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edited equations class
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@mtod92
mtod92 committed Dec 21, 2023
1 parent 26f7788 commit f74d3bf
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Showing 2 changed files with 27 additions and 24 deletions.
3 changes: 2 additions & 1 deletion equpy.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,8 @@ def __init__(self, equations, mass_conservation, species = None):
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
print(self.stoichiometry)
self.species = {'i':i for i in range(len(self.stoichiometry))} #placeholder for species name if not specified

class ChemicalReaction:
def __init__(
Expand Down
48 changes: 25 additions & 23 deletions equpy_test.ipynb
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"cells": [
{
"cell_type": "code",
"execution_count": 64,
"execution_count": 17,
"metadata": {},
"outputs": [
{
Expand All @@ -11,7 +11,7 @@
"{'divide': 'warn', 'over': 'warn', 'under': 'ignore', 'invalid': 'ignore'}"
]
},
"execution_count": 64,
"execution_count": 17,
"metadata": {},
"output_type": "execute_result"
}
Expand All @@ -27,15 +27,15 @@
},
{
"cell_type": "code",
"execution_count": 65,
"execution_count": 18,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"execution time --- 0.8813732802265822 milliseconds ---\n",
"execution time --- 0.9135236643781566 milliseconds ---\n",
"\n"
]
},
Expand Down Expand Up @@ -80,9 +80,20 @@
},
{
"cell_type": "code",
"execution_count": 75,
"execution_count": 16,
"metadata": {},
"outputs": [],
"outputs": [
{
"data": {
"text/plain": [
"{'i': 1}"
]
},
"execution_count": 16,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
"class ClassTest:\n",
" def __init__(self, equations, mass_conservation, species = None):\n",
Expand All @@ -91,10 +102,11 @@
" 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",
" 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"
"eq_system = ClassTest(N, C)\n",
"eq_system.species"
]
},
{
Expand Down Expand Up @@ -450,22 +462,19 @@
},
{
"cell_type": "code",
"execution_count": 85,
"execution_count": 21,
"metadata": {},
"outputs": [
{
"ename": "TypeError",
"evalue": "sequence item 0: expected str instance, numpy.ndarray found",
"evalue": "__call__() takes 1 positional argument but 2 were given",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mTypeError\u001b[0m Traceback (most recent call last)",
"\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"
"\u001b[0;32m<ipython-input-21-5e2c8a9a4bc1>\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, species)\u001b[0m\n\u001b[1;32m 12\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\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[0;32m---> 14\u001b[0;31m \u001b[0mprint\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;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 15\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[0;34m'i'\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[0mlen\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;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[1;32m 16\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mTypeError\u001b[0m: __call__() takes 1 positional argument but 2 were given"
]
}
],
Expand Down Expand Up @@ -516,13 +525,6 @@
"eq_system.species\n"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
},
{
"cell_type": "code",
"execution_count": null,
Expand Down

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