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#include <stdlib.h> |
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#include <string.h> |
3 |
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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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|
|
45 |
< |
inline double roundMe( double x ){ |
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return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
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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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} |
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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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|
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SimInfo::SimInfo(){ |
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bool SimInfo::addMolecule(Molecule* mol) { |
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MoleculeIterator 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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|
|
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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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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(); |
67 |
|
|
68 |
< |
haveRcut = 0; |
69 |
< |
haveRsw = 0; |
70 |
< |
boxIsInit = 0; |
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|
72 |
< |
resetTime = 1e99; |
68 |
> |
return true; |
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} else { |
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> |
return false; |
71 |
> |
} |
72 |
> |
} |
73 |
|
|
74 |
< |
orthoRhombic = 0; |
75 |
< |
orthoTolerance = 1E-6; |
76 |
< |
useInitXSstate = true; |
74 |
> |
bool SimInfo::removeMolecule(Molecule* mol) { |
75 |
> |
MoleculeIterator i; |
76 |
> |
i = std::find(molecules_.begin(), molecules_.end(), mol); |
77 |
|
|
78 |
< |
usePBC = 0; |
60 |
< |
useDirectionalAtoms = 0; |
61 |
< |
useLennardJones = 0; |
62 |
< |
useElectrostatics = 0; |
63 |
< |
useCharges = 0; |
64 |
< |
useDipoles = 0; |
65 |
< |
useSticky = 0; |
66 |
< |
useGayBerne = 0; |
67 |
< |
useEAM = 0; |
68 |
< |
useShapes = 0; |
69 |
< |
useFLARB = 0; |
78 |
> |
if (i != molecules_.end() ) { |
79 |
|
|
80 |
< |
useSolidThermInt = 0; |
81 |
< |
useLiquidThermInt = 0; |
80 |
> |
nAtoms_ -= mol->getNAtoms(); |
81 |
> |
nBonds_ -= mol->getNBonds(); |
82 |
> |
nBends_ -= mol->getNBends(); |
83 |
> |
nTorsions_ -= mol->getNTorsions(); |
84 |
> |
nRigidBodies_ -= mol->getNRigidBodies(); |
85 |
> |
nIntegrableObjects_ -= mol->getNIntegrableObjects(); |
86 |
> |
nCutoffGroups_ -= mol->getNCutoffGroups(); |
87 |
> |
nConstraints_ -= mol->getNConstraints(); |
88 |
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|
89 |
< |
haveCutoffGroups = false; |
89 |
> |
molecules_.erase(mol->getGlobalIndex()); |
90 |
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|
91 |
< |
excludes = Exclude::Instance(); |
91 |
> |
delete mol; |
92 |
> |
|
93 |
> |
return true; |
94 |
> |
} else { |
95 |
> |
return false; |
96 |
> |
} |
97 |
|
|
78 |
– |
myConfiguration = new SimState(); |
98 |
|
|
99 |
< |
has_minimizer = false; |
81 |
< |
the_minimizer =NULL; |
99 |
> |
} |
100 |
|
|
101 |
< |
ngroup = 0; |
101 |
> |
|
102 |
> |
Molecule* SimInfo::beginMolecule(MoleculeIterator& i) { |
103 |
> |
i = molecules_.begin(); |
104 |
> |
return i == molecules_.end() ? NULL : *i; |
105 |
> |
} |
106 |
|
|
107 |
+ |
Molecule* SimInfo::nextMolecule(MoleculeIterator& i) { |
108 |
+ |
++i; |
109 |
+ |
return i == molecules_.end() ? NULL : *i; |
110 |
|
} |
111 |
|
|
112 |
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|
113 |
< |
SimInfo::~SimInfo(){ |
113 |
> |
void SimInfo::calcNdf() { |
114 |
> |
int ndf_local; |
115 |
> |
MoleculeIterator i; |
116 |
> |
std::vector<StuntDouble*>::iterator j; |
117 |
> |
Molecule* mol; |
118 |
> |
StuntDouble* integrableObject; |
119 |
|
|
120 |
< |
delete myConfiguration; |
120 |
> |
ndf_local = 0; |
121 |
> |
|
122 |
> |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
123 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
124 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
125 |
|
|
126 |
< |
map<string, GenericData*>::iterator i; |
93 |
< |
|
94 |
< |
for(i = properties.begin(); i != properties.end(); i++) |
95 |
< |
delete (*i).second; |
126 |
> |
ndf_local += 3; |
127 |
|
|
128 |
< |
} |
128 |
> |
if (integrableObject->isDirectional()) { |
129 |
> |
if (integrableObject->isLinear()) { |
130 |
> |
ndf_local += 2; |
131 |
> |
} else { |
132 |
> |
ndf_local += 3; |
133 |
> |
} |
134 |
> |
} |
135 |
> |
|
136 |
> |
}//end for (integrableObject) |
137 |
> |
}// end for (mol) |
138 |
> |
|
139 |
> |
// n_constraints is local, so subtract them on each processor |
140 |
> |
ndf_local -= nConstraints_; |
141 |
|
|
142 |
< |
void SimInfo::setBox(double newBox[3]) { |
143 |
< |
|
144 |
< |
int i, j; |
145 |
< |
double tempMat[3][3]; |
142 |
> |
#ifdef IS_MPI |
143 |
> |
MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
144 |
> |
#else |
145 |
> |
ndf_ = ndf_local; |
146 |
> |
#endif |
147 |
|
|
148 |
< |
for(i=0; i<3; i++) |
149 |
< |
for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
148 |
> |
// nZconstraints is global, as are the 3 COM translations for the |
149 |
> |
// entire system: |
150 |
> |
ndf_ = ndf_ - 3 - nZconstraints; |
151 |
|
|
107 |
– |
tempMat[0][0] = newBox[0]; |
108 |
– |
tempMat[1][1] = newBox[1]; |
109 |
– |
tempMat[2][2] = newBox[2]; |
110 |
– |
|
111 |
– |
setBoxM( tempMat ); |
112 |
– |
|
152 |
|
} |
153 |
|
|
154 |
< |
void SimInfo::setBoxM( double theBox[3][3] ){ |
155 |
< |
|
117 |
< |
int i, j; |
118 |
< |
double FortranHmat[9]; // to preserve compatibility with Fortran the |
119 |
< |
// ordering in the array is as follows: |
120 |
< |
// [ 0 3 6 ] |
121 |
< |
// [ 1 4 7 ] |
122 |
< |
// [ 2 5 8 ] |
123 |
< |
double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
154 |
> |
void SimInfo::calcNdfRaw() { |
155 |
> |
int ndfRaw_local; |
156 |
|
|
157 |
< |
if( !boxIsInit ) boxIsInit = 1; |
157 |
> |
MoleculeIterator i; |
158 |
> |
std::vector<StuntDouble*>::iterator j; |
159 |
> |
Molecule* mol; |
160 |
> |
StuntDouble* integrableObject; |
161 |
|
|
162 |
< |
for(i=0; i < 3; i++) |
163 |
< |
for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
164 |
< |
|
165 |
< |
calcBoxL(); |
166 |
< |
calcHmatInv(); |
162 |
> |
// Raw degrees of freedom that we have to set |
163 |
> |
ndfRaw_local = 0; |
164 |
> |
|
165 |
> |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
166 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
167 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
168 |
|
|
169 |
< |
for(i=0; i < 3; i++) { |
170 |
< |
for (j=0; j < 3; j++) { |
171 |
< |
FortranHmat[3*j + i] = Hmat[i][j]; |
172 |
< |
FortranHmatInv[3*j + i] = HmatInv[i][j]; |
173 |
< |
} |
174 |
< |
} |
175 |
< |
|
176 |
< |
setFortranBox(FortranHmat, FortranHmatInv, &orthoRhombic); |
177 |
< |
|
169 |
> |
ndfRaw_local += 3; |
170 |
> |
|
171 |
> |
if (integrableObject->isDirectional()) { |
172 |
> |
if (integrableObject->isLinear()) { |
173 |
> |
ndfRaw_local += 2; |
174 |
> |
} else { |
175 |
> |
ndfRaw_local += 3; |
176 |
> |
} |
177 |
> |
} |
178 |
> |
|
179 |
> |
} |
180 |
> |
} |
181 |
> |
|
182 |
> |
#ifdef IS_MPI |
183 |
> |
MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
184 |
> |
#else |
185 |
> |
ndfRaw_ = ndfRaw_local; |
186 |
> |
#endif |
187 |
|
} |
143 |
– |
|
188 |
|
|
189 |
< |
void SimInfo::getBoxM (double theBox[3][3]) { |
189 |
> |
void SimInfo::calcNdfTrans() { |
190 |
> |
int ndfTrans_local; |
191 |
|
|
192 |
< |
int i, j; |
193 |
< |
for(i=0; i<3; i++) |
194 |
< |
for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
192 |
> |
ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_; |
193 |
> |
|
194 |
> |
|
195 |
> |
#ifdef IS_MPI |
196 |
> |
MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
197 |
> |
#else |
198 |
> |
ndfTrans_ = ndfTrans_local; |
199 |
> |
#endif |
200 |
> |
|
201 |
> |
ndfTrans_ = ndfTrans_ - 3 - nZconstraints; |
202 |
> |
|
203 |
|
} |
204 |
|
|
205 |
+ |
void SimInfo::addExcludePairs(Molecule* mol) { |
206 |
+ |
std::vector<Bond*>::iterator bondIter; |
207 |
+ |
std::vector<Bend*>::iterator bendIter; |
208 |
+ |
std::vector<Torsion*>::iterator torsionIter; |
209 |
+ |
Bond* bond; |
210 |
+ |
Bend* bend; |
211 |
+ |
Torsion* torsion; |
212 |
+ |
int a; |
213 |
+ |
int b; |
214 |
+ |
int c; |
215 |
+ |
int d; |
216 |
+ |
|
217 |
+ |
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
218 |
+ |
a = bond->getAtomA()->getGlobalIndex(); |
219 |
+ |
b = bond->getAtomB()->getGlobalIndex(); |
220 |
+ |
exclude_.addPair(a, b); |
221 |
+ |
} |
222 |
|
|
223 |
< |
void SimInfo::scaleBox(double scale) { |
224 |
< |
double theBox[3][3]; |
225 |
< |
int i, j; |
223 |
> |
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
224 |
> |
a = bend->getAtomA()->getGlobalIndex(); |
225 |
> |
b = bend->getAtomB()->getGlobalIndex(); |
226 |
> |
c = bend->getAtomC()->getGlobalIndex(); |
227 |
|
|
228 |
< |
// cerr << "Scaling box by " << scale << "\n"; |
228 |
> |
exclude_.addPair(a, b); |
229 |
> |
exclude_.addPair(a, c); |
230 |
> |
exclude_.addPair(b, c); |
231 |
> |
} |
232 |
|
|
233 |
< |
for(i=0; i<3; i++) |
234 |
< |
for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
233 |
> |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) { |
234 |
> |
a = torsion->getAtomA()->getGlobalIndex(); |
235 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
236 |
> |
c = torsion->getAtomC()->getGlobalIndex(); |
237 |
> |
d = torsion->getAtomD()->getGlobalIndex(); |
238 |
|
|
239 |
< |
setBoxM(theBox); |
239 |
> |
exclude_.addPair(a, b); |
240 |
> |
exclude_.addPair(a, c); |
241 |
> |
exclude_.addPair(a, d); |
242 |
> |
exclude_.addPair(b, c); |
243 |
> |
exclude_.addPair(b, d); |
244 |
> |
exclude_.addPair(c, d); |
245 |
> |
} |
246 |
|
|
247 |
+ |
|
248 |
|
} |
249 |
|
|
250 |
< |
void SimInfo::calcHmatInv( void ) { |
251 |
< |
|
252 |
< |
int oldOrtho; |
253 |
< |
int i,j; |
254 |
< |
double smallDiag; |
255 |
< |
double tol; |
256 |
< |
double sanity[3][3]; |
250 |
> |
void SimInfo::removeExcludePairs(Molecule* mol) { |
251 |
> |
std::vector<Bond*>::iterator bondIter; |
252 |
> |
std::vector<Bend*>::iterator bendIter; |
253 |
> |
std::vector<Torsion*>::iterator torsionIter; |
254 |
> |
Bond* bond; |
255 |
> |
Bend* bend; |
256 |
> |
Torsion* torsion; |
257 |
> |
int a; |
258 |
> |
int b; |
259 |
> |
int c; |
260 |
> |
int d; |
261 |
> |
|
262 |
> |
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
263 |
> |
a = bond->getAtomA()->getGlobalIndex(); |
264 |
> |
b = bond->getAtomB()->getGlobalIndex(); |
265 |
> |
exclude_.removePair(a, b); |
266 |
> |
} |
267 |
|
|
268 |
< |
invertMat3( Hmat, HmatInv ); |
268 |
> |
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
269 |
> |
a = bend->getAtomA()->getGlobalIndex(); |
270 |
> |
b = bend->getAtomB()->getGlobalIndex(); |
271 |
> |
c = bend->getAtomC()->getGlobalIndex(); |
272 |
|
|
273 |
< |
// check to see if Hmat is orthorhombic |
274 |
< |
|
275 |
< |
oldOrtho = orthoRhombic; |
273 |
> |
exclude_.removePair(a, b); |
274 |
> |
exclude_.removePair(a, c); |
275 |
> |
exclude_.removePair(b, c); |
276 |
> |
} |
277 |
|
|
278 |
< |
smallDiag = fabs(Hmat[0][0]); |
279 |
< |
if(smallDiag > fabs(Hmat[1][1])) smallDiag = fabs(Hmat[1][1]); |
280 |
< |
if(smallDiag > fabs(Hmat[2][2])) smallDiag = fabs(Hmat[2][2]); |
281 |
< |
tol = smallDiag * orthoTolerance; |
278 |
> |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextBond(torsionIter)) { |
279 |
> |
a = torsion->getAtomA()->getGlobalIndex(); |
280 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
281 |
> |
c = torsion->getAtomC()->getGlobalIndex(); |
282 |
> |
d = torsion->getAtomD()->getGlobalIndex(); |
283 |
|
|
284 |
< |
orthoRhombic = 1; |
285 |
< |
|
286 |
< |
for (i = 0; i < 3; i++ ) { |
287 |
< |
for (j = 0 ; j < 3; j++) { |
288 |
< |
if (i != j) { |
289 |
< |
if (orthoRhombic) { |
191 |
< |
if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
192 |
< |
} |
193 |
< |
} |
284 |
> |
exclude_.removePair(a, b); |
285 |
> |
exclude_.removePair(a, c); |
286 |
> |
exclude_.removePair(a, d); |
287 |
> |
exclude_.removePair(b, c); |
288 |
> |
exclude_.removePair(b, d); |
289 |
> |
exclude_.removePair(c, d); |
290 |
|
} |
195 |
– |
} |
291 |
|
|
197 |
– |
if( oldOrtho != orthoRhombic ){ |
198 |
– |
|
199 |
– |
if( orthoRhombic ) { |
200 |
– |
sprintf( painCave.errMsg, |
201 |
– |
"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 |
– |
} |
292 |
|
} |
293 |
|
|
225 |
– |
void SimInfo::calcBoxL( void ){ |
294 |
|
|
295 |
< |
double dx, dy, dz, dsq; |
295 |
> |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
296 |
> |
int curStampId; |
297 |
|
|
298 |
< |
// boxVol = Determinant of Hmat |
298 |
> |
//index from 0 |
299 |
> |
curStampId = molStampIds_.size(); |
300 |
|
|
301 |
< |
boxVol = matDet3( Hmat ); |
301 |
> |
moleculeStamps_.push_back(molStamp); |
302 |
> |
molStampIds_.insert(molStampIds_.end(), nmol, curStampId) |
303 |
> |
} |
304 |
|
|
305 |
< |
// boxLx |
234 |
< |
|
235 |
< |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
236 |
< |
dsq = dx*dx + dy*dy + dz*dz; |
237 |
< |
boxL[0] = sqrt( dsq ); |
238 |
< |
//maxCutoff = 0.5 * boxL[0]; |
305 |
> |
void SimInfo::update() { |
306 |
|
|
307 |
< |
// boxLy |
308 |
< |
|
309 |
< |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
310 |
< |
dsq = dx*dx + dy*dy + dz*dz; |
311 |
< |
boxL[1] = sqrt( dsq ); |
312 |
< |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
307 |
> |
|
308 |
> |
|
309 |
> |
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
310 |
> |
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
311 |
> |
std::vector<int> localToGlobalCutoffGroupIndex; |
312 |
> |
typename SimInfo::MoleculeIterator mi; |
313 |
> |
typename Molecule::AtomIterator ai; |
314 |
> |
typename Molecule::CutoffGroupIterator ci; |
315 |
> |
Molecule* mol; |
316 |
> |
Atom* atom; |
317 |
> |
CutoffGroup* cg; |
318 |
> |
mpiSimData parallelData; |
319 |
> |
int isError; |
320 |
|
|
321 |
+ |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
322 |
|
|
323 |
< |
// boxLz |
324 |
< |
|
325 |
< |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
326 |
< |
dsq = dx*dx + dy*dy + dz*dz; |
252 |
< |
boxL[2] = sqrt( dsq ); |
253 |
< |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
323 |
> |
//local index(index in DataStorge) of atom is important |
324 |
> |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
325 |
> |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
326 |
> |
} |
327 |
|
|
328 |
< |
//calculate the max cutoff |
329 |
< |
maxCutoff = calcMaxCutOff(); |
330 |
< |
|
331 |
< |
checkCutOffs(); |
328 |
> |
//local index of cutoff group is trivial, it only depends on the order of travesing |
329 |
> |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
330 |
> |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
331 |
> |
} |
332 |
> |
|
333 |
> |
} |
334 |
|
|
335 |
< |
} |
336 |
< |
|
337 |
< |
|
338 |
< |
double SimInfo::calcMaxCutOff(){ |
339 |
< |
|
340 |
< |
double ri[3], rj[3], rk[3]; |
341 |
< |
double rij[3], rjk[3], rki[3]; |
342 |
< |
double minDist; |
343 |
< |
|
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]; |
335 |
> |
//Setup Parallel Data and pass the index arrays to fortran |
336 |
> |
parallelData.nMolGlobal = getNMolGlobal(); |
337 |
> |
parallelData.nMolLocal = ; |
338 |
> |
parallelData.nAtomsGlobal = ; |
339 |
> |
parallelData.nAtomsLocal = ; |
340 |
> |
parallelData.nGroupsGlobal = ; |
341 |
> |
parallelData.nGroupsLocal = ; |
342 |
> |
parallelData.myNode = worldRank; |
343 |
> |
MPI_Comm_size(MPI_COMM_WORLD, &(parallelData->nProcessors)); |
344 |
|
|
345 |
< |
crossProduct3(ri, rj, rij); |
346 |
< |
distXY = dotProduct3(rk,rij) / norm3(rij); |
345 |
> |
setFsimParallel(parallelData, &(parallelData->nAtomsLocal), |
346 |
> |
&localToGlobalAtomIndex[0], &(parallelData->nGroupsLocal), |
347 |
> |
&localToGlobalCutoffGroupIndex[0], &isError); |
348 |
|
|
349 |
< |
crossProduct3(rj,rk, rjk); |
350 |
< |
distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
351 |
< |
|
352 |
< |
crossProduct3(rk,ri, rki); |
353 |
< |
distZX = dotProduct3(rj,rki) / norm3(rki); |
289 |
< |
|
290 |
< |
minDist = min(min(distXY, distYZ), distZX); |
291 |
< |
return minDist/2; |
292 |
< |
|
293 |
< |
} |
294 |
< |
|
295 |
< |
void SimInfo::wrapVector( double thePos[3] ){ |
296 |
< |
|
297 |
< |
int i; |
298 |
< |
double scaled[3]; |
299 |
< |
|
300 |
< |
if( !orthoRhombic ){ |
301 |
< |
// calc the scaled coordinates. |
302 |
< |
|
303 |
< |
|
304 |
< |
matVecMul3(HmatInv, thePos, scaled); |
305 |
< |
|
306 |
< |
for(i=0; i<3; i++) |
307 |
< |
scaled[i] -= roundMe(scaled[i]); |
308 |
< |
|
309 |
< |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
310 |
< |
|
311 |
< |
matVecMul3(Hmat, scaled, thePos); |
312 |
< |
|
313 |
< |
} |
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 |
< |
} |
332 |
< |
|
333 |
< |
|
334 |
< |
int SimInfo::getNDF(){ |
335 |
< |
int ndf_local; |
336 |
< |
|
337 |
< |
ndf_local = 0; |
338 |
< |
|
339 |
< |
for(int i = 0; i < integrableObjects.size(); i++){ |
340 |
< |
ndf_local += 3; |
341 |
< |
if (integrableObjects[i]->isDirectional()) { |
342 |
< |
if (integrableObjects[i]->isLinear()) |
343 |
< |
ndf_local += 2; |
344 |
< |
else |
345 |
< |
ndf_local += 3; |
349 |
> |
if (isError) { |
350 |
> |
sprintf(painCave.errMsg, |
351 |
> |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
352 |
> |
painCave.isFatal = 1; |
353 |
> |
simError(); |
354 |
|
} |
347 |
– |
} |
355 |
|
|
356 |
< |
// n_constraints is local, so subtract them on each processor: |
356 |
> |
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
357 |
> |
MPIcheckPoint(); |
358 |
|
|
351 |
– |
ndf_local -= n_constraints; |
359 |
|
|
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; |
360 |
|
} |
361 |
|
|
362 |
< |
int SimInfo::getNDFraw() { |
368 |
< |
int ndfRaw_local; |
362 |
> |
std::ostream& operator <<(ostream& o, SimInfo& info) { |
363 |
|
|
364 |
< |
// 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 |
< |
} |
382 |
< |
|
383 |
< |
#ifdef IS_MPI |
384 |
< |
MPI_Allreduce(&ndfRaw_local,&ndfRaw,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
385 |
< |
#else |
386 |
< |
ndfRaw = ndfRaw_local; |
387 |
< |
#endif |
388 |
< |
|
389 |
< |
return ndfRaw; |
364 |
> |
return o; |
365 |
|
} |
366 |
|
|
367 |
< |
int SimInfo::getNDFtranslational() { |
393 |
< |
int ndfTrans_local; |
394 |
< |
|
395 |
< |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
396 |
< |
|
397 |
< |
|
398 |
< |
#ifdef IS_MPI |
399 |
< |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
400 |
< |
#else |
401 |
< |
ndfTrans = ndfTrans_local; |
402 |
< |
#endif |
403 |
< |
|
404 |
< |
ndfTrans = ndfTrans - 3 - nZconstraints; |
405 |
< |
|
406 |
< |
return ndfTrans; |
407 |
< |
} |
408 |
< |
|
409 |
< |
int SimInfo::getTotIntegrableObjects() { |
410 |
< |
int nObjs_local; |
411 |
< |
int nObjs; |
412 |
< |
|
413 |
< |
nObjs_local = integrableObjects.size(); |
414 |
< |
|
415 |
< |
|
416 |
< |
#ifdef IS_MPI |
417 |
< |
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
418 |
< |
#else |
419 |
< |
nObjs = nObjs_local; |
420 |
< |
#endif |
421 |
< |
|
422 |
< |
|
423 |
< |
return nObjs; |
424 |
< |
} |
425 |
< |
|
426 |
< |
void SimInfo::refreshSim(){ |
427 |
< |
|
428 |
< |
simtype fInfo; |
429 |
< |
int isError; |
430 |
< |
int n_global; |
431 |
< |
int* excl; |
432 |
< |
|
433 |
< |
fInfo.dielect = 0.0; |
434 |
< |
|
435 |
< |
if( useDipoles ){ |
436 |
< |
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 ){ |
482 |
< |
|
483 |
< |
sprintf( painCave.errMsg, |
484 |
< |
"There was an error setting the simulation information in fortran.\n" ); |
485 |
< |
painCave.isFatal = 1; |
486 |
< |
painCave.severity = OOPSE_ERROR; |
487 |
< |
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 |
< |
} |
500 |
< |
|
501 |
< |
void SimInfo::setDefaultRcut( double theRcut ){ |
502 |
< |
|
503 |
< |
haveRcut = 1; |
504 |
< |
rCut = theRcut; |
505 |
< |
rList = rCut + 1.0; |
506 |
< |
|
507 |
< |
notifyFortranCutoffs( &rCut, &rSw, &rList ); |
508 |
< |
} |
509 |
< |
|
510 |
< |
void SimInfo::setDefaultRcut( double theRcut, double theRsw ){ |
511 |
< |
|
512 |
< |
rSw = theRsw; |
513 |
< |
setDefaultRcut( theRcut ); |
514 |
< |
} |
515 |
< |
|
516 |
< |
|
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 |
< |
|
551 |
< |
} |
552 |
< |
|
553 |
< |
void SimInfo::addProperty(GenericData* prop){ |
554 |
< |
|
555 |
< |
map<string, GenericData*>::iterator result; |
556 |
< |
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{ |
568 |
< |
|
569 |
< |
properties[prop->getID()] = prop; |
570 |
< |
|
571 |
< |
} |
572 |
< |
|
573 |
< |
} |
574 |
< |
|
575 |
< |
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 |
< |
} |
588 |
< |
|
589 |
< |
|
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 |
< |
|
639 |
< |
} |
367 |
> |
}//end namespace oopse |