[ase-users] Assistance Request for ASE Global Optimization Scripts for Molecular Crystals

[Adam Jackson]

Hi Grigory,

It looks like when the script creates a new “HarmonicPlusLennardJones” class it misses one of the default parameters expected by the LennardJones calculator. I think the simplest fix is to modify this line in ga_molecular_crystal_relax.py

    calc = HarmonicPlusLennardJones(epsilon=37.3 * kB, sigma=3.31, rc=12.,
                                    r0=1.12998, k=10.)

to include an “ro=None” argument. (Watch out for the r0 vs ro…)
It should also work to include “ro: None”  in the the default_parameters dictionary of HarmonicPlusLennardJones, a bit further down.

Because this class is part of a tutorial and not included in the main ASE code, I suppose it was not tested when the other classes were updated. Maybe these scripts could use a clean-up.

I hope that gets things back on track for you!

All the best,
Adam

From: ase-users <ase-users-bounces at listserv.fysik.dtu.dk> on behalf of ase-users-request at listserv.fysik.dtu.dk <ase-users-request at listserv.fysik.dtu.dk>
Date: Friday, 26 July 2024 at 11:25
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Subject: ase-users Digest, Vol 193, Issue 11
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Today's Topics:

   1. Assistance Request for ASE Global Optimization Scripts for
      Molecular Crystals (Grigory Livshits)


----------------------------------------------------------------------

Message: 1
Date: Thu, 25 Jul 2024 16:06:11 +0300
From: Grigory Livshits <grigory.livshits at gmail.com>
To: ase-users at listserv.fysik.dtu.dk
Subject: [ase-users] Assistance Request for ASE Global Optimization
        Scripts for Molecular Crystals
Message-ID:
        <CAA9T=aW7nc4RU06ThGoE4XnO5AbOnhOqFbcfHp81YZrwaMPQ1A at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Dear ASE Users,

I hope this message finds you well.

I am a beginner with the ASE software and seek your assistance with running
global optimization scripts for molecular crystals, following the guide
available at this ASE tutorial
<https://wiki.fysik.dtu.dk/ase/tutorials/ga/ga_molecular_crystal.html<https://wiki.fysik.dtu.dk/ase/tutorials/ga/ga_molecular_crystal.html>>.

While the ga_molecular_crystal_start.py script successfully creates the
starting population database gadb.db, I encounter an issue when running
ga_molecular_crystal_run.py. The script crashes within a few seconds, and
the following traceback is generated:

Traceback (most recent call last):
  File "/home/qnt/livshig1/ase/ga_molecular_crystal_run.py", line 57, in
<module>    relax(a)
  File "/home/qnt/livshig1/ase/ga_molecular_crystal_relax.py", line 24, in
relax
    calc = HarmonicPlusLennardJones(epsilon=37.3 * kB, sigma=3.31, rc=12.,
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/qnt/livshig1/ase/ga_molecular_crystal_relax.py", line 67, in
__init__
    LennardJones.__init__(self, **kwargs)
  File
"/home/qnt/livshig1/miniconda3/envs/ase/lib/python3.12/site-packages/ase-3.23.0-py3.12.egg/ase/calculators/lj.py",
line 162, in __init__
    if self.parameters.ro is None:
       ^^^^^^^^^^^^^^^^^^
  File
"/home/qnt/livshig1/miniconda3/envs/ase/lib/python3.12/site-packages/ase-3.23.0-py3.12.egg/ase/calculators/calculator.py",
line 424, in __getattr__
    return dict.__getattribute__(self, key)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: 'Parameters' object has no attribute 'ro'

For your reference, I am using ASE version 3.23.0 installed with Miniconda3
on Rocky Linux 9.4. I have also attempted running this script with ASE
version 3.22.0, but the issue persists.

I would greatly appreciate any suggestions or guidance on how to resolve
this issue.

Thank you in advance for your assistance.

Best regards,

Grigory Livshits
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