16
General Questions and Answers / Re: Error of VNL concerning band structure analyzer
« on: April 12, 2015, 12:26 »
OK. Thanks a lot.
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17
General Questions and Answers / Re: How to visualize electrostatic potential file in VNL
« on: April 9, 2015, 14:04 »
Hi,
The file format of LOCPOT is completely same to CHGCAR, hence if you can open CHGCAR successfully, you should also open LOCPOT. However, in your case, it didn't work. I think you may try to check the contents of LOCPOT and the calculation in your VASP.
Bests
The file format of LOCPOT is completely same to CHGCAR, hence if you can open CHGCAR successfully, you should also open LOCPOT. However, in your case, it didn't work. I think you may try to check the contents of LOCPOT and the calculation in your VASP.
Bests
18
General Questions and Answers / Re: Optimization parameters for convergence
« on: April 9, 2015, 13:47 »
Dear Dr. Kstokbro,
Thanks for your answers.
Usually I need to conduct DFT calculations for large systems composed of solids or oxides thin films. Did you mean ATK-DFT should be the fastest code when treating this kind of calculation? But the calculation for me isn't as fast as you said. I think some important parameters may not be very reasonable in my recent calculations.
To make it clear, the codes of a recent DFT calculation was pasted here. Could you give me some advice especially for the convergence criterion. This work of geometry optimization cost me 17 hours using one master and 3 slaves, which was much slower than other packages did.
Kindest bests
Fang
Thanks for your answers.
Usually I need to conduct DFT calculations for large systems composed of solids or oxides thin films. Did you mean ATK-DFT should be the fastest code when treating this kind of calculation? But the calculation for me isn't as fast as you said. I think some important parameters may not be very reasonable in my recent calculations.
To make it clear, the codes of a recent DFT calculation was pasted here. Could you give me some advice especially for the convergence criterion. This work of geometry optimization cost me 17 hours using one master and 3 slaves, which was much slower than other packages did.
Kindest bests
Fang
Code
# -------------------------------------------------------------
# Bulk configuration
# -------------------------------------------------------------
# Set up lattice
lattice = SimpleTetragonal(3.9909999371*Angstrom, 36.2396011353*Angstrom)
# Define elements
elements = [Platinum, Platinum, Platinum, Platinum, Platinum, Platinum,
Platinum, Platinum, Platinum, Platinum, Platinum, Platinum,
Platinum, Platinum, Platinum, Platinum, Platinum, Platinum, Barium,
Barium, Barium, Barium, Titanium, Titanium, Titanium, Titanium,
Titanium, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen,
Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen, Oxygen]
# Define coordinates
fractional_coordinates = [[ 0. , 0. , 0.054310001],
[ 0. , 0. , 0.162929997],
[ 0. , 0.5 , 0. ],
[ 0. , 0.5 , 0.108620003],
[ 0. , 0.5 , 0.217230007],
[ 0.5 , 0. , 0. ],
[ 0.5 , 0. , 0.108620003],
[ 0.5 , 0. , 0.217230007],
[ 0.5 , 0.5 , 0.054310001],
[ 0.5 , 0.5 , 0.162929997],
[ 0. , 0. , 0.945689976],
[ 0. , 0. , 0.837069988],
[ 0. , 0.5 , 0.891380012],
[ 0. , 0.5 , 0.782769978],
[ 0.5 , 0. , 0.891380012],
[ 0.5 , 0. , 0.782769978],
[ 0.5 , 0.5 , 0.945689976],
[ 0.5 , 0.5 , 0.837069988],
[ 0. , 0. , 0.331499994],
[ 0. , 0. , 0.443830013],
[ 0. , 0. , 0.556169987],
[ 0. , 0. , 0.668500006],
[ 0.5 , 0.5 , 0.276719987],
[ 0.5 , 0.5 , 0.389050007],
[ 0.5 , 0.5 , 0.501380026],
[ 0.5 , 0.5 , 0.613709986],
[ 0.5 , 0.5 , 0.726040006],
[ 0.5 , 0. , 0.275339991],
[ 0.5 , 0. , 0.38767001 ],
[ 0.5 , 0. , 0.5 ],
[ 0.5 , 0. , 0.612330019],
[ 0.5 , 0. , 0.724659979],
[ 0. , 0.5 , 0.275339991],
[ 0. , 0.5 , 0.38767001 ],
[ 0. , 0.5 , 0.5 ],
[ 0. , 0.5 , 0.612330019],
[ 0. , 0.5 , 0.724659979],
[ 0.5 , 0.5 , 0.331499994],
[ 0.5 , 0.5 , 0.443830013],
[ 0.5 , 0.5 , 0.556169987],
[ 0.5 , 0.5 , 0.668500006]]
# Set up configuration
bulk_configuration = BulkConfiguration(
bravais_lattice=lattice,
elements=elements,
fractional_coordinates=fractional_coordinates
)
# Add tags
bulk_configuration.addTags('Constraints')
# -------------------------------------------------------------
# Calculator
# -------------------------------------------------------------
#----------------------------------------
# Basis Set
#----------------------------------------
basis_set = [
GGABasis.Oxygen_DoubleZetaPolarized,
GGABasis.Titanium_DoubleZetaPolarized,
GGABasis.Barium_DoubleZetaPolarized,
GGABasis.Platinum_DoubleZetaPolarized,
]
#----------------------------------------
# Exchange-Correlation
#----------------------------------------
exchange_correlation = GGA.PBE
numerical_accuracy_parameters = NumericalAccuracyParameters(
k_point_sampling=(4, 4, 1),
)
calculator = LCAOCalculator(
basis_set=basis_set,
exchange_correlation=exchange_correlation,
numerical_accuracy_parameters=numerical_accuracy_parameters,
)
bulk_configuration.setCalculator(calculator)
nlprint(bulk_configuration)
bulk_configuration.update()
nlsave('fer_relax.nc', bulk_configuration)
constraints = [FixStrain(x=True, y=True, z=False), 2, 5]
bulk_configuration = OptimizeGeometry(
bulk_configuration,
max_forces=0.1*eV/Ang,
max_stress=0.05*eV/Ang**3,
max_steps=200,
max_step_length=0.2*Ang,
constraints=constraints,
trajectory_filename=None,
optimizer_method=LBFGS(),
)
nlsave('fer_relax.nc', bulk_configuration)
nlprint(bulk_configuration)
19
General Questions and Answers / Re: Error of VNL concerning band structure analyzer
« on: April 3, 2015, 10:02 »
Is it necessary to update the license for 2014.2?
20
General Questions and Answers / Error of VNL concerning band structure analyzer
« on: April 2, 2015, 02:58 »
Dear all,
Yesterday, I updated some add-on plugins for our VNL 2014.1. But when I wanted to open it in this morning, it presented an error.
Could you tell me how to fix this error?
Thank you in advance.
Bests
Fang
Yesterday, I updated some add-on plugins for our VNL 2014.1. But when I wanted to open it in this morning, it presented an error.
Could you tell me how to fix this error?
Thank you in advance.
Bests
Fang
21
General Questions and Answers / Re: Optimization parameters for convergence
« on: April 2, 2015, 02:49 »
Hi, Dr. Kstokbro,
Thanks a lot.
Do you have experience in the settings of max_forces and max_stress for large systems?
For the step length, is it a good manner to use the default value given by ATK?
Comparing with other electronic structure calculation packages in our group, ATK isn't very fast within the framework of ATK-DFT.
Bests
Thanks a lot.
Do you have experience in the settings of max_forces and max_stress for large systems?
For the step length, is it a good manner to use the default value given by ATK?
Comparing with other electronic structure calculation packages in our group, ATK isn't very fast within the framework of ATK-DFT.
Bests
22
General Questions and Answers / Optimization parameters for convergence
« on: April 1, 2015, 04:58 »
Dear all,
For the geometry optimization in ATK, we usually use the parameters including
For the small systems such as a five atoms unite cell, it's easy to get convergence. However, I found that sometimes it's not a trivial thing for large systems more that 50 atoms using ATK-DFT methods in VNL-ATK 2014.1. I think it should be caused the unreasonable optimization parameters setted by me.
As said by the official manual (http://www.quantumwise.com/documents/manuals/ATK-13.8/ReferenceManual/ref.optimizegeometry.html) , combining with my personal experience, max_forces is applied to atoms and the max_stress is applied to the cell. However, how to make them collaborate with each other effectively for large systems, together with max_steps and max_step_length?
In the VASP software, we usually set two converge criterion, one is energy and the other is force. ATK seems different from VASP in this aspect. Energy criterion is absent in ATK. I don't understand why ATK employs max_step_length (the maximum step length the optimizer may take). Especially, why angstrom is chosen to serve as its length unit?
Any comments are appreciated.
Thank you in advance.
Fang
For the geometry optimization in ATK, we usually use the parameters including
Code
OptimizeGeometry(
configuration,
max_forces,
max_stress,
max_steps,
max_step_length,
scf_restart_step_length,
constraints,
trajectory_filename,
disable_stress,
optimizer_method
)For the small systems such as a five atoms unite cell, it's easy to get convergence. However, I found that sometimes it's not a trivial thing for large systems more that 50 atoms using ATK-DFT methods in VNL-ATK 2014.1. I think it should be caused the unreasonable optimization parameters setted by me.
As said by the official manual (http://www.quantumwise.com/documents/manuals/ATK-13.8/ReferenceManual/ref.optimizegeometry.html) , combining with my personal experience, max_forces is applied to atoms and the max_stress is applied to the cell. However, how to make them collaborate with each other effectively for large systems, together with max_steps and max_step_length?
In the VASP software, we usually set two converge criterion, one is energy and the other is force. ATK seems different from VASP in this aspect. Energy criterion is absent in ATK. I don't understand why ATK employs max_step_length (the maximum step length the optimizer may take). Especially, why angstrom is chosen to serve as its length unit?
Any comments are appreciated.
Thank you in advance.
Fang
23
Installation and License Questions / Re: License error when parallelling on computing node
« on: November 19, 2014, 02:35 »
Hi, Dr. Anders Blom,
Yeah, you got the key to the problem. Last night, with the help of Dr. Dong from fermi-tech, I finally found the solution which is almost same to your reply.
Thank you for your advice about my posting. I have deleted the private information.
Bests
Fang
Yeah, you got the key to the problem. Last night, with the help of Dr. Dong from fermi-tech, I finally found the solution which is almost same to your reply.
Thank you for your advice about my posting. I have deleted the private information.
Bests
Fang
24
Installation and License Questions / License error when parallelling on computing node
« on: November 17, 2014, 14:12 »
Dear all,
The installed ATK with a floating license is in a SUGON high performance computer (SUGON-HPC) consisting of master node and many other computing nodes and storage nodes.
Before posting this topic, I have read the topics related to my problem in this forum and also asked help from HPC administrators and the cooperators of QuantumWise in China, but I still haven't got a nice solution.
Any comment is appreciated.
Bests.
Fang
The problem was soloved so I modify the content of this topic because of too many private information. Thanks to Dr. Anders's instructions.
The installed ATK with a floating license is in a SUGON high performance computer (SUGON-HPC) consisting of master node and many other computing nodes and storage nodes.
Before posting this topic, I have read the topics related to my problem in this forum and also asked help from HPC administrators and the cooperators of QuantumWise in China, but I still haven't got a nice solution.
Any comment is appreciated.
Bests.
Fang
The problem was soloved so I modify the content of this topic because of too many private information. Thanks to Dr. Anders's instructions.
25
General Questions and Answers / Re: Mulliken Population-Spin Polarised calculation
« on: November 10, 2014, 09:29 »
Hi, Jananikumar
In your case,
1.952 is the spin-up electrons and 2.142 is the spin-down electrons
Bests
Fang
In your case,
1.952 is the spin-up electrons and 2.142 is the spin-down electrons
Bests
Fang
26
General Questions and Answers / Re: meta-GGA is not recommended for geometry optimizations！Why?
« on: July 9, 2012, 16:24 »Yes and no.
It is not ATK - it is the functional itself.
The way they use in the paper originally, is that the optimize the structure using LDA and once they have optimized the structure they use their functional TB09
to recalculate the bandstructure etc.
Yeah, I see! Thank you, captain!
27
General Questions and Answers / Re: meta-GGA is not recommended for geometry optimizations！Why?
« on: July 9, 2012, 15:22 »The TB09 was constructed by the authors for giving accurate bandstructure (i.e. band gaps) of insulators and semi-conductors, it was never intended for giving good total energies and forces.
in conclusion, because we cannot get accurate information about bandstructure, it is not possible for ATK to define a proper derivative of the TB09 potential, and hence we also cannot get good total energies and forces, is it right?
thank you very much
28
General Questions and Answers / Re: meta-GGA is not recommended for geometry optimizations！Why?
« on: July 9, 2012, 15:09 »In order for a geometric optimization to be good, the total energy and forces ( the derivative with respect to the total energy) needs to be proper correlated. The exchange-correlation is part of this energy.
For the TB09 metaGGA which the one currently supported in ATK, it is not possible to define a proper derivative of the TB09 potential, and hence the total energy and the forces is not well correlated any more.
In the worst case, it can end up with having non-zero forces in the minimum or having zero forces in a non-extreme.
thank you, I've got it. It's very kind of you.
29
General Questions and Answers / meta-GGA is not recommended for geometry optimizations！Why?
« on: July 8, 2012, 03:51 »
In the morning, I found some information about meta-GGA from ATK manual.
It was stated that "A noteworthy detail about the meta-GGA exchange potential is that it can usually not be written as a derivative of an exchange functional. Therefore, meta-GGA is not recommended for geometry optimizations; for that, one should use standard GGA."
The question is why meta-GGA is not recommended fro geometry optimizations?
What's the relation between the exchange functional and geometry optimizations?
Thank you!
It was stated that "A noteworthy detail about the meta-GGA exchange potential is that it can usually not be written as a derivative of an exchange functional. Therefore, meta-GGA is not recommended for geometry optimizations; for that, one should use standard GGA."
The question is why meta-GGA is not recommended fro geometry optimizations?
What's the relation between the exchange functional and geometry optimizations?
Thank you!
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