The use of magnetic moment, kpoints, ionmov, supercells, and DOS
Posted: Mon Jun 15, 2020 7:04 pm
Hi,
I was trying to test a couple of different parameters related to the magnetic moment, kpoints and the ionmov, supercell but don't know if there's something wrong.
The compound is an Mn-oxide with an antiferromagnetic structure and I expect the Mn moment to be ~4 µB/ion but when I run the calculation I reach more than 6 Bohr magnetons which is far too much. Since the structure is hexagonaI would also need to calculate the kpoints centered at the Gamma point.
I would also like to run a relaxation of the atomic cores and the full cell relaxation using ionmov. Further I would like to know how supercells are made and how the electronic DOS is easiest plotted with nice graphs similar to the Sumo software used for VASP (https://sumo.readthedocs.io/en/latest/gallery.html ).
So, more specifically:
1) I would like to have a spin poarized DOS. To refine the magnetic moment I use a spin polarized calculation with
nsppol 2
nspden 2
nspinor 1
spinat with 0 0 4 on the magnetic atom positions as starting magnetic moments (I hope this is correctly understood)
However, I was told by the err file that I should use spinmagntarget, which I have put to 0. So I don't know which one decides the starting moment
------------------------------------------------------------------------
2) for kpoints I use
chksymbreak 0
ngkpt 4 4 4 for the grid resolution
shiftk 0 0 0 I assume this decides if it is Gamma centered or not?
-------------------------------------------------------------------------
3) to relax the atomic cores I use
ionmov 2
optcell 0
toldff 5.0d-5 the convergence criteria for the forces (can I change the units here?)
However, I don't understand if abinit has some specific priority when running, i.e., if electronic SCF is first made then secondly the ionmov step and then SCF again and then ionmov for each step in the convegence? Or does it skip the SCF and go directly to the ionmov and move around the atoms or cores? When I check the output file I only notice the ionmov written as step 1/1 so I don't undertstand if this step is done with each SCF or not. In VASP I think each SCF step includes a atomic or nucleus movement before running SCF again and repeating the movement of the atoms/cores. What is the procedure in abinit? If I set nstep 50 and toldff 5d-5, will the SCF stop when the forces have reached 5d-5 even before SCF has reached 50? and will it otherwise just continue until lthe limit 50 is reached?
--------------------------------------------------------------------------
4) I would like to try and test the difference in energies between different cell sizes, how do I get supercells in abinit? do I multiply the cell parameters with a scalar e.g., a 4 4 4 cell with 2*4 2*4 2*4 to show abinit that I want a supercell or do I need to make a cif with a cell X times larger? that is not practical for a supercell with sya, 500 atoms or larger to add each atom manually
---------------------------------------------------------------------------
5) I would like to make chained calculations so that I first calculate only SCF, then use the ionmov for atomic cores, and finally geometry.
Can I somehow link the ndtset so that each calculaltion continues from the latest results?
Also I didn't quite understand the use of the udtset, why is there 2 different values that add up to ndtset.
--------------------------------------------------------------------------
6) Currently I can only plot the eDOS by using the "abiopen.py *_GSR.nc --expose -sns=talk" from base tutorial 3 for silicon. But The band structure looks horrible and I doubt that people publish such ugly band structures, at least the ones I have obtained.
I have used the abipy obtion to create the k-path for the space group from a cif file, which is something like:
iscf -2
tolwfr 1d-16
# K-path in reduced coordinates:
ndivsm 10
kptopt -11
kptbounds
+0.00000 +0.00000 +0.00000 # $\Gamma$
+0.50000 +0.00000 +0.00000 # M
+0.33333 +0.33333 +0.00000 # K
+0.00000 +0.00000 +0.00000 # $\Gamma$
+0.00000 +0.00000 +0.50000 # A
+0.50000 +0.00000 +0.50000 # L
+0.33333 +0.33333 +0.50000 # H
+0.00000 +0.00000 +0.50000 # A
+0.50000 +0.00000 +0.50000 # L
+0.50000 +0.00000 +0.00000 # M
+0.33333 +0.33333 +0.00000 # K
+0.33333 +0.33333 +0.50000 # H
How is this information supposed to be used? When I try and plot the DOS as mentioned, I get a horrible band structure and total DOS. However, for the abipy k-path creator one should rerun a non-SCF using the information above, but nothing changes. So currently the accuracy and looks of the band structure and DOS plots are horrible and I don't know if they are reliable, or if I need to replot them somehow using a different software.
Is there a way to convert abinit output to vasp output files? that way I will be able to use the sumo software which is really fantastic but only made for VASP.
I would be grateful if somebody is able to help clearing these questions out for me, that would be extremely helpful.
/ssh77
I was trying to test a couple of different parameters related to the magnetic moment, kpoints and the ionmov, supercell but don't know if there's something wrong.
The compound is an Mn-oxide with an antiferromagnetic structure and I expect the Mn moment to be ~4 µB/ion but when I run the calculation I reach more than 6 Bohr magnetons which is far too much. Since the structure is hexagonaI would also need to calculate the kpoints centered at the Gamma point.
I would also like to run a relaxation of the atomic cores and the full cell relaxation using ionmov. Further I would like to know how supercells are made and how the electronic DOS is easiest plotted with nice graphs similar to the Sumo software used for VASP (https://sumo.readthedocs.io/en/latest/gallery.html ).
So, more specifically:
1) I would like to have a spin poarized DOS. To refine the magnetic moment I use a spin polarized calculation with
nsppol 2
nspden 2
nspinor 1
spinat with 0 0 4 on the magnetic atom positions as starting magnetic moments (I hope this is correctly understood)
However, I was told by the err file that I should use spinmagntarget, which I have put to 0. So I don't know which one decides the starting moment
------------------------------------------------------------------------
2) for kpoints I use
chksymbreak 0
ngkpt 4 4 4 for the grid resolution
shiftk 0 0 0 I assume this decides if it is Gamma centered or not?
-------------------------------------------------------------------------
3) to relax the atomic cores I use
ionmov 2
optcell 0
toldff 5.0d-5 the convergence criteria for the forces (can I change the units here?)
However, I don't understand if abinit has some specific priority when running, i.e., if electronic SCF is first made then secondly the ionmov step and then SCF again and then ionmov for each step in the convegence? Or does it skip the SCF and go directly to the ionmov and move around the atoms or cores? When I check the output file I only notice the ionmov written as step 1/1 so I don't undertstand if this step is done with each SCF or not. In VASP I think each SCF step includes a atomic or nucleus movement before running SCF again and repeating the movement of the atoms/cores. What is the procedure in abinit? If I set nstep 50 and toldff 5d-5, will the SCF stop when the forces have reached 5d-5 even before SCF has reached 50? and will it otherwise just continue until lthe limit 50 is reached?
--------------------------------------------------------------------------
4) I would like to try and test the difference in energies between different cell sizes, how do I get supercells in abinit? do I multiply the cell parameters with a scalar e.g., a 4 4 4 cell with 2*4 2*4 2*4 to show abinit that I want a supercell or do I need to make a cif with a cell X times larger? that is not practical for a supercell with sya, 500 atoms or larger to add each atom manually
---------------------------------------------------------------------------
5) I would like to make chained calculations so that I first calculate only SCF, then use the ionmov for atomic cores, and finally geometry.
Can I somehow link the ndtset so that each calculaltion continues from the latest results?
Also I didn't quite understand the use of the udtset, why is there 2 different values that add up to ndtset.
--------------------------------------------------------------------------
6) Currently I can only plot the eDOS by using the "abiopen.py *_GSR.nc --expose -sns=talk" from base tutorial 3 for silicon. But The band structure looks horrible and I doubt that people publish such ugly band structures, at least the ones I have obtained.
I have used the abipy obtion to create the k-path for the space group from a cif file, which is something like:
iscf -2
tolwfr 1d-16
# K-path in reduced coordinates:
ndivsm 10
kptopt -11
kptbounds
+0.00000 +0.00000 +0.00000 # $\Gamma$
+0.50000 +0.00000 +0.00000 # M
+0.33333 +0.33333 +0.00000 # K
+0.00000 +0.00000 +0.00000 # $\Gamma$
+0.00000 +0.00000 +0.50000 # A
+0.50000 +0.00000 +0.50000 # L
+0.33333 +0.33333 +0.50000 # H
+0.00000 +0.00000 +0.50000 # A
+0.50000 +0.00000 +0.50000 # L
+0.50000 +0.00000 +0.00000 # M
+0.33333 +0.33333 +0.00000 # K
+0.33333 +0.33333 +0.50000 # H
How is this information supposed to be used? When I try and plot the DOS as mentioned, I get a horrible band structure and total DOS. However, for the abipy k-path creator one should rerun a non-SCF using the information above, but nothing changes. So currently the accuracy and looks of the band structure and DOS plots are horrible and I don't know if they are reliable, or if I need to replot them somehow using a different software.
Is there a way to convert abinit output to vasp output files? that way I will be able to use the sumo software which is really fantastic but only made for VASP.
I would be grateful if somebody is able to help clearing these questions out for me, that would be extremely helpful.
/ssh77