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yangxuezhang金虫 (正式写手)
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[求助]
请大家帮忙看看siesta输入文件有哪些错误
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我这是第一次写输入文件，以前也没师兄做这个，也每个人问，希望高手不要嫌低级，帮我看一下，哪里有错误，不甚感激 SystemName Test for Ti3SiC2 SystemLabel Ti3SiC2 NumberOfAtoms 11 # Number of atoms NumberOfSpecies 3 # Number of species %block Chemical_Species_Label 1 22 Ti 2 6 C 3 14 Si %endblock Chemical_Species_Label PAO.BasisSize SZ #??? # Lattice, coordinates, k-sampling AtomicCoordinatesFormat ScaledCartesian # Format for coordinates AtomicCoorFormatOut Ang %block AtomicCoordinatesAndAtomicSpecies 0.000000000 0.000000000 0.000000000 1 0.000000000 0.000000000 4.401250000 3 0.000000000 0.000000000 13.20375 3 1.541000000 0.889696765 1.271081005 2 1.541000000 0.889696765 7.531419 2 0.000000000 1.779393530 10.073581 2 0.000000000 1.779393530 16.333919 2 0.000000000 1.779393530 2.385477481 1 0.000000000 1.779393530 6.4170225 1 1.541000000 0.889696765 11.1879775 1 1.541000000 0.889696765 15.2195225 1 %endblock AtomicCoordinatesAndAtomicSpecies LatticeConstant 3.082 Ang %block LatticeVectors 1.000 0.500 0.000 0.000 0.866 0.000 0.000 0.000 1.000 %endblock LatticeVectors kgrid_cutoff 7. Ang #????? # DFT, Grid, SCF XC.functional LDA # Exchange-correlation functional type XC.authors CA # Particular parametrization of xc func SpinPolarized .false. # Spin unpolarized calculation MeshCutoff 200. Ry # Equivalent planewave cutoff for the grid MaxSCFIterations 100 # Maximum number of SCF iterations per step DM.MixingWeight 0.3 # New DM amount for next SCF cycle DM.Tolerance 1.d-4 # Tolerance in maximum difference # between input and output DM DM.NumberPulay 3 # Number of SCF steps between pulay mixing # Eigenvalue problem: order-N or diagonalization SolutionMethod diagon # OrderN or Diagon ElectronicTemperature 5 K # Temp. for Fermi smearing # Molecular dynamics and relaxations MD.TypeOfRun cg # Type of dynamics: # Output options WriteCoorInitial WriteCoorStep WriteForces WriteKpoints .false. WriteEigenvalues .false. WriteKbands .false. WriteBands .false. WriteMullikenPop 1 # Write Mulliken Population Analysis WriteCoorXmol .false. WriteMDCoorXmol .false. WriteMDhistory .false. WriteCoorXmol .false. # Options for saving/reading information DM.UseSaveDM # Use DM Continuation files MD.UseSaveXV .false. # Use stored positions and velocities MD.UseSaveCG .false. # Use stored positions and velocities SaveRho # Write valence pseudocharge at the mesh SaveDeltaRho # Write RHOscf-RHOatm at the mesh SaveElectrostaticPotential .false. # Write the total elect. pot. at the mesh SaveTotalPotential .false. # Write the total pot. at the mesh WriteSiestaDim .false. # Write minimum dim to siesta.h and stop WriteDenchar # Write information for DENCHAR |
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yangxuezhang
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2楼2012-09-23 15:30:46
yangxuezhang
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这是提交后的scrip.err文件里面的 ERROR STOP from Node: 0 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- -------------------------------------------------------------------------- mpiexec has exited due to process rank 0 with PID 14863 on node dell745-2-1.local exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpiexec (as reported here). -------------------------------------------------------------------------- real 0m0.866s user 0m0.041s sys 0m0.054s |
3楼2012-09-23 15:46:12
zhangguangping
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4楼2012-09-24 21:04:14
yangxuezhang
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下面是*.out文件里面的，为了找错误，和前面的输入文件比，我注释掉了很多项，不过还是不行，不知道是什么问题 Siesta Version: siesta-3.1 Architecture : x86_64-unknown-linux-gnu--Intel Compiler flags: /opt/openmpi-intel11/bin/mpif90 -g -O2 PARALLEL version * Running on 2 nodes in parallel >> Start of run: 24-SEP-2012 15:08:55 *********************** * WELCOME TO SIESTA * *********************** reinit: Reading from standard input ************************** Dump of input data file **************************** SystemName Test for Ti3SiC2 SystemLabel Ti3SiC2 NumberOfAtoms 11 # Number of atoms NumberOfSpecies 3 # Number of species %block Chemical_Species_Label 1 22 Ti 2 6 C 3 14 Si %endblock Chemical_Species_Label #PAO.BasisSize SZ #??? # Lattice, coordinates, k-sampling AtomicCoordinatesFormat Ang # Format for coordinates AtomicCoorFormatOut Ang %block AtomicCoordinatesAndAtomicSpecies 0.000000000 0.000000000 0.000000000 1 0.000000000 0.000000000 4.401250000 3 0.000000000 0.000000000 13.20375 3 1.541000000 0.889696765 1.271081005 2 1.541000000 0.889696765 7.531419 2 0.000000000 1.779393530 10.073581 2 0.000000000 1.779393530 16.333919 2 0.000000000 1.779393530 2.385477481 1 0.000000000 1.779393530 6.4170225 1 1.541000000 0.889696765 11.1879775 1 1.541000000 0.889696765 15.2195225 1 %endblock AtomicCoordinatesAndAtomicSpecies LatticeConstant 3.082 Ang %block LatticeVectors 1.000 0.500 0.000 0.000 0.866 0.000 0.000 0.000 1.000 %endblock LatticeVectors #kgrid_cutoff 7. Ang #????? # DFT, Grid, SCF #XC.functional LDA # Exchange-correlation functional type #XC.authors CA # Particular parametrization of xc func #SpinPolarized .false. # Spin unpolarized calculation #MeshCutoff 200. Ry # Equivalent planewave cutoff for the grid #MaxSCFIterations 100 # Maximum number of SCF iterations per step #DM.MixingWeight 0.3 # New DM amount for next SCF cycle #DM.Tolerance 1.d-4 # Tolerance in maximum difference # between input and output DM #DM.NumberPulay 3 # Number of SCF steps between pulay mixing # Eigenvalue problem: order-N or diagonalization SolutionMethod diagon # OrderN or Diagon #ElectronicTemperature 5 K # Temp. for Fermi smearing # Molecular dynamics and relaxations #MD.TypeOfRun cg # Type of dynamics: # Output options #WriteCoorInitial #WriteCoorStep #WriteForces #WriteKpoints .false. #WriteEigenvalues .false. #WriteKbands .false. #WriteBands .false. #WriteMullikenPop 1 # Write Mulliken Population Analysis #WriteCoorXmol .false. #WriteMDCoorXmol .false. #WriteMDhistory .false. #WriteCoorXmol .false. # Options for saving/reading information #DM.UseSaveDM # Use DM Continuation files #MD.UseSaveXV .false. # Use stored positions and velocities #MD.UseSaveCG .false. # Use stored positions and velocities #SaveRho # Write valence pseudocharge at the mesh #SaveDeltaRho # Write RHOscf-RHOatm at the mesh #SaveElectrostaticPotential .false. # Write the total elect. pot. at the mesh #SaveTotalPotential .false. # Write the total pot. at the mesh #WriteSiestaDim .false. # Write minimum dim to siesta.h and stop #WriteDenchar # Write information for DENCHAR ************************** End of input data file ***************************** reinit: ----------------------------------------------------------------------- reinit: System Name: Test for Ti3SiC2 reinit: ----------------------------------------------------------------------- reinit: System Label: Ti3SiC2 reinit: ----------------------------------------------------------------------- initatom: Reading input for the pseudopotentials and atomic orbitals ---------- Species number: 1 Label: Ti Atomic number: 22 Species number: 2 Label: C Atomic number: 6 Species number: 3 Label: Si Atomic number: 14 Ground state valence configuration: 4s02 3d02 Reading pseudopotential information in formatted form from Ti.psf Pseudopotential generated from a relativistic atomic calculation There are spin-orbit pseudopotentials available Spin-orbit interaction is not included in this calculation Valence configuration for pseudopotential generation: 3s( 2.00) rc: 1.30 3p( 6.00) rc: 1.30 3d( 2.00) rc: 1.30 4f( 0.00) rc: 1.98 Ground state valence configuration: 2s02 2p02 Reading pseudopotential information in formatted form from C.psf Valence configuration for pseudopotential generation: 2s( 2.00) rc: 1.49 2p( 2.00) rc: 1.52 3d( 0.00) rc: 1.58 Ground state valence configuration: 3s02 3p02 Reading pseudopotential information in formatted form from Si.psf Valence configuration for pseudopotential generation: 3s( 2.00) rc: 1.89 3p( 2.00) rc: 1.89 3d( 0.00) rc: 1.89 4f( 0.00) rc: 1.89 Semicore shell(s) with 8 electrons included in the valence for Ti Ti must be in PAO.Basis (it has semicore states) ERROR STOP from Node: 0 希望大侠多多帮忙 |
5楼2012-09-26 14:53:20
zhangguangping
木虫 (著名写手)
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【答案】应助回帖
★ ★
yangxuezhang: 金币+2, ★有帮助 2012-09-30 15:17:02
yangxuezhang: 金币+2, ★有帮助 2012-09-30 15:17:02
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从输出文件中看出来，你计算中的Ti元素的赝势将8个本应该属于core的电子放到了价电子的考虑范围，这样可以更好的描述不同环境中的Ti的电子结构。但是你需要对Ti的基函数进行手动设置。而不能用简单的PAO.BasisSize SZ关键字，使用这个关键字默认只给价电子产生基函数。所以你需要使用 %block PAO.Basis %endblock PAO.Basis 来设置，比如 PAO.BasisSize DZP PAO.EnergyShift 100 meV 对应的C元素的基函数为： %block PAO.Basis C 2 # Species label, number of l-shells n=2 0 2 # n, l, Nzeta 4.633 3.432 1.000 1.000 n=2 1 2 P 1 # n, l, Nzeta, Polarization, NzetaPol 5.659 3.653 1.000 1.000 %endblock PAO.Basis 当然，这个与具体的赝势还有点关系。 你可以比照着这个对Ti进行一下设置，将那8个电子的基函数明确的写出来。我没有算过Ti,所以不会设置。 还有一个办法就是你可以使用一个没有semicore态电子的Ti赝势。你从官网上下载一个就是了。我看了一下官网上的LDA和GGA的Ti赝势就都没有semicore态。 http://icmab.cat/leem/siesta/Dat ... init/Tl_html/Tl.psf http://icmab.cat/leem/siesta/Dat ... init/Tl_html/Tl.psf |
6楼2012-09-26 15:22:26
yangxuezhang
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7楼2012-09-27 15:59:10
8楼2012-09-30 12:00:09
yangxuezhang
金虫 (正式写手)
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9楼2012-09-30 15:16:24
5