where can I find a file for molecules e.g: H2
For solids, I am using AMCSD (American Mineralogist Crystal Structure Database), but where can I find molecule files?
Add a comment
|
2 Answers
$\begingroup$
$\endgroup$
2
It is easy to create input of $\ce{H2}$ molecule inside QE input file directly or Generate cif or xyz file using ASE, VESTA, ATOMSK and other tool
from ase import build
model=build.molecule('H2',vacuum=5)
model.write('H2.cif',format='cif')
QE input
&control
calculation = 'relax'
prefix = 'h2'
pseudo_dir = '/home/anonymous/quantumEspresso_2019/SSSP_precision_pseudos'
/
&system
ibrav=1, celldm(1) =20,
nat=2, ntyp=1,
ecutwfc=30.0
/
&electrons
conv_thr=1e-8
/
&ions
ion_dynamics='bfgs'
/
ATOMIC_SPECIES
H 1.00784 H_ONCV_PBE-1.0.oncvpsp.upf
ATOMIC_POSITIONS (angstrom)
H 0.00 0.00 0.00
H 1.00 0.00 0.00
K_POINTS (automatic)
1 1 1 0 0 0
-
$\begingroup$ When do you used this code: "model=build.molecule('H2',vacuum=5) model.write('H2.cif',format='cif')" An XYZ file was created? $\endgroup$ Nov 11, 2022 at 10:27
-
$\begingroup$ Its cif format. There are several format you can export, check ase manual. $\endgroup$ Nov 11, 2022 at 12:28
$\begingroup$
$\endgroup$
If you need structures for other, more complex, molecules, you can use several online databases like:
ZINC
Welcome to ZINC, a free database of commercially-available compounds for virtual screening. ZINC contains over 230 million purchasable compounds in ready-to-dock, 3D formats. ZINC also contains over 750 million purchasable compounds you can search for analogs in under a minute.
ChemSpider
ChemSpider is a free chemical structure database providing fast text and structure search access to over 100 million structures from hundreds of data sources.
You can download your structure from one of these sites and then convert to QE input format.
