Hi Herbert,
Thanks for your suggestions. Will try gdis, sounds like what I am looking for. For the optimizer I did use conjugate gradients indeed. 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.
