def __init__(self):
"""
Class to interface commands with HPC
"""
config = load_config()['HPC']
for key, value in config.items():
setattr(self, key, value)
def __init__(self, **kwargs):
"""
Parameters
----------
**kwargs :
project_id: (str) Project ID \n
name: (str) Job name \n
array_size: (int) Number of jobs for array \n
email: (str) Email address for info \n
nodes: (int) Number of nodes \n
cores_per_node: (int) Number of cores per node \n
output_filename: (str) Filename of output file \n
error_filename: (str) Filename of error file \n
timelimit: (int) Time limit in hours \n
memory_per_cpu:(int) Memory settings
partition (str) Partition
processor: (str) CPU architecture
modules: (list) List of modules to be loaded
path_exe: (str) Path to executable \n
add_stop_array : (Bool), Add lines for stopping array jobs when calculation is converged. \n
If True is effective only if key 'array_size' is not None
add_automation : (str) , Automation script to add to the file.
add_lines_header : (List) , Lines to add in the header part of the file.
add_lines_body : (List) , Lines to add in the body part of the file.
"""
config = load_config()
default_settings = config['job_settings']
for key, value in default_settings.items():
setattr(self, key, value)
for key, value in kwargs.items():
if key in default_settings:
setattr(self, key, value)
else:
raise Exception(
'"%s" is not a possible argument \nPossible arguments are: %s'
% (key, self.settings.keys()))
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Nov 9 11:12:09 2020
@author: villa
"""
from matgendb.creator import VaspToDbTaskDrone
from pynter.__init__ import load_config
dbconfig = load_config()['dbconfig']
# for VaspJob we use pymatgen-db interface
class VaspJobDrone(VaspToDbTaskDrone):
"""
Subclass of VaspToDbTaskDrone in pymatgen-db (matgendb) package.
To set up the database for VaspJob we use the pymatgen-db package which already provides a useful
interface to the other pymatgen objects that are already used (like Structure or ComputedEntry).
This class helps to interface a VaspJob object with the database.
For documentation on input args (https://github.com/materialsproject/pymatgen-db/blob/master/matgendb/creator.py).
Warning: 'use_full_uri' has been set to False here to allow interface with VaspJob objects.
"""
def __init__(self, job, **kwargs):
for k,v in dbconfig['vasp'].items():
if k not in kwargs:
kwargs[k] = v
super().__init__(use_full_uri=False,**kwargs)
#!/usr/bin/env python
import os
import os.path as op
import time
from datetime import datetime
import subprocess
import schedule
from pynter.__init__ import load_config
config = load_config()
hostname = config['HPC']['hostname']
workdir = config['HPC']['workdir']
localdir = config['HPC']['localdir']
workdir = op.join(workdir, '') #ensure backslash at the end
localdir = op.join(localdir, '')
homedir = os.getenv("HOME")
wdir = os.path.join(homedir, '.sync_hpc')
if not os.path.exists(wdir):
os.makedirs(wdir)
os.chdir(wdir)
command = f"rsync -r -uavzh --exclude='core.*' --exclude='WAVECAR' -e ssh {hostname}:{workdir} {localdir}"
command = command.split(
) #subprocess.run() takes a list with the arguments of the command
def job(command):
proc = subprocess.run(command, capture_output=True, shell=False, text=True)
#!/usr/bin/env python
from pymatgen.ext.matproj import MPRester
from pymatgen.io.vasp.inputs import Poscar
import argparse as ap
from pynter.__init__ import load_config
API_KEY = load_config()['API_KEY']
with MPRester(API_KEY) as mpr:
class MPDatabase:
def __init__(self, mp_id=None):
"""
Class to retrieve data from Materials Project database
Parameters
----------
mp_id : (str), optional
Materials-ID. The default is None.
"""
self.mp_id = mp_id if mp_id else None
self.api_key = API_KEY
@property
def mp_rester(self):
return mpr
def args(self):
"""