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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 1534 by gezelter, Wed Dec 29 21:53:28 2010 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]  Vardeman & Gezelter, in progress (2009).
40	>	*/
41	>
42	>	/**
43	>	* @file SimInfo.hpp
44	>	* @author    tlin
45	>	* @date  11/02/2004
46	>	* @version 1.0
47	>	*/
48
49	<	#include <map>
50	<	#include <string>
49	>	#ifndef BRAINS_SIMMODEL_HPP
50	>	#define BRAINS_SIMMODEL_HPP
51	>
52	>	#include <iostream>
53	>	#include <set>
54	>	#include <utility>
55		#include <vector>
56
57	<	#include "primitives/Atom.hpp"
58	<	#include "primitives/RigidBody.hpp"
59	<	#include "primitives/Molecule.hpp"
60	<	#include "brains/Exclude.hpp"
61	<	#include "brains/SkipList.hpp"
62	<	#include "primitives/AbstractClasses.hpp"
63	<	#include "types/MakeStamps.hpp"
64	<	#include "brains/SimState.hpp"
65	<	#include "restraints/Restraints.hpp"
57	>	#include "brains/PairList.hpp"
58	>	#include "io/Globals.hpp"
59	>	#include "math/Vector3.hpp"
60	>	#include "math/SquareMatrix3.hpp"
61	>	#include "types/MoleculeStamp.hpp"
62	>	#include "UseTheForce/ForceField.hpp"
63	>	#include "utils/PropertyMap.hpp"
64	>	#include "utils/LocalIndexManager.hpp"
65	>	#include "nonbonded/SwitchingFunction.hpp"
66
67	<	#define __C
67	>	//another nonsense macro declaration
68	>	#define __OPENMD_C
69		#include "brains/fSimulation.h"
20	–	#include "utils/GenericData.hpp"
70
71	+	using namespace std;
72	+	namespace OpenMD{
73	+	enum CutoffMethod {
74	+	HARD,
75	+	SWITCHING_FUNCTION,
76	+	SHIFTED_POTENTIAL,
77	+	SHIFTED_FORCE
78	+	};
79
80	<	//#include "Minimizer.hpp"
81	<	//#include "minimizers/OOPSEMinimizer.hpp"
80	>	//forward decalration
81	>	class SnapshotManager;
82	>	class Molecule;
83	>	class SelectionManager;
84	>	class StuntDouble;
85
86	+	/**
87	+	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
88	+	*
89	+	* @brief One of the heavy-weight classes of OpenMD, SimInfo
90	+	* maintains objects and variables relating to the current
91	+	* simulation.  This includes the master list of Molecules.  The
92	+	* Molecule class maintains all of the concrete objects (Atoms,
93	+	* Bond, Bend, Torsions, Inversions, RigidBodies, CutoffGroups,
94	+	* Constraints). In both the single and parallel versions, Atoms and
95	+	* RigidBodies have both global and local indices.
96	+	*/
97	+	class SimInfo {
98	+	public:
99	+	typedef map<int, Molecule*>::iterator  MoleculeIterator;
100	+
101	+	/**
102	+	* Constructor of SimInfo
103	+	*
104	+	* @param molStampPairs MoleculeStamp Array. The first element of
105	+	* the pair is molecule stamp, the second element is the total
106	+	* number of molecules with the same molecule stamp in the system
107	+	*
108	+	* @param ff pointer of a concrete ForceField instance
109	+	*
110	+	* @param simParams
111	+	*/
112	+	SimInfo(ForceField* ff, Globals* simParams);
113	+	virtual ~SimInfo();
114
115	<	double roundMe( double x );
116	<	class OOPSEMinimizer;
117	<	class SimInfo{
115	>	/**
116	>	* Adds a molecule
117	>	*
118	>	* @return return true if adding successfully, return false if the
119	>	* molecule is already in SimInfo
120	>	*
121	>	* @param mol molecule to be added
122	>	*/
123	>	bool addMolecule(Molecule* mol);
124
125	<	public:
125	>	/**
126	>	* Removes a molecule from SimInfo
127	>	*
128	>	* @return true if removing successfully, return false if molecule
129	>	* is not in this SimInfo
130	>	*/
131	>	bool removeMolecule(Molecule* mol);
132
133	<	SimInfo();
134	<	~SimInfo();
133	>	/** Returns the total number of molecules in the system. */
134	>	int getNGlobalMolecules() {
135	>	return nGlobalMols_;
136	>	}
137
138	<	int n_atoms; // the number of atoms
139	<	Atom **atoms; // the array of atom objects
138	>	/** Returns the total number of atoms in the system. */
139	>	int getNGlobalAtoms() {
140	>	return nGlobalAtoms_;
141	>	}
142
143	<	vector<RigidBody*> rigidBodies;  // A vector of rigid bodies
144	<	vector<StuntDouble*> integrableObjects;
145	<
146	<	double tau[9]; // the stress tensor
143	>	/** Returns the total number of cutoff groups in the system. */
144	>	int getNGlobalCutoffGroups() {
145	>	return nGlobalCutoffGroups_;
146	>	}
147
148	<	int n_bonds;    // number of bends
149	<	int n_bends;    // number of bends
150	<	int n_torsions; // number of torsions
151	<	int n_oriented; // number of of atoms with orientation
152	<	int ndf;        // number of actual degrees of freedom
153	<	int ndfRaw;     // number of settable degrees of freedom
154	<	int ndfTrans;   // number of translational degrees of freedom
155	<	int nZconstraints; // the number of zConstraints
148	>	/**
149	>	* Returns the total number of integrable objects (total number of
150	>	* rigid bodies plus the total number of atoms which do not belong
151	>	* to the rigid bodies) in the system
152	>	*/
153	>	int getNGlobalIntegrableObjects() {
154	>	return nGlobalIntegrableObjects_;
155	>	}
156
157	<	int setTemp;   // boolean to set the temperature at each sampleTime
158	<	int resetIntegrator; // boolean to reset the integrator
157	>	/**
158	>	* Returns the total number of integrable objects (total number of
159	>	* rigid bodies plus the total number of atoms which do not belong
160	>	* to the rigid bodies) in the system
161	>	*/
162	>	int getNGlobalRigidBodies() {
163	>	return nGlobalRigidBodies_;
164	>	}
165
166	<	int n_dipoles; // number of dipoles
166	>	int getNGlobalConstraints();
167	>	/**
168	>	* Returns the number of local molecules.
169	>	* @return the number of local molecules
170	>	*/
171	>	int getNMolecules() {
172	>	return molecules_.size();
173	>	}
174
175	<	int n_exclude;
176	<	Exclude* excludes;  // the exclude list for ignoring pairs in fortran
177	<	int nGlobalExcludes;
178	<	int* globalExcludes; // same as above, but these guys participate in
62	<	// no long range forces.
175	>	/** Returns the number of local atoms */
176	>	unsigned int getNAtoms() {
177	>	return nAtoms_;
178	>	}
179
180	<	int* identArray;     // array of unique identifiers for the atoms
181	<	int* molMembershipArray;  // map of atom numbers onto molecule numbers
180	>	/** Returns the number of local bonds */
181	>	unsigned int getNBonds(){
182	>	return nBonds_;
183	>	}
184
185	<	int n_constraints; // the number of constraints on the system
185	>	/** Returns the number of local bends */
186	>	unsigned int getNBends() {
187	>	return nBends_;
188	>	}
189
190	<	int n_SRI;   // the number of short range interactions
190	>	/** Returns the number of local torsions */
191	>	unsigned int getNTorsions() {
192	>	return nTorsions_;
193	>	}
194
195	<	double lrPot; // the potential energy from the long range calculations.
195	>	/** Returns the number of local torsions */
196	>	unsigned int getNInversions() {
197	>	return nInversions_;
198	>	}
199	>	/** Returns the number of local rigid bodies */
200	>	unsigned int getNRigidBodies() {
201	>	return nRigidBodies_;
202	>	}
203
204	<	double Hmat[3][3];  // the periodic boundry conditions. The Hmat is the
205	<	// column vectors of the x, y, and z box vectors.
206	<	//   h1  h2  h3
207	<	// [ Xx  Yx  Zx ]
77	<	// [ Xy  Yy  Zy ]
78	<	// [ Xz  Yz  Zz ]
79	<	//
80	<	double HmatInv[3][3];
204	>	/** Returns the number of local integrable objects */
205	>	unsigned int getNIntegrableObjects() {
206	>	return nIntegrableObjects_;
207	>	}
208
209	<	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
210	<	double boxVol;
211	<	int orthoRhombic;
212	<
209	>	/** Returns the number of local cutoff groups */
210	>	unsigned int getNCutoffGroups() {
211	>	return nCutoffGroups_;
212	>	}
213
214	<	double dielectric;      // the dielectric of the medium for reaction field
214	>	/** Returns the total number of constraints in this SimInfo */
215	>	unsigned int getNConstraints() {
216	>	return nConstraints_;
217	>	}
218	>
219	>	/**
220	>	* Returns the first molecule in this SimInfo and intialize the iterator.
221	>	* @return the first molecule, return NULL if there is not molecule in this SimInfo
222	>	* @param i the iterator of molecule array (user shouldn't change it)
223	>	*/
224	>	Molecule* beginMolecule(MoleculeIterator& i);
225
226	<
227	<	int usePBC; // whether we use periodic boundry conditions.
228	<	int useDirectionalAtoms;
229	<	int useLennardJones;
230	<	int useElectrostatics;
231	<	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;
226	>	/**
227	>	* Returns the next avaliable Molecule based on the iterator.
228	>	* @return the next avaliable molecule, return NULL if reaching the end of the array
229	>	* @param i the iterator of molecule array
230	>	*/
231	>	Molecule* nextMolecule(MoleculeIterator& i);
232
233	<	double dt, run_time;           // the time step and total time
234	<	double sampleTime, statusTime; // the position and energy dump frequencies
235	<	double target_temp;            // the target temperature of the system
236	<	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;
233	>	/** Returns the number of degrees of freedom */
234	>	int getNdf() {
235	>	return ndf_ - getFdf();
236	>	}
237
238	<	int n_mol;           // n_molecules;
239	<	Molecule* molecules; // the array of molecules
240	<
241	<	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
238	>	/** Returns the number of raw degrees of freedom */
239	>	int getNdfRaw() {
240	>	return ndfRaw_;
241	>	}
242
243	<	OOPSEMinimizer* the_minimizer; // the energy minimizer
244	<	Restraints* restraint;
245	<	bool has_minimizer;
243	>	/** Returns the number of translational degrees of freedom */
244	>	int getNdfTrans() {
245	>	return ndfTrans_;
246	>	}
247
248	<	string finalName;  // the name of the eor file to be written
249	<	string sampleName; // the name of the dump file to be written
250	<	string statusName; // the name of the stat file to be written
248	>	/** sets the current number of frozen degrees of freedom */
249	>	void setFdf(int fdf) {
250	>	fdf_local = fdf;
251	>	}
252
253	<	int seed;                    //seed for random number generator
253	>	int getFdf();
254	>
255	>	//getNZconstraint and setNZconstraint ruin the coherence of
256	>	//SimInfo class, need refactoring
257	>
258	>	/** Returns the total number of z-constraint molecules in the system */
259	>	int getNZconstraint() {
260	>	return nZconstraint_;
261	>	}
262
263	<	int useSolidThermInt;  // is solid-state thermodynamic integration being used
264	<	int useLiquidThermInt; // is liquid thermodynamic integration being used
265	<	double thermIntLambda; // lambda for TI
266	<	double thermIntK;      // power of lambda for TI
267	<	double vRaw;           // unperturbed potential for TI
268	<	double vHarm;          // harmonic potential for TI
269	<	int i;                 // just an int
263	>	/**
264	>	* Sets the number of z-constraint molecules in the system.
265	>	*/
266	>	void setNZconstraint(int nZconstraint) {
267	>	nZconstraint_ = nZconstraint;
268	>	}
269	>
270	>	/** Returns the snapshot manager. */
271	>	SnapshotManager* getSnapshotManager() {
272	>	return sman_;
273	>	}
274
275	<	vector<double> mfact;
276	<	vector<int> FglobalGroupMembership;
277	<	int ngroup;
278	<	int* globalGroupMembership;
275	>	/** Sets the snapshot manager. */
276	>	void setSnapshotManager(SnapshotManager* sman);
277	>
278	>	/** Returns the force field */
279	>	ForceField* getForceField() {
280	>	return forceField_;
281	>	}
282
283	<	// refreshes the sim if things get changed (load balanceing, volume
284	<	// adjustment, etc.)
283	>	Globals* getSimParams() {
284	>	return simParams_;
285	>	}
286
287	<	void refreshSim( void );
288	<
287	>	/** Returns the velocity of center of mass of the whole system.*/
288	>	Vector3d getComVel();
289
290	<	// sets the internal function pointer to fortran.
290	>	/** Returns the center of the mass of the whole system.*/
291	>	Vector3d getCom();
292	>	/** Returns the center of the mass and Center of Mass velocity of
293	>	the whole system.*/
294	>	void getComAll(Vector3d& com,Vector3d& comVel);
295
296	+	/** Returns intertia tensor for the entire system and system
297	+	Angular Momentum.*/
298	+	void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
299	+
300	+	/** Returns system angular momentum */
301	+	Vector3d getAngularMomentum();
302
303	<	int getNDF();
304	<	int getNDFraw();
305	<	int getNDFtranslational();
306	<	int getTotIntegrableObjects();
307	<	void setBox( double newBox[3] );
308	<	void setBoxM( double newBox[3][3] );
309	<	void getBoxM( double theBox[3][3] );
310	<	void scaleBox( double scale );
311	<
168	<	void setDefaultRcut( double theRcut );
169	<	void setDefaultRcut( double theRcut, double theRsw );
170	<	void checkCutOffs( void );
171	<
172	<	double getRcut( void )  { return rCut; }
173	<	double getRlist( void ) { return rList; }
174	<	double getRsw( void )   { return rSw; }
175	<	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; }
181	<
182	<	void wrapVector( double thePos[3] );
183	<
184	<	SimState* getConfiguration( void ) { return myConfiguration; }
185	<
186	<	void addProperty(GenericData* prop);
187	<	GenericData* getProperty(const string& propName);
188	<	//vector<GenericData*>& getProperties()  {return properties;}
303	>	/** Returns volume of system as estimated by an ellipsoid defined
304	>	by the radii of gyration*/
305	>	void getGyrationalVolume(RealType &vol);
306	>	/** Overloaded version of gyrational volume that also returns
307	>	det(I) so dV/dr can be calculated*/
308	>	void getGyrationalVolume(RealType &vol, RealType &detI);
309	>	/** main driver function to interact with fortran during the
310	>	initialization and molecule migration */
311	>	void update();
312
313	<	int getSeed(void) {  return seed; }
314	<	void setSeed(int theSeed) {  seed = theSeed;}
313	>	/** Returns the local index manager */
314	>	LocalIndexManager* getLocalIndexManager() {
315	>	return &localIndexMan_;
316	>	}
317
318	<	private:
318	>	int getMoleculeStampId(int globalIndex) {
319	>	//assert(globalIndex < molStampIds_.size())
320	>	return molStampIds_[globalIndex];
321	>	}
322
323	<	SimState* myConfiguration;
323	>	/** Returns the molecule stamp */
324	>	MoleculeStamp* getMoleculeStamp(int id) {
325	>	return moleculeStamps_[id];
326	>	}
327
328	<	int boxIsInit, haveRcut, haveRsw;
328	>	/** Return the total number of the molecule stamps */
329	>	int getNMoleculeStamp() {
330	>	return moleculeStamps_.size();
331	>	}
332	>	/**
333	>	* Finds a molecule with a specified global index
334	>	* @return a pointer point to found molecule
335	>	* @param index
336	>	*/
337	>	Molecule* getMoleculeByGlobalIndex(int index) {
338	>	MoleculeIterator i;
339	>	i = molecules_.find(index);
340
341	<	double rList, rCut; // variables for the neighborlist
342	<	double rSw;         // the switching radius
341	>	return i != molecules_.end() ? i->second : NULL;
342	>	}
343
344	<	double maxCutoff;
344	>	int getGlobalMolMembership(int id){
345	>	return globalMolMembership_[id];
346	>	}
347
348	<	double distXY;
349	<	double distYZ;
350	<	double distZX;
207	<
208	<	void calcHmatInv( void );
209	<	void calcBoxL();
210	<	double calcMaxCutOff();
348	>	RealType getCutoffRadius() {
349	>	return cutoffRadius_;
350	>	}
351
352	<
353	<	//Addtional Properties of SimInfo
354	<	map<string, GenericData*> properties;
215	<	void getFortranGroupArrays(SimInfo* info,
216	<	vector<int>& FglobalGroupMembership,
217	<	vector<double>& mfact);
352	>	RealType getSwitchingRadius() {
353	>	return switchingRadius_;
354	>	}
355
356	+	RealType getListRadius() {
357	+	return listRadius_;
358	+	}
359	+
360	+	string getFinalConfigFileName() {
361	+	return finalConfigFileName_;
362	+	}
363
364	<	};
364	>	void setFinalConfigFileName(const string& fileName) {
365	>	finalConfigFileName_ = fileName;
366	>	}
367
368	+	string getRawMetaData() {
369	+	return rawMetaData_;
370	+	}
371	+	void setRawMetaData(const string& rawMetaData) {
372	+	rawMetaData_ = rawMetaData;
373	+	}
374	+
375	+	string getDumpFileName() {
376	+	return dumpFileName_;
377	+	}
378	+
379	+	void setDumpFileName(const string& fileName) {
380	+	dumpFileName_ = fileName;
381	+	}
382
383	<	#endif
383	>	string getStatFileName() {
384	>	return statFileName_;
385	>	}
386	>
387	>	void setStatFileName(const string& fileName) {
388	>	statFileName_ = fileName;
389	>	}
390	>
391	>	string getRestFileName() {
392	>	return restFileName_;
393	>	}
394	>
395	>	void setRestFileName(const string& fileName) {
396	>	restFileName_ = fileName;
397	>	}
398	>
399	>	/**
400	>	* Sets GlobalGroupMembership
401	>	* @see #SimCreator::setGlobalIndex
402	>	*/
403	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
404	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
405	>	globalGroupMembership_ = globalGroupMembership;
406	>	}
407	>
408	>	/**
409	>	* Sets GlobalMolMembership
410	>	* @see #SimCreator::setGlobalIndex
411	>	*/
412	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
413	>	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
414	>	globalMolMembership_ = globalMolMembership;
415	>	}
416	>
417	>
418	>	bool isFortranInitialized() {
419	>	return fortranInitialized_;
420	>	}
421	>
422	>	bool getCalcBoxDipole() {
423	>	return calcBoxDipole_;
424	>	}
425	>
426	>	bool getUseAtomicVirial() {
427	>	return useAtomicVirial_;
428	>	}
429	>
430	>	/**
431	>	* Adds property into property map
432	>	* @param genData GenericData to be added into PropertyMap
433	>	*/
434	>	void addProperty(GenericData* genData);
435	>
436	>	/**
437	>	* Removes property from PropertyMap by name
438	>	* @param propName the name of property to be removed
439	>	*/
440	>	void removeProperty(const string& propName);
441	>
442	>	/**
443	>	* clear all of the properties
444	>	*/
445	>	void clearProperties();
446	>
447	>	/**
448	>	* Returns all names of properties
449	>	* @return all names of properties
450	>	*/
451	>	vector<string> getPropertyNames();
452	>
453	>	/**
454	>	* Returns all of the properties in PropertyMap
455	>	* @return all of the properties in PropertyMap
456	>	*/
457	>	vector<GenericData*> getProperties();
458	>
459	>	/**
460	>	* Returns property
461	>	* @param propName name of property
462	>	* @return a pointer point to property with propName. If no property named propName
463	>	* exists, return NULL
464	>	*/
465	>	GenericData* getPropertyByName(const string& propName);
466	>
467	>	/**
468	>	* add all special interaction pairs (including excluded
469	>	* interactions) in a molecule into the appropriate lists.
470	>	*/
471	>	void addInteractionPairs(Molecule* mol);
472	>
473	>	/**
474	>	* remove all special interaction pairs which belong to a molecule
475	>	* from the appropriate lists.
476	>	*/
477	>	void removeInteractionPairs(Molecule* mol);
478	>
479	>
480	>	/** Returns the unique atom types of local processor in an array */
481	>	set<AtomType*> getUniqueAtomTypes();
482	>
483	>	/** Returns the set of atom types present in this simulation */
484	>	set<AtomType*> getSimulatedAtomTypes();
485	>
486	>	friend ostream& operator <<(ostream& o, SimInfo& info);
487	>
488	>	void getCutoff(RealType& rcut, RealType& rsw);
489	>
490	>	private:
491	>
492	>	/** fill up the simtype struct and other simulation-related variables */
493	>	void setupSimVariables();
494	>
495	>	/**
496	>	* Setup Fortran Simulation
497	>	* @see #setupFortranParallel
498	>	*/
499	>	void setupFortranSim();
500	>
501	>	/** Figure out the cutoff radius and cutoff method */
502	>	void setupCutoffs();
503	>	/** Figure out the switching radius and polynomial type for the switching function */
504	>	void setupSwitching();
505	>	/** Figure out the simulation variables associated with electrostatics */
506	>	void setupElectrostatics();
507	>	/** Figure out the neighbor list skin thickness */
508	>	void setupNeighborlists();
509	>
510	>	/** Determine if we need to accumulate the simulation box dipole */
511	>	void setupAccumulateBoxDipole();
512	>
513	>	/** Calculates the number of degress of freedom in the whole system */
514	>	void calcNdf();
515	>	void calcNdfRaw();
516	>	void calcNdfTrans();
517	>
518	>	/**
519	>	* Adds molecule stamp and the total number of the molecule with
520	>	* same molecule stamp in the whole system.
521	>	*/
522	>	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
523	>
524	>	// Other classes holdingn important information
525	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
526	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
527	>
528	>	///  Counts of local objects
529	>	int nAtoms_;              /**< number of atoms in local processor */
530	>	int nBonds_;              /**< number of bonds in local processor */
531	>	int nBends_;              /**< number of bends in local processor */
532	>	int nTorsions_;           /**< number of torsions in local processor */
533	>	int nInversions_;         /**< number of inversions in local processor */
534	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
535	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
536	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
537	>	int nConstraints_;        /**< number of constraints in local processors */
538	>
539	>	/// Counts of global objects
540	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
541	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
542	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
543	>	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
544	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
545	>
546	>	/// Degress of freedom
547	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
548	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
549	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
550	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
551	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
552	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
553	>
554	>	/// logicals
555	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
556	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
557	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
558	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
559	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
560	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
561	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
562	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
563	>
564	>	/// Data structures holding primary simulation objects
565	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
566	>	simtype fInfo_;                   /**< A dual struct shared by C++
567	>	and Fortran to pass
568	>	information about what types
569	>	of calculation are
570	>	required */
571	>
572	>	/// Stamps are templates for objects that are then used to create
573	>	/// groups of objects.  For example, a molecule stamp contains
574	>	/// information on how to build that molecule (i.e. the topology,
575	>	/// the atoms, the bonds, etc.)  Once the system is built, the
576	>	/// stamps are no longer useful.
577	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
578	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
579	>
580	>	/**
581	>	* A vector that maps between the global index of an atom, and the
582	>	* global index of cutoff group the atom belong to.  It is filled
583	>	* by SimCreator once and only once, since it never changed during
584	>	* the simulation.  It should be nGlobalAtoms_ in size.
585	>	*/
586	>	vector<int> globalGroupMembership_;
587	>
588	>	/**
589	>	* A vector that maps between the global index of an atom and the
590	>	* global index of the molecule the atom belongs to.  It is filled
591	>	* by SimCreator once and only once, since it is never changed
592	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
593	>	*/
594	>	vector<int> globalMolMembership_;
595	>
596	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
597	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
598	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
599	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
600	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
601	>
602	>	PropertyMap properties_;       /**< Generic Properties can be added */
603	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
604	>
605	>	/**
606	>	* The reason to have a local index manager is that when molecule
607	>	* is migrating to other processors, the atoms and the
608	>	* rigid-bodies will release their local indices to
609	>	* LocalIndexManager. Combining the information of molecule
610	>	* migrating to current processor, Migrator class can query the
611	>	* LocalIndexManager to make a efficient data moving plan.
612	>	*/
613	>	LocalIndexManager localIndexMan_;
614	>
615	>	// unparsed MetaData block for storing in Dump and EOR files:
616	>	string rawMetaData_;
617	>
618	>	// file names
619	>	string finalConfigFileName_;
620	>	string dumpFileName_;
621	>	string statFileName_;
622	>	string restFileName_;
623	>
624	>	RealType cutoffRadius_;         /**< cutoff radius for non-bonded interactions */
625	>	RealType switchingRadius_;      /**< inner radius of switching function */
626	>	RealType listRadius_;           /**< Verlet neighbor list radius */
627	>	RealType skinThickness_;        /**< Verlet neighbor list skin thickness */
628	>	CutoffMethod cutoffMethod_;     /**< Cutoff Method for most non-bonded interactions */
629	>	SwitchingFunctionType sft_;     /**< Type of switching function in use */
630	>
631	>	bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
632	>
633	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
634	>	the simulation box dipole moment */
635	>
636	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
637	>	Atomic Virials to calculate the pressure */
638	>
639	>	public:
640	>	/**
641	>	* return an integral objects by its global index. In MPI
642	>	* version, if the StuntDouble with specified global index does
643	>	* not belong to local processor, a NULL will be return.
644	>	*/
645	>	StuntDouble* getIOIndexToIntegrableObject(int index);
646	>	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
647	>
648	>	private:
649	>	vector<StuntDouble*> IOIndexToIntegrableObject;
650	>
651	>	public:
652	>
653	>	/**
654	>	* Finds the processor where a molecule resides
655	>	* @return the id of the processor which contains the molecule
656	>	* @param globalIndex global Index of the molecule
657	>	*/
658	>	int getMolToProc(int globalIndex) {
659	>	//assert(globalIndex < molToProcMap_.size());
660	>	return molToProcMap_[globalIndex];
661	>	}
662	>
663	>	/**
664	>	* Set MolToProcMap array
665	>	* @see #SimCreator::divideMolecules
666	>	*/
667	>	void setMolToProcMap(const vector<int>& molToProcMap) {
668	>	molToProcMap_ = molToProcMap;
669	>	}
670	>
671	>	private:
672	>
673	>	void setupFortranParallel();
674	>
675	>	/**
676	>	* The size of molToProcMap_ is equal to total number of molecules
677	>	* in the system.  It maps a molecule to the processor on which it
678	>	* resides. it is filled by SimCreator once and only once.
679	>	*/
680	>	vector<int> molToProcMap_;
681	>
682	>	};
683	>
684	>	} //namespace OpenMD
685	>	#endif //BRAINS_SIMMODEL_HPP
686	>

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 1534 by gezelter, Wed Dec 29 21:53:28 2010 UTC

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