# 6.4. geom with Gaussian

Tip

Gaussian is suitable for any clusters in gas phase, as long as you choose the correct model (pure, hybrid, or double-hybrid DFT, CCSD(T), and basis sets), but it is also expensive. So, this should only be used when there is no better ways.

In this Section, we just want to demonstrate how to use Gaussian with geom. Actually, it is possible that xTB is used first to get reliable structures, then Gaussian is used to refine, as discussed in Theoretical Background.

## 6.4.1. Example: (H2O)4(-)

Tip

The sample input and output files can be found in testfiles/geom/2-h2o4e-g16.

In this Section we will see how to use geom and Gaussian to do global optimization. Actually, this is exactly the same as we do in isomer with Gaussian: you just need to copy the commands to commands block.

The cluster we consider here is $$\left(\text{H}_2\text{O}\right)_4^{-}$$, an electron solvated in 4 water molecules. We will use the following input:

h2o4e.inp
 1lm_dir          h2o4e    # Save the local minima to this folder.
2num_calcs       50       # Total number of calculations.
3do_coarse_opt   yes      # no: Do NOT the coarse optimization.
4min_energy_gap  1.E-4    # When two energies differ smaller than
5                         # this value, they are treated as identical.
6                         # A negative number means do not remove
7                         # energetically degenerated ones.
8max_geom_iters  3000     # The maximum number of iterations for local optimization.
9                         # If it is less or equal than zero, then the number is unlimited.
10
11components
12    h2o.xyz 4
13    random 0 0 0 6 6 6
14    ****
15end
16
17savegjf
18  %chk=h2o4-$index$.chk
19  %nproc=48
20  %mem=30GB
21  $hash$MP2/aug-cc-pVTZ Opt Freq Output=wfn
22  $blank$
23  Initial guess generated from ABCluster, energy = $energy$
24  $blank$
25  -1 2
26  >>>>
27  h2o6-$index$.wfn
28end
29
30commands
31   xyz2gaussian optfile $inp$ > $xxx$.gjf
32   g16 < $xxx$.gjf > $xxx$.log 2>/dev/null
33   gaussian2xyz $xxx$.log > $out$
34end


You can see that, the commands to call Gaussian in commands is the same to the ones in isomer with Gaussian. We will calculate 50 structures and save them to heo4e. We also add a savegjf block to let geom save LMs in Gaussian job input format.

Also, we use random instead of box because we hope to get more flexible initial guess for global optimization.

The structure of $$\text{H}_2\text{O}$$ is:

h2o.xyz
13
2water
3O                  0.00000000    0.00000000   -0.11081188
4H                  0.00000000   -0.78397589    0.44324751
5H                 -0.00000000    0.78397589    0.44324751


The Gaussian input template is:

optfile
 1%nprocs=48
2%mem=20GB
3%chk=h2o4e.chk
4#N B3LYP/6-31++g(d) SCF(XQC) Geom(NoCrowd) Opt
5
6opt
7
8-1 2
9>>>>
10>>>>


Now you can run the global optimization:

$geom h2o4e.inp > h2o4e.out  After the optimization, the end of h2o4e.out is h2o4e.out  -- Result Report -- Results are energy-increasingly reordered. Structures of energies within 1.000E-04 are treated as degenerate. All minima are saved to "h2o4e". ------------------------------------------------------------------- # index Energy NaiveRMSD ------------------------------------------------------------------- 0 32 -305.73627036 0.00000000 1 8 -305.73593799 1.92341824 2 1 -305.73517045 1.95589313 3 47 -305.73433736 2.14224379 4 16 -305.73402914 1.52860669 5 33 -305.73371713 1.31278433 6 34 -305.73312443 0.94350149 7 25 -305.73243751 1.49950503 8 23 -305.73225990 1.78428545 9 38 -305.73083814 2.34486039 10 29 -305.73055667 1.64935620  So the global minimum is h2o4e/32.xyz, which is shown below. Interestingly, the anionic cluster optimized starting with the GM of neutral $$\left(\text{H}_2\text{O}\right)_4$$ is higher in energy than h2o4e/32.xyz by 1.37 kcal/mol at B3LYP/6-31g++(d). Tip We use B3LYP/6-31++g(d) to study the system. However, since the addition electron in this system may be very delocalized, very diffuse basis functions and high level of theory (beyond MP2) are needed to get reasonable results. That is why we let geom to generate GJF files for LMs. You can run more accurate calculations for the top 5 or 10 LMs to further refine the true GM. ## 6.4.2. Example: (CF3)4@C20 Tip The sample input and output files can be found in testfiles/geom/3-c20cf34-g16. It is argued that carbon cage like $$\text{C}_{20}$$ is an electron acceptor. So what will happen if some electron-withdrawing groups are attached? Let’s try to build a cluster of 4 $$\text{-CF}_3$$ on $$\text{C}_{20}$$. The structures of $$\text{C}_{20}$$ and $$\text{-CF}_{3}$$ are: c20.xyz  120 2C20 3C -1.20472114 0.39143763 1.65815580 4C -0.74455861 -1.02479702 1.65815580 5C 1.20472114 0.39143763 1.65815580 6C -0.00000000 1.26671877 1.65815580 7C 0.00000065 2.04959354 0.39143762 8C -1.20471985 1.65815687 -0.39143704 9C 1.20472125 1.65815590 -0.39143685 10C 0.74456049 1.02479624 -1.65815544 11C -0.74455796 1.02479756 -1.65815575 12C 1.20472204 -0.39143886 -1.65815486 13C 1.94927928 -0.63336012 -0.39143623 14C 1.94927917 0.63335933 0.39143808 15C 0.74455861 -1.02479702 1.65815580 16C 1.20472070 -1.65815601 0.39143808 17C 0.00000038 -2.04959369 -0.39143685 18C -1.20472033 -1.65815639 0.39143762 19C -1.94927899 -0.63336053 -0.39143704 20C -1.20472093 -0.39143845 -1.65815575 21C 0.00000048 -1.26672037 -1.65815458 22C -1.94927868 0.63336060 0.39143848  cf3.xyz 14 2CF3 3C 0.00000000 0.00000000 -0.36818188 4F -1.10227044 -0.63639614 0.08181821 5F 0.00000000 1.27279228 0.08181821 6F 1.10227044 -0.63639614 0.08181821  The input file is: c20cf34.inp  1lm_dir c20cf34 # Save the local minima to this folder. 2num_calcs 5 # Total number of calculations. 3do_coarse_opt yes # no: Do NOT the coarse optimization. 4min_energy_gap 1.E-4 # When two energies differ smaller than 5 # this value, they are treated as identical. 6 # A negative number means do not remove 7 # energetically degenerated ones. 8max_geom_iters 3000 # The maximum number of iterations for local optimization. 9 # If it is less or equal than zero, then the number is unlimited. 10 11components 12 c20.xyz 1 13 fix 0 0 0 0 0 0 14 **** 15 cf3.xyz 4 16 shell 1 1 1 2 3 4 0 0 0 3 3 3 17 **** 18end 19 20commands 21 xyz2gaussian optfile$inp$>$xxx$.gjf 22 g16 <$xxx$.gjf >$xxx$.log 2>/dev/null 23 gaussian2xyz$xxx$.log >$out$24end  From components, we can see that $$\text{C}_{20}$$ is fixed at (0, 0, 0) without rotation. Since its diameter is about 6 Å, we let the 4 $$\text{-CF}_{3}$$ groups form a shell on an ellipsoid centered at (0, 0, 0) with radii 3, 3, and 3. They point to the shell with an axis defined by the average of atom 1, 1, 1 and 2, 3, 4. This system is very expensive, so we do only 5 calculations. The Gaussian template is: optfile  1%nprocs=48 2%mem=20GB 3%chk=c20cf34.chk 4#N wB97XD/gen Opt 5 6opt 7 80 1 9>>>> 1021 25 29 33 116-31g(d) 12**** 13F 0 146-31g(d) 15**** 161 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 173-21g 18**** 19>>>>  Here, we choose wB97XD instead of B3LYP because the latter usually performs poorly for aromatic systems. After the first >>>>, we define the basis sets for different atoms to save the computational cost Tip This basis set canNOT be used in real scientific research. A better one is def2-SVP. For property calculations, triple-zeta and diffusion functions may be required. Now you can run the global optimization: $ geom c20cf34.inp > c20cf34.out


After the optimization, the end of c20cf34.out is

c20cf34.out
 -- Result Report --
Results are energy-increasingly reordered.
Structures of energies within 1.000E-04 are treated as degenerate.
All minima are saved to "c20cf34".
-------------------------------------------------------------------
#  index               Energy            NaiveRMSD
-------------------------------------------------------------------
0      2       -2107.38065472           0.00000000
1      0       -2107.38019685           1.83056800
2      1       -2107.37839045           3.12425180
3      3       -2107.37619597           3.38430408
4      4       -2106.56831104           2.73267963
-------------------------------------------------------------------


So the global minimum is c20cf34/2.xyz, which is shown below.