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root/group/trunk/OOPSE-2.0/src/io/Globals.cpp
Revision: 2365
Committed: Fri Oct 14 14:18:02 2005 UTC (18 years, 9 months ago) by chrisfen
File size: 12338 byte(s)
Log Message:
added default restraint spring constants into Globals

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    
54 tim 2364 #define DefineParameter(NAME,KEYWORD) \
55     NAME.setKeyword(KEYWORD); \
56     parameters_.insert(std::make_pair(std::string(KEYWORD), &NAME));
57 gezelter 1490
58 tim 2364 #define DefineOptionalParameter(NAME,KEYWORD) \
59     NAME.setKeyword(KEYWORD); NAME.setOptional(true); \
60     parameters_.insert(std::make_pair(std::string(KEYWORD), &NAME));
61 chrisfen 2101
62 tim 2364 #define DefineOptionalParameterWithDefaultValue(NAME,KEYWORD, DEFAULTVALUE) \
63     NAME.setKeyword(KEYWORD); NAME.setOptional(true); NAME.setDefaultValue(DEFAULTVALUE); \
64     parameters_.insert(std::make_pair(std::string(KEYWORD), &NAME));
65    
66 gezelter 1490 Globals::Globals(){
67 tim 2364
68     DefineParameter(ForceField, "forceField")
69     DefineParameter(NComponents, "nComponents")
70    
71     DefineOptionalParameter(TargetTemp, "targetTemp");
72     DefineOptionalParameter(Ensemble, "ensemble");
73     DefineOptionalParameter(Dt, "dt");
74     DefineOptionalParameter(RunTime, "runTime");
75     DefineOptionalParameter(InitialConfig, "initialConfig");
76     DefineOptionalParameter(FinalConfig, "finalConfig");
77     DefineOptionalParameter(NMol, "nMol");
78     DefineOptionalParameter(Density, "density");
79     DefineOptionalParameter(Box, "box");
80     DefineOptionalParameter(BoxX, "boxX");
81     DefineOptionalParameter(BoxY, "boxY");
82     DefineOptionalParameter(BoxZ, "boxZ");
83     DefineOptionalParameter(SampleTime, "sampleTime");
84     DefineOptionalParameter(ResetTime, "resetTime");
85     DefineOptionalParameter(StatusTime, "statusTime");
86     DefineOptionalParameter(CutoffRadius, "cutoffRadius");
87     DefineOptionalParameter(SwitchingRadius, "switchingRadius");
88     DefineOptionalParameter(Dielectric, "dielectric");
89     DefineOptionalParameter(TempSet, "tempSet");
90     DefineOptionalParameter(ThermalTime, "thermalTime");
91     DefineOptionalParameter(TargetPressure, "targetPressure");
92     DefineOptionalParameter(TauThermostat, "tauThermostat");
93     DefineOptionalParameter(TauBarostat, "tauBarostat");
94     DefineOptionalParameter(ZconsTime, "zconsTime");
95     DefineOptionalParameter(NZconstraints, "nZconstraints");
96     DefineOptionalParameter(ZconsTol, "zconsTol");
97     DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
98     DefineOptionalParameter(Seed, "seed");
99     DefineOptionalParameter(Minimizer, "minimizer");
100     DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
101     DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
102     DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
103     DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
104     DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
105     DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
106     DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
107     DefineOptionalParameter(ZconsGap, "zconsGap");
108     DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
109     DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
110     DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda");
111     DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
112     DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
113     DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
114     DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
115     DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
116     DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
117     DefineOptionalParameter(SurfaceTension, "surfaceTension");
118     DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
119     DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
120     DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
121     DefineOptionalParameter(StatFileFormat, "statFileFormat");
122    
123     DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
124     DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
125     DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
126     DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
127     DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);
128     DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
129     DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
130 chrisfen 2365 DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
131     DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
132     DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
133 tim 2364 DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 1.5);
134     DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
135     DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
136    
137 gezelter 1490 }
138    
139 tim 2364 int Globals::globalAssign( event* the_event ){
140 gezelter 1490
141 tim 2364 int key;
142     int token;
143     interface_assign_type the_type = the_event->evt.asmt.asmt_type;
144     char* lhs = the_event->evt.asmt.lhs;
145     std::string keyword(lhs);
146 chrisfen 2101
147 tim 2364 bool result;
148 gezelter 1490
149 tim 2364
150     ParamMap::iterator i =parameters_.find(keyword);
151     if (i != parameters_.end()) {
152     if( the_type == STRING ){
153     result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
154     if (!result ) {
155     sprintf(the_event->err_msg, "Error in parsing meta-data file!\n\t%s must be a string.\n", keyword.c_str() );
156     }
157     } else if( the_type == DOUBLE ){
158     result = i->second->setData(the_event->evt.asmt.rhs.dval);
159     if (!result )
160     sprintf(the_event->err_msg, "Error in parsing meta-data file!\n\t%s must be a double.\n", keyword.c_str() );
161     }
162     else if (the_type == INT ){
163     result = i->second->setData(the_event->evt.asmt.rhs.ival);
164     if (!result )
165     sprintf(the_event->err_msg, "Error in parsing meta-data file!\n\t%s must be an int.\n", keyword.c_str() );
166    
167     } else {
168    
169     }
170     }
171    
172     if (keyword == "nComponents" && getNComponents() > 0) {
173     components = new Component*[getNComponents()];
174     }else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
175     zConstraints = new ZconStamp*[getNZconstraints()];
176     }
177 gezelter 1490
178 tim 2364 return result;
179 gezelter 1490 }
180    
181     int Globals::newComponent( event* the_event ){
182    
183     current_component = new Component;
184     int index = the_event->evt.blk_index;
185     char err[200];
186    
187 tim 2364 if( haveNComponents() && index < getNComponents() )
188 gezelter 1490 components[index] = current_component;
189     else{
190 tim 2364 if( haveNComponents() ){
191 gezelter 1490 sprintf( err, "meta-data parsing error: %d out of nComponents range",
192     index );
193     the_event->err_msg = strdup( err );
194     return 0;
195     }
196     else{
197     the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
198     " first component declaration." );
199     return 0;
200     }
201     }
202    
203     return 1;
204     }
205    
206    
207    
208     int Globals::componentAssign( event* the_event ){
209    
210     switch( the_event->evt.asmt.asmt_type ){
211    
212     case STRING:
213     return current_component->assignString( the_event->evt.asmt.lhs,
214     the_event->evt.asmt.rhs.sval,
215     &(the_event->err_msg));
216     break;
217    
218     case DOUBLE:
219     return current_component->assignDouble( the_event->evt.asmt.lhs,
220     the_event->evt.asmt.rhs.dval,
221     &(the_event->err_msg));
222     break;
223    
224     case INT:
225     return current_component->assignInt( the_event->evt.asmt.lhs,
226     the_event->evt.asmt.rhs.ival,
227     &(the_event->err_msg));
228     break;
229    
230     default:
231     the_event->err_msg = strdup( "Globals error. Invalid component"
232     " assignment type" );
233     return 0;
234     break;
235     }
236     return 0;
237     }
238    
239     int Globals::componentEnd( event* the_event ){
240    
241     the_event->err_msg = current_component->checkMe();
242     if( the_event->err_msg != NULL ) return 0;
243    
244     return 1;
245     }
246    
247     int Globals::newZconstraint( event* the_event ){
248    
249    
250     int index = the_event->evt.blk_index;
251     char err[200];
252     current_zConstraint = new ZconStamp( index );
253    
254 tim 2364 if( haveNZconstraints() && index < getNZconstraints() )
255 gezelter 1490 zConstraints[index] = current_zConstraint;
256     else{
257 tim 2364 if( haveNZconstraints() ){
258 gezelter 1490 sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
259     index );
260     the_event->err_msg = strdup( err );
261     return 0;
262     }
263     else{
264     the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
265     " not given before"
266     " first zConstraint declaration." );
267     return 0;
268     }
269     }
270 tim 2364
271 gezelter 1490 return 1;
272     }
273    
274    
275    
276     int Globals::zConstraintAssign( event* the_event ){
277    
278     switch( the_event->evt.asmt.asmt_type ){
279    
280     case STRING:
281     return current_zConstraint->assignString( the_event->evt.asmt.lhs,
282     the_event->evt.asmt.rhs.sval,
283     &(the_event->err_msg));
284     break;
285    
286     case DOUBLE:
287     return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
288     the_event->evt.asmt.rhs.dval,
289     &(the_event->err_msg));
290     break;
291    
292     case INT:
293     return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
294     the_event->evt.asmt.rhs.ival,
295     &(the_event->err_msg));
296     break;
297    
298     default:
299     the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
300     " assignment type" );
301     return 0;
302     break;
303     }
304     return 0;
305     }
306    
307     int Globals::zConstraintEnd( event* the_event ){
308    
309     the_event->err_msg = current_zConstraint->checkMe();
310     if( the_event->err_msg != NULL ) return 0;
311    
312     return 1;
313     }
314    
315 tim 2364 char* Globals::checkMe( void ){
316 tim 2109
317 gezelter 1490
318 tim 2364 std::string err("The following required keywords are missing:\n");
319     short int have_err = 0;
320 gezelter 1490
321 tim 2364 ParamMap::iterator i;
322     for (i = parameters_.begin(); i != parameters_.end(); ++i) {
323     if (!i->second->isOptional() && i->second->empty()) {
324     err += i->second->getKeyword() + "\n";
325 gezelter 1490 }
326     }
327    
328 tim 2364 //@todo memory leak
329     if( have_err )
330     return strdup( err.c_str() );
331 gezelter 1490
332 tim 2364 return NULL;
333 gezelter 1490
334    
335     }
336    
337     int Globals::globalEnd( event* the_event ){
338    
339     the_event->err_msg = checkMe();
340     if( the_event->err_msg != NULL ) return 0;
341    
342     return 1;
343     }