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root/OpenMD/trunk/src/nonbonded/Electrostatic.cpp
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Comparing trunk/src/nonbonded/Electrostatic.cpp (file contents):
Revision 1981 by gezelter, Mon Apr 14 18:32:51 2014 UTC vs.
Revision 2070 by gezelter, Sat Mar 7 16:59:57 2015 UTC

# Line 66 | Line 66 | namespace OpenMD {
66   namespace OpenMD {
67    
68    Electrostatic::Electrostatic(): name_("Electrostatic"), initialized_(false),
69 –                                  forceField_(NULL), info_(NULL),
69                                    haveCutoffRadius_(false),
70                                    haveDampingAlpha_(false),
71                                    haveDielectric_(false),
72 <                                  haveElectroSplines_(false)
72 >                                  haveElectroSplines_(false),
73 >                                  info_(NULL), forceField_(NULL)
74 >                                  
75    {
76      flucQ_ = new FluctuatingChargeForces(info_);
77    }
# Line 768 | Line 769 | namespace OpenMD {
769      Tb.zero(); // Torque on site b
770      Ea.zero(); // Electric field at site a
771      Eb.zero(); // Electric field at site b
772 +    Pa = 0.0;  // Site potential at site a
773 +    Pb = 0.0;  // Site potential at site b
774      dUdCa = 0.0; // fluctuating charge force at site a
775      dUdCb = 0.0; // fluctuating charge force at site a
776      
# Line 842 | Line 845 | namespace OpenMD {
845        if (idat.excluded) {
846          *(idat.skippedCharge2) += C_a;
847        } else {
848 <        // only do the field if we're not excluded:
848 >        // only do the field and site potentials if we're not excluded:
849          Eb -= C_a *  pre11_ * dv01 * rhat;
850 +        Pb += C_a *  pre11_ * v01;
851        }
852      }
853      
# Line 851 | Line 855 | namespace OpenMD {
855        D_a = *(idat.dipole1);
856        rdDa = dot(rhat, D_a);
857        rxDa = cross(rhat, D_a);
858 <      if (!idat.excluded)
858 >      if (!idat.excluded) {
859          Eb -=  pre12_ * ((dv11-v11or) * rdDa * rhat + v11or * D_a);
860 +        Pb +=  pre12_ * v11 * rdDa;
861 +      }
862 +
863      }
864      
865      if (a_is_Quadrupole) {
# Line 862 | Line 869 | namespace OpenMD {
869        rQa = rhat * Q_a;
870        rdQar = dot(rhat, Qar);
871        rxQar = cross(rhat, Qar);
872 <      if (!idat.excluded)
872 >      if (!idat.excluded) {
873          Eb -= pre14_ * (trQa * rhat * dv21 + 2.0 * Qar * v22or
874                          + rdQar * rhat * (dv22 - 2.0*v22or));
875 +        Pb += pre14_ * (v21 * trQa + v22 * rdQar);
876 +      }
877      }
878      
879      if (b_is_Charge) {
# Line 878 | Line 887 | namespace OpenMD {
887        } else {
888          // only do the field if we're not excluded:
889          Ea += C_b *  pre11_ * dv01 * rhat;
890 +        Pa += C_b *  pre11_ * v01;
891 +
892        }
893      }
894      
# Line 885 | Line 896 | namespace OpenMD {
896        D_b = *(idat.dipole2);
897        rdDb = dot(rhat, D_b);
898        rxDb = cross(rhat, D_b);
899 <      if (!idat.excluded)
899 >      if (!idat.excluded) {
900          Ea += pre12_ * ((dv11-v11or) * rdDb * rhat + v11or * D_b);
901 +        Pa += pre12_ * v11 * rdDb;
902 +      }
903      }
904      
905      if (b_is_Quadrupole) {
# Line 896 | Line 909 | namespace OpenMD {
909        rQb = rhat * Q_b;
910        rdQbr = dot(rhat, Qbr);
911        rxQbr = cross(rhat, Qbr);
912 <      if (!idat.excluded)
912 >      if (!idat.excluded) {
913          Ea += pre14_ * (trQb * rhat * dv21 + 2.0 * Qbr * v22or
914                          + rdQbr * rhat * (dv22 - 2.0*v22or));
915 +        Pa += pre14_ * (v21 * trQb + v22 * rdQbr);
916 +      }
917      }
918          
919  
# Line 1099 | Line 1114 | namespace OpenMD {
1114        *(idat.eField2) += Eb * *(idat.electroMult);
1115      }
1116  
1117 +    if (idat.doSitePotential) {
1118 +      *(idat.sPot1) += Pa * *(idat.electroMult);
1119 +      *(idat.sPot2) += Pb * *(idat.electroMult);
1120 +    }
1121 +
1122      if (a_is_Fluctuating) *(idat.dVdFQ1) += dUdCa * *(idat.sw);
1123      if (b_is_Fluctuating) *(idat.dVdFQ2) += dUdCb * *(idat.sw);
1124  
# Line 1536 | Line 1556 | namespace OpenMD {
1556        mMin = 1;
1557      }
1558      pot += kPot;  
1559 +  }
1560 +
1561 +  void Electrostatic::getSitePotentials(Atom* a1, Atom* a2, bool excluded,
1562 +                                        RealType &spot1, RealType &spot2) {
1563 +
1564 +    if (!initialized_) {
1565 +      cerr << "initializing\n";
1566 +      initialize();
1567 +      cerr << "done\n";
1568 +    }
1569 +
1570 +    const RealType mPoleConverter = 0.20819434;
1571 +
1572 +    AtomType* atype1 = a1->getAtomType();
1573 +    AtomType* atype2 = a2->getAtomType();
1574 +    int atid1 = atype1->getIdent();
1575 +    int atid2 = atype2->getIdent();
1576 +    data1 = ElectrostaticMap[Etids[atid1]];
1577 +    data2 = ElectrostaticMap[Etids[atid2]];
1578 +
1579 +    Pa = 0.0;  // Site potential at site a
1580 +    Pb = 0.0;  // Site potential at site b
1581 +
1582 +    Vector3d d = a2->getPos() - a1->getPos();
1583 +    info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(d);
1584 +    RealType rij = d.length();
1585 +    // some variables we'll need independent of electrostatic type:
1586 +
1587 +    RealType ri = 1.0 /  rij;
1588 +    rhat = d  * ri;
1589 +      
1590 +
1591 +    if ((rij >= cutoffRadius_) || excluded) {
1592 +      spot1 = 0.0;
1593 +      spot2 = 0.0;
1594 +      return;
1595 +    }
1596 +
1597 +    // logicals
1598 +
1599 +    a_is_Charge = data1.is_Charge;
1600 +    a_is_Dipole = data1.is_Dipole;
1601 +    a_is_Quadrupole = data1.is_Quadrupole;
1602 +    a_is_Fluctuating = data1.is_Fluctuating;
1603 +
1604 +    b_is_Charge = data2.is_Charge;
1605 +    b_is_Dipole = data2.is_Dipole;
1606 +    b_is_Quadrupole = data2.is_Quadrupole;
1607 +    b_is_Fluctuating = data2.is_Fluctuating;
1608 +
1609 +    // Obtain all of the required radial function values from the
1610 +    // spline structures:
1611 +    
1612 +
1613 +    if (a_is_Charge || b_is_Charge) {
1614 +      v01 = v01s->getValueAt(rij);
1615 +    }
1616 +    if (a_is_Dipole || b_is_Dipole) {
1617 +      v11 = v11s->getValueAt(rij);
1618 +      v11or = ri * v11;
1619 +    }
1620 +    if (a_is_Quadrupole || b_is_Quadrupole) {
1621 +      v21 = v21s->getValueAt(rij);
1622 +      v22 = v22s->getValueAt(rij);
1623 +      v22or = ri * v22;
1624 +    }      
1625 +
1626 +    if (a_is_Charge) {
1627 +      C_a = data1.fixedCharge;
1628 +      
1629 +      if (a_is_Fluctuating) {
1630 +        C_a += a1->getFlucQPos();
1631 +      }
1632 +      
1633 +      Pb += C_a *  pre11_ * v01;      
1634 +    }
1635 +    
1636 +    if (a_is_Dipole) {
1637 +      D_a = a1->getDipole() * mPoleConverter;
1638 +      rdDa = dot(rhat, D_a);
1639 +      Pb +=  pre12_ * v11 * rdDa;      
1640 +    }
1641 +    
1642 +    if (a_is_Quadrupole) {
1643 +      Q_a = a1->getQuadrupole() * mPoleConverter;
1644 +      trQa =  Q_a.trace();
1645 +      Qar =   Q_a * rhat;
1646 +      rdQar = dot(rhat, Qar);
1647 +      Pb += pre14_ * (v21 * trQa + v22 * rdQar);      
1648 +    }
1649 +    
1650 +    if (b_is_Charge) {
1651 +      C_b = data2.fixedCharge;
1652 +      
1653 +      if (b_is_Fluctuating)
1654 +        C_b += a2->getFlucQPos();
1655 +      
1656 +      Pa += C_b *  pre11_ * v01;
1657 +    }
1658 +    
1659 +    if (b_is_Dipole) {
1660 +      D_b = a2->getDipole() * mPoleConverter;
1661 +      rdDb = dot(rhat, D_b);
1662 +      Pa += pre12_ * v11 * rdDb;
1663 +    }
1664 +    
1665 +    if (b_is_Quadrupole) {
1666 +      Q_a = a2->getQuadrupole() * mPoleConverter;
1667 +      trQb =  Q_b.trace();
1668 +      Qbr =   Q_b * rhat;
1669 +      rdQbr = dot(rhat, Qbr);
1670 +      Pa += pre14_ * (v21 * trQb + v22 * rdQbr);      
1671 +    }
1672 +
1673 +    spot1 = Pa;
1674 +    spot2 = Pb;
1675    }
1676   }

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