RE: [SIESTA-L] Problem using Vibra utility
Hi Sunetra, >From the website >https://urldefense.com/v3/__https://siesta-project.org/SIESTA_MATERIAL/Docs/list.html__;!!D9dNQwwGXtA!RxHJm2MCashIuvFYxBV08uyZ9nd_FhgAyf-fKq_B2IV5F0qFwZ1fkZKV3kVFn3_Lz9CdUVLk0GIKeeJ7VXzqNsL4$ > To leave the list just send an e-mail to sy...@uam.es<mailto:sy...@uam.es> with the following in its subject: SIGNOFF SIESTA-L The body of the message should be blank. Cheers, EL-Abed EL-ABED HAIDAR |Doctor of Philosophy (Science) |THE UNIVERSITY OF SYDNEY | NSW | 2006 Current Staff Scientist |NCI Australia<https://urldefense.com/v3/__http://www.nci.org.au/__;!!D9dNQwwGXtA!RxHJm2MCashIuvFYxBV08uyZ9nd_FhgAyf-fKq_B2IV5F0qFwZ1fkZKV3kVFn3_Lz9CdUVLk0GIKeeJ7VUXUnppL$ > |The Australian National University 143 Ward Road, Acton, ACT 2601 M: +61 416625261 E: el-abed.hai...@anu.edu.au<mailto:el-abed.hai...@anu.edu.au> Want the latest news from NCI? https://urldefense.com/v3/__http://nci.org.au/research-news/news/__;!!D9dNQwwGXtA!RxHJm2MCashIuvFYxBV08uyZ9nd_FhgAyf-fKq_B2IV5F0qFwZ1fkZKV3kVFn3_Lz9CdUVLk0GIKeeJ7VS6TSm4t$ Find out more about NCI: YouTube<https://urldefense.com/v3/__http://www.youtube.com/user/NCINationalFacility__;!!D9dNQwwGXtA!RxHJm2MCashIuvFYxBV08uyZ9nd_FhgAyf-fKq_B2IV5F0qFwZ1fkZKV3kVFn3_Lz9CdUVLk0GIKeeJ7VfJmi_-_$ > / Facebook<https://urldefense.com/v3/__https://www.facebook.com/NCIAustralia/__;!!D9dNQwwGXtA!RxHJm2MCashIuvFYxBV08uyZ9nd_FhgAyf-fKq_B2IV5F0qFwZ1fkZKV3kVFn3_Lz9CdUVLk0GIKeeJ7VdQNVBMA$ > / Twitter<https://urldefense.com/v3/__https://twitter.com/NCInews__;!!D9dNQwwGXtA!RxHJm2MCashIuvFYxBV08uyZ9nd_FhgAyf-fKq_B2IV5F0qFwZ1fkZKV3kVFn3_Lz9CdUVLk0GIKeeJ7Vc7tp_mE$ > / LinkedIn<https://urldefense.com/v3/__https://www.linkedin.com/company/national-computational-infrastructure/__;!!D9dNQwwGXtA!RxHJm2MCashIuvFYxBV08uyZ9nd_FhgAyf-fKq_B2IV5F0qFwZ1fkZKV3kVFn3_Lz9CdUVLk0GIKeeJ7VW6jSi4R$ > [NCI Australia logo black PNG transparent] [MHFAider Accredited Digital Badge] From: Sunetra Das<mailto:sunetra.das...@gmail.com> Sent: Friday, 15 September 2023 6:00 AM To: siesta-l@uam.es<mailto:siesta-l@uam.es> Subject: 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, mailto: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<mailto: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 pro
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 > > > > SolutionMethod diagon # OrderN or Diagon > > ElectronicTemperature 300 K# Temp. for Fermi smearing > > > > # Output options > > > > WriteCoorInitial > > WriteCoorStep > > WriteForces > > WriteMullikenPop1 # Write Mulliken Population Analysis > > WriteCoorXmol .false. > > WriteMDCoorXmol .false. > > WriteMDhistory .false. > > WriteCoorXmol .false. > > > > Once it is done I add the following lines to the input (as suggested > here: > > > https://urldefense.com/v3/__https://docs.siesta-project.org/projects/siesta/en/latest/tutorials/basic/vibrational-properties/Benzene/index.html__;!!D9dNQwwGXtA!UewEzyC8ZoPpI3i_PmoF3Vbbcs86V_CEf3F-hofbAGex6SS1dlsBvcgSPg7HdC2VlF
Re: [SIESTA-L] Problem using Vibra utility
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 > > SolutionMethod diagon # OrderN or Diagon > ElectronicTemperature 300 K# Temp. for Fermi smearing > > # Output options > > WriteCoorInitial > WriteCoorStep > WriteForces > WriteMullikenPop1 # Write Mulliken Population Analysis > WriteCoorXmol .false. > WriteMDCoorXmol .false. > WriteMDhistory .false. > WriteCoorXmol .false. > > Once it is done I add the following lines to the input (as suggested here: > https://urldefense.com/v3/__https://docs.siesta-project.org/projects/siesta/en/latest/tutorials/basic/vibrational-properties/Benzene/index.html__;!!D9dNQwwGXtA!UewEzyC8ZoPpI3i_PmoF3Vbbcs86V_CEf3F-hofbAGex6SS1dlsBvcgSPg7HdC2VlFmiZZGfJEXGqNlpcyY$ > ) and I run the vibra utility, obtaining this error message. The > SystemLabel.bands is formed but not the SystemLabel.vectors. > > Eigenvectors.true.# Compute both phonon eigenvalues and > eigenvectors > BandLinesScale pi/a > %block BandLines > 1 0.0 0.0 0.0 \Gamma # Only the Gamma point (enough for a molecule) > %endblock BandLines > > But when I run the vibra utility I always have this message: > > redata: System Name
[SIESTA-L] Problem using Vibra utility
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 SolutionMethod diagon # OrderN or Diagon ElectronicTemperature 300 K# Temp. for Fermi smearing # Output options WriteCoorInitial WriteCoorStep WriteForces WriteMullikenPop1 # Write Mulliken Population Analysis WriteCoorXmol .false. WriteMDCoorXmol .false. WriteMDhistory .false. WriteCoorXmol .false. Once it is done I add the following lines to the input (as suggested here: https://urldefense.com/v3/__https://docs.siesta-project.org/projects/siesta/en/latest/tutorials/basic/vibrational-properties/Benzene/index.html__;!!D9dNQwwGXtA!UewEzyC8ZoPpI3i_PmoF3Vbbcs86V_CEf3F-hofbAGex6SS1dlsBvcgSPg7HdC2VlFmiZZGfJEXGqNlpcyY$ ) and I run the vibra utility, obtaining this error message. The SystemLabel.bands is formed but not the SystemLabel.vectors. Eigenvectors.true.# Compute both phonon eigenvalues and eigenvectors BandLinesScale pi/a %block BandLines 1 0.0 0.0 0.0 \Gamma # Only the Gamma point (enough for a molecule) %endblock BandLines But when I run the vibra utility I always have this message: redata: System Name = vibra-2 redata: System Label = vibra-2 Number of Atoms = 164 Lattice Constant=1.88973 Bohr Lattice vectors (in units of Lattice Constant) = 17.82880 0.0 0.0 0.0 24.31472 0.0 0.0 0.0 25.23624 Lattice vectors (in Bohr) = 33.69156 0.0 0.0 0.0 45.94818 0.0 0.0 0.0 47.68960
