Re: [SIESTA-L] Phonons in CdSe
On Tue, 21 Nov 2006, marcel wrote: | Dear All, | | I'm doing some test calculations on bulk hexagonal CdSe. I want to calculate | the phonon dispersion. | (Im using the version of T. Archer, for LO-TO splitting and include BC in my | Siesta calculation. | The dielectric constants I use are from literature on measurements. ) | | I get perfect acoustic frequencies at 0.0 cm^(-1). | Lowest optical and highest optical frequency are underestimated by max. 2 % | from experiment. OK. | However, the mid-range frequencies are overestimated, up to 10%. | | So would you think this is ok, or should I further investigate the source of | this discrepancy? Marcel: it can be deduced from your message that you have this problem already in Gamma, and for the minimal cell. Did you check the effect of k-mesh? The forces and force constants may vary with it. Andrei Postnikov +-- Dr. Andrei Postnikov Tel. +33-387315873 - mobile +33-666784053 ---+ | Paul Verlaine University - Institute de Physique Electronique et Chimie, | | Laboratoire de Physique des Milieux Denses, 1 Bd Arago, F-57078 Metz, France | +-- [EMAIL PROTECTED] http://www.home.uni-osnabrueck.de/apostnik/ --+
Re: [SIESTA-L] atom label ordering problem
On Tue, 21 Nov 2006, Chu Chun FU wrote: | Dear Postnikov, | | I could but, I didn't since in principle the result should not depend on the | atom label ordering... | | Chu Chun Dear Chu Chun, What I mean is, if you for instance always set initial spin for type 2 only: if your type 2 is Fe it converges to magnetic solution as it should be, and if your type 2 is Cu it doesn't manage to induce enough spin on Fe and converges to a non-magnetic solution. Andrei
[SIESTA-L] Phonons in CdSe
Dear All, I'm doing some test calculations on bulk hexagonal CdSe. I want to calculate the phonon dispersion. (Im using the version of T. Archer, for LO-TO splitting and include BC in my Siesta calculation. The dielectric constants I use are from literature on measurements. ) I get perfect acoustic frequencies at 0.0 cm^(-1). Lowest optical and highest optical frequency are underestimated by max. 2 % from experiment. OK. However, the mid-range frequencies are overestimated, up to 10%. So would you think this is ok, or should I further investigate the source of this discrepancy? Greetings Marcel Mohr
Re: [SIESTA-L] atom label ordering problem
Dear Postnikov, I could but, I didn't since in principle the result should not depend on the atom label ordering... Chu Chun Andrei Postnikov wrote: On Tue, 21 Nov 2006, Chu Chun FU wrote: | Dear All, | | We are studying the FeCu system with Siesta and we have found some problems | related to the | labels (1 or 2) asigned to each chemical species. | | For example when considering the system containing 1 Fe atom and N-1 atoms of | Cu with BCC | structure (e.g. N = 54), the results (total energy and magnetic moment of Fe) | differ depending | on which atom is labeled as atom '1': | | If we put | | %block ChemicalSpeciesLabel | 1 29 Cu | 2 26 Fe | %endblock ChemicalSpeciesLabel | | we obtain reasonable values for total energy and magnetic moment for the Fe | atom (about 3 | mu_B). | | However when we change the order and put | | %block ChemicalSpeciesLabel | 1 26 Fe | 2 29 Cu | %endblock ChemicalSpeciesLabel | | we obtain a different value of total energy (0.6 eV higher) and zero magnetic | moment for Fe ! | | We wonder if anybody had a similar problem before ? or any idea on the origing | of this problem | ? Dear Chu Chun: and do you set %block DM.InitSpin differently, depending on which type is Fe ? Best regards, Andrei +-- Dr. Andrei Postnikov Tel. +33-387315873 - mobile +33-666784053 ---+ | Paul Verlaine University - Institute de Physique Electronique et Chimie, | | Laboratoire de Physique des Milieux Denses, 1 Bd Arago, F-57078 Metz, France | +-- [EMAIL PROTECTED] http://www.home.uni-osnabrueck.de/apostnik/ --+ -- Chu Chun FU DEN/DMN/SRMP CEA-Saclay 91191 Gif-sur-yvette Cedex France Tel: +33 1 69 08 29 32 Fax: +33 1 69 08 68 67 E-mail: [EMAIL PROTECTED]
Re: [SIESTA-L] atom label ordering problem
Dear Andrei, Excuse me, I mean I did not set explicitly in any casethe InitSpin of the system. Chu Chun Andrei Postnikov wrote: On Tue, 21 Nov 2006, Chu Chun FU wrote: | Dear All, | | We are studying the FeCu system with Siesta and we have found some problems | related to the | labels (1 or 2) asigned to each chemical species. | | For example when considering the system containing 1 Fe atom and N-1 atoms of | Cu with BCC | structure (e.g. N = 54), the results (total energy and magnetic moment of Fe) | differ depending | on which atom is labeled as atom '1': | | If we put | | %block ChemicalSpeciesLabel | 1 29 Cu | 2 26 Fe | %endblock ChemicalSpeciesLabel | | we obtain reasonable values for total energy and magnetic moment for the Fe | atom (about 3 | mu_B). | | However when we change the order and put | | %block ChemicalSpeciesLabel | 1 26 Fe | 2 29 Cu | %endblock ChemicalSpeciesLabel | | we obtain a different value of total energy (0.6 eV higher) and zero magnetic | moment for Fe ! | | We wonder if anybody had a similar problem before ? or any idea on the origing | of this problem | ? Dear Chu Chun: and do you set %block DM.InitSpin differently, depending on which type is Fe ? Best regards, Andrei +-- Dr. Andrei Postnikov Tel. +33-387315873 - mobile +33-666784053 ---+ | Paul Verlaine University - Institute de Physique Electronique et Chimie, | | Laboratoire de Physique des Milieux Denses, 1 Bd Arago, F-57078 Metz, France | +-- [EMAIL PROTECTED] http://www.home.uni-osnabrueck.de/apostnik/ --+ -- Chu Chun FU DEN/DMN/SRMP CEA-Saclay 91191 Gif-sur-yvette Cedex France Tel: +33 1 69 08 29 32 Fax: +33 1 69 08 68 67 E-mail: [EMAIL PROTECTED]
Re: [SIESTA-L] atom label ordering problem
On Tue, 21 Nov 2006, Chu Chun FU wrote: | Dear All, | | We are studying the FeCu system with Siesta and we have found some problems | related to the | labels (1 or 2) asigned to each chemical species. | | For example when considering the system containing 1 Fe atom and N-1 atoms of | Cu with BCC | structure (e.g. N = 54), the results (total energy and magnetic moment of Fe) | differ depending | on which atom is labeled as atom '1': | | If we put | | %block ChemicalSpeciesLabel | 1 29 Cu | 2 26 Fe | %endblock ChemicalSpeciesLabel | | we obtain reasonable values for total energy and magnetic moment for the Fe | atom (about 3 | mu_B). | | However when we change the order and put | | %block ChemicalSpeciesLabel | 1 26 Fe | 2 29 Cu | %endblock ChemicalSpeciesLabel | | we obtain a different value of total energy (0.6 eV higher) and zero magnetic | moment for Fe ! | | We wonder if anybody had a similar problem before ? or any idea on the origing | of this problem | ? Dear Chu Chun: and do you set %block DM.InitSpin differently, depending on which type is Fe ? Best regards, Andrei +-- Dr. Andrei Postnikov Tel. +33-387315873 - mobile +33-666784053 ---+ | Paul Verlaine University - Institute de Physique Electronique et Chimie, | | Laboratoire de Physique des Milieux Denses, 1 Bd Arago, F-57078 Metz, France | +-- [EMAIL PROTECTED] http://www.home.uni-osnabrueck.de/apostnik/ --+
Re: [SIESTA-L] atom label ordering problem
Dear Salvador, Thank you , actually I have made the changes in the atomic coordinate block accordingly, exactly as you said. Chu Chun Salvador Barraza-Lopez wrote: Hello Chu, The issue here is when you change the ordering on the Chamicalspecies block, you are changing the atomic species also in your coordinate set. Did you leave the coordinates unchanged? For instance, if an atom with coordinates X Y Z 1 was assigned to species 1, then by renaming the atomicspecies block this same atom now belongs to the complimentary specie (originally, to species 2). So you really need to change the atomicspecies block, and the labels on your coordinate set, which assign the atomic species to an atom at position XYZ. Best, Salvador. On Tue, 21 Nov 2006, Chu Chun FU wrote: Dear All, We are studying the FeCu system with Siesta and we have found some problems related to the labels (1 or 2) asigned to each chemical species. For example when considering the system containing 1 Fe atom and N-1 atoms of Cu with BCC structure (e.g. N = 54), the results (total energy and magnetic moment of Fe) differ depending on which atom is labeled as atom '1': If we put %block ChemicalSpeciesLabel 1 29 Cu 2 26 Fe %endblock ChemicalSpeciesLabel we obtain reasonable values for total energy and magnetic moment for the Fe atom (about 3 mu_B). However when we change the order and put %block ChemicalSpeciesLabel 1 26 Fe 2 29 Cu %endblock ChemicalSpeciesLabel we obtain a different value of total energy (0.6 eV higher) and zero magnetic moment for Fe ! We wonder if anybody had a similar problem before ? or any idea on the origing of this problem ? Thank you in advance for your information and help Chu Chun FU -- Chu Chun FU DEN/DMN/SRMP CEA-Saclay 91191 Gif-sur-yvette Cedex France Tel: +33 1 69 08 29 32 Fax: +33 1 69 08 68 67 E-mail: [EMAIL PROTECTED]
Re: [SIESTA-L] atom label ordering problem
Hello Chu, The issue here is when you change the ordering on the Chamicalspecies block, you are changing the atomic species also in your coordinate set. Did you leave the coordinates unchanged? For instance, if an atom with coordinates X Y Z 1 was assigned to species 1, then by renaming the atomicspecies block this same atom now belongs to the complimentary specie (originally, to species 2). So you really need to change the atomicspecies block, and the labels on your coordinate set, which assign the atomic species to an atom at position XYZ. Best, Salvador. On Tue, 21 Nov 2006, Chu Chun FU wrote: Dear All, We are studying the FeCu system with Siesta and we have found some problems related to the labels (1 or 2) asigned to each chemical species. For example when considering the system containing 1 Fe atom and N-1 atoms of Cu with BCC structure (e.g. N = 54), the results (total energy and magnetic moment of Fe) differ depending on which atom is labeled as atom '1': If we put %block ChemicalSpeciesLabel 1 29 Cu 2 26 Fe %endblock ChemicalSpeciesLabel we obtain reasonable values for total energy and magnetic moment for the Fe atom (about 3 mu_B). However when we change the order and put %block ChemicalSpeciesLabel 1 26 Fe 2 29 Cu %endblock ChemicalSpeciesLabel we obtain a different value of total energy (0.6 eV higher) and zero magnetic moment for Fe ! We wonder if anybody had a similar problem before ? or any idea on the origing of this problem ? Thank you in advance for your information and help Chu Chun FU
[SIESTA-L] atom label ordering problem
Dear All, We are studying the FeCu system with Siesta and we have found some problems related to the labels (1 or 2) asigned to each chemical species. For example when considering the system containing 1 Fe atom and N-1 atoms of Cu with BCC structure (e.g. N = 54), the results (total energy and magnetic moment of Fe) differ depending on which atom is labeled as atom '1': If we put %block ChemicalSpeciesLabel 1 29 Cu 2 26 Fe %endblock ChemicalSpeciesLabel we obtain reasonable values for total energy and magnetic moment for the Fe atom (about 3 mu_B). However when we change the order and put %block ChemicalSpeciesLabel 1 26 Fe 2 29 Cu %endblock ChemicalSpeciesLabel we obtain a different value of total energy (0.6 eV higher) and zero magnetic moment for Fe ! We wonder if anybody had a similar problem before ? or any idea on the origing of this problem ? Thank you in advance for your information and help Chu Chun FU -- Chu Chun FU DEN/DMN/SRMP CEA-Saclay 91191 Gif-sur-yvette Cedex France Tel: +33 1 69 08 29 32 Fax: +33 1 69 08 68 67 E-mail: [EMAIL PROTECTED]
Re: [SIESTA-L] About Atomic Forces.
On Tue, 21 Nov 2006, SuiYang wrote: | Dear SIESTA users: | I have used SIESTA to study the property of FePt systems.Here I have a question about the atomic forces SIESTA calculated: | When I am calculating the FePt unit cell(including 4 atoms) with its lattice constant around 4 ang.The corresponding atomic forces are around 0.02 eV/ang.When I am using the 2x2x2 supercell(including 32 atoms) as unit cell, with relatively the same atomic positions,and the lattice constant is changed to 8 ang to maintain it is the same bulk as the previous one,however ,the atomic forces are increased to around one hundred eV/ang. | | I also calculated another system using 3x3x3 supercell as unit cell, the forces are much even higher ,it seems the atomic force will increase with the number of atoms and the lattice constant. | | I am rather confused with its behavior,why there is such a drastic change in atomic forces and stress tensor while the bulk is the same, only the expression of it is different. | | I've attached both 1x1x1 and 2x2x2's input and output files,if needed. | I really need your help. | Dear SuiYang, As Riccardo pointed out, you are doing calculation with the default setting for k-points, that is just one k-point. This is no good when calculating bulk - in any case, metals. You can see that Siesta fails to converge your system - which is in fact metal with partially filled bands, - when using just one k-point and hence no dispersion; it just desperately swaps the Fermi energy back and forth: siesta: iscf Eharris(eV) E_KS(eV) FreeEng(eV) dDmax Ef(eV) ... siesta: 23-3027.3747-2953.1394-2953.2110 0.8298 2.5907 ... siesta: 98-3034.0919-2952.4118-2952.4146 0.8258 -2.0656 siesta: 99-3027.3736-2953.3750-2953.4466 0.8258 2.5911 Normally you should be wondered by this behavior before going any further... After you manage to get reasonable convergence of electronic properties, take into account that the forces are especially sensitive to the k-mesh, and (if you really need good forces, i.e. for phonons) you should check how they converge as you increase the number of k-points. Your forces are zero in your 4-atom cell, because the positions of atoms are symmetric with respect to the real-space mesh (defined by the Mesh cutoff, 200 Ry in your case), and the errors cancel. In order to see how good/bad the forces REALLY are, you can displace the atoms a bit from the symmetric positions, imposing the uniform shift (AtomicCoordinatesOrigin). In your 2x2x2-cell you have apparently the atoms situated at random with respect to the mesh along the Y-direction, and you see huge fluctuations of forces, which - in principle, i.e. apart from numerical errors - should be zero by symmetry: siesta: Atomic forces (eV/Ang): 10.01 94.7209640.06 2 -0.04 -94.7209750.03 30.04 -117.510866 -0.02 4 -0.05 117.5108590.00 I must confess I don't understand why X and Y behave differently, avan as they are completely equivalent with respect of atomic positions and mesh construction. I'd be glad to see somebody's comment on that. You did't need to provide .fdf separately because they are dumped at the beginning of each Siesta output anyway. I don't know what you are after in your study, but if I remember correctly, in real life FePt is magnetic, so that when you switch on the spin, this will affect your forces as well. Hope this helps, Andrei Postnikov +-- Dr. Andrei Postnikov Tel. +33-387315873 - mobile +33-666784053 ---+ | Paul Verlaine University - Institute de Physique Electronique et Chimie, | | Laboratoire de Physique des Milieux Denses, 1 Bd Arago, F-57078 Metz, France | +-- [EMAIL PROTECTED] http://www.home.uni-osnabrueck.de/apostnik/ --+
[SIESTA-L] Optical.Broaden
Dear Users, Hi, can some body tell me how to choose the Optical.Broaden value in the calculation of the imaginary part of epsilon apearing in *.EPSIMG file, in the case of clusters? Thanks. ___ Yahoo! Mail réinvente le mail ! Découvrez le nouveau Yahoo! Mail et son interface révolutionnaire. http://fr.mail.yahoo.com
Re: [SIESTA-L] About Atomic Forces.
Dear SuiYang, I have used SIESTA to study the property of FePt systems.Here I have a question about the atomic forces SIESTA calculated: When I am calculating the FePt unit cell(including 4 atoms) with its lattice constant around 4 ang.The corresponding atomic forces are around 0.02 eV/ang.When I am using the 2x2x2 supercell(including 32 atoms) as unit cell, with relatively the same atomic positions,and the lattice constant is changed to 8 ang to maintain it is the same bulk as the previous one,however ,the atomic forces are increased to around one hundred eV/ang. at least one problem that you are having concerns the number of k-points. If I understand correctly your FDF files, you're using Gamma point only for both systems. This is a problem for two reasons: 1) your cells are very small and a large number of k-points is possibly needed to be converged; 2) the number of k-points should be consistently scaled when you increase the size of the direct space cell (if you double it along the 3 axis, i.e. if you go from 1x1x1 to 2x2x2, the numer of k-points should be reduced by a factor 2 in the 3 axis as well). Riccardo -- Riccardo Rurali Escola Tècnica Superior d'Enginyeria (ETSE) Universitat Autònoma de Barcelona (UAB) Campus de la UAB 08193 Bellaterra (Barcelona) Spain tel.: +34 93 581 3531 fax.: +34 93 581 2600 e-mail: [EMAIL PROTECTED]
[SIESTA-L] About Atomic Forces.
Dear SIESTA users: I have used SIESTA to study the property of FePt systems.Here I have a question about the atomic forces SIESTA calculated: When I am calculating the FePt unit cell(including 4 atoms) with its lattice constant around 4 ang.The corresponding atomic forces are around 0.02 eV/ang.When I am using the 2x2x2 supercell(including 32 atoms) as unit cell, with relatively the same atomic positions,and the lattice constant is changed to 8 ang to maintain it is the same bulk as the previous one,however ,the atomic forces are increased to around one hundred eV/ang. I also calculated another system using 3x3x3 supercell as unit cell, the forces are much even higher ,it seems the atomic force will increase with the number of atoms and the lattice constant. I am rather confused with its behavior,why there is such a drastic change in atomic forces and stress tensor while the bulk is the same, only the expression of it is different. I've attached both 1x1x1 and 2x2x2's input and output files,if needed. I really need your help. Thanks In Advance. Best Wishes.. SuiYang 2006-11-21 FePt-1x1x1.out Description: Binary data FePt-1x1x1.fdf Description: Binary data FePt-2x2x2.out Description: Binary data FePt-2x2x2.fdf Description: Binary data
