In [1]:
from jLM.units import *
from jLM.RDME import Sim as RDMESim
from jLM.RegionBuilder import RegionBuilder
In [2]:
### Define our own solver class derived from MpdRdmeSolver
class MyOwnSolver(lm.MpdRdmeSolver):

	# The hookSimulation method defined here will be called at every frame write
	# time.  The return value is either 0 or 1, which will indicate if we
	# changed the state or not and need the lattice to be copied back to the GPU
	# before continuing.  If you do not return 1, your changes will not be
	# reflected.
	def hookSimulation(self, time, lattice):
		print("\n\nBegin hook of MyOwnSolver: Adding 1 particle of type C\n\n")
		lattice.addParticle(16,16,16,3);
		return 1

	def onBeginTrajectory(self, lattice):
		print(" *************************************")
		print("          H E L L O ! ! ! ! ! ! !")
		print(" *************************************")
		return 0


	def onEndTrajectory(self, lattice):
		print(" *************************************")
		print("    G O O D B Y E ! ! ! ! ! ! ! !")
		print(" *************************************")

		return 0

# End of MyOwnSolver class.  That's it!
In [3]:
outputFile = "extendrdme.lm"
latticeSpacing = nm(32)
In [4]:
m_size = micron(1.024, 1.024, 1.024)
lx, ly, lz = [int(round(cDim / latticeSpacing)) for cDim in m_size]
In [5]:
# Create our simulation object
sim = RDMESim("RDME Extension",
              outputFile,
              [lx, ly, lz],
              latticeSpacing,
              "default",
              "Byte",
              50e-6)
In [6]:
B = RegionBuilder(sim)
default = B.box(lx, ly, lz)
In [7]:
B.compose(
    (sim.region('default'), default)
)
In [8]:
with sim.construct():
    sim.species('A', texRepr = 'A', annotation = "Species A")
    sim.species('B', texRepr = 'B', annotation = "Species B")
    sim.species('C', texRepr = 'C', annotation = "Species C")
New Species
Index Name Annotation
1 A Species A
2 B Species B
3 C Species C
In [9]:
with sim.construct():
    sim.diffusionConst("dRate", 2.5e-12, texRepr = r'd_{Rate}', annotation = 'Default Diffusion Rate')
New diffusion constants
Index Name Value Annotation
0 $$d_{Rate}$$ 2.500 × 10-12 m2⋅s-1  Default Diffusion Rate
In [10]:
dc = sim.dc

with sim.construct():
    sim.transitionRate(None, None, None, dc.dRate)
In [11]:
with sim.construct():
    sim.rateConst('fRate', 0.5, order = 1, annotation = "First Order Reaction Rate")
New reaction rates
Index Name Value Annotation
0 $$k_{\mathrm{fRate}}$$ 0.500 s-1  First Order Reaction Rate
In [12]:
sp  = sim.sp
rc  = sim.rc
reg = sim.reg

with sim.construct():
    sim.reaction([sp.A], [sp.B], rc.fRate, annotation = "First Order Reaction", regions = [reg.default])
New reactions
Index Reaction Rate Regions Annotation
0 $$A\overset{k_{\mathrm{fRate}}}{\longrightarrow}B$$ 0.500 s-1  default First Order Reaction
In [13]:
with sim.construct():
    sim.distributeNumber(sp.A, reg.default, 1000)
    sim.distributeNumber(sp.B, reg.default, 1000)
In [14]:
sim.simulationTime = 10

hook_interval = ms(10)
sim.hookInterval = int(hook_interval / sim.timestep)

write_interval = ms(100)
sim.latticeWriteInterval = int(write_interval / sim.timestep)
sim.speciesWriteInterval = int(write_interval / sim.timestep)
In [15]:
solver = MyOwnSolver()
sim.finalize()
sim.run(solver = solver, cudaDevices = [0])

nodiffregion in finalize: []
2025-09-02 15:31:52) Info: Using 32 processor(s) and 1 CUDA device(s) per process.
2025-09-02 15:31:52) Info: Assigning 1.00 processor(s) and 1.00 CUDA device(s) per replicate.
2025-09-02 15:31:52) Info: Data output thread running.
2025-09-02 15:31:52) Info: MPDRDME: Rng seed: top word 1585160580, bottom word 1
 *************************************
          H E L L O ! ! ! ! ! ! !
 *************************************


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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




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Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C




Begin hook of MyOwnSolver: Adding 1 particle of type C


 *************************************
    G O O D B Y E ! ! ! ! ! ! ! !
 *************************************
2025-09-02 15:31:59) Info: Data output thread finished.
2025-09-02 15:31:59) Info: Simulation file closed.
Out[15]:

RDME Extension

Key

  • default

xy-plane; z-index=0

No description has been provided for this image
Simulation
Time step 50.000 µs
Simulation time 10.000 s
Lattice write interval 2.000 × 103 s
Particle count write interval 2.000 × 103 s
Number of replicates 1
Trajectory data
Replicate Simulated time Lattice times Count times Initial count Final count
0000001 10.000 s 101 101 2000 3001
Lattice
Dimensions 32 × 32 × 32
Particles per site 16
Bytes per particle 1
Lattice spacing 32.000 nm
Subvolume size 3.277 × 10-5 fl
Model summary
Output file extendrdme.lm
Number of species 3
Number of reactions 1
Number of region types 1
Number of rate constants 1
Number of diffusion constants 1
Number of placed particles 0
Region summary
Region Subvolumes Volume Particles Concentration Occupancy
default 32768 1.074 fl 3001 4.641 µM $0.57\,\%$