Changeset f7c19e for src

Timestamp:

Oct 6, 2011, 9:09:56 AM (13 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:

81c980b

Parents:

dc8827

git-author:

Frederik Heber <heber@…> (08/09/11 16:39:43)

git-committer:

Frederik Heber <heber@…> (10/06/11 09:09:56)

Message:

Some fixes to parsing files.

• MpqcParser::save() does not store all atoms but those given in the parameters.
• FIX: MoleculeListClass::AddHydrogenCorrection() and FilePresent() check with bad() and eof() whether file is missing or has ended.

Location:

src

Files:

• Parser/MpqcParser.cpp (modified) (2 diffs)
• moleculelist.cpp (modified) (3 diffs)
• parser.cpp (modified) (9 diffs)

src/Parser/MpqcParser.cpp

@@ -214 +214 @@
 {
   Vector center;
-  vector<atom *> allatoms = World::getInstance().getAllAtoms();
+//  vector<atom *> allatoms = World::getInstance().getAllAtoms();
 
   // calculate center
-  for (vector<atom *>::iterator runner = allatoms.begin();runner != allatoms.end(); ++runner)
+  for (std::vector<atom *>::const_iterator runner = atoms.begin();runner != atoms.end(); ++runner)
     center += (*runner)->getPosition();
-  center.Scale(1./(double)allatoms.size());
+  center.Scale(1./(double)atoms.size());
 
   // first without hessian
@@ -293 +293 @@
     *file << "\t{ atoms geometry } = {" << endl;
     // output of atoms
-    for (vector<atom *>::iterator AtomRunner = allatoms.begin(); AtomRunner != allatoms.end(); ++AtomRunner) {
+    for (std::vector<atom *>::const_iterator AtomRunner = atoms.begin(); AtomRunner != atoms.end(); ++AtomRunner) {
       (*AtomRunner)->OutputMPQCLine(file, &center);
     }

src/moleculelist.cpp

@@ -38 +38 @@
 #include "linkedcell.hpp"
 #include "molecule.hpp"
+#include "Parser/MpqcParser.hpp"
+#include "Parser/FormatParserStorage.hpp"
 #include "periodentafel.hpp"
 #include "tesselation.hpp"
@@ -341 +343 @@
     line += FITCONSTANTSUFFIX;
     input.open(line.c_str());
-    if (input == NULL) {
+    if (input.fail()) {
       DoeLog(0) && (eLog()<< Verbose(0) << endl << "Unable to open " << line << ", is the directory correct?" << endl);
       performCriticalExit();
@@ -615 +617 @@
       // and save as mpqc input file
       stringstream output;
-      FragmentName = prefix + FragmentNumber + ".conf";
+      FragmentName = prefix + FragmentNumber + ".conf.in";
       output << "Saving bond fragment No. " << FragmentNumber << "/" << FragmentCounter - 1 << " as mpqc input ... ";
-      if ((intermediateResult = World::getInstance().getConfig()->SaveMPQC(FragmentName.c_str(), (*ListRunner))))
+      std::ofstream outfile(FragmentName.c_str());
+      std::vector<atom *> atoms;
+      for (molecule::const_iterator iter = (*ListRunner)->begin(); iter != (*ListRunner)->end(); ++iter)
+        atoms.push_back(*iter);
+//      atoms.resize((*ListRunner)->getAtomCount());
+//      std::copy((*ListRunner)->begin(), (*ListRunner)->end(), atoms.begin());
+      FormatParserStorage::getInstance().getMpqc().save(&outfile, atoms);
+//      if ((intermediateResult = World::getInstance().getConfig()->SaveMPQC(FragmentName.c_str(), (*ListRunner))))
         output << " done.";
-      else
-        output << " failed.";
+//      else
+//        output << " failed.";
       LOG(3, output.str());
     }

src/parser.cpp

@@ -45 +45 @@
 
   input.open(filename, ios::in);
-  if (input == NULL) {
+  if (input.fail()) {
     if (!test)
       DoLog(0) && (Log() << Verbose(0) << endl << "FilePresent: Unable to open " << filename << ", is the directory correct?" << endl);
@@ -204 +204 @@
   char filename[1023];
 
-  //Log() << Verbose(1) << "Opening " << name << " ... "  << input << endl;
-  if (input.bad()) {
+  if (input.fail()) {
     DoeLog(1) && (eLog()<< Verbose(1) << endl << "MatrixContainer::ParseMatrix: Unable to parse istream." << endl);
     //performCriticalExit();
@@ -327 +326 @@
   file << name << FRAGMENTPREFIX << KEYSETFILE;
   input.open(file.str().c_str(), ios::in);
-  if (input == NULL) {
+  if (input.bad()) {
     DoLog(0) && (Log() << Verbose(0) << endl << "MatrixContainer::ParseFragmentMatrix: Unable to open " << file.str() << ", is the directory correct?" << endl);
     return false;
@@ -360 +359 @@
     file << name << FRAGMENTPREFIX << FragmentNumber << prefix << suffix;
     std::ifstream input(file.str().c_str());
+    DoLog(0) &&( Log() << Verbose(0) << "Opening " << file.str() << " ... " << endl);
     if (!ParseMatrix(input, skiplines, skipcolumns, i)) {
       input.close();
@@ -704 +704 @@
   input.open(line.str().c_str(), ios::in);
   //Log() << Verbose(0) << "Opening " << line.str() << " ... "  << input << endl;
-  if (input == NULL) {
+  if (input.fail()) {
     DoLog(0) && (Log() << Verbose(0) << endl << "ForceMatrix::ParseIndices: Unable to open " << line.str() << ", is the directory correct?" << endl);
     return false;
@@ -783 +783 @@
     file << name << FRAGMENTPREFIX << KEYSETFILE;
     input.open(file.str().c_str(), ios::in);
-    if (input == NULL) {
+    if (input.fail()) {
       DoLog(0) && (Log() << Verbose(0) << endl << "ForceMatrix::ParseFragmentMatrix: Unable to open " << file.str() << ", is the directory correct?" << endl);
       return false;
@@ -844 +844 @@
   input.open(line.str().c_str(), ios::in);
   //Log() << Verbose(0) << "Opening " << line.str() << " ... "  << input << endl;
-  if (input == NULL) {
+  if (input.fail()) {
     DoLog(0) && (Log() << Verbose(0) << endl << "HessianMatrix::ParseIndices: Unable to open " << line.str() << ", is the directory correct?" << endl);
     return false;
@@ -1015 +1015 @@
     file << name << FRAGMENTPREFIX << KEYSETFILE;
     input.open(file.str().c_str(), ios::in);
-    if (input == NULL) {
+    if (input.fail()) {
       DoLog(0) && (Log() << Verbose(0) << endl << "HessianMatrix::ParseFragmentMatrix: Unable to open " << file.str() << ", is the directory correct?" << endl);
       return false;
@@ -1101 +1101 @@
   file << name << FRAGMENTPREFIX << KEYSETFILE;
   input.open(file.str().c_str(), ios::in);
-  if (input == NULL) {
+  if (input.fail()) {
     DoLog(0) && (Log() << Verbose(0) << endl << "KeySetsContainer::ParseKeySets: Unable to open " << file.str() << ", is the directory correct?" << endl);
     return false;