atomic simulation enviornment

8/19/2019 Atomic Simulation Enviornment

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Atomic Simulation Environment - a Python library

Modern Tools for Spectroscopy on Advanced MaterialsLouvain-la-Neuve, September 15-17, 2014

Jens Jørgen Mortensen

Department of Physics

Technical University of Denmark

Overview of ASE

The Python language

The Atoms object

Building stuff (molecules, surfaces, ...)Doing stuff with atoms (MD, optimization, ...)

Databases

Installing ASE

Development of ASE


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What is ASE?

ASE is a Python library for working with atoms:

A S E p a c k a g e

A t o m s

p o s i t i o n s ,

a t o m i c n u m b e r s ,

. . .

C o n s t r a i n t s

F i x e d a t o m s ,

b o n d s , . . .

C a l c u l a t o r

A b i n i t , . . . , V A S P

F i l e I O

x y z , c i f , . . .

M o l e c u l a r D y n a m i c s

O p t i m i z a t i o n

V i s u a l i z e

R e a c t i o n p a t h s

N E B , D i m e r

V i b r a t i o n s

I n f r a r e d ,

P h o n o n s

A n a l y s i s

D O S , S T M i m a g e s

http://wiki.fysik.dtu.dk/ase

http://wiki.fysik.dtu.dk/asehttp://wiki.fysik.dtu.dk/ase


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A recipe for your atoms

from ase import Atoms

from ase.optimize import BFGS

from ase.calculators.nwchem import NWChem

from ase.io import write

h2 = Atoms(’H2’,

positions=[(0, 0, 0),

(0, 0, 0.7)])

h2.calc = NWChem(xc=’PBE’)

opt = BFGS(h2)

opt.run(fmax=0.02)write(’H2.xyz’, h2)

Units: eV and Å.


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An interactive recipe for your atoms

>>> from ase import Atoms

>>> from ase.optimize import BFGS

>>> from ase.calculators.nwchem import NWChem

>>> from ase.io import write

>>> h2 = Atoms(’H2’,

positions=[(0, 0, 0),

(0, 0, 0.7)])

>>> h2.calc = NWChem(xc=’PBE’)

>>> opt = BFGS(h2)

>>> opt.run(fmax=0.02)

BFGS: 0 19:10:49 -31.435229 2.2691

BFGS: 1 19:10:50 -31.490773 0.3740BFGS: 2 19:10:50 -31.492791 0.0630

BFGS: 3 19:10:51 -31.492848 0.0023

>>> write(’H2.xyz’, h2)

>>> h2.get_potential_energy()

-31.492847800329216


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What is Python?

http://www.python.org

Interpreted language

Dynamically typed

Easy to read and write, and very expressive

Great for scripting a calculation

Great for small and large programsOptimized for programmer productivity

Can be extended in C/C++/Fortran

General purpose language

Numpy: Base N-dimensional array packageScipy: Fundamental library for scientific computing

Matplotlib: Comprehensive 2D Plotting

Sympy: Symbolic mathematics.

http://www.python.org/http://www.python.org/


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The Atoms objectA t o m s

. . .

C o n s t r a i n t s C a l c u l a t o r

What’s inside?

Positions, atomic numbers, velocities, masses, initial magneticmoments, charges, tags

Unit cell

Boundary conditions

(Calculator)

(Constraints)

M h d d ib f h A bj


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Methods and attributes of the Atoms object

List methods:

a.pop() # remove last atom

a.append(’Xe’) # append xenon atom

a.extend(Atoms(’H2’)) # append 2 hydrogens

a[1] # second atom

del a[-3:] # delete three last atoms

Other methods: repeat(), translate(), center(),rotate(), get_distance(), get_angle(), get_momentsof_inertia(), ...Special attributes: positions, numbers, cell, pbc (Numpy n-darrays)

x1, x2 = a.positions[-2:, 0] # x-coords of

# last two atoms

a.positions[-2:, 0] += 0.1 # translate atoms

a.positions[:, 2].max() # maximum z-coord

B ildi h A bj


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Building the Atoms object

A t o m s

p o s i t i o n s ,


. . .

F i l e I O

x y z , c i f , . . .

D a t a b a s e

b u l k ( )

m o l e c u l e ( )

n a n o r i b b o n ( )

s u r f a c e ( )

B ildi th At bj t


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Building the Atoms object ...

from ase import Atoms

h2 = Atoms(’H2’, [(0, 0, 0), (0, 0, 0.74)])

from ase.structure import molecule

water = molecule(’H2O’)

from ase.lattice import bulk

si2 = bulk(’Si’)

from ase.lattice.spacegroup import crystal

rutile = crystal([’Ti’, ’O’],

basis=[(0, 0, 0), (u, u, 0)],

spacegroup=136,

cellpar=[a, a, c,

90, 90, 90])from ase.lattice.surface import fcc110

slab = fcc110(’Pt’, (2, 1, 7), a=4.0,

vacuum=6.0)

from ase.lattice.surface import add_adsorbate

add_adsorbate(slab, ’H’, site=’hollow’)

B ildi th At bj t ti d


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Building the Atoms object, continued ...

from ase.lattice.surface import surface

nasty_cut = surface(rutile, (1, 1, 0),

layers=5)from ase.io import read

q = read(’quarts.cif’)

import ase.db

con = ase.db.con(’mystuff.db’)

atoms = con.get_atoms(foo=’bar’, H=0)

# same as this:

atoms = read(’mystuff.db@foo=bar,H=0’)

ASE’ l l t


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ASE’s calculatorsA t o m s

C a l c u l a t o r

. . .

DFT, ab initio :

Abinit, Castep, ELK, Exciting, FHI-Aims, Fleur, Gaussian,

GPAW, Jacapo, JDFTx, NWChem, QuantumEspresso,

SIESTA, Turbomole, VASP

(Semi-)empirical potentials:

ASAP, DFTB+, EAM, EMT, Gromacs, Hotbit, LAMMPS,

Lennard-Jones, MOPAC, Morse

Optimization MD and minimum energy paths


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Optimization, MD and minimum energy pathsA t o m s

p o s i t i o n s ,


. . .

M o l e c u l a r D y n a m i c s

V e r l e t , L a n g e v i n ,

N P T , . . .

O p t i m i z a t i o n

B F G S , F I R E ,

M i n i m a h o p p i n g ,

B a s i n h o p p i n g , . . .

R e a c t i o n p a t h s

N E B , D i m e r

ASE database


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ASE-database

In each row we have:

Taxonomy:Atoms object (positions, atomic numbers, ...)ID, user-name, creation and modified timeConstraintsCalculator name and parameters

Energy, Forces, Stress tensor, dipole moment,magnetic moments

Folksonomy:

Key-value pairs

KeywordsAdditional stuff:

extra data (band structure, ...)

Back-ends: JSON, SQLite3 and PostgreSQL.

Dye sensitized solar cells1


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Dye sensitized solar cells

3 . 0 3 . 5 4 . 0 4 . 5 5 . 0

E

g a p

( e V )

7

6

5

4

3

2

E

n

e

r

g

y

(

e

V

)

1Kristian B. Ørnsø, Christian S. Pedersen, Juan M. Garca-Lastra and Kristian S.

Thygesen Optimizing porphyrins for dye sensitized solar cells using large-scale ab initio calculations Phys. Chem. Chem. Phys., 2014, 16, 16246-16254

A figure from Ørnsø et al (almost)


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A figure from Ørnsø et al. (almost)

import matplotlib.pyplot as plt

import ase.db

con = ase.db.connect(’dssc.db’)for M in [’Zn’, ’TiO’, ’H2’]:

gap = []

homo = []

lumo = []

for dct in con.select(metal=M,

anchor=’EthynPhA’):

gap.append(dct.E_gap)

homo.append(dct.E_HOMO)

lumo.append(dct.E_LUMO)plt.plot(gap, homo, ’o’)

plt.plot(gap, lumo, ’*’)

plt.ylabel(r’Energy (eV)’)

plt.xlabel(r’$E_{\mathrm{gap}}$ (eV)’)

plt.savefig(’homolumo.svg’)

Three types of calculators


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Three types of calculators

1) a) ASE writes input fileb) ASE starts Fortran/C/C++ code (maybe in parallel)c) ASE waits for Fortran/C/C++ code to finishd) ASE reads output file

2) Same as above, except that the Fortran code doesn’t stop -it waits for a new input file with new coordinates(QuantumEspresso, Dacapo).

3) Python solution (EMT, EAM, ...). For parallel calculations,

the Python interpreter runs on all processes (GPAW, ASAP)

Installing ASE


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Installing ASE

Requirements: Python and NumPy (ase-gui: PyGTK andMatplotlib)

$ SVN=https://svn.fysik.dtu.dk/projects

$ svn co $SVN/ase/trunk ase

$ cd ase

$ python setup.py install --user

$ python setup.py test # takes 1 min.

Where is what?ase/:

Source code.

tools/:Command-line tools

ase/doc/:

Documentation (source for web-page)

Questions


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Questions

How to get started?

http://wiki.fysik.dtu.dk/ase

http://docs.scipy.org/doc/numpy

http://www.python.org

How to get help?

Write to the ase-users mailing list.

How is ASE developed?

Mostly by volunteers. Coordination and discussions on the

ase-developers mailing list.

How to contribute?Please send us bug-reports, patches, code and ideas.

License?

LGPLv2.1+

Thanks

http://wiki.fysik.dtu.dk/asehttp://docs.scipy.org/doc/numpyhttp://www.python.org/http://www.python.org/http://docs.scipy.org/doc/numpyhttp://wiki.fysik.dtu.dk/ase


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Thanks

Andrew Peterson, Anthony Goodrow, Ask Hjorth Larsen, CarstenRostgaard, Christian Glinsvad, David Landis, Elvar Örn Jónsson, EricHermes, Felix Hanke, Gaël Donval, George Tritsaris, Glen Jenness,Heine Anton Hansen, Ivano Eligio Castelli, Jakob Blomquist, JakobSchiøtz, Janne Blomqvist, Janosch Michael Rauba, Jens Jørgen

Mortensen, Jesper Friis, Jesper Kleis, Jess Wellendorff Pedersen,Jingzhe Chen, John Kitchin, Jon Bergmann Maronsson, Jonas Bjork,Jussi Enkovaara, Karsten Wedel Jacobsen, Kristen Kaasbjerg, KristianBaruel Ørnsø, Lars Grabow, Lars Pastewka, Lasse Vilhelmsen, MarcinDulak, Marco Vanin, Markus Kaukonen, Mattias Slabanja, Michael

Walter, Mikkel Strange, Poul Georg Moses, Rolf Würdemann, SteenLysgaard, Stephan Schenk, Tao Jiang, Thomas Olsen, TristanMaxson, Troels Kofoed Jacobsen, ...

Extra material


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Extra material

How to use sys.argv, other ASE functions, for-loops and string

interpolation:import sys

from ase.lattice.surface import fcc111

from gpaw import GPAW, PW

a = float(sys.argv[1])k = int(sys.argv[2])

for n in range(1, 5):

slab = fcc111(’Cu’, size=(1, 1, n),

a=a, vacuum=5.0)

slab.calc = GPAW(mode=PW(ecut=400),kpts=(k, k, 1),

txt=’Cu%d .txt’ % n)

slab.get_potential_energy()

atomic simulation enviornment

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