Merge pull request #15 from UppASD/sld2

Sld2

Author: johanhellsvik

content/sld/DimerSLD/DimerpuSLDcoupled/inpsd.dat

@@ -20,20 +20,20 @@ ll        ./llfile.nosym
 mml      ./mmlfile.nosym
 Initlatt  3
 
-do_ld     Y
-mode      R
+do_ld     Y                    # Read lattice and spin-lattice Hamiltonians
+mode      R                    # Perform SLD simulation
 Nstep     20000
 timestep  1e-16
 damping   0.00
 lattdamp  0.00
 Temp      0.00
 
-do_lavrg   Y
+do_lavrg   Y                   # Measurement of average displacaments
 do_proj_lavrg   Y
 lavrg_step   10
 lavrg_buff   10
 
-do_ltottraj  Y
+do_ltottraj  Y                 # Measurements of displacments
 ltottraj_step  10
 ltottraj_buff  10
 
@@ -62,4 +62,12 @@ do_prn_binteff  Y
 binteff_step    10
 binteff_buff    10
 
-plotenergy   1
+ntraj   2                  # Measurements of individual spin trajectories
+1    10    10
+2    10    10
+
+lntraj   2                 # Measurements of individual displacament trajectories
+1    10    10
+2    10    10
+
+plotenergy   1             # Measurement of energies

content/sld/DimerSLD/DimerpuSLDcoupled/plotTrajDimerSLD.py

@@ -0,0 +1,57 @@
+import numpy as np
+import matplotlib.pyplot as plt
+import matplotlib as mpl
+plt.style.use('default')
+plt.rc("figure", facecolor="white")
+
+mtraj1=np.genfromtxt("trajectory.scnobase.001.1.out")
+mtraj2=np.genfromtxt("trajectory.scnobase.002.1.out")
+utraj1=np.genfromtxt("disptraj.scnobase.1.1.out")
+utraj2=np.genfromtxt("disptraj.scnobase.1.1.out")
+lattenergy=np.genfromtxt("lattenergy.scnobase.out")
+t0=0
+t1=2001
+
+# Plot the spin trajectories
+fig_mtraj = plt.figure()
+ax1 = fig_mtraj.add_subplot(111)
+ax1.plot(mtraj1[t0:t1,0],mtraj1[t0:t1,2], c='r', linestyle='--',linewidth=2.0)
+ax1.plot(mtraj1[t0:t1,0],mtraj1[t0:t1,3], c='g', linestyle='--',linewidth=2.0)
+ax1.plot(mtraj1[t0:t1,0],mtraj1[t0:t1,4], c='b', linestyle='--',linewidth=2.0)
+ax1.axis('tight')
+#plt.xlim([-12,12])
+#plt.ylim([0,80])
+plt.xticks(fontsize=16)
+plt.yticks(fontsize=16)
+plt.legend(['mx', 'my', 'mz'], fontsize=16)
+plt.show()
+fig_mtraj.savefig('figmtraj1.png', format='png', dpi=100)
+
+# Plot the displacement trajectories
+fig_utraj = plt.figure()
+ax1 = fig_utraj.add_subplot(111)
+ax1.plot(utraj1[t0:t1,0],utraj1[t0:t1,2], c='r', linestyle='--',linewidth=2.0)
+ax1.plot(utraj1[t0:t1,0],utraj1[t0:t1,3], c='g', linestyle='--',linewidth=2.0)
+ax1.plot(utraj1[t0:t1,0],utraj1[t0:t1,4], c='b', linestyle='--',linewidth=2.0)
+ax1.axis('tight')
+plt.xticks(fontsize=16)
+plt.yticks(fontsize=16)
+plt.legend(['ux', 'uy', 'uz'], fontsize=16)
+plt.show()
+fig_mtraj.savefig('figmtraj1.png', format='png', dpi=100)
+
+# Plot the energies of the SLD Hamiltonian
+fig_etraj = plt.figure()
+ax1 = fig_etraj.add_subplot(111)
+# Iter.     ld_potenrg      sd_potenrg      sld_potenrg     totpot_enrg     kin_enrg        tot_enrg       ionic temp   
+ax1.plot(lattenergy[t0:t1,0],lattenergy[t0:t1,1], c='r', linestyle='--',linewidth=2.0)
+ax1.plot(lattenergy[t0:t1,0],lattenergy[t0:t1,2], c='g', linestyle='--',linewidth=2.0)
+ax1.plot(lattenergy[t0:t1,0],lattenergy[t0:t1,3], c='b', linestyle='--',linewidth=2.0)
+ax1.plot(lattenergy[t0:t1,0],lattenergy[t0:t1,5], c='m', linestyle='--',linewidth=2.0)
+ax1.plot(lattenergy[t0:t1,0],lattenergy[t0:t1,6], c='k', linestyle='--',linewidth=2.0)
+ax1.axis('tight')
+plt.xticks(fontsize=16)
+plt.yticks(fontsize=16)
+plt.legend(['LL', 'SS', 'SSL', 'KIN', 'TOT'], fontsize=16)
+plt.show()
+fig_etraj.savefig('figetraj.png', format='png', dpi=100)

content/sld/sld.rst

@@ -1,49 +1,84 @@
 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``.
+
+In these exercises you will explore how a spin-lattice coupled systems can be set up for
+simulation with UppASD. The first two systems are a magnetic dimer and a magnetic trimer.
+For these systems input files are provided in two variants, either with the full set of
+interactions specified, or with only the irreducible set of interactions are specified.
+In the latter case the point group operations that are activated with the ``sym`` flag
+are used to work out the full set of couplings.
+
+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
 
-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
+* 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]_. Use the sccript ``plotTrajDimerSLD.py``.
+* Plot the time trajectories of spins (``trajectory.scnobase.001.1.out``, ``trajectory.scnobase.002.1.out``), and displacements (``disptraj.scnobase.1.1.out``, ``disptraj.scnobase.2.1.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.
+
+Exercise 2: SLD simulation for trimer
+-------------------------------------
+
+* Run a simulation for the example ``TrimerSLD/TrimerauSLD3site``.
+* Modify the plot script ``plotTrajDimerSLD.py`` that was used for the dimer, so that it can be used for the trimer.
+* Run a simulation for the example ``TrimerSLD/TrimerauSLD3siteSym``. Compare the input files contained in ``TrimerSLD/TrimerauSLD3siteSym`` with ``TrimerSLD/TrimerauSLD3site``. How do they differ?
+
+Exercise 3: Phonon and magnon spectra for bcc Fe
+------------------------------------------------
 
-bcc Fe
-------
 bccFeSLD       # bcc Fe with MM, LL and MML coupling. Uses cutoff in LL interaction
 
 	       # Variants available in the runbccFe*.sh scripts