exercise/02: equilibrium volume for fcc Cu

In this exercise we will practice how to get lattice parameters for fcc copper with EMTO code. The main idea is to calculate total energy vs. different volumes, \(E(\omega)\) curve, and fit to an “Equation of State” function. Here we choose “Morse function”:

\[E(\omega)=a+be^{-\lambda\omega}+ce^{-2\lambda\omega}\]

System-specific instructions

Select instructions for the system you are using:

TetralithLeonardo_Booster

Instructions for use on the NAISS cluster Tetralith (NSC)

Attention

make sure we are in the path at exercise/02

1. we could reuse the kstr, bmdl and shape from exercise/00

Hint

ln -vs ../00/kstr
ln -vs ../00/bmdl
ln -vs ../00/shape

2. base on 00/kgrn/cu.dat, change to different SWS and also the jobname and file name

Hint

for sws in `seq 2.60 0.02 2.76`
do
  sed -e "s/JOBNAM=.*/JOBNAM=cu_${sws}/" \
      -e "s/SWS......=......../SWS......=${sws}0000/" \
    ../00/kgrn/cu.dat > kgrn/cu_${sws}.dat
done
 
# maybe we need reduce the AMIX
      # -e 's/AMIX...=  0.100/AMIX...=  0.020/' \
# soft core apprixmation is important for equilibrium volume calculation 
      # -e 's/SOFC.=  N/SOFC.=  Y/' \

3. base on 00/kfcd/cu.dat change to different jobnam and file name

Hint

mkdir -vp kfcd
for sws in `seq 2.60 0.02 2.76`
do
  sed -e "s/JOBNAM...=.*/JOBNAM...=cu_${sws}/" \
      ../00/kfcd/cu.dat > kfcd/cu_${sws}.dat
done
# maybe we want to silence the output 
      # -e 's/MSGL..=  1/MSGL..=  0/' \

4. run all calculations and get \(E(\omega)\)

• submit all kgrn jobs to the queue, use following sbatch script.

TetralithLeonardo_Booster

cd kgrn
sbatch -A naiss2024-22-241 -c 2 -a 1-9 -t 10:00 ../../emto.sbatch

• check if the kgrn jobs are finished correctly.

  Hint

  cd kgrn
  grep -L "finished" *.prn
  

• submit all kfcd jobs to the queue, use following sbatch script.

TetralithLeonardo_Booster

cd kfcd 
sbatch -A naiss2024-22-241 -c 1 -a 1-9 -t 10:00 ../../emto.sbatch

5. get total energy vs. SWS from kfcd output

   Hint

   cd kfcd
   grep TOT-PBE *.prn
   

   here we choose PBE EXC

   #               EXC                                      5th                      8th
   cu_2.60.prn:    TOT-PBE         -102.553631 (Ry)    -102.553631 (Ry/site)   S=  2.600000 Bohr
   cu_2.62.prn:    TOT-PBE         -102.555746 (Ry)    -102.555746 (Ry/site)   S=  2.620000 Bohr
   cu_2.64.prn:    TOT-PBE         -102.557381 (Ry)    -102.557381 (Ry/site)   S=  2.640000 Bohr
   cu_2.66.prn:    TOT-PBE         -102.558531 (Ry)    -102.558531 (Ry/site)   S=  2.660000 Bohr
   cu_2.68.prn:    TOT-PBE         -102.559243 (Ry)    -102.559243 (Ry/site)   S=  2.680000 Bohr
   cu_2.70.prn:    TOT-PBE         -102.559439 (Ry)    -102.559439 (Ry/site)   S=  2.700000 Bohr
   cu_2.72.prn:    TOT-PBE         -102.559283 (Ry)    -102.559283 (Ry/site)   S=  2.720000 Bohr
   cu_2.74.prn:    TOT-PBE         -102.558814 (Ry)    -102.558814 (Ry/site)   S=  2.740000 Bohr
   cu_2.76.prn:    TOT-PBE         -102.558060 (Ry)    -102.558060 (Ry/site)   S=  2.760000 Bohr
   

   fit the 5th and 8th for morse function