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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 1953 by gezelter, Thu Dec 5 18:19:26 2013 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	>	int getNGlobalConstraints();
173	>	/**
174	>	* Returns the number of local molecules.
175	>	* @return the number of local molecules
176	>	*/
177	>	int getNMolecules() {
178	>	return molecules_.size();
179	>	}
180
181	<	int n_constraints; // the number of constraints on the system
181	>	/** Returns the number of local atoms */
182	>	unsigned int getNAtoms() {
183	>	return nAtoms_;
184	>	}
185
186	<	int n_SRI;   // the number of short range interactions
186	>	/** Returns the number of effective cutoff groups on local processor */
187	>	unsigned int getNLocalCutoffGroups();
188
189	<	double lrPot; // the potential energy from the long range calculations.
189	>	/** Returns the number of local bonds */
190	>	unsigned int getNBonds(){
191	>	return nBonds_;
192	>	}
193
194	<	double Hmat[3][3];  // the periodic boundry conditions. The Hmat is the
195	<	// column vectors of the x, y, and z box vectors.
196	<	//   h1  h2  h3
197	<	// [ Xx  Yx  Zx ]
198	<	// [ Xy  Yy  Zy ]
199	<	// [ Xz  Yz  Zz ]
200	<	//
201	<	double HmatInv[3][3];
194	>	/** Returns the number of local bends */
195	>	unsigned int getNBends() {
196	>	return nBends_;
197	>	}
198	>
199	>	/** Returns the number of local torsions */
200	>	unsigned int getNTorsions() {
201	>	return nTorsions_;
202	>	}
203
204	<	double boxL[3]; // The Lengths of the 3 column vectors of Hmat
205	<	double boxVol;
206	<	int orthoRhombic;
207	<
204	>	/** Returns the number of local inversions */
205	>	unsigned int getNInversions() {
206	>	return nInversions_;
207	>	}
208	>	/** Returns the number of local rigid bodies */
209	>	unsigned int getNRigidBodies() {
210	>	return nRigidBodies_;
211	>	}
212
213	<	double dielectric;      // the dielectric of the medium for reaction field
213	>	/** Returns the number of local integrable objects */
214	>	unsigned int getNIntegrableObjects() {
215	>	return nIntegrableObjects_;
216	>	}
217
218	<
219	<	int usePBC; // whether we use periodic boundry conditions.
220	<	int useLJ;
221	<	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;
218	>	/** Returns the number of local cutoff groups */
219	>	unsigned int getNCutoffGroups() {
220	>	return nCutoffGroups_;
221	>	}
222
223	<	double dt, run_time;           // the time step and total time
224	<	double sampleTime, statusTime; // the position and energy dump frequencies
225	<	double target_temp;            // the target temperature of the system
226	<	double thermalTime;            // the temp kick interval
227	<	double currentTime;            // Used primarily for correlation Functions
228	<	double resetTime;              // Use to reset the integrator periodically
229	<	short int have_target_temp;
223	>	/** Returns the total number of constraints in this SimInfo */
224	>	unsigned int getNConstraints() {
225	>	return nConstraints_;
226	>	}
227	>
228	>	/**
229	>	* Returns the first molecule in this SimInfo and intialize the iterator.
230	>	* @return the first molecule, return NULL if there is not molecule in this SimInfo
231	>	* @param i the iterator of molecule array (user shouldn't change it)
232	>	*/
233	>	Molecule* beginMolecule(MoleculeIterator& i);
234
235	<	int n_mol;           // n_molecules;
236	<	Molecule* molecules; // the array of molecules
237	<
238	<	int nComponents;           // the number of components in the system
239	<	int* componentsNmol;       // the number of molecules of each component
240	<	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
235	>	/**
236	>	* Returns the next avaliable Molecule based on the iterator.
237	>	* @return the next avaliable molecule, return NULL if reaching the end of the array
238	>	* @param i the iterator of molecule array
239	>	*/
240	>	Molecule* nextMolecule(MoleculeIterator& i);
241
242	<	OOPSEMinimizer* the_minimizer; // the energy minimizer
243	<	Restraints* restraint;
244	<	bool has_minimizer;
242	>	/** Returns the total number of fluctuating charges that are present */
243	>	int getNFluctuatingCharges() {
244	>	return nGlobalFluctuatingCharges_;
245	>	}
246
247	<	string finalName;  // the name of the eor file to be written
248	<	string sampleName; // the name of the dump file to be written
249	<	string statusName; // the name of the stat file to be written
247	>	/** Returns the number of degrees of freedom */
248	>	int getNdf() {
249	>	return ndf_ - getFdf();
250	>	}
251
252	<	int seed;                    //seed for random number generator
252	>	/** Returns the number of degrees of freedom (LOCAL) */
253	>	int getNdfLocal() {
254	>	return ndfLocal_;
255	>	}
256
257	<	int useSolidThermInt;  // is solid-state thermodynamic integration being used
258	<	int useLiquidThermInt; // is liquid thermodynamic integration being used
259	<	double thermIntLambda; // lambda for TI
260	<	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
257	>	/** Returns the number of raw degrees of freedom */
258	>	int getNdfRaw() {
259	>	return ndfRaw_;
260	>	}
261
262	<	vector<double> mfact;
263	<	vector<int> FglobalGroupMembership;
264	<	int ngroup;
265	<	int* globalGroupMembership;
262	>	/** Returns the number of translational degrees of freedom */
263	>	int getNdfTrans() {
264	>	return ndfTrans_;
265	>	}
266
267	<	// refreshes the sim if things get changed (load balanceing, volume
268	<	// adjustment, etc.)
267	>	/** sets the current number of frozen degrees of freedom */
268	>	void setFdf(int fdf) {
269	>	fdf_local = fdf;
270	>	}
271
272	<	void refreshSim( void );
273	<
272	>	int getFdf();
273	>
274	>	//getNZconstraint and setNZconstraint ruin the coherence of
275	>	//SimInfo class, need refactoring
276	>
277	>	/** Returns the total number of z-constraint molecules in the system */
278	>	int getNZconstraint() {
279	>	return nZconstraint_;
280	>	}
281
282	<	// sets the internal function pointer to fortran.
282	>	/**
283	>	* Sets the number of z-constraint molecules in the system.
284	>	*/
285	>	void setNZconstraint(int nZconstraint) {
286	>	nZconstraint_ = nZconstraint;
287	>	}
288	>
289	>	/** Returns the snapshot manager. */
290	>	SnapshotManager* getSnapshotManager() {
291	>	return sman_;
292	>	}
293	>	/** Returns the storage layout (computed by SimCreator) */
294	>	int getStorageLayout() {
295	>	return storageLayout_;
296	>	}
297	>	/** Sets the storage layout (computed by SimCreator) */
298	>	void setStorageLayout(int sl) {
299	>	storageLayout_ = sl;
300	>	}
301	>
302	>	/** Sets the snapshot manager. */
303	>	void setSnapshotManager(SnapshotManager* sman);
304	>
305	>	/** Returns the force field */
306	>	ForceField* getForceField() {
307	>	return forceField_;
308	>	}
309
310	<	void setInternal( setFortranSim_TD fSetup,
311	<	setFortranBox_TD fBox,
312	<	notifyFortranCutOff_TD fCut){
158	<	setFsimulation = fSetup;
159	<	setFortranBoxSize = fBox;
160	<	notifyFortranCutOffs = fCut;
161	<	}
310	>	Globals* getSimParams() {
311	>	return simParams_;
312	>	}
313
314	<	int getNDF();
315	<	int getNDFraw();
316	<	int getNDFtranslational();
317	<	int getTotIntegrableObjects();
318	<	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 );
314	>	void update();
315	>	/**
316	>	* Do final bookkeeping before Force managers need their data.
317	>	*/
318	>	void prepareTopology();
319
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; }
320
321	<	void wrapVector( double thePos[3] );
322	<
323	<	SimState* getConfiguration( void ) { return myConfiguration; }
324	<
190	<	void addProperty(GenericData* prop);
191	<	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;}
321	>	/** Returns the local index manager */
322	>	LocalIndexManager* getLocalIndexManager() {
323	>	return &localIndexMan_;
324	>	}
325
326	<	private:
326	>	int getMoleculeStampId(int globalIndex) {
327	>	//assert(globalIndex < molStampIds_.size())
328	>	return molStampIds_[globalIndex];
329	>	}
330
331	<	SimState* myConfiguration;
331	>	/** Returns the molecule stamp */
332	>	MoleculeStamp* getMoleculeStamp(int id) {
333	>	return moleculeStamps_[id];
334	>	}
335
336	<	int boxIsInit, haveRcut, haveRsw;
336	>	/** Return the total number of the molecule stamps */
337	>	int getNMoleculeStamp() {
338	>	return moleculeStamps_.size();
339	>	}
340	>	/**
341	>	* Finds a molecule with a specified global index
342	>	* @return a pointer point to found molecule
343	>	* @param index
344	>	*/
345	>	Molecule* getMoleculeByGlobalIndex(int index) {
346	>	MoleculeIterator i;
347	>	i = molecules_.find(index);
348
349	<	double rList, rCut; // variables for the neighborlist
350	<	double rSw;         // the switching radius
349	>	return i != molecules_.end() ? i->second : NULL;
350	>	}
351
352	<	double maxCutoff;
352	>	int getGlobalMolMembership(int id){
353	>	return globalMolMembership_[id];
354	>	}
355
356	<	double distXY;
357	<	double distYZ;
358	<	double distZX;
359	<
360	<	void calcHmatInv( void );
361	<	void calcBoxL();
214	<	double calcMaxCutOff();
356	>	/**
357	>	* returns a vector which maps the local atom index on this
358	>	* processor to the global atom index.  With only one processor,
359	>	* these should be identical.
360	>	*/
361	>	vector<int> getGlobalAtomIndices();
362
363	<	// private function to initialize the fortran side of the simulation
364	<	setFortranSim_TD setFsimulation;
363	>	/**
364	>	* returns a vector which maps the local cutoff group index on
365	>	* this processor to the global cutoff group index.  With only one
366	>	* processor, these should be identical.
367	>	*/
368	>	vector<int> getGlobalGroupIndices();
369
370	<	setFortranBox_TD setFortranBoxSize;
371	<
372	<	notifyFortranCutOff_TD notifyFortranCutOffs;
373	<
223	<	//Addtional Properties of SimInfo
224	<	map<string, GenericData*> properties;
225	<	void getFortranGroupArrays(SimInfo* info,
226	<	vector<int>& FglobalGroupMembership,
227	<	vector<double>& mfact);
370	>
371	>	string getFinalConfigFileName() {
372	>	return finalConfigFileName_;
373	>	}
374
375	+	void setFinalConfigFileName(const string& fileName) {
376	+	finalConfigFileName_ = fileName;
377	+	}
378
379	<	};
379	>	string getRawMetaData() {
380	>	return rawMetaData_;
381	>	}
382	>	void setRawMetaData(const string& rawMetaData) {
383	>	rawMetaData_ = rawMetaData;
384	>	}
385	>
386	>	string getDumpFileName() {
387	>	return dumpFileName_;
388	>	}
389	>
390	>	void setDumpFileName(const string& fileName) {
391	>	dumpFileName_ = fileName;
392	>	}
393
394	+	string getStatFileName() {
395	+	return statFileName_;
396	+	}
397	+
398	+	void setStatFileName(const string& fileName) {
399	+	statFileName_ = fileName;
400	+	}
401	+
402	+	string getRestFileName() {
403	+	return restFileName_;
404	+	}
405	+
406	+	void setRestFileName(const string& fileName) {
407	+	restFileName_ = fileName;
408	+	}
409
410	<	#endif
410	>	/**
411	>	* Sets GlobalGroupMembership
412	>	*/
413	>	void setGlobalGroupMembership(const vector<int>& ggm) {
414	>	assert(ggm.size() == static_cast<size_t>(nGlobalAtoms_));
415	>	globalGroupMembership_ = ggm;
416	>	}
417	>
418	>	/**
419	>	* Sets GlobalMolMembership
420	>	*/
421	>	void setGlobalMolMembership(const vector<int>& gmm) {
422	>	assert(gmm.size() == (static_cast<size_t>(nGlobalAtoms_ +
423	>	nGlobalRigidBodies_)));
424	>	globalMolMembership_ = gmm;
425	>	}
426	>
427	>
428	>	bool isTopologyDone() {
429	>	return topologyDone_;
430	>	}
431	>
432	>	bool getCalcBoxDipole() {
433	>	return calcBoxDipole_;
434	>	}
435	>
436	>	bool getUseAtomicVirial() {
437	>	return useAtomicVirial_;
438	>	}
439	>
440	>	/**
441	>	* Adds property into property map
442	>	* @param genData GenericData to be added into PropertyMap
443	>	*/
444	>	void addProperty(GenericData* genData);
445	>
446	>	/**
447	>	* Removes property from PropertyMap by name
448	>	* @param propName the name of property to be removed
449	>	*/
450	>	void removeProperty(const string& propName);
451	>
452	>	/**
453	>	* clear all of the properties
454	>	*/
455	>	void clearProperties();
456	>
457	>	/**
458	>	* Returns all names of properties
459	>	* @return all names of properties
460	>	*/
461	>	vector<string> getPropertyNames();
462	>
463	>	/**
464	>	* Returns all of the properties in PropertyMap
465	>	* @return all of the properties in PropertyMap
466	>	*/
467	>	vector<GenericData*> getProperties();
468	>
469	>	/**
470	>	* Returns property
471	>	* @param propName name of property
472	>	* @return a pointer point to property with propName. If no property named propName
473	>	* exists, return NULL
474	>	*/
475	>	GenericData* getPropertyByName(const string& propName);
476	>
477	>	/**
478	>	* add all special interaction pairs (including excluded
479	>	* interactions) in a molecule into the appropriate lists.
480	>	*/
481	>	void addInteractionPairs(Molecule* mol);
482	>
483	>	/**
484	>	* remove all special interaction pairs which belong to a molecule
485	>	* from the appropriate lists.
486	>	*/
487	>	void removeInteractionPairs(Molecule* mol);
488	>
489	>	/** Returns the set of atom types present in this simulation */
490	>	set<AtomType*> getSimulatedAtomTypes();
491	>
492	>	/** Returns the global count of atoms of a particular type */
493	>	int getGlobalCountOfType(AtomType* atype);
494	>
495	>	friend ostream& operator <<(ostream& o, SimInfo& info);
496	>
497	>	void getCutoff(RealType& rcut, RealType& rsw);
498	>
499	>	private:
500	>
501	>	/** fill up the simtype struct and other simulation-related variables */
502	>	void setupSimVariables();
503	>
504	>
505	>	/** Determine if we need to accumulate the simulation box dipole */
506	>	void setupAccumulateBoxDipole();
507	>
508	>	/** Calculates the number of degress of freedom in the whole system */
509	>	void calcNdf();
510	>	void calcNdfRaw();
511	>	void calcNdfTrans();
512	>
513	>	/**
514	>	* Adds molecule stamp and the total number of the molecule with
515	>	* same molecule stamp in the whole system.
516	>	*/
517	>	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
518	>
519	>	// Other classes holdingn important information
520	>	ForceField* forceField_; /**< provides access to defined atom types, bond types, etc. */
521	>	Globals* simParams_;     /**< provides access to simulation parameters set by user */
522	>
523	>	///  Counts of local objects
524	>	int nAtoms_;              /**< number of atoms in local processor */
525	>	int nBonds_;              /**< number of bonds in local processor */
526	>	int nBends_;              /**< number of bends in local processor */
527	>	int nTorsions_;           /**< number of torsions in local processor */
528	>	int nInversions_;         /**< number of inversions in local processor */
529	>	int nRigidBodies_;        /**< number of rigid bodies in local processor */
530	>	int nIntegrableObjects_;  /**< number of integrable objects in local processor */
531	>	int nCutoffGroups_;       /**< number of cutoff groups in local processor */
532	>	int nConstraints_;        /**< number of constraints in local processors */
533	>	int nFluctuatingCharges_; /**< number of fluctuating charges in local processor */
534	>
535	>	/// Counts of global objects
536	>	int nGlobalMols_;              /**< number of molecules in the system (GLOBAL) */
537	>	int nGlobalAtoms_;             /**< number of atoms in the system (GLOBAL) */
538	>	int nGlobalCutoffGroups_;      /**< number of cutoff groups in this system (GLOBAL) */
539	>	int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
540	>	int nGlobalRigidBodies_;       /**< number of rigid bodies in this system (GLOBAL) */
541	>	int nGlobalFluctuatingCharges_;/**< number of fluctuating charges in this system (GLOBAL) */
542	>	int nGlobalBonds_;              /**< number of bonds in the system */
543	>	int nGlobalBends_;              /**< number of bends in the system */
544	>	int nGlobalTorsions_;           /**< number of torsions in the system */
545	>	int nGlobalInversions_;         /**< number of inversions in the system */
546	>
547	>	/// Degress of freedom
548	>	int ndf_;          /**< number of degress of freedom (excludes constraints) (LOCAL) */
549	>	int ndfLocal_;     /**< number of degrees of freedom (LOCAL, excludes constraints) */
550	>	int fdf_local;     /**< number of frozen degrees of freedom (LOCAL) */
551	>	int fdf_;          /**< number of frozen degrees of freedom (GLOBAL) */
552	>	int ndfRaw_;       /**< number of degress of freedom (includes constraints),  (LOCAL) */
553	>	int ndfTrans_;     /**< number of translation degress of freedom, (LOCAL) */
554	>	int nZconstraint_; /**< number of  z-constraint molecules (GLOBAL) */
555	>
556	>	/// logicals
557	>	bool usesPeriodicBoundaries_; /**< use periodic boundary conditions? */
558	>	bool usesDirectionalAtoms_;   /**< are there atoms with position AND orientation? */
559	>	bool usesMetallicAtoms_;      /**< are there transition metal atoms? */
560	>	bool usesElectrostaticAtoms_; /**< are there electrostatic atoms? */
561	>	bool usesFluctuatingCharges_; /**< are there fluctuating charges? */
562	>	bool usesAtomicVirial_;       /**< are we computing atomic virials? */
563	>	bool requiresPrepair_;        /**< does this simulation require a pre-pair loop? */
564	>	bool requiresSkipCorrection_; /**< does this simulation require a skip-correction? */
565	>	bool requiresSelfCorrection_; /**< does this simulation require a self-correction? */
566	>
567	>	public:
568	>	bool usesElectrostaticAtoms() { return usesElectrostaticAtoms_; }
569	>	bool usesDirectionalAtoms() { return usesDirectionalAtoms_; }
570	>	bool usesFluctuatingCharges() { return usesFluctuatingCharges_; }
571	>	bool usesAtomicVirial() { return usesAtomicVirial_; }
572	>	bool requiresPrepair() { return requiresPrepair_; }
573	>	bool requiresSkipCorrection() { return requiresSkipCorrection_;}
574	>	bool requiresSelfCorrection() { return requiresSelfCorrection_;}
575	>
576	>	private:
577	>	/// Data structures holding primary simulation objects
578	>	map<int, Molecule*>  molecules_;  /**< map holding pointers to LOCAL molecules */
579	>
580	>	/// Stamps are templates for objects that are then used to create
581	>	/// groups of objects.  For example, a molecule stamp contains
582	>	/// information on how to build that molecule (i.e. the topology,
583	>	/// the atoms, the bonds, etc.)  Once the system is built, the
584	>	/// stamps are no longer useful.
585	>	vector<int> molStampIds_;                /**< stamp id for molecules in the system */
586	>	vector<MoleculeStamp*> moleculeStamps_;  /**< molecule stamps array */
587	>
588	>	/**
589	>	* A vector that maps between the global index of an atom, and the
590	>	* global index of cutoff group the atom belong to.  It is filled
591	>	* by SimCreator once and only once, since it never changed during
592	>	* the simulation.  It should be nGlobalAtoms_ in size.
593	>	*/
594	>	vector<int> globalGroupMembership_;
595	>	public:
596	>	vector<int> getGlobalGroupMembership() { return globalGroupMembership_; }
597	>	private:
598	>
599	>	/**
600	>	* A vector that maps between the global index of an atom and the
601	>	* global index of the molecule the atom belongs to.  It is filled
602	>	* by SimCreator once and only once, since it is never changed
603	>	* during the simulation. It shoudl be nGlobalAtoms_ in size.
604	>	*/
605	>	vector<int> globalMolMembership_;
606	>
607	>	/**
608	>	* A vector that maps between the local index of an atom and the
609	>	* index of the AtomType.
610	>	*/
611	>	vector<int> identArray_;
612	>	public:
613	>	vector<int> getIdentArray() { return identArray_; }
614	>
615	>	/**
616	>	* A vector that contains information about the local region of an
617	>	* atom (used for fluctuating charges, etc.)
618	>	*/
619	>	private:
620	>	vector<int> regions_;
621	>	public:
622	>	vector<int> getRegions() { return regions_; }
623	>	private:
624	>	/**
625	>	* A vector which contains the fractional contribution of an
626	>	* atom's mass to the total mass of the cutoffGroup that atom
627	>	* belongs to.  In the case of single atom cutoff groups, the mass
628	>	* factor for that atom is 1.  For massless atoms, the factor is
629	>	* also 1.
630	>	*/
631	>	vector<RealType> massFactors_;
632	>	public:
633	>	vector<RealType> getMassFactors() { return massFactors_; }
634	>
635	>	PairList* getExcludedInteractions() { return &excludedInteractions_; }
636	>	PairList* getOneTwoInteractions() { return &oneTwoInteractions_; }
637	>	PairList* getOneThreeInteractions() { return &oneThreeInteractions_; }
638	>	PairList* getOneFourInteractions() { return &oneFourInteractions_; }
639	>
640	>	private:
641	>
642	>	/// lists to handle atoms needing special treatment in the non-bonded interactions
643	>	PairList excludedInteractions_;  /**< atoms excluded from interacting with each other */
644	>	PairList oneTwoInteractions_;    /**< atoms that are directly Bonded */
645	>	PairList oneThreeInteractions_;  /**< atoms sharing a Bend */
646	>	PairList oneFourInteractions_;   /**< atoms sharing a Torsion */
647	>
648	>	PropertyMap properties_;       /**< Generic Properties can be added */
649	>	SnapshotManager* sman_;        /**< SnapshotManager (handles particle positions, etc.) */
650	>	int storageLayout_;            /**< Bits to tell how much data to store on each object */
651	>
652	>	/**
653	>	* The reason to have a local index manager is that when molecule
654	>	* is migrating to other processors, the atoms and the
655	>	* rigid-bodies will release their local indices to
656	>	* LocalIndexManager. Combining the information of molecule
657	>	* migrating to current processor, Migrator class can query the
658	>	* LocalIndexManager to make a efficient data moving plan.
659	>	*/
660	>	LocalIndexManager localIndexMan_;
661	>
662	>	// unparsed MetaData block for storing in Dump and EOR files:
663	>	string rawMetaData_;
664	>
665	>	// file names
666	>	string finalConfigFileName_;
667	>	string dumpFileName_;
668	>	string statFileName_;
669	>	string restFileName_;
670	>
671	>	bool topologyDone_;  /** flag to indicate whether the topology has
672	>	been scanned and all the relevant
673	>	bookkeeping has been done*/
674	>
675	>	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
676	>	the simulation box dipole moment */
677	>
678	>	bool useAtomicVirial_; /**< flag to indicate whether or not we use
679	>	Atomic Virials to calculate the pressure */
680	>
681	>	public:
682	>	/**
683	>	* return an integral objects by its global index. In MPI
684	>	* version, if the StuntDouble with specified global index does
685	>	* not belong to local processor, a NULL will be return.
686	>	*/
687	>	StuntDouble* getIOIndexToIntegrableObject(int index);
688	>	void setIOIndexToIntegrableObject(const vector<StuntDouble*>& v);
689	>
690	>	private:
691	>	vector<StuntDouble*> IOIndexToIntegrableObject;
692	>
693	>	public:
694	>
695	>	/**
696	>	* Finds the processor where a molecule resides
697	>	* @return the id of the processor which contains the molecule
698	>	* @param globalIndex global Index of the molecule
699	>	*/
700	>	int getMolToProc(int globalIndex) {
701	>	//assert(globalIndex < molToProcMap_.size());
702	>	return molToProcMap_[globalIndex];
703	>	}
704	>
705	>	/**
706	>	* Set MolToProcMap array
707	>	*/
708	>	void setMolToProcMap(const vector<int>& molToProcMap) {
709	>	molToProcMap_ = molToProcMap;
710	>	}
711	>
712	>	private:
713	>
714	>	/**
715	>	* The size of molToProcMap_ is equal to total number of molecules
716	>	* in the system.  It maps a molecule to the processor on which it
717	>	* resides. it is filled by SimCreator once and only once.
718	>	*/
719	>	vector<int> molToProcMap_;
720	>
721	>	};
722	>
723	>	} //namespace OpenMD
724	>	#endif //BRAINS_SIMMODEL_HPP
725	>

Comparing trunk/src/brains/SimInfo.hpp (property svn:keywords):
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Revision 1953 by gezelter, Thu Dec 5 18:19:26 2013 UTC

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