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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 1569 by gezelter, Thu May 26 13:55:04 2011 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/SwitchingFunction.hpp"
66
67	<	//another nonsense macro declaration
68	<	#define __C
69	<	#include "brains/fSimulation.h"
67	>	using namespace std;
68	>	namespace OpenMD{
69	>	//forward declaration
70	>	class SnapshotManager;
71	>	class Molecule;
72	>	class SelectionManager;
73	>	class StuntDouble;
74
75	<	namespace oopse{
75	>	/**
76	>	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
77	>	*
78	>	* @brief One of the heavy-weight classes of OpenMD, SimInfo
79	>	* maintains objects and variables relating to the current
80	>	* simulation.  This includes the master list of Molecules.  The
81	>	* Molecule class maintains all of the concrete objects (Atoms,
82	>	* Bond, Bend, Torsions, Inversions, RigidBodies, CutoffGroups,
83	>	* Constraints). In both the single and parallel versions, Atoms and
84	>	* RigidBodies have both global and local indices.
85	>	*/
86	>	class SimInfo {
87	>	public:
88	>	typedef map<int, Molecule*>::iterator  MoleculeIterator;
89	>
90	>	/**
91	>	* Constructor of SimInfo
92	>	*
93	>	* @param molStampPairs MoleculeStamp Array. The first element of
94	>	* the pair is molecule stamp, the second element is the total
95	>	* number of molecules with the same molecule stamp in the system
96	>	*
97	>	* @param ff pointer of a concrete ForceField instance
98	>	*
99	>	* @param simParams
100	>	*/
101	>	SimInfo(ForceField* ff, Globals* simParams);
102	>	virtual ~SimInfo();
103
104	<	//forward decalration
105	<	class SnapshotManager;
106	<	class Molecule;
107	<	class SelectionManager;
108	<	/**
109	<	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
110	<	* @brief As one of the heavy weight class of OOPSE, SimInfo
111	<	* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
112	<	* 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;
104	>	/**
105	>	* Adds a molecule
106	>	*
107	>	* @return return true if adding successfully, return false if the
108	>	* molecule is already in SimInfo
109	>	*
110	>	* @param mol molecule to be added
111	>	*/
112	>	bool addMolecule(Molecule* mol);
113
114	<	/**
115	<	* Constructor of SimInfo
116	<	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
117	<	* second element is the total number of molecules with the same molecule stamp in the system
118	<	* @param ff pointer of a concrete ForceField instance
119	<	* @param simParams
120	<	* @note
96	<	*/
97	<	SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams);
98	<	virtual ~SimInfo();
114	>	/**
115	>	* Removes a molecule from SimInfo
116	>	*
117	>	* @return true if removing successfully, return false if molecule
118	>	* is not in this SimInfo
119	>	*/
120	>	bool removeMolecule(Molecule* mol);
121
122	<	/**
123	<	* Adds a molecule
124	<	* @return return true if adding successfully, return false if the molecule is already in SimInfo
125	<	* @param mol molecule to be added
104	<	*/
105	<	bool addMolecule(Molecule* mol);
122	>	/** Returns the total number of molecules in the system. */
123	>	int getNGlobalMolecules() {
124	>	return nGlobalMols_;
125	>	}
126
127	<	/**
128	<	* Removes a molecule from SimInfo
129	<	* @return true if removing successfully, return false if molecule is not in this SimInfo
130	<	*/
111	<	bool removeMolecule(Molecule* mol);
127	>	/** Returns the total number of atoms in the system. */
128	>	int getNGlobalAtoms() {
129	>	return nGlobalAtoms_;
130	>	}
131
132	<	/** Returns the total number of molecules in the system. */
133	<	int getNGlobalMolecules() {
134	<	return nGlobalMols_;
135	<	}
132	>	/** Returns the total number of cutoff groups in the system. */
133	>	int getNGlobalCutoffGroups() {
134	>	return nGlobalCutoffGroups_;
135	>	}
136
137	<	/** Returns the total number of atoms in the system. */
138	<	int getNGlobalAtoms() {
139	<	return nGlobalAtoms_;
140	<	}
137	>	/**
138	>	* Returns the total number of integrable objects (total number of
139	>	* rigid bodies plus the total number of atoms which do not belong
140	>	* to the rigid bodies) in the system
141	>	*/
142	>	int getNGlobalIntegrableObjects() {
143	>	return nGlobalIntegrableObjects_;
144	>	}
145
146	<	/** Returns the total number of cutoff groups in the system. */
147	<	int getNGlobalCutoffGroups() {
148	<	return nGlobalCutoffGroups_;
149	<	}
146	>	/**
147	>	* Returns the total number of integrable objects (total number of
148	>	* rigid bodies plus the total number of atoms which do not belong
149	>	* to the rigid bodies) in the system
150	>	*/
151	>	int getNGlobalRigidBodies() {
152	>	return nGlobalRigidBodies_;
153	>	}
154
155	<	/**
156	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
157	<	* of atoms which do not belong to the rigid bodies) in the system
158	<	*/
159	<	int getNGlobalIntegrableObjects() {
160	<	return nGlobalIntegrableObjects_;
161	<	}
155	>	int getNGlobalConstraints();
156	>	/**
157	>	* Returns the number of local molecules.
158	>	* @return the number of local molecules
159	>	*/
160	>	int getNMolecules() {
161	>	return molecules_.size();
162	>	}
163
164	<	/**
165	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
166	<	* of atoms which do not belong to the rigid bodies) in the system
167	<	*/
140	<	int getNGlobalRigidBodies() {
141	<	return nGlobalRigidBodies_;
142	<	}
164	>	/** Returns the number of local atoms */
165	>	unsigned int getNAtoms() {
166	>	return nAtoms_;
167	>	}
168
169	<	int getNGlobalConstraints();
170	<	/**
171	<	* Returns the number of local molecules.
172	<	* @return the number of local molecules
148	<	*/
149	<	int getNMolecules() {
150	<	return molecules_.size();
151	<	}
169	>	/** Returns the number of local bonds */
170	>	unsigned int getNBonds(){
171	>	return nBonds_;
172	>	}
173
174	<	/** Returns the number of local atoms */
175	<	unsigned int getNAtoms() {
176	<	return nAtoms_;
177	<	}
174	>	/** Returns the number of local bends */
175	>	unsigned int getNBends() {
176	>	return nBends_;
177	>	}
178
179	<	/** Returns the number of local bonds */
180	<	unsigned int getNBonds(){
181	<	return nBonds_;
182	<	}
179	>	/** Returns the number of local torsions */
180	>	unsigned int getNTorsions() {
181	>	return nTorsions_;
182	>	}
183
184	<	/** Returns the number of local bends */
185	<	unsigned int getNBends() {
186	<	return nBends_;
187	<	}
184	>	/** Returns the number of local torsions */
185	>	unsigned int getNInversions() {
186	>	return nInversions_;
187	>	}
188	>	/** Returns the number of local rigid bodies */
189	>	unsigned int getNRigidBodies() {
190	>	return nRigidBodies_;
191	>	}
192
193	<	/** Returns the number of local torsions */
194	<	unsigned int getNTorsions() {
195	<	return nTorsions_;
196	<	}
193	>	/** Returns the number of local integrable objects */
194	>	unsigned int getNIntegrableObjects() {
195	>	return nIntegrableObjects_;
196	>	}
197
198	<	/** Returns the number of local rigid bodies */
199	<	unsigned int getNRigidBodies() {
200	<	return nRigidBodies_;
201	<	}
198	>	/** Returns the number of local cutoff groups */
199	>	unsigned int getNCutoffGroups() {
200	>	return nCutoffGroups_;
201	>	}
202
203	<	/** Returns the number of local integrable objects */
204	<	unsigned int getNIntegrableObjects() {
205	<	return nIntegrableObjects_;
206	<	}
182	<
183	<	/** Returns the number of local cutoff groups */
184	<	unsigned int getNCutoffGroups() {
185	<	return nCutoffGroups_;
186	<	}
187	<
188	<	/** Returns the total number of constraints in this SimInfo */
189	<	unsigned int getNConstraints() {
190	<	return nConstraints_;
191	<	}
203	>	/** Returns the total number of constraints in this SimInfo */
204	>	unsigned int getNConstraints() {
205	>	return nConstraints_;
206	>	}
207
208	<	/**
209	<	* Returns the first molecule in this SimInfo and intialize the iterator.
210	<	* @return the first molecule, return NULL if there is not molecule in this SimInfo
211	<	* @param i the iterator of molecule array (user shouldn't change it)
212	<	*/
213	<	Molecule* beginMolecule(MoleculeIterator& i);
208	>	/**
209	>	* Returns the first molecule in this SimInfo and intialize the iterator.
210	>	* @return the first molecule, return NULL if there is not molecule in this SimInfo
211	>	* @param i the iterator of molecule array (user shouldn't change it)
212	>	*/
213	>	Molecule* beginMolecule(MoleculeIterator& i);
214
215	<	/**
216	<	* Returns the next avaliable Molecule based on the iterator.
217	<	* @return the next avaliable molecule, return NULL if reaching the end of the array
218	<	* @param i the iterator of molecule array
219	<	*/
220	<	Molecule* nextMolecule(MoleculeIterator& i);
206	<
207	<	/** Returns the number of degrees of freedom */
208	<	int getNdf() {
209	<	return ndf_;
210	<	}
215	>	/**
216	>	* Returns the next avaliable Molecule based on the iterator.
217	>	* @return the next avaliable molecule, return NULL if reaching the end of the array
218	>	* @param i the iterator of molecule array
219	>	*/
220	>	Molecule* nextMolecule(MoleculeIterator& i);
221
222	<	/** Returns the number of raw degrees of freedom */
223	<	int getNdfRaw() {
224	<	return ndfRaw_;
225	<	}
222	>	/** Returns the number of degrees of freedom */
223	>	int getNdf() {
224	>	return ndf_ - getFdf();
225	>	}
226
227	<	/** Returns the number of translational degrees of freedom */
228	<	int getNdfTrans() {
229	<	return ndfTrans_;
230	<	}
227	>	/** Returns the number of raw degrees of freedom */
228	>	int getNdfRaw() {
229	>	return ndfRaw_;
230	>	}
231
232	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
232	>	/** Returns the number of translational degrees of freedom */
233	>	int getNdfTrans() {
234	>	return ndfTrans_;
235	>	}
236	>
237	>	/** sets the current number of frozen degrees of freedom */
238	>	void setFdf(int fdf) {
239	>	fdf_local = fdf;
240	>	}
241	>
242	>	int getFdf();
243	>
244	>	//getNZconstraint and setNZconstraint ruin the coherence of
245	>	//SimInfo class, need refactoring
246
247	<	/** Returns the total number of z-constraint molecules in the system */
248	<	int getNZconstraint() {
249	<	return nZconstraint_;
250	<	}
247	>	/** Returns the total number of z-constraint molecules in the system */
248	>	int getNZconstraint() {
249	>	return nZconstraint_;
250	>	}
251
252	<	/**
253	<	* Sets the number of z-constraint molecules in the system.
254	<	*/
255	<	void setNZconstraint(int nZconstraint) {
256	<	nZconstraint_ = nZconstraint;
257	<	}
252	>	/**
253	>	* Sets the number of z-constraint molecules in the system.
254	>	*/
255	>	void setNZconstraint(int nZconstraint) {
256	>	nZconstraint_ = nZconstraint;
257	>	}
258
259	<	/** Returns the snapshot manager. */
260	<	SnapshotManager* getSnapshotManager() {
261	<	return sman_;
262	<	}
259	>	/** Returns the snapshot manager. */
260	>	SnapshotManager* getSnapshotManager() {
261	>	return sman_;
262	>	}
263
264	<	/** Sets the snapshot manager. */
265	<	void setSnapshotManager(SnapshotManager* sman);
264	>	/** Sets the snapshot manager. */
265	>	void setSnapshotManager(SnapshotManager* sman);
266
267	<	/** Returns the force field */
268	<	ForceField* getForceField() {
269	<	return forceField_;
270	<	}
267	>	/** Returns the force field */
268	>	ForceField* getForceField() {
269	>	return forceField_;
270	>	}
271
272	<	Globals* getSimParams() {
273	<	return simParams_;
274	<	}
272	>	Globals* getSimParams() {
273	>	return simParams_;
274	>	}
275
276	<	/** Returns the velocity of center of mass of the whole system.*/
277	<	Vector3d getComVel();
276	>	/** Returns the velocity of center of mass of the whole system.*/
277	>	Vector3d getComVel();
278
279	<	/** Returns the center of the mass of the whole system.*/
280	<	Vector3d getCom();
279	>	/** Returns the center of the mass of the whole system.*/
280	>	Vector3d getCom();
281	>	/** Returns the center of the mass and Center of Mass velocity of
282	>	the whole system.*/
283	>	void getComAll(Vector3d& com,Vector3d& comVel);
284
285	<	/** main driver function to interact with fortran during the initialization and molecule migration */
286	<	void update();
285	>	/** Returns intertia tensor for the entire system and system
286	>	Angular Momentum.*/
287	>	void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
288	>
289	>	/** Returns system angular momentum */
290	>	Vector3d getAngularMomentum();
291
292	<	/** Returns the local index manager */
293	<	LocalIndexManager* getLocalIndexManager() {
294	<	return &localIndexMan_;
295	<	}
292	>	/** Returns volume of system as estimated by an ellipsoid defined
293	>	by the radii of gyration*/
294	>	void getGyrationalVolume(RealType &vol);
295	>	/** Overloaded version of gyrational volume that also returns
296	>	det(I) so dV/dr can be calculated*/
297	>	void getGyrationalVolume(RealType &vol, RealType &detI);
298
299	<	int getMoleculeStampId(int globalIndex) {
300	<	//assert(globalIndex < molStampIds_.size())
301	<	return molStampIds_[globalIndex];
302	<	}
299	>	void update();
300	>	/**
301	>	* Do final bookkeeping before Force managers need their data.
302	>	*/
303	>	void prepareTopology();
304
272	–	/** Returns the molecule stamp */
273	–	MoleculeStamp* getMoleculeStamp(int id) {
274	–	return moleculeStamps_[id];
275	–	}
305
306	<	/** Return the total number of the molecule stamps */
307	<	int getNMoleculeStamp() {
308	<	return moleculeStamps_.size();
309	<	}
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);
306	>	/** Returns the local index manager */
307	>	LocalIndexManager* getLocalIndexManager() {
308	>	return &localIndexMan_;
309	>	}
310
311	<	return i != molecules_.end() ? i->second : NULL;
312	<	}
311	>	int getMoleculeStampId(int globalIndex) {
312	>	//assert(globalIndex < molStampIds_.size())
313	>	return molStampIds_[globalIndex];
314	>	}
315
316	<	/** Calculate the maximum cutoff radius based on the atom types */
317	<	double calcMaxCutoffRadius();
316	>	/** Returns the molecule stamp */
317	>	MoleculeStamp* getMoleculeStamp(int id) {
318	>	return moleculeStamps_[id];
319	>	}
320
321	<	double getRcut() {
322	<	return rcut_;
323	<	}
321	>	/** Return the total number of the molecule stamps */
322	>	int getNMoleculeStamp() {
323	>	return moleculeStamps_.size();
324	>	}
325	>	/**
326	>	* Finds a molecule with a specified global index
327	>	* @return a pointer point to found molecule
328	>	* @param index
329	>	*/
330	>	Molecule* getMoleculeByGlobalIndex(int index) {
331	>	MoleculeIterator i;
332	>	i = molecules_.find(index);
333
334	<	double getRsw() {
335	<	return rsw_;
302	<	}
303	<
304	<	std::string getFinalConfigFileName() {
305	<	return finalConfigFileName_;
306	<	}
307	<
308	<	void setFinalConfigFileName(const std::string& fileName) {
309	<	finalConfigFileName_ = fileName;
310	<	}
334	>	return i != molecules_.end() ? i->second : NULL;
335	>	}
336
337	<	std::string getDumpFileName() {
338	<	return dumpFileName_;
339	<	}
315	<
316	<	void setDumpFileName(const std::string& fileName) {
317	<	dumpFileName_ = fileName;
318	<	}
337	>	int getGlobalMolMembership(int id){
338	>	return globalMolMembership_[id];
339	>	}
340
341	<	std::string getStatFileName() {
342	<	return statFileName_;
343	<	}
344	<
345	<	void setStatFileName(const std::string& fileName) {
346	<	statFileName_ = fileName;
326	<	}
341	>	/**
342	>	* returns a vector which maps the local atom index on this
343	>	* processor to the global atom index.  With only one processor,
344	>	* these should be identical.
345	>	*/
346	>	vector<int> getGlobalAtomIndices();
347
348	<	/**
349	<	* Sets GlobalGroupMembership
350	<	* @see #SimCreator::setGlobalIndex
351	<	*/
352	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
353	<	assert(globalGroupMembership.size() == nGlobalAtoms_);
334	<	globalGroupMembership_ = globalGroupMembership;
335	<	}
348	>	/**
349	>	* returns a vector which maps the local cutoff group index on
350	>	* this processor to the global cutoff group index.  With only one
351	>	* processor, these should be identical.
352	>	*/
353	>	vector<int> getGlobalGroupIndices();
354
355	<	/**
356	<	* Sets GlobalMolMembership
357	<	* @see #SimCreator::setGlobalIndex
358	<	*/
341	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
342	<	assert(globalMolMembership.size() == nGlobalAtoms_);
343	<	globalMolMembership_ = globalMolMembership;
344	<	}
355	>
356	>	string getFinalConfigFileName() {
357	>	return finalConfigFileName_;
358	>	}
359
360	+	void setFinalConfigFileName(const string& fileName) {
361	+	finalConfigFileName_ = fileName;
362	+	}
363
364	<	bool isFortranInitialized() {
365	<	return fortranInitialized_;
366	<	}
364	>	string getRawMetaData() {
365	>	return rawMetaData_;
366	>	}
367	>	void setRawMetaData(const string& rawMetaData) {
368	>	rawMetaData_ = rawMetaData;
369	>	}
370
371	<	//below functions are just forward functions
372	<	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
373	<	//the other hand, has-a relation need composing.
374	<	/**
375	<	* Adds property into property map
376	<	* @param genData GenericData to be added into PropertyMap
377	<	*/
358	<	void addProperty(GenericData* genData);
371	>	string getDumpFileName() {
372	>	return dumpFileName_;
373	>	}
374	>
375	>	void setDumpFileName(const string& fileName) {
376	>	dumpFileName_ = fileName;
377	>	}
378
379	<	/**
380	<	* Removes property from PropertyMap by name
381	<	* @param propName the name of property to be removed
382	<	*/
383	<	void removeProperty(const std::string& propName);
379	>	string getStatFileName() {
380	>	return statFileName_;
381	>	}
382	>
383	>	void setStatFileName(const string& fileName) {
384	>	statFileName_ = fileName;
385	>	}
386	>
387	>	string getRestFileName() {
388	>	return restFileName_;
389	>	}
390	>
391	>	void setRestFileName(const string& fileName) {
392	>	restFileName_ = fileName;
393	>	}
394
395	<	/**
396	<	* clear all of the properties
397	<	*/
398	<	void clearProperties();
395	>	/**
396	>	* Sets GlobalGroupMembership
397	>	* @see #SimCreator::setGlobalIndex
398	>	*/
399	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
400	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
401	>	globalGroupMembership_ = globalGroupMembership;
402	>	}
403
404	<	/**
405	<	* Returns all names of properties
406	<	* @return all names of properties
407	<	*/
408	<	std::vector<std::string> getPropertyNames();
404	>	/**
405	>	* Sets GlobalMolMembership
406	>	* @see #SimCreator::setGlobalIndex
407	>	*/
408	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
409	>	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
410	>	globalMolMembership_ = globalMolMembership;
411	>	}
412
377	–	/**
378	–	* Returns all of the properties in PropertyMap
379	–	* @return all of the properties in PropertyMap
380	–	*/
381	–	std::vector<GenericData*> getProperties();
413
414	<	/**
415	<	* Returns property
416	<	* @param propName name of property
417	<	* @return a pointer point to property with propName. If no property named propName
418	<	* exists, return NULL
419	<	*/
420	<	GenericData* getPropertyByName(const std::string& propName);
414	>	bool isTopologyDone() {
415	>	return topologyDone_;
416	>	}
417	>
418	>	bool getCalcBoxDipole() {
419	>	return calcBoxDipole_;
420	>	}
421
422	<	/**
423	<	* add all exclude pairs of a molecule into exclude list.
424	<	*/
394	<	void addExcludePairs(Molecule* mol);
422	>	bool getUseAtomicVirial() {
423	>	return useAtomicVirial_;
424	>	}
425
426	<	/**
427	<	* remove all exclude pairs which belong to a molecule from exclude list
428	<	*/
426	>	/**
427	>	* Adds property into property map
428	>	* @param genData GenericData to be added into PropertyMap
429	>	*/
430	>	void addProperty(GenericData* genData);
431
432	<	void removeExcludePairs(Molecule* mol);
432	>	/**
433	>	* Removes property from PropertyMap by name
434	>	* @param propName the name of property to be removed
435	>	*/
436	>	void removeProperty(const string& propName);
437
438	+	/**
439	+	* clear all of the properties
440	+	*/
441	+	void clearProperties();
442
443	<	SelectionManager* getSelectionManager() {
444	<	return selectMan_;
445	<	}
443	>	/**
444	>	* Returns all names of properties
445	>	* @return all names of properties
446	>	*/
447	>	vector<string> getPropertyNames();
448
449	<	/** Returns the unique atom types of local processor in an array */
450	<	std::set<AtomType*> getUniqueAtomTypes();
449	>	/**
450	>	* Returns all of the properties in PropertyMap
451	>	* @return all of the properties in PropertyMap
452	>	*/
453	>	vector<GenericData*> getProperties();
454	>
455	>	/**
456	>	* Returns property
457	>	* @param propName name of property
458	>	* @return a pointer point to property with propName. If no property named propName
459	>	* exists, return NULL
460	>	*/
461	>	GenericData* getPropertyByName(const string& propName);
462	>
463	>	/**
464	>	* add all special interaction pairs (including excluded
465	>	* interactions) in a molecule into the appropriate lists.
466	>	*/
467	>	void addInteractionPairs(Molecule* mol);
468	>
469	>	/**
470	>	* remove all special interaction pairs which belong to a molecule
471	>	* from the appropriate lists.
472	>	*/
473	>	void removeInteractionPairs(Molecule* mol);
474	>
475	>	/** Returns the set of atom types present in this simulation */
476	>	set<AtomType*> getSimulatedAtomTypes();
477
478	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
478	>	friend ostream& operator <<(ostream& o, SimInfo& info);
479
480	<	void getCutoff(double& rcut, double& rsw);
480	>	void getCutoff(RealType& rcut, RealType& rsw);
481
482	<	private:
482	>	private:
483
484	<	/** fill up the simtype struct*/
485	<	void setupSimType();
484	>	/** fill up the simtype struct and other simulation-related variables */
485	>	void setupSimVariables();
486
419	–	/**
420	–	* Setup Fortran Simulation
421	–	* @see #setupFortranParallel
422	–	*/
423	–	void setupFortranSim();
487
488	<	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
489	<	void setupCutoff();
488	>	/** Determine if we need to accumulate the simulation box dipole */
489	>	void setupAccumulateBoxDipole();
490
491	<	/** Calculates the number of degress of freedom in the whole system */
492	<	void calcNdf();
493	<	void calcNdfRaw();
494	<	void calcNdfTrans();
491	>	/** Calculates the number of degress of freedom in the whole system */
492	>	void calcNdf();
493	>	void calcNdfRaw();
494	>	void calcNdfTrans();
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);
496	>	/**
497	>	* Adds molecule stamp and the total number of the molecule with
498	>	* same molecule stamp in the whole system.
499	>	*/
500	>	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
501
502	<	ForceField* forceField_;
503	<	Globals* simParams_;
502	>	// Other classes holdingn important information
503	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
504	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
505
506	<	std::map<int, Molecule*>  molecules_; /**< Molecule array */
506	>	///  Counts of local objects
507	>	int nAtoms_;              /**< number of atoms in local processor */
508	>	int nBonds_;              /**< number of bonds in local processor */
509	>	int nBends_;              /**< number of bends in local processor */
510	>	int nTorsions_;           /**< number of torsions in local processor */
511	>	int nInversions_;         /**< number of inversions in local processor */
512	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
513	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
514	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
515	>	int nConstraints_;        /**< number of constraints in local processors */
516
517	<	//degress of freedom
518	<	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
519	<	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
520	<	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
521	<	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
522	<
523	<	//number of global objects
524	<	int nGlobalMols_;       /**< number of molecules in the system */
525	<	int nGlobalAtoms_;   /**< number of atoms in the system */
526	<	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
527	<	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
528	<	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
529	<	/**
530	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
458	<	* corresponding content is the global index of cutoff group this atom belong to.
459	<	* It is filled by SimCreator once and only once, since it never changed during the simulation.
460	<	*/
461	<	std::vector<int> globalGroupMembership_;
462	<
463	<	/**
464	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
465	<	* corresponding content is the global index of molecule this atom belong to.
466	<	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
467	<	*/
468	<	std::vector<int> globalMolMembership_;
517	>	/// Counts of global objects
518	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
519	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
520	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
521	>	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
522	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
523	>
524	>	/// Degress of freedom
525	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
526	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
527	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
528	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
529	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
530	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
531
532	<
533	<	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
534	<	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
535	<
536	<	//number of local objects
537	<	int nAtoms_;                        /**< number of atoms in local processor */
538	<	int nBonds_;                        /**< number of bonds in local processor */
539	<	int nBends_;                        /**< number of bends in local processor */
540	<	int nTorsions_;                    /**< number of torsions in local processor */
479	<	int nRigidBodies_;              /**< number of rigid bodies in local processor */
480	<	int nIntegrableObjects_;    /**< number of integrable objects in local processor */
481	<	int nCutoffGroups_;             /**< number of cutoff groups in local processor */
482	<	int nConstraints_;              /**< number of constraints in local processors */
532	>	/// logicals
533	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
534	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
535	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
536	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
537	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
538	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
539	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
540	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
541
542	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
543	<	Exclude exclude_;
544	<	PropertyMap properties_;                  /**< Generic Property */
545	<	SnapshotManager* sman_;               /**< SnapshotManager */
542	>	public:
543	>	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
544	>	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
545	>	bool usesMetallicAtoms() { return usesMetallicAtoms_; }
546	>	bool usesAtomicVirial() { return usesAtomicVirial_; }
547	>	bool requiresPrepair() { return requiresPrepair_; }
548	>	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
549	>	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
550
551	<	/**
552	<	* The reason to have a local index manager is that when molecule is migrating to other processors,
553	<	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
492	<	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
493	<	* to make a efficient data moving plan.
494	<	*/
495	<	LocalIndexManager localIndexMan_;
551	>	private:
552	>	/// Data structures holding primary simulation objects
553	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
554
555	<	//file names
556	<	std::string finalConfigFileName_;
557	<	std::string dumpFileName_;
558	<	std::string statFileName_;
555	>	/// Stamps are templates for objects that are then used to create
556	>	/// groups of objects.  For example, a molecule stamp contains
557	>	/// information on how to build that molecule (i.e. the topology,
558	>	/// the atoms, the bonds, etc.)  Once the system is built, the
559	>	/// stamps are no longer useful.
560	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
561	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
562
563	<	double rcut_;       /**< cutoff radius*/
564	<	double rsw_;        /**< radius of switching function*/
563	>	/**
564	>	* A vector that maps between the global index of an atom, and the
565	>	* global index of cutoff group the atom belong to.  It is filled
566	>	* by SimCreator once and only once, since it never changed during
567	>	* the simulation.  It should be nGlobalAtoms_ in size.
568	>	*/
569	>	vector<int> globalGroupMembership_;
570	>	public:
571	>	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
572	>	private:
573
574	<	bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
574	>	/**
575	>	* A vector that maps between the global index of an atom and the
576	>	* global index of the molecule the atom belongs to.  It is filled
577	>	* by SimCreator once and only once, since it is never changed
578	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
579	>	*/
580	>	vector<int> globalMolMembership_;
581
582	<	SelectionManager* selectMan_;
583	<	#ifdef IS_MPI
584	<	//in Parallel version, we need MolToProc
585	<	public:
586	<
587	<	/**
588	<	* Finds the processor where a molecule resides
589	<	* @return the id of the processor which contains the molecule
590	<	* @param globalIndex global Index of the molecule
591	<	*/
592	<	int getMolToProc(int globalIndex) {
593	<	//assert(globalIndex < molToProcMap_.size());
594	<	return molToProcMap_[globalIndex];
595	<	}
582	>	/**
583	>	* A vector that maps between the local index of an atom and the
584	>	* index of the AtomType.
585	>	*/
586	>	vector<int> identArray_;
587	>	public:
588	>	vector<int> getIdentArray() { return identArray_; }
589	>	private:
590	>
591	>	/**
592	>	* A vector which contains the fractional contribution of an
593	>	* atom's mass to the total mass of the cutoffGroup that atom
594	>	* belongs to.  In the case of single atom cutoff groups, the mass
595	>	* factor for that atom is 1.  For massless atoms, the factor is
596	>	* also 1.
597	>	*/
598	>	vector<RealType> massFactors_;
599	>	public:
600	>	vector<RealType> getMassFactors() { return massFactors_; }
601	>	private:
602
603	<	/**
604	<	* Set MolToProcMap array
605	<	* @see #SimCreator::divideMolecules
606	<	*/
607	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
608	<	molToProcMap_ = molToProcMap;
609	<	}
603	>
604	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
605	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
606	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
607	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
608	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
609	>
610	>	PropertyMap properties_;       /**< Generic Properties can be added */
611	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
612	>
613	>	/**
614	>	* The reason to have a local index manager is that when molecule
615	>	* is migrating to other processors, the atoms and the
616	>	* rigid-bodies will release their local indices to
617	>	* LocalIndexManager. Combining the information of molecule
618	>	* migrating to current processor, Migrator class can query the
619	>	* LocalIndexManager to make a efficient data moving plan.
620	>	*/
621	>	LocalIndexManager localIndexMan_;
622	>
623	>	// unparsed MetaData block for storing in Dump and EOR files:
624	>	string rawMetaData_;
625	>
626	>	// file names
627	>	string finalConfigFileName_;
628	>	string dumpFileName_;
629	>	string statFileName_;
630	>	string restFileName_;
631
530	–	private:
632
633	<	void setupFortranParallel();
633	>	bool topologyDone_;  /** flag to indicate whether the topology has
634	>	been scanned and all the relevant
635	>	bookkeeping has been done*/
636	>
637	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
638	>	the simulation box dipole moment */
639	>
640	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
641	>	Atomic Virials to calculate the pressure */
642	>
643	>	public:
644	>	/**
645	>	* return an integral objects by its global index. In MPI
646	>	* version, if the StuntDouble with specified global index does
647	>	* not belong to local processor, a NULL will be return.
648	>	*/
649	>	StuntDouble* getIOIndexToIntegrableObject(int index);
650	>	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
651	>
652	>	private:
653	>	vector<StuntDouble*> IOIndexToIntegrableObject;
654	>
655	>	public:
656	>
657	>	/**
658	>	* Finds the processor where a molecule resides
659	>	* @return the id of the processor which contains the molecule
660	>	* @param globalIndex global Index of the molecule
661	>	*/
662	>	int getMolToProc(int globalIndex) {
663	>	//assert(globalIndex < molToProcMap_.size());
664	>	return molToProcMap_[globalIndex];
665	>	}
666	>
667	>	/**
668	>	* Set MolToProcMap array
669	>	* @see #SimCreator::divideMolecules
670	>	*/
671	>	void setMolToProcMap(const vector<int>& molToProcMap) {
672	>	molToProcMap_ = molToProcMap;
673	>	}
674
675	<	/**
676	<	* The size of molToProcMap_ is equal to total number of molecules in the system.
677	<	*  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
678	<	* once.
679	<	*/
680	<	std::vector<int> molToProcMap_;
675	>	private:
676	>
677	>	/**
678	>	* The size of molToProcMap_ is equal to total number of molecules
679	>	* in the system.  It maps a molecule to the processor on which it
680	>	* resides. it is filled by SimCreator once and only once.
681	>	*/
682	>	vector<int> molToProcMap_;
683
684	<	#endif
684	>	};
685
686	<	};
544	<
545	<	} //namespace oopse
686	>	} //namespace OpenMD
687		#endif //BRAINS_SIMMODEL_HPP
688

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 1569 by gezelter, Thu May 26 13:55:04 2011 UTC

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