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#include <stdlib.h> |
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#include <string.h> |
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#include <math.h> |
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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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|
|
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#include <iostream> |
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using namespace std; |
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/** |
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* @file SimInfo.cpp |
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* @author tlin |
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* @date 11/02/2004 |
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* @version 1.0 |
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*/ |
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|
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#include <algorithm> |
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|
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#include "brains/SimInfo.hpp" |
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#define __C |
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#include "brains/fSimulation.h" |
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#include "utils/simError.h" |
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#include "UseTheForce/DarkSide/simulation_interface.h" |
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#include "UseTheForce/notifyCutoffs_interface.h" |
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#include "utils/MemoryUtils.hpp" |
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|
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//#include "UseTheForce/fortranWrappers.hpp" |
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namespace oopse { |
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|
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#include "math/MatVec3.h" |
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SimInfo::SimInfo() : nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
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nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), sman_(NULL){ |
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|
|
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#ifdef IS_MPI |
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#include "brains/mpiSimulation.hpp" |
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#endif |
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|
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inline double roundMe( double x ){ |
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return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
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} |
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|
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inline double min( double a, double b ){ |
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return (a < b ) ? a : b; |
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} |
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|
|
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SimInfo* currentInfo; |
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SimInfo::~SimInfo() { |
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MemoryUtils::deleteVectorOfPointer(molecules_); |
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delete sman_; |
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|
|
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SimInfo::SimInfo(){ |
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|
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n_constraints = 0; |
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nZconstraints = 0; |
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n_oriented = 0; |
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n_dipoles = 0; |
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ndf = 0; |
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ndfRaw = 0; |
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nZconstraints = 0; |
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the_integrator = NULL; |
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setTemp = 0; |
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thermalTime = 0.0; |
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currentTime = 0.0; |
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rCut = 0.0; |
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rSw = 0.0; |
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|
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haveRcut = 0; |
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haveRsw = 0; |
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boxIsInit = 0; |
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|
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resetTime = 1e99; |
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|
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orthoRhombic = 0; |
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orthoTolerance = 1E-6; |
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useInitXSstate = true; |
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|
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usePBC = 0; |
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useLJ = 0; |
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useSticky = 0; |
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useCharges = 0; |
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useDipoles = 0; |
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useReactionField = 0; |
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useGB = 0; |
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useEAM = 0; |
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useSolidThermInt = 0; |
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useLiquidThermInt = 0; |
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|
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haveCutoffGroups = false; |
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|
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excludes = Exclude::Instance(); |
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|
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myConfiguration = new SimState(); |
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|
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has_minimizer = false; |
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the_minimizer =NULL; |
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|
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ngroup = 0; |
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|
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} |
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|
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|
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SimInfo::~SimInfo(){ |
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> |
bool SimInfo::addMolecule(Molecule* mol) { |
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std::vector<Molecule*>::iterator i; |
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> |
i = std::find(molecules_.begin(), molecules_.end(), mol); |
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> |
if (i != molecules_.end() ) { |
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> |
molecules_.push_back(mol); |
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|
|
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delete myConfiguration; |
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nAtoms_ += mol->getNAtoms(); |
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nBonds_ += mol->getNBonds(); |
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> |
nBends_ += mol->getNBends(); |
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nTorsions_ += mol->getNTorsions(); |
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nRigidBodies_ += mol->getNRigidBodies(); |
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nIntegrableObjects_ += mol->getNIntegrableObjects(); |
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> |
nCutoffGroups_ += mol->getNCutoffGroups(); |
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nConstraints_ += mol->getNConstraints(); |
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|
|
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map<string, GenericData*>::iterator i; |
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|
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for(i = properties.begin(); i != properties.end(); i++) |
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delete (*i).second; |
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|
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return true; |
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} else { |
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return false; |
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} |
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|
} |
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|
|
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void SimInfo::setBox(double newBox[3]) { |
74 |
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|
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< |
int i, j; |
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double tempMat[3][3]; |
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> |
bool SimInfo::removeMolecule(Molecule* mol) { |
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std::vector<Molecule*>::iterator i; |
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> |
i = std::find(molecules_.begin(), molecules_.end(), mol); |
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|
|
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for(i=0; i<3; i++) |
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for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
77 |
> |
if (i != molecules_.end() ) { |
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molecules_.push_back(mol); |
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nAtoms_ -= mol->getNAtoms(); |
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nBonds_ -= mol->getNBonds(); |
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> |
nBends_ -= mol->getNBends(); |
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nTorsions_ -= mol->getNTorsions(); |
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nRigidBodies_ -= mol->getNRigidBodies(); |
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nIntegrableObjects_ -= mol->getNIntegrableObjects(); |
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nCutoffGroups_ -= mol->getNCutoffGroups(); |
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nConstraints_ -= mol->getNConstraints(); |
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|
|
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tempMat[0][0] = newBox[0]; |
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< |
tempMat[1][1] = newBox[1]; |
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< |
tempMat[2][2] = newBox[2]; |
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|
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< |
setBoxM( tempMat ); |
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< |
|
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< |
} |
110 |
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|
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< |
void SimInfo::setBoxM( double theBox[3][3] ){ |
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< |
|
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int i, j; |
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< |
double FortranHmat[9]; // to preserve compatibility with Fortran the |
115 |
< |
// ordering in the array is as follows: |
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< |
// [ 0 3 6 ] |
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// [ 1 4 7 ] |
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< |
// [ 2 5 8 ] |
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< |
double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
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< |
|
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if( !boxIsInit ) boxIsInit = 1; |
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|
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for(i=0; i < 3; i++) |
124 |
< |
for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
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< |
|
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< |
calcBoxL(); |
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< |
calcHmatInv(); |
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|
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< |
for(i=0; i < 3; i++) { |
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< |
for (j=0; j < 3; j++) { |
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FortranHmat[3*j + i] = Hmat[i][j]; |
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FortranHmatInv[3*j + i] = HmatInv[i][j]; |
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return true; |
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} else { |
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return false; |
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|
} |
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} |
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|
|
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– |
setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic); |
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|
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} |
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|
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|
|
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< |
void SimInfo::getBoxM (double theBox[3][3]) { |
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} |
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|
|
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< |
int i, j; |
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< |
for(i=0; i<3; i++) |
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for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
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< |
} |
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> |
|
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> |
Molecule* SimInfo::beginMolecule(std::vector<Molecule*>::iterator& i) { |
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i = molecules_.begin(); |
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> |
return i == molecules_.end() ? NULL : *i; |
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> |
} |
101 |
|
|
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< |
|
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< |
void SimInfo::scaleBox(double scale) { |
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double theBox[3][3]; |
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int i, j; |
152 |
< |
|
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< |
// cerr << "Scaling box by " << scale << "\n"; |
154 |
< |
|
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for(i=0; i<3; i++) |
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< |
for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
157 |
< |
|
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< |
setBoxM(theBox); |
159 |
< |
|
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> |
Molecule* SimInfo::nextMolecule(std::vector<Molecule*>::iterator& i) { |
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> |
++i; |
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> |
return i == molecules_.end() ? NULL : *i; |
105 |
|
} |
106 |
|
|
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– |
void SimInfo::calcHmatInv( void ) { |
163 |
– |
|
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– |
int oldOrtho; |
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– |
int i,j; |
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– |
double smallDiag; |
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– |
double tol; |
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– |
double sanity[3][3]; |
107 |
|
|
108 |
< |
invertMat3( Hmat, HmatInv ); |
108 |
> |
void SimInfo::calcNDF() { |
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> |
int ndf_local; |
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> |
std::vector<Molecule*>::iterator i; |
111 |
> |
std::vector<StuntDouble*>::iterator j; |
112 |
> |
Molecule* mol; |
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> |
StuntDouble* integrableObject; |
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|
|
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< |
// check to see if Hmat is orthorhombic |
173 |
< |
|
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< |
oldOrtho = orthoRhombic; |
175 |
< |
|
176 |
< |
smallDiag = fabs(Hmat[0][0]); |
177 |
< |
if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
178 |
< |
if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
179 |
< |
tol = smallDiag * orthoTolerance; |
180 |
< |
|
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< |
orthoRhombic = 1; |
182 |
< |
|
183 |
< |
for (i = 0; i < 3; i++ ) { |
184 |
< |
for (j = 0 ; j < 3; j++) { |
185 |
< |
if (i != j) { |
186 |
< |
if (orthoRhombic) { |
187 |
< |
if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
188 |
< |
} |
189 |
< |
} |
190 |
< |
} |
191 |
< |
} |
192 |
< |
|
193 |
< |
if( oldOrtho != orthoRhombic ){ |
115 |
> |
ndf_local = 0; |
116 |
|
|
117 |
< |
if( orthoRhombic ) { |
118 |
< |
sprintf( painCave.errMsg, |
119 |
< |
"OOPSE is switching from the default Non-Orthorhombic\n" |
198 |
< |
"\tto the faster Orthorhombic periodic boundary computations.\n" |
199 |
< |
"\tThis is usually a good thing, but if you wan't the\n" |
200 |
< |
"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
201 |
< |
"\tvariable ( currently set to %G ) smaller.\n", |
202 |
< |
orthoTolerance); |
203 |
< |
painCave.severity = OOPSE_INFO; |
204 |
< |
simError(); |
205 |
< |
} |
206 |
< |
else { |
207 |
< |
sprintf( painCave.errMsg, |
208 |
< |
"OOPSE is switching from the faster Orthorhombic to the more\n" |
209 |
< |
"\tflexible Non-Orthorhombic periodic boundary computations.\n" |
210 |
< |
"\tThis is usually because the box has deformed under\n" |
211 |
< |
"\tNPTf integration. If you wan't to live on the edge with\n" |
212 |
< |
"\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
213 |
< |
"\tvariable ( currently set to %G ) larger.\n", |
214 |
< |
orthoTolerance); |
215 |
< |
painCave.severity = OOPSE_WARNING; |
216 |
< |
simError(); |
217 |
< |
} |
218 |
< |
} |
219 |
< |
} |
117 |
> |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
118 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
119 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
120 |
|
|
121 |
< |
void SimInfo::calcBoxL( void ){ |
121 |
> |
ndf_local += 3; |
122 |
|
|
123 |
< |
double dx, dy, dz, dsq; |
124 |
< |
|
125 |
< |
// boxVol = Determinant of Hmat |
126 |
< |
|
127 |
< |
boxVol = matDet3( Hmat ); |
128 |
< |
|
129 |
< |
// boxLx |
130 |
< |
|
131 |
< |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
132 |
< |
dsq = dx*dx + dy*dy + dz*dz; |
233 |
< |
boxL[0] = sqrt( dsq ); |
234 |
< |
//maxCutoff = 0.5 * boxL[0]; |
235 |
< |
|
236 |
< |
// boxLy |
237 |
< |
|
238 |
< |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
239 |
< |
dsq = dx*dx + dy*dy + dz*dz; |
240 |
< |
boxL[1] = sqrt( dsq ); |
241 |
< |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
242 |
< |
|
243 |
< |
|
244 |
< |
// boxLz |
245 |
< |
|
246 |
< |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
247 |
< |
dsq = dx*dx + dy*dy + dz*dz; |
248 |
< |
boxL[2] = sqrt( dsq ); |
249 |
< |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
250 |
< |
|
251 |
< |
//calculate the max cutoff |
252 |
< |
maxCutoff = calcMaxCutOff(); |
253 |
< |
|
254 |
< |
checkCutOffs(); |
255 |
< |
|
256 |
< |
} |
257 |
< |
|
258 |
< |
|
259 |
< |
double SimInfo::calcMaxCutOff(){ |
260 |
< |
|
261 |
< |
double ri[3], rj[3], rk[3]; |
262 |
< |
double rij[3], rjk[3], rki[3]; |
263 |
< |
double minDist; |
264 |
< |
|
265 |
< |
ri[0] = Hmat[0][0]; |
266 |
< |
ri[1] = Hmat[1][0]; |
267 |
< |
ri[2] = Hmat[2][0]; |
268 |
< |
|
269 |
< |
rj[0] = Hmat[0][1]; |
270 |
< |
rj[1] = Hmat[1][1]; |
271 |
< |
rj[2] = Hmat[2][1]; |
272 |
< |
|
273 |
< |
rk[0] = Hmat[0][2]; |
274 |
< |
rk[1] = Hmat[1][2]; |
275 |
< |
rk[2] = Hmat[2][2]; |
123 |
> |
if (integrableObject->isDirectional()) { |
124 |
> |
if (integrableObject->isLinear()) { |
125 |
> |
ndf_local += 2; |
126 |
> |
} else { |
127 |
> |
ndf_local += 3; |
128 |
> |
} |
129 |
> |
} |
130 |
> |
|
131 |
> |
}//end for (integrableObject) |
132 |
> |
}// end for (mol) |
133 |
|
|
134 |
< |
crossProduct3(ri, rj, rij); |
135 |
< |
distXY = dotProduct3(rk,rij) / norm3(rij); |
134 |
> |
// n_constraints is local, so subtract them on each processor |
135 |
> |
ndf_local -= nConstraints_; |
136 |
|
|
137 |
< |
crossProduct3(rj,rk, rjk); |
138 |
< |
distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
137 |
> |
#ifdef IS_MPI |
138 |
> |
MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
139 |
> |
#else |
140 |
> |
ndf_ = ndf_local; |
141 |
> |
#endif |
142 |
|
|
143 |
< |
crossProduct3(rk,ri, rki); |
144 |
< |
distZX = dotProduct3(rj,rki) / norm3(rki); |
143 |
> |
// nZconstraints is global, as are the 3 COM translations for the |
144 |
> |
// entire system: |
145 |
> |
ndf_ = ndf_ - 3 - nZconstraints; |
146 |
|
|
286 |
– |
minDist = min(min(distXY, distYZ), distZX); |
287 |
– |
return minDist/2; |
288 |
– |
|
147 |
|
} |
148 |
|
|
149 |
< |
void SimInfo::wrapVector( double thePos[3] ){ |
149 |
> |
void SimInfo::calcNDFRaw() { |
150 |
> |
int ndfRaw_local; |
151 |
|
|
152 |
< |
int i; |
153 |
< |
double scaled[3]; |
152 |
> |
std::vector<Molecule*>::iterator i; |
153 |
> |
std::vector<StuntDouble*>::iterator j; |
154 |
> |
Molecule* mol; |
155 |
> |
StuntDouble* integrableObject; |
156 |
|
|
157 |
< |
if( !orthoRhombic ){ |
158 |
< |
// calc the scaled coordinates. |
298 |
< |
|
299 |
< |
|
300 |
< |
matVecMul3(HmatInv, thePos, scaled); |
157 |
> |
// Raw degrees of freedom that we have to set |
158 |
> |
ndfRaw_local = 0; |
159 |
|
|
160 |
< |
for(i=0; i<3; i++) |
161 |
< |
scaled[i] -= roundMe(scaled[i]); |
162 |
< |
|
305 |
< |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
306 |
< |
|
307 |
< |
matVecMul3(Hmat, scaled, thePos); |
160 |
> |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
161 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
162 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
163 |
|
|
164 |
< |
} |
310 |
< |
else{ |
311 |
< |
// calc the scaled coordinates. |
312 |
< |
|
313 |
< |
for(i=0; i<3; i++) |
314 |
< |
scaled[i] = thePos[i]*HmatInv[i][i]; |
315 |
< |
|
316 |
< |
// wrap the scaled coordinates |
317 |
< |
|
318 |
< |
for(i=0; i<3; i++) |
319 |
< |
scaled[i] -= roundMe(scaled[i]); |
320 |
< |
|
321 |
< |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
322 |
< |
|
323 |
< |
for(i=0; i<3; i++) |
324 |
< |
thePos[i] = scaled[i]*Hmat[i][i]; |
325 |
< |
} |
326 |
< |
|
327 |
< |
} |
164 |
> |
ndfRaw_local += 3; |
165 |
|
|
166 |
< |
|
167 |
< |
int SimInfo::getNDF(){ |
168 |
< |
int ndf_local; |
169 |
< |
|
170 |
< |
ndf_local = 0; |
171 |
< |
|
172 |
< |
for(int i = 0; i < integrableObjects.size(); i++){ |
173 |
< |
ndf_local += 3; |
174 |
< |
if (integrableObjects[i]->isDirectional()) { |
338 |
< |
if (integrableObjects[i]->isLinear()) |
339 |
< |
ndf_local += 2; |
340 |
< |
else |
341 |
< |
ndf_local += 3; |
166 |
> |
if (integrableObject->isDirectional()) { |
167 |
> |
if (integrableObject->isLinear()) { |
168 |
> |
ndfRaw_local += 2; |
169 |
> |
} else { |
170 |
> |
ndfRaw_local += 3; |
171 |
> |
} |
172 |
> |
} |
173 |
> |
|
174 |
> |
} |
175 |
|
} |
343 |
– |
} |
344 |
– |
|
345 |
– |
// n_constraints is local, so subtract them on each processor: |
346 |
– |
|
347 |
– |
ndf_local -= n_constraints; |
348 |
– |
|
349 |
– |
#ifdef IS_MPI |
350 |
– |
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
351 |
– |
#else |
352 |
– |
ndf = ndf_local; |
353 |
– |
#endif |
354 |
– |
|
355 |
– |
// nZconstraints is global, as are the 3 COM translations for the |
356 |
– |
// entire system: |
357 |
– |
|
358 |
– |
ndf = ndf - 3 - nZconstraints; |
359 |
– |
|
360 |
– |
return ndf; |
361 |
– |
} |
362 |
– |
|
363 |
– |
int SimInfo::getNDFraw() { |
364 |
– |
int ndfRaw_local; |
365 |
– |
|
366 |
– |
// Raw degrees of freedom that we have to set |
367 |
– |
ndfRaw_local = 0; |
368 |
– |
|
369 |
– |
for(int i = 0; i < integrableObjects.size(); i++){ |
370 |
– |
ndfRaw_local += 3; |
371 |
– |
if (integrableObjects[i]->isDirectional()) { |
372 |
– |
if (integrableObjects[i]->isLinear()) |
373 |
– |
ndfRaw_local += 2; |
374 |
– |
else |
375 |
– |
ndfRaw_local += 3; |
376 |
– |
} |
377 |
– |
} |
176 |
|
|
177 |
|
#ifdef IS_MPI |
178 |
< |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
178 |
> |
MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
179 |
|
#else |
180 |
< |
ndfRaw = ndfRaw_local; |
180 |
> |
ndfRaw_ = ndfRaw_local; |
181 |
|
#endif |
384 |
– |
|
385 |
– |
return ndfRaw; |
182 |
|
} |
183 |
|
|
184 |
< |
int SimInfo::getNDFtranslational() { |
185 |
< |
int ndfTrans_local; |
184 |
> |
void SimInfo::calcNDFTrans() { |
185 |
> |
int ndfTrans_local; |
186 |
|
|
187 |
< |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
187 |
> |
ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_; |
188 |
|
|
189 |
|
|
190 |
|
#ifdef IS_MPI |
191 |
< |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
191 |
> |
MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
192 |
|
#else |
193 |
< |
ndfTrans = ndfTrans_local; |
193 |
> |
ndfTrans_ = ndfTrans_local; |
194 |
|
#endif |
195 |
|
|
196 |
< |
ndfTrans = ndfTrans - 3 - nZconstraints; |
197 |
< |
|
402 |
< |
return ndfTrans; |
196 |
> |
ndfTrans_ = ndfTrans_ - 3 - nZconstraints; |
197 |
> |
|
198 |
|
} |
199 |
|
|
200 |
< |
int SimInfo::getTotIntegrableObjects() { |
201 |
< |
int nObjs_local; |
202 |
< |
int nObjs; |
203 |
< |
|
204 |
< |
nObjs_local = integrableObjects.size(); |
205 |
< |
|
206 |
< |
|
207 |
< |
#ifdef IS_MPI |
208 |
< |
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
209 |
< |
#else |
210 |
< |
nObjs = nObjs_local; |
416 |
< |
#endif |
417 |
< |
|
418 |
< |
|
419 |
< |
return nObjs; |
420 |
< |
} |
421 |
< |
|
422 |
< |
void SimInfo::refreshSim(){ |
423 |
< |
|
424 |
< |
simtype fInfo; |
425 |
< |
int isError; |
426 |
< |
int n_global; |
427 |
< |
int* excl; |
428 |
< |
|
429 |
< |
fInfo.dielect = 0.0; |
430 |
< |
|
431 |
< |
if( useDipoles ){ |
432 |
< |
if( useReactionField )fInfo.dielect = dielectric; |
433 |
< |
} |
434 |
< |
|
435 |
< |
fInfo.SIM_uses_PBC = usePBC; |
436 |
< |
//fInfo.SIM_uses_LJ = 0; |
437 |
< |
fInfo.SIM_uses_LJ = useLJ; |
438 |
< |
fInfo.SIM_uses_sticky = useSticky; |
439 |
< |
//fInfo.SIM_uses_sticky = 0; |
440 |
< |
fInfo.SIM_uses_charges = useCharges; |
441 |
< |
fInfo.SIM_uses_dipoles = useDipoles; |
442 |
< |
//fInfo.SIM_uses_dipoles = 0; |
443 |
< |
fInfo.SIM_uses_RF = useReactionField; |
444 |
< |
//fInfo.SIM_uses_RF = 0; |
445 |
< |
fInfo.SIM_uses_GB = useGB; |
446 |
< |
fInfo.SIM_uses_EAM = useEAM; |
447 |
< |
|
448 |
< |
n_exclude = excludes->getSize(); |
449 |
< |
excl = excludes->getFortranArray(); |
450 |
< |
|
451 |
< |
#ifdef IS_MPI |
452 |
< |
n_global = mpiSim->getNAtomsGlobal(); |
453 |
< |
#else |
454 |
< |
n_global = n_atoms; |
455 |
< |
#endif |
456 |
< |
|
457 |
< |
isError = 0; |
458 |
< |
|
459 |
< |
getFortranGroupArrays(this, FglobalGroupMembership, mfact); |
460 |
< |
//it may not be a good idea to pass the address of first element in vector |
461 |
< |
//since c++ standard does not require vector to be stored continuously in meomory |
462 |
< |
//Most of the compilers will organize the memory of vector continuously |
463 |
< |
setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
464 |
< |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
465 |
< |
&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError); |
466 |
< |
|
467 |
< |
if( isError ){ |
200 |
> |
void SimInfo::addExcludePairs(Molecule* mol) { |
201 |
> |
std::vector<Bond*>::iterator bondIter; |
202 |
> |
std::vector<Bend*>::iterator bendIter; |
203 |
> |
std::vector<Torsion*>::iterator torsionIter; |
204 |
> |
Bond* bond; |
205 |
> |
Bend* bend; |
206 |
> |
Torsion* torsion; |
207 |
> |
int a; |
208 |
> |
int b; |
209 |
> |
int c; |
210 |
> |
int d; |
211 |
|
|
212 |
< |
sprintf( painCave.errMsg, |
213 |
< |
"There was an error setting the simulation information in fortran.\n" ); |
214 |
< |
painCave.isFatal = 1; |
215 |
< |
painCave.severity = OOPSE_ERROR; |
216 |
< |
simError(); |
474 |
< |
} |
475 |
< |
|
476 |
< |
#ifdef IS_MPI |
477 |
< |
sprintf( checkPointMsg, |
478 |
< |
"succesfully sent the simulation information to fortran.\n"); |
479 |
< |
MPIcheckPoint(); |
480 |
< |
#endif // is_mpi |
481 |
< |
|
482 |
< |
this->ndf = this->getNDF(); |
483 |
< |
this->ndfRaw = this->getNDFraw(); |
484 |
< |
this->ndfTrans = this->getNDFtranslational(); |
485 |
< |
} |
212 |
> |
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
213 |
> |
a = bond->getAtomA()->getGlobalIndex(); |
214 |
> |
b = bond->getAtomB()->getGlobalIndex(); |
215 |
> |
exclude_.addPair(a, b); |
216 |
> |
} |
217 |
|
|
218 |
< |
void SimInfo::setDefaultRcut( double theRcut ){ |
219 |
< |
|
220 |
< |
haveRcut = 1; |
221 |
< |
rCut = theRcut; |
491 |
< |
rList = rCut + 1.0; |
492 |
< |
|
493 |
< |
notifyFortranCutoffs( &rCut, &rSw, &rList ); |
494 |
< |
} |
218 |
> |
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
219 |
> |
a = bend->getAtomA()->getGlobalIndex(); |
220 |
> |
b = bend->getAtomB()->getGlobalIndex(); |
221 |
> |
c = bend->getAtomC()->getGlobalIndex(); |
222 |
|
|
223 |
< |
void SimInfo::setDefaultRcut( double theRcut, double theRsw ){ |
223 |
> |
exclude_.addPair(a, b); |
224 |
> |
exclude_.addPair(a, c); |
225 |
> |
exclude_.addPair(b, c); |
226 |
> |
} |
227 |
|
|
228 |
< |
rSw = theRsw; |
229 |
< |
setDefaultRcut( theRcut ); |
230 |
< |
} |
228 |
> |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) { |
229 |
> |
a = torsion->getAtomA()->getGlobalIndex(); |
230 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
231 |
> |
c = torsion->getAtomC()->getGlobalIndex(); |
232 |
> |
d = torsion->getAtomD()->getGlobalIndex(); |
233 |
|
|
234 |
+ |
exclude_.addPair(a, b); |
235 |
+ |
exclude_.addPair(a, c); |
236 |
+ |
exclude_.addPair(a, d); |
237 |
+ |
exclude_.addPair(b, c); |
238 |
+ |
exclude_.addPair(b, d); |
239 |
+ |
exclude_.addPair(c, d); |
240 |
+ |
} |
241 |
|
|
503 |
– |
void SimInfo::checkCutOffs( void ){ |
504 |
– |
|
505 |
– |
if( boxIsInit ){ |
242 |
|
|
507 |
– |
//we need to check cutOffs against the box |
508 |
– |
|
509 |
– |
if( rCut > maxCutoff ){ |
510 |
– |
sprintf( painCave.errMsg, |
511 |
– |
"cutoffRadius is too large for the current periodic box.\n" |
512 |
– |
"\tCurrent Value of cutoffRadius = %G at time %G\n " |
513 |
– |
"\tThis is larger than half of at least one of the\n" |
514 |
– |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
515 |
– |
"\n" |
516 |
– |
"\t[ %G %G %G ]\n" |
517 |
– |
"\t[ %G %G %G ]\n" |
518 |
– |
"\t[ %G %G %G ]\n", |
519 |
– |
rCut, currentTime, |
520 |
– |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
521 |
– |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
522 |
– |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
523 |
– |
painCave.severity = OOPSE_ERROR; |
524 |
– |
painCave.isFatal = 1; |
525 |
– |
simError(); |
526 |
– |
} |
527 |
– |
} else { |
528 |
– |
// initialize this stuff before using it, OK? |
529 |
– |
sprintf( painCave.errMsg, |
530 |
– |
"Trying to check cutoffs without a box.\n" |
531 |
– |
"\tOOPSE should have better programmers than that.\n" ); |
532 |
– |
painCave.severity = OOPSE_ERROR; |
533 |
– |
painCave.isFatal = 1; |
534 |
– |
simError(); |
535 |
– |
} |
536 |
– |
|
243 |
|
} |
244 |
|
|
245 |
< |
void SimInfo::addProperty(GenericData* prop){ |
246 |
< |
|
247 |
< |
map<string, GenericData*>::iterator result; |
248 |
< |
result = properties.find(prop->getID()); |
249 |
< |
|
250 |
< |
//we can't simply use properties[prop->getID()] = prop, |
251 |
< |
//it will cause memory leak if we already contain a propery which has the same name of prop |
252 |
< |
|
253 |
< |
if(result != properties.end()){ |
245 |
> |
void SimInfo::removeExcludePairs(Molecule* mol) { |
246 |
> |
std::vector<Bond*>::iterator bondIter; |
247 |
> |
std::vector<Bend*>::iterator bendIter; |
248 |
> |
std::vector<Torsion*>::iterator torsionIter; |
249 |
> |
Bond* bond; |
250 |
> |
Bend* bend; |
251 |
> |
Torsion* torsion; |
252 |
> |
int a; |
253 |
> |
int b; |
254 |
> |
int c; |
255 |
> |
int d; |
256 |
|
|
257 |
< |
delete (*result).second; |
258 |
< |
(*result).second = prop; |
259 |
< |
|
260 |
< |
} |
261 |
< |
else{ |
257 |
> |
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
258 |
> |
a = bond->getAtomA()->getGlobalIndex(); |
259 |
> |
b = bond->getAtomB()->getGlobalIndex(); |
260 |
> |
exclude_.removePair(a, b); |
261 |
> |
} |
262 |
|
|
263 |
< |
properties[prop->getID()] = prop; |
263 |
> |
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
264 |
> |
a = bend->getAtomA()->getGlobalIndex(); |
265 |
> |
b = bend->getAtomB()->getGlobalIndex(); |
266 |
> |
c = bend->getAtomC()->getGlobalIndex(); |
267 |
|
|
268 |
< |
} |
269 |
< |
|
270 |
< |
} |
268 |
> |
exclude_.removePair(a, b); |
269 |
> |
exclude_.removePair(a, c); |
270 |
> |
exclude_.removePair(b, c); |
271 |
> |
} |
272 |
|
|
273 |
< |
GenericData* SimInfo::getProperty(const string& propName){ |
274 |
< |
|
275 |
< |
map<string, GenericData*>::iterator result; |
276 |
< |
|
277 |
< |
//string lowerCaseName = (); |
566 |
< |
|
567 |
< |
result = properties.find(propName); |
568 |
< |
|
569 |
< |
if(result != properties.end()) |
570 |
< |
return (*result).second; |
571 |
< |
else |
572 |
< |
return NULL; |
573 |
< |
} |
273 |
> |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) { |
274 |
> |
a = torsion->getAtomA()->getGlobalIndex(); |
275 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
276 |
> |
c = torsion->getAtomC()->getGlobalIndex(); |
277 |
> |
d = torsion->getAtomD()->getGlobalIndex(); |
278 |
|
|
279 |
< |
|
280 |
< |
void SimInfo::getFortranGroupArrays(SimInfo* info, |
281 |
< |
vector<int>& FglobalGroupMembership, |
282 |
< |
vector<double>& mfact){ |
283 |
< |
|
284 |
< |
Molecule* myMols; |
581 |
< |
Atom** myAtoms; |
582 |
< |
int numAtom; |
583 |
< |
double mtot; |
584 |
< |
int numMol; |
585 |
< |
int numCutoffGroups; |
586 |
< |
CutoffGroup* myCutoffGroup; |
587 |
< |
vector<CutoffGroup*>::iterator iterCutoff; |
588 |
< |
Atom* cutoffAtom; |
589 |
< |
vector<Atom*>::iterator iterAtom; |
590 |
< |
int atomIndex; |
591 |
< |
double totalMass; |
592 |
< |
|
593 |
< |
mfact.clear(); |
594 |
< |
FglobalGroupMembership.clear(); |
595 |
< |
|
596 |
< |
|
597 |
< |
// Fix the silly fortran indexing problem |
598 |
< |
#ifdef IS_MPI |
599 |
< |
numAtom = mpiSim->getNAtomsGlobal(); |
600 |
< |
#else |
601 |
< |
numAtom = n_atoms; |
602 |
< |
#endif |
603 |
< |
for (int i = 0; i < numAtom; i++) |
604 |
< |
FglobalGroupMembership.push_back(globalGroupMembership[i] + 1); |
605 |
< |
|
606 |
< |
|
607 |
< |
myMols = info->molecules; |
608 |
< |
numMol = info->n_mol; |
609 |
< |
for(int i = 0; i < numMol; i++){ |
610 |
< |
numCutoffGroups = myMols[i].getNCutoffGroups(); |
611 |
< |
for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); |
612 |
< |
myCutoffGroup != NULL; |
613 |
< |
myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
614 |
< |
|
615 |
< |
totalMass = myCutoffGroup->getMass(); |
616 |
< |
|
617 |
< |
for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); |
618 |
< |
cutoffAtom != NULL; |
619 |
< |
cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){ |
620 |
< |
mfact.push_back(cutoffAtom->getMass()/totalMass); |
621 |
< |
} |
279 |
> |
exclude_.removePair(a, b); |
280 |
> |
exclude_.removePair(a, c); |
281 |
> |
exclude_.removePair(a, d); |
282 |
> |
exclude_.removePair(b, c); |
283 |
> |
exclude_.removePair(b, d); |
284 |
> |
exclude_.removePair(c, d); |
285 |
|
} |
623 |
– |
} |
286 |
|
|
287 |
|
} |
288 |
+ |
|
289 |
+ |
|
290 |
+ |
}//end namespace oopse |