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root/OpenMD/trunk/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.
Revision 2011 by gezelter, Wed Aug 6 19:27:37 2014 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, 234107 (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
60	<	#define DefineParameter(NAME,KEYWORD)                              \
61	<	NAME.setKeyword(KEYWORD);                  \
62	<	parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));
60	>	DefineParameter(ForceField, "forceField");
61	>
62	>	DefineOptionalParameter(TargetTemp, "targetTemp");
63	>	DefineOptionalParameter(Ensemble, "ensemble");
64	>	DefineOptionalParameter(Dt, "dt");
65	>	DefineOptionalParameter(RunTime, "runTime");
66	>	DefineOptionalParameter(FinalConfig, "finalConfig");
67	>	DefineOptionalParameter(SampleTime, "sampleTime");
68	>	DefineOptionalParameter(ResetTime, "resetTime");
69	>	DefineOptionalParameter(StatusTime, "statusTime");
70	>	DefineOptionalParameter(CutoffRadius, "cutoffRadius");
71	>	DefineOptionalParameter(SwitchingRadius, "switchingRadius");
72	>	DefineOptionalParameter(TempSet, "tempSet");
73	>	DefineOptionalParameter(ThermalTime, "thermalTime");
74	>	DefineOptionalParameter(TargetPressure, "targetPressure");
75	>	DefineOptionalParameter(TauThermostat, "tauThermostat");
76	>	DefineOptionalParameter(TauBarostat, "tauBarostat");
77	>	DefineOptionalParameter(ZconsTime, "zconsTime");
78	>	DefineOptionalParameter(ZconsTol, "zconsTol");
79	>	DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
80	>	DefineOptionalParameter(Seed, "seed");
81	>	DefineOptionalParameter(ZconsGap, "zconsGap");
82	>	DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
83	>	DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
84	>	DefineOptionalParameter(ThermodynamicIntegrationLambda,
85	>	"thermodynamicIntegrationLambda");
86	>	DefineOptionalParameter(ThermodynamicIntegrationK,
87	>	"thermodynamicIntegrationK");
88	>	DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
89	>	DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
90	>	DefineOptionalParameter(DampingAlpha, "dampingAlpha");
91	>	DefineOptionalParameter(SurfaceTension, "surfaceTension");
92	>	DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
93	>	DefineOptionalParameter(ElectricField, "electricField");
94
95	<	#define DefineOptionalParameter(NAME,KEYWORD)                              \
96	<	NAME.setKeyword(KEYWORD); NAME.setOptional(true);                    \
97	<	parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));
95	>	DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
96	>	DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
97	>	DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
98	>	DefineOptionalParameter(HydroPropFile, "HydroPropFile");
99	>	DefineOptionalParameter(Viscosity, "viscosity");
100	>	DefineOptionalParameter(BeadSize, "beadSize");
101	>	DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
102	>	DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
103	>	DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
104	>	DefineOptionalParameter(UseMultipleTemperatureMethod,
105	>	"useMultipleTemperatureMethod");
106	>	DefineOptionalParameter(ElectrostaticSummationMethod,
107	>	"electrostaticSummationMethod");
108	>	DefineOptionalParameter(MTM_Ce, "MTM_Ce");
109	>	DefineOptionalParameter(MTM_G, "MTM_G");
110	>	DefineOptionalParameter(MTM_Io, "MTM_Io");
111	>	DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
112	>	DefineOptionalParameter(MTM_R, "MTM_R");
113	>	DefineOptionalParameter(Alpha, "alpha");
114	>	DefineOptionalParameter(ConstraintTime, "constraintTime");
115
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	–
72	–	DefineParameter(ForceField, "forceField")
73	–	DefineParameter(NComponents, "nComponents")
74	–
75	–	DefineOptionalParameter(TargetTemp, "targetTemp");
76	–	DefineOptionalParameter(Ensemble, "ensemble");
77	–	DefineOptionalParameter(Dt, "dt");
78	–	DefineOptionalParameter(RunTime, "runTime");
79	–	DefineOptionalParameter(InitialConfig, "initialConfig");
80	–	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");
87	–	DefineOptionalParameter(SampleTime, "sampleTime");
88	–	DefineOptionalParameter(ResetTime, "resetTime");
89	–	DefineOptionalParameter(StatusTime, "statusTime");
90	–	DefineOptionalParameter(CutoffRadius, "cutoffRadius");
91	–	DefineOptionalParameter(SwitchingRadius, "switchingRadius");
92	–	DefineOptionalParameter(Dielectric, "dielectric");
93	–	DefineOptionalParameter(TempSet, "tempSet");
94	–	DefineOptionalParameter(ThermalTime, "thermalTime");
95	–	DefineOptionalParameter(TargetPressure, "targetPressure");
96	–	DefineOptionalParameter(TauThermostat, "tauThermostat");
97	–	DefineOptionalParameter(TauBarostat, "tauBarostat");
98	–	DefineOptionalParameter(ZconsTime, "zconsTime");
99	–	DefineOptionalParameter(NZconstraints, "nZconstraints");
100	–	DefineOptionalParameter(ZconsTol, "zconsTol");
101	–	DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
102	–	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");
111	–	DefineOptionalParameter(ZconsGap, "zconsGap");
112	–	DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
113	–	DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
114	–	DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
115	–	DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
116	–	DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
117	–	DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
118	–	DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
119	–	DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
120	–	DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
121	–	DefineOptionalParameter(SurfaceTension, "surfaceTension");
122	–	DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
123	–	DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
124	–	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
116
117	<	DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
118	<	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
119	<	DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
120	<	DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
121	<	DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
122	<	DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
123	<	DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
124	<	DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
125	<	DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
126	<	DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
127	<	DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 1.5);
128	<	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
129	<	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
130	<	DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
117	>	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions,
118	>	"usePeriodicBoundaryConditions",
119	>	true);
120	>	DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial",
121	>	true);
122	>	DefineOptionalParameterWithDefaultValue(UseLongRangeCorrections,
123	>	"useLongRangeCorrections", true);
124	>	DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime",
125	>	false);
126	>	DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState,
127	>	"useInitialExtendedSystemState",
128	>	false);
129	>	DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance,
130	>	"orthoBoxTolerance", 1E-6);
131	>	DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod",
132	>	"SHIFTED_FORCE");
133	>	DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod,
134	>	"electrostaticScreeningMethod",
135	>	"DAMPED");
136	>	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
137	>	DefineOptionalParameterWithDefaultValue(CompressDumpFile,
138	>	"compressDumpFile", false);
139	>	DefineOptionalParameterWithDefaultValue(PrintHeatFlux, "printHeatFlux",
140	>	false);
141	>	DefineOptionalParameterWithDefaultValue(OutputForceVector,
142	>	"outputForceVector", false);
143	>	DefineOptionalParameterWithDefaultValue(OutputParticlePotential,
144	>	"outputParticlePotential", false);
145	>	DefineOptionalParameterWithDefaultValue(OutputElectricField,
146	>	"outputElectricField", false);
147	>	DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges,
148	>	"outputFluctuatingCharges", false);
149	>	DefineOptionalParameterWithDefaultValue(OutputSitePotential,
150	>	"outputSitePotential", false);
151	>	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness",
152	>	1.0);
153	>	DefineOptionalParameterWithDefaultValue(StatFileFormat,
154	>	"statFileFormat",
155	>	"TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
156	>	DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions,
157	>	"useSphericalBoundaryConditions",
158	>	false);
159	>	DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole,
160	>	"accumulateBoxDipole", false);
161	>	DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints",
162	>	false);
163	>	DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file",
164	>	"idealCrystal.in");
165	>	DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration,
166	>	"useThermodynamicIntegration",
167	>	false);
168	>	DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
169
170	<
171	<	}
170	>	deprecatedKeywords_.insert("nComponents");
171	>	deprecatedKeywords_.insert("nZconstraints");
172	>	deprecatedKeywords_.insert("initialConfig");
173	>	deprecatedKeywords_.insert("thermIntDistSpringConst");
174	>	deprecatedKeywords_.insert("thermIntThetaSpringConst");
175	>	deprecatedKeywords_.insert("thermIntOmegaSpringConst");
176	>	deprecatedKeywords_.insert("useSolidThermInt");
177	>	deprecatedKeywords_.insert("useLiquidThermInt");
178	>	deprecatedKeywords_.insert("minimizerMaxIter");
179	>	deprecatedKeywords_.insert("minimizerWriteFreq");
180	>	deprecatedKeywords_.insert("minimizerStepSize");
181	>	deprecatedKeywords_.insert("minimizerFTol");
182	>	deprecatedKeywords_.insert("minimizerGTol");
183	>	deprecatedKeywords_.insert("minimizerLSTol");
184	>	deprecatedKeywords_.insert("minimizerLSMaxIter");
185
186	<	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);
186	>
187		}
188
189	<	if (keyword == "nComponents" && getNComponents() > 0) {
190	<	components = new Component*[getNComponents()];
191	<	}else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
192	<	zConstraints = new ZconStamp*[getNZconstraints()];
189	>	Globals::~Globals() {
190	>	MemoryUtils::deletePointers(components_);
191	>	MemoryUtils::deletePointers(zconstraints_);
192	>	MemoryUtils::deletePointers(restraints_);
193	>	delete flucQpars_;
194	>	delete rnemdPars_;
195	>	delete minimizerPars_;
196		}
188	–
189	–	return result;
190	–	}
197
198	<	int Globals::newComponent( event* the_event ){
199	<
200	<	current_component = new Component;
201	<	int index = the_event->evt.blk_index;
202	<	char err[200];
203	<
204	<	if( haveNComponents() && index < getNComponents() )
205	<	components[index] = current_component;
206	<	else{
207	<	if( haveNComponents()  ){
208	<	sprintf( err, "meta-data parsing error: %d out of nComponents range",
209	<	index );
210	<	the_event->err_msg = strdup( err );
211	<	return 0;
212	<	}
213	<	else{
214	<	the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
215	<	" first component declaration." );
216	<	return 0;
217	<	}
218	<	}
219	<
220	<	return 1;
221	<	}
198	>	void Globals::validate() {
199	>	DataHolder::validate();
200	>
201	>	CheckParameter(ForceField, isNotEmpty());
202	>	CheckParameter(TargetTemp, isPositive());
203	>	CheckParameter(Ensemble, isEqualIgnoreCase("NVE") ||
204	>	isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") ||
205	>	isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") ||
206	>	isEqualIgnoreCase("NPTsz") || isEqualIgnoreCase("NPAT")  ||
207	>	isEqualIgnoreCase("NPA") ||
208	>	isEqualIgnoreCase("LANGEVINDYNAMICS") ||
209	>	isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") ||
210	>	isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") ||
211	>	isEqualIgnoreCase("NGT") ||
212	>	isEqualIgnoreCase("LANGEVINHULL") ||
213	>	isEqualIgnoreCase("LHULL") || isEqualIgnoreCase("SMIPD"));
214	>	CheckParameter(Dt, isPositive());
215	>	CheckParameter(RunTime, isPositive());
216	>	CheckParameter(FinalConfig, isNotEmpty());
217	>	CheckParameter(SampleTime, isNonNegative());
218	>	CheckParameter(ResetTime, isNonNegative());
219	>	CheckParameter(StatusTime, isNonNegative());
220	>	CheckParameter(CutoffRadius, isPositive());
221	>	CheckParameter(SwitchingRadius, isNonNegative());
222	>	CheckParameter(Dielectric, isPositive());
223	>	CheckParameter(ThermalTime,  isNonNegative());
224	>	CheckParameter(TauThermostat, isPositive());
225	>	CheckParameter(TauBarostat, isPositive());
226	>	CheckParameter(ZconsTime, isPositive());
227	>	CheckParameter(ZconsTol, isPositive());
228	>	CheckParameter(Seed, isPositive());
229	>	CheckParameter(ZconsGap, isPositive());
230	>	CheckParameter(ZconsFixtime, isPositive());
231	>	CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
232	>	CheckParameter(ThermodynamicIntegrationK, isPositive());
233	>	CheckParameter(ForceFieldVariant, isNotEmpty());
234	>	CheckParameter(ForceFieldFileName, isNotEmpty());
235	>	CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") ||
236	>	isEqualIgnoreCase("SWITCHED") ||
237	>	isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
238	>	isEqualIgnoreCase("SHIFTED_FORCE") ||
239	>	isEqualIgnoreCase("TAYLOR_SHIFTED") ||
240	>	isEqualIgnoreCase("EWALD_FULL"));
241	>	CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") ||
242	>	isEqualIgnoreCase("MAX") ||
243	>	isEqualIgnoreCase("TRADITIONAL"));
244	>	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") ||
245	>	isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") ||
246	>	isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
247	>	isEqualIgnoreCase("SHIFTED_FORCE") ||
248	>	isEqualIgnoreCase("REACTION_FIELD") ||
249	>	isEqualIgnoreCase("TAYLOR_SHIFTED"));
250	>	CheckParameter(ElectrostaticScreeningMethod,
251	>	isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
252	>	CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") ||
253	>	isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
254	>	CheckParameter(OrthoBoxTolerance, isPositive());
255	>	CheckParameter(DampingAlpha,isNonNegative());
256	>	CheckParameter(SkinThickness, isPositive());
257	>	CheckParameter(Viscosity, isNonNegative());
258	>	CheckParameter(BeadSize, isPositive());
259	>	CheckParameter(FrozenBufferRadius, isPositive());
260	>	CheckParameter(LangevinBufferRadius, isPositive());
261	>	CheckParameter(NeighborListNeighbors, isPositive());
262	>	CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") ||
263	>	isEqualIgnoreCase("AlphaShape"));
264	>	CheckParameter(Alpha, isPositive());
265	>
266	>	for(std::vector<Component*>::iterator i = components_.begin();
267	>	i != components_.end(); ++i) {
268	>	if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
269	>	std::ostringstream oss;
270	>	oss << "Globals Error: can not find molecule stamp for component "
271	>	<< (*i)->getType() << std::endl;
272	>	throw OpenMDException(oss.str());
273	>	}
274	>	}
275	>	}
276	>
277	>	bool Globals::addComponent(Component* comp) {
278	>	components_.push_back(comp);
279	>	return true;
280	>	}
281
282	+	bool Globals::addZConsStamp(ZConsStamp* zcons) {
283	+	zconstraints_.push_back(zcons);
284	+	return true;
285	+	}
286
287	+	bool Globals::addRestraintStamp(RestraintStamp* rest) {
288	+	restraints_.push_back(rest);
289	+	return true;
290	+	}
291
292	<	int Globals::componentAssign( event* the_event ){
292	>	bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
293	>	if (flucQpars_ != NULL)
294	>	delete flucQpars_;
295	>
296	>	flucQpars_ = fqp;
297	>	return true;
298	>	}
299
300	<	switch( the_event->evt.asmt.asmt_type ){
300	>	bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
301	>	if (rnemdPars_ != NULL)
302	>	delete rnemdPars_;
303
304	<	case STRING:
305	<	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;
304	>	rnemdPars_ = rnemdPars;
305	>	return true;
306		}
247	–	return 0;
248	–	}
307
308	<	int Globals::componentEnd( event* the_event ){
309	<
310	<	the_event->err_msg = current_component->checkMe();
253	<	if( the_event->err_msg != NULL ) return 0;
254	<
255	<	return 1;
256	<	}
257	<
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 ){
308	>	bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
309	>	if (minimizerPars_ != NULL)
310	>	delete minimizerPars_;
311
312	<	case STRING:
313	<	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;
312	>	minimizerPars_ = miniPars;
313	>	return true;
314		}
315	–	return 0;
316	–	}
315
316	<	int Globals::zConstraintEnd( event* the_event ){
317	<
318	<	the_event->err_msg = current_zConstraint->checkMe();
319	<	if( the_event->err_msg != NULL ) return 0;
320	<
321	<	return 1;
322	<	}
323	<
324	<	char* Globals::checkMe( void ){
325	<
326	<
327	<	std::string err("The following required keywords are missing:\n");
328	<	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";
316	>	bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
317	>	std::string molStampName = molStamp->getName();
318	>	std::map<std::string, MoleculeStamp*>::iterator i;
319	>	bool ret = false;
320	>	i = moleculeStamps_.find(molStampName);
321	>	if (i == moleculeStamps_.end()) {
322	>	moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
323	>	ret = true;
324	>	} else {
325	>	std::ostringstream oss;
326	>	oss << "Globals Error: Molecule Stamp " << molStamp->getName()
327	>	<< "appears multiple times\n";
328	>	throw OpenMDException(oss.str());
329		}
330	+	return ret;
331		}
338	–
339	–	CheckParameter(ForceField, isNotEmpty());
340	–	CheckParameter(NComponents,isPositive());
341	–	CheckParameter(TargetTemp, isPositive());
342	–	CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) ||
343	–	isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf"))||
344	–	isEqualIgnoreCase(std::string("NPTxyz")) );
345	–	CheckParameter(Dt, isPositive());
346	–	CheckParameter(RunTime, isPositive());
347	–	CheckParameter(InitialConfig, isNotEmpty());
348	–	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());
355	–	CheckParameter(SampleTime, isNonNegative());
356	–	CheckParameter(ResetTime, isNonNegative());
357	–	CheckParameter(StatusTime, isNonNegative());
358	–	CheckParameter(CutoffRadius, isPositive());
359	–	CheckParameter(SwitchingRadius, isNonNegative());
360	–	CheckParameter(Dielectric, isPositive());
361	–	CheckParameter(ThermalTime,  isNonNegative());
362	–	CheckParameter(TargetPressure,  isPositive());
363	–	CheckParameter(TauThermostat, isPositive());
364	–	CheckParameter(TauBarostat, isPositive());
365	–	CheckParameter(ZconsTime, isPositive());
366	–	CheckParameter(NZconstraints, isPositive());
367	–	CheckParameter(ZconsTol, isPositive());
368	–	//CheckParameter(ZconsForcePolicy,);
369	–	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());
378	–	CheckParameter(ZconsGap, isPositive());
379	–	CheckParameter(ZconsFixtime, isPositive());
380	–	CheckParameter(ThermodynamicIntegrationLambda, isPositive());
381	–	CheckParameter(ThermodynamicIntegrationK, isPositive());
382	–	CheckParameter(ForceFieldVariant, isNotEmpty());
383	–	CheckParameter(ForceFieldFileName, isNotEmpty());
384	–	CheckParameter(ThermIntDistSpringConst, isPositive());
385	–	CheckParameter(ThermIntThetaSpringConst, isPositive());
386	–	CheckParameter(ThermIntOmegaSpringConst, isPositive());
387	–	CheckParameter(SurfaceTension, isPositive());
388	–	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,);
392	–	CheckParameter(OrthoBoxTolerance, isPositive());
393	–	CheckParameter(ThermIntDistSpringConst, isPositive());
394	–	CheckParameter(ThermIntThetaSpringConst, isPositive());
395	–	CheckParameter(ThermIntOmegaSpringConst, isPositive());
396	–	CheckParameter(DampingAlpha,isPositive());
397	–	CheckParameter(SkinThickness, isPositive());
398	–
399	–	//@todo memory leak
400	–	if( have_err )
401	–	return strdup( err.c_str() );
402	–
403	–	return NULL;
404	–
405	–
332		}
407	–
408	–	int Globals::globalEnd( event* the_event ){
409	–
410	–	the_event->err_msg = checkMe();
411	–	if( the_event->err_msg != NULL ) return 0;
412	–
413	–	return 1;
414	–	}

Comparing trunk/src/io/Globals.cpp (property svn:keywords):
Revision 705 by chrisfen, Tue Nov 1 19:14:27 2005 UTC vs.
Revision 2011 by gezelter, Wed Aug 6 19:27:37 2014 UTC

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