This tutorial presents various applications of the static sigma editor. With it you can manipulate the QSGW static self-energy Σ0(k) in a variety of ways. The present tutorial displays some of the features of the editor in the context of some practical applications.
Questaal has two self-energy editors corresponding to the two forms of self energy in QSGW:
a static self-energy Σ0(k) that substitutes for the exchange-correlation potential in LDA, GGA, Hartree-Fock or LDA+U theory. Σ0(k) is static and hermitian, and generates a noninteracting hamiltonian H0 and a corresponding noninteracting Green’s function G0. This potential is the primary output of the the QSGW cycle and Σ0(k) (actually ) is saved on disk, usually in file sigm.ext. There are numerous ways to use and transform Σ0; most are accomplished through the Σ0(k) editor described here.
a frequency-dependent, nonhermitian self energy Σ(k,ω). The ω-dependence broadens the states; the non-hermitian part gives the quasiparticle a finite lifetime. This is not generated automatically, but must be done using a special setup, as described in this tutorial. Once the dynamical Σ(k,ω) is made, there is a corresponding dynamical self-energy editor to facilitate analysis.
Note: this page is under construction.
Follow the steps that create input files and carry out QSGW self-consistency in the Command Summary of the superlattice tutorial.
lmscell gasb -vz=11.5/11.43 --stack~scale=1/z~stretch=z^3~wsitex@short lmf ctrl.gasb --wsig:fbz cp sigm2.gasb sigm.gasb cp sites.gasb site.gasb lmf ctrl.gasb --rsig:fbz:rlxkp --iactiv --wsig:newkp cp sigm2.gasb sigm.gasb lmgwsc --wt --insul=14 --mpi=12,12 --tol=2e-5 --sym --getsigp --save= gasb-shear gasb > out.job mpix -n 16 lmf-MPIK ctrl.gasb > out.lmf
Table of Contents
- Change in sigma on Shearing Zincblende GaSb
- Reading and writing Real-Space sigm Files
- Spin Orbit Coupling in Fe
- As Antisite Defect
- Computers that do not use IEEE conventions for binary files.
- Static Sigma Editor instructions
- Additional Exercises
This tutorial uses the MPI parallel form of lmf. It assumes a script mpix is present in your path that runs an MPI job with # processors as follows:
mpix -n # MPI-job
mpix can be simply mpirun.
If you have compiled lmf in serial mode, you can run the tutorials here in serial mode, by omitting the
mpix -n #.
Change in sigma on Shearing Zincblende GaSb
Here we demonstrate how to modify the static self-energy in the presence of a lattice shear. The shear reduces the symmetry, and must be adapted accordingly. For demonstration purposes we build on the tutorial on building superlattices, and shear GaSb in the manner used in that tutorial.
Here we modify calculated for the zincblende lattice, using it as a starting point for a new QSGW with the sheared lattice. Of course the entire QSGW calculation could be redone from scratch, but with small shears like this one it is a reasonable approximation that the matrix elements of remain invariant under the shear. Here we will check how good that ansatz is. In any case the ansatz gives a good estimate for the self-consistent , avoiding the need to start from scratch.
To set up input conditions of the original zincblende structure, cut and paste the init file designed for InAs and GaSb shown in the superlattice tutorial and name it init.gasb. Then build the input file and carry out both LDA and QSGW self-consistency as described in detail in that tutorial. If you don’t want to read the tutorial, follow the instructions for Zincblende GaSb in the Command Summary, skipping the last part about drawing energy bands.
Assuming you followed instructions you will have run this step
mpix -n 16 lmf-MPIK ctrl.gasb > out.lmf
Find the gap :
grep gap out.lmf
You should find that the gap is 1.29 eV.
Now we are ready to make the shear. Use the superlattice editor built into lmscell to scale and stretch the lattice, so that (1) the basal plane matches that of InAs and (2) the shear conserves volume.
$ lmscell gasb -vz=11.5/11.43 --stack~scale=1/z~stretch=z^3~wsitex@short
In this instruction preprocessor variable z is set to the ratio of GaSb and InAs lattice constants and:
- ~scale=1/z scales the lattice constant by 1/z
- ~stretch=z^3 stretches the third lattice vector by z3
- ~wsitex@short saves the modified structure into into site file sites.gasb
The two scalings together preserve the volume.
Compare sites.gasb to site.gasb and note that that the lattice constant has been reduced while the third lattice vector p3 has been stretched.
The shear reduces the symmetry. To obtain for reduced symmetry, first write for points in the full Brillouin zone. Then for the sheared lattice, read this and write it again under reduced symmetry.
lmf ctrl.gasb --wsig:fbz cp sigm2.gasb sigm.gasb cp sites.gasb site.gasb lmf ctrl.gasb --rsig:fbz:rlxkp --iactiv --wsig:newkp cp sigm2.gasb sigm.gasb
- Steps (1) and (2) generate a sigm.gasb without any symmetry operations.
- Step (3) replaces the site containing the zincblende structure with the sheared structure
- Steps (4) and (5) read sigm.gasb for the full BZ and writes it for the reduced symmetry operations of the sheared lattice. Switch --rsig:fbz:rlxkp tells lmf that contains k points for the full Brillouin zone, and also to ignore the mismatch in the k sought and file values of k (k points are shifted because the lattice is sheared). Switch --wsig:newkp tells lmf to write for the symmetry of the sheared mesh.
mpix -n 16 lmf-MPIK ctrl.gasb --rs=1,0 -vnit=1 > out &
This segment of output shows the symmetry operations of the sheared lattice is much reduced from the 24 point group operations of the Zincblende lattice:
GROUPG: the following are sufficient to generate the space group: m(1,-1,0) m(1,-1,0)
This segment of output
iors : read restart file (binary, mesh density) remesh density from 20 * 20 * 20 to 20 * 20 * 21 use from restart file: ef window, pos(sheared), pnu ignore in restart file: *
indicates the given lattice is sheared relative to the contents in the restart file, rst.gasb. lmf can nevertheless read the file.
Look a little farther down can you can see the bandgap
VBmax = 0.097372 CBmin = 0.182519 gap = 0.085147 Ry = 1.15799 eV
With this ansatz for the gap is reduced from 1.29 eV to 1.16 eV.
Now make it self-consistent
lmgwsc --wt --insul=14 --mpi=12,12 --tol=2e-5 --sym --getsigp --save= gasb-shear gasb > out.job mpix -n 16 lmf-MPIK ctrl.gasb > out.lmf
You should find that the ansatz for is very close to the self-consistent one:
$ grep more out.job lmgwsc : iter 1 of 999 RMS change in sigma = 2.53E-05 Tolerance = 2e-5 more=T ... lmgwsc : iter 2 of 999 RMS change in sigma = 5.58E-06 Tolerance = 2e-5 more=F ...
Run lmf with the self-consistent and find the gap once again
mpix -n 16 lmf-MPIK ctrl.gasb --rs=1,0 -vnit=1 > out.lmf & grep gap out.lmf
It should be essentially unchanged from the 1.16 eV found earlier. See also Additional Exercises.
Reading and writing Real-Space sigm Files
Files associated with this tutorial are too large to be included with the basic distribution. Download and unpack the tarball FeTutorial.tar.gz and change to directory fetutorial.
cp input/* . cp bas2.tppc3.tpd4.sep12/rst.fe . cp bas2.tppc3.tpd4.sep12/nk12/* . ln -s -f sigm sigm.fe
If your computer hardware does not not-use-ieee-conventions-for-binary-files, see here before proceeding.
Verify that the input conditions result in a self-consistent potential.
rm -f mixm.fe log.fe mpix -n 12 lmf -vnit=1 --rs=1,0 ctrl.fe `cat switches-for-lm` > out.noso.001
If you want to carry out a corresponding LDA calculation, do:
cp bas2.tppc3.tpd4.sep12/rst.lda rst.fe rm -f mixm.fe log.fe mpix -n 12 lmf -vsig=0 -vnit=1 --rs=1,0 ctrl.fe `cat switches-for-lm` > out.noso.lda.001
Problems arise if you try to include use the given self-energy in a calculation with lower symmetry, e.g. a shear distortion or the addition of spin-orbit coupling. It immediately appears if you repeat the calculation lmf with spin-orbit coupling on (note tag SO in the input file!):
lmf -vso=1 -vnit=1 --rs=1,0 ctrl.fe `cat switches-for-lm`
This is because by the given Σ0xc is stored on a mesh of k-points. SO coupling reduces symmetry and requires that Σ0 be available on a different k-mesh.
You can work around this by saving Σ0 in a real space form; that is, map Σ0RL,R′L′(k) to Σ0RL,R′L′(T) = Σ0R+TL,R′L′. T is a crystal lattice translation vector; there are as many T-points as k points in k-space. The transformation is exact and no information is lost. (It is accomplished in practice using FFT techniques, and the original Σ0RL,R′L′(k) can be recovered by a Bloch sum.) Once generated Σ0(T) doesn’t depend on the number of k-points, so it is preferable in this context even while it is less compact.
Spin Orbit Coupling in Fe
As Antisite Defect
Computers that do not use IEEE conventions for binary files.
Files sigm._ext and rst._ext are stored in binary form following IEEE conventions. If your computer doesn’t read binary files in this format, do the following additional steps:
cp bas2.tppc3.tpd4.sep12/rsta.fe.gz . gunzip rsta.fe.gz gunzip sigma.fe.gz lmf -vnit=0 --rs=2,1 ctrl.fe `cat switches-for-lm` lmf ctrl.fe `cat switches-for-lm` --rsig:ascii --wsig cp sigm2.fe sigm
Static Sigma Editor instructions
This section documents the instruction set of static self-energy editor, built into lmf. You can operate it in interactive mode or in batch mode, or a mix, as described below.
Instructions are separated by a delimiter, the first character after the instruction (assumed in this documentation to be ”~”).\
Instructions are separated by a delimiter, the first character after --wsig (assumed in this documentation to be ”~”). Instructions often have optional arguments, also separated by a delimiter, the first character after the instruction (assumed in this documentation to be ”@”).\
Note: if you are operating the editor in batch mode, take care to differentiate the delimiters separating instructions from those separating optional arguments to an instruction.
- Interactive mode
- To operate lmscell in interactive mode, invoke
You should see:
Welcome to the static self-energy file editor. Enter '?' to see options. Option :
The editor operates interactively. It reads a command from standard input, executes the command, and returns to the Option prompt waiting for another instruction.
The editor will print a short summary of instructions if you type ? <RET> .
- Batch mode
- You can also run the editor in batch mode by stringing instructions together separated by a delimiter, e.g.
The delimiter ( ~ in this case), as the first character following --wsig. lmf will parse through all the commands sequentially until it encounters “quit” instruction ( ~q ) which causes it to exit. If no such instruction is encountered, lmf returns to the interactive mode.
The real space form of the static Σ0(R,R’) is accessible to edits. This consists of blocks connecting one site to another, given by the neighbor table. The neighbor table consists of a long list of pairs (pair-list) connecting two sites. Sites ib and jb are used below to denote the first and second sites in pair-list.
You can edit subsets of pair-list or the all of of them Σ0. There are various ways to specify the subset: they are given by specifying a set of conditions, called CONDITION below. For each pair if CONDITION is met, the pair is included in the subset.
CONDITION appears as an argument to several of the instructions.
It consists of some combination of the following:
- Either (or neither) of:
- ib=site-list must be in cluster centered at site ib
- ip=pair-list must be in pair-list
With this option you can additionally impose:
- jb=site-list site for 2nd element in pair must be jb
- jbx=site-list site for 2nd element in pair must not be jb
- Any (or none) of:
- onsite connecting vector must be zero
- offsite complement of onsite
- ib==jb center and neighbor have same site index
- ibnejb complement of ib==jb
- Tags r< and r> impose constraints on range:
r<#1 [p<#2 p1,p2,p3]pairs separated by distance r<#1
r>#1 [p<#2 p1,p2,p3]pairs separated by distance r>#1
p<#2 p1,p2,p3Both sites in the pair must be within neighborhood of fixed (p1,p2,p3), i.e. for each site, d = |(px-p1,py-p2,pz-p3)| where (px,py,pz) = site position.
- Conjugate pairs are assigned the status of the original
noconj suppresses this constraint
ib=2,3 r<.45 p<.45 -.25,-.25,-.25
- sum [#[,#]] : summarizes site pair table. Optional [#,#] gives detailed information about a specific range of pairs
- sum ib=#1,#2 : shows hamiltonian subblocks for sites in (#1,#2)
sum ib : summarizes hamiltonian subblocks for all sites
- scell[options] snam : map Σ0 into a supercell specified by site file snam.
- @sigq writes sigma(k)
- @sigrs writes sigma(T)
- @range=# limits the range of sigma(T) when matching
- @nq=#,#,# sets the supercell k mesh
sigbar #1 [#2] set avg sigma for high-lying states. Use argument #2 in spin polarized case
rssave [fn] write rs sigma Σ0 to file. If not specified, file name is rssigm.
readx [fn] read rs sigma and associated files to auxilliary storage for subsequent pasting into Σ0. If not specified, file name is rssigm.
- merge [sigbar] site-list merge pairs in Σ0x to corrresponding pairs in Σ0 for all pairs connected to sites in site-list
- merge [sigbar] 0 merge Σ0x into Σ0 for all pairs in common. Optional ‘-sigbar’ imports avg sigma from auxilliary filereducing size of rs sigma
The following instructions use CONDITION noted above. pairc is used to create a permanent list which becomes the default for other instructions. For any instruction you can create a temporary list. If you don’t specify a temporary list, the permanent list is used if it is defined; otherwise the list becomes the entire pair list.
Set permanent pair list according to CONDITION. If CONDITION is absent all pairs are included.
shows[options] r1,r2,c1,c2 [CONDITION]
Shows r1,r2,c1,c2 subblock of sigma. substitute ‘-‘ for r1,r2,c1,c2 to print entire block
- spin[options] [CONDITION]
For spin manipulations. Select one of the following options:
- @flip[=list] exchanges (up,down) spins
- @zers[=list] zero out spin-up - spin-dn
- @zerq[=list] zero out spin-up + spin-dn
Optional list performs function for pairs in list
- zero[options] [CONDITION]
Zero Σ0 for pairs specified by CONDITION
- @short reduce size of pair table and Σ0
- showp[options] [CONDITION]
List attributes of pairs satisfying CONDITION
- @rms also print rms sum of elements for each pair
- @sum print summary information only
For the GaSb shear demo, compare energy bnds for the ansatz and the self-consistent one. You should find them nearly identical.