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Comparing trunk/src/brains/SimInfo.hpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 1983 by gezelter, Tue Apr 15 20:36:19 2014 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, 234107 (2008).
39	>	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	>	*/
42	>
43	>	/**
44	>	* @file SimInfo.hpp
45	>	* @author    tlin
46	>	* @date  11/02/2004
47	>	* @version 1.0
48	>	*/
49
50	<	#include <map>
51	<	#include <string>
50	>	#ifndef BRAINS_SIMMODEL_HPP
51	>	#define BRAINS_SIMMODEL_HPP
52	>
53	>	#include <iostream>
54	>	#include <set>
55	>	#include <utility>
56		#include <vector>
57
58	<	#include "Atom.hpp"
59	<	#include "RigidBody.hpp"
60	<	#include "Molecule.hpp"
61	<	#include "Exclude.hpp"
62	<	#include "SkipList.hpp"
63	<	#include "AbstractClasses.hpp"
64	<	#include "MakeStamps.hpp"
65	<	#include "SimState.hpp"
66	<	#include "Restraints.hpp"
58	>	#include "brains/PairList.hpp"
59	>	#include "io/Globals.hpp"
60	>	#include "math/Vector3.hpp"
61	>	#include "math/SquareMatrix3.hpp"
62	>	#include "types/MoleculeStamp.hpp"
63	>	#include "brains/ForceField.hpp"
64	>	#include "utils/PropertyMap.hpp"
65	>	#include "utils/LocalIndexManager.hpp"
66	>	#include "nonbonded/SwitchingFunction.hpp"
67
68	<	#define __C
69	<	#include "fSimulation.h"
70	<	#include "fortranWrapDefines.hpp"
71	<	#include "GenericData.hpp"
68	>	using namespace std;
69	>	namespace OpenMD{
70	>	//forward declaration
71	>	class SnapshotManager;
72	>	class Molecule;
73	>	class SelectionManager;
74	>	class StuntDouble;
75
76	+	/**
77	+	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
78	+	*
79	+	* @brief One of the heavy-weight classes of OpenMD, SimInfo
80	+	* maintains objects and variables relating to the current
81	+	* simulation.  This includes the master list of Molecules.  The
82	+	* Molecule class maintains all of the concrete objects (Atoms,
83	+	* Bond, Bend, Torsions, Inversions, RigidBodies, CutoffGroups,
84	+	* Constraints). In both the single and parallel versions, Atoms and
85	+	* RigidBodies have both global and local indices.
86	+	*/
87	+	class SimInfo {
88	+	public:
89	+	typedef map<int, Molecule*>::iterator  MoleculeIterator;
90	+
91	+	/**
92	+	* Constructor of SimInfo
93	+	*
94	+	* @param ff pointer to a concrete ForceField instance
95	+	*
96	+	* @param simParams pointer to the simulation parameters in a Globals object
97	+	*/
98	+	SimInfo(ForceField* ff, Globals* simParams);
99	+	virtual ~SimInfo();
100
101	<	//#include "Minimizer.hpp"
102	<	//#include "OOPSEMinimizer.hpp"
101	>	/**
102	>	* Adds a molecule
103	>	*
104	>	* @return return true if adding successfully, return false if the
105	>	* molecule is already in SimInfo
106	>	*
107	>	* @param mol Molecule to be added
108	>	*/
109	>	bool addMolecule(Molecule* mol);
110
111	+	/**
112	+	* Removes a molecule from SimInfo
113	+	*
114	+	* @return true if removing successfully, return false if molecule
115	+	* is not in this SimInfo
116	+	*/
117	+	bool removeMolecule(Molecule* mol);
118
119	<	double roundMe( double x );
120	<	class OOPSEMinimizer;
121	<	class SimInfo{
119	>	/** Returns the total number of molecules in the system. */
120	>	int getNGlobalMolecules() {
121	>	return nGlobalMols_;
122	>	}
123
124	<	public:
124	>	/** Returns the total number of atoms in the system. */
125	>	int getNGlobalAtoms() {
126	>	return nGlobalAtoms_;
127	>	}
128
129	<	SimInfo();
130	<	~SimInfo();
129	>	/** Returns the total number of cutoff groups in the system. */
130	>	int getNGlobalCutoffGroups() {
131	>	return nGlobalCutoffGroups_;
132	>	}
133
134	<	int n_atoms; // the number of atoms
135	<	Atom **atoms; // the array of atom objects
134	>	/**
135	>	* Returns the total number of integrable objects (total number of
136	>	* rigid bodies plus the total number of atoms which do not belong
137	>	* to the rigid bodies) in the system
138	>	*/
139	>	int getNGlobalIntegrableObjects() {
140	>	return nGlobalIntegrableObjects_;
141	>	}
142
143	<	vector<RigidBody*> rigidBodies;  // A vector of rigid bodies
144	<	vector<StuntDouble*> integrableObjects;
145	<
146	<	double tau[9]; // the stress tensor
143	>	/**
144	>	* Returns the total number of integrable objects (total number of
145	>	* rigid bodies plus the total number of atoms which do not belong
146	>	* to the rigid bodies) in the system
147	>	*/
148	>	int getNGlobalRigidBodies() {
149	>	return nGlobalRigidBodies_;
150	>	}
151
152	<	int n_bonds;    // number of bends
153	<	int n_bends;    // number of bends
154	<	int n_torsions; // number of torsions
155	<	int n_oriented; // number of of atoms with orientation
49	<	int ndf;        // number of actual degrees of freedom
50	<	int ndfRaw;     // number of settable degrees of freedom
51	<	int ndfTrans;   // number of translational degrees of freedom
52	<	int nZconstraints; // the number of zConstraints
152	>	/** Returns the number of global bonds */
153	>	unsigned int getNGlobalBonds(){
154	>	return nGlobalBonds_;
155	>	}
156
157	<	int setTemp;   // boolean to set the temperature at each sampleTime
158	<	int resetIntegrator; // boolean to reset the integrator
157	>	/** Returns the number of global bends */
158	>	unsigned int getNGlobalBends() {
159	>	return nGlobalBends_;
160	>	}
161
162	<	int n_dipoles; // number of dipoles
162	>	/** Returns the number of global torsions */
163	>	unsigned int getNGlobalTorsions() {
164	>	return nGlobalTorsions_;
165	>	}
166
167	<	int n_exclude;
168	<	Exclude* excludes;  // the exclude list for ignoring pairs in fortran
169	<	int nGlobalExcludes;
170	<	int* globalExcludes; // same as above, but these guys participate in
63	<	// no long range forces.
167	>	/** Returns the number of global inversions */
168	>	unsigned int getNGlobalInversions() {
169	>	return nGlobalInversions_;
170	>	}
171
172	<	int* identArray;     // array of unique identifiers for the atoms
173	<	int* molMembershipArray;  // map of atom numbers onto molecule numbers
172	>	unsigned int getNGlobalConstraints() {
173	>	if (!hasNGlobalConstraints_) calcNConstraints();
174	>	return nGlobalConstraints_;
175	>	}
176	>	/**
177	>	* Returns the number of local molecules.
178	>	* @return the number of local molecules
179	>	*/
180	>	int getNMolecules() {
181	>	return molecules_.size();
182	>	}
183
184	<	int n_constraints; // the number of constraints on the system
184	>	/** Returns the number of local atoms */
185	>	unsigned int getNAtoms() {
186	>	return nAtoms_;
187	>	}
188
189	<	int n_SRI;   // the number of short range interactions
189	>	/** Returns the number of effective cutoff groups on local processor */
190	>	unsigned int getNLocalCutoffGroups();
191
192	<	double lrPot; // the potential energy from the long range calculations.
192	>	/** Returns the number of local bonds */
193	>	unsigned int getNBonds(){
194	>	return nBonds_;
195	>	}
196
197	<	double Hmat[3][3];  // the periodic boundry conditions. The Hmat is the
198	<	// column vectors of the x, y, and z box vectors.
199	<	//   h1  h2  h3
200	<	// [ Xx  Yx  Zx ]
78	<	// [ Xy  Yy  Zy ]
79	<	// [ Xz  Yz  Zz ]
80	<	//
81	<	double HmatInv[3][3];
197	>	/** Returns the number of local bends */
198	>	unsigned int getNBends() {
199	>	return nBends_;
200	>	}
201
202	<	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
203	<	double boxVol;
204	<	int orthoRhombic;
205	<
202	>	/** Returns the number of local torsions */
203	>	unsigned int getNTorsions() {
204	>	return nTorsions_;
205	>	}
206
207	<	double dielectric;      // the dielectric of the medium for reaction field
207	>	/** Returns the number of local inversions */
208	>	unsigned int getNInversions() {
209	>	return nInversions_;
210	>	}
211	>	/** Returns the number of local rigid bodies */
212	>	unsigned int getNRigidBodies() {
213	>	return nRigidBodies_;
214	>	}
215
216	<
217	<	int usePBC; // whether we use periodic boundry conditions.
218	<	int useLJ;
219	<	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;
216	>	/** Returns the number of local integrable objects */
217	>	unsigned int getNIntegrableObjects() {
218	>	return nIntegrableObjects_;
219	>	}
220
221	<	double dt, run_time;           // the time step and total time
222	<	double sampleTime, statusTime; // the position and energy dump frequencies
223	<	double target_temp;            // the target temperature of the system
224	<	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;
221	>	/** Returns the number of local cutoff groups */
222	>	unsigned int getNCutoffGroups() {
223	>	return nCutoffGroups_;
224	>	}
225
226	<	int n_mol;           // n_molecules;
227	<	Molecule* molecules; // the array of molecules
228	<
229	<	int nComponents;           // the number of components in the system
230	<	int* componentsNmol;       // the number of molecules of each component
231	<	MoleculeStamp** compStamps;// the stamps matching the components
232	<	LinkedMolStamp* headStamp; // list of stamps used in the simulation
233	<
234	<
235	<	char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. )
236	<	char mixingRule[100]; // the mixing rules for Lennard jones/van der walls
122	<	BaseIntegrator *the_integrator; // the integrator of the simulation
226	>	/** Returns the total number of constraints in this SimInfo */
227	>	unsigned int getNConstraints() {
228	>	return nConstraints_;
229	>	}
230	>
231	>	/**
232	>	* Returns the first molecule in this SimInfo and intialize the iterator.
233	>	* @return the first molecule, return NULL if there is not molecule in this SimInfo
234	>	* @param i the iterator of molecule array (user shouldn't change it)
235	>	*/
236	>	Molecule* beginMolecule(MoleculeIterator& i);
237
238	<	OOPSEMinimizer* the_minimizer; // the energy minimizer
239	<	Restraints* restraint;
240	<	bool has_minimizer;
238	>	/**
239	>	* Returns the next avaliable Molecule based on the iterator.
240	>	* @return the next avaliable molecule, return NULL if reaching the end of the array
241	>	* @param i the iterator of molecule array
242	>	*/
243	>	Molecule* nextMolecule(MoleculeIterator& i);
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	>	/** Returns the total number of fluctuating charges that are present */
246	>	int getNFluctuatingCharges() {
247	>	return nGlobalFluctuatingCharges_;
248	>	}
249
250	<	int seed;                    //seed for random number generator
250	>	/** Returns the number of degrees of freedom */
251	>	int getNdf() {
252	>	return ndf_ - getFdf();
253	>	}
254
255	<	int useSolidThermInt;  // is solid-state thermodynamic integration being used
256	<	int useLiquidThermInt; // is liquid thermodynamic integration being used
257	<	double thermIntLambda; // lambda for TI
258	<	double thermIntK;      // power of lambda for TI
138	<	double vRaw;           // unperturbed potential for TI
139	<	double vHarm;          // harmonic potential for TI
140	<	int i;                 // just an int
255	>	/** Returns the number of degrees of freedom (LOCAL) */
256	>	int getNdfLocal() {
257	>	return ndfLocal_;
258	>	}
259
260	<	vector<double> mfact;
261	<	vector<int> FglobalGroupMembership;
262	<	int ngroup;
263	<	int* globalGroupMembership;
260	>	/** Returns the number of raw degrees of freedom */
261	>	int getNdfRaw() {
262	>	return ndfRaw_;
263	>	}
264
265	<	// refreshes the sim if things get changed (load balanceing, volume
266	<	// adjustment, etc.)
265	>	/** Returns the number of translational degrees of freedom */
266	>	int getNdfTrans() {
267	>	return ndfTrans_;
268	>	}
269
270	<	void refreshSim( void );
271	<
270	>	/** sets the current number of frozen degrees of freedom */
271	>	void setFdf(int fdf) {
272	>	fdf_local = fdf;
273	>	}
274
275	<	// sets the internal function pointer to fortran.
275	>	int getFdf();
276	>
277	>	//getNZconstraint and setNZconstraint ruin the coherence of
278	>	//SimInfo class, need refactoring
279	>
280	>	/** Returns the total number of z-constraint molecules in the system */
281	>	int getNZconstraint() {
282	>	return nZconstraint_;
283	>	}
284
285	<	void setInternal( setFortranSim_TD fSetup,
286	<	setFortranBox_TD fBox,
287	<	notifyFortranCutOff_TD fCut){
288	<	setFsimulation = fSetup;
289	<	setFortranBoxSize = fBox;
290	<	notifyFortranCutOffs = fCut;
291	<	}
285	>	/**
286	>	* Sets the number of z-constraint molecules in the system.
287	>	*/
288	>	void setNZconstraint(int nZconstraint) {
289	>	nZconstraint_ = nZconstraint;
290	>	}
291	>
292	>	/** Returns the snapshot manager. */
293	>	SnapshotManager* getSnapshotManager() {
294	>	return sman_;
295	>	}
296	>	/** Returns the storage layout (computed by SimCreator) */
297	>	int getStorageLayout() {
298	>	return storageLayout_;
299	>	}
300	>	/** Sets the storage layout (computed by SimCreator) */
301	>	void setStorageLayout(int sl) {
302	>	storageLayout_ = sl;
303	>	}
304	>
305	>	/** Sets the snapshot manager. */
306	>	void setSnapshotManager(SnapshotManager* sman);
307	>
308	>	/** Returns the force field */
309	>	ForceField* getForceField() {
310	>	return forceField_;
311	>	}
312
313	<	int getNDF();
314	<	int getNDFraw();
315	<	int getNDFtranslational();
166	<	int getTotIntegrableObjects();
167	<	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 );
313	>	Globals* getSimParams() {
314	>	return simParams_;
315	>	}
316
317	<	double getRcut( void )  { return rCut; }
318	<	double getRlist( void ) { return rList; }
319	<	double getRsw( void )   { return rSw; }
320	<	double getMaxCutoff( void ) { return maxCutoff; }
321	<
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; }
317	>	void update();
318	>	/**
319	>	* Do final bookkeeping before Force managers need their data.
320	>	*/
321	>	void prepareTopology();
322
186	–	void wrapVector( double thePos[3] );
323
324	<	SimState* getConfiguration( void ) { return myConfiguration; }
325	<
326	<	void addProperty(GenericData* prop);
327	<	GenericData* getProperty(const string& propName);
192	<	//vector<GenericData*>& getProperties()  {return properties;}
193	<
194	<	int getSeed(void) {  return seed; }
195	<	void setSeed(int theSeed) {  seed = theSeed;}
324	>	/** Returns the local index manager */
325	>	LocalIndexManager* getLocalIndexManager() {
326	>	return &localIndexMan_;
327	>	}
328
329	<	private:
329	>	int getMoleculeStampId(int globalIndex) {
330	>	//assert(globalIndex < molStampIds_.size())
331	>	return molStampIds_[globalIndex];
332	>	}
333
334	<	SimState* myConfiguration;
334	>	/** Returns the molecule stamp */
335	>	MoleculeStamp* getMoleculeStamp(int id) {
336	>	return moleculeStamps_[id];
337	>	}
338
339	<	int boxIsInit, haveRcut, haveRsw;
339	>	/** Return the total number of the molecule stamps */
340	>	int getNMoleculeStamp() {
341	>	return moleculeStamps_.size();
342	>	}
343	>	/**
344	>	* Finds a molecule with a specified global index
345	>	* @return a pointer point to found molecule
346	>	* @param index
347	>	*/
348	>	Molecule* getMoleculeByGlobalIndex(int index) {
349	>	MoleculeIterator i;
350	>	i = molecules_.find(index);
351
352	<	double rList, rCut; // variables for the neighborlist
353	<	double rSw;         // the switching radius
352	>	return i != molecules_.end() ? i->second : NULL;
353	>	}
354
355	<	double maxCutoff;
355	>	int getGlobalMolMembership(int id){
356	>	return globalMolMembership_[id];
357	>	}
358
359	<	double distXY;
360	<	double distYZ;
361	<	double distZX;
362	<
363	<	void calcHmatInv( void );
364	<	void calcBoxL();
214	<	double calcMaxCutOff();
359	>	/**
360	>	* returns a vector which maps the local atom index on this
361	>	* processor to the global atom index.  With only one processor,
362	>	* these should be identical.
363	>	*/
364	>	vector<int> getGlobalAtomIndices();
365
366	<	// private function to initialize the fortran side of the simulation
367	<	setFortranSim_TD setFsimulation;
366	>	/**
367	>	* returns a vector which maps the local cutoff group index on
368	>	* this processor to the global cutoff group index.  With only one
369	>	* processor, these should be identical.
370	>	*/
371	>	vector<int> getGlobalGroupIndices();
372
373	<	setFortranBox_TD setFortranBoxSize;
374	<
375	<	notifyFortranCutOff_TD notifyFortranCutOffs;
376	<
223	<	//Addtional Properties of SimInfo
224	<	map<string, GenericData*> properties;
225	<	void getFortranGroupArrays(SimInfo* info,
226	<	vector<int>& FglobalGroupMembership,
227	<	vector<double>& mfact);
373	>
374	>	string getFinalConfigFileName() {
375	>	return finalConfigFileName_;
376	>	}
377
378	+	void setFinalConfigFileName(const string& fileName) {
379	+	finalConfigFileName_ = fileName;
380	+	}
381
382	<	};
382	>	string getRawMetaData() {
383	>	return rawMetaData_;
384	>	}
385	>	void setRawMetaData(const string& rawMetaData) {
386	>	rawMetaData_ = rawMetaData;
387	>	}
388	>
389	>	string getDumpFileName() {
390	>	return dumpFileName_;
391	>	}
392	>
393	>	void setDumpFileName(const string& fileName) {
394	>	dumpFileName_ = fileName;
395	>	}
396
397	+	string getStatFileName() {
398	+	return statFileName_;
399	+	}
400	+
401	+	void setStatFileName(const string& fileName) {
402	+	statFileName_ = fileName;
403	+	}
404	+
405	+	string getRestFileName() {
406	+	return restFileName_;
407	+	}
408	+
409	+	void setRestFileName(const string& fileName) {
410	+	restFileName_ = fileName;
411	+	}
412
413	<	#endif
413	>	/**
414	>	* Sets GlobalGroupMembership
415	>	*/
416	>	void setGlobalGroupMembership(const vector<int>& ggm) {
417	>	assert(ggm.size() == static_cast<size_t>(nGlobalAtoms_));
418	>	globalGroupMembership_ = ggm;
419	>	}
420	>
421	>	/**
422	>	* Sets GlobalMolMembership
423	>	*/
424	>	void setGlobalMolMembership(const vector<int>& gmm) {
425	>	assert(gmm.size() == (static_cast<size_t>(nGlobalAtoms_ +
426	>	nGlobalRigidBodies_)));
427	>	globalMolMembership_ = gmm;
428	>	}
429	>
430	>
431	>	bool isTopologyDone() {
432	>	return topologyDone_;
433	>	}
434	>
435	>	bool getCalcBoxDipole() {
436	>	return calcBoxDipole_;
437	>	}
438	>
439	>	bool getUseAtomicVirial() {
440	>	return useAtomicVirial_;
441	>	}
442	>
443	>	/**
444	>	* Adds property into property map
445	>	* @param genData GenericData to be added into PropertyMap
446	>	*/
447	>	void addProperty(GenericData* genData);
448	>
449	>	/**
450	>	* Removes property from PropertyMap by name
451	>	* @param propName the name of property to be removed
452	>	*/
453	>	void removeProperty(const string& propName);
454	>
455	>	/**
456	>	* clear all of the properties
457	>	*/
458	>	void clearProperties();
459	>
460	>	/**
461	>	* Returns all names of properties
462	>	* @return all names of properties
463	>	*/
464	>	vector<string> getPropertyNames();
465	>
466	>	/**
467	>	* Returns all of the properties in PropertyMap
468	>	* @return all of the properties in PropertyMap
469	>	*/
470	>	vector<GenericData*> getProperties();
471	>
472	>	/**
473	>	* Returns property
474	>	* @param propName name of property
475	>	* @return a pointer point to property with propName. If no property named propName
476	>	* exists, return NULL
477	>	*/
478	>	GenericData* getPropertyByName(const string& propName);
479	>
480	>	/**
481	>	* add all special interaction pairs (including excluded
482	>	* interactions) in a molecule into the appropriate lists.
483	>	*/
484	>	void addInteractionPairs(Molecule* mol);
485	>
486	>	/**
487	>	* remove all special interaction pairs which belong to a molecule
488	>	* from the appropriate lists.
489	>	*/
490	>	void removeInteractionPairs(Molecule* mol);
491	>
492	>	/** Returns the set of atom types present in this simulation */
493	>	set<AtomType*> getSimulatedAtomTypes();
494	>
495	>	/** Returns the global count of atoms of a particular type */
496	>	int getGlobalCountOfType(AtomType* atype);
497	>
498	>	friend ostream& operator <<(ostream& o, SimInfo& info);
499	>
500	>	void getCutoff(RealType& rcut, RealType& rsw);
501	>
502	>	private:
503	>
504	>	/** fill up the simtype struct and other simulation-related variables */
505	>	void setupSimVariables();
506	>
507	>
508	>	/** Determine if we need to accumulate the simulation box dipole */
509	>	void setupAccumulateBoxDipole();
510	>
511	>	/** Calculates the number of degress of freedom in the whole system */
512	>	void calcNdf();
513	>	void calcNdfRaw();
514	>	void calcNdfTrans();
515	>	void calcNConstraints();
516	>
517	>	/**
518	>	* Adds molecule stamp and the total number of the molecule with
519	>	* same molecule stamp in the whole system.
520	>	*/
521	>	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
522	>
523	>	// Other classes holdingn important information
524	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
525	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
526	>
527	>	///  Counts of local objects
528	>	int nAtoms_;              /**< number of atoms in local processor */
529	>	int nBonds_;              /**< number of bonds in local processor */
530	>	int nBends_;              /**< number of bends in local processor */
531	>	int nTorsions_;           /**< number of torsions in local processor */
532	>	int nInversions_;         /**< number of inversions in local processor */
533	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
534	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
535	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
536	>	int nConstraints_;        /**< number of constraints in local processors */
537	>	int nFluctuatingCharges_; /**< number of fluctuating charges in local processor */
538	>
539	>	/// Counts of global objects
540	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
541	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
542	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
543	>	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
544	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
545	>	int nGlobalFluctuatingCharges_;/**< number of fluctuating charges in this system (GLOBAL) */
546	>	int nGlobalBonds_;              /**< number of bonds in the system */
547	>	int nGlobalBends_;              /**< number of bends in the system */
548	>	int nGlobalTorsions_;           /**< number of torsions in the system */
549	>	int nGlobalInversions_;         /**< number of inversions in the system */
550	>	int nGlobalConstraints_;        /**< number of constraints in the system */
551	>	bool hasNGlobalConstraints_;
552	>
553	>	/// Degress of freedom
554	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
555	>	int ndfLocal_;     /**< number of degrees of freedom (LOCAL, excludes constraints) */
556	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
557	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
558	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
559	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
560	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
561	>
562	>	/// logicals
563	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
564	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
565	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
566	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
567	>	bool usesFluctuatingCharges_; /**< are there fluctuating charges? */
568	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
569	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
570	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
571	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
572	>
573	>	public:
574	>	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
575	>	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
576	>	bool usesFluctuatingCharges() { return usesFluctuatingCharges_; }
577	>	bool usesAtomicVirial() { return usesAtomicVirial_; }
578	>	bool requiresPrepair() { return requiresPrepair_; }
579	>	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
580	>	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
581	>
582	>	private:
583	>	/// Data structures holding primary simulation objects
584	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
585	>
586	>	/// Stamps are templates for objects that are then used to create
587	>	/// groups of objects.  For example, a molecule stamp contains
588	>	/// information on how to build that molecule (i.e. the topology,
589	>	/// the atoms, the bonds, etc.)  Once the system is built, the
590	>	/// stamps are no longer useful.
591	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
592	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
593	>
594	>	/**
595	>	* A vector that maps between the global index of an atom, and the
596	>	* global index of cutoff group the atom belong to.  It is filled
597	>	* by SimCreator once and only once, since it never changed during
598	>	* the simulation.  It should be nGlobalAtoms_ in size.
599	>	*/
600	>	vector<int> globalGroupMembership_;
601	>	public:
602	>	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
603	>	private:
604	>
605	>	/**
606	>	* A vector that maps between the global index of an atom and the
607	>	* global index of the molecule the atom belongs to.  It is filled
608	>	* by SimCreator once and only once, since it is never changed
609	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
610	>	*/
611	>	vector<int> globalMolMembership_;
612	>
613	>	/**
614	>	* A vector that maps between the local index of an atom and the
615	>	* index of the AtomType.
616	>	*/
617	>	vector<int> identArray_;
618	>	public:
619	>	vector<int> getIdentArray() { return identArray_; }
620	>
621	>	/**
622	>	* A vector that contains information about the local region of an
623	>	* atom (used for fluctuating charges, etc.)
624	>	*/
625	>	private:
626	>	vector<int> regions_;
627	>	public:
628	>	vector<int> getRegions() { return regions_; }
629	>	private:
630	>	/**
631	>	* A vector which contains the fractional contribution of an
632	>	* atom's mass to the total mass of the cutoffGroup that atom
633	>	* belongs to.  In the case of single atom cutoff groups, the mass
634	>	* factor for that atom is 1.  For massless atoms, the factor is
635	>	* also 1.
636	>	*/
637	>	vector<RealType> massFactors_;
638	>	public:
639	>	vector<RealType> getMassFactors() { return massFactors_; }
640	>
641	>	PairList* getExcludedInteractions() { return &excludedInteractions_; }
642	>	PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
643	>	PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
644	>	PairList* getOneFourInteractions() { return &oneFourInteractions_; }
645	>
646	>	private:
647	>
648	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
649	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
650	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
651	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
652	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
653	>
654	>	PropertyMap properties_;       /**< Generic Properties can be added */
655	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
656	>	int storageLayout_;            /**< Bits to tell how much data to store on each object */
657	>
658	>	/**
659	>	* The reason to have a local index manager is that when molecule
660	>	* is migrating to other processors, the atoms and the
661	>	* rigid-bodies will release their local indices to
662	>	* LocalIndexManager. Combining the information of molecule
663	>	* migrating to current processor, Migrator class can query the
664	>	* LocalIndexManager to make a efficient data moving plan.
665	>	*/
666	>	LocalIndexManager localIndexMan_;
667	>
668	>	// unparsed MetaData block for storing in Dump and EOR files:
669	>	string rawMetaData_;
670	>
671	>	// file names
672	>	string finalConfigFileName_;
673	>	string dumpFileName_;
674	>	string statFileName_;
675	>	string restFileName_;
676	>
677	>	bool topologyDone_;  /** flag to indicate whether the topology has
678	>	been scanned and all the relevant
679	>	bookkeeping has been done*/
680	>
681	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
682	>	the simulation box dipole moment */
683	>
684	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
685	>	Atomic Virials to calculate the pressure */
686	>
687	>	public:
688	>	/**
689	>	* return an integral objects by its global index. In MPI
690	>	* version, if the StuntDouble with specified global index does
691	>	* not belong to local processor, a NULL will be return.
692	>	*/
693	>	StuntDouble* getIOIndexToIntegrableObject(int index);
694	>	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
695	>
696	>	private:
697	>	vector<StuntDouble*> IOIndexToIntegrableObject;
698	>
699	>	public:
700	>
701	>	/**
702	>	* Finds the processor where a molecule resides
703	>	* @return the id of the processor which contains the molecule
704	>	* @param globalIndex global Index of the molecule
705	>	*/
706	>	int getMolToProc(int globalIndex) {
707	>	//assert(globalIndex < molToProcMap_.size());
708	>	return molToProcMap_[globalIndex];
709	>	}
710	>
711	>	/**
712	>	* Set MolToProcMap array
713	>	*/
714	>	void setMolToProcMap(const vector<int>& molToProcMap) {
715	>	molToProcMap_ = molToProcMap;
716	>	}
717	>
718	>	private:
719	>
720	>	/**
721	>	* The size of molToProcMap_ is equal to total number of molecules
722	>	* in the system.  It maps a molecule to the processor on which it
723	>	* resides. it is filled by SimCreator once and only once.
724	>	*/
725	>	vector<int> molToProcMap_;
726	>
727	>	};
728	>
729	>	} //namespace OpenMD
730	>	#endif //BRAINS_SIMMODEL_HPP
731	>

Comparing trunk/src/brains/SimInfo.hpp (property svn:keywords):
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