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Tutorials #38

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Sep 29, 2023
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37c7a84
rename first tutorial to basics
marjanalbooyeh Sep 5, 2023
99d7f02
edit text
marjanalbooyeh Sep 5, 2023
cc59edf
edit overview wording
marjanalbooyeh Sep 6, 2023
18e239d
rename files
marjanalbooyeh Sep 6, 2023
ab174cf
move advanced topics to tutorial 2
marjanalbooyeh Sep 6, 2023
e1d6671
introduce additional features with examples
marjanalbooyeh Sep 6, 2023
3d4ff2a
edit wording on system initialization
marjanalbooyeh Sep 7, 2023
e3d4800
explain scaling in system
marjanalbooyeh Sep 7, 2023
41bc987
update simulation text
marjanalbooyeh Sep 7, 2023
52697ad
add upate volume example
marjanalbooyeh Sep 7, 2023
322e505
add visualization
marjanalbooyeh Sep 7, 2023
6e48990
refactor sections in advanced tutorial
marjanalbooyeh Sep 7, 2023
79ba527
add content to simulation
marjanalbooyeh Sep 7, 2023
3922e0c
add information about logging
marjanalbooyeh Sep 7, 2023
dc93b98
minor edits
marjanalbooyeh Sep 7, 2023
7e08964
add example code for resume simulation
marjanalbooyeh Sep 8, 2023
38d814e
change mol name only if ff is provided
marjanalbooyeh Sep 8, 2023
86f9c44
testing cg tutorial code
marjanalbooyeh Sep 8, 2023
f004ca1
coarse graining overview
marjanalbooyeh Sep 11, 2023
a77a44b
structuring the sections
marjanalbooyeh Sep 11, 2023
ee4db46
Grammar fixes for tutorial 1
RainierBarrett Sep 11, 2023
cb54890
Grammar fixes for tutorial 2
RainierBarrett Sep 11, 2023
3b58d7f
Grammar fixes for tutorial 3
RainierBarrett Sep 11, 2023
b906484
finish the cg steps guide
marjanalbooyeh Sep 11, 2023
a315881
install gmso from source
marjanalbooyeh Sep 12, 2023
22623db
update code based on new gmso changes
marjanalbooyeh Sep 12, 2023
a2b5ef7
add gmso dependencies
marjanalbooyeh Sep 13, 2023
1d4d123
add missing .git from path
marjanalbooyeh Sep 13, 2023
4d66277
remove unyt version
marjanalbooyeh Sep 13, 2023
c7cd23d
unpin unyt version
marjanalbooyeh Sep 13, 2023
1cd1713
address some comments on tutorial #1
marjanalbooyeh Sep 14, 2023
12c2ebf
add a note about expanding factor in pack
marjanalbooyeh Sep 14, 2023
c9fcc55
merge changes from main
marjanalbooyeh Sep 15, 2023
ba11b02
minor edits on text and code
marjanalbooyeh Sep 18, 2023
5f1d5dc
add links to forcefields.py
marjanalbooyeh Sep 18, 2023
1dd755b
add a note about in-place changes of CG
marjanalbooyeh Sep 18, 2023
0ee6ddc
add .pickle to gitignore
marjanalbooyeh Sep 18, 2023
d6ced9a
Merge branch 'main' into tutorials
marjanalbooyeh Sep 18, 2023
50b3944
add fresnel to environment yaml files
marjanalbooyeh Sep 18, 2023
f543ce3
add fresnel visualizer to tutorial 1
marjanalbooyeh Sep 18, 2023
2059163
Merge branch 'main' into tutorials
marjanalbooyeh Sep 22, 2023
c69617a
add some text about thermostat
marjanalbooyeh Sep 22, 2023
a315561
minor changes on tutorial 2 and 3
marjanalbooyeh Sep 22, 2023
a2fcd3d
Merge branch 'cmelab:main' into tutorials
marjanalbooyeh Sep 29, 2023
8c3d92e
use apply_forcefield in tutorial 1
marjanalbooyeh Sep 29, 2023
a3afd19
update tutorial 1
marjanalbooyeh Sep 29, 2023
b4e2159
update the text and system apply ff
marjanalbooyeh Sep 29, 2023
4f714ac
use apply_forcefield in tutorial 3
marjanalbooyeh Sep 29, 2023
eac5fa9
remove old welding tutorial
marjanalbooyeh Sep 29, 2023
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1 change: 1 addition & 0 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ __pycache__/
# Tutorial/test files
*.gsd
*.txt
*.pickle

# Distribution / packaging
.Python
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1 change: 1 addition & 0 deletions environment-cpu.yml
Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ dependencies:
- symengine
- python-symengine
- sympy
- fresnel
- pip:
- git+https://github.com/mosdef-hub/gmso.git@main
- git+https://github.com/cmelab/cmeutils.git@master
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1 change: 1 addition & 0 deletions environment-gpu.yml
Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ dependencies:
- symengine
- python-symengine
- sympy
- fresnel
- pip:
- git+https://github.com/mosdef-hub/gmso.git@main
- git+https://github.com/cmelab/cmeutils.git@master
Expand Down
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