mirror of https://gitlab.com/QEF/q-e.git
373 lines
6.4 KiB
Bash
Executable File
373 lines
6.4 KiB
Bash
Executable File
#!/bin/sh
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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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# 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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$ECHO "This example shows how to use cp.x to perform"
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$ECHO "Born-Oppenheimer molecular dynamics using the"
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$ECHO "conjugate gradient minimization of the electronic"
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$ECHO "states. It shows also the use of ensemble-DFT"
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$ECHO "for metallic systems."
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$ECHO "The example shows a Si dimer"
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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="cp.x"
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PSEUDO_LIST="Si.pbe-rrkj.UPF"
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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" ; 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
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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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# check for pseudopotentials
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for FILE in $PSEUDO_LIST ; do
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if test ! -r $PSEUDO_DIR/$FILE ; then
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$ECHO
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$ECHO "Downloading $FILE to $PSEUDO_DIR...\c"
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$WGET $PSEUDO_DIR/$FILE \
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http://www.quantum-espresso.org/pseudo/1.3/UPF/$FILE 2> /dev/null
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fi
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if test $? != 0; then
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$ECHO
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$ECHO "ERROR: $PSEUDO_DIR/$FILE not existent or not readable"
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$ECHO "Aborting"
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exit 1
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fi
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done
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$ECHO " done"
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# how to run executables
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CP_COMMAND="$PARA_PREFIX $BIN_DIR/cp.x $PARA_POSTFIX"
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$ECHO
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$ECHO " running cp.x as: $CP_COMMAND"
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$ECHO
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# clean TMP_DIR
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$ECHO " cleaning $TMP_DIR...\c"
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rm -rf $TMP_DIR/*
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$ECHO " done"
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# molecular dynamics calculation
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cat > si2.ensemble-dyn.xml << EOF
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<?xml version="1.0" encoding="UTF-8"?>
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<input calculation="cp" prefix="Si_dimer">
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<cell type="qecell">
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<qecell ibrav="8" alat="10.0">
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<real rank="1" n1="5">
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1.0 1.5 0.0 0.0 0.0
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</real>
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</qecell>
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</cell>
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<atomic_species ntyp="1">
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<specie name="Si">
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<property name="mass">
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<real>28.086</real>
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</property>
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<property name="pseudofile">
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<string>Si.pbe-rrkj.UPF</string>
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</property>
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<property name="ion_radius">
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<real>0.8d0</real>
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</property>
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</specie>
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</atomic_species>
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<atomic_list units="bohr" nat="2" >
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<atom name="Si">
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<position ifx="1" ify="1" ifz="1">
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<real rank="1" n1="3">
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0.0 0.0 0.0
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</real>
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</position>
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</atom>
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<atom name="Si">
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<position ifx="1" ify="1" ifz="1">
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<real rank="1" n1="3">
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0.0 0.0 5.5
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</real>
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</position>
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</atom>
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</atomic_list>
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<field name="InputOutput">
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<parameter name="pseudo_dir">
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<string>
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$PSEUDO_DIR/
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</string>
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</parameter>
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<parameter name="outdir">
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<string>
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$TMP_DIR/
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</string>
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</parameter>
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<parameter name="restart_mode">
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<string>
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from_scratch
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</string>
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</parameter>
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<parameter name="iprint">
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<integer>
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10
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</integer>
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</parameter>
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<parameter name="tstress">
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<logical>
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TRUE
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</logical>
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</parameter>
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<parameter name="tprnfor">
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<logical>
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TRUE
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</logical>
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</parameter>
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<parameter name="startingwfc">
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<string>
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random
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</string>
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</parameter>
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<parameter name="ion_positions">
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<string>
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from_input
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</string>
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</parameter>
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</field>
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<field name="Numerics">
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<parameter name="ecutwfc">
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<real>
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15.0
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</real>
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</parameter>
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<parameter name="ecutrho">
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<real>
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60.0
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</real>
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</parameter>
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<parameter name="conv_thr">
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<real>
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1.d-6
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</real>
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</parameter>
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</field>
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<field name="Options">
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<parameter name="nbnd">
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<integer>
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8
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</integer>
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</parameter>
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<parameter name="occupations">
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<string>
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ensemble
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</string>
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</parameter>
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<parameter name="smearing">
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<string>
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fd
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</string>
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</parameter>
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<parameter name="degauss">
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<real>
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0.025
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</real>
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</parameter>
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</field>
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<field name="Fields">
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<parameter name="nspin">
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<integer>
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1
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</integer>
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</parameter>
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</field>
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<field name="CP">
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<!--nstep, dt, ion_dynamics e ion_temperature esistono anche nel PW
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ma nn sapevo in che field metterli -->
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<parameter name="nstep">
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<integer>
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5
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</integer>
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</parameter>
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<parameter name="dt">
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<real>
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10.0d0
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</real>
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</parameter>
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<parameter name="ion_dynamics">
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<string>
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damp
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</string>
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</parameter>
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<parameter name="ion_temperature">
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<string>
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not_controlled
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</string>
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</parameter>
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<!-- Da qui in poi esistono solo in CP-->
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<parameter name="isave">
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<integer>
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10
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</integer>
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</parameter>
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<parameter name="nr1b">
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<integer>
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20
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</integer>
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</parameter>
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<parameter name="nr2b">
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<integer>
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20
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</integer>
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</parameter>
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<parameter name="nr3b">
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<integer>
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20
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</integer>
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</parameter>
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<parameter name="emass">
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<real>
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1000.d0
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</real>
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</parameter>
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<parameter name="emass_cutoff">
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<real>
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4.d0
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</real>
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</parameter>
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<parameter name="orthogonalization">
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<string>
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Gram-Schmidt
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</string>
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</parameter>
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<parameter name="ampre">
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<real>
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0.02
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</real>
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</parameter>
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<parameter name="n_inner">
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<integer>
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8
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</integer>
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</parameter>
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<parameter name="tcg">
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<logical>
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TRUE
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</logical>
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</parameter>
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<parameter name="passop">
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<real>
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0.3
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</real>
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</parameter>
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<parameter name="maxiter">
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<integer>
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250
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</integer>
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</parameter>
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<!-- non esiste nel CP Help ion_damping -->
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<parameter name="ion_damping">
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<real>
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0.0
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</real>
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</parameter>
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<!-- -->
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<parameter name="greasp">
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<real>
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1.0
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</real>
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</parameter>
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</field>
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</input>
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EOF
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$ECHO " running the calculation BO-MD for Si-dimer...\c"
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$CP_COMMAND < si2.ensemble-dyn.xml > si2.ensemble-dyn.out
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check_failure $?
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$ECHO " done"
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$ECHO
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$ECHO "$EXAMPLE_DIR : done"
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