Merge pull request #41 from detrin/devel

Devel

.github/workflows/ci-short.yml

@@ -16,14 +16,11 @@ jobs:
           - '1.7'
         os:
           - ubuntu-latest
-        arch:
-          - x64
     steps:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
-          arch: ${{ matrix.arch }}
       - uses: actions/cache@v1
         env:
           cache-name: cache-artifacts

benchmark/benchmark.jl

@@ -21,7 +21,7 @@ import QuantumOpticsBase
 BenchmarkTools.DEFAULT_PARAMETERS.samples = 100
 
 # dic_commits = JSON.parsefile("test/benchmark_commits.json")
-open("benchmark/benchmark_commits.json","r") do f 
+open("benchmark/benchmark_commits.json", "r") do f
     global dic_commits = JSON.parse(f)
 end
 
@@ -34,18 +34,18 @@ println
 
 ## Aggregate building
 ### agg_dimer_small
-BenchmarkTools.DEFAULT_PARAMETERS.seconds = 5.
+BenchmarkTools.DEFAULT_PARAMETERS.seconds = 5.0
 t1_1 = @benchmark begin
     HR = 0.01
     shift = (2.0 * HR)
-    modes = [Mode(180., shift)]
+    modes = [Mode(180.0, shift)]
     mols = [
-        Molecule([Mode(300., shift)], 3, [12500., 12710.]),
-        Molecule([Mode(300., shift)], 3, [12500., 12690.])
+        Molecule([Mode(300.0, shift)], 3, [12500.0, 12710.0]),
+        Molecule([Mode(300.0, shift)], 3, [12500.0, 12690.0]),
     ]
 
     agg = Aggregate(mols)
-    for mol_i in 2:length(agg.molecules)
+    for mol_i = 2:length(agg.molecules)
         agg.coupling[mol_i, mol_i+1] = 200
         agg.coupling[mol_i+1, mol_i] = 200
     end
@@ -59,7 +59,7 @@ t1_1 = @benchmark begin
     Ham = getAggHamiltonian(agg, aggIndices, FCFact)
 
     Ham_bath = getAggHamiltonianBath(agg)
-    Ham_sys = getAggHamiltonianSystem(agg; groundEnergy=false)
+    Ham_sys = getAggHamiltonianSystem(agg; groundEnergy = false)
     b = GenericBasis([aggIndLen])
     b_sys = GenericBasis([size(Ham_sys, 1)])
     b_bath = GenericBasis([size(Ham_bath, 1)])
@@ -77,18 +77,18 @@ t1_1 = @benchmark begin
 end
 
 ### agg_dimer_medium
-BenchmarkTools.DEFAULT_PARAMETERS.seconds = 20.
+BenchmarkTools.DEFAULT_PARAMETERS.seconds = 20.0
 t1_2 = @benchmark begin
     HR = 0.01
     shift = (2.0 * HR)
-    modes = [Mode(180., shift)]
+    modes = [Mode(180.0, shift)]
     mols = [
-        Molecule([Mode(300., shift)], 7, [12500., 12710.]),
-        Molecule([Mode(300., shift)], 7, [12500., 12690.])
+        Molecule([Mode(300.0, shift)], 7, [12500.0, 12710.0]),
+        Molecule([Mode(300.0, shift)], 7, [12500.0, 12690.0]),
     ]
 
     agg = Aggregate(mols)
-    for mol_i in 2:length(agg.molecules)
+    for mol_i = 2:length(agg.molecules)
         agg.coupling[mol_i, mol_i+1] = 200
         agg.coupling[mol_i+1, mol_i] = 200
     end
@@ -102,7 +102,7 @@ t1_2 = @benchmark begin
     Ham = getAggHamiltonian(agg, aggIndices, FCFact)
 
     Ham_bath = getAggHamiltonianBath(agg)
-    Ham_sys = getAggHamiltonianSystem(agg; groundEnergy=false)
+    Ham_sys = getAggHamiltonianSystem(agg; groundEnergy = false)
     b = GenericBasis([aggIndLen])
     b_sys = GenericBasis([size(Ham_sys, 1)])
     b_bath = GenericBasis([size(Ham_bath, 1)])
@@ -120,28 +120,28 @@ t1_2 = @benchmark begin
 end
 
 ### agg_building
-BenchmarkTools.DEFAULT_PARAMETERS.seconds = 1.
+BenchmarkTools.DEFAULT_PARAMETERS.seconds = 1.0
 t1_4 = @benchmark begin
     HR = 0.01
     shift = (2.0 * HR)
-    modes = [Mode(180., shift)]
+    modes = [Mode(180.0, shift)]
     mols = [
-        Molecule([Mode(300., shift)], 7, [12500., 12710.]),
-        Molecule([Mode(300., shift)], 7, [12500., 12690.])
+        Molecule([Mode(300.0, shift)], 7, [12500.0, 12710.0]),
+        Molecule([Mode(300.0, shift)], 7, [12500.0, 12690.0]),
     ]
 
     agg = Aggregate(mols)
 end
 HR = 0.01
 shift = (2.0 * HR)
-modes = [Mode(180., shift)]
+modes = [Mode(180.0, shift)]
 mols = [
-    Molecule([Mode(300., shift)], 7, [12500., 12710.]),
-    Molecule([Mode(300., shift)], 7, [12500., 12690.])
+    Molecule([Mode(300.0, shift)], 7, [12500.0, 12710.0]),
+    Molecule([Mode(300.0, shift)], 7, [12500.0, 12690.0]),
 ]
 
 agg = Aggregate(mols)
-for mol_i in 2:length(agg.molecules)
+for mol_i = 2:length(agg.molecules)
     agg.coupling[mol_i, mol_i+1] = 200
     agg.coupling[mol_i+1, mol_i] = 200
 end
@@ -152,57 +152,57 @@ aggIndLen = length(aggIndices)
 base = GenericBasis([aggIndLen])
 
 ### getFranckCondonFactors
-BenchmarkTools.DEFAULT_PARAMETERS.seconds = 10.
+BenchmarkTools.DEFAULT_PARAMETERS.seconds = 10.0
 t1_5 = @benchmark begin
     FCFact = getFranckCondonFactors(agg, aggIndices)
 end
 FCFact = getFranckCondonFactors(agg, aggIndices)
 
 ### getFCProd
-BenchmarkTools.DEFAULT_PARAMETERS.seconds = 100.
+BenchmarkTools.DEFAULT_PARAMETERS.seconds = 100.0
 t1_6 = @benchmark begin
     FCProd = getFCProd(agg, FCFact, aggIndices, vibindices)
 end
 FCProd = getFCProd(agg, FCFact, aggIndices, vibindices)
 
 ### getFCProd
-BenchmarkTools.DEFAULT_PARAMETERS.seconds = 10.
+BenchmarkTools.DEFAULT_PARAMETERS.seconds = 10.0
 t1_7 = @benchmark begin
     Ham = getAggHamiltonian(agg, aggIndices, FCFact)
 end
 Ham = getAggHamiltonian(agg, aggIndices, FCFact)
 Ham_bath = getAggHamiltonianBath(agg)
-Ham_sys = getAggHamiltonianSystem(agg; groundEnergy=false)
+Ham_sys = getAggHamiltonianSystem(agg; groundEnergy = false)
 b = GenericBasis([aggIndLen])
 b_sys = GenericBasis([size(Ham_sys, 1)])
 b_bath = GenericBasis([size(Ham_bath, 1)])
 
 ### getAggHamiltonianInteraction
-BenchmarkTools.DEFAULT_PARAMETERS.seconds = 10.
+BenchmarkTools.DEFAULT_PARAMETERS.seconds = 10.0
 t1_8 = @benchmark begin
     Ham_int = getAggHamiltonianInteraction(agg, aggIndices, FCFact)
 end
 
 dic_commit["agg_dimer_small"] = t1_1.times # 27
 dic_commit["agg_dimer_medium"] = t1_2.times # 147
-dic_commit["agg_building"] = t1_4.times 
-dic_commit["getFranckCondonFactors"] = t1_5.times 
+dic_commit["agg_building"] = t1_4.times
+dic_commit["getFranckCondonFactors"] = t1_5.times
 dic_commit["getFCProd"] = t1_6.times
-dic_commit["getAggHamiltonian"] = t1_7.times  
-dic_commit["getAggHamiltonianInteraction"] = t1_8.times  
+dic_commit["getAggHamiltonian"] = t1_7.times
+dic_commit["getAggHamiltonianInteraction"] = t1_8.times
 
 
 ## Simulations
 HR = 0.01
 shift = (2.0 * HR)
-modes = [Mode(180., shift)]
+modes = [Mode(180.0, shift)]
 mols = [
-    Molecule([Mode(300., shift)], 3, [12500., 12710.]),
-    Molecule([Mode(300., shift)], 3, [12500., 12690.])
+    Molecule([Mode(300.0, shift)], 3, [12500.0, 12710.0]),
+    Molecule([Mode(300.0, shift)], 3, [12500.0, 12690.0]),
 ]
 
 agg = Aggregate(mols)
-for mol_i in 2:length(agg.molecules)
+for mol_i = 2:length(agg.molecules)
     agg.coupling[mol_i, mol_i+1] = 200
     agg.coupling[mol_i+1, mol_i] = 200
 end
@@ -217,7 +217,7 @@ Ham = getAggHamiltonian(agg, aggIndices, FCFact)
 basis = GenericBasis([length(aggIndices)])
 
 Ham_bath = getAggHamiltonianBath(agg)
-Ham_sys = getAggHamiltonianSystem(agg; groundEnergy=false)
+Ham_sys = getAggHamiltonianSystem(agg; groundEnergy = false)
 b = GenericBasis([aggIndLen])
 b_sys = GenericBasis([size(Ham_sys, 1)])
 b_bath = GenericBasis([size(Ham_bath, 1)])
@@ -237,15 +237,15 @@ H_lambda = diagm(H_lambda)
 
 t_max = 0.01
 t_count = 200
-t0 = 0.
+t0 = 0.0
 t_step = (t_max - t0) / (t_count)
 tspan = [t0:t_step:t_max;]
 T = 300
 mu_array = [[2, 1]]
 W0_1 = thermal_state(T, mu_array, Ham, vibindices, aggIndices; diagonalize = false)
 mu_array = [[1, 2]]
 W0_2 = thermal_state(T, mu_array, Ham, vibindices, aggIndices; diagonalize = false)
-W0 = 0.8*W0_1 + 0.2*W0_2
+W0 = 0.8 * W0_1 + 0.2 * W0_2
 W0 = DenseOperator(W0.basis_l, W0.basis_r, complex(W0.data))
 W0_bath = get_rho_bath(W0, agg, FCProd, aggIndices, vibindices)
 W0_bath = DenseOperator(W0_bath.basis_l, W0_bath.basis_r, complex(W0_bath.data))
@@ -258,19 +258,19 @@ t2_0 = @benchmark begin
 end
 
 ### evolutionExact
-BenchmarkTools.DEFAULT_PARAMETERS.seconds = 10.
+BenchmarkTools.DEFAULT_PARAMETERS.seconds = 10.0
 t2_1 = @benchmark begin
     op_array = evolutionExact(W0, tspan, Ham)
 end
 
 ### evolutionApproximate
-BenchmarkTools.DEFAULT_PARAMETERS.seconds = 2.
+BenchmarkTools.DEFAULT_PARAMETERS.seconds = 2.0
 t2_2 = @benchmark begin
     op_array = evolutionApproximate(W0, tspan, Ham)
 end
 
 ### schroedinger
-BenchmarkTools.DEFAULT_PARAMETERS.seconds = 1.
+BenchmarkTools.DEFAULT_PARAMETERS.seconds = 1.0
 psi0 = randstate(basis)
 t2_3 = @benchmark begin
     Tspan, psi_t = schroedinger(
@@ -284,7 +284,7 @@ t2_3 = @benchmark begin
 end
 
 ### schroedinger
-BenchmarkTools.DEFAULT_PARAMETERS.seconds = 10.
+BenchmarkTools.DEFAULT_PARAMETERS.seconds = 10.0
 t2_4 = @benchmark begin
     Tspan, rho_t = liouvilleVonNeumann(
         W0,
@@ -297,12 +297,14 @@ t2_4 = @benchmark begin
 end
 
 ### evolutionOperatorIterator
-BenchmarkTools.DEFAULT_PARAMETERS.seconds = 10.
+BenchmarkTools.DEFAULT_PARAMETERS.seconds = 10.0
 elLen = length(agg.molecules)
-rho_t_exact = zeros(ComplexF64, length(tspan), elLen+1, elLen+1)
+rho_t_exact = zeros(ComplexF64, length(tspan), elLen + 1, elLen + 1)
 t2_5 = @benchmark begin
     t_i = 0
-    foreach(evolutionOperatorIterator(Ham, tspan; diagonalize = false, approximate=true)) do U_op
+    foreach(
+        evolutionOperatorIterator(Ham, tspan; diagonalize = false, approximate = true),
+    ) do U_op
         t_i = t_i + 1
         # println(t_i / 150. * 100)
         W = U_op * W0 * U_op'
@@ -312,8 +314,21 @@ t2_5 = @benchmark begin
 end
 
 ### master_int
-BenchmarkTools.DEFAULT_PARAMETERS.seconds = 20.
-p = (Ham_S, Ham_int, H_lambda, H_S, H_Sinv, W0, W0_bath, agg, FCProd, aggIndices, vibindices, ComplexF64)
+BenchmarkTools.DEFAULT_PARAMETERS.seconds = 20.0
+p = (
+    Ham_S,
+    Ham_int,
+    H_lambda,
+    H_S,
+    H_Sinv,
+    W0,
+    W0_bath,
+    agg,
+    FCProd,
+    aggIndices,
+    vibindices,
+    ComplexF64,
+)
 t2_6 = @benchmark begin
     Tspan, W_t_master_int = master_int(
         W0,
@@ -322,12 +337,12 @@ t2_6 = @benchmark begin
         Ham_int;
         reltol = 1.0e-4,
         abstol = 1.0e-4,
-        alg = DelayDiffEq.MethodOfSteps(DelayDiffEq.Tsit5())
+        alg = DelayDiffEq.MethodOfSteps(DelayDiffEq.Tsit5()),
     )
 
     elLen = length(agg.molecules)
-    rho_t_master = zeros(ComplexF64, length(tspan), elLen+1, elLen+1)
-    for t_i in 1:length(tspan)
+    rho_t_master = zeros(ComplexF64, length(tspan), elLen + 1, elLen + 1)
+    for t_i = 1:length(tspan)
         t = tspan[t_i]
         U_op_S = evolutionOperator(Ham_sys, t)
         rho = trace_bath(W_t_master_int[t_i], agg, FCProd, aggIndices, vibindices)
@@ -337,40 +352,54 @@ t2_6 = @benchmark begin
 end
 
 ### evolutionOperatorIterator
-BenchmarkTools.DEFAULT_PARAMETERS.seconds = 20.
-p = (Ham_S, Ham_int, H_lambda, H_S, H_Sinv, Ham_B, W0, W0_bath, agg, FCProd, aggIndices, vibindices, ComplexF64)
+BenchmarkTools.DEFAULT_PARAMETERS.seconds = 20.0
+p = (
+    Ham_S,
+    Ham_int,
+    H_lambda,
+    H_S,
+    H_Sinv,
+    Ham_B,
+    W0,
+    W0_bath,
+    agg,
+    FCProd,
+    aggIndices,
+    vibindices,
+    ComplexF64,
+)
 t2_7 = @benchmark begin
     Tspan, rho_t_ansatz_int = master_ansatz(
         rho0,
         tspan,
         p;
         reltol = 1.0e-4,
         abstol = 1.0e-4,
-        alg = DelayDiffEq.MethodOfSteps(DelayDiffEq.Tsit5())
+        alg = DelayDiffEq.MethodOfSteps(DelayDiffEq.Tsit5()),
     )
-    
+
     elLen = length(agg.molecules)
-    rho_t_ansatz = zeros(ComplexF64, length(tspan), elLen+1, elLen+1)
-    for t_i in 1:length(tspan)
+    rho_t_ansatz = zeros(ComplexF64, length(tspan), elLen + 1, elLen + 1)
+    for t_i = 1:length(tspan)
         t = tspan[t_i]
         U_op_S = evolutionOperator(Ham_sys, t)
         rho = U_op_S * rho_t_ansatz_int[t_i] * U_op_S'
         rho_t_ansatz[t_i, :, :] = rho.data
     end
 end
 
-dic_commit["trace_bath"] = t2_0.times 
-dic_commit["evolutionExact"] = t2_1.times 
-dic_commit["evolutionApproximate"] = t2_2.times 
-dic_commit["schroedinger"] = t2_3.times 
-dic_commit["liouvilleVonNeumann"] = t2_4.times 
-dic_commit["evolutionOperatorIterator"] = t2_5.times 
-dic_commit["master_int"] = t2_6.times 
-dic_commit["master_ansatz"] = t2_7.times 
+dic_commit["trace_bath"] = t2_0.times
+dic_commit["evolutionExact"] = t2_1.times
+dic_commit["evolutionApproximate"] = t2_2.times
+dic_commit["schroedinger"] = t2_3.times
+dic_commit["liouvilleVonNeumann"] = t2_4.times
+dic_commit["evolutionOperatorIterator"] = t2_5.times
+dic_commit["master_int"] = t2_6.times
+dic_commit["master_ansatz"] = t2_7.times
 
 dic_commits[commit_hash] = dic_commit
 json_string = JSON.json(dic_commits)
 
-open("benchmark/benchmark_commits.json","w") do f 
-    write(f, json_string) 
-end
+open("benchmark/benchmark_commits.json", "w") do f
+    write(f, json_string)
+end

docs/make.jl

@@ -16,9 +16,7 @@ makedocs(
     pages = [
         "Home" => "index.md",
         "Documentation" => "documentation.md",
-        "Tutorials" => [
-            "Dimer" => "tutorials/dimer.md"
-            ]
+        "Tutorials" => ["Dimer" => "tutorials/dimer.md"],
     ],
 )