File Management

This article introduces how to manage files on Bohrium.

Click the Files button on the left sidebar of Bohrium to enter the File Management interface:

On this page, you can perform basic operations such as uploading, downloading, moving, copying, renaming, and deleting files in the /personal disk of the node. Additionally, you can preview and edit online both text files and structured files.

The file types and operations supported by Bohrium are detailed in the table below:

File Types	File Formats	Supported Operations
Structured Files	POSCAR, CONTCAR, CIF, XYZ	Online preview and edit
	dump, lammpstrj, pdb, sdf, mol, mol2	Online preview
Text Files	PY, CPP, JSON, LOG, XML, TXT and most other text formats	Online preview and edit
Image Files	JPEG, PNG, BMP, GIF, SVG	Online preview

The recognition rules adopted by Bohrium for identifying structural files are as follows:

• VASP Structure File Recognition

  • Files with the uppercase POSCAR or CONTCAR in the filename.
  • Files with the suffixes poscar, contcar, or vasp.

• LAMMPS Trajectory File Recognition

  • Files with the suffixes dump or lammpstrj.
  • Files with the prefix lammpstrj.

• Recognition of Other Structural Files

  • Files with the suffixes cif, pdb, sdf, mol, mol2, or xyz.

File download and upload

Download

Select the file in the Bohrium directory tree, and right-click Download to download the file from the /personal disk to your local computer.

Upload

On Bohrium, you can upload local files or folders to the /personal disk using three methods:

1. Click the Upload button to upload files and folders

2. Select the folder in the directory tree and right-click Upload

3. Drag and drop files or folders directly to the /personal directory tree to upload

Structured file visualization

Online preview

For structural files such as POSCAR, dump, xyz, and mol2, double-click the desired file in the directory tree on the left side of the Bohrium file management page to conveniently and quickly preview the structure.

In preview mode, you can view the lattice information of the structure. Additionally, you can translate and rotate the structure by holding Ctrl while dragging the mouse and simply dragging the mouse, respectively.

When the mouse hovers over an atom, the element name and coordinates of the atom will be displayed. After clicking to select the atom, its information will also be displayed in the structure information column on the right.

Online edit

Specifically, for POSCAR, CONTCAR, CIF, and single-frame structured XYZ format files, Bohrium now supports online editing of these structured files.

Click the slider on the left side of Start editing to enter editing mode, and then you can edit the structure file online. After editing, click the slider again to Save the file and finish editing.

In edit mode, you can modify the lattice size, add atom, edit atom and delete atom in the structure file.

Edit lattice

In edit mode, click the edit icon located to the right of Lattice to modify the size of the lattice.

Note: When editing the lattice, the distance between atoms will also be scaled proportionally.

Add atom

In edit mode, click Add Atom in the structure information column on the right. Select an atom from the periodic table and enter its Cartesian or fractional coordinates to add the atom to the structure file.

Edit Atom

In edit mode, after selecting an atom to be edited, click the Edit icon in the atom information column to modify the atom type and coordinates.

Delete atom

In edit mode, after selecting an atom to be edited, click the Delete icon in the atom information column or press the Del key to delete the atom.