Action_Thermostats
Add_AtomRandomPerturbation
Add_RotateAroundBondAction
Add_SelectAtomByNameAction
Adding_Graph_to_ChangeBondActions
Adding_MD_integration_tests
Adding_StructOpt_integration_tests
Automaking_mpqc_open
AutomationFragmentation_failures
Candidate_v1.6.0
Candidate_v1.6.1
ChangeBugEmailaddress
ChangingTestPorts
ChemicalSpaceEvaluator
Combining_Subpackages
Debian_Package_split
Debian_package_split_molecuildergui_only
Disabling_MemDebug
Docu_Python_wait
EmpiricalPotential_contain_HomologyGraph_documentation
Enable_parallel_make_install
Enhance_userguide
Enhanced_StructuralOptimization
Enhanced_StructuralOptimization_continued
Example_ManyWaysToTranslateAtom
Exclude_Hydrogens_annealWithBondGraph
FitPartialCharges_GlobalError
Fix_ChronosMutex
Fix_StatusMsg
Fix_StepWorldTime_single_argument
Fix_Verbose_Codepatterns
ForceAnnealing_goodresults
ForceAnnealing_oldresults
ForceAnnealing_tocheck
ForceAnnealing_with_BondGraph
ForceAnnealing_with_BondGraph_continued
ForceAnnealing_with_BondGraph_continued_betteresults
ForceAnnealing_with_BondGraph_contraction-expansion
GeometryObjects
Gui_displays_atomic_force_velocity
IndependentFragmentGrids_IntegrationTest
JobMarket_RobustOnKillsSegFaults
JobMarket_StableWorkerPool
JobMarket_unresolvable_hostname_fix
ODR_violation_mpqc_open
PartialCharges_OrthogonalSummation
PythonUI_with_named_parameters
QtGui_reactivate_TimeChanged_changes
Recreated_GuiChecks
RotateToPrincipalAxisSystem_UndoRedo
StoppableMakroAction
Subpackage_levmar
Subpackage_vmg
ThirdParty_MPQC_rebuilt_buildsystem
TremoloParser_IncreasedPrecision
TremoloParser_MultipleTimesteps
Ubuntu_1604_changes
stable
| Rev | Line | |
|---|
| [0b990d] | 1 | % emacs should use -*- KeyVal -*- mode
|
|---|
| 2 | % molecule specification
|
|---|
| 3 | molecule<Molecule>: (
|
|---|
| 4 | symmetry = C1
|
|---|
| 5 | { atoms geometry } = {
|
|---|
| 6 | H [ 0.088 2.006 1.438 ]
|
|---|
| 7 | O [ 0.123 3.193 0.000 ]
|
|---|
| 8 | H [ 0.088 2.006 -1.438 ]
|
|---|
| 9 | O [ 4.502 5.955 -0.000 ]
|
|---|
| 10 | H [ 2.917 4.963 -0.000 ]
|
|---|
| 11 | H [ 3.812 7.691 -0.000 ]
|
|---|
| 12 | }
|
|---|
| 13 | )
|
|---|
| 14 | % basis set specification
|
|---|
| 15 | basis<GaussianBasisSet>: (
|
|---|
| 16 | name = "STO-3G"
|
|---|
| 17 | molecule = $:molecule
|
|---|
| 18 | )
|
|---|
| 19 | mpqc: (
|
|---|
| 20 | checkpoint = no
|
|---|
| 21 | savestate = no
|
|---|
| 22 | % method for computing the molecule's energy
|
|---|
| 23 | mole<CLHF>: (
|
|---|
| 24 | molecule = $:molecule
|
|---|
| 25 | basis = $:basis
|
|---|
| 26 | coor = $..:coor
|
|---|
| 27 | memory = 16000000
|
|---|
| 28 | )
|
|---|
| 29 | % molecular coordinates for optimization
|
|---|
| 30 | coor<SymmMolecularCoor>: (
|
|---|
| 31 | molecule = $:molecule
|
|---|
| 32 | % give an internal coordinate generator that knows about the
|
|---|
| 33 | % hydrogen bond between atoms 2 and 5
|
|---|
| 34 | generator<IntCoorGen>: (
|
|---|
| 35 | molecule = $:molecule
|
|---|
| 36 | extra_bonds = [ 2 5 ]
|
|---|
| 37 | )
|
|---|
| 38 | )
|
|---|
| 39 | % optimizer object for the molecular geometry
|
|---|
| 40 | opt<QNewtonOpt>: (
|
|---|
| 41 | function = $..:mole
|
|---|
| 42 | update<BFGSUpdate>: ()
|
|---|
| 43 | convergence<MolEnergyConvergence>: (
|
|---|
| 44 | cartesian = yes
|
|---|
| 45 | energy = $..:..:mole
|
|---|
| 46 | )
|
|---|
| 47 | )
|
|---|
| 48 | )
|
|---|
Note:
See
TracBrowser
for help on using the repository browser.
