Hi everyone, and thanks to all of you who are still using Crystallica so many years later! I'm happy you've found it useful. This reply is for everyone who had problems with lattice planes in Mathematica 12, and I'm very sorry I haven't been able to react sooner. There was indeed a change in Mathematica that broke my code. Here's a fix you can make yourself:

1. Find and open the file Crystallica/PackageFiles/CrystalPlot.m within your Crystallica installation.

2. Find the following section of code:

   (*lattice planes: *)
   
   If[p3dQ||d2Q,
   oneplane[{h_,k_,l___},dist_]:=Cases[ContourPlot[{h,k}.{x,y}==dist,{x,0,sysdim[[1]]},{y,0,sysdim[[2]]},
   Evaluate[Sequence@@Join[FilterRules[options,Options[ContourPlot]],{Mesh->False,ContourLabels->False,ContourStyle->{Thick,Red}}]]],GraphicsComplex[x_,y__]:>GraphicsComplex[If[p3dQ,Join[#,{0}]&/@(x.lattvec[[{1,2},{1,2}]]),x.lattvec],y]],
   oneplane[{h_,k_,l_},dist_]:=Cases[ContourPlot3D[{h,k,l}.{x,y,z}==dist,{x,0,sysdim[[1]]},{y,0,sysdim[[2]]},{z,0,sysdim[[3]]},
   Evaluate[Sequence@@Join[FilterRules[options,Options[ContourPlot3D]],{Mesh->False,BoundaryStyle->None,ContourStyle->{Red,Opacity[.5]}}]]],GraphicsComplex[x_,y__]:>GraphicsComplex[x.lattvec,y]]
   ];
   planes=oneplane@@@(LatticePlanes/.options/.Options[CrystalPlot]);
   

3. Replace it with the following:

   (*lattice planes: *)
   
   If[p3dQ||d2Q,
   oneplane[{h_,k_,l___},dist_]:=Cases[ContourPlot[{h,k}.{x,y}==dist,{x,0,sysdim[[1]]},{y,0,sysdim[[2]]},
   Evaluate[Sequence@@Join[FilterRules[options,Options[ContourPlot]],{Mesh->False,ContourLabels->False,ContourStyle->{Thick,Red}}]]],GraphicsComplex[x_,y__]:>GraphicsComplex[If[p3dQ,Join[#,{0}]&/@(x.lattvec[[{1,2},{1,2}]]),x.lattvec],y],Infinity],
   oneplane[{h_,k_,l_},dist_]:=Cases[ContourPlot3D[{h,k,l}.{x,y,z}==dist,{x,0,sysdim[[1]]},{y,0,sysdim[[2]]},{z,0,sysdim[[3]]},
   Evaluate[Sequence@@Join[FilterRules[options,Options[ContourPlot3D]],{Mesh->False,BoundaryStyle->None,ContourStyle->{Red,Opacity[.5]}}]]],GraphicsComplex[x_,y__]:>GraphicsComplex[x.lattvec,y],Infinity]
   ];
   planes=oneplane@@@(LatticePlanes/.options/.Options[CrystalPlot]);
   

Yes, it's basically just addding two "Infinity"s. Based on a quick test, that should work for both 2D and 3D now.

Sorry again to leave you alone with this. I sadly haven't used Mathematica in a long time myself. I hope this fix still helps someone.

Hello Someone can help me, I try to do something simple and I can't get the dimensions of the stutructure that's going on? When you download the package, save it to a cart then install it by File -> Install -> Crystallica.m which you are doing wrong.

Hello Robert. I use Mathematica 12.1 under macOS Catalina ver. 10.15.7. I ran the same codes and got the exact output as yours.

I wonder why... perhaps the codes don't work in Ver. 12?

I also notice the double and triple bond visualization problem has gone in Ver. 12. I tried to run

ChemicalData["Benzene", "MoleculePlot"]

and the output is excellent: we can see the double bond in the benzene. I guess they implemented Bianca's codes in the new version.

Anyway, the VaspImport package is great (even though I use Quantum Espresso for my work.)

Thank you.

Welcome to Wolfram Community! Please make sure you know the rules: https://wolfr.am/READ-1ST

The rules explain how to format your code properly. If you do not format code, it may become corrupted and useless to other members. Please EDIT your posts and make sure code blocks start on a new paragraph and look framed and colored like this.

int = Integrate[1/(x^3 - 1), x];
Map[Framed, int, Infinity]

Bianca, This package looks great! Would you be willing to host it on github, since the Wolfram Library Archive link is not active?

Thanks, Jason

Just saw that you replied while I was drafting an edit to the post. I came up with a workaround, hope it's robust. Now my next goal is to find someway to download 3D structures for the 33,000 ChemicalData entities we don't have them for. Looking at ServiceConnect for this.....

Impressive!

Or, if you want to live dangerously:

conf=chem/.Thread[(types=DeleteDuplicates[chem])->Range[Length[types]]]

That happens, sometimes a much easier solution is possible, but you just don't see it somehow. Possibly one of the shortest (but not best) solution is:

conf = chem /. (# -> ++i & /@ (i = 0; DeleteDuplicates[chem]))

You can also import structures from files related to the VASP program.

I'll use the POSCAR of BN from the official VASP site - the second one on the page (although either one will work). Just copy the data to a plain text file and name it "POSCAR". We'll import it with the VaspImport package.

The VASP formats are obviously useful for you if you work with the VASP program, but even if you don't, you may want to use these files: Many other crystal structure programs can import and export them, so you can now exchange data easily between Crystallica and other applications. Also, the POSCAR format in particular is easy to export (I'll show that later), and comfortably readable for a human.

The VaspImport package can read various types of VASP input and output files, namely CONTCAR / POSCAR, OUTCAR, XDATCAR, and vasprun.xml. CONTCAR and POSCAR are essentially the same format and this will be our test case for import and export. These files store one crystal structure. The other three file types can store multiple structures and lots of other information. What exactly these multiple structures are will obviously depend on the type of calculation you did. They might be steps of a structural relaxation or a molecular dynamics run. VaspImport automatically detects the file type and returns all structures in the file, but as for CIF, the last one is usually the one we want.

Let's import our POSCAR:

Get["VaspImport`"];
VaspImport["POSCAR"]

... which returns:

{<|"lattice"->{{0.`,1.785`,1.785`},{1.785`,0.`,1.785`},{1.785`,1.785`,0.`}},"atomcoords"->{{0.`,0.`,0.`},{0.25`,0.25`,0.25`}},
"atomtypes"->{1,2},"chemical"->{},"name"->"Cubic BN","file"->"E:\\POSCAR"|>}

VaspImport always returns a list of structures so that you can consistently work with Last[VaspImport[...]] without thinking about the file type.

We can also connect VaspImport to Crystallica the same way we did for CifImport:

Needs["Crystallica`"];
Needs["VaspImport`"];
vaspPlot[file_,options___]:=With[{data=Last[VaspImport[file]]},
CrystalPlot[data["lattice"],data["atomcoords"],data["atomtypes"],options,AtomCol->data["chemical"]]];
vaspPlot["POSCAR",AtomCol->{"B","N"}]

(I added atom colours because this specific POSCAR doesn't contain chemical atom types; but in general, many files will contain types.)

If you had a file with multiple structures you could do fun things like animations, and you might learn a lot about the process you were simulating.

Alright, so let's take a look at exporting to POSCAR since I promised that it's so easy and useful. As you may have noticed from the VASP documentation, POSCARs can look differently depending on your needs and preferences; they can store cartesian coordinates, or you can scale lattice vectors by giving a total colume for the cell. We'll just go with a very basic export here:

vaspExport[file_,lattvec_,coord_,conf_,chem_,name_]:=Module[{sorted,content},
(*atoms have to be sorted by type: *)
sorted=CrystalChange[lattvec,coord,conf,SortQ->"weak"];
(*export the file: *)
Export[file,Join[
{StringSplit[name],{1.0}},
sorted[[1]],
{chem,Tally[sorted[[3]]][[All,2]],{"Direct"}},
sorted[[2]]
],"Table","FieldSeparators"->" "]
];

And here's a usage example:

vaspExport["myPOSCAR",3*IdentityMatrix[3],{{0,0,0},{.5,.5,.5}},{1,2},{"Cu","O"},"definitely not copper oxide"]

That works, but there's one little problem that some of you may have (I know I do): Maybe you actually want to run the POSCAR through VASP on a Linux cluster, but you use a different OS to prepare the POSCAR. Let me just tell you that Fortran won't enjoy the wrong linebreaks! So here's a version of the export that enforces Unix-style linebreaks. It's an ugly kludge, but for some reason I haven't found a more natural solution. If anyone knows the hidden export option that would do the same, please do let me know.

vaspExport[file_,lattvec_,coord_,conf_,chem_,name_]:=Module[{sorted,content},
(*atoms have to be sorted by type: *)
sorted=CrystalChange[lattvec,coord,conf,SortQ->"weak"];
(*the actual file contents: *)
content=Join[
{StringSplit[name],{1.0}},
sorted[[1]],
{chem,Tally[sorted[[3]]][[All,2]],{"Direct"}},
sorted[[2]]
];
(*convert to UNIX linebreaks (LF): *)
content=ToCharacterCode[ExportString[content,"Table","FieldSeparators"->" "]];
content=If[MemberQ[content,10],(*from LFCR or CRLF: *)DeleteCases[content,13],(*from CR: *)content/.{13->10}];
(*export: *)
Export[file,content,"Binary"]
];

And that's it for VASP import/export!