Merge branch 'inputarchive'

.gitignore

@@ -1,4 +1,6 @@
 *~
 _gitmsg.saved.txt
 docs/_build
+docs/_archives/recipes/slakos/download/*
+docs/_downloads/archives
 

README.rst

@@ -3,9 +3,23 @@ DFTB+ Recipes
 *************
 
 This repository contains the source of the DFTB+ Recipes book. The content is
-rendered on `dftbplus-recipes.readthedocs.io
-<http://dftbplus-recipes.readthedocs.io>`_.
+currently rendered on `dftbplus-recipes.readthedocs.io
+<http://dftbplus-recipes.readthedocs.io>`_. You can also render it locally by
+using the Sphinx documentation system.
 
-The material is licensed under the CC-BY-SA license (see `LICENSE <LICENSE>`_).
+This material is licensed under the CC-BY-SA license (see `LICENSE <LICENSE>`_).
 
 Contributions are very welcome!
+
+
+Technical notes
+===============
+
+* The book is written in the restructured text format and is contained in the
+  `docs/` folder. In order to process it, you need Sphinx version 1.8 or above.
+
+* Before the text of the book is built, the building system creates a tar.bz2
+  archive for each top level file/directory in the `docs/_archives/`
+  folder. Created archives will be then copied to the `docs/_downloads/archives`
+  folder. You may then reference those .tar.bz2 archives from within the text of
+  the book.

docs/_archives/_ignore

@@ -0,0 +1,2 @@
+*~
+recipes/slako/download/*

docs/_archives/recipes/basics/bandstruct/1_density/dftb_in.hsd

@@ -0,0 +1,54 @@
+Geometry = GenFormat {
+    6  F
+ Ti  O
+    1 1    0.4393045491E-02   -0.4394122690E-02   -0.4185505032E-06
+    2 1   -0.2456050838E+00   -0.7543932244E+00    0.5000007729E+00
+    3 2    0.1997217007E+00    0.2106836749E+00   -0.1813953963E-02
+    4 2   -0.4625010039E+00    0.4843137675E-01    0.4981557672E+00
+    5 2   -0.2106822274E+00   -0.1997223911E+00    0.1816384188E-02
+    6 2   -0.4843281768E-01   -0.5374990457E+00    0.5018414482E+00
+    0.0000000000E+00    0.0000000000E+00    0.0000000000E+00
+   -0.1903471721E+01    0.1903471721E+01    0.4864738245E+01
+    0.1903471721E+01   -0.1903471721E+01    0.4864738245E+01
+    0.1903471721E+01    0.1903471721E+01   -0.4864738245E+01
+}
+
+Hamiltonian = DFTB {
+  Scc = Yes
+  SccTolerance = 1e-5
+  SlaterKosterFiles = Type2FileNames {
+    Prefix = "../../../slakos/mio-ext/"
+    Separator = "-"
+    Suffix = ".skf"
+  }
+  MaxAngularMomentum {
+    Ti = "d"
+    O  = "p"
+  }
+  KPointsAndWeights = SupercellFolding {
+    4 0 0
+    0 4 0
+    0 0 4
+    0.5 0.5 0.5
+  }
+}
+
+Analysis {
+  ProjectStates {
+    Region {
+      Atoms = Ti
+      ShellResolved = Yes
+      Label = "dos_ti"
+    }
+    Region {
+      Atoms = O
+      ShellResolved = Yes
+      Label = "dos_o"
+     }
+  }
+}
+
+ParserOptions {
+  ParserVersion = 6
+}
+

docs/_archives/recipes/basics/bandstruct/1_density/run.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+set -e
+dftb+ > output
+dp_dos band.out dos_total.dat >> output
+dp_dos -w dos_ti.1.out dos_ti.s.dat >> output
+dp_dos -w dos_ti.2.out dos_ti.p.dat >> output
+dp_dos -w dos_ti.3.out dos_ti.d.dat >> output
+dp_dos -w dos_o.1.out dos_o.s.dat >> output
+dp_dos -w dos_o.2.out dos_o.p.dat >> output
+

docs/_archives/recipes/basics/bandstruct/2_bands/dftb_in.hsd

@@ -0,0 +1,39 @@
+Geometry = GenFormat {
+    6  F
+ Ti  O
+    1 1    0.4393045491E-02   -0.4394122690E-02   -0.4185505032E-06
+    2 1   -0.2456050838E+00   -0.7543932244E+00    0.5000007729E+00
+    3 2    0.1997217007E+00    0.2106836749E+00   -0.1813953963E-02
+    4 2   -0.4625010039E+00    0.4843137675E-01    0.4981557672E+00
+    5 2   -0.2106822274E+00   -0.1997223911E+00    0.1816384188E-02
+    6 2   -0.4843281768E-01   -0.5374990457E+00    0.5018414482E+00
+    0.0000000000E+00    0.0000000000E+00    0.0000000000E+00
+   -0.1903471721E+01    0.1903471721E+01    0.4864738245E+01
+    0.1903471721E+01   -0.1903471721E+01    0.4864738245E+01
+    0.1903471721E+01    0.1903471721E+01   -0.4864738245E+01
+}
+
+Hamiltonian = DFTB {
+  Scc = Yes
+  ReadInitialCharges = Yes
+  MaxSccIterations = 1
+  SlaterKosterFiles = Type2FileNames {
+    Prefix = "../../../slakos/mio-ext/"
+    Separator = "-"
+    Suffix = ".skf"
+  }
+  MaxAngularMomentum {
+    Ti = "d"
+    O  = "p"
+  }
+  KPointsAndWeights = Klines {
+    1   0.5   0.5  -0.5    # Z
+   20   0.0   0.0   0.0    # G
+   45   0.0   0.0   0.5    # X
+   10   0.25  0.25  0.25   # P
+  }
+}
+
+ParserOptions {
+  ParserVersion = 6
+}

docs/_archives/recipes/basics/bandstruct/2_bands/run.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+set -e
+cp ../1_density/charges.bin .
+dftb+ > output
+dp_bands band.out band >> output
+

docs/_archives/recipes/basics/firstcalc/dftb_in.hsd

@@ -0,0 +1,40 @@
+Geometry = GenFormat {
+3 C
+  O H
+
+  1 1  0.00000000000E+00 -0.10000000000E+01  0.00000000000E+00
+  2 2  0.00000000000E+00  0.00000000000E+00  0.78306400000E+00
+  3 2  0.00000000000E+00  0.00000000000E+00 -0.78306400000E+00
+}
+
+Driver = ConjugateGradient {
+  MovedAtoms = 1:-1
+  MaxForceComponent = 1E-4
+  MaxSteps = 100
+  OutputPrefix = "geom.out"
+}
+
+Hamiltonian = DFTB {
+  Scc = Yes
+  SlaterKosterFiles {
+    O-O = "../../slakos/mio-ext/O-O.skf"
+    O-H = "../../slakos/mio-ext/O-H.skf"
+    H-O = "../../slakos/mio-ext/H-O.skf"
+    H-H = "../../slakos/mio-ext/H-H.skf"
+  }
+  MaxAngularMomentum {
+    O = "p"
+    H = "s"
+  }
+}
+
+Options {}
+
+Analysis {
+  CalculateForces = Yes
+}
+
+ParserOptions {
+  ParserVersion = 6
+}
+

docs/_archives/recipes/basics/firstcalc/run.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+set -e
+dftb+ > output

docs/_archives/recipes/basics/waveplot/dftb_in.hsd

@@ -0,0 +1,40 @@
+Geometry = GenFormat {
+3  C
+ O H
+     1    1    0.00000000000E+00  -0.10000000000E+01   0.00000000000E+00
+     2    2    0.00000000000E+00   0.00000000000E+00   0.78306400000E+00
+     3    2    0.00000000000E+00   0.00000000000E+00  -0.78306400000E+00
+}
+
+Driver = ConjugateGradient {
+  MovedAtoms = 1:-1
+  MaxForceComponent = 1.0e-4
+  MaxSteps = 100
+  OutputPrefix = "geom.out"
+}
+
+Hamiltonian = DFTB {
+  Scc = Yes
+  SccTolerance = 1.0e-5
+  SlaterKosterFiles = Type2FileNames {
+    Prefix = "../../slakos/mio-ext/"
+    Separator = "-"
+    Suffix = ".skf"
+  }
+  MaxAngularMomentum = {
+    O = "p"
+    H = "s"
+  }
+}
+
+Options {
+  WriteDetailedXml = Yes
+}
+
+Analysis {
+  WriteEigenvectors = Yes
+}
+
+ParserOptions {
+  ParserVersion = 5
+}

docs/_archives/recipes/basics/waveplot/run.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+set -e
+dftb+ > output
+waveplot >> output

docs/_archives/recipes/basics/waveplot/waveplot_in.hsd

@@ -0,0 +1,29 @@
+# General options
+
+Options {
+  TotalChargeDensity = Yes             # Total density be plotted?
+  TotalChargeDifference = Yes          # Total density difference plotted?
+  ChargeDensity = Yes                  # Charge density for each state?
+  RealComponent = Yes                  # Plot real component of the wavefunction
+  PlottedSpins = 1 -1 
+  PlottedLevels =  4                   # Levels to plot
+  PlottedRegion =  OptimalCuboid {}    # Region to plot
+
+  NrOfPoints = 50 50 50                # Number of grid points in each direction
+  NrOfCachedGrids = -1                 # Nr of cached grids (speeds up things)
+  Verbose = Yes                        # Wanna see a lot of messages?
+}
+
+DetailedXml = "detailed.xml"           # File containing the detailed xml output
+                                       # of DFTB+
+EigenvecBin = "eigenvec.bin"           # File cointaining the binary eigenvecs
+
+
+# Definition of the basis
+Basis {
+  Resolution = 0.01
+  # Including mio-1-1.hsd. (If you use a set, which depends on other sets,
+  # the wfc.*.hsd files for each required set must be included in a similar
+  # way.)
+  <<+ "../../slakos/wfc/wfc.mio-1-1.hsd"  
+}

docs/_archives/recipes/scripts/get_slakos

@@ -0,0 +1,33 @@
+#!/bin/bash
+################################################################################
+# Downloads and unpacks slako related files from dftb.org
+################################################################################
+scriptdir="$(dirname $0)"
+root="$scriptdir/.."
+downloaddir="$root/slakos/download"
+downloadfile="$root/slakos/SLAKO_DOWNLOADS"
+slakourlprefix="http://www.dftb.org/fileadmin/DFTB/public/slako"
+
+echo "Downloading SLAKO archives:"
+for remotefile in $(cat $downloadfile); do
+  destdir=$(dirname $remotefile)
+  fname=$(basename $remotefile)
+  mkdir -p $downloaddir/$destdir
+
+  echo "Downloading $remotefile"
+  echo "wget -q -O $downloaddir/$destdir/$fname $slakourlprefix/$remotefile"
+  wget -q -O $downloaddir/$destdir/$fname $slakourlprefix/$remotefile
+  if [ $? -ne 0 ]; then
+    echo "DOWNLOAD FAILED for$ slakourlprefix/$remotefile" >&2
+  fi
+
+  if [ "$(basename $fname .tar.xz)" != "$fname" ]; then
+    echo "Unpacking archive $fname"
+    tar -x -C $downloaddir/$destdir -J -f $downloaddir/$destdir/$fname
+    if [ $? -ne 0 ]; then
+      echo "UNPACKING FAILED for $downloaddir/$destdir/$fname" >&2
+    fi
+    echo "Removing archive $fname"
+    rm -f $downloaddir/$destdir/$fname
+  fi
+done

docs/_archives/recipes/slakos/SLAKO_DOWNLOADS

@@ -0,0 +1,3 @@
+mio/mio-1-1.tar.xz
+mio/wfc.mio-1-1.hsd
+tiorg/tiorg-0-1.tar.xz

docs/_archives/recipes/slakos/mio-ext/C-C.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/C-C.skf

docs/_archives/recipes/slakos/mio-ext/C-H.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/C-H.skf

docs/_archives/recipes/slakos/mio-ext/C-N.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/C-N.skf

docs/_archives/recipes/slakos/mio-ext/C-O.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/C-O.skf

docs/_archives/recipes/slakos/mio-ext/C-P.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/C-P.skf

docs/_archives/recipes/slakos/mio-ext/C-S.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/C-S.skf

docs/_archives/recipes/slakos/mio-ext/C-Ti.skf

@@ -0,0 +1 @@
+../download/tiorg/tiorg-0-1/C-Ti.skf

docs/_archives/recipes/slakos/mio-ext/H-C.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/H-C.skf

docs/_archives/recipes/slakos/mio-ext/H-H.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/H-H.skf

docs/_archives/recipes/slakos/mio-ext/H-N.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/H-N.skf

docs/_archives/recipes/slakos/mio-ext/H-O.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/H-O.skf

docs/_archives/recipes/slakos/mio-ext/H-P.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/H-P.skf

docs/_archives/recipes/slakos/mio-ext/H-S.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/H-S.skf

docs/_archives/recipes/slakos/mio-ext/H-Ti.skf

@@ -0,0 +1 @@
+../download/tiorg/tiorg-0-1/H-Ti.skf

docs/_archives/recipes/slakos/mio-ext/LICENSE

@@ -0,0 +1,2 @@
+This folder contains the mio set and some of its extensions. Please consult the
+LICENSE files of the respective sets for further information.

docs/_archives/recipes/slakos/mio-ext/LICENSE.mio-1-1

@@ -0,0 +1 @@
+../download/mio/mio-1-1/LICENSE

docs/_archives/recipes/slakos/mio-ext/LICENSE.tiorg-0-1

@@ -0,0 +1 @@
+../download/tiorg/tiorg-0-1/LICENSE

docs/_archives/recipes/slakos/mio-ext/N-C.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/N-C.skf

docs/_archives/recipes/slakos/mio-ext/N-H.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/N-H.skf

docs/_archives/recipes/slakos/mio-ext/N-N.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/N-N.skf

docs/_archives/recipes/slakos/mio-ext/N-O.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/N-O.skf

docs/_archives/recipes/slakos/mio-ext/N-P.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/N-P.skf

docs/_archives/recipes/slakos/mio-ext/N-S.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/N-S.skf

docs/_archives/recipes/slakos/mio-ext/N-Ti.skf

@@ -0,0 +1 @@
+../download/tiorg/tiorg-0-1/N-Ti.skf

docs/_archives/recipes/slakos/mio-ext/O-C.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/O-C.skf

docs/_archives/recipes/slakos/mio-ext/O-H.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/O-H.skf

docs/_archives/recipes/slakos/mio-ext/O-N.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/O-N.skf

docs/_archives/recipes/slakos/mio-ext/O-O.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/O-O.skf

docs/_archives/recipes/slakos/mio-ext/O-P.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/O-P.skf

docs/_archives/recipes/slakos/mio-ext/O-S.skf

@@ -0,0 +1 @@
+../download/mio/mio-1-1/O-S.skf