CSE 111 | Project: Chemistry

W04 Project: Chemistry

Purpose

Prove that you can write a Python program that creates and uses compound lists.

Project

Background

You are an intern working for a government research facility. The chemistry lab has requested a program that will calculate the molar mass and the number of moles for a given quantity of a chemical compound. You have been assigned to create this program.

But I'm not a Chemist!

Often times you will be tasked to create programs where you might not fully understand the entire problem. When this happens you must rely on the requirements given to you by the user. For this problem you may not know what a mole or a molar mass is. Don't worry. The user knows what they are and can give you the necessary information to solve their problem.

User Requirements

The lead chemist Mariana Cardoso has asked you to create a program with the following requirements.

Ask the user for a chemical formula.
Ask the user for the amount of the compound in grams (this is the sample_mass).
Compute and display the molar mass.
Compute and display the number of moles.

Mariana has provided the following information:

A compound or molecule is described by a list of elements it contains. The element is identified by the element's symbol. If there is more than one atom of that element a number representing the number of atoms in the compound will follow the element's symbol. Here are some examples.
- H₂O (water) has 2 Hydrogen atoms and 1 Oxygen atom.
- C₆H₁₂O₆ (glucose) has 6 Carbon atoms, 12 Hydrogen atoms, and 6 Oxygen atoms.
To calculate the molar mass of a compound all you need to do is sum all of the weights of each atom in the compound.
To calculate the number of moles in a sample use the following formula:

number_of_moles =

sample_mass

molar_mass

Design

The requirements were sent to Alice Laurent, one of our software architects. She provided the following direction.

Alice developed the following program architecture. Use this information to create your program. As a junior programmer, you must use the functions defined by Alice, and the exact function names and parameters.

Function Specifications

Function Name	Parameters Return Type	Description
make_periodic_table	Parameters: (none) Returns: Dictionary	Returns a dictionary object which contains all of the elements of the periodic table. For each element the dictionary key should be the element's symbol. The value contains a list where the first item in the list is the element's name and the second item is the atomic mass.
compute_molar_mass	Parameters: symbol_quantity_list, periodic_table_dict Returns: float	Compute and return the total molar mass of all the elements listed in symbol_quantity_list. loop through the item's in the symbol_quantity_list For each item in the list use the element's symbol to lookup the atomic mass of the element in the periodic_table_dict dictionary. Multiply the elements atomic weight by the quantity of atoms for the element (from the symbol_quantity_list) and add that to the total mass. Return the total mass.
main	Parameters: (none) Returns: (none)	Asks the user for a chemical formula. Asks the user for the sample size in grams. Call parse_formula (from provided library) to get a list of elements in formula. (store in a vaiable). Call make_periodic_table function and store returned dictionary in variable. Call compute_molar_mass to calculate the molar mass. Pass in the periodic table dictionary and element list returned from the previous functions. Display the molar mass. Calculate Number of moles in the sample. Display the Number of moles.

Other helpful information.

While working on this project Alice discoverd that another programmer has already created a library that has a function named parse_formula for another project. This function does exactly what you need. You can use that library in your program to save time. The function is in the library formula.py

Milestone

Start your project by writing the outline of your program. Follow these steps:

Create a folder for this week's project, name it whatever you want.
Open the folder you just created in VSCode.
Create a file named chemistry.py.

Create the function make_periodic_table. When complete the function will return a dictionary that contains all of the elements in the periodic table. Your dictionary should look similar to this:

periodic_table_dict = {
  # symbol: [name, atomic_mass]
  "Ac": ["Actinium", 227],
  "Ag": ["Silver", 107.8682],
  "Al": ["Aluminum", 26.9815386],
  ⋮
  }

Full list of elements:

Mariana has provided this list of elements for you to use. It is also available in this text file elements.csv

Symbol	Name	Atomic Mass
Ac,	Actinium,	227
Ag,	Silver,	107.8682
Al,	Aluminum,	26.9815386
Ar,	Argon,	39.948
As,	Arsenic,	74.9216
At,	Astatine,	210
Au,	Gold,	196.966569
B,	Boron,	10.811
Ba,	Barium,	137.327
Be,	Beryllium,	9.012182
Bi,	Bismuth,	208.9804
Br,	Bromine,	79.904
C,	Carbon,	12.0107
Ca,	Calcium,	40.078
Cd,	Cadmium,	112.411
Ce,	Cerium,	140.116
Cl,	Chlorine,	35.453
Co,	Cobalt,	58.933195
Cr,	Chromium,	51.9961
Cs,	Cesium,	132.9054519
Cu,	Copper,	63.546
Dy,	Dysprosium,	162.5
Er,	Erbium,	167.259
Eu,	Europium,	151.964
F,	Fluorine,	18.9984032
Fe,	Iron,	55.845
Fr,	Francium,	223
Ga,	Gallium,	69.723
Gd,	Gadolinium,	157.25
Ge,	Germanium,	72.64
H,	Hydrogen,	1.00794
He,	Helium,	4.002602
Hf,	Hafnium,	178.49
Hg,	Mercury,	200.59
Ho,	Holmium,	164.93032
I,	Iodine,	126.90447
In,	Indium,	114.818
Ir,	Iridium,	192.217
K,	Potassium,	39.0983
Kr,	Krypton,	83.798
La,	Lanthanum,	138.90547
Li,	Lithium,	6.941
Lu,	Lutetium,	174.9668
Mg,	Magnesium,	24.305
Mn,	Manganese,	54.938045
Mo,	Molybdenum,	95.96
N,	Nitrogen,	14.0067
Na,	Sodium,	22.98976928
Nb,	Niobium,	92.90638
Nd,	Neodymium,	144.242
Ne,	Neon,	20.1797
Ni,	Nickel,	58.6934
Np,	Neptunium,	237
O,	Oxygen,	15.9994
Os,	Osmium,	190.23
P,	Phosphorus,	30.973762
Pa,	Protactinium,	231.03588
Pb,	Lead,	207.2
Pd,	Palladium,	106.42
Pm,	Promethium,	145
Po,	Polonium,	209
Pr,	Praseodymium,	140.90765
Pt,	Platinum,	195.084
Pu,	Plutonium,	244
Ra,	Radium,	226
Rb,	Rubidium,	85.4678
Re,	Rhenium,	186.207
Rh,	Rhodium,	102.9055
Rn,	Radon,	222
Ru,	Ruthenium,	101.07
S,	Sulfur,	32.065
Sb,	Antimony,	121.76
Sc,	Scandium,	44.955912
Se,	Selenium,	78.96
Si,	Silicon,	28.0855
Sm,	Samarium,	150.36
Sn,	Tin,	118.71
Sr,	Strontium,	87.62
Ta,	Tantalum,	180.94788
Tb,	Terbium,	158.92535
Tc,	Technetium,	98
Te,	Tellurium,	127.6
Th,	Thorium,	232.03806
Ti,	Titanium,	47.867
Tl,	Thallium,	204.3833
Tm,	Thulium,	168.93421
U,	Uranium,	238.02891
V,	Vanadium,	50.9415
W,	Tungsten,	183.84
Xe,	Xenon,	131.293
Y,	Yttrium,	88.90585
Yb,	Ytterbium,	173.054
Zn,	Zinc,	65.38
Zr,	Zirconium,	91.224

Add function main. For now just have the main function call make_periodic_table and print the returned table.
Include the following code at the bottom of your program to facilitate testing.
```
if __name__ == "__main__":
  main()
```

Testing

Verify that your program works correctly by following each step in this testing procedure:

Download the test_chemistry_milestone.py Python file and save it in the same folder where you saved your chemistry.py program. Run the test_chemistry_milestone.pyfile and ensure that the test passes. If the test functions does not pass, there is a mistake in your chemistry.py program. Read the output from pytest, fix the mistake, and run the test_chemistry_milestone.py file again until all the test functions pass.

============================== 1 passed in 0.04s ============================== 
PS C:\Users\cjlindstrom\cse111\chemistry> python .\test_chemistry_milestone.py
============================= test session starts =============================
platform win32 -- Python 3.13.0, pytest-8.3.4, pluggy-1.5.0 
cachedir: .pytest_cache
rootdir: C:\Users\cjlindstrom\cse111\chemistry
collected 1 item                                                                                                                                                           

test_chemistry_milestone.py::test_make_periodic_table PASSED             [100%]

============================== 1 passed in 0.04s ==============================

Milestone Submission

On or before the due date, return to Canvas and report your progress on this milestone.

Project Completion

Finish your project by completing the code for the compute_molar_mass and main functions. Ensure your code accomplishes the requirements specified above.

Download the formula.py Python file and save it in the same folder where you saved your chemistry.py program. The formula.py file includes a FormulaError class and a function named parse_formula. Both of them are complete and work correctly, and you should not change them.
Open the formula.py file in VS Code and read the triple quoted string at the top of the parse_formula function. As the triple quoted string states, the parse_formula function converts a chemical formula for a molecule, such as "C13H16N2O2" (melatonin), into a compound list, such as [["C", 13], ["H", 16], ["N", 2], ["O", 2]]. This compound list is known as a symbol_quantity_list because it contains the symbols of chemical elements and the quantity of atoms of each element that appear in a chemical formula.
Copy and paste the following import statement into your chemistry.py program at the top of your program. This statement will import the parse_formula function from the formula.py file into your chemistry.py program so that you can call the parse_formula function in your program.
```
from formula import parse_formula
```

Complete the compute_molar_mass function according to the program specifications.

Calculation Example:

This example might help you as you write your code. Consider a sample of glucose (C₆H₁₂O₆) with a mass of 12.37 grams. To use a molar mass calculator, a chemist enters

C6H12O6
12.37

The calculator computes the molar mass of glucose by doing the following:

Sum the number of atoms of each element in the formula for glucose:
6 carbon atoms
12 hydrogen atoms
6 oxygen atoms

Find the atomic mass of each element:

Symbol	Name	Atomic Mass
C	Carbon	12.0107
H	Hydrogen	1.00794
O	Oxygen	15.9994

Multiply the number of atoms by their atomic mass:

6	×	12.0107	=	72.0642
12	×	1.00794	=	12.09528
6	×	15.9994	=	95.9964

Add the results of the multiplications to get the molar mass of glucose:
72.0642 + 12.09528 + 95.9964 = 180.15588 grams/mole

Then the calculator divides the mass of the sample of glucose by the molar mass of glucose which results in the number of moles in the sample:

12.37 grams

180.15588 grams/mole

= 0.06866 moles

The calculator prints two results for the chemist to see:

the molar mass of glucose: 180.15588 grams/mole
the number of moles in the sample: 0.06866 moles

Hint: Don't forget index variables.

Remember when working with compound lists is is helpful to create variables that hold the index values of your data. For example, if I had a list that contains lists that describe people and their favorite color:

people=[['James','red'],['Julia','blue'],['Ricardo','yellow']]

The following code will print each person's name and favorite color.

for person in people:
  print(f"{person[0]}'s favorite color is {person[1]}")

If I use well named variables to hold the list index numbers my code is much easier to understand.

NAME_INDEX=0
COLOR_INDEX=1
for person in people:
  print(f"{person[NAME_INDEX]}'s favorite color is {person[COLOR_INDEX]}")

Complete the main function. Remove the code from the milestone and complete the main function according to the program Specifications.

Exceeding the Requirements

If your program fulfills the requirements for this assignment as described above, your program will earn 93% of the possible points. In order to earn the remaining 7% of points, you will need to add one or more features to your program so that it exceeds the requirements. Use your creativity to add features. Add a comment to the top of your code that explains your enhancement(s).

Document your enhancements:

If you choose to "exceed requirements" place a comment at the top of your code file that describes what you did to enhance your program.

Testing

Verify that your program works correctly by following each step in this testing procedure:

Download the test_chemistry.py Python file and save it in the same folder where you saved your chemistry.py program. Run the test_chemistry.py file and ensure that all three of the test functions pass. If any of the test functions don’t pass, there is a mistake in your chemistry.py program. Read the output from pytest, fix the mistake, and run the test_chemistry.py file again until all the test functions pass.

> python test_chemistry_2.py
=================== test session starts ====================
platform win32--Python 3.8.6, pytest-6.1.2, py-1.9.0, pluggy
rootdir: C:\Users\cse111\week04
collected 3 items
test_chemistry_2.py::test_make_periodic_table PASSED  [ 33%]
test_chemistry_2.py::test_parse_formula PASSED        [ 66%]
test_chemistry_2.py::test_compute_molar_mass PASSED   [100%]
==================== 3 passed in 0.17s =====================

Run your finished chemistry.py program. Enter the input shown below and ensure that your program prints the output shown below.

> python chemistry.py
Enter the molecular formula of the sample: C6H6
Enter the mass in grams of the sample: 25.04
78.11184 grams/mole
0.32057 moles

Project Submission

Return to Canvas and upload your chemistry.py file for feedback.

Don't get a zero!

If an error prevents your program from running to completion the grader will score your assignment with a 0 and request that you fix and resubmit your program. In other words, rather than submitting a program that doesn't work, it's best to ask for help to understand how to fix the problem before submitting your program.

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