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rlaplaza/opt_min_xtb_ase.py

Last active May 15, 2024 12:17
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opt_min_xtb_ase.py
#!/usr/bin/env python3
import os
import sys
import numpy as np
import ase
# New official implementation
from tblite.ase import TBLite as XTB3
from ase.io import read
from ase.units import fs, Hartree, Bohr, kB
from ase.optimize import LBFGS, MDMin
from ase.mep import NEB
from ase.io.trajectory import Trajectory
from ase.constraints import FixBondLengths, Hookean, FixAtoms
from ase.filters import ExpCellFilter, FrechetCellFilter
from ase.neighborlist import NeighborList, natural_cutoffs
import sys
path = "test.xyz"
name = "test"
mol = read(path)
# Can set up constraints etc. using ASE, too
mol.set_constraint(FixAtoms(indices=[atom.index for atom in mol if atom.symbol == 'C']))
# We could set harmonic constraints in atoms, etc. as
#bonds = []
#cutoffs = natural_cutoffs(mol)
#nl = NeighborList(cutoffs, self_interaction=False, bothways=True)
#nl.update(mol)
#cm = nl.get_connectivity_matrix(sparse=False)
#for n in range(cm.shape[0]):
# for m in range(n+1,cm.shape[1]):
# if cm[n,m] :
# bonds.append([n,m])
#for bond in bonds:
# mol.set_constraint(Hookean(bond[0],bond[1],k=10))
# Or simply fix them
#mol.set_constraint(FixBondLengths(bonds))
# Optimize to a minima
try:
mol.calc = XTB3(method="GFN2-xTB", max_iterations=1000)
opt = LBFGS(mol, trajectory=f"opt.traj", logfile=f"opt.log")
opt.run(fmax=0.02, steps=100)
traj = Trajectory(f"opt.traj")
# We can write any frame of the trajectory
ase.io.write(f"{name}_opt.xyz", traj[-1])
except Exception as m:
print(m)
Raw
test.xyz
134
-229.10631947
C 5.4083547045 -1.6912384040 -0.5607576677
C 4.9849409368 -2.4715181445 0.5525003406
C 5.8229402954 -3.4361681743 1.1404117752
C 7.0745132572 -3.6049726446 0.5889898338
C 7.5078995938 -2.8437266336 -0.5267655923
C 6.6969405826 -1.8944835391 -1.1039705425
C 4.3574506583 -0.7867263745 -0.8507821508
C 3.3008458758 -1.0994280047 0.0485553474
N 3.7355033641 -2.0829783892 0.9115996766
H 3.1792681187 -2.4627766159 1.6804932085
C 4.1838086112 0.1382700650 -1.9863309401
H 3.8195102168 1.1163159853 -1.6332785550
H 5.1215985088 0.2727296299 -2.5391254543
C 3.0951848292 -0.4210264867 -2.9736503197
H 2.8234053952 0.3625115930 -3.6891140676
H 3.5012946477 -1.2821278387 -3.5166632128
C 2.0453597035 -1.8257567806 -1.3266238240
N 1.9292573399 -0.8251070910 -2.2381437565
H 2.5546307535 -0.3935333359 0.4170893943
H 1.1650591648 -1.8925608647 -0.6805424933
O 0.7119582346 -1.3458119661 1.8822792287
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H -0.3330711525 -1.3172378047 4.2850619694
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H 8.5089205489 -3.0236988569 -0.9145015345
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C -2.2517578776 -1.5831734166 -2.7542718755
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C -2.7539178998 0.2484769150 -1.2731152577
H -1.0537758041 1.3653645780 -0.5574643222
C -3.1845492712 -0.8158469779 -2.0578745139
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C -1.7892489022 0.8824733325 2.1163061934
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C 3.5109118436 0.7802633821 3.0521589453
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C -4.1767122486 -0.8175518966 1.3848761013
C -5.1521139844 -1.6848017287 0.9055715947
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F -6.9433952572 -0.5308291216 1.9334897788
F -6.7446698854 -0.3433539922 -0.1928205080
F -7.4597645742 -2.1714914910 0.6600892627
C -4.8426851991 -2.9608530324 0.4463527652
C -3.5117954291 -3.3703397872 0.4928189184
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F -4.1288541840 -5.5325739446 -0.2782724193
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F -2.3025030405 -5.3685967429 0.8257604443
C -2.5185022084 -2.5279013915 0.9692258949
H 0.9190135951 0.4523290282 2.3163713403
H 1.1078666335 3.3080553030 3.1669403005
H 2.9973958838 1.3587139255 5.6881325739
H 1.4986740938 0.7877765962 4.9189957371
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H 0.0799526553 -3.9683876128 -0.6596589148
N 3.8751046722 -4.9160206449 -2.2235361455
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