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root/OpenMD/branches/development/src/io/Globals.hpp
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Comparing trunk/src/io/Globals.hpp (file contents):
Revision 603 by chrisfen, Fri Sep 16 16:07:39 2005 UTC vs.
Revision 1306 by chuckv, Thu Oct 16 18:25:36 2008 UTC

# Line 49 | Line 49
49   #include <string>
50   #include <map>
51  
52 – #include "io/BASS_interface.h"
52   #include "types/Component.hpp"
53 < #include "types/MakeStamps.hpp"
54 < #include "types/ZconStamp.hpp"
53 > #include "types/ZconsStamp.hpp"
54 > #include "types/MoleculeStamp.hpp"
55 > #include "utils/ParameterManager.hpp"
56  
57 + namespace oopse {
58 +  class Globals : public DataHolder {
59 +  public:
60 +    typedef std::pair<int, int> intPair;
61  
62 +    Globals();
63 +    virtual ~Globals();
64 +    
65 +    DeclareParameter(ForceField, std::string);
66 +    DeclareParameter(TargetTemp, RealType);
67 +    DeclareParameter(Ensemble, std::string);
68 +    DeclareParameter(Dt, RealType);
69 +    DeclareParameter(RunTime, RealType);
70 +    DeclareParameter(FinalConfig, std::string);
71 +    DeclareParameter(SampleTime, RealType);
72 +    DeclareParameter(ResetTime, RealType);
73 +    DeclareParameter(StatusTime, RealType);
74 +    DeclareParameter(CutoffRadius, RealType);
75 +    DeclareParameter(SwitchingRadius, RealType);
76 +    DeclareParameter(TempSet, bool);
77 +    DeclareParameter(ThermalTime, RealType);
78 +    DeclareParameter(UsePeriodicBoundaryConditions, bool);
79 +    DeclareParameter(TargetPressure, RealType);
80 +    DeclareParameter(UseAtomicVirial, bool);
81 +    DeclareParameter(TauThermostat, RealType);
82 +    DeclareParameter(TauBarostat, RealType);
83 +    DeclareParameter(ZconsTime, RealType);
84 +    DeclareParameter(ZconsTol, RealType);
85 +    DeclareParameter(ZconsForcePolicy, std::string);
86 +    DeclareParameter(Seed, int);
87 +    DeclareParameter(UseInitalTime, bool);
88 +    DeclareParameter(UseIntialExtendedSystemState, bool);
89 +    DeclareParameter(OrthoBoxTolerance, RealType);
90 +    DeclareParameter(Minimizer, std::string);
91 +    DeclareParameter(MinimizerMaxIter, RealType);
92 +    DeclareParameter(MinimizerWriteFrq, int);
93 +    DeclareParameter(MinimizerStepSize, RealType);
94 +    DeclareParameter(MinimizerFTol, RealType);
95 +    DeclareParameter(MinimizerGTol, RealType);
96 +    DeclareParameter(MinimizerLSTol, RealType);
97 +    DeclareParameter(MinimizerLSMaxIter, int);
98 +    DeclareParameter(ZconsGap, RealType);
99 +    DeclareParameter(ZconsFixtime, RealType);
100 +    DeclareParameter(ZconsUsingSMD, bool);
101 +    DeclareParameter(UseSolidThermInt, bool);
102 +    DeclareParameter(UseLiquidThermInt, bool);
103 +    DeclareParameter(ThermodynamicIntegrationLambda, RealType);
104 +    DeclareParameter(ThermodynamicIntegrationK, RealType);
105 +    DeclareParameter(ForceFieldVariant, std::string);
106 +    DeclareParameter(ForceFieldFileName, std::string);
107 +    DeclareParameter(ThermIntDistSpringConst, RealType);
108 +    DeclareParameter(ThermIntThetaSpringConst, RealType);
109 +    DeclareParameter(ThermIntOmegaSpringConst, RealType);
110 +    DeclareParameter(SurfaceTension, RealType);
111 +    DeclareParameter(PrintPressureTensor, bool);
112 +    DeclareParameter(TaggedAtomPair, intPair);
113 +    DeclareParameter(PrintTaggedPairDistance, bool);
114 +    DeclareParameter(ElectrostaticSummationMethod, std::string);
115 +    DeclareParameter(ElectrostaticScreeningMethod, std::string);
116 +    DeclareParameter(DampingAlpha, RealType);
117 +    DeclareParameter(Dielectric, RealType);
118 +    DeclareParameter(CutoffPolicy, std::string);
119 +    DeclareParameter(SwitchingFunctionType, std::string);
120 +    DeclareParameter(CompressDumpFile, bool);
121 +    DeclareParameter(OutputForceVector, bool);
122 +    DeclareParameter(SkinThickness, RealType);
123 +    DeclareParameter(StatFileFormat, std::string);    
124 +    DeclareParameter(HydroPropFile, std::string);
125 +    DeclareParameter(Viscosity, RealType);
126 +    DeclareParameter(BeadSize, RealType);  
127 +    DeclareParameter(UseSphericalBoundaryConditions, bool);
128 +    DeclareParameter(FrozenBufferRadius, RealType);
129 +    DeclareParameter(LangevinBufferRadius, RealType);
130 +    DeclareParameter(AccumulateBoxDipole, bool);
131 +    DeclareParameter(NeighborListNeighbors, int);
132 +    DeclareParameter(UseMultipleTemperatureMethod, bool);
133 +    DeclareParameter(MTM_Ce, RealType);
134 +    DeclareParameter(MTM_G, RealType);
135 +    DeclareParameter(MTM_Io, RealType);
136 +    DeclareParameter(MTM_Sigma, RealType);    
137 +    DeclareParameter(MTM_R, RealType);    
138 +    
139 +  public:
140 +    bool addComponent(Component* comp);
141 +    bool addZConsStamp(ZConsStamp* zcons);
142 +    bool addMoleculeStamp(MoleculeStamp* molStamp);
143 +    int getNComponents() {return components_.size();}
144 +    std::vector<Component*> getComponents() {return components_;}
145 +    Component* getComponentAt(int index) {return components_.at(index);}    
146 +    
147 +    int getNZconsStamps() {return zconstraints_.size();}
148 +    std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;}
149 +    ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);}    
150 +    
151 +    virtual void validate();
152 +  private:
153 +    
154 +    std::vector<Component*> components_;
155 +    std::vector<ZConsStamp*> zconstraints_;    
156 +    std::map<std::string, MoleculeStamp*> moleculeStamps_;
157 +    std::pair<int, int> taggedAtomPair_;
158  
59 – /**
60 – * @class Globals Globals.hpp "io/Globals.hpp"
61 – * @brief parsing and storing global parameters for simulation
62 – * @todo need refactorying
63 – */
64 – class Globals{
65 –  
66 – public:
67 –  
68 –  Globals();
69 –  ~Globals();
70 –
71 –  void initalize();
72 –  
73 –  int newComponent( event* the_event );
74 –  int componentAssign( event* the_event );
75 –  int componentEnd( event* the_event );
76 –
77 –  int newZconstraint( event* the_event );
78 –  int zConstraintAssign( event* the_event );
79 –  int zConstraintEnd( event* the_event );
80 –  
81 –  int globalAssign( event* the_event );
82 –  int globalEnd( event* the_event );
83 –
84 –  char*  getForceField( void )      { return force_field; }
85 –  int    getNComponents( void )     { return n_components; }
86 –  double getTargetTemp( void )      { return target_temp; }
87 –  double getTargetPressure( void )  { return target_pressure; }
88 –  double getQmass( void )           { return q_mass; }
89 –  double getTauThermostat( void )   { return tau_thermostat; }
90 –  double getTauBarostat( void )     { return tau_barostat; }
91 –  char*  getEnsemble( void )        { return ensemble; }
92 –  double getDt( void )              { return dt; }
93 –  double getRunTime( void )         { return run_time; }
94 –
95 –  int    getNzConstraints( void )   { return n_zConstraints; }
96 –  char*  getInitialConfig( void )   { return initial_config; }
97 –  char*  getFinalConfig( void )     { return final_config; }
98 –  int    getNMol( void )            { return n_mol; }
99 –  double getDensity( void )         { return density; }
100 –  double getBox( void )             { return box; }
101 –  double getBoxX( void )            { return box_x; }
102 –  double getBoxY( void )            { return box_y; }
103 –  double getBoxZ( void )            { return box_z; }
104 –  double getSampleTime( void )      { return sample_time; }
105 –  double getStatusTime( void )      { return status_time; }
106 –  double getResetTime( void )       { return resetTime; }
107 –  double getThermalTime( void )     { return thermal_time; }
108 –  double getDielectric( void )      { return dielectric; }
109 –  double getRcut( void )            { return rcut; }
110 –  double getRsw( void )             { return rsw; }
111 –  int    getTempSet( void )         { return tempSet; }
112 –  int    getUseInitTime( void )     { return useInitTime; }
113 –  int    getUseInitXSstate( void )  { return useInitXSstate; }
114 –  double getOrthoBoxTolerance(void) { return orthoBoxTolerance; }
115 –  int    getPBC( void )             { return usePBC; }
116 –  char*  getMixingRule( void)       { return mixingRule; }
117 –  double getZconsTime(void)         { return zcons_time; }
118 –  double getZconsTol(void)          { return zcons_tol; }
119 –  char*  getZconsForcePolicy(void)  { return zconsForcePolicy; }
120 –  double getZconsGap(void)          { return zcons_gap; }
121 –  double getZconsFixtime(void)      { return zcons_fixtime; }
122 –  int    getZconsUsingSMD(void)     { return zcons_using_smd; }
123 –  int    getSeed(void)              { return seed; }
124 –  char*  getMinimizer(void)         { return minimizer_name; }
125 –  int    getMinMaxIter(void)        { return minimizer_maxiteration; }
126 –  int    getMinWriteFrq(void)       { return minimizer_writefrq; }
127 –  double getMinStepSize(void)       { return minimizer_stepsize; }
128 –  double getMinFTol(void)           { return minimizer_ftol; }
129 –  double getMinGTol(void)           { return minimizer_gtol; }
130 –  double getMinLSTol(void)          { return minimizer_ls_tol; }
131 –  int    getMinLSMaxIter(void)      { return minimizer_ls_maxiteration; }
132 –  int    getUseSolidThermInt(void)  { return useSolidThermInt; }
133 –  int    getUseLiquidThermInt(void) { return useLiquidThermInt; }
134 –  double getThermIntLambda(void)    { return thermodynamic_integration_lambda; }
135 –  double getThermIntK(void)         { return thermodynamic_integration_k; }
136 –  char*  getForceFieldVariant( void ) { return forcefield_variant; }
137 –  char*  getForceFieldFileName()    { return forcefield_filename; }
138 –  double getDistSpringConst(void)   { return therm_int_dist_spring; }
139 –  double getThetaSpringConst(void)  { return therm_int_theta_spring; }
140 –  double getOmegaSpringConst(void)  { return therm_int_omega_spring; }
141 –  double getSurfaceTension(void)    { return surface_tension; }
142 –  bool   getPrintPressureTensor(void) { return print_pressure_tensor;}
143 –  char*  getElectrostaticSummationMethod(void) { return electrostaticSummationMethod; }
144 –  double getDampingAlpha(void)      { return dampingAlpha; }
145 –  char*  getCutoffPolicy(void)      { return cutoffPolicy; }
146 –  
147 –  short int haveDt( void )            { return have_dt; }
148 –  short int haveRunTime( void )       { return have_run_time; }
149 –  short int haveEnsemble( void )      { return have_ensemble; }
150 –  short int haveTargetTemp( void )    { return have_target_temp; }
151 –  short int haveInitialConfig( void ) { return have_initial_config; }
152 –  short int haveFinalConfig( void )   { return have_final_config; }
153 –  short int haveNMol( void )          { return have_n_mol; }
154 –  short int haveDensity( void )       { return have_density; }
155 –  short int haveBox( void )           { return have_box; }
156 –  short int haveBoxX( void )          { return have_box_x; }
157 –  short int haveBoxY( void )          { return have_box_y; }
158 –  short int haveBoxZ( void )          { return have_box_z; }
159 –  short int haveSampleTime( void )    { return have_sample_time; }
160 –  short int haveResetTime( void )     { return have_reset_time; }
161 –  short int haveStatusTime( void )    { return have_status_time; }
162 –  short int haveThermalTime( void )   { return have_thermal_time; }
163 –  short int haveRcut( void )          { return have_rcut; }
164 –  short int haveRsw( void )           { return have_rsw; }
165 –  short int haveDielectric( void )    { return have_dielectric; }
166 –  short int haveTempSet( void )       { return have_tempSet; }
167 –  short int haveTargetPressure( void ){ return have_target_pressure; }
168 –  short int haveQmass( void )         { return have_q_mass; }
169 –  short int haveTauThermostat( void ) { return have_tau_thermostat; }
170 –  short int haveTauBarostat( void )   { return have_tau_barostat; }
171 –  short int haveZconstraintTime(void) { return have_zcons_time; }
172 –  short int haveZconstraints( void )  { return have_zConstraints; }
173 –  short int haveZconsTol(void)        { return have_zcons_tol; }
174 –  short int haveZconsForcePolicy(void){ return have_zcons_force_policy; }
175 –  short int haveZConsGap(void)        { return have_zcons_gap; }
176 –  short int haveZConsFixTime(void)    { return have_zcons_fixtime; }
177 –  short int haveZConsUsingSMD(void)   { return have_zcons_using_smd; }  
178 –  short int haveSeed(void)            { return have_seed; }
179 –  short int haveMinimizer(void)       { return have_minimizer; }
180 –  short int haveMinMaxIter(void)      { return have_minimizer_maxiteration; }
181 –  short int haveMinWriteFrq(void)     { return have_minimizer_writefrq; }
182 –  short int haveMinStepSize(void)     { return have_minimizer_stepsize; }
183 –  short int haveMinFTol(void)         { return have_minimizer_ftol; }
184 –  short int haveMinGTol(void)         { return have_minimizer_gtol; }
185 –  short int haveMinLSTol(void)        { return have_minimizer_ls_tol; }
186 –  short int haveMinLSMaxIter(void)    { return have_minimizer_ls_maxiteration;}
187 –  short int haveThermIntLambda(void)  { return have_thermodynamic_integration_lambda; }
188 –  short int haveThermIntK(void)       { return have_thermodynamic_integration_k; }
189 –  short int haveForceFieldVariant(void)  { return have_forcefield_variant; }
190 –  short int haveForceFieldFileName(void) { return have_forcefield_filename; }
191 –  short int haveDistSpringConst(void)    { return have_dist_spring_constant; }
192 –  short int haveThetaSpringConst(void)   { return have_theta_spring_constant; }
193 –  short int haveOmegaSpringConst(void)   { return have_omega_spring_constant; }
194 –  short int haveSurfaceTension(void)     { return have_surface_tension; }
195 –  short int havePrintPressureTensor(void) {return have_print_pressure_tensor;}
196 –  short int haveElectrostaticSummationMethod(void) {return have_electro_sum_method;}
197 –  short int haveDampingAlpha(void)       { return have_damping_alpha; }
198 –  short int haveCutoffPolicy(void)       { return have_cutoff_policy; }
199 –
200 –  /* other accessors */
201 –  Component** getComponents( void )   { return components; }
202 –  ZconStamp** getZconStamp( void )    { return zConstraints; }
203 –  
204 – private:
205 –  
206 –
207 –  typedef std::map<std::string, int> CommandMapType;
208 –  CommandMapType command_table;
209 –
210 –  
211 –  char* checkMe( void );
212 –  
213 –  Component* current_component;
214 –  Component** components; // the array of components
215 –
216 –  ZconStamp* current_zConstraint;
217 –  ZconStamp** zConstraints; // the array of zConstraints
218 –
219 –  char force_field[100];
220 –  int n_components;
221 –  int n_zConstraints;
222 –  double target_temp;
223 –  double target_pressure;
224 –  char ensemble[100];
225 –  char mixingRule[100];
226 –  double dt;
227 –  double run_time;
228 –  char initial_config[120];
229 –  char final_config[120];
230 –  int n_mol;
231 –  double density;
232 –  double box;
233 –  double box_x, box_y, box_z;
234 –  double sample_time;
235 –  double status_time;
236 –  double resetTime;
237 –  double orthoBoxTolerance;
238 –  double thermal_time;
239 –  double rcut;
240 –  double rsw;
241 –  double dielectric;
242 –  int tempSet;
243 –  int useInitTime;
244 –  int useInitXSstate;
245 –  int usePBC;
246 –  double q_mass;
247 –  double tau_thermostat;
248 –  double tau_barostat;
249 –  double zcons_time;    
250 –  double zcons_tol;
251 –  char zconsForcePolicy[100];
252 –  double zcons_gap;
253 –  double zcons_fixtime;
254 –  int zcons_using_smd;
255 –  
256 –  int seed;
257 –  char minimizer_name[100];
258 –  int minimizer_maxiteration;
259 –  int minimizer_writefrq;
260 –  double minimizer_stepsize;
261 –  double minimizer_ftol;
262 –  double minimizer_gtol;
263 –  double minimizer_ls_tol;
264 –  int minimizer_ls_maxiteration;
265 –  int useSolidThermInt;
266 –  int useLiquidThermInt;
267 –  double thermodynamic_integration_lambda;
268 –  double thermodynamic_integration_k;
269 –  char forcefield_variant[100];
270 –  char forcefield_filename[100];
271 –  double therm_int_dist_spring;
272 –  double therm_int_theta_spring;
273 –  double therm_int_omega_spring;
274 –  double surface_tension;
275 –  bool print_pressure_tensor;
276 –  char electrostaticSummationMethod[100];
277 –  double dampingAlpha;
278 –  char cutoffPolicy[100];
279 –  
280 –  //required arguments
281 –  short int have_force_field, have_n_components, have_target_temp;
282 –  short int have_target_pressure, have_ensemble, have_dt, have_run_time;
283 –  
284 –  // optional arguments
285 –  short int have_initial_config, have_final_config, have_n_mol;
286 –  short int have_density, have_box, have_box_x, have_box_y, have_box_z;
287 –  short int have_sample_time, have_status_time, have_rcut, have_dielectric;
288 –  short int have_tempSet, have_thermal_time, have_rsw, have_q_mass;
289 –  short int have_tau_thermostat, have_tau_barostat;
290 –  short int have_zcons_time, have_zConstraints, have_n_zConstraints;
291 –  short int have_zcons_tol, have_seed;
292 –  short int have_zcons_force_policy, have_reset_time;
293 –  short int have_zcons_gap, have_zcons_fixtime;
294 –  short int have_zcons_using_smd;
295 –  short int have_minimizer, have_minimizer_maxiteration;
296 –  short int have_minimizer_writefrq, have_minimizer_stepsize;
297 –  short int have_minimizer_ftol, have_minimizer_gtol;
298 –  short int have_minimizer_ls_tol, have_minimizer_ls_maxiteration;
299 –  short int have_thermodynamic_integration_lambda;
300 –  short int have_thermodynamic_integration_k;
301 –  short int have_forcefield_variant;
302 –  short int have_forcefield_filename;  
303 –  short int have_dist_spring_constant;
304 –  short int have_theta_spring_constant;
305 –  short int have_omega_spring_constant;
306 –  short int have_surface_tension;
307 –  short int have_print_pressure_tensor;
308 –  short int have_electro_sum_method;
309 –  short int have_damping_alpha;
310 –  short int have_cutoff_policy;
159   };
160 <
160 > }
161   #endif
162 +

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