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root/OpenMD/branches/development/src/io/Globals.cpp

Comparing trunk/src/io/Globals.cpp (file contents):
Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC

#	Line 1 | Line 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
5	+	* non-exclusive, royalty free, license to use, modify and
6	+	* redistribute this software in source and binary code form, provided
7	+	* that the following conditions are met:
8	+	*
9	+	* 1. Acknowledgement of the program authors must be made in any
10	+	*    publication of scientific results based in part on use of the
11	+	*    program.  An acceptable form of acknowledgement is citation of
12	+	*    the article in which the program was described (Matthew
13	+	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	+	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	+	*    Parallel Simulation Engine for Molecular Dynamics,"
16	+	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	+	*
18	+	* 2. Redistributions of source code must retain the above copyright
19	+	*    notice, this list of conditions and the following disclaimer.
20	+	*
21	+	* 3. Redistributions in binary form must reproduce the above copyright
22	+	*    notice, this list of conditions and the following disclaimer in the
23	+	*    documentation and/or other materials provided with the
24	+	*    distribution.
25	+	*
26	+	* This software is provided "AS IS," without a warranty of any
27	+	* kind. All express or implied conditions, representations and
28	+	* warranties, including any implied warranty of merchantability,
29	+	* fitness for a particular purpose or non-infringement, are hereby
30	+	* excluded.  The University of Notre Dame and its licensors shall not
31	+	* be liable for any damages suffered by licensee as a result of
32	+	* using, modifying or distributing the software or its
33	+	* derivatives. In no event will the University of Notre Dame or its
34	+	* licensors be liable for any lost revenue, profit or data, or for
35	+	* direct, indirect, special, consequential, incidental or punitive
36	+	* damages, however caused and regardless of the theory of liability,
37	+	* arising out of the use of or inability to use software, even if the
38	+	* University of Notre Dame has been advised of the possibility of
39	+	* such damages.
40	+	*/
41	+
42		#include <stdlib.h>
43		#include <stdio.h>
44		#include <string.h>
45	+	#include <string>
46
47	<	#include "Globals.hpp"
48	<	#include "simError.h"
7	<	#ifdef IS_MPI
8	<	#include "mpiBASS.h"
9	<	#endif // is_mpi
47	>	#include "io/Globals.hpp"
48	>	#include "utils/simError.h"
49
50	<	/*
12	<	* The following section lists all of the defined tokens for the
13	<	* gloabal assignment statements. All are prefixed with a G_ to avoid
14	<	* stepping on any previously defined enumerations.
15	<	*
16	<	* NOTE: tokens start at 1, 0 is a resrved token number
17	<	*/
50	>	#include "io/ParamConstraint.hpp"
51
52	<	//required parameters
53	<	#define G_FORCEFIELD         1
54	<	#define G_NCOMPONENTS        2
22	<	#define G_TARGETTEMP         3
23	<	#define G_ENSEMBLE           4
24	<	#define G_DT                 5
25	<	#define G_RUNTIME            6
26	<
27	<	//optional parameters
28	<	#define G_INITIALCONFIG      7
29	<	#define G_FINALCONFIG        8
30	<	#define G_NMOL               9
31	<	#define G_DENSITY           10
32	<	#define G_BOX               11
33	<	#define G_BOXX              12
34	<	#define G_BOXY              13
35	<	#define G_BOXZ              14
36	<	#define G_SAMPLETIME        15
37	<	#define G_STATUSTIME        16
38	<	#define G_RCUT              17
39	<	#define G_RSW               18
40	<	#define G_DIELECTRIC        19
41	<	#define G_TEMPSET           20
42	<	#define G_THERMALTIME       21
43	<	#define G_USEPBC            22
44	<	#define G_MIXINGRULE        23
45	<	#define G_USERF             24
46	<	#define G_TARGETPRESSURE    25
47	<	#define G_TAUTHERMOSTAT     26
48	<	#define G_TAUBAROSTAT       27
49	<	#define G_ZCONSTIME         28
50	<	#define G_NZCONSTRAINTS     29
51	<	#define G_ZCONSTOL          30
52	<	#define G_ZCONSFORCEPOLICY  31
53	<	#define G_SEED              32
54	<	#define G_RESETTIME         33
55	<	#define G_USEINITTIME       34
56	<	#define G_USEINIT_XS_STATE  35
57	<	#define G_ORTHOBOXTOLERANCE 36
58	<	#define G_MINIMIZER         37
59	<	#define G_MIN_MAXITER       38
60	<	#define G_MIN_WRITEFRQ      39
61	<	#define G_MIN_STEPSIZE      40
62	<	#define G_MIN_FTOL          41
63	<	#define G_MIN_GTOL          42
64	<	#define G_MIN_LSTOL         43
65	<	#define G_MIN_LSMAXITER     44
66	<	#define G_ZCONSGAP          45
67	<	#define G_ZCONSFIXTIME      46
68	<	#define G_ZCONSUSINGSMD     47
69	<	#define G_USE_SOLID_THERM_INT     48
70	<	#define G_USE_LIQUID_THERM_INT    49
71	<	#define G_THERM_INT_LAMBDA  50
72	<	#define G_THERM_INT_K       51
73	<	#define G_FORCEFIELD_VARIANT 52
74	<
75	<	Globals::Globals(){
76	<	initalize();
77	<	}
78	<
79	<	Globals::~Globals(){
80	<	int i;
81	<
82	<	for( i=0; i<hash_size; i++ ){
83	<	if( command_table[i] != NULL ) delete command_table[i];
84	<	}
85	<	delete[] command_table;
86	<
87	<	if( components != NULL ){
88	<	for( i=0; i<n_components; i++ ) delete components[i];
89	<	delete[] components;
90	<	}
91	<	}
92	<
93	<	void Globals::initalize(){
94	<	int i;
95	<
96	<	hash_size = 23;
97	<	hash_shift = 4;
98	<
99	<	components = NULL;
100	<
101	<	command_table = new LinkedCommand*[hash_size];
102	<	for( i=0; i<hash_size; i++ ) command_table[i] = NULL;
103	<
104	<	addHash( "forceField",    G_FORCEFIELD );
105	<	addHash( "nComponents",   G_NCOMPONENTS );
106	<	addHash( "targetTemp",    G_TARGETTEMP );
107	<	addHash( "ensemble",      G_ENSEMBLE );
108	<
109	<	addHash( "dt",            G_DT );
110	<	addHash( "runTime",       G_RUNTIME );
111	<
112	<	addHash( "initialConfig", G_INITIALCONFIG );
113	<	addHash( "finalConfig",   G_FINALCONFIG );
114	<	addHash( "nMol",          G_NMOL );
115	<	addHash( "density",       G_DENSITY );
116	<	addHash( "box",           G_BOX );
117	<	addHash( "boxX",          G_BOXX );
118	<	addHash( "boxY",          G_BOXY );
119	<	addHash( "boxZ",          G_BOXZ );
120	<	addHash( "sampleTime",    G_SAMPLETIME );
121	<	addHash( "resetTime",     G_RESETTIME );
122	<	addHash( "statusTime",    G_STATUSTIME );
123	<	addHash( "cutoffRadius",  G_RCUT );
124	<	addHash( "switchingRadius",  G_RSW );
125	<	addHash( "dielectric",    G_DIELECTRIC );
126	<	addHash( "tempSet",       G_TEMPSET );
127	<	addHash( "thermalTime",   G_THERMALTIME );
128	<	addHash( "mixingRule",    G_MIXINGRULE);
129	<	addHash( "usePeriodicBoundaryConditions",        G_USEPBC);
130	<	addHash( "useReactionField",                     G_USERF );
131	<	addHash( "targetPressure",                       G_TARGETPRESSURE);
132	<	addHash( "tauThermostat",                        G_TAUTHERMOSTAT);
133	<	addHash( "tauBarostat",                          G_TAUBAROSTAT);
134	<	addHash( "zconsTime",                            G_ZCONSTIME);
135	<	addHash( "nZconstraints",                        G_NZCONSTRAINTS);
136	<	addHash( "zconsTol",                             G_ZCONSTOL);
137	<	addHash( "zconsForcePolicy",                     G_ZCONSFORCEPOLICY);
138	<	addHash( "seed",                                 G_SEED);
139	<	addHash( "useInitialTime",                       G_USEINITTIME);
140	<	addHash( "useInitialExtendedSystemState",        G_USEINIT_XS_STATE);
141	<	addHash( "orthoBoxTolerance",                    G_ORTHOBOXTOLERANCE);
142	<	addHash( "minimizer",                            G_MINIMIZER);
143	<	addHash( "minimizerMaxIter",                     G_MIN_MAXITER);
144	<	addHash( "minimizerWriteFrq",                    G_MIN_WRITEFRQ);
145	<	addHash( "minimizerStepSize",                    G_MIN_STEPSIZE);
146	<	addHash( "minimizerFTol",                        G_MIN_FTOL);
147	<	addHash( "minimizerGTol",                        G_MIN_GTOL);
148	<	addHash( "minimizerLSTol",                       G_MIN_LSTOL);
149	<	addHash( "minimizerLSMaxIter",                   G_MIN_LSMAXITER);
150	<	addHash( "zconsGap",                             G_ZCONSGAP);
151	<	addHash( "zconsFixtime",                         G_ZCONSFIXTIME);
152	<	addHash( "zconsUsingSMD",                        G_ZCONSUSINGSMD);
153	<	addHash( "useSolidThermInt",                     G_USE_SOLID_THERM_INT);
154	<	addHash( "useLiquidThermInt",                    G_USE_LIQUID_THERM_INT);
155	<	addHash( "thermodynamicIntegrationLambda",       G_THERM_INT_LAMBDA);
156	<	addHash( "thermodynamicIntegrationK",            G_THERM_INT_K);
157	<	addHash( "forceFieldVariant",                    G_FORCEFIELD_VARIANT);
158	<
159	<	strcpy( mixingRule,"standard");  //default mixing rules to standard.
160	<	usePBC = 1; //default  periodic boundry conditions to on
161	<	useRF  = 0;
162	<	useInitTime = 0; // default to pull init time from the init file
163	<	useInitXSstate = 0; // default to pull the extended state from the init file
164	<	orthoBoxTolerance = 1E-6;
165	<	useSolidThermInt = 0; // default solid-state thermodynamic integration to off
166	<	useLiquidThermInt = 0; // default liquid thermodynamic integration to off
167	<
168	<	have_force_field =  0;
169	<	have_n_components = 0;
170	<	have_target_temp =  0;
171	<	have_ensemble =     0;
172	<	have_dt =           0;
173	<	have_run_time =     0;
174	<
175	<	have_initial_config = 0;
176	<	have_final_config =   0;
177	<	have_n_mol =          0;
178	<	have_density =        0;
179	<	have_box =            0;
180	<	have_box_x =          0;
181	<	have_box_y =          0;
182	<	have_box_y =          0;
183	<	have_box_z =          0;
184	<	have_sample_time =    0;
185	<	have_status_time =    0;
186	<	have_reset_time =     0;
187	<	have_thermal_time =   0;
188	<	have_rcut =           0;
189	<	have_rsw =            0;
190	<	have_dielectric =     0;
191	<	have_tempSet =        0;
192	<	have_target_pressure =0;
193	<	have_q_mass =         0;
194	<	have_tau_thermostat = 0;
195	<	have_tau_barostat   = 0;
196	<	have_zcons_time     = 0;
197	<	have_n_zConstraints = 0;
198	<	have_zConstraints   = 0;
199	<	have_zcons_tol = 0;
200	<	have_zcons_gap = 0;
201	<	have_zcons_fixtime = 0;
202	<	have_zcons_using_smd = 0;
203	<	have_seed = 0;
204	<	have_minimizer = 0;
205	<	have_minimizer_maxiteration = 0;
206	<	have_minimizer_writefrq = 0;
207	<	have_minimizer_stepsize = 0;
208	<	have_minimizer_ftol = 0;
209	<	have_minimizer_gtol = 0;
210	<	have_minimizer_ls_tol = 0;
211	<	have_minimizer_ls_maxiteration = 0;
212	<	have_thermodynamic_integration_lambda = 0;
213	<	have_thermodynamic_integration_k = 0;
214	<	have_forcefield_variant = 0;
215	<
216	<	}
217	<
218	<	int Globals::newComponent( event* the_event ){
219	<
220	<	current_component = new Component;
221	<	int index = the_event->evt.blk_index;
222	<	char err[200];
223	<
224	<	if( have_n_components && index < n_components )
225	<	components[index] = current_component;
226	<	else{
227	<	if( have_n_components ){
228	<	sprintf( err, "meta-data parsing error: %d out of nComponents range",
229	<	index );
230	<	the_event->err_msg = strdup( err );
231	<	return 0;
232	<	}
233	<	else{
234	<	the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
235	<	" first component declaration." );
236	<	return 0;
237	<	}
238	<	}
52	>	namespace oopse {
53	>	Globals::Globals() {
54	>	DefineParameter(ForceField, "forceField")
55
56	<	return 1;
57	<	}
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	<
119	<	int Globals::componentAssign( event* the_event ){
246	<
247	<	switch( the_event->evt.asmt.asmt_type ){
118	>	deprecatedKeywords_.insert("nComponents");
119	>	deprecatedKeywords_.insert("nZconstraints");
120
249	–	case STRING:
250	–	return current_component->assignString( the_event->evt.asmt.lhs,
251	–	the_event->evt.asmt.rhs.sval,
252	–	&(the_event->err_msg));
253	–	break;
254	–
255	–	case DOUBLE:
256	–	return current_component->assignDouble( the_event->evt.asmt.lhs,
257	–	the_event->evt.asmt.rhs.dval,
258	–	&(the_event->err_msg));
259	–	break;
260	–
261	–	case INT:
262	–	return current_component->assignInt( the_event->evt.asmt.lhs,
263	–	the_event->evt.asmt.rhs.ival,
264	–	&(the_event->err_msg));
265	–	break;
266	–
267	–	default:
268	–	the_event->err_msg = strdup( "Globals error. Invalid component"
269	–	" assignment type" );
270	–	return 0;
271	–	break;
272	–	}
273	–	return 0;
121		}
122
123	<	int Globals::componentEnd( event* the_event ){
123	>	Globals::~Globals() {
124
278	–	the_event->err_msg = current_component->checkMe();
279	–	if( the_event->err_msg != NULL ) return 0;
125
281	–	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{
296	<	if( have_n_zConstraints ){
297	<	sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
298	<	index );
299	<	the_event->err_msg = strdup( err );
300	<	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{
303	<	the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
304	<	" not given before"
305	<	" first zConstraint declaration." );
306	<	return 0;
307	<	}
308	<	}
309	<
310	<	return 1;
186	>	}
187		}
312	–
313	–
314	–
315	–	int Globals::zConstraintAssign( event* the_event ){
316	–
317	–	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,
322	<	&(the_event->err_msg));
323	<	break;
324	<
325	<	case DOUBLE:
326	<	return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
327	<	the_event->evt.asmt.rhs.dval,
328	<	&(the_event->err_msg));
329	<	break;
330	<
331	<	case INT:
332	<	return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
333	<	the_event->evt.asmt.rhs.ival,
334	<	&(the_event->err_msg));
335	<	break;
336	<
337	<	default:
338	<	the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
339	<	" assignment type" );
340	<	return 0;
341	<	break;
342	<	}
343	<	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();
349	<	if( the_event->err_msg != NULL ) return 0;
350	<
351	<	return 1;
194	>	bool Globals::addZConsStamp(ZConsStamp* zcons) {
195	>	zconstraints_.push_back(zcons);
196	>	return true;
197		}
198
199	<	int Globals::globalAssign( event* the_event ){
200	<
201	<	int key;
202	<	int token;
203	<	interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
204	<	char* lhs = the_event->evt.asmt.lhs;
205	<	char err[300];
206	<
362	<	token = 0;
363	<	key = hash( lhs );
364	<	if( command_table[key] != NULL ) token = command_table[key]->match( lhs );
365	<
366	<	if( token ){
367	<
368	<	switch( token ){
369	<
370	<	case G_FORCEFIELD:
371	<	if( the_type == STRING ){
372	<	strcpy( force_field, the_event->evt.asmt.rhs.sval );
373	<	have_force_field = 1;
374	<	return 1;
375	<	}
376	<
377	<	the_event->err_msg =
378	<	strdup( "Error in parsing meta-data file!\n\tforceField was not a string assignment.\n" );
379	<	return 0;
380	<	break;
381	<
382	<	case G_NCOMPONENTS:
383	<	if( the_type == STRING ){
384	<	the_event->err_msg =
385	<	strdup("Error in parsing meta-data file!\n\tnComponents is not a double or an int.\n" );
386	<	return 0;
387	<	}
388	<
389	<	else if( the_type == DOUBLE ){
390	<	n_components = (int)the_event->evt.asmt.rhs.dval;
391	<	components = new Component*[n_components];
392	<	have_n_components = 1;
393	<	return 1;
394	<	}
395	<
396	<	else{
397	<	n_components = the_event->evt.asmt.rhs.ival;
398	<	components = new Component*[n_components];
399	<	have_n_components = 1;
400	<	return 1;
401	<	}
402	<	break;
403	<
404	<	case G_NZCONSTRAINTS:
405	<	if( the_type == STRING ){
406	<	the_event->err_msg =
407	<	strdup("Error in parsing meta-data file!\n\tnZconstraints is not a double or an int.\n" );
408	<	return 0;
409	<	}
410	<
411	<	else if( the_type == DOUBLE ){
412	<	n_zConstraints = (int)the_event->evt.asmt.rhs.dval;
413	<	zConstraints = new ZconStamp*[n_zConstraints];
414	<	have_n_zConstraints = 1;
415	<	return 1;
416	<	}
417	<
418	<	else{
419	<	n_zConstraints = the_event->evt.asmt.rhs.ival;
420	<	zConstraints = new ZconStamp*[n_zConstraints];
421	<	have_n_zConstraints = 1;
422	<	return 1;
423	<	}
424	<	break;
425	<
426	<	case G_TARGETTEMP:
427	<	switch( the_type ){
428	<
429	<	case STRING:
430	<	the_event->err_msg =
431	<	strdup( "Error in parsing meta-data file!\n\ttargetTemp is not a double or int.\n" );
432	<	return 0;
433	<	break;
434	<
435	<	case DOUBLE:
436	<	target_temp = the_event->evt.asmt.rhs.dval;
437	<	have_target_temp = 1;
438	<	return 1;
439	<	break;
440	<
441	<	case INT:
442	<	target_temp = (double)the_event->evt.asmt.rhs.ival;
443	<	have_target_temp = 1;
444	<	return 1;
445	<	break;
446	<
447	<	default:
448	<	the_event->err_msg =
449	<	strdup( "Error in parsing meta-data file!\n\ttargetTemp unrecognized.\n" );
450	<	return 0;
451	<	break;
452	<	}
453	<	break;
454	<
455	<	case G_ORTHOBOXTOLERANCE:
456	<	switch( the_type ){
457	<
458	<	case STRING:
459	<	the_event->err_msg =
460	<	strdup( "Error in parsing meta-data file!\n\torthoBoxTolerance is not a double or int.\n" );
461	<	return 0;
462	<	break;
463	<
464	<	case DOUBLE:
465	<	orthoBoxTolerance = the_event->evt.asmt.rhs.dval;
466	<	have_target_temp = 1;
467	<	return 1;
468	<	break;
469	<
470	<	case INT:
471	<	orthoBoxTolerance = (double)the_event->evt.asmt.rhs.ival;
472	<	have_target_temp = 1;
473	<	return 1;
474	<	break;
475	<
476	<	default:
477	<	the_event->err_msg =
478	<	strdup( "Global error.orthoBoxTolerance unrecognized.\n" );
479	<	return 0;
480	<	break;
481	<	}
482	<	break;
483	<
484	<	case G_ENSEMBLE:
485	<	if( the_type == STRING ){
486	<	strcpy( ensemble, the_event->evt.asmt.rhs.sval );
487	<	have_ensemble = 1;
488	<	return 1;
489	<	}
490	<
491	<	the_event->err_msg =
492	<	strdup( "Error in parsing meta-data file!\n\tensemble was not assigned to a string\n" );
493	<	return 0;
494	<	break;
495	<
496	<	case G_MIXINGRULE:
497	<	if( the_type == STRING ){
498	<	strcpy( mixingRule, the_event->evt.asmt.rhs.sval );
499	<	return 1;
500	<	}
501	<
502	<	the_event->err_msg =
503	<	strdup( "Error in parsing meta-data file!\n\tmixing rule was not assigned to a string\n" );
504	<	return 0;
505	<	break;
506	<
507	<	case G_DT:
508	<	switch( the_type ){
509	<
510	<	case STRING:
511	<	the_event->err_msg =
512	<	strdup( "Error in parsing meta-data file!\n\tdt is not a double or int.\n" );
513	<	return 0;
514	<	break;
515	<
516	<	case DOUBLE:
517	<	dt = the_event->evt.asmt.rhs.dval;
518	<	have_dt = 1;
519	<	return 1;
520	<	break;
521	<
522	<	case INT:
523	<	dt = (double)the_event->evt.asmt.rhs.ival;
524	<	have_dt = 1;
525	<	return 1;
526	<	break;
527	<
528	<	default:
529	<	the_event->err_msg =
530	<	strdup( "Error in parsing meta-data file!\n\tdt unrecognized.\n" );
531	<	return 0;
532	<	break;
533	<	}
534	<	break;
535	<
536	<	case G_RUNTIME:
537	<	switch( the_type ){
538	<
539	<	case STRING:
540	<	the_event->err_msg =
541	<	strdup( "Error in parsing meta-data file!\n\trunTime is not a double or int.\n" );
542	<	return 0;
543	<	break;
544	<
545	<	case DOUBLE:
546	<	run_time = the_event->evt.asmt.rhs.dval;
547	<	have_run_time = 1;
548	<	return 1;
549	<	break;
550	<
551	<	case INT:
552	<	run_time = (double)the_event->evt.asmt.rhs.ival;
553	<	have_run_time = 1;
554	<	return 1;
555	<	break;
556	<
557	<	default:
558	<	the_event->err_msg =
559	<	strdup( "Error in parsing meta-data file!\n\trunTime unrecognized.\n" );
560	<	return 0;
561	<	break;
562	<	}
563	<	break;
564	<
565	<	case G_INITIALCONFIG:
566	<	if( the_type == STRING ){
567	<	strcpy( initial_config, the_event->evt.asmt.rhs.sval );
568	<	have_initial_config = 1;
569	<	return 1;
570	<	}
571	<
572	<	the_event->err_msg =
573	<	strdup( "Error in parsing meta-data file!\n\tinitialConfig was not a string assignment.\n" );
574	<	return 0;
575	<	break;
576	<
577	<	case G_FINALCONFIG:
578	<	if( the_type == STRING ){
579	<	strcpy( final_config, the_event->evt.asmt.rhs.sval );
580	<	have_final_config = 1;
581	<	return 1;
582	<	}
583	<
584	<	the_event->err_msg =
585	<	strdup( "Error in parsing meta-data file!\n\tfinalConfig was not a string assignment.\n" );
586	<	return 0;
587	<	break;
588	<
589	<	case G_NMOL:
590	<	switch( the_type ){
591	<
592	<	case STRING:
593	<	the_event->err_msg =
594	<	strdup( "Error in parsing meta-data file!\n\tnMol is not a double or int.\n" );
595	<	return 0;
596	<	break;
597	<
598	<	case DOUBLE:
599	<	n_mol = (int)the_event->evt.asmt.rhs.dval;
600	<	have_n_mol = 1;
601	<	return 1;
602	<	break;
603	<
604	<	case INT:
605	<	n_mol = the_event->evt.asmt.rhs.ival;
606	<	have_n_mol = 1;
607	<	return 1;
608	<	break;
609	<
610	<	default:
611	<	the_event->err_msg =
612	<	strdup( "Error in parsing meta-data file!\n\tnMol unrecognized.\n" );
613	<	return 0;
614	<	break;
615	<	}
616	<	break;
617	<
618	<	case G_DENSITY:
619	<	switch( the_type ){
620	<
621	<	case STRING:
622	<	the_event->err_msg =
623	<	strdup( "Error in parsing meta-data file!\n\tdensity is not a double or int.\n" );
624	<	return 0;
625	<	break;
626	<
627	<	case DOUBLE:
628	<	density = the_event->evt.asmt.rhs.dval;
629	<	have_density = 1;
630	<	return 1;
631	<	break;
632	<
633	<	case INT:
634	<	density = (double)the_event->evt.asmt.rhs.ival;
635	<	have_density = 1;
636	<	return 1;
637	<	break;
638	<
639	<	default:
640	<	the_event->err_msg =
641	<	strdup( "Error in parsing meta-data file!\n\tdensity unrecognized.\n" );
642	<	return 0;
643	<	break;
644	<	}
645	<	break;
646	<
647	<	case G_BOX:
648	<	switch( the_type ){
649	<
650	<	case STRING:
651	<	the_event->err_msg =
652	<	strdup( "Error in parsing meta-data file!\n\tbox is not a double or int.\n" );
653	<	return 0;
654	<	break;
655	<
656	<	case DOUBLE:
657	<	box = the_event->evt.asmt.rhs.dval;
658	<	have_box = 1;
659	<	return 1;
660	<	break;
661	<
662	<	case INT:
663	<	box = (double)the_event->evt.asmt.rhs.ival;
664	<	have_box = 1;
665	<	return 1;
666	<	break;
667	<
668	<	default:
669	<	the_event->err_msg =
670	<	strdup( "Error in parsing meta-data file!\n\tbox unrecognized.\n" );
671	<	return 0;
672	<	break;
673	<	}
674	<	break;
675	<
676	<	case G_BOXX:
677	<	switch( the_type ){
678	<
679	<	case STRING:
680	<	the_event->err_msg =
681	<	strdup( "Error in parsing meta-data file!\n\tboxX is not a double or int.\n" );
682	<	return 0;
683	<	break;
684	<
685	<	case DOUBLE:
686	<	box_x = the_event->evt.asmt.rhs.dval;
687	<	have_box_x = 1;
688	<	return 1;
689	<	break;
690	<
691	<	case INT:
692	<	box_x = (double)the_event->evt.asmt.rhs.ival;
693	<	have_box_x = 1;
694	<	return 1;
695	<	break;
696	<
697	<	default:
698	<	the_event->err_msg =
699	<	strdup( "Error in parsing meta-data file!\n\tboxX unrecognized.\n" );
700	<	return 0;
701	<	break;
702	<	}
703	<	break;
704	<
705	<	case G_BOXY:
706	<	switch( the_type ){
707	<
708	<	case STRING:
709	<	the_event->err_msg =
710	<	strdup( "Error in parsing meta-data file!\n\tboxY is not a double or int.\n" );
711	<	return 0;
712	<	break;
713	<
714	<	case DOUBLE:
715	<	box_y = the_event->evt.asmt.rhs.dval;
716	<	have_box_y = 1;
717	<	return 1;
718	<	break;
719	<
720	<	case INT:
721	<	box_y = (double)the_event->evt.asmt.rhs.ival;
722	<	have_box_y = 1;
723	<	return 1;
724	<	break;
725	<
726	<	default:
727	<	the_event->err_msg =
728	<	strdup( "Error in parsing meta-data file!\n\tboxY unrecognized.\n" );
729	<	return 0;
730	<	break;
731	<	}
732	<	break;
733	<
734	<	case G_BOXZ:
735	<	switch( the_type ){
736	<
737	<	case STRING:
738	<	the_event->err_msg =
739	<	strdup( "Error in parsing meta-data file!\n\tboxZ is not a double or int.\n" );
740	<	return 0;
741	<	break;
742	<
743	<	case DOUBLE:
744	<	box_z = the_event->evt.asmt.rhs.dval;
745	<	have_box_z = 1;
746	<	return 1;
747	<	break;
748	<
749	<	case INT:
750	<	box_z = (double)the_event->evt.asmt.rhs.ival;
751	<	have_box_z = 1;
752	<	return 1;
753	<	break;
754	<
755	<	default:
756	<	the_event->err_msg =
757	<	strdup( "Error in parsing meta-data file!\n\tboxZ unrecognized.\n" );
758	<	return 0;
759	<	break;
760	<	}
761	<	break;
762	<
763	<	case G_SAMPLETIME:
764	<	switch( the_type ){
765	<
766	<	case STRING:
767	<	the_event->err_msg =
768	<	strdup( "Error in parsing meta-data file!\n\tsampleTime is not a double or int.\n" );
769	<	return 0;
770	<	break;
771	<
772	<	case DOUBLE:
773	<	sample_time = the_event->evt.asmt.rhs.dval;
774	<	have_sample_time = 1;
775	<	return 1;
776	<	break;
777	<
778	<	case INT:
779	<	sample_time = (double)the_event->evt.asmt.rhs.ival;
780	<	have_sample_time = 1;
781	<	return 1;
782	<	break;
783	<
784	<	default:
785	<	the_event->err_msg =
786	<	strdup( "Error in parsing meta-data file!\n\tsampleTime unrecognized.\n" );
787	<	return 0;
788	<	break;
789	<	}
790	<	break;
791	<
792	<	case G_STATUSTIME:
793	<	switch( the_type ){
794	<
795	<	case STRING:
796	<	the_event->err_msg =
797	<	strdup( "Error in parsing meta-data file!\n\tstatusTime is not a double or int.\n" );
798	<	return 0;
799	<	break;
800	<
801	<	case DOUBLE:
802	<	status_time = the_event->evt.asmt.rhs.dval;
803	<	have_status_time = 1;
804	<	return 1;
805	<	break;
806	<
807	<	case INT:
808	<	status_time = (double)the_event->evt.asmt.rhs.ival;
809	<	have_status_time = 1;
810	<	return 1;
811	<	break;
812	<
813	<	default:
814	<	the_event->err_msg =
815	<	strdup( "Error in parsing meta-data file!\n\tstatusTime unrecognized.\n" );
816	<	return 0;
817	<	break;
818	<	}
819	<	break;
820	<
821	<	case G_RESETTIME:
822	<	switch( the_type ){
823	<
824	<	case STRING:
825	<	the_event->err_msg =
826	<	strdup( "Error in parsing meta-data file!\n\tresetTime is not a double or int.\n" );
827	<	return 0;
828	<	break;
829	<
830	<	case DOUBLE:
831	<	resetTime = the_event->evt.asmt.rhs.dval;
832	<	have_reset_time = 1;
833	<	return 1;
834	<	break;
835	<
836	<	case INT:
837	<	resetTime = (double)the_event->evt.asmt.rhs.ival;
838	<	have_reset_time = 1;
839	<	return 1;
840	<	break;
841	<
842	<	default:
843	<	the_event->err_msg =
844	<	strdup( "Error in parsing meta-data file!\n\tresetTime unrecognized.\n" );
845	<	return 0;
846	<	break;
847	<	}
848	<	break;
849	<
850	<	case G_THERMALTIME:
851	<	switch( the_type ){
852	<
853	<	case STRING:
854	<	the_event->err_msg =
855	<	strdup( "Error in parsing meta-data file!\n\tthermalTime is not a double or int.\n" );
856	<	return 0;
857	<	break;
858	<
859	<	case DOUBLE:
860	<	thermal_time = the_event->evt.asmt.rhs.dval;
861	<	have_thermal_time = 1;
862	<	return 1;
863	<	break;
864	<
865	<	case INT:
866	<	thermal_time = (double)the_event->evt.asmt.rhs.ival;
867	<	have_thermal_time = 1;
868	<	return 1;
869	<	break;
870	<
871	<	default:
872	<	the_event->err_msg =
873	<	strdup( "Error in parsing meta-data file!\n\tthermalTime unrecognized.\n" );
874	<	return 0;
875	<	break;
876	<	}
877	<	break;
878	<
879	<	case G_RCUT:
880	<	switch( the_type ){
881	<
882	<	case STRING:
883	<	the_event->err_msg =
884	<	strdup( "Error in parsing meta-data file!\n\tcutoffRadius is not a double or int.\n" );
885	<	return 0;
886	<	break;
887	<
888	<	case DOUBLE:
889	<	rcut = the_event->evt.asmt.rhs.dval;
890	<	have_rcut = 1;
891	<	return 1;
892	<	break;
893	<
894	<	case INT:
895	<	rcut = (double)the_event->evt.asmt.rhs.ival;
896	<	have_rcut = 1;
897	<	return 1;
898	<	break;
899	<
900	<	default:
901	<	the_event->err_msg =
902	<	strdup( "Error in parsing meta-data file!\n\tcutoffRadius unrecognized.\n" );
903	<	return 0;
904	<	break;
905	<	}
906	<	break;
907	<
908	<	case G_RSW:
909	<	switch( the_type ){
910	<
911	<	case STRING:
912	<	the_event->err_msg =
913	<	strdup( "Error in parsing meta-data file!\n\tswitchingRadius is not a double or int.\n" );
914	<	return 0;
915	<	break;
916	<
917	<	case DOUBLE:
918	<	rsw = the_event->evt.asmt.rhs.dval;
919	<	have_rsw = 1;
920	<	return 1;
921	<	break;
922	<
923	<	case INT:
924	<	rsw = (double)the_event->evt.asmt.rhs.ival;
925	<	have_rsw = 1;
926	<	return 1;
927	<	break;
928	<
929	<	default:
930	<	the_event->err_msg =
931	<	strdup( "Error in parsing meta-data file!\n\tswitchingRadius unrecognized.\n" );
932	<	return 0;
933	<	break;
934	<	}
935	<	break;
936	<
937	<	case G_DIELECTRIC:
938	<	switch( the_type ){
939	<
940	<	case STRING:
941	<	the_event->err_msg =
942	<	strdup( "Error in parsing meta-data file!\n\tdielectric is not a double or int.\n" );
943	<	return 0;
944	<	break;
945	<
946	<	case DOUBLE:
947	<	dielectric = the_event->evt.asmt.rhs.dval;
948	<	have_dielectric = 1;
949	<	return 1;
950	<	break;
951	<
952	<	case INT:
953	<	dielectric = (double)the_event->evt.asmt.rhs.ival;
954	<	have_dielectric = 1;
955	<	return 1;
956	<	break;
957	<
958	<	default:
959	<	the_event->err_msg =
960	<	strdup( "Error in parsing meta-data file!\n\tdielectric unrecognized.\n" );
961	<	return 0;
962	<	break;
963	<	}
964	<	break;
965	<
966	<	case G_TEMPSET:
967	<	if( the_type == STRING ){
968	<
969	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) tempSet = 1;
970	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) tempSet = 0;
971	<	else{
972	<	the_event->err_msg =
973	<	strdup( "Error in parsing meta-data file!\n\ttempSet was not \"true\" or \"false\".\n" );
974	<	return 0;
975	<	}
976	<	have_tempSet = 1;
977	<	return 1;
978	<	}
979	<
980	<	the_event->err_msg =
981	<	strdup( "Error in parsing meta-data file!\n\ttempSet was not \"true\" or \"false\".\n" );
982	<	return 0;
983	<	break;
984	<
985	<	case G_USEINITTIME:
986	<	if( the_type == STRING ){
987	<
988	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useInitTime = 1;
989	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useInitTime = 0;
990	<	else{
991	<	the_event->err_msg =
992	<	strdup( "Error in parsing meta-data file!\n\tuseInitTime was not \"true\" or \"false\".\n" );
993	<	return 0;
994	<	}
995	<	return 1;
996	<	}
997	<
998	<	the_event->err_msg =
999	<	strdup( "Error in parsing meta-data file!\n\tuseInitTime was not \"true\" or \"false\".\n" );
1000	<	return 0;
1001	<	break;
1002	<
1003	<	case G_USEINIT_XS_STATE:
1004	<	if( the_type == STRING ){
1005	<
1006	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval ))
1007	<	useInitXSstate = 1;
1008	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval ))
1009	<	useInitXSstate = 0;
1010	<	else{
1011	<	the_event->err_msg =
1012	<	strdup( "Error in parsing meta-data file!\n\tuseInitExtendedSystemState was not \"true\" or \"false\".\n" );
1013	<	return 0;
1014	<	}
1015	<	return 1;
1016	<	}
1017	<
1018	<	the_event->err_msg =
1019	<	strdup( "Error in parsing meta-data file!\n\tuseInitExtendedSystemState was not \"true\" or \"false\".\n" );
1020	<	return 0;
1021	<	break;
1022	<
1023	<	case G_USEPBC:
1024	<	if( the_type == STRING ){
1025	<
1026	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) usePBC = 1;
1027	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) usePBC = 0;
1028	<	else{
1029	<	the_event->err_msg =
1030	<	strdup( "Error in parsing meta-data file!\n\tusePeriodicBoundaryConditions was not \"true\" or \"false\".\n" );
1031	<	return 0;
1032	<	}
1033	<	return 1;
1034	<	}
1035	<
1036	<	the_event->err_msg =
1037	<	strdup( "Error in parsing meta-data file!\n\tusePeriodicBoundaryConditions was not \"true\" or \"false\".\n" );
1038	<	return 0;
1039	<	break;
1040	<
1041	<	case G_USERF:
1042	<	if( the_type == STRING ){
1043	<
1044	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useRF = 1;
1045	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useRF = 0;
1046	<	else{
1047	<	the_event->err_msg =
1048	<	strdup( "Error in parsing meta-data file!\n\tuseReactionField was not \"true\" or \"false\".\n" );
1049	<	return 0;
1050	<	}
1051	<	return 1;
1052	<	}
1053	<
1054	<	the_event->err_msg =
1055	<	strdup( "Error in parsing meta-data file!\n\tuseReactionField was not \"true\" or \"false\".\n" );
1056	<	return 0;
1057	<	break;
1058	<
1059	<	case G_TARGETPRESSURE:
1060	<	switch( the_type ){
1061	<
1062	<	case STRING:
1063	<	the_event->err_msg =
1064	<	strdup( "Error in parsing meta-data file!\n\ttargetPressure is not a double or int.\n" );
1065	<	return 0;
1066	<	break;
1067	<
1068	<	case DOUBLE:
1069	<	target_pressure = the_event->evt.asmt.rhs.dval;
1070	<	have_target_pressure = 1;
1071	<	return 1;
1072	<	break;
1073	<
1074	<	case INT:
1075	<	target_pressure = (double)the_event->evt.asmt.rhs.ival;
1076	<	have_target_pressure = 1;
1077	<	return 1;
1078	<	break;
1079	<
1080	<	default:
1081	<	the_event->err_msg =
1082	<	strdup( "Error in parsing meta-data file!\n\ttargetPressure unrecognized.\n" );
1083	<	return 0;
1084	<	break;
1085	<	}
1086	<	break;
1087	<
1088	<	case G_TAUTHERMOSTAT:
1089	<	switch( the_type ){
1090	<
1091	<	case STRING:
1092	<	the_event->err_msg =
1093	<	strdup( "Error in parsing meta-data file!\n\ttauThermostat is not a double or int.\n" );
1094	<	return 0;
1095	<	break;
1096	<
1097	<	case DOUBLE:
1098	<	tau_thermostat = the_event->evt.asmt.rhs.dval;
1099	<	have_tau_thermostat = 1;
1100	<	return 1;
1101	<	break;
1102	<
1103	<	case INT:
1104	<	tau_thermostat = (double)the_event->evt.asmt.rhs.ival;
1105	<	have_tau_thermostat = 1;
1106	<	return 1;
1107	<	break;
1108	<
1109	<	default:
1110	<	the_event->err_msg =
1111	<	strdup( "Error in parsing meta-data file!\n\ttauThermostat unrecognized.\n" );
1112	<	return 0;
1113	<	break;
1114	<	}
1115	<	break;
1116	<
1117	<	case G_TAUBAROSTAT:
1118	<	switch( the_type ){
1119	<
1120	<	case STRING:
1121	<	the_event->err_msg =
1122	<	strdup( "Error in parsing meta-data file!\n\ttauBarostat is not a double or int.\n" );
1123	<	return 0;
1124	<	break;
1125	<
1126	<	case DOUBLE:
1127	<	tau_barostat = the_event->evt.asmt.rhs.dval;
1128	<	have_tau_barostat = 1;
1129	<	return 1;
1130	<	break;
1131	<
1132	<	case INT:
1133	<	tau_barostat = (double)the_event->evt.asmt.rhs.ival;
1134	<	have_tau_barostat = 1;
1135	<	return 1;
1136	<	break;
1137	<
1138	<	default:
1139	<	the_event->err_msg =
1140	<	strdup( "Error in parsing meta-data file!\n\ttauBarostat unrecognized.\n" );
1141	<	return 0;
1142	<	break;
1143	<	}
1144	<	break;
1145	<
1146	<	case G_ZCONSTIME:
1147	<	switch( the_type ){
1148	<
1149	<	case STRING:
1150	<	the_event->err_msg =
1151	<	strdup( "Error in parsing meta-data file!\n\tzcons_time is not a double or int.\n" );
1152	<	return 0;
1153	<	break;
1154	<
1155	<	case DOUBLE:
1156	<	zcons_time = the_event->evt.asmt.rhs.dval;
1157	<	have_zcons_time = 1;
1158	<	return 1;
1159	<	break;
1160	<
1161	<	case INT:
1162	<	zcons_time = (double)the_event->evt.asmt.rhs.ival;
1163	<	have_zcons_time = 1;
1164	<	return 1;
1165	<	break;
1166	<
1167	<	default:
1168	<	the_event->err_msg =
1169	<	strdup( "Error in parsing meta-data file!\n\tzcons_time unrecognized.\n" );
1170	<	return 0;
1171	<	break;
1172	<	}
1173	<	break;
1174	<
1175	<	case G_ZCONSTOL:
1176	<	switch( the_type ){
1177	<
1178	<	case STRING:
1179	<	the_event->err_msg =
1180	<	strdup( "Error in parsing meta-data file!\n\tzcons_tol is not a double or int.\n" );
1181	<	return 0;
1182	<	break;
1183	<
1184	<	case DOUBLE:
1185	<	zcons_tol = the_event->evt.asmt.rhs.dval;
1186	<	have_zcons_tol = 1;
1187	<	return 1;
1188	<	break;
1189	<
1190	<	case INT:
1191	<	zcons_tol = (double)the_event->evt.asmt.rhs.ival;
1192	<	have_zcons_tol = 1;
1193	<	return 1;
1194	<	break;
1195	<
1196	<	default:
1197	<	the_event->err_msg =
1198	<	strdup( "Error in parsing meta-data file!\n\tzcons_ol unrecognized.\n" );
1199	<	return 0;
1200	<	break;
1201	<	}
1202	<	break;
1203	<
1204	<	case G_ZCONSFORCEPOLICY:
1205	<	switch( the_type ){
1206	<
1207	<	case STRING:
1208	<	strcpy(zconsForcePolicy, the_event->evt.asmt.rhs.sval);
1209	<
1210	<	for(int i = 0; zconsForcePolicy[i] != '\0'; i++)
1211	<	{
1212	<	zconsForcePolicy[i] = toupper(zconsForcePolicy[i]);
1213	<	}
1214	<	have_zcons_force_policy = 1;
1215	<	return 1;
1216	<	break;
1217	<
1218	<	case DOUBLE:
1219	<	the_event->err_msg =
1220	<	strdup( "Error in parsing meta-data file!\n\tzconsForcePolicy is not a double or int.\n" );
1221	<	return 0;
1222	<	break;
1223	<
1224	<	case INT:
1225	<	the_event->err_msg =
1226	<	strdup( "Error in parsing meta-data file!\n\tzconsForcePolicy is not a double or int.\n" );
1227	<	return 0;
1228	<	break;
1229	<
1230	<	default:
1231	<	the_event->err_msg =
1232	<	strdup( "Error in parsing meta-data file!\n\tzconsForcePolicy unrecognized.\n" );
1233	<	return 0;
1234	<	break;
1235	<	}
1236	<	break;
1237	<
1238	<	case G_ZCONSGAP:
1239	<	switch( the_type ){
1240	<
1241	<	case STRING:
1242	<	the_event->err_msg =
1243	<	strdup( "Error in parsing meta-data file!\n\tzcons_gap is not a double or int.\n" );
1244	<	return 0;
1245	<	break;
1246	<
1247	<	case DOUBLE:
1248	<	zcons_gap = the_event->evt.asmt.rhs.dval;
1249	<	have_zcons_gap= 1;
1250	<	return 1;
1251	<	break;
1252	<
1253	<	case INT:
1254	<	zcons_gap= (double)the_event->evt.asmt.rhs.ival;
1255	<	have_zcons_gap= 1;
1256	<	return 1;
1257	<	break;
1258	<
1259	<	default:
1260	<	the_event->err_msg =
1261	<	strdup( "Error in parsing meta-data file!\n\tzcons_gap unrecognized.\n" );
1262	<	return 0;
1263	<	break;
1264	<	}
1265	<	break;
1266	<
1267	<	case G_ZCONSFIXTIME:
1268	<	switch( the_type ){
1269	<
1270	<	case STRING:
1271	<	the_event->err_msg =
1272	<	strdup( "Error in parsing meta-data file!\n\tzcons_fixtime is not a double or int.\n" );
1273	<	return 0;
1274	<	break;
1275	<
1276	<	case DOUBLE:
1277	<	zcons_fixtime= the_event->evt.asmt.rhs.dval;
1278	<	have_zcons_fixtime= 1;
1279	<	return 1;
1280	<	break;
1281	<
1282	<	case INT:
1283	<	zcons_fixtime= (double)the_event->evt.asmt.rhs.ival;
1284	<	have_zcons_fixtime= 1;
1285	<	return 1;
1286	<	break;
1287	<
1288	<	default:
1289	<	the_event->err_msg =
1290	<	strdup( "Error in parsing meta-data file!\n\tzcons_fixtime unrecognized.\n" );
1291	<	return 0;
1292	<	break;
1293	<	}
1294	<	break;
1295	<
1296	<	case G_ZCONSUSINGSMD:
1297	<	switch( the_type ){
1298	<
1299	<	case STRING:
1300	<	the_event->err_msg =
1301	<	strdup( "Error in parsing meta-data file!\n\tzcons_fixtime is not an  int.\n" );
1302	<	return 0;
1303	<	break;
1304	<
1305	<	case DOUBLE:
1306	<	the_event->err_msg =
1307	<	strdup( "Error in parsing meta-data file!\n\tzcons_fixtime is not an  int.\n" );
1308	<	return 0;
1309	<	break;
1310	<
1311	<	case INT:
1312	<	zcons_using_smd= the_event->evt.asmt.rhs.ival;
1313	<	have_zcons_using_smd= 1;
1314	<	return 1;
1315	<	break;
1316	<
1317	<	default:
1318	<	the_event->err_msg =
1319	<	strdup( "Error in parsing meta-data file!\n\tzcons_usingsmd unrecognized.\n" );
1320	<	return 0;
1321	<	break;
1322	<	}
1323	<	break;
1324	<
1325	<	case G_MINIMIZER:
1326	<	switch( the_type ){
1327	<
1328	<	case STRING:
1329	<	strcpy(minimizer_name, the_event->evt.asmt.rhs.sval);
1330	<
1331	<	for(int i = 0; zconsForcePolicy[i] != '\0'; i++){
1332	<	zconsForcePolicy[i] = toupper(zconsForcePolicy[i]);
1333	<	}
1334	<	have_minimizer= 1;
1335	<	return 1;
1336	<	break;
1337	<
1338	<	case DOUBLE:
1339	<	the_event->err_msg =
1340	<	strdup( "Error in parsing meta-data file!\n\tminimizer_name is not a double or int.\n" );
1341	<	return 0;
1342	<	break;
1343	<
1344	<	case INT:
1345	<	the_event->err_msg =
1346	<	strdup( "Error in parsing meta-data file!\n\tminimizer_name is not a double or int.\n" );
1347	<	return 0;
1348	<	break;
1349	<
1350	<	default:
1351	<	the_event->err_msg =
1352	<	strdup( "Error in parsing meta-data file!\n\tminimizer_name unrecognized.\n" );
1353	<	return 0;
1354	<	break;
1355	<	}
1356	<	break;
1357	<
1358	<	case G_MIN_MAXITER:
1359	<	switch( the_type ){
1360	<
1361	<	case STRING:
1362	<	the_event->err_msg =
1363	<	strdup( "Error in parsing meta-data file!\n\tminimizer_maxiteration is not a double or int.\n" );
1364	<	return 1;
1365	<	break;
1366	<
1367	<	case DOUBLE:
1368	<	minimizer_maxiteration = (int)the_event->evt.asmt.rhs.dval;
1369	<	have_minimizer_maxiteration = 1;
1370	<	return 1;
1371	<	break;
1372	<
1373	<	case INT:
1374	<	minimizer_maxiteration = the_event->evt.asmt.rhs.ival;
1375	<	have_minimizer_maxiteration = 1;
1376	<	return 1;
1377	<	break;
1378	<
1379	<	default:
1380	<	the_event->err_msg =
1381	<	strdup( "Error in parsing meta-data file!\n\tminimizer_maxiteration unrecognized.\n" );
1382	<	return 0;
1383	<	break;
1384	<	}
1385	<	break;
1386	<
1387	<	case G_MIN_WRITEFRQ:
1388	<	switch( the_type ){
1389	<
1390	<	case STRING:
1391	<	the_event->err_msg =
1392	<	strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq is not a double or int.\n" );
1393	<	return 1;
1394	<	break;
1395	<
1396	<	case DOUBLE:
1397	<	minimizer_writefrq= the_event->evt.asmt.rhs.dval;
1398	<	have_minimizer_writefrq = 1;
1399	<	return 1;
1400	<	break;
1401	<
1402	<	case INT:
1403	<	minimizer_writefrq= the_event->evt.asmt.rhs.ival;
1404	<	have_minimizer_writefrq = 1;
1405	<	return 1;
1406	<	break;
1407	<
1408	<	default:
1409	<	the_event->err_msg =
1410	<	strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq unrecognized.\n" );
1411	<	return 0;
1412	<	break;
1413	<	}
1414	<	break;
1415	<
1416	<	case G_MIN_STEPSIZE:
1417	<	switch( the_type ){
1418	<
1419	<	case STRING:
1420	<	the_event->err_msg =
1421	<	strdup( "Error in parsing meta-data file!\n\tminimizer_resetfrq is not a double or int.\n" );
1422	<	return 1;
1423	<	break;
1424	<
1425	<	case DOUBLE:
1426	<	minimizer_stepsize= the_event->evt.asmt.rhs.dval;
1427	<	have_minimizer_stepsize = 1;
1428	<	return 1;
1429	<	break;
1430	<
1431	<	case INT:
1432	<	minimizer_stepsize= the_event->evt.asmt.rhs.ival;
1433	<	have_minimizer_stepsize = 1;
1434	<	return 1;
1435	<	break;
1436	<
1437	<	default:
1438	<	the_event->err_msg =
1439	<	strdup( "Error in parsing meta-data file!\n\tminimizer_resetfrq unrecognized.\n" );
1440	<	return 0;
1441	<	break;
1442	<	}
1443	<	break;
1444	<
1445	<	case G_MIN_FTOL:
1446	<	switch( the_type ){
1447	<
1448	<	case STRING:
1449	<	the_event->err_msg =
1450	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ftol is not a double or int.\n" );
1451	<	return 1;
1452	<	break;
1453	<
1454	<	case DOUBLE:
1455	<	minimizer_ftol= the_event->evt.asmt.rhs.dval;
1456	<	have_minimizer_ftol = 1;
1457	<	return 1;
1458	<	break;
1459	<
1460	<	case INT:
1461	<	minimizer_ftol= the_event->evt.asmt.rhs.ival;
1462	<	have_minimizer_ftol = 1;
1463	<	return 1;
1464	<	break;
1465	<
1466	<	default:
1467	<	the_event->err_msg =
1468	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ftol unrecognized.\n" );
1469	<	return 0;
1470	<	break;
1471	<	}
1472	<	break;
1473	<
1474	<	case G_MIN_GTOL:
1475	<	switch( the_type ){
1476	<
1477	<	case STRING:
1478	<	the_event->err_msg =
1479	<	strdup( "Error in parsing meta-data file!\n\tminimizer_gtol is not a double or int.\n" );
1480	<	return 1;
1481	<	break;
1482	<
1483	<	case DOUBLE:
1484	<	minimizer_gtol= the_event->evt.asmt.rhs.dval;
1485	<	have_minimizer_gtol = 1;
1486	<	return 1;
1487	<	break;
1488	<
1489	<	case INT:
1490	<	minimizer_gtol= the_event->evt.asmt.rhs.ival;
1491	<	have_minimizer_gtol = 1;
1492	<	return 1;
1493	<	break;
1494	<
1495	<	default:
1496	<	the_event->err_msg =
1497	<	strdup( "Error in parsing meta-data file!\n\tminimizer_gtol unrecognized.\n" );
1498	<	return 0;
1499	<	break;
1500	<	}
1501	<	break;
1502	<
1503	<	case G_MIN_LSMAXITER:
1504	<	switch( the_type ){
1505	<
1506	<	case STRING:
1507	<	the_event->err_msg =
1508	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration is not a double or int.\n" );
1509	<	return 1;
1510	<	break;
1511	<
1512	<	case DOUBLE:
1513	<	minimizer_ls_maxiteration = the_event->evt.asmt.rhs.dval;
1514	<	have_minimizer_ls_maxiteration = 1;
1515	<	return 1;
1516	<	break;
1517	<
1518	<	case INT:
1519	<	minimizer_ls_maxiteration = the_event->evt.asmt.rhs.ival;
1520	<	have_minimizer_ls_maxiteration = 1;
1521	<	return 1;
1522	<	break;
1523	<
1524	<	default:
1525	<	the_event->err_msg =
1526	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration unrecognized.\n" );
1527	<	return 0;
1528	<	break;
1529	<	}
1530	<	break;
1531	<
1532	<	case G_MIN_LSTOL:
1533	<	switch( the_type ){
1534	<
1535	<	case STRING:
1536	<	the_event->err_msg =
1537	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_tol is not a double or int.\n" );
1538	<	return 1;
1539	<	break;
1540	<
1541	<	case DOUBLE:
1542	<	minimizer_ls_tol= the_event->evt.asmt.rhs.dval;
1543	<	have_minimizer_ls_tol = 1;
1544	<	return 1;
1545	<	break;
1546	<
1547	<	case INT:
1548	<	minimizer_ls_tol= the_event->evt.asmt.rhs.ival;
1549	<	have_minimizer_ls_tol = 1;
1550	<	return 1;
1551	<	break;
1552	<
1553	<	default:
1554	<	the_event->err_msg =
1555	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_tol unrecognized.\n" );
1556	<	return 0;
1557	<	break;
1558	<	}
1559	<	break;
1560	<
1561	<	// add more token cases here.
1562	<	case G_SEED:
1563	<	switch( the_type ){
1564	<
1565	<	case STRING:
1566	<	the_event->err_msg =
1567	<	strdup( "Error in parsing meta-data file!\n\tseed is not a string.\n" );
1568	<	return 0;
1569	<	return 0;
1570	<	break;
1571	<
1572	<	case DOUBLE:
1573	<	have_seed = 1;
1574	<	seed = (int)the_event->evt.asmt.rhs.dval;
1575	<	return 1;
1576	<	break;
1577	<
1578	<	case INT:
1579	<	have_seed = 1;
1580	<	seed =  the_event->evt.asmt.rhs.ival ;
1581	<	return 1;
1582	<	break;
1583	<
1584	<	default:
1585	<	the_event->err_msg =
1586	<	strdup( "Error in parsing meta-data file!\n\tseed unrecognized.\n" );
1587	<	return 0;
1588	<	break;
1589	<	}
1590	<	break;
1591	<
1592	<	case G_USE_SOLID_THERM_INT:
1593	<	if( the_type == STRING ){
1594	<
1595	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useSolidThermInt = 1;
1596	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useSolidThermInt = 0;
1597	<	else{
1598	<	the_event->err_msg =
1599	<	strdup( "Error in parsing meta-data file!\n\tuseSolidThermInt was not \"true\" or \"false\".\n" );
1600	<	return 0;
1601	<	}
1602	<	return 1;
1603	<	}
1604	<
1605	<	the_event->err_msg =
1606	<	strdup( "Error in parsing meta-data file!\n\tuseSolidThermInt was not \"true\" or \"false\".\n" );
1607	<	return 0;
1608	<	break;
1609	<
1610	<	case G_USE_LIQUID_THERM_INT:
1611	<	if( the_type == STRING ){
1612	<
1613	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useLiquidThermInt = 1;
1614	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useLiquidThermInt = 0;
1615	<	else{
1616	<	the_event->err_msg =
1617	<	strdup( "Error in parsing meta-data file!\n\tuseLiquidThermInt was not \"true\" or \"false\".\n" );
1618	<	return 0;
1619	<	}
1620	<	return 1;
1621	<	}
1622	<
1623	<	the_event->err_msg =
1624	<	strdup( "Error in parsing meta-data file!\n\tuseLiquidThermInt was not \"true\" or \"false\".\n" );
1625	<	return 0;
1626	<	break;
1627	<
1628	<	case G_THERM_INT_LAMBDA:
1629	<	switch( the_type ){
1630	<
1631	<	case STRING:
1632	<	the_event->err_msg =
1633	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationLambda is not a double or int.\n" );
1634	<	return 1;
1635	<	break;
1636	<
1637	<	case DOUBLE:
1638	<	thermodynamic_integration_lambda = the_event->evt.asmt.rhs.dval;
1639	<	have_thermodynamic_integration_lambda = 1;
1640	<	return 1;
1641	<	break;
1642	<
1643	<	case INT:
1644	<	thermodynamic_integration_lambda = (double)the_event->evt.asmt.rhs.dval;
1645	<	have_thermodynamic_integration_lambda = 1;
1646	<	return 1;
1647	<	break;
1648	<
1649	<	default:
1650	<	the_event->err_msg =
1651	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationLambda unrecognized.\n" );
1652	<	return 0;
1653	<	break;
1654	<	}
1655	<	break;
1656	<
1657	<	case G_THERM_INT_K:
1658	<	switch( the_type ){
1659	<
1660	<	case STRING:
1661	<	the_event->err_msg =
1662	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationK is not a double or int.\n" );
1663	<	return 1;
1664	<	break;
1665	<
1666	<	case DOUBLE:
1667	<	thermodynamic_integration_k = the_event->evt.asmt.rhs.dval;
1668	<	have_thermodynamic_integration_k = 1;
1669	<	return 1;
1670	<	break;
1671	<
1672	<	case INT:
1673	<	thermodynamic_integration_k = (double)the_event->evt.asmt.rhs.dval;
1674	<	have_thermodynamic_integration_k = 1;
1675	<	return 1;
1676	<	break;
1677	<
1678	<	default:
1679	<	the_event->err_msg =
1680	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationK unrecognized.\n" );
1681	<	return 0;
1682	<	break;
1683	<	}
1684	<	break;
1685	<	case G_FORCEFIELD_VARIANT:
1686	<	if( the_type == STRING ){
1687	<	strcpy( forcefield_variant, the_event->evt.asmt.rhs.sval );
1688	<	have_forcefield_variant = 1;
1689	<	return 1;
1690	<	}
1691	<
1692	<	the_event->err_msg =
1693	<	strdup( "Error in parsing meta-data file!\n\tforceFieldVariant was not a string assignment.\n" );
1694	<	return 0;
1695	<	break;
1696	<	// add more token cases here.
1697	<	}
1698	<	}
1699	<
1700	<	switch( the_type ){
1701	<
1702	<	case STRING:
1703	<	sprintf( err,
1704	<	"\tUnrecognized assignment:\n"
1705	<	"\t\t-> %s = %s\n",
1706	<	lhs, the_event->evt.asmt.rhs.sval );
1707	<	break;
1708	<
1709	<	case DOUBLE:
1710	<	sprintf( err,
1711	<	"\tUnrecognized assignment:\n"
1712	<	"\t\t-> %s = %lf\n",
1713	<	lhs, the_event->evt.asmt.rhs.dval );
1714	<	break;
1715	<
1716	<	case INT:
1717	<	sprintf( err,
1718	<	"\tUnrecognized assignment:\n"
1719	<	"\t\t-> %s = %d\n",
1720	<	lhs, the_event->evt.asmt.rhs.ival );
1721	<	break;
1722	<
1723	<	default:
1724	<	sprintf( err,
1725	<	"\tUnrecognized assignment:\n"
1726	<	"\t\t-> %s = ?\n",
1727	<	lhs );
1728	<	break;
1729	<	}
1730	<
1731	<	the_event->err_msg = strdup( err );
1732	<	return 0;
1733	<	}
1734	<
1735	<	char* Globals::checkMe( void ){
1736	<
1737	<	char err[300];
1738	<	short int have_err = 0;
1739	<
1740	<	strcpy( err, "The following required keywords are missing:\n" );
1741	<
1742	<	if( !have_force_field ){
1743	<	strcat( err, "\t\t->forceField\n" );
1744	<	have_err= 1;
1745	<	}
1746	<
1747	<	if( !have_n_components ){
1748	<	strcat( err, "\t\t->nComponents\n" );
1749	<	have_err= 1;
1750	<	}
1751	<
1752	<
1753	<	if ( !have_ensemble ) {
1754	<	// I'm not doing MD:
1755	<	if ( !have_minimizer ) {
1756	<	// I'm not doing MD or minimization:
1757	<	strcat( err, "\t\t->either ensemble or minimizer must be set!\n" );
1758	<	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 {
1760	–	// I'm a minimizer:
1761	–	}
1762	–	} else {
1763	–	// I *am* doing MD:
1764	–	if( !have_dt ){
1765	–	strcat( err, "\t\t->dt (timestep in fs)\n" );
1766	–	have_err= 1;
1767	–	}
1768	–	if( !have_run_time ){
1769	–	strcat( err, "\t\t->runTime (total run time in fs)\n" );
1770	–	have_err= 1;
1771	–	}
1772	–	}
1773	–
1774	–	if( have_err ) return strdup( err );
1775	–
1776	–	return NULL;
1777	–	}
208
1779	–	int Globals::globalEnd( event* the_event ){
1780	–
1781	–	the_event->err_msg = checkMe();
1782	–	if( the_event->err_msg != NULL ) return 0;
1783	–
1784	–	return 1;
1785	–	}
1786	–
1787	–	int Globals::hash( char* text ){
1788	–
1789	–	register unsigned short int i = 0; // loop counter
1790	–	int key = 0; // the hash key
1791	–
1792	–	while( text[i] != '\0' ){
1793	–
1794	–	key = ( ( key << hash_shift ) + text[i] ) % hash_size;
1795	–
1796	–	i++;
1797	–	}
1798	–
1799	–	if( key < 0 ){
1800	–
1801	–	// if the key is less than zero, we've had an overflow error
1802	–
1803	–	sprintf( painCave.errMsg,
1804	–	"There has been an overflow error in the Globals' hash key.");
1805	–	painCave.isFatal = 1;
1806	–	simError();
1807	–	#ifdef IS_MPI
1808	–	if( painCave.isEventLoop ){
1809	–	if( worldRank == 0 ) mpiInterfaceExit();
209		}
210	<	#endif //is_mpi
1812	<	}
1813	<
1814	<	return key;
210	>	return ret;
211		}
212	+
213
1817	–	void Globals::addHash( char* text, int token ){
1818	–
1819	–	int key;
1820	–	LinkedCommand* the_element;
1821	–
1822	–	the_element = new LinkedCommand;
1823	–	the_element->setValues( text, token );
1824	–
1825	–	key = hash( text );
1826	–
1827	–	the_element->setNext( command_table[key] );
1828	–	command_table[key] = the_element;
214		}

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