Re: [SIESTA-L] gnubands
dear saswata, gnubands comes with SIESTA, compile file gnubands.f in Utils directory. xmgrace is not a part of SIESTA, but a free program called grace, available from the web. it comes with many linux distros, I have it as a part of my Fedora. On 27/03/07, Saswata Bhattacharya [EMAIL PROTECTED] wrote: dear friends, i want to know whether gnubands and xmgrace are two software packages that comes with SIESTA package or not?I have installed SIESTA and it is running nicely but there i dont get access of the software gnubands and xmgrace.mostly i have read that to convert .bands file to .dat file we need gnubands.right?and to plot .band we need xmgrace software...but if in my SIESTA package these two are absent then how can i get access of these two?i mean how to plot the file .band to get the bands structure? next my question is how to plot the file .PDOS to visualize partial DOS? please help.i am waiting for your reply... with regards, Saswata Here's a new way to find what you're looking for - Yahoo! Answers -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED]
[SIESTA-L] gnubands
dear friends, i want to know whether gnubands and xmgrace are two software packages that comes with SIESTA package or not?I have installed SIESTA and it is running nicely but there i dont get access of the software gnubands and xmgrace.mostly i have read that to convert .bands file to .dat file we need gnubands.right?and to plot .band we need xmgrace software...but if in my SIESTA package these two are absent then how can i get access of these two?i mean how to plot the file .band to get the bands structure? next my question is how to plot the file .PDOS to visualize partial DOS? please help.i am waiting for your reply... with regards, Saswata - Heres a new way to find what you're looking for - Yahoo! Answers
Re: [SIESTA-L] FDF howto's
Vasilii FDF is an independent package on itself developed by Alberto Garcia and Jose M. Soler. If you take a look at the fdf directory within the Src dir of the siesta distribution, you'll get a feel of how to use it, with some sample fortran files. In addition you may want to check Util/SiestaSubroutine for what you want to do Emilio Vasilii Artyukhov wrote: Dear all, especially, the developers, Could someone briefly explain to me how to work with the FDF format? I'd like to use SIESTA as an external subroutine (I want to implement some simple form of metadynamics), and it seems a nice idea to make the driver program compatible with FDF. Best regards, Vasilii -- Emilio Artacho Department of Earth Sciences, University of Cambridge Downing Street, Cambridge CB2 3EQ, UK Tel. (+44/0) 1223 333480, Fax (+44/0) 1223 333450 [EMAIL PROTECTED], http://www.esc.cam.ac.uk/~emilio
[SIESTA-L] FDF howto's
Dear all, especially, the developers, Could someone briefly explain to me how to work with the FDF format? I'd like to use SIESTA as an external subroutine (I want to implement some simple form of metadynamics), and it seems a nice idea to make the driver program compatible with FDF. Best regards, Vasilii
Re: [SIESTA-L] how to calculate the values of strain tensor from forces or stress tensor?
If your system is not too large, I'd advise that you determine the relaxed lattice constants from a series of fixed-cell calculations, especially if the system is more or less symmetrical. Although your stresses seem quite low to me, I think that the only way to improve them might be, indeed, to lower the stress tolerance. Note that since you are using a finite integration grid, no one can guarantee that you will ever get zero stresses. So, check for the integration grid cutoff as well, you might have to increase it at some point. 2007/3/27, Yurko Natanzon [EMAIL PROTECTED]: Dear siesters, I'm thinking on increasing the accuracy of calculating elastic constants (i'm interested in shear ones but it doesn't matter). First I relax a lattice to get a stress tensor zero, and then make deformations to get a new stress tensor and calculate elastic constants. But in fact the stress tensor of relaxed lattice is not zero, it has a form like this one: -0.20 -0.56 0.000233 -0.56 0.53-0.33 0.000233-0.33 0.001350 the values of this tensor in fact influence the results of elastic constant calculations. In fact, if I get +1% deformation in one direction and -1% - I may get totally different values of stress tensor. Is there a way to take the influence of zero stress tensor into account? If I'll be able to know, which strain corresponds to this stress tensor, I can find the lattice vectors of ideally relaxed lattice, and this will solve the problem. I would be grateful for any advices regarding this. Of course, I may try to set StressTolerance and Force Tolerance to some low values, but this will take much more CG steps to fully relax the lattice and much more time. Also in some cases I can't fully relax the lattice because of constraints, but need to relax only several components of stress tensor. -- Yurko Natanzon PhD Student Henryk Niewodniczański Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED]
Re: [SIESTA-L] Restrict geometry optimization
Dear Gali Ádám: I also found the 'routine' of 'GeometryConstraints' in the manual. But it's too brief for me to use it. Would you mind send me some detail information about this trick? 2007/3/27, [EMAIL PROTECTED] [EMAIL PROTECTED]: Dear Yong Liu, The symmetry is NOT included basically in SIESTA. In some simple cases you can use some tricks in which you can still conserve the symmetry during relaxation (using fixed fractional coordinates, etc). In your case these tricks may not work. What you can still do is to use the constraints.f file in SIESTA which can be activated within GeometryConstraints block. By default, constraints.f file is a template source and your calculation would not be affected. However, you can write your specific constraints into this file using your specified atoms, etc, which will conserve the symmetry what you want to achieve. You have to compile the code again, and you will have such a code which will conserve the symmetry for your particular(!) input. This indeed works (with 1.3f version, for sure); for instance I could use for studying the migration of a defect in a crystal constrained in a chosen plane. Yours, Adam I'd like to apply a restrict geometry optimization considering the symmetry of the system, but from the manual I do not find the useful parameters. For instance, How can I fully optimize tetragonal PbTiO3 (P4mm, No.99) which has a=b!=c, Pb(0,0,x1), Ti(0.5,0.5,x2),O1(0,0.5,x3),O2(0.5,0,x3),O3(0.5,0.5,x4). I'm afraid that 'GeometryConstraints' is not good enough to deal with this work since the constrainsts of this parameter are not implemented, as mentioned in the manual. Is there any parameters provide a mode of structural relaxtion taking into account the symmetry of the system and how to use them? Thanks a lot in advance. --- Dr. Gali ÁdámAdam Gali, PhD Budapesti Műszaki és Department of Atomic Physics, Gazdaságtudományi Egyetem, Budapest University of Technology and Atomfizika Tanszék Economics Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest, Hungary telefon: 463-1580telephone: [36]-(1)-463-1580 fax: 463-4357fax: [36]-(1)-463-4357 e-mail: [EMAIL PROTECTED] http://www.fat.bme.hu/homepages/galia/index.en.html --- -- Best regards. - Liu, Yong, Ph D Institute of Inorganic Materials, Department of Materials Science and Engineering, Zhejiang University,PR China
Re: [SIESTA-L] Restrict geometry optimization
Dear Yurko Natanzon, Thank you for your answers, but I'm afraid that it do not work. I have done some calculation as you said. The fdf and output files are attached. For test purpose, the precision of the calculation is very low and only 2 CG steps are performed. After relaxation, the position of atoms do not follow the symmetry of P4mm, as can be seen from the output file outcoor: Final (unrelaxed) atomic coordinates (fractional): 0.00280.0030 -0.02131593 1 Pb 1 0.45760.45780.46938626 2 Ti 2 0.00310.49920.53442460 3 O 3 0.49830.00400.53442458 3 O 4 0.49930.49880.03276782 3 O 5 2007/3/27, Yurko Natanzon [EMAIL PROTECTED]: Dear Yong Liu, As far as I understood you want to keep a=b!=c and angles 90, 90 ,90 after relaxation, don't you? Then you don't need any geometry constraints, just make variablecell=true calculations. To my experience, the angles will not change or change a little (in my case smth like 89.999). Then use obtained lattice parameters and coordinates and repeat the relaxation but with VariableCell = false. Manually change angles to 90 90 90, if they were changed in previous run. This second calculation will relax atomic cooredinates only, not unit cell. On 27/03/07, Yong Liu [EMAIL PROTECTED] wrote: Dear all: I'd like to apply a restrict geometry optimization considering the symmetry of the system, but from the manual I do not find the useful parameters. For instance, How can I fully optimize tetragonal PbTiO3 (P4mm, No.99) which has a=b!=c, Pb(0,0,x1), Ti(0.5,0.5,x2),O1(0,0.5,x3),O2(0.5,0,x3),O3(0.5,0.5,x4). I'm afraid that 'GeometryConstraints' is not good enough to deal with this work since the constrainsts of this parameter are not implemented, as mentioned in the manual. Is there any parameters provide a mode of structural relaxtion taking into account the symmetry of the system and how to use them? Thanks a lot in advance. -- Best regards. - Liu, Yong, Ph D Institute of Inorganic Materials, Department of Materials Science and Engineering, Zhejiang University,PR China -- Yurko Natanzon PhD Student Henryk Niewodnicza��ski Institute of Nuclear Physics Polish Academy of Sciences ul. Radzikowskiego 152, 31-342 Kraków, Poland Email: [EMAIL PROTECTED], [EMAIL PROTECTED] -- Best regards. - Liu, Yong, Ph D Institute of Inorganic Materials, Department of Materials Science and Engineering, Zhejiang University,PR China pbtio3.out Description: Binary data pbtio3.fdf Description: application/vnd.fdf
Re: [SIESTA-L] Restrict geometry optimization
Dear Yong Liu, The symmetry is NOT included basically in SIESTA. In some simple cases you can use some tricks in which you can still conserve the symmetry during relaxation (using fixed fractional coordinates, etc). In your case these tricks may not work. What you can still do is to use the constraints.f file in SIESTA which can be activated within GeometryConstraints block. By default, constraints.f file is a template source and your calculation would not be affected. However, you can write your specific constraints into this file using your specified atoms, etc, which will conserve the symmetry what you want to achieve. You have to compile the code again, and you will have such a code which will conserve the symmetry for your particular(!) input. This indeed works (with 1.3f version, for sure); for instance I could use for studying the migration of a defect in a crystal constrained in a chosen plane. Yours, Adam I'd like to apply a restrict geometry optimization considering the symmetry of the system, but from the manual I do not find the useful parameters. For instance, How can I fully optimize tetragonal PbTiO3 (P4mm, No.99) which has a=b!=c, Pb(0,0,x1), Ti(0.5,0.5,x2),O1(0,0.5,x3),O2(0.5,0,x3),O3(0.5,0.5,x4). I'm afraid that 'GeometryConstraints' is not good enough to deal with this work since the constrainsts of this parameter are not implemented, as mentioned in the manual. Is there any parameters provide a mode of structural relaxtion taking into account the symmetry of the system and how to use them? Thanks a lot in advance. --- Dr. Gali ÁdámAdam Gali, PhD Budapesti Műszaki és Department of Atomic Physics, Gazdaságtudományi Egyetem, Budapest University of Technology and Atomfizika Tanszék Economics Budapest, Budafoki út 8., Budafoki út 8., H-, Budapest, Hungary telefon: 463-1580telephone: [36]-(1)-463-1580 fax: 463-4357fax: [36]-(1)-463-4357 e-mail: [EMAIL PROTECTED] http://www.fat.bme.hu/homepages/galia/index.en.html ---
[SIESTA-L] Restrict geometry optimization
Dear all: I'd like to apply a restrict geometry optimization considering the symmetry of the system, but from the manual I do not find the useful parameters. For instance, How can I fully optimize tetragonal PbTiO3 (P4mm, No.99) which has a=b!=c, Pb(0,0,x1), Ti(0.5,0.5,x2),O1(0,0.5,x3),O2(0.5 ,0,x3),O3(0.5,0.5,x4). I'm afraid that 'GeometryConstraints' is not good enough to deal with this work since the constrainsts of this parameter are not implemented, as mentioned in the manual. Is there any parameters provide a mode of structural relaxtion taking into account the symmetry of the system and how to use them? Thanks a lot in advance. -- Best regards. - Liu, Yong, Ph D Institute of Inorganic Materials, Department of Materials Science and Engineering, Zhejiang University,PR China
[SIESTA-L] Error in Cholesky factorisation in cdiag
Dear All, As I was trying to carry out the test run in the parallel mode for BaTiO3 as given in the Test file of SIESTA, I encounter the following errors: . * Maximum dynamic memory allocated =29 MB Error in Cholesky factorisation in cdiag Stopping Program from Node:0 Error in Cholesky factorisation in cdiag Error in Cholesky factorisation in cdiag Stopping Program from Node:6 Stopping Program from Node:5 Error in Cholesky factorisation in cdiag Stopping Program from Node:2 Error in Cholesky factorisation in cdiag Stopping Program from Node:4 Error in Cholesky factorisation in cdiag Stopping Program from Node:1 Error in Cholesky factorisation in cdiag Stopping Program from Node:3 Error in Cholesky factorisation in cdiag Stopping Program from Node:7 rank 4 in job 1 w06_59876 caused collective abort of all ranks exit status of rank 4: killed by signal 9 rank 1 in job 1 w06_59876 caused collective abort of all ranks exit status of rank 1: killed by signal 9 rank 0 in job 1 w06_59876 caused collective abort of all ranks exit status of rank 0: killed by signal 9 Could you please suggest me what needs to be done? With regards, sen
Re: [SIESTA-L] problem of compiling parallel siesta with mpich-ifc
Thank you!
