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Emergent Dynamics in Living Systems
InPartS Models
InPartSBiome.jl
Commits
d12d367f
Commit
d12d367f
authored
2 weeks ago
by
Ilias-Marios Sarris
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Update FieldParticleContainer to support arbitrary dimensions and abstract boxing
parent
7f1c3ae3
Branches
update-fieldcontainer-dimensions
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1 merge request
!9
Update FieldParticleContainer to support arbitrary dimensions and abstract boxing
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src/fieldcontainers.jl
+48
-45
48 additions, 45 deletions
src/fieldcontainers.jl
with
48 additions
and
45 deletions
src/fieldcontainers.jl
+
48
−
45
View file @
d12d367f
...
...
@@ -6,87 +6,90 @@ export FieldParticleContainer, FieldParticleObstacleContainer
###########################################################################################
# Field Particle Container : Use BoxGrid - no obstacles #
###########################################################################################
# both Field*Containers IGNORE THE DIMENSION PARAMETER and ONLY WORK IN 2D!!!!!111!!
mutable struct
FieldParticleContainer
{
N
,
PT
<:
AbstractParticle
,
FT
}
<:
AbstractParticleContainer
{
N
}
mutable struct
FieldParticleContainer
{
N
,
PT
<:
AbstractParticle
,
FT
}
<:
AbstractParticleContainer
{
N
}
particles
::
Vector
{
PT
}
field
::
Vector
{
FT
}
boxgrid
::
BoxGrid
{
2
,
Float64
,
PT
}
function
FieldParticleContainer
{
N
,
PT
,
FT
}()
where
{
N
,
PT
,
FT
}
if
N
!=
2
@warn
"FieldParticleContainer does not work with N ≠ 2 (yet)"
end
return
new
{
2
,
PT
,
FT
}(
PT
[],
FT
[])
boxgrid
::
AbstractBoxing
# Store any boxing type here (BoxGrid or NoBoxing)
function
FieldParticleContainer
{
N
,
PT
,
FT
}()
where
{
N
,
PT
<:
AbstractParticle
,
FT
}
# Instead of calling BoxGrid{N,Float64,PT}(), default to a no-op boxing
return
new
{
N
,
PT
,
FT
}(
PT
[],
FT
[],
NoBoxing
())
end
end
FieldParticleContainer
(
PT
::
Type
{
<:
AbstractParticle
},
FT
)
=
FieldParticleContainer
{
2
,
PT
,
FT
}()
function
initialize_pc!
(
sim
::
Simulation
{
<:
FieldParticleContainer
{
N
,
PT
}})
where
{
N
,
PT
<:
AbstractParticle
}
function
FieldParticleContainer
(
PT
::
Type
{
<:
AbstractParticle
},
FT
,
N
::
Int
)
return
FieldParticleContainer
{
N
,
PT
,
FT
}()
end
function
FieldParticleContainer
(
PT
::
Type
{
<:
AbstractParticle
{
N
}},
FT
)
where
{
N
}
return
FieldParticleContainer
{
N
,
PT
,
FT
}()
end
function
initialize_pc!
(
sim
::
Simulation
{
<:
FieldParticleContainer
{
N
,
PT
,
FT
}})
where
{
N
,
PT
<:
AbstractParticle
,
FT
}
# The 'BoxGrid{N,Float64,PT}(sim)' constructor calls `BoxGrid(sim)`
sim
.
particles
.
boxgrid
=
BoxGrid
{
N
,
Float64
,
PT
}(
sim
)
return
nothing
end
Base
.
push!
(
pc
::
FieldParticleContainer
,
x
)
=
push!
(
pc
.
particles
,
x
)
Base
.
append!
(
pc
::
FieldParticleContainer
,
xs
)
=
append!
(
pc
.
particles
,
xs
)
Base
.
push!
(
pc
::
FieldParticleContainer
,
p
)
=
push!
(
pc
.
particles
,
p
)
Base
.
append!
(
pc
::
FieldParticleContainer
,
ps
)
=
append!
(
pc
.
particles
,
ps
)
InPartS
.
particles
(
sim
::
Simulation
{
<:
FieldParticleContainer
})
=
sim
.
particles
.
particles
InPartS
.
particletype
(
::
FieldParticleContainer
{
N
,
PT
})
where
{
N
,
PT
}
=
PT
InPartS
.
flushadditions!
(
pc
::
FieldParticleContainer
,
ab
::
Vector
)
=
flushadditions!
(
pc
.
particles
,
ab
)
InPartS
.
flushdeletions!
(
pc
::
FieldParticleContainer
,
db
)
=
flushdeletions!
(
pc
.
particles
,
db
)
InPartS
.
particletype
(
::
FieldParticleContainer
{
N
,
PT
,
FT
})
where
{
N
,
PT
,
FT
}
=
PT
InPartS
.
flushadditions!
(
pc
::
FieldParticleContainer
,
newparticles
::
Vector
)
=
flushadditions!
(
pc
.
particles
,
newparticles
)
InPartS
.
flushdeletions!
(
pc
::
FieldParticleContainer
,
rmids
)
=
flushdeletions!
(
pc
.
particles
,
rmids
)
InPartS
.
findbyid
(
pc
::
FieldParticleContainer
,
id
)
=
findbyid
(
pc
.
particles
,
id
)
InPartS
.
setparticles!
(
pc
::
FieldParticleContainer
,
ps
)
=
(
empty!
(
pc
.
particles
);
append!
(
pc
.
particles
,
ps
))
InPartS
.
alldynamicobjects
(
sim
::
Simulation
{
<:
FieldParticleContainer
})
=
vcat
(
sim
.
particles
.
particles
,
sim
.
particles
.
field
)
## FORCE COMPUTATION ###########################################################
@forcedef
function
computeforces!
(
sim
::
Simulation
{
<:
FieldParticleContainer
})
@forcedef
function
InPartS.computeforces!
(
sim
::
Simulation
{
<:
FieldParticleContainer
})
pc
=
sim
.
particles
# Pairwise interactions among particles
pairwise_interactions
(
externalforces!
,
sim
,
pc
.
boxgrid
)
for
p
in
particles
(
sim
)
# Internal forces (e.g. springs) for each particle
for
p
in
pc
.
particles
internalforces!
(
p
,
sim
)
end
for
f
in
pc
.
field
# maybe more than one field
for
p
in
particles
(
sim
)
# Field–particle interactions
for
f
in
pc
.
field
for
p
in
pc
.
particles
fieldinteraction!
(
f
,
p
,
sim
)
end
end
end
function
Base.show
(
io
::
IO
,
::
MIME
"text/plain"
,
pc
::
FieldParticleContainer
{
PT
})
where
{
PT
}
print
(
io
,
"""FieldParticleContainer{
$
PT}
\t
$(PT)
:
$
(length(pc.particles))"""
)
end
# This definition is not strictly necessary but should help with speed
function
InPartS.propagate!
(
sim
::
Simulation
{
<:
FieldParticleContainer
},
dt
)
for
particle
∈
particles
(
sim
)
# Step each particle
for
particle
in
particles
(
sim
)
InPartS
.
step!
(
particle
,
dt
,
sim
)
end
for
f
ield
in
sim
.
particles
.
field
InPartS
.
step!
(
f
ield
,
dt
,
sim
)
# Step each field
for
f
in
sim
.
particles
.
field
InPartS
.
step!
(
f
,
dt
,
sim
)
end
flushdeletions!
(
sim
)
flushadditions!
(
sim
)
for
particle
∈
particles
(
sim
)
# Let each particle fold back into domain if needed, then reset
for
particle
in
particles
(
sim
)
fold_back!
(
particle
,
sim
.
domain
)
reset!
(
particle
,
sim
)
end
return
nothing
end
# Printing
function
Base.show
(
io
::
IO
,
::
MIME
"text/plain"
,
pc
::
FieldParticleContainer
{
N
,
PT
,
FT
})
where
{
N
,
PT
,
FT
}
print
(
io
,
"FieldParticleContainer{
$
N,
$
PT,
$
FT}
\n
"
)
print
(
io
,
" #particles = "
,
length
(
pc
.
particles
),
"
\n
"
)
print
(
io
,
" #fields = "
,
length
(
pc
.
field
),
"
\n
"
)
end
###########################################################################################
# Field Particle Obstacle Container : Use BoxGrid - obstacles #
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