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

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trunk/src/brains/SimInfo.hpp (file contents), Revision 384 by tim, Tue Mar 1 19:11:47 2005 UTC vs.
branches/development/src/brains/SimInfo.hpp (file contents), Revision 1467 by gezelter, Sat Jul 17 15:33:03 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	>	namespace OpenMD{
71
72	<	//forward decalration
73	<	class SnapshotManager;
74	<	class Molecule;
75	<	class SelectionManager;
76	<	/**
77	<	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
78	<	* @brief As one of the heavy weight class of OOPSE, SimInfo
79	<	* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
80	<	* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
81	<	* cutoff groups, constrains).
82	<	* Another major change is the index. No matter single version or parallel version,  atoms and
83	<	* rigid bodies have both global index and local index. Local index is not important to molecule as well as
84	<	* cutoff group.
85	<	*/
86	<	class SimInfo {
87	<	public:
88	<	typedef std::map<int, Molecule*>::iterator  MoleculeIterator;
72	>	//forward decalration
73	>	class SnapshotManager;
74	>	class Molecule;
75	>	class SelectionManager;
76	>	class StuntDouble;
77	>	/**
78	>	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
79	>	* @brief One of the heavy weight classes of OpenMD, SimInfo maintains a list of molecules.
80	>	* The Molecule class maintains all of the concrete objects
81	>	* (atoms, bond, bend, torsions, inversions, rigid bodies, cutoff groups,
82	>	* constraints). In both the single and parallel versions, atoms and
83	>	* rigid bodies have both global and local indices.  The local index is
84	>	* not relevant to molecules or cutoff groups.
85	>	*/
86	>	class SimInfo {
87	>	public:
88	>	typedef std::map<int, Molecule*>::iterator  MoleculeIterator;
89
90	<	/**
91	<	* Constructor of SimInfo
92	<	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
93	<	* second element is the total number of molecules with the same molecule stamp in the system
94	<	* @param ff pointer of a concrete ForceField instance
95	<	* @param simParams
96	<	* @note
97	<	*/
98	<	SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams);
99	<	virtual ~SimInfo();
90	>	/**
91	>	* Constructor of SimInfo
92	>	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
93	>	* second element is the total number of molecules with the same molecule stamp in the system
94	>	* @param ff pointer of a concrete ForceField instance
95	>	* @param simParams
96	>	* @note
97	>	*/
98	>	SimInfo(ForceField* ff, Globals* simParams);
99	>	virtual ~SimInfo();
100
101	<	/**
102	<	* Adds a molecule
103	<	* @return return true if adding successfully, return false if the molecule is already in SimInfo
104	<	* @param mol molecule to be added
105	<	*/
106	<	bool addMolecule(Molecule* mol);
101	>	/**
102	>	* Adds a molecule
103	>	* @return return true if adding successfully, return false if the molecule is already in SimInfo
104	>	* @param mol molecule to be added
105	>	*/
106	>	bool addMolecule(Molecule* mol);
107
108	<	/**
109	<	* Removes a molecule from SimInfo
110	<	* @return true if removing successfully, return false if molecule is not in this SimInfo
111	<	*/
112	<	bool removeMolecule(Molecule* mol);
108	>	/**
109	>	* Removes a molecule from SimInfo
110	>	* @return true if removing successfully, return false if molecule is not in this SimInfo
111	>	*/
112	>	bool removeMolecule(Molecule* mol);
113
114	<	/** Returns the total number of molecules in the system. */
115	<	int getNGlobalMolecules() {
116	<	return nGlobalMols_;
117	<	}
114	>	/** Returns the total number of molecules in the system. */
115	>	int getNGlobalMolecules() {
116	>	return nGlobalMols_;
117	>	}
118
119	<	/** Returns the total number of atoms in the system. */
120	<	int getNGlobalAtoms() {
121	<	return nGlobalAtoms_;
122	<	}
119	>	/** Returns the total number of atoms in the system. */
120	>	int getNGlobalAtoms() {
121	>	return nGlobalAtoms_;
122	>	}
123
124	<	/** Returns the total number of cutoff groups in the system. */
125	<	int getNGlobalCutoffGroups() {
126	<	return nGlobalCutoffGroups_;
127	<	}
124	>	/** Returns the total number of cutoff groups in the system. */
125	>	int getNGlobalCutoffGroups() {
126	>	return nGlobalCutoffGroups_;
127	>	}
128
129	<	/**
130	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
131	<	* of atoms which do not belong to the rigid bodies) in the system
132	<	*/
133	<	int getNGlobalIntegrableObjects() {
134	<	return nGlobalIntegrableObjects_;
135	<	}
129	>	/**
130	>	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
131	>	* of atoms which do not belong to the rigid bodies) in the system
132	>	*/
133	>	int getNGlobalIntegrableObjects() {
134	>	return nGlobalIntegrableObjects_;
135	>	}
136
137	<	/**
138	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
139	<	* of atoms which do not belong to the rigid bodies) in the system
140	<	*/
141	<	int getNGlobalRigidBodies() {
142	<	return nGlobalRigidBodies_;
143	<	}
137	>	/**
138	>	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
139	>	* of atoms which do not belong to the rigid bodies) in the system
140	>	*/
141	>	int getNGlobalRigidBodies() {
142	>	return nGlobalRigidBodies_;
143	>	}
144
145	<	int getNGlobalConstraints();
146	<	/**
147	<	* Returns the number of local molecules.
148	<	* @return the number of local molecules
149	<	*/
150	<	int getNMolecules() {
151	<	return molecules_.size();
152	<	}
145	>	int getNGlobalConstraints();
146	>	/**
147	>	* Returns the number of local molecules.
148	>	* @return the number of local molecules
149	>	*/
150	>	int getNMolecules() {
151	>	return molecules_.size();
152	>	}
153
154	<	/** Returns the number of local atoms */
155	<	unsigned int getNAtoms() {
156	<	return nAtoms_;
157	<	}
154	>	/** Returns the number of local atoms */
155	>	unsigned int getNAtoms() {
156	>	return nAtoms_;
157	>	}
158
159	<	/** Returns the number of local bonds */
160	<	unsigned int getNBonds(){
161	<	return nBonds_;
162	<	}
159	>	/** Returns the number of local bonds */
160	>	unsigned int getNBonds(){
161	>	return nBonds_;
162	>	}
163
164	<	/** Returns the number of local bends */
165	<	unsigned int getNBends() {
166	<	return nBends_;
167	<	}
164	>	/** Returns the number of local bends */
165	>	unsigned int getNBends() {
166	>	return nBends_;
167	>	}
168
169	<	/** Returns the number of local torsions */
170	<	unsigned int getNTorsions() {
171	<	return nTorsions_;
172	<	}
169	>	/** Returns the number of local torsions */
170	>	unsigned int getNTorsions() {
171	>	return nTorsions_;
172	>	}
173
174	<	/** Returns the number of local rigid bodies */
175	<	unsigned int getNRigidBodies() {
176	<	return nRigidBodies_;
177	<	}
174	>	/** Returns the number of local torsions */
175	>	unsigned int getNInversions() {
176	>	return nInversions_;
177	>	}
178	>	/** Returns the number of local rigid bodies */
179	>	unsigned int getNRigidBodies() {
180	>	return nRigidBodies_;
181	>	}
182
183	<	/** Returns the number of local integrable objects */
184	<	unsigned int getNIntegrableObjects() {
185	<	return nIntegrableObjects_;
186	<	}
183	>	/** Returns the number of local integrable objects */
184	>	unsigned int getNIntegrableObjects() {
185	>	return nIntegrableObjects_;
186	>	}
187
188	<	/** Returns the number of local cutoff groups */
189	<	unsigned int getNCutoffGroups() {
190	<	return nCutoffGroups_;
191	<	}
188	>	/** Returns the number of local cutoff groups */
189	>	unsigned int getNCutoffGroups() {
190	>	return nCutoffGroups_;
191	>	}
192
193	<	/** Returns the total number of constraints in this SimInfo */
194	<	unsigned int getNConstraints() {
195	<	return nConstraints_;
196	<	}
193	>	/** Returns the total number of constraints in this SimInfo */
194	>	unsigned int getNConstraints() {
195	>	return nConstraints_;
196	>	}
197
198	<	/**
199	<	* Returns the first molecule in this SimInfo and intialize the iterator.
200	<	* @return the first molecule, return NULL if there is not molecule in this SimInfo
201	<	* @param i the iterator of molecule array (user shouldn't change it)
202	<	*/
203	<	Molecule* beginMolecule(MoleculeIterator& i);
198	>	/**
199	>	* Returns the first molecule in this SimInfo and intialize the iterator.
200	>	* @return the first molecule, return NULL if there is not molecule in this SimInfo
201	>	* @param i the iterator of molecule array (user shouldn't change it)
202	>	*/
203	>	Molecule* beginMolecule(MoleculeIterator& i);
204
205	<	/**
206	<	* Returns the next avaliable Molecule based on the iterator.
207	<	* @return the next avaliable molecule, return NULL if reaching the end of the array
208	<	* @param i the iterator of molecule array
209	<	*/
210	<	Molecule* nextMolecule(MoleculeIterator& i);
206	<
207	<	/** Returns the number of degrees of freedom */
208	<	int getNdf() {
209	<	return ndf_;
210	<	}
205	>	/**
206	>	* Returns the next avaliable Molecule based on the iterator.
207	>	* @return the next avaliable molecule, return NULL if reaching the end of the array
208	>	* @param i the iterator of molecule array
209	>	*/
210	>	Molecule* nextMolecule(MoleculeIterator& i);
211
212	<	/** Returns the number of raw degrees of freedom */
213	<	int getNdfRaw() {
214	<	return ndfRaw_;
215	<	}
212	>	/** Returns the number of degrees of freedom */
213	>	int getNdf() {
214	>	return ndf_ - getFdf();
215	>	}
216
217	<	/** Returns the number of translational degrees of freedom */
218	<	int getNdfTrans() {
219	<	return ndfTrans_;
220	<	}
217	>	/** Returns the number of raw degrees of freedom */
218	>	int getNdfRaw() {
219	>	return ndfRaw_;
220	>	}
221
222	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
222	>	/** Returns the number of translational degrees of freedom */
223	>	int getNdfTrans() {
224	>	return ndfTrans_;
225	>	}
226	>
227	>	/** sets the current number of frozen degrees of freedom */
228	>	void setFdf(int fdf) {
229	>	fdf_local = fdf;
230	>	}
231	>
232	>	int getFdf();
233	>
234	>	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
235
236	<	/** Returns the total number of z-constraint molecules in the system */
237	<	int getNZconstraint() {
238	<	return nZconstraint_;
239	<	}
236	>	/** Returns the total number of z-constraint molecules in the system */
237	>	int getNZconstraint() {
238	>	return nZconstraint_;
239	>	}
240
241	<	/**
242	<	* Sets the number of z-constraint molecules in the system.
243	<	*/
244	<	void setNZconstraint(int nZconstraint) {
245	<	nZconstraint_ = nZconstraint;
246	<	}
241	>	/**
242	>	* Sets the number of z-constraint molecules in the system.
243	>	*/
244	>	void setNZconstraint(int nZconstraint) {
245	>	nZconstraint_ = nZconstraint;
246	>	}
247
248	<	/** Returns the snapshot manager. */
249	<	SnapshotManager* getSnapshotManager() {
250	<	return sman_;
251	<	}
248	>	/** Returns the snapshot manager. */
249	>	SnapshotManager* getSnapshotManager() {
250	>	return sman_;
251	>	}
252
253	<	/** Sets the snapshot manager. */
254	<	void setSnapshotManager(SnapshotManager* sman);
253	>	/** Sets the snapshot manager. */
254	>	void setSnapshotManager(SnapshotManager* sman);
255
256	<	/** Returns the force field */
257	<	ForceField* getForceField() {
258	<	return forceField_;
259	<	}
256	>	/** Returns the force field */
257	>	ForceField* getForceField() {
258	>	return forceField_;
259	>	}
260
261	<	Globals* getSimParams() {
262	<	return simParams_;
263	<	}
261	>	Globals* getSimParams() {
262	>	return simParams_;
263	>	}
264
265	<	/** Returns the velocity of center of mass of the whole system.*/
266	<	Vector3d getComVel();
265	>	/** Returns the velocity of center of mass of the whole system.*/
266	>	Vector3d getComVel();
267
268	<	/** Returns the center of the mass of the whole system.*/
269	<	Vector3d getCom();
268	>	/** Returns the center of the mass of the whole system.*/
269	>	Vector3d getCom();
270	>	/** Returns the center of the mass and Center of Mass velocity of the whole system.*/
271	>	void getComAll(Vector3d& com,Vector3d& comVel);
272
273	<	/** main driver function to interact with fortran during the initialization and molecule migration */
274	<	void update();
273	>	/** Returns intertia tensor for the entire system and system Angular Momentum.*/
274	>	void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
275	>
276	>	/** Returns system angular momentum */
277	>	Vector3d getAngularMomentum();
278
279	<	/** Returns the local index manager */
280	<	LocalIndexManager* getLocalIndexManager() {
281	<	return &localIndexMan_;
282	<	}
279	>	/** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/
280	>	void getGyrationalVolume(RealType &vol);
281	>	/** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/
282	>	void getGyrationalVolume(RealType &vol, RealType &detI);
283	>	/** main driver function to interact with fortran during the initialization and molecule migration */
284	>	void update();
285
286	<	int getMoleculeStampId(int globalIndex) {
287	<	//assert(globalIndex < molStampIds_.size())
288	<	return molStampIds_[globalIndex];
289	<	}
286	>	/** Returns the local index manager */
287	>	LocalIndexManager* getLocalIndexManager() {
288	>	return &localIndexMan_;
289	>	}
290
291	<	/** Returns the molecule stamp */
292	<	MoleculeStamp* getMoleculeStamp(int id) {
293	<	return moleculeStamps_[id];
294	<	}
291	>	int getMoleculeStampId(int globalIndex) {
292	>	//assert(globalIndex < molStampIds_.size())
293	>	return molStampIds_[globalIndex];
294	>	}
295
296	<	/** Return the total number of the molecule stamps */
297	<	int getNMoleculeStamp() {
298	<	return moleculeStamps_.size();
299	<	}
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);
296	>	/** Returns the molecule stamp */
297	>	MoleculeStamp* getMoleculeStamp(int id) {
298	>	return moleculeStamps_[id];
299	>	}
300
301	<	return i != molecules_.end() ? i->second : NULL;
302	<	}
301	>	/** Return the total number of the molecule stamps */
302	>	int getNMoleculeStamp() {
303	>	return moleculeStamps_.size();
304	>	}
305	>	/**
306	>	* Finds a molecule with a specified global index
307	>	* @return a pointer point to found molecule
308	>	* @param index
309	>	*/
310	>	Molecule* getMoleculeByGlobalIndex(int index) {
311	>	MoleculeIterator i;
312	>	i = molecules_.find(index);
313
314	<	/** Calculate the maximum cutoff radius based on the atom types */
315	<	double calcMaxCutoffRadius();
314	>	return i != molecules_.end() ? i->second : NULL;
315	>	}
316
317	<	double getRcut() {
318	<	return rcut_;
319	<	}
317	>	int getGlobalMolMembership(int id){
318	>	return globalMolMembership_[id];
319	>	}
320
321	<	double getRsw() {
322	<	return rsw_;
323	<	}
303	<
304	<	std::string getFinalConfigFileName() {
305	<	return finalConfigFileName_;
306	<	}
307	<
308	<	void setFinalConfigFileName(const std::string& fileName) {
309	<	finalConfigFileName_ = fileName;
310	<	}
321	>	RealType getRcut() {
322	>	return rcut_;
323	>	}
324
325	<	std::string getDumpFileName() {
326	<	return dumpFileName_;
327	<	}
315	<
316	<	void setDumpFileName(const std::string& fileName) {
317	<	dumpFileName_ = fileName;
318	<	}
325	>	RealType getRsw() {
326	>	return rsw_;
327	>	}
328
329	<	std::string getStatFileName() {
330	<	return statFileName_;
331	<	}
329	>	RealType getList() {
330	>	return rlist_;
331	>	}
332
333	<	void setStatFileName(const std::string& fileName) {
334	<	statFileName_ = fileName;
335	<	}
333	>	std::string getFinalConfigFileName() {
334	>	return finalConfigFileName_;
335	>	}
336
337	<	/**
338	<	* Sets GlobalGroupMembership
339	<	* @see #SimCreator::setGlobalIndex
331	<	*/
332	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
333	<	assert(globalGroupMembership.size() == nGlobalAtoms_);
334	<	globalGroupMembership_ = globalGroupMembership;
335	<	}
337	>	void setFinalConfigFileName(const std::string& fileName) {
338	>	finalConfigFileName_ = fileName;
339	>	}
340
341	<	/**
342	<	* Sets GlobalMolMembership
343	<	* @see #SimCreator::setGlobalIndex
344	<	*/
345	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
346	<	assert(globalMolMembership.size() == nGlobalAtoms_);
347	<	globalMolMembership_ = globalMolMembership;
348	<	}
341	>	std::string getRawMetaData() {
342	>	return rawMetaData_;
343	>	}
344	>	void setRawMetaData(const std::string& rawMetaData) {
345	>	rawMetaData_ = rawMetaData;
346	>	}
347	>
348	>	std::string getDumpFileName() {
349	>	return dumpFileName_;
350	>	}
351	>
352	>	void setDumpFileName(const std::string& fileName) {
353	>	dumpFileName_ = fileName;
354	>	}
355
356	+	std::string getStatFileName() {
357	+	return statFileName_;
358	+	}
359	+
360	+	void setStatFileName(const std::string& fileName) {
361	+	statFileName_ = fileName;
362	+	}
363	+
364	+	std::string getRestFileName() {
365	+	return restFileName_;
366	+	}
367	+
368	+	void setRestFileName(const std::string& fileName) {
369	+	restFileName_ = fileName;
370	+	}
371
372	<	bool isFortranInitialized() {
373	<	return fortranInitialized_;
374	<	}
372	>	/**
373	>	* Sets GlobalGroupMembership
374	>	* @see #SimCreator::setGlobalIndex
375	>	*/
376	>	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
377	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
378	>	globalGroupMembership_ = globalGroupMembership;
379	>	}
380	>
381	>	/**
382	>	* Sets GlobalMolMembership
383	>	* @see #SimCreator::setGlobalIndex
384	>	*/
385	>	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
386	>	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
387	>	globalMolMembership_ = globalMolMembership;
388	>	}
389	>
390	>
391	>	bool isFortranInitialized() {
392	>	return fortranInitialized_;
393	>	}
394
395	<	//below functions are just forward functions
396	<	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
397	<	//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);
395	>	bool getCalcBoxDipole() {
396	>	return calcBoxDipole_;
397	>	}
398
399	<	/**
400	<	* Removes property from PropertyMap by name
401	<	* @param propName the name of property to be removed
363	<	*/
364	<	void removeProperty(const std::string& propName);
399	>	bool getUseAtomicVirial() {
400	>	return useAtomicVirial_;
401	>	}
402
403	<	/**
404	<	* clear all of the properties
405	<	*/
406	<	void clearProperties();
403	>	//below functions are just forward functions
404	>	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
405	>	//the other hand, has-a relation need composing.
406	>	/**
407	>	* Adds property into property map
408	>	* @param genData GenericData to be added into PropertyMap
409	>	*/
410	>	void addProperty(GenericData* genData);
411
412	<	/**
413	<	* Returns all names of properties
414	<	* @return all names of properties
415	<	*/
416	<	std::vector<std::string> getPropertyNames();
412	>	/**
413	>	* Removes property from PropertyMap by name
414	>	* @param propName the name of property to be removed
415	>	*/
416	>	void removeProperty(const std::string& propName);
417
418	<	/**
419	<	* Returns all of the properties in PropertyMap
420	<	* @return all of the properties in PropertyMap
421	<	*/
381	<	std::vector<GenericData*> getProperties();
418	>	/**
419	>	* clear all of the properties
420	>	*/
421	>	void clearProperties();
422
423	<	/**
424	<	* Returns property
425	<	* @param propName name of property
426	<	* @return a pointer point to property with propName. If no property named propName
427	<	* exists, return NULL
388	<	*/
389	<	GenericData* getPropertyByName(const std::string& propName);
423	>	/**
424	>	* Returns all names of properties
425	>	* @return all names of properties
426	>	*/
427	>	std::vector<std::string> getPropertyNames();
428
429	<	/**
430	<	* add all exclude pairs of a molecule into exclude list.
431	<	*/
432	<	void addExcludePairs(Molecule* mol);
429	>	/**
430	>	* Returns all of the properties in PropertyMap
431	>	* @return all of the properties in PropertyMap
432	>	*/
433	>	std::vector<GenericData*> getProperties();
434
435	<	/**
436	<	* remove all exclude pairs which belong to a molecule from exclude list
437	<	*/
435	>	/**
436	>	* Returns property
437	>	* @param propName name of property
438	>	* @return a pointer point to property with propName. If no property named propName
439	>	* exists, return NULL
440	>	*/
441	>	GenericData* getPropertyByName(const std::string& propName);
442
443	<	void removeExcludePairs(Molecule* mol);
443	>	/**
444	>	* add all special interaction pairs (including excluded
445	>	* interactions) in a molecule into the appropriate lists.
446	>	*/
447	>	void addInteractionPairs(Molecule* mol);
448
449	+	/**
450	+	* remove all special interaction pairs which belong to a molecule
451	+	* from the appropriate lists.
452	+	*/
453	+	void removeInteractionPairs(Molecule* mol);
454
403	–	SelectionManager* getSelectionManager() {
404	–	return selectMan_;
405	–	}
455
456	<	/** Returns the unique atom types of local processor in an array */
457	<	std::set<AtomType*> getUniqueAtomTypes();
456	>	/** Returns the unique atom types of local processor in an array */
457	>	std::set<AtomType*> getUniqueAtomTypes();
458
459	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
459	>	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
460
461	<	void getCutoff(double& rcut, double& rsw);
461	>	void getCutoff(RealType& rcut, RealType& rsw);
462
463	<	private:
463	>	private:
464
465	<	/** fill up the simtype struct*/
466	<	void setupSimType();
465	>	/** fill up the simtype struct*/
466	>	void setupSimType();
467
468	<	/**
469	<	* Setup Fortran Simulation
470	<	* @see #setupFortranParallel
471	<	*/
472	<	void setupFortranSim();
468	>	/**
469	>	* Setup Fortran Simulation
470	>	* @see #setupFortranParallel
471	>	*/
472	>	void setupFortranSim();
473
474	<	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
475	<	void setupCutoff();
474	>	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
475	>	void setupCutoff();
476
477	<	/** Calculates the number of degress of freedom in the whole system */
478	<	void calcNdf();
430	<	void calcNdfRaw();
431	<	void calcNdfTrans();
477	>	/** Figure out which coulombic correction method to use and pass to fortran */
478	>	void setupElectrostaticSummationMethod( int isError );
479
480	<	/**
481	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
435	<	* system.
436	<	*/
437	<	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
480	>	/** Figure out which polynomial type to use for the switching function */
481	>	void setupSwitchingFunction();
482
483	<	ForceField* forceField_;
484	<	Globals* simParams_;
483	>	/** Determine if we need to accumulate the simulation box dipole */
484	>	void setupAccumulateBoxDipole();
485
486	<	std::map<int, Molecule*>  molecules_; /**< Molecule array */
486	>	/** Calculates the number of degress of freedom in the whole system */
487	>	void calcNdf();
488	>	void calcNdfRaw();
489	>	void calcNdfTrans();
490	>
491	>	ForceField* forceField_;
492	>	Globals* simParams_;
493	>
494	>	std::map<int, Molecule*>  molecules_; /**< Molecule array */
495	>
496	>	/**
497	>	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
498	>	* system.
499	>	*/
500	>	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
501
502	<	//degress of freedom
503	<	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
504	<	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
505	<	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
506	<	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
502	>	//degress of freedom
503	>	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
504	>	int fdf_local;       /**< number of frozen degrees of freedom */
505	>	int fdf_;            /**< number of frozen degrees of freedom */
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 */
509
510	<	//number of global objects
511	<	int nGlobalMols_;       /**< number of molecules in the system */
512	<	int nGlobalAtoms_;   /**< number of atoms in the system */
513	<	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
514	<	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
515	<	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
516	<	/**
517	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
518	<	* corresponding content is the global index of cutoff group this atom belong to.
519	<	* It is filled by SimCreator once and only once, since it never changed during the simulation.
520	<	*/
521	<	std::vector<int> globalGroupMembership_;
510	>	//number of global objects
511	>	int nGlobalMols_;       /**< number of molecules in the system */
512	>	int nGlobalAtoms_;   /**< number of atoms in the system */
513	>	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
514	>	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
515	>	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
516	>	/**
517	>	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
518	>	* corresponding content is the global index of cutoff group this atom belong to.
519	>	* It is filled by SimCreator once and only once, since it never changed during the simulation.
520	>	*/
521	>	std::vector<int> globalGroupMembership_;
522
523	<	/**
524	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
525	<	* corresponding content is the global index of molecule this atom belong to.
526	<	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
527	<	*/
528	<	std::vector<int> globalMolMembership_;
523	>	/**
524	>	* the size of globalMolMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
525	>	* corresponding content is the global index of molecule this atom belong to.
526	>	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
527	>	*/
528	>	std::vector<int> globalMolMembership_;
529
530
531	<	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
532	<	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
531	>	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
532	>	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
533
534	<	//number of local objects
535	<	int nAtoms_;                        /**< number of atoms in local processor */
536	<	int nBonds_;                        /**< number of bonds in local processor */
537	<	int nBends_;                        /**< number of bends in local processor */
538	<	int nTorsions_;                    /**< number of torsions in local processor */
539	<	int nRigidBodies_;              /**< number of rigid bodies in local processor */
540	<	int nIntegrableObjects_;    /**< number of integrable objects in local processor */
541	<	int nCutoffGroups_;             /**< number of cutoff groups in local processor */
542	<	int nConstraints_;              /**< number of constraints in local processors */
534	>	//number of local objects
535	>	int nAtoms_;              /**< number of atoms in local processor */
536	>	int nBonds_;              /**< number of bonds in local processor */
537	>	int nBends_;              /**< number of bends in local processor */
538	>	int nTorsions_;           /**< number of torsions in local processor */
539	>	int nInversions_;         /**< number of inversions in local processor */
540	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
541	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
542	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
543	>	int nConstraints_;        /**< number of constraints in local processors */
544
545	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
546	<	Exclude exclude_;
547	<	PropertyMap properties_;                  /**< Generic Property */
548	<	SnapshotManager* sman_;               /**< SnapshotManager */
545	>	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
546	>	PairList excludedInteractions_;
547	>	PairList oneTwoInteractions_;
548	>	PairList oneThreeInteractions_;
549	>	PairList oneFourInteractions_;
550	>	PropertyMap properties_;                  /**< Generic Property */
551	>	SnapshotManager* sman_;               /**< SnapshotManager */
552
553	<	/**
554	<	* The reason to have a local index manager is that when molecule is migrating to other processors,
555	<	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
556	<	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
557	<	* to make a efficient data moving plan.
558	<	*/
559	<	LocalIndexManager localIndexMan_;
553	>	/**
554	>	* The reason to have a local index manager is that when molecule is migrating to other processors,
555	>	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
556	>	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
557	>	* to make a efficient data moving plan.
558	>	*/
559	>	LocalIndexManager localIndexMan_;
560
561	<	//file names
562	<	std::string finalConfigFileName_;
499	<	std::string dumpFileName_;
500	<	std::string statFileName_;
561	>	// unparsed MetaData block for storing in Dump and EOR files:
562	>	std::string rawMetaData_;
563
564	<	double rcut_;       /**< cutoff radius*/
565	<	double rsw_;        /**< radius of switching function*/
564	>	//file names
565	>	std::string finalConfigFileName_;
566	>	std::string dumpFileName_;
567	>	std::string statFileName_;
568	>	std::string restFileName_;
569	>
570	>	RealType rcut_;       /**< cutoff radius*/
571	>	RealType rsw_;        /**< radius of switching function*/
572	>	RealType rlist_;      /**< neighbor list radius */
573
574	<	bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
574	>	int ljsp_; /**< use shifted potential for LJ*/
575	>	int ljsf_; /**< use shifted force for LJ*/
576
577	<	SelectionManager* selectMan_;
578	<	#ifdef IS_MPI
579	<	//in Parallel version, we need MolToProc
577	>	bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
578	>
579	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
580	>	the simulation box dipole moment */
581	>
582	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
583	>	Atomic Virials to calculate the pressure */
584	>
585		public:
586	+	/**
587	+	* return an integral objects by its global index. In MPI version, if the StuntDouble with specified
588	+	* global index does not belong to local processor, a NULL will be return.
589	+	*/
590	+	StuntDouble* getIOIndexToIntegrableObject(int index);
591	+	void setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v);
592	+	private:
593	+	std::vector<StuntDouble*> IOIndexToIntegrableObject;
594	+	//public:
595	+	//void setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v);
596	+	/**
597	+	* return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
598	+	* global index does not belong to local processor, a NULL will be return.
599	+	*/
600	+	//StuntDouble* getStuntDoubleFromGlobalIndex(int index);
601	+	//private:
602	+	//std::vector<StuntDouble*> sdByGlobalIndex_;
603	+
604	+	//in Parallel version, we need MolToProc
605	+	public:
606
607	<	/**
608	<	* Finds the processor where a molecule resides
609	<	* @return the id of the processor which contains the molecule
610	<	* @param globalIndex global Index of the molecule
611	<	*/
612	<	int getMolToProc(int globalIndex) {
613	<	//assert(globalIndex < molToProcMap_.size());
614	<	return molToProcMap_[globalIndex];
615	<	}
607	>	/**
608	>	* Finds the processor where a molecule resides
609	>	* @return the id of the processor which contains the molecule
610	>	* @param globalIndex global Index of the molecule
611	>	*/
612	>	int getMolToProc(int globalIndex) {
613	>	//assert(globalIndex < molToProcMap_.size());
614	>	return molToProcMap_[globalIndex];
615	>	}
616
617	<	/**
618	<	* Set MolToProcMap array
619	<	* @see #SimCreator::divideMolecules
620	<	*/
621	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
622	<	molToProcMap_ = molToProcMap;
623	<	}
617	>	/**
618	>	* Set MolToProcMap array
619	>	* @see #SimCreator::divideMolecules
620	>	*/
621	>	void setMolToProcMap(const std::vector<int>& molToProcMap) {
622	>	molToProcMap_ = molToProcMap;
623	>	}
624
625	<	private:
625	>	private:
626
627	<	void setupFortranParallel();
627	>	void setupFortranParallel();
628
629	<	/**
630	<	* The size of molToProcMap_ is equal to total number of molecules in the system.
631	<	*  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
632	<	* once.
633	<	*/
634	<	std::vector<int> molToProcMap_;
629	>	/**
630	>	* The size of molToProcMap_ is equal to total number of molecules
631	>	* in the system.  It maps a molecule to the processor on which it
632	>	* resides. it is filled by SimCreator once and only once.
633	>	*/
634	>	std::vector<int> molToProcMap_;
635
541	–	#endif
636
637	<	};
637	>	};
638
639	<	} //namespace oopse
639	>	} //namespace OpenMD
640		#endif //BRAINS_SIMMODEL_HPP
641

Comparing:
trunk/src/brains/SimInfo.hpp (property svn:keywords), Revision 384 by tim, Tue Mar 1 19:11:47 2005 UTC vs.
branches/development/src/brains/SimInfo.hpp (property svn:keywords), Revision 1467 by gezelter, Sat Jul 17 15:33:03 2010 UTC

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