Editing Examples for Quantum Espresso

Go back to [[Scripts_for_QE]]

Here are the input examples for a Quantum Espresso (QE) 6.1 for a H2O molecule in vacuum. The main program for single point calculations and geometry/cell optimisation is pw.x. 

save to USPP.001_G_D2H2O.in
<pre>
 &CONTROL
                 calculation = 'relax' ,
                restart_mode = 'from_scratch' ,
                  wf_collect = .true. ,
                      prefix = 'USPP.001_G_D2H2O' ,
                   verbosity = 'high' ,
               etot_conv_thr = 1.0D-9 ,
               forc_conv_thr = 1.0D-5 ,
                     tstress = .true. ,
                     tprnfor = .true. ,
                    !dipfield = .true. ,
                       nstep = 200 ,
 /
&SYSTEM
                      ibrav = 1,
                          A = 15 ,
                        nat = 3 ,
                       ntyp = 2,
                    ecutwfc = 40.0 , !J. Chem. Phys. 138, 194709
                    ecutrho = 320.0 ,!J. Chem. Phys. 138, 194709
                  input_dft = 'PBE' ,
                occupations = 'smearing' ,
                    degauss = 0.02 ,
                   smearing = 'gaussian' ,
                      nspin = 2 ,
    starting_magnetization(1) = 0.0,
    starting_magnetization(2) = 0.0,
                    vdw_corr = Grimme-D2, ! DFT-D2 dispersion correction
                       nosym = .true. !For isolated atom
            assume_isolated = 'makov-payne'
/
&ELECTRONS
           electron_maxstep = 800,
              conv_thr_init = 1e-4 ,
                   conv_thr = 1e-9 ,
                startingpot = 'atomic' ,
                startingwfc = 'random' ,
               adaptive_thr = .true. ,
                mixing_beta = 0.514,
            diagonalization = 'david' ,
/
&IONS
               ion_dynamics = 'bfgs' ,
           trust_radius_min =  1.D-5 ,
/
ATOMIC_SPECIES
   O   15.99990  O.pbe-van_ak.UPF
   H    1.00790  H.pbe-van_ak.UPF
ATOMIC_POSITIONS angstrom
O        4.960864866   4.932204696  10.000041372
H        5.926442340   5.064579477   9.999978448
H        4.592692795   5.834600215   9.99998018
K_POINTS Gamma
</pre>

to save to USPP.001_G_D2H2O.lsf12
<pre>
#!/bin/bash
#   - Dra. Nuria's Lopez Group  -
##########################################
# SGE Parameters
##########################################
#$ -S /bin/bash
#$ -N D2H2O
#$ -cwd
#$ -masterq c12m48ib.q
#$ -pe c12m48ib_mpi  12
#$ -m ae
#$ -M YOURMAIL@iciq.es
#$ -o $JOB_NAME.o$JOB_ID
#$ -e $JOB_NAME.e$JOB_ID
cat $TMP/machines.$JOB_ID >> $JOB_NAME.MACHINES.$JOB_ID
INPUT=USPP.001_G_D2H2O.in
OUTPUT=USPP.001_G_D2H2O.out1
# Set up the environment
. /etc/profile.d/modules.sh
module load quantum-espresso/6.1
#module load quantum-espresso/6.1_Env2
##########################################
# Running Job
##########################################
export ESPRESSO_PSEUDO=$HOME/espresso_pseudo
export ESPRESSO_TMPDIR=$HOME/espresso_tmp

export OMP_NUM_THREADS=1

echo $PWD >> $JOB_NAME.o$JOB_ID
echo $TMP >> $JOB_NAME.o$JOB_ID

time mpirun -np $NSLOTS $BIN_DIR/pw.x -input $INPUT > $OUTPUT
</pre>

save to USPP.001_G_D2H2O_LDOS.in
<pre>
 &PROJWFC
                      prefix = 'USPP.001_G_D2H2O' ,
                      !outdir = '/media/hnguyen/WAREHOUSE/tekla/espresso_tmp/SurfaceUSPP/001' ,
                      DeltaE = 0.01 ,
                        Emin = -15.0 ,
                        Emax = 15.0 ,
                      ngauss = 0,
                     degauss = 0.001469972, ! =0.02 eV
                     pawproj = .false. ,
 /
</pre>

save to USPP.001_G_D2H2O_LDOS.lsf12
<pre>
#!/bin/bash
#   - Dra. Nuria's Lopez Group  -
##########################################
# SGE Parameters
##########################################
#$ -S /bin/bash
#$ -N H2Oldos
#$ -cwd
#$ -masterq c12m48ib.q
#$ -pe c12m48ib_mpi  12
#$ -m ae
#$ -M YOURMAIL@iciq.es
#$ -o $JOB_NAME.o$JOB_ID
#$ -e $JOB_NAME.e$JOB_ID
cat $TMP/machines.$JOB_ID >> $JOB_NAME.MACHINES.$JOB_ID

PREFIXfolder=USPP.001_G_D2H2O
INPUT=${PREFIXfolder}_LDOS.in
OUTPUT=${PREFIXfolder}_LDOS.out
# Set up the environment
. /etc/profile.d/modules.sh
module load quantum-espresso/6.1

##########################################
# Running Job
##########################################
export ESPRESSO_PSEUDO=$HOME/espresso_pseudo
export ESPRESSO_TMPDIR=$HOME/espresso_tmp

export OMP_NUM_THREADS=1

echo $PWD >> $JOB_NAME.o$JOB_ID
echo $TMP >> $JOB_NAME.o$JOB_ID


time mpirun -np $NSLOTS $BIN_DIR/projwfc.x -input $INPUT > $OUTPUT
mkdir PDOS
mkdir PDOS/${PREFIXfolder}
mv *pdos* PDOS/${PREFIXfolder}/.
grep 'polarization' $OUTPUT > ${OUTPUT}.polarization
grep 'charge' $OUTPUT > ${OUTPUT}.charge
</pre>


--------------------------------------------------------------------



Before starting the calculation, you need to create two folder in your $HOME directory:

$HOME/espresso_pseudo where you put all your pseudo potentials (O.pbe-van_ak.UPF[http://www.quantum-espresso.org/pseudo/1.3/UPF/O.pbe-van_ak.UPF] and H.pbe-van_ak.UPF[http://www.quantum-espresso.org/pseudo/1.3/UPF/H.pbe-van_ak.UPF])

$HOME/espresso_tmp is where all the outputs will be. Put all the .in and .lsf12 files there. 

Then, edit in the files .lsf12 and replace
<pre>
#$ -M YOURMAIL@iciq.es > your email
</pre>

You can first submit the geometry optimisation job
qsub USPP.001_G_D2H2O.lsf12

When it is done, it will create a human readable output USPP.001_G_D2H2O.out1 and a folder USPP.001_G_D2H2O for restart and postprecessing.

 
if you want to visualize the output of the geometry optimisation, you will need to load quantum espresso module:

module load quantum-espresso/6.1
and then type
<pre>
pwo2xsf.sh -a USPP.001_G_D2H2O.out1 > USPP.001_G_D2H2O.out1.axsf
</pre>
This will create a file USPP.001_G_D2H2O.out1.axsf that can be opened with xcrysden.
 

You can, after the geometry optimisation, submit a PDOS calculation
<pre>
qsub USPP.001_G_D2H2O_LDOS.lsf12
</pre>
When finished, it will create a directory in PDOS/USPP.001_G_D2H2O_LDOS containing all the projected DOS and the total DOS (USPP.001_G_D2H2O.pdos_tot) in text format. You can used your favourite program to plot the DOS.
Löwdin charges will be in USPP.001_G_D2H2O_LDOS.out.charge and polarization will be in USPP.001_G_D2H2O_LDOS.out.polarization

Standard environ water solvent input
<pre>
 &ENVIRON
   !
   verbose = 0
   environ_thr = 1.d-1
   environ_type = 'water'
   tolrhopol = 1.d-11
   mixrhopol = 0.6
 /
</pre>

'''Bader Charge procedure:'''
 pw.x <math>\rightarrow</math> pp.x <math>\rightarrow</math> bader
NB: You MUST use PAW pseudopotential to compute Bader charges in QE. 

Step1: After a scf calculation you need to run
pp.x < INPUT > OUTPUT
<pre>
&INPUTPP
prefix = 'prefix' ,
filplot = 'prefix' ,
plot_num = 17,
/
&PLOT nfile = 1 ,
weight(1) = 1.0,
fileout = 'prefix.charge.cube' ,
iflag = 3 ,
output_format = 6 ,
/
</pre>
This will create a .cube file that can be read by the program bader (not included in QE). 	

Step2:
After step1, execute 
<pre>
bader -v file.charge.cube
</pre>
This will creates 3 files ACF.dat, AVF.dat, BCF.dat. 

ACF.dat contains the coordinates of each atom, the charge associated with it according to Bader partitioning, percentage of the whole according to Bader partitioning and the minimum distance to the surface. 

BCF.dat contains Bader maxima

AVF.dat  contains Bader volumes
 
For practical reasons, it is highly recommended to rename these files before scripting large data set.
A very simple script for step 2 for computing Bader charges. Recommended name: ''bader.sh''
<pre>
#!/bin/bash
#lazy script to compute Bader charges
PREFIX=Fe.USPP.001_2x2_145_full_D2_O1-PAW
bader -v ${PREFIX}.charge.cube
mv ACF.dat ${PREFIX}_ACF.dat
mv AVF.dat ${PREFIX}_AVF.dat
mv BCF.dat ${PREFIX}_BCF.dat
</pre>