def get_run_result():
random.seed(10)
subs_db = SubsMaterialsDatabase()
result_list = []
filterstring = {"purpose": "converged_ionic", "achievement": "running"}
for x in subs_db.find(filterstring):
id_ = x["_id"]
# hostname = x["hostname"]
basedir_prefix = x["basedir"]
calc = fakeVaspRunNode(basedir_prefix)
result_list.append(calc.run_result())
subs_db.delete_one({"_id": id_})
subs_db.add_files_under(basedir_prefix, StructureNode)
result = [x["converged_ionic"] for x in result_list]
counter = Counter(result)
print(counter, "True if converged")
n = subs_db.count_documents({"achievement": "executed"})
print(n, "executed")
def run_them():
random.seed(10)
subs_db = SubsMaterialsDatabase()
filterstring = {"purpose": "converged_ionic",
"achievement": "to_relax"}
for x in subs_db.find(filterstring):
id_ = x["_id"]
# hostname = x["hostname"]
basedir_prefix = x["basedir"]
# struc = StructureNode(basedir_prefix)
# kind = x["kind"]
# positionfile = x["positionfile"]
print("run", basedir_prefix)
calc = fakeVaspRunNode(basedir_prefix)
calc.place_files()
calc.run()
subs_db.delete_one({"_id": id_})
subs_db.add_files_under(basedir_prefix, StructureNode)
n = subs_db.count_documents({"achievement": "running"})
print(n, "running")
import os
import random
from pymatgen.core.structure import Structure
from pymatgen.analysis.structure_matcher import StructureMatcher
from subsMat.structure import SubsStructure
from subsMat.node import subs_elms_to_prefix, StructureNode
from subsMat.database import SubsMaterialsDatabase
if __name__ == "__main__":
random.seed(10)
subs_db = SubsMaterialsDatabase()
subs_elm_list = [[["Cu", "Fe"]]]
subs_elm_list.append([["Cu", "Ni"]])
subs_elm_list.append([["Cu", "Co"]])
for subs_elm in subs_elm_list:
print("substitute elements", subs_elm)
for x in subs_db.find_subs_elems(subs_elm):
basedir = x["basedir"]
positionfilename = x["positionfile"]
struc = StructureNode(basedir)
current_dir = struc.get_currentdir()
position_path = os.path.join(current_dir, positionfilename)
source_uuid = x["uuid"]
struc = SubsStructure.from_file(position_path)
new_struc = struc.substitute_elements(subs_elm)
from subsMat.database import SubsMaterialsDatabase
if __name__ == "__main__":
subs_db = SubsMaterialsDatabase()
subs_db.collection_remove()
print("collection is removed")
import random
from collections import Counter
from subsMat.database import SubsMaterialsDatabase
from subsMat.node import StructureNode
from subsMat.fakenode import fakeVaspRunNode
if __name__ == "__main__":
random.seed(10)
subs_db = SubsMaterialsDatabase()
filter = {"purpose": "converged_ionic", "achievement": "executed"}
result_list = []
for x in subs_db.find(filter):
id_ = x["_id"]
hostname = x["hostname"]
basedir_prefix = x["basedir"]
# current_dir = StructureNode(basedir_prefix).get_currentdir()
# kind = x["kind"]
# positionfile = x["positionfile"]
calc = fakeVaspRunNode(basedir_prefix)
result = calc.check_result()
result_list.append(result)
subs_db.delete_one({"_id": id_})
subs_db.add_files_under(basedir_prefix, StructureNode)
print(len(result_list), "data processed.")
# argparser = argparse.ArgumentParser()
# argparser.add_argument("--increase_data",
# default=False, action="store_true")
# args = argparser.parse_args()
action = ["step2"]
if True:
action.append("step1")
return action
action = parse_argument()
if "step1" in action:
metadata = {"purpose": "prototype", "achievement": "completed"}
subs_db = SubsMaterialsDatabase().\
initialize_with_dirs("Calc/MGI/mp-*", StructureNode)
n = subs_db.count_documents()
print("initial database size", n)
subs_elm_list = [[["Fe", "Cu"]]]
subs_elm_list.append([["Ni", "Cu"]])
subs_elm_list.append([["Cu", "Co"]])
subs_elm_list.append([["Zn", "Cu"]])
subs_elm_list.append([["Gd", "Y"]])
subs_elm_list.append([["Yb", "Y"]])
count_list = []
for subs_elm in subs_elm_list:
print("subsitute elements", subs_elm)