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<code>thermo</code> Calculations |
Utility Tools |
Examples and Guides |
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How to evaluate thermodynamical partition functions with the <i>thermo</i> submodule. |
/page/examples/utilities/utils_4.html |
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Calculations of the entropy or free energy require an evaluation of the rovibrational partition functions.
In publications such as Chem. Sci., 2021, 12, 6551-6568
we employ a modified and scaled rigid-rotor harmonic-oscillator (msRRHO) evaluation of the partition function.
While this can in principal be conducted at any level of theory (FF, SQM, DFT, etc.), the modified (i.e., interpolated) and scaled treatment is not necessarly available in any QM code.
Therefore, a standalone version of the thermo program is implemented in CREST that allows just that.
All that is required is the molecular input structure (for identification of rotational and translational partition functions), and the vibrational frequencies in a file called vibspectrum using a specific format.
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An example is shown for the thymine molecule below.
The vibspectrum file must simply be present in the same directory and is read automatically.
{% include image.html file="utils-example-4-1.png" alt="Thymine input structure" caption="Input structure of the thymine molecule used to obtain the vibrational frequencies." max-width=200 %}
command
{{site.data.icons.codefile}} struc.xyz
{{site.data.icons.codefile}} vibspectrum
{{site.data.icons.checkfile}} output
vibspectrum file must be present in the same directory and is not explicitly specified via the command line!" %}
O 1.6295236631 -1.6750880104 0.0273337989 C 0.8505026159 -0.7502234227 0.0134304505 N -0.5218781169 -0.9874374197 -0.0063526997 C -1.5401115163 -0.0659265702 -0.0253285595 O -2.7097403039 -0.3600312267 -0.0416029833 N -1.1000479488 1.2392522165 -0.0242265895 C 0.2235337218 1.5858124075 -0.0036680534 C 1.2067187753 0.6684447723 0.0152381391 C 2.6606979446 1.0088396987 0.0381263685 H -0.8083247148 -1.9604112352 -0.0073629285 H -1.8173110585 1.9499835714 -0.0379190725 H 0.4295022336 2.6464257401 -0.0036869221 H 2.8109266091 2.0846097420 0.0364195981 H 3.1545530447 0.5713072437 -0.8278672347 H 3.1254195278 0.5782828637 0.9235387765 {% endcapture %} {% include codecell.html content=inputfile style="font-size:10px" %}
Cite work conducted with this code as
• P.Pracht, F.Bohle, S.Grimme, PCCP, 2020, 22, 7169-7192. • S.Grimme, JCTC, 2019, 15, 2847-2862.
and for works involving QCG as
• S.Spicher, C.Plett, P.Pracht, A.Hansen, S.Grimme, JCTC, 2022, 18 (5), 3174-3189.
with help from: C.Bannwarth, F.Bohle, S.Ehlert, S.Grimme, C.Plett, P.Pracht, S.Spicher
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Command line input:
crest --thermo struc.xyz
Mol. weight /amu : 126.11 Rot. const. /MHz : 3209.69 1425.53 993.12 Rot. const. /cm-1 : 0.11 0.05 0.03 Symmetry: cs
...................................................
: SETUP :
:.................................................:
: # frequencies 39 :
: # imaginary freq. 0 :
: linear? F :
: symmetry cs :
: rotational number 1 :
: scaling factor 1.0000000 :
: rotor cutoff 25.0000000 cm⁻¹ :
: imag. cutoff -50.0000000 cm⁻¹ :
:.................................................:
mode ω/cm⁻¹ T·S(HO)/kcal·mol⁻¹ T·S(FR)/kcal·mol⁻¹ T·S(vib)
1 70.05 -1.23790 ( 98.40%) -0.95645 ( 1.60%) -1.23341
2 105.13 -1.00086 ( 99.68%) -0.83625 ( 0.32%) -1.00034
3 147.88 -0.80480 ( 99.92%) -0.73521 ( 0.08%) -0.80475
4 261.06 -0.49334 ( 99.99%) -0.56689 ( 0.01%) -0.49335
temp. (K) partition function enthalpy heat capacity entropy cal/mol cal/K/mol cal/K/mol J/K/mol 298.15 VIB 79.3 3380.390 24.301 20.012 ROT 0.407E+06 888.752 2.981 28.650 INT 0.323E+08 4269.143 27.282 48.662 TR 0.137E+28 1481.254 4.968 40.391 TOT 5750.3966 32.2500 89.0530 372.5979
T/K H(0)-H(T)+PV H(T)/Eh T*S/Eh G(T)/Eh
278.15 0.816352E-02 0.118775E+00 0.385087E-01 0.802659E-01
288.15 0.865677E-02 0.119268E+00 0.403947E-01 0.788731E-01
298.15 0.916384E-02 0.119775E+00 0.423120E-01 0.774629E-01 (used)
308.15 0.968460E-02 0.120296E+00 0.442601E-01 0.760355E-01
318.15 0.102189E-01 0.120830E+00 0.462389E-01 0.745910E-01
328.15 0.107666E-01 0.121378E+00 0.482481E-01 0.731295E-01
338.15 0.113275E-01 0.121939E+00 0.502874E-01 0.716511E-01
348.15 0.119015E-01 0.122513E+00 0.523565E-01 0.701560E-01
358.15 0.124883E-01 0.123099E+00 0.544552E-01 0.686442E-01
368.15 0.130878E-01 0.123699E+00 0.565831E-01 0.671158E-01
378.15 0.136998E-01 0.124311E+00 0.587399E-01 0.655710E-01
Overall wall time : 0h : 0m : 0s
CREST terminated normally. {% endcapture %} {% include codecell.html content=outfile style="font-size:10px" %}
By default, the evaluation is conducted for the partition functions at a temperature range from 278.15 to 378.15 K.
This can be changed with the --trange command.
Interpolation and scaling parameters of msRRHO can be adjusted with the --sthr and --fscal commands, respectively.
See the Keyword Documentation {{ site.data.icons.book }}.
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