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

Comparing trunk/src/io/Globals.cpp (file contents):
Revision 749 by tim, Wed Nov 16 23:10:02 2005 UTC vs.
Revision 2022 by gezelter, Fri Sep 26 22:22:28 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	<	using namespace oopse;
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	>	DefineOptionalParameter(UniformField, "uniformField");
95	>	//DefineOptionalParameter(PeriodicField, "periodicField");
96	>	//DefineOptionalParameter(PeriodicFieldStrength, "periodicFieldStrength");
97	>
98
99	<	Globals::Globals(){
100	<
101	<	DefineParameter(ForceField, "forceField")
102	<	DefineParameter(NComponents, "nComponents")
103	<
104	<	DefineOptionalParameter(TargetTemp, "targetTemp");
105	<	DefineOptionalParameter(Ensemble, "ensemble");
106	<	DefineOptionalParameter(Dt, "dt");
107	<	DefineOptionalParameter(RunTime, "runTime");
108	<	DefineOptionalParameter(InitialConfig, "initialConfig");
109	<	DefineOptionalParameter(FinalConfig, "finalConfig");
110	<	DefineOptionalParameter(NMol, "nMol");
111	<	DefineOptionalParameter(Density, "density");
112	<	DefineOptionalParameter(Box, "box");
113	<	DefineOptionalParameter(BoxX, "boxX");
114	<	DefineOptionalParameter(BoxY, "boxY");
115	<	DefineOptionalParameter(BoxZ, "boxZ");
116	<	DefineOptionalParameter(SampleTime, "sampleTime");
117	<	DefineOptionalParameter(ResetTime, "resetTime");
118	<	DefineOptionalParameter(StatusTime, "statusTime");
77	<	DefineOptionalParameter(CutoffRadius, "cutoffRadius");
78	<	DefineOptionalParameter(SwitchingRadius, "switchingRadius");
79	<	DefineOptionalParameter(Dielectric, "dielectric");
80	<	DefineOptionalParameter(TempSet, "tempSet");
81	<	DefineOptionalParameter(ThermalTime, "thermalTime");
82	<	DefineOptionalParameter(TargetPressure, "targetPressure");
83	<	DefineOptionalParameter(TauThermostat, "tauThermostat");
84	<	DefineOptionalParameter(TauBarostat, "tauBarostat");
85	<	DefineOptionalParameter(ZconsTime, "zconsTime");
86	<	DefineOptionalParameter(NZconstraints, "nZconstraints");
87	<	DefineOptionalParameter(ZconsTol, "zconsTol");
88	<	DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
89	<	DefineOptionalParameter(Seed, "seed");
90	<	DefineOptionalParameter(Minimizer, "minimizer");
91	<	DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
92	<	DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
93	<	DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
94	<	DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
95	<	DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
96	<	DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
97	<	DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
98	<	DefineOptionalParameter(ZconsGap, "zconsGap");
99	<	DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
100	<	DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
101	<	DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
102	<	DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
103	<	DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
104	<	DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
105	<	DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
106	<	DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
107	<	DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
108	<	DefineOptionalParameter(SurfaceTension, "surfaceTension");
109	<	DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
110	<	DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
111	<	DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
112	<	DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
113	<	DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
114	<	DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
115	<	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
116	<	DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
117	<	DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
118	<	DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
119	<	DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
120	<	DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
121	<	DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
122	<	DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
123	<	DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
124	<	DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
125	<	DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
126	<	DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
127	<	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
128	<	DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
99	>	DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
100	>	DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
101	>	DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
102	>	DefineOptionalParameter(HydroPropFile, "HydroPropFile");
103	>	DefineOptionalParameter(Viscosity, "viscosity");
104	>	DefineOptionalParameter(BeadSize, "beadSize");
105	>	DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
106	>	DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
107	>	DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
108	>	DefineOptionalParameter(UseMultipleTemperatureMethod,
109	>	"useMultipleTemperatureMethod");
110	>	DefineOptionalParameter(ElectrostaticSummationMethod,
111	>	"electrostaticSummationMethod");
112	>	DefineOptionalParameter(MTM_Ce, "MTM_Ce");
113	>	DefineOptionalParameter(MTM_G, "MTM_G");
114	>	DefineOptionalParameter(MTM_Io, "MTM_Io");
115	>	DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
116	>	DefineOptionalParameter(MTM_R, "MTM_R");
117	>	DefineOptionalParameter(Alpha, "alpha");
118	>	DefineOptionalParameter(ConstraintTime, "constraintTime");
119
120
121	<	}
121	>	DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions,
122	>	"usePeriodicBoundaryConditions",
123	>	true);
124	>	DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial",
125	>	true);
126	>	DefineOptionalParameterWithDefaultValue(UseLongRangeCorrections,
127	>	"useLongRangeCorrections", true);
128	>	DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime",
129	>	false);
130	>	DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState,
131	>	"useInitialExtendedSystemState",
132	>	false);
133	>	DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance,
134	>	"orthoBoxTolerance", 1E-6);
135	>	DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod",
136	>	"SHIFTED_FORCE");
137	>	DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod,
138	>	"electrostaticScreeningMethod",
139	>	"DAMPED");
140	>	DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
141	>	DefineOptionalParameterWithDefaultValue(CompressDumpFile,
142	>	"compressDumpFile", false);
143	>	DefineOptionalParameterWithDefaultValue(PrintHeatFlux, "printHeatFlux",
144	>	false);
145	>	DefineOptionalParameterWithDefaultValue(OutputForceVector,
146	>	"outputForceVector", false);
147	>	DefineOptionalParameterWithDefaultValue(OutputParticlePotential,
148	>	"outputParticlePotential", false);
149	>	DefineOptionalParameterWithDefaultValue(OutputElectricField,
150	>	"outputElectricField", false);
151	>	DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges,
152	>	"outputFluctuatingCharges", false);
153	>	DefineOptionalParameterWithDefaultValue(OutputSitePotential,
154	>	"outputSitePotential", false);
155	>	DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness",
156	>	1.0);
157	>	DefineOptionalParameterWithDefaultValue(StatFileFormat,
158	>	"statFileFormat",
159	>	"TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
160	>	DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions,
161	>	"useSphericalBoundaryConditions",
162	>	false);
163	>	DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole,
164	>	"accumulateBoxDipole", false);
165	>	DefineOptionalParameterWithDefaultValue(AccumulateBoxQuadrupole,
166	>	"accumulateBoxQuadrupole", false);
167	>	DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints",
168	>	false);
169	>	DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file",
170	>	"idealCrystal.in");
171	>	DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration,
172	>	"useThermodynamicIntegration",
173	>	false);
174	>	DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex");
175
176	<	Globals::~Globals(){
177	<	int i;
178	<	if( components != NULL ){
179	<	for( i=0; i< getNComponents(); i++ ) delete components[i];
180	<	delete[] components;
181	<	}
182	<
183	<	if( zConstraints != NULL ){
184	<	for( i=0; i< getNZconstraints(); i++ ) delete zConstraints[i];
185	<	delete[] zConstraints;
186	<	}
187	<
188	<	}
176	>	deprecatedKeywords_.insert("nComponents");
177	>	deprecatedKeywords_.insert("nZconstraints");
178	>	deprecatedKeywords_.insert("initialConfig");
179	>	deprecatedKeywords_.insert("thermIntDistSpringConst");
180	>	deprecatedKeywords_.insert("thermIntThetaSpringConst");
181	>	deprecatedKeywords_.insert("thermIntOmegaSpringConst");
182	>	deprecatedKeywords_.insert("useSolidThermInt");
183	>	deprecatedKeywords_.insert("useLiquidThermInt");
184	>	deprecatedKeywords_.insert("minimizerMaxIter");
185	>	deprecatedKeywords_.insert("minimizerWriteFreq");
186	>	deprecatedKeywords_.insert("minimizerStepSize");
187	>	deprecatedKeywords_.insert("minimizerFTol");
188	>	deprecatedKeywords_.insert("minimizerGTol");
189	>	deprecatedKeywords_.insert("minimizerLSTol");
190	>	deprecatedKeywords_.insert("minimizerLSMaxIter");
191	>	deprecatedKeywords_.insert("electricField");
192
193	<	int Globals::globalAssign( event* the_event ){
148	<	char errorMessage[65535];
149	<	int key;
150	<	interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
151	<	char* lhs = the_event->evt.asmt.lhs;
152	<	std::string keyword(lhs);
153	<
154	<	bool result = false;
155	<
156	<	/**@todo fix memory leak */
157	<	ParamMap::iterator i =parameters_.find(keyword);
158	<	if (i != parameters_.end()) {
159	<	if( the_type == STRING ){
160	<	result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
161	<	if (!result ) {
162	<	sprintf(errorMessage, "Error in parsing %s: expect %s, but get a string \"%s\".\n", keyword.c_str(), i->second->getParamType().c_str(), the_event->evt.asmt.rhs.sval);
163	<	the_event->err_msg = strdup(errorMessage);
164	<	}
165	<	} else if( the_type == DOUBLE ){
166	<	result = i->second->setData(the_event->evt.asmt.rhs.dval);
167	<	if (!result )
168	<	sprintf(errorMessage, "Error in parsing %s: expect %s, but get a double %f.\n", keyword.c_str(), i->second->getParamType().c_str(), the_event->evt.asmt.rhs.dval );
169	<	the_event->err_msg = strdup(errorMessage);
170	<	}
171	<	else if (the_type == INT ){
172	<	result = i->second->setData(the_event->evt.asmt.rhs.ival);
173	<	if (!result )
174	<	sprintf(errorMessage,  "Error in parsing %s: expect %s, but get an int %d.\n", keyword.c_str(), i->second->getParamType().c_str(), the_event->evt.asmt.rhs.ival );
175	<	the_event->err_msg = strdup(errorMessage);
176	<
177	<	} else {
178	<	sprintf(errorMessage,  "Internal error of parser\n");
179	<	the_event->err_msg = strdup(errorMessage);
180	<	}
181	<	} else {
182	<	sprintf(errorMessage,  "%s is an unrecognized keyword\n", keyword.c_str() );
183	<	the_event->err_msg = strdup(errorMessage);
193	>
194		}
195
196	<	if (keyword == "nComponents" && getNComponents() > 0) {
197	<	components = new Component*[getNComponents()];
198	<	}else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
199	<	zConstraints = new ZconStamp*[getNZconstraints()];
196	>	Globals::~Globals() {
197	>	MemoryUtils::deletePointers(components_);
198	>	MemoryUtils::deletePointers(zconstraints_);
199	>	MemoryUtils::deletePointers(restraints_);
200	>	delete flucQpars_;
201	>	delete rnemdPars_;
202	>	delete minimizerPars_;
203		}
191	–
192	–	return result;
193	–	}
204
205	<	int Globals::newComponent( event* the_event ){
206	<
197	<	current_component = new Component;
198	<	int index = the_event->evt.blk_index;
199	<	char err[200];
200	<
201	<	if( haveNComponents() && index < getNComponents() )
202	<	components[index] = current_component;
203	<	else{
204	<	if( haveNComponents()  ){
205	<	sprintf( err, "meta-data parsing error: %d out of nComponents range",
206	<	index );
207	<	the_event->err_msg = strdup( err );
208	<	return 0;
209	<	}
210	<	else{
211	<	the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
212	<	" first component declaration." );
213	<	return 0;
214	<	}
215	<	}
216	<
217	<	return 1;
218	<	}
205	>	void Globals::validate() {
206	>	DataHolder::validate();
207
208	+	CheckParameter(ForceField, isNotEmpty());
209	+	CheckParameter(TargetTemp, isPositive());
210	+	CheckParameter(Ensemble, isEqualIgnoreCase("NVE") ||
211	+	isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") ||
212	+	isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") ||
213	+	isEqualIgnoreCase("NPTsz") || isEqualIgnoreCase("NPAT")  ||
214	+	isEqualIgnoreCase("NPA") ||
215	+	isEqualIgnoreCase("LANGEVINDYNAMICS") ||
216	+	isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") ||
217	+	isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") ||
218	+	isEqualIgnoreCase("NGT") ||
219	+	isEqualIgnoreCase("LANGEVINHULL") ||
220	+	isEqualIgnoreCase("LHULL") || isEqualIgnoreCase("SMIPD"));
221	+	CheckParameter(Dt, isPositive());
222	+	CheckParameter(RunTime, isPositive());
223	+	CheckParameter(FinalConfig, isNotEmpty());
224	+	CheckParameter(SampleTime, isNonNegative());
225	+	CheckParameter(ResetTime, isNonNegative());
226	+	CheckParameter(StatusTime, isNonNegative());
227	+	CheckParameter(CutoffRadius, isPositive());
228	+	CheckParameter(SwitchingRadius, isNonNegative());
229	+	CheckParameter(Dielectric, isPositive());
230	+	CheckParameter(ThermalTime,  isNonNegative());
231	+	CheckParameter(TauThermostat, isPositive());
232	+	CheckParameter(TauBarostat, isPositive());
233	+	CheckParameter(ZconsTime, isPositive());
234	+	CheckParameter(ZconsTol, isPositive());
235	+	CheckParameter(Seed, isPositive());
236	+	CheckParameter(ZconsGap, isPositive());
237	+	CheckParameter(ZconsFixtime, isPositive());
238	+	CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
239	+	CheckParameter(ThermodynamicIntegrationK, isPositive());
240	+	CheckParameter(ForceFieldVariant, isNotEmpty());
241	+	CheckParameter(ForceFieldFileName, isNotEmpty());
242	+	CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") ||
243	+	isEqualIgnoreCase("SWITCHED") ||
244	+	isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
245	+	isEqualIgnoreCase("SHIFTED_FORCE") ||
246	+	isEqualIgnoreCase("TAYLOR_SHIFTED") ||
247	+	isEqualIgnoreCase("EWALD_FULL"));
248	+	CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") ||
249	+	isEqualIgnoreCase("MAX") ||
250	+	isEqualIgnoreCase("TRADITIONAL"));
251	+	CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") ||
252	+	isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") ||
253	+	isEqualIgnoreCase("SHIFTED_POTENTIAL") ||
254	+	isEqualIgnoreCase("SHIFTED_FORCE") ||
255	+	isEqualIgnoreCase("REACTION_FIELD") ||
256	+	isEqualIgnoreCase("TAYLOR_SHIFTED"));
257	+	CheckParameter(ElectrostaticScreeningMethod,
258	+	isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED"));
259	+	CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") ||
260	+	isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
261	+	CheckParameter(OrthoBoxTolerance, isPositive());
262	+	CheckParameter(DampingAlpha,isNonNegative());
263	+	CheckParameter(SkinThickness, isPositive());
264	+	CheckParameter(Viscosity, isNonNegative());
265	+	CheckParameter(BeadSize, isPositive());
266	+	CheckParameter(FrozenBufferRadius, isPositive());
267	+	CheckParameter(LangevinBufferRadius, isPositive());
268	+	CheckParameter(NeighborListNeighbors, isPositive());
269	+	CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") ||
270	+	isEqualIgnoreCase("AlphaShape"));
271	+	CheckParameter(Alpha, isPositive());
272	+
273	+	for(std::vector<Component*>::iterator i = components_.begin();
274	+	i != components_.end(); ++i) {
275	+	if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
276	+	std::ostringstream oss;
277	+	oss << "Globals Error: can not find molecule stamp for component "
278	+	<< (*i)->getType() << std::endl;
279	+	throw OpenMDException(oss.str());
280	+	}
281	+	}
282	+	}
283	+
284	+	bool Globals::addComponent(Component* comp) {
285	+	components_.push_back(comp);
286	+	return true;
287	+	}
288
289	+	bool Globals::addZConsStamp(ZConsStamp* zcons) {
290	+	zconstraints_.push_back(zcons);
291	+	return true;
292	+	}
293
294	<	int Globals::componentAssign( event* the_event ){
294	>	bool Globals::addRestraintStamp(RestraintStamp* rest) {
295	>	restraints_.push_back(rest);
296	>	return true;
297	>	}
298
299	<	switch( the_event->evt.asmt.asmt_type ){
299	>	bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) {
300	>	if (flucQpars_ != NULL)
301	>	delete flucQpars_;
302
303	<	case STRING:
304	<	return current_component->assignString( the_event->evt.asmt.lhs,
305	<	the_event->evt.asmt.rhs.sval,
306	<	&(the_event->err_msg));
307	<	break;
303	>	flucQpars_ = fqp;
304	>	return true;
305	>	}
306	>
307	>	bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) {
308	>	if (rnemdPars_ != NULL)
309	>	delete rnemdPars_;
310
311	<	case DOUBLE:
312	<	return current_component->assignDouble( the_event->evt.asmt.lhs,
234	<	the_event->evt.asmt.rhs.dval,
235	<	&(the_event->err_msg));
236	<	break;
237	<
238	<	case INT:
239	<	return current_component->assignInt( the_event->evt.asmt.lhs,
240	<	the_event->evt.asmt.rhs.ival,
241	<	&(the_event->err_msg));
242	<	break;
243	<
244	<	default:
245	<	the_event->err_msg = strdup( "Globals error. Invalid component"
246	<	" assignment type" );
247	<	return 0;
248	<	break;
311	>	rnemdPars_ = rnemdPars;
312	>	return true;
313		}
250	–	return 0;
251	–	}
314
315	<	int Globals::componentEnd( event* the_event ){
316	<
317	<	the_event->err_msg = current_component->checkMe();
256	<	if( the_event->err_msg != NULL ) return 0;
257	<
258	<	return 1;
259	<	}
260	<
261	<	int Globals::newZconstraint( event* the_event ){
262	<
263	<
264	<	int index = the_event->evt.blk_index;
265	<	char err[200];
266	<	current_zConstraint = new ZconStamp( index );
267	<
268	<	if( haveNZconstraints() && index < getNZconstraints() )
269	<	zConstraints[index] = current_zConstraint;
270	<	else{
271	<	if( haveNZconstraints() ){
272	<	sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
273	<	index );
274	<	the_event->err_msg = strdup( err );
275	<	return 0;
276	<	}
277	<	else{
278	<	the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
279	<	" not given before"
280	<	" first zConstraint declaration." );
281	<	return 0;
282	<	}
283	<	}
284	<
285	<	return 1;
286	<	}
287	<
288	<
289	<
290	<	int Globals::zConstraintAssign( event* the_event ){
291	<
292	<	switch( the_event->evt.asmt.asmt_type ){
315	>	bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) {
316	>	if (minimizerPars_ != NULL)
317	>	delete minimizerPars_;
318
319	<	case STRING:
320	<	return current_zConstraint->assignString( the_event->evt.asmt.lhs,
296	<	the_event->evt.asmt.rhs.sval,
297	<	&(the_event->err_msg));
298	<	break;
299	<
300	<	case DOUBLE:
301	<	return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
302	<	the_event->evt.asmt.rhs.dval,
303	<	&(the_event->err_msg));
304	<	break;
305	<
306	<	case INT:
307	<	return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
308	<	the_event->evt.asmt.rhs.ival,
309	<	&(the_event->err_msg));
310	<	break;
311	<
312	<	default:
313	<	the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
314	<	" assignment type" );
315	<	return 0;
316	<	break;
319	>	minimizerPars_ = miniPars;
320	>	return true;
321		}
318	–	return 0;
319	–	}
322
323	<	int Globals::zConstraintEnd( event* the_event ){
324	<
325	<	the_event->err_msg = current_zConstraint->checkMe();
326	<	if( the_event->err_msg != NULL ) return 0;
327	<
328	<	return 1;
329	<	}
330	<
331	<	char* Globals::checkMe( void ){
332	<
333	<
334	<	std::string err("The following required keywords are missing:\n");
335	<	short int have_err = 0;
334	<
335	<	ParamMap::iterator i;
336	<	for (i = parameters_.begin(); i != parameters_.end(); ++i) {
337	<	if (!i->second->isOptional() && i->second->empty()) {
338	<	err +=  i->second->getKeyword() + "\n";
323	>	bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
324	>	std::string molStampName = molStamp->getName();
325	>	std::map<std::string, MoleculeStamp*>::iterator i;
326	>	bool ret = false;
327	>	i = moleculeStamps_.find(molStampName);
328	>	if (i == moleculeStamps_.end()) {
329	>	moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
330	>	ret = true;
331	>	} else {
332	>	std::ostringstream oss;
333	>	oss << "Globals Error: Molecule Stamp " << molStamp->getName()
334	>	<< "appears multiple times\n";
335	>	throw OpenMDException(oss.str());
336		}
337	+	return ret;
338		}
341	–
342	–	CheckParameter(ForceField, isNotEmpty());
343	–	CheckParameter(NComponents,isPositive());
344	–	CheckParameter(TargetTemp, isPositive());
345	–	CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) ||
346	–	isEqualIgnoreCase(std::string("NVT")) ||
347	–	isEqualIgnoreCase(std::string("NPTi")) ||
348	–	isEqualIgnoreCase(std::string("NPTf")) ||
349	–	isEqualIgnoreCase(std::string("NPTxyz")) );
350	–	CheckParameter(Dt, isPositive());
351	–	CheckParameter(RunTime, isPositive());
352	–	CheckParameter(InitialConfig, isNotEmpty());
353	–	CheckParameter(FinalConfig, isNotEmpty());
354	–	CheckParameter(NMol, isPositive());
355	–	CheckParameter(Density, isPositive());
356	–	CheckParameter(Box, isPositive());
357	–	CheckParameter(BoxX, isPositive());
358	–	CheckParameter(BoxY, isPositive());
359	–	CheckParameter(BoxZ, isPositive());
360	–	CheckParameter(SampleTime, isNonNegative());
361	–	CheckParameter(ResetTime, isNonNegative());
362	–	CheckParameter(StatusTime, isNonNegative());
363	–	CheckParameter(CutoffRadius, isPositive());
364	–	CheckParameter(SwitchingRadius, isNonNegative());
365	–	CheckParameter(Dielectric, isPositive());
366	–	CheckParameter(ThermalTime,  isNonNegative());
367	–	CheckParameter(TargetPressure,  isPositive());
368	–	CheckParameter(TauThermostat, isPositive());
369	–	CheckParameter(TauBarostat, isPositive());
370	–	CheckParameter(ZconsTime, isPositive());
371	–	CheckParameter(NZconstraints, isPositive());
372	–	CheckParameter(ZconsTol, isPositive());
373	–	//CheckParameter(ZconsForcePolicy,);
374	–	CheckParameter(Seed, isPositive());
375	–	CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) ||
376	–	isEqualIgnoreCase(std::string("CG")));
377	–	CheckParameter(MinimizerMaxIter, isPositive());
378	–	CheckParameter(MinimizerWriteFrq, isPositive());
379	–	CheckParameter(MinimizerStepSize, isPositive());
380	–	CheckParameter(MinimizerFTol, isPositive());
381	–	CheckParameter(MinimizerGTol, isPositive());
382	–	CheckParameter(MinimizerLSTol, isPositive());
383	–	CheckParameter(MinimizerLSMaxIter, isPositive());
384	–	CheckParameter(ZconsGap, isPositive());
385	–	CheckParameter(ZconsFixtime, isPositive());
386	–	CheckParameter(ThermodynamicIntegrationLambda, isPositive());
387	–	CheckParameter(ThermodynamicIntegrationK, isPositive());
388	–	CheckParameter(ForceFieldVariant, isNotEmpty());
389	–	CheckParameter(ForceFieldFileName, isNotEmpty());
390	–	CheckParameter(ThermIntDistSpringConst, isPositive());
391	–	CheckParameter(ThermIntThetaSpringConst, isPositive());
392	–	CheckParameter(ThermIntOmegaSpringConst, isPositive());
393	–	CheckParameter(SurfaceTension, isPositive());
394	–	CheckParameter(ElectrostaticSummationMethod,
395	–	isEqualIgnoreCase(std::string("NONE")) ||
396	–	isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) ||
397	–	isEqualIgnoreCase(std::string("SHIFTED_FORCE")) ||
398	–	isEqualIgnoreCase(std::string("REACTION_FIELD")));
399	–	CheckParameter(ElectrostaticScreeningMethod,
400	–	isEqualIgnoreCase(std::string("UNDAMPED")) ||
401	–	isEqualIgnoreCase(std::string("DAMPED")));
402	–	CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) ||
403	–	isEqualIgnoreCase(std::string("MAX")) ||
404	–	isEqualIgnoreCase(std::string("TRADITIONAL")));
405	–	CheckParameter(SwitchingFunctionType,
406	–	isEqualIgnoreCase(std::string("CUBIC")) ||
407	–	isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL")));
408	–	//CheckParameter(StatFileFormat,);
409	–	//CheckParameter(MixingRule,);
410	–	CheckParameter(OrthoBoxTolerance, isPositive());
411	–	CheckParameter(ThermIntDistSpringConst, isPositive());
412	–	CheckParameter(ThermIntThetaSpringConst, isPositive());
413	–	CheckParameter(ThermIntOmegaSpringConst, isPositive());
414	–	CheckParameter(DampingAlpha,isNonNegative());
415	–	CheckParameter(SkinThickness, isPositive());
416	–
417	–	//@todo memory leak
418	–	if( have_err )
419	–	return strdup( err.c_str() );
420	–
421	–	return NULL;
422	–
423	–
339		}
425	–
426	–	int Globals::globalEnd( event* the_event ){
427	–
428	–	the_event->err_msg = checkMe();
429	–	if( the_event->err_msg != NULL ) return 0;
430	–
431	–	return 1;
432	–	}

Comparing trunk/src/io/Globals.cpp (property svn:keywords):
Revision 749 by tim, Wed Nov 16 23:10:02 2005 UTC vs.
Revision 2022 by gezelter, Fri Sep 26 22:22:28 2014 UTC

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