Scripting

JDFTx was designed with power users in mind and is packed with many neat features that make scripting complex sets of calculations really easy. Here we'll discover the flexibility of JDFTx by measuring elasticity (of a solid, not the code).

All previous examples used -i and -o to read commands from an input file and log to an output file respectively; one or both of these options may be omitted so that JDFTx reads from stdin and/or logs to stdout, allowing the program to be executed in a pipe.

We can combine this with the here document feature of bash to extract the energy vs. strain curve of bulk Pt with a very simple script (that never writes anything to disk):

#!/bin/bash
JDFTx=/path/to/jdftx  #Reminder: aliases don't work in scripts

#Loop over strains from -5% to +5%
for aScale in {95..105}; do

    #Compute a/2 in bohrs for the stretched lattice:
    aBy2=$(echo "scale=6; 3.92*$aScale*0.5/(100*0.5291772)" | bc)

    #Print the strain in percent as the first column:
    echo -n $((aScale-100)), " "

    #Run JDFTx to compute the energy (with input from a here document)
    #and use awk to extract and report the final energy from the log
    $JDFTx <<EOF | awk '$1=="IonicMinimize:" && $4=="F:" {print $5}'
        lattice \
            0.000 $aBy2 $aBy2 \
            $aBy2 0.000 $aBy2 \
            $aBy2 $aBy2 0.000
        ion-species Pt.fhi
        ion Pt 0 0 0  0

        kpoint-folding 4 4 4
        kpoint .5 .5 .5  1

        elec-ex-corr gga-pbe
        dump End None

        elec-n-bands 12
        elec-fermi-fillings 0 0.01
EOF
done

which produces output similar to:

-5  -2.669861355551623e+01
-4  -2.670472797610590e+01
-3  -2.670945662690582e+01
-2  -2.671274947286359e+01
-1  -2.671494598649965e+01
0  -2.671607957671839e+01
1  -2.671635927342334e+01
2  -2.671578666995583e+01
3  -2.671458307389652e+01
4  -2.671277432086174e+01
5  -2.671053667426573e+01

We can achieve the same using another feature: variable substitution in the input file. Create an input file BulkPt.in with:

:::bash
lattice \
    0.00000 ${aBy2} ${aBy2} \
    ${aBy2} 0.00000 ${aBy2} \
    ${aBy2} ${aBy2} 0.00000
ion-species Pt.fhi
ion Pt 0 0 0  0

kpoint-folding 4 4 4
kpoint .5 .5 .5  1

elec-ex-corr gga-pbe
dump End None

elec-n-bands 12
elec-fermi-fillings 0 0.01

and then the following bash script prints the energy vs strain curve:

#!/bin/bash
JDFTx=/path/to/jdftx  #Reminder: aliases don't work in scripts

#Loop over strains from -5% to +5%
for aScale in {95..105}; do

    #Compute a/2 in bohrs for the stretched lattice
    #Note that export makes this variable visible to child process jdftx
    export aBy2=$(echo "scale=6; 3.92*$aScale*0.5/(100*0.5291772)" | bc)

    #Print the strain in percent as the first column:
    echo -n $((aScale-100)), " "

    $JDFTx -i BulkPt.in | awk '$1=="IonicMinimize:" && $4=="F:" {print $5}'
done

Of course for this example, the first method is more elegant. The real power of this variable substitution lies in the fact that it happens before include commands are processed - this means that the input files can be dynamic by including different files depending on the environment!