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 705 by chrisfen, Tue Nov 1 19:14:27 2005 UTC vs.
branches/development/src/io/Globals.cpp (file contents), Revision 1749 by gezelter, Thu Jun 7 02:47:21 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	+
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(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
126	–	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(PrintHeatFlux, "printHeatFlux", false);
121	>	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false);
122	>	DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false);
123	>	DefineOptionalParameterWithDefaultValue(OutputElectricField, "outputElectricField", false);
124	>	DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, "outputFluctuatingCharges", false);
125		DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
126		DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
127	+	DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
128	+	DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
129
130	<
131	<	}
132	<
133	<	int Globals::globalAssign( event* the_event ){
145	<	char errorMessage[65535];
146	<	int key;
147	<	interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
148	<	char* lhs = the_event->evt.asmt.lhs;
149	<	std::string keyword(lhs);
150	<
151	<	bool result = false;
152	<
153	<	/**@todo fix memory leak */
154	<	ParamMap::iterator i =parameters_.find(keyword);
155	<	if (i != parameters_.end()) {
156	<	if( the_type == STRING ){
157	<	result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
158	<	if (!result ) {
159	<	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);
160	<	the_event->err_msg = strdup(errorMessage);
161	<	}
162	<	} else if( the_type == DOUBLE ){
163	<	result = i->second->setData(the_event->evt.asmt.rhs.dval);
164	<	if (!result )
165	<	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 );
166	<	the_event->err_msg = strdup(errorMessage);
167	<	}
168	<	else if (the_type == INT ){
169	<	result = i->second->setData(the_event->evt.asmt.rhs.ival);
170	<	if (!result )
171	<	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 );
172	<	the_event->err_msg = strdup(errorMessage);
173	<
174	<	} else {
175	<	sprintf(errorMessage,  "Internal error of parser\n");
176	<	the_event->err_msg = strdup(errorMessage);
177	<	}
178	<	} else {
179	<	sprintf(errorMessage,  "%s is an unrecognized keyword\n", keyword.c_str() );
180	<	the_event->err_msg = strdup(errorMessage);
181	<	}
182	<
183	<	if (keyword == "nComponents" && getNComponents() > 0) {
184	<	components = new Component*[getNComponents()];
185	<	}else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
186	<	zConstraints = new ZconStamp*[getNZconstraints()];
187	<	}
188	<
189	<	return result;
190	<	}
191	<
192	<	int Globals::newComponent( event* the_event ){
193	<
194	<	current_component = new Component;
195	<	int index = the_event->evt.blk_index;
196	<	char err[200];
197	<
198	<	if( haveNComponents() && index < getNComponents() )
199	<	components[index] = current_component;
200	<	else{
201	<	if( haveNComponents()  ){
202	<	sprintf( err, "meta-data parsing error: %d out of nComponents range",
203	<	index );
204	<	the_event->err_msg = strdup( err );
205	<	return 0;
206	<	}
207	<	else{
208	<	the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
209	<	" first component declaration." );
210	<	return 0;
211	<	}
212	<	}
213	<
214	<	return 1;
215	<	}
216	<
217	<
218	<
219	<	int Globals::componentAssign( event* the_event ){
220	<
221	<	switch( the_event->evt.asmt.asmt_type ){
222	<
223	<	case STRING:
224	<	return current_component->assignString( the_event->evt.asmt.lhs,
225	<	the_event->evt.asmt.rhs.sval,
226	<	&(the_event->err_msg));
227	<	break;
228	<
229	<	case DOUBLE:
230	<	return current_component->assignDouble( the_event->evt.asmt.lhs,
231	<	the_event->evt.asmt.rhs.dval,
232	<	&(the_event->err_msg));
233	<	break;
234	<
235	<	case INT:
236	<	return current_component->assignInt( the_event->evt.asmt.lhs,
237	<	the_event->evt.asmt.rhs.ival,
238	<	&(the_event->err_msg));
239	<	break;
240	<
241	<	default:
242	<	the_event->err_msg = strdup( "Globals error. Invalid component"
243	<	" assignment type" );
244	<	return 0;
245	<	break;
246	<	}
247	<	return 0;
248	<	}
249	<
250	<	int Globals::componentEnd( event* the_event ){
251	<
252	<	the_event->err_msg = current_component->checkMe();
253	<	if( the_event->err_msg != NULL ) return 0;
130	>	DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
131	>	DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
132	>	DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
133	>	DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
134
135	<	return 1;
136	<	}
135	>	deprecatedKeywords_.insert("nComponents");
136	>	deprecatedKeywords_.insert("nZconstraints");
137	>	deprecatedKeywords_.insert("initialConfig");
138	>	deprecatedKeywords_.insert("thermIntDistSpringConst");
139	>	deprecatedKeywords_.insert("thermIntThetaSpringConst");
140	>	deprecatedKeywords_.insert("thermIntOmegaSpringConst");
141	>	deprecatedKeywords_.insert("useSolidThermInt");
142	>	deprecatedKeywords_.insert("useLiquidThermInt");
143	>	deprecatedKeywords_.insert("minimizerMaxIter");
144	>	deprecatedKeywords_.insert("minimizerWriteFreq");
145	>	deprecatedKeywords_.insert("minimizerStepSize");
146	>	deprecatedKeywords_.insert("minimizerFTol");
147	>	deprecatedKeywords_.insert("minimizerGTol");
148	>	deprecatedKeywords_.insert("minimizerLSTol");
149	>	deprecatedKeywords_.insert("minimizerLSMaxIter");
150
258	–	int Globals::newZconstraint( event* the_event ){
259	–
260	–
261	–	int index = the_event->evt.blk_index;
262	–	char err[200];
263	–	current_zConstraint = new ZconStamp( index );
264	–
265	–	if( haveNZconstraints() && index < getNZconstraints() )
266	–	zConstraints[index] = current_zConstraint;
267	–	else{
268	–	if( haveNZconstraints() ){
269	–	sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
270	–	index );
271	–	the_event->err_msg = strdup( err );
272	–	return 0;
273	–	}
274	–	else{
275	–	the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
276	–	" not given before"
277	–	" first zConstraint declaration." );
278	–	return 0;
279	–	}
280	–	}
281	–
282	–	return 1;
283	–	}
284	–
285	–
286	–
287	–	int Globals::zConstraintAssign( event* the_event ){
288	–
289	–	switch( the_event->evt.asmt.asmt_type ){
151
291	–	case STRING:
292	–	return current_zConstraint->assignString( the_event->evt.asmt.lhs,
293	–	the_event->evt.asmt.rhs.sval,
294	–	&(the_event->err_msg));
295	–	break;
296	–
297	–	case DOUBLE:
298	–	return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
299	–	the_event->evt.asmt.rhs.dval,
300	–	&(the_event->err_msg));
301	–	break;
302	–
303	–	case INT:
304	–	return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
305	–	the_event->evt.asmt.rhs.ival,
306	–	&(the_event->err_msg));
307	–	break;
308	–
309	–	default:
310	–	the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
311	–	" assignment type" );
312	–	return 0;
313	–	break;
314	–	}
315	–	return 0;
152		}
153
154	<	int Globals::zConstraintEnd( event* the_event ){
155	<
156	<	the_event->err_msg = current_zConstraint->checkMe();
157	<	if( the_event->err_msg != NULL ) return 0;
322	<
323	<	return 1;
154	>	Globals::~Globals() {
155	>	MemoryUtils::deletePointers(components_);
156	>	MemoryUtils::deletePointers(zconstraints_);
157	>	MemoryUtils::deletePointers(restraints_);
158		}
159
160	<	char* Globals::checkMe( void ){
160	>	void Globals::validate() {
161	>	DataHolder::validate();
162
328	–
329	–	std::string err("The following required keywords are missing:\n");
330	–	short int have_err = 0;
331	–
332	–	ParamMap::iterator i;
333	–	for (i = parameters_.begin(); i != parameters_.end(); ++i) {
334	–	if (!i->second->isOptional() && i->second->empty()) {
335	–	err +=  i->second->getKeyword() + "\n";
336	–	}
337	–	}
338	–
163		CheckParameter(ForceField, isNotEmpty());
340	–	CheckParameter(NComponents,isPositive());
164		CheckParameter(TargetTemp, isPositive());
165	<	CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) ||
343	<	isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf"))||
344	<	isEqualIgnoreCase(std::string("NPTxyz")) );
165	>	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"));
166		CheckParameter(Dt, isPositive());
167		CheckParameter(RunTime, isPositive());
347	–	CheckParameter(InitialConfig, isNotEmpty());
168		CheckParameter(FinalConfig, isNotEmpty());
349	–	CheckParameter(NMol, isPositive());
350	–	CheckParameter(Density, isPositive());
351	–	CheckParameter(Box, isPositive());
352	–	CheckParameter(BoxX, isPositive());
353	–	CheckParameter(BoxY, isPositive());
354	–	CheckParameter(BoxZ, isPositive());
169		CheckParameter(SampleTime, isNonNegative());
170		CheckParameter(ResetTime, isNonNegative());
171		CheckParameter(StatusTime, isNonNegative());
#	Line 359 | Line 173 | char* Globals::checkMe( void ){
173		CheckParameter(SwitchingRadius, isNonNegative());
174		CheckParameter(Dielectric, isPositive());
175		CheckParameter(ThermalTime,  isNonNegative());
362	–	CheckParameter(TargetPressure,  isPositive());
176		CheckParameter(TauThermostat, isPositive());
177		CheckParameter(TauBarostat, isPositive());
178		CheckParameter(ZconsTime, isPositive());
366	–	CheckParameter(NZconstraints, isPositive());
179		CheckParameter(ZconsTol, isPositive());
368	–	//CheckParameter(ZconsForcePolicy,);
180		CheckParameter(Seed, isPositive());
370	–	CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
371	–	CheckParameter(MinimizerMaxIter, isPositive());
372	–	CheckParameter(MinimizerWriteFrq, isPositive());
373	–	CheckParameter(MinimizerStepSize, isPositive());
374	–	CheckParameter(MinimizerFTol, isPositive());
375	–	CheckParameter(MinimizerGTol, isPositive());
376	–	CheckParameter(MinimizerLSTol, isPositive());
377	–	CheckParameter(MinimizerLSMaxIter, isPositive());
181		CheckParameter(ZconsGap, isPositive());
182		CheckParameter(ZconsFixtime, isPositive());
183	<	CheckParameter(ThermodynamicIntegrationLambda, isPositive());
183	>	CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
184		CheckParameter(ThermodynamicIntegrationK, isPositive());
185		CheckParameter(ForceFieldVariant, isNotEmpty());
186		CheckParameter(ForceFieldFileName, isNotEmpty());
187	<	CheckParameter(ThermIntDistSpringConst, isPositive());
188	<	CheckParameter(ThermIntThetaSpringConst, isPositive());
189	<	CheckParameter(ThermIntOmegaSpringConst, isPositive());
190	<	CheckParameter(SurfaceTension, isPositive());
191	<	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("UNDAMPED_WOLF")) || isEqualIgnoreCase(std::string("DAMPED_WOLF")) || isEqualIgnoreCase(std::string("REACTION_FIELD")) );
389	<	CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
390	<	//CheckParameter(StatFileFormat,);
391	<	//CheckParameter(MixingRule,);
187	>	CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE"));
188	>	CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
189	>	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
190	>	CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
191	>	CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
192		CheckParameter(OrthoBoxTolerance, isPositive());
193	<	CheckParameter(ThermIntDistSpringConst, isPositive());
394	<	CheckParameter(ThermIntThetaSpringConst, isPositive());
395	<	CheckParameter(ThermIntOmegaSpringConst, isPositive());
396	<	CheckParameter(DampingAlpha,isPositive());
193	>	CheckParameter(DampingAlpha,isNonNegative());
194		CheckParameter(SkinThickness, isPositive());
195	+	CheckParameter(Viscosity, isNonNegative());
196	+	CheckParameter(BeadSize, isPositive());
197	+	CheckParameter(FrozenBufferRadius, isPositive());
198	+	CheckParameter(LangevinBufferRadius, isPositive());
199	+	CheckParameter(NeighborListNeighbors, isPositive());
200	+	CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape"));
201	+	CheckParameter(Alpha, isPositive());
202
203	<	//@todo memory leak
204	<	if( have_err )
205	<	return strdup( err.c_str() );
206	<
207	<	return NULL;
203	>	for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
204	>	if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
205	>	std::ostringstream oss;
206	>	oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
207	>	throw OpenMDException(oss.str());
208	>	}
209	>	}
210	>	}
211
212	+	bool Globals::addComponent(Component* comp) {
213	+	components_.push_back(comp);
214	+	return true;
215	+	}
216
217	+	bool Globals::addZConsStamp(ZConsStamp* zcons) {
218	+	zconstraints_.push_back(zcons);
219	+	return true;
220		}
221
222	<	int Globals::globalEnd( event* the_event ){
223	<
224	<	the_event->err_msg = checkMe();
225	<	if( the_event->err_msg != NULL ) return 0;
222	>	bool Globals::addRestraintStamp(RestraintStamp* rest) {
223	>	restraints_.push_back(rest);
224	>	return true;
225	>	}
226
227	<	return 1;
227	>	bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
228	>	if (flucQpars_ != NULL)
229	>	delete flucQpars_;
230	>
231	>	flucQpars_ = fqp;
232	>	return true;
233		}
234	+
235	+	bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
236	+	if (rnemdPars_ != NULL)
237	+	delete rnemdPars_;
238	+
239	+	rnemdPars_ = rnemdPars;
240	+	return true;
241	+	}
242	+
243	+	bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
244	+	if (minimizerPars_ != NULL)
245	+	delete minimizerPars_;
246	+
247	+	minimizerPars_ = miniPars;
248	+	return true;
249	+	}
250	+
251	+	bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
252	+	std::string molStampName = molStamp->getName();
253	+	std::map<std::string, MoleculeStamp*>::iterator i;
254	+	bool ret = false;
255	+	i = moleculeStamps_.find(molStampName);
256	+	if (i == moleculeStamps_.end()) {
257	+	moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
258	+	ret = true;
259	+	} else {
260	+	std::ostringstream oss;
261	+	oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
262	+	throw OpenMDException(oss.str());
263	+	}
264	+	return ret;
265	+	}
266	+
267	+
268	+	}

Comparing:
trunk/src/io/Globals.cpp (property svn:keywords), Revision 705 by chrisfen, Tue Nov 1 19:14:27 2005 UTC vs.
branches/development/src/io/Globals.cpp (property svn:keywords), Revision 1749 by gezelter, Thu Jun 7 02:47:21 2012 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

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