HISKP-LQCD · simone-romiti · Jan 19, 2023 · Jan 20, 2023 · Jan 22, 2023 · Jan 22, 2023
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -51,7 +51,6 @@ configure_file(
   set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS} -D_USE_OMP_")
 
   find_package(yaml-cpp)
-
   include_directories(${YAML_CPP_INCLUDE_DIR} ${YAML_CPP_INCLUDE_DIR}/yaml-cpp/)
 
   find_package(xtl)
@@ -60,6 +59,11 @@ configure_file(
   find_package(xtensor)
   include_directories(${xtensor_INCLUDE_DIRS} ${xtensor_INCLUDE_DIRS}/xtensor/)
 
+
+  if(${HIGHFIVE_FORMAT})
+    find_package(HighFive REQUIRED)
+  endif()
+
 # We could just have two `add_executable` blocks listing almost all source
 # files. However, CMake would then compile the source files twice, once for
 # each executable. The rationale is that different flags can be used for
@@ -90,9 +94,31 @@ add_executable(test-groups test.cc)
 add_executable(scaling scaling.cc)
 add_executable(try tryreduce.cc)
 
+set(test_progs "links" "smearing" "yaml")
+
+if(${HIGHFIVE_FORMAT})
+  set(test_progs ${test_progs} "h5-gen" "h5-dump")
+endif()
+
+set(test_progs_fullname "")
+foreach(target ${test_progs})
+  add_executable(test-${target}.exe test/${target}.cpp)
+  list(APPEND test_progs_fullname test-${target}.exe) # now FOO="a;b"
+endforeach(target)
+
+
+target_link_libraries(test-yaml.exe ${YAML_CPP_LIBRARIES})
+
+foreach(target ${test_progs_fullname})
+  if(${HIGHFIVE_FORMAT})
+    target_link_libraries(${target} HighFive)
+  endif()
+endforeach(target)
+
+
 target_link_directories(${CMAKE_PROJECT_NAME} PUBLIC ${YAML_CPP_LIBRARY_DIR})
 
-foreach(target u1-main su2-main su2-kramers test-groups scaling try)
+foreach(target u1-main su2-main su2-kramers test-groups scaling try ${test_progs_fullname})
   target_link_libraries(${target} su2 ${YAML_CPP_LIBRARIES})
 
   if(Boost_FOUND)
@@ -110,4 +136,9 @@ install(TARGETS ${PROJECT_NAME}
 install(TARGETS u1-main su2-main)
 install(TARGETS su2-kramers test-groups scaling try)
 
+# tests
+
+foreach(target ${test_progs})
+  install(TARGETS test-${target}.exe LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR})
+endforeach(target)
 
diff --git a/base_program.hpp b/base_program.hpp
@@ -12,7 +12,7 @@
 #pragma once
 
 #include "flat-energy_density.hh"
-#include "flat-gauge_energy.hpp"
+#include "gauge_energy.hh"
 #include "flat-sweep.hh" // flat spacetime
 #include "gaugeconfig.hh"
 #include "io.hh"
@@ -21,7 +21,7 @@
 #include "random_gauge_trafo.hh"
 // #include "rotating-energy_density.hpp" // rotating spacetime
 // #include "rotating-gauge_energy.hpp" // rotating spacetime
-//#include "rotating-sweep.hpp" // rotating spacetime
+// #include "rotating-sweep.hpp" // rotating spacetime
 #include "su2.hh"
 #include "u1.hh"
 #include "vectorfunctions.hh"
@@ -423,10 +423,9 @@ template <class Group, class sparam_type> class base_program {
       if ((*this).omeas.verbosity > 0) {
         std::cout << "## online measuring: J^{PC} glueball correlators.\n";
       }
-      if ((*this).omeas.glueball.correlator) {
-        omeasurements::meas_glueball_correlator<Group>(omeas.glueball.interpolator_type,
-                                                       U, i, (*this).omeas);
-      }
+
+      const std::string glb_interp = omeas.glueball.interpolator_type;
+      omeasurements::meas_glueball_correlator<Group>(glb_interp, U, i, (*this).omeas);
     }
     return;
   }

diff --git a/doc/users/2d-materials.csl → doc/2d-materials.csl b/doc/users/2d-materials.csl → doc/2d-materials.csl
diff --git a/doc/users/Makefile → doc/Makefile b/doc/users/Makefile → doc/Makefile
@@ -1,21 +1,18 @@
 # Makefile
 
 # file paths and variables
-STAGG = ./staggered_fermions.Rmd
-u1 = ./u1.Rmd
+main = ./main.Rmd
 
 define generate_html
 	Rscript -e 'library(rmarkdown); rmarkdown::render("$(1)", "html_document")'
+	Rscript -e 'library(rmarkdown); rmarkdown::render("$(1)", "pdf_document")'
 endef
 
-all: staggered u1
+all: main
 	make clean
 
-u1: $(u1)
-	$(call generate_html,$(u1))
-
-staggered: $(STAGG)
-	$(call generate_html,$(STAGG))
+main: $(main)
+	$(call generate_html,$(main))
 
 
 clean:

diff --git a/doc/README.md b/doc/README.md
@@ -0,0 +1,4 @@
+# Users guide
+
+This directory contains the users guide to this project.
+In order to produce the `html` and `pdf` output run `make all` from the present directory.
diff --git a/doc/users/biblio.bib → doc/biblio.bib b/doc/users/biblio.bib → doc/biblio.bib
diff --git a/doc/users/u1.Rmd → doc/howto.Rmd b/doc/users/u1.Rmd → doc/howto.Rmd
@@ -1,28 +1,7 @@
 ---
-title: u1
-author: Simone Romiti
 output: html_document
-bibliography: biblio.bib  
-csl: 2d-materials.csl
-link-citations: true
 ---
 
-## Introduction and main features
-
-This repository contains a program called `main-u1.cpp`, which is capable of both generating gauge configurations and doing measurements on them for a $U(1)$ theory in $d=2,3,4$ dimensions.
-At present the gauge configurations can be generated with the following Markov Chain Monte Carlo algorithms (see @gattringer2009quantum for the theoretical background):
-
-- Metropolis
-- Hybrid Monte Carlo
-
-The measurements can be generated either online (during the MCMC) or offline (on previously generated configurations). At present the supported observables are:
-
-- Plaquette standard and clover-improved energy
-- Glueball correlators
-- "pion" correlator
-- Wilson loops and static potential among $\bar{q} q$ pairs
-- Wilson gradient flow
-
 ## Program execution
 
 The `main-u1.cpp` program works using an input file `main.input` as follows:
@@ -101,7 +80,4 @@ WRITE DOCUMENTATION HERE
 - `Wloop`
 - `potential` block. 
 - `glueball` block. The user can specify the interpolators and the APE smearing parameters      
-- `gradient_flow` block
-
-## References
-
+- `gradient_flow` block
diff --git a/doc/main.Rmd b/doc/main.Rmd
@@ -0,0 +1,74 @@
+---
+title: Documentation `su2` project
+author: Simone Romiti
+output: 
+  html_document:
+    toc: true
+    theme: united
+bibliography: biblio.bib  
+csl: 2d-materials.csl
+link-citations: true
+---
+
+The present repository contains routines for numerical simulations of $SU(2)$ and $U(1)$ lattice gauge theories in $d=2,3,4$ dimensions.
+
+# Library routines
+
+The gauge configurations can be generated with the following Markov Chain Monte Carlo algorithms (see @gattringer2009quantum for the theoretical background):
+
+- Metropolis
+- Hybrid Monte Carlo
+
+The measurements can be generated either online (during the MCMC) or offline (on previously generated configurations). At present the supported observables are:
+
+- Plaquette standard and clover-improved energy
+- Glueball correlators
+- "pion" correlator
+- Wilson loops and static potential among $\bar{q} q$ pairs
+- Wilson gradient flow
+
+### Programs info
+
+- Programs: `main-u1.cpp` and `main-su2.cpp`
+- Parameters parsing: `yaml` input file
+- Input file example: see [./main.input](main.input)
+  Notes:
+  - Each run produces/updates a file named `nconf_counter.txt` in the directory storing the gauge configurations. This file contains a header line and the values below. An example:
+  ```
+  heat i path_conf
+  1 1140 ./confs/config_u1.4.4.1.16.b1.900000.1140
+  ```
+  - `restart` and `heat` cannot be passed simultaneously
+  - If `restart: true` is passed, the last configuration id and path are read from the `nconf_counter.txt` file.
+  - The program can do online and offline measurements
+
+##### `hadron` folder 
+
+In the `hadron/` folder are found scripts for data manipulation such that online measurements are more easily readable with the `R` library `hadron`: https://github.com/HISKP-LQCD/hadron:
+
+- `glueball.py`: converts the data for the interpolators and correlators of the glueball. 
+  1. This is done in a separate step and not directly in the `C++` code on purpose. One may want to generate configurations and do offline measurements afterwards in parallel (multiple jobs, one for each bunch of measurements).
+  2. The scripts takes care of deleting the files in the old format. For each choice of the parameters and interpolator type, only 4 files are saved in the corresponding folders:
+
+      - `iconf.dat` : list of trajectory indices that have been put in `hadron` format
+
+      - `pp.dat`, `pm.dat`, `mp.dat`, `mm.dat`: correlators
+
+  3. The storage space saved in this way is mostly negligible, but avoids potential filesystem slowdowns due to the access to large number of files. Besides, the analysis scripts won't have to cope with reading the configurations one by one.
+  4. The script uses the same input file used for the runs
+
+### tests
+
+In the `test/` folder the user can find various simple programs implementing the routines of this repository. For further details please look at the `test/README.md` file.
+
+# How to use the library
+
+```{r child = './howto.Rmd'}
+```
+
+# Theoretical background
+
+Fermions are included as a degenerate doublet using the staggered discretization.
+
+```{r child = './staggered_fermions.Rmd'}
+```
diff --git a/doc/users/main.input → doc/main.input b/doc/users/main.input → doc/main.input
diff --git a/doc/users/staggered_fermions.Rmd → doc/staggered_fermions.Rmd b/doc/users/staggered_fermions.Rmd → doc/staggered_fermions.Rmd
@@ -1,12 +1,14 @@
 ---
-title: Staggered fermions
-author: Simone Romiti
+#title: Staggered fermions
+#author: Simone Romiti
 output: html_document
-bibliography: biblio.bib  
-csl: 2d-materials.csl
-link-citations: true
+#bibliography: biblio.bib  
+#csl: 2d-materials.csl
+#link-citations: true
 ---
 
+## Staggered fermions
+
 For staggered fermions the Dirac operator is:
 
 $$

diff --git a/doc/bibliography.bib → doc/su2_partitioning/bibliography.bib b/doc/bibliography.bib → doc/su2_partitioning/bibliography.bib
diff --git a/doc/charge-notes.xoj → doc/su2_partitioning/charge-notes.xoj b/doc/charge-notes.xoj → doc/su2_partitioning/charge-notes.xoj
diff --git a/doc/doc.Rmd → doc/su2_partitioning/doc.Rmd b/doc/doc.Rmd → doc/su2_partitioning/doc.Rmd
diff --git a/doc/ref.txt → doc/su2_partitioning/ref.txt b/doc/ref.txt → doc/su2_partitioning/ref.txt
diff --git a/doc/reference-values.txt → doc/su2_partitioning/reference-values.txt b/doc/reference-values.txt → doc/su2_partitioning/reference-values.txt
diff --git a/doc/su2strong.R → doc/su2_partitioning/su2strong.R b/doc/su2strong.R → doc/su2_partitioning/su2strong.R
diff --git a/doc/u1strong.R → doc/su2_partitioning/u1strong.R b/doc/u1strong.R → doc/su2_partitioning/u1strong.R
diff --git a/doc/users/README.md b/doc/users/README.md
diff --git a/hadron/README.md b/hadron/README.md
@@ -0,0 +1,2 @@
+This folder contains scripts for formatting online (offline) measurements.
+Tha data is formatted such that is more easily readable by the routines of the "R" library "hadron": https://github.com/HISKP-LQCD/hadron