Added external_forces_file option to simulate_oxdna

mrdna/segmentmodel.py

@@ -3803,6 +3803,7 @@ E = 0 0 0
                            delta_rotation = 0.22,
                            verlet_skin = 0.5,
                            max_backbone_force = 100,
+                           external_forces_file = None
                        ):
 
         if seed is None:
@@ -3852,6 +3853,11 @@ E = 0 0 0
             delta_translation = ''
             delta_rotation = ''
 
+        if external_forces_file is None:
+            external_forces = "external_forces = 0"
+        else:
+            external_forces = "external_forces = 1\nexternal_forces_file = {}".format(external_forces_file)
+
         with open(filename,'w') as fh:
             fh.write("""##############################
 ####  PROGRAM PARAMETERS  ####
@@ -3882,6 +3888,8 @@ dt = {timestep}
 verlet_skin = {verlet_skin}
 {max_backbone_force}
 
+{external_forces}
+
 ##############################
 ####    INPUT / OUTPUT    ####
 ##############################
@@ -3897,7 +3905,6 @@ energy_file = {log_file}.energy.dat
 print_conf_interval = {print_conf_interval}
 print_energy_every = {print_energy_every}
 time_scale = linear
-external_forces = 0
 """.format( **locals() ))
 
     def simulate_oxdna(self, output_name, directory='.', output_directory='output', topology=None, configuration=None, oxDNA=None, **oxdna_args):

mrdna/simulate.py

@@ -54,16 +54,20 @@ def minimize_and_simulate_oxdna( model,
                                         print_energy_every = 10,
                                         **min_args)
 
-        model.simulate_oxdna(output_name = "{}-oxdna".format(output_name),
-                             topology = top,
-                             configuration = conf,
-                             num_steps = num_steps,
-                             print_conf_interval = output_period,
-                             print_energy_every = output_period,
-                             **oxdna_args)
+        top,conf = model.simulate_oxdna(output_name = "{}-oxdna".format(output_name),
+                                        topology = top,
+                                        configuration = conf,
+                                        num_steps = num_steps,
+                                        print_conf_interval = output_period,
+                                        print_energy_every = output_period,
+                                        **oxdna_args)
     finally:
         os.chdir(d_orig)
-        
+
+    try:
+        return top,conf
+    except:
+        pass
 
 def multiresolution_simulation( model, output_name, 
                                 job_id=None,