Import Materials from files in various formats

This tutorial explains how to import materials from files in various formats into the Materials Designer interface. With the help of notebook that uses ASE python package to extract structural information from files in multiple formats (CIF, POSCAR, etc., as supported by ASE). Some formats, like espresso-in and espresso-out can be inferred from the file content.

Step 0: Open Materials Designer

Start by opening an instance of the Materials Designer Interface for creating and designing new Materials structures on our platform.

Step 1: Open JupyterLite Environment

Open the JupyterLite Environment by navigating to "Advanced" > "JupyterLite Transformation" menu item in the Materials Designer interface.

Step 2: Open the Notebook

Open the "Materials import from files in ASE-supported formats" in the Introduction.ipynb notebook.

Step 3: Upload files

Double-click the uploads folder in the File Browser tab on the left to open it. Drag and drop the files you want to import into the field.

Step 4: Run the Notebook

Run the notebook by clicking the "Run All Cells" button in the toolbar or execute each cell by pressing "Shift + Enter" if you want to review results or change the code in the process.

Step 5: Review the Results and Submit

Materials should appear in the "Materials Out" dropdown at the bottom of the dialog. Select the material you want to work with and click "Submit" to load it into the Materials Designer.

In case ASE is unable to read the file, an error message will be printed stating the unreadable files and a table of available formats. In this case, you can try to fix the issue and re-run the notebook. The error with some files does not prevent other files from being read.

Additional Information

ASE

The information about ASE IO can be found here. The version of ASE used in the JupyterLite environment is 3.22.1 (as of 2024-04-05).

Supported Formats

ase.io.formats.ioformats provides the list of supported formats:

Format Name	File Extensions	Description
abinit-in	[]	ABINIT input file
abinit-out	[]	ABINIT output file
aims	['in']	FHI-aims geometry file
aims-output	[]	FHI-aims output
bundletrajectory	[]	ASE bundle trajectory
castep-castep	['castep']	CASTEP output file
castep-cell	['cell']	CASTEP geom file
castep-geom	['geom']	CASTEP trajectory file
castep-md	['md']	CASTEP molecular dynamics file
castep-phonon	['phonon']	CASTEP phonon file
cfg	[]	AtomEye configuration
cif	['cif']	CIF-file
cmdft	[]	CMDFT-file
cml	['cml']	Chemical json file
cp2k-dcd	['dcd']	CP2K DCD file
cp2k-restart	['restart']	CP2K restart file
crystal	['f34', '34']	Crystal fort.34 format
cube	['cube']	CUBE file
dacapo-text	[]	Dacapo text output
db	[]	ASE SQLite database file
dftb	[]	DftbPlus input file
dlp4	['config']	DL_POLY_4 CONFIG file
dlp-history	[]	DL_POLY HISTORY file
dmol-arc	[]	DMol3 arc file
dmol-car	['car']	DMol3 structure file
dmol-incoor	[]	DMol3 structure file
elk	[]	ELK atoms definition from GEOMETRY.OUT
elk-in	[]	ELK input file
eon	['con']	EON CON file
eps	[]	Encapsulated Postscript
espresso-in	['pwi']	Quantum espresso in file
espresso-out	['out', 'pwo']	Quantum espresso out file
exciting	[]	exciting input
extxyz	['xyz']	Extended XYZ file
findsym	[]	FINDSYM-format
gamess-us-out	[]	GAMESS-US output file
gamess-us-in	[]	GAMESS-US input file
gamess-us-punch	['dat']	GAMESS-US punchcard file
gaussian-in	['com', 'gjf']	Gaussian com (input) file
gaussian-out	['log']	Gaussian output file
acemolecule-out	[]	ACE output file
acemolecule-input	[]	ACE input file
gen	[]	DFTBPlus GEN format
gif	[]	Graphics interchange format
gpaw-out	[]	GPAW text output
gpumd	[]	GPUMD input file
gpw	[]	GPAW restart-file
gromacs	['gro']	Gromacs coordinates
gromos	['g96']	Gromos96 geometry file
html	[]	X3DOM HTML
json	['json']	ASE JSON database file
jsv	[]	JSV file format
lammps-dump-text	[]	LAMMPS text dump file
lammps-dump-binary	[]	LAMMPS binary dump file
lammps-data	[]	LAMMPS data file
magres	[]	MAGRES ab initio NMR data file
mol	[]	MDL Molfile
mp4	[]	MP4 animation
mustem	['xtl']	muSTEM xtl file
mysql	[]	ASE MySQL database file
netcdftrajectory	[]	AMBER NetCDF trajectory file
nomad-json	['nomad-json']	JSON from Nomad archive
nwchem-in	['nwi']	NWChem input file
nwchem-out	['nwo']	NWChem output file
octopus-in	[]	Octopus input file
proteindatabank	['pdb']	Protein Data Bank
png	[]	Portable Network Graphics
postgresql	[]	ASE PostgreSQL database file
pov	[]	Persistance of Vision
prismatic	[]	prismatic and computem XYZ-file
py	[]	Python file
sys	[]	qball sys file
qbox	[]	QBOX output file
res	['shelx']	SHELX format
rmc6f	['rmc6f']	RMCProfile
sdf	[]	SDF format
siesta-xv	[]	Siesta .XV file
struct	[]	WIEN2k structure file
struct_out	[]	SIESTA STRUCT file
traj	['traj']	ASE trajectory
turbomole	[]	TURBOMOLE coord file
turbomole-gradient	[]	TURBOMOLE gradient file
v-sim	['ascii']	V_Sim ascii file
vasp	['poscar']	VASP POSCAR/CONTCAR
vasp-out	[]	VASP OUTCAR file
vasp-xdatcar	[]	VASP XDATCAR file
vasp-xml	[]	VASP vasprun.xml file
vti	[]	VTK XML Image Data
vtu	['vtu']	VTK XML Unstructured Grid
wout	[]	Wannier90 output
x3d	[]	X3D
xsd	[]	Materials Studio file
xsf	[]	XCrySDen Structure File
xtd	[]	Materials Studio file
xyz	[]	XYZ-file