Demonstration of file storage of system concentration history, and stop-restart of simulation, for the reaction `A <-> B`,¶

with 1st-order kinetics in both directions, taken to equilibrium.

Same as experiment react_1_a, but with CSV file storage of the concentration history, and reaction stop-restart.

TAGS : "basic", "uniform compartment"¶

In [1]:

LAST_REVISED = "Aug. 29, 2025"
LIFE123_VERSION = "1.0.0rc6"         # Library version this experiment is based on

In [2]:

#import set_path            # Using MyBinder?  Uncomment this before running the next cell!
                            # Importing this module will add the project's home directory to sys.path

In [3]:

#import sys
#sys.path.append("C:/some_path/my_env_or_install")   # CHANGE to the folder containing your venv or libraries installation!
# NOTE: If any of the imports below can't find a module, uncomment the lines above, or try:  import set_path

import ipynbname
import life123

In [4]:

life123.check_version(LIFE123_VERSION)    # To check compatibility

OK

In [5]:

# Initialize logging (for the system state)
csv_log_file = ipynbname.name() + "_system_log.csv"   # Use the notebook base filename 
                                                      # IN CASE OF PROBLEMS, set manually to any desired name

In [ ]:

Initialize the Uniform-Compartment Simulation¶

In [6]:

# Instantiate the simulator and specify the chemicals
uc = life123.UniformCompartment()  

In [7]:

# We're now requesting that all System Concentration Data get logged in our previously-specified CSV file
uc.start_csv_log(csv_log_file)

-> CSV-format output will be LOGGED into the file 'react_1_b_system_log.csv' . An existing file by that name was over-written

In [8]:

# Reaction A <-> B , with 1st-order kinetics in both directions
uc.add_reaction(reactants="A", products="B", kF=3., kR=2.)

uc.describe_reactions()

Number of reactions: 1
0: A <-> B  (Elementary Unimolecular reaction)  (kF = 3 / kR = 2 / delta_G = -1,005.1 / K = 1.5 / Temp = 25 C)
Chemicals involved in the above reactions: ['A', 'B']

In [9]:

# Set the initial concentrations of all the chemicals
uc.set_conc({"A": 80., "B": 10.})

In [ ]:

This time (contrasted to experiment `react_1_a`) we'll be running the simulation in two parts¶

In [ ]:

Part 1 (early run)¶

In [10]:

uc.single_compartment_react(initial_step=0.1, target_end_time=0.2)   # The first part of our run

28 total variable step(s) taken in 0.00 min
Number of step re-do's because of elective soft aborts: 3
Norm usage: {'norm_A': 12, 'norm_B': 8, 'norm_C': 8, 'norm_D': 8}
System Time is now: 0.2117

In [11]:

uc.get_history()      # The system's concentrations history, saved during the run of single_compartment_react()

Out[11]:

	SYSTEM TIME	A	B	step	caption
0	0.000000	80.000000	10.000000		Set concentration
1	0.006400	78.592000	11.408000	1	1st reaction step
2	0.009600	77.910528	12.089472	2
3	0.013440	77.105846	12.894154	3
4	0.018048	76.158767	13.841233	4
5	0.023578	75.048458	14.951542	5
6	0.029107	73.968846	16.031154	6
7	0.034637	72.919083	17.080917	7
8	0.040166	71.898344	18.101656	8
9	0.045696	70.905827	19.094173	9
10	0.052332	69.747735	20.252265	10
11	0.058967	68.628067	21.371933	11
12	0.065603	67.545546	22.454454	12
13	0.072238	66.498940	23.501060	13
14	0.078874	65.487058	24.512942	14
15	0.085509	64.508749	25.491251	15
16	0.093472	63.373726	26.626274	16
17	0.101434	62.283893	27.716107	17
18	0.109397	61.237449	28.762551	18
19	0.117360	60.232668	29.767332	19
20	0.125322	59.267889	30.732111	20
21	0.134877	58.156249	31.843751	21
22	0.144433	57.097717	32.902283	22
23	0.153988	56.089758	33.910242	23
24	0.163543	55.129955	34.870045	24
25	0.175009	54.033218	35.966782	25
26	0.186475	52.999357	37.000643	26
27	0.197941	52.024769	37.975231	27
28	0.211701	50.922312	39.077688	28	last reaction step

In [12]:

uc.plot_history(show_intervals=True)

In [13]:

# We're nowhere near equilibrium yet!
uc.is_in_equilibrium()

0: A <-> B
Current concentrations: [A] = 50.92 ; [B] = 39.08
1. Ratio of reactant/product concentrations, adjusted for reaction orders: 0.767398
    Formula used:  [B] / [A]
2. Ratio of forward/reverse reaction rates: 1.5
Discrepancy between the two values: 48.84 %
Reaction is NOT in equilibrium (not within 1% tolerance)

Out[13]:

{False: [0]}

In [ ]:

Part 2 (late run)¶

In [14]:

initial_step = 0.013759414272    # We're choosing this value simply FOR DEMONSTRATION PURPOSES,
                                 # to remain in exact lockstep with the time course of experiment `react_1_a`

'''
If you run experiment `react_1_a`, you can determine what the next time step would have been, had we not stopped early this time.

    In experiment `react_1_a`, after running the simulation, you can issue:

    list(uc.get_history(t_start=0.21, t_end=0.23, columns="SYSTEM TIME"))

    and you will get:  [0.211700785152, 0.225460199424]

    Their difference is the initial_step we're using here.
''';

In [15]:

uc.single_compartment_react(initial_step=0.013759414272, target_end_time=1.0)   # The 2nd part of our run, to the final target end time

19 total variable step(s) taken in 0.00 min
Norm usage: {'norm_A': 14, 'norm_B': 14, 'norm_C': 14, 'norm_D': 14}
System Time is now: 1.1343

In [16]:

uc.get_history()   # The cumulative system's history

Out[16]:

	SYSTEM TIME	A	B	step	caption
0	0.000000	80.000000	10.000000		Set concentration
1	0.006400	78.592000	11.408000	1	1st reaction step
2	0.009600	77.910528	12.089472	2
3	0.013440	77.105846	12.894154	3
4	0.018048	76.158767	13.841233	4
5	0.023578	75.048458	14.951542	5
6	0.029107	73.968846	16.031154	6
7	0.034637	72.919083	17.080917	7
8	0.040166	71.898344	18.101656	8
9	0.045696	70.905827	19.094173	9
10	0.052332	69.747735	20.252265	10
11	0.058967	68.628067	21.371933	11
12	0.065603	67.545546	22.454454	12
13	0.072238	66.498940	23.501060	13
14	0.078874	65.487058	24.512942	14
15	0.085509	64.508749	25.491251	15
16	0.093472	63.373726	26.626274	16
17	0.101434	62.283893	27.716107	17
18	0.109397	61.237449	28.762551	18
19	0.117360	60.232668	29.767332	19
20	0.125322	59.267889	30.732111	20
21	0.134877	58.156249	31.843751	21
22	0.144433	57.097717	32.902283	22
23	0.153988	56.089758	33.910242	23
24	0.163543	55.129955	34.870045	24
25	0.175009	54.033218	35.966782	25
26	0.186475	52.999357	37.000643	26
27	0.197941	52.024769	37.975231	27
28	0.211701	50.922312	39.077688	28	last reaction step
29	0.225460	49.895700	40.104300	1	1st reaction step
30	0.239220	48.939717	41.060283	2
31	0.255731	47.871459	42.128541	3
32	0.272242	46.891393	43.108607	4
33	0.292056	45.812407	44.187593	5
34	0.311869	44.840314	45.159686	6
35	0.335646	43.789365	46.210635	7
36	0.359422	42.863355	47.136645	8
37	0.387953	41.884245	48.115755	9
38	0.422191	40.876927	49.123073	10
39	0.456429	40.042050	49.957950	11
40	0.497514	39.211704	50.788296	12
41	0.546817	38.419979	51.580021	13
42	0.605980	37.704113	52.295887	14
43	0.676975	37.099191	52.900809	15
44	0.762170	36.630965	53.369035	16
45	0.864404	36.308436	53.691564	17
46	0.987084	36.119241	53.880759	18
47	1.134300	36.031470	53.968530	19	last reaction step

In [17]:

uc.plot_history(show_intervals=True)

In [18]:

# Verify that the reaction has reached equilibrium
uc.is_in_equilibrium()

0: A <-> B
Current concentrations: [A] = 36.03 ; [B] = 53.97
1. Ratio of reactant/product concentrations, adjusted for reaction orders: 1.49782
    Formula used:  [B] / [A]
2. Ratio of forward/reverse reaction rates: 1.5
Discrepancy between the two values: 0.1456 %
Reaction IS in equilibrium (within 1% tolerance)

Out[18]:

True

In [ ]:

As we requested, a log of the concentration data, in CSV format, has ben saved in the following file:¶

In [19]:

csv_log_file

Out[19]:

'react_1_b_system_log.csv'

In [20]:

# Here's dump of the contents of that log file
with open(csv_log_file, 'r', encoding='utf8') as fh:
    file_contents = fh.read()
    print(file_contents)

SYSTEM TIME,A,B,step,caption
0.0,80.0,10.0,,Set concentration
0.006400000000000002,78.592,11.408000000000001,1,1st reaction step
0.009600000000000003,77.910528,12.089472,2,
0.013440000000000004,77.1058458624,12.894154137600001,3,
0.018048000000000005,76.15876717373031,13.841232826269698,4,
0.023577600000000004,75.04845757891101,14.951542421088993,5,
0.029107200000000007,73.96884582376929,16.031154176230725,6,
0.03463680000000001,72.91908317443371,17.080916825566298,7,
0.04016640000000001,71.89834436282696,18.101655637173042,8,
0.045696000000000014,70.90582693788352,19.094173062116482,9,
0.05233152000000001,69.7477353740692,20.252264625930806,10,
0.05896704000000001,68.62806650892247,21.371933491077524,11,
0.06560256000000002,67.54554556951605,22.45445443048395,12,
0.07223808000000002,66.49894007682887,23.501059923171127,13,
0.07887360000000003,65.48705844253587,24.512941557464124,14,
0.08550912000000004,64.50874861235279,25.491251387647203,15,
0.09347174400000004,63.373726382799354,26.62627361720064,16,
0.10143436800000004,62.2838929294738,27.716107070526196,17,
0.10939699200000004,61.237449146205506,28.762550853794487,18,
0.11735961600000004,60.23266755485373,29.767332445146263,19,
0.12532224000000003,59.26788945357223,30.732110546427762,20,
0.13487738880000003,58.15624872361806,31.84375127638193,21,
0.14443253760000002,57.09771745659816,32.90228254340183,22,
0.15398768640000002,56.0897583084074,33.910241691592596,23,
0.16354283520000001,55.12995515844305,34.87004484155694,24,
0.17500901376000003,54.033217749985546,35.96678225001445,25,
0.18647519232000004,52.999357276322066,37.00064272367793,26,
0.19794137088000005,52.02476894664434,37.97523105335565,27,
0.21170078515200005,50.92231177389454,39.07768822610545,28,
0.22546019942400006,49.89570042592975,40.10429957407024,1,1st reaction step
0.23921961369600006,48.93971693212988,41.06028306787011,2,
0.25573091082240007,47.871459377140354,42.12854062285964,3,
0.27224220794880005,46.89139341164059,43.1086065883594,4,
0.29205576450048004,45.81240721519991,44.18759278480008,5,
0.31186932105216003,44.84031378886753,45.15968621113246,6,
0.335645588914176,43.78936544572559,46.2106345542744,7,
0.359421856776192,42.863355249162076,47.13664475083792,8,
0.38795337821061116,41.88424541214457,48.11575458785542,9,
0.42219120393191417,40.87692656753266,49.123073432467336,10,
0.4564290296532172,40.042049758158775,49.95795024184122,11,
0.4975144205187808,39.21170378709872,50.78829621290127,12,
0.5468168895574572,38.41997915447455,51.580020845525446,13,
0.6059798524038689,37.704113470448206,52.29588652955179,14,
0.6769754078195629,37.099191058819024,52.90080894118097,15,
0.7621700743183957,36.630964980446095,53.3690350195539,16,
0.8644036741169949,36.30843587395681,53.69156412604318,17,
0.9870839938753141,36.11924081574702,53.88075918425297,18,
1.1343003775852971,36.031469807322495,53.9685301926775,19,

In [ ]:

Demonstration of file storage of system concentration history, and stop-restart of simulation, for the reaction A <-> B,¶

TAGS : "basic", "uniform compartment"¶

Initialize the Uniform-Compartment Simulation¶

This time (contrasted to experiment react_1_a) we'll be running the simulation in two parts¶

Part 1 (early run)¶

Part 2 (late run)¶

As we requested, a log of the concentration data, in CSV format, has ben saved in the following file:¶

Demonstration of file storage of system concentration history, and stop-restart of simulation, for the reaction `A <-> B`,¶

This time (contrasted to experiment `react_1_a`) we'll be running the simulation in two parts¶