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; }
  int    getUseRF( void )           { return useRF; }
  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; }
  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; }
  /* 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;
  int useRF;
  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;
  //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;
};

#endif
Revision:	507
Committed:	Fri Apr 15 22:04:00 2005 UTC (20 years ago) by gezelter
Original Path:	*trunk/src/io/Globals.hpp*
File size:	12703 byte(s)
Log Message:	xemacs has been drafted to perform our indentation services
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	2
45			#include <iostream>
46
47			#include <stdlib.h>
48			#include <vector>
49	tim	425	#include <string>
50			#include <map>
51	gezelter	2
52	tim	3	#include "io/BASS_interface.h"
53			#include "types/Component.hpp"
54			#include "types/MakeStamps.hpp"
55			#include "types/ZconStamp.hpp"
56	gezelter	2
57
58	gezelter	246
59	tim	425	/**
60			* @class Globals Globals.hpp "io/Globals.hpp"
61			* @brief parsing and storing global parameters for simulation
62			* @todo need refactorying
63			*/
64	gezelter	2	class Globals{
65
66	gezelter	507	public:
67	gezelter	2
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			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; }
120			char* getZconsForcePolicy(void) { return zconsForcePolicy; }
121			double getZconsGap(void) { return zcons_gap; }
122			double getZconsFixtime(void) { return zcons_fixtime; }
123			int getZconsUsingSMD(void) { return zcons_using_smd; }
124			int getSeed(void) { return seed; }
125			char* getMinimizer(void) { return minimizer_name; }
126			int getMinMaxIter(void) { return minimizer_maxiteration; }
127			int getMinWriteFrq(void) { return minimizer_writefrq; }
128			double getMinStepSize(void) { return minimizer_stepsize; }
129			double getMinFTol(void) { return minimizer_ftol; }
130			double getMinGTol(void) { return minimizer_gtol; }
131			double getMinLSTol(void) { return minimizer_ls_tol; }
132			int getMinLSMaxIter(void) { return minimizer_ls_maxiteration; }
133			int getUseSolidThermInt(void) { return useSolidThermInt; }
134			int getUseLiquidThermInt(void) { return useLiquidThermInt; }
135	chrisfen	417	double getThermIntLambda(void) { return thermodynamic_integration_lambda; }
136	gezelter	2	double getThermIntK(void) { return thermodynamic_integration_k; }
137			char* getForceFieldVariant( void ) { return forcefield_variant; }
138	tim	273	char* getForceFieldFileName() { return forcefield_filename;}
139	chrisfen	417	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	gezelter	2	short int haveDt( void ) { return have_dt; }
143			short int haveRunTime( void ) { return have_run_time; }
144			short int haveEnsemble( void ) { return have_ensemble; }
145			short int haveTargetTemp( void ) { return have_target_temp; }
146			short int haveInitialConfig( void ) { return have_initial_config; }
147			short int haveFinalConfig( void ) { return have_final_config; }
148			short int haveNMol( void ) { return have_n_mol; }
149			short int haveDensity( void ) { return have_density; }
150			short int haveBox( void ) { return have_box; }
151			short int haveBoxX( void ) { return have_box_x; }
152			short int haveBoxY( void ) { return have_box_y; }
153			short int haveBoxZ( void ) { return have_box_z; }
154			short int haveSampleTime( void ) { return have_sample_time; }
155			short int haveResetTime( void ) { return have_reset_time; }
156			short int haveStatusTime( void ) { return have_status_time; }
157			short int haveThermalTime( void ) { return have_thermal_time; }
158			short int haveRcut( void ) { return have_rcut; }
159			short int haveRsw( void ) { return have_rsw; }
160			short int haveDielectric( void ) { return have_dielectric; }
161			short int haveTempSet( void ) { return have_tempSet; }
162			short int haveTargetPressure( void ){ return have_target_pressure; }
163			short int haveQmass( void ) { return have_q_mass; }
164			short int haveTauThermostat( void ) { return have_tau_thermostat; }
165			short int haveTauBarostat( void ) { return have_tau_barostat; }
166			short int haveZconstraintTime(void) { return have_zcons_time; }
167			short int haveZconstraints( void ) { return have_zConstraints; }
168			short int haveZconsTol(void) { return have_zcons_tol; }
169			short int haveZconsForcePolicy(void){ return have_zcons_force_policy; }
170			short int haveZConsGap(void) { return have_zcons_gap; }
171			short int haveZConsFixTime(void) { return have_zcons_fixtime; }
172			short int haveZConsUsingSMD(void) { return have_zcons_using_smd; }
173			short int haveSeed(void) { return have_seed; }
174			short int haveMinimizer(void) { return have_minimizer; }
175			short int haveMinMaxIter(void) { return have_minimizer_maxiteration; }
176			short int haveMinWriteFrq(void) { return have_minimizer_writefrq; }
177			short int haveMinStepSize(void) { return have_minimizer_stepsize; }
178			short int haveMinFTol(void) { return have_minimizer_ftol; }
179			short int haveMinGTol(void) { return have_minimizer_gtol; }
180			short int haveMinLSTol(void) { return have_minimizer_ls_tol; }
181			short int haveMinLSMaxIter(void) { return have_minimizer_ls_maxiteration;}
182			short int haveThermIntLambda(void) { return have_thermodynamic_integration_lambda; }
183	chrisfen	417	short int haveThermIntK(void) { return have_thermodynamic_integration_k; }
184	gezelter	2	short int haveForceFieldVariant(void) { return have_forcefield_variant; }
185	chrisfen	417	short int haveForceFieldFileName(void) { return have_forcefield_filename; }
186			short int haveDistSpringConst(void) { return have_dist_spring_constant; }
187			short int haveThetaSpringConst(void) { return have_theta_spring_constant; }
188			short int haveOmegaSpringConst(void) { return have_omega_spring_constant; }
189	gezelter	2	/* other accessors */
190			Component** getComponents( void ) { return components; }
191			ZconStamp** getZconStamp( void ) { return zConstraints; }
192
193	gezelter	507	private:
194	gezelter	2
195	tim	425
196			typedef std::map<std::string, int> CommandMapType;
197			CommandMapType command_table;
198
199	gezelter	2
200			char* checkMe( void );
201
202			Component* current_component;
203			Component** components; // the array of components
204
205			ZconStamp* current_zConstraint;
206			ZconStamp** zConstraints; // the array of zConstraints
207
208			char force_field[100];
209			int n_components;
210			int n_zConstraints;
211			double target_temp;
212			double target_pressure;
213			char ensemble[100];
214			char mixingRule[100];
215			double dt;
216			double run_time;
217			char initial_config[120];
218			char final_config[120];
219			int n_mol;
220			double density;
221			double box;
222			double box_x, box_y, box_z;
223			double sample_time;
224			double status_time;
225			double resetTime;
226			double orthoBoxTolerance;
227			double thermal_time;
228			double rcut;
229			double rsw;
230			double dielectric;
231			int tempSet;
232			int useInitTime;
233			int useInitXSstate;
234			int usePBC;
235			int useRF;
236			double q_mass;
237			double tau_thermostat;
238			double tau_barostat;
239			double zcons_time;
240			double zcons_tol;
241			char zconsForcePolicy[100];
242			double zcons_gap;
243			double zcons_fixtime;
244			int zcons_using_smd;
245
246			int seed;
247			char minimizer_name[100];
248			int minimizer_maxiteration;
249			int minimizer_writefrq;
250			double minimizer_stepsize;
251			double minimizer_ftol;
252			double minimizer_gtol;
253			double minimizer_ls_tol;
254			int minimizer_ls_maxiteration;
255			int useSolidThermInt;
256			int useLiquidThermInt;
257			double thermodynamic_integration_lambda;
258			double thermodynamic_integration_k;
259			char forcefield_variant[100];
260	tim	273	char forcefield_filename[100];
261	chrisfen	417	double therm_int_dist_spring;
262			double therm_int_theta_spring;
263			double therm_int_omega_spring;
264	gezelter	2	//required arguments
265			short int have_force_field, have_n_components, have_target_temp;
266			short int have_target_pressure, have_ensemble, have_dt, have_run_time;
267
268			// optional arguments
269			short int have_initial_config, have_final_config, have_n_mol;
270			short int have_density, have_box, have_box_x, have_box_y, have_box_z;
271			short int have_sample_time, have_status_time, have_rcut, have_dielectric;
272			short int have_tempSet, have_thermal_time, have_rsw, have_q_mass;
273			short int have_tau_thermostat, have_tau_barostat;
274			short int have_zcons_time, have_zConstraints, have_n_zConstraints;
275			short int have_zcons_tol, have_seed;
276			short int have_zcons_force_policy, have_reset_time;
277			short int have_zcons_gap, have_zcons_fixtime;
278			short int have_zcons_using_smd;
279			short int have_minimizer, have_minimizer_maxiteration;
280			short int have_minimizer_writefrq, have_minimizer_stepsize;
281			short int have_minimizer_ftol, have_minimizer_gtol;
282			short int have_minimizer_ls_tol, have_minimizer_ls_maxiteration;
283			short int have_thermodynamic_integration_lambda;
284			short int have_thermodynamic_integration_k;
285			short int have_forcefield_variant;
286	tim	273	short int have_forcefield_filename;
287	chrisfen	417	short int have_dist_spring_constant;
288			short int have_theta_spring_constant;
289			short int have_omega_spring_constant;
290	gezelter	2	};
291
292			#endif