jmmshn

on run {input, parameters}
	tell application "iTerm"
		create window with default profile
		tell front window
			tell current session
				write text ("ranger " & "; exit")
			end tell
		end tell
	end tell
	return input

jmmshn

cat << EOF > FILENAME
#!/bin/bash
echo \$PWD
EOF

jmmshn

%env FW_CONFIG_FILE=/Users/lik/.atomate/config/FW_config.yaml
from pymatgen import Structure
from atomate.vasp.workflows.base.core import get_wf
from fireworks import LaunchPad,fw_config
fw_config.CONFIG_FILE_DIR # you can finetune the configuration for each project using this parameter
from atomate.vasp.powerups import add_modify_incar, add_additional_fields_to_taskdocs, add_priority
from pymongo import MongoClient
import json
from pymatgen import MPRester

jmmshn

import os
import tempfile

temp = tempfile.NamedTemporaryFile(mode='w+t')
try:
    temp.write(string)
    temp.seek(0)
    print (temp.name)
finally:
    temp.close()

jmmshn

cart_pos = np.dot(struct.lattice.matrix, frac_coord_vec)

jmmshn

db.getCollection("chgcar_fs.files").aggregate([  
    {$group: {
        _id: {task_id: "$metadata.task_id"},
        uniqueIds: {$addToSet: "$metadata.task_id"},
        count: {$sum: 1}
        }
    },
    {$match: { 
        count: {"$gt": 1}
        }

jmmshn

from maggma.stores import MongoStore
from pymatgen.analysis.structure_matcher import StructureMatcher, ElementComparator
from pymatgen import Structure
sm = StructureMatcher(comparator=ElementComparator(),
                           primitive_cell=False)
def check_fws( struct_in ):
    js_fw_store = MongoStore("", "",
                  host="",
                  username="",
                  password="",

jmmshn

from atomate.vasp.firetasks.parse_outputs import VaspDrone
drone = VaspDrone(parse_chgcar=True, parse_aeccar=True)
d = drone.assimilate('CALC_DIR')

jmmshn

atoms = AseAtomsAdaptor.get_atoms(struct)
import matplotlib.pyplot as plt
from ase.visualize.plot import plot_atoms
from ase.lattice.cubic import FaceCenteredCubic

fig, ax = plt.subplots(2,2)
plt.subplots_adjust(wspace=0, hspace=0)
rot=['0x,0y,0z', '90x,0y,0z', '0x,90y,0z', '0x,0y,90z']
for itr, a in enumerate(ax.flatten()):
    plot_atoms(atoms, a, radii=0.3, rotation=rot[itr], show_unit_cell=True, scale=0.5)

jmmshn

from fireworks import LaunchPad,fw_config
lpad = LaunchPad.auto_load()
# rerun the full workflow becuase you suck
l_incomplete = list(lpad.db['workflows'].find({'$or' :[{"state": "RUNNING"}, {"state": "FIZZLED"} ]}))
for fid in l_incomplete:
    for itr in sorted(fid['fw_states'].keys(), reverse=False):
        lpad.rerun_fw(int(itr))