Atomic Forces and Geometry Optimizaiton

What this tutorial is about

In this tutorial we will learn how to compute the excited state atomic forces of a molecular structure and how to use these to perform geometry optimization. Let’s start by importing the relevant modules

from pyxtp import xtp
from ase.io import write
from ase.build import molecule
from ase.optimize import GoodOldQuasiNewton

Define the molecular structure

We define here a CO molecule in its ground state geometry.

atoms = molecule('CO')

Configure the xtp calculator

We now define the xtp calculator and configure it to target particular forces. We can select which forces we want to compute with the method .select_force() of the calculator. We can choose to target different forces :

• energy='energy' : DFT total energy

• energy='singlets': BSE singlet energy

• energy='triplets': BSE triplet energy

• energy='qp': Quasi particile energy

For singlets, triplets and qp one can also specify which particular level to target to compute the forces. For example energy='singlets', level=0 will target the lowest lying singlet state.

# instantiate the calculator
calc = xtp(nthreads=2)

# select the force we want to use
calc.select_force(energy='singlets', level=0, dynamic=False)

# this allows to change all options
# calc.options.dftpackage.functional = 'PBE'
calc.options.dftpackage.basisset = 'def2-svp'
calc.options.dftpackage.auxbasisset = 'aux-def2-svp'

# set up the logger
calc.options.logging_file = 'CO_forces.log'

# set the calculator
atoms.calc = calc

Compute the forces

If you are simply interested in computing the forces, they can easily be accessed through the .get_forces() method

atoms.get_forces()

 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml

array([[-3.50937057e-08, -3.51647600e-08,  3.19442266e-01],
       [ 3.49658080e-08,  3.51434437e-08, -3.19442265e-01]])

Geometry optimization

Geometry optimization can be run by leveraging the intrinsic ASE capabilities. We can for example use the QuasiNewton method implemented in ASE to relax the molecular structre in the excited states we have just specified. We here fix the number of steps to 10 to limit the computational cost.

dyn = GoodOldQuasiNewton(atoms, trajectory='test.traj')
dyn.run(fmax=0.05, steps=10)
write('final.xyz', atoms)

 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml                    Step     Time          Energy          fmax
GoodOldQuasiNewton:    0 10:42:40     -113.101204        0.319442
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlnew radius 0.012247
eigenvalues 20.00 20.00 20.00
Corrected Newton step: abs(D) = 0.02
Abs Gbar estimate 0.0427706293433541
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:    1 10:43:26     -113.098913        0.319442
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlenergies -113.09891342922471 -113.10120446793198
reject step
new radius 0.006124
eigenvalues 20.00 20.00 20.00
Corrected Newton step: abs(D) = 0.02
Abs Gbar estimate 0.10842867600566072
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:    2 10:44:14     -113.100204        0.248356
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlenergies -113.10020359454678 -113.10120446793198
reject step
new radius 0.003062
eigenvalues 20.00 20.00 20.00
Corrected Newton step: abs(D) = 0.02
Abs Gbar estimate 0.15250769885421517
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:    3 10:45:02     -113.100741        0.282670
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlenergies -113.10074132944271 -113.10120446793198
reject step
new radius 0.001531
eigenvalues 20.00 20.00 20.00
Corrected Newton step: abs(D) = 0.02
Abs Gbar estimate 0.1773597107014855
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:    4 10:45:50     -113.100982        0.300957
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlenergies -113.1009823679633 -113.10120446793198
reject step
new radius 0.000765
eigenvalues 20.00 20.00 20.00
Corrected Newton step: abs(D) = 0.02
Abs Gbar estimate 0.19048884159370189
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:    5 10:46:37     -113.101096        0.310036
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlenergies -113.10109580257749 -113.10120446793198
reject step
new radius 0.000383
eigenvalues 20.00 20.00 20.00
Corrected Newton step: abs(D) = 0.02
Abs Gbar estimate 0.19722918827321428
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:    6 10:47:25     -113.101151        0.314725
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlenergies -113.10115073499155 -113.10120446793198
energy change; actual: 0.000054 estimated: -0.000171
Energy prediction factor 1.3134242658769528
Force prediction factor -1.452662740093484
Scale factors 0.364431 0.364431
new radius 0.000139
eigenvalues 8.15 20.00 20.00
Corrected Newton step: abs(D) = 0.06
Abs Gbar estimate 0.2002573710075848
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:    7 10:48:13     -113.101131        0.317235
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlenergies -113.1011308542795 -113.10115073499155
energy change; actual: 0.000020 estimated: -0.000062
Energy prediction factor 1.3181079930973942
Force prediction factor 0.12541719600876725
Scale factors 0.364431 0.510204
new radius 0.000100
eigenvalues 9.32 20.00 20.00
Corrected Newton step: abs(D) = 0.05
Abs Gbar estimate 0.1992781150792045
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:    8 10:49:00     -113.101117        0.316316
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlenergies -113.10111650360597 -113.1011308542795
energy change; actual: 0.000014 estimated: -0.000045
Energy prediction factor 1.3211361363852434
Force prediction factor 0.09444099148020789
Scale factors 0.364431 0.510204
new radius 0.000100
eigenvalues 10.30 20.00 20.00
Corrected Newton step: abs(D) = 0.04
Abs Gbar estimate 0.19827331853502042
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:    9 10:49:47     -113.101102        0.315588
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlenergies -113.1011020713832 -113.10111650360597
energy change; actual: 0.000014 estimated: -0.000045
Energy prediction factor 1.3237421664547542
Force prediction factor -0.31214063374505446
Scale factors 0.364431 0.364431
new radius 0.000100
eigenvalues 7.85 20.00 20.00
Corrected Newton step: abs(D) = 0.06
Abs Gbar estimate 0.19779293006551354
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:   10 10:50:34     -113.101088        0.315033
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xml