Merge pull request #20 from KennethQNgo/main

Reviewed final chapters

Author: simongravelle

Diff for: docs/source/chapters/chapter6.rst

@@ -1,7 +1,7 @@
 .. _chapter6-label:
 
-Monte Carlo dispace
-===================
+Monte Carlo displace
+====================
 
 .. figure:: ../projects/project1/avatar-dm.webp
     :alt: The fluid made of argon atoms and simulated using monte carlo and python.
@@ -16,7 +16,7 @@ Monte Carlo dispace
     :class: only-light
 
 Here, a Monte Carlo simulation is implemented where the only allowed move
-is a dispacement of the particles. The principle of such Monte Carlo
+is a displacement of the particles. The principle of such Monte Carlo
 simulation is the following:
 
 - 1) We start from a given intial configuration, and measure the potential

Diff for: docs/source/chapters/chapter8.rst

@@ -175,7 +175,7 @@ Let us also normalize the "desired_mu":
 
 .. code-block:: python
 
-    class MonteCarlo(Outputs):
+    class MonteCarlo(Measurements):
         def __init__(self,
             (...)
             self.nondimensionalize_units(["desired_temperature", "displace_mc"])
@@ -238,7 +238,7 @@ Test the code
 One can use a similar test as previously, but with an imposed chemical
 potential *desired_mu*:
 
-.. label:: start_test_9a_class
+.. label:: start_test_8a_class
 
 .. code-block:: python
 
@@ -297,7 +297,7 @@ potential *desired_mu*:
         # Run pytest programmatically
         pytest.main(["-s", __file__])
 
-.. label:: end_test_9a_class
+.. label:: end_test_8a_class
 
 The evolution of the potential energy as a function of the
 number of steps is written in the *Outputs/Epot.dat*.

Diff for: docs/source/chapters/chapter9.rst

@@ -76,7 +76,7 @@ Let us initialise swap counter:
 
 .. code-block:: python
 
-    class MonteCarlo(Outputs):
+    class MonteCarlo(Measurements):
         def __init__(self,
             (...)
             self.failed_move = 0
@@ -91,7 +91,7 @@ Complete the *__init__* method as follows:
 
 .. code-block:: python
 
-    class MonteCarlo(Outputs):
+    class MonteCarlo(Measurements):
         def __init__(self,
                     (...)
                     displace_mc = None,
@@ -105,7 +105,7 @@ and
 
 .. code-block:: python
 
-    class MonteCarlo(Outputs):
+    class MonteCarlo(Measurements):
         def __init__(self,
             (...)
             self.displace_mc = displace_mc
@@ -125,3 +125,81 @@ Finally, the *monte_carlo_exchange()* method must be included in the run:
             self.monte_carlo_swap()
 
 .. label:: end_MonteCarlo_class
+
+Test the code
+-------------
+
+Let's test the Monte Carlo swap.
+
+.. label:: start_test_9a_class
+
+.. code-block:: python
+
+    from MonteCarlo import MonteCarlo
+    from pint import UnitRegistry
+    ureg = UnitRegistry()
+    import os
+
+    # Define atom number of each group
+    nmb_1 = 50
+    nmb_2 = 50  # New group for testing swaps
+    # Define LJ parameters (sigma)
+    sig_1 = 3 * ureg.angstrom
+    sig_2 = 4 * ureg.angstrom  # Different sigma for group 2
+    # Define LJ parameters (epsilon)
+    eps_1 = 0.1 * ureg.kcal / ureg.mol
+    eps_2 = 0.15 * ureg.kcal / ureg.mol  # Different epsilon for group 2
+    # Define atom mass
+    mss_1 = 10 * ureg.gram / ureg.mol
+    mss_2 = 12 * ureg.gram / ureg.mol  # Different mass for group 2
+    # Define box size
+    L = 20 * ureg.angstrom
+    # Define a cut off
+    rc = 2.5 * sig_1
+    # Pick the desired temperature
+    T = 300 * ureg.kelvin
+
+    # Initialize the prepare object
+    mc = MonteCarlo(
+        ureg=ureg,
+        maximum_steps=100,
+        thermo_period=10,
+        dumping_period=10,
+        number_atoms=[nmb_1, nmb_2],  # Include two groups of atoms for swap
+        epsilon=[eps_1, eps_2],  # kcal/mol
+        sigma=[sig_1, sig_2],  # A
+        atom_mass=[mss_1, mss_2],  # g/mol
+        box_dimensions=[L, L, L],  # A
+        cut_off=rc,
+        thermo_outputs="Epot-press",
+        desired_temperature=T,  # K
+        neighbor=1,
+        swap_type=[0, 1]  # Enable Monte Carlo swap between groups 1 and 2
+    )
+
+    # Run the Monte Carlo simulation
+    mc.run()
+
+    # Test function using pytest
+    def test_output_files():
+        assert os.path.exists("Outputs/dump.mc.lammpstrj"), \
+            "Test failed: dump file was not created"
+        assert os.path.exists("Outputs/simulation.log"), \
+            "Test failed: log file was not created"
+        print("Test passed")
+
+    # Test the swap counters
+    def test_swap_counters():
+        assert mc.successful_swap + mc.failed_swap > 0, \
+            "Test failed: No swaps were attempted"
+        print("Swap test passed")
+
+    # If the script is run directly, execute the tests
+    if __name__ == "__main__":
+        import pytest
+        # Run pytest programmatically
+        pytest.main(["-s", __file__])
+
+.. label:: end_test_9a_class
+
+

Diff for: docs/source/projects/project1.rst

@@ -261,7 +261,7 @@ at the same time (if your computer has enough CPU core, if not, perform these
 calculations in serial):
 
 .. code-block:: python
-A
+
     if __name__ == "__main__":
         tau_values = np.round(np.logspace(-0.126, 0.882, 10),2)
         pool = multiprocessing.Pool()