Cassandra gmso

gmso/formats/mcf.py

@@ -67,18 +67,16 @@
             "!Molecular connectivity file\n"
             "!***************************************"
             "****************************************\n"
-            "!File {} written by gmso {} at {}\n\n".format(
-                filename, __version__, str(datetime.datetime.now())
-            )
+            f"!File {filename} written by gmso {__version__} "
+            f"at {str(datetime.datetime.now())}\n\n"
         )
 
         mcf.write(header)
         _write_atom_information(mcf, top, in_ring)
         _write_bond_information(mcf, top)
         _write_angle_information(mcf, top)
         _write_dihedral_information(mcf, top)
-        # TODO: Add improper information
-        # _write_improper_information(mcf, top)
+        _write_improper_information(mcf, top)
         _write_fragment_information(mcf, top, frag_list, frag_conn)
         _write_intrascaling_information(mcf, top)
 
@@ -107,7 +105,13 @@
     # Identify atoms in rings
     bond_graph = nx.Graph()
     bond_graph.add_edges_from(
-        [[bond.atom1.idx, bond.atom2.idx] for bond in top.bonds]
+        [
+            [
+                top.get_index(bond.connection_members[0]),
+                top.get_index(bond.connection_members[1]),
+            ]
+            for bond in top.bonds
+        ]
     )
     if len(top.bonds) == 0:
         warnings.warn(
@@ -119,7 +123,7 @@
         return in_ring, frag_list, frag_conn
 
     # Check if entire molecule is connected. Warn if not.
-    if nx.is_connected(bond_graph) == False:
+    if not nx.is_connected(bond_graph):
         raise ValueError(
             "Not all components of the molecule are connected. "
             "MCF files are for a single molecule and thus "
@@ -143,21 +147,24 @@
         i: list(bond_graph.neighbors(i))
         for i in range(bond_graph.number_of_nodes())
     }
-    # First ID fused rings
-    fused_rings = []
-    rings_to_remove = []
-    for i in range(len(all_rings)):
-        ring1 = all_rings[i]
-        for j in range(i + 1, len(all_rings)):
-            ring2 = all_rings[j]
-            shared_atoms = list(set(ring1) & set(ring2))
-            if len(shared_atoms) == 2:
-                fused_rings.append(list(set(ring1 + ring2)))
-                rings_to_remove.append(ring1)
-                rings_to_remove.append(ring2)
-    for ring in rings_to_remove:
-        all_rings.remove(ring)
-    all_rings = all_rings + fused_rings
+
+    # Handle fused/adjoining rings
+    rings_changed = True
+    while rings_changed:
+        rings_changed = False
+        for ring1 in all_rings:
+            if rings_changed:
+                break
+            for ring2 in all_rings:
+                if ring1 == ring2:
+                    continue
+                if len(set(ring1) & set(ring2)) > 0:
+                    all_rings.remove(ring1)
+                    all_rings.remove(ring2)
+                    all_rings.append(list(set(ring1 + ring2)))
+                    rings_changed = True
+                    break
+
     # ID fragments which contain a ring
     for ring in all_rings:
         adjacent_atoms = []
@@ -209,53 +216,54 @@
         Topology object
     in_ring : list
         Boolean for each atom idx True if atom belongs to a ring
-
     """
-    names = [site.name for site in top.sites]
-    types = [site.atom_type.name for site in top.sites]
+    # Based upon Cassandra; updated following 1.2.2 release
+    max_element_length = 6
+    max_atomtype_length = 20
+
+    # Sort to make sure the atom order matches the topology indexing
+    sorted_sites = [site for site in top.sites]
+    sorted_sites.sort(key=lambda site: top.get_index(site))
+    names = [site.name for site in sorted_sites]
+    types = [site.atom_type.name for site in sorted_sites]
 
     # Check constraints on atom type length and element name length
-    # TODO: Update these following Cassandra release
-    # to be more reasonable values
     n_unique_names = len(set(names))
     for name in names:
-        if len(name) > 2:
+        if len(name) > max_element_length:
             warnings.warn(
-                "Warning, name {} will be shortened "
-                "to two characters. Please confirm your final "
-                "MCF.".format(name)
+                f"Name: {name} will be shortened to {max_element_length}"
+                "characters. Please confirm your final MCF."
             )
 
     # Confirm that shortening names to two characters does not
     # cause two previously unique atom names to become identical.
-    names = [name[:2] for name in names]
+    names = [name[:max_element_length] for name in names]
     if len(set(names)) < n_unique_names:
         warnings.warn(
-            "Warning, the number of unique names has been "
-            "reduced due to shortening the name to two "
-            "characters."
+            "The number of unique names has been reduced due"
+            f"to shortening the name to {max_element_length} characters."
         )
 
     n_unique_types = len(set(types))
-    for itype in types:
-        if len(itype) > 6:
+    for type_ in types:
+        if len(type_) > max_atomtype_length:
             warnings.warn(
-                "Warning, type name {} will be shortened to six "
-                "characters as {}. Please confirm your final "
-                "MCF.".format(itype, itype[-6:])
+                f"Type name: {type_} will be shortened to "
+                f"{max_atomtype_length} characters as "
+                f"{type[-max_atomtype_length:]}. Please confirm your final MCF."
             )
-        types = [itype[-6:] for itype in types]
+        types = [itype[-max_atomtype_length:] for itype in types]
     if len(set(types)) < n_unique_types:
         warnings.warn(
-            "Warning, the number of unique atomtypes has been "
-            "reduced due to shortening the atomtype name to six "
-            "characters."
+            "The number of unique atomtypes has been reduced due to "
+            f"shortening the atomtype name to {max_atomtype_length} characters."
         )
 
     # Detect VDW style
     vdw_styles = set()
-    for site in top.sites:
-        vdw_styles.add(_get_vdw_style(site.atom_type))
+    for site in sorted_sites:
+        vdw_styles.add(_get_vdw_style(site))
     if len(vdw_styles) > 1:
         raise GMSOError(
             "More than one vdw_style detected. "
@@ -283,8 +291,8 @@
             "{:<4d}  "
             "{:<6s}  "
             "{:<2s}  "
-            "{:7.3f}  "
-            "{:7.3f}  ".format(
+            "{:8.4f}  "
+            "{:12.8f}  ".format(
                 idx + 1,
                 types[idx],
                 names[idx],
@@ -354,8 +362,9 @@
             "{:s}  "
             "{:10.5f}\n".format(
                 idx + 1,
-                bond.connection_members[0].idx + 1,  # TODO: Confirm the +1 here
-                bond.connection_members[1].idx + 1,
+                top.get_index(bond.connection_members[0])
+                + 1,  # TODO: Confirm the +1 here
+                top.get_index(bond.connection_members[1]) + 1,
                 "fixed",
                 bond.connection_type.parameters["r_eq"]
                 .in_units(u.Angstrom)
@@ -374,8 +383,6 @@
     top : Topology
         Topology object
     """
-    # TODO: Add support for fixed angles
-    angle_style = "harmonic"
     header = (
         "\n!Angle Format\n"
         "!index i j k type parameters\n"
@@ -387,27 +394,38 @@
     mcf.write("{:d}\n".format(len(top.angles)))
     for idx, angle in enumerate(top.angles):
         mcf.write(
-            "{:<4d}  "
-            "{:<4d}  "
-            "{:<4d}  "
-            "{:<4d}  "
-            "{:s}  "
-            "{:10.5f} "
-            "{:10.5f}\n".format(
-                idx + 1,
-                angle.connection_members[0].idx + 1,
-                angle.connection_members[1].idx
-                + 1,  # TODO: Confirm order for angles i-j-k
-                angle.connection_members[2].idx + 1,
-                angle_style,
-                (0.5 * angle.connection_type.parameters["k"] / u.kb)
-                .in_units("K/rad**2")
-                .value,  # TODO: k vs. k/2. conversion
-                angle.connection_type.parameters["theta_eq"]
-                .in_units(u.degree)
-                .value,
-            )
+            f"{idx + 1:<4d}  "
+            f"{top.get_index(angle.connection_members[0]) + 1:<4d}  "
+            f"{top.get_index(angle.connection_members[1]) + 1:<4d}  "
+            f"{top.get_index(angle.connection_members[2]) + 1:<4d}  "
         )
+        angle_style = _get_angle_style(angle)
+        if angle_style == "fixed":
+            mcf.write(
+                "{:s}  "
+                "{:10.5f}\n".format(
+                    angle_style,
+                    angle.connection_type.parameters["theta_eq"]
+                    .in_units(u.degree)
+                    .value,
+                )
+            )
+        elif angle_style == "harmonic":
+            mcf.write(
+                "{:s}  "
+                "{:10.5f} "
+                "{:10.5f}\n".format(
+                    angle_style,
+                    (0.5 * angle.connection_type.parameters["k"] / u.kb)
+                    .in_units("K/rad**2")
+                    .value,  # TODO: k vs. k/2. conversion
+                    angle.connection_type.parameters["theta_eq"]
+                    .in_units(u.degree)
+                    .value,
+                )
+            )
+        else:
+            raise GMSOError("Unsupported angle style for Cassandra MCF writer")
 
 
 def _write_dihedral_information(mcf, top):
@@ -419,8 +437,6 @@
         The file object of the Cassandra mcf being written
     top : Topology
         Topology object
-    dihedral_style : string
-        Dihedral style for Cassandra to use
     """
     # Dihedral info
     header = (
@@ -435,7 +451,6 @@
 
     mcf.write(header)
 
-    # TODO: Are impropers buried in dihedrals?
     mcf.write("{:d}\n".format(len(top.dihedrals)))
     for idx, dihedral in enumerate(top.dihedrals):
         mcf.write(
@@ -445,10 +460,10 @@
             "{:<4d}  "
             "{:<4d}  ".format(
                 idx + 1,
-                dihedral.connection_members[0].idx + 1,
-                dihedral.connection_members[1].idx + 1,
-                dihedral.connection_members[2].idx + 1,
-                dihedral.connection_members[3].idx + 1,
+                top.get_index(dihedral.connection_members[0]) + 1,
+                top.get_index(dihedral.connection_members[1]) + 1,
+                top.get_index(dihedral.connection_members[2]) + 1,
+                top.get_index(dihedral.connection_members[3]) + 1,
             )
         )
         dihedral_style = _get_dihedral_style(dihedral)
@@ -467,10 +482,6 @@
                 "{:10.5f}\n".format(
                     dihedral_style,
                     0.5
-                    * dihedral.connection_type.parameters["k0"]
-                    .in_units("kJ/mol")
-                    .value,
-                    0.5
                     * dihedral.connection_type.parameters["k1"]
                     .in_units("kJ/mol")
                     .value,
@@ -482,6 +493,10 @@
                     * dihedral.connection_type.parameters["k3"]
                     .in_units("kJ/mol")
                     .value,
+                    0.5
+                    * dihedral.connection_type.parameters["k4"]
+                    .in_units("kJ/mol")
+                    .value,
                 )
             )
         elif dihedral_style == "charmm":
@@ -542,19 +557,19 @@
     mcf.write(header)
     mcf.write("{:d}\n".format(len(top.impropers)))
 
-    improper_type = "harmonic"
+    improper_style = "harmonic"
     for i, improper in enumerate(top.impropers):
         mcf.write(
             "{:<4d}  {:<4d}  {:<4d}  {:<4d}  {:<4d}"
-            "  {:s}  {:8.3f}  {:8.3f}\n".format(
+            "  {:s}  {:10.5f}  {:10.5f}\n".format(
                 i + 1,
-                improper.atom1.idx + 1,
-                improper.atom2.idx + 1,
-                improper.atom3.idx + 1,
-                improper.atom4.idx + 1,
-                improper_type,
-                improper.type.psi_k * KCAL_TO_KJ,
-                improper.type.psi_eq,
+                top.get_index(improper.connection_members[0]) + 1,
+                top.get_index(improper.connection_members[1]) + 1,
+                top.get_index(improper.connection_members[2]) + 1,
+                top.get_index(improper.connection_members[3]) + 1,
+                improper_style,
+                0.5 * improper.connection_type.parameters["k"],
+                improper.connection_type.parameters["phi_eq"],
             )
         )
 
@@ -649,25 +664,38 @@
     accepted_potentials = (
         potential_templates["LennardJonesPotential"],
         potential_templates["MiePotential"],
+        potential_templates["FixedBondPotential"],
+        potential_templates["HarmonicBondPotential"],
         potential_templates["HarmonicAnglePotential"],
+        potential_templates["FixedAnglePotential"],
         potential_templates["PeriodicTorsionPotential"],
         potential_templates["OPLSTorsionPotential"],
         potential_templates["RyckaertBellemansTorsionPotential"],
     )
     check_compatibility(top, accepted_potentials)
 
 
-def _get_vdw_style(atom_type):
+def _get_vdw_style(site):
     """Return the vdw style."""
     vdw_styles = {
         "LJ": potential_templates["LennardJonesPotential"],
         "Mie": potential_templates["MiePotential"],
     }
 
-    return _get_potential_style(vdw_styles, atom_type)
+    return _get_potential_style(vdw_styles, site.atom_type)
+
+
+def _get_angle_style(angle):
+    """Return the angle style."""
+    angle_styles = {
+        "harmonic": potential_templates["HarmonicAnglePotential"],
+        "fixed": potential_templates["FixedAnglePotential"],
+    }
+
+    return _get_potential_style(angle_styles, angle.connection_type)
 
 
-def _get_dihedral_style(dihedral_type):
+def _get_dihedral_style(dihedral):
     """Return the dihedral style."""
     dihedral_styles = {
         "charmm": potential_templates["PeriodicTorsionPotential"],
@@ -676,7 +704,7 @@
         "ryckaert": potential_templates["RyckaertBellemansTorsionPotential"],
     }
 
-    return _get_potential_style(dihedral_styles, dihedral_type)
+    return _get_potential_style(dihedral_styles, dihedral.connection_type)
 
 
 def _get_potential_style(styles, potential):

gmso/lib/jsons/FixedAnglePotential.json

@@ -0,0 +1,8 @@
+{
+  "name": "FixedAnglePotential",
+  "expression": "DiracDelta(theta-theta_eq)",
+  "independent_variables": "theta",
+  "expected_parameters_dimensions": {
+    "theta_eq": "angle"
+  }
+}