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Merged
RagnarB83 merged 2 commits into from
Sep 24, 2026
Merged

Dlfind restart #522

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ba8e043
Add DL-FIND restart support
danielguion Sep 23, 2026
e089810
Improve DL-FIND NEB output logging
danielguion Sep 23, 2026
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103 changes: 83 additions & 20 deletions ash/interfaces/interface_dlfind.py
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ def DLFIND_optimizer(jobtype=None, theory=None, fragment=None, fragment2=None, c
hessian_choice="numfreq", inithessian=0,
numfreq_npoint=1, numfreq_displacement=0.005, numfreq_hessatoms=None,
numfreq_force_projection=None, print_atoms_list=None,
force_noPBC=False, PBC_format_option='CIF'):
force_noPBC=False, PBC_format_option='CIF', dump=None, restart=None):
"""
Wrapper function around DLFIND_optimizerClass
"""
Expand All @@ -46,7 +46,7 @@ def DLFIND_optimizer(jobtype=None, theory=None, fragment=None, fragment2=None, c
hessian_choice=hessian_choice, inithessian=inithessian,
numfreq_npoint=numfreq_npoint,numfreq_displacement=numfreq_displacement,
numfreq_hessatoms=numfreq_hessatoms,numfreq_force_projection=numfreq_force_projection,
print_atoms_list=print_atoms_list,
print_atoms_list=print_atoms_list, dump=dump, restart=restart,
force_noPBC=force_noPBC, PBC_format_option=PBC_format_option)

# If NumGrad then we wrap theory object into NumGrad class object
Expand All @@ -72,7 +72,7 @@ def __init__(self,jobtype=None, fragment=None, fragment2=None, theory=None, char
hessian_choice='numfreq', inithessian=None,
numfreq_npoint=1,numfreq_displacement=0.005,numfreq_force_projection=None,
numfreq_hessatoms=None, print_atoms_list=None,
force_noPBC=False, PBC_format_option='CIF'):
force_noPBC=False, PBC_format_option='CIF', dump=None, restart=None):

print_line_with_mainheader("DLFIND_optimizer initialization")
print()
Expand Down Expand Up @@ -180,6 +180,11 @@ def __init__(self,jobtype=None, fragment=None, fragment2=None, theory=None, char
self.tolerance_e=tolerance_e
# NEB
self.nimage=nimage

# DL-FIND restart/checkpoint options
self.dump=dump
self.restart=restart

#Dimer
self.delta=delta

Expand Down Expand Up @@ -231,7 +236,10 @@ def ash_e_g_func(coordinates, iimage, kiter, theory):
#PRINTING ACTIVE GEOMETRY IN EACH GEOMETRIC ITERATION
self.fragment.write_xyzfile(xyzfilename="Fragment-currentgeo.xyz")
if self.printlevel >= 1:
print(f"Current geometry (Å) in step {self.dlfind_opt_cycles} (print_atoms_list region)")
if self.icoord >= 100 and self.icoord < 150:
print(f"Current geometry (Å), NEB cycle {self.dlfind_neb_cycles + 1}, image {iimage} (print_atoms_list region)")
else:
print(f"Current geometry (Å) in step {self.dlfind_opt_cycles} (print_atoms_list region)")
print("---------------------------------------------------")
print_coords_for_atoms(R_phys, self.elems_phys, self.print_atoms_list)
print("")
Expand Down Expand Up @@ -279,7 +287,10 @@ def ash_e_g_func(coordinates, iimage, kiter, theory):
#PRINTING ACTIVE GEOMETRY IN EACH GEOMETRIC ITERATION
self.fragment.write_xyzfile(xyzfilename="Fragment-currentgeo.xyz")
if self.printlevel >= 1:
print(f"Current geometry (Å) in step {self.dlfind_opt_cycles} (print_atoms_list region)")
if self.icoord >= 100 and self.icoord < 150:
print(f"Current geometry (Å), NEB cycle {self.dlfind_neb_cycles + 1}, image {iimage} (print_atoms_list region)")
else:
print(f"Current geometry (Å) in step {self.dlfind_opt_cycles} (print_atoms_list region)")
print("---------------------------------------------------")
print_coords_for_atoms(coordinates_ang, self.fragment.elems, self.print_atoms_list)
print("")
Expand Down Expand Up @@ -371,7 +382,7 @@ def hess_func(coords):
# Create function to store results from DL-FIND
#@dlf_put_coords_wrapper
def store_results(a,nvar,switch, energy, coordinates, iam):
print("Called store_results with switch:", switch)
print("Called store_results with switch:", switch, flush=True)
if switch > 0:
coords = as_array(coordinates, (nvar,)).reshape(-1, 3)
coordinates_ang = coords*0.5291772109303
Expand All @@ -380,23 +391,30 @@ def store_results(a,nvar,switch, energy, coordinates, iam):
# Write out NEB path if switch -1
if self.icoord >= 100 and self.icoord < 150 and switch == -1:
self.dlfind_neb_cycles+=1
print("="*70)
print(f"DLFIND NEB-OPTIMIZATION CYCLE {self.dlfind_neb_cycles}")
print("="*70)
print("="*70, flush=True)
print(f"DLFIND NEB-OPTIMIZATION CYCLE {self.dlfind_neb_cycles}", flush=True)
print("="*70, flush=True)

for imageid in list(range(1,self.nimage)):
if imageid not in self.NEB_energies_dict or imageid not in self.NEB_geometries:
print(f"Error: Missing ASH NEB data for image {imageid}")
ashexit()
#print("Switch -1, writing out current NEB-path without CI")
with open("DLFIND_NEBpath_all.xyz", "a") as trajfile:
for imageid in list(range(1,self.nimage)):
trajfile.write(str(self.fragment.numatoms) + "\n")
trajfile.write(f"Image {imageid}. Energy: {self.NEB_energies_dict[imageid]} \n")
for el, cord in zip(self.fragment.elems, self.NEB_geometries[imageid]):
trajfile.write(el + " " + str(cord[0]) + " " + str(cord[1]) + " " + str(cord[2]) + "\n")
with open("DLFIND_NEBpath_current.xyz", "w") as trajfile:
with open("DLFIND_NEBpath_current.xyz.tmp", "w") as trajfile:
for imageid in list(range(1,self.nimage)):
trajfile.write(str(self.fragment.numatoms) + "\n")
trajfile.write(f"Image {imageid}. Energy: {self.NEB_energies_dict[imageid]} \n")
for el, cord in zip(self.fragment.elems, self.NEB_geometries[imageid]):
trajfile.write(el + " " + str(cord[0]) + " " + str(cord[1]) + " " + str(cord[2]) + "\n")

os.replace("DLFIND_NEBpath_current.xyz.tmp", "DLFIND_NEBpath_current.xyz")

# Writing out CI once it has been spawned
if nimage in self.NEB_geometries:
print("Writing out current trajectory for climbing image as: DLFIND_CIgeo_traj.xyz ")
Expand Down Expand Up @@ -673,24 +691,29 @@ def prepare_run(self):
iopt=self.iopt, maxcycle=self.maxcycle,tolerance=self.tolerance,
tolerance_e=self.tolerance_e, inithessian=self.inithessian,
nframe=nframe, nz=nz,
ncons=self.numcons, delta=self.delta,
ncons=self.numcons, delta=self.delta, dump=self.dump, restart=self.restart,
spec=self.spec, printl=self.printlevel, nimage=self.nimage)

# Delete old traj file before beginning
# Delete old traj files before beginning, unless this is a restart
remove_files=['DLFIND_opt_traj.xyz','DLFIND_dimertraj_1.xyz', 'DLFIND_dimertraj_2.xyz','DLFIND_dimertraj_3.xyz','DLFIND_NEBpath_current.xyz', 'DLFIND_NEBpath_all.xyz', 'DLFIND_CIgeo_traj.xyz']
print_if_level(f"Removing possible old files: {remove_files}", self.printlevel,2)
for rfile in remove_files:
try:
os.remove(rfile)
print_if_level(f"removed {rfile} ", self.printlevel,2)
except FileNotFoundError:
#print(f"file {rfile} not found")
pass

if self.restart in (None,0):
print_if_level(f"Removing possible old files: {remove_files}", self.printlevel,2)
for rfile in remove_files:
try:
os.remove(rfile)
print_if_level(f"removed {rfile} ", self.printlevel,2)
except FileNotFoundError:
pass
else:
print_if_level("Restart requested. Keeping existing DL-FIND files.", self.printlevel,2)

print_if_level(f"\nArguments passed to DL-FIND:", self.printlevel,2)
print_if_level(f"icoord: {self.icoord}", self.printlevel,2)
print_if_level(f"iopt: {self.iopt}", self.printlevel,2)
print_if_level(f"maxcycle: {self.maxcycle}", self.printlevel,2)
print_if_level(f"dump: {self.dump}", self.printlevel,2)
print_if_level(f"restart: {self.restart}", self.printlevel,2)
print_if_level(f"spec ({len(self.spec)}): {self.spec}", self.printlevel,2)
if self.icoord == 120:
print_if_level(f"NEB nimage: {self.nimage}", self.printlevel,2)
Expand All @@ -707,6 +730,46 @@ def run(self, theory=None, fragment=None, fragment2=None, constraints=None, char
self.NEB_energies_dict={}
self.NEB_geometries={}

# Restore ASH NEB bookkeeping on restart
if self.restart not in (None,0) and 100 <= self.icoord < 150:
# Restore previous ASH NEB cycle count
if os.path.isfile("DLFIND_NEBpath_all.xyz"):
with open("DLFIND_NEBpath_all.xyz") as f:
self.dlfind_neb_cycles = sum(1 for line in f if line.startswith("Image 1."))
print(f"Restart: restored ASH NEB cycle counter to {self.dlfind_neb_cycles}")

# Restore energies/geometries of the most recent complete NEB path
if os.path.isfile("DLFIND_NEBpath_current.xyz"):
print("Restart: restoring ASH NEB energies/geometries from DLFIND_NEBpath_current.xyz")
with open("DLFIND_NEBpath_current.xyz") as f:
lines = f.readlines()

i = 0
while i < len(lines):
natoms = int(lines[i].strip())
header = lines[i + 1].split()
imageid = int(header[1].rstrip("."))
energy = float(header[3])

coords = []
for j in range(natoms):
parts = lines[i + 2 + j].split()
coords.append([float(parts[1]), float(parts[2]), float(parts[3])])

self.NEB_energies_dict[imageid] = energy
self.NEB_geometries[imageid] = np.array(coords)

i += natoms + 2

print("Restored NEB images:", sorted(self.NEB_energies_dict.keys()))

expected_images = set(range(1,self.nimage))
restored_images = set(self.NEB_energies_dict.keys())
missing_images = expected_images - restored_images
if len(missing_images) > 0:
print(f"Error: Missing NEB restart data for images: {sorted(missing_images)}")
ashexit()

# Runcounter
self.runcounter=0

Expand Down
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