Re: [SIESTA-L] error in LDOS and PDOS
Hello Oleksandr and Pablo, Pablo, I wanted to calculate the PDOs over whole ranges of m therefore, I suppose that replacing * with -1 does not affect the result. If it is otherwise please let me know. What I am concerned about is that I have problem compiling the utilities with gfortran, for example, I can not compile pdosxml in the Util, since I receive errors as follows: gfortran -o pdos m_orbital_chooser.o m_pdos.o f2kcli.o pdos.o ../../Src/libxmlparser.a f2kcli.o: In function `__f2kcli_MOD_get_command_argument': f2kcli.F90:(.text+0xc2): undefined reference to `iargc_' f2kcli.F90:(.text+0x18e): undefined reference to `getarg_' f2kcli.F90:(.text+0x1d2): undefined reference to `getarg_' f2kcli.o: In function `__f2kcli_MOD_command_argument_count': f2kcli.F90:(.text+0x212): undefined reference to `iargc_' f2kcli.o: In function `__f2kcli_MOD_get_command': f2kcli.F90:(.text+0x232): undefined reference to `iargc_' f2kcli.F90:(.text+0x290): undefined reference to `getarg_' collect2: ld returned 1 exit status make: *** [pdos] Error 1 That is while I could compile Dr. Postnikov's tools easily. I know it may seems a personal problem, but I would be happy if you kindly let me know how to be able to compile the utils with gfort, while I have no privilage to have other compilers? Regards, Sarah
[SIESTA-L] error in LDOS and PDOS
Hi, I have compiled Siesta both with g95 and with gfortran. I want to calculate the PDOS and the LDOS of my system. I have managed to compile fmpdos from Dr. Postinikov's tools for the projected density of states and eig2dos in the Util for Local density of States both successfully with gfortran and once again with g95. But when I want to execute them I receive fortran runtime error: 1. a. with g95 for fmpdos I receive: *At line 242 of file fmpdos.f Traceback: not available, compile with -ftrace=frame or -ftrace=full Fortran runtime error: Bad integer for item 1 in list input* b. with gfortran I receive: At line 242 of file fmpdos.f Fortran runtime error: Bad integer for item 1 in list input 2. for eig2dos for both compilers I receive: At line 53 of file eig2dos.f (unit = 5, file = 'stdin') Fortran runtime error: Bad real number in item 1 of list input I do not have the privilage to use ifort or other compilers. Is there a solution for this problem using gfort or g95? Regards, Sarah
Re: [SIESTA-L] single excitation for unpolarized sturucture
Dear Marcos, In my calculation, when i compare the results of the single excitation with the off ones, I see a difference in the total energy. What could this difference stand for? Regards, On Mon, Apr 6, 2009 at 2:56 AM, Marcos Verissimo Alves marcos.veriss...@uclouvain.be wrote: I guess the issue here is not so much about being spin-polarized or not, but what the single excitation, as implemented in siesta, means. As stated in the manual, single excitation will get the electronic population of the HOMO (or maybe more generally, that of the first valence band) and promote it to the LUMO (first conduction band), creating an artificial excited state. One thing in which it certainly has an effect is on the equilibrium atomic geometry. In fact, the single excitation feature has been used to mimick an excited state in a PPV (or maybe PPP, now I'm not completely sure) to check for the equilibrium geometry of that state. Try looking in the publications list, I think it was published on PRL about two or three years ago by people in the siesta team (Emilio Artacho was in the list of authors, I guess). I have used it for another small polymer, but with no great effect on its geometry. So, the effect might strongly depend on which system you are working on, and I don't see a simple rule to say what the effect might be. I have a few hypothesis, but I'm really not sure about them. Maybe someone more knowledgeable could give a better insight? Cheers, Marcos Vous avez écrit / You have written / Lei ha scritto / Você escreveu... Sarah Lebedev Hello Siesta Users, I have always worked on the systems with no spin polarization and now I am interested to have the resilts of single excitation in Siesta. I would like to know if it is worth to calculate the single excitation for unpolarizaed structures? What differences these two will have? Regards, Sarah -- Dr. Marcos Verissimo Alves Post-Doctoral Fellow Unité de Physico-Chimie et de Physique des Matériaux (PCPM) Université Catholique de Louvain 1 Place Croix du Sud, B-1348 Louvain-la-Neuve Belgique -- Gort, Klaatu barada nikto. Klaatu barada nikto. Klaatu barada nikto. Free translation: Gort, Google is your friend. Google is your friend. Google is your friend.
[SIESTA-L] single excitation for unpolarized sturucture
Hello Siesta Users, I have always worked on the systems with no spin polarization and now I am interested to have the resilts of single excitation in Siesta. I would like to know if it is worth to calculate the single excitation for unpolarizaed structures? What differences these two will have? Regards, Sarah
[SIESTA-L] cross section calculation
Dear Siesta users, I am calculating the young modulus of nanowires. For that I need to have the cross section area of the wires. Is there a visualization tool that could give me the cross section area of such systems? Also, is it necessary that we include the passivating Hs in the cross section as well? Regards, sara
[SIESTA-L] charge density problem
Hello all, I am new handling siesta files that is why I ask this question. It is obvious that for plotting the charge densty at gamma point for LUMO and HOMO states I should use LocalDensityOfStates. My question is about arranging the energies in this block to get to the righ HOMO and LUMO states. If you have any experiences please let me know. Regards,
Re: [SIESTA-L] charge density problem
Thanks for the complete answer, it comes really useful to me. As I have read the mailing list, I have found that for finding the HOMO and LUMO we should look at the EIG file. Is it the only way to do so? On Sun, Feb 22, 2009 at 7:40 PM, Lucas Fernandez Seivane queve...@gmail.com wrote: Hi Sarah in the block you put the energy gap you want to plot. Therefore, you should run siesta twice and in two separate directories, one in a energy range that just contais the HOMO and another one for the LUMO If they are at HOMO: -3.29089 and LUMO: -3.17099 %block LocalDensityOfStates -3.31089 -3.27089 eV %endblock LocalDensityOfStates would plot the HOMO, and %block LocalDensityOfStates -3.18099 -3.16099 eV %endblock LocalDensityOfStates would do it for the LUMO. The zero of the energy is NOT Fermi energy! Regards On Sun, Feb 22, 2009 at 3:28 PM, Sarah Lebedev sarah.lebe...@gmail.com wrote: Hello all, I am new handling siesta files that is why I ask this question. It is obvious that for plotting the charge densty at gamma point for LUMO and HOMO states I should use LocalDensityOfStates. My question is about arranging the energies in this block to get to the righ HOMO and LUMO states. If you have any experiences please let me know. Regards,
Re: [SIESTA-L] Fwd: crystal energy calculation
Thanks so much for replying me. Regarding the GaN you have said, taking a bigger unitcell means forexample having 4 unit cells with 16 atoms, or the unit cell still has 4 atoms and we just increase the length of the cell? also, in GaN forexample again we have 2 Ga and 2 N in the unit cell, right, so how could I mention the basis I have for Ga as an example, because I have only mentioned the ghost atom with a negative sign of atomic number? All in all, how could I have a real Ga and a ghost Ga basis? Regards,
[SIESTA-L] Fwd: crystal energy calculation
*I am very sorry to re-send my email, but I really need to know the answer.* Dear Siesta users, I am sorry, I have not got my answer reading the whole archive about this subject. Therefore, I hope you would kindly let me know the answer of the following question: We all know that for the crystals we have the following relation: *Cohesive Energy (CE) = (energy of free atom) - (energy of atom in a crystal).* I am working on GaN bulk and nanostructures. 1. Regarding the energy of the free atom, as I read the archive, it seems that we have to consider the ghost atoms surrounding the main atom to get the enrgy of the free atom?! or, it is enough to have the right basis of the atom and calculate its energy? 2. energy of atom in a crystal: when we calculate the enery of the bulk, then how do we have the energy of the atom in the structure? 3. I would be grateful if you let me know the additional terms I have to consider in order to calculate the cohesive energy of a slab too. Regards, Sarah
[SIESTA-L] crystal energy calculation
Dear Siesta users, I am sorry, I have not got my answer reading the whole archive about this subject. Therefore, I hope you would kindly let me know the answer of the following question: We all know that for the crystals we have the following relation: *Cohesive Energy (CE) = (energy of free atom) - (energy of atom in a crystal).* I am working on GaN bulk and nanostructures. 1. Regarding the energy of the free atom, as I read the archive, it seems that we have to consider the ghost atoms surrounding the main atom to get the enrgy of the free atom?! or, it is enough to have the right basis of the atom and calculate its energy? 2. energy of atom in a crystal: when we calculate the enery of the bulk, then how do we have the energy of the atom in the structure? 3. I would be grateful if you let me know the additional terms I have to consider in order to calculate the cohesive energy of a slab too. Regards, Sarah
