thermo Calculations
How to evaluate thermodynamical partition functions with the thermo submodule.
Evaluating rotational/vibrational/translational partition functions
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.
An example is shown for the thymine molecule below. The vibspectrum file must simply be present in the same directory and is read automatically.
crest --thermo struc.xyz Note: The
vibspectrum file must be present in the same directory and is not explicitly specified via the command line!
15
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
$vibrational spectrum
# mode symmetry wave number IR intensity selection rules
# cm**(-1) (km*mol⁻¹) IR RAMAN
1 -0.00 0.00000 - -
2 -0.00 0.00000 - -
3 -0.00 0.00000 - -
4 0.00 0.00000 - -
5 0.00 0.00000 - -
6 0.00 0.00000 - -
7 a 70.05 0.38846 YES YES
8 a 105.13 0.44816 YES YES
9 a 147.88 4.81587 YES YES
10 a 261.06 3.14819 YES YES
11 a 301.90 0.50209 YES YES
12 a 360.79 7.68669 YES YES
13 a 377.25 25.99351 YES YES
14 a 431.27 13.50432 YES YES
15 a 522.33 2.07831 YES YES
16 a 583.19 4.66771 YES YES
17 a 587.91 102.69438 YES YES
18 a 664.09 13.87677 YES YES
19 a 685.26 10.36450 YES YES
20 a 720.79 217.35379 YES YES
21 a 755.25 2.31369 YES YES
22 a 777.49 2.22428 YES YES
23 a 860.72 15.31103 YES YES
24 a 958.79 1.79962 YES YES
25 a 1006.53 1.51584 YES YES
26 a 1035.98 6.36000 YES YES
27 a 1126.59 38.23933 YES YES
28 a 1153.10 45.04718 YES YES
29 a 1212.04 55.76099 YES YES
30 a 1273.30 29.07111 YES YES
31 a 1303.81 96.17203 YES YES
32 a 1327.48 68.41479 YES YES
33 a 1400.54 60.93027 YES YES
34 a 1410.68 139.45727 YES YES
35 a 1454.52 5.40728 YES YES
36 a 1472.57 1.05534 YES YES
37 a 1663.21 141.68596 YES YES
38 a 1739.67 685.35070 YES YES
39 a 1779.98 830.38911 YES YES
40 a 3016.25 8.53182 YES YES
41 a 3034.18 7.87679 YES YES
42 a 3052.46 20.26137 YES YES
43 a 3076.43 17.81182 YES YES
44 a 3398.16 26.97265 YES YES
45 a 3444.01 49.06620 YES YES
$end
==============================================
| |
| C R E S T |
| |
| Conformer-Rotamer Ensemble Sampling Tool |
| based on the GFN methods |
| P.Pracht, S.Grimme |
| Universitaet Bonn, MCTC |
==============================================
Version 2.12, Thu 19. Mai 16:32:32 CEST 2022
Using the xTB program. Compatible with xTB version 6.4.0
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
------------------------------------------------------------------------
-----------------
Wall Time Summary
-----------------
--------------------
Overall wall time : 0h : 0m : 0s
CREST terminated normally.
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 .