fix: evaluator unit bug#277
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leeping merged 2 commits intoleeping:masterfrom Feb 4, 2023
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Hm, I just tried study 022 and got the attached output. How did you get the reference optimize.out? Maybe you forgot to commit some other changes?
Also, I activated CI on this PR so we can see if I've just messed up my install of this branch. Sorry for the delay on that!
study 022 output
(forcebalance-test) jw@mba$ ForceBalance.py optimize.in
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
#======================================================================#
#| Welcome to ForceBalance version 1.9.4! =D |#
#| Force Field Optimization System |#
#| |#
#| Authors: |#
#| Lee-Ping Wang |#
#| Yudong Qiu, Keri A. McKiernan |#
#| Jeffrey R. Wagner, Hyesu Jang, Simon Boothroyd |#
#| Arthur Vigil, Erik G. Brandt, John Stoppelman |#
#| Johnny Israeli, Matt Thompson |#
#======================================================================#
`.:+@@###@'
,;'+###############.
+################':`
`.,,...####+.
,##### +##.
##### ######
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:####@ ####. ,####'
###### #### +###+
##### #### ###;
:## #### ++`
####``..:;+##############+`
.,:;;'++##################################`
`############################++++''';;;;;;;;;;;'';
,########':,.`` ####
####
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+`
Reading options from file: optimize.in
#========================================================#
#| Options at their default values are not printed |#
#| Use 'verbose_options True' to Enable |#
#========================================================#
Reading force field from file: smirnoff99Frosst_experimental.offxml
#=========================================================#
#| Starting parameter indices, physical values and IDs |#
#=========================================================#
0 [ 9.3800e+02 ] : Bonds/Bond/k/[#6X3:1]:[#6X3:2]
1 [ 1.4000e+00 ] : Bonds/Bond/length/[#6X3:1]:[#6X3:2]
2 [ 9.0000e+02 ] : Bonds/Bond/k/[#6X3a:1]-[#8X2H0:2]
3 [ 1.3230e+00 ] : Bonds/Bond/length/[#6X3a:1]-[#8X2H0:2]
4 [ 6.8000e+02 ] : Bonds/Bond/k/[#6X4:1]-[#1:2]
5 [ 1.0900e+00 ] : Bonds/Bond/length/[#6X4:1]-[#1:2]
6 [ 7.3400e+02 ] : Bonds/Bond/k/[#6X3:1]-[#1:2]
7 [ 1.0800e+00 ] : Bonds/Bond/length/[#6X3:1]-[#1:2]
8 [ 1.0950e+02 ] : Angles/Angle/angle/[#1:1]-[#6X4:2]-[#1:3]
9 [ 7.0000e+01 ] : Angles/Angle/k/[#1:1]-[#6X4:2]-[#1:3]
10 [ 1.2000e+02 ] : Angles/Angle/angle/[*:1]~[#6X3:2]~[*:3]
11 [ 1.4000e+02 ] : Angles/Angle/k/[*:1]~[#6X3:2]~[*:3]
12 [ 1.2000e+02 ] : Angles/Angle/angle/[#1:1]-[#6X3:2]~[*:3]
13 [ 1.0000e+02 ] : Angles/Angle/k/[#1:1]-[#6X3:2]~[*:3]
14 [ 1.2000e+02 ] : Angles/Angle/angle/[#6X3,#7:1]~;@[#8;r:2]~;@[#6X3,#7:3]
15 [ 1.4000e+02 ] : Angles/Angle/k/[#6X3,#7:1]~;@[#8;r:2]~;@[#6X3,#7:3]
16 [ 0.0000e+00 ] : ProperTorsions/Proper/k1/[*:1]~[#6X3:2]-[#6X4:3]-[*:4]
17 [ 3.6250e+00 ] : ProperTorsions/Proper/k1/[*:1]~[#6X3:2]:[#6X3:3]~[*:4]
18 [ 2.5000e+00 ] : ProperTorsions/Proper/k1/[*:1]-[#8X2:2]@[#6X3:3]~[*:4]
19 [ 1.4870e+00 ] : vdW/Atom/rmin_half/[#1:1]-[#6X4]
20 [ 1.5700e-02 ] : vdW/Atom/epsilon/[#1:1]-[#6X4]
21 [ 1.4590e+00 ] : vdW/Atom/rmin_half/[#1:1]-[#6X3]
22 [ 1.5000e-02 ] : vdW/Atom/epsilon/[#1:1]-[#6X3]
23 [ 1.9080e+00 ] : vdW/Atom/rmin_half/[#6X4:1]
24 [ 1.0940e-01 ] : vdW/Atom/epsilon/[#6X4:1]
25 [ 1.6837e+00 ] : vdW/Atom/rmin_half/[#8X2H0+0:1]
26 [ 1.7000e-01 ] : vdW/Atom/epsilon/[#8X2H0+0:1]
-----------------------------------------------------------
#=========================================================#
#| Rescaling Factors by Type (Lower Takes Precedence): |#
#=========================================================#
ProperTorsions/Proper/k1 : 3.62500e+00
Bonds/Bond/k : 1.00000e+01
Bonds/Bond/length : 1.00000e-01
Angles/Angle/k : 1.00000e+01
Angles/Angle/angle : 1.00000e+01
ProperTorsions/Proper/k : 1.00000e+01
vdW/Atom/epsilon : 1.00000e-01
vdW/Atom/rmin_half : 1.00000e-01
-----------------------------------------------------------
#========================================================#
#| Rescaling Types / Factors by Parameter Number: |#
#========================================================#
0 [ Bonds/Bond/k : 1.00000e+01 ] : Bonds/Bond/k/[#6X3:1]:[#6X3:2]
1 [ Bonds/Bond/length : 1.00000e-01 ] : Bonds/Bond/length/[#6X3:1]:[#6X3:2]
2 [ Bonds/Bond/k : 1.00000e+01 ] : Bonds/Bond/k/[#6X3a:1]-[#8X2H0:2]
3 [ Bonds/Bond/length : 1.00000e-01 ] : Bonds/Bond/length/[#6X3a:1]-[#8X2H0:2]
4 [ Bonds/Bond/k : 1.00000e+01 ] : Bonds/Bond/k/[#6X4:1]-[#1:2]
5 [ Bonds/Bond/length : 1.00000e-01 ] : Bonds/Bond/length/[#6X4:1]-[#1:2]
6 [ Bonds/Bond/k : 1.00000e+01 ] : Bonds/Bond/k/[#6X3:1]-[#1:2]
7 [ Bonds/Bond/length : 1.00000e-01 ] : Bonds/Bond/length/[#6X3:1]-[#1:2]
8 [ Angles/Angle/angle : 1.00000e+01 ] : Angles/Angle/angle/[#1:1]-[#6X4:2]-[#1:3]
9 [ Angles/Angle/k : 1.00000e+01 ] : Angles/Angle/k/[#1:1]-[#6X4:2]-[#1:3]
10 [ Angles/Angle/angle : 1.00000e+01 ] : Angles/Angle/angle/[*:1]~[#6X3:2]~[*:3]
11 [ Angles/Angle/k : 1.00000e+01 ] : Angles/Angle/k/[*:1]~[#6X3:2]~[*:3]
12 [ Angles/Angle/angle : 1.00000e+01 ] : Angles/Angle/angle/[#1:1]-[#6X3:2]~[*:3]
13 [ Angles/Angle/k : 1.00000e+01 ] : Angles/Angle/k/[#1:1]-[#6X3:2]~[*:3]
14 [ Angles/Angle/angle : 1.00000e+01 ] : Angles/Angle/angle/[#6X3,#7:1]~;@[#8;r:2]~;@[#6X3,#7:3]
15 [ Angles/Angle/k : 1.00000e+01 ] : Angles/Angle/k/[#6X3,#7:1]~;@[#8;r:2]~;@[#6X3,#7:3]
16 [ ProperTorsions/Proper/k : 1.00000e+01 ] : ProperTorsions/Proper/k1/[*:1]~[#6X3:2]-[#6X4:3]-[*:4]
17 [ ProperTorsions/Proper/k : 1.00000e+01 ] : ProperTorsions/Proper/k1/[*:1]~[#6X3:2]:[#6X3:3]~[*:4]
18 [ ProperTorsions/Proper/k : 1.00000e+01 ] : ProperTorsions/Proper/k1/[*:1]-[#8X2:2]@[#6X3:3]~[*:4]
19 [ vdW/Atom/rmin_half : 1.00000e-01 ] : vdW/Atom/rmin_half/[#1:1]-[#6X4]
20 [ vdW/Atom/epsilon : 1.00000e-01 ] : vdW/Atom/epsilon/[#1:1]-[#6X4]
21 [ vdW/Atom/rmin_half : 1.00000e-01 ] : vdW/Atom/rmin_half/[#1:1]-[#6X3]
22 [ vdW/Atom/epsilon : 1.00000e-01 ] : vdW/Atom/epsilon/[#1:1]-[#6X3]
23 [ vdW/Atom/rmin_half : 1.00000e-01 ] : vdW/Atom/rmin_half/[#6X4:1]
24 [ vdW/Atom/epsilon : 1.00000e-01 ] : vdW/Atom/epsilon/[#6X4:1]
25 [ vdW/Atom/rmin_half : 1.00000e-01 ] : vdW/Atom/rmin_half/[#8X2H0+0:1]
26 [ vdW/Atom/epsilon : 1.00000e-01 ] : vdW/Atom/epsilon/[#8X2H0+0:1]
----------------------------------------------------------
#========================================================#
#| Setup for force field |#
#========================================================#
fnms ['smirnoff99Frosst_experimental.offxml']
priors OrderedDict([('Bonds/Bond/k', 10.0), ('Bonds/Bond/length', 0.1), ('Angles/Angle/k', 10.0), ('Angles/Angle/angle', 10.0), ('ProperTorsions/Proper/k', 10.0), ('vdW/Atom/epsilon', 0.1), ('vdW/Atom/rmin_half', 0.1)])
----------------------------------------------------------
Backing up: optimize.tmp/optgeo to: optimize.bak/optgeo_2.tar.bz2
Reading optgeo options from file: targets/optgeo/optgeo_options.txt
/Users/jeffreywagner/conda/envs/forcebalance-test/lib/python3.9/site-packages/openff/interchange/components/interchange.py:339: UserWarning: Automatically up-converting BondHandler from version 0.3 to 0.4. Consider manually upgrading this BondHandler (or <Bonds> section in an OFFXML file) to 0.4 or newer. For more details, see https://openforcefield.github.io/standards/standards/smirnoff/#bonds.
warnings.warn(
Traceback (most recent call last):
File "/Users/jeffreywagner/conda/envs/forcebalance-test/lib/python3.9/site-packages/forcebalance-1.9.4-py3.9-macosx-10.9-x86_64.egg/EGG-INFO/scripts/ForceBalance.py", line 41, in Run_ForceBalance
objective = Objective(options, tgt_opts, forcefield)
File "/Users/jeffreywagner/conda/envs/forcebalance-test/lib/python3.9/site-packages/forcebalance-1.9.4-py3.9-macosx-10.9-x86_64.egg/forcebalance/objective.py", line 182, in __init__
else: Tgt = Implemented_Targets[opts['type']](options,opts,forcefield)
File "/Users/jeffreywagner/conda/envs/forcebalance-test/lib/python3.9/site-packages/forcebalance-1.9.4-py3.9-macosx-10.9-x86_64.egg/forcebalance/smirnoffio.py", line 686, in __init__
super(OptGeoTarget_SMIRNOFF,self).__init__(options,tgt_opts,forcefield)
File "/Users/jeffreywagner/conda/envs/forcebalance-test/lib/python3.9/site-packages/forcebalance-1.9.4-py3.9-macosx-10.9-x86_64.egg/forcebalance/opt_geo_target.py", line 79, in __init__
self.create_engines(engine_args)
File "/Users/jeffreywagner/conda/envs/forcebalance-test/lib/python3.9/site-packages/forcebalance-1.9.4-py3.9-macosx-10.9-x86_64.egg/forcebalance/smirnoffio.py", line 705, in create_engines
self.engines[sysname] = self.engine_(target=self, mol=M, name=sysname, pdb=pdbpath, mol2=mol2path, **engine_args)
File "/Users/jeffreywagner/conda/envs/forcebalance-test/lib/python3.9/site-packages/forcebalance-1.9.4-py3.9-macosx-10.9-x86_64.egg/forcebalance/smirnoffio.py", line 265, in __init__
super(SMIRNOFF,self).__init__(name=name, **kwargs)
File "/Users/jeffreywagner/conda/envs/forcebalance-test/lib/python3.9/site-packages/forcebalance-1.9.4-py3.9-macosx-10.9-x86_64.egg/forcebalance/openmmio.py", line 626, in __init__
super(OpenMM,self).__init__(name=name, **kwargs)
File "/Users/jeffreywagner/conda/envs/forcebalance-test/lib/python3.9/site-packages/forcebalance-1.9.4-py3.9-macosx-10.9-x86_64.egg/forcebalance/engine.py", line 80, in __init__
self.prepare(**kwargs)
File "/Users/jeffreywagner/conda/envs/forcebalance-test/lib/python3.9/site-packages/forcebalance-1.9.4-py3.9-macosx-10.9-x86_64.egg/forcebalance/smirnoffio.py", line 443, in prepare
self.xyz_omms.append((positions, box))
File "/Users/jeffreywagner/conda/envs/forcebalance-test/lib/python3.9/site-packages/openmm/unit/quantity.py", line 773, in append
raise TypeError("Cannot append item without units into list with units")
TypeError: Cannot append item without units into list with units
Author
|
I didn't have time to dive deep into this bug so I didn't try study022. I tried the tutorial04 in openff-evaluator and that scripts runs without raising error but the result is not fully correct. according to Originally posted by @mattwthompson in openforcefield/openff-evaluator#482 (comment) There are probably many more fixes necessary to make forcebalance work properly with evaluator 0.4.1 and openff-toolkit 0.11.* |
j-wags
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Feb 1, 2023
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Thanks @wenyan4work - It took me a while but I got this test running on my dinky laptop [1]. I reproduced the error in #276 and verified that this PR fixes it. Thanks for your patience!
[1] The key to getting this running in a reasonable amount of time on a GPU-less computer is to turn steps_per_iteration in these lines down to something like 5000. Since this is just a technical error instead of a numerical issue, I think this is sufficient to say I reproduced the bug and this patch fixes it.
Owner
|
Thank you! I'll merge this now, so that we have it for ForceBalance v1.9.5. |
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the unit system of openff-evaluator 0.3.9 has been changed to openff-units based on pint. So this simple fix is necessary.
Tested to work on openff-evaluator 0.4.1 / tutorial04
this PR fixes #276