Simulations: Difference between revisions
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===Special Usage Notes=== |
===Special Usage Notes=== |
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By default, LAMMPS normalizes the temperature by an amount (dof - d), where dof is the system's total number of degrees of freedom and d is the dimensionality of the simulation. |
By default, LAMMPS normalizes the temperature by an amount (dof - d), where dof is the system's total number of degrees of freedom and d is the dimensionality of the simulation. Subtracting d accounts for the center-of-mass motion of the system. This is correct except when there is a proper frame of reference for the system, e.g., in a Langevin dynamics simulation in which the implicit background solvent has zero average velocity. In this case it is necessary to use the command [http://lammps.sandia.gov/doc/compute_modify.html compute_modify] to ensure dof is used instead of (dof - d). An example is as follows. |
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<pre> |
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compute myTemp all temp |
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compute_modify myTemp extra 0 |
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thermo_modify temp myTemp |
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</pre> |
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== Monte Carlo simulations == |
== Monte Carlo simulations == |
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Revision as of 18:51, 7 June 2014
Introduction
Assorted topics relevant to programming particle-based simulation codes and to using these codes for the modeling of a wide range of systems, notably complex fluids.
Molecular dynamics simulations
Special Usage Notes
By default, LAMMPS normalizes the temperature by an amount (dof - d), where dof is the system's total number of degrees of freedom and d is the dimensionality of the simulation. Subtracting d accounts for the center-of-mass motion of the system. This is correct except when there is a proper frame of reference for the system, e.g., in a Langevin dynamics simulation in which the implicit background solvent has zero average velocity. In this case it is necessary to use the command compute_modify to ensure dof is used instead of (dof - d). An example is as follows.
compute myTemp all temp compute_modify myTemp extra 0 thermo_modify temp myTemp