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trunk/src/brains/SimInfo.hpp (file contents), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/brains/SimInfo.hpp (file contents), Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 UTC

#	Line 1 | Line 1
1	<	#ifndef __SIMINFO_H__
2	<	#define __SIMINFO_H__
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13	>	*    notice, this list of conditions and the following disclaimer in the
14	>	*    documentation and/or other materials provided with the
15	>	*    distribution.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
28	>	* arising out of the use of or inability to use software, even if the
29	>	* University of Notre Dame has been advised of the possibility of
30	>	* such damages.
31	>	*
32	>	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	>	* research, please cite the appropriate papers when you publish your
34	>	* work.  Good starting points are:
35	>	*
36	>	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	>	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	>	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	>	* [4]  Vardeman & Gezelter, in progress (2009).
40	>	*/
41	>
42	>	/**
43	>	* @file SimInfo.hpp
44	>	* @author    tlin
45	>	* @date  11/02/2004
46	>	* @version 1.0
47	>	*/
48
49	<	#include <map>
50	<	#include <string>
49	>	#ifndef BRAINS_SIMMODEL_HPP
50	>	#define BRAINS_SIMMODEL_HPP
51	>
52	>	#include <iostream>
53	>	#include <set>
54	>	#include <utility>
55		#include <vector>
56
57	<	#include "Atom.hpp"
58	<	#include "RigidBody.hpp"
59	<	#include "Molecule.hpp"
60	<	#include "Exclude.hpp"
61	<	#include "SkipList.hpp"
62	<	#include "AbstractClasses.hpp"
63	<	#include "MakeStamps.hpp"
64	<	#include "SimState.hpp"
65	<	#include "Restraints.hpp"
57	>	#include "brains/PairList.hpp"
58	>	#include "io/Globals.hpp"
59	>	#include "math/Vector3.hpp"
60	>	#include "math/SquareMatrix3.hpp"
61	>	#include "types/MoleculeStamp.hpp"
62	>	#include "UseTheForce/ForceField.hpp"
63	>	#include "utils/PropertyMap.hpp"
64	>	#include "utils/LocalIndexManager.hpp"
65	>	#include "nonbonded/Electrostatic.hpp"
66
67	<	#define __C
68	<	#include "fSimulation.h"
69	<	#include "fortranWrapDefines.hpp"
21	<	#include "GenericData.hpp"
67	>	//another nonsense macro declaration
68	>	#define __OPENMD_C
69	>	#include "brains/fSimulation.h"
70
71	+	namespace OpenMD{
72
73	<	//#include "Minimizer.hpp"
74	<	//#include "OOPSEMinimizer.hpp"
73	>	//forward decalration
74	>	class SnapshotManager;
75	>	class Molecule;
76	>	class SelectionManager;
77	>	class StuntDouble;
78	>	class Electrostatic;
79	>	/**
80	>	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
81	>	* @brief One of the heavy weight classes of OpenMD, SimInfo maintains a list of molecules.
82	>	* The Molecule class maintains all of the concrete objects
83	>	* (atoms, bond, bend, torsions, inversions, rigid bodies, cutoff groups,
84	>	* constraints). In both the single and parallel versions, atoms and
85	>	* rigid bodies have both global and local indices.  The local index is
86	>	* not relevant to molecules or cutoff groups.
87	>	*/
88	>	class SimInfo {
89	>	public:
90	>	typedef std::map<int, Molecule*>::iterator  MoleculeIterator;
91
92	+	/**
93	+	* Constructor of SimInfo
94	+	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
95	+	* second element is the total number of molecules with the same molecule stamp in the system
96	+	* @param ff pointer of a concrete ForceField instance
97	+	* @param simParams
98	+	* @note
99	+	*/
100	+	SimInfo(ForceField* ff, Globals* simParams);
101	+	virtual ~SimInfo();
102
103	<	double roundMe( double x );
104	<	class OOPSEMinimizer;
105	<	class SimInfo{
103	>	/**
104	>	* Adds a molecule
105	>	* @return return true if adding successfully, return false if the molecule is already in SimInfo
106	>	* @param mol molecule to be added
107	>	*/
108	>	bool addMolecule(Molecule* mol);
109
110	<	public:
110	>	/**
111	>	* Removes a molecule from SimInfo
112	>	* @return true if removing successfully, return false if molecule is not in this SimInfo
113	>	*/
114	>	bool removeMolecule(Molecule* mol);
115
116	<	SimInfo();
117	<	~SimInfo();
116	>	/** Returns the total number of molecules in the system. */
117	>	int getNGlobalMolecules() {
118	>	return nGlobalMols_;
119	>	}
120
121	<	int n_atoms; // the number of atoms
122	<	Atom **atoms; // the array of atom objects
121	>	/** Returns the total number of atoms in the system. */
122	>	int getNGlobalAtoms() {
123	>	return nGlobalAtoms_;
124	>	}
125
126	<	vector<RigidBody*> rigidBodies;  // A vector of rigid bodies
127	<	vector<StuntDouble*> integrableObjects;
128	<
129	<	double tau[9]; // the stress tensor
126	>	/** Returns the total number of cutoff groups in the system. */
127	>	int getNGlobalCutoffGroups() {
128	>	return nGlobalCutoffGroups_;
129	>	}
130
131	<	int n_bonds;    // number of bends
132	<	int n_bends;    // number of bends
133	<	int n_torsions; // number of torsions
134	<	int n_oriented; // number of of atoms with orientation
135	<	int ndf;        // number of actual degrees of freedom
136	<	int ndfRaw;     // number of settable degrees of freedom
137	<	int ndfTrans;   // number of translational degrees of freedom
52	<	int nZconstraints; // the number of zConstraints
131	>	/**
132	>	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
133	>	* of atoms which do not belong to the rigid bodies) in the system
134	>	*/
135	>	int getNGlobalIntegrableObjects() {
136	>	return nGlobalIntegrableObjects_;
137	>	}
138
139	<	int setTemp;   // boolean to set the temperature at each sampleTime
140	<	int resetIntegrator; // boolean to reset the integrator
139	>	/**
140	>	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
141	>	* of atoms which do not belong to the rigid bodies) in the system
142	>	*/
143	>	int getNGlobalRigidBodies() {
144	>	return nGlobalRigidBodies_;
145	>	}
146
147	<	int n_dipoles; // number of dipoles
147	>	int getNGlobalConstraints();
148	>	/**
149	>	* Returns the number of local molecules.
150	>	* @return the number of local molecules
151	>	*/
152	>	int getNMolecules() {
153	>	return molecules_.size();
154	>	}
155
156	<	int n_exclude;
157	<	Exclude* excludes;  // the exclude list for ignoring pairs in fortran
158	<	int nGlobalExcludes;
159	<	int* globalExcludes; // same as above, but these guys participate in
63	<	// no long range forces.
156	>	/** Returns the number of local atoms */
157	>	unsigned int getNAtoms() {
158	>	return nAtoms_;
159	>	}
160
161	<	int* identArray;     // array of unique identifiers for the atoms
162	<	int* molMembershipArray;  // map of atom numbers onto molecule numbers
161	>	/** Returns the number of local bonds */
162	>	unsigned int getNBonds(){
163	>	return nBonds_;
164	>	}
165
166	<	int n_constraints; // the number of constraints on the system
166	>	/** Returns the number of local bends */
167	>	unsigned int getNBends() {
168	>	return nBends_;
169	>	}
170
171	<	int n_SRI;   // the number of short range interactions
171	>	/** Returns the number of local torsions */
172	>	unsigned int getNTorsions() {
173	>	return nTorsions_;
174	>	}
175
176	<	double lrPot; // the potential energy from the long range calculations.
176	>	/** Returns the number of local torsions */
177	>	unsigned int getNInversions() {
178	>	return nInversions_;
179	>	}
180	>	/** Returns the number of local rigid bodies */
181	>	unsigned int getNRigidBodies() {
182	>	return nRigidBodies_;
183	>	}
184
185	<	double Hmat[3][3];  // the periodic boundry conditions. The Hmat is the
186	<	// column vectors of the x, y, and z box vectors.
187	<	//   h1  h2  h3
188	<	// [ Xx  Yx  Zx ]
78	<	// [ Xy  Yy  Zy ]
79	<	// [ Xz  Yz  Zz ]
80	<	//
81	<	double HmatInv[3][3];
185	>	/** Returns the number of local integrable objects */
186	>	unsigned int getNIntegrableObjects() {
187	>	return nIntegrableObjects_;
188	>	}
189
190	<	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
191	<	double boxVol;
192	<	int orthoRhombic;
193	<
190	>	/** Returns the number of local cutoff groups */
191	>	unsigned int getNCutoffGroups() {
192	>	return nCutoffGroups_;
193	>	}
194
195	<	double dielectric;      // the dielectric of the medium for reaction field
195	>	/** Returns the total number of constraints in this SimInfo */
196	>	unsigned int getNConstraints() {
197	>	return nConstraints_;
198	>	}
199	>
200	>	/**
201	>	* Returns the first molecule in this SimInfo and intialize the iterator.
202	>	* @return the first molecule, return NULL if there is not molecule in this SimInfo
203	>	* @param i the iterator of molecule array (user shouldn't change it)
204	>	*/
205	>	Molecule* beginMolecule(MoleculeIterator& i);
206
207	<
208	<	int usePBC; // whether we use periodic boundry conditions.
209	<	int useLJ;
210	<	int useSticky;
211	<	int useCharges;
212	<	int useDipoles;
96	<	int useReactionField;
97	<	int useGB;
98	<	int useEAM;
99	<	bool haveCutoffGroups;
100	<	bool useInitXSstate;
101	<	double orthoTolerance;
207	>	/**
208	>	* Returns the next avaliable Molecule based on the iterator.
209	>	* @return the next avaliable molecule, return NULL if reaching the end of the array
210	>	* @param i the iterator of molecule array
211	>	*/
212	>	Molecule* nextMolecule(MoleculeIterator& i);
213
214	<	double dt, run_time;           // the time step and total time
215	<	double sampleTime, statusTime; // the position and energy dump frequencies
216	<	double target_temp;            // the target temperature of the system
217	<	double thermalTime;            // the temp kick interval
107	<	double currentTime;            // Used primarily for correlation Functions
108	<	double resetTime;              // Use to reset the integrator periodically
109	<	short int have_target_temp;
214	>	/** Returns the number of degrees of freedom */
215	>	int getNdf() {
216	>	return ndf_ - getFdf();
217	>	}
218
219	<	int n_mol;           // n_molecules;
220	<	Molecule* molecules; // the array of molecules
221	<
222	<	int nComponents;           // the number of components in the system
115	<	int* componentsNmol;       // the number of molecules of each component
116	<	MoleculeStamp** compStamps;// the stamps matching the components
117	<	LinkedMolStamp* headStamp; // list of stamps used in the simulation
118	<
119	<
120	<	char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
121	<	char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
122	<	BaseIntegrator *the_integrator; // the integrator of the simulation
219	>	/** Returns the number of raw degrees of freedom */
220	>	int getNdfRaw() {
221	>	return ndfRaw_;
222	>	}
223
224	<	OOPSEMinimizer* the_minimizer; // the energy minimizer
225	<	Restraints* restraint;
226	<	bool has_minimizer;
224	>	/** Returns the number of translational degrees of freedom */
225	>	int getNdfTrans() {
226	>	return ndfTrans_;
227	>	}
228
229	<	string finalName;  // the name of the eor file to be written
230	<	string sampleName; // the name of the dump file to be written
231	<	string statusName; // the name of the stat file to be written
229	>	/** sets the current number of frozen degrees of freedom */
230	>	void setFdf(int fdf) {
231	>	fdf_local = fdf;
232	>	}
233
234	<	int seed;                    //seed for random number generator
234	>	int getFdf();
235	>
236	>	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
237	>
238	>	/** Returns the total number of z-constraint molecules in the system */
239	>	int getNZconstraint() {
240	>	return nZconstraint_;
241	>	}
242
243	<	int useSolidThermInt;  // is solid-state thermodynamic integration being used
244	<	int useLiquidThermInt; // is liquid thermodynamic integration being used
245	<	double thermIntLambda; // lambda for TI
246	<	double thermIntK;      // power of lambda for TI
247	<	double vRaw;           // unperturbed potential for TI
248	<	double vHarm;          // harmonic potential for TI
249	<	int i;                 // just an int
243	>	/**
244	>	* Sets the number of z-constraint molecules in the system.
245	>	*/
246	>	void setNZconstraint(int nZconstraint) {
247	>	nZconstraint_ = nZconstraint;
248	>	}
249	>
250	>	/** Returns the snapshot manager. */
251	>	SnapshotManager* getSnapshotManager() {
252	>	return sman_;
253	>	}
254
255	<	vector<double> mfact;
256	<	vector<int> FglobalGroupMembership;
257	<	int ngroup;
258	<	int* globalGroupMembership;
255	>	/** Sets the snapshot manager. */
256	>	void setSnapshotManager(SnapshotManager* sman);
257	>
258	>	/** Returns the force field */
259	>	ForceField* getForceField() {
260	>	return forceField_;
261	>	}
262
263	<	// refreshes the sim if things get changed (load balanceing, volume
264	<	// adjustment, etc.)
263	>	Globals* getSimParams() {
264	>	return simParams_;
265	>	}
266
267	<	void refreshSim( void );
268	<
267	>	/** Returns the velocity of center of mass of the whole system.*/
268	>	Vector3d getComVel();
269
270	<	// sets the internal function pointer to fortran.
270	>	/** Returns the center of the mass of the whole system.*/
271	>	Vector3d getCom();
272	>	/** Returns the center of the mass and Center of Mass velocity of the whole system.*/
273	>	void getComAll(Vector3d& com,Vector3d& comVel);
274
275	<	void setInternal( setFortranSim_TD fSetup,
276	<	setFortranBox_TD fBox,
277	<	notifyFortranCutOff_TD fCut){
278	<	setFsimulation = fSetup;
279	<	setFortranBoxSize = fBox;
160	<	notifyFortranCutOffs = fCut;
161	<	}
275	>	/** Returns intertia tensor for the entire system and system Angular Momentum.*/
276	>	void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
277	>
278	>	/** Returns system angular momentum */
279	>	Vector3d getAngularMomentum();
280
281	<	int getNDF();
282	<	int getNDFraw();
283	<	int getNDFtranslational();
284	<	int getTotIntegrableObjects();
285	<	void setBox( double newBox[3] );
286	<	void setBoxM( double newBox[3][3] );
169	<	void getBoxM( double theBox[3][3] );
170	<	void scaleBox( double scale );
171	<
172	<	void setDefaultRcut( double theRcut );
173	<	void setDefaultRcut( double theRcut, double theRsw );
174	<	void checkCutOffs( void );
281	>	/** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/
282	>	void getGyrationalVolume(RealType &vol);
283	>	/** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/
284	>	void getGyrationalVolume(RealType &vol, RealType &detI);
285	>	/** main driver function to interact with fortran during the initialization and molecule migration */
286	>	void update();
287
288	<	double getRcut( void )  { return rCut; }
289	<	double getRlist( void ) { return rList; }
290	<	double getRsw( void )   { return rSw; }
291	<	double getMaxCutoff( void ) { return maxCutoff; }
180	<
181	<	void setTime( double theTime ) { currentTime = theTime; }
182	<	void incrTime( double the_dt ) { currentTime += the_dt; }
183	<	void decrTime( double the_dt ) { currentTime -= the_dt; }
184	<	double getTime( void ) { return currentTime; }
185	<
186	<	void wrapVector( double thePos[3] );
288	>	/** Returns the local index manager */
289	>	LocalIndexManager* getLocalIndexManager() {
290	>	return &localIndexMan_;
291	>	}
292
293	<	SimState* getConfiguration( void ) { return myConfiguration; }
294	<
295	<	void addProperty(GenericData* prop);
296	<	GenericData* getProperty(const string& propName);
192	<	//vector<GenericData*>& getProperties()  {return properties;}
293	>	int getMoleculeStampId(int globalIndex) {
294	>	//assert(globalIndex < molStampIds_.size())
295	>	return molStampIds_[globalIndex];
296	>	}
297
298	<	int getSeed(void) {  return seed; }
299	<	void setSeed(int theSeed) {  seed = theSeed;}
298	>	/** Returns the molecule stamp */
299	>	MoleculeStamp* getMoleculeStamp(int id) {
300	>	return moleculeStamps_[id];
301	>	}
302
303	<	private:
303	>	/** Return the total number of the molecule stamps */
304	>	int getNMoleculeStamp() {
305	>	return moleculeStamps_.size();
306	>	}
307	>	/**
308	>	* Finds a molecule with a specified global index
309	>	* @return a pointer point to found molecule
310	>	* @param index
311	>	*/
312	>	Molecule* getMoleculeByGlobalIndex(int index) {
313	>	MoleculeIterator i;
314	>	i = molecules_.find(index);
315
316	<	SimState* myConfiguration;
316	>	return i != molecules_.end() ? i->second : NULL;
317	>	}
318
319	<	int boxIsInit, haveRcut, haveRsw;
319	>	int getGlobalMolMembership(int id){
320	>	return globalMolMembership_[id];
321	>	}
322
323	<	double rList, rCut; // variables for the neighborlist
324	<	double rSw;         // the switching radius
323	>	RealType getRcut() {
324	>	return rcut_;
325	>	}
326
327	<	double maxCutoff;
327	>	RealType getRsw() {
328	>	return rsw_;
329	>	}
330
331	<	double distXY;
332	<	double distYZ;
333	<	double distZX;
334	<
335	<	void calcHmatInv( void );
336	<	void calcBoxL();
337	<	double calcMaxCutOff();
331	>	RealType getList() {
332	>	return rlist_;
333	>	}
334	>
335	>	std::string getFinalConfigFileName() {
336	>	return finalConfigFileName_;
337	>	}
338
339	<	// private function to initialize the fortran side of the simulation
340	<	setFortranSim_TD setFsimulation;
339	>	void setFinalConfigFileName(const std::string& fileName) {
340	>	finalConfigFileName_ = fileName;
341	>	}
342
343	<	setFortranBox_TD setFortranBoxSize;
344	<
345	<	notifyFortranCutOff_TD notifyFortranCutOffs;
346	<
347	<	//Addtional Properties of SimInfo
348	<	map<string, GenericData*> properties;
349	<	void getFortranGroupArrays(SimInfo* info,
350	<	vector<int>& FglobalGroupMembership,
351	<	vector<double>& mfact);
343	>	std::string getRawMetaData() {
344	>	return rawMetaData_;
345	>	}
346	>	void setRawMetaData(const std::string& rawMetaData) {
347	>	rawMetaData_ = rawMetaData;
348	>	}
349	>
350	>	std::string getDumpFileName() {
351	>	return dumpFileName_;
352	>	}
353	>
354	>	void setDumpFileName(const std::string& fileName) {
355	>	dumpFileName_ = fileName;
356	>	}
357
358	+	std::string getStatFileName() {
359	+	return statFileName_;
360	+	}
361	+
362	+	void setStatFileName(const std::string& fileName) {
363	+	statFileName_ = fileName;
364	+	}
365	+
366	+	std::string getRestFileName() {
367	+	return restFileName_;
368	+	}
369	+
370	+	void setRestFileName(const std::string& fileName) {
371	+	restFileName_ = fileName;
372	+	}
373
374	<	};
374	>	/**
375	>	* Sets GlobalGroupMembership
376	>	* @see #SimCreator::setGlobalIndex
377	>	*/
378	>	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
379	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
380	>	globalGroupMembership_ = globalGroupMembership;
381	>	}
382
383	+	/**
384	+	* Sets GlobalMolMembership
385	+	* @see #SimCreator::setGlobalIndex
386	+	*/
387	+	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
388	+	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
389	+	globalMolMembership_ = globalMolMembership;
390	+	}
391
392	<	#endif
392	>
393	>	bool isFortranInitialized() {
394	>	return fortranInitialized_;
395	>	}
396	>
397	>	bool getCalcBoxDipole() {
398	>	return calcBoxDipole_;
399	>	}
400	>
401	>	bool getUseAtomicVirial() {
402	>	return useAtomicVirial_;
403	>	}
404	>
405	>	//below functions are just forward functions
406	>	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
407	>	//the other hand, has-a relation need composing.
408	>	/**
409	>	* Adds property into property map
410	>	* @param genData GenericData to be added into PropertyMap
411	>	*/
412	>	void addProperty(GenericData* genData);
413	>
414	>	/**
415	>	* Removes property from PropertyMap by name
416	>	* @param propName the name of property to be removed
417	>	*/
418	>	void removeProperty(const std::string& propName);
419	>
420	>	/**
421	>	* clear all of the properties
422	>	*/
423	>	void clearProperties();
424	>
425	>	/**
426	>	* Returns all names of properties
427	>	* @return all names of properties
428	>	*/
429	>	std::vector<std::string> getPropertyNames();
430	>
431	>	/**
432	>	* Returns all of the properties in PropertyMap
433	>	* @return all of the properties in PropertyMap
434	>	*/
435	>	std::vector<GenericData*> getProperties();
436	>
437	>	/**
438	>	* Returns property
439	>	* @param propName name of property
440	>	* @return a pointer point to property with propName. If no property named propName
441	>	* exists, return NULL
442	>	*/
443	>	GenericData* getPropertyByName(const std::string& propName);
444	>
445	>	/**
446	>	* add all special interaction pairs (including excluded
447	>	* interactions) in a molecule into the appropriate lists.
448	>	*/
449	>	void addInteractionPairs(Molecule* mol);
450	>
451	>	/**
452	>	* remove all special interaction pairs which belong to a molecule
453	>	* from the appropriate lists.
454	>	*/
455	>	void removeInteractionPairs(Molecule* mol);
456	>
457	>
458	>	/** Returns the unique atom types of local processor in an array */
459	>	std::set<AtomType*> getUniqueAtomTypes();
460	>
461	>	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
462	>
463	>	void getCutoff(RealType& rcut, RealType& rsw);
464	>
465	>	private:
466	>
467	>	/** fill up the simtype struct*/
468	>	void setupSimType();
469	>
470	>	/**
471	>	* Setup Fortran Simulation
472	>	* @see #setupFortranParallel
473	>	*/
474	>	void setupFortranSim();
475	>
476	>	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
477	>	void setupCutoff();
478	>
479	>	/** Figure out which coulombic correction method to use and pass to fortran */
480	>	void setupElectrostaticSummationMethod( int isError );
481	>
482	>	/** Figure out which polynomial type to use for the switching function */
483	>	void setupSwitchingFunction();
484	>
485	>	/** Determine if we need to accumulate the simulation box dipole */
486	>	void setupAccumulateBoxDipole();
487	>
488	>	/** Calculates the number of degress of freedom in the whole system */
489	>	void calcNdf();
490	>	void calcNdfRaw();
491	>	void calcNdfTrans();
492	>
493	>	ForceField* forceField_;
494	>	Globals* simParams_;
495	>
496	>	std::map<int, Molecule*>  molecules_; /**< Molecule array */
497	>
498	>	/**
499	>	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
500	>	* system.
501	>	*/
502	>	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
503	>
504	>	//degress of freedom
505	>	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
506	>	int fdf_local;       /**< number of frozen degrees of freedom */
507	>	int fdf_;            /**< number of frozen degrees of freedom */
508	>	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
509	>	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
510	>	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
511	>
512	>	//number of global objects
513	>	int nGlobalMols_;       /**< number of molecules in the system */
514	>	int nGlobalAtoms_;   /**< number of atoms in the system */
515	>	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
516	>	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
517	>	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
518	>	/**
519	>	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
520	>	* corresponding content is the global index of cutoff group this atom belong to.
521	>	* It is filled by SimCreator once and only once, since it never changed during the simulation.
522	>	*/
523	>	std::vector<int> globalGroupMembership_;
524	>
525	>	/**
526	>	* the size of globalMolMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
527	>	* corresponding content is the global index of molecule this atom belong to.
528	>	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
529	>	*/
530	>	std::vector<int> globalMolMembership_;
531	>
532	>
533	>	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
534	>	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
535	>
536	>	//number of local objects
537	>	int nAtoms_;              /**< number of atoms in local processor */
538	>	int nBonds_;              /**< number of bonds in local processor */
539	>	int nBends_;              /**< number of bends in local processor */
540	>	int nTorsions_;           /**< number of torsions in local processor */
541	>	int nInversions_;         /**< number of inversions in local processor */
542	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
543	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
544	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
545	>	int nConstraints_;        /**< number of constraints in local processors */
546	>
547	>	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
548	>	PairList excludedInteractions_;
549	>	PairList oneTwoInteractions_;
550	>	PairList oneThreeInteractions_;
551	>	PairList oneFourInteractions_;
552	>	PropertyMap properties_;                  /**< Generic Property */
553	>	SnapshotManager* sman_;               /**< SnapshotManager */
554	>
555	>	/**
556	>	* The reason to have a local index manager is that when molecule is migrating to other processors,
557	>	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
558	>	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
559	>	* to make a efficient data moving plan.
560	>	*/
561	>	LocalIndexManager localIndexMan_;
562	>
563	>	// unparsed MetaData block for storing in Dump and EOR files:
564	>	std::string rawMetaData_;
565	>
566	>	//file names
567	>	std::string finalConfigFileName_;
568	>	std::string dumpFileName_;
569	>	std::string statFileName_;
570	>	std::string restFileName_;
571	>
572	>	RealType rcut_;       /**< cutoff radius*/
573	>	RealType rsw_;        /**< radius of switching function*/
574	>	RealType rlist_;      /**< neighbor list radius */
575	>
576	>	int ljsp_; /**< use shifted potential for LJ*/
577	>	int ljsf_; /**< use shifted force for LJ*/
578	>
579	>	bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
580	>
581	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
582	>	the simulation box dipole moment */
583	>
584	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
585	>	Atomic Virials to calculate the pressure */
586	>
587	>	public:
588	>	/**
589	>	* return an integral objects by its global index. In MPI version, if the StuntDouble with specified
590	>	* global index does not belong to local processor, a NULL will be return.
591	>	*/
592	>	StuntDouble* getIOIndexToIntegrableObject(int index);
593	>	void setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v);
594	>	private:
595	>	std::vector<StuntDouble*> IOIndexToIntegrableObject;
596	>	//public:
597	>	//void setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v);
598	>	/**
599	>	* return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
600	>	* global index does not belong to local processor, a NULL will be return.
601	>	*/
602	>	//StuntDouble* getStuntDoubleFromGlobalIndex(int index);
603	>	//private:
604	>	//std::vector<StuntDouble*> sdByGlobalIndex_;
605	>
606	>	//in Parallel version, we need MolToProc
607	>	public:
608	>
609	>	/**
610	>	* Finds the processor where a molecule resides
611	>	* @return the id of the processor which contains the molecule
612	>	* @param globalIndex global Index of the molecule
613	>	*/
614	>	int getMolToProc(int globalIndex) {
615	>	//assert(globalIndex < molToProcMap_.size());
616	>	return molToProcMap_[globalIndex];
617	>	}
618	>
619	>	/**
620	>	* Set MolToProcMap array
621	>	* @see #SimCreator::divideMolecules
622	>	*/
623	>	void setMolToProcMap(const std::vector<int>& molToProcMap) {
624	>	molToProcMap_ = molToProcMap;
625	>	}
626	>
627	>	private:
628	>
629	>	void setupFortranParallel();
630	>
631	>	/**
632	>	* The size of molToProcMap_ is equal to total number of molecules
633	>	* in the system.  It maps a molecule to the processor on which it
634	>	* resides. it is filled by SimCreator once and only once.
635	>	*/
636	>	std::vector<int> molToProcMap_;
637	>
638	>
639	>	};
640	>
641	>	} //namespace OpenMD
642	>	#endif //BRAINS_SIMMODEL_HPP
643	>

Comparing:
trunk/src/brains/SimInfo.hpp (property svn:keywords), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/brains/SimInfo.hpp (property svn:keywords), Revision 1503 by gezelter, Sat Oct 2 19:54:41 2010 UTC

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