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Comparing trunk/src/nonbonded/Electrostatic.cpp (file contents):
Revision 1894 by gezelter, Fri Jun 21 23:21:58 2013 UTC vs.
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC

# Line 40 | Line 40
40   * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43 + #ifdef IS_MPI
44 + #include <mpi.h>
45 + #endif
46 +
47   #include <stdio.h>
48   #include <string.h>
49  
50   #include <cmath>
51 + #include <numeric>
52   #include "nonbonded/Electrostatic.hpp"
53   #include "utils/simError.h"
54   #include "types/NonBondedInteractionType.hpp"
# Line 55 | Line 60
60   #include "utils/PhysicalConstants.hpp"
61   #include "math/erfc.hpp"
62   #include "math/SquareMatrix.hpp"
63 + #include "primitives/Molecule.hpp"
64 + #include "flucq/FluctuatingChargeForces.hpp"
65  
66   namespace OpenMD {
67    
# Line 64 | Line 71 | namespace OpenMD {
71                                    haveDampingAlpha_(false),
72                                    haveDielectric_(false),
73                                    haveElectroSplines_(false)
74 <  {}
74 >  {
75 >    flucQ_ = new FluctuatingChargeForces(info_);
76 >  }
77    
78 +  void Electrostatic::setForceField(ForceField *ff) {
79 +    forceField_ = ff;
80 +    flucQ_->setForceField(forceField_);
81 +  }
82 +
83 +  void Electrostatic::setSimulatedAtomTypes(set<AtomType*> &simtypes) {
84 +    simTypes_ = simtypes;
85 +    flucQ_->setSimulatedAtomTypes(simTypes_);
86 +  }
87 +
88    void Electrostatic::initialize() {
89      
90      Globals* simParams_ = info_->getSimParams();
# Line 191 | Line 210 | namespace OpenMD {
210        simError();
211      }
212            
213 <    if (screeningMethod_ == DAMPED) {      
213 >    if (screeningMethod_ == DAMPED || summationMethod_ == esm_EWALD_FULL) {
214        if (!simParams_->haveDampingAlpha()) {
215          // first set a cutoff dependent alpha value
216          // we assume alpha depends linearly with rcut from 0 to 20.5 ang
217          dampingAlpha_ = 0.425 - cutoffRadius_* 0.02;
218 <        if (dampingAlpha_ < 0.0) dampingAlpha_ = 0.0;
200 <        
218 >        if (dampingAlpha_ < 0.0) dampingAlpha_ = 0.0;        
219          // throw warning
220          sprintf( painCave.errMsg,
221                   "Electrostatic::initialize: dampingAlpha was not specified in the\n"
# Line 213 | Line 231 | namespace OpenMD {
231        haveDampingAlpha_ = true;
232      }
233  
234 <    // find all of the Electrostatic atom Types:
235 <    ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes();
236 <    ForceField::AtomTypeContainer::MapTypeIterator i;
237 <    AtomType* at;
234 >
235 >    Etypes.clear();
236 >    Etids.clear();
237 >    FQtypes.clear();
238 >    FQtids.clear();
239 >    ElectrostaticMap.clear();
240 >    Jij.clear();
241 >    nElectro_ = 0;
242 >    nFlucq_ = 0;
243 >
244 >    Etids.resize( forceField_->getNAtomType(), -1);
245 >    FQtids.resize( forceField_->getNAtomType(), -1);
246 >
247 >    set<AtomType*>::iterator at;
248 >    for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {    
249 >      if ((*at)->isElectrostatic()) nElectro_++;
250 >      if ((*at)->isFluctuatingCharge()) nFlucq_++;
251 >    }
252      
253 <    for (at = atomTypes->beginType(i); at != NULL;
254 <         at = atomTypes->nextType(i)) {
255 <      
256 <      if (at->isElectrostatic())
225 <        addType(at);
253 >    Jij.resize(nFlucq_);
254 >
255 >    for (at = simTypes_.begin(); at != simTypes_.end(); ++at) {
256 >      if ((*at)->isElectrostatic()) addType(*at);
257      }  
258      
259      if (summationMethod_ == esm_REACTION_FIELD) {
# Line 250 | Line 281 | namespace OpenMD {
281        b3c = (5.0 * b2c + pow(2.0*a2, 3) * expTerm * invArootPi) / r2;
282        b4c = (7.0 * b3c + pow(2.0*a2, 4) * expTerm * invArootPi) / r2;
283        b5c = (9.0 * b4c + pow(2.0*a2, 5) * expTerm * invArootPi) / r2;
284 <      selfMult_ = b0c + a2 * invArootPi;
284 >      // Half the Smith self piece:
285 >      selfMult1_ = - a2 * invArootPi;
286 >      selfMult2_ = - 2.0 * a2 * a2 * invArootPi / 3.0;
287 >      selfMult4_ = - 4.0 * a2 * a2 * a2 * invArootPi / 5.0;
288      } else {
289        a2 = 0.0;
290        b0c = 1.0 / r;
# Line 259 | Line 293 | namespace OpenMD {
293        b3c = (5.0 * b2c) / r2;
294        b4c = (7.0 * b3c) / r2;
295        b5c = (9.0 * b4c) / r2;
296 <      selfMult_ = b0c;
296 >      selfMult1_ = 0.0;
297 >      selfMult2_ = 0.0;
298 >      selfMult4_ = 0.0;
299      }
300  
301      // higher derivatives of B_0 at the cutoff radius:
# Line 267 | Line 303 | namespace OpenMD {
303      db0c_2 =     -b1c + r2 * b2c;
304      db0c_3 =          3.0*r*b2c  - r2*r*b3c;
305      db0c_4 =          3.0*b2c  - 6.0*r2*b3c     + r2*r2*b4c;
306 <    db0c_5 =                    -15.0*r*b3c + 10.0*r2*r*b4c - r2*r2*r*b5c;
271 <    
306 >    db0c_5 =                    -15.0*r*b3c + 10.0*r2*r*b4c - r2*r2*r*b5c;  
307  
308 +    if (summationMethod_ != esm_EWALD_FULL) {
309 +      selfMult1_ -= b0c;
310 +      selfMult2_ += (db0c_2 + 2.0*db0c_1*ric) /  3.0;
311 +      selfMult4_ -= (db0c_4 + 4.0*db0c_3*ric) / 15.0;
312 +    }
313 +
314      // working variables for the splines:
315      RealType ri, ri2;
316      RealType b0, b1, b2, b3, b4, b5;
# Line 305 | Line 346 | namespace OpenMD {
346      vector<RealType> v31v, v32v;
347      vector<RealType> v41v, v42v, v43v;
348  
308 –    /*
309 –    vector<RealType> dv01v;
310 –    vector<RealType> dv11v;
311 –    vector<RealType> dv21v, dv22v;
312 –    vector<RealType> dv31v, dv32v;
313 –    vector<RealType> dv41v, dv42v, dv43v;
314 –    */
315 –
349      for (int i = 1; i < np_ + 1; i++) {
350        r = RealType(i) * dx;
351        rv.push_back(r);
# Line 476 | Line 509 | namespace OpenMD {
509  
510        case esm_SWITCHING_FUNCTION:
511        case esm_HARD:
512 +      case esm_EWALD_FULL:
513  
514          v01 = f;
515          v11 = g;
# Line 534 | Line 568 | namespace OpenMD {
568  
569          break;
570                  
537 –      case esm_EWALD_FULL:
571        case esm_EWALD_PME:
572        case esm_EWALD_SPME:
573        default :
# Line 563 | Line 596 | namespace OpenMD {
596        v41v.push_back(v41);
597        v42v.push_back(v42);
598        v43v.push_back(v43);
566 –      /*
567 –      dv01v.push_back(dv01);
568 –      dv11v.push_back(dv11);
569 –      dv21v.push_back(dv21);
570 –      dv22v.push_back(dv22);
571 –      dv31v.push_back(dv31);
572 –      dv32v.push_back(dv32);      
573 –      dv41v.push_back(dv41);
574 –      dv42v.push_back(dv42);
575 –      dv43v.push_back(dv43);
576 –      */
599      }
600  
601      // construct the spline structures and fill them with the values we've
# Line 597 | Line 619 | namespace OpenMD {
619      v42s->addPoints(rv, v42v);
620      v43s = new CubicSpline();
621      v43s->addPoints(rv, v43v);
600 –
601 –    /*
602 –    dv01s = new CubicSpline();
603 –    dv01s->addPoints(rv, dv01v);
604 –    dv11s = new CubicSpline();
605 –    dv11s->addPoints(rv, dv11v);
606 –    dv21s = new CubicSpline();
607 –    dv21s->addPoints(rv, dv21v);
608 –    dv22s = new CubicSpline();
609 –    dv22s->addPoints(rv, dv22v);
610 –    dv31s = new CubicSpline();
611 –    dv31s->addPoints(rv, dv31v);
612 –    dv32s = new CubicSpline();
613 –    dv32s->addPoints(rv, dv32v);
614 –    dv41s = new CubicSpline();
615 –    dv41s->addPoints(rv, dv41v);
616 –    dv42s = new CubicSpline();
617 –    dv42s->addPoints(rv, dv42v);
618 –    dv43s = new CubicSpline();
619 –    dv43s->addPoints(rv, dv43v);
620 –    */
622  
623      haveElectroSplines_ = true;
624  
# Line 625 | Line 626 | namespace OpenMD {
626    }
627        
628    void Electrostatic::addType(AtomType* atomType){
629 <
629 >    
630      ElectrostaticAtomData electrostaticAtomData;
631      electrostaticAtomData.is_Charge = false;
632      electrostaticAtomData.is_Dipole = false;
# Line 661 | Line 662 | namespace OpenMD {
662        electrostaticAtomData.slaterZeta = fqa.getSlaterZeta();
663      }
664  
665 <    pair<map<int,AtomType*>::iterator,bool> ret;    
666 <    ret = ElectrostaticList.insert( pair<int,AtomType*>(atomType->getIdent(),
667 <                                                        atomType) );
665 >    int atid = atomType->getIdent();
666 >    int etid = Etypes.size();
667 >    int fqtid = FQtypes.size();
668 >
669 >    pair<set<int>::iterator,bool> ret;    
670 >    ret = Etypes.insert( atid );
671      if (ret.second == false) {
672        sprintf( painCave.errMsg,
673                 "Electrostatic already had a previous entry with ident %d\n",
674 <               atomType->getIdent() );
674 >               atid);
675        painCave.severity = OPENMD_INFO;
676        painCave.isFatal = 0;
677        simError();        
678      }
679      
680 <    ElectrostaticMap[atomType] = electrostaticAtomData;  
680 >    Etids[ atid ] = etid;
681 >    ElectrostaticMap.push_back(electrostaticAtomData);
682  
683 <    // Now, iterate over all known types and add to the mixing map:
684 <    
685 <    map<AtomType*, ElectrostaticAtomData>::iterator it;
686 <    for( it = ElectrostaticMap.begin(); it != ElectrostaticMap.end(); ++it) {
687 <      AtomType* atype2 = (*it).first;
688 <      ElectrostaticAtomData eaData2 = (*it).second;
689 <      if (eaData2.is_Fluctuating && electrostaticAtomData.is_Fluctuating) {
690 <        
683 >    if (electrostaticAtomData.is_Fluctuating) {
684 >      ret = FQtypes.insert( atid );
685 >      if (ret.second == false) {
686 >        sprintf( painCave.errMsg,
687 >                 "Electrostatic already had a previous fluctuating charge entry with ident %d\n",
688 >                 atid );
689 >        painCave.severity = OPENMD_INFO;
690 >        painCave.isFatal = 0;
691 >        simError();        
692 >      }
693 >      FQtids[atid] = fqtid;
694 >      Jij[fqtid].resize(nFlucq_);
695 >
696 >      // Now, iterate over all known fluctuating and add to the
697 >      // coulomb integral map:
698 >      
699 >      std::set<int>::iterator it;
700 >      for( it = FQtypes.begin(); it != FQtypes.end(); ++it) {    
701 >        int etid2 = Etids[ (*it) ];
702 >        int fqtid2 = FQtids[ (*it) ];
703 >        ElectrostaticAtomData eaData2 = ElectrostaticMap[ etid2 ];
704          RealType a = electrostaticAtomData.slaterZeta;
705          RealType b = eaData2.slaterZeta;
706          int m = electrostaticAtomData.slaterN;
707          int n = eaData2.slaterN;
708 <
708 >        
709          // Create the spline of the coulombic integral for s-type
710          // Slater orbitals.  Add a 2 angstrom safety window to deal
711          // with cutoffGroups that have charged atoms longer than the
712          // cutoffRadius away from each other.
713 <
713 >        
714          RealType rval;
715          RealType dr = (cutoffRadius_ + 2.0) / RealType(np_ - 1);
716          vector<RealType> rvals;
# Line 709 | Line 727 | namespace OpenMD {
727          
728          CubicSpline* J = new CubicSpline();
729          J->addPoints(rvals, Jvals);
730 <        
731 <        pair<AtomType*, AtomType*> key1, key2;
732 <        key1 = make_pair(atomType, atype2);
733 <        key2 = make_pair(atype2, atomType);
734 <        
717 <        Jij[key1] = J;
718 <        Jij[key2] = J;
719 <      }
720 <    }
721 <
730 >        Jij[fqtid][fqtid2] = J;
731 >        Jij[fqtid2].resize( nFlucq_ );
732 >        Jij[fqtid2][fqtid] = J;
733 >      }      
734 >    }      
735      return;
736    }
737    
# Line 746 | Line 759 | namespace OpenMD {
759  
760      if (!initialized_) initialize();
761      
762 <    data1 = ElectrostaticMap[idat.atypes.first];
763 <    data2 = ElectrostaticMap[idat.atypes.second];
762 >    data1 = ElectrostaticMap[Etids[idat.atid1]];
763 >    data2 = ElectrostaticMap[Etids[idat.atid2]];
764  
765      U = 0.0;  // Potential
766      F.zero();  // Force
# Line 755 | Line 768 | namespace OpenMD {
768      Tb.zero(); // Torque on site b
769      Ea.zero(); // Electric field at site a
770      Eb.zero(); // Electric field at site b
771 +    Pa = 0.0;  // Site potential at site a
772 +    Pb = 0.0;  // Site potential at site b
773      dUdCa = 0.0; // fluctuating charge force at site a
774      dUdCb = 0.0; // fluctuating charge force at site a
775      
# Line 767 | Line 782 | namespace OpenMD {
782      // Excluded potential that is still computed for fluctuating charges
783      excluded_Pot= 0.0;
784  
770 –
785      // some variables we'll need independent of electrostatic type:
786  
787      ri = 1.0 /  *(idat.rij);
# Line 830 | Line 844 | namespace OpenMD {
844        if (idat.excluded) {
845          *(idat.skippedCharge2) += C_a;
846        } else {
847 <        // only do the field if we're not excluded:
847 >        // only do the field and site potentials if we're not excluded:
848          Eb -= C_a *  pre11_ * dv01 * rhat;
849 +        Pb += C_a *  pre11_ * v01;
850        }
851      }
852      
# Line 839 | Line 854 | namespace OpenMD {
854        D_a = *(idat.dipole1);
855        rdDa = dot(rhat, D_a);
856        rxDa = cross(rhat, D_a);
857 <      if (!idat.excluded)
857 >      if (!idat.excluded) {
858          Eb -=  pre12_ * ((dv11-v11or) * rdDa * rhat + v11or * D_a);
859 +        Pb +=  pre12_ * v11 * rdDa;
860 +      }
861 +
862      }
863      
864      if (a_is_Quadrupole) {
# Line 850 | Line 868 | namespace OpenMD {
868        rQa = rhat * Q_a;
869        rdQar = dot(rhat, Qar);
870        rxQar = cross(rhat, Qar);
871 <      if (!idat.excluded)
871 >      if (!idat.excluded) {
872          Eb -= pre14_ * (trQa * rhat * dv21 + 2.0 * Qar * v22or
873                          + rdQar * rhat * (dv22 - 2.0*v22or));
874 +        Pb += pre14_ * (v21 * trQa + v22 * rdQar);
875 +      }
876      }
877      
878      if (b_is_Charge) {
# Line 866 | Line 886 | namespace OpenMD {
886        } else {
887          // only do the field if we're not excluded:
888          Ea += C_b *  pre11_ * dv01 * rhat;
889 +        Pa += C_b *  pre11_ * v01;
890 +
891        }
892      }
893      
# Line 873 | Line 895 | namespace OpenMD {
895        D_b = *(idat.dipole2);
896        rdDb = dot(rhat, D_b);
897        rxDb = cross(rhat, D_b);
898 <      if (!idat.excluded)
898 >      if (!idat.excluded) {
899          Ea += pre12_ * ((dv11-v11or) * rdDb * rhat + v11or * D_b);
900 +        Pa += pre12_ * v11 * rdDb;
901 +      }
902      }
903      
904      if (b_is_Quadrupole) {
# Line 884 | Line 908 | namespace OpenMD {
908        rQb = rhat * Q_b;
909        rdQbr = dot(rhat, Qbr);
910        rxQbr = cross(rhat, Qbr);
911 <      if (!idat.excluded)
911 >      if (!idat.excluded) {
912          Ea += pre14_ * (trQb * rhat * dv21 + 2.0 * Qbr * v22or
913                          + rdQbr * rhat * (dv22 - 2.0*v22or));
914 +        Pa += pre14_ * (v21 * trQb + v22 * rdQbr);
915 +      }
916      }
917 <    
917 >        
918 >
919      if ((a_is_Fluctuating || b_is_Fluctuating) && idat.excluded) {
920 <      J = Jij[idat.atypes];
920 >      J = Jij[FQtids[idat.atid1]][FQtids[idat.atid2]];
921      }    
922 <    
922 >
923      if (a_is_Charge) {    
924        
925        if (b_is_Charge) {
926          pref =  pre11_ * *(idat.electroMult);      
927          U  += C_a * C_b * pref * v01;
928          F  += C_a * C_b * pref * dv01 * rhat;
929 <        
929 >
930          // If this is an excluded pair, there are still indirect
931          // interactions via the reaction field we must worry about:
932  
# Line 908 | Line 935 | namespace OpenMD {
935            indirect_Pot += rfContrib;
936            indirect_F   += rfContrib * 2.0 * ri * rhat;
937          }
938 <        
938 >
939          // Fluctuating charge forces are handled via Coulomb integrals
940          // for excluded pairs (i.e. those connected via bonds) and
941          // with the standard charge-charge interaction otherwise.
942  
943 <        if (idat.excluded) {          
943 >        if (idat.excluded) {
944            if (a_is_Fluctuating || b_is_Fluctuating) {
945              coulInt = J->getValueAt( *(idat.rij) );
946 <            if (a_is_Fluctuating)  dUdCa += coulInt * C_b;
947 <            if (b_is_Fluctuating)  dUdCb += coulInt * C_a;
948 <            excluded_Pot += C_a * C_b * coulInt;
922 <          }          
946 >            if (a_is_Fluctuating) dUdCa += C_b * coulInt;
947 >            if (b_is_Fluctuating) dUdCb += C_a * coulInt;          
948 >          }
949          } else {
950            if (a_is_Fluctuating) dUdCa += C_b * pref * v01;
951 <          if (a_is_Fluctuating) dUdCb += C_a * pref * v01;
952 <        }
951 >          if (b_is_Fluctuating) dUdCb += C_a * pref * v01;
952 >        }              
953        }
954  
955        if (b_is_Dipole) {
# Line 989 | Line 1015 | namespace OpenMD {
1015          F  -= pref * (rdDa * rdDb) * (dv22 - 2.0*v22or) * rhat;
1016          Ta += pref * ( v21 * DaxDb - v22 * rdDb * rxDa);
1017          Tb += pref * (-v21 * DaxDb - v22 * rdDa * rxDb);
992 –
1018          // Even if we excluded this pair from direct interactions, we
1019          // still have the reaction-field-mediated dipole-dipole
1020          // interaction:
# Line 1049 | Line 1074 | namespace OpenMD {
1074          trQaQb = QaQb.trace();
1075          rQaQb = rhat * QaQb;
1076          QaQbr = QaQb * rhat;
1077 <        QaxQb = cross(Q_a, Q_b);
1077 >        QaxQb = mCross(Q_a, Q_b);
1078          rQaQbr = dot(rQa, Qbr);
1079          rQaxQbr = cross(rQa, Qbr);
1080          
# Line 1080 | Line 1105 | namespace OpenMD {
1105          //             + 4.0 * cross(rhat, QbQar)
1106  
1107          Tb += pref * 2.0 * cross(rhat,Qbr) * rdQar * v43;
1083 –
1084 –        //  cerr << " tsum = " << Ta + Tb - cross(  *(idat.d) , F ) << "\n";
1108        }
1109      }
1110  
# Line 1090 | Line 1113 | namespace OpenMD {
1113        *(idat.eField2) += Eb * *(idat.electroMult);
1114      }
1115  
1116 +    if (idat.doSitePotential) {
1117 +      *(idat.sPot1) += Pa * *(idat.electroMult);
1118 +      *(idat.sPot2) += Pb * *(idat.electroMult);
1119 +    }
1120 +
1121      if (a_is_Fluctuating) *(idat.dVdFQ1) += dUdCa * *(idat.sw);
1122      if (b_is_Fluctuating) *(idat.dVdFQ2) += dUdCb * *(idat.sw);
1123  
# Line 1128 | Line 1156 | namespace OpenMD {
1156  
1157      if (!initialized_) initialize();
1158  
1159 <    ElectrostaticAtomData data = ElectrostaticMap[sdat.atype];
1159 >    ElectrostaticAtomData data = ElectrostaticMap[Etids[sdat.atid]];
1160      
1161      // logicals
1162      bool i_is_Charge = data.is_Charge;
1163      bool i_is_Dipole = data.is_Dipole;
1164 +    bool i_is_Quadrupole = data.is_Quadrupole;
1165      bool i_is_Fluctuating = data.is_Fluctuating;
1166      RealType C_a = data.fixedCharge;  
1167 <    RealType self, preVal, DadDa;
1168 <    
1167 >    RealType self(0.0), preVal, DdD, trQ, trQQ;
1168 >
1169 >    if (i_is_Dipole) {
1170 >      DdD = data.dipole.lengthSquare();
1171 >    }
1172 >        
1173      if (i_is_Fluctuating) {
1174        C_a += *(sdat.flucQ);
1175 <      // dVdFQ is really a force, so this is negative the derivative
1176 <      *(sdat.dVdFQ) -=  *(sdat.flucQ) * data.hardness + data.electronegativity;
1177 <      (*(sdat.excludedPot))[ELECTROSTATIC_FAMILY] += (*sdat.flucQ) *
1178 <        (*(sdat.flucQ) * data.hardness * 0.5 + data.electronegativity);
1175 >
1176 >      flucQ_->getSelfInteraction(sdat.atid, *(sdat.flucQ),  
1177 >                                 (*(sdat.excludedPot))[ELECTROSTATIC_FAMILY],
1178 >                                 *(sdat.flucQfrc) );
1179 >
1180      }
1181  
1182      switch (summationMethod_) {
# Line 1157 | Line 1191 | namespace OpenMD {
1191        }
1192  
1193        if (i_is_Dipole) {
1194 <        DadDa = data.dipole.lengthSquare();
1161 <        (*(sdat.pot))[ELECTROSTATIC_FAMILY] -= pre22_ * preRF_ * DadDa;
1194 >        (*(sdat.pot))[ELECTROSTATIC_FAMILY] -= pre22_ * preRF_ * DdD;
1195        }
1196        
1197        break;
1198        
1199      case esm_SHIFTED_FORCE:
1200      case esm_SHIFTED_POTENTIAL:
1201 <      if (i_is_Charge) {
1202 <        self = - selfMult_ * C_a * (C_a + *(sdat.skippedCharge)) * pre11_;
1203 <        (*(sdat.pot))[ELECTROSTATIC_FAMILY] += self;
1201 >    case esm_TAYLOR_SHIFTED:
1202 >    case esm_EWALD_FULL:
1203 >      if (i_is_Charge)
1204 >        self += selfMult1_ * pre11_ * C_a * (C_a + *(sdat.skippedCharge));      
1205 >      if (i_is_Dipole)
1206 >        self += selfMult2_ * pre22_ * DdD;      
1207 >      if (i_is_Quadrupole) {
1208 >        trQ = data.quadrupole.trace();
1209 >        trQQ = (data.quadrupole * data.quadrupole).trace();
1210 >        self += selfMult4_ * pre44_ * (2.0*trQQ + trQ*trQ);
1211 >        if (i_is_Charge)
1212 >          self -= selfMult2_ * pre14_ * 2.0 * C_a * trQ;
1213        }
1214 +      (*(sdat.pot))[ELECTROSTATIC_FAMILY] += self;      
1215        break;
1216      default:
1217        break;
# Line 1181 | Line 1224 | namespace OpenMD {
1224      // 12 angstroms seems to be a reasonably good guess for most
1225      // cases.
1226      return 12.0;
1227 +  }
1228 +
1229 +
1230 +  void Electrostatic::ReciprocalSpaceSum(RealType& pot) {
1231 +    
1232 +    RealType kPot = 0.0;
1233 +    RealType kVir = 0.0;
1234 +    
1235 +    const RealType mPoleConverter = 0.20819434; // converts from the
1236 +                                                // internal units of
1237 +                                                // Debye (for dipoles)
1238 +                                                // or Debye-angstroms
1239 +                                                // (for quadrupoles) to
1240 +                                                // electron angstroms or
1241 +                                                // electron-angstroms^2
1242 +    
1243 +    const RealType eConverter = 332.0637778; // convert the
1244 +                                             // Charge-Charge
1245 +                                             // electrostatic
1246 +                                             // interactions into kcal /
1247 +                                             // mol assuming distances
1248 +                                             // are measured in
1249 +                                             // angstroms.
1250 +
1251 +    Mat3x3d hmat = info_->getSnapshotManager()->getCurrentSnapshot()->getHmat();
1252 +    Vector3d box = hmat.diagonals();
1253 +    RealType boxMax = box.max();
1254 +    
1255 +    //int kMax = int(2.0 * M_PI / (pow(dampingAlpha_,2)*cutoffRadius_ * boxMax) );
1256 +    int kMax = 7;
1257 +    int kSqMax = kMax*kMax + 2;
1258 +    
1259 +    int kLimit = kMax+1;
1260 +    int kLim2 = 2*kMax+1;
1261 +    int kSqLim = kSqMax;
1262 +    
1263 +    vector<RealType> AK(kSqLim+1, 0.0);
1264 +    RealType xcl = 2.0 * M_PI / box.x();
1265 +    RealType ycl = 2.0 * M_PI / box.y();
1266 +    RealType zcl = 2.0 * M_PI / box.z();
1267 +    RealType rcl = 2.0 * M_PI / boxMax;
1268 +    RealType rvol = 2.0 * M_PI /(box.x() * box.y() * box.z());
1269 +    
1270 +    if(dampingAlpha_ < 1.0e-12) return;
1271 +    
1272 +    RealType ralph = -0.25/pow(dampingAlpha_,2);
1273 +    
1274 +    // Calculate and store exponential factors  
1275 +    
1276 +    vector<vector<RealType> > elc;
1277 +    vector<vector<RealType> > emc;
1278 +    vector<vector<RealType> > enc;
1279 +    vector<vector<RealType> > els;
1280 +    vector<vector<RealType> > ems;
1281 +    vector<vector<RealType> > ens;
1282 +    
1283 +    int nMax = info_->getNAtoms();
1284 +    
1285 +    elc.resize(kLimit+1);
1286 +    emc.resize(kLimit+1);
1287 +    enc.resize(kLimit+1);
1288 +    els.resize(kLimit+1);
1289 +    ems.resize(kLimit+1);
1290 +    ens.resize(kLimit+1);
1291 +
1292 +    for (int j = 0; j < kLimit+1; j++) {
1293 +      elc[j].resize(nMax);
1294 +      emc[j].resize(nMax);
1295 +      enc[j].resize(nMax);
1296 +      els[j].resize(nMax);
1297 +      ems[j].resize(nMax);
1298 +      ens[j].resize(nMax);
1299 +    }
1300 +    
1301 +    Vector3d t( 2.0 * M_PI );
1302 +    t.Vdiv(t, box);
1303 +
1304 +    SimInfo::MoleculeIterator mi;
1305 +    Molecule::AtomIterator ai;
1306 +    int i;
1307 +    Vector3d r;
1308 +    Vector3d tt;
1309 +    
1310 +    for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1311 +         mol = info_->nextMolecule(mi)) {
1312 +      for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1313 +          atom = mol->nextAtom(ai)) {  
1314 +        
1315 +        i = atom->getLocalIndex();
1316 +        r = atom->getPos();
1317 +        info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(r);
1318 +        
1319 +        tt.Vmul(t, r);
1320 +
1321 +        elc[1][i] = 1.0;
1322 +        emc[1][i] = 1.0;
1323 +        enc[1][i] = 1.0;
1324 +        els[1][i] = 0.0;
1325 +        ems[1][i] = 0.0;
1326 +        ens[1][i] = 0.0;
1327 +
1328 +        elc[2][i] = cos(tt.x());
1329 +        emc[2][i] = cos(tt.y());
1330 +        enc[2][i] = cos(tt.z());
1331 +        els[2][i] = sin(tt.x());
1332 +        ems[2][i] = sin(tt.y());
1333 +        ens[2][i] = sin(tt.z());
1334 +        
1335 +        for(int l = 3; l <= kLimit; l++) {
1336 +          elc[l][i]=elc[l-1][i]*elc[2][i]-els[l-1][i]*els[2][i];
1337 +          emc[l][i]=emc[l-1][i]*emc[2][i]-ems[l-1][i]*ems[2][i];
1338 +          enc[l][i]=enc[l-1][i]*enc[2][i]-ens[l-1][i]*ens[2][i];
1339 +          els[l][i]=els[l-1][i]*elc[2][i]+elc[l-1][i]*els[2][i];
1340 +          ems[l][i]=ems[l-1][i]*emc[2][i]+emc[l-1][i]*ems[2][i];
1341 +          ens[l][i]=ens[l-1][i]*enc[2][i]+enc[l-1][i]*ens[2][i];
1342 +        }
1343 +      }
1344 +    }
1345 +    
1346 +    // Calculate and store AK coefficients:
1347 +    
1348 +    RealType eksq = 1.0;
1349 +    RealType expf = 0.0;
1350 +    if (ralph < 0.0) expf = exp(ralph*rcl*rcl);
1351 +    for (i = 1; i <= kSqLim; i++) {
1352 +      RealType rksq = float(i)*rcl*rcl;
1353 +      eksq = expf*eksq;
1354 +      AK[i] = eConverter * eksq/rksq;
1355 +    }
1356 +    
1357 +    /*
1358 +     * Loop over all k vectors k = 2 pi (ll/Lx, mm/Ly, nn/Lz)
1359 +     * the values of ll, mm and nn are selected so that the symmetry of
1360 +     * reciprocal lattice is taken into account i.e. the following
1361 +     * rules apply.
1362 +     *
1363 +     * ll ranges over the values 0 to kMax only.
1364 +     *
1365 +     * mm ranges over 0 to kMax when ll=0 and over
1366 +     *            -kMax to kMax otherwise.
1367 +     * nn ranges over 1 to kMax when ll=mm=0 and over
1368 +     *            -kMax to kMax otherwise.
1369 +     *
1370 +     * Hence the result of the summation must be doubled at the end.    
1371 +     */
1372 +    
1373 +    std::vector<RealType> clm(nMax, 0.0);
1374 +    std::vector<RealType> slm(nMax, 0.0);
1375 +    std::vector<RealType> ckr(nMax, 0.0);
1376 +    std::vector<RealType> skr(nMax, 0.0);
1377 +    std::vector<RealType> ckc(nMax, 0.0);
1378 +    std::vector<RealType> cks(nMax, 0.0);
1379 +    std::vector<RealType> dkc(nMax, 0.0);
1380 +    std::vector<RealType> dks(nMax, 0.0);
1381 +    std::vector<RealType> qkc(nMax, 0.0);
1382 +    std::vector<RealType> qks(nMax, 0.0);
1383 +    std::vector<Vector3d> dxk(nMax, V3Zero);
1384 +    std::vector<Vector3d> qxk(nMax, V3Zero);
1385 +    RealType rl, rm, rn;
1386 +    Vector3d kVec;
1387 +    Vector3d Qk;
1388 +    Mat3x3d k2;
1389 +    RealType ckcs, ckss, dkcs, dkss, qkcs, qkss;
1390 +    int atid;
1391 +    ElectrostaticAtomData data;
1392 +    RealType C, dk, qk;
1393 +    Vector3d D;
1394 +    Mat3x3d  Q;
1395 +
1396 +    int mMin = kLimit;
1397 +    int nMin = kLimit + 1;
1398 +    for (int l = 1; l <= kLimit; l++) {
1399 +      int ll = l - 1;
1400 +      rl = xcl * float(ll);
1401 +      for (int mmm = mMin; mmm <= kLim2; mmm++) {
1402 +        int mm = mmm - kLimit;
1403 +        int m = abs(mm) + 1;
1404 +        rm = ycl * float(mm);
1405 +        // Set temporary products of exponential terms
1406 +        for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1407 +             mol = info_->nextMolecule(mi)) {
1408 +          for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1409 +              atom = mol->nextAtom(ai)) {
1410 +            
1411 +            i = atom->getLocalIndex();
1412 +            if(mm < 0) {
1413 +              clm[i]=elc[l][i]*emc[m][i]+els[l][i]*ems[m][i];
1414 +              slm[i]=els[l][i]*emc[m][i]-ems[m][i]*elc[l][i];
1415 +            } else {
1416 +              clm[i]=elc[l][i]*emc[m][i]-els[l][i]*ems[m][i];
1417 +              slm[i]=els[l][i]*emc[m][i]+ems[m][i]*elc[l][i];
1418 +            }
1419 +          }
1420 +        }
1421 +        for (int nnn = nMin; nnn <= kLim2; nnn++) {
1422 +          int nn = nnn - kLimit;          
1423 +          int n = abs(nn) + 1;
1424 +          rn = zcl * float(nn);
1425 +          // Test on magnitude of k vector:
1426 +          int kk=ll*ll + mm*mm + nn*nn;
1427 +          if(kk <= kSqLim) {
1428 +            kVec = Vector3d(rl, rm, rn);
1429 +            k2 = outProduct(kVec, kVec);
1430 +            // Calculate exp(ikr) terms
1431 +            for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1432 +                 mol = info_->nextMolecule(mi)) {
1433 +              for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1434 +                  atom = mol->nextAtom(ai)) {
1435 +                i = atom->getLocalIndex();
1436 +                
1437 +                if (nn < 0) {
1438 +                  ckr[i]=clm[i]*enc[n][i]+slm[i]*ens[n][i];
1439 +                  skr[i]=slm[i]*enc[n][i]-clm[i]*ens[n][i];
1440 +
1441 +                } else {
1442 +                  ckr[i]=clm[i]*enc[n][i]-slm[i]*ens[n][i];
1443 +                  skr[i]=slm[i]*enc[n][i]+clm[i]*ens[n][i];
1444 +                }
1445 +              }
1446 +            }
1447 +            
1448 +            // Calculate scalar and vector products for each site:
1449 +            
1450 +            for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1451 +                 mol = info_->nextMolecule(mi)) {
1452 +              for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1453 +                  atom = mol->nextAtom(ai)) {
1454 +                i = atom->getLocalIndex();
1455 +                int atid = atom->getAtomType()->getIdent();
1456 +                data = ElectrostaticMap[Etids[atid]];
1457 +                              
1458 +                if (data.is_Charge) {
1459 +                  C = data.fixedCharge;
1460 +                  if (atom->isFluctuatingCharge()) C += atom->getFlucQPos();
1461 +                  ckc[i] = C * ckr[i];
1462 +                  cks[i] = C * skr[i];
1463 +                }
1464 +                
1465 +                if (data.is_Dipole) {
1466 +                  D = atom->getDipole() * mPoleConverter;
1467 +                  dk = dot(D, kVec);
1468 +                  dxk[i] = cross(D, kVec);
1469 +                  dkc[i] = dk * ckr[i];
1470 +                  dks[i] = dk * skr[i];
1471 +                }
1472 +                if (data.is_Quadrupole) {
1473 +                  Q = atom->getQuadrupole() * mPoleConverter;
1474 +                  Qk = Q * kVec;                  
1475 +                  qk = dot(kVec, Qk);
1476 +                  qxk[i] = -cross(kVec, Qk);
1477 +                  qkc[i] = qk * ckr[i];
1478 +                  qks[i] = qk * skr[i];
1479 +                }              
1480 +              }
1481 +            }
1482 +
1483 +            // calculate vector sums
1484 +            
1485 +            ckcs = std::accumulate(ckc.begin(),ckc.end(),0.0);
1486 +            ckss = std::accumulate(cks.begin(),cks.end(),0.0);
1487 +            dkcs = std::accumulate(dkc.begin(),dkc.end(),0.0);
1488 +            dkss = std::accumulate(dks.begin(),dks.end(),0.0);
1489 +            qkcs = std::accumulate(qkc.begin(),qkc.end(),0.0);
1490 +            qkss = std::accumulate(qks.begin(),qks.end(),0.0);
1491 +            
1492 + #ifdef IS_MPI
1493 +            MPI_Allreduce(MPI_IN_PLACE, &ckcs, 1, MPI_REALTYPE,
1494 +                          MPI_SUM, MPI_COMM_WORLD);
1495 +            MPI_Allreduce(MPI_IN_PLACE, &ckss, 1, MPI_REALTYPE,
1496 +                          MPI_SUM, MPI_COMM_WORLD);
1497 +            MPI_Allreduce(MPI_IN_PLACE, &dkcs, 1, MPI_REALTYPE,
1498 +                          MPI_SUM, MPI_COMM_WORLD);
1499 +            MPI_Allreduce(MPI_IN_PLACE, &dkss, 1, MPI_REALTYPE,
1500 +                          MPI_SUM, MPI_COMM_WORLD);
1501 +            MPI_Allreduce(MPI_IN_PLACE, &qkcs, 1, MPI_REALTYPE,
1502 +                          MPI_SUM, MPI_COMM_WORLD);
1503 +            MPI_Allreduce(MPI_IN_PLACE, &qkss, 1, MPI_REALTYPE,
1504 +                          MPI_SUM, MPI_COMM_WORLD);
1505 + #endif        
1506 +            
1507 +            // Accumulate potential energy and virial contribution:
1508 +
1509 +            kPot += 2.0 * rvol * AK[kk]*((ckss+dkcs-qkss)*(ckss+dkcs-qkss)
1510 +                                         + (ckcs-dkss-qkcs)*(ckcs-dkss-qkcs));
1511 +
1512 +            kVir += 2.0 * rvol  * AK[kk]*(ckcs*ckcs+ckss*ckss
1513 +                                          +4.0*(ckss*dkcs-ckcs*dkss)
1514 +                                          +3.0*(dkcs*dkcs+dkss*dkss)
1515 +                                          -6.0*(ckss*qkss+ckcs*qkcs)
1516 +                                          +8.0*(dkss*qkcs-dkcs*qkss)
1517 +                                          +5.0*(qkss*qkss+qkcs*qkcs));
1518 +            
1519 +            // Calculate force and torque for each site:
1520 +            
1521 +            for (Molecule* mol = info_->beginMolecule(mi); mol != NULL;
1522 +                 mol = info_->nextMolecule(mi)) {
1523 +              for(Atom* atom = mol->beginAtom(ai); atom != NULL;
1524 +                  atom = mol->nextAtom(ai)) {
1525 +                
1526 +                i = atom->getLocalIndex();
1527 +                atid = atom->getAtomType()->getIdent();
1528 +                data = ElectrostaticMap[Etids[atid]];
1529 +
1530 +                RealType qfrc = AK[kk]*((cks[i]+dkc[i]-qks[i])*(ckcs-dkss-qkcs)
1531 +                                     - (ckc[i]-dks[i]-qkc[i])*(ckss+dkcs-qkss));
1532 +                RealType qtrq1 = AK[kk]*(skr[i]*(ckcs-dkss-qkcs)
1533 +                                         -ckr[i]*(ckss+dkcs-qkss));
1534 +                RealType qtrq2 = 2.0*AK[kk]*(ckr[i]*(ckcs-dkss-qkcs)
1535 +                                            +skr[i]*(ckss+dkcs-qkss));
1536 +              
1537 +                atom->addFrc( 4.0 * rvol * qfrc * kVec );
1538 +
1539 +                if (atom->isFluctuatingCharge()) {
1540 +                  atom->addFlucQFrc( - 2.0 * rvol * qtrq2 );
1541 +                }
1542 +                  
1543 +                if (data.is_Dipole) {
1544 +                  atom->addTrq( 4.0 * rvol * qtrq1 * dxk[i] );
1545 +                }
1546 +                if (data.is_Quadrupole) {
1547 +                  atom->addTrq( 4.0 * rvol * qtrq2 * qxk[i] );
1548 +                }
1549 +              }
1550 +            }
1551 +          }
1552 +        }
1553 +        nMin = 1;
1554 +      }
1555 +      mMin = 1;
1556 +    }
1557 +    pot += kPot;  
1558    }
1559   }

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