QC-JSON working prototype -- Jmol

[BobHanson]

I have a working prototype in Jmol now. Very simple to test.

Just:

1. download and unzip the [Jmol latest release] (https://sourceforge.net/projects/jmol/files/latest/download?source=files)
2. start Jmol.jar and open a file...console
3. load some Jmol-readable calculation output into Jmol using the load command or by drag-dropping into the application.
4. issue WRITE xxx.qcjson.

A directory of prototypes produced this way is now in the jmol-data qcjson directory.

It is designed just to cover the area that I will be interested in for Jmol. Specifically:

Anyway, it is working. The purpose of this is not to force an issue, just to explore what is needed.

And one of the things I found I needed was an indication of the orbital normalization mode; maybe this is not needed in the final business, but I suggest we have that, as it would allow direct conversion from legacy output such as we have here.

Bob

• overall format:

["magic number/version",
{metadata block}
{job block},
{job block},
....
]

• basic job/step hierarchy

{job block} ==
{
"metadata":{....},
"steps":[{step block}, {step block},...],
"mo_bases":{
basis id: {basis block},
basis id: {basis block},
....
}
}

{step block} ==
{
"metadata":{....},
"topology": {topology block},
"vibrations":[{vibration block}, {vibration block},..},
"molecular_orbitals":{molecular orbital block},
}

{topology block} ==
{
"atoms":{atom block}
}

{atom block} ==
{
"coords_units":["angstroms",1.88972613],
"coords":[ x1, y1, z1, x2, y2, z2,....],
"symbol":["_RLE_",...run-length-encoded data...],
"atom_number":["_RLE_",...run-length-encoded data...]
}

{molecular orbital block} ==
{
"orbitals":[{orbital block},{orbital block}...],
"__jmol_calculation_type":critical jmol data",
"basis_id":basis id,
"__jmol_normalized":boolean,
"orbitals_energy_units":["?","?"]
}

{basis block} ==
{
"gaussians":[GTO gaussians array of arrays],
"shells":[GTO shells array of arrays],
"slaters":[STO slaters array]
}

etc. (sorry, I know that is not complete...)

[berquist]

For others who were wondering how to run this quickly:

#!/bin/bash

stub=${1%.*}

cat <<EOF > ${stub}.spt
load ${1}
write ${stub}.qcjson
EOF

jmol -onl ${stub}.spt
rm ${stub}.spt

If you are using SSH, you must connect with -X even though no GUI is created.

[BobHanson]

Also, you shouldn't need -x if you use JmolData instead of Jmol, as that version is headless.

[berquist]

In that case, switch the jmol call to

java -jar /usr/share/jmol/JmolData.jar -onl ${stub}.spt

and the change the jar file path as necessary.