changing filepath

Author: AngelikaH123

chromo/mc/__init__.py

@@ -109,6 +109,8 @@ def _polymer_in_field(
         (default = None)
     """
     np.random.seed(random_seed)
+    print("output init "+ str(output_dir))
+    #print(log_directory)
     if mc_move_controllers is None:
         mc_move_controllers = all_moves(
             log_dir=output_dir,
@@ -179,6 +181,7 @@ def _polymer_in_field(
         print("Save point " + str(mc_count) + " completed")
 
     for polymer in polymers:
+        print("update log path " + str(output_dir))
         polymer.update_log_path(
             str(output_dir) + "/" + polymer.name + "_config_log.csv"
         )
@@ -226,6 +229,7 @@ def continue_polymer_in_field_simulation(
     random_seed : Optional[SEED]
         Random seed for replication of simulation (default = 0)
     """
+    # issue is somewhere here
     latest_output_subdir = get_latest_simulation(output_dir)
     latest_output_subdir_path = output_dir + "/" + latest_output_subdir
     polymer_names = find_polymers_in_output_dir(latest_output_subdir_path)

chromo/polymers.pyx

@@ -760,6 +760,7 @@ cdef class PolymerBase(TransformedObject):
         """
         if name is None:
             name = path.split("/")[-1].split(".")[0]
+            print("name" + str(name))
         df = pd.read_csv(path, header=[0, 1], index_col=0)
         return cls.from_dataframe(df, name)
 

chromo/run_simulation.py

@@ -127,8 +127,8 @@
     num_saves = num_snapshots,
     bead_amp_bounds = amp_bead_bounds,
     move_amp_bounds = amp_move_bounds,
-    output_dir = '/scratch/users/ahirsch1/output', # for running on sherlock
-    #output_dir = 'output',
+    #output_dir = '/scratch/users/ahirsch1', # for running on sherlock
+    output_dir = 'output',
     mc_move_controllers = moves_to_use,
     temperature_schedule = "no schedule",
     lt_schedule = "linear increase"

chromo/twist_schedule.py

@@ -31,3 +31,10 @@ def linear_increase(current_step, total_steps):
     return value
 def no_schedule():
     return 100
+#dynamic structure factor
+#density correlation function at differnet lengthscales
+#fouirer transform of density density correlation function
+#how much largest lengthscale of polymer is changing
+#correleation function of radius of gyration
+#how density fluctluation within polymer correlate in time
+#plot rmsd for different twist values

chromo/util/mc_stat.py

@@ -100,6 +100,8 @@ def create_log_file(self, ind: int):
             Index with which to append log file name
         """
         log_path = self.log_dir+"/"+self.log_file_prefix+str(ind)+".csv"
+        print("log dir in mc_stat "+str(self.log_dir))
+        print("prefix in mcstat " + str(self.log_file_prefix))
         column_labels = [
             "snapshot",
             "iteration",
@@ -209,7 +211,7 @@ def update_acceptance_rate(self, accept: float, log_update: int):
 
 
 class ConfigurationTracker(Tracker):
-    """Track progressive reconfiguraion of the polymer.
+    """Track progressive reconfiguration of the polymer.
     """
 
     def __init__(self, log_path: str, initial_config: np.ndarray):
@@ -218,7 +220,7 @@ def __init__(self, log_path: str, initial_config: np.ndarray):
         Parameters
         ----------
         log_path : str
-            Path to the output file for confiruation tracker
+            Path to the output file for configuration tracker
         initial_config : np.ndarray (N, 3)
             Initial polymer configuration; rows represent individual beads and
             columns represent (x, y, z) coordinates

chromo/view_past_simulation_output.py

@@ -150,15 +150,16 @@
 #print(ratio)
 
 def find_RMSD(array1, array2):
-
+    array1 = array1 - np.mean(array1, axis = 0)
+    array2 = array2 - np.mean(array2, axis = 0)
     RMSD = np.sqrt(
         1 / array1.shape[0] * np.sum(
             np.linalg.norm(array2 - array1, ord=1, axis=1)
             )
         )
 
     return RMSD
-
+# dot produt of end to end vector should be a decaying function over different snapshots
 num_equilibration = 70
 RMSD_list = []
 x_list = []