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nomad-lab
parser-cpmd
Commits
93cf2295
Commit
93cf2295
authored
4 years ago
by
temok-mx
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Updated README.md; added metadata.yml; the lead branch is now master, inactive branches became tags
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README.md
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README.md
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stages
:
-
test
testing
:
stage
:
test
script
:
-
cd .. && rm -rf nomad-lab-base
-
git clone --recursive git@gitlab.mpcdf.mpg.de:nomad-lab/nomad-lab-base.git
-
cd nomad-lab-base
-
git submodule foreach git checkout master
-
git submodule foreach git pull
-
sbt cpmd/test
-
export PYTHONEXE=/labEnv/bin/python
-
sbt cpmd/test
only
:
-
master
tags
:
-
test
-
spec2
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README.md
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This is
the main repository of the
[
NOMAD
](
https://www.nomad-coe.eu/
)
parser for
[
CPMD
](
http://www.cpmd.org/
)
.
This is
a NOMAD parser for
[
CPMD
](
https://www.cpmd.org/
)
. It will read CPMD input and
output files and provide all information in NOMAD's unified Metainfo based Archive format
.
# Example
```
python
from
cpmdparser
import
CPMDParser
import
matplotlib.pyplot
as
mpl
## Preparing code input and output file for uploading to NOMAD
NOMAD accepts
`.zip`
and
`.tar.gz`
archives as uploads. Each upload can contain arbitrary
files and directories. NOMAD will automatically try to choose the right parser for you files.
For each parser (i.e. for each supported code) there is one type of file that the respective
parser can recognize. We call these files
`mainfiles`
as they typically are the main
output file a code. For each
`mainfile`
that NOMAD discovers it will create an entry
in the database that users can search, view, and download. NOMAD will associate all files
in the same directory as files that also belong to that entry. Parsers
might also read information from these auxillary files. This way you can add more files
to an entry, even if the respective parser/code might not directly support it.
For cpmd please provide at least the files from this table if applicable to your
calculations (remember that you can provide more files if you want):
# 1. Initialize a parser with a set of default units.
default_units
=
[
"
eV
"
]
parser
=
CPMDParser
(
default_units
=
default_units
)
# 2. Parse a file
path
=
"
path/to/main.file
"
results
=
parser
.
parse
(
path
)
# 3. Query the results with using the id's created specifically for NOMAD.
scf_energies
=
results
[
"
energy_total_scf_iteration
"
]
mpl
.
plot
(
scf_energies
)
mpl
.
show
()
To create an upload with all calculations in a directory structure:
```
zip -r <upload-file>.zip <directory>/*
```
# Installation
The code is python 2 and python 3 compatible. First download and install
the nomadcore package:
Go to the
[
NOMAD upload page
](
https://nomad-lab.eu/prod/rae/gui/uploads
)
to upload files
or find instructions about how to upload files from the command line.
## Using the parser
```
sh
git clone https://gitlab.mpcdf.mpg.de/nomad-lab/python-common.git
cd
python-common
pip
install
-r
requirements.txt
pip
install
-e
.
You can use NOMAD's parsers and normalizers locally on your computer. You need to install
NOMAD's pypi package:
```
pip install
nomad-lab
```
T
hen download the metainfo definitions to the same folder where th
e
'python-common' repository was cloned
:
T
o parse code input/output from the command line, you can use NOMAD's command lin
e
interface (CLI) and print the processing results output to stdout
:
```
sh
git clone https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-meta-info.git
```
nomad parse --show-archive <path-to-file>
```
To parse a file in Python, you can program something like this:
```
python
import
sys
from
nomad.cli.parse
import
parse
,
normalize_all
Finally download and install the parser:
# match and run the parser
backend
=
parse
(
sys
.
argv
[
1
])
# run all normalizers
normalize_all
(
backend
)
```
sh
git clone https://gitlab.mpcdf.mpg.de/nomad-lab/parser-cpmd.git
cd
parser-cpmd
pip
install
-e
.
# get the 'main section' section_run as a metainfo object
section_run
=
backend
.
resource
.
contents
[
0
].
section_run
[
0
]
# get the same data as JSON serializable Python dict
python_dict
=
section_run
.
m_to_dict
()
```
## Developing the parser
Also install NOMAD's pypi package:
```
pip install nomad-lab
```
Clone the parser project and install it in development mode:
```
git clone https://gitlab.mpcdf.mpg.de/nomad-lab/parser-cpmd parser-cpmd
pip install -e parser-cpmd
```
# Notes
The parser is based on CPMD 4.1.
Running the parser now, will use the parser's Python code from the clone project.
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code-label
:
CPMD
code-label-style
:
all in capitals
code-url
:
https://www.cpmd.org/
parser-dir-name
:
dependencies/parsers/cpmd/
parser-git-url
:
https://gitlab.mpcdf.mpg.de/nomad-lab/parser-cpmd
parser-specific
:
'
'
table-of-files
:
'
'
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