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

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trunk/src/brains/SimInfo.hpp (file contents), Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
branches/development/src/brains/SimInfo.hpp (file contents), Revision 1577 by gezelter, Wed Jun 8 20:26:56 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	<	/**
146	<	* Returns the number of local molecules.
147	<	* @return the number of local molecules
148	<	*/
149	<	int getNMolecules() {
150	<	return molecules_.size();
151	<	}
169	>	/** Returns the number of effective cutoff groups on local processor */
170	>	unsigned int getNLocalCutoffGroups();
171
172	<	/** Returns the number of local atoms */
173	<	unsigned int getNAtoms() {
174	<	return nAtoms_;
175	<	}
172	>	/** Returns the number of local bonds */
173	>	unsigned int getNBonds(){
174	>	return nBonds_;
175	>	}
176
177	<	/** Returns the number of local bonds */
178	<	unsigned int getNBonds(){
179	<	return nBonds_;
180	<	}
177	>	/** Returns the number of local bends */
178	>	unsigned int getNBends() {
179	>	return nBends_;
180	>	}
181
182	<	/** Returns the number of local bends */
183	<	unsigned int getNBends() {
184	<	return nBends_;
185	<	}
182	>	/** Returns the number of local torsions */
183	>	unsigned int getNTorsions() {
184	>	return nTorsions_;
185	>	}
186
187	<	/** Returns the number of local torsions */
188	<	unsigned int getNTorsions() {
189	<	return nTorsions_;
190	<	}
187	>	/** Returns the number of local torsions */
188	>	unsigned int getNInversions() {
189	>	return nInversions_;
190	>	}
191	>	/** Returns the number of local rigid bodies */
192	>	unsigned int getNRigidBodies() {
193	>	return nRigidBodies_;
194	>	}
195
196	<	/** Returns the number of local rigid bodies */
197	<	unsigned int getNRigidBodies() {
198	<	return nRigidBodies_;
199	<	}
196	>	/** Returns the number of local integrable objects */
197	>	unsigned int getNIntegrableObjects() {
198	>	return nIntegrableObjects_;
199	>	}
200
201	<	/** Returns the number of local integrable objects */
202	<	unsigned int getNIntegrableObjects() {
203	<	return nIntegrableObjects_;
204	<	}
201	>	/** Returns the number of local cutoff groups */
202	>	unsigned int getNCutoffGroups() {
203	>	return nCutoffGroups_;
204	>	}
205
206	<	/** Returns the number of local cutoff groups */
207	<	unsigned int getNCutoffGroups() {
208	<	return nCutoffGroups_;
209	<	}
187	<
188	<	/** Returns the total number of constraints in this SimInfo */
189	<	unsigned int getNConstraints() {
190	<	return nConstraints_;
191	<	}
206	>	/** Returns the total number of constraints in this SimInfo */
207	>	unsigned int getNConstraints() {
208	>	return nConstraints_;
209	>	}
210
211	<	/**
212	<	* Returns the first molecule in this SimInfo and intialize the iterator.
213	<	* @return the first molecule, return NULL if there is not molecule in this SimInfo
214	<	* @param i the iterator of molecule array (user shouldn't change it)
215	<	*/
216	<	Molecule* beginMolecule(MoleculeIterator& i);
211	>	/**
212	>	* Returns the first molecule in this SimInfo and intialize the iterator.
213	>	* @return the first molecule, return NULL if there is not molecule in this SimInfo
214	>	* @param i the iterator of molecule array (user shouldn't change it)
215	>	*/
216	>	Molecule* beginMolecule(MoleculeIterator& i);
217
218	<	/**
219	<	* Returns the next avaliable Molecule based on the iterator.
220	<	* @return the next avaliable molecule, return NULL if reaching the end of the array
221	<	* @param i the iterator of molecule array
222	<	*/
223	<	Molecule* nextMolecule(MoleculeIterator& i);
218	>	/**
219	>	* Returns the next avaliable Molecule based on the iterator.
220	>	* @return the next avaliable molecule, return NULL if reaching the end of the array
221	>	* @param i the iterator of molecule array
222	>	*/
223	>	Molecule* nextMolecule(MoleculeIterator& i);
224
225	<	/** Returns the number of degrees of freedom */
226	<	int getNdf() {
227	<	return ndf_;
228	<	}
225	>	/** Returns the number of degrees of freedom */
226	>	int getNdf() {
227	>	return ndf_ - getFdf();
228	>	}
229
230	<	/** Returns the number of raw degrees of freedom */
231	<	int getNdfRaw() {
232	<	return ndfRaw_;
233	<	}
230	>	/** Returns the number of raw degrees of freedom */
231	>	int getNdfRaw() {
232	>	return ndfRaw_;
233	>	}
234
235	<	/** Returns the number of translational degrees of freedom */
236	<	int getNdfTrans() {
237	<	return ndfTrans_;
238	<	}
235	>	/** Returns the number of translational degrees of freedom */
236	>	int getNdfTrans() {
237	>	return ndfTrans_;
238	>	}
239
240	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
240	>	/** sets the current number of frozen degrees of freedom */
241	>	void setFdf(int fdf) {
242	>	fdf_local = fdf;
243	>	}
244	>
245	>	int getFdf();
246	>
247	>	//getNZconstraint and setNZconstraint ruin the coherence of
248	>	//SimInfo class, need refactoring
249
250	<	/** Returns the total number of z-constraint molecules in the system */
251	<	int getNZconstraint() {
252	<	return nZconstraint_;
253	<	}
250	>	/** Returns the total number of z-constraint molecules in the system */
251	>	int getNZconstraint() {
252	>	return nZconstraint_;
253	>	}
254
255	<	/**
256	<	* Sets the number of z-constraint molecules in the system.
257	<	*/
258	<	void setNZconstraint(int nZconstraint) {
259	<	nZconstraint_ = nZconstraint;
260	<	}
255	>	/**
256	>	* Sets the number of z-constraint molecules in the system.
257	>	*/
258	>	void setNZconstraint(int nZconstraint) {
259	>	nZconstraint_ = nZconstraint;
260	>	}
261
262	<	/** Returns the snapshot manager. */
263	<	SnapshotManager* getSnapshotManager() {
264	<	return sman_;
265	<	}
262	>	/** Returns the snapshot manager. */
263	>	SnapshotManager* getSnapshotManager() {
264	>	return sman_;
265	>	}
266
267	<	/** Sets the snapshot manager. */
268	<	void setSnapshotManager(SnapshotManager* sman);
267	>	/** Sets the snapshot manager. */
268	>	void setSnapshotManager(SnapshotManager* sman);
269
270	<	/** Returns the force field */
271	<	ForceField* getForceField() {
272	<	return forceField_;
273	<	}
270	>	/** Returns the force field */
271	>	ForceField* getForceField() {
272	>	return forceField_;
273	>	}
274
275	<	Globals* getSimParams() {
276	<	return simParams_;
277	<	}
275	>	Globals* getSimParams() {
276	>	return simParams_;
277	>	}
278
279	<	/** Returns the velocity of center of mass of the whole system.*/
280	<	Vector3d getComVel();
279	>	/** Returns the velocity of center of mass of the whole system.*/
280	>	Vector3d getComVel();
281
282	<	/** Returns the center of the mass of the whole system.*/
283	<	Vector3d getCom();
282	>	/** Returns the center of the mass of the whole system.*/
283	>	Vector3d getCom();
284	>	/** Returns the center of the mass and Center of Mass velocity of
285	>	the whole system.*/
286	>	void getComAll(Vector3d& com,Vector3d& comVel);
287
288	<	/** main driver function to interact with fortran during the initialization and molecule migration */
289	<	void update();
288	>	/** Returns intertia tensor for the entire system and system
289	>	Angular Momentum.*/
290	>	void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
291	>
292	>	/** Returns system angular momentum */
293	>	Vector3d getAngularMomentum();
294
295	<	/** Returns the local index manager */
296	<	LocalIndexManager* getLocalIndexManager() {
297	<	return &localIndexMan_;
298	<	}
295	>	/** Returns volume of system as estimated by an ellipsoid defined
296	>	by the radii of gyration*/
297	>	void getGyrationalVolume(RealType &vol);
298	>	/** Overloaded version of gyrational volume that also returns
299	>	det(I) so dV/dr can be calculated*/
300	>	void getGyrationalVolume(RealType &vol, RealType &detI);
301
302	<	int getMoleculeStampId(int globalIndex) {
303	<	//assert(globalIndex < molStampIds_.size())
304	<	return molStampIds_[globalIndex];
305	<	}
302	>	void update();
303	>	/**
304	>	* Do final bookkeeping before Force managers need their data.
305	>	*/
306	>	void prepareTopology();
307
272	–	/** Returns the molecule stamp */
273	–	MoleculeStamp* getMoleculeStamp(int id) {
274	–	return moleculeStamps_[id];
275	–	}
308
309	<	/** Return the total number of the molecule stamps */
310	<	int getNMoleculeStamp() {
311	<	return moleculeStamps_.size();
312	<	}
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);
309	>	/** Returns the local index manager */
310	>	LocalIndexManager* getLocalIndexManager() {
311	>	return &localIndexMan_;
312	>	}
313
314	<	return i != molecules_.end() ? i->second : NULL;
315	<	}
314	>	int getMoleculeStampId(int globalIndex) {
315	>	//assert(globalIndex < molStampIds_.size())
316	>	return molStampIds_[globalIndex];
317	>	}
318
319	<	/** Calculate the maximum cutoff radius based on the atom types */
320	<	double calcMaxCutoffRadius();
319	>	/** Returns the molecule stamp */
320	>	MoleculeStamp* getMoleculeStamp(int id) {
321	>	return moleculeStamps_[id];
322	>	}
323
324	<	double getRcut() {
325	<	return rcut_;
326	<	}
324	>	/** Return the total number of the molecule stamps */
325	>	int getNMoleculeStamp() {
326	>	return moleculeStamps_.size();
327	>	}
328	>	/**
329	>	* Finds a molecule with a specified global index
330	>	* @return a pointer point to found molecule
331	>	* @param index
332	>	*/
333	>	Molecule* getMoleculeByGlobalIndex(int index) {
334	>	MoleculeIterator i;
335	>	i = molecules_.find(index);
336
337	<	double getRsw() {
338	<	return rsw_;
302	<	}
303	<
304	<	std::string getFinalConfigFileName() {
305	<	return finalConfigFileName_;
306	<	}
307	<
308	<	void setFinalConfigFileName(const std::string& fileName) {
309	<	finalConfigFileName_ = fileName;
310	<	}
337	>	return i != molecules_.end() ? i->second : NULL;
338	>	}
339
340	<	std::string getDumpFileName() {
341	<	return dumpFileName_;
342	<	}
315	<
316	<	void setDumpFileName(const std::string& fileName) {
317	<	dumpFileName_ = fileName;
318	<	}
340	>	int getGlobalMolMembership(int id){
341	>	return globalMolMembership_[id];
342	>	}
343
344	<	std::string getStatFileName() {
345	<	return statFileName_;
346	<	}
347	<
348	<	void setStatFileName(const std::string& fileName) {
349	<	statFileName_ = fileName;
326	<	}
344	>	/**
345	>	* returns a vector which maps the local atom index on this
346	>	* processor to the global atom index.  With only one processor,
347	>	* these should be identical.
348	>	*/
349	>	vector<int> getGlobalAtomIndices();
350
351	<	/**
352	<	* Sets GlobalGroupMembership
353	<	* @see #SimCreator::setGlobalIndex
354	<	*/
355	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
356	<	assert(globalGroupMembership.size() == nGlobalAtoms_);
334	<	globalGroupMembership_ = globalGroupMembership;
335	<	}
351	>	/**
352	>	* returns a vector which maps the local cutoff group index on
353	>	* this processor to the global cutoff group index.  With only one
354	>	* processor, these should be identical.
355	>	*/
356	>	vector<int> getGlobalGroupIndices();
357
358	<	/**
359	<	* Sets GlobalMolMembership
360	<	* @see #SimCreator::setGlobalIndex
361	<	*/
341	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
342	<	assert(globalMolMembership.size() == nGlobalAtoms_);
343	<	globalMolMembership_ = globalMolMembership;
344	<	}
358	>
359	>	string getFinalConfigFileName() {
360	>	return finalConfigFileName_;
361	>	}
362
363	+	void setFinalConfigFileName(const string& fileName) {
364	+	finalConfigFileName_ = fileName;
365	+	}
366
367	<	bool isFortranInitialized() {
368	<	return fortranInitialized_;
369	<	}
367	>	string getRawMetaData() {
368	>	return rawMetaData_;
369	>	}
370	>	void setRawMetaData(const string& rawMetaData) {
371	>	rawMetaData_ = rawMetaData;
372	>	}
373
374	<	//below functions are just forward functions
375	<	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
376	<	//the other hand, has-a relation need composing.
377	<	/**
378	<	* Adds property into property map
379	<	* @param genData GenericData to be added into PropertyMap
380	<	*/
358	<	void addProperty(GenericData* genData);
374	>	string getDumpFileName() {
375	>	return dumpFileName_;
376	>	}
377	>
378	>	void setDumpFileName(const string& fileName) {
379	>	dumpFileName_ = fileName;
380	>	}
381
382	<	/**
383	<	* Removes property from PropertyMap by name
384	<	* @param propName the name of property to be removed
385	<	*/
386	<	void removeProperty(const std::string& propName);
382	>	string getStatFileName() {
383	>	return statFileName_;
384	>	}
385	>
386	>	void setStatFileName(const string& fileName) {
387	>	statFileName_ = fileName;
388	>	}
389	>
390	>	string getRestFileName() {
391	>	return restFileName_;
392	>	}
393	>
394	>	void setRestFileName(const string& fileName) {
395	>	restFileName_ = fileName;
396	>	}
397
398	<	/**
399	<	* clear all of the properties
400	<	*/
401	<	void clearProperties();
398	>	/**
399	>	* Sets GlobalGroupMembership
400	>	* @see #SimCreator::setGlobalIndex
401	>	*/
402	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
403	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
404	>	globalGroupMembership_ = globalGroupMembership;
405	>	}
406
407	<	/**
408	<	* Returns all names of properties
409	<	* @return all names of properties
410	<	*/
411	<	std::vector<std::string> getPropertyNames();
407	>	/**
408	>	* Sets GlobalMolMembership
409	>	* @see #SimCreator::setGlobalIndex
410	>	*/
411	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
412	>	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
413	>	globalMolMembership_ = globalMolMembership;
414	>	}
415
377	–	/**
378	–	* Returns all of the properties in PropertyMap
379	–	* @return all of the properties in PropertyMap
380	–	*/
381	–	std::vector<GenericData*> getProperties();
416
417	<	/**
418	<	* Returns property
419	<	* @param propName name of property
420	<	* @return a pointer point to property with propName. If no property named propName
421	<	* exists, return NULL
422	<	*/
423	<	GenericData* getPropertyByName(const std::string& propName);
417	>	bool isTopologyDone() {
418	>	return topologyDone_;
419	>	}
420	>
421	>	bool getCalcBoxDipole() {
422	>	return calcBoxDipole_;
423	>	}
424
425	<	/**
426	<	* add all exclude pairs of a molecule into exclude list.
427	<	*/
394	<	void addExcludePairs(Molecule* mol);
425	>	bool getUseAtomicVirial() {
426	>	return useAtomicVirial_;
427	>	}
428
429	<	/**
430	<	* remove all exclude pairs which belong to a molecule from exclude list
431	<	*/
429	>	/**
430	>	* Adds property into property map
431	>	* @param genData GenericData to be added into PropertyMap
432	>	*/
433	>	void addProperty(GenericData* genData);
434
435	<	void removeExcludePairs(Molecule* mol);
435	>	/**
436	>	* Removes property from PropertyMap by name
437	>	* @param propName the name of property to be removed
438	>	*/
439	>	void removeProperty(const string& propName);
440
441	+	/**
442	+	* clear all of the properties
443	+	*/
444	+	void clearProperties();
445
446	<	/** Returns the unique atom types of local processor in an array */
447	<	std::set<AtomType*> getUniqueAtomTypes();
448	<
449	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
446	>	/**
447	>	* Returns all names of properties
448	>	* @return all names of properties
449	>	*/
450	>	vector<string> getPropertyNames();
451
452	<	void getCutoff(double& rcut, double& rsw);
453	<
454	<	private:
452	>	/**
453	>	* Returns all of the properties in PropertyMap
454	>	* @return all of the properties in PropertyMap
455	>	*/
456	>	vector<GenericData*> getProperties();
457
458	<	/** fill up the simtype struct*/
459	<	void setupSimType();
458	>	/**
459	>	* Returns property
460	>	* @param propName name of property
461	>	* @return a pointer point to property with propName. If no property named propName
462	>	* exists, return NULL
463	>	*/
464	>	GenericData* getPropertyByName(const string& propName);
465
466	<	/**
467	<	* Setup Fortran Simulation
468	<	* @see #setupFortranParallel
469	<	*/
470	<	void setupFortranSim();
466	>	/**
467	>	* add all special interaction pairs (including excluded
468	>	* interactions) in a molecule into the appropriate lists.
469	>	*/
470	>	void addInteractionPairs(Molecule* mol);
471
472	<	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
473	<	void setupCutoff();
472	>	/**
473	>	* remove all special interaction pairs which belong to a molecule
474	>	* from the appropriate lists.
475	>	*/
476	>	void removeInteractionPairs(Molecule* mol);
477
478	<	/** Calculates the number of degress of freedom in the whole system */
479	<	void calcNdf();
426	<	void calcNdfRaw();
427	<	void calcNdfTrans();
428	<
429	<	/**
430	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
431	<	* system.
432	<	*/
433	<	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
434	<
435	<	ForceField* forceField_;
436	<	Globals* simParams_;
437	<
438	<	std::map<int, Molecule*>  molecules_; /**< Molecule array */
478	>	/** Returns the set of atom types present in this simulation */
479	>	set<AtomType*> getSimulatedAtomTypes();
480
481	<	//degress of freedom
441	<	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
442	<	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
443	<	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
444	<	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
445	<
446	<	//number of global objects
447	<	int nGlobalMols_;       /**< number of molecules in the system */
448	<	int nGlobalAtoms_;   /**< number of atoms in the system */
449	<	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
450	<	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
451	<	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
452	<	/**
453	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
454	<	* corresponding content is the global index of cutoff group this atom belong to.
455	<	* It is filled by SimCreator once and only once, since it never changed during the simulation.
456	<	*/
457	<	std::vector<int> globalGroupMembership_;
481	>	friend ostream& operator <<(ostream& o, SimInfo& info);
482
483	<	/**
460	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
461	<	* corresponding content is the global index of molecule this atom belong to.
462	<	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
463	<	*/
464	<	std::vector<int> globalMolMembership_;
465	<
483	>	void getCutoff(RealType& rcut, RealType& rsw);
484
485	<	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
468	<	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
469	<
470	<	//number of local objects
471	<	int nAtoms_;                        /**< number of atoms in local processor */
472	<	int nBonds_;                        /**< number of bonds in local processor */
473	<	int nBends_;                        /**< number of bends in local processor */
474	<	int nTorsions_;                    /**< number of torsions in local processor */
475	<	int nRigidBodies_;              /**< number of rigid bodies in local processor */
476	<	int nIntegrableObjects_;    /**< number of integrable objects in local processor */
477	<	int nCutoffGroups_;             /**< number of cutoff groups in local processor */
478	<	int nConstraints_;              /**< number of constraints in local processors */
485	>	private:
486
487	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
488	<	Exclude exclude_;
482	<	PropertyMap properties_;                  /**< Generic Property */
483	<	SnapshotManager* sman_;               /**< SnapshotManager */
487	>	/** fill up the simtype struct and other simulation-related variables */
488	>	void setupSimVariables();
489
485	–	/**
486	–	* The reason to have a local index manager is that when molecule is migrating to other processors,
487	–	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
488	–	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
489	–	* to make a efficient data moving plan.
490	–	*/
491	–	LocalIndexManager localIndexMan_;
490
491	<	//file names
492	<	std::string finalConfigFileName_;
495	<	std::string dumpFileName_;
496	<	std::string statFileName_;
491	>	/** Determine if we need to accumulate the simulation box dipole */
492	>	void setupAccumulateBoxDipole();
493
494	<	double rcut_;       /**< cutoff radius*/
495	<	double rsw_;        /**< radius of switching function*/
496	<
497	<	bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
494	>	/** Calculates the number of degress of freedom in the whole system */
495	>	void calcNdf();
496	>	void calcNdfRaw();
497	>	void calcNdfTrans();
498
499	<	#ifdef IS_MPI
500	<	//in Parallel version, we need MolToProc
501	<	public:
502	<
503	<	/**
508	<	* Finds the processor where a molecule resides
509	<	* @return the id of the processor which contains the molecule
510	<	* @param globalIndex global Index of the molecule
511	<	*/
512	<	int getMolToProc(int globalIndex) {
513	<	//assert(globalIndex < molToProcMap_.size());
514	<	return molToProcMap_[globalIndex];
515	<	}
499	>	/**
500	>	* Adds molecule stamp and the total number of the molecule with
501	>	* same molecule stamp in the whole system.
502	>	*/
503	>	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
504
505	<	/**
506	<	* Set MolToProcMap array
507	<	* @see #SimCreator::divideMolecules
508	<	*/
509	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
510	<	molToProcMap_ = molToProcMap;
511	<	}
505	>	// Other classes holdingn important information
506	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
507	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
508	>
509	>	///  Counts of local objects
510	>	int nAtoms_;              /**< number of atoms in local processor */
511	>	int nBonds_;              /**< number of bonds in local processor */
512	>	int nBends_;              /**< number of bends in local processor */
513	>	int nTorsions_;           /**< number of torsions in local processor */
514	>	int nInversions_;         /**< number of inversions in local processor */
515	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
516	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
517	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
518	>	int nConstraints_;        /**< number of constraints in local processors */
519
520	<	private:
520	>	/// Counts of global objects
521	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
522	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
523	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
524	>	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
525	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
526	>
527	>	/// Degress of freedom
528	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
529	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
530	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
531	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
532	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
533	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
534
535	<	void setupFortranParallel();
535	>	/// logicals
536	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
537	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
538	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
539	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
540	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
541	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
542	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
543	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
544	>
545	>	public:
546	>	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
547	>	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
548	>	bool usesMetallicAtoms() { return usesMetallicAtoms_; }
549	>	bool usesAtomicVirial() { return usesAtomicVirial_; }
550	>	bool requiresPrepair() { return requiresPrepair_; }
551	>	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
552	>	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
553	>
554	>	private:
555	>	/// Data structures holding primary simulation objects
556	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
557	>
558	>	/// Stamps are templates for objects that are then used to create
559	>	/// groups of objects.  For example, a molecule stamp contains
560	>	/// information on how to build that molecule (i.e. the topology,
561	>	/// the atoms, the bonds, etc.)  Once the system is built, the
562	>	/// stamps are no longer useful.
563	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
564	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
565	>
566	>	/**
567	>	* A vector that maps between the global index of an atom, and the
568	>	* global index of cutoff group the atom belong to.  It is filled
569	>	* by SimCreator once and only once, since it never changed during
570	>	* the simulation.  It should be nGlobalAtoms_ in size.
571	>	*/
572	>	vector<int> globalGroupMembership_;
573	>	public:
574	>	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
575	>	private:
576	>
577	>	/**
578	>	* A vector that maps between the global index of an atom and the
579	>	* global index of the molecule the atom belongs to.  It is filled
580	>	* by SimCreator once and only once, since it is never changed
581	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
582	>	*/
583	>	vector<int> globalMolMembership_;
584	>
585	>	/**
586	>	* A vector that maps between the local index of an atom and the
587	>	* index of the AtomType.
588	>	*/
589	>	vector<int> identArray_;
590	>	public:
591	>	vector<int> getIdentArray() { return identArray_; }
592	>	private:
593	>
594	>	/**
595	>	* A vector which contains the fractional contribution of an
596	>	* atom's mass to the total mass of the cutoffGroup that atom
597	>	* belongs to.  In the case of single atom cutoff groups, the mass
598	>	* factor for that atom is 1.  For massless atoms, the factor is
599	>	* also 1.
600	>	*/
601	>	vector<RealType> massFactors_;
602	>	public:
603	>	vector<RealType> getMassFactors() { return massFactors_; }
604	>
605	>	PairList getExcludedInteractions() { return excludedInteractions_; }
606	>	PairList getOneTwoInteractions() { return oneTwoInteractions_; }
607	>	PairList getOneThreeInteractions() { return oneThreeInteractions_; }
608	>	PairList getOneFourInteractions() { return oneFourInteractions_; }
609	>
610	>	private:
611	>
612	>
613	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
614	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
615	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
616	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
617	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
618	>
619	>	PropertyMap properties_;       /**< Generic Properties can be added */
620	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
621	>
622	>	/**
623	>	* The reason to have a local index manager is that when molecule
624	>	* is migrating to other processors, the atoms and the
625	>	* rigid-bodies will release their local indices to
626	>	* LocalIndexManager. Combining the information of molecule
627	>	* migrating to current processor, Migrator class can query the
628	>	* LocalIndexManager to make a efficient data moving plan.
629	>	*/
630	>	LocalIndexManager localIndexMan_;
631	>
632	>	// unparsed MetaData block for storing in Dump and EOR files:
633	>	string rawMetaData_;
634	>
635	>	// file names
636	>	string finalConfigFileName_;
637	>	string dumpFileName_;
638	>	string statFileName_;
639	>	string restFileName_;
640
529	–	/**
530	–	* The size of molToProcMap_ is equal to total number of molecules in the system.
531	–	*  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
532	–	* once.
533	–	*/
534	–	std::vector<int> molToProcMap_;
641
642	<	#endif
642	>	bool topologyDone_;  /** flag to indicate whether the topology has
643	>	been scanned and all the relevant
644	>	bookkeeping has been done*/
645	>
646	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
647	>	the simulation box dipole moment */
648	>
649	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
650	>	Atomic Virials to calculate the pressure */
651	>
652	>	public:
653	>	/**
654	>	* return an integral objects by its global index. In MPI
655	>	* version, if the StuntDouble with specified global index does
656	>	* not belong to local processor, a NULL will be return.
657	>	*/
658	>	StuntDouble* getIOIndexToIntegrableObject(int index);
659	>	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
660	>
661	>	private:
662	>	vector<StuntDouble*> IOIndexToIntegrableObject;
663	>
664	>	public:
665	>
666	>	/**
667	>	* Finds the processor where a molecule resides
668	>	* @return the id of the processor which contains the molecule
669	>	* @param globalIndex global Index of the molecule
670	>	*/
671	>	int getMolToProc(int globalIndex) {
672	>	//assert(globalIndex < molToProcMap_.size());
673	>	return molToProcMap_[globalIndex];
674	>	}
675	>
676	>	/**
677	>	* Set MolToProcMap array
678	>	* @see #SimCreator::divideMolecules
679	>	*/
680	>	void setMolToProcMap(const vector<int>& molToProcMap) {
681	>	molToProcMap_ = molToProcMap;
682	>	}
683	>
684	>	private:
685	>
686	>	/**
687	>	* The size of molToProcMap_ is equal to total number of molecules
688	>	* in the system.  It maps a molecule to the processor on which it
689	>	* resides. it is filled by SimCreator once and only once.
690	>	*/
691	>	vector<int> molToProcMap_;
692
693	<	};
693	>	};
694
695	<	} //namespace oopse
695	>	} //namespace OpenMD
696		#endif //BRAINS_SIMMODEL_HPP
697

Comparing:
trunk/src/brains/SimInfo.hpp (property svn:keywords), Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
branches/development/src/brains/SimInfo.hpp (property svn:keywords), Revision 1577 by gezelter, Wed Jun 8 20:26:56 2011 UTC

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