Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Ase interface - add stress & tested OTF parser #107

Merged
merged 53 commits into from
Nov 24, 2019
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
53 commits
Select commit Hold shift + click to select a range
ee564f3
fix a bug with 'update'
YuuuXie Oct 14, 2019
6843780
add Langevin MD
YuuuXie Oct 14, 2019
cf60e47
Merge branch 'master' of https://github.com/mir-group/flare into ase_…
YuuuXie Oct 16, 2019
735579e
ASE output tested with otf_parser
YuuuXie Oct 17, 2019
53903d1
ASE output tested with otf_parser
YuuuXie Oct 17, 2019
e5e6079
Merge branch 'master' of https://github.com/mir-group/flare into ase_…
YuuuXie Oct 17, 2019
08c1eb8
Delete .DS_Store
YuuuXie Oct 17, 2019
19fd43d
fix a numerical err of mgp
YuuuXie Oct 17, 2019
14832b5
Merge branch 'ase_interface' of https://github.com/mir-group/flare in…
YuuuXie Oct 17, 2019
a3be05b
Merge branch 'master' of https://github.com/mir-group/flare into ase_…
YuuuXie Oct 21, 2019
b4b5d9c
fix otf stds
YuuuXie Oct 27, 2019
44d93ce
merge with yu/parallel branch
YuuuXie Oct 27, 2019
9153b79
delete 'print' line
YuuuXie Oct 27, 2019
117744c
fix target_atoms with is_std_in_bound
YuuuXie Oct 27, 2019
1833fcb
add mgp stress
YuuuXie Oct 28, 2019
b366c98
add mgp stress to ase calculator
YuuuXie Oct 28, 2019
f629b01
fix f, v, vir order
YuuuXie Oct 28, 2019
4d09207
modify for tutorial
YuuuXie Oct 28, 2019
f845eed
add OTF tutorial of Al from test_OTF_qe.py
Oct 28, 2019
e2be1ae
Merge branch 'master' of https://github.com/mir-group/flare into ase_…
YuuuXie Oct 28, 2019
9af0448
Merge branch 'master' of https://github.com/mir-group/flare into ase_…
Oct 28, 2019
85d249a
Merge branch 'master' of https://github.com/mir-group/flare into ase_…
YuuuXie Oct 30, 2019
9c686f8
fix ase calculator stress
YuuuXie Oct 30, 2019
f64c562
Merge branch 'ase_interface' of https://github.com/mir-group/flare in…
YuuuXie Oct 30, 2019
dbc604b
MGP stress (in ASE) passed unit test
YuuuXie Oct 31, 2019
5f84cbc
fix small bugs
YuuuXie Oct 31, 2019
c3ad422
fix bug of ase logger
YuuuXie Oct 31, 2019
d5c83e2
add restart method
YuuuXie Nov 3, 2019
f38d3b5
logger write added_atoms.dat
YuuuXie Nov 3, 2019
f2aa7a0
tested restart
YuuuXie Nov 3, 2019
f2ad51f
add rescaling temperature
YuuuXie Nov 3, 2019
fff5086
fix add atom log
YuuuXie Nov 3, 2019
141a2d1
small fix of write_lmp_file
YuuuXie Nov 3, 2019
334b4a0
add tutorial of diamond training
YuuuXie Nov 4, 2019
2bd9af9
Merge branch 'ase_interface' of https://github.com/mir-group/flare in…
YuuuXie Nov 4, 2019
c288cda
add ase tutorial
YuuuXie Nov 4, 2019
00910e0
remove 'fixture'
YuuuXie Nov 4, 2019
ed169fc
Merge branch 'master' of https://github.com/mir-group/flare into ase_…
YuuuXie Nov 6, 2019
b401058
Merge branch 'master' of https://github.com/mir-group/flare into ase_…
YuuuXie Nov 22, 2019
364dbdd
add docstring
YuuuXie Nov 22, 2019
4eee436
change angle to cos_angle
YuuuXie Nov 22, 2019
df33b4a
add docstring
YuuuXie Nov 22, 2019
353e195
change angle to cos_angle
YuuuXie Nov 22, 2019
4679ae2
change rtol
YuuuXie Nov 22, 2019
7d35078
remove mass_dict
YuuuXie Nov 22, 2019
e2f6300
add docstring
YuuuXie Nov 22, 2019
ced63ab
fix build_bond_struc for 2-b only
YuuuXie Nov 23, 2019
e252060
adapt with changed lmp
YuuuXie Nov 23, 2019
ca42286
change lmp
YuuuXie Nov 23, 2019
47555ef
change qe setting
YuuuXie Nov 23, 2019
c13e213
change docstring
YuuuXie Nov 24, 2019
9e0f59a
Merge branch 'ase_interface' of https://github.com/mir-group/flare in…
YuuuXie Nov 24, 2019
1650142
Merge branch 'master' of https://github.com/mir-group/flare into ase_…
YuuuXie Nov 24, 2019
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
Binary file modified docs/build/doctrees/environment.pickle
Binary file not shown.
Binary file modified docs/build/doctrees/flare/env.doctree
Binary file not shown.
Binary file modified docs/build/doctrees/flare/gp.doctree
Binary file not shown.
Binary file modified docs/build/doctrees/flare/struc.doctree
Binary file not shown.
Binary file modified docs/build/doctrees/tutorials/al.doctree
Binary file not shown.
2 changes: 1 addition & 1 deletion docs/build/html/.buildinfo
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: c57d036cde002c820567db10171273a1
config: 6eae062ba94a7ff55a48f6ce3bd8a81b
tags: 645f666f9bcd5a90fca523b33c5a78b7
92 changes: 90 additions & 2 deletions docs/build/html/_static/basic.css
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
*
* Sphinx stylesheet -- basic theme.
*
* :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
* :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
Expand Down Expand Up @@ -231,6 +231,16 @@ a.headerlink {
visibility: hidden;
}

a.brackets:before,
span.brackets > a:before{
content: "[";
}

a.brackets:after,
span.brackets > a:after {
content: "]";
}

h1:hover > a.headerlink,
h2:hover > a.headerlink,
h3:hover > a.headerlink,
Expand Down Expand Up @@ -279,6 +289,12 @@ img.align-center, .figure.align-center, object.align-center {
margin-right: auto;
}

img.align-default, .figure.align-default {
display: block;
margin-left: auto;
margin-right: auto;
}

.align-left {
text-align: left;
}
Expand All @@ -287,6 +303,10 @@ img.align-center, .figure.align-center, object.align-center {
text-align: center;
}

.align-default {
text-align: center;
}

.align-right {
text-align: right;
}
Expand Down Expand Up @@ -358,6 +378,11 @@ table.align-center {
margin-right: auto;
}

table.align-default {
margin-left: auto;
margin-right: auto;
}

table caption span.caption-number {
font-style: italic;
}
Expand Down Expand Up @@ -391,6 +416,16 @@ table.citation td {
border-bottom: none;
}

th > p:first-child,
td > p:first-child {
margin-top: 0px;
}

th > p:last-child,
td > p:last-child {
margin-bottom: 0px;
}

/* -- figures --------------------------------------------------------------- */

div.figure {
Expand Down Expand Up @@ -460,11 +495,58 @@ ol.upperroman {
list-style: upper-roman;
}

li > p:first-child {
margin-top: 0px;
}

li > p:last-child {
margin-bottom: 0px;
}

dl.footnote > dt,
dl.citation > dt {
float: left;
}

dl.footnote > dd,
dl.citation > dd {
margin-bottom: 0em;
}

dl.footnote > dd:after,
dl.citation > dd:after {
content: "";
clear: both;
}

dl.field-list {
display: grid;
grid-template-columns: fit-content(30%) auto;
}

dl.field-list > dt {
font-weight: bold;
word-break: break-word;
padding-left: 0.5em;
padding-right: 5px;
}

dl.field-list > dt:after {
content: ":";
}

dl.field-list > dd {
padding-left: 0.5em;
margin-top: 0em;
margin-left: 0em;
margin-bottom: 0em;
}

dl {
margin-bottom: 15px;
}

dd p {
dd > p:first-child {
margin-top: 0px;
}

Expand Down Expand Up @@ -537,6 +619,12 @@ dl.glossary dt {
font-style: oblique;
}

.classifier:before {
font-style: normal;
margin: 0.5em;
content: ":";
}

abbr, acronym {
border-bottom: dotted 1px;
cursor: help;
Expand Down
7 changes: 3 additions & 4 deletions docs/build/html/_static/doctools.js
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
*
* Sphinx JavaScript utilities for all documentation.
*
* :copyright: Copyright 2007-2018 by the Sphinx team, see AUTHORS.
* :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
* :license: BSD, see LICENSE for details.
*
*/
Expand Down Expand Up @@ -87,14 +87,13 @@ jQuery.fn.highlightText = function(text, className) {
node.nextSibling));
node.nodeValue = val.substr(0, pos);
if (isInSVG) {
var bbox = span.getBBox();
var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
rect.x.baseVal.value = bbox.x;
var bbox = node.parentElement.getBBox();
rect.x.baseVal.value = bbox.x;
rect.y.baseVal.value = bbox.y;
rect.width.baseVal.value = bbox.width;
rect.height.baseVal.value = bbox.height;
rect.setAttribute('class', className);
var parentOfText = node.parentNode.parentNode;
addItems.push({
"parent": node.parentNode,
"target": rect});
Expand Down
Loading