Commit 50165f75 authored by Marco Govoni's avatar Marco Govoni
Browse files

Updated tutorial west_300

parent 1d43735c
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
<h1>RESTful Tutorials</h1> <h1>RESTful Tutorials</h1>
%% Cell type:markdown id: tags: %% 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. 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: %% Cell type:markdown id: tags:
We start by importing WESTPy and generating a ground state input file for methane. We start by importing WESTPy and generating a ground state input file for methane.
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
from westpy import * from westpy import *
``` ```
%%%% Output: stream %%%% Output: stream
_ _ _____ _____ _____ _ _ _____ _____ _____
| | | | ___/ ___|_ _| | | | | ___/ ___|_ _|
| | | | |__ \ `--. | |_ __ _ _ | | | | |__ \ `--. | |_ __ _ _
| |/\| | __| `--. \ | | '_ \| | | | | |/\| | __| `--. \ | | '_ \| | | |
\ /\ / |___/\__/ / | | |_) | |_| | \ /\ / |___/\__/ / | | |_) | |_| |
\/ \/\____/\____/ \_/ .__/ \__, | \/ \/\____/\____/ \_/ .__/ \__, |
| | __/ | | | __/ |
|_| |___/ |_| |___/
WEST version : 3.1.0 WEST version : 3.1.1
Today : 2018-09-19 15:02:57.396652 Today : 2018-09-19 15:33:45.581889
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
geom = Geometry() geom = Geometry()
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
geom.setCell((25,0,0),(0,25,0),(0,0,25)) geom.setCell((25,0,0),(0,25,0),(0,0,25))
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
geom.addAtomsFromOnlineXYZ( "http://www.west-code.org/doc/training/methane/CH4.xyz" ) geom.addAtomsFromOnlineXYZ( "http://www.west-code.org/doc/training/methane/CH4.xyz" )
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
geom.addSpecies( "C", "http://www.quantum-simulation.org/potentials/sg15_oncv/upf/C_ONCV_PBE-1.0.upf") 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") geom.addSpecies( "H", "http://www.quantum-simulation.org/potentials/sg15_oncv/upf/H_ONCV_PBE-1.0.upf")
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
gs = GroundState(geom,xc="PBE",ecut=40.0) gs = GroundState(geom,xc="PBE",ecut=40.0)
``` ```
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
gs.generateInputPW() gs.generateInputPW()
``` ```
%%%% Output: stream %%%% Output: stream
Generated file: pw.in Generated file: pw.in
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
We now create a session on the remote server. We now create a session on the remote server.
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
session = Session("marco.outatime@gmail.com") session = Session("your.email@domain.edu")
``` ```
%%%% Output: stream %%%% Output: stream
Check the inbox/spam folder of your email and click on the link to activate the session Check the inbox/spam folder of your email and click on the link to activate the session
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
status = session.status() session.status()
print(status)
``` ```
%%%% Output: stream %%%% Output: execute_result
{'Active': 'True', 'Time Left': '49 minutes'} {'Active': 'True', 'Time Left': '59 minutes'}
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` 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"] 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) pw_output = session.run("pw","pw.in","pw.out",download,3)
``` ```
%%%% Output: stream %%%% Output: stream
Requested to run executable pw on server imedevel.uchicago.edu Requested to run executable pw on server imedevel.uchicago.edu
Generated pw.out Generated pw.out
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
We now generate the input for `wstat.x`. We now generate the input for `wstat.x`.
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
data = {} data = {}
data["input_west"] = {} data["input_west"] = {}
data["input_west"]["qe_prefix"] = "calc" data["input_west"]["qe_prefix"] = "calc"
data["input_west"]["west_prefix"] = "calc" data["input_west"]["west_prefix"] = "calc"
data["input_west"]["outdir"] = "./" data["input_west"]["outdir"] = "./"
data["wstat_control"] = {} data["wstat_control"] = {}
data["wstat_control"]["wstat_calculation"] = "S" data["wstat_control"]["wstat_calculation"] = "S"
data["wstat_control"]["n_pdep_eigen"] = 5 data["wstat_control"]["n_pdep_eigen"] = 5
writeJsonFile("wstat.in",data) writeJsonFile("wstat.in",data)
``` ```
%%%% Output: stream %%%% Output: stream
File written : wstat.in File written : wstat.in
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
wstat_output = session.run("wstat","wstat.in","wstat.out",download,3) wstat_output = session.run("wstat","wstat.in","wstat.out",download,3)
``` ```
%%%% Output: stream %%%% Output: stream
Requested to run executable wstat on server imedevel.uchicago.edu Requested to run executable wstat on server imedevel.uchicago.edu
Session Expired! Invalid Request sent, Please recreate session and recheck your input. Generated wstat.out
the JSON object must be str, bytes or bytearray, not dict
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
We now generate the input for `wfreq.x`. We now generate the input for `wfreq.x`.
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
data = {}
data["wfreq_control"] = {} data["wfreq_control"] = {}
data["wfreq_control"]["wfreq_calculation"] = "XWGQ" data["wfreq_control"]["wfreq_calculation"] = "XWGQ"
data["wfreq_control"]["n_pdep_eigen_to_use"] = 50 data["wfreq_control"]["n_pdep_eigen_to_use"] = 5
data["wfreq_control"]["qp_bandrange"] = [1,5] data["wfreq_control"]["qp_bandrange"] = [1,5]
data["wfreq_control"]["n_refreq"] = 300 data["wfreq_control"]["n_refreq"] = 300
data["wfreq_control"]["ecut_refreq"] = 2.0 data["wfreq_control"]["ecut_refreq"] = 2.0
writeJsonFile("wfreq.in",data) writeJsonFile("wfreq.in",data)
``` ```
%%%% Output: stream %%%% Output: stream
File written : wfreq.in File written : wfreq.in
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
wfreq_output = session.run("wfreq","wfreq.in","wfreq.out",3) wfreq_output = session.run("wfreq","wfreq.in","wfreq.out",download,3)
``` ```
%%%% Output: stream %%%% Output: stream
Requested to run executable wfreq on server imedevel.uchicago.edu Requested to run executable wfreq on server imedevel.uchicago.edu
Server failed with the following error Generated wfreq.out
can only join an iterable
%% Cell type:markdown id: tags: %% Cell type:markdown id: tags:
We now stop the session. We now stop the session.
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
session.stop() session.stop()
``` ```
%%%% Output: execute_result
{'Success': 'Session removed and cleared'}
%% Cell type:code id: tags: %% Cell type:code id: tags:
``` python ``` python
``` ```
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment