307 >        rSwitch_ = simParams_->getSwitchingRadius();
308 >        if (rSwitch_ > rCut_) {        
309 >          sprintf(painCave.errMsg,
310 >                  "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
311 >                  "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
312 >          painCave.isFatal = 1;
313 >          painCave.severity = OPENMD_ERROR;
314 >          simError();
315 >        }
316 >      } else {      
317 >        rSwitch_ = 0.85 * rCut_;
318 >        sprintf(painCave.errMsg,
319 >                "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
320 >                "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
321 >                "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
322 >        painCave.isFatal = 0;
323 >        painCave.severity = OPENMD_WARNING;
324 >        simError();
325 >      }
326 >    } else {
327 >      if (mdFileVersion > 1) {
328 >        // throw an error if we define a switching radius and don't need one.
329 >        // older file versions should not do this.
330 >        if (simParams_->haveSwitchingRadius()) {
331 >          map<string, CutoffMethod>::const_iterator it;
332 >          string theMeth;
333 >          for (it = stringToCutoffMethod.begin();
334 >               it != stringToCutoffMethod.end(); ++it) {
335 >            if (it->second == cutoffMethod_) {
336 >              theMeth = it->first;
337 >              break;
338 >            }
339 >          }
340 >          sprintf(painCave.errMsg,
341 >                  "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
342 >                  "\tis not set to SWITCHED, so switchingRadius value\n"
343 >                  "\twill be ignored for this simulation\n", theMeth.c_str());
344 >          painCave.isFatal = 0;
345 >          painCave.severity = OPENMD_WARNING;
346 >          simError();
347 >        }
348 >      }
349 >      rSwitch_ = rCut_;
350 >    }
351      
352 +    // Default to cubic switching function.
353 +    sft_ = cubic;
354 +    if (simParams_->haveSwitchingFunctionType()) {
355 +      string funcType = simParams_->getSwitchingFunctionType();
356 +      toUpper(funcType);
357 +      if (funcType == "CUBIC") {
358 +        sft_ = cubic;
359 +      } else {
360 +        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
361 +          sft_ = fifth_order_poly;
362 +        } else {
363 +          // throw error        
364 +          sprintf( painCave.errMsg,
365 +                   "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
366 +                   "\tswitchingFunctionType must be one of: "
367 +                   "\"cubic\" or \"fifth_order_polynomial\".",
368 +                   funcType.c_str() );
369 +          painCave.isFatal = 1;
370 +          painCave.severity = OPENMD_ERROR;
371 +          simError();
372 +        }          
373 +      }
374 +    }
375 +    switcher_->setSwitchType(sft_);
376 +    switcher_->setSwitch(rSwitch_, rCut_);
377    }
378 +
379 +
380 +
381    
382 +  void ForceManager::initialize() {
383 +
384 +    if (!info_->isTopologyDone()) {
385 +
386 +      info_->update();
387 +      interactionMan_->setSimInfo(info_);
388 +      interactionMan_->initialize();
389 +
390 +      // We want to delay the cutoffs until after the interaction
391 +      // manager has set up the atom-atom interactions so that we can
392 +      // query them for suggested cutoff values
393 +      setupCutoffs();
394 +
395 +      info_->prepareTopology();      
396 +
397 +      doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
398 +      doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
399 +      if (doHeatFlux_) doParticlePot_ = true;
400 +
401 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
402 +  
403 +    }
404 +
405 +    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
406 +    
407 +    // Force fields can set options on how to scale van der Waals and
408 +    // electrostatic interactions for atoms connected via bonds, bends
409 +    // and torsions in this case the topological distance between
410 +    // atoms is:
411 +    // 0 = topologically unconnected
412 +    // 1 = bonded together
413 +    // 2 = connected via a bend
414 +    // 3 = connected via a torsion
415 +    
416 +    vdwScale_.reserve(4);
417 +    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
418 +
419 +    electrostaticScale_.reserve(4);
420 +    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
421 +
422 +    vdwScale_[0] = 1.0;
423 +    vdwScale_[1] = fopts.getvdw12scale();
424 +    vdwScale_[2] = fopts.getvdw13scale();
425 +    vdwScale_[3] = fopts.getvdw14scale();
426 +    
427 +    electrostaticScale_[0] = 1.0;
428 +    electrostaticScale_[1] = fopts.getelectrostatic12scale();
429 +    electrostaticScale_[2] = fopts.getelectrostatic13scale();
430 +    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
431 +    
432 +    if (info_->getSimParams()->haveElectricField()) {
433 +      ElectricField* eField = new ElectricField(info_);
434 +      perturbations_.push_back(eField);
435 +    }
436 +
437 +    usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
438 +    
439 +    fDecomp_->distributeInitialData();
440 +    
441 +    initialized_ = true;
442 +    
443 +  }
444 +  
445 +  void ForceManager::calcForces() {
446 +    
447 +    if (!initialized_) initialize();
448 +    
449 +    preCalculation();  
450 +    shortRangeInteractions();
451 +    longRangeInteractions();
452 +    postCalculation();    
453 +  }
454 +  
455    void ForceManager::preCalculation() {
456      SimInfo::MoleculeIterator mi;
457      Molecule* mol;
# Line 87 | Line 459 | namespace OpenMD {
459      Atom* atom;
460      Molecule::RigidBodyIterator rbIter;
461      RigidBody* rb;
462 +    Molecule::CutoffGroupIterator ci;
463 +    CutoffGroup* cg;
464      
465 <    // forces are zeroed here, before any are accumulated.
466 <    // NOTE: do not rezero the forces in Fortran.
465 >    // forces and potentials are zeroed here, before any are
466 >    // accumulated.
467      
468 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
469 +
470 +    snap->setBondPotential(0.0);
471 +    snap->setBendPotential(0.0);
472 +    snap->setTorsionPotential(0.0);
473 +    snap->setInversionPotential(0.0);
474 +
475 +    potVec zeroPot(0.0);
476 +    snap->setLongRangePotential(zeroPot);
477 +    snap->setExcludedPotentials(zeroPot);
478 +
479 +    snap->setRestraintPotential(0.0);
480 +    snap->setRawPotential(0.0);
481 +
482      for (mol = info_->beginMolecule(mi); mol != NULL;
483           mol = info_->nextMolecule(mi)) {
484 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
484 >      for(atom = mol->beginAtom(ai); atom != NULL;
485 >          atom = mol->nextAtom(ai)) {
486          atom->zeroForcesAndTorques();
487        }
488 <          
488 >      
489        //change the positions of atoms which belong to the rigidbodies
490        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
491             rb = mol->nextRigidBody(rbIter)) {
492          rb->zeroForcesAndTorques();
493        }        
494 <          
494 >      
495 >      if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
496 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
497 >            cg = mol->nextCutoffGroup(ci)) {
498 >          //calculate the center of mass of cutoff group
499 >          cg->updateCOM();
500 >        }
501 >      }      
502      }
503      
504      // Zero out the stress tensor
505 <    tau *= 0.0;
506 <    
505 >    stressTensor *= 0.0;
506 >    // Zero out the heatFlux
507 >    fDecomp_->setHeatFlux( Vector3d(0.0) );    
508    }
509    
510 <  void ForceManager::calcShortRangeInteraction() {
510 >  void ForceManager::shortRangeInteractions() {
511      Molecule* mol;
512      RigidBody* rb;
513      Bond* bond;
# Line 140 | Line 537 | namespace OpenMD {
537  
538        for (bond = mol->beginBond(bondIter); bond != NULL;
539             bond = mol->nextBond(bondIter)) {
540 <        bond->calcForce();
540 >        bond->calcForce(doParticlePot_);
541          bondPotential += bond->getPotential();
542        }
543  
# Line 148 | Line 545 | namespace OpenMD {
545             bend = mol->nextBend(bendIter)) {
546          
547          RealType angle;
548 <        bend->calcForce(angle);
548 >        bend->calcForce(angle, doParticlePot_);
549          RealType currBendPot = bend->getPotential();          
550          
551          bendPotential += bend->getPotential();
552 <        std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
552 >        map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
553          if (i == bendDataSets.end()) {
554            BendDataSet dataSet;
555            dataSet.prev.angle = dataSet.curr.angle = angle;
556            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
557            dataSet.deltaV = 0.0;
558 <          bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
558 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
559 >                                                                  dataSet));
560          }else {
561            i->second.prev.angle = i->second.curr.angle;
562            i->second.prev.potential = i->second.curr.potential;
# Line 172 | Line 570 | namespace OpenMD {
570        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
571             torsion = mol->nextTorsion(torsionIter)) {
572          RealType angle;
573 <        torsion->calcForce(angle);
573 >        torsion->calcForce(angle, doParticlePot_);
574          RealType currTorsionPot = torsion->getPotential();
575          torsionPotential += torsion->getPotential();
576 <        std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
576 >        map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
577          if (i == torsionDataSets.end()) {
578            TorsionDataSet dataSet;
579            dataSet.prev.angle = dataSet.curr.angle = angle;
580            dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
581            dataSet.deltaV = 0.0;
582 <          torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
582 >          torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
583          }else {
584            i->second.prev.angle = i->second.curr.angle;
585            i->second.prev.potential = i->second.curr.potential;
# Line 191 | Line 589 | namespace OpenMD {
589                                     i->second.prev.potential);
590          }      
591        }      
592 <
592 >      
593        for (inversion = mol->beginInversion(inversionIter);
594             inversion != NULL;
595             inversion = mol->nextInversion(inversionIter)) {
596          RealType angle;
597 <        inversion->calcForce(angle);
597 >        inversion->calcForce(angle, doParticlePot_);
598          RealType currInversionPot = inversion->getPotential();
599          inversionPotential += inversion->getPotential();
600 <        std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
600 >        map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
601          if (i == inversionDataSets.end()) {
602            InversionDataSet dataSet;
603            dataSet.prev.angle = dataSet.curr.angle = angle;
604            dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
605            dataSet.deltaV = 0.0;
606 <          inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
606 >          inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
607          }else {
608            i->second.prev.angle = i->second.curr.angle;
609            i->second.prev.potential = i->second.curr.potential;
# Line 216 | Line 614 | namespace OpenMD {
614          }      
615        }      
616      }
617 <    
618 <    RealType  shortRangePotential = bondPotential + bendPotential +
619 <      torsionPotential +  inversionPotential;    
617 >
618 > #ifdef IS_MPI
619 >    // Collect from all nodes.  This should eventually be moved into a
620 >    // SystemDecomposition, but this is a better place than in
621 >    // Thermo to do the collection.
622 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
623 >                              MPI::SUM);
624 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
625 >                              MPI::SUM);
626 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
627 >                              MPI::REALTYPE, MPI::SUM);
628 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
629 >                              MPI::REALTYPE, MPI::SUM);
630 > #endif
631 >
632      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
633 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
634 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
635 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
636 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
637 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
633 >
634 >    curSnapshot->setBondPotential(bondPotential);
635 >    curSnapshot->setBendPotential(bendPotential);
636 >    curSnapshot->setTorsionPotential(torsionPotential);
637 >    curSnapshot->setInversionPotential(inversionPotential);
638      
639 +    // RealType shortRangePotential = bondPotential + bendPotential +
640 +    //   torsionPotential +  inversionPotential;    
641 +
642 +    // curSnapshot->setShortRangePotential(shortRangePotential);
643    }
644    
645 <  void ForceManager::calcLongRangeInteraction() {
232 <    Snapshot* curSnapshot;
233 <    DataStorage* config;
234 <    RealType* frc;
235 <    RealType* pos;
236 <    RealType* trq;
237 <    RealType* A;
238 <    RealType* electroFrame;
239 <    RealType* rc;
240 <    RealType* particlePot;
241 <    
242 <    //get current snapshot from SimInfo
243 <    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
244 <    
245 <    //get array pointers
246 <    config = &(curSnapshot->atomData);
247 <    frc = config->getArrayPointer(DataStorage::dslForce);
248 <    pos = config->getArrayPointer(DataStorage::dslPosition);
249 <    trq = config->getArrayPointer(DataStorage::dslTorque);
250 <    A   = config->getArrayPointer(DataStorage::dslAmat);
251 <    electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
252 <    particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
645 >  void ForceManager::longRangeInteractions() {
646  
647 +
648 +    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
649 +    DataStorage* config = &(curSnapshot->atomData);
650 +    DataStorage* cgConfig = &(curSnapshot->cgData);
651 +
652      //calculate the center of mass of cutoff group
653 +
654      SimInfo::MoleculeIterator mi;
655      Molecule* mol;
656      Molecule::CutoffGroupIterator ci;
657      CutoffGroup* cg;
658 <    Vector3d com;
659 <    std::vector<Vector3d> rcGroup;
261 <    
262 <    if(info_->getNCutoffGroups() > 0){
263 <      
658 >
659 >    if(info_->getNCutoffGroups() > 0){      
660        for (mol = info_->beginMolecule(mi); mol != NULL;
661             mol = info_->nextMolecule(mi)) {
662          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
663              cg = mol->nextCutoffGroup(ci)) {
664 <          cg->getCOM(com);
269 <          rcGroup.push_back(com);
664 >          cg->updateCOM();
665          }
666 <      }// end for (mol)
272 <      
273 <      rc = rcGroup[0].getArrayPointer();
666 >      }      
667      } else {
668        // center of mass of the group is the same as position of the atom  
669        // if cutoff group does not exist
670 <      rc = pos;
670 >      cgConfig->position = config->position;
671 >      cgConfig->velocity = config->velocity;
672      }
673 +
674 +    fDecomp_->zeroWorkArrays();
675 +    fDecomp_->distributeData();
676      
677 <    //initialize data before passing to fortran
678 <    RealType longRangePotential[LR_POT_TYPES];
679 <    RealType lrPot = 0.0;
680 <    int isError = 0;
677 >    int cg1, cg2, atom1, atom2, topoDist;
678 >    Vector3d d_grp, dag, d, gvel2, vel2;
679 >    RealType rgrpsq, rgrp, r2, r;
680 >    RealType electroMult, vdwMult;
681 >    RealType vij;
682 >    Vector3d fij, fg, f1;
683 >    tuple3<RealType, RealType, RealType> cuts;
684 >    RealType rCutSq;
685 >    bool in_switching_region;
686 >    RealType sw, dswdr, swderiv;
687 >    vector<int> atomListColumn, atomListRow, atomListLocal;
688 >    InteractionData idat;
689 >    SelfData sdat;
690 >    RealType mf;
691 >    RealType vpair;
692 >    RealType dVdFQ1(0.0);
693 >    RealType dVdFQ2(0.0);
694 >    potVec longRangePotential(0.0);
695 >    potVec workPot(0.0);
696 >    potVec exPot(0.0);
697 >    Vector3d eField1(0.0);
698 >    Vector3d eField2(0.0);
699 >    vector<int>::iterator ia, jb;
700  
701 <    for (int i=0; i<LR_POT_TYPES;i++){
702 <      longRangePotential[i]=0.0; //Initialize array
703 <    }
701 >    int loopStart, loopEnd;
702 >
703 >    idat.vdwMult = &vdwMult;
704 >    idat.electroMult = &electroMult;
705 >    idat.pot = &workPot;
706 >    idat.excludedPot = &exPot;
707 >    sdat.pot = fDecomp_->getEmbeddingPotential();
708 >    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
709 >    idat.vpair = &vpair;
710 >    idat.dVdFQ1 = &dVdFQ1;
711 >    idat.dVdFQ2 = &dVdFQ2;
712 >    idat.eField1 = &eField1;
713 >    idat.eField2 = &eField2;  
714 >    idat.f1 = &f1;
715 >    idat.sw = &sw;
716 >    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
717 >    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
718 >    idat.doParticlePot = doParticlePot_;
719 >    idat.doElectricField = doElectricField_;
720 >    sdat.doParticlePot = doParticlePot_;
721      
722 <    doForceLoop(pos,
723 <                rc,
724 <                A,
725 <                electroFrame,
726 <                frc,
294 <                trq,
295 <                tau.getArrayPointer(),
296 <                longRangePotential,
297 <                particlePot,
298 <                &isError );
299 <    
300 <    if( isError ){
301 <      sprintf( painCave.errMsg,
302 <               "Error returned from the fortran force calculation.\n" );
303 <      painCave.isFatal = 1;
304 <      simError();
722 >    loopEnd = PAIR_LOOP;
723 >    if (info_->requiresPrepair() ) {
724 >      loopStart = PREPAIR_LOOP;
725 >    } else {
726 >      loopStart = PAIR_LOOP;
727      }
728 <    for (int i=0; i<LR_POT_TYPES;i++){
729 <      lrPot += longRangePotential[i]; //Quick hack
728 >    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
729 >    
730 >      if (iLoop == loopStart) {
731 >        bool update_nlist = fDecomp_->checkNeighborList();
732 >        if (update_nlist) {
733 >          if (!usePeriodicBoundaryConditions_)
734 >            Mat3x3d bbox = thermo->getBoundingBox();
735 >          neighborList = fDecomp_->buildNeighborList();
736 >        }
737 >      }
738 >
739 >      for (vector<pair<int, int> >::iterator it = neighborList.begin();
740 >             it != neighborList.end(); ++it) {
741 >                
742 >        cg1 = (*it).first;
743 >        cg2 = (*it).second;
744 >        
745 >        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
746 >
747 >        d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
748 >
749 >        curSnapshot->wrapVector(d_grp);        
750 >        rgrpsq = d_grp.lengthSquare();
751 >        rCutSq = cuts.second;
752 >
753 >        if (rgrpsq < rCutSq) {
754 >          idat.rcut = &cuts.first;
755 >          if (iLoop == PAIR_LOOP) {
756 >            vij = 0.0;
757 >            fij = V3Zero;
758 >            eField1 = V3Zero;
759 >            eField2 = V3Zero;
760 >          }
761 >          
762 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
763 >                                                     rgrp);
764 >
765 >          atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
766 >          atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
767 >
768 >          if (doHeatFlux_)
769 >            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
770 >
771 >          for (ia = atomListRow.begin();
772 >               ia != atomListRow.end(); ++ia) {            
773 >            atom1 = (*ia);
774 >
775 >            for (jb = atomListColumn.begin();
776 >                 jb != atomListColumn.end(); ++jb) {              
777 >              atom2 = (*jb);
778 >
779 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
780 >
781 >                vpair = 0.0;
782 >                workPot = 0.0;
783 >                exPot = 0.0;
784 >                f1 = V3Zero;
785 >                dVdFQ1 = 0.0;
786 >                dVdFQ2 = 0.0;
787 >
788 >                fDecomp_->fillInteractionData(idat, atom1, atom2);
789 >
790 >                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
791 >                vdwMult = vdwScale_[topoDist];
792 >                electroMult = electrostaticScale_[topoDist];
793 >
794 >                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
795 >                  idat.d = &d_grp;
796 >                  idat.r2 = &rgrpsq;
797 >                  if (doHeatFlux_)
798 >                    vel2 = gvel2;
799 >                } else {
800 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
801 >                  curSnapshot->wrapVector( d );
802 >                  r2 = d.lengthSquare();
803 >                  idat.d = &d;
804 >                  idat.r2 = &r2;
805 >                  if (doHeatFlux_)
806 >                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
807 >                }
808 >              
809 >                r = sqrt( *(idat.r2) );
810 >                idat.rij = &r;
811 >              
812 >                if (iLoop == PREPAIR_LOOP) {
813 >                  interactionMan_->doPrePair(idat);
814 >                } else {
815 >                  interactionMan_->doPair(idat);
816 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
817 >                  vij += vpair;
818 >                  fij += f1;
819 >                  stressTensor -= outProduct( *(idat.d), f1);
820 >                  if (doHeatFlux_)
821 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
822 >                }
823 >              }
824 >            }
825 >          }
826 >
827 >          if (iLoop == PAIR_LOOP) {
828 >            if (in_switching_region) {
829 >              swderiv = vij * dswdr / rgrp;
830 >              fg = swderiv * d_grp;
831 >              fij += fg;
832 >
833 >              if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
834 >                if (!fDecomp_->skipAtomPair(atomListRow[0],
835 >                                            atomListColumn[0],
836 >                                            cg1, cg2)) {
837 >                  stressTensor -= outProduct( *(idat.d), fg);
838 >                  if (doHeatFlux_)
839 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
840 >                }                
841 >              }
842 >          
843 >              for (ia = atomListRow.begin();
844 >                   ia != atomListRow.end(); ++ia) {            
845 >                atom1 = (*ia);                
846 >                mf = fDecomp_->getMassFactorRow(atom1);
847 >                // fg is the force on atom ia due to cutoff group's
848 >                // presence in switching region
849 >                fg = swderiv * d_grp * mf;
850 >                fDecomp_->addForceToAtomRow(atom1, fg);
851 >                if (atomListRow.size() > 1) {
852 >                  if (info_->usesAtomicVirial()) {
853 >                    // find the distance between the atom
854 >                    // and the center of the cutoff group:
855 >                    dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
856 >                    stressTensor -= outProduct(dag, fg);
857 >                    if (doHeatFlux_)
858 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
859 >                  }
860 >                }
861 >              }
862 >              for (jb = atomListColumn.begin();
863 >                   jb != atomListColumn.end(); ++jb) {              
864 >                atom2 = (*jb);
865 >                mf = fDecomp_->getMassFactorColumn(atom2);
866 >                // fg is the force on atom jb due to cutoff group's
867 >                // presence in switching region
868 >                fg = -swderiv * d_grp * mf;
869 >                fDecomp_->addForceToAtomColumn(atom2, fg);
870 >
871 >                if (atomListColumn.size() > 1) {
872 >                  if (info_->usesAtomicVirial()) {
873 >                    // find the distance between the atom
874 >                    // and the center of the cutoff group:
875 >                    dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
876 >                    stressTensor -= outProduct(dag, fg);
877 >                    if (doHeatFlux_)
878 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
879 >                  }
880 >                }
881 >              }
882 >            }
883 >            //if (!info_->usesAtomicVirial()) {
884 >            //  stressTensor -= outProduct(d_grp, fij);
885 >            //  if (doHeatFlux_)
886 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
887 >            //}
888 >          }
889 >        }
890 >      }
891 >
892 >      if (iLoop == PREPAIR_LOOP) {
893 >        if (info_->requiresPrepair()) {
894 >
895 >          fDecomp_->collectIntermediateData();
896 >
897 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
898 >            fDecomp_->fillSelfData(sdat, atom1);
899 >            interactionMan_->doPreForce(sdat);
900 >          }
901 >
902 >          fDecomp_->distributeIntermediateData();
903 >
904 >        }
905 >      }
906      }
907 +    
908 +    // collects pairwise information
909 +    fDecomp_->collectData();
910          
911 <    //store the tau and long range potential    
912 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
913 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
914 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
911 >    if (info_->requiresSelfCorrection()) {
912 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
913 >        fDecomp_->fillSelfData(sdat, atom1);
914 >        interactionMan_->doSelfCorrection(sdat);
915 >      }
916 >    }
917 >
918 >    // collects single-atom information
919 >    fDecomp_->collectSelfData();
920 >
921 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
922 >      *(fDecomp_->getPairwisePotential());
923 >
924 >    curSnapshot->setLongRangePotential(longRangePotential);
925 >    
926 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
927 >                                         *(fDecomp_->getExcludedPotential()));
928 >
929    }
930  
931    
932    void ForceManager::postCalculation() {
933 +
934 +    vector<Perturbation*>::iterator pi;
935 +    for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
936 +      (*pi)->applyPerturbation();
937 +    }
938 +
939      SimInfo::MoleculeIterator mi;
940      Molecule* mol;
941      Molecule::RigidBodyIterator rbIter;
942      RigidBody* rb;
943      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
944 <    
944 >  
945      // collect the atomic forces onto rigid bodies
946      
947      for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 328 | Line 949 | namespace OpenMD {
949        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
950             rb = mol->nextRigidBody(rbIter)) {
951          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
952 <        tau += rbTau;
952 >        stressTensor += rbTau;
953        }
954      }
955      
956   #ifdef IS_MPI
957 <    Mat3x3d tmpTau(tau);
958 <    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
338 <                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
957 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
958 >                              MPI::REALTYPE, MPI::SUM);
959   #endif
960 <    curSnapshot->statData.setTau(tau);
961 <  }
960 >    curSnapshot->setStressTensor(stressTensor);
961 >    
962 >    if (info_->getSimParams()->getUseLongRangeCorrections()) {
963 >      /*
964 >      RealType vol = curSnapshot->getVolume();
965 >      RealType Elrc(0.0);
966 >      RealType Wlrc(0.0);
967  
968 < } //end namespace OpenMD
968 >      set<AtomType*>::iterator i;
969 >      set<AtomType*>::iterator j;
970 >    
971 >      RealType n_i, n_j;
972 >      RealType rho_i, rho_j;
973 >      pair<RealType, RealType> LRI;
974 >      
975 >      for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
976 >        n_i = RealType(info_->getGlobalCountOfType(*i));
977 >        rho_i = n_i /  vol;
978 >        for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
979 >          n_j = RealType(info_->getGlobalCountOfType(*j));
980 >          rho_j = n_j / vol;
981 >          
982 >          LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
983 >
984 >          Elrc += n_i   * rho_j * LRI.first;
985 >          Wlrc -= rho_i * rho_j * LRI.second;
986 >        }
987 >      }
988 >      Elrc *= 2.0 * NumericConstant::PI;
989 >      Wlrc *= 2.0 * NumericConstant::PI;
990 >
991 >      RealType lrp = curSnapshot->getLongRangePotential();
992 >      curSnapshot->setLongRangePotential(lrp + Elrc);
993 >      stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
994 >      curSnapshot->setStressTensor(stressTensor);
995 >      */
996 >    
997 >    }
998 >  }
999 > }

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