Changeset c68c90

Timestamp:

May 30, 2010, 3:18:50 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:

72e36f

Parents:

1325ba

Message:

Added case '-A' (parsing bonds) to testsuite.

• ParseCommandLineOptions() - input was not delete'd, is now instantiated directly.
• molecule::CreateAdjacencyListFromDbondFile() was buggy, needed line-by-line parsing via stringstream ro fix.
• bond file has been created by storing bond information.

Files:

• src/builder.cpp (modified) (1 diff)
• src/molecule_graph.cpp (modified) (2 diffs)
• tests/regression/Molecules/1/pre/test.conf (added)
• tests/regression/Molecules/1/pre/test.dbond (added)
• tests/regression/testsuite.at (modified) (1 diff)

src/builder.cpp

@@ -1994 +1994 @@
               } else {
                 DoLog(0) && (Log() << Verbose(0) << "Parsing bonds from " << argv[argptr] << "." << endl);
-                ifstream *input = new ifstream(argv[argptr]);
-                mol->CreateAdjacencyListFromDbondFile(input);
-                input->close();
+                ifstream input(argv[argptr]);
+                mol->CreateAdjacencyListFromDbondFile(&input);
+                input.close();
                 argptr+=1;
               }

src/molecule_graph.cpp

@@ -12 +12 @@
 #include "element.hpp"
 #include "helpers.hpp"
+#include "info.hpp"
 #include "linkedcell.hpp"
 #include "lists.hpp"
@@ -54 +55 @@
 void molecule::CreateAdjacencyListFromDbondFile(ifstream *input)
 {
-
+  Info FunctionInfo(__func__);
   // 1 We will parse bonds out of the dbond file created by tremolo.
   int atom1, atom2;
   atom *Walker, *OtherWalker;
-
-  if (!input) {
-    DoLog(1) && (Log() << Verbose(1) << "Opening silica failed \n");
+  char line[MAXSTRINGSIZE];
+
+  if (input->fail()) {
+    DoeLog(0) && (eLog() << Verbose(0) << "Opening of bond file failed \n");
+    performCriticalExit();
   };
 
-  *input >> ws >> atom1;
-  *input >> ws >> atom2;
-  DoLog(1) && (Log() << Verbose(1) << "Scanning file\n");
+  // skip header
+  input->getline(line,MAXSTRINGSIZE);
+  DoLog(1) && (Log() << Verbose(1) << "Scanning file ... \n");
   while (!input->eof()) // Check whether we read everything already
   {
-    *input >> ws >> atom1;
-    *input >> ws >> atom2;
-
+    input->getline(line,MAXSTRINGSIZE);
+    stringstream zeile(line);
+    zeile >> atom1;
+    zeile >> atom2;
+
+    DoLog(2) && (Log() << Verbose(2) << "Looking for atoms " << atom1 << " and " << atom2 << "." << endl);
     if (atom2 < atom1) //Sort indices of atoms in order
       flip(atom1, atom2);

tests/regression/testsuite.at

@@ -208 +208 @@
 AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 3 -I], 0, [stdout], [stderr])
 AT_CHECK([fgrep "I scanned 31 molecules." stdout], 0, [ignore], [ignore])
+AT_CLEANUP
+
+
+AT_BANNER([MoleCuilder - Molecules])
+# 1. Bonds from file
+AT_SETUP([Graph - Bonds from file])
+AT_KEYWORDS([graph])
+AT_CHECK([/bin/cp -f ${abs_top_srcdir}/${AUTOTEST_PATH}/Molecules/1/pre/test.* .], 0)
+AT_CHECK([../../molecuilder test.conf -e ${abs_top_srcdir}/src/ -v 4 -A test.dbond], 0, [stdout], [stderr])
+AT_CHECK([fgrep "Looking for atoms 2 and 9." stdout], 0, [ignore], [ignore])
 AT_CLEANUP