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#include <iostream> |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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using namespace std; |
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|
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#include "simError.h" |
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#include "Atom.hpp" |
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|
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Atom::Atom(int theIndex, SimState* theConfig) { |
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|
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objType = OT_ATOM; |
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myConfig = theConfig; |
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hasCoords = false; |
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|
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has_dipole = 0; |
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has_charge = 0; |
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#include "primitives/Atom.hpp" |
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namespace OpenMD { |
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|
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index = theIndex; |
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offset = 0; |
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offsetX = offset; |
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offsetY = offset+1; |
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offsetZ = offset+2; |
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|
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Axx = 0; |
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Axy = Axx+1; |
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Axz = Axx+2; |
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|
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Ayx = Axx+3; |
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Ayy = Axx+4; |
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Ayz = Axx+5; |
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|
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Azx = Axx+6; |
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Azy = Axx+7; |
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Azz = Axx+8; |
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} |
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|
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void Atom::setIndex(int theIndex) { |
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index = theIndex; |
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} |
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|
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void Atom::setCoords(void){ |
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|
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if( myConfig->isAllocated() ){ |
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|
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myConfig->getAtomPointers( index, |
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&pos, |
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&vel, |
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&frc, |
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&trq, |
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&Amat, |
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&mu, |
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&ul); |
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Atom::Atom(AtomType* at) : StuntDouble(otAtom, &Snapshot::atomData), |
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atomType_(at) { |
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mass_ = at->getMass(); |
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} |
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else{ |
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sprintf( painCave.errMsg, |
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"Attempted to set Atom %d coordinates with an unallocated " |
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"SimState object.\n", index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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hasCoords = true; |
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|
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} |
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|
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void Atom::getPos( double theP[3] ){ |
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Mat3x3d Atom::getI() { |
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return Mat3x3d::identity(); |
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} |
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|
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if( hasCoords ){ |
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theP[0] = pos[offsetX]; |
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theP[1] = pos[offsetY]; |
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theP[2] = pos[offsetZ]; |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
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"Attempt to get Pos for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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void Atom::setPos( double theP[3] ){ |
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|
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if( hasCoords ){ |
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pos[offsetX] = theP[0]; |
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pos[offsetY] = theP[1]; |
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pos[offsetZ] = theP[2]; |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
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"Attempt to set Pos for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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void Atom::getVel( double theV[3] ){ |
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|
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if( hasCoords ){ |
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theV[0] = vel[offsetX]; |
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theV[1] = vel[offsetY]; |
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theV[2] = vel[offsetZ]; |
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} |
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else{ |
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std::vector<RealType> Atom::getGrad() { |
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std::vector<RealType> grad(3); |
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Vector3d force= getFrc(); |
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|
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sprintf( painCave.errMsg, |
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"Attempt to get vel for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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} |
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|
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void Atom::setVel( double theV[3] ){ |
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|
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if( hasCoords ){ |
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vel[offsetX] = theV[0]; |
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vel[offsetY] = theV[1]; |
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vel[offsetZ] = theV[2]; |
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} |
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else{ |
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grad[0] = -force[0]; |
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grad[1] = -force[1]; |
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grad[2] = -force[2]; |
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|
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sprintf( painCave.errMsg, |
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"Attempt to set vel for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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void Atom::getFrc( double theF[3] ){ |
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return grad; |
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} |
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|
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if( hasCoords ){ |
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theF[0] = frc[offsetX]; |
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theF[1] = frc[offsetY]; |
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theF[2] = frc[offsetZ]; |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
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"Attempt to get frc for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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void Atom::accept(BaseVisitor* v) { |
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v->visit(this); |
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} |
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} |
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|
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void Atom::addFrc( double theF[3] ){ |
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|
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if( hasCoords ){ |
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frc[offsetX] += theF[0]; |
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frc[offsetY] += theF[1]; |
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frc[offsetZ] += theF[2]; |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
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"Attempt to add frc for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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|
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void Atom::zeroForces( void ){ |
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|
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if( hasCoords ){ |
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frc[offsetX] = 0.0; |
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frc[offsetY] = 0.0; |
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frc[offsetZ] = 0.0; |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
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"Attempt to zero frc for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
