1 |
< |
#include <stdlib.h> |
2 |
< |
#include <string.h> |
3 |
< |
#include <math.h> |
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/* |
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> |
* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* non-exclusive, royalty free, license to use, modify and |
6 |
> |
* redistribute this software in source and binary code form, provided |
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> |
* that the following conditions are met: |
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> |
* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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> |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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> |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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> |
* Parallel Simulation Engine for Molecular Dynamics," |
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> |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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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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*/ |
48 |
|
|
49 |
< |
#include <iostream> |
50 |
< |
using namespace std; |
49 |
> |
#include <algorithm> |
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> |
#include <set> |
51 |
|
|
52 |
< |
#include "SimInfo.hpp" |
53 |
< |
#define __C |
54 |
< |
#include "fSimulation.h" |
55 |
< |
#include "simError.h" |
52 |
> |
#include "brains/SimInfo.hpp" |
53 |
> |
#include "math/Vector3.hpp" |
54 |
> |
#include "primitives/Molecule.hpp" |
55 |
> |
#include "UseTheForce/fCutoffPolicy.h" |
56 |
> |
#include "UseTheForce/fCoulombicCorrection.h" |
57 |
> |
#include "UseTheForce/doForces_interface.h" |
58 |
> |
#include "UseTheForce/notifyCutoffs_interface.h" |
59 |
> |
#include "utils/MemoryUtils.hpp" |
60 |
> |
#include "utils/simError.h" |
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> |
#include "selection/SelectionManager.hpp" |
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|
|
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– |
#include "fortranWrappers.hpp" |
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– |
|
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– |
#include "MatVec3.h" |
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|
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|
#ifdef IS_MPI |
64 |
< |
#include "mpiSimulation.hpp" |
65 |
< |
#endif |
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> |
#include "UseTheForce/mpiComponentPlan.h" |
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> |
#include "UseTheForce/DarkSide/simParallel_interface.h" |
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> |
#endif |
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|
|
68 |
< |
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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< |
|
25 |
< |
inline double min( double a, double b ){ |
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< |
return (a < b ) ? a : b; |
27 |
< |
} |
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> |
namespace oopse { |
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|
|
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SimInfo* currentInfo; |
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SimInfo::SimInfo(MakeStamps* stamps, std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, |
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ForceField* ff, Globals* simParams) : |
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stamps_(stamps), forceField_(ff), simParams_(simParams), |
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ndf_(0), ndfRaw_(0), ndfTrans_(0), nZconstraint_(0), |
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nGlobalMols_(0), nGlobalAtoms_(0), nGlobalCutoffGroups_(0), |
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nGlobalIntegrableObjects_(0), nGlobalRigidBodies_(0), |
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> |
nAtoms_(0), nBonds_(0), nBends_(0), nTorsions_(0), nRigidBodies_(0), |
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> |
nIntegrableObjects_(0), nCutoffGroups_(0), nConstraints_(0), |
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> |
sman_(NULL), fortranInitialized_(false) { |
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|
|
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< |
SimInfo::SimInfo(){ |
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|
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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 = 0; // number of atoms belong to cutoff groups |
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> |
int nGroups = 0; //total cutoff groups defined in meta-data file |
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> |
CutoffGroupStamp* cgStamp; |
87 |
> |
RigidBodyStamp* rbStamp; |
88 |
> |
int nRigidAtoms = 0; |
89 |
> |
|
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> |
for (i = molStampPairs.begin(); i !=molStampPairs.end(); ++i) { |
91 |
> |
molStamp = i->first; |
92 |
> |
nMolWithSameStamp = i->second; |
93 |
> |
|
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> |
addMoleculeStamp(molStamp, nMolWithSameStamp); |
95 |
|
|
96 |
< |
n_constraints = 0; |
97 |
< |
nZconstraints = 0; |
35 |
< |
n_oriented = 0; |
36 |
< |
n_dipoles = 0; |
37 |
< |
ndf = 0; |
38 |
< |
ndfRaw = 0; |
39 |
< |
nZconstraints = 0; |
40 |
< |
the_integrator = NULL; |
41 |
< |
setTemp = 0; |
42 |
< |
thermalTime = 0.0; |
43 |
< |
currentTime = 0.0; |
44 |
< |
rCut = 0.0; |
45 |
< |
rSw = 0.0; |
96 |
> |
//calculate atoms in molecules |
97 |
> |
nGlobalAtoms_ += molStamp->getNAtoms() *nMolWithSameStamp; |
98 |
|
|
47 |
– |
haveRcut = 0; |
48 |
– |
haveRsw = 0; |
49 |
– |
boxIsInit = 0; |
50 |
– |
|
51 |
– |
resetTime = 1e99; |
99 |
|
|
100 |
< |
orthoRhombic = 0; |
101 |
< |
orthoTolerance = 1E-6; |
102 |
< |
useInitXSstate = true; |
100 |
> |
//calculate atoms in cutoff groups |
101 |
> |
int nAtomsInGroups = 0; |
102 |
> |
int nCutoffGroupsInStamp = molStamp->getNCutoffGroups(); |
103 |
> |
|
104 |
> |
for (int j=0; j < nCutoffGroupsInStamp; j++) { |
105 |
> |
cgStamp = molStamp->getCutoffGroup(j); |
106 |
> |
nAtomsInGroups += cgStamp->getNMembers(); |
107 |
> |
} |
108 |
|
|
109 |
< |
usePBC = 0; |
110 |
< |
useLJ = 0; |
59 |
< |
useSticky = 0; |
60 |
< |
useCharges = 0; |
61 |
< |
useDipoles = 0; |
62 |
< |
useReactionField = 0; |
63 |
< |
useGB = 0; |
64 |
< |
useEAM = 0; |
65 |
< |
useSolidThermInt = 0; |
66 |
< |
useLiquidThermInt = 0; |
109 |
> |
nGroups += nCutoffGroupsInStamp * nMolWithSameStamp; |
110 |
> |
nCutoffAtoms += nAtomsInGroups * nMolWithSameStamp; |
111 |
|
|
112 |
< |
haveCutoffGroups = false; |
112 |
> |
//calculate atoms in rigid bodies |
113 |
> |
int nAtomsInRigidBodies = 0; |
114 |
> |
int nRigidBodiesInStamp = molStamp->getNRigidBodies(); |
115 |
> |
|
116 |
> |
for (int j=0; j < nRigidBodiesInStamp; j++) { |
117 |
> |
rbStamp = molStamp->getRigidBody(j); |
118 |
> |
nAtomsInRigidBodies += rbStamp->getNMembers(); |
119 |
> |
} |
120 |
|
|
121 |
< |
excludes = Exclude::Instance(); |
121 |
> |
nGlobalRigidBodies_ += nRigidBodiesInStamp * nMolWithSameStamp; |
122 |
> |
nRigidAtoms += nAtomsInRigidBodies * nMolWithSameStamp; |
123 |
> |
|
124 |
> |
} |
125 |
|
|
126 |
< |
myConfiguration = new SimState(); |
126 |
> |
//every free atom (atom does not belong to cutoff groups) is a cutoff group |
127 |
> |
//therefore the total number of cutoff groups in the system is equal to |
128 |
> |
//the total number of atoms minus number of atoms belong to cutoff group defined in meta-data |
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> |
//file plus the number of cutoff groups defined in meta-data file |
130 |
> |
nGlobalCutoffGroups_ = nGlobalAtoms_ - nCutoffAtoms + nGroups; |
131 |
|
|
132 |
< |
has_minimizer = false; |
133 |
< |
the_minimizer =NULL; |
132 |
> |
//every free atom (atom does not belong to rigid bodies) is an integrable object |
133 |
> |
//therefore the total number of integrable objects in the system is equal to |
134 |
> |
//the total number of atoms minus number of atoms belong to rigid body defined in meta-data |
135 |
> |
//file plus the number of rigid bodies defined in meta-data file |
136 |
> |
nGlobalIntegrableObjects_ = nGlobalAtoms_ - nRigidAtoms + nGlobalRigidBodies_; |
137 |
|
|
138 |
< |
ngroup = 0; |
138 |
> |
nGlobalMols_ = molStampIds_.size(); |
139 |
|
|
140 |
< |
wrapMeSimInfo( this ); |
141 |
< |
} |
140 |
> |
#ifdef IS_MPI |
141 |
> |
molToProcMap_.resize(nGlobalMols_); |
142 |
> |
#endif |
143 |
|
|
144 |
+ |
} |
145 |
|
|
146 |
< |
SimInfo::~SimInfo(){ |
146 |
> |
SimInfo::~SimInfo() { |
147 |
> |
std::map<int, Molecule*>::iterator i; |
148 |
> |
for (i = molecules_.begin(); i != molecules_.end(); ++i) { |
149 |
> |
delete i->second; |
150 |
> |
} |
151 |
> |
molecules_.clear(); |
152 |
> |
|
153 |
> |
delete stamps_; |
154 |
> |
delete sman_; |
155 |
> |
delete simParams_; |
156 |
> |
delete forceField_; |
157 |
> |
} |
158 |
|
|
159 |
< |
delete myConfiguration; |
159 |
> |
int SimInfo::getNGlobalConstraints() { |
160 |
> |
int nGlobalConstraints; |
161 |
> |
#ifdef IS_MPI |
162 |
> |
MPI_Allreduce(&nConstraints_, &nGlobalConstraints, 1, MPI_INT, MPI_SUM, |
163 |
> |
MPI_COMM_WORLD); |
164 |
> |
#else |
165 |
> |
nGlobalConstraints = nConstraints_; |
166 |
> |
#endif |
167 |
> |
return nGlobalConstraints; |
168 |
> |
} |
169 |
|
|
170 |
< |
map<string, GenericData*>::iterator i; |
171 |
< |
|
89 |
< |
for(i = properties.begin(); i != properties.end(); i++) |
90 |
< |
delete (*i).second; |
170 |
> |
bool SimInfo::addMolecule(Molecule* mol) { |
171 |
> |
MoleculeIterator i; |
172 |
|
|
173 |
< |
} |
173 |
> |
i = molecules_.find(mol->getGlobalIndex()); |
174 |
> |
if (i == molecules_.end() ) { |
175 |
|
|
176 |
< |
void SimInfo::setBox(double newBox[3]) { |
177 |
< |
|
178 |
< |
int i, j; |
179 |
< |
double tempMat[3][3]; |
180 |
< |
|
181 |
< |
for(i=0; i<3; i++) |
182 |
< |
for (j=0; j<3; j++) tempMat[i][j] = 0.0;; |
183 |
< |
|
184 |
< |
tempMat[0][0] = newBox[0]; |
185 |
< |
tempMat[1][1] = newBox[1]; |
104 |
< |
tempMat[2][2] = newBox[2]; |
105 |
< |
|
106 |
< |
setBoxM( tempMat ); |
176 |
> |
molecules_.insert(std::make_pair(mol->getGlobalIndex(), mol)); |
177 |
> |
|
178 |
> |
nAtoms_ += mol->getNAtoms(); |
179 |
> |
nBonds_ += mol->getNBonds(); |
180 |
> |
nBends_ += mol->getNBends(); |
181 |
> |
nTorsions_ += mol->getNTorsions(); |
182 |
> |
nRigidBodies_ += mol->getNRigidBodies(); |
183 |
> |
nIntegrableObjects_ += mol->getNIntegrableObjects(); |
184 |
> |
nCutoffGroups_ += mol->getNCutoffGroups(); |
185 |
> |
nConstraints_ += mol->getNConstraintPairs(); |
186 |
|
|
187 |
< |
} |
188 |
< |
|
189 |
< |
void SimInfo::setBoxM( double theBox[3][3] ){ |
190 |
< |
|
191 |
< |
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); |
119 |
< |
|
120 |
< |
if( !boxIsInit ) boxIsInit = 1; |
121 |
< |
|
122 |
< |
for(i=0; i < 3; i++) |
123 |
< |
for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
124 |
< |
|
125 |
< |
calcBoxL(); |
126 |
< |
calcHmatInv(); |
127 |
< |
|
128 |
< |
for(i=0; i < 3; i++) { |
129 |
< |
for (j=0; j < 3; j++) { |
130 |
< |
FortranHmat[3*j + i] = Hmat[i][j]; |
131 |
< |
FortranHmatInv[3*j + i] = HmatInv[i][j]; |
187 |
> |
addExcludePairs(mol); |
188 |
> |
|
189 |
> |
return true; |
190 |
> |
} else { |
191 |
> |
return false; |
192 |
|
} |
193 |
|
} |
194 |
|
|
195 |
< |
setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
196 |
< |
|
197 |
< |
} |
138 |
< |
|
195 |
> |
bool SimInfo::removeMolecule(Molecule* mol) { |
196 |
> |
MoleculeIterator i; |
197 |
> |
i = molecules_.find(mol->getGlobalIndex()); |
198 |
|
|
199 |
< |
void SimInfo::getBoxM (double theBox[3][3]) { |
199 |
> |
if (i != molecules_.end() ) { |
200 |
|
|
201 |
< |
int i, j; |
202 |
< |
for(i=0; i<3; i++) |
203 |
< |
for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]; |
204 |
< |
} |
201 |
> |
assert(mol == i->second); |
202 |
> |
|
203 |
> |
nAtoms_ -= mol->getNAtoms(); |
204 |
> |
nBonds_ -= mol->getNBonds(); |
205 |
> |
nBends_ -= mol->getNBends(); |
206 |
> |
nTorsions_ -= mol->getNTorsions(); |
207 |
> |
nRigidBodies_ -= mol->getNRigidBodies(); |
208 |
> |
nIntegrableObjects_ -= mol->getNIntegrableObjects(); |
209 |
> |
nCutoffGroups_ -= mol->getNCutoffGroups(); |
210 |
> |
nConstraints_ -= mol->getNConstraintPairs(); |
211 |
|
|
212 |
+ |
removeExcludePairs(mol); |
213 |
+ |
molecules_.erase(mol->getGlobalIndex()); |
214 |
|
|
215 |
< |
void SimInfo::scaleBox(double scale) { |
216 |
< |
double theBox[3][3]; |
217 |
< |
int i, j; |
215 |
> |
delete mol; |
216 |
> |
|
217 |
> |
return true; |
218 |
> |
} else { |
219 |
> |
return false; |
220 |
> |
} |
221 |
|
|
152 |
– |
// cerr << "Scaling box by " << scale << "\n"; |
222 |
|
|
223 |
< |
for(i=0; i<3; i++) |
155 |
< |
for (j=0; j<3; j++) theBox[i][j] = Hmat[i][j]*scale; |
223 |
> |
} |
224 |
|
|
225 |
< |
setBoxM(theBox); |
225 |
> |
|
226 |
> |
Molecule* SimInfo::beginMolecule(MoleculeIterator& i) { |
227 |
> |
i = molecules_.begin(); |
228 |
> |
return i == molecules_.end() ? NULL : i->second; |
229 |
> |
} |
230 |
|
|
231 |
< |
} |
231 |
> |
Molecule* SimInfo::nextMolecule(MoleculeIterator& i) { |
232 |
> |
++i; |
233 |
> |
return i == molecules_.end() ? NULL : i->second; |
234 |
> |
} |
235 |
|
|
161 |
– |
void SimInfo::calcHmatInv( void ) { |
162 |
– |
|
163 |
– |
int oldOrtho; |
164 |
– |
int i,j; |
165 |
– |
double smallDiag; |
166 |
– |
double tol; |
167 |
– |
double sanity[3][3]; |
236 |
|
|
237 |
< |
invertMat3( Hmat, HmatInv ); |
237 |
> |
void SimInfo::calcNdf() { |
238 |
> |
int ndf_local; |
239 |
> |
MoleculeIterator i; |
240 |
> |
std::vector<StuntDouble*>::iterator j; |
241 |
> |
Molecule* mol; |
242 |
> |
StuntDouble* integrableObject; |
243 |
|
|
244 |
< |
// check to see if Hmat is orthorhombic |
245 |
< |
|
246 |
< |
oldOrtho = orthoRhombic; |
244 |
> |
ndf_local = 0; |
245 |
> |
|
246 |
> |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
247 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
248 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
249 |
|
|
250 |
< |
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; |
250 |
> |
ndf_local += 3; |
251 |
|
|
252 |
< |
orthoRhombic = 1; |
253 |
< |
|
254 |
< |
for (i = 0; i < 3; i++ ) { |
255 |
< |
for (j = 0 ; j < 3; j++) { |
256 |
< |
if (i != j) { |
257 |
< |
if (orthoRhombic) { |
258 |
< |
if ( fabs(Hmat[i][j]) >= tol) orthoRhombic = 0; |
259 |
< |
} |
260 |
< |
} |
261 |
< |
} |
190 |
< |
} |
191 |
< |
|
192 |
< |
if( oldOrtho != orthoRhombic ){ |
252 |
> |
if (integrableObject->isDirectional()) { |
253 |
> |
if (integrableObject->isLinear()) { |
254 |
> |
ndf_local += 2; |
255 |
> |
} else { |
256 |
> |
ndf_local += 3; |
257 |
> |
} |
258 |
> |
} |
259 |
> |
|
260 |
> |
}//end for (integrableObject) |
261 |
> |
}// end for (mol) |
262 |
|
|
263 |
< |
if( orthoRhombic ) { |
264 |
< |
sprintf( painCave.errMsg, |
196 |
< |
"OOPSE is switching from the default Non-Orthorhombic\n" |
197 |
< |
"\tto the faster Orthorhombic periodic boundary computations.\n" |
198 |
< |
"\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 |
< |
} |
218 |
< |
} |
263 |
> |
// n_constraints is local, so subtract them on each processor |
264 |
> |
ndf_local -= nConstraints_; |
265 |
|
|
266 |
< |
void SimInfo::calcBoxL( void ){ |
266 |
> |
#ifdef IS_MPI |
267 |
> |
MPI_Allreduce(&ndf_local,&ndf_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
268 |
> |
#else |
269 |
> |
ndf_ = ndf_local; |
270 |
> |
#endif |
271 |
|
|
272 |
< |
double dx, dy, dz, dsq; |
272 |
> |
// nZconstraints_ is global, as are the 3 COM translations for the |
273 |
> |
// entire system: |
274 |
> |
ndf_ = ndf_ - 3 - nZconstraint_; |
275 |
|
|
276 |
< |
// boxVol = Determinant of Hmat |
276 |
> |
} |
277 |
|
|
278 |
< |
boxVol = matDet3( Hmat ); |
278 |
> |
void SimInfo::calcNdfRaw() { |
279 |
> |
int ndfRaw_local; |
280 |
|
|
281 |
< |
// boxLx |
282 |
< |
|
283 |
< |
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
284 |
< |
dsq = dx*dx + dy*dy + dz*dz; |
232 |
< |
boxL[0] = sqrt( dsq ); |
233 |
< |
//maxCutoff = 0.5 * boxL[0]; |
281 |
> |
MoleculeIterator i; |
282 |
> |
std::vector<StuntDouble*>::iterator j; |
283 |
> |
Molecule* mol; |
284 |
> |
StuntDouble* integrableObject; |
285 |
|
|
286 |
< |
// boxLy |
287 |
< |
|
288 |
< |
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
289 |
< |
dsq = dx*dx + dy*dy + dz*dz; |
290 |
< |
boxL[1] = sqrt( dsq ); |
291 |
< |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
286 |
> |
// Raw degrees of freedom that we have to set |
287 |
> |
ndfRaw_local = 0; |
288 |
> |
|
289 |
> |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
290 |
> |
for (integrableObject = mol->beginIntegrableObject(j); integrableObject != NULL; |
291 |
> |
integrableObject = mol->nextIntegrableObject(j)) { |
292 |
|
|
293 |
+ |
ndfRaw_local += 3; |
294 |
|
|
295 |
< |
// boxLz |
296 |
< |
|
297 |
< |
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
298 |
< |
dsq = dx*dx + dy*dy + dz*dz; |
299 |
< |
boxL[2] = sqrt( dsq ); |
300 |
< |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
295 |
> |
if (integrableObject->isDirectional()) { |
296 |
> |
if (integrableObject->isLinear()) { |
297 |
> |
ndfRaw_local += 2; |
298 |
> |
} else { |
299 |
> |
ndfRaw_local += 3; |
300 |
> |
} |
301 |
> |
} |
302 |
> |
|
303 |
> |
} |
304 |
> |
} |
305 |
> |
|
306 |
> |
#ifdef IS_MPI |
307 |
> |
MPI_Allreduce(&ndfRaw_local,&ndfRaw_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
308 |
> |
#else |
309 |
> |
ndfRaw_ = ndfRaw_local; |
310 |
> |
#endif |
311 |
> |
} |
312 |
|
|
313 |
< |
//calculate the max cutoff |
314 |
< |
maxCutoff = calcMaxCutOff(); |
252 |
< |
|
253 |
< |
checkCutOffs(); |
313 |
> |
void SimInfo::calcNdfTrans() { |
314 |
> |
int ndfTrans_local; |
315 |
|
|
316 |
< |
} |
316 |
> |
ndfTrans_local = 3 * nIntegrableObjects_ - nConstraints_; |
317 |
|
|
318 |
|
|
319 |
< |
double SimInfo::calcMaxCutOff(){ |
319 |
> |
#ifdef IS_MPI |
320 |
> |
MPI_Allreduce(&ndfTrans_local,&ndfTrans_,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
321 |
> |
#else |
322 |
> |
ndfTrans_ = ndfTrans_local; |
323 |
> |
#endif |
324 |
|
|
325 |
< |
double ri[3], rj[3], rk[3]; |
326 |
< |
double rij[3], rjk[3], rki[3]; |
327 |
< |
double minDist; |
325 |
> |
ndfTrans_ = ndfTrans_ - 3 - nZconstraint_; |
326 |
> |
|
327 |
> |
} |
328 |
|
|
329 |
< |
ri[0] = Hmat[0][0]; |
330 |
< |
ri[1] = Hmat[1][0]; |
331 |
< |
ri[2] = Hmat[2][0]; |
332 |
< |
|
333 |
< |
rj[0] = Hmat[0][1]; |
334 |
< |
rj[1] = Hmat[1][1]; |
335 |
< |
rj[2] = Hmat[2][1]; |
336 |
< |
|
337 |
< |
rk[0] = Hmat[0][2]; |
338 |
< |
rk[1] = Hmat[1][2]; |
339 |
< |
rk[2] = Hmat[2][2]; |
329 |
> |
void SimInfo::addExcludePairs(Molecule* mol) { |
330 |
> |
std::vector<Bond*>::iterator bondIter; |
331 |
> |
std::vector<Bend*>::iterator bendIter; |
332 |
> |
std::vector<Torsion*>::iterator torsionIter; |
333 |
> |
Bond* bond; |
334 |
> |
Bend* bend; |
335 |
> |
Torsion* torsion; |
336 |
> |
int a; |
337 |
> |
int b; |
338 |
> |
int c; |
339 |
> |
int d; |
340 |
|
|
341 |
< |
crossProduct3(ri, rj, rij); |
342 |
< |
distXY = dotProduct3(rk,rij) / norm3(rij); |
341 |
> |
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
342 |
> |
a = bond->getAtomA()->getGlobalIndex(); |
343 |
> |
b = bond->getAtomB()->getGlobalIndex(); |
344 |
> |
exclude_.addPair(a, b); |
345 |
> |
} |
346 |
|
|
347 |
< |
crossProduct3(rj,rk, rjk); |
348 |
< |
distYZ = dotProduct3(ri,rjk) / norm3(rjk); |
347 |
> |
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
348 |
> |
a = bend->getAtomA()->getGlobalIndex(); |
349 |
> |
b = bend->getAtomB()->getGlobalIndex(); |
350 |
> |
c = bend->getAtomC()->getGlobalIndex(); |
351 |
|
|
352 |
< |
crossProduct3(rk,ri, rki); |
353 |
< |
distZX = dotProduct3(rj,rki) / norm3(rki); |
352 |
> |
exclude_.addPair(a, b); |
353 |
> |
exclude_.addPair(a, c); |
354 |
> |
exclude_.addPair(b, c); |
355 |
> |
} |
356 |
|
|
357 |
< |
minDist = min(min(distXY, distYZ), distZX); |
358 |
< |
return minDist/2; |
359 |
< |
|
360 |
< |
} |
357 |
> |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
358 |
> |
a = torsion->getAtomA()->getGlobalIndex(); |
359 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
360 |
> |
c = torsion->getAtomC()->getGlobalIndex(); |
361 |
> |
d = torsion->getAtomD()->getGlobalIndex(); |
362 |
|
|
363 |
< |
void SimInfo::wrapVector( double thePos[3] ){ |
363 |
> |
exclude_.addPair(a, b); |
364 |
> |
exclude_.addPair(a, c); |
365 |
> |
exclude_.addPair(a, d); |
366 |
> |
exclude_.addPair(b, c); |
367 |
> |
exclude_.addPair(b, d); |
368 |
> |
exclude_.addPair(c, d); |
369 |
> |
} |
370 |
|
|
371 |
< |
int i; |
372 |
< |
double scaled[3]; |
371 |
> |
Molecule::RigidBodyIterator rbIter; |
372 |
> |
RigidBody* rb; |
373 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
374 |
> |
std::vector<Atom*> atoms = rb->getAtoms(); |
375 |
> |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
376 |
> |
for (int j = i + 1; j < atoms.size(); ++j) { |
377 |
> |
a = atoms[i]->getGlobalIndex(); |
378 |
> |
b = atoms[j]->getGlobalIndex(); |
379 |
> |
exclude_.addPair(a, b); |
380 |
> |
} |
381 |
> |
} |
382 |
> |
} |
383 |
|
|
384 |
< |
if( !orthoRhombic ){ |
296 |
< |
// calc the scaled coordinates. |
297 |
< |
|
384 |
> |
} |
385 |
|
|
386 |
< |
matVecMul3(HmatInv, thePos, scaled); |
386 |
> |
void SimInfo::removeExcludePairs(Molecule* mol) { |
387 |
> |
std::vector<Bond*>::iterator bondIter; |
388 |
> |
std::vector<Bend*>::iterator bendIter; |
389 |
> |
std::vector<Torsion*>::iterator torsionIter; |
390 |
> |
Bond* bond; |
391 |
> |
Bend* bend; |
392 |
> |
Torsion* torsion; |
393 |
> |
int a; |
394 |
> |
int b; |
395 |
> |
int c; |
396 |
> |
int d; |
397 |
|
|
398 |
< |
for(i=0; i<3; i++) |
399 |
< |
scaled[i] -= roundMe(scaled[i]); |
400 |
< |
|
401 |
< |
// calc the wrapped real coordinates from the wrapped scaled coordinates |
402 |
< |
|
306 |
< |
matVecMul3(Hmat, scaled, thePos); |
398 |
> |
for (bond= mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) { |
399 |
> |
a = bond->getAtomA()->getGlobalIndex(); |
400 |
> |
b = bond->getAtomB()->getGlobalIndex(); |
401 |
> |
exclude_.removePair(a, b); |
402 |
> |
} |
403 |
|
|
404 |
< |
} |
405 |
< |
else{ |
406 |
< |
// calc the scaled coordinates. |
407 |
< |
|
312 |
< |
for(i=0; i<3; i++) |
313 |
< |
scaled[i] = thePos[i]*HmatInv[i][i]; |
314 |
< |
|
315 |
< |
// wrap the scaled coordinates |
316 |
< |
|
317 |
< |
for(i=0; i<3; i++) |
318 |
< |
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 |
< |
|
326 |
< |
} |
404 |
> |
for (bend= mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) { |
405 |
> |
a = bend->getAtomA()->getGlobalIndex(); |
406 |
> |
b = bend->getAtomB()->getGlobalIndex(); |
407 |
> |
c = bend->getAtomC()->getGlobalIndex(); |
408 |
|
|
409 |
+ |
exclude_.removePair(a, b); |
410 |
+ |
exclude_.removePair(a, c); |
411 |
+ |
exclude_.removePair(b, c); |
412 |
+ |
} |
413 |
|
|
414 |
< |
int SimInfo::getNDF(){ |
415 |
< |
int ndf_local; |
414 |
> |
for (torsion= mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) { |
415 |
> |
a = torsion->getAtomA()->getGlobalIndex(); |
416 |
> |
b = torsion->getAtomB()->getGlobalIndex(); |
417 |
> |
c = torsion->getAtomC()->getGlobalIndex(); |
418 |
> |
d = torsion->getAtomD()->getGlobalIndex(); |
419 |
|
|
420 |
< |
ndf_local = 0; |
421 |
< |
|
422 |
< |
for(int i = 0; i < integrableObjects.size(); i++){ |
423 |
< |
ndf_local += 3; |
424 |
< |
if (integrableObjects[i]->isDirectional()) { |
425 |
< |
if (integrableObjects[i]->isLinear()) |
338 |
< |
ndf_local += 2; |
339 |
< |
else |
340 |
< |
ndf_local += 3; |
420 |
> |
exclude_.removePair(a, b); |
421 |
> |
exclude_.removePair(a, c); |
422 |
> |
exclude_.removePair(a, d); |
423 |
> |
exclude_.removePair(b, c); |
424 |
> |
exclude_.removePair(b, d); |
425 |
> |
exclude_.removePair(c, d); |
426 |
|
} |
427 |
+ |
|
428 |
+ |
Molecule::RigidBodyIterator rbIter; |
429 |
+ |
RigidBody* rb; |
430 |
+ |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
431 |
+ |
std::vector<Atom*> atoms = rb->getAtoms(); |
432 |
+ |
for (int i = 0; i < atoms.size() -1 ; ++i) { |
433 |
+ |
for (int j = i + 1; j < atoms.size(); ++j) { |
434 |
+ |
a = atoms[i]->getGlobalIndex(); |
435 |
+ |
b = atoms[j]->getGlobalIndex(); |
436 |
+ |
exclude_.removePair(a, b); |
437 |
+ |
} |
438 |
+ |
} |
439 |
+ |
} |
440 |
+ |
|
441 |
|
} |
442 |
|
|
344 |
– |
// n_constraints is local, so subtract them on each processor: |
443 |
|
|
444 |
< |
ndf_local -= n_constraints; |
444 |
> |
void SimInfo::addMoleculeStamp(MoleculeStamp* molStamp, int nmol) { |
445 |
> |
int curStampId; |
446 |
|
|
447 |
< |
#ifdef IS_MPI |
448 |
< |
MPI_Allreduce(&ndf_local,&ndf,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
350 |
< |
#else |
351 |
< |
ndf = ndf_local; |
352 |
< |
#endif |
447 |
> |
//index from 0 |
448 |
> |
curStampId = moleculeStamps_.size(); |
449 |
|
|
450 |
< |
// nZconstraints is global, as are the 3 COM translations for the |
451 |
< |
// entire system: |
450 |
> |
moleculeStamps_.push_back(molStamp); |
451 |
> |
molStampIds_.insert(molStampIds_.end(), nmol, curStampId); |
452 |
> |
} |
453 |
|
|
454 |
< |
ndf = ndf - 3 - nZconstraints; |
454 |
> |
void SimInfo::update() { |
455 |
|
|
456 |
< |
return ndf; |
360 |
< |
} |
456 |
> |
setupSimType(); |
457 |
|
|
458 |
< |
int SimInfo::getNDFraw() { |
459 |
< |
int ndfRaw_local; |
458 |
> |
#ifdef IS_MPI |
459 |
> |
setupFortranParallel(); |
460 |
> |
#endif |
461 |
|
|
462 |
< |
// Raw degrees of freedom that we have to set |
366 |
< |
ndfRaw_local = 0; |
462 |
> |
setupFortranSim(); |
463 |
|
|
464 |
< |
for(int i = 0; i < integrableObjects.size(); i++){ |
465 |
< |
ndfRaw_local += 3; |
466 |
< |
if (integrableObjects[i]->isDirectional()) { |
467 |
< |
if (integrableObjects[i]->isLinear()) |
468 |
< |
ndfRaw_local += 2; |
469 |
< |
else |
470 |
< |
ndfRaw_local += 3; |
464 |
> |
//setup fortran force field |
465 |
> |
/** @deprecate */ |
466 |
> |
int isError = 0; |
467 |
> |
|
468 |
> |
setupCoulombicCorrection( isError ); |
469 |
> |
|
470 |
> |
if(isError){ |
471 |
> |
sprintf( painCave.errMsg, |
472 |
> |
"ForceField error: There was an error initializing the forceField in fortran.\n" ); |
473 |
> |
painCave.isFatal = 1; |
474 |
> |
simError(); |
475 |
|
} |
476 |
< |
} |
476 |
> |
|
477 |
|
|
478 |
< |
#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 |
478 |
> |
setupCutoff(); |
479 |
|
|
480 |
< |
return ndfRaw; |
481 |
< |
} |
480 |
> |
calcNdf(); |
481 |
> |
calcNdfRaw(); |
482 |
> |
calcNdfTrans(); |
483 |
|
|
484 |
< |
int SimInfo::getNDFtranslational() { |
485 |
< |
int ndfTrans_local; |
484 |
> |
fortranInitialized_ = true; |
485 |
> |
} |
486 |
|
|
487 |
< |
ndfTrans_local = 3 * integrableObjects.size() - n_constraints; |
487 |
> |
std::set<AtomType*> SimInfo::getUniqueAtomTypes() { |
488 |
> |
SimInfo::MoleculeIterator mi; |
489 |
> |
Molecule* mol; |
490 |
> |
Molecule::AtomIterator ai; |
491 |
> |
Atom* atom; |
492 |
> |
std::set<AtomType*> atomTypes; |
493 |
|
|
494 |
+ |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
495 |
|
|
496 |
< |
#ifdef IS_MPI |
497 |
< |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
498 |
< |
#else |
499 |
< |
ndfTrans = ndfTrans_local; |
500 |
< |
#endif |
496 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
497 |
> |
atomTypes.insert(atom->getAtomType()); |
498 |
> |
} |
499 |
> |
|
500 |
> |
} |
501 |
|
|
502 |
< |
ndfTrans = ndfTrans - 3 - nZconstraints; |
502 |
> |
return atomTypes; |
503 |
> |
} |
504 |
|
|
505 |
< |
return ndfTrans; |
506 |
< |
} |
505 |
> |
void SimInfo::setupSimType() { |
506 |
> |
std::set<AtomType*>::iterator i; |
507 |
> |
std::set<AtomType*> atomTypes; |
508 |
> |
atomTypes = getUniqueAtomTypes(); |
509 |
> |
|
510 |
> |
int useLennardJones = 0; |
511 |
> |
int useElectrostatic = 0; |
512 |
> |
int useEAM = 0; |
513 |
> |
int useCharge = 0; |
514 |
> |
int useDirectional = 0; |
515 |
> |
int useDipole = 0; |
516 |
> |
int useGayBerne = 0; |
517 |
> |
int useSticky = 0; |
518 |
> |
int useStickyPower = 0; |
519 |
> |
int useShape = 0; |
520 |
> |
int useFLARB = 0; //it is not in AtomType yet |
521 |
> |
int useDirectionalAtom = 0; |
522 |
> |
int useElectrostatics = 0; |
523 |
> |
//usePBC and useRF are from simParams |
524 |
> |
int usePBC = simParams_->getPBC(); |
525 |
> |
int useRF = simParams_->getUseRF(); |
526 |
|
|
527 |
< |
int SimInfo::getTotIntegrableObjects() { |
528 |
< |
int nObjs_local; |
529 |
< |
int nObjs; |
527 |
> |
//loop over all of the atom types |
528 |
> |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
529 |
> |
useLennardJones |= (*i)->isLennardJones(); |
530 |
> |
useElectrostatic |= (*i)->isElectrostatic(); |
531 |
> |
useEAM |= (*i)->isEAM(); |
532 |
> |
useCharge |= (*i)->isCharge(); |
533 |
> |
useDirectional |= (*i)->isDirectional(); |
534 |
> |
useDipole |= (*i)->isDipole(); |
535 |
> |
useGayBerne |= (*i)->isGayBerne(); |
536 |
> |
useSticky |= (*i)->isSticky(); |
537 |
> |
useStickyPower |= (*i)->isStickyPower(); |
538 |
> |
useShape |= (*i)->isShape(); |
539 |
> |
} |
540 |
|
|
541 |
< |
nObjs_local = integrableObjects.size(); |
541 |
> |
if (useSticky || useStickyPower || useDipole || useGayBerne || useShape) { |
542 |
> |
useDirectionalAtom = 1; |
543 |
> |
} |
544 |
|
|
545 |
+ |
if (useCharge || useDipole) { |
546 |
+ |
useElectrostatics = 1; |
547 |
+ |
} |
548 |
|
|
549 |
< |
#ifdef IS_MPI |
550 |
< |
MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
413 |
< |
#else |
414 |
< |
nObjs = nObjs_local; |
415 |
< |
#endif |
549 |
> |
#ifdef IS_MPI |
550 |
> |
int temp; |
551 |
|
|
552 |
+ |
temp = usePBC; |
553 |
+ |
MPI_Allreduce(&temp, &usePBC, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
554 |
|
|
555 |
< |
return nObjs; |
556 |
< |
} |
555 |
> |
temp = useDirectionalAtom; |
556 |
> |
MPI_Allreduce(&temp, &useDirectionalAtom, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
557 |
|
|
558 |
< |
void SimInfo::refreshSim(){ |
558 |
> |
temp = useLennardJones; |
559 |
> |
MPI_Allreduce(&temp, &useLennardJones, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
560 |
|
|
561 |
< |
simtype fInfo; |
562 |
< |
int isError; |
425 |
< |
int n_global; |
426 |
< |
int* excl; |
561 |
> |
temp = useElectrostatics; |
562 |
> |
MPI_Allreduce(&temp, &useElectrostatics, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
563 |
|
|
564 |
< |
fInfo.dielect = 0.0; |
564 |
> |
temp = useCharge; |
565 |
> |
MPI_Allreduce(&temp, &useCharge, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
566 |
|
|
567 |
< |
if( useDipoles ){ |
568 |
< |
if( useReactionField )fInfo.dielect = dielectric; |
432 |
< |
} |
567 |
> |
temp = useDipole; |
568 |
> |
MPI_Allreduce(&temp, &useDipole, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
569 |
|
|
570 |
< |
fInfo.SIM_uses_PBC = usePBC; |
571 |
< |
//fInfo.SIM_uses_LJ = 0; |
436 |
< |
fInfo.SIM_uses_LJ = useLJ; |
437 |
< |
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; |
570 |
> |
temp = useSticky; |
571 |
> |
MPI_Allreduce(&temp, &useSticky, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
572 |
|
|
573 |
< |
n_exclude = excludes->getSize(); |
574 |
< |
excl = excludes->getFortranArray(); |
575 |
< |
|
576 |
< |
#ifdef IS_MPI |
577 |
< |
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); |
573 |
> |
temp = useStickyPower; |
574 |
> |
MPI_Allreduce(&temp, &useStickyPower, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
575 |
> |
|
576 |
> |
temp = useGayBerne; |
577 |
> |
MPI_Allreduce(&temp, &useGayBerne, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
578 |
|
|
579 |
< |
if( isError ){ |
579 |
> |
temp = useEAM; |
580 |
> |
MPI_Allreduce(&temp, &useEAM, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
581 |
> |
|
582 |
> |
temp = useShape; |
583 |
> |
MPI_Allreduce(&temp, &useShape, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
584 |
> |
|
585 |
> |
temp = useFLARB; |
586 |
> |
MPI_Allreduce(&temp, &useFLARB, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
587 |
> |
|
588 |
> |
temp = useRF; |
589 |
> |
MPI_Allreduce(&temp, &useRF, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
590 |
> |
|
591 |
> |
temp = useUW; |
592 |
> |
MPI_Allreduce(&temp, &useUW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
593 |
> |
|
594 |
> |
temp = useDW; |
595 |
> |
MPI_Allreduce(&temp, &useDW, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
596 |
|
|
597 |
< |
sprintf( painCave.errMsg, |
598 |
< |
"There was an error setting the simulation information in fortran.\n" ); |
599 |
< |
painCave.isFatal = 1; |
600 |
< |
painCave.severity = OOPSE_ERROR; |
601 |
< |
simError(); |
597 |
> |
#endif |
598 |
> |
|
599 |
> |
fInfo_.SIM_uses_PBC = usePBC; |
600 |
> |
fInfo_.SIM_uses_DirectionalAtoms = useDirectionalAtom; |
601 |
> |
fInfo_.SIM_uses_LennardJones = useLennardJones; |
602 |
> |
fInfo_.SIM_uses_Electrostatics = useElectrostatics; |
603 |
> |
fInfo_.SIM_uses_Charges = useCharge; |
604 |
> |
fInfo_.SIM_uses_Dipoles = useDipole; |
605 |
> |
fInfo_.SIM_uses_Sticky = useSticky; |
606 |
> |
fInfo_.SIM_uses_StickyPower = useStickyPower; |
607 |
> |
fInfo_.SIM_uses_GayBerne = useGayBerne; |
608 |
> |
fInfo_.SIM_uses_EAM = useEAM; |
609 |
> |
fInfo_.SIM_uses_Shapes = useShape; |
610 |
> |
fInfo_.SIM_uses_FLARB = useFLARB; |
611 |
> |
fInfo_.SIM_uses_RF = useRF; |
612 |
> |
|
613 |
> |
if( fInfo_.SIM_uses_Dipoles && fInfo_.SIM_uses_RF) { |
614 |
> |
|
615 |
> |
if (simParams_->haveDielectric()) { |
616 |
> |
fInfo_.dielect = simParams_->getDielectric(); |
617 |
> |
} else { |
618 |
> |
sprintf(painCave.errMsg, |
619 |
> |
"SimSetup Error: No Dielectric constant was set.\n" |
620 |
> |
"\tYou are trying to use Reaction Field without" |
621 |
> |
"\tsetting a dielectric constant!\n"); |
622 |
> |
painCave.isFatal = 1; |
623 |
> |
simError(); |
624 |
> |
} |
625 |
> |
|
626 |
> |
} else { |
627 |
> |
fInfo_.dielect = 0.0; |
628 |
> |
} |
629 |
> |
|
630 |
|
} |
474 |
– |
|
475 |
– |
#ifdef IS_MPI |
476 |
– |
sprintf( checkPointMsg, |
477 |
– |
"succesfully sent the simulation information to fortran.\n"); |
478 |
– |
MPIcheckPoint(); |
479 |
– |
#endif // is_mpi |
480 |
– |
|
481 |
– |
this->ndf = this->getNDF(); |
482 |
– |
this->ndfRaw = this->getNDFraw(); |
483 |
– |
this->ndfTrans = this->getNDFtranslational(); |
484 |
– |
} |
631 |
|
|
632 |
< |
void SimInfo::setDefaultRcut( double theRcut ){ |
633 |
< |
|
634 |
< |
haveRcut = 1; |
635 |
< |
rCut = theRcut; |
636 |
< |
rList = rCut + 1.0; |
637 |
< |
|
638 |
< |
notifyFortranCutOffs( &rCut, &rSw, &rList ); |
493 |
< |
} |
632 |
> |
void SimInfo::setupFortranSim() { |
633 |
> |
int isError; |
634 |
> |
int nExclude; |
635 |
> |
std::vector<int> fortranGlobalGroupMembership; |
636 |
> |
|
637 |
> |
nExclude = exclude_.getSize(); |
638 |
> |
isError = 0; |
639 |
|
|
640 |
< |
void SimInfo::setDefaultRcut( double theRcut, double theRsw ){ |
640 |
> |
//globalGroupMembership_ is filled by SimCreator |
641 |
> |
for (int i = 0; i < nGlobalAtoms_; i++) { |
642 |
> |
fortranGlobalGroupMembership.push_back(globalGroupMembership_[i] + 1); |
643 |
> |
} |
644 |
|
|
645 |
< |
rSw = theRsw; |
646 |
< |
setDefaultRcut( theRcut ); |
647 |
< |
} |
645 |
> |
//calculate mass ratio of cutoff group |
646 |
> |
std::vector<double> mfact; |
647 |
> |
SimInfo::MoleculeIterator mi; |
648 |
> |
Molecule* mol; |
649 |
> |
Molecule::CutoffGroupIterator ci; |
650 |
> |
CutoffGroup* cg; |
651 |
> |
Molecule::AtomIterator ai; |
652 |
> |
Atom* atom; |
653 |
> |
double totalMass; |
654 |
|
|
655 |
+ |
//to avoid memory reallocation, reserve enough space for mfact |
656 |
+ |
mfact.reserve(getNCutoffGroups()); |
657 |
+ |
|
658 |
+ |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
659 |
+ |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
660 |
|
|
661 |
< |
void SimInfo::checkCutOffs( void ){ |
662 |
< |
|
663 |
< |
if( boxIsInit ){ |
661 |
> |
totalMass = cg->getMass(); |
662 |
> |
for(atom = cg->beginAtom(ai); atom != NULL; atom = cg->nextAtom(ai)) { |
663 |
> |
mfact.push_back(atom->getMass()/totalMass); |
664 |
> |
} |
665 |
> |
|
666 |
> |
} |
667 |
> |
} |
668 |
> |
|
669 |
> |
//fill ident array of local atoms (it is actually ident of AtomType, it is so confusing !!!) |
670 |
> |
std::vector<int> identArray; |
671 |
> |
|
672 |
> |
//to avoid memory reallocation, reserve enough space identArray |
673 |
> |
identArray.reserve(getNAtoms()); |
674 |
|
|
675 |
< |
//we need to check cutOffs against the box |
675 |
> |
for(mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
676 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
677 |
> |
identArray.push_back(atom->getIdent()); |
678 |
> |
} |
679 |
> |
} |
680 |
> |
|
681 |
> |
//fill molMembershipArray |
682 |
> |
//molMembershipArray is filled by SimCreator |
683 |
> |
std::vector<int> molMembershipArray(nGlobalAtoms_); |
684 |
> |
for (int i = 0; i < nGlobalAtoms_; i++) { |
685 |
> |
molMembershipArray[i] = globalMolMembership_[i] + 1; |
686 |
> |
} |
687 |
|
|
688 |
< |
if( rCut > maxCutoff ){ |
688 |
> |
//setup fortran simulation |
689 |
> |
int nGlobalExcludes = 0; |
690 |
> |
int* globalExcludes = NULL; |
691 |
> |
int* excludeList = exclude_.getExcludeList(); |
692 |
> |
setFortranSim( &fInfo_, &nGlobalAtoms_, &nAtoms_, &identArray[0], &nExclude, excludeList , |
693 |
> |
&nGlobalExcludes, globalExcludes, &molMembershipArray[0], |
694 |
> |
&mfact[0], &nCutoffGroups_, &fortranGlobalGroupMembership[0], &isError); |
695 |
> |
|
696 |
> |
if( isError ){ |
697 |
> |
|
698 |
|
sprintf( painCave.errMsg, |
699 |
< |
"cutoffRadius is too large for the current periodic box.\n" |
511 |
< |
"\tCurrent Value of cutoffRadius = %G at time %G\n " |
512 |
< |
"\tThis is larger than half of at least one of the\n" |
513 |
< |
"\tperiodic box vectors. Right now, the Box matrix is:\n" |
514 |
< |
"\n" |
515 |
< |
"\t[ %G %G %G ]\n" |
516 |
< |
"\t[ %G %G %G ]\n" |
517 |
< |
"\t[ %G %G %G ]\n", |
518 |
< |
rCut, currentTime, |
519 |
< |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
520 |
< |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
521 |
< |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
522 |
< |
painCave.severity = OOPSE_ERROR; |
699 |
> |
"There was an error setting the simulation information in fortran.\n" ); |
700 |
|
painCave.isFatal = 1; |
701 |
+ |
painCave.severity = OOPSE_ERROR; |
702 |
|
simError(); |
703 |
< |
} |
704 |
< |
} else { |
705 |
< |
// initialize this stuff before using it, OK? |
706 |
< |
sprintf( painCave.errMsg, |
707 |
< |
"Trying to check cutoffs without a box.\n" |
708 |
< |
"\tOOPSE should have better programmers than that.\n" ); |
709 |
< |
painCave.severity = OOPSE_ERROR; |
532 |
< |
painCave.isFatal = 1; |
533 |
< |
simError(); |
703 |
> |
} |
704 |
> |
|
705 |
> |
#ifdef IS_MPI |
706 |
> |
sprintf( checkPointMsg, |
707 |
> |
"succesfully sent the simulation information to fortran.\n"); |
708 |
> |
MPIcheckPoint(); |
709 |
> |
#endif // is_mpi |
710 |
|
} |
535 |
– |
|
536 |
– |
} |
711 |
|
|
538 |
– |
void SimInfo::addProperty(GenericData* prop){ |
712 |
|
|
713 |
< |
map<string, GenericData*>::iterator result; |
714 |
< |
result = properties.find(prop->getID()); |
542 |
< |
|
543 |
< |
//we can't simply use properties[prop->getID()] = prop, |
544 |
< |
//it will cause memory leak if we already contain a propery which has the same name of prop |
545 |
< |
|
546 |
< |
if(result != properties.end()){ |
713 |
> |
#ifdef IS_MPI |
714 |
> |
void SimInfo::setupFortranParallel() { |
715 |
|
|
716 |
< |
delete (*result).second; |
717 |
< |
(*result).second = prop; |
718 |
< |
|
719 |
< |
} |
720 |
< |
else{ |
716 |
> |
//SimInfo is responsible for creating localToGlobalAtomIndex and localToGlobalGroupIndex |
717 |
> |
std::vector<int> localToGlobalAtomIndex(getNAtoms(), 0); |
718 |
> |
std::vector<int> localToGlobalCutoffGroupIndex; |
719 |
> |
SimInfo::MoleculeIterator mi; |
720 |
> |
Molecule::AtomIterator ai; |
721 |
> |
Molecule::CutoffGroupIterator ci; |
722 |
> |
Molecule* mol; |
723 |
> |
Atom* atom; |
724 |
> |
CutoffGroup* cg; |
725 |
> |
mpiSimData parallelData; |
726 |
> |
int isError; |
727 |
|
|
728 |
< |
properties[prop->getID()] = prop; |
728 |
> |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
729 |
|
|
730 |
+ |
//local index(index in DataStorge) of atom is important |
731 |
+ |
for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
732 |
+ |
localToGlobalAtomIndex[atom->getLocalIndex()] = atom->getGlobalIndex() + 1; |
733 |
+ |
} |
734 |
+ |
|
735 |
+ |
//local index of cutoff group is trivial, it only depends on the order of travesing |
736 |
+ |
for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) { |
737 |
+ |
localToGlobalCutoffGroupIndex.push_back(cg->getGlobalIndex() + 1); |
738 |
+ |
} |
739 |
+ |
|
740 |
+ |
} |
741 |
+ |
|
742 |
+ |
//fill up mpiSimData struct |
743 |
+ |
parallelData.nMolGlobal = getNGlobalMolecules(); |
744 |
+ |
parallelData.nMolLocal = getNMolecules(); |
745 |
+ |
parallelData.nAtomsGlobal = getNGlobalAtoms(); |
746 |
+ |
parallelData.nAtomsLocal = getNAtoms(); |
747 |
+ |
parallelData.nGroupsGlobal = getNGlobalCutoffGroups(); |
748 |
+ |
parallelData.nGroupsLocal = getNCutoffGroups(); |
749 |
+ |
parallelData.myNode = worldRank; |
750 |
+ |
MPI_Comm_size(MPI_COMM_WORLD, &(parallelData.nProcessors)); |
751 |
+ |
|
752 |
+ |
//pass mpiSimData struct and index arrays to fortran |
753 |
+ |
setFsimParallel(¶llelData, &(parallelData.nAtomsLocal), |
754 |
+ |
&localToGlobalAtomIndex[0], &(parallelData.nGroupsLocal), |
755 |
+ |
&localToGlobalCutoffGroupIndex[0], &isError); |
756 |
+ |
|
757 |
+ |
if (isError) { |
758 |
+ |
sprintf(painCave.errMsg, |
759 |
+ |
"mpiRefresh errror: fortran didn't like something we gave it.\n"); |
760 |
+ |
painCave.isFatal = 1; |
761 |
+ |
simError(); |
762 |
+ |
} |
763 |
+ |
|
764 |
+ |
sprintf(checkPointMsg, " mpiRefresh successful.\n"); |
765 |
+ |
MPIcheckPoint(); |
766 |
+ |
|
767 |
+ |
|
768 |
|
} |
557 |
– |
|
558 |
– |
} |
769 |
|
|
770 |
< |
GenericData* SimInfo::getProperty(const string& propName){ |
561 |
< |
|
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; |
572 |
< |
} |
770 |
> |
#endif |
771 |
|
|
772 |
+ |
double SimInfo::calcMaxCutoffRadius() { |
773 |
|
|
575 |
– |
void SimInfo::getFortranGroupArrays(SimInfo* info, |
576 |
– |
vector<int>& FglobalGroupMembership, |
577 |
– |
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 |
– |
|
774 |
|
|
775 |
< |
// Fix the silly fortran indexing problem |
775 |
> |
std::set<AtomType*> atomTypes; |
776 |
> |
std::set<AtomType*>::iterator i; |
777 |
> |
std::vector<double> cutoffRadius; |
778 |
> |
|
779 |
> |
//get the unique atom types |
780 |
> |
atomTypes = getUniqueAtomTypes(); |
781 |
> |
|
782 |
> |
//query the max cutoff radius among these atom types |
783 |
> |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
784 |
> |
cutoffRadius.push_back(forceField_->getRcutFromAtomType(*i)); |
785 |
> |
} |
786 |
> |
|
787 |
> |
double maxCutoffRadius = *(std::max_element(cutoffRadius.begin(), cutoffRadius.end())); |
788 |
|
#ifdef IS_MPI |
789 |
< |
numAtom = mpiSim->getNAtomsGlobal(); |
599 |
< |
#else |
600 |
< |
numAtom = n_atoms; |
789 |
> |
//pick the max cutoff radius among the processors |
790 |
|
#endif |
602 |
– |
for (int i = 0; i < numAtom; i++) |
603 |
– |
FglobalGroupMembership.push_back(globalGroupMembership[i] + 1); |
604 |
– |
|
791 |
|
|
792 |
< |
myMols = info->molecules; |
793 |
< |
numMol = info->n_mol; |
608 |
< |
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)){ |
792 |
> |
return maxCutoffRadius; |
793 |
> |
} |
794 |
|
|
795 |
< |
totalMass = myCutoffGroup->getMass(); |
796 |
< |
|
797 |
< |
for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); |
798 |
< |
cutoffAtom != NULL; |
799 |
< |
cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){ |
800 |
< |
mfact.push_back(cutoffAtom->getMass()/totalMass); |
801 |
< |
} |
795 |
> |
void SimInfo::getCutoff(double& rcut, double& rsw) { |
796 |
> |
|
797 |
> |
if (fInfo_.SIM_uses_Charges | fInfo_.SIM_uses_Dipoles | fInfo_.SIM_uses_RF) { |
798 |
> |
|
799 |
> |
if (!simParams_->haveRcut()){ |
800 |
> |
sprintf(painCave.errMsg, |
801 |
> |
"SimCreator Warning: No value was set for the cutoffRadius.\n" |
802 |
> |
"\tOOPSE will use a default value of 15.0 angstroms" |
803 |
> |
"\tfor the cutoffRadius.\n"); |
804 |
> |
painCave.isFatal = 0; |
805 |
> |
simError(); |
806 |
> |
rcut = 15.0; |
807 |
> |
} else{ |
808 |
> |
rcut = simParams_->getRcut(); |
809 |
> |
} |
810 |
> |
|
811 |
> |
if (!simParams_->haveRsw()){ |
812 |
> |
sprintf(painCave.errMsg, |
813 |
> |
"SimCreator Warning: No value was set for switchingRadius.\n" |
814 |
> |
"\tOOPSE will use a default value of\n" |
815 |
> |
"\t0.95 * cutoffRadius for the switchingRadius\n"); |
816 |
> |
painCave.isFatal = 0; |
817 |
> |
simError(); |
818 |
> |
rsw = 0.95 * rcut; |
819 |
> |
} else{ |
820 |
> |
rsw = simParams_->getRsw(); |
821 |
> |
} |
822 |
> |
|
823 |
> |
} else { |
824 |
> |
// if charge, dipole or reaction field is not used and the cutofff radius is not specified in |
825 |
> |
//meta-data file, the maximum cutoff radius calculated from forcefiled will be used |
826 |
> |
|
827 |
> |
if (simParams_->haveRcut()) { |
828 |
> |
rcut = simParams_->getRcut(); |
829 |
> |
} else { |
830 |
> |
//set cutoff radius to the maximum cutoff radius based on atom types in the whole system |
831 |
> |
rcut = calcMaxCutoffRadius(); |
832 |
> |
} |
833 |
> |
|
834 |
> |
if (simParams_->haveRsw()) { |
835 |
> |
rsw = simParams_->getRsw(); |
836 |
> |
} else { |
837 |
> |
rsw = rcut; |
838 |
> |
} |
839 |
> |
|
840 |
|
} |
841 |
|
} |
842 |
|
|
843 |
< |
} |
843 |
> |
void SimInfo::setupCutoff() { |
844 |
> |
getCutoff(rcut_, rsw_); |
845 |
> |
double rnblist = rcut_ + 1; // skin of neighbor list |
846 |
> |
|
847 |
> |
//Pass these cutoff radius etc. to fortran. This function should be called once and only once |
848 |
> |
|
849 |
> |
int cp = TRADITIONAL_CUTOFF_POLICY; |
850 |
> |
if (simParams_->haveCutoffPolicy()) { |
851 |
> |
std::string myPolicy = simParams_->getCutoffPolicy(); |
852 |
> |
if (myPolicy == "MIX") { |
853 |
> |
cp = MIX_CUTOFF_POLICY; |
854 |
> |
} else { |
855 |
> |
if (myPolicy == "MAX") { |
856 |
> |
cp = MAX_CUTOFF_POLICY; |
857 |
> |
} else { |
858 |
> |
if (myPolicy == "TRADITIONAL") { |
859 |
> |
cp = TRADITIONAL_CUTOFF_POLICY; |
860 |
> |
} else { |
861 |
> |
// throw error |
862 |
> |
sprintf( painCave.errMsg, |
863 |
> |
"SimInfo error: Unknown cutoffPolicy. (Input file specified %s .)\n\tcutoffPolicy must be one of: \"Mix\", \"Max\", or \"Traditional\".", myPolicy.c_str() ); |
864 |
> |
painCave.isFatal = 1; |
865 |
> |
simError(); |
866 |
> |
} |
867 |
> |
} |
868 |
> |
} |
869 |
> |
} |
870 |
> |
notifyFortranCutoffs(&rcut_, &rsw_, &rnblist, &cp); |
871 |
> |
} |
872 |
> |
|
873 |
> |
void SimInfo::setupCoulombicCorrection( int isError ) { |
874 |
> |
|
875 |
> |
int errorOut; |
876 |
> |
int cc = NONE; |
877 |
> |
double alphaVal; |
878 |
> |
|
879 |
> |
errorOut = isError; |
880 |
> |
|
881 |
> |
if (simParams_->haveCoulombicCorrection()) { |
882 |
> |
std::string myCorrection = simParams_->getCoulombicCorrection(); |
883 |
> |
if (myCorrection == "NONE") { |
884 |
> |
cc = NONE; |
885 |
> |
} else { |
886 |
> |
if (myCorrection == "UNDAMPED_WOLF") { |
887 |
> |
cc = UNDAMPED_WOLF; |
888 |
> |
} else { |
889 |
> |
if (myCorrection == "WOLF") { |
890 |
> |
cc = WOLF; |
891 |
> |
if (!simParams_->haveDampingAlpha()) { |
892 |
> |
//throw error |
893 |
> |
sprintf( painCave.errMsg, |
894 |
> |
"SimInfo warning: dampingAlpha was not specified in the input file. A default value of %f (1/ang) will be used for the Wolf Coulombic Correction.", simParams_->getDampingAlpha()); |
895 |
> |
painCave.isFatal = 0; |
896 |
> |
simError(); |
897 |
> |
} |
898 |
> |
alphaVal = simParams_->getDampingAlpha(); |
899 |
> |
} else { |
900 |
> |
if (myCorrection == "REACTION_FIELD") { |
901 |
> |
cc = REACTION_FIELD; |
902 |
> |
} else { |
903 |
> |
// throw error |
904 |
> |
sprintf( painCave.errMsg, |
905 |
> |
"SimInfo error: Unknown coulombicCorrection. (Input file specified %s .)\n\tcoulombicCorrection must be one of: \"none\", \"undamped_wolf\", \"wolf\", or \"reaction_field\".", myCorrection.c_str() ); |
906 |
> |
painCave.isFatal = 1; |
907 |
> |
simError(); |
908 |
> |
} |
909 |
> |
} |
910 |
> |
} |
911 |
> |
} |
912 |
> |
} |
913 |
> |
initFortranFF( &fInfo_.SIM_uses_RF, &cc, &alphaVal, &errorOut ); |
914 |
> |
} |
915 |
> |
|
916 |
> |
void SimInfo::addProperty(GenericData* genData) { |
917 |
> |
properties_.addProperty(genData); |
918 |
> |
} |
919 |
> |
|
920 |
> |
void SimInfo::removeProperty(const std::string& propName) { |
921 |
> |
properties_.removeProperty(propName); |
922 |
> |
} |
923 |
> |
|
924 |
> |
void SimInfo::clearProperties() { |
925 |
> |
properties_.clearProperties(); |
926 |
> |
} |
927 |
> |
|
928 |
> |
std::vector<std::string> SimInfo::getPropertyNames() { |
929 |
> |
return properties_.getPropertyNames(); |
930 |
> |
} |
931 |
> |
|
932 |
> |
std::vector<GenericData*> SimInfo::getProperties() { |
933 |
> |
return properties_.getProperties(); |
934 |
> |
} |
935 |
> |
|
936 |
> |
GenericData* SimInfo::getPropertyByName(const std::string& propName) { |
937 |
> |
return properties_.getPropertyByName(propName); |
938 |
> |
} |
939 |
> |
|
940 |
> |
void SimInfo::setSnapshotManager(SnapshotManager* sman) { |
941 |
> |
if (sman_ == sman) { |
942 |
> |
return; |
943 |
> |
} |
944 |
> |
delete sman_; |
945 |
> |
sman_ = sman; |
946 |
> |
|
947 |
> |
Molecule* mol; |
948 |
> |
RigidBody* rb; |
949 |
> |
Atom* atom; |
950 |
> |
SimInfo::MoleculeIterator mi; |
951 |
> |
Molecule::RigidBodyIterator rbIter; |
952 |
> |
Molecule::AtomIterator atomIter;; |
953 |
> |
|
954 |
> |
for (mol = beginMolecule(mi); mol != NULL; mol = nextMolecule(mi)) { |
955 |
> |
|
956 |
> |
for (atom = mol->beginAtom(atomIter); atom != NULL; atom = mol->nextAtom(atomIter)) { |
957 |
> |
atom->setSnapshotManager(sman_); |
958 |
> |
} |
959 |
> |
|
960 |
> |
for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) { |
961 |
> |
rb->setSnapshotManager(sman_); |
962 |
> |
} |
963 |
> |
} |
964 |
> |
|
965 |
> |
} |
966 |
> |
|
967 |
> |
Vector3d SimInfo::getComVel(){ |
968 |
> |
SimInfo::MoleculeIterator i; |
969 |
> |
Molecule* mol; |
970 |
> |
|
971 |
> |
Vector3d comVel(0.0); |
972 |
> |
double totalMass = 0.0; |
973 |
> |
|
974 |
> |
|
975 |
> |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
976 |
> |
double mass = mol->getMass(); |
977 |
> |
totalMass += mass; |
978 |
> |
comVel += mass * mol->getComVel(); |
979 |
> |
} |
980 |
> |
|
981 |
> |
#ifdef IS_MPI |
982 |
> |
double tmpMass = totalMass; |
983 |
> |
Vector3d tmpComVel(comVel); |
984 |
> |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
985 |
> |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
986 |
> |
#endif |
987 |
> |
|
988 |
> |
comVel /= totalMass; |
989 |
> |
|
990 |
> |
return comVel; |
991 |
> |
} |
992 |
> |
|
993 |
> |
Vector3d SimInfo::getCom(){ |
994 |
> |
SimInfo::MoleculeIterator i; |
995 |
> |
Molecule* mol; |
996 |
> |
|
997 |
> |
Vector3d com(0.0); |
998 |
> |
double totalMass = 0.0; |
999 |
> |
|
1000 |
> |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1001 |
> |
double mass = mol->getMass(); |
1002 |
> |
totalMass += mass; |
1003 |
> |
com += mass * mol->getCom(); |
1004 |
> |
} |
1005 |
> |
|
1006 |
> |
#ifdef IS_MPI |
1007 |
> |
double tmpMass = totalMass; |
1008 |
> |
Vector3d tmpCom(com); |
1009 |
> |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1010 |
> |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1011 |
> |
#endif |
1012 |
> |
|
1013 |
> |
com /= totalMass; |
1014 |
> |
|
1015 |
> |
return com; |
1016 |
> |
|
1017 |
> |
} |
1018 |
> |
|
1019 |
> |
std::ostream& operator <<(std::ostream& o, SimInfo& info) { |
1020 |
> |
|
1021 |
> |
return o; |
1022 |
> |
} |
1023 |
> |
|
1024 |
> |
|
1025 |
> |
/* |
1026 |
> |
Returns center of mass and center of mass velocity in one function call. |
1027 |
> |
*/ |
1028 |
> |
|
1029 |
> |
void SimInfo::getComAll(Vector3d &com, Vector3d &comVel){ |
1030 |
> |
SimInfo::MoleculeIterator i; |
1031 |
> |
Molecule* mol; |
1032 |
> |
|
1033 |
> |
|
1034 |
> |
double totalMass = 0.0; |
1035 |
> |
|
1036 |
> |
|
1037 |
> |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1038 |
> |
double mass = mol->getMass(); |
1039 |
> |
totalMass += mass; |
1040 |
> |
com += mass * mol->getCom(); |
1041 |
> |
comVel += mass * mol->getComVel(); |
1042 |
> |
} |
1043 |
> |
|
1044 |
> |
#ifdef IS_MPI |
1045 |
> |
double tmpMass = totalMass; |
1046 |
> |
Vector3d tmpCom(com); |
1047 |
> |
Vector3d tmpComVel(comVel); |
1048 |
> |
MPI_Allreduce(&tmpMass,&totalMass,1,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1049 |
> |
MPI_Allreduce(tmpCom.getArrayPointer(), com.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1050 |
> |
MPI_Allreduce(tmpComVel.getArrayPointer(), comVel.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1051 |
> |
#endif |
1052 |
> |
|
1053 |
> |
com /= totalMass; |
1054 |
> |
comVel /= totalMass; |
1055 |
> |
} |
1056 |
> |
|
1057 |
> |
/* |
1058 |
> |
Return intertia tensor for entire system and angular momentum Vector. |
1059 |
> |
|
1060 |
> |
|
1061 |
> |
[ Ixx -Ixy -Ixz ] |
1062 |
> |
J =| -Iyx Iyy -Iyz | |
1063 |
> |
[ -Izx -Iyz Izz ] |
1064 |
> |
*/ |
1065 |
> |
|
1066 |
> |
void SimInfo::getInertiaTensor(Mat3x3d &inertiaTensor, Vector3d &angularMomentum){ |
1067 |
> |
|
1068 |
> |
|
1069 |
> |
double xx = 0.0; |
1070 |
> |
double yy = 0.0; |
1071 |
> |
double zz = 0.0; |
1072 |
> |
double xy = 0.0; |
1073 |
> |
double xz = 0.0; |
1074 |
> |
double yz = 0.0; |
1075 |
> |
Vector3d com(0.0); |
1076 |
> |
Vector3d comVel(0.0); |
1077 |
> |
|
1078 |
> |
getComAll(com, comVel); |
1079 |
> |
|
1080 |
> |
SimInfo::MoleculeIterator i; |
1081 |
> |
Molecule* mol; |
1082 |
> |
|
1083 |
> |
Vector3d thisq(0.0); |
1084 |
> |
Vector3d thisv(0.0); |
1085 |
> |
|
1086 |
> |
double thisMass = 0.0; |
1087 |
> |
|
1088 |
> |
|
1089 |
> |
|
1090 |
> |
|
1091 |
> |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1092 |
> |
|
1093 |
> |
thisq = mol->getCom()-com; |
1094 |
> |
thisv = mol->getComVel()-comVel; |
1095 |
> |
thisMass = mol->getMass(); |
1096 |
> |
// Compute moment of intertia coefficients. |
1097 |
> |
xx += thisq[0]*thisq[0]*thisMass; |
1098 |
> |
yy += thisq[1]*thisq[1]*thisMass; |
1099 |
> |
zz += thisq[2]*thisq[2]*thisMass; |
1100 |
> |
|
1101 |
> |
// compute products of intertia |
1102 |
> |
xy += thisq[0]*thisq[1]*thisMass; |
1103 |
> |
xz += thisq[0]*thisq[2]*thisMass; |
1104 |
> |
yz += thisq[1]*thisq[2]*thisMass; |
1105 |
> |
|
1106 |
> |
angularMomentum += cross( thisq, thisv ) * thisMass; |
1107 |
> |
|
1108 |
> |
} |
1109 |
> |
|
1110 |
> |
|
1111 |
> |
inertiaTensor(0,0) = yy + zz; |
1112 |
> |
inertiaTensor(0,1) = -xy; |
1113 |
> |
inertiaTensor(0,2) = -xz; |
1114 |
> |
inertiaTensor(1,0) = -xy; |
1115 |
> |
inertiaTensor(1,1) = xx + zz; |
1116 |
> |
inertiaTensor(1,2) = -yz; |
1117 |
> |
inertiaTensor(2,0) = -xz; |
1118 |
> |
inertiaTensor(2,1) = -yz; |
1119 |
> |
inertiaTensor(2,2) = xx + yy; |
1120 |
> |
|
1121 |
> |
#ifdef IS_MPI |
1122 |
> |
Mat3x3d tmpI(inertiaTensor); |
1123 |
> |
Vector3d tmpAngMom; |
1124 |
> |
MPI_Allreduce(tmpI.getArrayPointer(), inertiaTensor.getArrayPointer(),9,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1125 |
> |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1126 |
> |
#endif |
1127 |
> |
|
1128 |
> |
return; |
1129 |
> |
} |
1130 |
> |
|
1131 |
> |
//Returns the angular momentum of the system |
1132 |
> |
Vector3d SimInfo::getAngularMomentum(){ |
1133 |
> |
|
1134 |
> |
Vector3d com(0.0); |
1135 |
> |
Vector3d comVel(0.0); |
1136 |
> |
Vector3d angularMomentum(0.0); |
1137 |
> |
|
1138 |
> |
getComAll(com,comVel); |
1139 |
> |
|
1140 |
> |
SimInfo::MoleculeIterator i; |
1141 |
> |
Molecule* mol; |
1142 |
> |
|
1143 |
> |
Vector3d thisr(0.0); |
1144 |
> |
Vector3d thisp(0.0); |
1145 |
> |
|
1146 |
> |
double thisMass; |
1147 |
> |
|
1148 |
> |
for (mol = beginMolecule(i); mol != NULL; mol = nextMolecule(i)) { |
1149 |
> |
thisMass = mol->getMass(); |
1150 |
> |
thisr = mol->getCom()-com; |
1151 |
> |
thisp = (mol->getComVel()-comVel)*thisMass; |
1152 |
> |
|
1153 |
> |
angularMomentum += cross( thisr, thisp ); |
1154 |
> |
|
1155 |
> |
} |
1156 |
> |
|
1157 |
> |
#ifdef IS_MPI |
1158 |
> |
Vector3d tmpAngMom; |
1159 |
> |
MPI_Allreduce(tmpAngMom.getArrayPointer(), angularMomentum.getArrayPointer(),3,MPI_DOUBLE,MPI_SUM, MPI_COMM_WORLD); |
1160 |
> |
#endif |
1161 |
> |
|
1162 |
> |
return angularMomentum; |
1163 |
> |
} |
1164 |
> |
|
1165 |
> |
|
1166 |
> |
}//end namespace oopse |
1167 |
> |
|