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root/OpenMD/trunk/src/brains/SimInfo.hpp

Comparing trunk/src/brains/SimInfo.hpp (file contents):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 1953 by gezelter, Thu Dec 5 18:19:26 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, 234107 (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	<	*/
132	<	int getNGlobalIntegrableObjects() {
133	<	return nGlobalIntegrableObjects_;
134	<	}
152	>	/** Returns the number of global bonds */
153	>	unsigned int getNGlobalBonds(){
154	>	return nGlobalBonds_;
155	>	}
156
157	<	/**
158	<	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
159	<	* of atoms which do not belong to the rigid bodies) in the system
160	<	*/
140	<	int getNGlobalRigidBodies() {
141	<	return nGlobalRigidBodies_;
142	<	}
157	>	/** Returns the number of global bends */
158	>	unsigned int getNGlobalBends() {
159	>	return nGlobalBends_;
160	>	}
161
162	<	int getNGlobalConstraints();
163	<	/**
164	<	* Returns the number of local molecules.
165	<	* @return the number of local molecules
148	<	*/
149	<	int getNMolecules() {
150	<	return molecules_.size();
151	<	}
162	>	/** Returns the number of global torsions */
163	>	unsigned int getNGlobalTorsions() {
164	>	return nGlobalTorsions_;
165	>	}
166
167	<	/** Returns the number of local atoms */
168	<	unsigned int getNAtoms() {
169	<	return nAtoms_;
170	<	}
167	>	/** Returns the number of global inversions */
168	>	unsigned int getNGlobalInversions() {
169	>	return nGlobalInversions_;
170	>	}
171
172	<	/** Returns the number of local bonds */
173	<	unsigned int getNBonds(){
174	<	return nBonds_;
175	<	}
172	>	int getNGlobalConstraints();
173	>	/**
174	>	* Returns the number of local molecules.
175	>	* @return the number of local molecules
176	>	*/
177	>	int getNMolecules() {
178	>	return molecules_.size();
179	>	}
180
181	<	/** Returns the number of local bends */
182	<	unsigned int getNBends() {
183	<	return nBends_;
184	<	}
181	>	/** Returns the number of local atoms */
182	>	unsigned int getNAtoms() {
183	>	return nAtoms_;
184	>	}
185
186	<	/** Returns the number of local torsions */
187	<	unsigned int getNTorsions() {
170	<	return nTorsions_;
171	<	}
186	>	/** Returns the number of effective cutoff groups on local processor */
187	>	unsigned int getNLocalCutoffGroups();
188
189	<	/** Returns the number of local rigid bodies */
190	<	unsigned int getNRigidBodies() {
191	<	return nRigidBodies_;
192	<	}
189	>	/** Returns the number of local bonds */
190	>	unsigned int getNBonds(){
191	>	return nBonds_;
192	>	}
193
194	<	/** Returns the number of local integrable objects */
195	<	unsigned int getNIntegrableObjects() {
196	<	return nIntegrableObjects_;
197	<	}
194	>	/** Returns the number of local bends */
195	>	unsigned int getNBends() {
196	>	return nBends_;
197	>	}
198
199	<	/** Returns the number of local cutoff groups */
200	<	unsigned int getNCutoffGroups() {
201	<	return nCutoffGroups_;
202	<	}
199	>	/** Returns the number of local torsions */
200	>	unsigned int getNTorsions() {
201	>	return nTorsions_;
202	>	}
203
204	<	/** Returns the total number of constraints in this SimInfo */
205	<	unsigned int getNConstraints() {
206	<	return nConstraints_;
207	<	}
208	<
209	<	/**
210	<	* Returns the first molecule in this SimInfo and intialize the iterator.
211	<	* @return the first molecule, return NULL if there is not molecule in this SimInfo
196	<	* @param i the iterator of molecule array (user shouldn't change it)
197	<	*/
198	<	Molecule* beginMolecule(MoleculeIterator& i);
204	>	/** Returns the number of local inversions */
205	>	unsigned int getNInversions() {
206	>	return nInversions_;
207	>	}
208	>	/** Returns the number of local rigid bodies */
209	>	unsigned int getNRigidBodies() {
210	>	return nRigidBodies_;
211	>	}
212
213	<	/**
214	<	* Returns the next avaliable Molecule based on the iterator.
215	<	* @return the next avaliable molecule, return NULL if reaching the end of the array
216	<	* @param i the iterator of molecule array
204	<	*/
205	<	Molecule* nextMolecule(MoleculeIterator& i);
213	>	/** Returns the number of local integrable objects */
214	>	unsigned int getNIntegrableObjects() {
215	>	return nIntegrableObjects_;
216	>	}
217
218	<	/** Returns the number of degrees of freedom */
219	<	int getNdf() {
220	<	return ndf_;
221	<	}
211	<
212	<	/** Returns the number of raw degrees of freedom */
213	<	int getNdfRaw() {
214	<	return ndfRaw_;
215	<	}
218	>	/** Returns the number of local cutoff groups */
219	>	unsigned int getNCutoffGroups() {
220	>	return nCutoffGroups_;
221	>	}
222
223	<	/** Returns the number of translational degrees of freedom */
224	<	int getNdfTrans() {
225	<	return ndfTrans_;
226	<	}
221	<
222	<	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
223	>	/** Returns the total number of constraints in this SimInfo */
224	>	unsigned int getNConstraints() {
225	>	return nConstraints_;
226	>	}
227
228	<	/** Returns the total number of z-constraint molecules in the system */
229	<	int getNZconstraint() {
230	<	return nZconstraint_;
231	<	}
228	>	/**
229	>	* Returns the first molecule in this SimInfo and intialize the iterator.
230	>	* @return the first molecule, return NULL if there is not molecule in this SimInfo
231	>	* @param i the iterator of molecule array (user shouldn't change it)
232	>	*/
233	>	Molecule* beginMolecule(MoleculeIterator& i);
234
235	<	/**
236	<	* Sets the number of z-constraint molecules in the system.
237	<	*/
238	<	void setNZconstraint(int nZconstraint) {
239	<	nZconstraint_ = nZconstraint;
240	<	}
235	>	/**
236	>	* Returns the next avaliable Molecule based on the iterator.
237	>	* @return the next avaliable molecule, return NULL if reaching the end of the array
238	>	* @param i the iterator of molecule array
239	>	*/
240	>	Molecule* nextMolecule(MoleculeIterator& i);
241	>
242	>	/** Returns the total number of fluctuating charges that are present */
243	>	int getNFluctuatingCharges() {
244	>	return nGlobalFluctuatingCharges_;
245	>	}
246	>
247	>	/** Returns the number of degrees of freedom */
248	>	int getNdf() {
249	>	return ndf_ - getFdf();
250	>	}
251	>
252	>	/** Returns the number of degrees of freedom (LOCAL) */
253	>	int getNdfLocal() {
254	>	return ndfLocal_;
255	>	}
256	>
257	>	/** Returns the number of raw degrees of freedom */
258	>	int getNdfRaw() {
259	>	return ndfRaw_;
260	>	}
261	>
262	>	/** Returns the number of translational degrees of freedom */
263	>	int getNdfTrans() {
264	>	return ndfTrans_;
265	>	}
266	>
267	>	/** sets the current number of frozen degrees of freedom */
268	>	void setFdf(int fdf) {
269	>	fdf_local = fdf;
270	>	}
271	>
272	>	int getFdf();
273	>
274	>	//getNZconstraint and setNZconstraint ruin the coherence of
275	>	//SimInfo class, need refactoring
276
277	<	/** Returns the snapshot manager. */
278	<	SnapshotManager* getSnapshotManager() {
279	<	return sman_;
280	<	}
277	>	/** Returns the total number of z-constraint molecules in the system */
278	>	int getNZconstraint() {
279	>	return nZconstraint_;
280	>	}
281
282	<	/** Sets the snapshot manager. */
283	<	void setSnapshotManager(SnapshotManager* sman);
282	>	/**
283	>	* Sets the number of z-constraint molecules in the system.
284	>	*/
285	>	void setNZconstraint(int nZconstraint) {
286	>	nZconstraint_ = nZconstraint;
287	>	}
288
289	<	/** Returns the force field */
290	<	ForceField* getForceField() {
291	<	return forceField_;
292	<	}
289	>	/** Returns the snapshot manager. */
290	>	SnapshotManager* getSnapshotManager() {
291	>	return sman_;
292	>	}
293	>	/** Returns the storage layout (computed by SimCreator) */
294	>	int getStorageLayout() {
295	>	return storageLayout_;
296	>	}
297	>	/** Sets the storage layout (computed by SimCreator) */
298	>	void setStorageLayout(int sl) {
299	>	storageLayout_ = sl;
300	>	}
301	>
302	>	/** Sets the snapshot manager. */
303	>	void setSnapshotManager(SnapshotManager* sman);
304	>
305	>	/** Returns the force field */
306	>	ForceField* getForceField() {
307	>	return forceField_;
308	>	}
309
310	<	Globals* getSimParams() {
311	<	return simParams_;
312	<	}
310	>	Globals* getSimParams() {
311	>	return simParams_;
312	>	}
313
314	<	/** Returns the velocity of center of mass of the whole system.*/
315	<	Vector3d getComVel();
314	>	void update();
315	>	/**
316	>	* Do final bookkeeping before Force managers need their data.
317	>	*/
318	>	void prepareTopology();
319
256	–	/** Returns the center of the mass of the whole system.*/
257	–	Vector3d getCom();
320
321	<	/** main driver function to interact with fortran during the initialization and molecule migration */
322	<	void update();
321	>	/** Returns the local index manager */
322	>	LocalIndexManager* getLocalIndexManager() {
323	>	return &localIndexMan_;
324	>	}
325
326	<	/** Returns the local index manager */
327	<	LocalIndexManager* getLocalIndexManager() {
328	<	return &localIndexMan_;
329	<	}
326	>	int getMoleculeStampId(int globalIndex) {
327	>	//assert(globalIndex < molStampIds_.size())
328	>	return molStampIds_[globalIndex];
329	>	}
330
331	<	int getMoleculeStampId(int globalIndex) {
332	<	//assert(globalIndex < molStampIds_.size())
333	<	return molStampIds_[globalIndex];
334	<	}
331	>	/** Returns the molecule stamp */
332	>	MoleculeStamp* getMoleculeStamp(int id) {
333	>	return moleculeStamps_[id];
334	>	}
335
336	<	/** Returns the molecule stamp */
337	<	MoleculeStamp* getMoleculeStamp(int id) {
338	<	return moleculeStamps_[id];
339	<	}
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
342	>	* @return a pointer point to found molecule
343	>	* @param index
344	>	*/
345	>	Molecule* getMoleculeByGlobalIndex(int index) {
346	>	MoleculeIterator i;
347	>	i = molecules_.find(index);
348
349	<	/** Return the total number of the molecule stamps */
350	<	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);
349	>	return i != molecules_.end() ? i->second : NULL;
350	>	}
351
352	<	return i != molecules_.end() ? i->second : NULL;
353	<	}
352	>	int getGlobalMolMembership(int id){
353	>	return globalMolMembership_[id];
354	>	}
355
356	<	/** Calculate the maximum cutoff radius based on the atom types */
357	<	double calcMaxCutoffRadius();
356	>	/**
357	>	* returns a vector which maps the local atom index on this
358	>	* processor to the global atom index.  With only one processor,
359	>	* these should be identical.
360	>	*/
361	>	vector<int> getGlobalAtomIndices();
362
363	<	double getRcut() {
364	<	return rcut_;
365	<	}
363	>	/**
364	>	* returns a vector which maps the local cutoff group index on
365	>	* this processor to the global cutoff group index.  With only one
366	>	* processor, these should be identical.
367	>	*/
368	>	vector<int> getGlobalGroupIndices();
369
300	–	double getRsw() {
301	–	return rsw_;
302	–	}
370
371	<	std::string getFinalConfigFileName() {
372	<	return finalConfigFileName_;
373	<	}
307	<
308	<	void setFinalConfigFileName(const std::string& fileName) {
309	<	finalConfigFileName_ = fileName;
310	<	}
371	>	string getFinalConfigFileName() {
372	>	return finalConfigFileName_;
373	>	}
374
375	<	std::string getDumpFileName() {
376	<	return dumpFileName_;
377	<	}
375	>	void setFinalConfigFileName(const string& fileName) {
376	>	finalConfigFileName_ = fileName;
377	>	}
378	>
379	>	string getRawMetaData() {
380	>	return rawMetaData_;
381	>	}
382	>	void setRawMetaData(const string& rawMetaData) {
383	>	rawMetaData_ = rawMetaData;
384	>	}
385
386	<	void setDumpFileName(const std::string& fileName) {
387	<	dumpFileName_ = fileName;
388	<	}
386	>	string getDumpFileName() {
387	>	return dumpFileName_;
388	>	}
389	>
390	>	void setDumpFileName(const string& fileName) {
391	>	dumpFileName_ = fileName;
392	>	}
393
394	<	std::string getStatFileName() {
395	<	return statFileName_;
396	<	}
394	>	string getStatFileName() {
395	>	return statFileName_;
396	>	}
397
398	<	void setStatFileName(const std::string& fileName) {
399	<	statFileName_ = fileName;
400	<	}
398	>	void setStatFileName(const string& fileName) {
399	>	statFileName_ = fileName;
400	>	}
401	>
402	>	string getRestFileName() {
403	>	return restFileName_;
404	>	}
405	>
406	>	void setRestFileName(const string& fileName) {
407	>	restFileName_ = fileName;
408	>	}
409
410	<	/**
411	<	* Sets GlobalGroupMembership
412	<	* @see #SimCreator::setGlobalIndex
413	<	*/
414	<	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
415	<	assert(globalGroupMembership.size() == nGlobalAtoms_);
416	<	globalGroupMembership_ = globalGroupMembership;
335	<	}
410	>	/**
411	>	* Sets GlobalGroupMembership
412	>	*/
413	>	void setGlobalGroupMembership(const vector<int>& ggm) {
414	>	assert(ggm.size() == static_cast<size_t>(nGlobalAtoms_));
415	>	globalGroupMembership_ = ggm;
416	>	}
417
418	<	/**
419	<	* Sets GlobalMolMembership
420	<	* @see #SimCreator::setGlobalIndex
421	<	*/
422	<	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
423	<	assert(globalMolMembership.size() == nGlobalAtoms_);
424	<	globalMolMembership_ = globalMolMembership;
425	<	}
418	>	/**
419	>	* Sets GlobalMolMembership
420	>	*/
421	>	void setGlobalMolMembership(const vector<int>& gmm) {
422	>	assert(gmm.size() == (static_cast<size_t>(nGlobalAtoms_ +
423	>	nGlobalRigidBodies_)));
424	>	globalMolMembership_ = gmm;
425	>	}
426
427
428	<	bool isFortranInitialized() {
429	<	return fortranInitialized_;
430	<	}
428	>	bool isTopologyDone() {
429	>	return topologyDone_;
430	>	}
431
432	<	//below functions are just forward functions
433	<	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
434	<	//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);
432	>	bool getCalcBoxDipole() {
433	>	return calcBoxDipole_;
434	>	}
435
436	<	/**
437	<	* Removes property from PropertyMap by name
438	<	* @param propName the name of property to be removed
363	<	*/
364	<	void removeProperty(const std::string& propName);
436	>	bool getUseAtomicVirial() {
437	>	return useAtomicVirial_;
438	>	}
439
440	<	/**
441	<	* clear all of the properties
442	<	*/
443	<	void clearProperties();
440	>	/**
441	>	* Adds property into property map
442	>	* @param genData GenericData to be added into PropertyMap
443	>	*/
444	>	void addProperty(GenericData* genData);
445
446	<	/**
447	<	* Returns all names of properties
448	<	* @return all names of properties
449	<	*/
450	<	std::vector<std::string> getPropertyNames();
446	>	/**
447	>	* Removes property from PropertyMap by name
448	>	* @param propName the name of property to be removed
449	>	*/
450	>	void removeProperty(const string& propName);
451
452	<	/**
453	<	* Returns all of the properties in PropertyMap
454	<	* @return all of the properties in PropertyMap
455	<	*/
381	<	std::vector<GenericData*> getProperties();
452	>	/**
453	>	* clear all of the properties
454	>	*/
455	>	void clearProperties();
456
457	<	/**
458	<	* Returns property
459	<	* @param propName name of property
460	<	* @return a pointer point to property with propName. If no property named propName
461	<	* exists, return NULL
388	<	*/
389	<	GenericData* getPropertyByName(const std::string& propName);
457	>	/**
458	>	* Returns all names of properties
459	>	* @return all names of properties
460	>	*/
461	>	vector<string> getPropertyNames();
462
463	<	/**
464	<	* add all exclude pairs of a molecule into exclude list.
465	<	*/
466	<	void addExcludePairs(Molecule* mol);
463	>	/**
464	>	* Returns all of the properties in PropertyMap
465	>	* @return all of the properties in PropertyMap
466	>	*/
467	>	vector<GenericData*> getProperties();
468
469	<	/**
470	<	* remove all exclude pairs which belong to a molecule from exclude list
471	<	*/
469	>	/**
470	>	* Returns property
471	>	* @param propName name of property
472	>	* @return a pointer point to property with propName. If no property named propName
473	>	* exists, return NULL
474	>	*/
475	>	GenericData* getPropertyByName(const string& propName);
476
477	<	void removeExcludePairs(Molecule* mol);
477	>	/**
478	>	* add all special interaction pairs (including excluded
479	>	* interactions) in a molecule into the appropriate lists.
480	>	*/
481	>	void addInteractionPairs(Molecule* mol);
482
483	+	/**
484	+	* remove all special interaction pairs which belong to a molecule
485	+	* from the appropriate lists.
486	+	*/
487	+	void removeInteractionPairs(Molecule* mol);
488
489	<	/** Returns the unique atom types of local processor in an array */
490	<	std::set<AtomType*> getUniqueAtomTypes();
489	>	/** Returns the set of atom types present in this simulation */
490	>	set<AtomType*> getSimulatedAtomTypes();
491	>
492	>	/** Returns the global count of atoms of a particular type */
493	>	int getGlobalCountOfType(AtomType* atype);
494
495	<	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
495	>	friend ostream& operator <<(ostream& o, SimInfo& info);
496
497	<	void getCutoff(double& rcut, double& rsw);
497	>	void getCutoff(RealType& rcut, RealType& rsw);
498
499	<	private:
499	>	private:
500
501	<	/** fill up the simtype struct*/
502	<	void setupSimType();
501	>	/** fill up the simtype struct and other simulation-related variables */
502	>	void setupSimVariables();
503
415	–	/**
416	–	* Setup Fortran Simulation
417	–	* @see #setupFortranParallel
418	–	*/
419	–	void setupFortranSim();
504
505	<	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
506	<	void setupCutoff();
505	>	/** Determine if we need to accumulate the simulation box dipole */
506	>	void setupAccumulateBoxDipole();
507
508	<	/** Calculates the number of degress of freedom in the whole system */
509	<	void calcNdf();
510	<	void calcNdfRaw();
511	<	void calcNdfTrans();
508	>	/** Calculates the number of degress of freedom in the whole system */
509	>	void calcNdf();
510	>	void calcNdfRaw();
511	>	void calcNdfTrans();
512
513	<	/**
514	<	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
515	<	* system.
516	<	*/
517	<	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
513	>	/**
514	>	* Adds molecule stamp and the total number of the molecule with
515	>	* same molecule stamp in the whole system.
516	>	*/
517	>	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
518
519	<	ForceField* forceField_;
520	<	Globals* simParams_;
519	>	// Other classes holdingn important information
520	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
521	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
522
523	<	std::map<int, Molecule*>  molecules_; /**< Molecule array */
523	>	///  Counts of local objects
524	>	int nAtoms_;              /**< number of atoms in local processor */
525	>	int nBonds_;              /**< number of bonds in local processor */
526	>	int nBends_;              /**< number of bends in local processor */
527	>	int nTorsions_;           /**< number of torsions in local processor */
528	>	int nInversions_;         /**< number of inversions in local processor */
529	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
530	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
531	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
532	>	int nConstraints_;        /**< number of constraints in local processors */
533	>	int nFluctuatingCharges_; /**< number of fluctuating charges in local processor */
534
535	<	//degress of freedom
536	<	int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
537	<	int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
538	<	int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
539	<	int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
540	<
541	<	//number of global objects
542	<	int nGlobalMols_;       /**< number of molecules in the system */
543	<	int nGlobalAtoms_;   /**< number of atoms in the system */
544	<	int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
545	<	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
546	<	int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
547	<	/**
548	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
549	<	* corresponding content is the global index of cutoff group this atom belong to.
550	<	* It is filled by SimCreator once and only once, since it never changed during the simulation.
551	<	*/
552	<	std::vector<int> globalGroupMembership_;
535	>	/// Counts of global objects
536	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
537	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
538	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
539	>	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
540	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
541	>	int nGlobalFluctuatingCharges_;/**< number of fluctuating charges in this system (GLOBAL) */
542	>	int nGlobalBonds_;              /**< number of bonds in the system */
543	>	int nGlobalBends_;              /**< number of bends in the system */
544	>	int nGlobalTorsions_;           /**< number of torsions in the system */
545	>	int nGlobalInversions_;         /**< number of inversions in the system */
546	>
547	>	/// Degress of freedom
548	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
549	>	int ndfLocal_;     /**< number of degrees of freedom (LOCAL, excludes constraints) */
550	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
551	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
552	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
553	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
554	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
555
556	<	/**
557	<	* the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
558	<	* corresponding content is the global index of molecule this atom belong to.
559	<	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
560	<	*/
561	<	std::vector<int> globalMolMembership_;
556	>	/// logicals
557	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
558	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
559	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
560	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
561	>	bool usesFluctuatingCharges_; /**< are there fluctuating charges? */
562	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
563	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
564	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
565	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
566
567	<
568	<	std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
569	<	std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */
570	<
571	<	//number of local objects
572	<	int nAtoms_;                        /**< number of atoms in local processor */
573	<	int nBonds_;                        /**< number of bonds in local processor */
574	<	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 */
567	>	public:
568	>	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
569	>	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
570	>	bool usesFluctuatingCharges() { return usesFluctuatingCharges_; }
571	>	bool usesAtomicVirial() { return usesAtomicVirial_; }
572	>	bool requiresPrepair() { return requiresPrepair_; }
573	>	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
574	>	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
575
576	<	simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
577	<	Exclude exclude_;
578	<	PropertyMap properties_;                  /**< Generic Property */
483	<	SnapshotManager* sman_;               /**< SnapshotManager */
576	>	private:
577	>	/// Data structures holding primary simulation objects
578	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
579
580	<	/**
581	<	* The reason to have a local index manager is that when molecule is migrating to other processors,
582	<	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
583	<	* information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
584	<	* to make a efficient data moving plan.
585	<	*/
586	<	LocalIndexManager localIndexMan_;
580	>	/// Stamps are templates for objects that are then used to create
581	>	/// groups of objects.  For example, a molecule stamp contains
582	>	/// information on how to build that molecule (i.e. the topology,
583	>	/// the atoms, the bonds, etc.)  Once the system is built, the
584	>	/// stamps are no longer useful.
585	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
586	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
587
588	<	//file names
589	<	std::string finalConfigFileName_;
590	<	std::string dumpFileName_;
591	<	std::string statFileName_;
588	>	/**
589	>	* A vector that maps between the global index of an atom, and the
590	>	* global index of cutoff group the atom belong to.  It is filled
591	>	* by SimCreator once and only once, since it never changed during
592	>	* the simulation.  It should be nGlobalAtoms_ in size.
593	>	*/
594	>	vector<int> globalGroupMembership_;
595	>	public:
596	>	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
597	>	private:
598
599	<	double rcut_;       /**< cutoff radius*/
600	<	double rsw_;        /**< radius of switching function*/
599	>	/**
600	>	* A vector that maps between the global index of an atom and the
601	>	* global index of the molecule the atom belongs to.  It is filled
602	>	* by SimCreator once and only once, since it is never changed
603	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
604	>	*/
605	>	vector<int> globalMolMembership_;
606
607	<	bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */
607	>	/**
608	>	* A vector that maps between the local index of an atom and the
609	>	* index of the AtomType.
610	>	*/
611	>	vector<int> identArray_;
612	>	public:
613	>	vector<int> getIdentArray() { return identArray_; }
614
615	<	#ifdef IS_MPI
616	<	//in Parallel version, we need MolToProc
617	<	public:
618	<
619	<	/**
620	<	* Finds the processor where a molecule resides
621	<	* @return the id of the processor which contains the molecule
622	<	* @param globalIndex global Index of the molecule
623	<	*/
624	<	int getMolToProc(int globalIndex) {
625	<	//assert(globalIndex < molToProcMap_.size());
626	<	return molToProcMap_[globalIndex];
627	<	}
615	>	/**
616	>	* A vector that contains information about the local region of an
617	>	* atom (used for fluctuating charges, etc.)
618	>	*/
619	>	private:
620	>	vector<int> regions_;
621	>	public:
622	>	vector<int> getRegions() { return regions_; }
623	>	private:
624	>	/**
625	>	* A vector which contains the fractional contribution of an
626	>	* atom's mass to the total mass of the cutoffGroup that atom
627	>	* belongs to.  In the case of single atom cutoff groups, the mass
628	>	* factor for that atom is 1.  For massless atoms, the factor is
629	>	* also 1.
630	>	*/
631	>	vector<RealType> massFactors_;
632	>	public:
633	>	vector<RealType> getMassFactors() { return massFactors_; }
634
635	<	/**
636	<	* Set MolToProcMap array
637	<	* @see #SimCreator::divideMolecules
638	<	*/
521	<	void setMolToProcMap(const std::vector<int>& molToProcMap) {
522	<	molToProcMap_ = molToProcMap;
523	<	}
524	<
525	<	private:
635	>	PairList* getExcludedInteractions() { return &excludedInteractions_; }
636	>	PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
637	>	PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
638	>	PairList* getOneFourInteractions() { return &oneFourInteractions_; }
639
640	<	void setupFortranParallel();
641	<
642	<	/**
643	<	* The size of molToProcMap_ is equal to total number of molecules in the system.
644	<	*  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
645	<	* once.
646	<	*/
534	<	std::vector<int> molToProcMap_;
640	>	private:
641	>
642	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
643	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
644	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
645	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
646	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
647
648	<	#endif
648	>	PropertyMap properties_;       /**< Generic Properties can be added */
649	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
650	>	int storageLayout_;            /**< Bits to tell how much data to store on each object */
651
652	<	};
652	>	/**
653	>	* The reason to have a local index manager is that when molecule
654	>	* is migrating to other processors, the atoms and the
655	>	* rigid-bodies will release their local indices to
656	>	* LocalIndexManager. Combining the information of molecule
657	>	* migrating to current processor, Migrator class can query the
658	>	* LocalIndexManager to make a efficient data moving plan.
659	>	*/
660	>	LocalIndexManager localIndexMan_;
661
662	<	} //namespace oopse
662	>	// unparsed MetaData block for storing in Dump and EOR files:
663	>	string rawMetaData_;
664	>
665	>	// file names
666	>	string finalConfigFileName_;
667	>	string dumpFileName_;
668	>	string statFileName_;
669	>	string restFileName_;
670	>
671	>	bool topologyDone_;  /** flag to indicate whether the topology has
672	>	been scanned and all the relevant
673	>	bookkeeping has been done*/
674	>
675	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
676	>	the simulation box dipole moment */
677	>
678	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
679	>	Atomic Virials to calculate the pressure */
680	>
681	>	public:
682	>	/**
683	>	* return an integral objects by its global index. In MPI
684	>	* version, if the StuntDouble with specified global index does
685	>	* not belong to local processor, a NULL will be return.
686	>	*/
687	>	StuntDouble* getIOIndexToIntegrableObject(int index);
688	>	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
689	>
690	>	private:
691	>	vector<StuntDouble*> IOIndexToIntegrableObject;
692	>
693	>	public:
694	>
695	>	/**
696	>	* Finds the processor where a molecule resides
697	>	* @return the id of the processor which contains the molecule
698	>	* @param globalIndex global Index of the molecule
699	>	*/
700	>	int getMolToProc(int globalIndex) {
701	>	//assert(globalIndex < molToProcMap_.size());
702	>	return molToProcMap_[globalIndex];
703	>	}
704	>
705	>	/**
706	>	* Set MolToProcMap array
707	>	*/
708	>	void setMolToProcMap(const vector<int>& molToProcMap) {
709	>	molToProcMap_ = molToProcMap;
710	>	}
711	>
712	>	private:
713	>
714	>	/**
715	>	* The size of molToProcMap_ is equal to total number of molecules
716	>	* in the system.  It maps a molecule to the processor on which it
717	>	* resides. it is filled by SimCreator once and only once.
718	>	*/
719	>	vector<int> molToProcMap_;
720	>
721	>	};
722	>
723	>	} //namespace OpenMD
724		#endif //BRAINS_SIMMODEL_HPP
725

Comparing trunk/src/brains/SimInfo.hpp (property svn:keywords):
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Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

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