1 |
mmeineke |
377 |
#ifndef __SIMINFO_H__ |
2 |
|
|
#define __SIMINFO_H__ |
3 |
|
|
|
4 |
tim |
658 |
#include <map> |
5 |
|
|
#include <string> |
6 |
|
|
#include <vector> |
7 |
mmeineke |
377 |
|
8 |
|
|
#include "Atom.hpp" |
9 |
|
|
#include "Molecule.hpp" |
10 |
|
|
#include "AbstractClasses.hpp" |
11 |
|
|
#include "MakeStamps.hpp" |
12 |
mmeineke |
670 |
#include "SimState.hpp" |
13 |
mmeineke |
377 |
|
14 |
|
|
#define __C |
15 |
|
|
#include "fSimulation.h" |
16 |
|
|
#include "fortranWrapDefines.hpp" |
17 |
tim |
658 |
#include "GenericData.hpp" |
18 |
tim |
1064 |
//#include "Minimizer.hpp" |
19 |
|
|
//#include "OOPSEMinimizer.hpp" |
20 |
mmeineke |
377 |
|
21 |
tim |
1064 |
class OOPSEMinimizer; |
22 |
mmeineke |
377 |
class SimInfo{ |
23 |
|
|
|
24 |
|
|
public: |
25 |
|
|
|
26 |
|
|
SimInfo(); |
27 |
tim |
660 |
~SimInfo(); |
28 |
mmeineke |
377 |
|
29 |
|
|
int n_atoms; // the number of atoms |
30 |
|
|
Atom **atoms; // the array of atom objects |
31 |
|
|
|
32 |
|
|
double tau[9]; // the stress tensor |
33 |
|
|
|
34 |
mmeineke |
787 |
int n_bonds; // number of bends |
35 |
|
|
int n_bends; // number of bends |
36 |
|
|
int n_torsions; // number of torsions |
37 |
|
|
int n_oriented; // number of of atoms with orientation |
38 |
|
|
int ndf; // number of actual degrees of freedom |
39 |
|
|
int ndfRaw; // number of settable degrees of freedom |
40 |
|
|
int ndfTrans; // number of translational degrees of freedom |
41 |
|
|
int nZconstraints; // the number of zConstraints |
42 |
mmeineke |
377 |
|
43 |
mmeineke |
787 |
int setTemp; // boolean to set the temperature at each sampleTime |
44 |
|
|
int resetIntegrator; // boolean to reset the integrator |
45 |
mmeineke |
377 |
|
46 |
mmeineke |
787 |
int n_dipoles; // number of dipoles |
47 |
mmeineke |
377 |
|
48 |
mmeineke |
626 |
|
49 |
mmeineke |
377 |
int n_exclude; // the # of pairs excluded from long range forces |
50 |
mmeineke |
427 |
Exclude** excludes; // the pairs themselves |
51 |
mmeineke |
377 |
|
52 |
|
|
int nGlobalExcludes; |
53 |
|
|
int* globalExcludes; // same as above, but these guys participate in |
54 |
|
|
// no long range forces. |
55 |
|
|
|
56 |
|
|
int* identArray; // array of unique identifiers for the atoms |
57 |
gezelter |
483 |
int* molMembershipArray; // map of atom numbers onto molecule numbers |
58 |
mmeineke |
377 |
|
59 |
|
|
int n_constraints; // the number of constraints on the system |
60 |
|
|
|
61 |
mmeineke |
787 |
int n_SRI; // the number of short range interactions |
62 |
mmeineke |
377 |
|
63 |
|
|
double lrPot; // the potential energy from the long range calculations. |
64 |
|
|
|
65 |
gezelter |
588 |
double Hmat[3][3]; // the periodic boundry conditions. The Hmat is the |
66 |
|
|
// column vectors of the x, y, and z box vectors. |
67 |
|
|
// h1 h2 h3 |
68 |
|
|
// [ Xx Yx Zx ] |
69 |
|
|
// [ Xy Yy Zy ] |
70 |
|
|
// [ Xz Yz Zz ] |
71 |
|
|
// |
72 |
|
|
double HmatInv[3][3]; |
73 |
mmeineke |
568 |
|
74 |
gezelter |
621 |
double boxL[3]; // The Lengths of the 3 column vectors of Hmat |
75 |
mmeineke |
572 |
double boxVol; |
76 |
|
|
int orthoRhombic; |
77 |
mmeineke |
568 |
|
78 |
|
|
|
79 |
mmeineke |
626 |
double dielectric; // the dielectric of the medium for reaction field |
80 |
mmeineke |
568 |
|
81 |
mmeineke |
377 |
|
82 |
|
|
int usePBC; // whether we use periodic boundry conditions. |
83 |
|
|
int useLJ; |
84 |
|
|
int useSticky; |
85 |
gezelter |
941 |
int useCharges; |
86 |
|
|
int useDipoles; |
87 |
mmeineke |
377 |
int useReactionField; |
88 |
|
|
int useGB; |
89 |
|
|
int useEAM; |
90 |
|
|
|
91 |
mmeineke |
855 |
bool useInitXSstate; |
92 |
|
|
double orthoTolerance; |
93 |
mmeineke |
377 |
|
94 |
|
|
double dt, run_time; // the time step and total time |
95 |
|
|
double sampleTime, statusTime; // the position and energy dump frequencies |
96 |
|
|
double target_temp; // the target temperature of the system |
97 |
|
|
double thermalTime; // the temp kick interval |
98 |
gezelter |
637 |
double currentTime; // Used primarily for correlation Functions |
99 |
mmeineke |
746 |
double resetTime; // Use to reset the integrator periodically |
100 |
mmeineke |
377 |
|
101 |
|
|
int n_mol; // n_molecules; |
102 |
|
|
Molecule* molecules; // the array of molecules |
103 |
|
|
|
104 |
mmeineke |
823 |
int nComponents; // the number of components in the system |
105 |
mmeineke |
377 |
int* componentsNmol; // the number of molecules of each component |
106 |
|
|
MoleculeStamp** compStamps;// the stamps matching the components |
107 |
|
|
LinkedMolStamp* headStamp; // list of stamps used in the simulation |
108 |
|
|
|
109 |
|
|
|
110 |
|
|
char ensemble[100]; // the enesemble of the simulation (NVT, NVE, etc. ) |
111 |
|
|
char mixingRule[100]; // the mixing rules for Lennard jones/van der walls |
112 |
mmeineke |
542 |
BaseIntegrator *the_integrator; // the integrator of the simulation |
113 |
mmeineke |
377 |
|
114 |
tim |
1064 |
OOPSEMinimizer* the_minimizer; // the energy minimizer |
115 |
tim |
1031 |
bool has_minimizer; |
116 |
|
|
|
117 |
mmeineke |
377 |
char finalName[300]; // the name of the eor file to be written |
118 |
|
|
char sampleName[300]; // the name of the dump file to be written |
119 |
|
|
char statusName[300]; // the name of the stat file to be written |
120 |
|
|
|
121 |
tim |
708 |
int seed; //seed for random number generator |
122 |
mmeineke |
377 |
// refreshes the sim if things get changed (load balanceing, volume |
123 |
|
|
// adjustment, etc.) |
124 |
|
|
|
125 |
|
|
void refreshSim( void ); |
126 |
|
|
|
127 |
|
|
|
128 |
|
|
// sets the internal function pointer to fortran. |
129 |
|
|
|
130 |
mmeineke |
836 |
void setInternal( setFortranSim_TD fSetup, |
131 |
|
|
setFortranBox_TD fBox, |
132 |
|
|
notifyFortranCutOff_TD fCut){ |
133 |
mmeineke |
377 |
setFsimulation = fSetup; |
134 |
|
|
setFortranBoxSize = fBox; |
135 |
mmeineke |
626 |
notifyFortranCutOffs = fCut; |
136 |
mmeineke |
377 |
} |
137 |
|
|
|
138 |
gezelter |
458 |
int getNDF(); |
139 |
|
|
int getNDFraw(); |
140 |
tim |
767 |
int getNDFtranslational(); |
141 |
gezelter |
458 |
|
142 |
gezelter |
457 |
void setBox( double newBox[3] ); |
143 |
gezelter |
588 |
void setBoxM( double newBox[3][3] ); |
144 |
|
|
void getBoxM( double theBox[3][3] ); |
145 |
gezelter |
574 |
void scaleBox( double scale ); |
146 |
mmeineke |
626 |
|
147 |
mmeineke |
841 |
void setDefaultRcut( double theRcut ); |
148 |
|
|
void setDefaultEcr( double theEcr ); |
149 |
|
|
void setDefaultEcr( double theEcr, double theEst ); |
150 |
gezelter |
845 |
void checkCutOffs( void ); |
151 |
gezelter |
457 |
|
152 |
mmeineke |
626 |
double getRcut( void ) { return rCut; } |
153 |
|
|
double getRlist( void ) { return rList; } |
154 |
|
|
double getEcr( void ) { return ecr; } |
155 |
|
|
double getEst( void ) { return est; } |
156 |
mmeineke |
797 |
double getMaxCutoff( void ) { return maxCutoff; } |
157 |
mmeineke |
626 |
|
158 |
mmeineke |
644 |
void setTime( double theTime ) { currentTime = theTime; } |
159 |
mmeineke |
790 |
void incrTime( double the_dt ) { currentTime += the_dt; } |
160 |
|
|
void decrTime( double the_dt ) { currentTime -= the_dt; } |
161 |
mmeineke |
644 |
double getTime( void ) { return currentTime; } |
162 |
mmeineke |
626 |
|
163 |
mmeineke |
568 |
void wrapVector( double thePos[3] ); |
164 |
|
|
|
165 |
gezelter |
588 |
void matMul3(double a[3][3], double b[3][3], double out[3][3]); |
166 |
|
|
void matVecMul3(double m[3][3], double inVec[3], double outVec[3]); |
167 |
|
|
void invertMat3(double in[3][3], double out[3][3]); |
168 |
mmeineke |
597 |
void transposeMat3(double in[3][3], double out[3][3]); |
169 |
|
|
void printMat3(double A[3][3]); |
170 |
|
|
void printMat9(double A[9]); |
171 |
gezelter |
588 |
double matDet3(double m[3][3]); |
172 |
tim |
763 |
double matTrace3(double m[3][3]); |
173 |
mmeineke |
670 |
|
174 |
tim |
781 |
void crossProduct3(double a[3],double b[3], double out[3]); |
175 |
|
|
double dotProduct3(double a[3], double b[3]); |
176 |
|
|
double length3(double a[3]); |
177 |
|
|
|
178 |
mmeineke |
670 |
SimState* getConfiguration( void ) { return myConfiguration; } |
179 |
gezelter |
588 |
|
180 |
tim |
658 |
void addProperty(GenericData* prop); |
181 |
|
|
GenericData* getProperty(const string& propName); |
182 |
|
|
vector<GenericData*> getProperties(); |
183 |
mmeineke |
670 |
|
184 |
tim |
708 |
int getSeed(void) { return seed; } |
185 |
|
|
void setSeed(int theSeed) { seed = theSeed;} |
186 |
|
|
|
187 |
mmeineke |
377 |
private: |
188 |
mmeineke |
626 |
|
189 |
mmeineke |
670 |
SimState* myConfiguration; |
190 |
|
|
|
191 |
mmeineke |
859 |
int boxIsInit, haveRcut, haveEcr; |
192 |
mmeineke |
626 |
|
193 |
|
|
double rList, rCut; // variables for the neighborlist |
194 |
|
|
double ecr; // the electrostatic cutoff radius |
195 |
|
|
double est; // the electrostatic skin thickness |
196 |
|
|
double maxCutoff; |
197 |
tim |
781 |
|
198 |
|
|
double distXY; |
199 |
|
|
double distYZ; |
200 |
|
|
double distZX; |
201 |
mmeineke |
855 |
|
202 |
|
|
|
203 |
mmeineke |
377 |
|
204 |
gezelter |
588 |
void calcHmatInv( void ); |
205 |
mmeineke |
568 |
void calcBoxL(); |
206 |
tim |
781 |
double calcMaxCutOff(); |
207 |
mmeineke |
568 |
|
208 |
gezelter |
845 |
|
209 |
mmeineke |
377 |
// private function to initialize the fortran side of the simulation |
210 |
mmeineke |
836 |
setFortranSim_TD setFsimulation; |
211 |
mmeineke |
377 |
|
212 |
mmeineke |
836 |
setFortranBox_TD setFortranBoxSize; |
213 |
mmeineke |
626 |
|
214 |
mmeineke |
836 |
notifyFortranCutOff_TD notifyFortranCutOffs; |
215 |
tim |
658 |
|
216 |
|
|
//Addtional Properties of SimInfo |
217 |
|
|
map<string, GenericData*> properties; |
218 |
mmeineke |
626 |
|
219 |
mmeineke |
377 |
}; |
220 |
|
|
|
221 |
|
|
|
222 |
|
|
|
223 |
|
|
#endif |