How to use NEWTONX-2.2
Description
NX is a general-purpose program package for simulating the dynamics of electronically excited molecules and molecular assemblies.
It is a platform for performing all steps of the simulation, from the generation of the initial conditions to the statistical analysis of the results.
The dynamics simulations are based on Mixed quantum-classical methods, which allow including nonadiabatic effects and treating the nuclei in full dimensionality.
The main method implemented in NX is Trajectory surface hopping.
Newton-X works interfaced with other quantum-chemistry programs. It also contains a collection of built-in analytical Hamiltonians.
NEWTONX-2.2 is installed on the cluster with the precompiled binaries.
To use newtonx you must edit your ".bashrc" file and add the following line:
export NX=/home/apps/Chem/newton-x2.2/bin
Then run the "source .bashrc" command to apply the changes.
In this section, we will simulate absorption spectrum with TURBOMOLE. The system is pyrazine and two singlet excited states will be included. The initial geometry distribution will be generated by a Wigner distribution in the ground vibrational state of the ground electronic state. The transition energies and moments will be also computed at TD-DFT(B3- LYP)/SV(P). 2.1 Geometry file creation 1. In the TUTORIAL directory (see Section 1.4 of manual) create a subdirectory called PYRAZINE_TDDFT_SPEC: mkdir PYRAZINE_TDDFT_SPEC 2. Move to this directory and create a file called pyrazine.xyz containing the geometry in XYZ format: cd PYRAZINE_TDDFT_SPEC vi pyrazine.xyz 10 N -0.000000 2.421234 1.397837 N -0.000000 0.003637 0.002163 C 0.000000 1.241014 2.044972 C -0.000000 0.033417 1.347829 C -0.000000 2.391454 0.052171 C 0.000000 1.183858 -0.644972 H 0.000000 1.271951 3.113613 H -0.000000 -0.907483 1.855431 H -0.000000 3.332354 -0.455431 H 0.000000 1.152921 -1.713613 This initial geometry can be created by hand with a text editor (like VI) or with any molecular editor like MOLDEN. It is the simple xyz Cartesian format in Angstrom. The first line contains the number of atoms and it is followed by a blank line. 3. Convert geometry into NEWTON-X format. $NX/xyz2nx < pyrazine.xyz <ENTER>