Re: [SIESTA-L] PAO-basis block for As
Don't forget to change the file run_script.sh SIESTA=$HOME/bin/siestayou have to change for the path where are your siesta are! In my case is SIESTA=/home/guilherme/Programas/siesta-3.2/Obj/siestaI don't know if this what's happening wrong if your simulation... ___Guilherme Maia Santos Doutorando (PhD student) Multifunctional Devices Development Lab - MDDL Departamento de Física - DF(Departament of physics) Universidade Estadual de Maringá - UEM (State University of Maringá) University of Texas at San Antonio - UTSA Em Quinta-feira, 11 de Junho de 2015 13:19, Abraham Hmiel escreveu: My guess regarding the compilation errors: there's no need to use sudo for this install, and your compiler in the makefile is pointing to f77, is it that the same compiler you used to install SIESTA? It doesn't have to be, but if SIESTA compiles you should use what works there. Your FC line should be pointing to f90, or whatever fortran compiler (pg90, ifort, ifc, gfortran, etc.) you used in the SIESTA install. Check your Obj/ folder in the SIESTA source tree for the arch.make. I could not reproduce your error when I used my own f77 compiler or f90 or gfortran so that's strange. Try using gfortran, perhaps? You should not have to edit the source code to get this utility to work. Just try a different compiler until you can get it to work. My gfortran is: GNU Fortran 95 (GCC) 4.1.2 20070115 and it compiles without error. Swarm is Open-MP enabled, so you could compile it in parallel as well. On Thu, Jun 11, 2015 at 6:29 AM, Ludwig, Stephan wrote: Hello Abraham, thank you for your suggestion. Unfortunately I have proplems to install the optimization programm.typing 'make swarm simplex' I receive the error message i1@QuanQal2:/home/siesta-3.2-pl-5/Util/Optimizer$ sudo make swarm simplexf77 -c io.f io_assign: Error on line 2: syntax error Warning on line 13: ignoring text after "end". Warning on line 13: local variable out never used Warning on line 13: local variable intend never used Error on line 13: Declaration error for intend: adjustable dimension on non-argument /usr/bin/f77: aborting compilation make: *** [io.o] Fehler 25 The io.f file looks like this SUBROUTINE io_assign(lun) integer intend(out) :: lun logical used integer iostat c c Looks for a free unit and assigns it to lun c do lun= 10, 99 inquire(unit=lun, opened=used, iostat=iostat) if (iostat .ne. 0) used = .true. if (.not. used) return enddo end SUBROUTINE io_assign Can you help me to find the syntax error? Best regards Stephan -Original message- From: Abraham Hmiel Sent: Wednesday 10th June 2015 17:42 To: Siesta, Self-Consistent DFT LCAO program, http://www.uam.es/siesta Subject: Re: [SIESTA-L] PAO-basis block for As Stephan, Creating a PAO basis set from scratch is a nontrivial exercise even for experts. The way I usually use involves the simplex tetrahedral method, which allows you to vary several parameters at a time and find their optimized values. There is an implementation included with SIESTA. Look in the Util/Optimizer folder of the siesta source tree. There are some examples there which will allow you to use the simplex method code in a basic manner for a water molecule to optimize basis set parameters. Take a look at the files and study them and run the example calculations. They're pretty quick. From there, it's not a big stretch to apply the principles to arsenic. You will still have to figure out the format of the PAO basis block corresponding to your pseudopotential and desired size of the basis set. You might try using As2S3 or solid arsenic as input, and optimize for bond length and total energy minimization. I'd offer that you might learn more doing it this way. Kind regards, On Wed, Jun 10, 2015 at 7:27 AM, Nick Papior Andersen wrote: I would suggest you ask your supervisor/professor (I suspect you have one?). 2015-06-10 16:24 GMT+02:00 Ludwig, Stephan : Hello everybody, I'm an absolute beginner in DFT calculations (I'm a Master student) and now I have to cope with a material containing Arsenid. The pseudopotential of As in the database has a semicore state so I have to implement the PAO-basis block in the fdf-file. I have no idea how to choose the parameters of this block to obtain reasonable results. I was able to start siesta by using a PAO-basis block which was originally designed for iron: %block PAO.Basis # Define Basis set As 1 # Species label, number of l-shells n=3 2 2 # n, l, Nzeta 6.000 0.000 1.000 1.000 %endblock PAO.Basis Can anybody please deliver a suitable PAO-basis and a pseudopotential for As. Or can anybody help me to find a suitable PAO-basis for the pseudopotential I use. You can find it in the attachment It would be a great help and I would learn a lot through it Thanks and regards Stephan Ludwig
Re: [SIESTA-L] Problems installing Util Optimizer
Did you make the change in the Makefile? # Choose compiler here. # Optimization flags are not really necessary, but do include # the OpenMP compiler flag if your system supports it and it is worth it. # #FC=ifort -openmp # -g -O1 -CB -ftrapuv # #FC=gfortran -fopenmp # You have choose between Ifort or Gfortran.. and erase the '#' if you choose the gfortan, do: # FC=gfortran -fopenmp #___ Guilherme Maia Santos Doutorando (PhD student) Multifunctional Devices Development Lab - MDDL Departamento de Física - DF (Departament of physics) Universidade Estadual de Maringá - UEM (State University of Maringá) University of Texas at San Antonio - UTSA Em Quinta-feira, 11 de Junho de 2015 8:35, "Ludwig, Stephan" escreveu: Problems installing Util Optimizer Hi, I want to optimize a Basis set for As. Unfortunately I have proplems to install the optimization programm. typing 'make swarm simplex' in 'siesta-3.2-pl-5/Util/Optimizer' I receive the error message i1@QuanQal2:/home/siesta-3.2-pl-5/Util/Optimizer$ sudo make swarm simplex f77 -c io.f io_assign: Error on line 2: syntax error Warning on line 13: ignoring text after "end". Warning on line 13: local variable out never used Warning on line 13: local variable intend never used Error on line 13: Declaration error for intend: adjustable dimension on non-argument /usr/bin/f77: aborting compilation make: *** [io.o] Fehler 25 The io.f file looks like this SUBROUTINE io_assign(lun) integer intend(out) :: lun logical used integer iostat c c Looks for a free unit and assigns it to lun c do lun= 10, 99 inquire(unit=lun, opened=used, iostat=iostat) if (iostat .ne. 0) used = .true. if (.not. used) return enddo end SUBROUTINE io_assign Can anybody help me to find the syntax error? Best regards Stephan
[SIESTA-L] Doubt about the contribution of the electrons of the Al in the PDOS and electron maps densities, anyone can help me?
Hi everyone, My research is about the AlFeO_3 compound... My question is about the Al+3 ... I already understood why in the Electron Maps Densities don't appear the Al... Like we can see in the figure attached. As the PseudoPotetial of the Al are only implicit the 3s2 and 3p1 orbitals, and all three electrons are given to the Oxygen, don't appear nothing where supposed appear the Al core, because looking in the figure of the maps, we can't see any density around the Al... (the circle in the middle of the figure have density very low..).. So I guess we can assume that the Al donated the three electron to Oxygen... But is shown in the Figure of the PDOS (Partial Density of States) the contribution of the Al 3s2 and 3p1... So.. my doubt is about that... I don't know if is a silly question, but... How can appear the contribution of the Al 3s2 and 3p1 if the Al loses those electrons? (as shown in the electron maps) Someone can give me some direction? Thanks!! ___ Guilherme Maia Santos Doutorando (PhD student) Multifunctional Devices Development Lab - MDDL Departamento de Física - DF (Departament of physics) Universidade Estadual de Maringá - UEM (State University of Maringá) University of Texas at San Antonio - UTSA
[SIESTA-L] Doubt about PAO.Basis in Siesta code. Can anyone help me?
Hello Siesta Users, There is a example to see which is the optimal radius for each of the orbitals in the Fe atom, so we have to change the block: %block PAO.Basis # Define Basis setFe 2 # Species label, number of l-shells n=4 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 6.800 6.468 <--- 1.000 1.000 n=3 2 2 # n, l, Nzeta 4.124 2.321 <--- 1.000 1.000 Al 2 # Species label, number of l-shells n=3 0 2 # n, l, Nzeta 5.669 5.130 <--- 1.000 1.000 n=3 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 7.279 5.960 <--- 1.000 1.000 O 2 # Species label, number of l-shells n=2 0 2 # n, l, Nzeta 3.305 2.510 <-- 1.000 1.000 n=2 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 3.937 2.574 <-- 1.000 1.000 %endblock PAO.Basis so if I want to change the rc, I have to change the both colum in the same time with the same proportion? Can I change one by one?There are some order to do that?Like, I have to change the orbital n=3... Or fisrt the O orbitals or Al... I don't know if it's clear my doubt...Thanks! Best Regards! ___Guilherme Maia SantosDoutorando (PhD student) Multifunctional Devices Development Lab - MDDL Departamento de Física - DF(Departament of physics) Universidade Estadual de Maringá - UEM (State University of Maringá) University of Texas at San Antonio - UTSA
[SIESTA-L] [***Posible SPAM***]Doubt about %block PAO.Basis...
Hello Siesta Users, There is a exampleto see which is the optimal radius for each of the orbitals in the Featom, so we have to change the block: %block PAO.Basis # Define Basis setFe 2 # Species label, number of l-shells n=4 0 2 P 1 # n, l, Nzeta 6.000 0.000 <- 1.000 1.000 n=3 2 2 # n, l, Nzeta 6.000 0.000<- 1.000 1.000%endblock PAO.Basis First, maintainingthe d orbitals to r c =4.0 Bohr, change the radius of the s orbitalsfrom 4.0 up to 8.0Bohrs in increments of, lets say, 0.5 Bohrs... that's is what ask todo..do this is OK!!But my doubt is, inmy system the block Pao.basis is: %block PAO.Basis # Define Basis setFe 2 # Species label, number of l-shells n=4 0 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 6.800 6.388 <--- 1.000 1.000 n=3 2 2 # n, l, Nzeta 4.124 2.321 <--- 1.000 1.000 (…)%endblock PAO.Basis the second colum isnot zero like in the example... so if I want to change the rc, I haveto change the both colum in the same time with the same proportion?Can I change one by one? I don't know if it's clear my doubt... Thanks!Best Regards! ___Guilherme Maia Santos Doutorando (PhD student) Multifunctional Devices Development Lab - MDDL Departamento de Física - DF(Departament of physics) Universidade Estadual de Maringá - UEM (State University of Maringá) University of Texas at San Antonio - UTSA
[SIESTA-L] Doubt about doped sample
Hello Siesta Users! I have one doubt about doped sample. In my case, my system is AlFeO3, there are 40 atoms in the cell (in the box), where 8 Fe, 8 Al and 24 O... But I wanna do a simulation with 2% of Nb in Iron sitio... So for me do that I have to create a supercell 6 times bigger than the original... So in the case I have 48 atoms of Iron, but I will change one of this for Nb... so in this way 2% of Nb in my system... But doing that, I have at least two problems... 1. Will increase a lot the number of Atoms, so requires more of my PC. 2. The system are ordered in this way... but I need the system disordered!! Someone know I better way for me do that?! Thanks! ___Guilherme Maia Santos
Re: [SIESTA-L] Band Structure - How build the block for the Orthorhombic system?
Hi Camps, I found other example... but still I couldn't understand exactly this positions... This is for the Silicon%block BandLines 1 1.5 1.5 0.0 K # Begin at K 38 0.0 0.0 0.0 \Gamma # 38 points from K to Gamma 36 0.0 2.0 0.0 X # 36 points from Gamma to X 18 1.0 2.0 0.0 W # 18 points from X to W 26 1.0 1.0 1.0 L # 26 points from W to L 31 0.0 0.0 0.0 \Gamma # 31 points from L to Gamma %endblock BandLinesHow I can find the best path for my sample?! The only position I understand it's for Gamma... and why this path?... I gave a quick read in the paper that you told me and didn't find... but I'll read again !! Thanks for the help! ___Guilherme Maia Santos "Se as pessoas são boas só por temerem o castigo e almejarem uma recompensa, então realmente somos um grupo muito desprezível."(Albert Einstein) Em Segunda-feira, 16 de Fevereiro de 2015 16:02, I. Camps escreveu: Hello Guilherme,Take a look in this link: en.Wikipedia.org/wiki/Brillouin_zoneThis is based in the paper Comp. Mat. Sci. 49 (2) 299-312, DOI: 10.1016/j.commatsci.2010.05.010Or any good Solid State Book.There is also a server named Bilbao Crystallographic Server: www.cryst.ehu.es Good reading. On Mon, Feb 16, 2015, 19:36 Guilherme Maia Sawyer wrote: Hi all, I'm trying to plot Band Structure using the gnuband (Util from Siesta)... But I have one doubt about %block BandLines that we have to write in the .fdf file... According the Siesta Manual, we usually write along the high-symmetry directions... but where I can find it?! In the manual : %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 BandLinesThis is for an FCC lattice... I tried to find this values for this lattice just to understand how build for my system... but nothing...My system it's a Orthorhombic...for this one.. which is the high-symmetry directions?! Thanks!
[SIESTA-L] Band Structure - How build the block for the Orthorhombic system?
Hi all, I'm trying to plot Band Structure using the gnuband (Util from Siesta)... But I have one doubt about %block BandLines that we have to write in the .fdf file... According the Siesta Manual, we usually write along the high-symmetry directions... but where I can find it?! In the manual : %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 BandLinesThis is for an FCC lattice... I tried to find this values for this lattice just to understand how build for my system... but nothing...My system it's a Orthorhombic...for this one.. which is the high-symmetry directions?! Thanks!
[SIESTA-L] About Pseudopotential and the program ATOM!
Hello users, I have one doubt and one problem about create a PseudoPotential...In the Tutorial, have the PseudoPotential for Iron... Fe.gga-cc.inp# # PS generation with core corrections # GGA (Perdew-Burke-Ernzerhof) XC , relativistic # pe Fe, GGA, rcore=0.70 tm2 3.0 n=Fe c=pbr 0.0 0.0 0.0 0.0 0.0 0.0 5 4 4 0 2.00 0.00 # 4s2 4 1 0.00 0.00 # 4p0 3 2 6.00 0.00 # 3d6 4 3 0.00 0.00 # 4f0 2.00 2.00 2.00 2.00 0.00 0.70 # | # Radius of pseudocore I ran and it's Ok... create the *.psf... everything ok! But something I didn't understand... 4 3 0.00 0.00 # 4f0 --> This line... why ?Why I can't change for 5 0 0.00 0.00 #5s0 ? I try to change and appear the error:cp: cannot stat ‘VPSOUT’: No such file or directory cp: cannot stat ‘VPSFMT’: No such file or directory and in the OUT file appear: error in pseudo - two up spin orbitals of the same angular momentum (0) exist And don't create the *.psf file... The reason I'm doing this is because I'm try to respect Electron configuration :1s2 2s2 2p6 3s2 3p6 4s2 3d6 4p0 5s0 I don't know if it's clear what I just said.. Kind Regards, Guilherme Maia.
Re: [SIESTA-L] My doubt is about sites occupation
Using the VCA program, when I mixed 65% of Fe and 35% of Al... appeared the error that a put in my last post... But I tried 90% of Fe and only 10% of Al... and it works!! But I need more... do you know what it's happening?! ___Guilherme Maia Santos "Se as pessoas são boas só por temerem o castigo e almejarem uma recompensa, então realmente somos um grupo muito desprezível."(Albert Einstein) Em Terça-feira, 4 de Novembro de 2014 13:24, Guilherme Maia Sawyer escreveu: Hi I. Camps, I used the VCA to generate the mix pseudopotential... But when I change my fdf, and run the Siesta appear this error: SPLIT: ERROR Orbital with angular momentum L= 2 not bound in the atom SPLIT: ERROR a cut off radius must be explicitly given ERROR STOP from Node: 0 ERROR STOP from Node: 0 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 I'm trying to find the error... but until now... I found nothing!! I put in attached my new FDF... ___Guilherme Maia Santos "Se as pessoas são boas só por temerem o castigo e almejarem uma recompensa, então realmente somos um grupo muito desprezível."(Albert Einstein) Em Segunda-feira, 3 de Novembro de 2014 7:44, I. Camps escreveu: Hello Guilherme, You have two choices: 1-) To use the Virtual Crystal Approximation 2-) Generate a bigger crystal cell (2x2x2, 3x3x3, etc.) and distribute your atoms accordingly. For the first option, you need a pseudopotential file that is a mix of both atom types (Fe and Al). Take a look in this links: http://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/html/thcastepdisorder.htm http://journals.aps.org/prb/abstract/10.1103/PhysRevB.61.7877 I am not aware if the program ATOM can generate a pseudo as a mix. For the second option, you should generate your disordered structure following some physics. I recommend to use the quase-entropy concept to chose which disordered structure are the good one. Take a look at this softwares: ATAT: http://www.brown.edu/Departments/Engineering/Labs/avdw/atat/ USPEX: http://uspex.stonybrook.edu/uspex.html []'s, @mps On Mon, Oct 20, 2014 at 2:06 PM, Guilherme Maia Sawyer wrote: My doubt is about sites occupation. In my compound there are 4 different sites, they are: Fe1 and Fe2 (occupied more by Iron) and Al1 and Al2 (occupied more by Alluminio). To do the simulation considering 100% of the sites Fe1 and Fe2 occupied by Iron and the other two by Alluminio, it's ok. But it's not correct! In the real system the Fe1 its 75% occupied by Iron, and 25% by Aluminio... and the same for the other sites...So ... how I can I do this?!I don't know if are clear what I just say... I put in attached my FDF ... but in that case I'm considering 100% of the sites Fe1 and Fe2 occupied by Iron and the other two by Alluminio.So... How I can rewrite my .fdf ? Really Thank!! ___Guilherme Maia Santos "Se as pessoas são boas só por temerem o castigo e almejarem uma recompensa, então realmente somos um grupo muito desprezível."(Albert Einstein)
Re: [SIESTA-L] My doubt is about sites occupation
Hi I. Camps, I used the VCA to generate the mix pseudopotential... But when I change my fdf, and run the Siesta appear this error: SPLIT: ERROR Orbital with angular momentum L= 2 not bound in the atom SPLIT: ERROR a cut off radius must be explicitly given ERROR STOP from Node: 0 ERROR STOP from Node: 0 application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0 I'm trying to find the error... but until now... I found nothing!! I put in attached my new FDF... ___Guilherme Maia Santos "Se as pessoas são boas só por temerem o castigo e almejarem uma recompensa, então realmente somos um grupo muito desprezível."(Albert Einstein) Em Segunda-feira, 3 de Novembro de 2014 7:44, I. Camps escreveu: Hello Guilherme, You have two choices: 1-) To use the Virtual Crystal Approximation 2-) Generate a bigger crystal cell (2x2x2, 3x3x3, etc.) and distribute your atoms accordingly. For the first option, you need a pseudopotential file that is a mix of both atom types (Fe and Al). Take a look in this links: http://www.tcm.phy.cam.ac.uk/castep/documentation/WebHelp/html/thcastepdisorder.htm http://journals.aps.org/prb/abstract/10.1103/PhysRevB.61.7877 I am not aware if the program ATOM can generate a pseudo as a mix. For the second option, you should generate your disordered structure following some physics. I recommend to use the quase-entropy concept to chose which disordered structure are the good one. Take a look at this softwares: ATAT: http://www.brown.edu/Departments/Engineering/Labs/avdw/atat/ USPEX: http://uspex.stonybrook.edu/uspex.html []'s, @mps On Mon, Oct 20, 2014 at 2:06 PM, Guilherme Maia Sawyer wrote: My doubt is about sites occupation. In my compound there are 4 different sites, they are: Fe1 and Fe2 (occupied more by Iron) and Al1 and Al2 (occupied more by Alluminio). To do the simulation considering 100% of the sites Fe1 and Fe2 occupied by Iron and the other two by Alluminio, it's ok. But it's not correct! In the real system the Fe1 its 75% occupied by Iron, and 25% by Aluminio... and the same for the other sites...So ... how I can I do this?!I don't know if are clear what I just say... I put in attached my FDF ... but in that case I'm considering 100% of the sites Fe1 and Fe2 occupied by Iron and the other two by Alluminio.So... How I can rewrite my .fdf ? Really Thank!! ___Guilherme Maia Santos "Se as pessoas são boas só por temerem o castigo e almejarem uma recompensa, então realmente somos um grupo muito desprezível."(Albert Einstein) AlFeO3.fdf Description: Binary data
[SIESTA-L] My doubt is about sites occupation
My doubt is about sites occupation. In my compound there are 4 different sites, they are: Fe1 and Fe2 (occupied more by Iron) and Al1 and Al2 (occupied more by Alluminio). To do the simulation considering 100% of the sites Fe1 and Fe2 occupied by Iron and the other two by Alluminio, it's ok. But it's not correct! In the real system the Fe1 its 75% occupied by Iron, and 25% by Aluminio... and the same for the other sites...So ... how I can I do this?!I don't know if are clear what I just say... I put in attached my FDF ... but in that case I'm considering 100% of the sites Fe1 and Fe2 occupied by Iron and the other two by Alluminio.So... How I can rewrite my .fdf ? Really Thank!! ___Guilherme Maia Santos "Se as pessoas são boas só por temerem o castigo e almejarem uma recompensa, então realmente somos um grupo muito desprezível."(Albert Einstein) AlFeO3.fdf Description: Binary data
Re: [SIESTA-L] siesta paralle
Hi... In the arch.make you try put: MPI_INCLUDE=/usr/local/include # indicates the directory where the header file "mpif.h" can be found on the present machine DEFS_MPI=-DMPI LIBS= -lscalapack -lblacs -lmpi -lblas - llapack ___ Guilherme Maia Santos "Se as pessoas são boas só por temerem o castigo e almejarem uma recompensa, então realmente somos um grupo muito desprezível." (Albert Einstein) Em Terça-feira, 3 de Dezembro de 2013 12:56, k.manzoorolajdad escreveu: hi every user i use centos 6.4 and install blas , atlas , lapack with yum. i use openmpi for scalapack for config i use: ../Src/configure --enable-mpi --enable-debug --with-scalapack=/usr/lib64/openmpi/lib/libscalapack.a --with-blacs=/usr/lib64/libblas.a --with-lapack=/usr/lib64/liblapack.a and edit arch.make and add -L in library address after that type make. but see error : /lib/libscalapack.a -L /usr/lib64/libblas.a -L /usr/lib64/liblapack.a -lblas inver.o: In function `inver_': /home/manzoor/Downloads/siesta-3.2-pl3/Src/inver.f:52: undefined reference to `dgetrf_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/inver.f:59: undefined reference to `dgetri_' m_pulay.o: In function `inverse': /home/manzoor/Downloads/siesta-3.2-pl3/Src/m_pulay.F90:549: undefined reference to `dgetrf_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/m_pulay.F90:557: undefined reference to `dgetri_' cdiag.o: In function `cdiag_': /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:259: undefined reference to `blacs_gridinfo_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:265: undefined reference to `descinit_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:429: undefined reference to `zhegvx_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:337: undefined reference to `blacs_gridinfo_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:338: undefined reference to `indxg2p_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:339: undefined reference to `indxg2p_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:343: undefined reference to `numroc_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:344: undefined reference to `numroc_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:345: undefined reference to `numroc_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:346: undefined reference to `numroc_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:437: undefined reference to `pzhegvx_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:438: undefined reference to `pzgemr2d_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:493: undefined reference to `pzpotrf_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:512: undefined reference to `pzhengst_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:536: undefined reference to `pzhemm_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:538: undefined reference to `pzgemm_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:637: undefined reference to `pzgemm_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:412: undefined reference to `pzgemr2d_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:413: undefined reference to `pzgemr2d_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:273: undefined reference to `numroc_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:274: undefined reference to `numroc_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:278: undefined reference to `descinit_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:359: undefined reference to `pjlaenv_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:361: undefined reference to `numroc_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:371: undefined reference to `iceil_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:443: undefined reference to `pzhegvx_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:423: undefined reference to `zhegv_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:491: undefined reference to `pzpotrf_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:255: undefined reference to `blacs_get_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:256: undefined reference to `blacs_gridinit_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:246: undefined reference to `blacs_get_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:247: undefined reference to `blacs_gridinit_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:568: undefined reference to `pzheevd_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:319: undefined reference to `ilaenv_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:319: undefined reference to `ilaenv_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:675: undefined reference to `pztrsm_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:676: undefined reference to `pzgemr2d_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:515: undefined reference to `pzhengst_' /home/manzoor/Downloads/siesta-3.2-pl3/Src/cdiag.F:487: undefined reference to `zpotrf_' /
[SIESTA-L] Problem to run Siesta in Parallel!
Hi everyone, This the deal , when I try to run siesta, e.g.: mpirun -np 4 /home/guilherme/siesta-3.2/Obj/siesta < AlFeO3.fdf | tee saida.out appeared the mensage: mpirun noticed that process rank 1 with PID 17811 on node guilherme-Inspiron-N5010 exited on signal 6 (Aborted). And when I change -np 4 to -np 1 like: mpirun -np 1 /home/guilherme/siesta-3.2/Obj/siesta < AlFeO3.fdf | tee saida.out it's ok... but this way it's a normal way... without parallel mode!! Anyone know what is going on?! Thanks! ___ Guilherme Maia Santos Grupo de Desenvolvimento de Dispositivos Multifuncionais Departamento de Física - Universidade Estadual de Maringá Av. Colombo, 5790. 87020-900 Maringá - Paraná - Brasil
[SIESTA-L] Doubt about AtomicCoordinatesAndAtomicSpecies!
Hi, I'm beginner in the Siesta software, and I have a doubt about the atoms that I put on the Input file, (.fdf) The material that I'm studying it's AlFeO3. This compound have a orthorhombic symmetry and space group Pna21, and the base have 10 atom. And the Formula Units per Cell are 8, so in my case there are 40 atoms ! in the %block AtomicCoordinatesAndAtomicSpecies I have to put only the atoms base (10 atoms) or the 40 atoms that have in unit cell? Thanks ___ Guilherme Maia Santos
