add "metal" Unit for Lammps #1098

thangckt · 2023-03-09T05:26:18Z

PR Summary:

add "metal" Unit for Lammps data file

PR Checklist

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

Up

Add smiles string conversion using pybel backend (mosdef-hub#1056)

Trim coordinate_transform.py, new features for spin method (mosdef-hub#1054)

up

Produce n=2 when ports are not capped (mosdef-hub#1069)

update

add support metal Unit Lammps

Add more notes about unit conversions to the hoomd functions (mosdef-hub#1062)

u

up

for more information, see https://pre-commit.ci

mbuild/formats/lammpsdata.py

for more information, see https://pre-commit.ci

codecov · 2023-03-09T05:54:18Z

Codecov Report

Patch coverage: 71.42% and project coverage change: -0.09 ⚠️

Comparison is base (7941ba4) 89.37% compared to head (bed7ec2) 89.29%.

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1098      +/-   ##
==========================================
- Coverage   89.37%   89.29%   -0.09%     
==========================================
  Files          61       61              
  Lines        6164     6173       +9     
==========================================
+ Hits         5509     5512       +3     
- Misses        655      661       +6

Impacted Files	Coverage Δ
mbuild/formats/lammpsdata.py	`93.15% <71.42%> (-1.22%)`	⬇️

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daico007

The PR looks good overall! Only a few comments. Thanks for your contribution!

mbuild/formats/lammpsdata.py

daico007 · 2023-03-09T11:41:23Z

Also, I think it worthwhile to add some unit test for the new unit_styles (if you have one available).

Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>

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Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>

mbuild/formats/lammpsdata.py

daico007 · 2023-03-10T14:35:47Z

Will merge after tests finished running

for more information, see https://pre-commit.ci

thangckt · 2023-05-24T12:03:46Z

Dear Prof. @daico007

can you help me with a letter of recommendation?
I will very much appreciate for that

Thank you so much.

daico007 · 2023-05-24T14:56:41Z

Hi @thangckt, I am currently still a PhD student so I don't know if I have the credential you're looking for, but I would be happy to help in any way that I can.

thangckt · 2023-05-25T09:25:02Z

@daico007
can I reach you on some message platforms?
my fb: thangckt5

thangckt added 30 commits May 13, 2022 00:52

Update lammpsdata.py

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Update lammpsdata.py

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Merge branch 'mosdef-hub:main' into thang

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Merge branch 'mosdef-hub:main' into thang

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Merge branch 'mosdef-hub:main' into thang

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Merge branch 'mosdef-hub:main' into thang

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Merge branch 'mosdef-hub:main' into thang

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Update compound.py

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Update compound.py

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Update compound.py

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Update compound.py

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Merge pull request #1 from mosdef-hub/main

9c051d6

Up

Merge pull request #2 from mosdef-hub/main

b51465f

Add smiles string conversion using pybel backend (mosdef-hub#1056)

Update environment-dev-win.yml

e467c4f

Update environment-dev.yml

0e48431

Update environment.yml

cd88f8c

Merge pull request #3 from mosdef-hub/main

db49817

Trim coordinate_transform.py, new features for spin method (mosdef-hub#1054)

Merge pull request #4 from mosdef-hub/main

b755f09

up

Merge pull request #5 from mosdef-hub/main

9999e5a

Produce n=2 when ports are not capped (mosdef-hub#1069)

Merge pull request #6 from mosdef-hub/main

4b5dada

update

Merge pull request #7 from thangckt/thang

b824580

add support metal Unit Lammps

Merge pull request #8 from mosdef-hub/main

e04541e

Add more notes about unit conversions to the hoomd functions (mosdef-hub#1062)

Merge pull request #9 from mosdef-hub/main

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Update lammpsdata.py

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Merge pull request #10 from mosdef-hub/main

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u

Update lammpsdata.py

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thangckt and others added 5 commits March 9, 2023 14:11

Merge pull request #11 from mosdef-hub/main

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Update lammpsdata.py

ca19625

Merge branch 'main' of https://github.com/thangckt/mbuild

56a263a

Delete oryx-build-commands.txt

f98644b

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

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thangckt and others added 2 commits March 9, 2023 14:39

Update lammpsdata.py

093f0c5

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

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daico007 reviewed Mar 9, 2023

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thangckt and others added 7 commits March 9, 2023 20:58

Update mbuild/formats/lammpsdata.py

54d1f65

Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>

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

9ac0b82

for more information, see https://pre-commit.ci

Update mbuild/formats/lammpsdata.py

b645d36

Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>

Update mbuild/formats/lammpsdata.py

acdd6d0

Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>

Update mbuild/formats/lammpsdata.py

6238215

Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>

Update mbuild/formats/lammpsdata.py

d899f59

Co-authored-by: Co Quach <43968221+daico007@users.noreply.github.com>

Merge branch 'main' into main

9c74d34

thangckt requested a review from daico007 March 10, 2023 14:22

daico007 reviewed Mar 10, 2023

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Update mbuild/formats/lammpsdata.py

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daico007 approved these changes Mar 10, 2023

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daico007 merged commit 00d8c77 into mosdef-hub:main Mar 10, 2023

thangckt mentioned this pull request Mar 14, 2023

Change dihedral phi to integer in lammpsdata.py as required by LAMMPS. #1092

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daico007 mentioned this pull request Mar 14, 2023

Dihedral phi in lammpsdata writer is incorrectly written as a float #1091

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add "metal" Unit for Lammps #1098

add "metal" Unit for Lammps #1098

thangckt commented Mar 9, 2023 •

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thangckt commented May 24, 2023 •

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daico007 commented May 24, 2023

thangckt commented May 25, 2023

add "metal" Unit for Lammps #1098

add "metal" Unit for Lammps #1098

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thangckt commented Mar 9, 2023 • edited Loading

PR Summary:

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