Interoperability With Other Tools
AtomsBase.jl
Cclib.jl provides interoperability with AtomsBase.jl by allowing to create AtomsBase systems.
The documentaiton below provides some essential functionality, such as creating and editing AtomsBase.jl systems.
For a detailed overview, or if you want to know how AtomsBase.jl operates behind the scenes, refer to its official documentation.
Creating AtomsBase Systems
We can load information contained in a Cclib.jl-supported file into a system by using the following functions:
make_flexible_system- for creating an AtomsBaseFlexibleSystem
# Input file can be found in the in the repo under "test" folder
julia> using Cclib
julia> using Unitful
julia> using AtomsBase
julia> box = [[3.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 3.0]]u"Å"
julia> boundary_conditions = [Periodic(), Periodic(), Periodic()]
julia> system = make_flexible_system("./water_mp2.out", box, boundary_conditions)
FlexibleSystem(H₂O, periodic = TTT):
bounding_box : [ 3 0 0;
0 3 0;
0 0 3]u"Å"
Atom(O, [ 0, 0, -0.0666785]u"Å")
Atom(H, [ 0, -0.790649, 0.529118]u"Å")
Atom(H, [ 0, 0.790649, 0.529118]u"Å")
.------.
/| |
O | |
| | |
|H.------.
|H /
*------*
make_isolated_system- for creating an AtomsBaseisolated_system
julia> using Cclib
julia> system = make_isolated_system("./water_mp2.out")
FlexibleSystem(H₂O, infinite):
Atom(O, [ 0, 0, -0.0666785]u"Å")
Atom(H, [ 0, -0.790649, 0.529118]u"Å")
Atom(H, [ 0, 0.790649, 0.529118]u"Å")get_atom_objects- for getting an array of AtomsBaseAtomobjects in case you need more control.
julia> using Cclib
julia> using AtomsBase
julia> mol = ccread("./water_mp2.out")
julia> atoms = get_atom_objects(mol)
julia> atoms[1]
Atom(O, atomic_number = 8, atomic_mass = 15.999 u):
position : [0,0,-0.066678532]u"Å"Accessing System Properties
In case we need to look at what our system contains, we can use regular keys to see available system-level properties and atomkeys to see available atom-level properties
julia> using Cclib
julia> using AtomsBase
julia> system = make_isolated_system("./water_mp2.out")
julia> keys(system)
(:bounding_box, :boundary_conditions)
julia> atomkeys(system)
(:position, :velocity, :atomic_symbol, :atomic_number, :atomic_mass)
julia> bounding_box(system)
[Inf a₀, 0.0 a₀, 0.0 a₀]
[0.0 a₀, Inf a₀, 0.0 a₀]
[0.0 a₀, 0.0 a₀, Inf a₀
julia> atomic_symbol(system)
3-element Vector{Symbol}:
:O
:H
:HUpdating and/or adding system properties
We can also update and/or add system properties by using update_system function that accepts keywords arguments. Below is an example of adding data that was parsed using ccread to a system.
julia> using Cclib
julia> mol = ccread("./water_mp2.out")
julia> system = make_isolated_system(mol);
julia> system = update_system(system; nbasis=mol["nbasis"])
julia> system[:nbasis]
7AtomsBase.jl-supported libraries
We can use data loaded with Cclib.jl to perform calculations using other libraries that use AtomsBase.jl, such as InteratomicPotentials.jl or DFTK.jl.
Let's first load some dependencies and make a system
julia> using Cclib
julia> using AtomsBase
julia> using Unitful
julia> using UnitfulAtomic
julia> using InteratomicPotentials
julia> using DFTK
julia> box = [[3.0, 0.0, 0.0], [0.0, 3.0, 0.0], [0.0, 0.0, 3.0]]u"Å"
julia> boundary_conditions = [Periodic(), Periodic(), Periodic()]
julia> system = make_flexible_system("./water_mp2.out", box, boundary_conditions);We can now perform calculate various properties of the system:
- using
InteratomicPotentials.jl
julia> ϵ = 1.0 * 1u"eV"
julia> σ = 0.25 * 1u"Å"
julia> rcutoff = 2.25 * 1u"Å"
julia> lj = LennardJones(ϵ, σ, rcutoff, [:N, :C, :O, :H])
julia> potential_energy(system, lj)
-8.061904291397444e-5 Eₕ- using
DFTK.jl
model = model_LDA(system; temperature=1e-3)
basis = PlaneWaveBasis(model; Ecut=15, kgrid=(3, 3, 3))
self_consistent_field(basis);
n Energy log10(ΔE) log10(Δρ) Diag Δtime
--- --------------- --------- --------- ---- ------
1 -38.18166038243 0.81 5.2
2 -45.38103756530 0.86 0.12 3.0 253ms
3 -45.54220597356 -0.79 -0.74 3.0 273ms
4 -45.55809718591 -1.80 -1.40 2.1 172ms
5 -45.55889514812 -3.10 -2.14 1.0 159ms
6 -45.55892123307 -4.58 -2.63 1.4 158ms
7 -45.55892315420 -5.72 -3.26 1.8 211ms
8 -45.55892314370 + -7.98 -3.57 1.2 113ms
9 -45.55892319258 -7.31 -3.92 2.0 189ms
10 -45.55892320440 -7.93 -4.94 1.1 142ms
11 -45.55892320464 -9.63 -4.96 2.0 185ms
12 -45.55892320468 -10.33 -5.44 1.0 134ms
13 -45.55892320469 -11.36 -6.15 2.0 158msFor a full list of tools that support AtomsBase.jl, refer to its official documentation.
Fermi.jl
We can use information loaded using Cclib and use it for Fermi.jl calculations, which accept atom numbers and XYZ coordinates as input. The latter is accessible using Cclib's getXYZ function.
Note that files may contain more than one geometry, in which case the index of the geometry can be specified by passing geomIdx argument to getXYZ. Be default, getXYZ will use the last read geometry.
julia> using Cclib
julia> using Fermi # make sure to install using "add Fermi#master"
julia> xyzfile = getXYZ("./test/data/Trp_polar.fchk")
julia> mol = Molecule(molstring=xyzfile)
julia> @set basis sto-3g
julia> @energy rhf # this line should produce something similar to what is below.
================================================================================
| Hartree-Fock |
| Module by |
| G.J.R Aroeira and M.M. Davis |
================================================================================
Collecting necessary integrals...
Done in 0.44575 s
Using GWH Guess
Molecule:
O 1.209153654800 1.766411818900 -0.017161397200
H 2.198480007500 1.797710062700 0.012116171900
H 0.919788188200 2.458018557000 0.629793883200
Charge: 0 Multiplicity: 1
Nuclear repulsion: 8.8880641737
Number of AOs: 7
Number of Doubly Occupied Orbitals: 5
Number of Virtual Spatial Orbitals: 2
Guess Energy -83.52857161946045
Iter. E[RHF] ΔE Dᵣₘₛ t DIIS damp
--------------------------------------------------------------------------------
1 -74.9454656296 -7.495e+01 1.011e-01 0.12 false 2.18
2 -74.8779931590 6.747e-02 4.129e-02 0.00 false 1.47
3 -74.7758359210 1.022e-01 3.788e-02 0.00 false 0.00
4 -74.9409547085 -1.651e-01 7.125e-02 0.06 true 0.00
5 -74.9649972656 -2.404e-02 4.621e-02 0.00 true 0.00
6 -74.9650022441 -4.979e-06 7.385e-04 0.00 true 0.00
7 -74.9650028906 -6.464e-07 2.615e-04 0.00 true 0.00
8 -74.9650028947 -4.112e-09 1.362e-05 0.00 true 0.00
9 -74.9650028947 -3.979e-13 1.273e-07 0.13 true 0.00
10 -74.9650028947 0.000e+00 4.229e-08 0.00 true 0.00
11 -74.9650028947 0.000e+00 1.605e-08 0.00 true 0.00
12 -74.9650028947 -2.842e-14 1.155e-09 0.00 true 0.00
13 -74.9650028947 -2.842e-14 2.004e-10 0.00 true 0.00
--------------------------------------------------------------------------------
RHF done in 0.43s
@Final RHF Energy -74.965002894685 Eₕ
• Orbitals Summary
Orbital Energy Occupancy
1 -20.2459299842 ↿⇂
2 -1.2522309022 ↿⇂
3 -0.6007847377 ↿⇂
4 -0.4490335937 ↿⇂
5 -0.3893764439 ↿⇂
6 0.5733840180
7 0.7039953043
✔ SCF Equations converged 😄
--------------------------------------------------------------------------------
⇒ Fermi Restricted Hartree--Fock Wave function
⋅ Basis: sto-3g
⋅ Energy: -74.96500289468506
⋅ Occ. Spatial Orbitals: 5
⋅ Vir. Spatial Orbitals: 2
Convergence: ΔE => 2.84e-14 Dᵣₘₛ => 2.00e-10