Re: [SIESTA-L] How do you construct initial coordinates?
I have a Fortran program that translates between a few periodic formats I use (mainly SIESTA input and output, CASTEP input and output and VASP POSCAR). As Bartek mentioned, gdis can be used to manipulate fdf files. You can also "cut and paste" a molecule (for example from an xyz file) into a periodic cell (for example onto a surface). Cheers, Herbert Mike Turchenkov wrote: Hello, let's share our methods of constructing initial coordinates for SIESTA. There is a lot of atomic structure apps under linux, but I didn't find anything better than use *.car format and then copy/paste its content into input.fdf with following manual edit. It is not very comfort, especially there is a lot of trial calculations. May be there is some apps that produce *.STRUCT_IN file directly? Which of them support periodic cell and symmetry operations? Mike. -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532
[SIESTA-L] Post-Doc position in Lyons: theoretical heterogeneous catalysis
[Sorry if you already got this email.] One Post-doc position, starting as soon as possible, is available in the field of Theoretical Chemistry at the Laboratory of Chemistry, Ecole Normale Supérieure de Lyon, France. Net salary between 2100-2300/month depending on experience. Position is for 18 months. The research project concerns the modeling of the solvent in a QM/MM molecular dynamic simulation. Indeed, most of the standard approaches resort to a static definition of the QM/MM partitioning: one molecule is either MM or QM. However, when dealing with reactions in solution, this can be a problem: some solvent molecule can become reactants or can act as electron attractors through hydrogen bonding for example. In order to deal with such cases, we want to implement the adaptive QM/MM scheme recently proposed by Bulo et al. (DOI:10.1021/ct900148e) into CPMD. The scheme will then be applied to the study of organic and biochemical reactions. One important application will be the mechanistic study of the imine formation in water under different pH conditions. This textbook reaction is of the utmost importance not only in organic synthesis, but also in the context of DNA damage. Applicants are expected to have a good background in either quantum chemistry or molecular dynamics. Knowledge of CPMD or CP2K is a requirement. Fluency in a high-level programming language, such as FORTRAN90 or/and Python would be a definite plus. Lyon's listing by UNESCO as a World Heritage Site gives recognition to the long history heritage of the city. It is also recognized for its gastronomy and last but not least, Lyon is a vivid city with thousands of students. Motivated candidates are invited to send their CV, including a short motivation for carrying out this project, list of publications, abstract of research results (1 page) and two recommendation letters by e-mail (preferred format pdf or plain text) to: Paul Fleurat-Lessard Laboratoire de Chimie, UMR CNRS 5182, École Normale Supérieure de Lyon 46, Allée d'Italie 69364 Lyon Cedex 07 France Phone: +33 4 72 72 81 54 Fax: +33 4 72 72 88 60 E-mail: Paul.Fleurat-Lessard at ens-lyon.fr Best regards, Paul. -- Fleurat-Lessard Paul, Lecturer e-mail: paul.fleurat-less...@ens-lyon.fr Laboratoire de Chimie Ecole Normale Supérieure de Lyon Tel: + 33 (0)4 72 72 81 54 46, Allée d'ItalieFax: + 33 (0)4 72 72 88 60 69364 Lyon Cedex 07
Re: [SIESTA-L] How do you construct initial coordinates?
On Mon, 2011-01-17 at 14:21 +0100, Mike Turchenkov wrote: > Hello, let's share our methods of constructing initial coordinates for > SIESTA. > > There is a lot of atomic structure apps under linux, but I didn't find > anything better than use *.car format and then copy/paste its content > into input.fdf with following manual edit. It is not very comfort, > especially there is a lot of trial calculations. > > May be there is some apps that produce *.STRUCT_IN file directly? > Which of them support periodic cell and symmetry operations? gdis is able to generate an fdf file directly. you might also want to try my plugin for zeobuilder - check the list archive for the links :) Groeten - Regards - Pozdrowienia, Bartek
Re: [SIESTA-L] How to start trial run?
Thanks, Bartek! So trial SIESTA run doesn't seem to be the best way to produce initial coordinates file.
[SIESTA-L] How do you construct initial coordinates?
Hello, let's share our methods of constructing initial coordinates for SIESTA. There is a lot of atomic structure apps under linux, but I didn't find anything better than use *.car format and then copy/paste its content into input.fdf with following manual edit. It is not very comfort, especially there is a lot of trial calculations. May be there is some apps that produce *.STRUCT_IN file directly? Which of them support periodic cell and symmetry operations? Mike.
Re: [SIESTA-L] band structure
Thank you very much. Magda 2011/1/17 Barraza-Lopez,Salvador > Hi Magda, > > For a given k-point, the bands file will have spin up and spin down > entries if the run was spin-polarized. To see where the spin down entries > start, look for a sudden jump in the eigenvalues (ie, from large positive > values back to negative ones) right at the middle of the dataset for any > k-point. > > Best regards, > -Salvador. > > -- > *From: *"Magdalena Birowska" > *To: *siesta-l@uam.es > *Sent: *Monday, January 17, 2011 6:26:53 AM > *Subject: *[SIESTA-L] band structure > > > I have performed Spin Polarized calculations. I would like to know how can > I > turn on spin down calculations in the file *.bands > > > Thanks in advance > Magda > > > > > > -- > Salvador Barraza-Lopez > Postdoctoral Fellow > School of Physics > The Georgia Institute of Technology > > Office N205 > 837 State Street Atlanta, Georgia 30332-0430 U.S.A > Tel: (404) 894-0892 Fax: (404) 894-9958 >
Re: [SIESTA-L] band structure
Hi Magda, For a given k-point, the bands file will have spin up and spin down entries if the run was spin-polarized. To see where the spin down entries start, look for a sudden jump in the eigenvalues (ie, from large positive values back to negative ones) right at the middle of the dataset for any k-point. Best regards, -Salvador. - Original Message - From: "Magdalena Birowska" To: siesta-l@uam.es Sent: Monday, January 17, 2011 6:26:53 AM Subject: [SIESTA-L] band structure I have performed Spin Polarized calculations. I would like to know how can I turn on spin down calculations in the file *.bands Thanks in advance Magda -- Salvador Barraza-Lopez Postdoctoral Fellow School of Physics The Georgia Institute of Technology Office N205 837 State Street Atlanta, Georgia 30332-0430 U.S.A Tel: (404) 894-0892 Fax: (404) 894-9958
[SIESTA-L] band structure
I have performed Spin Polarized calculations. I would like to know how can I turn on spin down calculations in the file *.bands Thanks in advance Magda
Re: [SIESTA-L] BSSE corrections
Hi Everyone, Thank you for your quick responses. @ Alaxander: >Does this work use SIESTA??? I thought that non-local XC functionals are not implemented in >SIESTA and the van der Waals interactions are added a posteriori as a force-field correction. >(i.e. the basis set has no relevance to vdW at all (in SIESTA)) Yes this work is using siesta, it is the trunk version. The stable versions of siesta do not have this feature yet and need to rely on force field corrections. @ Herbert: You mentioned for BSSE: >You can use this in siesta for energies, but not forces or geometry optimisation. I'm actually interested in forces since I intend to do phonon calculations, does this mean that BBSE corrections for the force constant calculation will not play much of a role? I have another question I tried doing calculations for my system with TZDP basis with 8 nodes and the memory requirement per thread was < 1.75 GB, but upon using a basis set > TZDP (given below) the memory requirement suddenly jumps upto > 6 GB per thread. I was wondering if using TZDP+BSSE or diffuse orbitals would reduce the memory requirement? Basis for C: %block PAO.Basis C.vdw2 0.0 n=2 0 3 P 0 0.0 0.0 0.0 n=2 1 3 P 3 0.0 0.0 0.0 %endblock PAO.Basis Regards, Juzar Thingna Department of Physics, Center for Computation Science and Engineering, National University of Singapore. On Mon, Jan 17, 2011 at 4:45 PM, Herbert Fruchtl < herbert.fruc...@st-andrews.ac.uk> wrote: > These are different, but related. issues: > > BSSE is an error that comes from the incompleteness of atom-centred basis > sets. > Basically, if you add atoms, you add basis functions. If you move atoms > closer > together, they can use each other's basis functions, which "improves" the > basis. The result is an artificial lowering of energies for compact > systems, > and therefore an attractive force. You can fix this by using counterpoise > correction, i.e. placing "ghost atoms" (basis functions without electrons > or > nuclei) where the atoms would be. You can use this in siesta for energies, > but > not forces or geometry optimisation. Just use the negative atomic number > (i.e. > -6 for a "ghost C"). > > Van-der-Waals forces are mainly based on dispersion, which is neglected or > badly > described by most DFT functionals. You can add an empirical force field > term, > based on work by Grimme. This is implemented in Siesta 3.0 (see section > 6.20 of > the manual). > > And finally, long-range interactions need diffuse basis functions. This > also > reduces BSSE (but doesn't remove it completely, and won't give you > dispersion). > You find an application example in Phys Rev B 79, 075441 (2009). In > practice, > you have to optimise basis functions. There is an example script in the > siesta > distribution, but it's tricky. > > HTH, > > Herbert > > Quoting Juzar Thingna : > > > Hello Everyone, > > > > I'm working with vdw interractions for C in a double wall carbon > nano-tube. > > What I have realized is that using the vdw requires very good basis set > and > > the regular DZP doesn't work anymore. Even TZDP is not sufficient, > according > > to Guillermo Roma慨-Pe愉ez et al. PRL, 103, 096102 (2009), they needed a > > TZDP optimized basis + BSSE corrections. > > Please could some explain of how to actually apply BSSE corrections? > > Also I read some discussions on the previous threads about using diffuse > > orbitals instead of BSSE, how do i use diffuse orbitals in siesta? > > > > If both the above options can be used I would like to know which one is > > computationally more efficient. > > > > P.S. If possible please could you provide examples. > > > > Regards, > > > > Juzar Thingna > > Department of Physics, > > Center for Computation Science and Engineering, > > National University of Singapore. > > > > > -- > Herbert Fruchtl > Senior Scientific Computing Officer > School of Chemistry, School of Mathematics and Statistics > University of St Andrews > -- > The University of St Andrews is a charity registered in Scotland: > No SC013532 > > > -- > University of St Andrews Webmail: https://webmail.st-andrews.ac.uk > >
Re: [SIESTA-L] BSSE corrections
These are different, but related. issues: BSSE is an error that comes from the incompleteness of atom-centred basis sets. Basically, if you add atoms, you add basis functions. If you move atoms closer together, they can use each other's basis functions, which "improves" the basis. The result is an artificial lowering of energies for compact systems, and therefore an attractive force. You can fix this by using counterpoise correction, i.e. placing "ghost atoms" (basis functions without electrons or nuclei) where the atoms would be. You can use this in siesta for energies, but not forces or geometry optimisation. Just use the negative atomic number (i.e. -6 for a "ghost C"). Van-der-Waals forces are mainly based on dispersion, which is neglected or badly described by most DFT functionals. You can add an empirical force field term, based on work by Grimme. This is implemented in Siesta 3.0 (see section 6.20 of the manual). And finally, long-range interactions need diffuse basis functions. This also reduces BSSE (but doesn't remove it completely, and won't give you dispersion). You find an application example in Phys Rev B 79, 075441 (2009). In practice, you have to optimise basis functions. There is an example script in the siesta distribution, but it's tricky. HTH, Herbert Quoting Juzar Thingna : > Hello Everyone, > > I'm working with vdw interractions for C in a double wall carbon nano-tube. > What I have realized is that using the vdw requires very good basis set and > the regular DZP doesn't work anymore. Even TZDP is not sufficient, according > to Guillermo Roma´n-Pe´rez et al. PRL, 103, 096102 (2009), they needed a > TZDP optimized basis + BSSE corrections. > Please could some explain of how to actually apply BSSE corrections? > Also I read some discussions on the previous threads about using diffuse > orbitals instead of BSSE, how do i use diffuse orbitals in siesta? > > If both the above options can be used I would like to know which one is > computationally more efficient. > > P.S. If possible please could you provide examples. > > Regards, > > Juzar Thingna > Department of Physics, > Center for Computation Science and Engineering, > National University of Singapore. > -- Herbert Fruchtl Senior Scientific Computing Officer School of Chemistry, School of Mathematics and Statistics University of St Andrews -- The University of St Andrews is a charity registered in Scotland: No SC013532 -- University of St Andrews Webmail: https://webmail.st-andrews.ac.uk
Re: [SIESTA-L] How to start trial run?
On Mon, 2011-01-17 at 05:29 +0100, Mike Turchenkov wrote: > Hello, I need to start trial run just to produce output files such as > siesta.STRUCT_OUT without real calculation. If I am not mistaken, STRUCT_OUT file is created *after* completing at least one CG or MD step, i.e. after SCF has converged. > I use supercell block in that trial run just to get supercell as one > sell in a normal run. > I tried to set > > MD.NumCGsteps 0 > ON.MaxNumIter 0 > MaxSCFIterations 0 '0' means no limits. Use '1' if you need to limit the whole cycle to only one step. Groeten - Regards - Pozdrowienia, Bartek
