python: Rename MC method reaction argument

For consistency with the integrator.run() method. Co-authored-by: Pablo Miguel Blanco Andrés <[email protected]>
espressomd · Feb 13, 2023 · 881d214 · 881d214
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commit 881d214
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Showing 11 changed files with 23 additions and 23 deletions.
diff --git a/doc/tutorials/constant_pH/constant_pH.ipynb b/doc/tutorials/constant_pH/constant_pH.ipynb
@@ -686,7 +686,7 @@
    "source": [
     "```python\n",
     "def equilibrate_reaction(reaction_steps=1):\n",
-    "    RE.reaction(reaction_steps=reaction_steps)\n",
+    "    RE.reaction(steps=reaction_steps)\n",
     "```"
    ]
   },
@@ -743,7 +743,7 @@
     "        if USE_WCA and np.random.random() < prob_integration:\n",
     "            system.integrator.run(integration_steps)\n",
     "        # we should do at least one reaction attempt per reactive particle\n",
-    "        RE.reaction(reaction_steps=reaction_steps)        \n",
+    "        RE.reaction(steps=reaction_steps)\n",
     "        num_As[i] = system.number_of_particles(type=type_A)\n",
     "```"
    ]

diff --git a/maintainer/benchmarks/mc_acid_base_reservoir.py b/maintainer/benchmarks/mc_acid_base_reservoir.py
@@ -259,7 +259,7 @@ def calc_donnan_coefficient(c_acid, I_res, charge=-1):
 
 
 def equilibrate_reaction(reaction_steps=1):
-    RE.reaction(reaction_steps=reaction_steps)
+    RE.reaction(steps=reaction_steps)
 
 
 def report_progress(system, i, next_i):
@@ -295,7 +295,7 @@ def report_progress(system, i, next_i):
 
         if MC_STEPS_PER_SAMPLE > 0:
             tick_MC = time.time()
-            RE.reaction(reaction_steps=MC_STEPS_PER_SAMPLE)
+            RE.reaction(steps=MC_STEPS_PER_SAMPLE)
             tock_MC = time.time()
 
         t_MC = (tock_MC - tick_MC) / MC_STEPS_PER_SAMPLE
@@ -332,7 +332,7 @@ def report_progress(system, i, next_i):
     for i in range(NUM_SAMPLES):
         if RUN_INTEGRATION:
             system.integrator.run(INTEGRATION_STEPS_PER_SAMPLE)
-        RE.reaction(reaction_steps=MC_STEPS_PER_SAMPLE)
+        RE.reaction(steps=MC_STEPS_PER_SAMPLE)
         n_A = system.number_of_particles(type=TYPES['A'])
         n_As.append(n_A)
         n_All = len(system.part)

diff --git a/samples/grand_canonical.py b/samples/grand_canonical.py
@@ -101,7 +101,7 @@
 # up the simulation
 RE.set_non_interacting_type(type=max(types) + 1)
 
-RE.reaction(reaction_steps=10000)
+RE.reaction(steps=10000)
 
 p3m = espressomd.electrostatics.P3M(prefactor=2.0, accuracy=1e-3)
 system.actors.add(p3m)
@@ -134,14 +134,14 @@
 system.thermostat.set_langevin(kT=temperature, gamma=.5, seed=42)
 
 # MC warmup
-RE.reaction(reaction_steps=1000)
+RE.reaction(steps=1000)
 
 n_int_cycles = 10000
 n_int_steps = 600
 num_As = []
 deviation = None
 for i in range(n_int_cycles):
-    RE.reaction(reaction_steps=10)
+    RE.reaction(steps=10)
     system.integrator.run(steps=n_int_steps)
     num_As.append(system.number_of_particles(type=1))
     if i > 2 and i % 50 == 0:

diff --git a/samples/reaction_ensemble_complex_reaction.py b/samples/reaction_ensemble_complex_reaction.py
@@ -100,10 +100,10 @@
 RE.set_non_interacting_type(type=max(types) + 1)
 
 # warmup
-RE.reaction(reaction_steps=200)
+RE.reaction(steps=200)
 
 for i in range(200):
-    RE.reaction(reaction_steps=10)
+    RE.reaction(steps=10)
     for _type in types:
         numbers[_type].append(system.number_of_particles(type=_type))
 

diff --git a/samples/reaction_methods.py b/samples/reaction_methods.py
@@ -107,7 +107,7 @@
 
 
 for i in range(10000):
-    RE.reaction(reaction_steps=1)
+    RE.reaction(steps=1)
     if i % 100 == 0:
         print(f"HA {system.number_of_particles(type=types['HA'])}",
               f"A- {system.number_of_particles(type=types['A-'])}",

diff --git a/src/python/espressomd/reaction_methods.py b/src/python/espressomd/reaction_methods.py
@@ -407,19 +407,19 @@ def _rebuild_reaction_cache(self):
         """
         self._reactions_cache = [x for x in self.reactions]
 
-    def reaction(self, reaction_steps):
+    def reaction(self, steps):
         """
         Performs randomly selected reactions.
 
         Parameters
         ----------
-        reaction_steps : :obj:`int`, optional
+        steps : :obj:`int`, optional
             The number of reactions to be performed at once, defaults to 1.
 
         """
         self.call_method("setup_bookkeeping_of_empty_pids")
         E_pot = self.call_method("potential_energy")
-        for _ in range(reaction_steps):
+        for _ in range(steps):
             reaction_id = self.call_method("get_random_reaction_index")
             E_pot = self.generic_oneway_reaction(reaction_id, E_pot)
 

diff --git a/testsuite/python/constant_pH.py b/testsuite/python/constant_pH.py
@@ -64,12 +64,12 @@ def test_ideal_alpha(self):
             default_charges=charges_dict)
 
         # equilibration
-        RE.reaction(reaction_steps=800)
+        RE.reaction(steps=800)
 
         # sampling
         alphas = []
         for _ in range(80):
-            RE.reaction(reaction_steps=15)
+            RE.reaction(steps=15)
             num_H = system.number_of_particles(type=types["H+"])
             num_HA = system.number_of_particles(type=types["HA"])
             num_A = system.number_of_particles(type=types["A-"])

diff --git a/testsuite/python/constant_pH_stats.py b/testsuite/python/constant_pH_stats.py
@@ -80,14 +80,14 @@ def test_ideal_titration_curve(self):
 
         # chemical warmup - get close to chemical equilibrium before we start
         # sampling
-        RE.reaction(reaction_steps=40 * N0)
+        RE.reaction(steps=40 * N0)
 
         average_NH = 0.0
         average_NHA = 0.0
         average_NA = 0.0
         num_samples = 1000
         for _ in range(num_samples):
-            RE.reaction(reaction_steps=10)
+            RE.reaction(steps=10)
             average_NH += system.number_of_particles(type=types["H+"])
             average_NHA += system.number_of_particles(type=types["HA"])
             average_NA += system.number_of_particles(type=types["A-"])

diff --git a/testsuite/python/reaction_bookkeeping.py b/testsuite/python/reaction_bookkeeping.py
@@ -88,7 +88,7 @@ def setUpClass(cls):
 
     def test_reaction_bookeeping(self):
         self.widom.calculate_particle_insertion_potential_energy(reaction_id=0)
-        self.cph.reaction(reaction_steps=100)
+        self.cph.reaction(steps=100)
 
         # Measure the chemical potential
         for _ in range(50):

diff --git a/testsuite/python/reaction_complex.py b/testsuite/python/reaction_complex.py
@@ -84,11 +84,11 @@ def test_equilibrium_concentrations(self):
         RE.set_non_interacting_type(type=max(types) + 1)
 
         # warmup
-        RE.reaction(reaction_steps=50)
+        RE.reaction(steps=50)
 
         numbers = {type_A: [], type_B: [], type_C: [], type_D: [], type_E: []}
         for _ in range(40):
-            RE.reaction(reaction_steps=6)
+            RE.reaction(steps=6)
             for key in types:
                 numbers[key].append(self.system.number_of_particles(type=key))
 

diff --git a/testsuite/python/reaction_ensemble.py b/testsuite/python/reaction_ensemble.py
@@ -97,14 +97,14 @@ def test_ideal_titration_curve(self):
 
         # chemical warmup - get close to chemical equilibrium before we start
         # sampling
-        RE.reaction(reaction_steps=5 * N0)
+        RE.reaction(steps=5 * N0)
 
         average_NH = 0.0
         average_NHA = 0.0
         average_NA = 0.0
         num_samples = 300
         for _ in range(num_samples):
-            RE.reaction(reaction_steps=10)
+            RE.reaction(steps=10)
             average_NH += system.number_of_particles(type=types["H+"])
             average_NHA += system.number_of_particles(type=types["HA"])
             average_NA += system.number_of_particles(type=types["A-"])