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

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trunk/src/io/Globals.cpp (file contents), Revision 765 by gezelter, Mon Nov 21 22:59:36 2005 UTC vs.
branches/development/src/io/Globals.cpp (file contents), Revision 1722 by gezelter, Thu May 24 14:23:40 2012 UTC

#	Line 1 | Line 1
1		/*
2	<	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		#include <stdlib.h>
#	Line 45 | Line 46
46		#include <string>
47
48		#include "io/Globals.hpp"
49	+	#include "io/ParamConstraint.hpp"
50	+	#include "utils/MemoryUtils.hpp"
51		#include "utils/simError.h"
49	–	#ifdef IS_MPI
50	–	#include "io/mpiBASS.h"
51	–	#endif // is_mpi
52
53	<	#include "io/ParamConstraint.hpp"
54	<
55	<	using namespace oopse;
56	<
57	<	Globals::Globals(){
58	<
53	>	namespace OpenMD {
54	>	Globals::Globals() {
55		DefineParameter(ForceField, "forceField")
60	–	DefineParameter(NComponents, "nComponents")
56
57		DefineOptionalParameter(TargetTemp, "targetTemp");
58		DefineOptionalParameter(Ensemble, "ensemble");
59		DefineOptionalParameter(Dt, "dt");
60		DefineOptionalParameter(RunTime, "runTime");
66	–	DefineOptionalParameter(InitialConfig, "initialConfig");
61		DefineOptionalParameter(FinalConfig, "finalConfig");
68	–	DefineOptionalParameter(NMol, "nMol");
69	–	DefineOptionalParameter(Density, "density");
70	–	DefineOptionalParameter(Box, "box");
71	–	DefineOptionalParameter(BoxX, "boxX");
72	–	DefineOptionalParameter(BoxY, "boxY");
73	–	DefineOptionalParameter(BoxZ, "boxZ");
62		DefineOptionalParameter(SampleTime, "sampleTime");
63		DefineOptionalParameter(ResetTime, "resetTime");
64		DefineOptionalParameter(StatusTime, "statusTime");
65		DefineOptionalParameter(CutoffRadius, "cutoffRadius");
66		DefineOptionalParameter(SwitchingRadius, "switchingRadius");
79	–	DefineOptionalParameter(Dielectric, "dielectric");
67		DefineOptionalParameter(TempSet, "tempSet");
68		DefineOptionalParameter(ThermalTime, "thermalTime");
69	<	DefineOptionalParameter(TargetPressure, "targetPressure");
69	>	DefineOptionalParameter(TargetPressure, "targetPressure");
70		DefineOptionalParameter(TauThermostat, "tauThermostat");
71		DefineOptionalParameter(TauBarostat, "tauBarostat");
72		DefineOptionalParameter(ZconsTime, "zconsTime");
86	–	DefineOptionalParameter(NZconstraints, "nZconstraints");
73		DefineOptionalParameter(ZconsTol, "zconsTol");
74		DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
75		DefineOptionalParameter(Seed, "seed");
76		DefineOptionalParameter(Minimizer, "minimizer");
77		DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
78	<	DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
78	>	DefineOptionalParameter(MinimizerWriteFreq, "minimizerWriteFreq");
79		DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
80		DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
81		DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
#	Line 102 | Line 88 | Globals::Globals(){
88		DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
89		DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
90		DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
91	<	DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
106	<	DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
107	<	DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
91	>	DefineOptionalParameter(DampingAlpha, "dampingAlpha");
92		DefineOptionalParameter(SurfaceTension, "surfaceTension");
93		DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
94	<	DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
95	<	DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
112	<	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
94	>	DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
95	>	DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
96		DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
97	<	DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
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(ElectrostaticSummationMethod, "electrostaticSummationMethod");
105	>	DefineOptionalParameter(MTM_Ce, "MTM_Ce");
106	>	DefineOptionalParameter(MTM_G, "MTM_G");
107	>	DefineOptionalParameter(MTM_Io, "MTM_Io");
108	>	DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
109	>	DefineOptionalParameter(MTM_R, "MTM_R");
110	>	DefineOptionalParameter(Alpha, "alpha");
111	>
112	>
113		DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
114	+	DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
115		DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
116		DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
117		DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
118	<	DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
119	<	DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
120	<	DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
121	<	DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
122	<	DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
123	<	DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
124	<	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
125	<	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
118	>	DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
119	>	DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
120	>	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
121	>	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false);
122	>	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false);
123	>	DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false);
124	>	DefineOptionalParameterWithDefaultValue(OutputElectricField, "outputElectricField", false);
125	>	DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, "outputFluctuatingCharges", false);
126		DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
127		DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
128	+	DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
129	+	DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
130
131	<
132	<	}
131	>	DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
132	>	DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
133	>	DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
134	>	DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
135	>	DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
136	>	DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
137	>	DefineOptionalParameterWithDefaultValue(RNEMD_targetJzKE, "RNEMD_targetJzKE", 0.0);
138	>	DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpx, "RNEMD_targetJzpx", 0.0);
139	>	DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpy, "RNEMD_targetJzpy", 0.0);
140	>	DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpz, "RNEMD_targetJzpz", 0.0);
141	>	DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
142	>	DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false);
143	>	DefineOptionalParameterWithDefaultValue(RNEMD_outputTemperature, "RNEMD_outputTemperature", false);
144	>	DefineOptionalParameterWithDefaultValue(RNEMD_outputVx, "RNEMD_outputVx", false);
145	>	DefineOptionalParameterWithDefaultValue(RNEMD_outputVy, "RNEMD_outputVy", false);
146	>	DefineOptionalParameterWithDefaultValue(RNEMD_outputXyzTemperature, "RNEMD_outputXyzTemperature", false);
147	>	DefineOptionalParameterWithDefaultValue(RNEMD_outputRotTemperature, "RNEMD_outputRotTemperature", false);
148
149	<	Globals::~Globals(){
150	<	int i;
151	<	if( components != NULL ){
152	<	for( i=0; i< getNComponents(); i++ ) delete components[i];
153	<	delete[] components;
154	<	}
155	<
156	<	if( zConstraints != NULL ){
157	<	for( i=0; i< getNZconstraints(); i++ ) delete zConstraints[i];
158	<	delete[] zConstraints;
143	<	}
144	<
145	<	}
149	>	DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
150	>	DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
151	>	DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
152	>	DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
153	>	DefineOptionalParameterWithDefaultValue(FlucQPropagator, "flucQ.propagator", "NVT");
154	>	DefineOptionalParameterWithDefaultValue(FlucQFriction, "flucQ.friction", 1600.0);
155	>	DefineOptionalParameterWithDefaultValue(FlucQTolerance, "flucQ.tolerance", 1.0e-6);
156	>	DefineOptionalParameterWithDefaultValue(FlucQMaxIterations, "flucQ.maxIterations", 100);
157	>	DefineOptionalParameterWithDefaultValue(FlucQTargetTemp, "flucQ.targetTemp", 1.0e-6);
158	>	DefineOptionalParameterWithDefaultValue(FlucQtauThermostat, "flucQ.tauThermostat", 10.0);
159
160	<	int Globals::globalAssign( event* the_event ){
161	<	char errorMessage[65535];
162	<	int key;
163	<	interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
164	<	char* lhs = the_event->evt.asmt.lhs;
165	<	std::string keyword(lhs);
166	<
167	<	bool result = false;
155	<
156	<	/**@todo fix memory leak */
157	<	ParamMap::iterator i =parameters_.find(keyword);
158	<	if (i != parameters_.end()) {
159	<	if( the_type == STRING ){
160	<	result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
161	<	if (!result ) {
162	<	sprintf(errorMessage, "Error in parsing %s: expect %s, but get a string \"%s\".\n", keyword.c_str(), i->second->getParamType().c_str(), the_event->evt.asmt.rhs.sval);
163	<	the_event->err_msg = strdup(errorMessage);
164	<	}
165	<	} else if( the_type == DOUBLE ){
166	<	result = i->second->setData(the_event->evt.asmt.rhs.dval);
167	<	if (!result )
168	<	sprintf(errorMessage, "Error in parsing %s: expect %s, but get a double %f.\n", keyword.c_str(), i->second->getParamType().c_str(), the_event->evt.asmt.rhs.dval );
169	<	the_event->err_msg = strdup(errorMessage);
170	<	}
171	<	else if (the_type == INT ){
172	<	result = i->second->setData(the_event->evt.asmt.rhs.ival);
173	<	if (!result )
174	<	sprintf(errorMessage,  "Error in parsing %s: expect %s, but get an int %d.\n", keyword.c_str(), i->second->getParamType().c_str(), the_event->evt.asmt.rhs.ival );
175	<	the_event->err_msg = strdup(errorMessage);
176	<
177	<	} else {
178	<	sprintf(errorMessage,  "Internal error of parser\n");
179	<	the_event->err_msg = strdup(errorMessage);
180	<	}
181	<	} else {
182	<	sprintf(errorMessage,  "%s is an unrecognized keyword\n", keyword.c_str() );
183	<	the_event->err_msg = strdup(errorMessage);
184	<	}
185	<
186	<	if (keyword == "nComponents" && getNComponents() > 0) {
187	<	components = new Component*[getNComponents()];
188	<	}else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
189	<	zConstraints = new ZconStamp*[getNZconstraints()];
190	<	}
191	<
192	<	return result;
193	<	}
194	<
195	<	int Globals::newComponent( event* the_event ){
196	<
197	<	current_component = new Component;
198	<	int index = the_event->evt.blk_index;
199	<	char err[200];
200	<
201	<	if( haveNComponents() && index < getNComponents() )
202	<	components[index] = current_component;
203	<	else{
204	<	if( haveNComponents()  ){
205	<	sprintf( err, "meta-data parsing error: %d out of nComponents range",
206	<	index );
207	<	the_event->err_msg = strdup( err );
208	<	return 0;
209	<	}
210	<	else{
211	<	the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
212	<	" first component declaration." );
213	<	return 0;
214	<	}
215	<	}
216	<
217	<	return 1;
218	<	}
219	<
220	<
221	<
222	<	int Globals::componentAssign( event* the_event ){
223	<
224	<	switch( the_event->evt.asmt.asmt_type ){
225	<
226	<	case STRING:
227	<	return current_component->assignString( the_event->evt.asmt.lhs,
228	<	the_event->evt.asmt.rhs.sval,
229	<	&(the_event->err_msg));
230	<	break;
231	<
232	<	case DOUBLE:
233	<	return current_component->assignDouble( the_event->evt.asmt.lhs,
234	<	the_event->evt.asmt.rhs.dval,
235	<	&(the_event->err_msg));
236	<	break;
160	>	deprecatedKeywords_.insert("nComponents");
161	>	deprecatedKeywords_.insert("nZconstraints");
162	>	deprecatedKeywords_.insert("initialConfig");
163	>	deprecatedKeywords_.insert("thermIntDistSpringConst");
164	>	deprecatedKeywords_.insert("thermIntThetaSpringConst");
165	>	deprecatedKeywords_.insert("thermIntOmegaSpringConst");
166	>	deprecatedKeywords_.insert("useSolidThermInt");
167	>	deprecatedKeywords_.insert("useLiquidThermInt");
168
238	–	case INT:
239	–	return current_component->assignInt( the_event->evt.asmt.lhs,
240	–	the_event->evt.asmt.rhs.ival,
241	–	&(the_event->err_msg));
242	–	break;
243	–
244	–	default:
245	–	the_event->err_msg = strdup( "Globals error. Invalid component"
246	–	" assignment type" );
247	–	return 0;
248	–	break;
249	–	}
250	–	return 0;
169		}
170
171	<	int Globals::componentEnd( event* the_event ){
172	<
173	<	the_event->err_msg = current_component->checkMe();
174	<	if( the_event->err_msg != NULL ) return 0;
257	<
258	<	return 1;
171	>	Globals::~Globals() {
172	>	MemoryUtils::deletePointers(components_);
173	>	MemoryUtils::deletePointers(zconstraints_);
174	>	MemoryUtils::deletePointers(restraints_);
175		}
176
177	<	int Globals::newZconstraint( event* the_event ){
178	<
177	>	void Globals::validate() {
178	>	DataHolder::validate();
179
264	–	int index = the_event->evt.blk_index;
265	–	char err[200];
266	–	current_zConstraint = new ZconStamp( index );
267	–
268	–	if( haveNZconstraints() && index < getNZconstraints() )
269	–	zConstraints[index] = current_zConstraint;
270	–	else{
271	–	if( haveNZconstraints() ){
272	–	sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
273	–	index );
274	–	the_event->err_msg = strdup( err );
275	–	return 0;
276	–	}
277	–	else{
278	–	the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
279	–	" not given before"
280	–	" first zConstraint declaration." );
281	–	return 0;
282	–	}
283	–	}
284	–
285	–	return 1;
286	–	}
287	–
288	–
289	–
290	–	int Globals::zConstraintAssign( event* the_event ){
291	–
292	–	switch( the_event->evt.asmt.asmt_type ){
293	–
294	–	case STRING:
295	–	return current_zConstraint->assignString( the_event->evt.asmt.lhs,
296	–	the_event->evt.asmt.rhs.sval,
297	–	&(the_event->err_msg));
298	–	break;
299	–
300	–	case DOUBLE:
301	–	return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
302	–	the_event->evt.asmt.rhs.dval,
303	–	&(the_event->err_msg));
304	–	break;
305	–
306	–	case INT:
307	–	return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
308	–	the_event->evt.asmt.rhs.ival,
309	–	&(the_event->err_msg));
310	–	break;
311	–
312	–	default:
313	–	the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
314	–	" assignment type" );
315	–	return 0;
316	–	break;
317	–	}
318	–	return 0;
319	–	}
320	–
321	–	int Globals::zConstraintEnd( event* the_event ){
322	–
323	–	the_event->err_msg = current_zConstraint->checkMe();
324	–	if( the_event->err_msg != NULL ) return 0;
325	–
326	–	return 1;
327	–	}
328	–
329	–	char* Globals::checkMe( void ){
330	–
331	–
332	–	std::string err("The following required keywords are missing:\n");
333	–	short int have_err = 0;
334	–
335	–	ParamMap::iterator i;
336	–	for (i = parameters_.begin(); i != parameters_.end(); ++i) {
337	–	if (!i->second->isOptional() && i->second->empty()) {
338	–	err +=  i->second->getKeyword() + "\n";
339	–	}
340	–	}
341	–
180		CheckParameter(ForceField, isNotEmpty());
343	–	CheckParameter(NComponents,isPositive());
181		CheckParameter(TargetTemp, isPositive());
182	<	CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) || isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf")) || isEqualIgnoreCase(std::string("NPTxyz")) );
182	>	CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPTsz") || isEqualIgnoreCase("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT") || isEqualIgnoreCase("LANGEVINHULL") || isEqualIgnoreCase("LHULL") || isEqualIgnoreCase("SMIPD"));
183		CheckParameter(Dt, isPositive());
184		CheckParameter(RunTime, isPositive());
348	–	CheckParameter(InitialConfig, isNotEmpty());
185		CheckParameter(FinalConfig, isNotEmpty());
350	–	CheckParameter(NMol, isPositive());
351	–	CheckParameter(Density, isPositive());
352	–	CheckParameter(Box, isPositive());
353	–	CheckParameter(BoxX, isPositive());
354	–	CheckParameter(BoxY, isPositive());
355	–	CheckParameter(BoxZ, isPositive());
186		CheckParameter(SampleTime, isNonNegative());
187		CheckParameter(ResetTime, isNonNegative());
188		CheckParameter(StatusTime, isNonNegative());
#	Line 360 | Line 190 | char* Globals::checkMe( void ){
190		CheckParameter(SwitchingRadius, isNonNegative());
191		CheckParameter(Dielectric, isPositive());
192		CheckParameter(ThermalTime,  isNonNegative());
363	–	CheckParameter(TargetPressure,  isPositive());
193		CheckParameter(TauThermostat, isPositive());
194		CheckParameter(TauBarostat, isPositive());
195		CheckParameter(ZconsTime, isPositive());
367	–	CheckParameter(NZconstraints, isPositive());
196		CheckParameter(ZconsTol, isPositive());
369	–	//CheckParameter(ZconsForcePolicy,);
197		CheckParameter(Seed, isPositive());
198	<	CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
198	>	CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
199		CheckParameter(MinimizerMaxIter, isPositive());
200	<	CheckParameter(MinimizerWriteFrq, isPositive());
200	>	CheckParameter(MinimizerWriteFreq, isPositive());
201		CheckParameter(MinimizerStepSize, isPositive());
202		CheckParameter(MinimizerFTol, isPositive());
203		CheckParameter(MinimizerGTol, isPositive());
#	Line 378 | Line 205 | char* Globals::checkMe( void ){
205		CheckParameter(MinimizerLSMaxIter, isPositive());
206		CheckParameter(ZconsGap, isPositive());
207		CheckParameter(ZconsFixtime, isPositive());
208	<	CheckParameter(ThermodynamicIntegrationLambda, isPositive());
208	>	CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
209		CheckParameter(ThermodynamicIntegrationK, isPositive());
210		CheckParameter(ForceFieldVariant, isNotEmpty());
211		CheckParameter(ForceFieldFileName, isNotEmpty());
212	<	CheckParameter(ThermIntDistSpringConst, isPositive());
213	<	CheckParameter(ThermIntThetaSpringConst, isPositive());
214	<	CheckParameter(ThermIntOmegaSpringConst, isPositive());
215	<	CheckParameter(SurfaceTension, isPositive());
216	<	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || isEqualIgnoreCase(std::string("SHIFTED_FORCE")) || isEqualIgnoreCase(std::string("REACTION_FIELD")));
390	<	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) || isEqualIgnoreCase(std::string("DAMPED")));
391	<	CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
392	<	CheckParameter(SwitchingFunctionType, isEqualIgnoreCase(std::string("CUBIC")) || isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL")));
393	<	//CheckParameter(StatFileFormat,);
394	<	//CheckParameter(MixingRule,);
212	>	CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE"));
213	>	CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
214	>	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
215	>	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
216	>	CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
217		CheckParameter(OrthoBoxTolerance, isPositive());
396	–	CheckParameter(ThermIntDistSpringConst, isPositive());
397	–	CheckParameter(ThermIntThetaSpringConst, isPositive());
398	–	CheckParameter(ThermIntOmegaSpringConst, isPositive());
218		CheckParameter(DampingAlpha,isNonNegative());
219		CheckParameter(SkinThickness, isPositive());
220	+	CheckParameter(Viscosity, isNonNegative());
221	+	CheckParameter(BeadSize, isPositive());
222	+	CheckParameter(FrozenBufferRadius, isPositive());
223	+	CheckParameter(LangevinBufferRadius, isPositive());
224	+	CheckParameter(NeighborListNeighbors, isPositive());
225	+	CheckParameter(RNEMD_exchangeTime, isPositive());
226	+	CheckParameter(RNEMD_nBins, isPositive() && isEven());
227	+	CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("KineticScaleVAM") || isEqualIgnoreCase("KineticScaleAM") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale") || isEqualIgnoreCase("ShiftScaleV") || isEqualIgnoreCase("ShiftScaleVAM"));
228	+	CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
229	+	CheckParameter(Alpha, isPositive());
230	+	CheckParameter(FlucQPropagator, isEqualIgnoreCase("NVT") || isEqualIgnoreCase("Langevin") || isEqualIgnoreCase("Minimizer") || isEqualIgnoreCase("Exact") );
231	+	CheckParameter(FlucQFriction, isNonNegative());
232	+	CheckParameter(FlucQTolerance, isPositive());
233	+	CheckParameter(FlucQMaxIterations, isPositive());
234	+	CheckParameter(FlucQTargetTemp,  isNonNegative());
235	+	CheckParameter(FlucQtauThermostat, isPositive());
236
237	<	//@todo memory leak
238	<	if( have_err )
239	<	return strdup( err.c_str() );
240	<
241	<	return NULL;
237	>	for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
238	>	if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
239	>	std::ostringstream oss;
240	>	oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
241	>	throw OpenMDException(oss.str());
242	>	}
243	>	}
244	>	}
245
246	+	bool Globals::addComponent(Component* comp) {
247	+	components_.push_back(comp);
248	+	return true;
249	+	}
250
251	+	bool Globals::addZConsStamp(ZConsStamp* zcons) {
252	+	zconstraints_.push_back(zcons);
253	+	return true;
254		}
255
256	<	int Globals::globalEnd( event* the_event ){
257	<
258	<	the_event->err_msg = checkMe();
259	<	if( the_event->err_msg != NULL ) return 0;
256	>	bool Globals::addRestraintStamp(RestraintStamp* rest) {
257	>	restraints_.push_back(rest);
258	>	return true;
259	>	}
260
261	<	return 1;
261	>	bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
262	>	std::string molStampName = molStamp->getName();
263	>	std::map<std::string, MoleculeStamp*>::iterator i;
264	>	bool ret = false;
265	>	i = moleculeStamps_.find(molStampName);
266	>	if (i == moleculeStamps_.end()) {
267	>	moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
268	>	ret = true;
269	>	} else {
270	>	std::ostringstream oss;
271	>	oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
272	>	throw OpenMDException(oss.str());
273	>	}
274	>	return ret;
275		}
276	+
277	+
278	+	}

Comparing:
trunk/src/io/Globals.cpp (property svn:keywords), Revision 765 by gezelter, Mon Nov 21 22:59:36 2005 UTC vs.
branches/development/src/io/Globals.cpp (property svn:keywords), Revision 1722 by gezelter, Thu May 24 14:23:40 2012 UTC

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