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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 1930 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
Revision 2488 by tim, Mon Dec 5 23:37:56 2005 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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 "utils/simError.h"
48	–	#ifdef IS_MPI
49	–	#include "io/mpiBASS.h"
50	–	#endif // is_mpi
49
50	<	/*
53	<	* The following section lists all of the defined tokens for the
54	<	* gloabal 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	<	*/
50	>	#include "io/ParamConstraint.hpp"
51
52	<	//required parameters
53	<	#define G_FORCEFIELD         1
54	<	#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	<
116	<	Globals::Globals(){
117	<	initalize();
118	<	}
119	<
120	<	Globals::~Globals(){
121	<	int i;
122	<
123	<	for( i=0; i<hash_size; i++ ){
124	<	if( command_table[i] != NULL ) delete command_table[i];
125	<	}
126	<	delete[] command_table;
127	<
128	<	if( components != NULL ){
129	<	for( i=0; i<n_components; i++ ) delete components[i];
130	<	delete[] components;
131	<	}
132	<	}
133	<
134	<	void Globals::initalize(){
135	<	int i;
136	<
137	<	hash_size = 23;
138	<	hash_shift = 4;
139	<
140	<	components = NULL;
141	<
142	<	command_table = new LinkedCommand*[hash_size];
143	<	for( i=0; i<hash_size; i++ ) command_table[i] = NULL;
144	<
145	<	addHash( "forceField",    G_FORCEFIELD );
146	<	addHash( "nComponents",   G_NCOMPONENTS );
147	<	addHash( "targetTemp",    G_TARGETTEMP );
148	<	addHash( "ensemble",      G_ENSEMBLE );
149	<
150	<	addHash( "dt",            G_DT );
151	<	addHash( "runTime",       G_RUNTIME );
152	<
153	<	addHash( "initialConfig", G_INITIALCONFIG );
154	<	addHash( "finalConfig",   G_FINALCONFIG );
155	<	addHash( "nMol",          G_NMOL );
156	<	addHash( "density",       G_DENSITY );
157	<	addHash( "box",           G_BOX );
158	<	addHash( "boxX",          G_BOXX );
159	<	addHash( "boxY",          G_BOXY );
160	<	addHash( "boxZ",          G_BOXZ );
161	<	addHash( "sampleTime",    G_SAMPLETIME );
162	<	addHash( "resetTime",     G_RESETTIME );
163	<	addHash( "statusTime",    G_STATUSTIME );
164	<	addHash( "cutoffRadius",  G_RCUT );
165	<	addHash( "switchingRadius",  G_RSW );
166	<	addHash( "dielectric",    G_DIELECTRIC );
167	<	addHash( "tempSet",       G_TEMPSET );
168	<	addHash( "thermalTime",   G_THERMALTIME );
169	<	addHash( "mixingRule",    G_MIXINGRULE);
170	<	addHash( "usePeriodicBoundaryConditions",        G_USEPBC);
171	<	addHash( "useReactionField",                     G_USERF );
172	<	addHash( "targetPressure",                       G_TARGETPRESSURE);
173	<	addHash( "tauThermostat",                        G_TAUTHERMOSTAT);
174	<	addHash( "tauBarostat",                          G_TAUBAROSTAT);
175	<	addHash( "zconsTime",                            G_ZCONSTIME);
176	<	addHash( "nZconstraints",                        G_NZCONSTRAINTS);
177	<	addHash( "zconsTol",                             G_ZCONSTOL);
178	<	addHash( "zconsForcePolicy",                     G_ZCONSFORCEPOLICY);
179	<	addHash( "seed",                                 G_SEED);
180	<	addHash( "useInitialTime",                       G_USEINITTIME);
181	<	addHash( "useInitialExtendedSystemState",        G_USEINIT_XS_STATE);
182	<	addHash( "orthoBoxTolerance",                    G_ORTHOBOXTOLERANCE);
183	<	addHash( "minimizer",                            G_MINIMIZER);
184	<	addHash( "minimizerMaxIter",                     G_MIN_MAXITER);
185	<	addHash( "minimizerWriteFrq",                    G_MIN_WRITEFRQ);
186	<	addHash( "minimizerStepSize",                    G_MIN_STEPSIZE);
187	<	addHash( "minimizerFTol",                        G_MIN_FTOL);
188	<	addHash( "minimizerGTol",                        G_MIN_GTOL);
189	<	addHash( "minimizerLSTol",                       G_MIN_LSTOL);
190	<	addHash( "minimizerLSMaxIter",                   G_MIN_LSMAXITER);
191	<	addHash( "zconsGap",                             G_ZCONSGAP);
192	<	addHash( "zconsFixtime",                         G_ZCONSFIXTIME);
193	<	addHash( "zconsUsingSMD",                        G_ZCONSUSINGSMD);
194	<	addHash( "useSolidThermInt",                     G_USE_SOLID_THERM_INT);
195	<	addHash( "useLiquidThermInt",                    G_USE_LIQUID_THERM_INT);
196	<	addHash( "thermodynamicIntegrationLambda",       G_THERM_INT_LAMBDA);
197	<	addHash( "thermodynamicIntegrationK",            G_THERM_INT_K);
198	<	addHash( "forceFieldVariant",                    G_FORCEFIELD_VARIANT);
199	<
200	<	strcpy( mixingRule,"standard");  //default mixing rules to standard.
201	<	usePBC = 1; //default  periodic boundry conditions to on
202	<	useRF  = 0;
203	<	useInitTime = 0; // default to pull init time from the init file
204	<	useInitXSstate = 0; // default to pull the extended state from the init file
205	<	orthoBoxTolerance = 1E-6;
206	<	useSolidThermInt = 0; // default solid-state thermodynamic integration to off
207	<	useLiquidThermInt = 0; // default liquid thermodynamic integration to off
208	<
209	<	have_force_field =  0;
210	<	have_n_components = 0;
211	<	have_target_temp =  0;
212	<	have_ensemble =     0;
213	<	have_dt =           0;
214	<	have_run_time =     0;
215	<
216	<	have_initial_config = 0;
217	<	have_final_config =   0;
218	<	have_n_mol =          0;
219	<	have_density =        0;
220	<	have_box =            0;
221	<	have_box_x =          0;
222	<	have_box_y =          0;
223	<	have_box_y =          0;
224	<	have_box_z =          0;
225	<	have_sample_time =    0;
226	<	have_status_time =    0;
227	<	have_reset_time =     0;
228	<	have_thermal_time =   0;
229	<	have_rcut =           0;
230	<	have_rsw =            0;
231	<	have_dielectric =     0;
232	<	have_tempSet =        0;
233	<	have_target_pressure =0;
234	<	have_q_mass =         0;
235	<	have_tau_thermostat = 0;
236	<	have_tau_barostat   = 0;
237	<	have_zcons_time     = 0;
238	<	have_n_zConstraints = 0;
239	<	have_zConstraints   = 0;
240	<	have_zcons_tol = 0;
241	<	have_zcons_gap = 0;
242	<	have_zcons_fixtime = 0;
243	<	have_zcons_using_smd = 0;
244	<	have_seed = 0;
245	<	have_minimizer = 0;
246	<	have_minimizer_maxiteration = 0;
247	<	have_minimizer_writefrq = 0;
248	<	have_minimizer_stepsize = 0;
249	<	have_minimizer_ftol = 0;
250	<	have_minimizer_gtol = 0;
251	<	have_minimizer_ls_tol = 0;
252	<	have_minimizer_ls_maxiteration = 0;
253	<	have_thermodynamic_integration_lambda = 0;
254	<	have_thermodynamic_integration_k = 0;
255	<	have_forcefield_variant = 0;
256	<
257	<	}
258	<
259	<	int Globals::newComponent( event* the_event ){
260	<
261	<	current_component = new Component;
262	<	int index = the_event->evt.blk_index;
263	<	char err[200];
264	<
265	<	if( have_n_components && index < n_components )
266	<	components[index] = current_component;
267	<	else{
268	<	if( have_n_components ){
269	<	sprintf( err, "meta-data parsing error: %d out of nComponents range",
270	<	index );
271	<	the_event->err_msg = strdup( err );
272	<	return 0;
273	<	}
274	<	else{
275	<	the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
276	<	" first component declaration." );
277	<	return 0;
278	<	}
279	<	}
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	<
288	<	switch( the_event->evt.asmt.asmt_type ){
118	>	deprecatedKeywords_.insert("nComponents");
119	>	deprecatedKeywords_.insert("nZconstraints");
120
290	–	case STRING:
291	–	return current_component->assignString( the_event->evt.asmt.lhs,
292	–	the_event->evt.asmt.rhs.sval,
293	–	&(the_event->err_msg));
294	–	break;
295	–
296	–	case DOUBLE:
297	–	return current_component->assignDouble( the_event->evt.asmt.lhs,
298	–	the_event->evt.asmt.rhs.dval,
299	–	&(the_event->err_msg));
300	–	break;
301	–
302	–	case INT:
303	–	return current_component->assignInt( the_event->evt.asmt.lhs,
304	–	the_event->evt.asmt.rhs.ival,
305	–	&(the_event->err_msg));
306	–	break;
307	–
308	–	default:
309	–	the_event->err_msg = strdup( "Globals error. Invalid component"
310	–	" assignment type" );
311	–	return 0;
312	–	break;
313	–	}
314	–	return 0;
121		}
122
123	<	int Globals::componentEnd( event* the_event ){
123	>	Globals::~Globals() {
124
319	–	the_event->err_msg = current_component->checkMe();
320	–	if( the_event->err_msg != NULL ) return 0;
125
322	–	return 1;
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{
337	<	if( have_n_zConstraints ){
338	<	sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
339	<	index );
340	<	the_event->err_msg = strdup( err );
341	<	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{
344	<	the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
345	<	" not given before"
346	<	" first zConstraint declaration." );
347	<	return 0;
348	<	}
349	<	}
350	<
351	<	return 1;
186	>	}
187		}
353	–
354	–
355	–
356	–	int Globals::zConstraintAssign( event* the_event ){
357	–
358	–	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,
363	<	&(the_event->err_msg));
364	<	break;
365	<
366	<	case DOUBLE:
367	<	return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
368	<	the_event->evt.asmt.rhs.dval,
369	<	&(the_event->err_msg));
370	<	break;
371	<
372	<	case INT:
373	<	return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
374	<	the_event->evt.asmt.rhs.ival,
375	<	&(the_event->err_msg));
376	<	break;
377	<
378	<	default:
379	<	the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
380	<	" assignment type" );
381	<	return 0;
382	<	break;
383	<	}
384	<	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();
390	<	if( the_event->err_msg != NULL ) return 0;
391	<
392	<	return 1;
194	>	bool Globals::addZConsStamp(ZConsStamp* zcons) {
195	>	zconstraints_.push_back(zcons);
196	>	return true;
197		}
394	–
395	–	int Globals::globalAssign( event* the_event ){
396	–
397	–	int key;
398	–	int token;
399	–	interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
400	–	char* lhs = the_event->evt.asmt.lhs;
401	–	char err[300];
402	–
403	–	token = 0;
404	–	key = hash( lhs );
405	–	if( command_table[key] != NULL ) token = command_table[key]->match( lhs );
406	–
407	–	if( token ){
408	–
409	–	switch( token ){
410	–
411	–	case G_FORCEFIELD:
412	–	if( the_type == STRING ){
413	–	strcpy( force_field, the_event->evt.asmt.rhs.sval );
414	–	have_force_field = 1;
415	–	return 1;
416	–	}
417	–
418	–	the_event->err_msg =
419	–	strdup( "Error in parsing meta-data file!\n\tforceField was not a string assignment.\n" );
420	–	return 0;
421	–	break;
422	–
423	–	case G_NCOMPONENTS:
424	–	if( the_type == STRING ){
425	–	the_event->err_msg =
426	–	strdup("Error in parsing meta-data file!\n\tnComponents is not a double or an int.\n" );
427	–	return 0;
428	–	}
429	–
430	–	else if( the_type == DOUBLE ){
431	–	n_components = (int)the_event->evt.asmt.rhs.dval;
432	–	components = new Component*[n_components];
433	–	have_n_components = 1;
434	–	return 1;
435	–	}
436	–
437	–	else{
438	–	n_components = the_event->evt.asmt.rhs.ival;
439	–	components = new Component*[n_components];
440	–	have_n_components = 1;
441	–	return 1;
442	–	}
443	–	break;
444	–
445	–	case G_NZCONSTRAINTS:
446	–	if( the_type == STRING ){
447	–	the_event->err_msg =
448	–	strdup("Error in parsing meta-data file!\n\tnZconstraints is not a double or an int.\n" );
449	–	return 0;
450	–	}
451	–
452	–	else if( the_type == DOUBLE ){
453	–	n_zConstraints = (int)the_event->evt.asmt.rhs.dval;
454	–	zConstraints = new ZconStamp*[n_zConstraints];
455	–	have_n_zConstraints = 1;
456	–	return 1;
457	–	}
458	–
459	–	else{
460	–	n_zConstraints = the_event->evt.asmt.rhs.ival;
461	–	zConstraints = new ZconStamp*[n_zConstraints];
462	–	have_n_zConstraints = 1;
463	–	return 1;
464	–	}
465	–	break;
466	–
467	–	case G_TARGETTEMP:
468	–	switch( the_type ){
469	–
470	–	case STRING:
471	–	the_event->err_msg =
472	–	strdup( "Error in parsing meta-data file!\n\ttargetTemp is not a double or int.\n" );
473	–	return 0;
474	–	break;
475	–
476	–	case DOUBLE:
477	–	target_temp = the_event->evt.asmt.rhs.dval;
478	–	have_target_temp = 1;
479	–	return 1;
480	–	break;
481	–
482	–	case INT:
483	–	target_temp = (double)the_event->evt.asmt.rhs.ival;
484	–	have_target_temp = 1;
485	–	return 1;
486	–	break;
487	–
488	–	default:
489	–	the_event->err_msg =
490	–	strdup( "Error in parsing meta-data file!\n\ttargetTemp unrecognized.\n" );
491	–	return 0;
492	–	break;
493	–	}
494	–	break;
495	–
496	–	case G_ORTHOBOXTOLERANCE:
497	–	switch( the_type ){
498	–
499	–	case STRING:
500	–	the_event->err_msg =
501	–	strdup( "Error in parsing meta-data file!\n\torthoBoxTolerance is not a double or int.\n" );
502	–	return 0;
503	–	break;
504	–
505	–	case DOUBLE:
506	–	orthoBoxTolerance = the_event->evt.asmt.rhs.dval;
507	–	have_target_temp = 1;
508	–	return 1;
509	–	break;
510	–
511	–	case INT:
512	–	orthoBoxTolerance = (double)the_event->evt.asmt.rhs.ival;
513	–	have_target_temp = 1;
514	–	return 1;
515	–	break;
516	–
517	–	default:
518	–	the_event->err_msg =
519	–	strdup( "Global error.orthoBoxTolerance unrecognized.\n" );
520	–	return 0;
521	–	break;
522	–	}
523	–	break;
524	–
525	–	case G_ENSEMBLE:
526	–	if( the_type == STRING ){
527	–	strcpy( ensemble, the_event->evt.asmt.rhs.sval );
528	–	have_ensemble = 1;
529	–	return 1;
530	–	}
531	–
532	–	the_event->err_msg =
533	–	strdup( "Error in parsing meta-data file!\n\tensemble was not assigned to a string\n" );
534	–	return 0;
535	–	break;
536	–
537	–	case G_MIXINGRULE:
538	–	if( the_type == STRING ){
539	–	strcpy( mixingRule, the_event->evt.asmt.rhs.sval );
540	–	return 1;
541	–	}
542	–
543	–	the_event->err_msg =
544	–	strdup( "Error in parsing meta-data file!\n\tmixing rule was not assigned to a string\n" );
545	–	return 0;
546	–	break;
547	–
548	–	case G_DT:
549	–	switch( the_type ){
550	–
551	–	case STRING:
552	–	the_event->err_msg =
553	–	strdup( "Error in parsing meta-data file!\n\tdt is not a double or int.\n" );
554	–	return 0;
555	–	break;
556	–
557	–	case DOUBLE:
558	–	dt = the_event->evt.asmt.rhs.dval;
559	–	have_dt = 1;
560	–	return 1;
561	–	break;
562	–
563	–	case INT:
564	–	dt = (double)the_event->evt.asmt.rhs.ival;
565	–	have_dt = 1;
566	–	return 1;
567	–	break;
568	–
569	–	default:
570	–	the_event->err_msg =
571	–	strdup( "Error in parsing meta-data file!\n\tdt unrecognized.\n" );
572	–	return 0;
573	–	break;
574	–	}
575	–	break;
576	–
577	–	case G_RUNTIME:
578	–	switch( the_type ){
579	–
580	–	case STRING:
581	–	the_event->err_msg =
582	–	strdup( "Error in parsing meta-data file!\n\trunTime is not a double or int.\n" );
583	–	return 0;
584	–	break;
585	–
586	–	case DOUBLE:
587	–	run_time = the_event->evt.asmt.rhs.dval;
588	–	have_run_time = 1;
589	–	return 1;
590	–	break;
591	–
592	–	case INT:
593	–	run_time = (double)the_event->evt.asmt.rhs.ival;
594	–	have_run_time = 1;
595	–	return 1;
596	–	break;
597	–
598	–	default:
599	–	the_event->err_msg =
600	–	strdup( "Error in parsing meta-data file!\n\trunTime unrecognized.\n" );
601	–	return 0;
602	–	break;
603	–	}
604	–	break;
605	–
606	–	case G_INITIALCONFIG:
607	–	if( the_type == STRING ){
608	–	strcpy( initial_config, the_event->evt.asmt.rhs.sval );
609	–	have_initial_config = 1;
610	–	return 1;
611	–	}
612	–
613	–	the_event->err_msg =
614	–	strdup( "Error in parsing meta-data file!\n\tinitialConfig was not a string assignment.\n" );
615	–	return 0;
616	–	break;
617	–
618	–	case G_FINALCONFIG:
619	–	if( the_type == STRING ){
620	–	strcpy( final_config, the_event->evt.asmt.rhs.sval );
621	–	have_final_config = 1;
622	–	return 1;
623	–	}
624	–
625	–	the_event->err_msg =
626	–	strdup( "Error in parsing meta-data file!\n\tfinalConfig was not a string assignment.\n" );
627	–	return 0;
628	–	break;
629	–
630	–	case G_NMOL:
631	–	switch( the_type ){
632	–
633	–	case STRING:
634	–	the_event->err_msg =
635	–	strdup( "Error in parsing meta-data file!\n\tnMol is not a double or int.\n" );
636	–	return 0;
637	–	break;
638	–
639	–	case DOUBLE:
640	–	n_mol = (int)the_event->evt.asmt.rhs.dval;
641	–	have_n_mol = 1;
642	–	return 1;
643	–	break;
644	–
645	–	case INT:
646	–	n_mol = the_event->evt.asmt.rhs.ival;
647	–	have_n_mol = 1;
648	–	return 1;
649	–	break;
650	–
651	–	default:
652	–	the_event->err_msg =
653	–	strdup( "Error in parsing meta-data file!\n\tnMol unrecognized.\n" );
654	–	return 0;
655	–	break;
656	–	}
657	–	break;
658	–
659	–	case G_DENSITY:
660	–	switch( the_type ){
661	–
662	–	case STRING:
663	–	the_event->err_msg =
664	–	strdup( "Error in parsing meta-data file!\n\tdensity is not a double or int.\n" );
665	–	return 0;
666	–	break;
667	–
668	–	case DOUBLE:
669	–	density = the_event->evt.asmt.rhs.dval;
670	–	have_density = 1;
671	–	return 1;
672	–	break;
673	–
674	–	case INT:
675	–	density = (double)the_event->evt.asmt.rhs.ival;
676	–	have_density = 1;
677	–	return 1;
678	–	break;
679	–
680	–	default:
681	–	the_event->err_msg =
682	–	strdup( "Error in parsing meta-data file!\n\tdensity unrecognized.\n" );
683	–	return 0;
684	–	break;
685	–	}
686	–	break;
687	–
688	–	case G_BOX:
689	–	switch( the_type ){
690	–
691	–	case STRING:
692	–	the_event->err_msg =
693	–	strdup( "Error in parsing meta-data file!\n\tbox is not a double or int.\n" );
694	–	return 0;
695	–	break;
696	–
697	–	case DOUBLE:
698	–	box = the_event->evt.asmt.rhs.dval;
699	–	have_box = 1;
700	–	return 1;
701	–	break;
702	–
703	–	case INT:
704	–	box = (double)the_event->evt.asmt.rhs.ival;
705	–	have_box = 1;
706	–	return 1;
707	–	break;
708	–
709	–	default:
710	–	the_event->err_msg =
711	–	strdup( "Error in parsing meta-data file!\n\tbox unrecognized.\n" );
712	–	return 0;
713	–	break;
714	–	}
715	–	break;
716	–
717	–	case G_BOXX:
718	–	switch( the_type ){
719	–
720	–	case STRING:
721	–	the_event->err_msg =
722	–	strdup( "Error in parsing meta-data file!\n\tboxX is not a double or int.\n" );
723	–	return 0;
724	–	break;
725	–
726	–	case DOUBLE:
727	–	box_x = the_event->evt.asmt.rhs.dval;
728	–	have_box_x = 1;
729	–	return 1;
730	–	break;
731	–
732	–	case INT:
733	–	box_x = (double)the_event->evt.asmt.rhs.ival;
734	–	have_box_x = 1;
735	–	return 1;
736	–	break;
737	–
738	–	default:
739	–	the_event->err_msg =
740	–	strdup( "Error in parsing meta-data file!\n\tboxX unrecognized.\n" );
741	–	return 0;
742	–	break;
743	–	}
744	–	break;
745	–
746	–	case G_BOXY:
747	–	switch( the_type ){
748	–
749	–	case STRING:
750	–	the_event->err_msg =
751	–	strdup( "Error in parsing meta-data file!\n\tboxY is not a double or int.\n" );
752	–	return 0;
753	–	break;
754	–
755	–	case DOUBLE:
756	–	box_y = the_event->evt.asmt.rhs.dval;
757	–	have_box_y = 1;
758	–	return 1;
759	–	break;
760	–
761	–	case INT:
762	–	box_y = (double)the_event->evt.asmt.rhs.ival;
763	–	have_box_y = 1;
764	–	return 1;
765	–	break;
766	–
767	–	default:
768	–	the_event->err_msg =
769	–	strdup( "Error in parsing meta-data file!\n\tboxY unrecognized.\n" );
770	–	return 0;
771	–	break;
772	–	}
773	–	break;
774	–
775	–	case G_BOXZ:
776	–	switch( the_type ){
777	–
778	–	case STRING:
779	–	the_event->err_msg =
780	–	strdup( "Error in parsing meta-data file!\n\tboxZ is not a double or int.\n" );
781	–	return 0;
782	–	break;
783	–
784	–	case DOUBLE:
785	–	box_z = the_event->evt.asmt.rhs.dval;
786	–	have_box_z = 1;
787	–	return 1;
788	–	break;
789	–
790	–	case INT:
791	–	box_z = (double)the_event->evt.asmt.rhs.ival;
792	–	have_box_z = 1;
793	–	return 1;
794	–	break;
795	–
796	–	default:
797	–	the_event->err_msg =
798	–	strdup( "Error in parsing meta-data file!\n\tboxZ unrecognized.\n" );
799	–	return 0;
800	–	break;
801	–	}
802	–	break;
803	–
804	–	case G_SAMPLETIME:
805	–	switch( the_type ){
806	–
807	–	case STRING:
808	–	the_event->err_msg =
809	–	strdup( "Error in parsing meta-data file!\n\tsampleTime is not a double or int.\n" );
810	–	return 0;
811	–	break;
812	–
813	–	case DOUBLE:
814	–	sample_time = the_event->evt.asmt.rhs.dval;
815	–	have_sample_time = 1;
816	–	return 1;
817	–	break;
818	–
819	–	case INT:
820	–	sample_time = (double)the_event->evt.asmt.rhs.ival;
821	–	have_sample_time = 1;
822	–	return 1;
823	–	break;
824	–
825	–	default:
826	–	the_event->err_msg =
827	–	strdup( "Error in parsing meta-data file!\n\tsampleTime unrecognized.\n" );
828	–	return 0;
829	–	break;
830	–	}
831	–	break;
832	–
833	–	case G_STATUSTIME:
834	–	switch( the_type ){
835	–
836	–	case STRING:
837	–	the_event->err_msg =
838	–	strdup( "Error in parsing meta-data file!\n\tstatusTime is not a double or int.\n" );
839	–	return 0;
840	–	break;
841	–
842	–	case DOUBLE:
843	–	status_time = the_event->evt.asmt.rhs.dval;
844	–	have_status_time = 1;
845	–	return 1;
846	–	break;
847	–
848	–	case INT:
849	–	status_time = (double)the_event->evt.asmt.rhs.ival;
850	–	have_status_time = 1;
851	–	return 1;
852	–	break;
853	–
854	–	default:
855	–	the_event->err_msg =
856	–	strdup( "Error in parsing meta-data file!\n\tstatusTime unrecognized.\n" );
857	–	return 0;
858	–	break;
859	–	}
860	–	break;
861	–
862	–	case G_RESETTIME:
863	–	switch( the_type ){
864	–
865	–	case STRING:
866	–	the_event->err_msg =
867	–	strdup( "Error in parsing meta-data file!\n\tresetTime is not a double or int.\n" );
868	–	return 0;
869	–	break;
870	–
871	–	case DOUBLE:
872	–	resetTime = the_event->evt.asmt.rhs.dval;
873	–	have_reset_time = 1;
874	–	return 1;
875	–	break;
876	–
877	–	case INT:
878	–	resetTime = (double)the_event->evt.asmt.rhs.ival;
879	–	have_reset_time = 1;
880	–	return 1;
881	–	break;
882	–
883	–	default:
884	–	the_event->err_msg =
885	–	strdup( "Error in parsing meta-data file!\n\tresetTime unrecognized.\n" );
886	–	return 0;
887	–	break;
888	–	}
889	–	break;
890	–
891	–	case G_THERMALTIME:
892	–	switch( the_type ){
893	–
894	–	case STRING:
895	–	the_event->err_msg =
896	–	strdup( "Error in parsing meta-data file!\n\tthermalTime is not a double or int.\n" );
897	–	return 0;
898	–	break;
899	–
900	–	case DOUBLE:
901	–	thermal_time = the_event->evt.asmt.rhs.dval;
902	–	have_thermal_time = 1;
903	–	return 1;
904	–	break;
905	–
906	–	case INT:
907	–	thermal_time = (double)the_event->evt.asmt.rhs.ival;
908	–	have_thermal_time = 1;
909	–	return 1;
910	–	break;
911	–
912	–	default:
913	–	the_event->err_msg =
914	–	strdup( "Error in parsing meta-data file!\n\tthermalTime unrecognized.\n" );
915	–	return 0;
916	–	break;
917	–	}
918	–	break;
919	–
920	–	case G_RCUT:
921	–	switch( the_type ){
922	–
923	–	case STRING:
924	–	the_event->err_msg =
925	–	strdup( "Error in parsing meta-data file!\n\tcutoffRadius is not a double or int.\n" );
926	–	return 0;
927	–	break;
928	–
929	–	case DOUBLE:
930	–	rcut = the_event->evt.asmt.rhs.dval;
931	–	have_rcut = 1;
932	–	return 1;
933	–	break;
934	–
935	–	case INT:
936	–	rcut = (double)the_event->evt.asmt.rhs.ival;
937	–	have_rcut = 1;
938	–	return 1;
939	–	break;
940	–
941	–	default:
942	–	the_event->err_msg =
943	–	strdup( "Error in parsing meta-data file!\n\tcutoffRadius unrecognized.\n" );
944	–	return 0;
945	–	break;
946	–	}
947	–	break;
198
199	<	case G_RSW:
200	<	switch( the_type ){
201	<
202	<	case STRING:
203	<	the_event->err_msg =
204	<	strdup( "Error in parsing meta-data file!\n\tswitchingRadius is not a double or int.\n" );
205	<	return 0;
206	<	break;
957	<
958	<	case DOUBLE:
959	<	rsw = the_event->evt.asmt.rhs.dval;
960	<	have_rsw = 1;
961	<	return 1;
962	<	break;
963	<
964	<	case INT:
965	<	rsw = (double)the_event->evt.asmt.rhs.ival;
966	<	have_rsw = 1;
967	<	return 1;
968	<	break;
969	<
970	<	default:
971	<	the_event->err_msg =
972	<	strdup( "Error in parsing meta-data file!\n\tswitchingRadius unrecognized.\n" );
973	<	return 0;
974	<	break;
975	<	}
976	<	break;
977	<
978	<	case G_DIELECTRIC:
979	<	switch( the_type ){
980	<
981	<	case STRING:
982	<	the_event->err_msg =
983	<	strdup( "Error in parsing meta-data file!\n\tdielectric is not a double or int.\n" );
984	<	return 0;
985	<	break;
986	<
987	<	case DOUBLE:
988	<	dielectric = the_event->evt.asmt.rhs.dval;
989	<	have_dielectric = 1;
990	<	return 1;
991	<	break;
992	<
993	<	case INT:
994	<	dielectric = (double)the_event->evt.asmt.rhs.ival;
995	<	have_dielectric = 1;
996	<	return 1;
997	<	break;
998	<
999	<	default:
1000	<	the_event->err_msg =
1001	<	strdup( "Error in parsing meta-data file!\n\tdielectric unrecognized.\n" );
1002	<	return 0;
1003	<	break;
1004	<	}
1005	<	break;
1006	<
1007	<	case G_TEMPSET:
1008	<	if( the_type == STRING ){
1009	<
1010	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) tempSet = 1;
1011	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) tempSet = 0;
1012	<	else{
1013	<	the_event->err_msg =
1014	<	strdup( "Error in parsing meta-data file!\n\ttempSet was not \"true\" or \"false\".\n" );
1015	<	return 0;
1016	<	}
1017	<	have_tempSet = 1;
1018	<	return 1;
1019	<	}
1020	<
1021	<	the_event->err_msg =
1022	<	strdup( "Error in parsing meta-data file!\n\ttempSet was not \"true\" or \"false\".\n" );
1023	<	return 0;
1024	<	break;
1025	<
1026	<	case G_USEINITTIME:
1027	<	if( the_type == STRING ){
1028	<
1029	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useInitTime = 1;
1030	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useInitTime = 0;
1031	<	else{
1032	<	the_event->err_msg =
1033	<	strdup( "Error in parsing meta-data file!\n\tuseInitTime was not \"true\" or \"false\".\n" );
1034	<	return 0;
1035	<	}
1036	<	return 1;
1037	<	}
1038	<
1039	<	the_event->err_msg =
1040	<	strdup( "Error in parsing meta-data file!\n\tuseInitTime was not \"true\" or \"false\".\n" );
1041	<	return 0;
1042	<	break;
1043	<
1044	<	case G_USEINIT_XS_STATE:
1045	<	if( the_type == STRING ){
1046	<
1047	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval ))
1048	<	useInitXSstate = 1;
1049	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval ))
1050	<	useInitXSstate = 0;
1051	<	else{
1052	<	the_event->err_msg =
1053	<	strdup( "Error in parsing meta-data file!\n\tuseInitExtendedSystemState was not \"true\" or \"false\".\n" );
1054	<	return 0;
1055	<	}
1056	<	return 1;
1057	<	}
1058	<
1059	<	the_event->err_msg =
1060	<	strdup( "Error in parsing meta-data file!\n\tuseInitExtendedSystemState was not \"true\" or \"false\".\n" );
1061	<	return 0;
1062	<	break;
1063	<
1064	<	case G_USEPBC:
1065	<	if( the_type == STRING ){
1066	<
1067	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) usePBC = 1;
1068	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) usePBC = 0;
1069	<	else{
1070	<	the_event->err_msg =
1071	<	strdup( "Error in parsing meta-data file!\n\tusePeriodicBoundaryConditions was not \"true\" or \"false\".\n" );
1072	<	return 0;
1073	<	}
1074	<	return 1;
1075	<	}
1076	<
1077	<	the_event->err_msg =
1078	<	strdup( "Error in parsing meta-data file!\n\tusePeriodicBoundaryConditions was not \"true\" or \"false\".\n" );
1079	<	return 0;
1080	<	break;
1081	<
1082	<	case G_USERF:
1083	<	if( the_type == STRING ){
1084	<
1085	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useRF = 1;
1086	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useRF = 0;
1087	<	else{
1088	<	the_event->err_msg =
1089	<	strdup( "Error in parsing meta-data file!\n\tuseReactionField was not \"true\" or \"false\".\n" );
1090	<	return 0;
1091	<	}
1092	<	return 1;
1093	<	}
1094	<
1095	<	the_event->err_msg =
1096	<	strdup( "Error in parsing meta-data file!\n\tuseReactionField was not \"true\" or \"false\".\n" );
1097	<	return 0;
1098	<	break;
1099	<
1100	<	case G_TARGETPRESSURE:
1101	<	switch( the_type ){
1102	<
1103	<	case STRING:
1104	<	the_event->err_msg =
1105	<	strdup( "Error in parsing meta-data file!\n\ttargetPressure is not a double or int.\n" );
1106	<	return 0;
1107	<	break;
1108	<
1109	<	case DOUBLE:
1110	<	target_pressure = the_event->evt.asmt.rhs.dval;
1111	<	have_target_pressure = 1;
1112	<	return 1;
1113	<	break;
1114	<
1115	<	case INT:
1116	<	target_pressure = (double)the_event->evt.asmt.rhs.ival;
1117	<	have_target_pressure = 1;
1118	<	return 1;
1119	<	break;
1120	<
1121	<	default:
1122	<	the_event->err_msg =
1123	<	strdup( "Error in parsing meta-data file!\n\ttargetPressure unrecognized.\n" );
1124	<	return 0;
1125	<	break;
1126	<	}
1127	<	break;
1128	<
1129	<	case G_TAUTHERMOSTAT:
1130	<	switch( the_type ){
1131	<
1132	<	case STRING:
1133	<	the_event->err_msg =
1134	<	strdup( "Error in parsing meta-data file!\n\ttauThermostat is not a double or int.\n" );
1135	<	return 0;
1136	<	break;
1137	<
1138	<	case DOUBLE:
1139	<	tau_thermostat = the_event->evt.asmt.rhs.dval;
1140	<	have_tau_thermostat = 1;
1141	<	return 1;
1142	<	break;
1143	<
1144	<	case INT:
1145	<	tau_thermostat = (double)the_event->evt.asmt.rhs.ival;
1146	<	have_tau_thermostat = 1;
1147	<	return 1;
1148	<	break;
1149	<
1150	<	default:
1151	<	the_event->err_msg =
1152	<	strdup( "Error in parsing meta-data file!\n\ttauThermostat unrecognized.\n" );
1153	<	return 0;
1154	<	break;
1155	<	}
1156	<	break;
1157	<
1158	<	case G_TAUBAROSTAT:
1159	<	switch( the_type ){
1160	<
1161	<	case STRING:
1162	<	the_event->err_msg =
1163	<	strdup( "Error in parsing meta-data file!\n\ttauBarostat is not a double or int.\n" );
1164	<	return 0;
1165	<	break;
1166	<
1167	<	case DOUBLE:
1168	<	tau_barostat = the_event->evt.asmt.rhs.dval;
1169	<	have_tau_barostat = 1;
1170	<	return 1;
1171	<	break;
1172	<
1173	<	case INT:
1174	<	tau_barostat = (double)the_event->evt.asmt.rhs.ival;
1175	<	have_tau_barostat = 1;
1176	<	return 1;
1177	<	break;
1178	<
1179	<	default:
1180	<	the_event->err_msg =
1181	<	strdup( "Error in parsing meta-data file!\n\ttauBarostat unrecognized.\n" );
1182	<	return 0;
1183	<	break;
1184	<	}
1185	<	break;
1186	<
1187	<	case G_ZCONSTIME:
1188	<	switch( the_type ){
1189	<
1190	<	case STRING:
1191	<	the_event->err_msg =
1192	<	strdup( "Error in parsing meta-data file!\n\tzcons_time is not a double or int.\n" );
1193	<	return 0;
1194	<	break;
1195	<
1196	<	case DOUBLE:
1197	<	zcons_time = the_event->evt.asmt.rhs.dval;
1198	<	have_zcons_time = 1;
1199	<	return 1;
1200	<	break;
1201	<
1202	<	case INT:
1203	<	zcons_time = (double)the_event->evt.asmt.rhs.ival;
1204	<	have_zcons_time = 1;
1205	<	return 1;
1206	<	break;
1207	<
1208	<	default:
1209	<	the_event->err_msg =
1210	<	strdup( "Error in parsing meta-data file!\n\tzcons_time unrecognized.\n" );
1211	<	return 0;
1212	<	break;
1213	<	}
1214	<	break;
1215	<
1216	<	case G_ZCONSTOL:
1217	<	switch( the_type ){
1218	<
1219	<	case STRING:
1220	<	the_event->err_msg =
1221	<	strdup( "Error in parsing meta-data file!\n\tzcons_tol is not a double or int.\n" );
1222	<	return 0;
1223	<	break;
1224	<
1225	<	case DOUBLE:
1226	<	zcons_tol = the_event->evt.asmt.rhs.dval;
1227	<	have_zcons_tol = 1;
1228	<	return 1;
1229	<	break;
1230	<
1231	<	case INT:
1232	<	zcons_tol = (double)the_event->evt.asmt.rhs.ival;
1233	<	have_zcons_tol = 1;
1234	<	return 1;
1235	<	break;
1236	<
1237	<	default:
1238	<	the_event->err_msg =
1239	<	strdup( "Error in parsing meta-data file!\n\tzcons_ol unrecognized.\n" );
1240	<	return 0;
1241	<	break;
1242	<	}
1243	<	break;
1244	<
1245	<	case G_ZCONSFORCEPOLICY:
1246	<	switch( the_type ){
1247	<
1248	<	case STRING:
1249	<	strcpy(zconsForcePolicy, the_event->evt.asmt.rhs.sval);
1250	<
1251	<	for(int i = 0; zconsForcePolicy[i] != '\0'; i++)
1252	<	{
1253	<	zconsForcePolicy[i] = toupper(zconsForcePolicy[i]);
1254	<	}
1255	<	have_zcons_force_policy = 1;
1256	<	return 1;
1257	<	break;
1258	<
1259	<	case DOUBLE:
1260	<	the_event->err_msg =
1261	<	strdup( "Error in parsing meta-data file!\n\tzconsForcePolicy is not a double or int.\n" );
1262	<	return 0;
1263	<	break;
1264	<
1265	<	case INT:
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	<	default:
1272	<	the_event->err_msg =
1273	<	strdup( "Error in parsing meta-data file!\n\tzconsForcePolicy unrecognized.\n" );
1274	<	return 0;
1275	<	break;
1276	<	}
1277	<	break;
1278	<
1279	<	case G_ZCONSGAP:
1280	<	switch( the_type ){
1281	<
1282	<	case STRING:
1283	<	the_event->err_msg =
1284	<	strdup( "Error in parsing meta-data file!\n\tzcons_gap is not a double or int.\n" );
1285	<	return 0;
1286	<	break;
1287	<
1288	<	case DOUBLE:
1289	<	zcons_gap = the_event->evt.asmt.rhs.dval;
1290	<	have_zcons_gap= 1;
1291	<	return 1;
1292	<	break;
1293	<
1294	<	case INT:
1295	<	zcons_gap= (double)the_event->evt.asmt.rhs.ival;
1296	<	have_zcons_gap= 1;
1297	<	return 1;
1298	<	break;
1299	<
1300	<	default:
1301	<	the_event->err_msg =
1302	<	strdup( "Error in parsing meta-data file!\n\tzcons_gap unrecognized.\n" );
1303	<	return 0;
1304	<	break;
1305	<	}
1306	<	break;
1307	<
1308	<	case G_ZCONSFIXTIME:
1309	<	switch( the_type ){
1310	<
1311	<	case STRING:
1312	<	the_event->err_msg =
1313	<	strdup( "Error in parsing meta-data file!\n\tzcons_fixtime is not a double or int.\n" );
1314	<	return 0;
1315	<	break;
1316	<
1317	<	case DOUBLE:
1318	<	zcons_fixtime= the_event->evt.asmt.rhs.dval;
1319	<	have_zcons_fixtime= 1;
1320	<	return 1;
1321	<	break;
1322	<
1323	<	case INT:
1324	<	zcons_fixtime= (double)the_event->evt.asmt.rhs.ival;
1325	<	have_zcons_fixtime= 1;
1326	<	return 1;
1327	<	break;
1328	<
1329	<	default:
1330	<	the_event->err_msg =
1331	<	strdup( "Error in parsing meta-data file!\n\tzcons_fixtime unrecognized.\n" );
1332	<	return 0;
1333	<	break;
1334	<	}
1335	<	break;
1336	<
1337	<	case G_ZCONSUSINGSMD:
1338	<	switch( the_type ){
1339	<
1340	<	case STRING:
1341	<	the_event->err_msg =
1342	<	strdup( "Error in parsing meta-data file!\n\tzcons_fixtime is not an  int.\n" );
1343	<	return 0;
1344	<	break;
1345	<
1346	<	case DOUBLE:
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 INT:
1353	<	zcons_using_smd= the_event->evt.asmt.rhs.ival;
1354	<	have_zcons_using_smd= 1;
1355	<	return 1;
1356	<	break;
1357	<
1358	<	default:
1359	<	the_event->err_msg =
1360	<	strdup( "Error in parsing meta-data file!\n\tzcons_usingsmd unrecognized.\n" );
1361	<	return 0;
1362	<	break;
1363	<	}
1364	<	break;
1365	<
1366	<	case G_MINIMIZER:
1367	<	switch( the_type ){
1368	<
1369	<	case STRING:
1370	<	strcpy(minimizer_name, the_event->evt.asmt.rhs.sval);
1371	<
1372	<	for(int i = 0; zconsForcePolicy[i] != '\0'; i++){
1373	<	zconsForcePolicy[i] = toupper(zconsForcePolicy[i]);
1374	<	}
1375	<	have_minimizer= 1;
1376	<	return 1;
1377	<	break;
1378	<
1379	<	case DOUBLE:
1380	<	the_event->err_msg =
1381	<	strdup( "Error in parsing meta-data file!\n\tminimizer_name is not a double or int.\n" );
1382	<	return 0;
1383	<	break;
1384	<
1385	<	case INT:
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	<	default:
1392	<	the_event->err_msg =
1393	<	strdup( "Error in parsing meta-data file!\n\tminimizer_name unrecognized.\n" );
1394	<	return 0;
1395	<	break;
1396	<	}
1397	<	break;
1398	<
1399	<	case G_MIN_MAXITER:
1400	<	switch( the_type ){
1401	<
1402	<	case STRING:
1403	<	the_event->err_msg =
1404	<	strdup( "Error in parsing meta-data file!\n\tminimizer_maxiteration is not a double or int.\n" );
1405	<	return 1;
1406	<	break;
1407	<
1408	<	case DOUBLE:
1409	<	minimizer_maxiteration = (int)the_event->evt.asmt.rhs.dval;
1410	<	have_minimizer_maxiteration = 1;
1411	<	return 1;
1412	<	break;
1413	<
1414	<	case INT:
1415	<	minimizer_maxiteration = the_event->evt.asmt.rhs.ival;
1416	<	have_minimizer_maxiteration = 1;
1417	<	return 1;
1418	<	break;
1419	<
1420	<	default:
1421	<	the_event->err_msg =
1422	<	strdup( "Error in parsing meta-data file!\n\tminimizer_maxiteration unrecognized.\n" );
1423	<	return 0;
1424	<	break;
1425	<	}
1426	<	break;
1427	<
1428	<	case G_MIN_WRITEFRQ:
1429	<	switch( the_type ){
1430	<
1431	<	case STRING:
1432	<	the_event->err_msg =
1433	<	strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq is not an int.\n" );
1434	<	return 1;
1435	<	break;
1436	<
1437	<	case DOUBLE:
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 INT:
1444	<	minimizer_writefrq= the_event->evt.asmt.rhs.ival;
1445	<	have_minimizer_writefrq = 1;
1446	<	return 1;
1447	<	break;
1448	<
1449	<	default:
1450	<	the_event->err_msg =
1451	<	strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq unrecognized.\n" );
1452	<	return 0;
1453	<	break;
1454	<	}
1455	<	break;
1456	<
1457	<	case G_MIN_STEPSIZE:
1458	<	switch( the_type ){
1459	<
1460	<	case STRING:
1461	<	the_event->err_msg =
1462	<	strdup( "Error in parsing meta-data file!\n\tminimizer_resetfrq is not a double or int.\n" );
1463	<	return 1;
1464	<	break;
1465	<
1466	<	case DOUBLE:
1467	<	minimizer_stepsize= the_event->evt.asmt.rhs.dval;
1468	<	have_minimizer_stepsize = 1;
1469	<	return 1;
1470	<	break;
1471	<
1472	<	case INT:
1473	<	minimizer_stepsize= the_event->evt.asmt.rhs.ival;
1474	<	have_minimizer_stepsize = 1;
1475	<	return 1;
1476	<	break;
1477	<
1478	<	default:
1479	<	the_event->err_msg =
1480	<	strdup( "Error in parsing meta-data file!\n\tminimizer_resetfrq unrecognized.\n" );
1481	<	return 0;
1482	<	break;
1483	<	}
1484	<	break;
1485	<
1486	<	case G_MIN_FTOL:
1487	<	switch( the_type ){
1488	<
1489	<	case STRING:
1490	<	the_event->err_msg =
1491	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ftol is not a double or int.\n" );
1492	<	return 1;
1493	<	break;
1494	<
1495	<	case DOUBLE:
1496	<	minimizer_ftol= the_event->evt.asmt.rhs.dval;
1497	<	have_minimizer_ftol = 1;
1498	<	return 1;
1499	<	break;
1500	<
1501	<	case INT:
1502	<	minimizer_ftol= the_event->evt.asmt.rhs.ival;
1503	<	have_minimizer_ftol = 1;
1504	<	return 1;
1505	<	break;
1506	<
1507	<	default:
1508	<	the_event->err_msg =
1509	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ftol unrecognized.\n" );
1510	<	return 0;
1511	<	break;
1512	<	}
1513	<	break;
1514	<
1515	<	case G_MIN_GTOL:
1516	<	switch( the_type ){
1517	<
1518	<	case STRING:
1519	<	the_event->err_msg =
1520	<	strdup( "Error in parsing meta-data file!\n\tminimizer_gtol is not a double or int.\n" );
1521	<	return 1;
1522	<	break;
1523	<
1524	<	case DOUBLE:
1525	<	minimizer_gtol= the_event->evt.asmt.rhs.dval;
1526	<	have_minimizer_gtol = 1;
1527	<	return 1;
1528	<	break;
1529	<
1530	<	case INT:
1531	<	minimizer_gtol= the_event->evt.asmt.rhs.ival;
1532	<	have_minimizer_gtol = 1;
1533	<	return 1;
1534	<	break;
1535	<
1536	<	default:
1537	<	the_event->err_msg =
1538	<	strdup( "Error in parsing meta-data file!\n\tminimizer_gtol unrecognized.\n" );
1539	<	return 0;
1540	<	break;
1541	<	}
1542	<	break;
1543	<
1544	<	case G_MIN_LSMAXITER:
1545	<	switch( the_type ){
1546	<
1547	<	case STRING:
1548	<	the_event->err_msg =
1549	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration is not an int.\n" );
1550	<	return 1;
1551	<	break;
1552	<
1553	<	case DOUBLE:
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 INT:
1560	<	minimizer_ls_maxiteration = the_event->evt.asmt.rhs.ival;
1561	<	have_minimizer_ls_maxiteration = 1;
1562	<	return 1;
1563	<	break;
1564	<
1565	<	default:
1566	<	the_event->err_msg =
1567	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration unrecognized.\n" );
1568	<	return 0;
1569	<	break;
1570	<	}
1571	<	break;
1572	<
1573	<	case G_MIN_LSTOL:
1574	<	switch( the_type ){
1575	<
1576	<	case STRING:
1577	<	the_event->err_msg =
1578	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_tol is not a double or int.\n" );
1579	<	return 1;
1580	<	break;
1581	<
1582	<	case DOUBLE:
1583	<	minimizer_ls_tol= the_event->evt.asmt.rhs.dval;
1584	<	have_minimizer_ls_tol = 1;
1585	<	return 1;
1586	<	break;
1587	<
1588	<	case INT:
1589	<	minimizer_ls_tol= the_event->evt.asmt.rhs.ival;
1590	<	have_minimizer_ls_tol = 1;
1591	<	return 1;
1592	<	break;
1593	<
1594	<	default:
1595	<	the_event->err_msg =
1596	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_tol unrecognized.\n" );
1597	<	return 0;
1598	<	break;
1599	<	}
1600	<	break;
1601	<
1602	<	// add more token cases here.
1603	<	case G_SEED:
1604	<	switch( the_type ){
1605	<
1606	<	case STRING:
1607	<	the_event->err_msg =
1608	<	strdup( "Error in parsing meta-data file!\n\tseed is not a string.\n" );
1609	<	return 0;
1610	<	return 0;
1611	<	break;
1612	<
1613	<	case DOUBLE:
1614	<	have_seed = 1;
1615	<	seed = (int)the_event->evt.asmt.rhs.dval;
1616	<	return 1;
1617	<	break;
1618	<
1619	<	case INT:
1620	<	have_seed = 1;
1621	<	seed =  the_event->evt.asmt.rhs.ival ;
1622	<	return 1;
1623	<	break;
1624	<
1625	<	default:
1626	<	the_event->err_msg =
1627	<	strdup( "Error in parsing meta-data file!\n\tseed unrecognized.\n" );
1628	<	return 0;
1629	<	break;
1630	<	}
1631	<	break;
1632	<
1633	<	case G_USE_SOLID_THERM_INT:
1634	<	if( the_type == STRING ){
1635	<
1636	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useSolidThermInt = 1;
1637	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useSolidThermInt = 0;
1638	<	else{
1639	<	the_event->err_msg =
1640	<	strdup( "Error in parsing meta-data file!\n\tuseSolidThermInt was not \"true\" or \"false\".\n" );
1641	<	return 0;
1642	<	}
1643	<	return 1;
1644	<	}
1645	<
1646	<	the_event->err_msg =
1647	<	strdup( "Error in parsing meta-data file!\n\tuseSolidThermInt was not \"true\" or \"false\".\n" );
1648	<	return 0;
1649	<	break;
1650	<
1651	<	case G_USE_LIQUID_THERM_INT:
1652	<	if( the_type == STRING ){
1653	<
1654	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useLiquidThermInt = 1;
1655	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useLiquidThermInt = 0;
1656	<	else{
1657	<	the_event->err_msg =
1658	<	strdup( "Error in parsing meta-data file!\n\tuseLiquidThermInt was not \"true\" or \"false\".\n" );
1659	<	return 0;
1660	<	}
1661	<	return 1;
1662	<	}
1663	<
1664	<	the_event->err_msg =
1665	<	strdup( "Error in parsing meta-data file!\n\tuseLiquidThermInt was not \"true\" or \"false\".\n" );
1666	<	return 0;
1667	<	break;
1668	<
1669	<	case G_THERM_INT_LAMBDA:
1670	<	switch( the_type ){
1671	<
1672	<	case STRING:
1673	<	the_event->err_msg =
1674	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationLambda is not a double or int.\n" );
1675	<	return 1;
1676	<	break;
1677	<
1678	<	case DOUBLE:
1679	<	thermodynamic_integration_lambda = the_event->evt.asmt.rhs.dval;
1680	<	have_thermodynamic_integration_lambda = 1;
1681	<	return 1;
1682	<	break;
1683	<
1684	<	case INT:
1685	<	thermodynamic_integration_lambda = (double)the_event->evt.asmt.rhs.dval;
1686	<	have_thermodynamic_integration_lambda = 1;
1687	<	return 1;
1688	<	break;
1689	<
1690	<	default:
1691	<	the_event->err_msg =
1692	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationLambda unrecognized.\n" );
1693	<	return 0;
1694	<	break;
1695	<	}
1696	<	break;
1697	<
1698	<	case G_THERM_INT_K:
1699	<	switch( the_type ){
1700	<
1701	<	case STRING:
1702	<	the_event->err_msg =
1703	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationK is not a double or int.\n" );
1704	<	return 1;
1705	<	break;
1706	<
1707	<	case DOUBLE:
1708	<	thermodynamic_integration_k = the_event->evt.asmt.rhs.dval;
1709	<	have_thermodynamic_integration_k = 1;
1710	<	return 1;
1711	<	break;
1712	<
1713	<	case INT:
1714	<	thermodynamic_integration_k = (double)the_event->evt.asmt.rhs.dval;
1715	<	have_thermodynamic_integration_k = 1;
1716	<	return 1;
1717	<	break;
1718	<
1719	<	default:
1720	<	the_event->err_msg =
1721	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationK unrecognized.\n" );
1722	<	return 0;
1723	<	break;
1724	<	}
1725	<	break;
1726	<	case G_FORCEFIELD_VARIANT:
1727	<	if( the_type == STRING ){
1728	<	strcpy( forcefield_variant, the_event->evt.asmt.rhs.sval );
1729	<	have_forcefield_variant = 1;
1730	<	return 1;
1731	<	}
1732	<
1733	<	the_event->err_msg =
1734	<	strdup( "Error in parsing meta-data file!\n\tforceFieldVariant was not a string assignment.\n" );
1735	<	return 0;
1736	<	break;
1737	<	// add more token cases here.
1738	<	}
1739	<	}
1740	<
1741	<	switch( the_type ){
1742	<
1743	<	case STRING:
1744	<	sprintf( err,
1745	<	"\tUnrecognized assignment:\n"
1746	<	"\t\t-> %s = %s\n",
1747	<	lhs, the_event->evt.asmt.rhs.sval );
1748	<	break;
1749	<
1750	<	case DOUBLE:
1751	<	sprintf( err,
1752	<	"\tUnrecognized assignment:\n"
1753	<	"\t\t-> %s = %lf\n",
1754	<	lhs, the_event->evt.asmt.rhs.dval );
1755	<	break;
1756	<
1757	<	case INT:
1758	<	sprintf( err,
1759	<	"\tUnrecognized assignment:\n"
1760	<	"\t\t-> %s = %d\n",
1761	<	lhs, the_event->evt.asmt.rhs.ival );
1762	<	break;
1763	<
1764	<	default:
1765	<	sprintf( err,
1766	<	"\tUnrecognized assignment:\n"
1767	<	"\t\t-> %s = ?\n",
1768	<	lhs );
1769	<	break;
1770	<	}
1771	<
1772	<	the_event->err_msg = strdup( err );
1773	<	return 0;
1774	<	}
1775	<
1776	<	char* Globals::checkMe( void ){
1777	<
1778	<	char err[300];
1779	<	short int have_err = 0;
1780	<
1781	<	strcpy( err, "The following required keywords are missing:\n" );
1782	<
1783	<	if( !have_force_field ){
1784	<	strcat( err, "\t\t->forceField\n" );
1785	<	have_err= 1;
1786	<	}
1787	<
1788	<	if( !have_n_components ){
1789	<	strcat( err, "\t\t->nComponents\n" );
1790	<	have_err= 1;
1791	<	}
1792	<
1793	<
1794	<	if ( !have_ensemble ) {
1795	<	// I'm not doing MD:
1796	<	if ( !have_minimizer ) {
1797	<	// I'm not doing MD or minimization:
1798	<	strcat( err, "\t\t->either ensemble or minimizer must be set!\n" );
1799	<	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 {
1804	<	// I *am* doing MD:
1805	<	if( !have_dt ){
1806	<	strcat( err, "\t\t->dt (timestep in fs)\n" );
1807	<	have_err= 1;
1808	<	}
1809	<	if( !have_run_time ){
1810	<	strcat( err, "\t\t->runTime (total run time in fs)\n" );
1811	<	have_err= 1;
1812	<	}
1813	<	}
1814	<
1815	<	if( have_err ) return strdup( err );
1816	<
1817	<	return NULL;
210	>	return ret;
211		}
212	+
213
1820	–	int Globals::globalEnd( event* the_event ){
1821	–
1822	–	the_event->err_msg = checkMe();
1823	–	if( the_event->err_msg != NULL ) return 0;
1824	–
1825	–	return 1;
214		}
1827	–
1828	–	int Globals::hash( char* text ){
1829	–
1830	–	register unsigned short int i = 0; // loop counter
1831	–	int key = 0; // the hash key
1832	–
1833	–	while( text[i] != '\0' ){
1834	–
1835	–	key = ( ( key << hash_shift ) + text[i] ) % hash_size;
1836	–
1837	–	i++;
1838	–	}
1839	–
1840	–	if( key < 0 ){
1841	–
1842	–	// if the key is less than zero, we've had an overflow error
1843	–
1844	–	sprintf( painCave.errMsg,
1845	–	"There has been an overflow error in the Globals' hash key.");
1846	–	painCave.isFatal = 1;
1847	–	simError();
1848	–	#ifdef IS_MPI
1849	–	if( painCave.isEventLoop ){
1850	–	if( worldRank == 0 ) mpiInterfaceExit();
1851	–	}
1852	–	#endif //is_mpi
1853	–	}
1854	–
1855	–	return key;
1856	–	}
1857	–
1858	–	void Globals::addHash( char* text, int token ){
1859	–
1860	–	int key;
1861	–	LinkedCommand* the_element;
1862	–
1863	–	the_element = new LinkedCommand;
1864	–	the_element->setValues( text, token );
1865	–
1866	–	key = hash( text );
1867	–
1868	–	the_element->setNext( command_table[key] );
1869	–	command_table[key] = the_element;
1870	–	}

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