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Particle in cell chemical calculation software
This project forked from paddywball/bdd21
Particle in cell chemical calculation software
###~~~~~~~~~~~~~~~~~~### Fluidity Chemistry Model ###~~~~~~~~~~~~~~~~~~### Fluidity Chemistry Model is a series of Python scripts which can be used together to estimate melt chemistry within a Fluidity model. For a full explanation of this modelling software please see Ball et al., (submitted to JGR Solid Earth). #-------------------- # Software Requirements python 2.7 numpy 1.16.5 h5py 2.9.0 re 2.2.1 pandas 0.24.2 scipy 1.2.1 os vtk glob mpi4py #-------------------- # Data Requirements A Fluidity model of mantle convection within which X coordinate, Y coordinate, Temperature, Melt Fraction, Melting Rate, Latent Heat of Melting, Particle ID and Processor ID recorded for each particle at each time step in a h5 file. vtu or pvtu files of each time step within the model #-------------------- # Example data files We include example data files for an edge-driven-convection model with a original oceanic thermal boundary layer thickness of 80 km. # Files used to generate fluidity model Constants.py Par_Pourquoi.flml Pourquoi.flml # h5 file with particle data Pourquoi.particles.SubMelt.h5part # vtu/pvtu files Pourquoi_*.pvtu Pourquoi_*/Pourquoi_*_*.vtu #-------------------- # Implementation Place following files in the same directory: # Script to calculate melt compositions from particle data Fluidity_Optimize_Parallel_Example.py # File including all the modules used in Fluidity_Optimize_Parallel_Example.py Fluidity_Chem_Mods.py # File including all datasets used in Fluidity_Optimize_Parallel_Example.py Fluidity_Chem_dict.py Place Fluidity model data files in the same directory as each other, not necessarilty the same directory as the data processing scripts. Edit lines 65-96 in Fluidity_Optimize_Parallel_Example.py to match the specific Fluidity model. Edit line 173 in Fluidity_Optimize_Parallel_Example.py to match the specific Fluidity model. Edit line 209 in Fluidity_Optimize_Parallel_Example.py to match the specific Fluidity model. To run the model, migrate to directory holding the python files and input the following command: mpirun -np 8 python Fluidity_Optimize_Parallel.py where 8 is changed to the number of processors that can be used. #-------------------- # Post Implementation Model yeilds one csv file for each processor used to run Fluidity_Optimize_Parallel.py Headers (i.e., first row) for all but one of the csv files should be removed and all csv files should be appended beneath the file with a header remaining. #-------------------- # Example Final Model Full_model.csv
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