* Re: zpasesopts problem
2021-06-02 17:00 ` Stephane Chazelas
@ 2021-06-02 17:23 ` Roger Mason
2021-06-02 20:30 ` gammafunction
0 siblings, 1 reply; 5+ messages in thread
From: Roger Mason @ 2021-06-02 17:23 UTC (permalink / raw)
To: zsh-users
Hello,
Stephane Chazelas writes:
> 2021-06-02 13:44:44 -0230, Roger Mason:
>
> You're not showing the full script, so we don't know what $argv
> contains at the time zparseopts is being invoked.
>
> I'd recommend you add a
>
> typeset -p argv
>
> before the zparseopts call.
>
> My guess would be that you're expecting $argv to be:
>
> typeset -a argv=( --symbol Si --rmt 1.55 --nocc 7 --vstates 1112 )
>
> but it's not, possibly because you've called "shift" too many
> times or with the wrong number as argument.
Here is the full script. It is rather long.
#!/usr/local/bin/zsh
action=$1
ELKVER=elk-7.1.14
case $action in
printall)
printbools="true"
printfloats="true"
printints="true"
printtexts="true"
;;
printbools)
printbools="true"
;;
printfloats)
printfloats="true"
;;
printints)
printints="true"
;;
printtexts)
printtexts="true"
;;
names)
nams="true"
;;
values)
vals="true"
;;
naval)
nvl="true"
;;
run)
run="true"
;;
*)
run="true"
;;
esac
if [[ $nams == true ]];then
names=($(awk '/! default values !/{flag=1;next}/! read from elk.in !/{flag=0}flag' \
$HOME/Software/Elk/$ELKVER-omp-fft/src/readinput.f90 \
| awk '!/!/' \
| awk '!/^if/'| awk '!/^allocate/' | awk '!/:/' \ | awk '{gsub(/ /,""); print}' \
| sed 's/[(]/_/g;s/:/_/g;s/)//g;s/,_/all_/g;s/,\([0-9]\)/_\1/g' | sort \
| awk '{gsub(/=/," "); print}' | sed 's/\.\([0-9][0-9]*\)d/\.\1e/g;s/\.d/\.e/g;s|45\.e0\*pi/180\.e0|0\.e0|g' \
| awk '{print $1}'))
# b=('--'${^tmp})
# c=$(printf '%s ' $b)
echo "Variable names:"
echo "$names"
fi
if [[ $vals == true ]];then
# These are all the default values corresponding to the options.
values=($(awk '/! default values !/{flag=1;next}/! read from elk.in !/{flag=0}flag' \
~/Software/Elk/$ELKVER-omp-fft/src/readinput.f90 \
| awk '!/!/' | awk '!/^if/'| awk '!/^allocate/' | awk '!/:/' \
| awk '{gsub(/ /,""); print}' | sed 's/[(]/_/g;s/:/_/g;s/)//g;s/,_/all_/g;s/,\([0-9]\)/_\1/g' | sort \
| awk '{gsub(/=/," "); print}' | sed 's/\.\([0-9][0-9]*\)d/\.\1e/g;s/\.d/\.e/g;s|45\.e0\*pi/180\.e0|0\.e0|g' \
| awk '{print $2}'))
# b=('--'${^tmp})
# c=$(printf '%s ' $b)
echo "Variable values:"
echo "$values"
fi
# This lists names & values together.
if [[ $nvl == true ]];then
# These are all the default values corresponding to the options.
naval=($(awk '/! default values !/{flag=1;next}/! read from elk.in !/{flag=0}flag' \
~/Software/Elk/$ELKVER-omp-fft/src/readinput.f90 \
| awk '!/!/' | awk '!/^if/'| awk '!/^allocate/' | awk '!/:/' \
| awk '{gsub(/ /,""); print}' | sed 's/[(]/_/g;s/:/_/g;s/)//g;s/,_/all_/g;s/,\([0-9]\)/_\1/g' | sort \
| awk '{gsub(/=/," "); print}' | sed 's/\.\([0-9][0-9]*\)d/\.\1e/g;s/\.d/\.e/g;s|45\.e0\*pi/180\.e0|0\.e0|g' \
| awk '{printf "%s\\t\\t%s\\n",$1, $2}'))
# b=('--'${^tmp})
# c=$(printf '%s ' $b)
echo "Variable names & values:"
echo "$naval"
fi
# Booleans only.
elkbools=($(awk '/! default values !/{flag=1;next}/! read from elk.in !/{flag=0}flag' \
~/Software/Elk/$ELKVER-omp-fft/src/readinput.f90 \
| awk '!/!/' | awk '!/^if/'| awk '!/^allocate/' | awk '!/:/' \
| awk '{gsub(/ /,""); print}' | sed 's/[(]/_/g;s/:/_/g;s/)//g;s/,_/all_/g;s/,\([0-9]\)/_\1/g' | sort \
| awk '{gsub(/=/," "); print}' | awk '{if ($2==".false." || $2==".true.") {print "-"$1":" }}'))
# These need special handling b/c they are groups of settings. There is probably a way to get them from readinput.f90.
# In addition they should be near the beginning of the elk.in so subsequent settings can override them.
elkbools=(-lowq: "${elkbools[@]}")
elkbools=(-highq: "${elkbools[@]}")
elkbools=(-vhighq: "${elkbools[@]}")
elkbools=(-uhighq: "${elkbools[@]}")
if [[ $printbools == true ]];then
echo "$elkbools"
fi
# Floats only.
elkfloats=($(awk '/! default values !/{flag=1;next}/! read from elk.in !/{flag=0}flag' \
~/Software/Elk/$ELKVER-omp-fft/src/readinput.f90 \
| awk '!/!/' | awk '!/^if/'| awk '!/^allocate/' | awk '!/:/' \
| awk '{gsub(/ /,""); print}' | sed 's/[(]/_/g;s/:/_/g;s/)//g;s/,_/all_/g;s/,\([0-9]\)/_\1/g' | sort \
| awk '{gsub(/=/," "); print}' | awk '$2 ~ /[0-9]+(\.)[0-9]*/ {print "-"$1":"}'))
if [[ $printfloats == true ]];then
echo "$elkfloats"
fi
# Integers only.
elkints=($(awk '/! default values !/{flag=1;next}/! read from elk.in !/{flag=0}flag' \
~/Software/Elk/$ELKVER-omp-fft/src/readinput.f90 \
| awk '!/!/' | awk '!/^if/'| awk '!/^allocate/' | awk '!/:/' | awk '!/xct/' \
| awk '{gsub(/ /,""); print}' | sed 's/[(]/_/g;s/:/_/g;s/)//g;s/,_/all_/g;s/,\([0-9]\)/_\1/g' | sort \
| awk '{gsub(/=/," "); print}' | awk '$2 ~ /[0-9][0-9]*/' | awk '$2 !~ /\./ {print "-"$1":"}'))
if [[ $printints == true ]];then
echo "$elkints"
fi
# Text only. Read as a string between \A\z.
# tasks is a list of integers that is not handled by elkints. They should be on separate lines.
# The newlines can be entered explicitly like this: '0\n 21'.
# ngridk is handled similarly, but using spaces vs \n.
elktexts=(-tasks: "${elktexts[@]}")
#elktexts=(-ngridk: "${elktexts[@]}")
elktexts+=($(awk '/! default values !/{flag=1;next}/! read from elk.in !/{flag=0}flag' \
~/Software/Elk/$ELKVER-omp-fft/src/readinput.f90 \
| awk '!/!/' | awk '!/^if/'| awk '!/^allocate/' | awk '!/:/' \
| awk '{gsub(/ /,""); print}' | sed 's/[(]/_/g;s/:/_/g;s/)//g;s/,_/all_/g;s/,\([0-9]\)/_\1/g' | sort \
| awk '{gsub(/=/," "); print}' | awk '$2 ~ /^\A[0-9][0-9]*\z/ {print "-"$1":"}'))
#elktexts=("${elktexts[@]}" -ngridk:)
if [[ $printtexts == true ]];then
echo "$elktexts"
fi
# ngridk. Needs special handling b/c it is an array. For some reason
# I could not get text like '1 1 1' to load into postgresql correctly.
zparseopts -D -E -A intarrays - -ngridk: -xctype:
zparseopts -D -E -A elkbools - $elkbools
zparseopts -D -E -A elkfloats - $elkfloats
zparseopts -D -E -A elkints - $elkints
zparseopts -D -E -A elktexts - $elktexts
# This accumulates most of the options that are used in elk.in
OPTSELK=""
kx=1;ky=1;kz=1 # Defaults
for key value in "${(@kv)intarrays}"; do
k=$(echo $key | tr -d '-')
${k}=${intarrays[$key]} 2>/dev/null # Discard error message: command not found:
if [[ $k == ngridk ]];then # extract kx,ky & kz for later use in postgres.
kx=$(echo "${value}" | awk '{print $1}')
ky=$(echo "${value}" | awk '{print $2}')
kz=$(echo "${value}" | awk '{print $3}')
fi
OPTSELK+="$k\n $value\n\n"
done
# echo "k = $k kx = $kx ky = $ky kz = $kz"
# exit 10
# If given on the command line, the command line versions will be used, otherwise the program defaults are used.
# Loop over the option names and set values to override the defaults.
for key value in "${(@kv)elkbools}"; do
k=$(echo $key | tr -d '-')
${k}=${elkbools[$key]} 2>/dev/null # Discard error message: command not found:
OPTSELK+="$k\n $value\n\n"
done
#echo $OPTSELK
for key value in "${(@kv)elkfloats}"; do
k=$(echo $key | tr -d '-')
${k}=${elkfloats[$key]} 2>/dev/null # Discard error message: command not found:
if [[ $k == sc ]];then # sc is used internally in the elk code vs elk.in.
k=$(echo $k | sed 's/sc/scale/g') # Should work on sc1, sc2 & sc3.
fi
if [[ $k == nempty0 ]];then # nempty0 is used internally in the elk code vs elk.in.
k=$(echo $k | sed 's/nempty0/nempty/g') # Remove 0
fi
OPTSELK+="$k\n $value\n\n"
done
# echo "$OPTSELK"
# exit 10
for key value in "${(@kv)elkints}"; do
k=$(echo $key | tr -d '-')
${k}=${elkints[$key]} 2>/dev/null # Discard error message: command not found:
OPTSELK+="$k\n $value\n\n"
done
for key value in "${(@kv)elktexts}"; do
k=$(echo $key | tr -d '-')
${k}=${elktexts[$key]} 2>/dev/null # Discard error message: command not found:
OPTSELK+="$k\n $value\n\n"
done
#echo $OPTSELK
# Other options This ensures that spsource is set in the species array
# even when not specified on the command line.
# zparseopts -D -E -A species - -spsource: -Z: -symbol: -name: -mass: -rmt: -nocc: -vstates:
# zparseopts -D -E -A species -spsource:
# spsource=${species[--spsource]:-/home/rmason/Software/Elk/$ELKVER/species/}
# species[--spsource]=${spsource}
# Z=${species[--Z]:-14}
# species[--Z]=${Z}
# symbol=${species[--symbol]:-Si}
# species[--symbol]=${symbol}
# name=${species[--name]:-silicon}
# species[--name]=${name}
# mass=${species[--mass]:-28.0855}
# species[--mass]=${mass}
# rmt=${species[--rmt]:-1.55}
# species[--rmt]=${rmt}
# nocc=${species[--nocc]:-1}
# species[--nocc]=${nocc}
# vstates=${species[--vstates]:-"1 0 1 1"}
# species[--vstates]=${vstates}
# Supercell options
zparseopts -D -E -A scopts -sx: -sy: -sz: -dry:
sx=${scopts[--sx]:-1}
sy=${scopts[--sy]:-1}
sz=${scopts[--sz]:-1}
dry=${scopts[--dry]:-no} # does not need to be retained for DB.
scopts[--sx]=${sx}
scopts[--sy]=${sy}
scopts[--sz]=${sz}
# echo "sx = $sx sy = $sy sz = $sz"
# exit 1
# Sbatch options
zparseopts -D -E -A sbopts -nodes: -mpitasks: -cppt: -memper: -time: -nodelist:
time=${sbopts[--time]:-00:30:00}
nnodes=${sbopts[--nodes]:-1} # number of nodes
mpitasks=${sbopts[--mpitasks]:-1} # number of MPI tasks
cpuper=${sbopts[--cppt]:-1} # cpus-per-task
memper=${sbopts[--mem]:-250} # memory per CPU
nodelist=${sbopts[--nodelist]:-} # no default so it does not need the re-insertion used for the others below.
sbopts[--nodes]=$nnodes
sbopts[--mpitasks]=$mpitasks
sbopts[--cpuper]=$cpuper
sbopts[--memper]=$memper
sbopts[--time]=$time
# Composition arguments
# NB: compositions with Al won't be charge balanced.
zparseopts -D -E -A comopts -xti: -xal:
# Composition arguments
xti=${comopts[--xti]-0}
xal=${comopts[--xal]-0}
comopts[--xti]=$xti
comopts[--xal]=$xal
# Job control options. If submit = no, the job is created along with
# the input tarball but nothing is sent to $target or submitted to
# slurm. Not stored in DB b/c if the job wasn't run there won't be a
# DB entry for the results.
zparseopts -D -E -A jbcopts - -submit:
submit=${jbcopts[--submit]:-yes}
# echo "Job submit = $submit"
# exit 3
if [[ ${dry} == yes ]];then
submit=no
scd="-d"
fi
# echo "submit = $submit dry = $scd"
# exit 10
# PostgreSQL options
zparseopts -D -E -A pgopts - -db:
db=${pgopts[--db]:-elk}
pgopts[--db]=$db
# Tar options
zparseopts -D -E -A taropts -tar:
tar=${taropts[--tar]:-zf}
# No tasks?
if [[ ! ${elktexts[--tasks]+x} ]];then
echo "The '--tasks' setting is mandatory."
exit 1
fi
# Species options
typeset -p argv
zparseopts -D -E -A species - -spsource:
spsource=${species[--spsource]:-/home/rmason/Software/Elk/$ELKVER/species/}
# If spsource = SpeciesGenerated, parse these options too.
if [[ $spsource == SpeciesGenerated ]];then
zparseopts -D -E - -symbol+:=chemsyms -rmt+:=rmts -nocc+:=noccs -vstate+:=vstates
echo "Parsing species options."
function addspecies()
{
ADDSPECIES+="species\n"
ADDSPECIES+=" $Z\n"
ADDSPECIES+=" '$symbol' '$name'\n"
ADDSPECIES+=" $mass\n"
ADDSPECIES+=" $rmt\n"
ADDSPECIES+=" $nocc\n"
ADDSPECIES+=" $states\n"
}
# This could be relaxed so that only the desired quantities need be
# specified. In that case the defaults need to be given in the case
# statements, somehow. Ugly.
if [[ ${#chemsyms} -ne ${#rmts} ]] || [[ ${#chemsyms} -ne ${#noccs} ]] || [[ ${#chemsyms} -ne ${#vstates} ]];then
echo "The numbers of chemical chemsyms, RMTs, occupation numbers and valence states do not match."
echo "#chemsyms = ${#chemsyms}, #rmts = ${#rmts}, #noccs = ${#noccs}, #vstates = ${#vstates}"
echo "Check your command line. Exiting."
exit -1
fi
# Additional species information to override the defaults.
ADDSPECIES=""
typeset -A helper
helper=($(seq 1 ${#chemsyms}))
echo "helper = $helper"
for item in ${(@v)helper}
do
echo "${chemsyms[$item]} ${rmts[$item]} ${noccs[$item]} ${vstates[$item]}"
case ${chemsyms[$item]} in
Si)
name=silicon
mass=28.0855
Z=14
symbol=${chemsyms[$item]}
rmt=${rmts[$item]}
nocc=${noccs[$item]}
states=${vstates[$item]}
addspecies
;;
O)
name=oxygen
mass=15.9994
Z=8
symbol=${chemsyms[$item]}
rmt=${rmts[$item]}
nocc=${noccs[$item]}
states=${vstates[$item]}
addspecies
;;
Ti)
name=titanium
mass=47.867
Z=22
symbol=${chemsyms[$item]}
rmt=${rmts[$item]}
nocc=${noccs[$item]}
states=${vstates[$item]}
addspecies
;;
Al)
name=aluminium
mass=26.981538
Z=13
symbol=${chemsyms[$item]}
rmt=${rmts[$item]}
nocc=${noccs[$item]}
states=${vstates[$item]}
addspecies
;;
*)
echo "${chemsyms[$item]} is not currently in the list of elements."
echo "Add it to the script or check your command line. Exiting."
exit -2
;;
esac
done
fi
And the output from typset -p argv is:
typeset -a argv=( filmperthite --spsource SpeciesGenerated Si --rmt 1.55 \
--nocc 7 --vstates 1112 )
So, the argument to --symbol is not being recognised.
Thanks,
Roger
^ permalink raw reply [flat|nested] 5+ messages in thread