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root/OpenMD/branches/development/src/brains/SimInfo.hpp

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trunk/src/brains/SimInfo.hpp (file contents), Revision 413 by tim, Wed Mar 9 17:30:29 2005 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	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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		/**
#	Line 54 | Line 54
54		#include <utility>
55		#include <vector>
56
57	<	#include "brains/Exclude.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		//another nonsense macro declaration
68	<	#define __C
68	>	#define __OPENMD_C
69		#include "brains/fSimulation.h"
70
71	<	namespace oopse{
71	>	namespace OpenMD{
72
73	<	//forward decalration
74	<	class SnapshotManager;
75	<	class Molecule;
76	<	class SelectionManager;
77	<	/**
78	<	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
79	<	* @brief As one of the heavy weight class of OOPSE, SimInfo
80	<	* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
81	<	* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
82	<	* cutoff groups, constrains).
83	<	* Another major change is the index. No matter single version or parallel version,  atoms and
84	<	* rigid bodies have both global index and local index. Local index is not important to molecule as well as
85	<	* cutoff group.
86	<	*/
87	<	class SimInfo {
88	<	public:
89	<	typedef std::map<int, Molecule*>::iterator  MoleculeIterator;
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(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams);
101	<	virtual ~SimInfo();
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	<	/**
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);
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	<	/**
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);
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	<	/** Returns the total number of molecules in the system. */
117	<	int getNGlobalMolecules() {
118	<	return nGlobalMols_;
119	<	}
116	>	/** Returns the total number of molecules in the system. */
117	>	int getNGlobalMolecules() {
118	>	return nGlobalMols_;
119	>	}
120
121	<	/** Returns the total number of atoms in the system. */
122	<	int getNGlobalAtoms() {
123	<	return nGlobalAtoms_;
124	<	}
121	>	/** Returns the total number of atoms in the system. */
122	>	int getNGlobalAtoms() {
123	>	return nGlobalAtoms_;
124	>	}
125
126	<	/** Returns the total number of cutoff groups in the system. */
127	<	int getNGlobalCutoffGroups() {
128	<	return nGlobalCutoffGroups_;
129	<	}
126	>	/** Returns the total number of cutoff groups in the system. */
127	>	int getNGlobalCutoffGroups() {
128	>	return nGlobalCutoffGroups_;
129	>	}
130
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	<	}
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	<	/**
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	<	}
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 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	<	}
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	<	/** Returns the number of local atoms */
157	<	unsigned int getNAtoms() {
158	<	return nAtoms_;
159	<	}
156	>	/** Returns the number of local atoms */
157	>	unsigned int getNAtoms() {
158	>	return nAtoms_;
159	>	}
160
161	<	/** Returns the number of local bonds */
162	<	unsigned int getNBonds(){
163	<	return nBonds_;
164	<	}
161	>	/** Returns the number of local bonds */
162	>	unsigned int getNBonds(){
163	>	return nBonds_;
164	>	}
165
166	<	/** Returns the number of local bends */
167	<	unsigned int getNBends() {
168	<	return nBends_;
169	<	}
166	>	/** Returns the number of local bends */
167	>	unsigned int getNBends() {
168	>	return nBends_;
169	>	}
170
171	<	/** Returns the number of local torsions */
172	<	unsigned int getNTorsions() {
173	<	return nTorsions_;
174	<	}
171	>	/** Returns the number of local torsions */
172	>	unsigned int getNTorsions() {
173	>	return nTorsions_;
174	>	}
175
176	<	/** Returns the number of local rigid bodies */
177	<	unsigned int getNRigidBodies() {
178	<	return nRigidBodies_;
179	<	}
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	<	/** Returns the number of local integrable objects */
186	<	unsigned int getNIntegrableObjects() {
187	<	return nIntegrableObjects_;
188	<	}
185	>	/** Returns the number of local integrable objects */
186	>	unsigned int getNIntegrableObjects() {
187	>	return nIntegrableObjects_;
188	>	}
189
190	<	/** Returns the number of local cutoff groups */
191	<	unsigned int getNCutoffGroups() {
192	<	return nCutoffGroups_;
193	<	}
190	>	/** Returns the number of local cutoff groups */
191	>	unsigned int getNCutoffGroups() {
192	>	return nCutoffGroups_;
193	>	}
194
195	<	/** Returns the total number of constraints in this SimInfo */
196	<	unsigned int getNConstraints() {
197	<	return nConstraints_;
198	<	}
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);
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	<	* 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);
206	<
207	<	/** Returns the number of degrees of freedom */
208	<	int getNdf() {
209	<	return ndf_;
210	<	}
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	<	/** Returns the number of raw degrees of freedom */
215	<	int getNdfRaw() {
216	<	return ndfRaw_;
217	<	}
214	>	/** Returns the number of degrees of freedom */
215	>	int getNdf() {
216	>	return ndf_ - getFdf();
217	>	}
218
219	<	/** Returns the number of translational degrees of freedom */
220	<	int getNdfTrans() {
221	<	return ndfTrans_;
222	<	}
219	>	/** Returns the number of raw degrees of freedom */
220	>	int getNdfRaw() {
221	>	return ndfRaw_;
222	>	}
223
224	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
224	>	/** Returns the number of translational degrees of freedom */
225	>	int getNdfTrans() {
226	>	return ndfTrans_;
227	>	}
228	>
229	>	/** sets the current number of frozen degrees of freedom */
230	>	void setFdf(int fdf) {
231	>	fdf_local = fdf;
232	>	}
233	>
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	<	}
238	>	/** Returns the total number of z-constraint molecules in the system */
239	>	int getNZconstraint() {
240	>	return nZconstraint_;
241	>	}
242
243	<	/**
244	<	* Sets the number of z-constraint molecules in the system.
245	<	*/
246	<	void setNZconstraint(int nZconstraint) {
247	<	nZconstraint_ = nZconstraint;
248	<	}
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	<	}
250	>	/** Returns the snapshot manager. */
251	>	SnapshotManager* getSnapshotManager() {
252	>	return sman_;
253	>	}
254
255	<	/** Sets the snapshot manager. */
256	<	void setSnapshotManager(SnapshotManager* sman);
255	>	/** Sets the snapshot manager. */
256	>	void setSnapshotManager(SnapshotManager* sman);
257
258	<	/** Returns the force field */
259	<	ForceField* getForceField() {
260	<	return forceField_;
261	<	}
258	>	/** Returns the force field */
259	>	ForceField* getForceField() {
260	>	return forceField_;
261	>	}
262
263	<	Globals* getSimParams() {
264	<	return simParams_;
265	<	}
263	>	Globals* getSimParams() {
264	>	return simParams_;
265	>	}
266
267	<	/** Returns the velocity of center of mass of the whole system.*/
268	<	Vector3d getComVel();
267	>	/** Returns the velocity of center of mass of the whole system.*/
268	>	Vector3d getComVel();
269
270	<	/** Returns the center of the mass of the whole system.*/
271	<	Vector3d getCom();
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	<	/** main driver function to interact with fortran during the initialization and molecule migration */
276	<	void update();
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	<	/** Returns the local index manager */
282	<	LocalIndexManager* getLocalIndexManager() {
283	<	return &localIndexMan_;
284	<	}
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	<	int getMoleculeStampId(int globalIndex) {
289	<	//assert(globalIndex < molStampIds_.size())
290	<	return molStampIds_[globalIndex];
291	<	}
288	>	/** Returns the local index manager */
289	>	LocalIndexManager* getLocalIndexManager() {
290	>	return &localIndexMan_;
291	>	}
292
293	<	/** Returns the molecule stamp */
294	<	MoleculeStamp* getMoleculeStamp(int id) {
295	<	return moleculeStamps_[id];
296	<	}
293	>	int getMoleculeStampId(int globalIndex) {
294	>	//assert(globalIndex < molStampIds_.size())
295	>	return molStampIds_[globalIndex];
296	>	}
297
298	<	/** Return the total number of the molecule stamps */
299	<	int getNMoleculeStamp() {
300	<	return moleculeStamps_.size();
301	<	}
281	<	/**
282	<	* Finds a molecule with a specified global index
283	<	* @return a pointer point to found molecule
284	<	* @param index
285	<	*/
286	<	Molecule* getMoleculeByGlobalIndex(int index) {
287	<	MoleculeIterator i;
288	<	i = molecules_.find(index);
298	>	/** Returns the molecule stamp */
299	>	MoleculeStamp* getMoleculeStamp(int id) {
300	>	return moleculeStamps_[id];
301	>	}
302
303	<	return i != molecules_.end() ? i->second : NULL;
304	<	}
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	<	/** Calculate the maximum cutoff radius based on the atom types */
317	<	double calcMaxCutoffRadius();
316	>	return i != molecules_.end() ? i->second : NULL;
317	>	}
318
319	<	double getRcut() {
320	<	return rcut_;
321	<	}
319	>	int getGlobalMolMembership(int id){
320	>	return globalMolMembership_[id];
321	>	}
322
323	<	double getRsw() {
324	<	return rsw_;
325	<	}
303	<
304	<	std::string getFinalConfigFileName() {
305	<	return finalConfigFileName_;
306	<	}
307	<
308	<	void setFinalConfigFileName(const std::string& fileName) {
309	<	finalConfigFileName_ = fileName;
310	<	}
323	>	RealType getRcut() {
324	>	return rcut_;
325	>	}
326
327	<	std::string getDumpFileName() {
328	<	return dumpFileName_;
329	<	}
315	<
316	<	void setDumpFileName(const std::string& fileName) {
317	<	dumpFileName_ = fileName;
318	<	}
327	>	RealType getRsw() {
328	>	return rsw_;
329	>	}
330
331	<	std::string getStatFileName() {
332	<	return statFileName_;
333	<	}
331	>	RealType getList() {
332	>	return rlist_;
333	>	}
334
335	<	void setStatFileName(const std::string& fileName) {
336	<	statFileName_ = fileName;
337	<	}
335	>	std::string getFinalConfigFileName() {
336	>	return finalConfigFileName_;
337	>	}
338
339	<	/**
340	<	* Sets GlobalGroupMembership
341	<	* @see #SimCreator::setGlobalIndex
331	<	*/
332	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
333	<	assert(globalGroupMembership.size() == nGlobalAtoms_);
334	<	globalGroupMembership_ = globalGroupMembership;
335	<	}
339	>	void setFinalConfigFileName(const std::string& fileName) {
340	>	finalConfigFileName_ = fileName;
341	>	}
342
343	<	/**
344	<	* Sets GlobalMolMembership
345	<	* @see #SimCreator::setGlobalIndex
346	<	*/
347	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
348	<	assert(globalMolMembership.size() == nGlobalAtoms_);
349	<	globalMolMembership_ = globalMolMembership;
350	<	}
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	<	bool isFortranInitialized() {
375	<	return fortranInitialized_;
376	<	}
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	>
393	>	bool isFortranInitialized() {
394	>	return fortranInitialized_;
395	>	}
396
397	<	//below functions are just forward functions
398	<	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
399	<	//the other hand, has-a relation need composing.
354	<	/**
355	<	* Adds property into property map
356	<	* @param genData GenericData to be added into PropertyMap
357	<	*/
358	<	void addProperty(GenericData* genData);
397	>	bool getCalcBoxDipole() {
398	>	return calcBoxDipole_;
399	>	}
400
401	<	/**
402	<	* Removes property from PropertyMap by name
403	<	* @param propName the name of property to be removed
363	<	*/
364	<	void removeProperty(const std::string& propName);
401	>	bool getUseAtomicVirial() {
402	>	return useAtomicVirial_;
403	>	}
404
405	<	/**
406	<	* clear all of the properties
407	<	*/
408	<	void clearProperties();
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	<	* Returns all names of properties
416	<	* @return all names of properties
417	<	*/
418	<	std::vector<std::string> getPropertyNames();
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	<	* Returns all of the properties in PropertyMap
422	<	* @return all of the properties in PropertyMap
423	<	*/
381	<	std::vector<GenericData*> getProperties();
420	>	/**
421	>	* clear all of the properties
422	>	*/
423	>	void clearProperties();
424
425	<	/**
426	<	* Returns property
427	<	* @param propName name of property
428	<	* @return a pointer point to property with propName. If no property named propName
429	<	* exists, return NULL
388	<	*/
389	<	GenericData* getPropertyByName(const std::string& propName);
425	>	/**
426	>	* Returns all names of properties
427	>	* @return all names of properties
428	>	*/
429	>	std::vector<std::string> getPropertyNames();
430
431	<	/**
432	<	* add all exclude pairs of a molecule into exclude list.
433	<	*/
434	<	void addExcludePairs(Molecule* mol);
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	<	* remove all exclude pairs which belong to a molecule from exclude list
439	<	*/
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	<	void removeExcludePairs(Molecule* mol);
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	<	/** Returns the unique atom types of local processor in an array */
458	<	std::set<AtomType*> getUniqueAtomTypes();
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);
461	>	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
462
463	<	void getCutoff(double& rcut, double& rsw);
463	>	void getCutoff(RealType& rcut, RealType& rsw);
464
465	<	private:
465	>	private:
466
467	<	/** fill up the simtype struct*/
468	<	void setupSimType();
467	>	/** fill up the simtype struct*/
468	>	void setupSimType();
469
470	<	/**
471	<	* Setup Fortran Simulation
472	<	* @see #setupFortranParallel
473	<	*/
474	<	void setupFortranSim();
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();
476	>	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
477	>	void setupCutoff();
478
479	<	/** Calculates the number of degress of freedom in the whole system */
480	<	void calcNdf();
426	<	void calcNdfRaw();
427	<	void calcNdfTrans();
479	>	/** Figure out which coulombic correction method to use and pass to fortran */
480	>	void setupElectrostaticSummationMethod( int isError );
481
482	<	/**
483	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
431	<	* system.
432	<	*/
433	<	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
482	>	/** Figure out which polynomial type to use for the switching function */
483	>	void setupSwitchingFunction();
484
485	<	ForceField* forceField_;
486	<	Globals* simParams_;
485	>	/** Determine if we need to accumulate the simulation box dipole */
486	>	void setupAccumulateBoxDipole();
487
488	<	std::map<int, Molecule*>  molecules_; /**< Molecule array */
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 ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
507	<	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
508	<	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
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_;
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 globalGroupMembership_  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_;
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 */
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 nRigidBodies_;              /**< number of rigid bodies in local processor */
542	<	int nIntegrableObjects_;    /**< number of integrable objects in local processor */
543	<	int nCutoffGroups_;             /**< number of cutoff groups in local processor */
544	<	int nConstraints_;              /**< number of constraints in local processors */
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	<	Exclude exclude_;
549	<	PropertyMap properties_;                  /**< Generic Property */
550	<	SnapshotManager* sman_;               /**< SnapshotManager */
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_;
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	<	//file names
564	<	std::string finalConfigFileName_;
495	<	std::string dumpFileName_;
496	<	std::string statFileName_;
563	>	// unparsed MetaData block for storing in Dump and EOR files:
564	>	std::string rawMetaData_;
565
566	<	double rcut_;       /**< cutoff radius*/
567	<	double rsw_;        /**< radius of switching function*/
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	<	bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
576	>	int ljsp_; /**< use shifted potential for LJ*/
577	>	int ljsf_; /**< use shifted force for LJ*/
578
579	<	#ifdef IS_MPI
580	<	//in Parallel version, we need MolToProc
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	<	}
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	<	}
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:
627	>	private:
628
629	<	void setupFortranParallel();
629	>	void setupFortranParallel();
630
631	<	/**
632	<	* The size of molToProcMap_ is equal to total number of molecules in the system.
633	<	*  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
634	<	* once.
635	<	*/
636	<	std::vector<int> molToProcMap_;
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
536	–	#endif
638
639	<	};
639	>	};
640
641	<	} //namespace oopse
641	>	} //namespace OpenMD
642		#endif //BRAINS_SIMMODEL_HPP
643

Comparing:
trunk/src/brains/SimInfo.hpp (property svn:keywords), Revision 413 by tim, Wed Mar 9 17:30:29 2005 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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