Rafael R. Pappalardo

Securty problem at mathchem web page.

2

Firefox refuses to connect to https://mathchem.iam.upr.si/ The message is: Did Not Connect: Potential Security Issue Firefox detected a potential security threat and did not continue to mathchem.iam.upr.si because this website...

XYZWriter odd behaviour

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## Expected behavior ## If I reorder some atoms I expect to get the right name along the right coordinates. Original coordinates: O 0.00000 0.00000 0.00000 N 2.00000 0.00000 0.00000...

Gradients only available up to Rn?

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**Describe the bug** When asking for gradients for atoms beyond Rn the output is NaN. I wonder if it is a bug. **To Reproduce** Steps to reproduce the behaviour: 1....

Sometimes I am interested in knowing the rmsd value for the modified structure. Now I need to run calculate_rmsd.py twice (with and without -p). With this simple change the rmsd...

Parser fails to read ORCA coordinates with dummy atoms

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The following input z-matrix ``` %coords ctyp internal charge 0 mult 1 pardef royl=1.4; row=2.501; roh=0.968; aoh=126.6; oylMDA=0. end coords C 0 0 0 0.000000 0.0000000 0.00000000 DA 1 0...

How difficult will be to include Cv in the output? Thanks a lot for sharing your work!

If I use numpy 1.20.3 all tests pass. But using numpy 1.21.2 the following messages appear: FAILED thermoanalysis/tests/test_thermochemistry.py::test_g16_thermochemistry - numpy.linalg.LinAlgError: Eigenvalues did not converge FAILED thermoanalysis/tests/test_thermochemistry.py::test_orca_thermochemistry - numpy.linalg.LinAlgError: Eigenvalues did...