mirror of https://gitlab.com/QEF/q-e.git
146 lines
3.7 KiB
Bash
Executable File
146 lines
3.7 KiB
Bash
Executable File
#!/bin/sh
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set -x
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# run from directory where this script is
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cd `echo $0 | sed 's/\(.*\)\/.*/\1/'` # extract pathname
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EXAMPLE_DIR=`pwd`
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export GMON_OUT_PREFIX=gmon.out
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# check whether echo has the -e option
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if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi
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$ECHO
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$ECHO "$EXAMPLE_DIR : starting"
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$ECHO
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$ECHO "This example shows how to use pioud.x to calculate an NVT"
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$ECHO "graphene Path Integral Molecular Dynamics simulation"
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$ECHO
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$ECHO "!!! Beware: pioud.x DOES NOT READ FROM STANDARD INPUT"
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$ECHO "!!! run as 'pioud.x -inp input_file_name > output_file_name'"
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$ECHO
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TMP_DIR=out
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# set the needed environment variables
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. ../../../environment_variables
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# required executables and pseudopotentials
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BIN_LIST="pioud.x"
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$ECHO
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$ECHO " executables directory: $BIN_DIR"
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$ECHO " pseudo directory: $PSEUDO_DIR"
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$ECHO " temporary directory: $TMP_DIR"
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$ECHO " checking that needed directories and files exist...\c"
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# check for directories
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for DIR in "$BIN_DIR" "$PSEUDO_DIR" ; do
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if test ! -d $DIR ; then
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$ECHO
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$ECHO "ERROR: $DIR not existent or not a directory"
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$ECHO "Aborting"
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exit 1
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fi
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done
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for DIR in "$TMP_DIR" "$EXAMPLE_DIR/results_parallel" ; do
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if test ! -d $DIR ; then
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mkdir $DIR
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fi
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done
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cd $EXAMPLE_DIR/results_parallel
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# check for executables
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for FILE in $BIN_LIST ; do
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if test ! -x $BIN_DIR/$FILE ; then
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$ECHO
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$ECHO "ERROR: $BIN_DIR/$FILE not existent or not executable"
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$ECHO "Aborting"
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exit 1
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fi
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done
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export OMP_NUM_THREADS=${SLURM_CPUS_PER_TASK}
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# how to run executables
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# PIOUD_COMMAND="$PARA_PREFIX $BIN_DIR/pioud.x $PARA_POSTFIX"
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PIOUD_COMMAND="mpirun -n 4 $BIN_DIR/pioud.x -ni 4"
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# PIOUD_COMMAND="mpirun -n 4 $BIN_DIR/pioud.x -ni 2"
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# PIOUD_COMMAND="mpirun -n 1 $BIN_DIR/pioud.x"
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$ECHO
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$ECHO " running Born-Oppenheimer PIOUD as: $PIOUD_COMMAND"
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$ECHO
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# clean TMP_DIR
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$ECHO " cleaning $TMP_DIR...\c"
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rm -rf $TMP_DIR/diamond*
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$ECHO " done"
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# clean current result DIR
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# $ECHO " cleaning $EXAMPLE_DIR/results_parallel...\c"
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# rm -rf $EXAMPLE_DIR/results_parallel
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# $ECHO " done"
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nbeadMD=4
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# NEB calculation. Automatic choice of the climbing image.
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cat > diamond.in << EOF
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BEGIN
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BEGIN_PIMD_INPUT
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&dynamics
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restart_pimd=.false.
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nbeadMD=$nbeadMD
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nunitcells=1 !! Just for atomic potentials not DFT.
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nblocks=4 !! not used check - only used for first run. restart not working -check
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nstep_block=4 !! not used check - only used for first run. restart not working -check
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iprint=1 !! Freqncy of output print
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run='pioud' !! verlet,ceriotti,pioud
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delt=0.004 !! for pioud, 41.32231 which is 1 fs in a.u., must be divided for sqrt(m_1) #time step
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tempMD=300.d0 !! temprature in Kelvin
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gammaMD=0.21d0 !! Damping parameter in(1/fs)
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delta_force=1.d-4 !! Just for atomic potentials not DFT.
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delta_harm=5.d-3 !! Just for atomic potentials not DFT.
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/
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END_PIMD_INPUT
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BEGIN_ENGINE_INPUT
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&CONTROL
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prefix = "diamond"
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outdir = "$TMP_DIR",
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pseudo_dir = "$PSEUDO_DIR",
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tstress = .true.
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/
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&SYSTEM
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ibrav = 2 ,
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nosym_evc= .true.
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a=3.56,
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nat = 2,
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ntyp = 1,
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nspin=1,
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ecutwfc = 25.0,
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ecutrho = 120.0,
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nbnd = 15,
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occupations='smearing',
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smearing='fd'
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degauss=0.001,
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/
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&ELECTRONS
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conv_thr = 1.D-8,
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mixing_beta = 0.3D0,
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/
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&IONS
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/
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ATOMIC_SPECIES
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C 12.0107 C.pbe-van_bm.UPF
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BEGIN_POSITIONS
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ATOMIC_POSITIONS crystal
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C 0.0 0.0 0.000000000
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C 0.12 0.12 0.12
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END_POSITIONS
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K_POINTS automatic
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4 4 4 0 0 0
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END_ENGINE_INPUT
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END
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EOF
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$ECHO " running Born-Oppenheimer pioud calculation... "
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$PIOUD_COMMAND -inp diamond.in > diamond.out
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check_failure $?
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$ECHO " done"
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# clean TMP_DIR
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#$ECHO " cleaning $TMP_DIR...\c"
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#rm -rf $TMP_DIR/pwscf*
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#$ECHO " done"
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