Merge branch 'develop'

Daniele Coslovich
2 parents d0f2fa19 a991e0bc
Showing 5 changed files with 79 additions and 15 deletions
atooms/backends/f90/f90.py
atooms/core/_version.py
atooms/trajectory/xyz.py
tests/test_f90.py
tests/test_xyz.py
@@ -62,9 +62,49 @@ class Interaction(_Interaction):
                  interaction='interaction.f90',
                  helpers='helpers.f90',
                  inline=True, debug=False):
+        """
+        The interaction model can be defined in three ways:
+
+        1) Passing a `model` string that matches any of the models
+        defined in the atooms-models database (ex. "lennard_jones" or
+        "gaussian_core")
+
+        2) Passing a `model` dictionary with "potential" and "cutoff"
+        keys and identical layout as the atooms-model database entries
+        (ex. https://gitlab.info-ufr.univ-montp2.fr/atooms/models/blob/master/atooms/models/lennard_jones.json)
+
+        3) Passing the `potential`, `cutoff`, `potential_parameters`
+        and `cutoff_parameters` parameters. The `potential` and
+        `cutoff` strings should match either
+        
+        a) potential and/or cutoff defined in atooms-models, such as
+        "lennard_jones" or "cut_and_shift", or
+
+        b) paths to Fortran 90 source codes that implement appropriate
+        routines following the interfaces defined by the atooms-models
+        package, see for instance
+        https://gitlab.info-ufr.univ-montp2.fr/atooms/models/blob/master/atooms/models/lennard_jones.f90
+        https://gitlab.info-ufr.univ-montp2.fr/atooms/models/blob/master/atooms/models/cut_shift.f90
+        for an example of the interface the routines should implement.
+
+        The parameters values are provided as dictionaries
+        (`potential_parameters` and `cutoff_parameters``) matching the
+        intent(in) variables entering the `setup()` routines of the
+        fortran modules.
+        """
         _Interaction.__init__(self, None)
  
+        if model and not hasattr(model, 'get'):
+            # This may be a string, so we look for the model in the
+            # atooms-models database and replace the string with the dictionary            
+            try:
+                from atooms.models import database
+                model = database[model]
+            except ImportError:
+                raise ValueError('could not find model {}'.format(model))
+                
         if model:
+            # At this stage we expect a model dictionary
             assert len(model.get('potential')) == 1
             assert len(model.get('cutoff')) == 1
             potential = model.get('potential')[0].get('path')
-__version__ = '2.5.4'
+__version__ = '2.6.0'
@@ -280,9 +280,10 @@ class TrajectoryXYZ(TrajectoryBase):
  
         else:
             # The comment line contains self descriptive fields
-            # TODO: accept extended xyz format
             # Remove spaces around : or = and replace = by :
             data = re.sub(r'\s*[=:]\s*', ':', data)
+            # Tolerate spaces between entries of vectors
+            data = re.sub(r'\s*,\s*', ',', data)
  
             # Fill metadata dictionary
             for e in data.split():
@@ -31,8 +31,8 @@ class Test(unittest.TestCase):
         db = atooms.models.load()
         model = db["lennard_jones"]
         particles = [Particle(position=[0.0, 0.0, 0.0], species=1),
-	             Particle(position=[1.0, 0.0, 0.0], species=1),
-	             Particle(position=[2.0, 0.0, 0.0], species=1)]
+                     Particle(position=[1.0, 0.0, 0.0], species=1),
+                     Particle(position=[2.0, 0.0, 0.0], species=1)]
         cell = Cell([10., 10., 10.])
         system = System(particles, cell)
         system.interaction = Interaction(model)
@@ -63,6 +63,11 @@ class Test(unittest.TestCase):
             system = trajectory[0]
             self.assertAlmostEqual(system.potential_energy(per_particle=True), -2.24379330538)
  
+    @unittest.skipIf(not HAS_MODELS, 'no atooms-models module')
+    def test_interface(self):
+        from atooms.backends.f90 import Interaction
+        interaction = Interaction("lennard_jones")
+            
     def tearDown(self):
         self.trajectory.close()
  
@@ -38,7 +38,7 @@ A -2.8 2.8 0.0
         with open(self.finp_meta, 'w') as fh:
             fh.write("""\
 2
-metafmt:space,comma columns:id,x,y,z mass:1.0,2.0 step:1 cell:5.0,5.0,5.0 
+metafmt:space,comma columns:id,x,y,z mass:1.0,2.0 step:1 cell:5.0,5.0,5.0
 A 1.0 -1.0 0.0
 B 2.9 -2.9 0.0
 """)
@@ -89,6 +89,21 @@ columns:field step:1
             x = t[0].particle[0].field
             self.assertEqual(x, 1.0)
  
+    def test_xyz_meta_with_spaces(self):
+        # Test fields
+        finp = '/tmp/test_xyz/spaces.xyz'
+        with open(finp, 'w') as fh:
+            fh.write("""\
+1
+columns:id step:1 cell:    1.0,   1.0,  1.0
+1
+""")
+        with self.Trajectory(finp) as t:
+            x = t[0].cell.side
+            self.assertEqual(x[0], 1.0)
+            self.assertEqual(x[1], 1.0)
+            self.assertEqual(x[2], 1.0)
+
     def test_xyz_meta(self):
         with self.Trajectory(self.finp_meta) as t:
             meta = t._read_comment(0)
@@ -185,11 +200,11 @@ columns:field step:1
         with open(finp, 'w') as fh:
             fh.write("""\
 2
-metafmt:space,comma columns:id,x,y,z step:1 cell:5.0,5.0,5.0 
+metafmt:space,comma columns:id,x,y,z step:1 cell:5.0,5.0,5.0
 B 1.0 -1.0 0.0
 A 2.9 -2.9 0.0
 2
-metafmt:space,comma columns:id,x,y,z step:2 cell:5.0,5.0,5.0 
+metafmt:space,comma columns:id,x,y,z step:2 cell:5.0,5.0,5.0
 C 1.0 -1.0 0.0
 B 2.9 -2.9 0.0
 """)
@@ -204,12 +219,12 @@ B 2.9 -2.9 0.0
         with open(finp, 'w') as fh:
             fh.write("""\
 3
-metafmt:space,comma columns:id,x,y,z,radius mass:1.0,2.0,3.0 step:1 cell:5.0,5.0,5.0 
+metafmt:space,comma columns:id,x,y,z,radius mass:1.0,2.0,3.0 step:1 cell:5.0,5.0,5.0
 B 1.0 -1.0 0.0 0.5
 A 2.9 -2.9 0.0 0.6
 C 2.9 -2.9 0.0 0.7
 3
-metafmt:space,comma columns:id,x,y,z,radius mass:2.0,3.0 step:1 cell:5.0,5.0,5.0 
+metafmt:space,comma columns:id,x,y,z,radius mass:2.0,3.0 step:1 cell:5.0,5.0,5.0
 C 1.0 -1.0 0.0 0.5
 B 2.9 -2.9 0.0 0.6
 B 2.9 -2.9 0.0 0.7
@@ -306,7 +321,7 @@ class TestNeighbors(unittest.TestCase):
 step:1 columns:neighbors*
 2 4
 1 3
-2 
+2
 1
 """)
         with TrajectoryNeighbors('/tmp/test_xyz/neighbors.xyz', offset=0) as th:
@@ -352,6 +367,9 @@ class TestSimpleXYZ(TestXYZ):
     def test_xyz_meta(self):
         pass
  
+    def test_xyz_meta_with_spaces(self):
+        pass
+
     def test_xyz_mass(self):
         pass
  
@@ -405,10 +423,10 @@ class TestUtils(unittest.TestCase):
 metafmt:space,comma columns:id,x,y,z step:1 cell:5.0,5.0,5.0
 B 1.0 -1.0 0.0
 1
-metafmt:space,comma columns:id,x,y,z step:2 cell:5.0,5.0,5.0 
+metafmt:space,comma columns:id,x,y,z step:2 cell:5.0,5.0,5.0
 B 2.9 -2.9 0.0
 1
-metafmt:space,comma columns:id,x,y,z step:4 cell:5.0,5.0,5.0 
+metafmt:space,comma columns:id,x,y,z step:4 cell:5.0,5.0,5.0
 B 2.9 -2.9 0.0
 """)
         with open('/tmp/test_xyz/2.xyz', 'w') as fh:
@@ -417,13 +435,13 @@ B 2.9 -2.9 0.0
 metafmt:space,comma columns:id,x,y,z step:2 cell:5.0,5.0,5.0
 B 1.0 -1.0 0.0
 1
-metafmt:space,comma columns:id,x,y,z step:3 cell:5.0,5.0,5.0 
+metafmt:space,comma columns:id,x,y,z step:3 cell:5.0,5.0,5.0
 B 2.9 -2.9 0.0
 1
-metafmt:space,comma columns:id,x,y,z step:4 cell:5.0,5.0,5.0 
+metafmt:space,comma columns:id,x,y,z step:4 cell:5.0,5.0,5.0
 B 2.9 -2.9 0.0
 1
-metafmt:space,comma columns:id,x,y,z step:5 cell:5.0,5.0,5.0 
+metafmt:space,comma columns:id,x,y,z step:5 cell:5.0,5.0,5.0
 B 2.9 -2.9 0.0
 """)