diff --git a/doc/src/Howto.rst b/doc/src/Howto.rst index a048c1b1c7..85c98bd6de 100644 --- a/doc/src/Howto.rst +++ b/doc/src/Howto.rst @@ -90,7 +90,6 @@ Packages howto Howto_peri Howto_manifold Howto_spins - Howto_cgdna Tutorials howto =============== diff --git a/doc/src/Howto_cgdna.rst b/doc/src/Howto_cgdna.rst deleted file mode 100644 index 0089df4a8d..0000000000 --- a/doc/src/Howto_cgdna.rst +++ /dev/null @@ -1,64 +0,0 @@ -Coarse-grained DNA and RNA -========================== - -The magnetic spin simulations are enabled by the SPIN package, whose -implementation is detailed in :ref:`Tranchida `. - -The model represents the simulation of atomic magnetic spins coupled -to lattice vibrations. The dynamics of those magnetic spins can be used -to simulate a broad range a phenomena related to magneto-elasticity, or -or to study the influence of defects on the magnetic properties of -materials. - -The magnetic spins are interacting with each others and with the -lattice via pair interactions. Typically, the magnetic exchange -interaction can be defined using the -:doc:`pair/spin/exchange ` command. This exchange -applies a magnetic torque to a given spin, considering the orientation -of its neighboring spins and their relative distances. -It also applies a force on the atoms as a function of the spin -orientations and their associated inter-atomic distances. - -The command :doc:`fix precession/spin ` allows to -apply a constant magnetic torque on all the spins in the system. This -torque can be an external magnetic field (Zeeman interaction), and an -uniaxial or cubic magnetic anisotropy. - -A Langevin thermostat can be applied to those magnetic spins using -:doc:`fix langevin/spin `. Typically, this thermostat -can be coupled to another Langevin thermostat applied to the atoms -using :doc:`fix langevin ` in order to simulate -thermostatted spin-lattice systems. - -The magnetic Gilbert damping can also be applied using :doc:`fix langevin/spin `. It allows to either dissipate -the thermal energy of the Langevin thermostat, or to perform a -relaxation of the magnetic configuration toward an equilibrium state. - -The command :doc:`fix setforce/spin ` allows to set the -components of the magnetic precession vectors (while erasing and -replacing the previously computed magnetic precession vectors on -the atom). -This command can be used to freeze the magnetic moment of certain -atoms in the simulation by zeroing their precession vector. - -The command :doc:`fix nve/spin ` can be used to -perform a symplectic integration of the combined dynamics of spins -and atomic motions. - -The minimization style :doc:`min/spin ` can be applied -to the spins to perform a minimization of the spin configuration. - -All the computed magnetic properties can be output by two main -commands. The first one is :doc:`compute spin `, that -enables to evaluate magnetic averaged quantities, such as the total -magnetization of the system along x, y, or z, the spin temperature, or -the magnetic energy. The second command is :doc:`compute property/atom `. It enables to output all the -per atom magnetic quantities. Typically, the orientation of a given -magnetic spin, or the magnetic force acting on this spin. - ----------- - -.. _Tranchida: - -**(Tranchida)** Tranchida, Plimpton, Thibaudeau and Thompson, -Journal of Computational Physics, 372, 406-425, (2018).