source: tests/regression/Parser/Mpqc/pre/water.in@ c0e28c

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
Last change on this file since c0e28c was c0e28c, checked in by Frederik Heber <heber@…>, 13 years ago

FIX: One could not load another pdb file due to local ids messing up.

  • We enhanced FormatParser_common now contains two maps to go from local to global and back again. Thi is necessary, as ids in a file only make sense within that file. We added the following functions: resetIdAssociations(), associateLocaltoGlobalId(), getGlobalId(), getLocalId().
  • adapted TremoloParser and PdbParser because they are the only formats that also contain bond information and where the associations are needed to translate the local connections into global ones.
  • removed SerialSet entirely from PdbParser, is replaced by new construct, in similar manner AtomIdMap for TremoloParser.
  • TEST: Added regression tests for all Parser to check for loading twice the same file.
  • Property mode set to 100644
File size: 459 bytes
Line 
1% Created by MoleCuilder
2mpqc: (
3 savestate = no
4 do_gradient = yes
5 mole<MBPT2>: (
6 basis = $:basis
7 molecule = $:molecule
8 memory = 16000000
9 reference<CLHF>: (
10 maxiter = 1000
11 basis = $:basis
12 molecule = $:molecule
13 memory = 16000000
14 )
15 )
16)
17molecule<Molecule>: (
18 unit = angstrom
19 { atoms geometry } = {
20 O [ -0.506 0 0 ]
21 H [ 0.253 0 0.504 ]
22 H [ 0.253 0 -0.504 ]
23 }
24)
25basis<GaussianBasisSet>: (
26 name = "3-21G"
27 molecule = $:molecule
28)
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