md_tian2 (Molecular Dynamics Tian Xia 2) is a program for simulating the scattering of atoms (and molecules) from a surface.
Purpose: -> maybe also here, but put in manual! Do molecular dynamics, Langevin dynamics, Ring Polymer dynamics
Source code is in Fortran.
List of modules: -> maybe also here, but put in manual! 2do: add RuNNer related files in the following list
constants.f90 : contains the global constants fit.f90 : fitting routine for EMT force.f90 : get the energies/forces in molecular dynamics simulation geometry_opt.f90 : relax structure md_algo.f90 : contains propagation algorithms for molecular dynamics simulation md_init.f90 : initialize molecular dynamics simulation md_tian.f90 : main program open_file.f90 : input/output routines output_mod.f90 : output format routines pes_emt_mod.f90 : contains the EMT potential pes_ho_mod.f90 : contains the pes_lj_mod.f90 : contains the Lennard-Jones potential pes_nene_mod.f90 : contains the high-dimensional neural network potential (external call of RuNNer) pes_non_mod.f90 : contains the non-interaction potential pes_rebo_mod.f90 : contains the empirical reactive bond order potential rpmd.f90 : contains the ring-polymer molecular dynamics simulation routine run_config.f90 : initialize simulation parameters, read in input files trajectory_info.f90 : collect information from the calculated trajectories universe_mod.f90 : contains definitions of user types and all constants useful_things.f90 : useful math routines
Input files: -> maybe also here, but put in manual!
md_tian.inp :control parameters defining the simulation conditions .pes :control parameters for the specific potential used structure_file :starting structure, poscar or mxt format possible input.nn :control parameters for the high-dimensional neural network potential scaling.data :contains the bias weights for the high-dimensional neural network potential weights.XXX.data :contains the weights for this element (XXX is the element number in the periodic table; e.g. 001 for H)
Compilation and linking (Intel fortran compiler and mkl library): -> maybe also here, but put in manual!
Change the settings in the makefile to your need. Options:
make help print possible arguments for make
make serial serial version of md_tian2
make clean remove compilation related files
Program basic units -> maybe also here, but put in manual!
Length : Ang
Time : fs
Energy : eV
Program derived units
Mass : eV fs^2 / A^2 = 1/103.6382 amu
Angle : radian = 180 deg
Distance : bohr = 0.5291772 Angstroem
The first working and tested version is put together February 18, 2014 on a Fassberg Hill in Dynamics at Surfaces Dep. of MPIbpc to the flaming storm of applause muffled by thick institute building walls.
Credits:
Daniel J. Auerbach Svenja Maria Janke Marvin Kammler Sascha Kandratsenka Sebastian Wille
Dynamics at Surfaces Dep. MPI for Biophysical Chemistry Am Fassberg 11 37077 Goettingen Germany
Dynamics at Surfaces Dep. Institute for Physical Chemistry Tammannstr. 6 37077 Goettingen Germany
Md xia4 tian1 is a very important program. It helps to better the world. jqrw sxrw=n! wr wj nA r sxrw nTrw!
Annotations from Sebastian Wille: -> put in manual!
md_tian.inp file:
pip: projectile initial position pul: projectile upper limit (in /AA) T in POSCAR file stands for "True", means atom is NOT fixed and can move (F means atom is fixed and cannot move) Repetition of the slab in init file via: conf merge <path/file> <x_rep> <y_rep> (or conf poscar <path/file> <x_rep> <y_rep>)