If a run a program written in julia as
sachin#localhost:$ julia mettis.jl then it runs sucessfully, without printing anything, though one print statement is in it.
And Secondly If run it as by going in julia:
sachin#localhost:$ julia
julia> include("mettis.jl")
main (generic function with 1 method)`
julia> main()
Then It gives some error.
I am puzzled why two style of executing is giving different result ?
Here is my code:
using ITensors
using Printf
function ITensors.op(::OpName"expτSS", ::SiteType"S=1/2", s1::Index, s2::Index; τ)
h =
1 / 2 * op("S+", s1) * op("S-", s2) +
1 / 2 * op("S-", s1) * op("S+", s2) +
op("Sz", s1) * op("Sz", s2)
return exp(τ * h)
end
function main(; N=10, cutoff=1E-8, δτ=0.1, beta_max=2.0)
# Make an array of 'site' indices
s = siteinds("S=1/2", N; conserve_qns=true)
# #show s
# Make gates (1,2),(2,3),(3,4),...
gates = ops([("expτSS", (n, n + 1), (τ=-δτ / 2,)) for n in 1:(N - 1)], s)
# Include gates in reverse order to complete Trotter formula
append!(gates, reverse(gates))
# Initial state is infinite-temperature mixed state
rho = MPO(s, "Id") ./ √2
#show inner(rho, H)
# Make H for measuring the energy
terms = OpSum()
for j in 1:(N - 1)
terms += 1 / 2, "S+", j, "S-", j + 1
terms += 1 / 2, "S-", j, "S+", j + 1
terms += "Sz", j, "Sz", j + 1
end
H = MPO(terms, s)
# Do the time evolution by applying the gates
# for Nsteps steps
for β in 0:δτ:beta_max
energy = inner(rho, H)
#printf("β = %.2f energy = %.8f\n", β, energy)
rho = apply(gates, rho; cutoff)main
rho = rho / tr(rho)
end
# #show energy
return nothing
end
There is nothing special about a function called main in Julia and defining a function is different from calling it. Consequently a file mettis.jl with the following code:
function main()
println("Hello, World!")
end
will not "do" anything when run (julia mettis.jl). However if you actually call the function at the end:
function main()
println("Hello, World!")
end
main()
you get the expected result
$ julia mettis.jl
Hello, World!
Related
I wrote a main function which uses a stochastic optimization algorithm (Particle Swarm Optimization) to found optimal solution for a ODE system. I would run 50 times to make sure the optimal can be found. At first, it operates normally, but now I found the calculation time would increase with iteration increases.
It cost less than 300s for first ten calculations, but it would increase to 500s for final calculation. It seems that it would cost 3~5 seconds more for each calculation. I have followed the high performance tips to optimize my code but it doesn't work.
I am sorry I don't know quite well how to upload my code before, here is the code I wrote below. But in this code, the experimental data is not loaded, I may need to find a way to upload data. In main function, with the increase of i, the time cost is increasing for each calculation.
Oh, by the way, I found another interesting phenomenon. I changed the number of calculations and the calculation time changed again. For first 20 calculations in main loop, each calculation cost about 300s, and the memory useage fluctuates significantly. But something I don't know happend, it is speeding up. It cost 1/4 time less time for each calculation, which is about 80s. And the memory useage became a straight line like this:
I knew the Julia would do pre-heating for first run and then speed up. But this situation seems different. This situation looks like Julia run slowly for first 20 calculation, and then it found a good way to optimize the memory useage and speed up. Then the program just run at full speed.
using CSV, DataFrames
using BenchmarkTools
using DifferentialEquations
using Statistics
using Dates
using Base.Threads
using Suppressor
function uniform(dim::Int, lb::Array{Float64, 1}, ub::Array{Float64, 1})
arr = rand(Float64, dim)
#inbounds for i in 1:dim; arr[i] = arr[i] * (ub[i] - lb[i]) + lb[i] end
return arr
end
mutable struct Problem
cost_func
dim::Int
lb::Array{Float64,1}
ub::Array{Float64,1}
end
mutable struct Particle
position::Array{Float64,1}
velocity::Array{Float64,1}
cost::Float64
best_position::Array{Float64,1}
best_cost::Float64
end
mutable struct Gbest
position::Array{Float64,1}
cost::Float64
end
function PSO(problem, data_dict; max_iter=100,population=100,c1=1.4962,c2=1.4962,w=0.7298,wdamp=1.0)
dim = problem.dim
lb = problem.lb
ub = problem.ub
cost_func = problem.cost_func
gbest, particles = initialize_particles(problem, population, data_dict)
# main loop
for iter in 1:max_iter
#threads for i in 1:population
particles[i].velocity .= w .* particles[i].velocity .+
c1 .* rand(dim) .* (particles[i].best_position .- particles[i].position) .+
c2 .* rand(dim) .* (gbest.position .- particles[i].position)
particles[i].position .= particles[i].position .+ particles[i].velocity
particles[i].position .= max.(particles[i].position, lb)
particles[i].position .= min.(particles[i].position, ub)
particles[i].cost = cost_func(particles[i].position,data_dict)
if particles[i].cost < particles[i].best_cost
particles[i].best_position = copy(particles[i].position)
particles[i].best_cost = copy(particles[i].cost)
if particles[i].best_cost < gbest.cost
gbest.position = copy(particles[i].best_position)
gbest.cost = copy(particles[i].best_cost)
end
end
end
w = w * wdamp
if iter % 50 == 1
println("Iteration " * string(iter) * ": Best Cost = " * string(gbest.cost))
println("Best Position = " * string(gbest.position))
println()
end
end
gbest, particles
end
function initialize_particles(problem, population,data_dict)
dim = problem.dim
lb = problem.lb
ub = problem.ub
cost_func = problem.cost_func
gbest_position = uniform(dim, lb, ub)
gbest = Gbest(gbest_position, cost_func(gbest_position,data_dict))
particles = []
for i in 1:population
position = uniform(dim, lb, ub)
velocity = zeros(dim)
cost = cost_func(position,data_dict)
best_position = copy(position)
best_cost = copy(cost)
push!(particles, Particle(position, velocity, cost, best_position, best_cost))
if best_cost < gbest.cost
gbest.position = copy(best_position)
gbest.cost = copy(best_cost)
end
end
return gbest, particles
end
function get_dict_label(beta::Int)
beta_str = lpad(beta,2,"0")
T_label = "Temperature_" * beta_str
M_label = "Mass_" * beta_str
MLR_label = "MLR_" * beta_str
return T_label, M_label, MLR_label
end
function get_error(x::Vector{Float64}, y::Vector{Float64})
numerator = sum((x.-y).^2)
denominator = var(x) * length(x)
numerator/denominator
end
function central_diff(x::AbstractArray{Float64}, y::AbstractArray{Float64})
# Central difference quotient
dydx = Vector{Float64}(undef, length(x))
dydx[2:end] .= diff(y) ./ diff(x)
#views dydx[2:end-1] .= (dydx[2:end-1] .+ dydx[3:end])./2
# Forward and Backward difference
dydx[1] = (y[2]-y[1])/(x[2]-x[1])
dydx[end] = (y[end]-y[end-1])/(x[end]-x[end-1])
return dydx
end
function decomposition!(dm,m,p,T)
# A-> residue + volitale
# B-> residue + volatile
beta,A1,E1,n1,k1,A2,E2,n2,k2,m1,m2 = p
R = 8.314
rxn1 = -m1 * exp(A1-E1/R/T) * max(m[1]/m1,0)^n1 / beta
rxn2 = -m2 * exp(A2-E2/R/T) * max(m[2]/m2,0)^n2 / beta
dm[1] = rxn1
dm[2] = rxn2
dm[3] = -k1 * rxn1 - k2 * rxn2
dm[4] = dm[1] + dm[2] + dm[3]
end
function read_file(file_path)
df = CSV.read(file_path, DataFrame)
data_dict = Dict{String, Vector{Float64}}()
for beta in 5:5:21
T_label, M_label, MLR_label = get_dict_label(beta)
T_data = collect(skipmissing(df[:, T_label]))
M_data = collect(skipmissing(df[:, M_label]))
T = T_data[T_data .< 780]
M = M_data[T_data .< 780]
data_dict[T_label] = T
data_dict[M_label] = M
data_dict[MLR_label] = central_diff(T, M)
end
return data_dict
end
function initial_condition(beta::Int64, ode_parameters::Array{Float64,1})
m_FR_initial = ode_parameters[end]
m_PVC_initial = 1 - m_FR_initial
T_span = (300.0, 800.0) # temperature range
p = [beta; ode_parameters; m_PVC_initial]
m0 = [p[end-1], p[end], 0.0, 1.0] # initial mass
return m0, T_span, p
end
function cost_func(ode_parameters, data_dict)
total_error = 0.0
for beta in 5:5:21
T_label, M_label, MLR_label= get_dict_label(beta)
T = data_dict[T_label]::Vector{Float64}
M = data_dict[M_label]::Vector{Float64}
MLR = data_dict[MLR_label]::Vector{Float64}
m0, T_span, p = initial_condition(beta,ode_parameters)
prob = ODEProblem(decomposition!,m0,T_span,p)
sol = solve(prob, AutoVern9(Rodas5(autodiff=false)),saveat=T,abstol=1e-8,reltol=1e-8,maxiters=1e4)
if sol.retcode != :Success
# println(1)
return Inf
else
M_sol = #view sol[end, :]
MLR_sol = central_diff(T, M_sol)::Array{Float64,1}
error1 = get_error(MLR, MLR_sol)::Float64
error2 = get_error(M, M_sol)::Float64
total_error += error1 + error2
end
end
total_error
end
function main()
flush(stdout)
total_time = 0
best_costs = []
file_path = raw"F:\17-Fabric\17-Fabric (Smoothed) TG.csv"
data_dict = read_file(file_path)
dimension = 9
lb = [5, 47450, 0.0, 0.0, 24.36, 148010, 0.0, 0.0, 1e-5]
ub = [25.79, 167700, 5, 1, 58.95, 293890, 5, 1, 0.25]
problem = Problem(cost_func,dimension,lb,ub)
global_best_cost = Inf
println("-"^100)
println("Running PSO ...")
population = 50
max_iter = 1001
println("The population is: ", population)
println("Max iteration is:", max_iter)
for i in 1:50 # The number of calculation
start_time = Dates.now()
println("Current iteration is: ", string(i))
gbest, particles = PSO(problem, data_dict, max_iter=max_iter, population=population)
if gbest.cost < global_best_cost
global_best_cost = gbest.cost
global_best_position = gbest.position
end
end_time = Dates.now()
time_duration = round(end_time-start_time, Second)
total_time += time_duration.value
push!(best_costs, gbest.cost)
println()
println("The Best is:")
println(gbest.cost)
println(gbest.position)
println("The calculation time is: " * string(time_duration))
println()
println("-"^50)
end
println('-'^100)
println("Global best cost is: ", global_best_cost)
println("Global best position is: ", global_best_position)
println(total_time)
best_costs
end
#suppress_err begin
#time global best_costs = main()
end
So, what is the possible mechanism for this? Is there a way to avoid this problem? Because If I increase the population and max iterations of particles, the time increased would be extremely large and thus is unacceptable.
And what is the possible mechanism for speed up the program I mentioned above? How to trigger this mechanism?
As the parameters of an ODE optimizes it can completely change its characteristics. Your equation could be getting more stiff and require different ODE solvers. There are many other related ways, but you can see how changing parameters could give such a performance issue. It's best to use methods like AutoTsit5(Rodas5()) and the like in such estimation cases because it's hard to know or guess what the performance will be like, and thus adaptiveness in the method choice can be crucial.
The renewal function for Weibull distribution m(t) with t = 10 is given as below.
I want to find the value of m(t). I wrote the following r code to compute m(t)
last_term = NULL
gamma_k = NULL
n = 50
for(k in 1:n){
gamma_k[k] = gamma(2*k + 1)/factorial(k)
}
for(j in 1: (n-1)){
prev = gamma_k[n-j]
last_term[j] = gamma(2*j + 1)/factorial(j)*prev
}
final_term = NULL
find_value = function(n){
for(i in 2:n){
final_term[i] = gamma_k[i] - sum(last_term[1:(i-1)])
}
return(final_term)
}
all_k = find_value(n)
af_sum = NULL
m_t = function(t){
for(k in 1:n){
af_sum[k] = (-1)^(k-1) * all_k[k] * t^(2*k)/gamma(2*k + 1)
}
return(sum(na.omit(af_sum)))
}
m_t(20)
The output is m(t) = 2.670408e+93. Does my iteratvie procedure correct? Thanks.
I don't think it will work. First, lets move Γ(2k+1) from denominator of m(t) into Ak. Thus, Ak will behave roughly as 1/k!.
In the nominator of the m(t) terms there is t2k, so roughly speaking you're computing sum with terms
100k/k!
From Stirling formula
k! ~ kk, making terms
(100/k)k
so yes, they will start to decrease and converge to something but after 100th term
Anyway, here is the code, you could try to improve it, but it breaks at k~70
N <- 20
A <- rep(0, N)
# compute A_k/gamma(2k+1) terms
ps <- 0.0 # previous sum
A[1] = 1.0
for(k in 2:N) {
ps <- ps + A[k-1]*gamma(2*(k-1) + 1)/factorial(k-1)
A[k] <- 1.0/factorial(k) - ps/gamma(2*k+1)
}
print(A)
t <- 10.0
t2 <- t*t
r <- 0.0
for(k in 1:N){
r <- r + (-t2)^k*A[k]
}
print(-r)
UPDATE
Ok, I calculated Ak as in your question, got the same answer. I want to estimate terms Ak/Γ(2k+1) from m(t), I believe it will be pretty much dominated by 1/k! term. To do that I made another array k!*Ak/Γ(2k+1), and it should be close to one.
Code
N <- 20
A <- rep(0.0, N)
psum <- function( pA, k ) {
ps <- 0.0
if (k >= 2) {
jmax <- k - 1
for(j in 1:jmax) {
ps <- ps + (gamma(2*j+1)/factorial(j))*pA[k-j]
}
}
ps
}
# compute A_k/gamma(2k+1) terms
A[1] = gamma(3)
for(k in 2:N) {
A[k] <- gamma(2*k+1)/factorial(k) - psum(A, k)
}
print(A)
B <- rep(0.0, N)
for(k in 1:N) {
B[k] <- (A[k]/gamma(2*k+1))*factorial(k)
}
print(B)
shows that
I got the same Ak values as you did.
Bk is indeed very close to 1
It means that term Ak/Γ(2k+1) could be replaced by 1/k! to get quick estimate of what we might get (with replacement)
m(t) ~= - Sum(k=1, k=Infinity) (-1)k (t2)k / k! = 1 - Sum(k=0, k=Infinity) (-t2)k / k!
This is actually well-known sum and it is equal to exp() with negative argument (well, you have to add term for k=0)
m(t) ~= 1 - exp(-t2)
Conclusions
Approximate value is positive. Probably will stay positive after all, Ak/Γ(2k+1) is a bit different from 1/k!.
We're talking about 1 - exp(-100), which is 1-3.72*10-44! And we're trying to compute it precisely summing and subtracting values on the order of 10100 or even higher. Even with MPFR I don't think this is possible.
Another approach is needed
OK, so I ended up going down a pretty different road on this. I have implemented a simple discretization of the integral equation which defines the renewal function:
m(t) = F(t) + integrate (m(t - s)*f(s), s, 0, t)
The integral is approximated with the rectangle rule. Approximating the integral for different values of t gives a system of linear equations. I wrote a function to generate the equations and extract a matrix of coefficients from it. After looking at some examples, I guessed a rule to define the coefficients directly and used that to generate solutions for some examples. In particular I tried shape = 2, t = 10, as in OP's example, with step = 0.1 (so 101 equations).
I found that the result agrees pretty well with an approximate result which I found in a paper (Baxter et al., cited in the code). Since the renewal function is the expected number of events, for large t it is approximately equal to t/mu where mu is the mean time between events; this is a handy way to know if we're anywhere in the neighborhood.
I was working with Maxima (http://maxima.sourceforge.net), which is not efficient for numerical stuff, but which makes it very easy to experiment with different aspects. At this point it would be straightforward to port the final, numerical stuff to another language such as Python.
Thanks to OP for suggesting the problem, and S. Pappadeux for insightful discussions. Here is the plot I got comparing the discretized approximation (red) with the approximation for large t (blue). Trying some examples with different step sizes, I saw that the values tend to increase a little as step size gets smaller, so I think the red line is probably a little low, and the blue line might be more nearly correct.
Here is my Maxima code:
/* discretize weibull renewal function and formulate system of linear equations
* copyright 2020 by Robert Dodier
* I release this work under terms of the GNU General Public License
*
* This is a program for Maxima, a computer algebra system.
* http://maxima.sourceforge.net/
*/
"Definition of the renewal function m(t):" $
renewal_eq: m(t) = F(t) + 'integrate (m(t - s)*f(s), s, 0, t);
"Approximate integral equation with rectangle rule:" $
discretize_renewal (delta_t, k) :=
if equal(k, 0)
then m(0) = F(0)
else m(k*delta_t) = F(k*delta_t)
+ m(k*delta_t)*f(0)*(delta_t / 2)
+ sum (m((k - j)*delta_t)*f(j*delta_t)*delta_t, j, 1, k - 1)
+ m(0)*f(k*delta_t)*(delta_t / 2);
make_eqs (n, delta_t) :=
makelist (discretize_renewal (delta_t, k), k, 0, n);
make_vars (n, delta_t) :=
makelist (m(k*delta_t), k, 0, n);
"Discretized integral equation and variables for n = 4, delta_t = 1/2:" $
make_eqs (4, 1/2);
make_vars (4, 1/2);
make_eqs_vars (n, delta_t) :=
[make_eqs (n, delta_t), make_vars (n, delta_t)];
load (distrib);
subst_pdf_cdf (shape, scale, e) :=
subst ([f = lambda ([x], pdf_weibull (x, shape, scale)), F = lambda ([x], cdf_weibull (x, shape, scale))], e);
matrix_from (eqs, vars) :=
(augcoefmatrix (eqs, vars),
[submatrix (%%, length(%%) + 1), - col (%%, length(%%) + 1)]);
"Subsitute Weibull pdf and cdf for shape = 2 into discretized equation:" $
apply (matrix_from, make_eqs_vars (4, 1/2));
subst_pdf_cdf (2, 1, %);
"Just the right-hand side matrix:" $
rhs_matrix_from (eqs, vars) :=
(map (rhs, eqs),
augcoefmatrix (%%, vars),
[submatrix (%%, length(%%) + 1), col (%%, length(%%) + 1)]);
"Generate the right-hand side matrix, instead of extracting it from equations:" $
generate_rhs_matrix (n, delta_t) :=
[delta_t * genmatrix (lambda ([i, j], if i = 1 and j = 1 then 0
elseif j > i then 0
elseif j = i then f(0)/2
elseif j = 1 then f(delta_t*(i - 1))/2
else f(delta_t*(i - j))), n + 1, n + 1),
transpose (makelist (F(k*delta_t), k, 0, n))];
"Generate numerical right-hand side matrix, skipping over formulas:" $
generate_rhs_matrix_numerical (shape, scale, n, delta_t) :=
block ([f, F, numer: true], local (f, F),
f: lambda ([x], pdf_weibull (x, shape, scale)),
F: lambda ([x], cdf_weibull (x, shape, scale)),
[genmatrix (lambda ([i, j], delta_t * if i = 1 and j = 1 then 0
elseif j > i then 0
elseif j = i then f(0)/2
elseif j = 1 then f(delta_t*(i - 1))/2
else f(delta_t*(i - j))), n + 1, n + 1),
transpose (makelist (F(k*delta_t), k, 0, n))]);
"Solve approximate integral equation (shape = 3, t = 1) via LU decomposition:" $
fpprintprec: 4 $
n: 20 $
t: 1;
[AA, bb]: generate_rhs_matrix_numerical (3, 1, n, t/n);
xx_by_lu: linsolve_by_lu (ident(n + 1) - AA, bb, floatfield);
"Iterative solution of approximate integral equation (shape = 3, t = 1):" $
xx: bb;
for i thru 10 do xx: AA . xx + bb;
xx - (AA.xx + bb);
xx_iterative: xx;
"Should find iterative and LU give same result:" $
xx_diff: xx_iterative - xx_by_lu[1];
sqrt (transpose(xx_diff) . xx_diff);
"Try shape = 2, t = 10:" $
n: 100 $
t: 10 $
[AA, bb]: generate_rhs_matrix_numerical (2, 1, n, t/n);
xx_by_lu: linsolve_by_lu (ident(n + 1) - AA, bb, floatfield);
"Baxter, et al., Eq. 3 (for large values of t) compared to discretization:" $
/* L.A. Baxter, E.M. Scheuer, D.J. McConalogue, W.R. Blischke.
* "On the Tabulation of the Renewal Function,"
* Econometrics, vol. 24, no. 2 (May 1982).
* H(t) is their notation for the renewal function.
*/
H(t) := t/mu + sigma^2/(2*mu^2) - 1/2;
tx_points: makelist ([float (k/n*t), xx_by_lu[1][k, 1]], k, 1, n);
plot2d ([H(u), [discrete, tx_points]], [u, 0, t]), mu = mean_weibull(2, 1), sigma = std_weibull(2, 1);
When f(x-1) is called, is it calling f(x) = x+10 or f(x) = if ...
Is this a tail recursion?
How should I rewrite it using static / dynamic allocation?
let fun f(x) = x + 10
in
let fun f(x) = if x < 1 then 0 else f(x-1)
in f(3)
end
end
Before addressing your questions, here are some observations about your code:
There are two functions f, one inside the other. They're different from one another.
To lessen this confusion you can rename the inner function to g:
let fun f(x) = x + 10
in
let fun g(x) = if x < 1 then 0 else g(x-1)
in g(3)
end
end
This clears up which function calls which by the following rules: The outer f is defined inside the outer in-end, but is immediately shadowed by the inner f. So any reference to f on the right-hand side of the inner fun f(x) = if ... is shadowed because fun enables self-recursion. And any reference to f within the inner in-end is shadowed
In the following tangential example the right-hand side of an inner declaration f does not shadow the outer f if we were using val rather than fun:
let fun f(x) = if (x mod 2 = 0) then x - 10 else x + 10
in
let val f = fn x => f(x + 2) * 2
in f(3)
end
end
If the inner f is renamed to g in this second piece of code, it'd look like:
let fun f(x) = if (x mod 2 = 0) then x - 10 else x + 10
in
let val g = fn x => f(x + 2) * 2
in g(3)
end
end
The important bit is that the f(x + 2) part was not rewritten into g(x + 2) because val means that references to f are outer fs, not the f being defined, because a val is not a self-recursive definition. So any reference to an f within that definition would have to depend on it being available in the outer scope.
But the g(3) bit is rewritten because between in-end, the inner f (now g) is shadowing. So whether it's a fun or a val does not matter with respect to the shadowing of let-in-end.
(There are some more details wrt. val rec and the exact scope of a let val f = ... that I haven't elaborated on.)
As for your questions,
You should be able to answer this now. A nice way to provide the answer is 1) rename the inner function for clarity, 2) evaluate the code by hand using substitution (one rewrite per line, ~> denoting a rewrite, so I don't mean an SML operator here).
Here's an example of how it'd look with my second example (not your code):
g(3)
~> (fn x => f(x + 2) * 2)(3)
~> f(3 + 2) * 2
~> f(5) * 2
~> (if (5 mod 2 = 0) then 5 - 10 else 5 + 10) * 2
~> (if (1 = 0) then 5 - 10 else 5 + 10) * 2
~> (5 + 10) * 2
~> 15 * 2
~> 30
Your evaluation by hand would look different and possibly conclude differently.
What is tail recursion? Provide a definition and ask if your code satisfies that definition.
I'm not sure what you mean by rewriting it using static / dynamic allocation. You'll have to elaborate.
I was wondering how I can convert this code from Matlab to R code. It seems this is the code for midpoint method. Any help would be highly appreciated.
% Usage: [y t] = midpoint(f,a,b,ya,n) or y = midpoint(f,a,b,ya,n)
% Midpoint method for initial value problems
%
% Input:
% f - Matlab inline function f(t,y)
% a,b - interval
% ya - initial condition
% n - number of subintervals (panels)
%
% Output:
% y - computed solution
% t - time steps
%
% Examples:
% [y t]=midpoint(#myfunc,0,1,1,10); here 'myfunc' is a user-defined function in M-file
% y=midpoint(inline('sin(y*t)','t','y'),0,1,1,10);
% f=inline('sin(y(1))-cos(y(2))','t','y');
% y=midpoint(f,0,1,1,10);
function [y t] = midpoint(f,a,b,ya,n)
h = (b - a) / n;
halfh = h / 2;
y(1,:) = ya;
t(1) = a;
for i = 1 : n
t(i+1) = t(i) + h;
z = y(i,:) + halfh * f(t(i),y(i,:));
y(i+1,:) = y(i,:) + h * f(t(i)+halfh,z);
end;
I have the R code for Euler method which is
euler <- function(f, h = 1e-7, x0, y0, xfinal) {
N = (xfinal - x0) / h
x = y = numeric(N + 1)
x[1] = x0; y[1] = y0
i = 1
while (i <= N) {
x[i + 1] = x[i] + h
y[i + 1] = y[i] + h * f(x[i], y[i])
i = i + 1
}
return (data.frame(X = x, Y = y))
}
so based on the matlab code, do I need to change h in euler method (R code) to (b - a) / n to modify Euler code to midpoint method?
Note
Broadly speaking, I agree with the expressed comments; however, I decided to vote up this question. (now deleted) This is due to the existence of matconv that facilitates this process.
Answer
Given your code, we could use matconv in the following manner:
pacman::p_load(matconv)
out <- mat2r(inMat = "input.m")
The created out object will attempt to translate Matlab code into R, however, the job is far from finished. If you inspect the out object you will see that it requires further work. Simple statements are usually translated correctly with Matlab comments % replaced with # and so forth but more complex statements may require a more detailed investigation. You could then inspect respective line and attempt to evaluate them to see where further work may be required, example:
eval(parse(text=out$rCode[1]))
NULL
(first line is a comment so the output is NULL)
My first Fortran lesson is to plot the probability density function of the radial Sturmian functions. In case you are interested, the radial Sturmian functions are used to graph the momentum space eigenfunctions for the hydrogen atom.
In order to produce these radial functions, one needs to first produce some polynomials called the Gegenbauer polynomials, denoted
Cba(x),
where a and b should be stacked atop each other. One needs these polynomials because the Sturmians (let's call them R_n,l) are defined like so,
R_n,l(p) = N pl⁄(p2 + k2)l+2 Cn - l - 1l + 1(p2 - k2⁄p2 + k2),
where N is a normalisation constant, p is the momentum, n is the principle quantum number, l is the angular momentum and k is a constant. The normalisation constant is there so that when I come to square this function, it will produce a probability distribution for the momentum of the electron in a hydrogen atom.
Gegenbauer polynomials are generated using the following recurrence relation:
Cnl(x) = 1⁄n[2(l + n - 1) x Cn - 1l(x) - (2l + n - 2)Cn - 2l(x)],
with C0l(x) = 1 and C1l(x) = 2lx, as you may have noticed, l is fixed but n is not. At the start of my program, I will specify both l and n and work out the Gegenbauer polynomial I need for the radial function I wish to plot.
The problems I am having with my code at the moment are all in my subroutine for working out the value of the Gegenbauer polynomial Cn-l-1l+1(p2 - k2⁄p2 + k2) for incremental values of p between 0 and 3. I keep getting the error
Unclassified statement at (1)
but I cannot see what the issue is.
program Radial_Plot
implicit none
real, parameter :: pi = 4*atan(1.0)
integer, parameter :: top = 1000, l = 50, n = 100
real, dimension(1:top) :: x, y
real increment
real :: a=0.0, b = 2.5, k = 0.3
integer :: i
real, dimension(1:top) :: C
increment = (b-a)/(real(top)-1)
x(1) = 0.0
do i = 2, top
x(i) = x(i-1) + increment
end do
Call Gegenbauer(top, n, l, k, C)
y = x*C
! y is the function that I shall be plotting between values a and b.
end program Radial_Plot
Subroutine Gegenbauer(top1, n1, l1, k1, CSub)
! This subroutine is my attempt to calculate the Gegenbauer polynomials evaluated at a certain number of values between c and d.
implicit none
integer :: top1, i, j, n1, l1
real :: k1, increment1, c, d
real, dimension(1:top1) :: x1
real, dimension(1:n1 - l1, 1:top1) :: C1
real, dimension(1:n1 - l1) :: CSub
c = 0.0
d = 3.0
k1 = 0.3
n1 = 50
l1 = 25
top1 = 1000
increment1 = (d - c)/(real(top1) - 1)
x1(1) = 0.0
do i = 2, top1
x1(i) = x1(i-1) + increment1
end do
do j = 1, top1
C1(1,j) = 1
C1(2,j) = 2(l1 + 1)(x1(i)^2 - k1^2)/(x1(i)^2 + k1^2)
! All the errors occurring here are all due to, and I quote, 'Unclassifiable statement at (1)', I can't see what the heck I have done wrong.
do i = 3, n1 - l1
C1(i,j) = 2(((l1 + 1)/n1) + 1)(x1(i)^2 - k1^2)/(x1(i)^2 + k1^2)C1(i,j-1) - ((2(l1+1)/n1) + 1)C1(i,j-2)
end do
CSub(j) = Cn(n1 - l1,j)^2
end do
return
end Subroutine Gegenbauer
As francesalus correctly pointed out, the problem is because you use ^ instead of ** for exponentiation. Additionally, you do not put * between the terms you are multiplying.
C1(1,j) = 1
C1(2,j) = 2*(l1 + 1)*(x1(i)**2 - k1**2)/(x1(i)**2 + k1**2)
do i = 3, n1 - l1
C1(i,j) = 2 * (((l1 + 1)/n1) + 1) * (x1(i)**2 - k1**2) / &
(x1(i)**2 + k1**2)*C1(i,j-1) - ((2(l1+1)/n1) + 1) * &
C1(i,j-2)
end do
CSub(j) = Cn(n1 - l1,j)**2
Since you are beginning I have some advice. Learn to put all subroutines and functions to modules (unless they are internal). There is no reason for the return statement at the and of the subroutine, similarly as a stop statement isn't necessary at the and of the program.