source: src/Actions/FragmentationAction/FragmentationAutomationAction.cpp@ ac9ca4

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Last change on this file since ac9ca4 was ac9ca4, checked in by Frederik Heber <heber@…>, 12 years ago

FragmentAction creates FragmentJobs if no output-types are given.

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1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010-2012 University of Bonn. All rights reserved.
5 *
6 *
7 * This file is part of MoleCuilder.
8 *
9 * MoleCuilder is free software: you can redistribute it and/or modify
10 * it under the terms of the GNU General Public License as published by
11 * the Free Software Foundation, either version 2 of the License, or
12 * (at your option) any later version.
13 *
14 * MoleCuilder is distributed in the hope that it will be useful,
15 * but WITHOUT ANY WARRANTY; without even the implied warranty of
16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
17 * GNU General Public License for more details.
18 *
19 * You should have received a copy of the GNU General Public License
20 * along with MoleCuilder. If not, see <http://www.gnu.org/licenses/>.
21 */
22
23/*
24 * FragmentationAutomationAction.cpp
25 *
26 * Created on: May 18, 2012
27 * Author: heber
28 */
29
30// include config.h
31#ifdef HAVE_CONFIG_H
32#include <config.h>
33#endif
34
35#include <boost/archive/text_iarchive.hpp>
36// boost asio needs specific operator new
37#include <boost/asio.hpp>
38
39#include "CodePatterns/MemDebug.hpp"
40
41// include headers that implement a archive in simple text format
42#include <boost/archive/text_oarchive.hpp>
43#include <boost/archive/text_iarchive.hpp>
44
45
46#include <boost/mpl/remove.hpp>
47#include <boost/lambda/lambda.hpp>
48
49#include <iostream>
50
51#include "CodePatterns/Assert.hpp"
52#include "CodePatterns/Info.hpp"
53#include "CodePatterns/Log.hpp"
54#include "JobMarket/Jobs/FragmentJob.hpp"
55
56#include "Fragmentation/Automation/createMatrixNrLookup.hpp"
57#include "Fragmentation/Automation/extractJobIds.hpp"
58#include "Fragmentation/Automation/FragmentationChargeDensity.hpp"
59#include "Fragmentation/Automation/FragmentJobQueue.hpp"
60#include "Fragmentation/Automation/FragmentationResults.hpp"
61#include "Fragmentation/Automation/MPQCFragmentController.hpp"
62#include "Fragmentation/Automation/parseKeySetFile.hpp"
63#include "Fragmentation/Automation/VMGDebugGridFragmentController.hpp"
64#include "Fragmentation/Automation/VMGFragmentController.hpp"
65#include "Fragmentation/EnergyMatrix.hpp"
66#include "Fragmentation/ForceMatrix.hpp"
67#include "Fragmentation/Fragmentation.hpp"
68#include "Fragmentation/Homology/HomologyContainer.hpp"
69#include "Fragmentation/Homology/HomologyGraph.hpp"
70#include "Fragmentation/KeySet.hpp"
71#include "Fragmentation/KeySetsContainer.hpp"
72#include "Fragmentation/SetValues/Fragment.hpp"
73#include "Fragmentation/SetValues/Histogram.hpp"
74#include "Fragmentation/SetValues/IndexedVectors.hpp"
75#include "Fragmentation/Summation/IndexSetContainer.hpp"
76#include "Fragmentation/Summation/writeTable.hpp"
77#include "Graph/DepthFirstSearchAnalysis.hpp"
78#include "Jobs/MPQCJob.hpp"
79#include "Jobs/MPQCData.hpp"
80#include "Jobs/MPQCData_printKeyNames.hpp"
81#ifdef HAVE_VMG
82#include "Jobs/VMGDebugGridJob.hpp"
83#include "Jobs/VMGJob.hpp"
84#include "Jobs/VMGData.hpp"
85#include "Jobs/VMGDataFused.hpp"
86#include "Jobs/VMGDataMap.hpp"
87#include "Jobs/VMGData_printKeyNames.hpp"
88#endif
89#include "World.hpp"
90
91#include <fstream>
92#include <iostream>
93#include <string>
94#include <vector>
95
96#include <boost/mpl/for_each.hpp>
97
98#include "Actions/FragmentationAction/FragmentationAutomationAction.hpp"
99
100using namespace MoleCuilder;
101
102// and construct the stuff
103#include "FragmentationAutomationAction.def"
104#include "Action_impl_pre.hpp"
105/** =========== define the function ====================== */
106
107class controller_AddOn;
108
109// needs to be defined for using the FragmentController
110controller_AddOn *getAddOn()
111{
112 return NULL;
113}
114
115/** Helper function to get number of atoms somehow.
116 *
117 * Here, we just parse the number of lines in the adjacency file as
118 * it should correspond to the number of atoms, except when some atoms
119 * are not bonded, but then fragmentation makes no sense.
120 *
121 * @param path path to the adjacency file
122 */
123size_t getNoAtomsFromAdjacencyFile(const std::string &path)
124{
125 size_t NoAtoms = 0;
126
127 // parse in special file to get atom count (from line count)
128 std::string filename(path);
129 filename += FRAGMENTPREFIX;
130 filename += ADJACENCYFILE;
131 std::ifstream adjacency(filename.c_str());
132 if (adjacency.fail()) {
133 LOG(0, endl << "getNoAtomsFromAdjacencyFile() - Unable to open " << filename << ", is the directory correct?");
134 return false;
135 }
136 std::string buffer;
137 while (getline(adjacency, buffer))
138 NoAtoms++;
139 LOG(1, "INFO: There are " << NoAtoms << " atoms.");
140
141 return NoAtoms;
142}
143
144
145
146/** Place results from FragmentResult into EnergyMatrix and ForceMatrix.
147 *
148 * @param fragmentData MPQCData resulting from the jobs
149 * @param MatrixNrLookup Lookup up-map from job id to fragment number
150 * @param FragmentCounter total number of fragments
151 * @param NoAtoms total number of atoms
152 * @param Energy energy matrix to be filled on return
153 * @param Force force matrix to be filled on return
154 * @return true - everything ok, false - else
155 */
156bool putResultsintoMatrices(
157 const std::map<JobId_t, MPQCData> &fragmentData,
158 const std::map< JobId_t, size_t > &MatrixNrLookup,
159 const size_t FragmentCounter,
160 const size_t NoAtoms,
161 EnergyMatrix &Energy,
162 ForceMatrix &Force)
163{
164 for (std::map<JobId_t, MPQCData>::const_iterator dataiter = fragmentData.begin();
165 dataiter != fragmentData.end(); ++dataiter) {
166 const MPQCData &extractedData = dataiter->second;
167 const JobId_t &jobid = dataiter->first;
168 std::map< JobId_t, size_t >::const_iterator nriter = MatrixNrLookup.find(jobid);
169 ASSERT( nriter != MatrixNrLookup.end(),
170 "putResultsintoMatrices() - MatrixNrLookup does not contain id "
171 +toString(jobid)+".");
172 // place results into EnergyMatrix ...
173 {
174 MatrixContainer::MatrixArray matrix;
175 matrix.resize(1);
176 matrix[0].resize(1, extractedData.energies.total);
177 if (!Energy.AddMatrix(
178 std::string("MPQCJob ")+toString(jobid),
179 matrix,
180 nriter->second)) {
181 ELOG(1, "Adding energy matrix failed.");
182 return false;
183 }
184 }
185 // ... and ForceMatrix (with two empty columns in front)
186 {
187 MatrixContainer::MatrixArray matrix;
188 const size_t rows = extractedData.forces.size();
189 matrix.resize(rows);
190 for (size_t i=0;i<rows;++i) {
191 const size_t columns = 2+extractedData.forces[i].size();
192 matrix[i].resize(columns, 0.);
193 // for (size_t j=0;j<2;++j)
194 // matrix[i][j] = 0.;
195 for (size_t j=2;j<columns;++j)
196 matrix[i][j] = extractedData.forces[i][j-2];
197 }
198 if (!Force.AddMatrix(
199 std::string("MPQCJob ")+toString(jobid),
200 matrix,
201 nriter->second)) {
202 ELOG(1, "Adding force matrix failed.");
203 return false;
204 }
205 }
206 }
207 // add one more matrix (not required for energy)
208 MatrixContainer::MatrixArray matrix;
209 matrix.resize(1);
210 matrix[0].resize(1, 0.);
211 if (!Energy.AddMatrix(std::string("MPQCJob total"), matrix, FragmentCounter))
212 return false;
213 // but for energy because we need to know total number of atoms
214 matrix.resize(NoAtoms);
215 for (size_t i = 0; i< NoAtoms; ++i)
216 matrix[i].resize(2+NDIM, 0.);
217 if (!Force.AddMatrix(std::string("MPQCJob total"), matrix, FragmentCounter))
218 return false;
219
220 return true;
221}
222
223/** Print MPQCData from received results.
224 *
225 * @param fragmentData MPQCData resulting from the jobs, associated to job id
226 * @param KeySetFilename filename with keysets to associate forces correctly
227 * @param NoAtoms total number of atoms
228 * @param full_sample summed up charge from fragments on return
229 */
230bool printReceivedMPQCResults(
231 const std::map<JobId_t, MPQCData> &fragmentData,
232 const std::string &KeySetFilename,
233 size_t NoAtoms)
234{
235 // create a vector of all job ids
236 std::vector<JobId_t> jobids;
237 std::transform(fragmentData.begin(),fragmentData.end(),
238 std::back_inserter(jobids),
239 boost::bind( &std::map<JobId_t,MPQCData>::value_type::first, boost::lambda::_1 )
240 );
241
242 // create lookup from job nr to fragment number
243 size_t FragmentCounter = 0;
244 const std::map< JobId_t, size_t > MatrixNrLookup=
245 createMatrixNrLookup(jobids, FragmentCounter);
246
247 // place results into maps
248 EnergyMatrix Energy;
249 ForceMatrix Force;
250 if (!putResultsintoMatrices(fragmentData, MatrixNrLookup, FragmentCounter, NoAtoms, Energy, Force))
251 return false;
252
253 if (!Energy.InitialiseIndices()) return false;
254
255 if (!Force.ParseIndices(KeySetFilename.c_str())) return false;
256
257 // initialise keysets
258 KeySetsContainer KeySet;
259 parseKeySetFile(KeySet, KeySetFilename, FragmentCounter, NonHydrogenKeySets);
260 KeySetsContainer ForceKeySet;
261 parseKeySetFile(ForceKeySet, KeySetFilename, FragmentCounter, HydrogenKeySets);
262
263 // combine all found data
264 if (!KeySet.ParseManyBodyTerms()) return false;
265
266 EnergyMatrix EnergyFragments;
267 ForceMatrix ForceFragments;
268 if (!EnergyFragments.AllocateMatrix(Energy.Header, Energy.MatrixCounter, Energy.RowCounter, Energy.ColumnCounter)) return false;
269 if (!ForceFragments.AllocateMatrix(Force.Header, Force.MatrixCounter, Force.RowCounter, Force.ColumnCounter)) return false;
270
271 if(!Energy.SetLastMatrix(0., 0)) return false;
272 if(!Force.SetLastMatrix(0., 2)) return false;
273
274 for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
275 // --------- sum up energy --------------------
276 LOG(1, "INFO: Summing energy of order " << BondOrder+1 << " ...");
277 if (!EnergyFragments.SumSubManyBodyTerms(Energy, KeySet, BondOrder)) return false;
278 if (!Energy.SumSubEnergy(EnergyFragments, NULL, KeySet, BondOrder, 1.)) return false;
279
280 // --------- sum up Forces --------------------
281 LOG(1, "INFO: Summing forces of order " << BondOrder+1 << " ...");
282 if (!ForceFragments.SumSubManyBodyTerms(Force, KeySet, BondOrder)) return false;
283 if (!Force.SumSubForces(ForceFragments, KeySet, BondOrder, 1.)) return false;
284 }
285
286 // for debugging print resulting energy and forces
287 LOG(1, "INFO: Resulting energy is " << Energy.Matrix[ FragmentCounter ][0][0]);
288 std::stringstream output;
289 for (int i=0; i< Force.RowCounter[FragmentCounter]; ++i) {
290 for (int j=0; j< Force.ColumnCounter[FragmentCounter]; ++j)
291 output << Force.Matrix[ FragmentCounter ][i][j] << " ";
292 output << "\n";
293 }
294 LOG(1, "INFO: Resulting forces are " << std::endl << output.str());
295
296 return true;
297}
298
299void writeToFile(const std::string &filename, const std::string contents)
300{
301 std::ofstream tablefile(filename.c_str());
302 tablefile << contents;
303 tablefile.close();
304}
305
306/** Print MPQCData from received results.
307 *
308 * @param results summed up results container
309 */
310void printReceivedFullResults(
311 const FragmentationResults &results)
312{
313 // print tables (without eigenvalues, they go extra)
314 {
315 typedef boost::mpl::remove<MPQCDataEnergyVector_t, MPQCDataFused::energy_eigenvalues>::type
316 MPQCDataEnergyVector_noeigenvalues_t;
317 const std::string energyresult =
318 writeTable<MPQCDataEnergyMap_t, MPQCDataEnergyVector_noeigenvalues_t >()(
319 results.Result_Energy_fused, results.getMaxLevel());
320 LOG(0, "Energy table is \n" << energyresult);
321 std::string filename;
322 filename += FRAGMENTPREFIX + std::string("_Energy.dat");
323 writeToFile(filename, energyresult);
324 }
325
326 if (results.Result_LongRange_fused.size() >= (results.getMaxLevel()-2))
327 {
328 const std::string gridresult =
329 writeTable<VMGDataMap_t, VMGDataVector_t >()(
330 results.Result_LongRange_fused, results.getMaxLevel(), 2);
331 LOG(0, "VMG table is \n" << gridresult);
332 std::string filename;
333 filename += FRAGMENTPREFIX + std::string("_VMGEnergy.dat");
334 writeToFile(filename, gridresult);
335 }
336
337 if (results.Result_LongRangeIntegrated_fused.size() >= (results.getMaxLevel()-2))
338 {
339 const std::string gridresult =
340 writeTable<VMGDataLongRangeMap_t, VMGDataLongRangeVector_t >()(
341 results.Result_LongRangeIntegrated_fused, results.getMaxLevel(), 2);
342 LOG(0, "LongRange table is \n" << gridresult);
343 std::string filename;
344 filename += FRAGMENTPREFIX + std::string("_LongRangeEnergy.dat");
345 writeToFile(filename, gridresult);
346 }
347
348 {
349 const std::string eigenvalueresult;
350 LOG(0, "Eigenvalue table is \n" << eigenvalueresult);
351 std::string filename;
352 filename += FRAGMENTPREFIX + std::string("_Eigenvalues.dat");
353 writeToFile(filename, eigenvalueresult);
354 }
355
356 {
357 const std::string forceresult =
358 writeTable<MPQCDataForceMap_t, MPQCDataForceVector_t>()(
359 results.Result_Force_fused, results.getMaxLevel());
360 LOG(0, "Force table is \n" << forceresult);
361 std::string filename;
362 filename += FRAGMENTPREFIX + std::string("_Forces.dat");
363 writeToFile(filename, forceresult);
364 }
365 // we don't want to print grid to a table
366 {
367 // print times (without flops for now)
368 typedef boost::mpl::remove<
369 boost::mpl::remove<MPQCDataTimeVector_t, MPQCDataFused::times_total_flops>::type,
370 MPQCDataFused::times_gather_flops>::type
371 MPQCDataTimeVector_noflops_t;
372 const std::string timesresult =
373 writeTable<MPQCDataTimeMap_t, MPQCDataTimeVector_noflops_t >()(
374 results.Result_Time_fused, results.getMaxLevel());
375 LOG(0, "Times table is \n" << timesresult);
376 std::string filename;
377 filename += FRAGMENTPREFIX + std::string("_Times.dat");
378 writeToFile(filename, timesresult);
379 }
380}
381
382bool appendToHomologyFile(
383 const boost::filesystem::path &homology_file,
384 const FragmentationResults &results,
385 const std::string &KeySetFilename)
386{
387 /// read homology container (if present)
388 HomologyContainer homology_container;
389 if (boost::filesystem::exists(homology_file)) {
390 std::ifstream returnstream(homology_file.string().c_str());
391 if (returnstream.good()) {
392 boost::archive::text_iarchive ia(returnstream);
393 ia >> homology_container;
394 } else {
395 ELOG(2, "Failed to parse from " << homology_file.string() << ".");
396 }
397 returnstream.close();
398 } else {
399 LOG(2, "Could not open " << homology_file.string()
400 << ", creating empty container.");
401 }
402
403 /// append all fragments to a HomologyContainer
404 HomologyContainer::container_t values;
405 const size_t FragmentCounter = results.Result_perIndexSet_Energy.size();
406
407 // convert KeySetContainer to IndexSetContainer
408 IndexSetContainer::ptr ForceContainer(new IndexSetContainer(results.getForceKeySet()));
409 const IndexSetContainer::Container_t &Indices = results.getContainer();
410 const IndexSetContainer::Container_t &ForceIndices = ForceContainer->getContainer();
411 IndexSetContainer::Container_t::const_iterator iter = Indices.begin();
412 IndexSetContainer::Container_t::const_iterator forceiter = ForceIndices.begin();
413 /// go through all fragments
414 for (;iter != Indices.end(); ++iter, ++forceiter) // go through each IndexSet
415 {
416 /// create new graph entry in HomologyContainer which is (key,value) type
417 LOG(1, "INFO: Creating new graph with " << **forceiter << ".");
418 HomologyGraph graph(**forceiter);
419 LOG(2, "DEBUG: Created graph " << graph << ".");
420 const IndexSet::ptr &index = *iter;
421 HomologyContainer::value_t value;
422
423 // obtain fragment as key
424 std::map<IndexSet::ptr, std::pair< MPQCDataFragmentMap_t, MPQCDataFragmentMap_t> >::const_iterator fragmentiter
425 = results.Result_perIndexSet_Fragment.find(index);
426 ASSERT( fragmentiter != results.Result_perIndexSet_Fragment.end(),
427 "appendToHomologyFile() - cannot find index "+toString(*index)
428 +" in FragmentResults.");
429 value.first = boost::fusion::at_key<MPQCDataFused::fragment>(fragmentiter->second.first);
430
431 // obtain energy as value
432 std::map<IndexSet::ptr, std::pair< MPQCDataEnergyMap_t, MPQCDataEnergyMap_t> >::const_iterator energyiter
433 = results.Result_perIndexSet_Energy.find(index);
434 ASSERT( energyiter != results.Result_perIndexSet_Energy.end(),
435 "appendToHomologyFile() - cannot find index "+toString(*index)
436 +" in FragmentResults.");
437 // value.second = boost::fusion::at_key<MPQCDataFused::energy_total>(energyiter->second.first); // values
438 value.second = boost::fusion::at_key<MPQCDataFused::energy_total>(energyiter->second.second); // contributions
439 values.insert( std::make_pair( graph, value) );
440 }
441 homology_container.insert(values);
442
443 LOG(1, "INFO: Listing all present atomic ids ...");
444 std::stringstream output;
445 for (World::AtomIterator iter = World::getInstance().getAtomIter();
446 iter != World::getInstance().atomEnd(); ++iter)
447 output << (*iter)->getId() << " ";
448 LOG(1, "INFO: { " << output.str() << "} .");
449
450 // for debugging: print container
451 LOG(1, "INFO: Listing all present homologies ...");
452 for (HomologyContainer::container_t::const_iterator iter =
453 homology_container.begin(); iter != homology_container.end(); ++iter) {
454 LOG(1, "INFO: graph " << iter->first << " has Fragment "
455 << iter->second.first << " and associated energy " << iter->second.second << ".");
456 }
457
458 /// store homology container again
459 std::ofstream outputstream(homology_file.string().c_str());
460 if (outputstream.good()) { // check if opened
461 boost::archive::text_oarchive oa(outputstream);
462 oa << homology_container;
463 if (outputstream.fail()) { // check if correctly written
464 LOG(1, "Failed to write to file " << homology_file.string() << ".");
465 return false;
466 } else
467 outputstream.close();
468 } else {
469 LOG(1, "Failed to open file " << homology_file.string()
470 << " for writing.");
471 return false;
472 }
473 return true;
474}
475
476Action::state_ptr FragmentationFragmentationAutomationAction::performCall() {
477 boost::asio::io_service io_service;
478
479 // TODO: Have io_service run in second thread and merge with current again eventually
480
481 // check some things prior to work
482 enum OutputType_t {
483 ToFiles,
484 ToJobs,
485 ToNone
486 };
487 enum OutputType_t outputtype = ToNone;
488 if (params.jobfiles.get().size() != 0) {
489 // we got no job files, hence we use FragmentJobQueue
490 if (params.path.get().size() == 0) {
491 ELOG(1, "Missing path to fragment files.");
492 return Action::failure;
493 }
494 outputtype = ToFiles;
495
496 // parse in fragment-jobs if given
497 if(!FragmentJobQueue::getInstance().addJobsFromFiles(
498 params.jobfiles.get(),
499 params.level.get()))
500 return Action::failure;
501 } else {
502 if (params.path.get().size() != 0) {
503 ELOG(2, "Path to fragment given although we use FragmentJobQueue.");
504 }
505 outputtype = ToJobs;
506 }
507
508 size_t Exitflag = 0;
509 std::map<JobId_t, MPQCData> fragmentData;
510 {
511 const size_t NumberJobs = FragmentJobQueue::getInstance().size();
512 MPQCFragmentController mpqccontroller(io_service);
513 mpqccontroller.setHost(params.host.get());
514 mpqccontroller.setPort(params.port.get());
515 // Phase One: obtain ids
516 mpqccontroller.requestIds(NumberJobs);
517
518 // Phase Two: add MPQCJobs and send
519 mpqccontroller.addJobsFromQueue();
520 mpqccontroller.run();
521
522 // Phase Three: calculate result
523 mpqccontroller.waitforResults(NumberJobs);
524 mpqccontroller.getResults(fragmentData);
525
526 Exitflag += mpqccontroller.getExitflag();
527 }
528
529#ifdef HAVE_VMG
530 if (params.DoLongrange.get()) {
531 if ( World::getInstance().getAllAtoms().size() == 0) {
532 ELOG(1, "Please load the full molecule into the world before starting this action.");
533 return Action::failure;
534 }
535
536 // obtain combined charge density
537 FragmentationChargeDensity summedChargeDensity(
538 fragmentData,
539 params.path.get());
540 const std::vector<SamplingGrid> full_sample = summedChargeDensity.getFullSampledGrid();
541
542 LOG(1, "INFO: There are " << fragmentData.size() << " short-range and "
543 << full_sample.size() << " level-wise long-range jobs.");
544
545 // Phase Four: obtain more ids
546 std::map<JobId_t, VMGData> longrangeData;
547 {
548 VMGFragmentController vmgcontroller(io_service);
549 vmgcontroller.setHost(params.host.get());
550 vmgcontroller.setPort(params.port.get());
551 const size_t NoJobs = fragmentData.size()+full_sample.size();
552 vmgcontroller.requestIds(NoJobs);
553
554 // Phase Five: create VMGJobs
555 const size_t near_field_cells = params.near_field_cells.get();
556 const size_t interpolation_degree = params.interpolation_degree.get();
557 if (!vmgcontroller.createLongRangeJobs(
558 fragmentData,
559 full_sample,
560 summedChargeDensity.getFragment(),
561 near_field_cells,
562 interpolation_degree))
563 return Action::failure;
564
565 // Phase Six: calculate result
566 vmgcontroller.waitforResults(NoJobs);
567 vmgcontroller.getResults(longrangeData);
568 ASSERT( NoJobs == longrangeData.size(),
569 "FragmentationFragmentationAutomationAction::performCall() - number of MPQCresults+"
570 +toString(full_sample.size())+"="+toString(NoJobs)
571 +" and VMGresults "+toString(longrangeData.size())+" don't match.");
572 Exitflag += vmgcontroller.getExitflag();
573 }
574
575 // remove full solution corresponding to full_sample from map (must be highest ids), has to be treated extra
576 std::map<JobId_t, VMGData>::iterator iter = longrangeData.end();
577 for (size_t i=0;i<full_sample.size();++i)
578 --iter;
579 std::map<JobId_t, VMGData>::iterator remove_iter = iter;
580 std::vector<VMGData> fullsolutionData;
581 for (; iter != longrangeData.end(); ++iter)
582 fullsolutionData.push_back(iter->second);
583 longrangeData.erase(remove_iter, longrangeData.end());
584
585 // Final phase: sum up and print result
586 FragmentationResults results(
587 fragmentData,
588 longrangeData,
589 params.path.get());
590 results(
591 fragmentData,
592 longrangeData,
593 fullsolutionData,
594 full_sample);
595 {
596 LOG(1, "INFO: Parsing fragment files from " << params.path.get() << ".");
597 printReceivedFullResults(results);
598 }
599
600 // append all keysets to homology file
601 if ((Exitflag == 0) && (!params.homology_file.get().empty())) {
602 const boost::filesystem::path &homology_file = params.homology_file.get();
603 if (homology_file.string() != "") {
604 LOG(1, "INFO: Appending HomologyGraphs to file " << homology_file.string() << ".");
605 if (!appendToHomologyFile(homology_file, results, params.path.get()))
606 Exitflag = 1;
607 }
608 }
609
610 std::map<JobId_t, std::string> debugData;
611 {
612 if (!full_sample.empty()) {
613 // create debug jobs for each level to print the summed-up potential to vtk files
614 VMGDebugGridFragmentController debugcontroller(io_service);
615 debugcontroller.setHost(params.host.get());
616 debugcontroller.setPort(params.port.get());
617 debugcontroller.requestIds(full_sample.size());
618 if (!debugcontroller.createDebugJobs(full_sample))
619 return Action::failure;
620 debugcontroller.waitforResults(full_sample.size());
621 debugcontroller.getResults(debugData);
622 Exitflag += debugcontroller.getExitflag();
623 }
624 }
625 }
626#else
627 // Final phase: print result
628 {
629 LOG(1, "INFO: Parsing fragment files from " << params.path.get() << ".");
630 printReceivedMPQCResults(
631 fragmentData,
632 params.path.get(),
633 getNoAtomsFromAdjacencyFile(params.path.get()));
634 }
635#endif
636
637 return (Exitflag == 0) ? Action::success : Action::failure;
638}
639
640Action::state_ptr FragmentationFragmentationAutomationAction::performUndo(Action::state_ptr _state) {
641 return Action::success;
642}
643
644Action::state_ptr FragmentationFragmentationAutomationAction::performRedo(Action::state_ptr _state){
645 return Action::success;
646}
647
648bool FragmentationFragmentationAutomationAction::canUndo() {
649 return false;
650}
651
652bool FragmentationFragmentationAutomationAction::shouldUndo() {
653 return false;
654}
655/** =========== end of function ====================== */
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