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

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trunk/src/brains/SimInfo.hpp (file contents), Revision 143 by chrisfen, Fri Oct 22 22:54:01 2004 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	<	#ifndef __SIMINFO_H__
2	<	#define __SIMINFO_H__
1	>	/*
2	>	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	>	*
4	>	* The University of Notre Dame grants you ("Licensee") a
5	>	* non-exclusive, royalty free, license to use, modify and
6	>	* redistribute this software in source and binary code form, provided
7	>	* that the following conditions are met:
8	>	*
9	>	* 1. Redistributions of source code must retain the above copyright
10	>	*    notice, this list of conditions and the following disclaimer.
11	>	*
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.
16	>	*
17	>	* This software is provided "AS IS," without a warranty of any
18	>	* kind. All express or implied conditions, representations and
19	>	* warranties, including any implied warranty of merchantability,
20	>	* fitness for a particular purpose or non-infringement, are hereby
21	>	* excluded.  The University of Notre Dame and its licensors shall not
22	>	* be liable for any damages suffered by licensee as a result of
23	>	* using, modifying or distributing the software or its
24	>	* derivatives. In no event will the University of Notre Dame or its
25	>	* licensors be liable for any lost revenue, profit or data, or for
26	>	* direct, indirect, special, consequential, incidental or punitive
27	>	* damages, however caused and regardless of the theory of liability,
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	>	/**
44	>	* @file SimInfo.hpp
45	>	* @author    tlin
46	>	* @date  11/02/2004
47	>	* @version 1.0
48	>	*/
49
50	<	#include <map>
51	<	#include <string>
50	>	#ifndef BRAINS_SIMMODEL_HPP
51	>	#define BRAINS_SIMMODEL_HPP
52	>
53	>	#include <iostream>
54	>	#include <set>
55	>	#include <utility>
56		#include <vector>
57
58	<	#include "primitives/Atom.hpp"
59	<	#include "primitives/RigidBody.hpp"
60	<	#include "primitives/Molecule.hpp"
61	<	#include "brains/Exclude.hpp"
62	<	#include "brains/SkipList.hpp"
63	<	#include "primitives/AbstractClasses.hpp"
64	<	#include "types/MakeStamps.hpp"
65	<	#include "brains/SimState.hpp"
66	<	#include "restraints/Restraints.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 "brains/ForceField.hpp"
64	>	#include "utils/PropertyMap.hpp"
65	>	#include "utils/LocalIndexManager.hpp"
66	>	#include "nonbonded/SwitchingFunction.hpp"
67
68	<	#define __C
69	<	#include "brains/fSimulation.h"
70	<	#include "utils/GenericData.hpp"
68	>	using namespace std;
69	>	namespace OpenMD{
70	>	//forward declaration
71	>	class SnapshotManager;
72	>	class Molecule;
73	>	class SelectionManager;
74	>	class StuntDouble;
75
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	<	//#include "Minimizer.hpp"
102	<	//#include "minimizers/OOPSEMinimizer.hpp"
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	+	* 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	<	double roundMe( double x );
120	<	class OOPSEMinimizer;
121	<	class SimInfo{
119	>	/** Returns the total number of molecules in the system. */
120	>	int getNGlobalMolecules() {
121	>	return nGlobalMols_;
122	>	}
123
124	<	public:
124	>	/** Returns the total number of atoms in the system. */
125	>	int getNGlobalAtoms() {
126	>	return nGlobalAtoms_;
127	>	}
128
129	<	SimInfo();
130	<	~SimInfo();
129	>	/** Returns the total number of cutoff groups in the system. */
130	>	int getNGlobalCutoffGroups() {
131	>	return nGlobalCutoffGroups_;
132	>	}
133
134	<	int n_atoms; // the number of atoms
135	<	Atom **atoms; // the array of atom objects
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	<	vector<RigidBody*> rigidBodies;  // A vector of rigid bodies
144	<	vector<StuntDouble*> integrableObjects;
145	<
146	<	double tau[9]; // the stress tensor
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	<	int n_bonds;    // number of bends
153	<	int n_bends;    // number of bends
154	<	int n_torsions; // number of torsions
155	<	int n_oriented; // number of of atoms with orientation
156	<	int ndf;        // number of actual degrees of freedom
157	<	int ndfRaw;     // number of settable degrees of freedom
158	<	int ndfTrans;   // number of translational degrees of freedom
159	<	int nZconstraints; // the number of zConstraints
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	<	int setTemp;   // boolean to set the temperature at each sampleTime
162	<	int resetIntegrator; // boolean to reset the integrator
161	>	/** Returns the number of local atoms */
162	>	unsigned int getNAtoms() {
163	>	return nAtoms_;
164	>	}
165
166	<	int n_dipoles; // number of dipoles
166	>	/** Returns the number of effective cutoff groups on local processor */
167	>	unsigned int getNLocalCutoffGroups();
168
169	<	int n_exclude;
170	<	Exclude* excludes;  // the exclude list for ignoring pairs in fortran
171	<	int nGlobalExcludes;
172	<	int* globalExcludes; // same as above, but these guys participate in
62	<	// no long range forces.
169	>	/** Returns the number of local bonds */
170	>	unsigned int getNBonds(){
171	>	return nBonds_;
172	>	}
173
174	<	int* identArray;     // array of unique identifiers for the atoms
175	<	int* molMembershipArray;  // map of atom numbers onto molecule numbers
174	>	/** Returns the number of local bends */
175	>	unsigned int getNBends() {
176	>	return nBends_;
177	>	}
178
179	<	int n_constraints; // the number of constraints on the system
179	>	/** Returns the number of local torsions */
180	>	unsigned int getNTorsions() {
181	>	return nTorsions_;
182	>	}
183
184	<	int n_SRI;   // the number of short range interactions
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	<	double lrPot; // the potential energy from the long range calculations.
193	>	/** Returns the number of local integrable objects */
194	>	unsigned int getNIntegrableObjects() {
195	>	return nIntegrableObjects_;
196	>	}
197
198	<	double Hmat[3][3];  // the periodic boundry conditions. The Hmat is the
199	<	// column vectors of the x, y, and z box vectors.
200	<	//   h1  h2  h3
201	<	// [ Xx  Yx  Zx ]
77	<	// [ Xy  Yy  Zy ]
78	<	// [ Xz  Yz  Zz ]
79	<	//
80	<	double HmatInv[3][3];
198	>	/** Returns the number of local cutoff groups */
199	>	unsigned int getNCutoffGroups() {
200	>	return nCutoffGroups_;
201	>	}
202
203	<	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
204	<	double boxVol;
205	<	int orthoRhombic;
206	<
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);
214
215	<	double dielectric;      // the dielectric of the medium for reaction field
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	<
223	<	int usePBC; // whether we use periodic boundry conditions.
224	<	int useDirectionalAtoms;
225	<	int useLennardJones;
93	<	int useElectrostatics;
94	<	int useCharges;
95	<	int useDipoles;
96	<	int useSticky;
97	<	int useGayBerne;
98	<	int useEAM;
99	<	int useShapes;
100	<	int useFLARB;
101	<	int useReactionField;
102	<	bool haveCutoffGroups;
103	<	bool useInitXSstate;
104	<	double orthoTolerance;
222	>	/** Returns the total number of fluctuating charges that are present */
223	>	int getNFluctuatingCharges() {
224	>	return nGlobalFluctuatingCharges_;
225	>	}
226
227	<	double dt, run_time;           // the time step and total time
228	<	double sampleTime, statusTime; // the position and energy dump frequencies
229	<	double target_temp;            // the target temperature of the system
230	<	double thermalTime;            // the temp kick interval
110	<	double currentTime;            // Used primarily for correlation Functions
111	<	double resetTime;              // Use to reset the integrator periodically
112	<	short int have_target_temp;
227	>	/** Returns the number of degrees of freedom */
228	>	int getNdf() {
229	>	return ndf_ - getFdf();
230	>	}
231
232	<	int n_mol;           // n_molecules;
233	<	Molecule* molecules; // the array of molecules
234	<
235	<	int nComponents;           // the number of components in the system
118	<	int* componentsNmol;       // the number of molecules of each component
119	<	MoleculeStamp** compStamps;// the stamps matching the components
120	<	LinkedMolStamp* headStamp; // list of stamps used in the simulation
121	<
122	<
123	<	char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
124	<	char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
125	<	BaseIntegrator *the_integrator; // the integrator of the simulation
232	>	/** Returns the number of degrees of freedom (LOCAL) */
233	>	int getNdfLocal() {
234	>	return ndfLocal_;
235	>	}
236
237	<	OOPSEMinimizer* the_minimizer; // the energy minimizer
238	<	Restraints* restraint;
239	<	bool has_minimizer;
237	>	/** Returns the number of raw degrees of freedom */
238	>	int getNdfRaw() {
239	>	return ndfRaw_;
240	>	}
241
242	<	string finalName;  // the name of the eor file to be written
243	<	string sampleName; // the name of the dump file to be written
244	<	string statusName; // the name of the stat file to be written
242	>	/** Returns the number of translational degrees of freedom */
243	>	int getNdfTrans() {
244	>	return ndfTrans_;
245	>	}
246
247	<	int seed;                    //seed for random number generator
247	>	/** sets the current number of frozen degrees of freedom */
248	>	void setFdf(int fdf) {
249	>	fdf_local = fdf;
250	>	}
251
252	<	int useSolidThermInt;  // is solid-state thermodynamic integration being used
253	<	int useLiquidThermInt; // is liquid thermodynamic integration being used
254	<	double thermIntLambda; // lambda for TI
255	<	double thermIntK;      // power of lambda for TI
256	<	double vRaw;           // unperturbed potential for TI
257	<	double vHarm;          // harmonic potential for TI
258	<	int i;                 // just an int
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	>	}
261
262	<	vector<double> mfact;
263	<	vector<int> FglobalGroupMembership;
264	<	int ngroup;
265	<	int* globalGroupMembership;
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	>	}
273
274	<	// refreshes the sim if things get changed (load balanceing, volume
275	<	// adjustment, etc.)
274	>	/** Sets the snapshot manager. */
275	>	void setSnapshotManager(SnapshotManager* sman);
276	>
277	>	/** Returns the force field */
278	>	ForceField* getForceField() {
279	>	return forceField_;
280	>	}
281
282	<	void refreshSim( void );
283	<
282	>	Globals* getSimParams() {
283	>	return simParams_;
284	>	}
285
286	<	// sets the internal function pointer to fortran.
286	>	void update();
287	>	/**
288	>	* Do final bookkeeping before Force managers need their data.
289	>	*/
290	>	void prepareTopology();
291
292
293	<	int getNDF();
294	<	int getNDFraw();
295	<	int getNDFtranslational();
296	<	int getTotIntegrableObjects();
163	<	void setBox( double newBox[3] );
164	<	void setBoxM( double newBox[3][3] );
165	<	void getBoxM( double theBox[3][3] );
166	<	void scaleBox( double scale );
167	<
168	<	void setDefaultRcut( double theRcut );
169	<	void setDefaultRcut( double theRcut, double theRsw );
170	<	void checkCutOffs( void );
293	>	/** Returns the local index manager */
294	>	LocalIndexManager* getLocalIndexManager() {
295	>	return &localIndexMan_;
296	>	}
297
298	<	double getRcut( void )  { return rCut; }
299	<	double getRlist( void ) { return rList; }
300	<	double getRsw( void )   { return rSw; }
301	<	double getMaxCutoff( void ) { return maxCutoff; }
176	<
177	<	void setTime( double theTime ) { currentTime = theTime; }
178	<	void incrTime( double the_dt ) { currentTime += the_dt; }
179	<	void decrTime( double the_dt ) { currentTime -= the_dt; }
180	<	double getTime( void ) { return currentTime; }
298	>	int getMoleculeStampId(int globalIndex) {
299	>	//assert(globalIndex < molStampIds_.size())
300	>	return molStampIds_[globalIndex];
301	>	}
302
303	<	void wrapVector( double thePos[3] );
303	>	/** Returns the molecule stamp */
304	>	MoleculeStamp* getMoleculeStamp(int id) {
305	>	return moleculeStamps_[id];
306	>	}
307
308	<	SimState* getConfiguration( void ) { return myConfiguration; }
309	<
310	<	void addProperty(GenericData* prop);
311	<	GenericData* getProperty(const string& propName);
312	<	//vector<GenericData*>& getProperties()  {return properties;}
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	<	int getSeed(void) {  return seed; }
322	<	void setSeed(int theSeed) {  seed = theSeed;}
321	>	return i != molecules_.end() ? i->second : NULL;
322	>	}
323
324	<	private:
324	>	int getGlobalMolMembership(int id){
325	>	return globalMolMembership_[id];
326	>	}
327
328	<	SimState* myConfiguration;
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	<	int boxIsInit, haveRcut, haveRsw;
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
342	<	double rList, rCut; // variables for the neighborlist
343	<	double rSw;         // the switching radius
342	>
343	>	string getFinalConfigFileName() {
344	>	return finalConfigFileName_;
345	>	}
346
347	<	double maxCutoff;
347	>	void setFinalConfigFileName(const string& fileName) {
348	>	finalConfigFileName_ = fileName;
349	>	}
350
351	<	double distXY;
352	<	double distYZ;
353	<	double distZX;
354	<
355	<	void calcHmatInv( void );
356	<	void calcBoxL();
357	<	double calcMaxCutOff();
351	>	string getRawMetaData() {
352	>	return rawMetaData_;
353	>	}
354	>	void setRawMetaData(const string& rawMetaData) {
355	>	rawMetaData_ = rawMetaData;
356	>	}
357	>
358	>	string getDumpFileName() {
359	>	return dumpFileName_;
360	>	}
361	>
362	>	void setDumpFileName(const string& fileName) {
363	>	dumpFileName_ = fileName;
364	>	}
365
366	<
367	<	//Addtional Properties of SimInfo
368	<	map<string, GenericData*> properties;
369	<	void getFortranGroupArrays(SimInfo* info,
370	<	vector<int>& FglobalGroupMembership,
371	<	vector<double>& mfact);
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	+	/**
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	<	};
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	<	#endif
399	>	bool isTopologyDone() {
400	>	return topologyDone_;
401	>	}
402	>
403	>	bool getCalcBoxDipole() {
404	>	return calcBoxDipole_;
405	>	}
406	>
407	>	bool getUseAtomicVirial() {
408	>	return useAtomicVirial_;
409	>	}
410	>
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	>	* 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	>	* clear all of the properties
425	>	*/
426	>	void clearProperties();
427	>
428	>	/**
429	>	* Returns all names of properties
430	>	* @return all names of properties
431	>	*/
432	>	vector<string> getPropertyNames();
433	>
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	>	* 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	>	/**
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 set of atom types present in this simulation */
461	>	set<AtomType*> getSimulatedAtomTypes();
462	>
463	>	friend ostream& operator <<(ostream& o, SimInfo& info);
464	>
465	>	void getCutoff(RealType& rcut, RealType& rsw);
466	>
467	>	private:
468	>
469	>	/** fill up the simtype struct and other simulation-related variables */
470	>	void setupSimVariables();
471	>
472	>
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();
480	>
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	>	// 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	>	///  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	>	/// 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	>	/// 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	>	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	>	private:
542	>	/// Data structures holding primary simulation objects
543	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
544	>
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	>	/**
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	>	/**
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	>	/**
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	>	PairList* getExcludedInteractions() { return &excludedInteractions_; }
593	>	PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
594	>	PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
595	>	PairList* getOneFourInteractions() { return &oneFourInteractions_; }
596	>
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	>
627	>
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	>	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	>	};
679	>
680	>	} //namespace OpenMD
681	>	#endif //BRAINS_SIMMODEL_HPP
682	>

Comparing:
trunk/src/brains/SimInfo.hpp (property svn:keywords), Revision 143 by chrisfen, Fri Oct 22 22:54:01 2004 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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