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root/OpenMD/trunk/src/io/Globals.hpp
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Comparing trunk/src/io/Globals.hpp (file contents):
Revision 598 by chrisfen, Thu Sep 15 00:14:35 2005 UTC vs.
Revision 770 by tim, Fri Dec 2 15:38:03 2005 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 +    Globals();
61 +    virtual ~Globals();
62 +    
63 +  DeclareParameter(ForceField, std::string);
64 +  DeclareParameter(TargetTemp, double);
65 +  DeclareParameter(Ensemble, std::string);
66 +  DeclareParameter(Dt, double);
67 +  DeclareParameter(RunTime, double);
68 +  DeclareParameter(InitialConfig, std::string);
69 +  DeclareParameter(FinalConfig, std::string);
70 +  DeclareParameter(SampleTime, double);
71 +  DeclareParameter(ResetTime, double);
72 +  DeclareParameter(StatusTime, double);
73 +  DeclareParameter(CutoffRadius, double);
74 +  DeclareParameter(SwitchingRadius, double);
75 +  DeclareParameter(Dielectric, double);
76 +  DeclareParameter(TempSet, bool);
77 +  DeclareParameter(ThermalTime, double);
78 +  DeclareParameter(MixingRule, std::string);
79 +  DeclareParameter(UsePeriodicBoundaryConditions, bool);
80 +  DeclareParameter(TargetPressure, double);
81 +  DeclareParameter(TauThermostat, double);
82 +  DeclareParameter(TauBarostat, double);
83 +  DeclareParameter(ZconsTime, double);
84 +  DeclareParameter(ZconsTol, double);
85 +  DeclareParameter(ZconsForcePolicy, std::string);
86 +  DeclareParameter(Seed, int);
87 +  DeclareParameter(UseInitalTime, bool);
88 +  DeclareParameter(UseIntialExtendedSystemState, bool);
89 +  DeclareParameter(OrthoBoxTolerance, double);
90 +  DeclareParameter(Minimizer, std::string);
91 +  DeclareParameter(MinimizerMaxIter, double);
92 +  DeclareParameter(MinimizerWriteFrq, int);
93 +  DeclareParameter(MinimizerStepSize, double);
94 +  DeclareParameter(MinimizerFTol, double);
95 +  DeclareParameter(MinimizerGTol, double);
96 +  DeclareParameter(MinimizerLSTol, double);
97 +  DeclareParameter(MinimizerLSMaxIter, int);
98 +  DeclareParameter(ZconsGap, double);
99 +  DeclareParameter(ZconsFixtime, double);
100 +  DeclareParameter(ZconsUsingSMD, bool);
101 +  DeclareParameter(UseSolidThermInt, bool);
102 +  DeclareParameter(UseLiquidThermInt, bool);
103 +  DeclareParameter(ThermodynamicIntegrationLambda, double);
104 +  DeclareParameter(ThermodynamicIntegrationK, double);
105 +  DeclareParameter(ForceFieldVariant, std::string);
106 +  DeclareParameter(ForceFieldFileName, std::string);
107 +  DeclareParameter(ThermIntDistSpringConst, double);
108 +  DeclareParameter(ThermIntThetaSpringConst, double);
109 +  DeclareParameter(ThermIntOmegaSpringConst, double);
110 +  DeclareParameter(SurfaceTension, double);
111 +  DeclareParameter(PrintPressureTensor, bool);
112 +  DeclareParameter(ElectrostaticSummationMethod, std::string);
113 +  DeclareParameter(ElectrostaticScreeningMethod, std::string);
114 +  DeclareParameter(DampingAlpha, double);
115 +  DeclareParameter(CutoffPolicy, std::string);
116 +  DeclareParameter(SwitchingFunctionType, std::string);
117 +  DeclareParameter(CompressDumpFile, bool);
118 +  DeclareParameter(OutputForceVector, bool);
119 +  DeclareParameter(SkinThickness, double);
120 +  DeclareParameter(StatFileFormat, std::string);    
121  
122 +  public:
123 +    bool addComponent(Component* comp);
124 +    bool addZConsStamp(ZConsStamp* zcons);
125 +    bool addMoleculeStamp(MoleculeStamp* molStamp);
126 +    int getNComponents() {return components_.size();}
127 +    std::vector<Component*> getComponents() {return components_;}
128 +    Component* getComponentAt(int index) {return components_.at(index);}    
129  
130 < /**
131 < * @class Globals Globals.hpp "io/Globals.hpp"
132 < * @brief parsing and storing global parameters for simulation
62 < * @todo need refactorying
63 < */
64 < class Globals{
65 <  
66 < public:
67 <  
68 <  Globals();
69 <  ~Globals();
130 >    int getNZconsStamps() {return zconstraints_.size();}
131 >    std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;}
132 >    ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);}    
133  
134 <  void initalize();
135 <  
136 <  int newComponent( event* the_event );
137 <  int componentAssign( event* the_event );
138 <  int componentEnd( event* the_event );
134 >    virtual void validate();
135 >  private:
136 >    std::vector<Component*> components_;
137 >    std::vector<ZConsStamp*> zconstraints_;    
138 >    std::map<std::string, MoleculeStamp*> moleculeStamps_;
139  
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 –  int    getUseRF( void )           { return useRF; }
117 –  char*  getMixingRule( void)       { return mixingRule; }
118 –  double getZconsTime(void)         { return zcons_time; }
119 –  double getZconsTol(void)          { return zcons_tol; }
120 –  char*  getZconsForcePolicy(void)  { return zconsForcePolicy; }
121 –  double getZconsGap(void)          { return zcons_gap; }
122 –  double getZconsFixtime(void)      { return zcons_fixtime; }
123 –  int    getZconsUsingSMD(void)     { return zcons_using_smd; }
124 –  int    getSeed(void)              { return seed; }
125 –  char*  getMinimizer(void)         { return minimizer_name; }
126 –  int    getMinMaxIter(void)        { return minimizer_maxiteration; }
127 –  int    getMinWriteFrq(void)       { return minimizer_writefrq; }
128 –  double getMinStepSize(void)       { return minimizer_stepsize; }
129 –  double getMinFTol(void)           { return minimizer_ftol; }
130 –  double getMinGTol(void)           { return minimizer_gtol; }
131 –  double getMinLSTol(void)          { return minimizer_ls_tol; }
132 –  int    getMinLSMaxIter(void)      { return minimizer_ls_maxiteration; }
133 –  int    getUseSolidThermInt(void)  { return useSolidThermInt; }
134 –  int    getUseLiquidThermInt(void) { return useLiquidThermInt; }
135 –  double getThermIntLambda(void)    { return thermodynamic_integration_lambda; }
136 –  double getThermIntK(void)         { return thermodynamic_integration_k; }
137 –  char*  getForceFieldVariant( void ) { return forcefield_variant; }
138 –  char*  getForceFieldFileName()    { return forcefield_filename; }
139 –  double getDistSpringConst(void)   { return therm_int_dist_spring; }
140 –  double getThetaSpringConst(void)  { return therm_int_theta_spring; }
141 –  double getOmegaSpringConst(void)  { return therm_int_omega_spring; }
142 –  double getSurfaceTension(void)    { return surface_tension; }
143 –  bool   getPrintPressureTensor(void) { return print_pressure_tensor;}
144 –  char*  getCoulombicCorrection(void) { return coulombicCorrection; }
145 –  double getDampingAlpha(void)      { return dampingAlpha; }
146 –  char*  getCutoffPolicy(void)      { return cutoffPolicy; }
147 –  
148 –  short int haveDt( void )            { return have_dt; }
149 –  short int haveRunTime( void )       { return have_run_time; }
150 –  short int haveEnsemble( void )      { return have_ensemble; }
151 –  short int haveTargetTemp( void )    { return have_target_temp; }
152 –  short int haveInitialConfig( void ) { return have_initial_config; }
153 –  short int haveFinalConfig( void )   { return have_final_config; }
154 –  short int haveNMol( void )          { return have_n_mol; }
155 –  short int haveDensity( void )       { return have_density; }
156 –  short int haveBox( void )           { return have_box; }
157 –  short int haveBoxX( void )          { return have_box_x; }
158 –  short int haveBoxY( void )          { return have_box_y; }
159 –  short int haveBoxZ( void )          { return have_box_z; }
160 –  short int haveSampleTime( void )    { return have_sample_time; }
161 –  short int haveResetTime( void )     { return have_reset_time; }
162 –  short int haveStatusTime( void )    { return have_status_time; }
163 –  short int haveThermalTime( void )   { return have_thermal_time; }
164 –  short int haveRcut( void )          { return have_rcut; }
165 –  short int haveRsw( void )           { return have_rsw; }
166 –  short int haveDielectric( void )    { return have_dielectric; }
167 –  short int haveTempSet( void )       { return have_tempSet; }
168 –  short int haveTargetPressure( void ){ return have_target_pressure; }
169 –  short int haveQmass( void )         { return have_q_mass; }
170 –  short int haveTauThermostat( void ) { return have_tau_thermostat; }
171 –  short int haveTauBarostat( void )   { return have_tau_barostat; }
172 –  short int haveZconstraintTime(void) { return have_zcons_time; }
173 –  short int haveZconstraints( void )  { return have_zConstraints; }
174 –  short int haveZconsTol(void)        { return have_zcons_tol; }
175 –  short int haveZconsForcePolicy(void){ return have_zcons_force_policy; }
176 –  short int haveZConsGap(void)        { return have_zcons_gap; }
177 –  short int haveZConsFixTime(void)    { return have_zcons_fixtime; }
178 –  short int haveZConsUsingSMD(void)   { return have_zcons_using_smd; }  
179 –  short int haveSeed(void)            { return have_seed; }
180 –  short int haveMinimizer(void)       { return have_minimizer; }
181 –  short int haveMinMaxIter(void)      { return have_minimizer_maxiteration; }
182 –  short int haveMinWriteFrq(void)     { return have_minimizer_writefrq; }
183 –  short int haveMinStepSize(void)     { return have_minimizer_stepsize; }
184 –  short int haveMinFTol(void)         { return have_minimizer_ftol; }
185 –  short int haveMinGTol(void)         { return have_minimizer_gtol; }
186 –  short int haveMinLSTol(void)        { return have_minimizer_ls_tol; }
187 –  short int haveMinLSMaxIter(void)    { return have_minimizer_ls_maxiteration;}
188 –  short int haveThermIntLambda(void)  { return have_thermodynamic_integration_lambda; }
189 –  short int haveThermIntK(void)       { return have_thermodynamic_integration_k; }
190 –  short int haveForceFieldVariant(void)  { return have_forcefield_variant; }
191 –  short int haveForceFieldFileName(void) { return have_forcefield_filename; }
192 –  short int haveDistSpringConst(void)    { return have_dist_spring_constant; }
193 –  short int haveThetaSpringConst(void)   { return have_theta_spring_constant; }
194 –  short int haveOmegaSpringConst(void)   { return have_omega_spring_constant; }
195 –  short int haveSurfaceTension(void)     { return have_surface_tension; }
196 –  short int havePrintPressureTensor(void) {return have_print_pressure_tensor;}
197 –  short int haveCoulombicCorrection(void) {return have_coulombic_correction;}
198 –  short int haveDampingAlpha(void)       { return have_damping_alpha; }
199 –  short int haveCutoffPolicy(void)       { return have_cutoff_policy; }
200 –
201 –  /* other accessors */
202 –  Component** getComponents( void )   { return components; }
203 –  ZconStamp** getZconStamp( void )    { return zConstraints; }
204 –  
205 – private:
206 –  
207 –
208 –  typedef std::map<std::string, int> CommandMapType;
209 –  CommandMapType command_table;
210 –
211 –  
212 –  char* checkMe( void );
213 –  
214 –  Component* current_component;
215 –  Component** components; // the array of components
216 –
217 –  ZconStamp* current_zConstraint;
218 –  ZconStamp** zConstraints; // the array of zConstraints
219 –
220 –  char force_field[100];
221 –  int n_components;
222 –  int n_zConstraints;
223 –  double target_temp;
224 –  double target_pressure;
225 –  char ensemble[100];
226 –  char mixingRule[100];
227 –  double dt;
228 –  double run_time;
229 –  char initial_config[120];
230 –  char final_config[120];
231 –  int n_mol;
232 –  double density;
233 –  double box;
234 –  double box_x, box_y, box_z;
235 –  double sample_time;
236 –  double status_time;
237 –  double resetTime;
238 –  double orthoBoxTolerance;
239 –  double thermal_time;
240 –  double rcut;
241 –  double rsw;
242 –  double dielectric;
243 –  int tempSet;
244 –  int useInitTime;
245 –  int useInitXSstate;
246 –  int usePBC;
247 –  int useRF;
248 –  double q_mass;
249 –  double tau_thermostat;
250 –  double tau_barostat;
251 –  double zcons_time;    
252 –  double zcons_tol;
253 –  char zconsForcePolicy[100];
254 –  double zcons_gap;
255 –  double zcons_fixtime;
256 –  int zcons_using_smd;
257 –  
258 –  int seed;
259 –  char minimizer_name[100];
260 –  int minimizer_maxiteration;
261 –  int minimizer_writefrq;
262 –  double minimizer_stepsize;
263 –  double minimizer_ftol;
264 –  double minimizer_gtol;
265 –  double minimizer_ls_tol;
266 –  int minimizer_ls_maxiteration;
267 –  int useSolidThermInt;
268 –  int useLiquidThermInt;
269 –  double thermodynamic_integration_lambda;
270 –  double thermodynamic_integration_k;
271 –  char forcefield_variant[100];
272 –  char forcefield_filename[100];
273 –  double therm_int_dist_spring;
274 –  double therm_int_theta_spring;
275 –  double therm_int_omega_spring;
276 –  double surface_tension;
277 –  bool print_pressure_tensor;
278 –  char coulombicCorrection[100];
279 –  double dampingAlpha;
280 –  char cutoffPolicy[100];
281 –  
282 –  //required arguments
283 –  short int have_force_field, have_n_components, have_target_temp;
284 –  short int have_target_pressure, have_ensemble, have_dt, have_run_time;
285 –  
286 –  // optional arguments
287 –  short int have_initial_config, have_final_config, have_n_mol;
288 –  short int have_density, have_box, have_box_x, have_box_y, have_box_z;
289 –  short int have_sample_time, have_status_time, have_rcut, have_dielectric;
290 –  short int have_tempSet, have_thermal_time, have_rsw, have_q_mass;
291 –  short int have_tau_thermostat, have_tau_barostat;
292 –  short int have_zcons_time, have_zConstraints, have_n_zConstraints;
293 –  short int have_zcons_tol, have_seed;
294 –  short int have_zcons_force_policy, have_reset_time;
295 –  short int have_zcons_gap, have_zcons_fixtime;
296 –  short int have_zcons_using_smd;
297 –  short int have_minimizer, have_minimizer_maxiteration;
298 –  short int have_minimizer_writefrq, have_minimizer_stepsize;
299 –  short int have_minimizer_ftol, have_minimizer_gtol;
300 –  short int have_minimizer_ls_tol, have_minimizer_ls_maxiteration;
301 –  short int have_thermodynamic_integration_lambda;
302 –  short int have_thermodynamic_integration_k;
303 –  short int have_forcefield_variant;
304 –  short int have_forcefield_filename;  
305 –  short int have_dist_spring_constant;
306 –  short int have_theta_spring_constant;
307 –  short int have_omega_spring_constant;
308 –  short int have_surface_tension;
309 –  short int have_print_pressure_tensor;
310 –  short int have_coulombic_correction;
311 –  short int have_damping_alpha;
312 –  short int have_cutoff_policy;
140   };
141 <
141 > }
142   #endif
143 +

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