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Comparing trunk/src/io/Globals.hpp (file contents):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 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. 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, 24107 (2008).          
39 > * [4]  Vardeman & Gezelter, in progress (2009).                        
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  
9 – #include "io/BASS_interface.h"
52   #include "types/Component.hpp"
53 < #include "io/LinkedCommand.hpp"
54 < #include "types/MakeStamps.hpp"
55 < #include "types/ZconStamp.hpp"
53 > #include "types/ZconsStamp.hpp"
54 > #include "types/RestraintStamp.hpp"
55 > #include "types/MoleculeStamp.hpp"
56 > #include "utils/ParameterManager.hpp"
57  
58 < using namespace std;
58 > namespace OpenMD {
59 >  class Globals : public DataHolder {
60 >  public:
61 >    typedef std::pair<int, int> intPair;
62  
63 < class Globals{
64 <  
65 < public:
66 <  
67 <  Globals();
68 <  ~Globals();
63 >    Globals();
64 >    virtual ~Globals();
65 >    
66 >    DeclareParameter(ForceField, std::string);
67 >    DeclareParameter(TargetTemp, RealType);
68 >    DeclareParameter(Ensemble, std::string);
69 >    DeclareParameter(Dt, RealType);
70 >    DeclareParameter(RunTime, RealType);
71 >    DeclareParameter(FinalConfig, std::string);
72 >    DeclareParameter(SampleTime, RealType);
73 >    DeclareParameter(ResetTime, RealType);
74 >    DeclareParameter(StatusTime, RealType);
75 >    DeclareParameter(CutoffRadius, RealType);
76 >    DeclareParameter(SwitchingRadius, RealType);
77 >    DeclareParameter(TempSet, bool);
78 >    DeclareParameter(ThermalTime, RealType);
79 >    DeclareParameter(UsePeriodicBoundaryConditions, bool);
80 >    DeclareParameter(TargetPressure, RealType);
81 >    DeclareParameter(UseAtomicVirial, bool);
82 >    DeclareParameter(TauThermostat, RealType);
83 >    DeclareParameter(TauBarostat, RealType);
84 >    DeclareParameter(ZconsTime, RealType);
85 >    DeclareParameter(ZconsTol, RealType);
86 >    DeclareParameter(ZconsForcePolicy, std::string);
87 >    DeclareParameter(Seed, unsigned long int);
88 >    DeclareParameter(UseInitalTime, bool);
89 >    DeclareParameter(UseIntialExtendedSystemState, bool);
90 >    DeclareParameter(OrthoBoxTolerance, RealType);
91 >    DeclareParameter(Minimizer, std::string);
92 >    DeclareParameter(MinimizerMaxIter, RealType);
93 >    DeclareParameter(MinimizerWriteFrq, int);
94 >    DeclareParameter(MinimizerStepSize, RealType);
95 >    DeclareParameter(MinimizerFTol, RealType);
96 >    DeclareParameter(MinimizerGTol, RealType);
97 >    DeclareParameter(MinimizerLSTol, RealType);
98 >    DeclareParameter(MinimizerLSMaxIter, int);
99 >    DeclareParameter(ZconsGap, RealType);
100 >    DeclareParameter(ZconsFixtime, RealType);
101 >    DeclareParameter(ZconsUsingSMD, bool);
102 >    DeclareParameter(UseThermodynamicIntegration, bool);
103 >    DeclareParameter(ThermodynamicIntegrationLambda, RealType);
104 >    DeclareParameter(ThermodynamicIntegrationK, RealType);
105 >    DeclareParameter(ForceFieldVariant, std::string);
106 >    DeclareParameter(ForceFieldFileName, std::string);
107 >    DeclareParameter(SurfaceTension, RealType);
108 >    DeclareParameter(PrintPressureTensor, bool);
109 >    DeclareParameter(TaggedAtomPair, intPair);
110 >    DeclareParameter(PrintTaggedPairDistance, bool);
111 >    DeclareParameter(ElectrostaticSummationMethod, std::string);
112 >    DeclareParameter(ElectrostaticScreeningMethod, std::string);
113 >    DeclareParameter(DampingAlpha, RealType);
114 >    DeclareParameter(Dielectric, RealType);
115 >    DeclareParameter(CutoffPolicy, std::string);
116 >    DeclareParameter(SwitchingFunctionType, std::string);
117 >    DeclareParameter(CompressDumpFile, bool);
118 >    DeclareParameter(OutputForceVector, bool);
119 >    DeclareParameter(SkinThickness, RealType);
120 >    DeclareParameter(StatFileFormat, std::string);    
121 >    DeclareParameter(HydroPropFile, std::string);
122 >    DeclareParameter(Viscosity, RealType);
123 >    DeclareParameter(BeadSize, RealType);  
124 >    DeclareParameter(ThermalConductivity, RealType);
125 >    DeclareParameter(ThermalLength, RealType);
126 >    DeclareParameter(UseSphericalBoundaryConditions, bool);
127 >    DeclareParameter(FrozenBufferRadius, RealType);
128 >    DeclareParameter(LangevinBufferRadius, RealType);
129 >    DeclareParameter(AccumulateBoxDipole, bool);
130 >    DeclareParameter(NeighborListNeighbors, int);
131 >    DeclareParameter(UseMultipleTemperatureMethod, bool);
132 >    DeclareParameter(MTM_Ce, RealType);
133 >    DeclareParameter(MTM_G, RealType);
134 >    DeclareParameter(MTM_Io, RealType);
135 >    DeclareParameter(MTM_Sigma, RealType);    
136 >    DeclareParameter(MTM_R, RealType);    
137 >    DeclareParameter(UseRNEMD, bool);
138 >    DeclareParameter(RNEMD_exchangeTime, RealType);
139 >    DeclareParameter(RNEMD_nBins, int);
140 >    DeclareParameter(RNEMD_logWidth, int);
141 >    DeclareParameter(RNEMD_exchangeType, std::string);
142 >    DeclareParameter(RNEMD_objectSelection, std::string);
143 >    DeclareParameter(RNEMD_targetFlux, RealType);
144 >    DeclareParameter(UseRestraints, bool);
145 >    DeclareParameter(Restraint_file, std::string);
146 >    
147 >  public:
148 >    bool addComponent(Component* comp);
149 >    bool addZConsStamp(ZConsStamp* zcons);
150 >    bool addRestraintStamp(RestraintStamp* rest);
151 >    bool addMoleculeStamp(MoleculeStamp* molStamp);
152 >    int getNComponents() {return components_.size();}
153 >    std::vector<Component*> getComponents() {return components_;}
154 >    Component* getComponentAt(int index) {return components_.at(index);}    
155 >    
156 >    int getNZconsStamps() {return zconstraints_.size();}
157 >    std::vector<ZConsStamp*> getZconsStamps() {return zconstraints_;}
158 >    ZConsStamp* getZconsStampAt(int index) {return zconstraints_.at(index);}    
159  
160 <  void initalize();
161 <  
162 <  int newComponent( event* the_event );
27 <  int componentAssign( event* the_event );
28 <  int componentEnd( event* the_event );
160 >    int getNRestraintStamps() {return restraints_.size();}
161 >    std::vector<RestraintStamp*> getRestraintStamps() {return restraints_;}
162 >    RestraintStamp* getRestraintStampAt(int index) {return restraints_.at(index);}    
163  
164 <  int newZconstraint( event* the_event );
165 <  int zConstraintAssign( event* the_event );
166 <  int zConstraintEnd( event* the_event );
167 <  
168 <  int globalAssign( event* the_event );
169 <  int globalEnd( event* the_event );
170 <
171 <  char*  getForceField( void )      { return force_field; }
172 <  int    getNComponents( void )     { return n_components; }
173 <  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; }
91 <
92 <  short int haveDt( void )            { return have_dt; }
93 <  short int haveRunTime( void )       { return have_run_time; }
94 <  short int haveEnsemble( void )      { return have_ensemble; }
95 <  short int haveTargetTemp( void )    { return have_target_temp; }
96 <  short int haveInitialConfig( void ) { return have_initial_config; }
97 <  short int haveFinalConfig( void )   { return have_final_config; }
98 <  short int haveNMol( void )          { return have_n_mol; }
99 <  short int haveDensity( void )       { return have_density; }
100 <  short int haveBox( void )           { return have_box; }
101 <  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; }
135 <
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
152 <
153 <  ZconStamp* current_zConstraint;
154 <  ZconStamp** zConstraints; // the array of zConstraints
155 <
156 <  char force_field[100];
157 <  int n_components;
158 <  int n_zConstraints;
159 <  double target_temp;
160 <  double target_pressure;
161 <  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];
208 <
209 <  //required arguments
210 <  short int have_force_field, have_n_components, have_target_temp;
211 <  short int have_target_pressure, have_ensemble, have_dt, have_run_time;
212 <  
213 <  // optional arguments
214 <  short int have_initial_config, have_final_config, have_n_mol;
215 <  short int have_density, have_box, have_box_x, have_box_y, have_box_z;
216 <  short int have_sample_time, have_status_time, have_rcut, have_dielectric;
217 <  short int have_tempSet, have_thermal_time, have_rsw, have_q_mass;
218 <  short int have_tau_thermostat, have_tau_barostat;
219 <  short int have_zcons_time, have_zConstraints, have_n_zConstraints;
220 <  short int have_zcons_tol, have_seed;
221 <  short int have_zcons_force_policy, have_reset_time;
222 <  short int have_zcons_gap, have_zcons_fixtime;
223 <  short int have_zcons_using_smd;
224 <  short int have_minimizer, have_minimizer_maxiteration;
225 <  short int have_minimizer_writefrq, have_minimizer_stepsize;
226 <  short int have_minimizer_ftol, have_minimizer_gtol;
227 <  short int have_minimizer_ls_tol, have_minimizer_ls_maxiteration;
228 <  short int have_thermodynamic_integration_lambda;
229 <  short int have_thermodynamic_integration_k;
230 <  short int have_forcefield_variant;
164 >    //std::string getRestraint_file(){
165 >    
166 >    virtual void validate();
167 >  private:
168 >    
169 >    std::vector<Component*> components_;
170 >    std::vector<ZConsStamp*> zconstraints_;    
171 >    std::vector<RestraintStamp*> restraints_;    
172 >    std::map<std::string, MoleculeStamp*> moleculeStamps_;
173 >    std::pair<int, int> taggedAtomPair_;
174   };
175 <
175 > }
176   #endif

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