QuantumATK Forum
QuantumATK => General Questions and Answers => Topic started by: kaypu on March 3, 2017, 08:22
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Dear QuantumWise staff:
In the process of gas adsorption, A stands for pristine adsorbate (such as graphene), B is gas molecule (for example CO), and C is the adsorbate with an absorbed gas molecule (graphene+CO). the adsorption process can be represent as A+B=C, the adsorption energy is defined as: Eads=EC-EA-EB. We can calculate the Total energy of A, B, and C respectively by ATK, and get adsorption energy. how to calculate enthalpy in the adsorption process by ATK?
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Assume that the contribution from phonons of substrates can be cancelled before and after the gas adsorption.
1. Calculate the vibration frequencies of an isolated gas molecule (i.e., the adsorbate);
2. Calculate the vibration frequencies only for the atoms belonging to the adsorbed molecules;
Following the formula in the following webpage to calculate the enthalpy for the adsorbate molecules before and after adsorption:
https://wiki.fysik.dtu.dk/ase/ase/thermochemistry/thermochemistry.html
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Assume that the contribution from phonons of substrates can be cancelled before and after the gas adsorption.
1. Calculate the vibration frequencies of an isolated gas molecule (i.e., the adsorbate);
2. Calculate the vibration frequencies only for the atoms belonging to the adsorbed molecules;
Following the formula in the following webpage to calculate the enthalpy for the adsorbate molecules before and after adsorption:
https://wiki.fysik.dtu.dk/ase/ase/thermochemistry/thermochemistry.html
Thank you zh, another question,
How to "Calculate the vibration frequencies only for the atoms belonging to the adsorbed molecules" Can the ATK do ProjectionList on selected atom?
BTW, i use ATK2014.3
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When you do the calculations of force constants and dynamic matrix, you can fix the atoms of substrate. In such case, only the atoms of adsorbate molecule will be made by small displacement to calculate the vibration frequencies.
see:
http://docs.quantumwise.com/manuals/Types/DynamicalMatrix/DynamicalMatrix.html#dynamicalmatrix-c
constraints(),
The list of constrained atoms.
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When you do the calculations of force constants and dynamic matrix, you can fix the atoms of substrate. In such case, only the atoms of adsorbate molecule will be made by small displacement to calculate the vibration frequencies.
see:
http://docs.quantumwise.com/manuals/Types/DynamicalMatrix/DynamicalMatrix.html#dynamicalmatrix-c
constraints(),
The list of constrained atoms.
Thank you zh, here is another question, the ATK does not work on constraints(),
***************************************************
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File "phonon.py", line 219
constraints(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19),
SyntaxError: non-keyword arg after keyword arg
File "phonon.py", line 219
constraints(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19),
SyntaxError: non-keyword arg after keyword arg
File "C20-NO-phonon.py", line 219
constraints(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19),
SyntaxError: non-keyword arg after keyword arg
File "C20-NO-phonon.py", line 219
constraints(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19),
SyntaxError: non-keyword arg after keyword arg
File "C20-NO-phonon.py", line 219
constraints(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19),
SyntaxError: non-keyword arg after keyword arg
File "C20-NO-phonon.py", line 219
constraints(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19),
SyntaxError: non-keyword arg after keyword arg
File "C20-NO-phonon.py", line 219
constraints(0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19),
SyntaxError: non-keyword arg after keyword arg
***************************************************
i use in ATK 2014.3, how to solve this problem?
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I just check the atk2014 version. This version doesn't support the constraints on atoms for dynamic matrix calculations. Please use the latest version of ATK.
http://www.quantumwise.com/documents/manuals/ATK-2014/ReferenceManual/index.html/ref.dynamicalmatrixparameters.html