Revised sld.rst

Author: johanhellsvik

content/sld/sld.rst

@@ -1,43 +1,70 @@
 Spin-lattice dynamics
 =====================
 
-SLD simulation of a dimer
--------------------------
+For ASD simulations, the minimal set of input files consists of ``inpsd.dat``, a ``posfile``,
+a ``momfile``, and a ``jfile``. In order to set up a SLD simulation with UppASD, this set of
+input files need to be augmented with a number of files, namely a ``phonfile``, an ``llfile``,
+and the coupling constants for a cross coupling Hamiltonian such as the third order
+spin-spin-displacement Hamiltonian contained in an ``mmlfile``.
+
+Exercise 1: SLD simulation of a dimer
+-------------------------------------
+
 In this example we are modeling a spin-lattice coupled magnetic dimer, with zero lattice
 damping and zero Gilbert damping, using velocity-Verlet or fixed-point iteration
 implicit midpoint solver. The full expressions for the Hamiltonian, the effective magnetic
 fields, and the interatomic forces are contained in Eqs. 27-31 in Ref. [Hellsvik2019]_. 
 
-The main input file ``inpsd.dat``
+The main input file ``inpsd.dat`` contains a number of additional blocks
 
 .. literalinclude:: DimerSLD/DimerpuSLDcoupled/inpsd.dat
 
-the  ``posfile`` The file contains the positions of the atoms in terms of basis vector coordinates in the unit cell.
+The  ``posfile`` contains the positions of the atoms in terms of basis vector coordinates in the unit cell.
 
 .. literalinclude:: DimerSLD/DimerpuSLDcoupled/posfile
 
-the ``momfile`` The file contains the magnetic moments of the atoms in the unit cell.
+The ``momfile`` contains the magnetic moments of the atoms in the unit cell.
 
 .. literalinclude:: DimerSLD/DimerpuSLDcoupled/momfile
 
-the ``jfile.nosym`` The file contains the exchange couplings within the system.
+The ``jfile.nosym`` contains the exchange couplings within the system.
 
 .. literalinclude:: DimerSLD/DimerpuSLDcoupled/jfile.nosym
 
-The ``phonfile`` File contains ionic masses, initial displacements and velocities. The columns are : site number, atom type, atomic mass, initial displacements and velocities in three different directions x, y, z.
+The ``phonfile`` file contains ionic masses, initial displacements and velocities.
+The first column is the ``site`` number, the second the atom ``type``,
+the third the ``atomic mass`` in atomic mass units, the 4-6th the Cartesian components
+of the initial displacements, the 7-9th columns the Cartesian components of the velocities.
 
 .. literalinclude:: DimerSLD/DimerpuSLDcoupled/phonfile
 
-The ``llfile.nosym`` File contains the harmonic force constants for a lattice. The columns are : site number, (not used), interaction vectors depending on maptype, 9 components of the harmonic force constants in the order of [xx, xy, xz, yx, yy, yz, zx, zy, zz].
+The ``llfile`` file contains the harmonic force constants.
+The first column is the ``site`` number, (not used), the 3rd-5th the interaction vectors
+(dependent on ``maptype``), and the 6-15th columns the components of the harmonic force
+constants in the order of *xx*, *xy*, *xz*, *yx*, *yy*, *yz*, *zx*, *zy*, *zz*.
 
 .. literalinclude:: DimerSLD/DimerpuSLDcoupled/llfile.nosym
 
-The ``mmlfile.nosym`` File contains the spin-lattice coupling (SLC) constants [see Eqs. 6-9 in Ref. [Hellsvik2019]_]. The columns from first row are : site number (atom i), site number of nearest neighbour mapping (atom j), interaction vectors for nearest neighbour site  (j-th) and displaced (k-th) atom depending on maptype. The columns from the second, third and fourth rows are : 9 components of SLC constants for the displacement of k-th atom along x, y, z respecively. The ordering of SLC components in each row are [xx, yx, zx, xy, yy, zy, xz, yz, zz]. For DimerSLD, the SLC constants are of :math:`A_{iji}` type.
+The ``mmlfile`` contains the spin-lattice coupling (SLC) constants
+[see Eqs. 6-9 in Ref. [Hellsvik2019]_]. The columns from first row are:
+site number (atom i), site number of nearest neighbour mapping (atom j),
+interaction vectors for nearest neighbour site (j-th) and displaced (k-th)
+atom depending on maptype. The columns from the second, third and fourth rows are:
+9 components of SLC constants for the displacement of k-th atom along x, y, z respectively.
+The ordering of SLC components in each row are [xx, yx, zx, xy, yy, zy, xz, yz, zz].
+For a dimer, the SLC constants are of :math:`A_{iji}` type, *i.e.* the displacement is always
+on one of the two atoms that are exchange coupled, given that no third site is present.
 
 .. literalinclude:: DimerSLD/DimerpuSLDcoupled/mmlfile.nosym
 
+* Run a simulation for the example ``DimerSLD/DimerpuSLDcoupled``. Which output files are generated?
+* Plot the time trajectories of the energies that are written to the file ``lattenergy.scnobase.out``. How do the energies evolve in time? Compare for Fig. 2 in [Hellsvik2019]_.
+* Plot the time trajectories of spins (``moment.scnobase.out``), and displacements (``disp.scnobase.out``). How do magnetic precession frequencies evolve in time? Compare for Fig. 3 in [Hellsvik2019]_.
+* Compare the input files contained in ``DimerSLD/DimerpuSLDcoupledSym`` with ``DimerSLD/DimerpuSLDcoupled``. How do they differ? Verify that the same Hamiltonians are set up within the UppASD simulation by comparing the ``struct.scnobase.out``, the ``lldata.scnobase.ou``, and the ``mmldata.scnobase.out`` files for the two different cases.
+
 SLD simulation for trimer
 -------------------------
+
 TrimerSLD      # Trimer SLD, atomic units, with different MML coupling,
                # either of :math:`A_{iji}` type or of :math:`A_{ijk}` type.
                # optional use of point group symmetries for the couplings