RMG-Electrochem

[mjohnson541]

Enables RMG to operate on solid electrolyte interface conditions in Li-ion batteries. Adds Li atoms, adds electrochemical reactions, adds a liquid-catalysis reactor and upgrades tree generation adding corrections for kinetic solvent effect.

[lgtm-com]

This pull request introduces 5 alerts when merging 10314f2 into 2a35d62 - view on LGTM.com

new alerts:

• 2 for Except block handles 'BaseException'
• 1 for Unused import
• 1 for Syntax error
• 1 for Unreachable code

[lgtm-com]

This pull request introduces 5 alerts when merging 4f6b5db into e3d0617 - view on LGTM.com

new alerts:

• 2 for Except block handles 'BaseException'
• 1 for Unused import
• 1 for Syntax error
• 1 for Unreachable code

[rwest]

I rebased, did a few interactive rebases to clean up some fixups and merge conflict markers that had gotten in there, and force pushed.

[rwest]

The database tests are failing, because some sample molecules are being made that are charged.

In family 1,2_Insertion_CO, a sample molecule made from node COS returns an unexpectedly charged molecule:
Sample molecule AdjList:
1 *4 O u0 p1 c+1 {2,T}
2 *1 C u0 p1 c-1 {1,T}


Origin Group AdjList:
1 *1 C     u0 p1 c-1 {2,T}
2 *4 [O,S] u0 p1 c+1 {1,T}

ERROR:root:
In family 1,2_Insertion_CO, a sample molecule made from node CO returns an unexpectedly charged molecule:
Sample molecule AdjList:
1 *4 O u0 p1 c+1 {2,T}
2 *1 C u0 p1 c-1 {1,T}


Origin Group AdjList:
1 *1 C u0 p1 c-1 {2,T}
2 *4 O u0 p1 c+1 {1,T}

ERROR:root:
In family 1,2_Insertion_CO, a sample molecule made from node CS returns an unexpectedly charged molecule:
Sample molecule AdjList:
1 *4 S u0 p1 c+1 {2,T}
2 *1 C u0 p1 c-1 {1,T}


Origin Group AdjList:
1 *1 C u0 p1 c-1 {2,T}
2 *4 S u0 p1 c+1 {1,T}

ERROR

Kinetics family 1,2_NH3_elimination: Entry is accessible? ... ERROR:root:
In family 1,2_NH3_elimination, a sample molecule made from node charged returns an unexpectedly charged molecule:
Sample molecule AdjList:
1 *2 N u0 p0 c+1 {2,S} {3,S} {4,S} {5,S}
2 *1 N u0 p1 c0 {1,S} {6,S} {7,S}
3 *3 N u0 p2 c-1 {1,S} {8,S}
4 *4 H u0 p0 c0 {1,S}
5    H u0 p0 c0 {1,S}
6    H u0 p0 c0 {2,S}
7    H u0 p0 c0 {2,S}
8    H u0 p0 c0 {3,S}


Origin Group AdjList:
1 *1 N u0 p1 c0 {2,S} {5,S} {6,S}
2 *2 N u0 p0 c+1 {1,S} {3,[S,D]} {4,S}
3 *3 N u0 p2 c-1 {2,[S,D]}
4 *4 H u0 p0 c0 {2,S}
5    H u0 p0 c0 {1,S}
6    H u0 p0 c0 {1,S}

ERROR:root:
In family 1,2_NH3_elimination, a sample molecule made from node chargedS returns an unexpectedly charged molecule:
Sample molecule AdjList:
1 *2 N u0 p0 c+1 {2,S} {3,S} {4,S} {5,S}
2 *1 N u0 p1 c0 {1,S} {6,S} {7,S}
3 *3 N u0 p2 c-1 {1,S} {8,S}
4 *4 H u0 p0 c0 {1,S}
5    H u0 p0 c0 {1,S}
6    H u0 p0 c0 {2,S}
7    H u0 p0 c0 {2,S}
8    H u0 p0 c0 {3,S}


Origin Group AdjList:
1 *1 N u0 p1 c0 {2,S} {5,S} {6,S}
2 *2 N u0 p0 c+1 {1,S} {3,S} {4,S}
3 *3 N u0 p2 c-1 {2,S}
4 *4 H u0 p0 c0 {2,S}
5    H u0 p0 c0 {1,S}
6    H u0 p0 c0 {1,S}

ERROR:root:
In family 1,2_NH3_elimination, a sample molecule made from node chargedD returns an unexpectedly charged molecule:
Sample molecule AdjList:
1 *1 N u0 p1 c0 {2,S} {5,S} {6,S}
2 *2 N u0 p0 c+1 {1,S} {3,D} {4,S}
3 *3 N u0 p2 c-1 {2,D}
4 *4 H u0 p0 c0 {2,S}
5    H u0 p0 c0 {1,S}
6    H u0 p0 c0 {1,S}


Origin Group AdjList:
1 *1 N u0 p1 c0 {2,S} {5,S} {6,S}
2 *2 N u0 p0 c+1 {1,S} {3,D} {4,S}
3 *3 N u0 p2 c-1 {2,D}
4 *4 H u0 p0 c0 {2,S}
5    H u0 p0 c0 {1,S}
6    H u0 p0 c0 {1,S}

ERROR
Kinetics family 1,2_NH3_elimination: Recipe applies to group entry? ... ERROR

Kinetics family R_Addition_CSm: Entry is accessible? ... ERROR:root:
In family R_Addition_CSm, a sample molecule made from node CSm returns an unexpectedly charged molecule:
Sample molecule AdjList:
1 *3 S u0 p1 c+1 {2,T}
2 *1 C u0 p1 c-1 {1,T}


Origin Group AdjList:
1 *3 S u0 p1 c+1 {2,T}
2 *1 C u0 p1 c-1 {1,T}

ERROR
Kinetics family R_Addition_CSm: Recipe applies to group entry? ... ERROR

Kinetics family Surface_Adsorption_vdW: Entry is accessible? ... ERROR:root:
In family Surface_Adsorption_vdW, a sample molecule made from node N2O returns an unexpectedly charged molecule:
Sample molecule AdjList:
1 *1 O u0 p2 c0 {2,D}
2    N u0 p0 c+1 {1,D} {3,D}
3    N u0 p2 c-1 {2,D}


Origin Group AdjList:
multiplicity [1]
1    N u0 p0 c+1 {2,D} {3,D}
2 *1 O u0 p2 c0 {1,D}
3    N u0 p2 c-1 {1,D}

ERROR
Kinetics family Surface_Adsorption_vdW: Recipe applies to group entry? ... ERROR

Solvation groups group: Entry is accessible? ... ERROR:root:Problem making sample molecule for group Cs-N5cHHH
1 * Cs u0 {2,S} {3,S} {4,S} {5,S}
2   N  u0 c+1 {1,S}
3   H  u0 {1,S}
4   H  u0 {1,S}
5   H  u0 {1,S}

ERROR:root:Problem making sample molecule for group Cs-N5cCsHH
1 * Cs u0 {2,S} {3,S} {4,S} {5,S}
2   N  u0 c+1 {1,S}
3   Cs u0 {1,S}
4   H  u0 {1,S}
5   H  u0 {1,S}

ERROR:root:
In family group, a sample molecule made from node Cs-N5cHHH returns an unexpectedly charged molecule:
Sample molecule AdjList:
1   N u0 p1 c+1 {2,S} {6,S}
2 * C u0 p0 c0 {1,S} {3,S} {4,S} {5,S}
3   H u0 p0 c0 {2,S}
4   H u0 p0 c0 {2,S}
5   H u0 p0 c0 {2,S}
6   H u0 p0 c0 {1,S}


Origin Group AdjList:
1 * Cs u0 {2,S} {3,S} {4,S} {5,S}
2   N  u0 c+1 {1,S}
3   H  u0 {1,S}
4   H  u0 {1,S}
5   H  u0 {1,S}

ERROR:root:
In family group, a sample molecule made from node Cs-N5cCsHH returns an unexpectedly charged molecule:
Sample molecule AdjList:
1   N u0 p1 c+1 {2,S} {9,S}
2 * C u0 p0 c0 {1,S} {3,S} {4,S} {5,S}
3   C u0 p0 c0 {2,S} {6,S} {7,S} {8,S}
4   H u0 p0 c0 {2,S}
5   H u0 p0 c0 {2,S}
6   H u0 p0 c0 {3,S}
7   H u0 p0 c0 {3,S}
8   H u0 p0 c0 {3,S}
9   H u0 p0 c0 {1,S}


Origin Group AdjList:
1 * Cs u0 {2,S} {3,S} {4,S} {5,S}
2   N  u0 c+1 {1,S}
3   Cs u0 {1,S}
4   H  u0 {1,S}
5   H  u0 {1,S}

ERROR

Thermo groups group: Entry is accessible? ... ERROR:root:Problem making sample molecule for group Sc
1 * S ux c+1

ERROR:root:
In family group, a sample molecule made from node Sc returns an unexpectedly charged molecule:
Sample molecule AdjList:
1 * S u0 p2 c+1 {2,S}
2   H u0 p0 c0 {1,S}


Origin Group AdjList:
1 * S ux c+1

ERROR

etc.

looks like they're probably mostly the same cause.
Any ideas @mjohnson541 ?

[mjohnson541]

Thanks for the help! I meant to get on this last weekend, but I've been ill and now I'm frantically trying to get some urgent calculations done. Hopefully I'll be working on this PR as soon as those launch.

At some point a month or so ago I think I figured out why that was happening, but I don't remember now. Skimming the sample molecule code doesn't seem to be jogging my memory.

[mjohnson541]

I have examples, but part of why they aren't on this branch yet is this isn't the complete PR, I didn't want to get in the way of the rebase, but I have the rest of the changes locally. I can try to get those added soon if we're ready.

[github-actions]

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.

[github-actions]

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.