molecular_dynamics
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molecular_dynamics [2009/11/26 09:56] prokop |
molecular_dynamics [2011/02/18 13:13] (current) |
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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 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''. | + | 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=0 | NVE ensemble | | ||
| Line 28: | Line 28: | ||
| </code> | </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. | + | 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 : ==== | ==== NH.optional : ==== | ||
| <code> | <code> | ||
| 4 !number of chains | 4 !number of chains | ||
| - | 1.2 ! | + | 1.2 ! mass of chain 1 |
| - | 1.2 ! | + | 1.2 ! mass of chain 2 |
| - | 1.2 ! | + | 1.2 ! mass of chain 3 |
| - | 1.2 ! | + | 1.2 ! mass of chain 4 |
| </code> | </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. | + | 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 : ==== | ==== fireball.in : ==== | ||
| Line 61: | Line 61: | ||
| &END | &END | ||
| </code> | </code> | ||
| + | All input files here:{{:fireball:md:input_files.tar.gz|input_files}} | ||
| ==== Output ==== | ==== Output ==== | ||
| - | 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: | + | 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: |
| <code> | <code> | ||
| awk '/ETOT/ {print 6$}' answer.xyz > T_dyn '' | awk '/ETOT/ {print 6$}' answer.xyz > T_dyn '' | ||
| Line 70: | Line 70: | ||
| where are the data in simple list. | 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. | + | Temperature during simulation of benzene hold on by velocity rescaling and Nose-Hoover thermostat during the simulation in Figure 1. |
molecular_dynamics.1259225781.txt.gz · Last modified: 2011/02/18 13:14 (external edit)
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