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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 1665 by gezelter, Tue Nov 22 20:38:56 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 54 | Line 55
55		#include <utility>
56		#include <vector>
57
58	<	#include "brains/Exclude.hpp"
58	>	#include "brains/PairList.hpp"
59		#include "io/Globals.hpp"
60		#include "math/Vector3.hpp"
61	+	#include "math/SquareMatrix3.hpp"
62		#include "types/MoleculeStamp.hpp"
63		#include "UseTheForce/ForceField.hpp"
64		#include "utils/PropertyMap.hpp"
65		#include "utils/LocalIndexManager.hpp"
66	+	#include "nonbonded/SwitchingFunction.hpp"
67
68	<	//another nonsense macro declaration
69	<	#define __C
70	<	#include "brains/fSimulation.h"
68	>	using namespace std;
69	>	namespace OpenMD{
70	>	//forward declaration
71	>	class SnapshotManager;
72	>	class Molecule;
73	>	class SelectionManager;
74	>	class StuntDouble;
75
76	<	namespace oopse{
76	>	/**
77	>	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
78	>	*
79	>	* @brief One of the heavy-weight classes of OpenMD, SimInfo
80	>	* maintains objects and variables relating to the current
81	>	* simulation.  This includes the master list of Molecules.  The
82	>	* Molecule class maintains all of the concrete objects (Atoms,
83	>	* Bond, Bend, Torsions, Inversions, RigidBodies, CutoffGroups,
84	>	* Constraints). In both the single and parallel versions, Atoms and
85	>	* RigidBodies have both global and local indices.
86	>	*/
87	>	class SimInfo {
88	>	public:
89	>	typedef map<int, Molecule*>::iterator  MoleculeIterator;
90	>
91	>	/**
92	>	* Constructor of SimInfo
93	>	*
94	>	* @param molStampPairs MoleculeStamp Array. The first element of
95	>	* the pair is molecule stamp, the second element is the total
96	>	* number of molecules with the same molecule stamp in the system
97	>	*
98	>	* @param ff pointer of a concrete ForceField instance
99	>	*
100	>	* @param simParams
101	>	*/
102	>	SimInfo(ForceField* ff, Globals* simParams);
103	>	virtual ~SimInfo();
104
105	<	//forward decalration
106	<	class SnapshotManager;
107	<	class Molecule;
108	<	class SelectionManager;
109	<	/**
110	<	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
111	<	* @brief As one of the heavy weight class of OOPSE, SimInfo
112	<	* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
113	<	* 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;
105	>	/**
106	>	* Adds a molecule
107	>	*
108	>	* @return return true if adding successfully, return false if the
109	>	* molecule is already in SimInfo
110	>	*
111	>	* @param mol molecule to be added
112	>	*/
113	>	bool addMolecule(Molecule* mol);
114
115	<	/**
116	<	* Constructor of SimInfo
117	<	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
118	<	* second element is the total number of molecules with the same molecule stamp in the system
119	<	* @param ff pointer of a concrete ForceField instance
120	<	* @param simParams
121	<	* @note
96	<	*/
97	<	SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams);
98	<	virtual ~SimInfo();
115	>	/**
116	>	* Removes a molecule from SimInfo
117	>	*
118	>	* @return true if removing successfully, return false if molecule
119	>	* is not in this SimInfo
120	>	*/
121	>	bool removeMolecule(Molecule* mol);
122
123	<	/**
124	<	* Adds a molecule
125	<	* @return return true if adding successfully, return false if the molecule is already in SimInfo
126	<	* @param mol molecule to be added
104	<	*/
105	<	bool addMolecule(Molecule* mol);
123	>	/** Returns the total number of molecules in the system. */
124	>	int getNGlobalMolecules() {
125	>	return nGlobalMols_;
126	>	}
127
128	<	/**
129	<	* Removes a molecule from SimInfo
130	<	* @return true if removing successfully, return false if molecule is not in this SimInfo
131	<	*/
111	<	bool removeMolecule(Molecule* mol);
128	>	/** Returns the total number of atoms in the system. */
129	>	int getNGlobalAtoms() {
130	>	return nGlobalAtoms_;
131	>	}
132
133	<	/** Returns the total number of molecules in the system. */
134	<	int getNGlobalMolecules() {
135	<	return nGlobalMols_;
136	<	}
133	>	/** Returns the total number of cutoff groups in the system. */
134	>	int getNGlobalCutoffGroups() {
135	>	return nGlobalCutoffGroups_;
136	>	}
137
138	<	/** Returns the total number of atoms in the system. */
139	<	int getNGlobalAtoms() {
140	<	return nGlobalAtoms_;
141	<	}
138	>	/**
139	>	* Returns the total number of integrable objects (total number of
140	>	* rigid bodies plus the total number of atoms which do not belong
141	>	* to the rigid bodies) in the system
142	>	*/
143	>	int getNGlobalIntegrableObjects() {
144	>	return nGlobalIntegrableObjects_;
145	>	}
146
147	<	/** Returns the total number of cutoff groups in the system. */
148	<	int getNGlobalCutoffGroups() {
149	<	return nGlobalCutoffGroups_;
150	<	}
147	>	/**
148	>	* Returns the total number of integrable objects (total number of
149	>	* rigid bodies plus the total number of atoms which do not belong
150	>	* to the rigid bodies) in the system
151	>	*/
152	>	int getNGlobalRigidBodies() {
153	>	return nGlobalRigidBodies_;
154	>	}
155
156	<	/**
157	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
158	<	* of atoms which do not belong to the rigid bodies) in the system
159	<	*/
160	<	int getNGlobalIntegrableObjects() {
161	<	return nGlobalIntegrableObjects_;
162	<	}
156	>	int getNGlobalConstraints();
157	>	/**
158	>	* Returns the number of local molecules.
159	>	* @return the number of local molecules
160	>	*/
161	>	int getNMolecules() {
162	>	return molecules_.size();
163	>	}
164
165	<	/**
166	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
167	<	* of atoms which do not belong to the rigid bodies) in the system
168	<	*/
140	<	int getNGlobalRigidBodies() {
141	<	return nGlobalRigidBodies_;
142	<	}
165	>	/** Returns the number of local atoms */
166	>	unsigned int getNAtoms() {
167	>	return nAtoms_;
168	>	}
169
170	<	int getNGlobalConstraints();
171	<	/**
146	<	* Returns the number of local molecules.
147	<	* @return the number of local molecules
148	<	*/
149	<	int getNMolecules() {
150	<	return molecules_.size();
151	<	}
170	>	/** Returns the number of effective cutoff groups on local processor */
171	>	unsigned int getNLocalCutoffGroups();
172
173	<	/** Returns the number of local atoms */
174	<	unsigned int getNAtoms() {
175	<	return nAtoms_;
176	<	}
173	>	/** Returns the number of local bonds */
174	>	unsigned int getNBonds(){
175	>	return nBonds_;
176	>	}
177
178	<	/** Returns the number of local bonds */
179	<	unsigned int getNBonds(){
180	<	return nBonds_;
181	<	}
178	>	/** Returns the number of local bends */
179	>	unsigned int getNBends() {
180	>	return nBends_;
181	>	}
182
183	<	/** Returns the number of local bends */
184	<	unsigned int getNBends() {
185	<	return nBends_;
186	<	}
183	>	/** Returns the number of local torsions */
184	>	unsigned int getNTorsions() {
185	>	return nTorsions_;
186	>	}
187
188	<	/** Returns the number of local torsions */
189	<	unsigned int getNTorsions() {
190	<	return nTorsions_;
191	<	}
188	>	/** Returns the number of local torsions */
189	>	unsigned int getNInversions() {
190	>	return nInversions_;
191	>	}
192	>	/** Returns the number of local rigid bodies */
193	>	unsigned int getNRigidBodies() {
194	>	return nRigidBodies_;
195	>	}
196
197	<	/** Returns the number of local rigid bodies */
198	<	unsigned int getNRigidBodies() {
199	<	return nRigidBodies_;
200	<	}
197	>	/** Returns the number of local integrable objects */
198	>	unsigned int getNIntegrableObjects() {
199	>	return nIntegrableObjects_;
200	>	}
201
202	<	/** Returns the number of local integrable objects */
203	<	unsigned int getNIntegrableObjects() {
204	<	return nIntegrableObjects_;
205	<	}
202	>	/** Returns the number of local cutoff groups */
203	>	unsigned int getNCutoffGroups() {
204	>	return nCutoffGroups_;
205	>	}
206
207	<	/** Returns the number of local cutoff groups */
208	<	unsigned int getNCutoffGroups() {
209	<	return nCutoffGroups_;
210	<	}
187	<
188	<	/** Returns the total number of constraints in this SimInfo */
189	<	unsigned int getNConstraints() {
190	<	return nConstraints_;
191	<	}
207	>	/** Returns the total number of constraints in this SimInfo */
208	>	unsigned int getNConstraints() {
209	>	return nConstraints_;
210	>	}
211
212	<	/**
213	<	* Returns the first molecule in this SimInfo and intialize the iterator.
214	<	* @return the first molecule, return NULL if there is not molecule in this SimInfo
215	<	* @param i the iterator of molecule array (user shouldn't change it)
216	<	*/
217	<	Molecule* beginMolecule(MoleculeIterator& i);
212	>	/**
213	>	* Returns the first molecule in this SimInfo and intialize the iterator.
214	>	* @return the first molecule, return NULL if there is not molecule in this SimInfo
215	>	* @param i the iterator of molecule array (user shouldn't change it)
216	>	*/
217	>	Molecule* beginMolecule(MoleculeIterator& i);
218
219	<	/**
220	<	* Returns the next avaliable Molecule based on the iterator.
221	<	* @return the next avaliable molecule, return NULL if reaching the end of the array
222	<	* @param i the iterator of molecule array
223	<	*/
224	<	Molecule* nextMolecule(MoleculeIterator& i);
219	>	/**
220	>	* Returns the next avaliable Molecule based on the iterator.
221	>	* @return the next avaliable molecule, return NULL if reaching the end of the array
222	>	* @param i the iterator of molecule array
223	>	*/
224	>	Molecule* nextMolecule(MoleculeIterator& i);
225
226	<	/** Returns the number of degrees of freedom */
227	<	int getNdf() {
228	<	return ndf_;
229	<	}
226	>	/** Returns the number of degrees of freedom */
227	>	int getNdf() {
228	>	return ndf_ - getFdf();
229	>	}
230
231	<	/** Returns the number of raw degrees of freedom */
232	<	int getNdfRaw() {
233	<	return ndfRaw_;
234	<	}
231	>	/** Returns the number of raw degrees of freedom */
232	>	int getNdfRaw() {
233	>	return ndfRaw_;
234	>	}
235
236	<	/** Returns the number of translational degrees of freedom */
237	<	int getNdfTrans() {
238	<	return ndfTrans_;
239	<	}
236	>	/** Returns the number of translational degrees of freedom */
237	>	int getNdfTrans() {
238	>	return ndfTrans_;
239	>	}
240
241	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
241	>	/** sets the current number of frozen degrees of freedom */
242	>	void setFdf(int fdf) {
243	>	fdf_local = fdf;
244	>	}
245	>
246	>	int getFdf();
247	>
248	>	//getNZconstraint and setNZconstraint ruin the coherence of
249	>	//SimInfo class, need refactoring
250
251	<	/** Returns the total number of z-constraint molecules in the system */
252	<	int getNZconstraint() {
253	<	return nZconstraint_;
254	<	}
251	>	/** Returns the total number of z-constraint molecules in the system */
252	>	int getNZconstraint() {
253	>	return nZconstraint_;
254	>	}
255
256	<	/**
257	<	* Sets the number of z-constraint molecules in the system.
258	<	*/
259	<	void setNZconstraint(int nZconstraint) {
260	<	nZconstraint_ = nZconstraint;
261	<	}
256	>	/**
257	>	* Sets the number of z-constraint molecules in the system.
258	>	*/
259	>	void setNZconstraint(int nZconstraint) {
260	>	nZconstraint_ = nZconstraint;
261	>	}
262
263	<	/** Returns the snapshot manager. */
264	<	SnapshotManager* getSnapshotManager() {
265	<	return sman_;
266	<	}
263	>	/** Returns the snapshot manager. */
264	>	SnapshotManager* getSnapshotManager() {
265	>	return sman_;
266	>	}
267
268	<	/** Sets the snapshot manager. */
269	<	void setSnapshotManager(SnapshotManager* sman);
268	>	/** Sets the snapshot manager. */
269	>	void setSnapshotManager(SnapshotManager* sman);
270
271	<	/** Returns the force field */
272	<	ForceField* getForceField() {
273	<	return forceField_;
274	<	}
271	>	/** Returns the force field */
272	>	ForceField* getForceField() {
273	>	return forceField_;
274	>	}
275
276	<	Globals* getSimParams() {
277	<	return simParams_;
278	<	}
276	>	Globals* getSimParams() {
277	>	return simParams_;
278	>	}
279
280	<	/** Returns the velocity of center of mass of the whole system.*/
281	<	Vector3d getComVel();
280	>	/** Returns the velocity of center of mass of the whole system.*/
281	>	Vector3d getComVel();
282
283	<	/** Returns the center of the mass of the whole system.*/
284	<	Vector3d getCom();
283	>	/** Returns the center of the mass of the whole system.*/
284	>	Vector3d getCom();
285	>	/** Returns the center of the mass and Center of Mass velocity of
286	>	the whole system.*/
287	>	void getComAll(Vector3d& com,Vector3d& comVel);
288
289	<	/** main driver function to interact with fortran during the initialization and molecule migration */
290	<	void update();
289	>	/** Returns intertia tensor for the entire system and system
290	>	Angular Momentum.*/
291	>	void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
292	>
293	>	/** Returns system angular momentum */
294	>	Vector3d getAngularMomentum();
295
296	<	/** Returns the local index manager */
297	<	LocalIndexManager* getLocalIndexManager() {
298	<	return &localIndexMan_;
299	<	}
296	>	/** Returns volume of system as estimated by an ellipsoid defined
297	>	by the radii of gyration*/
298	>	void getGyrationalVolume(RealType &vol);
299	>	/** Overloaded version of gyrational volume that also returns
300	>	det(I) so dV/dr can be calculated*/
301	>	void getGyrationalVolume(RealType &vol, RealType &detI);
302
303	<	int getMoleculeStampId(int globalIndex) {
304	<	//assert(globalIndex < molStampIds_.size())
305	<	return molStampIds_[globalIndex];
306	<	}
303	>	void update();
304	>	/**
305	>	* Do final bookkeeping before Force managers need their data.
306	>	*/
307	>	void prepareTopology();
308
272	–	/** Returns the molecule stamp */
273	–	MoleculeStamp* getMoleculeStamp(int id) {
274	–	return moleculeStamps_[id];
275	–	}
309
310	<	/** Return the total number of the molecule stamps */
311	<	int getNMoleculeStamp() {
312	<	return moleculeStamps_.size();
313	<	}
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);
310	>	/** Returns the local index manager */
311	>	LocalIndexManager* getLocalIndexManager() {
312	>	return &localIndexMan_;
313	>	}
314
315	<	return i != molecules_.end() ? i->second : NULL;
316	<	}
315	>	int getMoleculeStampId(int globalIndex) {
316	>	//assert(globalIndex < molStampIds_.size())
317	>	return molStampIds_[globalIndex];
318	>	}
319
320	<	/** Calculate the maximum cutoff radius based on the atom types */
321	<	double calcMaxCutoffRadius();
320	>	/** Returns the molecule stamp */
321	>	MoleculeStamp* getMoleculeStamp(int id) {
322	>	return moleculeStamps_[id];
323	>	}
324
325	<	double getRcut() {
326	<	return rcut_;
327	<	}
325	>	/** Return the total number of the molecule stamps */
326	>	int getNMoleculeStamp() {
327	>	return moleculeStamps_.size();
328	>	}
329	>	/**
330	>	* Finds a molecule with a specified global index
331	>	* @return a pointer point to found molecule
332	>	* @param index
333	>	*/
334	>	Molecule* getMoleculeByGlobalIndex(int index) {
335	>	MoleculeIterator i;
336	>	i = molecules_.find(index);
337
338	<	double getRsw() {
339	<	return rsw_;
302	<	}
303	<
304	<	std::string getFinalConfigFileName() {
305	<	return finalConfigFileName_;
306	<	}
307	<
308	<	void setFinalConfigFileName(const std::string& fileName) {
309	<	finalConfigFileName_ = fileName;
310	<	}
338	>	return i != molecules_.end() ? i->second : NULL;
339	>	}
340
341	<	std::string getDumpFileName() {
342	<	return dumpFileName_;
343	<	}
315	<
316	<	void setDumpFileName(const std::string& fileName) {
317	<	dumpFileName_ = fileName;
318	<	}
341	>	int getGlobalMolMembership(int id){
342	>	return globalMolMembership_[id];
343	>	}
344
345	<	std::string getStatFileName() {
346	<	return statFileName_;
347	<	}
345	>	/**
346	>	* returns a vector which maps the local atom index on this
347	>	* processor to the global atom index.  With only one processor,
348	>	* these should be identical.
349	>	*/
350	>	vector<int> getGlobalAtomIndices();
351	>
352	>	/**
353	>	* returns a vector which maps the local cutoff group index on
354	>	* this processor to the global cutoff group index.  With only one
355	>	* processor, these should be identical.
356	>	*/
357	>	vector<int> getGlobalGroupIndices();
358	>
359
360	<	void setStatFileName(const std::string& fileName) {
361	<	statFileName_ = fileName;
362	<	}
360	>	string getFinalConfigFileName() {
361	>	return finalConfigFileName_;
362	>	}
363
364	<	/**
365	<	* Sets GlobalGroupMembership
366	<	* @see #SimCreator::setGlobalIndex
331	<	*/
332	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
333	<	assert(globalGroupMembership.size() == nGlobalAtoms_);
334	<	globalGroupMembership_ = globalGroupMembership;
335	<	}
364	>	void setFinalConfigFileName(const string& fileName) {
365	>	finalConfigFileName_ = fileName;
366	>	}
367
368	<	/**
369	<	* Sets GlobalMolMembership
370	<	* @see #SimCreator::setGlobalIndex
371	<	*/
372	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
373	<	assert(globalMolMembership.size() == nGlobalAtoms_);
374	<	globalMolMembership_ = globalMolMembership;
375	<	}
368	>	string getRawMetaData() {
369	>	return rawMetaData_;
370	>	}
371	>	void setRawMetaData(const string& rawMetaData) {
372	>	rawMetaData_ = rawMetaData;
373	>	}
374	>
375	>	string getDumpFileName() {
376	>	return dumpFileName_;
377	>	}
378	>
379	>	void setDumpFileName(const string& fileName) {
380	>	dumpFileName_ = fileName;
381	>	}
382
383	+	string getStatFileName() {
384	+	return statFileName_;
385	+	}
386	+
387	+	void setStatFileName(const string& fileName) {
388	+	statFileName_ = fileName;
389	+	}
390	+
391	+	string getRestFileName() {
392	+	return restFileName_;
393	+	}
394	+
395	+	void setRestFileName(const string& fileName) {
396	+	restFileName_ = fileName;
397	+	}
398
399	<	bool isFortranInitialized() {
400	<	return fortranInitialized_;
401	<	}
399	>	/**
400	>	* Sets GlobalGroupMembership
401	>	* @see #SimCreator::setGlobalIndex
402	>	*/
403	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
404	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
405	>	globalGroupMembership_ = globalGroupMembership;
406	>	}
407	>
408	>	/**
409	>	* Sets GlobalMolMembership
410	>	* @see #SimCreator::setGlobalIndex
411	>	*/
412	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
413	>	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
414	>	globalMolMembership_ = globalMolMembership;
415	>	}
416	>
417	>
418	>	bool isTopologyDone() {
419	>	return topologyDone_;
420	>	}
421
422	<	//below functions are just forward functions
423	<	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
424	<	//the other hand, has-a relation need composing.
354	<	/**
355	<	* Adds property into property map
356	<	* @param genData GenericData to be added into PropertyMap
357	<	*/
358	<	void addProperty(GenericData* genData);
422	>	bool getCalcBoxDipole() {
423	>	return calcBoxDipole_;
424	>	}
425
426	<	/**
427	<	* Removes property from PropertyMap by name
428	<	* @param propName the name of property to be removed
363	<	*/
364	<	void removeProperty(const std::string& propName);
426	>	bool getUseAtomicVirial() {
427	>	return useAtomicVirial_;
428	>	}
429
430	<	/**
431	<	* clear all of the properties
432	<	*/
433	<	void clearProperties();
430	>	/**
431	>	* Adds property into property map
432	>	* @param genData GenericData to be added into PropertyMap
433	>	*/
434	>	void addProperty(GenericData* genData);
435
436	<	/**
437	<	* Returns all names of properties
438	<	* @return all names of properties
439	<	*/
440	<	std::vector<std::string> getPropertyNames();
436	>	/**
437	>	* Removes property from PropertyMap by name
438	>	* @param propName the name of property to be removed
439	>	*/
440	>	void removeProperty(const string& propName);
441
442	<	/**
443	<	* Returns all of the properties in PropertyMap
444	<	* @return all of the properties in PropertyMap
445	<	*/
381	<	std::vector<GenericData*> getProperties();
442	>	/**
443	>	* clear all of the properties
444	>	*/
445	>	void clearProperties();
446
447	<	/**
448	<	* Returns property
449	<	* @param propName name of property
450	<	* @return a pointer point to property with propName. If no property named propName
451	<	* exists, return NULL
388	<	*/
389	<	GenericData* getPropertyByName(const std::string& propName);
447	>	/**
448	>	* Returns all names of properties
449	>	* @return all names of properties
450	>	*/
451	>	vector<string> getPropertyNames();
452
453	<	/**
454	<	* add all exclude pairs of a molecule into exclude list.
455	<	*/
456	<	void addExcludePairs(Molecule* mol);
453	>	/**
454	>	* Returns all of the properties in PropertyMap
455	>	* @return all of the properties in PropertyMap
456	>	*/
457	>	vector<GenericData*> getProperties();
458
459	<	/**
460	<	* remove all exclude pairs which belong to a molecule from exclude list
461	<	*/
459	>	/**
460	>	* Returns property
461	>	* @param propName name of property
462	>	* @return a pointer point to property with propName. If no property named propName
463	>	* exists, return NULL
464	>	*/
465	>	GenericData* getPropertyByName(const string& propName);
466
467	<	void removeExcludePairs(Molecule* mol);
467	>	/**
468	>	* add all special interaction pairs (including excluded
469	>	* interactions) in a molecule into the appropriate lists.
470	>	*/
471	>	void addInteractionPairs(Molecule* mol);
472
473	+	/**
474	+	* remove all special interaction pairs which belong to a molecule
475	+	* from the appropriate lists.
476	+	*/
477	+	void removeInteractionPairs(Molecule* mol);
478
479	<	/** Returns the unique atom types of local processor in an array */
480	<	std::set<AtomType*> getUniqueAtomTypes();
479	>	/** Returns the set of atom types present in this simulation */
480	>	set<AtomType*> getSimulatedAtomTypes();
481
482	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
482	>	friend ostream& operator <<(ostream& o, SimInfo& info);
483
484	<	void getCutoff(double& rcut, double& rsw);
484	>	void getCutoff(RealType& rcut, RealType& rsw);
485
486	<	private:
486	>	private:
487
488	<	/** fill up the simtype struct*/
489	<	void setupSimType();
488	>	/** fill up the simtype struct and other simulation-related variables */
489	>	void setupSimVariables();
490
415	–	/**
416	–	* Setup Fortran Simulation
417	–	* @see #setupFortranParallel
418	–	*/
419	–	void setupFortranSim();
491
492	<	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
493	<	void setupCutoff();
492	>	/** Determine if we need to accumulate the simulation box dipole */
493	>	void setupAccumulateBoxDipole();
494
495	<	/** Calculates the number of degress of freedom in the whole system */
496	<	void calcNdf();
497	<	void calcNdfRaw();
498	<	void calcNdfTrans();
495	>	/** Calculates the number of degress of freedom in the whole system */
496	>	void calcNdf();
497	>	void calcNdfRaw();
498	>	void calcNdfTrans();
499
500	<	/**
501	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
502	<	* system.
503	<	*/
504	<	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
500	>	/**
501	>	* Adds molecule stamp and the total number of the molecule with
502	>	* same molecule stamp in the whole system.
503	>	*/
504	>	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
505
506	<	ForceField* forceField_;
507	<	Globals* simParams_;
506	>	// Other classes holdingn important information
507	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
508	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
509
510	<	std::map<int, Molecule*>  molecules_; /**< Molecule array */
510	>	///  Counts of local objects
511	>	int nAtoms_;              /**< number of atoms in local processor */
512	>	int nBonds_;              /**< number of bonds in local processor */
513	>	int nBends_;              /**< number of bends in local processor */
514	>	int nTorsions_;           /**< number of torsions in local processor */
515	>	int nInversions_;         /**< number of inversions in local processor */
516	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
517	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
518	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
519	>	int nConstraints_;        /**< number of constraints in local processors */
520
521	<	//degress of freedom
522	<	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
523	<	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
524	<	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
525	<	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
526	<
527	<	//number of global objects
528	<	int nGlobalMols_;       /**< number of molecules in the system */
529	<	int nGlobalAtoms_;   /**< number of atoms in the system */
530	<	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
531	<	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
532	<	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
533	<	/**
534	<	* 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_;
458	<
459	<	/**
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_;
521	>	/// Counts of global objects
522	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
523	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
524	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
525	>	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
526	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
527	>
528	>	/// Degress of freedom
529	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
530	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
531	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
532	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
533	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
534	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
535
536	<
537	<	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
538	<	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
539	<
540	<	//number of local objects
541	<	int nAtoms_;                        /**< number of atoms in local processor */
542	<	int nBonds_;                        /**< number of bonds in local processor */
543	<	int nBends_;                        /**< number of bends in local processor */
544	<	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 */
536	>	/// logicals
537	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
538	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
539	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
540	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
541	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
542	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
543	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
544	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
545
546	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
547	<	Exclude exclude_;
548	<	PropertyMap properties_;                  /**< Generic Property */
549	<	SnapshotManager* sman_;               /**< SnapshotManager */
546	>	public:
547	>	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
548	>	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
549	>	bool usesMetallicAtoms() { return usesMetallicAtoms_; }
550	>	bool usesAtomicVirial() { return usesAtomicVirial_; }
551	>	bool requiresPrepair() { return requiresPrepair_; }
552	>	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
553	>	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
554
555	<	/**
556	<	* The reason to have a local index manager is that when molecule is migrating to other processors,
557	<	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
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_;
555	>	private:
556	>	/// Data structures holding primary simulation objects
557	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
558
559	<	//file names
560	<	std::string finalConfigFileName_;
561	<	std::string dumpFileName_;
562	<	std::string statFileName_;
559	>	/// Stamps are templates for objects that are then used to create
560	>	/// groups of objects.  For example, a molecule stamp contains
561	>	/// information on how to build that molecule (i.e. the topology,
562	>	/// the atoms, the bonds, etc.)  Once the system is built, the
563	>	/// stamps are no longer useful.
564	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
565	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
566
567	<	double rcut_;       /**< cutoff radius*/
568	<	double rsw_;        /**< radius of switching function*/
567	>	/**
568	>	* A vector that maps between the global index of an atom, and the
569	>	* global index of cutoff group the atom belong to.  It is filled
570	>	* by SimCreator once and only once, since it never changed during
571	>	* the simulation.  It should be nGlobalAtoms_ in size.
572	>	*/
573	>	vector<int> globalGroupMembership_;
574	>	public:
575	>	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
576	>	private:
577
578	<	bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
578	>	/**
579	>	* A vector that maps between the global index of an atom and the
580	>	* global index of the molecule the atom belongs to.  It is filled
581	>	* by SimCreator once and only once, since it is never changed
582	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
583	>	*/
584	>	vector<int> globalMolMembership_;
585
586	<	#ifdef IS_MPI
587	<	//in Parallel version, we need MolToProc
588	<	public:
589	<
590	<	/**
591	<	* Finds the processor where a molecule resides
592	<	* @return the id of the processor which contains the molecule
593	<	* @param globalIndex global Index of the molecule
594	<	*/
595	<	int getMolToProc(int globalIndex) {
596	<	//assert(globalIndex < molToProcMap_.size());
597	<	return molToProcMap_[globalIndex];
598	<	}
586	>	/**
587	>	* A vector that maps between the local index of an atom and the
588	>	* index of the AtomType.
589	>	*/
590	>	vector<int> identArray_;
591	>	public:
592	>	vector<int> getIdentArray() { return identArray_; }
593	>	private:
594	>
595	>	/**
596	>	* A vector which contains the fractional contribution of an
597	>	* atom's mass to the total mass of the cutoffGroup that atom
598	>	* belongs to.  In the case of single atom cutoff groups, the mass
599	>	* factor for that atom is 1.  For massless atoms, the factor is
600	>	* also 1.
601	>	*/
602	>	vector<RealType> massFactors_;
603	>	public:
604	>	vector<RealType> getMassFactors() { return massFactors_; }
605
606	<	/**
607	<	* Set MolToProcMap array
608	<	* @see #SimCreator::divideMolecules
609	<	*/
610	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
611	<	molToProcMap_ = molToProcMap;
612	<	}
606	>	PairList* getExcludedInteractions() { return &excludedInteractions_; }
607	>	PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
608	>	PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
609	>	PairList* getOneFourInteractions() { return &oneFourInteractions_; }
610	>
611	>	private:
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
525	–	private:
641
642	<	void setupFortranParallel();
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	<	/**
685	<	* The size of molToProcMap_ is equal to total number of molecules in the system.
686	<	*  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
687	<	* once.
688	<	*/
689	<	std::vector<int> molToProcMap_;
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	<	#endif
693	>	};
694
695	<	};
539	<
540	<	} //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 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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