Merge pull request #96 from cmelab/surface-wetting

Add surface wetting module

Author: marjanalbooyeh

docs/source/modules.rst

@@ -15,3 +15,4 @@ Modules
    :maxdepth: 1
 
    welding
+   surface_wetting

docs/source/surface_wetting.rst

@@ -0,0 +1,23 @@
+Surface Wetting
+---------------
+
+.. py:currentmodule:flowermd.modules
+
+.. rubric:: Details
+
+.. automodule:: flowermd.modules.surface_wetting
+    :no-members:
+
+    .. autoclass:: DropletSimulation()
+        :members:
+        :no-index:
+
+    .. autoclass:: InterfaceBuilder()
+        :members:
+        :no-index:
+        :show-inheritance:
+
+    .. autoclass:: WettingSimulation()
+        :members:
+        :no-index:
+        :show-inheritance:

flowermd/base/molecule.py

@@ -31,7 +31,7 @@ class Molecule:
         Number of molecules to generate.
     force_field : flowermd.ForceField or a list of
         `hoomd.md.force.Force` objects, default=None
-        The force field to be applied to the molecule for parameterization.
+        The forcefield to be applied to the molecule for parameterization.
         Note that setting `force_field` does not actually apply the
         forcefield to the molecule. The forcefield in this step is mainly
         used for validation purposes.
@@ -430,8 +430,12 @@ class Polymer(Molecule):
         The smiles string of the monomer to generate.
     file : str, default None
         The file path to the monomer to generate.
-    force_field : str, default None
-        The force field to apply to the molecule.
+    force_field : flowermd.ForceField or a list of
+        `hoomd.md.force.Force` objects, default=None
+        The forcefield to be applied to the molecule for parameterization.
+        Note that setting `force_field` does not actually apply the
+        forcefield to the molecule. The forcefield in this step is mainly
+        used for validation purposes.
     bond_indices: list, default None
         The indices of the atoms to bond.
     bond_length: float, default None
@@ -502,13 +506,21 @@ class CoPolymer(Molecule):
         Class of the B-type monomer
     length : int, required
         The total number of monomers in the molecule
+    num_mols : int, required
+        Number of chains to generate.
     sequence : str, default None
         Manually define the sequence of 'A' and 'B' monomers.
         Leave as None if generating random sequences.
         Example: sequence = "AABAABAAB"
     AB_ratio : float, default 0.50
         The relative weight of A to B monomer types.
         Used when generating random sequences.
+    force_field : flowermd.ForceField or a list of
+        `hoomd.md.force.Force` objects, default=None
+        The forcefield to be applied to the molecule for parameterization.
+        Note that setting `force_field` does not actually apply the
+        forcefield to the molecule. The forcefield in this step is mainly
+        used for validation purposes.
     seed : int, default 24
         Set the seed used when generating random sequences
 

flowermd/base/simulation.py

@@ -612,7 +612,7 @@ def run_update_volume(
             Number of steps to run during volume update.
         period : int, required
             The number of steps ran between each box update iteration.
-        kT : int or hoomd.variant.Ramp, required
+        kT : float or hoomd.variant.Ramp, required
             The temperature to use during volume update.
         tau_kt : float, required
             Thermostat coupling period (in simulation time units).

flowermd/base/system.py

@@ -586,21 +586,27 @@ def apply_forcefield(
         if scale_charges and not remove_charges:
             self._scale_charges()
 
-        epsilons = [
-            s.atom_type.parameters["epsilon"] for s in self.gmso_system.sites
-        ]
-        sigmas = [
-            s.atom_type.parameters["sigma"] for s in self.gmso_system.sites
-        ]
-        masses = [s.mass for s in self.gmso_system.sites]
+        if not self._reference_values:
+            epsilons = [
+                s.atom_type.parameters["epsilon"]
+                for s in self.gmso_system.sites
+            ]
+            sigmas = [
+                s.atom_type.parameters["sigma"] for s in self.gmso_system.sites
+            ]
+            masses = [s.mass for s in self.gmso_system.sites]
 
-        energy_scale = np.max(epsilons) if self.auto_scale else 1.0
-        length_scale = np.max(sigmas) if self.auto_scale else 1.0
-        mass_scale = np.max(masses) if self.auto_scale else 1.0
+            energy_scale = np.max(epsilons) if self.auto_scale else 1.0
+            length_scale = np.max(sigmas) if self.auto_scale else 1.0
+            mass_scale = np.max(masses) if self.auto_scale else 1.0
 
-        self._reference_values["energy"] = energy_scale * epsilons[0].unit_array
-        self._reference_values["length"] = length_scale * sigmas[0].unit_array
-        self._reference_values["mass"] = mass_scale * masses[0].unit_array
+            self._reference_values["energy"] = (
+                energy_scale * epsilons[0].unit_array
+            )
+            self._reference_values["length"] = (
+                length_scale * sigmas[0].unit_array
+            )
+            self._reference_values["mass"] = mass_scale * masses[0].unit_array
 
         if remove_hydrogens:
             self.remove_hydrogens()

flowermd/library/surfaces.py

@@ -1,10 +1,13 @@
 """Recipes to generate surfaces using mBuild."""
 
+import mbuild as mb
 from mbuild.compound import Compound
 from mbuild.lattice import Lattice
 
+from flowermd.base import Molecule, System
 
-class Graphene(Compound):
+
+class Graphene(System):
     """Create a rectangular graphene layer or multiple layers.
 
     Parameters
@@ -15,10 +18,43 @@ class Graphene(Compound):
         Number of times to repeat graphene lattice in the y-direciton.
     n_layers: int, optional, default 1
         Number of times to repeat the complete layer in the normal direction.
+    force_field: force_field : flowermd.ForceField
+        The force field to be applied to the surface for paramaterizaiton.
+        Note that setting `force_field` does not actually apply the forcefield
+        to the molecule. The forcefield in this step is mainly used for
+        validation purposes.
+    reference_values : dict, required
+        A dictionary of reference values for the surface. The keys of the
+        dictionary are "length", "energy", and "mass". The values of the
+        dictionary are unyt quantities.
+    r_cut : float, required
+        The cutoff radius for the Lennard-Jones interactions.
     periodicity : tuple of bools, length=3, optional, default=(True, True, False) # noqa: E501
         Whether the Compound is periodic in the x, y, and z directions.
         If None is provided, the periodicity is set to `(False, False, False)`
         which is non-periodic in all directions.
+        auto_scale : bool, default=False
+        Set to true to use reduced simulation units.
+        distance, mass, and energy are scaled by the largest value
+        present in the system for each.
+    scale_charges : bool, default False
+        Set to true to scale charges to net zero.
+    remove_charges : bool, default False
+        Set to true to remove charges from the system.
+    remove_hydrogens : bool, default False
+        Set to true to remove hydrogen atoms from the system.
+        The masses and charges of the hydrogens are absorbed into
+        the heavy atoms they were bonded to.
+    pppm_resolution : tuple, default=(8, 8, 8)
+        The resolution used in
+        `hoomd.md.long_range.pppm.make_pppm_coulomb_force` representing
+        number of grid points in the x, y, and z directions.
+    ppmp_order : int, default=4
+        The order used in
+        `hoomd.md.long_range.pppm.make_pppm_coulomb_force` representing
+        number of grid points in each direction to assign charges to.
+    nlist_buffer : float, default=0.4
+        Neighborlist buffer for simulation cell.
 
     Notes
     -----
@@ -28,19 +64,38 @@ class Graphene(Compound):
     """
 
     def __init__(
-        self, x_repeat, y_repeat, n_layers, periodicity=(True, True, False)
+        self,
+        x_repeat,
+        y_repeat,
+        n_layers,
+        base_units=dict(),
+        periodicity=(True, True, False),
     ):
-        super(Graphene, self).__init__(periodicity=periodicity)
+        surface = mb.Compound(periodicity=periodicity)
         spacings = [0.425, 0.246, 0.35]
-        points = [[1 / 6, 0, 0], [1 / 2, 0, 0], [0, 0.5, 0], [2 / 3, 1 / 2, 0]]
+        points = [
+            [1 / 6, 0, 0],
+            [1 / 2, 0, 0],
+            [0, 1 / 2, 0],
+            [2 / 3, 1 / 2, 0],
+        ]
         lattice = Lattice(
             lattice_spacing=spacings,
             angles=[90, 90, 90],
             lattice_points={"A": points},
         )
-        carbon = Compound(name="C")
+        carbon = Compound(name="C", element="C")
         layers = lattice.populate(
             compound_dict={"A": carbon}, x=x_repeat, y=y_repeat, z=n_layers
         )
-        self.add(layers)
-        self.freud_generate_bonds("C", "C", dmin=0.14, dmax=0.145)
+        surface.add(layers)
+        surface.freud_generate_bonds("C", "C", dmin=0.14, dmax=0.145)
+        surface_mol = Molecule(num_mols=1, compound=surface)
+        super(Graphene, self).__init__(
+            molecules=[surface_mol],
+            density=1.0,
+            base_units=base_units,
+        )
+
+    def _build_system(self):
+        return self.all_molecules[0]

flowermd/modules/surface_wetting/__init__.py

@@ -0,0 +1,6 @@
+"""Surface wetting module for FlowerMD."""
+from .surface_wetting import (
+    DropletSimulation,
+    InterfaceBuilder,
+    WettingSimulation,
+)