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PhononIrep.wl
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(* ::Package:: *)
BeginPackage["PhononIrep`",{"SpaceGroupIrep`"}]
getcharandsymm ::usage = ""
phonopyIrepIO ::usage = ""
calcPhononIrep ::usage = "calcPhononIrep[{{\"supercell\"\[Rule]{a,b,c},
\"unitcell\" \[Rule] path of unitcell cell strcuture file,
\"force\" -> path of force constants file,
\"kset\"\[Rule]{{\!\(\*SubscriptBox[\(kx\), \(1\)]\),\!\(\*SubscriptBox[\(ky\), \(1\)]\),\!\(\*SubscriptBox[\(kz\), \(1\)]\)},{\!\(\*SubscriptBox[\(kx\), \(2\)]\),\!\(\*SubscriptBox[\(ky\), \(2\)]\),\!\(\*SubscriptBox[\(kz\), \(2\)]\)},...},
\"showRep\"\[Rule] True or False,
\"degeneracytolerance\" -> tolerance of determining the degeneracy in phonopy,
\"symprec\" -> tolerance of determining the symmetry in phonopy]
generates the irreducible representations for phonon of the k points in \"kset\" option, where for opinions \"supercell\", \"unitcell\", \"force\", \"kset\" are shoule be set almost every calculations, but for \"degeneracytolerance\" and \"symprec\" the default values are OK.\"showRep\" is a opinion that tell PhononIrep whether to show the results in a Grid form.";
Begin["`Private`"];
ss=StartExternalSession["Python"];
ExternalEvaluate[ss,"
import numpy as np
import phonopy
from phonopy.structure.symmetry import Symmetry
from phonopy.interface.vasp import write_vasp
def getcharandsymm(supercell,unitcell_filename,force_constants_filename,kset,symprec,degeneracy_tolerance):
chardict={}
ph = phonopy.load(supercell_matrix=supercell,
unitcell_filename=unitcell_filename,
force_constants_filename=force_constants_filename,
symprec=symprec)
write_vasp("<>"'POSCARasdasd'"<>",ph._primitive)
symm=Symmetry(ph._primitive, symprec=symprec).get_dataset()
symm=dict((k,symm[k]) for k in ('number','rotations','translations','transformation_matrix') if k in symm)
symm['rotations']=np.array(symm['rotations'],dtype='int64')
chardict['symmetry']=symm
for k in kset:
ph.set_irreps(k,
is_little_cogroup=False,
nac_q_direction=None,
degeneracy_tolerance=degeneracy_tolerance)
char={}
char['rotations']=np.array( ph._irreps._conventional_rotations,dtype='int64')
char['q-position']=ph._irreps._q
char['normal_modes']=[]
for i, deg_set in enumerate(ph._irreps._degenerate_sets):
char['normal_modes'].append({
'band_indices': [i+1 for i in deg_set],
'frequency': ph._irreps._freqs[deg_set[0]],
'characters': ph._irreps._characters[i]})
chardict[k]=char
return chardict
"];
Options[getcharandsymm] = {
"supercell" -> {1, 1, 1},
"unitcell" -> "POSCAR-unitcell",
"force" -> "FORCE_CONSTANTS",
"kset" -> {{0, 0, 0}},
"symprec" -> 0.0001,
"degeneracytolerance" -> 0.0001};
getcharandsymm[OptionsPattern[]] := Module[{
supercell = OptionValue["supercell"],
unitcell = OptionValue["unitcell"],
force = OptionValue["force"],
kset = N@OptionValue["kset"],
symprec = N@OptionValue["symprec"],
degeneracytolerance = N@OptionValue["degeneracytolerance"],output},
output=ExternalEvaluate[
ss, <|"Command" -> "getcharandsymm",
"Arguments" -> {supercell, unitcell, force, kset, symprec,
degeneracytolerance}|>];
output["symmetry"]= Rationalize/@Normal/@output["symmetry"];
(* Print[output];*)
output
];
phonopyIrepIO[char_] := Module[{nele, SymmData, CharData,
nsymm, SOC = 0, SymmetryOperation, NK, kvector,
PositionofPointGroupElement, BandChar,
OutputStr,
qpoints,
tm
},
SymmData = char["symmetry"];
qpoints = Drop[Keys[char], 1];
(*Print[qpoints];*)
tm=Rationalize[SymmData["transformation_matrix"],0.000001];
nsymm = Length@SymmData["rotations"];
SymmetryOperation =
Flatten/@Transpose@{#rotations,Mod[Round[N@#translations,0.00001],1] }&[SymmData];
(*Print[SymmetryOperation];*)
kvector = <||>;
BandChar = <||>;
PositionofPointGroupElement = <||>;
Do[
CharData = char[q];
nele = Last[Last[#"band_indices" & /@ CharData["normal_modes"]]];
kvector[q] = Normal@CharData["q-position"];
(*Print[SymmData["rotations"],CharData["rotations"]];*)
PositionofPointGroupElement[q] =
FirstPosition[# & /@
SymmData["rotations"], #] & /@
(Simplify[Inverse[tm] . # . tm] & /@ Normal@CharData["rotations"]);
(*Print[PositionofPointGroupElement,"\n",Normal@CharData["rotations"],"\n",SymmData["rotations"],"\n",
tm
];*)
PositionofPointGroupElement[q] =
Flatten[PositionofPointGroupElement[q]];
BandChar[
q] = {#"band_indices", #frequency, {N[Re[#], 10], N[Im[#], 10]}&/@ Chop@Normal[#characters]} & /@
CharData["normal_modes"];
(*Print[BandChar];*)
BandChar[q] = MapAt[{#[[1]], Length[#]} &, BandChar[q], {;; , 1}];
BandChar[q] = Flatten /@ BandChar[q];
, {q, qpoints}];
(*Print[BandChar];*)
OutputStr = StringRiffle[{nele}, " "];
OutputStr =
OutputStr <> "\n" <> ToString[SOC] <> "\n" <> ToString[nsymm] <>
"\n";
NK = Length[qpoints];
Do[
OutputStr = OutputStr <> str <> " 1 0 0 0 0 0 1 0" <> "\n",
{str, StringRiffle[#, " "] & /@ SymmetryOperation}];
OutputStr = OutputStr <> ToString[NK] <> "\n";
Do[
OutputStr = OutputStr <> StringRiffle[kvector[q], " "] <> "\n";
, {q, qpoints}];
Do[
OutputStr =
OutputStr <> ToString[Length[PositionofPointGroupElement[q]]] <>
"\n";
OutputStr =
OutputStr <> StringRiffle[PositionofPointGroupElement[q], " "] <>
"\n";
(*Print[PositionofPointGroupElement[q]];*)
Do[
OutputStr = OutputStr <> str <> "\n",
{str, StringRiffle[#, " "] & /@ BandChar[q]}];
, {q, qpoints}];
OutputStr;
Export[FileNameJoin[{$TemporaryDirectory, "trace.txt"}], OutputStr];
];
getBZtype[poscarFile_, prec_] :=
Module[{cell, sym, BCcell, brav, sgno, U, Q, t0, S, R, hsp,
bravtype}, cell = readPOSCAR[poscarFile];
sym = spglibGetSym[Values[cell][[1 ;; 3]], prec];
sgno = sym["number"];
brav = getSGLatt[sgno];
(*Print[brav];*)bravtype = checkBasVec[brav, cell[[1]]];
(*Print[bravtype];*)If[bravtype[[1]], bravtype = bravtype[[2]];
If[bravtype != "", brav = brav <> "(" <> bravtype <> ")"];
(*Print[checkBasVec[brav,BCcell[[1]]]];*)
hsp = N@BCHighSymKpt[brav][[;; , ;; 3]];
{brav, Select[hsp, #[[2]] == "" &]}, {t0, U} =
SGGenElem[sgno][[{2, 3}]];
{Q, S} = getQandS[sgno];
BCcell = cell;
BCcell["basVec"] =
Transpose@(S . sym["R"] . Transpose[cell["basVec"]] .
Inverse[sym["P"]] . Q . U) // Chop;
(*BCcell["pos"]=Inverse[Q.U].(sym["P"].#+sym["p0"])+t0&/@cell[
"pos"]//Chop;*)(*Print[cell,BCcell[[1]]];*)bravtype = "";
If[MemberQ[{"OrthBase", "OrthBody", "OrthFace", "TetrBody",
"TrigPrim"}, brav],
bravtype = checkBasVec[brav, BCcell[[1]]][[2]];
(*Print[checkBasVec[brav,BCcell[[1]]]];*)
brav = brav <> "(" <> bravtype <> ")";];
hsp = BCHighSymKpt[brav][[;; , ;; 3]];
hsp =
MapAt[Inverse[Transpose[Inverse[sym["P"]] . Q . U]] . # &,
hsp, {;; , 3}];
{bravtype, brav, Select[hsp, #[[2]] == "" &]}]
];
Options[calcPhononIrep] = {
"supercell" -> {1, 1, 1},
"unitcell" -> "POSCAR-unitcell",
"force" -> "FORCE_CONSTANTS",
"kset" -> {{0, 0, 0}},
"symprec" -> 0.0001,
"degeneracytolerance" -> 0.0001,
"showRep"->False};
calcPhononIrep[OptionsPattern[]] := Module[{
supercell = OptionValue["supercell"],
unitcell = OptionValue["unitcell"],
force = OptionValue["force"],
kset = N@OptionValue["kset"],
symprec = N@OptionValue["symprec"],
degeneracytolerance = N@OptionValue["degeneracytolerance"],
showRep = OptionValue["showRep"],
char, tracedata, tr, rep1,bztype
},
char = getcharandsymm[
"supercell" -> supercell,
"unitcell" -> unitcell,
"force" -> force,
"kset" -> kset,
"symprec" -> symprec,
"degeneracytolerance" -> degeneracytolerance];
phonopyIrepIO[char];
tracedata =
readVasp2trace[FileNameJoin[{$TemporaryDirectory, "trace.txt"}]];
(*tr = autoConvTraceToBC["C:\\Users\\zhang\\Documents\\POSCARasdasd", tracedata];*)
tr = autoConvTraceToBC[unitcell, tracedata];
bztype=getBZtype[unitcell,symprec][[1]];
bztype=StringCases[bztype,"("~~x_~~")"->x];
If[bztype=={},bztype="",bztype=bztype[[1]]];
(*Print[getBZtype[unitcell,symprec],bztype];*)
rep1 = getBandRep[char["symmetry"]["number"], bztype,
(*For SpaceGroupIrep <=1.03 use tr["trace"]]; otherwise use tr];*)
(*tr["trace"]];*)
tr];
(*Print[rep1];*)
Print["SG No:",char["symmetry"]["number"]];
If[showRep,showIrep[rep1];rep1,rep1]
];
showIrep[repoutput_]:=Module[{kpath,rep,kinfo,head},
{kpath,rep,kinfo}=repoutput/@Keys[repoutput];
(*Print[kinfo];*)
Do[
head=PadRight[{kinfo[[n]][[;;2]]},4,SpanFromLeft];
Print@Grid[Join[{head},{{"Band","Frequency","dim","Irep"}},rep[[n]]],Frame->All];
,{n,Length[kinfo]}]
]
End[];
EndPackage[];