Installation

It is recommended to install DFTTK under the anaconda environment. Under the linux command prompt (or anaconda powershell prompt for Windows), one can create a preferred directory and then run

  • Release version

pip install dfttk==0.3.4 #0.3.4 is latest which may change in a timely manner

  • Development version

git clone https://github.com/PhasesResearchLab/dfttk.git
cd dfttk
pip install -e .

  • Alpha interanal daily test version

git clone https://github.com/yiwang62/dfttk.git
cd dfttk
pip install -e .

to get the laste updates for the Alpha version based on one’s current version, run

git fetch origin
git checkout 20210826 #20210826 is a branch name which may be change in a timely manner

mkdir a folder named config whereever you want to followed by copy the file db.json, my_launchpad.yaml from your MongoDB manager into config/. See the section Config MongoDB

dfttk config -all --nodes 1 --ppn 16 --pmem 32gb -aci -M yourcomputer -qt yourbatch -mapi PMG_MAPI_KEY

where

vasp_psp is a place holding your vasp pseudopotentials
yourcomputer is your computer name, such as aci-rour, cori-knl, cori-ksw, bridges2, stampede2
yourbactch can be pbs, slurm
PMG_MAPI_KEY can be obtained by: Go to the materials project website, https://materialsproject.org/, under the API section, you will easily find you API Keys number.
finally, you need to change the account number and queue/partition number in the config/my_qadapter.yaml file

Config MongoDB

DFTTK needs MongoDB to manage DFT calculations and outputs. The users of DFTTK can either buy the commercial MongoDB database service or set up their own MongoDB server.

Ask the MongoDB system manager for two json files: one named db.json and another named my_launchpad.yaml and save them in a config folder wherever you choose.

db.json used by FireWorks through MongoDB to access the DFTTK output results, templated as follows.

{
    "database": "userid-results",
    "collection": "tasks",
    "admin_user": "userid",
    "admin_password": "pass1",
    "readonly_user": "userid-ro",
    "readonly_password": "pass2",
    "host": "146.186.149.69",
    "port": 27018,
    "aliases": {}
}

my_launchpad.yaml used by FireWorks through MongoDB for DFT job managements, templated as follows.

host: 146.186.149.69
name: userid-fws
password: pass3
port: 27018
ssl_ca_file: null
strm_lvl: INFO
user_indices: []
username: userid
wf_user_indices: []

Access MongoDB database from desktop

One can install robo3T from https://robomongo.org/. One needs to use the information from the db.json file to setup robo3T connection as indicated below

_images/robo3Tsetup.png

#note

  1. PSU-VM is a label of your choice to remark the MongoDB connection;

  2. 146.186.149.69 is the ip address of the MongoDB server;

  3. One needs to replace userid with the one (i.e. the value field of admin_user) from the db.json file together with the the value field of admin_password

YPHON

To postprocess the finite properties, the Yphon package is required. Yphon can be installed by run

cd ~
git clone https://github.com/yiwang62/YphonPackage
#Note: Usually the precompiled binaries should be executable in the common Linux/Unix environment. If not, do the following:

cd YphonPackage/YPHON/YPHON
make
#Note: If errors reported in the compiling stage, insert one line #define R_OK 1 after #include

For csh user: the command search path should be changed by inserting line below into the .cshrc (.tcshrc) file

set path = (. ~/YphonPackage/YPHON/YPHON $BIN_PATH $path)

For bsh user: the command search path should be changed by inserting the lines below into the .bash_profile (.bashrc) file

PATH=.:~/YphonPackage/YPHON/YPHON:$BIN_PATH:$PATH
export PATH