ENH: Expose simulation cell dimensions in insert-molecules (#38)

* FIX: include vector handling for command line arguments

* ENH: add flag for number of threads to mdrun

* ENH: expose cell_dim in BaseSimulationBuilder

force_gromacs/commands/base_gromacs_command.py

@@ -129,9 +129,11 @@ def _build_command(self):
         for flag, arg in self.command_options.items():
             if arg is None:
                 pass
-            elif type(arg) == bool:
+            elif isinstance(arg, bool):
                 command += ' {}'.format(flag)
             else:
+                if isinstance(arg, list):
+                    arg = ' '.join([str(item) for item in arg])
                 command += ' {} {}'.format(flag, arg)
 
         return command

force_gromacs/commands/gromacs_commands.py

@@ -139,7 +139,7 @@ class Gromacs_mdrun(BaseGromacsCommand):
                       '-cpo', '-cpi', '-rerun', '-ei',
                       '-awh', '-mp', '-mn', '-cpnum',
                       '-nocpnum', '-multidir', '-nsteps',
-                      '-maxh'])
+                      '-maxh', '-nt'])
 
     def _get_name(self):
         """Returns correct name syntax, depending on MPI run

force_gromacs/commands/tests/test_base_gromacs_command.py

@@ -15,16 +15,17 @@ class TestBaseGromacsCommand(TestCase):
     def setUp(self):
         # Create Gromacs command objects
         self.gromacs_command = BaseGromacsCommand(
-            flags=['-c', '-o', '-flag'],
+            flags=['-c', '-o', '-box', '-flag'],
             dry_run=True)
 
     def test___init__(self):
         self.assertEqual('gmx', self.gromacs_command.executable)
         self.assertListEqual(
-            ['-c', '-o', '-flag'], self.gromacs_command.flags
+            ['-c', '-o', '-box', '-flag'], self.gromacs_command.flags
         )
         self.assertEqual(
-            {'-c', '-o', '-flag', '-h'}, self.gromacs_command._flags)
+            {'-c', '-o', '-box', '-flag', '-h'},
+            self.gromacs_command._flags)
 
         self.assertTrue(self.gromacs_command.dry_run)
         self.assertEqual('', self.gromacs_command.user_input)
@@ -92,12 +93,14 @@ def test__build_command(self):
         self.gromacs_command.command_options = {
             '-c': 'coordinate',
             '-o': 'output',
+            '-box': [10, 10, 10],
             '-flag': True,
         }
         command = self.gromacs_command._build_command()
         self.assertIn('gmx', command)
         self.assertIn(' -c coordinate', command)
         self.assertIn(' -o output', command)
+        self.assertIn(' -box 10 10 10', command)
         self.assertIn(' -flag', command)
         self.assertNotIn('True', command)
 

force_gromacs/commands/tests/test_gromacs_commands.py

@@ -103,13 +103,15 @@ def test_insert_molecules(self):
             '-nmol': 30,
             '-not_a_flag': 60,
             '-o': 'test_output.gro',
+            '-box': [10, 10, 10],
             '-try': True}
 
         self.insert_molecules.command_options = input_options
         command = self.insert_molecules.bash_script()
         self.assertIn('insert-molecules', command)
         self.assertNotIn(' -cp test_coord.gro', command)
         self.assertIn(' -o test_output.gro', command)
+        self.assertIn(' -box 10 10 10', command)
         self.assertIn(' -try', command)
         self.assertIn(' -nmol 30', command)
         self.assertNotIn(' -not_a_flag 60', command)

force_gromacs/simulation_builders/base_gromacs_simulation_builder.py

@@ -4,7 +4,7 @@
 
 from traits.api import (
     HasTraits, Str, Int, Bool, Instance, Directory,
-    provides
+    provides, List, Float
 )
 
 from force_gromacs.io.gromacs_file_registry import GromacsFileRegistry
@@ -32,6 +32,9 @@ class BaseGromacsSimulationBuilder(HasTraits):
     #: Particle size of simulation
     size = Int()
 
+    #: Simulation cell dimensions in nm
+    cell_dim = List(Float, value=[0, 0, 0], maxlen=3, minlen=3)
+
     #: Length of simulation in time steps
     n_steps = Int()
 

force_gromacs/simulation_builders/tests/test_base_gromacs_simulation_builder.py

@@ -31,6 +31,7 @@ def test__init__(self):
 
         self.assertEqual('test_experiment', self.sim_builder.name)
         self.assertEqual(100, self.sim_builder.size)
+        self.assertListEqual([0, 0, 0], self.sim_builder.cell_dim)
         self.assertEqual(os.path.curdir, self.sim_builder.directory)
         self.assertEqual(
             os.path.join(os.path.curdir, 'test_experiment'),