[CP2K-user] [CP2K:13471] Visualize electron density during formation of a water molecule
hut... at chem.uzh.ch
hut... at chem.uzh.ch
Sun Jun 7 12:34:08 UTC 2020
Hi
this worked for me
&MOTION
&MD
ENSEMBLE NVT
STEPS 1000
TIMESTEP 0.25
&THERMOSTAT
TYPE CSVR
&CSVR
TIMECON 0.1
&END
&END THERMOSTAT
&END MD
&END MOTION
&SCF
ADDED_MOS 20
&DIAGONALIZATION
&END DIAGONALIZATION
&MIXING
ALPHA 0.1
&END MIXING
&SMEAR
METHOD FERMI_DIRAC
&END SMEAR
MAX_SCF 50
EPS_SCF 1.E-6
&END SCF
&MGRID
CUTOFF 200
&END
Use periodic boundary conditions, it makes the trajectory more smooth.
--------------------------------------------------------------
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
---------------------------------------------------------------
-----cp... at googlegroups.com wrote: -----
To: "cp2k" <cp... at googlegroups.com>
From: "Michael Hale"
Sent by: cp... at googlegroups.com
Date: 06/06/2020 07:01PM
Subject: Re: [CP2K:13471] Visualize electron density during formation of a water molecule
Well I filled out the input file as well as I could figure out from your tips. CP2K runs for a few minutes and then aborts with the error "KS energy is an abnormal value (NaN/Inf)". I tried setting a small MAX_SCF value, but it still hits that error. Any other tips? Here is my input file:
&GLOBAL
PROJECT water-formation
RUN_TYPE MD
PRINT_LEVEL LOW
&END GLOBAL
&MOTION
&MD
ENSEMBLE NVT
&THERMOSTAT
TYPE CSVR
&END THERMOSTAT
&END MD
&END MOTION
&FORCE_EVAL
&SUBSYS
&KIND H
BASIS_SET DZVP-GTH-PADE
POTENTIAL GTH-PADE-q1
&END KIND
&KIND O
BASIS_SET DZVP-GTH-PADE
POTENTIAL GTH-PADE-q6
&END KIND
&CELL
ABC 10 10 10
PERIODIC NONE
&END CELL
&COORD
H 4.0 4.0 4.66667
H 6.0 6.0 4.66667
O 5.0 5.0 5.66667
&END COORD
&END SUBSYS
&DFT
BASIS_SET_FILE_NAME data/BASIS_SET
POTENTIAL_FILE_NAME data/POTENTIAL
LSD
&SCF
ADDED_MOS 10
&DIAGONALIZATION
&END DIAGONALIZATION
&MIXING
METHOD BROYDEN_MIXING
&END MIXING
&SMEAR
METHOD FERMI_DIRAC
&END SMEAR
&END SCF
&XC
&XC_FUNCTIONAL PADE
&END XC_FUNCTIONAL
&END XC
&PRINT
&E_DENSITY_CUBE
&EACH
MD 1
&END EACH
FILENAME CUBE
&END E_DENSITY_CUBE
&END PRINT
&END DFT
&END FORCE_EVAL
On Thursday, June 4, 2020 at 10:10:06 AM UTC-4, Michael Hale wrote:
Great! Thank you. I'll look into those options and hopefully mess with it some more this weekend.
Is there much of a hobbyist community around computational chemistry? I'm a pretty experienced software developer, but still new to this. I know there are projects like Folding at Home which don't give you much control, and Chemistry Stack Exchange which is more just traditional Q&A. But I'd love to find community projects to help enhance digital chemistry textbooks with ab initio quantum MD animations of common reactions and such.
I actually first tried this during a weekend a couple of years ago. Here was the result:
https://www.youtube.com/watch?v=foG5LgFYb2o
I finally revisited it a week or two ago. I thought maybe just my initial conditions needed to be tweaked, but then I realized my simulation set up had deeper problems, haha. Thanks again for your help. I hope to post an update again soon.
On Thursday, June 4, 2020 at 9:26:25 AM UTC-4, jgh wrote: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
--------------------------------------------------------------
Juerg Hutter Phone : ++41 44 635 4491
Institut für Chemie C FAX : ++41 44 635 6838
Universität Zürich E-mail: h... at chem.uzh.ch
Winterthurerstrasse 190
CH-8057 Zürich, Switzerland
---------------------------------------------------------------
-----c... at googlegroups.com wrote: -----
To: "cp2k" <c... at googlegroups.com>
From: "Michael Hale"
Sent by: c... 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.
--
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to c... at googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/e90450de-cd30-4bad-ae96-96779a50764e%40googlegroups.com.
--
You received this message because you are subscribed to the Google Groups "cp2k" group.
To unsubscribe from this group and stop receiving emails from it, send an email to cp... at googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/cp2k/59156e08-bd00-4591-b2c1-878ac6010be5o%40googlegroups.com.
More information about the CP2K-user
mailing list