Changeset cabb46 for src/Parser

Timestamp:

Dec 5, 2010, 12:20:07 AM (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:

001f8a, ca03c7

Parents:

4fbca9c

git-author:

Frederik Heber <heber@…> (12/04/10 21:23:07)

git-committer:

Frederik Heber <heber@…> (12/05/10 00:20:07)

Message:

Extended LoadXyz and SaveXyz to any format.

• renamed ParserAction/LoadXyz -> MoleculeAction/Load (same with Save).
• also changed .def for both.
• LoadAction then uses stuff from InputAction but without output name setting.
• new function FormatParserStorage::put() which is opposite to get and stores world to a given ofstream with type from suffix.
• SaveAction uses new FormatParserStorage::put().
• short form of LodAction is "l" not "p"
• short form of SaveAction is "s", ScaleBox has no short form anymore

Testchanges:

• copied all from Simple_configuration/2/pre to ./post.
• changes to test.conf:

MaxPsiStep (if 0 given, then 3 is set).
MaxMinGapStopStep (if 0 given, then 1 is set).
InitMaxMinGapStopStep (if 0 given, then 1 is set).

• changes to test.pdb:

segName is tes (from _tes_t.pdb) not non.
Obtaining molecule names from pdb file's segName is not implemented yet.

• ParserCommonUnitTest::rewriteAnXyzTest(), we don't check for string equality but parse the output stream again and check whether first and second half of all atoms are equal with respect to position and element.
• all regression test that diff an xyz file now use -I '.*Created by....*'
• changed regression tests with respect to changed short forms.

Location:

src/Parser

Files:

• FormatParserStorage.cpp (modified) (1 diff)
• FormatParserStorage.hpp (modified) (1 diff)
• XyzParser.cpp (modified) (2 diffs)

src/Parser/FormatParserStorage.cpp

@@ -243 +243 @@
 }
 
+
+/** Stores world in an ostream depending on its suffix
+ * \param &output output stream
+ * \param suffix
+ * \return true - storing ok, false - suffix unknown
+ */
+bool FormatParserStorage::put(std::ostream &output, std::string suffix)
+{
+  if (suffix == ParserSuffixes[mpqc]) {
+    getMpqc().save(&output);
+  } else if (suffix == ParserSuffixes[pcp]) {
+    getPcp().save(&output);
+  } else if (suffix == ParserSuffixes[pdb]) {
+    getPdb().save(&output);
+  } else if (suffix == ParserSuffixes[tremolo]) {
+    getTremolo().save(&output);
+  } else if (suffix == ParserSuffixes[xyz]) {
+    getXyz().save(&output);
+  } else {
+    DoeLog(1) && (eLog() << Verbose(1) << "Unknown suffix " << suffix << " to for FormatParserStorage::put()." << endl);
+    return false;
+  }
+  return true;
+}
+
 /** Returns reference to the output MpqcParser, adds if not present.
  * \return reference to the output MpqcParser

src/Parser/FormatParserStorage.hpp

@@ -46 +46 @@
 
   bool get(std::istream &input, std::string suffix);
+  bool put(std::ostream &output, std::string suffix);
   MpqcParser &getMpqc();
   PcpParser &getPcp();

src/Parser/XyzParser.cpp

@@ -84 +84 @@
 void XyzParser::save(ostream* file) {
   DoLog(0) && (Log() << Verbose(0) << "Saving changes to xyz." << std::endl);
-  if (comment == "") {
+  //if (comment == "") {
     time_t now = time((time_t *)NULL);   // Get the system time and put it into 'now' as 'calender time'
     comment = "Created by molecuilder on ";
@@ -94 +94 @@
     else
       comment += time;
-  }
+  //}
   *file << World::getInstance().numAtoms() << endl << "\t" << comment << endl;