NEB Dynamics Documentation🔗
Welcome to the NEB Dynamics documentation! This software package provides tools for running automated minimum energy path (MEP) minimizations using the Nudged Elastic Band (NEB) method and its variants.
Overview🔗
NEB Dynamics is designed to: - Find transition states and reaction paths between chemical structures - Automatically split complex reaction pathways into elementary steps - Support multiple electronic structure engines (ChemCloud, QCOP, ASE-based calculators) - Provide geodesic interpolation for generating initial path guesses
Installation🔗
Detailed install/setup instructions are in:
That page includes:
uvandpipinstallation workflows- backend setup (including ChemCloud auth)
- optional
retropathssetup for network-growth features - verification commands
Quick Start🔗
import numpy as np
from qcio import Structure
from neb_dynamics import StructureNode, NEBInputs, ChainInputs
from neb_dynamics.engines.qcop import QCOPEngine
from neb_dynamics.neb import NEB
import neb_dynamics.chainhelpers as ch
from neb_dynamics import Chain
from neb_dynamics.optimizers.cg import ConjugateGradient
# 1. Define initial and final structures using embedded XYZ data
start_xyz = """17
Frame 0
C 0.885440409184 2.102076768875 0.627821743488
C 0.841612815857 1.115651130676 -0.247040778399
C -0.420807182789 0.556873917580 -0.838685691357
O -0.430870711803 0.798001468182 -2.239025592804
C -0.522329509258 -0.964021146297 -0.644988238811
C -0.715307652950 -1.349323630333 0.785972416401
C 0.097422197461 -2.135773420334 1.466876506805
H -0.267592728138 1.735007524490 -2.391090631485
H -1.386946558952 -1.296320080757 -1.227010726929
H 0.993258416653 -2.552916049957 1.031124353409
H -0.008914750069 2.554719924927 1.029638171196
H 1.820721507072 2.502734899521 0.982666194439
H 1.748645901680 0.692936420441 -0.660514891148
H -1.296261906624 1.040292620659 -0.372635990381
H 0.376222431660 -1.434682250023 -1.046772599220
H -1.611668467522 -0.956238925457 1.253052473068
H -0.102624341846 -2.409019231796 2.490613460541
"""
end_xyz = """17
Frame 29
C 0.576232671738 0.921668708324 0.825146675110
C 0.811691701412 1.315650582314 -0.631796598434
C -0.290672153234 0.930290937424 -1.571661710739
O -0.139186233282 0.584553778172 -2.709024667740
C -1.166546344757 -1.861497998238 -0.220005810261
C -0.774998486042 -1.183089017868 0.841198801994
C 0.589584112167 -0.601971745491 1.032947182655
H 0.880913138390 2.407624959946 -0.707833826542
H -2.171884059906 -2.235154390335 -0.311172336340
H 1.294490098953 -1.047748923302 0.330671131611
H -0.374946832657 1.333065629005 1.164748311043
H 1.358177542686 1.381788730621 1.429385662079
H 1.752718806267 0.898995816708 -0.990877032280
H -1.302031993866 1.039528012276 -1.137167930603
H -0.504405736923 -2.070925474167 -1.043461441994
H -1.469262003899 -0.993297398090 1.650624632835
H 0.930125653744 -0.819482147694 2.048279047012
"""
# Load structures from XYZ strings
start = Structure.from_xyz(start_xyz)
end = Structure.from_xyz(end_xyz)
# 2. Create nodes
start_node = StructureNode(structure=start)
end_node = StructureNode(structure=end)
# 3. Set up engine using ChemCloud
eng = QCOPEngine(compute_program="chemcloud")
# 4. Optimize endpoints
start_opt = eng.compute_geometry_optimization(start_node)
end_opt = eng.compute_geometry_optimization(end_node)
# 5. Create initial chain using geodesic interpolation
chain = Chain.model_validate({
'nodes': [start_opt[-1], end_opt[-1]],
'parameters': ChainInputs(k=0.1, delta_k=0.09)
})
initial_chain = ch.run_geodesic(chain, nimages=15)
# 6. Run NEB optimization
opt = ConjugateGradient(timestep=0.5)
nbi = NEBInputs(v=True)
n = NEB(initial_chain=initial_chain, parameters=nbi, optimizer=opt, engine=eng)
results = n.optimize_chain()
# 7. Visualize results
n.plot_opt_history(1)
ch.visualize_chain(n.optimized)