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Upload Structures¶

We support uploading structural data in the file formats containing the lattice geometry and the ionic positions of the crystal structure under investigation.

At present CIF, POSCAR and XYZ formats are supported ¹, ², ³. POSCAR format represents a standard way of defining and inputting crystal structure information to VASP code, one of the simulations engines incorporated into our platform. XYZ files are a common format for defining and inputting non-periodic molecular structures into simulation engines, such as NWChem⁴.

Open Upload Dialog¶

Open the Account Profile page and navigate to "Materials" tab. Then choose upload tool in the top right actions toolbar.

Select Files¶

Click Select Items tool in the actions toolbar, to open a file upload dialog. Through this dialog, select one or multiple files from the local filesystem. The files are processed by the web browser and arranged in a list prepared to be uploaded to our platform. This list also contains information about whether a certain file has already been used for uploading structural information before to avoid unnecessary repetitions.

Expand Content¶

Textual data contained in each file can be further visualized by clicking its corresponding entry, and then collapsed back by clicking second time. The same functionality can be accessed through Expand and Collapse tools located in the top-right actions toolbar of the page, upon selection of the relevant structure file.

Search¶

When large sets of files need to be imported at a single time, particular entries can be retrieved from the resulting list by filtering through the text bar at the top of the screen.

Tag¶

Users may tag structures with a list of keywords. This is especially resourceful when large datasets of imported files need to be retrieved or filtered later. The general guidelines for entering tags and attaching them to entities are presented here.

Tagging a Structure as Non-Periodic¶

Users may wish to create a non-periodic structure when they upload a new structure by adding "non-periodic" as a tag.

Set Filename Using File Content¶

A common feature of POSCAR and XYZ files is that the name of a structure may be written into the file itself. In POSCAR files the first line of the file often contains a string identifying the material. In XYZ files the second line of the file often contains a string identifying the material. To update the name of a file based on the contents (first line of a POSCAR file, or second line of an XYZ file) the user can select the button.

For example:

Original Name: material_0001.poscar

File Content:

H2O
1.0
  10.583540000     0.000000000     0.000000000
   0.000000000    10.583540000     0.000000000
   0.000000000     0.000000000    12.700250000
O H
1 2
direct
   0.000000000    0.500000000    0.000000000  O
   0.043139000    0.431029000    0.043078000  H
   0.036635000    0.576406000    0.035949000  H

New Name: H2O.poscar

Upload Files¶

Next, the selected files can be uploaded to the platform by clicking Upload in the actions toolbar.

View Materials¶

Once the files have been imported, they are added as entries to the Materials collection. The name of the material is read from the imported file, if possible. Chemical formula is used as a backup option.

Animation¶

The aforementioned steps are demonstrated in the animation below.