molecular_dynamics
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molecular_dynamics [2009/11/26 09:41] prokop created |
molecular_dynamics [2011/02/18 13:13] |
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| - | =====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 keyvord: 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 ichuench = 0. | ||
| - | |||
| - | <code> | ||
| - | 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. | ||
| - | </code> | ||
| - | |||
| - | Here is an example of answer.bas for benzene molecule. | ||
| - | |||
| - | <code> | ||
| - | 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 | ||
| - | </code> | ||
| - | |||
| - | 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 like bellow. | ||
| - | |||
| - | <code> | ||
| - | NH.optional | ||
| - | 4 !number of chains | ||
| - | 1.2 ! | ||
| - | 1.2 ! | ||
| - | 1.2 ! | ||
| - | 1.2 ! | ||
| - | </code> | ||
| - | |||
| - | 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 femtosecond.An example of fireball.in input file for clasical molecular dynamic is bellow. | ||
| - | |||
| - | <code> | ||
| - | 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 | ||
| - | </code> | ||
| - | |||
| - | The position and values of total energy and tomperature 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 Hoocer thermostat during the simulation in Figure 1. | ||
molecular_dynamics.txt ยท Last modified: 2011/02/18 13:13 (external edit)
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