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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 1570 by gezelter, Thu May 26 21:56:04 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 local bonds */
170	>	unsigned int getNBonds(){
171	>	return nBonds_;
172	>	}
173
174	<	int n_exclude;
175	<	Exclude* excludes;  // the exclude list for ignoring pairs in fortran
176	<	int nGlobalExcludes;
177	<	int* globalExcludes; // same as above, but these guys participate in
62	<	// no long range forces.
174	>	/** Returns the number of local bends */
175	>	unsigned int getNBends() {
176	>	return nBends_;
177	>	}
178
179	<	int* identArray;     // array of unique identifiers for the atoms
180	<	int* molMembershipArray;  // map of atom numbers onto molecule numbers
179	>	/** Returns the number of local torsions */
180	>	unsigned int getNTorsions() {
181	>	return nTorsions_;
182	>	}
183
184	<	int n_constraints; // the number of constraints on the system
184	>	/** Returns the number of local torsions */
185	>	unsigned int getNInversions() {
186	>	return nInversions_;
187	>	}
188	>	/** Returns the number of local rigid bodies */
189	>	unsigned int getNRigidBodies() {
190	>	return nRigidBodies_;
191	>	}
192
193	<	int n_SRI;   // the number of short range interactions
193	>	/** Returns the number of local integrable objects */
194	>	unsigned int getNIntegrableObjects() {
195	>	return nIntegrableObjects_;
196	>	}
197
198	<	double lrPot; // the potential energy from the long range calculations.
198	>	/** Returns the number of local cutoff groups */
199	>	unsigned int getNCutoffGroups() {
200	>	return nCutoffGroups_;
201	>	}
202
203	<	double Hmat[3][3];  // the periodic boundry conditions. The Hmat is the
204	<	// column vectors of the x, y, and z box vectors.
205	<	//   h1  h2  h3
206	<	// [ Xx  Yx  Zx ]
207	<	// [ Xy  Yy  Zy ]
208	<	// [ Xz  Yz  Zz ]
209	<	//
210	<	double HmatInv[3][3];
203	>	/** Returns the total number of constraints in this SimInfo */
204	>	unsigned int getNConstraints() {
205	>	return nConstraints_;
206	>	}
207	>
208	>	/**
209	>	* Returns the first molecule in this SimInfo and intialize the iterator.
210	>	* @return the first molecule, return NULL if there is not molecule in this SimInfo
211	>	* @param i the iterator of molecule array (user shouldn't change it)
212	>	*/
213	>	Molecule* beginMolecule(MoleculeIterator& i);
214
215	<	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
216	<	double boxVol;
217	<	int orthoRhombic;
218	<
215	>	/**
216	>	* Returns the next avaliable Molecule based on the iterator.
217	>	* @return the next avaliable molecule, return NULL if reaching the end of the array
218	>	* @param i the iterator of molecule array
219	>	*/
220	>	Molecule* nextMolecule(MoleculeIterator& i);
221
222	<	double dielectric;      // the dielectric of the medium for reaction field
222	>	/** Returns the number of degrees of freedom */
223	>	int getNdf() {
224	>	return ndf_ - getFdf();
225	>	}
226
227	<
228	<	int usePBC; // whether we use periodic boundry conditions.
229	<	int useDirectionalAtoms;
230	<	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;
227	>	/** Returns the number of raw degrees of freedom */
228	>	int getNdfRaw() {
229	>	return ndfRaw_;
230	>	}
231
232	<	double dt, run_time;           // the time step and total time
233	<	double sampleTime, statusTime; // the position and energy dump frequencies
234	<	double target_temp;            // the target temperature of the system
235	<	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;
232	>	/** Returns the number of translational degrees of freedom */
233	>	int getNdfTrans() {
234	>	return ndfTrans_;
235	>	}
236
237	<	int n_mol;           // n_molecules;
238	<	Molecule* molecules; // the array of molecules
239	<
240	<	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
237	>	/** sets the current number of frozen degrees of freedom */
238	>	void setFdf(int fdf) {
239	>	fdf_local = fdf;
240	>	}
241
242	<	OOPSEMinimizer* the_minimizer; // the energy minimizer
243	<	Restraints* restraint;
244	<	bool has_minimizer;
242	>	int getFdf();
243	>
244	>	//getNZconstraint and setNZconstraint ruin the coherence of
245	>	//SimInfo class, need refactoring
246	>
247	>	/** Returns the total number of z-constraint molecules in the system */
248	>	int getNZconstraint() {
249	>	return nZconstraint_;
250	>	}
251
252	<	string finalName;  // the name of the eor file to be written
253	<	string sampleName; // the name of the dump file to be written
254	<	string statusName; // the name of the stat file to be written
252	>	/**
253	>	* Sets the number of z-constraint molecules in the system.
254	>	*/
255	>	void setNZconstraint(int nZconstraint) {
256	>	nZconstraint_ = nZconstraint;
257	>	}
258	>
259	>	/** Returns the snapshot manager. */
260	>	SnapshotManager* getSnapshotManager() {
261	>	return sman_;
262	>	}
263
264	<	int seed;                    //seed for random number generator
264	>	/** Sets the snapshot manager. */
265	>	void setSnapshotManager(SnapshotManager* sman);
266	>
267	>	/** Returns the force field */
268	>	ForceField* getForceField() {
269	>	return forceField_;
270	>	}
271
272	<	int useSolidThermInt;  // is solid-state thermodynamic integration being used
273	<	int useLiquidThermInt; // is liquid thermodynamic integration being used
274	<	double thermIntLambda; // lambda for TI
140	<	double thermIntK;      // power of lambda for TI
141	<	double vRaw;           // unperturbed potential for TI
142	<	double vHarm;          // harmonic potential for TI
143	<	int i;                 // just an int
272	>	Globals* getSimParams() {
273	>	return simParams_;
274	>	}
275
276	<	vector<double> mfact;
277	<	vector<int> FglobalGroupMembership;
147	<	int ngroup;
148	<	int* globalGroupMembership;
276	>	/** Returns the velocity of center of mass of the whole system.*/
277	>	Vector3d getComVel();
278
279	<	// refreshes the sim if things get changed (load balanceing, volume
280	<	// adjustment, etc.)
279	>	/** Returns the center of the mass of the whole system.*/
280	>	Vector3d getCom();
281	>	/** Returns the center of the mass and Center of Mass velocity of
282	>	the whole system.*/
283	>	void getComAll(Vector3d& com,Vector3d& comVel);
284
285	<	void refreshSim( void );
286	<
285	>	/** Returns intertia tensor for the entire system and system
286	>	Angular Momentum.*/
287	>	void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
288	>
289	>	/** Returns system angular momentum */
290	>	Vector3d getAngularMomentum();
291
292	<	// sets the internal function pointer to fortran.
292	>	/** Returns volume of system as estimated by an ellipsoid defined
293	>	by the radii of gyration*/
294	>	void getGyrationalVolume(RealType &vol);
295	>	/** Overloaded version of gyrational volume that also returns
296	>	det(I) so dV/dr can be calculated*/
297	>	void getGyrationalVolume(RealType &vol, RealType &detI);
298
299	+	void update();
300	+	/**
301	+	* Do final bookkeeping before Force managers need their data.
302	+	*/
303	+	void prepareTopology();
304
159	–	int getNDF();
160	–	int getNDFraw();
161	–	int getNDFtranslational();
162	–	int getTotIntegrableObjects();
163	–	void setBox( double newBox[3] );
164	–	void setBoxM( double newBox[3][3] );
165	–	void getBoxM( double theBox[3][3] );
166	–	void scaleBox( double scale );
167	–
168	–	void setDefaultRcut( double theRcut );
169	–	void setDefaultRcut( double theRcut, double theRsw );
170	–	void checkCutOffs( void );
305
306	<	double getRcut( void )  { return rCut; }
307	<	double getRlist( void ) { return rList; }
308	<	double getRsw( void )   { return rSw; }
309	<	double getMaxCutoff( void ) { return maxCutoff; }
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; }
306	>	/** Returns the local index manager */
307	>	LocalIndexManager* getLocalIndexManager() {
308	>	return &localIndexMan_;
309	>	}
310
311	<	void wrapVector( double thePos[3] );
311	>	int getMoleculeStampId(int globalIndex) {
312	>	//assert(globalIndex < molStampIds_.size())
313	>	return molStampIds_[globalIndex];
314	>	}
315
316	<	SimState* getConfiguration( void ) { return myConfiguration; }
317	<
318	<	void addProperty(GenericData* prop);
319	<	GenericData* getProperty(const string& propName);
188	<	//vector<GenericData*>& getProperties()  {return properties;}
316	>	/** Returns the molecule stamp */
317	>	MoleculeStamp* getMoleculeStamp(int id) {
318	>	return moleculeStamps_[id];
319	>	}
320
321	<	int getSeed(void) {  return seed; }
322	<	void setSeed(int theSeed) {  seed = theSeed;}
321	>	/** Return the total number of the molecule stamps */
322	>	int getNMoleculeStamp() {
323	>	return moleculeStamps_.size();
324	>	}
325	>	/**
326	>	* Finds a molecule with a specified global index
327	>	* @return a pointer point to found molecule
328	>	* @param index
329	>	*/
330	>	Molecule* getMoleculeByGlobalIndex(int index) {
331	>	MoleculeIterator i;
332	>	i = molecules_.find(index);
333
334	<	private:
334	>	return i != molecules_.end() ? i->second : NULL;
335	>	}
336
337	<	SimState* myConfiguration;
337	>	int getGlobalMolMembership(int id){
338	>	return globalMolMembership_[id];
339	>	}
340
341	<	int boxIsInit, haveRcut, haveRsw;
341	>	/**
342	>	* returns a vector which maps the local atom index on this
343	>	* processor to the global atom index.  With only one processor,
344	>	* these should be identical.
345	>	*/
346	>	vector<int> getGlobalAtomIndices();
347
348	<	double rList, rCut; // variables for the neighborlist
349	<	double rSw;         // the switching radius
348	>	/**
349	>	* returns a vector which maps the local cutoff group index on
350	>	* this processor to the global cutoff group index.  With only one
351	>	* processor, these should be identical.
352	>	*/
353	>	vector<int> getGlobalGroupIndices();
354
355	<	double maxCutoff;
355	>
356	>	string getFinalConfigFileName() {
357	>	return finalConfigFileName_;
358	>	}
359
360	<	double distXY;
361	<	double distYZ;
362	<	double distZX;
207	<
208	<	void calcHmatInv( void );
209	<	void calcBoxL();
210	<	double calcMaxCutOff();
360	>	void setFinalConfigFileName(const string& fileName) {
361	>	finalConfigFileName_ = fileName;
362	>	}
363
364	<
365	<	//Addtional Properties of SimInfo
366	<	map<string, GenericData*> properties;
367	<	void getFortranGroupArrays(SimInfo* info,
368	<	vector<int>& FglobalGroupMembership,
369	<	vector<double>& mfact);
364	>	string getRawMetaData() {
365	>	return rawMetaData_;
366	>	}
367	>	void setRawMetaData(const string& rawMetaData) {
368	>	rawMetaData_ = rawMetaData;
369	>	}
370	>
371	>	string getDumpFileName() {
372	>	return dumpFileName_;
373	>	}
374	>
375	>	void setDumpFileName(const string& fileName) {
376	>	dumpFileName_ = fileName;
377	>	}
378
379	+	string getStatFileName() {
380	+	return statFileName_;
381	+	}
382	+
383	+	void setStatFileName(const string& fileName) {
384	+	statFileName_ = fileName;
385	+	}
386	+
387	+	string getRestFileName() {
388	+	return restFileName_;
389	+	}
390	+
391	+	void setRestFileName(const string& fileName) {
392	+	restFileName_ = fileName;
393	+	}
394
395	<	};
395	>	/**
396	>	* Sets GlobalGroupMembership
397	>	* @see #SimCreator::setGlobalIndex
398	>	*/
399	>	void setGlobalGroupMembership(const vector<int>& globalGroupMembership) {
400	>	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
401	>	globalGroupMembership_ = globalGroupMembership;
402	>	}
403
404	+	/**
405	+	* Sets GlobalMolMembership
406	+	* @see #SimCreator::setGlobalIndex
407	+	*/
408	+	void setGlobalMolMembership(const vector<int>& globalMolMembership) {
409	+	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
410	+	globalMolMembership_ = globalMolMembership;
411	+	}
412
413	<	#endif
413	>
414	>	bool isTopologyDone() {
415	>	return topologyDone_;
416	>	}
417	>
418	>	bool getCalcBoxDipole() {
419	>	return calcBoxDipole_;
420	>	}
421	>
422	>	bool getUseAtomicVirial() {
423	>	return useAtomicVirial_;
424	>	}
425	>
426	>	/**
427	>	* Adds property into property map
428	>	* @param genData GenericData to be added into PropertyMap
429	>	*/
430	>	void addProperty(GenericData* genData);
431	>
432	>	/**
433	>	* Removes property from PropertyMap by name
434	>	* @param propName the name of property to be removed
435	>	*/
436	>	void removeProperty(const string& propName);
437	>
438	>	/**
439	>	* clear all of the properties
440	>	*/
441	>	void clearProperties();
442	>
443	>	/**
444	>	* Returns all names of properties
445	>	* @return all names of properties
446	>	*/
447	>	vector<string> getPropertyNames();
448	>
449	>	/**
450	>	* Returns all of the properties in PropertyMap
451	>	* @return all of the properties in PropertyMap
452	>	*/
453	>	vector<GenericData*> getProperties();
454	>
455	>	/**
456	>	* Returns property
457	>	* @param propName name of property
458	>	* @return a pointer point to property with propName. If no property named propName
459	>	* exists, return NULL
460	>	*/
461	>	GenericData* getPropertyByName(const string& propName);
462	>
463	>	/**
464	>	* add all special interaction pairs (including excluded
465	>	* interactions) in a molecule into the appropriate lists.
466	>	*/
467	>	void addInteractionPairs(Molecule* mol);
468	>
469	>	/**
470	>	* remove all special interaction pairs which belong to a molecule
471	>	* from the appropriate lists.
472	>	*/
473	>	void removeInteractionPairs(Molecule* mol);
474	>
475	>	/** Returns the set of atom types present in this simulation */
476	>	set<AtomType*> getSimulatedAtomTypes();
477	>
478	>	friend ostream& operator <<(ostream& o, SimInfo& info);
479	>
480	>	void getCutoff(RealType& rcut, RealType& rsw);
481	>
482	>	private:
483	>
484	>	/** fill up the simtype struct and other simulation-related variables */
485	>	void setupSimVariables();
486	>
487	>
488	>	/** Determine if we need to accumulate the simulation box dipole */
489	>	void setupAccumulateBoxDipole();
490	>
491	>	/** Calculates the number of degress of freedom in the whole system */
492	>	void calcNdf();
493	>	void calcNdfRaw();
494	>	void calcNdfTrans();
495	>
496	>	/**
497	>	* Adds molecule stamp and the total number of the molecule with
498	>	* same molecule stamp in the whole system.
499	>	*/
500	>	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
501	>
502	>	// Other classes holdingn important information
503	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
504	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
505	>
506	>	///  Counts of local objects
507	>	int nAtoms_;              /**< number of atoms in local processor */
508	>	int nBonds_;              /**< number of bonds in local processor */
509	>	int nBends_;              /**< number of bends in local processor */
510	>	int nTorsions_;           /**< number of torsions in local processor */
511	>	int nInversions_;         /**< number of inversions in local processor */
512	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
513	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
514	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
515	>	int nConstraints_;        /**< number of constraints in local processors */
516	>
517	>	/// Counts of global objects
518	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
519	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
520	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
521	>	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
522	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
523	>
524	>	/// Degress of freedom
525	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
526	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
527	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
528	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
529	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
530	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
531	>
532	>	/// logicals
533	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
534	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
535	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
536	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
537	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
538	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
539	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
540	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
541	>
542	>	public:
543	>	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
544	>	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
545	>	bool usesMetallicAtoms() { return usesMetallicAtoms_; }
546	>	bool usesAtomicVirial() { return usesAtomicVirial_; }
547	>	bool requiresPrepair() { return requiresPrepair_; }
548	>	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
549	>	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
550	>
551	>	private:
552	>	/// Data structures holding primary simulation objects
553	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
554	>
555	>	/// Stamps are templates for objects that are then used to create
556	>	/// groups of objects.  For example, a molecule stamp contains
557	>	/// information on how to build that molecule (i.e. the topology,
558	>	/// the atoms, the bonds, etc.)  Once the system is built, the
559	>	/// stamps are no longer useful.
560	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
561	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
562	>
563	>	/**
564	>	* A vector that maps between the global index of an atom, and the
565	>	* global index of cutoff group the atom belong to.  It is filled
566	>	* by SimCreator once and only once, since it never changed during
567	>	* the simulation.  It should be nGlobalAtoms_ in size.
568	>	*/
569	>	vector<int> globalGroupMembership_;
570	>	public:
571	>	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
572	>	private:
573	>
574	>	/**
575	>	* A vector that maps between the global index of an atom and the
576	>	* global index of the molecule the atom belongs to.  It is filled
577	>	* by SimCreator once and only once, since it is never changed
578	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
579	>	*/
580	>	vector<int> globalMolMembership_;
581	>
582	>	/**
583	>	* A vector that maps between the local index of an atom and the
584	>	* index of the AtomType.
585	>	*/
586	>	vector<int> identArray_;
587	>	public:
588	>	vector<int> getIdentArray() { return identArray_; }
589	>	private:
590	>
591	>	/**
592	>	* A vector which contains the fractional contribution of an
593	>	* atom's mass to the total mass of the cutoffGroup that atom
594	>	* belongs to.  In the case of single atom cutoff groups, the mass
595	>	* factor for that atom is 1.  For massless atoms, the factor is
596	>	* also 1.
597	>	*/
598	>	vector<RealType> massFactors_;
599	>	public:
600	>	vector<RealType> getMassFactors() { return massFactors_; }
601	>
602	>	PairList getExcludedInteractions() { return excludedInteractions_; }
603	>	PairList getOneTwoInteractions() { return oneTwoInteractions_; }
604	>	PairList getOneThreeInteractions() { return oneThreeInteractions_; }
605	>	PairList getOneFourInteractions() { return oneFourInteractions_; }
606	>
607	>	private:
608	>
609	>
610	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
611	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
612	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
613	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
614	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
615	>
616	>	PropertyMap properties_;       /**< Generic Properties can be added */
617	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
618	>
619	>	/**
620	>	* The reason to have a local index manager is that when molecule
621	>	* is migrating to other processors, the atoms and the
622	>	* rigid-bodies will release their local indices to
623	>	* LocalIndexManager. Combining the information of molecule
624	>	* migrating to current processor, Migrator class can query the
625	>	* LocalIndexManager to make a efficient data moving plan.
626	>	*/
627	>	LocalIndexManager localIndexMan_;
628	>
629	>	// unparsed MetaData block for storing in Dump and EOR files:
630	>	string rawMetaData_;
631	>
632	>	// file names
633	>	string finalConfigFileName_;
634	>	string dumpFileName_;
635	>	string statFileName_;
636	>	string restFileName_;
637	>
638	>
639	>	bool topologyDone_;  /** flag to indicate whether the topology has
640	>	been scanned and all the relevant
641	>	bookkeeping has been done*/
642	>
643	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
644	>	the simulation box dipole moment */
645	>
646	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
647	>	Atomic Virials to calculate the pressure */
648	>
649	>	public:
650	>	/**
651	>	* return an integral objects by its global index. In MPI
652	>	* version, if the StuntDouble with specified global index does
653	>	* not belong to local processor, a NULL will be return.
654	>	*/
655	>	StuntDouble* getIOIndexToIntegrableObject(int index);
656	>	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
657	>
658	>	private:
659	>	vector<StuntDouble*> IOIndexToIntegrableObject;
660	>
661	>	public:
662	>
663	>	/**
664	>	* Finds the processor where a molecule resides
665	>	* @return the id of the processor which contains the molecule
666	>	* @param globalIndex global Index of the molecule
667	>	*/
668	>	int getMolToProc(int globalIndex) {
669	>	//assert(globalIndex < molToProcMap_.size());
670	>	return molToProcMap_[globalIndex];
671	>	}
672	>
673	>	/**
674	>	* Set MolToProcMap array
675	>	* @see #SimCreator::divideMolecules
676	>	*/
677	>	void setMolToProcMap(const vector<int>& molToProcMap) {
678	>	molToProcMap_ = molToProcMap;
679	>	}
680	>
681	>	private:
682	>
683	>	/**
684	>	* The size of molToProcMap_ is equal to total number of molecules
685	>	* in the system.  It maps a molecule to the processor on which it
686	>	* resides. it is filled by SimCreator once and only once.
687	>	*/
688	>	vector<int> molToProcMap_;
689	>
690	>	};
691	>
692	>	} //namespace OpenMD
693	>	#endif //BRAINS_SIMMODEL_HPP
694	>

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 1570 by gezelter, Thu May 26 21:56:04 2011 UTC

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