Fix compilation errors and add experimental batch support (#3)

* Add the cases for dispatching of cached networks depending on inputs, and for batched too.
Add new preallocated outputs for batched variantts

* BatchAccumulators

* Add NDMBatched

* fix import orders

* Add KLocal Tensor Operators

* Experimental SuperOperator problem

* chain length

* UnsafeArrays for manipulations

* Batched evaluate

* Plug points for Neural gpu

* Remove cuarrays

* Fix ambiguities in state generation batch

* Improve type stability and remove allocations

* Type stability for operator hamiltonian problem

* Fix optimisers behaviour

* When building batched derivative cache, don't reshape if not needed.

* Improve batched calculator

* v0.1.2

* update manifest

* Update test configuration

* backports

* fix travis

.github/workflows/Julia-tests.yml

@@ -7,20 +7,19 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        julia-version: [1.2.0, 1.3.0-rc3]
+        julia-version: [1.2, 1.3]
         os: [ubuntu-latest, macOS-latest]
 
     steps:
       - uses: actions/[email protected]
       - name: "Setup Julia environment ${{ matrix.julia-version }}"
-        uses: julia-actions/setup-julia@v0.2
+        uses: julia-actions/setup-julia@v1.0.1
         with:
           version: ${{ matrix.julia-version }}
       - name: "Run Tests"
         run: |
             julia --color=yes --project=@. -e 'using Pkg;
                             Pkg.activate();
                             Pkg.instantiate();
-                            Pkg.add(PackageSpec(url="https://github.com/PhilipVinc/QuantumLattices.jl"));
                             println("Instantiated");'
             julia --color=yes --project=@. -e "using Pkg; Pkg.test(coverage=true)"

.travis.yml

@@ -8,19 +8,16 @@ julia:
     - nightly
 matrix:
     allow_failures:
-        - julia: [1.3, nightly]
-        - os: osx
+        - julia: [nightly]
 notifications:
     email: false
 script:
     - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
     - travis_wait 20 julia --project=@. --color=yes -e 'using Pkg;
                             Pkg.activate();
-                            println("Instantiated");
+                            println("Activate");
                             Pkg.instantiate();
-                            Pkg.add(PackageSpec(url="https://github.com/PhilipVinc/QuantumLattices.jl"));
-                            println("Installed [QuantumLattices, Zygote]");
-                            println("Developed");
+                            println("Instantiate");                            
                             Pkg.test(coverage=true)';
 after_success:
     - julia -e 'using Pkg; cd(Pkg.dir("NeuralQuantum")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
@@ -32,7 +29,7 @@ jobs:
       os: linux
       script:
         - julia --project=docs/ -e 'using Pkg;
-                                    Pkg.add([PackageSpec(url="https://github.com/PhilipVinc/QuantumLattices.jl")]);
+                                    Pkg.activate();
                                     Pkg.add("Documenter");
                                     Pkg.develop(PackageSpec(path=pwd()));
                                     Pkg.instantiate()'

Manifest.toml

@@ -2,9 +2,9 @@
 
 [[AbstractFFTs]]
 deps = ["LinearAlgebra"]
-git-tree-sha1 = "380e36c66edfa099cd90116b24c1ce8cafccac40"
+git-tree-sha1 = "051c95d6836228d120f5f4b984dd5aba1624f716"
 uuid = "621f4979-c628-5d54-868e-fcf4e3e8185c"
-version = "0.4.1"
+version = "0.5.0"
 
 [[Adapt]]
 deps = ["LinearAlgebra"]
@@ -28,16 +28,10 @@ uuid = "9e28174c-4ba2-5203-b857-d8d62c4213ee"
 version = "0.8.10"
 
 [[BinaryProvider]]
-deps = ["Libdl", "Logging", "SHA"]
-git-tree-sha1 = "c7361ce8a2129f20b0e05a89f7070820cfed6648"
+deps = ["Libdl", "SHA"]
+git-tree-sha1 = "5b08ed6036d9d3f0ee6369410b830f8873d4024c"
 uuid = "b99e7846-7c00-51b0-8f62-c81ae34c0232"
-version = "0.5.6"
-
-[[CSTParser]]
-deps = ["Tokenize"]
-git-tree-sha1 = "c69698c3d4a7255bc1b4bc2afc09f59db910243b"
-uuid = "00ebfdb7-1f24-5e51-bd34-a7502290713f"
-version = "0.6.2"
+version = "0.5.8"
 
 [[CommonSubexpressions]]
 deps = ["Test"]
@@ -47,27 +41,21 @@ version = "0.2.0"
 
 [[Compat]]
 deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
-git-tree-sha1 = "84aa74986c5b9b898b0d1acaf3258741ee64754f"
+git-tree-sha1 = "ed2c4abadf84c53d9e58510b5fc48912c2336fbb"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "2.1.0"
+version = "2.2.0"
 
 [[Conda]]
 deps = ["JSON", "VersionParsing"]
 git-tree-sha1 = "9a11d428dcdc425072af4aea19ab1e8c3e01c032"
 uuid = "8f4d0f93-b110-5947-807f-2305c1781a2d"
 version = "1.3.0"
 
-[[Crayons]]
-deps = ["Test"]
-git-tree-sha1 = "f621b8ef51fd2004c7cf157ea47f027fdeac5523"
-uuid = "a8cc5b0e-0ffa-5ad4-8c14-923d3ee1735f"
-version = "4.0.0"
-
 [[DataStructures]]
 deps = ["InteractiveUtils", "OrderedCollections"]
-git-tree-sha1 = "517ce30aa57cdfae1ab444a7c0aef8bb86345bc2"
+git-tree-sha1 = "a1b652fb77ae8ca7ea328fa7ba5aa151036e5c10"
 uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
-version = "0.17.1"
+version = "0.17.6"
 
 [[Dates]]
 deps = ["Printf"]
@@ -84,40 +72,50 @@ uuid = "163ba53b-c6d8-5494-b064-1a9d43ac40c5"
 version = "0.0.4"
 
 [[DiffRules]]
-deps = ["Random", "Test"]
-git-tree-sha1 = "dc0869fb2f5b23466b32ea799bd82c76480167f7"
+deps = ["NaNMath", "Random", "SpecialFunctions"]
+git-tree-sha1 = "f734b5f6bc9c909027ef99f6d91d5d9e4b111eed"
 uuid = "b552c78f-8df3-52c6-915a-8e097449b14b"
-version = "0.0.10"
+version = "0.1.0"
 
 [[Distributed]]
 deps = ["Random", "Serialization", "Sockets"]
 uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
+[[DocStringExtensions]]
+deps = ["LibGit2", "Markdown", "Pkg", "Test"]
+git-tree-sha1 = "88bb0edb352b16608036faadcc071adda068582a"
+uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
+version = "0.8.1"
+
+[[Documenter]]
+deps = ["Base64", "Dates", "DocStringExtensions", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "REPL", "Test", "Unicode"]
+git-tree-sha1 = "0be9bf63e854a2408c2ecd3c600d68d4d87d8a73"
+uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+version = "0.24.2"
+
 [[FFTW]]
-deps = ["AbstractFFTs", "BinaryProvider", "Conda", "Libdl", "LinearAlgebra", "Reexport", "Test"]
-git-tree-sha1 = "6c5b420da0b8c12098048561b8d58f81adea506f"
+deps = ["AbstractFFTs", "BinaryProvider", "Conda", "Libdl", "LinearAlgebra", "Reexport"]
+git-tree-sha1 = "4cfd3d43819228b9e73ab46600d0af0aa5cedceb"
 uuid = "7a1cc6ca-52ef-59f5-83cd-3a7055c09341"
-version = "1.0.1"
+version = "1.1.0"
 
 [[FillArrays]]
 deps = ["LinearAlgebra", "Random", "SparseArrays"]
-git-tree-sha1 = "16974065d5bfa867446d3228bc63f05a440e910b"
+git-tree-sha1 = "1a9fe4e1323f38de0ba4da49eafd15b25ec62298"
 uuid = "1a297f60-69ca-5386-bcde-b61e274b549b"
-version = "0.7.2"
+version = "0.8.2"
 
 [[ForwardDiff]]
-deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "InteractiveUtils", "LinearAlgebra", "NaNMath", "Random", "SparseArrays", "SpecialFunctions", "StaticArrays", "Test"]
-git-tree-sha1 = "4c4d727f1b7e0092134fabfab6396b8945c1ea5b"
+deps = ["CommonSubexpressions", "DiffResults", "DiffRules", "NaNMath", "Random", "SpecialFunctions", "StaticArrays"]
+git-tree-sha1 = "da46ac97b17793eba44ff366dc6cb70f1238a738"
 uuid = "f6369f11-7733-5829-9624-2563aa707210"
-version = "0.10.3"
+version = "0.10.7"
 
 [[IRTools]]
 deps = ["InteractiveUtils", "MacroTools", "Test"]
-git-tree-sha1 = "5bdac064676287838868e3715d44d1129d8f2d26"
-repo-rev = "master"
-repo-url = "https://github.com/MikeInnes/IRTools.jl.git"
+git-tree-sha1 = "72421971e60917b8cd7737f9577c4f0f87eab306"
 uuid = "7869d1d1-7146-5819-86e3-90919afe41df"
-version = "0.2.3"
+version = "0.3.0"
 
 [[Inflate]]
 deps = ["Pkg", "Printf", "Random", "Test"]
@@ -161,10 +159,10 @@ uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
 [[MacroTools]]
-deps = ["CSTParser", "Compat", "DataStructures", "Test", "Tokenize"]
-git-tree-sha1 = "d6e9dedb8c92c3465575442da456aec15a89ff76"
+deps = ["Compat", "DataStructures", "Test"]
+git-tree-sha1 = "82921f0e3bde6aebb8e524efc20f4042373c0c06"
 uuid = "1914dd2f-81c6-5fcd-8719-6d5c9610ff09"
-version = "0.5.1"
+version = "0.5.2"
 
 [[Markdown]]
 deps = ["Base64"]
@@ -180,10 +178,9 @@ uuid = "872c559c-99b0-510c-b3b7-b6c96a88d5cd"
 version = "0.6.0"
 
 [[NaNMath]]
-deps = ["Compat"]
-git-tree-sha1 = "ce3b85e484a5d4c71dd5316215069311135fa9f2"
+git-tree-sha1 = "928b8ca9b2791081dc71a51c55347c27c618760f"
 uuid = "77ba4419-2d1f-58cd-9bb1-8ffee604a2e3"
-version = "0.3.2"
+version = "0.3.3"
 
 [[OrderedCollections]]
 deps = ["Random", "Serialization", "Test"]
@@ -193,9 +190,9 @@ version = "1.1.0"
 
 [[Parsers]]
 deps = ["Dates", "Test"]
-git-tree-sha1 = "ef0af6c8601db18c282d092ccbd2f01f3f0cd70b"
+git-tree-sha1 = "0139ba59ce9bc680e2925aec5b7db79065d60556"
 uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
-version = "0.3.7"
+version = "0.3.10"
 
 [[Pkg]]
 deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
@@ -275,9 +272,9 @@ version = "0.8.0"
 
 [[StaticArrays]]
 deps = ["LinearAlgebra", "Random", "Statistics"]
-git-tree-sha1 = "db23bbf50064c582b6f2b9b043c8e7e98ea8c0c6"
+git-tree-sha1 = "5a3bcb6233adabde68ebc97be66e95dcb787424c"
 uuid = "90137ffa-7385-5640-81b9-e52037218182"
-version = "0.11.0"
+version = "0.12.1"
 
 [[Statistics]]
 deps = ["LinearAlgebra", "SparseArrays"]
@@ -294,21 +291,15 @@ deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[TimerOutputs]]
-deps = ["Crayons", "Printf", "Test", "Unicode"]
-git-tree-sha1 = "b80671c06f8f8bae08c55d67b5ce292c5ae2660c"
+deps = ["Printf"]
+git-tree-sha1 = "311765af81bbb48d7bad01fb016d9c328c6ede03"
 uuid = "a759f4b9-e2f1-59dc-863e-4aeb61b1ea8f"
-version = "0.5.0"
-
-[[Tokenize]]
-git-tree-sha1 = "dfcdbbfb2d0370716c815cbd6f8a364efb6f42cf"
-uuid = "0796e94c-ce3b-5d07-9a54-7f471281c624"
-version = "0.5.6"
+version = "0.5.3"
 
 [[TupleTools]]
-deps = ["Random", "Test"]
-git-tree-sha1 = "b006524003142128cc6d36189dce337729aa0050"
+git-tree-sha1 = "62a7a6cd5a608ff71cecfdb612e67a0897836069"
 uuid = "9d95972d-f1c8-5527-a6e0-b4b365fa01f6"
-version = "1.1.0"
+version = "1.2.0"
 
 [[URIParser]]
 deps = ["Test", "Unicode"]
@@ -323,6 +314,11 @@ uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 [[Unicode]]
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 
+[[UnsafeArrays]]
+git-tree-sha1 = "1de6ef280110c7ad3c5d2f7a31a360b57a1bde21"
+uuid = "c4a57d5a-5b31-53a6-b365-19f8c011fbd6"
+version = "1.0.0"
+
 [[VersionParsing]]
 deps = ["Compat"]
 git-tree-sha1 = "c9d5aa108588b978bd859554660c8a5c4f2f7669"
@@ -331,16 +327,12 @@ version = "1.1.3"
 
 [[Zygote]]
 deps = ["DiffRules", "FFTW", "FillArrays", "ForwardDiff", "IRTools", "InteractiveUtils", "LinearAlgebra", "MacroTools", "NNlib", "NaNMath", "Random", "Requires", "SpecialFunctions", "Statistics", "ZygoteRules"]
-git-tree-sha1 = "bc6f84f1ac81f1d1548264dc0c1816252e1c62ef"
-repo-rev = "master"
-repo-url = "https://github.com/FluxML/Zygote.jl.git"
+git-tree-sha1 = "e4245b9c5362346e154b62842a89a18e0210b92b"
 uuid = "e88e6eb3-aa80-5325-afca-941959d7151f"
-version = "0.3.4"
+version = "0.4.1"
 
 [[ZygoteRules]]
 deps = ["MacroTools"]
-git-tree-sha1 = "c4c29b30b8ff3be13d4244e78be7df2a42bc54d0"
-repo-rev = "master"
-repo-url = "https://github.com/FluxML/ZygoteRules.jl.git"
+git-tree-sha1 = "b3b4882cc9accf6731a08cc39543fbc6b669dca8"
 uuid = "700de1a5-db45-46bc-99cf-38207098b444"
 version = "0.2.0"

Project.toml

@@ -1,11 +1,10 @@
 name = "NeuralQuantum"
 uuid = "eb923273-1014-53d4-802c-abcb7262255a"
 authors = ["Filippo Vicentini <[email protected]>"]
-version = "0.1.1"
+version = "0.1.2"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"
-IRTools = "7869d1d1-7146-5819-86e3-90919afe41df"
 IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153"
 LightGraphs = "093fc24a-ae57-5d10-9952-331d41423f4d"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
@@ -20,14 +19,16 @@ Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 Strided = "5e0ebb24-38b0-5f93-81fe-25c709ecae67"
+UnsafeArrays = "c4a57d5a-5b31-53a6-b365-19f8c011fbd6"
 Zygote = "e88e6eb3-aa80-5325-afca-941959d7151f"
-ZygoteRules = "700de1a5-db45-46bc-99cf-38207098b444"
 
 [compat]
+Zygote = ">= 0.4"
 julia = ">= 1.2"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 
 [targets]
 test = ["Test"]

README.md

@@ -18,14 +18,28 @@ pkg"add https://github.com/PhilipVinc/NeuralQuantum.jl"
 `QuantumLattices` is a custom package that allows defining new types of operators on a lattice.
 It's not needed natively but it is usefull to define hamiltonians on a lattice.
 
+Alternatively you may activate the project included in the manifest that comes with NeuralQuantum.
+
+
 ## Example
+The basic idea of the package is the following: you create an hamiltonian/lindbladian with QuantumOptics or QuantumLattices (the latter allows you to go to arbitrarily big lattices, but isn't yet very documented...).
+Then, you create a `SteadyStateProblem`, which performs some transformations on those operators to put them in the shaped necessary to optimize them efficiently.
+You also will probably need to create an `ObservablesProblem`, by providing it all the observables that you wish to monitor during the optimization.
+
+By default, if you don't provide the precision `Float32` is used.
+
+Then, you will pick a network, a sampler, and create an iterative sampler to sample the network.
+You must write the training loop by yourself. Check the documentation and the examples in the folder `examples/` to better understand how to do this.
+
+*IMPORTANT:* If you want to use multithreaded samplers (identified by a `MT` at the beginning of their name), you will launch one markov chain per julia thread. As such, you will get much better performance if you set `JULIA_NUM_THREADS` environment variable to the number of physical cores in your computer before launching julia. 
+
 ```
 # Load dependencies
 using NeuralQuantum, QuantumLattices
-using Printf, ValueHistoriesLogger, Logging, ValueHistories
+using Printf, Logging, ValueHistories
 
 # Select the numerical precision
-T      = Float64
+T      = Float32
 # Select how many sites you want
 Nsites = 6
 

examples/dissipative_spins_1d.jl

@@ -3,7 +3,7 @@ using NeuralQuantum, QuantumLattices
 using Logging, Printf, ValueHistories
 
 # Select the numerical precision
-T      = Float64
+T      = Float32
 # Select how many sites you want
 Nsites = 7
 
@@ -22,7 +22,7 @@ Sx  = QuantumLattices.LocalObservable(lind, sigmax, Nsites)
 Sy  = QuantumLattices.LocalObservable(lind, sigmay, Nsites)
 Sz  = QuantumLattices.LocalObservable(lind, sigmaz, Nsites)
 # Create the problem object with all the observables to be computed.
-oprob = ObservablesProblem(Sx, Sy, Sz)
+oprob = ObservablesProblem(T, Sx, Sy, Sz)
 
 
 # Define the Neural Network. A NDM with N visible spins and αa=2 and αh=1
@@ -33,7 +33,7 @@ cnet = cached(net)
 # Chose a sampler. Options are FullSumSampler() which sums over the whole space
 # ExactSampler() which does exact sampling or MCMCSamler which does a markov
 # chain.
-sampl = MCMCSampler(Metropolis(Nsites), 3000, burn=50)
+sampl = MCMCSampler(Metropolis(Nsites), 1000, burn=50)
 # Chose a sampler for the observables.
 osampl = FullSumSampler()
 
@@ -69,6 +69,8 @@ for i=1:110
     Optimisers.update!(optimizer, cnet, Δw)
 end
 
+using QuantumOptics, Plots
+
 # Optional: compute the exact solution
 ρ   = last(steadystate.master(lind)[2])
 ESx = real(expect(SparseOperator(Sx), ρ))