Merge branch 'linker_length' of github.com:SpakowitzLab/chromo into linker_length

Author: AngelikaH123

chromo/mc/__init__.py

@@ -156,7 +156,9 @@ def _polymer_in_field(
             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)
+                lt_change = twist_schedule.step_wise_increase(mc_count, num_saves)
+            elif lt_schedule == "increasing sawtooth":
+                lt_change = twist_schedule.increasing_sawtooth(mc_count, num_saves)
             elif lt_schedule == "no schedule":
                 lt_change = twist_schedule.no_schedule()
             else:

chromo/run_simulation.py

@@ -130,7 +130,7 @@
     output_dir = 'output',
     mc_move_controllers = moves_to_use,
     temperature_schedule = "no schedule",
-    lt_schedule = "linear increase"
+    lt_schedule = "logarithmic increase"
 )
 
 output_files = os.listdir(latest_sim)

chromo/twist_schedule.py

@@ -39,7 +39,6 @@ def logarithmic_increase(current_step, total_steps):
         result = 0
     return result
 
-
 # for lp
 def linear_increase(current_step, total_steps):
     max_value = 100
@@ -73,8 +72,6 @@ def increasing_sawtooth(current_step, total_steps):
     section_division = np.floor(
         current_step / (total_steps / num_sections))  # 10.5 is the section from 20 total sections
     if section_division % 2 == 0:
-        # we are in section 6
-        # result = result + (current_step%num_sections) - section_division
         result = result + (current_step % num_sections) * 4 - section_division - 14
     else:
         result = result - (current_step % num_sections) * 2.5 - section_division + 46
@@ -86,6 +83,22 @@ def increasing_sawtooth(current_step, total_steps):
         result = 0
     return result
 
+def increasing_sawtooth(current_step, total_steps):
+    num_blocks = 10
+    max_height = 100
+    step_height = max_height/num_blocks # each step has a height of 10
+    step_length = total_steps / num_blocks # so 20 is the length
+    division = current_step/step_length # so if we are at snapshot 105 we get 5.11
+    ceiling = np.ceil(division) # we are currently on the 6th step
+    result = step_height * ceiling # this is the height we are at in the 6th block
+
+    num_sections = num_blocks * 2 #if we are at 105
+    section_division = np.floor(current_step/(total_steps/num_sections)) # 10.5 is the section from 20 total sections
+    if section_division%2 == 0:
+        result = result + (current_step % num_sections) * 2 - section_division - 20
+    else:
+        result = result - (current_step%num_sections)*2 - section_division + 20
+    return result
 
 def no_schedule():
     return 100

chromo/util/temperature_schedule.py

@@ -25,8 +25,15 @@ def decreasing_stepwise(current_step, total_steps):
 
     return value
 def logarithmic_decrease(current_step, total_steps):
-    value = 1 - (0.9 ** (current_step / total_steps))
-    return value
+    if current_step == 0:
+    	return 1
+    ratio = current_step/total_steps
+    result = -1 * np.log(ratio/2)/5.5 -0.1
+    if result > 1:
+        result = 1
+    if result < 0:
+        result = 0
+    return result
 
 def linear_decrease(current_step, total_steps):
     slope = (0.1 - 1) / total_steps

slurm-32249165.out

@@ -0,0 +1,2 @@
+/scratch/users/ahirsch1/chromo_scratch/chromo/chromo/run_simulation.py:41: FutureWarning: The frame.append method is deprecated and will be removed from pandas in a future version. Use pandas.concat instead.
+  binders = chromo.binders.make_binder_collection([null_binder]) # gets relevant binder information from binder specified