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; }
  
  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; }

  /* 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];
  
  //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;
};

#endif
Revision:	2302
Committed:	Fri Sep 16 16:07:39 2005 UTC (18 years, 9 months ago) by chrisfen
File size:	13709 byte(s)
Log Message:	some fixes but even more breaking (cutting out the old way to do reaction field)
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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	gezelter	1490
45			#include <iostream>
46
47			#include <stdlib.h>
48			#include <vector>
49	tim	2109	#include <string>
50			#include <map>
51	gezelter	1490
52	tim	1492	#include "io/BASS_interface.h"
53			#include "types/Component.hpp"
54			#include "types/MakeStamps.hpp"
55			#include "types/ZconStamp.hpp"
56	gezelter	1490
57
58	gezelter	1930
59	tim	2109	/**
60			* @class Globals Globals.hpp "io/Globals.hpp"
61			* @brief parsing and storing global parameters for simulation
62			* @todo need refactorying
63			*/
64	gezelter	1490	class Globals{
65
66	gezelter	2204	public:
67	gezelter	1490
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	chrisfen	2279	double getThermIntLambda(void) { return thermodynamic_integration_lambda; }
135	gezelter	1490	double getThermIntK(void) { return thermodynamic_integration_k; }
136			char* getForceFieldVariant( void ) { return forcefield_variant; }
137	chrisfen	2279	char* getForceFieldFileName() { return forcefield_filename; }
138	chrisfen	2101	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	chrisfen	2279	double getSurfaceTension(void) { return surface_tension; }
142			bool getPrintPressureTensor(void) { return print_pressure_tensor;}
143	chrisfen	2302	char* getElectrostaticSummationMethod(void) { return electrostaticSummationMethod; }
144	chrisfen	2297	double getDampingAlpha(void) { return dampingAlpha; }
145	gezelter	2285	char* getCutoffPolicy(void) { return cutoffPolicy; }
146	tim	2233
147	gezelter	1490	short int haveDt( void ) { return have_dt; }
148			short int haveRunTime( void ) { return have_run_time; }
149			short int haveEnsemble( void ) { return have_ensemble; }
150			short int haveTargetTemp( void ) { return have_target_temp; }
151			short int haveInitialConfig( void ) { return have_initial_config; }
152			short int haveFinalConfig( void ) { return have_final_config; }
153			short int haveNMol( void ) { return have_n_mol; }
154			short int haveDensity( void ) { return have_density; }
155			short int haveBox( void ) { return have_box; }
156			short int haveBoxX( void ) { return have_box_x; }
157			short int haveBoxY( void ) { return have_box_y; }
158			short int haveBoxZ( void ) { return have_box_z; }
159			short int haveSampleTime( void ) { return have_sample_time; }
160			short int haveResetTime( void ) { return have_reset_time; }
161			short int haveStatusTime( void ) { return have_status_time; }
162			short int haveThermalTime( void ) { return have_thermal_time; }
163			short int haveRcut( void ) { return have_rcut; }
164			short int haveRsw( void ) { return have_rsw; }
165			short int haveDielectric( void ) { return have_dielectric; }
166			short int haveTempSet( void ) { return have_tempSet; }
167			short int haveTargetPressure( void ){ return have_target_pressure; }
168			short int haveQmass( void ) { return have_q_mass; }
169			short int haveTauThermostat( void ) { return have_tau_thermostat; }
170			short int haveTauBarostat( void ) { return have_tau_barostat; }
171			short int haveZconstraintTime(void) { return have_zcons_time; }
172			short int haveZconstraints( void ) { return have_zConstraints; }
173			short int haveZconsTol(void) { return have_zcons_tol; }
174			short int haveZconsForcePolicy(void){ return have_zcons_force_policy; }
175			short int haveZConsGap(void) { return have_zcons_gap; }
176			short int haveZConsFixTime(void) { return have_zcons_fixtime; }
177			short int haveZConsUsingSMD(void) { return have_zcons_using_smd; }
178			short int haveSeed(void) { return have_seed; }
179			short int haveMinimizer(void) { return have_minimizer; }
180			short int haveMinMaxIter(void) { return have_minimizer_maxiteration; }
181			short int haveMinWriteFrq(void) { return have_minimizer_writefrq; }
182			short int haveMinStepSize(void) { return have_minimizer_stepsize; }
183			short int haveMinFTol(void) { return have_minimizer_ftol; }
184			short int haveMinGTol(void) { return have_minimizer_gtol; }
185			short int haveMinLSTol(void) { return have_minimizer_ls_tol; }
186			short int haveMinLSMaxIter(void) { return have_minimizer_ls_maxiteration;}
187			short int haveThermIntLambda(void) { return have_thermodynamic_integration_lambda; }
188	chrisfen	2297	short int haveThermIntK(void) { return have_thermodynamic_integration_k; }
189	gezelter	2285	short int haveForceFieldVariant(void) { return have_forcefield_variant; }
190	chrisfen	2101	short int haveForceFieldFileName(void) { return have_forcefield_filename; }
191	gezelter	2285	short int haveDistSpringConst(void) { return have_dist_spring_constant; }
192			short int haveThetaSpringConst(void) { return have_theta_spring_constant; }
193			short int haveOmegaSpringConst(void) { return have_omega_spring_constant; }
194			short int haveSurfaceTension(void) { return have_surface_tension; }
195	tim	2238	short int havePrintPressureTensor(void) {return have_print_pressure_tensor;}
196	chrisfen	2302	short int haveElectrostaticSummationMethod(void) {return have_electro_sum_method;}
197	chrisfen	2297	short int haveDampingAlpha(void) { return have_damping_alpha; }
198	gezelter	2285	short int haveCutoffPolicy(void) { return have_cutoff_policy; }
199
200	gezelter	1490	/* other accessors */
201			Component** getComponents( void ) { return components; }
202			ZconStamp** getZconStamp( void ) { return zConstraints; }
203
204	gezelter	2204	private:
205	gezelter	1490
206	tim	2109
207			typedef std::map<std::string, int> CommandMapType;
208			CommandMapType command_table;
209
210	gezelter	1490
211			char* checkMe( void );
212
213			Component* current_component;
214			Component** components; // the array of components
215
216			ZconStamp* current_zConstraint;
217			ZconStamp** zConstraints; // the array of zConstraints
218
219			char force_field[100];
220			int n_components;
221			int n_zConstraints;
222			double target_temp;
223			double target_pressure;
224			char ensemble[100];
225			char mixingRule[100];
226			double dt;
227			double run_time;
228			char initial_config[120];
229			char final_config[120];
230			int n_mol;
231			double density;
232			double box;
233			double box_x, box_y, box_z;
234			double sample_time;
235			double status_time;
236			double resetTime;
237			double orthoBoxTolerance;
238			double thermal_time;
239			double rcut;
240			double rsw;
241			double dielectric;
242			int tempSet;
243			int useInitTime;
244			int useInitXSstate;
245			int usePBC;
246			double q_mass;
247			double tau_thermostat;
248			double tau_barostat;
249			double zcons_time;
250			double zcons_tol;
251			char zconsForcePolicy[100];
252			double zcons_gap;
253			double zcons_fixtime;
254			int zcons_using_smd;
255
256			int seed;
257			char minimizer_name[100];
258			int minimizer_maxiteration;
259			int minimizer_writefrq;
260			double minimizer_stepsize;
261			double minimizer_ftol;
262			double minimizer_gtol;
263			double minimizer_ls_tol;
264			int minimizer_ls_maxiteration;
265			int useSolidThermInt;
266			int useLiquidThermInt;
267			double thermodynamic_integration_lambda;
268			double thermodynamic_integration_k;
269			char forcefield_variant[100];
270	tim	1957	char forcefield_filename[100];
271	chrisfen	2101	double therm_int_dist_spring;
272			double therm_int_theta_spring;
273			double therm_int_omega_spring;
274	tim	2235	double surface_tension;
275	tim	2238	bool print_pressure_tensor;
276	chrisfen	2302	char electrostaticSummationMethod[100];
277	chrisfen	2297	double dampingAlpha;
278	gezelter	2285	char cutoffPolicy[100];
279	tim	2233
280	gezelter	1490	//required arguments
281			short int have_force_field, have_n_components, have_target_temp;
282			short int have_target_pressure, have_ensemble, have_dt, have_run_time;
283
284			// optional arguments
285			short int have_initial_config, have_final_config, have_n_mol;
286			short int have_density, have_box, have_box_x, have_box_y, have_box_z;
287			short int have_sample_time, have_status_time, have_rcut, have_dielectric;
288			short int have_tempSet, have_thermal_time, have_rsw, have_q_mass;
289			short int have_tau_thermostat, have_tau_barostat;
290			short int have_zcons_time, have_zConstraints, have_n_zConstraints;
291			short int have_zcons_tol, have_seed;
292			short int have_zcons_force_policy, have_reset_time;
293			short int have_zcons_gap, have_zcons_fixtime;
294			short int have_zcons_using_smd;
295			short int have_minimizer, have_minimizer_maxiteration;
296			short int have_minimizer_writefrq, have_minimizer_stepsize;
297			short int have_minimizer_ftol, have_minimizer_gtol;
298			short int have_minimizer_ls_tol, have_minimizer_ls_maxiteration;
299			short int have_thermodynamic_integration_lambda;
300			short int have_thermodynamic_integration_k;
301			short int have_forcefield_variant;
302	tim	1957	short int have_forcefield_filename;
303	chrisfen	2101	short int have_dist_spring_constant;
304			short int have_theta_spring_constant;
305			short int have_omega_spring_constant;
306	tim	2235	short int have_surface_tension;
307	tim	2238	short int have_print_pressure_tensor;
308	chrisfen	2302	short int have_electro_sum_method;
309	chrisfen	2297	short int have_damping_alpha;
310	gezelter	2285	short int have_cutoff_policy;
311	gezelter	1490	};
312
313			#endif