AuToGraFS

Original publication: "Automatic Topological Generator for Framework Structures".

This version is under active development. Bug hunting is very much going on, and there are still some old functionalities that are not yet reimplemented.

Installation

pip install AuToGraFS

For a development install:

git clone https://github.com/DCoupry/autografs.git
cd autografs
pip install -e ".[dev]"

Requirements

• Python >= 3.13
• ase, scipy, numpy, networkx, pandas, pymatgen, dill

Examples

From any Python script or command line:

from autografs import Autografs

mofgen = Autografs()
mof = mofgen.make(
    topology_name="pcu",
    sbu_names=["Zn_mof5_octahedral", "Benzene_linear"]
)
mof.write()

Custom databases can be accessed by passing the path during instantiation:

mofgen = Autografs(topology_path="my_topo_path", sbu_path="my_sbu_path")

When looping over both SBU and topologies, it is better to set the topology directly:

for topology_name in my_topology_names:
    mofgen.set_topology(topology_name=topology_name)
    for sbu_names in my_sbu_names:
        mof = mofgen.make(sbu_names=sbu_names)

Probabilistic SBU Selection

It is possible to pass more than one SBU of each shape, optionally with an associated probabilistic weight. This weight defaults to 1.0 / (number of similar SBU).

mof = mofgen.make(
    topology_name="pcu",
    sbu_names=[
        "Zn_mof5_octahedral",
        ("Benzene_linear", 2.0),
        ("Acetylene_linear", 0.5)
    ]
)
mof.write()

This is particularly helpful in combination with an initial supercell for statistically introducing defects:

mof = mofgen.make(
    topology_name="pcu",
    sbu_names=[
        ("Zn_mof5_octahedral", 2.0),
        ("defect_octahedral", 0.5),
        "Benzene_linear"
    ],
    supercell=(3, 3, 3)
)
mof.write()

Supercell Generation

Supercells can also be generated post-alignment:

supercell_6x6x6 = mof.get_supercell(m=2)
supercell_6x6x6.write()

Direct Modifications

Defects and modifications can be introduced at any time directly:

# Get the site directly
sbu = mof[7]

# Change all hydrogens to Fluorine
atoms = sbu.atoms.copy()
symbols = atoms.get_chemical_symbols()
symbols = [s if s != "H" else "F" for s in symbols]
atoms.set_chemical_symbols(symbols)

# By setting the atoms back, mmtypes and bonding are updated
sbu.set_atoms(atoms=atoms, analyze=True)

# Delete another SBU. H will cap the dangling bits.
del mof[8]
mof.write()

Rotation, Functionalization, and Flipping

# Rotate SBU 7 by 45 degrees
mof.rotate(index=7, angle=45.0)

# If a C* axis or reflection plane is detected in SBU 8, flip around it
mof.flip(index=8)

# Replace all functionalizable H sites with NH2
nh2 = mofgen.sbu["NH2_point_group"]
sites = mof.list_functionalizable_sites(symbol="H")
for site in sites:
    mof.functionalize(where=site, fg=nh2)
mof.write()

Monitoring Bonds and Types

from ase.visualize import view

# With the dummies included
mmtypes = mof.get_mmtypes()
bonds = mof.get_bonds()

# Without the dummies
atoms, bonds, mmtypes = mof.get_atoms(dummies=False)
view(atoms)

Direct Slot Mapping

If you know the shape of each slot and its index within the topology:

topology = mofgen.get_topology(topology_name="pcu")
sbu_dict = {}
for slot_index, slot_shape in topology.shapes.items():
    # Do something to choose an SBU
    sbu_dict[slot_index] = "chosen_sbu_name"

mof = mofgen.make(topology_name="pcu", sbu_dict=sbu_dict)
mof.write()

Accessing Databases

sbudict = mofgen.sbu
topodict = mofgen.topologies

Or using tools to find compatible objects:

sbu_list = mofgen.list_available_sbu(topology_name="pcu")
topology_list = mofgen.list_available_topologies(
    sbu_names=["Zn_mof5_octahedral", "Benzene_linear"]
)

Multi-Component Frameworks

AuToGraFS is aware of topologically equivalent positions and can generate multi-component frameworks:

sbu_dicts = mofgen.list_available_frameworks()
for sbu_dict in sbu_dicts:
    mof = mofgen.make(sbu_dict=sbu_dict)
    mof.view()

Atom Typing Utility

A useful utility assigns bond orders and UFF atom types to a structure:

from autografs.mmanalysis import analyze_mm
bonds, types = analyze_mm(sbu=mofgen.sbu["Zn_mof5_octahedral"])

License

MIT License - see LICENSE.txt for details.