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. 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'' |
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''. For instance one can use |
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Revision as of 18:02, 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. For instance one can use
compute myTemp all temp compute_modify myTemp extra 0 thermo_modify temp myTemp