mofbuilder.MetalOrganicFrameworkBuilder#

class mofbuilder.MetalOrganicFrameworkBuilder(comm=None, ostream=None, mof_family=None)[source]#

Bases: object

Orchestrates MOF building: load net and topology, place nodes and linkers, optimize, supercell, defects, write.

Set mof_family, node_metal, linker (xyz/molecule/SMILES), then call build() to get a Framework. sG: scaled and rotated net graph; eG: edge graph (V + EDGE nodes, XOO on edges); superG: supercell of sG.

Parameters:

comm (Optional[Any])
ostream (Optional[Any])
mof_family (Optional[str])

comm#: MPI communicator.

rank#: MPI rank of this process.

nodes#: MPI size (number of processes).

ostream#: Output stream for logging.

framework#: Framework instance (result of build()).

mof_family#: MOF family name (e.g. “HKUST-1”).

node_metal#: Metal type string for nodes.

dummy_atom_node#: Whether to add dummy atoms to nodes.

dummy_atom_node_dict#: Dict of dummy atom counts (set after node processing).

data_path#: Path to database directory.

frame_nodes#: FrameNode instance.

frame_linker#: FrameLinker instance.

frame_terminations#: FrameTermination instance.

frame_net#: FrameNet instance.

mof_top_library#: MofTopLibrary instance.

net_optimizer#: NetOptimizer instance.

mofwriter#: MofWriter instance.

defectgenerator#: TerminationDefectGenerator instance.

net_spacegroup#: Space group from net (set when net is loaded).

net_cell_info#: Cell parameters from net.

net_unit_cell#: 3x3 unit cell matrix from net.

net_unit_cell_inv#: Inverse of net_unit_cell.

node_connectivity#: Node connectivity from topology.

linker_connectivity#: Linker connectivity (topic) from topology.

net_sorted_nodes#: Sorted list of node names from net.

net_sorted_edges#: Sorted list of edges from net.

net_pair_vertex_edge#: Vertex-edge pairs from net.

linker_xyzfile#: Path to linker XYZ file (optional).

linker_molecule#: VeloxChem molecule for linker (optional).

linker_smiles#: SMILES string for linker (optional).

linker_charge#: Linker charge.

linker_multiplicity#: Linker multiplicity.

linker_center_data#: Center fragment data (set when linker is loaded).

linker_center_X_data#: Center X-atom data.

linker_outer_data#: Outer fragment(s) data.

linker_outer_X_data#: Outer X-atom data.

linker_frag_length#: Length of linker fragment.

linker_fake_edge#: Whether linker is fake (zero-length) edge.

node_data#: Node atom data (set when node is loaded).

node_X_data#: Node X-atom data.

termination#: Whether to use terminations.

termination_name#: Name of termination group (e.g. ‘acetate’).

termination_molecule#: Termination molecule (optional).

termination_data#: Termination atom data.

termination_X_data#: Termination X atoms.

termination_Y_data#: Termination Y atoms.

constant_length#: X-X bond length in Angstrom (default 1.54).

load_optimized_rotations#: Path to H5 file with saved rotations (optional).

skip_rotation_optimization#: If True, skip rotation optimization.

rotation_filename#: Path to save optimized rotations (optional).

frame_unit_cell#: 3x3 frame unit cell (set after build).

frame_cell_info#: Frame cell parameters.

supercell#: Supercell dimensions (nx, ny, nz).

remove_node_list#: List of node indices to remove (defects).

remove_edge_list#: List of edge indices to remove (defects).

_debug#: If True, print extra debug messages.

list_available_mof_families()[source]#

list_available_metals(mof_family=None)[source]#

Print available metals for the given (or current) MOF family from the topology library.

Parameters:: mof_family (str | None)
Return type:: None

list_available_terminations()[source]#

list_available_solvents()[source]#

load_framework()[source]#

optimize_framework()[source]#

make_supercell()[source]#

build()[source]#

Load net and topology, place nodes/linkers, optimize rotations and cell, build supercell (and defects). Returns self.framework.

Return type:: Framework