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edited equations class
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@mtod92
mtod92 committed Dec 21, 2023
1 parent bbb06ab commit 26f7788
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Showing 2 changed files with 115 additions and 30 deletions.
12 changes: 6 additions & 6 deletions equpy.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4,14 +4,14 @@
from typing import List, Tuple
from utils import eq_system_builder


class EquationSystem:
def __init__(self, equations: List[str], mass_conservation: List[str]) -> None:
self.stoichiometry, self.mass_conservation, self.species = eq_system_builder(
equations, mass_conservation
)
def __init__(self, equations, mass_conservation, species = None):
self.stoichiometry, self.mass_conservation, self.species = equations, mass_conservation, species
if isinstance(self.stoichiometry[0], str):
self.stoichiometry, self.mass_conservation, self.species = eq_system_builder(self.stoichiometry, self.mass_conservation)


if self.species == None:
self.species = {i:i for i in range(license(equations))} #placeholder for species name if not specified

class ChemicalReaction:
def __init__(
Expand Down
133 changes: 109 additions & 24 deletions equpy_test.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -2,16 +2,16 @@
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"execution_count": 64,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{'divide': 'warn', 'over': 'warn', 'under': 'ignore', 'invalid': 'warn'}"
"{'divide': 'warn', 'over': 'warn', 'under': 'ignore', 'invalid': 'ignore'}"
]
},
"execution_count": 1,
"execution_count": 64,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -27,15 +27,15 @@
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 65,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"execution time --- 0.5432817146460739 milliseconds ---\n",
"execution time --- 0.8813732802265822 milliseconds ---\n",
"\n"
]
},
Expand Down Expand Up @@ -78,6 +78,51 @@
"reaction.plotter()"
]
},
{
"cell_type": "code",
"execution_count": 75,
"metadata": {},
"outputs": [],
"source": [
"class ClassTest:\n",
" def __init__(self, equations, mass_conservation, species = None):\n",
" self.stoichiometry, self.mass_conservation, self.species = equations, mass_conservation, species\n",
" if isinstance(self.stoichiometry[0], str):\n",
" self.stoichiometry, self.mass_conservation, self.species = eq_system_builder(self.stoichiometry, self.mass_conservation)\n",
"\n",
" if self.species == None:\n",
" self.species = {i:i for i in range(len(equations))} #placeholder for species name if not specified\n",
"\n",
"\n",
"eq_system = ClassTest(reactions, mass_conservation)\n"
]
},
{
"cell_type": "code",
"execution_count": 36,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"<class 'str'>\n"
]
}
],
"source": [
"print(type(reactions[0]))\n",
"if type(reactions[0]) == 'str':\n",
" print('ciao')"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
Expand Down Expand Up @@ -117,19 +162,18 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 81,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"H2O = H+ + OH-; 1e-14\n",
"NH4+ = H+ + NH3; 5.75e-10\n",
"\n",
"execution time --- 10.820120065897196 milliseconds ---\n",
"\n",
"1, 0.0013, 7.6e-12, 0.099, 0.0013\n"
"ename": "NameError",
"evalue": "name 'EqSystem' is not defined",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mNameError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-81-b91d6e9c6c0d>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 4\u001b[0m \u001b[0mammonia_prot\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mEquilibrium\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m{\u001b[0m\u001b[0;34m'NH4+'\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m{\u001b[0m\u001b[0;34m'NH3'\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'H+'\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m10\u001b[0m\u001b[0;34m**\u001b[0m\u001b[0;34m-\u001b[0m\u001b[0;36m9.24\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;31m# same here\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 5\u001b[0m \u001b[0msubstances\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m[\u001b[0m\u001b[0mSpecies\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mfrom_formula\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mf\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mf\u001b[0m \u001b[0;32min\u001b[0m \u001b[0;34m'H2O OH- H+ NH3 NH4+'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msplit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m----> 6\u001b[0;31m \u001b[0meqsys\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mEqSystem\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0mwater_autop\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mammonia_prot\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0msubstances\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 7\u001b[0m \u001b[0mprint\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m'\\n'\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmap\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mstr\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0meqsys\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mrxns\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;31m# \"rxns\" short for \"reactions\"\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 8\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mNameError\u001b[0m: name 'EqSystem' is not defined"
]
}
],
Expand Down Expand Up @@ -406,23 +450,27 @@
},
{
"cell_type": "code",
"execution_count": 5,
"execution_count": 85,
"metadata": {},
"outputs": [
{
"ename": "TypeError",
"evalue": "__init__() takes 4 positional arguments but 6 were given",
"evalue": "sequence item 0: expected str instance, numpy.ndarray found",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-5-3d25a661764c>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 14\u001b[0m \u001b[0mC\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0marray\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m2\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m2\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m1\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 15\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 16\u001b[0;31m \u001b[0mreaction\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mChemicalReaction\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m{\u001b[0m\u001b[0;34m'A'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'B'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'C'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m2\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'AB2'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m3\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'AB2C'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m4\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mN\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mK\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mC\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mS\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 17\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdelta\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mreaction\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msolve\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m30\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m1e2\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 18\u001b[0m \u001b[0mreaction\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mplotter\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mTypeError\u001b[0m: __init__() takes 4 positional arguments but 6 were given"
"\u001b[0;32m<ipython-input-85-5e2c8a9a4bc1>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m 15\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 16\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 17\u001b[0;31m \u001b[0meq_system\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mEquationSystem\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mN\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mC\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 18\u001b[0m \u001b[0mreaction\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mChemicalReaction\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m{\u001b[0m\u001b[0;34m'A'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'B'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m1\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'C'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m2\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'AB2'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m3\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;34m'AB2C'\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;36m4\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mN\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mK\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mC\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mS\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 19\u001b[0m \u001b[0mx\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mdelta\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mreaction\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msolve\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;36m30\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m1e2\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0;36m0\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/Documents/git_repository_06_23/equpy/equpy.py\u001b[0m in \u001b[0;36m__init__\u001b[0;34m(self, equations, mass_conservation)\u001b[0m\n\u001b[1;32m 10\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0misinstance\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstoichiometry\u001b[0m\u001b[0;34m[\u001b[0m\u001b[0;36m0\u001b[0m\u001b[0;34m]\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstr\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 11\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstoichiometry\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmass_conservation\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mspecies\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0meq_system_builder\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mstoichiometry\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmass_conservation\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 12\u001b[0;31m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 13\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mspecies\u001b[0m \u001b[0;34m==\u001b[0m \u001b[0;32mNone\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 14\u001b[0m \u001b[0mself\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mspecies\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m{\u001b[0m\u001b[0mi\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0mi\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mi\u001b[0m \u001b[0;32min\u001b[0m \u001b[0mrange\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mlicense\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mequations\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m}\u001b[0m \u001b[0;31m#placeholder for species name if not specified\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/Documents/git_repository_06_23/equpy/utils.py\u001b[0m in \u001b[0;36meq_system_builder\u001b[0;34m(eq, mass_conservation)\u001b[0m\n\u001b[1;32m 108\u001b[0m \"\"\"\n\u001b[1;32m 109\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m--> 110\u001b[0;31m \u001b[0mN\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mspecies\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mdefine_reactions\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0meq\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 111\u001b[0m \u001b[0mC\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mdefine_conservations\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmass_conservation\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mn\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mspecies\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 112\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/Documents/git_repository_06_23/equpy/utils.py\u001b[0m in \u001b[0;36mdefine_reactions\u001b[0;34m(eq)\u001b[0m\n\u001b[1;32m 35\u001b[0m \"\"\"\n\u001b[1;32m 36\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 37\u001b[0;31m \u001b[0mspecies_set\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mdefine_species_set\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0meq\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 38\u001b[0m \u001b[0mn\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mlen\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mspecies_set\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 39\u001b[0m \u001b[0mspecies\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m{\u001b[0m\u001b[0mstring\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mindex\u001b[0m \u001b[0;32mfor\u001b[0m \u001b[0mindex\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstring\u001b[0m \u001b[0;32min\u001b[0m \u001b[0menumerate\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0msorted\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mspecies_set\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m}\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;32m~/Documents/git_repository_06_23/equpy/utils.py\u001b[0m in \u001b[0;36mdefine_species_set\u001b[0;34m(eq)\u001b[0m\n\u001b[1;32m 11\u001b[0m \u001b[0;34m-\u001b[0m \u001b[0meq\u001b[0m\u001b[0;34m:\u001b[0m \u001b[0mlist\u001b[0m \u001b[0mof\u001b[0m \u001b[0mequations\u001b[0m \u001b[0;32min\u001b[0m \u001b[0msymbolic\u001b[0m \u001b[0mform\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 12\u001b[0m \"\"\"\n\u001b[0;32m---> 13\u001b[0;31m \u001b[0me_\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m\" \"\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mjoin\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0meq\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 14\u001b[0m \u001b[0me_\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0me_\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0msplit\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m\" \"\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 15\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mTypeError\u001b[0m: sequence item 0: expected str instance, numpy.ndarray found"
]
}
],
"source": [
"from equpy import ChemicalReaction\n",
"from equpy import ChemicalReaction, EquationSystem\n",
"from utils import eq_system_builder\n",
"import numpy as np\n",
"import matplotlib.pyplot as plt\n",
Expand All @@ -437,13 +485,44 @@
"S = np.array([1, 2, 3])\n",
"C = np.array([[1, 0, 0, 1, 1],[0, 1, 0, 2, 2],[0, 0, 1, 0, 1]])\n",
"\n",
"\n",
"eq_system = EquationSystem(N, C)\n",
"reaction = ChemicalReaction({'A':0, 'B':1, 'C':2, 'AB2':3, 'AB2C':4}, N, K, C, S)\n",
"x, delta = reaction.solve(30, 1e2, 0)\n",
"reaction.plotter()\n",
"\n",
"np.linalg.norm(np.log(x)*1e-16)"
]
},
{
"cell_type": "code",
"execution_count": 84,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"{0: 0, 1: 1}"
]
},
"execution_count": 84,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"eq_system = ClassTest(N, C)\n",
"eq_system.stoichiometry\n",
"eq_system.species\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
Expand Down Expand Up @@ -522,22 +601,28 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 52,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"[1, 1, 0.1]"
"3"
]
},
"execution_count": 63,
"execution_count": 52,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"S"
"def test(a, b, c=None):\n",
" if c == None:\n",
" return a+b\n",
" else:\n",
" return a+b+c\n",
"\n",
"test(1,2)"
]
},
{
Expand Down

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