# jLM CME Imports
from jLM.CME import CMESimulation
from jLM.units import *
from jLM.LMLogger import *
from jLM.CMEPostProcessing import *

outputFile = "bimol.lm"

# Set up logging #
#  Here we define the amount of logging information that
#  pyLM will print when it is running.  The amount of
#  information will increase with the levels:
#    DEBUG > INFO > WARNING > ERROR > CRITICAL
import os
import logging

setLMLoggerLevel(logging.INFO)

# Specify Simulation #
# We begin by creating a CME Simulation that will 
#  include the whole problem definition.
sim = CMESimulation()

# Here we register the chemical species with simulation;
#  first by specifing the names of the chemical species
#  followed by the actual command to register those species
#  with the simulation.  The defineSpecies command can
#  be called multiple times and will add any new names
#  to the list of species.
species = ['A', 'B', 'C']
sim.defineSpecies(species)

# Add reactions to the simulation adding a bimolecular 
#  association reaction and a unimolecular dissociation
#  reaction. When more than one reactant is involved,
#  the list of reactant names should be passed as a 
#  tuple.
sim.addReaction(reactant = ('A', 'B'), product = 'C',        rate = 1.78e-4)
sim.addReaction(reactant = 'C',        product = ('A', 'B'), rate = 3.51e-1)

# Set our initial species counts
sim.addParticles(species = 'A', count = 1000)
sim.addParticles(species = 'B', count = 1000)
sim.addParticles(species = 'C', count = 0)

# Define simulation parameters: run for 10 seconds, 
#  saving data every ms. The simulation must be saved to 
#  disk using the save() command before the simulation can be run.
sim.setWriteInterval(ms(1))
sim.setSimulationTime(10)

os.system("rm -rf %s"%(outputFile))
sim.save(outputFile)

# Run the Simulation #
# Here we declare that the simulation will be run using the Gillespie 
#  algorithm and that we want 50 independent samplings of the
#  solution.
sim.run(filename = outputFile, method = "lm::cme::GillespieDSolver", replicates = 50)

  0%|          | 0/50 [00:00<?, ?it/s]

2025-09-02 15:31:25) Info: Using 32 processor(s) and 1 CUDA device(s) per process.
2025-09-02 15:31:25) Info: Assigning 1.00 processor(s) and 1.00 CUDA device(s) per replicate.
2025-09-02 15:31:25) Info: Data output thread running.
2025-09-02 15:31:25) Info: Seeding xorwow rng with top word 1 and bottom word 638137815
2025-09-02 15:31:25) Info: Data output thread finished.
2025-09-02 15:31:25) Info: Simulation file closed.

  2%|2         | 1/50 [00:00<00:13,  3.53it/s]

2025-09-02 15:31:25) Info: Using 32 processor(s) and 1 CUDA device(s) per process.
2025-09-02 15:31:25) Info: Assigning 1.00 processor(s) and 1.00 CUDA device(s) per replicate.
2025-09-02 15:31:25) Info: Data output thread running.
2025-09-02 15:31:25) Info: Seeding xorwow rng with top word 2 and bottom word 701077397
2025-09-02 15:31:25) Info: Data output thread finished.
2025-09-02 15:31:25) Info: Simulation file closed.
2025-09-02 15:31:25) Info: Using 32 processor(s) and 1 CUDA device(s) per process.
2025-09-02 15:31:25) Info: Assigning 1.00 processor(s) and 1.00 CUDA device(s) per replicate.
2025-09-02 15:31:25) Info: Data output thread running.
2025-09-02 15:31:25) Info: Seeding xorwow rng with top word 3 and bottom word 756620449
2025-09-02 15:31:25) Info: Data output thread finished.
2025-09-02 15:31:25) Info: Simulation file closed.

  6%|6         | 3/50 [00:00<00:05,  8.72it/s]

2025-09-02 15:31:25) Info: Using 32 processor(s) and 1 CUDA device(s) per process.
2025-09-02 15:31:25) Info: Assigning 1.00 processor(s) and 1.00 CUDA device(s) per replicate.
2025-09-02 15:31:25) Info: Data output thread running.
2025-09-02 15:31:25) Info: Seeding xorwow rng with top word 4 and bottom word 812079371
2025-09-02 15:31:25) Info: Data output thread finished.
2025-09-02 15:31:25) Info: Simulation file closed.
2025-09-02 15:31:25) Info: Using 32 processor(s) and 1 CUDA device(s) per process.
2025-09-02 15:31:25) Info: Assigning 1.00 processor(s) and 1.00 CUDA device(s) per replicate.
2025-09-02 15:31:25) Info: Data output thread running.
2025-09-02 15:31:25) Info: Seeding xorwow rng with top word 5 and bottom word 868027083
2025-09-02 15:31:25) Info: Data output thread finished.
2025-09-02 15:31:25) Info: Simulation file closed.

 10%|#         | 5/50 [00:00<00:03, 11.80it/s]

2025-09-02 15:31:25) Info: Using 32 processor(s) and 1 CUDA device(s) per process.
2025-09-02 15:31:25) Info: Assigning 1.00 processor(s) and 1.00 CUDA device(s) per replicate.
2025-09-02 15:31:25) Info: Data output thread running.
2025-09-02 15:31:25) Info: Seeding xorwow rng with top word 6 and bottom word 924908255
2025-09-02 15:31:25) Info: Data output thread finished.
2025-09-02 15:31:25) Info: Simulation file closed.
2025-09-02 15:31:25) Info: Using 32 processor(s) and 1 CUDA device(s) per process.
2025-09-02 15:31:25) Info: Assigning 1.00 processor(s) and 1.00 CUDA device(s) per replicate.
2025-09-02 15:31:25) Info: Data output thread running.
2025-09-02 15:31:26) Info: Seeding xorwow rng with top word 7 and bottom word 980936137
2025-09-02 15:31:26) Info: Data output thread finished.
2025-09-02 15:31:26) Info: Simulation file closed.

 14%|#4        | 7/50 [00:00<00:03, 13.81it/s]

2025-09-02 15:31:26) Info: Using 32 processor(s) and 1 CUDA device(s) per process.
2025-09-02 15:31:26) Info: Assigning 1.00 processor(s) and 1.00 CUDA device(s) per replicate.
2025-09-02 15:31:26) Info: Data output thread running.
2025-09-02 15:31:26) Info: Seeding xorwow rng with top word 8 and bottom word 36093979
2025-09-02 15:31:26) Info: Data output thread finished.
2025-09-02 15:31:26) Info: Simulation file closed.
2025-09-02 15:31:26) Info: Using 32 processor(s) and 1 CUDA device(s) per process.
2025-09-02 15:31:26) Info: Assigning 1.00 processor(s) and 1.00 CUDA device(s) per replicate.
2025-09-02 15:31:26) Info: Data output thread running.
2025-09-02 15:31:26) Info: Seeding xorwow rng with top word 9 and bottom word 91332080
2025-09-02 15:31:26) Info: Data output thread finished.
2025-09-02 15:31:26) Info: Simulation file closed.