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root/OpenMD/trunk/src/io/Globals.cpp

Comparing trunk/src/io/Globals.cpp (file contents):
Revision 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC vs.
Revision 1981 by gezelter, Mon Apr 14 18:32:51 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(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
125	–	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
126	–	DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
127	–	DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
128	–	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
129	–	DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
130	–	DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
131	–	DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
132	–	DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
133	–	DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
134	–	DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
135	–	DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
136	–	DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
137	–	DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
138	–	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
139	–	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
140	–	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
141	–	DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
142	–
116
117	<	}
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(SkinThickness, "skinThickness",
150	>	1.0);
151	>	DefineOptionalParameterWithDefaultValue(StatFileFormat,
152	>	"statFileFormat",
153	>	"TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
154	>	DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions,
155	>	"useSphericalBoundaryConditions",
156	>	false);
157	>	DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole,
158	>	"accumulateBoxDipole", false);
159	>	DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints",
160	>	false);
161	>	DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file",
162	>	"idealCrystal.in");
163	>	DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration,
164	>	"useThermodynamicIntegration",
165	>	false);
166	>	DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
167
168	<	int Globals::globalAssign( event* the_event ){
169	<	char errorMessage[65535];
170	<	int key;
171	<	interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
172	<	char* lhs = the_event->evt.asmt.lhs;
173	<	std::string keyword(lhs);
168	>	deprecatedKeywords_.insert("nComponents");
169	>	deprecatedKeywords_.insert("nZconstraints");
170	>	deprecatedKeywords_.insert("initialConfig");
171	>	deprecatedKeywords_.insert("thermIntDistSpringConst");
172	>	deprecatedKeywords_.insert("thermIntThetaSpringConst");
173	>	deprecatedKeywords_.insert("thermIntOmegaSpringConst");
174	>	deprecatedKeywords_.insert("useSolidThermInt");
175	>	deprecatedKeywords_.insert("useLiquidThermInt");
176	>	deprecatedKeywords_.insert("minimizerMaxIter");
177	>	deprecatedKeywords_.insert("minimizerWriteFreq");
178	>	deprecatedKeywords_.insert("minimizerStepSize");
179	>	deprecatedKeywords_.insert("minimizerFTol");
180	>	deprecatedKeywords_.insert("minimizerGTol");
181	>	deprecatedKeywords_.insert("minimizerLSTol");
182	>	deprecatedKeywords_.insert("minimizerLSMaxIter");
183
184	<	bool result = false;
154	<
155	<	/**@todo fix memory leak */
156	<	ParamMap::iterator i =parameters_.find(keyword);
157	<	if (i != parameters_.end()) {
158	<	if( the_type == STRING ){
159	<	result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
160	<	if (!result ) {
161	<	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);
162	<	the_event->err_msg = strdup(errorMessage);
163	<	}
164	<	} else if( the_type == DOUBLE ){
165	<	result = i->second->setData(the_event->evt.asmt.rhs.dval);
166	<	if (!result )
167	<	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 );
168	<	the_event->err_msg = strdup(errorMessage);
169	<	}
170	<	else if (the_type == INT ){
171	<	result = i->second->setData(the_event->evt.asmt.rhs.ival);
172	<	if (!result )
173	<	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 );
174	<	the_event->err_msg = strdup(errorMessage);
175	<
176	<	} else {
177	<	sprintf(errorMessage,  "Internal error of parser\n");
178	<	the_event->err_msg = strdup(errorMessage);
179	<	}
180	<	} else {
181	<	sprintf(errorMessage,  "%s is an unrecognized keyword\n", keyword.c_str() );
182	<	the_event->err_msg = strdup(errorMessage);
184	>
185		}
186
187	<	if (keyword == "nComponents" && getNComponents() > 0) {
188	<	components = new Component*[getNComponents()];
189	<	}else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
190	<	zConstraints = new ZconStamp*[getNZconstraints()];
187	>	Globals::~Globals() {
188	>	MemoryUtils::deletePointers(components_);
189	>	MemoryUtils::deletePointers(zconstraints_);
190	>	MemoryUtils::deletePointers(restraints_);
191	>	delete flucQpars_;
192	>	delete rnemdPars_;
193	>	delete minimizerPars_;
194		}
190	–
191	–	return result;
192	–	}
195
196	<	int Globals::newComponent( event* the_event ){
197	<
198	<	current_component = new Component;
199	<	int index = the_event->evt.blk_index;
200	<	char err[200];
201	<
202	<	if( haveNComponents() && index < getNComponents() )
203	<	components[index] = current_component;
204	<	else{
205	<	if( haveNComponents()  ){
206	<	sprintf( err, "meta-data parsing error: %d out of nComponents range",
207	<	index );
208	<	the_event->err_msg = strdup( err );
209	<	return 0;
210	<	}
211	<	else{
212	<	the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
213	<	" first component declaration." );
214	<	return 0;
215	<	}
216	<	}
217	<
218	<	return 1;
219	<	}
196	>	void Globals::validate() {
197	>	DataHolder::validate();
198	>
199	>	CheckParameter(ForceField, isNotEmpty());
200	>	CheckParameter(TargetTemp, isPositive());
201	>	CheckParameter(Ensemble, isEqualIgnoreCase("NVE") ||
202	>	isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") ||
203	>	isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") ||
204	>	isEqualIgnoreCase("NPTsz") || isEqualIgnoreCase("NPAT")  ||
205	>	isEqualIgnoreCase("LANGEVINDYNAMICS") ||
206	>	isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") ||
207	>	isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") ||
208	>	isEqualIgnoreCase("NGT") ||
209	>	isEqualIgnoreCase("LANGEVINHULL") ||
210	>	isEqualIgnoreCase("LHULL") || isEqualIgnoreCase("SMIPD"));
211	>	CheckParameter(Dt, isPositive());
212	>	CheckParameter(RunTime, isPositive());
213	>	CheckParameter(FinalConfig, isNotEmpty());
214	>	CheckParameter(SampleTime, isNonNegative());
215	>	CheckParameter(ResetTime, isNonNegative());
216	>	CheckParameter(StatusTime, isNonNegative());
217	>	CheckParameter(CutoffRadius, isPositive());
218	>	CheckParameter(SwitchingRadius, isNonNegative());
219	>	CheckParameter(Dielectric, isPositive());
220	>	CheckParameter(ThermalTime,  isNonNegative());
221	>	CheckParameter(TauThermostat, isPositive());
222	>	CheckParameter(TauBarostat, isPositive());
223	>	CheckParameter(ZconsTime, isPositive());
224	>	CheckParameter(ZconsTol, isPositive());
225	>	CheckParameter(Seed, isPositive());
226	>	CheckParameter(ZconsGap, isPositive());
227	>	CheckParameter(ZconsFixtime, isPositive());
228	>	CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
229	>	CheckParameter(ThermodynamicIntegrationK, isPositive());
230	>	CheckParameter(ForceFieldVariant, isNotEmpty());
231	>	CheckParameter(ForceFieldFileName, isNotEmpty());
232	>	CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") ||
233	>	isEqualIgnoreCase("SWITCHED") ||
234	>	isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
235	>	isEqualIgnoreCase("SHIFTED_FORCE") ||
236	>	isEqualIgnoreCase("TAYLOR_SHIFTED") ||
237	>	isEqualIgnoreCase("EWALD_FULL"));
238	>	CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") ||
239	>	isEqualIgnoreCase("MAX") ||
240	>	isEqualIgnoreCase("TRADITIONAL"));
241	>	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") ||
242	>	isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") ||
243	>	isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
244	>	isEqualIgnoreCase("SHIFTED_FORCE") ||
245	>	isEqualIgnoreCase("REACTION_FIELD") ||
246	>	isEqualIgnoreCase("TAYLOR_SHIFTED"));
247	>	CheckParameter(ElectrostaticScreeningMethod,
248	>	isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
249	>	CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") ||
250	>	isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
251	>	CheckParameter(OrthoBoxTolerance, isPositive());
252	>	CheckParameter(DampingAlpha,isNonNegative());
253	>	CheckParameter(SkinThickness, isPositive());
254	>	CheckParameter(Viscosity, isNonNegative());
255	>	CheckParameter(BeadSize, isPositive());
256	>	CheckParameter(FrozenBufferRadius, isPositive());
257	>	CheckParameter(LangevinBufferRadius, isPositive());
258	>	CheckParameter(NeighborListNeighbors, isPositive());
259	>	CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") ||
260	>	isEqualIgnoreCase("AlphaShape"));
261	>	CheckParameter(Alpha, isPositive());
262	>
263	>	for(std::vector<Component*>::iterator i = components_.begin();
264	>	i != components_.end(); ++i) {
265	>	if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
266	>	std::ostringstream oss;
267	>	oss << "Globals Error: can not find molecule stamp for component "
268	>	<< (*i)->getType() << std::endl;
269	>	throw OpenMDException(oss.str());
270	>	}
271	>	}
272	>	}
273	>
274	>	bool Globals::addComponent(Component* comp) {
275	>	components_.push_back(comp);
276	>	return true;
277	>	}
278
279	+	bool Globals::addZConsStamp(ZConsStamp* zcons) {
280	+	zconstraints_.push_back(zcons);
281	+	return true;
282	+	}
283
284	+	bool Globals::addRestraintStamp(RestraintStamp* rest) {
285	+	restraints_.push_back(rest);
286	+	return true;
287	+	}
288
289	<	int Globals::componentAssign( event* the_event ){
289	>	bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
290	>	if (flucQpars_ != NULL)
291	>	delete flucQpars_;
292	>
293	>	flucQpars_ = fqp;
294	>	return true;
295	>	}
296
297	<	switch( the_event->evt.asmt.asmt_type ){
297	>	bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
298	>	if (rnemdPars_ != NULL)
299	>	delete rnemdPars_;
300
301	<	case STRING:
302	<	return current_component->assignString( the_event->evt.asmt.lhs,
227	<	the_event->evt.asmt.rhs.sval,
228	<	&(the_event->err_msg));
229	<	break;
230	<
231	<	case DOUBLE:
232	<	return current_component->assignDouble( the_event->evt.asmt.lhs,
233	<	the_event->evt.asmt.rhs.dval,
234	<	&(the_event->err_msg));
235	<	break;
236	<
237	<	case INT:
238	<	return current_component->assignInt( the_event->evt.asmt.lhs,
239	<	the_event->evt.asmt.rhs.ival,
240	<	&(the_event->err_msg));
241	<	break;
242	<
243	<	default:
244	<	the_event->err_msg = strdup( "Globals error. Invalid component"
245	<	" assignment type" );
246	<	return 0;
247	<	break;
301	>	rnemdPars_ = rnemdPars;
302	>	return true;
303		}
249	–	return 0;
250	–	}
304
305	<	int Globals::componentEnd( event* the_event ){
306	<
307	<	the_event->err_msg = current_component->checkMe();
255	<	if( the_event->err_msg != NULL ) return 0;
256	<
257	<	return 1;
258	<	}
259	<
260	<	int Globals::newZconstraint( event* the_event ){
261	<
262	<
263	<	int index = the_event->evt.blk_index;
264	<	char err[200];
265	<	current_zConstraint = new ZconStamp( index );
266	<
267	<	if( haveNZconstraints() && index < getNZconstraints() )
268	<	zConstraints[index] = current_zConstraint;
269	<	else{
270	<	if( haveNZconstraints() ){
271	<	sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
272	<	index );
273	<	the_event->err_msg = strdup( err );
274	<	return 0;
275	<	}
276	<	else{
277	<	the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
278	<	" not given before"
279	<	" first zConstraint declaration." );
280	<	return 0;
281	<	}
282	<	}
283	<
284	<	return 1;
285	<	}
286	<
287	<
288	<
289	<	int Globals::zConstraintAssign( event* the_event ){
290	<
291	<	switch( the_event->evt.asmt.asmt_type ){
305	>	bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
306	>	if (minimizerPars_ != NULL)
307	>	delete minimizerPars_;
308
309	<	case STRING:
310	<	return current_zConstraint->assignString( the_event->evt.asmt.lhs,
295	<	the_event->evt.asmt.rhs.sval,
296	<	&(the_event->err_msg));
297	<	break;
298	<
299	<	case DOUBLE:
300	<	return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
301	<	the_event->evt.asmt.rhs.dval,
302	<	&(the_event->err_msg));
303	<	break;
304	<
305	<	case INT:
306	<	return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
307	<	the_event->evt.asmt.rhs.ival,
308	<	&(the_event->err_msg));
309	<	break;
310	<
311	<	default:
312	<	the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
313	<	" assignment type" );
314	<	return 0;
315	<	break;
309	>	minimizerPars_ = miniPars;
310	>	return true;
311		}
317	–	return 0;
318	–	}
312
313	<	int Globals::zConstraintEnd( event* the_event ){
314	<
315	<	the_event->err_msg = current_zConstraint->checkMe();
316	<	if( the_event->err_msg != NULL ) return 0;
317	<
318	<	return 1;
319	<	}
320	<
321	<	char* Globals::checkMe( void ){
322	<
323	<
324	<	std::string err("The following required keywords are missing:\n");
325	<	short int have_err = 0;
333	<
334	<	ParamMap::iterator i;
335	<	for (i = parameters_.begin(); i != parameters_.end(); ++i) {
336	<	if (!i->second->isOptional() && i->second->empty()) {
337	<	err +=  i->second->getKeyword() + "\n";
313	>	bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
314	>	std::string molStampName = molStamp->getName();
315	>	std::map<std::string, MoleculeStamp*>::iterator i;
316	>	bool ret = false;
317	>	i = moleculeStamps_.find(molStampName);
318	>	if (i == moleculeStamps_.end()) {
319	>	moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
320	>	ret = true;
321	>	} else {
322	>	std::ostringstream oss;
323	>	oss << "Globals Error: Molecule Stamp " << molStamp->getName()
324	>	<< "appears multiple times\n";
325	>	throw OpenMDException(oss.str());
326		}
327	+	return ret;
328		}
340	–
341	–	CheckParameter(ForceField, isNotEmpty());
342	–	CheckParameter(NComponents,isPositive());
343	–	CheckParameter(TargetTemp, isPositive());
344	–	CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) ||
345	–	isEqualIgnoreCase(std::string("NVT")) ||
346	–	isEqualIgnoreCase(std::string("NPTi")) ||
347	–	isEqualIgnoreCase(std::string("NPTf")) ||
348	–	isEqualIgnoreCase(std::string("NPTxyz")) );
349	–	CheckParameter(Dt, isPositive());
350	–	CheckParameter(RunTime, isPositive());
351	–	CheckParameter(InitialConfig, isNotEmpty());
352	–	CheckParameter(FinalConfig, isNotEmpty());
353	–	CheckParameter(NMol, isPositive());
354	–	CheckParameter(Density, isPositive());
355	–	CheckParameter(Box, isPositive());
356	–	CheckParameter(BoxX, isPositive());
357	–	CheckParameter(BoxY, isPositive());
358	–	CheckParameter(BoxZ, isPositive());
359	–	CheckParameter(SampleTime, isNonNegative());
360	–	CheckParameter(ResetTime, isNonNegative());
361	–	CheckParameter(StatusTime, isNonNegative());
362	–	CheckParameter(CutoffRadius, isPositive());
363	–	CheckParameter(SwitchingRadius, isNonNegative());
364	–	CheckParameter(Dielectric, isPositive());
365	–	CheckParameter(ThermalTime,  isNonNegative());
366	–	CheckParameter(TargetPressure,  isPositive());
367	–	CheckParameter(TauThermostat, isPositive());
368	–	CheckParameter(TauBarostat, isPositive());
369	–	CheckParameter(ZconsTime, isPositive());
370	–	CheckParameter(NZconstraints, isPositive());
371	–	CheckParameter(ZconsTol, isPositive());
372	–	//CheckParameter(ZconsForcePolicy,);
373	–	CheckParameter(Seed, isPositive());
374	–	CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) ||
375	–	isEqualIgnoreCase(std::string("CG")));
376	–	CheckParameter(MinimizerMaxIter, isPositive());
377	–	CheckParameter(MinimizerWriteFrq, isPositive());
378	–	CheckParameter(MinimizerStepSize, isPositive());
379	–	CheckParameter(MinimizerFTol, isPositive());
380	–	CheckParameter(MinimizerGTol, isPositive());
381	–	CheckParameter(MinimizerLSTol, isPositive());
382	–	CheckParameter(MinimizerLSMaxIter, isPositive());
383	–	CheckParameter(ZconsGap, isPositive());
384	–	CheckParameter(ZconsFixtime, isPositive());
385	–	CheckParameter(ThermodynamicIntegrationLambda, isPositive());
386	–	CheckParameter(ThermodynamicIntegrationK, isPositive());
387	–	CheckParameter(ForceFieldVariant, isNotEmpty());
388	–	CheckParameter(ForceFieldFileName, isNotEmpty());
389	–	CheckParameter(ThermIntDistSpringConst, isPositive());
390	–	CheckParameter(ThermIntThetaSpringConst, isPositive());
391	–	CheckParameter(ThermIntOmegaSpringConst, isPositive());
392	–	CheckParameter(SurfaceTension, isPositive());
393	–	CheckParameter(ElectrostaticSummationMethod,
394	–	isEqualIgnoreCase(std::string("NONE")) ||
395	–	isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) ||
396	–	isEqualIgnoreCase(std::string("SHIFTED_FORCE")) ||
397	–	isEqualIgnoreCase(std::string("REACTION_FIELD")));
398	–	CheckParameter(ElectrostaticScreeningMethod,
399	–	isEqualIgnoreCase(std::string("UNDAMPED")) ||
400	–	isEqualIgnoreCase(std::string("DAMPED")));
401	–	CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) ||
402	–	isEqualIgnoreCase(std::string("MAX")) ||
403	–	isEqualIgnoreCase(std::string("TRADITIONAL")));
404	–	CheckParameter(SwitchingFunctionType,
405	–	isEqualIgnoreCase(std::string("CUBIC")) ||
406	–	isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL")));
407	–	//CheckParameter(StatFileFormat,);
408	–	//CheckParameter(MixingRule,);
409	–	CheckParameter(OrthoBoxTolerance, isPositive());
410	–	CheckParameter(ThermIntDistSpringConst, isPositive());
411	–	CheckParameter(ThermIntThetaSpringConst, isPositive());
412	–	CheckParameter(ThermIntOmegaSpringConst, isPositive());
413	–	CheckParameter(DampingAlpha,isNonNegative());
414	–	CheckParameter(SkinThickness, isPositive());
415	–
416	–	//@todo memory leak
417	–	if( have_err )
418	–	return strdup( err.c_str() );
419	–
420	–	return NULL;
421	–
422	–
329		}
424	–
425	–	int Globals::globalEnd( event* the_event ){
426	–
427	–	the_event->err_msg = checkMe();
428	–	if( the_event->err_msg != NULL ) return 0;
429	–
430	–	return 1;
431	–	}

Comparing trunk/src/io/Globals.cpp (property svn:keywords):
Revision 726 by chrisfen, Fri Nov 11 15:22:11 2005 UTC vs.
Revision 1981 by gezelter, Mon Apr 14 18:32:51 2014 UTC

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