[SIESTA-L] Maximum dynamic memory allocated problem
Hi all I'm running one jobs in two different machines. In the first one, such job works without problems. however the second one i obtaine the next: New_DM. Step: 1 Initializing Density Matrix... InitMesh: MESH = 270 x 200 x 162 = 8748000 InitMesh: Mesh cutoff (required, used) = 200.000 201.285 Ry * Maximum dynamic memory allocated =36 MB And the jobs stops. I think the problem in the second machines is realted with the memory capacity. However, it machine have arond 6TB of available memory. Besides the machine tecnhician told me that it is not a memory related problem. Then, where is the problem in the second machine??? Thanks in advance Gregorio -- Gregorio García Moreno, PhD e-mail: gjgar...@ubu.es Department of Chemistry University of Burgos Plaza Misael Bañuelos s/n 09001 Burgos - Spain
Re: [SIESTA-L] Fullerene Band Structure
thanks I think the solution for my problem is firstly optimize the latticeconstat paremeter. Thanks El 19/12/2013 14:26, Riccardo Rurali escribió: On 12/19/13 2:02 PM, Gregorio García Moreno wrote: Then, how is there several papers about fullerenes bands structures (see for example) http://onlinelibrary.wiley.com/doi/10.1002/pssb.200879595/pdf Because in that paper fullerenes are packed in a fcc lattice in such a way that they DO interact with each other. The system is a crystal where at every lattice site you have a fullerene instead of an atom (apparently that is called a "fullerene-cubane cocrystal"). I think the idea is to put the fullerene is to use a fcc unit cell, but unit cell would be enough larg to avoid interaccion between different molecules. If you reduce your fcc cell lattice parameter you should recover the results of the paper you mention. That, incidentally, would be the bands structure of a molecular solid built with fullerenes, but not "the band structure of a fullerene" (there is no such thing). Good luck, Riccardo -- Gregorio García Moreno, PhD e-mail: gjgar...@ubu.es Department of Chemistry University of Burgos Plaza Misael Bañuelos s/n 09001 Burgos - Spain
Re: [SIESTA-L] Fullerene Band Structure
On 12/19/13 2:02 PM, Gregorio García Moreno wrote: Then, how is there several papers about fullerenes bands structures (see for example) http://onlinelibrary.wiley.com/doi/10.1002/pssb.200879595/pdf Because in that paper fullerenes are packed in a fcc lattice in such a way that they DO interact with each other. The system is a crystal where at every lattice site you have a fullerene instead of an atom (apparently that is called a "fullerene-cubane cocrystal"). I think the idea is to put the fullerene is to use a fcc unit cell, but unit cell would be enough larg to avoid interaccion between different molecules. If you reduce your fcc cell lattice parameter you should recover the results of the paper you mention. That, incidentally, would be the bands structure of a molecular solid built with fullerenes, but not "the band structure of a fullerene" (there is no such thing). Good luck, Riccardo -- Riccardo Rurali Institut de Ciència de Materials de Barcelona (ICMAB) Consejo Superior de Investigaciones Científicas (CSIC) Campus de Bellaterra 08193 Bellaterra (Barcelona) Spain tel.: +34 93 5801853 ext. 347 e-mail: rrur...@icmab.es http://www.icmab.es/dmmis/leem/ Man, the dope's that there's still hope
[SIESTA-L] GGA lattice optimization error criteria
Hello, Our group is working on some metal-oxide junctions. But it seems that reaching an ensemble of pseudopotentials that can work for all elements in our system is putting us in trouble. Anyway, the problem we have right now is Beryllium Oxide. We have used the available pseudopotential for Oxygen in siesta examples with r_C=1.15 Bohr. But for Beryllium we generated several pseudopotentials, some of the r-Cs that were even reported in previous works done by Siesta. But in the best case, the optimized lattice for wurtzite Bulk BeO comes to be: a=2.790527ang and c=4.524322ang about 3.5% more than experimental reports. The previous works have reported the optimized lattice results with ~2.5% error which seems to be reasonable for GGA. But ours no matter what pseudo we use surpasses 3.5% error!!! I have enclosed the input file as well. I would be very thankful if you kindly let us know if this error criteria is Ok or, does it come from the basis sets and pseudopotentials, or we should change a parameter in the input? Best Regards, Pedram Heidari beo.fdf Description: application/vnd.fdf
Re: [SIESTA-L] Fullerene Band Structure
Then, how is there several papers about fullerenes bands structures (see for example) http://onlinelibrary.wiley.com/doi/10.1002/pssb.200879595/pdf I think the idea is to put the fullerene is to use a fcc unit cell, but unit cell would be enough larg to avoid interaccion between different molecules. I'm think the problem is bandlines vectors, im compoting using other differents. But im not sure thanks El 19/12/2013 13:16, Riccardo Rurali escribió: Dear Gregorio, unless I'm missing something, your result seems correct: the fullerene is a non-periodic system, thus its band structure must be flat. Riccardo On 12/19/13 10:21 AM, Gregorio García Moreno wrote: Dear Siesta users, i', triying to calculate the band structure of a big fullerene (540 atoms) usign siesta. For this purpuse, i'm using and fcc unit cell with its corresponding K-point for the brillouin zone. The size of the unit cell has been selected for to avoid interaction between fullerenes. However, my lines are planes. I dont know where is my problem. I think, may be i'm not using a correct set of K-points for the fcc unit cell, or may be the latticevector are no correct. I dont know Could someone help me? At the end of the mail you can see my input file. Thanks in advance Gregorio WriteSiestaDim false# If true: writes dimensions and stops WriteCoorCeriustrue #Write format .cssr WriteCoorXmol true #Write format .xyz WriteMDXmoltrue#Write format .ani SaveRHO WriteMullikenPop 0# to write population analysis # 0 : (def) No writing # 1 : Atomic and orbital charges # 2 : 1 + overlap populations among atoms # 3 : 2 + id. among orbitals WriteEigenvaluestrue # It writes the hamiltonian eigenvalues for the sampling utility. # .EIG WriteKbands true # It writes the coordinates of the k vector defined for band plotting WriteBands true # To write the Hamiltonian eigen values corresponding to the k vectors writekpoints true # .bands latticeconstant 29.698 Ang NumberOfSpecies 1 # Number of species NumberOfAtoms 540 # Number of atoms KgridCutoff 07. Ang %block ChemicalSpeciesLabel 1 6 C %endblock ChemicalSpeciesLabel %block latticevectors 0.0 1.5 1.5 1.5 0.0 1.5 1.5 0.0 0.0 %endblock latticevectors PAO.BasisSize DZP # Size of PAO basis set : Double-Z PAO.BasisTypesplit # Type of PAO basis set : Split valence PAO.EnergyShift0.3 eV # to define the finite range of orbitals PAO.SplitNorm 0.15 xc.functional GGA # GGA xc.authorsPBE# Generalized Gradient Aproximation SpinPolarized false # Logical parameters are: yes or no MeshCutoff200. Ry# Mesh cutoff. real space mesh # SCF options MaxSCFIterations 300 # Maximum number of SCF iter DM.MixingWeight 0.25 # New DM amount for next SCF cycle DM.Tolerance 1.d-4 # Tolerance in maximum difference # between input and output DM DM.NumberPulay 4 NeglNonOverlapInt false # Neglect non-overlap interactions SolutionMethoddiagon# OrderN or Diagon ElectronicTemperature 5 meV# Temp. for Fermi smearing # MD options MD.TypeOfRun CG # Type of dynamics: MD.NumCGsteps 0 # Number of CG steps for # coordinate optimization MD.MaxCGDispl 0.1 Ang# Maximum atomic displacement # in one CG step (Bohr) MD.MaxForceTol 0.04 eV/Ang # Tolerance in the maximum MD.Variable.Cell true# Relax all the system cell and atoms. UseSaveDatatrue # For restart calculations. #* # Band structure #* BandLinesScale pi/a %block Bandlines 1. 1.5 1.5 0.0 K 15 0.0 0.0 0.0 \Gamma # 15 points from K to gamma 15 0.0 2.0 0.0 X 15 1.0 2.0 0.0 W 15 1.0 1.0 1.0 L 15 0.0 0.0 0.0 /Gamma %endblock Bandlines %block Atomic CoordinatesOrigin 0.0 0.0 0.0 %endblock AtomicCoordiantesOrigin #** # Density of States DOS #** %block ProjectedDensityOfSTates -5.0 1.0 0.200 700 eV %endblock ProjectedDensityOfStates #** # Atomic coordinates #*** AtomicCoordinatesFormat NotScaledCartesianAng # Format for coordinates %b
Re: [SIESTA-L] Fullerene Band Structure
Dear Gregorio, unless I'm missing something, your result seems correct: the fullerene is a non-periodic system, thus its band structure must be flat. Riccardo On 12/19/13 10:21 AM, Gregorio García Moreno wrote: Dear Siesta users, i', triying to calculate the band structure of a big fullerene (540 atoms) usign siesta. For this purpuse, i'm using and fcc unit cell with its corresponding K-point for the brillouin zone. The size of the unit cell has been selected for to avoid interaction between fullerenes. However, my lines are planes. I dont know where is my problem. I think, may be i'm not using a correct set of K-points for the fcc unit cell, or may be the latticevector are no correct. I dont know Could someone help me? At the end of the mail you can see my input file. Thanks in advance Gregorio WriteSiestaDim false# If true: writes dimensions and stops WriteCoorCeriustrue #Write format .cssr WriteCoorXmol true #Write format .xyz WriteMDXmoltrue#Write format .ani SaveRHO WriteMullikenPop 0# to write population analysis # 0 : (def) No writing # 1 : Atomic and orbital charges # 2 : 1 + overlap populations among atoms # 3 : 2 + id. among orbitals WriteEigenvaluestrue # It writes the hamiltonian eigenvalues for the sampling utility. # .EIG WriteKbands true # It writes the coordinates of the k vector defined for band plotting WriteBands true # To write the Hamiltonian eigen values corresponding to the k vectors writekpoints true # .bands latticeconstant 29.698 Ang NumberOfSpecies 1 # Number of species NumberOfAtoms 540 # Number of atoms KgridCutoff 07. Ang %block ChemicalSpeciesLabel 1 6 C %endblock ChemicalSpeciesLabel %block latticevectors 0.0 1.5 1.5 1.5 0.0 1.5 1.5 0.0 0.0 %endblock latticevectors PAO.BasisSize DZP # Size of PAO basis set : Double-Z PAO.BasisTypesplit # Type of PAO basis set : Split valence PAO.EnergyShift0.3 eV # to define the finite range of orbitals PAO.SplitNorm 0.15 xc.functional GGA # GGA xc.authorsPBE# Generalized Gradient Aproximation SpinPolarized false # Logical parameters are: yes or no MeshCutoff200. Ry# Mesh cutoff. real space mesh # SCF options MaxSCFIterations 300 # Maximum number of SCF iter DM.MixingWeight 0.25 # New DM amount for next SCF cycle DM.Tolerance 1.d-4 # Tolerance in maximum difference # between input and output DM DM.NumberPulay 4 NeglNonOverlapInt false # Neglect non-overlap interactions SolutionMethoddiagon# OrderN or Diagon ElectronicTemperature 5 meV# Temp. for Fermi smearing # MD options MD.TypeOfRun CG # Type of dynamics: MD.NumCGsteps 0 # Number of CG steps for # coordinate optimization MD.MaxCGDispl 0.1 Ang# Maximum atomic displacement # in one CG step (Bohr) MD.MaxForceTol 0.04 eV/Ang # Tolerance in the maximum MD.Variable.Cell true# Relax all the system cell and atoms. UseSaveDatatrue # For restart calculations. #* # Band structure #* BandLinesScale pi/a %block Bandlines 1. 1.5 1.5 0.0 K 15 0.0 0.0 0.0 \Gamma # 15 points from K to gamma 15 0.0 2.0 0.0 X 15 1.0 2.0 0.0 W 15 1.0 1.0 1.0 L 15 0.0 0.0 0.0 /Gamma %endblock Bandlines %block Atomic CoordinatesOrigin 0.0 0.0 0.0 %endblock AtomicCoordiantesOrigin #** # Density of States DOS #** %block ProjectedDensityOfSTates -5.0 1.0 0.200 700 eV %endblock ProjectedDensityOfStates #** # Atomic coordinates #*** AtomicCoordinatesFormat NotScaledCartesianAng # Format for coordinates %block AtomicCoordinatesAndAtomicSpecies 2.78083947 0.02742816 -11.17845346 1 etc %endblock AtomicCoordinatesAndAtomicSpecies -- Riccardo Rurali Institut de Ciència de Materials de Barcelona (ICMAB) Consejo Superior de Investigaciones Científicas (CSIC) Campus de Bellaterra 08193 Bellaterra (Barcelona) Spain tel.: +34 93 5801853 ext. 347 e-mail: rrur...@icmab.es http://www.icmab.es/dmmis/leem/ Man, the dope's that there's still hope
[SIESTA-L] Fullerene Band Structure
Dear Siesta users, i', triying to calculate the band structure of a big fullerene (540 atoms) usign siesta. For this purpuse, i'm using and fcc unit cell with its corresponding K-point for the brillouin zone. The size of the unit cell has been selected for to avoid interaction between fullerenes. However, my lines are planes. I dont know where is my problem. I think, may be i'm not using a correct set of K-points for the fcc unit cell, or may be the latticevector are no correct. I dont know Could someone help me? At the end of the mail you can see my input file. Thanks in advance Gregorio WriteSiestaDim false# If true: writes dimensions and stops WriteCoorCeriustrue #Write format .cssr WriteCoorXmol true #Write format .xyz WriteMDXmoltrue#Write format .ani SaveRHO WriteMullikenPop 0# to write population analysis # 0 : (def) No writing # 1 : Atomic and orbital charges # 2 : 1 + overlap populations among atoms # 3 : 2 + id. among orbitals WriteEigenvaluestrue # It writes the hamiltonian eigenvalues for the sampling utility. # .EIG WriteKbands true # It writes the coordinates of the k vector defined for band plotting WriteBands true # To write the Hamiltonian eigen values corresponding to the k vectors writekpoints true # .bands latticeconstant 29.698 Ang NumberOfSpecies 1 # Number of species NumberOfAtoms 540 # Number of atoms KgridCutoff 07. Ang %block ChemicalSpeciesLabel 1 6 C %endblock ChemicalSpeciesLabel %block latticevectors 0.0 1.5 1.5 1.5 0.0 1.5 1.5 0.0 0.0 %endblock latticevectors PAO.BasisSize DZP # Size of PAO basis set : Double-Z PAO.BasisTypesplit # Type of PAO basis set : Split valence PAO.EnergyShift0.3 eV # to define the finite range of orbitals PAO.SplitNorm 0.15 xc.functional GGA # GGA xc.authorsPBE# Generalized Gradient Aproximation SpinPolarized false # Logical parameters are: yes or no MeshCutoff200. Ry# Mesh cutoff. real space mesh # SCF options MaxSCFIterations 300 # Maximum number of SCF iter DM.MixingWeight 0.25 # New DM amount for next SCF cycle DM.Tolerance 1.d-4 # Tolerance in maximum difference # between input and output DM DM.NumberPulay 4 NeglNonOverlapInt false # Neglect non-overlap interactions SolutionMethoddiagon# OrderN or Diagon ElectronicTemperature 5 meV# Temp. for Fermi smearing # MD options MD.TypeOfRun CG # Type of dynamics: MD.NumCGsteps 0 # Number of CG steps for # coordinate optimization MD.MaxCGDispl 0.1 Ang# Maximum atomic displacement # in one CG step (Bohr) MD.MaxForceTol 0.04 eV/Ang # Tolerance in the maximum MD.Variable.Cell true# Relax all the system cell and atoms. UseSaveDatatrue # For restart calculations. #* # Band structure #* BandLinesScale pi/a %block Bandlines 1. 1.5 1.5 0.0 K 15 0.0 0.0 0.0 \Gamma # 15 points from K to gamma 15 0.0 2.0 0.0 X 15 1.0 2.0 0.0 W 15 1.0 1.0 1.0 L 15 0.0 0.0 0.0 /Gamma %endblock Bandlines %block Atomic CoordinatesOrigin 0.0 0.0 0.0 %endblock AtomicCoordiantesOrigin #** # Density of States DOS #** %block ProjectedDensityOfSTates -5.0 1.0 0.200 700 eV %endblock ProjectedDensityOfStates #** # Atomic coordinates #*** AtomicCoordinatesFormat NotScaledCartesianAng # Format for coordinates %block AtomicCoordinatesAndAtomicSpecies 2.78083947 0.02742816 -11.17845346 1 etc %endblock AtomicCoordinatesAndAtomicSpecies -- Gregorio García Moreno, PhD e-mail: gjgar...@ubu.es Department of Chemistry University of Burgos Plaza Misael Bañuelos s/n 09001 Burgos - Spain
[SIESTA-L] GGA lattice optimization error criteria
Hello, Our group is working on some metal-oxide junctions. But it seems that reaching an ensemble of pseudopotentials that can work for all elements in our system is putting us in trouble. Anyway, the problem we have right now is Beryllium Oxide. We have used the available pseudopotential for Oxygen in siesta examples with r_C=1.15 Bohr. But for Beryllium we generated several pseudopotentials, some of the r-Cs that were even reported in previous works done by Siesta. But in the best case, the optimized lattice for wurtzite Bulk BeO comes to be: a=2.790527ang and c=4.524322ang about 3.5% more than experimental reports. The previous works have reported the optimized lattice results with ~2.5% error which seems to be reasonable for GGA. But ours no matter what pseudo we use surpasses 3.5% error!!! I have enclosed the input file as well. I would be very thankful if you kindly let us know if this error criteria is Ok or, does it come from the basis sets and pseudopotentials, or we should change a parameter in the input? Best Regards, Pedram Heidari beo.fdf Description: application/vnd.fdf
