Re: [SIESTA-L] learning
STOP On Tue, 26 Dec, 2023, 2:30 am M Mohammadi, wrote: > how can i learn siesta from the biggening? > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence > (https://urldefense.com/v3/__http://www.max-centre.eu/__;!!D9dNQwwGXtA!TtP64JYx8M2cReaZheQmoWqos8mKglFNplOnM79Os0NWA6TYEtBU0QO6ewNMLRNfqyTzO32zxojIru5n4WnLoqY$ > ) > -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
Re: [SIESTA-L] Problem using Vibra utility
Hello, I want to unsubscribe from Siesta emails. Kindly cancel my email address from subscription. Thank you. Regards, Sunetra Das. On Thu, 14 Sep, 2023, 1:30 am Andrei Postnikov, < andrei.postni...@univ-lorraine.fr> wrote: > Dear Diego, > > as your case is q=0 only, you can try your luck > with my shortcut version of vibra, to be compiled from the attached zip. > It does not need an .fdf file, just .XV and .FC > (.XV serves just to identify the atoms; exact coordinates are not > important). > Tell me if you'd encounter any difficulties. > > Best regards > > Andrei Postnikov > > > - Le 12 Sep 23, à 12:16, Diego Lopez Alcala diego.lo...@uv.es a écrit > : > > > Dear Siesta users, > > > > I have been trying to compute the modes of vibrations of a molecule > adsorbed on > > a semiconducting monolayer, but I am having some problems. First I run > this > > input: > > > > # General System descriptors > > > > SystemName vibra-2 # Descriptive name of the system > > SystemLabel vibra-2# Short name for naming files > > > > NumberOfAtoms 164 # Number of atoms > > NumberOfSpecies 5 # Number of species > > > > md.typeofrun fc > > > > MD.FCFirst 151 > > MD.FCLast 164 > > > > AtomicCoordinatesFormat NotScaledCartesianAng > > > > MM.UnitsDistance Ang # what this program prints out DO NOT CHANGE > > MM.UnitsEnergyeV # what this program prints out DO NOT CHANGE > > MM.Grimme.S6 0.75 # Grimme-paper for PBE (correct for your > functional) > > MM.Grimme.D 20. # Grimme-paper (correct for your functional) > > %block MM.Potentials > > 1 1 Grimme111.94 3.124 # Cr, 10.1002/jcc.20495 > > 1 2 Grimme 80.39 3.245 # Cr / S > > 1 3 Grimme120.28 3.311 # Cr / Br > > 1 4 Grimme 45.06 3.014 # Cr / C > > 1 5 Grimme 12.74 2.563 # Cr / H > > 2 2 Grimme 57.73 3.366 # S, 10.1002/jcc.20495 > > 2 3 Grimme 86.38 3.432 # S / Br > > 2 4 Grimme 32.36 3.135 # S / C > > 2 5 Grimme 9.15 2.684 # S / H > > 3 3 Grimme129.24 3.498 # Br, 10.1002/jcc.20495 > > 3 4 Grimme 48.42 3.201 # Br / C > > 3 5 Grimme 13.69 2.750 # Br / H > > 4 4 Grimme 18.14 2.904 # C, 10.1002/jcc.20495 > > 4 5 Grimme 5.13 2.453 # C / H > > 5 5 Grimme 1.45 2.002 # H, 10.1002/jcc.20495 > > %endblock MM.Potentials > > > > %block Chemical_Species_Label > > 1 24 Cr > > 2 16 S > > 3 35 Br > > 46 C > > 51 H > > %endblock Chemical_Species_Label > > > > PAO.BasisSize SZ > > > > DFTU.ProjectorGenerationMethod 1 > > DFTU.PotentialShift .true. > > > > %block DFTU.Proj # Define DFTU projectors > > Cr 1 # Label, l_shells > > n=3 2 # n (opt if not using semicore levels),l,Softconf(opt) > > 4.00 0.0 # U(eV), J(eV) for this shell > > 0.0 # rc (Bohr), \omega(Bohr) (Fermi cutoff function) > > %endblock DFTU.Proj > > > > # Lattice, coordinates, k-sampling > > > > AtomicCoorFormatOut Ang > > > > %block AtomicCoordinatesAndAtomicSpecies > > 4.44717269 3.68308271 0.75902034 3 79.904 > > . > > . (Rest of atomic coordinates) > > . > > 5.10327585 14.06972694 8.19442056 5 1.007 > > %endblock AtomicCoordinatesAndAtomicSpecies > > > > LatticeConstant 1.0 Ang > > > > %block LatticeVectors > > 17.8287990.000.00 > >0.00 24.3147200.00 > >0.000.00 25.236237 > > %endblock LatticeVectors > > > > %block kgrid_Monkhorst_Pack > > 1 0 0 0.0 > > 0 1 0 0.0 > > 0 0 1 0.0 > > %endblock kgrid_Monkhorst_Pack > > > > # DFT, Grid, SCF > > > > XC.functional GGA # Exchange-correlation functional > type > > XC.authors PBE # Particular parametrization of xc > func > > SpinPolarized .true. # Spin unpolarized calculation > > MeshCutoff 400. Ry # Equivalent planewave cutoff for > the grid > > MaxSCFIterations300 # Maximum number of SCF iterations > per step > > SCF.DM.Converge true > > SCF.H.Converge true > > > > # Eigenvalue problem: order-N or diagonalization > > > > SolutionMetho
[SIESTA-L] different energies at the end of siesta output
Hello Siesta experts, Can anyone please tell me what are the different energy values mentioned at the end of any siesta output file? In the tutorials there is the mention of free energy only. Are there any references to know what all these energies are ? Thanks in advance for your help. Regards, Sunetra Das.
Re: [SIESTA-L] Spin polarized calculation
Dear Emilio sir , Thank you very much for your help. On 25 September 2018 at 14:06, Emilio Artacho wrote: > Dear Sunetra > > InitSpin just sets up the initial density matrix to start the > self-consistency cycle. The spin polarisation at the end > of the SCF will be whatever spin-polarised DFT predicts > including the sin polarisation on atoms that you did not > include in the InitSpin block. > > The initialisation is needed because > > - the non-polarised solution is still a solution (saddle point but > a minimum until you break the spin symmetry), if both spin up and > spin down densities were equal at the start they would remain equal > till the end. (Siesta defaults to a vanilla ferromagnetic initialisation > when spin polarised is true, just to allow the calculation to escape > the spin-symmetric solution). > > - If the solution (minimum) is spin-polarised, there is always more > than one (e.g. if there is a ferromagnetic solution, there will be always > at least two, total spin being up or down). There can also be > different minima as ferromagnetic and antiferro, etc. As in any > minimisation with local minima, you’ll find one or the other > depending where you start from. What matters at the end > is the actual minima (solutions), especially the one (ones) with > lowest energy. But you have to ind them and for that you have > to try different starting points. > > Emilio > > > > On Sep 24, 2018, at 7:44 AM, Sunetra Das > wrote: > > > > Dear siesta experts, > > > > Please help me clarify a confusion, as I am unable to clear my doubt > from the manual. I am using siesta 4.0 version. > > > > I want to study the effect of doping on a non-magnetic system. I have > carried out spin polazied calculation on the pristine system and the > resulting total magnetic moment was zero. I did the same with a single > dopant atom with non zero total magnetic moment. Now after I introduce two > dopant atoms, I want to see if the atoms are ferromagnetically coupled or > antiferromagnetically, in ground state. I use the data block DM.InitSpin to > define the spin directions of the two dopant atoms only. I have also turned > the spin polarization option to .true.. Do I need to specify the spin > directions of the atoms of the doped system in the DM.InitSpin data block > or turning the spin polarization to .true. takes care of the atomic spins > outside the datablock? > > > > I want to see how the local magnetic moment of the atoms in the doped > system changes with introduction of dopant atoms. > > > > I have assumed the spins to be collinear. > > > > Thank you. > > Regards, > > Sunetra Das. > >
[SIESTA-L] Spin polarized calculation
Dear siesta experts, Please help me clarify a confusion, as I am unable to clear my doubt from the manual. I am using siesta 4.0 version. I want to study the effect of doping on a non-magnetic system. I have carried out spin polazied calculation on the pristine system and the resulting total magnetic moment was zero. I did the same with a single dopant atom with non zero total magnetic moment. Now after I introduce two dopant atoms, I want to see if the atoms are ferromagnetically coupled or antiferromagnetically, in ground state. I use the data block DM.InitSpin to define the spin directions of the two dopant atoms only. I have also turned the spin polarization option to .true.. Do I need to specify the spin directions of the atoms of the doped system in the DM.InitSpin data block or turning the spin polarization to .true. takes care of the atomic spins outside the datablock? I want to see how the local magnetic moment of the atoms in the doped system changes with introduction of dopant atoms. I have assumed the spins to be collinear. Thank you. Regards, Sunetra Das.
[SIESTA-L] cell vector not converged
Dear experts, I am trying to converge my system unitcell structure for k - mesh values. Even though the Free Energy value has converged for less denser mesh, the unit cell parameter has not converged for even 21x21x1 k mesh. The system is a 2D one with 3 atoms in the unit cell. I am attaching the file containing the k values and the corresponding free energy and cell parameter values along with the plotted graph. please have a look and help me. Is the free energy convergence enough? I have used systems before where I have checked if both the parameters have converged for a given k mesh. Thank you. Regards, Sunetra Das pse.dat Description: Netscape Proxy Auto Config
Re: [SIESTA-L] optimization
Dear Saif, I followed your instructions and have been able to achieve the stable configuration of my system. Thank you very much. Regards, Sunetra On 2 July 2018 at 20:41, Sunetra Das wrote: > Thank you very much for your kind help. > > > On Mon 2 Jul, 2018, 1:32 AM sullah, wrote: > >> Dear Sunetra, >> >> These links might be helpful. >> >> http://www.home.uni-osnabrueck.de/apostnik/Lectures/SIESTA-tuto.pdf >> >> http://personales.unican.es/junqueraj/JavierJunquera_ >> files/Metodos/Basis/Energy-Shift/Energy-Shift.pdf >> >> Best, >> >> Em 28.06.2018 17:38, Sunetra Das escreveu: >> >> Thank you Saif, >> I will use tighter force convergence like you said. >> >> Regarding the other three parameters, i.e. ElectronicTemperature , >> PAO.EnergyShift , and PAO.SplitNorm, how do I test the convergence ? I did >> not understand the basis set optimization from the tutorials. All I know is >> that PAO.EnergyShift has to be some positive number and PAO.SplitNorm >> should lie between the values 0.05 to 0.5, from the manual. Could you >> please tell me what to do and how to check the optimum values for these >> parameters? >> >> Regards, >> Sunetra >> >> On 28 June 2018 at 21:33, sullah wrote: >> >>> Dear Sunetra, >>> >>> It seems that the issue is due to the bad convergence criteria. >>> Generally, 1.d-6 is a good value for forces but for phonons, you may need >>> 1.d-8 (you are using DM.Tolerance 1.d-4). >>> >>> Furthermore, you are using (ElectronicTemperature 400 K, >>> PAO.EnergyShift 0.35 eV >>> PAO.SplitNorm 0.4), are you sure you need these values. Did you check >>> the convergence wrt the different values of these parameters ( especially >>> the EnergyShift and SplitNorm)? >>> >>> Best, >>> >>> Saif >>> >>> Em 27.06.2018 12:42, Sunetra Das escreveu: >>> >>> Hello Sullah, >>> >>> I have attached the input fdf file for your understanding of the >>> possible issue. >>> >>> Regards, >>> Sunetra >>> >>> On 26 June 2018 at 02:53, sullah wrote: >>> >>>> Dear Sunetra, >>>> >>>> It is difficult to say anything without taking a look at your input >>>> file(s). How many negative frequencies do you have at gamma? What is (are) >>>> the value(s) of the negative frequency(ies)? >>>> >>>> Anyways, this may be due to the bad convergence. I guess you are using >>>> the DZP basis set which is sufficient in most of the cases. Try to increase >>>> the value of mesh cutoff and keep a tight criterion for forces. >>>> >>>> I hope it helps. >>>> >>>> Best, >>>> >>>> >>>> Em 25.06.2018 01:31, Sunetra Das escreveu: >>>> >>>> Hello experts, >>>> >>>> I have been trying to optimize a 2D structure with 3 atoms in the unit >>>> cell. I am using CG by varying the cell dimensions. I have optimized the >>>> k-points and mesh cutoff. But no matter how many times I try to relax the >>>> structure, it is giving a negative phonon frequency at the gamma point. The >>>> structure is experimentally achieved structure with available .cif file. >>>> The cell dimensions achieved after relaxation are the same as the >>>> experimentally achieved one, with less than 2% deviation, and theoretical >>>> work publications show that the structure should come out to a stable one >>>> with no negative frequencies. >>>> >>>> Where can be the issue? I am using fully relativistic .psf files and >>>> spin-polarization is on. Can basis set optimization be an issue? >>>> Help please. >>>> >>>> Regards, >>>> Sunetra Das. >>>> >>>> >>>> >>> >>
Re: [SIESTA-L] optimization
Thank you very much for your kind help. On Mon 2 Jul, 2018, 1:32 AM sullah, wrote: > Dear Sunetra, > > These links might be helpful. > > http://www.home.uni-osnabrueck.de/apostnik/Lectures/SIESTA-tuto.pdf > > > http://personales.unican.es/junqueraj/JavierJunquera_files/Metodos/Basis/Energy-Shift/Energy-Shift.pdf > > Best, > > Em 28.06.2018 17:38, Sunetra Das escreveu: > > Thank you Saif, > I will use tighter force convergence like you said. > > Regarding the other three parameters, i.e. ElectronicTemperature , > PAO.EnergyShift , and PAO.SplitNorm, how do I test the convergence ? I did > not understand the basis set optimization from the tutorials. All I know is > that PAO.EnergyShift has to be some positive number and PAO.SplitNorm > should lie between the values 0.05 to 0.5, from the manual. Could you > please tell me what to do and how to check the optimum values for these > parameters? > > Regards, > Sunetra > > On 28 June 2018 at 21:33, sullah wrote: > >> Dear Sunetra, >> >> It seems that the issue is due to the bad convergence criteria. >> Generally, 1.d-6 is a good value for forces but for phonons, you may need >> 1.d-8 (you are using DM.Tolerance 1.d-4). >> >> Furthermore, you are using (ElectronicTemperature 400 K, PAO.EnergyShift >> 0.35 eV >> PAO.SplitNorm 0.4), are you sure you need these values. Did you check the >> convergence wrt the different values of these parameters ( especially the >> EnergyShift and SplitNorm)? >> >> Best, >> >> Saif >> >> Em 27.06.2018 12:42, Sunetra Das escreveu: >> >> Hello Sullah, >> >> I have attached the input fdf file for your understanding of the possible >> issue. >> >> Regards, >> Sunetra >> >> On 26 June 2018 at 02:53, sullah wrote: >> >>> Dear Sunetra, >>> >>> It is difficult to say anything without taking a look at your input >>> file(s). How many negative frequencies do you have at gamma? What is (are) >>> the value(s) of the negative frequency(ies)? >>> >>> Anyways, this may be due to the bad convergence. I guess you are using >>> the DZP basis set which is sufficient in most of the cases. Try to increase >>> the value of mesh cutoff and keep a tight criterion for forces. >>> >>> I hope it helps. >>> >>> Best, >>> >>> >>> Em 25.06.2018 01:31, Sunetra Das escreveu: >>> >>> Hello experts, >>> >>> I have been trying to optimize a 2D structure with 3 atoms in the unit >>> cell. I am using CG by varying the cell dimensions. I have optimized the >>> k-points and mesh cutoff. But no matter how many times I try to relax the >>> structure, it is giving a negative phonon frequency at the gamma point. The >>> structure is experimentally achieved structure with available .cif file. >>> The cell dimensions achieved after relaxation are the same as the >>> experimentally achieved one, with less than 2% deviation, and theoretical >>> work publications show that the structure should come out to a stable one >>> with no negative frequencies. >>> >>> Where can be the issue? I am using fully relativistic .psf files and >>> spin-polarization is on. Can basis set optimization be an issue? >>> Help please. >>> >>> Regards, >>> Sunetra Das. >>> >>> >>> >> >
Re: [SIESTA-L] optimization
Thank you Saif, I will use tighter force convergence like you said. Regarding the other three parameters, i.e. ElectronicTemperature , PAO.EnergyShift , and PAO.SplitNorm, how do I test the convergence ? I did not understand the basis set optimization from the tutorials. All I know is that PAO.EnergyShift has to be some positive number and PAO.SplitNorm should lie between the values 0.05 to 0.5, from the manual. Could you please tell me what to do and how to check the optimum values for these parameters? Regards, Sunetra On 28 June 2018 at 21:33, sullah wrote: > Dear Sunetra, > > It seems that the issue is due to the bad convergence criteria. Generally, > 1.d-6 is a good value for forces but for phonons, you may need 1.d-8 (you > are using DM.Tolerance 1.d-4). > > Furthermore, you are using (ElectronicTemperature 400 K, PAO.EnergyShift > 0.35 eV > PAO.SplitNorm 0.4), are you sure you need these values. Did you check the > convergence wrt the different values of these parameters ( especially the > EnergyShift and SplitNorm)? > > Best, > > Saif > > Em 27.06.2018 12:42, Sunetra Das escreveu: > > Hello Sullah, > > I have attached the input fdf file for your understanding of the possible > issue. > > Regards, > Sunetra > > On 26 June 2018 at 02:53, sullah wrote: > >> Dear Sunetra, >> >> It is difficult to say anything without taking a look at your input >> file(s). How many negative frequencies do you have at gamma? What is (are) >> the value(s) of the negative frequency(ies)? >> >> Anyways, this may be due to the bad convergence. I guess you are using >> the DZP basis set which is sufficient in most of the cases. Try to increase >> the value of mesh cutoff and keep a tight criterion for forces. >> >> I hope it helps. >> >> Best, >> >> >> Em 25.06.2018 01:31, Sunetra Das escreveu: >> >> Hello experts, >> >> I have been trying to optimize a 2D structure with 3 atoms in the unit >> cell. I am using CG by varying the cell dimensions. I have optimized the >> k-points and mesh cutoff. But no matter how many times I try to relax the >> structure, it is giving a negative phonon frequency at the gamma point. The >> structure is experimentally achieved structure with available .cif file. >> The cell dimensions achieved after relaxation are the same as the >> experimentally achieved one, with less than 2% deviation, and theoretical >> work publications show that the structure should come out to a stable one >> with no negative frequencies. >> >> Where can be the issue? I am using fully relativistic .psf files and >> spin-polarization is on. Can basis set optimization be an issue? >> Help please. >> >> Regards, >> Sunetra Das. >> >> >> >
Re: [SIESTA-L] optimization
Hello again, The system is getting stuck in a local minimum, it seems. How to bring the system to global minimum? Any help is highly appreciated. Thanks in advance. Sunetra. On 25 June 2018 at 10:01, Sunetra Das wrote: > Hello experts, > > I have been trying to optimize a 2D structure with 3 atoms in the unit > cell. I am using CG by varying the cell dimensions. I have optimized the > k-points and mesh cutoff. But no matter how many times I try to relax the > structure, it is giving a negative phonon frequency at the gamma point. The > structure is experimentally achieved structure with available .cif file. > The cell dimensions achieved after relaxation are the same as the > experimentally achieved one, with less than 2% deviation, and theoretical > work publications show that the structure should come out to a stable one > with no negative frequencies. > > Where can be the issue? I am using fully relativistic .psf files and > spin-polarization is on. Can basis set optimization be an issue? > Help please. > > Regards, > Sunetra Das. >
[SIESTA-L] optimization
Hello experts, I have been trying to optimize a 2D structure with 3 atoms in the unit cell. I am using CG by varying the cell dimensions. I have optimized the k-points and mesh cutoff. But no matter how many times I try to relax the structure, it is giving a negative phonon frequency at the gamma point. The structure is experimentally achieved structure with available .cif file. The cell dimensions achieved after relaxation are the same as the experimentally achieved one, with less than 2% deviation, and theoretical work publications show that the structure should come out to a stable one with no negative frequencies. Where can be the issue? I am using fully relativistic .psf files and spin-polarization is on. Can basis set optimization be an issue? Help please. Regards, Sunetra Das.
[SIESTA-L] gga pseudopotentials
Hello SIESTA users, I saw that the siesta website ( https://departments.icmab.es/leem/siesta/Databases/Pseudopotentials/periodictable-gga-abinit.html) does not have the GGA pseudopotentials for the elements La (atomic # 57) and W (atomic #74). Can anyone please tell me, from where can I get norm-conserving GGA psedopotential files for the said two elements? Or can anyone kindly share their input files for these two elements' pseudopotentials? Thanks in advance. Regards, Sunetra Das
Re: [SIESTA-L] Spin polarised band structure
Thank you all very much, especially Nick sir. I have successfully calculated the spin Polarized band structure of my system using the new band calculating code in siesta 4.0. Regards, Sunetra. On Fri 4 May, 2018, 1:36 AM Nick Papior, wrote: > > 2018-05-02 8:53 GMT+02:00 Sunetra Das : > >> Thank you every one for your help. >> >> All this time I have been using gnuplot utility code to calculate band >> structures for spin-polarized systems but instead of getting two output >> files, one for each spin, I was getting a single output file. Does that >> mean I have to modify the gnubands.f code each time accordingly to >> calculate the bands for a specific spin, recompile and run the code >> ? >> > No. > In version 4.0 gnubands there is a flag that lets you choose the > spin-index (gnubands -s 1|2). Please note that you probably need to use > new.gnubands.f90 (which will be the new default in the later 4.0 releases). > >> I am using 4.0 version of SIESTA. >> >> Regards, >> Sunetra Das. >> >> On 1 May 2018 at 13:05, Nick Papior wrote: >> >>> As far as I know, all versions of siesta can plot the band structure of >>> spin-polarized calculations. >>> >>> The gnubands utility post-processes the .bands file into gnuplot data >>> files which may be used to plot spin-polarized band structures. >>> >>> In versions 4.0 and later the gnubands utility has more options such >>> that one can extract each spin-component individually. This is easier in >>> the sense that you can extract bandstructure per spin to individual files. >>> >>> To plot the bandstructure you have to use your favourite plotting >>> utility. gnubands creates input ready to plot in gnuplot. >>> Prior versions to 4.0 >>> >>> 2018-04-30 11:10 GMT+02:00 Sunetra Das : >>> >>>> Dear fellow SIESTA users, >>>> >>>> I would like to know if SIESTA can plot spin-polarized band structure >>>> of a given system? In which of the latest version of the software can I >>>> find the feature to draw spin-polarized band structure? Any help is highly >>>> appreciated. >>>> >>>> Thanks in advance. >>>> >>>> Regards, >>>> Sunetra Das >>>> >>> >>> >>> >>> -- >>> Kind regards Nick >>> >> >> > > > -- > Kind regards Nick >
[SIESTA-L] eig2bxsf code error
Dear all SIESTA users, I am trying to use the post processing code eig2bxsf for mu system, which is giving me the following error: *Specify SystemLabel (or 'siesta' if none): GeC Found and opened: GeC.XV Found and opened: GeC.EIG nkp= 79 nbands= 418 is= 1 homo, lumo= 67 68 spin 1: band gap between bands67 and 68 is= 2 homo, lumo= 64 65 spin 2: band gap between bands64 and65 Found and opened: GeC.KPNo. of divisions seems to be 12 12 0 Full No. of k-points on general grid: 169Program received signal SIGFPE: Floating-point exception - erroneous arithmetic operation.Backtrace for this error:#0 0x7F00CB3EC777#1 0x7F00CB3ECD7E#2 0x7F00CB040CAF#3 0x40264E in ene2bxsf at eig2bxsf.f:159 (discriminator 2)Floating point exception (core dumped)* How to solve this error? Please help me in this regard. Thank you in advance. Regards, Sunetra Das.
Re: [SIESTA-L] Spin polarised band structure
Thank you every one for your help. All this time I have been using gnuplot utility code to calculate band structures for spin-polarized systems but instead of getting two output files, one for each spin, I was getting a single output file. Does that mean I have to modify the gnubands.f code each time accordingly to calculate the bands for a specific spin, recompile and run the code ? I am using 4.0 version of SIESTA. Regards, Sunetra Das. On 1 May 2018 at 13:05, Nick Papior wrote: > As far as I know, all versions of siesta can plot the band structure of > spin-polarized calculations. > > The gnubands utility post-processes the .bands file into gnuplot data > files which may be used to plot spin-polarized band structures. > > In versions 4.0 and later the gnubands utility has more options such that > one can extract each spin-component individually. This is easier in the > sense that you can extract bandstructure per spin to individual files. > > To plot the bandstructure you have to use your favourite plotting utility. > gnubands creates input ready to plot in gnuplot. > Prior versions to 4.0 > > 2018-04-30 11:10 GMT+02:00 Sunetra Das : > >> Dear fellow SIESTA users, >> >> I would like to know if SIESTA can plot spin-polarized band structure of >> a given system? In which of the latest version of the software can I find >> the feature to draw spin-polarized band structure? Any help is highly >> appreciated. >> >> Thanks in advance. >> >> Regards, >> Sunetra Das >> > > > > -- > Kind regards Nick >
[SIESTA-L] Spin polarised band structure
Dear fellow SIESTA users, I would like to know if SIESTA can plot spin-polarized band structure of a given system? In which of the latest version of the software can I find the feature to draw spin-polarized band structure? Any help is highly appreciated. Thanks in advance. Regards, Sunetra Das
[SIESTA-L] convergence with respect to k mesh
Dear Siesta users, I have been trying to optimize a 32 atom 2D supercell of Germanium Carbide. For that I am trying to test the convergence of my system with respect to the k-mesh value. Following according to the siesta hands on tutorial, I have run optimization of the system with k-mesh value starting from 4x4x1 up to 30x30x1. Now even though the lattice parameter has obtained a constant value from 20x20x1 k-mesh, the free energy values are fluctuating very much, even near 30x30x1 k-mesh. I am attaching a data file listing the k-mesh used and the corresponding free energies, lattice parameters and pressures. #kfree_energy(eV) a(Ang)press(kBar) #--- 4-4404.68656913.0719191.58775270 5-4404.69200913.0719261.57574542 6-4404.68364413.0719201.58159257 7-4404.69038313.0719181.58333081 8-4404.69046813.0719201.58158769 9-4404.65695013.0719181.58728229 10-4404.68947913.0719201.58758950 11-4404.65124213.0719231.55663793 12-4404.65243013.0719241.55242216 13-4404.65278513.0719241.55406592 14-4404.69045313.0719171.58822447 15-4404.69032613.0719201.58736858 16-4404.64894613.0719241.58553524 17-4404.69040913.0719191.58581311 18-4404.65669513.0719241.51914825 19-4404.64795313.0719231.56108155 20-4404.65682313.0719241.51265983 21-4404.66229813.0719241.56920158 22-4404.66009913.0719251.57130732 23-4404.65439413.0719241.52465516 24-4404.66623513.0719241.56528804 25-4404.65527313.0719241.51864296 26-4404.65496913.0719241.57698239 27-4404.65402613.0719241.51899044 28-4404.66068613.0719241.57076477 29-4404.64796513.0719241.58495969 30-4404.65091813.0719241.58155660 I have been optimizing the above structure with spin-polarization turned ON. Is it the reason why the free energy values are not reaching a converged value? Should I carry out the convergence tests with spin-polarization option turned off and turn it on only while calculating bands, DOS and other properties? Please help me in this regard. Thank YOu in advance. Sunetra Das
Re: [SIESTA-L] Auxiliary supercell needs to be larger than naive one...
Thank you Sir, for your kind help. On 8 February 2018 at 10:51, Nick Papior wrote: > Dear Sunetra, > > You can try and set this variable: > > NaiveAuxiliaryCell true > > and sometimes this may help as well: > FixAuxiliaryCell true > > 2018-02-07 10:16 GMT+01:00 Sunetra Das : > >> Dear SIESTA users, >> >> I have a 2D supercell of 32 atoms which structure I have relaxed. Then I >> wanted to calculate the optical and magnetic properties of this relaxed >> structure. >> In the output file I a getting the following warning, which I do not know >> how to solve: >> >> >> >> >> >> >> >> >> >> *Naive supercell factors: 222Auxiliary supercell needs to be >> larger than naive one...Auxiliary supercell needs to be larger than naive >> one...superc: Internal auxiliary supercell: 3 x 2 x 2 = >> 12superc: Number of atoms, orbitals, and projectors:384 5040 >> 5424Auxiliary supercell needs to be larger than naive one...Auxiliary >> supercell needs to be larger than naive one...* >> Can somebody please help me in this regard as to Which options to modify >> so that this is solved? >> >> Thank You. >> Regards, >> Sunetra Das. >> >> > > > -- > Kind regards Nick >
[SIESTA-L] Auxiliary supercell needs to be larger than naive one...
Dear SIESTA users, I have a 2D supercell of 32 atoms which structure I have relaxed. Then I wanted to calculate the optical and magnetic properties of this relaxed structure. In the output file I a getting the following warning, which I do not know how to solve: *Naive supercell factors: 222Auxiliary supercell needs to be larger than naive one...Auxiliary supercell needs to be larger than naive one...superc: Internal auxiliary supercell: 3 x 2 x 2 = 12superc: Number of atoms, orbitals, and projectors:384 5040 5424Auxiliary supercell needs to be larger than naive one...Auxiliary supercell needs to be larger than naive one...* Can somebody please help me in this regard as to Which options to modify so that this is solved? Thank You. Regards, Sunetra Das.
Re: [SIESTA-L] Bands at lower energies
Dear All, Thank you very much for answering my query. I have been trying to reproduce the TDOS for a reported half metallic system, as well, and the Fermi level in this case is lying in a region with non-zero DOS for both the spins, even though the DOS looks the same as reported in published data. Here the relative positioning of the Fermi level with the bands did change the nature of the studied structure. Where am I going wrong? If someone please elaborates this to me, I will be thankful. Regards, Sunetra Das. On 2 February 2018 at 11:23, Nick Papior wrote: > A Fermi level is *only* well defined for metallic systems where there are > no band-gabs. When determining the Fermi level for gabbed materials it may > be arbitrarily chosen in the gabbed region. > > Often one chooses the fermi level to lie *exactly* in the middle of the > gab. However you have to manually shift the energies in the band-structure. > > Note that the important thing is that the number of electrons at the Fermi > level corresponds to the valence charge. With this in mind it should be > clear why the fermi level cannot be uniquely determined for gabbed > materials. > > 2018-02-01 9:12 GMT+01:00 Sunetra Das : > >> Dear all Siesta users, >> >> I am trying to calculate and reproduce the band structure for a certain >> 2D system. The band structure of the system has already been calculated >> using a different software and published. Even though the band structure >> remains the same when calculated using Siesta, the bands are forming at >> lower energy values with respect to the Fermi level. >> How to correct this mismatch and get the bands at their correct energies? >> In my calculation the Fermi level lies near the conduction band whereas in >> the already published data the Fermi level lies very close to the valence >> band. Is there any way to correct for this discrepancy? >> The calculations have been performaned in GGA-PBE exchange correlation >> functional as was done in published data. >> Any suggestion is humbly appreciated. >> >> Thankfully, >> Sunetra Das. >> > > > > -- > Kind regards Nick >
[SIESTA-L] Bands at lower energies
Dear all Siesta users, I am trying to calculate and reproduce the band structure for a certain 2D system. The band structure of the system has already been calculated using a different software and published. Even though the band structure remains the same when calculated using Siesta, the bands are forming at lower energy values with respect to the Fermi level. How to correct this mismatch and get the bands at their correct energies? In my calculation the Fermi level lies near the conduction band whereas in the already published data the Fermi level lies very close to the valence band. Is there any way to correct for this discrepancy? The calculations have been performaned in GGA-PBE exchange correlation functional as was done in published data. Any suggestion is humbly appreciated. Thankfully, Sunetra Das.
[SIESTA-L] optical properties and electronic transitions
Dear SIESTA users, I have performed optical property calculation for my system but confused how to tally the obtained results with various inter/intraband transitions? I am not sure if the transitions are interband or intraband as well. Can someone please enlighten me in this regard or guide me towards some reference? Is there any code included in the siesta package which might help in determining the bands across which electronic transitions are taking place to give the obtained optical results? If no code is available then how to determine the corresponding bands across which the transitions are taking place? Any suggestion is very much appreciated. Thanks in advance. Regards, Sunetra Das
Re: [SIESTA-L] problem with converging mesh-cutoff and K-grid points
Thank you Javier Junquera Sir. On 27 December 2017 at 17:00, Javier Junquera wrote: > > Dear Sunetra: > > Take look at: > > http://personales.unican.es/junqueraj/JavierJunquera_ > files/Metodos/Hands-on-session.html > > And then follow the links to: > > 5. Converging the simulations > > Exercise 4. Convergence of the simulation with respect the MeshCutoff. > The egg box effect. > > Hope this helps, > > Best regards, > > Javier > > > El 26 dic 2017, a las 4:32, Sunetra Das > escribió: > > Dear Andrei Postnikov Sir, > > Can you please guide me in how to do the 'eggbox test' ? I have gone > through the tutorials and examples but am still unclear on how to do that > test for a system. Will be very much thankful if you let me know the steps > on testing the eggbox effect and eliminating it. I have seen the term > 'eggbox energy' in siesta output file after completion of a run, but > confused what to decipher from it. > Thanking you and awaiting a reply. > > Warm regards and wishing you a happy new year in advance, > Sunetra Das. > > On 25 December 2017 at 19:52, Andrei Postnikov lorraine.fr> wrote: > >> Dear Najmeh, >> >> you are worrying about z-components of forces >> and try to help it by increasing the k(xy) mesh. It means that your >> bands dispersion becomes ever better in the plane, >> however, I don't think this would have an important effect on the >> z-force! >> >> Three observations: >> >> 1) >> Do you really have a problem? >> Your z-forces on atoms 1 and 2 do nicely sum up to zero within 0.001 - >> that is fine, - >> and the fact that they (individually) fluctuate with k simply reveals the >> fact >> that your structure is not at equilibrium. Try to get a better >> equilibrium - see 2). >> If you ultimate goal is phonons, why don't you calculate just Gamma >> and check if you get the acoustic modes close enough to zero? >> >> 2) >> In order to suppress fluctuations of forces / energy, >> the MeshCutoff is probably much more important that k-mesh. >> Apparently you tried 300 Ry and did not increase it any further. >> It might be not sufficient, depending on pseudos / basis. >> (However, it might well be OK in your case, see 1). >> In order to understand what's going on, the eggbox test >> (rigidly moving all the atoms... along Z, your "problematic" direction) >> for different values of MeshCutoff would help. >> With insufficient MeshCutoff, the increase of the k-mesh alone won't >> help you. >> (and... do you really need 20 Ang in the z-direction? You only need >> so much that the basis functions won't overlap). >> >> 3) >> The k-mesh is not a variational parameter, >> so you cannot expect a systematic lowering of the total energy >> (although it usually happens, albeit with fluctuations). >> For the phonon calculations, the total energy as such (i.e., >> its absolute value) is irrelevant anyway. >> >> Best regards >> >> Andrei Postnikov >> >> >> - Najmeh Honari a écrit : >> > >> Dear >> > Siesta users, >> >> > >> > >> >> I’m >> > trying to simulate 2D borophene δ*6*, in order to calculate phonon >> dispersion of the material. I did convergence >> > test for mesh-cut-off and k-points. I selected mesh cutoff=300Ry and >> started >> > k-grid from 12x12x1 and increased it to 40x40x1. The issue is that >> neither “total >> > energy” nor the “forces on atoms” are converged in other words >> fluctuations of >> > energies and forces are obsereved. Here are a table of some energy and >> forces >> > for different k-grid meshes of borophene >> > structure: >> >> > >> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> >> > >> >> K-grid >> >> > >> > >> >> Total >> > Energy (eV) >> >> > >> > >> >> Atomic >> > forces (eV/A) >> >> > >> >> > >> >> 15x15 >> >> > >> > >> >> -206.414196 >> >> > >> > >> >> 1 -0.01 -0.05 >> > -0.131499 >> >> > >> >> 2 -0.02 -0.04
Re: [SIESTA-L] Fwd: problem with converging mesh-cutoff and K-grid points
Dear Andrei Postnikov Sir, Can you please guide me in how to do the 'eggbox test' ? I have gone through the tutorials and examples but am still unclear on how to do that test for a system. Will be very much thankful if you let me know the steps on testing the eggbox effect and eliminating it. I have seen the term 'eggbox energy' in siesta output file after completion of a run, but confused what to decipher from it. Thanking you and awaiting a reply. Warm regards and wishing you a happy new year in advance, Sunetra Das. On 25 December 2017 at 19:52, Andrei Postnikov < andrei.postni...@univ-lorraine.fr> wrote: > Dear Najmeh, > > you are worrying about z-components of forces > and try to help it by increasing the k(xy) mesh. It means that your > bands dispersion becomes ever better in the plane, > however, I don't think this would have an important effect on the z-force! > > Three observations: > > 1) > Do you really have a problem? > Your z-forces on atoms 1 and 2 do nicely sum up to zero within 0.001 - > that is fine, - > and the fact that they (individually) fluctuate with k simply reveals the > fact > that your structure is not at equilibrium. Try to get a better equilibrium > - see 2). > If you ultimate goal is phonons, why don't you calculate just Gamma > and check if you get the acoustic modes close enough to zero? > > 2) > In order to suppress fluctuations of forces / energy, > the MeshCutoff is probably much more important that k-mesh. > Apparently you tried 300 Ry and did not increase it any further. > It might be not sufficient, depending on pseudos / basis. > (However, it might well be OK in your case, see 1). > In order to understand what's going on, the eggbox test > (rigidly moving all the atoms... along Z, your "problematic" direction) > for different values of MeshCutoff would help. > With insufficient MeshCutoff, the increase of the k-mesh alone won't help > you. > (and... do you really need 20 Ang in the z-direction? You only need > so much that the basis functions won't overlap). > > 3) > The k-mesh is not a variational parameter, > so you cannot expect a systematic lowering of the total energy > (although it usually happens, albeit with fluctuations). > For the phonon calculations, the total energy as such (i.e., > its absolute value) is irrelevant anyway. > > Best regards > > Andrei Postnikov > > > - Najmeh Honari a écrit : > > > Dear > > Siesta users, > > > > > > > I’m > > trying to simulate 2D borophene δ*6*, in order to calculate phonon > dispersion of the material. I did convergence > > test for mesh-cut-off and k-points. I selected mesh cutoff=300Ry and > started > > k-grid from 12x12x1 and increased it to 40x40x1. The issue is that > neither “total > > energy” nor the “forces on atoms” are converged in other words > fluctuations of > > energies and forces are obsereved. Here are a table of some energy and > forces > > for different k-grid meshes of borophene > > structure: > > > > >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> > > > > > K-grid > > > > > > > Total > > Energy (eV) > > > > > > > Atomic > > forces (eV/A) > > > > > > > > 15x15 > > > > > > > -206.414196 > > > > > > > 1 -0.01 -0.05 > > -0.131499 > > > > > 2 -0.02 -0.040.131227 > > > > > > > > 17x17 > > > > > > > -206.410794 > > > > > > > 10.00 -0.03 > > -0.423281 > > > > > 20.04 -0.010.423056 > > > > > > > > 20x20 > > > > > > > -206.413284 > > > > > > > 10.01 -0.06 > > -0.287325 > > > > > 2 -0.020.020.287087 > > > > > > > > 23x23 > > > > > > > -206.414429 > > > > > > > 10.00 -0.00 > > -0.355986 > > > > > 2 -0.02 -0.050.355733 > > > > > > > > 25x25 > > > > > > > -206.423565 > > > > > > > 1 -0.01 -0.00 > > -0.416997 > > > > > 2 -0.02 -0.030.416772 > > > > > > > > 27x27 > > > > > > > -206.424037 > > > > > > &
Re: [SIESTA-L] error in parallel installation
Dear Nick Sir, Thank you for your guidance. Which one should I use for all the compilations? mpich or openmpi? I have tried using openmpi for all compilations, blacs and siesta and the other related packages. Then the installation gets completed error free, but which running siesta in parallel, I get the following error message: *Program received signal SIGSEGV: Segmentation fault - invalid memory reference.Backtrace for this error:Program received signal SIGSEGV: Segmentation fault - invalid memory reference.Backtrace for this error:Program received signal SIGSEGV: Segmentation fault - invalid memory reference.Backtrace for this error:Program received signal SIGSEGV: Segmentation fault - invalid memory reference.Backtrace for this error:#0 0x7FB354DAA6F7#1 0x7FB354DAAD3E#2 0x7FB35409326F#0 0x7F6E0BF3B6F7#1 0x7F6E0BF3BD3E#2 0x7F6E0B22426F#3 0x7FB35510DE2A#3 0x7F6E0C29EE2A#0 0x7F94B84896F7#1 0x7F94B8489D3E#2 0x7F94B777226F#3 0x7F94B87ECE2A#0 0x7F6CDA7CF6F7#1 0x7F6CDA7CFD3E#2 0x7F6CD9AB826F#3 0x7F6CDAB32E2A#4 0x7319B3 in BI_TransUserComm#5 0x72B476 in blacs_gridmap_#6 0x72B1B8 in blacs_gridinit_#4 0x7319B3 in BI_TransUserComm#7 0x4AE8AC in cdiag_ at cdiag.F:247#5 0x72B476 in blacs_gridmap_#4 0x7319B3 in BI_TransUserComm#8 0x434AD1 in diagk_ at diagk.F:177#6 0x72B1B8 in blacs_gridinit_#5 0x72B476 in blacs_gridmap_#9 0x4230FE in diagon_ at diagon.F:305#4 0x7319B3 in BI_TransUserComm#6 0x72B1B8 in blacs_gridinit_#5 0x72B476 in blacs_gridmap_#10 0x4C584E in __m_compute_dm_MOD_compute_dm at compute_dm.F:60#6 0x72B1B8 in blacs_gridinit_#11 0x4DD8A5 in __m_siesta_forces_MOD_siesta_forces at siesta_forces.F:80#7 0x4AE8AC in cdiag_ at cdiag.F:247#7 0x4AE8AC in cdiag_ at cdiag.F:247#8 0x434AD1 in diagk_ at diagk.F:177#8 0x434AD1 in diagk_ at diagk.F:177#9 0x4230FE in diagon_ at diagon.F:305#7 0x4AE8AC in cdiag_ at cdiag.F:247#9 0x4230FE in diagon_ at diagon.F:305#10 0x4C584E in __m_compute_dm_MOD_compute_dm at compute_dm.F:60#8 0x434AD1 in diagk_ at diagk.F:177#10 0x4C584E in __m_compute_dm_MOD_compute_dm at compute_dm.F:60#11 0x4DD8A5 in __m_siesta_forces_MOD_siesta_forces at siesta_forces.F:80#11 0x4DD8A5 in __m_siesta_forces_MOD_siesta_forces at siesta_forces.F:80#9 0x4230FE in diagon_ at diagon.F:305#10 0x4C584E in __m_compute_dm_MOD_compute_dm at compute_dm.F:60#11 0x4DD8A5 in __m_siesta_forces_MOD_siesta_forces at siesta_forces.F:80--mpirun noticed that process rank 2 with PID 0 on node loadbalancer exited on signal 11 (Segmentation fault).* Please help me out in this regard. What does the error mean and how can it be solved? Thank you. Respectfully, Sunetra Das
[SIESTA-L] 'Segmentation fault - invalid memory reference' when running siesta in parallel
Hello siesta users, I am getting the following error whenever I am running siesta-3.2-pl3 in parallel. Can anyone please tell me what these errors mean? Any help is appreciated. *Program received signal SIGSEGV: Segmentation fault - invalid memory reference.Backtrace for this error:Program received signal SIGSEGV: Segmentation fault - invalid memory reference.Backtrace for this error:Program received signal SIGSEGV: Segmentation fault - invalid memory reference.Backtrace for this error:Program received signal SIGSEGV: Segmentation fault - invalid memory reference.Backtrace for this error:#0 0x7FB354DAA6F7#1 0x7FB354DAAD3E#2 0x7FB35409326F#0 0x7F6E0BF3B6F7#1 0x7F6E0BF3BD3E#2 0x7F6E0B22426F#3 0x7FB35510DE2A#3 0x7F6E0C29EE2A#0 0x7F94B84896F7#1 0x7F94B8489D3E#2 0x7F94B777226F#3 0x7F94B87ECE2A#0 0x7F6CDA7CF6F7#1 0x7F6CDA7CFD3E#2 0x7F6CD9AB826F#3 0x7F6CDAB32E2A#4 0x7319B3 in BI_TransUserComm#5 0x72B476 in blacs_gridmap_#6 0x72B1B8 in blacs_gridinit_#4 0x7319B3 in BI_TransUserComm#7 0x4AE8AC in cdiag_ at cdiag.F:247#5 0x72B476 in blacs_gridmap_#4 0x7319B3 in BI_TransUserComm#8 0x434AD1 in diagk_ at diagk.F:177#6 0x72B1B8 in blacs_gridinit_#5 0x72B476 in blacs_gridmap_#9 0x4230FE in diagon_ at diagon.F:305#4 0x7319B3 in BI_TransUserComm#6 0x72B1B8 in blacs_gridinit_#5 0x72B476 in blacs_gridmap_#10 0x4C584E in __m_compute_dm_MOD_compute_dm at compute_dm.F:60#6 0x72B1B8 in blacs_gridinit_#11 0x4DD8A5 in __m_siesta_forces_MOD_siesta_forces at siesta_forces.F:80#7 0x4AE8AC in cdiag_ at cdiag.F:247#7 0x4AE8AC in cdiag_ at cdiag.F:247#8 0x434AD1 in diagk_ at diagk.F:177#8 0x434AD1 in diagk_ at diagk.F:177#9 0x4230FE in diagon_ at diagon.F:305#7 0x4AE8AC in cdiag_ at cdiag.F:247#9 0x4230FE in diagon_ at diagon.F:305#10 0x4C584E in __m_compute_dm_MOD_compute_dm at compute_dm.F:60#8 0x434AD1 in diagk_ at diagk.F:177#10 0x4C584E in __m_compute_dm_MOD_compute_dm at compute_dm.F:60#11 0x4DD8A5 in __m_siesta_forces_MOD_siesta_forces at siesta_forces.F:80#11 0x4DD8A5 in __m_siesta_forces_MOD_siesta_forces at siesta_forces.F:80#9 0x4230FE in diagon_ at diagon.F:305#10 0x4C584E in __m_compute_dm_MOD_compute_dm at compute_dm.F:60#11 0x4DD8A5 in __m_siesta_forces_MOD_siesta_forces at siesta_forces.F:80--mpirun noticed that process rank 2 with PID 0 on node loadbalancer exited on signal 11 (Segmentation fault).* Thank you in advance. Sincerely, Sunetra Das.
[SIESTA-L] error in parallel installation
ep/SIESTA-PARALLEL/BLACS/LIB/blacsF77init_MPI-LINUX-0.aSCALAPACK_LIBS=/home/joydeep/SIESTA-PARALLEL/scalapack-1.8.0/libscalapack.aCOMP_LIBS=dc_lapack.aNETCDF_LIBS=NETCDF_INTERFACE=LIBS=$(SCALAPACK_LIBS) $(BLACS_LIBS) $(LAPACK_LIBS) $(BLAS_LIBS) $(NETCDF_LIBS)#SIESTA needs an F90 interface to MPI#This will give you SIESTA's own implementation#If your compiler vendor offers an alternative, you may change#to it here.MPI_INTERFACE=libmpi_f90.aMPI_INCLUDE=.#Dependency rules are created by autoconf according to whether#discrete preprocessing is necessary or not..F.o:$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_fixed_F) $<.F90.o:$(FC) -c $(FFLAGS) $(INCFLAGS) $(FPPFLAGS) $(FPPFLAGS_free_F90) $<.f.o:$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_fixed_f) $<.f90.o:$(FC) -c $(FFLAGS) $(INCFLAGS) $(FCFLAGS_free_f90) $<* Any suggestion would be appreciated. Please help me in solving the issue. Thank you in advance. Regards, Sunetra Das
Re: [SIESTA-L] siesta-4.0 version vibra
Hello all, Please pardon me my mistake, the version of siesta I am using for 'vibra' is seista-3.0-b Thank You. Sincerely, Sunetra Das On 2 September 2017 at 10:39, Sunetra Das wrote: > Hello SIESTA users, > > I am using the vibra package of siesta-4.0 version to check the phonon > frequencies for my 32 atom planar system. Upon running 'fcbuild' I have not > faced any issue but while calculation the force constant matrix, I am > getting the following error: > > NOTE: orbital pair 1 172 (at least) is multiply connected. > NOTE: Harmless for Gamma calculations, except if a COHP analysis is > intended. > > I am clueless about the above NOTEs shown in the output file. What does > the 'orbital pair 1' , '172 (atleast) is multiply connected' indicate and > how can I solve the issue? I have never come across such warnings, if it is > at all a warning to be worried about. > > Any suggestion is highly appreciated. > > Thank you. > > Sunetra Das >
[SIESTA-L] siesta-4.0 version vibra
Hello SIESTA users, I am using the vibra package of siesta-4.0 version to check the phonon frequencies for my 32 atom planar system. Upon running 'fcbuild' I have not faced any issue but while calculation the force constant matrix, I am getting the following error: NOTE: orbital pair 1 172 (at least) is multiply connected. NOTE: Harmless for Gamma calculations, except if a COHP analysis is intended. I am clueless about the above NOTEs shown in the output file. What does the 'orbital pair 1' , '172 (atleast) is multiply connected' indicate and how can I solve the issue? I have never come across such warnings, if it is at all a warning to be worried about. Any suggestion is highly appreciated. Thank you. Sunetra Das
Re: [SIESTA-L] Plotting Bandstructure in Siesta
Hello All, In regard to the ongoing discussion about band structure, I have a query since I am newly working in this field of computational solid state physics. While calculating band structure, Is it absolutely necessary that I calculate the band structure of a unit cell and not of a supercell? If during structural relaxation I am using a supercell, will the calculated band structure of a supercell be the same as that of a unit cell band structure in that case? How do I get the unit cell parameters from the supercell relaxation output? Is there any code to extract the unit cell data from the SIESTA output files for a supercell? Any hints in this regard is highly appreciated. Thank you in advance. Sunetra Das Dept. of Physics, MMC College, Kolkata, India. On 6 July 2017 at 01:40, Ritwik Vatsyayan wrote: > Dear Aakanksha, > I am using XCrysDen version 1.5.60. > > > Regards, > Ritwik > > On Mon, Jul 3, 2017 at 1:53 AM, AAKANKSHA SUD > wrote: > >> Dear Ritwik >> I am happy that my suggestions were helpful to you. I was just >> wondering that how did you open .xyz file in xcrysden because such files >> cannot be opened in it. Perhaps you are using some other version.I would >> really appreciate if you could tell me that which version of xcrysden are >> you using that supports .xyz file. >> >> Thanks >> Aakanksha >> -- >> From: Ritwik Vatsyayan >> Sent: 7/3/2017 1:30 AM >> >> To: siesta-l@uam.es >> Subject: Re: [SIESTA-L] Plotting Bandstructure in Siesta >> >> Dear Aakanksha, >> Thank you so much for that tip. I was >> normally using the .xyz file generated from siesta run after optimizing the >> geometry, but I guess that will not give the information about the >> k-points. >> I really appreciate your time and effort in this. >> >> Best Regards, >> Ritwik >> >> On Sat, Jul 1, 2017 at 7:24 AM, AAKANKSHA SUD < >> aakankshasood0...@gmail.com> wrote: >> >>> Hi ritwik >>> Could you please elaborate the steps you followed. First you have to >>> optimise the geometry . So after optimisation you will get .xv file. There >>> is a utility in siesta xv2xsf . Use that to generate .xsf file.Now open >>> that file in xcrysden and generate the kpoints. After that do the >>> calculation for bandstructure. Hope it helps. >>> >>> Regards >>> Aakanksha >>> -- >>> From: Ritwik Vatsyayan >>> Sent: 7/1/2017 1:31 AM >>> To: siesta-l@uam.es >>> Subject: Re: [SIESTA-L] Plotting Bandstructure in Siesta >>> >>> Dear Aakanksha, >>>Thank you for suggesting XCrysDen. I >>> wanted to know that when you are using xcrysden to generate the k-points, >>> what is the extension of the file you use as the input? I tried using the >>> SystemLabel.xyz file, but it doesn't give me the option for making k-path. >>> Is there some other file generated by Siesta which can be used? >>> >>> Regards, >>> Ritwik Vatsyayan >>> >>> On Thu, Jun 29, 2017 at 1:59 AM, AAKANKSHA SUD < >>> aakankshasood0...@gmail.com> wrote: >>> >>>> Hi Ritwik >>>> It would be better if you use xcrysden to know the high symmetry pts. >>>> And using xcrysden you can easily generate the kpoints based on the >>>> brillouin zone.and its necessary to use a cyclic closed path. We are >>>> defining a region of brilliouin zone and by repeating it we can define >>>> whole zone so its necessary to specify the cyclic path. And specifying the >>>> number of intersections between two k points is also necessary. Regarding >>>> the reciprocal lattice vectors or fractional it depends like in which >>>> coordinates you are specifying the kpoints. I insist that you should use >>>> xcrysden or some other kpoint generating software . >>>> >>>> Hope it helps.. >>>> >>>> Regards >>>> Aakanksha >>>> -- >>>> From: Ritwik Vatsyayan >>>> Sent: 6/29/2017 1:32 AM >>>> To: siesta-l@uam.es >>>> Subject: [SIESTA-L] Plotting Bandstructure in Siesta >>>> >>>> Dear Siesta Users, >>>> I am working on a system with a >>>> hexagonal lattice, and I want to plot the bandstructure for the same. >>>> I read online at: https://lampx
[SIESTA-L] unable to attain global minimum
Dear all SIESTA users, I have been trying to optimize a 2D structure (slab) using CG scheme. I am using DZP basis set and a relativistic pseudopotential for my system. I am tweaking the flags MD.MaxforceTol and DM.Energy.Tolerance to get the lowest energy stable configuration. Even though the phonon curve shows my relaxed structure to be a stable one, the actual structure is coming out very much different from the already published structure. I have checked that the published structure is also a stable one, using phonon. Now I think that the structure obtained by me is getting trapped in a local minimum on the PES. What is the method in SIESTA to know for sure and check that my structure has attained the global minimum or not? Also what to do to bring the configuration out of a local minimum and make it attain attain the global minimum? Will a different scheme other than CG help? Any suggestion is very much appreciated. Thank you in advance. Sunetra Das.
[SIESTA-L] Relativistic pseudopotential and spin polarization
Dear Siesta users, I am using a fully relativistic pseudopotential file for one of my calculations. Is it absolutely essential that I keep the SpinPolarized option to .true. ? Thanks in advance. Regards, Sunetra Das.
Re: [SIESTA-L] structure optimization
The results came out to be the same even after using a less stricter convergence criteria. Thank you all for helping. Regards, Sunetra. On 16 April 2017 at 03:18, berna uyanık wrote: > May be, decreasing value of MaxForceTol helps. > > 2017-04-14 23:17 GMT+03:00 : > >> Is there any physical reason why you think that the hexagonal symmetry >> must preserve? >> >> Ruslan Zhachuk >> >> Sent from my iPhone >> >> On 14 апр. 2017 г., at 17:09, Sunetra Das >> wrote: >> >> Hello SIESTA users, >> >> I am facing a difficulty during while trying to fully relax a 32 atom >> graphene like 2D system with and without a single vacancy, in the middle of >> the srtucture. >> A part of my input .fdf file is given below: >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> *DM.Tolerance 1.d-3DM.Require.Energy.Convergence >> TDM.Energy.Tolerance 1.d-5 eVPAO.BasisSize DZPPAO.EnergyShift 0.3 >> eVMD.TypeOfRun CGMaxSCFIterations 3000MD.NumCGsteps >> 3000MD.VariableCell TMD.MaxForceTol0.02 eV/AngMeshCutoff300 >> RyDM.MixingWeight 0.02DM.NumberPulay 3WriteCoorXmol >> TWriteMullikenPop0XC.functional GGAXC.authors >> PBESolutionMethod diagonElectronicTemperature 300 K* >> The lattice constant of the system, the bond length and bond angle used >> by me has already been reported in a reputed journal, as a stable one. I >> have not used any constraints in my structure. I have created a 4x4x1 >> supercell using the reported dimensions and trying to optimize the >> structure with the siesta code version 3.2-pl-5. The problem I am facing is >> that the optimized structure is no longer of the symmetry I started with. >> The structure is no longer a hexagonal honeycomb one anymore. >> Also while using a vacancy defect in the structure the atoms are getting >> asymmetrically arranged breaking any symmetry that was present there. >> Now my question is, are there any more parameters that I should have >> specified in the input .fdf file? >> Or, will a change in the .psf file can bring about any improvement in the >> optimization? >> Also, if I apply some constraints like fixing the bond angles or that my >> structure should relax only in a single plane, then how can I say that all >> the atoms in my structure are FULLY relaxed? >> >> Please kindly help me in this regard. I feel like I am missing some >> important parameter in my .fdf file. >> Thank you. >> >> Regards, >> Sunetra Das. >> >> >
Re: [SIESTA-L] structure optimization
Dear Zain, Thank you for your reply. I have viewed the unit cell as well as the 4x4x1 supercell in softwares like Vesta and Xcrysden. Before relaxation it seemed okay, like the structure I had wanted to draw. I will check again, though. I have relaxed the 2 atom unit cell both in atomic positions as well as in cell dimensions. Used the relaxed coordinates and cell dimensions to form the supercell. There is a parameter MD.MaxCGDispl which uses a default value of 0.2 Bohr. Should I try playing with that ? Thank you. Regards, Sunetra Das
Re: [SIESTA-L] structure optimization
Dear Ruslan Zhachuk, Thank you for replying. The hexagonal planar structure has already been reported to be a stable one. The group which published the results however used a different software. I wanted to reproduce their result using Siesta before carrying out with furthur studies. Regards, Sunetra Das
Re: [SIESTA-L] structure optimization
Dear Berna, The run terminated without any error. So there shouldn't be any such error message in the log or output file. Thank you. Regards, Sunetra Das. On 16-Apr-2017 11:15 AM, "Sunetra Das" wrote: > Dear Zain, > > Thank you for your reply. > I have viewed the unit cell as well as the 4x4x1 supercell in softwares > like Vesta and Xcrysden. Before relaxation it seemed okay, like the > structure I had wanted to draw. > I will check again, though. > I have relaxed the 2 atom unit cell both in atomic positions as well as in > cell dimensions. Used the relaxed coordinates and cell dimensions to form > the supercell. > > There is a parameter MD.MaxCGDispl which uses a default value of 0.2 Bohr. > Should I try playing with that ? > > Thank you. > Regards, > Sunetra Das >
[SIESTA-L] structure optimization
Hello SIESTA users, I am facing a difficulty during while trying to fully relax a 32 atom graphene like 2D system with and without a single vacancy, in the middle of the srtucture. A part of my input .fdf file is given below: *DM.Tolerance 1.d-3DM.Require.Energy.Convergence TDM.Energy.Tolerance 1.d-5 eVPAO.BasisSize DZPPAO.EnergyShift 0.3 eVMD.TypeOfRun CGMaxSCFIterations 3000MD.NumCGsteps 3000MD.VariableCell TMD.MaxForceTol0.02 eV/AngMeshCutoff300 RyDM.MixingWeight 0.02DM.NumberPulay 3WriteCoorXmol TWriteMullikenPop0XC.functional GGAXC.authors PBESolutionMethod diagonElectronicTemperature 300 K* The lattice constant of the system, the bond length and bond angle used by me has already been reported in a reputed journal, as a stable one. I have not used any constraints in my structure. I have created a 4x4x1 supercell using the reported dimensions and trying to optimize the structure with the siesta code version 3.2-pl-5. The problem I am facing is that the optimized structure is no longer of the symmetry I started with. The structure is no longer a hexagonal honeycomb one anymore. Also while using a vacancy defect in the structure the atoms are getting asymmetrically arranged breaking any symmetry that was present there. Now my question is, are there any more parameters that I should have specified in the input .fdf file? Or, will a change in the .psf file can bring about any improvement in the optimization? Also, if I apply some constraints like fixing the bond angles or that my structure should relax only in a single plane, then how can I say that all the atoms in my structure are FULLY relaxed? Please kindly help me in this regard. I feel like I am missing some important parameter in my .fdf file. Thank you. Regards, Sunetra Das.
Re: [SIESTA-L] siesta-4.0-b2 installation error
Thank you Nick, (and also Alberto) I have managed to install siesta-4.0 according to Alberto's instructions. But now I am finding error while trying to run a job. I am using the same .fdf and .psf file to run a structure relaxation job using the siesta-4.0 executable, as I had used in siesta-3.2-pl-5, but this time it is showing me 'presence of ghost state' error. And the code stops. How can the same set of input and pp files show different results for two different versions of the same executable file? Has anyone else also faced this issue? Where lies the problem, can anybody please help me? Thanking all, Sunetra.
[SIESTA-L] siesta-4.0-b2 installation error
Dear All, I am getting the following error while trying to install siesta-4.0-b2: *m_dminim.o: In function `minim_cg_sparse':/home/sunetra/Desktop/siesta-4.0-b2/Src/m_dminim.F90:1724: undefined reference to `dsytrf_'/home/sunetra/Desktop/siesta-4.0-b2/Src/m_dminim.F90:1728: undefined reference to `dsytri_'m_zminim.o: In function `minim_cg':/home/sunetra/Desktop/siesta-4.0-b2/Src/m_zminim.F90:996: undefined reference to `zhetrf_'/home/sunetra/Desktop/siesta-4.0-b2/Src/m_zminim.F90:1000: undefined reference to `zhetri_'m_zminim.o: In function `minim_cg_sparse':/home/sunetra/Desktop/siesta-4.0-b2/Src/m_zminim.F90:1864: undefined reference to `zhetrf_'/home/sunetra/Desktop/siesta-4.0-b2/Src/m_zminim.F90:1868: undefined reference to `zhetri_'m_svd.o: In function `__m_svd_MOD_solve_with_svd':/home/sunetra/Desktop/siesta-4.0-b2/Src/m_svd.F90:59: undefined reference to `dgelss_'collect2: error: ld returned 1 exit statusmake: *** [siesta] Error 1* Kindly help me in this regard as I need to upgrade from my current siesta version 3.2-pl-5. Thanks in advance. Sunetra Das
[SIESTA-L] siesta-4.1-b2 installation error
Dear forum members, I am facing the following error message when trying to install siesta-4.1-b2: *sunetra@sunetra-Inspiron:~/Desktop/siesta-4.1-b2/Src$ ./configurebash: ./configure: No such file or directorysunetra@sunetra-Inspiron:~/Desktop/siesta-4.1-b2/Src$ cp arch.make ../Objsunetra@sunetra-Inspiron:~/Desktop/siesta-4.1-b2/Src$ cd ../Objsunetra@sunetra-Inspiron:~/Desktop/siesta-4.1-b2/Obj$ makeCompilation architecture to be used: If this is not what you want, create the rightarch.make file using the models in Src/SysHit ^C to abort...==> Incorporating information about present compilation (compiler and flags)make "FPPFLAGS=" compinfo.omake[1]: Entering directory `/home/sunetra/Desktop/siesta-4.1-b2/Obj'make[1]: *** No rule to make target `compinfo.o'. Stop.make[1]: Leaving directory `/home/sunetra/Desktop/siesta-4.1-b2/Obj'make: *** [version] Error 2* Please guide me through my problem. Thank you.
Re: [SIESTA-L] VIBRA package
Okay. Will update and let the forum know. Thank you. -- SUNETRA DAS
[SIESTA-L] VIBRA package
Hello SIESTA users, I am new to SIESTA and trying to calculate the phonon dispersion curves for a given optimized structure using the VIBRA package included with the original software. But every time I am running 'vibrator' it is showing me runtime error as shown below: *At line 618 of file vibrator.f (unit = 11, file = 'Ind.vectors')Fortran runtime error: Sequential READ or WRITE not allowed after EOF marker, possibly use REWIND or BACKSPACE* How to correct this error, can anybody please help me with it? How and where to use a REWIND or a BACKSPACE ? Even after the error I am getting output files. Is it by any chance giving erroneous outputs due to this error?
