| [edecba] | 1 | /*
 | 
|---|
 | 2 |  * Project: MoleCuilder
 | 
|---|
 | 3 |  * Description: creates and alters molecular systems
 | 
|---|
 | 4 |  * Copyright (C)  2010-2012 University of Bonn. All rights reserved.
 | 
|---|
| [94d5ac6] | 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/>.
 | 
|---|
| [edecba] | 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 | 
 | 
|---|
| [6ca578] | 41 | #include <boost/assign.hpp>
 | 
|---|
 | 42 | 
 | 
|---|
 | 43 | #include "CodePatterns/Assert.hpp"
 | 
|---|
| [edecba] | 44 | #include "CodePatterns/Info.hpp"
 | 
|---|
 | 45 | #include "CodePatterns/Log.hpp"
 | 
|---|
 | 46 | #include "JobMarket/Controller/FragmentController.hpp"
 | 
|---|
 | 47 | #include "JobMarket/Jobs/FragmentJob.hpp"
 | 
|---|
 | 48 | 
 | 
|---|
 | 49 | #include "Atom/atom.hpp"
 | 
|---|
| [d12d621] | 50 | #include "Box.hpp"
 | 
|---|
| [edecba] | 51 | #include "Fragmentation/EnergyMatrix.hpp"
 | 
|---|
 | 52 | #include "Fragmentation/ForceMatrix.hpp"
 | 
|---|
 | 53 | #include "Fragmentation/Fragmentation.hpp"
 | 
|---|
| [e06820] | 54 | #include "Fragmentation/SetValues/Histogram.hpp"
 | 
|---|
| [e13990b] | 55 | #include "Fragmentation/SetValues/IndexedVectors.hpp"
 | 
|---|
| [edecba] | 56 | #include "Fragmentation/HydrogenSaturation_enum.hpp"
 | 
|---|
| [6ca578] | 57 | #include "Fragmentation/KeySet.hpp"
 | 
|---|
| [edecba] | 58 | #include "Fragmentation/KeySetsContainer.hpp"
 | 
|---|
| [286e36] | 59 | #include "Fragmentation/Summation/printSum.hpp"
 | 
|---|
| [edecba] | 60 | #include "Graph/DepthFirstSearchAnalysis.hpp"
 | 
|---|
| [28e894] | 61 | #include "Jobs/MPQCJob.hpp"
 | 
|---|
| [4bc75d] | 62 | #include "Jobs/MPQCData.hpp"
 | 
|---|
| [1f66c7] | 63 | #include "Jobs/MPQCData_printKeyNames.hpp"
 | 
|---|
| [d12d621] | 64 | #include "LinearAlgebra/RealSpaceMatrix.hpp"
 | 
|---|
| [69c733] | 65 | #ifdef HAVE_VMG
 | 
|---|
 | 66 | #include "Jobs/VMGJob.hpp"
 | 
|---|
 | 67 | #endif
 | 
|---|
| [edecba] | 68 | #include "molecule.hpp"
 | 
|---|
 | 69 | #include "World.hpp"
 | 
|---|
 | 70 | 
 | 
|---|
 | 71 | #include <iostream>
 | 
|---|
 | 72 | #include <string>
 | 
|---|
 | 73 | #include <vector>
 | 
|---|
 | 74 | 
 | 
|---|
| [8cae4c] | 75 | #include <boost/mpl/for_each.hpp>
 | 
|---|
 | 76 | 
 | 
|---|
| [edecba] | 77 | #include "Actions/FragmentationAction/FragmentationAutomationAction.hpp"
 | 
|---|
 | 78 | 
 | 
|---|
 | 79 | using namespace MoleCuilder;
 | 
|---|
 | 80 | 
 | 
|---|
| [6ca578] | 81 | using namespace boost::assign;
 | 
|---|
 | 82 | 
 | 
|---|
| [edecba] | 83 | // and construct the stuff
 | 
|---|
 | 84 | #include "FragmentationAutomationAction.def"
 | 
|---|
 | 85 | #include "Action_impl_pre.hpp"
 | 
|---|
 | 86 | /** =========== define the function ====================== */
 | 
|---|
 | 87 | 
 | 
|---|
 | 88 | class controller_AddOn;
 | 
|---|
 | 89 | 
 | 
|---|
 | 90 | // needs to be defined for using the FragmentController
 | 
|---|
 | 91 | controller_AddOn *getAddOn()
 | 
|---|
 | 92 | {
 | 
|---|
 | 93 |   return NULL;
 | 
|---|
 | 94 | }
 | 
|---|
 | 95 | 
 | 
|---|
| [d12d621] | 96 | const int LEVEL = 5;
 | 
|---|
 | 97 | 
 | 
|---|
| [edecba] | 98 | /** Creates a MPQCCommandJob with argument \a filename.
 | 
|---|
 | 99 |  *
 | 
|---|
 | 100 |  * @param jobs created job is added to this vector
 | 
|---|
 | 101 |  * @param command mpqc command to execute
 | 
|---|
 | 102 |  * @param filename filename being argument to job
 | 
|---|
 | 103 |  * @param nextid id for this job
 | 
|---|
 | 104 |  */
 | 
|---|
 | 105 | void parsejob(
 | 
|---|
 | 106 |     std::vector<FragmentJob::ptr> &jobs,
 | 
|---|
 | 107 |     const std::string &command,
 | 
|---|
 | 108 |     const std::string &filename,
 | 
|---|
 | 109 |     const JobId_t nextid)
 | 
|---|
 | 110 | {
 | 
|---|
 | 111 |   std::ifstream file;
 | 
|---|
 | 112 |   file.open(filename.c_str());
 | 
|---|
 | 113 |   ASSERT( file.good(), "parsejob() - file "+filename+" does not exist.");
 | 
|---|
 | 114 |   std::string output((std::istreambuf_iterator<char>(file)),
 | 
|---|
 | 115 |       std::istreambuf_iterator<char>());
 | 
|---|
| [d12d621] | 116 |   double begin[NDIM] = { 0., 0., 0. };
 | 
|---|
 | 117 |   const RealSpaceMatrix& M = World::getInstance().getDomain().getM();
 | 
|---|
 | 118 |   const double size = M.at(0,0);
 | 
|---|
 | 119 |   ASSERT( M.determinant() == size*size*size,
 | 
|---|
 | 120 |       "parsejob() - current domain matrix "+toString(M)+" is not cubic.");
 | 
|---|
 | 121 |   const int level = LEVEL;
 | 
|---|
 | 122 |   FragmentJob::ptr testJob( new MPQCJob(nextid, output, begin, size, level) );
 | 
|---|
| [edecba] | 123 |   jobs.push_back(testJob);
 | 
|---|
 | 124 |   file.close();
 | 
|---|
 | 125 |   LOG(1, "INFO: Added MPQCCommandJob from file "+filename+".");
 | 
|---|
 | 126 | }
 | 
|---|
 | 127 | 
 | 
|---|
 | 128 | /** Helper function to get number of atoms somehow.
 | 
|---|
 | 129 |  *
 | 
|---|
 | 130 |  * Here, we just parse the number of lines in the adjacency file as
 | 
|---|
 | 131 |  * it should correspond to the number of atoms, except when some atoms
 | 
|---|
 | 132 |  * are not bonded, but then fragmentation makes no sense.
 | 
|---|
 | 133 |  *
 | 
|---|
 | 134 |  * @param path path to the adjacency file
 | 
|---|
 | 135 |  */
 | 
|---|
 | 136 | size_t getNoAtomsFromAdjacencyFile(const std::string &path)
 | 
|---|
 | 137 | {
 | 
|---|
 | 138 |   size_t NoAtoms = 0;
 | 
|---|
 | 139 | 
 | 
|---|
 | 140 |   // parse in special file to get atom count (from line count)
 | 
|---|
 | 141 |   std::string filename(path);
 | 
|---|
 | 142 |   filename += FRAGMENTPREFIX;
 | 
|---|
 | 143 |   filename += ADJACENCYFILE;
 | 
|---|
 | 144 |   std::ifstream adjacency(filename.c_str());
 | 
|---|
 | 145 |   if (adjacency.fail()) {
 | 
|---|
 | 146 |     LOG(0, endl << "getNoAtomsFromAdjacencyFile() - Unable to open " << filename << ", is the directory correct?");
 | 
|---|
 | 147 |     return false;
 | 
|---|
 | 148 |   }
 | 
|---|
 | 149 |   std::string buffer;
 | 
|---|
 | 150 |   while (getline(adjacency, buffer))
 | 
|---|
 | 151 |     NoAtoms++;
 | 
|---|
 | 152 |   LOG(1, "INFO: There are " << NoAtoms << " atoms.");
 | 
|---|
 | 153 | 
 | 
|---|
 | 154 |   return NoAtoms;
 | 
|---|
 | 155 | }
 | 
|---|
 | 156 | 
 | 
|---|
| [2764e0] | 157 | /** Extracts MPQCData from received vector of FragmentResults.
 | 
|---|
 | 158 |  *
 | 
|---|
 | 159 |  * @param results results to extract MPQCData from
 | 
|---|
 | 160 |  * @param fragmentData on return array filled with extracted MPQCData
 | 
|---|
 | 161 |  */
 | 
|---|
 | 162 | void ConvertFragmentResultToMPQCData(
 | 
|---|
 | 163 |     const std::vector<FragmentResult::ptr> &results,
 | 
|---|
 | 164 |     std::vector<MPQCData> &fragmentData)
 | 
|---|
 | 165 | {
 | 
|---|
 | 166 |   // extract results
 | 
|---|
 | 167 |   fragmentData.clear();
 | 
|---|
 | 168 |   fragmentData.reserve(results.size());
 | 
|---|
 | 169 | 
 | 
|---|
 | 170 |   LOG(2, "DEBUG: Parsing now through " << results.size() << " results.");
 | 
|---|
 | 171 |   for (std::vector<FragmentResult::ptr>::const_iterator iter = results.begin();
 | 
|---|
 | 172 |       iter != results.end(); ++iter) {
 | 
|---|
 | 173 |     //LOG(1, "RESULT: job #"+toString((*iter)->getId())+": "+toString((*iter)->result));
 | 
|---|
 | 174 |     MPQCData extractedData;
 | 
|---|
 | 175 |     std::stringstream inputstream((*iter)->result);
 | 
|---|
 | 176 |     LOG(2, "DEBUG: First 50 characters FragmentResult's string: "+(*iter)->result.substr(0, 50));
 | 
|---|
 | 177 |     boost::archive::text_iarchive ia(inputstream);
 | 
|---|
 | 178 |     ia >> extractedData;
 | 
|---|
 | 179 |     LOG(1, "INFO: extracted data is " << extractedData << ".");
 | 
|---|
 | 180 |     fragmentData.push_back(extractedData);
 | 
|---|
 | 181 |   }
 | 
|---|
 | 182 | 
 | 
|---|
 | 183 |   ASSERT( results.size() == fragmentData.size(),
 | 
|---|
 | 184 |       "ConvertFragmentResultToMPQCData() - the number of extracted data differs from the number of results.");
 | 
|---|
 | 185 | }
 | 
|---|
| [edecba] | 186 | 
 | 
|---|
 | 187 | /** Print MPQCData from received results.
 | 
|---|
 | 188 |  *
 | 
|---|
| [2764e0] | 189 |  * @param results results with ids to associate with fragment number
 | 
|---|
 | 190 |  * @param fragmentData MPQCData resulting from the jobs
 | 
|---|
| [edecba] | 191 |  * @param KeySetFilename filename with keysets to associate forces correctly
 | 
|---|
 | 192 |  * @param NoAtoms total number of atoms
 | 
|---|
 | 193 |  */
 | 
|---|
 | 194 | bool printReceivedMPQCResults(
 | 
|---|
 | 195 |     const std::vector<FragmentResult::ptr> &results,
 | 
|---|
| [2764e0] | 196 |     const std::vector<MPQCData> &fragmentData,
 | 
|---|
| [edecba] | 197 |     const std::string &KeySetFilename,
 | 
|---|
 | 198 |     size_t NoAtoms)
 | 
|---|
 | 199 | {
 | 
|---|
 | 200 |   EnergyMatrix Energy;
 | 
|---|
 | 201 |   EnergyMatrix EnergyFragments;
 | 
|---|
 | 202 |   ForceMatrix Force;
 | 
|---|
 | 203 |   ForceMatrix ForceFragments;
 | 
|---|
 | 204 | 
 | 
|---|
 | 205 |   // align fragments
 | 
|---|
 | 206 |   std::map< JobId_t, size_t > MatrixNrLookup;
 | 
|---|
 | 207 |   size_t FragmentCounter = 0;
 | 
|---|
 | 208 |   {
 | 
|---|
 | 209 |     // bring ids in order ...
 | 
|---|
 | 210 |     typedef std::map< JobId_t, FragmentResult::ptr> IdResultMap_t;
 | 
|---|
 | 211 |     IdResultMap_t IdResultMap;
 | 
|---|
 | 212 |     for (std::vector<FragmentResult::ptr>::const_iterator iter = results.begin();
 | 
|---|
 | 213 |         iter != results.end(); ++iter) {
 | 
|---|
 | 214 |   #ifndef NDEBUG
 | 
|---|
 | 215 |       std::pair< IdResultMap_t::iterator, bool> inserter =
 | 
|---|
 | 216 |   #endif
 | 
|---|
 | 217 |       IdResultMap.insert( make_pair((*iter)->getId(), *iter) );
 | 
|---|
 | 218 |       ASSERT( inserter.second,
 | 
|---|
| [d12d621] | 219 |           "ExtractMPQCDataFromResults() - two results have same id "
 | 
|---|
| [edecba] | 220 |           +toString((*iter)->getId())+".");
 | 
|---|
 | 221 |     }
 | 
|---|
 | 222 |     // ... and fill lookup
 | 
|---|
 | 223 |     for(IdResultMap_t::const_iterator iter = IdResultMap.begin();
 | 
|---|
 | 224 |         iter != IdResultMap.end(); ++iter)
 | 
|---|
 | 225 |       MatrixNrLookup.insert( make_pair(iter->first, FragmentCounter++) );
 | 
|---|
 | 226 |   }
 | 
|---|
 | 227 |   LOG(1, "INFO: There are " << FragmentCounter << " fragments.");
 | 
|---|
 | 228 | 
 | 
|---|
| [2764e0] | 229 |   std::vector<MPQCData>::const_iterator dataiter = fragmentData.begin();
 | 
|---|
 | 230 |   std::vector<FragmentResult::ptr>::const_iterator resultiter = results.begin();
 | 
|---|
 | 231 |   for (; dataiter != fragmentData.end(); ++dataiter, ++resultiter) {
 | 
|---|
 | 232 |     const MPQCData &extractedData = *dataiter;
 | 
|---|
| [edecba] | 233 |     // place results into EnergyMatrix ...
 | 
|---|
 | 234 |     {
 | 
|---|
 | 235 |       MatrixContainer::MatrixArray matrix;
 | 
|---|
 | 236 |       matrix.resize(1);
 | 
|---|
| [a9558f] | 237 |       matrix[0].resize(1, extractedData.energies.total);
 | 
|---|
| [edecba] | 238 |       if (!Energy.AddMatrix(
 | 
|---|
| [2764e0] | 239 |           std::string("MPQCJob ")+toString((*resultiter)->getId()),
 | 
|---|
| [edecba] | 240 |           matrix,
 | 
|---|
| [2764e0] | 241 |           MatrixNrLookup[(*resultiter)->getId()])) {
 | 
|---|
| [edecba] | 242 |         ELOG(1, "Adding energy matrix failed.");
 | 
|---|
 | 243 |         return false;
 | 
|---|
 | 244 |       }
 | 
|---|
 | 245 |     }
 | 
|---|
 | 246 |     // ... and ForceMatrix (with two empty columns in front)
 | 
|---|
 | 247 |     {
 | 
|---|
 | 248 |       MatrixContainer::MatrixArray matrix;
 | 
|---|
 | 249 |       const size_t rows = extractedData.forces.size();
 | 
|---|
 | 250 |       matrix.resize(rows);
 | 
|---|
 | 251 |       for (size_t i=0;i<rows;++i) {
 | 
|---|
 | 252 |         const size_t columns = 2+extractedData.forces[i].size();
 | 
|---|
 | 253 |         matrix[i].resize(columns, 0.);
 | 
|---|
 | 254 |   //      for (size_t j=0;j<2;++j)
 | 
|---|
 | 255 |   //        matrix[i][j] = 0.;
 | 
|---|
 | 256 |         for (size_t j=2;j<columns;++j)
 | 
|---|
 | 257 |           matrix[i][j] = extractedData.forces[i][j-2];
 | 
|---|
 | 258 |       }
 | 
|---|
 | 259 |       if (!Force.AddMatrix(
 | 
|---|
| [2764e0] | 260 |           std::string("MPQCJob ")+toString((*resultiter)->getId()),
 | 
|---|
| [edecba] | 261 |           matrix,
 | 
|---|
| [2764e0] | 262 |           MatrixNrLookup[(*resultiter)->getId()])) {
 | 
|---|
| [edecba] | 263 |         ELOG(1, "Adding force matrix failed.");
 | 
|---|
 | 264 |         return false;
 | 
|---|
 | 265 |       }
 | 
|---|
 | 266 |     }
 | 
|---|
 | 267 |   }
 | 
|---|
 | 268 |   // add one more matrix (not required for energy)
 | 
|---|
 | 269 |   MatrixContainer::MatrixArray matrix;
 | 
|---|
 | 270 |   matrix.resize(1);
 | 
|---|
 | 271 |   matrix[0].resize(1, 0.);
 | 
|---|
 | 272 |   if (!Energy.AddMatrix(std::string("MPQCJob total"), matrix, FragmentCounter))
 | 
|---|
 | 273 |     return false;
 | 
|---|
 | 274 |   // but for energy because we need to know total number of atoms
 | 
|---|
 | 275 |   matrix.resize(NoAtoms);
 | 
|---|
 | 276 |   for (size_t i = 0; i< NoAtoms; ++i)
 | 
|---|
 | 277 |     matrix[i].resize(2+NDIM, 0.);
 | 
|---|
 | 278 |   if (!Force.AddMatrix(std::string("MPQCJob total"), matrix, FragmentCounter))
 | 
|---|
 | 279 |     return false;
 | 
|---|
 | 280 | 
 | 
|---|
| [6ca578] | 281 |   // initialise indices
 | 
|---|
 | 282 |   KeySetsContainer KeySet;
 | 
|---|
| [edecba] | 283 |   if (!Energy.InitialiseIndices()) return false;
 | 
|---|
 | 284 | 
 | 
|---|
 | 285 |   if (!Force.ParseIndices(KeySetFilename.c_str())) return false;
 | 
|---|
 | 286 | 
 | 
|---|
 | 287 |   if (!KeySet.ParseKeySets(KeySetFilename.c_str(), Force.RowCounter, Force.MatrixCounter)) return false;
 | 
|---|
 | 288 | 
 | 
|---|
| [6ca578] | 289 |   /// prepare for OrthogonalSummation
 | 
|---|
 | 290 | 
 | 
|---|
 | 291 |   // gather all present indices in AllIndices
 | 
|---|
 | 292 |   IndexSet::ptr AllIndices(new IndexSet);
 | 
|---|
 | 293 |   for (KeySetsContainer::ArrayOfIntVectors::const_iterator iter = KeySet.KeySets.begin();
 | 
|---|
 | 294 |       iter != KeySet.KeySets.end(); ++iter)
 | 
|---|
 | 295 |     for(KeySetsContainer::IntVector::const_iterator keyiter = (*iter).begin();
 | 
|---|
 | 296 |         keyiter != (*iter).end(); ++keyiter) {
 | 
|---|
 | 297 |       if (*keyiter != -1)
 | 
|---|
 | 298 |         (*AllIndices) += *keyiter;
 | 
|---|
 | 299 |     }
 | 
|---|
 | 300 |   LOG(1, "INFO: AllIndices is " << AllIndices << ".");
 | 
|---|
 | 301 |   // create container with all keysets
 | 
|---|
 | 302 |   IndexSetContainer::ptr container(new IndexSetContainer(AllIndices));
 | 
|---|
 | 303 |   for (KeySetsContainer::ArrayOfIntVectors::const_iterator iter = KeySet.KeySets.begin();
 | 
|---|
 | 304 |       iter != KeySet.KeySets.end(); ++iter) {
 | 
|---|
 | 305 |     IndexSet tempset;
 | 
|---|
 | 306 |     for(KeySetsContainer::IntVector::const_iterator keyiter = (*iter).begin();
 | 
|---|
 | 307 |         keyiter != (*iter).end(); ++keyiter)
 | 
|---|
 | 308 |       if (*keyiter != -1)
 | 
|---|
 | 309 |         tempset += *keyiter;
 | 
|---|
 | 310 |     container->insert(tempset);
 | 
|---|
 | 311 |   }
 | 
|---|
 | 312 |   // create the map of all keysets
 | 
|---|
 | 313 |   SubsetMap::ptr subsetmap(new SubsetMap(*container));
 | 
|---|
 | 314 | 
 | 
|---|
| [e13990b] | 315 |   /// convert all MPQCData to MPQCDataMap_t
 | 
|---|
| [8cae4c] | 316 |   {
 | 
|---|
 | 317 |     // energy_t
 | 
|---|
 | 318 |     std::vector<MPQCDataEnergyMap_t> MPQCData_Energy_fused;
 | 
|---|
 | 319 |     MPQCData_Energy_fused.reserve(fragmentData.size());
 | 
|---|
 | 320 |     for(std::vector<MPQCData>::const_iterator dataiter = fragmentData.begin();
 | 
|---|
 | 321 |         dataiter != fragmentData.end(); ++dataiter) {
 | 
|---|
 | 322 |       const MPQCData &extractedData = *dataiter;
 | 
|---|
 | 323 |       LOG(2, "DEBUG: Current extracted Data is " << extractedData << ".");
 | 
|---|
 | 324 |       MPQCDataEnergyMap_t instance;
 | 
|---|
 | 325 |       boost::fusion::at_key<MPQCDataFused::energy_total>(instance) = extractedData.energies.total;
 | 
|---|
 | 326 |       boost::fusion::at_key<MPQCDataFused::energy_nuclear_repulsion>(instance) = extractedData.energies.nuclear_repulsion;
 | 
|---|
| [adccae] | 327 |       boost::fusion::at_key<MPQCDataFused::energy_electron_coulomb>(instance) = extractedData.energies.electron_coulomb;
 | 
|---|
 | 328 |       boost::fusion::at_key<MPQCDataFused::energy_electron_exchange>(instance) = extractedData.energies.electron_exchange;
 | 
|---|
| [8cae4c] | 329 |       boost::fusion::at_key<MPQCDataFused::energy_correlation>(instance) = extractedData.energies.correlation;
 | 
|---|
 | 330 |       boost::fusion::at_key<MPQCDataFused::energy_overlap>(instance) = extractedData.energies.overlap;
 | 
|---|
 | 331 |       boost::fusion::at_key<MPQCDataFused::energy_kinetic>(instance) = extractedData.energies.kinetic;
 | 
|---|
 | 332 |       boost::fusion::at_key<MPQCDataFused::energy_hcore>(instance) = extractedData.energies.hcore;
 | 
|---|
| [dde8ec] | 333 |       boost::fusion::at_key<MPQCDataFused::energy_eigenvalues>(instance) = extractedData.energies.eigenvalues;
 | 
|---|
| [8cae4c] | 334 |       MPQCData_Energy_fused.push_back(instance);
 | 
|---|
 | 335 |     }
 | 
|---|
| [965e2f] | 336 | 
 | 
|---|
| [8cae4c] | 337 |     // forces
 | 
|---|
| [e13990b] | 338 |     const IndexSetContainer::Container_t &indices = container->getContainer();
 | 
|---|
 | 339 |     ASSERT( indices.size() == fragmentData.size(),
 | 
|---|
 | 340 |         "FragmentationAutomationAction::performCall() - indices and fragmentData differ in size.");
 | 
|---|
| [8cae4c] | 341 |     std::vector<MPQCDataForceMap_t> MPQCData_Force_fused;
 | 
|---|
 | 342 |     MPQCData_Force_fused.reserve(fragmentData.size());
 | 
|---|
| [e13990b] | 343 |     std::vector<MPQCData>::const_iterator dataiter = fragmentData.begin();
 | 
|---|
 | 344 |     IndexSetContainer::Container_t::const_iterator indexiter = indices.begin();
 | 
|---|
 | 345 |     for(;dataiter != fragmentData.end(); ++dataiter, ++indexiter) {
 | 
|---|
| [8cae4c] | 346 |       const MPQCData &extractedData = *dataiter;
 | 
|---|
 | 347 |       LOG(2, "DEBUG: Current extracted Data is " << extractedData << ".");
 | 
|---|
 | 348 |       MPQCDataForceMap_t instance;
 | 
|---|
| [e13990b] | 349 |       boost::fusion::at_key<MPQCDataFused::forces>(instance) =
 | 
|---|
 | 350 |           IndexedVectors(**indexiter, extractedData.forces);
 | 
|---|
| [8cae4c] | 351 |       MPQCData_Force_fused.push_back(instance);
 | 
|---|
 | 352 |     }
 | 
|---|
| [6ca578] | 353 | 
 | 
|---|
| [8cae4c] | 354 |     // times
 | 
|---|
 | 355 |     std::vector<MPQCDataTimeMap_t> MPQCData_Time_fused;
 | 
|---|
 | 356 |     MPQCData_Time_fused.reserve(fragmentData.size());
 | 
|---|
 | 357 |     for(std::vector<MPQCData>::const_iterator dataiter = fragmentData.begin();
 | 
|---|
 | 358 |         dataiter != fragmentData.end(); ++dataiter) {
 | 
|---|
 | 359 |       const MPQCData &extractedData = *dataiter;
 | 
|---|
 | 360 |       LOG(2, "DEBUG: Current extracted Data is " << extractedData << ".");
 | 
|---|
 | 361 |       MPQCDataTimeMap_t instance;
 | 
|---|
 | 362 |       boost::fusion::at_key<MPQCDataFused::times_walltime>(instance) = extractedData.times.walltime;
 | 
|---|
 | 363 |       boost::fusion::at_key<MPQCDataFused::times_cputime>(instance) = extractedData.times.cputime;
 | 
|---|
 | 364 |       boost::fusion::at_key<MPQCDataFused::times_flops>(instance) = extractedData.times.flops;
 | 
|---|
 | 365 |       MPQCData_Time_fused.push_back(instance);
 | 
|---|
 | 366 |     }
 | 
|---|
 | 367 | 
 | 
|---|
 | 368 |     // create a vector of all job ids
 | 
|---|
 | 369 |     std::vector<JobId_t> jobids(results.size(), JobId::IllegalJob);
 | 
|---|
 | 370 |     std::transform(results.begin(), results.end(), jobids.begin(),
 | 
|---|
 | 371 |         boost::bind(&FragmentResult::getId,
 | 
|---|
 | 372 |             boost::bind(&FragmentResult::ptr::operator->, _1)));
 | 
|---|
 | 373 | 
 | 
|---|
 | 374 |     // sum up and print energies
 | 
|---|
 | 375 |     boost::mpl::for_each<MPQCDataEnergyVector_t>(
 | 
|---|
 | 376 |         printSum<MPQCDataEnergyMap_t>(
 | 
|---|
 | 377 |             subsetmap,
 | 
|---|
 | 378 |             MPQCData_Energy_fused,
 | 
|---|
 | 379 |             jobids,
 | 
|---|
 | 380 |             container->getContainer(),
 | 
|---|
 | 381 |             MatrixNrLookup)
 | 
|---|
 | 382 |         );
 | 
|---|
 | 383 | 
 | 
|---|
| [e13990b] | 384 |     // sum up and print forces
 | 
|---|
 | 385 |     boost::mpl::for_each<MPQCDataForceVector_t>(
 | 
|---|
 | 386 |         printSum<MPQCDataForceMap_t>(
 | 
|---|
 | 387 |             subsetmap,
 | 
|---|
 | 388 |             MPQCData_Force_fused,
 | 
|---|
 | 389 |             jobids,
 | 
|---|
 | 390 |             container->getContainer(),
 | 
|---|
 | 391 |             MatrixNrLookup)
 | 
|---|
 | 392 |         );
 | 
|---|
| [8cae4c] | 393 | 
 | 
|---|
 | 394 |     // TODO: Times should just be summed not orthogonalized
 | 
|---|
 | 395 | //    // sum up and print times
 | 
|---|
 | 396 | //    boost::mpl::for_each<MPQCDataTimeVector_t>(
 | 
|---|
 | 397 | //        printSum<MPQCDataTimeMap_t>(
 | 
|---|
 | 398 | //            subsetmap,
 | 
|---|
 | 399 | //            MPQCData_Time_fused,
 | 
|---|
 | 400 | //            jobids,
 | 
|---|
 | 401 | //            container->getContainer(),
 | 
|---|
 | 402 | //            MatrixNrLookup)
 | 
|---|
 | 403 | //        );
 | 
|---|
 | 404 |   }
 | 
|---|
| [56df37] | 405 | 
 | 
|---|
| [6ca578] | 406 |   // combine all found data
 | 
|---|
| [edecba] | 407 |   if (!KeySet.ParseManyBodyTerms()) return false;
 | 
|---|
 | 408 | 
 | 
|---|
 | 409 |   if (!EnergyFragments.AllocateMatrix(Energy.Header, Energy.MatrixCounter, Energy.RowCounter, Energy.ColumnCounter)) return false;
 | 
|---|
 | 410 |   if (!ForceFragments.AllocateMatrix(Force.Header, Force.MatrixCounter, Force.RowCounter, Force.ColumnCounter)) return false;
 | 
|---|
 | 411 | 
 | 
|---|
 | 412 |   if(!Energy.SetLastMatrix(0., 0)) return false;
 | 
|---|
 | 413 |   if(!Force.SetLastMatrix(0., 2)) return false;
 | 
|---|
 | 414 | 
 | 
|---|
 | 415 |   for (int BondOrder=0;BondOrder<KeySet.Order;BondOrder++) {
 | 
|---|
 | 416 |     // --------- sum up energy --------------------
 | 
|---|
 | 417 |     LOG(1, "INFO: Summing energy of order " << BondOrder+1 << " ...");
 | 
|---|
 | 418 |     if (!EnergyFragments.SumSubManyBodyTerms(Energy, KeySet, BondOrder)) return false;
 | 
|---|
 | 419 |     if (!Energy.SumSubEnergy(EnergyFragments, NULL, KeySet, BondOrder, 1.)) return false;
 | 
|---|
 | 420 | 
 | 
|---|
 | 421 |     // --------- sum up Forces --------------------
 | 
|---|
 | 422 |     LOG(1, "INFO: Summing forces of order " << BondOrder+1 << " ...");
 | 
|---|
 | 423 |     if (!ForceFragments.SumSubManyBodyTerms(Force, KeySet, BondOrder)) return false;
 | 
|---|
 | 424 |     if (!Force.SumSubForces(ForceFragments, KeySet, BondOrder, 1.)) return false;
 | 
|---|
 | 425 |   }
 | 
|---|
 | 426 | 
 | 
|---|
 | 427 |   // for debugging print resulting energy and forces
 | 
|---|
 | 428 |   LOG(1, "INFO: Resulting energy is " << Energy.Matrix[ FragmentCounter ][0][0]);
 | 
|---|
 | 429 |   std::stringstream output;
 | 
|---|
 | 430 |   for (int i=0; i< Force.RowCounter[FragmentCounter]; ++i) {
 | 
|---|
 | 431 |     for (int j=0; j< Force.ColumnCounter[FragmentCounter]; ++j)
 | 
|---|
 | 432 |       output << Force.Matrix[ FragmentCounter ][i][j] << " ";
 | 
|---|
 | 433 |     output << "\n";
 | 
|---|
 | 434 |   }
 | 
|---|
 | 435 |   LOG(1, "INFO: Resulting forces are " << std::endl << output.str());
 | 
|---|
 | 436 | 
 | 
|---|
 | 437 |   return true;
 | 
|---|
 | 438 | }
 | 
|---|
 | 439 | 
 | 
|---|
 | 440 | 
 | 
|---|
| [c5324f] | 441 | void RunService(
 | 
|---|
 | 442 |     boost::asio::io_service &io_service,
 | 
|---|
 | 443 |     std::string message)
 | 
|---|
 | 444 | {
 | 
|---|
 | 445 |   message = std::string("io_service: ") + message;
 | 
|---|
 | 446 |   io_service.reset();
 | 
|---|
 | 447 |   Info info(message.c_str());
 | 
|---|
 | 448 |   io_service.run();
 | 
|---|
 | 449 | }
 | 
|---|
| [edecba] | 450 | 
 | 
|---|
| [c5324f] | 451 | void requestIds(
 | 
|---|
 | 452 |     FragmentController &controller,
 | 
|---|
 | 453 |     const FragmentationFragmentationAutomationAction::FragmentationFragmentationAutomationParameters ¶ms,
 | 
|---|
 | 454 |     const size_t numberjobs)
 | 
|---|
 | 455 | {
 | 
|---|
 | 456 |   controller.requestIds(params.host.get(), params.port.get(), numberjobs);
 | 
|---|
 | 457 | }
 | 
|---|
 | 458 | 
 | 
|---|
 | 459 | bool createJobsFromFiles(
 | 
|---|
 | 460 |     FragmentController &controller,
 | 
|---|
 | 461 |     const FragmentationFragmentationAutomationAction::FragmentationFragmentationAutomationParameters ¶ms,
 | 
|---|
 | 462 |     const std::vector< boost::filesystem::path > &jobfiles)
 | 
|---|
 | 463 | {
 | 
|---|
 | 464 |   std::vector<FragmentJob::ptr> jobs;
 | 
|---|
 | 465 |   for (std::vector< boost::filesystem::path >::const_iterator iter = jobfiles.begin();
 | 
|---|
 | 466 |       iter != jobfiles .end(); ++iter) {
 | 
|---|
 | 467 |     const std::string &filename = (*iter).string();
 | 
|---|
 | 468 |     if (boost::filesystem::exists(filename)) {
 | 
|---|
 | 469 |       const JobId_t next_id = controller.getAvailableId();
 | 
|---|
 | 470 |       LOG(1, "INFO: Creating MPQCCommandJob with filename'"
 | 
|---|
 | 471 |           +filename+"', and id "+toString(next_id)+".");
 | 
|---|
 | 472 |       parsejob(jobs, params.executable.get().string(), filename, next_id);
 | 
|---|
 | 473 |     } else {
 | 
|---|
 | 474 |       ELOG(1, "Fragment job "+filename+" does not exist.");
 | 
|---|
 | 475 |       return false;
 | 
|---|
| [edecba] | 476 |     }
 | 
|---|
 | 477 |   }
 | 
|---|
| [c5324f] | 478 |   controller.addJobs(jobs);
 | 
|---|
 | 479 |   controller.sendJobs(params.host.get(), params.port.get());
 | 
|---|
 | 480 |   return true;
 | 
|---|
 | 481 | }
 | 
|---|
 | 482 | 
 | 
|---|
| [69c733] | 483 | #ifdef HAVE_VMG
 | 
|---|
 | 484 | bool createLongRangeJobs(
 | 
|---|
 | 485 |     FragmentController &controller,
 | 
|---|
 | 486 |     const FragmentationFragmentationAutomationAction::FragmentationFragmentationAutomationParameters ¶ms,
 | 
|---|
| [d12d621] | 487 |     const std::vector<MPQCData> &fragmentData)
 | 
|---|
| [69c733] | 488 | {
 | 
|---|
 | 489 |   std::vector<FragmentJob::ptr> jobs;
 | 
|---|
| [d12d621] | 490 |   // add one job for each fragment as the short-range correction which we need
 | 
|---|
 | 491 |   // to subtract from the obtained full potential to get the long-range part only
 | 
|---|
 | 492 |   for (std::vector<MPQCData>::const_iterator iter = fragmentData.begin();
 | 
|---|
 | 493 |       iter != fragmentData.end(); ++iter) {
 | 
|---|
| [69c733] | 494 |     const JobId_t next_id = controller.getAvailableId();
 | 
|---|
 | 495 |     LOG(1, "INFO: Creating VMGJob.");
 | 
|---|
| [d12d621] | 496 |     FragmentJob::ptr testJob(
 | 
|---|
| [28c025] | 497 |         new VMGJob(next_id, iter->sampled_grid) );
 | 
|---|
| [69c733] | 498 |     jobs.push_back(testJob);
 | 
|---|
 | 499 |   }
 | 
|---|
| [d12d621] | 500 | 
 | 
|---|
 | 501 |   // add one more job for the full calculation
 | 
|---|
 | 502 |   // TODO: Here, we actually have to combine all the other sampled_grids
 | 
|---|
 | 503 |   {
 | 
|---|
 | 504 |     const int level = LEVEL;
 | 
|---|
 | 505 |     const int GRID = pow(2, level);
 | 
|---|
| [28c025] | 506 |     std::vector<double> full_sample(GRID*GRID*GRID, 0.);
 | 
|---|
| [d12d621] | 507 |     double begin[NDIM] = { 0., 0., 0. };
 | 
|---|
 | 508 |     const RealSpaceMatrix& M = World::getInstance().getDomain().getM();
 | 
|---|
 | 509 |     const double size = M.at(0,0);
 | 
|---|
 | 510 |     ASSERT( M.determinant() == size*size*size,
 | 
|---|
 | 511 |         "createLongRangeJobs() - current domain matrix "+toString(M)+" is not cubic.");
 | 
|---|
| [28c025] | 512 |     const SamplingGrid full_sampled_grid(begin, size, level, full_sample);
 | 
|---|
| [d12d621] | 513 |     const JobId_t next_id = controller.getAvailableId();
 | 
|---|
 | 514 |     FragmentJob::ptr testJob(
 | 
|---|
| [28c025] | 515 |         new VMGJob(next_id, full_sampled_grid) );
 | 
|---|
| [d12d621] | 516 |     jobs.push_back(testJob);
 | 
|---|
 | 517 |   }
 | 
|---|
 | 518 | 
 | 
|---|
 | 519 |   // then send jobs to controller
 | 
|---|
| [69c733] | 520 |   controller.addJobs(jobs);
 | 
|---|
 | 521 |   controller.sendJobs(params.host.get(), params.port.get());
 | 
|---|
 | 522 |   return true;
 | 
|---|
 | 523 | }
 | 
|---|
 | 524 | #endif
 | 
|---|
 | 525 | 
 | 
|---|
| [c5324f] | 526 | void WaitforResults(
 | 
|---|
 | 527 |     boost::asio::io_service &io_service,
 | 
|---|
 | 528 |     FragmentController &controller,
 | 
|---|
 | 529 |     const FragmentationFragmentationAutomationAction::FragmentationFragmentationAutomationParameters ¶ms,
 | 
|---|
 | 530 |     const size_t NoExpectedResults
 | 
|---|
 | 531 |     )
 | 
|---|
 | 532 | {
 | 
|---|
| [edecba] | 533 |   size_t NoCalculatedResults = 0;
 | 
|---|
| [c5324f] | 534 |   while (NoCalculatedResults != NoExpectedResults) {
 | 
|---|
| [edecba] | 535 |     // wait a bit
 | 
|---|
 | 536 |     boost::asio::deadline_timer timer(io_service);
 | 
|---|
 | 537 |     timer.expires_from_now(boost::posix_time::milliseconds(500));
 | 
|---|
 | 538 |     timer.wait();
 | 
|---|
 | 539 |     // then request status
 | 
|---|
| [bd81f9] | 540 |     controller.checkResults(params.host.get(), params.port.get());
 | 
|---|
| [c5324f] | 541 |     RunService(io_service, "Checking on results");
 | 
|---|
 | 542 | 
 | 
|---|
| [edecba] | 543 |     const std::pair<size_t, size_t> JobStatus = controller.getJobStatus();
 | 
|---|
 | 544 |     LOG(1, "INFO: #" << JobStatus.first << " are waiting in the queue and #" << JobStatus.second << " jobs are calculated so far.");
 | 
|---|
 | 545 |     NoCalculatedResults = JobStatus.second;
 | 
|---|
 | 546 |   }
 | 
|---|
| [c5324f] | 547 | }
 | 
|---|
 | 548 | 
 | 
|---|
 | 549 | 
 | 
|---|
 | 550 | Action::state_ptr FragmentationFragmentationAutomationAction::performCall() {
 | 
|---|
 | 551 |   boost::asio::io_service io_service;
 | 
|---|
 | 552 |   FragmentController controller(io_service);
 | 
|---|
 | 553 | 
 | 
|---|
 | 554 |   // TODO: Have io_service run in second thread and merge with current again eventually
 | 
|---|
 | 555 | 
 | 
|---|
 | 556 |   // Phase One: obtain ids
 | 
|---|
 | 557 |   std::vector< boost::filesystem::path > jobfiles = params.jobfiles.get();
 | 
|---|
 | 558 |   requestIds(controller, params, jobfiles.size());
 | 
|---|
 | 559 |   RunService(io_service, "Requesting ids");
 | 
|---|
 | 560 | 
 | 
|---|
| [69c733] | 561 |   // Phase Two: create and add MPQCJobs
 | 
|---|
| [c5324f] | 562 |   if (!createJobsFromFiles(controller, params, jobfiles))
 | 
|---|
 | 563 |     return Action::failure;
 | 
|---|
| [69c733] | 564 |   RunService(io_service, "Adding MPQCJobs");
 | 
|---|
| [c5324f] | 565 | 
 | 
|---|
 | 566 |   // Phase Three: calculate result
 | 
|---|
 | 567 |   WaitforResults(io_service, controller, params, jobfiles.size());
 | 
|---|
| [bd81f9] | 568 |   controller.receiveResults(params.host.get(), params.port.get());
 | 
|---|
| [69c733] | 569 |   RunService(io_service, "Requesting short-range results");
 | 
|---|
| [2764e0] | 570 |   std::vector<FragmentResult::ptr> MPQCresults = controller.getReceivedResults();
 | 
|---|
 | 571 |   std::vector<MPQCData> fragmentData;
 | 
|---|
 | 572 |   ConvertFragmentResultToMPQCData(MPQCresults, fragmentData);
 | 
|---|
| [c5324f] | 573 | 
 | 
|---|
| [69c733] | 574 |   // print intermediate short-range results
 | 
|---|
| [edecba] | 575 |   {
 | 
|---|
| [bd81f9] | 576 |     LOG(1, "INFO: Parsing fragment files from " << params.path.get() << ".");
 | 
|---|
| [edecba] | 577 |     printReceivedMPQCResults(
 | 
|---|
| [69c733] | 578 |         MPQCresults,
 | 
|---|
| [2764e0] | 579 |         fragmentData,
 | 
|---|
| [bd81f9] | 580 |         params.path.get(),
 | 
|---|
 | 581 |         getNoAtomsFromAdjacencyFile(params.path.get()));
 | 
|---|
| [edecba] | 582 |   }
 | 
|---|
| [69c733] | 583 | 
 | 
|---|
 | 584 | #ifdef HAVE_VMG
 | 
|---|
 | 585 |   if (params.DoLongrange.get()) {
 | 
|---|
 | 586 |   // Phase Four: obtain more ids
 | 
|---|
| [2764e0] | 587 |   requestIds(controller, params, fragmentData.size()+1);
 | 
|---|
| [69c733] | 588 |   RunService(io_service, "Requesting ids");
 | 
|---|
 | 589 | 
 | 
|---|
 | 590 |   // Phase Five: create VMGJobs
 | 
|---|
| [d12d621] | 591 |   if (!createLongRangeJobs(controller, params, fragmentData))
 | 
|---|
| [69c733] | 592 |     return Action::failure;
 | 
|---|
 | 593 |   RunService(io_service, "Adding VMGJobs");
 | 
|---|
 | 594 | 
 | 
|---|
 | 595 |   // Phase Six: calculate result
 | 
|---|
| [2764e0] | 596 |   WaitforResults(io_service, controller, params, fragmentData.size()+1);
 | 
|---|
| [69c733] | 597 |   controller.receiveResults(params.host.get(), params.port.get());
 | 
|---|
 | 598 |   RunService(io_service, "Requesting long-range results");
 | 
|---|
 | 599 |   std::vector<FragmentResult::ptr> VMGresults = controller.getReceivedResults();
 | 
|---|
| [2764e0] | 600 |   ASSERT( MPQCresults.size()+1 == VMGresults.size(),
 | 
|---|
 | 601 |       "FragmentationFragmentationAutomationAction::performCall() - number of MPQCresultd and VMGresults don't match.");
 | 
|---|
 | 602 | 
 | 
|---|
 | 603 |   // Final phase: print result
 | 
|---|
 | 604 |   {
 | 
|---|
 | 605 |     LOG(1, "INFO: Parsing fragment files from " << params.path.get() << ".");
 | 
|---|
 | 606 |     printReceivedMPQCResults(
 | 
|---|
 | 607 |         MPQCresults,
 | 
|---|
 | 608 |         fragmentData,
 | 
|---|
 | 609 |         params.path.get(),
 | 
|---|
 | 610 |         getNoAtomsFromAdjacencyFile(params.path.get()));
 | 
|---|
 | 611 |   }
 | 
|---|
| [69c733] | 612 |   }
 | 
|---|
 | 613 | #endif
 | 
|---|
| [edecba] | 614 |   size_t Exitflag = controller.getExitflag();
 | 
|---|
 | 615 | 
 | 
|---|
 | 616 |   return (Exitflag == 0) ? Action::success : Action::failure;
 | 
|---|
 | 617 | }
 | 
|---|
 | 618 | 
 | 
|---|
 | 619 | Action::state_ptr FragmentationFragmentationAutomationAction::performUndo(Action::state_ptr _state) {
 | 
|---|
 | 620 |   return Action::success;
 | 
|---|
 | 621 | }
 | 
|---|
 | 622 | 
 | 
|---|
 | 623 | Action::state_ptr FragmentationFragmentationAutomationAction::performRedo(Action::state_ptr _state){
 | 
|---|
 | 624 |   return Action::success;
 | 
|---|
 | 625 | }
 | 
|---|
 | 626 | 
 | 
|---|
 | 627 | bool FragmentationFragmentationAutomationAction::canUndo() {
 | 
|---|
 | 628 |   return false;
 | 
|---|
 | 629 | }
 | 
|---|
 | 630 | 
 | 
|---|
 | 631 | bool FragmentationFragmentationAutomationAction::shouldUndo() {
 | 
|---|
 | 632 |   return false;
 | 
|---|
 | 633 | }
 | 
|---|
 | 634 | /** =========== end of function ====================== */
 | 
|---|