MOF Builder - VeloxChem Docs

import veloxchem as vlx

mof = vlx.MofBuilder()

There are several predefined families of MOFs defined in VeloxChem.

mof.show_available_mof_families()

Available MOF Family:
UiO-66 UiO-67 UiO-68 PCN-222 MOF-545 NU-1000 PCN-224 MOF-525 MOF-535 MOF-808 MOF-818 PCN-777 NU-901 MIL-100 PCN-228 PCN-229 PCN-230 MIL-101

To build a target MOF, you need to:

Assign MOF family.
Assign the node metal type.
Specify the name of the file containing the linker in xyz-format.
Set the supercell size, where (1,1,1) refers to the primitive cell.

mof.mof_family = "UiO-66"
mof.node_metal = "Zr"
mof.linker_xyz_file = "../input_files/linker.xyz"
mof.supercell = (1, 1, 1)

mof.build()

UiO-66 selected
available metal nodes: ['Zr', 'Hf']
please select a metal node
will search template cif files in /Users/panor/miniconda3/envs/vlxman/lib/python3.12/site-packages/veloxchem/database/template_database
fcu.cif is found in template_database
fcu.cif will be used for MOF building
Zr node is selected
found the file including ['12c', 'Zr']
File copied from /Users/panor/miniconda3/envs/vlxman/lib/python3.12/site-packages/veloxchem/database/nodes_database/12c_Zr.pdb to nodes/12c_Zr.pdb
nodes/12c_Zr.pdb is fetched
default node without dummy atoms will be usednodes/12c_Zr.pdb
nodes will be saved in nodes
found the file including ['12c', 'Zr']
2 is selected for linker splitting
center is a cycle
center_nodes: [6, np.int64(7), np.int64(8), np.int64(30), 29, 27, 10, np.int64(11), np.int64(12), np.int64(13), np.int64(19), 18, 16, 15] center_class: cycle 2
[12, 13]
ditopic linker: center is a cycle
find connected X in edge:   24
find connected X in edge:   39
pairXs: [24, 39]
linker_center_frag: 46 [18, 33]
linker edge fragment edges/diedge.pdb is saved and will be used for MOF building
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                     Preparation is completed                     
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MOF builder is ready to build
ditopic mof builder driver is called
 no symmetry operation
 no symmetry operation
trying to read pdb file nodes/12c_Zr.pdb
trying to read pdb file edges/diedge.pdb
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                     start to optimize the rotations                     
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optimize_rotations_step1
optimize_rotations information:
opt_method: L-BFGS-B


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                     rotations optimization completed                     
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                     start to optimize the cell parameters                     
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Optimized New Cell Parameters: [39.35195 39.35195 39.35195 90.      90.      90.     ] 
Template Cell Parameters: [14.1421, 14.1421, 14.1421, 90.0, 90.0, 90.0]
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                     cell parameters optimization completed                     
--------------------------------------------------------------------------------
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                Building time cost: 0.70098 seconds 
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main fragment of the MOF cell is kept
node_res_num:  14
edge_res_num:  36
term_res_num:  96

mof.show(residue_indices=True, residue_names=False)

node_res_num:  14
edge_res_num:  36
term_res_num:  96

We can introduce defects by removing linkers or nodes. As an example, let us remove the four linkers facing the viewer.

mof.remove(linkers=[18, 24, 30, 36], update_node_termination=True)

mof.show(residue_indices=True)

node_res_num:  14
edge_res_num:  32
term_res_num:  104

Input files can be written for subsequent molecular dynamics simulations using GROMACS.

mof.write_gromacs_files()