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Comparing trunk/src/io/Globals.hpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 710 by chrisfen, Wed Nov 2 20:36:25 2005 UTC

# Line 1 | Line 1
1 < #ifndef __GLOBALS_H__
2 < #define __GLOBALS_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. Acknowledgement of the program authors must be made in any
10 > *    publication of scientific results based in part on use of the
11 > *    program.  An acceptable form of acknowledgement is citation of
12 > *    the article in which the program was described (Matthew
13 > *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 > *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 > *    Parallel Simulation Engine for Molecular Dynamics,"
16 > *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 > *
18 > * 2. Redistributions of source code must retain the above copyright
19 > *    notice, this list of conditions and the following disclaimer.
20 > *
21 > * 3. Redistributions in binary form must reproduce the above copyright
22 > *    notice, this list of conditions and the following disclaimer in the
23 > *    documentation and/or other materials provided with the
24 > *    distribution.
25 > *
26 > * This software is provided "AS IS," without a warranty of any
27 > * kind. All express or implied conditions, representations and
28 > * warranties, including any implied warranty of merchantability,
29 > * fitness for a particular purpose or non-infringement, are hereby
30 > * excluded.  The University of Notre Dame and its licensors shall not
31 > * be liable for any damages suffered by licensee as a result of
32 > * using, modifying or distributing the software or its
33 > * derivatives. In no event will the University of Notre Dame or its
34 > * licensors be liable for any lost revenue, profit or data, or for
35 > * direct, indirect, special, consequential, incidental or punitive
36 > * damages, however caused and regardless of the theory of liability,
37 > * arising out of the use of or inability to use software, even if the
38 > * University of Notre Dame has been advised of the possibility of
39 > * such damages.
40 > */
41 >
42 > #ifndef IO_GLOBALS_HPP
43 > #define IO_GLOBALS_HPP
44  
45   #include <iostream>
46  
47   #include <stdlib.h>
48   #include <vector>
49 + #include <string>
50 + #include <map>
51  
52 < #include "BASS_interface.h"
53 < #include "Component.hpp"
54 < #include "LinkedCommand.hpp"
55 < #include "MakeStamps.hpp"
56 < #include "ZconStamp.hpp"
52 > #include "io/BASS_interface.h"
53 > #include "types/Component.hpp"
54 > #include "types/MakeStamps.hpp"
55 > #include "types/ZconStamp.hpp"
56 > #include "utils/CaseConversion.hpp"
57  
58 < using namespace std;
58 > template<typename T>
59 > struct ParameterTraits;
60  
61 < class Globals{
62 <  
63 < public:
64 <  
21 <  Globals();
22 <  ~Globals();
61 > //string
62 > template<>                    
63 > struct ParameterTraits<std::string>{
64 >  typedef std::string RepType;       // Representation type of the value
65  
66 <  void initalize();
67 <  
68 <  int newComponent( event* the_event );
69 <  int componentAssign( event* the_event );
70 <  int componentEnd( event* the_event );
66 > template<typename T> static bool    convert(T v, RepType& r){return false;} // !NB everything is ok
67 > template<typename T> static RepType convert(T v)            {RepType tmp; convert(v,tmp);return tmp;}
68 >  static bool convert(RepType v, RepType& r) { r = v; return true;}
69 >  static std::string getParamType() { return "string";}  
70 > };
71 > //bool
72 > template<>                    
73 > struct ParameterTraits<bool>{
74 >  typedef bool RepType;
75 >  template<typename T> static bool    convert(T, RepType&){return false;}
76 >  template<typename T> static RepType convert(T v)        {RepType tmp; convert(v,tmp);return tmp;}
77 >  static bool convert(std::string v, RepType& r) {
78 >    oopse::toLower(v);
79 >    bool result = false;
80 >    if (v == "true") {
81 >        r = true;
82 >        result = true;
83 >    } else if (v == "false") {
84 >        r = false;
85 >        result = true;
86 >    }
87 >    
88 >     return result;
89 >  }
90 >  static std::string getParamType() { return "bool";}  
91 > };
92  
93 <  int newZconstraint( event* the_event );
94 <  int zConstraintAssign( event* the_event );
95 <  int zConstraintEnd( event* the_event );
96 <  
97 <  int globalAssign( event* the_event );
98 <  int globalEnd( event* the_event );
99 <
100 <  char*  getForceField( void )      { return force_field; }
101 <  int    getNComponents( void )     { return n_components; }
39 <  double getTargetTemp( void )      { return target_temp; }
40 <  double getTargetPressure( void )  { return target_pressure; }
41 <  double getQmass( void )           { return q_mass; }
42 <  double getTauThermostat( void )   { return tau_thermostat; }
43 <  double getTauBarostat( void )     { return tau_barostat; }
44 <  char*  getEnsemble( void )        { return ensemble; }
45 <  double getDt( void )              { return dt; }
46 <  double getRunTime( void )         { return run_time; }
47 <
48 <  int    getNzConstraints( void )   { return n_zConstraints; }
49 <  char*  getInitialConfig( void )   { return initial_config; }
50 <  char*  getFinalConfig( void )     { return final_config; }
51 <  int    getNMol( void )            { return n_mol; }
52 <  double getDensity( void )         { return density; }
53 <  double getBox( void )             { return box; }
54 <  double getBoxX( void )            { return box_x; }
55 <  double getBoxY( void )            { return box_y; }
56 <  double getBoxZ( void )            { return box_z; }
57 <  double getSampleTime( void )      { return sample_time; }
58 <  double getStatusTime( void )      { return status_time; }
59 <  double getResetTime( void )       { return resetTime; }
60 <  double getThermalTime( void )     { return thermal_time; }
61 <  double getDielectric( void )      { return dielectric; }
62 <  double getRcut( void )            { return rcut; }
63 <  double getRsw( void )             { return rsw; }
64 <  int    getTempSet( void )         { return tempSet; }
65 <  int    getUseInitTime( void )     { return useInitTime; }
66 <  int    getUseInitXSstate( void )  { return useInitXSstate; }
67 <  double getOrthoBoxTolerance(void) { return orthoBoxTolerance; }
68 <  int    getPBC( void )             { return usePBC; }
69 <  int    getUseRF( void )           { return useRF; }
70 <  char*  getMixingRule( void)       { return mixingRule; }
71 <  double getZconsTime(void)         { return zcons_time; }
72 <  double getZconsTol(void)          { return zcons_tol; }
73 <  char*  getZconsForcePolicy(void)  { return zconsForcePolicy; }
74 <  double getZconsGap(void)          { return zcons_gap; }
75 <  double getZconsFixtime(void)      { return zcons_fixtime; }
76 <  int    getZconsUsingSMD(void)     { return zcons_using_smd; }
77 <  int    getSeed(void)              { return seed; }
78 <  char*  getMinimizer(void)         { return minimizer_name; }
79 <  int    getMinMaxIter(void)        { return minimizer_maxiteration; }
80 <  int    getMinWriteFrq(void)       { return minimizer_writefrq; }
81 <  double getMinStepSize(void)       { return minimizer_stepsize; }
82 <  double getMinFTol(void)           { return minimizer_ftol; }
83 <  double getMinGTol(void)           { return minimizer_gtol; }
84 <  double getMinLSTol(void)          { return minimizer_ls_tol; }
85 <  int    getMinLSMaxIter(void)      { return minimizer_ls_maxiteration; }
86 <  int    getUseSolidThermInt(void)  { return useSolidThermInt; }
87 <  int    getUseLiquidThermInt(void) { return useLiquidThermInt; }
88 <  double getThermIntLambda(void)    { return thermodynamic_integration_lambda; }
89 <  double getThermIntK(void)         { return thermodynamic_integration_k; }
90 <  char*  getForceFieldVariant( void ) { return forcefield_variant; }
93 > //int  
94 > template<>
95 > struct ParameterTraits<int>{
96 >    typedef int RepType;
97 >    template<typename T> static bool    convert(T, RepType&){return false;}
98 >    template<typename T> static RepType convert(T v)        {RepType tmp; convert(v,tmp);return tmp;}
99 >    static bool convert(RepType v, RepType& r)            { r=v; return true;}
100 >    static std::string getParamType() { return "int";}  
101 > };
102  
103 <  short int haveDt( void )            { return have_dt; }
104 <  short int haveRunTime( void )       { return have_run_time; }
105 <  short int haveEnsemble( void )      { return have_ensemble; }
106 <  short int haveTargetTemp( void )    { return have_target_temp; }
107 <  short int haveInitialConfig( void ) { return have_initial_config; }
108 <  short int haveFinalConfig( void )   { return have_final_config; }
109 <  short int haveNMol( void )          { return have_n_mol; }
110 <  short int haveDensity( void )       { return have_density; }
111 <  short int haveBox( void )           { return have_box; }
112 <  short int haveBoxX( void )          { return have_box_x; }
102 <  short int haveBoxY( void )          { return have_box_y; }
103 <  short int haveBoxZ( void )          { return have_box_z; }
104 <  short int haveSampleTime( void )    { return have_sample_time; }
105 <  short int haveResetTime( void )     { return have_reset_time; }
106 <  short int haveStatusTime( void )    { return have_status_time; }
107 <  short int haveThermalTime( void )   { return have_thermal_time; }
108 <  short int haveRcut( void )          { return have_rcut; }
109 <  short int haveRsw( void )           { return have_rsw; }
110 <  short int haveDielectric( void )    { return have_dielectric; }
111 <  short int haveTempSet( void )       { return have_tempSet; }
112 <  short int haveTargetPressure( void ){ return have_target_pressure; }
113 <  short int haveQmass( void )         { return have_q_mass; }
114 <  short int haveTauThermostat( void ) { return have_tau_thermostat; }
115 <  short int haveTauBarostat( void )   { return have_tau_barostat; }
116 <  short int haveZconstraintTime(void) { return have_zcons_time; }
117 <  short int haveZconstraints( void )  { return have_zConstraints; }
118 <  short int haveZconsTol(void)        { return have_zcons_tol; }
119 <  short int haveZconsForcePolicy(void){ return have_zcons_force_policy; }
120 <  short int haveZConsGap(void)        { return have_zcons_gap; }
121 <  short int haveZConsFixTime(void)    { return have_zcons_fixtime; }
122 <  short int haveZConsUsingSMD(void)   { return have_zcons_using_smd; }  
123 <  short int haveSeed(void)            { return have_seed; }
124 <  short int haveMinimizer(void)       { return have_minimizer; }
125 <  short int haveMinMaxIter(void)      { return have_minimizer_maxiteration; }
126 <  short int haveMinWriteFrq(void)     { return have_minimizer_writefrq; }
127 <  short int haveMinStepSize(void)     { return have_minimizer_stepsize; }
128 <  short int haveMinFTol(void)         { return have_minimizer_ftol; }
129 <  short int haveMinGTol(void)         { return have_minimizer_gtol; }
130 <  short int haveMinLSTol(void)        { return have_minimizer_ls_tol; }
131 <  short int haveMinLSMaxIter(void)    { return have_minimizer_ls_maxiteration;}
132 <  short int haveThermIntLambda(void)  { return have_thermodynamic_integration_lambda; }
133 <  short int haveThermIntK(void)       { return have_thermodynamic_integration_k; }
134 <  short int haveForceFieldVariant(void) { return have_forcefield_variant; }
103 > //double
104 > template<>                    
105 > struct ParameterTraits<double>{
106 >    typedef double RepType;
107 >    template<typename T> static bool    convert(T, RepType&){return false;}
108 >    template<typename T> static RepType convert(T v)        {RepType tmp; convert(v,tmp);return tmp;}
109 >    static bool convert(RepType v, RepType& r)            {r=v; return true;}
110 >    static bool convert(int v, RepType& r)                {r = static_cast<double>(v); return true;}
111 >    static std::string getParamType() { return "double";}    
112 > };
113  
136 –  /* other accessors */
137 –  Component** getComponents( void )   { return components; }
138 –  ZconStamp** getZconStamp( void )    { return zConstraints; }
139 –  
140 – private:
141 –  
142 –  int hash_size;
143 –  int hash_shift;
144 –  int hash( char* text );
145 –  void addHash( char* text, int token );
146 –  LinkedCommand** command_table;
147 –  
148 –  char* checkMe( void );
149 –  
150 –  Component* current_component;
151 –  Component** components; // the array of components
114  
115 <  ZconStamp* current_zConstraint;
116 <  ZconStamp** zConstraints; // the array of zConstraints
115 > class ParameterBase {
116 >  public:    
117 >    ParameterBase() : keyword_(), optional_(false), defaultValue_(false), empty_(true) {}
118 >    virtual ~ParameterBase() {}
119 >    bool isOptional() {return optional_;}
120 >    void setOptional(bool optional) {optional_ = optional;}
121 >    bool hasDefaultValue() {return defaultValue_;}
122 >    virtual bool isValid() { return true;}
123 >    const std::string& getKeyword() {return keyword_;}
124 >    void setKeyword(const std::string& keyword) { keyword_ = keyword;}
125 >    bool empty() {return empty_;}
126 >    virtual bool setData(std::string) = 0;
127 >    virtual bool setData(int) = 0;
128 >    virtual bool setData(double) = 0;
129 >    virtual std::string getParamType() = 0;
130 >  protected:
131 >    std::string keyword_;
132 >    bool optional_;
133 >    bool defaultValue_;
134 >    bool empty_;
135 > };
136  
137 <  char force_field[100];
138 <  int n_components;
139 <  int n_zConstraints;
140 <  double target_temp;
141 <  double target_pressure;
142 <  char ensemble[100];
162 <  char mixingRule[100];
163 <  double dt;
164 <  double run_time;
165 <  char initial_config[120];
166 <  char final_config[120];
167 <  int n_mol;
168 <  double density;
169 <  double box;
170 <  double box_x, box_y, box_z;
171 <  double sample_time;
172 <  double status_time;
173 <  double resetTime;
174 <  double orthoBoxTolerance;
175 <  double thermal_time;
176 <  double rcut;
177 <  double rsw;
178 <  double dielectric;
179 <  int tempSet;
180 <  int useInitTime;
181 <  int useInitXSstate;
182 <  int usePBC;
183 <  int useRF;
184 <  double q_mass;
185 <  double tau_thermostat;
186 <  double tau_barostat;
187 <  double zcons_time;    
188 <  double zcons_tol;
189 <  char zconsForcePolicy[100];
190 <  double zcons_gap;
191 <  double zcons_fixtime;
192 <  int zcons_using_smd;
193 <  
194 <  int seed;
195 <  char minimizer_name[100];
196 <  int minimizer_maxiteration;
197 <  int minimizer_writefrq;
198 <  double minimizer_stepsize;
199 <  double minimizer_ftol;
200 <  double minimizer_gtol;
201 <  double minimizer_ls_tol;
202 <  int minimizer_ls_maxiteration;
203 <  int useSolidThermInt;
204 <  int useLiquidThermInt;
205 <  double thermodynamic_integration_lambda;
206 <  double thermodynamic_integration_k;
207 <  char forcefield_variant[100];
137 > template<class ParamType>
138 > class Parameter : public ParameterBase{
139 >   public:    
140 >    typedef ParameterTraits<ParamType> ValueType;
141 >     void setDefaultValue(const ParamType& value) {data_ = value; defaultValue_ = true;}
142 >     ParamType getData() { return data_;}
143  
144 <  //required arguments
145 <  short int have_force_field, have_n_components, have_target_temp;
146 <  short int have_target_pressure, have_ensemble, have_dt, have_run_time;
147 <  
148 <  // optional arguments
149 <  short int have_initial_config, have_final_config, have_n_mol;
150 <  short int have_density, have_box, have_box_x, have_box_y, have_box_z;
151 <  short int have_sample_time, have_status_time, have_rcut, have_dielectric;
152 <  short int have_tempSet, have_thermal_time, have_rsw, have_q_mass;
153 <  short int have_tau_thermostat, have_tau_barostat;
154 <  short int have_zcons_time, have_zConstraints, have_n_zConstraints;
155 <  short int have_zcons_tol, have_seed;
156 <  short int have_zcons_force_policy, have_reset_time;
157 <  short int have_zcons_gap, have_zcons_fixtime;
158 <  short int have_zcons_using_smd;
159 <  short int have_minimizer, have_minimizer_maxiteration;
160 <  short int have_minimizer_writefrq, have_minimizer_stepsize;
161 <  short int have_minimizer_ftol, have_minimizer_gtol;
162 <  short int have_minimizer_ls_tol, have_minimizer_ls_maxiteration;
163 <  short int have_thermodynamic_integration_lambda;
164 <  short int have_thermodynamic_integration_k;
165 <  short int have_forcefield_variant;
144 >    virtual bool setData(std::string sval) {
145 >        return internalSetData<std::string>(sval);
146 >    }
147 >    virtual bool setData(int ival) {
148 >        return internalSetData<int>(ival);
149 >    }
150 >    
151 >    virtual bool setData(double dval) {
152 >        return internalSetData<double>(dval);
153 >    }
154 >
155 >    virtual std::string getParamType() { return ParameterTraits<ParamType>::getParamType();}
156 >   private:
157 >     template<class T> bool internalSetData(T data) {
158 >        ParamType tmp;
159 >        bool result = ValueType::convert(data, tmp);
160 >        if (result) {
161 >            empty_ = false;
162 >            data_ = tmp;
163 >        }
164 >        return result;
165 >     }
166 >    
167 >   private:
168 >     ParamType data_;
169 >      
170   };
171  
172 + #define DeclareParameter(NAME, TYPE)         \
173 +    private:                                                   \
174 +      Parameter<TYPE> NAME;                                     \
175 +    public:                                                      \
176 +      bool have##NAME() { return !NAME.empty();}  \
177 +      TYPE get##NAME() { return NAME.getData();}
178 +
179 +
180 + class Globals {
181 +  public:
182 +    Globals();
183 +    
184 +  DeclareParameter(ForceField, std::string);
185 +  DeclareParameter(NComponents, int);  
186 +  DeclareParameter(TargetTemp, double);
187 +  DeclareParameter(Ensemble, std::string);
188 +  DeclareParameter(Dt, double);
189 +  DeclareParameter(RunTime, double);
190 +  DeclareParameter(InitialConfig, std::string);
191 +  DeclareParameter(FinalConfig, std::string);
192 +  DeclareParameter(NMol, int);
193 +  DeclareParameter(Density, double);
194 +  DeclareParameter(Box, double);
195 +  DeclareParameter(BoxX, double);
196 +  DeclareParameter(BoxY, double);
197 +  DeclareParameter(BoxZ, double);
198 +  DeclareParameter(SampleTime, double);
199 +  DeclareParameter(ResetTime, double);
200 +  DeclareParameter(StatusTime, double);
201 +  DeclareParameter(CutoffRadius, double);
202 +  DeclareParameter(SwitchingRadius, double);
203 +  DeclareParameter(Dielectric, double);
204 +  DeclareParameter(TempSet, bool);
205 +  DeclareParameter(ThermalTime, double);
206 +  DeclareParameter(MixingRule, std::string);
207 +  DeclareParameter(UsePeriodicBoundaryConditions, bool);
208 +  DeclareParameter(TargetPressure, double);
209 +  DeclareParameter(TauThermostat, double);
210 +  DeclareParameter(TauBarostat, double);
211 +  DeclareParameter(ZconsTime, double);
212 +  DeclareParameter(NZconstraints, int);
213 +  DeclareParameter(ZconsTol, double);
214 +  DeclareParameter(ZconsForcePolicy, std::string);
215 +  DeclareParameter(Seed, int);
216 +  DeclareParameter(UseInitalTime, bool);
217 +  DeclareParameter(UseIntialExtendedSystemState, bool);
218 +  DeclareParameter(OrthoBoxTolerance, double);
219 +  DeclareParameter(Minimizer, std::string);
220 +  DeclareParameter(MinimizerMaxIter, double);
221 +  DeclareParameter(MinimizerWriteFrq, int);
222 +  DeclareParameter(MinimizerStepSize, double);
223 +  DeclareParameter(MinimizerFTol, double);
224 +  DeclareParameter(MinimizerGTol, double);
225 +  DeclareParameter(MinimizerLSTol, double);
226 +  DeclareParameter(MinimizerLSMaxIter, int);
227 +  DeclareParameter(ZconsGap, double);
228 +  DeclareParameter(ZconsFixtime, double);
229 +  DeclareParameter(ZconsUsingSMD, bool);
230 +  DeclareParameter(UseSolidThermInt, bool);
231 +  DeclareParameter(UseLiquidThermInt, bool);
232 +  DeclareParameter(ThermodynamicIntegrationLambda, double);
233 +  DeclareParameter(ThermodynamicIntegrationK, double);
234 +  DeclareParameter(ForceFieldVariant, std::string);
235 +  DeclareParameter(ForceFieldFileName, std::string);
236 +  DeclareParameter(ThermIntDistSpringConst, double);
237 +  DeclareParameter(ThermIntThetaSpringConst, double);
238 +  DeclareParameter(ThermIntOmegaSpringConst, double);
239 +  DeclareParameter(SurfaceTension, double);
240 +  DeclareParameter(PrintPressureTensor, bool);
241 +  DeclareParameter(ElectrostaticSummationMethod, std::string);
242 +  DeclareParameter(ScreeningMethod, std::string);
243 +  DeclareParameter(DampingAlpha, double);
244 +  DeclareParameter(CutoffPolicy, std::string);
245 +  DeclareParameter(CompressDumpFile, bool);
246 +  DeclareParameter(SkinThickness, double);
247 +  DeclareParameter(StatFileFormat, std::string);    
248 +
249 +  private:
250 +    typedef std::map<std::string, ParameterBase*> ParamMap;
251 +    ParamMap parameters_;
252 +    
253 +    Component* current_component;
254 +    Component** components; // the array of components
255 +
256 +    ZconStamp* current_zConstraint;
257 +    ZconStamp** zConstraints; // the array of zConstraints
258 +
259 +    char* checkMe();
260 +
261 +  public:
262 +    int newComponent( event* the_event );
263 +    int componentAssign( event* the_event );
264 +    int componentEnd( event* the_event );
265 +
266 +    int newZconstraint( event* the_event );
267 +    int zConstraintAssign( event* the_event );
268 +    int zConstraintEnd( event* the_event );
269 +  
270 +    int globalAssign( event* the_event );
271 +    int globalEnd( event* the_event );    
272 +
273 +    ZconStamp** getZconStamp() {return zConstraints;}
274 +    Component** getComponents() {return components;}
275 + };
276   #endif
277 +

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