diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index de04aeb..8abd263 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.10.0","generation_timestamp":"2024-01-17T00:21:14","documenter_version":"1.2.1"}} \ No newline at end of file +{"documenter":{"julia_version":"1.10.1","generation_timestamp":"2024-02-21T14:41:15","documenter_version":"1.2.1"}} \ No newline at end of file diff --git a/dev/index.html b/dev/index.html index 9039f61..d0b0495 100644 --- a/dev/index.html +++ b/dev/index.html @@ -1,9 +1,9 @@ Home · Packmol.jl
GitHub

Packmol.jl

Packmol.jl is in very early stages of development.

See also

MolSimToolkit.jl/Packmol-Input-Creator

Reference

Packmol.run_packmol — Function
run_packmol()
-run_packmol(input_file::String)

Runs the packmol executable with the input file input_file. This will run the classical http://m3g.iqm.unicamp.br/packmol program, which is a pre-compiled binary. The input file is a text file with the same syntax as the packmol input files.

If no input file is provided, a file explorer will be opened to choose the input file.

source
Packmol.pack_monoatomic! — Function
pack_monoatomic!(positions::AbstractVector{<:SVector{N,T}}, unitcell, tol)

Pack a monoatomic system with iniital positions x and distance tolerance tol, into the unitcell defined by unitcell, considering periodic boundary conditions.

The unitcell can be a vector, in the case of orthorhombic cells, or a matrix, in the case of triclinic cells.

The coordinates and the unitcells can be two- or three-dimensional.

Example

julia> using Packmol, StaticArrays
+run_packmol(input_file::String)

Runs the packmol executable with the input file input_file. This will run the classical http://m3g.iqm.unicamp.br/packmol program, which is a pre-compiled binary. The input file is a text file with the same syntax as the packmol input files.

If no input file is provided, a file explorer will be opened to choose the input file.

source
Packmol.pack_monoatomic! — Function
pack_monoatomic!(positions::AbstractVector{<:SVector{N,T}}, unitcell, tol)

Pack a monoatomic system with iniital positions x and distance tolerance tol, into the unitcell defined by unitcell, considering periodic boundary conditions.

The unitcell can be a vector, in the case of orthorhombic cells, or a matrix, in the case of triclinic cells.

The coordinates and the unitcells can be two- or three-dimensional.

Example

julia> using Packmol, StaticArrays
 
 julia> coordinates = 100 * rand(SVector{3,Float64}, 10^5);
 
 julia> unitcell = [100.0, 100.0, 100.0]; tolerance = 2.0;
 
-julia> pack_monoatomic!(coordinates, unitcell, tolerance)

After packing, the coordinates array will have updated positions for the atoms without overlaps.

source
+julia> pack_monoatomic!(coordinates, unitcell, tolerance)

After packing, the coordinates array will have updated positions for the atoms without overlaps.

source