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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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useDirectionalAtoms = 0; |
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useLennardJones = 0; |
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useElectrostatics = 0; |
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useCharges = 0; |
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useDipoles = 0; |
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useSticky = 0; |
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useGayBerne = 0; |
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useEAM = 0; |
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useShapes = 0; |
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useFLARB = 0; |
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|
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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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> |
globalIndexToMol_.insert(make_pair(mol->getGlobalIndex(), mol)); |
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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]) { |
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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;; |
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> |
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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< |
} |
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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 |
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// 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++) |
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< |
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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> |
globalIndexToMol_.erase(mol->getGlobalIndex()); |
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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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> |
} |
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|
|
| 104 |
< |
|
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< |
void SimInfo::scaleBox(double scale) { |
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< |
double theBox[3][3]; |
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< |
int i, j; |
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< |
|
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< |
// cerr << "Scaling box by " << scale << "\n"; |
| 158 |
< |
|
| 159 |
< |
for(i=0; i<3; i++) |
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< |
for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
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< |
|
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< |
setBoxM(theBox); |
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< |
|
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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; |
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|
} |
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|
|
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– |
void SimInfo::calcHmatInv( void ) { |
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– |
|
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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]; |
| 109 |
|
|
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< |
invertMat3( Hmat, HmatInv ); |
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> |
void SimInfo::calcNdf() { |
| 111 |
> |
int ndf_local; |
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> |
std::vector<Molecule*>::iterator i; |
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> |
std::vector<StuntDouble*>::iterator j; |
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> |
Molecule* mol; |
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> |
StuntDouble* integrableObject; |
| 116 |
|
|
| 117 |
< |
// check to see if Hmat is orthorhombic |
| 177 |
< |
|
| 178 |
< |
oldOrtho = orthoRhombic; |
| 179 |
< |
|
| 180 |
< |
smallDiag = fabs(Hmat[0][0]); |
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< |
if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
| 182 |
< |
if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
| 183 |
< |
tol = smallDiag * orthoTolerance; |
| 184 |
< |
|
| 185 |
< |
orthoRhombic = 1; |
| 186 |
< |
|
| 187 |
< |
for (i = 0; i < 3; i++ ) { |
| 188 |
< |
for (j = 0 ; j < 3; j++) { |
| 189 |
< |
if (i != j) { |
| 190 |
< |
if (orthoRhombic) { |
| 191 |
< |
if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
| 192 |
< |
} |
| 193 |
< |
} |
| 194 |
< |
} |
| 195 |
< |
} |
| 196 |
< |
|
| 197 |
< |
if( oldOrtho != orthoRhombic ){ |
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> |
ndf_local = 0; |
| 118 |
|
|
| 119 |
< |
if( orthoRhombic ) { |
| 120 |
< |
sprintf( painCave.errMsg, |
| 121 |
< |
"OOPSE is switching from the default Non-Orthorhombic\n" |
| 202 |
< |
"\tto the faster Orthorhombic periodic boundary computations.\n" |
| 203 |
< |
"\tThis is usually a good thing, but if you wan't the\n" |
| 204 |
< |
"\tNon-Orthorhombic computations, make the orthoBoxTolerance\n" |
| 205 |
< |
"\tvariable ( currently set to %G ) smaller.\n", |
| 206 |
< |
orthoTolerance); |
| 207 |
< |
painCave.severity = OOPSE_INFO; |
| 208 |
< |
simError(); |
| 209 |
< |
} |
| 210 |
< |
else { |
| 211 |
< |
sprintf( painCave.errMsg, |
| 212 |
< |
"OOPSE is switching from the faster Orthorhombic to the more\n" |
| 213 |
< |
"\tflexible Non-Orthorhombic periodic boundary computations.\n" |
| 214 |
< |
"\tThis is usually because the box has deformed under\n" |
| 215 |
< |
"\tNPTf integration. If you wan't to live on the edge with\n" |
| 216 |
< |
"\tthe Orthorhombic computations, make the orthoBoxTolerance\n" |
| 217 |
< |
"\tvariable ( currently set to %G ) larger.\n", |
| 218 |
< |
orthoTolerance); |
| 219 |
< |
painCave.severity = OOPSE_WARNING; |
| 220 |
< |
simError(); |
| 221 |
< |
} |
| 222 |
< |
} |
| 223 |
< |
} |
| 119 |
> |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
| 120 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 121 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 122 |
|
|
| 123 |
< |
void SimInfo::calcBoxL( void ){ |
| 123 |
> |
ndf_local += 3; |
| 124 |
|
|
| 125 |
< |
double dx, dy, dz, dsq; |
| 126 |
< |
|
| 127 |
< |
// boxVol = Determinant of Hmat |
| 128 |
< |
|
| 129 |
< |
boxVol = matDet3( Hmat ); |
| 130 |
< |
|
| 131 |
< |
// boxLx |
| 132 |
< |
|
| 133 |
< |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
| 134 |
< |
dsq = dx*dx + dy*dy + dz*dz; |
| 237 |
< |
boxL[0] = sqrt( dsq ); |
| 238 |
< |
//maxCutoff = 0.5 * boxL[0]; |
| 239 |
< |
|
| 240 |
< |
// boxLy |
| 241 |
< |
|
| 242 |
< |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
| 243 |
< |
dsq = dx*dx + dy*dy + dz*dz; |
| 244 |
< |
boxL[1] = sqrt( dsq ); |
| 245 |
< |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
| 246 |
< |
|
| 247 |
< |
|
| 248 |
< |
// boxLz |
| 249 |
< |
|
| 250 |
< |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
| 251 |
< |
dsq = dx*dx + dy*dy + dz*dz; |
| 252 |
< |
boxL[2] = sqrt( dsq ); |
| 253 |
< |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
| 254 |
< |
|
| 255 |
< |
//calculate the max cutoff |
| 256 |
< |
maxCutoff = calcMaxCutOff(); |
| 257 |
< |
|
| 258 |
< |
checkCutOffs(); |
| 259 |
< |
|
| 260 |
< |
} |
| 261 |
< |
|
| 262 |
< |
|
| 263 |
< |
double SimInfo::calcMaxCutOff(){ |
| 264 |
< |
|
| 265 |
< |
double ri[3], rj[3], rk[3]; |
| 266 |
< |
double rij[3], rjk[3], rki[3]; |
| 267 |
< |
double minDist; |
| 268 |
< |
|
| 269 |
< |
ri[0] = Hmat[0][0]; |
| 270 |
< |
ri[1] = Hmat[1][0]; |
| 271 |
< |
ri[2] = Hmat[2][0]; |
| 272 |
< |
|
| 273 |
< |
rj[0] = Hmat[0][1]; |
| 274 |
< |
rj[1] = Hmat[1][1]; |
| 275 |
< |
rj[2] = Hmat[2][1]; |
| 276 |
< |
|
| 277 |
< |
rk[0] = Hmat[0][2]; |
| 278 |
< |
rk[1] = Hmat[1][2]; |
| 279 |
< |
rk[2] = Hmat[2][2]; |
| 125 |
> |
if (integrableObject->isDirectional()) { |
| 126 |
> |
if (integrableObject->isLinear()) { |
| 127 |
> |
ndf_local += 2; |
| 128 |
> |
} else { |
| 129 |
> |
ndf_local += 3; |
| 130 |
> |
} |
| 131 |
> |
} |
| 132 |
> |
|
| 133 |
> |
}//end for (integrableObject) |
| 134 |
> |
}// end for (mol) |
| 135 |
|
|
| 136 |
< |
crossProduct3(ri, rj, rij); |
| 137 |
< |
distXY = dotProduct3(rk,rij) / norm3(rij); |
| 136 |
> |
// n_constraints is local, so subtract them on each processor |
| 137 |
> |
ndf_local -= nConstraints_; |
| 138 |
|
|
| 139 |
< |
crossProduct3(rj,rk, rjk); |
| 140 |
< |
distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
| 139 |
> |
#ifdef IS_MPI |
| 140 |
> |
MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 141 |
> |
#else |
| 142 |
> |
ndf_ = ndf_local; |
| 143 |
> |
#endif |
| 144 |
|
|
| 145 |
< |
crossProduct3(rk,ri, rki); |
| 146 |
< |
distZX = dotProduct3(rj,rki) / norm3(rki); |
| 145 |
> |
// nZconstraints is global, as are the 3 COM translations for the |
| 146 |
> |
// entire system: |
| 147 |
> |
ndf_ = ndf_ - 3 - nZconstraints; |
| 148 |
|
|
| 290 |
– |
minDist = min(min(distXY, distYZ), distZX); |
| 291 |
– |
return minDist/2; |
| 292 |
– |
|
| 149 |
|
} |
| 150 |
|
|
| 151 |
< |
void SimInfo::wrapVector( double thePos[3] ){ |
| 151 |
> |
void SimInfo::calcNdfRaw() { |
| 152 |
> |
int ndfRaw_local; |
| 153 |
|
|
| 154 |
< |
int i; |
| 155 |
< |
double scaled[3]; |
| 154 |
> |
std::vector<Molecule*>::iterator i; |
| 155 |
> |
std::vector<StuntDouble*>::iterator j; |
| 156 |
> |
Molecule* mol; |
| 157 |
> |
StuntDouble* integrableObject; |
| 158 |
|
|
| 159 |
< |
if( !orthoRhombic ){ |
| 160 |
< |
// calc the scaled coordinates. |
| 302 |
< |
|
| 303 |
< |
|
| 304 |
< |
matVecMul3(HmatInv, thePos, scaled); |
| 159 |
> |
// Raw degrees of freedom that we have to set |
| 160 |
> |
ndfRaw_local = 0; |
| 161 |
|
|
| 162 |
< |
for(i=0; i<3; i++) |
| 163 |
< |
scaled[i] -= roundMe(scaled[i]); |
| 164 |
< |
|
| 309 |
< |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
| 310 |
< |
|
| 311 |
< |
matVecMul3(Hmat, scaled, thePos); |
| 162 |
> |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
| 163 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
| 164 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
| 165 |
|
|
| 166 |
< |
} |
| 314 |
< |
else{ |
| 315 |
< |
// calc the scaled coordinates. |
| 316 |
< |
|
| 317 |
< |
for(i=0; i<3; i++) |
| 318 |
< |
scaled[i] = thePos[i]*HmatInv[i][i]; |
| 319 |
< |
|
| 320 |
< |
// wrap the scaled coordinates |
| 321 |
< |
|
| 322 |
< |
for(i=0; i<3; i++) |
| 323 |
< |
scaled[i] -= roundMe(scaled[i]); |
| 324 |
< |
|
| 325 |
< |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
| 326 |
< |
|
| 327 |
< |
for(i=0; i<3; i++) |
| 328 |
< |
thePos[i] = scaled[i]*Hmat[i][i]; |
| 329 |
< |
} |
| 330 |
< |
|
| 331 |
< |
} |
| 166 |
> |
ndfRaw_local += 3; |
| 167 |
|
|
| 168 |
< |
|
| 169 |
< |
int SimInfo::getNDF(){ |
| 170 |
< |
int ndf_local; |
| 171 |
< |
|
| 172 |
< |
ndf_local = 0; |
| 173 |
< |
|
| 174 |
< |
for(int i = 0; i < integrableObjects.size(); i++){ |
| 175 |
< |
ndf_local += 3; |
| 176 |
< |
if (integrableObjects[i]->isDirectional()) { |
| 342 |
< |
if (integrableObjects[i]->isLinear()) |
| 343 |
< |
ndf_local += 2; |
| 344 |
< |
else |
| 345 |
< |
ndf_local += 3; |
| 168 |
> |
if (integrableObject->isDirectional()) { |
| 169 |
> |
if (integrableObject->isLinear()) { |
| 170 |
> |
ndfRaw_local += 2; |
| 171 |
> |
} else { |
| 172 |
> |
ndfRaw_local += 3; |
| 173 |
> |
} |
| 174 |
> |
} |
| 175 |
> |
|
| 176 |
> |
} |
| 177 |
|
} |
| 347 |
– |
} |
| 348 |
– |
|
| 349 |
– |
// n_constraints is local, so subtract them on each processor: |
| 350 |
– |
|
| 351 |
– |
ndf_local -= n_constraints; |
| 352 |
– |
|
| 353 |
– |
#ifdef IS_MPI |
| 354 |
– |
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 355 |
– |
#else |
| 356 |
– |
ndf = ndf_local; |
| 357 |
– |
#endif |
| 358 |
– |
|
| 359 |
– |
// nZconstraints is global, as are the 3 COM translations for the |
| 360 |
– |
// entire system: |
| 361 |
– |
|
| 362 |
– |
ndf = ndf - 3 - nZconstraints; |
| 363 |
– |
|
| 364 |
– |
return ndf; |
| 365 |
– |
} |
| 366 |
– |
|
| 367 |
– |
int SimInfo::getNDFraw() { |
| 368 |
– |
int ndfRaw_local; |
| 369 |
– |
|
| 370 |
– |
// Raw degrees of freedom that we have to set |
| 371 |
– |
ndfRaw_local = 0; |
| 372 |
– |
|
| 373 |
– |
for(int i = 0; i < integrableObjects.size(); i++){ |
| 374 |
– |
ndfRaw_local += 3; |
| 375 |
– |
if (integrableObjects[i]->isDirectional()) { |
| 376 |
– |
if (integrableObjects[i]->isLinear()) |
| 377 |
– |
ndfRaw_local += 2; |
| 378 |
– |
else |
| 379 |
– |
ndfRaw_local += 3; |
| 380 |
– |
} |
| 381 |
– |
} |
| 178 |
|
|
| 179 |
|
#ifdef IS_MPI |
| 180 |
< |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 180 |
> |
MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 181 |
|
#else |
| 182 |
< |
ndfRaw = ndfRaw_local; |
| 182 |
> |
ndfRaw_ = ndfRaw_local; |
| 183 |
|
#endif |
| 388 |
– |
|
| 389 |
– |
return ndfRaw; |
| 184 |
|
} |
| 185 |
|
|
| 186 |
< |
int SimInfo::getNDFtranslational() { |
| 187 |
< |
int ndfTrans_local; |
| 186 |
> |
void SimInfo::calcNdfTrans() { |
| 187 |
> |
int ndfTrans_local; |
| 188 |
|
|
| 189 |
< |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
| 189 |
> |
ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_; |
| 190 |
|
|
| 191 |
|
|
| 192 |
|
#ifdef IS_MPI |
| 193 |
< |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 193 |
> |
MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 194 |
|
#else |
| 195 |
< |
ndfTrans = ndfTrans_local; |
| 195 |
> |
ndfTrans_ = ndfTrans_local; |
| 196 |
|
#endif |
| 197 |
|
|
| 198 |
< |
ndfTrans = ndfTrans - 3 - nZconstraints; |
| 199 |
< |
|
| 406 |
< |
return ndfTrans; |
| 198 |
> |
ndfTrans_ = ndfTrans_ - 3 - nZconstraints; |
| 199 |
> |
|
| 200 |
|
} |
| 201 |
|
|
| 202 |
< |
int SimInfo::getTotIntegrableObjects() { |
| 203 |
< |
int nObjs_local; |
| 204 |
< |
int nObjs; |
| 202 |
> |
void SimInfo::addExcludePairs(Molecule* mol) { |
| 203 |
> |
std::vector<Bond*>::iterator bondIter; |
| 204 |
> |
std::vector<Bend*>::iterator bendIter; |
| 205 |
> |
std::vector<Torsion*>::iterator torsionIter; |
| 206 |
> |
Bond* bond; |
| 207 |
> |
Bend* bend; |
| 208 |
> |
Torsion* torsion; |
| 209 |
> |
int a; |
| 210 |
> |
int b; |
| 211 |
> |
int c; |
| 212 |
> |
int d; |
| 213 |
> |
|
| 214 |
> |
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
| 215 |
> |
a = bond->getAtomA()->getGlobalIndex(); |
| 216 |
> |
b = bond->getAtomB()->getGlobalIndex(); |
| 217 |
> |
exclude_.addPair(a, b); |
| 218 |
> |
} |
| 219 |
|
|
| 220 |
< |
nObjs_local = integrableObjects.size(); |
| 220 |
> |
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
| 221 |
> |
a = bend->getAtomA()->getGlobalIndex(); |
| 222 |
> |
b = bend->getAtomB()->getGlobalIndex(); |
| 223 |
> |
c = bend->getAtomC()->getGlobalIndex(); |
| 224 |
|
|
| 225 |
+ |
exclude_.addPair(a, b); |
| 226 |
+ |
exclude_.addPair(a, c); |
| 227 |
+ |
exclude_.addPair(b, c); |
| 228 |
+ |
} |
| 229 |
|
|
| 230 |
< |
#ifdef IS_MPI |
| 231 |
< |
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 232 |
< |
#else |
| 233 |
< |
nObjs = nObjs_local; |
| 234 |
< |
#endif |
| 230 |
> |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) { |
| 231 |
> |
a = torsion->getAtomA()->getGlobalIndex(); |
| 232 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
| 233 |
> |
c = torsion->getAtomC()->getGlobalIndex(); |
| 234 |
> |
d = torsion->getAtomD()->getGlobalIndex(); |
| 235 |
|
|
| 236 |
+ |
exclude_.addPair(a, b); |
| 237 |
+ |
exclude_.addPair(a, c); |
| 238 |
+ |
exclude_.addPair(a, d); |
| 239 |
+ |
exclude_.addPair(b, c); |
| 240 |
+ |
exclude_.addPair(b, d); |
| 241 |
+ |
exclude_.addPair(c, d); |
| 242 |
+ |
} |
| 243 |
|
|
| 244 |
< |
return nObjs; |
| 244 |
> |
|
| 245 |
|
} |
| 246 |
|
|
| 247 |
< |
void SimInfo::refreshSim(){ |
| 248 |
< |
|
| 249 |
< |
simtype fInfo; |
| 250 |
< |
int isError; |
| 251 |
< |
int n_global; |
| 252 |
< |
int* excl; |
| 253 |
< |
|
| 254 |
< |
fInfo.dielect = 0.0; |
| 255 |
< |
|
| 256 |
< |
if( useDipoles ){ |
| 257 |
< |
if( useReactionField )fInfo.dielect = dielectric; |
| 437 |
< |
} |
| 438 |
< |
|
| 439 |
< |
fInfo.SIM_uses_PBC = usePBC; |
| 440 |
< |
|
| 441 |
< |
if (useSticky || useDipoles || useGayBerne || useShapes) { |
| 442 |
< |
useDirectionalAtoms = 1; |
| 443 |
< |
fInfo.SIM_uses_DirectionalAtoms = useDirectionalAtoms; |
| 444 |
< |
} |
| 445 |
< |
|
| 446 |
< |
fInfo.SIM_uses_LennardJones = useLennardJones; |
| 447 |
< |
|
| 448 |
< |
if (useCharges || useDipoles) { |
| 449 |
< |
useElectrostatics = 1; |
| 450 |
< |
fInfo.SIM_uses_Electrostatics = useElectrostatics; |
| 451 |
< |
} |
| 452 |
< |
|
| 453 |
< |
fInfo.SIM_uses_Charges = useCharges; |
| 454 |
< |
fInfo.SIM_uses_Dipoles = useDipoles; |
| 455 |
< |
fInfo.SIM_uses_Sticky = useSticky; |
| 456 |
< |
fInfo.SIM_uses_GayBerne = useGayBerne; |
| 457 |
< |
fInfo.SIM_uses_EAM = useEAM; |
| 458 |
< |
fInfo.SIM_uses_Shapes = useShapes; |
| 459 |
< |
fInfo.SIM_uses_FLARB = useFLARB; |
| 460 |
< |
fInfo.SIM_uses_RF = useReactionField; |
| 461 |
< |
|
| 462 |
< |
n_exclude = excludes->getSize(); |
| 463 |
< |
excl = excludes->getFortranArray(); |
| 464 |
< |
|
| 465 |
< |
#ifdef IS_MPI |
| 466 |
< |
n_global = mpiSim->getNAtomsGlobal(); |
| 467 |
< |
#else |
| 468 |
< |
n_global = n_atoms; |
| 469 |
< |
#endif |
| 470 |
< |
|
| 471 |
< |
isError = 0; |
| 472 |
< |
|
| 473 |
< |
getFortranGroupArrays(this, FglobalGroupMembership, mfact); |
| 474 |
< |
//it may not be a good idea to pass the address of first element in vector |
| 475 |
< |
//since c++ standard does not require vector to be stored continuously in meomory |
| 476 |
< |
//Most of the compilers will organize the memory of vector continuously |
| 477 |
< |
setFortranSim( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl, |
| 478 |
< |
&nGlobalExcludes, globalExcludes, molMembershipArray, |
| 479 |
< |
&mfact[0], &ngroup, &FglobalGroupMembership[0], &isError); |
| 480 |
< |
|
| 481 |
< |
if( isError ){ |
| 247 |
> |
void SimInfo::removeExcludePairs(Molecule* mol) { |
| 248 |
> |
std::vector<Bond*>::iterator bondIter; |
| 249 |
> |
std::vector<Bend*>::iterator bendIter; |
| 250 |
> |
std::vector<Torsion*>::iterator torsionIter; |
| 251 |
> |
Bond* bond; |
| 252 |
> |
Bend* bend; |
| 253 |
> |
Torsion* torsion; |
| 254 |
> |
int a; |
| 255 |
> |
int b; |
| 256 |
> |
int c; |
| 257 |
> |
int d; |
| 258 |
|
|
| 259 |
< |
sprintf( painCave.errMsg, |
| 260 |
< |
"There was an error setting the simulation information in fortran.\n" ); |
| 261 |
< |
painCave.isFatal = 1; |
| 262 |
< |
painCave.severity = OOPSE_ERROR; |
| 263 |
< |
simError(); |
| 488 |
< |
} |
| 489 |
< |
|
| 490 |
< |
#ifdef IS_MPI |
| 491 |
< |
sprintf( checkPointMsg, |
| 492 |
< |
"succesfully sent the simulation information to fortran.\n"); |
| 493 |
< |
MPIcheckPoint(); |
| 494 |
< |
#endif // is_mpi |
| 495 |
< |
|
| 496 |
< |
this->ndf = this->getNDF(); |
| 497 |
< |
this->ndfRaw = this->getNDFraw(); |
| 498 |
< |
this->ndfTrans = this->getNDFtranslational(); |
| 499 |
< |
} |
| 259 |
> |
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
| 260 |
> |
a = bond->getAtomA()->getGlobalIndex(); |
| 261 |
> |
b = bond->getAtomB()->getGlobalIndex(); |
| 262 |
> |
exclude_.removePair(a, b); |
| 263 |
> |
} |
| 264 |
|
|
| 265 |
< |
void SimInfo::setDefaultRcut( double theRcut ){ |
| 266 |
< |
|
| 267 |
< |
haveRcut = 1; |
| 268 |
< |
rCut = theRcut; |
| 505 |
< |
rList = rCut + 1.0; |
| 506 |
< |
|
| 507 |
< |
notifyFortranCutoffs( &rCut, &rSw, &rList ); |
| 508 |
< |
} |
| 265 |
> |
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
| 266 |
> |
a = bend->getAtomA()->getGlobalIndex(); |
| 267 |
> |
b = bend->getAtomB()->getGlobalIndex(); |
| 268 |
> |
c = bend->getAtomC()->getGlobalIndex(); |
| 269 |
|
|
| 270 |
< |
void SimInfo::setDefaultRcut( double theRcut, double theRsw ){ |
| 270 |
> |
exclude_.removePair(a, b); |
| 271 |
> |
exclude_.removePair(a, c); |
| 272 |
> |
exclude_.removePair(b, c); |
| 273 |
> |
} |
| 274 |
|
|
| 275 |
< |
rSw = theRsw; |
| 276 |
< |
setDefaultRcut( theRcut ); |
| 277 |
< |
} |
| 275 |
> |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) { |
| 276 |
> |
a = torsion->getAtomA()->getGlobalIndex(); |
| 277 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
| 278 |
> |
c = torsion->getAtomC()->getGlobalIndex(); |
| 279 |
> |
d = torsion->getAtomD()->getGlobalIndex(); |
| 280 |
|
|
| 281 |
+ |
exclude_.removePair(a, b); |
| 282 |
+ |
exclude_.removePair(a, c); |
| 283 |
+ |
exclude_.removePair(a, d); |
| 284 |
+ |
exclude_.removePair(b, c); |
| 285 |
+ |
exclude_.removePair(b, d); |
| 286 |
+ |
exclude_.removePair(c, d); |
| 287 |
+ |
} |
| 288 |
|
|
| 517 |
– |
void SimInfo::checkCutOffs( void ){ |
| 518 |
– |
|
| 519 |
– |
if( boxIsInit ){ |
| 520 |
– |
|
| 521 |
– |
//we need to check cutOffs against the box |
| 522 |
– |
|
| 523 |
– |
if( rCut > maxCutoff ){ |
| 524 |
– |
sprintf( painCave.errMsg, |
| 525 |
– |
"cutoffRadius is too large for the current periodic box.\n" |
| 526 |
– |
"\tCurrent Value of cutoffRadius = %G at time %G\n " |
| 527 |
– |
"\tThis is larger than half of at least one of the\n" |
| 528 |
– |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
| 529 |
– |
"\n" |
| 530 |
– |
"\t[ %G %G %G ]\n" |
| 531 |
– |
"\t[ %G %G %G ]\n" |
| 532 |
– |
"\t[ %G %G %G ]\n", |
| 533 |
– |
rCut, currentTime, |
| 534 |
– |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
| 535 |
– |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
| 536 |
– |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
| 537 |
– |
painCave.severity = OOPSE_ERROR; |
| 538 |
– |
painCave.isFatal = 1; |
| 539 |
– |
simError(); |
| 540 |
– |
} |
| 541 |
– |
} else { |
| 542 |
– |
// initialize this stuff before using it, OK? |
| 543 |
– |
sprintf( painCave.errMsg, |
| 544 |
– |
"Trying to check cutoffs without a box.\n" |
| 545 |
– |
"\tOOPSE should have better programmers than that.\n" ); |
| 546 |
– |
painCave.severity = OOPSE_ERROR; |
| 547 |
– |
painCave.isFatal = 1; |
| 548 |
– |
simError(); |
| 549 |
– |
} |
| 550 |
– |
|
| 289 |
|
} |
| 290 |
|
|
| 553 |
– |
void SimInfo::addProperty(GenericData* prop){ |
| 291 |
|
|
| 292 |
< |
map<string, GenericData*>::iterator result; |
| 293 |
< |
result = properties.find(prop->getID()); |
| 557 |
< |
|
| 558 |
< |
//we can't simply use properties[prop->getID()] = prop, |
| 559 |
< |
//it will cause memory leak if we already contain a propery which has the same name of prop |
| 560 |
< |
|
| 561 |
< |
if(result != properties.end()){ |
| 562 |
< |
|
| 563 |
< |
delete (*result).second; |
| 564 |
< |
(*result).second = prop; |
| 565 |
< |
|
| 566 |
< |
} |
| 567 |
< |
else{ |
| 292 |
> |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
| 293 |
> |
int curStampId; |
| 294 |
|
|
| 295 |
< |
properties[prop->getID()] = prop; |
| 295 |
> |
//index from 0 |
| 296 |
> |
curStampId = molStampIds_.size(); |
| 297 |
|
|
| 298 |
< |
} |
| 299 |
< |
|
| 298 |
> |
moleculeStamps_.push_back(molStamp); |
| 299 |
> |
molStampIds_.insert(molStampIds_.end(), nmol, curStampId) |
| 300 |
|
} |
| 301 |
|
|
| 302 |
< |
GenericData* SimInfo::getPropertyByName(const string& propName){ |
| 576 |
< |
|
| 577 |
< |
map<string, GenericData*>::iterator result; |
| 578 |
< |
|
| 579 |
< |
//string lowerCaseName = (); |
| 580 |
< |
|
| 581 |
< |
result = properties.find(propName); |
| 582 |
< |
|
| 583 |
< |
if(result != properties.end()) |
| 584 |
< |
return (*result).second; |
| 585 |
< |
else |
| 586 |
< |
return NULL; |
| 587 |
< |
} |
| 302 |
> |
std::ostream& operator <<(ostream& o, SimInfo& info) { |
| 303 |
|
|
| 304 |
< |
|
| 590 |
< |
void SimInfo::getFortranGroupArrays(SimInfo* info, |
| 591 |
< |
vector<int>& FglobalGroupMembership, |
| 592 |
< |
vector<double>& mfact){ |
| 593 |
< |
|
| 594 |
< |
Molecule* myMols; |
| 595 |
< |
Atom** myAtoms; |
| 596 |
< |
int numAtom; |
| 597 |
< |
double mtot; |
| 598 |
< |
int numMol; |
| 599 |
< |
int numCutoffGroups; |
| 600 |
< |
CutoffGroup* myCutoffGroup; |
| 601 |
< |
vector<CutoffGroup*>::iterator iterCutoff; |
| 602 |
< |
Atom* cutoffAtom; |
| 603 |
< |
vector<Atom*>::iterator iterAtom; |
| 604 |
< |
int atomIndex; |
| 605 |
< |
double totalMass; |
| 606 |
< |
|
| 607 |
< |
mfact.clear(); |
| 608 |
< |
FglobalGroupMembership.clear(); |
| 609 |
< |
|
| 610 |
< |
|
| 611 |
< |
// Fix the silly fortran indexing problem |
| 612 |
< |
#ifdef IS_MPI |
| 613 |
< |
numAtom = mpiSim->getNAtomsGlobal(); |
| 614 |
< |
#else |
| 615 |
< |
numAtom = n_atoms; |
| 616 |
< |
#endif |
| 617 |
< |
for (int i = 0; i < numAtom; i++) |
| 618 |
< |
FglobalGroupMembership.push_back(globalGroupMembership[i] + 1); |
| 619 |
< |
|
| 620 |
< |
|
| 621 |
< |
myMols = info->molecules; |
| 622 |
< |
numMol = info->n_mol; |
| 623 |
< |
for(int i = 0; i < numMol; i++){ |
| 624 |
< |
numCutoffGroups = myMols[i].getNCutoffGroups(); |
| 625 |
< |
for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); |
| 626 |
< |
myCutoffGroup != NULL; |
| 627 |
< |
myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){ |
| 628 |
< |
|
| 629 |
< |
totalMass = myCutoffGroup->getMass(); |
| 630 |
< |
|
| 631 |
< |
for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); |
| 632 |
< |
cutoffAtom != NULL; |
| 633 |
< |
cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){ |
| 634 |
< |
mfact.push_back(cutoffAtom->getMass()/totalMass); |
| 635 |
< |
} |
| 636 |
< |
} |
| 637 |
< |
} |
| 638 |
< |
|
| 304 |
> |
return o; |
| 305 |
|
} |
| 306 |
+ |
|
| 307 |
+ |
}//end namespace oopse |
