inp files for molden

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Stine
Posts: 7
Joined: 12 Nov 2013, 10:55
First name(s): Stine
Middle name(s): Tetzschner
Last name(s): Olsen
Affiliation: University of Copenhagen
Country: Denmark

inp files for molden

Post by Stine » 12 Dec 2013, 15:38

Hi

I have a problem with generating the .inp files which can be used in Molden to illustrate the charge density, since only the .out file is generated. I had no problems in the old version of Dalton. Any suggestions?

Best regards
Stine

My submit script is:

navn=${PWD##*/stine/}
navn2=${PWD##*/stine/PhD/PrisOpgave/}

molfil=${1:?"du glemte angive mol fil"}
kerne=${molfil%.mol}
LLpol='polfil'

# polarization calculation

cat > $LLpol <<EOF
#!/bin/bash
# @ environment = COPY_ALL
# @ job_type = parallel
# @ job_name = ${navn2}pol
# @ error = \$(Host).\$(Cluster).err
# @ output = \$(Host).\$(Cluster).out
# @ wall_clock_limit =5330:00:00
# @ class = kemi6
# @ notification = never
# @ resources = ConsumableCpus(4) ConsumableMemory(4gb)
# @ queue

cd $LOADL_STEP_INITDIR
echo "Running on "`hostname`
date
SCR=/scratch/\$LOADL_STEP_ID

# EXPORT OPENMPI HERE
source /kemi/stine/.openmpi

# EXPORT INTEL STUFF HERE
source /software/kemi/intel/Compiler/composer_xe_2013/bin/compilervars.sh intel64

/kemi/stine/Dalton2013/DALTON-2013.0-Source/build/dalton -t /scratch/\$LOADL_STEP_ID -N 4 -M 4000 -d -o $navn/polar/${kerne}Molden.out $navn/*moldenpolar.dal $navn/$molfil $navn/${kerne}.guld

cp \$SCR/molden.inp $navn/polar/${kerne}POP.inp
cp \$SCR/DALTON.PROP $navn/polar/${kerne}POP.PROP
cp \$SCR/SIRIUS.RST $navn/polar/${kerne}POP.rst

date
echo ========= Job finished ===================

EOF

llsubmit $LLpol

rm -f $LLpol[/code][/color]

erik
Posts: 14
Joined: 12 Dec 2013, 12:43
First name(s): Erik
Middle name(s): Donovan
Last name(s): Hedegård
Affiliation: University of Southern Denmark
Country: Denmark
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Re: inp files for molden

Post by erik » 12 Dec 2013, 16:51

Hi Stine

The molden.inp file is also packed in the "your_job".taz.gz file. Unpack this file and it should be there

With best regards
Erik

Stine
Posts: 7
Joined: 12 Nov 2013, 10:55
First name(s): Stine
Middle name(s): Tetzschner
Last name(s): Olsen
Affiliation: University of Copenhagen
Country: Denmark

Re: inp files for molden

Post by Stine » 13 Dec 2013, 09:31

Thanks, the problem is just that I cannot find the tar file an that is why I tried to generate the .inp file. I looked up in the manual and found that the tar file should be generated by default (could be non-generated by the keyword -noarch), however, I cannot find it.

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magnus
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Affiliation: Aarhus University
Country: Denmark

Re: inp files for molden

Post by magnus » 13 Dec 2013, 11:21

You can use the -get option to copy files from the scratch directory. To get the molden.inp file you should then use

Code: Select all

-get "molden.inp"
The dalton script deletes the scratch files by default after the calculation stops which is probably the reason why you can't copy the file afterwards. The -D option can be used to avoid deleting the scratch files but then you should be careful if you run the same job again without deleting the scratch files because dalton will then use the old files.

Stine
Posts: 7
Joined: 12 Nov 2013, 10:55
First name(s): Stine
Middle name(s): Tetzschner
Last name(s): Olsen
Affiliation: University of Copenhagen
Country: Denmark

Re: inp files for molden

Post by Stine » 13 Dec 2013, 11:23

Thanks:) I will try that.

erik
Posts: 14
Joined: 12 Dec 2013, 12:43
First name(s): Erik
Middle name(s): Donovan
Last name(s): Hedegård
Affiliation: University of Southern Denmark
Country: Denmark
Contact:

Re: inp files for molden

Post by erik » 13 Dec 2013, 13:08

The -get option should work, yes. I'm a bit mystified that you do not get *any* tar.gz file... It should be copied to the run-directory per. default or there should at least be a meesage saying something like
"your_file.tar.gz has not been created and has thus not been copied to /fend03/someDIR/"

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