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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1489 by gezelter, Tue Aug 10 18:34:59 2010 UTC vs.
Revision 1787 by gezelter, Wed Aug 29 18:13:11 2012 UTC

# Line 36 | Line 36
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).                        
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   /**
# Line 47 | Line 48
48   * @version 1.0
49   */
50  
51 +
52   #include "brains/ForceManager.hpp"
53   #include "primitives/Molecule.hpp"
52 – #include "UseTheForce/doForces_interface.h"
54   #define __OPENMD_C
54 – #include "UseTheForce/DarkSide/fInteractionMap.h"
55   #include "utils/simError.h"
56   #include "primitives/Bond.hpp"
57   #include "primitives/Bend.hpp"
58   #include "primitives/Torsion.hpp"
59   #include "primitives/Inversion.hpp"
60 + #include "nonbonded/NonBondedInteraction.hpp"
61 + #include "perturbations/ElectricField.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 <                                               NBforcesInitialized_(false) {
73 <    lj_ = LJ::Instance();
74 <    lj_->setForceField(info_->getForceField());
71 >  ForceManager::ForceManager(SimInfo * info) : info_(info) {
72 >    forceField_ = info_->getForceField();
73 >    interactionMan_ = new InteractionManager();
74 >    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
75 >  }
76  
77 <    gb_ = GB::Instance();
78 <    gb_->setForceField(info_->getForceField());
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 >    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 >    if (simParams_->haveMDfileVersion())
117 >      mdFileVersion = simParams_->getMDfileVersion();
118 >    else
119 >      mdFileVersion = 0;
120 >  
121 >    if (simParams_->haveCutoffRadius()) {
122 >      rCut_ = simParams_->getCutoffRadius();
123 >    } else {      
124 >      if (info_->usesElectrostaticAtoms()) {
125 >        sprintf(painCave.errMsg,
126 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
127 >                "\tOpenMD will use a default value of 12.0 angstroms"
128 >                "\tfor the cutoffRadius.\n");
129 >        painCave.isFatal = 0;
130 >        painCave.severity = OPENMD_INFO;
131 >        simError();
132 >        rCut_ = 12.0;
133 >      } else {
134 >        RealType thisCut;
135 >        set<AtomType*>::iterator i;
136 >        set<AtomType*> atomTypes;
137 >        atomTypes = info_->getSimulatedAtomTypes();        
138 >        for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
139 >          thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
140 >          rCut_ = max(thisCut, rCut_);
141 >        }
142 >        sprintf(painCave.errMsg,
143 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
144 >                "\tOpenMD will use %lf angstroms.\n",
145 >                rCut_);
146 >        painCave.isFatal = 0;
147 >        painCave.severity = OPENMD_INFO;
148 >        simError();
149 >      }
150 >    }
151  
152 <    sticky_ = Sticky::Instance();
153 <    sticky_->setForceField(info_->getForceField());
152 >    fDecomp_->setUserCutoff(rCut_);
153 >    interactionMan_->setCutoffRadius(rCut_);
154  
155 <    eam_ = EAM::Instance();
156 <    eam_->setForceField(info_->getForceField());
155 >    map<string, CutoffMethod> stringToCutoffMethod;
156 >    stringToCutoffMethod["HARD"] = HARD;
157 >    stringToCutoffMethod["SWITCHED"] = SWITCHED;
158 >    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
159 >    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
160 >  
161 >    if (simParams_->haveCutoffMethod()) {
162 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
163 >      map<string, CutoffMethod>::iterator i;
164 >      i = stringToCutoffMethod.find(cutMeth);
165 >      if (i == stringToCutoffMethod.end()) {
166 >        sprintf(painCave.errMsg,
167 >                "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
168 >                "\tShould be one of: "
169 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
170 >                cutMeth.c_str());
171 >        painCave.isFatal = 1;
172 >        painCave.severity = OPENMD_ERROR;
173 >        simError();
174 >      } else {
175 >        cutoffMethod_ = i->second;
176 >      }
177 >    } else {
178 >      if (mdFileVersion > 1) {
179 >        sprintf(painCave.errMsg,
180 >                "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
181 >                "\tOpenMD will use SHIFTED_FORCE.\n");
182 >        painCave.isFatal = 0;
183 >        painCave.severity = OPENMD_INFO;
184 >        simError();
185 >        cutoffMethod_ = SHIFTED_FORCE;        
186 >      } else {
187 >        // handle the case where the old file version was in play
188 >        // (there should be no cutoffMethod, so we have to deduce it
189 >        // from other data).        
190  
191 <    sc_ = SC::Instance();
192 <    sc_->setForceField(info_->getForceField());
193 <  }
194 <
195 <  void ForceManager::calcForces() {
191 >        sprintf(painCave.errMsg,
192 >                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
193 >                "\tOpenMD found a file which does not set a cutoffMethod.\n"
194 >                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
195 >                "\tbehavior of the older (version 1) code.  To remove this\n"
196 >                "\twarning, add an explicit cutoffMethod and change the top\n"
197 >                "\tof the file so that it begins with <OpenMD version=2>\n");
198 >        painCave.isFatal = 0;
199 >        painCave.severity = OPENMD_WARNING;
200 >        simError();            
201 >                
202 >        // The old file version tethered the shifting behavior to the
203 >        // electrostaticSummationMethod keyword.
204 >        
205 >        if (simParams_->haveElectrostaticSummationMethod()) {
206 >          string myMethod = simParams_->getElectrostaticSummationMethod();
207 >          toUpper(myMethod);
208 >        
209 >          if (myMethod == "SHIFTED_POTENTIAL") {
210 >            cutoffMethod_ = SHIFTED_POTENTIAL;
211 >          } else if (myMethod == "SHIFTED_FORCE") {
212 >            cutoffMethod_ = SHIFTED_FORCE;
213 >          }
214 >        
215 >          if (simParams_->haveSwitchingRadius())
216 >            rSwitch_ = simParams_->getSwitchingRadius();
217 >
218 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
219 >            if (simParams_->haveSwitchingRadius()){
220 >              sprintf(painCave.errMsg,
221 >                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
222 >                      "\tA value was set for the switchingRadius\n"
223 >                      "\teven though the electrostaticSummationMethod was\n"
224 >                      "\tset to %s\n", myMethod.c_str());
225 >              painCave.severity = OPENMD_WARNING;
226 >              painCave.isFatal = 1;
227 >              simError();            
228 >            }
229 >          }
230 >          if (abs(rCut_ - rSwitch_) < 0.0001) {
231 >            if (cutoffMethod_ == SHIFTED_FORCE) {              
232 >              sprintf(painCave.errMsg,
233 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
234 >                      "\tcutoffRadius and switchingRadius are set to the\n"
235 >                      "\tsame value.  OpenMD will use shifted force\n"
236 >                      "\tpotentials instead of switching functions.\n");
237 >              painCave.isFatal = 0;
238 >              painCave.severity = OPENMD_WARNING;
239 >              simError();            
240 >            } else {
241 >              cutoffMethod_ = SHIFTED_POTENTIAL;
242 >              sprintf(painCave.errMsg,
243 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
244 >                      "\tcutoffRadius and switchingRadius are set to the\n"
245 >                      "\tsame value.  OpenMD will use shifted potentials\n"
246 >                      "\tinstead of switching functions.\n");
247 >              painCave.isFatal = 0;
248 >              painCave.severity = OPENMD_WARNING;
249 >              simError();            
250 >            }
251 >          }
252 >        }
253 >      }
254 >    }
255 >
256 >    map<string, CutoffPolicy> stringToCutoffPolicy;
257 >    stringToCutoffPolicy["MIX"] = MIX;
258 >    stringToCutoffPolicy["MAX"] = MAX;
259 >    stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
260 >
261 >    string cutPolicy;
262 >    if (forceFieldOptions_.haveCutoffPolicy()){
263 >      cutPolicy = forceFieldOptions_.getCutoffPolicy();
264 >    }else if (simParams_->haveCutoffPolicy()) {
265 >      cutPolicy = simParams_->getCutoffPolicy();
266 >    }
267 >
268 >    if (!cutPolicy.empty()){
269 >      toUpper(cutPolicy);
270 >      map<string, CutoffPolicy>::iterator i;
271 >      i = stringToCutoffPolicy.find(cutPolicy);
272 >
273 >      if (i == stringToCutoffPolicy.end()) {
274 >        sprintf(painCave.errMsg,
275 >                "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
276 >                "\tShould be one of: "
277 >                "MIX, MAX, or TRADITIONAL\n",
278 >                cutPolicy.c_str());
279 >        painCave.isFatal = 1;
280 >        painCave.severity = OPENMD_ERROR;
281 >        simError();
282 >      } else {
283 >        cutoffPolicy_ = i->second;
284 >      }
285 >    } else {
286 >      sprintf(painCave.errMsg,
287 >              "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
288 >              "\tOpenMD will use TRADITIONAL.\n");
289 >      painCave.isFatal = 0;
290 >      painCave.severity = OPENMD_INFO;
291 >      simError();
292 >      cutoffPolicy_ = TRADITIONAL;        
293 >    }
294 >
295 >    fDecomp_->setCutoffPolicy(cutoffPolicy_);
296 >        
297 >    // create the switching function object:
298 >
299 >    switcher_ = new SwitchingFunction();
300 >  
301 >    if (cutoffMethod_ == SWITCHED) {
302 >      if (simParams_->haveSwitchingRadius()) {
303 >        rSwitch_ = simParams_->getSwitchingRadius();
304 >        if (rSwitch_ > rCut_) {        
305 >          sprintf(painCave.errMsg,
306 >                  "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
307 >                  "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
308 >          painCave.isFatal = 1;
309 >          painCave.severity = OPENMD_ERROR;
310 >          simError();
311 >        }
312 >      } else {      
313 >        rSwitch_ = 0.85 * rCut_;
314 >        sprintf(painCave.errMsg,
315 >                "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
316 >                "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
317 >                "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
318 >        painCave.isFatal = 0;
319 >        painCave.severity = OPENMD_WARNING;
320 >        simError();
321 >      }
322 >    } else {
323 >      if (mdFileVersion > 1) {
324 >        // throw an error if we define a switching radius and don't need one.
325 >        // older file versions should not do this.
326 >        if (simParams_->haveSwitchingRadius()) {
327 >          map<string, CutoffMethod>::const_iterator it;
328 >          string theMeth;
329 >          for (it = stringToCutoffMethod.begin();
330 >               it != stringToCutoffMethod.end(); ++it) {
331 >            if (it->second == cutoffMethod_) {
332 >              theMeth = it->first;
333 >              break;
334 >            }
335 >          }
336 >          sprintf(painCave.errMsg,
337 >                  "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
338 >                  "\tis not set to SWITCHED, so switchingRadius value\n"
339 >                  "\twill be ignored for this simulation\n", theMeth.c_str());
340 >          painCave.isFatal = 0;
341 >          painCave.severity = OPENMD_WARNING;
342 >          simError();
343 >        }
344 >      }
345 >      rSwitch_ = rCut_;
346 >    }
347      
348 <    if (!info_->isFortranInitialized()) {
348 >    // Default to cubic switching function.
349 >    sft_ = cubic;
350 >    if (simParams_->haveSwitchingFunctionType()) {
351 >      string funcType = simParams_->getSwitchingFunctionType();
352 >      toUpper(funcType);
353 >      if (funcType == "CUBIC") {
354 >        sft_ = cubic;
355 >      } else {
356 >        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
357 >          sft_ = fifth_order_poly;
358 >        } else {
359 >          // throw error        
360 >          sprintf( painCave.errMsg,
361 >                   "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
362 >                   "\tswitchingFunctionType must be one of: "
363 >                   "\"cubic\" or \"fifth_order_polynomial\".",
364 >                   funcType.c_str() );
365 >          painCave.isFatal = 1;
366 >          painCave.severity = OPENMD_ERROR;
367 >          simError();
368 >        }          
369 >      }
370 >    }
371 >    switcher_->setSwitchType(sft_);
372 >    switcher_->setSwitch(rSwitch_, rCut_);
373 >  }
374 >
375 >
376 >
377 >  
378 >  void ForceManager::initialize() {
379 >
380 >    if (!info_->isTopologyDone()) {
381 >
382        info_->update();
383 +      interactionMan_->setSimInfo(info_);
384 +      interactionMan_->initialize();
385 +
386 +      // We want to delay the cutoffs until after the interaction
387 +      // manager has set up the atom-atom interactions so that we can
388 +      // query them for suggested cutoff values
389 +      setupCutoffs();
390 +
391 +      info_->prepareTopology();      
392 +
393 +      doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
394 +      doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
395 +      if (doHeatFlux_) doParticlePot_ = true;
396 +
397 +      doElectricField_ = info_->getSimParams()->getOutputElectricField();
398 +  
399      }
400 +
401 +    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
402      
403 <    preCalculation();
403 >    // Force fields can set options on how to scale van der Waals and
404 >    // electrostatic interactions for atoms connected via bonds, bends
405 >    // and torsions in this case the topological distance between
406 >    // atoms is:
407 >    // 0 = topologically unconnected
408 >    // 1 = bonded together
409 >    // 2 = connected via a bend
410 >    // 3 = connected via a torsion
411      
412 <    calcShortRangeInteraction();
412 >    vdwScale_.reserve(4);
413 >    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
414  
415 <    calcLongRangeInteraction();
415 >    electrostaticScale_.reserve(4);
416 >    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
417  
418 <    postCalculation();
418 >    vdwScale_[0] = 1.0;
419 >    vdwScale_[1] = fopts.getvdw12scale();
420 >    vdwScale_[2] = fopts.getvdw13scale();
421 >    vdwScale_[3] = fopts.getvdw14scale();
422      
423 +    electrostaticScale_[0] = 1.0;
424 +    electrostaticScale_[1] = fopts.getelectrostatic12scale();
425 +    electrostaticScale_[2] = fopts.getelectrostatic13scale();
426 +    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
427 +    
428 +    if (info_->getSimParams()->haveElectricField()) {
429 +      ElectricField* eField = new ElectricField(info_);
430 +      perturbations_.push_back(eField);
431 +    }
432 +
433 +    fDecomp_->distributeInitialData();
434 +
435 +    initialized_ = true;
436 +
437    }
438 +
439 +  void ForceManager::calcForces() {
440 +    
441 +    if (!initialized_) initialize();
442 +
443 +    preCalculation();  
444 +    shortRangeInteractions();
445 +    longRangeInteractions();
446 +    postCalculation();    
447 +  }
448    
449    void ForceManager::preCalculation() {
450      SimInfo::MoleculeIterator mi;
# Line 101 | Line 453 | namespace OpenMD {
453      Atom* atom;
454      Molecule::RigidBodyIterator rbIter;
455      RigidBody* rb;
456 +    Molecule::CutoffGroupIterator ci;
457 +    CutoffGroup* cg;
458      
459 <    // forces are zeroed here, before any are accumulated.
460 <    // NOTE: do not rezero the forces in Fortran.
459 >    // forces and potentials are zeroed here, before any are
460 >    // accumulated.
461      
462 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
463 +
464 +    snap->setBondPotential(0.0);
465 +    snap->setBendPotential(0.0);
466 +    snap->setTorsionPotential(0.0);
467 +    snap->setInversionPotential(0.0);
468 +
469 +    potVec zeroPot(0.0);
470 +    snap->setLongRangePotential(zeroPot);
471 +    snap->setExcludedPotentials(zeroPot);
472 +
473 +    snap->setRestraintPotential(0.0);
474 +    snap->setRawPotential(0.0);
475 +
476      for (mol = info_->beginMolecule(mi); mol != NULL;
477           mol = info_->nextMolecule(mi)) {
478 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
478 >      for(atom = mol->beginAtom(ai); atom != NULL;
479 >          atom = mol->nextAtom(ai)) {
480          atom->zeroForcesAndTorques();
481        }
482 <          
482 >      
483        //change the positions of atoms which belong to the rigidbodies
484        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
485             rb = mol->nextRigidBody(rbIter)) {
486          rb->zeroForcesAndTorques();
487        }        
488 <          
488 >      
489 >      if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
490 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
491 >            cg = mol->nextCutoffGroup(ci)) {
492 >          //calculate the center of mass of cutoff group
493 >          cg->updateCOM();
494 >        }
495 >      }      
496      }
497      
498      // Zero out the stress tensor
499 <    tau *= 0.0;
500 <    
499 >    stressTensor *= 0.0;
500 >    // Zero out the heatFlux
501 >    fDecomp_->setHeatFlux( Vector3d(0.0) );    
502    }
503    
504 <  void ForceManager::calcShortRangeInteraction() {
504 >  void ForceManager::shortRangeInteractions() {
505      Molecule* mol;
506      RigidBody* rb;
507      Bond* bond;
# Line 154 | Line 531 | namespace OpenMD {
531  
532        for (bond = mol->beginBond(bondIter); bond != NULL;
533             bond = mol->nextBond(bondIter)) {
534 <        bond->calcForce();
534 >        bond->calcForce(doParticlePot_);
535          bondPotential += bond->getPotential();
536        }
537  
# Line 162 | Line 539 | namespace OpenMD {
539             bend = mol->nextBend(bendIter)) {
540          
541          RealType angle;
542 <        bend->calcForce(angle);
542 >        bend->calcForce(angle, doParticlePot_);
543          RealType currBendPot = bend->getPotential();          
544          
545          bendPotential += bend->getPotential();
546 <        std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
546 >        map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
547          if (i == bendDataSets.end()) {
548            BendDataSet dataSet;
549            dataSet.prev.angle = dataSet.curr.angle = angle;
550            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
551            dataSet.deltaV = 0.0;
552 <          bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
552 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
553 >                                                                  dataSet));
554          }else {
555            i->second.prev.angle = i->second.curr.angle;
556            i->second.prev.potential = i->second.curr.potential;
# Line 186 | Line 564 | namespace OpenMD {
564        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
565             torsion = mol->nextTorsion(torsionIter)) {
566          RealType angle;
567 <        torsion->calcForce(angle);
567 >        torsion->calcForce(angle, doParticlePot_);
568          RealType currTorsionPot = torsion->getPotential();
569          torsionPotential += torsion->getPotential();
570 <        std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
570 >        map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
571          if (i == torsionDataSets.end()) {
572            TorsionDataSet dataSet;
573            dataSet.prev.angle = dataSet.curr.angle = angle;
574            dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
575            dataSet.deltaV = 0.0;
576 <          torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
576 >          torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
577          }else {
578            i->second.prev.angle = i->second.curr.angle;
579            i->second.prev.potential = i->second.curr.potential;
# Line 205 | Line 583 | namespace OpenMD {
583                                     i->second.prev.potential);
584          }      
585        }      
586 <
586 >      
587        for (inversion = mol->beginInversion(inversionIter);
588             inversion != NULL;
589             inversion = mol->nextInversion(inversionIter)) {
590          RealType angle;
591 <        inversion->calcForce(angle);
591 >        inversion->calcForce(angle, doParticlePot_);
592          RealType currInversionPot = inversion->getPotential();
593          inversionPotential += inversion->getPotential();
594 <        std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
594 >        map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
595          if (i == inversionDataSets.end()) {
596            InversionDataSet dataSet;
597            dataSet.prev.angle = dataSet.curr.angle = angle;
598            dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
599            dataSet.deltaV = 0.0;
600 <          inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
600 >          inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
601          }else {
602            i->second.prev.angle = i->second.curr.angle;
603            i->second.prev.potential = i->second.curr.potential;
# Line 230 | Line 608 | namespace OpenMD {
608          }      
609        }      
610      }
611 <    
612 <    RealType  shortRangePotential = bondPotential + bendPotential +
613 <      torsionPotential +  inversionPotential;    
611 >
612 > #ifdef IS_MPI
613 >    // Collect from all nodes.  This should eventually be moved into a
614 >    // SystemDecomposition, but this is a better place than in
615 >    // Thermo to do the collection.
616 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
617 >                              MPI::SUM);
618 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
619 >                              MPI::SUM);
620 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
621 >                              MPI::REALTYPE, MPI::SUM);
622 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
623 >                              MPI::REALTYPE, MPI::SUM);
624 > #endif
625 >
626      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
627 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
628 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
629 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
630 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
631 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
627 >
628 >    curSnapshot->setBondPotential(bondPotential);
629 >    curSnapshot->setBendPotential(bendPotential);
630 >    curSnapshot->setTorsionPotential(torsionPotential);
631 >    curSnapshot->setInversionPotential(inversionPotential);
632      
633 +    // RealType shortRangePotential = bondPotential + bendPotential +
634 +    //   torsionPotential +  inversionPotential;    
635 +
636 +    // curSnapshot->setShortRangePotential(shortRangePotential);
637    }
638    
639 <  void ForceManager::calcLongRangeInteraction() {
246 <    Snapshot* curSnapshot;
247 <    DataStorage* config;
248 <    RealType* frc;
249 <    RealType* pos;
250 <    RealType* trq;
251 <    RealType* A;
252 <    RealType* electroFrame;
253 <    RealType* rc;
254 <    RealType* particlePot;
255 <    
256 <    //get current snapshot from SimInfo
257 <    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
258 <    
259 <    //get array pointers
260 <    config = &(curSnapshot->atomData);
261 <    frc = config->getArrayPointer(DataStorage::dslForce);
262 <    pos = config->getArrayPointer(DataStorage::dslPosition);
263 <    trq = config->getArrayPointer(DataStorage::dslTorque);
264 <    A   = config->getArrayPointer(DataStorage::dslAmat);
265 <    electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
266 <    particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
639 >  void ForceManager::longRangeInteractions() {
640  
641 +
642 +    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
643 +    DataStorage* config = &(curSnapshot->atomData);
644 +    DataStorage* cgConfig = &(curSnapshot->cgData);
645 +
646      //calculate the center of mass of cutoff group
647 +
648      SimInfo::MoleculeIterator mi;
649      Molecule* mol;
650      Molecule::CutoffGroupIterator ci;
651      CutoffGroup* cg;
652 <    Vector3d com;
653 <    std::vector<Vector3d> rcGroup;
275 <    
276 <    if(info_->getNCutoffGroups() > 0){
277 <      
652 >
653 >    if(info_->getNCutoffGroups() > 0){      
654        for (mol = info_->beginMolecule(mi); mol != NULL;
655             mol = info_->nextMolecule(mi)) {
656          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
657              cg = mol->nextCutoffGroup(ci)) {
658 <          cg->getCOM(com);
283 <          rcGroup.push_back(com);
658 >          cg->updateCOM();
659          }
660 <      }// end for (mol)
286 <      
287 <      rc = rcGroup[0].getArrayPointer();
660 >      }      
661      } else {
662        // center of mass of the group is the same as position of the atom  
663        // if cutoff group does not exist
664 <      rc = pos;
664 >      cgConfig->position = config->position;
665 >      cgConfig->velocity = config->velocity;
666      }
667 +
668 +    fDecomp_->zeroWorkArrays();
669 +    fDecomp_->distributeData();
670      
671 <    //initialize data before passing to fortran
672 <    RealType longRangePotential[LR_POT_TYPES];
673 <    RealType lrPot = 0.0;
674 <    Vector3d totalDipole;
675 <    int isError = 0;
671 >    int cg1, cg2, atom1, atom2, topoDist;
672 >    Vector3d d_grp, dag, d, gvel2, vel2;
673 >    RealType rgrpsq, rgrp, r2, r;
674 >    RealType electroMult, vdwMult;
675 >    RealType vij;
676 >    Vector3d fij, fg, f1;
677 >    tuple3<RealType, RealType, RealType> cuts;
678 >    RealType rCutSq;
679 >    bool in_switching_region;
680 >    RealType sw, dswdr, swderiv;
681 >    vector<int> atomListColumn, atomListRow, atomListLocal;
682 >    InteractionData idat;
683 >    SelfData sdat;
684 >    RealType mf;
685 >    RealType vpair;
686 >    RealType dVdFQ1(0.0);
687 >    RealType dVdFQ2(0.0);
688 >    potVec longRangePotential(0.0);
689 >    potVec workPot(0.0);
690 >    potVec exPot(0.0);
691 >    Vector3d eField1(0.0);
692 >    Vector3d eField2(0.0);
693 >    vector<int>::iterator ia, jb;
694  
695 <    for (int i=0; i<LR_POT_TYPES;i++){
696 <      longRangePotential[i]=0.0; //Initialize array
697 <    }
695 >    int loopStart, loopEnd;
696 >
697 >    idat.vdwMult = &vdwMult;
698 >    idat.electroMult = &electroMult;
699 >    idat.pot = &workPot;
700 >    idat.excludedPot = &exPot;
701 >    sdat.pot = fDecomp_->getEmbeddingPotential();
702 >    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
703 >    idat.vpair = &vpair;
704 >    idat.dVdFQ1 = &dVdFQ1;
705 >    idat.dVdFQ2 = &dVdFQ2;
706 >    idat.eField1 = &eField1;
707 >    idat.eField2 = &eField2;  
708 >    idat.f1 = &f1;
709 >    idat.sw = &sw;
710 >    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
711 >    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
712 >    idat.doParticlePot = doParticlePot_;
713 >    idat.doElectricField = doElectricField_;
714 >    sdat.doParticlePot = doParticlePot_;
715      
716 <    doForceLoop(pos,
717 <                rc,
718 <                A,
719 <                electroFrame,
720 <                frc,
309 <                trq,
310 <                tau.getArrayPointer(),
311 <                longRangePotential,
312 <                particlePot,
313 <                &isError );
314 <    
315 <    if( isError ){
316 <      sprintf( painCave.errMsg,
317 <               "Error returned from the fortran force calculation.\n" );
318 <      painCave.isFatal = 1;
319 <      simError();
716 >    loopEnd = PAIR_LOOP;
717 >    if (info_->requiresPrepair() ) {
718 >      loopStart = PREPAIR_LOOP;
719 >    } else {
720 >      loopStart = PAIR_LOOP;
721      }
722 <    for (int i=0; i<LR_POT_TYPES;i++){
723 <      lrPot += longRangePotential[i]; //Quick hack
722 >    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
723 >    
724 >      if (iLoop == loopStart) {
725 >        bool update_nlist = fDecomp_->checkNeighborList();
726 >        if (update_nlist)
727 >          neighborList = fDecomp_->buildNeighborList();
728 >      }            
729 >
730 >      for (vector<pair<int, int> >::iterator it = neighborList.begin();
731 >             it != neighborList.end(); ++it) {
732 >                
733 >        cg1 = (*it).first;
734 >        cg2 = (*it).second;
735 >        
736 >        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
737 >
738 >        d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
739 >
740 >        curSnapshot->wrapVector(d_grp);        
741 >        rgrpsq = d_grp.lengthSquare();
742 >        rCutSq = cuts.second;
743 >
744 >        if (rgrpsq < rCutSq) {
745 >          idat.rcut = &cuts.first;
746 >          if (iLoop == PAIR_LOOP) {
747 >            vij = 0.0;
748 >            fij = V3Zero;
749 >          }
750 >          
751 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
752 >                                                     rgrp);
753 >
754 >          atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
755 >          atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
756 >
757 >          if (doHeatFlux_)
758 >            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
759 >
760 >          for (ia = atomListRow.begin();
761 >               ia != atomListRow.end(); ++ia) {            
762 >            atom1 = (*ia);
763 >
764 >            for (jb = atomListColumn.begin();
765 >                 jb != atomListColumn.end(); ++jb) {              
766 >              atom2 = (*jb);
767 >
768 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
769 >
770 >                vpair = 0.0;
771 >                workPot = 0.0;
772 >                exPot = 0.0;
773 >                f1 = V3Zero;
774 >                dVdFQ1 = 0.0;
775 >                dVdFQ2 = 0.0;
776 >
777 >                fDecomp_->fillInteractionData(idat, atom1, atom2);
778 >
779 >                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
780 >                vdwMult = vdwScale_[topoDist];
781 >                electroMult = electrostaticScale_[topoDist];
782 >
783 >                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
784 >                  idat.d = &d_grp;
785 >                  idat.r2 = &rgrpsq;
786 >                  if (doHeatFlux_)
787 >                    vel2 = gvel2;
788 >                } else {
789 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
790 >                  curSnapshot->wrapVector( d );
791 >                  r2 = d.lengthSquare();
792 >                  idat.d = &d;
793 >                  idat.r2 = &r2;
794 >                  if (doHeatFlux_)
795 >                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
796 >                }
797 >              
798 >                r = sqrt( *(idat.r2) );
799 >                idat.rij = &r;
800 >              
801 >                if (iLoop == PREPAIR_LOOP) {
802 >                  interactionMan_->doPrePair(idat);
803 >                } else {
804 >                  interactionMan_->doPair(idat);
805 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
806 >                  vij += vpair;
807 >                  fij += f1;
808 >                  stressTensor -= outProduct( *(idat.d), f1);
809 >                  if (doHeatFlux_)
810 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
811 >                }
812 >              }
813 >            }
814 >          }
815 >
816 >          if (iLoop == PAIR_LOOP) {
817 >            if (in_switching_region) {
818 >              swderiv = vij * dswdr / rgrp;
819 >              fg = swderiv * d_grp;
820 >              fij += fg;
821 >
822 >              if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
823 >                stressTensor -= outProduct( *(idat.d), fg);
824 >                if (doHeatFlux_)
825 >                  fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
826 >                
827 >              }
828 >          
829 >              for (ia = atomListRow.begin();
830 >                   ia != atomListRow.end(); ++ia) {            
831 >                atom1 = (*ia);                
832 >                mf = fDecomp_->getMassFactorRow(atom1);
833 >                // fg is the force on atom ia due to cutoff group's
834 >                // presence in switching region
835 >                fg = swderiv * d_grp * mf;
836 >                fDecomp_->addForceToAtomRow(atom1, fg);
837 >                if (atomListRow.size() > 1) {
838 >                  if (info_->usesAtomicVirial()) {
839 >                    // find the distance between the atom
840 >                    // and the center of the cutoff group:
841 >                    dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
842 >                    stressTensor -= outProduct(dag, fg);
843 >                    if (doHeatFlux_)
844 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
845 >                  }
846 >                }
847 >              }
848 >              for (jb = atomListColumn.begin();
849 >                   jb != atomListColumn.end(); ++jb) {              
850 >                atom2 = (*jb);
851 >                mf = fDecomp_->getMassFactorColumn(atom2);
852 >                // fg is the force on atom jb due to cutoff group's
853 >                // presence in switching region
854 >                fg = -swderiv * d_grp * mf;
855 >                fDecomp_->addForceToAtomColumn(atom2, fg);
856 >
857 >                if (atomListColumn.size() > 1) {
858 >                  if (info_->usesAtomicVirial()) {
859 >                    // find the distance between the atom
860 >                    // and the center of the cutoff group:
861 >                    dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
862 >                    stressTensor -= outProduct(dag, fg);
863 >                    if (doHeatFlux_)
864 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
865 >                  }
866 >                }
867 >              }
868 >            }
869 >            //if (!info_->usesAtomicVirial()) {
870 >            //  stressTensor -= outProduct(d_grp, fij);
871 >            //  if (doHeatFlux_)
872 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
873 >            //}
874 >          }
875 >        }
876 >      }
877 >
878 >      if (iLoop == PREPAIR_LOOP) {
879 >        if (info_->requiresPrepair()) {
880 >
881 >          fDecomp_->collectIntermediateData();
882 >
883 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
884 >            fDecomp_->fillSelfData(sdat, atom1);
885 >            interactionMan_->doPreForce(sdat);
886 >          }
887 >
888 >          fDecomp_->distributeIntermediateData();
889 >
890 >        }
891 >      }
892      }
893      
894 <    // grab the simulation box dipole moment if specified
895 <    if (info_->getCalcBoxDipole()){
896 <      getAccumulatedBoxDipole(totalDipole.getArrayPointer());
897 <      
898 <      curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
899 <      curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
900 <      curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
894 >    // collects pairwise information
895 >    fDecomp_->collectData();
896 >        
897 >    if (info_->requiresSelfCorrection()) {
898 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
899 >        fDecomp_->fillSelfData(sdat, atom1);
900 >        interactionMan_->doSelfCorrection(sdat);
901 >      }
902      }
903 +
904 +    // collects single-atom information
905 +    fDecomp_->collectSelfData();
906 +
907 +    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
908 +      *(fDecomp_->getPairwisePotential());
909 +
910 +    curSnapshot->setLongRangePotential(longRangePotential);
911      
912 <    //store the tau and long range potential    
913 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
914 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
337 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
912 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
913 >                                         *(fDecomp_->getExcludedPotential()));
914 >
915    }
916  
917    
918    void ForceManager::postCalculation() {
919 +
920 +    vector<Perturbation*>::iterator pi;
921 +    for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
922 +      (*pi)->applyPerturbation();
923 +    }
924 +
925      SimInfo::MoleculeIterator mi;
926      Molecule* mol;
927      Molecule::RigidBodyIterator rbIter;
928      RigidBody* rb;
929      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
930 <    
930 >  
931      // collect the atomic forces onto rigid bodies
932      
933      for (mol = info_->beginMolecule(mi); mol != NULL;
# Line 352 | Line 935 | namespace OpenMD {
935        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
936             rb = mol->nextRigidBody(rbIter)) {
937          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
938 <        tau += rbTau;
938 >        stressTensor += rbTau;
939        }
940      }
941      
942   #ifdef IS_MPI
943 <    Mat3x3d tmpTau(tau);
944 <    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
362 <                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
943 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
944 >                              MPI::REALTYPE, MPI::SUM);
945   #endif
946 <    curSnapshot->statData.setTau(tau);
946 >    curSnapshot->setStressTensor(stressTensor);
947 >    
948    }
366 –
949   } //end namespace OpenMD

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