Accept log_file option for model.simulate() to redirect arbd stdout

mrdna/model/arbdmodel.py

@@ -705,7 +705,7 @@ class ArbdModel(PdbModel):
         if typeA != typeB:
             self.nbSchemes.append( (nbScheme, typeB, typeA) )
 
-    def simulate(self, output_name, output_directory='output', num_steps=100000000, timestep=None, gpu=0, output_period=1e4, arbd=None, directory='.', replicas=1):
+    def simulate(self, output_name, output_directory='output', num_steps=100000000, timestep=None, gpu=0, output_period=1e4, arbd=None, directory='.', replicas=1, log_file=None):
         assert(type(gpu) is int)
         num_steps = int(num_steps)
 
@@ -761,10 +761,16 @@ class ArbdModel(PdbModel):
             cmd = tuple(str(x) for x in cmd)
 
             print("Running ARBD with: %s" % " ".join(cmd))
-            process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
-            for line in process.stdout:
-                sys.stdout.write(line)
-                sys.stdout.flush()
+            if log_file is None or (hasattr(log_file,'write') and callable(log_file.write)):
+                fd = sys.stdout if log_file is None else log_file
+                process = subprocess.Popen(cmd, stdout=subprocess.PIPE, universal_newlines=True)
+                for line in process.stdout:
+                    fd.write(line)
+                    fd.flush()
+            else:
+                with open(log_file,'w') as fd:
+                    process = subprocess.Popen(cmd, stdout=log_file, universal_newlines=True)
+                    process.communicate()
 
         except:
             raise