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([[-7.24753590e-10, -6.89226454e-10,  3.19440044e-01],
       [ 7.24753590e-10,  6.89226454e-10, -3.19440044e-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 06:21:04     -113.101204        0.319440
 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 0.04276932980238802
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:    1 06:21:51     -113.098913        0.319440
 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 -113.09891342922477 -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 0.10842660626643877
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:    2 06:22:38     -113.100204        0.248363
 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 -113.10020359454666 -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 0.15250524485582462
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:    3 06:23:27     -113.100741        0.282673
 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 -113.1007413294429 -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 0.1773570642068088
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:    4 06:24:14     -113.100982        0.300959
 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 -113.10098236796318 -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 0.1904860988339735
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:    5 06:25:01     -113.101096        0.310037
 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 -113.10109580257742 -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 0.19722639741950215
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:    6 06:25:48     -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 -113.10115073499158 -113.10120446793198
energy change; actual: 0.000054 estimated: -0.000171
Energy prediction factor 1.3134264644138955
Force prediction factor -1.454263580093323
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 0.20025704473783704
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:    7 06:26:35     -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 -113.10113085427956 -113.10115073499158
energy change; actual: 0.000020 estimated: -0.000062
Energy prediction factor 1.3181085147193217
Force prediction factor 0.1256862086102094
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 0.19927781457133076
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:    8 06:27:23     -113.101117        0.316315
 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 -113.10111650360605 -113.10113085427956
energy change; actual: 0.000014 estimated: -0.000045
Energy prediction factor 1.3211364931113176
Force prediction factor 0.09444601279311975
Scale factors 0.364431 0.510204
new radius 0.000100
eigenvalues 10.29 20.00 20.00
Corrected Newton step: abs(D) = 0.04
Abs Gbar estimate 0.19827335461237972
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:    9 06:28:10     -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 -113.10110207138328 -113.10111650360605
energy change; actual: 0.000014 estimated: -0.000045
Energy prediction factor 1.3237422638563556
Force prediction factor -0.3123596933194114
Scale factors 0.364431 0.364431
new radius 0.000100
eigenvalues 7.84 20.00 20.00
Corrected Newton step: abs(D) = 0.06
Abs Gbar estimate 0.19779336189209498
 Using 2 threads
... ... Reading structure from CO.xyz
... ... Saving data to CO.orb
... ... Writing output to CO_summary.xmlGoodOldQuasiNewton:   10 06:28:56     -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