メニュー
Atomic Simulation Environment (ASE) for atomistic simulations: structure building, geometry optimization, NEB, molecular dynamics, and trajectory analysis.
デフォルトでは、最初にソースを確認する Prompt が選択されています。直接コマンドに切り替えるか、ローカルコピーをダウンロードすることもできます。
インストールを決める前に、SKILL.md と SkillsMP に表示されている付属ファイルをお読みください。
Codex または Claude でインストール この Prompt をコピーして Codex、Claude、または他のアシスタントに貼り付けると、Skill ページを確認してインストールできます。
直接コマンドでは確認用 Prompt が省略されます。実行前にソースを確認してください。
npx skills add https://github.com/xjtulyc/awesome-rosetta-skills --skill ase-atomisticコマンドは1行のまま表示されます。コピー前に横へスクロールして全体を確認してください。
ローカルで確認しますか？SkillsMP が現在取得できるファイルをダウンロードできます。
Astronomical data analysis with astropy and astroquery — FITS I/O, WCS transforms, catalog cross-matching, aperture photometry, and CMB power spectra.
Seismological data analysis with ObsPy — FDSN waveform download, response removal, phase picking, moment tensor inversion, and seismicity mapping.
Download and analyze oceanographic data from Copernicus Marine Service and Argo floats using copernicusmarine, gsw, and xarray.
SOC 職業分類に基づく
SKILL.md を表示中
| name | ase-atomistic |
| description | Atomic Simulation Environment (ASE) for atomistic simulations: structure building, geometry optimization, NEB, molecular dynamics, and trajectory analysis. |
| tags | ["ase","atomistic-simulation","chemistry","molecular-dynamics","dft","computational-chemistry"] |
| version | 1.0.0 |
| authors | [{"name":"awesome-rosetta-skills contributors","github":"@awesome-rosetta-skills"}] |
| license | MIT |
| platforms | ["claude-code","codex","gemini-cli","cursor"] |
| dependencies | ["ase>=3.22.0","numpy>=1.24.0","scipy>=1.11.0","matplotlib>=3.7.0"] |
| last_updated | 2026-03-17 |
The Atomic Simulation Environment (ASE) is the de-facto Python toolkit for setting up, running, and analyzing atomistic simulations. This skill covers structure building, geometry optimization, transition state searches, molecular dynamics, and trajectory analysis — with the EMT empirical potential as a dependency-free calculator.
ASE provides factory functions for common structure types.
from ase import Atoms
from ase.build import bulk, surface, molecule, fcc111, add_adsorbate
from ase.visualize import view # requires ASE GUI or nglview in Jupyter
import numpy as np
def build_structures_demo():
"""
Demonstrate building bulk, surface, molecule, and nanoparticle structures.
"""
# --- Bulk FCC copper ---
cu_bulk = bulk("Cu", crystalstructure="fcc", a=3.615, cubic=True)
print(f"Cu bulk: {len(cu_bulk)} atoms, cell = {cu_bulk.cell.diagonal().round(3)}")
# --- FCC(111) surface slab ---
def build_fcc_slab(element, miller, layers, vacuum=10.0, supercell=(2, 2)):
"""
Build an FCC surface slab.
Parameters
----------
element : str
Chemical symbol, e.g. 'Pt', 'Cu', 'Au'.
miller : tuple
Miller index, e.g. (1, 1, 1).
layers : int
Number of atomic layers.
vacuum : float
Vacuum thickness in Angstrom (added on both sides).
supercell : tuple
(nx, ny) supercell repetitions.
Returns
-------
slab : ase.Atoms
Surface slab with vacuum.
"""
from ase.build import fcc111, fcc110, fcc100
miller_map = {
(1, 1, 1): fcc111,
(1, 1, 0): fcc110,
(1, 0, 0): fcc100,
}
builder = miller_map.get(miller, fcc111)
slab = builder(element, size=(supercell[0], supercell[1], layers), vacuum=vacuum)
return slab
pt_slab = build_fcc_slab("Pt", (1, 1, 1), layers=4, vacuum=12.0, supercell=(3, 3))
print(f"Pt(111) slab: {len(pt_slab)} atoms")
print(f" Cell: {pt_slab.cell.diagonal().round(3)} Å")
print(f" Species: {set(pt_slab.get_chemical_symbols())}")
# --- Small molecules ---
co = molecule("CO")
h2o = molecule("H2O")
print(f"\nCO bond length: {co.get_distance(0, 1):.4f} Å")
print(f"H2O O-H bond: {h2o.get_distance(0, 1):.4f} Å")
print(f"H2O H-O-H angle: {h2o.get_angle(1, 0, 2):.2f}°")
# --- Custom Atoms object ---
h2 = Atoms(
symbols="HH",
positions=[[0, 0, 0], [0, 0, 0.74]],
cell=[10, 10, 10],
pbc=False,
)
print(f"\nH2 molecule: bond = {h2.get_distance(0, 1):.4f} Å")
# --- Nanoparticle (FCC icosahedron) ---
from ase.cluster import Icosahedron
np_Au = Icosahedron("Au", noshells=3)
print(f"\nAu nanoparticle: {len(np_Au)} atoms (Icosahedron, 3 shells)")
return pt_slab, co, h2
if __name__ == "__main__":
slab, co, h2 = build_structures_demo()
from ase.io import read, write
from ase.build import bulk, molecule
import os
def io_demo(output_dir="/tmp/ase_io_demo"):
"""
Demonstrate reading and writing structure files in various formats.
Supported formats: CIF, POSCAR/CONTCAR, XYZ, extXYZ, cube, cif, pdb, ...
"""
os.makedirs(output_dir, exist_ok=True)
# Build a test structure
cu = bulk("Cu", "fcc", a=3.615)
h2o = molecule("H2O")
# --- Write formats ---
write(f"{output_dir}/cu_bulk.vasp", cu, format="vasp") # POSCAR
write(f"{output_dir}/cu_bulk.cif", cu, format="cif") # CIF
write(f"{output_dir}/h2o.xyz", h2o, format="xyz") # XYZ
write(f"{output_dir}/h2o_ext.xyz", h2o, format="extxyz") # Extended XYZ
print(f"Wrote files to {output_dir}/")
for fname in os.listdir(output_dir):
fpath = f"{output_dir}/{fname}"
atoms = read(fpath)
print(f" {fname:25s}: {len(atoms):3d} atoms, formula={atoms.get_chemical_formula()}")
# --- Read a trajectory (multiple frames) ---
from ase.io.trajectory import Trajectory
from ase.calculators.emt import EMT
from ase.optimize import BFGS
traj_path = f"{output_dir}/test_traj.traj"
atoms = h2o.copy()
atoms.calc = EMT()
with Trajectory(traj_path, "w", atoms) as traj:
# Perturb and write a few frames
rng = np.random.default_rng(0)
for i in range(5):
atoms.positions += 0.05 * rng.standard_normal(atoms.positions.shape)
atoms.get_potential_energy() # trigger calc
traj.write(atoms)
# Read back all frames
frames = read(traj_path, index=":")
print(f"\nTrajectory: {len(frames)} frames, {len(frames[0])} atoms per frame")
energies = [f.get_potential_energy() for f in frames]
print(f"Energies: {[f'{e:.4f}' for e in energies]}")
return output_dir
import numpy as np
if __name__ == "__main__":
io_demo()
from ase.calculators.emt import EMT
from ase.optimize import BFGS, LBFGS, BFGSLineSearch
from ase.build import molecule
from ase.constraints import FixAtoms
import numpy as np
def optimize_geometry(atoms, calculator=None, fmax=0.01, optimizer="BFGS",
max_steps=500, trajectory_file=None):
"""
Optimize atomic positions to minimize forces.
Parameters
----------
atoms : ase.Atoms
Structure to optimize.
calculator : ase Calculator or None
If None, uses EMT (works for metals).
fmax : float
Convergence criterion: max force component in eV/Å.
optimizer : str
'BFGS', 'LBFGS', or 'BFGSLineSearch'.
max_steps : int
Maximum optimization steps.
trajectory_file : str or None
Path to save trajectory; None = no save.
Returns
-------
atoms : ase.Atoms (in-place modified)
converged : bool
"""
if calculator is None:
calculator = EMT()
atoms = atoms.copy()
atoms.calc = calculator
optimizer_map = {"BFGS": BFGS, "LBFGS": LBFGS, "BFGSLineSearch": BFGSLineSearch}
Opt = optimizer_map.get(optimizer, BFGS)
opt = Opt(atoms, logfile=None, trajectory=trajectory_file)
converged = opt.run(fmax=fmax, steps=max_steps)
e_final = atoms.get_potential_energy()
f_max = np.abs(atoms.get_forces()).max()
print(f"Geometry optimization ({optimizer}):")
print(f" Converged: {converged}")
print(f" Steps: {opt.nsteps}")
print(f" Energy: {e_final:.6f} eV")
print(f" Max force: {f_max:.6f} eV/Å")
return atoms, converged
def optimize_molecule_demo():
"""Optimize H2O geometry and compute properties."""
h2o = molecule("H2O")
h2o.calc = EMT()
print(f"Before optimization:")
print(f" Energy: {h2o.get_potential_energy():.6f} eV")
print(f" Max force: {np.abs(h2o.get_forces()).max():.6f} eV/Å")
h2o_opt, converged = optimize_geometry(h2o, fmax=0.001)
print(f"\nAfter optimization:")
print(f" O-H bond 1: {h2o_opt.get_distance(0, 1):.4f} Å")
print(f" O-H bond 2: {h2o_opt.get_distance(0, 2):.4f} Å")
print(f" H-O-H angle: {h2o_opt.get_angle(1, 0, 2):.2f}°")
return h2o_opt
def optimize_slab_with_constraints():
"""Optimize a surface slab with bottom layers fixed."""
from ase.build import fcc111
slab = fcc111("Pt", size=(2, 2, 4), vacuum=10.0)
slab.calc = EMT()
# Fix bottom 2 layers
n_bottom = len(slab) // 2
constraint = FixAtoms(indices=list(range(n_bottom)))
slab.set_constraint(constraint)
print(f"\nSlab optimization with FixAtoms constraint:")
print(f" {n_bottom} atoms fixed, {len(slab) - n_bottom} atoms free")
slab_opt, _ = optimize_geometry(slab, fmax=0.05, optimizer="LBFGS")
return slab_opt
if __name__ == "__main__":
h2o_opt = optimize_molecule_demo()
slab_opt = optimize_slab_with_constraints()
import numpy as np
from ase.calculators.emt import EMT
from ase.build import fcc111, add_adsorbate, molecule
from ase.optimize import BFGS
from ase.neb import NEB
from ase.constraints import FixAtoms
import matplotlib.pyplot as plt
def run_neb(initial, final, n_images=7, calculator_class=EMT, fmax=0.05):
"""
Run a Nudged Elastic Band calculation to find the minimum energy path.
Parameters
----------
initial : ase.Atoms
Initial state (relaxed).
final : ase.Atoms
Final state (relaxed).
n_images : int
Number of intermediate images (not counting endpoints).
calculator_class : callable
ASE calculator factory, e.g. EMT.
fmax : float
Force convergence threshold in eV/Å.
Returns
-------
images : list of ase.Atoms
All NEB images (initial + intermediate + final).
neb : NEB object
"""
# Build intermediate images by interpolation
images = [initial.copy()]
for _ in range(n_images):
images.append(initial.copy())
images.append(final.copy())
# Assign calculator to each intermediate image
for image in images[1:-1]:
image.calc = calculator_class()
# Linear interpolation
neb = NEB(images, climb=True, k=0.1)
neb.interpolate(method="idpp") # IDPP is smoother than linear for molecules
# Optimize
opt = BFGS(neb, logfile=None)
opt.run(fmax=fmax, steps=300)
print(f"NEB optimization steps: {opt.nsteps}")
return images, neb
def plot_neb_path(images):
"""Plot the NEB energy profile (MEP)."""
energies = [img.get_potential_energy() for img in images]
e_ref = energies[0]
reaction_coord = np.linspace(0, 1, len(energies))
activation_barrier = max(energies) - e_ref
reaction_energy = energies[-1] - e_ref
fig, ax = plt.subplots(figsize=(8, 5))
ax.plot(reaction_coord, [e - e_ref for e in energies], "o-", color="steelblue",
lw=2, ms=8, label="NEB images")
ax.fill_between(reaction_coord, [e - e_ref for e in energies], alpha=0.15, color="steelblue")
ax.axhline(0, color="gray", ls="--", lw=0.8)
ax.axhline(activation_barrier, color="red", ls=":", lw=1.5,
label=f"Barrier = {activation_barrier:.3f} eV")
ax.set_xlabel("Reaction Coordinate")
ax.set_ylabel("Energy (eV)")
ax.set_title("NEB Minimum Energy Path")
ax.legend()
print(f"\nNEB results:")
print(f" Activation barrier: {activation_barrier:.4f} eV")
print(f" Reaction energy: {reaction_energy:.4f} eV")
plt.tight_layout()
plt.show()
return activation_barrier, reaction_energy
def neb_demo():
"""
Demonstrate NEB for H2 dissociation on a flat potential (EMT demo).
Uses a simple displacement as the reaction coordinate.
"""
from ase import Atoms
# Initial: H2 molecule (bound)
initial = Atoms("H2", positions=[[0, 0, 0], [0, 0, 0.74]])
initial.calc = EMT()
opt = BFGS(initial, logfile=None)
opt.run(fmax=0.01)
# Final: H atoms separated
final = Atoms("H2", positions=[[0, 0, 0], [0, 0, 3.0]])
final.calc = EMT()
opt_f = BFGS(final, logfile=None)
opt_f.run(fmax=0.01)
print("H2 dissociation NEB:")
print(f" Initial energy: {initial.get_potential_energy():.4f} eV")
print(f" Final energy: {final.get_potential_energy():.4f} eV")
images, neb_obj = run_neb(initial, final, n_images=5, fmax=0.05)
barrier, delta_e = plot_neb_path(images)
return images
if __name__ == "__main__":
neb_demo()
import numpy as np
from ase import Atoms, units
from ase.build import bulk, molecule
from ase.calculators.emt import EMT
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase.md.verlet import VelocityVerlet
from ase.md.langevin import Langevin
from ase.io.trajectory import Trajectory
import matplotlib.pyplot as plt
def run_nvt_md(atoms, T=300, steps=1000, dt=1.0, friction=0.01,
trajectory_file=None, log_interval=10):
"""
Run NVT (constant temperature) molecular dynamics using Langevin thermostat.
Parameters
----------
atoms : ase.Atoms
Structure with calculator already set.
T : float
Target temperature in Kelvin.
steps : int
Total MD steps.
dt : float
Timestep in femtoseconds.
friction : float
Langevin friction coefficient (1/fs).
trajectory_file : str or None
Save trajectory to this file.
log_interval : int
Log energy/temperature every N steps.
Returns
-------
log : dict
Dictionary with 'time', 'temperature', 'potential_energy', 'kinetic_energy'.
"""
MaxwellBoltzmannDistribution(atoms, temperature_K=T)
dyn = Langevin(
atoms,
timestep=dt * units.fs,
temperature_K=T,
friction=friction / units.fs,
logfile=None,
)
log = {"time": [], "temperature": [], "potential_energy": [], "kinetic_energy": []}
if trajectory_file:
traj = Trajectory(trajectory_file, "w", atoms)
dyn.attach(traj.write, interval=log_interval)
def record():
log["time"].append(dyn.get_time() / units.fs)
log["temperature"].append(atoms.get_temperature())
log["potential_energy"].append(atoms.get_potential_energy())
log["kinetic_energy"].append(atoms.get_kinetic_energy())
dyn.attach(record, interval=log_interval)
dyn.run(steps)
if trajectory_file:
traj.close()
print(f"\nNVT MD completed:")
print(f" Steps: {steps}, dt = {dt} fs, T_target = {T} K")
print(f" T_mean = {np.mean(log['temperature']):.1f} K")
print(f" T_std = {np.std(log['temperature']):.2f} K")
return log
def run_nve_md(atoms, steps=500, dt=1.0, trajectory_file=None):
"""
Run NVE (microcanonical) MD using Velocity Verlet.
Energy should be approximately conserved.
"""
dyn = VelocityVerlet(atoms, timestep=dt * units.fs, logfile=None)
log = {"time": [], "total_energy": [], "temperature": []}
def record():
log["time"].append(dyn.get_time() / units.fs)
e_pot = atoms.get_potential_energy()
e_kin = atoms.get_kinetic_energy()
log["total_energy"].append(e_pot + e_kin)
log["temperature"].append(atoms.get_temperature())
dyn.attach(record, interval=5)
dyn.run(steps)
e_total = np.array(log["total_energy"])
drift = (e_total[-1] - e_total[0]) / abs(e_total[0]) * 100
print(f"\nNVE MD: total energy drift = {drift:.4f}%")
return log
def md_demo():
"""Run NVT MD on bulk Cu and plot thermodynamic observables."""
cu = bulk("Cu", "fcc", a=3.615, cubic=True) * (2, 2, 2)
cu.calc = EMT()
# Equilibrate at 500K
MaxwellBoltzmannDistribution(cu, temperature_K=500)
log = run_nvt_md(cu, T=500, steps=2000, dt=2.0, friction=0.02, log_interval=20)
fig, axes = plt.subplots(2, 1, figsize=(10, 7), sharex=True)
axes[0].plot(log["time"], log["temperature"], color="tomato", lw=0.8)
axes[0].axhline(500, color="black", ls="--", lw=1, label="T_target = 500 K")
axes[0].set_ylabel("Temperature (K)")
axes[0].legend()
axes[0].set_title("NVT MD — Bulk Cu at 500 K")
e_pot = np.array(log["potential_energy"])
e_kin = np.array(log["kinetic_energy"])
axes[1].plot(log["time"], e_pot, label="Potential", color="steelblue", lw=0.8)
axes[1].plot(log["time"], e_kin, label="Kinetic", color="darkorange", lw=0.8)
axes[1].plot(log["time"], e_pot + e_kin, label="Total", color="black", lw=1.2, ls="--")
axes[1].set_xlabel("Time (fs)")
axes[1].set_ylabel("Energy (eV)")
axes[1].legend()
plt.tight_layout()
plt.show()
return log
if __name__ == "__main__":
md_demo()
import numpy as np
from ase.io import read
from ase.geometry import get_distances
import matplotlib.pyplot as plt
def compute_rdf(trajectory, species_pair=None, rmax=6.0, nbins=100):
"""
Compute the radial distribution function g(r) from a trajectory.
Parameters
----------
trajectory : list of ase.Atoms
MD frames.
species_pair : tuple of str or None
e.g. ('Cu', 'Cu'). If None, uses all pairs.
rmax : float
Maximum distance in Å.
nbins : int
Number of histogram bins.
Returns
-------
r_centers : ndarray
Bin center distances.
g_r : ndarray
RDF values.
"""
dr = rmax / nbins
r_edges = np.linspace(0, rmax, nbins + 1)
r_centers = 0.5 * (r_edges[:-1] + r_edges[1:])
hist = np.zeros(nbins)
n_frames = len(trajectory)
for atoms in trajectory:
symbols = np.array(atoms.get_chemical_symbols())
N = len(atoms)
if species_pair is not None:
s1, s2 = species_pair
idx1 = np.where(symbols == s1)[0]
idx2 = np.where(symbols == s2)[0]
else:
idx1 = idx2 = np.arange(N)
for i in idx1:
for j in idx2:
if i >= j:
continue
r = atoms.get_distance(i, j, mic=True)
if r < rmax:
bin_idx = int(r / dr)
if bin_idx < nbins:
hist[bin_idx] += 2 # count both i->j and j->i
# Normalize to ideal gas
n_frames_norm = n_frames
cell_volume = np.mean([atoms.get_volume() for atoms in trajectory])
N_avg = np.mean([len(a) for a in trajectory])
rho = N_avg / cell_volume # number density
for k, (r_lo, r_hi) in enumerate(zip(r_edges[:-1], r_edges[1:])):
shell_vol = 4 * np.pi / 3 * (r_hi**3 - r_lo**3)
norm = rho * shell_vol * N_avg * n_frames_norm
g_r_k = hist[k] / (norm + 1e-12)
hist[k] = g_r_k
return r_centers, hist
def compute_msd(trajectory, species=None):
"""
Compute the Mean Squared Displacement as a function of time lag.
Parameters
----------
trajectory : list of ase.Atoms
MD frames (equal time spacing assumed).
species : str or None
If given, compute MSD only for this element.
Returns
-------
tau : ndarray
Time lags (in frame units).
msd : ndarray
MSD in Ų.
"""
n_frames = len(trajectory)
if species is not None:
ref_atoms = trajectory[0]
indices = [i for i, s in enumerate(ref_atoms.get_chemical_symbols()) if s == species]
else:
indices = list(range(len(trajectory[0])))
positions = np.array([atoms.positions[indices] for atoms in trajectory])
max_lag = n_frames // 2
msd = np.zeros(max_lag)
counts = np.zeros(max_lag)
for lag in range(1, max_lag):
disp = positions[lag:] - positions[:n_frames - lag]
msd[lag] = np.mean(np.sum(disp**2, axis=-1))
counts[lag] = n_frames - lag
return np.arange(max_lag), msd
def compute_rmsd(trajectory, reference=None):
"""
Compute RMSD of each frame relative to a reference structure.
Returns rmsd array in Å.
"""
if reference is None:
reference = trajectory[0]
ref_pos = reference.positions
rmsd_values = []
for atoms in trajectory:
disp = atoms.positions - ref_pos
rmsd = np.sqrt(np.mean(np.sum(disp**2, axis=-1)))
rmsd_values.append(rmsd)
return np.array(rmsd_values)
def trajectory_analysis_demo():
"""Generate an MD trajectory and perform full analysis."""
from ase.build import bulk
from ase.calculators.emt import EMT
from ase.md.langevin import Langevin
from ase.md.velocitydistribution import MaxwellBoltzmannDistribution
from ase import units
# Build system and run MD
cu = bulk("Cu", "fcc", a=3.615, cubic=True) * (3, 3, 3)
cu.calc = EMT()
MaxwellBoltzmannDistribution(cu, temperature_K=800)
dyn = Langevin(cu, timestep=2.0 * units.fs, temperature_K=800,
friction=0.01 / units.fs, logfile=None)
trajectory = []
def save_frame():
trajectory.append(cu.copy())
trajectory[-1].calc = None # don't keep calculator in trajectory
dyn.attach(save_frame, interval=5)
dyn.run(2000)
print(f"Collected {len(trajectory)} trajectory frames")
# Compute RDF
r, g_r = compute_rdf(trajectory[-50:], species_pair=("Cu", "Cu"), rmax=8.0, nbins=80)
# Compute MSD
tau, msd = compute_msd(trajectory, species="Cu")
# Compute RMSD
rmsd_vals = compute_rmsd(trajectory)
fig, axes = plt.subplots(1, 3, figsize=(15, 4))
axes[0].plot(r, g_r, color="steelblue", lw=1.5)
axes[0].axhline(1, color="gray", ls="--", lw=0.8, label="Ideal gas limit")
axes[0].set_xlabel("r (Å)")
axes[0].set_ylabel("g(r)")
axes[0].set_title("Radial Distribution Function — Cu")
axes[0].set_xlim(0, 8)
axes[0].legend()
valid = tau[1:] > 0
axes[1].plot(tau[1:][valid], msd[1:][valid], color="darkorange", lw=1.5)
axes[1].set_xlabel("Time lag (frames × 10 fs)")
axes[1].set_ylabel("MSD (Ų)")
axes[1].set_title("Mean Squared Displacement")
axes[2].plot(np.arange(len(rmsd_vals)) * 10, rmsd_vals, color="tomato", lw=1)
axes[2].set_xlabel("Time (fs)")
axes[2].set_ylabel("RMSD (Å)")
axes[2].set_title("RMSD from Initial Structure")
plt.tight_layout()
plt.show()
return trajectory, r, g_r, msd
if __name__ == "__main__":
trajectory_analysis_demo()
Compute the adsorption energy of CO on a Pt(111) surface using EMT.
import numpy as np
from ase.build import fcc111, molecule, add_adsorbate
from ase.calculators.emt import EMT
from ase.optimize import LBFGS
from ase.constraints import FixAtoms
import matplotlib.pyplot as plt
def co_adsorption_on_pt111(layers=4, vacuum=12.0, supercell=(3, 3)):
"""
Calculate the adsorption energy of CO on Pt(111).
E_ads = E(slab+CO) - E(slab) - E(CO)
Positive E_ads means adsorption is favorable (exothermic).
Adsorption sites tested: top, bridge, hollow-fcc, hollow-hcp
"""
def build_clean_slab():
slab = fcc111("Pt", size=(supercell[0], supercell[1], layers), vacuum=vacuum)
# Fix bottom half of slab
n_fix = len(slab) // 2
slab.set_constraint(FixAtoms(indices=list(range(n_fix))))
return slab
def relax(atoms, fmax=0.05, label=""):
atoms.calc = EMT()
opt = LBFGS(atoms, logfile=None)
opt.run(fmax=fmax, steps=300)
e = atoms.get_potential_energy()
print(f" {label:25s}: E = {e:.4f} eV, steps = {opt.nsteps}")
return atoms, e
# 1. Relax clean slab
print("Relaxing clean Pt(111) slab...")
slab_clean, e_slab = relax(build_clean_slab(), label="Clean Pt(111)")
# 2. Relax isolated CO molecule
print("Relaxing CO molecule...")
co = molecule("CO")
co.cell = [15, 15, 15]
co.center()
co.pbc = True
co_relaxed, e_co = relax(co, label="CO molecule")
print(f" CO bond length: {co_relaxed.get_distance(0, 1):.4f} Å")
# 3. Test adsorption on top site
adsorption_results = {}
sites = {
"top": ("ontop", (0, 0)),
"bridge": ("bridge", (0, 0)),
"fcc": ("fcc", (0, 0)),
"hcp": ("hcp", (0, 0)),
}
print("\nCalculating adsorption energies on different sites:")
for site_name, (site_type, offset) in sites.items():
slab_co = build_clean_slab()
slab_co.calc = EMT()
co_mol = molecule("CO")
try:
add_adsorbate(slab_co, co_mol, height=1.8, position=site_type)
except Exception:
# Fallback: add CO manually on top of a surface atom
surface_layer = [a for a in slab_co if a.tag == 1]
if surface_layer:
top_pos = slab_co[surface_layer[0].index].position[:2]
add_adsorbate(slab_co, co_mol, height=1.8, position=top_pos)
else:
add_adsorbate(slab_co, co_mol, height=1.8)
# Fix bottom layers
n_fix = (len(slab_co) - len(co_mol)) // 2
slab_co.set_constraint(FixAtoms(indices=list(range(n_fix))))
slab_co_relaxed, e_slab_co = relax(slab_co, label=f"Pt(111)+CO/{site_name}")
e_ads = e_slab + e_co - e_slab_co
adsorption_results[site_name] = {
"e_ads": e_ads,
"e_total": e_slab_co,
}
print("\n" + "=" * 45)
print("Adsorption Energies Summary:")
print("=" * 45)
for site, data in adsorption_results.items():
print(f" {site:8s}: E_ads = {data['e_ads']:+.4f} eV")
best_site = max(adsorption_results, key=lambda s: adsorption_results[s]["e_ads"])
print(f"\n Most stable site: {best_site}")
# Plot
sites_list = list(adsorption_results.keys())
e_ads_list = [adsorption_results[s]["e_ads"] for s in sites_list]
fig, ax = plt.subplots(figsize=(7, 4))
bars = ax.bar(sites_list, e_ads_list,
color=["green" if e > 0 else "tomato" for e in e_ads_list], alpha=0.8)
ax.axhline(0, color="black", lw=0.8)
ax.set_ylabel("E_ads (eV)")
ax.set_title("CO Adsorption Energy on Pt(111) Sites")
ax.bar_label(bars, fmt="%.3f", padding=3)
plt.tight_layout()
plt.show()
return adsorption_results
if __name__ == "__main__":
results = co_adsorption_on_pt111()
import numpy as np
from ase.build import molecule
from ase.calculators.emt import EMT
from ase.optimize import BFGS
from ase.vibrations import Vibrations
import matplotlib.pyplot as plt
def geometry_and_phonons(mol_name="H2O", outdir="/tmp/ase_vib"):
"""
(b) Full workflow:
1. Optimize geometry of a molecule
2. Compute vibrational modes (numerical Hessian)
3. Compute infrared intensities (if dipoles available)
4. Plot vibrational spectrum
Parameters
----------
mol_name : str
ASE molecule name, e.g. 'H2O', 'NH3', 'CH4'.
outdir : str
Directory to store vibrational calculation files.
"""
import os
os.makedirs(outdir, exist_ok=True)
# 1. Build and optimize
atoms = molecule(mol_name)
atoms.cell = [15, 15, 15]
atoms.center()
atoms.pbc = False
atoms.calc = EMT()
print(f"{'='*50}")
print(f"Molecule: {mol_name}, N_atoms = {len(atoms)}")
print(f"{'='*50}")
# Pre-optimization energy
e0 = atoms.get_potential_energy()
f0_max = np.abs(atoms.get_forces()).max()
print(f"Initial: E = {e0:.4f} eV, |F|_max = {f0_max:.4f} eV/Å")
opt = BFGS(atoms, logfile=None)
opt.run(fmax=0.001, steps=1000)
e_opt = atoms.get_potential_energy()
f_opt_max = np.abs(atoms.get_forces()).max()
print(f"Optimized: E = {e_opt:.4f} eV, |F|_max = {f_opt_max:.6f} eV/Å")
print(f"Relaxation: ΔE = {e_opt - e0:.4f} eV, steps = {opt.nsteps}")
# Print bond lengths and angles
print("\nGeometry:")
symbols = atoms.get_chemical_symbols()
if mol_name == "H2O":
print(f" O-H1: {atoms.get_distance(0, 1):.4f} Å")
print(f" O-H2: {atoms.get_distance(0, 2):.4f} Å")
print(f" H-O-H: {atoms.get_angle(1, 0, 2):.2f}°")
elif mol_name == "NH3":
for i in range(1, 4):
print(f" N-H{i}: {atoms.get_distance(0, i):.4f} Å")
# 2. Vibrational analysis
print(f"\nComputing vibrational modes (numerical Hessian)...")
vib = Vibrations(atoms, name=f"{outdir}/{mol_name}_vib", delta=0.01)
vib.run()
vib.summary(log="-") # print summary to stdout
# Get vibrational energies
vib_energies = vib.get_energies()
real_modes = [e for e in vib_energies if e.real > 1e-3 and abs(e.imag) < 1e-3]
imaginary_modes = [e for e in vib_energies if abs(e.imag) > 1.0]
print(f"\nVibrational frequencies (real modes):")
for i, e in enumerate(real_modes):
freq_cm1 = e.real * 8065.5 # eV → cm^-1
freq_thz = e.real * 241.8 # eV → THz
print(f" Mode {i+1}: {freq_cm1:.1f} cm⁻¹ ({freq_thz:.2f} THz)")
if imaginary_modes:
print(f" WARNING: {len(imaginary_modes)} imaginary mode(s) found.")
# Zero-point energy
zpe = vib.get_zero_point_energy()
print(f"\nZero-point energy: {zpe:.4f} eV")
# 3. Plot vibrational spectrum (Gaussian broadening)
freq_range = np.linspace(0, 5000, 2000) # cm^-1
spectrum = np.zeros_like(freq_range)
sigma = 30.0 # broadening in cm^-1
for e in real_modes:
freq_cm1 = e.real * 8065.5
spectrum += np.exp(-0.5 * ((freq_range - freq_cm1) / sigma) ** 2)
fig, axes = plt.subplots(2, 1, figsize=(10, 7))
# Stick spectrum
for e in real_modes:
freq_cm1 = e.real * 8065.5
axes[0].axvline(freq_cm1, ymin=0, ymax=1, color="steelblue", lw=2, alpha=0.8)
axes[0].set_xlim(0, 5000)
axes[0].set_ylabel("Intensity (arb.)")
axes[0].set_title(f"{mol_name} Vibrational Frequencies (Stick Spectrum)")
axes[0].set_xlabel("Wavenumber (cm⁻¹)")
# Broadened spectrum
axes[1].plot(freq_range, spectrum, color="darkorange", lw=1.5)
axes[1].fill_between(freq_range, spectrum, alpha=0.3, color="darkorange")
axes[1].set_xlim(0, 5000)
axes[1].set_xlabel("Wavenumber (cm⁻¹)")
axes[1].set_ylabel("Intensity (arb.)")
axes[1].set_title(f"{mol_name} IR Spectrum (σ={sigma} cm⁻¹)")
plt.tight_layout()
plt.show()
# Cleanup
vib.clean()
return atoms, vib_energies
if __name__ == "__main__":
atoms_h2o, vib_h2o = geometry_and_phonons("H2O")
atoms_nh3, vib_nh3 = geometry_and_phonons("NH3")
| Task | ASE API |
|---|---|
| Build FCC bulk | bulk("Cu", "fcc", a=3.615) |
| Build surface slab | fcc111("Pt", size=(3,3,4), vacuum=10.0) |
| Build molecule | molecule("H2O") |
| Add adsorbate | add_adsorbate(slab, mol, height=1.8) |
| Fix atoms (constraint) | FixAtoms(indices=[...]) |
| Read structure file | read("file.cif") |
| Write structure file | write("out.vasp", atoms, format="vasp") |
| Set EMT calculator | atoms.calc = EMT() |
| Get potential energy | atoms.get_potential_energy() |
| Get forces | atoms.get_forces() |
| Optimize geometry (BFGS) | BFGS(atoms); opt.run(fmax=0.01) |
| Optimize geometry (LBFGS) | LBFGS(atoms); opt.run(fmax=0.05) |
| NVT Langevin MD | Langevin(atoms, dt*units.fs, T, friction/units.fs) |
| NVE Verlet MD | VelocityVerlet(atoms, dt*units.fs) |
| Maxwell-Boltzmann velocities | MaxwellBoltzmannDistribution(atoms, temperature_K=T) |
| NEB transition state | NEB(images, climb=True); BFGS(neb).run(fmax=0.05) |
| Vibrational analysis | Vibrations(atoms); vib.run(); vib.summary() |
| Get bond distance | atoms.get_distance(i, j, mic=True) |
| Get bond angle | atoms.get_angle(i, j, k) |
| Calculator | Use case | Availability |
|---|---|---|
| EMT | FCC metals (quick testing) | Built into ASE |
| GPAW | DFT, PAW method | pip install gpaw |
| VASP | DFT, plane waves | License required |
| CP2K | DFT, mixed Gaussian/PW | Free, open source |
| LAMMPS | Classical MD, many potentials | Free, open source |
| Psi4 / ORCA | Quantum chemistry | Free/academic |