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handle vdW in coverage dependence 2D extraction functions
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@mjohnson541
mjohnson541 committed Jan 8, 2025
1 parent c5b8abb commit b7fdc1b
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Showing 2 changed files with 63 additions and 10 deletions.
36 changes: 28 additions & 8 deletions pynta/coveragedependence.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -1739,7 +1739,7 @@ def get_configs_of_concern(tree_interaction_regressor,configs,coad_stable_sites,
return configs_of_concern

def load_coverage_delta(d,ad_energy_dict,slab,metal,facet,sites,site_adjacency,ts_pynta_dir=None,allowed_structure_site_structures=None,
out_file_name="out",vib_file_name="vib",is_ad=None):
out_file_name="out",vib_file_name="vib",is_ad=None,keep_binding_vdW_bonds=False,keep_vdW_surface_bonds=False):

try:
info = json.load(open(os.path.join(d,"info.json")))
Expand All @@ -1755,7 +1755,9 @@ def load_coverage_delta(d,ad_energy_dict,slab,metal,facet,sites,site_adjacency,t

if not is_ts:
try:
admol,neighbor_sites,ninds = generate_adsorbate_2D(atoms, sites, site_adjacency, len(slab), max_dist=np.inf, cut_multidentate_off_num=None, allowed_structure_site_structures=allowed_structure_site_structures)
admol,neighbor_sites,ninds = generate_adsorbate_2D(atoms, sites, site_adjacency, len(slab), max_dist=np.inf, cut_multidentate_off_num=None,
allowed_structure_site_structures=allowed_structure_site_structures,
keep_binding_vdW_bonds=keep_binding_vdW_bonds,keep_vdW_surface_bonds=keep_vdW_surface_bonds)
except (SiteOccupationException,TooManyElectronsException,ValueError) as e:
return None,None,None,None

Expand Down Expand Up @@ -1792,7 +1794,9 @@ def load_coverage_delta(d,ad_energy_dict,slab,metal,facet,sites,site_adjacency,t
ts_info_path = os.path.join(ts_path,"info.json")

try:
admol,neighbor_sites,ninds = generate_TS_2D(atoms, ts_info_path, metal, facet, sites, site_adjacency, len(slab), imag_freq_path=os.path.join(d,"vib.0.traj"), max_dist=np.inf, allowed_structure_site_structures=allowed_structure_site_structures)
admol,neighbor_sites,ninds = generate_TS_2D(atoms, ts_info_path, metal, facet, sites, site_adjacency, len(slab), imag_freq_path=os.path.join(d,"vib.0.traj"),
max_dist=np.inf, allowed_structure_site_structures=allowed_structure_site_structures,
keep_binding_vdW_bonds=keep_binding_vdW_bonds,keep_vdW_surface_bonds=keep_vdW_surface_bonds)
except (SiteOccupationException,TooManyElectronsException, ValueError) as e:
return None,None,None,None
try:
Expand Down Expand Up @@ -1882,11 +1886,24 @@ def extract_sample(d,ad_energy_dict,slab,metal,facet,sites,site_adjacency,pynta_
# vibdata = get_vibdata(os.path.join(d,out_file_name+".xyz"),os.path.join(d,vib_file_name+".json"),len(slab))
# except:
# vibdata = None

keep_binding_vdW_bonds=False
keep_vdW_surface_bonds=False

try:
with open(os.path.join(d,"info.json"),'r') as f:
info = json.load(f)
except:
mol = Molecule().from_adjacency_list(info["adjlist"])
for bd in mol.get_all_edges():
if bd.order == 0:
if bd.atom1.is_surface_site() or bd.atom2.is_surface_site():
keep_binding_vdW_bonds = True
m = mol.copy(deep=True)
b = m.get_bond(m.atoms[mol.atoms.index(bd.atom1)],m.atoms[mol.atoms.index(bd.atom2)])
m.remove_bond(b)
out = m.split()
if len(out) == 1: #vdW bond is not only thing connecting adsorbate to surface
keep_vdW_surface_bonds = True
except FileNotFoundError:
info = None

if is_ad is None:
Expand Down Expand Up @@ -1930,13 +1947,15 @@ def extract_sample(d,ad_energy_dict,slab,metal,facet,sites,site_adjacency,pynta_

admol,neighbor_sites,ninds,dE = load_coverage_delta(d,ad_energy_dict,slab,metal,facet,sites,site_adjacency,
ts_pynta_dir=pynta_dir,allowed_structure_site_structures=allowed_structure_site_structures,
out_file_name=out_file_name,vib_file_name=vib_file_name,is_ad=is_ad)
out_file_name=out_file_name,vib_file_name=vib_file_name,is_ad=is_ad,
keep_binding_vdW_bonds=keep_binding_vdW_bonds,keep_vdW_surface_bonds=keep_vdW_surface_bonds)


if is_ad:
try:
admol_init,neighbor_sites_init,ninds_init = generate_adsorbate_2D(atoms_init, sites, site_adjacency, nslab,
max_dist=None, cut_multidentate_off_num=cut_multidentate_off_num, allowed_structure_site_structures=allowed_structure_site_structures)
max_dist=None, cut_multidentate_off_num=cut_multidentate_off_num, allowed_structure_site_structures=allowed_structure_site_structures,
keep_binding_vdW_bonds=keep_binding_vdW_bonds,keep_vdW_surface_bonds=keep_vdW_surface_bonds)
except TooManyElectronsException:
admol_init = None
neighbor_sites_init = None
Expand All @@ -1955,7 +1974,8 @@ def extract_sample(d,ad_energy_dict,slab,metal,facet,sites,site_adjacency,pynta_
try:
admol_init,neighbor_sites_init,ninds_init = generate_TS_2D(atoms_init, info_path, metal, facet, sites, site_adjacency, nslab,
imag_freq_path=imag_freq_path, max_dist=None, cut_multidentate_off_num=cut_multidentate_off_num,
allowed_structure_site_structures=allowed_structure_site_structures)
allowed_structure_site_structures=allowed_structure_site_structures,
keep_binding_vdW_bonds=keep_binding_vdW_bonds,keep_vdW_surface_bonds=keep_vdW_surface_bonds)
except TooManyElectronsException as e:
valid = False
admol_init = None
Expand Down
37 changes: 35 additions & 2 deletions pynta/main.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -699,9 +699,26 @@ def setup_active_learning_loop(self):

for ts in self.transition_states.keys():
info_path = os.path.join(self.pynta_run_directory,ts,"info.json")
with open(info_path) as f:
info = json.load(f)
mol = Molecule().from_adjacency_list(info["adjlist"])
keep_binding_vdW_bonds=False
keep_vdW_surface_bonds=False
for bd in mol.get_all_edges():
if bd.order == 0:
if bd.atom1.is_surface_site() or bd.atom2.is_surface_site():
keep_binding_vdW_bonds = True
m = mol.copy(deep=True)
b = m.get_bond(m.atoms(mol.atoms.index(bd.atom1)),m.atoms[mol.atoms.index(bd.atom2)])
m.remove_bond(b)
out = m.split()
if len(out) == 1: #vdW bond is not only thing connecting adsorbate to surface
keep_vdW_surface_bonds = True

atoms = read(admol_name_path_dict[ts])
st,_,_ = generate_TS_2D(atoms, info_path, self.metal, self.surface_type, self.sites, self.site_adjacency, self.nslab,
max_dist=np.inf, allowed_structure_site_structures=allowed_structure_site_structures)
max_dist=np.inf, allowed_structure_site_structures=allowed_structure_site_structures,
keep_binding_vdW_bonds=keep_binding_vdW_bonds,keep_vdW_surface_bonds=keep_vdW_surface_bonds)
admol_name_structure_dict[ts] = st
with open(info_path,"r") as f:
info = json.load(f)
Expand All @@ -713,12 +730,28 @@ def setup_active_learning_loop(self):
p = os.path.join(self.pynta_run_directory,"Adsorbates",ad)
with open(os.path.join(p,"info.json")) as f:
info = json.load(f)

mol = Molecule().from_adjacency_list(info["adjlist"])

if mol.contains_surface_site():
keep_binding_vdW_bonds=False
keep_vdW_surface_bonds=False
for bd in mol.get_all_edges():
if bd.order == 0:
if bd.atom1.is_surface_site() or bd.atom2.is_surface_site():
keep_binding_vdW_bonds = True
m = mol.copy(deep=True)
b = m.get_bond(m.atoms(mol.atoms.index(bd.atom1)),m.atoms[mol.atoms.index(bd.atom2)])
m.remove_bond(b)
out = m.split()
if len(out) == 1: #vdW bond is not only thing connecting adsorbate to surface
keep_vdW_surface_bonds = True

ad_xyz = get_best_adsorbate_xyz(p,self.sites,self.nslab)
admol_name_path_dict[ad] = ad_xyz
atoms = read(ad_xyz)
st,_,_ = generate_adsorbate_2D(atoms, self.sites, self.site_adjacency, self.nslab, max_dist=np.inf, allowed_structure_site_structures=allowed_structure_site_structures)
st,_,_ = generate_adsorbate_2D(atoms, self.sites, self.site_adjacency, self.nslab, max_dist=np.inf, allowed_structure_site_structures=allowed_structure_site_structures,
keep_binding_vdW_bonds=keep_binding_vdW_bonds,keep_vdW_surface_bonds=keep_vdW_surface_bonds)
admol_name_structure_dict[ad] = st

calculation_directories = [] #identify pairs directories
Expand Down

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