31
General Questions and Answers / Re: DFTB basis set
« on: November 29, 2023, 13:11 »Thank you very much!
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Thank you very much!
32
General Questions and Answers / Phase/Magnitude of Transmission through Molecular Orbitals
« on: November 22, 2023, 16:34 »
Hello,
Please, How can I have access to the phase and transmission contribution of each molecular orbital in a molecular junction? I want to reproduce the pictures 6 and 7 of the paper <https://doi.org/10.1063/5.0141577>. I also attached the images from the paper.
Best,
Joseane
Please, How can I have access to the phase and transmission contribution of each molecular orbital in a molecular junction? I want to reproduce the pictures 6 and 7 of the paper <https://doi.org/10.1063/5.0141577>. I also attached the images from the paper.
Best,
Joseane
33
General Questions and Answers / Re: optimize_cell flag Error
« on: November 22, 2023, 10:16 »
Dear,
Thank you. So if I use < disable_stress=True > means the same in my version (2021.06)?
Best,
Joseane
Thank you. So if I use < disable_stress=True > means the same in my version (2021.06)?
Best,
Joseane
34
General Questions and Answers / Optimization in OneProbe Configuration
« on: November 21, 2023, 15:35 »
Hello 
I am trying to optimize a system surface+molecule using SurfaceConfiguration instead of slab method. However, I don't know the right way to proceed for the optimization. The calculator needs to be DeviceLCAOCalculator, but for optimization seems that I cannot use OptimizeDeviceConfiguration class. If I use the OptimizeGeometry I still need add constrains by myself to fix the atoms from left electrode and the electrode repetition?
For writing the input, comparing with two probe configuration script, the only difference is the boundary conditions, right?
Best,
Joseane
I am trying to optimize a system surface+molecule using SurfaceConfiguration instead of slab method. However, I don't know the right way to proceed for the optimization. The calculator needs to be DeviceLCAOCalculator, but for optimization seems that I cannot use OptimizeDeviceConfiguration class. If I use the OptimizeGeometry I still need add constrains by myself to fix the atoms from left electrode and the electrode repetition?
For writing the input, comparing with two probe configuration script, the only difference is the boundary conditions, right?
Best,
Joseane
35
General Questions and Answers / Re: Basis set for Hydrogen
« on: October 9, 2023, 11:00 »
All right, thank you!
36
General Questions and Answers / optimize_cell flag Error
« on: October 4, 2023, 10:02 »
Hello,
I am trying to optimize a bulk configuration without change the unit cell. However I got an error that this flag does not belong to the class OptimizeGeometry! Please, What could be the problem?
My script:
bulk_configuration = nlread('/path/bulk.hdf5', BulkConfiguration)[0]
# -------------------------------------------------------------
# Optimize Geometry
# -------------------------------------------------------------
constraints = None
bulk_configuration = OptimizeGeometry(
bulk_configuration,
max_forces=0.02*eV/Ang,
max_steps=50,
max_step_length=0.2*Ang,
constraints=constraints,
optimize_cell=False,
trajectory_filename='bulk_trajectory.hdf5',
restart_strategy=RestartFromTrajectory(),
disable_stress=True,
optimizer_method=LBFGS(),
)
nlsave('bulk.hdf5', bulk_configuration)
nlprint(bulk_configuration)
The error:
File "bulk.py", line 9, in <module>
bulk_configuration = OptimizeGeometry(
TypeError: OptimizeGeometry() got an unexpected keyword argument 'optimize_cell'
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 38
/tmp2/slurmd/job143810/slurm_script : ligne 50 : 261141 Erreur de segmentation mpiexec -n 44 atkpython $job.py > $job.out
I am trying to optimize a bulk configuration without change the unit cell. However I got an error that this flag does not belong to the class OptimizeGeometry! Please, What could be the problem?
My script:
bulk_configuration = nlread('/path/bulk.hdf5', BulkConfiguration)[0]
# -------------------------------------------------------------
# Optimize Geometry
# -------------------------------------------------------------
constraints = None
bulk_configuration = OptimizeGeometry(
bulk_configuration,
max_forces=0.02*eV/Ang,
max_steps=50,
max_step_length=0.2*Ang,
constraints=constraints,
optimize_cell=False,
trajectory_filename='bulk_trajectory.hdf5',
restart_strategy=RestartFromTrajectory(),
disable_stress=True,
optimizer_method=LBFGS(),
)
nlsave('bulk.hdf5', bulk_configuration)
nlprint(bulk_configuration)
The error:
File "bulk.py", line 9, in <module>
bulk_configuration = OptimizeGeometry(
TypeError: OptimizeGeometry() got an unexpected keyword argument 'optimize_cell'
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 38
/tmp2/slurmd/job143810/slurm_script : ligne 50 : 261141 Erreur de segmentation mpiexec -n 44 atkpython $job.py > $job.out
37
General Questions and Answers / Re: Basis set for Hydrogen
« on: October 4, 2023, 09:49 »
So it seems like there's no big difference in the calculation if I choose one or the other. Thank you!
38
General Questions and Answers / DFTB basis set
« on: September 12, 2023, 16:23 »
Dear,
Please, is it possible set different basis set for different atoms in DFTB scheme? I have a system cluster-molecule-cluster, and I want to keep the symmetry closer to fcc bulk structure. I used the Wulff constructor and I want to optimise with clusters of different sizes. I suppose that for ~20 Au atoms the LCAOCalculator will be nice. However, more than 100 atoms for each cluster, I suppose it is better use DFTB. The gold is coordinate with sulphur and my molecule contains C, N , H and Fe. Seeing the AtomicData page on documentation, I believe that could be good use the basis set auorg-1-1 for the Au, mio-1-1 for H,C,N and S, and trans3d-0-1 for Fe. However, how can I do this?
Please, is it possible set different basis set for different atoms in DFTB scheme? I have a system cluster-molecule-cluster, and I want to keep the symmetry closer to fcc bulk structure. I used the Wulff constructor and I want to optimise with clusters of different sizes. I suppose that for ~20 Au atoms the LCAOCalculator will be nice. However, more than 100 atoms for each cluster, I suppose it is better use DFTB. The gold is coordinate with sulphur and my molecule contains C, N , H and Fe. Seeing the AtomicData page on documentation, I believe that could be good use the basis set auorg-1-1 for the Au, mio-1-1 for H,C,N and S, and trans3d-0-1 for Fe. However, how can I do this?
40
General Questions and Answers / Basis set for Hydrogen
« on: August 29, 2023, 17:03 »
Dear all,
Please, what is the difference between use confined orbital for the Hydrogen atom and use directly the python class HydrogenOrbital? Are there some documentation explain better the HydrogenOrbital class (for example, the mathematical expression of the function )?
Please, what is the difference between use confined orbital for the Hydrogen atom and use directly the python class HydrogenOrbital? Are there some documentation explain better the HydrogenOrbital class (for example, the mathematical expression of the function )?
41
General Questions and Answers / HSE+U
« on: July 7, 2023, 17:13 »
Dear all,
Please, is it possible in QuantumATK use DFT+U with a Hybrid functional like HSE?
Please, is it possible in QuantumATK use DFT+U with a Hybrid functional like HSE?
42
General Questions and Answers / Re: QuantumATK doesn't read optimized structure
« on: April 5, 2023, 17:26 »
All right. Since I tried different ways without success, the solution that I found was drop it in the builder and save the coordinates of optimized structure to do one scf calculation that I can use the hdf5 file later. Thank you for your reply!
43
General Questions and Answers / Re: QuantumATK doesn't read optimized structure
« on: March 31, 2023, 09:47 »
Thanks for your reply. Unfortunately it didn't work. I tried 0, 1, -1, -2 just to check and all of them gives the error "IndexError: list index out of range".
44
General Questions and Answers / QuantumATK doesn't read optimized structure
« on: March 30, 2023, 11:17 »
Dear all,
Please, I am trying to read the optimized structure of a junction but doesn't work. The part of the code is bellow:
device_configuration = nlread(filename='/home/jalmeida/MyProjects/junction/opt.hdf5',
class_type=DeviceConfiguration,
object_id='optimizedeviceconfiguration')
However, I got the error:
NL.ComputerScienceUtilities.Exceptions.NLTypeError: The parameter 'configuration' must be an instance of one of the following: MoleculeConfiguration, BulkConfiguration, SurfaceConfiguration, DeviceConfiguration.
The image of the objects is attached. probably I need to declare somehow the 'Optimized Configuration' to describe well where my DeviceConfiguration is. Thanks in advance!
Have a nice day,
SANTOS ALMEIDA, Joseane.
Please, I am trying to read the optimized structure of a junction but doesn't work. The part of the code is bellow:
device_configuration = nlread(filename='/home/jalmeida/MyProjects/junction/opt.hdf5',
class_type=DeviceConfiguration,
object_id='optimizedeviceconfiguration')
However, I got the error:
NL.ComputerScienceUtilities.Exceptions.NLTypeError: The parameter 'configuration' must be an instance of one of the following: MoleculeConfiguration, BulkConfiguration, SurfaceConfiguration, DeviceConfiguration.
The image of the objects is attached. probably I need to declare somehow the 'Optimized Configuration' to describe well where my DeviceConfiguration is. Thanks in advance!
Have a nice day,
SANTOS ALMEIDA, Joseane.