[CP2K-user] [CP2K:13450] Visualize electron density during formation of a water molecule

[hut... at chem.uzh.ch]

Hi

What I would do:

Small basis e.g. DZVP
LSD
SCF with Diagonalization and Broyden mixing, use all MOs
Fermi-Dirac Smearing with high temperature
NVT MD with velocity rescaling to get rid of excessive energy
Print CUBE file automatically during MD 

regards

Juerg Hutter
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Juerg Hutter                         Phone : ++41 44 635 4491
Institut für Chemie C                FAX   : ++41 44 635 6838
Universität Zürich                   E-mail: hut... at chem.uzh.ch
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
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-----cp... at googlegroups.com wrote: -----
To: "cp2k" <cp... at googlegroups.com>
From: "Michael Hale" 
Sent by: cp... at googlegroups.com
Date: 06/04/2020 05:08AM
Subject: [CP2K:13450] Visualize electron density during formation of a water molecule

Hey, sorry for the basic question. I've skimmed some computational chemistry books, but I still find the CP2K documentation a bit overwhelming. I'm trying to put two hydrogens an an oxygen atom near each other and watch the spontaneous assembly of a water molecule. I can make the input file and have CP2K output the forces on the atoms and a cube file that I can use to make a 3D visualization of the electron density in Mathematica. Then I update the atom positions with a simple velocity Verlet update and run CP2K again. The resulting animation looks how I want stylistically, but the behavior is clearly not accurate. The atoms come together and bounce off of each other and come back together and bounce off harder. They keep getting more energy and bouncing farther and farther away until they fly apart instead of bonding together.

Is the error that the energy calculation for the forces and electron density isn't converging and causing the erratic behavior? Is the error probably in the way I'm updating the atom positions manually? Can I use the CP2K molecular dynamics functionality to do multiple steps of the simulation at once while also outputting the cube file of the electron density for each step? Is this type of simulation of the formation of small molecules within the scope of CP2K? It seems most people typically assume the molecules are already formed and they just want to simulate how those molecules interact, not how atoms come together to form the small molecules.

This is all just for fun. I just want to watch the animations and see how "sticky" the atoms and molecules are. Thanks for any help and guidance you might provide.  
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