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Revision 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC vs.
Revision 1850 by gezelter, Wed Feb 20 15:39:39 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 "parallel/ForceDecomposition.hpp"
60 < //#include "parallel/SerialDecomposition.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) {
72 < #ifdef IS_MPI
73 <    decomp_ = new ForceDecomposition(info_);
69 < #else
70 <    //  decomp_ = new SerialDecomposition(info);
71 < #endif
70 >  ForceManager::ForceManager(SimInfo * info) : info_(info) {
71 >    forceField_ = info_->getForceField();
72 >    interactionMan_ = new InteractionManager();
73 >    fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
74    }
75 <
76 <  void ForceManager::calcForces() {
75 >
76 >  /**
77 >   * setupCutoffs
78 >   *
79 >   * Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
80 >   * and cutoffPolicy
81 >   *
82 >   * cutoffRadius : realType
83 >   *  If the cutoffRadius was explicitly set, use that value.
84 >   *  If the cutoffRadius was not explicitly set:
85 >   *      Are there electrostatic atoms?  Use 12.0 Angstroms.
86 >   *      No electrostatic atoms?  Poll the atom types present in the
87 >   *      simulation for suggested cutoff values (e.g. 2.5 * sigma).
88 >   *      Use the maximum suggested value that was found.
89 >   *
90 >   * cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
91 >   *                        or SHIFTED_POTENTIAL)
92 >   *      If cutoffMethod was explicitly set, use that choice.
93 >   *      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
94 >   *
95 >   * cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
96 >   *      If cutoffPolicy was explicitly set, use that choice.
97 >   *      If cutoffPolicy was not explicitly set, use TRADITIONAL
98 >   *
99 >   * switchingRadius : realType
100 >   *  If the cutoffMethod was set to SWITCHED:
101 >   *      If the switchingRadius was explicitly set, use that value
102 >   *          (but do a sanity check first).
103 >   *      If the switchingRadius was not explicitly set: use 0.85 *
104 >   *      cutoffRadius_
105 >   *  If the cutoffMethod was not set to SWITCHED:
106 >   *      Set switchingRadius equal to cutoffRadius for safety.
107 >   */
108 >  void ForceManager::setupCutoffs() {
109      
110 +    Globals* simParams_ = info_->getSimParams();
111 +    ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
112 +    int mdFileVersion;
113 +    rCut_ = 0.0; //Needs a value for a later max() call;  
114 +    
115 +    if (simParams_->haveMDfileVersion())
116 +      mdFileVersion = simParams_->getMDfileVersion();
117 +    else
118 +      mdFileVersion = 0;
119 +  
120 +    // We need the list of simulated atom types to figure out cutoffs
121 +    // as well as long range corrections.
122  
123 <    if (!info_->isFortranInitialized()) {
124 <      info_->update();
125 <      nbiMan_->setSimInfo(info_);
126 <      nbiMan_->initialize();
127 <      decomp_->distributeInitialData();
128 <      info_->setupFortran();
123 >    set<AtomType*>::iterator i;
124 >    set<AtomType*> atomTypes_;
125 >    atomTypes_ = info_->getSimulatedAtomTypes();
126 >
127 >    if (simParams_->haveCutoffRadius()) {
128 >      rCut_ = simParams_->getCutoffRadius();
129 >    } else {      
130 >      if (info_->usesElectrostaticAtoms()) {
131 >        sprintf(painCave.errMsg,
132 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
133 >                "\tOpenMD will use a default value of 12.0 angstroms"
134 >                "\tfor the cutoffRadius.\n");
135 >        painCave.isFatal = 0;
136 >        painCave.severity = OPENMD_INFO;
137 >        simError();
138 >        rCut_ = 12.0;
139 >      } else {
140 >        RealType thisCut;
141 >        for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
142 >          thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
143 >          rCut_ = max(thisCut, rCut_);
144 >        }
145 >        sprintf(painCave.errMsg,
146 >                "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
147 >                "\tOpenMD will use %lf angstroms.\n",
148 >                rCut_);
149 >        painCave.isFatal = 0;
150 >        painCave.severity = OPENMD_INFO;
151 >        simError();
152 >      }
153 >    }
154 >
155 >    fDecomp_->setUserCutoff(rCut_);
156 >    interactionMan_->setCutoffRadius(rCut_);
157 >
158 >    map<string, CutoffMethod> stringToCutoffMethod;
159 >    stringToCutoffMethod["HARD"] = HARD;
160 >    stringToCutoffMethod["SWITCHED"] = SWITCHED;
161 >    stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;    
162 >    stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
163 >  
164 >    if (simParams_->haveCutoffMethod()) {
165 >      string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
166 >      map<string, CutoffMethod>::iterator i;
167 >      i = stringToCutoffMethod.find(cutMeth);
168 >      if (i == stringToCutoffMethod.end()) {
169 >        sprintf(painCave.errMsg,
170 >                "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
171 >                "\tShould be one of: "
172 >                "HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
173 >                cutMeth.c_str());
174 >        painCave.isFatal = 1;
175 >        painCave.severity = OPENMD_ERROR;
176 >        simError();
177 >      } else {
178 >        cutoffMethod_ = i->second;
179 >      }
180 >    } else {
181 >      if (mdFileVersion > 1) {
182 >        sprintf(painCave.errMsg,
183 >                "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
184 >                "\tOpenMD will use SHIFTED_FORCE.\n");
185 >        painCave.isFatal = 0;
186 >        painCave.severity = OPENMD_INFO;
187 >        simError();
188 >        cutoffMethod_ = SHIFTED_FORCE;        
189 >      } else {
190 >        // handle the case where the old file version was in play
191 >        // (there should be no cutoffMethod, so we have to deduce it
192 >        // from other data).        
193 >
194 >        sprintf(painCave.errMsg,
195 >                "ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
196 >                "\tOpenMD found a file which does not set a cutoffMethod.\n"
197 >                "\tOpenMD will attempt to deduce a cutoffMethod using the\n"
198 >                "\tbehavior of the older (version 1) code.  To remove this\n"
199 >                "\twarning, add an explicit cutoffMethod and change the top\n"
200 >                "\tof the file so that it begins with <OpenMD version=2>\n");
201 >        painCave.isFatal = 0;
202 >        painCave.severity = OPENMD_WARNING;
203 >        simError();            
204 >                
205 >        // The old file version tethered the shifting behavior to the
206 >        // electrostaticSummationMethod keyword.
207 >        
208 >        if (simParams_->haveElectrostaticSummationMethod()) {
209 >          string myMethod = simParams_->getElectrostaticSummationMethod();
210 >          toUpper(myMethod);
211 >        
212 >          if (myMethod == "SHIFTED_POTENTIAL") {
213 >            cutoffMethod_ = SHIFTED_POTENTIAL;
214 >          } else if (myMethod == "SHIFTED_FORCE") {
215 >            cutoffMethod_ = SHIFTED_FORCE;
216 >          }
217 >        
218 >          if (simParams_->haveSwitchingRadius())
219 >            rSwitch_ = simParams_->getSwitchingRadius();
220 >
221 >          if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
222 >            if (simParams_->haveSwitchingRadius()){
223 >              sprintf(painCave.errMsg,
224 >                      "ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
225 >                      "\tA value was set for the switchingRadius\n"
226 >                      "\teven though the electrostaticSummationMethod was\n"
227 >                      "\tset to %s\n", myMethod.c_str());
228 >              painCave.severity = OPENMD_WARNING;
229 >              painCave.isFatal = 1;
230 >              simError();            
231 >            }
232 >          }
233 >          if (abs(rCut_ - rSwitch_) < 0.0001) {
234 >            if (cutoffMethod_ == SHIFTED_FORCE) {              
235 >              sprintf(painCave.errMsg,
236 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
237 >                      "\tcutoffRadius and switchingRadius are set to the\n"
238 >                      "\tsame value.  OpenMD will use shifted force\n"
239 >                      "\tpotentials instead of switching functions.\n");
240 >              painCave.isFatal = 0;
241 >              painCave.severity = OPENMD_WARNING;
242 >              simError();            
243 >            } else {
244 >              cutoffMethod_ = SHIFTED_POTENTIAL;
245 >              sprintf(painCave.errMsg,
246 >                      "ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
247 >                      "\tcutoffRadius and switchingRadius are set to the\n"
248 >                      "\tsame value.  OpenMD will use shifted potentials\n"
249 >                      "\tinstead of switching functions.\n");
250 >              painCave.isFatal = 0;
251 >              painCave.severity = OPENMD_WARNING;
252 >              simError();            
253 >            }
254 >          }
255 >        }
256 >      }
257 >    }
258 >
259 >    map<string, CutoffPolicy> stringToCutoffPolicy;
260 >    stringToCutoffPolicy["MIX"] = MIX;
261 >    stringToCutoffPolicy["MAX"] = MAX;
262 >    stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;    
263 >
264 >    string cutPolicy;
265 >    if (forceFieldOptions_.haveCutoffPolicy()){
266 >      cutPolicy = forceFieldOptions_.getCutoffPolicy();
267 >    }else if (simParams_->haveCutoffPolicy()) {
268 >      cutPolicy = simParams_->getCutoffPolicy();
269 >    }
270 >
271 >    if (!cutPolicy.empty()){
272 >      toUpper(cutPolicy);
273 >      map<string, CutoffPolicy>::iterator i;
274 >      i = stringToCutoffPolicy.find(cutPolicy);
275 >
276 >      if (i == stringToCutoffPolicy.end()) {
277 >        sprintf(painCave.errMsg,
278 >                "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
279 >                "\tShould be one of: "
280 >                "MIX, MAX, or TRADITIONAL\n",
281 >                cutPolicy.c_str());
282 >        painCave.isFatal = 1;
283 >        painCave.severity = OPENMD_ERROR;
284 >        simError();
285 >      } else {
286 >        cutoffPolicy_ = i->second;
287 >      }
288 >    } else {
289 >      sprintf(painCave.errMsg,
290 >              "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
291 >              "\tOpenMD will use TRADITIONAL.\n");
292 >      painCave.isFatal = 0;
293 >      painCave.severity = OPENMD_INFO;
294 >      simError();
295 >      cutoffPolicy_ = TRADITIONAL;        
296      }
297 +
298 +    fDecomp_->setCutoffPolicy(cutoffPolicy_);
299 +        
300 +    // create the switching function object:
301 +
302 +    switcher_ = new SwitchingFunction();
303 +  
304 +    if (cutoffMethod_ == SWITCHED) {
305 +      if (simParams_->haveSwitchingRadius()) {
306 +        rSwitch_ = simParams_->getSwitchingRadius();
307 +        if (rSwitch_ > rCut_) {        
308 +          sprintf(painCave.errMsg,
309 +                  "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
310 +                  "than the cutoffRadius(%f)\n", rSwitch_, rCut_);
311 +          painCave.isFatal = 1;
312 +          painCave.severity = OPENMD_ERROR;
313 +          simError();
314 +        }
315 +      } else {      
316 +        rSwitch_ = 0.85 * rCut_;
317 +        sprintf(painCave.errMsg,
318 +                "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
319 +                "\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
320 +                "\tswitchingRadius = %f. for this simulation\n", rSwitch_);
321 +        painCave.isFatal = 0;
322 +        painCave.severity = OPENMD_WARNING;
323 +        simError();
324 +      }
325 +    } else {
326 +      if (mdFileVersion > 1) {
327 +        // throw an error if we define a switching radius and don't need one.
328 +        // older file versions should not do this.
329 +        if (simParams_->haveSwitchingRadius()) {
330 +          map<string, CutoffMethod>::const_iterator it;
331 +          string theMeth;
332 +          for (it = stringToCutoffMethod.begin();
333 +               it != stringToCutoffMethod.end(); ++it) {
334 +            if (it->second == cutoffMethod_) {
335 +              theMeth = it->first;
336 +              break;
337 +            }
338 +          }
339 +          sprintf(painCave.errMsg,
340 +                  "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
341 +                  "\tis not set to SWITCHED, so switchingRadius value\n"
342 +                  "\twill be ignored for this simulation\n", theMeth.c_str());
343 +          painCave.isFatal = 0;
344 +          painCave.severity = OPENMD_WARNING;
345 +          simError();
346 +        }
347 +      }
348 +      rSwitch_ = rCut_;
349 +    }
350      
351 <    preCalculation();  
352 <    calcShortRangeInteraction();
353 <    calcLongRangeInteraction();
354 <    postCalculation();
351 >    // Default to cubic switching function.
352 >    sft_ = cubic;
353 >    if (simParams_->haveSwitchingFunctionType()) {
354 >      string funcType = simParams_->getSwitchingFunctionType();
355 >      toUpper(funcType);
356 >      if (funcType == "CUBIC") {
357 >        sft_ = cubic;
358 >      } else {
359 >        if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
360 >          sft_ = fifth_order_poly;
361 >        } else {
362 >          // throw error        
363 >          sprintf( painCave.errMsg,
364 >                   "ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
365 >                   "\tswitchingFunctionType must be one of: "
366 >                   "\"cubic\" or \"fifth_order_polynomial\".",
367 >                   funcType.c_str() );
368 >          painCave.isFatal = 1;
369 >          painCave.severity = OPENMD_ERROR;
370 >          simError();
371 >        }          
372 >      }
373 >    }
374 >    switcher_->setSwitchType(sft_);
375 >    switcher_->setSwitch(rSwitch_, rCut_);
376 >  }
377 >
378 >
379 >
380 >  
381 >  void ForceManager::initialize() {
382 >
383 >    if (!info_->isTopologyDone()) {
384 >
385 >      info_->update();
386 >      interactionMan_->setSimInfo(info_);
387 >      interactionMan_->initialize();
388 >
389 >      // We want to delay the cutoffs until after the interaction
390 >      // manager has set up the atom-atom interactions so that we can
391 >      // query them for suggested cutoff values
392 >      setupCutoffs();
393 >
394 >      info_->prepareTopology();      
395 >
396 >      doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
397 >      doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
398 >      if (doHeatFlux_) doParticlePot_ = true;
399 >
400 >      doElectricField_ = info_->getSimParams()->getOutputElectricField();
401 >  
402 >    }
403 >
404 >    ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
405      
406 +    // Force fields can set options on how to scale van der Waals and
407 +    // electrostatic interactions for atoms connected via bonds, bends
408 +    // and torsions in this case the topological distance between
409 +    // atoms is:
410 +    // 0 = topologically unconnected
411 +    // 1 = bonded together
412 +    // 2 = connected via a bend
413 +    // 3 = connected via a torsion
414 +    
415 +    vdwScale_.reserve(4);
416 +    fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
417 +
418 +    electrostaticScale_.reserve(4);
419 +    fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
420 +
421 +    vdwScale_[0] = 1.0;
422 +    vdwScale_[1] = fopts.getvdw12scale();
423 +    vdwScale_[2] = fopts.getvdw13scale();
424 +    vdwScale_[3] = fopts.getvdw14scale();
425 +    
426 +    electrostaticScale_[0] = 1.0;
427 +    electrostaticScale_[1] = fopts.getelectrostatic12scale();
428 +    electrostaticScale_[2] = fopts.getelectrostatic13scale();
429 +    electrostaticScale_[3] = fopts.getelectrostatic14scale();    
430 +    
431 +    if (info_->getSimParams()->haveElectricField()) {
432 +      ElectricField* eField = new ElectricField(info_);
433 +      perturbations_.push_back(eField);
434 +    }
435 +
436 +    fDecomp_->distributeInitialData();
437 +
438 +    initialized_ = true;
439 +
440    }
441 +
442 +  void ForceManager::calcForces() {
443 +    
444 +    if (!initialized_) initialize();
445 +
446 +    preCalculation();  
447 +    shortRangeInteractions();
448 +    longRangeInteractions();
449 +    postCalculation();    
450 +  }
451    
452    void ForceManager::preCalculation() {
453      SimInfo::MoleculeIterator mi;
# Line 99 | Line 459 | namespace OpenMD {
459      Molecule::CutoffGroupIterator ci;
460      CutoffGroup* cg;
461      
462 <    // forces are zeroed here, before any are accumulated.
463 <    // NOTE: do not rezero the forces in Fortran.
462 >    // forces and potentials are zeroed here, before any are
463 >    // accumulated.
464      
465 +    Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
466 +
467 +    snap->setBondPotential(0.0);
468 +    snap->setBendPotential(0.0);
469 +    snap->setTorsionPotential(0.0);
470 +    snap->setInversionPotential(0.0);
471 +
472 +    potVec zeroPot(0.0);
473 +    snap->setLongRangePotential(zeroPot);
474 +    snap->setExcludedPotentials(zeroPot);
475 +
476 +    snap->setRestraintPotential(0.0);
477 +    snap->setRawPotential(0.0);
478 +
479      for (mol = info_->beginMolecule(mi); mol != NULL;
480           mol = info_->nextMolecule(mi)) {
481 <      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
481 >      for(atom = mol->beginAtom(ai); atom != NULL;
482 >          atom = mol->nextAtom(ai)) {
483          atom->zeroForcesAndTorques();
484        }
485 <          
485 >      
486        //change the positions of atoms which belong to the rigidbodies
487        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
488             rb = mol->nextRigidBody(rbIter)) {
489          rb->zeroForcesAndTorques();
490        }        
491 <
491 >      
492        if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
118 –        std::cerr << "should not see me \n";
493          for(cg = mol->beginCutoffGroup(ci); cg != NULL;
494              cg = mol->nextCutoffGroup(ci)) {
495            //calculate the center of mass of cutoff group
# Line 123 | Line 497 | namespace OpenMD {
497          }
498        }      
499      }
126 –  
127 –    // Zero out the stress tensor
128 –    tau *= 0.0;
500      
501 +    // Zero out the stress tensor
502 +    stressTensor *= 0.0;
503 +    // Zero out the heatFlux
504 +    fDecomp_->setHeatFlux( Vector3d(0.0) );    
505    }
506    
507 <  void ForceManager::calcShortRangeInteraction() {
507 >  void ForceManager::shortRangeInteractions() {
508      Molecule* mol;
509      RigidBody* rb;
510      Bond* bond;
# Line 159 | Line 534 | namespace OpenMD {
534  
535        for (bond = mol->beginBond(bondIter); bond != NULL;
536             bond = mol->nextBond(bondIter)) {
537 <        bond->calcForce();
537 >        bond->calcForce(doParticlePot_);
538          bondPotential += bond->getPotential();
539        }
540  
# Line 167 | Line 542 | namespace OpenMD {
542             bend = mol->nextBend(bendIter)) {
543          
544          RealType angle;
545 <        bend->calcForce(angle);
545 >        bend->calcForce(angle, doParticlePot_);
546          RealType currBendPot = bend->getPotential();          
547          
548          bendPotential += bend->getPotential();
549 <        std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
549 >        map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
550          if (i == bendDataSets.end()) {
551            BendDataSet dataSet;
552            dataSet.prev.angle = dataSet.curr.angle = angle;
553            dataSet.prev.potential = dataSet.curr.potential = currBendPot;
554            dataSet.deltaV = 0.0;
555 <          bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
555 >          bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
556 >                                                                  dataSet));
557          }else {
558            i->second.prev.angle = i->second.curr.angle;
559            i->second.prev.potential = i->second.curr.potential;
# Line 191 | Line 567 | namespace OpenMD {
567        for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
568             torsion = mol->nextTorsion(torsionIter)) {
569          RealType angle;
570 <        torsion->calcForce(angle);
570 >        torsion->calcForce(angle, doParticlePot_);
571          RealType currTorsionPot = torsion->getPotential();
572          torsionPotential += torsion->getPotential();
573 <        std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
573 >        map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
574          if (i == torsionDataSets.end()) {
575            TorsionDataSet dataSet;
576            dataSet.prev.angle = dataSet.curr.angle = angle;
577            dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
578            dataSet.deltaV = 0.0;
579 <          torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
579 >          torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
580          }else {
581            i->second.prev.angle = i->second.curr.angle;
582            i->second.prev.potential = i->second.curr.potential;
# Line 210 | Line 586 | namespace OpenMD {
586                                     i->second.prev.potential);
587          }      
588        }      
589 <
589 >      
590        for (inversion = mol->beginInversion(inversionIter);
591             inversion != NULL;
592             inversion = mol->nextInversion(inversionIter)) {
593          RealType angle;
594 <        inversion->calcForce(angle);
594 >        inversion->calcForce(angle, doParticlePot_);
595          RealType currInversionPot = inversion->getPotential();
596          inversionPotential += inversion->getPotential();
597 <        std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
597 >        map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
598          if (i == inversionDataSets.end()) {
599            InversionDataSet dataSet;
600            dataSet.prev.angle = dataSet.curr.angle = angle;
601            dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
602            dataSet.deltaV = 0.0;
603 <          inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
603 >          inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
604          }else {
605            i->second.prev.angle = i->second.curr.angle;
606            i->second.prev.potential = i->second.curr.potential;
# Line 235 | Line 611 | namespace OpenMD {
611          }      
612        }      
613      }
614 <    
615 <    RealType  shortRangePotential = bondPotential + bendPotential +
616 <      torsionPotential +  inversionPotential;    
614 >
615 > #ifdef IS_MPI
616 >    // Collect from all nodes.  This should eventually be moved into a
617 >    // SystemDecomposition, but this is a better place than in
618 >    // Thermo to do the collection.
619 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
620 >                              MPI::SUM);
621 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
622 >                              MPI::SUM);
623 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
624 >                              MPI::REALTYPE, MPI::SUM);
625 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
626 >                              MPI::REALTYPE, MPI::SUM);
627 > #endif
628 >
629      Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
630 <    curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
631 <    curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
632 <    curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
633 <    curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
634 <    curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
630 >
631 >    curSnapshot->setBondPotential(bondPotential);
632 >    curSnapshot->setBendPotential(bendPotential);
633 >    curSnapshot->setTorsionPotential(torsionPotential);
634 >    curSnapshot->setInversionPotential(inversionPotential);
635      
636 +    // RealType shortRangePotential = bondPotential + bendPotential +
637 +    //   torsionPotential +  inversionPotential;    
638 +
639 +    // curSnapshot->setShortRangePotential(shortRangePotential);
640    }
641    
642 <  void ForceManager::calcLongRangeInteraction() {
251 <    Snapshot* curSnapshot;
252 <    DataStorage* config;
253 <    DataStorage* cgConfig;
254 <    RealType* frc;
255 <    RealType* pos;
256 <    RealType* trq;
257 <    RealType* A;
258 <    RealType* electroFrame;
259 <    RealType* rc;
260 <    RealType* particlePot;
261 <    
262 <    //get current snapshot from SimInfo
263 <    curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
264 <    
265 <    //get array pointers
266 <    config = &(curSnapshot->atomData);
267 <    cgConfig = &(curSnapshot->cgData);
268 <    frc = config->getArrayPointer(DataStorage::dslForce);
269 <    pos = config->getArrayPointer(DataStorage::dslPosition);
270 <    trq = config->getArrayPointer(DataStorage::dslTorque);
271 <    A   = config->getArrayPointer(DataStorage::dslAmat);
272 <    electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
273 <    particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
642 >  void ForceManager::longRangeInteractions() {
643  
644 <    if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
645 <      std::cerr << "should not see me \n";
646 <      rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
644 >
645 >    Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
646 >    DataStorage* config = &(curSnapshot->atomData);
647 >    DataStorage* cgConfig = &(curSnapshot->cgData);
648 >
649 >    //calculate the center of mass of cutoff group
650 >
651 >    SimInfo::MoleculeIterator mi;
652 >    Molecule* mol;
653 >    Molecule::CutoffGroupIterator ci;
654 >    CutoffGroup* cg;
655 >
656 >    if(info_->getNCutoffGroups() > 0){      
657 >      for (mol = info_->beginMolecule(mi); mol != NULL;
658 >           mol = info_->nextMolecule(mi)) {
659 >        for(cg = mol->beginCutoffGroup(ci); cg != NULL;
660 >            cg = mol->nextCutoffGroup(ci)) {
661 >          cg->updateCOM();
662 >        }
663 >      }      
664      } else {
665        // center of mass of the group is the same as position of the atom  
666        // if cutoff group does not exist
667 <      rc = pos;
667 >      cgConfig->position = config->position;
668 >      cgConfig->velocity = config->velocity;
669      }
670 +
671 +    fDecomp_->zeroWorkArrays();
672 +    fDecomp_->distributeData();
673      
674 <    //initialize data before passing to fortran
675 <    RealType longRangePotential[LR_POT_TYPES];
676 <    RealType lrPot = 0.0;
677 <    int isError = 0;
674 >    int cg1, cg2, atom1, atom2, topoDist;
675 >    Vector3d d_grp, dag, d, gvel2, vel2;
676 >    RealType rgrpsq, rgrp, r2, r;
677 >    RealType electroMult, vdwMult;
678 >    RealType vij;
679 >    Vector3d fij, fg, f1;
680 >    tuple3<RealType, RealType, RealType> cuts;
681 >    RealType rCutSq;
682 >    bool in_switching_region;
683 >    RealType sw, dswdr, swderiv;
684 >    vector<int> atomListColumn, atomListRow, atomListLocal;
685 >    InteractionData idat;
686 >    SelfData sdat;
687 >    RealType mf;
688 >    RealType vpair;
689 >    RealType dVdFQ1(0.0);
690 >    RealType dVdFQ2(0.0);
691 >    potVec longRangePotential(0.0);
692 >    potVec workPot(0.0);
693 >    potVec exPot(0.0);
694 >    Vector3d eField1(0.0);
695 >    Vector3d eField2(0.0);
696 >    vector<int>::iterator ia, jb;
697  
698 <    for (int i=0; i<LR_POT_TYPES;i++){
699 <      longRangePotential[i]=0.0; //Initialize array
698 >    int loopStart, loopEnd;
699 >
700 >    idat.vdwMult = &vdwMult;
701 >    idat.electroMult = &electroMult;
702 >    idat.pot = &workPot;
703 >    idat.excludedPot = &exPot;
704 >    sdat.pot = fDecomp_->getEmbeddingPotential();
705 >    sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
706 >    idat.vpair = &vpair;
707 >    idat.dVdFQ1 = &dVdFQ1;
708 >    idat.dVdFQ2 = &dVdFQ2;
709 >    idat.eField1 = &eField1;
710 >    idat.eField2 = &eField2;  
711 >    idat.f1 = &f1;
712 >    idat.sw = &sw;
713 >    idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
714 >    idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
715 >    idat.doParticlePot = doParticlePot_;
716 >    idat.doElectricField = doElectricField_;
717 >    sdat.doParticlePot = doParticlePot_;
718 >    
719 >    loopEnd = PAIR_LOOP;
720 >    if (info_->requiresPrepair() ) {
721 >      loopStart = PREPAIR_LOOP;
722 >    } else {
723 >      loopStart = PAIR_LOOP;
724      }
725 +    for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
726      
727 <    decomp_->distributeData();
727 >      if (iLoop == loopStart) {
728 >        bool update_nlist = fDecomp_->checkNeighborList();
729 >        if (update_nlist)
730 >          neighborList = fDecomp_->buildNeighborList();
731 >      }            
732  
733 <    int nLoops = 1;
734 <    for (int iLoop = 0; iLoop < nLoops; iLoop++) {
735 <      doForceLoop(pos,
736 <                  rc,
737 <                  A,
738 <                  electroFrame,
739 <                  frc,
302 <                  trq,
303 <                  tau.getArrayPointer(),
304 <                  longRangePotential,
305 <                  particlePot,
306 <                  &isError );  
733 >      for (vector<pair<int, int> >::iterator it = neighborList.begin();
734 >             it != neighborList.end(); ++it) {
735 >                
736 >        cg1 = (*it).first;
737 >        cg2 = (*it).second;
738 >        
739 >        cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
740  
741 <      if (nLoops > 1) {
309 <        decomp_->collectIntermediateData();
310 <        decomp_->distributeIntermediateData();
311 <      }
312 <    }
313 <  
314 <    decomp_->collectData();
741 >        d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
742  
743 <    if( isError ){
744 <      sprintf( painCave.errMsg,
745 <               "Error returned from the fortran force calculation.\n" );
746 <      painCave.isFatal = 1;
747 <      simError();
748 <    }
749 <    for (int i=0; i<LR_POT_TYPES;i++){
750 <      lrPot += longRangePotential[i]; //Quick hack
743 >        curSnapshot->wrapVector(d_grp);        
744 >        rgrpsq = d_grp.lengthSquare();
745 >        rCutSq = cuts.second;
746 >
747 >        if (rgrpsq < rCutSq) {
748 >          idat.rcut = &cuts.first;
749 >          if (iLoop == PAIR_LOOP) {
750 >            vij = 0.0;
751 >            fij = V3Zero;
752 >            eField1 = V3Zero;
753 >            eField2 = V3Zero;
754 >          }
755 >          
756 >          in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
757 >                                                     rgrp);
758 >
759 >          atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
760 >          atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
761 >
762 >          if (doHeatFlux_)
763 >            gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
764 >
765 >          for (ia = atomListRow.begin();
766 >               ia != atomListRow.end(); ++ia) {            
767 >            atom1 = (*ia);
768 >
769 >            for (jb = atomListColumn.begin();
770 >                 jb != atomListColumn.end(); ++jb) {              
771 >              atom2 = (*jb);
772 >
773 >              if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
774 >
775 >                vpair = 0.0;
776 >                workPot = 0.0;
777 >                exPot = 0.0;
778 >                f1 = V3Zero;
779 >                dVdFQ1 = 0.0;
780 >                dVdFQ2 = 0.0;
781 >
782 >                fDecomp_->fillInteractionData(idat, atom1, atom2);
783 >
784 >                topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
785 >                vdwMult = vdwScale_[topoDist];
786 >                electroMult = electrostaticScale_[topoDist];
787 >
788 >                if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
789 >                  idat.d = &d_grp;
790 >                  idat.r2 = &rgrpsq;
791 >                  if (doHeatFlux_)
792 >                    vel2 = gvel2;
793 >                } else {
794 >                  d = fDecomp_->getInteratomicVector(atom1, atom2);
795 >                  curSnapshot->wrapVector( d );
796 >                  r2 = d.lengthSquare();
797 >                  idat.d = &d;
798 >                  idat.r2 = &r2;
799 >                  if (doHeatFlux_)
800 >                    vel2 = fDecomp_->getAtomVelocityColumn(atom2);
801 >                }
802 >              
803 >                r = sqrt( *(idat.r2) );
804 >                idat.rij = &r;
805 >              
806 >                if (iLoop == PREPAIR_LOOP) {
807 >                  interactionMan_->doPrePair(idat);
808 >                } else {
809 >                  interactionMan_->doPair(idat);
810 >                  fDecomp_->unpackInteractionData(idat, atom1, atom2);
811 >                  vij += vpair;
812 >                  fij += f1;
813 >                  stressTensor -= outProduct( *(idat.d), f1);
814 >                  if (doHeatFlux_)
815 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
816 >                }
817 >              }
818 >            }
819 >          }
820 >
821 >          if (iLoop == PAIR_LOOP) {
822 >            if (in_switching_region) {
823 >              swderiv = vij * dswdr / rgrp;
824 >              fg = swderiv * d_grp;
825 >              fij += fg;
826 >
827 >              if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
828 >                if (!fDecomp_->skipAtomPair(atomListRow[0],
829 >                                            atomListColumn[0],
830 >                                            cg1, cg2)) {
831 >                  stressTensor -= outProduct( *(idat.d), fg);
832 >                  if (doHeatFlux_)
833 >                    fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
834 >                }                
835 >              }
836 >          
837 >              for (ia = atomListRow.begin();
838 >                   ia != atomListRow.end(); ++ia) {            
839 >                atom1 = (*ia);                
840 >                mf = fDecomp_->getMassFactorRow(atom1);
841 >                // fg is the force on atom ia due to cutoff group's
842 >                // presence in switching region
843 >                fg = swderiv * d_grp * mf;
844 >                fDecomp_->addForceToAtomRow(atom1, fg);
845 >                if (atomListRow.size() > 1) {
846 >                  if (info_->usesAtomicVirial()) {
847 >                    // find the distance between the atom
848 >                    // and the center of the cutoff group:
849 >                    dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
850 >                    stressTensor -= outProduct(dag, fg);
851 >                    if (doHeatFlux_)
852 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
853 >                  }
854 >                }
855 >              }
856 >              for (jb = atomListColumn.begin();
857 >                   jb != atomListColumn.end(); ++jb) {              
858 >                atom2 = (*jb);
859 >                mf = fDecomp_->getMassFactorColumn(atom2);
860 >                // fg is the force on atom jb due to cutoff group's
861 >                // presence in switching region
862 >                fg = -swderiv * d_grp * mf;
863 >                fDecomp_->addForceToAtomColumn(atom2, fg);
864 >
865 >                if (atomListColumn.size() > 1) {
866 >                  if (info_->usesAtomicVirial()) {
867 >                    // find the distance between the atom
868 >                    // and the center of the cutoff group:
869 >                    dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
870 >                    stressTensor -= outProduct(dag, fg);
871 >                    if (doHeatFlux_)
872 >                      fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
873 >                  }
874 >                }
875 >              }
876 >            }
877 >            //if (!info_->usesAtomicVirial()) {
878 >            //  stressTensor -= outProduct(d_grp, fij);
879 >            //  if (doHeatFlux_)
880 >            //     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
881 >            //}
882 >          }
883 >        }
884 >      }
885 >
886 >      if (iLoop == PREPAIR_LOOP) {
887 >        if (info_->requiresPrepair()) {
888 >
889 >          fDecomp_->collectIntermediateData();
890 >
891 >          for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
892 >            fDecomp_->fillSelfData(sdat, atom1);
893 >            interactionMan_->doPreForce(sdat);
894 >          }
895 >
896 >          fDecomp_->distributeIntermediateData();
897 >
898 >        }
899 >      }
900      }
901 +    
902 +    // collects pairwise information
903 +    fDecomp_->collectData();
904          
905 <    //store the tau and long range potential    
906 <    curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
907 <    curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
908 <    curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
905 >    if (info_->requiresSelfCorrection()) {
906 >      for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
907 >        fDecomp_->fillSelfData(sdat, atom1);
908 >        interactionMan_->doSelfCorrection(sdat);
909 >      }
910 >    }
911 >
912 >    // collects single-atom information
913 >    fDecomp_->collectSelfData();
914 >
915 >    longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
916 >      *(fDecomp_->getPairwisePotential());
917 >
918 >    curSnapshot->setLongRangePotential(longRangePotential);
919 >    
920 >    curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
921 >                                         *(fDecomp_->getExcludedPotential()));
922 >
923    }
924  
925    
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;
# Line 344 | Line 943 | namespace OpenMD {
943        for (rb = mol->beginRigidBody(rbIter); rb != NULL;
944             rb = mol->nextRigidBody(rbIter)) {
945          Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
946 <        tau += rbTau;
946 >        stressTensor += rbTau;
947        }
948      }
949      
950   #ifdef IS_MPI
951 <    Mat3x3d tmpTau(tau);
952 <    MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
354 <                  9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
951 >    MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
952 >                              MPI::REALTYPE, MPI::SUM);
953   #endif
954 <    curSnapshot->statData.setTau(tau);
955 <  }
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 > }

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