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Update classical.py and xmlio.py #168

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Jul 4, 2024
Merged

Update classical.py and xmlio.py #168

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124cf0f
Update classical.py
Ethan-Norch Feb 22, 2024
5c789c3
Update xmlio.py
Ethan-Norch Feb 23, 2024
f7cccc9
Update classical.py
Ethan-Norch Feb 23, 2024
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4 changes: 4 additions & 0 deletions dmff/api/xmlio.py
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Original file line number Diff line number Diff line change
Expand Up @@ -123,6 +123,8 @@ def parseForce(self, nodes):
inner = {}
inner["name"] = child.tag
inner["attrib"] = child.attrib
if child.text is not None:
inner["formula"] = child.text
ret["node"].append(inner)
return ret

Expand Down Expand Up @@ -178,6 +180,8 @@ def writeXML(
for node in force_info["node"]:
subnode = ET.SubElement(fnode, node["name"])
subnode.attrib = genStrDict(node["attrib"])
if "formula" in node:
subnode.text = node["formula"]

tree = ET.ElementTree(root)
xmlstr = minidom.parseString(ET.tostring(root)).toprettyxml(indent=" ")
Expand Down
12 changes: 6 additions & 6 deletions dmff/generators/classical.py
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@WangXinyan940 WangXinyan940 Mar 7, 2024 •
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Here the mask in PeriodicTorsionForce is designed to control if tuning the whole term, including phase and k.

Original file line number Diff line number Diff line change
Expand Up @@ -897,7 +897,7 @@ def overwrite(self, paramset):
proper_phase = paramset[self.name]["proper_phase"]
proper_k = paramset[self.name]["proper_k"]
proper_shift = paramset[self.name]["proper_shift"]
proper_msks = paramset.mask[self.name]["proper"]
proper_msks = paramset.mask[self.name]["proper_phase"]
for nnode, key in enumerate(self.proper_keys):
self.ffinfo["Forces"][self.name]["node"][proper_node_indices[nnode]]["attrib"] = {
}
Expand Down Expand Up @@ -929,7 +929,7 @@ def overwrite(self, paramset):
improper_phase = paramset[self.name]["improper_phase"]
improper_k = paramset[self.name]["improper_k"]
improper_shift = paramset[self.name]["improper_shift"]
improper_msks = paramset.mask[self.name]["improper"]
improper_msks = paramset.mask[self.name]["improper_phase"]
for nnode, key in enumerate(self.imp_keys):
self.ffinfo["Forces"][self.name]["node"][improper_node_indices[nnode]]["attrib"] = {
}
Expand Down Expand Up @@ -2028,9 +2028,9 @@ def overwrite(self, paramset: ParamSet) -> None:
"""
radius = paramset[self.name]["radius"]
scale = paramset[self.name]["scale"]
for i in self.ffinfo.perParticleParamIndices:
self.ffinfo["Forces"][self.name]["node"][i]["attrib"]["radius"] = str(radius[i])
self.ffinfo["Forces"][self.name]["node"][i]["attrib"]["scale"] = str(scale[i])
for j, i in enumerate(self.perParticleParamIndices):
self.ffinfo["Forces"][self.name]["node"][i]["attrib"]["radius"] = str(radius[j])
self.ffinfo["Forces"][self.name]["node"][i]["attrib"]["scale"] = str(scale[j])

def _find_key_index(self, key: Tuple[str]) -> int:
"""
Expand Down Expand Up @@ -2109,4 +2109,4 @@ def potential_fn(positions: jnp.ndarray, box: jnp.ndarray, pairs: jnp.ndarray, p
return potential_fn


_DMFFGenerators["CustomGBForce"] = CustomGBGenerator
_DMFFGenerators["CustomGBForce"] = CustomGBGenerator
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