Bug for constraints type "xyz" in run_json.py

[yudongqiu]

Source code:

geomeTRIC/geometric/run_json.py

Line 138 in 5f2fa0b

const_rep.extend([x + 1 for x in constraint["indices"]])

Explanation:

Four constraint types are supported, namely ["xyz", "distance", "angle", "dihedral"], the current implementation is correct for the last three, such as distance 1 2 or angle 1 2 3, but is incorrect for the "xyz", because to freeze the xyz of atoms 0-2, it will generate string "xyz 1 2 3", which will trigger an error by geomeTRIC. The correct string should be "xyz 1-3" or "xyz 1,2,3"

Solution:

For the special case of constraint type "xyz", it would be useful to call the nifty.commadash() function instead of adding indices:
old:

const_rep.extend([x + 1 for x in constraint["indices"]])

new:

from geometric.nifty import commadash
...

if constraint["type"] == "xyz":
    const_rep.append(commadash(constraint["indices"]))
else:
    const_rep.extend([x + 1 for x in constraint["indices"]])

[leeping]

Could you submit a PR with this change? :) Does this affect anything outside of geomeTRIC (i.e. things on the QCFractal side)?

[yudongqiu]

Sure. I think if QCFractal tries to call geometric.run_json.geometric_run_json() with the "xyz" constraints, it will result in an error in the current implementation. Fixing the bug here should fix it for QCFractal, too.

[dgasmith]

+1 for @yudongqiu's comment. Since we pass through options this will work just fine.