diff --git a/julia-docs/dev/docstrings.html b/julia-docs/dev/docstrings.html index e1bfa80..d333fb8 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 3b00813..b307461 100644 Binary files a/julia-docs/dev/medyan-tutorial.zip and b/julia-docs/dev/medyan-tutorial.zip differ diff --git a/julia-docs/dev/reference/fileformats.html b/julia-docs/dev/reference/fileformats.html index e5d0eab..1922965 100644 --- a/julia-docs/dev/reference/fileformats.html +++ b/julia-docs/dev/reference/fileformats.html @@ -285,7 +285,7 @@

"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/sitemap.xml b/julia-docs/dev/sitemap.xml
index 9d29be2..7d42dd6 100644
--- a/julia-docs/dev/sitemap.xml
+++ b/julia-docs/dev/sitemap.xml
@@ -2,251 +2,251 @@
 
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.set_chemboundary--0aa6e4e95c60f9f7.html
-    2024-05-13T18:03:16.507Z
+    2024-05-19T10:17:31.778Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.chem_adddiffusingcount--2264be341b81a600.html
-    2024-05-13T18:03:16.571Z
+    2024-05-19T10:17:31.818Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.chem_removelink_2mon--e25a3fd69f791cd0.html
-    2024-05-13T18:03:16.491Z
+    2024-05-19T10:17:31.762Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.boundary_cylinder-33a45da15f9672d3.html
-    2024-05-13T18:03:16.515Z
+    2024-05-19T10:17:31.802Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.vertexstate-450b7005d2acebe8.html
-    2024-05-13T18:03:16.563Z
+    2024-05-19T10:17:31.810Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.add_link_2mon_site--b9548c4a2d23aac9.html
-    2024-05-13T18:03:16.503Z
+    2024-05-19T10:17:31.774Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.link2monstate-9845e7e08620ea8a.html
-    2024-05-13T18:03:16.519Z
+    2024-05-19T10:17:31.802Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.mon_plusvector-b7271c7721602813.html
-    2024-05-13T18:03:16.511Z
+    2024-05-19T10:17:31.782Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.load_snapshot--e534be293ce74465.html
-    2024-05-13T18:03:16.567Z
+    2024-05-19T10:17:31.814Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.set_mechboundary--b5e26b6b690256aa.html
-    2024-05-13T18:03:16.503Z
+    2024-05-19T10:17:31.774Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.boundary_plane-2caa9b52b3b3f0cc.html
-    2024-05-13T18:03:16.567Z
+    2024-05-19T10:17:31.814Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.chem_depolymerize--a5f262191e484dd4.html
-    2024-05-13T18:03:16.515Z
+    2024-05-19T10:17:31.786Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.mon_minimized-5b17adaf7d8a4f62.html
-    2024-05-13T18:03:16.519Z
+    2024-05-19T10:17:31.802Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.defer_chem_caching--9538a1c449f3da93.html
-    2024-05-13T18:03:16.507Z
+    2024-05-19T10:17:31.778Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.boundary_box-060d4c56df40146a.html
-    2024-05-13T18:03:16.507Z
+    2024-05-19T10:17:31.778Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.add_diffusion_coeff--a77d1ef833cfdedd.html
-    2024-05-13T18:03:16.503Z
+    2024-05-19T10:17:31.774Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.chem_setmonomerstate--ed756af0de4db0ca.html
-    2024-05-13T18:03:16.571Z
+    2024-05-19T10:17:31.818Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.link2monsitemonomerstatematch-c495443de74016ce.html
-    2024-05-13T18:03:16.527Z
+    2024-05-19T10:17:31.810Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.membranesitediffusing-66734014eb12ddb1.html
-    2024-05-13T18:03:16.519Z
+    2024-05-19T10:17:31.802Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.chem_removefilament--f36888837f14bad7.html
-    2024-05-13T18:03:16.491Z
+    2024-05-19T10:17:31.766Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.grididat-8671e01413346deb.html
-    2024-05-13T18:03:16.563Z
+    2024-05-19T10:17:31.810Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.fil_node_mon_ids-b1d3d66a81296343.html
-    2024-05-13T18:03:16.523Z
+    2024-05-19T10:17:31.806Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.agentnames-948e6a24b4fb0cb5.html
-    2024-05-13T18:03:16.567Z
+    2024-05-19T10:17:31.814Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.chem_polymerize--7a5e88ac36e4ccbf.html
-    2024-05-13T18:03:16.519Z
+    2024-05-19T10:17:31.802Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.chem_setlink_2mon_state--82213403237b28e5.html
-    2024-05-13T18:03:16.575Z
+    2024-05-19T10:17:31.822Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/base.empty--418304748816268d.html
-    2024-05-13T18:03:16.523Z
+    2024-05-19T10:17:31.806Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.decimated2monsiteminanglerange-fc006e574376cfff.html
-    2024-05-13T18:03:16.511Z
+    2024-05-19T10:17:31.782Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.adapt_membranes--1d26092defd0f4fa.html
-    2024-05-13T18:03:16.515Z
+    2024-05-19T10:17:31.786Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.fil_mon_states-3db9714621903b78.html
-    2024-05-13T18:03:16.495Z
+    2024-05-19T10:17:31.770Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.boundary-f1e7be79002a27f8.html
-    2024-05-13T18:03:16.499Z
+    2024-05-19T10:17:31.774Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.newfilament_rand--432ec27232aad41e.html
-    2024-05-13T18:03:16.491Z
+    2024-05-19T10:17:31.766Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/base.length-7ea31a421de7d258.html
-    2024-05-13T18:03:16.523Z
+    2024-05-19T10:17:31.806Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/mon_link_2mon_sites.html
-    2024-05-13T18:03:15.035Z
+    2024-05-19T10:17:30.486Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/decimated_2mon_sites.html
-    2024-05-13T18:03:15.035Z
+    2024-05-19T10:17:30.490Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/link_2mon_sites.html
-    2024-05-13T18:03:15.039Z
+    2024-05-19T10:17:30.494Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/util/math/cuboidslicing.html
-    2024-05-13T18:03:15.035Z
+    2024-05-19T10:17:30.490Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/trajectory-io/snapshot.html
-    2024-05-13T18:03:16.487Z
+    2024-05-19T10:17:31.758Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/sys_def.html
-    2024-05-13T18:03:15.027Z
+    2024-05-19T10:17:30.482Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/sever_filament.html
-    2024-05-13T18:03:15.035Z
+    2024-05-19T10:17:30.490Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/filamentsites.html
-    2024-05-13T18:03:15.039Z
+    2024-05-19T10:17:30.490Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/membrane/membranesites.html
-    2024-05-13T18:03:15.035Z
+    2024-05-19T10:17:30.490Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.mon_3states-6c16efb303a60058.html
-    2024-05-13T18:03:16.523Z
+    2024-05-19T10:17:31.806Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.cadherinparams-b70febdaf4c8fba5.html
-    2024-05-13T18:03:16.579Z
+    2024-05-19T10:17:31.826Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.add_membranesitereaction--59d1fe245302e071.html
-    2024-05-13T18:03:16.511Z
+    2024-05-19T10:17:31.782Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.fil_num_unmin_ends-813ffc641f9ac9da.html
-    2024-05-13T18:03:16.503Z
+    2024-05-19T10:17:31.778Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.compute_all_membrane_geometry-_system-05b4d2a32e31560c.html
-    2024-05-13T18:03:16.575Z
+    2024-05-19T10:17:31.822Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/base.haskey-e7d3f961991e2663.html
-    2024-05-13T18:03:16.563Z
+    2024-05-19T10:17:31.814Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.cubicgrid-fe4b7cc2dceb0431.html
-    2024-05-13T18:03:16.571Z
+    2024-05-19T10:17:31.818Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.addfilamentendsite--95612d72d1fda05f.html
-    2024-05-13T18:03:16.507Z
+    2024-05-19T10:17:31.778Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/base.iterate-5228367cd62c0bf2.html
-    2024-05-13T18:03:16.491Z
+    2024-05-19T10:17:31.766Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.refresh_chem_cache--f90ebca1f896ad2c.html
-    2024-05-13T18:03:16.579Z
+    2024-05-19T10:17:31.826Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.add_link_2mon--b801c872b8ff168a.html
-    2024-05-13T18:03:16.499Z
+    2024-05-19T10:17:31.774Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.randompoint-83e939bdee528294.html
-    2024-05-13T18:03:16.507Z
+    2024-05-19T10:17:31.778Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.vertexname-2d87a6a86cabc4f5.html
-    2024-05-13T18:03:16.575Z
+    2024-05-19T10:17:31.822Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.addmembranediffusingcount_rand--7b719dca63a36b1b.html
-    2024-05-13T18:03:16.511Z
+    2024-05-19T10:17:31.786Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.filamentsitegeneral-0d87ce44fed17b2c.html
-    2024-05-13T18:03:16.527Z
+    2024-05-19T10:17:31.810Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.link2monsitecount-ab4fcc1eb50c2313.html
-    2024-05-13T18:03:16.563Z
+    2024-05-19T10:17:31.814Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.addfilamentend_reaction--83ec3db37b4e2130.html
-    2024-05-13T18:03:16.583Z
+    2024-05-19T10:17:31.830Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.link2monsitemotorcatch-0185d4c95b91e30b.html
-    2024-05-13T18:03:16.503Z
+    2024-05-19T10:17:31.778Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.chem_newfilament--7a45f2860949bee3.html
-    2024-05-13T18:03:16.575Z
+    2024-05-19T10:17:31.822Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.membranespeciesparams-548fecb643fc2599.html
-    2024-05-13T18:03:16.563Z
+    2024-05-19T10:17:31.814Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.addpossiblecadherinsite--ae8586daa0b5454a.html
-    2024-05-13T18:03:16.519Z
+    2024-05-19T10:17:31.802Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/reference/sitesinfo.html
@@ -286,246 +286,246 @@
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.set_time--a6dd8f73f68a3759.html
-    2024-05-13T18:03:16.567Z
+    2024-05-19T10:17:31.814Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/base.copy-4ca5eb8401ab10b2.html
-    2024-05-13T18:03:16.491Z
+    2024-05-19T10:17:31.766Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/base.setindex--725f722fff4cfa6d.html
-    2024-05-13T18:03:16.563Z
+    2024-05-19T10:17:31.810Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.addfilamentsite--eb6bfd871a21b6f4.html
-    2024-05-13T18:03:16.567Z
+    2024-05-19T10:17:31.814Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/base.---a21e771ed8ea7d6f.html
-    2024-05-13T18:03:16.575Z
+    2024-05-19T10:17:31.822Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.addfilament_reaction--63195cbff2ab4237.html
-    2024-05-13T18:03:16.579Z
+    2024-05-19T10:17:31.826Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.centerof-e902b9bb7b2a6caf.html
-    2024-05-13T18:03:16.571Z
+    2024-05-19T10:17:31.818Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.addreactioncallback--9c9d46adeded2d88.html
-    2024-05-13T18:03:16.523Z
+    2024-05-19T10:17:31.806Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.sever_filament--a0475617dc0fbf93.html
-    2024-05-13T18:03:16.499Z
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     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.num_filtypes-b9943bbf7a9c7781.html
-    2024-05-13T18:03:16.523Z
+    2024-05-19T10:17:31.806Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.link2monsiteslipbond-2cec57cbea12864e.html
-    2024-05-13T18:03:16.499Z
+    2024-05-19T10:17:31.770Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.mon_position-83983d8916347411.html
-    2024-05-13T18:03:16.507Z
+    2024-05-19T10:17:31.778Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.link2monparams-d960d08f0808df0c.html
-    2024-05-13T18:03:16.519Z
+    2024-05-19T10:17:31.806Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.link2monsiteone-9886bc1476194731.html
-    2024-05-13T18:03:16.495Z
+    2024-05-19T10:17:31.770Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.run_chemistry--dda22fac5c555b9e.html
-    2024-05-13T18:03:16.571Z
+    2024-05-19T10:17:31.818Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.adddiffusingcount_rand--9d3ddfabbceeef92.html
-    2024-05-13T18:03:16.519Z
+    2024-05-19T10:17:31.802Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.add_decimated_2mon_site--ad56e7ee56067940.html
-    2024-05-13T18:03:16.499Z
+    2024-05-19T10:17:31.774Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.set_enable_cylinder_volume_exclusion--38c20ab68ab8bf1a.html
-    2024-05-13T18:03:16.511Z
+    2024-05-19T10:17:31.782Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.addunbindinglink_2mon_site--76d17dbe625169cd.html
-    2024-05-13T18:03:16.511Z
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     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.mon_exists-898c415a5eddc619.html
-    2024-05-13T18:03:16.503Z
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     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/context.html
-    2024-05-13T18:03:16.479Z
+    2024-05-19T10:17:31.754Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/membrane/meshadapt.html
-    2024-05-13T18:03:15.031Z
+    2024-05-19T10:17:30.486Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/auxprocs.html
-    2024-05-13T18:03:16.483Z
+    2024-05-19T10:17:31.758Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/filamentendsites.html
-    2024-05-13T18:03:16.487Z
+    2024-05-19T10:17:31.758Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/grids.html
-    2024-05-13T18:03:15.031Z
+    2024-05-19T10:17:30.486Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/util/stableindex.html
-    2024-05-13T18:03:16.483Z
+    2024-05-19T10:17:31.754Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/cadherins/possiblecadherinsite.html
-    2024-05-13T18:03:15.039Z
+    2024-05-19T10:17:30.494Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/boundary.html
-    2024-05-13T18:03:15.031Z
+    2024-05-19T10:17:30.486Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/minimize_energy.html
-    2024-05-13T18:03:16.483Z
+    2024-05-19T10:17:31.758Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.link_2mon_state-6d59dcd98ed7e303.html
-    2024-05-13T18:03:16.491Z
+    2024-05-19T10:17:31.762Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.link2monsitemotorstall-deb10f7964d5bef9.html
-    2024-05-13T18:03:16.579Z
+    2024-05-19T10:17:31.826Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.add_filament_params--74c7d0081157ca31.html
-    2024-05-13T18:03:16.567Z
+    2024-05-19T10:17:31.818Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.filter_grididat-58a94154d21e32b0.html
-    2024-05-13T18:03:16.567Z
+    2024-05-19T10:17:31.814Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/base.push--8715d52e2302aaeb.html
-    2024-05-13T18:03:16.563Z
+    2024-05-19T10:17:31.810Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.addmembranesite--892875b2c079002d.html
-    2024-05-13T18:03:16.495Z
+    2024-05-19T10:17:31.770Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.decimated2monsiterange-8afd8f3188bbcd4a.html
-    2024-05-13T18:03:16.515Z
+    2024-05-19T10:17:31.786Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.addcadherin--3c757785fa097c75.html
-    2024-05-13T18:03:16.503Z
+    2024-05-19T10:17:31.778Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.addreaction--da9bd35e7d1df7c3.html
-    2024-05-13T18:03:16.515Z
+    2024-05-19T10:17:31.786Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.link_2mon_endnames-5d0bca4b8e2e3509.html
-    2024-05-13T18:03:16.527Z
+    2024-05-19T10:17:31.810Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.context-736368ed32b08894.html
-    2024-05-13T18:03:16.519Z
+    2024-05-19T10:17:31.802Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.filtype_fil_ids-d333c38b9f9b3584.html
-    2024-05-13T18:03:16.563Z
+    2024-05-19T10:17:31.810Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.cadherinstate-0cd5353e58a90ec2.html
-    2024-05-13T18:03:16.507Z
+    2024-05-19T10:17:31.778Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/base.delete--56ef520341df3c06.html
-    2024-05-13T18:03:16.495Z
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     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.boundary_capsule-1700142f310bd9db.html
-    2024-05-13T18:03:16.567Z
+    2024-05-19T10:17:31.814Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.filamentendsitegeneral-7a32ac96fb4364ea.html
-    2024-05-13T18:03:16.575Z
+    2024-05-19T10:17:31.822Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/base.getindex-f593dde852851bc8.html
-    2024-05-13T18:03:16.503Z
+    2024-05-19T10:17:31.774Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.vertex_state-aa3350c08b68b63a.html
-    2024-05-13T18:03:16.515Z
+    2024-05-19T10:17:31.786Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.resolve_all_filament_mesh_crossing--a8be83a7d2ad65c7.html
-    2024-05-13T18:03:16.583Z
+    2024-05-19T10:17:31.826Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.mon_position_plusvector-927d0affbbdfef6f.html
-    2024-05-13T18:03:16.491Z
+    2024-05-19T10:17:31.766Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/nlsolversbase.value---d4fdd3b317023c0e.html
-    2024-05-13T18:03:16.563Z
+    2024-05-19T10:17:31.810Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.is_chem_cache_valid-8336a8adc58a252f.html
-    2024-05-13T18:03:16.571Z
+    2024-05-19T10:17:31.818Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.sysdef-c0c4da7a2b3d4fef.html
-    2024-05-13T18:03:16.579Z
+    2024-05-19T10:17:31.826Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.monlink2monsiteone-77707f45e082c27e.html
-    2024-05-13T18:03:16.579Z
+    2024-05-19T10:17:31.826Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.addcadherinsite--9e21ac42968d0196.html
-    2024-05-13T18:03:16.511Z
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     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.monomername-bb517706cb60c4f5.html
-    2024-05-13T18:03:16.507Z
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     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.num_vertexwithstate-3cf6fcd964588d37.html
-    2024-05-13T18:03:16.527Z
+    2024-05-19T10:17:31.810Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.chem_newlink_2mon--e4f84fe5cfa9a727.html
-    2024-05-13T18:03:16.499Z
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     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.minimize_energy--84c4aeab5457d3ee.html
-    2024-05-13T18:03:16.575Z
+    2024-05-19T10:17:31.822Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.fil_node_positions-618a66637eb50781.html
-    2024-05-13T18:03:16.511Z
+    2024-05-19T10:17:31.782Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.chem_addfixedcount--0286edfebf8ea5e6.html
-    2024-05-13T18:03:16.571Z
+    2024-05-19T10:17:31.818Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.newmembrane--a714b4a1c87062be.html
-    2024-05-13T18:03:16.567Z
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diff --git a/julia-docs/dev/tutorials/1install.html b/julia-docs/dev/tutorials/1install.html
index e59e57b..710f94d 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 1.10.3
 Commit 0b4590a5507 (2024-04-30 10:59 UTC)
diff --git a/julia-docs/dev/tutorials/2rdme.html b/julia-docs/dev/tutorials/2rdme.html
index 2830649..28644ef 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

 

-

+

 

     

-