Comments (2)
I found the issue, it is from the reaction mechanism I fed into the mkm file. I wasn't careful with the empty site balancing.
from catmap.
Hello @lrjohnson494, I just encountered similar issue at the moment, 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 yours.
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*(-7*kf[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. Your kind assistance will be highly appreciated.
from catmap.
Related Issues (20)
- TYPE_ERROR HOT 2
- How to export the result data in *.txt format ?
- Blank squares in output plots HOT 8
- the tutorial ORR scaling
- Tutorial update request
- How to include pre-determined activation barriers
- Adsorbate interaction tutorial
- regarding getting error in my .py file when i am running it. anyone could help me in this
- How to analyze reaction conditions as a function of a just one thermodynamic discriptor?
- solved after updating catmap - finding adsorbate-adsorbate interaction parameters (Python 3) HOT 1
- ValueError: Frequency vectors have different lengths HOT 1
- Error with manually defined species_name HOT 1
- How to output the clean site results?
- Changing name of "formation_energy" field in input files to better reflect what that term represents
- How to calculate an integral_formation_energy? HOT 4
- NameError: name 'null' is not defined HOT 1
- How to get free_energy_dict
- Error Running CatMAP reactionModel HOT 2
- CatMAP on Jupyter HOT 1
- calculation of formation energy of isomer(molecule)
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from catmap.