src/io/Globals.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
#ifndef IO_GLOBALS_HPP
#define IO_GLOBALS_HPP

#include <iostream>

#include <stdlib.h>
#include <vector>
#include <string>
#include <map>

#include "io/BASS_interface.h"
#include "types/Component.hpp"
#include "types/MakeStamps.hpp"
#include "types/ZconStamp.hpp"


/**
 * @class Globals Globals.hpp "io/Globals.hpp"
 * @brief parsing and storing global parameters for simulation 
 * @todo need refactorying
 */
class Globals{
  
 public:
  
  Globals();
  ~Globals();

  void initalize();
  
  int newComponent( event* the_event );
  int componentAssign( event* the_event );
  int componentEnd( event* the_event );

  int newZconstraint( event* the_event );
  int zConstraintAssign( event* the_event );
  int zConstraintEnd( event* the_event );
  
  int globalAssign( event* the_event );
  int globalEnd( event* the_event );
 
  char*  getForceField( void )      { return force_field; }
  int    getNComponents( void )     { return n_components; }
  double getTargetTemp( void )      { return target_temp; }
  double getTargetPressure( void )  { return target_pressure; }
  double getQmass( void )           { return q_mass; }
  double getTauThermostat( void )   { return tau_thermostat; }
  double getTauBarostat( void )     { return tau_barostat; }
  char*  getEnsemble( void )        { return ensemble; }
  double getDt( void )              { return dt; }
  double getRunTime( void )         { return run_time; }
 
  int    getNzConstraints( void )   { return n_zConstraints; }
  char*  getInitialConfig( void )   { return initial_config; }
  char*  getFinalConfig( void )     { return final_config; }
  int    getNMol( void )            { return n_mol; }
  double getDensity( void )         { return density; }
  double getBox( void )             { return box; }
  double getBoxX( void )            { return box_x; }
  double getBoxY( void )            { return box_y; }
  double getBoxZ( void )            { return box_z; }
  double getSampleTime( void )      { return sample_time; }
  double getStatusTime( void )      { return status_time; }
  double getResetTime( void )       { return resetTime; }
  double getThermalTime( void )     { return thermal_time; }
  double getDielectric( void )      { return dielectric; }
  double getRcut( void )            { return rcut; }
  double getRsw( void )             { return rsw; }
  int    getTempSet( void )         { return tempSet; }
  int    getUseInitTime( void )     { return useInitTime; }
  int    getUseInitXSstate( void )  { return useInitXSstate; }
  double getOrthoBoxTolerance(void) { return orthoBoxTolerance; }
  int    getPBC( void )             { return usePBC; }
  char*  getMixingRule( void)       { return mixingRule; }
  double getZconsTime(void)         { return zcons_time; }
  double getZconsTol(void)          { return zcons_tol; }
  char*  getZconsForcePolicy(void)  { return zconsForcePolicy; }
  double getZconsGap(void)          { return zcons_gap; }
  double getZconsFixtime(void)      { return zcons_fixtime; }
  int    getZconsUsingSMD(void)     { return zcons_using_smd; }
  int    getSeed(void)              { return seed; }
  char*  getMinimizer(void)         { return minimizer_name; }
  int    getMinMaxIter(void)        { return minimizer_maxiteration; }
  int    getMinWriteFrq(void)       { return minimizer_writefrq; }
  double getMinStepSize(void)       { return minimizer_stepsize; }
  double getMinFTol(void)           { return minimizer_ftol; }
  double getMinGTol(void)           { return minimizer_gtol; }
  double getMinLSTol(void)          { return minimizer_ls_tol; }
  int    getMinLSMaxIter(void)      { return minimizer_ls_maxiteration; }
  int    getUseSolidThermInt(void)  { return useSolidThermInt; }
  int    getUseLiquidThermInt(void) { return useLiquidThermInt; }
  double getThermIntLambda(void)    { return thermodynamic_integration_lambda; }
  double getThermIntK(void)         { return thermodynamic_integration_k; }
  char*  getForceFieldVariant( void ) { return forcefield_variant; }
  char*  getForceFieldFileName()    { return forcefield_filename; }
  double getDistSpringConst(void)   { return therm_int_dist_spring; }
  double getThetaSpringConst(void)  { return therm_int_theta_spring; }
  double getOmegaSpringConst(void)  { return therm_int_omega_spring; }
  double getSurfaceTension(void)    { return surface_tension; }
  bool   getPrintPressureTensor(void) { return print_pressure_tensor;}
  char*  getElectrostaticSummationMethod(void) { return electrostaticSummationMethod; }
  double getDampingAlpha(void)      { return dampingAlpha; }
  char*  getCutoffPolicy(void)      { return cutoffPolicy; }
  bool   getCompressDumpFile(void)  { return compressDumpFile;}
  
  short int haveDt( void )            { return have_dt; }
  short int haveRunTime( void )       { return have_run_time; }
  short int haveEnsemble( void )      { return have_ensemble; }
  short int haveTargetTemp( void )    { return have_target_temp; }
  short int haveInitialConfig( void ) { return have_initial_config; }
  short int haveFinalConfig( void )   { return have_final_config; }
  short int haveNMol( void )          { return have_n_mol; }
  short int haveDensity( void )       { return have_density; }
  short int haveBox( void )           { return have_box; }
  short int haveBoxX( void )          { return have_box_x; }
  short int haveBoxY( void )          { return have_box_y; }
  short int haveBoxZ( void )          { return have_box_z; }
  short int haveSampleTime( void )    { return have_sample_time; }
  short int haveResetTime( void )     { return have_reset_time; }
  short int haveStatusTime( void )    { return have_status_time; }
  short int haveThermalTime( void )   { return have_thermal_time; }
  short int haveRcut( void )          { return have_rcut; }
  short int haveRsw( void )           { return have_rsw; }
  short int haveDielectric( void )    { return have_dielectric; }
  short int haveTempSet( void )       { return have_tempSet; }
  short int haveTargetPressure( void ){ return have_target_pressure; }
  short int haveQmass( void )         { return have_q_mass; }
  short int haveTauThermostat( void ) { return have_tau_thermostat; }
  short int haveTauBarostat( void )   { return have_tau_barostat; }
  short int haveZconstraintTime(void) { return have_zcons_time; }
  short int haveZconstraints( void )  { return have_zConstraints; }
  short int haveZconsTol(void)        { return have_zcons_tol; }
  short int haveZconsForcePolicy(void){ return have_zcons_force_policy; }
  short int haveZConsGap(void)        { return have_zcons_gap; }
  short int haveZConsFixTime(void)    { return have_zcons_fixtime; }
  short int haveZConsUsingSMD(void)   { return have_zcons_using_smd; }  
  short int haveSeed(void)            { return have_seed; }
  short int haveMinimizer(void)       { return have_minimizer; }
  short int haveMinMaxIter(void)      { return have_minimizer_maxiteration; }
  short int haveMinWriteFrq(void)     { return have_minimizer_writefrq; }
  short int haveMinStepSize(void)     { return have_minimizer_stepsize; }
  short int haveMinFTol(void)         { return have_minimizer_ftol; }
  short int haveMinGTol(void)         { return have_minimizer_gtol; }
  short int haveMinLSTol(void)        { return have_minimizer_ls_tol; }
  short int haveMinLSMaxIter(void)    { return have_minimizer_ls_maxiteration;}
  short int haveThermIntLambda(void)  { return have_thermodynamic_integration_lambda; }
  short int haveThermIntK(void)       { return have_thermodynamic_integration_k; }
  short int haveForceFieldVariant(void)  { return have_forcefield_variant; }
  short int haveForceFieldFileName(void) { return have_forcefield_filename; }
  short int haveDistSpringConst(void)    { return have_dist_spring_constant; }
  short int haveThetaSpringConst(void)   { return have_theta_spring_constant; }
  short int haveOmegaSpringConst(void)   { return have_omega_spring_constant; }
  short int haveSurfaceTension(void)     { return have_surface_tension; }
  short int havePrintPressureTensor(void) {return have_print_pressure_tensor;}
  short int haveElectrostaticSummationMethod(void) {return have_electro_sum_method;}
  short int haveDampingAlpha(void)       { return have_damping_alpha; }
  short int haveCutoffPolicy(void)       { return have_cutoff_policy; }
  short int haveCompressDumpfile(void)   { return have_compress_dumpfile; }

  /* other accessors */
  Component** getComponents( void )   { return components; }
  ZconStamp** getZconStamp( void )    { return zConstraints; }
  
 private:
  

  typedef std::map<std::string, int> CommandMapType;
  CommandMapType command_table;

  
  char* checkMe( void );
  
  Component* current_component;
  Component** components; // the array of components

  ZconStamp* current_zConstraint;
  ZconStamp** zConstraints; // the array of zConstraints

  char force_field[100];
  int n_components;
  int n_zConstraints;
  double target_temp;
  double target_pressure;
  char ensemble[100];
  char mixingRule[100];
  double dt;
  double run_time;
  char initial_config[120];
  char final_config[120];
  int n_mol;
  double density;
  double box;
  double box_x, box_y, box_z;
  double sample_time;
  double status_time;
  double resetTime;
  double orthoBoxTolerance;
  double thermal_time;
  double rcut;
  double rsw;
  double dielectric;
  int tempSet;
  int useInitTime;
  int useInitXSstate;
  int usePBC;
  double q_mass;
  double tau_thermostat;
  double tau_barostat;
  double zcons_time;    
  double zcons_tol;
  char zconsForcePolicy[100];
  double zcons_gap;
  double zcons_fixtime;
  int zcons_using_smd;
  
  int seed;
  char minimizer_name[100];
  int minimizer_maxiteration;
  int minimizer_writefrq;
  double minimizer_stepsize;
  double minimizer_ftol;
  double minimizer_gtol;
  double minimizer_ls_tol;
  int minimizer_ls_maxiteration;
  int useSolidThermInt;
  int useLiquidThermInt;
  double thermodynamic_integration_lambda;
  double thermodynamic_integration_k;
  char forcefield_variant[100];
  char forcefield_filename[100];
  double therm_int_dist_spring;
  double therm_int_theta_spring;
  double therm_int_omega_spring;
  double surface_tension;
  bool print_pressure_tensor;
  char electrostaticSummationMethod[100];
  double dampingAlpha;
  char cutoffPolicy[100];
  bool compressDumpFile;
  
  //required arguments
  short int have_force_field, have_n_components, have_target_temp;
  short int have_target_pressure, have_ensemble, have_dt, have_run_time;
  
  // optional arguments
  short int have_initial_config, have_final_config, have_n_mol;
  short int have_density, have_box, have_box_x, have_box_y, have_box_z;
  short int have_sample_time, have_status_time, have_rcut, have_dielectric;
  short int have_tempSet, have_thermal_time, have_rsw, have_q_mass;
  short int have_tau_thermostat, have_tau_barostat;
  short int have_zcons_time, have_zConstraints, have_n_zConstraints;
  short int have_zcons_tol, have_seed;
  short int have_zcons_force_policy, have_reset_time;
  short int have_zcons_gap, have_zcons_fixtime;
  short int have_zcons_using_smd;
  short int have_minimizer, have_minimizer_maxiteration;
  short int have_minimizer_writefrq, have_minimizer_stepsize;
  short int have_minimizer_ftol, have_minimizer_gtol;
  short int have_minimizer_ls_tol, have_minimizer_ls_maxiteration;
  short int have_thermodynamic_integration_lambda;
  short int have_thermodynamic_integration_k;
  short int have_forcefield_variant;
  short int have_forcefield_filename;  
  short int have_dist_spring_constant;
  short int have_theta_spring_constant;
  short int have_omega_spring_constant;
  short int have_surface_tension;
  short int have_print_pressure_tensor;
  short int have_electro_sum_method;
  short int have_damping_alpha;
  short int have_cutoff_policy;
  short int have_compress_dumpfile;
};

#endif
Revision:	2308
Committed:	Fri Sep 16 23:04:47 2005 UTC (18 years, 9 months ago) by chuckv
File size:	13910 byte(s)
Log Message:	Added keywords for compressed dump files.
#	Content
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"
54	#include "types/MakeStamps.hpp"
55	#include "types/ZconStamp.hpp"
56
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:
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	bool getCompressDumpFile(void) { return compressDumpFile;}
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 haveElectrostaticSummationMethod(void) {return have_electro_sum_method;}
198	short int haveDampingAlpha(void) { return have_damping_alpha; }
199	short int haveCutoffPolicy(void) { return have_cutoff_policy; }
200	short int haveCompressDumpfile(void) { return have_compress_dumpfile; }
201
202	/* other accessors */
203	Component** getComponents( void ) { return components; }
204	ZconStamp** getZconStamp( void ) { return zConstraints; }
205
206	private:
207
208
209	typedef std::map<std::string, int> CommandMapType;
210	CommandMapType command_table;
211
212
213	char* checkMe( void );
214
215	Component* current_component;
216	Component** components; // the array of components
217
218	ZconStamp* current_zConstraint;
219	ZconStamp** zConstraints; // the array of zConstraints
220
221	char force_field[100];
222	int n_components;
223	int n_zConstraints;
224	double target_temp;
225	double target_pressure;
226	char ensemble[100];
227	char mixingRule[100];
228	double dt;
229	double run_time;
230	char initial_config[120];
231	char final_config[120];
232	int n_mol;
233	double density;
234	double box;
235	double box_x, box_y, box_z;
236	double sample_time;
237	double status_time;
238	double resetTime;
239	double orthoBoxTolerance;
240	double thermal_time;
241	double rcut;
242	double rsw;
243	double dielectric;
244	int tempSet;
245	int useInitTime;
246	int useInitXSstate;
247	int usePBC;
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 electrostaticSummationMethod[100];
279	double dampingAlpha;
280	char cutoffPolicy[100];
281	bool compressDumpFile;
282
283	//required arguments
284	short int have_force_field, have_n_components, have_target_temp;
285	short int have_target_pressure, have_ensemble, have_dt, have_run_time;
286
287	// optional arguments
288	short int have_initial_config, have_final_config, have_n_mol;
289	short int have_density, have_box, have_box_x, have_box_y, have_box_z;
290	short int have_sample_time, have_status_time, have_rcut, have_dielectric;
291	short int have_tempSet, have_thermal_time, have_rsw, have_q_mass;
292	short int have_tau_thermostat, have_tau_barostat;
293	short int have_zcons_time, have_zConstraints, have_n_zConstraints;
294	short int have_zcons_tol, have_seed;
295	short int have_zcons_force_policy, have_reset_time;
296	short int have_zcons_gap, have_zcons_fixtime;
297	short int have_zcons_using_smd;
298	short int have_minimizer, have_minimizer_maxiteration;
299	short int have_minimizer_writefrq, have_minimizer_stepsize;
300	short int have_minimizer_ftol, have_minimizer_gtol;
301	short int have_minimizer_ls_tol, have_minimizer_ls_maxiteration;
302	short int have_thermodynamic_integration_lambda;
303	short int have_thermodynamic_integration_k;
304	short int have_forcefield_variant;
305	short int have_forcefield_filename;
306	short int have_dist_spring_constant;
307	short int have_theta_spring_constant;
308	short int have_omega_spring_constant;
309	short int have_surface_tension;
310	short int have_print_pressure_tensor;
311	short int have_electro_sum_method;
312	short int have_damping_alpha;
313	short int have_cutoff_policy;
314	short int have_compress_dumpfile;
315	};
316
317	#endif