Calculating
Molecular Coordinates and Intermolecular Geometry and Interaction
The programs are written in
FORTRAN, and compiled by gfortran on windows 10.
Step 1. Convert atomic
coordinates in cif using trcif.
Step 2. Copy the atomic
coordinates and the lattice constants in at.dat to pcal8.dat. Add symmetry
operations.
Step 3. Run pcal8. The output
file at8.dat contains molecular coordinates, intermolecular geometry, and the
6-exp potentials.
Step 4. Run qcal8. The potential energy is calculated as a function of the
dihedral angle.
See, T. Mori, CrystEngComm. 25,
6266-6278 (2023).
|
Input File |
Source |
Windows |
Output File |
|
at.dat |
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q-dependence |
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j-dependence |
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September 25,
2023
Quadrupole moments
|
Input File |
Source |
Windows |
Output File |
|
QM.out |
June 17, 2025
Easy transformation to Molecular Coordinates
|
Input File |
Source |
Windows |
Output File |
|
at.cif |
mc.xyz, at.dat |
||
|
at.cif, trmc.dat |
mc.xyz, at.dat |
(1) Open the cif file of the target molecule. Display a single molecule.
If there are more than two molecules, delete. Save as at.cif.
(2) Download and
copy trmc2.exe in the same folder, and run by double clicking.
(3) Open mc.xyz, and project along the c axis. The projection onto
the molecular plane. (x: molecular long axis. y: short axis. z: vertical axis)
(4) For Gaussian,
copy the coordinates from mc.xyz by a text editor.
For ADF, import the coordinates from mc.xyz.
(5) If trmc2.exe
does not correctly make the molecular coordinates, select the using atoms as
111100111111111111,
or a blank line and 4 (for the first four atoms), or a blank line and 3 10 (for
using from the third to the tenth atoms)
in trmc.dat,
and run trmc3.exe. trmc2.exe uses all non-hydrogen atoms, and the atom numbering
follows the output in at.dat. To remove the alkyl chains, use trmc3.exe.
January 3,
2026
