[SIESTA-L] NetCDF error while compiling siesta
Dear Experts, While compiling siesta-4.0b-485 parallely on cluster i am facing problem regarding NetCDF. As i am new user so i don't know how to solve this error. while compiling i am getting following error *use netcdf 1Fatal Error: Can't open module file 'netcdf.mod' for reading at (1): No such file or directorymake: *** [iogrid_netcdf.o] Error 1* I have also attached my arch.make file which is copied from http://pelios.csx.cam.ac.uk/~mc321/siesta.html. Kindly look into this and try to solve my problem -- warm regards Amrish Sharma Ph.D. Research Scholar Punjabi University,Patiala Punjab (India)
[SIESTA-L] vdw calculations
heloo users I am studing the interaction between two carbon nanoforms. Initially i have done structural optimization using siesta 3.2 . After that i use "siesta-4.0b-485" for "vdw interaction" . I have done vdw interaction using "VDW" as "XC.functional" and "DRSLL" as "XC.Author". After single point calculations i have got atomic forces as much higher than from my optimized geometry in siesta 3.2. i want to know Why i am getting this? Also tell me does my calculations are accurate or not ? -- warm regards amrish sharma JRF, DST-SERB Research Project Punjabi University Patiala (India)
[SIESTA-L] compilation error during 4.0b
hello users. while compiling siesta 4.0b serially i get this error collect2: ld returned 1 exit status make: *** [siesta] Error 1 if u have any solution kindly let me know. your answer are highly valuable to me. -- warm regards amrish sharma
[SIESTA-L] pdos in siesta
dear user i want to plot pdos file. using partial dos block in my fdf i get .pdos file but i don't know how to proceed further kindly help. -- warm regards amrish sharma
[SIESTA-L] vdw pseudos
hii all users. I want to study the interaction between different carbon nanoforms. For that can anybody explain how can i generate vdw pseudos? In atom manual there is no explanation for this -- warm regards amrish sharma Project Fellow DST-SERB Project Punjabi University Patiala
Re: [SIESTA-L] unable to generate .band file
dear monica thanks for your kind reply i have do what u have said.. after that i got the same result .band file donot generated On Wed, Aug 10, 2016 at 2:46 PM, Monica Garcia wrote: > Dear Amrish, > > Please delete the line “WriteBands .true.” in your .fdf input file. The > .band file is generated when the default SIESTA parameter is used: > “WriteBands .false.” Otherwise the information is only written in the > output file. > > Best regards, > Mónica > > Support > Simune Atomistics > Tolosa Hiribidea 76 | 20018 Donostia - San Sebastián | Spain > T.: +34 943 57 40 42 | supp...@simune.eu | www. > simune.eu <http://www.simune.eu/> > > On 10 Aug 2016, at 10:19, amrish sharma wrote: > > hii all > > i unable to generate .band file for my system . i have attached .fdf file > also. kindly help > > -- > warm regards > > amrish sharma > > > > -- warm regards amrish sharma
[SIESTA-L] unable to generate .band file
hii all i unable to generate .band file for my system . i have attached .fdf file also. kindly help -- warm regards amrish sharma c.fdf Description: Binary data
Re: [SIESTA-L] Error in Cholesky factorisation
THANKS NICK PROBLEM HAS BEEN SOLVED On Wed, Aug 10, 2016 at 12:47 PM, Nick Papior wrote: > Typically when factorizations error out it is because atoms come too close > to each other, this line in your outfile says that: > siesta: WARNING: Atoms 239 240 too close: rij =0.00 Ang > > Basically you have two atoms on top of each other. Besides being > non-physical the factorization has problems. > > 2016-08-10 9:09 GMT+02:00 amrish sharma : > >> >> when i run my job in siesta after some time i got this error. as a source >> i have attached my outfile also. kindly help in solving this >> >> >> Error in Cholesky factorisation in rdiag >> ERROR STOP from Node:0 >> Aborted >> >> -- >> warm regards >> >> amrish sharma >> > > > > -- > Kind regards Nick > -- warm regards amrish sharma
Re: [SIESTA-L] band structure
%block BandLines 1 1.000 1.000 1.000 L # Begin at L 20 0.000 0.000 0.000 \Gamma # 20 points from L to gamma 25 2.000 0.000 0.000 X # 25 points from gamma to X 30 2.000 2.000 2.000 \Gamma # 30 points from X to gamma %endblock BandLines WHAT DOES THIS MATRIX TYPE NUMBERS REPRESENT EX. 1.0 1.0 1.0 LIKE IN L ETC. On Wed, Aug 10, 2016 at 12:53 PM, Nick Papior wrote: > Please read the manual from page 71. > > Note this is the manual 4.0 located here: > https://launchpad.net/siesta/4.0/4.0/+download/siesta.pdf > > 2016-08-10 8:35 GMT+02:00 amrish sharma : > >> hii all user >> >> i want to know how to get band structure plot in siesta ? >> >> -- >> warm regards >> >> amrish sharma >> > > > > -- > Kind regards Nick > -- warm regards amrish sharma
[SIESTA-L] Error in Cholesky factorisation
when i run my job in siesta after some time i got this error. as a source i have attached my outfile also. kindly help in solving this Error in Cholesky factorisation in rdiag ERROR STOP from Node:0 Aborted -- warm regards amrish sharma outfile Description: Binary data
[SIESTA-L] band structure
hii all user i want to know how to get band structure plot in siesta ? -- warm regards amrish sharma
[SIESTA-L] siesta trunk compilation
hii all i want to install siesta trunk 462. after creating arch.make file as soon as i type "make" command it showed message "make: *** No targets. Stop." what does this means. how can i compile the code -- warm regards amrish sharma
Re: [SIESTA-L] fdf parameters
thanks andrei i use that workstation because i have no other option to carry out calculations. and for siesta use because our group is familiar with siesta code only so we have good command over it that why i use. as u have mention first carry out calculation on small system then shift it to bigger one , now i want to ask i stabilize parameter upto 200 atoms can i use them to carry out work on 500 atom ? On Fri, Jul 22, 2016 at 2:38 PM, Andrei Postnikov < andrei.postni...@univ-lorraine.fr> wrote: > Dear Amrish: > > Let's sort things out: > 1. The *energy shift* is about constructing your basis functions. There > is nothing you need to test > on a huge supercell. Make the usual tests on small (minimal; single cell) > systems > to be sure that your basis set construction permits you to obtain the > reasonable description > (of whatever your aims are: lattice parameters, bulk modulus, ...) > 2. The *mesh cutoff*, as it seems to me, a priori is not supposed to > depend on the supercell size. > Again, after you test it on prototype small systems, you can use the same > value > for large supercell. > 3 *my workstation is not so powerful to deal with system like 500 atoms*... > - then: > why use such workstation? Or: why use 500 atoms? Or: why use Siesta? > > Best regards > > Andrei > > > i am facing problem in my fdf file to take value of some parameters like > mesh cutt off and energy shift parameters. my workstation is not so > powerful to deal with system like 500 atoms so i don't want to waste time > while test calculations on these parameters. > can any one explain an alternate way to get approximate but the accurate > value of mesh cutt off and energy shift for system consisting 500 atoms. > > -- > warm regards > > amrish sharma > research scholar > Dr. Isha Mudahar group > punjabi university > patialahii all > > > -- warm regards amrish sharma
[SIESTA-L] vander wall potential
hii all i want to know how can i give vander wall potential parameter in my fdf file. -- warm regards amrish sharma research scholar Dr.Isha Mudahar group Punjabi University Patiala
[SIESTA-L] fdf parameters
hii all i am facing problem in my fdf file to take value of some parameters like mesh cutt off and energy shift parameters. my workstation is not so powerful to deal with system like 500 atoms so i don't want to waste time while test calculations on these parameters.can any one explain an alternate way to get approximate but the accurate value of mesh cutt off and energy shift for system consisting 500 atoms. -- warm regards amrish sharma research scholar Dr. Isha Mudahar group punjabi university patiala
[SIESTA-L] geometric constraint
dear SIESTA users, i want to freeze some atoms out of complex and then allowed to relax the geometry . i want to run it for 100 CG.steps. but after 20 steps jobs were stopped by giving total energy at the end . but system was not fully converged . what's the reason behind it. i have attached input file also with some parameters. -- warm regards amrish sharma c.fdf Description: Binary data
