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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 1581 by gezelter, Mon Jun 13 22:13:12 2011 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
68	<	#include "brains/fSimulation.h"
69	<	#include "utils/GenericData.hpp"
67	>	using namespace std;
68	>	namespace OpenMD{
69	>	//forward declaration
70	>	class SnapshotManager;
71	>	class Molecule;
72	>	class SelectionManager;
73	>	class StuntDouble;
74
75	+	/**
76	+	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
77	+	*
78	+	* @brief One of the heavy-weight classes of OpenMD, SimInfo
79	+	* maintains objects and variables relating to the current
80	+	* simulation.  This includes the master list of Molecules.  The
81	+	* Molecule class maintains all of the concrete objects (Atoms,
82	+	* Bond, Bend, Torsions, Inversions, RigidBodies, CutoffGroups,
83	+	* Constraints). In both the single and parallel versions, Atoms and
84	+	* RigidBodies have both global and local indices.
85	+	*/
86	+	class SimInfo {
87	+	public:
88	+	typedef map<int, Molecule*>::iterator  MoleculeIterator;
89	+
90	+	/**
91	+	* Constructor of SimInfo
92	+	*
93	+	* @param molStampPairs MoleculeStamp Array. The first element of
94	+	* the pair is molecule stamp, the second element is the total
95	+	* number of molecules with the same molecule stamp in the system
96	+	*
97	+	* @param ff pointer of a concrete ForceField instance
98	+	*
99	+	* @param simParams
100	+	*/
101	+	SimInfo(ForceField* ff, Globals* simParams);
102	+	virtual ~SimInfo();
103
104	<	//#include "Minimizer.hpp"
105	<	//#include "minimizers/OOPSEMinimizer.hpp"
104	>	/**
105	>	* Adds a molecule
106	>	*
107	>	* @return return true if adding successfully, return false if the
108	>	* molecule is already in SimInfo
109	>	*
110	>	* @param mol molecule to be added
111	>	*/
112	>	bool addMolecule(Molecule* mol);
113
114	+	/**
115	+	* Removes a molecule from SimInfo
116	+	*
117	+	* @return true if removing successfully, return false if molecule
118	+	* is not in this SimInfo
119	+	*/
120	+	bool removeMolecule(Molecule* mol);
121
122	<	double roundMe( double x );
123	<	class OOPSEMinimizer;
124	<	class SimInfo{
122	>	/** Returns the total number of molecules in the system. */
123	>	int getNGlobalMolecules() {
124	>	return nGlobalMols_;
125	>	}
126
127	<	public:
127	>	/** Returns the total number of atoms in the system. */
128	>	int getNGlobalAtoms() {
129	>	return nGlobalAtoms_;
130	>	}
131
132	<	SimInfo();
133	<	~SimInfo();
132	>	/** Returns the total number of cutoff groups in the system. */
133	>	int getNGlobalCutoffGroups() {
134	>	return nGlobalCutoffGroups_;
135	>	}
136
137	<	int n_atoms; // the number of atoms
138	<	Atom **atoms; // the array of atom objects
137	>	/**
138	>	* Returns the total number of integrable objects (total number of
139	>	* rigid bodies plus the total number of atoms which do not belong
140	>	* to the rigid bodies) in the system
141	>	*/
142	>	int getNGlobalIntegrableObjects() {
143	>	return nGlobalIntegrableObjects_;
144	>	}
145
146	<	vector<RigidBody*> rigidBodies;  // A vector of rigid bodies
147	<	vector<StuntDouble*> integrableObjects;
148	<
149	<	double tau[9]; // the stress tensor
146	>	/**
147	>	* Returns the total number of integrable objects (total number of
148	>	* rigid bodies plus the total number of atoms which do not belong
149	>	* to the rigid bodies) in the system
150	>	*/
151	>	int getNGlobalRigidBodies() {
152	>	return nGlobalRigidBodies_;
153	>	}
154
155	<	int n_bonds;    // number of bends
156	<	int n_bends;    // number of bends
157	<	int n_torsions; // number of torsions
158	<	int n_oriented; // number of of atoms with orientation
159	<	int ndf;        // number of actual degrees of freedom
160	<	int ndfRaw;     // number of settable degrees of freedom
161	<	int ndfTrans;   // number of translational degrees of freedom
162	<	int nZconstraints; // the number of zConstraints
155	>	int getNGlobalConstraints();
156	>	/**
157	>	* Returns the number of local molecules.
158	>	* @return the number of local molecules
159	>	*/
160	>	int getNMolecules() {
161	>	return molecules_.size();
162	>	}
163
164	<	int setTemp;   // boolean to set the temperature at each sampleTime
165	<	int resetIntegrator; // boolean to reset the integrator
164	>	/** Returns the number of local atoms */
165	>	unsigned int getNAtoms() {
166	>	return nAtoms_;
167	>	}
168
169	<	int n_dipoles; // number of dipoles
169	>	/** Returns the number of effective cutoff groups on local processor */
170	>	unsigned int getNLocalCutoffGroups();
171
172	<	int n_exclude;
173	<	Exclude* excludes;  // the exclude list for ignoring pairs in fortran
174	<	int nGlobalExcludes;
175	<	int* globalExcludes; // same as above, but these guys participate in
62	<	// no long range forces.
172	>	/** Returns the number of local bonds */
173	>	unsigned int getNBonds(){
174	>	return nBonds_;
175	>	}
176
177	<	int* identArray;     // array of unique identifiers for the atoms
178	<	int* molMembershipArray;  // map of atom numbers onto molecule numbers
177	>	/** Returns the number of local bends */
178	>	unsigned int getNBends() {
179	>	return nBends_;
180	>	}
181
182	<	int n_constraints; // the number of constraints on the system
182	>	/** Returns the number of local torsions */
183	>	unsigned int getNTorsions() {
184	>	return nTorsions_;
185	>	}
186
187	<	int n_SRI;   // the number of short range interactions
187	>	/** Returns the number of local torsions */
188	>	unsigned int getNInversions() {
189	>	return nInversions_;
190	>	}
191	>	/** Returns the number of local rigid bodies */
192	>	unsigned int getNRigidBodies() {
193	>	return nRigidBodies_;
194	>	}
195
196	<	double lrPot; // the potential energy from the long range calculations.
196	>	/** Returns the number of local integrable objects */
197	>	unsigned int getNIntegrableObjects() {
198	>	return nIntegrableObjects_;
199	>	}
200
201	<	double Hmat[3][3];  // the periodic boundry conditions. The Hmat is the
202	<	// column vectors of the x, y, and z box vectors.
203	<	//   h1  h2  h3
204	<	// [ Xx  Yx  Zx ]
77	<	// [ Xy  Yy  Zy ]
78	<	// [ Xz  Yz  Zz ]
79	<	//
80	<	double HmatInv[3][3];
201	>	/** Returns the number of local cutoff groups */
202	>	unsigned int getNCutoffGroups() {
203	>	return nCutoffGroups_;
204	>	}
205
206	<	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
207	<	double boxVol;
208	<	int orthoRhombic;
209	<
206	>	/** Returns the total number of constraints in this SimInfo */
207	>	unsigned int getNConstraints() {
208	>	return nConstraints_;
209	>	}
210	>
211	>	/**
212	>	* Returns the first molecule in this SimInfo and intialize the iterator.
213	>	* @return the first molecule, return NULL if there is not molecule in this SimInfo
214	>	* @param i the iterator of molecule array (user shouldn't change it)
215	>	*/
216	>	Molecule* beginMolecule(MoleculeIterator& i);
217
218	<	double dielectric;      // the dielectric of the medium for reaction field
218	>	/**
219	>	* Returns the next avaliable Molecule based on the iterator.
220	>	* @return the next avaliable molecule, return NULL if reaching the end of the array
221	>	* @param i the iterator of molecule array
222	>	*/
223	>	Molecule* nextMolecule(MoleculeIterator& i);
224
225	<
226	<	int usePBC; // whether we use periodic boundry conditions.
227	<	int useDirectionalAtoms;
228	<	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;
225	>	/** Returns the number of degrees of freedom */
226	>	int getNdf() {
227	>	return ndf_ - getFdf();
228	>	}
229
230	<	double dt, run_time;           // the time step and total time
231	<	double sampleTime, statusTime; // the position and energy dump frequencies
232	<	double target_temp;            // the target temperature of the system
233	<	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;
230	>	/** Returns the number of raw degrees of freedom */
231	>	int getNdfRaw() {
232	>	return ndfRaw_;
233	>	}
234
235	<	int n_mol;           // n_molecules;
236	<	Molecule* molecules; // the array of molecules
237	<
238	<	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
235	>	/** Returns the number of translational degrees of freedom */
236	>	int getNdfTrans() {
237	>	return ndfTrans_;
238	>	}
239
240	<	OOPSEMinimizer* the_minimizer; // the energy minimizer
241	<	Restraints* restraint;
242	<	bool has_minimizer;
240	>	/** sets the current number of frozen degrees of freedom */
241	>	void setFdf(int fdf) {
242	>	fdf_local = fdf;
243	>	}
244
245	<	string finalName;  // the name of the eor file to be written
246	<	string sampleName; // the name of the dump file to be written
247	<	string statusName; // the name of the stat file to be written
245	>	int getFdf();
246	>
247	>	//getNZconstraint and setNZconstraint ruin the coherence of
248	>	//SimInfo class, need refactoring
249	>
250	>	/** Returns the total number of z-constraint molecules in the system */
251	>	int getNZconstraint() {
252	>	return nZconstraint_;
253	>	}
254
255	<	int seed;                    //seed for random number generator
255	>	/**
256	>	* Sets the number of z-constraint molecules in the system.
257	>	*/
258	>	void setNZconstraint(int nZconstraint) {
259	>	nZconstraint_ = nZconstraint;
260	>	}
261	>
262	>	/** Returns the snapshot manager. */
263	>	SnapshotManager* getSnapshotManager() {
264	>	return sman_;
265	>	}
266
267	<	int useSolidThermInt;  // is solid-state thermodynamic integration being used
268	<	int useLiquidThermInt; // is liquid thermodynamic integration being used
269	<	double thermIntLambda; // lambda for TI
270	<	double thermIntK;      // power of lambda for TI
271	<	double vRaw;           // unperturbed potential for TI
272	<	double vHarm;          // harmonic potential for TI
273	<	int i;                 // just an int
267	>	/** Sets the snapshot manager. */
268	>	void setSnapshotManager(SnapshotManager* sman);
269	>
270	>	/** Returns the force field */
271	>	ForceField* getForceField() {
272	>	return forceField_;
273	>	}
274
275	<	vector<double> mfact;
276	<	vector<int> FglobalGroupMembership;
277	<	int ngroup;
148	<	int* globalGroupMembership;
275	>	Globals* getSimParams() {
276	>	return simParams_;
277	>	}
278
279	<	// refreshes the sim if things get changed (load balanceing, volume
280	<	// adjustment, etc.)
279	>	/** Returns the velocity of center of mass of the whole system.*/
280	>	Vector3d getComVel();
281
282	<	void refreshSim( void );
283	<
282	>	/** Returns the center of the mass of the whole system.*/
283	>	Vector3d getCom();
284	>	/** Returns the center of the mass and Center of Mass velocity of
285	>	the whole system.*/
286	>	void getComAll(Vector3d& com,Vector3d& comVel);
287
288	<	// sets the internal function pointer to fortran.
288	>	/** Returns intertia tensor for the entire system and system
289	>	Angular Momentum.*/
290	>	void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
291	>
292	>	/** Returns system angular momentum */
293	>	Vector3d getAngularMomentum();
294
295	+	/** Returns volume of system as estimated by an ellipsoid defined
296	+	by the radii of gyration*/
297	+	void getGyrationalVolume(RealType &vol);
298	+	/** Overloaded version of gyrational volume that also returns
299	+	det(I) so dV/dr can be calculated*/
300	+	void getGyrationalVolume(RealType &vol, RealType &detI);
301
302	<	int getNDF();
303	<	int getNDFraw();
304	<	int getNDFtranslational();
305	<	int getTotIntegrableObjects();
306	<	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 );
302	>	void update();
303	>	/**
304	>	* Do final bookkeeping before Force managers need their data.
305	>	*/
306	>	void prepareTopology();
307
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; }
308
309	<	void wrapVector( double thePos[3] );
310	<
311	<	SimState* getConfiguration( void ) { return myConfiguration; }
312	<
186	<	void addProperty(GenericData* prop);
187	<	GenericData* getProperty(const string& propName);
188	<	//vector<GenericData*>& getProperties()  {return properties;}
309	>	/** Returns the local index manager */
310	>	LocalIndexManager* getLocalIndexManager() {
311	>	return &localIndexMan_;
312	>	}
313
314	<	int getSeed(void) {  return seed; }
315	<	void setSeed(int theSeed) {  seed = theSeed;}
314	>	int getMoleculeStampId(int globalIndex) {
315	>	//assert(globalIndex < molStampIds_.size())
316	>	return molStampIds_[globalIndex];
317	>	}
318
319	<	private:
319	>	/** Returns the molecule stamp */
320	>	MoleculeStamp* getMoleculeStamp(int id) {
321	>	return moleculeStamps_[id];
322	>	}
323
324	<	SimState* myConfiguration;
324	>	/** Return the total number of the molecule stamps */
325	>	int getNMoleculeStamp() {
326	>	return moleculeStamps_.size();
327	>	}
328	>	/**
329	>	* Finds a molecule with a specified global index
330	>	* @return a pointer point to found molecule
331	>	* @param index
332	>	*/
333	>	Molecule* getMoleculeByGlobalIndex(int index) {
334	>	MoleculeIterator i;
335	>	i = molecules_.find(index);
336
337	<	int boxIsInit, haveRcut, haveRsw;
337	>	return i != molecules_.end() ? i->second : NULL;
338	>	}
339
340	<	double rList, rCut; // variables for the neighborlist
341	<	double rSw;         // the switching radius
340	>	int getGlobalMolMembership(int id){
341	>	return globalMolMembership_[id];
342	>	}
343
344	<	double maxCutoff;
344	>	/**
345	>	* returns a vector which maps the local atom index on this
346	>	* processor to the global atom index.  With only one processor,
347	>	* these should be identical.
348	>	*/
349	>	vector<int> getGlobalAtomIndices();
350
351	<	double distXY;
352	<	double distYZ;
353	<	double distZX;
354	<
355	<	void calcHmatInv( void );
356	<	void calcBoxL();
210	<	double calcMaxCutOff();
351	>	/**
352	>	* returns a vector which maps the local cutoff group index on
353	>	* this processor to the global cutoff group index.  With only one
354	>	* processor, these should be identical.
355	>	*/
356	>	vector<int> getGlobalGroupIndices();
357
358	<
359	<	//Addtional Properties of SimInfo
360	<	map<string, GenericData*> properties;
361	<	void getFortranGroupArrays(SimInfo* info,
216	<	vector<int>& FglobalGroupMembership,
217	<	vector<double>& mfact);
358	>
359	>	string getFinalConfigFileName() {
360	>	return finalConfigFileName_;
361	>	}
362
363	+	void setFinalConfigFileName(const string& fileName) {
364	+	finalConfigFileName_ = fileName;
365	+	}
366
367	<	};
367	>	string getRawMetaData() {
368	>	return rawMetaData_;
369	>	}
370	>	void setRawMetaData(const string& rawMetaData) {
371	>	rawMetaData_ = rawMetaData;
372	>	}
373	>
374	>	string getDumpFileName() {
375	>	return dumpFileName_;
376	>	}
377	>
378	>	void setDumpFileName(const string& fileName) {
379	>	dumpFileName_ = fileName;
380	>	}
381
382	+	string getStatFileName() {
383	+	return statFileName_;
384	+	}
385	+
386	+	void setStatFileName(const string& fileName) {
387	+	statFileName_ = fileName;
388	+	}
389	+
390	+	string getRestFileName() {
391	+	return restFileName_;
392	+	}
393	+
394	+	void setRestFileName(const string& fileName) {
395	+	restFileName_ = fileName;
396	+	}
397
398	<	#endif
398	>	/**
399	>	* Sets GlobalGroupMembership
400	>	* @see #SimCreator::setGlobalIndex
401	>	*/
402	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
403	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
404	>	globalGroupMembership_ = globalGroupMembership;
405	>	}
406	>
407	>	/**
408	>	* Sets GlobalMolMembership
409	>	* @see #SimCreator::setGlobalIndex
410	>	*/
411	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
412	>	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
413	>	globalMolMembership_ = globalMolMembership;
414	>	}
415	>
416	>
417	>	bool isTopologyDone() {
418	>	return topologyDone_;
419	>	}
420	>
421	>	bool getCalcBoxDipole() {
422	>	return calcBoxDipole_;
423	>	}
424	>
425	>	bool getUseAtomicVirial() {
426	>	return useAtomicVirial_;
427	>	}
428	>
429	>	/**
430	>	* Adds property into property map
431	>	* @param genData GenericData to be added into PropertyMap
432	>	*/
433	>	void addProperty(GenericData* genData);
434	>
435	>	/**
436	>	* Removes property from PropertyMap by name
437	>	* @param propName the name of property to be removed
438	>	*/
439	>	void removeProperty(const string& propName);
440	>
441	>	/**
442	>	* clear all of the properties
443	>	*/
444	>	void clearProperties();
445	>
446	>	/**
447	>	* Returns all names of properties
448	>	* @return all names of properties
449	>	*/
450	>	vector<string> getPropertyNames();
451	>
452	>	/**
453	>	* Returns all of the properties in PropertyMap
454	>	* @return all of the properties in PropertyMap
455	>	*/
456	>	vector<GenericData*> getProperties();
457	>
458	>	/**
459	>	* Returns property
460	>	* @param propName name of property
461	>	* @return a pointer point to property with propName. If no property named propName
462	>	* exists, return NULL
463	>	*/
464	>	GenericData* getPropertyByName(const string& propName);
465	>
466	>	/**
467	>	* add all special interaction pairs (including excluded
468	>	* interactions) in a molecule into the appropriate lists.
469	>	*/
470	>	void addInteractionPairs(Molecule* mol);
471	>
472	>	/**
473	>	* remove all special interaction pairs which belong to a molecule
474	>	* from the appropriate lists.
475	>	*/
476	>	void removeInteractionPairs(Molecule* mol);
477	>
478	>	/** Returns the set of atom types present in this simulation */
479	>	set<AtomType*> getSimulatedAtomTypes();
480	>
481	>	friend ostream& operator <<(ostream& o, SimInfo& info);
482	>
483	>	void getCutoff(RealType& rcut, RealType& rsw);
484	>
485	>	private:
486	>
487	>	/** fill up the simtype struct and other simulation-related variables */
488	>	void setupSimVariables();
489	>
490	>
491	>	/** Determine if we need to accumulate the simulation box dipole */
492	>	void setupAccumulateBoxDipole();
493	>
494	>	/** Calculates the number of degress of freedom in the whole system */
495	>	void calcNdf();
496	>	void calcNdfRaw();
497	>	void calcNdfTrans();
498	>
499	>	/**
500	>	* Adds molecule stamp and the total number of the molecule with
501	>	* same molecule stamp in the whole system.
502	>	*/
503	>	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
504	>
505	>	// Other classes holdingn important information
506	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
507	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
508	>
509	>	///  Counts of local objects
510	>	int nAtoms_;              /**< number of atoms in local processor */
511	>	int nBonds_;              /**< number of bonds in local processor */
512	>	int nBends_;              /**< number of bends in local processor */
513	>	int nTorsions_;           /**< number of torsions in local processor */
514	>	int nInversions_;         /**< number of inversions in local processor */
515	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
516	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
517	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
518	>	int nConstraints_;        /**< number of constraints in local processors */
519	>
520	>	/// Counts of global objects
521	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
522	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
523	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
524	>	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
525	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
526	>
527	>	/// Degress of freedom
528	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
529	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
530	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
531	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
532	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
533	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
534	>
535	>	/// logicals
536	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
537	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
538	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
539	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
540	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
541	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
542	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
543	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
544	>
545	>	public:
546	>	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
547	>	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
548	>	bool usesMetallicAtoms() { return usesMetallicAtoms_; }
549	>	bool usesAtomicVirial() { return usesAtomicVirial_; }
550	>	bool requiresPrepair() { return requiresPrepair_; }
551	>	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
552	>	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
553	>
554	>	private:
555	>	/// Data structures holding primary simulation objects
556	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
557	>
558	>	/// Stamps are templates for objects that are then used to create
559	>	/// groups of objects.  For example, a molecule stamp contains
560	>	/// information on how to build that molecule (i.e. the topology,
561	>	/// the atoms, the bonds, etc.)  Once the system is built, the
562	>	/// stamps are no longer useful.
563	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
564	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
565	>
566	>	/**
567	>	* A vector that maps between the global index of an atom, and the
568	>	* global index of cutoff group the atom belong to.  It is filled
569	>	* by SimCreator once and only once, since it never changed during
570	>	* the simulation.  It should be nGlobalAtoms_ in size.
571	>	*/
572	>	vector<int> globalGroupMembership_;
573	>	public:
574	>	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
575	>	private:
576	>
577	>	/**
578	>	* A vector that maps between the global index of an atom and the
579	>	* global index of the molecule the atom belongs to.  It is filled
580	>	* by SimCreator once and only once, since it is never changed
581	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
582	>	*/
583	>	vector<int> globalMolMembership_;
584	>
585	>	/**
586	>	* A vector that maps between the local index of an atom and the
587	>	* index of the AtomType.
588	>	*/
589	>	vector<int> identArray_;
590	>	public:
591	>	vector<int> getIdentArray() { return identArray_; }
592	>	private:
593	>
594	>	/**
595	>	* A vector which contains the fractional contribution of an
596	>	* atom's mass to the total mass of the cutoffGroup that atom
597	>	* belongs to.  In the case of single atom cutoff groups, the mass
598	>	* factor for that atom is 1.  For massless atoms, the factor is
599	>	* also 1.
600	>	*/
601	>	vector<RealType> massFactors_;
602	>	public:
603	>	vector<RealType> getMassFactors() { return massFactors_; }
604	>
605	>	PairList getExcludedInteractions() { return excludedInteractions_; }
606	>	PairList getOneTwoInteractions() { return oneTwoInteractions_; }
607	>	PairList getOneThreeInteractions() { return oneThreeInteractions_; }
608	>	PairList getOneFourInteractions() { return oneFourInteractions_; }
609	>
610	>	private:
611	>
612	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
613	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
614	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
615	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
616	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
617	>
618	>	PropertyMap properties_;       /**< Generic Properties can be added */
619	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
620	>
621	>	/**
622	>	* The reason to have a local index manager is that when molecule
623	>	* is migrating to other processors, the atoms and the
624	>	* rigid-bodies will release their local indices to
625	>	* LocalIndexManager. Combining the information of molecule
626	>	* migrating to current processor, Migrator class can query the
627	>	* LocalIndexManager to make a efficient data moving plan.
628	>	*/
629	>	LocalIndexManager localIndexMan_;
630	>
631	>	// unparsed MetaData block for storing in Dump and EOR files:
632	>	string rawMetaData_;
633	>
634	>	// file names
635	>	string finalConfigFileName_;
636	>	string dumpFileName_;
637	>	string statFileName_;
638	>	string restFileName_;
639	>
640	>
641	>	bool topologyDone_;  /** flag to indicate whether the topology has
642	>	been scanned and all the relevant
643	>	bookkeeping has been done*/
644	>
645	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
646	>	the simulation box dipole moment */
647	>
648	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
649	>	Atomic Virials to calculate the pressure */
650	>
651	>	public:
652	>	/**
653	>	* return an integral objects by its global index. In MPI
654	>	* version, if the StuntDouble with specified global index does
655	>	* not belong to local processor, a NULL will be return.
656	>	*/
657	>	StuntDouble* getIOIndexToIntegrableObject(int index);
658	>	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
659	>
660	>	private:
661	>	vector<StuntDouble*> IOIndexToIntegrableObject;
662	>
663	>	public:
664	>
665	>	/**
666	>	* Finds the processor where a molecule resides
667	>	* @return the id of the processor which contains the molecule
668	>	* @param globalIndex global Index of the molecule
669	>	*/
670	>	int getMolToProc(int globalIndex) {
671	>	//assert(globalIndex < molToProcMap_.size());
672	>	return molToProcMap_[globalIndex];
673	>	}
674	>
675	>	/**
676	>	* Set MolToProcMap array
677	>	* @see #SimCreator::divideMolecules
678	>	*/
679	>	void setMolToProcMap(const vector<int>& molToProcMap) {
680	>	molToProcMap_ = molToProcMap;
681	>	}
682	>
683	>	private:
684	>
685	>	/**
686	>	* The size of molToProcMap_ is equal to total number of molecules
687	>	* in the system.  It maps a molecule to the processor on which it
688	>	* resides. it is filled by SimCreator once and only once.
689	>	*/
690	>	vector<int> molToProcMap_;
691	>
692	>	};
693	>
694	>	} //namespace OpenMD
695	>	#endif //BRAINS_SIMMODEL_HPP
696	>

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 1581 by gezelter, Mon Jun 13 22:13:12 2011 UTC

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