source: src/Parser/TremoloParser.cpp@ 38f991

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Last change on this file since 38f991 was 81c980b, checked in by Frederik Heber <heber@…>, 13 years ago

Added new action to set the ATOMDATA in tremolo's .data output file.

  • new action is set-tremolo-atomdata in ParserAction.
  • added regression test.
  • Property mode set to 100644
File size: 25.3 KB
Line 
1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010 University of Bonn. All rights reserved.
5 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
6 */
7
8/*
9 * TremoloParser.cpp
10 *
11 * Created on: Mar 2, 2010
12 * Author: metzler
13 */
14
15// include config.h
16#ifdef HAVE_CONFIG_H
17#include <config.h>
18#endif
19
20#include "CodePatterns/MemDebug.hpp"
21
22#include "CodePatterns/Assert.hpp"
23#include "CodePatterns/Log.hpp"
24#include "CodePatterns/toString.hpp"
25#include "CodePatterns/Verbose.hpp"
26#include "TremoloParser.hpp"
27#include "World.hpp"
28#include "WorldTime.hpp"
29#include "atom.hpp"
30#include "Bond/bond.hpp"
31#include "element.hpp"
32#include "molecule.hpp"
33#include "periodentafel.hpp"
34#include "Descriptors/AtomIdDescriptor.hpp"
35#include <map>
36#include <vector>
37
38#include <boost/tokenizer.hpp>
39#include <iostream>
40#include <iomanip>
41
42using namespace std;
43
44/**
45 * Constructor.
46 */
47TremoloParser::TremoloParser() {
48 knownKeys["x"] = TremoloKey::x;
49 knownKeys["u"] = TremoloKey::u;
50 knownKeys["F"] = TremoloKey::F;
51 knownKeys["stress"] = TremoloKey::stress;
52 knownKeys["Id"] = TremoloKey::Id;
53 knownKeys["neighbors"] = TremoloKey::neighbors;
54 knownKeys["imprData"] = TremoloKey::imprData;
55 knownKeys["GroupMeasureTypeNo"] = TremoloKey::GroupMeasureTypeNo;
56 knownKeys["type"] = TremoloKey::type;
57 knownKeys["extType"] = TremoloKey::extType;
58 knownKeys["name"] = TremoloKey::name;
59 knownKeys["resName"] = TremoloKey::resName;
60 knownKeys["chainID"] = TremoloKey::chainID;
61 knownKeys["resSeq"] = TremoloKey::resSeq;
62 knownKeys["occupancy"] = TremoloKey::occupancy;
63 knownKeys["tempFactor"] = TremoloKey::tempFactor;
64 knownKeys["segID"] = TremoloKey::segID;
65 knownKeys["Charge"] = TremoloKey::Charge;
66 knownKeys["charge"] = TremoloKey::charge;
67 knownKeys["GrpTypeNo"] = TremoloKey::GrpTypeNo;
68 knownKeys["torsion"] = TremoloKey::torsion;
69
70 createKnownTypesByIdentity();
71
72 // default behavior: use all possible keys on output
73 for (std::map<std::string, TremoloKey::atomDataKey>::iterator iter = knownKeys.begin(); iter != knownKeys.end(); ++iter)
74 usedFields.push_back(iter->first);
75
76 // and noKey afterwards(!) such that it is not used in usedFields
77 knownKeys[" "] = TremoloKey::noKey; // with this we can detect invalid keys
78
79 // invert knownKeys for debug output
80 for (std::map<std::string, TremoloKey::atomDataKey>::iterator iter = knownKeys.begin(); iter != knownKeys.end(); ++iter)
81 knownKeyNames.insert( make_pair( iter->second, iter->first) );
82
83 additionalAtomData.clear();
84}
85
86/**
87 * Destructor.
88 */
89TremoloParser::~TremoloParser() {
90 std::cerr << "Clearing usedFields." << std::endl;
91 usedFields.clear();
92 additionalAtomData.clear();
93 atomIdMap.clear();
94 knownKeys.clear();
95}
96
97/**
98 * Loads atoms from a tremolo-formatted file.
99 *
100 * \param tremolo file
101 */
102void TremoloParser::load(istream* file) {
103 string line;
104 string::size_type location;
105
106 // reset atomIdMap, for we now get new serials
107 atomIdMap.clear();
108 std::cerr << "Clearing usedFields." << std::endl;
109 usedFields.clear();
110
111 molecule *newmol = World::getInstance().createMolecule();
112 newmol->ActiveFlag = true;
113 // TODO: Remove the insertion into molecule when saving does not depend on them anymore. Also, remove molecule.hpp include
114 World::getInstance().getMolecules()->insert(newmol);
115 while (file->good()) {
116 std::getline(*file, line, '\n');
117 if (usedFields.empty()) {
118 location = line.find("ATOMDATA", 0);
119 if (location != string::npos) {
120 parseAtomDataKeysLine(line, location + 8);
121 }
122 }
123 if (line.length() > 0 && line.at(0) != '#') {
124 readAtomDataLine(line, newmol);
125 }
126 }
127 // refresh atom::nr and atom::name
128 newmol->getAtomCount();
129
130 DoLog(3) && (Log() << Verbose(3) << "usedFields after load contains: " << usedFields << std::endl);
131
132 processNeighborInformation();
133 adaptImprData();
134 adaptTorsion();
135}
136
137/**
138 * Saves the \a atoms into as a tremolo file.
139 *
140 * \param file where to save the state
141 * \param atoms atoms to store
142 */
143void TremoloParser::save(ostream* file, const std::vector<atom *> &AtomList) {
144 DoLog(0) && (Log() << Verbose(0) << "Saving changes to tremolo." << std::endl);
145
146 vector<atom*>::const_iterator atomIt;
147 /*vector<string>::iterator it;*/
148 vector<string>::iterator it = unique(usedFields.begin(), usedFields.end()); // skips all duplicates in the vector
149
150
151 DoLog(3) && (Log() << Verbose(3) << "usedFields before save contains: " << usedFields << std::endl);
152
153 DoLog(3) && (Log() << Verbose(3) << "additionalAtomData contains: " << additionalAtomData << std::endl);
154
155 DoLog(3) && (Log() << Verbose(3) << "additionalAtomData contains: " << additionalAtomData << std::endl);
156
157 *file << "# ATOMDATA";
158 for (it=usedFields.begin(); it < usedFields.end(); it++) {
159 *file << "\t" << *it;
160 }
161 *file << endl;
162 for (atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
163 saveLine(file, *atomIt);
164 }
165}
166
167/**
168 * Sets the keys for which data should be written to the stream when save is
169 * called.
170 *
171 * \param string of field names with the same syntax as for an ATOMDATA line
172 * but without the prexix "ATOMDATA"
173 */
174void TremoloParser::setFieldsForSave(std::string atomDataLine) {
175 parseAtomDataKeysLine(atomDataLine, 0);
176}
177
178
179/**
180 * Writes one line of tremolo-formatted data to the provided stream.
181 *
182 * \param stream where to write the line to
183 * \param reference to the atom of which information should be written
184 */
185void TremoloParser::saveLine(ostream* file, atom* currentAtom) {
186 /* vector<string>::iterator it;*/
187 vector<string>::iterator it = unique(usedFields.begin(), usedFields.end()); // skips all duplicates in the vector
188
189 TremoloKey::atomDataKey currentField;
190
191 DoLog(4) && (Log() << Verbose(4) << "INFO: Saving atom " << *currentAtom << ", its father id is " << currentAtom->GetTrueFather()->getId() << std::endl);
192
193 for (it = usedFields.begin(); it != usedFields.end(); it++) {
194 currentField = knownKeys[it->substr(0, it->find("="))];
195 switch (currentField) {
196 case TremoloKey::x :
197 // for the moment, assume there are always three dimensions
198 DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << currentAtom->getPosition() << std::endl);
199 *file << currentAtom->at(0) << "\t";
200 *file << currentAtom->at(1) << "\t";
201 *file << currentAtom->at(2) << "\t";
202 break;
203 case TremoloKey::u :
204 // for the moment, assume there are always three dimensions
205 DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << currentAtom->getAtomicVelocity() << std::endl);
206 *file << currentAtom->getAtomicVelocity()[0] << "\t";
207 *file << currentAtom->getAtomicVelocity()[1] << "\t";
208 *file << currentAtom->getAtomicVelocity()[2] << "\t";
209 break;
210 case TremoloKey::type :
211 if (additionalAtomData.count(currentAtom->getId())) {
212 if (additionalAtomData[currentAtom->getId()].get(currentField) != "-") {
213 DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << additionalAtomData[currentAtom->getId()].get(currentField) << std::endl);
214 *file << additionalAtomData[currentAtom->getId()].get(currentField) << "\t";
215 } else {
216 DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " default value: " << currentAtom->getType()->getSymbol() << std::endl);
217 *file << currentAtom->getType()->getSymbol() << "\t";
218 }
219 } else if (additionalAtomData.count(currentAtom->GetTrueFather()->getId())) {
220 if (additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField) != "-") {
221 DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " stuff from father: " << additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField) << std::endl);
222 *file << additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField) << "\t";
223 } else {
224 DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " default value from father: " << currentAtom->GetTrueFather()->getType()->getSymbol() << std::endl);
225 *file << currentAtom->GetTrueFather()->getType()->getSymbol() << "\t";
226 }
227 } else {
228 DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " its default value: " << currentAtom->getType()->getSymbol() << std::endl);
229 *file << currentAtom->getType()->getSymbol() << "\t";
230 }
231 break;
232 case TremoloKey::Id :
233 DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << currentAtom->getId()+1 << std::endl);
234 *file << currentAtom->getId()+1 << "\t";
235 break;
236 case TremoloKey::neighbors :
237 DoLog(3) && (Log() << Verbose(3) << "Writing type " << knownKeyNames[currentField] << std::endl);
238 writeNeighbors(file, atoi(it->substr(it->find("=") + 1, 1).c_str()), currentAtom);
239 break;
240 case TremoloKey::resSeq :
241 if (additionalAtomData.count(currentAtom->getId())) {
242 DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << additionalAtomData[currentAtom->getId()].get(currentField) << std::endl);
243 *file << additionalAtomData[currentAtom->getId()].get(currentField);
244 } else if (currentAtom->getMolecule() != NULL) {
245 DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " its own id: " << currentAtom->getMolecule()->getId()+1 << std::endl);
246 *file << setw(4) << currentAtom->getMolecule()->getId()+1;
247 } else {
248 DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " default value: " << defaultAdditionalData.get(currentField) << std::endl);
249 *file << defaultAdditionalData.get(currentField);
250 }
251 *file << "\t";
252 break;
253 default :
254 if (additionalAtomData.count(currentAtom->getId())) {
255 DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << ": " << additionalAtomData[currentAtom->getId()].get(currentField) << std::endl);
256 *file << additionalAtomData[currentAtom->getId()].get(currentField);
257 } else if (additionalAtomData.count(currentAtom->GetTrueFather()->getId())) {
258 DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " stuff from father: " << additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField) << std::endl);
259 *file << additionalAtomData[currentAtom->GetTrueFather()->getId()].get(currentField);
260 } else {
261 DoLog(3) && (Log() << Verbose(3) << "Writing for type " << knownKeyNames[currentField] << " the default: " << defaultAdditionalData.get(currentField) << std::endl);
262 *file << defaultAdditionalData.get(currentField);
263 }
264 *file << "\t";
265 break;
266 }
267 }
268
269 *file << endl;
270}
271
272/**
273 * Writes the neighbor information of one atom to the provided stream.
274 *
275 * Note that ListOfBonds of WorldTime::CurrentTime is used.
276 *
277 * \param stream where to write neighbor information to
278 * \param number of neighbors
279 * \param reference to the atom of which to take the neighbor information
280 */
281void TremoloParser::writeNeighbors(ostream* file, int numberOfNeighbors, atom* currentAtom) {
282 const BondList& ListOfBonds = currentAtom->getListOfBonds();
283 // sort bonded indices
284 typedef std::set<atomId_t> sortedIndices;
285 sortedIndices sortedBonds;
286 for (BondList::const_iterator iter = ListOfBonds.begin();
287 iter != ListOfBonds.end(); ++iter)
288 sortedBonds.insert((*iter)->GetOtherAtom(currentAtom)->getId());
289 // print indices
290 sortedIndices::const_iterator currentBond = sortedBonds.begin();
291 for (int i = 0; i < numberOfNeighbors; i++) {
292 *file << (currentBond != sortedBonds.end() ? (*currentBond)+1 : 0) << "\t";
293 if (currentBond != sortedBonds.end())
294 ++currentBond;
295 }
296}
297
298/**
299 * Stores keys from the ATOMDATA line.
300 *
301 * \param line to parse the keys from
302 * \param with which offset the keys begin within the line
303 */
304void TremoloParser::parseAtomDataKeysLine(string line, int offset) {
305 string keyword;
306 stringstream lineStream;
307
308 lineStream << line.substr(offset);
309 std::cerr << "Clearing usedFields in parseAtomDataKeysLine." << std::endl;
310 usedFields.clear();
311 while (lineStream.good()) {
312 lineStream >> keyword;
313 if (knownKeys[keyword.substr(0, keyword.find("="))] == TremoloKey::noKey) {
314 // TODO: throw exception about unknown key
315 cout << "Unknown key: " << keyword << " is not part of the tremolo format specification." << endl;
316 break;
317 }
318 usedFields.push_back(keyword);
319 }
320 //DoLog(1) && (Log() << Verbose(1) << "INFO: " << usedFields << std::endl);
321}
322
323/** Sets the properties per atom to print to .data file by parsing line from
324 * \a atomdata_string.
325 *
326 * We just call \sa TremoloParser::parseAtomDataKeysLine() which is left
327 * private.,
328 *
329 * @param atomdata_string line to parse with space-separated values
330 */
331void TremoloParser::setAtomData(const std::string &atomdata_string)
332{
333 parseAtomDataKeysLine(atomdata_string, 0);
334}
335
336
337/**
338 * Reads one data line of a tremolo file and interprets it according to the keys
339 * obtained from the ATOMDATA line.
340 *
341 * \param line to parse as an atom
342 * \param *newmol molecule to add atom to
343 */
344void TremoloParser::readAtomDataLine(string line, molecule *newmol = NULL) {
345 vector<string>::iterator it;
346 stringstream lineStream;
347 atom* newAtom = World::getInstance().createAtom();
348 TremoloAtomInfoContainer *atomInfo = NULL;
349 additionalAtomData[newAtom->getId()] = TremoloAtomInfoContainer(); // fill with default values
350 atomInfo = &additionalAtomData[newAtom->getId()];
351 TremoloKey::atomDataKey currentField;
352 ConvertTo<double> toDouble;
353 ConvertTo<int> toInt;
354 Vector tempVector;
355
356 // setup tokenizer, splitting up white-spaced entries
357 typedef boost::tokenizer<boost::char_separator<char> >
358 tokenizer;
359 boost::char_separator<char> whitespacesep(" \t");
360 tokenizer tokens(line, whitespacesep);
361 ASSERT(tokens.begin() != tokens.end(),
362 "TremoloParser::readAtomDataLine - empty string, need at least ' '!");
363 tokenizer::iterator tok_iter = tokens.begin();
364 // then associate each token to each file
365 for (it = usedFields.begin(); it < usedFields.end(); it++) {
366 const std::string keyName = it->substr(0, it->find("="));
367 currentField = knownKeys[keyName];
368 const string word = *tok_iter;
369 DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with remaining data " << word << std::endl);
370 switch (currentField) {
371 case TremoloKey::x :
372 // for the moment, assume there are always three dimensions
373 for (int i=0;i<NDIM;i++) {
374 ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for x["+toString(i)+"]!");
375 DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
376 newAtom->set(i, toDouble(*tok_iter));
377 tok_iter++;
378 }
379 break;
380 case TremoloKey::u :
381 // for the moment, assume there are always three dimensions
382 for (int i=0;i<NDIM;i++) {
383 ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for u["+toString(i)+"]!");
384 DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
385 tempVector[i] = toDouble(*tok_iter);
386 tok_iter++;
387 }
388 newAtom->setAtomicVelocity(tempVector);
389 break;
390 case TremoloKey::type :
391 {
392 ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
393 DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
394 std::string element(knownTypes[(*tok_iter)]);
395 // put type name into container for later use
396 atomInfo->set(currentField, *tok_iter);
397 DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing element " << (*tok_iter) << " as " << element << " according to KnownTypes." << std::endl);
398 tok_iter++;
399 newAtom->setType(World::getInstance().getPeriode()->FindElement(element));
400 ASSERT(newAtom->getType(), "Type was not set for this atom");
401 break;
402 }
403 case TremoloKey::Id :
404 ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
405 DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
406 atomIdMap[toInt(*tok_iter)] = newAtom->getId();
407 tok_iter++;
408 break;
409 case TremoloKey::neighbors :
410 for (int i=0;i<atoi(it->substr(it->find("=") + 1, 1).c_str());i++) {
411 ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
412 DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
413 lineStream << *tok_iter << "\t";
414 tok_iter++;
415 }
416 readNeighbors(&lineStream,
417 atoi(it->substr(it->find("=") + 1, 1).c_str()), newAtom->getId());
418 break;
419 default :
420 ASSERT(tok_iter != tokens.end(), "TremoloParser::readAtomDataLine() - no value for "+keyName+"!");
421 DoLog(4) && (Log() << Verbose(4) << "INFO: Parsing key " << keyName << " with next token " << *tok_iter << std::endl);
422 atomInfo->set(currentField, *tok_iter);
423 tok_iter++;
424 break;
425 }
426 }
427 if (newmol != NULL) {
428 //DoLog(0) && (Log() << Verbose(0) << "New Atom: " << *newAtom << " with type " << newAtom->getType()->getName() << std::endl);
429 newmol->AddAtom(newAtom);
430 }
431}
432
433/**
434 * Reads neighbor information for one atom from the input.
435 *
436 * \param line stream where to read the information from
437 * \param numberOfNeighbors number of neighbors to read
438 * \param atomid world id of the atom the information belongs to
439 */
440void TremoloParser::readNeighbors(stringstream* line, int numberOfNeighbors, int atomId) {
441 int neighborId = 0;
442 for (int i = 0; i < numberOfNeighbors; i++) {
443 *line >> neighborId;
444 // 0 is used to fill empty neighbor positions in the tremolo file.
445 if (neighborId > 0) {
446 DoLog(4) && (Log() << Verbose(4)
447 << "Atom with global id " << atomId
448 << " has neighbour with serial " << neighborId
449 << std::endl);
450 additionalAtomData[atomId].neighbors.push_back(neighborId);
451 }
452 }
453}
454
455/**
456 * Checks whether the provided name is within the list of used fields.
457 *
458 * \param field name to check
459 *
460 * \return true if the field name is used
461 */
462bool TremoloParser::isUsedField(string fieldName) {
463 bool fieldNameExists = false;
464 for (vector<string>::iterator usedField = usedFields.begin(); usedField != usedFields.end(); usedField++) {
465 if (usedField->substr(0, usedField->find("=")) == fieldName)
466 fieldNameExists = true;
467 }
468
469 return fieldNameExists;
470}
471
472
473/**
474 * Adds the collected neighbor information to the atoms in the world. The atoms
475 * are found by their current ID and mapped to the corresponding atoms with the
476 * Id found in the parsed file.
477 */
478void TremoloParser::processNeighborInformation() {
479 if (!isUsedField("neighbors")) {
480 return;
481 }
482
483 for(map<int, TremoloAtomInfoContainer>::iterator currentInfo = additionalAtomData.begin();
484 currentInfo != additionalAtomData.end(); currentInfo++
485 ) {
486 if (!currentInfo->second.neighbors_processed) {
487 for(vector<int>::iterator neighbor = currentInfo->second.neighbors.begin();
488 neighbor != currentInfo->second.neighbors.end(); neighbor++
489 ) {
490// DoLog(1) && (Log() << Verbose(1) << "Creating bond between ("
491// << currentInfo->first
492// << ") and ("
493// << atomIdMap[*neighbor] << "|" << *neighbor << ")" << std::endl);
494 World::getInstance().getAtom(AtomById(currentInfo->first))
495 ->addBond(WorldTime::getTime(), World::getInstance().getAtom(AtomById(atomIdMap[*neighbor])));
496 }
497 currentInfo->second.neighbors_processed = true;
498 }
499 }
500}
501
502/**
503 * Replaces atom IDs read from the file by the corresponding world IDs. All IDs
504 * IDs of the input string will be replaced; expected separating characters are
505 * "-" and ",".
506 *
507 * \param string in which atom IDs should be adapted
508 *
509 * \return input string with modified atom IDs
510 */
511string TremoloParser::adaptIdDependentDataString(string data) {
512 // there might be no IDs
513 if (data == "-") {
514 return "-";
515 }
516
517 char separator;
518 int id;
519 stringstream line, result;
520 line << data;
521
522 line >> id;
523 result << atomIdMap[id];
524 while (line.good()) {
525 line >> separator >> id;
526 result << separator << atomIdMap[id];
527 }
528
529 return result.str();
530}
531
532/**
533 * Corrects the atom IDs in each imprData entry to the corresponding world IDs
534 * as they might differ from the originally read IDs.
535 */
536void TremoloParser::adaptImprData() {
537 if (!isUsedField("imprData")) {
538 return;
539 }
540
541 for(map<int, TremoloAtomInfoContainer>::iterator currentInfo = additionalAtomData.begin();
542 currentInfo != additionalAtomData.end(); currentInfo++
543 ) {
544 currentInfo->second.imprData = adaptIdDependentDataString(currentInfo->second.imprData);
545 }
546}
547
548/**
549 * Corrects the atom IDs in each torsion entry to the corresponding world IDs
550 * as they might differ from the originally read IDs.
551 */
552void TremoloParser::adaptTorsion() {
553 if (!isUsedField("torsion")) {
554 return;
555 }
556
557 for(map<int, TremoloAtomInfoContainer>::iterator currentInfo = additionalAtomData.begin();
558 currentInfo != additionalAtomData.end(); currentInfo++
559 ) {
560 currentInfo->second.torsion = adaptIdDependentDataString(currentInfo->second.torsion);
561 }
562}
563
564/** Creates knownTypes as the identity, e.g. H -> H, He -> He, ... .
565 *
566 */
567void TremoloParser::createKnownTypesByIdentity()
568{
569 // remove old mapping
570 knownTypes.clear();
571 // make knownTypes the identity mapping
572 const periodentafel *periode = World::getInstance().getPeriode();
573 for (periodentafel::const_iterator iter = periode->begin();
574 iter != periode->end();
575 ++iter) {
576 knownTypes.insert( make_pair(iter->second->getSymbol(), iter->second->getSymbol()) );
577 }
578}
579
580/** Parses a .potentials file and creates from it the knownTypes file.
581 *
582 * @param file input stream of .potentials file
583 */
584void TremoloParser::parseKnownTypes(std::istream &file)
585{
586 const periodentafel *periode = World::getInstance().getPeriode();
587 // remove old mapping
588 knownTypes.clear();
589
590 DoLog(3) && (Log() << Verbose(3) << "additionalAtomData contains: " << additionalAtomData << std::endl);
591
592 // parse in file
593 typedef boost::tokenizer<boost::char_separator<char> >
594 tokenizer;
595 boost::char_separator<char> tokensep(":\t ,;");
596 boost::char_separator<char> equalitysep("\t =");
597 std::string line;
598 while (file.good()) {
599 std::getline( file, line );
600 DoLog(4) && (Log() << Verbose(4) << "INFO: full line of parameters is '" << line << "'" << std::endl);
601 if (line.find("particle:") != string::npos) {
602 DoLog(3) && (Log() << Verbose(3) << "INFO: found line '" << line << "' containing keyword 'particle:'." << std::endl);
603 tokenizer tokens(line, tokensep);
604 ASSERT(tokens.begin() != tokens.end(),
605 "TremoloParser::parseKnownTypes() - line with 'particle:' but no particles separated by comma.");
606 // look for particle_type
607 std::string particle_type("NULL");
608 std::string element_type("NULL");
609 for (tokenizer::iterator tok_iter = tokens.begin();
610 tok_iter != tokens.end();
611 ++tok_iter) {
612 if ((*tok_iter).find("particle_type") != string::npos) {
613 DoLog(3) && (Log() << Verbose(3) << "INFO: found line '" << line << "' containing keyword 'particle_type'." << std::endl);
614 tokenizer token((*tok_iter), equalitysep);
615 ASSERT(token.begin() != token.end(),
616 "TremoloParser::parseKnownTypes() - could not split particle_type by equality sign");
617 tokenizer::iterator particle_iter = token.begin();
618 particle_iter++;
619 particle_type = *particle_iter;
620 }
621 if ((*tok_iter).find("element_name") != string::npos) {
622 DoLog(3) && (Log() << Verbose(3) << "INFO: found line '" << line << "' containing keyword 'element_name'." << std::endl);
623 tokenizer token((*tok_iter), equalitysep);
624 ASSERT(token.begin() != token.end(),
625 "TremoloParser::parseKnownTypes() - could not split particle_type by equality sign");
626 tokenizer::iterator element_iter = token.begin();
627 element_iter++;
628 element_type = *element_iter;
629 }
630 }
631 if ((particle_type != "NULL") && (element_type != "NULL")) {
632 if (periode->FindElement(element_type) != NULL) {
633 DoLog(1) && (Log() << Verbose(1) << "INFO: Added Type " << particle_type << " as reference to element " << element_type << "." << std::endl);
634 knownTypes.insert( make_pair (particle_type, element_type) );
635 } else {
636 DoeLog(1) && (Log() << Verbose(1) << "INFO: Either Type " << particle_type << " or " << element_type << " could not be recognized." << std::endl);
637 }
638 } else {
639 DoeLog(1) && (Log() << Verbose(1) << "INFO: Desired element " << element_type << " is not known." << std::endl);
640 }
641 }
642 }
643
644}
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