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west-public
westpy
Commits
50165f75
Commit
50165f75
authored
Sep 19, 2018
by
Marco Govoni
Browse files
Updated tutorial west_300
parent
1d43735c
Changes
1
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Side-by-side
doc/tutorials/westpy_300.ipynb
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50165f75
%% Cell type:markdown id: tags:
<h1>
RESTful Tutorials
</h1>
%% Cell type:markdown id: tags:
We will show here how to interact with the remote server where the
`pw.x`
,
`wstat.x`
and
`wfreq.x`
are already installed.
%% Cell type:markdown id: tags:
We start by importing WESTPy and generating a ground state input file for methane.
%% Cell type:code id: tags:
```
python
from
westpy
import
*
```
%%%% Output: stream
_ _ _____ _____ _____
| | | | ___/ ___|_ _|
| | | | |__ \ `--. | |_ __ _ _
| |/\| | __| `--. \ | | '_ \| | | |
\ /\ / |___/\__/ / | | |_) | |_| |
\/ \/\____/\____/ \_/ .__/ \__, |
| | __/ |
|_| |___/
WEST version : 3.1.
0
Today : 2018-09-19 15:
02:57.396652
WEST version : 3.1.
1
Today : 2018-09-19 15:
33:45.581889
%% Cell type:code id: tags:
```
python
geom
=
Geometry
()
```
%% Cell type:code id: tags:
```
python
geom
.
setCell
((
25
,
0
,
0
),(
0
,
25
,
0
),(
0
,
0
,
25
))
```
%% Cell type:code id: tags:
```
python
geom
.
addAtomsFromOnlineXYZ
(
"http://www.west-code.org/doc/training/methane/CH4.xyz"
)
```
%% Cell type:code id: tags:
```
python
geom
.
addSpecies
(
"C"
,
"http://www.quantum-simulation.org/potentials/sg15_oncv/upf/C_ONCV_PBE-1.0.upf"
)
geom
.
addSpecies
(
"H"
,
"http://www.quantum-simulation.org/potentials/sg15_oncv/upf/H_ONCV_PBE-1.0.upf"
)
```
%% Cell type:code id: tags:
```
python
gs
=
GroundState
(
geom
,
xc
=
"PBE"
,
ecut
=
40.0
)
```
%% Cell type:code id: tags:
```
python
gs
.
generateInputPW
()
```
%%%% Output: stream
Generated file: pw.in
%% Cell type:markdown id: tags:
We now create a session on the remote server.
%% Cell type:code id: tags:
```
python
session
=
Session
(
"
marco.outatime@gmail.com
"
)
session
=
Session
(
"
your.email@domain.edu
"
)
```
%%%% Output: stream
Check the inbox/spam folder of your email and click on the link to activate the session
%% Cell type:code id: tags:
```
python
status
=
session
.
status
()
print
(
status
)
session
.
status
()
```
%%%% Output:
stream
%%%% Output:
execute_result
{'Active': 'True', 'Time Left': '
4
9 minutes'}
{'Active': 'True', 'Time Left': '
5
9 minutes'}
%% Cell type:code id: tags:
```
python
download
=
[
"http://www.quantum-simulation.org/potentials/sg15_oncv/upf/C_ONCV_PBE-1.0.upf"
,
"http://www.quantum-simulation.org/potentials/sg15_oncv/upf/H_ONCV_PBE-1.0.upf"
]
pw_output
=
session
.
run
(
"pw"
,
"pw.in"
,
"pw.out"
,
download
,
3
)
```
%%%% Output: stream
Requested to run executable pw on server imedevel.uchicago.edu
Generated pw.out
%% Cell type:markdown id: tags:
We now generate the input for
`wstat.x`
.
%% Cell type:code id: tags:
```
python
data
=
{}
data
[
"input_west"
]
=
{}
data
[
"input_west"
][
"qe_prefix"
]
=
"calc"
data
[
"input_west"
][
"west_prefix"
]
=
"calc"
data
[
"input_west"
][
"outdir"
]
=
"./"
data
[
"wstat_control"
]
=
{}
data
[
"wstat_control"
][
"wstat_calculation"
]
=
"S"
data
[
"wstat_control"
][
"n_pdep_eigen"
]
=
5
writeJsonFile
(
"wstat.in"
,
data
)
```
%%%% Output: stream
File written : wstat.in
%% Cell type:code id: tags:
```
python
wstat_output
=
session
.
run
(
"wstat"
,
"wstat.in"
,
"wstat.out"
,
download
,
3
)
```
%%%% Output: stream
Requested to run executable wstat on server imedevel.uchicago.edu
Session Expired! Invalid Request sent, Please recreate session and recheck your input.
the JSON object must be str, bytes or bytearray, not dict
Generated wstat.out
%% Cell type:markdown id: tags:
We now generate the input for
`wfreq.x`
.
%% Cell type:code id: tags:
```
python
data
=
{}
data
[
"wfreq_control"
]
=
{}
data
[
"wfreq_control"
][
"wfreq_calculation"
]
=
"XWGQ"
data
[
"wfreq_control"
][
"n_pdep_eigen_to_use"
]
=
5
0
data
[
"wfreq_control"
][
"n_pdep_eigen_to_use"
]
=
5
data
[
"wfreq_control"
][
"qp_bandrange"
]
=
[
1
,
5
]
data
[
"wfreq_control"
][
"n_refreq"
]
=
300
data
[
"wfreq_control"
][
"ecut_refreq"
]
=
2.0
writeJsonFile
(
"wfreq.in"
,
data
)
```
%%%% Output: stream
File written : wfreq.in
%% Cell type:code id: tags:
```
python
wfreq_output
=
session
.
run
(
"wfreq"
,
"wfreq.in"
,
"wfreq.out"
,
3
)
wfreq_output
=
session
.
run
(
"wfreq"
,
"wfreq.in"
,
"wfreq.out"
,
download
,
3
)
```
%%%% Output: stream
Requested to run executable wfreq on server imedevel.uchicago.edu
Server failed with the following error
can only join an iterable
Generated wfreq.out
%% Cell type:markdown id: tags:
We now stop the session.
%% Cell type:code id: tags:
```
python
session
.
stop
()
```
%%%% Output: execute_result
{'Success': 'Session removed and cleared'}
%% Cell type:code id: tags:
```
python
```
...
...
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