The following actions uses node12 which is deprecated and will be forced to run on node16: actions/checkout@v2, codecov/codecov-action@v2. For more info: https://github.blog/changelog/2023-06-13-github-actions-all-actions-will-run-on-node16-instead-of-node12-by-default/

failed to run `@example` block in src/examples/hubbard_chain_checkpoint.md:28-580 ```@example hubbard_chain_checkpoint using LinearAlgebra using Random using Printf using MPI # Import JLD2 package for write checkpoints during the simulation # to file as a binary file. using JLD2 using SmoQyDQMC import SmoQyDQMC.LatticeUtilities as lu import SmoQyDQMC.JDQMCFramework as dqmcf import SmoQyDQMC.JDQMCMeasurements as dqmcm # initialize MPI MPI.Init() # Define top-level function for running DQMC simulation function run_hubbard_chain_simulation(sID, U, μ, β, L, N_burnin, N_updates, N_bins; filepath = ".") # Initialize the MPI communicator. comm = MPI.COMM_WORLD # Construct the foldername the data will be written to. datafolder_prefix = @sprintf "hubbard_chain_U%.2f_mu%.2f_L%d_b%.2f" U μ L β # Get the MPI comm rank, which fixes the process ID (pID). pID = MPI.Comm_rank(comm) # Initialize an instance of the SimulationInfo type. simulation_info = SimulationInfo( filepath = filepath, datafolder_prefix = datafolder_prefix, sID = sID, pID = pID ) # Define checkpoint filename. # We implement three checkpoint files, an old, current and new one, # that get cycled through to ensure a checkpoint file always exists in the off # chance that the simulation is killed while a checkpoint is getting written to file. # Additionally, each simulation that is running in parallel with MPI will have their own # checkpoints written to file. datafolder = simulation_info.datafolder sID = simulation_info.sID pID = simulation_info.pID checkpoint_name_old = @sprintf "checkpoint_sID%d_pID%d_old.jld2" sID pID checkpoint_filename_old = joinpath(datafolder, checkpoint_name_old) checkpoint_name_current = @sprintf "checkpoint_sID%d_pID%d_current.jld2" sID pID checkpoint_filename_current = joinpath(datafolder, checkpoint_name_current) checkpoint_name_new = @sprintf "checkpoint_sID%d_pID%d_new.jld2" sID pID checkpoint_filename_new = joinpath(datafolder, checkpoint_name_new) ###################################################### ### DEFINE SOME RELEVANT DQMC SIMULATION PARAMETERS ## ###################################################### # Set the discretization in imaginary time for the DQMC simulation. Δτ = 0.10 # This flag indicates whether or not to use the checkboard approximation to # represent the exponentiated hopping matrix exp(-Δτ⋅K) checkerboard = false # Whether the propagator matrices should be represented using the # symmetric form B = exp(-Δτ⋅K/2)⋅exp(-Δτ⋅V)⋅exp(-Δτ⋅K/2) # or the asymetric form B = exp(-Δτ⋅V)⋅exp(-Δτ⋅K) symmetric = false # Set the initial period in imaginary time slices with which the Green's function matrices # will be recomputed using a numerically stable procedure. n_stab = 10 # Specify the maximum allowed error in any element of the Green's function matrix that is # corrected by performing numerical stabiliziation. δG_max = 1e-6 # Initialize variables to keep track of the largest numerical error in the # Green's function matrices corrected by numerical stabalization. δG = 0.0 δθ = 0.0 ####################### ### DEFINE THE MODEL ## ####################### # Initialize an instance of the type UnitCell. unit_cell = lu.UnitCell(lattice_vecs = [[1.0]], basis_vecs = [[0.0]]) # Initialize an instance of the type Lattice. lattice = lu.Lattice( L = [L], periodic = [true] ) # Initialize an instance of the ModelGeometry type. model_geometry = ModelGeometry(unit_cell, lattice) # Define the nearest-neighbor bond for a 1D chain. bond = lu.Bond(orbitals = (1,1), displacement = [1]) # Add this bond to the model, by adding it to the ModelGeometry type. bond_id = add_bond!(model_geometry, bond) # Define nearest-neighbor hopping amplitude, setting the energy sc

failed to run `@example` block in src/examples/hubbard_chain_mpi.md:26-426 ```@example hubbard_chain_mpi using LinearAlgebra using Random using Printf using MPI using SmoQyDQMC import SmoQyDQMC.LatticeUtilities as lu import SmoQyDQMC.JDQMCFramework as dqmcf import SmoQyDQMC.JDQMCMeasurements as dqmcm # initialize MPI MPI.Init() # Define top-level function for running DQMC simulation function run_hubbard_chain_simulation(sID, U, μ, β, L, N_burnin, N_updates, N_bins; filepath = ".") # Initialize the MPI communicator. comm = MPI.COMM_WORLD # Construct the foldername the data will be written to. datafolder_prefix = @sprintf "hubbard_chain_U%.2f_mu%.2f_L%d_b%.2f" U μ L β # Get the MPI comm rank, which fixes the process ID (pID). pID = MPI.Comm_rank(comm) # Initialize an instance of the SimulationInfo type. simulation_info = SimulationInfo( filepath = filepath, datafolder_prefix = datafolder_prefix, sID = sID, pID = pID ) # Synchronize all the MPI processes. # Here we need to make sure the data folder is initialized before letting # all the various processes move beyond this point. MPI.Barrier(comm) # Initialize a random number generator that will be used throughout the simulation. seed = abs(rand(Int)) rng = Xoshiro(seed) # Set the discretization in imaginary time for the DQMC simulation. Δτ = 0.10 # Calculate the length of the imaginary time axis, Lτ = β/Δτ. Lτ = dqmcf.eval_length_imaginary_axis(β, Δτ) # This flag indicates whether or not to use the checkboard approximation to # represent the exponentiated hopping matrix exp(-Δτ⋅K) checkerboard = false # Whether the propagator matrices should be represented using the # symmetric form B = exp(-Δτ⋅K/2)⋅exp(-Δτ⋅V)⋅exp(-Δτ⋅K/2) # or the asymetric form B = exp(-Δτ⋅V)⋅exp(-Δτ⋅K) symmetric = false # Set the initial period in imaginary time slices with which the Green's function matrices # will be recomputed using a numerically stable procedure. n_stab = 10 # Specify the maximum allowed error in any element of the Green's function matrix that is # corrected by performing numerical stabiliziation. δG_max = 1e-6 # Calculate the bins size. bin_size = div(N_updates, N_bins) # Initialize a dictionary to store additional information about the simulation. additional_info = Dict( "dG_max" => δG_max, "N_burnin" => N_burnin, "N_updates" => N_updates, "N_bins" => N_bins, "bin_size" => bin_size, "local_acceptance_rate" => 0.0, "reflection_acceptance_rate" => 0.0, "n_stab_init" => n_stab, "symmetric" => symmetric, "checkerboard" => checkerboard, "seed" => seed, ) ####################### ### DEFINE THE MODEL ## ####################### # Initialize an instance of the type UnitCell. unit_cell = lu.UnitCell(lattice_vecs = [[1.0]], basis_vecs = [[0.0]]) # Initialize an instance of the type Lattice. lattice = lu.Lattice( L = [L], periodic = [true] ) # Initialize an instance of the ModelGeometry type. model_geometry = ModelGeometry(unit_cell, lattice) # Define the nearest-neighbor bond for a 1D chain. bond = lu.Bond(orbitals = (1,1), displacement = [1]) # Add this bond to the model, by adding it to the ModelGeometry type. bond_id = add_bond!(model_geometry, bond) # Define nearest-neighbor hopping amplitude, setting the energy scale for the system. t = 1.0 # Define the tight-binding model tight_binding_model = TightBindingModel( model_geometry = model_geometry, t_bonds = [bond], # defines hopping t_mean = [t], # defines corresponding hopping amplitude μ = μ, # set chemical potential ϵ_mean = [0.] # set the (mean) on-site energy ) # Initialize the Hubbard interaction in the model. hubbard_model = HubbardModel( shif

no doc found for reference '[`SmoQyDQMC`](@ref)' in src/api.md.

no doc found for reference '[`initialize`](@ref)' in src/api.md.

no doc found for reference '[`FouerierMassMatrix`](@ref)' in src/api.md.

no doc found for reference '[`LOCAL_MEASUREMENTS`](@ref)' in src/api.md.

no doc found for reference '[`composite_correlation_stats`](@ref)' in src/api.md.

no doc found for reference '[`measure_ssh_sgn_switch`](@ref)' in src/api.md.

no doc found for reference '[`SmoQyDQMC`](@ref)' in src/examples/hubbard_chain.md.

28 docstrings not included in the manual: SmoQyDQMC.momentum_to_kinetic_energy :: Union{Tuple{E}, Tuple{SmoQyDQMC.FourierMassMatrix{E}, Matrix{E}}} where E<:AbstractFloat SmoQyDQMC.reset! :: Union{Tuple{SmoQyDQMC.CorrelationContainer{D, T}}, Tuple{T}, Tuple{D}} where {D, T<:AbstractFloat} SmoQyDQMC.calculate_exp_K! :: Union{Tuple{E}, Tuple{T}, Tuple{AbstractPropagator{T, E}, FermionPathIntegral{T, E}, Int64}} where {T, E} SmoQyDQMC.calculate_exp_K! :: Union{Tuple{P}, Tuple{E}, Tuple{T}, Tuple{Vector{P}, FermionPathIntegral{T, E}}} where {T, E, P<:AbstractPropagator{T, E}} SmoQyDQMC.reverse_partially_wrap_greens :: Union{Tuple{P}, Tuple{E}, Tuple{T}, Tuple{Matrix{T}, P}, Tuple{Matrix{T}, P, Matrix{T}}} where {T, E, P<:AbstractPropagator{T, E}} SmoQyDQMC.CorrelationContainer :: Tuple{Int64, DataType, Bool} SmoQyDQMC.CorrelationContainer SmoQyDQMC.initialize_correlation_measurement! :: Union{Tuple{}, Tuple{N}, Tuple{D}, Tuple{T}} where {T<:AbstractFloat, D, N} SmoQyDQMC.allocate_propagators :: Union{Tuple{FermionPathIntegral{T, E}}, Tuple{E}, Tuple{T}} where {T, E} SmoQyDQMC.measure_ssh_sgn_switch :: Union{Tuple{E}, Tuple{T}, Tuple{ElectronPhononParameters{T, E}, TightBindingParameters{T, E}, Int64}} where {T<:Number, E<:AbstractFloat} SmoQyDQMC.bosonic_action_derivative! :: Union{Tuple{E}, Tuple{T}, Tuple{Matrix{T}, ElectronPhononParameters{T, E}}} where {T, E} LinearAlgebra.mul! :: Union{Tuple{E}, Tuple{Matrix, SmoQyDQMC.FourierMassMatrix{E}, Matrix}, Tuple{Matrix, SmoQyDQMC.FourierMassMatrix{E}, Matrix, E}} where E<:AbstractFloat SmoQyDQMC.std_x_qho :: Union{Tuple{T}, Tuple{T, T, T}} where T<:AbstractFloat SmoQyDQMC.swap! :: Union{Tuple{T}, Tuple{AbstractArray{T}, AbstractArray{T}}} where T SmoQyDQMC.update! :: Union{Tuple{E}, Tuple{T}, Tuple{FermionPathIntegral{T, E}, SmoQyDQMC.HolsteinParameters{E}, Matrix{E}, Int64}} where {T, E} SmoQyDQMC.update! :: Union{Tuple{E}, Tuple{T}, Tuple{FermionPathIntegral{T, E}, SmoQyDQMC.SSHParameters{T}, Matrix{E}, Int64}} where {T, E} SmoQyDQMC.update! :: Union{Tuple{E}, Tuple{T}, Tuple{FermionPathIntegral{T, E}, FermionPathIntegral{T, E}, ElectronPhononParameters{T, E}, Matrix{E}}, Tuple{FermionPathIntegral{T, E}, FermionPathIntegral{T, E}, ElectronPhononParameters{T, E}, Matrix{E}, Matrix{E}}} where {T, E} SmoQyDQMC.LOCAL_MEASUREMENTS SmoQyDQMC.calculate_exp_V! :: Union{Tuple{E}, Tuple{T}, Tuple{AbstractPropagator{T, E}, FermionPathIntegral{T, E}, Int64}} where {T, E} SmoQyDQMC.calculate_exp_V! :: Union{Tuple{P}, Tuple{E}, Tuple{T}, Tuple{Vector{P}, FermionPathIntegral{T, E}}} where {T, E, P<:AbstractPropagator{T, E}} SmoQyDQMC.save :: Union{Tuple{T}, Tuple{D}, Tuple{String, SmoQyDQMC.CorrelationContainer{D, T}}} where {D, T<:AbstractFloat} SmoQyDQMC.bosonic_action :: Union{Tuple{ElectronPhononParameters{T, E}}, Tuple{E}, Tuple{T}} where {T, E} LinearAlgebra.lmul! :: Union{Tuple{E}, Tuple{SmoQyDQMC.FourierMassMatrix{E}, Matrix{E}}, Tuple{SmoQyDQMC.FourierMassMatrix{E}, Matrix{E}, E}} where E<:AbstractFloat SmoQyDQMC.fermionic_action_derivative! :: Union{Tuple{P}, Tuple{E}, Tuple{T}, Tuple{AbstractMatrix{E}, Matrix{T}, E, T, E, T, ElectronPhononParameters{T, E}, FermionGreensCalculator{T, E}, Vector{P}}} where {T<:Number, E<:AbstractFloat, P<:AbstractPropagator{T, E}} SmoQyDQMC.reduced_mass :: Union{Tuple{T}, Tuple{T, T}} where T<:AbstractFloat SmoQyDQMC.save_simulation_info :: Union{Tuple{SimulationInfo}, Tuple{SimulationInfo, Any}} SmoQyDQMC.forward_partially_wrap_greens :: Union{Tuple{P}, Tuple{E}, Tuple{T}, Tuple{Matrix{T}, P}, Tuple{Matrix{T}, P, Matrix{T}}} where {T, E, P<:AbstractPropagator{T, E}} SmoQyDQMC.velocity_to_kinetic_energy :: Union{Tuple{E}, Tuple{SmoQyDQMC.FourierMassMatrix{E}, Matrix{E}}} where E<:AbstractFloat These are docstrings in the checked modules (configured with the modules keyword) that are not included in @docs or @autodocs blocks.