Added examples for finite temperature exercises.

Author: aibergman

content/finitetemp/SimpleCubic/inpsd.dat

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+simid simpcube
+ncell     10        10       10                 System size            
+BC        P         P         P                 Boundary conditions (0=vacuum, P=periodic)
+cell      1.00000   0.00000   0.00000         
+          0.00000   1.00000   0.00000
+          0.00000   0.00000   1.00000
+Sym       1                                     Symmetry of lattice (0 for no, 1 for cubic, 2 for 2d cubic, 3 for hexagonal)
+do_prnstruct 1
+
+posfile      ./posfile
+momfile      ./momfile
+exchange     ./jfile
+
+Initmag     3                                   Initial config of moments (1=random, 2=cone, 3=spec., 4=file)
+
+ip_mode     N
+ip_mcanneal 1
+            5000  300.0 1.00e-16 0.95
+
+mode        S
+Temp        300.00          K                    Temperature of the system
+hfield      0.00000   0.00000   0.00000          Static H field
+
+damping     0.01                                 Damping parameter (gamma)
+nstep       10000                                Number of time-steps
+timestep    1.000e-16       s                    The time step-size for the SDE-solver
+
+plotenergy  1                                    Sample energies
+do_avrg     Y                                    Measure averages
+do_cumu     Y                                    Sample cumulative averages
+do_spintemp Y                                    Measure spin temperature

content/finitetemp/SimpleCubic/jfile

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+1 1  1.0       0.0       0.0       0.80000000000000
+1 1  1.0       1.0       0.0       0.50000000000000

content/finitetemp/SimpleCubic/momfile

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+1 1 1.00 0.0 0.0 1.0 

content/finitetemp/SimpleCubic/posfile

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+1 1   0.000000  0.000000  0.000000

content/finitetemp/SingleSpin/inpsd.dat

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+simid     SingleSP 
+ncell     1         1         1                 System size
+BC        0         0         0                 Boundary conditions (0=vacuum,P=periodic)
+cell      0.00000   0.00000   0.00000
+          0.00000   0.00000   0.00000
+          0.00000   0.00000   0.00000
+Sym       0                                     Symmetry of lattice (0 for no, 1 for cubic, 2 for 2d cubic, 3 for hexagonal)
+do_prnstruct 2                                  Print lattice structure (0=no, 1=yes, 2=coordinates only)
+
+posfile    ./posfile
+exchange   ./jfile
+momfile    ./momfile
+anisotropy ./kfile
+
+Mensemble 1                                     Number of samples in ensemble averaging
+Initmag   3                                     (1=random, 2=cone, 3=spec., 4=file)
+
+ip_mode   N                                     Initial phase parameters
+
+mode      S                                     S=SD, M=MC
+temp      5.00                                 Measurement phase parameters
+damping   0.50000                               --
+Nstep     150000                                  --
+timestep  1.000e-15                             --
+
+do_avrg   Y                                     Measure averages
+avrg_step 100 
+
+do_tottraj Y                                    Measure moments
+tottraj_step       10000
+tottraj_buff       10                           time step, buffer size
+
+do_cumu Y
+
+real_time_measure Y

content/finitetemp/SingleSpin/jfile

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+ 1 1    0.0    0.0    1.0    0.0000

content/finitetemp/SingleSpin/kfile

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+ 1 1   -0.100   0.0    0.0   0.0   1.0   0.0

content/finitetemp/SingleSpin/momfile

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+1 1 1.00000   0.00000  0.0000  1.0000

content/finitetemp/SingleSpin/posfile

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+1   1   0.0 0.0 0.0                    

content/finitetemp/finitetemp.rst

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 Finite temperatures
 ===================
+
+
+Statistics
+----------
+In this exercise we will investigate how statistics affect simulated measurables.
+
+A single spin with an uniaxial anisotropy has a bi-stable, Ising like, magnetic state. At finite temperatures the stability of the magnetic state is not finite
+but follows an exponential (Arrhenius) relaxation behaviour. As seen in the lecture, ensemble averaging can be crucial for the analysis of such systems.
+
+ * Investigate the amount of statistics that is needed to say something relevant about the life time of the magnetic state of the system. 
+ 
+ * Does the need of statistics change with system parameters? (temperature, anisotropy, external field)
+
+ * Extra: Can you fit the relaxation behaviour to an `Arrhenius function <https://en.wikipedia.org/wiki/Arrhenius_equation>`_? 
+
+You can do a similar analysis for a finite 1d-chain by either modifying the single spin example, or 
+starting from the `SimpleSystems/HeisChain <https://github.com/UppASD/UppASD/tree/master/examples/SimpleSystems/HeisChain>`_ example.
+
+ * Is there a difference by performing ensemble averaging compared to just increasing the system size?
+
+ * Does the exchange interaction magnitude affect the stability of the spin chains?
+
+An accessible article for those interested in spin chains and statistics can be found here: `A. Vindigni Inorganica Chimica Acta, 361 3731 (2008) <https://www.sciencedirect.com/science/article/abs/pii/S0020169308001588>`_.
+
+
+
+Thermalization
+--------------
+In this exercise the thermalization rates in spin simulations will be investigated. 
+
+As mentioned in the lecture, thermalising the system before performing measurements is crucial for ensuring relevant results. 
+Here we will investigate this for a simple cubic model system.
+
+The initial ``inpsd.dat`` file looks as follows 
+
+.. literalinclude:: SimpleCubic/inpsd.dat
+
+and the almost trivial ``posfile`` and ``momfile`` are written as 
+
+.. literalinclude:: SimpleCubic/posfile
+.. literalinclude:: SimpleCubic/momfile
+
+The ``jfile``, that will be changed during the exercise initially can look like
+
+.. literalinclude:: SimpleCubic/jfile
+
+i.e. including nearest and next-nearest neighbours on the cubic lattice. Notice that since ``sym 1`` is given in ``inpsd.dat``, the ``jfile`` can be kept to a minimum of two lines.
+
+ * Starting with the inputs as defined above, vary the simulation method and damping (where applicable) to investigate the thermalization rate of the system.
+
+ * Is the thermalization faster when going from low to high temperatures or vice versa? Anything particular happening around Tc?
+
+ * Change the sign of the next-nearest neighbour and redo the study. Is the magnetization a good measurable for determining the thermalization now?
+
+Phase diagrams
+--------------
+
+
+Minimization
+------------