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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 629 by chuckv, Mon Sep 26 15:58:17 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 "io/BASS_interface.h"
53   #include "types/Component.hpp"
11 – #include "io/LinkedCommand.hpp"
54   #include "types/MakeStamps.hpp"
55   #include "types/ZconStamp.hpp"
56  
15 – using namespace std;
57  
58 +
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:
66 > public:
67    
68    Globals();
69    ~Globals();
# Line 61 | Line 108 | class Globals{ (public)
108    double getDielectric( void )      { return dielectric; }
109    double getRcut( void )            { return rcut; }
110    double getRsw( void )             { return rsw; }
111 +  double getSkinThickness(void)     { return skinThickness;}
112    int    getTempSet( void )         { return tempSet; }
113    int    getUseInitTime( void )     { return useInitTime; }
114    int    getUseInitXSstate( void )  { return useInitXSstate; }
115    double getOrthoBoxTolerance(void) { return orthoBoxTolerance; }
116    int    getPBC( void )             { return usePBC; }
69 –  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; }
# Line 88 | Line 135 | class Globals{ (public)
135    double getThermIntLambda(void)    { return thermodynamic_integration_lambda; }
136    double getThermIntK(void)         { return thermodynamic_integration_k; }
137    char*  getForceFieldVariant( void ) { return forcefield_variant; }
138 <
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*  getElectrostaticSummationMethod(void) { return electrostaticSummationMethod; }
145 >  double getDampingAlpha(void)      { return dampingAlpha; }
146 >  char*  getCutoffPolicy(void)      { return cutoffPolicy; }
147 >  bool   getCompressDumpFile(void)  { return compressDumpFile;}
148 >  
149    short int haveDt( void )            { return have_dt; }
150    short int haveRunTime( void )       { return have_run_time; }
151    short int haveEnsemble( void )      { return have_ensemble; }
# Line 131 | Line 188 | class Globals{ (public)
188    short int haveMinLSMaxIter(void)    { return have_minimizer_ls_maxiteration;}
189    short int haveThermIntLambda(void)  { return have_thermodynamic_integration_lambda; }
190    short int haveThermIntK(void)       { return have_thermodynamic_integration_k; }
191 <  short int haveForceFieldVariant(void) { return have_forcefield_variant; }
191 >  short int haveForceFieldVariant(void)  { return have_forcefield_variant; }
192 >  short int haveForceFieldFileName(void) { return have_forcefield_filename; }
193 >  short int haveDistSpringConst(void)    { return have_dist_spring_constant; }
194 >  short int haveThetaSpringConst(void)   { return have_theta_spring_constant; }
195 >  short int haveOmegaSpringConst(void)   { return have_omega_spring_constant; }
196 >  short int haveSurfaceTension(void)     { return have_surface_tension; }
197 >  short int havePrintPressureTensor(void) {return have_print_pressure_tensor;}
198 >  short int haveElectrostaticSummationMethod(void) {return have_electro_sum_method;}
199 >  short int haveDampingAlpha(void)       { return have_damping_alpha; }
200 >  short int haveCutoffPolicy(void)       { return have_cutoff_policy; }
201 >  short int haveCompressDumpfile(void)   { return have_compress_dumpfile; }
202 >  short int haveSkinThickness(void)      {return have_skin_thickness; }
203  
204    /* other accessors */
205    Component** getComponents( void )   { return components; }
206    ZconStamp** getZconStamp( void )    { return zConstraints; }
207    
208 < private:
208 > private:
209    
210 <  int hash_size;
211 <  int hash_shift;
212 <  int hash( char* text );
213 <  void addHash( char* text, int token );
146 <  LinkedCommand** command_table;
210 >
211 >  typedef std::map<std::string, int> CommandMapType;
212 >  CommandMapType command_table;
213 >
214    
215    char* checkMe( void );
216    
# Line 175 | Line 242 | class Globals{ (public)
242    double thermal_time;
243    double rcut;
244    double rsw;
245 +  double skinThickness;
246    double dielectric;
247    int tempSet;
248    int useInitTime;
249    int useInitXSstate;
250    int usePBC;
183 –  int useRF;
251    double q_mass;
252    double tau_thermostat;
253    double tau_barostat;
# Line 205 | Line 272 | class Globals{ (public)
272    double thermodynamic_integration_lambda;
273    double thermodynamic_integration_k;
274    char forcefield_variant[100];
275 <
275 >  char forcefield_filename[100];
276 >  double therm_int_dist_spring;
277 >  double therm_int_theta_spring;
278 >  double therm_int_omega_spring;
279 >  double surface_tension;
280 >  bool print_pressure_tensor;
281 >  char electrostaticSummationMethod[100];
282 >  double dampingAlpha;
283 >  char cutoffPolicy[100];
284 >  bool compressDumpFile;
285 >  
286    //required arguments
287    short int have_force_field, have_n_components, have_target_temp;
288    short int have_target_pressure, have_ensemble, have_dt, have_run_time;
# Line 228 | Line 305 | class Globals{ (public)
305    short int have_thermodynamic_integration_lambda;
306    short int have_thermodynamic_integration_k;
307    short int have_forcefield_variant;
308 +  short int have_forcefield_filename;  
309 +  short int have_dist_spring_constant;
310 +  short int have_theta_spring_constant;
311 +  short int have_omega_spring_constant;
312 +  short int have_surface_tension;
313 +  short int have_print_pressure_tensor;
314 +  short int have_electro_sum_method;
315 +  short int have_damping_alpha;
316 +  short int have_cutoff_policy;
317 +  short int have_compress_dumpfile;
318 +  short int have_skin_thickness;
319   };
320  
321   #endif

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