Add HOOMD Supports #696

daico007 · 2022-10-05T07:30:23Z

[WIP] Start adding supports for HOOMD. Goal is to convert a typed GMSO Topology to a HOOMD state (gsd snapshot) and all the required forces.

carried over code from gsd writer, instead of saving the gsd file, just return the snapshot object

lgtm-com · 2022-10-11T07:05:54Z

This pull request introduces 3 alerts when merging 49f62ff into 691371c - view on LGTM.com

new alerts:

2 for Unused import
1 for Except block handles 'BaseException'

…t_hoomd_sim

lgtm-com · 2022-10-11T16:24:24Z

This pull request introduces 3 alerts when merging 1486fd0 into bc557dd - view on LGTM.com

new alerts:

2 for Unused import
1 for Except block handles 'BaseException'

codecov · 2022-10-11T16:28:05Z

Codecov Report

Patch coverage: 90.78% and project coverage change: -0.27 ⚠️

Comparison is base (c735cc3) 92.27% compared to head (bc51366) 92.01%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #696      +/-   ##
==========================================
- Coverage   92.27%   92.01%   -0.27%     
==========================================
  Files          65       66       +1     
  Lines        5890     6336     +446     
==========================================
+ Hits         5435     5830     +395     
- Misses        455      506      +51

Impacted Files	Coverage Δ
gmso/utils/sorting.py	`86.27% <84.78%> (-13.73%)`	⬇️
gmso/external/convert_hoomd.py	`91.03% <91.03%> (ø)`
gmso/external/__init__.py	`100.00% <100.00%> (ø)`
gmso/external/convert_mbuild.py	`94.73% <100.00%> (+0.03%)`	⬆️
gmso/formats/gsd.py	`100.00% <100.00%> (+1.38%)`	⬆️
gmso/formats/mcf.py	`54.16% <100.00%> (ø)`
gmso/formats/top.py	`88.42% <100.00%> (ø)`
gmso/utils/compatibility.py	`96.66% <100.00%> (+0.11%)`	⬆️
gmso/utils/geometry.py	`88.88% <100.00%> (ø)`
gmso/utils/io.py	`96.82% <100.00%> (+0.27%)`	⬆️

... and 2 files with indirect coverage changes

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lgtm-com · 2022-10-16T07:20:23Z

This pull request introduces 3 alerts when merging b682255 into bc557dd - view on LGTM.com

new alerts:

2 for Unused import
1 for Except block handles 'BaseException'

lgtm-com · 2022-10-17T21:04:00Z

This pull request introduces 2 alerts when merging 20dc383 into bc557dd - view on LGTM.com

new alerts:

2 for Unused import

Pending refining + better unit conversions

lgtm-com · 2022-10-18T06:43:37Z

This pull request introduces 2 alerts when merging 9b04d30 into bc557dd - view on LGTM.com

new alerts:

2 for Unused import

lgtm-com · 2022-10-21T19:48:51Z

This pull request introduces 2 alerts when merging 54bbd9e into bc557dd - view on LGTM.com

new alerts:

2 for Unused import

…t_hoomd_sim

lgtm-com · 2022-12-07T20:35:31Z

This pull request introduces 2 alerts when merging 61849cc into 6bcdfcc - view on LGTM.com

new alerts:

2 for Unused import

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…t_hoomd_sim

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chrisjonesBSU

I commented a couple questions, and some things to watch out for. I haven't tried using this yet, I'll be sure to do that ASAP.

gmso/external/convert_hoomd.py

chrisjonesBSU · 2023-01-26T21:35:11Z

gmso/external/convert_hoomd.py

+    return angle_forces
+
+
+def _parse_dihedral_forces(top, potential_types, potential_refs, base_units):


In this funciton, do we need to make sure any values for angles are in the correct units, similar to what you're doing in the _parse_angles function?

gmso/external/convert_hoomd.py

chrisjonesBSU · 2023-01-31T17:13:06Z

I tested this out in a notebook. It seems to be working well for methane. See my comments above about making sure we use radians.

I also tried it out with ethane so we have dihedrals, and the performance suffers quite a bit.

import mbuild as mb
import gmso
import forcefield_utilities as ffutils
from gmso.external.convert_hoomd import to_hoomd_forcefield 
from gmso.external.convert_mbuild import from_mbuild
from gmso.parameterization import apply

mol = mb.load("CC", smiles=True)
box = mb.packing.fill_box(compound=mol, n_compounds=20, box=[2,2,2])
oplsaa = ffutils.FoyerFFs().load('oplsaa').to_gmso_ff()
gmso_box = from_mbuild(box)
apply(top=gmso_box, forcefields=oplsaa, identify_connections=True)

forcefield = to_hoomd_forcefield(top=gmso_box)

When I use 40 methane molecules the to_hoomd_forcefield call takes about 200ms to run

When I use 20 ethane molecules the to_hoomd_forcefield call takes takes over 4 minutes to run

The slow down must be somewhere in parsing dihedrals, since methane doesn't contain any.

daico007 · 2023-01-31T17:40:04Z

Good catch! I also just realized the performance issue last night but haven't pinpoint where the bottleneck is. From your comment, I will start with the dihedral type parsing.

chrisjonesBSU · 2023-02-13T18:07:20Z

I think we should implement auto_scale in the same way it's done in create_hoomd_forcefield in mBuild. Has there been any discussion about this that I missed, or is this something that is potentially handled elsewhere in GMSO?

chrisjonesBSU · 2023-02-13T21:44:14Z

I think we should implement auto_scale in the same way it's done in create_hoomd_forcefield in mBuild. Has there been any discussion about this that I missed, or is this something that is potentially handled elsewhere in GMSO?

Also, I can plan on contributing this part of the PR if it is something we want in to_hoomd_forcefield

daico007 · 2023-02-13T22:17:38Z

@chrisjonesBSU please do! I don't think we make any decision about the autoscale stuff and I just forgot about that altogether

…t_hoomd_sim

…into support_hoomd_sim

…t_hoomd_sim

chrisjonesBSU

Looks good. Auto scale seems to be working as expected. What do you think about returning the base_units dict along with the forcefield? This is basically what we do in mbuild's create_hoomd_forcefield.

Also, looks like there are a few commented out lines from when you were troubleshooting things.

I think this is ready after we decide whether or not to include base_units in the return statement.

gmso/external/convert_hoomd.py

chrisjonesBSU

One note to fix the import, I'll push this change real quick, just wanted to document it.

gmso/external/convert_hoomd.py

Make r_cut a requried arguement for to_hoomd_forcefield. Temporarily disable lrc_cache since it's could behave in a weird manners. Fix related issues with the inputs of check_compatibility

gmso/external/convert_hoomd.py

+from gmso.utils.conversions import (
+    convert_opls_to_ryckaert,
+    convert_ryckaert_to_opls,
+)


gmso/utils/io.py

@@ -4,6 +4,7 @@
 import os
 import sys
 import textwrap
+from tempfile import TemporaryFile


gmso/utils/io.py

 except ImportError:
    has_gsd = False

+try:
+    import hoomd


gmso/external/convert_hoomd.py

+from gmso.utils.sorting import (
+    natural_sort,
+    sort_connection_members,
+    sort_member_types,
+)


gmso/utils/compatibility.py

@@ -1,5 +1,8 @@
 """Determine if the parametrized gmso.topology can be written to an engine."""
+from functools import lru_cache


gmso/external/convert_hoomd.py

+from unyt.array import allclose_units
+
+from gmso.core.views import PotentialFilters
+from gmso.exceptions import GMSOError, NotYetImplementedWarning


chrisjonesBSU

LGTM! It seems to be working great. Thanks for working on this @daico007.

daico007 · 2023-04-21T21:02:33Z

Cool, thank you for reviewing @chrisjonesBSU! I will let this sit a bit in case anyone want to drop a comment/review. I will merge this PR early next week.

gmso/external/convert_hoomd.py

…t_hoomd_sim

gmso/tests/test_hoomd.py

+        oplsaa = ffutils.FoyerFFs().load("oplsaa").to_gmso_ff()
+        top = apply(top, oplsaa, remove_untyped=True)
+
+        gmso_snapshot, snapshot_base_units = to_hoomd_snapshot(


gmso/tests/test_hoomd.py

+        oplsaa = ffutils.FoyerFFs().load("oplsaa").to_gmso_ff()
+        top = apply(top, oplsaa, remove_untyped=True)
+
+        gmso_snapshot, snapshot_base_units = to_hoomd_snapshot(


gmso/tests/test_hoomd.py

+        gmso_snapshot, snapshot_base_units = to_hoomd_snapshot(
+            top, base_units=base_units
+        )
+        gmso_forces, forces_base_units = to_hoomd_forcefield(


gmso/tests/test_hoomd.py

+        gmso_snapshot, snapshot_base_units = to_hoomd_snapshot(
+            top, base_units=base_units
+        )
+        gmso_forces, forces_base_units = to_hoomd_forcefield(


Co Quach added 2 commits October 5, 2022 02:27

Method to convert to gsd snapshot

ee8b7e9

carried over code from gsd writer, instead of saving the gsd file, just return the snapshot object

Add scaffold for hoomd forcefield writer

49f62ff

Merge branch 'main' of https://github.com/mosdef-hub/gmso into suppor…

1486fd0

…t_hoomd_sim

fix typo

b682255

Merge branch

20dc383

Add some conversions fucntionalities

9b04d30

Pending refining + better unit conversions

Check point for HOOMD forcefield conversion - units

54bbd9e

daico007 added 2 commits November 7, 2022 11:26

starting work on base_units conversion

4c00063

Merge branch 'main' of https://github.com/mosdef-hub/gmso into suppor…

61849cc

…t_hoomd_sim

daico007 added 3 commits December 12, 2022 11:09

Checkpoint - converting units

43ba657

Merge branch 'main' of https://github.com/mosdef-hub/gmso into suppor…

40e002e

…t_hoomd_sim

add unit conversions for hoomd forcefield

5c98901

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chrisjonesBSU reviewed Jan 26, 2023

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daico007 marked this pull request as ready for review January 26, 2023 22:08

Merge branch 'main' into support_hoomd_sim

90698d8

chrisjonesBSU reviewed Jan 31, 2023

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daico007 and others added 2 commits January 31, 2023 11:40

Merge branch 'main' into support_hoomd_sim

a3c74a7

Address performance issue, add pairs parser, special pair force parsers.

b914f1f

rearrange helper functions, fix bug

417e4b8

bc118 mentioned this pull request Feb 14, 2023

Upgrade to mbuild 0.16.0 after the bug fix affecting the test_gmso_charmm_writer.py unit test is fixed GOMC-WSU/MoSDeF-GOMC#49

Closed

daico007 and others added 7 commits March 9, 2023 06:18

Merge branch 'main' into support_hoomd_sim

0f736db

Merge branch 'main' of https://github.com/mosdef-hub/gmso into suppor…

7ca60c8

…t_hoomd_sim

Merge branch 'support_hoomd_sim' of https://github.com/daico007/gmso …

ba09584

…into support_hoomd_sim

Merge branch 'main' of https://github.com/mosdef-hub/gmso into suppor…

0dfb291

…t_hoomd_sim

initial implementation of auto_scale

c0a2328

working version of auto_scale, may need to do some clean up

9cc18fc

combine auto_scale into validate base units

98be559

chrisjonesBSU reviewed Apr 14, 2023

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Remove commented line, return base_units

19d3e6e

chrisjonesBSU reviewed Apr 17, 2023

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gmso/external/convert_hoomd.py Outdated Show resolved Hide resolved

fix gsd.hoomd import

fd79f68

chrisjonesBSU reviewed Apr 18, 2023

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daico007 added 4 commits April 18, 2023 15:58

Various fixes

5ad3e0d

Make r_cut a requried arguement for to_hoomd_forcefield. Temporarily disable lrc_cache since it's could behave in a weird manners. Fix related issues with the inputs of check_compatibility

update testing files

5fcc7e1

add else clause for sorting

c6220a7

Add auto_scale test and fix bug with auto_scale

f3d22a4

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chrisjonesBSU approved these changes Apr 21, 2023

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daico007 added 2 commits April 24, 2023 09:53

Merge branch 'main' of https://github.com/mosdef-hub/gmso into suppor…

0d89f96

…t_hoomd_sim

add but fix and test for amu base unit

bc51366

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daico007 merged commit 35aa77f into mosdef-hub:main Apr 24, 2023

daico007 mentioned this pull request May 2, 2023

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Add HOOMD Supports #696

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daico007 commented Apr 21, 2023

		return angle_forces


		def _parse_dihedral_forces(top, potential_types, potential_refs, base_units):

		@@ -1,5 +1,8 @@
		"""Determine if the parametrized gmso.topology can be written to an engine."""
		from functools import lru_cache

Add HOOMD Supports #696

Add HOOMD Supports #696

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