Adding some documentation for HMC

lib/qcd/hmc/UsingHMC.md

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+Using HMC in Grid version 0.5.1
+
+These are the instructions to use the Generalised HMC on Grid version 0.5.1.
+Disclaimer: GRID is still under active development so any information here can be changed in future releases.
+
+
+Command line options
+===================
+(relevant file GenericHMCrunner.h)
+The initial configuration can be changed at the command line using 
+--StartType <your choice>
+valid choices, one among these
+HotStart, ColdStart, TepidStart, CheckpointStart
+default: HotStart
+
+example
+./My_hmc_exec  --StartType HotStart
+
+The CheckpointStart option uses the prefix for the configurations and rng seed files defined in your executable and the initial configuration is specified by
+--StartTrajectory <integer>
+default: 0
+
+The number of trajectories for a specific run are specified at command line by
+--Trajectories <integer>
+default: 1
+
+The number of thermalization steps (i.e. steps when the Metropolis acceptance check is turned off) is specified by
+--Thermalizations <integer>
+default: 10
+
+
+Any other parameter is defined in the source for the executable.
+
+HMC controls
+===========
+
+The lines 
+
+  std::vector<int> SerSeed({1, 2, 3, 4, 5});
+  std::vector<int> ParSeed({6, 7, 8, 9, 10});
+
+define the seeds for the serial and the parallel RNG.
+
+The line 
+
+  TheHMC.MDparameters.set(20, 1.0);// MDsteps, traj length
+
+declares the number of molecular dynamics steps and the total trajectory length.
+
+
+Actions
+======
+
+Action names are defined in the file
+lib/qcd/Actions.h
+
+Gauge actions list:
+
+WilsonGaugeActionR;
+WilsonGaugeActionF;
+WilsonGaugeActionD;
+PlaqPlusRectangleActionR;
+PlaqPlusRectangleActionF;
+PlaqPlusRectangleActionD;
+IwasakiGaugeActionR;
+IwasakiGaugeActionF;
+IwasakiGaugeActionD;
+SymanzikGaugeActionR;
+SymanzikGaugeActionF;
+SymanzikGaugeActionD;
+
+
+ConjugateWilsonGaugeActionR;
+ConjugateWilsonGaugeActionF;
+ConjugateWilsonGaugeActionD;
+ConjugatePlaqPlusRectangleActionR;
+ConjugatePlaqPlusRectangleActionF;
+ConjugatePlaqPlusRectangleActionD;
+ConjugateIwasakiGaugeActionR;
+ConjugateIwasakiGaugeActionF;
+ConjugateIwasakiGaugeActionD;
+ConjugateSymanzikGaugeActionR;
+ConjugateSymanzikGaugeActionF;
+ConjugateSymanzikGaugeActionD;
+
+
+ScalarActionR;
+ScalarActionF;
+ScalarActionD;
+
+
+each of these action accept one single parameter at creation time (beta).
+Example for creating a Symanzik action with beta=4.0
+
+	SymanzikGaugeActionR(4.0)
+
+The suffixes R,F,D in the action names refer to the Real
+(the precision is defined at compile time by the --enable-precision flag in the configure),
+Float and Double, that force the precision of the action to be 32, 64 bit respectively.
+
+
+
+
+
+
+
+