Make thermo output accessable through PyLammps

Thermo data of the last run is now accessable through the `last_run.thermo`
property. This is a dictionary containing the data columns of thermo output.
All run data is kept as list and can be found in the `runs` property.
See issue #144

python/lammps.py

@@ -436,6 +436,42 @@ class Atom2D(Atom):
             self.lmp.eval("fy[%d]" % self.index))
 
 
+def get_thermo_data(output):
+    """ traverse output of runs and extract thermo data columns """
+    if isinstance(output, str):
+        lines = output.splitlines()
+    else:
+        lines = output
+
+    runs = []
+    columns = []
+    in_run = False
+
+    for line in lines:
+        if line.startswith("Memory usage per processor"):
+            in_run = True
+        elif in_run and len(columns) == 0:
+            # first line after memory usage are column names
+            columns = line.split()
+
+            current_run = {}
+
+            for col in columns:
+                current_run[col] = []
+
+        elif line.startswith("Loop time of "):
+            in_run = False
+            columns = None
+            thermo_data = namedtuple('ThermoData', list(current_run.keys()))(*list(current_run.values()))
+            r = {'thermo' : thermo_data }
+            runs.append(namedtuple('Run', list(r.keys()))(*list(r.values())))
+        elif in_run and len(columns) > 0:
+            values = [float(x) for x in line.split()]
+
+            for i, col in enumerate(columns):
+                current_run[col].append(values[i])
+    return runs
+
 class PyLammps(object):
   """
   More Python-like wrapper for LAMMPS (e.g., for iPython)
@@ -455,6 +491,7 @@ class PyLammps(object):
       self.lmp = lammps(name=name,cmdargs=cmdargs,ptr=None,comm=comm)
     print("LAMMPS output is captured by PyLammps wrapper")
     self._cmd_history = []
+    self.runs = []
 
   def __del__(self):
     if self.lmp: self.lmp.close()
@@ -480,6 +517,17 @@ class PyLammps(object):
     self.lmp.command(cmd)
     self._cmd_history.append(cmd)
 
+  def run(self, *args, **kwargs):
+    output = self.__getattr__('run')(*args, **kwargs)
+    self.runs += get_thermo_data(output)
+    return output
+
+  @property
+  def last_run(self):
+    if len(self.runs) > 0:
+        return self.runs[-1]
+    return None
+
   @property
   def atoms(self):
     return AtomList(self)