#!/bin/sh # run from directory where this script is cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname EXAMPLE_DIR=`pwd` # check whether echo has the -e option if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi $ECHO $ECHO "$EXAMPLE_DIR : starting" $ECHO $ECHO "This example shows how to use pw.x with vdw-DF functional. In the" $ECHO "first part a cell relaxation of graphite will be calculated and" $ECHO "then the energy of two water molecules far apart will be computed." $ECHO "Optionally, at the end, you can see how to set up a force relaxation" $ECHO "of an Argon dimer, not activated by default in the distribution." # set the needed environment variables . ../../../environment_variables # required executables and pseudopotentials BIN_LIST="pw.x generate_vdW_kernel_table.x" PSEUDO_LIST="C.pbe-rrkjus.UPF O.pbe-rrkjus.UPF H.pbe-rrkjus.UPF" VDW_TABLE="vdW_kernel_table" $ECHO $ECHO " executables directory: $BIN_DIR" $ECHO " pseudo directory: $PSEUDO_DIR" $ECHO " temporary directory: $TMP_DIR" $ECHO " checking that needed directories and files exist...\c" # check for directories for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do if test ! -d $DIR ; then $ECHO $ECHO "ERROR: $DIR not existent or not a directory" $ECHO "Aborting" exit 1 fi done for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results" ; do if test ! -d $DIR ; then mkdir $DIR fi done cd $EXAMPLE_DIR/results # check for executables for FILE in $BIN_LIST ; do if test ! -x $BIN_DIR/$FILE ; then $ECHO $ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable" $ECHO "Aborting" exit 1 fi done # check for pseudopotentials for FILE in $PSEUDO_LIST ; do if test ! -r $PSEUDO_DIR/$FILE ; then $ECHO $ECHO "Downloading $FILE to $PSEUDO_DIR...\c" $WGET $PSEUDO_DIR/$FILE $NETWORK_PSEUDO/$FILE 2> /dev/null fi if test $? != 0; then $ECHO $ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable" $ECHO "Aborting" exit 1 fi done $ECHO " done" # how to run executables PW_COMMAND="$PARA_PREFIX $BIN_DIR/pw.x $PARA_POSTFIX" GEN_COMMAND="$PARA_PREFIX $BIN_DIR/generate_vdW_kernel_table.x $PARA_POSTFIX" # check for vdw kernel table if test ! -r $PSEUDO_DIR/$VDW_TABLE ; then $ECHO " " $ECHO " " $ECHO " WARNING: $PSEUDO_DIR/$VDW_TABLE not existent or not readable" $ECHO " WARNING: a new table will be generated, this process will" $ECHO " WARNING: probably take about 20 mins (depending on your cpu" $ECHO " WARNING: power and configuration)." $ECHO $ECHO " Generating $VDW_TABLE...\c" if $GEN_COMMAND ; then if test ! -r $VDW_TABLE ; then $ECHO " ERROR: cannot generate vdW_kernel_table !!" exit 1 fi $ECHO "done ! Table moved to $PSEUDO_DIR" mv $VDW_TABLE $PSEUDO_DIR fi fi $ECHO " done" # Print how we run executables $ECHO $ECHO " running pw.x as: $PW_COMMAND" $ECHO # # Graphite cell relaxation # cat > graphite.scf.in << EOF &control calculation = 'vc-relax' restart_mode='from_scratch', prefix='graphite', tstress = .true. tprnfor = .true. pseudo_dir = '$PSEUDO_DIR', outdir='$TMP_DIR' forc_conv_thr = 1.0D-3 / &system ibrav = 4 celldm(1) = 4.6411700000 celldm(3) = 2.7264000000 nat = 4 ntyp = 1 occupations = 'fixed' smearing = 'mv' degauss = 0.02 ecutwfc = 30.0 ecutrho = 180.0 input_dft = 'vdW-DF' / &electrons conv_thr = 1.0d-8 / &ions / &cell press_conv_thr = 0.5D0 press = 0.D0 cell_dynamics = 'bfgs' cell_dofree = 'z' / ATOMIC_SPECIES C 12.00 C.pbe-rrkjus.UPF ATOMIC_POSITIONS {alat} C 0.0000000000 0.0000000000 0.0000000000 C 0.0000000000 0.5773502692 0.0000000000 C 0.0000000000 0.0000000000 1.3632000000 C 0.5000000000 0.2886751346 1.3632000000 K_POINTS automatic 4 4 4 1 1 1 EOF $ECHO " running the graphite cell relaxation...\c" $PW_COMMAND < graphite.scf.in > graphite.scf.out check_failure $? $ECHO " done" # clean TMP_DIR $ECHO " cleaning $TMP_DIR...\c" rm -rf $TMP_DIR/graphite* $ECHO " done" # # self-consistent calculation # for water molecules # cat > water.scf.in << EOF &control calculation = 'scf' restart_mode='from_scratch', prefix='water_vdw', tstress = .true. tprnfor = .true. pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' verbosity = 'high' / &system ibrav = 8 celldm(1) = 15 celldm(2) = 0.954545454545455 celldm(3) = 1.22727272727273 nat = 6 ntyp = 2 occupations = 'fixed' ecutwfc = 30.0 ecutrho = 180.0 input_dft = 'vdW-DF' / &electrons conv_thr = 1.0d-8 / ATOMIC_SPECIES O 15.9994 O.pbe-rrkjus.UPF H 1.00794 H.pbe-rrkjus.UPF ATOMIC_POSITIONS {angstrom} O -0.000000 0.013129 -0.057535 H -0.000000 0.779069 -0.656064 H 0.000000 0.389646 0.845802 O 0.000000 0.887109 2.818248 H -0.774530 0.521469 3.280767 H 0.774530 0.521469 3.280767 K_POINTS gamma EOF $ECHO " running the scf calculation for water molecules...\c" $PW_COMMAND < water.scf.in > water.scf.out check_failure $? $ECHO " done" # clean TMP_DIR $ECHO " cleaning $TMP_DIR...\c" rm -rf $TMP_DIR/water_vdw* $ECHO " done" # # self-consistent calculation # for Argon dimer # cat > Ar.scf.in << EOF &control calculation = 'scf' restart_mode='from_scratch', prefix='Ar_vdw', tstress = .true. tprnfor = .true. pseudo_dir = '$PSEUDO_DIR/', outdir='$TMP_DIR/' verbosity = 'high' forc_conv_thr = 1.0d-4 / &system ibrav = 8 celldm(1) = 19 celldm(2) = 1 celldm(3) = 1.47368421052632 nat = 2 ntyp = 1 occupations = 'fixed' ecutwfc = 80.0 input_dft = 'vdW-DF' / &electrons conv_thr = 1.0d-11 / &ions ion_dynamics = 'bfgs' / ATOMIC_SPECIES Ar 36.00 Ar.pz-rrkj.UPF ATOMIC_POSITIONS {angstrom} Ar 0.000000 0.000000 0.000000 Ar 0.000000 0.000000 4.500000 K_POINTS gamma EOF $ECHO " running the scf calculation for argon dimer...\c" #$PW_COMMAND < Ar.scf.in > Ar.scf.out #check_failure $? #$ECHO " done" # clean TMP_DIR $ECHO " cleaning $TMP_DIR...\c" rm -rf $TMP_DIR/ar_vdw* $ECHO " done" $ECHO $ECHO "$EXAMPLE_DIR : done"