Hello, I’m working on enabling geomeTRIC optimizations in place of OptKing in our software that uses psi4.
From the geometric documentation about constraints I had assumed atoms should be indexed at 1. Which was stated on the website “Atoms are numbered sequentially starting from 1.”
However, I’m seeing an error RuntimeError: Constraints refer to higher atom indices than the number of atoms when I try to constrain the last atom in a system.
I assume that we should be indexing at 0 for atom numbers instead and I see now in the Psi4 documentation that there are examples with atom 0 in the constraints.
I’m mostly writing to confirm there is a change in using the psi4 interface to geometric since the difference doesn’t seem to be documented anywhere I can find.
I found this problem in a complex environment for our software, but was able to replicate it in a more simple conda environment (on a linux machine running Ubuntu 20):
conda create -n psi4_example python==3.9 psi4==1.7+6ce35a5 geometric==1.0 numpy==1.21.6 -c psi4 -c conda-forge
With this python script:
import psi4
molecule = psi4.geometry("""
C 0.833 1.221 -0.504
H 1.482 2.086 -0.518
C 1.379 -0.055 -0.486
H 2.453 -0.184 -0.483
C 0.546 -1.167 -0.474
H 0.971 -2.162 -0.466
C -0.833 -1.001 -0.475
H -1.482 -1.867 -0.468
C -1.379 0.275 -0.490
H -2.453 0.404 -0.491
C -0.546 1.386 -0.506
H -0.971 2.381 -0.524
no_com
no_reorient
""")
psi4.set_options({
"maxiter": 100,
"g_convergence": "gau"
})
geometric_keywords = {
'coordsys' : 'tric',
'constraints' : {
'freeze' : [{'type' : 'dihedral',
'indices' : [9, 10, 11, 12]}]
}
}
psi4.optimize('hf/cc-pvdz', engine='geometric', optimizer_keywords=geometric_keywords)