mofbuilder.md.GromacsForcefieldMerger#
- class mofbuilder.md.GromacsForcefieldMerger(comm=None, ostream=None)[source]#
Bases:
objectMain class responsible for assembling and merging GROMACS forcefield files for MOF simulations.
- Parameters:
comm (Any | None)
ostream (veloxchem.outputstream.OutputStream | None)
- comm#
MPI communicator for parallel execution.
- Type:
mpi4py.MPI.Comm
- rank#
Rank of the current MPI process.
- Type:
int
- nodes#
Total number of MPI processes.
- Type:
int
- ostream#
Output stream for logging.
- Type:
OutputStream
- database_dir#
Directory containing reference forcefield database.
- Type:
Optional[str]
- target_dir#
Output directory for all generated files.
- Type:
Optional[str]
- node_metal_type#
Type of metal node in the MOF.
- Type:
Optional[str]
- dummy_atom_node#
Whether to use dummy atoms for the node (default: False).
- Type:
bool
- termination_name#
Name of termination group for the structure.
- Type:
Optional[str]
- linker_itp_dir#
Directory holding linker .itp files.
- Type:
str
- linker_name#
Name of the linker molecule.
- Type:
Optional[str]
- residues_info#
Dictionary mapping residue names to copy number.
- Type:
Optional[Dict[str, int]]
- mof_name#
Name for the MOF/model (used for the top file).
- Type:
Optional[str]
- other_residues#
List of additional residues that can be included.
- Type:
List[str]
- solvents_name#
List or tuple of solvent names.
- Type:
Optional[Sequence[str]]
- solvents_dict#
Maps solvent names to their info, including Molecule object.
- Type:
Optional[Dict[str, Dict[str, Any]]]
- _debug#
If True, print extensive debug information.
- Type:
bool
- top_path#
The path to the generated .top file (written upon generation).
- Type:
Optional[Path]