Updates to energy minimization routines #1061

chrisiacovella · 2022-11-12T06:02:27Z

PR Summary:

A few extensions to the existing energy minimization functions for compounds. In particular, changes were made to support additional OpenBabel features.

General operations:
1- After energy minimization, shift the Compound to the original COM; this behavior can be toggled with the shift_com variable. Default behavior will be to shift to the original COM. For example, toggle the shift off via:
dodecane = Alkane(n=12) dodecane.energy_minimize(steps=1000,shift_com=False)

2- Rather than retaining the COM position, the user can specify an "anchor" within the Compound. After energy minimization, the Compound is shifted such that the position (or COM as the case may be) of the anchor is unchanged. Example usage:

dodecane = Alkane(n=12) anchor_point = dodecane.labels['chain'].labels['CH3'][0] dodecane.energy_minimize(steps=10000,shift_com=False, anchor=anchor_point)

OpenBabel specific:
1- Energy minimization call will accept a list of Compounds whose positions will be fixed during energy minimization. Note, positions are not truly fixed, but have a strong harmonic energy term associated between the particle and its original position. This can apply to a Compound at any level, as the code will loop over all successors to fix any particle in the Compound. Example usage:

dodecane = Alkane(n=12) point0 = dodecane.labels['chain'].labels['CH3'][0] dodecane.energy_minimize(steps=1000,shift_com=False, fixed_compounds=point0)

Note, can also specify which directions to fix:

dodecane = Alkane(n=12) point0 = dodecane.labels['chain'].labels['CH3'][0] point1 = dodecane.labels['chain'].labels['monomer'][0] fixed = [ [ point0, (True, True, True)], [ point1, (False, False, True)] ] dodecane.energy_minimize(steps=1000,shift_com=False, fixed_compounds=fixed)

2- Distance constraints...a list of Compound pairs and the constrained distance. This must be between Compounds that represent atoms; cannot be between Compounds which contain other Compounds or multiple particles. The code will check to ensure only are applying to Compounds without children. Example usage:

dodecane = Alkane(n=12) point0 = dodecane.labels['chain'].labels['CH3'][0].labels['C'][0] point1 = dodecane.labels['chain'].labels['CH3'][1].labels['C'][0] dodecane.energy_minimize(steps=10000,shift_com=False, distance_constraints=[ [(point0, point1), 0.5 ]])

3- Will accept a list of Compounds to ignore during energy minimization. These Compounds will not have any parameters assigned during energy minimization from the force field, and will have their positions "fixed" (as described above). Note, interactions for ignore particles can be set by a user, e.g., via a distance constraint. This can apply to a Compound at any level, as the code will loop over all successors to fix any particle in the Compound. Example usage:

dodecane = Alkane(n=12) helium = mb.Compound(pos=dodecane.labels['chain'].labels['monomer'][5].pos+[0.0,0.0,0.05], name='He', element='He') dodecane.add(helium) dodecane.energy_minimize(shift_com=False, ignore_compounds=helium)

Can combine ignore_compounds with distance constraints, to, e.g., allow the COM of several atoms to be tied to the position of an associated coarse-grained bead.

PR Checklist

Includes appropriate unit test(s)
Appropriate docstring(s) are added/updated
Code is (approximately) PEP8 compliant
Issue(s) raised/addressed?

…straints, with various checking/parsing of input

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codecov · 2022-11-12T06:21:12Z

Codecov Report

Attention: Patch coverage is 90.47619% with 10 lines in your changes missing coverage. Please review.

Project coverage is 90.69%. Comparing base (d051e79) to head (2a2d467).
Report is 141 commits behind head on main.

Files with missing lines	Patch %	Lines
mbuild/compound.py	90.47%	10 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1061      +/-   ##
==========================================
- Coverage   90.69%   90.69%   -0.01%     
==========================================
  Files          57       57              
  Lines        5397     5500     +103     
==========================================
+ Hits         4895     4988      +93     
- Misses        502      512      +10

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chrisiacovella · 2022-11-18T21:41:33Z

I put together two notebooks demonstrating the usage (these will eventually be merged into the main tutorials). https://github.com/chrisiacovella/mbuild_energy_minimization

CalCraven

Looking good, such an exciting feature!

mbuild/compound.py

mbuild/tests/test_compound.py

fixing typo Co-authored-by: CalCraven <54594941+CalCraven@users.noreply.github.com>

fix more typos in comments Co-authored-by: CalCraven <54594941+CalCraven@users.noreply.github.com>

…e tests of errors

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mbuild/compound.py

daico007

Looks good, only a few comments to shorten the codes. The logic looks fine, the sanity checks can be a bit disruptive of the flow (may be have those as a helper method?).

mbuild/compound.py

daico007 · 2022-11-30T20:17:49Z

mbuild/compound.py

+                if len(fixed_compounds) == 2:
+                    # At this point in the code, we only want to see if the second element in the list
+                    # is a Compound. If it is a Compound we don't need to santize the input.
+                    # If it is not a Compound, (e.g., if the list passed is of the form  [Compound, [True, true,True]],


Suggested change

# If it is not a Compound, (e.g., if the list passed is of the form [Compound, [True, true,True]],

# If it is not a Compound, (e.g., if the list passed is of the form [Compound, [bool, bool, bool]],

mbuild/compound.py

CalCraven

LGTM! A few minor suggestions I'm seconding from @daico007.

mbuild/compound.py

CalCraven · 2022-12-01T14:16:26Z

mbuild/compound.py

+            An individual Compound or list of Compounds that will have their
+            position fixed during energy minimization. Note, positions are fixed
+            using a restraining potential and thus may change slightly.
+            Position fixing will apply to all Particles (i.e., atoms) that exist


Are we capitalizing or not capitalizing the word particle? I would maybe suggest no, since we really do want people to understand that these are really Compounds.

mbuild/compound.py

CalCraven · 2022-12-01T14:30:07Z

mbuild/compound.py

+                        if id(p1) == id(particle):
+                            pid = index
+                            if all_true == True:
+                                ob_constraints.AddAtomConstraint(pid)


I think this get's fixed by the suggest made hy @daico007 in line 2486 to 2498.

… additional tests.

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chrisiacovella · 2022-12-02T21:23:25Z

I think I got all the comments and suggestions incorporated.

daico007

Only one final bit and everything LGTM!

daico007 · 2022-12-05T17:26:34Z

mbuild/compound.py

+                        elif dims[0] == True:
+                            ob_constraints.AddAtomXConstraint(pid)
+                        elif dims[1] == True:
+                            ob_constraints.AddAtomYConstraint(pid)
+                        elif dims[2] == True:
+                            ob_constraints.AddAtomZConstraint(pid)


Suggested change

elif dims[0] == True:

ob_constraints.AddAtomXConstraint(pid)

elif dims[1] == True:

ob_constraints.AddAtomYConstraint(pid)

elif dims[2] == True:

ob_constraints.AddAtomZConstraint(pid)

else:

if dims[0] == True:

ob_constraints.AddAtomXConstraint(pid)

if dims[1] == True:

ob_constraints.AddAtomYConstraint(pid)

if dims[2] == True:

ob_constraints.AddAtomZConstraint(pid)

Unless they are mutually exclusive, I think they should belong to individual if block

Christopher Iacovella and others added 4 commits October 31, 2022 12:12

add COM shifting and anchoring

ebe51d9

added code to set fixed compounds, ignored compounds and distance con…

5f01cae

…straints, with various checking/parsing of input

added in tests and fixed input parsing

cc5d7a2

Merge branch 'mosdef-hub:main' into e_min

a310818

chrisiacovella added the enhancement label Nov 12, 2022

[pre-commit.ci] auto fixes from pre-commit.com hooks

38b6f8c

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chrisiacovella requested a review from CalCraven November 12, 2022 06:04

CalCraven requested changes Nov 21, 2022

View reviewed changes

chrisiacovella and others added 5 commits November 22, 2022 16:51

Update mbuild/compound.py

c516764

fixing typo Co-authored-by: CalCraven <54594941+CalCraven@users.noreply.github.com>

Update mbuild/compound.py

a74f38b

fixing typo Co-authored-by: CalCraven <54594941+CalCraven@users.noreply.github.com>

Update mbuild/compound.py

8fbe4f6

fix more typos in comments Co-authored-by: CalCraven <54594941+CalCraven@users.noreply.github.com>

updated energy minimization functions based on feedback and added mor…

74fd2ea

…e tests of errors

[pre-commit.ci] auto fixes from pre-commit.com hooks

5ac9576

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chrisiacovella requested a review from CalCraven November 30, 2022 19:03

Merge branch 'main' into e_min

c62f707

chrisiacovella requested a review from daico007 November 30, 2022 19:04

daico007 reviewed Nov 30, 2022

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daico007 reviewed Nov 30, 2022

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CalCraven approved these changes Dec 1, 2022

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Christopher Iacovella and others added 5 commits December 1, 2022 13:43

particle_idx list added to speed index calculation

d179ad0

addressed comments, streamlined input validation/checking, added some…

fa99c89

… additional tests.

not sure how I managed to conflict my own branch.

374301e

[pre-commit.ci] auto fixes from pre-commit.com hooks

ef76dd5

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Merge branch 'main' into e_min

3da22a1

chrisiacovella requested a review from daico007 December 2, 2022 21:23

daico007 reviewed Dec 5, 2022

View reviewed changes

addressed comment missed about constraining individual dimensions

2a2d467

chrisiacovella requested a review from daico007 December 5, 2022 18:00

daico007 approved these changes Dec 5, 2022

View reviewed changes

daico007 merged commit ee91caa into mosdef-hub:main Dec 5, 2022

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Updates to energy minimization routines #1061

Updates to energy minimization routines #1061

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daico007 Dec 5, 2022

	# If it is not a Compound, (e.g., if the list passed is of the form [Compound, [True, true,True]],
	# If it is not a Compound, (e.g., if the list passed is of the form [Compound, [bool, bool, bool]],

Updates to energy minimization routines #1061

Updates to energy minimization routines #1061

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chrisiacovella commented Nov 12, 2022 • edited Loading

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