Octopus输入文件实例
周铁戈
Octopus是一款开源的第一性原理计算软件，采用密度泛函理论（DFT）计算体系基态。可以利用的交换关联泛函有LDA、GGA、Meta-GGA 和OEP等。能够采用含时密度泛函理论（TDDFT）计算体系的响应，给出体系实空间的电荷密度的实时演化。周期体系的TDDFT计算是Octopus软件相对于其他第一性原理计算软件的突出优点。
笔者曾利用Octopus软件对铁基超导体、铜氧化物超导体和Nb单质超导进行了一系列研究，主要计算体系电荷密度随时间的演化，借此探索超导电子的配对机制。本文给出作者研究的三个体系的Octopus输入文件，仅供参考。
一、铁基超导体KFeSe的TDDFT计算。首先要计算出体系的基态，即设定CalculationMode = gs，然后再修改为CalculationMode = td，进行TDDFT计算。计算中笔者使用外加时变电场激发体系电荷密度的变化，激发之后撤销外加电场，最后给出体系电荷密度的自由振动。下面是输入文件：
CalculationMode = td
PeriodicDimensions = 3
BoxShape = parallelepiped
ExperimentalFeatures = yes
EigenSolver = rmmdiis
ConvRelDens = 1.0e-7
ExcessCharge = 2.0 # 减少2个价电子
MaximumIter = 600
Output = density
OutputFormat = cube
UnitsOutput = eV_Angstrom
a = 1.0*angstrom
%Species
"Fe" | species_pseudo | hubbard_l | 2 | hubbard_u | 4.5/27.21138
%
PseudopotentialSet = hscv_pbe
DFTULevel = dft_u_empirical
%LatticeParameters
a | a | a
%
%LatticeVectors
3.9479032341976 | 0.0000000000000 | 0.0000000000000
0.0000000000000 | 3.9479032335976 | 0.0000000000000
0.0000000000000 | 0.0000000000000 | 12.2633618360410
%
%ReducedCoordinates
"Fe" | 0.000000000000 | 0.500000000000 | 0.250000000000
"Fe" | 0.000000000000 | 0.500000000000 | 0.750000000000
"Fe" | 0.500000000000 | 0.000000000000 | 0.250000000000
"Fe" | 0.500000000000 | 0.000000000000 | 0.750000000000
"Se" | 0.000000000000 | 0.000000000000 | 0.368205065662
"Se" | 0.000000000000 | 0.000000000000 | 0.631794934337
"Se" | 0.500000000000 | 0.500000000000 | 0.868206065663
"Se" | 0.500000000000 | 0.500000000000 | 0.131793934337
"K" | 0.000000000000 | 0.000000000000 | 0.000000000000
"K" | 0.500000000000 | 0.500000000000 | 0.500000000000
%
Spacing = 0.35
FromScratch = no
ParDomains = no
ParKPoints = auto
SpinComponents = polarized
GuessMagnetDensity = user_defined
%AtomsMagnetDirection
5.0
5.0
-5.0
-5.0
0.0
0.0
0.0
0.0
0.0
0.0
%
LCAOStart= lcao_states
%KPointsGrid
6 | 6 | 4
%
KPointsUseSymmetries = no
KPointsUseTimeReversal = no
ExtraStates = 15
FilterPotentials = filter_none
AOThreshold = 0.05
OutputLDA_U = occ_matrices + effectiveU
Tf = 20/eV
dt = 0.002/eV
TDPropagator = aetrs
TDMaxSteps = Tf/dt
TDTimeStep = dt
amplitude = 1*eV/angstrom
omega = 1.8*eV
tau0 = 5.0/eV
t0 = tau0
%TDExternalFields
electric_field | 1 | 1 | 1 | omega | "envelope_cos"
%
%TDFunctions
"envelope_cos" | tdf_cosinoidal | amplitude | tau0 | t0
%
TDOutput = laser + multipoles
二、铜氧化物超导体TlBa2CaCu2O7的TDDFT研究，采用轻微改变一个Tl原子的位置产生电荷扰动。具体计算中先把一个Tl原子偏离平衡位置，计算基态，然后把Tl原子位置复原，再进行TDDFT计算。下面是输入文件：
CalculationMode = td
PeriodicDimensions = 3
BoxShape = parallelepiped
ExperimentalFeatures = yes
EigenSolver = rmmdiis
ConvRelDens = 1.0e-6
MaximumIter = 650
Output = density
OutputFormat = cube
UnitsOutput = eV_Angstrom
a = 1.0*angstrom
%Species
"Cu" | species_pseudo | hubbard_l | 2
%
PseudopotentialSet = hscv_pbe
DFTULevel = dft_u_acbn0
#DFTULevel = dft_u_empirical
%LatticeParameters
a | a | a
%
%LatticeVectors
5.3999928121 | 0.0000000000 | 0.0000000000
0.0000000000 | 5.3999921647 | 0.0000000000
0.0000000000 | 0.0000000000 | 12.8208424994
%
%ReducedCoordinates
"Tl" | 0.500000000000 | 0.500000000000 | 0.500000000000
"Tl" | 0.000000000000 | 0.000000000000 | 0.500000000000
"Ba" | 0.500000000000 | 0.000000000000 | 0.289365868572
"Ba" | 0.000000000000 | 0.500000000000 | 0.289365858572
"Ba" | 0.500000000000 | 0.000000000000 | 0.710634131496
"Ba" | 0.000000000000 | 0.500000000000 | 0.710634131496
"Ca" | 0.500000000000 | 0.000000000000 | 0.000000000000
"Ca" | 0.000000000000 | 0.500000000000 | 0.000000000000
"Cu" | 0.500000000000 | 0.500000000000 | 0.132782612859
"Cu" | 0.000000000000 | 0.000000000000 | 0.132782612859
"Cu" | 0.500000000000 | 0.500000000000 | 0.867217418172
"Cu" | 0.000000000000 | 0.000000000000 | 0.867217418172
"O" | 0.750000000000 | 0.250000000000 | 0.120153183183
"O" | 0.250000000000 | 0.749999950000 | 0.120153123183
"O" | 0.750000000000 | 0.250000000000 | 0.879846846795
"O" | 0.250000000000 | 0.749999957000 | 0.879846846795
"O" | 0.750000000000 | 0.749999957000 | 0.120153183183
"O" | 0.250000000000 | 0.250000000000 | 0.120153183183
"O" | 0.750000000000 | 0.749999957000 | 0.879846816795
"O" | 0.250000000000 | 0.250000000000 | 0.879846843795
"O" | 0.500000000000 | 0.500000000000 | 0.328394882794
"O" | 0.000000000000 | 0.000000000000 | 0.328393482794
"O" | 0.500000000000 | 0.500000000000 | 0.671606517238
"O" | 0.000000000000 | 0.000000000000 | 0.671605517238
"O" | 0.500000000000 | 0.000000000000 | 0.500000000000
"O" | 0.000000000000 | 0.500000000000 | 0.500000000000
%
Spacing = 0.39
FromScratch = yes
ParDomains = no
ParKPoints = auto
SpinComponents = polarized
GuessMagnetDensity = user_defined
%AtomsMagnetDirection
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
3.0
-3.0
3.0
-3.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
0.0
%
LCAOStart= lcao_states
%KPointsGrid
2 | 2 | 1
%
KPointsUseSymmetries = no
KPointsUseTimeReversal = no
ExtraStates = 25
FilterPotentials = filter_none
AOThreshold = 0.04
OutputLDA_U = occ_matrices + effectiveU
TDFreezeU = yes
Tf = 40/eV
dt = 0.002/eV
TDPropagator = aetrs
TDMaxSteps = Tf/dt
TDTimeStep = dt
三、Nb单值超导的TDDFT研究，Nb不符合同位素效应。采用随时间变化电场产生扰动，外加电场在一定时间后消失，研究电荷自由振荡的规律。下面是输入文件：
CalculationMode = td
PeriodicDimensions = 3
BoxShape = parallelepiped
ExperimentalFeatures = yes
EigenSolver = rmmdiis
ConvRelDens = 1.0e-6
MaximumIter = 450
Output = density
OutputFormat = cube
UnitsOutput = eV_Angstrom
SmearingFunction = fermi_dirac
a = 1.0*angstrom
%Species
"Nb" | species_pseudo
%
PseudopotentialSet = hscv_pbe
#DFTULevel = dft_u_acbn0
#DFTULevel = dft_u_empirical
%LatticeParameters
a | a | a
%
%LatticeVectors
6.6012001000047 | 0.0000000000000 | 0.0000000000000
0.0000000000000 | 6.6012001000047 | 0.0000000000000
0.0000000000000 | 0.0000000000000 | 6.6012008000047
%
%ReducedCoordinates
"Nb" | 0.000000 | 0.000000 | 0.000000
"Nb" | 0.250000 | 0.250000 | 0.250000
"Nb" | 0.500000 | 0.000000 | 0.000000
"Nb" | 0.750000 | 0.250000 | 0.250000
"Nb" | -0.000000 | 0.500000 | 0.000000
"Nb" | 0.250000 | 0.750000 | 0.250000
"Nb" | 0.500000 | 0.500000 | 0.000000
"Nb" | 0.750000 | 0.750000 | 0.250000
"Nb" | -0.000000 | -0.000000 | 0.500000
"Nb" | 0.250000 | 0.250000 | 0.750000
"Nb" | 0.500000 | -0.000000 | 0.500000
"Nb" | 0.750000 | 0.250000 | 0.750000
"Nb" | -0.000000 | 0.500000 | 0.500000
"Nb" | 0.250000 | 0.750000 | 0.750000
"Nb" | 0.500000 | 0.500000 | 0.500000
"Nb" | 0.750000 | 0.750000 | 0.750000
%
Spacing = 0.35
FromScratch = yes
ParDomains = no
ParKPoints = auto
SpinComponents = polarized
GuessMagnetDensity = paramagnetic
LCAOStart= lcao_states
%KPointsGrid
4 | 4 | 4
%
KPointsUseSymmetries = no
KPointsUseTimeReversal = no
ExtraStates = 25
FilterPotentials = filter_none
AOThreshold = 0.04
OutputLDA_U = occ_matrices + effectiveU
OutputInterval = 50
TDFreezeU = yes
Tf = 40/eV
dt = 0.002/eV
TDPropagator = aetrs
TDMaxSteps = Tf/dt
TDTimeStep = dt
amplitude = 1*eV/angstrom
omega = 1.8*eV
tau0 = 10.0/eV
t0 = tau0
%TDExternalFields
electric_field | 1 | 1 | 1 | omega | "envelope_cos"
%
%TDFunctions
"envelope_cos" | tdf_cosinoidal | amplitude | tau0 | t0
%
TDOutput = laser + multipoles
转载本文请联系原作者获取授权，同时请注明本文来自周铁戈科学网博客。
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