121
General Questions and Answers / Re: How to restar the calculation because of exceeding walktime?
« on: March 22, 2016, 04:33 »
I have read this chapter before. But it can't provide me useful methods. Thank you.
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122
General Questions and Answers / How to restar the calculation because of exceeding walktime?
« on: March 22, 2016, 02:56 »
Dear staffs, I want to restar the calculation which stops due to exceeding walktime.I modify the origin script as following:
#----------------------------------------
# Device Calculator
#----------------------------------------
calculator = DeviceLCAOCalculator(
contour_parameters=contour_parameters,
electrode_calculators=
[left_electrode_calculator, right_electrode_calculator],
)
device_configuration.setCalculator(calculator)
nlprint(device_configuration)
device_configuration = nlread("/tmp/checkpoint48792306.nc")[0]
device_configuration.update(force_restart=True)
nlsave('aIV.nc', device_configuration)
I calculate by means of the cluster,using node65.However,the cluster tell me "/tmp/checkpoint48792306.nc, was not found - please check correct path and name" I don't know how to do.
#----------------------------------------
# Device Calculator
#----------------------------------------
calculator = DeviceLCAOCalculator(
contour_parameters=contour_parameters,
electrode_calculators=
[left_electrode_calculator, right_electrode_calculator],
)
device_configuration.setCalculator(calculator)
nlprint(device_configuration)
device_configuration = nlread("/tmp/checkpoint48792306.nc")[0]
device_configuration.update(force_restart=True)
nlsave('aIV.nc', device_configuration)
I calculate by means of the cluster,using node65.However,the cluster tell me "/tmp/checkpoint48792306.nc, was not found - please check correct path and name" I don't know how to do.
123
General Questions and Answers / Are there other ways to construct a graphene nanoribbon?
« on: March 21, 2016, 09:29 »
Dear staffs:when I want to construct a graphene nanoribbon,I can make it as tutorails teach me: extract the unit cell from "nanoribbon" plugins, set parameters, optimize the unit cell and repeat the optimized cell along the Z direction.
I just want to ask: are there other ways to construct a graphene nanoribbon?
For example: (1). extract the unit cell from database by typing "graphene" . (2).considering the construction of graphene is monolayer, expand vacuum in the non-periodic direction (the default direction is the C direction). (3). optimize the cell with DFT, set K-points 27*27*1. (4).transform to the orthogonal cell, swap axes, be sure that the transportation direction is the Z direction. (5).repeat the orthogonal cell along the Z direction.
Or:(1). extract the unit cell from database by typing "graphene" .(2). transform to the orthogonal cell, swap axes, be sure that the transportation direction is the Z direction. (3). expand vacuum in the non-periodic direction (assum that the A direction is non-periodic). (4) optimize the cell with DFT, set K-points 1*27*27. (5). repeat the optimized cell along the Z direction.
Can I construct the correct graphene nanoribbon in ways described above?
Thank you very much!
I just want to ask: are there other ways to construct a graphene nanoribbon?
For example: (1). extract the unit cell from database by typing "graphene" . (2).considering the construction of graphene is monolayer, expand vacuum in the non-periodic direction (the default direction is the C direction). (3). optimize the cell with DFT, set K-points 27*27*1. (4).transform to the orthogonal cell, swap axes, be sure that the transportation direction is the Z direction. (5).repeat the orthogonal cell along the Z direction.
Or:(1). extract the unit cell from database by typing "graphene" .(2). transform to the orthogonal cell, swap axes, be sure that the transportation direction is the Z direction. (3). expand vacuum in the non-periodic direction (assum that the A direction is non-periodic). (4) optimize the cell with DFT, set K-points 1*27*27. (5). repeat the optimized cell along the Z direction.
Can I construct the correct graphene nanoribbon in ways described above?
Thank you very much!
124
General Questions and Answers / Why do we modify values of primitive vectors when study a monolayer nanoribbon
« on: March 10, 2016, 10:34 »
Dear QuantumWise Staffs,when I analyze band structures of a monolayer nanoribbon,I am told to expand vaccum around the unit cell before caculations. Does it mean that VNL only shows one visible unit cell, although there are many hidden unit cells around the particular one ? Increasing values of primitive vectors is to avoid effects of neighbor unit cells on the particular one, is that ture?
By the way,is the result same by manipluting primitive vectors in Lattice parameters or using sliders in Stretch Cell?
Looking forward to your reply.
Best regards
By the way,is the result same by manipluting primitive vectors in Lattice parameters or using sliders in Stretch Cell?
Looking forward to your reply.
Best regards