From ff4b1f70820064a82adf00f51ec9aae733b62a43 Mon Sep 17 00:00:00 2001 From: "Documenter.jl" Date: Tue, 24 Sep 2024 16:37:49 -0400 Subject: [PATCH] build based on 5d5afc2 --- julia-docs/dev/docstrings.html | 246 ++++++++++---------- julia-docs/dev/medyan-tutorial.zip | Bin 751808 -> 751869 bytes julia-docs/dev/reference/fileformats.html | 68 +++--- julia-docs/dev/sitemap.xml | 264 +++++++++++----------- julia-docs/dev/tutorials/1install.html | 2 +- julia-docs/dev/tutorials/2rdme.html | 34 +-- julia-docs/dev/tutorials/3treadmill.html | 66 +++--- 7 files changed, 340 insertions(+), 340 deletions(-) diff --git a/julia-docs/dev/docstrings.html b/julia-docs/dev/docstrings.html index 0993693..9f55544 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 c9cf44a9c23b36b3c319e20c83b3fcf0b430ab50..be49ec50368dd3dac1e943221f3644c9604264df 100644 GIT binary patch delta 23551 zcmV(&K;gf@@h$!FEgMiv0|XQR00;;G001EXF!VwQqFMj|r33*09g`7T6PHgB3k{R+ z^B9p+HUuctsmhU!EoGnd3;D_KKHS~@FV%;?zsvXU_(e}fre3YA$)pr&30}tTymleR zE-5!zU9RSn-~H~t|GUwL`xl@7`OVAEZ?A9fsJ*`1-8|sC|L1>xceQ&E4|hc3{#{o5 z!7kX6dsIrM;P9c79|1-IU6W=3a(_SZ{(q*ojDMVe*q1*|JHGga)kFM!hqq2&y;{n* zSfszBZ;%5gf^x&>P)xZb)A)i!Uc46Wpl{dwxf*`#si 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z7#?ju@hl`a7+yE>iA=%=q`0{F=~pf?h?3;``^qE@%tGM($3mL!t^;~P;q7Etnu~D& zbB4k+ZFOX^k)61>vG>6Yx~*cxEYR zvXC>HBq8u42DU-cA^kmhTeO*eLV$NOY^qz2Nr)h7Gh7u;1{mo!fZ@EP`=l8yk)y^i zfTa~}83SWCScCax#=yiY!2bbCPlRJEe6N{|fg@F9!6e4WDH}|v*}^(+$HF=X0x{wj zL=pvRaga!dW27vcLC$^_{BqW{|<~a#KW6bdNMel0LM)z z0ghXEIwp1`psR4HpfLe%@6P)%*1I3}!ZZ<{>e>9)8w8N9Z)kN4W<9w{voB1#d zbPM!*4Cn+N4BOzg9$!Kt0pDXJ6npPAD)~=_r%(LtECFcrIudIB#w4(2E6nwsy8mLw zdXhMBbc2I8dJ5)>wiRxhrKgx)R`C1AOhE#UXQ0p0-M4ZZj9us)i|yk!_9>{Tr`EQopm1 epdF|seh{Vyo)i>%MU1jTJ5X^Bets05aQ_2Y7EUk# diff --git a/julia-docs/dev/reference/fileformats.html b/julia-docs/dev/reference/fileformats.html index 47f3a44..306438f 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"])

 

 
3×1914 Matrix{Int64}:
@@ -1131,7 +1131,7 @@ 
Example snapshot

 
 🔢 vertlist
 
-

+

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

 

 
3×959 Matrix{Float64}:
@@ -1146,7 +1146,7 @@ 
Example snapshot

 
 🔢 id
 
-

+

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

 

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

 
 optional 🔢 copynumbers
 
-

+

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

 

 
3×959 Matrix{Int64}:
diff --git a/julia-docs/dev/sitemap.xml b/julia-docs/dev/sitemap.xml
index b4ec1fa..c7aa52d 100644
--- a/julia-docs/dev/sitemap.xml
+++ b/julia-docs/dev/sitemap.xml
@@ -2,530 +2,530 @@
 
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.set_chemboundary--0aa6e4e95c60f9f7.html
-    2024-09-20T00:49:17.013Z
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     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/cadherins/possiblecadherinsite.html
-    2024-09-20T00:49:15.577Z
+    2024-09-24T20:34:46.785Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/boundary.html
-    2024-09-20T00:49:15.565Z
+    2024-09-24T20:34:46.781Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/src/minimize_energy.html
-    2024-09-20T00:49:16.989Z
+    2024-09-24T20:34:48.225Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.link_2mon_state-6d59dcd98ed7e303.html
-    2024-09-20T00:49:16.993Z
+    2024-09-24T20:34:48.229Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.link2monsitemotorstall-deb10f7964d5bef9.html
-    2024-09-20T00:49:17.057Z
+    2024-09-24T20:34:48.293Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.add_filament_params--74c7d0081157ca31.html
-    2024-09-20T00:49:17.049Z
+    2024-09-24T20:34:48.285Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.filter_grididat-58a94154d21e32b0.html
-    2024-09-20T00:49:17.045Z
+    2024-09-24T20:34:48.281Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/base.push--8715d52e2302aaeb.html
-    2024-09-20T00:49:17.041Z
+    2024-09-24T20:34:48.277Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.addmembranesite--892875b2c079002d.html
-    2024-09-20T00:49:16.997Z
+    2024-09-24T20:34:48.233Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.decimated2monsiterange-8afd8f3188bbcd4a.html
-    2024-09-20T00:49:17.021Z
+    2024-09-24T20:34:48.269Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.addcadherin--3c757785fa097c75.html
-    2024-09-20T00:49:17.009Z
+    2024-09-24T20:34:48.241Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.addreaction--da9bd35e7d1df7c3.html
-    2024-09-20T00:49:17.021Z
+    2024-09-24T20:34:48.265Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.link_2mon_endnames-5d0bca4b8e2e3509.html
-    2024-09-20T00:49:17.041Z
+    2024-09-24T20:34:48.277Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.context-736368ed32b08894.html
-    2024-09-20T00:49:17.025Z
+    2024-09-24T20:34:48.269Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.filtype_fil_ids-d333c38b9f9b3584.html
-    2024-09-20T00:49:17.045Z
+    2024-09-24T20:34:48.277Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.cadherinstate-0cd5353e58a90ec2.html
-    2024-09-20T00:49:17.013Z
+    2024-09-24T20:34:48.245Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/base.delete--56ef520341df3c06.html
-    2024-09-20T00:49:17.001Z
+    2024-09-24T20:34:48.233Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.boundary_capsule-1700142f310bd9db.html
-    2024-09-20T00:49:17.049Z
+    2024-09-24T20:34:48.281Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.filamentendsitegeneral-7a32ac96fb4364ea.html
-    2024-09-20T00:49:17.053Z
+    2024-09-24T20:34:48.289Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/base.getindex-f593dde852851bc8.html
-    2024-09-20T00:49:17.005Z
+    2024-09-24T20:34:48.241Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.vertex_state-aa3350c08b68b63a.html
-    2024-09-20T00:49:17.017Z
+    2024-09-24T20:34:48.265Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.resolve_all_filament_mesh_crossing--a8be83a7d2ad65c7.html
-    2024-09-20T00:49:17.061Z
+    2024-09-24T20:34:48.297Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.mon_position_plusvector-927d0affbbdfef6f.html
-    2024-09-20T00:49:16.997Z
+    2024-09-24T20:34:48.229Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/nlsolversbase.value---d4fdd3b317023c0e.html
-    2024-09-20T00:49:17.045Z
+    2024-09-24T20:34:48.277Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.is_chem_cache_valid-8336a8adc58a252f.html
-    2024-09-20T00:49:17.049Z
+    2024-09-24T20:34:48.285Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.sysdef-c0c4da7a2b3d4fef.html
-    2024-09-20T00:49:17.061Z
+    2024-09-24T20:34:48.297Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.monlink2monsiteone-77707f45e082c27e.html
-    2024-09-20T00:49:17.057Z
+    2024-09-24T20:34:48.293Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.addcadherinsite--9e21ac42968d0196.html
-    2024-09-20T00:49:17.013Z
+    2024-09-24T20:34:48.249Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.monomername-bb517706cb60c4f5.html
-    2024-09-20T00:49:17.009Z
+    2024-09-24T20:34:48.245Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.num_vertexwithstate-3cf6fcd964588d37.html
-    2024-09-20T00:49:17.041Z
+    2024-09-24T20:34:48.277Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.chem_newlink_2mon--e4f84fe5cfa9a727.html
-    2024-09-20T00:49:17.001Z
+    2024-09-24T20:34:48.237Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.minimize_energy--84c4aeab5457d3ee.html
-    2024-09-20T00:49:17.057Z
+    2024-09-24T20:34:48.293Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.fil_node_positions-618a66637eb50781.html
-    2024-09-20T00:49:17.013Z
+    2024-09-24T20:34:48.249Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.chem_addfixedcount--0286edfebf8ea5e6.html
-    2024-09-20T00:49:17.049Z
+    2024-09-24T20:34:48.285Z
   
   
     https://medyan-dev.github.io/julia-docs/dev/docstrings/medyan.newmembrane--a714b4a1c87062be.html
-    2024-09-20T00:49:17.049Z
+    2024-09-24T20:34:48.281Z
   
 
diff --git a/julia-docs/dev/tutorials/1install.html b/julia-docs/dev/tutorials/1install.html
index 0d29b48..bbc1346 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 1.10.5
 Commit 6f3fdf7b362 (2024-08-27 14:19 UTC)
diff --git a/julia-docs/dev/tutorials/2rdme.html b/julia-docs/dev/tutorials/2rdme.html
index 5706fe4..3a2dae4 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

 

-

+

 

     

-