ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE-2.0/src/io/Globals.cpp
Revision: 2425
Committed: Fri Nov 11 15:22:11 2005 UTC (18 years, 8 months ago) by chrisfen
File size: 17295 byte(s)
Log Message: 
added in a 5th order polynomial switching function option

File Contents

# User Rev Content
1 gezelter 2088 /*
2 gezelter 1930 * Copyright (c) 2005 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
19     * notice, this list of conditions and the following disclaimer.
20     *
21     * 3. Redistributions in binary form must reproduce the above copyright
22     * notice, this list of conditions and the following disclaimer in the
23     * documentation and/or other materials provided with the
24     * distribution.
25     *
26     * This software is provided "AS IS," without a warranty of any
27     * kind. All express or implied conditions, representations and
28     * warranties, including any implied warranty of merchantability,
29     * fitness for a particular purpose or non-infringement, are hereby
30     * excluded. The University of Notre Dame and its licensors shall not
31     * be liable for any damages suffered by licensee as a result of
32     * using, modifying or distributing the software or its
33     * derivatives. In no event will the University of Notre Dame or its
34     * licensors be liable for any lost revenue, profit or data, or for
35     * direct, indirect, special, consequential, incidental or punitive
36     * damages, however caused and regardless of the theory of liability,
37     * arising out of the use of or inability to use software, even if the
38     * University of Notre Dame has been advised of the possibility of
39     * such damages.
40     */
41    
42 gezelter 1490 #include <stdlib.h>
43     #include <stdio.h>
44     #include <string.h>
45 tim 2364 #include <string>
46 gezelter 1490
47 tim 1492 #include "io/Globals.hpp"
48     #include "utils/simError.h"
49 gezelter 1490 #ifdef IS_MPI
50 tim 1492 #include "io/mpiBASS.h"
51 gezelter 1490 #endif // is_mpi
52    
53 tim 2371 #include "io/ParamConstraint.hpp"
54 gezelter 1490
55 tim 2364 #define DefineParameter(NAME,KEYWORD) \
56     NAME.setKeyword(KEYWORD); \
57     parameters_.insert(std::make_pair(std::string(KEYWORD), &NAME));
58 gezelter 1490
59 tim 2364 #define DefineOptionalParameter(NAME,KEYWORD) \
60     NAME.setKeyword(KEYWORD); NAME.setOptional(true); \
61     parameters_.insert(std::make_pair(std::string(KEYWORD), &NAME));
62 chrisfen 2101
63 tim 2364 #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 tim 2371 #define CheckParameter(NAME, CONSTRAINT) \
68 tim 2373 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 tim 2371
70 gezelter 1490 Globals::Globals(){
71 tim 2364
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 chrisfen 2415 DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
125 tim 2364 DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
126 chrisfen 2425 DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
127 tim 2364 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 chrisfen 2365 DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
135     DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
136     DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
137 chrisfen 2415 DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
138 tim 2364 DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
139 chrisfen 2425 DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
140 tim 2364 DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
141 tim 2380 DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
142    
143 tim 2364
144 gezelter 1490 }
145    
146 tim 2364 int Globals::globalAssign( event* the_event ){
147 tim 2373 char errorMessage[65535];
148 tim 2364 int key;
149     interface_assign_type the_type = the_event->evt.asmt.asmt_type;
150     char* lhs = the_event->evt.asmt.lhs;
151     std::string keyword(lhs);
152 chrisfen 2101
153 tim 2372 bool result = false;
154 gezelter 1490
155 tim 2373 /**@todo fix memory leak */
156 tim 2364 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 tim 2373 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 tim 2364 }
164     } else if( the_type == DOUBLE ){
165     result = i->second->setData(the_event->evt.asmt.rhs.dval);
166     if (!result )
167 tim 2373 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 tim 2364 }
170     else if (the_type == INT ){
171     result = i->second->setData(the_event->evt.asmt.rhs.ival);
172     if (!result )
173 tim 2373 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 tim 2364
176     } else {
177 tim 2373 sprintf(errorMessage, "Internal error of parser\n");
178     the_event->err_msg = strdup(errorMessage);
179 tim 2364 }
180 tim 2373 } else {
181     sprintf(errorMessage, "%s is an unrecognized keyword\n", keyword.c_str() );
182     the_event->err_msg = strdup(errorMessage);
183 tim 2364 }
184    
185     if (keyword == "nComponents" && getNComponents() > 0) {
186     components = new Component*[getNComponents()];
187     }else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
188     zConstraints = new ZconStamp*[getNZconstraints()];
189     }
190 gezelter 1490
191 tim 2364 return result;
192 gezelter 1490 }
193    
194     int Globals::newComponent( event* the_event ){
195    
196     current_component = new Component;
197     int index = the_event->evt.blk_index;
198     char err[200];
199    
200 tim 2364 if( haveNComponents() && index < getNComponents() )
201 gezelter 1490 components[index] = current_component;
202     else{
203 tim 2364 if( haveNComponents() ){
204 gezelter 1490 sprintf( err, "meta-data parsing error: %d out of nComponents range",
205     index );
206     the_event->err_msg = strdup( err );
207     return 0;
208     }
209     else{
210     the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
211     " first component declaration." );
212     return 0;
213     }
214     }
215    
216     return 1;
217     }
218    
219    
220    
221     int Globals::componentAssign( event* the_event ){
222    
223     switch( the_event->evt.asmt.asmt_type ){
224    
225     case STRING:
226     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;
248     }
249     return 0;
250     }
251    
252     int Globals::componentEnd( event* the_event ){
253    
254     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 tim 2364 if( haveNZconstraints() && index < getNZconstraints() )
268 gezelter 1490 zConstraints[index] = current_zConstraint;
269     else{
270 tim 2364 if( haveNZconstraints() ){
271 gezelter 1490 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 tim 2364
284 gezelter 1490 return 1;
285     }
286    
287    
288    
289     int Globals::zConstraintAssign( event* the_event ){
290    
291     switch( the_event->evt.asmt.asmt_type ){
292    
293     case STRING:
294     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;
316     }
317     return 0;
318     }
319    
320     int Globals::zConstraintEnd( event* the_event ){
321    
322     the_event->err_msg = current_zConstraint->checkMe();
323     if( the_event->err_msg != NULL ) return 0;
324    
325     return 1;
326     }
327    
328 tim 2364 char* Globals::checkMe( void ){
329 tim 2109
330 gezelter 1490
331 tim 2364 std::string err("The following required keywords are missing:\n");
332     short int have_err = 0;
333 gezelter 1490
334 tim 2364 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";
338 gezelter 1490 }
339     }
340    
341 tim 2371 CheckParameter(ForceField, isNotEmpty());
342     CheckParameter(NComponents,isPositive());
343     CheckParameter(TargetTemp, isPositive());
344 chrisfen 2425 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 tim 2371 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 chrisfen 2425 CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) ||
375     isEqualIgnoreCase(std::string("CG")));
376 tim 2371 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 chrisfen 2425 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 tim 2371 //CheckParameter(StatFileFormat,);
408     //CheckParameter(MixingRule,);
409     CheckParameter(OrthoBoxTolerance, isPositive());
410     CheckParameter(ThermIntDistSpringConst, isPositive());
411     CheckParameter(ThermIntThetaSpringConst, isPositive());
412     CheckParameter(ThermIntOmegaSpringConst, isPositive());
413 chrisfen 2415 CheckParameter(DampingAlpha,isNonNegative());
414 tim 2371 CheckParameter(SkinThickness, isPositive());
415    
416 tim 2364 //@todo memory leak
417     if( have_err )
418     return strdup( err.c_str() );
419 gezelter 1490
420 tim 2364 return NULL;
421 gezelter 1490
422    
423     }
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     }