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Merge pull request #371 from edbennett/hmc-documentation-update

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update documentation for GenericHMCRunner - thanks
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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. 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. Disclaimer: Grid is still under active development so any information here can be changed in future releases.
Command line options ## Command line options
===================
(relevant file GenericHMCrunner.h) (relevant file `GenericHMCrunner.h`)
The initial configuration can be changed at the command line using The initial configuration can be changed at the command line using
--StartType <your choice> `--StartingType STARTING_TYPE`, where `STARTING_TYPE` is one of
valid choices, one among these `HotStart`, `ColdStart`, `TepidStart`, and `CheckpointStart`.
HotStart, ColdStart, TepidStart, CheckpointStart Default: `--StartingType HotStart`
default: HotStart
example Example:
./My_hmc_exec --StartType HotStart ```
./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 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> `--StartingTrajectory STARTING_TRAJECTORY`, where `STARTING_TRAJECTORY` is an integer.
default: 0 Default: `--StartingTrajectory 0`
The number of trajectories for a specific run are specified at command line by The number of trajectories for a specific run are specified at command line by
--Trajectories <integer> `--Trajectories TRAJECTORIES`, where `TRAJECTORIES` is an integer.
default: 1 Default: `--Trajectories 1`
The number of thermalization steps (i.e. steps when the Metropolis acceptance check is turned off) is specified by The number of thermalization steps (i.e. steps when the Metropolis acceptance check is turned off) is specified by
--Thermalizations <integer> `--Thermalizations THERMALIZATIONS`, where `THERMALIZATIONS` is an integer.
default: 10 Default: `--Thermalizations 10`
Any other parameter is defined in the source for the executable. Any other parameter is defined in the source for the executable.
HMC controls ## HMC controls
===========
The lines The lines
```
std::vector<int> SerSeed({1, 2, 3, 4, 5}); std::vector<int> SerSeed({1, 2, 3, 4, 5});
std::vector<int> ParSeed({6, 7, 8, 9, 10}); std::vector<int> ParSeed({6, 7, 8, 9, 10});
```
define the seeds for the serial and the parallel RNG. define the seeds for the serial and the parallel RNG.
The line The line
```
TheHMC.MDparameters.set(20, 1.0);// MDsteps, traj length TheHMC.MDparameters.set(20, 1.0);// MDsteps, traj length
```
declares the number of molecular dynamics steps and the total trajectory length. declares the number of molecular dynamics steps and the total trajectory length.
Actions ## Actions
======
Action names are defined in the file Action names are defined in the directory `Grid/qcd/action`.
lib/qcd/Actions.h
Gauge actions list: Gauge actions list (from `Grid/qcd/action/gauge/Gauge.h`):
```
WilsonGaugeActionR; WilsonGaugeActionR;
WilsonGaugeActionF; WilsonGaugeActionF;
WilsonGaugeActionD; WilsonGaugeActionD;
@ -68,8 +70,9 @@ IwasakiGaugeActionD;
SymanzikGaugeActionR; SymanzikGaugeActionR;
SymanzikGaugeActionF; SymanzikGaugeActionF;
SymanzikGaugeActionD; SymanzikGaugeActionD;
```
```
ConjugateWilsonGaugeActionR; ConjugateWilsonGaugeActionR;
ConjugateWilsonGaugeActionF; ConjugateWilsonGaugeActionF;
ConjugateWilsonGaugeActionD; ConjugateWilsonGaugeActionD;
@ -82,26 +85,23 @@ ConjugateIwasakiGaugeActionD;
ConjugateSymanzikGaugeActionR; ConjugateSymanzikGaugeActionR;
ConjugateSymanzikGaugeActionF; ConjugateSymanzikGaugeActionF;
ConjugateSymanzikGaugeActionD; 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; ScalarActionR;
ScalarActionF; ScalarActionF;
ScalarActionD; ScalarActionD;
```
The suffixes `R`, `F`, `D` in the action names refer to the `Real`
each of these action accept one single parameter at creation time (beta). (the precision is defined at compile time by the `--enable-precision` flag in the configure),
Example for creating a Symanzik action with beta=4.0 `Float` and `Double`, that force the precision of the action to be 32, 64 bit respectively.
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.