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Fix bug of patching "class" field in Lennard-Jones potential #70

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Merged
merged 4 commits into from
Nov 22, 2022
Merged

Fix bug of patching "class" field in Lennard-Jones potential #70

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533981f
Hook jax force to generator for intra potentials
WangXinyan940 Nov 15, 2022
9fcd2fc
Let NeighborList.update return (N, 3) pairs with colv_map information
WangXinyan940 Nov 22, 2022
d0cd7a3
Update nblist.py
WangXinyan940 Nov 22, 2022
92b35ef
bugfix: correctly recognize if the LJForce card uses type or class
WangXinyan940 Nov 22, 2022
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4 changes: 2 additions & 2 deletions dmff/common/nblist.py
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Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ def allocate(self, positions: jnp.ndarray, box: Optional[jnp.ndarray] = None):
self.nblist = self.neighborlist_fn.allocate(positions)
else:
self.update(positions, box)
return self.nblist
return self.pairs

def update(self, positions: jnp.ndarray, box: Optional[jnp.ndarray] = None):
""" A function to update a neighbor list given a new set of positions and a previously allocated neighbor list.
Expand All @@ -59,7 +59,7 @@ def update(self, positions: jnp.ndarray, box: Optional[jnp.ndarray] = None):
self.nblist = self.nblist.update(positions)
else:
self.nblist = self.nblist.update(positions, box)
return self.nblist
return self.pairs

@property
def pairs(self):
Expand Down
8 changes: 6 additions & 2 deletions dmff/generators/classical.py
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Original file line number Diff line number Diff line change
Expand Up @@ -97,6 +97,7 @@ def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
map_param = np.array(map_param, dtype=int)

bforce = HarmonicBondJaxForce(map_atom1, map_atom2, map_param)
self._force_latest = bforce

def potential_fn(positions, box, pairs, params):
return bforce.get_energy(positions, box, pairs,
Expand Down Expand Up @@ -163,6 +164,7 @@ def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):

aforce = HarmonicAngleJaxForce(map_atom1, map_atom2, map_atom3,
map_param)
self._force_latest = aforce

def potential_fn(positions, box, pairs, params):
return aforce.get_energy(positions, box, pairs,
Expand Down Expand Up @@ -384,6 +386,8 @@ def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
jnp.array(map_impr_param[p], dtype=int), p)
for p in range(1, self.max_pred_impr + 1)
]
self._props_latest = props
self._imprs_latest = imprs

def potential_fn(positions, box, pairs, params):
prop_sum = sum([
Expand Down Expand Up @@ -822,8 +826,8 @@ def createForce(self, system, data, nonbondedMethod, nonbondedCutoff,

map_lj = jnp.array(maps["sigma"])

ifType = len(self.fftree.get_attribs("LennardJonesForce/Atom",
"type")) != 0
ifType = len([i for i in self.fftree.get_attribs("LennardJonesForce/Atom",
"type") if i is not None]) != 0
if ifType:
atom_labels = self.fftree.get_attribs("LennardJonesForce/Atom",
"type")
Expand Down