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Tutorial 1 - Lennard-Jones #3881

Merged
merged 49 commits into from
Sep 30, 2020
Merged

Tutorial 1 - Lennard-Jones #3881

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7128010
change indexing in the sampling loop
schlaicha Aug 31, 2020
a571818
omit default value in for loop
Sep 3, 2020
0999091
Add a first exercise to tutorial01
Sep 3, 2020
72f7550
Merge branch 'python' into tutorial01_lj
schlaicha Sep 3, 2020
61abad6
Improve links to doc
Sep 3, 2020
bb79a90
Convert irrelevant code cell to hint in markdown
Sep 3, 2020
405014d
Exercise thermostat langevin
Sep 3, 2020
364c7c0
WIP: Add exercise to create particles
Sep 3, 2020
d3f8514
Init notes for tutor file
Sep 3, 2020
254812d
LJ Tutorial: Tutor's notes
RudolfWeeber Sep 4, 2020
02013c5
Unify notation
Sep 4, 2020
d900324
Reformat alternative solution to avoid convertion to python code
Sep 4, 2020
1c5e908
Replace force_cap warmup by steepest descent
Sep 4, 2020
e8cb3b5
More points for tutors
Sep 4, 2020
7562149
Remove alternative solution path
Sep 4, 2020
1c2f127
Fix typo
schlaicha Sep 4, 2020
e7a961b
Fix typo
schlaicha Sep 4, 2020
e42007c
Fix typo
schlaicha Sep 4, 2020
426f8e6
Use ESPResSo in favor of Espresso
schlaicha Sep 4, 2020
4ba0765
Use steepest descent integrator
Sep 4, 2020
5104cdf
Improve overlap removal
Sep 9, 2020
0ed1854
Fix energy minimization
Sep 14, 2020
356b7fa
Rewrite main integration loop
Sep 14, 2020
41d1e2d
Remove standard deviation estimate
Sep 14, 2020
5c470b6
(Re-)add RDF calculation
Sep 14, 2020
697bda0
Make RDF comparison work
Sep 23, 2020
c9e2817
Remove MSD and redundant parts
Sep 23, 2020
0d7726a
Remove obsolete test for global standard error
Sep 23, 2020
e259d6e
Remove obsolete statement about the core in C
Sep 23, 2020
97a4602
Improve testing
Sep 24, 2020
394b27c
Merge branch 'python' into tutorial01_lj
schlaicha Sep 24, 2020
32836a8
Refine tests
Sep 24, 2020
6f172c0
formatting change
Sep 24, 2020
e350433
Adapt naming convention
schlaicha Sep 28, 2020
0daa839
Adapt to PEP naming convention
schlaicha Sep 28, 2020
f270798
Remove energy convergence criterion for steepest descent
schlaicha Sep 28, 2020
14202ce
Add more explanation for initial force calculation
schlaicha Sep 28, 2020
2c3f041
Add forgotten link
schlaicha Sep 28, 2020
fecbdaf
Fix TOC to pass CI tests
schlaicha Sep 28, 2020
a537af4
Update doc/tutorials/01-lennard_jones/NotesForTutor.md
schlaicha Sep 30, 2020
01db3ef
Apply suggestions from code review
schlaicha Sep 30, 2020
2e0daad
Apply suggestions from code review
schlaicha Sep 30, 2020
675353c
Formatting
jngrad Sep 30, 2020
d358649
Remove custom Python kernel metadata
jngrad Sep 30, 2020
4e7ee29
Remove LaTeX plugin metadata
jngrad Sep 30, 2020
6426cbf
Fix overlapping legends in matplotlib plot
jngrad Sep 30, 2020
d6b4d97
Fix handling of matplotlib in hidden cells
jngrad Sep 30, 2020
b5dd583
Add plot legend
jngrad Sep 30, 2020
d8b8a8f
Merge branch 'python' into tutorial01_lj
kodiakhq[bot] Sep 30, 2020
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