New answers tagged python
3
votes
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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2
votes
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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3
votes
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:
...
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7
votes
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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6
votes
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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6
votes
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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4
votes
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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3
votes
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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5
votes
Accepted
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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8
votes
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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8
votes
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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11
votes
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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3
votes
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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4
votes
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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3
votes
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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3
votes
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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3
votes
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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5
votes
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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10
votes
Accepted
Generate structure using atomic coordinates
To understand the new coordinates after altering the bond length of the C-O bonds you can use the below approach:
Let us first visualize the positions of all the atoms before and after altering the ...
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