Quantum Espresso¶
PWSCF (Regular Package)¶
If you have the cif file for your structure, then you can use Tools on Materials Cloud to get the input file.
For our system (examples/Pt111-CO.cif, you can view this from github ), the input file for pw.x in Quantum Espresso is:
&CONTROL
calculation = 'scf' # The type of calculation that you want to make
etot_conv_thr = 1.8000000000d-04 # convergence criteria for total energy
forc_conv_thr = 1.0000000000d-04 # convergence criteria for total force
outdir = './out/' # the output folder
prefix = 'aiida' # the prefix, used for output files
pseudo_dir = './pseudo/' # the folder for pseudopotential
tprnfor = .true. # print the force in the end
tstress = .true. # print the stress of the cell in the end
verbosity = 'low' # how much information do you want to print
/
&SYSTEM
degauss = 1.4699723600d-02 # value for gaussian-smearing
ecutrho = 8.0000000000d+02 # cutoff energy for electronic density
ecutwfc = 1.0000000000d+02 # cutoff energy for wave function
ibrav = 0 # means we need to specify cell parameter in the CELL_PARAMETERS part
nat = 18 # number of atoms in our system
ntyp = 3 # number of types of atoms in our system
occupations = 'smearing'
smearing = 'cold'
/
&ELECTRONS
conv_thr = 3.6000000000d-09 # convergence criteria for self-consistent field calculation
electron_maxstep = 80 # maximum number of steps of SCF loop
mixing_beta = 4.0000000000d-01 # value for mixing the old electronic density with the new one. Like the "training rate" in ML.
/
ATOMIC_SPECIES # specify the types of atoms and the corresponding pseudopotential
C 12.011 C.pbesol-n-kjpaw_psl.1.0.0.UPF
O 15.9994 O.pbesol-n-kjpaw_psl.0.1.UPF
Pt 195.08 pt_pbesol_v1.4.uspp.F.UPF
ATOMIC_POSITIONS crystal # the geometric coordinates of the system, really important!
Pt 0.5000000000 0.5000000000 0.3750000000
Pt -0.0000000000 -0.0000000000 0.3750000000
Pt 0.5000000000 -0.0000000000 0.3750000000
Pt -0.0000000000 0.5000000000 0.3750000000
Pt 0.1666700000 0.1666700000 0.4583300000
Pt 0.6666700000 0.6666700000 0.4583300000
Pt 0.1666700000 0.6666700000 0.4583300000
Pt 0.6666700000 0.1666700000 0.4583300000
Pt 0.8333300000 0.8333300000 0.5416700000
Pt 0.3333300000 0.3333300000 0.5416700000
Pt 0.8333300000 0.3333300000 0.5416700000
Pt 0.3333300000 0.8333300000 0.5416700000
Pt 0.5000000000 0.5000000000 0.6250000000
Pt -0.0000000000 0.0000000000 0.6250000000
Pt 0.5000000000 0.0000000000 0.6250000000
Pt -0.0000000000 0.5000000000 0.6250000000
C 0.5000000000 0.5000000000 0.6685200000
O 0.5000000000 0.5000000000 0.7120400000
K_POINTS automatic # The k-point mesh for the system.
7 7 2 0 0 0
CELL_PARAMETERS angstrom
5.6285700000 0.0000000000 0.0000000000
2.8142850000 4.8744846070 0.0000000000
0.0000000000 0.0000000000 27.5742000000
Then you can use pw.x -i INP_PWSCF > OUT_PWSCF to execute and get the energy of your structure.
If we want to use DFT+U and spin polarization, there are several parameters that we need to add to the input file.
# for DFT+U settings
lda_plus_u = .true.
hubbard_u(1) = 5.0
# for spin-polarization settings
nspin = 2
tot_magnetization = #some number
starting_magnetization(1) = 0.1
starting_ns_eigenvalue(1, 1, 1) = 1.0 # this is for finely tuning the initial magnetization, the first number is the index of the orbital (e.g. for d band it ranges from 1 to 5), the second number is the index of spin (1 or 2), the third number is the index of the atom (see that in ATOMIC SPECIES in the input file).
# if you want to constrain the magnetic moment
&ELECTRONS
mixing_fixed_ns = 10 # In 10 SCF steps, the magnetic moment will be the same as mentioned in starting_ns_eigenvalue.
PHonon Package (ph.x)¶
Step 1: Do the geometric optimization on the structure
Step 2: Get the optimized structure, then create another file called INP_PH for the ph.x software.
An example of INP_PH is shown in below:
Normal modes for CO2
&inputph
tr2_ph=1.0d-14,
prefix='CO2',
amass(1)=12.010,
amass(2)=15.999,
outdir='$TMP_DIR'
epsil=.true.,
trans=.true.,
asr=.true.
fildyn='dmat.co2'
nat_todo = 2
/
0.0 0.0 0.0
1 3 # the index for the atoms that we want to calculate (usually the adsorbates)
The execution of the ph.x can be written as: ph.x -i INP_PH > OUT_PH.
Note
The file listed in here needs to be adjusted to your own system.
DOS (dos.x) and PDOS (projwfc.x)¶
In Quantum Espresso, the procedure for calculating DOS or PDOS has 4 steps:
Step 1: Do the geometric optimization of the structure, you can see that in How to calculate the energy and do geometric relaxation on a chemical system?
Step 2: Do the SCF calculation (replace the calculation from relax/vc-relax to scf)
Step 3: Keep the output file and do the NSCF calculation (replace the calculation from scf to nscf)
Step 4: In the same directory, create a file named INP_PROJWFC, the content is shown in below:
&PROJWFC
DeltaE = 0.01
ngauss = 0
degauss = 0.015
Emin = -40
Emax = 40
Then you can use projwfc.x to execute it: projwfc.x -i INP_PROJWFC > OUT_PROJWFC. For calculating DOS, you can use dos.x, the input parameters can be seen in this link
After that, you can use pp.x to do the post-process procedure, or you can use python or other softwares to do the plotting and further analysis.