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]> 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] > > ( +44 (0)131 451 3259 > > ________________________________ > > > > ------------------------------ > > 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. >
