Hi Tobias,
You need to set the WriteCoorStep value. Here's a section from a random input I
once ran:
WriteCoorInital true
WriteCoorStep true
WriteForces true
WriteCoorXmol true
WriteCoorCerius false
WriteMDXmol true
WriteMDhistory true
The first two lines tell it to write the geometry (initial and in every step)
into the output file. WriteCoorXmol tells it to write the final geometry into
<seed>.xyz. WriteMDXmol creates <seed>.ANI, which has the format of an xyz movie
(I usually create a link "ln -s test.ANI trj.xyz". As I mentioned before, the
xyz format doesn't contain cell information, but is more reliable when used with
gdis. Anything with MD in it also applies to geometry optimisation (which you
can just see as a special case of dynamics).
HTH,
Herbert
On 04/02/14 13:38, Kraemer, Tobias wrote:
Dear Herbert,
I have installed gdis in the meantime. I was able to open the fdf file without
problems,
And I can nicely visualise the unit cell that I used as input. However, gdis
doesn't find
Any coordinates in the SIESTA output (you refer to this as the .sot file). I am
not sure
I am looking at the right file. My output doesn't contain coordinates which are
updated
During the run, only the input geometry in the @reading standard input"
section, later on
Only forces are reported.
Best
Tobias
-----Original Message-----
From: [email protected] [mailto:[email protected]] On Behalf Of
Herbert Fruchtl
Sent: 28 January 2014 11:53
To: [email protected]
Subject: Re: [SIESTA-L] Structure does not converge
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>
________________________________
----------------------------------------------------------------------
----------
Sunday Times Scottish University of the Year 2011-2013 Top in the UK
for student experience Fourth university in the UK and top in Scotland
(National Student Survey 2012)
We invite research leaders and ambitious early career researchers to
join us in leading and driving research in key inter-disciplinary
themes. Please see www.hw.ac.uk/researchleaders
<http://www.hw.ac.uk/researchleaders> for further information and how to apply.
Heriot-Watt University is a Scottish charity registered under charity
number SC000278.
----------------------------------------------------------------------
----------
Sunday Times Scottish University of the Year 2011-2013 Top in the UK
for student experience Fourth university in the UK and top in Scotland
(National Student Survey 2012)
We invite research leaders and ambitious early career researchers to
join us in leading and driving research in key inter-disciplinary
themes. Please see www.hw.ac.uk/researchleaders for further information and how
to apply.
Heriot-Watt University is a Scottish charity registered under charity
number SC000278.
--
Herbert Fruchtl
Senior Scientific Computing Officer
School of Chemistry, School of Mathematics and Statistics University of St
Andrews
--
The University of St Andrews is a charity registered in Scotland:
No SC013532
-----
Sunday Times Scottish University of the Year 2011-2013
Top in the UK for student experience
Fourth university in the UK and top in Scotland (National Student Survey 2012)
We invite research leaders and ambitious early career researchers to
join us in leading and driving research in key inter-disciplinary themes.
Please see www.hw.ac.uk/researchleaders for further information and how
to apply.
Heriot-Watt University is a Scottish charity
registered under charity number SC000278.
--
Herbert Fruchtl
Senior Scientific Computing Officer
School of Chemistry, School of Mathematics and Statistics
University of St Andrews
--
The University of St Andrews is a charity registered in Scotland:
No SC013532
