preparing to run simulation with linear modulation of twist persistance length

Author: AngelikaH123

chromo/mc/__init__.py

@@ -51,7 +51,6 @@ def _polymer_in_field(
     path_to_run_script: Optional[str] = None,
     path_to_chem_mods: Optional[List[str]] = None,
     run_command: Optional[str] = None,
-    #lt_value_adjust = 1,
     **kwargs
 ):
     """
@@ -142,27 +141,29 @@ def _polymer_in_field(
                 temperature_adjust_factor = temp_schedule.logarithmic_decrease(mc_count, num_saves)
             elif temperature_schedule == "decreasing stepwise":
                 temperature_adjust_factor = temp_schedule.decreasing_stepwise(mc_count, num_saves)
+            elif temperature_schedule == "no schedule":
+                temperature_adjust_factor = temp_schedule.no_schedule()
             else:
                 print("Not a valid temperature schedule option")
         else:
-            temperature_adjust_factor = 1
+            print("Missing lt schedule option")
 
         if lt_schedule is not None:
             if lt_schedule == "logarithmic increase":
-                #print(mc_count)
-                #print(num_saves)
                 lt_change = twist_schedule.logarithmic_increase(mc_count, num_saves)
             elif lt_schedule == "linear increase":
                 lt_change = twist_schedule.linear_increase(mc_count, num_saves)
             elif lt_schedule == "increasing stepwise":
                 lt_change = twist_schedule.increasing_stepwise(mc_count, num_saves)
+            elif lt_schedule == "no schedule":
+                lt_change = twist_schedule.no_schedule()
             else:
                 print("Not a valid lt schedule option")
         else:
-            lt_change = 1
+            print("Missing lt schedule option")
         #print("lt change " + str(lt_change))
 
-        temperature_adjust_factor=1
+        temperature_adjust_factor = 1
         lt_value_adjust= lt_change
 
         decorator_timed_path(output_dir)(mc_sim)(

chromo/mc/mc_sim.pyx

@@ -33,7 +33,6 @@ cpdef void mc_sim(
     list mc_move_controllers, Udf field, double mu_adjust_factor,
     long random_seed, double temperature_adjust_factor, double lt_value_adjust
 ):
-    print('Hi')
     """Perform Monte Carlo simulation.
 
     Pseudocode
@@ -88,24 +87,15 @@ cpdef void mc_sim(
             if controller.move.move_on == 1:
                 for j in range(controller.move.num_per_cycle):
                     for i in range(len(polymers)):
-                        #print("start lt")
-                        #print(polymers[i].lt)
                         polymers[i].lt = lt_value_adjust
-                        polymers[i]._find_parameters(polymers[i].bead_length)
+                        polymers[i]._find_parameters(polymers[i].bead_length) # coding best practice: accessing protected member of a class from outside the class?
                         poly = polymers[i]
-
-                        #print("lt change factor")
-                        #print(lt_value_adjust)
-                        #print("new lt value " + str(polymers[i].lt ))
-
-
                         active_field = active_fields[i]
                         mc_step(
                             controller.move, poly, readerproteins, field,
                             active_field, temperature_adjust_factor
                         )
             controller.update_amplitudes()
-    #print(poly.lt)
 
 
 cpdef void mc_step(
@@ -136,6 +126,8 @@ cpdef void mc_step(
         Field affecting polymer in Monte Carlo step
     active_field: bool
         Indicator of whether or not the field is active for the polymer
+    temperature_adjust_factor: double
+        Divide the energy value used to select accepted moves by this factor
     """
     cdef double dE, exp_dE
     cdef int check_field = 0

chromo/run_simulation.py

@@ -25,7 +25,7 @@
 from chromo.util.reproducibility import get_unique_subfolder_name
 import chromo.util.poly_stat as ps
 import datetime
-import chromo.util.temperature_schedule as temperature
+
 
 pst_time = datetime.datetime.utcnow() + datetime.timedelta(hours=-7)
 
@@ -65,7 +65,6 @@
     lp=lp,
     lt=lt,
     binder_names=np.array(["null_reader"]),
-    #lt_schedule = "logarithmic increase"
 )
 
 # shows a plot of the polymer object
@@ -117,6 +116,9 @@
 # count number of accepted moves for different conditions
 mc_steps_per_snapshot = 40000
 
+
+
+
 mc.polymer_in_field(
     polymers = [polymer],
     binders = binders,
@@ -127,16 +129,10 @@
     move_amp_bounds = amp_move_bounds,
     output_dir = 'output',
     mc_move_controllers = moves_to_use,
-    temperature_schedule = "linear decrease",
+    temperature_schedule = "no schedule",
     lt_schedule = "linear increase"
 )
 
-
-#temperature_schedule: Optional[Callable[[float],float]] = None
-# Load names of polymer configuration output files
-# 206 is with 200 snapshots of twist with alternating 15 and 25
-# 130 is without twist with alternating 15 and 25
-#latest_sim = "output/sim_206"
 output_files = os.listdir(latest_sim)
 
 output_files = [
@@ -226,10 +222,9 @@
         if monomer_separation[i] > 0
     ]
 )
-# monomer_separation_kuhn = monomer_separation * (bead_spacing / lp / 2)
+
 monomer_separation_kuhn = monomer_separation * (np.mean(bead_spacing) / lp / 2) # check that this is acceptable
-# do calc with same bead spacing
-# 
+
 
 lp = 100 # try 53
 kuhn_length = 2 * lp

chromo/twist_schedule.py

@@ -1,3 +1,4 @@
+
 class Schedule:
     """Class representation of the simulated annealing schedule.
 
@@ -27,4 +28,6 @@ def logarithmic_increase(current_step, total_steps):
 
 def linear_increase(current_step, total_steps):
     value =  (current_step/total_steps) * 100
-    return value
+    return value
+def no_schedule():
+    return 100

chromo/util/temperature_schedule.py

@@ -32,4 +32,6 @@ def linear_decrease(current_step, total_steps):
     slope = (0.1 - 1) / total_steps
     value = 1 + slope * current_step
     return value
+def no_schedule():
+    return 1