Dear Frank! Thank you, your advice was helpful - I now examine the behavior of different GridCellSampling. And to select correct parameters for the geometry optimization in my case I found an article with similar studies of CeO2 solid solutions (due to low defect concentration limit they performed only internal optimization with parameters equal that of purre CeO2). http://www.pnas.org/content/103/10/3518.full
Best wishes, Maxim 2013/11/25 Frank Maier <[email protected]> > Hi Maxim, > > In the graph from my previous mail, normal_main is the DNA base pair > adenine:thymine. The identical simulation with Grid Cell Sampling turned on > is displayed by gridcell_main. So you might also try to use > Gridcellsampling to further reduce the max. tot. forces, because your > MeshCutoff with 800 Ry is pretty large already for my experience. > > Maybe a few others, who simulate a similar system to yours have a few > further ideas, because my system consists of isolated molecules only :-) I > also never played with the MD.MaxCGDispl or DM.Tolerance. > > Best wishes, > Frank > > > On 11/25/2013 09:28 AM, Максим Арсентьев wrote: > > Sorry for my sluggishness - the picture above vise versa - it seems that > higher MD.MaxCGDispl gives higher forces, but maybe they will decrease > faster... > Also my MeshCutoff is already 800 because of Ce > > Best wishes, Maxim. > > > 2013/11/25 Максим Арсентьев <[email protected]> > >> Dear Frank! >> >> It seems for "normal_main" that you never reach 0.04 eV/Angstrom. How >> to fix that? >> And here is mt result (seems that MD.MaxCGDispl 0.15 Ang and >> DM.Tolerance 0.00001 behave better). >> >> Best wishes, Maxim. >> >> >> 2013/11/22 <[email protected]> >> >> A fluctuation in max. forces is normal. Attached is a max. force graph of >>> a few CG geometry optimizations I did of isolated molecules. >>> >>> Further details are in the following PDF: (keyword EggBox Effect) >>> http://www.home.uni-osnabrueck.de/apostnik/Lectures/SIESTA-tuto.pdf >>> >>> So the lower the max. force is, the less CG steps are required in my >>> experience and only then can you achieve low MD.MaxForceTol values. >>> >>> To reduce the max. forces you have to increase the finess of the real >>> space grid, by either increasing the MeshCutOff value or making use of >>> GridCellSampling: >>> >>> http://departments.icmab.es/leem/siesta/Documentation/Manuals/siesta-3.1-manual/node47.html >>> >>> >>> Best wishes, >>> Frank >>> >>> >>> > I'm doing geometry optimisation if I correctly set it (as I understand >>> > it's >>> > by default) >>> > >>> > Best Wishes, Maxim. >>> > >>> > >>> > 2013/11/22 Herbert Fruchtl <[email protected]> >>> > >>> >> Just to clarify: You are doing MD, not a geometry optimisation, and >>> you >>> >> are surprised that the forces don't go to zero? What are you trying to >>> >> find? For a minimum energy structure, you need a geometry >>> optimisation. >>> >> In >>> >> an MD simulation the total (potential+kinetic) energy should remain >>> >> constant (depending on your ensemble...), but the forces will vary. >>> >> >>> >> Herbert >>> >> >>> >> >>> >> On 22/11/2013 08:58, Максим Арсентьев wrote: >>> >> >>> >>> Dear Sebastian! >>> >>> >>> >>> My calculations convverge at each MD cycle (about 300-400 SCF >>> cycles), >>> >>> but max force oscillate (about 0.1-0.04 eV/anstrom) and I can not >>> >>> finish >>> >>> MD, and am already at 63 cycle and the calculation cycle is still >>> >>> going, >>> >>> although the system is quite large and contains 47 atoms. My counter >>> >>> question to all: does this oscillation of forces normal? >>> >>> I would like to strict DM.Tolerance to 0.00001 (it is VERY important >>> to >>> >>> accurate calculation of forces) and to limit MD.MaxCGDispl . >>> >>> >>> >>> Best Wishes, >>> >>> Maxim >>> >>> >>> >>> >>> >>> 2013/11/21 Sebastian Caicedo Davila >>> >>> <[email protected] >>> >>> <mailto:[email protected]>> >>> >>> >>> >>> >>> >>> Hello Diana!! >>> >>> >>> >>> Thanks a lot for your suggestion! I'll give it a try and maybe >>> I'll >>> >>> be bothering you again, if it is not an imposition, of course. >>> >>> >>> >>> Gracias de nuevo, y saludos desde tu tierra! >>> >>> >>> >>> Sebastian Caicedo Davila >>> >>> Bionanoelectronics Research Group >>> >>> School of electrical and electronics engineering >>> >>> Universidad del Valle >>> >>> Cali - Colombia. >>> >>> >>> >>> >>> >>> >>> >>> On Nov 21, 2013, at 11:02 AM, <[email protected] >>> >>> <mailto:[email protected]>> <[email protected] >>> >>> <mailto:[email protected]>> wrote: >>> >>> >>> >>> Hello Sebastian, >>> >>>> >>> >>>> I have had similar problems with convergence of the scf cycle. >>> >>>> They were solved when I changed from Pulay mixing to Broyden >>> >>>> mixing for the charge density. >>> >>>> >>> >>>> Usually if something doesn't converge in 250 cycles, it probably >>> >>>> never will. Also you can play with the DM.Tolerance. For very >>> >>>> difficult systems I set it to 0.0008 and then restart from that >>> DM >>> >>>> file with a stringer convergence criterion. >>> >>>> >>> >>>> Here is the settings I am using for my calculations: >>> >>>> >>> >>>> #--------------------Convergence of >>> SCF--------------------------- >>> >>>> ---- >>> >>>> MeshCutoff 200.0 Ry # Default value PW cutoff >>> >>>> for grid >>> >>>> >>> >>>> >>> >>>> MaxSCFIterations 250 # Maximum number of SCF >>> >>>> iter >>> >>>> DM.NumberBroyden 3 >>> >>>> DM.MixingWeight 0.01 # New DM amount for >>> next >>> >>>> SCF cycle >>> >>>> DM.Tolerance 0.0001 # Tolerance in maximum >>> >>>> difference >>> >>>> DM.UseSaveDM .false. # to use continuation >>> >>>> files >>> >>>> >>> >>>> DM.NumberKick 100 >>> >>>> DM.KickMixingWeight 0.01 >>> >>>> #---------------------------------- >>> >>>> >>> >>>> Suerte! >>> >>>> >>> >>>> PS: yo tambien soy caleña! >>> >>>> >>> >>>> Diana M. Otálvaro >>> >>>> PhD Candidate >>> >>>> >>> >>>> Computational Material Science >>> >>>> MESA+ Institute of Nanotechnology >>> >>>> University of Twente. >>> >>>> Enschede, Nederland >>> >>>> ------------------------------------------------------------ >>> >>>> ------------ >>> >>>> *From:*[email protected] <mailto:[email protected]> >>> >>>> [[email protected] <mailto:[email protected]>] on >>> >>>> >>> >>>> behalf of Максим Арсентьев [[email protected] >>> >>>> <mailto:[email protected]>] >>> >>>> *Sent:*Wednesday, November 20, 2013 7:29 AM >>> >>>> *To:*[email protected] <mailto:[email protected]> >>> >>>> *Subject:*Re: [SIESTA-L] Convergence problem on heterostructure. >>> >>>> >>> >>>> >>> >>>> I forgot to tell you - besides DM.MixingWeight 0.05 I also set >>> >>>> PAO.EnergyShift to 65 meV as >>> >>>> herehttp://www.nature.com/nnano/journal/v7/n9/extref/ >>> >>>> nnano.2012.127-s2.txt . >>> >>>> >>> >>>> >>> >>>> Best wishes, >>> >>>> Dr. Maxim Arsent'ev >>> >>>> Laboratory of inorganic synthesis >>> >>>> Institute of Silicate Chemistry of RAS >>> >>>> >>> >>>> >>> >>>> 2013/11/18 Mahmoud Hammouri<[email protected] <mailto:[email protected]>> >>> >>>> >>> >>>> >>> >>>> You could also try to increase the non-equilibrium contour >>> >>>> points. >>> >>>> >>> >>>> Mahmoud >>> >>>> >>> >>>> >>> >>>> On Nov 18, 2013, at 11:22, "Sebastián Cauce do Dávila" >>> >>>> <[email protected] >>> >>>> <mailto:[email protected]>> wrote: >>> >>>> >>> >>>> Thank you very much for your suggestion. I will give it a >>> >>>> try! >>> >>>>> >>> >>>>> Sebastián Caicedo Dávila >>> >>>>> Bionanoelectronics research group >>> >>>>> School of electrical and electronics engineering >>> >>>>> Universidad del Valle >>> >>>>> Cali - Colombia >>> >>>>> >>> >>>>> >>> >>>>> On 18/11/2013, at 11:50, Максим Арсентьев >>> >>>>> <[email protected] <mailto:[email protected]>> >>> wrote: >>> >>>>> >>> >>>>> I also try some siesta only six months, but for a more >>> >>>>>> heterogeneous structure I noticed that the reduction >>> >>>>>> DM.MixingWeight reduces oscillations in convergence, so >>> try >>> >>>>>> to play with it (decrease DM.MixingWeight). See >>> >>>>>> http://www.nature.com/nnano/journal/v7/n9/extref/nnano. >>> >>>>>> 2012.127-s2.txt >>> >>>>>> Maybe someone will tell something else. >>> >>>>>> >>> >>>>>> >>> >>>>>> 2013/11/18 Sebastian Caicedo >>> >>>>>> D.<[email protected] >>> >>>>>> <mailto:[email protected]>> >>> >>>>>> >>> >>>>>> >>> >>>>>> Dear Siesta/Transiesta users, >>> >>>>>> >>> >>>>>> I've been using the software for a couple months and >>> >>>>>> made some calculations of InAs and InP unit cell quite >>> >>>>>> successfully. Now I intend to work on transiesta >>> >>>>>> calculations of a heterostructure of both these >>> >>>>>> materials (InAs bulk with InP barriers). As a first >>> >>>>>> approach I want to simulate a couple of InAs unit >>> cells >>> >>>>>> and the barriers shall be unit cells of InP, just to >>> get >>> >>>>>> a qualitative idea. The electrodes .TSHS files were >>> >>>>>> obtained from the previous calculations of the InAs >>> unit >>> >>>>>> cell. I wanted first to run a siesta calculation of >>> the >>> >>>>>> whole heterostructure, so I can take a look at the >>> >>>>>> eigenvalues and define a correct value for the >>> parameter >>> >>>>>> TS.ComplexContour.Emin, as suggested in the manual. >>> >>>>>> >>> >>>>>> The structure has 120 atoms and I'm using LDA >>> >>>>>> Pseudopotentials, obtained from the siesta webpage. >>> (In >>> >>>>>> Pseudo includes semicore electrons, so we have enough >>> >>>>>> electrons to build a zinc-blende structure). The issue >>> >>>>>> is that after 1000 SCF steps, the energy doesn't >>> >>>>>> converge at all. I'm doing a Gamma-point calculation, >>> >>>>>> but even when I make the k-grid 1x1x15 it doesn't work >>> >>>>>> either. >>> >>>>>> >>> >>>>>> I used the same MeshCutoff as for the individual >>> >>>>>> materials unit cell an 200Ry and I increased the >>> Energy >>> >>>>>> Shift, so the calculation would be a bit faster though >>> >>>>>> less precise. >>> >>>>>> >>> >>>>>> I attach the Input (INPUT.fdf, STRUCTURE.fdf) and >>> output >>> >>>>>> files. >>> >>>>>> >>> >>>>>> I would really appreciate any suggestions. >>> >>>>>> >>> >>>>>> sincerely >>> >>>>>> >>> >>>>>> Sebastian Caicedo Davila >>> >>>>>> Bionanoelectronics Group >>> >>>>>> School of Electrical and Electronics Engineering >>> >>>>>> Universidad del Valle >>> >>>>>> Cali-Colombia >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> >>> >>>>>> -- >>> >>>>>> Best wishes, >>> >>>>>> Dr. Maxim Arsent'ev >>> >>>>>> Laboratory of inorganic synthesis >>> >>>>>> Institute of Silicate Chemistry of RAS >>> >>>>>> >>> >>>>> >>> >>>> >>> >>>> >>> >>>> >>> >>>> -- >>> >>>> Best wishes, >>> >>>> Dr. Maxim Arsent'ev >>> >>>> Laboratory of inorganic synthesis >>> >>>> Institute of Silicate Chemistry of RAS >>> >>>> >>> >>> >>> >>> >>> >>> >>> >>> >>> >>> -- >>> >>> Best wishes, >>> >>> Dr. Maxim Arsent'ev >>> >>> Laboratory of inorganic synthesis >>> >>> Institute of Silicate Chemistry of RAS >>> >>> >>> >> >>> >> >>> >> -- >>> >> 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 >>> >> >>> > >>> > >>> > >>> > -- >>> > Best wishes, >>> > Dr. Maxim Arsent'ev >>> > Laboratory of inorganic synthesis >>> > Institute of Silicate Chemistry of RAS >>> > >>> >> >> >> >> -- >> Best wishes, >> Dr. Maxim Arsent'ev >> Laboratory of inorganic synthesis >> Institute of Silicate Chemistry of RAS >> > > > > -- > Best wishes, > Dr. Maxim Arsent'ev > Laboratory of inorganic synthesis > Institute of Silicate Chemistry of RAS > > > -- Best wishes, Dr. Maxim Arsent'ev Laboratory of inorganic synthesis Institute of Silicate Chemistry of RAS
