Re: [SIESTA-L] Phonon-DOS
Hei, It might be possible for IR intensities using ase package (https://wiki.fysik.dtu.dk/ase/). Unfortunately the ASE-implementation does not fully support siesta calculation for IR intensities (the calculation of dipole moment is not there for siesta but it should be easy to add). Alternatively maybe siesta3.0 has it??? terveisin Markus 2009/7/5 karim rezouali rezoual...@yahoo.fr: Dear All, Is there any a way to calculate phonon density of states? Karim -- --www=http://www.iki.fi/markus.kaukonen --markus.kauko...@iki.fi --office: N102 Nano building FIN-02015 TKK --home: Viinirinne 3 F 12, 02630 Espoo, FIN --tel: h 045-1242068, w 4518694, 050-5112785 --Rikos ei kannata, eika maatalous --Suomessa. (Paimio 1998) ---
[SIESTA-L] Fermid: qtot,sumq= 2687.9999999999736 NaN
Dear Siesta, I'm trying to run a two crossed nanotube (14,0) calculation with ~672 atoms and diagonal solution method (the full input fdf-file below). Getting the following error with a computer that should have plenty of memory (10GB) and with Siesta 2.02 I tested additionally taking either of the nanotubes away (taking half of the coordinates away from the fdf file) and that was no problem. Also tried orderN but got crap. Any help would be appreciated, terveisin, Markus ==OUTPUT BEGINS== siesta: == Begin CG move = 0 == outcell: Unit cell vectors (Ang): 50.000.000.00 0.00 25.9419360.00 0.000.00 25.941936 outcell: Cell vector modules (Ang) : 50.00 25.941936 25.941936 outcell: Cell angles (23,13,12) (deg): 90. 90. 90. outcell: Cell volume (Ang**3): 33649.2009 InitMesh: MESH = 432 x 240 x 240 =24883200 InitMesh: Mesh cutoff (required, used) = 200.000 206.314 Ry * Maximum dynamic memory allocated = 920 MB stepf: Fermi-Dirac step function Fermid: Iteration has not converged. Fermid: qtot,sumq= 2687.99736 NaN Fermid: Iteration has not converged. Stopping Program from Node:0 ==INPUT BEGINS== SystemName 2 (14,0) crossed Carbon Nanotubes SystemLabel nanotube NumberOfAtoms 672 NumberOfSpecies 1 WriteCoorXmol T PAO.BasisType split PAO.BasisSize SZP PAO.EnergyShift 50 meV #Diag.DivideAndConquer F %block ChemicalSpeciesLabel 1 6 C %endblock ChemicalSpeciesLabel LatticeConstant 1.00 Ang %block LatticeVectors 50.00 0.00 0.00 0.0025.94193550.00 0.00 0.0025.9419355 %endblock LatticeVectors %block kgridMonkhorstPack 1 0 0 0.0 0 1 0 0.0 0 0 1 0.0 %endblock kgridMonkhorstPack MeshCutoff 200.0 Ry XC.functional GGA XC.authors revPBE MaxSCFIterations500 SolutionMethod Diagon MD.TypeOfRunCG MD.NumCGsteps 0 MD.UseSaveXVT MD.UseSaveCGT AtomicCoordinatesFormat NotScaledCartesianAng %block AtomicCoordinatesAndAtomicSpecies 5.56445112.251794 0.00 1 C 1 5.42419711.528201 1.238286 1 C 2 5.01292512.251874 2.414149 1 C 3 4.35038111.528286 3.469063 1 C 4 3.46906312.251820 4.350381 1 C 5 2.41414911.528233 5.012925 1 C 6 1.23828612.251905 5.424196 1 C 7 -0.0011.528312 5.564451 1 C 8 -1.23828712.251905 5.424196 1 C 9 -2.41414911.528233 5.012926 1 C 10 -3.46906312.251820 4.350382 1 C 11 -4.35038111.528286 3.469063 1 C 12 -5.01292512.251873 2.414149 1 C 13 -5.42419711.528201 1.238286 1 C 14 -5.56445112.251793 0.00 1 C 15 -5.42419711.528201-1.238287 1 C 16 -5.01292512.251874-2.414149 1 C 17 -4.35038111.528286-3.469063 1 C 18 -3.46906312.251820-4.350381 1 C 19 -2.41414911.528233-5.012925 1 C 20 -1.23828612.251905-5.424196 1 C 21 -0.0011.528312-5.564451 1 C 22 1.23828712.251905-5.424196 1 C 23 2.41414911.528233-5.012926 1 C 24 3.46906312.251820-4.350382 1 C 25 4.35038111.528286-3.469063 1 C 26 5.01292512.251873-2.414149 1 C 27 5.42419711.528202-1.238287 1 C 28 5.42419710.090079 1.238286 1 C 29 5.012925 9.366406 2.414149 1 C 30 4.35038110.089995 3.469063 1 C 31 3.469063 9.366461 4.350381 1 C 32 2.41414910.090047 5.012925 1 C 33 1.238285 9.366375 5.424196 1 C 34 -0.0010.089967 5.564451 1 C 35 -1.238286 9.366374 5.424196 1 C 36 -2.41414910.090048 5.012925 1 C 37 -3.469063 9.366460 4.350382 1 C 38 -4.35038110.089994 3.469062 1 C 39 -5.012925 9.366407 2.414149 1 C 40 -5.42419710.090078 1.238286 1 C 41 -5.564451 9.366486 0.00 1 C 42 -5.42419610.090079-1.238287 1 C 43 -5.012925
[SIESTA-L] Fwd: Fermid: qtot,sumq= 2687.9999999999736 NaN
Sorry the previous message (Fermid: qtot,sumq= 2687.99736 NaN), I had messed up with compilers, now siesta 2.02 works fine. Markus
[SIESTA-L] infrared intensities, solved?
Dear Siesta, There was no response to my infrared question (see below). Luckily, they have now implemented infrared intensities in the ASE package which can drive Siesta. https://wiki.fysik.dtu.dk/ase/ Terveisin Markus Dear Siesta, In the manual (siesta 2.0.2 page 41) it is said: The Born efective charges allow the calculation of LO-TO splittings and infrared activities. The version of the Vibra utility code in which these magnitudes are calculated is not yet distributed with Siesta, but can be obtained form Tom Archer (arch...@tcd.ie). Is this info still valid? I emailed arch...@tcd.ie in december 2008 and got no response. Terveisin Markus -- --www=http://www.iki.fi/markus.kaukonen --markus.kauko...@iki.fi --office: N102 Nano building FIN-02015 TKK --home: Viinirinne 3 F 12, 02630 Espoo, FIN --tel: h 045-1242068, w 4518694, 050-5112785 --Rikos ei kannata, eika maatalous --Suomessa. (Paimio 1998) ---
[SIESTA-L] infrared peak intensities ?
Dear Siesta, In the manual (siesta 2.0.2 page 41) it is said: The Born efective charges allow the calculation of LO-TO splittings and infrared activities. The version of the Vibra utility code in which these magnitudes are calculated is not yet distributed with Siesta, but can be obtained form Tom Archer (arch...@tcd.ie). Is this info still valid? I emailed arch...@tcd.ie in december 2008 and got no response. Terveisin Markus -- --www=http://www.iki.fi/markus.kaukonen --markus.kauko...@iki.fi --office: N102 Nano building FIN-02015 TKK --home: Viinirinne 3 F 12, 02630 Espoo, FIN --tel: h 045-1242068, w 4518694, 050-5112785 --Rikos ei kannata, eika maatalous --Suomessa. (Paimio 1998) ---
[SIESTA-L] On tutorials
Dear Siesta, The amplitude of variations of the sum of forces (around zero), periodic with the step of the real-space mesh, does indeed depend on MeshCutoff and can be gradually suppressed when increasing the latter. See tutorials on the Siesta web page on this subject. Best regards Andrei Postnikov What I have found on Siesta tutorials page is a random collection of lecture notes, not very suitable for self studies over internet. It would be great if somebody who knows Siesta and is not under threat of unemployment in the near future (ie a person with a permanent position) could offer his/her time for one month to prepare some decent tutorials for Siesta. I have in mind something in line they have in a classical MM package amber (http://ambermd.org/tutorials/), that is excellent stuff. Some issues one could deal with: - What should be tested and how for converged results (with an example) - How to test a pseudopotential (with an example) - What to do if scf cycles do not converge with solution method diagonal and standard settings in the input file (with an example). - When to use orderN method? To which systems it is good/bad. What can be done in case of poor convergence (with examples). I understand that for a program free of charge one should be thankful for what one gets, but anyway... Terveisin, Markus -- --www=http://www.iki.fi/markus.kaukonen --markus.kauko...@iki.fi --office: N102 Nano building FIN-02015 TKK --home: Viinirinne 3 F 12, 02630 Espoo, FIN --tel: h 045-1242068, w 4518694, 050-5112785 --Rikos ei kannata, eika maatalous --Suomessa. (Paimio 1998) ---
[SIESTA-L] Reproducing VASP k-points
Dear Siesta, In VASP manual it is stated (http://cms.mpi.univie.ac.at/vasp/vasp/node61.html) We strongly recommend to use only Gamma centered grids for hexagonal lattices. Many tests we have performed indicate that the energy converges significantly faster with $\Gamma$ centered grids than with standard Monkhorst Pack grids. Grids generated with the ``M'' setting in the third line, in fact do not have full hexagonal symmerty. Question: I'd like to reproduce some VASP data (substitutional Pt on graphene, 98 atoms) using something as close as possible to VASP's Monkhorst Pack 4x4x1 Mesh, Gamma centered grid. Is this possible using Siesta or what what would be the best option? Can one give k-points explicitly one by one? Terveisin Markus -- --www=http://www.iki.fi/markus.kaukonen --markus.kauko...@iki.fi --office: N102 Nano building FIN-02015 TKK --home: Viinirinne 3 F 12, 02630 Espoo, FIN --tel: h 045-1242068, w 4518694, 050-5112785 --Rikos ei kannata, eika maatalous --Suomessa. (Paimio 1998) ---
