finish test 00,01,02,03

content/00lectures.md

@@ -5,3 +5,189 @@
 
 
 ## Basic About How to Run EMTO Code
+
+|exe     |function|
+|--------|---|
+|bmdl    |Calculates the Madelung potentials|
+|kstr    |Computes the energy dependent slope matrix in real space.|
+|shape   |Computes the so called shape function, which transforms any integral over the unit cell into an integral over a sphere surrounding the unit cell.|
+|kgrn_cpa|Solves the actual self-consistent Kohn-Sham equations And calculate the Full charge density|
+|kfcd_cpa|Evaluate the total energy functional from the full charge density generated by kgrn|
+
+### Running dependence of EMTO subprograms
+
+```{image} img/001.svg
+:width: 400px
+:align: center
+```
+
+Commands to run the code looks like:
+```
+exe < input
+```
+
+#### Exercise 00
+
+```bash
+tree 00
+
+```
+
+
+```{caution}
+EMTO input files have very strict format, an extra space may cause some problems.
+```
+#### KSTR
+
+```{code-block}
+:caption: The input file (kstr/fcc.dat) of kstr for the *fcc* primitive cell
+:emphasize-lines: 2,3,4,8,9,13
+:lineno-start: 1
+KSTR      HP......=N                               22 Jan 08
+JOBNAM...=fcc        MSGL.=  1 MODE...=B STORE..=Y HIGH...=Y
+DIR001=smx/
+DIR006=./
+Slope matrices, fcc (spdf), (kappa*w)^2= 0.0
+NL.....= 4 NLH...=11 NLW...= 9 NDER..= 6 ITRANS= 3 NPRN..= 0
+(K*W)^2..=  0.000000 DMAX....=    1.7000 RWATS...=      0.10
+NQ3...=  1 LAT...= 2 IPRIM.= 0 NGHBP.=13 NQR2..= 0
+A........= 1.0000000 B.......= 1.0000000 C.......= 1.0000000
+BSX......= 0.5000000 BSY.....= 0.5000000 BSZ.....= 0.0000000
+BSX......= 0.0000000 BSY.....= 0.5000000 BSZ.....= 0.5000000
+BSX......= 0.5000000 BSY.....= 0.0000000 BSZ.....= 0.5000000
+QX(IQ)...= 0.0000000 QY......= 0.0000000 QZ......= 0.0000000
+a/w(IQ)..= 0.70 0.70 0.70 0.70
+LAMDA....=    2.5000 AMAX....=    4.5000 BMAX....=    4.5000
+```
+
+A part of the input file of `kstr` describes the lattice informations:
+- Total number of sites is set by NQ3.
+- The symmetry is set by `LAT`, more in the [online manual](https://emto.gitlab.io/manual/manual.html#kstr).
+- The lattice parameters are renormalized to the length of first lattice vector A (`A=1`).
+- **Cartesian Coordinates** are used for sites/"atom" with `QX,QY,QZ`.
+
+Commands for run the `kstr`:
+- `DIR006=./` and `JOBNAM...=fcc`: a file `fcc.prn` will be generated in the current directory.
+- `DIR001=smx`: "slop matrix" will save to `smx/fcc.tfh`.
+
+```
+kstr < fcc.dat
+```
+
+Or add `time` in front to have a feeling about the how much time each code consumes:
+
+```bash
+time kstr < fcc.dat
+```
+
+`MSGL.=  0` silence the screen printing.
+
+#### BMDL
+
+```{code-block}
+:caption: The input file (bmdl/fcc.dat) of `bmdl`
+:emphasize-lines: 2,3,8,9,10,11,12,13
+:lineno-start: 1
+BMDL      HP......=N                               22 Jan 08
+JOBNAM...=fcc        MSGL.=  1 NPRN.=  0
+DIR001=mdl/
+DIR006=
+Madelung potential for fcc bulk
+NL.....= 7
+LAMDA....=      2.50 AMAX....=      4.50 BMAX....=      4.50
+NQ....=  1 LAT...= 2 IPRIM.= 0 NQR2..= 0
+A........= 1.0000000 B.......= 1.0000000 C.......= 1.0000000
+BSX......= 0.5000000 BSY.....= 0.5000000 BSZ.....= 0.0000000
+BSX......= 0.0000000 BSY.....= 0.5000000 BSZ.....= 0.5000000
+BSX......= 0.5000000 BSY.....= 0.0000000 BSZ.....= 0.5000000
+QX(IQ)...= 0.0000000 QY......= 0.0000000 QZ......= 0.0000000
+```
+
+The Lattice information must be consistent with `kstr`, and the output files will be `./fcc.prn` and `mdl/fcc.mdl`
+
+#### SHAPE
+
+The input file (shape/fcc.dat) for `bmdl` contains similar lattice information as `kstr`:
+
+```{code-block}
+:emphasize-lines: 2,3,4
+:lineno-start: 1
+HAPE     HP......=N                             22 Jan 08
+JOBNAM...=fcc        MSGL.=  1
+FOR001=../kstr/smx/fcc.tfh
+DIR002=shp/
+DIR006=./
+Lmax..= 30 NSR..=129 NFI..= 11
+NPRN..=  0 IVEF.=  3
+```
+
+`FOR001=../kstr/smx/fcc.tfh` shows `shape` needs the "slop matrix" from the result of `kstr`. 
+The output will be `shp/fcc.shp`.
+
+```{hint}
+`kstr,bmdl` and `shape` only contains lattice information with a reduced unit, 
+They could be reused for any system which present with same lattice setup.
+```
+
+#### KGRN
+
+
+```{code-block}
+:emphasize-lines: 2,4,8,10,24,26
+:lineno-start: 1
+KGRN                                               13 Oct 12
+JOBNAM=cu
+STRT..=  A MSGL.=  0 EXPAN.= S FCD..=  Y FUNC..= SCA
+FOR001=../kstr/smx/fcc.tfh
+FOR001=../kstr/smx/fcc30.tfh
+DIR002=pot/
+DIR003=pot/
+FOR004=../bmdl/mdl/fcc.mdl
+DIR006=
+DIR009=pot/
+DIR010=chd/
+DIR011=/tmp/
+Self-consistent KKR calculation for fcc Cu
+Band: 10 lines
+NITER.= 50 NLIN.= 31 NPRN.=  0 NCPA.=  7 NT...=  1 MNTA.=  1
+MODE..= 3D FRC..=  N DOS..=  N OPS..=  N AFM..=  P CRT..=  M
+Lmaxh.=  8 Lmaxt=  4 NFI..= 31 FIXG.=  2 SHF..=  0 SOFC.=  N
+KMSH...= G IBZ..=  2 NKX..=  0 NKY..= 13 NKZ..=  0 FBZ..=  N
+KMSH2..= G IBZ2.=  1 NKX2.=  4 NKY2.=  0 NKZ2.= 51
+ZMSH...= C NZ1..= 16 NZ2..=  8 NZ3..=  8 NRES.=  4 NZD.=1500
+DEPTH..=  1.000 IMAGZ.=  0.020 EPS...=  0.200 ELIM..= -1.000
+AMIX...=  0.100 EFMIX.=  1.000 VMTZ..=  0.000 MMOM..=  0.000
+TOLE...= 1.d-07 TOLEF.= 1.d-07 TOLCPA= 1.d-06 TFERMI=  500.0 (K)
+SWS......=2.686842   NSWS.=  1 DSWS..=   0.05 ALPCPA= 0.6020
+Setup: 2 + NQ*NS lines
+EFGS...=  0.000 HX....=  0.100 NX...=  5 NZ0..=  6 STMP..= N
+Symb   IQ IT ITA NZ  CONC   Sm(s)  S(ws) WS(wst) QTR SPLT Fix
+Cu      1  1  1  29  1.000  1.000  1.000  1.000  0.0  0.0  N
+Atom:  4 lines + NT*NTA*6 lines
+IEX...=  4 NP..= 251 NES..= 15 NITER=100 IWAT.=  0 NPRNA=  0
+VMIX.....=  0.300000 RWAT....=  3.500000 RMAX....= 20.000000
+DX.......=  0.030000 DR1.....=  0.002000 TEST....=  1.00E-12
+TESTE....=  1.00E-12 TESTY...=  1.00E-12 TESTV...=  1.00E-12
+Cu
+Iz=  29 Norb= 10 Ion=  0 Config= 3d10_4s1
+n      1  2  2  2  3  3  3  3  3  4
+Kappa -1 -1  1 -2 -1  1 -2  2 -3 -1
+Occup  2  2  2  4  2  2  4  4  6  1
+Valen  0  0  0  0  0  0  0  1  1  1
+```
+- need `chd` and `pot` folder to be exist.
+- `JOBNAM=cu` will decide the output files start with `cu`: cu.prn, chd/cu.chd, pot/cu.pot …
+- `FOR001=../kstr/smx/fcc.tfh` and `FOR004=../bmdl/mdl/fcc.mdl`.
+- `IBZ..=  2` should consistent with `LAT=2` in `kstr` and `bmdl` for `fcc`.
+- `NITER.= 50`, `TOLE...= 1.d-07 TOLEF.= 1.d-07`, \
+check with `egrep "erre|Converged|NOS|Finished" cu.prn`.
+- `AMIX...=  0.100` mixing factor for new charge.
+- `SWS......=2.686842`: The average Wigner-Seitz radius (bohr) to scale the lattice.
+
+```{math}
+N(\epsilon_F)=\frac{1}{2\pi i}\oint_{\epsilon_F} G(z)~dz
+```
+```{image} img/contour_dos.svg
+:width: 800px
+:align: center
+```

content/conf.py

@@ -125,4 +125,4 @@ class TypealongDirective(_BaseCRDirective):
 
 def setup(app):
     for obj in DIRECTIVES:
-        app.add_directive(obj.cssname(), obj)
+        app.add_directive(obj.get_cssname(), obj)

content/exercise/00/bmdl/fcc.dat

@@ -0,0 +1,11 @@
+BMDL      HP......=N                               22 Jan 08
+JOBNAM...=fcc        MSGL.=  1 NPRN.=  0
+DIR001=mdl/
+DIR006=
+Madelung potential for fcc bulk
+NL.....= 7
+LAMDA....=      2.50 AMAX....=      4.50 BMAX....=      4.50
+NQ....=  1 LAT...= 2 IPRIM.= 1 NQR2..= 0
+A........=     1.000 B.......=     1.000 C.......=     1.000
+ALFA.....=      90.0 BETA....=      90.0 GAMMA...=      90.0
+QX(1)....=       0.0 QY(1)...=       0.0 QZ(1)...=       0.0

content/exercise/00/kfcd/cu.dat

@@ -0,0 +1,10 @@
+KFCD      MSGL..=  1                               22 Jan 08
+JOBNAM...=cu
+STRNAM...=fcc
+DIR001=../kstr/smx/
+DIR002=../kgrn/chd/
+DIR003=../shape/shp/
+DIR004=../bmdl/mdl/
+DIR006=./
+Lmaxs.= 30 NTH..= 41 NFI..= 81 FPOT..= N
+OVCOR.=  Y UBG..=  N NPRN.=  0

content/exercise/00/kgrn/cu.dat

@@ -0,0 +1,39 @@
+KGRN                                               13 Oct 12
+JOBNAM=cu 
+STRT..=  A MSGL.=  0 EXPAN.= S FCD..=  Y FUNC..= SCA
+FOR001=../kstr/smx/fcc.tfh
+FOR001=../kstr/smx/fcc30.tfh
+DIR002=pot/
+DIR003=pot/
+FOR004=../bmdl/mdl/fcc.mdl
+DIR006=
+DIR009=pot/
+DIR010=chd/
+DIR011=/tmp/
+Self-consistent KKR calculation for fcc Cu
+Band: 10 lines
+NITER.= 50 NLIN.= 31 NPRN.=  0 NCPA.=  7 NT...=  1 MNTA.=  1
+MODE..= 3D FRC..=  N DOS..=  N OPS..=  N AFM..=  P CRT..=  M
+Lmaxh.=  8 Lmaxt=  4 NFI..= 31 FIXG.=  2 SHF..=  0 SOFC.=  N
+KMSH...= G IBZ..=  2 NKX..=  0 NKY..= 37 NKZ..=  0 FBZ..=  N
+KMSH2..= G IBZ2.=  1 NKX2.=  4 NKY2.=  0 NKZ2.= 51
+ZMSH...= C NZ1..= 16 NZ2..=  8 NZ3..=  8 NRES.=  4 NZD.=1500
+DEPTH..=  1.000 IMAGZ.=  0.020 EPS...=  0.200 ELIM..= -1.000
+AMIX...=  0.100 EFMIX.=  1.000 VMTZ..=  0.000 MMOM..=  0.000
+TOLE...= 1.d-07 TOLEF.= 1.d-07 TOLCPA= 1.d-06 TFERMI=  500.0 (K)
+SWS......=2.686842   NSWS.=  1 DSWS..=   0.05 ALPCPA= 0.6020
+Setup: 2 + NQ*NS lines
+EFGS...=  0.000 HX....=  0.100 NX...=  5 NZ0..=  6 STMP..= N
+Symb   IQ IT ITA NZ  CONC   Sm(s)  S(ws) WS(wst) QTR SPLT Fix
+Cu      1  1  1  29  1.000  1.000  1.000  1.000  0.0  0.0  N
+Atom:  4 lines + NT*NTA*6 lines
+IEX...=  4 NP..= 251 NES..= 15 NITER=100 IWAT.=  0 NPRNA=  0
+VMIX.....=  0.300000 RWAT....=  3.500000 RMAX....= 20.000000
+DX.......=  0.030000 DR1.....=  0.002000 TEST....=  1.00E-12
+TESTE....=  1.00E-12 TESTY...=  1.00E-12 TESTV...=  1.00E-12
+Cu
+Iz=  29 Norb= 10 Ion=  0 Config= 3d10_4s1
+n      1  2  2  2  3  3  3  3  3  4
+Kappa -1 -1  1 -2 -1  1 -2  2 -3 -1
+Occup  2  2  2  4  2  2  4  4  6  1
+Valen  0  0  0  0  0  0  0  1  1  1

content/exercise/00/kstr/fcc.dat

@@ -0,0 +1,15 @@
+KSTR      HP......=N                               22 Jan 08
+JOBNAM...=fcc        MSGL.=  0 MODE...=B STORE..=Y HIGH...=Y
+DIR001=smx/
+DIR006=./
+Slope matrices, fcc (spdf), (kappa*w)^2= 0.0
+NL.....= 4 NLH...=11 NLW...= 9 NDER..= 6 ITRANS= 3 NPRN..= 0
+(K*W)^2..=  0.000000 DMAX....=    1.7000 RWATS...=      0.10
+NQ3...=  1 LAT...= 2 IPRIM.= 0 NGHBP.=13 NQR2..= 0
+A........= 1.0000000 B.......= 1.0000000 C.......= 1.0000000
+BSX......= 0.5000000 BSY.....= 0.5000000 BSZ.....= 0.0000000
+BSX......= 0.0000000 BSY.....= 0.5000000 BSZ.....= 0.5000000
+BSX......= 0.5000000 BSY.....= 0.0000000 BSZ.....= 0.5000000
+QX(IQ)...= 0.0000000 QY......= 0.0000000 QZ......= 0.0000000
+a/w(IQ)..= 0.70 0.70 0.70 0.70
+LAMDA....=    2.5000 AMAX....=    4.5000 BMAX....=    4.5000

content/exercise/00/shape/fcc.dat

@@ -0,0 +1,7 @@
+SHAPE     HP......=N                             22 Jan 08
+JOBNAM...=fcc        MSGL.=  1
+FOR001=../kstr/smx/fcc.tfh
+DIR002=shp/
+DIR006=./
+Lmax..= 30 NSR..=129 NFI..= 11
+NPRN..=  0 IVEF.=  3

content/exercise/solutions/00/bmdl/fcc.dat

@@ -0,0 +1,13 @@
+BMDL      HP......=N                               22 Jan 08
+JOBNAM...=fcc        MSGL.=  1 NPRN.=  0
+DIR001=mdl/
+DIR006=
+Madelung potential for fcc bulk
+NL.....= 7
+LAMDA....=      2.50 AMAX....=      4.50 BMAX....=      4.50
+NQ....=  1 LAT...= 2 IPRIM.= 0 NQR2..= 0
+A........= 1.0000000 B.......= 1.0000000 C.......= 1.0000000
+BSX......= 0.5000000 BSY.....= 0.5000000 BSZ.....= 0.0000000
+BSX......= 0.0000000 BSY.....= 0.5000000 BSZ.....= 0.5000000
+BSX......= 0.5000000 BSY.....= 0.0000000 BSZ.....= 0.5000000
+QX(IQ)...= 0.0000000 QY......= 0.0000000 QZ......= 0.0000000

content/exercise/solutions/00/clean.sh

@@ -0,0 +1 @@
+rm -fv */*.prn */*/*

content/exercise/solutions/00/kfcd/cu.dat

@@ -0,0 +1,10 @@
+KFCD      MSGL..=  1                               22 Jan 08
+JOBNAM...=cu
+STRNAM...=fcc
+DIR001=../kstr/smx/
+DIR002=../kgrn/chd/
+DIR003=../shape/shp/
+DIR004=../bmdl/mdl/
+DIR006=./
+Lmaxs.= 30 NTH..= 41 NFI..= 81 FPOT..= N
+OVCOR.=  Y UBG..=  N NPRN.=  0

content/exercise/solutions/00/kgrn/cu.dat

@@ -0,0 +1,39 @@
+KGRN                                               13 Oct 12
+JOBNAM=cu 
+STRT..=  A MSGL.=  0 EXPAN.= S FCD..=  Y FUNC..= SCA
+FOR001=../kstr/smx/fcc.tfh
+FOR001=../kstr/smx/fcc30.tfh
+DIR002=pot/
+DIR003=pot/
+FOR004=../bmdl/mdl/fcc.mdl
+DIR006=
+DIR009=pot/
+DIR010=chd/
+DIR011=/tmp/
+Self-consistent KKR calculation for fcc Cu
+Band: 10 lines
+NITER.= 50 NLIN.= 31 NPRN.=  0 NCPA.=  7 NT...=  1 MNTA.=  1
+MODE..= 3D FRC..=  N DOS..=  N OPS..=  N AFM..=  P CRT..=  M
+Lmaxh.=  8 Lmaxt=  4 NFI..= 31 FIXG.=  2 SHF..=  0 SOFC.=  N
+KMSH...= G IBZ..=  2 NKX..=  0 NKY..= 13 NKZ..=  0 FBZ..=  N
+KMSH2..= G IBZ2.=  1 NKX2.=  4 NKY2.=  0 NKZ2.= 51
+ZMSH...= C NZ1..= 16 NZ2..=  8 NZ3..=  8 NRES.=  4 NZD.=1500
+DEPTH..=  1.000 IMAGZ.=  0.020 EPS...=  0.200 ELIM..= -1.000
+AMIX...=  0.100 EFMIX.=  1.000 VMTZ..=  0.000 MMOM..=  0.000
+TOLE...= 1.d-07 TOLEF.= 1.d-07 TOLCPA= 1.d-06 TFERMI=  500.0 (K)
+SWS......=2.686842   NSWS.=  1 DSWS..=   0.05 ALPCPA= 0.6020
+Setup: 2 + NQ*NS lines
+EFGS...=  0.000 HX....=  0.100 NX...=  5 NZ0..=  6 STMP..= N
+Symb   IQ IT ITA NZ  CONC   Sm(s)  S(ws) WS(wst) QTR SPLT Fix
+Cu      1  1  1  29  1.000  1.000  1.000  1.000  0.0  0.0  N
+Atom:  4 lines + NT*NTA*6 lines
+IEX...=  4 NP..= 251 NES..= 15 NITER=100 IWAT.=  0 NPRNA=  0
+VMIX.....=  0.300000 RWAT....=  3.500000 RMAX....= 20.000000
+DX.......=  0.030000 DR1.....=  0.002000 TEST....=  1.00E-12
+TESTE....=  1.00E-12 TESTY...=  1.00E-12 TESTV...=  1.00E-12
+Cu
+Iz=  29 Norb= 10 Ion=  0 Config= 3d10_4s1
+n      1  2  2  2  3  3  3  3  3  4
+Kappa -1 -1  1 -2 -1  1 -2  2 -3 -1
+Occup  2  2  2  4  2  2  4  4  6  1
+Valen  0  0  0  0  0  0  0  1  1  1

content/exercise/solutions/00/kstr/fcc.dat

@@ -0,0 +1,15 @@
+KSTR      HP......=N                               22 Jan 08
+JOBNAM...=fcc        MSGL.=  0 MODE...=B STORE..=Y HIGH...=Y
+DIR001=smx/
+DIR006=./
+Slope matrices, fcc (spdf), (kappa*w)^2= 0.0
+NL.....= 4 NLH...=11 NLW...= 9 NDER..= 6 ITRANS= 3 NPRN..= 0
+(K*W)^2..=  0.000000 DMAX....=    1.7000 RWATS...=      0.10
+NQ3...=  1 LAT...= 2 IPRIM.= 0 NGHBP.=13 NQR2..= 0
+A........= 1.0000000 B.......= 1.0000000 C.......= 1.0000000
+BSX......= 0.5000000 BSY.....= 0.5000000 BSZ.....= 0.0000000
+BSX......= 0.0000000 BSY.....= 0.5000000 BSZ.....= 0.5000000
+BSX......= 0.5000000 BSY.....= 0.0000000 BSZ.....= 0.5000000
+QX(IQ)...= 0.0000000 QY......= 0.0000000 QZ......= 0.0000000
+a/w(IQ)..= 0.70 0.70 0.70 0.70
+LAMDA....=    2.5000 AMAX....=    4.5000 BMAX....=    4.5000