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trunk/src/brains/SimInfo.hpp (file contents), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/brains/SimInfo.hpp (file contents), Revision 1545 by gezelter, Fri Apr 8 21:25:19 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
67	>	//another nonsense macro declaration
68	>	#define __OPENMD_C
69		#include "brains/fSimulation.h"
20	–	#include "UseTheForce/fortranWrapDefines.hpp"
21	–	#include "utils/GenericData.hpp"
70
71	+	using namespace std;
72	+	namespace OpenMD{
73	+	//forward decalration
74	+	class SnapshotManager;
75	+	class Molecule;
76	+	class SelectionManager;
77	+	class StuntDouble;
78
79	<	//#include "Minimizer.hpp"
80	<	//#include "minimizers/OOPSEMinimizer.hpp"
79	>	/**
80	>	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
81	>	*
82	>	* @brief One of the heavy-weight classes of OpenMD, SimInfo
83	>	* maintains objects and variables relating to the current
84	>	* simulation.  This includes the master list of Molecules.  The
85	>	* Molecule class maintains all of the concrete objects (Atoms,
86	>	* Bond, Bend, Torsions, Inversions, RigidBodies, CutoffGroups,
87	>	* Constraints). In both the single and parallel versions, Atoms and
88	>	* RigidBodies have both global and local indices.
89	>	*/
90	>	class SimInfo {
91	>	public:
92	>	typedef map<int, Molecule*>::iterator  MoleculeIterator;
93	>
94	>	/**
95	>	* Constructor of SimInfo
96	>	*
97	>	* @param molStampPairs MoleculeStamp Array. The first element of
98	>	* the pair is molecule stamp, the second element is the total
99	>	* number of molecules with the same molecule stamp in the system
100	>	*
101	>	* @param ff pointer of a concrete ForceField instance
102	>	*
103	>	* @param simParams
104	>	*/
105	>	SimInfo(ForceField* ff, Globals* simParams);
106	>	virtual ~SimInfo();
107
108	+	/**
109	+	* Adds a molecule
110	+	*
111	+	* @return return true if adding successfully, return false if the
112	+	* molecule is already in SimInfo
113	+	*
114	+	* @param mol molecule to be added
115	+	*/
116	+	bool addMolecule(Molecule* mol);
117
118	<	double roundMe( double x );
119	<	class OOPSEMinimizer;
120	<	class SimInfo{
118	>	/**
119	>	* Removes a molecule from SimInfo
120	>	*
121	>	* @return true if removing successfully, return false if molecule
122	>	* is not in this SimInfo
123	>	*/
124	>	bool removeMolecule(Molecule* mol);
125
126	<	public:
126	>	/** Returns the total number of molecules in the system. */
127	>	int getNGlobalMolecules() {
128	>	return nGlobalMols_;
129	>	}
130
131	<	SimInfo();
132	<	~SimInfo();
131	>	/** Returns the total number of atoms in the system. */
132	>	int getNGlobalAtoms() {
133	>	return nGlobalAtoms_;
134	>	}
135
136	<	int n_atoms; // the number of atoms
137	<	Atom **atoms; // the array of atom objects
136	>	/** Returns the total number of cutoff groups in the system. */
137	>	int getNGlobalCutoffGroups() {
138	>	return nGlobalCutoffGroups_;
139	>	}
140
141	<	vector<RigidBody*> rigidBodies;  // A vector of rigid bodies
142	<	vector<StuntDouble*> integrableObjects;
143	<
144	<	double tau[9]; // the stress tensor
141	>	/**
142	>	* Returns the total number of integrable objects (total number of
143	>	* rigid bodies plus the total number of atoms which do not belong
144	>	* to the rigid bodies) in the system
145	>	*/
146	>	int getNGlobalIntegrableObjects() {
147	>	return nGlobalIntegrableObjects_;
148	>	}
149
150	<	int n_bonds;    // number of bends
151	<	int n_bends;    // number of bends
152	<	int n_torsions; // number of torsions
153	<	int n_oriented; // number of of atoms with orientation
154	<	int ndf;        // number of actual degrees of freedom
155	<	int ndfRaw;     // number of settable degrees of freedom
156	<	int ndfTrans;   // number of translational degrees of freedom
157	<	int nZconstraints; // the number of zConstraints
150	>	/**
151	>	* Returns the total number of integrable objects (total number of
152	>	* rigid bodies plus the total number of atoms which do not belong
153	>	* to the rigid bodies) in the system
154	>	*/
155	>	int getNGlobalRigidBodies() {
156	>	return nGlobalRigidBodies_;
157	>	}
158
159	<	int setTemp;   // boolean to set the temperature at each sampleTime
160	<	int resetIntegrator; // boolean to reset the integrator
159	>	int getNGlobalConstraints();
160	>	/**
161	>	* Returns the number of local molecules.
162	>	* @return the number of local molecules
163	>	*/
164	>	int getNMolecules() {
165	>	return molecules_.size();
166	>	}
167
168	<	int n_dipoles; // number of dipoles
168	>	/** Returns the number of local atoms */
169	>	unsigned int getNAtoms() {
170	>	return nAtoms_;
171	>	}
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 number of degrees of freedom */
227	>	int getNdf() {
228	>	return ndf_ - getFdf();
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 raw degrees of freedom */
232	>	int getNdfRaw() {
233	>	return ndfRaw_;
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 translational degrees of freedom */
237	>	int getNdfTrans() {
238	>	return ndfTrans_;
239	>	}
240
241	<	OOPSEMinimizer* the_minimizer; // the energy minimizer
242	<	Restraints* restraint;
243	<	bool has_minimizer;
241	>	/** sets the current number of frozen degrees of freedom */
242	>	void setFdf(int fdf) {
243	>	fdf_local = fdf;
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	>	int getFdf();
247	>
248	>	//getNZconstraint and setNZconstraint ruin the coherence of
249	>	//SimInfo class, need refactoring
250	>
251	>	/** Returns the total number of z-constraint molecules in the system */
252	>	int getNZconstraint() {
253	>	return nZconstraint_;
254	>	}
255
256	<	int seed;                    //seed for random number generator
256	>	/**
257	>	* Sets the number of z-constraint molecules in the system.
258	>	*/
259	>	void setNZconstraint(int nZconstraint) {
260	>	nZconstraint_ = nZconstraint;
261	>	}
262	>
263	>	/** Returns the snapshot manager. */
264	>	SnapshotManager* getSnapshotManager() {
265	>	return sman_;
266	>	}
267
268	<	int useSolidThermInt;  // is solid-state thermodynamic integration being used
269	<	int useLiquidThermInt; // is liquid thermodynamic integration being used
270	<	double thermIntLambda; // lambda for TI
271	<	double thermIntK;      // power of lambda for TI
272	<	double vRaw;           // unperturbed potential for TI
273	<	double vHarm;          // harmonic potential for TI
274	<	int i;                 // just an int
268	>	/** Sets the snapshot manager. */
269	>	void setSnapshotManager(SnapshotManager* sman);
270	>
271	>	/** Returns the force field */
272	>	ForceField* getForceField() {
273	>	return forceField_;
274	>	}
275
276	<	vector<double> mfact;
277	<	vector<int> FglobalGroupMembership;
278	<	int ngroup;
145	<	int* globalGroupMembership;
276	>	Globals* getSimParams() {
277	>	return simParams_;
278	>	}
279
280	<	// refreshes the sim if things get changed (load balanceing, volume
281	<	// adjustment, etc.)
280	>	/** Returns the velocity of center of mass of the whole system.*/
281	>	Vector3d getComVel();
282
283	<	void refreshSim( void );
284	<
283	>	/** Returns the center of the mass of the whole system.*/
284	>	Vector3d getCom();
285	>	/** Returns the center of the mass and Center of Mass velocity of
286	>	the whole system.*/
287	>	void getComAll(Vector3d& com,Vector3d& comVel);
288
289	<	// sets the internal function pointer to fortran.
289	>	/** Returns intertia tensor for the entire system and system
290	>	Angular Momentum.*/
291	>	void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
292	>
293	>	/** Returns system angular momentum */
294	>	Vector3d getAngularMomentum();
295
296	<	void setInternal( setFortranSim_TD fSetup,
297	<	setFortranBox_TD fBox,
298	<	notifyFortranCutOff_TD fCut){
299	<	setFsimulation = fSetup;
300	<	setFortranBoxSize = fBox;
301	<	notifyFortranCutOffs = fCut;
161	<	}
296	>	/** Returns volume of system as estimated by an ellipsoid defined
297	>	by the radii of gyration*/
298	>	void getGyrationalVolume(RealType &vol);
299	>	/** Overloaded version of gyrational volume that also returns
300	>	det(I) so dV/dr can be calculated*/
301	>	void getGyrationalVolume(RealType &vol, RealType &detI);
302
303	<	int getNDF();
304	<	int getNDFraw();
305	<	int getNDFtranslational();
306	<	int getTotIntegrableObjects();
307	<	void setBox( double newBox[3] );
168	<	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 );
303	>	void update();
304	>	/**
305	>	* Setup Fortran Simulation
306	>	*/
307	>	void setupFortran();
308
176	–	double getRcut( void )  { return rCut; }
177	–	double getRlist( void ) { return rList; }
178	–	double getRsw( void )   { return rSw; }
179	–	double getMaxCutoff( void ) { return maxCutoff; }
180	–
181	–	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; }
309
310	<	void wrapVector( double thePos[3] );
310	>	/** Returns the local index manager */
311	>	LocalIndexManager* getLocalIndexManager() {
312	>	return &localIndexMan_;
313	>	}
314
315	<	SimState* getConfiguration( void ) { return myConfiguration; }
316	<
317	<	void addProperty(GenericData* prop);
318	<	GenericData* getProperty(const string& propName);
192	<	//vector<GenericData*>& getProperties()  {return properties;}
315	>	int getMoleculeStampId(int globalIndex) {
316	>	//assert(globalIndex < molStampIds_.size())
317	>	return molStampIds_[globalIndex];
318	>	}
319
320	<	int getSeed(void) {  return seed; }
321	<	void setSeed(int theSeed) {  seed = theSeed;}
320	>	/** Returns the molecule stamp */
321	>	MoleculeStamp* getMoleculeStamp(int id) {
322	>	return moleculeStamps_[id];
323	>	}
324
325	<	private:
325	>	/** Return the total number of the molecule stamps */
326	>	int getNMoleculeStamp() {
327	>	return moleculeStamps_.size();
328	>	}
329	>	/**
330	>	* Finds a molecule with a specified global index
331	>	* @return a pointer point to found molecule
332	>	* @param index
333	>	*/
334	>	Molecule* getMoleculeByGlobalIndex(int index) {
335	>	MoleculeIterator i;
336	>	i = molecules_.find(index);
337
338	<	SimState* myConfiguration;
338	>	return i != molecules_.end() ? i->second : NULL;
339	>	}
340
341	<	int boxIsInit, haveRcut, haveRsw;
341	>	int getGlobalMolMembership(int id){
342	>	return globalMolMembership_[id];
343	>	}
344	>
345	>	string getFinalConfigFileName() {
346	>	return finalConfigFileName_;
347	>	}
348
349	<	double rList, rCut; // variables for the neighborlist
350	<	double rSw;         // the switching radius
349	>	void setFinalConfigFileName(const string& fileName) {
350	>	finalConfigFileName_ = fileName;
351	>	}
352
353	<	double maxCutoff;
353	>	string getRawMetaData() {
354	>	return rawMetaData_;
355	>	}
356	>	void setRawMetaData(const string& rawMetaData) {
357	>	rawMetaData_ = rawMetaData;
358	>	}
359	>
360	>	string getDumpFileName() {
361	>	return dumpFileName_;
362	>	}
363	>
364	>	void setDumpFileName(const string& fileName) {
365	>	dumpFileName_ = fileName;
366	>	}
367
368	<	double distXY;
369	<	double distYZ;
370	<	double distZX;
371	<
372	<	void calcHmatInv( void );
373	<	void calcBoxL();
374	<	double calcMaxCutOff();
368	>	string getStatFileName() {
369	>	return statFileName_;
370	>	}
371	>
372	>	void setStatFileName(const string& fileName) {
373	>	statFileName_ = fileName;
374	>	}
375	>
376	>	string getRestFileName() {
377	>	return restFileName_;
378	>	}
379	>
380	>	void setRestFileName(const string& fileName) {
381	>	restFileName_ = fileName;
382	>	}
383
384	<	// private function to initialize the fortran side of the simulation
385	<	setFortranSim_TD setFsimulation;
384	>	/**
385	>	* Sets GlobalGroupMembership
386	>	* @see #SimCreator::setGlobalIndex
387	>	*/
388	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
389	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
390	>	globalGroupMembership_ = globalGroupMembership;
391	>	}
392
393	<	setFortranBox_TD setFortranBoxSize;
394	<
395	<	notifyFortranCutOff_TD notifyFortranCutOffs;
396	<
397	<	//Addtional Properties of SimInfo
398	<	map<string, GenericData*> properties;
399	<	void getFortranGroupArrays(SimInfo* info,
400	<	vector<int>& FglobalGroupMembership,
227	<	vector<double>& mfact);
393	>	/**
394	>	* Sets GlobalMolMembership
395	>	* @see #SimCreator::setGlobalIndex
396	>	*/
397	>	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
398	>	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
399	>	globalMolMembership_ = globalMolMembership;
400	>	}
401
402
403	<	};
403	>	bool isFortranInitialized() {
404	>	return fortranInitialized_;
405	>	}
406	>
407	>	bool getCalcBoxDipole() {
408	>	return calcBoxDipole_;
409	>	}
410
411	+	bool getUseAtomicVirial() {
412	+	return useAtomicVirial_;
413	+	}
414
415	<	#endif
415	>	/**
416	>	* Adds property into property map
417	>	* @param genData GenericData to be added into PropertyMap
418	>	*/
419	>	void addProperty(GenericData* genData);
420	>
421	>	/**
422	>	* Removes property from PropertyMap by name
423	>	* @param propName the name of property to be removed
424	>	*/
425	>	void removeProperty(const string& propName);
426	>
427	>	/**
428	>	* clear all of the properties
429	>	*/
430	>	void clearProperties();
431	>
432	>	/**
433	>	* Returns all names of properties
434	>	* @return all names of properties
435	>	*/
436	>	vector<string> getPropertyNames();
437	>
438	>	/**
439	>	* Returns all of the properties in PropertyMap
440	>	* @return all of the properties in PropertyMap
441	>	*/
442	>	vector<GenericData*> getProperties();
443	>
444	>	/**
445	>	* Returns property
446	>	* @param propName name of property
447	>	* @return a pointer point to property with propName. If no property named propName
448	>	* exists, return NULL
449	>	*/
450	>	GenericData* getPropertyByName(const string& propName);
451	>
452	>	/**
453	>	* add all special interaction pairs (including excluded
454	>	* interactions) in a molecule into the appropriate lists.
455	>	*/
456	>	void addInteractionPairs(Molecule* mol);
457	>
458	>	/**
459	>	* remove all special interaction pairs which belong to a molecule
460	>	* from the appropriate lists.
461	>	*/
462	>	void removeInteractionPairs(Molecule* mol);
463	>
464	>	/** Returns the set of atom types present in this simulation */
465	>	set<AtomType*> getSimulatedAtomTypes();
466	>
467	>	friend ostream& operator <<(ostream& o, SimInfo& info);
468	>
469	>	void getCutoff(RealType& rcut, RealType& rsw);
470	>
471	>	private:
472	>
473	>	/** fill up the simtype struct and other simulation-related variables */
474	>	void setupSimVariables();
475	>
476	>
477	>	/** Determine if we need to accumulate the simulation box dipole */
478	>	void setupAccumulateBoxDipole();
479	>
480	>	/** Calculates the number of degress of freedom in the whole system */
481	>	void calcNdf();
482	>	void calcNdfRaw();
483	>	void calcNdfTrans();
484	>
485	>	/**
486	>	* Adds molecule stamp and the total number of the molecule with
487	>	* same molecule stamp in the whole system.
488	>	*/
489	>	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
490	>
491	>	// Other classes holdingn important information
492	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
493	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
494	>
495	>	///  Counts of local objects
496	>	int nAtoms_;              /**< number of atoms in local processor */
497	>	int nBonds_;              /**< number of bonds in local processor */
498	>	int nBends_;              /**< number of bends in local processor */
499	>	int nTorsions_;           /**< number of torsions in local processor */
500	>	int nInversions_;         /**< number of inversions in local processor */
501	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
502	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
503	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
504	>	int nConstraints_;        /**< number of constraints in local processors */
505	>
506	>	/// Counts of global objects
507	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
508	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
509	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
510	>	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
511	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
512	>
513	>	/// Degress of freedom
514	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
515	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
516	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
517	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
518	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
519	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
520	>
521	>	/// logicals
522	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
523	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
524	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
525	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
526	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
527	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
528	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
529	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
530	>
531	>	public:
532	>	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
533	>	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
534	>	bool usesMetallicAtoms() { return usesMetallicAtoms_; }
535	>
536	>	private:
537	>	/// Data structures holding primary simulation objects
538	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
539	>	simtype fInfo_;                   /**< A dual struct shared by C++
540	>	and Fortran to pass
541	>	information about what types
542	>	of calculation are
543	>	required */
544	>
545	>	/// Stamps are templates for objects that are then used to create
546	>	/// groups of objects.  For example, a molecule stamp contains
547	>	/// information on how to build that molecule (i.e. the topology,
548	>	/// the atoms, the bonds, etc.)  Once the system is built, the
549	>	/// stamps are no longer useful.
550	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
551	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
552	>
553	>	/**
554	>	* A vector that maps between the global index of an atom, and the
555	>	* global index of cutoff group the atom belong to.  It is filled
556	>	* by SimCreator once and only once, since it never changed during
557	>	* the simulation.  It should be nGlobalAtoms_ in size.
558	>	*/
559	>	vector<int> globalGroupMembership_;
560	>
561	>	/**
562	>	* A vector that maps between the global index of an atom and the
563	>	* global index of the molecule the atom belongs to.  It is filled
564	>	* by SimCreator once and only once, since it is never changed
565	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
566	>	*/
567	>	vector<int> globalMolMembership_;
568	>
569	>	/**
570	>	* A vector that maps between the local index of an atom and the
571	>	* index of the AtomType.
572	>	*/
573	>	vector<int> identArray_;
574	>	public:
575	>	vector<int> getIdentArray() { return identArray_; }
576	>	private:
577	>
578	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
579	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
580	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
581	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
582	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
583	>
584	>	PropertyMap properties_;       /**< Generic Properties can be added */
585	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
586	>
587	>	/**
588	>	* The reason to have a local index manager is that when molecule
589	>	* is migrating to other processors, the atoms and the
590	>	* rigid-bodies will release their local indices to
591	>	* LocalIndexManager. Combining the information of molecule
592	>	* migrating to current processor, Migrator class can query the
593	>	* LocalIndexManager to make a efficient data moving plan.
594	>	*/
595	>	LocalIndexManager localIndexMan_;
596	>
597	>	// unparsed MetaData block for storing in Dump and EOR files:
598	>	string rawMetaData_;
599	>
600	>	// file names
601	>	string finalConfigFileName_;
602	>	string dumpFileName_;
603	>	string statFileName_;
604	>	string restFileName_;
605	>
606	>
607	>	bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
608	>
609	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
610	>	the simulation box dipole moment */
611	>
612	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
613	>	Atomic Virials to calculate the pressure */
614	>
615	>	public:
616	>	/**
617	>	* return an integral objects by its global index. In MPI
618	>	* version, if the StuntDouble with specified global index does
619	>	* not belong to local processor, a NULL will be return.
620	>	*/
621	>	StuntDouble* getIOIndexToIntegrableObject(int index);
622	>	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
623	>
624	>	private:
625	>	vector<StuntDouble*> IOIndexToIntegrableObject;
626	>
627	>	public:
628	>
629	>	/**
630	>	* Finds the processor where a molecule resides
631	>	* @return the id of the processor which contains the molecule
632	>	* @param globalIndex global Index of the molecule
633	>	*/
634	>	int getMolToProc(int globalIndex) {
635	>	//assert(globalIndex < molToProcMap_.size());
636	>	return molToProcMap_[globalIndex];
637	>	}
638	>
639	>	/**
640	>	* Set MolToProcMap array
641	>	* @see #SimCreator::divideMolecules
642	>	*/
643	>	void setMolToProcMap(const vector<int>& molToProcMap) {
644	>	molToProcMap_ = molToProcMap;
645	>	}
646	>
647	>	private:
648	>
649	>	/**
650	>	* The size of molToProcMap_ is equal to total number of molecules
651	>	* in the system.  It maps a molecule to the processor on which it
652	>	* resides. it is filled by SimCreator once and only once.
653	>	*/
654	>	vector<int> molToProcMap_;
655	>
656	>	};
657	>
658	>	} //namespace OpenMD
659	>	#endif //BRAINS_SIMMODEL_HPP
660	>

Comparing:
trunk/src/brains/SimInfo.hpp (property svn:keywords), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/brains/SimInfo.hpp (property svn:keywords), Revision 1545 by gezelter, Fri Apr 8 21:25:19 2011 UTC

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