| 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 SimCreatorr.hpp |
| 28 |
* @author tlin |
| 29 |
* @date 11/02/2004 |
| 30 |
* @time 12:126am |
| 31 |
* @version 1.0 |
| 32 |
*/ |
| 33 |
|
| 34 |
#ifndef BRAINS_SIMCREATOR_HPP |
| 35 |
#define BRAINS_SIMCREATOR_HPP |
| 36 |
|
| 37 |
|
| 38 |
#include "primitives/Molecule.hpp" |
| 39 |
#include "brans/SimInfo.hpp" |
| 40 |
#include "types/MakeStamps.hpp" |
| 41 |
#include "io/Globals.hpp" |
| 42 |
#include "UseTheForce/ForceField.hpp" |
| 43 |
|
| 44 |
namespace oopse { |
| 45 |
|
| 46 |
/** |
| 47 |
* @class SimCreator SimCreator.hpp "brains/SimCreator.hpp" |
| 48 |
* @brief |
| 49 |
*/ |
| 50 |
class SimCreator { |
| 51 |
public: |
| 52 |
|
| 53 |
/** |
| 54 |
* Setup Simulation |
| 55 |
* @return a pointer to SimInfo |
| 56 |
* @param mdfile the meta-data file name |
| 57 |
*/ |
| 58 |
SimInfo* createSim(char* mdfile); |
| 59 |
|
| 60 |
protected: |
| 61 |
|
| 62 |
/** |
| 63 |
* Parses the meta-data file |
| 64 |
* @param mdfile |
| 65 |
* @param stamps |
| 66 |
* @param globals |
| 67 |
*/ |
| 68 |
void parseFile(const std::string mdFileName, MakeStamps* stamps, Globals* globals); |
| 69 |
|
| 70 |
#ifdef IS_MPI |
| 71 |
/** |
| 72 |
* Divide the molecules among the processors |
| 73 |
*/ |
| 74 |
void divideMolecules(); |
| 75 |
#endif //is_mpi |
| 76 |
|
| 77 |
/** create the molecules belong to current processor*/ |
| 78 |
virtual void createMolecules(); |
| 79 |
|
| 80 |
/** |
| 81 |
* Sets the global index for atoms, rigidbodies and cutoff groups and fill up |
| 82 |
* globalGroupMembership and globalMolMembership arrays which map atoms' |
| 83 |
* global index to the global index of the groups (or molecules) they belong to. |
| 84 |
* These array are never changed during the simulation. |
| 85 |
*/ |
| 86 |
void setGlobalIndex(); |
| 87 |
|
| 88 |
private: |
| 89 |
|
| 90 |
/** Extracts the molecules stamps and adds them into SimInfo class */ |
| 91 |
void compList(MakeStamps* stamps, Globals* globals, |
| 92 |
std::vector<std::pair<MoleculeStamp*, int> >& moleculeStamps) ; |
| 93 |
|
| 94 |
/** Initialize fortran, mainly set the cutoff radius and setup*/ |
| 95 |
void initFortran(SimInfo* info); |
| 96 |
|
| 97 |
/** Figure out the cutoff radius and pass it to fortran */ |
| 98 |
void setCutoff(SimInfo* info); |
| 99 |
|
| 100 |
std::string mdFileName_; //save the meta-data file name which may be used later |
| 101 |
}; |
| 102 |
|
| 103 |
} //end namespace oopse |
| 104 |
#endif //BRAINS_SIMCREATOR_HPP |
