Changeset ccb487 for src/Parser/TremoloParser.cpp

Timestamp:

Apr 3, 2012, 7:58:43 AM (14 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, Candidate_v1.7.0, 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:

08a0f52

Parents:

a275b3

git-author:

Frederik Heber <heber@…> (03/15/12 17:29:54)

git-committer:

Frederik Heber <heber@…> (04/03/12 07:58:43)

Message:

TremoloParser now always writes current domain as "# Box ..." into file.

• This is important, as format tremolo is essentially also a domain preserving type (i.e. tremolo reads Box from .data file).
• TESTFIX: The following regression tests have a "' Box ..." line added to their .data files: Domain/RepeatBox, Filling/FillVoidWithMolecule, Molecules/Copy, Molecules/CreateMicelle, Parser/Tremolo-SetAtomdata.
• FIX: Forgot to add testsuite-fill-void-with-tenside-molecule.at to Makefile.am

File:

• src/Parser/TremoloParser.cpp (modified) (3 diffs)

src/Parser/TremoloParser.cpp

@@ -29 +29 @@
 #include "Atom/atom.hpp"
 #include "Bond/bond.hpp"
+#include "Box.hpp"
 #include "Descriptors/AtomIdDescriptor.hpp"
 #include "Element/element.hpp"
 #include "Element/periodentafel.hpp"
+#include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "molecule.hpp"
 #include "MoleculeListClass.hpp"
@@ -171 +173 @@
   }
 
-  // store
+  // store Atomdata line
   *file << "# ATOMDATA";
   for (it=usedFields.begin(); it < usedFields.end(); it++) {
@@ -177 +179 @@
   }
   *file << endl;
+
+  // store Box info
+  *file << "# Box";
+  const RealSpaceMatrix &M = World::getInstance().getDomain().getM();
+  for (size_t i=0; i<NDIM;++i)
+    for (size_t j=0; j<NDIM;++j)
+      *file << "\t" << M.at(i,j);
+  *file << std::endl;
+
+  // store particles
   for (atomIt = AtomList.begin(); atomIt != AtomList.end(); atomIt++) {
     saveLine(file, *atomIt);