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yangxuezhang金蟲(chóng) (正式寫(xiě)手)
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[求助]
請(qǐng)大家?guī)兔纯磗iesta輸入文件有哪些錯(cuò)誤
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我這是第一次寫(xiě)輸入文件，以前也沒(méi)師兄做這個(gè)，也每個(gè)人問(wèn)，希望高手不要嫌低級(jí)，幫我看一下，哪里有錯(cuò)誤，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
金蟲(chóng) (正式寫(xiě)手)
- 應(yīng)助: 6 (幼兒園)
- 金幣: 2250.4
- 散金: 216
- 紅花: 5
- 帖子: 564
- 在線: 211.1小時(shí)
- 蟲(chóng)號(hào): 1967414
- 注冊(cè): 2012-09-01
- 性別: GG
- 專(zhuān)業(yè): 凝聚態(tài)物性I:結(jié)構(gòu)、力學(xué)和
2樓2012-09-23 15:30:46
yangxuezhang
金蟲(chóng) (正式寫(xiě)手)
- 應(yīng)助: 6 (幼兒園)
- 金幣: 2250.4
- 散金: 216
- 紅花: 5
- 帖子: 564
- 在線: 211.1小時(shí)
- 蟲(chóng)號(hào): 1967414
- 注冊(cè): 2012-09-01
- 性別: GG
- 專(zhuān)業(yè): 凝聚態(tài)物性I:結(jié)構(gòu)、力學(xué)和
|
這是提交后的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樓2012-09-23 15:46:12
zhangguangping
木蟲(chóng) (著名寫(xiě)手)
- 1ST強(qiáng)帖: 23
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- 專(zhuān)業(yè): 原子和分子物理
4樓2012-09-24 21:04:14
yangxuezhang
金蟲(chóng) (正式寫(xiě)手)
- 應(yīng)助: 6 (幼兒園)
- 金幣: 2250.4
- 散金: 216
- 紅花: 5
- 帖子: 564
- 在線: 211.1小時(shí)
- 蟲(chóng)號(hào): 1967414
- 注冊(cè): 2012-09-01
- 性別: GG
- 專(zhuān)業(yè): 凝聚態(tài)物性I:結(jié)構(gòu)、力學(xué)和
|
下面是*.out文件里面的，為了找錯(cuò)誤，和前面的輸入文件比，我注釋掉了很多項(xiàng)，不過(guò)還是不行，不知道是什么問(wèn)題 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 希望大俠多多幫忙 |
5樓2012-09-26 14:53:20
zhangguangping
木蟲(chóng) (著名寫(xiě)手)
- 1ST強(qiáng)帖: 23
- 應(yīng)助: 71 (初中生)
- 貴賓: 0.031
- 金幣: 1973.1
- 散金: 9059
- 紅花: 79
- 帖子: 2681
- 在線: 2128.8小時(shí)
- 蟲(chóng)號(hào): 529624
- 注冊(cè): 2008-03-20
- 性別: GG
- 專(zhuān)業(yè): 原子和分子物理
【答案】應(yīng)助回帖
★ ★
yangxuezhang: 金幣+2, ★有幫助 2012-09-30 15:17:02
yangxuezhang: 金幣+2, ★有幫助 2012-09-30 15:17:02
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從輸出文件中看出來(lái)，你計(jì)算中的Ti元素的贗勢(shì)將8個(gè)本應(yīng)該屬于core的電子放到了價(jià)電子的考慮范圍，這樣可以更好的描述不同環(huán)境中的Ti的電子結(jié)構(gòu)。但是你需要對(duì)Ti的基函數(shù)進(jìn)行手動(dòng)設(shè)置。而不能用簡(jiǎn)單的PAO.BasisSize SZ關(guān)鍵字，使用這個(gè)關(guān)鍵字默認(rèn)只給價(jià)電子產(chǎn)生基函數(shù)。所以你需要使用 %block PAO.Basis %endblock PAO.Basis 來(lái)設(shè)置，比如 PAO.BasisSize DZP PAO.EnergyShift 100 meV 對(duì)應(yīng)的C元素的基函數(shù)為： %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 當(dāng)然，這個(gè)與具體的贗勢(shì)還有點(diǎn)關(guān)系。 你可以比照著這個(gè)對(duì)Ti進(jìn)行一下設(shè)置，將那8個(gè)電子的基函數(shù)明確的寫(xiě)出來(lái)。我沒(méi)有算過(guò)Ti,所以不會(huì)設(shè)置。 還有一個(gè)辦法就是你可以使用一個(gè)沒(méi)有semicore態(tài)電子的Ti贗勢(shì)。你從官網(wǎng)上下載一個(gè)就是了。我看了一下官網(wǎng)上的LDA和GGA的Ti贗勢(shì)就都沒(méi)有semicore態(tài)。 http://icmab.cat/leem/siesta/Dat ... init/Tl_html/Tl.psf http://icmab.cat/leem/siesta/Dat ... init/Tl_html/Tl.psf |
6樓2012-09-26 15:22:26
yangxuezhang
金蟲(chóng) (正式寫(xiě)手)
- 應(yīng)助: 6 (幼兒園)
- 金幣: 2250.4
- 散金: 216
- 紅花: 5
- 帖子: 564
- 在線: 211.1小時(shí)
- 蟲(chóng)號(hào): 1967414
- 注冊(cè): 2012-09-01
- 性別: GG
- 專(zhuān)業(yè): 凝聚態(tài)物性I:結(jié)構(gòu)、力學(xué)和
7樓2012-09-27 15:59:10
8樓2012-09-30 12:00:09
yangxuezhang
金蟲(chóng) (正式寫(xiě)手)
- 應(yīng)助: 6 (幼兒園)
- 金幣: 2250.4
- 散金: 216
- 紅花: 5
- 帖子: 564
- 在線: 211.1小時(shí)
- 蟲(chóng)號(hào): 1967414
- 注冊(cè): 2012-09-01
- 性別: GG
- 專(zhuān)業(yè): 凝聚態(tài)物性I:結(jié)構(gòu)、力學(xué)和
9樓2012-09-30 15:16:24
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