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update documentation for GenericHMCRunner

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Grid/qcd/hmc/UsingHMC.md
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Using HMC in Grid version 0.5.1
# Using HMC in Grid
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.
These are the instructions to use the Generalised HMC on Grid as of commit `749b802`.
Disclaimer: Grid is still under active development so any information here can be changed in future releases.
Command line options
===================
(relevant file GenericHMCrunner.h)
## 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
`--StartingType STARTING_TYPE`, where `STARTING_TYPE` is one of
`HotStart`, `ColdStart`, `TepidStart`, and `CheckpointStart`.
Default: `--StartingType HotStart`
example
./My_hmc_exec --StartType HotStart
Example:
```
./My_hmc_exec --StartingType 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 `CheckpointStart` option uses the prefix for the configurations and rng seed files defined in your executable and the initial configuration is specified by
`--StartingTrajectory STARTING_TRAJECTORY`, where `STARTING_TRAJECTORY` is an integer.
Default: `--StartingTrajectory 0`
The number of trajectories for a specific run are specified at command line by
--Trajectories <integer>
default: 1
`--Trajectories TRAJECTORIES`, where `TRAJECTORIES` is an integer.
Default: `--Trajectories 1`
The number of thermalization steps (i.e. steps when the Metropolis acceptance check is turned off) is specified by
--Thermalizations <integer>
default: 10
`--Thermalizations THERMALIZATIONS`, where `THERMALIZATIONS` is an integer.
Default: `--Thermalizations 10`
Any other parameter is defined in the source for the executable.
HMC controls
===========
## 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
======
## Actions
Action names are defined in the file
lib/qcd/Actions.h
Action names are defined in the directory `Grid/qcd/action`.
Gauge actions list:
Gauge actions list (from `Grid/qcd/action/gauge/Gauge.h`):
```
WilsonGaugeActionR;
WilsonGaugeActionF;
WilsonGaugeActionD;
@ -68,8 +70,9 @@ IwasakiGaugeActionD;
SymanzikGaugeActionR;
SymanzikGaugeActionF;
SymanzikGaugeActionD;
```
```
ConjugateWilsonGaugeActionR;
ConjugateWilsonGaugeActionF;
ConjugateWilsonGaugeActionD;
@ -82,26 +85,23 @@ ConjugateIwasakiGaugeActionD;
ConjugateSymanzikGaugeActionR;
ConjugateSymanzikGaugeActionF;
ConjugateSymanzikGaugeActionD;
```
Each of these action accepts one single parameter at creation time (beta).
Example for creating a Symanzik action with beta=4.0
```
SymanzikGaugeActionR(4.0)
```
Scalar actions list (from `Grid/qcd/action/scalar/Scalar.h`):
```
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.
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.