This repo is created to share all the code about theoretical and computational chemistry developed by the author when working in Prof. Jun Li research group at Department of Chemistry, Tsinghua University, China.
The code are developed to help with the input or output of some popular computational chemistry software such as Gaussian, ADF, Molpro, NWChem, CP2K, VASP and Dmol3. 
Most of the code are develped using Perl or Python, so as to be easily portable.

This is a more detailed description of all scripts in each subdirectory of the TCCL-Code.
1. ADF
ADFDFTB2mov.py : Read the output of geometry optimization calculation with DFTB method in ADF, extract the cartesian coordinates and energy of each optimization step, output the optimization trajectory in XYZ format.
ADFDFTB2xyz.py : Read the output of geometry optimization calculation with DFTB method in ADF, extract the cartesian coordinates and energy of the last optimization step, output the geometry in XYZ format.
adflog2xyz.pl : Read the logfile of geometry optimization calculation with DFT method in ADF, extract the Cartesian coordinates and energy of the last step, output the geometry in XYZ format.
2. CP2K
cp2kdimerfe.py : Read the output of transition state optimization calculation with Dimer method using the CP2K package, extract the energy and Max Gradient of each optimization step. The result will be stored in fe.dat file. 
cp2kfreq2mov.pl : Read the output of the vibrational analysis calculation using the CP2K package, extract the vibrational mode for each frequency, export the animation in XYZ format for each mode.
cp2klog2xyz.pl： Read the *-pos-1.xyz file of geometry optimization calculation using the CP2K package, extract the Cartesian coordinates and energy of the last step and export it in XYZ format.
cp2knebforces.pl： Read the output of transition state optimization calculation with NEB method using the CP2K package, extract the maximum force of each replicas.
elpot_plot.pl ：Read the cube file generated by v-hartree calculation using CP2K package, calculating the average value of the V-hartree potential in Z direction.
cp2kdimerlog2xyz.pl：Read the *-pos-1.xyz file of transition state optimization calculation using CP2K package, get the geometry of the last optimization step. Get the energy of the last step from the fe.dat file generated by cp2kdimerfe.py script. Output the geometry and energy in XYZ format.
cp2kfreq.pl：Read the output of vibrational analysis calculation using CP2K, get the list of all the vibrational frequencies and label all the imaginary frequencies. Export the result to freq.date file.
GetCP2KDimerVector.py：Read the restart file of transition state search with Dimer method using the CP2K package, extract the DimerVector section, and export the DimerVector to the MODECAR format.
3. DMol3
dmolcar2xyz.pl: Read the .car file generated by Material Studio program, and convert it to XYZ file.
dmolcar2xyz.py: Read the .car file generated by Material Studio program, and convert it to XYZ file. If "-s" option is used, the atoms in the .car file will be sorted by its element type and the coordinates at Z direction. 
dmollog2xyz.pl：Read the output file of geometry optimization calculation using Dmol3 program, get the cartesioan coordinates and energy of the last optimization step.
xyz2arc.pl：Read an XYZ file and convert it to an .arc file which could be read by Material Studio program. If the XYZ file is a trajectory file with many geometries in XYZ format, all these geometries will be read and converted. The .arc file generated could be used to play animation of the trajectory. If a POSCAR or CONTCAR file exists in the current directory, the periodic boundary condition (PBC) will be read from the POSCAR or CONTCAR file, so the .arc file will have PBC. Note that the .arc file is almost the same to the .car file.
xyz2dmolcar.pl ：Convert a single XYZ file to the .car file for dmol3 program.
4. Gaussian
g03log2xyz.pl : Read the output file of geometry optimization calculation by Gaussian proram, extract the last geometry and its energy, export it in XYZ format.
5. Molpro
OrbPrint++_1.1.pl : Read the orbital composition of Molpro calculation ane output the orbital composition in a more friendly way. Open-Shell, Closed Shell calculation ans Natural orbitals are supported.
6. NWChem
nwlog2xyz.pl : Read the output file of geometry optimization calculation by NWChem program, extract the energy and coordinates of the last step, export the result in XYZ format.
7. VASP
vasp2xyz.pl: Using the vtsts scripts to convert the CONTCAR file to XYZ file and extract the cooresponding energy from the OUTCAR file. Put the energy in the second line of the XYZ file.
8. TwoElectronHF
HFCalc.f90: A simple two-electron Hartree-Fock program using sto-3G basis set. The program can calculate the ground state energy of H2 or HeH+. The program is written in Fortran 90. The framework of the program is based on the appendix in the book  Modern Quantum Chemistry: Introduction to advanced Electronic Structure Theory written by Szabo, A and Ostlund N S. 
9. Misc
freq2zpe.pl : Read all the vibrational frequencies from freq.dat file and calculate the vibrational Zero Point Energy.
xyz2neb.pl：Given the XYZ coordinates of the initial state, final states and the number of replicas, generate the images for NEB calculation using a linsear interpolation method. The coordinates of the replicas will be exported as XYZ files.
xyzshrink.py： Read the XYZ file produced by Molecular Dynamics calculation by a certain interval, so as to shrink the size of the trajectory file. For example, for a trajectory file with 1000 steps, set the interval to be 10, the xyzshrink.py file will read geometry 1, 11, 21 ... 991 from the trajectory file.