Dynamic Quantum Chemistry Workflow#
NOTE: Make sure to use Python 3.9 or higher for this, pymatgen package does not support Python 3.8 or lower.
In this tutorial, we discuss how covalent can be used to construct and manage dynamic workflows that are common in quantum-chemical simulations. In this example, given a crystal structure, we seek to do the following:
Relax the atomic positions and cell volume for the structure (i.e. find the local minimum energy configuration).
Carve all possible surface slabs of the relaxed structure.
For each generated slab, relax the atomic positions of each structure.
This will be done using the materials informatics library Pymatgen and a machine learned interatomic potential called M3GNet. Because the number of slabs is only known at runtime, this is a dynamic workflow and we must take advantage of the sublattice feature in Covalent to properly dispatch the workflow.
First, we need to install the necessary Python packages from the provided requirements.txt file (e.g. pip install -r requirements.txt). These are printed below:
[1]:
with open("requirements.txt", "r") as file:
for line in file:
print(line.rstrip())
covalent
pymatgen[relaxation]==2023.9.25
If you’re using mac then you might also have to install the following packages with homebrew as:
brew install freetype pkg-config libpng
Once that is done, we can import the necessary functions for this tutorial:
[2]:
import covalent as ct
from pymatgen.core import Structure
from pymatgen.core.surface import generate_all_slabs
We then will make sure the Covalent server is started:
[3]:
ct.covalent_start()
Covalent server is already running.
Now we will define the individual compute tasks. The first Electron we will define is a relax_structure function, which takes in a Pymatgen Structure object as the input and runs the relaxation calculation using M3GNet. It returns an updated Structure object. This process can be thought of as the compute-heavy task.
[4]:
@ct.electron
def relax_structure(structure, relax_cell=True):
return structure.relax(relax_cell=relax_cell)
Now we will define a separate Electron called carve_slabs that takes in a Structure object and carves all plausible surface slabs, which it returns as a list of new Structure objects. This is a relatively quick task, but we still need to define it as an Electron so that it can be used appropriately in the workflow.
[5]:
@ct.electron
def carve_slabs(structure, max_index=1, min_slab_size=10.0, min_vacuum_size=10.0):
slabs = generate_all_slabs(
structure,
max_index,
min_slab_size,
min_vacuum_size,
)
return slabs
Now, for the most subtle but important bit. We need to define a sublattice that will take in the list of slabs and relax each individual slab using the previously defined relax_structure Electron. The sublattice is crucial here because the number of slabs is only determined at runtime and will vary depending on the input Structure object.
[6]:
@ct.electron
@ct.lattice
def relax_slabs(slabs):
return [relax_structure(slab, relax_cell=False) for slab in slabs]
With these individual Electron objects defined, we can now define the overall workflow that stitches them together and forms a Lattice. As introduced at the start of this tutorial, there are three major sets of tasks, and those are reflected by the three functions defined above.
[7]:
@ct.lattice
def workflow(structure):
relaxed_structure = relax_structure(structure)
slabs = carve_slabs(relaxed_structure)
relaxed_slabs = relax_slabs(slabs)
return relaxed_slabs
Now we can create an example Structure as the input for our workflow. Its structure is shown below.
[8]:
structure = Structure(
lattice=[[0, 2.13, 2.13], [2.13, 0, 2.13], [2.13, 2.13, 0]],
species=["Mg", "O"],
coords=[[0, 0, 0], [0.5, 0.5, 0.5]],
)
And we finally take this input Structure and run it through our newly created workflow.
[9]:
dispatch_id = ct.dispatch(workflow)(structure)
results = ct.get_result(dispatch_id, wait=True)
The workflow in the Covalent UI looks like the following. Note that when you click on the sublattice in the UI, it will open up a new view that shows the individual tasks that were run.
The image below shows the input structure on the left and one of the four generated slabs on the right.
And this is the output of the workflow:
[10]:
print(results)
Lattice Result
==============
status: COMPLETED
result: [Structure Summary
Lattice
abc : 3.012274887854692 3.012274887854692 30.122748878546922
angles : 120.00000000000001 120.00000000000001 59.99999999999999
volume : 193.27193999999994
A : 2.608706576064084 0.0 -1.5061374439273467
B : 0.8695688586880276 2.4595121467478056 -1.5061374439273467
C : 0.0 0.0 30.122748878546922
pbc : True True True
PeriodicSite: Mg (-0.06335, -0.04479, 2.149) [-0.01821, -0.01821, 0.06954]
PeriodicSite: O (1.804, 1.275, -0.6412) [0.5186, 0.5186, 0.03057]
PeriodicSite: Mg (-0.04308, -0.03047, 5.197) [-0.01239, -0.01239, 0.1713]
PeriodicSite: O (1.762, 1.246, 2.298) [0.5064, 0.5064, 0.1269]
PeriodicSite: Mg (-0.03833, -0.0271, 8.217) [-0.01102, -0.01102, 0.2717]
PeriodicSite: O (1.776, 1.255, 5.335) [0.5105, 0.5105, 0.2281]
PeriodicSite: Mg (-0.03796, -0.02684, 11.23) [-0.01091, -0.01091, 0.3717]
PeriodicSite: O (1.788, 1.265, 8.369) [0.5141, 0.5141, 0.3292]
PeriodicSite: Mg (-0.01275, -0.009017, 14.29) [-0.003666, -0.003666, 0.4739]
PeriodicSite: O (1.762, 1.246, 11.34) [0.5066, 0.5066, 0.427], Structure Summary
Lattice
abc : 3.012274887854692 3.012274887854692 30.122748878546922
angles : 120.00000000000001 59.99999999999999 90.0
volume : 193.2719399999999
A : 2.608706576064084 0.0 1.5061374439273465
B : 0.8695688586880287 2.459512146747805 -1.5061374439273467
C : 0.0 0.0 30.122748878546922
pbc : True True True
PeriodicSite: Mg (-0.003667, 0.005186, 1.512) [-0.002108, 0.002108, 0.05042]
PeriodicSite: O (1.742, 1.226, 1.502) [0.5015, 0.4985, 0.0497]
PeriodicSite: Mg (0.004204, -0.005944, 4.511) [0.002417, -0.002417, 0.1495]
PeriodicSite: O (1.737, 1.233, 4.523) [0.4985, 0.5015, 0.1503]
PeriodicSite: Mg (-2.373e-07, 1.452e-07, 7.531) [-1.106e-07, 5.904e-08, 0.25]
PeriodicSite: O (1.739, 1.23, 7.531) [0.5, 0.5, 0.25]
PeriodicSite: Mg (-0.004206, 0.005949, 10.55) [-0.002419, 0.002419, 0.3505]
PeriodicSite: O (1.742, 1.226, 10.54) [0.5015, 0.4985, 0.3497]
PeriodicSite: Mg (0.003665, -0.005183, 13.55) [0.002107, -0.002107, 0.4496]
PeriodicSite: O (1.737, 1.233, 13.56) [0.4985, 0.5015, 0.4503], Structure Summary
Lattice
abc : 3.012274887854692 5.217413152128169 48.196398205675074
angles : 30.000000000000014 59.99999999999999 73.22134511903964
volume : 309.2351039999999
A : 2.608706576064084 0.0 1.5061374439273465
B : -0.869568858688028 2.4595121467478056 4.518412331782038
C : 0.0 0.0 48.196398205675074
pbc : True True True
PeriodicSite: Mg (0.1339, -0.01997, 2.027) [0.04861, -0.008121, 0.04131]
PeriodicSite: O (1.084, 1.0, 3.395) [0.5509, 0.4068, 0.01508]
PeriodicSite: Mg (0.1856, 0.2225, 4.95) [0.1013, 0.09047, 0.09106]
PeriodicSite: O (0.9559, 1.166, 6.628) [0.5245, 0.4742, 0.07668]
PeriodicSite: Mg (0.09665, 0.08853, 8.116) [0.04905, 0.036, 0.1635]
PeriodicSite: O (0.9216, 1.175, 9.7) [0.5125, 0.4777, 0.1405]
PeriodicSite: Mg (0.04673, 0.1156, 11.22) [0.03359, 0.04702, 0.2272]
PeriodicSite: O (0.8436, 1.125, 12.85) [0.4758, 0.4574, 0.2088]
PeriodicSite: Mg (-0.005373, 0.07126, 14.32) [0.007599, 0.02897, 0.2941]
PeriodicSite: O (0.7974, 1.125, 15.94) [0.4581, 0.4574, 0.2735]
PeriodicSite: Mg (-0.06382, 0.06227, 17.43) [-0.01603, 0.02532, 0.3598]
PeriodicSite: O (0.7609, 1.136, 19.01) [0.4456, 0.4618, 0.3373]
PeriodicSite: Mg (-0.07782, 0.05423, 20.47) [-0.02248, 0.02205, 0.4233]
PeriodicSite: O (0.7283, 1.092, 22.08) [0.4271, 0.4439, 0.4032]
PeriodicSite: Mg (-0.1775, 0.196, 23.65) [-0.04147, 0.07969, 0.4846]
PeriodicSite: O (0.727, 1.229, 25.1) [0.4452, 0.4996, 0.46], Structure Summary
Lattice
abc : 3.012274887854692 5.217413152128169 42.17184842996569
angles : 29.99999999999997 59.999999999999986 54.735610317245346
volume : 270.58071599999977
A : 2.608706576064084 0.0 1.5061374439273465
B : 0.8695688586880266 2.4595121467478043 4.51841233178204
C : 0.0 0.0 42.17184842996569
pbc : True True True
PeriodicSite: Mg (-0.02746, -0.07768, 1.554) [2.276e-07, -0.03158, 0.04023]
PeriodicSite: O (1.734, 1.216, 4.527) [0.5, 0.4945, 0.0365]
PeriodicSite: Mg (0.02554, 0.07223, 4.474) [1.088e-06, 0.02937, 0.1029]
PeriodicSite: O (1.746, 1.25, 7.518) [0.5, 0.5081, 0.106]
PeriodicSite: Mg (0.004413, 0.01248, 7.523) [1.247e-07, 0.005074, 0.1778]
PeriodicSite: O (1.736, 1.22, 10.55) [0.5, 0.4962, 0.1791]
PeriodicSite: Mg (5.245e-07, 2.488e-06, 10.54) [-1.362e-07, 1.012e-06, 0.25]
PeriodicSite: O (1.739, 1.23, 13.56) [0.5, 0.5, 0.25]
PeriodicSite: Mg (-0.004412, -0.01248, 13.56) [-5.311e-08, -0.005073, 0.3222]
PeriodicSite: O (1.742, 1.239, 16.56) [0.5, 0.5038, 0.3209]
PeriodicSite: Mg (-0.02554, -0.07224, 16.61) [-3.741e-08, -0.02937, 0.3971]
PeriodicSite: O (1.732, 1.21, 19.59) [0.5, 0.4919, 0.394]
PeriodicSite: Mg (0.02746, 0.07767, 19.53) [-2.13e-08, 0.03158, 0.4598]
PeriodicSite: O (1.744, 1.243, 22.58) [0.5, 0.5055, 0.4635]]
input args: None
input kwargs: None
error: None
start_time: 2024-01-07 18:47:40.318085
end_time: 2024-01-07 18:47:50.077092
results_dir: /Users/neptune/.cache/covalent/results/0de284ad-fecb-4c76-ba03-c4dd8d8b3103
dispatch_id: 0de284ad-fecb-4c76-ba03-c4dd8d8b3103
Node Outputs
------------
relax_structure(0): Full Formula (Mg1 O1)
Reduced Formula: MgO
abc : 3.012275 3.012275 3.012275
angles: 60.000000 60.000000 60.000000
pbc : True True True
Sites (2)
# SP a b c
--- ---- --- --- ---
0 Mg 0 0 0
1 O 0.5 0.5 0.5
:parameter:Full Formula (Mg1 O1)
Reduced Formula: MgO
abc : 3.012275 3.012275 3.012275
angles: 60.000000 60.000000 60.000000
pbc : True True True
Sites (2)
# SP a b c
--- ---- --- --- ---
0 Mg 0 0 0
1 O 0.5 0.5 0.5(1): Full Formula (Mg1 O1)
Reduced Formula: MgO
abc : 3.012275 3.012275 3.012275
angles: 60.000000 60.000000 60.000000
pbc : True True True
Sites (2)
# SP a b c
--- ---- --- --- ---
0 Mg 0 0 0
1 O 0.5 0.5 0.5
carve_slabs(2): [Structure Summary
Lattice
abc : 3.012274887854692 3.012274887854692 30.122748878546922
angles : 120.00000000000001 120.00000000000001 59.99999999999999
volume : 193.27193999999994
A : 2.608706576064084 0.0 -1.5061374439273467
B : 0.8695688586880276 2.4595121467478056 -1.5061374439273467
C : 0.0 0.0 30.122748878546922
pbc : True True True
PeriodicSite: Mg (0.0, 0.0, 2.259) [0.0, 0.0, 0.075]
PeriodicSite: O (1.739, 1.23, -0.7531) [0.5, 0.5, 0.025]
PeriodicSite: Mg (0.0, 0.0, 5.271) [0.0, 0.0, 0.175]
PeriodicSite: O (1.739, 1.23, 2.259) [0.5, 0.5, 0.125]
PeriodicSite: Mg (0.0, 0.0, 8.284) [0.0, 0.0, 0.275]
PeriodicSite: O (1.739, 1.23, 5.271) [0.5, 0.5, 0.225]
PeriodicSite: Mg (0.0, 0.0, 11.3) [0.0, 0.0, 0.375]
PeriodicSite: O (1.739, 1.23, 8.284) [0.5, 0.5, 0.325]
PeriodicSite: Mg (0.0, 0.0, 14.31) [0.0, 0.0, 0.475]
PeriodicSite: O (1.739, 1.23, 11.3) [0.5, 0.5, 0.425], Structure Summary
Lattice
abc : 3.012274887854692 3.012274887854692 30.122748878546922
angles : 120.00000000000001 59.99999999999999 90.0
volume : 193.2719399999999
A : 2.608706576064084 0.0 1.5061374439273465
B : 0.8695688586880287 2.459512146747805 -1.5061374439273467
C : 0.0 0.0 30.122748878546922
pbc : True True True
PeriodicSite: Mg (0.0, 0.0, 1.506) [0.0, 0.0, 0.05]
PeriodicSite: O (1.739, 1.23, 1.506) [0.5, 0.5, 0.05]
PeriodicSite: Mg (0.0, 0.0, 4.518) [0.0, 0.0, 0.15]
PeriodicSite: O (1.739, 1.23, 4.518) [0.5, 0.5, 0.15]
PeriodicSite: Mg (0.0, 0.0, 7.531) [0.0, 0.0, 0.25]
PeriodicSite: O (1.739, 1.23, 7.531) [0.5, 0.5, 0.25]
PeriodicSite: Mg (0.0, 0.0, 10.54) [0.0, 0.0, 0.35]
PeriodicSite: O (1.739, 1.23, 10.54) [0.5, 0.5, 0.35]
PeriodicSite: Mg (0.0, 0.0, 13.56) [0.0, 0.0, 0.45]
PeriodicSite: O (1.739, 1.23, 13.56) [0.5, 0.5, 0.45], Structure Summary
Lattice
abc : 3.012274887854692 5.217413152128169 48.196398205675074
angles : 30.000000000000014 59.99999999999999 73.22134511903964
volume : 309.2351039999999
A : 2.608706576064084 0.0 1.5061374439273465
B : -0.869568858688028 2.4595121467478056 4.518412331782038
C : 0.0 0.0 48.196398205675074
pbc : True True True
PeriodicSite: Mg (0.0, 0.0, 2.259) [0.0, 0.0, 0.04688]
PeriodicSite: O (0.8696, 1.23, 3.765) [0.5, 0.5, 0.01562]
PeriodicSite: Mg (0.0, 0.0, 5.271) [0.0, 0.0, 0.1094]
PeriodicSite: O (0.8696, 1.23, 6.778) [0.5, 0.5, 0.07812]
PeriodicSite: Mg (0.0, 0.0, 8.284) [0.0, 0.0, 0.1719]
PeriodicSite: O (0.8696, 1.23, 9.79) [0.5, 0.5, 0.1406]
PeriodicSite: Mg (0.0, 0.0, 11.3) [0.0, 0.0, 0.2344]
PeriodicSite: O (0.8696, 1.23, 12.8) [0.5, 0.5, 0.2031]
PeriodicSite: Mg (0.0, 0.0, 14.31) [0.0, 0.0, 0.2969]
PeriodicSite: O (0.8696, 1.23, 15.81) [0.5, 0.5, 0.2656]
PeriodicSite: Mg (0.0, 0.0, 17.32) [0.0, 0.0, 0.3594]
PeriodicSite: O (0.8696, 1.23, 18.83) [0.5, 0.5, 0.3281]
PeriodicSite: Mg (0.0, 0.0, 20.33) [0.0, 0.0, 0.4219]
PeriodicSite: O (0.8696, 1.23, 21.84) [0.5, 0.5, 0.3906]
PeriodicSite: Mg (0.0, 0.0, 23.35) [0.0, 0.0, 0.4844]
PeriodicSite: O (0.8696, 1.23, 24.85) [0.5, 0.5, 0.4531], Structure Summary
Lattice
abc : 3.012274887854692 5.217413152128169 42.17184842996569
angles : 29.99999999999997 59.999999999999986 54.735610317245346
volume : 270.58071599999977
A : 2.608706576064084 0.0 1.5061374439273465
B : 0.8695688586880266 2.4595121467478043 4.51841233178204
C : 0.0 0.0 42.17184842996569
pbc : True True True
PeriodicSite: Mg (0.0, 0.0, 1.506) [0.0, 0.0, 0.03571]
PeriodicSite: O (1.739, 1.23, 4.518) [0.5, 0.5, 0.03571]
PeriodicSite: Mg (0.0, 0.0, 4.518) [0.0, 0.0, 0.1071]
PeriodicSite: O (1.739, 1.23, 7.531) [0.5, 0.5, 0.1071]
PeriodicSite: Mg (0.0, 0.0, 7.531) [0.0, 0.0, 0.1786]
PeriodicSite: O (1.739, 1.23, 10.54) [0.5, 0.5, 0.1786]
PeriodicSite: Mg (0.0, 0.0, 10.54) [0.0, 0.0, 0.25]
PeriodicSite: O (1.739, 1.23, 13.56) [0.5, 0.5, 0.25]
PeriodicSite: Mg (0.0, 0.0, 13.56) [0.0, 0.0, 0.3214]
PeriodicSite: O (1.739, 1.23, 16.57) [0.5, 0.5, 0.3214]
PeriodicSite: Mg (0.0, 0.0, 16.57) [0.0, 0.0, 0.3929]
PeriodicSite: O (1.739, 1.23, 19.58) [0.5, 0.5, 0.3929]
PeriodicSite: Mg (0.0, 0.0, 19.58) [0.0, 0.0, 0.4643]
PeriodicSite: O (1.739, 1.23, 22.59) [0.5, 0.5, 0.4643]]
:sublattice:relax_slabs(3): [Structure Summary
Lattice
abc : 3.012274887854692 3.012274887854692 30.122748878546922
angles : 120.00000000000001 120.00000000000001 59.99999999999999
volume : 193.27193999999994
A : 2.608706576064084 0.0 -1.5061374439273467
B : 0.8695688586880276 2.4595121467478056 -1.5061374439273467
C : 0.0 0.0 30.122748878546922
pbc : True True True
PeriodicSite: Mg (-0.06335, -0.04479, 2.149) [-0.01821, -0.01821, 0.06954]
PeriodicSite: O (1.804, 1.275, -0.6412) [0.5186, 0.5186, 0.03057]
PeriodicSite: Mg (-0.04308, -0.03047, 5.197) [-0.01239, -0.01239, 0.1713]
PeriodicSite: O (1.762, 1.246, 2.298) [0.5064, 0.5064, 0.1269]
PeriodicSite: Mg (-0.03833, -0.0271, 8.217) [-0.01102, -0.01102, 0.2717]
PeriodicSite: O (1.776, 1.255, 5.335) [0.5105, 0.5105, 0.2281]
PeriodicSite: Mg (-0.03796, -0.02684, 11.23) [-0.01091, -0.01091, 0.3717]
PeriodicSite: O (1.788, 1.265, 8.369) [0.5141, 0.5141, 0.3292]
PeriodicSite: Mg (-0.01275, -0.009017, 14.29) [-0.003666, -0.003666, 0.4739]
PeriodicSite: O (1.762, 1.246, 11.34) [0.5066, 0.5066, 0.427], Structure Summary
Lattice
abc : 3.012274887854692 3.012274887854692 30.122748878546922
angles : 120.00000000000001 59.99999999999999 90.0
volume : 193.2719399999999
A : 2.608706576064084 0.0 1.5061374439273465
B : 0.8695688586880287 2.459512146747805 -1.5061374439273467
C : 0.0 0.0 30.122748878546922
pbc : True True True
PeriodicSite: Mg (-0.003667, 0.005186, 1.512) [-0.002108, 0.002108, 0.05042]
PeriodicSite: O (1.742, 1.226, 1.502) [0.5015, 0.4985, 0.0497]
PeriodicSite: Mg (0.004204, -0.005944, 4.511) [0.002417, -0.002417, 0.1495]
PeriodicSite: O (1.737, 1.233, 4.523) [0.4985, 0.5015, 0.1503]
PeriodicSite: Mg (-2.373e-07, 1.452e-07, 7.531) [-1.106e-07, 5.904e-08, 0.25]
PeriodicSite: O (1.739, 1.23, 7.531) [0.5, 0.5, 0.25]
PeriodicSite: Mg (-0.004206, 0.005949, 10.55) [-0.002419, 0.002419, 0.3505]
PeriodicSite: O (1.742, 1.226, 10.54) [0.5015, 0.4985, 0.3497]
PeriodicSite: Mg (0.003665, -0.005183, 13.55) [0.002107, -0.002107, 0.4496]
PeriodicSite: O (1.737, 1.233, 13.56) [0.4985, 0.5015, 0.4503], Structure Summary
Lattice
abc : 3.012274887854692 5.217413152128169 48.196398205675074
angles : 30.000000000000014 59.99999999999999 73.22134511903964
volume : 309.2351039999999
A : 2.608706576064084 0.0 1.5061374439273465
B : -0.869568858688028 2.4595121467478056 4.518412331782038
C : 0.0 0.0 48.196398205675074
pbc : True True True
PeriodicSite: Mg (0.1339, -0.01997, 2.027) [0.04861, -0.008121, 0.04131]
PeriodicSite: O (1.084, 1.0, 3.395) [0.5509, 0.4068, 0.01508]
PeriodicSite: Mg (0.1856, 0.2225, 4.95) [0.1013, 0.09047, 0.09106]
PeriodicSite: O (0.9559, 1.166, 6.628) [0.5245, 0.4742, 0.07668]
PeriodicSite: Mg (0.09665, 0.08853, 8.116) [0.04905, 0.036, 0.1635]
PeriodicSite: O (0.9216, 1.175, 9.7) [0.5125, 0.4777, 0.1405]
PeriodicSite: Mg (0.04673, 0.1156, 11.22) [0.03359, 0.04702, 0.2272]
PeriodicSite: O (0.8436, 1.125, 12.85) [0.4758, 0.4574, 0.2088]
PeriodicSite: Mg (-0.005373, 0.07126, 14.32) [0.007599, 0.02897, 0.2941]
PeriodicSite: O (0.7974, 1.125, 15.94) [0.4581, 0.4574, 0.2735]
PeriodicSite: Mg (-0.06382, 0.06227, 17.43) [-0.01603, 0.02532, 0.3598]
PeriodicSite: O (0.7609, 1.136, 19.01) [0.4456, 0.4618, 0.3373]
PeriodicSite: Mg (-0.07782, 0.05423, 20.47) [-0.02248, 0.02205, 0.4233]
PeriodicSite: O (0.7283, 1.092, 22.08) [0.4271, 0.4439, 0.4032]
PeriodicSite: Mg (-0.1775, 0.196, 23.65) [-0.04147, 0.07969, 0.4846]
PeriodicSite: O (0.727, 1.229, 25.1) [0.4452, 0.4996, 0.46], Structure Summary
Lattice
abc : 3.012274887854692 5.217413152128169 42.17184842996569
angles : 29.99999999999997 59.999999999999986 54.735610317245346
volume : 270.58071599999977
A : 2.608706576064084 0.0 1.5061374439273465
B : 0.8695688586880266 2.4595121467478043 4.51841233178204
C : 0.0 0.0 42.17184842996569
pbc : True True True
PeriodicSite: Mg (-0.02746, -0.07768, 1.554) [2.276e-07, -0.03158, 0.04023]
PeriodicSite: O (1.734, 1.216, 4.527) [0.5, 0.4945, 0.0365]
PeriodicSite: Mg (0.02554, 0.07223, 4.474) [1.088e-06, 0.02937, 0.1029]
PeriodicSite: O (1.746, 1.25, 7.518) [0.5, 0.5081, 0.106]
PeriodicSite: Mg (0.004413, 0.01248, 7.523) [1.247e-07, 0.005074, 0.1778]
PeriodicSite: O (1.736, 1.22, 10.55) [0.5, 0.4962, 0.1791]
PeriodicSite: Mg (5.245e-07, 2.488e-06, 10.54) [-1.362e-07, 1.012e-06, 0.25]
PeriodicSite: O (1.739, 1.23, 13.56) [0.5, 0.5, 0.25]
PeriodicSite: Mg (-0.004412, -0.01248, 13.56) [-5.311e-08, -0.005073, 0.3222]
PeriodicSite: O (1.742, 1.239, 16.56) [0.5, 0.5038, 0.3209]
PeriodicSite: Mg (-0.02554, -0.07224, 16.61) [-3.741e-08, -0.02937, 0.3971]
PeriodicSite: O (1.732, 1.21, 19.59) [0.5, 0.4919, 0.394]
PeriodicSite: Mg (0.02746, 0.07767, 19.53) [-2.13e-08, 0.03158, 0.4598]
PeriodicSite: O (1.744, 1.243, 22.58) [0.5, 0.5055, 0.4635]]
:parameter:<covalent._workflow.lattice.Lattice object at 0x2cf2d97f0>(4): <covalent._workflow.lattice.Lattice object at 0x2cf2d97f0>
:parameter:{"executor": "dask", "workflow_executor": "dask", "hooks": {}, "executor_data": {}, "workflow_executor_data": {}, "qelectron_data_exists": false}(5): {"executor": "dask", "workflow_executor": "dask", "hooks": {}, "executor_data": {}, "workflow_executor_data": {}, "qelectron_data_exists": false}
:postprocess:reconstruct(6): [Structure Summary
Lattice
abc : 3.012274887854692 3.012274887854692 30.122748878546922
angles : 120.00000000000001 120.00000000000001 59.99999999999999
volume : 193.27193999999994
A : 2.608706576064084 0.0 -1.5061374439273467
B : 0.8695688586880276 2.4595121467478056 -1.5061374439273467
C : 0.0 0.0 30.122748878546922
pbc : True True True
PeriodicSite: Mg (-0.06335, -0.04479, 2.149) [-0.01821, -0.01821, 0.06954]
PeriodicSite: O (1.804, 1.275, -0.6412) [0.5186, 0.5186, 0.03057]
PeriodicSite: Mg (-0.04308, -0.03047, 5.197) [-0.01239, -0.01239, 0.1713]
PeriodicSite: O (1.762, 1.246, 2.298) [0.5064, 0.5064, 0.1269]
PeriodicSite: Mg (-0.03833, -0.0271, 8.217) [-0.01102, -0.01102, 0.2717]
PeriodicSite: O (1.776, 1.255, 5.335) [0.5105, 0.5105, 0.2281]
PeriodicSite: Mg (-0.03796, -0.02684, 11.23) [-0.01091, -0.01091, 0.3717]
PeriodicSite: O (1.788, 1.265, 8.369) [0.5141, 0.5141, 0.3292]
PeriodicSite: Mg (-0.01275, -0.009017, 14.29) [-0.003666, -0.003666, 0.4739]
PeriodicSite: O (1.762, 1.246, 11.34) [0.5066, 0.5066, 0.427], Structure Summary
Lattice
abc : 3.012274887854692 3.012274887854692 30.122748878546922
angles : 120.00000000000001 59.99999999999999 90.0
volume : 193.2719399999999
A : 2.608706576064084 0.0 1.5061374439273465
B : 0.8695688586880287 2.459512146747805 -1.5061374439273467
C : 0.0 0.0 30.122748878546922
pbc : True True True
PeriodicSite: Mg (-0.003667, 0.005186, 1.512) [-0.002108, 0.002108, 0.05042]
PeriodicSite: O (1.742, 1.226, 1.502) [0.5015, 0.4985, 0.0497]
PeriodicSite: Mg (0.004204, -0.005944, 4.511) [0.002417, -0.002417, 0.1495]
PeriodicSite: O (1.737, 1.233, 4.523) [0.4985, 0.5015, 0.1503]
PeriodicSite: Mg (-2.373e-07, 1.452e-07, 7.531) [-1.106e-07, 5.904e-08, 0.25]
PeriodicSite: O (1.739, 1.23, 7.531) [0.5, 0.5, 0.25]
PeriodicSite: Mg (-0.004206, 0.005949, 10.55) [-0.002419, 0.002419, 0.3505]
PeriodicSite: O (1.742, 1.226, 10.54) [0.5015, 0.4985, 0.3497]
PeriodicSite: Mg (0.003665, -0.005183, 13.55) [0.002107, -0.002107, 0.4496]
PeriodicSite: O (1.737, 1.233, 13.56) [0.4985, 0.5015, 0.4503], Structure Summary
Lattice
abc : 3.012274887854692 5.217413152128169 48.196398205675074
angles : 30.000000000000014 59.99999999999999 73.22134511903964
volume : 309.2351039999999
A : 2.608706576064084 0.0 1.5061374439273465
B : -0.869568858688028 2.4595121467478056 4.518412331782038
C : 0.0 0.0 48.196398205675074
pbc : True True True
PeriodicSite: Mg (0.1339, -0.01997, 2.027) [0.04861, -0.008121, 0.04131]
PeriodicSite: O (1.084, 1.0, 3.395) [0.5509, 0.4068, 0.01508]
PeriodicSite: Mg (0.1856, 0.2225, 4.95) [0.1013, 0.09047, 0.09106]
PeriodicSite: O (0.9559, 1.166, 6.628) [0.5245, 0.4742, 0.07668]
PeriodicSite: Mg (0.09665, 0.08853, 8.116) [0.04905, 0.036, 0.1635]
PeriodicSite: O (0.9216, 1.175, 9.7) [0.5125, 0.4777, 0.1405]
PeriodicSite: Mg (0.04673, 0.1156, 11.22) [0.03359, 0.04702, 0.2272]
PeriodicSite: O (0.8436, 1.125, 12.85) [0.4758, 0.4574, 0.2088]
PeriodicSite: Mg (-0.005373, 0.07126, 14.32) [0.007599, 0.02897, 0.2941]
PeriodicSite: O (0.7974, 1.125, 15.94) [0.4581, 0.4574, 0.2735]
PeriodicSite: Mg (-0.06382, 0.06227, 17.43) [-0.01603, 0.02532, 0.3598]
PeriodicSite: O (0.7609, 1.136, 19.01) [0.4456, 0.4618, 0.3373]
PeriodicSite: Mg (-0.07782, 0.05423, 20.47) [-0.02248, 0.02205, 0.4233]
PeriodicSite: O (0.7283, 1.092, 22.08) [0.4271, 0.4439, 0.4032]
PeriodicSite: Mg (-0.1775, 0.196, 23.65) [-0.04147, 0.07969, 0.4846]
PeriodicSite: O (0.727, 1.229, 25.1) [0.4452, 0.4996, 0.46], Structure Summary
Lattice
abc : 3.012274887854692 5.217413152128169 42.17184842996569
angles : 29.99999999999997 59.999999999999986 54.735610317245346
volume : 270.58071599999977
A : 2.608706576064084 0.0 1.5061374439273465
B : 0.8695688586880266 2.4595121467478043 4.51841233178204
C : 0.0 0.0 42.17184842996569
pbc : True True True
PeriodicSite: Mg (-0.02746, -0.07768, 1.554) [2.276e-07, -0.03158, 0.04023]
PeriodicSite: O (1.734, 1.216, 4.527) [0.5, 0.4945, 0.0365]
PeriodicSite: Mg (0.02554, 0.07223, 4.474) [1.088e-06, 0.02937, 0.1029]
PeriodicSite: O (1.746, 1.25, 7.518) [0.5, 0.5081, 0.106]
PeriodicSite: Mg (0.004413, 0.01248, 7.523) [1.247e-07, 0.005074, 0.1778]
PeriodicSite: O (1.736, 1.22, 10.55) [0.5, 0.4962, 0.1791]
PeriodicSite: Mg (5.245e-07, 2.488e-06, 10.54) [-1.362e-07, 1.012e-06, 0.25]
PeriodicSite: O (1.739, 1.23, 13.56) [0.5, 0.5, 0.25]
PeriodicSite: Mg (-0.004412, -0.01248, 13.56) [-5.311e-08, -0.005073, 0.3222]
PeriodicSite: O (1.742, 1.239, 16.56) [0.5, 0.5038, 0.3209]
PeriodicSite: Mg (-0.02554, -0.07224, 16.61) [-3.741e-08, -0.02937, 0.3971]
PeriodicSite: O (1.732, 1.21, 19.59) [0.5, 0.4919, 0.394]
PeriodicSite: Mg (0.02746, 0.07767, 19.53) [-2.13e-08, 0.03158, 0.4598]
PeriodicSite: O (1.744, 1.243, 22.58) [0.5, 0.5055, 0.4635]]