Changeset 35b698 for src/molecule_fragmentation.cpp

Timestamp:

Jun 23, 2010, 3:52:50 PM (15 years ago)

Author:

Frederik Heber <heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable

Children:

d0fbec

Parents:

dc0d21

git-author:

Frederik Heber <heber@…> (06/23/10 15:20:35)

git-committer:

Frederik Heber <heber@…> (06/23/10 15:52:50)

Message:

BIG CHANGE: config::load and config::save in ParseCommandLineOptions() and main() replaced with FormatParser replacements.

Fragmentation:

• FragmentMolecule() - configuration is not needed anymore, but a path (including prefix)
• class molecule:
  • lots of changes from char * to std:string (due to above): LinearInterpolationBetweenConfiguration(), CheckOrderAtSite(), StoreBondsToFile(), StoreAdjacencyToFile(), CheckAdjacencyFileAgainstMolecule(), CheckAdjacencyFileAgainstMolecule_Init(), ParseOrderAtSiteFromFile(), StoreOrderAtSiteFile(), StoreForcesFile(), ScanAdaptiveFileIntoMap(), StoreForcesFile(), AddHydrogenCorrection(), OutputConfigForListOfFragments()
  • in all above functions, also stringstreams have been replaced by simple strings and file != NULL by file.good()
  • no more CalculateOrbitals(), shifted to class PcpParser
• FragmentationAction: argument of -f is now the prefix, molecule is obtained by molecule-by-id
• no more strcpy needed in: MoleculeLinearInterpolationofTrajectoriesAction, MoleculeSaveAdjacencyAction, MoleculeSaveBondsAction
• oldmenu::FragmentAtoms() - needs to ask for path with prefix now
• config: RetrieveConfigPathAndName() and configpath removed (replaced by above path with prefix)
• changes due to this removal: SaveConfig(), config::Load(), config::LoadOld()

• FIX: MoleculeFillWithMoleculeAction: filler atoms have to be removed before the system can be stored to file.
• FIX: PcpParser::load() - has to put the molecule also into World's MoleculeListClass (otherwise the name cannot be set right after loading)

• ParseCommandLineOptions()
  • new parameter BondGraphFileName and creation of bond graph is done in main()
  • no more config::load, just parser->load(), ConfigFileName is set extra and we always set configPresent to present.
  • FIX: filename is only set when no molecule was allocated before
  • FIX: case 't' and 'f' had wrong argc checks
• main()
  • FormatParserStorage is set with mpqc, pcp and xyz
  • BondGraph is constructed from new string BondGrapghFileName

• new Libparser.a
• all sources from PARSER subdir are compiled into libparser such that only ParserUnitTest is recompiled.

Testfixes:

• testsuite-fragmentation - changes to due to different -f calling syntax.
• most of the xyz files had to be replaced due to a single whitespace at the end of each entry: Domain/6, Simple_configuration/2, Simple_configuration/3, Simple_configuration/4, Simple_configuration/5, Simple_configuration/8
• in many cases were the number orbitals (and thus MaxMinStopStep) wrong: Filling/1, Simple_configuration/4, Simple_configuration/5

Signed-off-by: Frederik Heber <heber@…>

File:

• src/molecule_fragmentation.cpp (modified) (20 diffs)

src/molecule_fragmentation.cpp

@@ -82 +82 @@
  * -# Scans TEFactors file and sets the TEFactor of each key set in the temporary graph accordingly
  * Finally, the temporary graph is inserted into the given \a FragmentList for return.
- * \param *out output stream for debugging
- * \param *path path to file
+ * \param &path path to file
  * \param *FragmentList empty, filled on return
  * \return true - parsing successfully, false - failure on parsing (FragmentList will be NULL)
  */
-bool ParseKeySetFile(char *path, Graph *&FragmentList)
+bool ParseKeySetFile(std::string &path, Graph *&FragmentList)
 {
   bool status = true;
@@ -94 +93 @@
   GraphTestPair testGraphInsert;
   int NumberOfFragments = 0;
-  char filename[MAXSTRINGSIZE];
+  string filename;
 
   if (FragmentList == NULL) { // check list pointer
@@ -102 +101 @@
   // 1st pass: open file and read
   DoLog(1) && (Log() << Verbose(1) << "Parsing the KeySet file ... " << endl);
-  sprintf(filename, "%s/%s%s", path, FRAGMENTPREFIX, KEYSETFILE);
-  InputFile.open(filename);
-  if (InputFile != NULL) {
+  filename = path + KEYSETFILE;
+  InputFile.open(filename.c_str());
+  if (InputFile.good()) {
     // each line represents a new fragment
     char buffer[MAXSTRINGSIZE];
@@ -181 +180 @@
 
 /** Stores key sets to file.
- * \param *out output stream for debugging
  * \param KeySetList Graph with Keysets
- * \param *path path to file
+ * \param &path path to file
  * \return true - file written successfully, false - writing failed
  */
-bool StoreKeySetFile(Graph &KeySetList, char *path)
-{
-  ofstream output;
+bool StoreKeySetFile(Graph &KeySetList, std::string &path)
+{
   bool status =  true;
-  string line;
+  string line = path + KEYSETFILE;
+  ofstream output(line.c_str());
 
   // open KeySet file
-  line = path;
-  line.append("/");
-  line += FRAGMENTPREFIX;
-  line += KEYSETFILE;
-  output.open(line.c_str(), ios::out);
   DoLog(1) && (Log() << Verbose(1) << "Saving key sets of the total graph ... ");
-  if(output != NULL) {
+  if(output.good()) {
     for(Graph::iterator runner = KeySetList.begin(); runner != KeySetList.end(); runner++) {
       for (KeySet::iterator sprinter = (*runner).first.begin();sprinter != (*runner).first.end(); sprinter++) {
@@ -302 +295 @@
 
 /** Scans the adaptive order file and insert (index, value) into map.
- * \param *out output stream for debugging
- * \param *path path to ENERGYPERFRAGMENT file (may be NULL if Order is non-negative)
+ * \param &path path to ENERGYPERFRAGMENT file (may be NULL if Order is non-negative)
  * \param &IndexedKeySetList list to find key set for a given index \a No
  * \return adaptive criteria list from file
  */
-map<int, pair<double,int> > * ScanAdaptiveFileIntoMap(char *path, map<int,KeySet> &IndexKeySetList)
+map<int, pair<double,int> > * ScanAdaptiveFileIntoMap(std::string &path, map<int,KeySet> &IndexKeySetList)
 {
   map<int, pair<double,int> > *AdaptiveCriteriaList = new map<int, pair<double,int> >;
@@ -313 +305 @@
   double Value = 0.;
   char buffer[MAXSTRINGSIZE];
-  sprintf(buffer, "%s/%s%s.dat", path, FRAGMENTPREFIX, ENERGYPERFRAGMENT);
-  ifstream InputFile(buffer, ios::in);
+  string filename = path + ENERGYPERFRAGMENT;
+  ifstream InputFile(filename.c_str());
+
+  if (InputFile.fail()) {
+    DoeLog(1) && (eLog() << Verbose(1) << "Cannot find file " << filename << "." << endl);
+    return AdaptiveCriteriaList;
+  }
 
   if (CountLinesinFile(InputFile) > 0) {
@@ -419 +416 @@
 
 /** Checks whether the OrderAtSite is still below \a Order at some site.
- * \param *out output stream for debugging
  * \param *AtomMask defines true/false per global Atom::nr to mask in/out each nuclear site, used to activate given number of site to increment order adaptively
  * \param *GlobalKeySetList list of keysets with global ids (valid in "this" molecule) needed for adaptive increase
  * \param Order desired Order if positive, desired exponent in threshold criteria if negative (0 is single-step)
  * \param *MinimumRingSize array of max. possible order to avoid loops
- * \param *path path to ENERGYPERFRAGMENT file (may be NULL if Order is non-negative)
+ * \param path path to ENERGYPERFRAGMENT file (may be NULL if Order is non-negative)
  * \return true - needs further fragmentation, false - does not need fragmentation
  */
-bool molecule::CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, char *path)
+bool molecule::CheckOrderAtSite(bool *AtomMask, Graph *GlobalKeySetList, int Order, int *MinimumRingSize, std::string path)
 {
   bool status = false;
@@ -585 +581 @@
  * of vertex indices: Global always means the index in "this" molecule, whereas local refers to the molecule or
  * subgraph in the MoleculeListClass.
- * \param *out output stream for debugging
  * \param Order up to how many neighbouring bonds a fragment contains in BondOrderScheme::BottumUp scheme
- * \param *configuration configuration for writing config files for each fragment
+ * \param &prefix path and prefix of the bond order configs to be written
  * \return 1 - continue, 2 - stop (no fragmentation occured)
  */
-int molecule::FragmentMolecule(int Order, config *configuration)
+int molecule::FragmentMolecule(int Order, std::string &prefix)
 {
   MoleculeListClass *BondFragments = NULL;
@@ -624 +619 @@
 
   // === compare it with adjacency file ===
-  FragmentationToDo = FragmentationToDo && CheckAdjacencyFileAgainstMolecule(configuration->configpath, ListOfAtoms);
+  FragmentationToDo = FragmentationToDo && CheckAdjacencyFileAgainstMolecule(prefix, ListOfAtoms);
   delete[](ListOfAtoms);
 
@@ -658 +653 @@
 
   // ===== 3. if structure still valid, parse key set file and others =====
-  FragmentationToDo = FragmentationToDo && ParseKeySetFile(configuration->configpath, ParsedFragmentList);
+  FragmentationToDo = FragmentationToDo && ParseKeySetFile(prefix, ParsedFragmentList);
 
   // ===== 4. check globally whether there's something to do actually (first adaptivity check)
-  FragmentationToDo = FragmentationToDo && ParseOrderAtSiteFromFile(configuration->configpath);
+  FragmentationToDo = FragmentationToDo && ParseOrderAtSiteFromFile(prefix);
 
   // =================================== Begin of FRAGMENTATION ===============================
@@ -672 +667 @@
   AtomMask[getAtomCount()] = false;
   FragmentationToDo = false;  // if CheckOrderAtSite just ones recommends fragmentation, we will save fragments afterwards
-  while ((CheckOrder = CheckOrderAtSite(AtomMask, ParsedFragmentList, Order, MinimumRingSize, configuration->configpath))) {
+  while ((CheckOrder = CheckOrderAtSite(AtomMask, ParsedFragmentList, Order, MinimumRingSize, prefix))) {
     FragmentationToDo = FragmentationToDo || CheckOrder;
     AtomMask[getAtomCount()] = true;   // last plus one entry is used as marker that we have been through this loop once already in CheckOrderAtSite()
@@ -727 +722 @@
     KeySet test = (*runner).first;
     DoLog(0) && (Log() << Verbose(0) << "Fragment No." << (*runner).second.first << " with TEFactor " << (*runner).second.second << "." << endl);
-    BondFragments->insert(StoreFragmentFromKeySet(test, configuration));
+    BondFragments->insert(StoreFragmentFromKeySet(test, World::getInstance().getConfig()));
     k++;
   }
@@ -739 +734 @@
 
     DoLog(1) && (Log() << Verbose(1) << "Writing " << BondFragments->ListOfMolecules.size() << " possible bond fragmentation configs" << endl);
-    if (BondFragments->OutputConfigForListOfFragments(configuration, SortIndex))
+    if (BondFragments->OutputConfigForListOfFragments(prefix, SortIndex))
       DoLog(1) && (Log() << Verbose(1) << "All configs written." << endl);
     else
@@ -745 +740 @@
 
     // store force index reference file
-    BondFragments->StoreForcesFile(configuration->configpath, SortIndex);
+    BondFragments->StoreForcesFile(prefix, SortIndex);
 
     // store keysets file
-    StoreKeySetFile(TotalGraph, configuration->configpath);
+    StoreKeySetFile(TotalGraph, prefix);
 
     {
       // store Adjacency file
-      char filename[MAXSTRINGSIZE];
-      strcpy(filename, FRAGMENTPREFIX);
-      strcat(filename, ADJACENCYFILE);
-      StoreAdjacencyToFile(configuration->configpath, filename);
+      std::string filename = prefix + ADJACENCYFILE;
+      StoreAdjacencyToFile(filename);
     }
 
     // store Hydrogen saturation correction file
-    BondFragments->AddHydrogenCorrection(configuration->configpath);
+    BondFragments->AddHydrogenCorrection(prefix);
 
     // store adaptive orders into file
-    StoreOrderAtSiteFile(configuration->configpath);
+    StoreOrderAtSiteFile(prefix);
 
     // restore orbital and Stop values
-    CalculateOrbitals(*configuration);
+    //CalculateOrbitals(*configuration);
 
     // free memory for bond part
@@ -782 +775 @@
 /** Stores pairs (Atom::nr, Atom::AdaptiveOrder) into file.
  * Atoms not present in the file get "-1".
- * \param *out output stream for debugging
- * \param *path path to file ORDERATSITEFILE
+ * \param &path path to file ORDERATSITEFILE
  * \return true - file writable, false - not writable
  */
-bool molecule::StoreOrderAtSiteFile(char *path)
-{
-  stringstream line;
+bool molecule::StoreOrderAtSiteFile(std::string &path)
+{
+  string line;
   ofstream file;
 
-  line << path << "/" << FRAGMENTPREFIX << ORDERATSITEFILE;
-  file.open(line.str().c_str());
+  line = path + ORDERATSITEFILE;
+  file.open(line.c_str());
   DoLog(1) && (Log() << Verbose(1) << "Writing OrderAtSite " << ORDERATSITEFILE << " ... " << endl);
-  if (file != NULL) {
+  if (file.good()) {
     ActOnAllAtoms( &atom::OutputOrder, &file );
     file.close();
@@ -800 +792 @@
     return true;
   } else {
-    DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line.str() << "." << endl);
+    DoLog(1) && (Log() << Verbose(1) << "failed to open file " << line << "." << endl);
     return false;
   }
@@ -807 +799 @@
 /** Parses pairs(Atom::nr, Atom::AdaptiveOrder) from file and stores in molecule's Atom's.
  * Atoms not present in the file get "0".
- * \param *out output stream for debugging
- * \param *path path to file ORDERATSITEFILEe
+ * \param &path path to file ORDERATSITEFILEe
  * \return true - file found and scanned, false - file not found
  * \sa ParseKeySetFile() and CheckAdjacencyFileAgainstMolecule() as this is meant to be used in conjunction with the two
  */
-bool molecule::ParseOrderAtSiteFromFile(char *path)
+bool molecule::ParseOrderAtSiteFromFile(std::string &path)
 {
   unsigned char *OrderArray = new unsigned char[getAtomCount()];
@@ -818 +809 @@
   bool status;
   int AtomNr, value;
-  stringstream line;
+  string line;
   ifstream file;
 
@@ -827 +818 @@
 
   DoLog(1) && (Log() << Verbose(1) << "Begin of ParseOrderAtSiteFromFile" << endl);
-  line << path << "/" << FRAGMENTPREFIX << ORDERATSITEFILE;
-  file.open(line.str().c_str());
-  if (file != NULL) {
+  line = path + ORDERATSITEFILE;
+  file.open(line.c_str());
+  if (file.good()) {
     while (!file.eof()) { // parse from file
       AtomNr = -1;
@@ -850 +841 @@
     status = true;
   } else {
-    DoLog(1) && (Log() << Verbose(1) << "\t ... failed to open file " << line.str() << "." << endl);
+    DoLog(1) && (Log() << Verbose(1) << "\t ... failed to open file " << line << "." << endl);
     status = false;
   }