Add tutorial from DFTB+ school 2022

docs/_archives/recipes/electronicdynamics/driving/dftb_in.hsd

@@ -1,39 +1,37 @@
 InputVersion = 20.1
 
 Geometry = GenFormat {
-    <<< "coords.gen"
+  <<< "coords.gen"
 }
 
-Driver = {}
-
 Hamiltonian = DFTB {
-    SCC = Yes
-    SCCTolerance = 1.0e-7
-    SlaterKosterFiles = Type2FileNames {
-        Prefix = "../../slakos/download/3ob/3ob-3-1/"
-        Separator = "-"
-        Suffix = ".skf"
-    }
-    MaxAngularMomentum = {
-        Mg = "p"
-        C = "p"
-        N = "p"
-        O = "p"
-        H = "s"
-    }
-    Filling = Fermi {
-        Temperature [K] = 300
-    }
+  Scc = Yes
+  SccTolerance = 1.0e-7
+  SlaterKosterFiles = Type2FileNames {
+    Prefix = "../../slakos/download/3ob/3ob-3-1/"
+    Separator = "-"
+    Suffix = ".skf"
+  }
+  MaxAngularMomentum {
+    Mg = "p"
+    C = "p"
+    N = "p"
+    O = "p"
+    H = "s"
+  }
+  Filling = Fermi {
+    Temperature [K] = 300
+  }
 }
 
-ElectronDynamics = {
-    Steps = 60000
-    TimeStep [au] = 0.2
-    Perturbation = Laser {
-        PolarizationDirection = -0.08808129 0.99564018 -0.03069709
-        LaserEnergy [eV] = 1.94944
-    }
-    FieldStrength [V/A] = 0.0001
-    Populations = Yes
-    WriteFrequency = 100
+ElectronDynamics {
+  Steps = 60000
+  TimeStep [au] = 0.2
+  Perturbation = Laser {
+    PolarizationDirection = -0.08808129 0.99564018 -0.03069709
+    LaserEnergy [eV] = 1.94944
+  }
+  FieldStrength [V/A] = 0.0001
+  Populations = Yes
+  WriteFrequency = 100
 }

docs/_archives/recipes/electronicdynamics/ehrenfest/dftb_in.hsd

@@ -1,38 +1,38 @@
 InputVersion = 20.1
 
 Geometry = GenFormat {
-    <<< "coords.gen"
+  <<< "coords.gen"
 }
 
 Hamiltonian = DFTB {
-    SCC = Yes
-    SCCTolerance = 1.0E-9
-    MaxAngularMomentum = {
-        C = "p"
-        H = "s"
-    }
-    Filling = Fermi {
-        Temperature [Kelvin] = 30
-    }
-    SlaterKosterFiles = Type2FileNames {
-        Prefix = "../../slakos/download/3ob/3ob-3-1/"
-        Separator = "-"
-        Suffix = ".skf"
-    }
+  Scc = Yes
+  SccTolerance = 1.0E-9
+  MaxAngularMomentum {
+    C = "p"
+    H = "s"
+  }
+  Filling = Fermi {
+    Temperature [Kelvin] = 30
+  }
+  SlaterKosterFiles = Type2FileNames {
+    Prefix = "../../slakos/download/3ob/3ob-3-1/"
+    Separator = "-"
+    Suffix = ".skf"
+  }
 }
 
-ElectronDynamics = {
-    Steps = 100000
-    TimeStep [au] = 0.1
-    Perturbation = Laser {
-        PolarizationDirection = 0.00000001 0.61419463 -0.78915459
-        LaserEnergy [eV] = 6.834
-    }
-    EnvelopeShape = Sin2 {
-        Time1 [fs] = 10.0
-    }
-    FieldStrength [V/A] = 0.10
-    IonDynamics = Yes
-    InitialTemperature [K] = 0.0
-    Populations = Yes
+ElectronDynamics {
+  Steps = 100000
+  TimeStep [au] = 0.1
+  Perturbation = Laser {
+    PolarizationDirection = 0.00000001 0.61419463 -0.78915459
+    LaserEnergy [eV] = 6.834
+  }
+  EnvelopeShape = Sin2 {
+    Time1 [fs] = 10.0
+  }
+  FieldStrength [V/A] = 0.10
+  IonDynamics = Yes
+  InitialTemperature [K] = 0.0
+  Populations = Yes
 }

docs/_archives/recipes/electronicdynamics/spectrum/dftb_in.hsd

@@ -1,37 +1,36 @@
 InputVersion = 20.1
 
 Geometry = GenFormat {
-    <<< "coords.gen"
+  <<< "coords.gen"
 }
 
-Driver = {}
+Driver {}
 
 Hamiltonian = DFTB {
-    SCC = Yes
-    SCCTolerance = 1.0e-7
-    SlaterKosterFiles = Type2FileNames {
-        Prefix = "../../slakos/download/3ob/3ob-3-1/"
-        Separator = "-"
-        Suffix = ".skf"
-    }
-    MaxAngularMomentum = {
-        Mg = "p"
-        C = "p"
-        N = "p"
-        O = "p"
-        H = "s"
-    }
-    Charge = 0.0
-    Filling = Fermi {
-        Temperature [K] = 300
-    }
+  Scc = Yes
+  SccTolerance = 1.0e-7
+  SlaterKosterFiles = Type2FileNames {
+    Prefix = "../../slakos/download/3ob/3ob-3-1/"
+    Separator = "-"
+    Suffix = ".skf"
+  }
+  MaxAngularMomentum {
+    Mg = "p"
+    C = "p"
+    N = "p"
+    O = "p"
+    H = "s"
+  }
+  Filling = Fermi {
+    Temperature [K] = 300
+  }
 }
 
-ElectronDynamics = {
-    Steps = 20000
-    TimeStep [au] = 0.2
-    Perturbation = Kick {
-        PolarizationDirection = all
-    }
-    FieldStrength [V/A] = 0.001
+ElectronDynamics {
+  Steps = 20000
+  TimeStep [au] = 0.2
+  Perturbation = Kick {
+    PolarizationDirection = "all"
+  }
+  FieldStrength [V/A] = 0.001
 }

docs/_archives/recipes/electronicdynamics/tutorial/01_spectra_and_laser/01_carbazole/01_spectrum/coords.gen

@@ -0,0 +1,24 @@
+22 C
+C H N
+     1   1  -5.1728644000E-01  -7.2571119000E-01   5.5846500000E-03
+     2   1   8.5078177000E-01  -1.1301429800E+00   2.0378600000E-03
+     3   1   1.2261304100E+00  -2.4865873900E+00  -1.5372900000E-03
+     4   1   1.9994598000E-01  -3.4347336900E+00  -4.3233500000E-03
+     5   2   2.2839472400E+00  -2.7882631200E+00  -3.3389800000E-03
+     6   1  -1.1562943300E+00  -3.0498598500E+00  -2.9476600000E-03
+     7   2   4.5464746000E-01  -4.5055579500E+00  -8.7991900000E-03
+     8   1  -1.5299440000E+00  -1.7037797500E+00   2.9104100000E-03
+     9   2  -1.9330937600E+00  -3.8293745100E+00  -7.3501000000E-03
+    10   2  -2.5921016000E+00  -1.4158925700E+00   3.5784700000E-03
+    11   1  -5.1730828000E-01   7.2567935000E-01   5.8213800000E-03
+    12   1   8.5080047000E-01   1.1301031400E+00   0.0000000000E+00
+    13   3   1.6513735600E+00  -1.0210000000E-05   0.0000000000E+00
+    14   1  -1.5297530300E+00   1.7038648900E+00   8.4112200000E-03
+    15   1  -1.1559873900E+00   3.0499477100E+00   1.8125700000E-03
+    16   2  -2.5920072900E+00   1.4162563500E+00   1.4849170000E-02
+    17   1   2.0031694000E-01   3.4347032300E+00  -7.4452800000E-03
+    18   2  -1.9327718800E+00   3.8294924100E+00   2.8904500000E-03
+    19   1   1.2263781800E+00   2.4864970000E+00  -7.6315500000E-03
+    20   2   2.2841771200E+00   2.7882250200E+00  -1.4735950000E-02
+    21   2   4.5487270000E-01   4.5055017500E+00  -1.5258710000E-02
+    22   2   2.6797365300E+00  -1.0210000000E-05  -4.1508500000E-03

docs/_archives/recipes/electronicdynamics/tutorial/01_spectra_and_laser/01_carbazole/01_spectrum/dftb_in.hsd_spec

@@ -0,0 +1,29 @@
+InputVersion = 21.2
+
+Geometry = GenFormat {
+  <<< "coords.gen"
+}
+
+Hamiltonian = DFTB {
+  Scc = Yes
+  SccTolerance = 1e-7  
+  MaxAngularMomentum {
+    C = "p"
+    H = "s"
+    N = "p"
+  }
+  SlaterKosterFiles = Type2FileNames {
+    Prefix = "../../../../../slakos/download/mio/mio-1-1/"
+    Separator = "-"
+    Suffix = ".skf"
+  }
+}
+
+ElectronDynamics {
+  Steps =                         # define the time window
+  TimeStep [au] =                 # resolution of the spectrum
+  Perturbation = Kick {           # must be a kick (Dirac delta)
+    PolarizationDirection =       # desired direction/s
+  }
+  FieldStrength [V/A] =           # field strength of the perturbation
+}

docs/_archives/recipes/electronicdynamics/tutorial/01_spectra_and_laser/01_carbazole/02_laser/coords.gen

@@ -0,0 +1,24 @@
+22 C
+C H N
+     1   1  -5.1728644000E-01  -7.2571119000E-01   5.5846500000E-03
+     2   1   8.5078177000E-01  -1.1301429800E+00   2.0378600000E-03
+     3   1   1.2261304100E+00  -2.4865873900E+00  -1.5372900000E-03
+     4   1   1.9994598000E-01  -3.4347336900E+00  -4.3233500000E-03
+     5   2   2.2839472400E+00  -2.7882631200E+00  -3.3389800000E-03
+     6   1  -1.1562943300E+00  -3.0498598500E+00  -2.9476600000E-03
+     7   2   4.5464746000E-01  -4.5055579500E+00  -8.7991900000E-03
+     8   1  -1.5299440000E+00  -1.7037797500E+00   2.9104100000E-03
+     9   2  -1.9330937600E+00  -3.8293745100E+00  -7.3501000000E-03
+    10   2  -2.5921016000E+00  -1.4158925700E+00   3.5784700000E-03
+    11   1  -5.1730828000E-01   7.2567935000E-01   5.8213800000E-03
+    12   1   8.5080047000E-01   1.1301031400E+00   0.0000000000E+00
+    13   3   1.6513735600E+00  -1.0210000000E-05   0.0000000000E+00
+    14   1  -1.5297530300E+00   1.7038648900E+00   8.4112200000E-03
+    15   1  -1.1559873900E+00   3.0499477100E+00   1.8125700000E-03
+    16   2  -2.5920072900E+00   1.4162563500E+00   1.4849170000E-02
+    17   1   2.0031694000E-01   3.4347032300E+00  -7.4452800000E-03
+    18   2  -1.9327718800E+00   3.8294924100E+00   2.8904500000E-03
+    19   1   1.2263781800E+00   2.4864970000E+00  -7.6315500000E-03
+    20   2   2.2841771200E+00   2.7882250200E+00  -1.4735950000E-02
+    21   2   4.5487270000E-01   4.5055017500E+00  -1.5258710000E-02
+    22   2   2.6797365300E+00  -1.0210000000E-05  -4.1508500000E-03

docs/_archives/recipes/electronicdynamics/tutorial/01_spectra_and_laser/01_carbazole/02_laser/dftb_in.hsd_laser

@@ -0,0 +1,39 @@
+InputVersion = 21.2
+
+Geometry = GenFormat {
+  <<< "coords.gen"
+}
+
+Hamiltonian = DFTB {
+  Scc = Yes
+  SccTolerance = 1e-7  
+  MaxAngularMomentum {
+    C = "p"
+    H = "s"
+    N = "p"
+  }
+  SlaterKosterFiles = Type2FileNames {
+    Prefix = "../../../../slakos/download/mio-1-1/"
+    Separator = "-"
+    Suffix = ".skf"
+  }
+}
+
+ElectronDynamics {
+  Steps = 10000
+  TimeStep [au] = 0.2
+  Perturbation = Laser {             # Laser type perturbation
+    PolarizationDirection =          # calculate with calc_timeprop_maxpoldir
+    LaserEnergy [eV] =               # energy of interest 
+  }                                    
+  FieldStrength [V/A] = 0.001
+  Populations = Yes                  # to write GS-MP projected populations during dynamic
+}
+
+Options {
+  WriteDetailedXml = Yes             # needed for waveplot
+}
+
+Analysis {
+  WriteEigenvectors = Yes            # needed for waveplot
+}

docs/_archives/recipes/electronicdynamics/tutorial/01_spectra_and_laser/01_carbazole/02_laser/waveplot_in.hsd_

@@ -0,0 +1,29 @@
+# General options
+
+Options {
+  RealComponent = Yes                # Plot real component of the wavefunction
+  PlottedSpins = 1 -1
+  PlottedLevels =                    ### Levels (Orbitals) 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
+                                     # Both files must be asked for the user in the
+                                     # input for DFTB+ calculation (they are not default
+                                     # printed)
+
+
+# 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" ### Path for Wave function coeffiecients for waveplot
+}

docs/_archives/recipes/electronicdynamics/tutorial/01_spectra_and_laser/02_PDI/coords.gen

@@ -0,0 +1,42 @@
+40 C
+C H N O
+     1   1  -2.8702011600E+00   0.0000000000E+00   0.0000000000E+00
+     2   1  -1.4362663100E+00   0.0000000000E+00   1.3000000000E-07
+     3   1  -3.5889101500E+00  -1.2350464400E+00  -2.3000000000E-07
+     4   1  -2.8813199700E+00  -2.4379174600E+00  -2.1000000000E-07
+     5   1  -1.4787678500E+00  -2.4440123700E+00   1.1000000000E-07
+     6   1  -7.3366388000E-01  -1.2519893100E+00   3.1000000000E-07
+     7   1  -3.5889101500E+00   1.2350464400E+00   0.0000000000E+00
+     8   1  -2.8813199600E+00   2.4379174600E+00   5.0000000000E-08
+     9   1  -1.4787678400E+00   2.4440123900E+00   0.0000000000E+00
+    10   1  -7.3366389000E-01   1.2519893100E+00   2.0000000000E-08
+    11   1   7.3366387000E-01  -1.2519893000E+00   5.5000000000E-07
+    12   1   1.4362663200E+00   1.0000000000E-08   2.6000000000E-07
+    13   1   7.3366387000E-01   1.2519893100E+00  -7.0000000000E-08
+    14   1   1.4787678400E+00  -2.4440123700E+00   9.5000000000E-07
+    15   1   2.8813199500E+00  -2.4379174700E+00   9.2000000000E-07
+    16   1   3.5889101400E+00  -1.2350464400E+00   5.1000000000E-07
+    17   1   2.8702011700E+00   2.0000000000E-08   2.3000000000E-07
+    18   1   3.5889101600E+00   1.2350464500E+00  -1.2000000000E-07
+    19   1   2.8813199600E+00   2.4379174700E+00  -5.4000000000E-07
+    20   1   1.4787678400E+00   2.4440123700E+00  -5.2000000000E-07
+    21   2  -3.4335673000E+00  -3.3896396100E+00  -4.6000000000E-07
+    22   2  -9.7502556000E-01  -3.4212878700E+00   1.4000000000E-07
+    23   2  -3.4335673300E+00   3.3896396100E+00   9.0000000000E-08
+    24   2  -9.7502557000E-01   3.4212879000E+00  -4.0000000000E-08
+    25   2   9.7502555000E-01  -3.4212878600E+00   1.2900000000E-06
+    26   2   3.4335673000E+00  -3.3896396100E+00   1.2100000000E-06
+    27   2   9.7502554000E-01   3.4212878700E+00  -8.9000000000E-07
+    28   2   3.4335672900E+00   3.3896396300E+00  -8.6000000000E-07
+    29   1  -5.0766344400E+00  -1.2425131600E+00  -6.6000000000E-07
+    30   1  -5.0766344500E+00   1.2425131500E+00  -4.0000000000E-08
+    31   1   5.0766344400E+00  -1.2425131700E+00   2.2000000000E-07
+    32   1   5.0766344600E+00   1.2425131600E+00  -6.0000000000E-08
+    33   3  -5.7159981400E+00   0.0000000000E+00  -4.1000000000E-07
+    34   3   5.7159981500E+00  -1.0000000000E-08   6.0000000000E-08
+    35   4  -5.7484785000E+00  -2.2718608200E+00  -1.2300000000E-06
+    36   4  -5.7484785300E+00   2.2718608200E+00   2.2000000000E-07
+    37   4   5.7484785100E+00  -2.2718608300E+00   1.1000000000E-07
+    38   4   5.7484785500E+00   2.2718607900E+00  -1.6000000000E-07
+    39   2  -6.7494873900E+00   0.0000000000E+00  -5.7000000000E-07
+    40   2   6.7494873800E+00  -4.0000000000E-08  -2.0000000000E-08