Unit tests for bias.py and umbrella.py

Tests the harmonic bias with image and grad functions. Tests umbrella sampling with n windows. Added warning if >1 configurations are identical in US

mltrain/__init__.py

@@ -4,6 +4,7 @@
 from mltrain.system import System
 from mltrain.box import Box
 from mltrain.bias import Bias
+from mltrain.umbrella import UmbrellaSampling
 from mltrain import md
 from mltrain import potentials
 from mltrain.training import selection
@@ -17,7 +18,9 @@
            'Molecule',
            'System',
            'Box',
+           'Bias',
+           'UmbrellaSampling',
            'md',
            'selection',
-           'potentials',
-           'Bias']
+           'potentials'
+           ]

mltrain/bias.py

@@ -62,7 +62,7 @@ def __init__(self,
             {to_add, to_subtract, to_average}: (list) Indices of the atoms
             which are combined in some way to define the reaction rxn_coord
         """
-        self.s = reference
+        self.ref = reference
         self.kappa = kappa
 
         if len(kwargs) != 1:
@@ -90,14 +90,14 @@ def __init__(self,
     def __call__(self, atom_pair_list, atoms):
         """Value of the bias for set of atom pairs in atoms"""
 
-        return 0.5 * self.kappa * (self.func(atom_pair_list, atoms) - self.s)**2
+        return 0.5 * self.kappa * (self.func(atom_pair_list, atoms) - self.ref)**2
 
     def grad(self, atom_pair_list, atoms):
         """Gradient of the biasing potential a set of atom pairs in atoms"""
 
         return (self.kappa
                 * self.func.grad(atom_pair_list, atoms)
-                * (self.func(atom_pair_list, atoms) - self.s))
+                * (self.func(atom_pair_list, atoms) - self.ref))
 
     def adjust_potential_energy(self, atoms):
         """Adjust the energy of a set of atoms using the bias function"""
@@ -145,7 +145,7 @@ def grad(self, atom_pair_list, atoms):
         r_i,m:   i (= x, y or z) position of atom in pair m, m'
         ||r_m||: Euclidean distance between atoms in pair m, m'
         """
-        
+
         derivative = np.zeros(shape=(len(atoms), 3))
 
         num_pairs = len(atom_pair_list)

mltrain/md.py

@@ -82,6 +82,7 @@ def run_mlp_md(configuration: 'mltrain.Configuration',
 
     ase_atoms = configuration.ase_atoms
     ase_atoms.set_calculator(mlp.ase_calculator)
+
     if bias is not None:
         ase_atoms.set_constraint(bias)
 

mltrain/tests/init.xyz

@@ -0,0 +1,8 @@
+6
+Lattice="50.000000 0.000000 0.000000 0.000000 50.000000 0.000000 0.000000 0.000000 50.000000" Properties=species:S:1:pos:R:3 
+C -0.21149 -0.00789 0.00649 
+Cl 1.61172 0.05744 -0.01468 
+H -0.55360 -0.55147 -0.87761 
+H -0.53377 -0.52342 0.91466 
+H -0.59944 1.01358 -0.00511 
+Cl -3.31830 -0.12221 0.04350