--- trunk/src/primitives/Atom.cpp 2004/09/24 16:27:58 3 +++ trunk/src/primitives/Atom.cpp 2012/08/22 02:28:28 1782 @@ -1,185 +1,78 @@ -#include +/* + * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. + * + * The University of Notre Dame grants you ("Licensee") a + * non-exclusive, royalty free, license to use, modify and + * redistribute this software in source and binary code form, provided + * that the following conditions are met: + * + * 1. Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * + * 2. Redistributions in binary form must reproduce the above copyright + * notice, this list of conditions and the following disclaimer in the + * documentation and/or other materials provided with the + * distribution. + * + * This software is provided "AS IS," without a warranty of any + * kind. All express or implied conditions, representations and + * warranties, including any implied warranty of merchantability, + * fitness for a particular purpose or non-infringement, are hereby + * excluded. The University of Notre Dame and its licensors shall not + * be liable for any damages suffered by licensee as a result of + * using, modifying or distributing the software or its + * derivatives. In no event will the University of Notre Dame or its + * licensors be liable for any lost revenue, profit or data, or for + * direct, indirect, special, consequential, incidental or punitive + * damages, however caused and regardless of the theory of liability, + * arising out of the use of or inability to use software, even if the + * University of Notre Dame has been advised of the possibility of + * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). + * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). + */ -using namespace std; - -#include "utils/simError.h" +#include "utils/NumericConstant.hpp" #include "primitives/Atom.hpp" +#include "types/FluctuatingChargeAdapter.hpp" -Atom::Atom(int theIndex, SimState* theConfig) { - - objType = OT_ATOM; - myConfig = theConfig; - hasCoords = false; - - has_dipole = 0; - has_charge = 0; +namespace OpenMD { - index = theIndex; - offset = 0; - offsetX = offset; - offsetY = offset+1; - offsetZ = offset+2; - - Axx = 0; - Axy = Axx+1; - Axz = Axx+2; - - Ayx = Axx+3; - Ayy = Axx+4; - Ayz = Axx+5; - - Azx = Axx+6; - Azy = Axx+7; - Azz = Axx+8; -} - -void Atom::setIndex(int theIndex) { - index = theIndex; -} - -void Atom::setCoords(void){ - - if( myConfig->isAllocated() ){ - - myConfig->getAtomPointers( index, - &pos, - &vel, - &frc, - &trq, - &Amat, - &mu, - &ul); + Atom::Atom(AtomType* at) : StuntDouble(otAtom, &Snapshot::atomData), + atomType_(at) { + mass_ = at->getMass(); + if (at->isFluctuatingCharge()) { + FluctuatingChargeAdapter fca = FluctuatingChargeAdapter(at); + chargeMass_ = fca.getChargeMass(); + } else { + chargeMass_ = NumericConstant::infinity; + } } - else{ - sprintf( painCave.errMsg, - "Attempted to set Atom %d coordinates with an unallocated " - "SimState object.\n", index ); - painCave.isFatal = 1; - simError(); - } - - hasCoords = true; - -} -void Atom::getPos( double theP[3] ){ + Mat3x3d Atom::getI() { + return Mat3x3d::identity(); + } - if( hasCoords ){ - theP[0] = pos[offsetX]; - theP[1] = pos[offsetY]; - theP[2] = pos[offsetZ]; - } - else{ - - sprintf( painCave.errMsg, - "Attempt to get Pos for atom %d before coords set.\n", - index ); - painCave.isFatal = 1; - simError(); - } -} - -void Atom::setPos( double theP[3] ){ - - if( hasCoords ){ - pos[offsetX] = theP[0]; - pos[offsetY] = theP[1]; - pos[offsetZ] = theP[2]; - } - else{ - - sprintf( painCave.errMsg, - "Attempt to set Pos for atom %d before coords set.\n", - index ); - painCave.isFatal = 1; - simError(); - } -} - -void Atom::getVel( double theV[3] ){ - - if( hasCoords ){ - theV[0] = vel[offsetX]; - theV[1] = vel[offsetY]; - theV[2] = vel[offsetZ]; - } - else{ + std::vector Atom::getGrad() { + std::vector grad(3); + Vector3d force= getFrc(); - sprintf( painCave.errMsg, - "Attempt to get vel for atom %d before coords set.\n", - index ); - painCave.isFatal = 1; - simError(); - } - -} - -void Atom::setVel( double theV[3] ){ - - if( hasCoords ){ - vel[offsetX] = theV[0]; - vel[offsetY] = theV[1]; - vel[offsetZ] = theV[2]; - } - else{ + grad[0] = -force[0]; + grad[1] = -force[1]; + grad[2] = -force[2]; - sprintf( painCave.errMsg, - "Attempt to set vel for atom %d before coords set.\n", - index ); - painCave.isFatal = 1; - simError(); - } -} - -void Atom::getFrc( double theF[3] ){ + return grad; + } - if( hasCoords ){ - theF[0] = frc[offsetX]; - theF[1] = frc[offsetY]; - theF[2] = frc[offsetZ]; - } - else{ - - sprintf( painCave.errMsg, - "Attempt to get frc for atom %d before coords set.\n", - index ); - painCave.isFatal = 1; - simError(); - } + void Atom::accept(BaseVisitor* v) { + v->visit(this); + } } - -void Atom::addFrc( double theF[3] ){ - - if( hasCoords ){ - frc[offsetX] += theF[0]; - frc[offsetY] += theF[1]; - frc[offsetZ] += theF[2]; - } - else{ - - sprintf( painCave.errMsg, - "Attempt to add frc for atom %d before coords set.\n", - index ); - painCave.isFatal = 1; - simError(); - } -} - - -void Atom::zeroForces( void ){ - - if( hasCoords ){ - frc[offsetX] = 0.0; - frc[offsetY] = 0.0; - frc[offsetZ] = 0.0; - } - else{ - - sprintf( painCave.errMsg, - "Attempt to zero frc for atom %d before coords set.\n", - index ); - painCave.isFatal = 1; - simError(); - } -} -