Quantum-Espresso
the poor man's plane-vawe code

1. find the best code for the problem

the chemists' choice

http://www.bannedbygaussian.org

http://gaussian.com/silly/

go for Siesta instead...

"etalon code"

Gaussian

+ orthonormal

+ independent of atomic positions

+ no BSSE

± naturally periodic
 

– many functions needed

– localised functions difficult to represent

Why plane-wave?

What can QE do

• Ground-state calculations.
• Structural Optimization.
• Transition states and minimum energy paths.
• Ab-initio molecular dynamics.
• Response properties (DFPT).
• Spectroscopic properties.
• Quantum Transport.
• Platforms.

It is based on density-functional theory, plane waves, and pseudopotentials.

Platforms: (really! also cell phones and playstations)

3. benchmark

we skip this for now, but it is important

parallelization of the code vs parallelization against some of the parameters

FFT is important, gnu-compiler vs intel + MKL

Parallelization of QE

Parallelization on k-points:

• guarantees (almost) linear scaling if the number of k-points is a multiple of the number of pools;
• requires little communications (suitable for ethernet communications);
• reduces the required memory per processor by distributing wavefunctions (but not other quantities like the charge density), unless you set disk_io='high'.

Parallelization on PWs:

• yields good to very good scaling, especially if the number of processors in a pool is a divisor of N3 and Nr3 (the dimensions along the z-axis of the FFT grids, nr3 and nr3s, which coincide for NCPPs);
• requires heavy communications (suitable for Gigabit ethernet up to 4, 8 CPUs at most, specialized communication hardware needed for 8 or more processors );
• yields almost linear reduction of memory per processor with the number of processors in the pool.

kooplex-edu

2db XeonE5645@2.40GHz

Atoms & kpoints

ATOMIC_SPECIES
 Si  28.086  Si.pz-vbc.UPF
ATOMIC_POSITIONS alat
 Si 0.00 0.00 0.00
 Si 0.25 0.25 0.25

#K_POINTS tpiba
# this is also a comment: next line, number of k-points
# 2
# 0.25 0.25 0.25  1.0
# 0.25 0.25 0.75  3.0

K_POINTS automatic
 2 2 2 1 1 1

Atoms & kpoints

ATOMIC_SPECIES
 Si  28.086  Si.pz-vbc.UPF
ATOMIC_POSITIONS alat
 Si 0.00 0.00 0.00
 Si 0.25 0.25 0.25

#K_POINTS tpiba
# this is also a comment: next line, number of k-points
# 2
# 0.25 0.25 0.25  1.0
# 0.25 0.25 0.75  3.0

K_POINTS automatic
 2 2 2 1 1 1

Atoms & kpoints

ATOMIC_SPECIES
 Si  28.086  Si.pz-vbc.UPF
ATOMIC_POSITIONS alat
 Si 0.00 0.00 0.00
 Si 0.25 0.25 0.25

#K_POINTS tpiba
# 2
# 0.25 0.25 0.25  1.0
# 0.25 0.25 0.75  3.0

K_POINTS automatic
 2 2 2 1 1 1

4. ... run calculation

run erhm what?

ls pwscfdir/bin:       alpha2f.x     dos.x      fd_ifc.x          generate_rVV10_kernel_table.x  iotk_print_kinds.x  molecularpdos.x       plan_avg.x  projwfc.x       pwi2xsf.x     sumpdos.x
average.x     dynmat.x   fd.x              generate_vdW_kernel_table.x    iotk.x              neb.x                 plotband.x  pw2bgw.x        pw.x          wannier_ham.x
bands.x       epa.x      fermi_proj.x      ibrav2cell.x                   kpoints.x           open_grid.x           plotproj.x  pw2gw.x         q2qstar.x     wannier_plot.x
bgw2pw.x      epsilon.x  fermi_velocity.x  importexport_binary.x          lambda.x            path_interpolation.x  plotrho.x   pw2wannier90.x  q2r.x         wfck2r.x
cell2ibrav.x  ev.x       fqha.x            initial_state.x                manypw.x            phcg.x                pmw.x       pwcond.x        q2trans_fd.x
dist.x        fd_ef.x    fs.x              iotk                           matdyn.x            ph.x                  pp.x        pw_export.x   q2trans.x

PWSCF executables

• pw.x : Plane-Wave Self-Consistent Field
• ph.x : phonons with Density-Functional Perturbation Theory
• cp.x : Car-Parrinello Molecular Dynamics
• neb.x : energy barriers and reaction pathways through the Nudged Elastic Band method
• pwcond.x : ballistic conductance
• dos.x bands.x pp.x ... : various utilities for data postprocessing
   
• pwgui : a Graphical User Interface, producing input data files for PWscf
• ld1.x : (atomic) a program for atomic calculations and generation of pseudopotentials

Example 1

Convergency tests

- download pseudo (LDA+PAW for Si)

PART 1

- change ecutwfc (10, 20, ... Ry) & run

- find total energies

- plot results & find the converged ecutwfc

PART2

- set ecutwfc to converged value

- increase kpoint set 2x2x2 ... 9x9x9 & run

- plot results & find the converged k-set

wget <link>

pw.x < infile >outfile

grep '!' outfile

go to my_example1 folder

Example2

Geometry optimization by hand

- set ecutwfc, k-set (from my_example1)

- change unit cell parameter

A=5.3 -- 5.5 in 0.02 steps (Ångström) & run

- find total energies

- plot & fit parabola

pw.x < infile >outfile

grep '!' outfile

go to my_example2 folder

experimental cell parameter A=5.341Å

Example3

Geometry optimization by built-in method

- add calculation='vc-relax' to control block

- add &cell + &ion blocks (even if they are empty)

- find final coordinates (in units of original lattice constant ...)

- compare result with "handy method"

calculation switch

pw.x < infile >outfile

go to my_example3 folder

Example4

Band structure

- optimized structure, scf run with k-set

- add calculation='bands'
     nbnd= number_of_bands
     k-path in BZ

- run pw.x again

- bands.x to create gnuplot-compatible output (with .gnu extension)

- plotband.x (writes plot scripts)

pw.x < scf.in >scf.out

pw.x <bands.in > bands.out

bands.x < band2.in >band2.out

go to my_example4 folder

Band structure of bulk Si

Example5

Density of states

- setup scf calculation

- setup dos calculation & run

- plot DOS

- DOS is ugly

   - increase kpoints & change degauss value, 0.001, 0.01, 0.1 ... etc.

   - add occupations='tetrahedra' to scf & remove degauss from dos input

- DOS is pretty

pw.x < infile >outfile

dos.x <dos.in >dos.out

mpirun -np 6 pw.x

manual

go to my_example5 folder

DOS of bulk silicon

Example6

Bulk modulus

- add tstress=.true. tag to  &control block
 

- change the volume size by ±0.5%, ±1.0%, ...

- find the stress tensor in output, differentiate numerically & get the units right ...

go to my_example6 folder

Alternatively, set target stress to some value, perform geometry optimization, work out the bulk modulus...