simplify force definitino and fix tests

Author: simongravelle

docs/source/chapters/chapter4.rst

@@ -264,7 +264,7 @@ Compute_potential
 Computing the potential energy of the system is central to the energy minimizer,
 as the value of the potential is used to decide if the trial is accepted or
 rejected. Add the following method called *compute_potential()*  to the *Utilities*
-class.
+class:
 
 .. label:: start_Utilities_class
 
@@ -289,6 +289,10 @@ class.
     
 .. label:: end_Utilities_class
 
+Measuring the distance is an important step of computing the potential. Let us
+do it using a dedicated method. Add the following method to the *Utilities*
+class as well:
+
 .. label:: start_Utilities_class
 
 .. code-block:: python
@@ -308,6 +312,10 @@ class.
 
 .. label:: end_Utilities_class
 
+Finally, the energy minimization requires the computation of the minimum
+force in the system. Although not very different from the potential measurement,
+let us create a new method that is dedicated solely to measuring forces:
+
 .. label:: start_Utilities_class
 
 .. code-block:: python
@@ -345,11 +353,10 @@ class.
     
 .. label:: end_Utilities_class
 
-Here, the method is a little bit complicated, because three types of outputs can
-be requested by the user: *force-vector*, *force-matrix*, and *potential*. The last
-one, *potential*, simply returns the value of the potential energy for the entire system.
-If *force-vector* or *force-matrix* are selected instead, then the individual forces
-between atoms are returned.
+Here, two types of outputs can
+be requested by the user: *force-vector*, and *force-matrix*. 
+The *force-matrix* option will be useful for pressure calculation, see
+:ref:`chapter7-label`.
 
 Wrap in box
 -----------

docs/source/chapters/chapter5.rst

@@ -84,7 +84,7 @@ All quantities are re-dimensionalized before getting outputed.
         if code.thermo_period is not None:
             if code.step % code.thermo_period == 0:
                 if code.step == 0:
-                    Epot = code.compute_potential(output="potential") \
+                    Epot = code.compute_potential() \
                         * code.reference_energy  # kcal/mol
                 else:
                     Epot = code.Epot * code.reference_energy  # kcal/mol

docs/source/chapters/chapter6.rst

@@ -50,7 +50,7 @@ Let us add a method named *monte_carlo_move* to the *MonteCarlo* class:
             try: # try using the last saved Epot, if it exists
                 initial_Epot = self.Epot
             except: # If self.Epot does not exists yet, calculate it
-                initial_Epot = self.compute_potential(output="potential")
+                initial_Epot = self.compute_potential()
             # Make a copy of the initial atoms positions
             initial_positions = copy.deepcopy(self.atoms_positions)
             # Pick an atom id randomly
@@ -63,7 +63,7 @@ Let us add a method named *monte_carlo_move* to the *MonteCarlo* class:
                 move = np.append((np.random.random(2) - 0.5) * self.displace_mc, 0)
             self.atoms_positions[atom_id] += move
             # Measure the optential energy of the new configuration
-            trial_Epot = self.compute_potential(output="potential")
+            trial_Epot = self.compute_potential()
             # Evaluate whether the new configuration should be kept or not
             beta =  1/self.desired_temperature
             delta_E = trial_Epot-initial_Epot

docs/source/chapters/chapter7.rst

@@ -49,7 +49,7 @@ Let us add the following method to the *Utilities* class.
             temperature = self.desired_temperature # for MC, simply use the desired temperature
         p_ideal = Ndof*temperature/(volume*self.dimensions)
         # Compute the non-ideal contribution
-        distances_forces = np.sum(self.compute_potential(output="force-matrix")*self.evaluate_rij_matrix())
+        distances_forces = np.sum(self.compute_force(return_vector = False)*self.evaluate_rij_matrix())
         p_nonideal = distances_forces/(volume*self.dimensions)
         # Final pressure
         self.pressure = p_ideal+p_nonideal

tests/build-documentation.py

@@ -18,7 +18,7 @@
     os.mkdir("generated-codes/")
 
 # loop on the different chapter
-for chapter_id in [1, 2, 3, 4]: #, 5, 6, 7]:
+for chapter_id in [1, 2, 3, 4, 5, 6, 7]:
     # for each chapter, create the corresponding code
     RST_EXISTS, created_tests, folder = sphinx_to_python(path_to_docs, chapter_id)
     if RST_EXISTS: