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Update to Julia 1.10 synthax #2

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a932943
Update to Julia 1.10 synthax
Bachibouzouk Jul 22, 2024
32936bf
Add .toml files in place of REQUIRE
Bachibouzouk Jul 22, 2024
a327c37
Update README
Bachibouzouk Jul 22, 2024
82f9086
Add example dependencies
Bachibouzouk Jul 22, 2024
ee08458
Update basic.jl to julia 1.10
Bachibouzouk Jul 22, 2024
af8af17
Adapt example diamond.jl
Bachibouzouk Jul 22, 2024
ac3b985
Update needed packages for basic.jl
Bachibouzouk Aug 14, 2024
d00904f
Fix dropdims
Bachibouzouk Aug 14, 2024
d0880ce
Fix broadcasting
Bachibouzouk Aug 14, 2024
d3501ad
Replace flipdim() with reverse()
Bachibouzouk Aug 14, 2024
adbca62
Add module for writedlm function
Bachibouzouk Aug 14, 2024
cb43315
Fix example vibrational.jl
Bachibouzouk Aug 14, 2024
9af9626
Adapt examples for newer Julia version
Bachibouzouk Aug 14, 2024
2106574
Protect LineshapeLUT from broadcasting in R1
Bachibouzouk Aug 15, 2024
513b4be
Replace Complex128 by ComplexF64
Bachibouzouk Aug 15, 2024
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1,434 changes: 1,434 additions & 0 deletions Manifest.toml
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23 changes: 23 additions & 0 deletions Project.toml
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Original file line number Diff line number Diff line change
@@ -0,0 +1,23 @@
name = "Mbo"
uuid = "abb35812-7e48-465d-8fd2-5263f57cc2e0"
authors = ["Samuel Palato <>"]
version = "0.1.0"

[deps]
DSP = "717857b8-e6f2-59f4-9121-6e50c889abd2"
DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
FFTW = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
PlotlyJS = "f0f68f2c-4968-5e81-91da-67840de0976a"
Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
Rsvg = "c4c386cf-5103-5370-be45-f3a111cca3b8"
Runner = "847b7089-1ebf-4e83-b33e-c3c97d2ccb04"
YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"

[compat]
julia = "1.10"

[workspace]
projects = ["test", "src"]
17 changes: 16 additions & 1 deletion README.md
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Expand Up @@ -67,7 +67,22 @@ tell me if it breaks!)
Once julia is installed, open `julia` and type:

```julia
julia> Pkg.clone("https://github.com/spalato/Mbo.jl")
julia> ]
```

Then
```julia
@v1.10 pkg> activate /path/to this repository/
```
Your terminal should then look like

```julia
Mbo.jl pkg>
```
Finally precompile the package with

```julia
Mbo.jl pkg> precompile
```

Documentation
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4 changes: 0 additions & 4 deletions REQUIRE
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This file was deleted.

28 changes: 14 additions & 14 deletions examples/aimd_full/linear_xcf.jl
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Expand Up @@ -16,7 +16,7 @@ end
function run(args)
t0 = now()
cfgf = args[1]
info("Loading parameters from $(cfgf)")
@info("Loading parameters from $(cfgf)")
cfg = open(YAML.load, cfgf)
states_fn = cfg["states_fn"]
cf_fn = cfg["cf_fn"]
Expand All @@ -26,17 +26,17 @@ t2 = convert.(Float64, cfg["t2"])
t3 = convert.(Float64, cfg["t3"])
σ = cfg["sigma"]

info("Loading energies from $states_fn")
@info("Loading energies from $states_fn")
states = readdlm(states_fn)
energies = states[:,1]
tdm = states[:,2]
info("States count: $(size(states)[1])")
info("Loading CF from $cf_fn")
@info("States count: $(size(states)[1])")
@info("Loading CF from $cf_fn")
cfs = parse_cf(cf_fn)
info("CF count: $(length(cfs))")
@info("CF count: $(length(cfs))")

# build system
info("Building system...")
@info("Building system...")
t0_sys = now()
s = System("G")
#energy!(s, "G", 0)
Expand All @@ -57,33 +57,33 @@ for (i, j) in keys(cfs)
lut = LineshapeLUT(t->(GriddedCF(cfs[i,j], dt)(t)+g_inhomo(t, ev2angphz(σ))), lut_grid)
lineshape!(s, ti, tj, lut)
end
info(" Took $(now()-t0_sys)")
info("Number of order 1 Hilbert Paths: $(length(collect(hilbert_paths(s, 1))))")
info("Number of order 3 Hilbert Paths: $(length(collect(hilbert_paths(s, 3))))")
@info(" Took $(now()-t0_sys)")
@info("Number of order 1 Hilbert Paths: $(length(collect(hilbert_paths(s, 1))))")
@info("Number of order 3 Hilbert Paths: $(length(collect(hilbert_paths(s, 3))))")

grd_lin = TimeGrid(t1)

t0_calc = now()
out_root = cfg["rootname"]

# compute them separately
totlin = zeros(Complex128, size(grd_lin))
totlin = zeros(ComplexF64, size(grd_lin))
for p in hilbert_paths(s, 1)
rlin = linear(grd_lin, s, p)
#writedlm(out_root*"_lin_$(p.p[2]).txt", [grid(grd_lin)[1] real(rlin) imag(rlin)])
totlin += rlin
end
info("Saving to $(out_root)_rlin.txt")
@info("Saving to $(out_root)_rlin.txt")
writedlm("$(out_root)_rlin.txt", [grid(grd_lin)[1] real(totlin) imag(totlin)])

totlin[1] *= 0.5
s_lin = fftshift(ifft(totlin))
f_lin = fftshift(fftfreq(size(grd_lin)[1], 1/(grd_lin.times[1][2]-grd_lin.times[1][1])))
info("Saving linear spectrum to $(out_root)_slin.txt")
@info("Saving linear spectrum to $(out_root)_slin.txt")
writedlm("$(out_root)_slin.txt", [f_lin real(s_lin) imag(s_lin)])

info(" Took $(now()-t0_calc)")
info("Total runtime: $(now()-t0)")
@info(" Took $(now()-t0_calc)")
@info("Total runtime: $(now()-t0)")
end # run

run(ARGS)
8 changes: 4 additions & 4 deletions examples/aimd_full/spec_abs.jl
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Expand Up @@ -10,13 +10,13 @@ function run(cfgf, root, outf)
inf_n = root*"_sn.bin"
in_r = open(inf_r, "r+")
in_n = open(inf_n, "r+")
s_r = Mmap.mmap(in_r, Array{Complex128, 3}, sz)
s_n = Mmap.mmap(in_n, Array{Complex128, 3}, sz)
s_r = Mmap.mmap(in_r, Array{ComplexF64, 3}, sz)
s_n = Mmap.mmap(in_n, Array{ComplexF64, 3}, sz)
out = open(outf, "w+")
try
spec_abs = Mmap.mmap(out, Array{Complex128, 3}, sz)
spec_abs = Mmap.mmap(out, Array{ComplexF64, 3}, sz)
spec_abs[:] = copy(s_n)
spec_abs[2:end,:,:] += flipdim(s_r[2:end,:,:], 1)
spec_abs[2:end,:,:] += reverse(s_r[2:end,:,:], dims=1)
finally
close(out)
close(in_r)
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4 changes: 2 additions & 2 deletions examples/aimd_full/spec_ft.jl
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Expand Up @@ -7,11 +7,11 @@ function run(cfgf, infn, outf)
cfg = open(YAML.load, cfgf)
sz = tuple(map(length, cfg["t$i"] for i=1:3)...)
inf = open(infn, "r+")
sig = Mmap.mmap(inf, Array{Complex128, 3}, sz)
sig = Mmap.mmap(inf, Array{ComplexF64, 3}, sz)
sig[1,:,:] *= 0.5
sig[:,:,1] *= 0.5
out = open(outf, "w+")
spec2d = Mmap.mmap(out, Array{Complex128, 3}, sz)
spec2d = Mmap.mmap(out, Array{ComplexF64, 3}, sz)
fill!(spec2d, 0)
spec2d[:] = fftshift(ifft(sig, (1,3)), (1,3))
close(out)
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32 changes: 16 additions & 16 deletions examples/aimd_full/third_order_xcf.jl
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Expand Up @@ -15,7 +15,7 @@ end
function run(args)
t0 = now()
cfgf = args[1]
info("Loading parameters from $(cfgf)")
@info("Loading parameters from $(cfgf)")
cfg = open(YAML.load, cfgf)
root = cfg["rootname"]
states_fn = cfg["states_fn"]
Expand All @@ -26,17 +26,17 @@ t2 = convert.(Float64, cfg["t2"])
t3 = convert.(Float64, cfg["t3"])
σ = cfg["sigma"]

info("Loading energies from $states_fn")
@info("Loading energies from $states_fn")
states = readdlm(states_fn)
energies = states[:,1]
tdm = states[:,2]
info("States count: $(size(states)[1])")
info("Loading CF from $cf_fn")
@info("States count: $(size(states)[1])")
@info("Loading CF from $cf_fn")
cfs = parse_cf(cf_fn)
info("CF count: $(length(cfs))")
@info("CF count: $(length(cfs))")

# build system
info("Building system...")
@info("Building system...")
t0_sys = now()
s = System("G")
frame = ev2angphz(cfg["e_frame"])
Expand All @@ -53,24 +53,24 @@ for (i, j) in keys(cfs)
lut = LineshapeLUT(t->(GriddedCF(cfs[i,j], 1.0)(t)+g_inhomo(t, ev2angphz(σ))), lut_grid)
lineshape!(s, ti, tj, lut)
end
info(" Took $(now()-t0_sys)")
info("Number of order 1 Hilbert Paths: $(length(collect(hilbert_paths(s, 1))))")
info("Number of order 3 Hilbert Paths: $(length(collect(hilbert_paths(s, 3))))")
@info(" Took $(now()-t0_sys)")
@info("Number of order 1 Hilbert Paths: $(length(collect(hilbert_paths(s, 1))))")
@info("Number of order 3 Hilbert Paths: $(length(collect(hilbert_paths(s, 3))))")

info("Preparing calculation of third order response")
@info("Preparing calculation of third order response")
grd_trd = TimeGrid(t1, t2, t3)
info("Grid size: $(size(grd_trd))")
@info("Grid size: $(size(grd_trd))")

rr_fn = root*"_rr.bin"
rn_fn = root*"_rn.bin"
info("Saving rephasing to: $rr_fn")
info("Saving nonrephasing to: $rr_fn")
@info("Saving rephasing to: $rr_fn")
@info("Saving nonrephasing to: $rr_fn")
rr_out = open(rr_fn, "w+")
rn_out = open(rn_fn, "w+")
rr = Mmap.mmap(rr_out, Array{Complex128, 3}, size(grd_trd))
rn = Mmap.mmap(rn_out, Array{Complex128, 3}, size(grd_trd))
rr = Mmap.mmap(rr_out, Array{ComplexF64, 3}, size(grd_trd))
rn = Mmap.mmap(rn_out, Array{ComplexF64, 3}, size(grd_trd))
pm = Progress(4*length(collect(hilbert_paths(s, 3))))
info("Computing third order response")
@info("Computing third order response")
t0_third = now()
rr .+= R2(grd_trd, s, pm)
rr .+= R3(grd_trd, s, pm)
Expand Down
8 changes: 4 additions & 4 deletions examples/aimd_static/spec_abs.jl
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Expand Up @@ -10,13 +10,13 @@ function run(cfgf, root, outf)
inf_n = root*"_sn.bin"
in_r = open(inf_r, "r+")
in_n = open(inf_n, "r+")
s_r = Mmap.mmap(in_r, Array{Complex128, 3}, sz)
s_n = Mmap.mmap(in_n, Array{Complex128, 3}, sz)
s_r = Mmap.mmap(in_r, Array{ComplexF64, 3}, sz)
s_n = Mmap.mmap(in_n, Array{ComplexF64, 3}, sz)
out = open(outf, "w+")
try
spec_abs = Mmap.mmap(out, Array{Complex128, 3}, sz)
spec_abs = Mmap.mmap(out, Array{ComplexF64, 3}, sz)
spec_abs[:] = copy(s_n)
spec_abs[2:end,:,:] += flipdim(s_r[2:end,:,:], 1)
spec_abs[2:end,:,:] += reverse(s_r[2:end,:,:], dims=1)
finally
close(out)
close(in_r)
Expand Down
4 changes: 2 additions & 2 deletions examples/aimd_static/spec_ft.jl
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Expand Up @@ -7,11 +7,11 @@ function run(cfgf, infn, outf)
cfg = open(YAML.load, cfgf)
sz = tuple(map(length, cfg["t$i"] for i=1:3)...)
inf = open(infn, "r+")
sig = Mmap.mmap(inf, Array{Complex128, 3}, sz)
sig = Mmap.mmap(inf, Array{ComplexF64, 3}, sz)
sig[1,:,:] *= 0.5
sig[:,:,1] *= 0.5
out = open(outf, "w+")
spec2d = Mmap.mmap(out, Array{Complex128, 3}, sz)
spec2d = Mmap.mmap(out, Array{ComplexF64, 3}, sz)
fill!(spec2d, 0)
spec2d[:] = fftshift(ifft(sig, (1,3)), (1,3))
close(out)
Expand Down
32 changes: 16 additions & 16 deletions examples/aimd_static/third_order_xc.jl
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Expand Up @@ -10,7 +10,7 @@ end
function run(args)
t0 = now()
cfgf = args[1]
info("Loading parameters from $(cfgf)")
@info("Loading parameters from $(cfgf)")
cfg = open(YAML.load, cfgf)
states_fn = cfg["states_fn"]
cf_fn = cfg["xcorr_fn"]
Expand All @@ -20,17 +20,17 @@ t2 = convert.(Float64, cfg["t2"])
t3 = convert.(Float64, cfg["t3"])
sigma = cfg["sigma"]

info("Loading energies from $states_fn")
@info("Loading energies from $states_fn")
states = readdlm(states_fn)
energies = states[:,1]
tdm = states[:,2]
info("States count: $(size(states)[1])")
info("Loading correlation matrix from $cf_fn")
@info("States count: $(size(states)[1])")
@info("Loading correlation matrix from $cf_fn")
corrm = parse_corr(cf_fn)
info("Correlation count: $(length(corrm))")
@info("Correlation count: $(length(corrm))")

# build system
info("Building system...")
@info("Building system...")
t0_sys = now()
s = System("G")
frame = ev2angphz(cfg["e_frame"])
Expand All @@ -54,28 +54,28 @@ for i=1:size(corrm)[1], j=1:size(corrm)[2]
#end
lineshape!(s, ti, tj, lut)
end
info(" Took $(now()-t0_sys)")
info("Number of order 1 Hilbert Paths: $(length(collect(hilbert_paths(s, 1))))")
info("Number of order 3 Hilbert Paths: $(length(collect(hilbert_paths(s, 3))))")
@info(" Took $(now()-t0_sys)")
@info("Number of order 1 Hilbert Paths: $(length(collect(hilbert_paths(s, 1))))")
@info("Number of order 3 Hilbert Paths: $(length(collect(hilbert_paths(s, 3))))")

grd_lin = TimeGrid(t1)

info("Computing linear responses separately.")
@info("Computing linear responses separately.")
t0_calc = now()
out_root = "$(splitext(basename(states_fn))[1])_$(splitext(basename(cf_fn))[1])"

# compute them separately
totlin = zeros(Complex128, size(grd_lin))
totlin = zeros(ComplexF64, size(grd_lin))
for p in hilbert_paths(s, 1)
rlin = linear(grd_lin, s, p)
totlin += rlin
out_lin = out_root*"_lin_"*join(p.p[2:end-1], "-")*".txt"
info("Saving linear to: $out_lin")
@info("Saving linear to: $out_lin")
writedlm(out_lin, [grid(grd_lin)[1] real(rlin) imag(rlin)])
end
writedlm(out_root*"_lin_tot.txt", [grid(grd_lin)[1] real(totlin) imag(totlin)])
info(" Took $(now()-t0_calc)")
info("Preparing calculation of third order response")
@info(" Took $(now()-t0_calc)")
@info("Preparing calculation of third order response")
grd_trd = TimeGrid(t1, t2, t3)
info("Grid size: $(size(grd_trd))")

Expand All @@ -85,8 +85,8 @@ info("Saving rephasing to: $rr_fn")
info("Saving nonrephasing to: $rr_fn")
rr_out = open(rr_fn, "w+")
rn_out = open(rn_fn, "w+")
rr = Mmap.mmap(rr_out, Array{Complex128, 3}, size(grd_trd))
rn = Mmap.mmap(rn_out, Array{Complex128, 3}, size(grd_trd))
rr = Mmap.mmap(rr_out, Array{ComplexF64, 3}, size(grd_trd))
rn = Mmap.mmap(rn_out, Array{ComplexF64, 3}, size(grd_trd))
pm = Progress(4*length(collect(hilbert_paths(s, 3))))
info("Computing third order response")
t0_third = now()
Expand Down
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