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trunk/src/brains/SimInfo.hpp (file contents), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/brains/SimInfo.hpp (file contents), Revision 1744 by gezelter, Tue Jun 5 18:07:08 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 "Atom.hpp"
59	<	#include "RigidBody.hpp"
60	<	#include "Molecule.hpp"
61	<	#include "Exclude.hpp"
62	<	#include "SkipList.hpp"
63	<	#include "AbstractClasses.hpp"
64	<	#include "MakeStamps.hpp"
65	<	#include "SimState.hpp"
66	<	#include "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 "fSimulation.h"
70	<	#include "fortranWrapDefines.hpp"
71	<	#include "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 molStampPairs MoleculeStamp Array. The first element of
95	+	* the pair is molecule stamp, the second element is the total
96	+	* number of molecules with the same molecule stamp in the system
97	+	*
98	+	* @param ff pointer of a concrete ForceField instance
99	+	*
100	+	* @param simParams
101	+	*/
102	+	SimInfo(ForceField* ff, Globals* simParams);
103	+	virtual ~SimInfo();
104
105	<	//#include "Minimizer.hpp"
106	<	//#include "OOPSEMinimizer.hpp"
105	>	/**
106	>	* Adds a molecule
107	>	*
108	>	* @return return true if adding successfully, return false if the
109	>	* molecule is already in SimInfo
110	>	*
111	>	* @param mol molecule to be added
112	>	*/
113	>	bool addMolecule(Molecule* mol);
114
115	+	/**
116	+	* Removes a molecule from SimInfo
117	+	*
118	+	* @return true if removing successfully, return false if molecule
119	+	* is not in this SimInfo
120	+	*/
121	+	bool removeMolecule(Molecule* mol);
122
123	<	double roundMe( double x );
124	<	class OOPSEMinimizer;
125	<	class SimInfo{
123	>	/** Returns the total number of molecules in the system. */
124	>	int getNGlobalMolecules() {
125	>	return nGlobalMols_;
126	>	}
127
128	<	public:
128	>	/** Returns the total number of atoms in the system. */
129	>	int getNGlobalAtoms() {
130	>	return nGlobalAtoms_;
131	>	}
132
133	<	SimInfo();
134	<	~SimInfo();
133	>	/** Returns the total number of cutoff groups in the system. */
134	>	int getNGlobalCutoffGroups() {
135	>	return nGlobalCutoffGroups_;
136	>	}
137
138	<	int n_atoms; // the number of atoms
139	<	Atom **atoms; // the array of atom objects
138	>	/**
139	>	* Returns the total number of integrable objects (total number of
140	>	* rigid bodies plus the total number of atoms which do not belong
141	>	* to the rigid bodies) in the system
142	>	*/
143	>	int getNGlobalIntegrableObjects() {
144	>	return nGlobalIntegrableObjects_;
145	>	}
146
147	<	vector<RigidBody*> rigidBodies;  // A vector of rigid bodies
148	<	vector<StuntDouble*> integrableObjects;
149	<
150	<	double tau[9]; // the stress tensor
147	>	/**
148	>	* Returns the total number of integrable objects (total number of
149	>	* rigid bodies plus the total number of atoms which do not belong
150	>	* to the rigid bodies) in the system
151	>	*/
152	>	int getNGlobalRigidBodies() {
153	>	return nGlobalRigidBodies_;
154	>	}
155
156	<	int n_bonds;    // number of bends
157	<	int n_bends;    // number of bends
158	<	int n_torsions; // number of torsions
159	<	int n_oriented; // number of of atoms with orientation
160	<	int ndf;        // number of actual degrees of freedom
161	<	int ndfRaw;     // number of settable degrees of freedom
162	<	int ndfTrans;   // number of translational degrees of freedom
163	<	int nZconstraints; // the number of zConstraints
156	>	int getNGlobalConstraints();
157	>	/**
158	>	* Returns the number of local molecules.
159	>	* @return the number of local molecules
160	>	*/
161	>	int getNMolecules() {
162	>	return molecules_.size();
163	>	}
164
165	<	int setTemp;   // boolean to set the temperature at each sampleTime
166	<	int resetIntegrator; // boolean to reset the integrator
165	>	/** Returns the number of local atoms */
166	>	unsigned int getNAtoms() {
167	>	return nAtoms_;
168	>	}
169
170	<	int n_dipoles; // number of dipoles
170	>	/** Returns the number of effective cutoff groups on local processor */
171	>	unsigned int getNLocalCutoffGroups();
172
173	<	int n_exclude;
174	<	Exclude* excludes;  // the exclude list for ignoring pairs in fortran
175	<	int nGlobalExcludes;
176	<	int* globalExcludes; // same as above, but these guys participate in
63	<	// no long range forces.
173	>	/** Returns the number of local bonds */
174	>	unsigned int getNBonds(){
175	>	return nBonds_;
176	>	}
177
178	<	int* identArray;     // array of unique identifiers for the atoms
179	<	int* molMembershipArray;  // map of atom numbers onto molecule numbers
178	>	/** Returns the number of local bends */
179	>	unsigned int getNBends() {
180	>	return nBends_;
181	>	}
182
183	<	int n_constraints; // the number of constraints on the system
183	>	/** Returns the number of local torsions */
184	>	unsigned int getNTorsions() {
185	>	return nTorsions_;
186	>	}
187
188	<	int n_SRI;   // the number of short range interactions
188	>	/** Returns the number of local torsions */
189	>	unsigned int getNInversions() {
190	>	return nInversions_;
191	>	}
192	>	/** Returns the number of local rigid bodies */
193	>	unsigned int getNRigidBodies() {
194	>	return nRigidBodies_;
195	>	}
196
197	<	double lrPot; // the potential energy from the long range calculations.
197	>	/** Returns the number of local integrable objects */
198	>	unsigned int getNIntegrableObjects() {
199	>	return nIntegrableObjects_;
200	>	}
201
202	<	double Hmat[3][3];  // the periodic boundry conditions. The Hmat is the
203	<	// column vectors of the x, y, and z box vectors.
204	<	//   h1  h2  h3
205	<	// [ Xx  Yx  Zx ]
78	<	// [ Xy  Yy  Zy ]
79	<	// [ Xz  Yz  Zz ]
80	<	//
81	<	double HmatInv[3][3];
202	>	/** Returns the number of local cutoff groups */
203	>	unsigned int getNCutoffGroups() {
204	>	return nCutoffGroups_;
205	>	}
206
207	<	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
208	<	double boxVol;
209	<	int orthoRhombic;
210	<
207	>	/** Returns the total number of constraints in this SimInfo */
208	>	unsigned int getNConstraints() {
209	>	return nConstraints_;
210	>	}
211	>
212	>	/**
213	>	* Returns the first molecule in this SimInfo and intialize the iterator.
214	>	* @return the first molecule, return NULL if there is not molecule in this SimInfo
215	>	* @param i the iterator of molecule array (user shouldn't change it)
216	>	*/
217	>	Molecule* beginMolecule(MoleculeIterator& i);
218
219	<	double dielectric;      // the dielectric of the medium for reaction field
219	>	/**
220	>	* Returns the next avaliable Molecule based on the iterator.
221	>	* @return the next avaliable molecule, return NULL if reaching the end of the array
222	>	* @param i the iterator of molecule array
223	>	*/
224	>	Molecule* nextMolecule(MoleculeIterator& i);
225
226	<
227	<	int usePBC; // whether we use periodic boundry conditions.
228	<	int useLJ;
229	<	int useSticky;
94	<	int useCharges;
95	<	int useDipoles;
96	<	int useReactionField;
97	<	int useGB;
98	<	int useEAM;
99	<	bool haveCutoffGroups;
100	<	bool useInitXSstate;
101	<	double orthoTolerance;
226	>	/** Returns the total number of fluctuating charges that are present */
227	>	int getNFluctuatingCharges() {
228	>	return nGlobalFluctuatingCharges_;
229	>	}
230
231	<	double dt, run_time;           // the time step and total time
232	<	double sampleTime, statusTime; // the position and energy dump frequencies
233	<	double target_temp;            // the target temperature of the system
234	<	double thermalTime;            // the temp kick interval
107	<	double currentTime;            // Used primarily for correlation Functions
108	<	double resetTime;              // Use to reset the integrator periodically
109	<	short int have_target_temp;
231	>	/** Returns the number of degrees of freedom */
232	>	int getNdf() {
233	>	return ndf_ - getFdf();
234	>	}
235
236	<	int n_mol;           // n_molecules;
237	<	Molecule* molecules; // the array of molecules
238	<
239	<	int nComponents;           // the number of components in the system
115	<	int* componentsNmol;       // the number of molecules of each component
116	<	MoleculeStamp** compStamps;// the stamps matching the components
117	<	LinkedMolStamp* headStamp; // list of stamps used in the simulation
118	<
119	<
120	<	char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
121	<	char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
122	<	BaseIntegrator *the_integrator; // the integrator of the simulation
236	>	/** Returns the number of degrees of freedom (LOCAL) */
237	>	int getNdfLocal() {
238	>	return ndfLocal_;
239	>	}
240
241	<	OOPSEMinimizer* the_minimizer; // the energy minimizer
242	<	Restraints* restraint;
243	<	bool has_minimizer;
241	>	/** Returns the number of raw degrees of freedom */
242	>	int getNdfRaw() {
243	>	return ndfRaw_;
244	>	}
245
246	<	string finalName;  // the name of the eor file to be written
247	<	string sampleName; // the name of the dump file to be written
248	<	string statusName; // the name of the stat file to be written
246	>	/** Returns the number of translational degrees of freedom */
247	>	int getNdfTrans() {
248	>	return ndfTrans_;
249	>	}
250
251	<	int seed;                    //seed for random number generator
251	>	/** sets the current number of frozen degrees of freedom */
252	>	void setFdf(int fdf) {
253	>	fdf_local = fdf;
254	>	}
255
256	<	int useSolidThermInt;  // is solid-state thermodynamic integration being used
257	<	int useLiquidThermInt; // is liquid thermodynamic integration being used
258	<	double thermIntLambda; // lambda for TI
259	<	double thermIntK;      // power of lambda for TI
260	<	double vRaw;           // unperturbed potential for TI
261	<	double vHarm;          // harmonic potential for TI
262	<	int i;                 // just an int
256	>	int getFdf();
257	>
258	>	//getNZconstraint and setNZconstraint ruin the coherence of
259	>	//SimInfo class, need refactoring
260	>
261	>	/** Returns the total number of z-constraint molecules in the system */
262	>	int getNZconstraint() {
263	>	return nZconstraint_;
264	>	}
265
266	<	vector<double> mfact;
267	<	vector<int> FglobalGroupMembership;
268	<	int ngroup;
269	<	int* globalGroupMembership;
266	>	/**
267	>	* Sets the number of z-constraint molecules in the system.
268	>	*/
269	>	void setNZconstraint(int nZconstraint) {
270	>	nZconstraint_ = nZconstraint;
271	>	}
272	>
273	>	/** Returns the snapshot manager. */
274	>	SnapshotManager* getSnapshotManager() {
275	>	return sman_;
276	>	}
277
278	<	// refreshes the sim if things get changed (load balanceing, volume
279	<	// adjustment, etc.)
278	>	/** Sets the snapshot manager. */
279	>	void setSnapshotManager(SnapshotManager* sman);
280	>
281	>	/** Returns the force field */
282	>	ForceField* getForceField() {
283	>	return forceField_;
284	>	}
285
286	<	void refreshSim( void );
287	<
286	>	Globals* getSimParams() {
287	>	return simParams_;
288	>	}
289
290	<	// sets the internal function pointer to fortran.
290	>	/** Returns the velocity of center of mass of the whole system.*/
291	>	Vector3d getComVel();
292
293	<	void setInternal( setFortranSim_TD fSetup,
294	<	setFortranBox_TD fBox,
295	<	notifyFortranCutOff_TD fCut){
296	<	setFsimulation = fSetup;
297	<	setFortranBoxSize = fBox;
160	<	notifyFortranCutOffs = fCut;
161	<	}
293	>	/** Returns the center of the mass of the whole system.*/
294	>	Vector3d getCom();
295	>	/** Returns the center of the mass and Center of Mass velocity of
296	>	the whole system.*/
297	>	void getComAll(Vector3d& com,Vector3d& comVel);
298
299	<	int getNDF();
300	<	int getNDFraw();
301	<	int getNDFtranslational();
302	<	int getTotIntegrableObjects();
303	<	void setBox( double newBox[3] );
304	<	void setBoxM( double newBox[3][3] );
169	<	void getBoxM( double theBox[3][3] );
170	<	void scaleBox( double scale );
171	<
172	<	void setDefaultRcut( double theRcut );
173	<	void setDefaultRcut( double theRcut, double theRsw );
174	<	void checkCutOffs( void );
299	>	/** Returns intertia tensor for the entire system and system
300	>	Angular Momentum.*/
301	>	void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
302	>
303	>	/** Returns system angular momentum */
304	>	Vector3d getAngularMomentum();
305
306	<	double getRcut( void )  { return rCut; }
307	<	double getRlist( void ) { return rList; }
308	<	double getRsw( void )   { return rSw; }
309	<	double getMaxCutoff( void ) { return maxCutoff; }
310	<
311	<	void setTime( double theTime ) { currentTime = theTime; }
182	<	void incrTime( double the_dt ) { currentTime += the_dt; }
183	<	void decrTime( double the_dt ) { currentTime -= the_dt; }
184	<	double getTime( void ) { return currentTime; }
306	>	/** Returns volume of system as estimated by an ellipsoid defined
307	>	by the radii of gyration*/
308	>	void getGyrationalVolume(RealType &vol);
309	>	/** Overloaded version of gyrational volume that also returns
310	>	det(I) so dV/dr can be calculated*/
311	>	void getGyrationalVolume(RealType &vol, RealType &detI);
312
313	<	void wrapVector( double thePos[3] );
313	>	void update();
314	>	/**
315	>	* Do final bookkeeping before Force managers need their data.
316	>	*/
317	>	void prepareTopology();
318
188	–	SimState* getConfiguration( void ) { return myConfiguration; }
189	–
190	–	void addProperty(GenericData* prop);
191	–	GenericData* getProperty(const string& propName);
192	–	//vector<GenericData*>& getProperties()  {return properties;}
319
320	<	int getSeed(void) {  return seed; }
321	<	void setSeed(int theSeed) {  seed = theSeed;}
320	>	/** Returns the local index manager */
321	>	LocalIndexManager* getLocalIndexManager() {
322	>	return &localIndexMan_;
323	>	}
324
325	<	private:
325	>	int getMoleculeStampId(int globalIndex) {
326	>	//assert(globalIndex < molStampIds_.size())
327	>	return molStampIds_[globalIndex];
328	>	}
329
330	<	SimState* myConfiguration;
330	>	/** Returns the molecule stamp */
331	>	MoleculeStamp* getMoleculeStamp(int id) {
332	>	return moleculeStamps_[id];
333	>	}
334
335	<	int boxIsInit, haveRcut, haveRsw;
335	>	/** Return the total number of the molecule stamps */
336	>	int getNMoleculeStamp() {
337	>	return moleculeStamps_.size();
338	>	}
339	>	/**
340	>	* Finds a molecule with a specified global index
341	>	* @return a pointer point to found molecule
342	>	* @param index
343	>	*/
344	>	Molecule* getMoleculeByGlobalIndex(int index) {
345	>	MoleculeIterator i;
346	>	i = molecules_.find(index);
347
348	<	double rList, rCut; // variables for the neighborlist
349	<	double rSw;         // the switching radius
348	>	return i != molecules_.end() ? i->second : NULL;
349	>	}
350
351	<	double maxCutoff;
351	>	int getGlobalMolMembership(int id){
352	>	return globalMolMembership_[id];
353	>	}
354
355	<	double distXY;
356	<	double distYZ;
357	<	double distZX;
358	<
359	<	void calcHmatInv( void );
360	<	void calcBoxL();
214	<	double calcMaxCutOff();
355	>	/**
356	>	* returns a vector which maps the local atom index on this
357	>	* processor to the global atom index.  With only one processor,
358	>	* these should be identical.
359	>	*/
360	>	vector<int> getGlobalAtomIndices();
361
362	<	// private function to initialize the fortran side of the simulation
363	<	setFortranSim_TD setFsimulation;
362	>	/**
363	>	* returns a vector which maps the local cutoff group index on
364	>	* this processor to the global cutoff group index.  With only one
365	>	* processor, these should be identical.
366	>	*/
367	>	vector<int> getGlobalGroupIndices();
368
369	<	setFortranBox_TD setFortranBoxSize;
370	<
371	<	notifyFortranCutOff_TD notifyFortranCutOffs;
372	<
223	<	//Addtional Properties of SimInfo
224	<	map<string, GenericData*> properties;
225	<	void getFortranGroupArrays(SimInfo* info,
226	<	vector<int>& FglobalGroupMembership,
227	<	vector<double>& mfact);
369	>
370	>	string getFinalConfigFileName() {
371	>	return finalConfigFileName_;
372	>	}
373
374	+	void setFinalConfigFileName(const string& fileName) {
375	+	finalConfigFileName_ = fileName;
376	+	}
377
378	<	};
378	>	string getRawMetaData() {
379	>	return rawMetaData_;
380	>	}
381	>	void setRawMetaData(const string& rawMetaData) {
382	>	rawMetaData_ = rawMetaData;
383	>	}
384	>
385	>	string getDumpFileName() {
386	>	return dumpFileName_;
387	>	}
388	>
389	>	void setDumpFileName(const string& fileName) {
390	>	dumpFileName_ = fileName;
391	>	}
392
393	+	string getStatFileName() {
394	+	return statFileName_;
395	+	}
396	+
397	+	void setStatFileName(const string& fileName) {
398	+	statFileName_ = fileName;
399	+	}
400	+
401	+	string getRestFileName() {
402	+	return restFileName_;
403	+	}
404	+
405	+	void setRestFileName(const string& fileName) {
406	+	restFileName_ = fileName;
407	+	}
408
409	<	#endif
409	>	/**
410	>	* Sets GlobalGroupMembership
411	>	* @see #SimCreator::setGlobalIndex
412	>	*/
413	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
414	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
415	>	globalGroupMembership_ = globalGroupMembership;
416	>	}
417	>
418	>	/**
419	>	* Sets GlobalMolMembership
420	>	* @see #SimCreator::setGlobalIndex
421	>	*/
422	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
423	>	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
424	>	globalMolMembership_ = globalMolMembership;
425	>	}
426	>
427	>
428	>	bool isTopologyDone() {
429	>	return topologyDone_;
430	>	}
431	>
432	>	bool getCalcBoxDipole() {
433	>	return calcBoxDipole_;
434	>	}
435	>
436	>	bool getUseAtomicVirial() {
437	>	return useAtomicVirial_;
438	>	}
439	>
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	>	* 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	>	* clear all of the properties
454	>	*/
455	>	void clearProperties();
456	>
457	>	/**
458	>	* Returns all names of properties
459	>	* @return all names of properties
460	>	*/
461	>	vector<string> getPropertyNames();
462	>
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	>	* 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	>	/**
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 set of atom types present in this simulation */
490	>	set<AtomType*> getSimulatedAtomTypes();
491	>
492	>	friend ostream& operator <<(ostream& o, SimInfo& info);
493	>
494	>	void getCutoff(RealType& rcut, RealType& rsw);
495	>
496	>	private:
497	>
498	>	/** fill up the simtype struct and other simulation-related variables */
499	>	void setupSimVariables();
500	>
501	>
502	>	/** Determine if we need to accumulate the simulation box dipole */
503	>	void setupAccumulateBoxDipole();
504	>
505	>	/** Calculates the number of degress of freedom in the whole system */
506	>	void calcNdf();
507	>	void calcNdfRaw();
508	>	void calcNdfTrans();
509	>
510	>	/**
511	>	* Adds molecule stamp and the total number of the molecule with
512	>	* same molecule stamp in the whole system.
513	>	*/
514	>	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
515	>
516	>	// Other classes holdingn important information
517	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
518	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
519	>
520	>	///  Counts of local objects
521	>	int nAtoms_;              /**< number of atoms in local processor */
522	>	int nBonds_;              /**< number of bonds in local processor */
523	>	int nBends_;              /**< number of bends in local processor */
524	>	int nTorsions_;           /**< number of torsions in local processor */
525	>	int nInversions_;         /**< number of inversions in local processor */
526	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
527	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
528	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
529	>	int nConstraints_;        /**< number of constraints in local processors */
530	>	int nFluctuatingCharges_; /**< number of fluctuating charges in local processor */
531	>
532	>	/// Counts of global objects
533	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
534	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
535	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
536	>	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
537	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
538	>	int nGlobalFluctuatingCharges_;/**< number of fluctuating charges in this system (GLOBAL) */
539	>
540	>
541	>	/// Degress of freedom
542	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
543	>	int ndfLocal_;     /**< number of degrees of freedom (LOCAL, excludes constraints) */
544	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
545	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
546	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
547	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
548	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
549	>
550	>	/// logicals
551	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
552	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
553	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
554	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
555	>	bool usesFluctuatingCharges_; /**< are there fluctuating charges? */
556	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
557	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
558	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
559	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
560	>
561	>	public:
562	>	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
563	>	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
564	>	bool usesFluctuatingCharges() { return usesFluctuatingCharges_; }
565	>	bool usesAtomicVirial() { return usesAtomicVirial_; }
566	>	bool requiresPrepair() { return requiresPrepair_; }
567	>	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
568	>	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
569	>
570	>	private:
571	>	/// Data structures holding primary simulation objects
572	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
573	>
574	>	/// Stamps are templates for objects that are then used to create
575	>	/// groups of objects.  For example, a molecule stamp contains
576	>	/// information on how to build that molecule (i.e. the topology,
577	>	/// the atoms, the bonds, etc.)  Once the system is built, the
578	>	/// stamps are no longer useful.
579	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
580	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
581	>
582	>	/**
583	>	* A vector that maps between the global index of an atom, and the
584	>	* global index of cutoff group the atom belong to.  It is filled
585	>	* by SimCreator once and only once, since it never changed during
586	>	* the simulation.  It should be nGlobalAtoms_ in size.
587	>	*/
588	>	vector<int> globalGroupMembership_;
589	>	public:
590	>	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
591	>	private:
592	>
593	>	/**
594	>	* A vector that maps between the global index of an atom and the
595	>	* global index of the molecule the atom belongs to.  It is filled
596	>	* by SimCreator once and only once, since it is never changed
597	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
598	>	*/
599	>	vector<int> globalMolMembership_;
600	>
601	>	/**
602	>	* A vector that maps between the local index of an atom and the
603	>	* index of the AtomType.
604	>	*/
605	>	vector<int> identArray_;
606	>	public:
607	>	vector<int> getIdentArray() { return identArray_; }
608	>	private:
609	>
610	>	/**
611	>	* A vector which contains the fractional contribution of an
612	>	* atom's mass to the total mass of the cutoffGroup that atom
613	>	* belongs to.  In the case of single atom cutoff groups, the mass
614	>	* factor for that atom is 1.  For massless atoms, the factor is
615	>	* also 1.
616	>	*/
617	>	vector<RealType> massFactors_;
618	>	public:
619	>	vector<RealType> getMassFactors() { return massFactors_; }
620	>
621	>	PairList* getExcludedInteractions() { return &excludedInteractions_; }
622	>	PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
623	>	PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
624	>	PairList* getOneFourInteractions() { return &oneFourInteractions_; }
625	>
626	>	private:
627	>
628	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
629	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
630	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
631	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
632	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
633	>
634	>	PropertyMap properties_;       /**< Generic Properties can be added */
635	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
636	>
637	>	/**
638	>	* The reason to have a local index manager is that when molecule
639	>	* is migrating to other processors, the atoms and the
640	>	* rigid-bodies will release their local indices to
641	>	* LocalIndexManager. Combining the information of molecule
642	>	* migrating to current processor, Migrator class can query the
643	>	* LocalIndexManager to make a efficient data moving plan.
644	>	*/
645	>	LocalIndexManager localIndexMan_;
646	>
647	>	// unparsed MetaData block for storing in Dump and EOR files:
648	>	string rawMetaData_;
649	>
650	>	// file names
651	>	string finalConfigFileName_;
652	>	string dumpFileName_;
653	>	string statFileName_;
654	>	string restFileName_;
655	>
656	>
657	>	bool topologyDone_;  /** flag to indicate whether the topology has
658	>	been scanned and all the relevant
659	>	bookkeeping has been done*/
660	>
661	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
662	>	the simulation box dipole moment */
663	>
664	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
665	>	Atomic Virials to calculate the pressure */
666	>
667	>	public:
668	>	/**
669	>	* return an integral objects by its global index. In MPI
670	>	* version, if the StuntDouble with specified global index does
671	>	* not belong to local processor, a NULL will be return.
672	>	*/
673	>	StuntDouble* getIOIndexToIntegrableObject(int index);
674	>	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
675	>
676	>	private:
677	>	vector<StuntDouble*> IOIndexToIntegrableObject;
678	>
679	>	public:
680	>
681	>	/**
682	>	* Finds the processor where a molecule resides
683	>	* @return the id of the processor which contains the molecule
684	>	* @param globalIndex global Index of the molecule
685	>	*/
686	>	int getMolToProc(int globalIndex) {
687	>	//assert(globalIndex < molToProcMap_.size());
688	>	return molToProcMap_[globalIndex];
689	>	}
690	>
691	>	/**
692	>	* Set MolToProcMap array
693	>	* @see #SimCreator::divideMolecules
694	>	*/
695	>	void setMolToProcMap(const vector<int>& molToProcMap) {
696	>	molToProcMap_ = molToProcMap;
697	>	}
698	>
699	>	private:
700	>
701	>	/**
702	>	* The size of molToProcMap_ is equal to total number of molecules
703	>	* in the system.  It maps a molecule to the processor on which it
704	>	* resides. it is filled by SimCreator once and only once.
705	>	*/
706	>	vector<int> molToProcMap_;
707	>
708	>	};
709	>
710	>	} //namespace OpenMD
711	>	#endif //BRAINS_SIMMODEL_HPP
712	>

Comparing:
trunk/src/brains/SimInfo.hpp (property svn:keywords), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/brains/SimInfo.hpp (property svn:keywords), Revision 1744 by gezelter, Tue Jun 5 18:07:08 2012 UTC

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