howto:langevin_regions
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- | ====== How to Perform Molecular Dynamics With A Sub Set of Atoms Undergoing NVT Langevin Dynamics And The Rest Undergoing NVE Born-Oppenheimer Dynamics ====== | + | This page has been moved to: https:// |
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- | In this tutorial, we are going to show the reader how to perform Langevin molecular dynamics for a sub set of atoms in the simulation cell, with the rest of the atoms undergoing Born-Oppenheimer molecular dynamics. We assume the reader has already got the basic knowhow of performing molecular dynamics using CP2K. | + | |
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- | To be able to perform this calculation, | + | |
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- | We will use a simple 64 atoms face centred cubic bulk Si as an example. The system will start from a relaxed ground state structure (i.e. a geometry optimisation calculation | + | |
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- | The example files are contained in {{:howto: | + | |
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- | ===== Input Flags ===== | + | |
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- | All we need to do to perform this calculation is to add/modify a few flags in the [[http:// | + | |
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- | The relevant sections for the example are listed below: | + | |
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- | In the [[http:// | + | |
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- | <code CP2K> | + | |
- | ENSEMBLE LANGEVIN | + | |
- | </ | + | |
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- | This ensures we will be doing Langevin molecular dynamics. The method of applying mixed NVE and NVT dynamics //only works// if Langevin MD is switched on. | + | |
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- | The important thing to do next is to define the thermal regions, which controls whether each region will be performing NVT Langevin MD or NVE Born-Oppenheimer MD. In our example, we have (inside [[http:// | + | |
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- | <code CP2K> | + | |
- | & | + | |
- | DO_LANGEVIN_DEFAULT F | + | |
- | & | + | |
- | TEMPERATURE $temp | + | |
- | DO_LANGEVIN T | + | |
- | LIST 1..24 | + | |
- | &END DEFINE_REGION | + | |
- | & | + | |
- | # TEMPERATURE $temp | + | |
- | DO_LANGEVIN F | + | |
- | LIST 25..64 | + | |
- | &END DEFINE_REGION | + | |
- | & | + | |
- | & | + | |
- | &END LANGEVIN_REGIONS | + | |
- | &END PRINT | + | |
- | &END THERMAL_REGION | + | |
- | </ | + | |
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- | The [[http:// | + | |
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- | Each of the subsections | + | |
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- | <code CP2K> | + | |
- | & | + | |
- | TEMPERATURE $temp | + | |
- | DO_LANGEVIN T | + | |
- | LIST 1..24 | + | |
- | &END DEFINE_REGION | + | |
- | </ | + | |
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- | defines a thermal region. | + | |
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- | By default, '' | + | |
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- | In our example, we have defined two regions. The first region contains atoms 1 to 24, undergoing NVT Langevin MD with target temperature of 500 K, and the second region contains atoms 25 to 64, undergoing NVE Born-Oppenheimer MD. Note that since '' | + | |
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- | The [[http:// | + | |
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- | Information on the NVT and NVE regions may be printed out by using the [[http:// | + | |
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- | <code CP2K> | + | |
- | & | + | |
- | & | + | |
- | &END LANGEVIN_REGIONS | + | |
- | &END PRINT | + | |
- | </ | + | |
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- | Simply add the subsection [[http:// | + | |
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- | ===== Importance of Initial Velocity To Consistency Of Calculations ===== | + | |
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- | If the initial velocities of the atoms are not explicitly defined in the input, CP2K will randomise the atomic velocities to give an initial temperature corresponding to the target temperature defined by [[http:// | + | |
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- | Due to the stochastic nature of Langevin MD, the trajectories of the atoms generated as a result of the pseudo-random number generators will be dependent on the initial velocities of the atoms. Therefore, if you are to perform to two calculations with the same physical thermal regions setup, but do not specify the initial velocities, there is a chance that the velocities and energies at each MD step can be different for the two calculations. This can arise, in the cases where the setups are physically the same, but computationally different in terms of input setup: for example: setting '' | + |
howto/langevin_regions.1598004913.txt.gz · Last modified: 2020/08/21 10:15 by 127.0.0.1