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--- howto:atat [2018/01/11 14:32]
alopis
+++ howto:atat [2021/12/09 16:42] (current)
@@ Line 1: / Line 1: @@
-====== Running ATAT (The Alloy-Theoretic Automated Toolkit)======
+====== Running ATAT (The Alloy-Theoretic Automated Toolkit) ======
-This describes the use of ATAT which employs QE (Quantum Espresso 6.1.0).  Anton Lopis  11 Jan 2017
+[[http://www.brown.edu/Departments/Engineering/Labs/avdw/atat/]]
+This describes the use of ATAT on Lengau and employs QE (Quantum Espresso 6.1.0).  Anton Lopis  11 Jan 2017
 Please find the files at   **/apps/chpc/chem/ATAT/3.36/CHPC_Running** including pbs submission/bash script and input files (see below as well).
@@ Line 10: / Line 13: @@
-One needs the following files:
+===== One needs the following files: =====
 . maps.pbs
@@ Line 24: / Line 27: @@
-One needs to edit the pbs submit script file maps.pbs appropriately:
+===== One needs to edit the pbs submit script file maps.pbs appropriately: =====
 .** Choose the number of nodes that QE will run most efficiently on for your size of QM problem**. In the listed example I have specified 2 nodes, however I have not checked, and perhaps only one node might have been more efficient.
@@ Line 44: / Line 52: @@
-One needs to edit the file "runstruct_qe" appropriately:
+===== One needs to edit the file "runstruct_qe" appropriately: =====
 . The appropriate PseudoDIR (it could remain as one used for all jobs).
@@ Line 64: / Line 74: @@
 #PBS -m be
 #PBS -M none
-#PBS -o /mnt/lustre/users/alopis/ATAT_testing/out
+#PBS -o /mnt/lustre/users/alopis/ATAT_testing.out
-#PBS -e /mnt/lustre/users/alopis/ATAT_testing/error
+#PBS -e /mnt/lustre/users/alopis/ATAT_testing.error
 #PBS
@@ Line 87: / Line 97: @@
 touch stop
 </file>
+<file bash runstruct_qe>
+#!/bin/bash
+# This bash scrpit is for the interface between ATAT and Quantum-ESPRESSO v5.0
+# The final result will be in eV unit
+# Produced by GAO Zhe, Mater. Sci & Eng, Seoul Nat'l Univ., S. Korea
+# email to gaozhe1983(a)snu.ac.kr
+# Set the k-points density in reciprocal space
+KPPRA=1000
+# Set the command to run pw.x, for example,
+# if you wanna run it with 4 cores/cpus, set it
+# as "$MPI_PATH/mpirun -n 4 $QE_PATH/pw.x"
+#export QESPRESSO=/apps/chpc/chem/qespresso/6.1.0
+PWCOMMAND="$QESPRESSO/bin/pw.x"
+# Set some calculation parameters here, which contents:
+# cut-off energy for wave-functions and charge density;
+# gaussian broadening parameter for smearing;
+# especially, the directory where restore your pseudo-potential files.
+# Definitely, you can directly set these and some other parameters
+# in the input file-creating part.
+########################################################################
+# Recommand from the official manual of Quantum-ESPRESSO:              #
+# for Norm-Conserving pseudo-potential, the cut-off for charge density #
+# does not need to be setted (or, 4 times of ecutwfc).                 #
+# But for ultrasoft pseudo-potential, set the cut-off for charge       #
+# density to 8~10 times of cut-off for wavefunctions.                  #
+########################################################################
+PseudoDIR=/mnt/lustre/users/alopis/ATAT_testing/Pseudo
+CUT_WFC=50
+CUT_CHG=520
+DEGAUSS=0.5
+# Try to find the parameter setting file, which contents the
+# information for species of elements
+# If this file does not exist, the script will stop
+ParamFile=/mnt/lustre/users/alopis/ATAT_testing/qe.param
+if [ ! -e $ParamFile ]; then
+  ParamFile="../qe.param"
+  if [ ! -e $ParamFile ]; then
+    ParamFile="../../qe.param"
+    if [ ! -e $ParamFile ]; then
+     echo " Cannot find the param file qe.param, stop the code!"
+     exit 1
+    fi
+  fi
+fi
+# Create the fist part of input file for QE v5.0
+cat > pwscf.in <<EOF
+&control
+   calculation = 'vc-relax' ,
+   prefix = 'pwscf' ,
+   outdir = './temp/' ,
+   pseudo_dir = '$PseudoDIR/' ,
+   disk_io = 'none' ,
+   etot_conv_thr = 1.0d-10 ,
+   forc_conv_thr = 1.0d-5 ,
+/
+&system
+   ibrav = 0 ,
+   celldm(1) = 1.889725989 ,
+   ecutwfc = ${CUT_WFC} ,
+   ecutrho = ${CUT_CHG} ,
+   occupations = 'smearing' ,
+   smearing = 'mv' ,
+   degauss = ${DEGAUSS} ,
+EOF
+# Find the atom number and elements number
+# Then, write them into the input file
+NAT=`cellcvrt -f < str.out | tail -n +7 | wc -l`
+NTYPE=`cellcvrt -f < str.out | tail -n +7 | awk '{print $4}' | sort -u | wc -l`
+echo "   nat = $NAT , " >> pwscf.in
+echo "   ntyp = $NTYPE , " >> pwscf.in
+# Create the temp input file, which corresponds to
+# the second big part. After creating, it will be
+# attached follow the former one and deleted.
+cat > pwscf.tmp <<EOF
+/
+&electrons
+   conv_thr = 1.0d-10 ,
+   diagonalization = 'david' ,
+   mixing_mode = 'plain' ,
+   startingpot = 'atomic' ,
+   startingwfc = 'atomic+random' ,
+   mixing_beta = 0.6 ,
+/
+&ions
+   ion_dynamics = 'bfgs' ,
+/
+&cell
+   cell_dynamics = 'bfgs' ,
+   cell_factor = 2.0 ,
+   press = 0.0 ,
+   press_conv_thr = 1.0d-3 ,
+/
+CELL_PARAMETERS alat
+EOF
+cat pwscf.tmp >> pwscf.in
+rm -f pwscf.tmp
+# Find and write the lattice vector information
+cat str.out | cellcvrt -c -sig=9 | tail -n +4 | head -3 >> pwscf.in
+# Find and write the information for element type, mass
+# and pseudo-potential files' name
+echo "ATOMIC_SPECIES" >> pwscf.in
+INT=1
+while [ "$INT" -le "$NTYPE" ]; do
+  KIND=pp`cellcvrt -f < str.out | tail -n +7 | awk '{print $4}' | sort -u | head -${INT} | tail -1`
+  grep "$KIND" $ParamFile | awk '{print "  " $2, $3, $4}' >> pwscf.in
+  let "$((INT++))"
+done
+# Find and write the atoms' position to input file
+echo "ATOMIC_POSITIONS angstrom" >> pwscf.in
+cat str.out | cellcvrt -c -sig=9 | tail -n +7 | awk '{print "  " $4,  $1,  $2,  $3 }' >> pwscf.in
+# Find the k-points mesh, the mesh will be created
+# by Monkhorst-Pack method
+echo "K_POINTS automatic" >> pwscf.in
+nbat=`cellcvrt -pn < str.out`
+echo "  " `( echo $KPPRA $nbat | awk '{print $1/$2}' ; cat str.out | cellcvrt -f | head -3 ) | kmesh -q -r`   0  0  0 >> pwscf.in
+# Run pw.x for calculation
+nproc=`cat $PBS_NODEFILE | wc -l`
+#mpirun -np 24 $PWCOMMAND < pwscf.in > pwscf.out
+mpirun -np $nproc $PWCOMMAND < pwscf.in > pwscf.out
+# Abstract the final total energy to "energy" file
+# in the unit of eV
+FERy=`grep '!' pwscf.out | tail -1 | cut -c 35-50`
+FEeV=`echo "scale=15; $FERy*13.605698066" | bc -l`
+echo "$FEeV" > energy
+</file>
 <file txt lat.in>
 .155  3.155  3.155  90  90  90
 .5   0.5   0.5
 -0.5   0.5   0.5
 -0.5  -0.5   0.5
 .0  0.0  0.0  Mo,W
-~
+</file>
+<file txt qe.param>
+# The rule for make atomic_species card:
+# set the ppXXX as the name of certain line
+# then, write down the elemental symbol, mass
+# and pseudo-potential name info.
+ppW     W   183.80   W.GTH_LDA.UPF
+ppMo    Mo  12.011   Mo.GTH_LDA.UPF
 </file>

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