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Improved water model error handling #523

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Merged
RagnarB83 merged 2 commits into from
Sep 24, 2026
+20 −6
Merged

Improved water model error handling #523

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a72a651
Improved water model error handling
UpsilonAlpha Sep 24, 2026
6019d78
Fix indentation and formatting in interface_OpenMM.py
UpsilonAlpha Sep 24, 2026
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26 changes: 20 additions & 6 deletions ash/interfaces/interface_OpenMM.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2750,9 +2750,15 @@ def OpenMM_Modeller(pdbfile=None, forcefield_object=None, forcefield=None, xmlfi
# Define a forcefield if using XML-files
if xmlfile is not None:
print("XMfile:", xmlfile)
print("Water model:", watermodel)
print("Water xmlfile:", waterxmlfile)
#Basic checks
if watermodel is None:
print("Water model not provided, using tip3p as default for solvation")
modeller_solvent_name = "tip3p"
elif watermodel.lower() == "tip3p":
modeller_solvent_name = "tip3p"
else:
modeller_solvent_name = watermodel

if extraxmlfile is not None:
print("Using extra XML file:", extraxmlfile)
#Checking if file exists first before continuing
Expand All @@ -2766,16 +2772,24 @@ def OpenMM_Modeller(pdbfile=None, forcefield_object=None, forcefield=None, xmlfi
forcefield_obj = openmm_app.forcefield.ForceField(xmlfile,extraxmlfile)
elif extraxmlfile is None and waterxmlfile is not None:
forcefield_obj = openmm_app.forcefield.ForceField(xmlfile,waterxmlfile)
print("Water xmlfile:", waterxmlfile)
elif extraxmlfile is not None and waterxmlfile is not None:
forcefield_obj = openmm_app.forcefield.ForceField(xmlfile,extraxmlfile,waterxmlfile)
print("Water xmlfile:", waterxmlfile)

elif forcefield_object is not None:
print("Using forcefield object provided")
forcefield_obj= forcefield_object

if watermodel is not None or waterxmlfile is not None:
print("Warning: watermodel/waterxmlfile ignored when forcefield_object is supplied")
if watermodel is None:
print("Water model not provided, using tip3p as default for solvation")
modeller_solvent_name = "tip3p"
elif watermodel.lower() == "tip3p":
modeller_solvent_name = "tip3p"
else:
modeller_solvent_name = watermodel

if waterxmlfile is not None:
print("Warning: waterxmlfile ignored when forcefield_object is supplied")

else:
print("You must provide a forcefield name, forcefieldobject or xmlfile keywords!")
Expand Down Expand Up @@ -5844,7 +5858,7 @@ def get_free_energy_from_biasfiles(temperature,biasfactor,CV1_gridwith,CV2_gridw
if CV2_gridwith == None:
full_bias=np.zeros((CV1_gridwith))
else:
full_bias=np.zeros((CV2_gridwith,CV1_gridwith))
full_bias=np.zeros((CV2_gridwith,CV1_gridwith))

#Looping over bias-files
print("full_bias shape:", full_bias.shape)
Expand Down
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