[SIESTA-L] help fiel for make.arch?
Just to make sure, is there a help file that describes in detail all the options and flags in make.arch file for a semiexperienced user? thanks JOnas
[SIESTA-L] ./configure: Permission denied
Hi, I am not sure why, but when I download, unpack siesta-2.0.2 cd into Src and try ./configure it gives me [r...@mr9540 Src]# ./configure -bash: ./configure: Permission denied [r...@mr9540 Src]# I am loged in as a root so now I am puzzled why is the permission denied. Does it have anything to do with the code itself? thanks Jonas
Re: [SIESTA-L] ./configure: Permission denied
yep, looks like this was the problem. thanks Jonas --- On Thu, 5/14/09, Edan Scriven e...@physics.uq.edu.au wrote: From: Edan Scriven e...@physics.uq.edu.au Subject: Re: [SIESTA-L] ./configure: Permission denied To: SIESTA-L@listserv.uam.es Date: Thursday, May 14, 2009, 6:12 PM In the absence of any other information and assuming your compiler is working fine, did you check that the configure file is executable? Edit: sorry for the accidental extra post. Edan. On 15/05/2009, at 10:18 AM, Jonas Baltrusaitis wrote: Hi, I am not sure why, but when I download, unpack siesta-2.0.2 cd into Src and try ./configure it gives me [r...@mr9540 Src]# ./configure -bash: ./configure: Permission denied [r...@mr9540 Src]# I am loged in as a root so now I am puzzled why is the permission denied. Does it have anything to do with the code itself? thanks Jonas
Re: [SIESTA-L] ./configure: Permission denied
yep, found it, thanks. When I compile it with default options and run it in parallel via PBS I get mpirun noticed that job rank 0 with PID 18442 on node compute-0-2 exited on signal 6 (Aborted). What generically can cause this error so I can recompile it and run it properly? thanks Jonas --- On Thu, 5/14/09, Ravi Agrawal raviagrawal2...@u.northwestern.edu wrote: From: Ravi Agrawal raviagrawal2...@u.northwestern.edu Subject: Re: [SIESTA-L] ./configure: Permission denied To: SIESTA-L@listserv.uam.es Date: Thursday, May 14, 2009, 6:29 PM Jonas, You might have to change the permissions of the file and make it an executable. If you can't do that somehow, you should try this: . ./configure Hope it works. Regards, Ravi On Thu, May 14, 2009 at 7:18 PM, Jonas Baltrusaitis jasiu...@yahoo.com wrote: Hi, I am not sure why, but when I download, unpack siesta-2.0.2 cd into Src and try ./configure it gives me [r...@mr9540 Src]# ./configure -bash: ./configure: Permission denied [r...@mr9540 Src]# I am loged in as a root so now I am puzzled why is the permission denied. Does it have anything to do with the code itself? thanks Jonas -- PhD Candidate Espinosa Research Group Mechanical Engineering Northwestern University 2145 Sheridan Road, Tech Bldg. Evanston, IL 60208 - 3111 Phone: (847) - 467 - 7673
[SIESTA-L] create new account?
Please, is there a way to finally create a new account so I can download the software. Now I have no idea what's going on as I requested it more than a week ago but nothing happened: it hasn't been rejected nor approved Jonas Baltrusaitis University of Iowa
[SIESTA-L] new account
Hi, are new accounts to download SIESTA still being created, as I requested online last week but didn't get any response. Or should I send a paper copy? thanks Jonas Baltrusaitis University of Iowa
[SIESTA-L] approving a new account
Hi, just out of curiosity, how long does it take to approve a new account? Or is the process of sending the paper version still in effect, as opposed to the email based registration? thanks Jonas Baltrusaitis University of Iowa
Re: [SIESTA-L] single input to perform several tasks
very useful, thanks --- On Sun, 5/3/09, Marcos Verissimo Alves marcos.veriss...@uclouvain.be wrote: From: Marcos Verissimo Alves marcos.veriss...@uclouvain.be Subject: Re: [SIESTA-L] single input to perform several tasks To: SIESTA-L@listserv.uam.es Date: Sunday, May 3, 2009, 3:36 PM Not really, but you can make a bash script to do this (find an example attached after he end of the explanation). What this script does is: 1) Creates three files to be included for the three different siesta runs, with the appropriate parameters for each calculation. 2) Creates three fdf files that will be changed fro run to run only in the include file to be read. 3) Runs siesta three times with appropriate names for each run, reading the output from the previous calculation. To make sure, copies the STRUCT_OUT and XV files to new ones with the name of the corresponding run. This is because I am not sure if a phonon calculation will output a struct/xv file for each displacement. Of course, you should replace whatever X appears in the script with the appropriate parameters... Cheers, Marcos #!/bin/bash cat task.relax EOF MeshCutoff XXX Ry MD.TypeOfRun CG MD.NumCGSteps500 #... all other parameters related to relaxation here ... %block kgrid_Monkhorst_Pack xx xx xx x.x xx xx xx x.x xx xx xx x.x %endblock kgrid_Monkhorst_Pack EOF cat task.phonon EOF MeshCutoff XXX Ry MD.TypeOfRun FC #... all other parameters related to phonon calculations here ... %block kgrid_Monkhorst_Pack xx xx xx x.x xx xx xx x.x xx xx xx x.x %endblock kgrid_Monkhorst_Pack EOF cat task.pdos_ldos EOF MeshCutoff XXX Ry MD.TypeOfRun CG MD.NumCGSteps000 %block ProjectedDensityOfStates xxx xxx xxx xxx eV %endblock ProjectedDensityOfStates %block LocalDensityOfStates xxx xxx eV %endblock LocalDensityOfStates %block kgrid_Monkhorst_Pack xx xx xx x.x xx xx xx x.x xx xx xx x.x %endblock kgrid_Monkhorst_Pack EOF for run in relax pdos_ldos phonon do #In the first run, the blah.relax.STRUCT_OUT file will not exist. #It doesn't matter, all that will happen is an error that will not stop #the rest of the script from being executed - I'm not caring much about #programming elegance here :) cp blah.relax.STRUCT_OUT blah.STRUCT_IN cat blah.$run.fdf EOF SystemName blah SystemLabelblah %include task.$run MD.UseStructFile .true. AtomicCoordinatesFormat Fractional %block AtomicCoordinatesAndAtomicSpecies ... Place the atomic coordinates in fractional format here. ... They will be overridden by the pdos and phonon run, which ... will read the coordinates from file from the STRUCT_IN file %endblock AtomicCoordinatesAndAtomicSpecies #rest of fdf file flags that will not change #from one run to the other come here EOF mpirun -np X siesta blah.$run.fdf blah.$run.out cp blah.STRUCT_OUT blah.$run.STRUCT_OUT done Vous avez écrit / You have written / Lei ha scritto / Você escreveu... Jonas Baltrusaitis Hi, I was just wondering if there is a way to setup a single input to perform several consecutive tasks, e.g. geometry optimization followed by frequency calculation followed by DOS and PDOS calculations? Similar to Gaussian or NWChem where one input can be used for numerous tasks thanks Jonas Baltrusaitis University of Iowa -- Dr. Marcos Verissimo Alves Post-Doctoral Fellow Unité de Physico-Chimie et de Physique des Matériaux (PCPM) Université Catholique de Louvain 1 Place Croix du Sud, B-1348 Louvain-la-Neuve Belgique -- Gort, Klaatu barada nikto. Klaatu barada nikto. Klaatu barada nikto. Free translation: Gort, Google is your friend. Google is your friend. Google is your friend.
[SIESTA-L] single input to perform several tasks
Hi, I was just wondering if there is a way to setup a single input to perform several consecutive tasks, e.g. geometry optimization followed by frequency calculation followed by DOS and PDOS calculations? Similar to Gaussian or NWChem where one input can be used for numerous tasks thanks Jonas Baltrusaitis University of Iowa
