Skip to content

fix(unittest): fix classical UTs and remove double check of cutoff distance in potential calculation. #49

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 2 commits into from
Jul 5, 2022
Merged

fix(unittest): fix classical UTs and remove double check of cutoff distance in potential calculation. #49

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
0a0f70d
fix(tests): Add attribute to choose improper order
WangXinyan940 Jul 5, 2022
e75620e
fix(classical): remove double check of cutoff distance in potential f…
WangXinyan940 Jul 5, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 0 additions & 2 deletions dmff/classical/inter.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -198,8 +198,6 @@ def get_rf_energy(dr_vec, chrgprod, box):
if self.ifPBC:
dr_vec = v_pbc_shift(dr_vec, box, jnp.linalg.inv(box))
dr_norm = jnp.linalg.norm(dr_vec, axis=1)
chrgprod = chrgprod[dr_norm <= self.r_cut]
dr_norm = dr_norm[dr_norm <= self.r_cut]

dr_inv = 1.0 / dr_norm
E = (
Expand Down
2 changes: 1 addition & 1 deletion tests/data/impr1.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
<Bond atomName1="N1" atomName2="N4"/>
</Residue>
</Residues>
<PeriodicTorsionForce>
<PeriodicTorsionForce ordering="amber">
<Improper type1="n1" type2="n2" type3="n3" type4="n4" periodicity1="1" phase1="0.0" k1="2.092"/>
</PeriodicTorsionForce>
</ForceField>
2 changes: 1 addition & 1 deletion tests/data/wild1.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
<Bond atomName1="N3" atomName2="N4"/>
</Residue>
</Residues>
<PeriodicTorsionForce>
<PeriodicTorsionForce ordering="amber">
<Proper type1="" type2="n2" type3="n3" type4="" periodicity1="1" phase1="0.0" k1="2.092" periodicity2="2" phase2="0.0" k2="2.092" periodicity3="3" phase3="0.0" k3="2.092" periodicity4="4" phase4="0.0" k4="2.092"/>
</PeriodicTorsionForce>
</ForceField>
2 changes: 1 addition & 1 deletion tests/data/wild2.xml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@
<Bond atomName1="N1" atomName2="N4"/>
</Residue>
</Residues>
<PeriodicTorsionForce>
<PeriodicTorsionForce ordering="amber">
<Improper type1="n1" type2="" type3="" type4="n4" periodicity1="1" phase1="0.0" k1="2.092"/>
</PeriodicTorsionForce>
</ForceField>