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root/group/trunk/OOPSE-2.0/src/io/Globals.cpp

Comparing trunk/OOPSE-2.0/src/io/Globals.cpp (file contents):
Revision 2233 by tim, Thu May 19 04:28:26 2005 UTC vs.
Revision 2515 by tim, Fri Dec 16 18:26:41 2005 UTC

#	Line 42 | Line 42
42		#include <stdlib.h>
43		#include <stdio.h>
44		#include <string.h>
45	+	#include <string>
46
47		#include "io/Globals.hpp"
48	+	#include "io/ParamConstraint.hpp"
49	+	#include "utils/MemoryUtils.hpp"
50		#include "utils/simError.h"
48	–	#ifdef IS_MPI
49	–	#include "io/mpiBASS.h"
50	–	#endif // is_mpi
51
52	<	/*
53	<	* The following section lists all of the defined tokens for the
54	<	* global assignment statements. All are prefixed with a G_ to avoid
55	<	* stepping on any previously defined enumerations.
56	<	*
57	<	* NOTE: tokens start at 1, 0 is a resrved token number
58	<	*/
59	<
60	<	//required parameters
61	<	#define G_FORCEFIELD         1
62	<	#define G_NCOMPONENTS        2
63	<	#define G_TARGETTEMP         3
64	<	#define G_ENSEMBLE           4
65	<	#define G_DT                 5
66	<	#define G_RUNTIME            6
67	<
68	<	//optional parameters
69	<	#define G_INITIALCONFIG      7
70	<	#define G_FINALCONFIG        8
71	<	#define G_NMOL               9
72	<	#define G_DENSITY           10
73	<	#define G_BOX               11
74	<	#define G_BOXX              12
75	<	#define G_BOXY              13
76	<	#define G_BOXZ              14
77	<	#define G_SAMPLETIME        15
78	<	#define G_STATUSTIME        16
79	<	#define G_RCUT              17
80	<	#define G_RSW               18
81	<	#define G_DIELECTRIC        19
82	<	#define G_TEMPSET           20
83	<	#define G_THERMALTIME       21
84	<	#define G_USEPBC            22
85	<	#define G_MIXINGRULE        23
86	<	#define G_USERF             24
87	<	#define G_TARGETPRESSURE    25
88	<	#define G_TAUTHERMOSTAT     26
89	<	#define G_TAUBAROSTAT       27
90	<	#define G_ZCONSTIME         28
91	<	#define G_NZCONSTRAINTS     29
92	<	#define G_ZCONSTOL          30
93	<	#define G_ZCONSFORCEPOLICY  31
94	<	#define G_SEED              32
95	<	#define G_RESETTIME         33
96	<	#define G_USEINITTIME       34
97	<	#define G_USEINIT_XS_STATE  35
98	<	#define G_ORTHOBOXTOLERANCE 36
99	<	#define G_MINIMIZER         37
100	<	#define G_MIN_MAXITER       38
101	<	#define G_MIN_WRITEFRQ      39
102	<	#define G_MIN_STEPSIZE      40
103	<	#define G_MIN_FTOL          41
104	<	#define G_MIN_GTOL          42
105	<	#define G_MIN_LSTOL         43
106	<	#define G_MIN_LSMAXITER     44
107	<	#define G_ZCONSGAP          45
108	<	#define G_ZCONSFIXTIME      46
109	<	#define G_ZCONSUSINGSMD     47
110	<	#define G_USE_SOLID_THERM_INT     48
111	<	#define G_USE_LIQUID_THERM_INT    49
112	<	#define G_THERM_INT_LAMBDA  50
113	<	#define G_THERM_INT_K       51
114	<	#define G_FORCEFIELD_VARIANT 52
115	<	#define G_FORCEFIELD_FILENAME 53
116	<	#define G_THERM_INT_DIST_SPRING  54
117	<	#define G_THERM_INT_THETA_SPRING 55
118	<	#define G_THERM_INT_OMEGA_SPRING 56
119	<	#define G_TARGETSTRESS 57
120	<
121	<	Globals::Globals(){
122	<	initalize();
123	<	}
124	<
125	<	Globals::~Globals(){
126	<	int i;
127	<	if( components != NULL ){
128	<	for( i=0; i<n_components; i++ ) delete components[i];
129	<	delete[] components;
130	<	}
131	<	}
132	<
133	<	void Globals::initalize(){
134	<	int i;
135	<
136	<	components = NULL;
137	<
138	<	command_table.insert(CommandMapType::value_type("forceField", G_FORCEFIELD));
139	<	command_table.insert(CommandMapType::value_type("nComponents", G_NCOMPONENTS));
140	<	command_table.insert(CommandMapType::value_type("targetTemp", G_TARGETTEMP));
141	<	command_table.insert(CommandMapType::value_type("ensemble", G_ENSEMBLE));
142	<	command_table.insert(CommandMapType::value_type("dt", G_DT));
143	<	command_table.insert(CommandMapType::value_type("runTime", G_RUNTIME));
144	<	command_table.insert(CommandMapType::value_type("initialConfig", G_INITIALCONFIG));
145	<	command_table.insert(CommandMapType::value_type("finalConfig", G_FINALCONFIG));
146	<	command_table.insert(CommandMapType::value_type("nMol", G_NMOL));
147	<	command_table.insert(CommandMapType::value_type("density", G_DENSITY));
148	<	command_table.insert(CommandMapType::value_type("box", G_BOX));
149	<	command_table.insert(CommandMapType::value_type("boxX", G_BOXX));
150	<	command_table.insert(CommandMapType::value_type("boxY", G_BOXY));
151	<	command_table.insert(CommandMapType::value_type("boxZ", G_BOXZ));
152	<	command_table.insert(CommandMapType::value_type("sampleTime", G_SAMPLETIME));
153	<	command_table.insert(CommandMapType::value_type("resetTime", G_RESETTIME));
154	<	command_table.insert(CommandMapType::value_type("statusTime", G_STATUSTIME));
155	<	command_table.insert(CommandMapType::value_type("cutoffRadius", G_RCUT));
156	<	command_table.insert(CommandMapType::value_type("switchingRadius", G_RSW));
157	<	command_table.insert(CommandMapType::value_type("dielectric", G_DIELECTRIC));
158	<	command_table.insert(CommandMapType::value_type("tempSet", G_TEMPSET));
159	<	command_table.insert(CommandMapType::value_type("thermalTime", G_THERMALTIME));
160	<	command_table.insert(CommandMapType::value_type("mixingRule", G_MIXINGRULE));
161	<	command_table.insert(CommandMapType::value_type("usePeriodicBoundaryConditions", G_USEPBC));
162	<	command_table.insert(CommandMapType::value_type("useReactionField", G_USERF));
163	<	command_table.insert(CommandMapType::value_type("targetPressure", G_TARGETPRESSURE));
164	<	command_table.insert(CommandMapType::value_type("tauThermostat", G_TAUTHERMOSTAT));
165	<	command_table.insert(CommandMapType::value_type("tauBarostat", G_TAUBAROSTAT));
166	<	command_table.insert(CommandMapType::value_type("zconsTime", G_ZCONSTIME));
167	<	command_table.insert(CommandMapType::value_type("nZconstraints", G_NZCONSTRAINTS));
168	<	command_table.insert(CommandMapType::value_type("zconsTol", G_ZCONSTOL));
169	<	command_table.insert(CommandMapType::value_type("zconsForcePolicy", G_ZCONSFORCEPOLICY));
170	<	command_table.insert(CommandMapType::value_type("seed", G_SEED));
171	<	command_table.insert(CommandMapType::value_type("useInitialTime", G_USEINITTIME));
172	<	command_table.insert(CommandMapType::value_type("useInitialExtendedSystemState", G_USEINIT_XS_STATE));
173	<	command_table.insert(CommandMapType::value_type("orthoBoxTolerance", G_ORTHOBOXTOLERANCE));
174	<	command_table.insert(CommandMapType::value_type("minimizer", G_MINIMIZER));
175	<	command_table.insert(CommandMapType::value_type("minimizerMaxIter", G_MIN_MAXITER));
176	<	command_table.insert(CommandMapType::value_type("minimizerWriteFrq", G_MIN_WRITEFRQ));
177	<	command_table.insert(CommandMapType::value_type("minimizerStepSize", G_MIN_STEPSIZE));
178	<	command_table.insert(CommandMapType::value_type("minimizerFTol", G_MIN_FTOL));
179	<	command_table.insert(CommandMapType::value_type("minimizerGTol", G_MIN_GTOL));
180	<	command_table.insert(CommandMapType::value_type("minimizerLSTol", G_MIN_LSTOL));
181	<	command_table.insert(CommandMapType::value_type("minimizerLSMaxIter", G_MIN_LSMAXITER));
182	<	command_table.insert(CommandMapType::value_type("zconsGap", G_ZCONSGAP));
183	<	command_table.insert(CommandMapType::value_type("zconsFixtime", G_ZCONSFIXTIME));
184	<	command_table.insert(CommandMapType::value_type("zconsUsingSMD", G_ZCONSUSINGSMD));
185	<	command_table.insert(CommandMapType::value_type("useSolidThermInt", G_USE_SOLID_THERM_INT));
186	<	command_table.insert(CommandMapType::value_type("useLiquidThermInt", G_USE_LIQUID_THERM_INT));
187	<	command_table.insert(CommandMapType::value_type("thermodynamicIntegrationLambda", G_THERM_INT_LAMBDA));
188	<	command_table.insert(CommandMapType::value_type("thermodynamicIntegrationK", G_THERM_INT_K));
189	<	command_table.insert(CommandMapType::value_type("forceFieldVariant", G_FORCEFIELD_VARIANT));
190	<	command_table.insert(CommandMapType::value_type("forceFieldFileName", G_FORCEFIELD_FILENAME));
191	<	command_table.insert(CommandMapType::value_type("thermIntDistSpringConst", G_THERM_INT_DIST_SPRING));
192	<	command_table.insert(CommandMapType::value_type("thermIntThetaSpringConst", G_THERM_INT_THETA_SPRING));
193	<	command_table.insert(CommandMapType::value_type("thermIntOmegaSpringConst", G_THERM_INT_OMEGA_SPRING));
194	<	command_table.insert(CommandMapType::value_type("targetStress", G_TARGETSTRESS));
195	<
196	<
197	<	strcpy( mixingRule,"standard");  //default mixing rules to standard.
198	<	usePBC = 1; //default  periodic boundry conditions to on
199	<	useRF  = 0;
200	<	useInitTime = 0; // default to pull init time from the init file
201	<	useInitXSstate = 0; // default to pull the extended state from the init file
202	<	orthoBoxTolerance = 1E-6;
203	<	useSolidThermInt = 0; // default solid-state thermodynamic integration to off
204	<	useLiquidThermInt = 0; // default liquid thermodynamic integration to off
205	<
206	<	have_force_field =  0;
207	<	have_n_components = 0;
208	<	have_target_temp =  0;
209	<	have_ensemble =     0;
210	<	have_dt =           0;
211	<	have_run_time =     0;
212	<
213	<	have_initial_config = 0;
214	<	have_final_config =   0;
215	<	have_n_mol =          0;
216	<	have_density =        0;
217	<	have_box =            0;
218	<	have_box_x =          0;
219	<	have_box_y =          0;
220	<	have_box_y =          0;
221	<	have_box_z =          0;
222	<	have_sample_time =    0;
223	<	have_status_time =    0;
224	<	have_reset_time =     0;
225	<	have_thermal_time =   0;
226	<	have_rcut =           0;
227	<	have_rsw =            0;
228	<	have_dielectric =     0;
229	<	have_tempSet =        0;
230	<	have_target_pressure =0;
231	<	have_q_mass =         0;
232	<	have_tau_thermostat = 0;
233	<	have_tau_barostat   = 0;
234	<	have_zcons_time     = 0;
235	<	have_n_zConstraints = 0;
236	<	have_zConstraints   = 0;
237	<	have_zcons_tol = 0;
238	<	have_zcons_gap = 0;
239	<	have_zcons_fixtime = 0;
240	<	have_zcons_using_smd = 0;
241	<	have_seed = 0;
242	<	have_minimizer = 0;
243	<	have_minimizer_maxiteration = 0;
244	<	have_minimizer_writefrq = 0;
245	<	have_minimizer_stepsize = 0;
246	<	have_minimizer_ftol = 0;
247	<	have_minimizer_gtol = 0;
248	<	have_minimizer_ls_tol = 0;
249	<	have_minimizer_ls_maxiteration = 0;
250	<	have_thermodynamic_integration_lambda = 0;
251	<	have_thermodynamic_integration_k = 0;
252	<	have_forcefield_variant = 0;
253	<	have_forcefield_filename = 0;
254	<	have_dist_spring_constant =  0;
255	<	have_theta_spring_constant = 0;
256	<	have_omega_spring_constant = 0;
257	<	have_targetStress = 0;
258	<	}
259	<
260	<	int Globals::newComponent( event* the_event ){
261	<
262	<	current_component = new Component;
263	<	int index = the_event->evt.blk_index;
264	<	char err[200];
265	<
266	<	if( have_n_components && index < n_components )
267	<	components[index] = current_component;
268	<	else{
269	<	if( have_n_components ){
270	<	sprintf( err, "meta-data parsing error: %d out of nComponents range",
271	<	index );
272	<	the_event->err_msg = strdup( err );
273	<	return 0;
274	<	}
275	<	else{
276	<	the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
277	<	" first component declaration." );
278	<	return 0;
279	<	}
280	<	}
52	>	namespace oopse {
53	>	Globals::Globals() {
54	>	DefineParameter(ForceField, "forceField")
55
56	<	return 1;
57	<	}
58	<
56	>	DefineOptionalParameter(TargetTemp, "targetTemp");
57	>	DefineOptionalParameter(Ensemble, "ensemble");
58	>	DefineOptionalParameter(Dt, "dt");
59	>	DefineOptionalParameter(RunTime, "runTime");
60	>	DefineOptionalParameter(InitialConfig, "initialConfig");
61	>	DefineOptionalParameter(FinalConfig, "finalConfig");
62	>	DefineOptionalParameter(SampleTime, "sampleTime");
63	>	DefineOptionalParameter(ResetTime, "resetTime");
64	>	DefineOptionalParameter(StatusTime, "statusTime");
65	>	DefineOptionalParameter(CutoffRadius, "cutoffRadius");
66	>	DefineOptionalParameter(SwitchingRadius, "switchingRadius");
67	>	DefineOptionalParameter(Dielectric, "dielectric");
68	>	DefineOptionalParameter(TempSet, "tempSet");
69	>	DefineOptionalParameter(ThermalTime, "thermalTime");
70	>	DefineOptionalParameter(TargetPressure, "targetPressure");
71	>	DefineOptionalParameter(TauThermostat, "tauThermostat");
72	>	DefineOptionalParameter(TauBarostat, "tauBarostat");
73	>	DefineOptionalParameter(ZconsTime, "zconsTime");
74	>	DefineOptionalParameter(ZconsTol, "zconsTol");
75	>	DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
76	>	DefineOptionalParameter(Seed, "seed");
77	>	DefineOptionalParameter(Minimizer, "minimizer");
78	>	DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
79	>	DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
80	>	DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
81	>	DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
82	>	DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
83	>	DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
84	>	DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
85	>	DefineOptionalParameter(ZconsGap, "zconsGap");
86	>	DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
87	>	DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
88	>	DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
89	>	DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
90	>	DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
91	>	DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
92	>	DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
93	>	DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
94	>	DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
95	>	DefineOptionalParameter(SurfaceTension, "surfaceTension");
96	>	DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
97	>	DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
98	>	DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
99	>	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
100	>	DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
101	>	DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
102	>	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
103	>	DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
104	>	DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
105	>	DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
106	>	DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
107	>	DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
108	>	DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
109	>	DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
110	>	DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
111	>	DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
112	>	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
113	>	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
114	>	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
115	>	DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
116
117
118	<	int Globals::componentAssign( event* the_event ){
119	<
289	<	switch( the_event->evt.asmt.asmt_type ){
118	>	deprecatedKeywords_.insert("nComponents");
119	>	deprecatedKeywords_.insert("nZconstraints");
120
291	–	case STRING:
292	–	return current_component->assignString( the_event->evt.asmt.lhs,
293	–	the_event->evt.asmt.rhs.sval,
294	–	&(the_event->err_msg));
295	–	break;
296	–
297	–	case DOUBLE:
298	–	return current_component->assignDouble( the_event->evt.asmt.lhs,
299	–	the_event->evt.asmt.rhs.dval,
300	–	&(the_event->err_msg));
301	–	break;
302	–
303	–	case INT:
304	–	return current_component->assignInt( the_event->evt.asmt.lhs,
305	–	the_event->evt.asmt.rhs.ival,
306	–	&(the_event->err_msg));
307	–	break;
308	–
309	–	default:
310	–	the_event->err_msg = strdup( "Globals error. Invalid component"
311	–	" assignment type" );
312	–	return 0;
313	–	break;
314	–	}
315	–	return 0;
121		}
122
123	<	int Globals::componentEnd( event* the_event ){
124	<
125	<	the_event->err_msg = current_component->checkMe();
321	<	if( the_event->err_msg != NULL ) return 0;
322	<
323	<	return 1;
123	>	Globals::~Globals() {
124	>	MemoryUtils::deletePointers(components_);
125	>	MemoryUtils::deletePointers(zconstraints_);
126		}
127
128	<	int Globals::newZconstraint( event* the_event ){
129	<
128	>	void Globals::validate() {
129	>	DataHolder::validate();
130
131	<	int index = the_event->evt.blk_index;
132	<	char err[200];
133	<	current_zConstraint = new ZconStamp( index );
134	<
135	<	have_zConstraints = 1;
131	>	CheckParameter(ForceField, isNotEmpty());
132	>	CheckParameter(TargetTemp, isPositive());
133	>	CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) || isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf")) || isEqualIgnoreCase(std::string("NPTxyz")) );
134	>	CheckParameter(Dt, isPositive());
135	>	CheckParameter(RunTime, isPositive());
136	>	CheckParameter(InitialConfig, isNotEmpty());
137	>	CheckParameter(FinalConfig, isNotEmpty());
138	>	CheckParameter(SampleTime, isNonNegative());
139	>	CheckParameter(ResetTime, isNonNegative());
140	>	CheckParameter(StatusTime, isNonNegative());
141	>	CheckParameter(CutoffRadius, isPositive());
142	>	CheckParameter(SwitchingRadius, isNonNegative());
143	>	CheckParameter(Dielectric, isPositive());
144	>	CheckParameter(ThermalTime,  isNonNegative());
145	>	CheckParameter(TargetPressure,  isPositive());
146	>	CheckParameter(TauThermostat, isPositive());
147	>	CheckParameter(TauBarostat, isPositive());
148	>	CheckParameter(ZconsTime, isPositive());
149	>	CheckParameter(ZconsTol, isPositive());
150	>	CheckParameter(Seed, isPositive());
151	>	CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
152	>	CheckParameter(MinimizerMaxIter, isPositive());
153	>	CheckParameter(MinimizerWriteFrq, isPositive());
154	>	CheckParameter(MinimizerStepSize, isPositive());
155	>	CheckParameter(MinimizerFTol, isPositive());
156	>	CheckParameter(MinimizerGTol, isPositive());
157	>	CheckParameter(MinimizerLSTol, isPositive());
158	>	CheckParameter(MinimizerLSMaxIter, isPositive());
159	>	CheckParameter(ZconsGap, isPositive());
160	>	CheckParameter(ZconsFixtime, isPositive());
161	>	CheckParameter(ThermodynamicIntegrationLambda, isPositive());
162	>	CheckParameter(ThermodynamicIntegrationK, isPositive());
163	>	CheckParameter(ForceFieldVariant, isNotEmpty());
164	>	CheckParameter(ForceFieldFileName, isNotEmpty());
165	>	CheckParameter(ThermIntDistSpringConst, isPositive());
166	>	CheckParameter(ThermIntThetaSpringConst, isPositive());
167	>	CheckParameter(ThermIntOmegaSpringConst, isPositive());
168	>	CheckParameter(SurfaceTension, isPositive());
169	>	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || isEqualIgnoreCase(std::string("SHIFTED_FORCE")) || isEqualIgnoreCase(std::string("REACTION_FIELD")));
170	>	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) || isEqualIgnoreCase(std::string("DAMPED")));
171	>	CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
172	>	CheckParameter(SwitchingFunctionType, isEqualIgnoreCase(std::string("CUBIC")) || isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL")));
173	>	//CheckParameter(StatFileFormat,);
174	>	//CheckParameter(MixingRule,);
175	>	CheckParameter(OrthoBoxTolerance, isPositive());
176	>	CheckParameter(ThermIntDistSpringConst, isPositive());
177	>	CheckParameter(ThermIntThetaSpringConst, isPositive());
178	>	CheckParameter(ThermIntOmegaSpringConst, isPositive());
179	>	CheckParameter(DampingAlpha,isNonNegative());
180	>	CheckParameter(SkinThickness, isPositive());
181
182	<	if( have_n_zConstraints && index < n_zConstraints )
183	<	zConstraints[index] = current_zConstraint;
184	<	else{
338	<	if( have_n_zConstraints ){
339	<	sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
340	<	index );
341	<	the_event->err_msg = strdup( err );
342	<	return 0;
182	>	for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
183	>	if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
184	>	std::cout << "Globals Error: can not find molecule stamp for component" << std::endl;
185		}
186	<	else{
345	<	the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
346	<	" not given before"
347	<	" first zConstraint declaration." );
348	<	return 0;
349	<	}
350	<	}
351	<
352	<	return 1;
186	>	}
187		}
354	–
355	–
356	–
357	–	int Globals::zConstraintAssign( event* the_event ){
358	–
359	–	switch( the_event->evt.asmt.asmt_type ){
188
189	<	case STRING:
190	<	return current_zConstraint->assignString( the_event->evt.asmt.lhs,
191	<	the_event->evt.asmt.rhs.sval,
364	<	&(the_event->err_msg));
365	<	break;
366	<
367	<	case DOUBLE:
368	<	return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
369	<	the_event->evt.asmt.rhs.dval,
370	<	&(the_event->err_msg));
371	<	break;
372	<
373	<	case INT:
374	<	return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
375	<	the_event->evt.asmt.rhs.ival,
376	<	&(the_event->err_msg));
377	<	break;
378	<
379	<	default:
380	<	the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
381	<	" assignment type" );
382	<	return 0;
383	<	break;
384	<	}
385	<	return 0;
189	>	bool Globals::addComponent(Component* comp) {
190	>	components_.push_back(comp);
191	>	return true;
192		}
193
194	<	int Globals::zConstraintEnd( event* the_event ){
195	<
196	<	the_event->err_msg = current_zConstraint->checkMe();
391	<	if( the_event->err_msg != NULL ) return 0;
392	<
393	<	return 1;
194	>	bool Globals::addZConsStamp(ZConsStamp* zcons) {
195	>	zconstraints_.push_back(zcons);
196	>	return true;
197		}
395	–
396	–	int Globals::globalAssign( event* the_event ){
397	–
398	–	int key;
399	–	int token;
400	–	interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
401	–	char* lhs = the_event->evt.asmt.lhs;
402	–	char err[300];
403	–
404	–	token = 0;
405	–
406	–	CommandMapType::iterator iter;
407	–	std::string keyword(lhs);
408	–	iter = command_table.find(keyword);
409	–	if (iter != command_table.end()) {
410	–	token = iter->second;
411	–	}
412	–
413	–	if( token ){
414	–
415	–	switch( token ){
416	–
417	–	case G_FORCEFIELD:
418	–	if( the_type == STRING ){
419	–	strcpy( force_field, the_event->evt.asmt.rhs.sval );
420	–	have_force_field = 1;
421	–	return 1;
422	–	}
423	–
424	–	the_event->err_msg =
425	–	strdup( "Error in parsing meta-data file!\n\tforceField was not a string assignment.\n" );
426	–	return 0;
427	–	break;
428	–
429	–	case G_NCOMPONENTS:
430	–	if( the_type == STRING ){
431	–	the_event->err_msg =
432	–	strdup("Error in parsing meta-data file!\n\tnComponents is not a double or an int.\n" );
433	–	return 0;
434	–	}
435	–
436	–	else if( the_type == DOUBLE ){
437	–	n_components = (int)the_event->evt.asmt.rhs.dval;
438	–	components = new Component*[n_components];
439	–	have_n_components = 1;
440	–	return 1;
441	–	}
442	–
443	–	else{
444	–	n_components = the_event->evt.asmt.rhs.ival;
445	–	components = new Component*[n_components];
446	–	have_n_components = 1;
447	–	return 1;
448	–	}
449	–	break;
450	–
451	–	case G_NZCONSTRAINTS:
452	–	if( the_type == STRING ){
453	–	the_event->err_msg =
454	–	strdup("Error in parsing meta-data file!\n\tnZconstraints is not a double or an int.\n" );
455	–	return 0;
456	–	}
457	–
458	–	else if( the_type == DOUBLE ){
459	–	n_zConstraints = (int)the_event->evt.asmt.rhs.dval;
460	–	zConstraints = new ZconStamp*[n_zConstraints];
461	–	have_n_zConstraints = 1;
462	–	return 1;
463	–	}
464	–
465	–	else{
466	–	n_zConstraints = the_event->evt.asmt.rhs.ival;
467	–	zConstraints = new ZconStamp*[n_zConstraints];
468	–	have_n_zConstraints = 1;
469	–	return 1;
470	–	}
471	–	break;
472	–
473	–	case G_TARGETTEMP:
474	–	switch( the_type ){
475	–
476	–	case STRING:
477	–	the_event->err_msg =
478	–	strdup( "Error in parsing meta-data file!\n\ttargetTemp is not a double or int.\n" );
479	–	return 0;
480	–	break;
481	–
482	–	case DOUBLE:
483	–	target_temp = the_event->evt.asmt.rhs.dval;
484	–	have_target_temp = 1;
485	–	return 1;
486	–	break;
487	–
488	–	case INT:
489	–	target_temp = (double)the_event->evt.asmt.rhs.ival;
490	–	have_target_temp = 1;
491	–	return 1;
492	–	break;
493	–
494	–	default:
495	–	the_event->err_msg =
496	–	strdup( "Error in parsing meta-data file!\n\ttargetTemp unrecognized.\n" );
497	–	return 0;
498	–	break;
499	–	}
500	–	break;
501	–
502	–	case G_ORTHOBOXTOLERANCE:
503	–	switch( the_type ){
504	–
505	–	case STRING:
506	–	the_event->err_msg =
507	–	strdup( "Error in parsing meta-data file!\n\torthoBoxTolerance is not a double or int.\n" );
508	–	return 0;
509	–	break;
510	–
511	–	case DOUBLE:
512	–	orthoBoxTolerance = the_event->evt.asmt.rhs.dval;
513	–	have_target_temp = 1;
514	–	return 1;
515	–	break;
516	–
517	–	case INT:
518	–	orthoBoxTolerance = (double)the_event->evt.asmt.rhs.ival;
519	–	have_target_temp = 1;
520	–	return 1;
521	–	break;
522	–
523	–	default:
524	–	the_event->err_msg =
525	–	strdup( "Global error.orthoBoxTolerance unrecognized.\n" );
526	–	return 0;
527	–	break;
528	–	}
529	–	break;
530	–
531	–	case G_ENSEMBLE:
532	–	if( the_type == STRING ){
533	–	strcpy( ensemble, the_event->evt.asmt.rhs.sval );
534	–	have_ensemble = 1;
535	–	return 1;
536	–	}
537	–
538	–	the_event->err_msg =
539	–	strdup( "Error in parsing meta-data file!\n\tensemble was not assigned to a string\n" );
540	–	return 0;
541	–	break;
542	–
543	–	case G_MIXINGRULE:
544	–	if( the_type == STRING ){
545	–	strcpy( mixingRule, the_event->evt.asmt.rhs.sval );
546	–	return 1;
547	–	}
548	–
549	–	the_event->err_msg =
550	–	strdup( "Error in parsing meta-data file!\n\tmixing rule was not assigned to a string\n" );
551	–	return 0;
552	–	break;
553	–
554	–	case G_DT:
555	–	switch( the_type ){
556	–
557	–	case STRING:
558	–	the_event->err_msg =
559	–	strdup( "Error in parsing meta-data file!\n\tdt is not a double or int.\n" );
560	–	return 0;
561	–	break;
562	–
563	–	case DOUBLE:
564	–	dt = the_event->evt.asmt.rhs.dval;
565	–	have_dt = 1;
566	–	return 1;
567	–	break;
568	–
569	–	case INT:
570	–	dt = (double)the_event->evt.asmt.rhs.ival;
571	–	have_dt = 1;
572	–	return 1;
573	–	break;
574	–
575	–	default:
576	–	the_event->err_msg =
577	–	strdup( "Error in parsing meta-data file!\n\tdt unrecognized.\n" );
578	–	return 0;
579	–	break;
580	–	}
581	–	break;
582	–
583	–	case G_RUNTIME:
584	–	switch( the_type ){
585	–
586	–	case STRING:
587	–	the_event->err_msg =
588	–	strdup( "Error in parsing meta-data file!\n\trunTime is not a double or int.\n" );
589	–	return 0;
590	–	break;
591	–
592	–	case DOUBLE:
593	–	run_time = the_event->evt.asmt.rhs.dval;
594	–	have_run_time = 1;
595	–	return 1;
596	–	break;
597	–
598	–	case INT:
599	–	run_time = (double)the_event->evt.asmt.rhs.ival;
600	–	have_run_time = 1;
601	–	return 1;
602	–	break;
603	–
604	–	default:
605	–	the_event->err_msg =
606	–	strdup( "Error in parsing meta-data file!\n\trunTime unrecognized.\n" );
607	–	return 0;
608	–	break;
609	–	}
610	–	break;
611	–
612	–	case G_INITIALCONFIG:
613	–	if( the_type == STRING ){
614	–	strcpy( initial_config, the_event->evt.asmt.rhs.sval );
615	–	have_initial_config = 1;
616	–	return 1;
617	–	}
618	–
619	–	the_event->err_msg =
620	–	strdup( "Error in parsing meta-data file!\n\tinitialConfig was not a string assignment.\n" );
621	–	return 0;
622	–	break;
623	–
624	–	case G_FINALCONFIG:
625	–	if( the_type == STRING ){
626	–	strcpy( final_config, the_event->evt.asmt.rhs.sval );
627	–	have_final_config = 1;
628	–	return 1;
629	–	}
630	–
631	–	the_event->err_msg =
632	–	strdup( "Error in parsing meta-data file!\n\tfinalConfig was not a string assignment.\n" );
633	–	return 0;
634	–	break;
635	–
636	–	case G_NMOL:
637	–	switch( the_type ){
638	–
639	–	case STRING:
640	–	the_event->err_msg =
641	–	strdup( "Error in parsing meta-data file!\n\tnMol is not a double or int.\n" );
642	–	return 0;
643	–	break;
644	–
645	–	case DOUBLE:
646	–	n_mol = (int)the_event->evt.asmt.rhs.dval;
647	–	have_n_mol = 1;
648	–	return 1;
649	–	break;
650	–
651	–	case INT:
652	–	n_mol = the_event->evt.asmt.rhs.ival;
653	–	have_n_mol = 1;
654	–	return 1;
655	–	break;
656	–
657	–	default:
658	–	the_event->err_msg =
659	–	strdup( "Error in parsing meta-data file!\n\tnMol unrecognized.\n" );
660	–	return 0;
661	–	break;
662	–	}
663	–	break;
664	–
665	–	case G_DENSITY:
666	–	switch( the_type ){
667	–
668	–	case STRING:
669	–	the_event->err_msg =
670	–	strdup( "Error in parsing meta-data file!\n\tdensity is not a double or int.\n" );
671	–	return 0;
672	–	break;
673	–
674	–	case DOUBLE:
675	–	density = the_event->evt.asmt.rhs.dval;
676	–	have_density = 1;
677	–	return 1;
678	–	break;
679	–
680	–	case INT:
681	–	density = (double)the_event->evt.asmt.rhs.ival;
682	–	have_density = 1;
683	–	return 1;
684	–	break;
685	–
686	–	default:
687	–	the_event->err_msg =
688	–	strdup( "Error in parsing meta-data file!\n\tdensity unrecognized.\n" );
689	–	return 0;
690	–	break;
691	–	}
692	–	break;
693	–
694	–	case G_BOX:
695	–	switch( the_type ){
696	–
697	–	case STRING:
698	–	the_event->err_msg =
699	–	strdup( "Error in parsing meta-data file!\n\tbox is not a double or int.\n" );
700	–	return 0;
701	–	break;
702	–
703	–	case DOUBLE:
704	–	box = the_event->evt.asmt.rhs.dval;
705	–	have_box = 1;
706	–	return 1;
707	–	break;
708	–
709	–	case INT:
710	–	box = (double)the_event->evt.asmt.rhs.ival;
711	–	have_box = 1;
712	–	return 1;
713	–	break;
714	–
715	–	default:
716	–	the_event->err_msg =
717	–	strdup( "Error in parsing meta-data file!\n\tbox unrecognized.\n" );
718	–	return 0;
719	–	break;
720	–	}
721	–	break;
722	–
723	–	case G_BOXX:
724	–	switch( the_type ){
725	–
726	–	case STRING:
727	–	the_event->err_msg =
728	–	strdup( "Error in parsing meta-data file!\n\tboxX is not a double or int.\n" );
729	–	return 0;
730	–	break;
731	–
732	–	case DOUBLE:
733	–	box_x = the_event->evt.asmt.rhs.dval;
734	–	have_box_x = 1;
735	–	return 1;
736	–	break;
737	–
738	–	case INT:
739	–	box_x = (double)the_event->evt.asmt.rhs.ival;
740	–	have_box_x = 1;
741	–	return 1;
742	–	break;
743	–
744	–	default:
745	–	the_event->err_msg =
746	–	strdup( "Error in parsing meta-data file!\n\tboxX unrecognized.\n" );
747	–	return 0;
748	–	break;
749	–	}
750	–	break;
751	–
752	–	case G_BOXY:
753	–	switch( the_type ){
754	–
755	–	case STRING:
756	–	the_event->err_msg =
757	–	strdup( "Error in parsing meta-data file!\n\tboxY is not a double or int.\n" );
758	–	return 0;
759	–	break;
760	–
761	–	case DOUBLE:
762	–	box_y = the_event->evt.asmt.rhs.dval;
763	–	have_box_y = 1;
764	–	return 1;
765	–	break;
766	–
767	–	case INT:
768	–	box_y = (double)the_event->evt.asmt.rhs.ival;
769	–	have_box_y = 1;
770	–	return 1;
771	–	break;
772	–
773	–	default:
774	–	the_event->err_msg =
775	–	strdup( "Error in parsing meta-data file!\n\tboxY unrecognized.\n" );
776	–	return 0;
777	–	break;
778	–	}
779	–	break;
780	–
781	–	case G_BOXZ:
782	–	switch( the_type ){
783	–
784	–	case STRING:
785	–	the_event->err_msg =
786	–	strdup( "Error in parsing meta-data file!\n\tboxZ is not a double or int.\n" );
787	–	return 0;
788	–	break;
789	–
790	–	case DOUBLE:
791	–	box_z = the_event->evt.asmt.rhs.dval;
792	–	have_box_z = 1;
793	–	return 1;
794	–	break;
795	–
796	–	case INT:
797	–	box_z = (double)the_event->evt.asmt.rhs.ival;
798	–	have_box_z = 1;
799	–	return 1;
800	–	break;
801	–
802	–	default:
803	–	the_event->err_msg =
804	–	strdup( "Error in parsing meta-data file!\n\tboxZ unrecognized.\n" );
805	–	return 0;
806	–	break;
807	–	}
808	–	break;
809	–
810	–	case G_SAMPLETIME:
811	–	switch( the_type ){
812	–
813	–	case STRING:
814	–	the_event->err_msg =
815	–	strdup( "Error in parsing meta-data file!\n\tsampleTime is not a double or int.\n" );
816	–	return 0;
817	–	break;
818	–
819	–	case DOUBLE:
820	–	sample_time = the_event->evt.asmt.rhs.dval;
821	–	have_sample_time = 1;
822	–	return 1;
823	–	break;
824	–
825	–	case INT:
826	–	sample_time = (double)the_event->evt.asmt.rhs.ival;
827	–	have_sample_time = 1;
828	–	return 1;
829	–	break;
830	–
831	–	default:
832	–	the_event->err_msg =
833	–	strdup( "Error in parsing meta-data file!\n\tsampleTime unrecognized.\n" );
834	–	return 0;
835	–	break;
836	–	}
837	–	break;
838	–
839	–	case G_STATUSTIME:
840	–	switch( the_type ){
841	–
842	–	case STRING:
843	–	the_event->err_msg =
844	–	strdup( "Error in parsing meta-data file!\n\tstatusTime is not a double or int.\n" );
845	–	return 0;
846	–	break;
847	–
848	–	case DOUBLE:
849	–	status_time = the_event->evt.asmt.rhs.dval;
850	–	have_status_time = 1;
851	–	return 1;
852	–	break;
853	–
854	–	case INT:
855	–	status_time = (double)the_event->evt.asmt.rhs.ival;
856	–	have_status_time = 1;
857	–	return 1;
858	–	break;
859	–
860	–	default:
861	–	the_event->err_msg =
862	–	strdup( "Error in parsing meta-data file!\n\tstatusTime unrecognized.\n" );
863	–	return 0;
864	–	break;
865	–	}
866	–	break;
867	–
868	–	case G_RESETTIME:
869	–	switch( the_type ){
870	–
871	–	case STRING:
872	–	the_event->err_msg =
873	–	strdup( "Error in parsing meta-data file!\n\tresetTime is not a double or int.\n" );
874	–	return 0;
875	–	break;
876	–
877	–	case DOUBLE:
878	–	resetTime = the_event->evt.asmt.rhs.dval;
879	–	have_reset_time = 1;
880	–	return 1;
881	–	break;
882	–
883	–	case INT:
884	–	resetTime = (double)the_event->evt.asmt.rhs.ival;
885	–	have_reset_time = 1;
886	–	return 1;
887	–	break;
888	–
889	–	default:
890	–	the_event->err_msg =
891	–	strdup( "Error in parsing meta-data file!\n\tresetTime unrecognized.\n" );
892	–	return 0;
893	–	break;
894	–	}
895	–	break;
896	–
897	–	case G_THERMALTIME:
898	–	switch( the_type ){
899	–
900	–	case STRING:
901	–	the_event->err_msg =
902	–	strdup( "Error in parsing meta-data file!\n\tthermalTime is not a double or int.\n" );
903	–	return 0;
904	–	break;
905	–
906	–	case DOUBLE:
907	–	thermal_time = the_event->evt.asmt.rhs.dval;
908	–	have_thermal_time = 1;
909	–	return 1;
910	–	break;
911	–
912	–	case INT:
913	–	thermal_time = (double)the_event->evt.asmt.rhs.ival;
914	–	have_thermal_time = 1;
915	–	return 1;
916	–	break;
917	–
918	–	default:
919	–	the_event->err_msg =
920	–	strdup( "Error in parsing meta-data file!\n\tthermalTime unrecognized.\n" );
921	–	return 0;
922	–	break;
923	–	}
924	–	break;
925	–
926	–	case G_RCUT:
927	–	switch( the_type ){
928	–
929	–	case STRING:
930	–	the_event->err_msg =
931	–	strdup( "Error in parsing meta-data file!\n\tcutoffRadius is not a double or int.\n" );
932	–	return 0;
933	–	break;
934	–
935	–	case DOUBLE:
936	–	rcut = the_event->evt.asmt.rhs.dval;
937	–	have_rcut = 1;
938	–	return 1;
939	–	break;
940	–
941	–	case INT:
942	–	rcut = (double)the_event->evt.asmt.rhs.ival;
943	–	have_rcut = 1;
944	–	return 1;
945	–	break;
946	–
947	–	default:
948	–	the_event->err_msg =
949	–	strdup( "Error in parsing meta-data file!\n\tcutoffRadius unrecognized.\n" );
950	–	return 0;
951	–	break;
952	–	}
953	–	break;
954	–
955	–	case G_RSW:
956	–	switch( the_type ){
957	–
958	–	case STRING:
959	–	the_event->err_msg =
960	–	strdup( "Error in parsing meta-data file!\n\tswitchingRadius is not a double or int.\n" );
961	–	return 0;
962	–	break;
963	–
964	–	case DOUBLE:
965	–	rsw = the_event->evt.asmt.rhs.dval;
966	–	have_rsw = 1;
967	–	return 1;
968	–	break;
969	–
970	–	case INT:
971	–	rsw = (double)the_event->evt.asmt.rhs.ival;
972	–	have_rsw = 1;
973	–	return 1;
974	–	break;
975	–
976	–	default:
977	–	the_event->err_msg =
978	–	strdup( "Error in parsing meta-data file!\n\tswitchingRadius unrecognized.\n" );
979	–	return 0;
980	–	break;
981	–	}
982	–	break;
983	–
984	–	case G_DIELECTRIC:
985	–	switch( the_type ){
986	–
987	–	case STRING:
988	–	the_event->err_msg =
989	–	strdup( "Error in parsing meta-data file!\n\tdielectric is not a double or int.\n" );
990	–	return 0;
991	–	break;
992	–
993	–	case DOUBLE:
994	–	dielectric = the_event->evt.asmt.rhs.dval;
995	–	have_dielectric = 1;
996	–	return 1;
997	–	break;
998	–
999	–	case INT:
1000	–	dielectric = (double)the_event->evt.asmt.rhs.ival;
1001	–	have_dielectric = 1;
1002	–	return 1;
1003	–	break;
1004	–
1005	–	default:
1006	–	the_event->err_msg =
1007	–	strdup( "Error in parsing meta-data file!\n\tdielectric unrecognized.\n" );
1008	–	return 0;
1009	–	break;
1010	–	}
1011	–	break;
1012	–
1013	–	case G_TEMPSET:
1014	–	if( the_type == STRING ){
1015	–
1016	–	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) tempSet = 1;
1017	–	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) tempSet = 0;
1018	–	else{
1019	–	the_event->err_msg =
1020	–	strdup( "Error in parsing meta-data file!\n\ttempSet was not \"true\" or \"false\".\n" );
1021	–	return 0;
1022	–	}
1023	–	have_tempSet = 1;
1024	–	return 1;
1025	–	}
1026	–
1027	–	the_event->err_msg =
1028	–	strdup( "Error in parsing meta-data file!\n\ttempSet was not \"true\" or \"false\".\n" );
1029	–	return 0;
1030	–	break;
1031	–
1032	–	case G_USEINITTIME:
1033	–	if( the_type == STRING ){
1034	–
1035	–	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useInitTime = 1;
1036	–	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useInitTime = 0;
1037	–	else{
1038	–	the_event->err_msg =
1039	–	strdup( "Error in parsing meta-data file!\n\tuseInitTime was not \"true\" or \"false\".\n" );
1040	–	return 0;
1041	–	}
1042	–	return 1;
1043	–	}
1044	–
1045	–	the_event->err_msg =
1046	–	strdup( "Error in parsing meta-data file!\n\tuseInitTime was not \"true\" or \"false\".\n" );
1047	–	return 0;
1048	–	break;
1049	–
1050	–	case G_USEINIT_XS_STATE:
1051	–	if( the_type == STRING ){
1052	–
1053	–	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval ))
1054	–	useInitXSstate = 1;
1055	–	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval ))
1056	–	useInitXSstate = 0;
1057	–	else{
1058	–	the_event->err_msg =
1059	–	strdup( "Error in parsing meta-data file!\n\tuseInitExtendedSystemState was not \"true\" or \"false\".\n" );
1060	–	return 0;
1061	–	}
1062	–	return 1;
1063	–	}
1064	–
1065	–	the_event->err_msg =
1066	–	strdup( "Error in parsing meta-data file!\n\tuseInitExtendedSystemState was not \"true\" or \"false\".\n" );
1067	–	return 0;
1068	–	break;
1069	–
1070	–	case G_USEPBC:
1071	–	if( the_type == STRING ){
1072	–
1073	–	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) usePBC = 1;
1074	–	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) usePBC = 0;
1075	–	else{
1076	–	the_event->err_msg =
1077	–	strdup( "Error in parsing meta-data file!\n\tusePeriodicBoundaryConditions was not \"true\" or \"false\".\n" );
1078	–	return 0;
1079	–	}
1080	–	return 1;
1081	–	}
1082	–
1083	–	the_event->err_msg =
1084	–	strdup( "Error in parsing meta-data file!\n\tusePeriodicBoundaryConditions was not \"true\" or \"false\".\n" );
1085	–	return 0;
1086	–	break;
1087	–
1088	–	case G_USERF:
1089	–	if( the_type == STRING ){
1090	–
1091	–	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useRF = 1;
1092	–	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useRF = 0;
1093	–	else{
1094	–	the_event->err_msg =
1095	–	strdup( "Error in parsing meta-data file!\n\tuseReactionField was not \"true\" or \"false\".\n" );
1096	–	return 0;
1097	–	}
1098	–	return 1;
1099	–	}
1100	–
1101	–	the_event->err_msg =
1102	–	strdup( "Error in parsing meta-data file!\n\tuseReactionField was not \"true\" or \"false\".\n" );
1103	–	return 0;
1104	–	break;
1105	–
1106	–	case G_TARGETPRESSURE:
1107	–	switch( the_type ){
1108	–
1109	–	case STRING:
1110	–	the_event->err_msg =
1111	–	strdup( "Error in parsing meta-data file!\n\ttargetPressure is not a double or int.\n" );
1112	–	return 0;
1113	–	break;
1114	–
1115	–	case DOUBLE:
1116	–	target_pressure = the_event->evt.asmt.rhs.dval;
1117	–	have_target_pressure = 1;
1118	–	return 1;
1119	–	break;
1120	–
1121	–	case INT:
1122	–	target_pressure = (double)the_event->evt.asmt.rhs.ival;
1123	–	have_target_pressure = 1;
1124	–	return 1;
1125	–	break;
1126	–
1127	–	default:
1128	–	the_event->err_msg =
1129	–	strdup( "Error in parsing meta-data file!\n\ttargetPressure unrecognized.\n" );
1130	–	return 0;
1131	–	break;
1132	–	}
1133	–	break;
1134	–
1135	–	case G_TAUTHERMOSTAT:
1136	–	switch( the_type ){
1137	–
1138	–	case STRING:
1139	–	the_event->err_msg =
1140	–	strdup( "Error in parsing meta-data file!\n\ttauThermostat is not a double or int.\n" );
1141	–	return 0;
1142	–	break;
1143	–
1144	–	case DOUBLE:
1145	–	tau_thermostat = the_event->evt.asmt.rhs.dval;
1146	–	have_tau_thermostat = 1;
1147	–	return 1;
1148	–	break;
1149	–
1150	–	case INT:
1151	–	tau_thermostat = (double)the_event->evt.asmt.rhs.ival;
1152	–	have_tau_thermostat = 1;
1153	–	return 1;
1154	–	break;
1155	–
1156	–	default:
1157	–	the_event->err_msg =
1158	–	strdup( "Error in parsing meta-data file!\n\ttauThermostat unrecognized.\n" );
1159	–	return 0;
1160	–	break;
1161	–	}
1162	–	break;
1163	–
1164	–	case G_TAUBAROSTAT:
1165	–	switch( the_type ){
1166	–
1167	–	case STRING:
1168	–	the_event->err_msg =
1169	–	strdup( "Error in parsing meta-data file!\n\ttauBarostat is not a double or int.\n" );
1170	–	return 0;
1171	–	break;
1172	–
1173	–	case DOUBLE:
1174	–	tau_barostat = the_event->evt.asmt.rhs.dval;
1175	–	have_tau_barostat = 1;
1176	–	return 1;
1177	–	break;
1178	–
1179	–	case INT:
1180	–	tau_barostat = (double)the_event->evt.asmt.rhs.ival;
1181	–	have_tau_barostat = 1;
1182	–	return 1;
1183	–	break;
1184	–
1185	–	default:
1186	–	the_event->err_msg =
1187	–	strdup( "Error in parsing meta-data file!\n\ttauBarostat unrecognized.\n" );
1188	–	return 0;
1189	–	break;
1190	–	}
1191	–	break;
1192	–
1193	–	case G_ZCONSTIME:
1194	–	switch( the_type ){
1195	–
1196	–	case STRING:
1197	–	the_event->err_msg =
1198	–	strdup( "Error in parsing meta-data file!\n\tzcons_time is not a double or int.\n" );
1199	–	return 0;
1200	–	break;
1201	–
1202	–	case DOUBLE:
1203	–	zcons_time = the_event->evt.asmt.rhs.dval;
1204	–	have_zcons_time = 1;
1205	–	return 1;
1206	–	break;
1207	–
1208	–	case INT:
1209	–	zcons_time = (double)the_event->evt.asmt.rhs.ival;
1210	–	have_zcons_time = 1;
1211	–	return 1;
1212	–	break;
1213	–
1214	–	default:
1215	–	the_event->err_msg =
1216	–	strdup( "Error in parsing meta-data file!\n\tzcons_time unrecognized.\n" );
1217	–	return 0;
1218	–	break;
1219	–	}
1220	–	break;
198
199	<	case G_ZCONSTOL:
200	<	switch( the_type ){
201	<
202	<	case STRING:
203	<	the_event->err_msg =
204	<	strdup( "Error in parsing meta-data file!\n\tzcons_tol is not a double or int.\n" );
205	<	return 0;
206	<	break;
1230	<
1231	<	case DOUBLE:
1232	<	zcons_tol = the_event->evt.asmt.rhs.dval;
1233	<	have_zcons_tol = 1;
1234	<	return 1;
1235	<	break;
1236	<
1237	<	case INT:
1238	<	zcons_tol = (double)the_event->evt.asmt.rhs.ival;
1239	<	have_zcons_tol = 1;
1240	<	return 1;
1241	<	break;
1242	<
1243	<	default:
1244	<	the_event->err_msg =
1245	<	strdup( "Error in parsing meta-data file!\n\tzcons_ol unrecognized.\n" );
1246	<	return 0;
1247	<	break;
1248	<	}
1249	<	break;
1250	<
1251	<	case G_ZCONSFORCEPOLICY:
1252	<	switch( the_type ){
1253	<
1254	<	case STRING:
1255	<	strcpy(zconsForcePolicy, the_event->evt.asmt.rhs.sval);
1256	<
1257	<	for(int i = 0; zconsForcePolicy[i] != '\0'; i++)
1258	<	{
1259	<	zconsForcePolicy[i] = toupper(zconsForcePolicy[i]);
1260	<	}
1261	<	have_zcons_force_policy = 1;
1262	<	return 1;
1263	<	break;
1264	<
1265	<	case DOUBLE:
1266	<	the_event->err_msg =
1267	<	strdup( "Error in parsing meta-data file!\n\tzconsForcePolicy is not a double or int.\n" );
1268	<	return 0;
1269	<	break;
1270	<
1271	<	case INT:
1272	<	the_event->err_msg =
1273	<	strdup( "Error in parsing meta-data file!\n\tzconsForcePolicy is not a double or int.\n" );
1274	<	return 0;
1275	<	break;
1276	<
1277	<	default:
1278	<	the_event->err_msg =
1279	<	strdup( "Error in parsing meta-data file!\n\tzconsForcePolicy unrecognized.\n" );
1280	<	return 0;
1281	<	break;
1282	<	}
1283	<	break;
1284	<
1285	<	case G_ZCONSGAP:
1286	<	switch( the_type ){
1287	<
1288	<	case STRING:
1289	<	the_event->err_msg =
1290	<	strdup( "Error in parsing meta-data file!\n\tzcons_gap is not a double or int.\n" );
1291	<	return 0;
1292	<	break;
1293	<
1294	<	case DOUBLE:
1295	<	zcons_gap = the_event->evt.asmt.rhs.dval;
1296	<	have_zcons_gap= 1;
1297	<	return 1;
1298	<	break;
1299	<
1300	<	case INT:
1301	<	zcons_gap= (double)the_event->evt.asmt.rhs.ival;
1302	<	have_zcons_gap= 1;
1303	<	return 1;
1304	<	break;
1305	<
1306	<	default:
1307	<	the_event->err_msg =
1308	<	strdup( "Error in parsing meta-data file!\n\tzcons_gap unrecognized.\n" );
1309	<	return 0;
1310	<	break;
1311	<	}
1312	<	break;
1313	<
1314	<	case G_ZCONSFIXTIME:
1315	<	switch( the_type ){
1316	<
1317	<	case STRING:
1318	<	the_event->err_msg =
1319	<	strdup( "Error in parsing meta-data file!\n\tzcons_fixtime is not a double or int.\n" );
1320	<	return 0;
1321	<	break;
1322	<
1323	<	case DOUBLE:
1324	<	zcons_fixtime= the_event->evt.asmt.rhs.dval;
1325	<	have_zcons_fixtime= 1;
1326	<	return 1;
1327	<	break;
1328	<
1329	<	case INT:
1330	<	zcons_fixtime= (double)the_event->evt.asmt.rhs.ival;
1331	<	have_zcons_fixtime= 1;
1332	<	return 1;
1333	<	break;
1334	<
1335	<	default:
1336	<	the_event->err_msg =
1337	<	strdup( "Error in parsing meta-data file!\n\tzcons_fixtime unrecognized.\n" );
1338	<	return 0;
1339	<	break;
1340	<	}
1341	<	break;
1342	<
1343	<	case G_ZCONSUSINGSMD:
1344	<	switch( the_type ){
1345	<
1346	<	case STRING:
1347	<	the_event->err_msg =
1348	<	strdup( "Error in parsing meta-data file!\n\tzcons_fixtime is not an  int.\n" );
1349	<	return 0;
1350	<	break;
1351	<
1352	<	case DOUBLE:
1353	<	the_event->err_msg =
1354	<	strdup( "Error in parsing meta-data file!\n\tzcons_fixtime is not an  int.\n" );
1355	<	return 0;
1356	<	break;
1357	<
1358	<	case INT:
1359	<	zcons_using_smd= the_event->evt.asmt.rhs.ival;
1360	<	have_zcons_using_smd= 1;
1361	<	return 1;
1362	<	break;
1363	<
1364	<	default:
1365	<	the_event->err_msg =
1366	<	strdup( "Error in parsing meta-data file!\n\tzcons_usingsmd unrecognized.\n" );
1367	<	return 0;
1368	<	break;
1369	<	}
1370	<	break;
1371	<
1372	<	case G_MINIMIZER:
1373	<	switch( the_type ){
1374	<
1375	<	case STRING:
1376	<	strcpy(minimizer_name, the_event->evt.asmt.rhs.sval);
1377	<
1378	<	for(int i = 0; zconsForcePolicy[i] != '\0'; i++){
1379	<	zconsForcePolicy[i] = toupper(zconsForcePolicy[i]);
1380	<	}
1381	<	have_minimizer= 1;
1382	<	return 1;
1383	<	break;
1384	<
1385	<	case DOUBLE:
1386	<	the_event->err_msg =
1387	<	strdup( "Error in parsing meta-data file!\n\tminimizer_name is not a double or int.\n" );
1388	<	return 0;
1389	<	break;
1390	<
1391	<	case INT:
1392	<	the_event->err_msg =
1393	<	strdup( "Error in parsing meta-data file!\n\tminimizer_name is not a double or int.\n" );
1394	<	return 0;
1395	<	break;
1396	<
1397	<	default:
1398	<	the_event->err_msg =
1399	<	strdup( "Error in parsing meta-data file!\n\tminimizer_name unrecognized.\n" );
1400	<	return 0;
1401	<	break;
1402	<	}
1403	<	break;
1404	<
1405	<	case G_MIN_MAXITER:
1406	<	switch( the_type ){
1407	<
1408	<	case STRING:
1409	<	the_event->err_msg =
1410	<	strdup( "Error in parsing meta-data file!\n\tminimizer_maxiteration is not a double or int.\n" );
1411	<	return 1;
1412	<	break;
1413	<
1414	<	case DOUBLE:
1415	<	minimizer_maxiteration = (int)the_event->evt.asmt.rhs.dval;
1416	<	have_minimizer_maxiteration = 1;
1417	<	return 1;
1418	<	break;
1419	<
1420	<	case INT:
1421	<	minimizer_maxiteration = the_event->evt.asmt.rhs.ival;
1422	<	have_minimizer_maxiteration = 1;
1423	<	return 1;
1424	<	break;
1425	<
1426	<	default:
1427	<	the_event->err_msg =
1428	<	strdup( "Error in parsing meta-data file!\n\tminimizer_maxiteration unrecognized.\n" );
1429	<	return 0;
1430	<	break;
1431	<	}
1432	<	break;
1433	<
1434	<	case G_MIN_WRITEFRQ:
1435	<	switch( the_type ){
1436	<
1437	<	case STRING:
1438	<	the_event->err_msg =
1439	<	strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq is not an int.\n" );
1440	<	return 1;
1441	<	break;
1442	<
1443	<	case DOUBLE:
1444	<	the_event->err_msg =
1445	<	strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq is not an  int.\n" );
1446	<	return 1;
1447	<	break;
1448	<
1449	<	case INT:
1450	<	minimizer_writefrq= the_event->evt.asmt.rhs.ival;
1451	<	have_minimizer_writefrq = 1;
1452	<	return 1;
1453	<	break;
1454	<
1455	<	default:
1456	<	the_event->err_msg =
1457	<	strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq unrecognized.\n" );
1458	<	return 0;
1459	<	break;
1460	<	}
1461	<	break;
1462	<
1463	<	case G_MIN_STEPSIZE:
1464	<	switch( the_type ){
1465	<
1466	<	case STRING:
1467	<	the_event->err_msg =
1468	<	strdup( "Error in parsing meta-data file!\n\tminimizer_resetfrq is not a double or int.\n" );
1469	<	return 1;
1470	<	break;
1471	<
1472	<	case DOUBLE:
1473	<	minimizer_stepsize= the_event->evt.asmt.rhs.dval;
1474	<	have_minimizer_stepsize = 1;
1475	<	return 1;
1476	<	break;
1477	<
1478	<	case INT:
1479	<	minimizer_stepsize= the_event->evt.asmt.rhs.ival;
1480	<	have_minimizer_stepsize = 1;
1481	<	return 1;
1482	<	break;
1483	<
1484	<	default:
1485	<	the_event->err_msg =
1486	<	strdup( "Error in parsing meta-data file!\n\tminimizer_resetfrq unrecognized.\n" );
1487	<	return 0;
1488	<	break;
1489	<	}
1490	<	break;
1491	<
1492	<	case G_MIN_FTOL:
1493	<	switch( the_type ){
1494	<
1495	<	case STRING:
1496	<	the_event->err_msg =
1497	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ftol is not a double or int.\n" );
1498	<	return 1;
1499	<	break;
1500	<
1501	<	case DOUBLE:
1502	<	minimizer_ftol= the_event->evt.asmt.rhs.dval;
1503	<	have_minimizer_ftol = 1;
1504	<	return 1;
1505	<	break;
1506	<
1507	<	case INT:
1508	<	minimizer_ftol= the_event->evt.asmt.rhs.ival;
1509	<	have_minimizer_ftol = 1;
1510	<	return 1;
1511	<	break;
1512	<
1513	<	default:
1514	<	the_event->err_msg =
1515	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ftol unrecognized.\n" );
1516	<	return 0;
1517	<	break;
1518	<	}
1519	<	break;
1520	<
1521	<	case G_MIN_GTOL:
1522	<	switch( the_type ){
1523	<
1524	<	case STRING:
1525	<	the_event->err_msg =
1526	<	strdup( "Error in parsing meta-data file!\n\tminimizer_gtol is not a double or int.\n" );
1527	<	return 1;
1528	<	break;
1529	<
1530	<	case DOUBLE:
1531	<	minimizer_gtol= the_event->evt.asmt.rhs.dval;
1532	<	have_minimizer_gtol = 1;
1533	<	return 1;
1534	<	break;
1535	<
1536	<	case INT:
1537	<	minimizer_gtol= the_event->evt.asmt.rhs.ival;
1538	<	have_minimizer_gtol = 1;
1539	<	return 1;
1540	<	break;
1541	<
1542	<	default:
1543	<	the_event->err_msg =
1544	<	strdup( "Error in parsing meta-data file!\n\tminimizer_gtol unrecognized.\n" );
1545	<	return 0;
1546	<	break;
1547	<	}
1548	<	break;
1549	<
1550	<	case G_MIN_LSMAXITER:
1551	<	switch( the_type ){
1552	<
1553	<	case STRING:
1554	<	the_event->err_msg =
1555	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration is not an int.\n" );
1556	<	return 1;
1557	<	break;
1558	<
1559	<	case DOUBLE:
1560	<	the_event->err_msg =
1561	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration is not an int.\n" );
1562	<	return 1;
1563	<	break;
1564	<
1565	<	case INT:
1566	<	minimizer_ls_maxiteration = the_event->evt.asmt.rhs.ival;
1567	<	have_minimizer_ls_maxiteration = 1;
1568	<	return 1;
1569	<	break;
1570	<
1571	<	default:
1572	<	the_event->err_msg =
1573	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration unrecognized.\n" );
1574	<	return 0;
1575	<	break;
1576	<	}
1577	<	break;
1578	<
1579	<	case G_MIN_LSTOL:
1580	<	switch( the_type ){
1581	<
1582	<	case STRING:
1583	<	the_event->err_msg =
1584	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_tol is not a double or int.\n" );
1585	<	return 1;
1586	<	break;
1587	<
1588	<	case DOUBLE:
1589	<	minimizer_ls_tol= the_event->evt.asmt.rhs.dval;
1590	<	have_minimizer_ls_tol = 1;
1591	<	return 1;
1592	<	break;
1593	<
1594	<	case INT:
1595	<	minimizer_ls_tol= the_event->evt.asmt.rhs.ival;
1596	<	have_minimizer_ls_tol = 1;
1597	<	return 1;
1598	<	break;
1599	<
1600	<	default:
1601	<	the_event->err_msg =
1602	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_tol unrecognized.\n" );
1603	<	return 0;
1604	<	break;
1605	<	}
1606	<	break;
1607	<
1608	<	// add more token cases here.
1609	<	case G_SEED:
1610	<	switch( the_type ){
1611	<
1612	<	case STRING:
1613	<	the_event->err_msg =
1614	<	strdup( "Error in parsing meta-data file!\n\tseed is not a string.\n" );
1615	<	return 0;
1616	<	return 0;
1617	<	break;
1618	<
1619	<	case DOUBLE:
1620	<	have_seed = 1;
1621	<	seed = (int)the_event->evt.asmt.rhs.dval;
1622	<	return 1;
1623	<	break;
1624	<
1625	<	case INT:
1626	<	have_seed = 1;
1627	<	seed =  the_event->evt.asmt.rhs.ival ;
1628	<	return 1;
1629	<	break;
1630	<
1631	<	default:
1632	<	the_event->err_msg =
1633	<	strdup( "Error in parsing meta-data file!\n\tseed unrecognized.\n" );
1634	<	return 0;
1635	<	break;
1636	<	}
1637	<	break;
1638	<
1639	<	case G_USE_SOLID_THERM_INT:
1640	<	if( the_type == STRING ){
1641	<
1642	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useSolidThermInt = 1;
1643	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useSolidThermInt = 0;
1644	<	else{
1645	<	the_event->err_msg =
1646	<	strdup( "Error in parsing meta-data file!\n\tuseSolidThermInt was not \"true\" or \"false\".\n" );
1647	<	return 0;
1648	<	}
1649	<	return 1;
1650	<	}
1651	<
1652	<	the_event->err_msg =
1653	<	strdup( "Error in parsing meta-data file!\n\tuseSolidThermInt was not \"true\" or \"false\".\n" );
1654	<	return 0;
1655	<	break;
1656	<
1657	<	case G_USE_LIQUID_THERM_INT:
1658	<	if( the_type == STRING ){
1659	<
1660	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useLiquidThermInt = 1;
1661	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useLiquidThermInt = 0;
1662	<	else{
1663	<	the_event->err_msg =
1664	<	strdup( "Error in parsing meta-data file!\n\tuseLiquidThermInt was not \"true\" or \"false\".\n" );
1665	<	return 0;
1666	<	}
1667	<	return 1;
1668	<	}
1669	<
1670	<	the_event->err_msg =
1671	<	strdup( "Error in parsing meta-data file!\n\tuseLiquidThermInt was not \"true\" or \"false\".\n" );
1672	<	return 0;
1673	<	break;
1674	<
1675	<	case G_THERM_INT_LAMBDA:
1676	<	switch( the_type ){
1677	<
1678	<	case STRING:
1679	<	the_event->err_msg =
1680	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationLambda is not a double or int.\n" );
1681	<	return 1;
1682	<	break;
1683	<
1684	<	case DOUBLE:
1685	<	thermodynamic_integration_lambda = the_event->evt.asmt.rhs.dval;
1686	<	have_thermodynamic_integration_lambda = 1;
1687	<	return 1;
1688	<	break;
1689	<
1690	<	case INT:
1691	<	thermodynamic_integration_lambda = (double)the_event->evt.asmt.rhs.dval;
1692	<	have_thermodynamic_integration_lambda = 1;
1693	<	return 1;
1694	<	break;
1695	<
1696	<	default:
1697	<	the_event->err_msg =
1698	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationLambda unrecognized.\n" );
1699	<	return 0;
1700	<	break;
1701	<	}
1702	<	break;
1703	<
1704	<	case G_THERM_INT_K:
1705	<	switch( the_type ){
1706	<
1707	<	case STRING:
1708	<	the_event->err_msg =
1709	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationK is not a double or int.\n" );
1710	<	return 1;
1711	<	break;
1712	<
1713	<	case DOUBLE:
1714	<	thermodynamic_integration_k = the_event->evt.asmt.rhs.dval;
1715	<	have_thermodynamic_integration_k = 1;
1716	<	return 1;
1717	<	break;
1718	<
1719	<	case INT:
1720	<	thermodynamic_integration_k = (double)the_event->evt.asmt.rhs.dval;
1721	<	have_thermodynamic_integration_k = 1;
1722	<	return 1;
1723	<	break;
1724	<
1725	<	default:
1726	<	the_event->err_msg =
1727	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationK unrecognized.\n" );
1728	<	return 0;
1729	<	break;
1730	<	}
1731	<	break;
1732	<
1733	<	case G_FORCEFIELD_VARIANT:
1734	<	if( the_type == STRING ){
1735	<	strcpy( forcefield_variant, the_event->evt.asmt.rhs.sval );
1736	<	have_forcefield_variant = 1;
1737	<	return 1;
1738	<	}
1739	<
1740	<	the_event->err_msg =
1741	<	strdup( "Error in parsing meta-data file!\n\tforceFieldVariant was not a string assignment.\n" );
1742	<	return 0;
1743	<	break;
1744	<	// add more token cases here.
1745	<
1746	<	case G_FORCEFIELD_FILENAME:
1747	<	if( the_type == STRING ){
1748	<	strcpy( forcefield_filename, the_event->evt.asmt.rhs.sval );
1749	<	have_forcefield_filename = 1;
1750	<	return 1;
1751	<	}
1752	<
1753	<	the_event->err_msg =
1754	<	strdup( "Error in parsing meta-data file!\n\tforceFieldFileName was not a string assignment.\n" );
1755	<	return 0;
1756	<	break;
1757	<
1758	<	case G_THERM_INT_DIST_SPRING:
1759	<	switch( the_type ){
1760	<
1761	<	case STRING:
1762	<	the_event->err_msg =
1763	<	strdup( "Error in parsing meta-data file!\n\tthermIntDistSpringConst is not a double or int.\n" );
1764	<	return 1;
1765	<	break;
1766	<
1767	<	case DOUBLE:
1768	<	therm_int_dist_spring = the_event->evt.asmt.rhs.dval;
1769	<	have_dist_spring_constant = 1;
1770	<	return 1;
1771	<	break;
1772	<
1773	<	case INT:
1774	<	therm_int_dist_spring = (double)the_event->evt.asmt.rhs.dval;
1775	<	have_dist_spring_constant = 1;
1776	<	return 1;
1777	<	break;
1778	<
1779	<	default:
1780	<	the_event->err_msg =
1781	<	strdup( "Error in parsing meta-data file!\n\tthermIntDistSpringConst unrecognized.\n" );
1782	<	return 0;
1783	<	break;
1784	<	}
1785	<	break;
1786	<
1787	<	case G_THERM_INT_THETA_SPRING:
1788	<	switch( the_type ){
1789	<
1790	<	case STRING:
1791	<	the_event->err_msg =
1792	<	strdup( "Error in parsing meta-data file!\n\tthermIntThetaSpringConst is not a double or int.\n" );
1793	<	return 1;
1794	<	break;
1795	<
1796	<	case DOUBLE:
1797	<	therm_int_theta_spring = the_event->evt.asmt.rhs.dval;
1798	<	have_theta_spring_constant = 1;
1799	<	return 1;
1800	<	break;
1801	<
1802	<	case INT:
1803	<	therm_int_theta_spring = (double)the_event->evt.asmt.rhs.dval;
1804	<	have_theta_spring_constant = 1;
1805	<	return 1;
1806	<	break;
1807	<
1808	<	default:
1809	<	the_event->err_msg =
1810	<	strdup( "Error in parsing meta-data file!\n\tthermIntThetaSpringConst unrecognized.\n" );
1811	<	return 0;
1812	<	break;
1813	<	}
1814	<	break;
1815	<
1816	<	case G_THERM_INT_OMEGA_SPRING:
1817	<	switch( the_type ){
1818	<
1819	<	case STRING:
1820	<	the_event->err_msg =
1821	<	strdup( "Error in parsing meta-data file!\n\tthermIntOmegaSpringConst is not a double or int.\n" );
1822	<	return 1;
1823	<	break;
1824	<
1825	<	case DOUBLE:
1826	<	therm_int_omega_spring = the_event->evt.asmt.rhs.dval;
1827	<	have_omega_spring_constant = 1;
1828	<	return 1;
1829	<	break;
1830	<
1831	<	case INT:
1832	<	therm_int_omega_spring = (double)the_event->evt.asmt.rhs.dval;
1833	<	have_omega_spring_constant = 1;
1834	<	return 1;
1835	<	break;
1836	<
1837	<	default:
1838	<	the_event->err_msg =
1839	<	strdup( "Error in parsing meta-data file!\n\tthermIntOmegaSpringConst unrecognized.\n" );
1840	<	return 0;
1841	<	break;
1842	<	}
1843	<	break;
1844	<
1845	<	case G_THERM_INT_THETA_SPRING:
1846	<	switch( the_type ){
1847	<
1848	<	case STRING:
1849	<	the_event->err_msg =
1850	<	strdup( "Error in parsing meta-data file!\n\ttargetStress is not a double or int.\n" );
1851	<	return 1;
1852	<	break;
1853	<
1854	<	case DOUBLE:
1855	<	target_stress= the_event->evt.asmt.rhs.dval;
1856	<	have_targetstress = 1;
1857	<	return 1;
1858	<	break;
1859	<
1860	<	case INT:
1861	<	target_stress = (double)the_event->evt.asmt.rhs.dval;
1862	<	have_targetstress = 1;
1863	<	return 1;
1864	<	break;
1865	<
1866	<	default:
1867	<	the_event->err_msg =
1868	<	strdup( "Error in parsing meta-data file!\n\tttargetStress unrecognized.\n" );
1869	<	return 0;
1870	<	break;
1871	<	}
1872	<	break;
1873	<
1874	<
1875	<
1876	<	// add more token cases here.
1877	<	}
1878	<	}
1879	<
1880	<	switch( the_type ){
1881	<
1882	<	case STRING:
1883	<	sprintf( err,
1884	<	"\tUnrecognized assignment:\n"
1885	<	"\t\t-> %s = %s\n",
1886	<	lhs, the_event->evt.asmt.rhs.sval );
1887	<	break;
1888	<
1889	<	case DOUBLE:
1890	<	sprintf( err,
1891	<	"\tUnrecognized assignment:\n"
1892	<	"\t\t-> %s = %lf\n",
1893	<	lhs, the_event->evt.asmt.rhs.dval );
1894	<	break;
1895	<
1896	<	case INT:
1897	<	sprintf( err,
1898	<	"\tUnrecognized assignment:\n"
1899	<	"\t\t-> %s = %d\n",
1900	<	lhs, the_event->evt.asmt.rhs.ival );
1901	<	break;
1902	<
1903	<	default:
1904	<	sprintf( err,
1905	<	"\tUnrecognized assignment:\n"
1906	<	"\t\t-> %s = ?\n",
1907	<	lhs );
1908	<	break;
1909	<	}
1910	<
1911	<	the_event->err_msg = strdup( err );
1912	<	return 0;
1913	<	}
1914	<
1915	<	char* Globals::checkMe( void ){
1916	<
1917	<	char err[300];
1918	<	short int have_err = 0;
1919	<
1920	<	strcpy( err, "The following required keywords are missing:\n" );
1921	<
1922	<	if( !have_force_field ){
1923	<	strcat( err, "\t\t->forceField\n" );
1924	<	have_err= 1;
1925	<	}
1926	<
1927	<	if( !have_n_components ){
1928	<	strcat( err, "\t\t->nComponents\n" );
1929	<	have_err= 1;
1930	<	}
1931	<
1932	<
1933	<	if ( !have_ensemble ) {
1934	<	// I'm not doing MD:
1935	<	if ( !have_minimizer ) {
1936	<	// I'm not doing MD or minimization:
1937	<	strcat( err, "\t\t->either ensemble or minimizer must be set!\n" );
1938	<	have_err = 1;
199	>	bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
200	>	std::string molStampName = molStamp->getName();
201	>	std::map<std::string, MoleculeStamp*>::iterator i;
202	>	bool ret = false;
203	>	i = moleculeStamps_.find(molStampName);
204	>	if (i == moleculeStamps_.end()) {
205	>	moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
206	>	ret = true;
207		} else {
208	<	// I'm a minimizer:
208	>	std::cout << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
209		}
210	<	} else {
1943	<	// I *am* doing MD:
1944	<	if( !have_dt ){
1945	<	strcat( err, "\t\t->dt (timestep in fs)\n" );
1946	<	have_err= 1;
1947	<	}
1948	<	if( !have_run_time ){
1949	<	strcat( err, "\t\t->runTime (total run time in fs)\n" );
1950	<	have_err= 1;
1951	<	}
1952	<	}
1953	<
1954	<	if( have_err ) return strdup( err );
1955	<
1956	<	return NULL;
210	>	return ret;
211		}
212	+
213
1959	–	int Globals::globalEnd( event* the_event ){
1960	–
1961	–	the_event->err_msg = checkMe();
1962	–	if( the_event->err_msg != NULL ) return 0;
1963	–
1964	–	return 1;
214		}
1966	–

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