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

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trunk/src/brains/SimInfo.hpp (file contents), Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
branches/development/src/brains/SimInfo.hpp (file contents), Revision 1528 by gezelter, Fri Dec 17 20:11:05 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
66		//another nonsense macro declaration
67	<	#define __C
67	>	#define __OPENMD_C
68		#include "brains/fSimulation.h"
69
70	<	namespace oopse{
70	>	using namespace std;
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"
77	<	* @brief As one of the heavy weight class of OOPSE, SimInfo
78	<	* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
79	<	* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
80	<	* cutoff groups, constrains).
81	<	* Another major change is the index. No matter single version or parallel version,  atoms and
82	<	* rigid bodies have both global index and local index. Local index is not important to molecule as well as
83	<	* cutoff group.
84	<	*/
85	<	class SimInfo {
86	<	public:
87	<	typedef std::map<int, Molecule*>::iterator  MoleculeIterator;
73	>	enum CutoffMethod {
74	>	HARD,
75	>	SWITCHING_FUNCTION,
76	>	SHIFTED_POTENTIAL,
77	>	SHIFTED_FORCE
78	>	};
79
80	<	/**
81	<	* Constructor of SimInfo
82	<	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
83	<	* second element is the total number of molecules with the same molecule stamp in the system
84	<	* @param ff pointer of a concrete ForceField instance
94	<	* @param simParams
95	<	* @note
96	<	*/
97	<	SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams);
98	<	virtual ~SimInfo();
80	>	//forward decalration
81	>	class SnapshotManager;
82	>	class Molecule;
83	>	class SelectionManager;
84	>	class StuntDouble;
85
86	<	/**
87	<	* Adds a molecule
88	<	* @return return true if adding successfully, return false if the molecule is already in SimInfo
89	<	* @param mol molecule to be added
90	<	*/
91	<	bool addMolecule(Molecule* mol);
86	>	/**
87	>	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
88	>	*
89	>	* @brief One of the heavy-weight classes of OpenMD, SimInfo
90	>	* maintains objects and variables relating to the current
91	>	* simulation.  This includes the master list of Molecules.  The
92	>	* Molecule class maintains all of the concrete objects (Atoms,
93	>	* Bond, Bend, Torsions, Inversions, RigidBodies, CutoffGroups,
94	>	* Constraints). In both the single and parallel versions, Atoms and
95	>	* RigidBodies have both global and local indices.
96	>	*/
97	>	class SimInfo {
98	>	public:
99	>	typedef map<int, Molecule*>::iterator  MoleculeIterator;
100	>
101	>	/**
102	>	* Constructor of SimInfo
103	>	*
104	>	* @param molStampPairs MoleculeStamp Array. The first element of
105	>	* the pair is molecule stamp, the second element is the total
106	>	* number of molecules with the same molecule stamp in the system
107	>	*
108	>	* @param ff pointer of a concrete ForceField instance
109	>	*
110	>	* @param simParams
111	>	*/
112	>	SimInfo(ForceField* ff, Globals* simParams);
113	>	virtual ~SimInfo();
114
115	<	/**
116	<	* Removes a molecule from SimInfo
117	<	* @return true if removing successfully, return false if molecule is not in this SimInfo
118	<	*/
119	<	bool removeMolecule(Molecule* mol);
115	>	/**
116	>	* Adds a molecule
117	>	*
118	>	* @return return true if adding successfully, return false if the
119	>	* molecule is already in SimInfo
120	>	*
121	>	* @param mol molecule to be added
122	>	*/
123	>	bool addMolecule(Molecule* mol);
124
125	<	/** Returns the total number of molecules in the system. */
126	<	int getNGlobalMolecules() {
127	<	return nGlobalMols_;
128	<	}
125	>	/**
126	>	* Removes a molecule from SimInfo
127	>	*
128	>	* @return true if removing successfully, return false if molecule
129	>	* is not in this SimInfo
130	>	*/
131	>	bool removeMolecule(Molecule* mol);
132
133	<	/** Returns the total number of atoms in the system. */
134	<	int getNGlobalAtoms() {
135	<	return nGlobalAtoms_;
136	<	}
133	>	/** Returns the total number of molecules in the system. */
134	>	int getNGlobalMolecules() {
135	>	return nGlobalMols_;
136	>	}
137
138	<	/** Returns the total number of cutoff groups in the system. */
139	<	int getNGlobalCutoffGroups() {
140	<	return nGlobalCutoffGroups_;
141	<	}
138	>	/** Returns the total number of atoms in the system. */
139	>	int getNGlobalAtoms() {
140	>	return nGlobalAtoms_;
141	>	}
142
143	<	/**
144	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
145	<	* of atoms which do not belong to the rigid bodies) in the system
146	<	*/
132	<	int getNGlobalIntegrableObjects() {
133	<	return nGlobalIntegrableObjects_;
134	<	}
143	>	/** Returns the total number of cutoff groups in the system. */
144	>	int getNGlobalCutoffGroups() {
145	>	return nGlobalCutoffGroups_;
146	>	}
147
148	<	/**
149	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
150	<	* of atoms which do not belong to the rigid bodies) in the system
151	<	*/
152	<	int getNGlobalRigidBodies() {
153	<	return nGlobalRigidBodies_;
154	<	}
148	>	/**
149	>	* Returns the total number of integrable objects (total number of
150	>	* rigid bodies plus the total number of atoms which do not belong
151	>	* to the rigid bodies) in the system
152	>	*/
153	>	int getNGlobalIntegrableObjects() {
154	>	return nGlobalIntegrableObjects_;
155	>	}
156
157	<	int getNGlobalConstraints();
158	<	/**
159	<	* Returns the number of local molecules.
160	<	* @return the number of local molecules
161	<	*/
162	<	int getNMolecules() {
163	<	return molecules_.size();
164	<	}
157	>	/**
158	>	* Returns the total number of integrable objects (total number of
159	>	* rigid bodies plus the total number of atoms which do not belong
160	>	* to the rigid bodies) in the system
161	>	*/
162	>	int getNGlobalRigidBodies() {
163	>	return nGlobalRigidBodies_;
164	>	}
165
166	<	/** Returns the number of local atoms */
167	<	unsigned int getNAtoms() {
168	<	return nAtoms_;
169	<	}
166	>	int getNGlobalConstraints();
167	>	/**
168	>	* Returns the number of local molecules.
169	>	* @return the number of local molecules
170	>	*/
171	>	int getNMolecules() {
172	>	return molecules_.size();
173	>	}
174
175	<	/** Returns the number of local bonds */
176	<	unsigned int getNBonds(){
177	<	return nBonds_;
178	<	}
175	>	/** Returns the number of local atoms */
176	>	unsigned int getNAtoms() {
177	>	return nAtoms_;
178	>	}
179
180	<	/** Returns the number of local bends */
181	<	unsigned int getNBends() {
182	<	return nBends_;
183	<	}
180	>	/** Returns the number of local bonds */
181	>	unsigned int getNBonds(){
182	>	return nBonds_;
183	>	}
184
185	<	/** Returns the number of local torsions */
186	<	unsigned int getNTorsions() {
187	<	return nTorsions_;
188	<	}
185	>	/** Returns the number of local bends */
186	>	unsigned int getNBends() {
187	>	return nBends_;
188	>	}
189
190	<	/** Returns the number of local rigid bodies */
191	<	unsigned int getNRigidBodies() {
192	<	return nRigidBodies_;
193	<	}
190	>	/** Returns the number of local torsions */
191	>	unsigned int getNTorsions() {
192	>	return nTorsions_;
193	>	}
194
195	<	/** Returns the number of local integrable objects */
196	<	unsigned int getNIntegrableObjects() {
197	<	return nIntegrableObjects_;
198	<	}
195	>	/** Returns the number of local torsions */
196	>	unsigned int getNInversions() {
197	>	return nInversions_;
198	>	}
199	>	/** Returns the number of local rigid bodies */
200	>	unsigned int getNRigidBodies() {
201	>	return nRigidBodies_;
202	>	}
203
204	<	/** Returns the number of local cutoff groups */
205	<	unsigned int getNCutoffGroups() {
206	<	return nCutoffGroups_;
207	<	}
204	>	/** Returns the number of local integrable objects */
205	>	unsigned int getNIntegrableObjects() {
206	>	return nIntegrableObjects_;
207	>	}
208
209	<	/** Returns the total number of constraints in this SimInfo */
210	<	unsigned int getNConstraints() {
211	<	return nConstraints_;
212	<	}
209	>	/** Returns the number of local cutoff groups */
210	>	unsigned int getNCutoffGroups() {
211	>	return nCutoffGroups_;
212	>	}
213	>
214	>	/** Returns the total number of constraints in this SimInfo */
215	>	unsigned int getNConstraints() {
216	>	return nConstraints_;
217	>	}
218
219	<	/**
220	<	* Returns the first molecule in this SimInfo and intialize the iterator.
221	<	* @return the first molecule, return NULL if there is not molecule in this SimInfo
222	<	* @param i the iterator of molecule array (user shouldn't change it)
223	<	*/
224	<	Molecule* beginMolecule(MoleculeIterator& i);
219	>	/**
220	>	* Returns the first molecule in this SimInfo and intialize the iterator.
221	>	* @return the first molecule, return NULL if there is not molecule in this SimInfo
222	>	* @param i the iterator of molecule array (user shouldn't change it)
223	>	*/
224	>	Molecule* beginMolecule(MoleculeIterator& i);
225
226	<	/**
227	<	* Returns the next avaliable Molecule based on the iterator.
228	<	* @return the next avaliable molecule, return NULL if reaching the end of the array
229	<	* @param i the iterator of molecule array
230	<	*/
231	<	Molecule* nextMolecule(MoleculeIterator& i);
226	>	/**
227	>	* Returns the next avaliable Molecule based on the iterator.
228	>	* @return the next avaliable molecule, return NULL if reaching the end of the array
229	>	* @param i the iterator of molecule array
230	>	*/
231	>	Molecule* nextMolecule(MoleculeIterator& i);
232
233	<	/** Returns the number of degrees of freedom */
234	<	int getNdf() {
235	<	return ndf_;
236	<	}
233	>	/** Returns the number of degrees of freedom */
234	>	int getNdf() {
235	>	return ndf_ - getFdf();
236	>	}
237
238	<	/** Returns the number of raw degrees of freedom */
239	<	int getNdfRaw() {
240	<	return ndfRaw_;
241	<	}
238	>	/** Returns the number of raw degrees of freedom */
239	>	int getNdfRaw() {
240	>	return ndfRaw_;
241	>	}
242
243	<	/** Returns the number of translational degrees of freedom */
244	<	int getNdfTrans() {
245	<	return ndfTrans_;
246	<	}
243	>	/** Returns the number of translational degrees of freedom */
244	>	int getNdfTrans() {
245	>	return ndfTrans_;
246	>	}
247
248	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
248	>	/** sets the current number of frozen degrees of freedom */
249	>	void setFdf(int fdf) {
250	>	fdf_local = fdf;
251	>	}
252	>
253	>	int getFdf();
254	>
255	>	//getNZconstraint and setNZconstraint ruin the coherence of
256	>	//SimInfo class, need refactoring
257
258	<	/** Returns the total number of z-constraint molecules in the system */
259	<	int getNZconstraint() {
260	<	return nZconstraint_;
261	<	}
258	>	/** Returns the total number of z-constraint molecules in the system */
259	>	int getNZconstraint() {
260	>	return nZconstraint_;
261	>	}
262
263	<	/**
264	<	* Sets the number of z-constraint molecules in the system.
265	<	*/
266	<	void setNZconstraint(int nZconstraint) {
267	<	nZconstraint_ = nZconstraint;
268	<	}
263	>	/**
264	>	* Sets the number of z-constraint molecules in the system.
265	>	*/
266	>	void setNZconstraint(int nZconstraint) {
267	>	nZconstraint_ = nZconstraint;
268	>	}
269
270	<	/** Returns the snapshot manager. */
271	<	SnapshotManager* getSnapshotManager() {
272	<	return sman_;
273	<	}
270	>	/** Returns the snapshot manager. */
271	>	SnapshotManager* getSnapshotManager() {
272	>	return sman_;
273	>	}
274
275	<	/** Sets the snapshot manager. */
276	<	void setSnapshotManager(SnapshotManager* sman);
275	>	/** Sets the snapshot manager. */
276	>	void setSnapshotManager(SnapshotManager* sman);
277
278	<	/** Returns the force field */
279	<	ForceField* getForceField() {
280	<	return forceField_;
281	<	}
278	>	/** Returns the force field */
279	>	ForceField* getForceField() {
280	>	return forceField_;
281	>	}
282
283	<	Globals* getSimParams() {
284	<	return simParams_;
285	<	}
283	>	Globals* getSimParams() {
284	>	return simParams_;
285	>	}
286
287	<	/** Returns the velocity of center of mass of the whole system.*/
288	<	Vector3d getComVel();
287	>	/** Returns the velocity of center of mass of the whole system.*/
288	>	Vector3d getComVel();
289
290	<	/** Returns the center of the mass of the whole system.*/
291	<	Vector3d getCom();
290	>	/** Returns the center of the mass of the whole system.*/
291	>	Vector3d getCom();
292	>	/** Returns the center of the mass and Center of Mass velocity of
293	>	the whole system.*/
294	>	void getComAll(Vector3d& com,Vector3d& comVel);
295
296	<	/** main driver function to interact with fortran during the initialization and molecule migration */
297	<	void update();
296	>	/** Returns intertia tensor for the entire system and system
297	>	Angular Momentum.*/
298	>	void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
299	>
300	>	/** Returns system angular momentum */
301	>	Vector3d getAngularMomentum();
302
303	<	/** Returns the local index manager */
304	<	LocalIndexManager* getLocalIndexManager() {
305	<	return &localIndexMan_;
306	<	}
303	>	/** Returns volume of system as estimated by an ellipsoid defined
304	>	by the radii of gyration*/
305	>	void getGyrationalVolume(RealType &vol);
306	>	/** Overloaded version of gyrational volume that also returns
307	>	det(I) so dV/dr can be calculated*/
308	>	void getGyrationalVolume(RealType &vol, RealType &detI);
309	>	/** main driver function to interact with fortran during the
310	>	initialization and molecule migration */
311	>	void update();
312
313	<	int getMoleculeStampId(int globalIndex) {
314	<	//assert(globalIndex < molStampIds_.size())
315	<	return molStampIds_[globalIndex];
316	<	}
313	>	/** Returns the local index manager */
314	>	LocalIndexManager* getLocalIndexManager() {
315	>	return &localIndexMan_;
316	>	}
317
318	<	/** Returns the molecule stamp */
319	<	MoleculeStamp* getMoleculeStamp(int id) {
320	<	return moleculeStamps_[id];
321	<	}
318	>	int getMoleculeStampId(int globalIndex) {
319	>	//assert(globalIndex < molStampIds_.size())
320	>	return molStampIds_[globalIndex];
321	>	}
322
323	<	/** Return the total number of the molecule stamps */
324	<	int getNMoleculeStamp() {
325	<	return moleculeStamps_.size();
326	<	}
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);
323	>	/** Returns the molecule stamp */
324	>	MoleculeStamp* getMoleculeStamp(int id) {
325	>	return moleculeStamps_[id];
326	>	}
327
328	<	return i != molecules_.end() ? i->second : NULL;
329	<	}
328	>	/** Return the total number of the molecule stamps */
329	>	int getNMoleculeStamp() {
330	>	return moleculeStamps_.size();
331	>	}
332	>	/**
333	>	* Finds a molecule with a specified global index
334	>	* @return a pointer point to found molecule
335	>	* @param index
336	>	*/
337	>	Molecule* getMoleculeByGlobalIndex(int index) {
338	>	MoleculeIterator i;
339	>	i = molecules_.find(index);
340
341	<	/** Calculate the maximum cutoff radius based on the atom types */
342	<	double calcMaxCutoffRadius();
341	>	return i != molecules_.end() ? i->second : NULL;
342	>	}
343
344	<	double getRcut() {
345	<	return rcut_;
346	<	}
344	>	int getGlobalMolMembership(int id){
345	>	return globalMolMembership_[id];
346	>	}
347
348	<	double getRsw() {
349	<	return rsw_;
350	<	}
303	<
304	<	std::string getFinalConfigFileName() {
305	<	return finalConfigFileName_;
306	<	}
307	<
308	<	void setFinalConfigFileName(const std::string& fileName) {
309	<	finalConfigFileName_ = fileName;
310	<	}
348	>	RealType getCutoffRadius() {
349	>	return cutoffRadius_;
350	>	}
351
352	<	std::string getDumpFileName() {
353	<	return dumpFileName_;
354	<	}
352	>	RealType getSwitchingRadius() {
353	>	return switchingRadius_;
354	>	}
355	>
356	>	RealType getListRadius() {
357	>	return listRadius_;
358	>	}
359
360	<	void setDumpFileName(const std::string& fileName) {
361	<	dumpFileName_ = fileName;
362	<	}
360	>	string getFinalConfigFileName() {
361	>	return finalConfigFileName_;
362	>	}
363
364	<	std::string getStatFileName() {
365	<	return statFileName_;
366	<	}
364	>	void setFinalConfigFileName(const string& fileName) {
365	>	finalConfigFileName_ = fileName;
366	>	}
367	>
368	>	string getRawMetaData() {
369	>	return rawMetaData_;
370	>	}
371	>	void setRawMetaData(const string& rawMetaData) {
372	>	rawMetaData_ = rawMetaData;
373	>	}
374
375	<	void setStatFileName(const std::string& fileName) {
376	<	statFileName_ = fileName;
377	<	}
375	>	string getDumpFileName() {
376	>	return dumpFileName_;
377	>	}
378
379	<	std::string getRestFileName() {
380	<	return restFileName_;
381	<	}
331	<
332	<	void setRestFileName(const std::string& fileName) {
333	<	restFileName_ = fileName;
334	<	}
379	>	void setDumpFileName(const string& fileName) {
380	>	dumpFileName_ = fileName;
381	>	}
382
383	<	/**
384	<	* Sets GlobalGroupMembership
385	<	* @see #SimCreator::setGlobalIndex
386	<	*/
387	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
388	<	assert(globalGroupMembership.size() == nGlobalAtoms_);
389	<	globalGroupMembership_ = globalGroupMembership;
390	<	}
383	>	string getStatFileName() {
384	>	return statFileName_;
385	>	}
386	>
387	>	void setStatFileName(const string& fileName) {
388	>	statFileName_ = fileName;
389	>	}
390	>
391	>	string getRestFileName() {
392	>	return restFileName_;
393	>	}
394	>
395	>	void setRestFileName(const string& fileName) {
396	>	restFileName_ = fileName;
397	>	}
398
399	<	/**
400	<	* Sets GlobalMolMembership
401	<	* @see #SimCreator::setGlobalIndex
402	<	*/
403	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
404	<	assert(globalMolMembership.size() == nGlobalAtoms_);
405	<	globalMolMembership_ = globalMolMembership;
406	<	}
399	>	/**
400	>	* Sets GlobalGroupMembership
401	>	* @see #SimCreator::setGlobalIndex
402	>	*/
403	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
404	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
405	>	globalGroupMembership_ = globalGroupMembership;
406	>	}
407
408	+	/**
409	+	* Sets GlobalMolMembership
410	+	* @see #SimCreator::setGlobalIndex
411	+	*/
412	+	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
413	+	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
414	+	globalMolMembership_ = globalMolMembership;
415	+	}
416
417	<	bool isFortranInitialized() {
418	<	return fortranInitialized_;
419	<	}
417	>
418	>	bool isFortranInitialized() {
419	>	return fortranInitialized_;
420	>	}
421
422	<	//below functions are just forward functions
423	<	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
424	<	//the other hand, has-a relation need composing.
362	<	/**
363	<	* Adds property into property map
364	<	* @param genData GenericData to be added into PropertyMap
365	<	*/
366	<	void addProperty(GenericData* genData);
422	>	bool getCalcBoxDipole() {
423	>	return calcBoxDipole_;
424	>	}
425
426	<	/**
427	<	* Removes property from PropertyMap by name
428	<	* @param propName the name of property to be removed
371	<	*/
372	<	void removeProperty(const std::string& propName);
426	>	bool getUseAtomicVirial() {
427	>	return useAtomicVirial_;
428	>	}
429
430	<	/**
431	<	* clear all of the properties
432	<	*/
433	<	void clearProperties();
430	>	/**
431	>	* Adds property into property map
432	>	* @param genData GenericData to be added into PropertyMap
433	>	*/
434	>	void addProperty(GenericData* genData);
435
436	<	/**
437	<	* Returns all names of properties
438	<	* @return all names of properties
439	<	*/
440	<	std::vector<std::string> getPropertyNames();
436	>	/**
437	>	* Removes property from PropertyMap by name
438	>	* @param propName the name of property to be removed
439	>	*/
440	>	void removeProperty(const string& propName);
441
442	<	/**
443	<	* Returns all of the properties in PropertyMap
444	<	* @return all of the properties in PropertyMap
445	<	*/
389	<	std::vector<GenericData*> getProperties();
442	>	/**
443	>	* clear all of the properties
444	>	*/
445	>	void clearProperties();
446
447	<	/**
448	<	* Returns property
449	<	* @param propName name of property
450	<	* @return a pointer point to property with propName. If no property named propName
451	<	* exists, return NULL
396	<	*/
397	<	GenericData* getPropertyByName(const std::string& propName);
447	>	/**
448	>	* Returns all names of properties
449	>	* @return all names of properties
450	>	*/
451	>	vector<string> getPropertyNames();
452
453	<	/**
454	<	* add all exclude pairs of a molecule into exclude list.
455	<	*/
456	<	void addExcludePairs(Molecule* mol);
453	>	/**
454	>	* Returns all of the properties in PropertyMap
455	>	* @return all of the properties in PropertyMap
456	>	*/
457	>	vector<GenericData*> getProperties();
458
459	<	/**
460	<	* remove all exclude pairs which belong to a molecule from exclude list
461	<	*/
459	>	/**
460	>	* Returns property
461	>	* @param propName name of property
462	>	* @return a pointer point to property with propName. If no property named propName
463	>	* exists, return NULL
464	>	*/
465	>	GenericData* getPropertyByName(const string& propName);
466
467	<	void removeExcludePairs(Molecule* mol);
467	>	/**
468	>	* add all special interaction pairs (including excluded
469	>	* interactions) in a molecule into the appropriate lists.
470	>	*/
471	>	void addInteractionPairs(Molecule* mol);
472
473	+	/**
474	+	* remove all special interaction pairs which belong to a molecule
475	+	* from the appropriate lists.
476	+	*/
477	+	void removeInteractionPairs(Molecule* mol);
478
479	<	/** Returns the unique atom types of local processor in an array */
480	<	std::set<AtomType*> getUniqueAtomTypes();
479	>
480	>	/** Returns the unique atom types of local processor in an array */
481	>	set<AtomType*> getUniqueAtomTypes();
482	>
483	>	/** Returns the set of atom types present in this simulation */
484	>	set<AtomType*> getSimulatedAtomTypes();
485
486	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
486	>	friend ostream& operator <<(ostream& o, SimInfo& info);
487
488	<	void getCutoff(double& rcut, double& rsw);
488	>	void getCutoff(RealType& rcut, RealType& rsw);
489
490	<	private:
490	>	private:
491
492	<	/** fill up the simtype struct*/
493	<	void setupSimType();
492	>	/** fill up the simtype struct*/
493	>	void setupSimType();
494
495	<	/**
496	<	* Setup Fortran Simulation
497	<	* @see #setupFortranParallel
498	<	*/
499	<	void setupFortranSim();
495	>	/**
496	>	* Setup Fortran Simulation
497	>	* @see #setupFortranParallel
498	>	*/
499	>	void setupFortranSim();
500
501	<	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
502	<	void setupCutoff();
501	>	/** Figure out the cutoff radius */
502	>	void setupCutoffRadius();
503	>	/** Figure out the cutoff method */
504	>	void setupCutoffMethod();
505	>	/** Figure out the switching radius */
506	>	void setupSwitchingRadius();
507	>	/** Figure out the neighbor list skin thickness */
508	>	void setupSkinThickness();
509	>	/** Figure out which polynomial type to use for the switching function */
510	>	void setupSwitchingFunction();
511
512	<	/** Calculates the number of degress of freedom in the whole system */
513	<	void calcNdf();
434	<	void calcNdfRaw();
435	<	void calcNdfTrans();
512	>	/** Determine if we need to accumulate the simulation box dipole */
513	>	void setupAccumulateBoxDipole();
514
515	<	/**
516	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
517	<	* system.
518	<	*/
441	<	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
515	>	/** Calculates the number of degress of freedom in the whole system */
516	>	void calcNdf();
517	>	void calcNdfRaw();
518	>	void calcNdfTrans();
519
520	<	ForceField* forceField_;
521	<	Globals* simParams_;
520	>	/**
521	>	* Adds molecule stamp and the total number of the molecule with
522	>	* same molecule stamp in the whole system.
523	>	*/
524	>	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
525
526	<	std::map<int, Molecule*>  molecules_; /**< Molecule array */
527	<
528	<	//degress of freedom
449	<	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
450	<	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
451	<	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
452	<	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
453	<
454	<	//number of global objects
455	<	int nGlobalMols_;       /**< number of molecules in the system */
456	<	int nGlobalAtoms_;   /**< number of atoms in the system */
457	<	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
458	<	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
459	<	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
460	<	/**
461	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
462	<	* corresponding content is the global index of cutoff group this atom belong to.
463	<	* It is filled by SimCreator once and only once, since it never changed during the simulation.
464	<	*/
465	<	std::vector<int> globalGroupMembership_;
466	<
467	<	/**
468	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
469	<	* corresponding content is the global index of molecule this atom belong to.
470	<	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
471	<	*/
472	<	std::vector<int> globalMolMembership_;
526	>	// Other classes holdingn important information
527	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
528	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
529
530	+	///  Counts of local objects
531	+	int nAtoms_;              /**< number of atoms in local processor */
532	+	int nBonds_;              /**< number of bonds in local processor */
533	+	int nBends_;              /**< number of bends in local processor */
534	+	int nTorsions_;           /**< number of torsions in local processor */
535	+	int nInversions_;         /**< number of inversions in local processor */
536	+	int nRigidBodies_;        /**< number of rigid bodies in local processor */
537	+	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
538	+	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
539	+	int nConstraints_;        /**< number of constraints in local processors */
540
541	<	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
542	<	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
543	<
544	<	//number of local objects
545	<	int nAtoms_;                        /**< number of atoms in local processor */
546	<	int nBonds_;                        /**< number of bonds in local processor */
547	<	int nBends_;                        /**< number of bends in local processor */
548	<	int nTorsions_;                    /**< number of torsions in local processor */
549	<	int nRigidBodies_;              /**< number of rigid bodies in local processor */
550	<	int nIntegrableObjects_;    /**< number of integrable objects in local processor */
551	<	int nCutoffGroups_;             /**< number of cutoff groups in local processor */
552	<	int nConstraints_;              /**< number of constraints in local processors */
541	>	/// Counts of global objects
542	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
543	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
544	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
545	>	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
546	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
547	>
548	>	/// Degress of freedom
549	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
550	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
551	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
552	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
553	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
554	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
555
556	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
557	<	Exclude exclude_;
558	<	PropertyMap properties_;                  /**< Generic Property */
559	<	SnapshotManager* sman_;               /**< SnapshotManager */
556	>	/// logicals
557	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
558	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
559	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
560	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
561	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
562	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
563	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
564	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
565
566	<	/**
567	<	* The reason to have a local index manager is that when molecule is migrating to other processors,
568	<	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
569	<	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
570	<	* to make a efficient data moving plan.
571	<	*/
572	<	LocalIndexManager localIndexMan_;
566	>	/// Data structures holding primary simulation objects
567	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
568	>	simtype fInfo_;                   /**< A dual struct shared by C++
569	>	and Fortran to pass
570	>	information about what types
571	>	of calculation are
572	>	required */
573	>
574	>	/// Stamps are templates for objects that are then used to create
575	>	/// groups of objects.  For example, a molecule stamp contains
576	>	/// information on how to build that molecule (i.e. the topology,
577	>	/// the atoms, the bonds, etc.)  Once the system is built, the
578	>	/// stamps are no longer useful.
579	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
580	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
581
582	<	//file names
583	<	std::string finalConfigFileName_;
584	<	std::string dumpFileName_;
585	<	std::string statFileName_;
586	<	std::string restFileName_;
587	<
588	<	double rcut_;       /**< cutoff radius*/
508	<	double rsw_;        /**< radius of switching function*/
582	>	/**
583	>	* A vector that maps between the global index of an atom, and the
584	>	* global index of cutoff group the atom belong to.  It is filled
585	>	* by SimCreator once and only once, since it never changed during
586	>	* the simulation.  It should be nGlobalAtoms_ in size.
587	>	*/
588	>	vector<int> globalGroupMembership_;
589
590	<	bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
590	>	/**
591	>	* A vector that maps between the global index of an atom and the
592	>	* global index of the molecule the atom belongs to.  It is filled
593	>	* by SimCreator once and only once, since it is never changed
594	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
595	>	*/
596	>	vector<int> globalMolMembership_;
597	>
598	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
599	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
600	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
601	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
602	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
603
604	<	#ifdef IS_MPI
605	<	//in Parallel version, we need MolToProc
514	<	public:
515	<
516	<	/**
517	<	* Finds the processor where a molecule resides
518	<	* @return the id of the processor which contains the molecule
519	<	* @param globalIndex global Index of the molecule
520	<	*/
521	<	int getMolToProc(int globalIndex) {
522	<	//assert(globalIndex < molToProcMap_.size());
523	<	return molToProcMap_[globalIndex];
524	<	}
604	>	PropertyMap properties_;       /**< Generic Properties can be added */
605	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
606
607	<	/**
608	<	* Set MolToProcMap array
609	<	* @see #SimCreator::divideMolecules
610	<	*/
611	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
612	<	molToProcMap_ = molToProcMap;
613	<	}
607	>	/**
608	>	* The reason to have a local index manager is that when molecule
609	>	* is migrating to other processors, the atoms and the
610	>	* rigid-bodies will release their local indices to
611	>	* LocalIndexManager. Combining the information of molecule
612	>	* migrating to current processor, Migrator class can query the
613	>	* LocalIndexManager to make a efficient data moving plan.
614	>	*/
615	>	LocalIndexManager localIndexMan_;
616	>
617	>	// unparsed MetaData block for storing in Dump and EOR files:
618	>	string rawMetaData_;
619	>
620	>	// file names
621	>	string finalConfigFileName_;
622	>	string dumpFileName_;
623	>	string statFileName_;
624	>	string restFileName_;
625
626	<	private:
626	>	RealType cutoffRadius_;         /**< cutoff radius for non-bonded interactions */
627	>	RealType switchingRadius_;      /**< inner radius of switching function */
628	>	RealType listRadius_;           /**< Verlet neighbor list radius */
629	>	RealType skinThickness_;        /**< Verlet neighbor list skin thickness */
630	>	CutoffMethod cutoffMethod_;     /**< Cutoff Method for most non-bonded interactions */
631
632	<	void setupFortranParallel();
632	>	bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
633	>
634	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
635	>	the simulation box dipole moment */
636	>
637	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
638	>	Atomic Virials to calculate the pressure */
639	>
640	>	public:
641	>	/**
642	>	* return an integral objects by its global index. In MPI
643	>	* version, if the StuntDouble with specified global index does
644	>	* not belong to local processor, a NULL will be return.
645	>	*/
646	>	StuntDouble* getIOIndexToIntegrableObject(int index);
647	>	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
648	>
649	>	private:
650	>	vector<StuntDouble*> IOIndexToIntegrableObject;
651	>
652	>	public:
653	>
654	>	/**
655	>	* Finds the processor where a molecule resides
656	>	* @return the id of the processor which contains the molecule
657	>	* @param globalIndex global Index of the molecule
658	>	*/
659	>	int getMolToProc(int globalIndex) {
660	>	//assert(globalIndex < molToProcMap_.size());
661	>	return molToProcMap_[globalIndex];
662	>	}
663	>
664	>	/**
665	>	* Set MolToProcMap array
666	>	* @see #SimCreator::divideMolecules
667	>	*/
668	>	void setMolToProcMap(const vector<int>& molToProcMap) {
669	>	molToProcMap_ = molToProcMap;
670	>	}
671
672	<	/**
539	<	* The size of molToProcMap_ is equal to total number of molecules in the system.
540	<	*  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
541	<	* once.
542	<	*/
543	<	std::vector<int> molToProcMap_;
672	>	private:
673
674	<	#endif
674	>	void setupFortranParallel();
675	>
676	>	/**
677	>	* The size of molToProcMap_ is equal to total number of molecules
678	>	* in the system.  It maps a molecule to the processor on which it
679	>	* resides. it is filled by SimCreator once and only once.
680	>	*/
681	>	vector<int> molToProcMap_;
682
683	<	};
683	>	};
684
685	<	} //namespace oopse
685	>	} //namespace OpenMD
686		#endif //BRAINS_SIMMODEL_HPP
687

Comparing:
trunk/src/brains/SimInfo.hpp (property svn:keywords), Revision 417 by chrisfen, Thu Mar 10 15:10:24 2005 UTC vs.
branches/development/src/brains/SimInfo.hpp (property svn:keywords), Revision 1528 by gezelter, Fri Dec 17 20:11:05 2010 UTC

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