1 |
< |
/* |
2 |
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* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
3 |
< |
* |
4 |
< |
* Contact: oopse@oopse.org |
5 |
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* |
6 |
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* This program is free software; you can redistribute it and/or |
7 |
< |
* modify it under the terms of the GNU Lesser General Public License |
8 |
< |
* as published by the Free Software Foundation; either version 2.1 |
9 |
< |
* of the License, or (at your option) any later version. |
10 |
< |
* All we ask is that proper credit is given for our work, which includes |
11 |
< |
* - but is not limited to - adding the above copyright notice to the beginning |
12 |
< |
* of your source code files, and to any copyright notice that you may distribute |
13 |
< |
* with programs based on this work. |
14 |
< |
* |
15 |
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* This program is distributed in the hope that it will be useful, |
16 |
< |
* but WITHOUT ANY WARRANTY; without even the implied warranty of |
17 |
< |
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
18 |
< |
* GNU Lesser General Public License for more details. |
19 |
< |
* |
20 |
< |
* You should have received a copy of the GNU Lesser General Public License |
21 |
< |
* along with this program; if not, write to the Free Software |
22 |
< |
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
23 |
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* |
24 |
< |
*/ |
25 |
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|
26 |
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/** |
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* @file SimInfo.hpp |
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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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*/ |
32 |
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|
33 |
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#ifndef BRAINS_SIMMODEL_HPP |
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#define BRAINS_SIMMODEL_HPP |
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#include <vector> |
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#include <iostream> |
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|
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#include "brains/fSimulation.h" |
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#include "primitives/Molecule.hpp" |
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#include "utils/PropertyMap.hpp" |
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|
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namespace oopse{ |
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|
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/** |
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* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" |
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* @brief |
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*/ |
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class SimInfo { |
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public: |
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SimInfo(); |
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virtual ~SimInfo(); |
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|
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/** |
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* Adds a molecule |
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* @return return true if adding successfully, return false if the molecule is already in SimInfo |
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* @param mol molecule to be added |
57 |
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*/ |
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bool addMolecule(Molecule* mol); |
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|
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/** |
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* Removes a molecule from SimInfo |
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* @return true if removing successfully, return false if molecule is not in this SimInfo |
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*/ |
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bool removeMolecule(Molecule* mol); |
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|
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/** |
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* Returns the number of molecules. |
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* @return the number of molecules in this SimInfo |
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*/ |
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int getNMolecules() { |
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return molecules_.size(); |
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} |
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|
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/** Returns the total number of atoms in this SimInfo */ |
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unsigned int getNAtoms() { |
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return nAtoms_; |
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} |
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|
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/** Returns the total number of bonds in this SimInfo */ |
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unsigned int getNBonds(){ |
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return nBonds_; |
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} |
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|
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/** Returns the total number of bends in this SimInfo */ |
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unsigned int getNBends() { |
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return nBends_; |
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} |
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|
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/** Returns the total number of torsions in this SimInfo */ |
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unsigned int getNTorsions() { |
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return nTorsions_; |
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} |
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|
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/** Returns the total number of rigid bodies in this SimInfo */ |
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unsigned int getNRigidBodies() { |
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return nRigidBodies_; |
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} |
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|
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/** Returns the total number of integrable objects in this SimInfo */ |
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unsigned int getNIntegrableObjects() { |
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return nIntegrableObjects_; |
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} |
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|
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/** Returns the total number of cutoff groups in this SimInfo */ |
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unsigned int getNCutoffGroups() { |
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return nCutoffGroups_; |
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} |
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|
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/** Returns the total number of constraints in this SimInfo */ |
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unsigned int getNConstraints() { |
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return nConstraints_; |
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} |
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|
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/** |
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* Returns the first molecule in this SimInfo and intialize the iterator. |
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* @return the first molecule, return NULL if there is not molecule in this SimInfo |
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* @param i the iterator of molecule array (user shouldn't change it) |
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*/ |
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Molecule* beginMolecule(std::vector<Molecule*>::iterator& i); |
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|
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/** |
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* Returns the next avaliable Molecule based on the iterator. |
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* @return the next avaliable molecule, return NULL if reaching the end of the array |
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* @param i the iterator of molecule array |
125 |
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*/ |
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Molecule* nextMolecule(std::vector<Molecule*>::iterator& i); |
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|
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/** Returns the number of degrees of freedom */ |
129 |
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int getNDF() { |
130 |
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return ndf_; |
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} |
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|
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/** Returns the number of raw degrees of freedom */ |
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int getNDFRaw() { |
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return ndfRaw_; |
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} |
137 |
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|
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/** Returns the number of translational degrees of freedom */ |
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int getNDFTrans() { |
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return ndfTrans_; |
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} |
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|
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/** Returns the snapshot manager. */ |
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SnapshotManager* getSnapshotManager() { |
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return sman_; |
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} |
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|
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/** Sets the snapshot manager. */ |
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void setSnapshotManager(SnapshotManager* sman) { |
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sman_ = sman; |
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} |
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|
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ForceField* getForceField() { |
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return forceField_; |
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} |
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|
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void setForceField(ForceField* ff) { |
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forceField_ = ff; |
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} |
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private: |
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|
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void calcNDF(); |
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void calcNDFRaw(); |
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void calcNDFTrans(); |
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|
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int ndf_; |
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int ndfRaw_; |
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int ndfTrans_; |
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|
170 |
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int nAtoms_; |
171 |
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int nBonds_; |
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int nBends_; |
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int nTorsions_; |
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int nRigidBodies_; |
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int nIntegrableObjects_; |
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int nCutoffGroups_; |
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int nConstraints_; |
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|
179 |
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simtype fInfo; |
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Exclude excludeList; |
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ForceField* forceField_; |
182 |
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|
183 |
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std::vector<Molecule*> molecules_; /**< Molecule array */ |
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PropertyMap properties_; /** Generic Property */ |
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SnapshotManager* sman_; /** SnapshotManager */ |
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|
187 |
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}; |
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|
189 |
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} //namespace oopse |
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#endif //BRAINS_SIMMODEL_HPP |
1 |
> |
/* |
2 |
> |
* Copyright (C) 2000-2004 Object Oriented Parallel Simulation Engine (OOPSE) project |
3 |
> |
* |
4 |
> |
* Contact: oopse@oopse.org |
5 |
> |
* |
6 |
> |
* This program is free software; you can redistribute it and/or |
7 |
> |
* modify it under the terms of the GNU Lesser General Public License |
8 |
> |
* as published by the Free Software Foundation; either version 2.1 |
9 |
> |
* of the License, or (at your option) any later version. |
10 |
> |
* All we ask is that proper credit is given for our work, which includes |
11 |
> |
* - but is not limited to - adding the above copyright notice to the beginning |
12 |
> |
* of your source code files, and to any copyright notice that you may distribute |
13 |
> |
* with programs based on this work. |
14 |
> |
* |
15 |
> |
* This program is distributed in the hope that it will be useful, |
16 |
> |
* but WITHOUT ANY WARRANTY; without even the implied warranty of |
17 |
> |
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
18 |
> |
* GNU Lesser General Public License for more details. |
19 |
> |
* |
20 |
> |
* You should have received a copy of the GNU Lesser General Public License |
21 |
> |
* along with this program; if not, write to the Free Software |
22 |
> |
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. |
23 |
> |
* |
24 |
> |
*/ |
25 |
> |
|
26 |
> |
/** |
27 |
> |
* @file SimInfo.hpp |
28 |
> |
* @author tlin |
29 |
> |
* @date 11/02/2004 |
30 |
> |
* @version 1.0 |
31 |
> |
*/ |
32 |
> |
|
33 |
> |
#ifndef BRAINS_SIMMODEL_HPP |
34 |
> |
#define BRAINS_SIMMODEL_HPP |
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> |
|
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> |
#include <iostream> |
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#include <set> |
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#include <utility> |
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#include <vector> |
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|
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#include "brains/Exclude.hpp" |
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> |
#include "io/Globals.hpp" |
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> |
#include "math/Vector3.hpp" |
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> |
#include "types/MoleculeStamp.hpp" |
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> |
#include "UseTheForce/ForceField.hpp" |
46 |
> |
#include "utils/PropertyMap.hpp" |
47 |
> |
#include "utils/LocalIndexManager.hpp" |
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> |
|
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> |
//another nonsense macro declaration |
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#define __C |
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#include "brains/fSimulation.h" |
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|
53 |
> |
namespace oopse{ |
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|
55 |
> |
//forward decalration |
56 |
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class SnapshotManager; |
57 |
> |
class Molecule; |
58 |
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|
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/** |
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* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" |
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* @brief As one of the heavy weight class of OOPSE, SimInfo |
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> |
* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules. |
63 |
> |
* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies, |
64 |
> |
* cutoff groups, constrains). |
65 |
> |
* Another major change is the index. No matter single version or parallel version, atoms and |
66 |
> |
* rigid bodies have both global index and local index. Local index is not important to molecule as well as |
67 |
> |
* cutoff group. |
68 |
> |
*/ |
69 |
> |
class SimInfo { |
70 |
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public: |
71 |
> |
typedef std::map<int, Molecule*>::iterator MoleculeIterator; |
72 |
> |
|
73 |
> |
/** |
74 |
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* Constructor of SimInfo |
75 |
> |
* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the |
76 |
> |
* second element is the total number of molecules with the same molecule stamp in the system |
77 |
> |
* @param ff pointer of a concrete ForceField instance |
78 |
> |
* @param globals |
79 |
> |
* @note |
80 |
> |
*/ |
81 |
> |
SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* globals); |
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virtual ~SimInfo(); |
83 |
> |
|
84 |
> |
/** |
85 |
> |
* Adds a molecule |
86 |
> |
* @return return true if adding successfully, return false if the molecule is already in SimInfo |
87 |
> |
* @param mol molecule to be added |
88 |
> |
*/ |
89 |
> |
bool addMolecule(Molecule* mol); |
90 |
> |
|
91 |
> |
/** |
92 |
> |
* Removes a molecule from SimInfo |
93 |
> |
* @return true if removing successfully, return false if molecule is not in this SimInfo |
94 |
> |
*/ |
95 |
> |
bool removeMolecule(Molecule* mol); |
96 |
> |
|
97 |
> |
/** Returns the total number of molecules in the system. */ |
98 |
> |
int getNGlobalMolecules() { |
99 |
> |
return nGlobalMols_; |
100 |
> |
} |
101 |
> |
|
102 |
> |
/** Returns the total number of atoms in the system. */ |
103 |
> |
int getNGlobalAtoms() { |
104 |
> |
return nGlobalAtoms_; |
105 |
> |
} |
106 |
> |
|
107 |
> |
/** Returns the total number of cutoff groups in the system. */ |
108 |
> |
int getNGlobalCutoffGroups() { |
109 |
> |
return nGlobalCutoffGroups_; |
110 |
> |
} |
111 |
> |
|
112 |
> |
/** |
113 |
> |
* Returns the total number of integrable objects (total number of rigid bodies plus the total number |
114 |
> |
* of atoms which do not belong to the rigid bodies) in the system |
115 |
> |
*/ |
116 |
> |
int getNGlobalIntegrableObjects() { |
117 |
> |
return nGlobalIntegrableObjects_; |
118 |
> |
} |
119 |
> |
|
120 |
> |
/** |
121 |
> |
* Returns the number of local molecules. |
122 |
> |
* @return the number of local molecules |
123 |
> |
*/ |
124 |
> |
int getNMolecules() { |
125 |
> |
return molecules_.size(); |
126 |
> |
} |
127 |
> |
|
128 |
> |
/** Returns the number of local atoms */ |
129 |
> |
unsigned int getNAtoms() { |
130 |
> |
return nAtoms_; |
131 |
> |
} |
132 |
> |
|
133 |
> |
/** Returns the number of local bonds */ |
134 |
> |
unsigned int getNBonds(){ |
135 |
> |
return nBonds_; |
136 |
> |
} |
137 |
> |
|
138 |
> |
/** Returns the number of local bends */ |
139 |
> |
unsigned int getNBends() { |
140 |
> |
return nBends_; |
141 |
> |
} |
142 |
> |
|
143 |
> |
/** Returns the number of local torsions */ |
144 |
> |
unsigned int getNTorsions() { |
145 |
> |
return nTorsions_; |
146 |
> |
} |
147 |
> |
|
148 |
> |
/** Returns the number of local rigid bodies */ |
149 |
> |
unsigned int getNRigidBodies() { |
150 |
> |
return nRigidBodies_; |
151 |
> |
} |
152 |
> |
|
153 |
> |
/** Returns the number of local integrable objects */ |
154 |
> |
unsigned int getNIntegrableObjects() { |
155 |
> |
return nIntegrableObjects_; |
156 |
> |
} |
157 |
> |
|
158 |
> |
/** Returns the number of local cutoff groups */ |
159 |
> |
unsigned int getNCutoffGroups() { |
160 |
> |
return nCutoffGroups_; |
161 |
> |
} |
162 |
> |
|
163 |
> |
/** Returns the total number of constraints in this SimInfo */ |
164 |
> |
unsigned int getNConstraints() { |
165 |
> |
return nConstraints_; |
166 |
> |
} |
167 |
> |
|
168 |
> |
/** |
169 |
> |
* Returns the first molecule in this SimInfo and intialize the iterator. |
170 |
> |
* @return the first molecule, return NULL if there is not molecule in this SimInfo |
171 |
> |
* @param i the iterator of molecule array (user shouldn't change it) |
172 |
> |
*/ |
173 |
> |
Molecule* beginMolecule(MoleculeIterator& i); |
174 |
> |
|
175 |
> |
/** |
176 |
> |
* Returns the next avaliable Molecule based on the iterator. |
177 |
> |
* @return the next avaliable molecule, return NULL if reaching the end of the array |
178 |
> |
* @param i the iterator of molecule array |
179 |
> |
*/ |
180 |
> |
Molecule* nextMolecule(MoleculeIterator& i); |
181 |
> |
|
182 |
> |
/** Returns the number of degrees of freedom */ |
183 |
> |
int getNdf() { |
184 |
> |
return ndf_; |
185 |
> |
} |
186 |
> |
|
187 |
> |
/** Returns the number of raw degrees of freedom */ |
188 |
> |
int getNdfRaw() { |
189 |
> |
return ndfRaw_; |
190 |
> |
} |
191 |
> |
|
192 |
> |
/** Returns the number of translational degrees of freedom */ |
193 |
> |
int getNdfTrans() { |
194 |
> |
return ndfTrans_; |
195 |
> |
} |
196 |
> |
|
197 |
> |
//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying |
198 |
> |
|
199 |
> |
/** Returns the total number of z-constraint molecules in the system */ |
200 |
> |
int getNZconstraint() { |
201 |
> |
return nZconstraint_; |
202 |
> |
} |
203 |
> |
|
204 |
> |
/** |
205 |
> |
* Sets the number of z-constraint molecules in the system. |
206 |
> |
*/ |
207 |
> |
void setNZconstraint(int nZconstraint) { |
208 |
> |
nZconstraint_ = nZconstraint; |
209 |
> |
} |
210 |
> |
|
211 |
> |
/** Returns the snapshot manager. */ |
212 |
> |
SnapshotManager* getSnapshotManager() { |
213 |
> |
return sman_; |
214 |
> |
} |
215 |
> |
|
216 |
> |
/** Sets the snapshot manager. */ |
217 |
> |
void setSnapshotManager(SnapshotManager* sman) { |
218 |
> |
sman_ = sman; |
219 |
> |
} |
220 |
> |
|
221 |
> |
/** Returns the force field */ |
222 |
> |
ForceField* getForceField() { |
223 |
> |
return forceField_; |
224 |
> |
} |
225 |
> |
|
226 |
> |
Globals* getGlobals() { |
227 |
> |
return globals_; |
228 |
> |
} |
229 |
> |
|
230 |
> |
/** Returns the velocity of center of mass of the whole system.*/ |
231 |
> |
Vector3d getComVel(); |
232 |
> |
|
233 |
> |
/** Returns the center of the mass of the whole system.*/ |
234 |
> |
Vector3d getCom(); |
235 |
> |
|
236 |
> |
/** Returns the seed (used for random number generator) */ |
237 |
> |
int getSeed() { |
238 |
> |
return seed_; |
239 |
> |
} |
240 |
> |
|
241 |
> |
/** Sets the seed*/ |
242 |
> |
void setSeed(int seed) { |
243 |
> |
seed_ = seed; |
244 |
> |
} |
245 |
> |
|
246 |
> |
/** main driver function to interact with fortran during the initialization and molecule migration */ |
247 |
> |
void update(); |
248 |
> |
|
249 |
> |
/** Returns the local index manager */ |
250 |
> |
LocalIndexManager* getLocalIndexManager() { |
251 |
> |
return &localIndexMan_; |
252 |
> |
} |
253 |
> |
|
254 |
> |
int getMoleculeStampId(int globalIndex) { |
255 |
> |
//assert(globalIndex < molStampIds_.size()) |
256 |
> |
return molStampIds_[globalIndex]; |
257 |
> |
} |
258 |
> |
|
259 |
> |
/** Returns the molecule stamp */ |
260 |
> |
MoleculeStamp* getMoleculeStamp(int id) { |
261 |
> |
return moleculeStamps_[id]; |
262 |
> |
} |
263 |
> |
|
264 |
> |
/** |
265 |
> |
* Finds a molecule with a specified global index |
266 |
> |
* @return a pointer point to found molecule |
267 |
> |
* @param index |
268 |
> |
*/ |
269 |
> |
Molecule* getMoleculeByGlobalIndex(int index) { |
270 |
> |
MoleculeIterator i; |
271 |
> |
i = molecules_.find(index); |
272 |
> |
|
273 |
> |
return i != molecules_.end() ? i->second : NULL; |
274 |
> |
} |
275 |
> |
|
276 |
> |
/** Calculate the maximum cutoff radius based on the atom types */ |
277 |
> |
double calcMaxCutoffRadius(); |
278 |
> |
|
279 |
> |
double getRcut() { |
280 |
> |
return rcut_; |
281 |
> |
} |
282 |
> |
|
283 |
> |
double getRsw() { |
284 |
> |
return rsw_; |
285 |
> |
} |
286 |
> |
|
287 |
> |
std::string getFinalConfigFileName() { |
288 |
> |
return finalConfigFileName_; |
289 |
> |
} |
290 |
> |
|
291 |
> |
void setFinalConfigFileName(const std::string& fileName) { |
292 |
> |
finalConfigFileName_ = fileName; |
293 |
> |
} |
294 |
> |
|
295 |
> |
std::string getDumpFileName() { |
296 |
> |
return dumpFileName_; |
297 |
> |
} |
298 |
> |
|
299 |
> |
void setDumpFileName(const std::string& fileName) { |
300 |
> |
dumpFileName_ = fileName; |
301 |
> |
} |
302 |
> |
|
303 |
> |
std::string getStatFileName() { |
304 |
> |
return statFileName_; |
305 |
> |
} |
306 |
> |
|
307 |
> |
void setStatFileName(const std::string& fileName) { |
308 |
> |
statFileName_ = fileName; |
309 |
> |
} |
310 |
> |
|
311 |
> |
/** |
312 |
> |
* Returns the pointer of internal globalGroupMembership_ array. This array will be filled by SimCreator class |
313 |
> |
* @see #SimCreator::setGlobalIndex |
314 |
> |
*/ |
315 |
> |
int* getGlobalGroupMembershipPointer() { |
316 |
> |
return &globalGroupMembership_[0]; |
317 |
> |
} |
318 |
> |
|
319 |
> |
/** |
320 |
> |
* Returns the pointer of internal globalMolMembership_ array. This array will be filled by SimCreator class |
321 |
> |
* @see #SimCreator::setGlobalIndex |
322 |
> |
*/ |
323 |
> |
int* getGlobalMolMembershipPointer() { |
324 |
> |
return &globalMolMembership_[0]; |
325 |
> |
} |
326 |
> |
|
327 |
> |
|
328 |
> |
bool isFortranInitialized() { |
329 |
> |
return fortranInitialized_; |
330 |
> |
} |
331 |
> |
|
332 |
> |
//below functions are just forward functions |
333 |
> |
//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the |
334 |
> |
//the other hand, has-a relation need composing. |
335 |
> |
/** |
336 |
> |
* Adds property into property map |
337 |
> |
* @param genData GenericData to be added into PropertyMap |
338 |
> |
*/ |
339 |
> |
void addProperty(GenericData* genData); |
340 |
> |
|
341 |
> |
/** |
342 |
> |
* Removes property from PropertyMap by name |
343 |
> |
* @param propName the name of property to be removed |
344 |
> |
*/ |
345 |
> |
void removeProperty(const std::string& propName); |
346 |
> |
|
347 |
> |
/** |
348 |
> |
* clear all of the properties |
349 |
> |
*/ |
350 |
> |
void clearProperties(); |
351 |
> |
|
352 |
> |
/** |
353 |
> |
* Returns all names of properties |
354 |
> |
* @return all names of properties |
355 |
> |
*/ |
356 |
> |
std::vector<std::string> getPropertyNames(); |
357 |
> |
|
358 |
> |
/** |
359 |
> |
* Returns all of the properties in PropertyMap |
360 |
> |
* @return all of the properties in PropertyMap |
361 |
> |
*/ |
362 |
> |
std::vector<GenericData*> getProperties(); |
363 |
> |
|
364 |
> |
/** |
365 |
> |
* Returns property |
366 |
> |
* @param propName name of property |
367 |
> |
* @return a pointer point to property with propName. If no property named propName |
368 |
> |
* exists, return NULL |
369 |
> |
*/ |
370 |
> |
GenericData* getPropertyByName(const std::string& propName); |
371 |
> |
|
372 |
> |
friend std::ostream& operator <<(ostream& o, SimInfo& info); |
373 |
> |
|
374 |
> |
private: |
375 |
> |
|
376 |
> |
|
377 |
> |
/** Returns the unique atom types of local processor in an array */ |
378 |
> |
std::set<AtomType*> getUniqueAtomTypes(); |
379 |
> |
|
380 |
> |
/** fill up the simtype struct*/ |
381 |
> |
void setupSimType(); |
382 |
> |
|
383 |
> |
/** |
384 |
> |
* Setup Fortran Simulation |
385 |
> |
* @see #setupFortranParallel |
386 |
> |
*/ |
387 |
> |
void setupFortranSim(); |
388 |
> |
|
389 |
> |
/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */ |
390 |
> |
void setupCutoff(); |
391 |
> |
|
392 |
> |
/** Calculates the number of degress of freedom in the whole system */ |
393 |
> |
void calcNdf(); |
394 |
> |
void calcNdfRaw(); |
395 |
> |
void calcNdfTrans(); |
396 |
> |
|
397 |
> |
void addExcludePairs(Molecule* mol); |
398 |
> |
void removeExcludePairs(Molecule* mol); |
399 |
> |
|
400 |
> |
/** |
401 |
> |
* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole |
402 |
> |
* system. |
403 |
> |
*/ |
404 |
> |
void addMoleculeStamp(MoleculeStamp* molStamp, int nmol); |
405 |
> |
|
406 |
> |
std::map<int, Molecule*> molecules_; /**< Molecule array */ |
407 |
> |
|
408 |
> |
//degress of freedom |
409 |
> |
int ndf_; /**< number of degress of freedom (excludes constraints), ndf_ is local */ |
410 |
> |
int ndfRaw_; /**< number of degress of freedom (includes constraints), ndfRaw_ is local */ |
411 |
> |
int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */ |
412 |
> |
int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */ |
413 |
> |
|
414 |
> |
//number of global objects |
415 |
> |
int nGlobalMols_; /**< number of molecules in the system */ |
416 |
> |
int nGlobalAtoms_; /**< number of atoms in the system */ |
417 |
> |
int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */ |
418 |
> |
int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */ |
419 |
> |
|
420 |
> |
/** |
421 |
> |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
422 |
> |
* corresponding content is the global index of cutoff group this atom belong to. |
423 |
> |
* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
424 |
> |
*/ |
425 |
> |
std::vector<int> globalGroupMembership_; |
426 |
> |
|
427 |
> |
/** |
428 |
> |
* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the |
429 |
> |
* corresponding content is the global index of molecule this atom belong to. |
430 |
> |
* It is filled by SimCreator once and only once, since it is never changed during the simulation. |
431 |
> |
*/ |
432 |
> |
std::vector<int> globalMolMembership_; |
433 |
> |
|
434 |
> |
|
435 |
> |
std::vector<int> molStampIds_; /**< stamp id array of all molecules in the system */ |
436 |
> |
std::vector<MoleculeStamp*> moleculeStamps_; /**< molecule stamps array */ |
437 |
> |
|
438 |
> |
//number of local objects |
439 |
> |
int nAtoms_; /**< number of atoms in local processor */ |
440 |
> |
int nBonds_; /**< number of bonds in local processor */ |
441 |
> |
int nBends_; /**< number of bends in local processor */ |
442 |
> |
int nTorsions_; /**< number of torsions in local processor */ |
443 |
> |
int nRigidBodies_; /**< number of rigid bodies in local processor */ |
444 |
> |
int nIntegrableObjects_; /**< number of integrable objects in local processor */ |
445 |
> |
int nCutoffGroups_; /**< number of cutoff groups in local processor */ |
446 |
> |
int nConstraints_; /**< number of constraints in local processors */ |
447 |
> |
|
448 |
> |
simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/ |
449 |
> |
Exclude exclude_; |
450 |
> |
ForceField* forceField_; |
451 |
> |
PropertyMap properties_; /**< Generic Property */ |
452 |
> |
SnapshotManager* sman_; /**< SnapshotManager */ |
453 |
> |
Globals* globals_; |
454 |
> |
int seed_; /**< seed for random number generator */ |
455 |
> |
|
456 |
> |
/** |
457 |
> |
* The reason to have a local index manager is that when molecule is migrating to other processors, |
458 |
> |
* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the |
459 |
> |
* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager |
460 |
> |
* to make a efficient data moving plan. |
461 |
> |
*/ |
462 |
> |
LocalIndexManager localIndexMan_; |
463 |
> |
|
464 |
> |
//file names |
465 |
> |
std::string finalConfigFileName_; |
466 |
> |
std::string dumpFileName_; |
467 |
> |
std::string statFileName_; |
468 |
> |
|
469 |
> |
double rcut_; /**< cutoff radius*/ |
470 |
> |
double rsw_; /**< radius of switching function*/ |
471 |
> |
|
472 |
> |
bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */ |
473 |
> |
|
474 |
> |
#ifdef IS_MPI |
475 |
> |
//in Parallel version, we need MolToProc |
476 |
> |
public: |
477 |
> |
|
478 |
> |
/** |
479 |
> |
* Finds the processor where a molecule resides |
480 |
> |
* @return the id of the processor which contains the molecule |
481 |
> |
* @param globalIndex global Index of the molecule |
482 |
> |
*/ |
483 |
> |
int getMolToProc(int globalIndex) { |
484 |
> |
//assert(globalIndex < molToProcMap_.size()); |
485 |
> |
return molToProcMap_[globalIndex]; |
486 |
> |
} |
487 |
> |
|
488 |
> |
/** |
489 |
> |
* Returns the pointer of internal molToProcMap array. This array will be filled by SimCreator class |
490 |
> |
* @see #SimCreator::divideMolecules |
491 |
> |
*/ |
492 |
> |
int* getMolToProcMapPointer() { |
493 |
> |
return &molToProcMap_[0]; |
494 |
> |
} |
495 |
> |
|
496 |
> |
private: |
497 |
> |
|
498 |
> |
void setupFortranParallel(); |
499 |
> |
|
500 |
> |
/** |
501 |
> |
* The size of molToProcMap_ is equal to total number of molecules in the system. |
502 |
> |
* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only |
503 |
> |
* once. |
504 |
> |
*/ |
505 |
> |
std::vector<int> molToProcMap_; |
506 |
> |
#endif |
507 |
> |
|
508 |
> |
}; |
509 |
> |
|
510 |
> |
} //namespace oopse |
511 |
> |
#endif //BRAINS_SIMMODEL_HPP |