Error Running CatMAP reactionModel

[Shedo28]

Hello CatMAP community, I just encountered similar issue @lrjohnson494 posted sometimes in 2018. I've been trying all day to resolve it but to no avail. I've perused my .mkm file (rxn expression file), all sites including empty sites are balanced.

I have no issue with the compilation as I've ran several jobs after compiling CatMAP. Below are the output errors, which I guess are similar to those of @lrjohnson494.

Traceback (most recent call last): File "mkm_job.py", line 7, in File "/home/shed/.local/lib/python3.8/site-packages/catmap/model.py", line 260, in run self.descriptor_space_analysis() File "/home/shed/.local/lib/python3.8/site-packages/catmap/model.py", line 324, in descriptor_space_analysis self.mapper.get_output_map(self.descriptor_ranges,self.resolution) File "/home/shed/.local/lib/python3.8/site-packages/catmap/mappers/mapper_base.py", line 89, in get_output_map self.solver.compile() File "/home/shed/.local/lib/python3.8/site-packages/catmap/solvers/steady_state_solver.py", line 429, in compile self.generate_static_functions() File "/home/shed/.local/lib/python3.8/site-packages/catmap/model.py", line 357, in generate_static_functions exec(func_string, globals(), locs) File "", line 730 J[0][0] = 0 + 2(-7kf[7]theta[10]s[0]s[0]s[0]s[0]s[0]s[0] + (kfkBT[7])dEf[7][0]theta[10]s[0]s[0]s[0]s[0]s[0]s[0]s[0] - kr[7](-6theta[0]s[0]s[0]s[0]s[0]s[0] + 2s[0]theta[0]) - (krkBT[7])dEr[7][0]theta[0]theta[0]s[0]s[0]s[0]s[0]s[0]s[0]) + 1(-6kf[12]theta[12]theta[21]s[0]s[0]s[0]s[0]s[0] + (kfkBT[12])dEf[12][0]theta[12]theta[21]s[0]s[0]s[0]s[0]s[0]s[0] - kr[12](-5theta[0]s[0]s[0]s[0]s[0] + 1s[0])theta[2]theta[21] - (krkBT[12])dEr[12][0]theta[0]theta[2]theta[21]s[0]s[0]s[0]s[0]s[0]) + 1(-6kf[16]theta[11]theta[21]s[0]s[0]s[0]s[0]s[0] + (kfkBT[16])dEf[16][0]theta[11]theta[21]s[0]s[0]s[0]s[0]s[0]s[0] - kr[16](-5theta[0]s[0]s[0]s[0]s[0] + 1s[0])theta[1]theta[21] - (krkBT[16])dEr[16][0]theta[0]theta[1]theta[21]s[0]s[0]s[0]s[0]s[0]) + 1(-5kf[20]theta[14]theta[21]theta[21]s[0]s[0]s[0]s[0] + (kfkBT[20])dEf[20][0]theta[14]theta[21]theta[21]s[0]s[0]s[0]s[0]s[0] - kr[20](-4theta[0]s[0]s[0]s[0] + 1s[0])theta[4]theta[21]theta[21] - (krkBT[20])dEr[20][0]theta[0]theta[4]theta[21]theta[21]s[0]s[0]s[0]s[0]) + 1(-5kf[27]theta[13]theta[21]theta[21]s[0]s[0]s[0]s[0] + (kfkBT[27])dEf[27][0]theta[13]theta[21]theta[21]s[0]s[0]s[0]s[0]s[0] - kr[27](-4theta[0]s[0]s[0]s[0] + 1s[0])theta[3]theta[21]theta[21] - (krkBT[27])dEr[27][0]theta[0]theta[3]theta[21]theta[21]s[0]s[0]s[0]s[0]) + 1(-4kf[40]theta[15]theta[21]theta[21]theta[21]s[0]s[0]s[0] + (kfkBT[40])dEf[40][0]theta[15]theta[21]theta[21]theta[21]s[0]s[0]s[0]s[0] - kr[40](-3theta[0]s[0]s[0] + 1s[0])theta[5]theta[21]theta[21]theta[21] - (krkBT[40])dEr[40][0]theta[0]theta[5]theta[21]theta[21]theta[21]s[0]s[0]*s[0]) ^ SyntaxError: invalid syntax

Please everyone in the community, I need a resolution to this as soon as possible. Your kind assistance will be highly appreciated.

[ajmedford]

This error happens when the string that is generated for your kinetic equation is not valid for some reason. CatMAP auto-generates the long string you see (starting with J[0,0]) and then executes it to "compile" the equations. My strong suspicion is that this arises due to an error in the mkm file, but it may be difficult to debug. Try to create a "minimal working example" (a simpler reaction that reproduces the error) and share the mkm file as well as the resulting error.

[Shedo28]

@ajmedford Thank you Prof. for the response. I am also sorry for the late reply, I've been on leave for quite sometimes.

You are absolutely right, the issue was from my .mkm file. There were lots of improper material balances. I have sorted it. Thanks once again. EG_dehydrogenation.mkm.txt