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#include <iostream> |
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/* |
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* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
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* |
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* Contact: oopse@oopse.org |
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* |
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* This program is free software; you can redistribute it and/or |
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* modify it under the terms of the GNU Lesser General Public License |
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* as published by the Free Software Foundation; either version 2.1 |
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* of the License, or (at your option) any later version. |
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* All we ask is that proper credit is given for our work, which includes |
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* - but is not limited to - adding the above copyright notice to the beginning |
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* of your source code files, and to any copyright notice that you may distribute |
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* with programs based on this work. |
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* |
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* This program is distributed in the hope that it will be useful, |
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* but WITHOUT ANY WARRANTY; without even the implied warranty of |
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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* GNU Lesser General Public License for more details. |
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* |
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* You should have received a copy of the GNU Lesser General Public License |
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* along with this program; if not, write to the Free Software |
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* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
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* |
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*/ |
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using namespace std; |
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#include "utils/simError.h" |
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#include "primitives/Atom.hpp" |
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namespace oopse { |
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Atom::Atom(int theIndex, SimState* theConfig) { |
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Atom::Atom(AtomType* at) : StuntDouble(otAtom, &Snapshot::atomData) ,atomType_(at) { |
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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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|
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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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void Atom::setIndex(int theIndex) { |
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index = theIndex; |
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} |
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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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void Atom::setCoords(void){ |
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std::vector<double> Atom::getGrad() { |
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vector<double> grad(3); |
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Vector3d force= getFrc(); |
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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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} |
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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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|
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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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grad[0] = -force[0]; |
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grad[1] = -force[1]; |
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grad[2] = -force[2]; |
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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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return grad; |
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} |
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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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void Atom::setVel( double theV[3] ){ |
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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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|
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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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|
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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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} |
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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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void Atom::zeroForces( void ){ |
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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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|
