AuToGraFS

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

.. _here: http://pubs.acs.org/doi/abs/10.1021/jp507643v

__ here_

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

TODO:

Medium priority:

• offer an isotropic scaling option
• the symmetry axes detection has trouble with planar shapes
• more robust mmanalysis module

Low priority:

• unit testing coverage is non-existant
• documentation writing
• better handling of the databases:
  • precomputing sbu-topologies correspondance
  • use better format than pickle

Install:

.. highlight:: bash

$ pip install --user --upgrade AuToGraFS

For a manual install, first install the dependencies,

1. python >=3.4
2. ase, scipy, numpy<1.15.0

then clone this repository and add it to you pythonpath::

$ cd $HOME
$ git clone https://github.com/DCoupry/autografs.git
$ export PYTHONPATH=$HOME/autografs:$PYTHONPATH`

Examples:

From any python script or command line:

.. highlight:: python

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 instanciation

mofgen = Autografs(topology_path="my_topo_path",sbu_path="my_sbu_path") mof = mofgen.set_topology(topology_name=custom_topology_name,sbu_name=custom_sbu_names)

When looping over both SBU and topologies, it is better to set the topology directly (here, my_topologies and my_sbu_names are appropriate dummy colletions)

for topologi_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)

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 can also be generated post-alignement, carrying everything done before.

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

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()

Methods are also available for the rotation, functionalization and flipping.

rotate the sbu 7 buy 45 degrees

mof.rotate(index=7,angle=45.0)

if a C* axis or reflection plane is detected

in the 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(self,symbol="H") for site in sites: mof.functionalize(where=site,fg=nh2) mof.write()

At any moment, we can monitor the bonding matrix and mmtypes, or get a cleaned version without dummies.

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)

If you know the shape of each slot and its index within the topology, it is possible to directly pass a dictionary mapping the SBU to a particular slot.

method to investigate the topology shapes and slots

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"

now pass it directly

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

You can access the databases as dictionaries using the following:

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"])

AAuToGraFS is also aware of topologically equivalent positions, and can generate multi components frameworks with minimal effort.

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

A useful utility is the Atom typer, which 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"])