Re: [SIESTA-L] undefined reference to `getarg_' undefined reference to `iargc_'

Thank you for answer. I used both siesta-2.0.1 and siesta-2.0.2 and denchar does not compile with gfortran on both. This is how I solved the problem: edit file f2kcli.f90 : replace #ifndef GFORTRAN with #ifdef __GFORTRAN__ Regards Ruslan Zhachuk 2009/7/28 Lifeng Sun > Hi, > > The URL you re

[SIESTA-L] undefined reference to `getarg_' undefined reference to `iargc_'

Dear Siesta users, in page http://fisica.ehu.es/ag/siesta-extra/release.notes_2.0.2 there is stntence But when somebody try to compile denchar with gfortran immediatly receives an error /home/zhachuk/siesta-2.0.1/Src/f2kcli.F90:212: undefined reference to `getarg_' f2kcli.o: In function `__f2k

[SIESTA-L] Please, help with DENCHAR...

Dear siesta users, as far as I understand the only tool capable to plot wave functions in Siesta is Denchar. Unfortunately I got following error during compilation and cannot proceed. This error is mentioned in mailing list archive, but I found no solution published. Please, help... Ruslan zhac.

[SIESTA-L] DENCHAR compilation error

Dear siesta users, while trying to compile denchar program I am getting this error message (below). Does anybody know how to fix it? Regards Ruslan Zhachuk zhac...@solaris:~/siesta-2.0.1/Src> make denchar gfortran -c -g -O2 -DFC_HAVE_FLUSH -DFC_HAVE_ABORT f2kcli.F90 gfortran -c -g -O2 -DFC_HA

[SIESTA-L] How to specify PAO.Basis manually?

Dear Siesta users, I had Sr atom (2 valence s-electrons) with DZP basis set. This results in following basis: %block PAO.Basis # Define Basis set Sr-adatom 1# Species label, number of l-shells n=5 0 2 P 1 # n, l, Nzeta, Pola

Re: [SIESTA-L] WARNING: High Pressure calculation!

Dear Andrei, >this seems to be a too "loosely defined" question; >"will be Siesta accurate enough" with which basis, cutoffs etc.? basis set DZP mesh cutoff 200 Ry I did test calculations for Si(100) (unreconstructed and unrelaxed) surface energy in Siesta, the Esurf is very close to published v

[SIESTA-L] WARNING: High Pressure calculation!

Dear Siesta users, recently Andrei Postnikov wrote a small tutorial on Siesta http://www.home.uni-osnabrueck.de/apostnik/Lectures/SIESTA-tuto.pdf He wrote: "one cannot a priori expect equally good performance of basis over a large range of bond lengths and, say, pressures: as the pressure is vary

Re: [SIESTA-L] empty output in plstm

The vectors are Ok in fdf file. I found the source of problem. Siesta and plstm were compiled with different compilers (gfortran and ifort). So that plstm could not correctly read LDOS file produced by Siesta. Ruslan 2009/5/16 Sushil Auluck > hi, > you cell vectors look wrong. one component is

[SIESTA-L] empty output in plstm

Dear SIESTA users, I am trying to make constant-height image of Si(111)-7x7 (not rectangular unit cell). After running plstm I got file with "0" bytes. The output of plstm is below. The values of cell vectors are strange. What can be the problem? Ruslan sie...@hpc-suvir1:~/siesta-2.0.2/Util/my-

[SIESTA-L] STM image for not rectangular cell: Si(111)-7x7

Dear SIESTA users, I have a problem with generation of STM images for not rectangular cell: Si(111)-7x7. Earlier I did some STM image simulations for rectangular cell without any problems. For constant-current images I use WSxM software. When I try to open LDOS file this software crashes. For con

[SIESTA-L] basis size problem

Dear siesta users, when I try to specify basis size "TZDP" I get the following error message: size_name: incorrect basis-size option specified, active options are: SZ, SZP, DZ, DZP, and STANDARD How can I activate TZDP? It is explicitly mentioned in The Siesta method for ab initio order-N mate

[SIESTA-L] Maximum dynamic memory allocated

Dear siesta users, can anybody explain me what the " Maximum dynamic memory allocated" means just before the self-consistency cycle begins? In parallel calculations (ParallelOverK, k-points: 4 4 1) when I use 1 CPU Maximum dynamic memory allocated=158 MB 2 CPU Maximum dynamic memory allocated

[SIESTA-L] Parallel run - request for resources in PBS Pro

Dear SIESTA users, can you help me to write request for resources for parallel run. It looks like when this request is incorrect the job stops. We are using PBS Pro 9.2 system. The request string looks like this: #PBS -l select=3:ncpus=3:mpiprocs=3:mem=6GB The system I am studying is Si slab ab

[SIESTA-L] Errors in PARALLEL run: collective abort of all ranks

Dear SIESTA users, could you please help me to resolve the problem with parallel run. It works fine with Diag.ParallelOverK .true. But in default mode (paralell over orbitals) I have errors. The test system is very small, just slab of 8 Si atoms. Regards, Ruslan The errors are as following: Si

[SIESTA-L] simulated STM images (not LDOS)

Dear SIESTA users, recently I found a paper Phys. Rev. Lett. 94 (2005) 056103 which describe new effective method to simulate realistic STM images. It is not just LDOS plot, the authors calculate wave fucntions of tip and surface independently and then simulate the current, assuming that tip does

[SIESTA-L] Accurate Si surface formation energy

Dear SIESTA users, I need to calculate Si unreconstructed and unrelaxed surface formation energy very accurately. Previously I used another atomic orbitals based code, AIMPRO and found that it gives big error. The relation I used is Esurf=(Etot-uN)/2 Esurf - surface energy Etot - total energy of

Re: [SIESTA-L] H-passivation

You just set the H atom in the direction of Si bond at the distance, corresponding to the length of Si-H bond. As I remember it is approximately 1.5 Angstrom. Keep the coordinates of H atom and Si atom connected to it fixed during structure optimization. You don't need to relax them. Regards, Rusl

Re: [SIESTA-L] PAO.EnergyShift convergence problem

Dear Andrei, thank you for quick reply. I have some experience with AIMPRO which is also based on atom-centered basis functions, but it does not have parameters like EnergyShift, EnergySplit, nothing similar. What we usually did is we calculated theoretical bulk lattice constant and then used it

[SIESTA-L] PAO.EnergyShift convergence problem

Dear SIESTA users, I have difficulties trying to converge calculation with respect to PAO.EnergyShift. The system is 8 layers silicon slab, hydrogenated. The total energy varies strongly with PAO.EnergyShift parameter: PAO.EnergyShift Etot 300 meV -21007.7361 eV 250 meV

[SIESTA-L] PAO.BasisSizes problem

Dear SIESTA users, I have problem with specifying different basis sets for different atoms. The manual is not clear in this respect. Could you please show me the correct input for fdf file? Kind regards Ruslan P.S. Below are list of files in folder, error message and my fdf file. LIST OF FILES

Re: [SIESTA-L] surface energy with h passivation

Dear Chol-Jun Yu, the method is explained in detail in: A.A. Stekolnikov, J. Furthmueller, and F. Bechstedt, Phys. Rev. B 65, 115318 (2002). Try to read this first. Kind regards Ruslan 2008/11/17 Chol-Jun Yu <[EMAIL PROTECTED]> > Dear all, > > could anyone teach me how to calculate the surf

[SIESTA-L] parameters for Si slab calculation

Dear SIESTA users, I need to model STM image of clean Si surface, i.e. to get LDOS. All important calculations I did in AIMPRO code and now I need only STM image, so the calculation does not need to be very accurate. I moved to SIESTA since AIMPRO has no STM utility. But I am new to SIESTA and ha

[SIESTA-L] The sense of MeshCutoff parameter in SIESTA

Dear SIESTA users, could you please explain me the sense of MeshCutoff parameter in SIESTA? The manual is short in this respect: - MeshCutoff: Defines the equivalent plane wave cutoff for the grid. Default value: 100 Ry - I can understand energy cutoff parameter in plane-wa

[SIESTA-L] multiple LDOS output

Dear SIESTA users, how to generate output for multiple LDOS, each one with its own Uinitial and Ufinal? The system is quite large (about 200 Si atoms) and it takes a long time for SCF to get solution. And then I got only one LDOS for single Uinitial and Ufinal values. Should I save some values f

[SIESTA-L] plstm problem

Dear SIESTA users, I am using OpenSUSE Linux 10.3 and installed following packages to compile SIESTA utilities: 1) gcc-fortran (4.2) //The system GNU Compiler 2) gcc42-fortran (4.2.1_20070724) //The GNU Fortran Compiler and Support Files 3) libgfortran 42 (4.2.1_20070724) //The GNU Fortran Compile