CP2K Open Source Molecular Dynamics

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exercises:common:ensemble [2022/10/31 16:13] – jglanexercises:common:ensemble [2022/10/31 17:28] (current) – [NVT Ensemble] jglan
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-====== Lennard-Jones liquids ======+====== Ensembles (Lennard-Jones liquids) ======
 In this exercise, you will simulate a fluid of monoatomic particles that interact with a Lennard-Jones potential. The method to be used is molecular dynamics (MD) with periodic boundary conditions using CP2K. The aim is to explore the method, calculate the radial distribution function $g(r)$ and investigate a variety of ensembles. In this exercise, you will simulate a fluid of monoatomic particles that interact with a Lennard-Jones potential. The method to be used is molecular dynamics (MD) with periodic boundary conditions using CP2K. The aim is to explore the method, calculate the radial distribution function $g(r)$ and investigate a variety of ensembles.
  
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 The radial distribution function, (or pair correlation function) $g(r)$, in a system of particles (atoms, molecules, colloids, etc.), describes how the density varies as a function of distance from a reference particle. The radial distribution function, (or pair correlation function) $g(r)$, in a system of particles (atoms, molecules, colloids, etc.), describes how the density varies as a function of distance from a reference particle.
  
-===== NVE ensemble  =====+===== NVE Ensemble  =====
  
 In this section, we provide you with an example CP2K input for an MD calculation. In this section, we provide you with an example CP2K input for an MD calculation.
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 ===== NVT Ensemble  ===== ===== NVT Ensemble  =====
  
-In the previous sections, you have already run NVE ensemble molecular dynamics calculations for liquid Ar. In this section, we will focus on the NVT and NPT ensembles.+In the previous sections, you have already run NVE ensemble molecular dynamics calculations for liquid Ar. In this section, we will focus on the NVT ensembles.  
 + 
 +Although the most popular Nose-Hoover thermostat is commonly-used in other MD codes, the original Nose-Hoover thermostat has an ergodic issue. This has been solved by Mark Tuckerman et al. See [[https://doi.org/10.1063/1.463940 |Nose-Hoover Chain Thermostat]]  
 +In CP2K, the default length of the Nose-Hoover chain is set to 3. (See Manual [[https://manual.cp2k.org/cp2k-2022_1-branch/CP2K_INPUT/MOTION/MD/THERMOSTAT/NOSE.html| %MOTION%MD%THERMOSTAT%NOSE]]) 
  
 To set up an NVT calculation, change the settings in the &MD section as shown below: To set up an NVT calculation, change the settings in the &MD section as shown below:
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       REGION MASSIVE       REGION MASSIVE
       &NOSE                    #Uses the Nose-Hoover thermostat       &NOSE                    #Uses the Nose-Hoover thermostat
-        TIMECON 1000           #timeconstant of the thermostat chain, how often does thermostat adjust your system +        TIMECON 100           #timeconstant of the thermostat chain, how often does the thermostat adjust your system 
       &END NOSE       &END NOSE
     &END     &END
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 +Alternatively, one can also use [[https://manual.cp2k.org/cp2k-2022_1-branch/CP2K_INPUT/MOTION/MD/THERMOSTAT/CSVR.html| Canonical sampling through velocity rescaling
 +(CSVR)]] as developed by Giovanni [[https://doi.org/10.1063/1.2408420 |Bussi et al. ]]
 +  &MD
 +    ENSEMBLE NVT
 +    STEPS 3000
 +    TIMESTEP 5
 +    TEMPERATURE 298
 +    &THERMOSTAT
 +      &CSVR                    
 +        TIMECON 100           #timeconstant of the CSVR, how often does the thermostat adjust your system 
 +      &END CSVR
 +    &END
 +  &END MD
 +  
 ===== NPT Ensemble  ===== ===== NPT Ensemble  =====
  
exercises/common/ensemble.1667232808.txt.gz · Last modified: 2022/10/31 16:13 by jglan