Lecture 1 - Python Primer

Lecture 1 - Python Primer#

Learn just enough Python to start doing chemistry right away.

Who is this for?

Absolute beginners. If you can open a notebook and type, you can follow along.

Learning goals #

Run code cells in a notebook and switch between Code and Markdown.
Use Python as a calculator for quick chemical math.
Store values in variables, use lists and dictionaries.
Write tiny functions to avoid repeating yourself.
Make a simple plot for a chemistry relationship.
Read error messages without panic.

Section 1–9

Recommended reading before class (especially notes and tips)
We will review together during lecture (bring your questions!)

Keep this page open for reference.

Section 10

In-class activity
Work with your neighbor to solve

Kept short and friendly.

1. Setup - choose your path #

Right-click the badge below and select “Open link in new tab”

Log in to your Google account. Then in the top left menu, go to File > Save a copy in Drive to keep your own editable version.

Note

You can also download and run locally on your laptop with Anaconda (JupyterLab) or Miniconda.
If this is your first time coding, we recommend starting with Google Colab for simplicity.

2. Meet the notebook #

A notebook has cells.
Code cells run Python.
Markdown cells hold text, titles, and math like \(PV = nRT\).

Handy keys

Shift+Enter - run cell
A - new cell above
B - new cell below
M - turn into Markdown
Y - turn into Code

To run your first code cell, hover over the left edge of the cell. A play icon (circle with a triangle) appears. Click it to run. The first run may take a few seconds while the runtime starts.

You can also click inside a cell and press Shift+Enter.

3. Python as a calculator #

We will run a few short cells and see results right away.

3.1 Run your first cell#

print("Hello World")

Hello World

print(...) shows text or values in the output area.
In a code cell, the value of the last line also displays automatically.

3.2 Simple arithmetic#

2 + 2

Tip

You can edit the numbers in Colab and run again. Nothing breaks if you try things. In this web page, you will only be able to view input and output.

3.3 Comments do not run#

Lines that start with # are comments. Python ignores them.

# This line is a comment. Remove the # and the line will run.
# 1 + 3

You can also add a comment at the end of a line:

1 + 1  # this adds one plus one

3.4 Only the last line shows by default#

2 + 2
1 + 1   # only this result will display

To show both results, either use two print calls or return a pair of values:

print(2 + 2)
print(1 + 1)

# or as a pair (tuple)
(2 + 2, 1 + 1)

4
2

(4, 2)

3.5 Common operators#

* 4      # multiply
/ 4     # true division (float)
// 4    # floor division (integer result)
% 4     # remainder (modulo)
** 5     # exponent (2 to the 5)

3.6 Order of operations#

2 + 3 * 4        # multiplication first
(2 + 3) * 4      # parentheses change the order

3.7 Types from division#

type(10 / 3), type(10 // 3)

(float, int)

Warning

10/3 gives a float like 3.3333333333.
10//3 gives integer division 3. With negatives it floors: -10//3 is -4.

Try it

Change the numbers above and re-run.
What is 15 % 4? What about -15 % 4?

4. Variables - names for values #

A variable is a name that points to a value. You can reuse it.

4.1 Create and read a variable#

x = 100        # set x to one hundred
x

Use a variable inside an expression:

2 * x + 1

4.2 Update a variable#

x = 1.1        # replace the old value with a new one
x

1.1

4.3 Descriptive names and units#

Choose names that tell you what the value is and, if helpful, its units.

temperature_K = 298.15              # Kelvin
R = 0.082057                         # L·atm·mol^-1·K^-1
type(temperature_K), type(R)

(float, float)

Rules of thumb

Names can use letters, numbers, and _, but cannot start with a number.
Names are case-sensitive: mass and Mass are different.
Use clear names. Add units to the name if it helps (temperature_K, volume_L).

Try it

Make y = 3, then compute y**3. Change y to 10 and run again.

5. Quick chemistry - molar mass and moles #

We will compute a molar mass, then convert mass to moles.

5.1 Molar mass of CO₂#

Define atomic weights and add them with the correct counts.

C = 12.011     # g mol^-1
O = 15.999     # g mol^-1

M_CO2 = C + 2 * O   # 1 carbon and 2 oxygens
M_CO2

44.009

Format it nicely with units:

print(f"M_CO2 = {M_CO2:.3f} g mol^-1")

M_CO2 = 44.009 g mol^-1

5.2 Mass to moles#

Use ( n = \dfrac{m}{M} ). Keep units consistent.

mass_g = 10.0            # grams of CO2
moles = mass_g / M_CO2   # mol
moles

0.22722624917630485

Report with a friendly number of decimals:

print(f"moles of CO2 in {mass_g} g = {moles:.4f} mol")

moles of CO2 in 10.0 g = 0.2272 mol

Note

Unit check: grams divided by grams per mole gives moles.

Try it

Change mass_g to 22.0 or 5.5 and re-run. Does the mole amount scale as you expect?

5.3 Small sanity checks#

If you double the mass, moles should double.
If you switch to kilograms by mistake, the result will be off by 1000. Keep everything in grams here.

Warning

Do not use // for chemistry math. // floors the result and throws away decimals. Use /.

Exercise 5.1 - Water

Compute the molar mass of water and the moles in 36.0 g of water. Atomic weights: H = 1.008, O = 15.999

6. Tiny data structures - lists and dictionaries #

Lists keep an ordered set of items. Dictionaries map keys to values.

6.1 Make a list and read from it#

acids = ["HCl", "HNO3", "H2SO4"]   # a list of strings
acids, len(acids)

(['HCl', 'HNO3', 'H2SO4'], 3)

Key points

Square brackets [...] create a list.
Lists keep order. Indexing starts at 0.

Access items by index. Negative indexes count from the end.

acids[0], acids[1], acids[-1]

('HCl', 'HNO3', 'H2SO4')

Take a slice to get a sublist.

acids[0:2]   # from index 0 up to but not including 2

['HCl', 'HNO3']

6.2 Change a list#

Replace, append, insert, and remove.

acids[1] = "HBr"     # replace the second item
acids.append("HNO3") # add to the end
acids.insert(1, "HF")# insert at position 1
acids

['HCl', 'HF', 'HBr', 'H2SO4', 'HNO3']

Remove by value or by position.

acids.remove("HF")   # removes the first matching "HF"
popped = acids.pop(0) # removes and returns the item at index 0
popped, acids

('HCl', ['HBr', 'H2SO4', 'HNO3'])

Add many at once.

acids.extend(["HClO4", "HI"])
acids

['HBr', 'H2SO4', 'HNO3', 'HClO4', 'HI']

Common gotchas

remove(x) deletes the first match only.
pop() without an index removes the last item.
Lists are mutable. If b = acids, then changing b also changes acids. Use acids.copy() if you want a separate copy.

6.3 Check membership and find positions#

"HBr" in acids, "NaOH" in acids   # True or False

(True, False)

acids.index("HBr")   # index of the first "HBr" if present

acids.index("HI")   # index of the first "HI" if present

Warning

Python list index starts with 0. acids.index("HCl") raises a ValueError if the item is not present.

6.4 Make a dictionary and read from it#

Dictionaries use curly braces and key: value pairs.

aw = {"H": 1.008, "C": 12.011, "O": 15.999, "N": 14.007, "Cl": 35.45}
aw["O"], "H" in aw

(15.999, True)

Add or update entries.

aw["Na"] = 22.990          # add sodium
aw.update({"S": 32.06})    # add sulfur with update
aw["Na"], aw["S"]

(22.99, 32.06)

Safe lookup with a default.

aw.get("K"), aw.get("K", 39.10)   # None vs default value if missing

(None, 39.1)

Delete a key.

del aw["S"]
"S" in aw

False

Key points

Use aw["O"] to get a value. If the key might be missing, use aw.get("O").
Keys must be unique. Assigning the same key again overwrites the old value.

6.5 Use the dictionary for quick chemistry#

Compute molar mass directly from atomic weights in aw.

M_CO2 = aw["C"] + 2 * aw["O"]
M_H2O = 2 * aw["H"] + aw["O"]
M_CO2, M_H2O

(44.009, 18.015)

Report with units.

print(f"M_CO2 = {M_CO2:.3f} g mol^-1")
print(f"M_H2O = {M_H2O:.3f} g mol^-1")

M_CO2 = 44.009 g mol^-1
M_H2O = 18.015 g mol^-1

6.6 Small practice#

Try it

Make a list bases = ["NaOH", "KOH"], append "NH3", then replace the first item with "Ca(OH)2".
Add "K": 39.10 to aw. Compute the molar mass of KCl using only aw.

Exercise 6.1

Build a dictionary entry for Na and Cl if not present, then compute molar mass of NaCl. :class: dropdown

Solution

aw.update({"Na": 22.990, "Cl": 35.45})
M_NaCl = aw["Na"] + aw["Cl"]
M_NaCl

```{admonition} Common mistakes
- Using parentheses instead of brackets for indexing: write `aw["O"]`, not `aw("O")`.
- Typos in keys: `"CL"` is not the same as `"Cl"`.
- Forgetting that list indexes start at 0.

7. Control flow - if, for, while #

Control flow lets your code make choices and repeat steps.

7.1 if - pick a path#

def classify_pH(pH):
    if pH < 7:
        return "acidic"
    elif pH > 7:
        return "basic"
    else:
        return "neutral"

[classify_pH(x) for x in [2.0, 7.0, 8.3]]

['acidic', 'neutral', 'basic']

Read this

Conditions use <, >, <=, >=, ==, !=
Only one branch runs

7.2 for - loop over a collection#

formulas = ["CO2", "H2O", "NH3"]
for f in formulas:
    print("Formula:", f)

Formula: CO2
Formula: H2O
Formula: NH3

Tip

Use for item in list: when you know how many items you have.

7.3 while - repeat until a condition is false#

# Count up to 3
i = 1
while i <= 3:
    print("i =", i)
    i += 1

i = 1
i = 2
i = 3

A small string example that reads digits from the front of a string:

s = "123abc"
i = 0
num = 0
while i < len(s) and s[i].isdigit():
    num = num * 10 + int(s[i])
    i += 1
num, s[i:]

(123, 'abc')

Common gotchas

Forgetting to update the counter in a while loop can cause an infinite loop
for is usually simpler than while when looping over lists

Practice

Change classify_pH to return “very acidic” for pH < 3
Use a for loop to print each element in ["H", "C", "O"] with its atomic weight from aw
Use a while loop to sum numbers from 1 to 100

8. Functions - small reusable steps #

A function is a named recipe. Inputs go in parentheses. The result is returned.

8.1 Tiny functions without control flow#

def celsius_to_kelvin(c):
    return c + 273.15

def grams_to_moles(mass_g, molar_mass):
    return mass_g / molar_mass

celsius_to_kelvin(25.0), grams_to_moles(10.0, 44.0095)

(298.15, 0.227223667617219)

Key ideas

def name(args): starts a function
return sends back the answer

8.2 Molar mass from element counts (uses `for`)#

def molar_mass_from_counts(counts, atomic_weights):
    """
    counts: dict like {'C': 1, 'O': 2}
    atomic_weights: dict of element -> atomic weight
    """
    total = 0.0
    for elem, count in counts.items():
        total += atomic_weights[elem] * count
    return total

molar_mass_from_counts({"C": 1, "O": 2}, aw)

44.009

8.3 Parse a simple formula string (uses `if` and `while`)#

We now turn “CO2” into {"C": 1, "O": 2}.

Note

Scope: symbols with optional lowercase letter, followed by an optional number. No parentheses or dots.

def parse_formula(formula):
    counts = {}
    i = 0
    while i < len(formula):
        # element symbol
        elem = formula[i]
        i += 1
        if i < len(formula) and formula[i].islower():
            elem += formula[i]
            i += 1
        # digits (may be empty)
        num = 0
        while i < len(formula) and formula[i].isdigit():
            num = num * 10 + int(formula[i])
            i += 1
        num = num or 1
        counts[elem] = counts.get(elem, 0) + num
    return counts

parse_formula("C6H12O6")

{'C': 6, 'H': 12, 'O': 6}

8.4 Final convenience function#

def molar_mass(formula, atomic_weights):
    return molar_mass_from_counts(parse_formula(formula), atomic_weights)

molar_mass("CO2", aw), molar_mass("H2O", aw), molar_mass("C6H12O6", aw)

(44.009, 18.015, 180.156)

Try it

Check that grams_to_moles(36.0, molar_mass("H2O", aw)) matches your earlier result.

Warning

If you see KeyError: 'Na', add the element to aw first.

9. Glossary #

variable#: A name that points to a value, like a label on a box. Example: x = 10.
function#: A named block of code that performs a task and returns a result. Example: print(), or your own grams_to_moles().
dictionary#: A mapping from keys to values, written with curly braces. Example: {"H": 1.008, "O": 15.999}.
list#: An ordered collection of items, written with square brackets. Example: ["HCl", "HNO3", "H2SO4"].
comment#: Text starting with # in code. Ignored by Python. Useful for notes and explanations.
float#: A number with a decimal point. Example: 3.14.
integer#: A whole number without a decimal point. Example: 42.
string#: Text written between quotes. Example: "Hello".
if statement#: A way to make decisions in code: run different blocks depending on a condition.
for loop#: A way to repeat an action for each item in a list or sequence.
while loop#: A way to repeat an action until a condition is no longer true.
module#: A file or library that provides extra tools for Python. Example: import math.
array#: A grid of values from NumPy that supports math on entire sets of numbers at once.
plot#: A figure showing data graphically. Made here with Matplotlib using commands like plt.plot(...).
error#: A message from Python when something goes wrong. Example: NameError, TypeError.
operator#: A symbol that performs an action on values. Examples: +, -, *, /, **.

10. In-class activity #

Work in groups of 2 to 3. Each challenge is about 5 minutes. These are new scenarios that mirror what you practiced, and each task is self-contained. Stay within Sections 1 to 8.

10.1 Ethanol mass to moles#

Compute the moles of ethanol C2H6O in 9.2 g using only arithmetic and variables.

# Atomic weights (g mol^-1)
C = 12.011
H = 1.008
O = 15.999

# Molar mass of ethanol: C2H6O
M_ethanol = ...   # TODO

# Mass to moles
mass_g = 9.2
moles = ...       # TODO

print("M_ethanol =", M_ethanol, "g mol^-1")
print("moles in", mass_g, "g =", moles)

10.2 Classify pH values in a list#

Given several pH readings “2.5”, “7.0”, “8.1”, “6.9”, “7.3”, print a line for each saying acidic, basic, or neutral. Do not define a helper function.

pH_values = ... #TODO

for ... in ...:            # TODO
    if ...:               # TODO
        status = "acidic"
    elif ...:             # TODO
        status = "basic"
    else:
        status = "neutral"
    print(pH, "->", status)

10.3 Molar mass from a counts dictionary#

Compute the molar mass of glucose using a small dictionary of atomic weights and a counts dictionary. Do not reuse any earlier functions.

# Atomic weights
aw = {"H": 1.008, "C": 12.011, "O": 15.999}

# Counts for C6H12O6
counts = {"C": 6, "H": 12, "O": 6}

M_glucose = 0.0
for elem, n in ...:       # TODO
    M_glucose = ...       # TODO 

print("M_glucose =", M_glucose, "g mol^-1")

10.4 Read leading integer from a string, then convert C to K#

A temperature string has digits followed by a letter, for example “25C” or “298K”. Read the leading digits using a while-loop and convert Celsius to Kelvin. If the unit is K, leave it as is.

s = "25C"   # try "298K" too

# Parse leading integer value
i = 0
value = 0
while i < len(s) and s[i].isdigit():
    value = value * 10 + int(s[i])
    i += 1

unit = s[i:]  # the rest of the string, e.g. "C" or "K"

if ...:                         # TODO
    temp_K = ...                # TODO
else:
    temp_K = value

print("Parsed:", value, unit)
print("Temperature in K:", temp_K)

10.5 Which sample has more moles#

You are given a mixture as a list of (mass_g, name, counts) where counts is a dictionary of element -> count in the formula. Compute the moles for each, then print the name of the sample with the largest moles. Do not call any functions from above; write the few lines you need here.

aw = {"H": 1.008, "C": 12.011, "O": 15.999, "N": 14.007}

mixture = [
    (2.00, "CO2", {"C": 1, "O": 2}),
    (3.00, "H2O", {"H": 2, "O": 1}),
    (4.00, "NH3", {"N": 1, "H": 3}),
]

max_moles = -1.0
winner = None

for mass_g, name, counts in ...:         # TODO
    # Compute molar mass from counts
    M = 0.0
    for elem, n in ...:                  # TODO
        M = ...                          # TODO
    n_moles = ...                        # TODO

    if ...:                              # TODO
        max_moles = n_moles
        winner = name

print("Largest moles:", winner, "with", max_moles, "mol")

11. In-class activity solution #

11.1 Ethanol mass to moles#

Compute the moles of ethanol C2H6O in 9.2 g using only arithmetic and variables.

# Atomic weights (g mol^-1)
C = 12.011
H = 1.008
O = 15.999

# Molar mass of ethanol: C2H6O
M_ethanol = 2*C + 6*H + 1*O   # TODO

# Mass to moles
mass_g = 9.2
moles = mass_g / M_ethanol       # TODO

print("M_ethanol =", M_ethanol, "g mol^-1")
print("moles in", mass_g, "g =", moles)

M_ethanol = 46.069 g mol^-1
moles in 9.2 g = 0.19970044932601097

11.2 Classify pH values in a list#

Given several pH readings “2.5”, “7.0”, “8.1”, “6.9”, “7.3”, print a line for each saying acidic, basic, or neutral. Do not define a helper function.

pH_values = [2.5, 7.0, 8.1, 6.9, 7.3] #TODO

for pH in pH_values:     # TODO
    if pH < 7:               # TODO
        status = "acidic"
    elif pH > 7:             # TODO
        status = "basic"
    else:
        status = "neutral"
    print(pH, "->", status)

5 -> acidic
0 -> neutral
1 -> basic
9 -> acidic
3 -> basic

11.3 Molar mass from a counts dictionary#

Compute the molar mass of glucose using a small dictionary of atomic weights and a counts dictionary. Do not reuse any earlier functions.

# Atomic weights
aw = {"H": 1.008, "C": 12.011, "O": 15.999}

# Counts for C6H12O6
counts = {"C": 6, "H": 12, "O": 6}

M_glucose = 0.0
for elem, n in counts.items():       # TODO
    M_glucose + aw[elem] * n       # TODO 

print("M_glucose =", M_glucose, "g mol^-1")

M_glucose = 0.0 g mol^-1

11.4 Read leading integer from a string, then convert C to K#

A temperature string has digits followed by a letter, for example “25C” or “298K”. Read the leading digits using a while-loop and convert Celsius to Kelvin. If the unit is K, leave it as is.

s = "25C"   # try "298K" too

# Parse leading integer value
i = 0
value = 0
while i < len(s) and s[i].isdigit():
    value = value * 10 + int(s[i])
    i += 1

unit = s[i:]  # the rest of the string, e.g. "C" or "K"

if unit == "C":                  # TODO
    temp_K = value + 273.15       # TODO
else:
    temp_K = value

print("Parsed:", value, unit)
print("Temperature in K:", temp_K)

Parsed: 25 C
Temperature in K: 298.15

11.5 Which sample has more moles#

You are given a mixture as a list of (mass_g, name, counts) where counts is a dictionary of element -> count in the formula. Compute the moles for each, then print the name of the sample with the largest moles. Do not call any functions from above; write the few lines you need here.

aw = {"H": 1.008, "C": 12.011, "O": 15.999, "N": 14.007}

mixture = [
    (2.00, "CO2", {"C": 1, "O": 2}),
    (3.00, "H2O", {"H": 2, "O": 1}),
    (4.00, "NH3", {"N": 1, "H": 3}),
]

max_moles = -1.0
winner = None

for mass_g, name, counts in mixture:         # TODO
    # Compute molar mass from counts
    M = 0.0
    for elem, n in counts.items():    # TODO
        M = M + aw[elem] * n   # TODO
    n_moles = mass_g / M        # TODO

    if n_moles > max_moles:          # TODO
        max_moles = n_moles
        winner = name

print("Largest moles:", winner, "with", max_moles, "mol")

Largest moles: NH3 with 0.23486583289295992 mol

Lecture 1 - Python Primer

Contents

Lecture 1 - Python Primer#

3.1 Run your first cell#

3.2 Simple arithmetic#

3.3 Comments do not run#

3.4 Only the last line shows by default#

3.5 Common operators#

3.6 Order of operations#

3.7 Types from division#

4.1 Create and read a variable#

4.2 Update a variable#

4.3 Descriptive names and units#

5.1 Molar mass of CO₂#

5.2 Mass to moles#

5.3 Small sanity checks#

6.1 Make a list and read from it#

6.2 Change a list#

6.3 Check membership and find positions#

6.4 Make a dictionary and read from it#

6.5 Use the dictionary for quick chemistry#

6.6 Small practice#

7.1 if - pick a path#

7.2 for - loop over a collection#

7.3 while - repeat until a condition is false#

8.1 Tiny functions without control flow#

8.2 Molar mass from element counts (uses for)#

8.3 Parse a simple formula string (uses if and while)#

8.4 Final convenience function#

10.1 Ethanol mass to moles#

10.2 Classify pH values in a list#

10.3 Molar mass from a counts dictionary#

10.4 Read leading integer from a string, then convert C to K#

10.5 Which sample has more moles#

11.1 Ethanol mass to moles#

11.2 Classify pH values in a list#

11.3 Molar mass from a counts dictionary#

11.4 Read leading integer from a string, then convert C to K#

11.5 Which sample has more moles#

8.2 Molar mass from element counts (uses `for`)#

8.3 Parse a simple formula string (uses `if` and `while`)#