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TBpack v0.5.0 - Optimus
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Documentation for ElectronicBands1D, optimization module
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Vasil Saroka committed Feb 19, 2022
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6 changes: 3 additions & 3 deletions PacletInfo.m
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(* Paclet Info File *)

(* created 2021/04/08*)
(* created 2022/02/19*)

Paclet[
Name -> "TBpack",
Version -> "0.4.0",
Version -> "0.5.0",
MathematicaVersion -> "10.0+",
Description -> "Tight-binding calculations in Mathematica.",
Creator -> "Vasil Saroka <[email protected]>",
Expand All @@ -24,7 +24,7 @@
URL -> "https://github.com/vasilsaroka/TBpack",
Support -> "https://t.me/vasilsaroka",
Icon -> "Logo_3.png",
UUID -> "MaTeX documentation embeded",
UUID -> "TBpack-e9a2c698-48f6-49e0-8194-d7cd44976257",
Location -> "https://github.com/vasilsaroka/TBpack",
Extensions ->
{
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2 changes: 1 addition & 1 deletion TBpack/CustomTicks.m
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Expand Up @@ -625,7 +625,7 @@ x is plot coordinate (so b^x is true exponentiated coordinate)
*)


Options[LogTicks]={ExtraTicks->{},TickPreTransformation->Identity,TickPostTransformation->Identity,ShowFirst->True,ShowLast->True,ShowTickLabels->True,ShowMinorTicks->True,TickLabelStart->0,TickLabelStep->1,TickRange->{-Infinity,Infinity},TickLabelRange->{-Infinity,Infinity},DecimalDigits->Automatic,MajorTickLength->0.010,MinorTickLength->0.005,TickLengthScale->1,TickDirection->In,TickReverse->False,MajorTickStyle->{},MinorTickStyle->{},MinorTickIndexRange->{1,Infinity},LogPlot->False};
Options[LogTicks]={ExtraTicks->{},TickPreTransformation->Identity,TickPostTransformation->Identity,ShowFirst->True,ShowLast->True,ShowTickLabels->True,ShowMinorTicks->True,TickLabelStart->0,TickLabelStep->1,TickRange->{-Infinity,Infinity},TickLabelRange->{-Infinity,Infinity},DecimalDigits->Automatic,MajorTickLength->0.010,MinorTickLength->0.005,TickLengthScale->1,TickDirection->Inward,TickReverse->False,MajorTickStyle->{},MinorTickStyle->{},MinorTickIndexRange->{1,Infinity},LogPlot->False};


LogTicks::oldsyntax="The number of minor subdivisions no longer needs to be specified for LogTicks (see CustomTicks manual for new syntax).";LogTicks::minorsubdivs="Number of minor subdivisions `1` specified for LogTicks is not 1 or \[LeftCeiling]base\[RightCeiling]-1 (i.e., \[LeftCeiling]base\[RightCeiling]-2 tick marks) and so is being ignored.";
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229 changes: 221 additions & 8 deletions TBpack/DataAnalysis.m
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Expand Up @@ -7,7 +7,7 @@
ListOfBonds::usage = "ListOfBonds[\*StyleBox[\"unitcell\",\"TI\"], \*StyleBox[\"bondlength\",\"TI\"]] returns point pairs from \*StyleBox[\"unitcell\",\"TI\"] such that distance between the points is \*StyleBox[\"bondlength\",\"TI\"] \[PlusMinus] 0.05 \[Angstrom].
ListOfBonds[\*StyleBox[\"unitcell\",\"TI\"], \*StyleBox[\"bondlength\",\"TI\"], BondLengthDelta \[Rule] \*StyleBox[\"value\",\"TI\"]] returns point pairs from \*StyleBox[\"unitcell\",\"TI\"] such that distance between the points is \*StyleBox[\"bondlength\",\"TI\"] \[PlusMinus] \*StyleBox[\"value\",\"TI\"] \[Angstrom].
ListOfBonds[\*StyleBox[\"unitcell\",\"TI\"], \*StyleBox[\"bondlength\",\"TI\"], Dimentionality \[Rule] 2] returns a list of pairs \*RowBox[{\"{\", \"{\", StyleBox[SubscriptBox[\"x\",\"1\"],\"TI\"], \",\" , StyleBox[SubscriptBox[\"y\",\"1\"],\"TI\"] , \"}\" , \",\" , \"{\", StyleBox[SubscriptBox[\"x\",\"2\"],\"TI\"], \",\", StyleBox[SubscriptBox[\"y\",\"2\"],\"TI\"] ,\"}\" ,\"}\"}].";
AtomicStructure::usage = "AtomicStructure[{\*StyleBox[\"unitcell\",\"TI\"], \*StyleBox[\"tr\",\"TI\"], \*StyleBox[SubscriptBox[\"a\",\"0\"],\"TI\"]}] returns the ball-and-stick model of a \*StyleBox[\"system\",\"TI\"] specified by unit cell \*StyleBox[\"unitcell\",\"TI\"], translation vector \*StyleBox[\"tr\",\"TI\"] and the lattice constant \*StyleBox[SubscriptBox[\"a\",\"0\"],\"TI\"].
AtomicStructure::usage = "AtomicStructure[{\*StyleBox[\"unitcell\",\"TI\"], \*StyleBox[\"tr\",\"TI\"], \*StyleBox[SubscriptBox[\"a\",\"0\"],\"TI\"]}] returns the ball-and-stick model of a \*StyleBox[\"system\",\"TI\"] specified by the unit cell \*StyleBox[\"unitcell\",\"TI\"], translation vector \*StyleBox[\"tr\",\"TI\"] and the lattice constant \*StyleBox[SubscriptBox[\"a\",\"0\"],\"TI\"].
AtomicStructure[\*StyleBox[\"system\",\"TI\"], \*StyleBox[\"options\",\"TI\"]] uses option settings specified in \*StyleBox[\"options\",\"TI\"].
AtomicStructure[\*StyleBox[\"system\",\"TI\"], NumberOfUnitCells \[Rule] \*StyleBox[\"value\",\"TI\"]] returns the number of unit cells set by \*StyleBox[\"value\",\"TI\"].
AtomicStructure[\*StyleBox[\"system\",\"TI\"], Dimensionality \[Rule] 2] returns the \*StyleBox[\"system\",\"TI\"] projection to the \*StyleBox[\"xy\",\"TI\"]-plane.
Expand Down Expand Up @@ -53,14 +53,23 @@
PlotGrid[\!\(\*StyleBox[\"plist\",\"TI\"], ImageSize \[Rule] {\*StyleBox[\"width\",\"TI\"], \*StyleBox[\"height\",\"TI\"] }\)] produces image with the specified \*StyleBox[\"width\",\"TI\"] and \*StyleBox[\"height\",\"TI\"].
PlotGrid[\!\(\*StyleBox[\"plist\",\"TI\"], ImagePadding \[Rule] {{\*StyleBox[\"left\",\"TI\"], \*StyleBox[\"right\",\"TI\"]}, {\*StyleBox[\"bottom\",\"TI\"], \*StyleBox[\"top\",\"TI\"] }\)] produces image with the specified \*StyleBox[\"left\",\"TI\"], \*StyleBox[\"right\",\"TI\"], \*StyleBox[\"bottom\",\"TI\"] and \*StyleBox[\"top\",\"TI\"] image paddings around the tiled plots.";

ReadElectronicBands1D::usage = "ReadElectronicBands1D[] imports data from an output text file of \*StyleBox[\"ElectronicBands1D\",\"TI\"] function,
ReadElectronicBands1D[\!\(\*StyleBox[\"options\",\"TI\"] \)] imports data using the specified \*StyleBox[\"options\",\"TI\"].
ReadElectronicBands1D[\!\(Path2File \[Rule] \*StyleBox[\"path\",\"TI\"] \)] imports data from the file in a directory specified with \*StyleBox[\"path\",\"TI\"].
ReadElectronicBands1D[\!\(FileName \[Rule] \*StyleBox[\"fname\",\"TI\"] \)] imports data from the file specified with \*StyleBox[\"fname\",\"TI\"].
ReadElectronicBands1D[\!\(Output \[Rule] \*StyleBox[\"form\",\"TI\"] \)] imports data from the file in a form specified with \*StyleBox[\"form\",\"TI\"]:
\"\*StyleBox[\"Standard\",\"TI\"]\" returns the standard return of \*StyleBox[\"ElectronicBands1D\",\"TI\"] (default),
\"\*StyleBox[\"System\",\"TI\"]\" returns the list of the unit cell \*StyleBox[\"unitcell\",\"TI\"], translation vector \*StyleBox[\"tr\",\"TI\"] and the lattice constant \*StyleBox[SubscriptBox[\"a\",\"0\"],\"TI\"] to be used as an input for \*StyleBox[\"AtomicStructure\",\"TI\"] function,
\"\*StyleBox[\"Fields\",\"TI\"]\" returns the list of external electric and magnetic fields that were used in the calculations by \*StyleBox[\"ElectronicBands1D\",\"TI\"],
\"\*StyleBox[\"StructuralParameters\",\"TI\"]\" returns the list of hopping distances and hopping distance delta that were used in the calculations by \*StyleBox[\"ElectronicBands1D\",\"TI\"].
";



(* Options *)
NumberOfUnitCells::usage = "Option setting the number of unit cell to be displayed.";
Dimensionality::usage = "Option setting the number of dimensions used in displaying an object.";
AtomEnumeration::usage = "Option taking values \*StyleBox[\"True\",\"TI\"] or \*StyleBox[\"False\",\"TI\"] specifying if the atom numbers should be displayed."
BondLengthDelta::usage = "Option setting in \[Angstrom] the maximum deviation of the bond length in the unit cell from the explicitly specified bond length value.";
AtomColor::usage = "Option setting the color of the atoms displayed in graphical objects.";
BondColor::usage = "Option setting the color of the bonds displayed in graphical objects."
TextColor::usage = "Option setting the color of the text displayed in graphical objects."
Expand All @@ -78,7 +87,8 @@
XTickLen::usage = "Option in some plotting functions setting the length of ticks for x-axis scaled to the height of the plot.";
YTickDirection::usage = "Option in some plotting functions setting \*StyleBox[\"Inward\",\"TI\"], \*StyleBox[\"Outward\",\"TI\"] or \*StyleBox[\"Both\",\"TI\"] direction of ticks for y-axis."
XTickDirection::usage = "Option in some plotting functions setting \*StyleBox[\"Inward\",\"TI\"], \*StyleBox[\"Outward\",\"TI\"] or \*StyleBox[\"Both\",\"TI\"] direction of ticks for x-axis."
TicksPattern::usage = "Option is some plotting functions setting a pattern of the frame ticks displaying: {{\*StyleBox[\"left\",\"TI\"], \*StyleBox[\"right\",\"TI\"]}, {\*StyleBox[\"bottom\",\"TI\"], \*StyleBox[\"top\",\"TI\"]}}, where \*StyleBox[\"left\",\"TI\"], \*StyleBox[\"right\",\"TI\"], \*StyleBox[\"bottom\",\"TI\"] and \*StyleBox[\"top\",\"TI\"] are \*StyleBox[\"True\",\"TI\"] or \*StyleBox[\"False\",\"TI\"]."
TicksPattern::usage = "Option in some plotting functions setting a pattern of the frame ticks displaying: {{\*StyleBox[\"left\",\"TI\"], \*StyleBox[\"right\",\"TI\"]}, {\*StyleBox[\"bottom\",\"TI\"], \*StyleBox[\"top\",\"TI\"]}}, where \*StyleBox[\"left\",\"TI\"], \*StyleBox[\"right\",\"TI\"], \*StyleBox[\"bottom\",\"TI\"] and \*StyleBox[\"top\",\"TI\"] are \*StyleBox[\"True\",\"TI\"] or \*StyleBox[\"False\",\"TI\"]."
Output::usage = "Option specifying a form of the output for such functions as \*StyleBox[\"ReadElectronicBands1D\",\"TI\"].";

(* Constants *)
TBpackPalette::usage = "The list of standard colors used by default in plotting functions.";
Expand All @@ -88,12 +98,12 @@

Options[ListOfBonds] = {
Dimensionality -> 3,
BondLengthDelta -> 0.05
TBpack`BondLengthDelta -> 0.05
};
ListOfBonds[unitcell_List, bondlength_, OptionsPattern[]] := Module[
{
dim = OptionValue[Dimensionality],
delta = OptionValue[BondLengthDelta],
delta = OptionValue[TBpack`BondLengthDelta],
len, vec,
bondlist = {}
},
Expand Down Expand Up @@ -121,7 +131,7 @@
SyntaxInformation[ListOfBonds] = {"ArgumentsPattern" -> {_, _, OptionsPattern[]}};

Options[AtomicStructure] = {
BondLengthDelta -> 0.05,
TBpack`BondLengthDelta -> 0.05,
NumberOfUnitCells -> 1,
Dimensionality -> 3,
AtomEnumeration -> False,
Expand All @@ -135,7 +145,7 @@
(* 2D structure visualization is not included *)
AtomicStructure[system_List, OptionsPattern[]]:=Module[
{
bondlengthdelta = OptionValue[BondLengthDelta],
bondlengthdelta = OptionValue[TBpack`BondLengthDelta],
lim = OptionValue[NumberOfUnitCells],
dim = OptionValue[Dimensionality],
acolor = OptionValue[AtomColor],
Expand Down Expand Up @@ -722,7 +732,7 @@



(* this function is modified code from stackexchange:
(* this function is the modified code from stackexchange:
https://mathematica.stackexchange.com/questions/6877/do-i-have-to-\code-each-case-of-this-grid-full-of-plots-separately/6882#6882
*)

Expand Down Expand Up @@ -819,6 +829,209 @@
](* end Module *)]; (* end Catch *)
SyntaxInformation[PlotGrid] = {"ArgumentsPattern" -> {_, OptionsPattern[]}};


Options[ReadElectronicBands1D] = {
TBpack`Path2File -> Automatic(* Path2Save from ElectronicBands1D *),
TBpack`FileName -> Automatic(* last file in the list of files for the directory given by Path *),
Output -> "Standard" (* standard output of ElectronicBands1D *)
(*
System: {unitcell,T,a0};
StructuralParameters: {hoppinddistances,hoppingdistancedelta};
Fields: {efield,bgield}
*)
};
ReadElectronicBands1D[OptionsPattern[]] := Block[
{
output = OptionValue[Output],
path = OptionValue[TBpack`Path2File],
fname = OptionValue[TBpack`FileName],
data, evpos,
pos, pos2, pos3,
bands,
hoppingintegrals,
overlappingintegrals,
strain,
edgecorrections,
modelname,
len,
evec, v,

indfun, prc
},

(* path and file name *)
If[
path === Automatic,
path = Options[TBpack`ElectronicBands1D, TBpack`Path2Save][[1, 2]]
](* end If *);

If[
fname === Automatic,
SetDirectory[Options[TBpack`ElectronicBands1D, TBpack`Path2Save][[1, 2]]];
fname = Last[FileNames["ElectronicBands1D*"]]
](* end If *);

data = ReadList[FileNameJoin[{path, fname}], Word, RecordLists -> True];

Switch[
output,
"System",
(* system under consideration *)
pos = Position[data, {"#", __ , "under", "consideration:",___}][[1, 1]];
pos2 = Position[data, {"#", "Translation", "vector", __, "Angstrom"}][[1, 1]];
pos3 = Position[data, {"#", "Hopping", "distances,", "Angstrom"}][[1, 1]];
{
(* unit cell *)
ToExpression[data[[pos + 2 ;; pos2 - 1]]],
(* translation vector *)
ToExpression[data[[pos2 + 1]]],
(* lattice constant *)
ToExpression[data[[pos3 + 2, 4]]]
},
"Fields",
(* Efield *)
pos = Position[data, {"#", "Electric", "field", __, "V/Angstrom"}][[1, 1]];
pos2 = Position[data, {"#", "Magnetic", "field", __, "T"}][[1, 1]];
{
(*efield*)
ToExpression[data[[pos + 1]]],
(*bfield*)
ToExpression[data[[pos2 + 1]]]
},
"StructuralParameters",
(* structural parameters *)
pos = Position[data, {"#", "Hopping", "distances,", "Angstrom"}][[1, 1]];
pos2 = Position[data, {"#", "Hopping", "distance", "delta,", "Angstrom"}][[1, 1]];
{
(*hoppingdistances*)
ToExpression[data[[pos + 1 ;; pos2 - 1, 4]]],
(*hoppingdistancedelta*)
ToExpression[data[[pos2 + 1, 3]]]
},
"Standard",
(* auxilliary functions *)
indfun[list_] := Block[
{
ilist
},
ilist = First /@ StringPosition[list[[1]], {"t", "_"}];
RotateLeft[{1, 0, 0} + ToExpression@StringTake[list[[1]],
{
{ilist[[1]] + 1, ilist[[2]] - 1},
{ilist[[2]] + 1, ilist[[3]] - 1},
{ilist[[3]] + 1, -1}
}
]](* end RotateLeft *)
](* end Block *);

(* partition list of strings into a list of real and/or complex numbers *)
prc[tlist_] := Block[
{
l, elist, i
},
l = Length[tlist];
elist = {};
i = 1;
While[
i <= l,
If[
i > l - 3,
AppendTo[elist, ToExpression[tlist[[i]]]];
i += 1,
If[
SameQ["I", tlist[[i + 3]]],
AppendTo[
elist,
ToExpression[StringJoin[tlist[[i ;; i + 3]]]]
];
i += 4,
AppendTo[elist, ToExpression[tlist[[i]]]];
i += 1
](*end If*)
](* end If *)
](* end While *);
elist
](* end Block *);

(*hoppingintegrals*)
pos = Position[data, {"#", "Hopping", "integrals,", "eV"}][[1, 1]];
pos2 = Position[data, {"#", "Overlapping", "integrals"}][[1, 1]];
hoppingintegrals = ToExpression[StringJoin[#[[3 ;; All]]]] & /@ (data[[pos + 1 ;; pos2 - 1]]);


(*overlappingintegrals*)
pos = pos2;
pos2 = Position[data, {"#", "Strain", "exponent"}][[1, 1]];
overlappingintegrals =
ToExpression[StringJoin[#[[3 ;; All]]]] & /@ (data[[
pos + 1 ;; pos2 - 1]]);

(*strain*)
pos = pos2;
pos2 = Position[data, {"#", "Edge", "corrections,", "eV"}][[1, 1]];
strain =
ToExpression[StringJoin[data[[pos + 1 ;; pos2 - 1, 3 ;; All]]]];

(*edgecorrections*)
pos = pos2;
pos2 = Position[data, {"#", _, "system", "under", "consideration:",___}][[1, 1]];
edgecorrections =
ArrayReshape[
ToExpression[StringJoin[#[[3 ;; All]]]] & /@ (data[[
pos + 1 ;; pos2 - 1]]), indfun@(data[[pos2 - 1]])];

(*modelname*)
pos = Position[data, {"#", "Model", "name:", ___}][[1, 1]];
modelname = StringJoin @@ data[[pos, 4 ;; All]];

evpos = Position[data, {"#", "Eigenvectors:"}];
If[
evpos === {},
pos = Position[data, {"#", "Electronic", "band", "structure:"}][[1, 1]];
pos2 = Position[data, {"#", "Finished", "on", ___}][[1, 1]];
bands = prc /@ (data[[pos + 2 ;; pos2 - 1]]);
{
bands,
{hoppingintegrals,
overlappingintegrals,
strain,
edgecorrections,
modelname}
}
,
pos = Position[data, {"#", "Electronic", "band", "structure:"}][[1, 1]];
pos2 = evpos[[1, 1]];
bands = prc /@ (data[[pos + 2 ;; pos2 - 1]]);

pos = pos2;
pos2 = Position[data, {"#", "Velocity", "operator", "matrices:"}][[1, 1]];
len = Length[bands] - 1;
evec = Partition[prc /@ (data[[pos + 1 ;; pos2 - 1]]), len];

pos = pos2;
pos2 = Position[data, {"#", "Finished", "on", ___}][[1, 1]];
v = Flatten[#, {{2}, {3}, {1}}] & /@ Fold[
Partition,
prc /@ (data[[pos + 1 ;; pos2 - 1]]),
{len, 3}
](* end Fold *);
{
bands,
evec,
v,
{hoppingintegrals,
overlappingintegrals,
strain,
edgecorrections,
modelname}
}
](* end If *)

](* end Switch *)

](* end Block *)
SyntaxInformation[ReadElectronicBands1D] = {"ArgumentsPattern" -> {OptionsPattern[]}};

End[] (* End Private Context *)

EndPackage[]
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