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_mpqc_open
Subpackage_vmg
ThirdParty_MPQC_rebuilt_buildsystem
TremoloParser_IncreasedPrecision
TremoloParser_MultipleTimesteps
Ubuntu_1604_changes
stable
| Line | |
|---|
| 1 | % molecule specification
|
|---|
| 2 | molecule<Molecule>: (
|
|---|
| 3 | symmetry = C1
|
|---|
| 4 | angstroms = yes
|
|---|
| 5 | { atoms geometry } = {
|
|---|
| 6 | N [ 0.51607603 0.04519735 -0.95614194 ]
|
|---|
| 7 | H [ -0.19547589 0.17839942 -1.65845361 ]
|
|---|
| 8 | C [ 0.03095251 -0.69526932 0.25445565 ]
|
|---|
| 9 | C [ -0.06456519 0.77121302 0.60822996 ]
|
|---|
| 10 | H [ 0.85374037 1.04857415 -0.32020191 ]
|
|---|
| 11 | H [ -0.88816493 -1.22489056 0.08294898 ]
|
|---|
| 12 | H [ 0.79530751 -1.28353418 0.71918150 ]
|
|---|
| 13 | H [ -1.04787041 1.16031014 0.35868556 ]
|
|---|
| 14 | }
|
|---|
| 15 | )
|
|---|
| 16 | % basis set specification
|
|---|
| 17 | basis<GaussianBasisSet>: (
|
|---|
| 18 | name = "STO-3G"
|
|---|
| 19 | molecule = $:molecule
|
|---|
| 20 | )
|
|---|
| 21 | mpqc: (
|
|---|
| 22 | restart = no
|
|---|
| 23 | checkpoint = yes
|
|---|
| 24 | savestate = no
|
|---|
| 25 | % molecular coordinates for optimization
|
|---|
| 26 | coor<SymmMolecularCoor>: (
|
|---|
| 27 | molecule = $:molecule
|
|---|
| 28 | generator<IntCoorGen>: (
|
|---|
| 29 | molecule = $:molecule
|
|---|
| 30 | )
|
|---|
| 31 | followed<SumIntCoor>:(
|
|---|
| 32 | coor: [
|
|---|
| 33 | <StreSimpleCo>:(atoms = [1 5])
|
|---|
| 34 | <StreSimpleCo>:(atoms = [4 5])
|
|---|
| 35 | ]
|
|---|
| 36 | coef = [ 1.0 -1.0]
|
|---|
| 37 | )
|
|---|
| 38 | )
|
|---|
| 39 | % method for computing the molecule's energy
|
|---|
| 40 | mole<CLHF>: (
|
|---|
| 41 | molecule = $:molecule
|
|---|
| 42 | basis = $:basis
|
|---|
| 43 | coor = $..:coor
|
|---|
| 44 | memory = 16000000
|
|---|
| 45 | )
|
|---|
| 46 | % optimizer object for the molecular geometry
|
|---|
| 47 | opt<EFCOpt>: (
|
|---|
| 48 | max_iterations = 1
|
|---|
| 49 | function = $..:mole
|
|---|
| 50 | transition_state = yes
|
|---|
| 51 | hessian = [ [ -0.1 ] ]
|
|---|
| 52 | mode_following = yes
|
|---|
| 53 | update<PowellUpdate>: ()
|
|---|
| 54 | convergence<MolEnergyConvergence>: (
|
|---|
| 55 | cartesian = yes
|
|---|
| 56 | energy = $..:..:mole
|
|---|
| 57 | )
|
|---|
| 58 | )
|
|---|
| 59 | )
|
|---|
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