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fix(inter): fix numerical problem in sqrt function of LJ potential #51

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Merged
merged 2 commits into from
Jul 6, 2022
Merged

fix(inter): fix numerical problem in sqrt function of LJ potential #51

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2956d89
fix(classical): avoid creating empty dict in impr parameters
WangXinyan940 Jul 6, 2022
4055f11
fix(inter): add 1e-12 as eps value in jnp.sqrt function
WangXinyan940 Jul 6, 2022
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26 changes: 22 additions & 4 deletions dmff/api.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1823,6 +1823,16 @@ def render(self, filename):
def getParameters(self):
return self.paramtree

def updateParameters(self, paramtree):
def update_iter(node, ref):
for key in ref:
if isinstance(ref[key], dict):
update_iter(node[key], ref[key])
else:
node[key] = ref[key]

update_iter(self.paramtree, paramtree)


class HarmonicBondJaxGenerator:
def __init__(self, ff):
Expand Down Expand Up @@ -1996,6 +2006,9 @@ def extract(self):
prop_phase[f"{npred}"])
self.paramtree[self.name]["prop_k"][f"{npred}"] = jnp.array(
prop_k[f"{npred}"])
if self.max_pred_prop == 0:
del self.paramtree[self.name]["prop_phase"]
del self.paramtree[self.name]["prop_k"]

# impropers
impr_phase = defaultdict(list)
Expand All @@ -2021,14 +2034,17 @@ def extract(self):
impr_phase[f"{npred}"])
self.paramtree[self.name]["impr_k"][f"{npred}"] = jnp.array(
impr_k[f"{npred}"])
if self.max_pred_impr == 0:
del self.paramtree[self.name]["impr_phase"]
del self.paramtree[self.name]["impr_k"]

def overwrite(self):
propers = self.fftree.get_nodes("PeriodicTorsionForce/Proper")
impropers = self.fftree.get_nodes("PeriodicTorsionForce/Improper")
prop_data = [{} for _ in propers]
impr_data = [{} for _ in impropers]
# make propers
for periodicity in range(1, self.max_pred_prop):
for periodicity in range(1, self.max_pred_prop+1):
nterms = len(
self.paramtree[self.name][f"prop_phase"][f"{periodicity}"])
for nitem in range(nterms):
Expand All @@ -2040,10 +2056,11 @@ def overwrite(self):
order = self.meta[f"prop_order"][f"{periodicity}"][nitem]
prop_data[nodeidx][f"phase{order}"] = phase
prop_data[nodeidx][f"k{order}"] = k
self.fftree.set_node("PeriodicTorsionForce/Proper", prop_data)
if "prop_phase" in self.paramtree[self.name]:
self.fftree.set_node("PeriodicTorsionForce/Proper", prop_data)

# make impropers
for periodicity in range(1, self.max_pred_impr):
for periodicity in range(1, self.max_pred_impr+1):
nterms = len(
self.paramtree[self.name][f"impr_phase"][f"{periodicity}"])
for nitem in range(nterms):
Expand All @@ -2055,7 +2072,8 @@ def overwrite(self):
order = self.meta[f"impr_order"][f"{periodicity}"][nitem]
impr_data[nodeidx][f"phase{order}"] = phase
impr_data[nodeidx][f"k{order}"] = k
self.fftree.set_node("PeriodicTorsionForce/Improper", impr_data)
if "impr_phase" in self.paramtree[self.name]:
self.fftree.set_node("PeriodicTorsionForce/Improper", impr_data)

def createForce(self, sys, data, nonbondedMethod, nonbondedCutoff, args):
proper_matcher = TypeMatcher(self.fftree,
Expand Down
3 changes: 1 addition & 2 deletions dmff/classical/inter.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,7 +63,7 @@ def get_energy(positions, box, pairs, epsilon, sigma, epsfix, sigfix, mscales):

eps_m1 = jnp.repeat(epsilon.reshape((-1, 1)), epsilon.shape[0], axis=1)
eps_m2 = eps_m1.T
eps_mat = jnp.sqrt(eps_m1 * eps_m2)
eps_mat = jnp.sqrt(eps_m1 * eps_m2 + 1e-12)
sig_m1 = jnp.repeat(sigma.reshape((-1, 1)), sigma.shape[0], axis=1)
sig_m2 = sig_m1.T
sig_mat = (sig_m1 + sig_m2) * 0.5
Expand All @@ -85,7 +85,6 @@ def get_energy(positions, box, pairs, epsilon, sigma, epsfix, sigfix, mscales):
eps_scale = eps * mscale_pair

E_inter = get_LJ_energy(dr_vec, sig, eps_scale, box)

return jnp.sum(E_inter * mask)

return get_energy
Expand Down