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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 "primitives/Molecule.hpp" |
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> |
#include "UseTheForce/doForces_interface.h" |
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> |
#include "UseTheForce/notifyCutoffs_interface.h" |
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> |
#include "utils/MemoryUtils.hpp" |
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#include "utils/simError.h" |
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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(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
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> |
ForceField* ff, Globals* globals) : |
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> |
forceField_(ff), globals_(globals), nAtoms_(0), nBonds_(0), |
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> |
nBends_(0), nTorsions_(0), nRigidBodies_(0), nIntegrableObjects_(0), |
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> |
nCutoffGroups_(0), nConstraints_(0), nZconstraint_(0), sman_(NULL), |
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> |
fortranInitialized_(false) { |
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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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> |
std::vector<std::pair<MoleculeStamp*, int> >::iterator i; |
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> |
MoleculeStamp* molStamp; |
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> |
int nMolWithSameStamp; |
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> |
int nCutoffAtoms; // number of atoms belong to cutoff groups |
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> |
int nGroups; //total cutoff groups defined in meta-data file |
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> |
CutoffGroupStamp* cgStamp; |
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> |
int nAtomsInGroups; |
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> |
int nCutoffGroupsInStamp; |
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|
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> |
RigidBodyStamp* rbStamp; |
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> |
int nAtomsInRigidBodies; |
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> |
int nRigidBodiesInStamp; |
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> |
int nRigidAtoms; |
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> |
int nRigidBodies; |
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> |
|
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> |
nGlobalAtoms_ = 0; |
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> |
|
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> |
nGroups = 0; |
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> |
nCutoffAtoms = 0; |
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> |
nRigidBodies = 0; |
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> |
|
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for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
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molStamp = i->first; |
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nMolWithSameStamp = i->second; |
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> |
|
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addMoleculeStamp(molStamp, nMolWithSameStamp); |
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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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> |
//calculate atoms in molecules |
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> |
nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; |
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|
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SimInfo* currentInfo; |
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|
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< |
SimInfo::SimInfo(){ |
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> |
//calculate atoms in cutoff groups |
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> |
nAtomsInGroups = 0; |
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> |
nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
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> |
|
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> |
for (int j=0; j < nCutoffGroupsInStamp; j++) { |
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> |
cgStamp = molStamp->getCutoffGroup(j); |
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> |
nAtomsInGroups += cgStamp->getNMembers(); |
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> |
} |
| 90 |
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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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> |
nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
| 92 |
> |
nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
| 93 |
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|
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< |
haveRcut = 0; |
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< |
haveRsw = 0; |
| 96 |
< |
boxIsInit = 0; |
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< |
|
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< |
resetTime = 1e99; |
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> |
//calculate atoms in rigid bodies |
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> |
nAtomsInRigidBodies = 0; |
| 96 |
> |
nRigidBodiesInStamp = molStamp->getNCutoffGroups(); |
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> |
|
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> |
for (int j=0; j < nRigidBodiesInStamp; j++) { |
| 99 |
> |
rbStamp = molStamp->getRigidBody(j); |
| 100 |
> |
nRigidBodiesInStamp += rbStamp->getNMembers(); |
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> |
} |
| 102 |
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|
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< |
orthoRhombic = 0; |
| 104 |
< |
orthoTolerance = 1E-6; |
| 105 |
< |
useInitXSstate = true; |
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> |
nRigidBodies += nRigidBodiesInStamp * nMolWithSameStamp; |
| 104 |
> |
nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp; |
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> |
|
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> |
} |
| 107 |
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|
| 108 |
< |
usePBC = 0; |
| 109 |
< |
useLJ = 0; |
| 110 |
< |
useSticky = 0; |
| 111 |
< |
useCharges = 0; |
| 112 |
< |
useDipoles = 0; |
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< |
useReactionField = 0; |
| 63 |
< |
useGB = 0; |
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< |
useEAM = 0; |
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< |
useSolidThermInt = 0; |
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< |
useLiquidThermInt = 0; |
| 108 |
> |
//every free atom (atom does not belong to cutoff groups) is a cutoff group |
| 109 |
> |
//therefore the total number of cutoff groups in the system is equal to |
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> |
//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data |
| 111 |
> |
//file plus the number of cutoff groups defined in meta-data file |
| 112 |
> |
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
| 113 |
|
|
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< |
haveCutoffGroups = false; |
| 114 |
> |
//every free atom (atom does not belong to rigid bodies) is a rigid body |
| 115 |
> |
//therefore the total number of cutoff groups in the system is equal to |
| 116 |
> |
//the total number of atoms minus number of atoms belong to rigid body defined in meta-data |
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> |
//file plus the number of rigid bodies defined in meta-data file |
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> |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nRigidBodies; |
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|
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< |
excludes = Exclude::Instance(); |
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> |
//initialize globalGroupMembership_, every element of this array will be 0 |
| 121 |
> |
globalGroupMembership_.insert(globalGroupMembership_.end(), nGlobalAtoms_, 0); |
| 122 |
|
|
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< |
myConfiguration = new SimState(); |
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> |
nGlobalMols_ = molStampIds_.size(); |
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|
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< |
has_minimizer = false; |
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< |
the_minimizer =NULL; |
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> |
#ifdef IS_MPI |
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> |
molToProcMap_.resize(nGlobalMols_); |
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> |
#endif |
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> |
|
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> |
} |
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|
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< |
ngroup = 0; |
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> |
SimInfo::~SimInfo() { |
| 132 |
> |
//MemoryUtils::deleteVectorOfPointer(molecules_); |
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|
|
| 134 |
< |
wrapMeSimInfo( this ); |
| 134 |
> |
MemoryUtils::deleteVectorOfPointer(moleculeStamps_); |
| 135 |
> |
|
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> |
delete sman_; |
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> |
delete globals_; |
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> |
delete forceField_; |
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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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> |
MoleculeIterator i; |
| 145 |
|
|
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< |
delete myConfiguration; |
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> |
i = molecules_.find(mol->getGlobalIndex()); |
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> |
if (i != molecules_.end() ) { |
| 148 |
|
|
| 149 |
< |
map<string, GenericData*>::iterator i; |
| 150 |
< |
|
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< |
for(i = properties.begin(); i != properties.end(); i++) |
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< |
delete (*i).second; |
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> |
molecules_.insert(make_pair(mol->getGlobalIndex(), mol)); |
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> |
|
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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(); |
| 159 |
|
|
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+ |
return true; |
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+ |
} else { |
| 162 |
+ |
return false; |
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+ |
} |
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|
} |
| 165 |
|
|
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< |
void SimInfo::setBox(double newBox[3]) { |
| 167 |
< |
|
| 168 |
< |
int i, j; |
| 97 |
< |
double tempMat[3][3]; |
| 166 |
> |
bool SimInfo::removeMolecule(Molecule* mol) { |
| 167 |
> |
MoleculeIterator i; |
| 168 |
> |
i = molecules_.find(mol->getGlobalIndex()); |
| 169 |
|
|
| 170 |
< |
for(i=0; i<3; i++) |
| 100 |
< |
for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
| 170 |
> |
if (i != molecules_.end() ) { |
| 171 |
|
|
| 172 |
< |
tempMat[0][0] = newBox[0]; |
| 173 |
< |
tempMat[1][1] = newBox[1]; |
| 174 |
< |
tempMat[2][2] = newBox[2]; |
| 172 |
> |
assert(mol == i->second); |
| 173 |
> |
|
| 174 |
> |
nAtoms_ -= mol->getNAtoms(); |
| 175 |
> |
nBonds_ -= mol->getNBonds(); |
| 176 |
> |
nBends_ -= mol->getNBends(); |
| 177 |
> |
nTorsions_ -= mol->getNTorsions(); |
| 178 |
> |
nRigidBodies_ -= mol->getNRigidBodies(); |
| 179 |
> |
nIntegrableObjects_ -= mol->getNIntegrableObjects(); |
| 180 |
> |
nCutoffGroups_ -= mol->getNCutoffGroups(); |
| 181 |
> |
nConstraints_ -= mol->getNConstraints(); |
| 182 |
|
|
| 183 |
< |
setBoxM( tempMat ); |
| 183 |
> |
molecules_.erase(mol->getGlobalIndex()); |
| 184 |
|
|
| 185 |
< |
} |
| 185 |
> |
delete mol; |
| 186 |
> |
|
| 187 |
> |
return true; |
| 188 |
> |
} else { |
| 189 |
> |
return false; |
| 190 |
> |
} |
| 191 |
|
|
| 110 |
– |
void SimInfo::setBoxM( double theBox[3][3] ){ |
| 111 |
– |
|
| 112 |
– |
int i, j; |
| 113 |
– |
double FortranHmat[9]; // to preserve compatibility with Fortran the |
| 114 |
– |
// ordering in the array is as follows: |
| 115 |
– |
// [ 0 3 6 ] |
| 116 |
– |
// [ 1 4 7 ] |
| 117 |
– |
// [ 2 5 8 ] |
| 118 |
– |
double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
| 192 |
|
|
| 193 |
< |
if( !boxIsInit ) boxIsInit = 1; |
| 193 |
> |
} |
| 194 |
|
|
| 195 |
< |
for(i=0; i < 3; i++) |
| 196 |
< |
for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
| 197 |
< |
|
| 198 |
< |
calcBoxL(); |
| 199 |
< |
calcHmatInv(); |
| 195 |
> |
|
| 196 |
> |
Molecule* SimInfo::beginMolecule(MoleculeIterator& i) { |
| 197 |
> |
i = molecules_.begin(); |
| 198 |
> |
return i == molecules_.end() ? NULL : i->second; |
| 199 |
> |
} |
| 200 |
|
|
| 201 |
< |
for(i=0; i < 3; i++) { |
| 202 |
< |
for (j=0; j < 3; j++) { |
| 203 |
< |
FortranHmat[3*j + i] = Hmat[i][j]; |
| 131 |
< |
FortranHmatInv[3*j + i] = HmatInv[i][j]; |
| 132 |
< |
} |
| 133 |
< |
} |
| 134 |
< |
|
| 135 |
< |
setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
| 136 |
< |
|
| 201 |
> |
Molecule* SimInfo::nextMolecule(MoleculeIterator& i) { |
| 202 |
> |
++i; |
| 203 |
> |
return i == molecules_.end() ? NULL : i->second; |
| 204 |
|
} |
| 138 |
– |
|
| 205 |
|
|
| 140 |
– |
void SimInfo::getBoxM (double theBox[3][3]) { |
| 206 |
|
|
| 207 |
< |
int i, j; |
| 208 |
< |
for(i=0; i<3; i++) |
| 209 |
< |
for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
| 210 |
< |
} |
| 207 |
> |
void SimInfo::calcNdf() { |
| 208 |
> |
int ndf_local; |
| 209 |
> |
MoleculeIterator i; |
| 210 |
> |
std::vector<StuntDouble*>::iterator j; |
| 211 |
> |
Molecule* mol; |
| 212 |
> |
StuntDouble* integrableObject; |
| 213 |
|
|
| 214 |
+ |
ndf_local = 0; |
| 215 |
+ |
|
| 216 |
+ |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
| 217 |
+ |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 218 |
+ |
integrableObject = mol->nextIntegrableObject(j)) { |
| 219 |
|
|
| 220 |
< |
void SimInfo::scaleBox(double scale) { |
| 149 |
< |
double theBox[3][3]; |
| 150 |
< |
int i, j; |
| 220 |
> |
ndf_local += 3; |
| 221 |
|
|
| 222 |
< |
// cerr << "Scaling box by " << scale << "\n"; |
| 222 |
> |
if (integrableObject->isDirectional()) { |
| 223 |
> |
if (integrableObject->isLinear()) { |
| 224 |
> |
ndf_local += 2; |
| 225 |
> |
} else { |
| 226 |
> |
ndf_local += 3; |
| 227 |
> |
} |
| 228 |
> |
} |
| 229 |
> |
|
| 230 |
> |
}//end for (integrableObject) |
| 231 |
> |
}// end for (mol) |
| 232 |
> |
|
| 233 |
> |
// n_constraints is local, so subtract them on each processor |
| 234 |
> |
ndf_local -= nConstraints_; |
| 235 |
|
|
| 236 |
< |
for(i=0; i<3; i++) |
| 237 |
< |
for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
| 236 |
> |
#ifdef IS_MPI |
| 237 |
> |
MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 238 |
> |
#else |
| 239 |
> |
ndf_ = ndf_local; |
| 240 |
> |
#endif |
| 241 |
|
|
| 242 |
< |
setBoxM(theBox); |
| 242 |
> |
// nZconstraints_ is global, as are the 3 COM translations for the |
| 243 |
> |
// entire system: |
| 244 |
> |
ndf_ = ndf_ - 3 - nZconstraint_; |
| 245 |
|
|
| 246 |
|
} |
| 247 |
|
|
| 248 |
< |
void SimInfo::calcHmatInv( void ) { |
| 249 |
< |
|
| 163 |
< |
int oldOrtho; |
| 164 |
< |
int i,j; |
| 165 |
< |
double smallDiag; |
| 166 |
< |
double tol; |
| 167 |
< |
double sanity[3][3]; |
| 248 |
> |
void SimInfo::calcNdfRaw() { |
| 249 |
> |
int ndfRaw_local; |
| 250 |
|
|
| 251 |
< |
invertMat3( Hmat, HmatInv ); |
| 251 |
> |
MoleculeIterator i; |
| 252 |
> |
std::vector<StuntDouble*>::iterator j; |
| 253 |
> |
Molecule* mol; |
| 254 |
> |
StuntDouble* integrableObject; |
| 255 |
|
|
| 256 |
< |
// check to see if Hmat is orthorhombic |
| 257 |
< |
|
| 258 |
< |
oldOrtho = orthoRhombic; |
| 256 |
> |
// Raw degrees of freedom that we have to set |
| 257 |
> |
ndfRaw_local = 0; |
| 258 |
> |
|
| 259 |
> |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
| 260 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 261 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 262 |
|
|
| 263 |
< |
smallDiag = fabs(Hmat[0][0]); |
| 176 |
< |
if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
| 177 |
< |
if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
| 178 |
< |
tol = smallDiag * orthoTolerance; |
| 263 |
> |
ndfRaw_local += 3; |
| 264 |
|
|
| 265 |
< |
orthoRhombic = 1; |
| 266 |
< |
|
| 267 |
< |
for (i = 0; i < 3; i++ ) { |
| 268 |
< |
for (j = 0 ; j < 3; j++) { |
| 269 |
< |
if (i != j) { |
| 270 |
< |
if (orthoRhombic) { |
| 271 |
< |
if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
| 272 |
< |
} |
| 273 |
< |
} |
| 265 |
> |
if (integrableObject->isDirectional()) { |
| 266 |
> |
if (integrableObject->isLinear()) { |
| 267 |
> |
ndfRaw_local += 2; |
| 268 |
> |
} else { |
| 269 |
> |
ndfRaw_local += 3; |
| 270 |
> |
} |
| 271 |
> |
} |
| 272 |
> |
|
| 273 |
> |
} |
| 274 |
|
} |
| 190 |
– |
} |
| 191 |
– |
|
| 192 |
– |
if( oldOrtho != orthoRhombic ){ |
| 275 |
|
|
| 276 |
< |
if( orthoRhombic ) { |
| 277 |
< |
sprintf( painCave.errMsg, |
| 278 |
< |
"OOPSE is switching from the default Non-Orthorhombic\n" |
| 279 |
< |
"\tto the faster Orthorhombic periodic boundary computations.\n" |
| 280 |
< |
"\tThis is usually a good thing, but if you wan't the\n" |
| 199 |
< |
"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
| 200 |
< |
"\tvariable ( currently set to %G ) smaller.\n", |
| 201 |
< |
orthoTolerance); |
| 202 |
< |
painCave.severity = OOPSE_INFO; |
| 203 |
< |
simError(); |
| 204 |
< |
} |
| 205 |
< |
else { |
| 206 |
< |
sprintf( painCave.errMsg, |
| 207 |
< |
"OOPSE is switching from the faster Orthorhombic to the more\n" |
| 208 |
< |
"\tflexible Non-Orthorhombic periodic boundary computations.\n" |
| 209 |
< |
"\tThis is usually because the box has deformed under\n" |
| 210 |
< |
"\tNPTf integration. If you wan't to live on the edge with\n" |
| 211 |
< |
"\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
| 212 |
< |
"\tvariable ( currently set to %G ) larger.\n", |
| 213 |
< |
orthoTolerance); |
| 214 |
< |
painCave.severity = OOPSE_WARNING; |
| 215 |
< |
simError(); |
| 216 |
< |
} |
| 217 |
< |
} |
| 276 |
> |
#ifdef IS_MPI |
| 277 |
> |
MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 278 |
> |
#else |
| 279 |
> |
ndfRaw_ = ndfRaw_local; |
| 280 |
> |
#endif |
| 281 |
|
} |
| 282 |
|
|
| 283 |
< |
void SimInfo::calcBoxL( void ){ |
| 283 |
> |
void SimInfo::calcNdfTrans() { |
| 284 |
> |
int ndfTrans_local; |
| 285 |
|
|
| 286 |
< |
double dx, dy, dz, dsq; |
| 286 |
> |
ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_; |
| 287 |
|
|
| 224 |
– |
// boxVol = Determinant of Hmat |
| 288 |
|
|
| 289 |
< |
boxVol = matDet3( Hmat ); |
| 289 |
> |
#ifdef IS_MPI |
| 290 |
> |
MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 291 |
> |
#else |
| 292 |
> |
ndfTrans_ = ndfTrans_local; |
| 293 |
> |
#endif |
| 294 |
|
|
| 295 |
< |
// boxLx |
| 296 |
< |
|
| 297 |
< |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
| 231 |
< |
dsq = dx*dx + dy*dy + dz*dz; |
| 232 |
< |
boxL[0] = sqrt( dsq ); |
| 233 |
< |
//maxCutoff = 0.5 * boxL[0]; |
| 295 |
> |
ndfTrans_ = ndfTrans_ - 3 - nZconstraint_; |
| 296 |
> |
|
| 297 |
> |
} |
| 298 |
|
|
| 299 |
< |
// boxLy |
| 300 |
< |
|
| 301 |
< |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
| 302 |
< |
dsq = dx*dx + dy*dy + dz*dz; |
| 303 |
< |
boxL[1] = sqrt( dsq ); |
| 304 |
< |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
| 299 |
> |
void SimInfo::addExcludePairs(Molecule* mol) { |
| 300 |
> |
std::vector<Bond*>::iterator bondIter; |
| 301 |
> |
std::vector<Bend*>::iterator bendIter; |
| 302 |
> |
std::vector<Torsion*>::iterator torsionIter; |
| 303 |
> |
Bond* bond; |
| 304 |
> |
Bend* bend; |
| 305 |
> |
Torsion* torsion; |
| 306 |
> |
int a; |
| 307 |
> |
int b; |
| 308 |
> |
int c; |
| 309 |
> |
int d; |
| 310 |
> |
|
| 311 |
> |
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
| 312 |
> |
a = bond->getAtomA()->getGlobalIndex(); |
| 313 |
> |
b = bond->getAtomB()->getGlobalIndex(); |
| 314 |
> |
exclude_.addPair(a, b); |
| 315 |
> |
} |
| 316 |
|
|
| 317 |
+ |
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
| 318 |
+ |
a = bend->getAtomA()->getGlobalIndex(); |
| 319 |
+ |
b = bend->getAtomB()->getGlobalIndex(); |
| 320 |
+ |
c = bend->getAtomC()->getGlobalIndex(); |
| 321 |
|
|
| 322 |
< |
// boxLz |
| 323 |
< |
|
| 324 |
< |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
| 325 |
< |
dsq = dx*dx + dy*dy + dz*dz; |
| 247 |
< |
boxL[2] = sqrt( dsq ); |
| 248 |
< |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
| 322 |
> |
exclude_.addPair(a, b); |
| 323 |
> |
exclude_.addPair(a, c); |
| 324 |
> |
exclude_.addPair(b, c); |
| 325 |
> |
} |
| 326 |
|
|
| 327 |
< |
//calculate the max cutoff |
| 328 |
< |
maxCutoff = calcMaxCutOff(); |
| 329 |
< |
|
| 330 |
< |
checkCutOffs(); |
| 327 |
> |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
| 328 |
> |
a = torsion->getAtomA()->getGlobalIndex(); |
| 329 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
| 330 |
> |
c = torsion->getAtomC()->getGlobalIndex(); |
| 331 |
> |
d = torsion->getAtomD()->getGlobalIndex(); |
| 332 |
|
|
| 333 |
+ |
exclude_.addPair(a, b); |
| 334 |
+ |
exclude_.addPair(a, c); |
| 335 |
+ |
exclude_.addPair(a, d); |
| 336 |
+ |
exclude_.addPair(b, c); |
| 337 |
+ |
exclude_.addPair(b, d); |
| 338 |
+ |
exclude_.addPair(c, d); |
| 339 |
+ |
} |
| 340 |
+ |
|
| 341 |
+ |
|
| 342 |
|
} |
| 343 |
|
|
| 344 |
+ |
void SimInfo::removeExcludePairs(Molecule* mol) { |
| 345 |
+ |
std::vector<Bond*>::iterator bondIter; |
| 346 |
+ |
std::vector<Bend*>::iterator bendIter; |
| 347 |
+ |
std::vector<Torsion*>::iterator torsionIter; |
| 348 |
+ |
Bond* bond; |
| 349 |
+ |
Bend* bend; |
| 350 |
+ |
Torsion* torsion; |
| 351 |
+ |
int a; |
| 352 |
+ |
int b; |
| 353 |
+ |
int c; |
| 354 |
+ |
int d; |
| 355 |
+ |
|
| 356 |
+ |
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
| 357 |
+ |
a = bond->getAtomA()->getGlobalIndex(); |
| 358 |
+ |
b = bond->getAtomB()->getGlobalIndex(); |
| 359 |
+ |
exclude_.removePair(a, b); |
| 360 |
+ |
} |
| 361 |
|
|
| 362 |
< |
double SimInfo::calcMaxCutOff(){ |
| 362 |
> |
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
| 363 |
> |
a = bend->getAtomA()->getGlobalIndex(); |
| 364 |
> |
b = bend->getAtomB()->getGlobalIndex(); |
| 365 |
> |
c = bend->getAtomC()->getGlobalIndex(); |
| 366 |
|
|
| 367 |
< |
double ri[3], rj[3], rk[3]; |
| 368 |
< |
double rij[3], rjk[3], rki[3]; |
| 369 |
< |
double minDist; |
| 367 |
> |
exclude_.removePair(a, b); |
| 368 |
> |
exclude_.removePair(a, c); |
| 369 |
> |
exclude_.removePair(b, c); |
| 370 |
> |
} |
| 371 |
|
|
| 372 |
< |
ri[0] = Hmat[0][0]; |
| 373 |
< |
ri[1] = Hmat[1][0]; |
| 374 |
< |
ri[2] = Hmat[2][0]; |
| 372 |
> |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
| 373 |
> |
a = torsion->getAtomA()->getGlobalIndex(); |
| 374 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
| 375 |
> |
c = torsion->getAtomC()->getGlobalIndex(); |
| 376 |
> |
d = torsion->getAtomD()->getGlobalIndex(); |
| 377 |
|
|
| 378 |
< |
rj[0] = Hmat[0][1]; |
| 379 |
< |
rj[1] = Hmat[1][1]; |
| 380 |
< |
rj[2] = Hmat[2][1]; |
| 378 |
> |
exclude_.removePair(a, b); |
| 379 |
> |
exclude_.removePair(a, c); |
| 380 |
> |
exclude_.removePair(a, d); |
| 381 |
> |
exclude_.removePair(b, c); |
| 382 |
> |
exclude_.removePair(b, d); |
| 383 |
> |
exclude_.removePair(c, d); |
| 384 |
> |
} |
| 385 |
|
|
| 386 |
< |
rk[0] = Hmat[0][2]; |
| 273 |
< |
rk[1] = Hmat[1][2]; |
| 274 |
< |
rk[2] = Hmat[2][2]; |
| 275 |
< |
|
| 276 |
< |
crossProduct3(ri, rj, rij); |
| 277 |
< |
distXY = dotProduct3(rk,rij) / norm3(rij); |
| 386 |
> |
} |
| 387 |
|
|
| 279 |
– |
crossProduct3(rj,rk, rjk); |
| 280 |
– |
distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
| 388 |
|
|
| 389 |
< |
crossProduct3(rk,ri, rki); |
| 390 |
< |
distZX = dotProduct3(rj,rki) / norm3(rki); |
| 389 |
> |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
| 390 |
> |
int curStampId; |
| 391 |
|
|
| 392 |
< |
minDist = min(min(distXY, distYZ), distZX); |
| 393 |
< |
return minDist/2; |
| 394 |
< |
|
| 392 |
> |
//index from 0 |
| 393 |
> |
curStampId = molStampIds_.size(); |
| 394 |
> |
|
| 395 |
> |
moleculeStamps_.push_back(molStamp); |
| 396 |
> |
molStampIds_.insert(molStampIds_.end(), nmol, curStampId); |
| 397 |
|
} |
| 398 |
|
|
| 399 |
< |
void SimInfo::wrapVector( double thePos[3] ){ |
| 399 |
> |
void SimInfo::update() { |
| 400 |
|
|
| 401 |
< |
int i; |
| 293 |
< |
double scaled[3]; |
| 401 |
> |
setupSimType(); |
| 402 |
|
|
| 403 |
< |
if( !orthoRhombic ){ |
| 404 |
< |
// calc the scaled coordinates. |
| 405 |
< |
|
| 403 |
> |
#ifdef IS_MPI |
| 404 |
> |
setupFortranParallel(); |
| 405 |
> |
#endif |
| 406 |
|
|
| 407 |
< |
matVecMul3(HmatInv, thePos, scaled); |
| 300 |
< |
|
| 301 |
< |
for(i=0; i<3; i++) |
| 302 |
< |
scaled[i] -= roundMe(scaled[i]); |
| 303 |
< |
|
| 304 |
< |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
| 305 |
< |
|
| 306 |
< |
matVecMul3(Hmat, scaled, thePos); |
| 407 |
> |
setupFortranSim(); |
| 408 |
|
|
| 409 |
< |
} |
| 410 |
< |
else{ |
| 411 |
< |
// calc the scaled coordinates. |
| 409 |
> |
//setup fortran force field |
| 410 |
> |
/** @deprecate */ |
| 411 |
> |
int isError = 0; |
| 412 |
> |
initFortranFF( &fInfo_.SIM_uses_RF , &isError ); |
| 413 |
> |
if(isError){ |
| 414 |
> |
sprintf( painCave.errMsg, |
| 415 |
> |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
| 416 |
> |
painCave.isFatal = 1; |
| 417 |
> |
simError(); |
| 418 |
> |
} |
| 419 |
> |
|
| 420 |
|
|
| 421 |
< |
for(i=0; i<3; i++) |
| 422 |
< |
scaled[i] = thePos[i]*HmatInv[i][i]; |
| 423 |
< |
|
| 424 |
< |
// wrap the scaled coordinates |
| 425 |
< |
|
| 426 |
< |
for(i=0; i<3; i++) |
| 427 |
< |
scaled[i] -= roundMe(scaled[i]); |
| 319 |
< |
|
| 320 |
< |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
| 321 |
< |
|
| 322 |
< |
for(i=0; i<3; i++) |
| 323 |
< |
thePos[i] = scaled[i]*Hmat[i][i]; |
| 324 |
< |
} |
| 325 |
< |
|
| 421 |
> |
setupCutoff(); |
| 422 |
> |
|
| 423 |
> |
calcNdf(); |
| 424 |
> |
calcNdfRaw(); |
| 425 |
> |
calcNdfTrans(); |
| 426 |
> |
|
| 427 |
> |
fortranInitialized_ = true; |
| 428 |
|
} |
| 429 |
|
|
| 430 |
+ |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
| 431 |
+ |
SimInfo::MoleculeIterator mi; |
| 432 |
+ |
Molecule* mol; |
| 433 |
+ |
Molecule::AtomIterator ai; |
| 434 |
+ |
Atom* atom; |
| 435 |
+ |
std::set<AtomType*> atomTypes; |
| 436 |
|
|
| 437 |
< |
int SimInfo::getNDF(){ |
| 330 |
< |
int ndf_local; |
| 437 |
> |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 438 |
|
|
| 439 |
< |
ndf_local = 0; |
| 440 |
< |
|
| 441 |
< |
for(int i = 0; i < integrableObjects.size(); i++){ |
| 442 |
< |
ndf_local += 3; |
| 336 |
< |
if (integrableObjects[i]->isDirectional()) { |
| 337 |
< |
if (integrableObjects[i]->isLinear()) |
| 338 |
< |
ndf_local += 2; |
| 339 |
< |
else |
| 340 |
< |
ndf_local += 3; |
| 439 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 440 |
> |
atomTypes.insert(atom->getAtomType()); |
| 441 |
> |
} |
| 442 |
> |
|
| 443 |
|
} |
| 342 |
– |
} |
| 444 |
|
|
| 445 |
< |
// n_constraints is local, so subtract them on each processor: |
| 445 |
> |
return atomTypes; |
| 446 |
> |
} |
| 447 |
|
|
| 448 |
< |
ndf_local -= n_constraints; |
| 448 |
> |
void SimInfo::setupSimType() { |
| 449 |
> |
std::set<AtomType*>::iterator i; |
| 450 |
> |
std::set<AtomType*> atomTypes; |
| 451 |
> |
atomTypes = getUniqueAtomTypes(); |
| 452 |
> |
|
| 453 |
> |
int useLennardJones = 0; |
| 454 |
> |
int useElectrostatic = 0; |
| 455 |
> |
int useEAM = 0; |
| 456 |
> |
int useCharge = 0; |
| 457 |
> |
int useDirectional = 0; |
| 458 |
> |
int useDipole = 0; |
| 459 |
> |
int useGayBerne = 0; |
| 460 |
> |
int useSticky = 0; |
| 461 |
> |
int useShape = 0; |
| 462 |
> |
int useFLARB = 0; //it is not in AtomType yet |
| 463 |
> |
int useDirectionalAtom = 0; |
| 464 |
> |
int useElectrostatics = 0; |
| 465 |
> |
//usePBC and useRF are from globals |
| 466 |
> |
bool usePBC = globals_->getPBC(); |
| 467 |
> |
bool useRF = globals_->getUseRF(); |
| 468 |
|
|
| 469 |
< |
#ifdef IS_MPI |
| 470 |
< |
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 471 |
< |
#else |
| 472 |
< |
ndf = ndf_local; |
| 473 |
< |
#endif |
| 469 |
> |
//loop over all of the atom types |
| 470 |
> |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 471 |
> |
useLennardJones |= (*i)->isLennardJones(); |
| 472 |
> |
useElectrostatic |= (*i)->isElectrostatic(); |
| 473 |
> |
useEAM |= (*i)->isEAM(); |
| 474 |
> |
useCharge |= (*i)->isCharge(); |
| 475 |
> |
useDirectional |= (*i)->isDirectional(); |
| 476 |
> |
useDipole |= (*i)->isDipole(); |
| 477 |
> |
useGayBerne |= (*i)->isGayBerne(); |
| 478 |
> |
useSticky |= (*i)->isSticky(); |
| 479 |
> |
useShape |= (*i)->isShape(); |
| 480 |
> |
} |
| 481 |
|
|
| 482 |
< |
// nZconstraints is global, as are the 3 COM translations for the |
| 483 |
< |
// entire system: |
| 482 |
> |
if (useSticky || useDipole || useGayBerne || useShape) { |
| 483 |
> |
useDirectionalAtom = 1; |
| 484 |
> |
} |
| 485 |
|
|
| 486 |
< |
ndf = ndf - 3 - nZconstraints; |
| 486 |
> |
if (useCharge || useDipole) { |
| 487 |
> |
useElectrostatics = 1; |
| 488 |
> |
} |
| 489 |
|
|
| 490 |
< |
return ndf; |
| 491 |
< |
} |
| 490 |
> |
#ifdef IS_MPI |
| 491 |
> |
int temp; |
| 492 |
|
|
| 493 |
< |
int SimInfo::getNDFraw() { |
| 494 |
< |
int ndfRaw_local; |
| 493 |
> |
temp = usePBC; |
| 494 |
> |
MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 495 |
|
|
| 496 |
< |
// Raw degrees of freedom that we have to set |
| 497 |
< |
ndfRaw_local = 0; |
| 496 |
> |
temp = useDirectionalAtom; |
| 497 |
> |
MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 498 |
|
|
| 499 |
< |
for(int i = 0; i < integrableObjects.size(); i++){ |
| 500 |
< |
ndfRaw_local += 3; |
| 370 |
< |
if (integrableObjects[i]->isDirectional()) { |
| 371 |
< |
if (integrableObjects[i]->isLinear()) |
| 372 |
< |
ndfRaw_local += 2; |
| 373 |
< |
else |
| 374 |
< |
ndfRaw_local += 3; |
| 375 |
< |
} |
| 376 |
< |
} |
| 377 |
< |
|
| 378 |
< |
#ifdef IS_MPI |
| 379 |
< |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 380 |
< |
#else |
| 381 |
< |
ndfRaw = ndfRaw_local; |
| 382 |
< |
#endif |
| 499 |
> |
temp = useLennardJones; |
| 500 |
> |
MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 501 |
|
|
| 502 |
< |
return ndfRaw; |
| 503 |
< |
} |
| 502 |
> |
temp = useElectrostatics; |
| 503 |
> |
MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 504 |
|
|
| 505 |
< |
int SimInfo::getNDFtranslational() { |
| 506 |
< |
int ndfTrans_local; |
| 505 |
> |
temp = useCharge; |
| 506 |
> |
MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 507 |
|
|
| 508 |
< |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
| 508 |
> |
temp = useDipole; |
| 509 |
> |
MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 510 |
|
|
| 511 |
+ |
temp = useSticky; |
| 512 |
+ |
MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 513 |
|
|
| 514 |
< |
#ifdef IS_MPI |
| 515 |
< |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 395 |
< |
#else |
| 396 |
< |
ndfTrans = ndfTrans_local; |
| 397 |
< |
#endif |
| 514 |
> |
temp = useGayBerne; |
| 515 |
> |
MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 516 |
|
|
| 517 |
< |
ndfTrans = ndfTrans - 3 - nZconstraints; |
| 517 |
> |
temp = useEAM; |
| 518 |
> |
MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 519 |
|
|
| 520 |
< |
return ndfTrans; |
| 521 |
< |
} |
| 520 |
> |
temp = useShape; |
| 521 |
> |
MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 522 |
|
|
| 523 |
< |
int SimInfo::getTotIntegrableObjects() { |
| 524 |
< |
int nObjs_local; |
| 406 |
< |
int nObjs; |
| 523 |
> |
temp = useFLARB; |
| 524 |
> |
MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 525 |
|
|
| 526 |
< |
nObjs_local = integrableObjects.size(); |
| 526 |
> |
temp = useRF; |
| 527 |
> |
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
| 528 |
> |
|
| 529 |
> |
#endif |
| 530 |
|
|
| 531 |
+ |
fInfo_.SIM_uses_PBC = usePBC; |
| 532 |
+ |
fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom; |
| 533 |
+ |
fInfo_.SIM_uses_LennardJones = useLennardJones; |
| 534 |
+ |
fInfo_.SIM_uses_Electrostatics = useElectrostatics; |
| 535 |
+ |
fInfo_.SIM_uses_Charges = useCharge; |
| 536 |
+ |
fInfo_.SIM_uses_Dipoles = useDipole; |
| 537 |
+ |
fInfo_.SIM_uses_Sticky = useSticky; |
| 538 |
+ |
fInfo_.SIM_uses_GayBerne = useGayBerne; |
| 539 |
+ |
fInfo_.SIM_uses_EAM = useEAM; |
| 540 |
+ |
fInfo_.SIM_uses_Shapes = useShape; |
| 541 |
+ |
fInfo_.SIM_uses_FLARB = useFLARB; |
| 542 |
+ |
fInfo_.SIM_uses_RF = useRF; |
| 543 |
|
|
| 544 |
< |
#ifdef IS_MPI |
| 412 |
< |
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 413 |
< |
#else |
| 414 |
< |
nObjs = nObjs_local; |
| 415 |
< |
#endif |
| 544 |
> |
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
| 545 |
|
|
| 546 |
+ |
if (globals_->haveDielectric()) { |
| 547 |
+ |
fInfo_.dielect = globals_->getDielectric(); |
| 548 |
+ |
} else { |
| 549 |
+ |
sprintf(painCave.errMsg, |
| 550 |
+ |
"SimSetup Error: No Dielectric constant was set.\n" |
| 551 |
+ |
"\tYou are trying to use Reaction Field without" |
| 552 |
+ |
"\tsetting a dielectric constant!\n"); |
| 553 |
+ |
painCave.isFatal = 1; |
| 554 |
+ |
simError(); |
| 555 |
+ |
} |
| 556 |
+ |
|
| 557 |
+ |
} else { |
| 558 |
+ |
fInfo_.dielect = 0.0; |
| 559 |
+ |
} |
| 560 |
|
|
| 418 |
– |
return nObjs; |
| 561 |
|
} |
| 562 |
|
|
| 563 |
< |
void SimInfo::refreshSim(){ |
| 563 |
> |
void SimInfo::setupFortranSim() { |
| 564 |
> |
int isError; |
| 565 |
> |
int nExclude; |
| 566 |
> |
std::vector<int> fortranGlobalGroupMembership; |
| 567 |
> |
|
| 568 |
> |
nExclude = exclude_.getSize(); |
| 569 |
> |
isError = 0; |
| 570 |
|
|
| 571 |
< |
simtype fInfo; |
| 572 |
< |
int isError; |
| 573 |
< |
int n_global; |
| 574 |
< |
int* excl; |
| 571 |
> |
//globalGroupMembership_ is filled by SimCreator |
| 572 |
> |
for (int i = 0; i < nGlobalAtoms_; i++) { |
| 573 |
> |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
| 574 |
> |
} |
| 575 |
|
|
| 576 |
< |
fInfo.dielect = 0.0; |
| 576 |
> |
//calculate mass ratio of cutoff group |
| 577 |
> |
std::vector<double> mfact; |
| 578 |
> |
SimInfo::MoleculeIterator mi; |
| 579 |
> |
Molecule* mol; |
| 580 |
> |
Molecule::CutoffGroupIterator ci; |
| 581 |
> |
CutoffGroup* cg; |
| 582 |
> |
Molecule::AtomIterator ai; |
| 583 |
> |
Atom* atom; |
| 584 |
> |
double totalMass; |
| 585 |
|
|
| 586 |
< |
if( useDipoles ){ |
| 587 |
< |
if( useReactionField )fInfo.dielect = dielectric; |
| 588 |
< |
} |
| 586 |
> |
//to avoid memory reallocation, reserve enough space for mfact |
| 587 |
> |
mfact.reserve(getNCutoffGroups()); |
| 588 |
> |
|
| 589 |
> |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 590 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 591 |
|
|
| 592 |
< |
fInfo.SIM_uses_PBC = usePBC; |
| 593 |
< |
//fInfo.SIM_uses_LJ = 0; |
| 594 |
< |
fInfo.SIM_uses_LJ = useLJ; |
| 595 |
< |
fInfo.SIM_uses_sticky = useSticky; |
| 438 |
< |
//fInfo.SIM_uses_sticky = 0; |
| 439 |
< |
fInfo.SIM_uses_charges = useCharges; |
| 440 |
< |
fInfo.SIM_uses_dipoles = useDipoles; |
| 441 |
< |
//fInfo.SIM_uses_dipoles = 0; |
| 442 |
< |
fInfo.SIM_uses_RF = useReactionField; |
| 443 |
< |
//fInfo.SIM_uses_RF = 0; |
| 444 |
< |
fInfo.SIM_uses_GB = useGB; |
| 445 |
< |
fInfo.SIM_uses_EAM = useEAM; |
| 592 |
> |
totalMass = cg->getMass(); |
| 593 |
> |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
| 594 |
> |
mfact.push_back(atom->getMass()/totalMass); |
| 595 |
> |
} |
| 596 |
|
|
| 597 |
< |
n_exclude = excludes->getSize(); |
| 598 |
< |
excl = excludes->getFortranArray(); |
| 449 |
< |
|
| 450 |
< |
#ifdef IS_MPI |
| 451 |
< |
n_global = mpiSim->getNAtomsGlobal(); |
| 452 |
< |
#else |
| 453 |
< |
n_global = n_atoms; |
| 454 |
< |
#endif |
| 455 |
< |
|
| 456 |
< |
isError = 0; |
| 457 |
< |
|
| 458 |
< |
getFortranGroupArrays(this, FglobalGroupMembership, mfact); |
| 459 |
< |
//it may not be a good idea to pass the address of first element in vector |
| 460 |
< |
//since c++ standard does not require vector to be stored continuously in meomory |
| 461 |
< |
//Most of the compilers will organize the memory of vector continuously |
| 462 |
< |
setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
| 463 |
< |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
| 464 |
< |
&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError); |
| 597 |
> |
} |
| 598 |
> |
} |
| 599 |
|
|
| 600 |
< |
if( isError ){ |
| 600 |
> |
//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!) |
| 601 |
> |
std::vector<int> identArray; |
| 602 |
> |
|
| 603 |
> |
//to avoid memory reallocation, reserve enough space identArray |
| 604 |
> |
identArray.reserve(getNAtoms()); |
| 605 |
|
|
| 606 |
< |
sprintf( painCave.errMsg, |
| 607 |
< |
"There was an error setting the simulation information in fortran.\n" ); |
| 608 |
< |
painCave.isFatal = 1; |
| 609 |
< |
painCave.severity = OOPSE_ERROR; |
| 610 |
< |
simError(); |
| 611 |
< |
} |
| 612 |
< |
|
| 606 |
> |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 607 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 608 |
> |
identArray.push_back(atom->getIdent()); |
| 609 |
> |
} |
| 610 |
> |
} |
| 611 |
> |
|
| 612 |
> |
//fill molMembershipArray |
| 613 |
> |
//molMembershipArray is filled by SimCreator |
| 614 |
> |
std::vector<int> molMembershipArray(nGlobalAtoms_); |
| 615 |
> |
for (int i = 0; i < nGlobalAtoms_; i++) { |
| 616 |
> |
molMembershipArray.push_back(globalMolMembership_[i] + 1); |
| 617 |
> |
} |
| 618 |
> |
|
| 619 |
> |
//setup fortran simulation |
| 620 |
> |
//gloalExcludes and molMembershipArray should go away (They are never used) |
| 621 |
> |
//why the hell fortran need to know molecule? |
| 622 |
> |
//OOPSE = Object-Obfuscated Parallel Simulation Engine |
| 623 |
> |
int nGlobalExcludes = 0; |
| 624 |
> |
int* globalExcludes = NULL; |
| 625 |
> |
int* excludeList = exclude_.getExcludeList(); |
| 626 |
> |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
| 627 |
> |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
| 628 |
> |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
| 629 |
> |
|
| 630 |
> |
if( isError ){ |
| 631 |
> |
|
| 632 |
> |
sprintf( painCave.errMsg, |
| 633 |
> |
"There was an error setting the simulation information in fortran.\n" ); |
| 634 |
> |
painCave.isFatal = 1; |
| 635 |
> |
painCave.severity = OOPSE_ERROR; |
| 636 |
> |
simError(); |
| 637 |
> |
} |
| 638 |
> |
|
| 639 |
|
#ifdef IS_MPI |
| 640 |
< |
sprintf( checkPointMsg, |
| 641 |
< |
"succesfully sent the simulation information to fortran.\n"); |
| 642 |
< |
MPIcheckPoint(); |
| 640 |
> |
sprintf( checkPointMsg, |
| 641 |
> |
"succesfully sent the simulation information to fortran.\n"); |
| 642 |
> |
MPIcheckPoint(); |
| 643 |
|
#endif // is_mpi |
| 480 |
– |
|
| 481 |
– |
this->ndf = this->getNDF(); |
| 482 |
– |
this->ndfRaw = this->getNDFraw(); |
| 483 |
– |
this->ndfTrans = this->getNDFtranslational(); |
| 644 |
|
} |
| 645 |
|
|
| 486 |
– |
void SimInfo::setDefaultRcut( double theRcut ){ |
| 487 |
– |
|
| 488 |
– |
haveRcut = 1; |
| 489 |
– |
rCut = theRcut; |
| 490 |
– |
rList = rCut + 1.0; |
| 491 |
– |
|
| 492 |
– |
notifyFortranCutOffs( &rCut, &rSw, &rList ); |
| 493 |
– |
} |
| 646 |
|
|
| 647 |
< |
void SimInfo::setDefaultRcut( double theRcut, double theRsw ){ |
| 647 |
> |
#ifdef IS_MPI |
| 648 |
> |
void SimInfo::setupFortranParallel() { |
| 649 |
> |
|
| 650 |
> |
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
| 651 |
> |
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
| 652 |
> |
std::vector<int> localToGlobalCutoffGroupIndex; |
| 653 |
> |
SimInfo::MoleculeIterator mi; |
| 654 |
> |
Molecule::AtomIterator ai; |
| 655 |
> |
Molecule::CutoffGroupIterator ci; |
| 656 |
> |
Molecule* mol; |
| 657 |
> |
Atom* atom; |
| 658 |
> |
CutoffGroup* cg; |
| 659 |
> |
mpiSimData parallelData; |
| 660 |
> |
int isError; |
| 661 |
|
|
| 662 |
< |
rSw = theRsw; |
| 498 |
< |
setDefaultRcut( theRcut ); |
| 499 |
< |
} |
| 662 |
> |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 663 |
|
|
| 664 |
+ |
//local index(index in DataStorge) of atom is important |
| 665 |
+ |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 666 |
+ |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
| 667 |
+ |
} |
| 668 |
|
|
| 669 |
< |
void SimInfo::checkCutOffs( void ){ |
| 670 |
< |
|
| 671 |
< |
if( boxIsInit ){ |
| 672 |
< |
|
| 673 |
< |
//we need to check cutOffs against the box |
| 674 |
< |
|
| 675 |
< |
if( rCut > maxCutoff ){ |
| 676 |
< |
sprintf( painCave.errMsg, |
| 677 |
< |
"cutoffRadius is too large for the current periodic box.\n" |
| 678 |
< |
"\tCurrent Value of cutoffRadius = %G at time %G\n " |
| 679 |
< |
"\tThis is larger than half of at least one of the\n" |
| 680 |
< |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
| 681 |
< |
"\n" |
| 682 |
< |
"\t[ %G %G %G ]\n" |
| 683 |
< |
"\t[ %G %G %G ]\n" |
| 684 |
< |
"\t[ %G %G %G ]\n", |
| 685 |
< |
rCut, currentTime, |
| 686 |
< |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
| 687 |
< |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
| 688 |
< |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
| 689 |
< |
painCave.severity = OOPSE_ERROR; |
| 690 |
< |
painCave.isFatal = 1; |
| 691 |
< |
simError(); |
| 692 |
< |
} |
| 693 |
< |
} else { |
| 694 |
< |
// initialize this stuff before using it, OK? |
| 695 |
< |
sprintf( painCave.errMsg, |
| 696 |
< |
"Trying to check cutoffs without a box.\n" |
| 697 |
< |
"\tOOPSE should have better programmers than that.\n" ); |
| 698 |
< |
painCave.severity = OOPSE_ERROR; |
| 699 |
< |
painCave.isFatal = 1; |
| 700 |
< |
simError(); |
| 701 |
< |
} |
| 535 |
< |
|
| 669 |
> |
//local index of cutoff group is trivial, it only depends on the order of travesing |
| 670 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
| 671 |
> |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
| 672 |
> |
} |
| 673 |
> |
|
| 674 |
> |
} |
| 675 |
> |
|
| 676 |
> |
//fill up mpiSimData struct |
| 677 |
> |
parallelData.nMolGlobal = getNGlobalMolecules(); |
| 678 |
> |
parallelData.nMolLocal = getNMolecules(); |
| 679 |
> |
parallelData.nAtomsGlobal = getNGlobalAtoms(); |
| 680 |
> |
parallelData.nAtomsLocal = getNAtoms(); |
| 681 |
> |
parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
| 682 |
> |
parallelData.nGroupsLocal = getNCutoffGroups(); |
| 683 |
> |
parallelData.myNode = worldRank; |
| 684 |
> |
MPI_Comm_size(MPI_COMM_WORLD, &(parallelData->nProcessors)); |
| 685 |
> |
|
| 686 |
> |
//pass mpiSimData struct and index arrays to fortran |
| 687 |
> |
setFsimParallel(parallelData, &(parallelData->nAtomsLocal), |
| 688 |
> |
&localToGlobalAtomIndex[0], &(parallelData->nGroupsLocal), |
| 689 |
> |
&localToGlobalCutoffGroupIndex[0], &isError); |
| 690 |
> |
|
| 691 |
> |
if (isError) { |
| 692 |
> |
sprintf(painCave.errMsg, |
| 693 |
> |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
| 694 |
> |
painCave.isFatal = 1; |
| 695 |
> |
simError(); |
| 696 |
> |
} |
| 697 |
> |
|
| 698 |
> |
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
| 699 |
> |
MPIcheckPoint(); |
| 700 |
> |
|
| 701 |
> |
|
| 702 |
|
} |
| 703 |
|
|
| 704 |
< |
void SimInfo::addProperty(GenericData* prop){ |
| 704 |
> |
#endif |
| 705 |
|
|
| 706 |
< |
map<string, GenericData*>::iterator result; |
| 707 |
< |
result = properties.find(prop->getID()); |
| 708 |
< |
|
| 709 |
< |
//we can't simply use properties[prop->getID()] = prop, |
| 710 |
< |
//it will cause memory leak if we already contain a propery which has the same name of prop |
| 711 |
< |
|
| 712 |
< |
if(result != properties.end()){ |
| 706 |
> |
double SimInfo::calcMaxCutoffRadius() { |
| 707 |
> |
|
| 708 |
> |
|
| 709 |
> |
std::set<AtomType*> atomTypes; |
| 710 |
> |
std::set<AtomType*>::iterator i; |
| 711 |
> |
std::vector<double> cutoffRadius; |
| 712 |
> |
|
| 713 |
> |
//get the unique atom types |
| 714 |
> |
atomTypes = getUniqueAtomTypes(); |
| 715 |
> |
|
| 716 |
> |
//query the max cutoff radius among these atom types |
| 717 |
> |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 718 |
> |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
| 719 |
> |
} |
| 720 |
> |
|
| 721 |
> |
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
| 722 |
> |
#ifdef IS_MPI |
| 723 |
> |
//pick the max cutoff radius among the processors |
| 724 |
> |
#endif |
| 725 |
> |
|
| 726 |
> |
return maxCutoffRadius; |
| 727 |
> |
} |
| 728 |
> |
|
| 729 |
> |
void SimInfo::setupCutoff() { |
| 730 |
> |
double rcut_; //cutoff radius |
| 731 |
> |
double rsw_; //switching radius |
| 732 |
|
|
| 733 |
< |
delete (*result).second; |
| 734 |
< |
(*result).second = prop; |
| 735 |
< |
|
| 736 |
< |
} |
| 737 |
< |
else{ |
| 733 |
> |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
| 734 |
> |
|
| 735 |
> |
if (!globals_->haveRcut()){ |
| 736 |
> |
sprintf(painCave.errMsg, |
| 737 |
> |
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
| 738 |
> |
"\tOOPSE will use a default value of 15.0 angstroms" |
| 739 |
> |
"\tfor the cutoffRadius.\n"); |
| 740 |
> |
painCave.isFatal = 0; |
| 741 |
> |
simError(); |
| 742 |
> |
rcut_ = 15.0; |
| 743 |
> |
} else{ |
| 744 |
> |
rcut_ = globals_->getRcut(); |
| 745 |
> |
} |
| 746 |
|
|
| 747 |
< |
properties[prop->getID()] = prop; |
| 747 |
> |
if (!globals_->haveRsw()){ |
| 748 |
> |
sprintf(painCave.errMsg, |
| 749 |
> |
"SimCreator Warning: No value was set for switchingRadius.\n" |
| 750 |
> |
"\tOOPSE will use a default value of\n" |
| 751 |
> |
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
| 752 |
> |
painCave.isFatal = 0; |
| 753 |
> |
simError(); |
| 754 |
> |
rsw_ = 0.95 * rcut_; |
| 755 |
> |
} else{ |
| 756 |
> |
rsw_ = globals_->getRsw(); |
| 757 |
> |
} |
| 758 |
|
|
| 759 |
< |
} |
| 759 |
> |
} else { |
| 760 |
> |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
| 761 |
> |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
| 762 |
> |
|
| 763 |
> |
if (globals_->haveRcut()) { |
| 764 |
> |
rcut_ = globals_->getRcut(); |
| 765 |
> |
} else { |
| 766 |
> |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
| 767 |
> |
rcut_ = calcMaxCutoffRadius(); |
| 768 |
> |
} |
| 769 |
> |
|
| 770 |
> |
if (globals_->haveRsw()) { |
| 771 |
> |
rsw_ = globals_->getRsw(); |
| 772 |
> |
} else { |
| 773 |
> |
rsw_ = rcut_; |
| 774 |
> |
} |
| 775 |
|
|
| 776 |
+ |
} |
| 777 |
+ |
|
| 778 |
+ |
double rnblist = rcut_ + 1; // skin of neighbor list |
| 779 |
+ |
|
| 780 |
+ |
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
| 781 |
+ |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist); |
| 782 |
|
} |
| 783 |
|
|
| 784 |
< |
GenericData* SimInfo::getProperty(const string& propName){ |
| 785 |
< |
|
| 562 |
< |
map<string, GenericData*>::iterator result; |
| 563 |
< |
|
| 564 |
< |
//string lowerCaseName = (); |
| 565 |
< |
|
| 566 |
< |
result = properties.find(propName); |
| 567 |
< |
|
| 568 |
< |
if(result != properties.end()) |
| 569 |
< |
return (*result).second; |
| 570 |
< |
else |
| 571 |
< |
return NULL; |
| 784 |
> |
void SimInfo::addProperty(GenericData* genData) { |
| 785 |
> |
properties_.addProperty(genData); |
| 786 |
|
} |
| 787 |
|
|
| 788 |
+ |
void SimInfo::removeProperty(const std::string& propName) { |
| 789 |
+ |
properties_.removeProperty(propName); |
| 790 |
+ |
} |
| 791 |
|
|
| 792 |
< |
void SimInfo::getFortranGroupArrays(SimInfo* info, |
| 793 |
< |
vector<int>& FglobalGroupMembership, |
| 794 |
< |
vector<double>& mfact){ |
| 578 |
< |
|
| 579 |
< |
Molecule* myMols; |
| 580 |
< |
Atom** myAtoms; |
| 581 |
< |
int numAtom; |
| 582 |
< |
double mtot; |
| 583 |
< |
int numMol; |
| 584 |
< |
int numCutoffGroups; |
| 585 |
< |
CutoffGroup* myCutoffGroup; |
| 586 |
< |
vector<CutoffGroup*>::iterator iterCutoff; |
| 587 |
< |
Atom* cutoffAtom; |
| 588 |
< |
vector<Atom*>::iterator iterAtom; |
| 589 |
< |
int atomIndex; |
| 590 |
< |
double totalMass; |
| 591 |
< |
|
| 592 |
< |
mfact.clear(); |
| 593 |
< |
FglobalGroupMembership.clear(); |
| 594 |
< |
|
| 792 |
> |
void SimInfo::clearProperties() { |
| 793 |
> |
properties_.clearProperties(); |
| 794 |
> |
} |
| 795 |
|
|
| 796 |
< |
// Fix the silly fortran indexing problem |
| 797 |
< |
#ifdef IS_MPI |
| 798 |
< |
numAtom = mpiSim->getNAtomsGlobal(); |
| 799 |
< |
#else |
| 800 |
< |
numAtom = n_atoms; |
| 801 |
< |
#endif |
| 802 |
< |
for (int i = 0; i < numAtom; i++) |
| 603 |
< |
FglobalGroupMembership.push_back(globalGroupMembership[i] + 1); |
| 604 |
< |
|
| 796 |
> |
std::vector<std::string> SimInfo::getPropertyNames() { |
| 797 |
> |
return properties_.getPropertyNames(); |
| 798 |
> |
} |
| 799 |
> |
|
| 800 |
> |
std::vector<GenericData*> SimInfo::getProperties() { |
| 801 |
> |
return properties_.getProperties(); |
| 802 |
> |
} |
| 803 |
|
|
| 804 |
< |
myMols = info->molecules; |
| 805 |
< |
numMol = info->n_mol; |
| 806 |
< |
for(int i = 0; i < numMol; i++){ |
| 609 |
< |
numCutoffGroups = myMols[i].getNCutoffGroups(); |
| 610 |
< |
for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); |
| 611 |
< |
myCutoffGroup != NULL; |
| 612 |
< |
myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
| 804 |
> |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
| 805 |
> |
return properties_.getPropertyByName(propName); |
| 806 |
> |
} |
| 807 |
|
|
| 808 |
< |
totalMass = myCutoffGroup->getMass(); |
| 809 |
< |
|
| 616 |
< |
for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); |
| 617 |
< |
cutoffAtom != NULL; |
| 618 |
< |
cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){ |
| 619 |
< |
mfact.push_back(cutoffAtom->getMass()/totalMass); |
| 620 |
< |
} |
| 621 |
< |
} |
| 622 |
< |
} |
| 808 |
> |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
| 809 |
> |
sman_ = sman; |
| 810 |
|
|
| 811 |
+ |
Molecule* mol; |
| 812 |
+ |
RigidBody* rb; |
| 813 |
+ |
Atom* atom; |
| 814 |
+ |
SimInfo::MoleculeIterator mi; |
| 815 |
+ |
Molecule::RigidBodyIterator rbIter; |
| 816 |
+ |
Molecule::AtomIterator atomIter;; |
| 817 |
+ |
|
| 818 |
+ |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
| 819 |
+ |
|
| 820 |
+ |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
| 821 |
+ |
atom->setSnapshotManager(sman_); |
| 822 |
+ |
} |
| 823 |
+ |
|
| 824 |
+ |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
| 825 |
+ |
rb->setSnapshotManager(sman_); |
| 826 |
+ |
} |
| 827 |
+ |
} |
| 828 |
+ |
|
| 829 |
|
} |
| 830 |
+ |
|
| 831 |
+ |
std::ostream& operator <<(ostream& o, SimInfo& info) { |
| 832 |
+ |
|
| 833 |
+ |
return o; |
| 834 |
+ |
} |
| 835 |
+ |
|
| 836 |
+ |
}//end namespace oopse |
