Hybrid engine: Use lowest energy¶
Note: This example requires AMS2023 or later.
If you are unsure of the lowest energy spin state for a structure, the safest way is to try multiple different possibilities. Starting from AMS2023, this can be done with the AMS Hybrid engine together with the option DynamicFactors=UseLowestEnergy.
In this example, the hybrid engine is used to replay a PES Scan of a dissociating hydrogen peroxide molecule. For each bond length, both singlet and triplet states are evaluated. The resulting energy-vs-bond-length curve will only give the lowest energy for each bond length. This can be useful if you want to import such a bond scan into for example ParAMS for parametrization.
You may also try to optimize the spin using the OptimizeSpinRound feature of the ADF engine. This can be done in combination with an ElectronicTemperature. The energies are then not as accurate.
Example usage: (Download UseLowestEnergy.py)
#!/usr/bin/env plams
import matplotlib.pyplot as plt
"""
Example showing the UseLowestEnergy feature of the Hybrid engine and the OptimizeSpinRound feature of the ADF engine.
A bond scan is performed on hydrogen peroxide with UFF. The resulting
structures are then recalculated with DFT using four different setups. In
particular, one setup uses the Hybrid engine with DynamicFactors=UseLowestEnergy.
Another uses the ADF engine with OptimizeSpinRound in combination with an ElectronicTemperature.
In the end, the results of energy vs. bond length are plotted.
To run this example:
$AMSBIN/plams UseLowestEnergy.py
"""
def main():
#config.job.runscript.nproc = 1 # uncomment to run all jobs in serial
pesscan_job = initial_pesscan()
rkf = pesscan_job.results.rkfpath()
singlet_job = replay_job(rkf, 'singlet')
triplet_job = replay_job(rkf, 'triplet')
hybrid_job = replay_job(rkf, 'hybrid')
optimizespin_job = replay_job(rkf, 'optimizespin')
# or load the finished jobs from disk:
#pesscan_job = AMSJob.load_external('plams_workdir.002/initial_pesscan/ams.rkf')
#rkf = pesscan_job.results.rkfpath()
#singlet_job = AMSJob.load_external('plams_workdir.002/singlet/ams.rkf')
#triplet_job = AMSJob.load_external('plams_workdir.002/triplet/ams.rkf')
#hybrid_job = AMSJob.load_external('plams_workdir.002/hybrid/ams.rkf')
#optimizespin_job = AMSJob.load_external('plams_workdir.002/optimizespin/ams.rkf')
plot_results(singlet_job, triplet_job, hybrid_job, optimizespin_job)
def initial_pesscan():
""" Run a bond scan for hydrogen peroxide with UFF. Returns the finished job """
mol = from_smiles('OO') # hydrogen peroxide
s = Settings()
s.input.ams.Task = 'PESScan'
s.input.ams.PESScan.ScanCoordinate.nPoints = 7
# Scan O-O bond length (atoms 1 and 2) between 1.2 and 2.5 Å
s.input.ams.PESScan.ScanCoordinate.Distance = '2 1 1.2 2.5'
s.input.ForceField.Type = 'UFF'
job = AMSJob(settings=s, molecule=mol, name='initial_pesscan')
job.run()
return job
def singlet_settings(header=''):
s = Settings()
s.Unrestricted = 'No'
s.XC.GGA = 'PBE'
s.Basis.Type = 'DZP'
s.SCF.Iterations = 100
s._h = header
return s
def triplet_settings(header=''):
s = Settings()
s.Unrestricted = 'Yes'
s.SpinPolarization = 2
s.XC.GGA = 'PBE'
s.Basis.Type = 'DZP'
s.SCF.Iterations = 100
s._h = header
return s
def hybrid_settings():
""" Look at the file plams_workdir/hybrid/hybrid.in to see how the below is translated into text input for the hybrid engine """
s = Settings()
s.input.Hybrid.Energy.DynamicFactors = 'UseLowestEnergy'
s.input.Hybrid.Energy.Term = [ 'Region=* EngineID=Singlet',
'Region=* EngineID=Triplet' ]
s.input.Hybrid.Engine = [ singlet_settings('ADF Singlet'),
triplet_settings('ADF Triplet') ]
return s
def replay_job(rkf, engine='hybrid'):
""" Replay the structures from the UFF pesscan with ADF. Use three different engines:
Hybrid: This will run all structures with both Singlet and Triplet and pick the lowest energy
Singlet: This runs all structures using the Singlet settings
Triplet: This runs all structures using the Triplet settings
Returns the finished job
"""
s = Settings()
if engine == 'hybrid':
s = hybrid_settings()
elif engine == 'singlet':
s.input.adf = singlet_settings()
elif engine == 'triplet':
s.input.adf = triplet_settings()
elif engine == 'optimizespin':
s.input.adf = triplet_settings()
s.input.adf.Occupations = 'ElectronicTemperature=300 OptimizeSpinRound=0.05'
s.input.ams.Task = 'Replay'
s.input.ams.Replay.File = rkf
job = AMSJob(settings=s, name=engine)
job.run()
return job
def plot_results(singlet_job, triplet_job, hybrid_job, optimizespin_job):
"""
Generate a plot of the energy vs. bond length for the three different jobs. Saves a plot to pesplot.png.
"""
bondlengths = singlet_job.results.get_pesscan_results()['RaveledPESCoords'][0]
bondlengths = Units.convert(bondlengths, 'bohr', 'angstrom')
singlet_pes = singlet_job.results.get_pesscan_results()['PES']
triplet_pes = triplet_job.results.get_pesscan_results()['PES']
hybrid_pes = hybrid_job.results.get_pesscan_results()['PES']
hybrid_pes = [x-0.005 for x in hybrid_pes] # slightly downshift for visual clarity when plotting
optimizespin_pes = optimizespin_job.results.get_pesscan_results()['PES']
optimizespin_pes = [x-0.010 for x in optimizespin_pes] # slightly downshift for visual clarity when plotting
plt.plot(bondlengths, singlet_pes)
plt.plot(bondlengths, triplet_pes)
plt.plot(bondlengths, hybrid_pes)
plt.plot(bondlengths, optimizespin_pes)
plt.title("PES Scan for hydrogen peroxide")
plt.xlabel("O-O bond length (Å)")
plt.ylabel("Energy (hartree)")
plt.legend(["Singlet", "Triplet", "Hybrid: Lowest energy (slightly shifted)", "Optimized spin (slightly shifted)"])
plt.savefig("pesplot.png")
plt.show()
if __name__ == '__main__':
main()