Merge branch 'MD_section'

dftbplus · Dec 10, 2018 · c0f1e5b · c0f1e5b
2 parents f390954 + c831bbf
commit c0f1e5b
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diff --git a/docs/Makefile b/docs/Makefile
@@ -17,4 +17,4 @@ help:
 # Catch-all target: route all unknown targets to Sphinx using the new
 # "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
 %: Makefile
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
diff --git a/docs/_archives/recipes/moleculardynamics/XLBOMD/dftb_in.hsd b/docs/_archives/recipes/moleculardynamics/XLBOMD/dftb_in.hsd
@@ -0,0 +1,143 @@
+Geometry = GenFormat {
+38 C
+C O H
+     1   1  -3.2103390000E-01   6.4976606000E-01   6.1134966000E-01
+     2   1   9.6328881000E-01   2.6810143600E+00   2.4672770000E-02
+     3   1   3.7008025000E-01  -1.9148818000E-01  -3.4608252000E-01
+     4   1   1.7062543300E+00   1.8667277800E+00  -9.7432192000E-01
+     5   1  -4.6635000000E-04   2.0405072500E+00   8.3279825000E-01
+     6   1   1.3552255700E+00   4.6696619000E-01  -1.1164276800E+00
+     7   1  -1.2084626700E+00   3.5055440000E-02   1.4611567900E+00
+     8   1   1.2838829500E+00   4.0436668700E+00   2.3580619000E-01
+     9   1   1.7368624000E-01  -1.5974433500E+00  -5.6605157000E-01
+    10   1   2.7167114800E+00   2.5171334100E+00  -1.7385943600E+00
+    11   1  -6.7994802000E-01   2.7815041000E+00   1.8784723000E+00
+    12   1   2.1407047300E+00  -2.9303542000E-01  -2.0652228400E+00
+    13   1  -1.9292987000E+00   7.5069414000E-01   2.4361290700E+00
+    14   1   6.4765831000E-01   4.7324463100E+00   1.2977432600E+00
+    15   1   8.3835424000E-01  -2.2447042900E+00  -1.5758687500E+00
+    16   1   3.4495481300E+00   1.6997917600E+00  -2.6509048200E+00
+    17   1  -1.6506211100E+00   2.1200052600E+00   2.7154073500E+00
+    18   1  -3.6777644000E-01   4.1391518900E+00   2.0732747000E+00
+    19   1   1.9139484800E+00  -1.6634948600E+00  -2.2349815200E+00
+    20   1   3.1011552300E+00   3.5961796000E-01  -2.8927181400E+00
+    21   1  -2.4832568600E+00   2.8190296100E+00   3.7147392800E+00
+    22   1  -1.0551337700E+00   4.8836022000E+00   3.2217757000E+00
+    23   1   2.5647743600E+00  -2.3565660000E+00  -3.3888315300E+00
+    24   1   3.8672443600E+00  -3.7443306000E-01  -3.9283627100E+00
+    25   2  -2.2570870700E+00   4.2401457300E+00   3.7669234400E+00
+    26   2   3.5670952200E+00  -1.7034416800E+00  -4.2202391900E+00
+    27   2  -3.4531757200E+00   2.3849873100E+00   4.3012718900E+00
+    28   2  -8.5119925000E-01   5.9864947800E+00   3.6250608000E+00
+    29   2   2.2689106300E+00  -3.4863053800E+00  -3.6642365400E+00
+    30   2   4.8047915300E+00   1.0340452000E-01  -4.5201062700E+00
+    31   3  -1.3310748400E+00  -1.0903765300E+00   1.3043519700E+00
+    32   3   2.0065768900E+00   4.5267732800E+00  -4.6496078000E-01
+    33   3  -7.6392979000E-01  -2.1566928200E+00  -3.6773373000E-01
+    34   3   2.8953294300E+00   3.6457328500E+00  -1.6719959800E+00
+    35   3  -2.6358745700E+00   2.0275311000E-01   3.0872061600E+00
+    36   3   1.0561540100E+00   5.6545207000E+00   1.6511110400E+00
+    37   3   4.3113722000E-01  -3.2352289900E+00  -1.8495723100E+00
+    38   3   4.2695602000E+00   2.1622890000E+00  -3.2672901100E+00
+}
+
+Driver = VelocityVerlet{
+ TimeStep [fs] = 0.5
+ Thermostat = None {}
+
+ # extended Lagrangian dynamics, using the 'fast' option
+ XlbomdFast {
+   IntegrationSteps = 5
+   Scale = 0.5           # scalekappa (only for fast option with 1 scf cycle)
+   TransientSteps = 10
+ }
+
+ # Specify the initial velocities of the atoms to avoid having a 'burn
+ # in' period to get to a 'typical' microstate
+ Velocities [AA/ps] { # This is the same unit as xyz format output
+      0.63060001     10.71652407      0.41599521
+     -4.78167517     -0.67726160      6.81193886
+      3.98425977      1.00737908    -10.59008962
+     -5.00836769     -4.17503533      6.23338156
+     -6.98937694     -6.67991962     13.49283670
+      2.60129853      2.94191649     -6.17377828
+      5.45307788      4.06412641    -12.66174802
+     -7.65333453     -3.97065257      6.97104050
+    -10.13358053      2.65525500      1.71478235
+      2.43208042      7.32942823      4.28579643
+     -4.30000399      3.49584166      3.08283261
+      2.24408800     -6.45559687      0.04066731
+     -1.94541508      3.92663760     -0.72998677
+      5.60486436      3.94060376     -3.20947636
+      3.53019985      4.56545155     -1.48062150
+      7.81517642      2.25960070      4.82188329
+     -0.50193981     -4.94744725      3.06413849
+     -0.19059520      4.33561964      2.36256475
+      0.09466765     -0.51960301      5.72471343
+      4.47619173      7.41074772      1.11201016
+      3.27922874     -5.35329287     -2.56702569
+      3.99264878     -8.45260216     -4.11369388
+     -1.77619915     -3.53622712     -7.62449802
+      7.38469860     -1.25504906      0.63982263
+     -4.58383155      2.77913648     -3.36202315
+      2.57174728      3.16284242     -2.42263621
+     -1.51584311      4.83348853     -8.50814642
+      3.19719689     -5.10152266      4.80391910
+     -1.82283885     -4.42665140     -0.61092820
+      0.70148376    -13.29987273      5.73299098
+    -48.12863500      6.61689320     -3.55300242
+     -7.79595968      7.24986202     -7.89475790
+     19.47014048    -24.23046733    -19.62986878
+    -22.48734706      8.85056458      5.45198051
+     -8.26315843     12.84226567    -16.40492287
+    -27.33024406     29.56557052    -25.50583462
+    -20.88278228      1.24410318    -14.82956937
+     16.44412954     -1.14851662     13.23381502
+ }
+ Steps = 20000
+ MovedAtoms = 1:-1
+}
+
+
+Hamiltonian = DFTB {
+
+  # use the corrected forces for XL-BOMD
+  ForceEvaluation = Dynamics
+
+  SCC = Yes
+  SCCTolerance = 1e-6
+  Filling = Fermi {
+    Temperature [Kelvin] = 400
+  }
+  SlaterKosterFiles = Type2FileNames {
+   Prefix = "../../slakos/mio-ext/"
+   Separator = "-"
+   Suffix = ".skf" 
+  }
+  MaxAngularMomentum = {
+    H = "s"
+    O = "p"
+    C = "p"
+  }
+}
+
+Options = {
+  RandomSeed = 3871906
+  # speed up a bit by suppressing some file writing
+  WriteDetailedOut = No
+}
+
+Analysis {
+  # speed up a bit by suppressing some file writing
+  WriteBandOut = No
+}
+
+# This file uses the 5th input format
+ParserOptions = {
+  ParserVersion = 5
+}
+
+# if run in MPI parallel, allow openMP threads to be used
+Parallel = {
+  UseOmpThreads = Yes
+}
diff --git a/docs/_archives/recipes/moleculardynamics/annealSW/80_SW.gen b/docs/_archives/recipes/moleculardynamics/annealSW/80_SW.gen
@@ -0,0 +1,86 @@
+   80  S
+  C
+    1 1    0.1648525975E-01    0.3339375770E-02   -0.1449893017E-13
+    2 1    0.1279516987E+01    0.7045157680E+00   -0.1676027794E-13
+    3 1    0.1280478521E+01    0.2125402847E+01   -0.2097300060E-14
+    4 1    0.1490777082E-02    0.2779311605E+01    0.2935886213E-14
+    5 1    0.2540281607E+01    0.1019161293E-01   -0.5182676120E-14
+    6 1    0.3787129256E+01    0.7359286395E+00    0.7903185288E-15
+    7 1    0.3790327881E+01    0.2172431462E+01   -0.5619857797E-14
+    8 1    0.2531545960E+01    0.2859456954E+01    0.4788167914E-14
+    9 1    0.5030840382E+01    0.1291565710E-01   -0.1918944832E-14
+   10 1    0.6274551509E+01    0.7359286395E+00    0.2481487713E-14
+   11 1    0.6271352883E+01    0.2172431462E+01    0.5133686018E-14
+   12 1    0.5030840382E+01    0.2923766691E+01    0.6492488486E-14
+   13 1    0.7521399157E+01    0.1019161293E-01   -0.5978408211E-14
+   14 1    0.8782163778E+01    0.7045157680E+00   -0.6536196879E-15
+   15 1    0.8781202243E+01    0.2125402847E+01   -0.2647696342E-14
+   16 1    0.7530134804E+01    0.2859456954E+01    0.1789190487E-14
+   17 1    0.1004519550E+02    0.3339375770E-02    0.4621676408E-14
+   18 1    0.1131939087E+02    0.6771346577E+00    0.6515236400E-14
+   19 1    0.1131939087E+02    0.2087442349E+01   -0.7156293021E-14
+   20 1    0.1006018999E+02    0.2779311605E+01   -0.1095477921E-14
+   21 1   -0.1290776676E-01    0.4188149914E+01   -0.9477614019E-14
+   22 1    0.1223619913E+01    0.4898927029E+01   -0.1774157467E-13
+   23 1    0.1127444141E+01    0.6300308320E+01   -0.1193127746E-14
+   24 1   -0.6727740356E-01    0.7039297094E+01    0.1029189575E-13
+   25 1    0.2523882483E+01    0.4290572302E+01    0.6340155648E-14
+   26 1    0.3756046015E+01    0.5078957871E+01    0.1784263120E-14
+   27 1    0.3582340242E+01    0.6514063172E+01    0.7291073026E-14
+   28 1    0.2288717784E+01    0.7039867946E+01    0.1077349939E-13
+   29 1    0.5030840382E+01    0.4371868719E+01   -0.1667270744E-13
+   30 1    0.6305634749E+01    0.5078957871E+01    0.2790218036E-14
+   31 1    0.6479340523E+01    0.6514063172E+01   -0.1063474793E-13
+   32 1    0.5694079105E+01    0.7748261840E+01    0.3096589887E-14
+   33 1    0.7537798282E+01    0.4290572302E+01    0.4475801595E-14
+   34 1    0.8838060851E+01    0.4898927029E+01    0.2298442782E-13
+   35 1    0.8934236623E+01    0.6300308320E+01    0.4519756146E-14
+   36 1    0.7772962980E+01    0.7039867946E+01   -0.2778986918E-14
+   37 1    0.1007458853E+02    0.4188149914E+01   -0.3752445507E-13
+   38 1    0.1131939087E+02    0.4886577718E+01   -0.1319312362E-13
+   39 1    0.1131939087E+02    0.6305607971E+01    0.1033815503E-13
+   40 1    0.1012895817E+02    0.7039297094E+01   -0.3311109057E-14
+   41 1   -0.6727740356E-01    0.8457226586E+01    0.2479255151E-14
+   42 1    0.1127444141E+01    0.9196215361E+01   -0.9443316341E-14
+   43 1    0.1223619913E+01    0.1059759665E+02   -0.2669173999E-13
+   44 1   -0.1290776676E-01    0.1130837377E+02    0.8336866111E-14
+   45 1    0.2288717784E+01    0.8456655734E+01    0.1091218030E-13
+   46 1    0.3582340241E+01    0.8982460509E+01    0.8522399357E-14
+   47 1    0.3756046015E+01    0.1041756581E+02    0.3206079020E-16
+   48 1    0.2523882483E+01    0.1120595138E+02    0.6505288603E-14
+   49 1    0.4367601660E+01    0.7748261840E+01    0.5057325132E-14
+   50 1    0.6479340523E+01    0.8982460509E+01   -0.5058202645E-14
+   51 1    0.6305634749E+01    0.1041756581E+02    0.1574584305E-14
+   52 1    0.5030840382E+01    0.1112465496E+02    0.7048305389E-14
+   53 1    0.7772962980E+01    0.8456655734E+01   -0.4839603456E-14
+   54 1    0.8934236623E+01    0.9196215361E+01    0.1428018262E-14
+   55 1    0.8838060851E+01    0.1059759665E+02    0.3762055666E-14
+   56 1    0.7537798282E+01    0.1120595138E+02   -0.7732729645E-14
+   57 1    0.1012895817E+02    0.8457226586E+01    0.3983598038E-15
+   58 1    0.1131939087E+02    0.9190915709E+01    0.2561726110E-14
+   59 1    0.1131939087E+02    0.1060994596E+02    0.5133084686E-14
+   60 1    0.1007458853E+02    0.1130837377E+02    0.2079838615E-13
+   61 1    0.1490777077E-02    0.1271721208E+02    0.8056728699E-14
+   62 1    0.1280478521E+01    0.1337112083E+02    0.1713045148E-13
+   63 1    0.1279516987E+01    0.1479200791E+02   -0.3781203824E-14
+   64 1    0.1648525975E-01    0.1549318430E+02   -0.1571410647E-13
+   65 1    0.2531545960E+01    0.1263706673E+02    0.2627584982E-14
+   66 1    0.3790327881E+01    0.1332409222E+02    0.1053759811E-13
+   67 1    0.3787129256E+01    0.1476059504E+02    0.9125083489E-14
+   68 1    0.2540281607E+01    0.1548633207E+02   -0.4008197376E-13
+   69 1    0.5030840382E+01    0.1257275699E+02    0.4143561473E-14
+   70 1    0.6271352883E+01    0.1332409222E+02    0.2388187886E-14
+   71 1    0.6274551509E+01    0.1476059504E+02    0.1660513829E-14
+   72 1    0.5030840382E+01    0.1548360802E+02    0.9133522457E-14
+   73 1    0.7530134804E+01    0.1263706673E+02   -0.5694968685E-14
+   74 1    0.8781202243E+01    0.1337112083E+02   -0.5951206215E-14
+   75 1    0.8782163778E+01    0.1479200791E+02    0.7730915932E-15
+   76 1    0.7521399157E+01    0.1548633207E+02    0.5820145495E-14
+   77 1    0.1006018999E+02    0.1271721208E+02    0.9890522498E-14
+   78 1    0.1131939087E+02    0.1340908133E+02    0.8886924557E-14
+   79 1    0.1131939087E+02    0.1481938902E+02    0.2667200131E-14
+   80 1    0.1004519550E+02    0.1549318430E+02    0.3500993482E-14
+    0.0000000000E+00    0.0000000000E+00    0.0000000000E+00
+    0.0000000000E+00    0.1690529857E+02    0.0000000000E+00
+    0.1257710097E+02    0.0000000000E+00    0.0000000000E+00
+    0.0000000000E+00    0.0000000000E+00    0.1000000000E+03
diff --git a/docs/_archives/recipes/moleculardynamics/annealSW/dftb_in.hsd b/docs/_archives/recipes/moleculardynamics/annealSW/dftb_in.hsd
@@ -0,0 +1,77 @@
+Geometry = GenFormat {
+  <<< 80_SW.gen
+}
+
+Driver = VelocityVerlet {
+
+  # Using a thermostat, so conserved properties of dynamics are less #
+  # important
+  TimeStep [Femtosecond] = 2.0
+
+  Thermostat = Andersen {
+
+    # Probabalistically replaces atomic velocities from a
+    # Maxwell-Boltzmann distribution    
+    ReselectProbability = 0.2
+    ReselectIndividually = Yes
+
+    # Simulated annealing profile for the temperature
+    Temperature [Kelvin] = TemperatureProfile {
+      constant      1    100.0 # Start
+      linear      499   5500.0 # Ramp up
+      constant    200   5500.0 # 'cook'
+      linear      500    100.0 # Quench
+    }
+
+    AdaptFillingTemp = Yes # Adjust electron temperature to match
+
+  }
+
+  Barostat { # Apply presure control
+    Pressure [Pa] = 1.0E5
+    Timescale [ps] = 0.1
+  }
+
+  MDRestartFrequency = 10 # Only write output every 10 steps
+
+  OutputPrefix = "geo_end"
+
+}
+
+Hamiltonian = DFTB {
+
+  MaxAngularMomentum {
+    C = "p"
+  }
+
+  Charge = 0.0
+
+  Filling = Fermi {} # electronic temperature is controlled by the
+  # thermostat
+
+  SlaterKosterFiles = Type2FileNames {
+    Prefix = "../../slakos/mio-ext/"
+    Separator = "-"
+    Suffix = ".skf"
+  }
+
+  # Gamma point - use more accurate sampling for a realistic calculation
+  KPointsAndWeights {
+    0 0 0 1.0
+  }
+
+}
+
+Options {
+
+  MullikenAnalysis = No
+  WriteBandOut = No
+
+  WriteDetailedOut = No
+  RandomSeed = 589105024 # specify the rand number generator
+  # starting seed
+}
+
+ParserOptions {
+  ParserVersion = 4
+}