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tsh8167木虫 (小有名气)
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【求助】算分子能谱的时候结果全都为负数，是问题引起的？ 已有4人参与
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我在计算双探针体系中的分子能谱的时候，得出的数据是从-9942.9到-5474.78，这是我加入一个硝基后出现的错误。 但是加另一种氨基和没加侧基团所计算的结果都是正常的。这三种体系都是用同一种方法构建，都用SZP基组进行了优化。 请问，我的计算是什么地方发生了错误？有哪些原因可以导致上述的错误发生？？ 期待高手指教。 [ Last edited by tsh8167 on 2010-6-28 at 11:29 ] |
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tsh8167
木虫 (小有名气)
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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. 输入文件的参数设置、计算部分： # 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 ] |
7楼2010-06-30 11:16:15
2楼2010-06-24 17:15:00
tsh8167
木虫 (小有名气)
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3楼2010-06-24 17:43:19
4楼2010-06-25 22:41:36
