From c22024f6aa225756aca7407ac067fd9b483b8571 Mon Sep 17 00:00:00 2001 From: "Documenter.jl" Date: Tue, 25 Jun 2024 17:39:20 -0400 Subject: [PATCH] build based on f090446 --- julia-docs/dev/docstrings.html | 246 +++++++------- julia-docs/dev/medyan-tutorial.zip | Bin 676120 -> 676128 bytes julia-docs/dev/reference/fileformats.html | 68 ++-- julia-docs/dev/search.json | 4 +- julia-docs/dev/sitemap.xml | 264 +++++++-------- julia-docs/dev/tutorials/1install.html | 2 +- julia-docs/dev/tutorials/2rdme.html | 36 +- .../figure-html/cell-14-output-2.svg | 320 +++++++++--------- julia-docs/dev/tutorials/3treadmill.html | 66 ++-- 9 files changed, 503 insertions(+), 503 deletions(-) diff --git a/julia-docs/dev/docstrings.html b/julia-docs/dev/docstrings.html index ab7a208..c515ae0 100644 --- a/julia-docs/dev/docstrings.html +++ b/julia-docs/dev/docstrings.html @@ -298,617 +298,617 @@

Docstrings

- + Base.:* - + Base.copy - + Base.delete! - + Base.empty! - + Base.getindex - + Base.haskey - + Base.iterate - + Base.length - + Base.push! - + Base.setindex! - + MEDYAN.AgentNames - + MEDYAN.Boundary - + MEDYAN.CadherinParams - + MEDYAN.CadherinState - + MEDYAN.Context - + MEDYAN.CubicGrid - + MEDYAN.Decimated2MonSiteMinAngleRange - + MEDYAN.Decimated2MonSiteRange - + MEDYAN.FilamentEndSiteGeneral - + MEDYAN.FilamentSiteGeneral - + MEDYAN.Link2MonParams - + MEDYAN.Link2MonSiteCount - + MEDYAN.Link2MonSiteMonomerStateMatch - + MEDYAN.Link2MonSiteMotorCatch - + MEDYAN.Link2MonSiteMotorStall - + MEDYAN.Link2MonSiteOne - + MEDYAN.Link2MonSiteSlipBond - + MEDYAN.Link2MonState - + MEDYAN.MembraneSiteDiffusing - + MEDYAN.MembraneSpeciesParams - + MEDYAN.MonLink2MonSiteOne - + MEDYAN.MonomerName - + MEDYAN.SysDef - + MEDYAN.VertexName - + MEDYAN.VertexState - + MEDYAN.adapt_membranes! - + MEDYAN.add_decimated_2mon_site! - + MEDYAN.add_diffusion_coeff! - + MEDYAN.add_filament_params! - + MEDYAN.add_link_2mon! - + MEDYAN.add_link_2mon_site! - + MEDYAN.add_membranesitereaction! - + MEDYAN.addcadherin! - + MEDYAN.addcadherinsite! - + MEDYAN.adddiffusingcount_rand! - + MEDYAN.addfilament_reaction! - + MEDYAN.addfilamentend_reaction! - + MEDYAN.addfilamentendsite! - + MEDYAN.addfilamentsite! - + MEDYAN.addmembranediffusingcount_rand! - + MEDYAN.addmembranesite! - + MEDYAN.addpossiblecadherinsite! - + MEDYAN.addreaction! - + MEDYAN.addreactioncallback! - + MEDYAN.addunbindinglink_2mon_site! - + MEDYAN.boundary_box - + MEDYAN.boundary_capsule - + MEDYAN.boundary_cylinder - + MEDYAN.boundary_plane - + MEDYAN.centerof - + MEDYAN.chem_adddiffusingcount! - + MEDYAN.chem_addfixedcount! - + MEDYAN.chem_depolymerize! - + MEDYAN.chem_newfilament! - + MEDYAN.chem_newlink_2mon! - + MEDYAN.chem_polymerize! - + MEDYAN.chem_removefilament! - + MEDYAN.chem_removelink_2mon! - + MEDYAN.chem_setlink_2mon_state! - + MEDYAN.chem_setmonomerstate! - + MEDYAN.compute_all_membrane_geometry!_system - + MEDYAN.defer_chem_caching! - + MEDYAN.fil_mon_states - + MEDYAN.fil_node_mon_ids - + MEDYAN.fil_node_positions - + MEDYAN.fil_num_unmin_ends - + MEDYAN.filter_grididat - + MEDYAN.filtype_fil_ids - + MEDYAN.grididat - + MEDYAN.is_chem_cache_valid - + MEDYAN.link_2mon_endnames - + MEDYAN.link_2mon_state - + MEDYAN.load_snapshot! - + MEDYAN.minimize_energy! - + MEDYAN.mon_3states - + MEDYAN.mon_exists - + MEDYAN.mon_minimized - + MEDYAN.mon_plusvector - + MEDYAN.mon_position - + MEDYAN.mon_position_plusvector - + MEDYAN.newfilament_rand! - + MEDYAN.newmembrane! - + MEDYAN.num_filtypes - + MEDYAN.num_vertexwithstate - + MEDYAN.randompoint - + MEDYAN.refresh_chem_cache! - + MEDYAN.resolve_all_filament_mesh_crossing! - + MEDYAN.run_chemistry! - + MEDYAN.set_chemboundary! - + MEDYAN.set_enable_cylinder_volume_exclusion! - + MEDYAN.set_mechboundary! - + MEDYAN.set_time! - + MEDYAN.sever_filament! - + MEDYAN.vertex_state - + NLSolversBase.value!! - + src/auxprocs.jl - + src/boundary.jl - + src/cadherins/possiblecadherinsite.jl - + src/context.jl - + src/decimated_2mon_sites.jl - + src/filamentendsites.jl - + src/filamentsites.jl - + src/grids.jl - + src/link_2mon_sites.jl - + src/membrane/membranesites.jl - + src/membrane/meshadapt.jl - + src/minimize_energy.jl - + src/mon_link_2mon_sites.jl - + src/sever_filament.jl - + src/sys_def.jl - + src/trajectory-io/snapshot.jl - + src/util/math/cuboidslicing.jl - + src/util/stableindex.jl diff --git a/julia-docs/dev/medyan-tutorial.zip b/julia-docs/dev/medyan-tutorial.zip index 25834916b0b4b76c2ec5b4b7f843775f65408283..584cb8e911b9d332340a2f8936b3020392231657 100644 GIT binary patch delta 28476 zcmV(;K-<5VqA8%FDH~8r0|XQR00;;G001EXZ|r!eAX)$b`2qm|9g~rc6Ok@9e|Mo9 z5FrATG~L!F^Rl}PH>&$*GCdqiXc5IJVkZ33$@GqQZW_nf=_@AKUz{^Or@ z_qf^K|Nj5_{b%Av@EiTv@7~AzO{AyAMfJhJ9^Pp z#Y4-Q=b%DxIXTOHGgcbsed9G2f1XXu>a*Yd?!W)L)Q88L&;R`9#h2T=?XH&ByUqO* z{`UX;&+l$GPwZ(|D|>tw1%0t`I>qLN;K3PuX;DFBCwQ_-ixNd_QTyWaXTN)X-V}Nw 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zpr^DTHKaoe3IO*e{}659$Mhe8f+*-fWgvI)jG!SuI#3ef0#(z&VKx#$%B*mMM?|qNU;;&fu>`DOOoT(LVuC|k zPdX#K5FRsZCdkE#>&);77!_beMgcDBtSNX?V1^^8DnG;g&`~)q9rkuHR*6dr*|31b zKxZY^_JjqL1uj%$g;zB$6+{iUff$99Sm8BRTlbG4wH}V4kPEJNn-#9NydLW=#|A0_ z!3|i^+W=<e=bzOut(`1{}wp@XzJ zKwcy(3J;>-041O@4p10*z=j94E#QhkWSpP~f)`Te1Rapa(*Hm{Xpj>WM?N+DS4nb# zVn_z_e-*?9uc8=efD3d(YB~P{*&$mrD2F`E`&YG~;pxf;{YJx?Hz`Uz51xm@&Vz!; zb0v6CP6I9*WZjBK0nMKW<&jjie9L%2Z(By;P(#y8xcK2oU<53=jS6M>X2 zz};E?^p9eP9$tW>d%69u=l(Vx4b-Cp=L+P3YY5!=zZ!P%Xd!DJxS;pm{}3tEzyl}i z0ujW{2l7FTyr2X;K8C#T2GPlZWplis9AXM$Lo2 zf-w26iggSWgqQm(ZLB!e#;1hV&&-v2XM{O5lmHLf)WiSh-a-zU3BmJ3((r#KUqgH* zXkH#pi;e{WDfCGQo~P3A#x4qSLbrrLQix0#o~+aGe*Q1f1W-5r2olKr1_6Dl2;82j z>lx*T%tYXB4ZCASiwN9dn!8wm7Cp1T8?-1W0L6=fqKIOsRTQ42GJ#l!@IV3zh*k@Z z<*pbU=IbCVZW0480`2gAeO5hLC;=rTD-Jj4`{0alK#dOwSfQdbq6+WUX9V8PSs~MC zg8$y;)S@9nS-4k9(jW?GK@VLZ#q6Bd7l_vMdFP0P=%>h!#LR@<)(B*G33vpik0pPi801um~g| z0|ym3gB4F@Ku)IryjJkPyEuFscb&t!5y^sT!13alxCulZVN>$)h=2}z`a#LTkyo5z zv7$V@5j)F)Qiw??TMqOGNQIyrIZzd{k%wo0k_A?Lm4|olU5H!(zAxSEJY$?txdMDD zFob3l;G-Jnz!~F!S`|Tj$YX#IgcfMvK@3%dTeAN8$EFO>Ok;)T3?V+mcM+agyfc3Y z8N{dpmnyypmpVWH2jfGl7vcM7@sGdA&JRLH$Xy9e)W*gij0d$Ufx3X)um6&B(34+; z#Ag$P95Ve)_}@99^!qR8*x!U?P@OWo6I(*l%J8c82A~;b@B-wa0;&VIkY|D$5++8$ z`@IT0ka~nzqNEC&=ZXH9nIL8jxUn%+xFf-&e=s40R)Y^7k0|~kacb~1B%{HSbv1ag zDAQxbWp#M+957%-sXBaGoM-;GAPb7-tOa<p@bWcE!io`n zIH7^bX92Q6Ey-}^;0Fg@pauFv;C(R-MGvuTz|r+whU=jp{I87|Vl{wATXN|C$Bzu) VV4%hSA0rGwdi"medyan"<

header.json["medyan"] contains static metadata about the simulation that is constant over time.

Example header.json "medyan" value

-
+
using MEDYAN
 import JSON3
 cinit, s = MEDYAN.example_all_sites_context()
@@ -397,7 +397,7 @@ 
Snapshot group

 

 
Snapshot Versioning

 
The snapshot format is versioned by the “version” attribute. The current snapshot version is:

-

+

 
using MEDYAN
 MEDYAN.SNAPSHOT_VERSION

 

@@ -419,7 +419,7 @@ 
“#expe
 

 

 
Example snapshot

-

+

 
using MEDYAN
 using SmallZarrGroups
 cinit, s = MEDYAN.example_all_sites_context()
@@ -453,7 +453,7 @@ 
Example snapshot

 
 time (s)
 
-

+

 
attrs(group)["time (s)"]

 

 
0.0

@@ -466,7 +466,7 @@ 
Example snapshot

 
 version
 
-

+

 
attrs(group)["version"]

 

 
"0.8.0"

@@ -479,7 +479,7 @@ 
Example snapshot

 
 uuid
 
-

+

 
attrs(group)["uuid"]

 

 
"37eee81f-88ae-4d11-b6b3-d38e1ccf0a08"

@@ -507,7 +507,7 @@ 
Example snapshot

 
 diffusingcounts
 
-

+

 
collect(group["diffusingcounts"])

 

 
2×4 Matrix{Int32}:
@@ -523,7 +523,7 @@ 
Example snapshot

 
 fixedcounts
 
-

+

 
collect(group["fixedcounts"])

 

 
2×4 Matrix{Float64}:
@@ -570,7 +570,7 @@ 
Example snapshot

 
 🔢 capsules
 
-

+

 
collect(group["chemboundary/capsules"])

 

 
8×1 Matrix{Float64}:
@@ -591,7 +591,7 @@ 
Example snapshot

 
 🔢 planes
 
-

+

 
collect(group["chemboundary/planes"])

 

 
4×6 Matrix{Float64}:
@@ -638,7 +638,7 @@ 
Example snapshot

 
 position_scale
 
-

+

 
attrs(group["filaments"])["position_scale"]

 

 
3

@@ -669,7 +669,7 @@ 
Example snapshot

 
 🔢 endloadforces
 
-

+

 
collect(group["filaments/1/endloadforces"])

 

 
2×2 Matrix{Float64}:
@@ -684,7 +684,7 @@ 
Example snapshot

 
 🔢 fids
 
-

+

 
collect(group["filaments/1/fids"])

 

 
2-element Vector{Int32}:
@@ -698,7 +698,7 @@ 
Example snapshot

 
 🔢 minusend_num_notminimized
 
-

+

 
collect(group["filaments/1/minusend_num_notminimized"])

 

 
2-element Vector{Int32}:
@@ -712,7 +712,7 @@ 
Example snapshot

 
 🔢 plusend_num_notminimized
 
-

+

 
collect(group["filaments/1/plusend_num_notminimized"])

 

 
2-element Vector{Int32}:
@@ -726,7 +726,7 @@ 
Example snapshot

 
 🔢 num_cylinders
 
-

+

 
collect(group["filaments/1/num_cylinders"])

 

 
2-element Vector{Int32}:
@@ -740,7 +740,7 @@ 
Example snapshot

 
 🔢 num_monomers
 
-

+

 
collect(group["filaments/1/num_monomers"])

 

 
2-element Vector{Int32}:
@@ -754,7 +754,7 @@ 
Example snapshot

 
 🔢 node_mids
 
-

+

 
collect(group["filaments/1/node_mids"])

 

 
2-element Vector{Int32}:
@@ -775,7 +775,7 @@ 
Example snapshot

 
 🔢 nodepositions
 
-

+

 
collect(group["filaments/1/nodepositions"])

 

 
4×3 Matrix{Float64}:
@@ -791,7 +791,7 @@ 
Example snapshot

 
 🔢 monomerstates
 
-

+

 
collect(group["filaments/1/monomerstates"])

 

 
18-element Vector{UInt8}:
@@ -868,7 +868,7 @@ 
Example snapshot

 
 num_link_2mons
 
-

+

 
attrs(group["link_2mons/1"])["num_link_2mons"]

 

 
2

@@ -880,7 +880,7 @@ 
Example snapshot

 
 next_lid
 
-

+

 
attrs(group["link_2mons/1"])["next_lid"]

 

 
3

@@ -896,7 +896,7 @@ 
Example snapshot

 
 🔢 endnames
 
-

+

 
collect(group["link_2mons/1/endnames"])

 

 
2×6 Matrix{Int64}:
@@ -919,7 +919,7 @@ 
Example snapshot

 
 🔢 lids
 
-

+

 
collect(group["link_2mons/1/lids"])

 

 
2-element Vector{Int64}:
@@ -937,7 +937,7 @@ 
Example snapshot

 
Default: default link_2mon_state

 
See MEDYAN.chem_setlink_2mon_state! and MEDYAN.Link2MonState

 
The state of a link_2mon, organized in a nested struct of vector like form. Any static arrays will be unwrapped into a tuple of vectors, in column major order. The “name” attribute of each subgroup and dataset is the corresponding property name in the StructArray Any property in the default state that isn’t in the snapshot will stay at its default value.

-

+

 
group["link_2mons/1/state"]

 

 
📂
@@ -980,7 +980,7 @@ 
Example snapshot

 
 🔢 capsules
 
-

+

 
collect(group["mechboundary/capsules"])

 

 
8×1 Matrix{Float64}:
@@ -1001,7 +1001,7 @@ 
Example snapshot

 
 🔢 planes
 
-

+

 
collect(group["mechboundary/planes"])

 

 
4×6 Matrix{Float64}:
@@ -1047,7 +1047,7 @@ 
Example snapshot

 
 num_membranes
 
-

+

 
attrs(group["membranes"])["num_membranes"]

 

 
1

@@ -1059,7 +1059,7 @@ 
Example snapshot

 
 position_scale
 
-

+

 
attrs(group["membranes"])["position_scale"]

 

 
3

@@ -1101,7 +1101,7 @@ 
Example snapshot

 
 type_id
 
-

+

 
attrs(group["membranes/1"])["type_id"]

 

 
1

@@ -1116,7 +1116,7 @@ 
Example snapshot

 
 🔢 trilist
 
-

+

 
collect(group["membranes/1/trilist"])

 

 
3×1956 Matrix{Int64}:
@@ -1131,7 +1131,7 @@ 
Example snapshot

 
 🔢 vertlist
 
-

+

 
collect(group["membranes/1/vertlist"])

 

 
3×980 Matrix{Float64}:
@@ -1146,7 +1146,7 @@ 
Example snapshot

 
 🔢 id
 
-

+

 
collect(group["membranes/1/id"])

 

 
980-element Vector{Int64}:
@@ -1184,7 +1184,7 @@ 
Example snapshot

 
 optional 🔢 copynumbers
 
-

+

 
collect(group["membranes/1/copynumbers"])

 

 
3×980 Matrix{Int64}:
diff --git a/julia-docs/dev/search.json b/julia-docs/dev/search.json
index e07174e..8c80ca3 100644
--- a/julia-docs/dev/search.json
+++ b/julia-docs/dev/search.json
@@ -1416,7 +1416,7 @@
     "href": "tutorials/2rdme.html",
     "title": "2. Rock Paper Scissors Stochastic Reaction Diffusion",
     "section": "",
-    "text": "Inspired by:\nhttps://www.youtube.com/watch?v=TORwMc2AaRE&t=0s\n\n\nOpen a julia REPL or jupyter notebook using the medyan-tutorial environment you created in tutorial 1.\nLoad MEDYAN with MEDYANVis for visualization\n\nusing MEDYAN\nusing MEDYANVis\nusing CairoMakie\nusing Random\nusing SmallZarrGroups\nRandom.seed!(1234);\n\n\n\n\nThe first step is declaring the names of agents in the system.\nThis system will contain three diffusing species.\n\nagent_names = MEDYAN.AgentNames(;\n    diffusingspeciesnames=[\n        :R, # Rock\n        :P, # Paper\n        :S, # Scissors\n    ],\n)\n\nMEDYAN.AgentNames([:R, :P, :S], Symbol[], Symbol[], Symbol[], Tuple{Symbol, Vector{Symbol}}[], Symbol[], Symbol[], Symbol[])\n\n\n\n\n\nAfter the agent names are declared, the system can be defined.\nThis is done by constructing a MEDYAN.SysDef object from the agent_names and then mutating it to add parameters, reactions, and callbacks.\n\ns = MEDYAN.SysDef(agent_names)\n\nMEDYAN.SysDef\n Diffusing species:\n  R: 0.0 nm²/s\n  P: 0.0 nm²/s\n  S: 0.0 nm²/s\n\n\nAdd a diffusion coefficient of 1E6 nm²/s to all species. All units are based on nm, s, pN\nadd_diffusion_coeff!\n\nD = 1E6\nadd_diffusion_coeff!(s, :R, D) # nm²/s\nadd_diffusion_coeff!(s, :P, D) # nm²/s\nadd_diffusion_coeff!(s, :S, D) # nm²/s\n\nMEDYAN.SysDef\n Diffusing species:\n  R: 1.0e6 nm²/s\n  P: 1.0e6 nm²/s\n  S: 1.0e6 nm²/s\n\n\nAdd reactions, paper “beats” rock, scissors “beats” paper, rock “beats” scissors. In this simulation “beats” means convert to self type.\nIn this case because the reaction is between two diffusing species, it has units of nm³/s. You can think of this as the volume where if exactly one of each reactant existed the rate would be 1 per second.\naddreaction!\n\nrate = 50.0*(500.0^3) # nm³/s\naddreaction!(s,\n    \"diffusing.P + diffusing.R --> 2diffusing.P\",\n    rate,\n    1,\n)\naddreaction!(s,\n    \"diffusing.S + diffusing.P --> 2diffusing.S\",\n    rate,\n    1,\n)\naddreaction!(s,\n    \"diffusing.R + diffusing.S --> 2diffusing.R\",\n    rate,\n    1,\n)\n\nMEDYAN.SysDef\n Diffusing species:\n  R: 1.0e6 nm²/s\n  P: 1.0e6 nm²/s\n  S: 1.0e6 nm²/s\n Compartment reactions without callbacks:\n  \"diffusing.P + diffusing.R --> 2diffusing.P\" 6.25e9 nm³/s\n  \"diffusing.S + diffusing.P --> 2diffusing.S\" 6.25e9 nm³/s\n  \"diffusing.R + diffusing.S --> 2diffusing.R\" 6.25e9 nm³/s\n\n\n\n\n\nAll simulations run in a grid.\nThis is a box that contains the simulation.\nThe grid is composed of chemistry voxels, small cubes that can have different counts of the various diffusing species.\nCreate a 50 by 50 by 1 grid of 500 nm side length voxels.\n\nL = 50\ngrid = CubicGrid((L,L,1),500.0)\n\nCubicGrid([50, 50, 1], 500.0)\n\n\n\n\n\nThe Context is the object the handles the state of a running simulation.\nCreate a Context using s and grid\n\nc = MEDYAN.Context(s, grid)\n\nMEDYAN.Context at time 0.0s in CubicGrid([50, 50, 1], 500.0)\n\n\n\n\n\nThe context starts empty.\nDistribute 2000 of each species randomly to the chem voxels by mutating the context.\nadddiffusingcount_rand!\n\nadddiffusingcount_rand!(c, s.diffusing.R, 2000)\nadddiffusingcount_rand!(c, s.diffusing.P, 2000)\nadddiffusingcount_rand!(c, s.diffusing.S, 2000)\n\n\n\n\nRun chemistry for 1.0s and visualize the results.\n\nvis = Visualizer()\nsetvisible!(vis[\"/Grid\"], false)\nsetvisible!(vis[\"/Axes\"], false)\nsetvisible!(vis[\"/Background\"], false)\n\nIf you open the visualizer in a browser with open(vis) and run the following you should get an animated version of below.\n\nfor i in 1:100\n    run_chemistry!(c, 0.01)\n    MEDYANVis.drawdiffusing!(vis[\"diffusing\"], c.grid, c.chemistryengine, s; size = 0.8)\n    sleep(0.02)\nend\n\n\n\n    \n    \n    \n    \n\n\n\n\n\nNext we will see how to plot quantities from the simulation.\nIf you want to analyze a trajectory in detail, or load a system state, one method is to use snapshots. For details see snapshot group reference\nMEDYAN.load_snapshot! can be used to reload snapshots, this is very useful for restarting simulations, or changing the simulation state in a different programming language, but not needed in this tutorial.\nSmallZarrGroups.jl can be used to save/load snapshot groups to/from disk, in zip files, or in directories.\nRun chemistry for another 1.0s and store a snapshot every 0.01s in a vector.\n\nusing SmallZarrGroups\nsnapshots = ZGroup[]\nfor i in 1:100\n    run_chemistry!(c, 0.01)\n    push!(snapshots, MEDYAN.snapshot(c))\nend\n\nNow that the simulation is done the results can be analyzed. For longer simulations, these snapshots should be saved to disk with for example:\nSmallZarrGroups.save_dir(\"snapshot$i.zarr.zip\",MEDYAN.snapshot(c))\nto avoid needed to rerun the simulation and to avoid using too much RAM.\n\ntotal_rocks = Int[]\ntotal_papers = Int[]\ntotal_scissors = Int[]\ntimes = Float64[]\nfor group in snapshots\n    totals = sum(collect(group[\"diffusingcounts\"]);dims=2)\n    push!(times, attrs(group)[\"time (s)\"])\n    push!(total_rocks, totals[s.diffusing.R])\n    push!(total_papers, totals[s.diffusing.P])\n    push!(total_scissors, totals[s.diffusing.S])\nend\n\n\nfigure, axis, lineplot = lines(times, total_rocks; label=\"rock\")\nlines!(times, total_papers; label=\"paper\")\nlines!(times, total_scissors; label=\"scissors\")\nlines!(\n    times,\n    total_scissors.+total_papers.+total_rocks;\n    label=\"combined\")\naxislegend()\ncurrent_figure()\n\n┌ Warning: Found `resolution` in the theme when creating a `Scene`. The `resolution` keyword for `Scene`s and `Figure`s has been deprecated. Use `Figure(; size = ...` or `Scene(; size = ...)` instead, which better reflects that this is a unitless size and not a pixel resolution. The key could also come from `set_theme!` calls or related theming functions.\n└ @ Makie ~/.julia/packages/Makie/We6MY/src/scenes.jl:227\n\n\n\n\n\n\n\n\n\nIf you are using VSCode or Jupyter the figure will be displayed.\nIf you are using the REPL, save the figure as a PDF to view it.\nsave(\"tutorial2-plot.pdf\", current_figure())",
+    "text": "Inspired by:\nhttps://www.youtube.com/watch?v=TORwMc2AaRE&t=0s\n\n\nOpen a julia REPL or jupyter notebook using the medyan-tutorial environment you created in tutorial 1.\nLoad MEDYAN with MEDYANVis for visualization\n\nusing MEDYAN\nusing MEDYANVis\nusing CairoMakie\nusing Random\nusing SmallZarrGroups\nRandom.seed!(1234);\n\n\n\n\nThe first step is declaring the names of agents in the system.\nThis system will contain three diffusing species.\n\nagent_names = MEDYAN.AgentNames(;\n    diffusingspeciesnames=[\n        :R, # Rock\n        :P, # Paper\n        :S, # Scissors\n    ],\n)\n\nMEDYAN.AgentNames([:R, :P, :S], Symbol[], Symbol[], Symbol[], Tuple{Symbol, Vector{Symbol}}[], Symbol[], Symbol[], Symbol[])\n\n\n\n\n\nAfter the agent names are declared, the system can be defined.\nThis is done by constructing a MEDYAN.SysDef object from the agent_names and then mutating it to add parameters, reactions, and callbacks.\n\ns = MEDYAN.SysDef(agent_names)\n\nMEDYAN.SysDef\n Diffusing species:\n  R: 0.0 nm²/s\n  P: 0.0 nm²/s\n  S: 0.0 nm²/s\n\n\nAdd a diffusion coefficient of 1E6 nm²/s to all species. All units are based on nm, s, pN\nadd_diffusion_coeff!\n\nD = 1E6\nadd_diffusion_coeff!(s, :R, D) # nm²/s\nadd_diffusion_coeff!(s, :P, D) # nm²/s\nadd_diffusion_coeff!(s, :S, D) # nm²/s\n\nMEDYAN.SysDef\n Diffusing species:\n  R: 1.0e6 nm²/s\n  P: 1.0e6 nm²/s\n  S: 1.0e6 nm²/s\n\n\nAdd reactions, paper “beats” rock, scissors “beats” paper, rock “beats” scissors. In this simulation “beats” means convert to self type.\nIn this case because the reaction is between two diffusing species, it has units of nm³/s. You can think of this as the volume where if exactly one of each reactant existed the rate would be 1 per second.\naddreaction!\n\nrate = 50.0*(500.0^3) # nm³/s\naddreaction!(s,\n    \"diffusing.P + diffusing.R --> 2diffusing.P\",\n    rate,\n    1,\n)\naddreaction!(s,\n    \"diffusing.S + diffusing.P --> 2diffusing.S\",\n    rate,\n    1,\n)\naddreaction!(s,\n    \"diffusing.R + diffusing.S --> 2diffusing.R\",\n    rate,\n    1,\n)\n\nMEDYAN.SysDef\n Diffusing species:\n  R: 1.0e6 nm²/s\n  P: 1.0e6 nm²/s\n  S: 1.0e6 nm²/s\n Compartment reactions without callbacks:\n  \"diffusing.P + diffusing.R --> 2diffusing.P\" 6.25e9 nm³/s\n  \"diffusing.S + diffusing.P --> 2diffusing.S\" 6.25e9 nm³/s\n  \"diffusing.R + diffusing.S --> 2diffusing.R\" 6.25e9 nm³/s\n\n\n\n\n\nAll simulations run in a grid.\nThis is a box that contains the simulation.\nThe grid is composed of chemistry voxels, small cubes that can have different counts of the various diffusing species.\nCreate a 50 by 50 by 1 grid of 500 nm side length voxels.\n\nL = 50\ngrid = CubicGrid((L,L,1),500.0)\n\nCubicGrid([50, 50, 1], 500.0)\n\n\n\n\n\nThe Context is the object the handles the state of a running simulation.\nCreate a Context using s and grid\n\nc = MEDYAN.Context(s, grid)\n\nMEDYAN.Context at time 0.0s in CubicGrid([50, 50, 1], 500.0)\n\n\n\n\n\nThe context starts empty.\nDistribute 2000 of each species randomly to the chem voxels by mutating the context.\nadddiffusingcount_rand!\n\nadddiffusingcount_rand!(c, s.diffusing.R, 2000)\nadddiffusingcount_rand!(c, s.diffusing.P, 2000)\nadddiffusingcount_rand!(c, s.diffusing.S, 2000)\n\n\n\n\nRun chemistry for 1.0s and visualize the results.\n\nvis = Visualizer()\nsetvisible!(vis[\"/Grid\"], false)\nsetvisible!(vis[\"/Axes\"], false)\nsetvisible!(vis[\"/Background\"], false)\n\nIf you open the visualizer in a browser with open(vis) and run the following you should get an animated version of below.\n\nfor i in 1:100\n    run_chemistry!(c, 0.01)\n    MEDYANVis.drawdiffusing!(vis[\"diffusing\"], c.grid, c.chemistryengine, s; size = 0.8)\n    sleep(0.02)\nend\n\n\n\n    \n    \n    \n    \n\n\n\n\n\nNext we will see how to plot quantities from the simulation.\nIf you want to analyze a trajectory in detail, or load a system state, one method is to use snapshots. For details see snapshot group reference\nMEDYAN.load_snapshot! can be used to reload snapshots, this is very useful for restarting simulations, or changing the simulation state in a different programming language, but not needed in this tutorial.\nSmallZarrGroups.jl can be used to save/load snapshot groups to/from disk, in zip files, or in directories.\nRun chemistry for another 1.0s and store a snapshot every 0.01s in a vector.\n\nusing SmallZarrGroups\nsnapshots = ZGroup[]\nfor i in 1:100\n    run_chemistry!(c, 0.01)\n    push!(snapshots, MEDYAN.snapshot(c))\nend\n\nNow that the simulation is done the results can be analyzed. For longer simulations, these snapshots should be saved to disk with for example:\nSmallZarrGroups.save_dir(\"snapshot$i.zarr.zip\",MEDYAN.snapshot(c))\nto avoid needed to rerun the simulation and to avoid using too much RAM.\n\ntotal_rocks = Int[]\ntotal_papers = Int[]\ntotal_scissors = Int[]\ntimes = Float64[]\nfor group in snapshots\n    totals = sum(collect(group[\"diffusingcounts\"]);dims=2)\n    push!(times, attrs(group)[\"time (s)\"])\n    push!(total_rocks, totals[s.diffusing.R])\n    push!(total_papers, totals[s.diffusing.P])\n    push!(total_scissors, totals[s.diffusing.S])\nend\n\n\nfigure, axis, lineplot = lines(times, total_rocks; label=\"rock\")\nlines!(times, total_papers; label=\"paper\")\nlines!(times, total_scissors; label=\"scissors\")\nlines!(\n    times,\n    total_scissors.+total_papers.+total_rocks;\n    label=\"combined\")\naxislegend()\ncurrent_figure()\n\n┌ Warning: Found `resolution` in the theme when creating a `Scene`. The `resolution` keyword for `Scene`s and `Figure`s has been deprecated. Use `Figure(; size = ...` or `Scene(; size = ...)` instead, which better reflects that this is a unitless size and not a pixel resolution. The key could also come from `set_theme!` calls or related theming functions.\n└ @ Makie ~/.julia/packages/Makie/qMluh/src/scenes.jl:227\n\n\n\n\n\n\n\n\n\nIf you are using VSCode or Jupyter the figure will be displayed.\nIf you are using the REPL, save the figure as a PDF to view it.\nsave(\"tutorial2-plot.pdf\", current_figure())",
     "crumbs": [
       "Tutorials",
       "2. Rock Paper Scissors Stochastic Reaction Diffusion"
@@ -1504,7 +1504,7 @@
     "href": "tutorials/2rdme.html#snapshots-and-plotting",
     "title": "2. Rock Paper Scissors Stochastic Reaction Diffusion",
     "section": "",
-    "text": "Next we will see how to plot quantities from the simulation.\nIf you want to analyze a trajectory in detail, or load a system state, one method is to use snapshots. For details see snapshot group reference\nMEDYAN.load_snapshot! can be used to reload snapshots, this is very useful for restarting simulations, or changing the simulation state in a different programming language, but not needed in this tutorial.\nSmallZarrGroups.jl can be used to save/load snapshot groups to/from disk, in zip files, or in directories.\nRun chemistry for another 1.0s and store a snapshot every 0.01s in a vector.\n\nusing SmallZarrGroups\nsnapshots = ZGroup[]\nfor i in 1:100\n    run_chemistry!(c, 0.01)\n    push!(snapshots, MEDYAN.snapshot(c))\nend\n\nNow that the simulation is done the results can be analyzed. For longer simulations, these snapshots should be saved to disk with for example:\nSmallZarrGroups.save_dir(\"snapshot$i.zarr.zip\",MEDYAN.snapshot(c))\nto avoid needed to rerun the simulation and to avoid using too much RAM.\n\ntotal_rocks = Int[]\ntotal_papers = Int[]\ntotal_scissors = Int[]\ntimes = Float64[]\nfor group in snapshots\n    totals = sum(collect(group[\"diffusingcounts\"]);dims=2)\n    push!(times, attrs(group)[\"time (s)\"])\n    push!(total_rocks, totals[s.diffusing.R])\n    push!(total_papers, totals[s.diffusing.P])\n    push!(total_scissors, totals[s.diffusing.S])\nend\n\n\nfigure, axis, lineplot = lines(times, total_rocks; label=\"rock\")\nlines!(times, total_papers; label=\"paper\")\nlines!(times, total_scissors; label=\"scissors\")\nlines!(\n    times,\n    total_scissors.+total_papers.+total_rocks;\n    label=\"combined\")\naxislegend()\ncurrent_figure()\n\n┌ Warning: Found `resolution` in the theme when creating a `Scene`. The `resolution` keyword for `Scene`s and `Figure`s has been deprecated. Use `Figure(; size = ...` or `Scene(; size = ...)` instead, which better reflects that this is a unitless size and not a pixel resolution. The key could also come from `set_theme!` calls or related theming functions.\n└ @ Makie ~/.julia/packages/Makie/We6MY/src/scenes.jl:227\n\n\n\n\n\n\n\n\n\nIf you are using VSCode or Jupyter the figure will be displayed.\nIf you are using the REPL, save the figure as a PDF to view it.\nsave(\"tutorial2-plot.pdf\", current_figure())",
+    "text": "Next we will see how to plot quantities from the simulation.\nIf you want to analyze a trajectory in detail, or load a system state, one method is to use snapshots. For details see snapshot group reference\nMEDYAN.load_snapshot! can be used to reload snapshots, this is very useful for restarting simulations, or changing the simulation state in a different programming language, but not needed in this tutorial.\nSmallZarrGroups.jl can be used to save/load snapshot groups to/from disk, in zip files, or in directories.\nRun chemistry for another 1.0s and store a snapshot every 0.01s in a vector.\n\nusing SmallZarrGroups\nsnapshots = ZGroup[]\nfor i in 1:100\n    run_chemistry!(c, 0.01)\n    push!(snapshots, MEDYAN.snapshot(c))\nend\n\nNow that the simulation is done the results can be analyzed. For longer simulations, these snapshots should be saved to disk with for example:\nSmallZarrGroups.save_dir(\"snapshot$i.zarr.zip\",MEDYAN.snapshot(c))\nto avoid needed to rerun the simulation and to avoid using too much RAM.\n\ntotal_rocks = Int[]\ntotal_papers = Int[]\ntotal_scissors = Int[]\ntimes = Float64[]\nfor group in snapshots\n    totals = sum(collect(group[\"diffusingcounts\"]);dims=2)\n    push!(times, attrs(group)[\"time (s)\"])\n    push!(total_rocks, totals[s.diffusing.R])\n    push!(total_papers, totals[s.diffusing.P])\n    push!(total_scissors, totals[s.diffusing.S])\nend\n\n\nfigure, axis, lineplot = lines(times, total_rocks; label=\"rock\")\nlines!(times, total_papers; label=\"paper\")\nlines!(times, total_scissors; label=\"scissors\")\nlines!(\n    times,\n    total_scissors.+total_papers.+total_rocks;\n    label=\"combined\")\naxislegend()\ncurrent_figure()\n\n┌ Warning: Found `resolution` in the theme when creating a `Scene`. The `resolution` keyword for `Scene`s and `Figure`s has been deprecated. Use `Figure(; size = ...` or `Scene(; size = ...)` instead, which better reflects that this is a unitless size and not a pixel resolution. The key could also come from `set_theme!` calls or related theming functions.\n└ @ Makie ~/.julia/packages/Makie/qMluh/src/scenes.jl:227\n\n\n\n\n\n\n\n\n\nIf you are using VSCode or Jupyter the figure will be displayed.\nIf you are using the REPL, save the figure as a PDF to view it.\nsave(\"tutorial2-plot.pdf\", current_figure())",
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       "Tutorials",
       "2. Rock Paper Scissors Stochastic Reaction Diffusion"
diff --git a/julia-docs/dev/sitemap.xml b/julia-docs/dev/sitemap.xml
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-    2024-06-13T00:35:09.160Z
+    2024-06-25T21:34:18.575Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.fil_node_positions-618a66637eb50781.html
-    2024-06-13T00:35:09.096Z
+    2024-06-25T21:34:18.531Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.chem_addfixedcount--0286edfebf8ea5e6.html
-    2024-06-13T00:35:09.152Z
+    2024-06-25T21:34:18.571Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.newmembrane--a714b4a1c87062be.html
-    2024-06-13T00:35:09.152Z
+    2024-06-25T21:34:18.567Z
   
 
diff --git a/julia-docs/dev/tutorials/1install.html b/julia-docs/dev/tutorials/1install.html
index 0762aae..cde7e79 100644
--- a/julia-docs/dev/tutorials/1install.html
+++ b/julia-docs/dev/tutorials/1install.html
@@ -247,7 +247,7 @@ 
1. Installing MEDYAN.jl

 
Install julia

 
MEDYAN.jl is a julia package so first install the julia programming language.

 
This tutorial was generated using:

-

+

 

 
Julia Version 1.10.4
 Commit 48d4fd48430 (2024-06-04 10:41 UTC)
diff --git a/julia-docs/dev/tutorials/2rdme.html b/julia-docs/dev/tutorials/2rdme.html
index 7a0d99f..e7eb0c2 100644
--- a/julia-docs/dev/tutorials/2rdme.html
+++ b/julia-docs/dev/tutorials/2rdme.html
@@ -276,7 +276,7 @@ 
2. Rock Paper Scissors Stochastic Reaction Diffusion

 
Setup

 
Open a julia REPL or jupyter notebook using the medyan-tutorial environment you created in tutorial 1.

 
Load MEDYAN with MEDYANVis for visualization

-

+

 
using MEDYAN
 using MEDYANVis
 using CairoMakie
@@ -289,7 +289,7 @@ 
Setup

 
Declaring agent names

 
The first step is declaring the names of agents in the system.

 
This system will contain three diffusing species.

-

+

 
agent_names = MEDYAN.AgentNames(;
     diffusingspeciesnames=[
         :R, # Rock
@@ -306,7 +306,7 @@ 
Declaring agent name
 
Defining System

 
After the agent names are declared, the system can be defined.

 
This is done by constructing a MEDYAN.SysDef object from the agent_names and then mutating it to add parameters, reactions, and callbacks.

-

+

 
s = MEDYAN.SysDef(agent_names)

 

 
MEDYAN.SysDef
@@ -318,7 +318,7 @@ 
Defining System

 

 
Add a diffusion coefficient of 1E6 nm²/s to all species. All units are based on nm, s, pN

 
add_diffusion_coeff!

-

+

 
D = 1E6
 add_diffusion_coeff!(s, :R, D) # nm²/s
 add_diffusion_coeff!(s, :P, D) # nm²/s
@@ -334,7 +334,7 @@ 
Defining System

 
Add reactions, paper “beats” rock, scissors “beats” paper, rock “beats” scissors. In this simulation “beats” means convert to self type.

 
In this case because the reaction is between two diffusing species, it has units of nm³/s. You can think of this as the volume where if exactly one of each reactant existed the rate would be 1 per second.

 
addreaction!

-

+

 
rate = 50.0*(500.0^3) # nm³/s
 addreaction!(s,
     "diffusing.P + diffusing.R --> 2diffusing.P",
@@ -370,7 +370,7 @@ 
Creating a grid

 
This is a box that contains the simulation.

 
The grid is composed of chemistry voxels, small cubes that can have different counts of the various diffusing species.

 
Create a 50 by 50 by 1 grid of 500 nm side length voxels.

-

+

 
L = 50
 grid = CubicGrid((L,L,1),500.0)

 

@@ -382,7 +382,7 @@ 
Creating a grid

 
Creating a Context

 
The Context is the object the handles the state of a running simulation.

 
Create a Context using s and grid

-

+

 
c = MEDYAN.Context(s, grid)

 

 
MEDYAN.Context at time 0.0s in CubicGrid([50, 50, 1], 500.0)

@@ -394,7 +394,7 @@ 
Add agents to th
 
The context starts empty.

 
Distribute 2000 of each species randomly to the chem voxels by mutating the context.

 
adddiffusingcount_rand!

-

+

 
adddiffusingcount_rand!(c, s.diffusing.R, 2000)
 adddiffusingcount_rand!(c, s.diffusing.P, 2000)
 adddiffusingcount_rand!(c, s.diffusing.S, 2000)

@@ -403,24 +403,24 @@ 
Add agents to th
 

 
Run chemistry

 
Run chemistry for 1.0s and visualize the results.

-

+

 
vis = Visualizer()
 setvisible!(vis["/Grid"], false)
 setvisible!(vis["/Axes"], false)
 setvisible!(vis["/Background"], false)

 

 
If you open the visualizer in a browser with open(vis) and run the following you should get an animated version of below.

-

+

 
for i in 1:100
     run_chemistry!(c, 0.01)
     MEDYANVis.drawdiffusing!(vis["diffusing"], c.grid, c.chemistryengine, s; size = 0.8)
     sleep(0.02)
 end

 

-

+

 

     

-