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

Comparing trunk/src/io/Globals.cpp (file contents):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 1331 by gezelter, Thu Apr 2 16:04:52 2009 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 "io/Globals.hpp"
48	+	#include "io/ParamConstraint.hpp"
49	+	#include "utils/MemoryUtils.hpp"
50		#include "utils/simError.h"
7	–	#ifdef IS_MPI
8	–	#include "io/mpiBASS.h"
9	–	#endif // is_mpi
51
52	<	/*
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	<	*/
52	>	namespace oopse {
53	>	Globals::Globals() {
54	>	DefineParameter(ForceField, "forceField")
55	>
56	>	DefineOptionalParameter(TargetTemp, "targetTemp");
57	>	DefineOptionalParameter(Ensemble, "ensemble");
58	>	DefineOptionalParameter(Dt, "dt");
59	>	DefineOptionalParameter(RunTime, "runTime");
60	>	DefineOptionalParameter(FinalConfig, "finalConfig");
61	>	DefineOptionalParameter(SampleTime, "sampleTime");
62	>	DefineOptionalParameter(ResetTime, "resetTime");
63	>	DefineOptionalParameter(StatusTime, "statusTime");
64	>	DefineOptionalParameter(CutoffRadius, "cutoffRadius");
65	>	DefineOptionalParameter(SwitchingRadius, "switchingRadius");
66	>	DefineOptionalParameter(TempSet, "tempSet");
67	>	DefineOptionalParameter(ThermalTime, "thermalTime");
68	>	DefineOptionalParameter(TargetPressure, "targetPressure");
69	>	DefineOptionalParameter(TauThermostat, "tauThermostat");
70	>	DefineOptionalParameter(TauBarostat, "tauBarostat");
71	>	DefineOptionalParameter(ZconsTime, "zconsTime");
72	>	DefineOptionalParameter(ZconsTol, "zconsTol");
73	>	DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
74	>	DefineOptionalParameter(Seed, "seed");
75	>	DefineOptionalParameter(Minimizer, "minimizer");
76	>	DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
77	>	DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
78	>	DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
79	>	DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
80	>	DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
81	>	DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
82	>	DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
83	>	DefineOptionalParameter(ZconsGap, "zconsGap");
84	>	DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
85	>	DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
86	>	DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
87	>	DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
88	>	DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89	>	DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90	>	DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91	>	DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
92	>	DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
93	>	DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
94	>	DefineOptionalParameter(SurfaceTension, "surfaceTension");
95	>	DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
96	>	DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
97	>	DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
98	>	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
99	>	DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
100	>	DefineOptionalParameter(HydroPropFile, "HydroPropFile");
101	>	DefineOptionalParameter(Viscosity, "viscosity");
102	>	DefineOptionalParameter(BeadSize, "beadSize");
103	>	DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
104	>	DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
105	>	DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
106	>	DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
107	>	DefineOptionalParameter(MTM_Ce, "MTM_Ce");
108	>	DefineOptionalParameter(MTM_G, "MTM_G");
109	>	DefineOptionalParameter(MTM_Io, "MTM_Io");
110	>	DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
111	>	DefineOptionalParameter(MTM_R, "MTM_R");
112	>
113
19	–	//required parameters
20	–	#define G_FORCEFIELD         1
21	–	#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;
114
115	<	hash_size = 23;
116	<	hash_shift = 4;
117	<
118	<	components = NULL;
119	<
120	<	command_table = new LinkedCommand*[hash_size];
121	<	for( i=0; i<hash_size; i++ ) command_table[i] = NULL;
122	<
123	<	addHash( "forceField",    G_FORCEFIELD );
124	<	addHash( "nComponents",   G_NCOMPONENTS );
125	<	addHash( "targetTemp",    G_TARGETTEMP );
126	<	addHash( "ensemble",      G_ENSEMBLE );
127	<
128	<	addHash( "dt",            G_DT );
129	<	addHash( "runTime",       G_RUNTIME );
130	<
131	<	addHash( "initialConfig", G_INITIALCONFIG );
132	<	addHash( "finalConfig",   G_FINALCONFIG );
133	<	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);
115	>	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
116	>	DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
117	>	DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
118	>	DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
119	>	DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
120	>	DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
121	>	DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
122	>	DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
123	>	DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
124	>	DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
125	>	DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
126	>	DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
127	>	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
128	>	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
129	>	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
130	>	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
131	>	DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
132	>	DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
133	>	DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
134
135	<	strcpy( mixingRule,"standard");  //default mixing rules to standard.
136	<	usePBC = 1; //default  periodic boundry conditions to on
137	<	useRF  = 0;
138	<	useInitTime = 0; // default to pull init time from the init file
139	<	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;
135	>	DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
136	>	DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
137	>	DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 15);
138	>	DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
139	>	DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
140
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;
141
142	<	}
143	<
144	<	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	<	}
239	<
240	<	return 1;
241	<	}
242	<
243	<
244	<
245	<	int Globals::componentAssign( event* the_event ){
246	<
247	<	switch( the_event->evt.asmt.asmt_type ){
142	>	deprecatedKeywords_.insert("nComponents");
143	>	deprecatedKeywords_.insert("nZconstraints");
144	>	deprecatedKeywords_.insert("initialConfig");
145
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;
146		}
147
148	<	int Globals::componentEnd( event* the_event ){
149	<
150	<	the_event->err_msg = current_component->checkMe();
279	<	if( the_event->err_msg != NULL ) return 0;
280	<
281	<	return 1;
148	>	Globals::~Globals() {
149	>	MemoryUtils::deletePointers(components_);
150	>	MemoryUtils::deletePointers(zconstraints_);
151		}
152
153	<	int Globals::newZconstraint( event* the_event ){
154	<
153	>	void Globals::validate() {
154	>	DataHolder::validate();
155
156	<	int index = the_event->evt.blk_index;
157	<	char err[200];
158	<	current_zConstraint = new ZconStamp( index );
159	<
160	<	have_zConstraints = 1;
156	>	CheckParameter(ForceField, isNotEmpty());
157	>	CheckParameter(TargetTemp, isPositive());
158	>	CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT") || isEqualIgnoreCase("SMIPD"));
159	>	CheckParameter(Dt, isPositive());
160	>	CheckParameter(RunTime, isPositive());
161	>	CheckParameter(FinalConfig, isNotEmpty());
162	>	CheckParameter(SampleTime, isNonNegative());
163	>	CheckParameter(ResetTime, isNonNegative());
164	>	CheckParameter(StatusTime, isNonNegative());
165	>	CheckParameter(CutoffRadius, isPositive());
166	>	CheckParameter(SwitchingRadius, isNonNegative());
167	>	CheckParameter(Dielectric, isPositive());
168	>	CheckParameter(ThermalTime,  isNonNegative());
169	>	CheckParameter(TauThermostat, isPositive());
170	>	CheckParameter(TauBarostat, isPositive());
171	>	CheckParameter(ZconsTime, isPositive());
172	>	CheckParameter(ZconsTol, isPositive());
173	>	CheckParameter(Seed, isPositive());
174	>	CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
175	>	CheckParameter(MinimizerMaxIter, isPositive());
176	>	CheckParameter(MinimizerWriteFrq, isPositive());
177	>	CheckParameter(MinimizerStepSize, isPositive());
178	>	CheckParameter(MinimizerFTol, isPositive());
179	>	CheckParameter(MinimizerGTol, isPositive());
180	>	CheckParameter(MinimizerLSTol, isPositive());
181	>	CheckParameter(MinimizerLSMaxIter, isPositive());
182	>	CheckParameter(ZconsGap, isPositive());
183	>	CheckParameter(ZconsFixtime, isPositive());
184	>	CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
185	>	CheckParameter(ThermodynamicIntegrationK, isPositive());
186	>	CheckParameter(ForceFieldVariant, isNotEmpty());
187	>	CheckParameter(ForceFieldFileName, isNotEmpty());
188	>	CheckParameter(ThermIntDistSpringConst, isPositive());
189	>	CheckParameter(ThermIntThetaSpringConst, isPositive());
190	>	CheckParameter(ThermIntOmegaSpringConst, isPositive());
191	>	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
192	>	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
193	>	CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
194	>	CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
195	>	//CheckParameter(StatFileFormat,);
196	>	CheckParameter(OrthoBoxTolerance, isPositive());
197	>	CheckParameter(ThermIntDistSpringConst, isPositive());
198	>	CheckParameter(ThermIntThetaSpringConst, isPositive());
199	>	CheckParameter(ThermIntOmegaSpringConst, isPositive());
200	>	CheckParameter(DampingAlpha,isNonNegative());
201	>	CheckParameter(SkinThickness, isPositive());
202	>	CheckParameter(Viscosity, isNonNegative());
203	>	CheckParameter(BeadSize, isPositive());
204	>	CheckParameter(FrozenBufferRadius, isPositive());
205	>	CheckParameter(LangevinBufferRadius, isPositive());
206	>	CheckParameter(NeighborListNeighbors, isPositive());
207	>	CheckParameter(RNEMD_swapTime, isPositive());
208	>	CheckParameter(RNEMD_nBins, isPositive());
209	>	CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));
210
211	<	if( have_n_zConstraints && index < n_zConstraints )
212	<	zConstraints[index] = current_zConstraint;
213	<	else{
214	<	if( have_n_zConstraints ){
215	<	sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
298	<	index );
299	<	the_event->err_msg = strdup( err );
300	<	return 0;
211	>	for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
212	>	if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
213	>	std::ostringstream oss;
214	>	oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
215	>	throw OOPSEException(oss.str());
216		}
217	<	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;
217	>	}
218		}
312	–
313	–
314	–
315	–	int Globals::zConstraintAssign( event* the_event ){
316	–
317	–	switch( the_event->evt.asmt.asmt_type ){
219
220	<	case STRING:
221	<	return current_zConstraint->assignString( the_event->evt.asmt.lhs,
222	<	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;
220	>	bool Globals::addComponent(Component* comp) {
221	>	components_.push_back(comp);
222	>	return true;
223		}
224
225	<	int Globals::zConstraintEnd( event* the_event ){
226	<
227	<	the_event->err_msg = current_zConstraint->checkMe();
349	<	if( the_event->err_msg != NULL ) return 0;
350	<
351	<	return 1;
225	>	bool Globals::addZConsStamp(ZConsStamp* zcons) {
226	>	zconstraints_.push_back(zcons);
227	>	return true;
228		}
353	–
354	–	int Globals::globalAssign( event* the_event ){
355	–
356	–	int key;
357	–	int token;
358	–	interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
359	–	char* lhs = the_event->evt.asmt.lhs;
360	–	char err[300];
361	–
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;
229
230	<	case G_THERMALTIME:
231	<	switch( the_type ){
232	<
233	<	case STRING:
234	<	the_event->err_msg =
235	<	strdup( "Error in parsing meta-data file!\n\tthermalTime is not a double or int.\n" );
236	<	return 0;
237	<	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;
230	>	bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
231	>	std::string molStampName = molStamp->getName();
232	>	std::map<std::string, MoleculeStamp*>::iterator i;
233	>	bool ret = false;
234	>	i = moleculeStamps_.find(molStampName);
235	>	if (i == moleculeStamps_.end()) {
236	>	moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
237	>	ret = true;
238		} else {
239	<	// I'm a minimizer:
239	>	std::ostringstream oss;
240	>	oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
241	>	throw OOPSEException(oss.str());
242		}
243	<	} 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;
243	>	return ret;
244		}
245	+
246
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;
247		}
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();
1810	–	}
1811	–	#endif //is_mpi
1812	–	}
1813	–
1814	–	return key;
1815	–	}
1816	–
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;
1829	–	}

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