Improvements from review

.gitignore

@@ -29,4 +29,5 @@ fort.*
 *.log
 *.agr
 *.pdf
-*.eps
+*.eps
+*.pyc

CMakeLists.txt

@@ -72,21 +72,25 @@ set(FORTRAN_SRC_DIR ${SRC_DIR}/fortran)
 set(LIB_DIR ${FORTRAN_SRC_DIR}/lib)
 
 set(LIB_FILES
-    mod_error_handling.f90
+    mod_io_utils.F90
     mod_constants.f90
     mod_misc.f90
 	mod_misc_maths.f90
 	mod_misc_linalg.f90
-	mod_edit_geom.f90
-    mod_extended_geom.f90
-	mod_elements.f90
+	mod_dist_calcs.f90
+    mod_geom_utils.f90
+    mod_geom_extd.f90
+	mod_element_utils.f90
 	mod_evaluator.f90
-	mod_atom_adder.f90
+	mod_place_methods.f90
+    mod_viability.f90
+    mod_distribs.f90
+    mod_distribs_host.f90
 )
 
 set(SPECIAL_LIB_FILES
-  mod_rw_geom.f90
-  mod_evolver.f90
+  mod_geom_rw.f90
+  mod_distribs_container.f90
   mod_generator.f90
   # mod_generator_sub.f90
 )

app/inputs.f90

@@ -1,8 +1,9 @@
 module inputs
   !! Module for reading input files and setting global variables.
-  use misc_raffle, only: file_check,flagmaker, icount, to_lower
-  use generator, only: stoichiometry_type
-  use constants, only: real12, verbose, pi
+  use raffle__misc, only: file_check,flagmaker, icount, to_lower
+  use raffle__generator, only: stoichiometry_type
+  use raffle__constants, only: real32, pi
+  use raffle__io_utils
   implicit none
 
 
@@ -21,29 +22,31 @@ module inputs
   public :: bond_pairs, pair_radii
 
   public :: set_global_vars
+  public :: verbose
 
 
   logical :: lseed
 
+  integer :: verbose
   integer :: seed !random seed
   integer :: num_structures ! number of structures to generate
   integer :: task ! task setting (defines the RAFFLE task)
   type(stoichiometry_type), dimension(:), allocatable :: stoich ! stoichiometry of species to add
 
   integer :: vdW, volvar
 
-  real(real12), dimension(3) :: cutoff_min_list, cutoff_max_list
-  real(real12), dimension(3) :: width_list, sigma_list
+  real(real32), dimension(3) :: cutoff_min_list, cutoff_max_list
+  real(real32), dimension(3) :: width_list, sigma_list
 
-  real(real12), dimension(:), allocatable :: element_energies
-  real(real12), dimension(:), allocatable :: pair_radii
+  real(real32), dimension(:), allocatable :: element_energies
+  real(real32), dimension(:), allocatable :: pair_radii
   character(3), dimension(:), allocatable :: element_symbols
   character(3), dimension(:,:), allocatable :: bond_pairs
 
   integer, dimension(3) :: grid = [0, 0, 0]
-  real(real12) :: grid_spacing = 0._real12
-  real(real12), dimension(5) :: method_probab = &
-       [1._real12, 0.1_real12, 0.5_real12, 0.5_real12, 1._real12]
+  real(real32) :: grid_spacing = 0._real32
+  real(real32), dimension(5) :: method_probab = &
+       [1._real32, 0.1_real32, 0.5_real32, 0.5_real32, 1._real32]
 
   character(1024), dimension(:), allocatable :: database_list ! list of directories containing input database
   character(1024) :: database_format !format of input file (POSCAR, XYZ, etc.
@@ -81,7 +84,7 @@ subroutine set_global_vars()
     !---------------------------------------------------------------------------
     ! Reads flags and assigns to variables
     !---------------------------------------------------------------------------
-    flagloop: do i=0,command_argument_count()-1
+    flagloop: do i=0,command_argument_count()
        empty=.false.
        if (skip) then
           skip=.false.
@@ -119,6 +122,10 @@ subroutine set_global_vars()
        !------------------------------------------------------------------------
        elseif(index(buffer,'-v').eq.1)then
           flag="-v"
+          call print_build_info()
+          stop 0
+       elseif(index(buffer,'--verbose').eq.1)then
+          flag="--verbose"
           call flagmaker(buffer,flag,i,skip,empty)
           if(.not.empty) read(buffer,*) verbose
        elseif(index(buffer,'-h').eq.1)then
@@ -182,9 +189,9 @@ subroutine read_input_file(file_name)
     character(1024) :: stoichiometry, database, buffer, energies, &
          bond_radii
     !! Strings buffers to hold input values (usually derived types).
-    real(real12), dimension(3) :: width, sigma
+    real(real32), dimension(3) :: width, sigma
     !! Width and sigma values for distribution functions.
-    real(real12) :: void, rand, walk, grow, min
+    real(real32) :: void, rand, walk, grow, min
     !! Placement method probabilities.
     character(50), dimension(3) :: cutoff_min, cutoff_max
     !! Cutoff values for distribution functions.
@@ -213,12 +220,12 @@ subroutine read_input_file(file_name)
     output_dir = "iteration1"
     cutoff_min = "-1.0"
     cutoff_max = "-1.0"
-    width = -1._real12
-    sigma = -1._real12
+    width = -1._real32
+    sigma = -1._real32
     database_format = "vasprun.xml"
-    void = 0._real12; rand = 0._real12
-    walk = 0._real12; grow = 0._real12
-    min = 0._real12
+    void = 0._real32; rand = 0._real32
+    walk = 0._real32; grow = 0._real32
+    min = 0._real32
     !---------------------------------------------------------------------------
     ! read namelists from input file
     !---------------------------------------------------------------------------
@@ -263,7 +270,7 @@ subroutine read_input_file(file_name)
     method_probab = [void, rand, walk, grow, min]
     if(all(abs(method_probab).lt.1.E-6))then
        method_probab = &
-            [1._real12, 0.1_real12, 0.5_real12, 0.5_real12, 1._real12]
+            [1._real32, 0.1_real32, 0.5_real32, 0.5_real32, 1._real32]
       end if
 
     if(trim(stoichiometry).ne."")then
@@ -349,23 +356,23 @@ function read_value_from_string(string) result(output)
     ! Arguments
     character(*), intent(in) :: string
     !! Input string.
-    real(real12) :: output
+    real(real32) :: output
     !! Output value.
 
     ! Local variables
     integer :: k, pos
     !! Loop index, position.
-    real(real12) :: variable, power
+    real(real32) :: variable, power
     !! Variable and power values.
     character(:), allocatable :: string_
     !! Copy of input string.
     character(12) :: numeric_set = "0123456789.-"
     !! Numeric set.
 
     pos = 1
-    output = 1._real12
-    variable = 0._real12
-    power = 1._real12
+    output = 1._real32
+    variable = 0._real32
+    power = 1._real32
     string_ = trim(to_lower(string))
     loop: do
        !! read until first non-numeric character
@@ -382,20 +389,20 @@ function read_value_from_string(string) result(output)
 
        pos = pos + k - 1
        !! identify what the next character is (*, /, pi)
-       !! if *, then change power factor to 1._real12
-       !! if /, then change power factor to -1._real12
-       !! if pi, then change power factor to 1._real12 and variable = pi
+       !! if *, then change power factor to 1._real32
+       !! if /, then change power factor to -1._real32
+       !! if pi, then change power factor to 1._real32 and variable = pi
        !! if blank space, move pos to next non-space character and cycle
        !! if end of string, exit loop
 
        if (string_(pos:pos).eq."*")then
-          power = 1._real12
+          power = 1._real32
           pos = pos + 1
        elseif(string_(pos:pos).eq."/")then
-          power = -1._real12
+          power = -1._real32
           pos = pos + 1
        elseif(string_(pos:pos+1).eq."pi")then
-          power = 1._real12
+          power = 1._real32
           output = output * pi ** power
           pos = pos + 2
        end if

app/main.f90

@@ -1,12 +1,12 @@
 program raffle_program
   !! Main program for the interface-based random structure search
-  use constants, only: real12
-  use error_handling, only: stop_program
-  use misc_raffle, only: touch
+  use raffle__constants, only: real32
+  use raffle__io_utils, only: stop_program
+  use raffle__misc, only: touch
   use inputs
   use read_structures, only: get_evolved_gvectors_from_data
-  use raffle, only: raffle_generator_type, gvector_container_type
-  use rw_geom, only: geom_read, geom_write
+  use raffle, only: raffle_generator_type, distribs_container_type
+  use raffle__geom_rw, only: geom_read, geom_write
   implicit none
 
   ! Local variables
@@ -17,7 +17,7 @@ program raffle_program
   character(:), allocatable :: next_dir
   !! Next directory name
 
-  real(real12), dimension(:), allocatable :: tmp_energies
+  real(real32), dimension(:), allocatable :: tmp_energies
   !! Temporary array for element energies
   character(len=3), dimension(:), allocatable :: tmp_symbols
   !! Temporary array for element symbols
@@ -78,7 +78,7 @@ program raffle_program
   generator%distributions = get_evolved_gvectors_from_data( &
        input_dir    = database_list, &
        file_format  = database_format, &
-       gvector_container_template = gvector_container_type(&
+       distribs_container_template = distribs_container_type(&
             width = width_list, &
             sigma = sigma_list, &
             cutoff_min = cutoff_min_list, &

app/mod_read_structures.f90

@@ -4,12 +4,12 @@ module read_structures
   !! This module takes a list of directories and reads in the structures from
   !! the contained files. The structures are then converted to a set of
   !! generalised vectors (gvectors, aka distribution functions).
-  use constants, only: real12
-  use misc_raffle, only: grep
-  use misc_linalg, only: modu
-  use rw_geom, only: basis_type, geom_read, geom_write, igeom_input
+  use raffle__constants, only: real32
+  use raffle__misc, only: grep
+  use raffle__misc_linalg, only: modu
+  use raffle__geom_rw, only: basis_type, geom_read, geom_write, igeom_input
   use rw_vasprun, only: get_energy_from_vasprun, get_structure_from_vasprun
-  use evolver, only: gvector_container_type
+  use raffle__distribs_container, only: distribs_container_type
 #ifdef ENABLE_ATHENA
   use machine_learning, only: network_setup, &
        network_train, network_train_graph, &
@@ -28,19 +28,19 @@ module read_structures
 
 !###############################################################################
   function get_evolved_gvectors_from_data(input_dir, &
-       file_format, gvector_container_template) &
-       result(gvector_container)
+       file_format, distribs_container_template) &
+       result(distribs_container)
     !! Read structures from the input directories and evolve them to gvectors.
     implicit none
 
     ! Arguments
     character(*), dimension(..), intent(in) :: input_dir
     !! List of directories containing the structures to be read.
-    type(gvector_container_type), intent(in), optional :: &
-         gvector_container_template
-    !! Optional. A template gvector_container to be used.
-    type(gvector_container_type), allocatable :: gvector_container
-    !! The gvector_container containing the evolved gvectors.
+    type(distribs_container_type), intent(in), optional :: &
+         distribs_container_template
+    !! Optional. A template distribs_container to be used.
+    type(distribs_container_type), allocatable :: distribs_container
+    !! The distribs_container containing the evolved gvectors.
     character(*), intent(in), optional :: file_format
     !! Optional. The format of the input files. Default is vasprun.xml.
 
@@ -51,7 +51,7 @@ function get_evolved_gvectors_from_data(input_dir, &
     !! The format of the input files.
     integer :: num_structures
     !! The number of structures read.
-    real(real12) :: energy
+    real(real32) :: energy
     !! The energy of the structure.
     character(50) :: buffer
     !! A buffer for reading strings.
@@ -71,19 +71,19 @@ function get_evolved_gvectors_from_data(input_dir, &
 #ifdef ENABLE_ATHENA
     type(graph_type), dimension(:), allocatable :: graphs
     !! Graph representations of the structures.
-    real(real12), dimension(:), allocatable :: &
+    real(real32), dimension(:), allocatable :: &
          labels, labels_train, labels_validate
     !! The labels for the structures.
-    real(real12), dimension(:,:), allocatable :: &
+    real(real32), dimension(:,:), allocatable :: &
          dataset, data_train, data_validate
     !! The dataset for the structures.
 #endif
 
 
-    if(present(gvector_container_template)) then
-       gvector_container = gvector_container_template
+    if(present(distribs_container_template)) then
+       distribs_container = distribs_container_template
     else
-       gvector_container = gvector_container_type()
+       distribs_container = distribs_container_type()
     end if
 
     if(present(file_format)) then
@@ -104,9 +104,9 @@ function get_evolved_gvectors_from_data(input_dir, &
        ifile_format = 0
     end if
 
-    ! inquire(file='gvector_container.dat', exist=success)
+    ! inquire(file='distribs_container.dat', exist=success)
     ! if(success) then
-    !    call gvector_container%read('gvector_container.dat')
+    !    call distribs_container%read('distribs_container.dat')
     !    goto 100
     ! end if
     ! ! For each new run of the code, it should populate a new directory and ...
@@ -179,15 +179,15 @@ function get_evolved_gvectors_from_data(input_dir, &
                   basis%energy, &
                   ( trim(basis%spec(j)%name), basis%spec(j)%num, &
                   j=1, basis%nspec )
-             call gvector_container%add(basis)
+             call distribs_container%add(basis)
           end do
           cycle
        end select
 
        write(*,*) &
             "Found structure: ", trim(adjustl(structure_list(i))), &
             " with energy: ", basis%energy
-       call gvector_container%add(basis)
+       call distribs_container%add(basis)
        num_structures = num_structures + 1
 
        ! ! STORE THE ENERGY IN AN ARRAY
@@ -198,7 +198,7 @@ function get_evolved_gvectors_from_data(input_dir, &
 
 
 
-100 call gvector_container%evolve()
+100 call distribs_container%evolve()
 
 
 #ifdef ENABLE_ATHENA