ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/src/io/Globals.cpp (file contents):
Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
Revision 1423 by gezelter, Tue Mar 30 15:05:13 2010 UTC

#	Line 1 | Line 1
1	<	/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
1	>	/*
2	>	* Copyright (c) 2005, 2010 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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
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"
48	–	#ifdef IS_MPI
49	–	#include "io/mpiBASS.h"
50	–	#endif // is_mpi
51
52	<	/*
53	<	* The following section lists all of the defined tokens for the
54	<	* 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 OpenMD {
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(MinimizerWriteFreq, "minimizerWriteFreq");
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(SurfaceTension, "surfaceTension");
92	>	DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
93	>	DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
94	>	DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
95	>	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
96	>	DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
97	>	DefineOptionalParameter(HydroPropFile, "HydroPropFile");
98	>	DefineOptionalParameter(Viscosity, "viscosity");
99	>	DefineOptionalParameter(BeadSize, "beadSize");
100	>	DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
101	>	DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
102	>	DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
103	>	DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
104	>	DefineOptionalParameter(MTM_Ce, "MTM_Ce");
105	>	DefineOptionalParameter(MTM_G, "MTM_G");
106	>	DefineOptionalParameter(MTM_Io, "MTM_Io");
107	>	DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
108	>	DefineOptionalParameter(MTM_R, "MTM_R");
109	>	DefineOptionalParameter(Alpha, "alpha");
110
111	<	//required parameters
112	<	#define G_FORCEFIELD         1
113	<	#define G_NCOMPONENTS        2
114	<	#define G_TARGETTEMP         3
115	<	#define G_ENSEMBLE           4
116	<	#define G_DT                 5
117	<	#define G_RUNTIME            6
111	>
112	>	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
113	>	DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
114	>	DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
115	>	DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
116	>	DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
117	>	DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
118	>	DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
119	>	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
120	>	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
121	>	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
122	>	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
123	>	DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
124	>	DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
125	>	DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
126
127	<	//optional parameters
128	<	#define G_INITIALCONFIG      7
129	<	#define G_FINALCONFIG        8
130	<	#define G_NMOL               9
131	<	#define G_DENSITY           10
132	<	#define G_BOX               11
133	<	#define G_BOXX              12
134	<	#define G_BOXY              13
135	<	#define G_BOXZ              14
136	<	#define G_SAMPLETIME        15
137	<	#define G_STATUSTIME        16
79	<	#define G_RCUT              17
80	<	#define G_RSW               18
81	<	#define G_DIELECTRIC        19
82	<	#define G_TEMPSET           20
83	<	#define G_THERMALTIME       21
84	<	#define G_USEPBC            22
85	<	#define G_MIXINGRULE        23
86	<	#define G_USERF             24
87	<	#define G_TARGETPRESSURE    25
88	<	#define G_TAUTHERMOSTAT     26
89	<	#define G_TAUBAROSTAT       27
90	<	#define G_ZCONSTIME         28
91	<	#define G_NZCONSTRAINTS     29
92	<	#define G_ZCONSTOL          30
93	<	#define G_ZCONSFORCEPOLICY  31
94	<	#define G_SEED              32
95	<	#define G_RESETTIME         33
96	<	#define G_USEINITTIME       34
97	<	#define G_USEINIT_XS_STATE  35
98	<	#define G_ORTHOBOXTOLERANCE 36
99	<	#define G_MINIMIZER         37
100	<	#define G_MIN_MAXITER       38
101	<	#define G_MIN_WRITEFRQ      39
102	<	#define G_MIN_STEPSIZE      40
103	<	#define G_MIN_FTOL          41
104	<	#define G_MIN_GTOL          42
105	<	#define G_MIN_LSTOL         43
106	<	#define G_MIN_LSMAXITER     44
107	<	#define G_ZCONSGAP          45
108	<	#define G_ZCONSFIXTIME      46
109	<	#define G_ZCONSUSINGSMD     47
110	<	#define G_USE_SOLID_THERM_INT     48
111	<	#define G_USE_LIQUID_THERM_INT    49
112	<	#define G_THERM_INT_LAMBDA  50
113	<	#define G_THERM_INT_K       51
114	<	#define G_FORCEFIELD_VARIANT 52
115	<	#define G_FORCEFIELD_FILENAME 53
116	<	Globals::Globals(){
117	<	initalize();
118	<	}
127	>	DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
128	>	DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
129	>	DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
130	>	DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
131	>	DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
132	>	DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
133	>	DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
134	>	DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
135	>	DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
136	>	DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
137	>	DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
138
120	–	Globals::~Globals(){
121	–	int i;
139
140	<	for( i=0; i<hash_size; i++ ){
141	<	if( command_table[i] != NULL ) delete command_table[i];
142	<	}
143	<	delete[] command_table;
144	<
145	<	if( components != NULL ){
146	<	for( i=0; i<n_components; i++ ) delete components[i];
147	<	delete[] components;
148	<	}
132	<	}
133	<
134	<	void Globals::initalize(){
135	<	int i;
136	<
137	<	hash_size = 23;
138	<	hash_shift = 4;
139	<
140	<	components = NULL;
141	<
142	<	command_table = new LinkedCommand*[hash_size];
143	<	for( i=0; i<hash_size; i++ ) command_table[i] = NULL;
144	<
145	<	addHash( "forceField",    G_FORCEFIELD );
146	<	addHash( "nComponents",   G_NCOMPONENTS );
147	<	addHash( "targetTemp",    G_TARGETTEMP );
148	<	addHash( "ensemble",      G_ENSEMBLE );
149	<
150	<	addHash( "dt",            G_DT );
151	<	addHash( "runTime",       G_RUNTIME );
152	<
153	<	addHash( "initialConfig", G_INITIALCONFIG );
154	<	addHash( "finalConfig",   G_FINALCONFIG );
155	<	addHash( "nMol",          G_NMOL );
156	<	addHash( "density",       G_DENSITY );
157	<	addHash( "box",           G_BOX );
158	<	addHash( "boxX",          G_BOXX );
159	<	addHash( "boxY",          G_BOXY );
160	<	addHash( "boxZ",          G_BOXZ );
161	<	addHash( "sampleTime",    G_SAMPLETIME );
162	<	addHash( "resetTime",     G_RESETTIME );
163	<	addHash( "statusTime",    G_STATUSTIME );
164	<	addHash( "cutoffRadius",  G_RCUT );
165	<	addHash( "switchingRadius",  G_RSW );
166	<	addHash( "dielectric",    G_DIELECTRIC );
167	<	addHash( "tempSet",       G_TEMPSET );
168	<	addHash( "thermalTime",   G_THERMALTIME );
169	<	addHash( "mixingRule",    G_MIXINGRULE);
170	<	addHash( "usePeriodicBoundaryConditions",        G_USEPBC);
171	<	addHash( "useReactionField",                     G_USERF );
172	<	addHash( "targetPressure",                       G_TARGETPRESSURE);
173	<	addHash( "tauThermostat",                        G_TAUTHERMOSTAT);
174	<	addHash( "tauBarostat",                          G_TAUBAROSTAT);
175	<	addHash( "zconsTime",                            G_ZCONSTIME);
176	<	addHash( "nZconstraints",                        G_NZCONSTRAINTS);
177	<	addHash( "zconsTol",                             G_ZCONSTOL);
178	<	addHash( "zconsForcePolicy",                     G_ZCONSFORCEPOLICY);
179	<	addHash( "seed",                                 G_SEED);
180	<	addHash( "useInitialTime",                       G_USEINITTIME);
181	<	addHash( "useInitialExtendedSystemState",        G_USEINIT_XS_STATE);
182	<	addHash( "orthoBoxTolerance",                    G_ORTHOBOXTOLERANCE);
183	<	addHash( "minimizer",                            G_MINIMIZER);
184	<	addHash( "minimizerMaxIter",                     G_MIN_MAXITER);
185	<	addHash( "minimizerWriteFrq",                    G_MIN_WRITEFRQ);
186	<	addHash( "minimizerStepSize",                    G_MIN_STEPSIZE);
187	<	addHash( "minimizerFTol",                        G_MIN_FTOL);
188	<	addHash( "minimizerGTol",                        G_MIN_GTOL);
189	<	addHash( "minimizerLSTol",                       G_MIN_LSTOL);
190	<	addHash( "minimizerLSMaxIter",                   G_MIN_LSMAXITER);
191	<	addHash( "zconsGap",                             G_ZCONSGAP);
192	<	addHash( "zconsFixtime",                         G_ZCONSFIXTIME);
193	<	addHash( "zconsUsingSMD",                        G_ZCONSUSINGSMD);
194	<	addHash( "useSolidThermInt",                     G_USE_SOLID_THERM_INT);
195	<	addHash( "useLiquidThermInt",                    G_USE_LIQUID_THERM_INT);
196	<	addHash( "thermodynamicIntegrationLambda",       G_THERM_INT_LAMBDA);
197	<	addHash( "thermodynamicIntegrationK",            G_THERM_INT_K);
198	<	addHash( "forceFieldVariant",                    G_FORCEFIELD_VARIANT);
199	<	addHash( "forceFieldFileName",                    G_FORCEFIELD_FILENAME);
200	<
201	<	strcpy( mixingRule,"standard");  //default mixing rules to standard.
202	<	usePBC = 1; //default  periodic boundry conditions to on
203	<	useRF  = 0;
204	<	useInitTime = 0; // default to pull init time from the init file
205	<	useInitXSstate = 0; // default to pull the extended state from the init file
206	<	orthoBoxTolerance = 1E-6;
207	<	useSolidThermInt = 0; // default solid-state thermodynamic integration to off
208	<	useLiquidThermInt = 0; // default liquid thermodynamic integration to off
209	<
210	<	have_force_field =  0;
211	<	have_n_components = 0;
212	<	have_target_temp =  0;
213	<	have_ensemble =     0;
214	<	have_dt =           0;
215	<	have_run_time =     0;
216	<
217	<	have_initial_config = 0;
218	<	have_final_config =   0;
219	<	have_n_mol =          0;
220	<	have_density =        0;
221	<	have_box =            0;
222	<	have_box_x =          0;
223	<	have_box_y =          0;
224	<	have_box_y =          0;
225	<	have_box_z =          0;
226	<	have_sample_time =    0;
227	<	have_status_time =    0;
228	<	have_reset_time =     0;
229	<	have_thermal_time =   0;
230	<	have_rcut =           0;
231	<	have_rsw =            0;
232	<	have_dielectric =     0;
233	<	have_tempSet =        0;
234	<	have_target_pressure =0;
235	<	have_q_mass =         0;
236	<	have_tau_thermostat = 0;
237	<	have_tau_barostat   = 0;
238	<	have_zcons_time     = 0;
239	<	have_n_zConstraints = 0;
240	<	have_zConstraints   = 0;
241	<	have_zcons_tol = 0;
242	<	have_zcons_gap = 0;
243	<	have_zcons_fixtime = 0;
244	<	have_zcons_using_smd = 0;
245	<	have_seed = 0;
246	<	have_minimizer = 0;
247	<	have_minimizer_maxiteration = 0;
248	<	have_minimizer_writefrq = 0;
249	<	have_minimizer_stepsize = 0;
250	<	have_minimizer_ftol = 0;
251	<	have_minimizer_gtol = 0;
252	<	have_minimizer_ls_tol = 0;
253	<	have_minimizer_ls_maxiteration = 0;
254	<	have_thermodynamic_integration_lambda = 0;
255	<	have_thermodynamic_integration_k = 0;
256	<	have_forcefield_variant = 0;
257	<	have_forcefield_filename = 0;
258	<
140	>	deprecatedKeywords_.insert("nComponents");
141	>	deprecatedKeywords_.insert("nZconstraints");
142	>	deprecatedKeywords_.insert("initialConfig");
143	>	deprecatedKeywords_.insert("thermIntDistSpringConst");
144	>	deprecatedKeywords_.insert("thermIntThetaSpringConst");
145	>	deprecatedKeywords_.insert("thermIntOmegaSpringConst");
146	>	deprecatedKeywords_.insert("useSolidThermInt");
147	>	deprecatedKeywords_.insert("useLiquidThermInt");
148	>
149		}
150
151	<	int Globals::newComponent( event* the_event ){
152	<
153	<	current_component = new Component;
154	<	int index = the_event->evt.blk_index;
265	<	char err[200];
266	<
267	<	if( have_n_components && index < n_components )
268	<	components[index] = current_component;
269	<	else{
270	<	if( have_n_components ){
271	<	sprintf( err, "meta-data parsing error: %d out of nComponents range",
272	<	index );
273	<	the_event->err_msg = strdup( err );
274	<	return 0;
275	<	}
276	<	else{
277	<	the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
278	<	" first component declaration." );
279	<	return 0;
280	<	}
281	<	}
282	<
283	<	return 1;
151	>	Globals::~Globals() {
152	>	MemoryUtils::deletePointers(components_);
153	>	MemoryUtils::deletePointers(zconstraints_);
154	>	MemoryUtils::deletePointers(restraints_);
155		}
156
157	+	void Globals::validate() {
158	+	DataHolder::validate();
159
160	+	CheckParameter(ForceField, isNotEmpty());
161	+	CheckParameter(TargetTemp, isPositive());
162	+	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"));
163	+	CheckParameter(Dt, isPositive());
164	+	CheckParameter(RunTime, isPositive());
165	+	CheckParameter(FinalConfig, isNotEmpty());
166	+	CheckParameter(SampleTime, isNonNegative());
167	+	CheckParameter(ResetTime, isNonNegative());
168	+	CheckParameter(StatusTime, isNonNegative());
169	+	CheckParameter(CutoffRadius, isPositive());
170	+	CheckParameter(SwitchingRadius, isNonNegative());
171	+	CheckParameter(Dielectric, isPositive());
172	+	CheckParameter(ThermalTime,  isNonNegative());
173	+	CheckParameter(TauThermostat, isPositive());
174	+	CheckParameter(TauBarostat, isPositive());
175	+	CheckParameter(ZconsTime, isPositive());
176	+	CheckParameter(ZconsTol, isPositive());
177	+	CheckParameter(Seed, isPositive());
178	+	CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
179	+	CheckParameter(MinimizerMaxIter, isPositive());
180	+	CheckParameter(MinimizerWriteFreq, isPositive());
181	+	CheckParameter(MinimizerStepSize, isPositive());
182	+	CheckParameter(MinimizerFTol, isPositive());
183	+	CheckParameter(MinimizerGTol, isPositive());
184	+	CheckParameter(MinimizerLSTol, isPositive());
185	+	CheckParameter(MinimizerLSMaxIter, isPositive());
186	+	CheckParameter(ZconsGap, isPositive());
187	+	CheckParameter(ZconsFixtime, isPositive());
188	+	CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
189	+	CheckParameter(ThermodynamicIntegrationK, isPositive());
190	+	CheckParameter(ForceFieldVariant, isNotEmpty());
191	+	CheckParameter(ForceFieldFileName, isNotEmpty());
192	+	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
193	+	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
194	+	CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
195	+	CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
196	+	//CheckParameter(StatFileFormat,);
197	+	CheckParameter(OrthoBoxTolerance, isPositive());
198	+	CheckParameter(DampingAlpha,isNonNegative());
199	+	CheckParameter(SkinThickness, isPositive());
200	+	CheckParameter(Viscosity, isNonNegative());
201	+	CheckParameter(BeadSize, isPositive());
202	+	CheckParameter(FrozenBufferRadius, isPositive());
203	+	CheckParameter(LangevinBufferRadius, isPositive());
204	+	CheckParameter(NeighborListNeighbors, isPositive());
205	+	CheckParameter(RNEMD_exchangeTime, isPositive());
206	+	CheckParameter(RNEMD_nBins, isPositive() && isEven());
207	+	CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale"));
208	+	CheckParameter(RNEMD_targetFlux, isNonNegative());
209	+	CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
210	+	CheckParameter(Alpha, isPositive());
211
212	<	int Globals::componentAssign( event* the_event ){
213	<
214	<	switch( the_event->evt.asmt.asmt_type ){
215	<
216	<	case STRING:
217	<	return current_component->assignString( the_event->evt.asmt.lhs,
218	<	the_event->evt.asmt.rhs.sval,
295	<	&(the_event->err_msg));
296	<	break;
297	<
298	<	case DOUBLE:
299	<	return current_component->assignDouble( the_event->evt.asmt.lhs,
300	<	the_event->evt.asmt.rhs.dval,
301	<	&(the_event->err_msg));
302	<	break;
303	<
304	<	case INT:
305	<	return current_component->assignInt( the_event->evt.asmt.lhs,
306	<	the_event->evt.asmt.rhs.ival,
307	<	&(the_event->err_msg));
308	<	break;
309	<
310	<	default:
311	<	the_event->err_msg = strdup( "Globals error. Invalid component"
312	<	" assignment type" );
313	<	return 0;
314	<	break;
212	>
213	>	for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
214	>	if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
215	>	std::ostringstream oss;
216	>	oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
217	>	throw OpenMDException(oss.str());
218	>	}
219		}
316	–	return 0;
220		}
318	–
319	–	int Globals::componentEnd( event* the_event ){
320	–
321	–	the_event->err_msg = current_component->checkMe();
322	–	if( the_event->err_msg != NULL ) return 0;
323	–
324	–	return 1;
325	–	}
326	–
327	–	int Globals::newZconstraint( event* the_event ){
221
222	<
223	<	int index = the_event->evt.blk_index;
224	<	char err[200];
332	<	current_zConstraint = new ZconStamp( index );
333	<
334	<	have_zConstraints = 1;
335	<
336	<	if( have_n_zConstraints && index < n_zConstraints )
337	<	zConstraints[index] = current_zConstraint;
338	<	else{
339	<	if( have_n_zConstraints ){
340	<	sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
341	<	index );
342	<	the_event->err_msg = strdup( err );
343	<	return 0;
344	<	}
345	<	else{
346	<	the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
347	<	" not given before"
348	<	" first zConstraint declaration." );
349	<	return 0;
350	<	}
351	<	}
352	<
353	<	return 1;
222	>	bool Globals::addComponent(Component* comp) {
223	>	components_.push_back(comp);
224	>	return true;
225		}
226
227	<
228	<
229	<	int Globals::zConstraintAssign( event* the_event ){
359	<
360	<	switch( the_event->evt.asmt.asmt_type ){
361	<
362	<	case STRING:
363	<	return current_zConstraint->assignString( the_event->evt.asmt.lhs,
364	<	the_event->evt.asmt.rhs.sval,
365	<	&(the_event->err_msg));
366	<	break;
367	<
368	<	case DOUBLE:
369	<	return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
370	<	the_event->evt.asmt.rhs.dval,
371	<	&(the_event->err_msg));
372	<	break;
373	<
374	<	case INT:
375	<	return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
376	<	the_event->evt.asmt.rhs.ival,
377	<	&(the_event->err_msg));
378	<	break;
379	<
380	<	default:
381	<	the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
382	<	" assignment type" );
383	<	return 0;
384	<	break;
385	<	}
386	<	return 0;
227	>	bool Globals::addZConsStamp(ZConsStamp* zcons) {
228	>	zconstraints_.push_back(zcons);
229	>	return true;
230		}
231
232	<	int Globals::zConstraintEnd( event* the_event ){
233	<
234	<	the_event->err_msg = current_zConstraint->checkMe();
392	<	if( the_event->err_msg != NULL ) return 0;
393	<
394	<	return 1;
232	>	bool Globals::addRestraintStamp(RestraintStamp* rest) {
233	>	restraints_.push_back(rest);
234	>	return true;
235		}
396	–
397	–	int Globals::globalAssign( event* the_event ){
398	–
399	–	int key;
400	–	int token;
401	–	interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
402	–	char* lhs = the_event->evt.asmt.lhs;
403	–	char err[300];
404	–
405	–	token = 0;
406	–	key = hash( lhs );
407	–	if( command_table[key] != NULL ) token = command_table[key]->match( lhs );
408	–
409	–	if( token ){
410	–
411	–	switch( token ){
412	–
413	–	case G_FORCEFIELD:
414	–	if( the_type == STRING ){
415	–	strcpy( force_field, the_event->evt.asmt.rhs.sval );
416	–	have_force_field = 1;
417	–	return 1;
418	–	}
419	–
420	–	the_event->err_msg =
421	–	strdup( "Error in parsing meta-data file!\n\tforceField was not a string assignment.\n" );
422	–	return 0;
423	–	break;
424	–
425	–	case G_NCOMPONENTS:
426	–	if( the_type == STRING ){
427	–	the_event->err_msg =
428	–	strdup("Error in parsing meta-data file!\n\tnComponents is not a double or an int.\n" );
429	–	return 0;
430	–	}
431	–
432	–	else if( the_type == DOUBLE ){
433	–	n_components = (int)the_event->evt.asmt.rhs.dval;
434	–	components = new Component*[n_components];
435	–	have_n_components = 1;
436	–	return 1;
437	–	}
438	–
439	–	else{
440	–	n_components = the_event->evt.asmt.rhs.ival;
441	–	components = new Component*[n_components];
442	–	have_n_components = 1;
443	–	return 1;
444	–	}
445	–	break;
446	–
447	–	case G_NZCONSTRAINTS:
448	–	if( the_type == STRING ){
449	–	the_event->err_msg =
450	–	strdup("Error in parsing meta-data file!\n\tnZconstraints is not a double or an int.\n" );
451	–	return 0;
452	–	}
453	–
454	–	else if( the_type == DOUBLE ){
455	–	n_zConstraints = (int)the_event->evt.asmt.rhs.dval;
456	–	zConstraints = new ZconStamp*[n_zConstraints];
457	–	have_n_zConstraints = 1;
458	–	return 1;
459	–	}
460	–
461	–	else{
462	–	n_zConstraints = the_event->evt.asmt.rhs.ival;
463	–	zConstraints = new ZconStamp*[n_zConstraints];
464	–	have_n_zConstraints = 1;
465	–	return 1;
466	–	}
467	–	break;
468	–
469	–	case G_TARGETTEMP:
470	–	switch( the_type ){
471	–
472	–	case STRING:
473	–	the_event->err_msg =
474	–	strdup( "Error in parsing meta-data file!\n\ttargetTemp is not a double or int.\n" );
475	–	return 0;
476	–	break;
477	–
478	–	case DOUBLE:
479	–	target_temp = the_event->evt.asmt.rhs.dval;
480	–	have_target_temp = 1;
481	–	return 1;
482	–	break;
483	–
484	–	case INT:
485	–	target_temp = (double)the_event->evt.asmt.rhs.ival;
486	–	have_target_temp = 1;
487	–	return 1;
488	–	break;
489	–
490	–	default:
491	–	the_event->err_msg =
492	–	strdup( "Error in parsing meta-data file!\n\ttargetTemp unrecognized.\n" );
493	–	return 0;
494	–	break;
495	–	}
496	–	break;
497	–
498	–	case G_ORTHOBOXTOLERANCE:
499	–	switch( the_type ){
500	–
501	–	case STRING:
502	–	the_event->err_msg =
503	–	strdup( "Error in parsing meta-data file!\n\torthoBoxTolerance is not a double or int.\n" );
504	–	return 0;
505	–	break;
506	–
507	–	case DOUBLE:
508	–	orthoBoxTolerance = the_event->evt.asmt.rhs.dval;
509	–	have_target_temp = 1;
510	–	return 1;
511	–	break;
512	–
513	–	case INT:
514	–	orthoBoxTolerance = (double)the_event->evt.asmt.rhs.ival;
515	–	have_target_temp = 1;
516	–	return 1;
517	–	break;
518	–
519	–	default:
520	–	the_event->err_msg =
521	–	strdup( "Global error.orthoBoxTolerance unrecognized.\n" );
522	–	return 0;
523	–	break;
524	–	}
525	–	break;
526	–
527	–	case G_ENSEMBLE:
528	–	if( the_type == STRING ){
529	–	strcpy( ensemble, the_event->evt.asmt.rhs.sval );
530	–	have_ensemble = 1;
531	–	return 1;
532	–	}
533	–
534	–	the_event->err_msg =
535	–	strdup( "Error in parsing meta-data file!\n\tensemble was not assigned to a string\n" );
536	–	return 0;
537	–	break;
538	–
539	–	case G_MIXINGRULE:
540	–	if( the_type == STRING ){
541	–	strcpy( mixingRule, the_event->evt.asmt.rhs.sval );
542	–	return 1;
543	–	}
544	–
545	–	the_event->err_msg =
546	–	strdup( "Error in parsing meta-data file!\n\tmixing rule was not assigned to a string\n" );
547	–	return 0;
548	–	break;
549	–
550	–	case G_DT:
551	–	switch( the_type ){
552	–
553	–	case STRING:
554	–	the_event->err_msg =
555	–	strdup( "Error in parsing meta-data file!\n\tdt is not a double or int.\n" );
556	–	return 0;
557	–	break;
558	–
559	–	case DOUBLE:
560	–	dt = the_event->evt.asmt.rhs.dval;
561	–	have_dt = 1;
562	–	return 1;
563	–	break;
564	–
565	–	case INT:
566	–	dt = (double)the_event->evt.asmt.rhs.ival;
567	–	have_dt = 1;
568	–	return 1;
569	–	break;
570	–
571	–	default:
572	–	the_event->err_msg =
573	–	strdup( "Error in parsing meta-data file!\n\tdt unrecognized.\n" );
574	–	return 0;
575	–	break;
576	–	}
577	–	break;
578	–
579	–	case G_RUNTIME:
580	–	switch( the_type ){
581	–
582	–	case STRING:
583	–	the_event->err_msg =
584	–	strdup( "Error in parsing meta-data file!\n\trunTime is not a double or int.\n" );
585	–	return 0;
586	–	break;
587	–
588	–	case DOUBLE:
589	–	run_time = the_event->evt.asmt.rhs.dval;
590	–	have_run_time = 1;
591	–	return 1;
592	–	break;
593	–
594	–	case INT:
595	–	run_time = (double)the_event->evt.asmt.rhs.ival;
596	–	have_run_time = 1;
597	–	return 1;
598	–	break;
599	–
600	–	default:
601	–	the_event->err_msg =
602	–	strdup( "Error in parsing meta-data file!\n\trunTime unrecognized.\n" );
603	–	return 0;
604	–	break;
605	–	}
606	–	break;
607	–
608	–	case G_INITIALCONFIG:
609	–	if( the_type == STRING ){
610	–	strcpy( initial_config, the_event->evt.asmt.rhs.sval );
611	–	have_initial_config = 1;
612	–	return 1;
613	–	}
614	–
615	–	the_event->err_msg =
616	–	strdup( "Error in parsing meta-data file!\n\tinitialConfig was not a string assignment.\n" );
617	–	return 0;
618	–	break;
619	–
620	–	case G_FINALCONFIG:
621	–	if( the_type == STRING ){
622	–	strcpy( final_config, the_event->evt.asmt.rhs.sval );
623	–	have_final_config = 1;
624	–	return 1;
625	–	}
626	–
627	–	the_event->err_msg =
628	–	strdup( "Error in parsing meta-data file!\n\tfinalConfig was not a string assignment.\n" );
629	–	return 0;
630	–	break;
631	–
632	–	case G_NMOL:
633	–	switch( the_type ){
634	–
635	–	case STRING:
636	–	the_event->err_msg =
637	–	strdup( "Error in parsing meta-data file!\n\tnMol is not a double or int.\n" );
638	–	return 0;
639	–	break;
640	–
641	–	case DOUBLE:
642	–	n_mol = (int)the_event->evt.asmt.rhs.dval;
643	–	have_n_mol = 1;
644	–	return 1;
645	–	break;
646	–
647	–	case INT:
648	–	n_mol = the_event->evt.asmt.rhs.ival;
649	–	have_n_mol = 1;
650	–	return 1;
651	–	break;
652	–
653	–	default:
654	–	the_event->err_msg =
655	–	strdup( "Error in parsing meta-data file!\n\tnMol unrecognized.\n" );
656	–	return 0;
657	–	break;
658	–	}
659	–	break;
660	–
661	–	case G_DENSITY:
662	–	switch( the_type ){
663	–
664	–	case STRING:
665	–	the_event->err_msg =
666	–	strdup( "Error in parsing meta-data file!\n\tdensity is not a double or int.\n" );
667	–	return 0;
668	–	break;
669	–
670	–	case DOUBLE:
671	–	density = the_event->evt.asmt.rhs.dval;
672	–	have_density = 1;
673	–	return 1;
674	–	break;
675	–
676	–	case INT:
677	–	density = (double)the_event->evt.asmt.rhs.ival;
678	–	have_density = 1;
679	–	return 1;
680	–	break;
681	–
682	–	default:
683	–	the_event->err_msg =
684	–	strdup( "Error in parsing meta-data file!\n\tdensity unrecognized.\n" );
685	–	return 0;
686	–	break;
687	–	}
688	–	break;
689	–
690	–	case G_BOX:
691	–	switch( the_type ){
692	–
693	–	case STRING:
694	–	the_event->err_msg =
695	–	strdup( "Error in parsing meta-data file!\n\tbox is not a double or int.\n" );
696	–	return 0;
697	–	break;
698	–
699	–	case DOUBLE:
700	–	box = the_event->evt.asmt.rhs.dval;
701	–	have_box = 1;
702	–	return 1;
703	–	break;
704	–
705	–	case INT:
706	–	box = (double)the_event->evt.asmt.rhs.ival;
707	–	have_box = 1;
708	–	return 1;
709	–	break;
710	–
711	–	default:
712	–	the_event->err_msg =
713	–	strdup( "Error in parsing meta-data file!\n\tbox unrecognized.\n" );
714	–	return 0;
715	–	break;
716	–	}
717	–	break;
718	–
719	–	case G_BOXX:
720	–	switch( the_type ){
721	–
722	–	case STRING:
723	–	the_event->err_msg =
724	–	strdup( "Error in parsing meta-data file!\n\tboxX is not a double or int.\n" );
725	–	return 0;
726	–	break;
727	–
728	–	case DOUBLE:
729	–	box_x = the_event->evt.asmt.rhs.dval;
730	–	have_box_x = 1;
731	–	return 1;
732	–	break;
733	–
734	–	case INT:
735	–	box_x = (double)the_event->evt.asmt.rhs.ival;
736	–	have_box_x = 1;
737	–	return 1;
738	–	break;
739	–
740	–	default:
741	–	the_event->err_msg =
742	–	strdup( "Error in parsing meta-data file!\n\tboxX unrecognized.\n" );
743	–	return 0;
744	–	break;
745	–	}
746	–	break;
747	–
748	–	case G_BOXY:
749	–	switch( the_type ){
750	–
751	–	case STRING:
752	–	the_event->err_msg =
753	–	strdup( "Error in parsing meta-data file!\n\tboxY is not a double or int.\n" );
754	–	return 0;
755	–	break;
756	–
757	–	case DOUBLE:
758	–	box_y = the_event->evt.asmt.rhs.dval;
759	–	have_box_y = 1;
760	–	return 1;
761	–	break;
762	–
763	–	case INT:
764	–	box_y = (double)the_event->evt.asmt.rhs.ival;
765	–	have_box_y = 1;
766	–	return 1;
767	–	break;
768	–
769	–	default:
770	–	the_event->err_msg =
771	–	strdup( "Error in parsing meta-data file!\n\tboxY unrecognized.\n" );
772	–	return 0;
773	–	break;
774	–	}
775	–	break;
776	–
777	–	case G_BOXZ:
778	–	switch( the_type ){
779	–
780	–	case STRING:
781	–	the_event->err_msg =
782	–	strdup( "Error in parsing meta-data file!\n\tboxZ is not a double or int.\n" );
783	–	return 0;
784	–	break;
785	–
786	–	case DOUBLE:
787	–	box_z = the_event->evt.asmt.rhs.dval;
788	–	have_box_z = 1;
789	–	return 1;
790	–	break;
791	–
792	–	case INT:
793	–	box_z = (double)the_event->evt.asmt.rhs.ival;
794	–	have_box_z = 1;
795	–	return 1;
796	–	break;
797	–
798	–	default:
799	–	the_event->err_msg =
800	–	strdup( "Error in parsing meta-data file!\n\tboxZ unrecognized.\n" );
801	–	return 0;
802	–	break;
803	–	}
804	–	break;
805	–
806	–	case G_SAMPLETIME:
807	–	switch( the_type ){
808	–
809	–	case STRING:
810	–	the_event->err_msg =
811	–	strdup( "Error in parsing meta-data file!\n\tsampleTime is not a double or int.\n" );
812	–	return 0;
813	–	break;
814	–
815	–	case DOUBLE:
816	–	sample_time = the_event->evt.asmt.rhs.dval;
817	–	have_sample_time = 1;
818	–	return 1;
819	–	break;
820	–
821	–	case INT:
822	–	sample_time = (double)the_event->evt.asmt.rhs.ival;
823	–	have_sample_time = 1;
824	–	return 1;
825	–	break;
826	–
827	–	default:
828	–	the_event->err_msg =
829	–	strdup( "Error in parsing meta-data file!\n\tsampleTime unrecognized.\n" );
830	–	return 0;
831	–	break;
832	–	}
833	–	break;
834	–
835	–	case G_STATUSTIME:
836	–	switch( the_type ){
837	–
838	–	case STRING:
839	–	the_event->err_msg =
840	–	strdup( "Error in parsing meta-data file!\n\tstatusTime is not a double or int.\n" );
841	–	return 0;
842	–	break;
843	–
844	–	case DOUBLE:
845	–	status_time = the_event->evt.asmt.rhs.dval;
846	–	have_status_time = 1;
847	–	return 1;
848	–	break;
849	–
850	–	case INT:
851	–	status_time = (double)the_event->evt.asmt.rhs.ival;
852	–	have_status_time = 1;
853	–	return 1;
854	–	break;
855	–
856	–	default:
857	–	the_event->err_msg =
858	–	strdup( "Error in parsing meta-data file!\n\tstatusTime unrecognized.\n" );
859	–	return 0;
860	–	break;
861	–	}
862	–	break;
236
237	<	case G_RESETTIME:
238	<	switch( the_type ){
239	<
240	<	case STRING:
241	<	the_event->err_msg =
242	<	strdup( "Error in parsing meta-data file!\n\tresetTime is not a double or int.\n" );
243	<	return 0;
244	<	break;
872	<
873	<	case DOUBLE:
874	<	resetTime = the_event->evt.asmt.rhs.dval;
875	<	have_reset_time = 1;
876	<	return 1;
877	<	break;
878	<
879	<	case INT:
880	<	resetTime = (double)the_event->evt.asmt.rhs.ival;
881	<	have_reset_time = 1;
882	<	return 1;
883	<	break;
884	<
885	<	default:
886	<	the_event->err_msg =
887	<	strdup( "Error in parsing meta-data file!\n\tresetTime unrecognized.\n" );
888	<	return 0;
889	<	break;
890	<	}
891	<	break;
892	<
893	<	case G_THERMALTIME:
894	<	switch( the_type ){
895	<
896	<	case STRING:
897	<	the_event->err_msg =
898	<	strdup( "Error in parsing meta-data file!\n\tthermalTime is not a double or int.\n" );
899	<	return 0;
900	<	break;
901	<
902	<	case DOUBLE:
903	<	thermal_time = the_event->evt.asmt.rhs.dval;
904	<	have_thermal_time = 1;
905	<	return 1;
906	<	break;
907	<
908	<	case INT:
909	<	thermal_time = (double)the_event->evt.asmt.rhs.ival;
910	<	have_thermal_time = 1;
911	<	return 1;
912	<	break;
913	<
914	<	default:
915	<	the_event->err_msg =
916	<	strdup( "Error in parsing meta-data file!\n\tthermalTime unrecognized.\n" );
917	<	return 0;
918	<	break;
919	<	}
920	<	break;
921	<
922	<	case G_RCUT:
923	<	switch( the_type ){
924	<
925	<	case STRING:
926	<	the_event->err_msg =
927	<	strdup( "Error in parsing meta-data file!\n\tcutoffRadius is not a double or int.\n" );
928	<	return 0;
929	<	break;
930	<
931	<	case DOUBLE:
932	<	rcut = the_event->evt.asmt.rhs.dval;
933	<	have_rcut = 1;
934	<	return 1;
935	<	break;
936	<
937	<	case INT:
938	<	rcut = (double)the_event->evt.asmt.rhs.ival;
939	<	have_rcut = 1;
940	<	return 1;
941	<	break;
942	<
943	<	default:
944	<	the_event->err_msg =
945	<	strdup( "Error in parsing meta-data file!\n\tcutoffRadius unrecognized.\n" );
946	<	return 0;
947	<	break;
948	<	}
949	<	break;
950	<
951	<	case G_RSW:
952	<	switch( the_type ){
953	<
954	<	case STRING:
955	<	the_event->err_msg =
956	<	strdup( "Error in parsing meta-data file!\n\tswitchingRadius is not a double or int.\n" );
957	<	return 0;
958	<	break;
959	<
960	<	case DOUBLE:
961	<	rsw = the_event->evt.asmt.rhs.dval;
962	<	have_rsw = 1;
963	<	return 1;
964	<	break;
965	<
966	<	case INT:
967	<	rsw = (double)the_event->evt.asmt.rhs.ival;
968	<	have_rsw = 1;
969	<	return 1;
970	<	break;
971	<
972	<	default:
973	<	the_event->err_msg =
974	<	strdup( "Error in parsing meta-data file!\n\tswitchingRadius unrecognized.\n" );
975	<	return 0;
976	<	break;
977	<	}
978	<	break;
979	<
980	<	case G_DIELECTRIC:
981	<	switch( the_type ){
982	<
983	<	case STRING:
984	<	the_event->err_msg =
985	<	strdup( "Error in parsing meta-data file!\n\tdielectric is not a double or int.\n" );
986	<	return 0;
987	<	break;
988	<
989	<	case DOUBLE:
990	<	dielectric = the_event->evt.asmt.rhs.dval;
991	<	have_dielectric = 1;
992	<	return 1;
993	<	break;
994	<
995	<	case INT:
996	<	dielectric = (double)the_event->evt.asmt.rhs.ival;
997	<	have_dielectric = 1;
998	<	return 1;
999	<	break;
1000	<
1001	<	default:
1002	<	the_event->err_msg =
1003	<	strdup( "Error in parsing meta-data file!\n\tdielectric unrecognized.\n" );
1004	<	return 0;
1005	<	break;
1006	<	}
1007	<	break;
1008	<
1009	<	case G_TEMPSET:
1010	<	if( the_type == STRING ){
1011	<
1012	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) tempSet = 1;
1013	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) tempSet = 0;
1014	<	else{
1015	<	the_event->err_msg =
1016	<	strdup( "Error in parsing meta-data file!\n\ttempSet was not \"true\" or \"false\".\n" );
1017	<	return 0;
1018	<	}
1019	<	have_tempSet = 1;
1020	<	return 1;
1021	<	}
1022	<
1023	<	the_event->err_msg =
1024	<	strdup( "Error in parsing meta-data file!\n\ttempSet was not \"true\" or \"false\".\n" );
1025	<	return 0;
1026	<	break;
1027	<
1028	<	case G_USEINITTIME:
1029	<	if( the_type == STRING ){
1030	<
1031	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useInitTime = 1;
1032	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useInitTime = 0;
1033	<	else{
1034	<	the_event->err_msg =
1035	<	strdup( "Error in parsing meta-data file!\n\tuseInitTime was not \"true\" or \"false\".\n" );
1036	<	return 0;
1037	<	}
1038	<	return 1;
1039	<	}
1040	<
1041	<	the_event->err_msg =
1042	<	strdup( "Error in parsing meta-data file!\n\tuseInitTime was not \"true\" or \"false\".\n" );
1043	<	return 0;
1044	<	break;
1045	<
1046	<	case G_USEINIT_XS_STATE:
1047	<	if( the_type == STRING ){
1048	<
1049	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval ))
1050	<	useInitXSstate = 1;
1051	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval ))
1052	<	useInitXSstate = 0;
1053	<	else{
1054	<	the_event->err_msg =
1055	<	strdup( "Error in parsing meta-data file!\n\tuseInitExtendedSystemState was not \"true\" or \"false\".\n" );
1056	<	return 0;
1057	<	}
1058	<	return 1;
1059	<	}
1060	<
1061	<	the_event->err_msg =
1062	<	strdup( "Error in parsing meta-data file!\n\tuseInitExtendedSystemState was not \"true\" or \"false\".\n" );
1063	<	return 0;
1064	<	break;
1065	<
1066	<	case G_USEPBC:
1067	<	if( the_type == STRING ){
1068	<
1069	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) usePBC = 1;
1070	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) usePBC = 0;
1071	<	else{
1072	<	the_event->err_msg =
1073	<	strdup( "Error in parsing meta-data file!\n\tusePeriodicBoundaryConditions was not \"true\" or \"false\".\n" );
1074	<	return 0;
1075	<	}
1076	<	return 1;
1077	<	}
1078	<
1079	<	the_event->err_msg =
1080	<	strdup( "Error in parsing meta-data file!\n\tusePeriodicBoundaryConditions was not \"true\" or \"false\".\n" );
1081	<	return 0;
1082	<	break;
1083	<
1084	<	case G_USERF:
1085	<	if( the_type == STRING ){
1086	<
1087	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useRF = 1;
1088	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useRF = 0;
1089	<	else{
1090	<	the_event->err_msg =
1091	<	strdup( "Error in parsing meta-data file!\n\tuseReactionField was not \"true\" or \"false\".\n" );
1092	<	return 0;
1093	<	}
1094	<	return 1;
1095	<	}
1096	<
1097	<	the_event->err_msg =
1098	<	strdup( "Error in parsing meta-data file!\n\tuseReactionField was not \"true\" or \"false\".\n" );
1099	<	return 0;
1100	<	break;
1101	<
1102	<	case G_TARGETPRESSURE:
1103	<	switch( the_type ){
1104	<
1105	<	case STRING:
1106	<	the_event->err_msg =
1107	<	strdup( "Error in parsing meta-data file!\n\ttargetPressure is not a double or int.\n" );
1108	<	return 0;
1109	<	break;
1110	<
1111	<	case DOUBLE:
1112	<	target_pressure = the_event->evt.asmt.rhs.dval;
1113	<	have_target_pressure = 1;
1114	<	return 1;
1115	<	break;
1116	<
1117	<	case INT:
1118	<	target_pressure = (double)the_event->evt.asmt.rhs.ival;
1119	<	have_target_pressure = 1;
1120	<	return 1;
1121	<	break;
1122	<
1123	<	default:
1124	<	the_event->err_msg =
1125	<	strdup( "Error in parsing meta-data file!\n\ttargetPressure unrecognized.\n" );
1126	<	return 0;
1127	<	break;
1128	<	}
1129	<	break;
1130	<
1131	<	case G_TAUTHERMOSTAT:
1132	<	switch( the_type ){
1133	<
1134	<	case STRING:
1135	<	the_event->err_msg =
1136	<	strdup( "Error in parsing meta-data file!\n\ttauThermostat is not a double or int.\n" );
1137	<	return 0;
1138	<	break;
1139	<
1140	<	case DOUBLE:
1141	<	tau_thermostat = the_event->evt.asmt.rhs.dval;
1142	<	have_tau_thermostat = 1;
1143	<	return 1;
1144	<	break;
1145	<
1146	<	case INT:
1147	<	tau_thermostat = (double)the_event->evt.asmt.rhs.ival;
1148	<	have_tau_thermostat = 1;
1149	<	return 1;
1150	<	break;
1151	<
1152	<	default:
1153	<	the_event->err_msg =
1154	<	strdup( "Error in parsing meta-data file!\n\ttauThermostat unrecognized.\n" );
1155	<	return 0;
1156	<	break;
1157	<	}
1158	<	break;
1159	<
1160	<	case G_TAUBAROSTAT:
1161	<	switch( the_type ){
1162	<
1163	<	case STRING:
1164	<	the_event->err_msg =
1165	<	strdup( "Error in parsing meta-data file!\n\ttauBarostat is not a double or int.\n" );
1166	<	return 0;
1167	<	break;
1168	<
1169	<	case DOUBLE:
1170	<	tau_barostat = the_event->evt.asmt.rhs.dval;
1171	<	have_tau_barostat = 1;
1172	<	return 1;
1173	<	break;
1174	<
1175	<	case INT:
1176	<	tau_barostat = (double)the_event->evt.asmt.rhs.ival;
1177	<	have_tau_barostat = 1;
1178	<	return 1;
1179	<	break;
1180	<
1181	<	default:
1182	<	the_event->err_msg =
1183	<	strdup( "Error in parsing meta-data file!\n\ttauBarostat unrecognized.\n" );
1184	<	return 0;
1185	<	break;
1186	<	}
1187	<	break;
1188	<
1189	<	case G_ZCONSTIME:
1190	<	switch( the_type ){
1191	<
1192	<	case STRING:
1193	<	the_event->err_msg =
1194	<	strdup( "Error in parsing meta-data file!\n\tzcons_time is not a double or int.\n" );
1195	<	return 0;
1196	<	break;
1197	<
1198	<	case DOUBLE:
1199	<	zcons_time = the_event->evt.asmt.rhs.dval;
1200	<	have_zcons_time = 1;
1201	<	return 1;
1202	<	break;
1203	<
1204	<	case INT:
1205	<	zcons_time = (double)the_event->evt.asmt.rhs.ival;
1206	<	have_zcons_time = 1;
1207	<	return 1;
1208	<	break;
1209	<
1210	<	default:
1211	<	the_event->err_msg =
1212	<	strdup( "Error in parsing meta-data file!\n\tzcons_time unrecognized.\n" );
1213	<	return 0;
1214	<	break;
1215	<	}
1216	<	break;
1217	<
1218	<	case G_ZCONSTOL:
1219	<	switch( the_type ){
1220	<
1221	<	case STRING:
1222	<	the_event->err_msg =
1223	<	strdup( "Error in parsing meta-data file!\n\tzcons_tol is not a double or int.\n" );
1224	<	return 0;
1225	<	break;
1226	<
1227	<	case DOUBLE:
1228	<	zcons_tol = the_event->evt.asmt.rhs.dval;
1229	<	have_zcons_tol = 1;
1230	<	return 1;
1231	<	break;
1232	<
1233	<	case INT:
1234	<	zcons_tol = (double)the_event->evt.asmt.rhs.ival;
1235	<	have_zcons_tol = 1;
1236	<	return 1;
1237	<	break;
1238	<
1239	<	default:
1240	<	the_event->err_msg =
1241	<	strdup( "Error in parsing meta-data file!\n\tzcons_ol unrecognized.\n" );
1242	<	return 0;
1243	<	break;
1244	<	}
1245	<	break;
1246	<
1247	<	case G_ZCONSFORCEPOLICY:
1248	<	switch( the_type ){
1249	<
1250	<	case STRING:
1251	<	strcpy(zconsForcePolicy, the_event->evt.asmt.rhs.sval);
1252	<
1253	<	for(int i = 0; zconsForcePolicy[i] != '\0'; i++)
1254	<	{
1255	<	zconsForcePolicy[i] = toupper(zconsForcePolicy[i]);
1256	<	}
1257	<	have_zcons_force_policy = 1;
1258	<	return 1;
1259	<	break;
1260	<
1261	<	case DOUBLE:
1262	<	the_event->err_msg =
1263	<	strdup( "Error in parsing meta-data file!\n\tzconsForcePolicy is not a double or int.\n" );
1264	<	return 0;
1265	<	break;
1266	<
1267	<	case INT:
1268	<	the_event->err_msg =
1269	<	strdup( "Error in parsing meta-data file!\n\tzconsForcePolicy is not a double or int.\n" );
1270	<	return 0;
1271	<	break;
1272	<
1273	<	default:
1274	<	the_event->err_msg =
1275	<	strdup( "Error in parsing meta-data file!\n\tzconsForcePolicy unrecognized.\n" );
1276	<	return 0;
1277	<	break;
1278	<	}
1279	<	break;
1280	<
1281	<	case G_ZCONSGAP:
1282	<	switch( the_type ){
1283	<
1284	<	case STRING:
1285	<	the_event->err_msg =
1286	<	strdup( "Error in parsing meta-data file!\n\tzcons_gap is not a double or int.\n" );
1287	<	return 0;
1288	<	break;
1289	<
1290	<	case DOUBLE:
1291	<	zcons_gap = the_event->evt.asmt.rhs.dval;
1292	<	have_zcons_gap= 1;
1293	<	return 1;
1294	<	break;
1295	<
1296	<	case INT:
1297	<	zcons_gap= (double)the_event->evt.asmt.rhs.ival;
1298	<	have_zcons_gap= 1;
1299	<	return 1;
1300	<	break;
1301	<
1302	<	default:
1303	<	the_event->err_msg =
1304	<	strdup( "Error in parsing meta-data file!\n\tzcons_gap unrecognized.\n" );
1305	<	return 0;
1306	<	break;
1307	<	}
1308	<	break;
1309	<
1310	<	case G_ZCONSFIXTIME:
1311	<	switch( the_type ){
1312	<
1313	<	case STRING:
1314	<	the_event->err_msg =
1315	<	strdup( "Error in parsing meta-data file!\n\tzcons_fixtime is not a double or int.\n" );
1316	<	return 0;
1317	<	break;
1318	<
1319	<	case DOUBLE:
1320	<	zcons_fixtime= the_event->evt.asmt.rhs.dval;
1321	<	have_zcons_fixtime= 1;
1322	<	return 1;
1323	<	break;
1324	<
1325	<	case INT:
1326	<	zcons_fixtime= (double)the_event->evt.asmt.rhs.ival;
1327	<	have_zcons_fixtime= 1;
1328	<	return 1;
1329	<	break;
1330	<
1331	<	default:
1332	<	the_event->err_msg =
1333	<	strdup( "Error in parsing meta-data file!\n\tzcons_fixtime unrecognized.\n" );
1334	<	return 0;
1335	<	break;
1336	<	}
1337	<	break;
1338	<
1339	<	case G_ZCONSUSINGSMD:
1340	<	switch( the_type ){
1341	<
1342	<	case STRING:
1343	<	the_event->err_msg =
1344	<	strdup( "Error in parsing meta-data file!\n\tzcons_fixtime is not an  int.\n" );
1345	<	return 0;
1346	<	break;
1347	<
1348	<	case DOUBLE:
1349	<	the_event->err_msg =
1350	<	strdup( "Error in parsing meta-data file!\n\tzcons_fixtime is not an  int.\n" );
1351	<	return 0;
1352	<	break;
1353	<
1354	<	case INT:
1355	<	zcons_using_smd= the_event->evt.asmt.rhs.ival;
1356	<	have_zcons_using_smd= 1;
1357	<	return 1;
1358	<	break;
1359	<
1360	<	default:
1361	<	the_event->err_msg =
1362	<	strdup( "Error in parsing meta-data file!\n\tzcons_usingsmd unrecognized.\n" );
1363	<	return 0;
1364	<	break;
1365	<	}
1366	<	break;
1367	<
1368	<	case G_MINIMIZER:
1369	<	switch( the_type ){
1370	<
1371	<	case STRING:
1372	<	strcpy(minimizer_name, the_event->evt.asmt.rhs.sval);
1373	<
1374	<	for(int i = 0; zconsForcePolicy[i] != '\0'; i++){
1375	<	zconsForcePolicy[i] = toupper(zconsForcePolicy[i]);
1376	<	}
1377	<	have_minimizer= 1;
1378	<	return 1;
1379	<	break;
1380	<
1381	<	case DOUBLE:
1382	<	the_event->err_msg =
1383	<	strdup( "Error in parsing meta-data file!\n\tminimizer_name is not a double or int.\n" );
1384	<	return 0;
1385	<	break;
1386	<
1387	<	case INT:
1388	<	the_event->err_msg =
1389	<	strdup( "Error in parsing meta-data file!\n\tminimizer_name is not a double or int.\n" );
1390	<	return 0;
1391	<	break;
1392	<
1393	<	default:
1394	<	the_event->err_msg =
1395	<	strdup( "Error in parsing meta-data file!\n\tminimizer_name unrecognized.\n" );
1396	<	return 0;
1397	<	break;
1398	<	}
1399	<	break;
1400	<
1401	<	case G_MIN_MAXITER:
1402	<	switch( the_type ){
1403	<
1404	<	case STRING:
1405	<	the_event->err_msg =
1406	<	strdup( "Error in parsing meta-data file!\n\tminimizer_maxiteration is not a double or int.\n" );
1407	<	return 1;
1408	<	break;
1409	<
1410	<	case DOUBLE:
1411	<	minimizer_maxiteration = (int)the_event->evt.asmt.rhs.dval;
1412	<	have_minimizer_maxiteration = 1;
1413	<	return 1;
1414	<	break;
1415	<
1416	<	case INT:
1417	<	minimizer_maxiteration = the_event->evt.asmt.rhs.ival;
1418	<	have_minimizer_maxiteration = 1;
1419	<	return 1;
1420	<	break;
1421	<
1422	<	default:
1423	<	the_event->err_msg =
1424	<	strdup( "Error in parsing meta-data file!\n\tminimizer_maxiteration unrecognized.\n" );
1425	<	return 0;
1426	<	break;
1427	<	}
1428	<	break;
1429	<
1430	<	case G_MIN_WRITEFRQ:
1431	<	switch( the_type ){
1432	<
1433	<	case STRING:
1434	<	the_event->err_msg =
1435	<	strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq is not an int.\n" );
1436	<	return 1;
1437	<	break;
1438	<
1439	<	case DOUBLE:
1440	<	the_event->err_msg =
1441	<	strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq is not an  int.\n" );
1442	<	return 1;
1443	<	break;
1444	<
1445	<	case INT:
1446	<	minimizer_writefrq= the_event->evt.asmt.rhs.ival;
1447	<	have_minimizer_writefrq = 1;
1448	<	return 1;
1449	<	break;
1450	<
1451	<	default:
1452	<	the_event->err_msg =
1453	<	strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq unrecognized.\n" );
1454	<	return 0;
1455	<	break;
1456	<	}
1457	<	break;
1458	<
1459	<	case G_MIN_STEPSIZE:
1460	<	switch( the_type ){
1461	<
1462	<	case STRING:
1463	<	the_event->err_msg =
1464	<	strdup( "Error in parsing meta-data file!\n\tminimizer_resetfrq is not a double or int.\n" );
1465	<	return 1;
1466	<	break;
1467	<
1468	<	case DOUBLE:
1469	<	minimizer_stepsize= the_event->evt.asmt.rhs.dval;
1470	<	have_minimizer_stepsize = 1;
1471	<	return 1;
1472	<	break;
1473	<
1474	<	case INT:
1475	<	minimizer_stepsize= the_event->evt.asmt.rhs.ival;
1476	<	have_minimizer_stepsize = 1;
1477	<	return 1;
1478	<	break;
1479	<
1480	<	default:
1481	<	the_event->err_msg =
1482	<	strdup( "Error in parsing meta-data file!\n\tminimizer_resetfrq unrecognized.\n" );
1483	<	return 0;
1484	<	break;
1485	<	}
1486	<	break;
1487	<
1488	<	case G_MIN_FTOL:
1489	<	switch( the_type ){
1490	<
1491	<	case STRING:
1492	<	the_event->err_msg =
1493	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ftol is not a double or int.\n" );
1494	<	return 1;
1495	<	break;
1496	<
1497	<	case DOUBLE:
1498	<	minimizer_ftol= the_event->evt.asmt.rhs.dval;
1499	<	have_minimizer_ftol = 1;
1500	<	return 1;
1501	<	break;
1502	<
1503	<	case INT:
1504	<	minimizer_ftol= the_event->evt.asmt.rhs.ival;
1505	<	have_minimizer_ftol = 1;
1506	<	return 1;
1507	<	break;
1508	<
1509	<	default:
1510	<	the_event->err_msg =
1511	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ftol unrecognized.\n" );
1512	<	return 0;
1513	<	break;
1514	<	}
1515	<	break;
1516	<
1517	<	case G_MIN_GTOL:
1518	<	switch( the_type ){
1519	<
1520	<	case STRING:
1521	<	the_event->err_msg =
1522	<	strdup( "Error in parsing meta-data file!\n\tminimizer_gtol is not a double or int.\n" );
1523	<	return 1;
1524	<	break;
1525	<
1526	<	case DOUBLE:
1527	<	minimizer_gtol= the_event->evt.asmt.rhs.dval;
1528	<	have_minimizer_gtol = 1;
1529	<	return 1;
1530	<	break;
1531	<
1532	<	case INT:
1533	<	minimizer_gtol= the_event->evt.asmt.rhs.ival;
1534	<	have_minimizer_gtol = 1;
1535	<	return 1;
1536	<	break;
1537	<
1538	<	default:
1539	<	the_event->err_msg =
1540	<	strdup( "Error in parsing meta-data file!\n\tminimizer_gtol unrecognized.\n" );
1541	<	return 0;
1542	<	break;
1543	<	}
1544	<	break;
1545	<
1546	<	case G_MIN_LSMAXITER:
1547	<	switch( the_type ){
1548	<
1549	<	case STRING:
1550	<	the_event->err_msg =
1551	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration is not an int.\n" );
1552	<	return 1;
1553	<	break;
1554	<
1555	<	case DOUBLE:
1556	<	the_event->err_msg =
1557	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration is not an int.\n" );
1558	<	return 1;
1559	<	break;
1560	<
1561	<	case INT:
1562	<	minimizer_ls_maxiteration = the_event->evt.asmt.rhs.ival;
1563	<	have_minimizer_ls_maxiteration = 1;
1564	<	return 1;
1565	<	break;
1566	<
1567	<	default:
1568	<	the_event->err_msg =
1569	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration unrecognized.\n" );
1570	<	return 0;
1571	<	break;
1572	<	}
1573	<	break;
1574	<
1575	<	case G_MIN_LSTOL:
1576	<	switch( the_type ){
1577	<
1578	<	case STRING:
1579	<	the_event->err_msg =
1580	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_tol is not a double or int.\n" );
1581	<	return 1;
1582	<	break;
1583	<
1584	<	case DOUBLE:
1585	<	minimizer_ls_tol= the_event->evt.asmt.rhs.dval;
1586	<	have_minimizer_ls_tol = 1;
1587	<	return 1;
1588	<	break;
1589	<
1590	<	case INT:
1591	<	minimizer_ls_tol= the_event->evt.asmt.rhs.ival;
1592	<	have_minimizer_ls_tol = 1;
1593	<	return 1;
1594	<	break;
1595	<
1596	<	default:
1597	<	the_event->err_msg =
1598	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_tol unrecognized.\n" );
1599	<	return 0;
1600	<	break;
1601	<	}
1602	<	break;
1603	<
1604	<	// add more token cases here.
1605	<	case G_SEED:
1606	<	switch( the_type ){
1607	<
1608	<	case STRING:
1609	<	the_event->err_msg =
1610	<	strdup( "Error in parsing meta-data file!\n\tseed is not a string.\n" );
1611	<	return 0;
1612	<	return 0;
1613	<	break;
1614	<
1615	<	case DOUBLE:
1616	<	have_seed = 1;
1617	<	seed = (int)the_event->evt.asmt.rhs.dval;
1618	<	return 1;
1619	<	break;
1620	<
1621	<	case INT:
1622	<	have_seed = 1;
1623	<	seed =  the_event->evt.asmt.rhs.ival ;
1624	<	return 1;
1625	<	break;
1626	<
1627	<	default:
1628	<	the_event->err_msg =
1629	<	strdup( "Error in parsing meta-data file!\n\tseed unrecognized.\n" );
1630	<	return 0;
1631	<	break;
1632	<	}
1633	<	break;
1634	<
1635	<	case G_USE_SOLID_THERM_INT:
1636	<	if( the_type == STRING ){
1637	<
1638	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useSolidThermInt = 1;
1639	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useSolidThermInt = 0;
1640	<	else{
1641	<	the_event->err_msg =
1642	<	strdup( "Error in parsing meta-data file!\n\tuseSolidThermInt was not \"true\" or \"false\".\n" );
1643	<	return 0;
1644	<	}
1645	<	return 1;
1646	<	}
1647	<
1648	<	the_event->err_msg =
1649	<	strdup( "Error in parsing meta-data file!\n\tuseSolidThermInt was not \"true\" or \"false\".\n" );
1650	<	return 0;
1651	<	break;
1652	<
1653	<	case G_USE_LIQUID_THERM_INT:
1654	<	if( the_type == STRING ){
1655	<
1656	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useLiquidThermInt = 1;
1657	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useLiquidThermInt = 0;
1658	<	else{
1659	<	the_event->err_msg =
1660	<	strdup( "Error in parsing meta-data file!\n\tuseLiquidThermInt was not \"true\" or \"false\".\n" );
1661	<	return 0;
1662	<	}
1663	<	return 1;
1664	<	}
1665	<
1666	<	the_event->err_msg =
1667	<	strdup( "Error in parsing meta-data file!\n\tuseLiquidThermInt was not \"true\" or \"false\".\n" );
1668	<	return 0;
1669	<	break;
1670	<
1671	<	case G_THERM_INT_LAMBDA:
1672	<	switch( the_type ){
1673	<
1674	<	case STRING:
1675	<	the_event->err_msg =
1676	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationLambda is not a double or int.\n" );
1677	<	return 1;
1678	<	break;
1679	<
1680	<	case DOUBLE:
1681	<	thermodynamic_integration_lambda = the_event->evt.asmt.rhs.dval;
1682	<	have_thermodynamic_integration_lambda = 1;
1683	<	return 1;
1684	<	break;
1685	<
1686	<	case INT:
1687	<	thermodynamic_integration_lambda = (double)the_event->evt.asmt.rhs.dval;
1688	<	have_thermodynamic_integration_lambda = 1;
1689	<	return 1;
1690	<	break;
1691	<
1692	<	default:
1693	<	the_event->err_msg =
1694	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationLambda unrecognized.\n" );
1695	<	return 0;
1696	<	break;
1697	<	}
1698	<	break;
1699	<
1700	<	case G_THERM_INT_K:
1701	<	switch( the_type ){
1702	<
1703	<	case STRING:
1704	<	the_event->err_msg =
1705	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationK is not a double or int.\n" );
1706	<	return 1;
1707	<	break;
1708	<
1709	<	case DOUBLE:
1710	<	thermodynamic_integration_k = the_event->evt.asmt.rhs.dval;
1711	<	have_thermodynamic_integration_k = 1;
1712	<	return 1;
1713	<	break;
1714	<
1715	<	case INT:
1716	<	thermodynamic_integration_k = (double)the_event->evt.asmt.rhs.dval;
1717	<	have_thermodynamic_integration_k = 1;
1718	<	return 1;
1719	<	break;
1720	<
1721	<	default:
1722	<	the_event->err_msg =
1723	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationK unrecognized.\n" );
1724	<	return 0;
1725	<	break;
1726	<	}
1727	<	break;
1728	<	case G_FORCEFIELD_VARIANT:
1729	<	if( the_type == STRING ){
1730	<	strcpy( forcefield_variant, the_event->evt.asmt.rhs.sval );
1731	<	have_forcefield_variant = 1;
1732	<	return 1;
1733	<	}
1734	<
1735	<	the_event->err_msg =
1736	<	strdup( "Error in parsing meta-data file!\n\tforceFieldVariant was not a string assignment.\n" );
1737	<	return 0;
1738	<	break;
1739	<	// add more token cases here.
1740	<
1741	<	case G_FORCEFIELD_FILENAME:
1742	<	if( the_type == STRING ){
1743	<	strcpy( forcefield_filename, the_event->evt.asmt.rhs.sval );
1744	<	have_forcefield_filename = 1;
1745	<	return 1;
1746	<	}
1747	<
1748	<	the_event->err_msg =
1749	<	strdup( "Error in parsing meta-data file!\n\tforceFieldFileName was not a string assignment.\n" );
1750	<	return 0;
1751	<	break;
1752	<	// add more token cases here.
1753	<	}
1754	<	}
1755	<
1756	<	switch( the_type ){
1757	<
1758	<	case STRING:
1759	<	sprintf( err,
1760	<	"\tUnrecognized assignment:\n"
1761	<	"\t\t-> %s = %s\n",
1762	<	lhs, the_event->evt.asmt.rhs.sval );
1763	<	break;
1764	<
1765	<	case DOUBLE:
1766	<	sprintf( err,
1767	<	"\tUnrecognized assignment:\n"
1768	<	"\t\t-> %s = %lf\n",
1769	<	lhs, the_event->evt.asmt.rhs.dval );
1770	<	break;
1771	<
1772	<	case INT:
1773	<	sprintf( err,
1774	<	"\tUnrecognized assignment:\n"
1775	<	"\t\t-> %s = %d\n",
1776	<	lhs, the_event->evt.asmt.rhs.ival );
1777	<	break;
1778	<
1779	<	default:
1780	<	sprintf( err,
1781	<	"\tUnrecognized assignment:\n"
1782	<	"\t\t-> %s = ?\n",
1783	<	lhs );
1784	<	break;
1785	<	}
1786	<
1787	<	the_event->err_msg = strdup( err );
1788	<	return 0;
1789	<	}
1790	<
1791	<	char* Globals::checkMe( void ){
1792	<
1793	<	char err[300];
1794	<	short int have_err = 0;
1795	<
1796	<	strcpy( err, "The following required keywords are missing:\n" );
1797	<
1798	<	if( !have_force_field ){
1799	<	strcat( err, "\t\t->forceField\n" );
1800	<	have_err= 1;
1801	<	}
1802	<
1803	<	if( !have_n_components ){
1804	<	strcat( err, "\t\t->nComponents\n" );
1805	<	have_err= 1;
1806	<	}
1807	<
1808	<
1809	<	if ( !have_ensemble ) {
1810	<	// I'm not doing MD:
1811	<	if ( !have_minimizer ) {
1812	<	// I'm not doing MD or minimization:
1813	<	strcat( err, "\t\t->either ensemble or minimizer must be set!\n" );
1814	<	have_err = 1;
237	>	bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
238	>	std::string molStampName = molStamp->getName();
239	>	std::map<std::string, MoleculeStamp*>::iterator i;
240	>	bool ret = false;
241	>	i = moleculeStamps_.find(molStampName);
242	>	if (i == moleculeStamps_.end()) {
243	>	moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
244	>	ret = true;
245		} else {
246	<	// I'm a minimizer:
246	>	std::ostringstream oss;
247	>	oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
248	>	throw OpenMDException(oss.str());
249		}
250	<	} else {
1819	<	// I *am* doing MD:
1820	<	if( !have_dt ){
1821	<	strcat( err, "\t\t->dt (timestep in fs)\n" );
1822	<	have_err= 1;
1823	<	}
1824	<	if( !have_run_time ){
1825	<	strcat( err, "\t\t->runTime (total run time in fs)\n" );
1826	<	have_err= 1;
1827	<	}
1828	<	}
1829	<
1830	<	if( have_err ) return strdup( err );
1831	<
1832	<	return NULL;
250	>	return ret;
251		}
252	+
253
1835	–	int Globals::globalEnd( event* the_event ){
1836	–
1837	–	the_event->err_msg = checkMe();
1838	–	if( the_event->err_msg != NULL ) return 0;
1839	–
1840	–	return 1;
254		}
1842	–
1843	–	int Globals::hash( char* text ){
1844	–
1845	–	register unsigned short int i = 0; // loop counter
1846	–	int key = 0; // the hash key
1847	–
1848	–	while( text[i] != '\0' ){
1849	–
1850	–	key = ( ( key << hash_shift ) + text[i] ) % hash_size;
1851	–
1852	–	i++;
1853	–	}
1854	–
1855	–	if( key < 0 ){
1856	–
1857	–	// if the key is less than zero, we've had an overflow error
1858	–
1859	–	sprintf( painCave.errMsg,
1860	–	"There has been an overflow error in the Globals' hash key.");
1861	–	painCave.isFatal = 1;
1862	–	simError();
1863	–	#ifdef IS_MPI
1864	–	if( painCave.isEventLoop ){
1865	–	if( worldRank == 0 ) mpiInterfaceExit();
1866	–	}
1867	–	#endif //is_mpi
1868	–	}
1869	–
1870	–	return key;
1871	–	}
1872	–
1873	–	void Globals::addHash( char* text, int token ){
1874	–
1875	–	int key;
1876	–	LinkedCommand* the_element;
1877	–
1878	–	the_element = new LinkedCommand;
1879	–	the_element->setValues( text, token );
1880	–
1881	–	key = hash( text );
1882	–
1883	–	the_element->setNext( command_table[key] );
1884	–	command_table[key] = the_element;
1885	–	}

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines