Check isomorphism of lists with 4+ species #2303

zhaoyangwx · 2022-05-09T13:52:07Z

Motivation or Problem

Sometimes need to compare reaction with 4+ reactants/products.

Description of Changes

Added checking for list with 4+ reactants/products.
Added limitation of list length to prevent too long input causing hanging.
Improved performance by adjusting sequence to avoid unnecessary calculation of list length.

Testing

Tested with simplified program:

list1 = [1,2,3,4,6,5]
list2 = [6,5,2,4,1,3]
list3 = [6,2,3,1,1,4]
list4 = [7,2,3,1,5,4]
def same(x,y):
	return (x==y)
def issamelist(l1,l2):
	l1=l1[:]
	l2=l2[:]
	x=0
	while x<len(l1):
		found_y = False
		for y in range(len(l2)):
			if same(l1[x],l2[y]):
				found_y = True
				del l1[x]
				x-=1
				del l2[y]
				break
		if not(found_y):
			return False
		x+=1
	return (len(l1)==0) and (len(l2)==0)
print(issamelist(list1,list2))
print(issamelist(list1,list3))
print(issamelist(list1,list4))
print(list1)

######output######
True
False
False
[1, 2, 3, 4, 6, 5]

Reviewer Tips

maximum_length may be adjusted

codecov · 2023-05-12T23:51:24Z

Codecov Report

Merging #2303 (5dc8434) into main (d643642) will decrease coverage by 0.44%.
The diff coverage is n/a.

❗ Current head 5dc8434 differs from pull request most recent head 9e798f0. Consider uploading reports for the commit 9e798f0 to get more accurate results

@@            Coverage Diff             @@
##             main    #2303      +/-   ##
==========================================
- Coverage   48.54%   48.11%   -0.44%     
==========================================
  Files         110      110              
  Lines       30812    30625     -187     
  Branches     8054     7988      -66     
==========================================
- Hits        14959    14734     -225     
- Misses      14329    14363      +34     
- Partials     1524     1528       +4

see 21 files with indirect coverage changes

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Sometimes need to compare reaction with 4+ reactants/products. Improved performance by avoid unnecessary calculation of list length.

Updated comparison for two lists with same elements but different sequence.

Reduce calculations

Argument list changes cause error when compiling. No need to add new argument maximum_length. Also no need to define individual function in list comparison.

github-actions · 2023-07-24T23:45:22Z

Regression Testing Results

⚠️ One or more regression tests failed.
Please download the failed results and run the tests locally or check the log to see why.

Detailed regression test results.

Regression test aromatics:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:23
Current: Execution time (DD:HH:MM:SS): 00:00:01:16
Reference: Memory used: 2097.70 MB
Current: Memory used: 2090.73 MB

aromatics Passed Core Comparison ✅

Original model has 15 species.
Test model has 15 species. ✅
Original model has 11 reactions.
Test model has 11 reactions. ✅

aromatics Passed Edge Comparison ✅

Original model has 106 species.
Test model has 106 species. ✅
Original model has 358 reactions.
Test model has 358 reactions. ✅

Details

Observables Test Case: Aromatics Comparison

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions!

aromatics Passed Observable Testing ✅

Regression test liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:47
Current: Execution time (DD:HH:MM:SS): 00:00:02:35
Reference: Memory used: 2216.73 MB
Current: Memory used: 2214.77 MB

liquid_oxidation Failed Core Comparison ❌

Original model has 37 species.
Test model has 37 species. ✅
Original model has 216 reactions.
Test model has 215 reactions. ❌
The original model has 1 reactions that the tested model does not have. ❌
rxn: CCO[O](31) <=> [OH](22) + CC=O(69) origin: intra_H_migration

Non-identical kinetics! ❌
original:
rxn: CCCC(C)O[O](20) + CCCCCO[O](104) <=> oxygen(1) + CCCC(C)[O](61) + CCCCC[O](127) origin: Peroxyl_Disproportionation
tested:
rxn: CCCC(C)O[O](20) + CCCCCO[O](103) <=> oxygen(1) + CCCC(C)[O](64) + CCCCC[O](128) origin: Peroxyl_Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	3.77	4.45	4.86	5.14	5.48	5.68	5.96	6.09
k(T):	7.83	7.49	7.23	7.02	6.68	6.42	5.95	5.61

kinetics: Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(3.756,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R""")
kinetics: Arrhenius(A=(3.18266e+20,'cm^3/(mol*s)'), n=-2.694, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing""")
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing

liquid_oxidation Failed Edge Comparison ❌

Original model has 202 species.
Test model has 202 species. ✅
Original model has 1610 reactions.
Test model has 1613 reactions. ❌
The original model has 2 reactions that the tested model does not have. ❌
rxn: CCO[O](31) <=> [OH](22) + CC=O(69) origin: intra_H_migration
rxn: CCCCCO[O](104) + CCCCCO[O](104) <=> oxygen(1) + CCCCC=O(106) + CCCCCO(130) origin: Peroxyl_Termination
The tested model has 5 reactions that the original model does not have. ❌
rxn: CCO[O](31) <=> C[CH]OO(70) origin: intra_H_migration
rxn: C[CH]CCCO(157) + CCCCCO[O](103) <=> CC=CCCO(192) + CCCCCOO(105) origin: Disproportionation
rxn: C[CH]CCCO(157) + CCCCCO[O](103) <=> C=CCCCO(193) + CCCCCOO(105) origin: Disproportionation
rxn: C[CH]CCCO(157) + C[CH]CCCO(157) <=> CC=CCCO(192) + CCCCCO(130) origin: Disproportionation
rxn: C[CH]CCCO(157) + C[CH]CCCO(157) <=> C=CCCCO(193) + CCCCCO(130) origin: Disproportionation

Non-identical kinetics! ❌
original:
rxn: CCCC(C)O[O](20) + CCCCCO[O](104) <=> oxygen(1) + CCCC(C)[O](61) + CCCCC[O](127) origin: Peroxyl_Disproportionation
tested:
rxn: CCCC(C)O[O](20) + CCCCCO[O](103) <=> oxygen(1) + CCCC(C)[O](64) + CCCCC[O](128) origin: Peroxyl_Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	3.77	4.45	4.86	5.14	5.48	5.68	5.96	6.09
k(T):	7.83	7.49	7.23	7.02	6.68	6.42	5.95	5.61

kinetics: Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(3.756,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R""")
kinetics: Arrhenius(A=(3.18266e+20,'cm^3/(mol*s)'), n=-2.694, Ea=(0,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing""")
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing

Non-identical kinetics! ❌
original:
rxn: CCCCCO[O](104) + CC(CC(C)OO)O[O](103) <=> oxygen(1) + CCCCC[O](127) + CC([O])CC(C)OO(129) origin: Peroxyl_Disproportionation
tested:
rxn: CCCCCO[O](103) + CC(CC(C)OO)O[O](104) <=> oxygen(1) + CCCCC[O](128) + CC([O])CC(C)OO(127) origin: Peroxyl_Disproportionation

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	7.79	7.46	7.21	7.00	6.67	6.41	5.94	5.60
k(T):	3.52	4.27	4.71	5.01	5.39	5.61	5.91	6.06

kinetics: Arrhenius(A=(3.18266e+20,'cm^3/(mol*s)'), n=-2.694, Ea=(0.053,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing Ea raised from 0.0 to 0.2 kJ/mol to match endothermicity of reaction.""")
kinetics: Arrhenius(A=(3.2e+12,'cm^3/(mol*s)'), n=0, Ea=(4.096,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R""")
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing
Ea raised from 0.0 to 0.2 kJ/mol to match endothermicity of reaction.
kinetics: Estimated from node Root_Ext-5R-R_7R!H->C_N-7C-inRing_Ext-5R-R

Details

Observables Test Case: liquid_oxidation Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

liquid_oxidation Passed Observable Testing ✅

Regression test nitrogen:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:44
Current: Execution time (DD:HH:MM:SS): 00:00:01:37
Reference: Memory used: 2214.09 MB
Current: Memory used: 2204.93 MB

nitrogen Failed Core Comparison ❌

Original model has 41 species.
Test model has 41 species. ✅
Original model has 360 reactions.
Test model has 359 reactions. ❌
The original model has 1 reactions that the tested model does not have. ❌
rxn: HNO(48) + HCO(13) <=> NO(38) + CH2O(18) origin: H_Abstraction

nitrogen Failed Edge Comparison ❌

Original model has 132 species.
Test model has 132 species. ✅
Original model has 997 reactions.
Test model has 995 reactions. ❌

Non-identical thermo! ❌
original: O1[C]=N1
tested: O1[C]=N1

Hf(300K)	S(300K)	Cp(300K)	Cp(400K)	Cp(500K)	Cp(600K)	Cp(800K)	Cp(1000K)	Cp(1500K)
141.64	58.66	12.26	12.27	12.09	11.96	12.26	12.72	12.15
116.46	53.90	11.62	12.71	13.49	13.96	14.14	13.85	13.58

thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(oxirene) + radical(CdJ-NdO)
thermo: Thermo group additivity estimation: group(O2s-CdN3d) + group(N3d-OCd) + group(Cd-HN3dO) + ring(Cyclopropene) + radical(CdJ-NdO)
The original model has 2 reactions that the tested model does not have. ❌
rxn: HNO(48) + HCO(13) <=> NO(38) + CH2O(18) origin: H_Abstraction
rxn: HON(T)(83) + HCO(13) <=> NO(38) + CH2O(18) origin: Disproportionation

Non-identical kinetics! ❌
original:
rxn: NCO(66) <=> O1[C]=N1(126) origin: Intra_R_Add_Endocyclic
tested:
rxn: NCO(66) <=> O1[C]=N1(126) origin: Intra_R_Add_Endocyclic

k(1bar)	300K	400K	500K	600K	800K	1000K	1500K	2000K
k(T):	-66.25	-46.19	-34.19	-26.21	-16.28	-10.36	-2.54	1.31
k(T):	-49.54	-33.65	-24.16	-17.85	-10.01	-5.35	0.80	3.82

kinetics: Arrhenius(A=(6.95187e+18,'s^-1'), n=-1.628, Ea=(111.271,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H""")
kinetics: Arrhenius(A=(6.95187e+18,'s^-1'), n=-1.628, Ea=(88.327,'kcal/mol'), T0=(1,'K'), comment="""Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H""")
Identical kinetics comments:
kinetics: Estimated from node Backbone0_N-2R!H-inRing_N-1R!H-inRing_Sp-2R!H-1R!H

Details

Observables Test Case: NC Comparison

✅ All Observables varied by less than 0.200 on average between old model and new model in all conditions!

nitrogen Passed Observable Testing ✅

Regression test oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:02:50
Current: Execution time (DD:HH:MM:SS): 00:00:02:38
Reference: Memory used: 2084.02 MB
Current: Memory used: 2079.10 MB

oxidation Passed Core Comparison ✅

Original model has 59 species.
Test model has 59 species. ✅
Original model has 694 reactions.
Test model has 694 reactions. ✅

oxidation Passed Edge Comparison ✅

Original model has 230 species.
Test model has 230 species. ✅
Original model has 1526 reactions.
Test model has 1526 reactions. ✅

Details

Observables Test Case: Oxidation Comparison

✅ All Observables varied by less than 0.500 on average between old model and new model in all conditions!

oxidation Passed Observable Testing ✅

Regression test sulfur:

Reference: Execution time (DD:HH:MM:SS): 00:00:01:08
Current: Execution time (DD:HH:MM:SS): 00:00:01:03
Reference: Memory used: 2183.30 MB
Current: Memory used: 2184.46 MB

sulfur Passed Core Comparison ✅

Original model has 27 species.
Test model has 27 species. ✅
Original model has 74 reactions.
Test model has 74 reactions. ✅

sulfur Failed Edge Comparison ❌

Original model has 89 species.
Test model has 89 species. ✅
Original model has 227 reactions.
Test model has 227 reactions. ✅
The original model has 1 reactions that the tested model does not have. ❌
rxn: O(4) + SO2(15) (+N2) <=> SO3(16) (+N2) origin: primarySulfurLibrary
The tested model has 1 reactions that the original model does not have. ❌
rxn: O(4) + SO2(15) (+N2) <=> SO3(16) (+N2) origin: primarySulfurLibrary

Details

Observables Test Case: SO2 Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

sulfur Passed Observable Testing ✅

Regression test superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:00:43
Current: Execution time (DD:HH:MM:SS): 00:00:00:39
Reference: Memory used: 2322.90 MB
Current: Memory used: 2362.60 MB

superminimal Passed Core Comparison ✅

Original model has 13 species.
Test model has 13 species. ✅
Original model has 21 reactions.
Test model has 21 reactions. ✅

superminimal Passed Edge Comparison ✅

Original model has 18 species.
Test model has 18 species. ✅
Original model has 28 reactions.
Test model has 28 reactions. ✅

Regression test RMS_constantVIdealGasReactor_superminimal:

Reference: Execution time (DD:HH:MM:SS): 00:00:03:21
Current: Execution time (DD:HH:MM:SS): 00:00:03:02
Reference: Memory used: 2753.11 MB
Current: Memory used: 2727.98 MB

RMS_constantVIdealGasReactor_superminimal Passed Core Comparison ✅

Original model has 13 species.
Test model has 13 species. ✅
Original model has 19 reactions.
Test model has 19 reactions. ✅

RMS_constantVIdealGasReactor_superminimal Passed Edge Comparison ✅

Original model has 13 species.
Test model has 13 species. ✅
Original model has 19 reactions.
Test model has 19 reactions. ✅

Details

Observables Test Case: RMS_constantVIdealGasReactor_superminimal Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

RMS_constantVIdealGasReactor_superminimal Passed Observable Testing ✅

Regression test RMS_CSTR_liquid_oxidation:

Reference: Execution time (DD:HH:MM:SS): 00:00:08:16
Current: Execution time (DD:HH:MM:SS): 00:00:07:35
Reference: Memory used: 2712.73 MB
Current: Memory used: 2699.08 MB

RMS_CSTR_liquid_oxidation Failed Core Comparison ❌

Original model has 37 species.
Test model has 37 species. ✅
Original model has 232 reactions.
Test model has 233 reactions. ❌
The tested model has 1 reactions that the original model does not have. ❌
rxn: CCO[O](34) <=> [OH](22) + CC=O(62) origin: intra_H_migration

RMS_CSTR_liquid_oxidation Failed Edge Comparison ❌

Original model has 206 species.
Test model has 206 species. ✅
Original model has 1508 reactions.
Test model has 1508 reactions. ✅
The original model has 2 reactions that the tested model does not have. ❌
rxn: CCCO[O](35) <=> CC[CH]OO(45) origin: intra_H_migration
rxn: CCO[O](34) <=> C[CH]OO(62) origin: intra_H_migration
The tested model has 2 reactions that the original model does not have. ❌
rxn: CCO[O](34) <=> [OH](22) + CC=O(62) origin: intra_H_migration
rxn: CCCO[O](36) <=> [OH](22) + CCC=O(50) origin: intra_H_migration

Details

Observables Test Case: RMS_CSTR_liquid_oxidation Comparison

✅ All Observables varied by less than 0.100 on average between old model and new model in all conditions!

RMS_CSTR_liquid_oxidation Passed Observable Testing ✅

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JacksonBurns · 2023-07-25T12:22:23Z

@rwest this needs unit tests - could we wait and merge after #2504 and write them in the new pytest style?

github-actions · 2023-10-24T08:08:02Z

This pull request is being automatically marked as stale because it has not received any interaction in the last 90 days. Please leave a comment if this is still a relevant pull request, otherwise it will automatically be closed in 30 days.

zhaoyangwx closed this May 9, 2022

zhaoyangwx reopened this May 9, 2022

JacksonBurns force-pushed the patch-1 branch from 5dc8434 to 8ef56d9 Compare June 26, 2023 12:22

zhaoyangwx added 6 commits July 24, 2023 17:12

Check isomorphism of lists with 4+ species

7fc0bbc

Sometimes need to compare reaction with 4+ reactants/products. Improved performance by avoid unnecessary calculation of list length.

Update reaction.py

4bc76a6

Fix comparison problem

d92833e

Updated comparison for two lists with same elements but different sequence.

Update reaction.py

0587a8f

Reduce calculations

Fix compile error

9e255bb

Argument list changes cause error when compiling. No need to add new argument maximum_length. Also no need to define individual function in list comparison.

Fix typo

9e798f0

rwest force-pushed the patch-1 branch from 8ef56d9 to 9e798f0 Compare July 24, 2023 21:12

github-actions bot added the stale stale issue/PR as determined by actions bot label Oct 24, 2023

github-actions bot added the abandoned abandoned issue/PR as determined by actions bot label Nov 24, 2023

github-actions bot closed this Nov 24, 2023

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Check isomorphism of lists with 4+ species #2303

Check isomorphism of lists with 4+ species #2303

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zhaoyangwx commented May 9, 2022 •

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github-actions bot commented Jul 24, 2023

Regression test aromatics:

Regression test liquid_oxidation:

Regression test nitrogen:

Regression test oxidation:

Regression test sulfur:

Regression test superminimal:

Regression test RMS_constantVIdealGasReactor_superminimal:

Regression test RMS_CSTR_liquid_oxidation:

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Check isomorphism of lists with 4+ species #2303

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Motivation or Problem

Description of Changes

Testing

Reviewer Tips

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github-actions bot commented Jul 24, 2023

Regression Testing Results

Regression test aromatics:

Regression test liquid_oxidation:

Regression test nitrogen:

Regression test oxidation:

Regression test sulfur:

Regression test superminimal:

Regression test RMS_constantVIdealGasReactor_superminimal:

Regression test RMS_CSTR_liquid_oxidation:

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JacksonBurns commented Jul 25, 2023

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