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

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trunk/src/io/Globals.cpp (file contents), Revision 710 by chrisfen, Wed Nov 2 20:36:25 2005 UTC vs.
branches/development/src/io/Globals.cpp (file contents), Revision 1746 by gezelter, Wed Jun 6 02:18:54 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"
53	>	namespace OpenMD {
54	>	Globals::Globals() {
55	>
56	>	flucQpars_ = new FluctuatingChargeParameters();
57	>	rnemdPars_ = new RNEMDParameters();
58	>	minimizerPars_ = new MinimizerParameters();
59
55	–	#define DefineParameter(NAME,KEYWORD)                              \
56	–	NAME.setKeyword(KEYWORD);                  \
57	–	parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));
58	–
59	–	#define DefineOptionalParameter(NAME,KEYWORD)                              \
60	–	NAME.setKeyword(KEYWORD); NAME.setOptional(true);                    \
61	–	parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));
62	–
63	–	#define DefineOptionalParameterWithDefaultValue(NAME,KEYWORD, DEFAULTVALUE)                              \
64	–	NAME.setKeyword(KEYWORD); NAME.setOptional(true); NAME.setDefaultValue(DEFAULTVALUE);                      \
65	–	parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));
66	–
67	–	#define CheckParameter(NAME, CONSTRAINT)                              \
68	–	if (!NAME.empty()) { if (!(CONSTRAINT)(NAME.getData())) { sprintf(painCave.errMsg,"Error in checking %s : should be %s\n",NAME.getKeyword().c_str(),(CONSTRAINT).getConstraintDescription().c_str()); painCave.isFatal = 1; painCave.severity = OOPSE_ERROR; simError();} }
69	–
70	–	Globals::Globals(){
71	–
60		DefineParameter(ForceField, "forceField")
73	–	DefineParameter(NComponents, "nComponents")
61
62		DefineOptionalParameter(TargetTemp, "targetTemp");
63		DefineOptionalParameter(Ensemble, "ensemble");
64		DefineOptionalParameter(Dt, "dt");
65		DefineOptionalParameter(RunTime, "runTime");
79	–	DefineOptionalParameter(InitialConfig, "initialConfig");
66		DefineOptionalParameter(FinalConfig, "finalConfig");
81	–	DefineOptionalParameter(NMol, "nMol");
82	–	DefineOptionalParameter(Density, "density");
83	–	DefineOptionalParameter(Box, "box");
84	–	DefineOptionalParameter(BoxX, "boxX");
85	–	DefineOptionalParameter(BoxY, "boxY");
86	–	DefineOptionalParameter(BoxZ, "boxZ");
67		DefineOptionalParameter(SampleTime, "sampleTime");
68		DefineOptionalParameter(ResetTime, "resetTime");
69		DefineOptionalParameter(StatusTime, "statusTime");
70		DefineOptionalParameter(CutoffRadius, "cutoffRadius");
71		DefineOptionalParameter(SwitchingRadius, "switchingRadius");
92	–	DefineOptionalParameter(Dielectric, "dielectric");
72		DefineOptionalParameter(TempSet, "tempSet");
73		DefineOptionalParameter(ThermalTime, "thermalTime");
74	<	DefineOptionalParameter(TargetPressure, "targetPressure");
74	>	DefineOptionalParameter(TargetPressure, "targetPressure");
75		DefineOptionalParameter(TauThermostat, "tauThermostat");
76		DefineOptionalParameter(TauBarostat, "tauBarostat");
77		DefineOptionalParameter(ZconsTime, "zconsTime");
99	–	DefineOptionalParameter(NZconstraints, "nZconstraints");
78		DefineOptionalParameter(ZconsTol, "zconsTol");
79		DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
80		DefineOptionalParameter(Seed, "seed");
103	–	DefineOptionalParameter(Minimizer, "minimizer");
104	–	DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
105	–	DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
106	–	DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
107	–	DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
108	–	DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
109	–	DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
110	–	DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
81		DefineOptionalParameter(ZconsGap, "zconsGap");
82		DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
83		DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
#	Line 115 | Line 85 | Globals::Globals(){
85		DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
86		DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
87		DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
88	<	DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
119	<	DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
120	<	DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
88	>	DefineOptionalParameter(DampingAlpha, "dampingAlpha");
89		DefineOptionalParameter(SurfaceTension, "surfaceTension");
90		DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
91	+	DefineOptionalParameter(PrintHeatFlux, "printHeatFlux");
92	+	DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
93	+	DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
94	+	DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
95	+	DefineOptionalParameter(HydroPropFile, "HydroPropFile");
96	+	DefineOptionalParameter(Viscosity, "viscosity");
97	+	DefineOptionalParameter(BeadSize, "beadSize");
98	+	DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
99	+	DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
100	+	DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
101	+	DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
102		DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
103	<	DefineOptionalParameter(ScreeningMethod, "screeningMethod");
104	<	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
103	>	DefineOptionalParameter(MTM_Ce, "MTM_Ce");
104	>	DefineOptionalParameter(MTM_G, "MTM_G");
105	>	DefineOptionalParameter(MTM_Io, "MTM_Io");
106	>	DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
107	>	DefineOptionalParameter(MTM_R, "MTM_R");
108	>	DefineOptionalParameter(Alpha, "alpha");
109	>
110
127	–	DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
111		DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
112	+	DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
113		DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
114		DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
115		DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
116	<	DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
117	<	DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
118	<	DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
119	<	DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
120	<	DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
121	<	DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 1.5);
122	<	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
116	>	DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
117	>	DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
118	>	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
119	>	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false);
120	>	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false);
121	>	DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false);
122	>	DefineOptionalParameterWithDefaultValue(OutputElectricField, "outputElectricField", false);
123	>	DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, "outputFluctuatingCharges", false);
124		DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
125		DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
126	+	DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
127	+	DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
128
129	<
130	<	}
131	<
132	<	int Globals::globalAssign( event* the_event ){
146	<	char errorMessage[65535];
147	<	int key;
148	<	interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
149	<	char* lhs = the_event->evt.asmt.lhs;
150	<	std::string keyword(lhs);
151	<
152	<	bool result = false;
153	<
154	<	/**@todo fix memory leak */
155	<	ParamMap::iterator i =parameters_.find(keyword);
156	<	if (i != parameters_.end()) {
157	<	if( the_type == STRING ){
158	<	result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
159	<	if (!result ) {
160	<	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);
161	<	the_event->err_msg = strdup(errorMessage);
162	<	}
163	<	} else if( the_type == DOUBLE ){
164	<	result = i->second->setData(the_event->evt.asmt.rhs.dval);
165	<	if (!result )
166	<	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 );
167	<	the_event->err_msg = strdup(errorMessage);
168	<	}
169	<	else if (the_type == INT ){
170	<	result = i->second->setData(the_event->evt.asmt.rhs.ival);
171	<	if (!result )
172	<	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 );
173	<	the_event->err_msg = strdup(errorMessage);
174	<
175	<	} else {
176	<	sprintf(errorMessage,  "Internal error of parser\n");
177	<	the_event->err_msg = strdup(errorMessage);
178	<	}
179	<	} else {
180	<	sprintf(errorMessage,  "%s is an unrecognized keyword\n", keyword.c_str() );
181	<	the_event->err_msg = strdup(errorMessage);
182	<	}
183	<
184	<	if (keyword == "nComponents" && getNComponents() > 0) {
185	<	components = new Component*[getNComponents()];
186	<	}else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
187	<	zConstraints = new ZconStamp*[getNZconstraints()];
188	<	}
189	<
190	<	return result;
191	<	}
192	<
193	<	int Globals::newComponent( event* the_event ){
194	<
195	<	current_component = new Component;
196	<	int index = the_event->evt.blk_index;
197	<	char err[200];
198	<
199	<	if( haveNComponents() && index < getNComponents() )
200	<	components[index] = current_component;
201	<	else{
202	<	if( haveNComponents()  ){
203	<	sprintf( err, "meta-data parsing error: %d out of nComponents range",
204	<	index );
205	<	the_event->err_msg = strdup( err );
206	<	return 0;
207	<	}
208	<	else{
209	<	the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
210	<	" first component declaration." );
211	<	return 0;
212	<	}
213	<	}
214	<
215	<	return 1;
216	<	}
217	<
218	<
219	<
220	<	int Globals::componentAssign( event* the_event ){
221	<
222	<	switch( the_event->evt.asmt.asmt_type ){
223	<
224	<	case STRING:
225	<	return current_component->assignString( the_event->evt.asmt.lhs,
226	<	the_event->evt.asmt.rhs.sval,
227	<	&(the_event->err_msg));
228	<	break;
229	<
230	<	case DOUBLE:
231	<	return current_component->assignDouble( the_event->evt.asmt.lhs,
232	<	the_event->evt.asmt.rhs.dval,
233	<	&(the_event->err_msg));
234	<	break;
235	<
236	<	case INT:
237	<	return current_component->assignInt( the_event->evt.asmt.lhs,
238	<	the_event->evt.asmt.rhs.ival,
239	<	&(the_event->err_msg));
240	<	break;
241	<
242	<	default:
243	<	the_event->err_msg = strdup( "Globals error. Invalid component"
244	<	" assignment type" );
245	<	return 0;
246	<	break;
247	<	}
248	<	return 0;
249	<	}
250	<
251	<	int Globals::componentEnd( event* the_event ){
252	<
253	<	the_event->err_msg = current_component->checkMe();
254	<	if( the_event->err_msg != NULL ) return 0;
129	>	DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
130	>	DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
131	>	DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
132	>	DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
133
134	<	return 1;
135	<	}
134	>	deprecatedKeywords_.insert("nComponents");
135	>	deprecatedKeywords_.insert("nZconstraints");
136	>	deprecatedKeywords_.insert("initialConfig");
137	>	deprecatedKeywords_.insert("thermIntDistSpringConst");
138	>	deprecatedKeywords_.insert("thermIntThetaSpringConst");
139	>	deprecatedKeywords_.insert("thermIntOmegaSpringConst");
140	>	deprecatedKeywords_.insert("useSolidThermInt");
141	>	deprecatedKeywords_.insert("useLiquidThermInt");
142	>	deprecatedKeywords_.insert("minimizerMaxIter");
143	>	deprecatedKeywords_.insert("minimizerWriteFreq");
144	>	deprecatedKeywords_.insert("minimizerStepSize");
145	>	deprecatedKeywords_.insert("minimizerFTol");
146	>	deprecatedKeywords_.insert("minimizerGTol");
147	>	deprecatedKeywords_.insert("minimizerLSTol");
148	>	deprecatedKeywords_.insert("minimizerLSMaxIter");
149
259	–	int Globals::newZconstraint( event* the_event ){
260	–
261	–
262	–	int index = the_event->evt.blk_index;
263	–	char err[200];
264	–	current_zConstraint = new ZconStamp( index );
265	–
266	–	if( haveNZconstraints() && index < getNZconstraints() )
267	–	zConstraints[index] = current_zConstraint;
268	–	else{
269	–	if( haveNZconstraints() ){
270	–	sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
271	–	index );
272	–	the_event->err_msg = strdup( err );
273	–	return 0;
274	–	}
275	–	else{
276	–	the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
277	–	" not given before"
278	–	" first zConstraint declaration." );
279	–	return 0;
280	–	}
281	–	}
282	–
283	–	return 1;
284	–	}
285	–
286	–
287	–
288	–	int Globals::zConstraintAssign( event* the_event ){
289	–
290	–	switch( the_event->evt.asmt.asmt_type ){
150
292	–	case STRING:
293	–	return current_zConstraint->assignString( the_event->evt.asmt.lhs,
294	–	the_event->evt.asmt.rhs.sval,
295	–	&(the_event->err_msg));
296	–	break;
297	–
298	–	case DOUBLE:
299	–	return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
300	–	the_event->evt.asmt.rhs.dval,
301	–	&(the_event->err_msg));
302	–	break;
303	–
304	–	case INT:
305	–	return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
306	–	the_event->evt.asmt.rhs.ival,
307	–	&(the_event->err_msg));
308	–	break;
309	–
310	–	default:
311	–	the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
312	–	" assignment type" );
313	–	return 0;
314	–	break;
315	–	}
316	–	return 0;
151		}
152
153	<	int Globals::zConstraintEnd( event* the_event ){
154	<
155	<	the_event->err_msg = current_zConstraint->checkMe();
156	<	if( the_event->err_msg != NULL ) return 0;
323	<
324	<	return 1;
153	>	Globals::~Globals() {
154	>	MemoryUtils::deletePointers(components_);
155	>	MemoryUtils::deletePointers(zconstraints_);
156	>	MemoryUtils::deletePointers(restraints_);
157		}
158
159	<	char* Globals::checkMe( void ){
159	>	void Globals::validate() {
160	>	DataHolder::validate();
161
329	–
330	–	std::string err("The following required keywords are missing:\n");
331	–	short int have_err = 0;
332	–
333	–	ParamMap::iterator i;
334	–	for (i = parameters_.begin(); i != parameters_.end(); ++i) {
335	–	if (!i->second->isOptional() && i->second->empty()) {
336	–	err +=  i->second->getKeyword() + "\n";
337	–	}
338	–	}
339	–
162		CheckParameter(ForceField, isNotEmpty());
341	–	CheckParameter(NComponents,isPositive());
163		CheckParameter(TargetTemp, isPositive());
164	<	CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) ||
344	<	isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf"))||
345	<	isEqualIgnoreCase(std::string("NPTxyz")) );
164	>	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"));
165		CheckParameter(Dt, isPositive());
166		CheckParameter(RunTime, isPositive());
348	–	CheckParameter(InitialConfig, isNotEmpty());
167		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());
168		CheckParameter(SampleTime, isNonNegative());
169		CheckParameter(ResetTime, isNonNegative());
170		CheckParameter(StatusTime, isNonNegative());
#	Line 360 | Line 172 | char* Globals::checkMe( void ){
172		CheckParameter(SwitchingRadius, isNonNegative());
173		CheckParameter(Dielectric, isPositive());
174		CheckParameter(ThermalTime,  isNonNegative());
363	–	CheckParameter(TargetPressure,  isPositive());
175		CheckParameter(TauThermostat, isPositive());
176		CheckParameter(TauBarostat, isPositive());
177		CheckParameter(ZconsTime, isPositive());
367	–	CheckParameter(NZconstraints, isPositive());
178		CheckParameter(ZconsTol, isPositive());
369	–	//CheckParameter(ZconsForcePolicy,);
179		CheckParameter(Seed, isPositive());
371	–	CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
372	–	CheckParameter(MinimizerMaxIter, isPositive());
373	–	CheckParameter(MinimizerWriteFrq, isPositive());
374	–	CheckParameter(MinimizerStepSize, isPositive());
375	–	CheckParameter(MinimizerFTol, isPositive());
376	–	CheckParameter(MinimizerGTol, isPositive());
377	–	CheckParameter(MinimizerLSTol, isPositive());
378	–	CheckParameter(MinimizerLSMaxIter, isPositive());
180		CheckParameter(ZconsGap, isPositive());
181		CheckParameter(ZconsFixtime, isPositive());
182	<	CheckParameter(ThermodynamicIntegrationLambda, isPositive());
182	>	CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
183		CheckParameter(ThermodynamicIntegrationK, isPositive());
184		CheckParameter(ForceFieldVariant, isNotEmpty());
185		CheckParameter(ForceFieldFileName, isNotEmpty());
186	<	CheckParameter(ThermIntDistSpringConst, isPositive());
187	<	CheckParameter(ThermIntThetaSpringConst, isPositive());
188	<	CheckParameter(ThermIntOmegaSpringConst, isPositive());
189	<	CheckParameter(SurfaceTension, isPositive());
190	<	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || isEqualIgnoreCase(std::string("SHIFTED_FORCE"))  || isEqualIgnoreCase(std::string("REACTION_FIELD")));
390	<	CheckParameter(ScreeningMethod, 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(StatFileFormat,);
393	<	//CheckParameter(MixingRule,);
186	>	CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE"));
187	>	CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
188	>	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
189	>	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
190	>	CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
191		CheckParameter(OrthoBoxTolerance, isPositive());
192	<	CheckParameter(ThermIntDistSpringConst, isPositive());
396	<	CheckParameter(ThermIntThetaSpringConst, isPositive());
397	<	CheckParameter(ThermIntOmegaSpringConst, isPositive());
398	<	CheckParameter(DampingAlpha,isPositive());
192	>	CheckParameter(DampingAlpha,isNonNegative());
193		CheckParameter(SkinThickness, isPositive());
194	+	CheckParameter(Viscosity, isNonNegative());
195	+	CheckParameter(BeadSize, isPositive());
196	+	CheckParameter(FrozenBufferRadius, isPositive());
197	+	CheckParameter(LangevinBufferRadius, isPositive());
198	+	CheckParameter(NeighborListNeighbors, isPositive());
199	+	CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
200	+	CheckParameter(Alpha, isPositive());
201
202	<	//@todo memory leak
203	<	if( have_err )
204	<	return strdup( err.c_str() );
205	<
206	<	return NULL;
202	>	for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
203	>	if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
204	>	std::ostringstream oss;
205	>	oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
206	>	throw OpenMDException(oss.str());
207	>	}
208	>	}
209	>	}
210
211	+	bool Globals::addComponent(Component* comp) {
212	+	components_.push_back(comp);
213	+	return true;
214	+	}
215
216	+	bool Globals::addZConsStamp(ZConsStamp* zcons) {
217	+	zconstraints_.push_back(zcons);
218	+	return true;
219		}
220
221	<	int Globals::globalEnd( event* the_event ){
222	<
223	<	the_event->err_msg = checkMe();
224	<	if( the_event->err_msg != NULL ) return 0;
221	>	bool Globals::addRestraintStamp(RestraintStamp* rest) {
222	>	restraints_.push_back(rest);
223	>	return true;
224	>	}
225
226	<	return 1;
226	>	bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
227	>	if (flucQpars_ != NULL)
228	>	delete flucQpars_;
229	>
230	>	flucQpars_ = fqp;
231	>	return true;
232		}
233	+
234	+	bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
235	+	if (rnemdPars_ != NULL)
236	+	delete rnemdPars_;
237	+
238	+	rnemdPars_ = rnemdPars;
239	+	return true;
240	+	}
241	+
242	+	bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
243	+	if (minimizerPars_ != NULL)
244	+	delete minimizerPars_;
245	+
246	+	minimizerPars_ = miniPars;
247	+	return true;
248	+	}
249	+
250	+	bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
251	+	std::string molStampName = molStamp->getName();
252	+	std::map<std::string, MoleculeStamp*>::iterator i;
253	+	bool ret = false;
254	+	i = moleculeStamps_.find(molStampName);
255	+	if (i == moleculeStamps_.end()) {
256	+	moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
257	+	ret = true;
258	+	} else {
259	+	std::ostringstream oss;
260	+	oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
261	+	throw OpenMDException(oss.str());
262	+	}
263	+	return ret;
264	+	}
265	+
266	+
267	+	}

Comparing:
trunk/src/io/Globals.cpp (property svn:keywords), Revision 710 by chrisfen, Wed Nov 2 20:36:25 2005 UTC vs.
branches/development/src/io/Globals.cpp (property svn:keywords), Revision 1746 by gezelter, Wed Jun 6 02:18:54 2012 UTC

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