A rust-written backend lib for edit and generation of lattice 3D-models compatible with CASTEP and Materials Studio.
This library is 100% written in rust. Currently, it has the following features:
1. I/O of existing .msi format model files. However the format for atom parsing is strict for the moment.
2. Edit atoms and lattice information in the model.
1. Edit the element information, atom ID, xyz coordinates of target atom.
2. Read/Write the lattice vectors.
3. Geometry transformation of the model:
1. Translation to desired positions
2. Rotate by axis-angle definition.
4. Place any molecules into a lattice, with necessary information provided:
1. The number and identities of atoms used to coordinate with the lattice.
2. The geometry information to determine the molecule direction in 3d space.
5. Export the seedfiles for CASTEP task, including:
- *.cell - necessary file for CASTEP task. Can be visualized in many simple and lightweight model viewing software. E.g. VESTA.
- *.trjaux, *.kptaux
- *.param
- *.msi - can be visualized in Materials Studio.
- Copy potential files used for CASTEP standalone mode. (Potential files are not provided and included in this repository and library)
- Miscellaneous files.
- Auto-generation of a perl script to instruct the Materials Studio to generate .xsd from .msi.
6. Parallel batch processing for model edit, molecule placement onto the lattice, and exports, supported by rayon.
- The detailed workflow for iteration is implemented by yourself.
7. Configure with YAML format files.
YAML filesThis lib is designed to be controlled with specific YAML files.
YAML file for project level control provides the following fields:base_model_loc: path to the base model msi file. This lattice model is used for the consequent batch editing and adsorbate placement.element_table_loc: path to the element table YAML file. It will include the elements that will be involved in your project.adsorbate_table_loc: path to the adsorbate information YAML file. It records the necessary information to deal with the placement of adsorbates.potentials_loc: path to the CASTEP potential files directory.export_loc: path to export your results.coord_sites: An array recording the target coordination sites that will be used in your lattice models. It has the following format for example:
coord_sites:
- name: c1
atom_id: 41
- name: c2
atom_id: 42
The name field is for naming your exported models. The atom_id field is consistent with the id in msi file, which is one-indexed.coord_cases: You will describe the possible coordination cases between the lattice and adsorbates. Currently, the library is designed to handle cases with coordination atoms up to two. For example:
coord_cases:
<ul>
<li>name: double
cases: [[41,42], [42,54], [54,53], [53,52], [41, 40], [41, 73], [42, 73]]</li>
<li>name: single
cases: [[41, null], [42, null], [54, null], [53, null], [52, null], [40, null], [73, null]]
This YAML describes the necessary information of elements, for writing cell and finding corresponding potential files.
Example structures:
Element_info:
- element: C
atomic_num: 6
LCAO: 2
mass: 12.0109996796
pot: C_00PBE.usp
spin: 0
- element: H
atomic_num: 0
LCAO: 1
mass: 1.0080000162
pot: H_00PBE.usp
spin: 0
This YAML file describes the necessary information about the adsorbate, which is key to the placement workflow of adsorbates onto the lattice.
Example structures: ``` directory: C2pathwaysads Adsorbates: - name: CO coordAtomIds: [1] stemAtomIds: [1,2] planeAtomIds: [1,2,2] vertical: true bSym: false upperAtomId: 2 atomNums: 2 pathName: ethylene - name: CHO coordAtomIds: [1] stemAtomIds: [2, 3] planeAtomIds: [1, 2, 3] vertical: true bSym: false upperAtomId: 2 atomNums: 3 pathName: ethylene
``
Thedirectoryfield tells the code where to locate the adsorbatemsifiles. ThepathNamefield helps the code to find the adsorbate: Currently this lib is designed to find the adsorbate according to the path:./{directory}/{pathName}path/{adsorbatename}.msi`.