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 425 by tim, Thu Mar 10 20:28:17 2005 UTC vs.
Revision 1341 by skuang, Fri May 8 19:47:05 2009 UTC

#	Line 42 | Line 42
42		#include <stdlib.h>
43		#include <stdio.h>
44		#include <string.h>
45	+	#include <string>
46
47		#include "io/Globals.hpp"
48	+	#include "io/ParamConstraint.hpp"
49	+	#include "utils/MemoryUtils.hpp"
50		#include "utils/simError.h"
48	–	#ifdef IS_MPI
49	–	#include "io/mpiBASS.h"
50	–	#endif // is_mpi
51
52	<	/*
53	<	* The following section lists all of the defined tokens for the
54	<	* global assignment statements. All are prefixed with a G_ to avoid
55	<	* stepping on any previously defined enumerations.
56	<	*
57	<	* NOTE: tokens start at 1, 0 is a resrved token number
58	<	*/
59	<
60	<	//required parameters
61	<	#define G_FORCEFIELD         1
62	<	#define G_NCOMPONENTS        2
63	<	#define G_TARGETTEMP         3
64	<	#define G_ENSEMBLE           4
65	<	#define G_DT                 5
66	<	#define G_RUNTIME            6
67	<
68	<	//optional parameters
69	<	#define G_INITIALCONFIG      7
70	<	#define G_FINALCONFIG        8
71	<	#define G_NMOL               9
72	<	#define G_DENSITY           10
73	<	#define G_BOX               11
74	<	#define G_BOXX              12
75	<	#define G_BOXY              13
76	<	#define G_BOXZ              14
77	<	#define G_SAMPLETIME        15
78	<	#define G_STATUSTIME        16
79	<	#define G_RCUT              17
80	<	#define G_RSW               18
81	<	#define G_DIELECTRIC        19
82	<	#define G_TEMPSET           20
83	<	#define G_THERMALTIME       21
84	<	#define G_USEPBC            22
85	<	#define G_MIXINGRULE        23
86	<	#define G_USERF             24
87	<	#define G_TARGETPRESSURE    25
88	<	#define G_TAUTHERMOSTAT     26
89	<	#define G_TAUBAROSTAT       27
90	<	#define G_ZCONSTIME         28
91	<	#define G_NZCONSTRAINTS     29
92	<	#define G_ZCONSTOL          30
93	<	#define G_ZCONSFORCEPOLICY  31
94	<	#define G_SEED              32
95	<	#define G_RESETTIME         33
96	<	#define G_USEINITTIME       34
97	<	#define G_USEINIT_XS_STATE  35
98	<	#define G_ORTHOBOXTOLERANCE 36
99	<	#define G_MINIMIZER         37
100	<	#define G_MIN_MAXITER       38
101	<	#define G_MIN_WRITEFRQ      39
102	<	#define G_MIN_STEPSIZE      40
103	<	#define G_MIN_FTOL          41
104	<	#define G_MIN_GTOL          42
105	<	#define G_MIN_LSTOL         43
106	<	#define G_MIN_LSMAXITER     44
107	<	#define G_ZCONSGAP          45
108	<	#define G_ZCONSFIXTIME      46
109	<	#define G_ZCONSUSINGSMD     47
110	<	#define G_USE_SOLID_THERM_INT     48
111	<	#define G_USE_LIQUID_THERM_INT    49
112	<	#define G_THERM_INT_LAMBDA  50
113	<	#define G_THERM_INT_K       51
114	<	#define G_FORCEFIELD_VARIANT 52
115	<	#define G_FORCEFIELD_FILENAME 53
116	<	#define G_THERM_INT_DIST_SPRING  54
117	<	#define G_THERM_INT_THETA_SPRING 55
118	<	#define G_THERM_INT_OMEGA_SPRING 56
119	<
120	<	Globals::Globals(){
121	<	initalize();
122	<	}
123	<
124	<	Globals::~Globals(){
125	<	int i;
126	<	if( components != NULL ){
127	<	for( i=0; i<n_components; i++ ) delete components[i];
128	<	delete[] components;
129	<	}
130	<	}
131	<
132	<	void Globals::initalize(){
133	<	int i;
134	<
135	<	components = NULL;
136	<
137	<	command_table.insert(CommandMapType::value_type("forceField", G_FORCEFIELD));
138	<	command_table.insert(CommandMapType::value_type("nComponents", G_NCOMPONENTS));
139	<	command_table.insert(CommandMapType::value_type("targetTemp", G_TARGETTEMP));
140	<	command_table.insert(CommandMapType::value_type("ensemble", G_ENSEMBLE));
141	<	command_table.insert(CommandMapType::value_type("dt", G_DT));
142	<	command_table.insert(CommandMapType::value_type("runTime", G_RUNTIME));
143	<	command_table.insert(CommandMapType::value_type("initialConfig", G_INITIALCONFIG));
144	<	command_table.insert(CommandMapType::value_type("finalConfig", G_FINALCONFIG));
145	<	command_table.insert(CommandMapType::value_type("nMol", G_NMOL));
146	<	command_table.insert(CommandMapType::value_type("density", G_DENSITY));
147	<	command_table.insert(CommandMapType::value_type("box", G_BOX));
148	<	command_table.insert(CommandMapType::value_type("boxX", G_BOXX));
149	<	command_table.insert(CommandMapType::value_type("boxY", G_BOXY));
150	<	command_table.insert(CommandMapType::value_type("boxZ", G_BOXZ));
151	<	command_table.insert(CommandMapType::value_type("sampleTime", G_SAMPLETIME));
152	<	command_table.insert(CommandMapType::value_type("resetTime", G_RESETTIME));
153	<	command_table.insert(CommandMapType::value_type("statusTime", G_STATUSTIME));
154	<	command_table.insert(CommandMapType::value_type("cutoffRadius", G_RCUT));
155	<	command_table.insert(CommandMapType::value_type("switchingRadius", G_RSW));
156	<	command_table.insert(CommandMapType::value_type("dielectric", G_DIELECTRIC));
157	<	command_table.insert(CommandMapType::value_type("tempSet", G_TEMPSET));
158	<	command_table.insert(CommandMapType::value_type("thermalTime", G_THERMALTIME));
159	<	command_table.insert(CommandMapType::value_type("mixingRule", G_MIXINGRULE));
160	<	command_table.insert(CommandMapType::value_type("usePeriodicBoundaryConditions", G_USEPBC));
161	<	command_table.insert(CommandMapType::value_type("useReactionField", G_USERF));
162	<	command_table.insert(CommandMapType::value_type("targetPressure", G_TARGETPRESSURE));
163	<	command_table.insert(CommandMapType::value_type("tauThermostat", G_TAUTHERMOSTAT));
164	<	command_table.insert(CommandMapType::value_type("tauBarostat", G_TAUBAROSTAT));
165	<	command_table.insert(CommandMapType::value_type("zconsTime", G_ZCONSTIME));
166	<	command_table.insert(CommandMapType::value_type("nZconstraints", G_NZCONSTRAINTS));
167	<	command_table.insert(CommandMapType::value_type("zconsTol", G_ZCONSTOL));
168	<	command_table.insert(CommandMapType::value_type("zconsForcePolicy", G_ZCONSFORCEPOLICY));
169	<	command_table.insert(CommandMapType::value_type("seed", G_SEED));
170	<	command_table.insert(CommandMapType::value_type("useInitialTime", G_USEINITTIME));
171	<	command_table.insert(CommandMapType::value_type("useInitialExtendedSystemState", G_USEINIT_XS_STATE));
172	<	command_table.insert(CommandMapType::value_type("orthoBoxTolerance", G_ORTHOBOXTOLERANCE));
173	<	command_table.insert(CommandMapType::value_type("minimizer", G_MINIMIZER));
174	<	command_table.insert(CommandMapType::value_type("minimizerMaxIter", G_MIN_MAXITER));
175	<	command_table.insert(CommandMapType::value_type("minimizerWriteFrq", G_MIN_WRITEFRQ));
176	<	command_table.insert(CommandMapType::value_type("minimizerStepSize", G_MIN_STEPSIZE));
177	<	command_table.insert(CommandMapType::value_type("minimizerFTol", G_MIN_FTOL));
178	<	command_table.insert(CommandMapType::value_type("minimizerGTol", G_MIN_GTOL));
179	<	command_table.insert(CommandMapType::value_type("minimizerLSTol", G_MIN_LSTOL));
180	<	command_table.insert(CommandMapType::value_type("minimizerLSMaxIter", G_MIN_LSMAXITER));
181	<	command_table.insert(CommandMapType::value_type("zconsGap", G_ZCONSGAP));
182	<	command_table.insert(CommandMapType::value_type("zconsFixtime", G_ZCONSFIXTIME));
183	<	command_table.insert(CommandMapType::value_type("zconsUsingSMD", G_ZCONSUSINGSMD));
184	<	command_table.insert(CommandMapType::value_type("useSolidThermInt", G_USE_SOLID_THERM_INT));
185	<	command_table.insert(CommandMapType::value_type("useLiquidThermInt", G_USE_LIQUID_THERM_INT));
186	<	command_table.insert(CommandMapType::value_type("thermodynamicIntegrationLambda", G_THERM_INT_LAMBDA));
187	<	command_table.insert(CommandMapType::value_type("thermodynamicIntegrationK", G_THERM_INT_K));
188	<	command_table.insert(CommandMapType::value_type("forceFieldVariant", G_FORCEFIELD_VARIANT));
189	<	command_table.insert(CommandMapType::value_type("forceFieldFileName", G_FORCEFIELD_FILENAME));
190	<	command_table.insert(CommandMapType::value_type("thermIntDistSpringConst", G_THERM_INT_DIST_SPRING));
191	<	command_table.insert(CommandMapType::value_type("thermIntThetaSpringConst", G_THERM_INT_THETA_SPRING));
192	<	command_table.insert(CommandMapType::value_type("thermIntOmegaSpringConst", G_THERM_INT_OMEGA_SPRING));
193	<
194	<
195	<	strcpy( mixingRule,"standard");  //default mixing rules to standard.
196	<	usePBC = 1; //default  periodic boundry conditions to on
197	<	useRF  = 0;
198	<	useInitTime = 0; // default to pull init time from the init file
199	<	useInitXSstate = 0; // default to pull the extended state from the init file
200	<	orthoBoxTolerance = 1E-6;
201	<	useSolidThermInt = 0; // default solid-state thermodynamic integration to off
202	<	useLiquidThermInt = 0; // default liquid thermodynamic integration to off
203	<
204	<	have_force_field =  0;
205	<	have_n_components = 0;
206	<	have_target_temp =  0;
207	<	have_ensemble =     0;
208	<	have_dt =           0;
209	<	have_run_time =     0;
210	<
211	<	have_initial_config = 0;
212	<	have_final_config =   0;
213	<	have_n_mol =          0;
214	<	have_density =        0;
215	<	have_box =            0;
216	<	have_box_x =          0;
217	<	have_box_y =          0;
218	<	have_box_y =          0;
219	<	have_box_z =          0;
220	<	have_sample_time =    0;
221	<	have_status_time =    0;
222	<	have_reset_time =     0;
223	<	have_thermal_time =   0;
224	<	have_rcut =           0;
225	<	have_rsw =            0;
226	<	have_dielectric =     0;
227	<	have_tempSet =        0;
228	<	have_target_pressure =0;
229	<	have_q_mass =         0;
230	<	have_tau_thermostat = 0;
231	<	have_tau_barostat   = 0;
232	<	have_zcons_time     = 0;
233	<	have_n_zConstraints = 0;
234	<	have_zConstraints   = 0;
235	<	have_zcons_tol = 0;
236	<	have_zcons_gap = 0;
237	<	have_zcons_fixtime = 0;
238	<	have_zcons_using_smd = 0;
239	<	have_seed = 0;
240	<	have_minimizer = 0;
241	<	have_minimizer_maxiteration = 0;
242	<	have_minimizer_writefrq = 0;
243	<	have_minimizer_stepsize = 0;
244	<	have_minimizer_ftol = 0;
245	<	have_minimizer_gtol = 0;
246	<	have_minimizer_ls_tol = 0;
247	<	have_minimizer_ls_maxiteration = 0;
248	<	have_thermodynamic_integration_lambda = 0;
249	<	have_thermodynamic_integration_k = 0;
250	<	have_forcefield_variant = 0;
251	<	have_forcefield_filename = 0;
252	<	have_dist_spring_constant =  0;
253	<	have_theta_spring_constant = 0;
254	<	have_omega_spring_constant = 0;
255	<	}
256	<
257	<	int Globals::newComponent( event* the_event ){
258	<
259	<	current_component = new Component;
260	<	int index = the_event->evt.blk_index;
261	<	char err[200];
262	<
263	<	if( have_n_components && index < n_components )
264	<	components[index] = current_component;
265	<	else{
266	<	if( have_n_components ){
267	<	sprintf( err, "meta-data parsing error: %d out of nComponents range",
268	<	index );
269	<	the_event->err_msg = strdup( err );
270	<	return 0;
271	<	}
272	<	else{
273	<	the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
274	<	" first component declaration." );
275	<	return 0;
276	<	}
277	<	}
52	>	namespace oopse {
53	>	Globals::Globals() {
54	>	DefineParameter(ForceField, "forceField")
55
56	<	return 1;
57	<	}
56	>	DefineOptionalParameter(TargetTemp, "targetTemp");
57	>	DefineOptionalParameter(Ensemble, "ensemble");
58	>	DefineOptionalParameter(Dt, "dt");
59	>	DefineOptionalParameter(RunTime, "runTime");
60	>	DefineOptionalParameter(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
114	+
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	+	DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
136	+	DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
137	+	DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
138	+	DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
139	+	DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
140	+
141
142	<	int Globals::componentAssign( event* the_event ){
143	<
144	<	switch( the_event->evt.asmt.asmt_type ){
142	>	deprecatedKeywords_.insert("nComponents");
143	>	deprecatedKeywords_.insert("nZconstraints");
144	>	deprecatedKeywords_.insert("initialConfig");
145
288	–	case STRING:
289	–	return current_component->assignString( the_event->evt.asmt.lhs,
290	–	the_event->evt.asmt.rhs.sval,
291	–	&(the_event->err_msg));
292	–	break;
293	–
294	–	case DOUBLE:
295	–	return current_component->assignDouble( the_event->evt.asmt.lhs,
296	–	the_event->evt.asmt.rhs.dval,
297	–	&(the_event->err_msg));
298	–	break;
299	–
300	–	case INT:
301	–	return current_component->assignInt( the_event->evt.asmt.lhs,
302	–	the_event->evt.asmt.rhs.ival,
303	–	&(the_event->err_msg));
304	–	break;
305	–
306	–	default:
307	–	the_event->err_msg = strdup( "Globals error. Invalid component"
308	–	" assignment type" );
309	–	return 0;
310	–	break;
311	–	}
312	–	return 0;
146		}
147
148	<	int Globals::componentEnd( event* the_event ){
149	<
150	<	the_event->err_msg = current_component->checkMe();
318	<	if( the_event->err_msg != NULL ) return 0;
319	<
320	<	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() && isEven());
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",
337	<	index );
338	<	the_event->err_msg = strdup( err );
339	<	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{
342	<	the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
343	<	" not given before"
344	<	" first zConstraint declaration." );
345	<	return 0;
346	<	}
347	<	}
348	<
349	<	return 1;
217	>	}
218		}
351	–
352	–
353	–
354	–	int Globals::zConstraintAssign( event* the_event ){
355	–
356	–	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,
361	<	&(the_event->err_msg));
362	<	break;
363	<
364	<	case DOUBLE:
365	<	return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
366	<	the_event->evt.asmt.rhs.dval,
367	<	&(the_event->err_msg));
368	<	break;
369	<
370	<	case INT:
371	<	return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
372	<	the_event->evt.asmt.rhs.ival,
373	<	&(the_event->err_msg));
374	<	break;
375	<
376	<	default:
377	<	the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
378	<	" assignment type" );
379	<	return 0;
380	<	break;
381	<	}
382	<	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();
388	<	if( the_event->err_msg != NULL ) return 0;
389	<
390	<	return 1;
225	>	bool Globals::addZConsStamp(ZConsStamp* zcons) {
226	>	zconstraints_.push_back(zcons);
227	>	return true;
228		}
392	–
393	–	int Globals::globalAssign( event* the_event ){
394	–
395	–	int key;
396	–	int token;
397	–	interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
398	–	char* lhs = the_event->evt.asmt.lhs;
399	–	char err[300];
400	–
401	–	token = 0;
402	–
403	–	CommandMapType::iterator iter;
404	–	std::string keyword(lhs);
405	–	iter = command_table.find(keyword);
406	–	if (iter != command_table.end()) {
407	–	token = iter->second;
408	–	}
409	–
410	–	if( token ){
411	–
412	–	switch( token ){
413	–
414	–	case G_FORCEFIELD:
415	–	if( the_type == STRING ){
416	–	strcpy( force_field, the_event->evt.asmt.rhs.sval );
417	–	have_force_field = 1;
418	–	return 1;
419	–	}
420	–
421	–	the_event->err_msg =
422	–	strdup( "Error in parsing meta-data file!\n\tforceField was not a string assignment.\n" );
423	–	return 0;
424	–	break;
425	–
426	–	case G_NCOMPONENTS:
427	–	if( the_type == STRING ){
428	–	the_event->err_msg =
429	–	strdup("Error in parsing meta-data file!\n\tnComponents is not a double or an int.\n" );
430	–	return 0;
431	–	}
432	–
433	–	else if( the_type == DOUBLE ){
434	–	n_components = (int)the_event->evt.asmt.rhs.dval;
435	–	components = new Component*[n_components];
436	–	have_n_components = 1;
437	–	return 1;
438	–	}
439	–
440	–	else{
441	–	n_components = the_event->evt.asmt.rhs.ival;
442	–	components = new Component*[n_components];
443	–	have_n_components = 1;
444	–	return 1;
445	–	}
446	–	break;
447	–
448	–	case G_NZCONSTRAINTS:
449	–	if( the_type == STRING ){
450	–	the_event->err_msg =
451	–	strdup("Error in parsing meta-data file!\n\tnZconstraints is not a double or an int.\n" );
452	–	return 0;
453	–	}
454	–
455	–	else if( the_type == DOUBLE ){
456	–	n_zConstraints = (int)the_event->evt.asmt.rhs.dval;
457	–	zConstraints = new ZconStamp*[n_zConstraints];
458	–	have_n_zConstraints = 1;
459	–	return 1;
460	–	}
461	–
462	–	else{
463	–	n_zConstraints = the_event->evt.asmt.rhs.ival;
464	–	zConstraints = new ZconStamp*[n_zConstraints];
465	–	have_n_zConstraints = 1;
466	–	return 1;
467	–	}
468	–	break;
469	–
470	–	case G_TARGETTEMP:
471	–	switch( the_type ){
472	–
473	–	case STRING:
474	–	the_event->err_msg =
475	–	strdup( "Error in parsing meta-data file!\n\ttargetTemp is not a double or int.\n" );
476	–	return 0;
477	–	break;
478	–
479	–	case DOUBLE:
480	–	target_temp = the_event->evt.asmt.rhs.dval;
481	–	have_target_temp = 1;
482	–	return 1;
483	–	break;
484	–
485	–	case INT:
486	–	target_temp = (double)the_event->evt.asmt.rhs.ival;
487	–	have_target_temp = 1;
488	–	return 1;
489	–	break;
490	–
491	–	default:
492	–	the_event->err_msg =
493	–	strdup( "Error in parsing meta-data file!\n\ttargetTemp unrecognized.\n" );
494	–	return 0;
495	–	break;
496	–	}
497	–	break;
498	–
499	–	case G_ORTHOBOXTOLERANCE:
500	–	switch( the_type ){
501	–
502	–	case STRING:
503	–	the_event->err_msg =
504	–	strdup( "Error in parsing meta-data file!\n\torthoBoxTolerance is not a double or int.\n" );
505	–	return 0;
506	–	break;
507	–
508	–	case DOUBLE:
509	–	orthoBoxTolerance = the_event->evt.asmt.rhs.dval;
510	–	have_target_temp = 1;
511	–	return 1;
512	–	break;
513	–
514	–	case INT:
515	–	orthoBoxTolerance = (double)the_event->evt.asmt.rhs.ival;
516	–	have_target_temp = 1;
517	–	return 1;
518	–	break;
519	–
520	–	default:
521	–	the_event->err_msg =
522	–	strdup( "Global error.orthoBoxTolerance unrecognized.\n" );
523	–	return 0;
524	–	break;
525	–	}
526	–	break;
527	–
528	–	case G_ENSEMBLE:
529	–	if( the_type == STRING ){
530	–	strcpy( ensemble, the_event->evt.asmt.rhs.sval );
531	–	have_ensemble = 1;
532	–	return 1;
533	–	}
534	–
535	–	the_event->err_msg =
536	–	strdup( "Error in parsing meta-data file!\n\tensemble was not assigned to a string\n" );
537	–	return 0;
538	–	break;
539	–
540	–	case G_MIXINGRULE:
541	–	if( the_type == STRING ){
542	–	strcpy( mixingRule, the_event->evt.asmt.rhs.sval );
543	–	return 1;
544	–	}
545	–
546	–	the_event->err_msg =
547	–	strdup( "Error in parsing meta-data file!\n\tmixing rule was not assigned to a string\n" );
548	–	return 0;
549	–	break;
550	–
551	–	case G_DT:
552	–	switch( the_type ){
553	–
554	–	case STRING:
555	–	the_event->err_msg =
556	–	strdup( "Error in parsing meta-data file!\n\tdt is not a double or int.\n" );
557	–	return 0;
558	–	break;
559	–
560	–	case DOUBLE:
561	–	dt = the_event->evt.asmt.rhs.dval;
562	–	have_dt = 1;
563	–	return 1;
564	–	break;
565	–
566	–	case INT:
567	–	dt = (double)the_event->evt.asmt.rhs.ival;
568	–	have_dt = 1;
569	–	return 1;
570	–	break;
571	–
572	–	default:
573	–	the_event->err_msg =
574	–	strdup( "Error in parsing meta-data file!\n\tdt unrecognized.\n" );
575	–	return 0;
576	–	break;
577	–	}
578	–	break;
579	–
580	–	case G_RUNTIME:
581	–	switch( the_type ){
582	–
583	–	case STRING:
584	–	the_event->err_msg =
585	–	strdup( "Error in parsing meta-data file!\n\trunTime is not a double or int.\n" );
586	–	return 0;
587	–	break;
588	–
589	–	case DOUBLE:
590	–	run_time = the_event->evt.asmt.rhs.dval;
591	–	have_run_time = 1;
592	–	return 1;
593	–	break;
594	–
595	–	case INT:
596	–	run_time = (double)the_event->evt.asmt.rhs.ival;
597	–	have_run_time = 1;
598	–	return 1;
599	–	break;
600	–
601	–	default:
602	–	the_event->err_msg =
603	–	strdup( "Error in parsing meta-data file!\n\trunTime unrecognized.\n" );
604	–	return 0;
605	–	break;
606	–	}
607	–	break;
608	–
609	–	case G_INITIALCONFIG:
610	–	if( the_type == STRING ){
611	–	strcpy( initial_config, the_event->evt.asmt.rhs.sval );
612	–	have_initial_config = 1;
613	–	return 1;
614	–	}
615	–
616	–	the_event->err_msg =
617	–	strdup( "Error in parsing meta-data file!\n\tinitialConfig was not a string assignment.\n" );
618	–	return 0;
619	–	break;
620	–
621	–	case G_FINALCONFIG:
622	–	if( the_type == STRING ){
623	–	strcpy( final_config, the_event->evt.asmt.rhs.sval );
624	–	have_final_config = 1;
625	–	return 1;
626	–	}
627	–
628	–	the_event->err_msg =
629	–	strdup( "Error in parsing meta-data file!\n\tfinalConfig was not a string assignment.\n" );
630	–	return 0;
631	–	break;
632	–
633	–	case G_NMOL:
634	–	switch( the_type ){
635	–
636	–	case STRING:
637	–	the_event->err_msg =
638	–	strdup( "Error in parsing meta-data file!\n\tnMol is not a double or int.\n" );
639	–	return 0;
640	–	break;
641	–
642	–	case DOUBLE:
643	–	n_mol = (int)the_event->evt.asmt.rhs.dval;
644	–	have_n_mol = 1;
645	–	return 1;
646	–	break;
647	–
648	–	case INT:
649	–	n_mol = the_event->evt.asmt.rhs.ival;
650	–	have_n_mol = 1;
651	–	return 1;
652	–	break;
653	–
654	–	default:
655	–	the_event->err_msg =
656	–	strdup( "Error in parsing meta-data file!\n\tnMol unrecognized.\n" );
657	–	return 0;
658	–	break;
659	–	}
660	–	break;
661	–
662	–	case G_DENSITY:
663	–	switch( the_type ){
664	–
665	–	case STRING:
666	–	the_event->err_msg =
667	–	strdup( "Error in parsing meta-data file!\n\tdensity is not a double or int.\n" );
668	–	return 0;
669	–	break;
670	–
671	–	case DOUBLE:
672	–	density = the_event->evt.asmt.rhs.dval;
673	–	have_density = 1;
674	–	return 1;
675	–	break;
676	–
677	–	case INT:
678	–	density = (double)the_event->evt.asmt.rhs.ival;
679	–	have_density = 1;
680	–	return 1;
681	–	break;
682	–
683	–	default:
684	–	the_event->err_msg =
685	–	strdup( "Error in parsing meta-data file!\n\tdensity unrecognized.\n" );
686	–	return 0;
687	–	break;
688	–	}
689	–	break;
690	–
691	–	case G_BOX:
692	–	switch( the_type ){
693	–
694	–	case STRING:
695	–	the_event->err_msg =
696	–	strdup( "Error in parsing meta-data file!\n\tbox is not a double or int.\n" );
697	–	return 0;
698	–	break;
699	–
700	–	case DOUBLE:
701	–	box = the_event->evt.asmt.rhs.dval;
702	–	have_box = 1;
703	–	return 1;
704	–	break;
705	–
706	–	case INT:
707	–	box = (double)the_event->evt.asmt.rhs.ival;
708	–	have_box = 1;
709	–	return 1;
710	–	break;
711	–
712	–	default:
713	–	the_event->err_msg =
714	–	strdup( "Error in parsing meta-data file!\n\tbox unrecognized.\n" );
715	–	return 0;
716	–	break;
717	–	}
718	–	break;
719	–
720	–	case G_BOXX:
721	–	switch( the_type ){
722	–
723	–	case STRING:
724	–	the_event->err_msg =
725	–	strdup( "Error in parsing meta-data file!\n\tboxX is not a double or int.\n" );
726	–	return 0;
727	–	break;
728	–
729	–	case DOUBLE:
730	–	box_x = the_event->evt.asmt.rhs.dval;
731	–	have_box_x = 1;
732	–	return 1;
733	–	break;
734	–
735	–	case INT:
736	–	box_x = (double)the_event->evt.asmt.rhs.ival;
737	–	have_box_x = 1;
738	–	return 1;
739	–	break;
740	–
741	–	default:
742	–	the_event->err_msg =
743	–	strdup( "Error in parsing meta-data file!\n\tboxX unrecognized.\n" );
744	–	return 0;
745	–	break;
746	–	}
747	–	break;
748	–
749	–	case G_BOXY:
750	–	switch( the_type ){
751	–
752	–	case STRING:
753	–	the_event->err_msg =
754	–	strdup( "Error in parsing meta-data file!\n\tboxY is not a double or int.\n" );
755	–	return 0;
756	–	break;
757	–
758	–	case DOUBLE:
759	–	box_y = the_event->evt.asmt.rhs.dval;
760	–	have_box_y = 1;
761	–	return 1;
762	–	break;
763	–
764	–	case INT:
765	–	box_y = (double)the_event->evt.asmt.rhs.ival;
766	–	have_box_y = 1;
767	–	return 1;
768	–	break;
769	–
770	–	default:
771	–	the_event->err_msg =
772	–	strdup( "Error in parsing meta-data file!\n\tboxY unrecognized.\n" );
773	–	return 0;
774	–	break;
775	–	}
776	–	break;
777	–
778	–	case G_BOXZ:
779	–	switch( the_type ){
780	–
781	–	case STRING:
782	–	the_event->err_msg =
783	–	strdup( "Error in parsing meta-data file!\n\tboxZ is not a double or int.\n" );
784	–	return 0;
785	–	break;
786	–
787	–	case DOUBLE:
788	–	box_z = the_event->evt.asmt.rhs.dval;
789	–	have_box_z = 1;
790	–	return 1;
791	–	break;
792	–
793	–	case INT:
794	–	box_z = (double)the_event->evt.asmt.rhs.ival;
795	–	have_box_z = 1;
796	–	return 1;
797	–	break;
798	–
799	–	default:
800	–	the_event->err_msg =
801	–	strdup( "Error in parsing meta-data file!\n\tboxZ unrecognized.\n" );
802	–	return 0;
803	–	break;
804	–	}
805	–	break;
806	–
807	–	case G_SAMPLETIME:
808	–	switch( the_type ){
809	–
810	–	case STRING:
811	–	the_event->err_msg =
812	–	strdup( "Error in parsing meta-data file!\n\tsampleTime is not a double or int.\n" );
813	–	return 0;
814	–	break;
815	–
816	–	case DOUBLE:
817	–	sample_time = the_event->evt.asmt.rhs.dval;
818	–	have_sample_time = 1;
819	–	return 1;
820	–	break;
821	–
822	–	case INT:
823	–	sample_time = (double)the_event->evt.asmt.rhs.ival;
824	–	have_sample_time = 1;
825	–	return 1;
826	–	break;
827	–
828	–	default:
829	–	the_event->err_msg =
830	–	strdup( "Error in parsing meta-data file!\n\tsampleTime unrecognized.\n" );
831	–	return 0;
832	–	break;
833	–	}
834	–	break;
835	–
836	–	case G_STATUSTIME:
837	–	switch( the_type ){
838	–
839	–	case STRING:
840	–	the_event->err_msg =
841	–	strdup( "Error in parsing meta-data file!\n\tstatusTime is not a double or int.\n" );
842	–	return 0;
843	–	break;
844	–
845	–	case DOUBLE:
846	–	status_time = the_event->evt.asmt.rhs.dval;
847	–	have_status_time = 1;
848	–	return 1;
849	–	break;
850	–
851	–	case INT:
852	–	status_time = (double)the_event->evt.asmt.rhs.ival;
853	–	have_status_time = 1;
854	–	return 1;
855	–	break;
856	–
857	–	default:
858	–	the_event->err_msg =
859	–	strdup( "Error in parsing meta-data file!\n\tstatusTime unrecognized.\n" );
860	–	return 0;
861	–	break;
862	–	}
863	–	break;
864	–
865	–	case G_RESETTIME:
866	–	switch( the_type ){
867	–
868	–	case STRING:
869	–	the_event->err_msg =
870	–	strdup( "Error in parsing meta-data file!\n\tresetTime is not a double or int.\n" );
871	–	return 0;
872	–	break;
873	–
874	–	case DOUBLE:
875	–	resetTime = the_event->evt.asmt.rhs.dval;
876	–	have_reset_time = 1;
877	–	return 1;
878	–	break;
879	–
880	–	case INT:
881	–	resetTime = (double)the_event->evt.asmt.rhs.ival;
882	–	have_reset_time = 1;
883	–	return 1;
884	–	break;
885	–
886	–	default:
887	–	the_event->err_msg =
888	–	strdup( "Error in parsing meta-data file!\n\tresetTime unrecognized.\n" );
889	–	return 0;
890	–	break;
891	–	}
892	–	break;
893	–
894	–	case G_THERMALTIME:
895	–	switch( the_type ){
896	–
897	–	case STRING:
898	–	the_event->err_msg =
899	–	strdup( "Error in parsing meta-data file!\n\tthermalTime is not a double or int.\n" );
900	–	return 0;
901	–	break;
902	–
903	–	case DOUBLE:
904	–	thermal_time = the_event->evt.asmt.rhs.dval;
905	–	have_thermal_time = 1;
906	–	return 1;
907	–	break;
908	–
909	–	case INT:
910	–	thermal_time = (double)the_event->evt.asmt.rhs.ival;
911	–	have_thermal_time = 1;
912	–	return 1;
913	–	break;
914	–
915	–	default:
916	–	the_event->err_msg =
917	–	strdup( "Error in parsing meta-data file!\n\tthermalTime unrecognized.\n" );
918	–	return 0;
919	–	break;
920	–	}
921	–	break;
922	–
923	–	case G_RCUT:
924	–	switch( the_type ){
925	–
926	–	case STRING:
927	–	the_event->err_msg =
928	–	strdup( "Error in parsing meta-data file!\n\tcutoffRadius is not a double or int.\n" );
929	–	return 0;
930	–	break;
931	–
932	–	case DOUBLE:
933	–	rcut = the_event->evt.asmt.rhs.dval;
934	–	have_rcut = 1;
935	–	return 1;
936	–	break;
937	–
938	–	case INT:
939	–	rcut = (double)the_event->evt.asmt.rhs.ival;
940	–	have_rcut = 1;
941	–	return 1;
942	–	break;
943	–
944	–	default:
945	–	the_event->err_msg =
946	–	strdup( "Error in parsing meta-data file!\n\tcutoffRadius unrecognized.\n" );
947	–	return 0;
948	–	break;
949	–	}
950	–	break;
951	–
952	–	case G_RSW:
953	–	switch( the_type ){
954	–
955	–	case STRING:
956	–	the_event->err_msg =
957	–	strdup( "Error in parsing meta-data file!\n\tswitchingRadius is not a double or int.\n" );
958	–	return 0;
959	–	break;
960	–
961	–	case DOUBLE:
962	–	rsw = the_event->evt.asmt.rhs.dval;
963	–	have_rsw = 1;
964	–	return 1;
965	–	break;
966	–
967	–	case INT:
968	–	rsw = (double)the_event->evt.asmt.rhs.ival;
969	–	have_rsw = 1;
970	–	return 1;
971	–	break;
972	–
973	–	default:
974	–	the_event->err_msg =
975	–	strdup( "Error in parsing meta-data file!\n\tswitchingRadius unrecognized.\n" );
976	–	return 0;
977	–	break;
978	–	}
979	–	break;
980	–
981	–	case G_DIELECTRIC:
982	–	switch( the_type ){
983	–
984	–	case STRING:
985	–	the_event->err_msg =
986	–	strdup( "Error in parsing meta-data file!\n\tdielectric is not a double or int.\n" );
987	–	return 0;
988	–	break;
989	–
990	–	case DOUBLE:
991	–	dielectric = the_event->evt.asmt.rhs.dval;
992	–	have_dielectric = 1;
993	–	return 1;
994	–	break;
995	–
996	–	case INT:
997	–	dielectric = (double)the_event->evt.asmt.rhs.ival;
998	–	have_dielectric = 1;
999	–	return 1;
1000	–	break;
1001	–
1002	–	default:
1003	–	the_event->err_msg =
1004	–	strdup( "Error in parsing meta-data file!\n\tdielectric unrecognized.\n" );
1005	–	return 0;
1006	–	break;
1007	–	}
1008	–	break;
1009	–
1010	–	case G_TEMPSET:
1011	–	if( the_type == STRING ){
1012	–
1013	–	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) tempSet = 1;
1014	–	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) tempSet = 0;
1015	–	else{
1016	–	the_event->err_msg =
1017	–	strdup( "Error in parsing meta-data file!\n\ttempSet was not \"true\" or \"false\".\n" );
1018	–	return 0;
1019	–	}
1020	–	have_tempSet = 1;
1021	–	return 1;
1022	–	}
1023	–
1024	–	the_event->err_msg =
1025	–	strdup( "Error in parsing meta-data file!\n\ttempSet was not \"true\" or \"false\".\n" );
1026	–	return 0;
1027	–	break;
1028	–
1029	–	case G_USEINITTIME:
1030	–	if( the_type == STRING ){
1031	–
1032	–	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useInitTime = 1;
1033	–	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useInitTime = 0;
1034	–	else{
1035	–	the_event->err_msg =
1036	–	strdup( "Error in parsing meta-data file!\n\tuseInitTime was not \"true\" or \"false\".\n" );
1037	–	return 0;
1038	–	}
1039	–	return 1;
1040	–	}
1041	–
1042	–	the_event->err_msg =
1043	–	strdup( "Error in parsing meta-data file!\n\tuseInitTime was not \"true\" or \"false\".\n" );
1044	–	return 0;
1045	–	break;
1046	–
1047	–	case G_USEINIT_XS_STATE:
1048	–	if( the_type == STRING ){
1049	–
1050	–	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval ))
1051	–	useInitXSstate = 1;
1052	–	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval ))
1053	–	useInitXSstate = 0;
1054	–	else{
1055	–	the_event->err_msg =
1056	–	strdup( "Error in parsing meta-data file!\n\tuseInitExtendedSystemState was not \"true\" or \"false\".\n" );
1057	–	return 0;
1058	–	}
1059	–	return 1;
1060	–	}
1061	–
1062	–	the_event->err_msg =
1063	–	strdup( "Error in parsing meta-data file!\n\tuseInitExtendedSystemState was not \"true\" or \"false\".\n" );
1064	–	return 0;
1065	–	break;
1066	–
1067	–	case G_USEPBC:
1068	–	if( the_type == STRING ){
1069	–
1070	–	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) usePBC = 1;
1071	–	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) usePBC = 0;
1072	–	else{
1073	–	the_event->err_msg =
1074	–	strdup( "Error in parsing meta-data file!\n\tusePeriodicBoundaryConditions was not \"true\" or \"false\".\n" );
1075	–	return 0;
1076	–	}
1077	–	return 1;
1078	–	}
1079	–
1080	–	the_event->err_msg =
1081	–	strdup( "Error in parsing meta-data file!\n\tusePeriodicBoundaryConditions was not \"true\" or \"false\".\n" );
1082	–	return 0;
1083	–	break;
1084	–
1085	–	case G_USERF:
1086	–	if( the_type == STRING ){
1087	–
1088	–	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useRF = 1;
1089	–	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useRF = 0;
1090	–	else{
1091	–	the_event->err_msg =
1092	–	strdup( "Error in parsing meta-data file!\n\tuseReactionField was not \"true\" or \"false\".\n" );
1093	–	return 0;
1094	–	}
1095	–	return 1;
1096	–	}
1097	–
1098	–	the_event->err_msg =
1099	–	strdup( "Error in parsing meta-data file!\n\tuseReactionField was not \"true\" or \"false\".\n" );
1100	–	return 0;
1101	–	break;
1102	–
1103	–	case G_TARGETPRESSURE:
1104	–	switch( the_type ){
1105	–
1106	–	case STRING:
1107	–	the_event->err_msg =
1108	–	strdup( "Error in parsing meta-data file!\n\ttargetPressure is not a double or int.\n" );
1109	–	return 0;
1110	–	break;
1111	–
1112	–	case DOUBLE:
1113	–	target_pressure = the_event->evt.asmt.rhs.dval;
1114	–	have_target_pressure = 1;
1115	–	return 1;
1116	–	break;
1117	–
1118	–	case INT:
1119	–	target_pressure = (double)the_event->evt.asmt.rhs.ival;
1120	–	have_target_pressure = 1;
1121	–	return 1;
1122	–	break;
1123	–
1124	–	default:
1125	–	the_event->err_msg =
1126	–	strdup( "Error in parsing meta-data file!\n\ttargetPressure unrecognized.\n" );
1127	–	return 0;
1128	–	break;
1129	–	}
1130	–	break;
1131	–
1132	–	case G_TAUTHERMOSTAT:
1133	–	switch( the_type ){
1134	–
1135	–	case STRING:
1136	–	the_event->err_msg =
1137	–	strdup( "Error in parsing meta-data file!\n\ttauThermostat is not a double or int.\n" );
1138	–	return 0;
1139	–	break;
1140	–
1141	–	case DOUBLE:
1142	–	tau_thermostat = the_event->evt.asmt.rhs.dval;
1143	–	have_tau_thermostat = 1;
1144	–	return 1;
1145	–	break;
1146	–
1147	–	case INT:
1148	–	tau_thermostat = (double)the_event->evt.asmt.rhs.ival;
1149	–	have_tau_thermostat = 1;
1150	–	return 1;
1151	–	break;
1152	–
1153	–	default:
1154	–	the_event->err_msg =
1155	–	strdup( "Error in parsing meta-data file!\n\ttauThermostat unrecognized.\n" );
1156	–	return 0;
1157	–	break;
1158	–	}
1159	–	break;
1160	–
1161	–	case G_TAUBAROSTAT:
1162	–	switch( the_type ){
1163	–
1164	–	case STRING:
1165	–	the_event->err_msg =
1166	–	strdup( "Error in parsing meta-data file!\n\ttauBarostat is not a double or int.\n" );
1167	–	return 0;
1168	–	break;
1169	–
1170	–	case DOUBLE:
1171	–	tau_barostat = the_event->evt.asmt.rhs.dval;
1172	–	have_tau_barostat = 1;
1173	–	return 1;
1174	–	break;
1175	–
1176	–	case INT:
1177	–	tau_barostat = (double)the_event->evt.asmt.rhs.ival;
1178	–	have_tau_barostat = 1;
1179	–	return 1;
1180	–	break;
1181	–
1182	–	default:
1183	–	the_event->err_msg =
1184	–	strdup( "Error in parsing meta-data file!\n\ttauBarostat unrecognized.\n" );
1185	–	return 0;
1186	–	break;
1187	–	}
1188	–	break;
1189	–
1190	–	case G_ZCONSTIME:
1191	–	switch( the_type ){
1192	–
1193	–	case STRING:
1194	–	the_event->err_msg =
1195	–	strdup( "Error in parsing meta-data file!\n\tzcons_time is not a double or int.\n" );
1196	–	return 0;
1197	–	break;
1198	–
1199	–	case DOUBLE:
1200	–	zcons_time = the_event->evt.asmt.rhs.dval;
1201	–	have_zcons_time = 1;
1202	–	return 1;
1203	–	break;
1204	–
1205	–	case INT:
1206	–	zcons_time = (double)the_event->evt.asmt.rhs.ival;
1207	–	have_zcons_time = 1;
1208	–	return 1;
1209	–	break;
1210	–
1211	–	default:
1212	–	the_event->err_msg =
1213	–	strdup( "Error in parsing meta-data file!\n\tzcons_time unrecognized.\n" );
1214	–	return 0;
1215	–	break;
1216	–	}
1217	–	break;
1218	–
1219	–	case G_ZCONSTOL:
1220	–	switch( the_type ){
1221	–
1222	–	case STRING:
1223	–	the_event->err_msg =
1224	–	strdup( "Error in parsing meta-data file!\n\tzcons_tol is not a double or int.\n" );
1225	–	return 0;
1226	–	break;
1227	–
1228	–	case DOUBLE:
1229	–	zcons_tol = the_event->evt.asmt.rhs.dval;
1230	–	have_zcons_tol = 1;
1231	–	return 1;
1232	–	break;
1233	–
1234	–	case INT:
1235	–	zcons_tol = (double)the_event->evt.asmt.rhs.ival;
1236	–	have_zcons_tol = 1;
1237	–	return 1;
1238	–	break;
1239	–
1240	–	default:
1241	–	the_event->err_msg =
1242	–	strdup( "Error in parsing meta-data file!\n\tzcons_ol unrecognized.\n" );
1243	–	return 0;
1244	–	break;
1245	–	}
1246	–	break;
1247	–
1248	–	case G_ZCONSFORCEPOLICY:
1249	–	switch( the_type ){
1250	–
1251	–	case STRING:
1252	–	strcpy(zconsForcePolicy, the_event->evt.asmt.rhs.sval);
1253	–
1254	–	for(int i = 0; zconsForcePolicy[i] != '\0'; i++)
1255	–	{
1256	–	zconsForcePolicy[i] = toupper(zconsForcePolicy[i]);
1257	–	}
1258	–	have_zcons_force_policy = 1;
1259	–	return 1;
1260	–	break;
1261	–
1262	–	case DOUBLE:
1263	–	the_event->err_msg =
1264	–	strdup( "Error in parsing meta-data file!\n\tzconsForcePolicy is not a double or int.\n" );
1265	–	return 0;
1266	–	break;
1267	–
1268	–	case INT:
1269	–	the_event->err_msg =
1270	–	strdup( "Error in parsing meta-data file!\n\tzconsForcePolicy is not a double or int.\n" );
1271	–	return 0;
1272	–	break;
1273	–
1274	–	default:
1275	–	the_event->err_msg =
1276	–	strdup( "Error in parsing meta-data file!\n\tzconsForcePolicy unrecognized.\n" );
1277	–	return 0;
1278	–	break;
1279	–	}
1280	–	break;
1281	–
1282	–	case G_ZCONSGAP:
1283	–	switch( the_type ){
1284	–
1285	–	case STRING:
1286	–	the_event->err_msg =
1287	–	strdup( "Error in parsing meta-data file!\n\tzcons_gap is not a double or int.\n" );
1288	–	return 0;
1289	–	break;
1290	–
1291	–	case DOUBLE:
1292	–	zcons_gap = the_event->evt.asmt.rhs.dval;
1293	–	have_zcons_gap= 1;
1294	–	return 1;
1295	–	break;
1296	–
1297	–	case INT:
1298	–	zcons_gap= (double)the_event->evt.asmt.rhs.ival;
1299	–	have_zcons_gap= 1;
1300	–	return 1;
1301	–	break;
1302	–
1303	–	default:
1304	–	the_event->err_msg =
1305	–	strdup( "Error in parsing meta-data file!\n\tzcons_gap unrecognized.\n" );
1306	–	return 0;
1307	–	break;
1308	–	}
1309	–	break;
1310	–
1311	–	case G_ZCONSFIXTIME:
1312	–	switch( the_type ){
1313	–
1314	–	case STRING:
1315	–	the_event->err_msg =
1316	–	strdup( "Error in parsing meta-data file!\n\tzcons_fixtime is not a double or int.\n" );
1317	–	return 0;
1318	–	break;
1319	–
1320	–	case DOUBLE:
1321	–	zcons_fixtime= the_event->evt.asmt.rhs.dval;
1322	–	have_zcons_fixtime= 1;
1323	–	return 1;
1324	–	break;
1325	–
1326	–	case INT:
1327	–	zcons_fixtime= (double)the_event->evt.asmt.rhs.ival;
1328	–	have_zcons_fixtime= 1;
1329	–	return 1;
1330	–	break;
1331	–
1332	–	default:
1333	–	the_event->err_msg =
1334	–	strdup( "Error in parsing meta-data file!\n\tzcons_fixtime unrecognized.\n" );
1335	–	return 0;
1336	–	break;
1337	–	}
1338	–	break;
1339	–
1340	–	case G_ZCONSUSINGSMD:
1341	–	switch( the_type ){
1342	–
1343	–	case STRING:
1344	–	the_event->err_msg =
1345	–	strdup( "Error in parsing meta-data file!\n\tzcons_fixtime is not an  int.\n" );
1346	–	return 0;
1347	–	break;
1348	–
1349	–	case DOUBLE:
1350	–	the_event->err_msg =
1351	–	strdup( "Error in parsing meta-data file!\n\tzcons_fixtime is not an  int.\n" );
1352	–	return 0;
1353	–	break;
1354	–
1355	–	case INT:
1356	–	zcons_using_smd= the_event->evt.asmt.rhs.ival;
1357	–	have_zcons_using_smd= 1;
1358	–	return 1;
1359	–	break;
1360	–
1361	–	default:
1362	–	the_event->err_msg =
1363	–	strdup( "Error in parsing meta-data file!\n\tzcons_usingsmd unrecognized.\n" );
1364	–	return 0;
1365	–	break;
1366	–	}
1367	–	break;
1368	–
1369	–	case G_MINIMIZER:
1370	–	switch( the_type ){
1371	–
1372	–	case STRING:
1373	–	strcpy(minimizer_name, the_event->evt.asmt.rhs.sval);
1374	–
1375	–	for(int i = 0; zconsForcePolicy[i] != '\0'; i++){
1376	–	zconsForcePolicy[i] = toupper(zconsForcePolicy[i]);
1377	–	}
1378	–	have_minimizer= 1;
1379	–	return 1;
1380	–	break;
1381	–
1382	–	case DOUBLE:
1383	–	the_event->err_msg =
1384	–	strdup( "Error in parsing meta-data file!\n\tminimizer_name is not a double or int.\n" );
1385	–	return 0;
1386	–	break;
1387	–
1388	–	case INT:
1389	–	the_event->err_msg =
1390	–	strdup( "Error in parsing meta-data file!\n\tminimizer_name is not a double or int.\n" );
1391	–	return 0;
1392	–	break;
1393	–
1394	–	default:
1395	–	the_event->err_msg =
1396	–	strdup( "Error in parsing meta-data file!\n\tminimizer_name unrecognized.\n" );
1397	–	return 0;
1398	–	break;
1399	–	}
1400	–	break;
1401	–
1402	–	case G_MIN_MAXITER:
1403	–	switch( the_type ){
1404	–
1405	–	case STRING:
1406	–	the_event->err_msg =
1407	–	strdup( "Error in parsing meta-data file!\n\tminimizer_maxiteration is not a double or int.\n" );
1408	–	return 1;
1409	–	break;
1410	–
1411	–	case DOUBLE:
1412	–	minimizer_maxiteration = (int)the_event->evt.asmt.rhs.dval;
1413	–	have_minimizer_maxiteration = 1;
1414	–	return 1;
1415	–	break;
1416	–
1417	–	case INT:
1418	–	minimizer_maxiteration = the_event->evt.asmt.rhs.ival;
1419	–	have_minimizer_maxiteration = 1;
1420	–	return 1;
1421	–	break;
1422	–
1423	–	default:
1424	–	the_event->err_msg =
1425	–	strdup( "Error in parsing meta-data file!\n\tminimizer_maxiteration unrecognized.\n" );
1426	–	return 0;
1427	–	break;
1428	–	}
1429	–	break;
1430	–
1431	–	case G_MIN_WRITEFRQ:
1432	–	switch( the_type ){
1433	–
1434	–	case STRING:
1435	–	the_event->err_msg =
1436	–	strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq is not an int.\n" );
1437	–	return 1;
1438	–	break;
1439	–
1440	–	case DOUBLE:
1441	–	the_event->err_msg =
1442	–	strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq is not an  int.\n" );
1443	–	return 1;
1444	–	break;
1445	–
1446	–	case INT:
1447	–	minimizer_writefrq= the_event->evt.asmt.rhs.ival;
1448	–	have_minimizer_writefrq = 1;
1449	–	return 1;
1450	–	break;
1451	–
1452	–	default:
1453	–	the_event->err_msg =
1454	–	strdup( "Error in parsing meta-data file!\n\tminimizer_writefrq unrecognized.\n" );
1455	–	return 0;
1456	–	break;
1457	–	}
1458	–	break;
229
230	<	case G_MIN_STEPSIZE:
231	<	switch( the_type ){
232	<
233	<	case STRING:
234	<	the_event->err_msg =
235	<	strdup( "Error in parsing meta-data file!\n\tminimizer_resetfrq is not a double or int.\n" );
236	<	return 1;
237	<	break;
1468	<
1469	<	case DOUBLE:
1470	<	minimizer_stepsize= the_event->evt.asmt.rhs.dval;
1471	<	have_minimizer_stepsize = 1;
1472	<	return 1;
1473	<	break;
1474	<
1475	<	case INT:
1476	<	minimizer_stepsize= the_event->evt.asmt.rhs.ival;
1477	<	have_minimizer_stepsize = 1;
1478	<	return 1;
1479	<	break;
1480	<
1481	<	default:
1482	<	the_event->err_msg =
1483	<	strdup( "Error in parsing meta-data file!\n\tminimizer_resetfrq unrecognized.\n" );
1484	<	return 0;
1485	<	break;
1486	<	}
1487	<	break;
1488	<
1489	<	case G_MIN_FTOL:
1490	<	switch( the_type ){
1491	<
1492	<	case STRING:
1493	<	the_event->err_msg =
1494	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ftol is not a double or int.\n" );
1495	<	return 1;
1496	<	break;
1497	<
1498	<	case DOUBLE:
1499	<	minimizer_ftol= the_event->evt.asmt.rhs.dval;
1500	<	have_minimizer_ftol = 1;
1501	<	return 1;
1502	<	break;
1503	<
1504	<	case INT:
1505	<	minimizer_ftol= the_event->evt.asmt.rhs.ival;
1506	<	have_minimizer_ftol = 1;
1507	<	return 1;
1508	<	break;
1509	<
1510	<	default:
1511	<	the_event->err_msg =
1512	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ftol unrecognized.\n" );
1513	<	return 0;
1514	<	break;
1515	<	}
1516	<	break;
1517	<
1518	<	case G_MIN_GTOL:
1519	<	switch( the_type ){
1520	<
1521	<	case STRING:
1522	<	the_event->err_msg =
1523	<	strdup( "Error in parsing meta-data file!\n\tminimizer_gtol is not a double or int.\n" );
1524	<	return 1;
1525	<	break;
1526	<
1527	<	case DOUBLE:
1528	<	minimizer_gtol= the_event->evt.asmt.rhs.dval;
1529	<	have_minimizer_gtol = 1;
1530	<	return 1;
1531	<	break;
1532	<
1533	<	case INT:
1534	<	minimizer_gtol= the_event->evt.asmt.rhs.ival;
1535	<	have_minimizer_gtol = 1;
1536	<	return 1;
1537	<	break;
1538	<
1539	<	default:
1540	<	the_event->err_msg =
1541	<	strdup( "Error in parsing meta-data file!\n\tminimizer_gtol unrecognized.\n" );
1542	<	return 0;
1543	<	break;
1544	<	}
1545	<	break;
1546	<
1547	<	case G_MIN_LSMAXITER:
1548	<	switch( the_type ){
1549	<
1550	<	case STRING:
1551	<	the_event->err_msg =
1552	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration is not an int.\n" );
1553	<	return 1;
1554	<	break;
1555	<
1556	<	case DOUBLE:
1557	<	the_event->err_msg =
1558	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration is not an int.\n" );
1559	<	return 1;
1560	<	break;
1561	<
1562	<	case INT:
1563	<	minimizer_ls_maxiteration = the_event->evt.asmt.rhs.ival;
1564	<	have_minimizer_ls_maxiteration = 1;
1565	<	return 1;
1566	<	break;
1567	<
1568	<	default:
1569	<	the_event->err_msg =
1570	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_maxiteration unrecognized.\n" );
1571	<	return 0;
1572	<	break;
1573	<	}
1574	<	break;
1575	<
1576	<	case G_MIN_LSTOL:
1577	<	switch( the_type ){
1578	<
1579	<	case STRING:
1580	<	the_event->err_msg =
1581	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_tol is not a double or int.\n" );
1582	<	return 1;
1583	<	break;
1584	<
1585	<	case DOUBLE:
1586	<	minimizer_ls_tol= the_event->evt.asmt.rhs.dval;
1587	<	have_minimizer_ls_tol = 1;
1588	<	return 1;
1589	<	break;
1590	<
1591	<	case INT:
1592	<	minimizer_ls_tol= the_event->evt.asmt.rhs.ival;
1593	<	have_minimizer_ls_tol = 1;
1594	<	return 1;
1595	<	break;
1596	<
1597	<	default:
1598	<	the_event->err_msg =
1599	<	strdup( "Error in parsing meta-data file!\n\tminimizer_ls_tol unrecognized.\n" );
1600	<	return 0;
1601	<	break;
1602	<	}
1603	<	break;
1604	<
1605	<	// add more token cases here.
1606	<	case G_SEED:
1607	<	switch( the_type ){
1608	<
1609	<	case STRING:
1610	<	the_event->err_msg =
1611	<	strdup( "Error in parsing meta-data file!\n\tseed is not a string.\n" );
1612	<	return 0;
1613	<	return 0;
1614	<	break;
1615	<
1616	<	case DOUBLE:
1617	<	have_seed = 1;
1618	<	seed = (int)the_event->evt.asmt.rhs.dval;
1619	<	return 1;
1620	<	break;
1621	<
1622	<	case INT:
1623	<	have_seed = 1;
1624	<	seed =  the_event->evt.asmt.rhs.ival ;
1625	<	return 1;
1626	<	break;
1627	<
1628	<	default:
1629	<	the_event->err_msg =
1630	<	strdup( "Error in parsing meta-data file!\n\tseed unrecognized.\n" );
1631	<	return 0;
1632	<	break;
1633	<	}
1634	<	break;
1635	<
1636	<	case G_USE_SOLID_THERM_INT:
1637	<	if( the_type == STRING ){
1638	<
1639	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useSolidThermInt = 1;
1640	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useSolidThermInt = 0;
1641	<	else{
1642	<	the_event->err_msg =
1643	<	strdup( "Error in parsing meta-data file!\n\tuseSolidThermInt was not \"true\" or \"false\".\n" );
1644	<	return 0;
1645	<	}
1646	<	return 1;
1647	<	}
1648	<
1649	<	the_event->err_msg =
1650	<	strdup( "Error in parsing meta-data file!\n\tuseSolidThermInt was not \"true\" or \"false\".\n" );
1651	<	return 0;
1652	<	break;
1653	<
1654	<	case G_USE_LIQUID_THERM_INT:
1655	<	if( the_type == STRING ){
1656	<
1657	<	if( !strcasecmp( "true", the_event->evt.asmt.rhs.sval )) useLiquidThermInt = 1;
1658	<	else if( !strcasecmp( "false", the_event->evt.asmt.rhs.sval )) useLiquidThermInt = 0;
1659	<	else{
1660	<	the_event->err_msg =
1661	<	strdup( "Error in parsing meta-data file!\n\tuseLiquidThermInt was not \"true\" or \"false\".\n" );
1662	<	return 0;
1663	<	}
1664	<	return 1;
1665	<	}
1666	<
1667	<	the_event->err_msg =
1668	<	strdup( "Error in parsing meta-data file!\n\tuseLiquidThermInt was not \"true\" or \"false\".\n" );
1669	<	return 0;
1670	<	break;
1671	<
1672	<	case G_THERM_INT_LAMBDA:
1673	<	switch( the_type ){
1674	<
1675	<	case STRING:
1676	<	the_event->err_msg =
1677	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationLambda is not a double or int.\n" );
1678	<	return 1;
1679	<	break;
1680	<
1681	<	case DOUBLE:
1682	<	thermodynamic_integration_lambda = the_event->evt.asmt.rhs.dval;
1683	<	have_thermodynamic_integration_lambda = 1;
1684	<	return 1;
1685	<	break;
1686	<
1687	<	case INT:
1688	<	thermodynamic_integration_lambda = (double)the_event->evt.asmt.rhs.dval;
1689	<	have_thermodynamic_integration_lambda = 1;
1690	<	return 1;
1691	<	break;
1692	<
1693	<	default:
1694	<	the_event->err_msg =
1695	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationLambda unrecognized.\n" );
1696	<	return 0;
1697	<	break;
1698	<	}
1699	<	break;
1700	<
1701	<	case G_THERM_INT_K:
1702	<	switch( the_type ){
1703	<
1704	<	case STRING:
1705	<	the_event->err_msg =
1706	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationK is not a double or int.\n" );
1707	<	return 1;
1708	<	break;
1709	<
1710	<	case DOUBLE:
1711	<	thermodynamic_integration_k = the_event->evt.asmt.rhs.dval;
1712	<	have_thermodynamic_integration_k = 1;
1713	<	return 1;
1714	<	break;
1715	<
1716	<	case INT:
1717	<	thermodynamic_integration_k = (double)the_event->evt.asmt.rhs.dval;
1718	<	have_thermodynamic_integration_k = 1;
1719	<	return 1;
1720	<	break;
1721	<
1722	<	default:
1723	<	the_event->err_msg =
1724	<	strdup( "Error in parsing meta-data file!\n\tthermodynamicIntegrationK unrecognized.\n" );
1725	<	return 0;
1726	<	break;
1727	<	}
1728	<	break;
1729	<
1730	<	case G_FORCEFIELD_VARIANT:
1731	<	if( the_type == STRING ){
1732	<	strcpy( forcefield_variant, the_event->evt.asmt.rhs.sval );
1733	<	have_forcefield_variant = 1;
1734	<	return 1;
1735	<	}
1736	<
1737	<	the_event->err_msg =
1738	<	strdup( "Error in parsing meta-data file!\n\tforceFieldVariant was not a string assignment.\n" );
1739	<	return 0;
1740	<	break;
1741	<	// add more token cases here.
1742	<
1743	<	case G_FORCEFIELD_FILENAME:
1744	<	if( the_type == STRING ){
1745	<	strcpy( forcefield_filename, the_event->evt.asmt.rhs.sval );
1746	<	have_forcefield_filename = 1;
1747	<	return 1;
1748	<	}
1749	<
1750	<	the_event->err_msg =
1751	<	strdup( "Error in parsing meta-data file!\n\tforceFieldFileName was not a string assignment.\n" );
1752	<	return 0;
1753	<	break;
1754	<
1755	<	case G_THERM_INT_DIST_SPRING:
1756	<	switch( the_type ){
1757	<
1758	<	case STRING:
1759	<	the_event->err_msg =
1760	<	strdup( "Error in parsing meta-data file!\n\tthermIntDistSpringConst is not a double or int.\n" );
1761	<	return 1;
1762	<	break;
1763	<
1764	<	case DOUBLE:
1765	<	therm_int_dist_spring = the_event->evt.asmt.rhs.dval;
1766	<	have_dist_spring_constant = 1;
1767	<	return 1;
1768	<	break;
1769	<
1770	<	case INT:
1771	<	therm_int_dist_spring = (double)the_event->evt.asmt.rhs.dval;
1772	<	have_dist_spring_constant = 1;
1773	<	return 1;
1774	<	break;
1775	<
1776	<	default:
1777	<	the_event->err_msg =
1778	<	strdup( "Error in parsing meta-data file!\n\tthermIntDistSpringConst unrecognized.\n" );
1779	<	return 0;
1780	<	break;
1781	<	}
1782	<	break;
1783	<
1784	<	case G_THERM_INT_THETA_SPRING:
1785	<	switch( the_type ){
1786	<
1787	<	case STRING:
1788	<	the_event->err_msg =
1789	<	strdup( "Error in parsing meta-data file!\n\tthermIntThetaSpringConst is not a double or int.\n" );
1790	<	return 1;
1791	<	break;
1792	<
1793	<	case DOUBLE:
1794	<	therm_int_theta_spring = the_event->evt.asmt.rhs.dval;
1795	<	have_theta_spring_constant = 1;
1796	<	return 1;
1797	<	break;
1798	<
1799	<	case INT:
1800	<	therm_int_theta_spring = (double)the_event->evt.asmt.rhs.dval;
1801	<	have_theta_spring_constant = 1;
1802	<	return 1;
1803	<	break;
1804	<
1805	<	default:
1806	<	the_event->err_msg =
1807	<	strdup( "Error in parsing meta-data file!\n\tthermIntThetaSpringConst unrecognized.\n" );
1808	<	return 0;
1809	<	break;
1810	<	}
1811	<	break;
1812	<
1813	<	case G_THERM_INT_OMEGA_SPRING:
1814	<	switch( the_type ){
1815	<
1816	<	case STRING:
1817	<	the_event->err_msg =
1818	<	strdup( "Error in parsing meta-data file!\n\tthermIntOmegaSpringConst is not a double or int.\n" );
1819	<	return 1;
1820	<	break;
1821	<
1822	<	case DOUBLE:
1823	<	therm_int_omega_spring = the_event->evt.asmt.rhs.dval;
1824	<	have_omega_spring_constant = 1;
1825	<	return 1;
1826	<	break;
1827	<
1828	<	case INT:
1829	<	therm_int_omega_spring = (double)the_event->evt.asmt.rhs.dval;
1830	<	have_omega_spring_constant = 1;
1831	<	return 1;
1832	<	break;
1833	<
1834	<	default:
1835	<	the_event->err_msg =
1836	<	strdup( "Error in parsing meta-data file!\n\tthermIntOmegaSpringConst unrecognized.\n" );
1837	<	return 0;
1838	<	break;
1839	<	}
1840	<	break;
1841	<	// add more token cases here.
1842	<	}
1843	<	}
1844	<
1845	<	switch( the_type ){
1846	<
1847	<	case STRING:
1848	<	sprintf( err,
1849	<	"\tUnrecognized assignment:\n"
1850	<	"\t\t-> %s = %s\n",
1851	<	lhs, the_event->evt.asmt.rhs.sval );
1852	<	break;
1853	<
1854	<	case DOUBLE:
1855	<	sprintf( err,
1856	<	"\tUnrecognized assignment:\n"
1857	<	"\t\t-> %s = %lf\n",
1858	<	lhs, the_event->evt.asmt.rhs.dval );
1859	<	break;
1860	<
1861	<	case INT:
1862	<	sprintf( err,
1863	<	"\tUnrecognized assignment:\n"
1864	<	"\t\t-> %s = %d\n",
1865	<	lhs, the_event->evt.asmt.rhs.ival );
1866	<	break;
1867	<
1868	<	default:
1869	<	sprintf( err,
1870	<	"\tUnrecognized assignment:\n"
1871	<	"\t\t-> %s = ?\n",
1872	<	lhs );
1873	<	break;
1874	<	}
1875	<
1876	<	the_event->err_msg = strdup( err );
1877	<	return 0;
1878	<	}
1879	<
1880	<	char* Globals::checkMe( void ){
1881	<
1882	<	char err[300];
1883	<	short int have_err = 0;
1884	<
1885	<	strcpy( err, "The following required keywords are missing:\n" );
1886	<
1887	<	if( !have_force_field ){
1888	<	strcat( err, "\t\t->forceField\n" );
1889	<	have_err= 1;
1890	<	}
1891	<
1892	<	if( !have_n_components ){
1893	<	strcat( err, "\t\t->nComponents\n" );
1894	<	have_err= 1;
1895	<	}
1896	<
1897	<
1898	<	if ( !have_ensemble ) {
1899	<	// I'm not doing MD:
1900	<	if ( !have_minimizer ) {
1901	<	// I'm not doing MD or minimization:
1902	<	strcat( err, "\t\t->either ensemble or minimizer must be set!\n" );
1903	<	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 {
1908	<	// I *am* doing MD:
1909	<	if( !have_dt ){
1910	<	strcat( err, "\t\t->dt (timestep in fs)\n" );
1911	<	have_err= 1;
1912	<	}
1913	<	if( !have_run_time ){
1914	<	strcat( err, "\t\t->runTime (total run time in fs)\n" );
1915	<	have_err= 1;
1916	<	}
1917	<	}
1918	<
1919	<	if( have_err ) return strdup( err );
1920	<
1921	<	return NULL;
243	>	return ret;
244		}
245	+
246
1924	–	int Globals::globalEnd( event* the_event ){
1925	–
1926	–	the_event->err_msg = checkMe();
1927	–	if( the_event->err_msg != NULL ) return 0;
1928	–
1929	–	return 1;
247		}
1931	–

Diff Legend

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