def test_linear_ts():
"""
compute a first approximation to the TS.
"""
# Read the Molecule from file
cnc = Molecule('test/test_files/C-N-C.mol', 'mol')
# User define Settings
settings = Settings()
settings.functional = "pbe"
settings.basis = "SZ"
settings.specific.dftb.dftb.scc
constraint1 = Distance(1, 5)
constraint2 = Distance(3, 4)
# scan input
pes = PES(cnc, constraints=[constraint1, constraint2],
offset=[2.3, 2.3], get_current_values=False,
nsteps=2, stepsize=[0.1, 0.1])
# returns a set of results object containing the output of
# each point in the scan
lt = pes.scan([dftb, adf], settings)
# Gets the object presenting the molecule
# with the maximum energy calculated from the scan
apprTS = select_max(lt, "energy")
# Run the TS optimization, using the default TS template
ts = run(apprTS)
expected_energy = -3.219708290363864
assert abs(ts.energy - expected_energy) < 0.02
scan = {
'constraint': [constraint1, constraint2],
'surface': {
'nsteps': 6,
'start': [2.3, 2.3],
'stepsize': [0.1, 0.1]
}
}
# returns a set of results object containing the output of
# each point in the scan
lt = PES_scan([dftb, adf], settings, cnc, scan)
# Gets the object presenting the molecule
# with the maximum energy calculated from the scan
apprTS = select_max(lt, "energy")
appr_hess = dftb(templates.freq.overlay(settings), apprTS.molecule)
t = Settings()
t.specific.adf.geometry.inithess = appr_hess.archive.path
# Run the TS optimization with ADF, using initial hessian from DFTB freq calculation
ts = run(adf(templates.ts.overlay(settings).overlay(t), appr_hess.molecule),
n_processes=1)
# Retrieve the molecular coordinates
mol = ts.molecule
r1 = mol.atoms[0].coords
r2 = mol.atoms[4].coords
p_freq = adf(templates.freq.overlay(settings), p.molecule, job_name=name + "_p_freq")
# Prepare scan
pes_jobs = []
for d in range(6):
consset = Settings()
consset.constraint.update(bond1.get_settings(2.0 + d * 0.1))
consset.constraint.update(bond2.get_settings(2.0 + d * 0.1))
pes_name = name + "_pes_" + str(d)
pes_dftb = dftb(templates.geometry.overlay(settings).overlay(consset), p.molecule, job_name=pes_name + "_DFTB")
pes = adf(templates.singlepoint.overlay(settings), pes_dftb.molecule, job_name=pes_name)
pes_jobs.append(pes)
# Get the result with the maximum energy
apprTS = select_max(gather(*pes_jobs), 'energy')
# Calculate the DFTB hessian
DFTBfreq = dftb(templates.freq.overlay(settings), apprTS.molecule, job_name=name + "_freq_DFTB")
# Run the TS optimization, using the initial hession from DFTB
t = Settings()
t.inithess = DFTBfreq.hessian
TS = adf(templates.ts.overlay(settings).overlay(t), DFTBfreq.molecule, job_name=name + "_TS")
# Perform a freq calculation
# freq_setting = Settings()
# freq_setting.specific.adf.geometry.frequencies = ""
# freq_setting.specific.adf.geometry.__block_replace = True
# TSfreq = adf(templates.geometry.overlay(settings).overlay(freq_setting), TS.molecule, job_name=name + "_freq")
TSfreq = adf(templates.freq.overlay(settings), TS.molecule, job_name=name + "_freq")
# Add the jobs to the job list
pjob = adf(
templates.geometry.overlay(settings),
dftb(templates.geometry.overlay(settings),
pmol, job_name=name + "_p_DFTB").molecule,
job_name=name + "_p")
# Prepare TS jobs
# Define PES
pes = PES(pjob.molecule, constraints=[bond1, bond2],
offset=[2.0, 2.0], get_current_values=False, nsteps=5, stepsize=[0.1, 0.1])
# pesscan: gathered (promised) result objects for each point in the scan
pesscan = pes.scan([dftb, adf], settings, job_name=name + "_PES")
# Get the result with the maximum energy
apprTS = select_max(pesscan, 'energy')
# Calculate the DFTB hessian
DFTBfreq = dftb(templates.freq.overlay(settings), apprTS.molecule, job_name=name + "_DFTBfreq")
# Run the TS optimization, using the initial hession from DFTB
t = Settings()
t.inithess = DFTBfreq.hessian
TS = adf(templates.ts.overlay(settings).overlay(t), DFTBfreq.molecule, job_name=name + "_TS")
# Perform a freq calculation
TSfreq = adf(templates.freq.overlay(settings), TS.molecule, job_name=name + "_freq")
# Add the jobs to the job list
job_list.append(gather(r1job, r2job, pjob, TSfreq, TS.optcycles))