Calculating Molecular Coordinates and Intermolecular Geometry and Interaction

The programs are written in FORTRAN, and compiled by gfortran on windows 11.

Step 1. Convert atomic coordinates in cif using trcifg4 or trmc3. Use trmc3.zip or trcifg4.zip.

Step 2. Copy the atomic coordinates and the lattice constants in at.dat to pcal.dat. Add symmetry operations. Use pcal.zip.

Step 3. Run pcal. Calculation of intermolecular potentials in the actual geometry and parallel displacement.
The output file at.dat contains molecular coordinates, intermolecular geometry, and the 6-exp potentials.

(Coordinates of parallel-displaced molecules are generated.)
Step 4. Run qcal. Calculation of intermolecular potentials by changing the dihedral angle. Use qcal.zip.

(Coordinates of herringbone structures with varying the dihedral angle are generated.)

See, T. Mori, CrystEngComm. 25, 6266-6278 (2023).

Instructions

Input File	Source	Windows	Output File	zip
trcifg.dat	trcif8.f trcifg4.f	trcif8.exe trcifg4.exe	at.dat	trcifg4.zip
pcal8.dat pcal8_pentacene.dat	pcal8.f	pcal8.exe	at8.dat
pcal.dat	pcal658.f	pcal658.exe		pcal.zip
pcal.dat	pcalC.f	pcalC.exe		pcalC.zip	For charge-transfer complex
at8.dat	qcal8.f qcal8x.f	qcal.exe qcal8x.exe	qcal8.out	qcal.zip
q-dependence	qcal88LNNO.f	qcal88LNNO.exe
j-dependence	qcal154.f	qcal154.exe

September 25, 2023

Quadrupole moments

Input File	Source	Windows	Output File
QM.dat	Q5.f	Q5.exe	QM.out

June 17, 2025

Easy transformation to Molecular Coordinates

Input File	Source	Windows	Output File	zip
at.cif	trmc2.f	trmc2.exe	mc.xyz, at.dat
at.cif, trmc.dat	trmc3.f	trmc3.exe	mc.xyz, at.dat	trmc3.zip

(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 trmc3.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. Otherwise 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

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