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
| Rev | Line | |
|---|
| [3493da] | 1 | bin-start
|
|---|
| 2 | bin-width
|
|---|
| 3 | bin-end
|
|---|
| 4 | output-file
|
|---|
| 5 | bin-output-file
|
|---|
| 6 | periodic
|
|---|
| 7 | elements
|
|---|
| 8 | position
|
|---|
| 9 | molecule-by-id
|
|---|
| 10 | add-atom
|
|---|
| 11 | domain-position
|
|---|
| 12 | change-element
|
|---|
| 13 | rotate-around-origin
|
|---|
| 14 | save-selected-atoms
|
|---|
| 15 | translate-atoms
|
|---|
| 16 | bond-table
|
|---|
| 17 | element-db
|
|---|
| 18 | fastparsing
|
|---|
| 19 | actionname
|
|---|
| 20 | set-random-number-distribution
|
|---|
| 21 | random-number-distribution-parameters
|
|---|
| 22 | set-random-number-engine
|
|---|
| 23 | random-number-engine-parameters
|
|---|
| 24 | verbose
|
|---|
| 25 | fragment-molecule
|
|---|
| 26 | distance
|
|---|
| 27 | order
|
|---|
| 28 | depth-first-search
|
|---|
| 29 | bond-file
|
|---|
| 30 | skiplines
|
|---|
| 31 | offset
|
|---|
| 32 | change-molname
|
|---|
| 33 | copy-molecule
|
|---|
| 34 | fill-void
|
|---|
| 35 | distances
|
|---|
| 36 | distance-to-molecule
|
|---|
| 37 | random-atom-displacement
|
|---|
| 38 | random-molecule-displacement
|
|---|
| 39 | distance-to-boundary
|
|---|
| 40 | DoRotate
|
|---|
| 41 | fill-molecule
|
|---|
| 42 | MaxDistance
|
|---|
| 43 | start-step
|
|---|
| 44 | interpolation-steps
|
|---|
| 45 | end-step
|
|---|
| 46 | id-mapping
|
|---|
| 47 | load
|
|---|
| 48 | rotate-around-self
|
|---|
| 49 | axis
|
|---|
| 50 | rotate-to-principal-axis-system
|
|---|
| 51 | save-adjacency
|
|---|
| 52 | save-bonds
|
|---|
| 53 | save-selected-molecules
|
|---|
| 54 | save-temperature
|
|---|
| 55 | suspend-in-water
|
|---|
| 56 | verlet-integration
|
|---|
| 57 | deltat
|
|---|
| 58 | MDSteps
|
|---|
| 59 | keep-fixed-CenterOfMass
|
|---|
| 60 | parse-tremolo-potentials
|
|---|
| 61 | set-mpqc-parameters
|
|---|
| 62 | set-output
|
|---|
| 63 | set-tremolo-atomdata
|
|---|
| 64 | select-atoms-inside-cuboid
|
|---|
| 65 | angle-x
|
|---|
| 66 | angle-y
|
|---|
| 67 | angle-z
|
|---|
| 68 | select-atoms-inside-sphere
|
|---|
| 69 | select-atom-by-element
|
|---|
| 70 | select-atom-by-id
|
|---|
| 71 | select-molecules-by-formula
|
|---|
| 72 | select-molecule-by-id
|
|---|
| 73 | select-molecules-by-name
|
|---|
| 74 | select-molecule-by-order
|
|---|
| 75 | unselect-atoms-inside-cuboid
|
|---|
| 76 | unselect-atoms-inside-sphere
|
|---|
| 77 | unselect-atom-by-element
|
|---|
| 78 | unselect-atom-by-id
|
|---|
| 79 | unselect-molecules-by-formula
|
|---|
| 80 | unselect-molecule-by-id
|
|---|
| 81 | unselect-molecules-by-name
|
|---|
| 82 | unselect-molecule-by-order
|
|---|
| 83 | convex-file
|
|---|
| 84 | nonconvex-file
|
|---|
| 85 | nonconvex-envelope
|
|---|
| 86 | add-empty-boundary
|
|---|
| 87 | center-in-box
|
|---|
| 88 | change-box
|
|---|
| 89 | input
|
|---|
| [072f0e] | 90 | output-as
|
|---|
| [3493da] | 91 | repeat-box
|
|---|
| 92 | scale-box
|
|---|
| 93 | default-molname
|
|---|
| 94 | set-world-time
|
|---|
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