Re: [SIESTA-L] Compilation error, How to start siesta programming
Dear Murali, Dear all, I have been trying to compile Siesta using f95 compiler and was not successful. Recently, i received help from one of the users to use g95 or gfortran compiler. As i used it, i could compile it successfully but when i started to run some programs that are available in Tests directory, i was successful in some cases while in most others, it gave the error of Fortran runtime error: Allocating negative dynamic error. That behavior is really strange, I've just compiled Siesta with g95 and it works. Maybe your compiler version is old. Also you can use the following compiler flags: -Wall -fbounds-check -ftrace=full When i had run program on fe, i got the results but when i tried to run h2o, h2oZ and most other examples in the Test directory, it resulted in runtime error. Please help me to overcome this error as i am not able to run the programs properly. My second question is that i am trying very new to do coding in siesta and so, i am asking you the steps in which i have to start and the files that are required to run any new program. Take a look at the Tests directory, it contains all the files needed to perform several simulations. Is it sufficient to go through the siesta manual before i embark on programming. Kindly tell me what are the steps needed to start programming in siesta. Well, if you want to develop a new extension to siesta you should start getting familiar with the different parts of the program: sparse matrix (hamiltonian, overlap), how the different matrix elements are calculated (matel.f, dhscf.f), how the orbitals are generated (atom.f) etc. Without more details I can't provide more information. Regards, Eduardo Thank you all very much Yours T.Murali Krishna Here’s a new way to find what you're looking for - Yahoo! Answers
Re: [SIESTA-L] Geo-Optimization
Dear Neil, In order to optimize geometry you must use the variable MD.TypeOfRun CG The Zmatrix is a way (there are others) to provide the atomic positions. The relevant part of the siesta manual is: http://www.uam.es/departamentos/ciencias/fismateriac/siesta/ manual-2.0/node20.html Regards, Eduardo On 03/04/2007, at 6:54, Neil Dixon wrote: Dear Friends, I am a new user of SIESTA.I want to know how to Optimize Geometry of a system by using SIESTA.I have got a very faint idea about Zmatrix and Constraints.are those commands deals with Geometry optimization?if so just tell me in few words,how this thing is done? please help me. Regards, Neil Don't be flakey. Get Yahoo! Mail for Mobile and always stay connected to friends.
Re: [SIESTA-L] About workfunction
Dear Septhiroth, You can use the MacroAve utility in the siesta/utils directory. In your siesta calculation, you need to ask for the electrostatic potential output SaveElectrostaticPotential .true. This will provide the electrostatic potential in .VH file. Run macroave.x after editing macroave.in, specifying the system name etc. This will give you a planar average in .PAV file, which I think is what you want. Cheers, Rainer On 09/04/2007, at 6:06 PM, Septhiroth Lo wrote: Dear All: I want know a system workfunction.So how can i get the coulomb potential distribution of a system using SIESTA? Because i want to polt one direction (ex:along Z axis) V.S coulomb potential. Thanks for help.
Re: [SIESTA-L] optimization of the lattice constant of GaN:Wurtzitestructure
Dear Mu J. Helien, The possible use of Z-matrix or constr.f file (use constraints) was discussed in the SIESTA list about one week ago. You should look at those messages how you can set symmetry for a particular input in SIESTA. Nevertheless, by using i) well-tested pseudopotentials ii) good basis compatible with the psuedopotentials iii) other well-converged parameters (Eshift, MeshCutoff, K-points, force criteria, stress criteria) the calculations should give automatically 'almost' symmetric structure after optimization since that should be the most stable configuration. If it is not the case then one of the afore-mentioned condition is not fulfilled. GaN is very tricky due to Ga 3d orbitals. I suggest first to check the convergence of some parameters on cubic GaN (it is a simpler structure and you can easily impose the symmetry by fixing the fractional coordinates), and look at what is happening during optimization without any constraints. If everything seems to be fine then you can switch to wurtzite GaN and re-check everything. Yours, Adam Gali I want to optimize the lattice constant of GaN of Wurtzite structure.Since the u fractional coordinate of N atom has to be optimized, so I choose MD.Variable-Cell:T and didn't fix the fractional coordinates of all atoms. But when SCF calculations are converged, the fractional coordinates are changed significantly and the symmetry of the cell are broken. I wonder if there is someone who met similar problem and would you like to tell me how to solve this problem? Thank you very much. Before: Ga 0. 0.6667 0. Ga 0.6667 0. 0.5000 N 0. 0.6667 0.3748 N 0.6667 0. -0.1252 outcell: Cell vector modules (Ang) :3.0999323.0999325.130500 outcell: Cell angles (23,13,12) (deg): 90. 90.119.9985 After: 0.284243760.60773737 -0.15293678 1 Ga 1 0.77520.342650060.48122587 1 Ga 2 0.270943530.627445310.50909357 2 N 3 0.786042940.32298514 -0.17115702 2 N 4 outcell: Cell vector modules (Ang) :3.0996403.1048344.925811 outcell: Cell angles (23,13,12) (deg): 90.5244 88.9666119.7208 --- 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 ---
