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

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trunk/src/brains/SimInfo.hpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/SimInfo.hpp (file contents), Revision 1848 by gezelter, Mon Feb 4 21:13:46 2013 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;
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	<	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
113	<	* @brief As one of the heavy weight class of OOPSE, SimInfo
114	<	* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
115	<	* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
116	<	* cutoff groups, constrains).
117	<	* 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;
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	<	* Constructor of SimInfo
121	<	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
122	<	* second element is the total number of molecules with the same molecule stamp in the system
93	<	* @param ff pointer of a concrete ForceField instance
94	<	* @param simParams
95	<	* @note
96	<	*/
97	<	SimInfo(std::vector<std::pair<MoleculeStamp*, int> >& molStampPairs, ForceField* ff, Globals* simParams);
98	<	virtual ~SimInfo();
119	>	/** Returns the total number of molecules in the system. */
120	>	int getNGlobalMolecules() {
121	>	return nGlobalMols_;
122	>	}
123
124	<	/**
125	<	* Adds a molecule
126	<	* @return return true if adding successfully, return false if the molecule is already in SimInfo
127	<	* @param mol molecule to be added
104	<	*/
105	<	bool addMolecule(Molecule* mol);
124	>	/** Returns the total number of atoms in the system. */
125	>	int getNGlobalAtoms() {
126	>	return nGlobalAtoms_;
127	>	}
128
129	<	/**
130	<	* Removes a molecule from SimInfo
131	<	* @return true if removing successfully, return false if molecule is not in this SimInfo
132	<	*/
111	<	bool removeMolecule(Molecule* mol);
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 molecules in the system. */
135	<	int getNGlobalMolecules() {
136	<	return nGlobalMols_;
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 atoms in the system. */
144	<	int getNGlobalAtoms() {
145	<	return nGlobalAtoms_;
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	<	/** Returns the total number of cutoff groups in the system. */
153	<	int getNGlobalCutoffGroups() {
154	<	return nGlobalCutoffGroups_;
155	<	}
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	<	*/
132	<	int getNGlobalIntegrableObjects() {
133	<	return nGlobalIntegrableObjects_;
134	<	}
161	>	/** Returns the number of local atoms */
162	>	unsigned int getNAtoms() {
163	>	return nAtoms_;
164	>	}
165
166	<	/**
167	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
138	<	* of atoms which do not belong to the rigid bodies) in the system
139	<	*/
140	<	int getNGlobalRigidBodies() {
141	<	return nGlobalRigidBodies_;
142	<	}
166	>	/** Returns the number of effective cutoff groups on local processor */
167	>	unsigned int getNLocalCutoffGroups();
168
169	<	int getNGlobalConstraints();
170	<	/**
171	<	* Returns the number of local molecules.
172	<	* @return the number of local molecules
148	<	*/
149	<	int getNMolecules() {
150	<	return molecules_.size();
151	<	}
169	>	/** Returns the number of local bonds */
170	>	unsigned int getNBonds(){
171	>	return nBonds_;
172	>	}
173
174	<	/** Returns the number of local atoms */
175	<	unsigned int getNAtoms() {
176	<	return nAtoms_;
177	<	}
174	>	/** Returns the number of local bends */
175	>	unsigned int getNBends() {
176	>	return nBends_;
177	>	}
178
179	<	/** Returns the number of local bonds */
180	<	unsigned int getNBonds(){
181	<	return nBonds_;
182	<	}
179	>	/** Returns the number of local torsions */
180	>	unsigned int getNTorsions() {
181	>	return nTorsions_;
182	>	}
183
184	<	/** Returns the number of local bends */
185	<	unsigned int getNBends() {
186	<	return nBends_;
187	<	}
184	>	/** Returns the number of local torsions */
185	>	unsigned int getNInversions() {
186	>	return nInversions_;
187	>	}
188	>	/** Returns the number of local rigid bodies */
189	>	unsigned int getNRigidBodies() {
190	>	return nRigidBodies_;
191	>	}
192
193	<	/** Returns the number of local torsions */
194	<	unsigned int getNTorsions() {
195	<	return nTorsions_;
196	<	}
193	>	/** Returns the number of local integrable objects */
194	>	unsigned int getNIntegrableObjects() {
195	>	return nIntegrableObjects_;
196	>	}
197
198	<	/** Returns the number of local rigid bodies */
199	<	unsigned int getNRigidBodies() {
200	<	return nRigidBodies_;
201	<	}
198	>	/** Returns the number of local cutoff groups */
199	>	unsigned int getNCutoffGroups() {
200	>	return nCutoffGroups_;
201	>	}
202
203	<	/** Returns the number of local integrable objects */
204	<	unsigned int getNIntegrableObjects() {
205	<	return nIntegrableObjects_;
206	<	}
182	<
183	<	/** Returns the number of local cutoff groups */
184	<	unsigned int getNCutoffGroups() {
185	<	return nCutoffGroups_;
186	<	}
187	<
188	<	/** Returns the total number of constraints in this SimInfo */
189	<	unsigned int getNConstraints() {
190	<	return nConstraints_;
191	<	}
203	>	/** Returns the total number of constraints in this SimInfo */
204	>	unsigned int getNConstraints() {
205	>	return nConstraints_;
206	>	}
207
208	<	/**
209	<	* Returns the first molecule in this SimInfo and intialize the iterator.
210	<	* @return the first molecule, return NULL if there is not molecule in this SimInfo
211	<	* @param i the iterator of molecule array (user shouldn't change it)
212	<	*/
213	<	Molecule* beginMolecule(MoleculeIterator& i);
208	>	/**
209	>	* Returns the first molecule in this SimInfo and intialize the iterator.
210	>	* @return the first molecule, return NULL if there is not molecule in this SimInfo
211	>	* @param i the iterator of molecule array (user shouldn't change it)
212	>	*/
213	>	Molecule* beginMolecule(MoleculeIterator& i);
214
215	<	/**
216	<	* Returns the next avaliable Molecule based on the iterator.
217	<	* @return the next avaliable molecule, return NULL if reaching the end of the array
218	<	* @param i the iterator of molecule array
219	<	*/
220	<	Molecule* nextMolecule(MoleculeIterator& i);
206	<
207	<	/** Returns the number of degrees of freedom */
208	<	int getNdf() {
209	<	return ndf_;
210	<	}
215	>	/**
216	>	* Returns the next avaliable Molecule based on the iterator.
217	>	* @return the next avaliable molecule, return NULL if reaching the end of the array
218	>	* @param i the iterator of molecule array
219	>	*/
220	>	Molecule* nextMolecule(MoleculeIterator& i);
221
222	<	/** Returns the number of raw degrees of freedom */
223	<	int getNdfRaw() {
224	<	return ndfRaw_;
225	<	}
222	>	/** Returns the total number of fluctuating charges that are present */
223	>	int getNFluctuatingCharges() {
224	>	return nGlobalFluctuatingCharges_;
225	>	}
226
227	<	/** Returns the number of translational degrees of freedom */
228	<	int getNdfTrans() {
229	<	return ndfTrans_;
230	<	}
227	>	/** Returns the number of degrees of freedom */
228	>	int getNdf() {
229	>	return ndf_ - getFdf();
230	>	}
231
232	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
233	<
234	<	/** Returns the total number of z-constraint molecules in the system */
235	<	int getNZconstraint() {
226	<	return nZconstraint_;
227	<	}
232	>	/** Returns the number of degrees of freedom (LOCAL) */
233	>	int getNdfLocal() {
234	>	return ndfLocal_;
235	>	}
236
237	<	/**
238	<	* Sets the number of z-constraint molecules in the system.
239	<	*/
240	<	void setNZconstraint(int nZconstraint) {
241	<	nZconstraint_ = nZconstraint;
242	<	}
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 snapshot manager. */
258	<	SnapshotManager* getSnapshotManager() {
259	<	return sman_;
260	<	}
257	>	/** Returns the total number of z-constraint molecules in the system */
258	>	int getNZconstraint() {
259	>	return nZconstraint_;
260	>	}
261
262	<	/** Sets the snapshot manager. */
263	<	void setSnapshotManager(SnapshotManager* sman);
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 force field */
270	<	ForceField* getForceField() {
271	<	return forceField_;
272	<	}
269	>	/** Returns the snapshot manager. */
270	>	SnapshotManager* getSnapshotManager() {
271	>	return sman_;
272	>	}
273	>	/** Returns the storage layout (computed by SimCreator) */
274	>	int getStorageLayout() {
275	>	return storageLayout_;
276	>	}
277	>	/** Sets the storage layout (computed by SimCreator) */
278	>	void setStorageLayout(int sl) {
279	>	storageLayout_ = sl;
280	>	}
281	>
282	>	/** Sets the snapshot manager. */
283	>	void setSnapshotManager(SnapshotManager* sman);
284	>
285	>	/** Returns the force field */
286	>	ForceField* getForceField() {
287	>	return forceField_;
288	>	}
289
290	<	Globals* getSimParams() {
291	<	return simParams_;
292	<	}
290	>	Globals* getSimParams() {
291	>	return simParams_;
292	>	}
293
294	<	/** Returns the velocity of center of mass of the whole system.*/
295	<	Vector3d getComVel();
294	>	void update();
295	>	/**
296	>	* Do final bookkeeping before Force managers need their data.
297	>	*/
298	>	void prepareTopology();
299
256	–	/** Returns the center of the mass of the whole system.*/
257	–	Vector3d getCom();
300
301	<	/** Returns the seed (used for random number generator) */
302	<	int getSeed() {
303	<	return seed_;
304	<	}
301	>	/** Returns the local index manager */
302	>	LocalIndexManager* getLocalIndexManager() {
303	>	return &localIndexMan_;
304	>	}
305
306	<	/** Sets the seed*/
307	<	void setSeed(int seed) {
308	<	seed_ = seed;
309	<	}
306	>	int getMoleculeStampId(int globalIndex) {
307	>	//assert(globalIndex < molStampIds_.size())
308	>	return molStampIds_[globalIndex];
309	>	}
310
311	<	/** main driver function to interact with fortran during the initialization and molecule migration */
312	<	void update();
311	>	/** Returns the molecule stamp */
312	>	MoleculeStamp* getMoleculeStamp(int id) {
313	>	return moleculeStamps_[id];
314	>	}
315
316	<	/** Returns the local index manager */
317	<	LocalIndexManager* getLocalIndexManager() {
318	<	return &localIndexMan_;
319	<	}
316	>	/** Return the total number of the molecule stamps */
317	>	int getNMoleculeStamp() {
318	>	return moleculeStamps_.size();
319	>	}
320	>	/**
321	>	* Finds a molecule with a specified global index
322	>	* @return a pointer point to found molecule
323	>	* @param index
324	>	*/
325	>	Molecule* getMoleculeByGlobalIndex(int index) {
326	>	MoleculeIterator i;
327	>	i = molecules_.find(index);
328
329	<	int getMoleculeStampId(int globalIndex) {
330	<	//assert(globalIndex < molStampIds_.size())
279	<	return molStampIds_[globalIndex];
280	<	}
329	>	return i != molecules_.end() ? i->second : NULL;
330	>	}
331
332	<	/** Returns the molecule stamp */
333	<	MoleculeStamp* getMoleculeStamp(int id) {
334	<	return moleculeStamps_[id];
285	<	}
332	>	int getGlobalMolMembership(int id){
333	>	return globalMolMembership_[id];
334	>	}
335
336	<	/** Return the total number of the molecule stamps */
337	<	int getNMoleculeStamp() {
338	<	return moleculeStamps_.size();
339	<	}
340	<	/**
341	<	* Finds a molecule with a specified global index
293	<	* @return a pointer point to found molecule
294	<	* @param index
295	<	*/
296	<	Molecule* getMoleculeByGlobalIndex(int index) {
297	<	MoleculeIterator i;
298	<	i = molecules_.find(index);
336	>	/**
337	>	* returns a vector which maps the local atom index on this
338	>	* processor to the global atom index.  With only one processor,
339	>	* these should be identical.
340	>	*/
341	>	vector<int> getGlobalAtomIndices();
342
343	<	return i != molecules_.end() ? i->second : NULL;
344	<	}
343	>	/**
344	>	* returns a vector which maps the local cutoff group index on
345	>	* this processor to the global cutoff group index.  With only one
346	>	* processor, these should be identical.
347	>	*/
348	>	vector<int> getGlobalGroupIndices();
349
350	<	/** Calculate the maximum cutoff radius based on the atom types */
351	<	double calcMaxCutoffRadius();
350	>
351	>	string getFinalConfigFileName() {
352	>	return finalConfigFileName_;
353	>	}
354
355	<	double getRcut() {
356	<	return rcut_;
357	<	}
355	>	void setFinalConfigFileName(const string& fileName) {
356	>	finalConfigFileName_ = fileName;
357	>	}
358
359	<	double getRsw() {
360	<	return rsw_;
361	<	}
359	>	string getRawMetaData() {
360	>	return rawMetaData_;
361	>	}
362	>	void setRawMetaData(const string& rawMetaData) {
363	>	rawMetaData_ = rawMetaData;
364	>	}
365
366	<	std::string getFinalConfigFileName() {
367	<	return finalConfigFileName_;
368	<	}
366	>	string getDumpFileName() {
367	>	return dumpFileName_;
368	>	}
369
370	<	void setFinalConfigFileName(const std::string& fileName) {
371	<	finalConfigFileName_ = fileName;
372	<	}
370	>	void setDumpFileName(const string& fileName) {
371	>	dumpFileName_ = fileName;
372	>	}
373
374	<	std::string getDumpFileName() {
375	<	return dumpFileName_;
376	<	}
374	>	string getStatFileName() {
375	>	return statFileName_;
376	>	}
377
378	<	void setDumpFileName(const std::string& fileName) {
379	<	dumpFileName_ = fileName;
380	<	}
381	<
382	<	std::string getStatFileName() {
383	<	return statFileName_;
384	<	}
385	<
386	<	void setStatFileName(const std::string& fileName) {
387	<	statFileName_ = fileName;
388	<	}
378	>	void setStatFileName(const string& fileName) {
379	>	statFileName_ = fileName;
380	>	}
381	>
382	>	string getRestFileName() {
383	>	return restFileName_;
384	>	}
385	>
386	>	void setRestFileName(const string& fileName) {
387	>	restFileName_ = fileName;
388	>	}
389
390	<	/**
391	<	* Sets GlobalGroupMembership
392	<	* @see #SimCreator::setGlobalIndex
393	<	*/
394	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
395	<	assert(globalGroupMembership.size() == nGlobalAtoms_);
396	<	globalGroupMembership_ = globalGroupMembership;
345	<	}
390	>	/**
391	>	* Sets GlobalGroupMembership
392	>	*/
393	>	void setGlobalGroupMembership(const vector<int>& ggm) {
394	>	assert(ggm.size() == static_cast<size_t>(nGlobalAtoms_));
395	>	globalGroupMembership_ = ggm;
396	>	}
397
398	<	/**
399	<	* Sets GlobalMolMembership
400	<	* @see #SimCreator::setGlobalIndex
401	<	*/
402	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
403	<	assert(globalMolMembership.size() == nGlobalAtoms_);
404	<	globalMolMembership_ = globalMolMembership;
405	<	}
398	>	/**
399	>	* Sets GlobalMolMembership
400	>	*/
401	>	void setGlobalMolMembership(const vector<int>& gmm) {
402	>	assert(gmm.size() == (static_cast<size_t>(nGlobalAtoms_ +
403	>	nGlobalRigidBodies_)));
404	>	globalMolMembership_ = gmm;
405	>	}
406
407
408	<	bool isFortranInitialized() {
409	<	return fortranInitialized_;
410	<	}
408	>	bool isTopologyDone() {
409	>	return topologyDone_;
410	>	}
411
412	<	//below functions are just forward functions
413	<	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
414	<	//the other hand, has-a relation need composing.
364	<	/**
365	<	* Adds property into property map
366	<	* @param genData GenericData to be added into PropertyMap
367	<	*/
368	<	void addProperty(GenericData* genData);
412	>	bool getCalcBoxDipole() {
413	>	return calcBoxDipole_;
414	>	}
415
416	<	/**
417	<	* Removes property from PropertyMap by name
418	<	* @param propName the name of property to be removed
373	<	*/
374	<	void removeProperty(const std::string& propName);
416	>	bool getUseAtomicVirial() {
417	>	return useAtomicVirial_;
418	>	}
419
420	<	/**
421	<	* clear all of the properties
422	<	*/
423	<	void clearProperties();
420	>	/**
421	>	* Adds property into property map
422	>	* @param genData GenericData to be added into PropertyMap
423	>	*/
424	>	void addProperty(GenericData* genData);
425
426	<	/**
427	<	* Returns all names of properties
428	<	* @return all names of properties
429	<	*/
430	<	std::vector<std::string> getPropertyNames();
426	>	/**
427	>	* Removes property from PropertyMap by name
428	>	* @param propName the name of property to be removed
429	>	*/
430	>	void removeProperty(const string& propName);
431
432	<	/**
433	<	* Returns all of the properties in PropertyMap
434	<	* @return all of the properties in PropertyMap
435	<	*/
391	<	std::vector<GenericData*> getProperties();
432	>	/**
433	>	* clear all of the properties
434	>	*/
435	>	void clearProperties();
436
437	<	/**
438	<	* Returns property
439	<	* @param propName name of property
440	<	* @return a pointer point to property with propName. If no property named propName
441	<	* exists, return NULL
398	<	*/
399	<	GenericData* getPropertyByName(const std::string& propName);
437	>	/**
438	>	* Returns all names of properties
439	>	* @return all names of properties
440	>	*/
441	>	vector<string> getPropertyNames();
442
443	<	/**
444	<	* add all exclude pairs of a molecule into exclude list.
445	<	*/
446	<	void addExcludePairs(Molecule* mol);
443	>	/**
444	>	* Returns all of the properties in PropertyMap
445	>	* @return all of the properties in PropertyMap
446	>	*/
447	>	vector<GenericData*> getProperties();
448
449	<	/**
450	<	* remove all exclude pairs which belong to a molecule from exclude list
451	<	*/
449	>	/**
450	>	* Returns property
451	>	* @param propName name of property
452	>	* @return a pointer point to property with propName. If no property named propName
453	>	* exists, return NULL
454	>	*/
455	>	GenericData* getPropertyByName(const string& propName);
456
457	<	void removeExcludePairs(Molecule* mol);
458	<
459	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
457	>	/**
458	>	* add all special interaction pairs (including excluded
459	>	* interactions) in a molecule into the appropriate lists.
460	>	*/
461	>	void addInteractionPairs(Molecule* mol);
462	>
463	>	/**
464	>	* remove all special interaction pairs which belong to a molecule
465	>	* from the appropriate lists.
466	>	*/
467	>	void removeInteractionPairs(Molecule* mol);
468	>
469	>	/** Returns the set of atom types present in this simulation */
470	>	set<AtomType*> getSimulatedAtomTypes();
471
472	<	private:
472	>	friend ostream& operator <<(ostream& o, SimInfo& info);
473
474	+	void getCutoff(RealType& rcut, RealType& rsw);
475
476	<	/** Returns the unique atom types of local processor in an array */
418	<	std::set<AtomType*> getUniqueAtomTypes();
476	>	private:
477
478	<	/** fill up the simtype struct*/
479	<	void setupSimType();
478	>	/** fill up the simtype struct and other simulation-related variables */
479	>	void setupSimVariables();
480
423	–	/**
424	–	* Setup Fortran Simulation
425	–	* @see #setupFortranParallel
426	–	*/
427	–	void setupFortranSim();
481
482	<	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
483	<	void setupCutoff();
482	>	/** Determine if we need to accumulate the simulation box dipole */
483	>	void setupAccumulateBoxDipole();
484
485	<	/** Calculates the number of degress of freedom in the whole system */
486	<	void calcNdf();
487	<	void calcNdfRaw();
488	<	void calcNdfTrans();
485	>	/** Calculates the number of degress of freedom in the whole system */
486	>	void calcNdf();
487	>	void calcNdfRaw();
488	>	void calcNdfTrans();
489
490	<	/**
491	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
492	<	* system.
493	<	*/
494	<	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
490	>	/**
491	>	* Adds molecule stamp and the total number of the molecule with
492	>	* same molecule stamp in the whole system.
493	>	*/
494	>	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
495
496	<	ForceField* forceField_;
497	<	Globals* simParams_;
496	>	// Other classes holdingn important information
497	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
498	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
499
500	<	std::map<int, Molecule*>  molecules_; /**< Molecule array */
500	>	///  Counts of local objects
501	>	int nAtoms_;              /**< number of atoms in local processor */
502	>	int nBonds_;              /**< number of bonds in local processor */
503	>	int nBends_;              /**< number of bends in local processor */
504	>	int nTorsions_;           /**< number of torsions in local processor */
505	>	int nInversions_;         /**< number of inversions in local processor */
506	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
507	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
508	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
509	>	int nConstraints_;        /**< number of constraints in local processors */
510	>	int nFluctuatingCharges_; /**< number of fluctuating charges in local processor */
511
512	<	//degress of freedom
513	<	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
514	<	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
515	<	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
516	<	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
517	<
518	<	//number of global objects
519	<	int nGlobalMols_;       /**< number of molecules in the system */
520	<	int nGlobalAtoms_;   /**< number of atoms in the system */
521	<	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
522	<	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
523	<	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
524	<	/**
525	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
526	<	* corresponding content is the global index of cutoff group this atom belong to.
527	<	* It is filled by SimCreator once and only once, since it never changed during the simulation.
528	<	*/
465	<	std::vector<int> globalGroupMembership_;
466	<
467	<	/**
468	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
469	<	* corresponding content is the global index of molecule this atom belong to.
470	<	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
471	<	*/
472	<	std::vector<int> globalMolMembership_;
512	>	/// Counts of global objects
513	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
514	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
515	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
516	>	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
517	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
518	>	int nGlobalFluctuatingCharges_;/**< number of fluctuating charges in this system (GLOBAL) */
519	>
520	>
521	>	/// Degress of freedom
522	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
523	>	int ndfLocal_;     /**< number of degrees of freedom (LOCAL, excludes constraints) */
524	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
525	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
526	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
527	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
528	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
529
530	<
531	<	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
532	<	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
533	<
534	<	//number of local objects
535	<	int nAtoms_;                        /**< number of atoms in local processor */
536	<	int nBonds_;                        /**< number of bonds in local processor */
537	<	int nBends_;                        /**< number of bends in local processor */
538	<	int nTorsions_;                    /**< number of torsions in local processor */
539	<	int nRigidBodies_;              /**< number of rigid bodies in local processor */
484	<	int nIntegrableObjects_;    /**< number of integrable objects in local processor */
485	<	int nCutoffGroups_;             /**< number of cutoff groups in local processor */
486	<	int nConstraints_;              /**< number of constraints in local processors */
530	>	/// logicals
531	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
532	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
533	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
534	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
535	>	bool usesFluctuatingCharges_; /**< are there fluctuating charges? */
536	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
537	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
538	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
539	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
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 */
544	<	SnapshotManager* sman_;               /**< SnapshotManager */
541	>	public:
542	>	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
543	>	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
544	>	bool usesFluctuatingCharges() { return usesFluctuatingCharges_; }
545	>	bool usesAtomicVirial() { return usesAtomicVirial_; }
546	>	bool requiresPrepair() { return requiresPrepair_; }
547	>	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
548	>	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
549
550	<	int seed_; /**< seed for random number generator */
550	>	private:
551	>	/// Data structures holding primary simulation objects
552	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
553
554	<	/**
555	<	* The reason to have a local index manager is that when molecule is migrating to other processors,
556	<	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
557	<	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
558	<	* to make a efficient data moving plan.
559	<	*/
560	<	LocalIndexManager localIndexMan_;
554	>	/// Stamps are templates for objects that are then used to create
555	>	/// groups of objects.  For example, a molecule stamp contains
556	>	/// information on how to build that molecule (i.e. the topology,
557	>	/// the atoms, the bonds, etc.)  Once the system is built, the
558	>	/// stamps are no longer useful.
559	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
560	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
561
562	<	//file names
563	<	std::string finalConfigFileName_;
564	<	std::string dumpFileName_;
565	<	std::string statFileName_;
562	>	/**
563	>	* A vector that maps between the global index of an atom, and the
564	>	* global index of cutoff group the atom belong to.  It is filled
565	>	* by SimCreator once and only once, since it never changed during
566	>	* the simulation.  It should be nGlobalAtoms_ in size.
567	>	*/
568	>	vector<int> globalGroupMembership_;
569	>	public:
570	>	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
571	>	private:
572
573	<	double rcut_;       /**< cutoff radius*/
574	<	double rsw_;        /**< radius of switching function*/
573	>	/**
574	>	* A vector that maps between the global index of an atom and the
575	>	* global index of the molecule the atom belongs to.  It is filled
576	>	* by SimCreator once and only once, since it is never changed
577	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
578	>	*/
579	>	vector<int> globalMolMembership_;
580
581	<	bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
582	<
583	<	#ifdef IS_MPI
584	<	//in Parallel version, we need MolToProc
585	<	public:
586	<
587	<	/**
588	<	* Finds the processor where a molecule resides
589	<	* @return the id of the processor which contains the molecule
590	<	* @param globalIndex global Index of the molecule
591	<	*/
592	<	int getMolToProc(int globalIndex) {
593	<	//assert(globalIndex < molToProcMap_.size());
594	<	return molToProcMap_[globalIndex];
595	<	}
581	>	/**
582	>	* A vector that maps between the local index of an atom and the
583	>	* index of the AtomType.
584	>	*/
585	>	vector<int> identArray_;
586	>	public:
587	>	vector<int> getIdentArray() { return identArray_; }
588	>	private:
589	>
590	>	/**
591	>	* A vector which contains the fractional contribution of an
592	>	* atom's mass to the total mass of the cutoffGroup that atom
593	>	* belongs to.  In the case of single atom cutoff groups, the mass
594	>	* factor for that atom is 1.  For massless atoms, the factor is
595	>	* also 1.
596	>	*/
597	>	vector<RealType> massFactors_;
598	>	public:
599	>	vector<RealType> getMassFactors() { return massFactors_; }
600
601	<	/**
602	<	* Set MolToProcMap array
603	<	* @see #SimCreator::divideMolecules
604	<	*/
531	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
532	<	molToProcMap_ = molToProcMap;
533	<	}
534	<
535	<	private:
601	>	PairList* getExcludedInteractions() { return &excludedInteractions_; }
602	>	PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
603	>	PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
604	>	PairList* getOneFourInteractions() { return &oneFourInteractions_; }
605
606	<	void setupFortranParallel();
606	>	private:
607	>
608	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
609	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
610	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
611	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
612	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
613	>
614	>	PropertyMap properties_;       /**< Generic Properties can be added */
615	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
616	>	int storageLayout_;            /**< Bits to tell how much data to store on each object */
617	>
618	>	/**
619	>	* The reason to have a local index manager is that when molecule
620	>	* is migrating to other processors, the atoms and the
621	>	* rigid-bodies will release their local indices to
622	>	* LocalIndexManager. Combining the information of molecule
623	>	* migrating to current processor, Migrator class can query the
624	>	* LocalIndexManager to make a efficient data moving plan.
625	>	*/
626	>	LocalIndexManager localIndexMan_;
627	>
628	>	// unparsed MetaData block for storing in Dump and EOR files:
629	>	string rawMetaData_;
630	>
631	>	// file names
632	>	string finalConfigFileName_;
633	>	string dumpFileName_;
634	>	string statFileName_;
635	>	string restFileName_;
636	>
637	>	bool topologyDone_;  /** flag to indicate whether the topology has
638	>	been scanned and all the relevant
639	>	bookkeeping has been done*/
640	>
641	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
642	>	the simulation box dipole moment */
643	>
644	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
645	>	Atomic Virials to calculate the pressure */
646	>
647	>	public:
648	>	/**
649	>	* return an integral objects by its global index. In MPI
650	>	* version, if the StuntDouble with specified global index does
651	>	* not belong to local processor, a NULL will be return.
652	>	*/
653	>	StuntDouble* getIOIndexToIntegrableObject(int index);
654	>	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
655	>
656	>	private:
657	>	vector<StuntDouble*> IOIndexToIntegrableObject;
658	>
659	>	public:
660	>
661	>	/**
662	>	* Finds the processor where a molecule resides
663	>	* @return the id of the processor which contains the molecule
664	>	* @param globalIndex global Index of the molecule
665	>	*/
666	>	int getMolToProc(int globalIndex) {
667	>	//assert(globalIndex < molToProcMap_.size());
668	>	return molToProcMap_[globalIndex];
669	>	}
670	>
671	>	/**
672	>	* Set MolToProcMap array
673	>	*/
674	>	void setMolToProcMap(const vector<int>& molToProcMap) {
675	>	molToProcMap_ = molToProcMap;
676	>	}
677
678	<	/**
679	<	* The size of molToProcMap_ is equal to total number of molecules in the system.
680	<	*  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
681	<	* once.
682	<	*/
683	<	std::vector<int> molToProcMap_;
684	<	#endif
678	>	private:
679	>
680	>	/**
681	>	* The size of molToProcMap_ is equal to total number of molecules
682	>	* in the system.  It maps a molecule to the processor on which it
683	>	* resides. it is filled by SimCreator once and only once.
684	>	*/
685	>	vector<int> molToProcMap_;
686
687	<	};
687	>	};
688
689	<	} //namespace oopse
689	>	} //namespace OpenMD
690		#endif //BRAINS_SIMMODEL_HPP
691

Comparing:
trunk/src/brains/SimInfo.hpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/SimInfo.hpp (property svn:keywords), Revision 1848 by gezelter, Mon Feb 4 21:13:46 2013 UTC

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