sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
5404304f74dd433351757f523100716bc2ef5d7e2619ff9ce70fb7936bd9c8bc | Julia | 7,597 | 212 | """
EigData
A struct for storing eigenvalue data associated with k-points.
# Fields
- `kp::Matrix{Float64}`: A matrix where each column represents a k-point.
- `Es::Matrix{Float64}`: A matrix where each column represents the eigenvalues corresponding to the respective k-point.
"""
struct EigData
kp :: Matrix... |
156aaf7efe88296ef814c73b6910638c00b9eb193b9b9c167490085abcf23c03 | Julia | 7,687 | 205 | ##
using Pkg
script_dir = @__DIR__ # Get the directory of the current script
project_root = joinpath(script_dir, "..", "..") # Get the path to the parent directory (the project root)
Pkg.activate(project_root) # Activate the project
Pkg.instantiate() # download all the required packages
using LinearRNNforFMRIdigitaltw... |
a8c9b5464f71532de799b4b48b6d00ed6926dd9e46f1e1478c32eb89e474def2 | Julia | 7,760 | 160 | """
run_calculation(::Val{:standard}, comm, conf::Config; rank=0, nranks=1)
Performs a standard calculation for an effective Hamiltonian model.
# Arguments
- `::Val{:standard}`: A type parameter indicating that this function performs a standard calculation.
- `comm`: The MPI communicator used for parallel process... |
fc703c19f21834c6e4ff2c3bbb0ea846678b4af371dfb79dea0b407f800436ca | Julia | 7,783 | 197 | """
struct Config
A configuration structure that holds options and blocks of tags in dictionaries.
# Fields
- `options::Dict{String, String}`: A dictionary holding configuration options.
- `blocks::Dict{String, Dict{String, String}}`: A dictionary holding configuration blocks.
"""
struct Config
options :: Dic... |
533314f6ca82d27d69d1a0eafe1c35730f8303261feaef85a8198c4c07c4f667 | Julia | 7,884 | 178 | mutable struct ZebrafishHMM_G3_NoSym_Full_Exp <: HiddenMarkovModels.AbstractHMM
pinit_turn::Float64
const transition_matrix::Matrix{Float64} # T[i,j] = probability of transitions i -> j
σforw::Float64
turn::Gamma{Float64}
forward_displacement::Gamma{Float64}
turn_displacement::Gamma{Float64}
... |
b0616f935e22b302ad033a50f3bbd8508f52673af55223c3eb26a8926b3da22b | Julia | 7,886 | 202 | const loss_to_n = Dict{String, Int64}("MAE" => 1, "MSE" => 2)
"""
struct Loss
A structure representing a (weighted) loss function for evaluating the difference between predicted and true values. The loss is calculated based on a given norm, with optional weights applied to the errors along the prediction and obse... |
877f43c8ea577dd31fb428e18913bc86a6af5a15b1f0b744a39b5afb02b32f60 | Julia | 7,940 | 196 | ##
using Pkg
script_dir = @__DIR__ # Get the directory of the current script
project_root = joinpath(script_dir, "..", "..", "..") # Get the path to the parent directory (the project root)
Pkg.activate(project_root) # Activate the project
#Pkg.instantiate() # download all the required packages
using LinearAlgebra, Sta... |
0c16c1b639ed9d26bb25709c4ba2be5b6207100603e2c0d18d77447efe4f67a5 | Julia | 8,169 | 180 | """
write_hr(Hr, Rs; filename="hamster_hr", tol=1e-8, verbose=1)
Writes Hamiltonian data `Hr` and corresponding lattice vectors `Rs` to a file.
# Arguments:
- `Hr`: A vector of matrices where each `Hr[R]` contains the Hamiltonian elements corresponding to the lattice vector `Rs[:, R]`.
- `Rs`: A 2D array where ea... |
1d8225591e7169568be56ff312dc76cf3b2bd360689c9e3cd4ab1b418e67e834 | Julia | 8,175 | 188 | mutable struct ZebrafishHMM_G3_Sym_Full_Exp <: HiddenMarkovModels.AbstractHMM
pinit_turn::Float64
const transition_matrix::Matrix{Float64} # T[i,j] = probability of transitions i -> j
σforw::Float64
turn::Gamma{Float64}
forward_displacement::Gamma{Float64}
turn_displacement::Gamma{Float64}
f... |
bb4bdc20f1312633939e574c5328bea39e7909922a4e8a679c4813c2bff86ac3 | Julia | 8,214 | 305 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
#! format: off
... |
59f2cc5e9b7d70e7ef62698f0258834357772a0c2563557753c77992943a8f3f | Julia | 8,287 | 220 | ##
using Pkg
script_dir = @__DIR__
project_root = joinpath(script_dir, "..", "..")
Pkg.activate(project_root)
Pkg.instantiate() # Ensure dependencies are available
using LinearRNNforFMRIdigitaltwins.FMRICommon
using LinearRNNforFMRIdigitaltwins.Utils
using LinearRNNforFMRIdigitaltwins.ESN
using LinearAlgebra, Interpo... |
dc100af7bd23b51fa147ef1d7ad300d7574c352733c234511d757949193d1d45 | Julia | 8,318 | 175 | """
hyper_optimize(param_values, params, comm, conf; rank=0, nranks=1, verbosity=get_verbosity(conf)) -> Float64
Evaluate a given set of hyperparameters by updating a configuration and running an optimization calculation.
# Arguments
- `param_values::Vector{Float64}`: Numerical values for each parameter to be opt... |
7d8d0ecfe14b009a1c20b4cc829c1b85b0480c960fe5916d5d6e4f491a718d68 | Julia | 8,320 | 356 | """
str_to_orb(str::String)
Convert an orbital name given as a string to its corresponding orbital object.
# Arguments
- `str::String`: The name of the orbital as a string. Valid strings include `"s"`, `"px"`, `"py"`, `"pz"`, `"dz2"`, `"dxy"`, `"dxz"`, `"dyz"`, `"dx2_y2"`, `"sp3"`, `"sp3dr2"`, `"pxdx2"`, `"pydy2"... |
119185941d36972838865a312d36fafb4bce77f9b823757343efc3c2963a93eb | Julia | 8,334 | 211 | """
mutable struct SOCModel{V, M}
A mutable struct representing a model for Spin-Orbit Coupling (SOC) effects.
# Type Parameters
- `V`: Type representing a structure-specific ion labeling or identifier.
- `M`: Type of the matrices describing SOC interactions, e.g., `Matrix{ComplexF64}`.
# Fields
- `params::Vecto... |
0d36594892bec642a609d7aec234aab37b498bee0298954974170f5150284fe3 | Julia | 8,367 | 358 | """
str_to_orb(str::String)
Convert an orbital name given as a string to its corresponding orbital object.
# Arguments
- `str::String`: The name of the orbital as a string. Valid strings include `"s"`, `"px"`, `"py"`, `"pz"`, `"dz2"`, `"dxy"`, `"dxz"`, `"dyz"`, `"dx2_y2"`, `"sp3"`, `"sp3dr2"`, `"pxdx2"`, `"pydy2"... |
4e7fd4e87be19ad4586ea313bb15b30ac14c2452a2a818d87ac6921306794e56 | Julia | 8,409 | 186 | const ndict = Dict(1=>R1, 2=>R2, 3=>R3, 4=>R4, 5=>R5, 6=>R6)
const mdict = Dict(0=>"σ", 1=>"π", 2=>"δ")
const mdict_inv = Dict('σ'=>0, 'π'=>1, 'δ'=>2)
const ldict = Dict(0=>"s", 1=>"p", 2=>"d")
const ldict_inv = Dict('s'=>0, 'p'=>1, 'd'=>2)
"""
IonLabel(types::SVector{2, UInt8})
A structure representing a label f... |
bfc4a280d7f6eaeb63ede6923d170424e8713bd090d4f7e3a3cfd7c9566b48b1 | Julia | 8,740 | 217 | struct EffectiveHamiltonian{T, S1, S2, IT}
Nstrc :: Int64
models :: T
systems :: Vector{String}
sp_mode :: S1
sp_diag :: S2
sp_tol :: Float64
sp_iterators :: IT
soc :: Bool
Rs :: Vector{Matrix{Float64}}
end
function EffectiveHamiltonian(strcs, bases, comm, conf=get_empty_conf();
... |
814ee74c6ce69bc993e27eb9d82d5910259904a5999b20707da788d66dd4de9d | Julia | 8,878 | 236 | ### A Pluto.jl notebook ###
# v0.20.13
using Markdown
using InteractiveUtils
# ╔═╡ 66a6d5b1-729f-49ea-8404-9c0ce48d9973
import Pkg, Revise; Pkg.activate(Base.current_project())
# ╔═╡ 9674b801-5acf-4f76-b494-4aa8cb8ab012
using Statistics: mean, std
# ╔═╡ dca0d89a-744f-11ef-1dde-71bceb3d228e
md"# Imports"
# ╔═╡ 47c0... |
ad90ed5cfe06166cfa6e4ee11072c32f21b9c957c4e1d19df3a83d226242bd6a | Julia | 8,968 | 283 | """
ewald_sum(pos, q, lattice; kwargs...)
Compute electrostatic potentials and energies using Ewald-type methods
(Ewald, Wolf, Zahn, etc.).
This function combines real-space and reciprocal-space contributions
(depending on `method`) and returns per-site potentials together with
energy components.
# Arguments
- `... |
1b4a29ed87f69bd078da354502561edefba6375c820ea4fc1d3082e0cd879569 | Julia | 9,024 | 233 | """
mutable struct SOCModel{V, M}
A mutable struct representing a model for Spin-Orbit Coupling (SOC) effects.
# Type Parameters
- `V`: Type representing a structure-specific ion labeling or identifier.
- `M`: Type of the matrices describing SOC interactions, e.g., `Matrix{ComplexF64}`.
# Fields
- `params::Vecto... |
afa0fdaddf1d7b1e3ec4b5b092e5c5eb337c5dbd4c2c118a45fea871a76a6470 | Julia | 9,211 | 226 | struct EffectiveHamiltonian{T, S1, S2, IT}
Nstrc :: Int64
models :: T
systems :: Vector{String}
sp_mode :: S1
sp_diag :: S2
sp_tol :: Float64
sp_iterators :: IT
soc :: Bool
Rs :: Vector{Matrix{Float64}}
end
function EffectiveHamiltonian(strcs, bases, comm, conf=get_empty_conf();
... |
b0f043977fa90fa2b48ade6f5d1ba23e0efdaac8c446faecd0cb72643fdbebd6 | Julia | 9,379 | 191 | using Lux, Zygote, Distributions, Optimisers, Random, MLUtils
using ComponentArrays
using Statistics
using DataFrames, CSV
include("functions.jl")
rng = Random.default_rng()
Random.seed!(1)
Nid = 3000
Nid_val = 1000
Nruns = 100
Sim_covs = 2
time_const = []
time_lin = []
time_NN = []
loss_const = []
loss_lin = []
l... |
6be39d9fd7b217d8eb52dc71002939b0ce2a6d9afd8adf848dacd761b1e45944 | Julia | 9,451 | 269 | """
struct Config
A configuration structure that holds options and blocks of tags in dictionaries.
# Fields
- `options::Dict{String, String}`: A dictionary holding configuration options.
- `blocks::Dict{String, Dict{String, String}}`: A dictionary holding configuration blocks.
"""
struct Config
options :: Dic... |
f4671cc18ee28457f46a547c3c9594d8570c5cf6f8316a64086bc1fe013815c9 | Julia | 9,518 | 198 | """
PointGrid
A data structure for organizing and managing points in a 3D simulation cell by dividing the space into equally-sized cubic boxes.
The `PointGrid` structure stores grid points for atom positions, allowing for efficient spatial queries and neighbor searches.
# Fields:
- `grid_size::Float64`: The siz... |
75236432c3d335e73e6eab2897f0bea26968591f02a3335a8a4d8c8bef130f5f | Julia | 9,528 | 198 | """
PointGrid
A data structure for organizing and managing points in a 3D simulation cell by dividing the space into equally-sized cubic boxes.
The `PointGrid` structure stores grid points for atom positions, allowing for efficient spatial queries and neighbor searches.
# Fields:
- `grid_size::Float64`: The siz... |
ee753fa0173e21712aeb6387342d9162236722c5bd002a4ecddbdc08923832db | Julia | 9,531 | 355 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
#! format: off
... |
0a2c10ee0a58e40a7ec305e28d060e249723163ee0b7882b3c6ce0f04ed619eb | Julia | 9,630 | 203 | using Lux, Zygote, Distributions, Optimisers, Random, MLUtils
using ComponentArrays
using Statistics
using DataFrames, CSV
include("functions_real_data.jl")
# df = CSV.read("e2.csv", DataFrame)
# rename!(df, :status => :state)
# df_validation, df_train = train_test_data_split(df, 0.2)
df_train = CSV.read("training_... |
f38bbba63f47e083de3e6eb1d21f5daa2b35a88251d8dd53a0f6d759e02558ea | Julia | 9,632 | 285 | """
EwaldOnsites{P,T,N}
Container for electrostatic onsite corrections computed from Ewald-type
methods (Ewald, Wolf, Zahn) over a set of structures.
This struct stores per-atom electrostatic potentials (mean-centered
per species) together with the metadata required to map them onto TB
onsite parameters.
# Field... |
c64badc6dfa99c0c8a778934ca4cded07b01e8093ad0b54777c259c9687950fc | Julia | 10,341 | 262 | """
TBModel
A mutable struct representing a tight-binding model.
# Fields
- `h::Matrix{SparseMatrixCSC{Float64, Int64}}`: A matrix where each element is a sparse matrix representing the geometry tensor.
- `parameter_labels::Vector`: A vector containing the label for each parameter.
- `V::Vector{Float64}`: A vecto... |
64ae2cb819e9ea387c81c7626fd18b62077ad9968d3edc04a8c46f54e7397165 | Julia | 10,454 | 271 | ### A Pluto.jl notebook ###
# v0.19.46
using Markdown
using InteractiveUtils
# ╔═╡ b5cd5128-01f9-4d63-a757-1ee9882a0f54
import Pkg, Revise; Pkg.activate(Base.current_project())
# ╔═╡ 16867f62-2fd0-4e52-80c9-5962e615ee98
using Makie: @L_str
# ╔═╡ d53d040f-5998-40cc-9b7f-69da402f1cce
using DataFrames: DataFrame
# ╔═... |
f2ca6ec95790a66468f6c90cda19444b9e9b47be8a0b048f2f5ab25110638d3a | Julia | 10,493 | 319 | module FMRICommon
using LinearAlgebra, MultivariateStats, StatsBase
using LinearRNNforFMRIdigitaltwins.Utils
using Interpolations, DelimitedFiles
# Export constants and functions
export load_patient_data, compute_area_indices, process_patient_data, process_patient_data_complete,
process_patient_data_complete!,
... |
0d42061b7fdcec630c29a3931e9fc58c892c73b438f0a8d33fc400b634580a1c | Julia | 10,589 | 251 | path = joinpath(@__DIR__, "test_files")
@testset "Test Config indices" begin
# Test 1: no validation, no Nconf_min
conf = get_empty_config()
set_value!(conf, "Nconf", "Supercell", 100)
set_value!(conf, "Nconf_min", "Supercell", 1)
set_value!(conf, "Nconf_max", "Supercell", 1000)
config_indices,... |
53f1da871cf3603a77023cf0815e79c3aa8e9a852f97541c3859be825113c81f | Julia | 10,651 | 297 | function train_test_data_split(df, frac)
state = df.state
unique_state = unique(state)
Number_of_groups = length(unique_state)
Nobs_grouped_state = similar(unique_state)
for i in eachindex(unique_state)
Nobs_grouped_state[i] = (count(state .== unique_state[i]) )
end
Nobs_group_test... |
3e8dba731707e956a4e083e4f72fb21d83a7b4ed94afe3bc3e8354b76bac84d9 | Julia | 10,678 | 323 | # Needed packages
using Microstructure, Fibers, Flux
using Plots, Statistics
using LaTeXStrings
using Plots.PlotMeasures
export axon_da_sensitivity,
sensitivity_plot, eval_plt, logs_plt, nn_eval, nn_estimate, sigma_level_smt
"""
Calculate the sensitivity range for axon diameter index with PA signal from a single ... |
bc4c8a0889692bd73d310f7ca3a87a7b8d5df049fc160428b55fe23fcfc81a96 | Julia | 10,699 | 262 | ##
using Pkg
script_dir = @__DIR__ # Get the directory of the current script
project_root = joinpath(script_dir, "..", "..", "..") # Get the path to the parent directory (the project root)
Pkg.activate(project_root) # Activate the project
#Pkg.instantiate() # download all the required packages
using LinearAlgebra, Sta... |
479bd31f622146cbb32cf4b6e76df425d97dbde187e6b137a03ee8a2d933efdd | Julia | 10,775 | 431 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
#! format: off
... |
a5c58b2fd45e1a9e34f2f7370236a4ad1bc9143ba13520dc52ae54a35d8d0f2a | Julia | 10,874 | 390 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
#! format: off
... |
cfa8aa4652433a6211810dbb6cac7973bba2a0f17dcd4d7e5a51bcf413221b56 | Julia | 10,992 | 235 | """
optimize_model!(ham_train, ham_val, optim, dl, prof, conf=get_empty_config(); verbosity=get_verbosity(conf), Nbatch=get_nbatch(conf), validate=get_validate(conf), rank=0, nranks=1)
Optimizes the model by performing training and optional validation steps.
# Arguments
- `ham_train`: The Hamiltonian model used f... |
ec38e3728ab8cdf7521416535d5b47ac0455f8a683865b60a76505c7f312bb9b | Julia | 10,996 | 235 | """
optimize_model!(ham_train, ham_val, optim, dl, prof, conf=get_empty_config(); verbosity=get_verbosity(conf), Nbatch=get_nbatch(conf), validate=get_validate(conf), rank=0, nranks=1)
Optimizes the model by performing training and optional validation steps.
# Arguments
- `ham_train`: The Hamiltonian model used f... |
0e00e4540fb693c33e7d04a7299ed2e855152df87badf4a6d8d965233289258f | Julia | 11,029 | 320 | using ProgressMeter
export pre_allocate, empty_chain!, create_chain, threading
"""
This method runs multi-threads MCMC estimation on dMRI data using a specified biophysical model, calls the voxel threading
method and save estimated parameters as nifti files. `savedir` includes both output path and file name prefix.
... |
dc3dff869ff509fb6f3c5938576373b6f0e454d86cbb5e8f4130ce9952e8cb33 | Julia | 11,176 | 330 | #=
3D lattice gas model, in the presence of an Ising surface (membrane), coupled via tethers.
Hamiltonian:
H = -Jb*sum(ni*nj) -Jm*sum(si*sj)-Jt*sum(ni)-mu*sum(ni),
where the first and fourth terms are for bulk.
The second term sums over all the Ising spins in the membrane.
The third term is summed over all the indi... |
a82a4e6b5b36955729dc64b0876222ef5bd3a9b029447184ab72443e4c550feb | Julia | 11,202 | 457 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
#! format: off
... |
9e0a1125fc4619f9b357e58b88fc5aeff97f72909e837d35a70dc69db5d7776a | Julia | 11,277 | 291 | """
mutable struct HamiltonianKernel{T1, T2}
A kernel structure used for computing weighted similarity functions.
# Fields
- `ws :: Vector{Float64}`: Weights for each sample point.
- `xs :: Vector{T1}`: Sample points.
- `sim_params :: T2`: Parameters for the similarity function.
"""
mutable struct HamiltonianKern... |
9633e275f0aa5e1adb914028a46e1c0d9777f4615ad3ccc27e79da33392b03c7 | Julia | 11,458 | 216 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# ╔═╡ c61f5cd6-023f-11ef-343e-6b895c2b8f54
import Pkg, Revise; Pkg.activate(Base.current_project())
# ╔═╡ 4ec29bd5-35ca-4cf2-8305-148816cb2f5f
using HiddenMarkovModels: logdensityof, baum_welch, transition_matrix, initial_distribution, viter... |
9b9465693981fa8f13e988ab65827e65335fb6c6793f2d0fd497c9bf4f4ca51e | Julia | 11,472 | 275 | #––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––#
# MACAQUE VS MARMOSET - DISTRIBUTED WORKING MEMORY #
#––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––#
#––––––––––––––––––––––––––––––––––––––––––––––––––––#
# ... |
9775f8c5c5ff5ecd2fab80dce4a043981dde2ca4a2c4f54392c333bb414449f7 | Julia | 11,479 | 251 | """
run_calculation(::Val{:standard}, comm, conf::Config; rank=0, nranks=1)
Performs a standard calculation for an effective Hamiltonian model, computing either the eigenvalues or the Hamiltonian itself for a given set of structures.
# Workflow
1. **Configuration Sampling**
- Retrieve configuration indices ... |
59737f54a1c9a7a49902b6789c51192d0f138e52a3a459a493c8f8db5a8df8a0 | Julia | 11,526 | 281 | ##
using Pkg
script_dir = @__DIR__
project_root = joinpath(script_dir, "..", "..")
Pkg.activate(project_root)
Pkg.instantiate() # Ensure dependencies are available
using LinearRNNforFMRIdigitaltwins.FMRICommon
using LinearRNNforFMRIdigitaltwins.Utils
using LinearRNNforFMRIdigitaltwins.ESN
using LinearAlgebra, Interpo... |
6881e48dc73b55a350be96f17f37d576e20e57308034174144fc621b6964b8ec | Julia | 11,558 | 298 | """
TBModel
A mutable struct representing a tight-binding model.
# Fields
- `h::Matrix{SparseMatrixCSC{Float64, Int64}}`: A matrix where each element is a sparse matrix representing the geometry tensor.
- `parameter_labels::Vector`: A vector containing the label for each parameter.
- `V::Vector{Float64}`: A vecto... |
38c0977261206964dc81115be95f7ddfb730da578fe4ea1dd38bf8edc7720c6d | Julia | 11,601 | 280 | """
fcut(r, rcut)
Cut-off function whose value smoothly transitions to zero as `r` approaches `rcut`.
Ensures continuity by using a cosine-based smoothing function.
# Arguments
- `r`: The input distance.
- `rcut`: The cutoff radius beyond which the function returns zero.
- `rcut_tol`: A tolerance applied to the c... |
2f0d9c971d6ac474c443bfd599ed6e58fe297106bb8c38312cde6c88d18647f6 | Julia | 11,860 | 345 | ###########################################################
####### Functions for data generation and manipulation ####
###########################################################
function transform_transvec(transitionvector, statevector, endstate)
transformed_transitionvector = deepcopy(transitionvector)
for i... |
d85b62cb59a7721652bf63efe26f2c12e89f55ada3156a9e19ac9d25eff65c31 | Julia | 11,941 | 275 | mutable struct ZebrafishHMM_G3_Sym_Full <: HiddenMarkovModels.AbstractHMM
pinit_turn::Float64
const transition_matrix::Matrix{Float64} # T[i,j] = probability of transitions i -> j
σforw::Float64
turn::Gamma{Float64}
forward_displacement::Gamma{Float64}
turn_displacement::Gamma{Float64}
forwa... |
c40fe2211af5a18e1e2e3cb0391ff1714c211a0c5e9e9ee58f12fba10ffa4520 | Julia | 12,038 | 284 | """
get_tb_descriptor(model, strc, conf)
Calculate the TB descriptor for a given a TB `model`, a structure `strc` and a TBConfig file `conf`.
"""
function get_tb_descriptor(h, V, strc::Structure, basis, conf::Config; rcut=get_ml_rcut(conf), rcut_tol=get_rcut_tol(conf), apply_distortion=get_apply_distortion(conf), ... |
218ae66cb9c43a6ddb05ea03230e671c56b2d78d7198e7376955736fb1d6e9d2 | Julia | 12,376 | 334 | module ESN
using LinearAlgebra, Random, Statistics, SparseArrays, SpecialFunctions
mutable struct NetType
netSize::Int # number of nodes
ν::Vector{Float64} # net state, firing rate
τ::Vector{Float64} # time constants
J::Union{Matrix{Float64},SparseMatrixCSC{Float64, Int64}} # synaptic matrix
Jext::... |
ae9f1c9e7ab070ab74da86d7bb5f09bafc5ffa3abf051fe45acd8d55d2843ccf | Julia | 13,103 | 319 | """
get_soc_matrices(strc::Structure) -> Vector{BlockDiagonal}
Precompute the spin-orbit coupling (SOC) matrices for a given structure.
"""
function get_soc_matrices(strc::Structure, basis::Basis, conf=get_empty_config(); verbosity=get_verbosity(conf))
atom_axes_list = get_axes_from_orbitals(basis.orbitals)
... |
b24a4208dd5b6db0b2880789e8c3750339b160c335bc369e5a24d3a0d14514c2 | Julia | 13,145 | 320 | """
get_soc_matrices(strc::Structure) -> Vector{BlockDiagonal}
Precompute the spin-orbit coupling (SOC) matrices for a given structure.
"""
function get_soc_matrices(strc::Structure, basis::Basis, conf=get_empty_config(); verbosity=get_verbosity(conf))
atom_axes_list = get_axes_from_orbitals(basis.orbitals)
... |
483da8f7e46e5b9edca865b89c3e336b371d87395dda0c863e4819c25c1c7389 | Julia | 13,263 | 283 | """
struct Basis{Orb, Ov, P, R}
A data structure that represents the basis of a system, containing information about orbitals, overlap integrals, parameters, and precomputed radial functions (RLLM).
# Fields
- `orbitals::Orb`: A collection of orbitals for each ion in the system. This typically contains the orbita... |
71e4e5d5e59441c4be08fb92f9b67fb13ee167534d603b79d4bc907a48d07201 | Julia | 13,346 | 315 | """
get_tb_descriptor(model, strc, conf)
Calculate the TB descriptor for a given a TB `model`, a structure `strc` and a TBConfig file `conf`.
"""
function get_tb_descriptor(h, V, strc::Structure, basis, conf::Config;
rcut=get_ml_rcut(conf),
rcut_tol=get_rcu... |
d51f236070e8fd2367910711c5508af7e31480e926c86e95b4ec6a1134902110 | Julia | 13,390 | 418 | ##
using Pkg
script_dir = @__DIR__ # Get the directory of the current script
project_root = joinpath(script_dir, "..", "..") # Get the path to the parent directory (the project root)
Pkg.activate(project_root) # Activate the project
#Pkg.instantiate() # download all the required packages
using LinearRNNforFMRIdigitalt... |
a3b97e9ca7f82e57ff45ffcf5de7fb09e78d3166a9319be09dd2eb3d4e0d06e0 | Julia | 14,074 | 300 | """
HamsterProfiler
A data structure for tracking and managing profiling information during an iterative process, including loss, timing, and verbosity settings.
# Fields
- `L_train::Matrix{Float64}`: A 2D array where each row corresponds to training loss values for a specific batch across iterations.
- `L_val::V... |
f22fd04aa90054769d5a0fafb05fbaeabe48b50d5b155ff545993b8995b7ff5a | Julia | 14,195 | 307 | #––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––#
# MACAQUE VS MARMOSET - DISTRIBUTED WORKING MEMORY #
#––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––––#
#––––––––––––––––––––––––––––––––––––––––––––––––––––#
# ... |
aef952c06a9e05aa3399001eeae297c4d9b0262de4d9c98e6afe613e7d943dd4 | Julia | 14,309 | 271 | """
exp_2πi(k⃗, R⃗)
Calculate the phase factor exp(2πik⃗⋅R⃗).
"""
@inline exp_2πi(R⃗, k⃗) = @. exp(2π*im * $*(R⃗', k⃗))
get_empty_complex_hamiltonians(Nε, NkR, mode=Dense()) = Matrix{ComplexF64}[zeros(ComplexF64, Nε, Nε) for _ in 1:NkR]
get_empty_complex_hamiltonians(Nε, NkR, ::Sparse) = SparseMatrixCSC{Compl... |
5e9a6eba44a7329efc2f89eb3a6dda31abb6e2a1dd36614c6b75e16198e9f3b5 | Julia | 14,417 | 369 | # Definitions of biophysical models.
#
# This script builds model structs with fields of tissue compartments and signal fractions,
# and forward functions inferencing signals from the model struct and imaging protocol.
export model_signals,
SANDI,
SANDIdot,
MTE_SANDI,
ExCaliber,
MTE_SMT,
print_... |
a79ecb706a745a2600f4695c2396779d78e8a185e0beb9e0ba203687d9124b17 | Julia | 14,502 | 355 | ### A Pluto.jl notebook ###
# v0.20.13
using Markdown
using InteractiveUtils
# ╔═╡ 34bee668-5efa-472b-9093-e082daf4a796
import Pkg, Revise; Pkg.activate(Base.current_project())
# ╔═╡ 353a003c-acc2-4632-b8c5-3765ace40490
using Statistics: mean, std
# ╔═╡ 6d701605-96b1-4dfe-a806-4841fd1c6b48
using Distributions: Gamm... |
9c0b041dd03c66153b92be014520887ef31925239d4d59df75a598101e72a5c8 | Julia | 14,544 | 363 | """
fcut(r, rcut)
Cut-off function whose value smoothly transitions to zero as `r` approaches `rcut`.
Ensures continuity by using a cosine-based smoothing function.
# Arguments
- `r`: The input distance.
- `rcut`: The cutoff radius beyond which the function returns zero.
- `rcut_tol`: A tolerance applied to the c... |
78628736d428e348dcd745d2286d834dbf9dc9c1a42c697148a9a9954f9a81f2 | Julia | 14,805 | 380 | """
mutable struct HamiltonianKernel{T1, T2}
A kernel structure used for computing weighted similarity functions.
# Fields
- `ws :: Vector{Float64}`: Weights for each sample point.
- `xs :: Vector{T1}`: Sample points.
- `sim_params :: T2`: Parameters for the similarity function.
"""
mutable struct HamiltonianKern... |
55a0a705e38679c64ab8fb37250b9631511d9b938beaeaa920b9d30657ffed5c | Julia | 14,868 | 348 | ### A Pluto.jl notebook ###
# v0.20.0
using Markdown
using InteractiveUtils
# ╔═╡ 7752ef77-6a36-4f65-b9c9-40bb3f4ace3f
import Pkg, Revise; Pkg.activate(Base.current_project())
# ╔═╡ 703dc739-beab-45ef-a68f-770f47144b60
using Statistics: mean, std, cor
# ╔═╡ 3fe7f379-9cc0-438f-8a35-b5d5431acb39
md"# Imports"
# ╔═╡ ... |
95524f8f2b56d38a358af1c2a470842837d22770c4d32c4d179edfe271b5ae12 | Julia | 14,901 | 584 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
#! format: off
... |
c2c4eb7ad1fa608dd9b8788e1c927dafe6944599ba2b0eef46e0fa5c454fa4e7 | Julia | 15,526 | 361 | """
get_systems(conf) -> Vector{String}
Return the list of system names available for a given configuration `conf`.
# Arguments
- `conf`: A configuration object.
# Returns
- `Vector{String}`: A list of system names (HDF5 group names or a single system).
"""
function get_systems(conf)
strc_file = get_xdatcar(... |
80fdc33bea39acb41b3843be936aa7d9412ac498fcb255cb469567e697359a83 | Julia | 15,754 | 389 | ### A Pluto.jl notebook ###
# v0.20.5
using Markdown
using InteractiveUtils
# ╔═╡ 7f95a967-426a-465f-bad4-671372ea1092
import Pkg, Revise; Pkg.activate(Base.current_project())
# ╔═╡ 7d355591-dddd-4463-97b1-d53e223bd6b3
using Statistics: mean
# ╔═╡ 8398c332-235b-4f6c-ab1e-8b5fd62d2d5a
using Distributions: Gamma
# ╔... |
27c52eae3cd488fba9be0aae7f84a801a9a0fbe79bbaa16d5b814f9ea8ea27d3 | Julia | 15,788 | 389 | """
get_systems(conf) -> Vector{String}
Return the list of system names available for a given configuration `conf`.
# Arguments
- `conf`: A configuration object.
# Returns
- `Vector{String}`: A list of system names (HDF5 group names or a single system).
"""
function get_systems(conf)
strc_file = get_xdatcar(... |
cb0f557a34061490a081ea163d9663c822c4f0bad84858aee775acd4f8a8c552 | Julia | 15,822 | 645 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# ╔═╡ b63457db-6045-4981-8f70-96a3906c1eb7
begin
using Pkg
Pkg.activate(Base.current_project())
Pkg.instantiate()
# loading usefules
using PlutoLinks
using PlutoUI
end
# ╔═╡ 82f4a87c-636f-4159-92fd-ad773bd089cb
begin
using BrainRBMju... |
46c96f06731a933c4be6f16542db68bfd43f3502d695534b2d8b3d215961ce97 | Julia | 16,101 | 326 | """
ParameterLabel(nnlabel::Int64, ion_label::IonLabel, overlap_label::SVector{3, Int64})
Represents a tight-binding (TB) parameter label by uniquely identifying it based on its nearest neighbor (NN) label, ion label,
and overlap label.
# Fields
- `nnlabel::Int64`: An integer representing the nearest neighbor (N... |
a7c0a4ec2b40acd9e16b900b4543a938871533ee7475f6baac4f8cc42e541da9 | Julia | 16,783 | 377 | import Base.copy
abstract type MatrixElement end
"""
TBOverlap{T<:MatrixElement, OC<:OrbitalConfiguration}
Represents a tight-binding (TB) overlap used in calculations, characterized by its type, orbital configuration, and ion label. This represents one interaction term.
# Fields
- `type::T`: Specifies the type... |
f25555c4c8eba5826cad1a1b539c541247e2c913417ff17725ac4f34331a632f | Julia | 17,463 | 389 | """
struct Basis{Orb, Ov, P, R}
A data structure that represents the basis of a system, containing information about orbitals, overlap integrals, parameters, and precomputed radial functions (RLLM).
# Fields
- `orbitals::Orb`: A collection of orbitals for each ion in the system. This typically contains the orbita... |
fd2275521672e9bdb14dbb8a5018083c69421aa0415e5ddcd973488addc67d38 | Julia | 17,736 | 615 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
#! format: off
... |
ec1865fffafae420f6a4d537459f50802ace0004749e21ba2cc21ad22475c024 | Julia | 18,231 | 483 | # This script builds compartment structs with fields of relevant tissue parameters and
# forward functions inferencing signals from the compartment model and imaging protocol.
using LinearAlgebra, SpecialFunctions
export Cylinder,
Stick,
Zeppelin,
Iso,
Sphere,
compartment_signals,
Compartmen... |
2acdf47458cc002a6cd22d978d8ff449f5419aefccfd7e2c7009862d66488547 | Julia | 18,946 | 484 | ### A Pluto.jl notebook ###
# v0.20.13
using Markdown
using InteractiveUtils
# ╔═╡ bfb8b4b5-eee8-47a5-8f55-e23ad3ddbaa9
import Pkg, Revise; Pkg.activate(Base.current_project())
# ╔═╡ 2bcdddad-4227-4c56-b452-cff43bec2d41
using Makie: @L_str
# ╔═╡ 76c368ee-0aa9-4d8e-b815-d006ec9ae3db
using DataFrames: DataFrame
# ╔═... |
6e3a6fdf9f0621b1cfa2412d718f564afc7faf6df5197703fd4b6d64b942dd3b | Julia | 18,971 | 632 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
#! format: off
... |
a638efc818eb1d6d01bf3ec39130e526e9c4a2b911895f7aac623825f6dcd915 | Julia | 19,106 | 477 | #----------------------
# Interactive Workflow for algorithm exploration and test
#----------------------
##
using Pkg
script_dir = @__DIR__ # Get the directory of the current script
project_root = joinpath(script_dir, "..", "..") # Get the path to the parent directory (the project root)
Pkg.activate(project_root) # Ac... |
56405d1ae593e2f6bbe11c7127a78a556092f46ec619da86d6208138de17d4eb | Julia | 19,777 | 486 | ### A Pluto.jl notebook ###
# v0.20.0
using Markdown
using InteractiveUtils
# ╔═╡ 673c2edc-3667-4834-b489-cdc1d8eec407
import Pkg, Revise; Pkg.activate(Base.current_project())
# ╔═╡ 9fcb9477-1365-42e5-b29a-a7e20feddd41
using DataFrames: DataFrame
# ╔═╡ ef3f2f53-d4de-4878-95c2-027d2d34ae9e
using Statistics: mean
# ... |
8ce8598621751d59db5557a9af5986e6aa4978241a3ff8d0aaf93a31c081f5f2 | Julia | 20,311 | 711 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# ╔═╡ 859e9214-3568-11f0-2108-85a2152204f2
begin
using Pkg
Pkg.activate(Base.current_project())
Pkg.instantiate()
# loading usefules
using PlutoLinks
using PlutoUI
end
# ╔═╡ 6c2c8e99-3c8b-4823-80ca-d3af7049a897
begin
using BrainRBMju... |
79a1865d2f52fa45ad44b4cb0251b32447ba2971644c90de1155239f94285bc8 | Julia | 20,358 | 506 | """
write_hr(Hr, Rs; filename="hamster_hr", tol=1e-8, verbose=1)
Writes Hamiltonian data `Hr` and corresponding lattice vectors `Rs` to a file.
# Arguments:
- `Hr`: A vector of matrices where each `Hr[R]` contains the Hamiltonian elements corresponding to the lattice vector `Rs[:, R]`.
- `Rs`: A 2D array where ea... |
38a0462e950e083a6025c374b88a0319a92bfa7223e33a13e3bb70ac07ce071a | Julia | 20,682 | 422 | ### A Pluto.jl notebook ###
# v0.20.5
using Markdown
using InteractiveUtils
# ╔═╡ 82fb3325-81b1-4516-a57a-721f991282f7
import Pkg, Revise; Pkg.activate(Base.current_project())
# ╔═╡ a3deaeb2-12df-4f1e-97a8-e14dc8aab28f
using Statistics: median, std, mean
# ╔═╡ b1ddac8e-2fab-4d13-852c-6b19adb1594e
using Makie: @L_st... |
7b8e737f6acca4645f1a201a81262ef4ad0e913b06c549072901fd8f34209abd | Julia | 22,783 | 846 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
#! format: off
... |
6f499a39ce8b2931f656380e1dd3b7d4bab9eccbc817098fd5c4e75106a0352b | Julia | 24,261 | 733 |
using ProgressMeter
using Flux, Distributions, Random, Statistics
export NetworkArg,
TrainingArg,
prepare_training,
create_mlp,
sigma_level,
generate_samples,
train_loop!,
training,
test,
save_mlp,
load_mlp,
nn_estimate,
save_nn_maps,
losses_rmse,
losses_corr,
... |
3fd0c6951bcc847b11fd3637f3d17392317c77b1b4a01e832851b7c1a92800a4 | Julia | 24,710 | 781 | # I/O functions for images and protocols
# Including functions to fit measurements to spherical harmonic bases
using Fibers, DelimitedFiles, Statistics, StaticArrays
export dMRI,
Protocol,
spherical_fit,
spherical_mean,
dmri_write,
dmri_read,
dmri_read_times,
dmri_read_times!,
dmri_rea... |
a1640d3dc26d14b3b7b6291ea69e77862314f08cc3e9a9008ac54d9fdc554bf7 | Julia | 24,835 | 896 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
#! format: off
... |
1abf7f84dc0938a01f4c8727d637d91b993f6fd8962e0c66a105b41fba766cb5 | Julia | 25,837 | 765 | ### A Pluto.jl notebook ###
# v0.20.4
using Markdown
using InteractiveUtils
# ╔═╡ c596973a-d074-4ad4-b6b5-4f7e3449c99b
begin
projectdir = dirname(Base.current_project())
import Pkg
Pkg.activate(projectdir)
Pkg.instantiate()
using Pollen
using DataFrames
using CSV
using WGLMakie
... |
2e72c9370f0f2c72da700b2e5ca9092af9c085344c0d4b8f00953de944cdc820 | Julia | 28,826 | 880 | # MCMC estimation
using Random, Distributions, StaticArrays
export Sampler,
Noisemodel,
mcmc!,
subsampler,
logp_gauss,
logp_rician,
update!,
increment!,
getsubfield,
draw_samples,
draw_samples!,
findsubfield
"""
Noisemodel(logpdf::Function,
sigma_start::Float64,
... |
58e5420a8942f483ac0d2808c2de9d05412bcf8613d0f815b613252101fd0552 | Julia | 32,265 | 782 | ### A Pluto.jl notebook ###
# v0.20.0
using Markdown
using InteractiveUtils
# ╔═╡ c7a4ca53-587c-4984-b712-b125e57a0aa8
import Pkg, Revise; Pkg.activate(Base.current_project())
# ╔═╡ 30c525d5-1060-4a30-ab48-57944716e6fa
using DataFrames: DataFrame
# ╔═╡ b296c9fe-2a8b-462d-8227-0db4bf747610
using Statistics: mean
# ... |
e3442d68fa7a7f384720def4f93b998c61582a492dc75770b0936047dc7b1a6d | Julia | 35,371 | 783 | ### A Pluto.jl notebook ###
# v0.20.0
using Markdown
using InteractiveUtils
# ╔═╡ 7f95a967-426a-465f-bad4-671372ea1092
import Pkg, Revise; Pkg.activate(Base.current_project())
# ╔═╡ c797f3ce-6d16-47e1-8728-82399f2133a9
using DataFrames: DataFrame
# ╔═╡ 7d355591-dddd-4463-97b1-d53e223bd6b3
using Statistics: mean
# ... |
7cee72e50773dc77fd784d41f9ea11ab9f9fe76514fceaf33d1b69142c1e1485 | Julia | 35,922 | 1,147 | ### A Pluto.jl notebook ###
# v0.20.4
using Markdown
using InteractiveUtils
# ╔═╡ a76f6dfc-7bdd-4110-a88f-271a17c6a7c6
begin
projectdir = dirname(Base.current_project())
import Pkg
Pkg.activate(projectdir)
Pkg.instantiate()
using Pollen
using DataFrames
using CSV
using WGLMakie
... |
8e822d60676c96e5bfea47fd1b488d774803099d2a540fd3380d147a3e432fc7 | Julia | 46,771 | 1,308 | ### A Pluto.jl notebook ###
# v0.20.4
using Markdown
using InteractiveUtils
# ╔═╡ 5b13b446-3e34-4637-bc4e-aa14fcc8d813
# ╠═╡ show_logs = false
begin
projectdir = dirname(Base.current_project())
import Pkg
Pkg.activate(projectdir)
Pkg.instantiate()
using Pollen
using DataFrames
using CSV... |
0196508d8faa845ba98c479b2a92a6a784a38b2b6e697bb59af9145e7fffbf5e | Julia | 47,241 | 1,658 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
#! format: off
... |
4f22742a554d7555c7fccab8c2924271156efb85cd68804ea9374369ad66b779 | Julia | 51,833 | 1,822 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
#! format: off
... |
fd698cbe48df90aa2376b0b4debd9eaf15dea341159f301db267214fdb8e0d3f | Julia | 53,922 | 2,133 | ### A Pluto.jl notebook ###
# v0.20.6
using Markdown
using InteractiveUtils
# This Pluto notebook uses @bind for interactivity. When running this notebook outside of Pluto, the following 'mock version' of @bind gives bound variables a default value (instead of an error).
macro bind(def, element)
#! format: off
... |
f57cc25a323dc3332b4de84f7dec1c3cee0ac29b22a93449292129e50451bdf0 | Jupyter | 49 | 5 | # %% [markdown]
# # Quickstart
# %% [markdown]
|
10ea197f5c16063ab8eaee1b2255f48e6ec4ffb3baf71ff6727e1f00e74d9831 | Jupyter | 51 | 6 | # %%
import pandas as pd
import numpy as np
# %%
|
20340740b80d1345c786988c2fa4b1836e1c86ce248320396b0fe4bda7811d66 | Jupyter | 51 | 11 | # %%
!pip freeze
# %%
!pwd
# %%
!ls /test
# %%
|
3d807ffdeba1d155d3a3a5807570d61439725ab9f5676e990a8d55d4a1e68127 | Jupyter | 56 | 8 | # %% [markdown]
# # Quickstart
# %%
# %% [markdown]
|
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