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molecular_dynamics

Molecular dynamics

In this section we describe how to simulate molecular dynamics in NVT and NVE ensembles. In the canonical ensemble are N,V,T respectively N,V,E conserved. There are implemented two methods to hold temperature constant in fireball. The first one is velocity rescaling and the second is Nose- Hoover chain thermostat. These options are driven by keyword: iensemble that controls which statistical ensemble will used within the simulation. In particular, to run free dynamics without any structural optimization method, one needs to set iquench = 0.

iensemble=0 NVE ensemble
iensemble=1 NVT ensemble with velocity rescaling
iensemble=2 NVT with a Nose-Hoover chain thermostat and velocity-verlet
iensemble=3 NVE with velocity-verlet integrator

Here is an example of answer.bas for benzene molecule:

answer.bas :

         12
   6     -4.183081     -4.008593     -0.000092
   6     -3.047805     -3.090020      0.004490
   6     -3.275844     -1.647830      0.001899
   6     -4.639523     -1.125588      0.002371
   6     -5.775305     -2.043508      0.000193
   6     -5.546619     -3.485699     -0.007522
   1     -6.432266     -4.204789     -0.015592
   1     -4.005535     -5.135519     -0.000976
   1     -1.983459     -3.500264      0.005183
   1     -2.389446     -0.929457     -0.002861
   1     -4.816925      0.001517     -0.000293
   1     -6.839935     -1.633156     -0.001403

In the case of Nose-Hoover thermostat we can choose number of chains and mass of extra additional degree of fredom. This values are set in file NH.optional placed in work directory.

NH.optional :

4               !number of chains
1.2             ! mass of chain 1
1.2             ! mass of chain 2
1.2             ! mass of chain 3
1.2             ! mass of chain 4

Temperature of system is set by keywords T_initial and T_final in section &OPTION&. Time step of ionic motion is defined through a standard keyword dt in femtoseconds. An example of fireball.in input file for classical molecular dynamic is below.

fireball.in :

&OPTION
basisfile = answer.bas 
iquench = 0
iendtemp = 0
T_initial = 500
T_final = 500
iensemble = 2
icluster = 1
nstepf = 200
dt = 0.1
iqout = 3
ifixcharge = 0
&END

&OUTPUT
iwrtxyz = 1
&END

All input files here:input_files

Output

The position and values of total energy and temperature are written into output file answer.xyz if the keyword iwrtxyz=1. To simplier plotting the values of temperature we can import tepmerature value from the file answer.xyz to another file e.g. T_dyn by command:

awk '/ETOT/ {print 6$}' answer.xyz > T_dyn '' 

where are the data in simple list.

Temperature during simulation of benzene hold on by velocity rescaling and Nose-Hoover thermostat during the simulation in Figure 1.

molecular_dynamics.txt · Last modified: 2011/02/18 13:13 (external edit)