Fix accidental elimination of torsions after 0.11.0 release #208

jchodera · 2022-07-10T03:00:30Z

Bugfixes:

Fix critical bug introduced in Remove debug prints. #198 that resulted in torsions being omitted from template-generated systems

Minor improvements:

Change how we measure relative deviation in vectors to avoid underflow.

jchodera · 2022-07-10T03:53:39Z

Hm, I'm not sure why this is happening. There is a significant energy discrepancy for '[H]C(=O)[H]' in openmmforcefields/tests/test_template_generators.py::TestSMIRNOFFTemplateGenerator::test_energies, but none of the individual components has a significant difference:

Force components:
component                      relative deviation
NonbondedForce                       0.0000000000
HarmonicBondForce                    0.0000000000
HarmonicAngleForce                   0.0000000000
TOTAL                                0.0000858405

jchodera · 2022-07-10T04:26:22Z

The System created by the SMIRNOFFTemplateGenerator appears to be missing impropers.
Investigating further.

jchodera · 2022-07-10T20:33:47Z

OK, what is currently happening is that the OpenFF toolkit generates an OpenMM System containing a SMIRNOFF improper:

<?xml version="1.0" ?>
<System openmmVersion="7.7" type="System" version="1">
	<PeriodicBoxVectors>
		<A x="2" y="0" z="0"/>
		<B x="0" y="2" z="0"/>
		<C x="0" y="0" z="2"/>
	</PeriodicBoxVectors>
	<Particles>
		<Particle mass="12.01078"/>
		<Particle mass="15.99943"/>
		<Particle mass="1.007947"/>
		<Particle mass="1.007947"/>
	</Particles>
	<Constraints/>
	<Forces>
		<Force forceGroup="0" name="PeriodicTorsionForce" type="PeriodicTorsionForce" usesPeriodic="0" version="2">
			<Torsions>
				<Torsion k="1.5341333333333336" p1="0" p2="1" p3="2" p4="3" periodicity="2" phase="3.141592653589793"/>
				<Torsion k="1.5341333333333336" p1="0" p2="2" p3="3" p4="1" periodicity="2" phase="3.141592653589793"/>
				<Torsion k="1.5341333333333336" p1="0" p2="3" p3="1" p4="2" periodicity="2" phase="3.141592653589793"/>
			</Torsions>
		</Force>
		<Force alpha="0" cutoff=".9" dispersionCorrection="1" ewaldTolerance=".0005" exceptionsUsePeriodic="0" forceGroup="0" includeDirectSpace="1" ljAlpha="0" ljnx="0" ljny="0" ljnz="0" method="0" name="NonbondedForce" nx="0" ny="0" nz="0" recipForceGroup="-1" rfDielectric="78.3" switchingDistance="-1" type="NonbondedForce" useSwitchingFunction="0" version="4">
			<GlobalParameters/>
			<ParticleOffsets/>
			<ExceptionOffsets/>
			<Particles>
				<Particle eps=".359824" q=".5632600113749504" sig=".3399669508423535"/>
				<Particle eps=".87864" q="-.5147399976849556" sig=".2959921901149463"/>
				<Particle eps=".06276" q="-.024260006844997406" sig=".2510552587719476"/>
				<Particle eps=".06276" q="-.024260006844997406" sig=".2510552587719476"/>
			</Particles>
			<Exceptions>
				<Exception eps="0" p1="0" p2="1" q="0" sig="1"/>
				<Exception eps="0" p1="0" p2="2" q="0" sig="1"/>
				<Exception eps="0" p1="1" p2="2" q="0" sig="1"/>
				<Exception eps="0" p1="0" p2="3" q="0" sig="1"/>
				<Exception eps="0" p1="1" p2="3" q="0" sig="1"/>
				<Exception eps="0" p1="2" p2="3" q="0" sig="1"/>
			</Exceptions>
		</Force>
		<Force forceGroup="0" name="HarmonicBondForce" type="HarmonicBondForce" usesPeriodic="0" version="2">
			<Bonds>
				<Bond d=".12290000000000001" k="476976.00000000006" p1="0" p2="1"/>
				<Bond d=".10800000000000001" k="307105.60000000003" p1="0" p2="2"/>
				<Bond d=".10800000000000001" k="307105.60000000003" p1="0" p2="3"/>
			</Bonds>
		</Force>
		<Force forceGroup="0" name="HarmonicAngleForce" type="HarmonicAngleForce" usesPeriodic="0" version="2">
			<Angles>
				<Angle a="2.0943951023931953" k="418.40000000000003" p1="1" p2="0" p3="2"/>
				<Angle a="2.0943951023931953" k="418.40000000000003" p1="1" p2="0" p3="3"/>
				<Angle a="2.0943951023931953" k="292.88" p1="2" p2="0" p3="3"/>
			</Angles>
		</Force>
	</Forces>
</System>

But the torsion processing part of convert_system_to_ffxml() is not generating torsion terms for the improper:

<ForceField>
  <AtomTypes>
    <Type name="[H]C(=O)[H]$C1#0" element="C" mass="12.01078" class="[H]C(=O)[H]$C1#0"/>
    <Type name="[H]C(=O)[H]$O1#1" element="O" mass="15.99943" class="[H]C(=O)[H]$O1#1"/>
    <Type name="[H]C(=O)[H]$H1#2" element="H" mass="1.007947" class="[H]C(=O)[H]$H1#2"/>
    <Type name="[H]C(=O)[H]$H2#3" element="H" mass="1.007947" class="[H]C(=O)[H]$H2#3"/>
  </AtomTypes>
  <NonbondedForce coulomb14scale="0.833333" lj14scale="0.5">
    <UseAttributeFromResidue name="charge"/>
    <Atom sigma="0.3399669508423535" epsilon="0.359824" class="[H]C(=O)[H]$C1#0"/>
    <Atom sigma="0.2959921901149463" epsilon="0.87864" class="[H]C(=O)[H]$O1#1"/>
    <Atom sigma="0.2510552587719476" epsilon="0.06276" class="[H]C(=O)[H]$H1#2"/>
    <Atom sigma="0.2510552587719476" epsilon="0.06276" class="[H]C(=O)[H]$H2#3"/>
  </NonbondedForce>
  <HarmonicBondForce>
    <Bond class1="[H]C(=O)[H]$C1#0" class2="[H]C(=O)[H]$O1#1" length="0.12290000000000001" k="476976.00000000006"/>
    <Bond class1="[H]C(=O)[H]$C1#0" class2="[H]C(=O)[H]$H1#2" length="0.10800000000000001" k="307105.60000000003"/>
    <Bond class1="[H]C(=O)[H]$C1#0" class2="[H]C(=O)[H]$H2#3" length="0.10800000000000001" k="307105.60000000003"/>
  </HarmonicBondForce>
  <HarmonicAngleForce>
    <Angle class1="[H]C(=O)[H]$O1#1" class2="[H]C(=O)[H]$C1#0" class3="[H]C(=O)[H]$H1#2" angle="2.0943951023931953" k="418.40000000000003"/>
    <Angle class1="[H]C(=O)[H]$O1#1" class2="[H]C(=O)[H]$C1#0" class3="[H]C(=O)[H]$H2#3" angle="2.0943951023931953" k="418.40000000000003"/>
    <Angle class1="[H]C(=O)[H]$H1#2" class2="[H]C(=O)[H]$C1#0" class3="[H]C(=O)[H]$H2#3" angle="2.0943951023931953" k="292.88"/>
  </HarmonicAngleForce>
  <Residues>
    <Residue name="[H]C(=O)[H]">
      <Atom name="C1" type="[H]C(=O)[H]$C1#0" charge="0.5632600113749504"/>
      <Atom name="O1" type="[H]C(=O)[H]$O1#1" charge="-0.5147399976849556"/>
      <Atom name="H1" type="[H]C(=O)[H]$H1#2" charge="-0.024260006844997406"/>
      <Atom name="H2" type="[H]C(=O)[H]$H2#3" charge="-0.024260006844997406"/>
      <Bond atomName1="C1" atomName2="O1"/>
      <Bond atomName1="C1" atomName2="H1"/>
      <Bond atomName1="C1" atomName2="H2"/>
    </Residue>
  </Residues>
</ForceField>

jchodera · 2022-07-10T20:42:51Z

OK, it looks like some critical code was removed in #198, a PR that was intended to eliminate extra debug printing but instead may have eliminated critical code needed to correctly convert all torsions for SMIRNOFF and Espaloma. Specifically, this change was one of the important deletions.

jchodera · 2022-07-10T20:47:37Z

Fortunately, it looks like this bug didn't make it into a release!

…nverted into templates

jchodera · 2022-07-10T22:26:01Z

@yuanqing-wang: I'm running into a type error with the tests parameterizing acetone with espaloma 0.2.2:

2022-07-10T22:14:21.2517660Z openmmforcefields/tests/test_template_generators.py:136: 
2022-07-10T22:14:21.2518497Z _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
2022-07-10T22:14:21.2519397Z openmmforcefields/tests/test_template_generators.py:131: in test_add_molecules
2022-07-10T22:14:21.2520339Z     system = forcefield.createSystem(openmm_topology, nonbondedMethod=NoCutoff)
2022-07-10T22:14:21.2521471Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/openmm/app/forcefield.py:1212: in createSystem
2022-07-10T22:14:21.2522587Z     templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds)
2022-07-10T22:14:21.2523839Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/openmm/app/forcefield.py:1417: in _matchAllResiduesToTemplates
2022-07-10T22:14:21.2524908Z     if generator(self, res):
2022-07-10T22:14:21.2526141Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/openmmforcefields-0+untagged.1.g7f40898-py3.10.egg/openmmforcefields/generators/template_generators.py:304: in generator
2022-07-10T22:14:21.2534583Z     ffxml_contents = self.generate_residue_template(molecule)
2022-07-10T22:14:21.2536082Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/openmmforcefields-0+untagged.1.g7f40898-py3.10.egg/openmmforcefields/generators/template_generators.py:1629: in generate_residue_template
2022-07-10T22:14:21.2537140Z     molecule_graph = esp.Graph(molecule)
2022-07-10T22:14:21.2538121Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/espaloma/graphs/graph.py:62: in __init__
2022-07-10T22:14:21.2539044Z     heterograph = self.get_heterograph_from_graph_and_mol(
2022-07-10T22:14:21.2540284Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/espaloma/graphs/graph.py:126: in get_heterograph_from_graph_and_mol
2022-07-10T22:14:21.2541312Z     heterograph = esp.graphs.utils.read_heterogeneous_graph.from_homogeneous_and_mol(
2022-07-10T22:14:21.2542775Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/espaloma/graphs/utils/read_heterogeneous_graph.py:272: in from_homogeneous_and_mol
2022-07-10T22:14:21.2543789Z     hg = dgl.heterograph({key: list(value) for key, value in hg.items()})
2022-07-10T22:14:21.2544827Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/dgl/convert.py:350: in heterograph
2022-07-10T22:14:21.2545792Z     (sparse_fmt, arrays), urange, vrange = utils.graphdata2tensors(
2022-07-10T22:14:21.2546856Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/dgl/utils/data.py:179: in graphdata2tensors
2022-07-10T22:14:21.2547732Z     src, dst = elist2tensor(data, idtype)
2022-07-10T22:14:21.2548688Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/dgl/utils/data.py:32: in elist2tensor
2022-07-10T22:14:21.2549584Z     return F.tensor(u, idtype), F.tensor(v, idtype)
2022-07-10T22:14:21.2550381Z _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
2022-07-10T22:14:21.2550830Z 
2022-07-10T22:14:21.2551192Z data = [0.0, 1.0, 2.0, 3.0], dtype = torch.int64
2022-07-10T22:14:21.2551608Z 
2022-07-10T22:14:21.2551951Z     def tensor(data, dtype=None):
2022-07-10T22:14:21.2552696Z         if isinstance(data, numbers.Number):
2022-07-10T22:14:21.2553407Z             data = [data]
2022-07-10T22:14:21.2554221Z         if isinstance(data, list) and len(data) > 0 and isinstance(data[0], th.Tensor):
2022-07-10T22:14:21.2555140Z             # prevent GPU->CPU->GPU copies
2022-07-10T22:14:21.2555870Z             if data[0].ndim == 0:
2022-07-10T22:14:21.2556613Z                 # zero dimenion scalar tensors
2022-07-10T22:14:21.2557372Z                 return th.stack(data)
2022-07-10T22:14:21.2558123Z         if isinstance(data, th.Tensor):
2022-07-10T22:14:21.2558928Z             return th.as_tensor(data, dtype=dtype, device=data.device)
2022-07-10T22:14:21.2559660Z         else:
2022-07-10T22:14:21.2560380Z >           return th.as_tensor(data, dtype=dtype)
2022-07-10T22:14:21.2561307Z E           TypeError: 'numpy.float64' object cannot be interpreted as an integer
2022-07-10T22:14:21.2561790Z 
2022-07-10T22:14:21.2562375Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/dgl/backend/pytorch/tensor.py:46: TypeError

Could this be due to a version issue? Here's how we are installing espaloma and its dependencies in the unit tests:
https://github.com/openmm/openmmforcefields/blob/master/devtools/conda-envs/test_env.yaml#L41-L50

yuanqing-wang · 2022-07-11T01:05:57Z

This looks like a DGL error. Let me double check.

…

On Jul 10, 2022, at 6:26 PM, John Chodera ***@***.***> wrote: @yuanqing-wang: I'm running into a type error with the tests parameterizing acetone with espaloma 0.2.2: 2022-07-10T22:14:21.2517660Z openmmforcefields/tests/test_template_generators.py:136: 2022-07-10T22:14:21.2518497Z _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2022-07-10T22:14:21.2519397Z openmmforcefields/tests/test_template_generators.py:131: in test_add_molecules 2022-07-10T22:14:21.2520339Z system = forcefield.createSystem(openmm_topology, nonbondedMethod=NoCutoff) 2022-07-10T22:14:21.2521471Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/openmm/app/forcefield.py:1212: in createSystem 2022-07-10T22:14:21.2522587Z templateForResidue = self._matchAllResiduesToTemplates(data, topology, residueTemplates, ignoreExternalBonds) 2022-07-10T22:14:21.2523839Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/openmm/app/forcefield.py:1417: in _matchAllResiduesToTemplates 2022-07-10T22:14:21.2524908Z if generator(self, res): 2022-07-10T22:14:21.2526141Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/openmmforcefields-0+untagged.1.g7f40898-py3.10.egg/openmmforcefields/generators/template_generators.py:304: in generator 2022-07-10T22:14:21.2534583Z ffxml_contents = self.generate_residue_template(molecule) 2022-07-10T22:14:21.2536082Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/openmmforcefields-0+untagged.1.g7f40898-py3.10.egg/openmmforcefields/generators/template_generators.py:1629: in generate_residue_template 2022-07-10T22:14:21.2537140Z molecule_graph = esp.Graph(molecule) 2022-07-10T22:14:21.2538121Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/espaloma/graphs/graph.py:62: in __init__ 2022-07-10T22:14:21.2539044Z heterograph = self.get_heterograph_from_graph_and_mol( 2022-07-10T22:14:21.2540284Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/espaloma/graphs/graph.py:126: in get_heterograph_from_graph_and_mol 2022-07-10T22:14:21.2541312Z heterograph = esp.graphs.utils.read_heterogeneous_graph.from_homogeneous_and_mol( 2022-07-10T22:14:21.2542775Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/espaloma/graphs/utils/read_heterogeneous_graph.py:272: in from_homogeneous_and_mol 2022-07-10T22:14:21.2543789Z hg = dgl.heterograph({key: list(value) for key, value in hg.items()}) 2022-07-10T22:14:21.2544827Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/dgl/convert.py:350: in heterograph 2022-07-10T22:14:21.2545792Z (sparse_fmt, arrays), urange, vrange = utils.graphdata2tensors( 2022-07-10T22:14:21.2546856Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/dgl/utils/data.py:179: in graphdata2tensors 2022-07-10T22:14:21.2547732Z src, dst = elist2tensor(data, idtype) 2022-07-10T22:14:21.2548688Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/dgl/utils/data.py:32: in elist2tensor 2022-07-10T22:14:21.2549584Z return F.tensor(u, idtype), F.tensor(v, idtype) 2022-07-10T22:14:21.2550381Z _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 2022-07-10T22:14:21.2550830Z 2022-07-10T22:14:21.2551192Z data = [0.0, 1.0, 2.0, 3.0], dtype = torch.int64 2022-07-10T22:14:21.2551608Z 2022-07-10T22:14:21.2551951Z def tensor(data, dtype=None): 2022-07-10T22:14:21.2552696Z if isinstance(data, numbers.Number): 2022-07-10T22:14:21.2553407Z data = [data] 2022-07-10T22:14:21.2554221Z if isinstance(data, list) and len(data) > 0 and isinstance(data[0], th.Tensor): 2022-07-10T22:14:21.2555140Z # prevent GPU->CPU->GPU copies 2022-07-10T22:14:21.2555870Z if data[0].ndim == 0: 2022-07-10T22:14:21.2556613Z # zero dimenion scalar tensors 2022-07-10T22:14:21.2557372Z return th.stack(data) 2022-07-10T22:14:21.2558123Z if isinstance(data, th.Tensor): 2022-07-10T22:14:21.2558928Z return th.as_tensor(data, dtype=dtype, device=data.device) 2022-07-10T22:14:21.2559660Z else: 2022-07-10T22:14:21.2560380Z > return th.as_tensor(data, dtype=dtype) 2022-07-10T22:14:21.2561307Z E TypeError: 'numpy.float64' object cannot be interpreted as an integer 2022-07-10T22:14:21.2561790Z 2022-07-10T22:14:21.2562375Z /usr/share/miniconda/envs/test/lib/python3.10/site-packages/dgl/backend/pytorch/tensor.py:46: TypeError Could this be due to a version issue? Here's how we are installing espaloma and its dependencies in the unit tests: https://github.com/openmm/openmmforcefields/blob/master/devtools/conda-envs/test_env.yaml#L41-L50 — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.

yuanqing-wang · 2022-07-11T01:22:05Z

@jchodera could you list the pytorch and dgl versions used to produce that error?

jchodera · 2022-07-11T01:30:43Z

Here are the versions that were installed in the conda environment:

    + pytorch                              1.11.0  cpu_py310h75c9ab6_2      conda-forge/linux-64       47 MB
    + dgl                                   0.8.2  py310_0                  dglteam/linux-64            5 MB

jchodera · 2022-07-11T17:30:46Z

@yuanqing-wang : Do you think we need to pin the DGL version for now?

yuanqing-wang · 2022-07-11T17:41:48Z

I think we might have to. I’ll come up with a solution in a few hours.

…

On Jul 11, 2022, at 1:30 PM, John Chodera ***@***.***> wrote: @yuanqing-wang <https://github.com/yuanqing-wang> : Do you think we need to pin the DGL version for now? — Reply to this email directly, view it on GitHub <#208 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGLMHA7FAVVRLZOVK5MLQ6LVTRK5DANCNFSM53EJICNA>. You are receiving this because you were mentioned.

yuanqing-wang · 2022-07-11T19:10:59Z

@jchodera fixed. could you try with the current espaloma master branch

yuanqing-wang · 2022-07-11T19:11:45Z

I accidentally had a float as graph index which was tolerated by older dgl but not newer versions.

jchodera · 2022-07-12T05:24:20Z

@yuanqing-wang : Thanks! It looks like this works, though there is a segfault on osx.
Can you cut a new release with this bugfix?

We can debug the osx failure separately.

yuanqing-wang · 2022-07-12T19:31:16Z

@jchodera new release here: https://github.com/choderalab/espaloma/releases/tag/0.2.3

Change how we measure relative deviation in vectors to avoid underflow.

7095e66

Refactor to eliminate some duplication and add debug XML output

8cb7979

jchodera added 3 commits July 9, 2022 21:33

More debug information

ddd4503

Fix bug in refactored code

08afe16

Fix and generalize tests to produce more useful error message

29e186f

jchodera changed the title ~~Fix test failures~~ Critical bugfix: Torsions (propers and impropers) were not being added to template-generated systems Jul 10, 2022

jchodera added bug high-priority labels Jul 10, 2022

jchodera added this to the 0.11.1 milestone Jul 10, 2022

jchodera self-assigned this Jul 10, 2022

jchodera added 3 commits July 10, 2022 16:49

Fix critical bug introduced in PR #198 that meant no torsions were co…

583be46

…nverted into templates

Reduce number of molecules for CI tests

95afb47

Remove voluminous debug output

975773c

jchodera requested a review from mikemhenry July 11, 2022 03:57

jchodera changed the title ~~Critical bugfix: Torsions (propers and impropers) were not being added to template-generated systems~~ Fix accidental elimination of torsions after 0.11.0 release Jul 11, 2022

jchodera mentioned this pull request Jul 11, 2022

Exception: Relative force deviation for [H]C(=O)[H] #204

Closed

Test against espaloma master to see if bugfix addresses test failure

b8cd9a0

jchodera marked this pull request as ready for review July 12, 2022 05:24

jchodera merged commit 815dfd1 into master Jul 12, 2022

jchodera deleted the fix-tests branch July 12, 2022 05:26

Fix accidental elimination of torsions after 0.11.0 release #208

Fix accidental elimination of torsions after 0.11.0 release #208

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jchodera commented Jul 10, 2022 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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Bugfixes:

Minor improvements:

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jchodera commented Jul 10, 2022 •

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jchodera commented Jul 10, 2022 •

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