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tsh8167

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[交流] 【求助】算分子能譜的時(shí)候結(jié)果全都為負(fù)數(shù)，是問(wèn)題引起的？已有4人參與

我在計(jì)算雙探針體系中的分子能譜的時(shí)候，得出的數(shù)據(jù)是從-9942.9到-5474.78，這是我加入一個(gè)硝基后出現(xiàn)的錯(cuò)誤。
但是加另一種氨基和沒(méi)加側(cè)基團(tuán)所計(jì)算的結(jié)果都是正常的。這三種體系都是用同一種方法構(gòu)建，都用SZP基組進(jìn)行了優(yōu)化。
請(qǐng)問(wèn)，我的計(jì)算是什么地方發(fā)生了錯(cuò)誤？有哪些原因可以導(dǎo)致上述的錯(cuò)誤發(fā)生？？
期待高手指教。

[ Last edited by tsh8167 on 2010-6-28 at 11:29 ]

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redhaier

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tsh8167(金幣+1): 2010-06-25 09:36:22
qasd(金幣+1):謝謝 2010-06-28 20:11:38

what data?DOS?

引用回帖:

Originally posted by tsh8167 at 2010-06-24 15:41:57:
我在計(jì)算雙探針體系中的分子能譜的時(shí)候，得出的數(shù)據(jù)是從-9942.9到-5474.78，這是我加入一個(gè)硝基后出現(xiàn)的錯(cuò)誤。
但是加另一種氨基和沒(méi)加側(cè)基團(tuán)所計(jì)算的結(jié)果都是正常的。這三種體系都是用同一種方法構(gòu)建，都用 ...

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2樓2010-06-24 17:15:00

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是Energy Spectrum

引用回帖:

Originally posted by redhaier at 2010-06-24 17:15:00:
what data?DOS?

[ Last edited by tsh8167 on 2010-6-24 at 17:44 ]

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3樓2010-06-24 17:43:19

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redhaier

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hedaors(金幣+1):謝謝交流 2010-06-25 22:47:19
tsh8167(金幣+1):謝謝，我試試 2010-06-26 17:31:22

Ok, they should be the same, try to decrease the lower energy bound in the green function
integral contour.

引用回帖:

Originally posted by tsh8167 at 2010-06-24 17:43:19:
是Energy Spectrum

[ Last edited by tsh8167 on 2010-6-24 at 17:44 ]

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4樓2010-06-25 22:41:36

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tsh8167

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[quote]Originally posted by redhaier at 2010-06-25 22:41:36:
Ok, they should be the same, try to decrease the lower energy bound in the green function
integral contour.

我試了，計(jì)算結(jié)果還是那樣，

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5樓2010-06-27 10:28:58

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redhaier

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tsh8167(金幣+1): 2010-06-30 11:16:28
gavinliu7390(金幣+1):謝謝交流！ 2010-07-04 10:16:06

It is hard to say why since there is no input file.

引用回帖:

Originally posted by tsh8167 at 2010-06-27 10:28:58:
[quote]Originally posted by redhaier at 2010-06-25 22:41:36:
Ok, they should be the same, try to decrease the lower energy bound in the green function
integral contour.

我試了，計(jì)算結(jié)果 ...

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6樓2010-06-28 19:54:31

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tsh8167

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[quote]Originally posted by redhaier at 2010-06-28 19:54:31:
It is hard to say why since there is no input file.

輸入文件的參數(shù)設(shè)置、計(jì)算部分：

# Set up electrodes
electrode_configuration = PeriodicAtomConfiguration(
electrode_cell,
electrode_elements,
electrode_coordinates
)

# Set up two-probe configuration
twoprobe_configuration = TwoProbeConfiguration(
(electrode_configuration,electrode_configuration),
scattering_elements,
scattering_coordinates,
electrode_repetitions=[[3,3],[3,3]],
equivalent_atoms=([0,0],[2,77])
)
if processIsMaster(): nlPrint(twoprobe_configuration)
if processIsMaster(): file.addToSample(twoprobe_configuration, 'twoprobe_configuration')

######################################################################
# Central region parameters
######################################################################
exchange_correlation_type = LDA.PZ

iteration_mixing_parameters = iterationMixingParameters(
algorithm = IterationMixing.Pulay,
diagonal_mixing_parameter = 0.1,
quantity = IterationMixing.Hamiltonian,
history_steps = 6
)

electron_density_parameters = electronDensityParameters(
mesh_cutoff = 150.0*Rydberg
)

basis_set_parameters = basisSetParameters(
type = SingleZetaPolarized,
radial_sampling_dr = 0.001*Bohr,
energy_shift = 0.01*Rydberg,
delta_rinn = 0.8,
v0 = 40.0*Rydberg,
charge = 0.0,
split_norm = 0.15
)

iteration_control_parameters = iterationControlParameters(
tolerance = 1e-005,
criterion = IterationControl.TotalEnergy,
max_steps = 100
)

electrode_voltages = (0.0,0.0)*Volt

two_probe_algorithm_parameters = twoProbeAlgorithmParameters(
electrode_constraint = ElectrodeConstraints.Off,
initial_density_type = InitialDensityType.EquivalentBulk
)

energy_contour_integral_parameters = energyContourIntegralParameters(
circle_points = 30,
integral_lower_bound = 3*Rydberg,
fermi_line_points = 10,
fermi_function_poles = 4,
real_axis_infinitesimal = 0.01*electronVolt,
real_axis_point_density = 0.02*electronVolt
)

two_center_integral_parameters = twoCenterIntegralParameters(
cutoff = 2500.0*Rydberg,
points = 1024
)

######################################################################
# Left electrode parameters
######################################################################
left_electrode_electron_density_parameters = electronDensityParameters(
mesh_cutoff = 150.0*Rydberg
)

left_electrode_iteration_control_parameters = iterationControlParameters(
tolerance = 1e-005,
criterion = IterationControl.TotalEnergy,
max_steps = 100
)

left_electrode_brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters(
monkhorst_pack_parameters = (3, 3, 100)
)

left_electrode_iteration_mixing_parameters = iterationMixingParameters(
algorithm = IterationMixing.Pulay,
diagonal_mixing_parameter = 0.1,
quantity = IterationMixing.Hamiltonian,
history_steps = 6
)

left_electrode_eigenstate_occupation_parameters = eigenstateOccupationParameters(
temperature = 300.0*Kelvin
)

######################################################################
# Collect left electrode parameters
######################################################################
left_electrode_parameters = ElectrodeParameters(
brillouin_zone_integration_parameters = left_electrode_brillouin_zone_integration_parameters,
electron_density_parameters = left_electrode_electron_density_parameters,
eigenstate_occupation_parameters = left_electrode_eigenstate_occupation_parameters,
iteration_mixing_parameters = left_electrode_iteration_mixing_parameters,
iteration_control_parameters = left_electrode_iteration_control_parameters
)

######################################################################
# Right electrode parameters
######################################################################
right_electrode_electron_density_parameters = electronDensityParameters(
mesh_cutoff = 150.0*Rydberg
)

right_electrode_iteration_control_parameters = iterationControlParameters(
tolerance = 1e-005,
criterion = IterationControl.TotalEnergy,
max_steps = 100
)

right_electrode_brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters(
monkhorst_pack_parameters = (3, 3, 100)
)

right_electrode_iteration_mixing_parameters = iterationMixingParameters(
algorithm = IterationMixing.Pulay,
diagonal_mixing_parameter = 0.1,
quantity = IterationMixing.Hamiltonian,
history_steps = 6
)

right_electrode_eigenstate_occupation_parameters = eigenstateOccupationParameters(
temperature = 300.0*Kelvin
)

######################################################################
# Collect right electrode parameters
######################################################################
right_electrode_parameters = ElectrodeParameters(
brillouin_zone_integration_parameters = right_electrode_brillouin_zone_integration_parameters,
electron_density_parameters = right_electrode_electron_density_parameters,
eigenstate_occupation_parameters = right_electrode_eigenstate_occupation_parameters,
iteration_mixing_parameters = right_electrode_iteration_mixing_parameters,
iteration_control_parameters = right_electrode_iteration_control_parameters
)

######################################################################
# Initialize self-consistent field calculation
######################################################################
two_probe_method = TwoProbeMethod(
electrode_parameters = (left_electrode_parameters,right_electrode_parameters),
exchange_correlation_type = exchange_correlation_type,
iteration_mixing_parameters = iteration_mixing_parameters,
electron_density_parameters = electron_density_parameters,
basis_set_parameters = basis_set_parameters,
iteration_control_parameters = iteration_control_parameters,
energy_contour_integral_parameters = energy_contour_integral_parameters,
two_center_integral_parameters = two_center_integral_parameters,
electrode_voltages = electrode_voltages,
algorithm_parameters = two_probe_algorithm_parameters
)
if processIsMaster(): nlPrint(two_probe_method)

# Restore self consistent calculation from check point file
scf = restoreSelfConsistentCalculation(
filename = 'D:/VNL/newmolecule/newmolecule-Au-NO2/newmolecule-Au-NO2-opt.nc'
)

runtime_parameters = runtimeParameters(
verbosity_level = 5,
checkpoint_filename = 'D:/VNL/newmolecule/newmolecule-Au-NO2/newmolecule-Au-NO2.nc'
)

# Using initial density from self consistent calculation
scf = executeSelfConsistentCalculation(
twoprobe_configuration,
two_probe_method,
initial_calculation = scf,
runtime_parameters = runtime_parameters
)
######################################################################
# Calculate physical properties
######################################################################
projected_hamiltonian_energy_spectrum = calculateProjectedHamiltonianEnergySpectrum(
self_consistent_calculation = scf,
projection_atoms = (0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77)
)
if processIsMaster(): nlPrint(projected_hamiltonian_energy_spectrum)
if processIsMaster(): file.addToSample(projected_hamiltonian_energy_spectrum, 'twoprobe_configuration', 'Projected Hamiltonian Energy Spectrum')

import numpy
transmission_spectrum = calculateTransmissionSpectrum(
self_consistent_calculation = scf,
energies = numpy.arange(-2.0, 2.0+0.002, 0.02)*electronVolt,
brillouin_zone_integration_parameters = brillouinZoneIntegrationParameters((1, 1)),
green_function_infinitesimal = 0.0001*electronVolt
)
if processIsMaster(): nlPrint(transmission_spectrum)
if processIsMaster(): file.addToSample(transmission_spectrum, 'twoprobe_configuration', 'Transmission Spectrum')

[ Last edited by tsh8167 on 2010-6-30 at 11:18 ]

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7樓2010-06-30 11:16:15

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lvjian8596(金幣+2):感謝交流！ 2010-07-04 09:23:45
tsh8167(金幣+1):謝謝交流 2010-07-04 09:37:51

你看下你說(shuō)的out文件，肯定每個(gè)原子上的電子數(shù)為0.這是叫做一個(gè)什么計(jì)算溢出。跟你選取什么基函數(shù)等沒(méi)什么關(guān)系。你可以試著優(yōu)化下結(jié)構(gòu)，再重新算�；蛘呱晕⒃龃蠓肿优c電極間的距離（如兩邊都增大0.1唉）。

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8樓2010-07-04 06:36:05

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tsh8167

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引用回帖:

Originally posted by panjinbo87 at 2010-07-04 06:36:05:
你看下你說(shuō)的out文件，肯定每個(gè)原子上的電子數(shù)為0.這是叫做一個(gè)什么計(jì)算溢出。跟你選取什么基函數(shù)等沒(méi)什么關(guān)系。你可以試著優(yōu)化下結(jié)構(gòu)，再重新算�；蛘呱晕⒃龃蠓肿优c電極間的距離（如兩邊都增大0.1唉）。

out文件：
# Electrodes 0 and 1
# -----------------------------------------------------------------------------
# Index  Element  x (Ang)  y (Ang)  z (Ang)
   0    Au    0.00    0.00    0.00
   1    Au    0.00    1.66    2.35
   2    Au    1.44    0.83    4.71
# -----------------------------------------------------------------------------
# Supercell Vectors
# -----------------------------------------------------------------------------
# Vector number  x (Ang)  y (Ang)  z (Ang)
            0    2.88    0.00    0.00
            1 -1.44    2.50    0.00
            2    0.00    0.00    7.06
# -----------------------------------------------------------------------------
# Two Probe Method
# -----------------------------------------------------------------------------

# -----------------------------------------------------------------------------
# Basis Set Parameters
# -----------------------------------------------------------------------------
Type             = SZP
Radial Sampling dr = 0.001 Bohr
Energy Shift    = 0.01 Rydberg
Delta R(inner)    = 0.8
v0                = 40 Rydberg
Charge          = 0
Split Norm       = 0.15
Element          = All

# -----------------------------------------------------------------------------
# Exchange Correlation
# -----------------------------------------------------------------------------
Exchange Correlation Type = LDA.PZ

# -----------------------------------------------------------------------------
# ElectronDensityParameters
# -----------------------------------------------------------------------------
Mesh Cutoff       = 150.00 Rydberg

# -----------------------------------------------------------------------------
# Two Center Integral Parameters
# -----------------------------------------------------------------------------
Cutoff          = 2500.0 Rydberg
Number Of Points = 1024

# -----------------------------------------------------------------------------
# Iteration Mixing Parameters
# -----------------------------------------------------------------------------
Algorithm                = Pulay
Diagonal Mixing Parameter = 0.1
Quantity                = Hamiltonian
History Steps          = 6

# -----------------------------------------------------------------------------
# Iteration Control Parameters
# -----------------------------------------------------------------------------
Tolerance  = 1e-005
Criterion  = TotalEnergy
Max. Steps = 100

# -----------------------------------------------------------------------------
# Energy Contour Integral Parameters
# -----------------------------------------------------------------------------
Circle Points          = 30
Integral Lower Bound = 3 Rydberg
Fermi Function Poles = 4
Real Axis Infinitesimal = 0.01 eV
Real Axis Point Density = 0.02 eV

# -----------------------------------------------------------------------------
# Electrode Voltages
# -----------------------------------------------------------------------------
Voltage at Electrode 0 = 0.00 V
Voltage at Electrode 1 = 0.00 V

# -----------------------------------------------------------------------------
# TwoProbe Algorithm Parameters
# -----------------------------------------------------------------------------
Electrode Constraint = ElectrodeConstraints.Off
Initial Density Type = InitialDensityType.EquivalentBulk

# sc  0 : q = -0.00341 e
# sc  1 : q = -0.00341 e  dRho = 4.2404E-009
# sc  2 : q = -0.00341 e  Etot = 171607.35005 Ry  dRho = 4.1350E-011
# sc  3 : q = -0.00341 e  Etot = 171607.35006 Ry  dRho = 3.9736E-010  dEtot = 5.6953E-006 Ry
# -----------------------------------------------------------------------------
# Energy Spectrum
# -----------------------------------------------------------------------------
# Energy (eV)
   -9942.95
   -9932.08
   -9930.06
   -9923.08
   -9923.03
   -9917.18
   -9914.21
   -9911.05
   -9908.87
   -9908.56
   -9905.48
   -9903.00
   -9902.30
   -9899.47
   -9897.87
   -9896.94
   -9896.45
   -9895.84
   -9894.46
  **中間部分省略****
   -6235.33
   -6235.28
   -6235.25
   -6234.25
   -6234.24
   -6234.16
   -5942.77
   -5942.37
   -5936.24
   -5936.10
   -5936.04
   -5935.39
   -5935.31
   -5934.71
   -5919.22
   -5919.20
   -5919.17
   -5918.54
   -5918.48
   -5918.31
   -5918.04
   -5918.03
   -5911.29
   -5911.12
   -5507.89
   -5485.27
   -5485.24
   -5485.07
   -5484.65
   -5484.57
   -5484.55
   -5474.77
   -5474.77
# -----------------------------------------------------------------------------
# Transmission Spectrum
# -----------------------------------------------------------------------------
# Energy (eV) Coefficient
      -2.00       0.0000
      -1.98       0.0000
      -1.96       0.0000
      -1.94       0.0000
      -1.92       0.0000
      -1.90       0.0000
      -1.88       0.0000
      -1.86       0.0000
      -1.84       0.0000
      -1.82       0.0000
      -1.80       0.0000
      -1.78       0.0000
      -1.76       0.0000
      -1.74       0.0000
      -1.72       0.0000
      -1.70       0.0000
      -1.68       0.0000
      -1.66       0.0000
      -1.64       0.0000
      -1.62       0.0000
      -1.60       0.0000
      -1.58       0.0000
      -1.56       0.0000
      -1.54       0.0000
      -1.52       0.0000
      -1.50       0.0000
      -1.48       0.0000
      -1.46       0.0000
      -1.44       0.0000
      -1.42       0.0000
      -1.40       0.0000
      -1.38       0.0000
      -1.36       0.0000
      -1.34       0.0000
      -1.32       0.0000
      -1.30       0.0000
      -1.28       0.0000
      -1.26       0.0000
      -1.24       0.0000
      -1.22       0.0000
      -1.20       0.0000
      -1.18       0.0000
      -1.16       0.0000
      -1.14       0.0000
      -1.12       0.0000
      -1.10       0.0000
      -1.08       0.0000
      -1.06       0.0000
      -1.04       0.0000
      -1.02       0.0000
      -1.00       0.0000
      -0.98       0.0000
      -0.96       0.0000
      -0.94       0.0000
      -0.92       0.0000
      -0.90       0.0000
      -0.88       0.0000
      -0.86       0.0000
      -0.84       0.0000
      -0.82       0.0000
      -0.80       0.0000
      -0.78       0.0000
      -0.76       0.0000
      -0.74       0.0000
      -0.72       0.0000
      -0.70       0.0000
      -0.68       0.0000
      -0.66       0.0000
      -0.64       0.0000
      -0.62       0.0000
      -0.60       0.0000
      -0.58       0.0000
      -0.56       0.0000
      -0.54       0.0000
      -0.52       0.0000
      -0.50       0.0000
      -0.48       0.0000
      -0.46       0.0000
      -0.44       0.0000
      -0.42       0.0000
      -0.40       0.0000
      -0.38       0.0000
      -0.36       0.0000
      -0.34       0.0000
      -0.32       0.0000
      -0.30       0.0000
      -0.28       0.0000
      -0.26       0.0000
      -0.24       0.0000
      -0.22       0.0000
      -0.20       0.0000
      -0.18       0.0000
      -0.16       0.0000
      -0.14       0.0000
      -0.12       0.0000
      -0.10       0.0000
      -0.08       0.0000
      -0.06       0.0000
      -0.04       0.0000
      -0.02       0.0000
      0.00       0.0000
      0.02       0.0000
      0.04       0.0000
      0.06       0.0000
      0.08       0.0000
      0.10       0.0000
      0.12       0.0000
      0.14       0.0000
      0.16       0.0000
      0.18       0.0000
      0.20       0.0000
      0.22       0.0000
      0.24       0.0000
      0.26       0.0000
      0.28       0.0000
      0.30       0.0000
      0.32       0.0000
      0.34       0.0000
      0.36       0.0000
      0.38       0.0000
      0.40       0.0000
      0.42       0.0000
      0.44       0.0000
      0.46       0.0000
      0.48       0.0000
      0.50       0.0000
      0.52       0.0000
      0.54       0.0000
      0.56       0.0000
      0.58       0.0000
      0.60       0.0000
      0.62       0.0000
      0.64       0.0000
      0.66       0.0000
      0.68       0.0000
      0.70       0.0000
      0.72       0.0000
      0.74       0.0000
      0.76       0.0000
      0.78       0.0000
      0.80       0.0000
      0.82       0.0000
      0.84       0.0000
      0.86       0.0000
      0.88       0.0000
      0.90       0.0000
      0.92       0.0000
      0.94       0.0000
      0.96       0.0000
      0.98       0.0000
      1.00       0.0000
      1.02       0.0000
      1.04       0.0000
      1.06       0.0000
      1.08       0.0000
      1.10       0.0000
      1.12       0.0000
      1.14       0.0000
      1.16       0.0000
      1.18       0.0000
      1.20       0.0000
      1.22       0.0000
      1.24       0.0000
      1.26       0.0000
      1.28       0.0000
      1.30       0.0000
      1.32       0.0000
      1.34       0.0000
      1.36       0.0000
      1.38       0.0000
      1.40       0.0000
      1.42       0.0000
      1.44       0.0000
      1.46       0.0000
      1.48       0.0000
      1.50       0.0000
      1.52       0.0000
      1.54       0.0000
      1.56       0.0000
      1.58       0.0000
      1.60       0.0000
      1.62       0.0000
      1.64       0.0000
      1.66       0.0000
      1.68       0.0000
      1.70       0.0000
      1.72       0.0000
      1.74       0.0000
      1.76       0.0000
      1.78       0.0000
      1.80       0.0000
      1.82       0.0000
      1.84       0.0000
      1.86       0.0000
      1.88       0.0000
      1.90       0.0000
      1.92       0.0000
      1.94       0.0000
      1.96       0.0000
      1.98       0.0000
      2.00       0.0000

贊一下

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9樓2010-07-04 09:41:17

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tsh8167

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引用回帖:

Originally posted by panjinbo87 at 2010-07-04 06:36:05:
你看下你說(shuō)的out文件，肯定每個(gè)原子上的電子數(shù)為0.這是叫做一個(gè)什么計(jì)算溢出。跟你選取什么基函數(shù)等沒(méi)什么關(guān)系。你可以試著優(yōu)化下結(jié)構(gòu)，再重新算。或者稍微增大分子與電極間的距離（如兩邊都增大0.1唉）。

電極與分子間的距離我選取的是一個(gè)能量最低值，這是我經(jīng)過(guò)計(jì)算得出的結(jié)果。也進(jìn)行過(guò)再次優(yōu)化，結(jié)果也是一樣。
我現(xiàn)在考慮的是，是不是我的電極表面原子選取過(guò)少，導(dǎo)致兩相鄰分子間的結(jié)構(gòu)發(fā)生交叉？？目前我把金表面原子從3*3改為4*4，重新進(jìn)行優(yōu)化，目前優(yōu)化正在進(jìn)行中。
不知道我的這種考慮是不是正確的？還請(qǐng)大俠指教。

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