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nomad-lab
analytics-toolkit-tutorials
Commits
9e2690cd
Commit
9e2690cd
authored
Feb 03, 2017
by
Angelo Ziletti
Browse files
Change path to prod-022 (prod-017 was deleted).
parent
91e0df9c
Changes
3
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beaker-notebooks/Embedding.bkr
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beaker-notebooks/LASSO_L0.bkr
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beaker-notebooks/SOAP_similarity.bkr
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...
...
@@ -90,7 +90,7 @@
"
<!--label style=\"color: #20335d;font-weight: 900; font-size: 15pt;\"> Visualizing global similarity</label-->
",
"
</p>
",
"
<hr
style=
\"border-width:2px\"
>
",
"
<p
style=
\"font-size:
15
px
;\"
>
developed by Carl Poelking, Angelo Ziletti, Luca Ghiringhelli and Gábor Csányi [version 2017-0
1-27
]
</p>
",
"
<p
style=
\"font-size:
15
px
;\"
>
developed by Carl Poelking, Angelo Ziletti, Luca Ghiringhelli and Gábor Csányi [version 2017-0
2-03
]
</p>
",
" ",
"
<p
style=
\"font-size:
15
px
;\"
>
<b>
Machine learning method:
</b>
Nonlinear dimensionality reduction based on SOAP similarity kernel
<br>
",
" ",
...
...
@@ -571,8 +571,8 @@
"object": "
<script>
\
nvar
beaker
=
bkHelper
.
getBeakerObject
().
beakerObj
;
\
n
</script>
\n
<script>
\
nvar
run_soap
=
function
()
{
\
n
$
(
\
"
#plot_result_button
\"
).removeClass(
\"
active
\"
).addClass(
\"
disabled
\"
);
\n
get_options();
\n
beaker.evaluate(
\"
cell_soap_run
\"
);
\n
};
\n
\n
var show_hide = function(tag, bt_tag) {
\n
$(
\"
#
\"
+tag).toggle();
\n
$(
\"
#
\"
+bt_tag).toggleClass(
\"
active
\"
);
\n
/*if ($(
\"
#
\"
+bt_tag).attr(
\"
clicked
\"
)) {
\n
$(
\"
#
\"
+bt_tag).css('background-color','lightgray');
\n
$(
\"
#
\"
+bt_tag).attr(
\"
clicked
\"
, 0)
\n
}
\n
else {
\n
$(
\"
#
\"
+bt_tag).css('background-color','red');
\n
$(
\"
#
\"
+bt_tag).attr(
\"
clicked
\"
, 1)
\n
}*/
\n
}
\n\n
var allow = function(yesno) {
\n
if (yesno) {
\n
$(
\"
#option_el_spec_dens
\"
).removeAttr('disabled');
\n
$(
\"
#atomic_density_type
\"
).val('number_density').change();
\n
}
\n
else {
\n
if ($(
\"
#atomic_density_type
\"
).val() ==
\"
number_density
\"
) {
\n
$(
\"
#atomic_density_type
\"
).val('number_density_generic').change();
\n
}
\n
$(
\"
#option_el_spec_dens
\"
).attr('disabled', 'disabled');
\n
}
\n
}
\n
\n
var reset_soap = function() {
\n
beaker.evaluate(
\"
cell_soap_gui
\"
);
\n
};
\n
\n
var get_options = function() {
\n
\n
// Determine kernel adaptor function
\n
// [i.e., choose from specific/generic/global-specific/global-generic]
\n
var density_type = $(
\"
#atomic_density_type
\"
).val();
\n
var adaptor_type =
\"
?
\"
;
\n
if (density_type ==
\"
number_density
\"
) {
\n
adaptor_type =
\"
specific
\"
;
\n
}
\n
else { // element-agnostic, core charge, valence charge, electronegativity
\n
adaptor_type =
\"
generic
\"
;
\n
}
\n
var kernel_method = $(
\"
#kernel_method
\"
).val();
\n
if (kernel_method ==
\"
global
\"
) {
\n
adaptor_type =
\"
global-
\"
+ adaptor_type;
\n
}
\n
\n
var n_procs = parseInt($(
\"
#exe_n_procs
\"
).val());
\n
if ($(
\"
#threading_mode
\"
).val() ==
\"
single_threaded
\"
) n_procs = 1;
\n
\n
beaker.options = {
\n
\"
run
\"
: {
\n
\"
config_folder
\"
: $(
\"
#dataset_example
\"
).val(),
\n
\"
n_configs
\"
: -1,
\n
\"
n_procs
\"
: n_procs,
\n
\"
n_blocksize
\"
: parseInt($(
\"
#exe_batch_size
\"
).val()),
\n
\"
queue
\"
:
\"
?
\"
,
\n
\"
walltime
\"
: 12,
\n
\"
out_folder
\"
:
\"
out.kernel
\"
,
\n
\"
verbose
\"
: false
\n
},
\n
\"
atomic_density
\"
: {
\n
\"
density_type
\"
: $(
\"
#atomic_density_type
\"
).val(),
\n
\"
atomic_radius
\"
: parseFloat($(
\"
#atomic_density_atomic_radius
\"
).val()),
\n
\"
use_covrad
\"
: $(
\"
#atomic_density_use_covrad:checked
\"
).val() ==
\"
true
\"\n
},
\n
\"
kernel
\"
: {
\n
\"
method
\"
: kernel_method
\n
},
\n
\"
basekernel
\"
: {
\n
\"
kernel.type
\"
:
\"
dot
\"
,
\n
\"
kernel.delta
\"
: 1.0,
\n
\"
kernel.xi
\"
: parseFloat($(
\"
#basekernel_kernel_xi
\"
).val())
\n
},
\n
\"
laplacian
\"
: {
\n
\"
inverse_dist
\"
: true,
\n
\"
coulomb
\"
: true,
\n
\"
scale
\"
: 0.01,
\n
\"
eta
\"
: 1.0,
\n
\"
gamma
\"
: 0.01,
\n
\"
optimize_eta_gamma
\"
: false
\n
},
\n
\"
dimred
\"
: {
\n
\"
method
\"
: $(
\"
#dimred_method
\"
).val()
\n
},
\n
\"
graph
\"
: {
\n
\"
descriptor
\"
:
\"
soap
\"
,
\n
\"
pca
\"
:
\"
none
\"
,
\n
\"
hierarchical
\"
: $(
\"
#kernel_hierarchical
\"
).val() ==
\"
true
\"
,
\n
\"
r0
\"
: 1.0,
\n
\"
alpha
\"
: 2.0,
\n
\"
n_levels
\"
: 3,
\n
\"
optimize_hierarchy
\"
: false
\n
},
\n
\"
lamatch
\"
: {
\n
\"
gamma
\"
: 0.3,
\n
\"
optimize_rematch
\"
: false
\n
},
\n
\"
descriptor
\"
: {
\n
\"
soap
\"
: {
\n
\"
spectrum.gradients
\"
: false,
\n
\"
spectrum.2l1_norm
\"
: false,
\n
\"
radialbasis.type
\"
:
\"
gaussian
\"
,
\n
\"
radialbasis.mode
\"
: $(
\"
#soap_radialbasis_mode
\"
).val(),
\n
\"
radialbasis.N
\"
: parseInt($(
\"
#soap_radialbasis_N
\"
).val()),
\n
\"
radialbasis.sigma
\"
: parseFloat($(
\"
#soap_radialbasis_sigma
\"
).val()),
\n
\"
radialbasis.integration_steps
\"
: 15,
\n
\"
radialcutoff.Rc
\"
: parseFloat($(
\"
#soap_radialbasis_Rc
\"
).val()),
\n
\"
radialcutoff.Rc_width
\"
: parseFloat($(
\"
#soap_radialbasis_sigma
\"
).val()),
\n
\"
radialcutoff.type
\"
:
\"
heaviside
\"
,
\n
\"
radialcutoff.center_weight
\"
: 1.0,
\n
\"
angularbasis.type
\"
:
\"
spherical-harmonic
\"
,
\n
\"
angularbasis.L
\"
: parseInt($(
\"
#soap_angularbasis_L
\"
).val()),
\n
\"
kernel.type
\"
:
\"
dot
\"
,
\n
\"
kernel.adaptor
\"
: adaptor_type,
\n
\"
kernel.delta
\"
: 1.0,
\n
\"
kernel.xi
\"
: parseFloat($(
\"
#basekernel_kernel_xi
\"
).val()),
\n
\"
exclude_centers
\"
: [],
\n
\"
exclude_targets
\"
: [],
\n
\"
type_list
\"
: [
\"
C
\"
]
\n
}
\n
}
\n
};
\n\n
};
\n
\n
beaker.view_result = function(result_link) {
\n
$(
\"
#plot_result_button
\"
).attr(
\"
href
\"
, result_link);
\n
$(
\"
#plot_result_button
\"
).removeClass(
\"
disabled
\"
); //.addClass(
\"
active
\"
);
\n
}
\n
</script>
\n
<style
type=
\"text/css\"
>
\
n
.in11f
{
\n
width
:
3.5em
;
\n
}
\
n
.in3d
{
\n
width
:
5em
;
\n
}
\
n
.select_main
{
\n
width
:
20em
;
\n
}
\
n
.btn.active
,
.btn
:active
{
\n
background
:
#cecece
;
\n
text-decoration
:
none
;
\n
}
\
n</style>
\n\n
<p
style=
\"color:#20335d;
font-weight:900
;
font-size:18pt
;\"
>
Control options
<br>
</p><hr
style=
\"border-width:2px\"
>
<p></p>
\n \n \n
<table
class=
\"glosim_control\"
>
\n \n
<!-- DATASETS -->
\n
<tbody><tr
style=
\"line-height:40px\"
>
\n
<td><b>
Dataset examples
</b>
</td>
\n
<td>
\n
<select
class=
\"select_main\"
id=
\"dataset_example\"
>
\n
<option
value=
\"zcrs\"
onclick=
\"allow(0)\"
selected=
\"\"
>
Zincblende / Rocksalt
</option>
\n
<option
value=
\"gdb\"
onclick=
\"allow(1)\"
>
GDB7
</option>
\n
</select>
\n
<!--button class=\"btn btn-xs active\" onclick='show_hide(\"in_detail_1\")' style=\"border:1;\" >\\></button-->
\n
<button
id=
\"toggle_detail_1\"
type=
\"button\"
class=
\"btn
btn-xs
\"
onclick=
\"show_hide("in_detail_1",
&
quot
;
toggle_detail_1
&
quot
;)\"
>
Configure
</button>
\n
<!--button id=\"toggle_detail_1\"type=\"button\" onclick='show_hide(\"in_detail_1\", \"toggle_detail_1\")'>Configure</button-->
\n
<g
id=
\"in_detail_1\"
hidden=
\"\"
>
Subsample structures
<input
id=
\"exe_batch_size\"
value=
\"200\"
min=
\"50\"
max=
\"1000\"
step=
\"50\"
class=
\"in3d\"
type=
\"number\"
>
</g>
\n
</td>
\n
</tr>
\n \n
<!-- ATOMIC DENSITY -->
\n
<tr
style=
\"line-height:40px\"
>
\n
<td><b>
Atomic density
</b>
</td>
\n
<td>
\n
<select
class=
\"select_main\"
id=
\"atomic_density_type\"
>
\n
<option
id=
\"option_el_agno_dens\"
value=
\"number_density_generic\"
selected=
\"\"
>
Density type: element-agnostic density
</option>
\n
<option
id=
\"option_el_spec_dens\"
value=
\"number_density\"
disabled=
\"\"
>
Density type: element-specific density
</option>
\n
<option
value=
\"valence_charge_density\"
>
Density type: valence charge
</option>
\n
<option
value=
\"z_density\"
>
Density type: core charge
</option>
\n
<option
value=
\"elneg_density\"
>
Density type: electronegativity
</option>
\n
</select>
\n
<button
id=
\"toggle_detail_2\"
type=
\"button\"
class=
\"btn
btn-xs
\"
onclick=
\"show_hide("in_detail_2",
&
quot
;
toggle_detail_2
&
quot
;)\"
>
Configure
</button>
\n
<g
id=
\"in_detail_2\"
hidden=
\"\"
>
Use covalent radii
<input
id=
\"atomic_density_use_covrad\"
value=
\"true\"
unchecked=
\"\"
type=
\"checkbox\"
>
\n
Constant atomic radius (Angstrom)
<input
id=
\"atomic_density_atomic_radius\"
value=
\"0.5\"
min=
\"0.0\"
max=
\"2.0\"
step=
\"0.1\"
class=
\"in11f\"
type=
\"number\"
>
</g>
\n
</td>
\n
</tr>
\n \n
<!-- BASIS SET -->
\n
<tr
style=
\"line-height:40px\"
>
\n
<td><b>
Basis set
</b>
</td>
\n
<td>
\n
<select
class=
\"select_main\"
id=
\"soap_radialbasis_mode\"
>
\n
<option
value=
\"adaptive\"
>
Radial basis: adaptive
</option>
\n
<option
value=
\"equispaced\"
>
Radial basis: equispaced
</option>
\n
</select>
\n
<button
id=
\"toggle_detail_3\"
type=
\"button\"
class=
\"btn
btn-xs
\"
onclick=
\"show_hide("in_detail_3",
&
quot
;
toggle_detail_3
&
quot
;)\"
>
Configure
</button>
\n
<g
id=
\"in_detail_3\"
hidden=
\"\"
>
\n
Radial functions N =
<input
id=
\"soap_radialbasis_N\"
value=
\"9\"
min=
\"1\"
max=
\"14\"
step=
\"1\"
class=
\"in11f\"
type=
\"number\"
>
\n
Radial cutoff (equispaced only)
<input
id=
\"soap_radialbasis_Rc\"
value=
\"3.5\"
min=
\"0.1\"
max=
\"10.0\"
step=
\"0.1\"
class=
\"in11f\"
type=
\"number\"
>
\n
Radial Gaussian width
<input
id=
\"soap_radialbasis_sigma\"
value=
\"0.5\"
min=
\"0.1\"
max=
\"3.0\"
step=
\"0.1\"
class=
\"in11f\"
type=
\"number\"
>
\n
Angular functions L =
<input
id=
\"soap_angularbasis_L\"
value=
\"6\"
min=
\"1\"
max=
\"14\"
step=
\"1\"
class=
\"in11f\"
type=
\"number\"
>
\n
</g>
\n
</td>
\n
</tr>
\n \n
<!-- BASE KERNEL -->
\n
<tr
style=
\"line-height:40px\"
>
\n
<td><b>
Base kernel
</b>
</td>
\n
<td>
\n
<select
class=
\"select_main\"
id=
\"basekernel_method\"
>
\n
<option
value=
\"dot\"
>
Dot-product kernel
</option>
\n
<option
value=
\"laplacian\"
disabled=
\"\"
>
Laplacian kernel
</option>
\n
<option
value=
\"gaussian\"
disabled=
\"\"
>
Gaussian kernel
</option>
\n
</select>
\n
<button
id=
\"toggle_detail_4\"
type=
\"button\"
class=
\"btn
btn-xs
\"
onclick=
\"show_hide("in_detail_4",
&
quot
;
toggle_detail_4
&
quot
;)\"
>
Configure
</button>
\n
<g
id=
\"in_detail_4\"
hidden=
\"\"
>
\n
Exponent
<input
id=
\"basekernel_kernel_xi\"
value=
\"3.0\"
min=
\"0.1\"
max=
\"5.0\"
step=
\"0.1\"
class=
\"in11f\"
type=
\"number\"
>
\n
</g>
\n
</td>
\n
</tr>
\n \n
<!-- TOP KERNEL -->
\n
<tr
style=
\"line-height:40px\"
>
\n
<td><b>
Top kernel
</b>
</td>
\n
<td>
\n
<select
class=
\"select_main\"
id=
\"kernel_method\"
>
\n
<option
value=
\"global\"
selected=
\"\"
>
Global average (coherent)
</option>
\n
<option
value=
\"average\"
>
Global average (incoherent)
</option>
\n
<option
value=
\"rematch\"
>
Regularized-entropy match
</option>
\n
<option
value=
\"laplacian\"
>
Laplacian Markov random field
</option>
\n
</select>
\n
<button
id=
\"toggle_detail_5\"
type=
\"button\"
class=
\"btn
btn-xs
\"
onclick=
\"show_hide("in_detail_5",
&
quot
;
toggle_detail_5
&
quot
;)\"
>
Configure
</button>
\n
<g
id=
\"in_detail_5\"
hidden=
\"\"
>
\n
Mode
\n
<select
id=
\"kernel_hierarchical\"
>
\n
<option
value=
\"false\"
>
single-level
</option>
\n
<option
value=
\"true\"
>
hierarchical
</option>
\n
</select>
\n
Graph Laplacian
\n
<select
id=
\"opt_top_kernel_hierarchy\"
>
\n
<option
value=
\"invdist\"
>
inverse distance
</option>
\n
<option
value=
\"coulomb\"
>
Coulomb matrix
</option>
\n
</select>
\n
Levels
<input
id=
\"graph:n_levels\"
value=
\"1\"
min=
\"1\"
max=
\"5\"
step=
\"1\"
class=
\"in11f\"
type=
\"number\"
>
\n
Base radius
<input
id=
\"graph:r0\"
value=
\"1.0\"
min=
\"0.1\"
max=
\"5.0\"
step=
\"0.1\"
class=
\"in11f\"
type=
\"number\"
>
\n
Scale
<input
id=
\"graph:alpha\"
value=
\"2.0\"
min=
\"0.1\"
max=
\"5.0\"
step=
\"0.1\"
class=
\"in11f\"
type=
\"number\"
>
\n
</g>
\n
</td>
\n
</tr>
\n \n
<!-- KERNEL DECOMPOSITION -->
\n
<tr
style=
\"line-height:40px\"
>
\n
<td><b>
Embedding
</b>
</td>
\n
<td>
\n
<select
class=
\"select_main\"
id=
\"dimred_method\"
>
\n
<option
value=
\"kernelpca\"
selected=
\"\"
>
Kernel PCA
</option>
\n
<option
value=
\"mds\"
>
Multi-dimensional scaling
</option>
\n
</select>
\n
<button
id=
\"toggle_detail_6\"
type=
\"button\"
class=
\"btn
btn-xs
\"
onclick=
\"show_hide("in_detail_6",
&
quot
;
toggle_detail_6
&
quot
;)\"
>
Configure
</button>
\n
<g
id=
\"in_detail_6\"
hidden=
\"\"
>
\n
Distance metric (MDS)
\n
<select
id=
\"dimred_distance\"
>
\n
<option
value=
\"dot\"
>
Hypersphere chord
</option>
\n
</select>
\n
</g>
\n
</td>
\n
</tr>
\n \n
<!-- EXECUTION -->
\n
<tr
style=
\"line-height:40px\"
>
\n
<td><b>
Parallel execution
</b></td>
\n
<td>
\n
<select
class=
\"select_main\"
id=
\"threading_mode\"
>
\n
<option
value=
\"single_threaded\"
>
Single-threaded
</option>
\n
<option
value=
\"multi_threaded\"
selected=
\"\"
>
Multi-threaded
</option>
\n
</select>
\n
<button
id=
\"toggle_detail_7\"
type=
\"button\"
class=
\"btn
btn-xs
\"
onclick=
\"show_hide("in_detail_7",
&
quot
;
toggle_detail_7
&
quot
;)\"
>
Configure
</button>
\n
<g
id=
\"in_detail_7\"
hidden=
\"\"
>
\n
Number of cores
<input
id=
\"exe_n_procs\"
value=
\"2\"
min=
\"1\"
max=
\"4\"
step=
\"1\"
class=
\"in11f\"
type=
\"number\"
>
\n
Batch size
<input
id=
\"exe_batch_size_parallel\"
value=
\"200\"
min=
\"50\"
max=
\"1000\"
step=
\"50\"
class=
\"in3d\"
type=
\"number\"
>
</g>
\n
</td>
\n
</tr>
\n \n
</tbody></table>
\n \n
<hr
style=
\"border-width:2px\"
>
\n \n
<button
class=
\"btn
btn-default
\"
onclick=
\"run_soap()\"
>
RUN SOAP
</button>
\n
<button
class=
\"btn
btn-default
\"
onclick=
\"reset_soap()\"
>
RESET SOAP
</button>
\n
<label
title=
\"Activate
once
run
is
complete.
\"
>
\n
<a
href=
\"#\"
target=
\"_blank\"
class=
\"btn
btn-primary
disabled
\"
id=
\"plot_result_button\"
>
View 2D similarity map
</a>
\n
</label>
\n\n
<!-- \nGDB7:\nel-spec + cov-radii + re-match + pca\nel-agno - cov-radii + re-match + pca\n\nRS/ZB\ncore-chrg + cov-radii + re-match + pca\nel-agno - cov-radii + re-match + pca\n-->
"
},
"selectedType": "BeakerDisplay",
"elapsedTime":
0
,
"height": 46
5
"elapsedTime":
1
,
"height": 46
6
},
"evaluatorReader": true,
"lineCount": 306,
...
...
@@ -640,7 +640,7 @@
"
#
LOAD
DATA
,
CONVERT
TO
ASE
",
"
logger.info
(\"
Loading
data
(%
s
)
...\"
%
options
['
run
']['
config_folder
'])",
"
if
options
['
run
']['
config_folder
'
] =
=
'
zcrs
'
:
",
"
data_folder=
'/parsed/prod-0
17
/FhiAimsParser2.0.0/RWApItBGtGUDsfMVlHKqrjUQ4rShT/'
",
"
data_folder=
'/parsed/prod-0
22
/FhiAimsParser2.0.0
-2-gf9335c4
/RWApItBGtGUDsfMVlHKqrjUQ4rShT/'
",
"
json_list =
get_json_list(",
"
method=
'folder'
,
",
"
drop_duplicates=
True,
",
...
...
@@ -756,7 +756,7 @@
"selectedType": "Results",
"state": {},
"pluginName": "IPython",
"shellId": "
685C15C25B544E2D849B1938008390FD
",
"shellId": "
A1E72F9FF9EF4FA68AC9A7FD1424AD63
",
"height": 222,
"dataresult": [
"HARTREE_TO_EV",
...
...
@@ -846,7 +846,7 @@
"update_node",
"util"
],
"elapsedTime":
42257
"elapsedTime":
34386
},
"evaluatorReader": true,
"lineCount": 165,
...
...
@@ -2055,8 +2055,8 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
"shellId": "
685C15C25B544E2D849B1938008390FD
",
"elapsedTime": 2
057
"shellId": "
A1E72F9FF9EF4FA68AC9A7FD1424AD63
",
"elapsedTime": 2
322
},
"evaluatorReader": true,
"lineCount": 1190,
...
...
@@ -2178,9 +2178,9 @@
"state": {},
"selectedType": "Hidden",
"pluginName": "IPython",
"shellId": "
685C15C25B544E2D849B1938008390FD
",
"shellId": "
A1E72F9FF9EF4FA68AC9A7FD1424AD63
",
"height": 78,
"elapsedTime": 4
05
"elapsedTime": 4
28
},
"evaluatorReader": true,
"lineCount": 103,
...
...
@@ -2264,9 +2264,9 @@
"state": {},
"selectedType": "Results",
"pluginName": "IPython",
"shellId": "
685C15C25B544E2D849B1938008390FD
",
"shellId": "
A1E72F9FF9EF4FA68AC9A7FD1424AD63
",
"height": 1462,
"elapsedTime":
3335
"elapsedTime":
9310
},
"evaluatorReader": true,
"lineCount": 65,
...
...
@@ -2288,7 +2288,7 @@
"selectedType": "BeakerDisplay",
"pluginName": "JavaScript",
"height": 78,
"elapsedTime":
39
"elapsedTime":
65
},
"evaluatorReader": true,
"lineCount": 2,
...
...
@@ -2330,7 +2330,7 @@
"viewer_result": "similarity-map",
"options": {
"run": {
"config_folder": "
gdb
",
"config_folder": "
zcrs
",
"n_configs": -1,
"n_procs": 2,
"n_blocksize": 200,
...
...
@@ -2340,7 +2340,7 @@
"verbose": false
},
"atomic_density": {
"density_type": "number_density",
"density_type": "number_density
_generic
",
"atomic_radius": 0.5,
"use_covrad": false
},
...
...
@@ -2392,7 +2392,7 @@
"angularbasis.type": "spherical-harmonic",
"angularbasis.L": 6,
"kernel.type": "dot",
"kernel.adaptor": "global-
specif
ic",
"kernel.adaptor": "global-
gener
ic",
"kernel.delta": 1,
"kernel.xi": 3,
"exclude_centers": [],
...
...
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