github pages v0.1

docs/_config.yml

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+theme: jekyll-theme-minimal

docs/make.jl

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+using Documenter
+#include("../src/QSWalk.jl")
+using QSWalk
+
+# same for contributing and license
+cp(normpath(@__FILE__, "../../LICENSE"), normpath(@__FILE__, "../src/license.md"); force=true)
+
+
+
+makedocs(
+    modules     = [QSWalk],
+    format      = :html,
+    sitename    = "QSWalk",
+    clean       = true,
+    doctest     = true,
+    checkdocs   = :exports,
+    assets 	= ["assets/logo.ico"],
+    pages       = Any[
+		"Home"				=> "index.md",
+        "GKSL master equation" => "gksl.md",
+    	"Demoralization"   => "demoralization.md",
+        "Contributing"		=> "contributing.md",
+        "Citing"	       	=> "citing.md",
+		"Licence"			=> "license.md",
+    ]
+)
+
+deploydocs(
+    deps        = nothing,
+    make        = nothing,
+    repo        = "github.com/QuantumWalks/QSWalk.jl",
+    target      = "build",
+    julia       = "0.6",
+    osname      = "linux"
+)
+
+
+#rm(normpath(@__FILE__, "src/license.md"))

docs/src/citing.md

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+## Usage and citing
+
+
+In case of citing, please use the following BibTeX form:
+
+```tex
+@article{glos2018qswalk,
+  title={QSWalk. jl: Julia package for quantum stochastic walks analysis},
+  author={Glos, Adam and Miszczak, Jaros{\l}aw Adam and Ostaszewski, Mateusz},
+  journal={arXiv preprint arXiv:1801.01294},
+  year={2018}
+}
+```
+
+Our package was already used in papers concerning quantum attacks
+* Adam Glos, Jarosław Adam Miszczak, and Mateusz Ostaszewski. 'Limiting properties of stochastic quantum walks on directed graphs.' Journal of Physics A: Mathematical and Theoretical 51.3 (2017): 035304.
+* Krzysztof Domino, Adam Glos, and Mateusz Ostaszewski. 'Superdiffusive quantum stochastic walk definable on arbitrary directed graph'. Quantum Information & Computation, 17(11-12), 973-986.
+
+In case You have used our package for your research, we will be grateful for any information about the paper or the package. With your consent we will provide a link to the paper here.

docs/src/contributing.md

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+## Bugs
+
+In the case, you noticed some bugs, please start with an issue with a minimal
+working example of not-working code. If *Exception* is thrown, please provide an
+exception message as well.  If no *Exception* is thrown, but the result is
+wrong, please provide in the issue message correct answer.
+
+In the case you make a pull request, please add a not-working example as a test.
+
+## Improvements
+
+If you can provide a code, which works faster than already existing, please
+check its efficiency for various input data. 
+
+We welcome any ideas concerning the readability and logic of the code as well.
+
+## Development guidelines
+* Post an issue.
+* Wait until the discussion ends.
+* Create assertions on argument types and other requirements.
+* Include necessary references.
+* Write tests.

docs/src/demoralization.md

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+```@meta
+DocTestSetup = quote
+   using QSWalk
+end
+```
+
+## Nonmoralizing model
+
+Global interaction quantum stochastic walk suffers for creating additional connections. For
+removing such effect, nonmoralizing quantum stochastic walk was introduced, see [here](http://www.rintonpress.com/journals/qiconline.html#v17n1112).
+Such model is constructed in several steps. First, the dimensionality is increased, hence to each
+vertex multidimensional subspaces is attached. Then, Hamiltonian and Lindblad
+operator is increased, furthermore additional Hamiltonian called "local Hamiltonian".
+is introduced.
+
+Below we present additional functionalities typical for nonmoralizing quantum
+stochastic walk. By default the the operator is generalized as in the original [paper](http://www.rintonpress.com/journals/qiconline.html#v17n1112).
+
+```@index
+Order = [:type, :function]
+Modules = [QSWalk]
+Pages   = ["demoralization.md"]
+```
+
+## Full docs
+
+```@docs
+Vertex
+VertexSet
+nm_measurement
+nm_loc_ham
+nm_init
+default_nm_loc_ham
+make_vertex_set
+vlist
+subspace
+fourier_matrix
+vertexsetsize
+```

docs/src/gksl.md

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+```@meta
+DocTestSetup = quote
+   using QSWalk
+end
+```
+
+## GKSL master equation
+
+GKSL master equation is general continuous-time open quantum evolution. The master equation base on to form of operators: the Hamiltonian, which describes the evolution of closed system, and the Lindbladian operators which describes the evolution of open system. Basic facts in context of quantum stochastic walks can found [here](https://journals.aps.org/pra/abstract/10.1103/PhysRevA.81.022323). For local interaction, where each Lindblad operator is a matrix with single nonzero element, we created a `local_lind` function which splits matrix into mentioned operators.
+
+Below we present a documentation of basic function used for simulating GKSL master equation.
+
+```@index
+Order = [:type, :function]
+Modules = [QSWalk]
+Pages   = ["gksl.md"]
+```
+
+## Full docs
+
+```@docs
+ket
+bra
+ketbra
+proj
+res
+unres
+evolve_generator(::AbstractMatrix{<:Number}, ::AbstractVector{<:AbstractMatrix{<:Number}}, ::AbstractMatrix{<:Number}, ::Real)
+evolve_operator
+evolve(::AbstractMatrix{<:Number}, ::AbstractMatrix{<:Number})
+local_lind
+```

docs/src/index.md

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+## Welcome to QSWalk.jl
+
+*QSWalk.jl* is a package providing implementation of open continuous-time quantum walk evolution based on GKSL master equation. In particular we have implemented function useful for analysing local interaction, global interaction and nonmoralizing global interaction stochastic quantum walk models.
+
+In GitHub we present an [examples](https://github.com/QuantumWalks/QSWalk.jl/) in .ipynb and .jl extension. The present most of the functionalities of the package. Furthermore, for package explanation we refer the user to our [paper](https://arxiv.org/abs/1801.01294) describing the package, and
+for the basic papers describing and introducing quantum stochastic models:
+* [Quantum stochastic walks: A generalization of classical random walks and quantum walks](https://journals.aps.org/pra/abstract/10.1103/PhysRevA.81.022323) by Whitfield, Rodríguez-Rosario, and Aspuru-Guzik,
+* [Superdiffusive quantum stochastic walk definable on arbitrary directed graph](http://www.rintonpress.com/journals/qiconline.html#v17n1112) by Domino, Glos, and Ostaszewski,
+* [Properties of quantum stochastic walks from the asymptotic scaling exponent](http://www.rintonpress.com/journals/qiconline.html#v18n34) by Domino, Glos, Ostaszewski, Pawela, and Sadowski.

docs/src/license.md

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+MIT License
+
+Copyright (c) 2017-2018 Adam Glos, Jarosław Adam Miszczak, Mateusz Ostaszewski
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

examples/ex01_path_propagation.jl

@@ -8,7 +8,6 @@
 using QSWalk
 using PyPlot # for plot
 using LightGraphs # for PathGraph
-using LinearAlgebra
 
 
 # ## Evolution on path graph for fixed time, global vs local interaction
@@ -38,7 +37,7 @@ rho_local = evolve(op_local, proj(midpoint, dim), timepoint);
 
 # To plot the result of the cannonical measurement, we take a diagonal of the states. Note that both *rhoglobal* and *rholocal* are complex matrices, hence we need to take the real part only. Argument *positions* is generated assuming that *midpoint* (the initial position) is at 0. Note that we have very heavy tails in the global interaction case, which confirms fast propagation in this model.
 
-positions = (collect(1:dim) .- midpoint)
+positions = (collect(1:dim) - midpoint)
 plot(positions, real.(diag(rho_local)), "k")
 plot(positions, real.(diag(rho_global)), "b")
 xlabel("position")
@@ -75,7 +74,7 @@ local_states = evolve(op_local, proj(midpoint, dim), timepoints);
 
 secmoment_global = Float64[]
 secmoment_local = Float64[]
-positions = (collect(1:dim) .- midpoint)
+positions = (collect(1:dim) - midpoint)
 
 for (rho_global, rho_local) = zip(global_states, local_states)
   push!(secmoment_global, sum(positions.^2 .* diag(rho_global)))
@@ -90,4 +89,3 @@ plot(timepoints, secmoment_global, "b")
 xlabel("t")
 ylabel(L"\mu_2")
 show()
-