Re: [SIESTA-L] FW: compressive/tensile stress

Hi, Search your output file for lines beginning with "Stress-tensor-Voigt (kbar)". If they read something like -20.0 0.0 0.0 0.0 0.0 0.0 then it is really compression. Conversely, for tension you'd get +20.0 ... Of course this assumes you've run some energy minimization up to convergence. Best,

Re: [SIESTA-L] Siesta compilation problem

Hi, You're missing scalapck (parallel lapack). Regards, Roberto On 10/03/2014 08:29 PM, Nilesh Dhumal wrote: Hello, I am trying to compile siesta in parallel and I am getting following error. I have attached the make file. Could you tell whats going wrong? Thanks, Nilesh

Re: [SIESTA-L] [***Posible SPAM***]

Hi, I think you are missunderstanding the distance axis of the pseudopotential components: r=2 (a.u.) means 2 Bohr, which is about 1 Angstrom. Regards, Roberto On 06/22/2015 05:17 PM, woso...@df.ufpe.br wrote: Dear users My name is William Sosa the purpose of this email is about of some pr

Re: [SIESTA-L] [***Posible SPAM***]

Hello William, Your output says nothing to me, in the first place, how do you know you're having a problem?. Mesh cutoff refers to the grid size for numerical integrations in real space (different thing from plane wave codes). Values in the range 300 to 500 Ry should be pretty fine. The larger t

Re: [SIESTA-L] run parallel siesta

Hi, Fetch the man pages for command "mpirun". Generally, it is something like mpirun -np nproc < input.fdf > output.out where "nproc" is the number of parallell processes you want. On the other hand, if you must go through a queuing system, then better ask your local admin. Regards,

Re: [SIESTA-L] run parallel siesta

Hi, That's because you're giving "mpirun" the wrong version. Let's call siesta.exe the parallell version you've compiled, then type mpirun -np nproc siesta.exe < input.fdf > output By the way, if you're using a real cluster (instead of a single multicore machine), do not forget the "--

Re: [SIESTA-L] fixed cell side calculation

Hi, Try killing the corresponding stress component, stress(3,3)=0 or something like that. R. On 08/26/2015 04:35 PM, sanjayna...@jncasr.ac.in wrote: Dear SIESTA Users, Can any body suggest me what exactly I have to write to fix a particular cell-side in constr.f

Re: [SIESTA-L] How to eliminate or reduce vibration among molecules?

Hi, I don't know what you mean exactly by "eliminate vibration", but check the manual for the GeometryConstraints block. For instance, you could fix individual coordinates, or kill forces, etc. Regards, Roberto On 09/09/2015 12:01 PM, Hongyu Shen wrote: Dear SIESTA users, I wonder if the SIES

[SIESTA-L] Voigt convention for stress

Dear developers, Let me point out a small inconsistency in the way siesta outputs stress, that confused me for a while: The off-diagonal elements of "Stress-tensor-Voigt" are written in the order 12,23,13 (write_subs.F). This is at variance with the standard convention, 23,13,12, which by the way

Re: [SIESTA-L] error while using Vibra utility

Hi, So, how big is your (vibrating) unit cell ?, 50 atoms ?. Each atom of the unit cell is responsible for 6*50=300 rows in the *.FC file. Thus, for 600 rows you must have a unit cell of 2 atoms. I bet this is not what you want; probably your FCfirst and/or FClast are wrong. Regards, Roberto O

Re: [SIESTA-L] error while using Vibra utility

Just a small bit: strictly your FC file must containt 600+1 rows. R. On 10/02/2015 09:28 AM, pooja pu wrote: Hello Yes it has two atoms in the unit cell the fcfirst and fclast are at 26 and 27 atom. Thanks a lot Pooja On 2 Oct 2015 17:50, "RCP" mailto:pasia...@cnea.gov.ar>>

Re: [SIESTA-L] error while using Vibra utility

then it has 600 rows with 3 collumn here is that .FC file and a input FCbuilder fdf. thanks pooja On Fri, Oct 2, 2015 at 6:10 PM, RCP wrote: Just a small bit: strictly your FC file must containt 600+1 rows. R. On 10/02/2015 09:28 AM, pooja pu wrote: Hello Yes it has two atoms in the unit

Re: [SIESTA-L] Minimum split_norm parameter

Hi, Default split norm parameter for DZ basis is 0.15, but for some of your pseudos/species this is not possible. Just choose a larger PAO.SplitNorm (check the manual). Best, Roberto On 10/25/2015 03:55 PM, Hamidreza Balangi wrote: Hi Dear friends, I encountered to run my system with the

[SIESTA-L] Puzzled about ParallelOverK feature

Dear everyone, I seem to have a misunderstanding on how the Diag.ParallellOverK feature works, any comment would be much appreciated. I've got a large metallic cell, though still with 9 k-points, that runs on a quad PC; moreover, routine diagkp shows k-points are distributed round robin among pr

Re: [SIESTA-L] Puzzled about ParallelOverK feature

ization is not everything in the program, check your TIMES file to figure out whether it _is_ the diagonalization or a mixture. 2015-11-02 19:42 GMT+01:00 RCP mailto:pasia...@cnea.gov.ar>>: Dear everyone, I seem to have a misunderstanding on how the Diag.ParallellOverK feat

Re: [SIESTA-L] Puzzled about ParallelOverK feature

other hand for np=5 the time taken would be something like 2* 1/0.80 = 2.5, or even shorter, 1/0.80 + 1 = 2.25. ¿What is flawed with this argument?. Best regards, Roberto On 11/02/2015 05:50 PM, Nick Papior wrote: 2015-11-02 21:37 GMT+01:00 RCP mailto:pasia...@cnea.gov.ar>>: T

Re: [SIESTA-L] Puzzled about ParallelOverK feature

ormance. -Salvador *From:* siesta-l-requ...@uam.es on behalf of Nick Papior *Sent:* Monday, November 2, 2015 4:08 PM *To:* siesta-l@uam.es *Subject:* Re: [SIESTA-L] Puzzled about ParallelOverK feature 2015-11-02 22:37 GMT+01:00 RCP mailto:pasia...@cnea.gov.ar>>: Hi Nick, Plea

Re: [SIESTA-L] Puzzled about ParallelOverK feature

-- Take care, Roberto On 11/03/2015 08:28 AM, Nick Papior wrote: 2015-11-03 12:10 GMT+01:00 RCP mailto:pasia...@cnea.gov.ar>>: Hi, Thanks for your time and sharing of wisdom. In general terms I do agree with you Nick, in the sense that running several sequential

Re: [SIESTA-L] Puzzled about ParallelOverK feature

function used. 2015-11-03 14:03 GMT+01:00 Nick Papior mailto:nickpap...@gmail.com>>: That is crazy, and it is _amazing_! Nevertheless, I would still not recommend you do these kind of things. 2015-11-03 13:37 GMT+01:00 RCP mailto:pasia...@cnea.gov.ar>>:

Re: [SIESTA-L] Segmentation fault-like error in siesta

Hi, No, it is not segmentation fault. The complaint stems from the file "mol1_gas_phase_3.67_ang.XV" that it is trying to read. Either it is not there at all or is incomplete (end-of-file) R. On 11/06/2015 07:39 AM, Sukanya Ghosh wrote: Dear siesta-users, I am facing some weird kind of problem

Re: [SIESTA-L] Segmentation fault-like error in siesta

Hi, I haven't done much MD with Siesta, but recall that restarting might be a bit tricky. 1) First, you've run out of computing time, so check you're restarting from a well defined state. 2) You must set MD.UseSave.XV to .true. in the input data file. 3) You must have a *.RESTART file, generated b

Re: [SIESTA-L] Segmentation fault-like error in siesta

ther ask your administrator to increase running time (I would prefer this option), or to reduce your number of steps so that the file is written ok. -Salvador From: siesta-l-requ...@uam.es on behalf of RCP Sent: Friday, November 6, 2015 12:00 PM To: siesta-l

Re: [SIESTA-L] "Error in Cholesky factorisation in cdiag" during geometry optimization

Hi. Sometimes disabling the DivideAndConquer option helps. Good luck, Roberto On 11/21/2015 02:06 AM, LinZhengzhe wrote: Dear SIESTA Users, When I performed geometry optimization using SIESTA, sometimes it stopped abnormally with "Error in Cholesky factorisation in cdiag" after dozens of hund

Re: [SIESTA-L] siesta + kgrid-cutoff parameter

Hi, On 11/24/2015 09:20 AM, azar ostovan wrote: Dear, siesta users The kgrid-cutoff parameter no need in the calculation with kgrid_Monkhorst_Pack block? Correct, kgrid-cutoff sets the M&P grid for you. Roughly you may think of it as the density of k-points: the larger the value the tight

Re: [SIESTA-L] Max job run time

Hi, No, there isn't. But there are several counters you may play with, e.g. MD.NumCGSteps. Besides, if you are running through a queuing system, the maximum time allowed is set in the queue properties: once reached the job will surelly (safely?) be killed ... R. On 11/24/2015 09:59 AM, Thong, Aar

Re: [SIESTA-L] siesta + kgrid-cutoff parameter

xtend the structure in z-direction? Warm regards azar On Tue, Nov 24, 2015 at 4:22 PM, RCP wrote: Hi, On 11/24/2015 09:20 AM, azar ostovan wrote: Dear, siesta users The kgrid-cutoff parameter no need in the calculation with kgrid_Monkhorst_Pack block? Correct, kgrid-cutoff sets the M&

Re: [SIESTA-L] Parallel compile and run

Hi, The problem is not MPI but your data file. So, try a data file you know it works, even if in serial mode. You could grab one from the Tests folder, or, better still, run the the tests, it is a good policy. Cheers, Roberto On 06/23/2016 05:46 PM, Mahmood Naderan wrote: Hi, As a cluster ad

Re: [SIESTA-L] Parallel compile and run

If your code was compiled for parallel execution, it should clearly say so in the head of the outpur file, just before the welcome banner. Regards, Roberto On 06/23/2016 08:04 PM, Mahmood Naderan wrote: The serial mode works for that fdf. Regards, Mahmood

Re: [SIESTA-L] Parallel compile and run

Hi, On 07/03/2016 03:40 PM, Mahmood Naderan wrote: ... mahmood@cluster:~$ mpirun -np 2 /export/apps/chemistry/siesta-3.2/ObjPar/siesta < file.fdf Siesta Version:                                       siesta-3.2 Architecture : x86_64-unknown-linux-gnu--un

Re: [SIESTA-L] Parallel compile and run

* Running in serial mode Start of run: 5-JUL-2016 1:47:51 *** * WELCOME TO SIESTA * *** ​Do you have any idea?​ Regards, Mahmood On Mon, Jul 4, 2016 at 4:53 PM, RCP wrote: Hi, This is saying your fo

Re: [SIESTA-L] Parallel compile and run

You must have a version of the netcdf library newer than mine. Those do not include the fortran interface anymore. Now, the latter is a separate package, but can't recall its name. It should be more or less obvious, search the web. Also, netcdf is optional for Siesta. You might comment it altoget

Re: [SIESTA-L] Parallel compile and run

Seems your linker does not search /usr/lib64/openmpi/lib for libraries. So, yes, try -L/usr/lib64/openmpi/lib in the LDFLAGS R. On 07/05/2016 12:31 PM, Mahmood Naderan wrote: I searched a lot about the parallel compilation of siesta and saw some question on the list. However, they don't r

Re: [SIESTA-L] Parallel compile and run

Of course I have those libraries because I did compile them by myself (Slackware Linux distro). Probably you don't need them because the package in your distro is organized differently. Namely, -lmpiblacs alone might already work. Anyway, check the contents of blacs-openmpi-devel.x86

Re: [SIESTA-L] Parallel compile and run

As you can see it is saying PARALLEL version, but I see "Running in serial mode with MPI". What does that mean? Ok, no problem. It means you just typed "siesta", so openMPI handles it as a serial code. More info: root@cluster:ObjPar# ldd siesta        linux-vdso.so.1 => (0x

Re: [SIESTA-L] Parallel compile and run

Hi Mahmood, I know next to nothing about Rocks, so I'll leave that to more knowledgeable people, On 07/08/2016 12:44 PM, Mahmood Naderan wrote: ... ​As I borrowed From Robert (RCP). I have to change those line, but I am not sure what to do. Here is my suggestion LAPACK

Re: [SIESTA-L] Choice of r_c values in pseudopotentials with atomic orbitals

Hi, On 07/14/2016 03:40 PM, Tristan Truttmann wrote: Dear all, I would greatly appreciate if somebody could answer my questions about generating pseudopotentials for SIESTA. I am wondering how I should choose r_c. In plane wave programs, I know that the r_c values must be chosen as a compromi

Re: [SIESTA-L] Question: Proper SolutionMethod for relaxing large systems

Hi, I'm not an expert here, but the naive answer is "use order N method". However, that depends on the physics of your system, for instance, O(N) cannot be applied to metals. Regards, Roberto On 08/01/2016 05:42 PM, Bahareh Fakhraei wrote: Hello every one, For relaxing the large systems (mo

Re: [SIESTA-L] Wrong Species Error

Your last line in %block AtomicCoordinatesAndAtomicSpecies is blank. On 08/09/2016 12:59 PM, Arturo Toro wrote: Hello, After trying to run the program numerous times, I keep receiving the same error. I've attached the fdf file itself and included the error message I keep receiving as well. I h

Re: [SIESTA-L] Wrong Species Error

Yeah !, I found that by myself ... after sending my response. Siesta is smart indeed :-). Cheers ! R. On 08/10/2016 05:04 AM, Nick Papior wrote: One is allowed to have blanks in the coordinates block, for instance this is read as expected: %block AtomicCoordinatesAndAtomicSpecies  # This is a

Re: [SIESTA-L] Errors for the compiling siesta 4.0

Hi, Your (lapack + blas + scalapack + blacs) setup in the arch.make file is wrong. Have a look at the example Makefiles included with the distribution to have an idea on how to set those variables correctly. Regards, Roberto On 08/11/2016 08:07 AM, 田 凡 wrote: Dear everyone, I am recently try

Re: [SIESTA-L] Expected output is not written

Hi, This may not be the reason why your job is not running, however the line MD.UseStructureFile .true. is wrong (MD.UseStructFile, see sec. 6.4.4 in manual). Are you providing a structure file or not ?. If so, be careful because then "any other structural information will be ignored". Take

Re: [SIESTA-L] Error in installation of Parallel version of Siesta-4.1-b1 on cluster

Hi, The message is pretty clear: the compiler used in your MPI library is different from the one you're using to compile Siesta. That's a nasty thing about *.mod files. No cure other than using the same compiler. Regards, Roberto PD: Eventualy, you might try to rebuild the MPI package using your

Re: [SIESTA-L] Error in installation of Parallel version of Siesta-4.1-b1 on cluster

indly help me. Thanking You Regards Rajan On Wed, Nov 9, 2016 at 7:32 AM, RCP mailto:pasia...@cnea.gov.ar>> wrote: Hi, The message is pretty clear: the compiler used in your MPI library is different from the one you're using to compile Siesta. That's a nasty thing

Re: [SIESTA-L] Cutoff radii for psedopotentials generation

Hi, search */Contrib for file atom_table.txt Roberto On 12/11/2016 01:45 PM, Riya Rogers wrote: Dear All In oder to generate psedopotentials for different exchange n correlation functionals, I am using ATOM program but kindly tell me how to put cutoff radii for different shells? Is there any s

Re: [SIESTA-L] NetCDF error while compiling siesta

Hi, There have been many reports of issues with netCDF on the mail list. Yours looks like not having netCDF library installed, while at the same time specifying netCFD support in the arch-make. That *.mod file comes with the library. Thus either, install netCDF (be aware the fortran interface is

Re: [SIESTA-L] .XV File For A Relaxed Structure

Hi, On 02/01/2017 08:54 AM, Seyed Mohammad Tabatabaei wrote: Dear all, I have a question about the information contained in an XV file and I would be really grateful if anyone helps. Here is my problem: Suppose I want to relax a system until all the forces acting on atoms are smaller than 0.01

Re: [SIESTA-L] Installation problem with transiesta.

Hi, Try commenting the line on netcdf interface, #NETCDF_INTERFACE=libnetcdf_f90.a Regards, Roberto On 02/19/2017 12:14 AM, acharya k.l.n. wrote: Hi All, Â I am trying to install transiesta with mpi and netcdf using the attached arch.make file,but I get the following error. make: *** No r

Re: [SIESTA-L] siesta-4.1-b2 MPI spin-orbit crashes with Error in Cholesky factorisation in cdiag

Hi, Have you tried the default settings for these two below ? Diag.DivideAndConquer .true. Diag.NoExpert .false. Regards, Roberto On 02/20/2017 02:34 PM, Aurelio Gallardo Caparrós wrote: Hi! I'm using siesta-4.1-b2 MPI compiled in a cluster. spin-orbit calculations with more than one core

Re: [SIESTA-L] Resume Siesta Calculations

Hi, My experience with static relaxations (e.g. CG) : just start from scratch but using the last set of coordinates you've got. Most likely the last DM output file (check DM.UseSaveDM) will not help in those cases, so don't forget to delete it (of course you might try anyway, at worst by loosing

Re: [SIESTA-L] Siesta calcuations run with more number of processors

Hi, Not sure how to interpret your question. 1) It is always possible to run an MPI-parallell application (such as SIESTA) in serial mode: just leave out the "mpirun" keyword from the command line. 2) Generally, it is not possible, say, to join the power of different cores for running a

Re: [SIESTA-L] FC calculation continuation

Hi Tao, No, it is not possible. That's why I had to tinker with the source in order to do what you want, and for that same reason. Now my MD.FCfirst and MD.FClast really mean individual displacements. Those changes are not difficult to implement, I might even send you the involved sources if can

Re: [SIESTA-L] scf convergence problem

Hi Marco, I have no experience with your system, however my default choice of smearing parameters (metals) are OccupationFunction FD ElectronicTemperature 0.15 eV Also your PAO.EnergyShift 0.005 Ry, might be less than optimal (basis functions too wide, default is 0.02 Ry). Last but not l

Re: [SIESTA-L] [***Posible SPAM***]Sin Asunto/Subject is blank

Hi, Look for line 23 in the source of siesta.F, the traceback says the problem starts there. You'll get an idea of what the program was doing. "Segmentation fault" is too generic an error to say anything precise, wrong data or-what-not might be a possible cause. Regards, Roberto On 05/09/201

Re: [SIESTA-L] structure relaxation by PBEsol - electronic structure PBE

Hi Mohammad, I'll assume you're using CG type of run, then 1) Use MD.MaxStressTol=0.01 GPa, i.e., stricter than default 1 GPa. 2) When you do this " ... when I start from PBEsol optimized structure and relax it with PBE,..." make sure there are no files from PBEsol hanging around in the s

Re: [SIESTA-L] ghsot atom in a 5times5 monolayer supercell

Hi, Gohst atoms do not introduce extra charge, only extra basis functions. This helps the electron density to further relax, thus energies will be lower. Search for "BSSE" in the list archives, there have been several discussions on the subject. Regards, Roberto On 06/06/2017 07:48 AM, MB MB

Re: [SIESTA-L] Difference between fee energy and total energy

Hi, Nothing special, indeed that would be my expectation, because both values depend on the "smearing" parameter (and method) being used. The latter is just a mathematical trick to help convergence of Brillouin zone integrations, a troublesome issue in the case of metals. There is no Physics in th

Re: [SIESTA-L] isotope effect

Hi Marco On 07/04/2017 03:08 AM, Marco Fronzi wrote: Hi everyone, I would like to calculate the deuterium adsorption energy on diamond. However, I am not sure how to setup the input parameters or generate a pseudopotential (if this is possible). Does anyone have experience on this? 99.9 % su

Re: [SIESTA-L] How to deal with the Pseudo-potential for alkali atoms

Hi, Have a look at */atom/Contrib/atom_table.txt (TM pseudos form JL Martin himself). On 07/05/2017 09:45 AM, Fen Hong wrote: Dear Siesta-users How to deal with the Pseudo-potential for alkali atoms? As we know, there is only one electron on the valence part. No problem, just include "semi

Re: [SIESTA-L] How to deal with the Pseudo-potential for alkali atoms

EasyMail <http://clkde.tradedoubler.com/click?p=259740&a=2839228&g=0&url=https%3a%2f%2fwww.microsoft.com%2fstore%2fp%2fEasyMail+for+Gmail%2f9nblggh626nc%3fcid%3dsignature>/ 2017-07-06 6:57 GMT+09:00 RCP mailto:pasia...@cnea.gov.ar>>: Hi, Have a look at */atom/Con

Re: [SIESTA-L] Restart without scf loop

Hi, A wild guess: have you tryed "MaxSCFIterations 0" ? Regards, Roberto On 07/23/2017 11:28 PM, Nicolas Duchêne wrote: Hi all, I was wondering if there was a way to restart a “calculationâ€� without actually entering the scf convergence loop. For example, I have a converged calculation,

Re: [SIESTA-L] Data in SystemLabel.vectors

Hi, they are the eigenvectors of the dynamical matrix, normalized to 1, thus unitless. You can interpret them in physical space by noting their coordinates mean $\sqrt(m_i) x_i$ (mass and Cartesian deviation). Bye, bye, Roberto PS: in particular your example corresponds to an unstable mode On 08

Re: [SIESTA-L] help

Hi, Search the manual for the block Geometry.Constraints. There is a cell-vector keyword there that you might find useful. Regards, Roberto On 09/22/2017 01:06 PM, nasrin estaji wrote: Hi, I am a graduate student in solid state physics, and studying mechanical properties of metals based on DFT

Re: [SIESTA-L] help

# stress 4 5 6 %endblock GeometryConstraints# when I use MD.variable cell true with this option all lattice vectors relaxed, and when I use MD.variable cell False non of them will be relaxed. I want just one of them will be fix. I will thanks alot for your respons. Â regards. On Sat, Sep 23, 2017 at 1

Re: [SIESTA-L] Is it Possible to make a movie in SIESTA?

Hi, that's exactly the *.ANI file. Search the manual. Regards, Roberto On 09/25/2017 01:51 AM, Rishi Sreedhar wrote: Dear SIESTA community, I was wondering if it would be possible to get the cartesian output of the input molecular cluster whilst SIESTA is running; like say after every 10-20 CG

Re: [SIESTA-L] USPEX and SIESTA

Hi, I know nothing about your problem but : Why are you missing redirection symbol, < , before input.fdf ? Regards Roberto On 11/23/2017 02:10 AM, Rishi Sreedhar wrote: Dear SIESTA users, Does anyone here have experience interfacing USPEX with SIESTA for molecular crystal prediction? I've been

Re: [SIESTA-L] error in parallel installation

Hi, Try linking bare BLACS library after BLACSCINIT and BLACSF77INIT. Also I do suggest upgrading to a newer scalapack (2.0.x) that come with blacs stuff already incorporated. Good luck, Roberto On 12/20/2017 08:30 AM, Sunetra Das wrote: Dear Siesta users, I have been trying to install sies

Re: [SIESTA-L] 'Segmentation fault - invalid memory reference' when running siesta in parallel

Troubles with your BLACS library, most likely. Have you tested it before? Regards, Roberto On 12/21/2017 03:09 PM, Sunetra Das wrote: Hello siesta users, I am getting the following error whenever I am running siesta-3.2-pl3 in parallel. Can anyone please tell me what these errors mean? Any help

Re: [SIESTA-L] mpi run issue with 4.0.2

Hi, I see you've made some progress. May be the problem's size is too small, have you tried other inputs ? Cheers, Roberto On 07/22/2018 12:53 PM, Mahmood Naderan wrote: Hi When I run the latest version 4.0.2 (mpi version) I see that not all processor numbers I specified are utilized. Sounds odd

Re: [SIESTA-L] phonon calculations

Hi, Just run different jobs for consecutive ranges of atom index by using keywords MD.FCfirst and MD.FClast, like MD.FCfirst=1 MD.FClast=10, MD.FCfirst=11 MD.FClast= ...MD.FClast=(nb of atoms in cell). Then catenate all FC files in that same order. Regards, Roberto On 08/15/2018 08:49 AM, Najmeh

Re: [SIESTA-L] problem with Vibra and name.FC

Hi, Probably you forgot to delete the first line of *.FCn files for n > 1 ?. ("Force constants matrix" string). Bye, Roberto On 09/27/2018 01:40 PM, sullah wrote: Dear all, I calculated phonons for a unit-cell containing 12 atoms with a supercell translation of 1x1x1. Everything was smooth. Th

Re: [SIESTA-L] Help with Indium Pseudopotentials.

Hi, It means Siesta cannot use that pseudo because of the ghost state. You may try generating your own using the ATOM program with the input file provided in Siesta's homepage (In-4d.inp). I see that the parameters in the latter file are different from the ones in your *.psf file. Moreover, your'

Re: [SIESTA-L] Total energy of my supercell was calculated to be lower than that of the optimized unit cell.

Hi Yang Mino, Try running the perfect lattice case also using 39 unit cells. Check the parameters (e.g. k-point mesh) are the same as in the stacking fault run. Thus you'd have two calculatins fully comparable. Hopefully, the deffect energy will be positive. Good luck, Roberto On 04/12/18 06:54

Re: [SIESTA-L] unit's physical dimensions don't match

Hi, On 25/02/19 17:23, Mina Sedighi wrote: Dear Siesta users and developers, I am performing a CG simulation on a battery system. at the first of simulation I receive the following error: ERROR FDF module: fdf_convfac: unit's physical dimensions don't match: eV , Ry/Bohr ... *** here

Re: [SIESTA-L] Installation Problem

Hello Vipin, Just type "f77" at the command prompt to find out if it is there or not. Anyway, f77 is not what you want, but something like mpif90 or mpifort or ..., to be assigned to variable FC in arch.make. Suggestion: grab one of those arch.make in Src/Sys that best suits your system (you'd b

Re: [SIESTA-L] ABOUT LATTICE parameters block which i could not find its answer in manual or mail

Hi, On 06/11/19 06:53, El-abed Haidar wrote: Good evening, Concerning the Block Lattice parameters if i have the following: # UNIT CELL LatticeConstant 1.0 Ang %block LatticeParameters 21.5476 11.3581 20.090.0 90.0-94.56 %endblock LatticeP

Re: [SIESTA-L] [SIESTA] Performing geometrical optimization

Hi, In your main fdf data file set keywords MD.TypeOfRun CG (conjugate gradients) MD.VariableCell .true. (fully flexible box) This will do using default values for other parameters. Have a look at the user's guide for other choices and fine tuning. Goo

Re: [SIESTA-L] how to define the value of rc to generate pseudo potential

Hi, Have a look at ./Contrib/atom_table.txt within the Atom tree, that file provides sensible values to start. bye, Roberto On 27/06/20 06:11, niuniubiubiu chen wrote: Hi, As I am trying to generate pseudopotential from Atom. Will any body please spare your valuable time to guide me that how

Re: [SIESTA-L] Total energy

Hello, May I contribute my 0.01 ?. According to Eq.(21) in, Kresse & Furthmüller, Comp. Mat. Sci. 6 (1996) 15-50 a good estimate for the (T=0K) DFT energy is 1/2(Etot +FreeEng), and this is the recipe I've always used. Regards, Roberto On 22/06/2022 13:11, Francisco Garcia wrote: Thanks  f

Re: [SIESTA-L] Total energy

f the two energies for T=0 makes sense. Thanks again! On Wed, Jun 22, 2022 at 3:01 PM RCP <mailto:pasia...@cnea.gov.ar>> wrote: Hello, May I contribute my 0.01 ?. According to Eq.(21) in,    Kresse & Furthmüller, Comp. Mat. Sci. 6 (1996) 15-50 a good estimate

Re: [SIESTA-L] Siesta parallel version installation on HPC

Hi, those are routines from the BLAS library, seems you're missing it. Check your arch.make file. Bye, Roberto On 22/06/2022 18:14, Ghazanfari, Sarah wrote: Hello all, I am trying to compile siesta in parallel version; however, I face the following errors. I greatly appreciate it if someone ca

[SIESTA-L] Question on VCA approach

Dear developers, I'd like to know if there is a specific reference for the method of mixing pseudopotentials implemented in the VCA mixps utility. Are general refs. such as these two below suitable? L. Bellaiche & D. Vanderbilt, Phys. Rev. B 61(12), 7877 (2000) N.J. Ramer & A.M. Rappe, J. Phys.

Re: [SIESTA-L] Geometry Optimization Problem

Hi Walter, Have you tried "position from 1 to 68" ?. That's exactly what the manual example quotes. Bye, Roberto Walter Cañón wrote: Dear Siesta Users, i had try to perform a geometry optimization of some atoms only, using geometry constrains in Siesta3 I havd try diferent set of parameters

Re: [SIESTA-L] how to find bulk modulus for hexagonal cell

Hi Andrei, Vasili Vasili, MD.ConstantVolume is not what we want. In any method the volume varies though only a small amount apost...@uni-osnabrueck.de wrote: Still, I don't understand the formula P = B \delta V / V in two aspects: 1) what is \delta? A difference? Between what and what? \delt

Re: [SIESTA-L] how to find bulk modulus for hexagonal cell

Hi Hongyi, Hongyi Zhao wrote: ... I usually obtain the bulk modulus by fitting the Birch–Murnaghan equation of state. But it seems that the P = B \delta V / V is more simple in form than Birch–Murnaghan equation of state. I've two issues about this method: 1- Comparison with the result

Re: [SIESTA-L] siesta help

Hi, This is something absent in the older version 2.x.y , namely, it appeared with version 3.x.y . Agreement of results between the two versions convinced me that the message is harmless. It would be nice however if, e.g., some of the developers, can give a hint on what's going on. Regards,

Re: [SIESTA-L] How to obtain the strain energy for a system.

Hi, Hongyi Zhao wrote: ... 1- As for the total energy, should we use the final energy for E_KS, i.e., something like the following one in the ouput file of siesta: siesta: E_KS(eV) =-2456.6000 Yes. Moreover, there should be a further line "total energy" or so, that should match

Re: [SIESTA-L] Harris vs KS energy in restart with 2.0.2

Hi Herbert, I don't have experience with metallic slabs, but with bulk metals. Good convergence to me always meant almost exact match between Harris and KS energies. Thus those 5.8 eV of your 1st run do not sound ok to me. Moreover, I like the results of your 2nd run, and believe that your 3rd ru

Re: [SIESTA-L] About k_sampling

Hi, Roland Gillen wrote: snipped However, in SIESTA we could also define the supercell (and thus the MP grid) by something like %block kgrid_Monkhorst_Pack a d 00.0 0 b 00.0 0 0 c0.0 %endblock kgrid_Monkhorst_Pack I thought th

Re: [SIESTA-L] about the polarized orbital when doing basis optimization

Hello Guangping, Your troubles are not due to polarization orbitals, but to the way the simplex method works. Namely, for a multiple-zeta optimization you have to make sure that the ranges where the cut-off radii are chosen from DO NOT intersect. Consider, for instance, that the largest r_c f

Re: [SIESTA-L] about the polarized orbital when doing basis optimization

Of course you should, otherwise Siesta does not know about soft confinement. Think that Siesta itself is used for basis generation and you write "E" there, don't you ? Regards. R. Guangping Zhang wrote: Dear Alberto, Thanks very much. I have learnt much that can and can not be found in

[SIESTA-L] To the list Admin

Dear Administrator, Is it possible to remove from the list the following two addresses ? wel...@postech.ac.kr and rod...@postech.ac.kr Whenever I post to the list I got a message from their postmaster with "Inbox Full" stuff, a bit annoying indeed ... This must be valid for

Re: [SIESTA-L] How to apply force on the atoms to the certain vector direction?

Hi, Do exactly the same, namely, write down your force in its cartesian components ;-) Best, Roberto Kyoungmin Min wrote: Dear SIESTA users, I would like to apply for to the specific atoms to the specific direction. I understand that I need to modify the constr.f file by adding a line l

Re: [SIESTA-L] information of FORCE_STRESS

Hello Guillermina, It's just the ordinary stress, as seen in the standard output ( possibly in some funny units, don't remember right now ), namely, how does the cell energy react to (uniform) cell deformations, divided by cell volume. Not an atomic property ( but a sort of average though

Re: [SIESTA-L] MPI Compile Error

Hi David, You might want to try the attached arch.make. It's for gfortran + openmpi on a Slackware 13.0 box. I hacked it from one of the supplied, and must be edited in a few places in order to match your exact paths and libraries. Regards, Roberto David Noriega wrote: I'm trying to bui

Re: [SIESTA-L] MPI Compile Error

Does openmpi work correctly for you ?, have you tried it before ?. There should be no need of that " /opt/openmpi/include " , because mpif90 already takes care. Also, I see that "parallel" in your path; you changed it from the standard "Obj", right ?. Besides, you know that a parallel binary

Re: [SIESTA-L] MPI Compile Error

Hi, As far as I understand, it derives from sources in turn produced through a scripting process that works upon the files in ./Src/MPI . R. David Noriega wrote: SNIPPED ... figure out whats going wrong. What is this mod file and why is it missing?

Re: [SIESTA-L] MPI Compile Error

It is too small a case, not representative, try a bigger one. Mine does explode on that with "failure to converge standard eigenproblem". No problems, however, for larger boxes. I believe the two procs interfere with each other when diagonalizing such a small case: mine explodes yours gets stuck

Re: [SIESTA-L] MPI Compile Error

Ooops !, no, no. I mean put more atoms in the box. Try, say, Ba_2TiO_3 test case, that should work. R. David Noriega wrote: You mean the number of cpus? OK I'll try again with 8 instead of 2. On Thu, Oct 6, 2011 at 1:22 PM, RCP wrote: It is too small a case, not representative,

Re: [SIESTA-L] MPI Compile Error

ur compilation. Regards Henrik 2011/10/6 David Noriega You mean the number of cpus? OK I'll try again with 8 instead of 2. On Thu, Oct 6, 2011 at 1:22 PM, RCP wrote: It is too small a case, not representative, try a bigger one. Mine does explode on that with "failur

Re: [SIESTA-L] MPI Compile Error

BTW, by commenting out the line " Diag.DivideAndConquer .false. " in fe.fdf ( thus effectively setting it to .true. ) mine does not crash anymore: it works ;-) R. RCP wrote: Hi, Well, it might be an MPI issue, or a Scalapack issue, or something with the orbital's blo

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