singroup / critcatworks

Workflow manager for DFT simulations on nanocluster databases using Fireworks

critcatworks

CritCatWorks is a workflow manager for DFT simulations on nanocluster databases built on Fireworks. The documentation along with tutorials is available at https://singroup.github.io/critcatworks/

Quick example

# This example will only run if you have a connection to a mongodb database
# containing a nanocluster simulation (Execute nanocluster workflow to get
# one). username, password, extdb_ids along with template_path and 
# worker_target_path need to be provided

from fireworks import LaunchPad, Workflow
import pathlib
import os, sys
import getpass
from critcatworks.database import mylaunchpad
from critcatworks.workflows.coverage import get_coverage_workflow

USERNAME = "myusername"
PASSWORD = getpass.getpass()

# set up the LaunchPad and reset it
launchpad = mylaunchpad.create_launchpad(USERNAME, PASSWORD)

# simple coverage workflow
wf = get_coverage_workflow(username = USERNAME, 
    password = PASSWORD,
    template_path = str(pathlib.Path("./templates/triton_gopt.inp").resolve()), 
    worker_target_path = "/path/to/my/calculation/directory/",
    extdb_ids = [245,],                          # unique identifier of your nanocluster structure in your mongodb database
    reference_energy = -1.16195386047558 * 0.5,  # half h2 total energy as reference
    adsorbate_name = "H",
    max_iterations = 4,                          # coverage workflow iterations
    adsite_types = ["top", "hollow", ],          # initial population of the adsorption sites on the nanocluster
    n_max_restarts = 1,                          # one DFT restart upon failure
    skip_dft = False,
    bond_length = 1.5,                           # converges when no adsorbates are as close as the specified bond length
    n_remaining = 80,                            # initial reduction of adsorbates to this number 
    extdb_connect = {"db_name": "ncdb"},         # default database is testdb. use this for production runs
)   

# store workflow on launchpad
launchpad.add_wf(wf)

Installation

critcatworks

0. virtual environment recommended virtualenv --python=python3 critcatenv source critcatenv/bin/activate

1. Download this repository

git clone [email protected]:SINGROUP/dscribe.git

2. Go inside this repository cd critcatworks

3. slightly modified NOMAD CP2K parser Installation

This step will become obsolete once the cp2k parser is available through pip

pip install numpy cython

cd nomad_parser/python-common
pip install -r requirements.txt
pip install -e .

cd ../parser-cp2k
pip install -e .

4. critcatworks installation

cd ../../
python3 setup.py install

--

steps 3 and 4 are automatically executed by

./easily_install_all.sh

critcatworks's Issues

Reference

Maybe a good idea to give a link to Fireworks somewhere.