Hi Tobias,
Try gdis for visualisation. It can shoe you a movie from a .sot (standard SIESTA
output), even though it sometimes does it wrong. Haven't found out yet when this
happens. You can also create an xyz (not periodic, but readable by most viewing
programs) movie with the WriteMDxmol flag. Rename the .ANI file to something
ending with .xyz.
Which optimizer do you use? I find CG safest.
HTH,
Herbert
On 28/01/14 10:07, Kraemer, Tobias wrote:
Dear Abraham,
Thanks for your detailed response. I did check the convergence of my
calculations, and I should have included this in
My previous post. So here is what happens in this calculation:
1)The force oscillates quite significantly within the set 500 optimisation
steps, and taken that the MaxForceTol is set to 0.04 eV/Ang,
This seems to be far from convergence to me. Here is a snapshot of the last 10
steps.
Max 0.580458 constrained
Max 0.174727 constrained
Max 0.082654 constrained
Max 0.080264 constrained
Max 0.115938 constrained
Max 0.354063 constrained
Max 0.164293 constrained
Max 0.236174 constrained
Max 0.114993 constrained
Max 0.060479 constrained
2)The unit cell seems to undergo some significant change, at least to my eye.
outcell: Cell vector modules (Ang) : 9.534700 11.749500 15.878700
outcell: Cell vector modules (Ang) : 9.675640 11.898404 16.056706
outcell: Cell vector modules (Ang) : 9.901185 12.136756 16.341658
[...]
outcell: Cell vector modules (Ang) : 9.017619 11.059155 15.490068
outcell: Cell vector modules (Ang) : 9.018024 11.060081 15.486998
outcell: Cell vector modules (Ang) : 9.018673 11.061565 15.482088
outcell: Cell vector modules (Ang) : 9.018155 11.060380 15.486008
outcell: Cell vector modules (Ang) : 9.018614 11.058782 15.482515
outcell: Cell vector modules (Ang) : 9.018461 11.059315 15.483680
outcell: Cell vector modules (Ang) : 9.020634 11.060348 15.484791
outcell: Cell vector modules (Ang) : 9.024112 11.062001 15.486571
Inspecting the last structure, I can at least say that the structure does not
blow-up or do anything that is unpredicted (I am looking at
This from the perspective of someone who has done gas phase DFT / ab initio
calculations on molecular/cluster systems, but I guess
There is some common ground here). I need to figure out a way though how to
visualise single steps of the optimisation itself,
Like I would do in one of my more regular calculations. I am sure there must be
a way to do this with XCrysden (the program I am using
Currently).
So following what you have said in your email, I will try your suggestions and
play around with the optimisation protocol.
However, what still worries me is if this possibly has something to do with the
(downloaded) pseudopotentials I have chosen.
I feel there are a lot of things that can go wrong here....
Anyways, I will keep you posted. Thanks again for your comments.
Tobias
*From:*[email protected] [mailto:[email protected]] *On Behalf Of
*Abrah
am Hmiel
*Sent:* 24 January 2014 20:40
*To:* Siesta, Self-Consistent DFT LCAO program, http://www.uam.es/siesta
*Subject:* Re: [SIESTA-L] Structure does not converge
Tobias,
I'm curious, what do the results of the following commands look like?
1) fgrep "constrained" 1.out
2) fgrep "outcell: Cell vector modules (Ang)" 1.out
*where 1.out is the name of the output log file
You don't have to print them and send them our way, as they'll be very large,
but what can you say about them in general? Are the forces fluctuating about a
small amount that isn't quite as small as the threshold you've chosen? Are the
lattice parameters very different from what you started with? Is everything
blowing up?
In general, this is what I do. Instead of doing one relaxation with a very large
number of CG steps, perform several in steps, making sure the UseSaveData flag
is set to true so that you don't have to come up with a new density matrix each
time and can use the previous CG trajectory information as well:
1) Do one with MD.NumCGSteps ~ 10 and MD.MaxCGDispl ~ 0.15 Ang, to perform a
very coarse relaxation (it is unlikely you will meet the threshold, and that's
okay. You're not done). Call the output file 1.out or something like that.
2) Do one with MD.NumCGSteps ~ 20 and MD.MaxCGDispl ~ 0.05 Ang, to perform a
coarse relaxation. Call the output file 2.out
3) Do one with MD.NumCGSteps ~ 20 and MD.MaxCGDispl ~ 0.01 Ang, to perform a
finer relaxation. Call the output file 3.out
...
as many successive steps as you need with as much fineness as desired or until
you meet your force convergence criteria, at which point you will have a relaxed
structure. If 'everything is blowing up' then you may have to take another look
at your simulation parameters. Sometimes choosing the wrong Pulay mixing
parameters will prevent your simulation from falling into a convergence basin,
so another look at that may be helpful. Transition metals sometimes call for
using small (~0.01 or smaller) DM.MixingWeight with a kick every several steps
(see the manual).
Warm regards,
--
*Abraham Hmiel*
Katherine Belz Groves Fellow in Nanoscience
Xue Group, SUNY College of Nanoscale Science and Engineering
http://abehmiel.net/about
On Fri, Jan 24, 2014 at 1:09 PM, Kraemer, Tobias <[email protected]
<mailto:[email protected]>> wrote:
Dear SIESTA users,
I am very new to the SIESTA code, so to start with I am familiarising myself
with the protocols involved to run
calculations with the code. I am trying to reproduce some numbers from a paper,
where a crystal structure
(triclinic system) of a Ru-allyl complex was relaxed (Organometallics, 2013, 32,
3784). I have set up a SIESTA input for relaxing
this structure, using PBE with the default DZP basis sets for all atoms, along
with pseudopotentials from the SIESTA
database (I am aware that this might not be the best choice, but to start with
it might be a fair option). The calculation
seems to fail to converge to a minimum structure and stops after the default 500
opt cycles. This makes me suspicious,
since my feeling is that the structure should have converged within 500 cycles.
The SCF cycles converge fine.
I have attached my input file below, the structure is read in from an external
xyz file (attached). I have used as many
default settings for the moment as possible. I would appreciate if you could
share your experience and advice on this subject.
Is such an input in principle a good starting point for the task at hand? What
could I improve?
Would the use of a Monkhorst-Pack grid be a better choice? There are some other
Questions regarding dispersion corrections but first I need to play around with
what I
understand from the manual.
Kind regards, thanks for everybody’s help. Really trying to learn how to get
reliable results.
Tobias
SystemName [Ru(AcCN)2(Cp*)(eta3-phenylallyl) unit cell
SystemLabel ru_allyl
NumberOfAtoms 160
NumberOfSpecies 7
WriteMullikenPop 1
%block ChemicalSpeciesLabel
1 44 Ru # Species index, atomic number, species label
2 15 P
3 9 F
4 8 O
5 7 N
6 6 C
7 1 H
%endblock ChemicalSpeciesLabel
MeshCutoff 400.0 Ry
NetCharge 0.00
XC.functional GGA
XC.authors PBE
SpinPolarized .false.
DM.NumberPulay 4
DM.MixingWeight 0.3
DM.UseSaveDM .true.
NeglNonOverlapInt False
AtomicCoordinatesFormat NotScaledCartesianAng
AtomicCoordinatesAndAtomicSpecies < ru_allylinput.xyz
LatticeConstant 1.0 Ang
%block LatticeParameters
9.5347 11.7495 15.8787 109.395 96.719 100.965
%endblock LatticeParameters
WriteCoorXmol True
WriteForces .true.
WriteMullikenPop 1
SaveDeltaRho .true.
MD.TypeOfRun cg # Type of dynamics: Conjugate gradients
MD.NumCGsteps 500 # number of CG steps
MD.MaxCGDispl 0.15 Ang
MD.MaxForceTol 0.04 eV/Ang
MD.UseSaveXV yes
MD.VariableCell .true.
________________________________
Dr. Tobias Kraemer
Research Associate
Institute of Chemical Sciences
School of Engineering & Physical Sciences
Heriot-Watt University
Edinburgh EH14 4AS
United Kingdom
* [email protected] <mailto:[email protected]>
( +44 (0)131 451 3259 <tel:%2B44%20%280%29131%20451%203259>
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We invite research leaders and ambitious early career researchers to join us in
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