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Using OpenBabel's gen3d in a Python notebook

The command-line --gen3d option can do a variety of things, including coordinate generation, some force field cleanup, and a quick conformer search. As mentioned in ...
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Lennard Jones Clusters in Python

Potential The Lennard-Jones potential has a simple form: $$V_{\rm LJ} (r) = 4\epsilon \left[ \left( \frac \sigma r \right)^{12} - \left( \frac \sigma r \right)^{6} \right].$$ In python, this could ...
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Accepted

Using OpenBabel's gen3d in a Python notebook

Here is a simple python recipe in addition to the CLI approach mentioned in the other answer, for more details see the docs: ...

Using OpenBabel's gen3d in a Python notebook

From the openbabel documentation : Open Babel will not generate coordinates unless asked, so while a conversion from SMILES to SDF will generate a valid SDF file, the resulting file will not contain ...
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Constrained optimisation on a hypersphere

I'll propose a slightly different Lagrangian expression:  L = E' + g^T \Delta x + \frac{1}{2} \Delta x^T H \Delta x + \frac{1}{2} \gamma \Delta x^T \Delta x - \frac{1}{2} \lambda (p^T p - k). \tag{1}...
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How can I build the wheels necessary for a quick installation of PySCFad on a "compute node"?

I finally got it working! Explanation of the error The above procedure installed the "main" branch of "pyscf_properties" rather than the "ad" branch. It seems that due ...
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How to make a Python code that can extract interatomic distances, angles and dihedrals from an xyz file

RDKIT Getting the distance between atoms, angle and dihedral between atoms can be achieved with a python library called rdkit. For the sake of brevity, I will demonstrate using a simple compound: ...
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Which Python packages, APIs or online databases may be used for a Python script to find bond dissociation energy between two arbitrary atoms?

PySCF Bond dissociation energies are either found by laboratory experiments followed by spectroscopic analysis, or by ab initio calculations. Secondary research could be done to find bond dissociation ...
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Unexpected atoms while working with XYZ files in rdkit

Here is a demo how to work with MolFromXYZ. You can choose rdDetermineBonds.DetermineConnectivity for bonds or ...
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Easy ways to generate "teaching" band structures in Python?

Another package (sisl) can do the same thing, but a bit more verbose and dynamic. (disclaimer, I am the author). One of sisl's main goal is to interact with large TB models, and thus the complexity of ...
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Running an ORCA calculation from Python

As the other answers and comments have suggested, the problem is probably coming from how Python is launching ORCA. Because I cannot see any reason the job should run from command line, but not from ...
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Accepted

Running an ORCA calculation from Python

I ran your script on my PC with Python and it ran perfectly fine. Here are all of the required PC specifications: System Specs ...
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Running an ORCA calculation from Python

What you are thinking of is a workflow manager. I have recently had some success with Signac -- it automates repetitive calculations over a parameter space, automatically saving state between subtasks ...
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Generate structure using atomic coordinates

The easiest way to do this IMHO is through Open Babel / Pybel, particularly if you want to set a lot of bonds. BTW, reading from XYZ, the bond orders are interpreted, but not always exactly. In ...
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How to calculate phase regions using CALPHAD for higher order systems (>3 elements)?

I assume someone at TCSAB (which market Thermo-Calc) can answer this better but as I participated in developing TC a long time ago and now I work on a similar free software called OpenCalphad (I ...
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Accepted

Is PySCF able to print checkpoint files during a CISD calculation?

As far as I know, there isn't a native way to do this, e.g. an option that can be passed to CISD. The dump_chk option is never passed to ...
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How to create png files of right angle Lewis notation

I have created a python library called pychemprojections to create such visualisations of 2D molecule projections. (Made the first release an hour ago 😁) It can be installed with pip like this: <...
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Python script for Metropolis Monte Carlo (global optimisation)

A properly-run Metropolis Monte Carlo algorithm does not perform global optimisation. It returns the stationary distribution of a random process. In this case, you have specified an acceptance rule ...
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