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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 1808 by gezelter, Mon Oct 22 20:42:10 2012 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"
63	>	#include "brains/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 ff pointer to a concrete ForceField instance
95	>	*
96	>	* @param simParams pointer to the simulation parameters in a Globals object
97	>	*/
98	>	SimInfo(ForceField* ff, Globals* simParams);
99	>	virtual ~SimInfo();
100
101	<	//forward decalration
102	<	class SnapshotManager;
103	<	class Molecule;
104	<	class SelectionManager;
105	<	/**
106	<	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
107	<	* @brief As one of the heavy weight class of OOPSE, SimInfo
108	<	* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
109	<	* 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;
101	>	/**
102	>	* Adds a molecule
103	>	*
104	>	* @return return true if adding successfully, return false if the
105	>	* molecule is already in SimInfo
106	>	*
107	>	* @param mol Molecule to be added
108	>	*/
109	>	bool addMolecule(Molecule* mol);
110
111	<	/**
112	<	* Constructor of SimInfo
113	<	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
114	<	* second element is the total number of molecules with the same molecule stamp in the system
115	<	* @param ff pointer of a concrete ForceField instance
116	<	* @param simParams
117	<	* @note
96	<	*/
97	<	SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams);
98	<	virtual ~SimInfo();
111	>	/**
112	>	* Removes a molecule from SimInfo
113	>	*
114	>	* @return true if removing successfully, return false if molecule
115	>	* is not in this SimInfo
116	>	*/
117	>	bool removeMolecule(Molecule* mol);
118
119	<	/**
120	<	* Adds a molecule
121	<	* @return return true if adding successfully, return false if the molecule is already in SimInfo
122	<	* @param mol molecule to be added
104	<	*/
105	<	bool addMolecule(Molecule* mol);
119	>	/** Returns the total number of molecules in the system. */
120	>	int getNGlobalMolecules() {
121	>	return nGlobalMols_;
122	>	}
123
124	<	/**
125	<	* Removes a molecule from SimInfo
126	<	* @return true if removing successfully, return false if molecule is not in this SimInfo
127	<	*/
111	<	bool removeMolecule(Molecule* mol);
124	>	/** Returns the total number of atoms in the system. */
125	>	int getNGlobalAtoms() {
126	>	return nGlobalAtoms_;
127	>	}
128
129	<	/** Returns the total number of molecules in the system. */
130	<	int getNGlobalMolecules() {
131	<	return nGlobalMols_;
132	<	}
129	>	/** Returns the total number of cutoff groups in the system. */
130	>	int getNGlobalCutoffGroups() {
131	>	return nGlobalCutoffGroups_;
132	>	}
133
134	<	/** Returns the total number of atoms in the system. */
135	<	int getNGlobalAtoms() {
136	<	return nGlobalAtoms_;
137	<	}
134	>	/**
135	>	* Returns the total number of integrable objects (total number of
136	>	* rigid bodies plus the total number of atoms which do not belong
137	>	* to the rigid bodies) in the system
138	>	*/
139	>	int getNGlobalIntegrableObjects() {
140	>	return nGlobalIntegrableObjects_;
141	>	}
142
143	<	/** Returns the total number of cutoff groups in the system. */
144	<	int getNGlobalCutoffGroups() {
145	<	return nGlobalCutoffGroups_;
146	<	}
143	>	/**
144	>	* Returns the total number of integrable objects (total number of
145	>	* rigid bodies plus the total number of atoms which do not belong
146	>	* to the rigid bodies) in the system
147	>	*/
148	>	int getNGlobalRigidBodies() {
149	>	return nGlobalRigidBodies_;
150	>	}
151
152	<	/**
153	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
154	<	* of atoms which do not belong to the rigid bodies) in the system
155	<	*/
156	<	int getNGlobalIntegrableObjects() {
157	<	return nGlobalIntegrableObjects_;
158	<	}
152	>	int getNGlobalConstraints();
153	>	/**
154	>	* Returns the number of local molecules.
155	>	* @return the number of local molecules
156	>	*/
157	>	int getNMolecules() {
158	>	return molecules_.size();
159	>	}
160
161	<	/**
162	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
163	<	* of atoms which do not belong to the rigid bodies) in the system
164	<	*/
140	<	int getNGlobalRigidBodies() {
141	<	return nGlobalRigidBodies_;
142	<	}
161	>	/** Returns the number of local atoms */
162	>	unsigned int getNAtoms() {
163	>	return nAtoms_;
164	>	}
165
166	<	int getNGlobalConstraints();
167	<	/**
146	<	* Returns the number of local molecules.
147	<	* @return the number of local molecules
148	<	*/
149	<	int getNMolecules() {
150	<	return molecules_.size();
151	<	}
166	>	/** Returns the number of effective cutoff groups on local processor */
167	>	unsigned int getNLocalCutoffGroups();
168
169	<	/** Returns the number of local atoms */
170	<	unsigned int getNAtoms() {
171	<	return nAtoms_;
172	<	}
169	>	/** Returns the number of local bonds */
170	>	unsigned int getNBonds(){
171	>	return nBonds_;
172	>	}
173
174	<	/** Returns the number of local bonds */
175	<	unsigned int getNBonds(){
176	<	return nBonds_;
177	<	}
174	>	/** Returns the number of local bends */
175	>	unsigned int getNBends() {
176	>	return nBends_;
177	>	}
178
179	<	/** Returns the number of local bends */
180	<	unsigned int getNBends() {
181	<	return nBends_;
182	<	}
179	>	/** Returns the number of local torsions */
180	>	unsigned int getNTorsions() {
181	>	return nTorsions_;
182	>	}
183
184	<	/** Returns the number of local torsions */
185	<	unsigned int getNTorsions() {
186	<	return nTorsions_;
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 rigid bodies */
194	<	unsigned int getNRigidBodies() {
195	<	return nRigidBodies_;
196	<	}
193	>	/** Returns the number of local integrable objects */
194	>	unsigned int getNIntegrableObjects() {
195	>	return nIntegrableObjects_;
196	>	}
197
198	<	/** Returns the number of local integrable objects */
199	<	unsigned int getNIntegrableObjects() {
200	<	return nIntegrableObjects_;
201	<	}
198	>	/** Returns the number of local cutoff groups */
199	>	unsigned int getNCutoffGroups() {
200	>	return nCutoffGroups_;
201	>	}
202
203	<	/** Returns the number of local cutoff groups */
204	<	unsigned int getNCutoffGroups() {
205	<	return nCutoffGroups_;
206	<	}
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);
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 degrees of freedom */
223	<	int getNdf() {
224	<	return ndf_;
225	<	}
222	>	/** Returns the total number of fluctuating charges that are present */
223	>	int getNFluctuatingCharges() {
224	>	return nGlobalFluctuatingCharges_;
225	>	}
226
227	<	/** Returns the number of raw degrees of freedom */
228	<	int getNdfRaw() {
229	<	return ndfRaw_;
230	<	}
227	>	/** Returns the number of degrees of freedom */
228	>	int getNdf() {
229	>	return ndf_ - getFdf();
230	>	}
231
232	<	/** Returns the number of translational degrees of freedom */
233	<	int getNdfTrans() {
234	<	return ndfTrans_;
235	<	}
232	>	/** Returns the number of degrees of freedom (LOCAL) */
233	>	int getNdfLocal() {
234	>	return ndfLocal_;
235	>	}
236
237	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
237	>	/** Returns the number of raw degrees of freedom */
238	>	int getNdfRaw() {
239	>	return ndfRaw_;
240	>	}
241	>
242	>	/** Returns the number of translational degrees of freedom */
243	>	int getNdfTrans() {
244	>	return ndfTrans_;
245	>	}
246	>
247	>	/** sets the current number of frozen degrees of freedom */
248	>	void setFdf(int fdf) {
249	>	fdf_local = fdf;
250	>	}
251	>
252	>	int getFdf();
253	>
254	>	//getNZconstraint and setNZconstraint ruin the coherence of
255	>	//SimInfo class, need refactoring
256
257	<	/** Returns the total number of z-constraint molecules in the system */
258	<	int getNZconstraint() {
259	<	return nZconstraint_;
260	<	}
257	>	/** Returns the total number of z-constraint molecules in the system */
258	>	int getNZconstraint() {
259	>	return nZconstraint_;
260	>	}
261
262	<	/**
263	<	* Sets the number of z-constraint molecules in the system.
264	<	*/
265	<	void setNZconstraint(int nZconstraint) {
266	<	nZconstraint_ = nZconstraint;
267	<	}
262	>	/**
263	>	* Sets the number of z-constraint molecules in the system.
264	>	*/
265	>	void setNZconstraint(int nZconstraint) {
266	>	nZconstraint_ = nZconstraint;
267	>	}
268
269	<	/** Returns the snapshot manager. */
270	<	SnapshotManager* getSnapshotManager() {
271	<	return sman_;
272	<	}
269	>	/** Returns the snapshot manager. */
270	>	SnapshotManager* getSnapshotManager() {
271	>	return sman_;
272	>	}
273
274	<	/** Sets the snapshot manager. */
275	<	void setSnapshotManager(SnapshotManager* sman);
274	>	/** Sets the snapshot manager. */
275	>	void setSnapshotManager(SnapshotManager* sman);
276
277	<	/** Returns the force field */
278	<	ForceField* getForceField() {
279	<	return forceField_;
280	<	}
277	>	/** Returns the force field */
278	>	ForceField* getForceField() {
279	>	return forceField_;
280	>	}
281
282	<	Globals* getSimParams() {
283	<	return simParams_;
284	<	}
282	>	Globals* getSimParams() {
283	>	return simParams_;
284	>	}
285
286	<	/** Returns the velocity of center of mass of the whole system.*/
287	<	Vector3d getComVel();
286	>	void update();
287	>	/**
288	>	* Do final bookkeeping before Force managers need their data.
289	>	*/
290	>	void prepareTopology();
291
256	–	/** Returns the center of the mass of the whole system.*/
257	–	Vector3d getCom();
292
293	<	/** main driver function to interact with fortran during the initialization and molecule migration */
294	<	void update();
293	>	/** Returns the local index manager */
294	>	LocalIndexManager* getLocalIndexManager() {
295	>	return &localIndexMan_;
296	>	}
297
298	<	/** Returns the local index manager */
299	<	LocalIndexManager* getLocalIndexManager() {
300	<	return &localIndexMan_;
301	<	}
298	>	int getMoleculeStampId(int globalIndex) {
299	>	//assert(globalIndex < molStampIds_.size())
300	>	return molStampIds_[globalIndex];
301	>	}
302
303	<	int getMoleculeStampId(int globalIndex) {
304	<	//assert(globalIndex < molStampIds_.size())
305	<	return molStampIds_[globalIndex];
306	<	}
303	>	/** Returns the molecule stamp */
304	>	MoleculeStamp* getMoleculeStamp(int id) {
305	>	return moleculeStamps_[id];
306	>	}
307
308	<	/** Returns the molecule stamp */
309	<	MoleculeStamp* getMoleculeStamp(int id) {
310	<	return moleculeStamps_[id];
311	<	}
308	>	/** Return the total number of the molecule stamps */
309	>	int getNMoleculeStamp() {
310	>	return moleculeStamps_.size();
311	>	}
312	>	/**
313	>	* Finds a molecule with a specified global index
314	>	* @return a pointer point to found molecule
315	>	* @param index
316	>	*/
317	>	Molecule* getMoleculeByGlobalIndex(int index) {
318	>	MoleculeIterator i;
319	>	i = molecules_.find(index);
320
321	<	/** Return the total number of the molecule stamps */
322	<	int getNMoleculeStamp() {
279	<	return moleculeStamps_.size();
280	<	}
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);
321	>	return i != molecules_.end() ? i->second : NULL;
322	>	}
323
324	<	return i != molecules_.end() ? i->second : NULL;
325	<	}
324	>	int getGlobalMolMembership(int id){
325	>	return globalMolMembership_[id];
326	>	}
327
328	<	/** Calculate the maximum cutoff radius based on the atom types */
329	<	double calcMaxCutoffRadius();
328	>	/**
329	>	* returns a vector which maps the local atom index on this
330	>	* processor to the global atom index.  With only one processor,
331	>	* these should be identical.
332	>	*/
333	>	vector<int> getGlobalAtomIndices();
334
335	<	double getRcut() {
336	<	return rcut_;
337	<	}
335	>	/**
336	>	* returns a vector which maps the local cutoff group index on
337	>	* this processor to the global cutoff group index.  With only one
338	>	* processor, these should be identical.
339	>	*/
340	>	vector<int> getGlobalGroupIndices();
341
300	–	double getRsw() {
301	–	return rsw_;
302	–	}
342
343	<	std::string getFinalConfigFileName() {
344	<	return finalConfigFileName_;
345	<	}
307	<
308	<	void setFinalConfigFileName(const std::string& fileName) {
309	<	finalConfigFileName_ = fileName;
310	<	}
343	>	string getFinalConfigFileName() {
344	>	return finalConfigFileName_;
345	>	}
346
347	<	std::string getDumpFileName() {
348	<	return dumpFileName_;
349	<	}
315	<
316	<	void setDumpFileName(const std::string& fileName) {
317	<	dumpFileName_ = fileName;
318	<	}
347	>	void setFinalConfigFileName(const string& fileName) {
348	>	finalConfigFileName_ = fileName;
349	>	}
350
351	<	std::string getStatFileName() {
352	<	return statFileName_;
353	<	}
351	>	string getRawMetaData() {
352	>	return rawMetaData_;
353	>	}
354	>	void setRawMetaData(const string& rawMetaData) {
355	>	rawMetaData_ = rawMetaData;
356	>	}
357
358	<	void setStatFileName(const std::string& fileName) {
359	<	statFileName_ = fileName;
360	<	}
361	<
362	<	/**
363	<	* Sets GlobalGroupMembership
364	<	* @see #SimCreator::setGlobalIndex
331	<	*/
332	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
333	<	assert(globalGroupMembership.size() == nGlobalAtoms_);
334	<	globalGroupMembership_ = globalGroupMembership;
335	<	}
336	<
337	<	/**
338	<	* Sets GlobalMolMembership
339	<	* @see #SimCreator::setGlobalIndex
340	<	*/
341	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
342	<	assert(globalMolMembership.size() == nGlobalAtoms_);
343	<	globalMolMembership_ = globalMolMembership;
344	<	}
358	>	string getDumpFileName() {
359	>	return dumpFileName_;
360	>	}
361	>
362	>	void setDumpFileName(const string& fileName) {
363	>	dumpFileName_ = fileName;
364	>	}
365
366	+	string getStatFileName() {
367	+	return statFileName_;
368	+	}
369	+
370	+	void setStatFileName(const string& fileName) {
371	+	statFileName_ = fileName;
372	+	}
373	+
374	+	string getRestFileName() {
375	+	return restFileName_;
376	+	}
377	+
378	+	void setRestFileName(const string& fileName) {
379	+	restFileName_ = fileName;
380	+	}
381
382	<	bool isFortranInitialized() {
383	<	return fortranInitialized_;
384	<	}
382	>	/**
383	>	* Sets GlobalGroupMembership
384	>	*/
385	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
386	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
387	>	globalGroupMembership_ = globalGroupMembership;
388	>	}
389	>
390	>	/**
391	>	* Sets GlobalMolMembership
392	>	*/
393	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
394	>	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
395	>	globalMolMembership_ = globalMolMembership;
396	>	}
397	>
398	>
399	>	bool isTopologyDone() {
400	>	return topologyDone_;
401	>	}
402
403	<	//below functions are just forward functions
404	<	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
405	<	//the other hand, has-a relation need composing.
354	<	/**
355	<	* Adds property into property map
356	<	* @param genData GenericData to be added into PropertyMap
357	<	*/
358	<	void addProperty(GenericData* genData);
403	>	bool getCalcBoxDipole() {
404	>	return calcBoxDipole_;
405	>	}
406
407	<	/**
408	<	* Removes property from PropertyMap by name
409	<	* @param propName the name of property to be removed
363	<	*/
364	<	void removeProperty(const std::string& propName);
407	>	bool getUseAtomicVirial() {
408	>	return useAtomicVirial_;
409	>	}
410
411	<	/**
412	<	* clear all of the properties
413	<	*/
414	<	void clearProperties();
411	>	/**
412	>	* Adds property into property map
413	>	* @param genData GenericData to be added into PropertyMap
414	>	*/
415	>	void addProperty(GenericData* genData);
416
417	<	/**
418	<	* Returns all names of properties
419	<	* @return all names of properties
420	<	*/
421	<	std::vector<std::string> getPropertyNames();
417	>	/**
418	>	* Removes property from PropertyMap by name
419	>	* @param propName the name of property to be removed
420	>	*/
421	>	void removeProperty(const string& propName);
422
423	<	/**
424	<	* Returns all of the properties in PropertyMap
425	<	* @return all of the properties in PropertyMap
426	<	*/
381	<	std::vector<GenericData*> getProperties();
423	>	/**
424	>	* clear all of the properties
425	>	*/
426	>	void clearProperties();
427
428	<	/**
429	<	* Returns property
430	<	* @param propName name of property
431	<	* @return a pointer point to property with propName. If no property named propName
432	<	* exists, return NULL
388	<	*/
389	<	GenericData* getPropertyByName(const std::string& propName);
428	>	/**
429	>	* Returns all names of properties
430	>	* @return all names of properties
431	>	*/
432	>	vector<string> getPropertyNames();
433
434	<	/**
435	<	* add all exclude pairs of a molecule into exclude list.
436	<	*/
437	<	void addExcludePairs(Molecule* mol);
434	>	/**
435	>	* Returns all of the properties in PropertyMap
436	>	* @return all of the properties in PropertyMap
437	>	*/
438	>	vector<GenericData*> getProperties();
439
440	<	/**
441	<	* remove all exclude pairs which belong to a molecule from exclude list
442	<	*/
440	>	/**
441	>	* Returns property
442	>	* @param propName name of property
443	>	* @return a pointer point to property with propName. If no property named propName
444	>	* exists, return NULL
445	>	*/
446	>	GenericData* getPropertyByName(const string& propName);
447
448	<	void removeExcludePairs(Molecule* mol);
448	>	/**
449	>	* add all special interaction pairs (including excluded
450	>	* interactions) in a molecule into the appropriate lists.
451	>	*/
452	>	void addInteractionPairs(Molecule* mol);
453
454	+	/**
455	+	* remove all special interaction pairs which belong to a molecule
456	+	* from the appropriate lists.
457	+	*/
458	+	void removeInteractionPairs(Molecule* mol);
459
460	<	/** Returns the unique atom types of local processor in an array */
461	<	std::set<AtomType*> getUniqueAtomTypes();
460	>	/** Returns the set of atom types present in this simulation */
461	>	set<AtomType*> getSimulatedAtomTypes();
462
463	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
463	>	friend ostream& operator <<(ostream& o, SimInfo& info);
464
465	<	void getCutoff(double& rcut, double& rsw);
465	>	void getCutoff(RealType& rcut, RealType& rsw);
466
467	<	private:
467	>	private:
468
469	<	/** fill up the simtype struct*/
470	<	void setupSimType();
469	>	/** fill up the simtype struct and other simulation-related variables */
470	>	void setupSimVariables();
471
415	–	/**
416	–	* Setup Fortran Simulation
417	–	* @see #setupFortranParallel
418	–	*/
419	–	void setupFortranSim();
472
473	<	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
474	<	void setupCutoff();
473	>	/** Determine if we need to accumulate the simulation box dipole */
474	>	void setupAccumulateBoxDipole();
475
476	<	/** Calculates the number of degress of freedom in the whole system */
477	<	void calcNdf();
478	<	void calcNdfRaw();
479	<	void calcNdfTrans();
476	>	/** Calculates the number of degress of freedom in the whole system */
477	>	void calcNdf();
478	>	void calcNdfRaw();
479	>	void calcNdfTrans();
480
481	<	/**
482	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
483	<	* system.
484	<	*/
485	<	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
481	>	/**
482	>	* Adds molecule stamp and the total number of the molecule with
483	>	* same molecule stamp in the whole system.
484	>	*/
485	>	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
486
487	<	ForceField* forceField_;
488	<	Globals* simParams_;
487	>	// Other classes holdingn important information
488	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
489	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
490
491	<	std::map<int, Molecule*>  molecules_; /**< Molecule array */
491	>	///  Counts of local objects
492	>	int nAtoms_;              /**< number of atoms in local processor */
493	>	int nBonds_;              /**< number of bonds in local processor */
494	>	int nBends_;              /**< number of bends in local processor */
495	>	int nTorsions_;           /**< number of torsions in local processor */
496	>	int nInversions_;         /**< number of inversions in local processor */
497	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
498	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
499	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
500	>	int nConstraints_;        /**< number of constraints in local processors */
501	>	int nFluctuatingCharges_; /**< number of fluctuating charges in local processor */
502
503	<	//degress of freedom
504	<	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
505	<	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
506	<	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
507	<	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
508	<
509	<	//number of global objects
510	<	int nGlobalMols_;       /**< number of molecules in the system */
511	<	int nGlobalAtoms_;   /**< number of atoms in the system */
512	<	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
513	<	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
514	<	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
515	<	/**
516	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
517	<	* corresponding content is the global index of cutoff group this atom belong to.
518	<	* It is filled by SimCreator once and only once, since it never changed during the simulation.
519	<	*/
457	<	std::vector<int> globalGroupMembership_;
503	>	/// Counts of global objects
504	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
505	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
506	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
507	>	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
508	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
509	>	int nGlobalFluctuatingCharges_;/**< number of fluctuating charges in this system (GLOBAL) */
510	>
511	>
512	>	/// Degress of freedom
513	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
514	>	int ndfLocal_;     /**< number of degrees of freedom (LOCAL, excludes constraints) */
515	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
516	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
517	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
518	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
519	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
520
521	<	/**
522	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
523	<	* corresponding content is the global index of molecule this atom belong to.
524	<	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
525	<	*/
526	<	std::vector<int> globalMolMembership_;
521	>	/// logicals
522	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
523	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
524	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
525	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
526	>	bool usesFluctuatingCharges_; /**< are there fluctuating charges? */
527	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
528	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
529	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
530	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
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 */
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 */
532	>	public:
533	>	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
534	>	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
535	>	bool usesFluctuatingCharges() { return usesFluctuatingCharges_; }
536	>	bool usesAtomicVirial() { return usesAtomicVirial_; }
537	>	bool requiresPrepair() { return requiresPrepair_; }
538	>	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
539	>	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
540
541	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
542	<	Exclude exclude_;
543	<	PropertyMap properties_;                  /**< Generic Property */
483	<	SnapshotManager* sman_;               /**< SnapshotManager */
541	>	private:
542	>	/// Data structures holding primary simulation objects
543	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
544
545	<	/**
546	<	* The reason to have a local index manager is that when molecule is migrating to other processors,
547	<	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
548	<	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
549	<	* to make a efficient data moving plan.
550	<	*/
551	<	LocalIndexManager localIndexMan_;
545	>	/// Stamps are templates for objects that are then used to create
546	>	/// groups of objects.  For example, a molecule stamp contains
547	>	/// information on how to build that molecule (i.e. the topology,
548	>	/// the atoms, the bonds, etc.)  Once the system is built, the
549	>	/// stamps are no longer useful.
550	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
551	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
552
553	<	//file names
554	<	std::string finalConfigFileName_;
555	<	std::string dumpFileName_;
556	<	std::string statFileName_;
553	>	/**
554	>	* A vector that maps between the global index of an atom, and the
555	>	* global index of cutoff group the atom belong to.  It is filled
556	>	* by SimCreator once and only once, since it never changed during
557	>	* the simulation.  It should be nGlobalAtoms_ in size.
558	>	*/
559	>	vector<int> globalGroupMembership_;
560	>	public:
561	>	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
562	>	private:
563
564	<	double rcut_;       /**< cutoff radius*/
565	<	double rsw_;        /**< radius of switching function*/
564	>	/**
565	>	* A vector that maps between the global index of an atom and the
566	>	* global index of the molecule the atom belongs to.  It is filled
567	>	* by SimCreator once and only once, since it is never changed
568	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
569	>	*/
570	>	vector<int> globalMolMembership_;
571
572	<	bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
572	>	/**
573	>	* A vector that maps between the local index of an atom and the
574	>	* index of the AtomType.
575	>	*/
576	>	vector<int> identArray_;
577	>	public:
578	>	vector<int> getIdentArray() { return identArray_; }
579	>	private:
580	>
581	>	/**
582	>	* A vector which contains the fractional contribution of an
583	>	* atom's mass to the total mass of the cutoffGroup that atom
584	>	* belongs to.  In the case of single atom cutoff groups, the mass
585	>	* factor for that atom is 1.  For massless atoms, the factor is
586	>	* also 1.
587	>	*/
588	>	vector<RealType> massFactors_;
589	>	public:
590	>	vector<RealType> getMassFactors() { return massFactors_; }
591
592	<	#ifdef IS_MPI
593	<	//in Parallel version, we need MolToProc
594	<	public:
595	<
507	<	/**
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	<	}
592	>	PairList* getExcludedInteractions() { return &excludedInteractions_; }
593	>	PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
594	>	PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
595	>	PairList* getOneFourInteractions() { return &oneFourInteractions_; }
596
597	<	/**
598	<	* Set MolToProcMap array
599	<	* @see #SimCreator::divideMolecules
600	<	*/
601	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
602	<	molToProcMap_ = molToProcMap;
603	<	}
597	>	private:
598	>
599	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
600	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
601	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
602	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
603	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
604	>
605	>	PropertyMap properties_;       /**< Generic Properties can be added */
606	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
607	>
608	>	/**
609	>	* The reason to have a local index manager is that when molecule
610	>	* is migrating to other processors, the atoms and the
611	>	* rigid-bodies will release their local indices to
612	>	* LocalIndexManager. Combining the information of molecule
613	>	* migrating to current processor, Migrator class can query the
614	>	* LocalIndexManager to make a efficient data moving plan.
615	>	*/
616	>	LocalIndexManager localIndexMan_;
617	>
618	>	// unparsed MetaData block for storing in Dump and EOR files:
619	>	string rawMetaData_;
620	>
621	>	// file names
622	>	string finalConfigFileName_;
623	>	string dumpFileName_;
624	>	string statFileName_;
625	>	string restFileName_;
626
525	–	private:
627
628	<	void setupFortranParallel();
628	>	bool topologyDone_;  /** flag to indicate whether the topology has
629	>	been scanned and all the relevant
630	>	bookkeeping has been done*/
631	>
632	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
633	>	the simulation box dipole moment */
634	>
635	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
636	>	Atomic Virials to calculate the pressure */
637	>
638	>	public:
639	>	/**
640	>	* return an integral objects by its global index. In MPI
641	>	* version, if the StuntDouble with specified global index does
642	>	* not belong to local processor, a NULL will be return.
643	>	*/
644	>	StuntDouble* getIOIndexToIntegrableObject(int index);
645	>	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
646	>
647	>	private:
648	>	vector<StuntDouble*> IOIndexToIntegrableObject;
649	>
650	>	public:
651	>
652	>	/**
653	>	* Finds the processor where a molecule resides
654	>	* @return the id of the processor which contains the molecule
655	>	* @param globalIndex global Index of the molecule
656	>	*/
657	>	int getMolToProc(int globalIndex) {
658	>	//assert(globalIndex < molToProcMap_.size());
659	>	return molToProcMap_[globalIndex];
660	>	}
661	>
662	>	/**
663	>	* Set MolToProcMap array
664	>	*/
665	>	void setMolToProcMap(const vector<int>& molToProcMap) {
666	>	molToProcMap_ = molToProcMap;
667	>	}
668
669	<	/**
670	<	* The size of molToProcMap_ is equal to total number of molecules in the system.
671	<	*  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
672	<	* once.
673	<	*/
674	<	std::vector<int> molToProcMap_;
669	>	private:
670	>
671	>	/**
672	>	* The size of molToProcMap_ is equal to total number of molecules
673	>	* in the system.  It maps a molecule to the processor on which it
674	>	* resides. it is filled by SimCreator once and only once.
675	>	*/
676	>	vector<int> molToProcMap_;
677
678	<	#endif
678	>	};
679
680	<	};
539	<
540	<	} //namespace oopse
680	>	} //namespace OpenMD
681		#endif //BRAINS_SIMMODEL_HPP
682

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 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

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