Updating for version 0.7.0. Adding HMC docs

_pages/docs/using_hmc.md

@@ -0,0 +1,119 @@
+---
+layout: single
+title : "Documentation"
+author_profile: false
+excerpt: "Using HMC"
+header:
+  overlay_color: "#5DADE2"
+permalink: /docs/theories/hmc/
+sidebar:
+  nav : docs
+---
+
+
+### Using HMC
+
+Using HMC in Grid version 0.7.0
+
+These are the instructions to use the Generalised HMC on Grid version 0.7.0.
+Disclaimer: GRID is still under active development so any information provided here can be changed in future releases.
+
+
+Command line options
+===================
+(relevant file GenericHMCrunner.h)
+List of command line options, specific for HMC
+
+* ```--StartingType  <string>```  
+
+Choices: HotStart, ColdStart, TepidStart, CheckpointStart
+
+* ```--StartingTrajectory <integer>```
+
+Only for CheckpointStart, ignored otherwise. 
+Expected format of the filename is ```<config prefix>.<integer>``` for the configuration and ```<rng file prefix>.<integer>```
+
+* ```--Trajectories <integer>```
+
+Number of trajectories in this run, excluding the thermalization steps. Default: 1.
+
+* ```--Thermalizations <integers>```
+
+Default: 10
+
+* ```--ParameterFile <string>```
+
+The filename for the input parameters deserialisation.
+
+All of them, except the starting trajectory, can be overridden by the input file (but this behaviour can be easily changed by the user writing the source file).
+
+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.
+
+
+
+