Merge pull request #18 from talassio/master

Miscelaneous updates (second batch)

libRALFit/CMakeLists.txt

@@ -14,12 +14,13 @@ set(CMAKE_EXE_LINKER_FLAGS "-Wl,-export-dynamic")
 
 # Set the source files that we're going to compile
 set ( SRC_FILES
-        src/ral_nlls_double.f90
+  src/ral_nlls_double.f90
 	src/ral_nlls_internal.f90
 	src/ral_nlls_dtrs_double.f90
 	src/ral_nlls_symbols.f90
 	src/ral_nlls_ciface.f90
 	src/ral_nlls_workspaces.f90
+  src/ral_nlls_printing.f90
 	)	
 
 # Support for CMAKE_BUILD_TYPE={Debug,Release,Profile}

libRALFit/doc/C/howtouse.rst

@@ -239,10 +239,6 @@ The derived data type for holding options
    
    **Printing Controls**
    
-   .. c:member:: int error 
-		 
-		 |error|
-		 Default is 6.
    .. c:member:: int out 
 
 		 |out|
@@ -255,6 +251,18 @@ The derived data type for holding options
 		 .. include:: ../common/options_print_level.txt
 			      
 		 Default is 0.
+
+   .. c:member:: bool print_options
+
+     |print_options|
+
+     Default is false.
+
+   .. c:member:: int print_header
+
+     |print_header|
+
+     Default is 30.
       
    **Choice of Algorithm**
 
@@ -580,6 +588,10 @@ The derived data type for holding information
    .. c:member:: character external_name(81)
 
 		 |external_name|
+
+   .. c:member:: double step
+
+     |step|
    
 
 The workspace derived data type

libRALFit/doc/Fortran/howtouse.rst

@@ -308,17 +308,21 @@ The derived data type for holding options
    This is used to hold controlling data. The components  are automatically given default values in the definition of the type.
 
    **Printing Controls**
-
-   :f integer error [default=6]: |error|
+
    :f integer out [default=6]: |out|
+
    :f integer print_level [default=0]: |print_level|
 
 				       .. include:: ../common/options_print_level.txt
+
+   :f logical print_options [default=false]: |print_options|
+
+   :f integer print_header [default=30]: |print_header|
 
    **Choice of Algorithm**
-				   
+
    :f integer model [default=3]: |model| 
-				 
+
 	     			 .. include:: ../common/options_model.txt
 
    :f integer type_of_method [default=1]: |type_of_method|
@@ -476,6 +480,8 @@ The derived data type for holding information
    :f integer external_return: |external_return|
 
    :f character external_name(80): |external_name|
+
+   :f real step: |step|
 
 
 The workspace derived data type

libRALFit/doc/Python/howtouse.rst

@@ -83,11 +83,6 @@ Controlling data is sent to the subroutine using a Python dictionary.  A descrip
 
    **Printing Controls**
 
-   * error (int)
-
-		 |error|
-		 Default is 6.
-
    * out (int)
 
 		 |out|
@@ -100,6 +95,18 @@ Controlling data is sent to the subroutine using a Python dictionary.  A descrip
 		 .. include:: ../common/options_print_level.txt
 
 		 Default is 0.
+
+   * print_options (bool)
+
+     |print_options|
+
+     Default is false.
+
+   * print_header (int)
+
+     |print_header|
+
+     Default is 30.
 
    **Choice of Algorithm**
 
@@ -393,3 +400,6 @@ This is used to hold information about the progress of the algorithm.
 
 		 |scaled_g|
 
+   *  step (float)
+     |step|
+

libRALFit/doc/common/errors.rst

@@ -29,9 +29,11 @@ Possible values are:
     * - -13
       -  Error accessing pre-allocated workspace.
     * - -14
-      -  Unsupported value in type_of_method
+      -  Unsupported value in ``type_of_method``.
+    * - -15
+      -  Unsupported value of ``inner_method`` passed in options.
     * - -101
-      -  Unsupported model in dogleg (``nlls_method = 1``).
+      -  Unsupported model in dogleg (``nlls_method=1``).
     * - -201
       -  All eigenvalues are imaginary (``nlls_method=2``).
     * - -202
@@ -44,3 +46,9 @@ Possible values are:
       -  No progress being made in ``more_sorensen`` subroutine (``nlls_method=3``).
     * - -401
       - ``model = 4`` selected, but ``exact_second_derivatives`` is set to ``false``. 
+    * - -900
+      - Illegal value of ``print_level`` in options array. Valid range is 0 to 5. 
+    * - -950
+      - Combination of method/regularization options not yet implemented
+    * - -999
+      - Unexpected error occured

libRALFit/doc/common/inform.rst

@@ -28,8 +28,10 @@
 
 .. |norm_g| replace:: holds the gradient of the objective function at the best estimate of the solution determined by the package.
 
-.. |scaled_g| replace:: holds the gradient of the objective function at the best estimate of the solution determined by the package.
+.. |scaled_g| replace:: holds a scaled version of the gradient of the objective function at the best estimate of the solution determined by the package.
 
 .. |external_return| replace:: gives the error code that was returned by a call to an external routine.
 
 .. |external_name| replace:: holds the name of the external code that flagged an error.
+
+.. |step| replace:: holds the size of the last step taken.

libRALFit/doc/common/options.rst

@@ -1,18 +1,24 @@
-.. |error| replace:: the Fortran unit number for error messages.  If it is negative, these messages will be suppressed.
-
 .. |out| replace::  the Fortran unit number for general messages. If it is negative, these messages will be suppressed.
 
 .. |print_level| replace:: controls the level of output required.  Options are:
 
 .. !+----+------------------------------------------------------------------------+
-.. !| <1 | No informational output will occur.                                    |
+.. !|  0 | No informational output will occur.                                    |
+.. !+----+------------------------------------------------------------------------+
+.. !|  1 | Prints a brief summary when finished.                                  |
+.. !+----+------------------------------------------------------------------------+
+.. !|  2 | Gives a one-line summary for each iteration.                           |
 .. !+----+------------------------------------------------------------------------+
-.. !|  1 | Gives a one-line summary for each iteration.                           |
-.. ! +----+------------------------------------------------------------------------+
-.. !|  2 | As 1, plus gives a summary of the inner iteration for each iteration.  |
+.. !|  3 | As 2, but with more details.                                           |
 .. !+----+------------------------------------------------------------------------+
-.. !|  3 | As 2, plus gives more verbose (debugging) output.                      |
+.. !|  4 | As 3, plus gives a summary of the inner iteration for each iteration.  |
 .. !+----+------------------------------------------------------------------------+
+.. !|  5 | As 4, plus gives more verbose (debugging) output.                      |
+.. !+----+------------------------------------------------------------------------+
+
+.. |print_options| replace:: determines whether to print a list of all options and their values at the beggining of the solve.
+
+.. |print_header| replace:: prints the column header every ``print_header`` iterations when ``print_level > 1``.
 
 .. |maxit| replace:: gives the number of iterations the algorithm is allowed to take before being stopped.  This is not accessed if |nlls_iterate| is used. 
 

libRALFit/doc/common/options_print_level.txt

@@ -1,10 +1,14 @@
 .. list-table::
 
-   * - < 1			
+   * - 0
      - No informational output will occur.
-   * - 1 
+   * - 1
+     - Prints a brief summary when finished.
+   * - 2
      - Gives a one-line summary for each iteration. 
-   * - 2 
-     - As 1, plus gives a summary of the inner iteration for each iteration.
-   * - 3 
-     - As 2, plus gives more verbose (debugging) output.
+   * - 3
+     - As 2, but with more details. 
+   * - 4 
+     - As 3, plus gives a summary of the inner iteration for each iteration.
+   * - 5 
+     - As 4, plus gives more verbose (debugging) output.

libRALFit/doc/conf.py

@@ -265,20 +265,23 @@
 #####################################################
 # add LaTeX macros 
 
-f = file('common/RALFit_header.sty')
+f = open('common/RALFit_header.sty', 'r')
+flines = f.readlines()
+
 
 try:
     imgmath_latex_preamble  # check whether this is already defined
 except NameError:
     imgmath_latex_preamble = ""
 
-for macro in f:
+for macro in flines:
     # used when building latex and pdf versions
     latex_elements['preamble'] += macro + '\n'
     # used when building html version
     imgmath_latex_preamble += macro + '\n'
 # (from http://stackoverflow.com/questions/9728292/creating-latex-math-macros-within-sphinx)
 
+f.close()
 #####################################################
 
 # Grouping the document tree into LaTeX files. List of tuples

libRALFit/doc/info_type.tex

@@ -26,6 +26,7 @@
 \scalarreal{scaled\_g} that holds the gradient of the objective function at the best estimate of the solution determined by the package.
 \scalarinteger{external\_return} that gives the error code that was returned by a call to an external routine.
 \scalarcharacter{external\_name}{80} that holds the name of the external code that flagged an error.
+\scalarreal{step} holds the size of the last step taken.
 \end{description}
 
 

libRALFit/doc/options_type.tex

@@ -16,10 +16,6 @@
 \noindent {\bf Components that control printing}
 \begin{description}
 
-\scalarinteger{error}
-with default value {\tt 6} that is used as the \conly{Fortran }unit number for error messages. 
-If it is negative, these messages will be suppressed.
-
 \scalarinteger{out}
 with default value {\tt 6} that is used as the \conly{Fortran }unit number for general messages. If it is negative, these messages will be suppressed.
 
@@ -34,6 +30,12 @@
 The default is {\tt print\_level} $=$ 0.
 \end{description}
 
+\scalarlogical{print_options}
+with default value {\tt false}, determines whether to print a list of all options and their values at the beggining of the solve.
+
+\scalarinteger{print_header}
+with default value {\tt 30}, it will print the column header every 30 iterations when {\tt print\_level} is greater than 1.
+
 \noindent {\bf Components that control the main iteration}.
 
 \begin{description}

libRALFit/example/Fortran/Lanczos.f90

@@ -28,7 +28,7 @@ subroutine eval_r(status, n, m, x, r, params)
        r(1:m) = params%y(:) &
             - x(1)*exp(-x(2)*params%t(:)) &
             - x(3)*exp(-x(4)*params%t(:)) &
-            - x(5)*exp(-x(6)*params%t(:)) 
+            - x(5)*exp(-x(n)*params%t(:))
     end select
 
     status = 0 ! success
@@ -50,7 +50,7 @@ subroutine eval_J(status, n, m, x, J, params)
          J(2*m+1:3*m) = -exp(-x(4)*params%t(1:m))                     ! J_i3
          J(3*m+1:4*m) = +params%t(1:m) * x(3) * exp(-x(4)*params%t(1:m))! J_i4
          J(4*m+1:5*m) = -exp(-x(6)*params%t(1:m))                     ! J_i5
-         J(5*m+1:6*m) = +params%t(1:m) * x(5) * exp(-x(6)*params%t(1:m))! J_i6
+         J(5*m+1:6*m) = +params%t(1:m) * x(5) * exp(-x(n)*params%t(1:m))! J_i6
     end select
 
 
@@ -93,7 +93,7 @@ subroutine eval_HP(status, n, m, x, y, HP, params)
       class(params_base_type), intent(inout) :: params
 
       integer :: i
-
+      status = 0
       HP(1:n*m) = 0.0
       select type(params)
       type is (params_type)
@@ -130,7 +130,6 @@ program lanczos
   integer :: m,n
   real(wp), allocatable :: x(:)
   type(params_type) :: params
-  integer :: inner_method
   real(wp) :: tic, toc
 
   ! data to be fitted
@@ -191,7 +190,7 @@ program lanczos
   allocate(x(n))
   x = (/ 1.2, 0.3, 5.6, 5.5, 6.5, 7.6 /) ! SP 1
 
-  options%print_level = 1
+  options%print_level = 4
   options%exact_second_derivatives = .true.
   options%model = 4
   options%nlls_method = 3

libRALFit/example/Fortran/nlls_example.f90

@@ -26,7 +26,7 @@ subroutine eval_r(status, n, m, x, r, params)
       real(wp) :: x1, x2
 
       x1 = x(1)
-      x2 = x(2)
+      x2 = x(n)
       select type(params)
       type is(params_type)
          r(1:m) = x1 * exp(x2*params%t(:)) - params%y(:)
@@ -48,7 +48,7 @@ subroutine eval_J(status, n, m, x, J, params)
       real(wp) :: x1, x2
 
       x1 = x(1)
-      x2 = x(2)
+      x2 = x(n)
       select type(params)
       type is(params_type)
          J(  1:  m) = exp(x2*params%t(1:m))                     ! J_i1

libRALFit/example/Fortran/nlls_example2.f90

@@ -26,7 +26,7 @@ subroutine eval_r(status, n, m, x, r, params)
       real(wp) :: x1, x2
 
       x1 = x(1)
-      x2 = x(2)
+      x2 = x(n)
       select type(params)
       type is(params_type)
          r(1:m) = x1 * exp(x2*params%t(:)) - params%y(:)
@@ -48,7 +48,7 @@ subroutine eval_J(status, n, m, x, J, params)
       real(wp) :: x1, x2
 
       x1 = x(1)
-      x2 = x(2)
+      x2 = x(n)
       select type(params)
       type is(params_type)
          J(  1:  m) = exp(x2*params%t(1:m))                     ! J_i1
@@ -125,7 +125,6 @@ program nlls_example2
    real(wp), allocatable :: x(:)
    type(params_type) :: params
    integer :: inner_method
-
    ! Data to be fitted
    m = 5
    allocate(params%t(m), params%y(m))
@@ -137,12 +136,11 @@ program nlls_example2
    allocate(x(n))
 
    options%model = 4
-   options%type_of_method = 3
+   options%type_of_method = 2
    options%nlls_method = 4
    options%exact_second_derivatives = .true. 
    options%maxit = 50
-
-   options%print_level = 1
+   options%print_level = 4
 
    do inner_method = 1,3
 

libRALFit/include/ral_nlls.h

@@ -27,9 +27,10 @@ typedef double ral_nllspkgtype_d_;
 struct ral_nlls_options_d {
   int f_arrays; /* Use 1-based indexing if true(!=0) else 0-based */
 
-  int error; /* Fortran output stream for error messages */
   int out;   /* Fortran output stream for general messages */
   int print_level; /* levels of print output */
+  bool print_options; /* print all options? */
+  int print_header; /*=k; print one-liner header every k-th iteration */
   int maxit; /* maximum number of iterations */
   int model; /* what model to use? */
   int type_of_method; /* what method to use? */
@@ -101,6 +102,7 @@ struct ral_nlls_inform_d {
   ral_nllspkgtype_d_ scaled_g;
   int external_return;
   char external_name[81];
+  ral_nllspkgtype_d_ step;
 };
 
 /* Set default values of options */