Python code kit for generating input files of intermolecular rigid scan calculations.
(1) A .txt file including atom coordinates of two molecules, and scan information. An example is shown following, you can find this example file in the /example folder.
101 61 101 162 10 -1.33
H 2.87743800 6.17226100 2.06448600
C 3.41666700 5.88600900 1.16582400
C 4.76477800 5.02306500 -1.08527100
C 4.58285000 5.14083300 1.29223300
C 2.85882400 6.14752400 -0.09092800
C 3.62082800 5.79663600 -1.21185000
( . . . . . . )
C -1.37202368 0.25836733 16.58099407
C 1.80309832 -3.02537363 13.07640301
Bq -0.00047997 0.00208209 13.33691324
In the first line, users need to give: (a) number of atoms in molecule A, (b) number of atoms in molecule B, (c) target atom in molecule A, (d) target atom in molecule B, (e) number of scan step, (f) step size of each scan. Then following with Cartesian coordinates of molecule A and B.
In this example, molecule A is [10]CPP, molecule B is C60. [10]CPP have 100 atoms with 1 Bq atom, total 101 atom, and C60 have 61 atoms since 1 Bq atom also be included. We want to scan the distance between two Bq atoms (atoms number: 101 and 162) in 10 steps with -1.33 step size.
(2) A .txt file including Gaussian calculation setup.
%nprocshared=8
%mem=10GB
%chk=
#p rb3lyp/6-31g(d) counterpoise=2
0 1 0 1 0 1
Users can specify the CPU cores, memory, routine line, charge and spin multiplicity. If you want to keep checkpoint file, please include %chk= in this file (you don't need to write the checkpoint file name here).
Run int.Scan from Terminal, make sure file (1) and (2) in step 1 are in the same directory. Input the file location of file (1), and press ENTER, the Gaussian input files and a .xyz file including the geometries of each scan step would be saved in the same location as the .txt files.
*******************************************************************************
* *
* i n t . S c a n *
* *
* ====================== Version 1.0 for macOS ====================== *
* Release date: 2022-01-30 *
* *
* -- Catch me with -- *
* E-mail [email protected] *
* Homepage https://wongzit.github.io *
* *
*******************************************************************************
PRESS Ctrl+c to exit the program.
int.Scan input file (.txt):
(e.g.: /intScan/examples/10cpp_c60.txt)
/Users/wangzhe/Desktop/10cpp_c60/10cpp_c60.txt
The trajectory of C60 in [10]CPP:
If BSSE (counter=2 or counterpoise=2) is included in file (2), the fragment data will also be included in the generated Gaussian input files.
With BSSE:
H(Fragment=1) -4.944644 -4.906682 -2.289024
H(Fragment=1) -2.877416 -6.172317 -2.064427
H(Fragment=1) -3.265775 -6.050711 2.206495
C(Fragment=2) -1.80485887 3.02852116 4.28662042
C(Fragment=2) -1.88434133 2.51907695 5.64214841
C(Fragment=2) -0.74835384 2.47866864 6.4353001
Without BSSE:
H -4.944644 -4.906682 -2.289024
H -2.877416 -6.172317 -2.064427
H -3.265775 -6.050711 2.206495
C -1.80485887 3.02852116 4.28662042
C -1.88434133 2.51907695 5.64214841
C -0.74835384 2.47866864 6.4353001
If Bq atoms are included in file (1), the generated Gaussian input files would delete these Bq atoms, but Bq atoms would be remain in the generated .xyz file.
For single point energy calculations, users can use int.Scan(enex) script to extracting electronic energies in each step. The source code could be found in this repo.
Users can use int.Scan(chkend) to check whether the calculations were terminated normally.
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