Merge branch 'develop' of http://greatfire.uchicago.edu/west-devel/West into dfpt_band_parallel

IO_kernel/pdep_db.f90

@@ -160,7 +160,7 @@ MODULE pdep_db
           CALL json%add("dielectric_matrix.pdep",jval)
           !
           OPEN(NEWUNIT= iunit, FILE= summary_file )
-          CALL json%print_file( iunit )
+          CALL json%print( iunit )
           CLOSE( iunit )
           !
           CALL json%destroy()
@@ -173,7 +173,7 @@ MODULE pdep_db
       IF ( mpime == root ) THEN
          !
          CALL json%initialize()
-         CALL json%load_file( filename = summary_file )
+         CALL json%load( filename = summary_file )
          !
          CALL json%info('dielectric_matrix.pdep',n_children=n_elements)
          write_element = n_elements + 1
@@ -193,7 +193,7 @@ MODULE pdep_db
          CALL json%add('dielectric_matrix.pdep('//TRIM(ADJUSTL(label_i))//').eigenvec' , eigenpot_filename(1:n_pdep_eigen))
          !
          OPEN( NEWUNIT=iunit, FILE=summary_file )
-         CALL json%print_file( iunit )
+         CALL json%print( iunit )
          CLOSE( iunit )
          CALL json%destroy()
          !
@@ -321,7 +321,7 @@ MODULE pdep_db
       IF ( mpime == root ) THEN
          !
          CALL json%initialize()
-         CALL json%load_file( filename = TRIM(ADJUSTL(wstat_save_dir)) // "/summary.json" )
+         CALL json%load( filename = TRIM(ADJUSTL(wstat_save_dir)) // "/summary.json" )
          IF( json%failed() ) THEN 
             CALL errore("", "Cannot open: " // TRIM(ADJUSTL(wstat_save_dir)) // "/summary.json", 1 )
          ENDIF 

IO_kernel/wfreq_db.f90

@@ -72,7 +72,7 @@ MODULE wfreq_db
          !
          CALL json%initialize()
          !
-         CALL json%load_file(filename=TRIM(logfile))
+         CALL json%load(filename=TRIM(logfile))
          !
          l_generate_plot = .FALSE.
          l_optics = .FALSE.
@@ -157,7 +157,7 @@ MODULE wfreq_db
          ENDDO
          !
          OPEN( NEWUNIT=iunit, FILE=TRIM( logfile ) )
-         CALL json%print_file( iunit )
+         CALL json%print( iunit )
          CLOSE( iunit )
          CALL json%destroy()
          !

Libraries/Json/README

 ==========================================
-Based on the library: json-fortran v 6.3.0
+Based on the library: json-fortran v 8.2.1
 ==========================================
 JSON-Fortran: A Fortran 2008 JSON API
 <https://github.com/jacobwilliams/json-fortran>
 
-Copyright (c) 2014-2018, Jacob Williams
+Copyright (c) 2014-2020, Jacob Williams
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification,

Libraries/Json/json_get_scalar_by_path.inc

+    type(json_value),pointer :: p
+
+    if (present(default)) then
+        value = default
+    else
+        value = default_if_not_specified
+    end if
+
+    if ( json%exception_thrown ) then
+       call flag_not_found(found)
+       return
+    end if
+
+    nullify(p)
+    call json%get(me=me, path=path, p=p)
+
+    if (.not. associated(p)) then
+        call json%throw_exception('Error in '//routine//':'//&
+                                  ' Unable to resolve path: '// trim(path),found)
+    else
+        call json%get(p,value)
+    end if
+
+    if ( json%exception_thrown ) then
+        if ( present(found) .or. present(default)) then
+            call flag_not_found(found)
+            if (present(default)) value = default
+            call json%clear_exceptions()
+        end if
+    else
+        if ( present(found) ) found = .true.
+    end if

Libraries/Json/json_get_vec_by_path.inc

+    type(json_value),pointer :: p
+
+    if ( json%exception_thrown ) then
+        if (present(default)) vec = default
+        call flag_not_found(found)
+        return
+    end if
+
+    nullify(p)
+    call json%get(me=me, path=path, p=p)
+
+    if (.not. associated(p)) then
+        call json%throw_exception('Error in '//routine//':'//&
+                                  ' Unable to resolve path: '// trim(path),found)
+    else
+        call json%get(p,vec)
+    end if
+
+    if ( json%exception_thrown ) then
+        if ( present(found) .or. present(default)) then
+            call flag_not_found(found)
+            if (present(default)) vec = default
+            call json%clear_exceptions()
+        end if
+    else
+        if ( present(found) ) found = .true.
+    end if

Libraries/Json/json_get_vec_by_path_alloc.inc

+    type(json_value),pointer :: p
+
+    if ( json%exception_thrown ) then
+        if (present(default)) then
+            vec = default
+            if (present(default_ilen)) then
+                ilen = default_ilen
+            else
+                allocate(ilen(size(default)))
+                ilen = len(default)
+            end if
+        end if
+        call flag_not_found(found)
+        return
+    end if
+
+    nullify(p)
+    call json%get(me=me, path=path, p=p)
+
+    if (.not. associated(p)) then
+        call json%throw_exception('Error in '//routine//':'//&
+                                  ' Unable to resolve path: '// trim(path),found)
+    else
+        call json%get(p,vec,ilen)
+    end if
+
+    if ( json%exception_thrown ) then
+        if ( present(found) .or. present(default)) then
+            call flag_not_found(found)
+            if (present(default)) then
+                vec = default
+                if (present(default_ilen)) then
+                    ilen = default_ilen
+                else
+                    allocate(ilen(size(default)))
+                    ilen = len(default)
+                end if
+            end if
+            call json%clear_exceptions()
+        end if
+    else
+        if ( present(found) ) found = .true.
+    end if

Libraries/Json/json_initialize_arguments.inc

 !  The argument list for the various `initialize` subroutines.
+!
+!  See also: json_initialize_dummy_arguments.inc
 
 logical(LK),intent(in),optional :: verbose
   !! mainly useful for debugging (default is false)
@@ -13,7 +15,7 @@ integer(IK),intent(in),optional :: spaces_per_tab
 logical(LK),intent(in),optional :: strict_type_checking
   !! if true, no integer, double, or logical type
   !! conversions are done for the `get` routines
-  !! (default is false)
+  !! (default is false).
 logical(LK),intent(in),optional :: trailing_spaces_significant
   !! for name and path comparisons, is trailing
   !! space to be considered significant.
@@ -30,20 +32,21 @@ logical(LK),intent(in),optional :: unescape_strings
   !! string is returned from [[json_get_string]]
   !! and similar routines. If true [default],
   !! then the string is returned unescaped.
-character(kind=CK,len=1),intent(in),optional :: comment_char
-  !! If present, this character is used
+character(kind=CK,len=*),intent(in),optional :: comment_char
+  !! If present, these characters are used
   !! to denote comments in the JSON file,
   !! which will be ignored if present.
-  !! Example: `!` or `#`. Setting this
+  !! Example: `!`, `#`, or `/!#`. Setting this
   !! to a blank string disables the
-  !! ignoring of comments. (Default is `!`).
+  !! ignoring of comments. (Default is `/!#`).
 integer(IK),intent(in),optional :: path_mode
   !! How the path strings are interpreted in the
   !! `get_by_path` routines:
-  !! * 1 -- Default mode (see [[json_get_by_path_default]])
-  !! * 2 -- as RFC 6901 "JSON Pointer" paths
+  !!
+  !! * 1 : Default mode (see [[json_get_by_path_default]])
+  !! * 2 : as RFC 6901 "JSON Pointer" paths
   !!   (see [[json_get_by_path_rfc6901]])
-  !! * 3 -- JSONPath "bracket-notation"
+  !! * 3 : JSONPath "bracket-notation"
   !!   see [[json_get_by_path_jsonpath_bracket]])
 character(kind=CK,len=1),intent(in),optional :: path_separator
   !! The `path` separator to use
@@ -71,10 +74,41 @@ logical(LK),intent(in),optional :: escape_solidus
   !! * If True then the solidus "`/`" is always escaped
   !!   "`\/`" when serializing JSON
   !! * If False [default], then it is not escaped.
+  !!
   !! Note that this option does not affect parsing
   !! (both escaped and unescaped are still valid in
   !! all cases).
 logical(LK),intent(in),optional :: stop_on_error
   !! If an exception is raised, then immediately quit.
   !! (Default is False).
-
+integer(IK),intent(in),optional :: null_to_real_mode
+  !! if `strict_type_checking=false`:
+  !!
+  !! * 1 : an exception will be raised if
+  !!   try to retrieve a `null` as a real.
+  !! * 2 : a `null` retrieved as a real
+  !!   will return a NaN. [default]
+  !! * 3 : a `null` retrieved as a real
+  !!   will return 0.0.
+integer(IK),intent(in),optional :: non_normal_mode
+  !! How to serialize NaN, Infinity, and
+  !! -Infinity real values:
+  !!
+  !! * 1 : as strings (e.g., "NaN",
+  !!   "Infinity", "-Infinity") [default]
+  !! * 2 : as JSON `null` values
+logical(LK),intent(in),optional :: use_quiet_nan
+  !! * If true [default], `null_to_real_mode=2`
+  !!   and [[string_to_real]] will use
+  !!   `ieee_quiet_nan` for NaN values.
+  !! * If false,
+  !!   `ieee_signaling_nan` will be used.
+logical(LK),intent(in),optional :: strict_integer_type_checking
+  !! * If false, when parsing JSON, if an integer numeric value
+  !!   cannot be converted to an integer (`integer(IK)`),
+  !!   then an attempt is then make to convert it
+  !!   to a real (`real(RK)`).
+  !! * If true, an exception will be raised if the integer
+  !!   value cannot be read.
+  !!
+  !! (default is true)
\ No newline at end of file

Libraries/Json/json_initialize_dummy_arguments.inc

+!  The dummy argument list for the various `initialize` subroutines.
+!
+!  See also: json_initialize_argument.inc
+
+verbose,&
+compact_reals,&
+print_signs,&
+real_format,&
+spaces_per_tab,&
+strict_type_checking,&
+trailing_spaces_significant,&
+case_sensitive_keys,&
+no_whitespace,&
+unescape_strings,&
+comment_char,&
+path_mode,&
+path_separator,&
+compress_vectors,&
+allow_duplicate_keys,&
+escape_solidus,&
+stop_on_error,&
+null_to_real_mode,&
+non_normal_mode,&
+use_quiet_nan, &
+strict_integer_type_checking &
\ No newline at end of file

Libraries/Json/json_kinds.f90

@@ -59,6 +59,10 @@
 !      integer(kind=int32) [4 bytes]
 #endif
 !      .
+!
+!@note In addition to the real kind specified by `RK`, interfaces for
+!      the real kinds with less precision are also provided in the library,
+!      but all are converted to `real(RK)` variables internally.
 
     module json_kinds
 
@@ -68,6 +72,15 @@
 
     private
 
+! used for the reals with less precision
+! than the default precision:
+#ifndef REAL32
+    public :: real32
+#endif
+#ifdef REAL128
+    public :: real64
+#endif
+
 #ifdef REAL32
     integer,parameter,public :: RK = real32   !! Default real kind [4 bytes]
 #elif REAL64
@@ -92,7 +105,7 @@
 
     !*********************************************************
     !>
-    !  Processor dependendant 'DEFAULT' character kind.
+    !  Processor dependent 'DEFAULT' character kind.
     !  This is 1 byte for the Intel and Gfortran compilers.
     integer,parameter,public :: CDK = selected_char_kind('DEFAULT')
     !*********************************************************

Libraries/Json/json_module.f90

@@ -65,6 +65,7 @@
                                json_array,  &
                                json_logical,&
                                json_integer,&
+                               json_real,   &
                                json_double, &
                                json_string
     use json_value_module

Libraries/Json/json_parameters.f90

@@ -29,13 +29,16 @@
                                                  !! (see [[json_file_variable_info]] and [[json_info]])
     integer(IK),parameter :: json_array     = 3  !! Array JSON data type
                                                  !! (see [[json_file_variable_info]] and [[json_info]])
-    integer(IK),parameter :: json_logical   = 4  !! Logical JSON data type
+    integer(IK),parameter :: json_logical   = 4  !! Logical JSON data type (`logical(LK)`)
                                                  !! (see [[json_file_variable_info]] and [[json_info]])
-    integer(IK),parameter :: json_integer   = 5  !! Integer JSON data type
+    integer(IK),parameter :: json_integer   = 5  !! Integer JSON data type (`integer(IK)`)
+                                                 !! (see [[json_file_variable_info]] and [[json_info]]).
+    integer(IK),parameter :: json_real      = 6  !! Real number JSON data type (`real(RK)`)
                                                  !! (see [[json_file_variable_info]] and [[json_info]])
-    integer(IK),parameter :: json_double    = 6  !! Double JSON data type
+    integer(IK),parameter :: json_string    = 7  !! String JSON data type (`character(kind=CK)`)
                                                  !! (see [[json_file_variable_info]] and [[json_info]])
-    integer(IK),parameter :: json_string    = 7  !! String JSON data type
+    integer(IK),parameter :: json_double    = json_real  !! Equivalent to `json_real` for
+                                                         !! backward compatibility.
 
     !special JSON characters
     character(kind=CK,len=*),parameter :: space           = CK_' '  !! space character
@@ -45,9 +48,11 @@
     character(kind=CK,len=*),parameter :: end_array       = CK_']'  !! end of a JSON array
     character(kind=CK,len=*),parameter :: delimiter       = CK_','  !! delimiter for JSON
     character(kind=CK,len=*),parameter :: colon_char      = CK_':'  !! colon character for JSON
-    character(kind=CK,len=*),parameter :: start_array_alt = CK_'('  !! alternate start of JSON array for [[json_get_by_path_default]]
-    character(kind=CK,len=*),parameter :: end_array_alt   = CK_')'  !! alternate end of JSON array for [[json_get_by_path_default]]
-    character(kind=CK,len=*),parameter :: root            = CK_'$'  !! root for [[json_get_by_path_default]]
+    character(kind=CK,len=*),parameter :: start_array_alt = CK_'('  !! alternate start of JSON array for
+                                                                    !! [[json_get_by_path_default]]
+    character(kind=CK,len=*),parameter :: end_array_alt   = CK_')'  !! alternate end of JSON array for
+                                                                    !! [[json_get_by_path_default]]
+    character(kind=CK,len=*),parameter :: root            = achar(36, kind=CK)  !! (`$`) root for [[json_get_by_path_default]]
     character(kind=CK,len=*),parameter :: this            = CK_'@'  !! 'this' for [[json_get_by_path_default]]
     character(kind=CK,len=*),parameter :: dot             = CK_'.'  !! path separator for [[json_get_by_path_default]]
     character(kind=CK,len=*),parameter :: tilde           = CK_'~'  !! RFC 6901 escape character
@@ -62,9 +67,17 @@
     character(kind=CK,len=*),parameter :: slash           = achar(47, kind=CK) !! JSON special character
     character(kind=CK,len=*),parameter :: backslash       = achar(92, kind=CK) !! JSON special character
 
+
+
+    !> default real number format statement (for writing real values to strings and files).
+    !  Note that this can be overridden by calling [[json_initialize]].
+#ifdef REAL32
+    character(kind=CDK,len=*),parameter :: default_real_fmt = '(ss,E17.8E3)'
+#elif REAL128
+    character(kind=CDK,len=*),parameter :: default_real_fmt = '(ss,E46.35E5)'
+#else
     character(kind=CDK,len=*),parameter :: default_real_fmt = '(ss,E27.17E4)'
-        !! default real number format statement (for writing real values to strings and files).
-        !! Note that this can be overridden by calling [[json_initialize]].
+#endif
 
     character(kind=CK,len=*),parameter :: star = CK_'*' !! for invalid numbers and
                                                         !! list-directed real output
@@ -111,17 +124,22 @@
         !! 6 = sign + leading 0 + decimal + 'E' + exponent sign + 1 extra
     character(kind=CDK,len=*),parameter :: int_fmt  = '(ss,I0)' !! minimum width format for integers
 
-    integer(IK),parameter :: max_integer_str_len = 256 !! maximum string length of an integer.
-                                                       !! This is totally arbitrary (any way
-                                                       !! to get the compiler to tell us this?)
+    integer(IK),parameter :: max_integer_str_len = 256_IK !! maximum string length of an integer.
+                                                          !! This is totally arbitrary (any way
+                                                          !! to get the compiler to tell us this?)
 
-    integer(IK),parameter :: chunk_size = 100_IK  !! for allocatable strings: allocate chunks of this size
+    integer(IK),parameter :: chunk_size = 256_IK  !! for allocatable strings: allocate chunks of this size
     integer(IK),parameter :: unit2str = -1_IK  !! unit number to cause stuff to be
                                                !! output to strings rather than files.
                                                !! See 9.5.6.12 in the F2003/08 standard
+    character(kind=CK,len=*),parameter :: blank_chunk = repeat(space, chunk_size) !! a blank string
 
     integer(IK),parameter :: seq_chunk_size = 256_IK !! chunk size for reading sequential files
 
+    integer(IK),parameter :: stream_chunk_size = 256_IK !! chunk size for reading stream files
+
+    integer(IK),parameter :: print_str_chunk_size = 1000_IK !! chunk size for writing JSON to a string
+
     integer(IK),parameter :: pushed_char_size = 10_IK !! size for `pushed_char`
                                                       !! array in [[json_core(type)]]
 

Libraries/Json/json_string_utilities.f90

@@ -11,6 +11,7 @@
 
     module json_string_utilities
 
+    use,intrinsic :: ieee_arithmetic
     use json_kinds
     use json_parameters
 
@@ -120,21 +121,22 @@
     integer(IK),intent(out)             :: ival       !! the integer value
     logical(LK),intent(out)             :: status_ok  !! true if there were no errors
 
-    !character(kind=CDK,len=:),allocatable :: digits
-    character(len=:),allocatable :: digits
+    character(kind=CDK,len=:),allocatable :: digits
     integer(IK) :: ndigits_digits,ndigits,ierr
 
     ! Compute how many digits we need to read
     ndigits = 2*len_trim(str)
-    ndigits_digits = floor(log10(real(ndigits)))+1
-    !allocate(character(kind=CK,len=ndigits_digits) :: digits)
-    allocate(character(len=ndigits_digits) :: digits)
-    write(digits,'(I0)') ndigits !gfortran will have a runtime error with * edit descriptor here
-    ! gfortran bug: '*' edit descriptor for ISO_10646 strings does bad stuff.
-    read(str,'(I'//trim(digits)//')',iostat=ierr) ival   !string to integer
-
-    ! error check:
-    status_ok = (ierr==0)
+    if (ndigits/=0) then
+        ndigits_digits = floor(log10(real(ndigits)))+1
+        allocate(character(kind=CDK,len=ndigits_digits) :: digits)
+        write(digits,'(I0)') ndigits !gfortran will have a runtime error with * edit descriptor here
+        ! gfortran bug: '*' edit descriptor for ISO_10646 strings does bad stuff.
+        read(str,'(I'//trim(digits)//')',iostat=ierr) ival   !string to integer
+        ! error check:
+        status_ok = (ierr==0)
+    else
+        status_ok = .false.
+    end if
     if (.not. status_ok) ival = 0_IK
 
     end subroutine string_to_integer
@@ -147,10 +149,11 @@
 !  Convert a real value to a string.
 !
 !### Modified
-!  * Izaak Beekman : 02/24/2015 : added the compact option.
+!  * Izaak Beekman  : 02/24/2015 : added the compact option.
 !  * Jacob Williams : 10/27/2015 : added the star option.