From e05c3ef1b3419c65004e5931a0b56e3b314b13c5 Mon Sep 17 00:00:00 2001 From: "Documenter.jl" Date: Mon, 1 Jul 2024 08:21:14 +0000 Subject: [PATCH] build based on ede4407 --- dev/.documenter-siteinfo.json | 2 +- dev/api/index.html | 4 ++-- dev/generated/fitting_snap/index.html | 2 +- dev/generated/snap/index.html | 2 +- dev/index.html | 2 +- 5 files changed, 6 insertions(+), 6 deletions(-) diff --git a/dev/.documenter-siteinfo.json b/dev/.documenter-siteinfo.json index aa3909d..1790e74 100644 --- a/dev/.documenter-siteinfo.json +++ b/dev/.documenter-siteinfo.json @@ -1 +1 @@ -{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-06-27T21:54:19","documenter_version":"1.5.0"}} \ No newline at end of file +{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-01T08:21:11","documenter_version":"1.5.0"}} \ No newline at end of file diff --git a/dev/api/index.html b/dev/api/index.html index 1f18d79..002cec7 100644 --- a/dev/api/index.html +++ b/dev/api/index.html @@ -1,5 +1,5 @@ -API · LAMMPS.jl

API

LAMMPS.LMP — Type
LMP(f::Function, args=String[], comm=nothing)

Create a new LAMMPS instance and call f on that instance while returning the result from f.

source
LAMMPS.LMP — Type
LMP(args::Vector{String}=String[], comm::Union{Nothing, MPI.Comm}=nothing)

Create a new LAMMPS instance while passing in a list of strings as if they were command-line arguments for the LAMMPS executable.

For a full ist of Command-line options see: https://docs.lammps.org/Run_options.html

source
LAMMPS.command — Method
command(lmp::LMP, cmd::Union{String, Array{String}})

Process LAMMPS input commands from a String or from an Array of Strings.

For a full list of commands see: https://docs.lammps.org/commands_list.html

This function processes a multi-line string similar to a block of commands from a file. The string may have multiple lines (separated by newline characters) and also single commands may be distributed over multiple lines with continuation characters (’&’). Those lines are combined by removing the ‘&’ and the following newline character. After this processing the string is handed to LAMMPS for parsing and executing.

Arrays of Strings get concatenated into a single String inserting newline characters as needed.

LAMMPS.jl 0.4.1

Multiline string support """ and support for array of strings was added. Prior versions of LAMMPS.jl ignore newline characters.

Examples

LMP(["-screen", "none"]) do lmp
+API · LAMMPS.jl
API
LAMMPS.LMP — Type
LMP(f::Function, args=String[], comm=nothing)
Create a new LAMMPS instance and call f on that instance while returning the result from f.
source
LAMMPS.LMP — Type
LMP(args::Vector{String}=String[], comm::Union{Nothing, MPI.Comm}=nothing)
Create a new LAMMPS instance while passing in a list of strings as if they were command-line arguments for the LAMMPS executable.
For a full ist of Command-line options see: https://docs.lammps.org/Run_options.html
source
LAMMPS.command — Method
command(lmp::LMP, cmd::Union{String, Array{String}})
Process LAMMPS input commands from a String or from an Array of Strings.
For a full list of commands see: https://docs.lammps.org/commands_list.html
This function processes a multi-line string similar to a block of commands from a file. The string may have multiple lines (separated by newline characters) and also single commands may be distributed over multiple lines with continuation characters (’&’). Those lines are combined by removing the ‘&’ and the following newline character. After this processing the string is handed to LAMMPS for parsing and executing.
Arrays of Strings get concatenated into a single String inserting newline characters as needed.
LAMMPS.jl 0.4.1
Multiline string support """ and support for array of strings was added. Prior versions of LAMMPS.jl ignore newline characters.
Examples
LMP(["-screen", "none"]) do lmp
     command(lmp, """
         atom_modify map yes
         region cell block 0 2 0 2 0 2
@@ -12,4 +12,4 @@
         group even id 2 4 6 8
         group odd id 1 3 5 7
     """)
-end
source
LAMMPS.extract_variable — Function
extract_variable(lmp::LMP, name, group)
Extracts the data from a LAMMPS variable. When the variable is either an equal-style compatible variable, a vector-style variable, or an atom-style variable, the variable is evaluated and the corresponding value(s) returned. Variables of style internal are compatible with equal-style variables, if they return a numeric value. For other variable styles, their string value is returned.
source
LAMMPS.gather — Function
gather(lmp::LMP, name::String, T::Union{Type{Int32}, Type{Float64}}, ids::Union{Nothing, Array{Int32}}=nothing)
Gather the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities from all processes. By default (when ids=nothing), this method collects data from all atoms in consecutive order according to their IDs. The optional parameter ids determines for which subset of atoms the requested data will be gathered. The returned data will then be ordered according to ids
Compute entities have the prefix c_, fix entities use the prefix f_, and per-atom entites have no prefix.
The returned Array is decoupled from the internal state of the LAMMPS instance.
Type Verification
Due to how the underlying C-API works, it's not possible to verify the element data-type of fix or compute style data. Supplying the wrong data-type will not throw an error but will result in nonsensical output
ids
The optional parameter ids only works, if there is a map defined. For example by doing: command(lmp, "atom_modify map yes") However, LAMMPS only issues a warning if that's the case, which unfortuately cannot be detected through the underlying API. Starting form LAMMPS version 17 Apr 2024 this should no longer be an issue, as LAMMPS then throws an error instead of a warning.
source
LAMMPS.get_category_ids — Function
get_category_ids(lmp::LMP, category::String, buffer_size::Integer=50)
Look up the names of entities within a certain category.
Valid categories are: compute, dump, fix, group, molecule, region, and variable. names longer than buffer_size will be truncated to fit inside the buffer.
source
LAMMPS.get_natoms — Method
get_natoms(lmp::LMP)::Int64
Get the total number of atoms in the LAMMPS instance.
Will be precise up to 53-bit signed integer due to the underlying lammps_get_natoms returning a Float64.
source
LAMMPS.locate — Method
locate()
Locate the LAMMPS library currently being used, by LAMMPS.jl
source
LAMMPS.scatter! — Method
scatter!(lmp::LMP, name::String, data::VecOrMat{T}, ids::Union{Nothing, Array{Int32}}=nothing) where T<:Union{Int32, Float64}
Scatter the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entity in data to all processes. By default (when ids=nothing), this method scatters data to all atoms in consecutive order according to their IDs. The optional parameter ids determines to which subset of atoms the data will be scattered.
Compute entities have the prefix c_, fix entities use the prefix f_, and per-atom entites have no prefix.
Type Verification
Due to how the underlying C-API works, it's not possible to verify the element data-type of fix or compute style data. Supplying the wrong data-type will not throw an error but will result in nonsensical date being supplied to the LAMMPS instance.
ids
The optional parameter ids only works, if there is a map defined. For example by doing: command(lmp, "atom_modify map yes") However, LAMMPS only issues a warning if that's the case, which unfortuately cannot be detected through the underlying API. Starting form LAMMPS version 17 Apr 2024 this should no longer be an issue, as LAMMPS then throws an error instead of a warning.
source
LAMMPS.set_library! — Method
set_library!(path)
Change the library path used by LAMMPS.jl for liblammps.so to path.
Note
You will need to restart Julia to use the new library.
Warning
Due to a bug in Julia (until 1.6.5 and 1.7.1), setting preferences in transitive dependencies is broken (https://github.com/JuliaPackaging/Preferences.jl/issues/24). To fix this either update your version of Julia, or add LAMMPS_jll as a direct dependency to your project.
source

+end
source
LAMMPS.extract_variable — Function
extract_variable(lmp::LMP, name, group)

Extracts the data from a LAMMPS variable. When the variable is either an equal-style compatible variable, a vector-style variable, or an atom-style variable, the variable is evaluated and the corresponding value(s) returned. Variables of style internal are compatible with equal-style variables, if they return a numeric value. For other variable styles, their string value is returned.

source
LAMMPS.gather — Function
gather(lmp::LMP, name::String, T::Union{Type{Int32}, Type{Float64}}, ids::Union{Nothing, Array{Int32}}=nothing)

Gather the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entities from all processes. By default (when ids=nothing), this method collects data from all atoms in consecutive order according to their IDs. The optional parameter ids determines for which subset of atoms the requested data will be gathered. The returned data will then be ordered according to ids

Compute entities have the prefix c_, fix entities use the prefix f_, and per-atom entites have no prefix.

The returned Array is decoupled from the internal state of the LAMMPS instance.

Type Verification

Due to how the underlying C-API works, it's not possible to verify the element data-type of fix or compute style data. Supplying the wrong data-type will not throw an error but will result in nonsensical output

ids

The optional parameter ids only works, if there is a map defined. For example by doing: command(lmp, "atom_modify map yes") However, LAMMPS only issues a warning if that's the case, which unfortuately cannot be detected through the underlying API. Starting form LAMMPS version 17 Apr 2024 this should no longer be an issue, as LAMMPS then throws an error instead of a warning.

source
LAMMPS.get_category_ids — Function
get_category_ids(lmp::LMP, category::String, buffer_size::Integer=50)

Look up the names of entities within a certain category.

Valid categories are: compute, dump, fix, group, molecule, region, and variable. names longer than buffer_size will be truncated to fit inside the buffer.

source
LAMMPS.get_natoms — Method
get_natoms(lmp::LMP)::Int64

Get the total number of atoms in the LAMMPS instance.

Will be precise up to 53-bit signed integer due to the underlying lammps_get_natoms returning a Float64.

source
LAMMPS.locate — Method
locate()

Locate the LAMMPS library currently being used, by LAMMPS.jl

source
LAMMPS.scatter! — Method
scatter!(lmp::LMP, name::String, data::VecOrMat{T}, ids::Union{Nothing, Array{Int32}}=nothing) where T<:Union{Int32, Float64}

Scatter the named per-atom, per-atom fix, per-atom compute, or fix property/atom-based entity in data to all processes. By default (when ids=nothing), this method scatters data to all atoms in consecutive order according to their IDs. The optional parameter ids determines to which subset of atoms the data will be scattered.

Compute entities have the prefix c_, fix entities use the prefix f_, and per-atom entites have no prefix.

Type Verification

Due to how the underlying C-API works, it's not possible to verify the element data-type of fix or compute style data. Supplying the wrong data-type will not throw an error but will result in nonsensical date being supplied to the LAMMPS instance.

ids

The optional parameter ids only works, if there is a map defined. For example by doing: command(lmp, "atom_modify map yes") However, LAMMPS only issues a warning if that's the case, which unfortuately cannot be detected through the underlying API. Starting form LAMMPS version 17 Apr 2024 this should no longer be an issue, as LAMMPS then throws an error instead of a warning.

source
LAMMPS.set_library! — Method
set_library!(path)

Change the library path used by LAMMPS.jl for liblammps.so to path.

Note

You will need to restart Julia to use the new library.

Warning

Due to a bug in Julia (until 1.6.5 and 1.7.1), setting preferences in transitive dependencies is broken (https://github.com/JuliaPackaging/Preferences.jl/issues/24). To fix this either update your version of Julia, or add LAMMPS_jll as a direct dependency to your project.

source
diff --git a/dev/generated/fitting_snap/index.html b/dev/generated/fitting_snap/index.html index 6999c27..b024c30 100644 --- a/dev/generated/fitting_snap/index.html +++ b/dev/generated/fitting_snap/index.html @@ -202,4 +202,4 @@ 1732.92, 1688.68, 2.55 1687.87, 1712.33, 1.45 1726.56, 1611.73, 6.65 -1685.35, 1731.82, 2.76

This page was generated using Literate.jl.

+1685.35, 1731.82, 2.76

This page was generated using Literate.jl.

diff --git a/dev/generated/snap/index.html b/dev/generated/snap/index.html index 8a9b872..c7f7b5c 100644 --- a/dev/generated/snap/index.html +++ b/dev/generated/snap/index.html @@ -74,4 +74,4 @@ const M = 48 # number of input files const N1 = 96 # number of atoms of the first type const N2 = 96 # number of atoms of the second type -A, ncoeff = calculate_snap_bispectrum(DATA, rcut, twojmax, M, N1, N2)
([96.0 714.8921306293827 … 1336.492540361043 432.0280579642445; 96.0 741.6379436413091 … 1254.106124342181 545.8425828497783; … ; 96.0 737.1339390521061 … 1253.9195498524505 539.1307198276115; 96.0 738.856450472822 … 1254.9583526931956 551.4702122992459], 31)

This page was generated using Literate.jl.

+A, ncoeff = calculate_snap_bispectrum(DATA, rcut, twojmax, M, N1, N2)
([96.0 714.8921306293827 … 1336.492540361043 432.0280579642445; 96.0 741.6379436413091 … 1254.106124342181 545.8425828497783; … ; 96.0 737.1339390521061 … 1253.9195498524505 539.1307198276115; 96.0 738.856450472822 … 1254.9583526931956 551.4702122992459], 31)

This page was generated using Literate.jl.

diff --git a/dev/index.html b/dev/index.html index a58a0de..87c1d79 100644 --- a/dev/index.html +++ b/dev/index.html @@ -1,2 +1,2 @@ -Home · LAMMPS.jl
+Home · LAMMPS.jl