[SIESTA-L] request help to simulate 75ZrO2 + 12.5CeO2 + 12.5Al2O3 material

with our modest career in the study of materials (mol %) 75ZrO2 + 12.5CeO2 + 12.5Al2O3, we need your help to simulate this type of material within the framework of SIESTA Code. In particular, we do not understand which cell to select and how to arrange the atoms there (CIF file is attached). Best

Re: [SIESTA-L] Convergence problem on heterostructure.

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

Re: [SIESTA-L] Convergence problem on heterostructure.

Dávila Bionanoelectronics research group School of electrical and electronics engineering Universidad del Valle Cali - Colombia On 18/11/2013, at 11:50, Максим Арсентьев ars21031...@gmail.com wrote: I also try some siesta only six months, but for a more heterogeneous structure I noticed

Re: [SIESTA-L] Convergence problem on heterostructure.

! PS: yo tambien soy caleña! Diana M. Otálvaro PhD Candidate Computational Material Science MESA+ Institute of Nanotechnology University of Twente. Enschede, Nederland -- *From:* siesta-l-requ...@uam.es [siesta-l-requ...@uam.es] on behalf of Максим Арсентьев

Re: [SIESTA-L] Convergence problem on heterostructure.

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

Re: [SIESTA-L] Convergence problem on heterostructure.

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

Re: [SIESTA-L] Convergence problem on heterostructure.

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 ars21031...@gmail.com Dear Frank

Re: [SIESTA-L] Convergence problem on heterostructure.

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

[SIESTA-L] Is it possible to engage in a computer simulation on a usual PC?

Dear Siesta users! I want to know is it possible to engage in a computer simulation on a usual PC. My config. is Core i7 3770 (3.4Ghz), 16GB RAM. How many users use usual PC for writing articles, does anyone uses Beowulf clusters? If so, pls give link how to build a Beowulf cluster -- Best

Re: [SIESTA-L] Help

Dear Kausala! - if in output file *** symbols, or convergence oscillates - set DM.MixingWeight 0.05 and PAO.EnergyShift to 65 meV as here http://www.nature.com/nnano/journal/v7/n9/extref/nnano.2012.127-s2.txt - set smaller PAO.EnergyShift 0.001 Ry, 0.005 Ry or 0.01 Ry, see

Re: [SIESTA-L] how to get a structure without strain after siesta relaxation

Dear, Dexi! You can vary residual strain by MD.MaxStressTol. Use CG, relax with MD.VariableCell False first, then input coordinates obtained to a new file with MD.VariableCell True. Note you may need to shift some atoms manually before geometry optimization: if all atoms are in 2D plane, then all

Re: [SIESTA-L] how to get a structure without strain after siesta relaxation

? And ifkgrid Monkhorst Pack option can be reserved at the same time? Yours Sincerely! Dexishao 2014-07-21 4:55 GMT+08:00 Максим Арсентьев ars21031...@gmail.com: Dear, Dexi! You can vary residual strain by MD.MaxStressTol. Use CG, relax with MD.VariableCell False first, then input

[SIESTA-L] how to get a structure without strain after siesta relaxation

was told that when MD.VariableCell is setted True, then we can not use block kgrid_Monkhorst_Pack option . Thanks very much . 2014-07-21 15:31 GMT+08:00 Максим Арсентьев ars21031...@gmail.com javascript:_e(%7B%7D,'cvml','ars21031...@gmail.com');: You right, you should perform 2 structural

Re: [SIESTA-L] how to get a structure without strain after siesta relaxation

in the structual optimazition. 2014-07-21 20:10 GMT+08:00 Максим Арсентьев ars21031...@gmail.com: When you perform internal optimization with MD.VariableCell false, cell parameters are fixed, so if you further perform full opt. with this option true cell parameters will be the same. So in both

Re: [SIESTA-L] convergence test

structual relaxation additionally. Is it all right? Thanks for all your replay! ( PS: I‘m so sorry but the service is just out of work.I'll upload my input fdf file as soon as it recovers.) Dexi Shao 2014-07-25 1:14 GMT+08:00 Максим Арсентьев ars21031...@gmail.com: Dear Dexi! You should

Re: [SIESTA-L] Ask for the W pseudopotential used in siesta

I do no thave it, but you can look at input file file for it in atom_table.txt in Pseudo\atom\Contrib directory (for this you should compare atom tutorials). Also maybe you can find it in previous siesta mailshots. Maybe someone else will be able to send it. Pls. post it here and results of tests

Re: [SIESTA-L] Ask for the W pseudopotential used in siesta

complete, not compare sorry 2014-07-26 16:07 GMT+04:00 Максим Арсентьев ars21031...@gmail.com: I do no thave it, but you can look at input file file for it in atom_table.txt in Pseudo\atom\Contrib directory (for this you should compare atom tutorials). Also maybe you can find it in previous

Re: [SIESTA-L] convergence test

Максим Арсентьев ars21031...@gmail.com: Yes, you right. To clarify 1st keep fixed high meshcutoff and vary kpoint - select kpoint and keep it fixed but vary meshcutoff Maybe this can be vice versa, or not,but possibly it is not so important (final value of meshcutoff about 350-400 Ry

Re: [SIESTA-L] convergence test

It's in French. Best wishes, Maxim. 2014-07-26 17:36 GMT+04:00 邵德喜 dxshao...@gmail.com: Thanks very much.Is it Spanish? I can't understant it ,but I 'll try my best to catch it . Dexi Shao 2014-07-26 21:24 GMT+08:00 Максим Арсентьев ars21031...@gmail.com: more easily to take only max

Re: [SIESTA-L] AuH2 example

Dear Chiu, I gave you this link because I was using these tutorials to create input for geometry optimization of graphene based systems. Unfortunately all I have now is my smartphone and I didn't ever used transiesta, so I can not help you to answer the question. Best wishes, Maxim.

Re: [SIESTA-L] how to process issues about strains(2)

Dear Dexi! There are variables which were created specially for these purposes - MD.TargetPressure and MD.TargetStress 2014-08-17 13:06 GMT+04:00 邵德喜 dxshao...@gmail.com: Suppose we have got the structure without strain,then how to get the structure with small strain? In my opinion,I

Re: [SIESTA-L] get an unreasonable structure from siesta

:42 GMT+08:00 Максим Арсентьев ars21031...@gmail.com: For geometry setting see http://dipc.ehu.es/frederiksen/tstutorial/index.php/Zig-zag_graphene_nanoribbon and http://dipc.ehu.es/frederiksen/tstutorial/index.php/AuH2-example пятница, 8 августа 2014 г. пользователь Максим Арсентьев написал

Re: [SIESTA-L] how to process issues about strains(2)

the OUTPUT file. Is that all right? 2014-08-17 21:15 GMT+08:00 Максим Арсентьев ars21031...@gmail.com: Yes, maybe first change lattice parameter by hand and fix shape of cell (MD.VariableCell false). You should obtain pressure and stress in your output. Then you can enter these values

Re: [SIESTA-L] get an unreasonable structure from siesta

For example, you can use 2 atomic layers instead of 5 (Fig. 4a), etc. 2014-08-18 21:35 GMT+04:00 Максим Арсентьев ars21031...@gmail.com: Dear Chui! How much atoms in your system. Remember, that than you double number of atoms calculations become an order longer (SolutonMethod diagon

Re: [SIESTA-L] how to process issues about strains(2)

?Or just keep k-grid and Meshcutoff same as that without strain? Thanks very much! Dexi Shao 2014-08-19 1:40 GMT+08:00 Максим Арсентьев ars21031...@gmail.com: The third is MD.VariableCell true. Correct, repeat again that before any full geom. optim. (MD.VariableCell true) you should relax

Re: [SIESTA-L] get an unreasonable structure from siesta

metal bulk, so you can check your parameters and it will be very fast. You can check your results with plane wave GGA calculations https://materialsproject.org/tasks/mp-134 2014-08-19 15:07 GMT+04:00 Максим Арсентьев ars21031...@gmail.com: Dear Chui! Sometimes geometry optim. itself is stack

Re: [SIESTA-L] get an unreasonable structure from siesta

to experiment with smaller system. You get get 2.84A for GGA or LDA? 2014-08-19 15:53 GMT+04:00 joyce79928cc . joyce79...@gmail.com: Dear Максим Арсентьев: I have calculate the Al bulk and test the k-grid for convergence. I get 2.84A lattice constant and k-grid equals to 40 bohr

Re: [SIESTA-L] get an unreasonable structure from siesta

ususally gives lattice constants lower than GGA and it is not correct to compare LDA and GGA maybe 2014-08-19 16:47 GMT+04:00 joyce79928cc . joyce79...@gmail.com: Dear Максим Арсентьев: I can't understand why 1st layer should be fixed? 1st layer connect to vacuum! 2.84A is LDA's result

Re: [SIESTA-L] how to process issues about strains(2)

much k points have to be increased? Sent from Yahoo Mail for iPhone https://overview.mail.yahoo.com?.src=iOS -- * From: * Максим Арсентьев ars21031...@gmail.com; * To: * siesta-l@uam.es siesta-l@uam.es; * Subject: * Re: [SIESTA-L] how to process issues about

Re: [SIESTA-L] lattice constant problem

PLs give us the link of the literature. K point grid should be more dense. Did you properly entered coordinates (cartesian are for ortogonal system)? 2014-08-21 21:04 GMT+04:00 Suman Chowdhury sumanchowdhur...@gmail.com: But after optimization the 2D sheet no longer remains 2D. It must have

Re: [SIESTA-L] lattice constant problem

getting the structure which I want but with zero z coordinate and with much much longer lattice constant. Cartesian coordinate can be of any system not necessarily of orthogonal system. On Fri, Aug 22, 2014 at 1:28 AM, Максим Арсентьев ars21031...@gmail.com wrote: PLs give us the link

Re: [SIESTA-L] cgvc: No target stress found

1. no 2. this was only for check (MD.TargetPressure and MD.TargetStress from the OUTPUT file in the first structual opt of STRAINED CELL) left it default what about check? the results may be close, not exactly the same. Best wishes, Maxim 2014-08-25 13:28 GMT+04:00 邵德喜 dxshao...@gmail.com:

Re: [SIESTA-L] Fwd: Forceful termination of the program

Dear Suman! I use MD.UseSaveXV with XV file for starting a new calculation (I checked this option) You can check these variables using light examples (with low computational cost) 2014-08-31 17:49 GMT+04:00 Suman Chowdhury sumanchowdhur...@gmail.com: -- Forwarded message --

Re: [SIESTA-L] error “qcn0 : NaN” in transiesta calculation

Dear Dexi, Maybe try strict params: PAO.EnergyShift65 meV DM.MixingWeight0.1 DM.NumberPulay2 What is your system? 2015-03-05 13:35 GMT+04:00 Guangping Zhang zgp...@126.com: Hi Dexi, I suspect your job converged to a very bad position. You can see this from the SCF

Re: [SIESTA-L] substrates

add vacuum layer upwand the monolayer and substrate, so you can get this calc 2016-03-14 11:25 GMT+04:00 pooja pu : > hello gud people, > > with regards > > To all siesta users noble metal monolayers are not stable in free standing > but are stable with substrates,. >

Re: [SIESTA-L] substrates

ou > have to energetically minimize. > > Regards, > Aaron > > > On 14/03/16 09:37, pooja pu wrote: > > i'll create vaccum...but how to put a monolayer on the substrate??? > > On Mon, Mar 14, 2016 at 2:52 PM, Максим Арсентьев <ars21031...@gmail.com> >

Re: [SIESTA-L] substrates

this stress should be the same in monolayer and substrate with opposite sign 2016-03-14 14:23 GMT+04:00 Максим Арсентьев <ars21031...@gmail.com>: > yes, mismatch strain due to mismatch of cell parameters of monolayer and > substrate. So shrink and expand both of them separately to

Re: [SIESTA-L] substrates

take cif files from internet, e g from https://materialsproject.org/ look papers which face of InSe is most stable construct from them layers 2016-03-14 15:47 GMT+04:00 pooja pu : > how do we simulate substrates.. like we have Au (1 1 1) surface and > InSe surface as a

Re: [SIESTA-L] substrates

gt; > > On Tue, Mar 15, 2016 at 1:00 AM, Максим Арсентьев <ars21031...@gmail.com> > wrote: > >> *vacuum layer >> >> 2016-03-14 22:30 GMT+03:00 Максим Арсентьев <ars21031...@gmail.com>: >> >>> so InSe is substrate? take this CIF >>> htt

Re: [SIESTA-L] substrates

so InSe is substrate? take this CIF https://materialsproject.org/materials/mp-22691/ and add layer upwards 2016-03-14 14:59 GMT+03:00 Максим Арсентьев <ars21031...@gmail.com>: > take cif files from internet, e g from https://materialsproject.org/ > look papers which face of InSe is

Re: [SIESTA-L] substrates

*vacuum layer 2016-03-14 22:30 GMT+03:00 Максим Арсентьев <ars21031...@gmail.com>: > so InSe is substrate? take this CIF > https://materialsproject.org/materials/mp-22691/ and add layer upwards > > 2016-03-14 14:59 GMT+03:00 Максим Арсентьев <ars21031...@gmail.com>:

Re: [SIESTA-L] Fwd: Electronic temperature default value and unit

It is smearing. When F-D is used, then it is real temperature of your system, if M-V it is not It is correct, if your system is nonmetalliuc 2016-03-20 10:07 GMT+03:00 RAJAN SINGH : > > Dear Siesta Users > > I read the manual where electronic temperature is written as

Re: [SIESTA-L] Fwd: Electronic temperature default value and unit

state > energy of system? > > Regards > Rajan > > Sent from my Sony Xperia™ smartphone > > > Максим Арсентьев <ars21031...@gmail.com> wrote: > > It is smearing. > When F-D is used, then it is real temperature of your system, if M-V it is > not > It is corr

Re: [SIESTA-L] Problems of the way to get the result of PDOS

to plot pdos you need activate PDOS block, e.g. %block ProjectedDensityOfStates -20.00 10.00 0.200 500 eV %endblock ProjectedDensityOfStates then plot *.PDOS file in e.g. excel for others use Postnikov utilites http://www.home.uni-osnabrueck.de/apostnik/download.html 2016-07-25 16:38 GMT+04:00

Re: [SIESTA-L] Band structure for doped ZGNR

to use a theory to help you with this task. One of >> them is the use of quase random structures where the "best" structure is >> generated based in disorder and entropy. >> >> On Sat, Jul 30, 2016, 17:51 Максим Арсентьев <ars21031...@gmail.com> >> wrote

Re: [SIESTA-L] Band structure for doped ZGNR

will do a massive >> work. >> >> For example, if you have 100 Atmos, and a dropping concentration of 5% >> (replace 5 atoms), you have to explore all the combination: 7.5E7. >> >> With the quase random structures theory, you get the best (must >> r

[SIESTA-L] phase transition

Dear siesta users, I want to simulate a phase transition. Please advice me which of MD type of run use, also possible examples of input files. "Anneal" seems reproduce some result similar to the result I need. Regards, Maxim.

[SIESTA-L] phase transitions via ab initio molecular dynamics

Hi everybody, I want to perform AIMD study of phase transition in Li2FeSiO4. Does anyone how much time (picoseconds) needed for phase to transform? I simulate at 300K but it is still stable after 40 picoseconds. Maybe to faster the equilibration it its better to heat it, although in real

Re: [SIESTA-L] How to get the net charge of individual atom

Mulliken are quite good, http://faculty.ims.uconn.edu/~alpay/Selected_Publications/2007_JPCM01.pdf 2016-09-07 21:01 GMT+04:00 Barnali Bhattacharya : > Dear Sir/Madam > > I am a siesta user and trying to calculate net charge of individual atom > of bilayer graphene

Re: [SIESTA-L] vdw-df calculation

that means take gga fhi pseudos from siesta link and write this to input file: XC.Functional VDW XC.authors DRSLL 2016-09-27 19:48 GMT+04:00 ZARA NBSH : > Dear Siesta users, > I found this question in mailing list but found no answer to

Re: [SIESTA-L] Not convergence in transiesta

hi, play with DM.MixingWeight and DM.NumberPulay. I recently had the same problem - when I set DM.MixingWeight 0.05 and DM.NumberPulay to 2 all come better. 2016-12-10 23:38 GMT+03:00 Leila Mikaeilzadeh : > > I'm using siesta 4.0b-485 version of siesta/transiesta with

Re: [SIESTA-L] Not convergence in transiesta

play with those two 2016-12-11 1:48 GMT+03:00 Максим Арсентьев <ars21031...@gmail.com>: > hi, > play with DM.MixingWeight and DM.NumberPulay. > I recently had the same problem - when I set DM.MixingWeight 0.05 and > DM.NumberPulay to 2 all come better. > > 2016-12-

Re: [SIESTA-L] Stars in the output file

hi, DM.numberpulay decrease, DM.mixingweight decrease 2016-12-02 16:23 GMT+04:00 Nick Papior : > It means that the number of digits is too large, so it can't be printed. > As a rule of thumb, if this happens you are so far from the minimum that > self-consistency will

[SIESTA-L] COHP curves

Dear siesta users, I used siesta to plot COHP curves in spin-polarized case and got absolutely symmetrical (along abscissa axis) COHP curves for spin up and down. What does it mean? -- Best wishes, Maxim Arsent'ev, Ph.D. (Chemistry) Laboratory of research of nanostructures Institute of Silicate

Re: [SIESTA-L] Software for cluster coordinates

vesta 2017-05-02 10:34 GMT+04:00 Ahmad Ali : > hello all, > If Anyone know the software that can be used to generate atomic > coordinates of nano-cluster. e.g. GaAs. suggest me please. > -- Best wishes, Maxim Arsent'ev, Ph.D. (Chemistry) Laboratory of research of

Re: [SIESTA-L] Software for cluster coordinates

http://jp-minerals.org/vesta/en/ 2017-05-03 0:02 GMT+04:00 Максим Арсентьев <ars21031...@gmail.com>: > vesta > > 2017-05-02 10:34 GMT+04:00 Ahmad Ali <mphysicis...@gmail.com>: > >> hello all, >> If Anyone know the software that can be used to generate atomic

Re: [SIESTA-L] structure optimisation problem

Play with DM.numberpulay and dm.mixingweight it sometimes helps -- Best wishes, Maxim Arsent'ev, Ph.D. (Chemistry) Laboratory of research of nanostructures Institute of Silicate Chemistry of RAS

Re: [SIESTA-L] Application of strain in SIESTA

look MD.TargetStress variable in manual https://departments.icmab.es/leem/siesta/Documentation/Manuals/siesta-4.0.pdf so you can apply external stress on your structrure remember siesta does not like very high pressures, but another plane-wave codes can do them (i seen this suggestion in the

[SIESTA-L] BiBO3 bandstructure calculation

Dear Siesta Users and Developers, I'm trying to calculate band structure of monoclinic (MCL) cell of BiBO3. Is my choice of points is correct? Also I concern in my choice of MeshCutoff. SystemName BiBO3 SystemLabel BiBO3 NumberOfAtoms 20 SpinPolarized .true. NumberOfSpecies 3 %block

[SIESTA-L] Atom binary

Dear siesta users and developers, Does anybody have binary file for the latest version of atom program. Bests, Maxim Arsentev, ISC RAS

Re: [SIESTA-L] << Debian 9.8+Intel+NetCDF >>

Dear siesta users and developers, Does anybody have binary file for the latest version of atom program. Bests, Maxim Arsentev, ISC RAS пн, 22 апр 2019 г., 23:03 Nick Papior : > You have a mixed usage of FPPFLAGS_* and LDFLAGS. So in the end you don't > have the include directories for NetCDF

[SIESTA-L] NoseParrinelloRahman (npr MD) cell explodes

Dear All， I used npr algorithm for graphite cell, but cell explodes 1) do i need to use anneal to avoid exploding 2) does the gamma point not enough, or cell too small 3) what about pressure - should i use 1 atm pressure for the object heating to some temperature? which pressure should I use for

[SIESTA-L] NoseParrinelloRahman (npr MD) cell explodes

Dear All， I used npr algorithm for graphite cell, but cell explodes # MgCO3 in primitive cell. SZ. Nose-Parrinello-Rahman. # SystemName MgCo3 R-3c -- SZ, 50 R -- NPR at 10 Gpa, 500K SystemLabel md_npr NumberOfSpecies 1 NumberOfAtoms 12 %block ChemicalSpeciesLabel 1 6 C %endblock

[SIESTA-L] ICOHP and bond strength

Dear SIESTA users, I'm trying to calculate the bond strength in diamond using SIESTA. I got 9.0 eV for integrated ICOHP for C-C bond in agreement with the results from other papers like this one https://www.sciencedirect.com/science/article/abs/pii/S0008622319302945 . Is it possible to exactly