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472dc1c
check html window
Apr 13, 2021
35420ba
change index.rst of branch devel
Apr 14, 2021
cabe8ba
Merge tag 'v2.0.0.a0' into devel
Apr 14, 2021
8ac43e5
Merge branch 'devel' of https://github.com/deepmodeling/deepmd-kit int…
Apr 14, 2021
36adf85
Re-structured doc
Apr 14, 2021
f62e5ce
Re-structured Doc
Apr 14, 2021
8dc480b
Re-structured Doc
Apr 14, 2021
f7c000f
Re-structured Doc
Apr 14, 2021
6e92359
Re-structured Doc
Apr 14, 2021
d2bd1ea
Re-structured Doc
Apr 14, 2021
0a994c2
Re-structured Doc
Apr 15, 2021
420822c
Re-structured Doc
Apr 15, 2021
ba1bc7b
Set theme jekyll-theme-cayman
tuoping Apr 15, 2021
dfe2193
Create index.md
tuoping Apr 15, 2021
2c46ffd
Re-structured Doc
Apr 15, 2021
25cf687
Re-structured Doc
Apr 15, 2021
484c9d9
Re-structured index.rst and seperated install.rst into 3 files;
Apr 16, 2021
1a55647
Same as before
Apr 16, 2021
a65a50f
Edited license.rst and credits.rst
Apr 19, 2021
bc68f89
same as before
Apr 19, 2021
fcc85a7
Modified pair-style-deepmd syntax part
Apr 20, 2021
38f713b
Fixed the collapsed table in getting-started#prepare-data by adding e…
Apr 20, 2021
19ff8a3
Added sphinx-markdown-table in requirements.txt
Apr 20, 2021
32e4a68
modified getting-started.md compared with deepmodeling/deepmd-kit/devel
Apr 20, 2021
52a182e
Modification after Merge
Apr 21, 2021
eae6661
modified superlinks in getting-started.md
Apr 21, 2021
328df53
same
Apr 21, 2021
35f46fb
Something is imperfect with the url. I can't link to #section in anot…
Apr 21, 2021
aa00bc8
changed LICENSE to url; deleted whatsnew, application-examples and kn…
Apr 22, 2021
df02d99
Merge remote-tracking branch 'refs/remotes/origin/devel' into devel
Apr 22, 2021
45956f6
corrected subsection links
Apr 22, 2021
c626b55
testing external section links
Apr 22, 2021
2f7c49c
same
Apr 22, 2021
940d08d
changed all the superlinks in getting-started.md from markdown format…
Apr 22, 2021
563a705
same
Apr 22, 2021
a28afd5
Update doc/conf.py
tuoping Apr 22, 2021
a9619bb
Update doc/getting-started.md
tuoping Apr 22, 2021
b38d538
added some descriptor/scripts in api.rst; Changed the user names of c…
Apr 22, 2021
3bed245
Merge branch 'devel' of https://github.com/tuoping/deepmd-kit into devel
Apr 22, 2021
006e7d1
Changed parser from recommonmark to myst, so the header-anchors in ge…
Apr 24, 2021
40c6ae2
add myst-parser in requirements
Apr 24, 2021
f0bdb8b
move doc dependence packages from requirements.txt to setup.py
Apr 25, 2021
dfc0484
changed contributor's order in credits.rst
Apr 26, 2021
c60523f
change whatsnew
Apr 26, 2021
fa48beb
change highlights in 2.0 in README.md
Apr 27, 2021
72c2c0e
Update README.md
tuoping Apr 27, 2021
46e843b
Merge remote-tracking branch 'TP/devel' into devel
Apr 27, 2021
ebb2419
Add CONTRIBUTING.md
Apr 29, 2021
990f1cb
Fixed some minor mistakes.
Apr 29, 2021
18c00a2
changed document for training inputs from train-input.rst to train-in…
Apr 29, 2021
fe084a3
Fixed links under "highlights in kit2.0.0".
tuoping Apr 30, 2021
9c2115e
Checked all the links, and made sure they work both in markdown mode …
May 3, 2021
74269c0
Sorry, fixed a broken link in CONTRIBUTING.md.
May 3, 2021
2bd50a6
Asigned language 'bash' for codes in CONTRIBUTING.md; Corrected a typ…
May 6, 2021
ea0acb7
Update CONTRIBUTING.md
amcadmus May 8, 2021
671be8d
fix typo in README.md
amcadmus May 8, 2021
e7a0589
Update README.md
amcadmus May 8, 2021
3735a8f
Update credits.rst
amcadmus May 8, 2021
25406a6
merge from deepmodeling
May 10, 2021
ad8bf83
Merge branch 'devel' of https://github.com/deepmodeling/deepmd-kit int…
May 10, 2021
383cfa9
Changed entries in troubleshooting/index.md and development/index.md …
May 12, 2021
7daa801
Merge branch 'devel' of https://github.com/tuoping/deepmd-kit into devel
May 12, 2021
e1cda02
Optimized the mkindex function in conf.py
May 12, 2021
d9db26f
Debuged conf.py
May 12, 2021
9d54f35
Itemized presentation in troubleshooting/index.md and development/ind…
May 14, 2021
475a899
Update rcut.md
amcadmus May 14, 2021
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64 changes: 27 additions & 37 deletions doc/conf.py
Original file line number Diff line number Diff line change
Expand Up @@ -15,47 +15,37 @@
import recommonmark
from recommonmark.transform import AutoStructify

def mkindex_troubleshooting():
oldfindex = open("troubleshooting/index.md", "r")
_oldlist = oldfindex.readlines()
oldlist = _oldlist[4:]
def mkindex(dirname):
dirname = dirname + "/"
oldfindex = open(dirname + "index.md", "r")
oldlist = oldfindex.readlines()
oldfindex.close()

newfindex = open("troubleshooting/index.md", "a")
for root, dirs, files in os.walk("./troubleshooting/", topdown=False):
for name in files:
if (name == "index.md"):
continue
if (name[-3:] == ".md"):
longname = "- ["+name[:-3]+"]("+name+")\n"
if (longname not in oldlist):
newfindex.write(longname)

newfindex.close()

def mkindex_development():
oldfindex = open("development/index.md", "r")
_oldlist = oldfindex.readlines()
oldlist = _oldlist[2:]
oldfindex.close()
oldnames = []
for entry in oldlist:
_name = entry[entry.find("(")+1 : entry.find(")")]
oldnames.append(_name)

newfindex = open("development/index.md", "a")
for root, dirs, files in os.walk("./development/", topdown=False):
for name in files:
if (name == "index.md"):
continue
if (name[-3:] == ".md"):
longname = "- ["+name[:-3]+"]("+name+")\n"
if (longname not in oldlist):
newfindex.write(longname)
else:
if (name[-4:] == ".rst"):
longname = "- ["+name[:-4]+"]("+name+")\n"
if (longname not in oldlist):
newfindex.write(longname)
newfindex = open(dirname + "index.md", "a")
for root, dirs, files in os.walk(dirname, topdown=False):
newnames = [name for name in files if name != "index.md" and name not in oldnames]
for name in newnames:
f = open(dirname + name, "r")
_lines = f.readlines()
for _headline in _lines:
_headline = _headline.strip("#")
headline = _headline.strip()
if (len(headline) == 0 or headline[0] == "." or headline[0] == "="):
continue
else:
break
longname = "- ["+headline+"]"+"("+name+")\n"
newfindex.write(longname)


newfindex.close()


# -- Project information -----------------------------------------------------

project = 'DeePMD-kit'
Expand All @@ -76,8 +66,8 @@ def mkindex_development():
# 'sphinx.ext.autosummary'
# ]

mkindex_troubleshooting()
mkindex_development()
mkindex("troubleshooting")
mkindex("development")

extensions = [
"sphinx_rtd_theme",
Expand Down
4 changes: 2 additions & 2 deletions doc/development/index.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Developer Guide

- [coding-conventions](coding-conventions.rst)
- [api](api.rst)
- [API](api.rst)
- [Coding Conventions](coding-conventions.rst)
9 changes: 6 additions & 3 deletions doc/troubleshooting/index.md
Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,9 @@
In consequence of various differences of computers or systems, problems may occur. Some common circumstances are listed as follows.
If other unexpected problems occur, you're welcome to contact us for help.

- [installation](installation.md)
- [md-version-compatibility](md-version-compatibility.md)
- [model-compatability](model-compatability.md)

- [Installation](installation.md)
- [The temperature undulates violently during early stages of MD](md-energy-undulation.md)
- [MD: cannot run LAMMPS after installing a new version of DeePMD-kit](md-version-compatibility.md)
- [Model compatability](model-compatability.md)
- [Do we need to set rcut < half boxsize ?](rcut.md)
5 changes: 5 additions & 0 deletions doc/troubleshooting/md-energy-undulation.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
# The temperature undulates violently during early stages of MD

This is probably because your structure is too far from the equlibrium configuration.

Although, to make sure the potential model is truly accurate, we recommend to check model deviation.
7 changes: 7 additions & 0 deletions doc/troubleshooting/rcut.md
Original file line number Diff line number Diff line change
@@ -0,0 +1,7 @@
# Do we need to set rcut < half boxsize ?

When seeking the neighbors of atom i under periodic boundary condition, deepmd-kit considers all j atoms within cutoff R<sub>cut</sub> from atom i in all mirror cells.

So there is no limitation on the setting of R<sub>cut</sub>.

PS: The reason why some softwares require R<sub>cut</sub> < half boxsize is that they only consider the nearest mirrors from the center cell. Deepmd-kit is totally different from them.