RE: [SIESTA-L] GGA+U
Sure Mohan Sent from Mail for Windows 10 From: Mina Sedighi Sent: 16 March 2019 02:33 To: siesta-l Subject: [SIESTA-L] GGA+U Dear Siesta users and developers, Is there any possibility of performing GGA+U simulations by Siesta? Regards, Mina
RE: [SIESTA-L] Procedure to calculate electron localization functionand charge density plot
Go through my website www.drmlv.in It may help you. Sent from Mail for Windows 10 From: Ananya Rajpoot Sent: 14 March 2019 02:39 To: siesta-l@uam.es Subject: [SIESTA-L] Procedure to calculate electron localization functionand charge density plot Dear users, Can anyone suggest tutorials explaining the procedure to calculate electron localization function and density plots and also how to analyse them. Thanks in advance... Regards Anaya
RE: [SIESTA-L] Error while running make
Read manual carefully and check the availability of arch.make file in the directory. Sent from Mail for Windows 10 From: Bassel Baker Sent: 21 June 2018 01:33 To: siesta-l@uam.es Subject: [SIESTA-L] Error while running make Hi all, I'm installing Siesta 4.0.1: While I'm running make under Obj directory, I'm getting: make: *** No targets. Stop. I successfully run ./configure under Src directory. Any advice? Thanks Bassel Best Regards
[SIESTA-L] compilation error in tbtrans using netcdf4 in siesta4.1b2
Dear Siesta Users and developers I am trying to compile tbtrans using netcdf4 in siesta4.1b2. I have successfully installed NetCDF4 using the method mentioned in the link : http://www.mail-archive.com/siesta-l@uam.es/msg09275.html I am simply using gfortran in compilation. My arch.make file is attached herewith. During transiesta compilation error message shown is : /4.4.0/include -I/home/drmohanlv/build/netcdf/4.4.0/include nf_ncdf.f90 nf_ncdf.f90:2342.28: real(dp), allocatable :: r 1 Error: Scalar object 'r' at (1) may not be ALLOCATABLE nf_ncdf.f90:2133.28: real(sp), allocatable :: r 1 Error: Scalar object 'r' at (1) may not be ALLOCATABLE make[2]: *** [nf_ncdf.o] Error 1 make[2]: Leaving directory `/home/drmohanlv/siesta-4.1-b2/Obj/NCDF/src' make[1]: *** [lib] Error 2 make[1]: Leaving directory `/home/drmohanlv/siesta-4.1-b2/Obj/NCDF' make: *** [libncdf.a] Error 2 And during tbtrans compilation the error message shown : gfortran -c -O2 -fPIC -ftree-vectorize -I../../ -I/home/drmohanlv/build/netcdf/4.4.0/include nf_ncdf.f90 nf_ncdf.f90:2342.28: real(dp), allocatable :: r 1 Error: Scalar object 'r' at (1) may not be ALLOCATABLE nf_ncdf.f90:2133.28: real(sp), allocatable :: r 1 Error: Scalar object 'r' at (1) may not be ALLOCATABLE make[1]: *** [nf_ncdf.o] Error 1 make[1]: Leaving directory `/home/drmohanlv/siesta-4.1-b2/Util/TS/TBtrans/NCDF/src' make: *** [libncdf.a] Error 2 Without Netcdf4 both compilation was completed successfully. And similar errors are obtained in siesta4.1b3 too. pls help me to sort this issues. Thanking you in advanced. Dr Mohan L Verma Prof & Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 Sent from Mail for Windows 10 arch.make Description: Binary data
[SIESTA-L] Fw: No change observed in Magnetic properties using GGA and GGA+U in siesta-4.1-b2
Show original message On Wednesday, 14 June 2017 1:15 PM, Dr. Mohan L. Verma <drmoha...@yahoo.com> wrote: Dear siesta users and developers I tried to calculate magnetic properties of Fe3SnC and related other structures using GGA and GGA+U methodology. A slight change in magnetic moment is observed in between GGA and GGA+U. When I changed U values from 2 to 8 eV. No relative change is found in total energy values and magnetic moment of system obtained using GGA+U. The fdf file of the system under study is attached herewith. This is prepared using siesta manual and test file there in siesta-4.1.b2. The outpul file is also attached. pls help me and suggest the method of selection of U as well as correction in my fdf file (if any). Thanking you in advance. Dr Mohan L Verma Prof & Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 Fe3SnC.fdf Description: application/vnd.fdf Fe3SnC.out Description: Binary data
[SIESTA-L] No change observed in Magnetic properties using GGA and GGA+U in siesta-4.1-b2
Dear siesta users and developers I tried to calculate magnetic properties of Fe3SnC and related other structures using GGA and GGA+U methodology. A slight change in magnetic moment is observed in between GGA and GGA+U. When I changed U values from 2 to 8 eV. No relative change is found in total energy values and magnetic moment of system obtained using GGA+U. The fdf file of the system under study is attached herewith. This is prepared using siesta manual and test file there in siesta-4.1.b2. The outpul file is also attached. pls help me and suggest the method of selection of U as well as correction in my fdf file (if any). Thanking you in advance. Dr Mohan L Verma Prof & Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 Fe3SnC.fdf Description: application/vnd.fdf Fe3SnC.out Description: Binary data
Re: [SIESTA-L] label of DOS and transmission spectra
Dear Anita No difference in the behaviour of system under study in both cases. In case of E-Ef the Fermi energy level is shifted to zero, so no need to mention necessarily the Fermi energy in figure as well as in Text. mohan Dr Mohan L Verma Prof & Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 email : drmoha...@gmail.com On Saturday, 18 June 2016 3:05 AM, anita dameh <anita.da@gmail.com> wrote: Dear Transiesta users,I am a new transiesta user and noticed in the most papers figures such as DOS, transmission spectra and ... reported verses the E-Ef not versus the E(electron energy).what is the differences? and why it is better? best,Anita
Re: [SIESTA-L] about unit in PDOS and DOS
Dear Mayuri Which type of variation you have observed? pls mention clearly and if possible send the pics of both plots. Dr Mohan L Verma Prof & Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 On Friday, 17 June 2016 12:14 PM, Mayuri Vaghela <mayurivaghel...@gmail.com> wrote: hi to all siesta users,i have calculated PDOS and DOS for Hg using both SIESTA and quantum espresso but i found variation in both graphs so i confuse weather unit problem or any other, please clear my doubt.thanking you in advance...
Re: [SIESTA-L] Conformation of made structure
Dear Jeetu Try Avogadro or Jmol to create graphene structure and find xyz coordinates of structure. The you can create fdf input file for further use in siesta. All the best. Dr Mohan L Verma Prof Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 email : drmoha...@gmail.com On Thursday, 2 July 2015 3:42 PM, Jeetu Donderiya jeetudonderiya2...@gmail.com wrote: Dear Siesta Developers and Users I don't understand, how can i make input fdf file for graphene mono layer sheet? while there is no graphical interface with siesta code. If i want to calculate band structure of graphene, which parameter should I define? and how shall I be conform, my structure is that as desired like bended graphene stucture. Please help me to get out of this. Many thanks. Best regards, Jeetu donderiya Research Scholar ITM GOI, Gwalior
Re: [SIESTA-L] TranSiesta Error after trying to run a fast example
Dear Sharma ji Please read the manual carefully and start from beginning i.e. from the compilation of transiesta. we are using siesta-trunk-462. In order to compile transiesta in series Use following steps : 1. download siesta-trunk-462 from : http://departments.icmab.es/leem/siesta/CodeAccess/Code/downloads.html and extract it in home directory now go to Obj dir and configure using : $ /home/drmohanlv/siesta-trunk-462/Obj/ sh ../Src/obj_setup.sh then $ /home/drmohanlv/siesta-trunk-462/Obj/ ../Src/configure finally compile transiesta using $ /home/drmohanlv/siesta-trunk-462/Obj/ make transiesta this will generate a transiesta binary file in this directory. copy binary file to /home/drmohanlv/bin/ directory by $ /home/drmohanlv/siesta-trunk-462/Obj/ cp transiesta ~/bin now for compilation of tbtrans go to $ /home/drmohanlv/siesta-trunk-462/Util/TBTrans_rep/ and only type make this will generate tbtrans binary file for further use copy binary file to /home/drmohanlv/bin/ directory by $ /home/drmohanlv/siesta-trunk-462/Obj/ cp tbtrans ~/bin After above compilation of transiesta and tbtrans you can run the examples in the test directory. All the best. Dr Mohan L Verma Prof Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 email : drmoha...@gmail.com On Friday, 26 June 2015 10:39 PM, Jaehwan Kweon janikw...@gmail.com wrote: that is probably because there is no executable transiesta file in /your_directory/siesta-3.2/Obj so, you need to check whether files are successfully compiled try this.. $cd siesta-3.2/Obj/$make clean$make transiesta$cp /directory/siesta/Obj/transiesta /usr/local/bin good luck! On Sat, Jun 27, 2015 at 1:39 AM, jv sharma jvnano...@gmail.com wrote: I am still getting the same error, after doing this. That is, like this: jv@jv-desktop:~/siesta-3.2/Examples/TranSiesta/Elec/OUT_Test$ transiesta elec.fast.fdf elec.fast.out transiesta: command not found jv@jv-desktop:~/siesta-3.2/Examples/TranSiesta/Elec/OUT_Test$ On Fri, Jun 26, 2015 at 10:01 PM, Raha khalili khadije.khal...@gmail.com wrote: Hi, You can try this: export PATH= /your_directory/siesta-3.2/Obj:$PATH Best, Raha On Fri, Jun 26, 2015 at 6:05 PM, jv sharma jvnano...@gmail.com wrote: On Fri, Jun 26, 2015 at 9:18 PM, Jaehwan Kweon janikw...@gmail.com wrote: you would better install transiesta first $cd siesta-3.2/Obj/$make transiesta then$cp /directory/siesta/Obj/transiesta /usr/local/bin Now I get like this: jv@jv-desktop:~$ cp /directory/siesta-3.2/Obj/transiesta /usr/local/bin cp: cannot stat ‘/directory/siesta-3.2/Obj/transiesta’: No such file or directory jv@jv-desktop:~$ On Sat, Jun 27, 2015 at 12:36 AM, jv sharma jvnano...@gmail.com wrote: On Fri, Jun 26, 2015 at 4:28 PM, 毛飞 200921220...@mail.bnu.edu.cn wrote: Hi, Sarma It seems that the transiesta can not be found by the system. Do you add the absolute path of the executable transiesta in the environment variable $PATH? You can test if it is added in the $PATH by typing “which transiesta” in the command line. I got like this: jv@jv-desktop:~$ which transiesta jv@jv-desktop:~$ I do not understand this. Good luck. Fei MaoUSC 在2015-06-26，jv sharma jvnano...@gmail.com 写道: -原始邮件- 发件人: jv sharma jvnano...@gmail.com 发送时间: 2015年6月26日 星期五 收件人: siesta-l@uam.es 抄送: nickpap...@gmail.com 主题: [SIESTA-L] TranSiesta Error after trying to run a fast example Dear Siesta Community, I get the following after trying to run a fast example in TranSiesta: jv@jv-desktop:~/siesta-3.2/Examples/TranSiesta/Elec/OUT_Test$ transiesta elec.fast.fdf elec.fast.out transiesta: command not found Please help me to get out of this. Many thanks. Best regards, JVN Sarma, India. -- Jaehwan KweonSungkyunkwan University(SKKU) SKKU Advanced Institute of Nanotechnology(SAINT)2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi 440 - 746, Republic of Korea Office:+82-31-299-4871C.P.#: 010-5145-8388E-mail: janikw...@gmail.com zaih...@skku.edu -- -- Jaehwan KweonSungkyunkwan University(SKKU) SKKU Advanced Institute of Nanotechnology(SAINT)2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi 440 - 746, Republic of Korea Office:+82-31-299-4871C.P.#: 010-5145-8388E-mail: janikw...@gmail.com zaih...@skku.edu
Re: [SIESTA-L] generate si.band file
in siesta/Tests dir a test file is given for Si bands run. Try that and run it for your Si system making necessary blocks in your input fdf file. all the best. Dr Mohan L Verma Prof Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 drmoha...@gmail.com On Thursday, 4 June 2015 5:04 PM, Uma Shankar Sharma ussharma...@gmail.com wrote: Check your input file Dr U S Sharma On Jun 4, 2015 4:55 PM, Jeetu Donderiya jeetudonderiya2...@gmail.com wrote: Hello How to generate si.band file? when i run siesta, there is no such file.
Re: [SIESTA-L] ABOUT SIESTA EXECUTABLES
Dear Anant If you have compiled siesta successfully, Then go to ~/siesta-3.2/Util and run build_all.sh this will creat maximum important utilities binary files for further use Dr Mohan L Verma Prof Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 drmoha...@gmail.com On Wednesday, 15 April 2015 5:12 PM, Nick Papior Andersen nickpap...@gmail.com wrote: 2015-04-15 13:34 GMT+02:00 ANANT VIJAY anantvijay...@gmail.com: Sir , I can compile and execute things with .f90 files sucsessfully but not with .f files, now all the utilities are not compiled from .f90 files but .f files so I need .f90 files only for those utilities.Although i can compile the files .f extention but they do not run at all I am sorry, I do not understand your inquiry then... for example when i execute ./plstm and then enters it does not give any messages. ANANT VIJAY VARMA M.Tech. STUDENT CENTER FOR CONVERGING TECHNOLOGIES UNIVERSITY OF RAJASTHAN JAIPUR On Wed, Apr 15, 2015 at 4:56 PM, Nick Papior Andersen nickpap...@gmail.com wrote: 2015-04-15 13:21 GMT+02:00 ANANT VIJAY anantvijay...@gmail.com: well all I am asking is for .f90 files (if someone have) of all the utilities in utility folder only, as I am not able to compile and execute the .f files correctly but .f90 only.So as you said .f90 source files for all utilities is all I need. This implies that you have a faulty compiler. Which compiler are you using?Regular gcc/gfortran compiles all the sources just fine. To be clear, can you compile all the .f90 and execute the utilities successfully? The utilities have not been ported to fortran 90, some have but far from all. This is because nearly all compilers are backwards compatible and can easily compile the .f files.What you are requesting is non-existing to my knowledge. Thank you for your reply. ANANT VIJAY VARMA M.Tech. STUDENT CENTER FOR CONVERGING TECHNOLOGIES UNIVERSITY OF RAJASTHAN JAIPUR On Tue, Apr 14, 2015 at 7:47 PM, I. Camps ica...@gmail.com wrote: Dear Anant, You should EVER ask to a stranger to send you executable files! One of the good things of SIESTA is that you have access to the source files. Then you can compile your own executable files in your own platform in a risk free manner.. If you have .f90 sources files, you have to compile them using a Fortran 90 compiler (gfortran, Intel, gcc, etc.) in the same way you compile .f files. Regards, []'s, @mps On Tue, Apr 14, 2015 at 9:30 AM, ANANT VIJAY anantvijay...@gmail.com wrote: Sir, As i mentioned plstm for LDOS, gnubands, and all other which are being compiled by .f extension fortran files. It would be really helpful if you send me either executables compiled from .f90 extension files or files themselves. thank you for your reply. On 4/9/15, Uma Shankar Sharma ussharma...@gmail.com wrote: Mention clearly, which executable is not compiled Dr U S Sharma RJIT Tekanpur On Apr 9, 2015 7:46 PM, ANANT VIJAY anantvijay...@gmail.com wrote: HELLO EVERYONE Please send me if you have siesta EXECUTABLES compiled from .f90 fortran files. I am not able to run many of the utility files. like plstm ,gnubands, etc. ANANT VIJAY VARMA M.Tech. STUDENT CENTER FOR CONVERGING TECHNOLOGIES UNIVERSITY OF RAJASTHAN JAIPUR -- ANANT VIJAY VARMA M.Tech. STUDENT CENTER FOR CONVERGING TECHNOLOGIES UNIVERSITY OF RAJASTHAN JAIPUR -- Kind regards Nick -- Kind regards Nick
Re: [SIESTA-L] Properties Calculation
dear younas You can compute all mentioned properties using siesta. The manual of siesta is well written for all properties and sufficient test files are also given. all the best. Dr Mohan L Verma Prof Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 On Tuesday, 31 March 2015 7:53 PM, Younas Khan younaskhan.phys...@gmail.com wrote: Hi all. I am new to SIESTA. I just wanted to know that can we calculate optical, structural, electronic and mechanical properties of a material using SIESTA? If yes, then what blocks should be included in the input file. Thanks in advance. Younas Khan
Re: [SIESTA-L] Denchar can't read the coordinates
can you send your input file ? and your CUBE file too ? Dr Mohan L Verma Prof Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 On Wednesday, 4 February 2015 9:53 PM, Li-Biao libiao19900...@163.com wrote: Dear siesta users,I'm doing first-principles calculations with siesta-3.1,recently.When I was running denchar,I find that there is no input coordinates in the running interface.But after the program run out,the cube file can't be read By Xcrysden. I don't know what's wrong with it.I wish someone can help me.
Re: [SIESTA-L] TranSIESTA Calculation
Dear Mohammad I am not getting how you are increasing the required vector length in z direction. Go thought the output file keenly, may be some difference (if any ) will be there. Can you please send me your fdf file for first two cases. Dr Mohan L Verma Prof Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 drmoha...@gmail.com On Monday, 17 November 2014 2:03 PM, Seyed Mohammad Tabatabaei smt...@gmail.com wrote: Dear SIESTA Users, I have a few conceptual questions about TranSIESTA and would be really grateful if you help me with them. In fact, the answer to these questions is quite important for my calculations. I have used TranSIESTA to study the current in an 8-AGNR system. My system consists of 16X7=112 carbon atoms. 16 atoms make the left electrode, 5X16=80 atoms make the scattering region, and 16 atoms make the right electrode. As the transport direction is along the z direction, my system would look like this along the z direction: ... + Left 16 atoms + Scat. region 80 atoms + Right 16 atoms + Left 16 atoms + Scat. region 80 atoms + Right 16 atoms + ... I successfully calculated the current in this case for a particular bias. Then, I increased the length of the vector along the z direction by about 3 Angs and repeated the calculation. Note that I only increased the length of the vector and did not add any atoms. All the other settings in the .fdf file was kept intact. In this case, my system looked like the following: ... + Vacuum of about 3 Angs + Left 16 atoms + Scat. region 80 atoms + Right 16 atoms + Vacuum of about 3 Angs + Left 16 atoms + Scat. region 80 atoms + Right 16 atoms + ... Interestingly, I found almost identical current values as the ones obtained in the case with no vacuum. Finally, I increased the void to 10 Angs without modifying any other settings. In this case, although the DM did not converged in 1000 iterations, the code calculated currents similar to the ones obtained for no vacuum but with about 40 percent deviation. My questions are the following: 1- Does the neighboring scattering regions affect each other in the scattering region calculation? What is the difference between calculations which do not include any vacuum with calculations which consider, say a 10 Angs, vacuum? 2- How should I make the code converge when I increase the void to 10 Angs? How should I modify my .fdf code in the case with vacuum so that I can obtain identical currents to the case with no vacuum. Sorry for my bother-making. I am trying to simulate a system with TranSIESTA which contains quite different left and right electrodes that cannot come into direct contact without the scattering region in between. The only way for me is to introduce vacuum between neighboring scattering regions. In brief, I would be really grateful if you tell me how can I determine the size of the sufficient vacuum between neighboring scattering regions so that my results can be credible. Best wishes, Mohammad,
Re: [SIESTA-L] How to restart Siesta?
Dears If your *.fdf file contains : UseSaveData true DM.UseSaveDMtrue MD.UseSaveXVtrue MD.UseSaveCGtrue then when you use the command for siesta run, siesta may be start from the last ending point. All the best. Dr Mohan L Verma Prof Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 On Sunday, 21 September 2014 11:29 AM, Suman Chowdhury sumanchowdhur...@gmail.com wrote: Few weeks ago I had also posted a similar question in the forum.. On Sun, Sep 21, 2014 at 6:55 AM, Julio Henrique juliohenri...@msn.com wrote: I had simulations interrupted by prolonged lack of electricity. How to restart from where it was interrupted? Is it possible? Thank's. Julio Henrique. -- Junior research fellow Dept. of Physics, University of Calcutta Kolkata- 79, West Bengal, India. Ph no-+91-9830512232
Re: [SIESTA-L] error in TranSiesta Installation
Dear Manjeet During configuration give the path of lapack and blas then make transiesta or alternatively you can try transiesta in siesta-trunk-462. I have compiled transiesta without giving the path of separate lapack and blas insiesta-trunk-462 . All the best. Dr Mohan L Verma Prof Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 On Tuesday, 2 September 2014 11:38 AM, Nick Papior Andersen nickpap...@gmail.com wrote: It cannot find your lapack library. Ensure you have -Lpath to liblapack.a in the LIBS environment variable. 2014-09-02 5:57 GMT+00:00 Manjeet Bhatia manjeetbhati...@gmail.com: Dear Siesta Users, When I try to install TranSiesta in siesta-3.2 package I came across the following error: nts.o m_ts_iodm.o m_ts_io.o m_ts_scattering.o m_ts_contour.o m_ts_electrode.o m_ts_in_siesta.o libfdf.a \ \ dc_lapack.a liblapack.a libblas.a `FoX/FoX-config --libs --wcml` dc_lapack.a liblapack.a libblas.a m_ts_aux_rout.o: In function `__m_ts_aux_rout_MOD_csolveg': /home/manjeet/siesta-3.2/Src/m_ts_aux_rout.F:347: undefined reference to `zgesv_' collect2: ld returned 1 exit status make: *** [transiesta] Error 1 Could you please tell me the possible cause of the error? Although I installed siesta successfully. Manjeet -- Kind regards Nick
Re: [SIESTA-L] version 3.2 : siesta = transiesta??
for transiesta you should try siesta-trunk-462 ... Dr Mohan L Verma Prof Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 On Friday, 8 August 2014 9:18 PM, Karolina Milowska karolina.milow...@gmail.com wrote: Dear Toufik, from manual: 1) go to Obj directory and type: sh ../Src/obj_setup.sh 2) then type ../Src/configure 3) The standard Siesta executable (obtained as described in Section 2) does not include the TranSiesta modules. In order to use the TranSiesta capabilities, you must compile the Siesta package as indicated in this Section. In this way, the compilation is done using the appropriate preprocessor flags needed to include the TranSiesta modules in the binary file. To generate a binary of Siesta which includes the TranSiesta capabilities, just type: $ make transiesta using the appropriate arch.make file for your system (note that you do not need to make any modification on your arch.make file: you can use the same one that you have used to make a standard Siesta compilation in your system). The Makefile takes care of defining the appro- priate preprocessor flag -DTRANSIESTA so that the TranSiesta modules and modifications are compiled and incorporated into the binary. Upon successful compilation, the binary file transiesta will be generated, containing an executable version of Siesta with TranSiesta capabilities. You will get executable file called: transiesta not siesta. So, to run the program type ./transiesta Bests, Karolina Milowska 2014-08-08 15:37 GMT+00:00 toufik esssakhri tou...@hotmail.fr: and this is my question how to do transiesta calculation using this version. From: nickpap...@gmail.com Date: Fri, 8 Aug 2014 11:29:12 + To: siesta-l@uam.es Subject: Re: [SIESTA-L] version 3.2 : siesta = transiesta?? Please read the manual carefully on how to utilize transiesta. It is very well explained. (you are using siesta, not transiesta in your calculation) 2014-08-08 8:54 GMT+00:00 toufik esssakhri tou...@hotmail.fr: what's exactally gone wrong?? this is the first lines of the output Siesta Version: siesta-3.2-pl-5 Architecture : x86_64-centos-linux-intel--openmpi Compiler flags: mpif90 -O0 PARALLEL version * Running on 4 nodes in parallel Start of run: 8-AUG-2014 10:49:58 *** * WELCOME TO SIESTA * *** reinit: Reading from standard input ** Dump of input data file SystemName elec.fast SystemLabel elec.fast == == From: nickpap...@gmail.com Date: Thu, 7 Aug 2014 21:47:57 + To: siesta-l@uam.es Subject: Re: [SIESTA-L] version 3.2 : siesta = transiesta?? Then you have done something wrong. The output will tell you whether it has transiesta supported or not (check the first 5 lines of the output) 2014-08-07 20:34 GMT+00:00 toufik esssakhri tou...@hotmail.fr: Thanks, one other question : To do transiesta calculation should i do export executable= transiesta (or siesta)?? Because i have done the calcution of the hydrogen, at the end i don't have the elect.fast.TSHS Best regards, Taoufik --- Message initial --- De : Nick Papior Andersen nickpap...@gmail.com Envoyé : 7 août 2014 23:30 A : siesta-l@uam.es Objet : Re: [SIESTA-L] version 3.2 : siesta = transiesta?? 2014-08-07 13:23 GMT+00:00 toufik esssakhri tou...@hotmail.fr: dear all, i have one question please In version 3.2, is transiesta = siesta (which is included)?? transiesta /= siesta. Both are included, you compile them by: make siesta or make transiesta cheers, Taoufik -- Kind regards Nick -- Kind regards Nick -- Kind regards Nick
Re: [SIESTA-L] Running the VIBRA PACKAGE
can you send me your input files ...? mohan On Sunday, 13 July 2014 8:39 PM, Bishal Bhattarai bishalbhattarai...@gmail.com wrote: Thanks very much for the earlier help but I am still stuck and unable to perform anything in the utilities. The siesta I compiled works well so does eig2dos but I am having trouble with the vibra package. As you said last time, I did the modification in the vibra.h file in siesta, still I am getting some error. I tried this will all the possible version of siesta but it's not working in any one of them. The error it says is, fcbuild sih.fdf (my initial input file ) At line 119 of file recoor.f (unit = 5, file = 'stdin') Fortran runtime error: Bad real number in item 1 of list input Every bit of Help will be really helpful. On Fri, Jul 11, 2014 at 2:43 AM, Dr. Mohan L. Verma drmoha...@yahoo.com wrote: hey Bishal.. Go to ~/siesta/Util/vibra/src and modify in the line no. 22 in vibra.h parameter (maxa = 8) to parameter (maxa = 64) and recompile fcbuild and vibrator simply using make. I think this will work. all the best. Dr Mohan L Verma Prof Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 drmoha...@gmail.com On Friday, 11 July 2014 9:56 AM, Bishal Bhattarai bishalbhattarai...@gmail.com wrote: Nick Papior Andersen, Thanks for your earlier Reply. I did the following steps till now, (compile siesta) cd Obj sh ../Src/obj_setup.sh cd ../Pseudo/atom make cd ../../Util sh build_all.sh This this generated both executable file for the fcbuild.f vibrator.f in the Util/Vibra/Src package. Now the description says that it will use a .fdf file as an input and it creates an .fdf file as an output. Is this the same fdf file used during the run of siesta or is it from my output files or i have to have a new input file ?? I also tried. fcbuild sih.fdf (my initial input file ) it gives the error as redata: System Name = SIH1 redata: System Label = SIH1 Number of Atoms = 64 chkdim: ERROR: In fcbuild, dimension maxa = 8. It must be at least 64 i have already generated a .FC file for the phonon relaxation. I am doing it in the siesta 3.1 version. EVERY BIT of information and Suggestion will be fully appreciated. Thankyou. Sincerely, Bishal Bhattarai Ohio University, USA On Thu, Jul 10, 2014 at 2:04 AM, Nick Papior Andersen nickpap...@gmail.com wrote: You should run make and not try to compile it yourself. :) Almost all applications in siesta utilities are compiled using makefiles. At least for 3.1 and above, I do not know about the 2.0.2 version. 2014-07-10 3:06 GMT+00:00 bishalbhattarai...@gmail.com: HELLO, I am a new person in SIESTA. I need to do some phonon calculations with the SIESTA. I have already got the sample.FC file after running the siesta with my Input .fdf file. How can I use these collected files after the simulations to run in the vibra package. How can i compile first the fcbuild.f file in SIESTA-2.0.2 or SIESTA-3.1 package ? Can I do this ? $ f95 fcbuild.f -o fcbuild but it says an error !!! fcbuild.f:29.72: use fdf 1 Fatal Error: Can't open module file 'fdf.mod' for reading at (1): No such file or directory Hoping for a kind reply. Sincerely, Bishal Bhattarai Ohio University,USA -- Kind regards Nick
Re: [SIESTA-L] Running the VIBRA PACKAGE
hey Bishal.. Go to ~/siesta/Util/vibra/src and modify in the line no. 22 in vibra.h parameter (maxa = 8) to parameter (maxa = 64) and recompile fcbuild and vibrator simply using make. I think this will work. all the best. Dr Mohan L Verma Prof Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 drmoha...@gmail.com On Friday, 11 July 2014 9:56 AM, Bishal Bhattarai bishalbhattarai...@gmail.com wrote: Nick Papior Andersen, Thanks for your earlier Reply. I did the following steps till now, (compile siesta) cd Obj sh ../Src/obj_setup.sh cd ../Pseudo/atom make cd ../../Util sh build_all.sh This this generated both executable file for the fcbuild.f vibrator.f in the Util/Vibra/Src package. Now the description says that it will use a .fdf file as an input and it creates an .fdf file as an output. Is this the same fdf file used during the run of siesta or is it from my output files or i have to have a new input file ?? I also tried. fcbuild sih.fdf (my initial input file ) it gives the error as redata: System Name = SIH1 redata: System Label = SIH1 Number of Atoms = 64 chkdim: ERROR: In fcbuild, dimension maxa = 8. It must be at least 64 i have already generated a .FC file for the phonon relaxation. I am doing it in the siesta 3.1 version. EVERY BIT of information and Suggestion will be fully appreciated. Thankyou. Sincerely, Bishal Bhattarai Ohio University, USA On Thu, Jul 10, 2014 at 2:04 AM, Nick Papior Andersen nickpap...@gmail.com wrote: You should run make and not try to compile it yourself. :) Almost all applications in siesta utilities are compiled using makefiles. At least for 3.1 and above, I do not know about the 2.0.2 version. 2014-07-10 3:06 GMT+00:00 bishalbhattarai...@gmail.com: HELLO, I am a new person in SIESTA. I need to do some phonon calculations with the SIESTA. I have already got the sample.FC file after running the siesta with my Input .fdf file. How can I use these collected files after the simulations to run in the vibra package. How can i compile first the fcbuild.f file in SIESTA-2.0.2 or SIESTA-3.1 package ? Can I do this ? $ f95 fcbuild.f -o fcbuild but it says an error !!! fcbuild.f:29.72: use fdf 1 Fatal Error: Can't open module file 'fdf.mod' for reading at (1): No such file or directory Hoping for a kind reply. Sincerely, Bishal Bhattarai Ohio University,USA -- Kind regards Nick
Re: [SIESTA-L] transport calculation
Hey Toufik If you want .. you can start from this link : http://dipc.ehu.es/frederiksen/tstutorial/index.php/Main_Page Dr Mohan L Verma Prof Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 On Thursday, 10 July 2014 8:45 PM, toufik esssakhri tou...@hotmail.fr wrote: Dear all, i want to do transport properties in the metal/oxyde junction using TRANSIESTA, i don't find documentation. Please, there is anyone help me how to proceed?? cheers
[SIESTA-L] elastic properties study of polymeric system
Dear Siesta users and developers I have a simple but fundamental question, Can I use siesta to study the elastic properties of polymers like PEO, PPY etc. If yes then suggest me the limitations or further directions. Thanking you all in advance. Dr Mohan L Verma Prof Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020
Re: [SIESTA-L] elastic properties study of polymeric system
hey Herbert Thanks a lot for promt response. mohan On Friday, 13 June 2014 5:23 PM, Herbert Fruchtl herbert.fruc...@st-andrews.ac.uk wrote: Dear Mohan, If your material is (or can be approximated as) crystalline with a unit cell of manageable size, you can use SIESTA to model it. A paper I came across lately (but haven't actually gotten around to read in detail, so I don't vouch for it) compares the performance of SIESTA and a plane-wave code (VASP) for calculating elastic properties. Have a look: First principles prediction of the elastic, electronic, and optical properties of Sb2S3 and Sb2Se3 compounds H. Koc, Amirullah M. Mamedovb, E. Deligozc, H. Ozisikd Solid State Sciences, Volume 14, Issue 8, August 2012, Pages 1211-1220, ISSN 1293-2558, http://dx.doi.org/10.1016/j.solidstatesciences.2012.06.003. Or, if you don't have access to the journal: http://arxiv.org/pdf/1205.3344.pdf I am sure you can find more examples. HTH, Herbert On 13/06/14 11:28, Dr. Mohan L. Verma wrote: Dear Siesta users and developers I have a simple but fundamental question, Can I use siesta to study the elastic properties of polymers like PEO, PPY etc. If yes then suggest me the limitations or further directions. Thanking you all in advance. Dr Mohan L Verma Prof Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532
Re: [SIESTA-L] how to compile the TBTrans in the version siesta-trunk-458
Toufik You may use jmol and/or avogadro and/or VESTA to generate coordinates of your supercell and make fdf input file for siesta run. all the best Dr Mohan L Verma Prof Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 On Tuesday, 10 June 2014 2:32 PM, toufik esssakhri tou...@hotmail.fr wrote: Dear all, I am a beginner user of Siesta and I am trying to do calculations for the very known hybrid system metal/oxyde junction. i need to use a tetragonal supercell, so how can i build it or define the atomic positions with siesta. i can extract the positions using XCrySDen for example but how put it in the .fdf file Please do guide me, it is very urgent for me. From: nickpap...@gmail.com Date: Tue, 10 Jun 2014 09:16:45 +0200 To: siesta-l@uam.es Subject: Re: [SIESTA-L] how to compile the TBTrans in the version siesta-trunk-458 Try and do (in the tbtrans directory): make clean rm -rf MPI make Might I also suggest you to try the tbtrans version in TBTrans_rep. 2014-06-10 5:00 GMT+02:00 xu yuehua xu11249...@gmail.com: Hi all : i have used the attached arch,make file to compile the siesta and transiesta, and no error presented when they are compiling. but when i cd Util/TBTrans, and use make command to compile the TBTrans the errors came out, Compilation architecture to be used: x86_64-unknown-linux-gnu--unknown If that is not what you want, give the correct value to the variable SIESTA_SYS in your shell environment. (mkdir -p MPI; cd MPI ; make -f /public/home/yhxu/siesta-trunk-458/Util/TBTrans/../../Src/MPI/Makefile FC=mpif90 VPATH=/public/home/yhxu/siesta-trunk-458/Util/TBTrans/../../Src/MPI \ MAKEFILES=/public/home/yhxu/siesta-trunk-458/Util/TBTrans/../../Src/MPI/Makefile ARCH_MAKE=../../../Obj/arch.make \ FFLAGS=-g -O1 module_built) make[1]: Entering directory `/public/home/yhxu/siesta-trunk-458/Util/TBTrans/MPI' ../../../Obj/arch.make:60: warning: overriding commands for target `.F.o' ../../../Obj/arch.make:60: warning: ignoring old commands for target `.F.o' ../../../Obj/arch.make:62: warning: overriding commands for target `.F90.o' ../../../Obj/arch.make:62: warning: ignoring old commands for target `.F90.o' ../../../Obj/arch.make:64: warning: overriding commands for target `.f.o' ../../../Obj/arch.make:64: warning: ignoring old commands for target `.f.o' ../../../Obj/arch.make:66: warning: overriding commands for target `.f90.o' ../../../Obj/arch.make:66: warning: ignoring old commands for target `.f90.o' /public/home/yhxu/siesta-trunk-458/Util/TBTrans/../../Src/MPI/Makefile:30: warning: overriding commands for target `Interfaces.f90' /public/home/yhxu/siesta-trunk-458/Util/TBTrans/../../Src/MPI/Makefile:30: warning: ignoring old commands for target `Interfaces.f90' /public/home/yhxu/siesta-trunk-458/Util/TBTrans/../../Src/MPI/Makefile:30: warning: overriding commands for target `V_S.uses' /public/home/yhxu/siesta-trunk-458/Util/TBTrans/../../Src/MPI/Makefile:30: warning: ignoring old commands for target `V_S.uses' /public/home/yhxu/siesta-trunk-458/Util/TBTrans/../../Src/MPI/Makefile:30: warning: overriding commands for target `VS.uses' /public/home/yhxu/siesta-trunk-458/Util/TBTrans/../../Src/MPI/Makefile:30: warning: ignoring old commands for target `VS.uses' /public/home/yhxu/siesta-trunk-458/Util/TBTrans/../../Src/MPI/Makefile:35: warning: overriding commands for target `kind_explorer' /public/home/yhxu/siesta-trunk-458/Util/TBTrans/../../Src/MPI/Makefile:35: warning: ignoring old commands for target `kind_explorer' /public/home/yhxu/siesta-trunk-458/Util/TBTrans/../../Src/MPI/Makefile:40: warning: overriding commands for target `module_built' /public/home/yhxu/siesta-trunk-458/Util/TBTrans/../../Src/MPI/Makefile:40: warning: ignoring old commands for target `module_built' /public/home/yhxu/siesta-trunk-458/Util/TBTrans/../../Src/MPI/Makefile:45: warning: overriding commands for target `libmpi_f90.a' /public/home/yhxu/siesta-trunk-458/Util/TBTrans/../../Src/MPI/Makefile:45: warning: ignoring old commands for target `libmpi_f90.a' /public/home/yhxu/siesta-trunk-458/Util/TBTrans/../../Src/MPI/Makefile:49: warning: overriding commands for target `clean' /public/home/yhxu/siesta-trunk-458/Util/TBTrans/../../Src/MPI/Makefile:49: warning: ignoring old commands for target `clean' mpif90 -c -g -O1 -I/public/home/yhxu/intel/impi/4.0.0.028/include64/ /public/home/yhxu/siesta-trunk-458/Util/TBTrans/../../Src/MPI/mpi__include.f90 if [ -z 4 8 ] ; then make kind_explorer ; fi The kind numbers for single and double precision reals follow sh /public/home/yhxu/siesta-trunk-458/Util/TBTrans/../../Src/MPI/generate.sh 4 8 === Generating module files from templates... 4 8 mpif90 -c -g -O1 -I/public/home/yhxu/intel/impi/4.0.0.028/include64/ -DMPI -DFC_HAVE_FLUSH -DFC_HAVE_ABORT
Re: [SIESTA-L] charge density
Dear I found xcrysden ( http://www.xcrysden.org/) is best to plot charge density. Use rho2xsf utility for the same. Dr Mohan L Verma Prof Head Department of Applied Physics FET,SSGI Shri Shankaracharya Technical Campus-Junwani, Bhilai (Chhattisgrah) INDIA 490020 On Wednesday, 4 June 2014 1:07 PM, Nick Papior Andersen nickpap...@gmail.com wrote: 1. You can use the grid2cube utility in Util/Grid to generate cube files from the binary grid files (SystemLabel.RHO). 2. You can use the cdf2cube utility in Util/Grid to generate cube files from the NetCDF grid files (Rho.grid.nc). Then follow instructions on showing cube files in vmd, basically they are: vmd cube-file Option Graphics - Representations Select first Style in list and do: Drawing Method - Isosurface I prefer to have the isosurface shown as a solid surface, this can be achieved using: Draw - Solid Surface Then play around in VMD :) 2014-06-04 9:01 GMT+02:00 berna uyanık bernauya...@gmail.com: Hi. VMD's supporting files is here: http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/ You should convert your files to supporting files. On Wed, Jun 4, 2014 at 9:38 AM, Suman Chowdhury sumanchowdhur...@gmail.com wrote: Dear user, Can anyone know how to plot charge density through siesta by using vmd visualization tool. -- Junior research fellow Dept. of Physics, University of Calcutta Kolkata- 79, West Bengal, India. Ph no-+91-9830512232 -- Kind regards Nick
Re: [SIESTA-L] Problem makeing TBTrans
Did to compile transiesta ? Use the same lapack and blas library for tbtrans. During compilation of transiesta if you get same error message then during configuration before using make in SRC directory. you may give the path for lapack and blas library installed out of siesta/transiesta. I did in this way... and its working in siesta-trunk.XXX versions.. mohan On Tuesday, 25 March 2014 11:57 PM, Behnaz Bagheri behnaz.bagher...@gmail.com wrote: Dear Siesta users, I am totally new to siesta and transiesta. I tried to use TBTrans in Utill file and typed make there but I got this error massage which I don't know how to solve: echo ***Please see top of Makefile f95: error: dc_lapack.a: No such file or directory f95: error: liblapack.a: No such file or directory f95: error: zgesv_lapack.a: No such file or directory f95: error: libblas.a: No such file or directory ***Please see top of Makefile I looked at the top of Makefile but I don't know how to solve the problem. I've attached the error and the Makefile. I really appreciate you help. With kind regards, Behnaz
[SIESTA-L] siesta in parallel compilation error
Dear sirsta users and developes WE ARE MAKING PARALLEL SIESTA WITH OPENMPI gfortan BUT WE HAVE THE FOLLOWING ERROR. I HOPE SOME OF YOU MIGHT RESOLVE THIS:... SIESTA'S arch.make FILE: - .SUFFIXES: .SUFFIXES: .f .F .o .a .f90 .F90 SIESTA_ARCH=i686-pc-linux-gnu--unknown FPP= FPP_OUTPUT= FC = /opt/pool/openmpi/bin/mpif90 CC = /opt/pool/openmpi/bin/mpicc RANLIB=ranlib SYS=nag SP_KIND=4 DP_KIND=8 KINDS=$(SP_KIND) $(DP_KIND) FFLAGS=-g -O2 FPPFLAGS= -DFC_HAVE_FLUSH -DFC_HAVE_ABORT LDFLAGS= ARFLAGS_EXTRA= FCFLAGS_fixed_f= FCFLAGS_free_f90= FPPFLAGS_fixed_F= FPPFLAGS_free_F90= BLAS_LIBS=/opt/[pool/openmpi/librefblas.a LAPACK_LIBS=/opt/pool/openmpi/liblapack.a BLACS_LIBS=/opt/pool/openmpi/blacsCinit_MPI-LINUX-0.a /opt/pool/openmpi/blacsF77init_MPI-LINUX-0.a /opt/pool/openmpi/blacs_MPI-LINUX-0.a SCALAPACK_LIBS=/opt/pool/openmpi/libscalapack.a COMP_LIBS=dc_lapack.a liblapack.a libblas.a NETCDF_LIBS= NETCDF_INTERFACE= LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(NETCDF_LIBS) #SIESTA needs an F90 interface to MPI #This will give you SIESTA's own implementation #If your compiler vendor offers an alternative, you may change #to it here. MPI_INTERFACE=/opt/pool/openmpi/lib/libmpi_f77.a MPI_INCLUDE=/opt/pool/openmpi/include #Dependency rules are created by autoconf according to whether #discrete preprocessing is necessary or not. .F.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $ .F90.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $ .f.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $ .f90.o: $(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90) $ ___ ERROR FORMED AFTER MAKE INSTRUCTION: [user@siesta12 Obj]$ make Compilation architecture to be used: i686-pc-linux-gnu--unknown If this is not what you want, create the right arch.make file using the models in Src/Sys Hit ^C to abort... (cd FoX; touch arch.make ; \ CONFIGURE=/home/user/siesta-3.1/Src/FoX/configure; \ $CONFIGURE VPATH=/home/user/siesta-3.1/Src/FoX \ FC=/usr/local/bin/mpif90 FCFLAGS=-g -O2 \ --enable-wcml || false ) checking build system type... i686-pc-linux-gnu checking host system type... i686-pc-linux-gnu checking for linker flag to name executables... -o checking for Fortran compiler default output file name... conftest checking whether the Fortran compiler works... configure: error: cannot run Fortran compiled programs. If you meant to cross compile, use `--host'. See `config.log' for more details. make: *** [FoX/.config] Error 1 Dr Mohan L Verma
Re: [SIESTA-L] Properties of ZnFeO using siesta
google it yaar. you can get the atomic structure easily. or if you know the structure you can draw using avogadro type molecular editor anf find the coordinates to use in siesa input file Dr Mohan L verma From: acharya k.l.n. acharya4...@gmail.com To: siesta-l@uam.es Sent: Monday, 25 June 2012 8:42 AM Subject: [SIESTA-L] Properties of ZnFeO using siesta Hi all, I wish to calculate the magnetic properties of Zincferrite (Spinel structure). but, i am facing a problem with the atomic positions block. how to give the atomic coordinates for Zinc ferrite structure. please help.. -- With Regards, K L N Acharya, M.Tech., Nanoelectronics, SASTRA UNIVERSITY, Thanjavur.
Re: [SIESTA-L] problem in running tests
dear Dr goker just give the complete path of siesta in the test.mk in siesta=../.../../siesta then run the make in tests Dr Mohan L Verma --- On Mon, 19/3/12, Ali Ihsan Goker aihsan.go...@bilecik.edu.tr wrote: From: Ali Ihsan Goker aihsan.go...@bilecik.edu.tr Subject: [SIESTA-L] problem in running tests To: siesta-l@uam.es Date: Monday, 19 March, 2012, 12:27 PM Dear all, I just downloaded nad installed Siesta in my linux machine. I followed the instructions in the manual (including copying an arch.make file to Obj directory) and the compilation was successful, however, when I tried to ru nthe tests, each time I get the following error == Running SIESTA as ../../../siesta /bin/sh: ../../../siesta: not found make: *** [completed_work] Error 127 Can anyone help me what this might be due to? Thanks Dr. Ali Goker
Re: [SIESTA-L] denchar
dear pradeep pls send me input files along with other supporting file to run.. probably i may give the answer.. Mohan L Verma SSTC Bhilai drmoha...@gmail.com --- On Wed, 7/3/12, Pradeep Kumar pradeep.tachy...@gmail.com wrote: From: Pradeep Kumar pradeep.tachy...@gmail.com Subject: [SIESTA-L] denchar To: siesta-l@uam.es Date: Wednesday, 7 March, 2012, 1:31 AM Dear siesta users I am a new user. when i run denchar post processing code to compute the densities and wavefunctions using the command: denchar Si.fdf i have the following error: At line 792 of file /home/pradeep/siesta-3.1/Util/Denchar/Src/../../../Src/fdf/fdf.f (unit = 5, file = 'stdin') Fortran runtime error: Illegal seek I check the file fdf.f but at line 792, i did not see this. please help thanks in advance -- Pradeep Kumar India
[SIESTA-L] Posible SPAM: Urgent Help
Hello, How are you doing today?I traveled down to Spain for an important program in Madrid and unfortunately for me the hotel i lodged got caught-up by fire. All my valuables including cash and cell phones were destroyed during the inferno and the hotel's phone line was also disconnected. I will explain details when i return. Please i need your financial assistance for me to relocate to another hotel and also get another flight ticket. As soon as I get home I would refund it immediately.Please I need you to get back to me as soon as possible if you can help me out of here today. Best Regards, M L Verma
Re: [SIESTA-L] Steps for SIESTA 3 Installation
read the user mannual carefully it is given in detail. Mohan L Verma From: Mohammad Jane Alam lt;mjalam...@gmail.comgt; To: siesta-l@uam.es Sent: Thursday, 29 September 2011 6:24 AM Subject: [SIESTA-L] Steps for SIESTA 3 Installation Hello Let me know the steps for siesta installation on fedora. -- Mohammad Jane Alam Research Scholar Physics Department A.M.U. Aligarh
Re: [SIESTA-L] Too many warnings when compiling tbtrans: extra tokens at end of #endif directive
Dear Zhao I obtained the same warnings during the compilation of tbtrans in siesta-3.0-b. But still the tbtrans is running well for further utilization. Mohan L Verma --- On Sat, 6/8/11, Hongyi Zhao hongyi.z...@gmail.com wrote: From: Hongyi Zhao hongyi.z...@gmail.com Subject: [SIESTA-L] Too many warnings when compiling tbtrans: extra tokens at end of #endif directive To: siesta-l@uam.es Date: Saturday, 6 August, 2011, 1:19 AM Hi all, I can compile the tbtrans within siesta-3.0-rc2 successfully, but I always meet the following warnings: - m_tbt_kpts.F90:20: warning: extra tokens at end of #endif directive m_tbt_kpts.F90:45: warning: extra tokens at end of #endif directive m_tbt_kpts.F90:92: warning: extra tokens at end of #endif directive m_tbt_kpts.F90:101: warning: extra tokens at end of #endif directive m_tbt_kpts.F90:145: warning: extra tokens at end of #endif directive m_tbt_kpts.F90:193: warning: extra tokens at end of #endif directive f95 -c -g -O2 -DFC_HAVE_FLUSH -DFC_HAVE_ABORT tsread2.F f95 -c -g -O2 -DFC_HAVE_FLUSH -DFC_HAVE_ABORT m_tbt_gf.F90 f95 -c -g -O2 -DFC_HAVE_FLUSH -DFC_HAVE_ABORT hamil2.F f95 -c -g -O2 /home/werner/software/siesta最新版/siesta-3.0-rc2/Util /TBTrans/../../Src/nag.f f95 -c -g -O2 -DFC_HAVE_FLUSH -DFC_HAVE_ABORT tbtrans.F tbtrans.F:47: warning: extra tokens at end of #endif directive tbtrans.F:87: warning: extra tokens at end of #endif directive tbtrans.F:138: warning: extra tokens at end of #endif directive tbtrans.F:168: warning: extra tokens at end of #endif directive tbtrans.F:181: warning: extra tokens at end of #endif directive tbtrans.F:238: warning: extra tokens at end of #endif directive tbtrans.F:251: warning: extra tokens at end of #endif directive tbtrans.F:308: warning: extra tokens at end of #endif directive tbtrans.F:482: warning: extra tokens at end of #endif directive tbtrans.F:499: warning: extra tokens at end of #endif directive tbtrans.F:513: warning: extra tokens at end of #endif directive tbtrans.F:688: warning: extra tokens at end of #endif directive tbtrans.F:710: warning: extra tokens at end of #endif directive tbtrans.F:847: warning: extra tokens at end of #endif directive tbtrans.F:863: warning: extra tokens at end of #endif directive tbtrans.F:894: warning: extra tokens at end of #endif directive tbtrans.F:1182: warning: extra tokens at end of #endif directive tbtrans.F:1195: warning: extra tokens at end of #endif directive f95 -c -g -O2 -DFC_HAVE_FLUSH -DFC_HAVE_ABORT transmission.F f95 -c -g -O2 -DFC_HAVE_FLUSH -DFC_HAVE_ABORT calc_green.F f95 -c -g -O2 cdiag_local.f f95 -c -g -O2 -DFC_HAVE_FLUSH -DFC_HAVE_ABORT getsfe.F f95 -c -g -O2 -DFC_HAVE_FLUSH -DFC_HAVE_ABORT mkRealContour.F f95 -c -g -O2 -DFC_HAVE_FLUSH -DFC_HAVE_ABORT reinit_tb.F f95 -c -g -O2 -DFC_HAVE_FLUSH -DFC_HAVE_ABORT setupkham2.F f95 -c -g -O2 -DFC_HAVE_FLUSH -DFC_HAVE_ABORT TSiohs.F TSiohs.F:55: warning: extra tokens at end of #endif directive TSiohs.F:94: warning: extra tokens at end of #endif directive TSiohs.F:109: warning: extra tokens at end of #endif directive TSiohs.F:127: warning: extra tokens at end of #endif directive TSiohs.F:142: warning: extra tokens at end of #endif directive TSiohs.F:152: warning: extra tokens at end of #endif directive TSiohs.F:159: warning: extra tokens at end of #endif directive TSiohs.F:169: warning: extra tokens at end of #endif directive TSiohs.F:178: warning: extra tokens at end of #endif directive TSiohs.F:189: warning: extra tokens at end of #endif directive TSiohs.F:196: warning: extra tokens at end of #endif directive TSiohs.F:202: warning: extra tokens at end of #endif directive TSiohs.F:226: warning: extra tokens at end of #endif directive TSiohs.F:239: warning: extra tokens at end of #endif directive TSiohs.F:254: warning: extra tokens at end of #endif directive TSiohs.F:269: warning: extra tokens at end of #endif directive TSiohs.F:286: warning: extra tokens at end of #endif directive TSiohs.F:294: warning: extra tokens at end of #endif directive - Any hints? Regards -- Hongyi Zhao hongyi.z...@gmail.com Institute of Semiconductors, Chinese Academy of Sciences GnuPG DSA: 0xD108493
[SIESTA-L] regarding the dispersion of ions in conducting polymers
--- On Mon, 18/7/11, Dr. Mohan L. Verma drmoha...@yahoo.com wrote: From: Dr. Mohan L. Verma drmoha...@yahoo.com Subject: regarding the dispersion of ions in conducting polymers To: siesta-l@uam.es Date: Monday, 18 July, 2011, 1:45 AM Dear all siesta users and developers I am interested to study the change in the electronic structure of an ion dispersed (eg. Ag+ K= etc.) conducting polymers. My doubts are : 1. Is this possible using siesta? 2. I am submitting here an input file in which Ag and I atoms are dispersed in PEO. What necessary correction should be made to fulfill my aim? 3. Should I have a pseudopotenials for ions? 4. May I get detailed help from anyone who can suggest me literature for the same Thanking you all in advanced. Yours truly Mohan L Verma Computational Nanoionics research laboratory Shri Shankaracharya Group of Institution-Junwani Bhilai (Chhattisgarh) INDIA 490020 email : drmoha...@yahoo.com, ml.ve...@sscet.ac.in peo5agi.fdf Description: application/vnd.fdf
[SIESTA-L] Dr. Mohan L. Verma invites you to connect
Join Dr. Mohan L. Verma on Yahoo! Messenger. Hi! Come join me on Yahoo! Messenger so we can chat, share files, watch videos and more. Stay in the loop with all your friends. Get started : http://invite.msg.yahoo.com/invite?op=acceptintl=insig=24t1fVGSn52WtHwi2N08D29m2k8ScHWgzxMHw460OFm40.X077PQZuvIJgxM * Stay connected at home, at work, or on the go * Have fun with games, emoticons, and more * Join a community of over 100 million people from around the world Join Your Friends : http://invite.msg.yahoo.com/invite?op=acceptintl=insig=24t1fVGSn52WtHwi2N08D29m2k8ScHWgzxMHw460OFm40.X077PQZuvIJgxM -- this email was sent to you by an automated system - please do not reply directly
[SIESTA-L] difference in DOS plots
Dear siesta developers and users I am not an expert in electronic structure calculation as well as siesta. But I am trying to use siesta 3.0 (rc2) version in fedora-10 using f95. I have two quries: 1. when i increase the number of atoms in input file I found there is in increase in the value of band gape Eg in the systemlevel.EIG file.Why it is so? Can any one explain to my error. 2. The DOS plot (i) using systemlevel.DOS generated by siesta and (ii) using the systemlevel. DOS generated by eig2dos utility are different peak positions and bradning too. why? which one is more reliable? I am analysing ionic solids like AgI AgCl using Pseudopotential developed by Abinit. Thanking you in advance. yours truely Dr Mohan l verma Condensed matter physics research lab Department of Applied Physics Shri Shankaracharya college of engineering and technology-Junwani Bhilai (Chhattisgarh)INDIA 490020
Re: [SIESTA-L] difference in DOS plots
Dear Marcos Thank you very much for the prompt response. Mohan --- On Thu, 29/7/10, Marcos Veríssimo Alves marcos.verissimo.al...@gmail.com wrote: From: Marcos Veríssimo Alves marcos.verissimo.al...@gmail.com Subject: Re: [SIESTA-L] difference in DOS plots To: siesta-l@uam.es Date: Thursday, 29 July, 2010, 6:29 AM Mohan, 1) The band gap should remains the same independently of the number of atoms in your system. One thing that occurs to me right now is that you could be increasing the supercell size but be maintaining the same k-point sampling of the smaller cell. This means that effectively you are increasing the k-point sampling with respect to the one for the smaller cell (think about band-folding and the size of the BZ when you increase the cell size in real space) and this will reflect in your band gap, if your k-point sampling is not good enough for the smaller cell. Are you doing two different supercell sizes with the same specification of the MP grid? Without more information on how you are proceeding one can only do wild guesses, which are good for nothing most of the time... 2) Most probably the version of eig2dos.f you are using does already shift the points so as to set th Fermi level to zero. If this is so, then plotting the DOS that comes out of siesta by the PDOS block with the energies (x-axis) shifted by the fermi level would yield equal peak positions. Check eig2dos.f to see if the energies are shifted or not, or plot the DOS that comes directly out of siesta in the way I am suggesting. Please be more specific about your procedures, and give as much info as possible. It takes some time in the short run but saves a lot of work in a longer run. Marcos On Thu, Jul 29, 2010 at 9:41 AM, Dr. Mohan L. Verma drmoha...@yahoo.com wrote: Dear siesta developers and users I am not an expert in electronic structure calculation as well as siesta. But I am trying to use siesta 3.0 (rc2) version in fedora-10 using f95. I have two quries: 1. when i increase the number of atoms in input file I found there is in increase in the value of band gape Eg in the systemlevel.EIG file.Why it is so? Can any one explain to my error. 2. The DOS plot (i) using systemlevel.DOS generated by siesta and (ii) using the systemlevel. DOS generated by eig2dos utility are different peak positions and bradning too. why? which one is more reliable? I am analysing ionic solids like AgI AgCl using Pseudopotential developed by Abinit. Thanking you in advance. yours truely Dr Mohan l verma Condensed matter physics research lab Department of Applied Physics Shri Shankaracharya college of engineering and technology-Junwani Bhilai (Chhattisgarh)INDIA 490020
Re: [SIESTA-L] sies2xsf compilation problem
Dear Mr Mitra I am also interested for the same binary code. Please send me. But I am using fedora 10 with f95 and gfortran. Can I use this code as siesta utilities for my system. Thanking you in advanced. yours truly Mohan L Verma Condensed Matter Physics Research Lab Deptt of Applied Physics SSCET-Bhilai (Chhattisgarh) INDIA --- On Thu, 15/7/10, Madan Mithra. L. M madan.mit...@gmail.com wrote: From: Madan Mithra. L. M madan.mit...@gmail.com Subject: Re: [SIESTA-L] sies2xsf compilation problem To: siesta-l@uam.es Date: Thursday, 15 July, 2010, 1:34 PM Dear Malgorzata, I have the binary of 'sies2xsf' for win32 as well as linux (ifort9). I can send you both if you wish to receive them. - Madan 2010/7/15 m...@amu.edu.pl: Hello Siesta users, I'm trying to compile sies2xsf program but with no success. I've changed the compilation options in Makefile for Sies2xsf as for Siesta's arch.make (f95) Any suggestions? Regards, Malgorzata -- Madan Mithra .L.M Senior Research Fellow Dept.of Physics Indian Institute of Science Bangalore - 560 012 INDIA . Phone : 91-80-22932313 (Lab) FAX : (080) 360 2602
Re: [SIESTA-L] Electrodes of Transiesta
Dear sir Would you send me the reprints of the articles listed in your mail? I am also interested to study them. Thanks. Dr Mohan L Verma D --- On Fri, 2/7/10, Julian Niño oso.a.2...@gmail.com wrote: From: Julian Niño oso.a.2...@gmail.com Subject: Re: [SIESTA-L] Electrodes of Transiesta To: siesta-l@uam.es Date: Friday, 2 July, 2010, 6:36 PM yes, you can see this articles: 1) http://jcp.aip.org/jcpsa6/v115/i4/p1661_s1 2) http://pubs.acs.org/doi/abs/10.1021/jp901091a 3) http://www3.interscience.wiley.com/journal/112159306/abstract?CRETRY=1SRETRY=0 4) http://prb.aps.org/abstract/PRB/v73/i16/e165402 5) http://iopscience.iop.org/1367-2630/11/12/125003?ejredirect=migration 6) http://www.sciencedirect.com/science?_ob=ArticleURL_udi=B6TVX-47TWS85-3_user=687356_coverDate=03%2F10%2F2003_rdoc=12_fmt =high_orig=browse_srch=doc-info%28%23toc%235546%232003%23994729998%23396502%23FLA%23display%23Volume%29_cdi=5546_sort=d_ docanchor=_ct=35_acct=C37898_version=1_urlVersion=0_userid=687356md5=35ce95caee5a9347379c0917cdf4a637 2010/7/3 庄家康 zhuangjiak...@gmail.com Dear All, I have a quick question: Can I just use several layers(i.e isolated atom clusters surrounded by a vaccum box) of metal as the electrodes? Thanks. JK -- - - - - - -
[SIESTA-L] wfsx2wfs error
Dear siesta users and developers hellow to all I am trying to convert AgCl.WFSX file to AgCl.WFS for further use in DENCHAR utility. I have f95 and gfortran in my fedora-10. when i use the cammand :in siesta-3.0-b/Utils/WFS ./wfsx2wAgCl.WFSXAgCl.WFS I found an errir message like : at line 36 of file wfsx2wfs.f(unit=10, file=' ') Fortarn runtime error: File 'WFSX' does not exist I am not very expert in fortran programming. and iam also new in siesta. So please can anyone help me to proceed furher in this work. Thanking you in advance with regards Yours Mohan L Verma Department of Applied Physics Shri Shankaracharya College of Engineering and technology-junwani bhilai chhattisgarh )INDIA)
Re: [SIESTA-L] error using gnupdos.f utility for PDOS plotting
Dera macros thanking you for promt response. I am using pdosxml utility successfully. Mohan --- On Thu, 3/6/10, Marcos Veríssimo Alves marcos.verissimo.al...@gmail.com wrote: From: Marcos Veríssimo Alves marcos.verissimo.al...@gmail.com Subject: Re: [SIESTA-L] error using gnupdos.f utility for PDOS plotting To: siesta-l@uam.es Date: Thursday, 3 June, 2010, 10:14 AM Mohan, You can try using the pdosxml utility that comes with Siesta. It works very well, the only inconvenient being the need to re-compile it every time you need different information. However it's so fast to do it that it compensates for the ease of use. Marcos On Thu, Jun 3, 2010 at 3:11 PM, Dr. Mohan L. Verma drmoha...@yahoo.com wrote: Dear siesta users and developers hellow to all I am trying to use the utility programme gnupdos.f programme developed by Tom Archer in the year 2004 received from the mailing list for my file AgCl.PDOS adding four line as per instruction given 1000 1 5 true in this file. when I used the cammand ./gnupdosAgCl.PDOSagclpdos.gplot I found the error message: At line 50 of file gnupdos.f (unit=5, file = 'stdin') Fortran runtime error : Bad real number in item 501 of list input can anyone help me to resolve this problem. ??. I am new in the siesta as well as fortran programming too. Yours truly Dr Mohan L Verma Condensed Matter Physics Research Lab Department of Applied Physics Shri Shankarcharya College of Engineering Technology-Junwani Bhilai (Chhattisgarh) INDIA 490020
Re: [SIESTA-L] about the eig2dos code
Dear martin In the assined number Ef 0.200 500 -20.00 10.00 the value of eta is missing. What is this and the assined value of eta will be yours truely Dr Mohan L Verma --- On Tue, 18/5/10, Jackie Wan jackiewa...@yahoo.com wrote: From: Jackie Wan jackiewa...@yahoo.com Subject: Re: [SIESTA-L] about the eig2dos code To: siesta-l@uam.es Date: Tuesday, 18 May, 2010, 9:49 AM Dear Martin, Thank you very much. Cheers, Wan From: Martin Zoloff mezol...@gmail.com To: siesta-l@uam.es Sent: Tue, May 18, 2010 7:48:49 PM Subject: Re: [SIESTA-L] about the eig2dos code Dear Wan, There is a brief explanation in the commented text at the beggining of the eig2dos code. You have to modify by hand the EIG file you obtained from the siesta calculation in order to add the missing values,ie the broadening constant, the number of points and the energy window. The first line of your modified EIG file should have then 4 extra numbers apart fron the fermi level energy. It should look something like this: Ef 0.200 500 -20.00 10.00 then you run the code: ./eig2dos systemlabel.EIG systemlabel.DOS and the DOS file produced can be plotted with xmgrace or gnuplot, for example. Hope this helps... Cheers, Martin On Tue, May 18, 2010 at 4:20 AM, Jackie Wan jackiewa...@yahoo.com wrote: Dear All, When tackle the result, one of the file Systemlable.EIG file, in order to plot the dos of bulk system. I use the code in the Util dir. I am confused about the eig2dos code. Thank you for your time to have a look. in the Siesta's Src/ioeig.f file: (in line 54-62 as below:) call io_assign( iu ) open( iu, file=fname, form='formatted', status='unknown' ) write(iu,(f14.4)) ef/eV write(iu,(3i6)) no, min(ns,2), nk do ik = 1,nk write(iu,(i5,10f12.5,/,(5x,10f12.5))) ik, ((eo(io,is,ik)/eV,io=1,no),is=1,nspin) enddo the Util/eig2dos.f: line 53-54: read(5,*) ef, eta, ne, emin, emax read(5,*) nband, nspin, nk As in the Systemlabel.EIG the first line only the fermi value writed, as the ioeig.f presented. My question is how can we set the value of 'eta, ne, emin, emax' in the eig2dos code? Anyone please give any simple explanation. Thank you very much in advance! Best regards, Wan -- Universidad Nacional de Córdoba Facultad de Ciencias Químicas Departamento de Matemática y Física Edificio Integrador - Subsuelo Ciudad Universitaria X5000HUA - Córdoba Argentina Tel/Fax. +54 351 434-4972
[SIESTA-L] error message during the compilation of transiesta
dear sir/madam I am very new for siesta and transiesta as well as linux. I am trying using siesta-3.0-b. when I tried to compile transiesta in the Obj directory using the commands : Obj $ sh ../Src/obj_setup.sh then ..Src/configuration make transiesta I found an error message : /home/siesta-3.0-b/Src/m_ts_aux_rout.F:344 : undefined reference to 'zgesv_' collect2: ld returned 1 exit status make: ***[transiesta] error 1 please help to overcome this error. I am not fully skilled with fortran too. Its my learning stage. So your help will be very benificial for my work. Yours truly Dr Mohan L Verma Condensed Matter physics Research Lab Department of Applied Physics Shri Shankaracharya College of Engineering technology- Bhilai chhattisgarh ( INDIA) 490020 The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. http://in.yahoo.com/
