ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/nonbonded/Electrostatic.cpp
(Generate patch)

Comparing trunk/src/nonbonded/Electrostatic.cpp (file contents):
Revision 1993 by gezelter, Tue Apr 29 17:32:31 2014 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 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 263 | Line 264 | namespace OpenMD {
264      
265      RealType b0c, b1c, b2c, b3c, b4c, b5c;
266      RealType db0c_1, db0c_2, db0c_3, db0c_4, db0c_5;
267 <    RealType a2, expTerm, invArootPi;
267 >    RealType a2, expTerm, invArootPi(0.0);
268      
269      RealType r = cutoffRadius_;
270      RealType r2 = r * r;
# Line 1164 | Line 1165 | namespace OpenMD {
1165      bool i_is_Quadrupole = data.is_Quadrupole;
1166      bool i_is_Fluctuating = data.is_Fluctuating;
1167      RealType C_a = data.fixedCharge;  
1168 <    RealType self(0.0), preVal, DdD, trQ, trQQ;
1168 >    RealType self(0.0), preVal, DdD(0.0), trQ, trQQ;
1169  
1170      if (i_is_Dipole) {
1171        DdD = data.dipole.lengthSquare();
# Line 1556 | Line 1557 | namespace OpenMD {
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   }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines