I started to learn how to use atomate, specially for surface/adsorption calculations workflow. At first I started with the tutorial “High-throughput workflows for determining adsorption energies on solid surfaces.” I tried with the following code taken from the link with some modifications: Slab relaxation and MongoDB output missing.
from pymatgen.core import Structure, Lattice, Molecule
from pymatgen.ext.matproj import MPRester
from pymatgen.analysis.adsorption import *
from pymatgen.core.surface import generate_all_slabs
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from matplotlib import pyplot as plt
from fireworks import LaunchPad
from atomate.vasp.config import DB_FILE
mpr = MPRester(‘az2g1nSIOQkZRCJv’)
lpad = LaunchPad.auto_load()
lpad.reset(’’, require_password=False)
from atomate.vasp.workflows.base.adsorption import get_wf_slab
struct = mpr.get_structure_by_material_id(“mp-30”) # fcc Cu
#print(struct)
slabs = generate_all_slabs(struct, 2, 5.0, 10.0, center_slab=True)
#print(slabs)
slab_dict = {slab.miller_index:slab for slab in slabs}
#print(slab_dict)
Cu_slab_111 = slab_dict[(1, 1, 1)]
#print(Cu_slab_111)
asf_Cu_111 = AdsorbateSiteFinder(Cu_slab_111)
ads_sites = asf_Cu_111.find_adsorption_sites()
#print(ads_sites)
co = Molecule(“CO”, [[0, 0, 0], [0, 0, 1.23]])
h = Molecule(“H”, [[0, 0, 0]])
wf = get_wf_slab(Cu_slab_111,adsorbates=[co,h],db_file=DB_FILE)
lpad.add_wf(wf)
But we have found the following errors :
lpad.reset(’’, require_password=False)
File “/apps/compilers/anaconda3/2020/lib/python3.8/site-packages/fireworks/core/launchpad.py”, line 345, in reset
not require_password and self.workflows.count() <= max_reset_wo_password):
File “/apps/compilers/anaconda3/2020/lib/python3.8/site-packages/pymongo/collection.py”, line 1906, in count
return self._count(cmd, collation, session)
File “/apps/compilers/anaconda3/2020/lib/python3.8/site-packages/pymongo/collection.py”, line 1679, in _count
return self.__database.client._retryable_read(
File “/apps/compilers/anaconda3/2020/lib/python3.8/site-packages/pymongo/mongo_client.py”, line 1514, in _retryable_read
server = self._select_server(
File “/apps/compilers/anaconda3/2020/lib/python3.8/site-packages/pymongo/mongo_client.py”, line 1346, in _select_server
server = topology.select_server(server_selector)
File “/apps/compilers/anaconda3/2020/lib/python3.8/site-packages/pymongo/topology.py”, line 244, in select_server
return random.choice(self.select_servers(selector,
File “/apps/compilers/anaconda3/2020/lib/python3.8/site-packages/pymongo/topology.py”, line 202, in select_servers
server_descriptions = self._select_servers_loop(
File “/apps/compilers/anaconda3/2020/lib/python3.8/site-packages/pymongo/topology.py”, line 218, in _select_servers_loop
raise ServerSelectionTimeoutError(
pymongo.errors.ServerSelectionTimeoutError: localhost:27017: [Errno 111] Connection refused, Timeout: 30s, Topology Description: <TopologyDescription id: 6128d647aff9caafc46d6e0d, topology_type: Single, servers: [<ServerDescription (‘localhost’, 27017) server_type: Unknown, rtt: None, error=AutoReconnect(‘localhost:27017: [Errno 111] Connection refused’)>]>
Is this a problem related to installation or some problem in code? If you kindly suggest any solution it will very helpful for me. Thanks in advance.