Install and Use ASE (Atomic Simulation Environment) in Ubuntu Linux

To install, I tried,

pip install --upgrade --user ase

/home/user/...../pip/_vendor/requests/__init__.py:83: RequestsDependencyWarning: Old version of cryptography ([1, 2, 3]) may cause slowdown.
  warnings.warn(warning, RequestsDependencyWarning)
Collecting ase
  Downloading https://files.pythonhosted.org/packages/b4/52/df21f492fbd/ase-3.18.0.tar.gz (1.8MB)
    100% |████████████████████████████████| 1.8MB 21.2MB/s 
    Complete output from command python setup.py egg_info:
    Python 3.5 or later is required!
    
    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-install-tSeI9W/ase/
You are using pip version 18.0, however version 19.2.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.

Then, I tried since "Python 3.5 or later is required!" is given.

pip3 install --upgrade --user ase

Now, I get

Installing collected packages: ase
  Found existing installation: ase 3.17.0
    Uninstalling ase-3.17.0:
      Successfully uninstalled ase-3.17.0
Successfully installed ase-3.18.0

(Earlier I have installed ase 3.17.0. Now it is updated to 3.18.0)


Then I tested the installation using

ase test

========== Summary ==========
Number of tests   317
Passes:           229
Failures:           0
Errors:             0
Skipped:           88
=============================
Test suite passed!
Time elapsed: 167.4 s

Now, ase is successfully installed.

Now, how to use for calculations? Lets try.

Now I tested ase in real calculation.

I checked the example given in this page https://wiki.fysik.dtu.dk/ase/tutorials/surface.html

Saved following script in a file (ase_example.py)

from ase import Atoms
from ase.calculators.emt import EMT
from ase.constraints import FixAtoms
from ase.optimize import QuasiNewton
from ase.build import fcc111, add_adsorbate

h = 1.85
d = 1.10

slab = fcc111('Cu', size=(4, 4, 2), vacuum=10.0)

slab.set_calculator(EMT())
e_slab = slab.get_potential_energy()

molecule = Atoms('2N', positions=[(0., 0., 0.), (0., 0., d)])
molecule.set_calculator(EMT())
e_N2 = molecule.get_potential_energy()

add_adsorbate(slab, molecule, h, 'ontop')
constraint = FixAtoms(mask=[a.symbol != 'N' for a in slab])
slab.set_constraint(constraint)
dyn = QuasiNewton(slab, trajectory='N2Cu.traj')
dyn.run(fmax=0.05)

print('Adsorption energy:', e_slab + e_N2 - slab.get_potential_energy())

Then, I run the python script (ase_example.py) as follow.

python3 ase_example.py

Now, I got following output.

                Step[ FC]     Time          Energy          fmax
*Force-consistent energies used in optimization.
BFGSLineSearch:    0[  0] 12:55:55       11.689927*       1.0797
BFGSLineSearch:    1[  2] 12:55:55       11.670814*       0.4090
BFGSLineSearch:    2[  4] 12:55:55       11.625880*       0.0409
Adsorption energy: 0.32351942231809083

This means that, the installation is successful and ready for calculations.
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