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 57388c9 was d2596b, checked in by Frederik Heber <heber@…>, 13 years ago |
|
Added XmlParser for parsing configurations for ScaFaCoS generic test code.
- XML is parsed via pugixml which is placed in subfolder pugixml in src/Parser.
- NOTE: pugixml does not import/export double with high enough precision.
Hence, we always obtain strings and convert them ourselves.
- also added unit test on the new parser.
- NOTE: Unit test is failing as charges are not yet written correctly, hence
marked as XFAIL.
|
-
Property mode
set to
100644
|
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File size:
937 bytes
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| 1 | # Project: MoleCuilder
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| 2 | #
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| 3 | # heber@ins.uni-bonn.de
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| 4 |
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| 5 | MoleCuilder
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| 6 |
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| 7 | ... is a tool that started as a mean to edit pcp configuration files (adding/
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| 8 | removing groups of atoms, measuring bond lengths and so forth), grew forth into
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| 9 | a many-body fragmentation test base of a new method coined BOSSANOVA (Bond
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| 10 | Order diSSection in an ANOVA (ANalysis Of VAriance) - like fashion). It spilled
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| 11 | out configuration files for each fragment and included joining and analyzing
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| 12 | programs, to put together the partial energies and forces of each fragment to
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| 13 | the total energy and forces. Since then it has evolved into a complete toolbox
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| 14 | for creating molecular systems and worlds.
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| 15 |
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| 16 |
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| 17 | INSTALLATION NOTES
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| 18 | ==================
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| 19 |
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| 20 | The following packages are needed
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| 21 | * GCC or alike
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| 22 | * GSL (GNU Scientific Library, available at http://www.gnu.org/software/gsl)
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| 23 | * Boost 1.4 or newer
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| 24 | * PugiXML (is provided in src/Parser/pugixml)
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| 25 |
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| 26 | LINKS
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| 27 | =====
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| 28 | [1] http://www.ins.uni-bonn.de/
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