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root/group/trunk/OOPSE-3.0/src/io/Globals.cpp
Revision: 2415
Committed: Thu Nov 3 23:12:27 2005 UTC (18 years, 7 months ago) by chrisfen
File size: 17021 byte(s)
Log Message:
improvements in shifted-force

File Contents

# Content
1 /*
2 * 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 #include <stdlib.h>
43 #include <stdio.h>
44 #include <string.h>
45 #include <string>
46
47 #include "io/Globals.hpp"
48 #include "utils/simError.h"
49 #ifdef IS_MPI
50 #include "io/mpiBASS.h"
51 #endif // is_mpi
52
53 #include "io/ParamConstraint.hpp"
54
55 #define DefineParameter(NAME,KEYWORD) \
56 NAME.setKeyword(KEYWORD); \
57 parameters_.insert(std::make_pair(std::string(KEYWORD), &NAME));
58
59 #define DefineOptionalParameter(NAME,KEYWORD) \
60 NAME.setKeyword(KEYWORD); NAME.setOptional(true); \
61 parameters_.insert(std::make_pair(std::string(KEYWORD), &NAME));
62
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
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(SkinThickness, "skinThickness", 1.0);
140 DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");
141
142
143 }
144
145 int Globals::globalAssign( event* the_event ){
146 char errorMessage[65535];
147 int key;
148 interface_assign_type the_type = the_event->evt.asmt.asmt_type;
149 char* lhs = the_event->evt.asmt.lhs;
150 std::string keyword(lhs);
151
152 bool result = false;
153
154 /**@todo fix memory leak */
155 ParamMap::iterator i =parameters_.find(keyword);
156 if (i != parameters_.end()) {
157 if( the_type == STRING ){
158 result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
159 if (!result ) {
160 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);
161 the_event->err_msg = strdup(errorMessage);
162 }
163 } else if( the_type == DOUBLE ){
164 result = i->second->setData(the_event->evt.asmt.rhs.dval);
165 if (!result )
166 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 );
167 the_event->err_msg = strdup(errorMessage);
168 }
169 else if (the_type == INT ){
170 result = i->second->setData(the_event->evt.asmt.rhs.ival);
171 if (!result )
172 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 );
173 the_event->err_msg = strdup(errorMessage);
174
175 } else {
176 sprintf(errorMessage, "Internal error of parser\n");
177 the_event->err_msg = strdup(errorMessage);
178 }
179 } else {
180 sprintf(errorMessage, "%s is an unrecognized keyword\n", keyword.c_str() );
181 the_event->err_msg = strdup(errorMessage);
182 }
183
184 if (keyword == "nComponents" && getNComponents() > 0) {
185 components = new Component*[getNComponents()];
186 }else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
187 zConstraints = new ZconStamp*[getNZconstraints()];
188 }
189
190 return result;
191 }
192
193 int Globals::newComponent( event* the_event ){
194
195 current_component = new Component;
196 int index = the_event->evt.blk_index;
197 char err[200];
198
199 if( haveNComponents() && index < getNComponents() )
200 components[index] = current_component;
201 else{
202 if( haveNComponents() ){
203 sprintf( err, "meta-data parsing error: %d out of nComponents range",
204 index );
205 the_event->err_msg = strdup( err );
206 return 0;
207 }
208 else{
209 the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
210 " first component declaration." );
211 return 0;
212 }
213 }
214
215 return 1;
216 }
217
218
219
220 int Globals::componentAssign( event* the_event ){
221
222 switch( the_event->evt.asmt.asmt_type ){
223
224 case STRING:
225 return current_component->assignString( the_event->evt.asmt.lhs,
226 the_event->evt.asmt.rhs.sval,
227 &(the_event->err_msg));
228 break;
229
230 case DOUBLE:
231 return current_component->assignDouble( the_event->evt.asmt.lhs,
232 the_event->evt.asmt.rhs.dval,
233 &(the_event->err_msg));
234 break;
235
236 case INT:
237 return current_component->assignInt( the_event->evt.asmt.lhs,
238 the_event->evt.asmt.rhs.ival,
239 &(the_event->err_msg));
240 break;
241
242 default:
243 the_event->err_msg = strdup( "Globals error. Invalid component"
244 " assignment type" );
245 return 0;
246 break;
247 }
248 return 0;
249 }
250
251 int Globals::componentEnd( event* the_event ){
252
253 the_event->err_msg = current_component->checkMe();
254 if( the_event->err_msg != NULL ) return 0;
255
256 return 1;
257 }
258
259 int Globals::newZconstraint( event* the_event ){
260
261
262 int index = the_event->evt.blk_index;
263 char err[200];
264 current_zConstraint = new ZconStamp( index );
265
266 if( haveNZconstraints() && index < getNZconstraints() )
267 zConstraints[index] = current_zConstraint;
268 else{
269 if( haveNZconstraints() ){
270 sprintf( err, "meta-data parsing error: %d out of nZconstraints range",
271 index );
272 the_event->err_msg = strdup( err );
273 return 0;
274 }
275 else{
276 the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
277 " not given before"
278 " first zConstraint declaration." );
279 return 0;
280 }
281 }
282
283 return 1;
284 }
285
286
287
288 int Globals::zConstraintAssign( event* the_event ){
289
290 switch( the_event->evt.asmt.asmt_type ){
291
292 case STRING:
293 return current_zConstraint->assignString( the_event->evt.asmt.lhs,
294 the_event->evt.asmt.rhs.sval,
295 &(the_event->err_msg));
296 break;
297
298 case DOUBLE:
299 return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
300 the_event->evt.asmt.rhs.dval,
301 &(the_event->err_msg));
302 break;
303
304 case INT:
305 return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
306 the_event->evt.asmt.rhs.ival,
307 &(the_event->err_msg));
308 break;
309
310 default:
311 the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
312 " assignment type" );
313 return 0;
314 break;
315 }
316 return 0;
317 }
318
319 int Globals::zConstraintEnd( event* the_event ){
320
321 the_event->err_msg = current_zConstraint->checkMe();
322 if( the_event->err_msg != NULL ) return 0;
323
324 return 1;
325 }
326
327 char* Globals::checkMe( void ){
328
329
330 std::string err("The following required keywords are missing:\n");
331 short int have_err = 0;
332
333 ParamMap::iterator i;
334 for (i = parameters_.begin(); i != parameters_.end(); ++i) {
335 if (!i->second->isOptional() && i->second->empty()) {
336 err += i->second->getKeyword() + "\n";
337 }
338 }
339
340 CheckParameter(ForceField, isNotEmpty());
341 CheckParameter(NComponents,isPositive());
342 CheckParameter(TargetTemp, isPositive());
343 CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) ||
344 isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf"))||
345 isEqualIgnoreCase(std::string("NPTxyz")) );
346 CheckParameter(Dt, isPositive());
347 CheckParameter(RunTime, isPositive());
348 CheckParameter(InitialConfig, isNotEmpty());
349 CheckParameter(FinalConfig, isNotEmpty());
350 CheckParameter(NMol, isPositive());
351 CheckParameter(Density, isPositive());
352 CheckParameter(Box, isPositive());
353 CheckParameter(BoxX, isPositive());
354 CheckParameter(BoxY, isPositive());
355 CheckParameter(BoxZ, isPositive());
356 CheckParameter(SampleTime, isNonNegative());
357 CheckParameter(ResetTime, isNonNegative());
358 CheckParameter(StatusTime, isNonNegative());
359 CheckParameter(CutoffRadius, isPositive());
360 CheckParameter(SwitchingRadius, isNonNegative());
361 CheckParameter(Dielectric, isPositive());
362 CheckParameter(ThermalTime, isNonNegative());
363 CheckParameter(TargetPressure, isPositive());
364 CheckParameter(TauThermostat, isPositive());
365 CheckParameter(TauBarostat, isPositive());
366 CheckParameter(ZconsTime, isPositive());
367 CheckParameter(NZconstraints, isPositive());
368 CheckParameter(ZconsTol, isPositive());
369 //CheckParameter(ZconsForcePolicy,);
370 CheckParameter(Seed, isPositive());
371 CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
372 CheckParameter(MinimizerMaxIter, isPositive());
373 CheckParameter(MinimizerWriteFrq, isPositive());
374 CheckParameter(MinimizerStepSize, isPositive());
375 CheckParameter(MinimizerFTol, isPositive());
376 CheckParameter(MinimizerGTol, isPositive());
377 CheckParameter(MinimizerLSTol, isPositive());
378 CheckParameter(MinimizerLSMaxIter, isPositive());
379 CheckParameter(ZconsGap, isPositive());
380 CheckParameter(ZconsFixtime, isPositive());
381 CheckParameter(ThermodynamicIntegrationLambda, isPositive());
382 CheckParameter(ThermodynamicIntegrationK, isPositive());
383 CheckParameter(ForceFieldVariant, isNotEmpty());
384 CheckParameter(ForceFieldFileName, isNotEmpty());
385 CheckParameter(ThermIntDistSpringConst, isPositive());
386 CheckParameter(ThermIntThetaSpringConst, isPositive());
387 CheckParameter(ThermIntOmegaSpringConst, isPositive());
388 CheckParameter(SurfaceTension, isPositive());
389 CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || isEqualIgnoreCase(std::string("SHIFTED_FORCE")) || isEqualIgnoreCase(std::string("REACTION_FIELD")));
390 CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) || isEqualIgnoreCase(std::string("DAMPED")));
391 CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
392 //CheckParameter(StatFileFormat,);
393 //CheckParameter(MixingRule,);
394 CheckParameter(OrthoBoxTolerance, isPositive());
395 CheckParameter(ThermIntDistSpringConst, isPositive());
396 CheckParameter(ThermIntThetaSpringConst, isPositive());
397 CheckParameter(ThermIntOmegaSpringConst, isPositive());
398 CheckParameter(DampingAlpha,isNonNegative());
399 CheckParameter(SkinThickness, isPositive());
400
401 //@todo memory leak
402 if( have_err )
403 return strdup( err.c_str() );
404
405 return NULL;
406
407
408 }
409
410 int Globals::globalEnd( event* the_event ){
411
412 the_event->err_msg = checkMe();
413 if( the_event->err_msg != NULL ) return 0;
414
415 return 1;
416 }