primer to cantherm 27 th sept 2013 shamel merchant
TRANSCRIPT
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Primer to CanTherm
27th Sept 2013
Shamel Merchant
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What is CanTherm
CanTherm1. Thermodynamic
Properties2. Kinetic rate
coefficients
Gaussian
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What is CanTherm
CanTherm is written in python and can be used for the following calculations
1. Thermodynamic properties of stable molecule (H298, S , Cp(T) )
2. High pressure limit rate coefficients
3. Pressure dependent rate coefficients for entire network using either Modified Strong Collision, Reservoir State or Chemically Significant Eigenvalue (CSE) approximations
Theory manual : https://github.com/GreenGroup/CanTherm/blob/master/manual.pdf
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Running CanTherm
For Green group folks it is easiest to use virtual environment setup on pharos on my account (or alternatively on Connie’s)
1. Activate virtualenvsource /home/shamel/virtualenv/bin/activate
2. Navigate to your input directory
3. Run CanTherm python /home/shamel/RMG-Py/cantherm.py input.py
4. Deactivate virtualenvdeactivate
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Calculating thermodynamic properties of stable species
What do you need ?– Gaussian log file containing optimized structure and energy– Gaussian log file for frequency job with keyword iop(7/33=1) (only if you
want hindered rotors)– Gaussian log file for every hindered rotor scan of the system (only if you
want hindered rotors)– Species file for CanTherm – Input file for CanTherm
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Species file
C2H6
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Species file
atoms = { 'C': 2, 'H': 6,}
bonds ={'C-C': 1, 'C-H': 6,}
1. Define the number and type of atoms in the molecule
2. Define the different bonds in the molecule, optional. We have corrections only for CBS-QB3 right now
3. Linearity of moleculelinear = False (or True for molecule like acetylene)
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Species file
4. Statistical factors and spin multiplicity
externalSymmetry = 6
spinMultiplicity = 1
opticalIsomers = 1
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Statistical factors include symmetry number and chirality correction
Statistical factors are typically introduced via the partition function, Q
– Partition functions are multiplied by chirality contribution, divided by the symmetry number
's
Q Q
symmetry number: a positive integer
chirality contribution: 2 if chiral; 1 otherwise;(the number of optical isomers)
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Statistical effects enter into entropy, equilibrium constants, A-factors, etc.
' ' ...rot int transrot int
sQ q q q
1'rot rot
rot
q q
,int
1 1' 'int vib rotor i vib rotor
i rotor,i
q q q q q
' lnS S R
chirality correction
externalsymmetry number
rotorsymmetry number(s)
internalpartition function
rotor,irot
rotationalpartition function
overallpartition function
s
entropy
Gibbs free energy reaction rate coefficients
1
'reactantseq eq
products
K K
reaction equilibrium constants
saddle point
( ) '( )reactantsTST TSTk T k T
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External symmetry number“The symmetry number of a molecule is obtained by imagining all identical atoms to be labeled, and then counting the number of different but equivalent arrangements that can be obtained by rotating (but not reflecting) the molecule.”—IUPAC Gold Book
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How to figure out external symmetry number
Point group uniquely determines external symmetry number
http://cccbdb.nist.gov/thermo.asp
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Determining point group
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Easy way of calculating the point group
Note: This can be inaccurate, check by making the tolerance loose.
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Determining spin multiplicity
Spin multiplicity is determined by the 2S+1 rule
Multiplicity = 2 (1/2) + 1 = 2 (Doublet)
Multiplicity = 2 (0) + 1 = 1 (Singlet)
Multiplicity = 2 (1) + 1 = 3 (Triplet)
Radical
Paired electron
Unpaired electron
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Determining chirality
• A molecular configuration is chiral if and only if its mirror image is non-superposable
• Carbon atom bonded to 4 distinct ligands?Sufficient for chiral center (“local” chirality)Neither necessary nor sufficient for overall chirality
Chirality can also arise from:Axial chirality (helicity)Planar chiralityInherent chirality
• A molecular configuration is not chiral if it contains a plane of symmetry
• Certain conformations can have chiral molecular configurations even when the molecule is not optically active
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Easy way of calculating chirality
Point groups (circled above) lacking σv, σd, σh (planes of symmetry) and Sn (improper rotation axis) symmetry elements correspond to chiral molecular configurations
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Statistical effects are easy to get wrong
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Species file
5. Energy, geometry and frequencies
energy = { 'CBS-QB3': GaussianLog('ethane_cbsqb3.log'), ‘CCSD(T)-F12/cc-pVDZ-F12': -79.64199436,}
geometry = GaussianLog('ethane_cbsqb3.log')frequencies = GaussianLog('ethane_cbsqb3.log')
Energy in Hartrees does not include ZPE
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Species file
6. Hindered rotors
rotors = [ HinderedRotor(scanLog=GaussianLog('ethane_scan_1.log'), pivots=[1,5], top=[1,2,3,4], symmetry=3, fit='best‘),]
Internal symmetry number of 3
Fit potential to Fourier series or cosine
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Input file for thermo
modelChemistry = “CBS-QB3“
frequencyScaleFactor = 0.99useHinderedRotors = TrueuseBondCorrections = False
species('C2H6', 'C2H6.py')statmech('C2H6')thermo('C2H6', 'NASA')
Which model chemistry energy you want to use? (Remember your species file can have multiple methods)
Frequency scale factor
Output the thermo in NASA or Wilhoit form
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Cantherm Thermo Output
Scroll down to the bottom of output.py:
This is the info needed to make anentry to a thermo library
Also the most commonly listed parameters in literature.
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To calculate the high pressure limit rate coefficient
You need to setup the species file for all the species in your system
Setup the input file for transition state
Setup input file for the reaction
TS
In all will need to setup 5 files to calculate the rate coefficient
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Input file for rate coefficient
modelChemistry = "CBS-QB3“frequencyScaleFactor = 0.99useHinderedRotors = TrueuseBondCorrections = False
species('H', '../../species/H/H.py')species('C2H4', '../../species/C2H4/ethene.py')species('C2H5', '../../species/C2H5/ethyl.py')transitionState('TS', 'TS.py')
reaction( label = 'H + C2H4 <=> C2H5', reactants = ['H', 'C2H4'], products = ['C2H5'], transitionState = 'TS', tunneling='Eckart',)
Location of the species file
Definition of the reaction
Model chemistry
kinetics('H + C2H4 <=> C2H5') Calculate the kinetics
Type of tunneling Eckart or Wigner
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Cantherm Kinetics Output
Scroll down to the bottom of output.py:
This is what you need for an entry to reaction libraryDegeneracy is factored into A-factor
Error from fitting is NOT total error on kinetics
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Changing pressure can dramatically changeproduct branching ratios in multi-well networks.
E(kJ/mol)
high pressuremoderate pressurelow pressure
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Questions