agarny’s gists

agarny / hh52.cpp

Last active July 4, 2023 02:54

Compute the HH52 model 1,000 times

agarny / output.txt

Created March 28, 2020 06:55

QtWebKit: trying to build version 5.212.0 alpha4 on Windows

	**********************************************************************
	** Visual Studio 2017 Developer Command Prompt v15.9.18
	** Copyright (c) 2017 Microsoft Corporation
	**********************************************************************
	[vcvarsall.bat] Environment initialized for: 'x64'
	-- The C compiler identification is MSVC 19.16.27034.0
	-- The CXX compiler identification is MSVC 19.16.27034.0
	-- Check for working C compiler: C:/Program Files (x86)/Microsoft Visual Studio/2017/Community/VC/Tools/MSVC/14.16.27023/bin/Hostx64/x64/cl.exe
	-- Check for working C compiler: C:/Program Files (x86)/Microsoft Visual Studio/2017/Community/VC/Tools/MSVC/14.16.27023/bin/Hostx64/x64/cl.exe -- works
	-- Detecting C compiler ABI info

agarny / main_ADAN-218_original_2_0.cellml

Created January 24, 2020 01:06

This file has been truncated, but you can view the full file.

	<?xml version='1.0' encoding='UTF-8'?>
	<model name="CardiovascularSystem" xmlns="http://www.cellml.org/cellml/2.0#" xmlns:cellml="http://www.cellml.org/cellml/2.0#">
	<units name="mm">
	<unit prefix="milli" units="metre"/>
	</units>
	<units name="m2">
	<unit exponent="2" units="metre"/>
	</units>
	<units name="mm2">
	<unit exponent="2" prefix="milli" units="metre"/>

agarny / main_ADAN-218_original.cellml

Created January 24, 2020 01:05

This file has been truncated, but you can view the full file.

	<?xml version='1.0' encoding='UTF-8'?>
	<model name="CardiovascularSystem" xmlns="http://www.cellml.org/cellml/1.0#">
	<units name="mm">
	<unit prefix="milli" units="metre"/>
	</units>
	<units name="m2">
	<unit exponent="2" units="metre"/>
	</units>
	<units name="mm2">
	<unit exponent="2" prefix="milli" units="metre"/>

agarny / output.txt

Created January 23, 2020 02:03

Output from idaRoberts_dns without yp0 values and without a Jacobian approximation

	idaRoberts_dns: Robertson kinetics DAE serial example problem for IDA
	Three equation chemical kinetics problem.

	Linear solver: DENSE, with user-supplied Jacobian.
	Tolerance parameters: rtol = 0.0001 atol = 1e-08 1e-06 1e-06
	Initial conditions y0 = (1 0 0)
	Constraints and id not used.

	-----------------------------------------------------------------------
	t y1 y2 y3 \| nst k h

agarny / idaRoberts_dns.c

Created January 23, 2020 02:03

idaRoberts_dns without yp0 values and without a Jacobian approximation

	/* -----------------------------------------------------------------
	* Programmer(s): Allan Taylor, Alan Hindmarsh and
	* Radu Serban @ LLNL
	* -----------------------------------------------------------------
	* SUNDIALS Copyright Start
	* Copyright (c) 2002-2020, Lawrence Livermore National Security
	* and Southern Methodist University.
	* All rights reserved.
	*
	* See the top-level LICENSE and NOTICE files for details.

agarny / plot_csv.py

Last active January 24, 2020 02:21

Plot data contained in a CSV file

	import csv
	import matplotlib.pyplot as plt
	import sys

	t = []
	y = []

	with open(sys.argv[1], 'r') as csv_file:
	for row_nb, row in enumerate(csv.reader(csv_file)):
	if row_nb == 0:

agarny / parabola_dae_model.sedml

Created October 10, 2019 23:44

SED-ML L1V4: example showing how to use CVODE+KINSOL

	<?xml version='1.0' encoding='UTF-8'?>
	<sedML level="1" version="4" xmlns="http://sed-ml.org/sed-ml/level1/version4" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
	<listOfModels>
	<model id="model" language="urn:sedml:language:cellml.1_0" source="parabola_dae_model.cellml"/>
	</listOfModels>
	<listOfSimulations>
	<uniformTimeCourse id="simulation1" initialTime="0" numberOfSteps="1000" outputEndTime="1000" outputStartTime="0">
	<algorithm kisaoID="KISAO:0000019">
	<listOfAlgorithmParameters>
	<algorithmParameter kisaoID="KISAO:0000211" value="1e-07"/>

agarny / noble_model_1962.sedml

Created October 9, 2019 20:37

SED-ML L1V4: example showing how to plot dV/dt

	<?xml version='1.0' encoding='UTF-8'?>
	<sedML level="1" version="4" xmlns="http://sed-ml.org/sed-ml/level1/version4" xmlns:cellml="http://www.cellml.org/cellml/1.0#">
	<listOfModels>
	<model id="model" language="urn:sedml:language:cellml.1_0" source="noble_model_1962.cellml"/>
	</listOfModels>
	<listOfSimulations>
	<uniformTimeCourse id="simulation1" initialTime="0" numberOfSteps="1000" outputEndTime="1000" outputStartTime="0">
	<algorithm kisaoID="KISAO:0000019">
	<listOfAlgorithmParameters>
	<algorithmParameter kisaoID="KISAO:0000211" value="1e-07"/>

agarny / zhang.py

Created July 28, 2019 17:29

	from math import *

	import numpy as np

	def initializeConstants(states, variables):
	states[0] = 0.092361701692
	states[1] = 0.015905380261
	states[2] = 0.01445216109
	states[3] = 0.04804900895
	states[4] = 0.48779845203

Alan Garny agarny