Fix viability

.gitignore

@@ -17,4 +17,7 @@ settings.json
 example/example_files/database*
 **/POSCAR*
 iteration/
-*.traj
+*.traj
+*.png
+*.param
+fort.*

CMakeLists.txt

@@ -72,6 +72,7 @@ set(FORTRAN_SRC_DIR ${SRC_DIR}/fortran)
 set(LIB_DIR ${FORTRAN_SRC_DIR}/lib)
 
 set(LIB_FILES
+    mod_error_handling.f90
     mod_constants.f90
     mod_misc.f90
 	mod_misc_maths.f90

README.md

@@ -50,29 +50,67 @@ Then, the path to the install directory (`${HOME}/.local/raffle`) needs to be ad
 
 ### Fortran
 
-For Fortran, CMake is required (fpm in the future, hopefully). The Python library installation can be turned off.
+For Fortran, either fpm or cmake are required.
+
+#### fpm
+
+fpm installation is as follows:
+
 ```
-mkdir build
-cd build
-cmake -DBUILD_PYTHON=Off ..
-make install
+fpm build --profile release
 ```
 
-This is a quick how-to guide for using RAFFLE.
+This will install both the Fortran library and the Fortran application for RAFFLE.
+The library can then be called from other fpm-built Fortran programs through normal means (usually referencing the location of RAFFLE in the program's own `fpm.toml` file).
+The application can be run using **(NOTE: The application is not a priority for development, so is less likely to work)**:
+```
+fpm run
+```
 
-First, compile using
-``` 
-make
+The library can be tested to ensure compilation was successful **(NOTE: Unit tests currently only provide minimal code coverage)**:
+```
+fpm test --profile release
 ```
 
-## Using
+#### cmake
 
-First, you need to ensure that the following file exists in the directory in which you run RAFFLE:
+cmake installation is as follows:
+```
+mkdir build
+cd build
+cmake [-DBUILD_PYTHON=Off] ..
+make install
 ```
-chem.in
+The optional filed (dentoted with `[...]`) can be used to turn off installation of the Python library.
+This will build the library in the build/ directory. All library files will then be found in:
 ```
+${HOME}/.local/raffle
+```
+Inside this directory, the following files will be generated:
+```
+include/raffle.mod
+lib/libraffle.a
+```
+
+To check whether RAFFLE has installed correctly and that the compilation works as expected, the following command can be run:
+```
+ctest
+```
+This runs the unit tests (found in the `test` directory) to ensure procedures output as expected.
+
+
+## Examples
+
+After the library has been installed, a set of example programs can be found in the `example` directory (note, the `test` directory is for unit tests to ensure each procedure in the library produces expected outputs after compilation, they are not really needed to be looked at by potential users).
+
+The `example/executable` example uses a shell script to run the Fortran installed application.
+It uses a user-editable input file `param.in` in the same directory to change values of the RAFFLE generator and provided database.
+
+The `example/wrapper` directory contains a set of `run_*.py` files that show how RAFFLE can be called using Python to implement it into existing random structure search workflows.
+These examples are the recommended ones to run.
+To successfully run them, follow the above installation instructions for Python, then go to the `example/wrapper` directory and run one of the scripts.
+
 
-Each of these files should follow the format found in the current repository. They should each have a header line that starts with "#" and contains the word "element". The example headers should then be followed for filling in data. For the elements.dat, the energy provided can be whatever you want to use as a reference energy. This energy is used for calculating formation energy. The example uses energy/atom of the bulk phase of the element.
 <!-- 
 Next, after the code is compiled, the way to run it is as follows:
 ```

app/inputs.f90

@@ -9,7 +9,7 @@ module inputs
   private
 
   public :: vdW, volvar
-  public :: bins, method_probab
+  public :: grid, grid_spacing, method_probab
   public :: seed
   public :: num_structures, task
   public :: stoich
@@ -40,7 +40,8 @@ module inputs
   character(3), dimension(:), allocatable :: element_symbols
   character(3), dimension(:,:), allocatable :: bond_pairs
 
-  integer, dimension(3) :: bins
+  integer, dimension(3) :: grid = [0, 0, 0]
+  real(real12) :: grid_spacing = 0._real12
   real(real12), dimension(3) :: method_probab = [1._real12, 1._real12, 1._real12]
 
   character(1024), dimension(:), allocatable :: database_list ! list of directories containing input database
@@ -197,7 +198,8 @@ subroutine read_input_file(file_name)
     !---------------------------------------------------------------------------
     ! set up namelists for input file
     !---------------------------------------------------------------------------
-    namelist /setup/        task, filename_host, seed, method_probab, bins, &
+    namelist /setup/        task, filename_host, seed, method_probab, grid, &
+                            grid_spacing, &
                             database_format, database, verbose, output_dir
     namelist /structure/    num_structures,stoichiometry
     namelist /volume/       vdW, volvar

app/main.f90

@@ -1,5 +1,6 @@
 program raffle_program
   use constants, only: real12
+  use error_handling, only: stop_program
   use misc_raffle, only: touch
   use inputs
   use read_structures, only: get_evolved_gvectors_from_data
@@ -48,8 +49,7 @@ program raffle_program
   case(2)
      write(*,*) "Running HOST_RSS"
   case default
-     write(*,*) "Invalid option"
-     stop 1
+     call stop_program("Invalid option")
   end select
 
 
@@ -103,7 +103,13 @@ program raffle_program
   open(newunit=unit, file=filename_host, status='old')
   call geom_read(unit, generator%host)
   close(unit)
-  generator%bins = bins
+  if(grid_spacing.gt.1.E-6.and.all(grid.ne.0))then
+     call stop_program('Cannot specify grid spacing and grid at the same time')
+  elseif(grid_spacing.gt.1.E-6)then
+     call generator%set_grid(grid_spacing = grid_spacing)
+  elseif(all(grid.ne.0))then
+     call generator%set_grid(grid = grid)
+  end if
 
 
   !-----------------------------------------------------------------------------

cmake/CodeCoverage.cmake

@@ -140,7 +140,7 @@ include(CMakeParseArguments)
 option(CODE_COVERAGE_VERBOSE "Verbose information" FALSE)
 
 # Check prereqs
-find_program( GCOV_PATH gcov )
+find_program( GCOV_PATH gcov-14 gcov )
 find_program( LCOV_PATH  NAMES lcov lcov.bat lcov.exe lcov.perl)
 find_program( FASTCOV_PATH NAMES fastcov fastcov.py )
 find_program( GENHTML_PATH NAMES genhtml genhtml.perl genhtml.bat )

example/example_files/POSCAR_graphite_missing_layer

@@ -0,0 +1,15 @@
+C
+    1.000000000
+    1.233645631   -2.136736911    0.000000000
+    1.233645631    2.136736911    0.000000000
+    0.000000000    0.000000000   15.606146000
+C    
+6
+Direct
+    0.000000000    0.000000000    0.125000000
+    0.000000000    0.000000000    0.375000000
+    0.000000000    0.000000000    0.875000000
+    0.333333333    0.666666667    0.125000000
+    0.666666667    0.333333333    0.375000000
+    0.666666667    0.333333333    0.875000000
+

example/example_files/POSCAR_host_BaTiO3

@@ -0,0 +1,13 @@
+BaTiO3
+1.0
+4.01 0.00 0.00
+0.00 4.01 0.00
+0.00 0.00 8.02
+Ba Ti O
+1 1 3
+Direct
+0.0 0.0 0.0
+0.5 0.5 0.25
+0.5 0.5 0.0
+0.5 0.0 0.25
+0.0 0.5 0.25

example/example_files/POSCAR_host_diamond

@@ -0,0 +1,16 @@
+C8
+    1.000000000
+    3.560745109    0.000000000    0.000000000
+    0.000000000    3.560745109    0.000000000
+    0.000000000    0.000000000    7.121490218
+C
+8
+Direct
+    0.000000000    0.000000000    0.000000000
+    0.500000000    0.500000000    0.000000000
+    0.500000000    0.000000000    0.250000000
+    0.000000000    0.500000000    0.250000000
+    0.250000000    0.250000000    0.125000000
+    0.750000000    0.750000000    0.125000000
+    0.750000000    0.250000000    0.375000000
+    0.250000000    0.750000000    0.375000000

example/example_files/POSCAR_host_graphene

@@ -0,0 +1,26 @@
+C4
+    1.000000000
+    3.700936892   -6.410210733    0.000000000
+    3.700936892    6.410210733    0.000000000
+    0.000000000    0.000000000    7.803073000
+C    
+18
+Direct
+    0.000000000    0.000000000    0.250000000
+    0.333333333    0.000000000    0.250000000
+    0.666666667    0.000000000    0.250000000
+    0.000000000    0.333333333    0.250000000
+    0.333333333    0.333333333    0.250000000
+    0.666666667    0.333333333    0.250000000
+    0.000000000    0.666666667    0.250000000
+    0.333333333    0.666666667    0.250000000
+    0.666666667    0.666666667    0.250000000
+    0.111111111    0.222222222    0.250000000
+    0.444444444    0.222222222    0.250000000
+    0.777777778    0.222222222    0.250000000
+    0.111111111    0.555555556    0.250000000
+    0.444444444    0.555555556    0.250000000
+    0.777777778    0.555555556    0.250000000
+    0.111111111    0.888888889    0.250000000
+    0.444444444    0.888888889    0.250000000
+    0.777777778    0.888888889    0.250000000

example/example_files/POSCAR_host_graphite_vacancy

@@ -0,0 +1,44 @@
+C4
+    1.000000000
+    3.700936892   -6.410210733    0.000000000
+    3.700936892    6.410210733    0.000000000
+    0.000000000    0.000000000    7.803073000
+C    
+35
+Direct
+    0.000000000    0.000000000    0.250000000
+    0.333333333    0.000000000    0.250000000
+    0.666666667    0.000000000    0.250000000
+    0.000000000    0.333333333    0.250000000
+    0.333333333    0.333333333    0.250000000
+    0.666666667    0.333333333    0.250000000
+    0.000000000    0.666666667    0.250000000
+    0.333333333    0.666666667    0.250000000
+    0.666666667    0.666666667    0.250000000
+    0.000000000    0.000000000    0.750000000
+    0.333333333    0.000000000    0.750000000
+    0.666666667    0.000000000    0.750000000
+    0.000000000    0.333333333    0.750000000
+    0.333333333    0.333333333    0.750000000
+    0.666666667    0.333333333    0.750000000
+    0.000000000    0.666666667    0.750000000
+    0.333333333    0.666666667    0.750000000
+    0.666666667    0.666666667    0.750000000
+    0.111111111    0.222222222    0.250000000
+    0.444444444    0.222222222    0.250000000
+    0.777777778    0.222222222    0.250000000
+    0.111111111    0.555555556    0.250000000
+    0.444444444    0.555555556    0.250000000
+    0.777777778    0.555555556    0.250000000
+    0.111111111    0.888888889    0.250000000
+    0.444444444    0.888888889    0.250000000
+    0.777777778    0.888888889    0.250000000
+    0.222222222    0.111111111    0.750000000
+    0.555555556    0.111111111    0.750000000
+    0.888888889    0.111111111    0.750000000
+    0.222222222    0.444444444    0.750000000
+    0.555555556    0.444444444    0.750000000
+    0.888888889    0.444444444    0.750000000
+    0.222222222    0.777777778    0.750000000
+    0.555555556    0.777777778    0.750000000
+