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 #Note for Windows:

  1. Open your anaconda powershell prompt and run as administrator.

  2. Go to the location where you want to install DFTTK.

  • Release version

pip install dfttk

  • 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 .

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 -mapi PMG_MAPI_KEY

where

For the system other than aci, “-aci” should be replace by “-psp vasp_psp/” where vasp_psp is a place holding your vasp pseudopotentials
yourcomputer is your computer name, such as aci-vasp5, aci-vasp6, 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

  • Additional steps for installation in Windows

One need to add two environmental variables by right click Windows symbol located in the lower left corner -> system -> (scrolling down to) Advanced system settings -> Environmental variales -> “New..” button

HOME - create a Windows environmental variale named ‘HOME’, something similiar to “C:Usersxxxxx” where xxxxx is your login in user name
FW_CONFIG_FILE - create a Windows environmental variale named ‘FW_CONFIG_FILE’ pointed to the ‘config’ folder

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

Job submission/run

Pymatgen task to MongoDB from Windows, MacOS, or Linux

dfttk run –wf robust –f POSCAR –l

Submit DFT job only in Linux

qlaunch singleshot; or
qlaunch rapidfire