Merge pull request #332 from chrisbrahms/helium

make "HeJ" the default helium

docs/src/scans.md

@@ -8,7 +8,7 @@ import PyPlot: plt
 
 a = 125e-6
 flength = 3
-gas = :HeJ
+gas = :He
 λ0 = 800e-9
 τfwhm = 10e-15
 λlims = (100e-9, 4e-6)

examples/simple_interface/scan.jl

@@ -4,7 +4,7 @@ import PyPlot: plt
 # Fixed parameters:
 a = 125e-6
 flength = 3
-gas = :HeJ
+gas = :He
 
 λ0 = 800e-9
 τfwhm = 10e-15

src/Interface.jl

@@ -364,8 +364,6 @@ function prop_capillary_args(radius, flength, gas, pressure;
     plasma = isnothing(plasma) ? !envelope : plasma
     thg = isnothing(thg) ? !envelope : thg
 
-    gas = (gas == :He) ? :HeJ : gas
-
     grid = makegrid(flength, λ0, λlims, trange, envelope, thg, δt)
     mode_s = makemode_s(modes, flength, radius, gas, pressure, model, loss, pol)
     check_orth(mode_s)

src/PhysData.jl

@@ -45,9 +45,10 @@ const amg = atm/(k_B*273.15)
 "Atomic mass unit"
 const m_u = ustrip(CODATA2014.m_u)
 
-const gas = (:Air, :He, :HeJ, :Ne, :Ar, :Kr, :Xe, :N2, :H2, :O2, :CH4, :SF6, :N2O, :D2)
+const gas = (:Air, :He, :HeJ, :HeB, :Ne, :Ar, :Kr, :Xe, :N2, :H2, :O2, :CH4, :SF6, :N2O, :D2)
 const gas_str = Dict(
     :He => "He",
+    :HeB => "He",
     :HeJ => "He",
     :Ar => "Ar",
     :Ne => "Neon",
@@ -142,13 +143,13 @@ calculated from Sellmeier expansions.
 """
 function sellmeier_gas(material::Symbol)
     dens = dens_1bar_0degC[material]
-    if material == :He
+    if material == :HeB
         B1 = 4977.77e-8
         C1 = 28.54e-6
         B2 = 1856.94e-8
         C2 = 7.76e-3
         return γ_Börzsönyi(B1/dens, C1, B2/dens, C2)
-    elseif material == :HeJ
+    elseif material == :He || material == :HeJ
         B1 = 2.16463842e-05
         C1 = -6.80769781e-04
         B2 = 2.10561127e-07
@@ -570,7 +571,7 @@ References:
 function γ3_gas(material::Symbol; source=nothing)
     # TODO: More Bishop/Shelton; Wahlstrand updated values.
     if source === nothing
-        if material in (:He, :HeJ, :Ne, :Ar, :Kr, :Xe, :N2)
+        if material in (:He, :HeB, :HeJ, :Ne, :Ar, :Kr, :Xe, :N2)
             source = :Lehmeier
         elseif material in (:H2, :CH4, :SF6, :D2)
             source = :Shelton
@@ -585,7 +586,7 @@ function γ3_gas(material::Symbol; source=nothing)
     if source == :Lehmeier
         dens = dens_1atm_0degC[material]
         # Table 1 in [3]
-        if material in (:He, :HeJ)
+        if material in (:He, :HeB, :HeJ)
             fac = 1
         elseif material == :Ne
             fac = 1.8
@@ -708,7 +709,7 @@ Return the first ionisation potential of the `material` in a specific unit (defa
 Possible units are `:SI`, `:atomic` and `:eV`.
 """
 function ionisation_potential(material; unit=:SI)
-    if material in (:He, :HeJ)
+    if material in (:He, :HeB, :HeJ)
         Ip = 0.9036
     elseif material == :Ne
         Ip = 0.7925
@@ -764,7 +765,7 @@ function quantum_numbers(material)
         return 4, 1, 1
     elseif material == :Xe
         return 5, 1, 1
-    elseif material in (:He, :HeJ)
+    elseif material in (:He, :HeB, :HeJ)
         return 1, 0, 1
     elseif material == :O2
         return 2, 0, 0.53 # https://doi.org/10.1016/S0030-4018(99)00113-3

src/Scans.jl

@@ -171,7 +171,7 @@ Make an appropriate file name for an `HDF5Output` or `prop_capillary` output for
 ```
 scan = Scan("scan_example"; energy=collect(range(5e-6, 200e-6; length=64)))
 runscan(scan) do scanidx, energyi
-    prop_capillary(125e-6, 3, :HeJ, 0.8; λ0=800e-9, τfwhm=10e-15, energy=energyi
+    prop_capillary(125e-6, 3, :He, 0.8; λ0=800e-9, τfwhm=10e-15, energy=energyi
                    filepath=makefilename(scan, scanidx))
 end
 ```
@@ -251,7 +251,7 @@ The exact subset and order of scan points which is run depends on `scan.exec`, s
 ```
 scan = Scan("scan_example"; energy=collect(range(5e-6, 200e-6; length=64)))
 runscan(scan) do scanidx, energyi
-    prop_capillary(125e-6, 3, :HeJ, 0.8; λ0=800e-9, τfwhm=10e-15, energy=energyi)
+    prop_capillary(125e-6, 3, :He, 0.8; λ0=800e-9, τfwhm=10e-15, energy=energyi)
 end
 ```
 """

test/test_capillary.jl

@@ -11,10 +11,10 @@ import Luna.PhysData: wlfreq
     λ = 800e-9
     ω = wlfreq(λ)
     a = 125e-6
-    m = Capillary.MarcatiliMode(a, :He, 1.0, model=:reduced)
+    m = Capillary.MarcatiliMode(a, :HeB, 1.0, model=:reduced)
     @test isapprox(Capillary.losslength(m, ω), 7.0593180702769, rtol=1e-5)
     @test isapprox(Capillary.dB_per_m(m, ω), 0.6152074146252722, rtol=1e-5)
-    @test Capillary.dB_per_m(m, ω) ≈ 8*Capillary.dB_per_m(Capillary.MarcatiliMode(2a, :He, 1.0, model=:reduced), ω)
+    @test Capillary.dB_per_m(m, ω) ≈ 8*Capillary.dB_per_m(Capillary.MarcatiliMode(2a, :HeB, 1.0, model=:reduced), ω)
 end
 
 @testset "normalisation" begin
@@ -55,17 +55,17 @@ end
     @testset "n = $n" for n = 1:6
         @testset "m = $m" for m = 1:6
             # With the exception of HE65 specifically, all of these also pass with rtol=1e-20
-            mode = Capillary.MarcatiliMode(a, :He, 1.0, n=n, m=m)
+            mode = Capillary.MarcatiliMode(a, :HeB, 1.0, n=n, m=m)
             Ni, Nerr = N(mode)
             @test isapprox(Modes.N(mode), Ni, atol=Nerr, rtol=1e-7)
             aeff, aefferr = Aeff(mode)
             @test isapprox(Modes.Aeff(mode), aeff, rtol=1e-7, atol=aefferr)
         end
     end
-    m = Capillary.MarcatiliMode(a, :He, 1.0, n=0, kind=:TE)
+    m = Capillary.MarcatiliMode(a, :HeB, 1.0, n=0, kind=:TE)
     @test Modes.N(m) ≈ N(m)[1]
     @test Modes.Aeff(m) ≈ Aeff(m)[1]
-    m = Capillary.MarcatiliMode(a, :He, 1.0, n=0, kind=:TM)
+    m = Capillary.MarcatiliMode(a, :HeB, 1.0, n=0, kind=:TM)
     @test Modes.N(m) ≈ N(m)[1]
     @test Modes.Aeff(m) ≈ Aeff(m)[1]
 
@@ -75,7 +75,7 @@ end
     afun = let a0=a0, aL=aL, L=L
         afun(z) = a0 + (aL-a0)*z/L
     end
-    m = Capillary.MarcatiliMode(afun, :He, 1, loss=false, model=:full)
+    m = Capillary.MarcatiliMode(afun, :HeB, 1, loss=false, model=:full)
     @test Modes.N(m) ≈ N(m)[1]
     @test Modes.N(m, z=L/2) ≈ N(m, z=L/2)[1]
     @test Modes.N(m, z=L) ≈ N(m, z=L)[1]
@@ -87,22 +87,22 @@ end
 
 @testset "β, α" begin
     a = 125e-6
-    m = Capillary.MarcatiliMode(a, :He, 1.0, model=:reduced)
+    m = Capillary.MarcatiliMode(a, :HeB, 1.0, model=:reduced)
     λ = 1e-9 .* collect(range(70, stop=7300, length=128))
     ω = wlfreq.(λ)
     @test all(isfinite.(Capillary.β.(m, ω)))
     @test all(isreal.(Capillary.β.(m, ω)))
-    @test all(isreal.(Capillary.β.(Capillary.MarcatiliMode(a, :He, 1.0, model=:reduced), ω)))
-    @test all(isreal.(Capillary.β.(Capillary.MarcatiliMode(a, :He, 10.0, model=:reduced), ω)))
-    @test all(isreal.(Capillary.β.(Capillary.MarcatiliMode(a, :He, 50.0, model=:reduced), ω)))
+    @test all(isreal.(Capillary.β.(Capillary.MarcatiliMode(a, :HeB, 1.0, model=:reduced), ω)))
+    @test all(isreal.(Capillary.β.(Capillary.MarcatiliMode(a, :HeB, 10.0, model=:reduced), ω)))
+    @test all(isreal.(Capillary.β.(Capillary.MarcatiliMode(a, :HeB, 50.0, model=:reduced), ω)))
     @test all(isfinite.(Capillary.α.(m, ω)))
     @test all(isreal.(Capillary.α.(m, ω)))
 end
 
 @testset "ZDW/Aeff" begin
-    @test abs(1e9*Capillary.zdw(Capillary.MarcatiliMode(125e-6, :He, 0.4, model=:reduced)) - 379) < 1
-    @test abs(1e9*Capillary.zdw(Capillary.MarcatiliMode(75e-6, :He, 5.9, model=:reduced)) - 562) < 1
-    @test Capillary.Aeff(Capillary.MarcatiliMode(75e-6, :He, 1.0, model=:reduced)) ≈ 8.42157534886545e-09
+    @test abs(1e9*Capillary.zdw(Capillary.MarcatiliMode(125e-6, :HeB, 0.4, model=:reduced)) - 379) < 1
+    @test abs(1e9*Capillary.zdw(Capillary.MarcatiliMode(75e-6, :HeB, 5.9, model=:reduced)) - 562) < 1
+    @test Capillary.Aeff(Capillary.MarcatiliMode(75e-6, :HeB, 1.0, model=:reduced)) ≈ 8.42157534886545e-09
 end
 
 
@@ -143,12 +143,12 @@ end
     @test isapprox(Capillary.dispersion(m, 5, ω), 2.64991510536236e-73, rtol=5e-5)
     @test isapprox(Capillary.zdw(m), 7.225347947615157e-07, rtol=2e-8)
     @test isapprox(Capillary.α(m, ω), 0.0290115706883820, rtol=1e-14)
-    @test Capillary.Aeff(Capillary.MarcatiliMode(75e-6, :He, 1.0)) ≈ 8.42157534886545e-09
+    @test Capillary.Aeff(Capillary.MarcatiliMode(75e-6, :HeB, 1.0)) ≈ 8.42157534886545e-09
 end
 
 @testset "to_space" begin
-    ms = (Capillary.MarcatiliMode(125e-6, :He, 1.0),
-          Capillary.MarcatiliMode(125e-6, :He, 1.0, m=2, ϕ=π/2))
+    ms = (Capillary.MarcatiliMode(125e-6, :HeB, 1.0),
+          Capillary.MarcatiliMode(125e-6, :HeB, 1.0, m=2, ϕ=π/2))
     components = :xy
     xs = (10e-6, π/7)
     ts = Modes.ToSpace(ms, components=components)

test/test_ionisation.jl

@@ -4,7 +4,7 @@ import NumericalIntegration: integrate, SimpsonEven
 
 @test Ionisation.ionrate_ADK(:He, 1e10) ≈ 1.2416371415312408e-18
 @test Ionisation.ionrate_ADK(:He, 2e10) ≈ 1.0772390893742478
-@test Ionisation.ionrate_ADK(:HeJ, 2e10) ≈ 1.0772390893742478
+@test Ionisation.ionrate_ADK(:HeB, 2e10) ≈ 1.0772390893742478
 @test Ionisation.ionrate_ADK(:Ar , 7e9) ≈ 2.4422306306649472e-08
 @test Ionisation.ionrate_ADK(:Ar , 8e9) ≈ 4.494711488416766e-05
 

test/test_modes.jl

@@ -10,15 +10,15 @@ import Luna.PhysData: wlfreq
 
 
 @testset "delegation" begin
-    m = Modes.delegated(Capillary.MarcatiliMode(75e-6, :He, 5.9))
+    m = Modes.delegated(Capillary.MarcatiliMode(75e-6, :HeB, 5.9))
     @test Modes.Aeff(m) ≈ 8.42157534886545e-09
     @test abs(1e9*Modes.zdw(m) - 562) < 1
     n(m, ω; z=0) = real(Modes.neff(m, ω; z=z))
-    m2 = Modes.delegated(Capillary.MarcatiliMode(75e-6, :He, 1.0), neff=n)
+    m2 = Modes.delegated(Capillary.MarcatiliMode(75e-6, :HeB, 1.0), neff=n)
     @test Modes.α(m2, 2e15) == 0
     @test Modes.α(m2, wlfreq(800e-9)) == 0
 
-    cm = Capillary.MarcatiliMode(75e-6, :He, 5.9)
+    cm = Capillary.MarcatiliMode(75e-6, :HeB, 5.9)
     dm = Modes.delegated(cm)
     @test Modes.Aeff(dm) ≈ 8.42157534886545e-09
 
@@ -49,7 +49,7 @@ end
 
 @testset "overlap" begin
 a = 100e-6
-m = Capillary.MarcatiliMode(a, :He, 1.0, model=:reduced)
+m = Capillary.MarcatiliMode(a, :HeB, 1.0, model=:reduced)
 r = collect(range(0, a, length=2^16))
 unm = sf_bessel_zero_Jnu(0, 1)
 Er = besselj.(0, unm*r/a) # spatial profile of the HE11 mode - overlap should be perfect
@@ -63,7 +63,7 @@ Er = besselj.(0, unm*r/a) # spatial profile of HE12 - overlap should be 0
 fac = collect(range(0.3, stop=0.9, length=128))
 ηn = zero(fac)
 r = collect(range(0, 4a, length=2^16))
-m = Capillary.MarcatiliMode(a, :He, 1.0, model=:reduced, m=1)
+m = Capillary.MarcatiliMode(a, :HeB, 1.0, model=:reduced, m=1)
 for i in eachindex(fac)
     w0 = fac[i]*a
     Er = Maths.gauss.(r, w0/sqrt(2))
@@ -78,7 +78,7 @@ w0 = fac*a
 Er = Maths.gauss.(r, w0/sqrt(2))
 s = 0
 for mi = 1:10
-    m = Capillary.MarcatiliMode(a, :He, 1.0, model=:reduced, m=mi)
+    m = Capillary.MarcatiliMode(a, :HeB, 1.0, model=:reduced, m=mi)
     η = Modes.overlap(m, r, Er, dim=1)[1]
     s += abs2(η[1])
 end
@@ -122,8 +122,8 @@ energy1 = ert(Etr1)
 energy2 = ert(Etr2)
 @test ert(Etr) ≈ energy1 + energy2
 
-m1 = Capillary.MarcatiliMode(a, :He, 1.0, model=:reduced, m=1)
-m2 = Capillary.MarcatiliMode(a, :He, 1.0, model=:reduced, m=2)
+m1 = Capillary.MarcatiliMode(a, :HeB, 1.0, model=:reduced, m=1)
+m2 = Capillary.MarcatiliMode(a, :HeB, 1.0, model=:reduced, m=2)
 Eωm1 = Modes.overlap(m1, q.r, Eωr; dim=2, norm=false)
 Eωm2 = Modes.overlap(m2, q.r, Eωr; dim=2, norm=false)
 
@@ -189,8 +189,8 @@ energy1 = ert(Etr1)
 energy2 = ert(Etr2)
 @test ert(Etr) ≈ energy1 + energy2
 
-modes = (Capillary.MarcatiliMode(a, :He, 1.0, model=:reduced, m=1),
-         Capillary.MarcatiliMode(a, :He, 1.0, model=:reduced, m=2))
+modes = (Capillary.MarcatiliMode(a, :HeB, 1.0, model=:reduced, m=1),
+         Capillary.MarcatiliMode(a, :HeB, 1.0, model=:reduced, m=2))
 newgrid = Grid.RealGrid(1, 800e-9, (160e-9, 3000e-9), 1e-12)
 
 Eωm = Modes.overlap(modes, newgrid, grid, q.r, Eωr)
@@ -375,7 +375,7 @@ end # testset "makemodes"
 @testset "spatial field and fluence" begin
     a = 100e-6
     flength = 0.1
-    gas = :He
+    gas = :HeB
     pressure = 1
     λ0 = 800e-9
     τfwhm = 30e-15

test/test_physdata.jl

@@ -3,12 +3,12 @@ import Luna: PhysData
 
 @testset "All" begin
 @testset "Exceptions" begin
-    @test_throws DomainError PhysData.ref_index(:Hello, 800e-9)
+    @test_throws DomainError PhysData.ref_index(:HeBllo, 800e-9)
 end
 
 @testset "refractive indices" begin
-    @test PhysData.ref_index(:He, 800e-9) ≈ 1.000031950041203
-    @test PhysData.ref_index(:He, 800e-9, 10) ≈ 1.0003180633169397
+    @test PhysData.ref_index(:HeB, 800e-9) ≈ 1.000031950041203
+    @test PhysData.ref_index(:HeB, 800e-9, 10) ≈ 1.0003180633169397
     @test PhysData.ref_index(:SiO2, 800e-9, lookup=false) ≈ 1.4533172548587419
     @test PhysData.ref_index(:SiO2, 400e-9, lookup=false) ≈ 1.4701161185594052
     @test PhysData.ref_index(:SiO2, PhysData.eV_to_m(6)) ≈ 1.543
@@ -20,13 +20,13 @@ end
 
 @testset "Function equivalence" begin
     @test PhysData.ref_index_fun(:SiO2)(800e-9) == PhysData.ref_index(:SiO2, 800e-9)
-    @test PhysData.ref_index_fun(:He)(800e-9) == PhysData.ref_index(:He, 800e-9)
+    @test PhysData.ref_index_fun(:HeB)(800e-9) == PhysData.ref_index(:HeB, 800e-9)
 end
 
 @testset "Dispersion" begin
     @test PhysData.dispersion(2, :SiO2, 800e-9, lookup=false) ≈ 3.61619983e-26
-    @test isapprox(PhysData.dispersion(2, :He, 800e-9), 9.373942337550116e-31, rtol=1e-5)
-    @test isapprox(PhysData.dispersion(2, :He, 800e-9, 10), 9.33043805928079e-30, rtol=1e-5)
+    @test isapprox(PhysData.dispersion(2, :HeB, 800e-9), 9.373942337550116e-31, rtol=1e-5)
+    @test isapprox(PhysData.dispersion(2, :HeB, 800e-9, 10), 9.33043805928079e-30, rtol=1e-5)
 end
 
 @testset "glasses" begin
@@ -48,12 +48,12 @@ end
 end
 
 @testset "Nonlinear coefficients" begin
-    @test_broken PhysData.χ3(:He, 1) ≈ 1.2617371645226101e-27
+    @test_broken PhysData.χ3(:HeB, 1) ≈ 1.2617371645226101e-27
     @test PhysData.χ3(:Ar, 1) ≈ 2.964158749949189e-26
-    @test_broken PhysData.n2(:He, 1) ≈ 3.5647819877255427e-25
-    @test PhysData.n2(:He, 2) ≈ 7.125642138007481e-25
-    @test_broken PhysData.n2.(:He, [1, 2]) ≈ [3.5647819877255427e-25, 7.125642138007481e-25]
-    @test_broken PhysData.n2.([:He, :Ne], 1) ≈ [3.5647819877255427e-25, 6.416061508801999e-25]
+    @test_broken PhysData.n2(:HeB, 1) ≈ 3.5647819877255427e-25
+    @test PhysData.n2(:HeB, 2) ≈ 7.125642138007481e-25
+    @test_broken PhysData.n2.(:HeB, [1, 2]) ≈ [3.5647819877255427e-25, 7.125642138007481e-25]
+    @test_broken PhysData.n2.([:HeB, :Ne], 1) ≈ [3.5647819877255427e-25, 6.416061508801999e-25]
     for gas in PhysData.gas[2:end] # Don't have γ3 for Air
         @test isreal(PhysData.n2(gas, 1))
     end
@@ -67,11 +67,11 @@ end
     @test isapprox(PhysData.density(:Ar, 2.0, 294.0), 4.933761614600933e25, rtol=4e-13)
     @test isapprox(PhysData.density(:Ar, 40.0, 294.0), 1.0101579129300146e27, rtol=2e-11)
     @test isapprox(PhysData.density(:Ar, 400.0, 294.0), 9.270757850984163e27, rtol=3e-10)
-    @test_broken isapprox(PhysData.density(:He, 0.002, 294.0), 4.927180563885407e22, rtol=7e-16)
-    @test_broken isapprox(PhysData.density(:He, 0.02, 294.0), 4.927137517453137e23, rtol=2e-16)
-    @test_broken isapprox(PhysData.density(:He, 2.0, 294.0), 4.9224080868066745e25, rtol=2e-13)
-    @test_broken isapprox(PhysData.density(:He, 40.0, 294.0), 9.66755645602771e26, rtol=6e-16)
-    @test_broken isapprox(PhysData.density(:He, 400.0, 294.0), 8.309132317978155e27, rtol=1e-13)
+    @test_broken isapprox(PhysData.density(:HeB, 0.002, 294.0), 4.927180563885407e22, rtol=7e-16)
+    @test_broken isapprox(PhysData.density(:HeB, 0.02, 294.0), 4.927137517453137e23, rtol=2e-16)
+    @test_broken isapprox(PhysData.density(:HeB, 2.0, 294.0), 4.9224080868066745e25, rtol=2e-13)
+    @test_broken isapprox(PhysData.density(:HeB, 40.0, 294.0), 9.66755645602771e26, rtol=6e-16)
+    @test_broken isapprox(PhysData.density(:HeB, 400.0, 294.0), 8.309132317978155e27, rtol=1e-13)
     @test isapprox(PhysData.density(:Xe, 0.002, 294.0), 4.927238737907382e22, rtol=7e-16)
     @test isapprox(PhysData.density(:Xe, 0.02, 294.0), 4.92771934762324e23, rtol=2e-16)
     @test isapprox(PhysData.density(:Xe, 2.0, 294.0), 4.981603290885485e25, rtol=9e-16)
@@ -89,9 +89,9 @@ end
     @test isapprox(PhysData.density(:H2, 40.0, 294.0), 9.624525613497868e26, rtol=6e-16)
     @test isapprox(PhysData.density(:H2, 400.0, 294.0), 7.840662987579036e27, rtol=6e-16)
     # temperature range
-    @test_broken isapprox(PhysData.density(:He, 10.0, 10.0), 9.218927214187151e27, rtol=6e-16)
-    @test_broken isapprox(PhysData.density(:He, 10.0, 100.0), 7.142310177179197e26, rtol=6e-16)
-    @test_broken isapprox(PhysData.density(:He, 10.0, 1000.0), 7.234660811823096e25, rtol=6e-13)
+    @test_broken isapprox(PhysData.density(:HeB, 10.0, 10.0), 9.218927214187151e27, rtol=6e-16)
+    @test_broken isapprox(PhysData.density(:HeB, 10.0, 100.0), 7.142310177179197e26, rtol=6e-16)
+    @test_broken isapprox(PhysData.density(:HeB, 10.0, 1000.0), 7.234660811823096e25, rtol=6e-13)
     @test isapprox(PhysData.density(:Xe, 10.0, 170.0), 1.336261228046876e28, rtol=6e-16)
     @test isapprox(PhysData.density(:Xe, 10.0, 700.0), 1.0361035050644844e26, rtol=6e-13)
     @test isapprox(PhysData.density(:N2, 10.0, 100.0), 1.4849593021049305e28, rtol=6e-7)

test/test_processing.jl

@@ -223,7 +223,7 @@ end
 @testset "scanproc" begin
     a = 125e-6
     flength = 0.1
-    gas = :HeJ
+    gas = :He
 
     λ0 = 800e-9
     τfwhm = 10e-15