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Jonathan Guyer guyer

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guyer / newton.ipynb
Created May 13, 2016 18:07
Jupyter notebook demonstrating Newton iterations in FIPy
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@guyer
guyer / crazycoupling1.ipynb
Last active July 14, 2016 16:17
Jupyter notebooks illustrating different ways to couple two equations over different spatial domains in FiPy
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@guyer
guyer / interpolationsDiscretizationsAndGradientsOhMy.ipynb
Last active October 18, 2020 19:04
IPython notebook illustrating some FiPy discretization and interpolation behavior
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guyer / exAztecOO.py
Last active March 5, 2018 19:59
PyTrilnos script that demonstrates memory leak even after calling `del`
#! ${PYTHON_EXECUTABLE}
# -*- python -*-
# @HEADER
# ***********************************************************************
#
# PyTrilinos: Python Interfaces to Trilinos Packages
# Copyright (2014) Sandia Corporation
#
# Under the terms of Contract DE-AC04-94AL85000 with Sandia
@guyer
guyer / conda-fipydependencies.txt
Last active April 5, 2018 02:53
conda install gmsh differences
This file has been truncated, but you can view the full file.
DEBUG conda.gateways.logging:set_verbosity(148): verbosity set to 3
TRACE conda.gateways.disk.test:file_path_is_writable(23): checking path is writable /data/guyer/miniconda2/pkgs/urls.txt
DEBUG conda.core.package_cache_data:_check_writable(236): package cache directory '/data/guyer/miniconda2/pkgs' writable: True
Solving environment: ...working... DEBUG conda.core.solve:solve_final_state(141): solving prefix /data/guyer/miniconda2/envs/fipy12
specs_to_remove: frozenset([])
specs_to_add: frozenset([MatchSpec(name=LowerStrMatch('scipy')), MatchSpec(name=LowerStrMatch('gmsh')), MatchSpec(name=LowerStrMatch('mpi4py')), MatchSpec(name=LowerStrMatch('python')), MatchSpec(name=LowerStrMatch('mayavi')), MatchSpec(name=LowerStrMatch('matplotlib')), MatchSpec(name=LowerStrMatch('trilinos')), MatchSpec(name=LowerStrMatch('pysparse')), MatchSpec(name=LowerStrMatch('numpy')), MatchSpec(name=LowerStrMatch('nomkl'))])
prune: False
TRACE conda.gateways.disk.test:file_path_is_writable(23): checking path is writable /us
@guyer
guyer / nix-shell_output.txt
Created September 5, 2018 20:44
nix output for FiPy on Mac OS X
$ nix-shell --pure
warning: dumping very large path (> 256 MiB); this may run out of memory
these derivations will be built:
/nix/store/yfyl2cq05lswwb47vj71h5fbzwpj5rk4-scikit-fmm-0.0.9.tar.gz.drv
/nix/store/2ykvqyvfp41rc1hq2vk4ys66c4msyl07-python2.7-scikit-fmm-0.0.9.drv
/nix/store/ap25cv9l4gig0sw0vxh3a4vbh967n90w-gmsh-3.0.6.drv
/nix/store/hmzya72gq1j92fj60zn2labci3ww2mlb-python2.7-tkinter-2.7.14.drv
/nix/store/mmyaxmp7zcsxnkzpiinp1q5xmfaka8is-pysparse-1.1.1-dev.tar.gz.drv
/nix/store/y86g8gr18ajb2frcis2dv474jaa1dpi3-python2.7-pysparse-1.1.1-dev.drv
/nix/store/p0kriliyjc5cgygyr4j2r1gx42qw1v17-fipy.drv
@guyer
guyer / coupledAdvectionDiffusionReaction.py
Created February 14, 2019 17:47
Cleaned up script to address [StackOverflow question](https://stackoverflow.com/q/53977269/2019542)
from fipy import *
g = 0.66
L = 10.
nx = 1000
mu1 = 1.
mu2 = 1.
K = 1.
D1 = 1.
D2 = 1.
@guyer
guyer / PCM_thermal_v0-SendOut.py
Last active April 8, 2019 21:28
Revisions to DeSantis thermal FiPy problem
# -*- coding: utf-8 -*-
"""
Created on Tue Apr 2 15:14:40 2019
@author: ddesantis
"""
from fipy import *
import numpy as np
import matplotlib.pyplot as plt
@guyer
guyer / gist:ab57a69ffa1f228eb599cc0d7cb37f2a
Created May 28, 2019 18:11
Gmsh output from conversion of TThe .geo file for https://stackoverflow.com/q/56341375/2019542
$ gmsh test2D.geo -3 -nopopup -format msh -o teset2D.msh
Info : Running 'gmsh test2D.geo -3 -nopopup -format msh -o teset2D.msh' [Gmsh 3.0.6, 1 node, max. 1 thread]
Info : Started on Tue May 28 14:08:46 2019
Info : Reading 'test2D.geo'...
Info : Done reading 'test2D.geo'
Info : Finalized high order topology of periodic connections
Info : Meshing 1D...
Info : Meshing curve 5 (Line)
Info : Meshing curve 6 (Line)
Info : Meshing curve 7 (Line)
@guyer
guyer / monod_kinetics.py
Last active June 9, 2019 13:13
Example script from https://github.com/usnistgov/fipy/issues/649
from fipy import CellVariable, Grid1D,Viewer, TransientTerm, DiffusionTerm, ImplicitSourceTerm
from fipy.tools import numerix
size, dl, q = 100, 3e-6, 14.1
Ds, Ks = 1e-4, 5.8e-4
order = 2
dt = dl ** 2 / (2 * Ds)
mesh = Grid1D(dx=dl, nx=size)
phi_s = CellVariable(name='substrate', mesh=mesh)