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
def example_freqs():
"""
This examples illustrates the possibility to use different packages interchangeably.
Analytical frequencies are not available for B3LYP in ADF
This workflow captures the resulting error and submits the same job to ORCA.
"""
# Generate water molecule
water = molkit.from_smiles('[OH2]', forcefield='mmff')
# Pre-optimize the water molecule
opt_water = dftb(templates.geometry, water, job_name="dftb_geometry")
jobs = []
# Generate freq jobs for 3 functionals
for functional in ['pbe', 'b3lyp', 'blyp']:
s = Settings()
s.basis = 'DZ'
s.functional = functional
# Try to perform the jobs with adf or orca, take result from first successful calculation
freqjob = find_first_job(is_successful, [adf, orca],
templates.freq.overlay(s),
opt_water.molecule,
job_name=functional)
jobs.append(freqjob)
# Run workflow
results = run(gather(*jobs), n_processes=1)
# extrac results
freqs = [r.frequencies[-3:] for r in results]
functionals = ['pbe', 'b3lyp', 'blyp']
# Print the result
table = [
"{:10s}{:10.3f}{:10.3f}{:10.3f}\n".format(fun, *fs)
for fun, fs in zip(functionals, freqs)
]
print(table)
return freqs
def example_freqs():
"""
This examples illustrates the possibility to use different packages interchangeably.
Analytical frequencies are not available for B3LYP in ADF
This workflow captures the resulting error and submits the same job to ORCA.
"""
# Generate water molecule
water = molkit.from_smiles('[OH2]', forcefield='mmff')
# Pre-optimize the water molecule
opt_water = dftb(templates.geometry, water, job_name="dftb_geometry")
jobs = []
# Generate freq jobs for 3 functionals
for functional in ['pbe', 'b3lyp', 'blyp']:
s = Settings()
s.basis = 'DZ'
s.functional = functional
# Try to perform the jobs with adf or orca, take result from first successful calculation
freqjob = find_first_job(is_successful, [adf, orca], templates.freq.overlay(s),
opt_water.molecule, job_name=functional)
jobs.append(freqjob)
# Run workflow
results = run(gather(*jobs), n_processes=1)
# extrac results
freqs = [r.frequencies[-3:] for r in results]
functionals = ['pbe', 'b3lyp', 'blyp']
# Print the result
table = ["{:10s}{:10.3f}{:10.3f}{:10.3f}\n".format(fun, *fs)
for fun, fs in zip(functionals, freqs)]
print(table)
return freqs
def bond_distance(r1, r2):
return sqrt(sum((x - y)**2 for x, y in zip(r1, r2)))
# ========== =============
plams.init()
# Read the Molecule from file
cnc = Molecule('C-N-C.mol', 'mol')
# User define Settings
settings = Settings()
settings.functional = "pbe"
settings.basis = "TZ2P"
settings.specific.dftb.dftb.scc
constraint1 = "dist 1 5"
constraint2 = "dist 3 4"
# scan input
scan = {
'constraint': [constraint1, constraint2],
'surface': {
'nsteps': 6,
'start': [2.3, 2.3],
'stepsize': [0.1, 0.1]
}
}
["ac17", "C#C", "[NH]=[O+][O-]", "C1NOOC=1"],
["ac18", "C#C", "O=[O+][O-]", "C1OOOC=1"],
["ac19", "C#C", "[CH2]=[S+][CH2-]", "C1CSCC=1"],
["ac20", "C#C", "[CH2]=[S+][NH-]", "C1CSNC=1"],
["ac21", "C#C", "[CH2]=[S+][O-]", "C1CSOC=1"],
["ac22", "C#C", "[NH]=[S+][NH-]", "C1NSNC=1"],
["ac23", "C#C", "[NH]=[S+][O-]", "C1NSOC=1"],
["ac24", "C#C", "O=[S+][O-]", "C1OSOC=1"]]
# Bonds to be formed (based on atom numbers in de product)
bond1 = Distance(0, 1)
bond2 = Distance(3, 4)
# User define Settings
settings = Settings()
settings.functional = "b3lyp"
settings.specific.orca.basis.basis = "_6_31G"
settings.specific.orca.basis.pol = "_d"
settings.specific.orca.basis.diff = "_p"
settings.specific.dftb.dftb.scc.ndiis = 4
settings.specific.dftb.dftb.scc.Mixing = 0.1
settings.specific.dftb.dftb.scc.iterations = 300
job_list = []
# Loop over all reactions
for name, r1_smiles, r2_smiles, p_smiles in reactions:
# Prepare reactant1 job
r1_mol = molkit.from_smiles(r1_smiles)
r1_dftb = dftb(templates.geometry.overlay(settings), r1_mol, job_name=name + "_r1_DFTB")
["ac17", "C#C", "[NH]=[O+][O-]", "C1NOOC=1"],
["ac18", "C#C", "O=[O+][O-]", "C1OOOC=1"],
["ac19", "C#C", "[CH2]=[S+][CH2-]", "C1CSCC=1"],
["ac20", "C#C", "[CH2]=[S+][NH-]", "C1CSNC=1"],
["ac21", "C#C", "[CH2]=[S+][O-]", "C1CSOC=1"],
["ac22", "C#C", "[NH]=[S+][NH-]", "C1NSNC=1"],
["ac23", "C#C", "[NH]=[S+][O-]", "C1NSOC=1"],
["ac24", "C#C", "O=[S+][O-]", "C1OSOC=1"]]
# Bonds to be formed (based on atom numbers in de product)
bond1 = Distance(0, 1)
bond2 = Distance(3, 4)
# User define Settings
settings = Settings()
settings.functional = "B3LYP_G"
settings.specific.orca.basis.basis = "_6_31G"
settings.specific.orca.basis.pol = "_d"
settings.specific.orca.basis.diff = "_p"
settings.specific.orca.pal.nprocs = 8
settings.specific.orca.geom.MaxIter = 200
settings.specific.dftb.dftb.scc.ndiis = 4
settings.specific.dftb.dftb.scc.Mixing = 0.1
settings.specific.dftb.dftb.scc.iterations = 300
job_list = []
# Loop over all reactions
for name, r1_smiles, r2_smiles, p_smiles in reactions:
# Prepare reactant1 job
r1_mol = molkit.from_smiles(r1_smiles)