MD/arcos Changeset - d6faa5ffcedf · Centrum Wiskunde & Informatica (CWI)

Changeset - d6faa5ffcedf

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! ! !

Margreet Nool - 10 years ago 2014-07-04 17:10:21
greta@timor.sen.cwi.nl

install arcos

13 files changed:

Makefile

Makefile.config

Makefile.inc

README

arcos_f90/src/Makefile

arcos_f90/src/cdr_advect_diffu_vec.f90

414

arcos_f90/src/cdr_advect_diffu_wrap.c

doc/README

doc/doxygen_config_file

1624

doc/figures/figure2.eps

1921

doc/figures/grids.eps

435

doc/figures/grids.fig

167

doc/figures/grids.png

bin+new file

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Makefile

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@@ new file 100644 @@
 include 	Makefile.inc
 include 	Makefile.config
 SOURCE_DIR	= src
 FISH90_DIR	= fish90/src
 F90_DIR		= arcos_f90/src
 CONFIG_DIR	= libconfig-1.4.9/lib
 SUBDIRS		= $(F90_DIR) $(FISH90_DIR) $(SOURCE_DIR) $(CONFIG_DIR)
 CLEANDIRS	= $(SUBDIRS:%=clean-%)
 .PHONY:		all allclean $(SUBDIRS) $(CLEANDIRS)
 # Default Target is to build everything
 all: $(SUBDIRS)
 allclean: $(CLEANDIRS) clean
 $(SUBDIRS):
 	$(MAKE) -C $@
 $(CLEANDIRS):
 	$(MAKE) -C $(@:clean-%=%) clean
 clean:
 	$(RM) $(SOURCE_DIR)/*.o ./arcos

Makefile.config

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@@ new file 100644 @@
 # This file defines the Makefile variables that are used to compile
 # the PHARCOS programs and  libraries. Edit this file as needed.
 # The C compiler and compiler options.
 CC		:= gcc
 #CC		:= pgcc
 CFLAGS		= -g -pg -O3
 # CFLAGS	= -openmp -D_GNU_SOURCE -O3 -ipo -openmp-report0 #-gcc-version=400
 # The Fortran 90 compiler and compiler options. Leave empty to
 # disable Fortran 90 support.
 F90 		:= gfortran -I../lib
 #F90		:= pgf90 -g -pg -I../lib
 #F90FLAGS	= -nofor-main -O3
 F90FLAGS	= -O3
 FFLAGS		= -O3
 DEBUG_LEVEL	:= 1
 DFLAGS		= -DCOMPILING_HOSTNAME=\"$(HOSTNAME)\" -DDEBUG_LEVEL=1
 # Search directories for include files and libraries.
 INCLUDEDIR1	= ../include
 INCLUDEDIR2	= ../fish90/include
 INCLUDES	= -I $(INCLUDEDIR1) -I $(INCLUDEDIR2)
 LIBDIRS		=
 INCDIRS		=
 # Command for creating static library.
 AR		= ar -rcsv
 # Other commands.
 MV		= mv -f

Makefile.inc

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@@ new file 100644 @@
 # This file defines common Makefile variables and rules that are used
 # to compile the FISHPACK libraries. Normally, this
 # file does not have to be modified; see the file Makefile.conf.
 # The names of the fishpack libraries.
 FISHPACK_LIB	= libfishpack.a
 FISH90_LIB	= libfish90.a
 # Commands to compile and link C and Fortran 90 code.
 Compile		= $(CC) $(CFLAGS) $(DFLAGS) $(addprefix -I,$(INCDIRS)) \
 		        -o $@ -c $<
 LinkExe		= $(CC) $(addprefix -L,$(LIBDIRS)) -o $@ $^ \
 		        $(F90FLAGS) $(addprefix -l,$(LIBS))
 CompileF90	= $(F90) $(F90FLAGS) $(addprefix -I,$(INCDIRS)) \
 		         -o $@ -c $<
 LinkF90Exe	= $(F90) $(addprefix -L,$(LIBDIRS)) -o $@ $^ \
 		         $(F90FLAGS) $(addprefix -l,$(LIBS))
 CompileF	= $(F90) $(F90FLAGS) $(addprefix -I,$(INCDIRS)) \
 		         -o $@ -c $<
 Compilef	= $(F90) $(FFLAGS) $(addprefix -I,$(INCDIRS)) \
 		         -o $@ -c $<
 # Implicit rules for compiling C and Fortran source files.
 %.o:		%.c
 		$(Compile)
 %.o:		%.f90
 		$(CompileF90)
 %.o:		%.F
 		$(CompileF)
 %.o:		%.f
 		$(Compilef)

README

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@@ new file 100644 @@
 To create the executable arcos:
 - first create library libconfig.
   Go to directory libconfig-1.4.9/lib  and give the following command
   make all
 - next, return to the root directory pharcos and give the following command
   make all
 Now you have the executable arcos, which needs the input files from
 directory input. ./arcos also needs an output directory. The name is given in
 /input/default.cfg by "output_dir". Here we chose directory output.
 If output does not exist, create this directory:
 make output
 In this directory many files for visualization will be written. For more details see the documentation:
 file:///?????

arcos_f90/src/Makefile

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@@ new file 100644 @@
 TOPDIR	:= ../..
 include	$(TOPDIR)/Makefile.config
 include	$(TOPDIR)/Makefile.inc
 .PHONY:	all
 all:	lib
 SRCF	= cdr_advect_diffu_vec.f90
 SRCC	= cdr_advect_diffu_wrap.c
 INCDIRS	= ../../include
 OBJF	=$(subst .f90,.o,$(SRCF))
 OBJC	=$(subst .c,.o,$(SRCC))
 OBJ := $(OBJF) $(OBJC)
 LIB	=../lib/libarcos.a
 lib : $(LIB)
 $(LIB) : $(OBJ)
 	$(AR) $@ $?
 clean:
 	rm -f $(LIB) $(OBJ) *~

arcos_f90/src/cdr_advect_diffu_vec.f90

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@@ new file 100644 @@
 !> @file cdr_advect_diffu_vec.f90
 !! @brief This code replaces the original c code of cdr_advect_diffu in file
 !!  cdr.c
 !!
 !! @author Margreet Nool
 !!
 !!     The arrays er_array and ez_array are in C stored as
 !!     1D arrays. In the wrapper routine cdr_advect_diffu_wrap.c it is
 !!     checked of their sizes, er_len, ez_len are equal to rmax-by-zmax.
 !!
 !!     Note that these are NOT the r0, z0 we received.  The idea here is that
 !!     RZ(array, r0, z0) will produce the correct result, where the allocated
 !!     array looks like (in the picture, r0, z0 ARE the received ones).
 !!     Note: in the picture there is only one buffer cell, while we actually
 !!     allocate two.
 !!
 !!      +--------------+--------------+...+--------------+--------------+
 !!      |r0 - 1, z0 - 1|              |   |              |              |
 !!      +--------------+--------------+...+--------------+--------------+
 !!      |              |   r0, z0     |   |              |              |
 !!      +--------------+--------------+...+--------------+--------------+
 !!                    ...             |...|             ...
 !!      +--------------+--------------+...+--------------+--------------+
 !!      |              |              |   |r1 - 1, z1 - 1|              |
 !!      +--------------+--------------+...+--------------+--------------+
 !!      |              |              |   |              |    r1, z1    |
 !!      +--------------+--------------+...+--------------+--------------+
 !!
 !!     but the rows z0 +/- 1 and the columns r0 +/- 1 do not belong to the
 !!     physical space and are used only to specify boundary conditions.
 !!
 !!     In the C routines r0, and z0 are zero, and the calculations start
 !!     at the third element (r0-2, r0-1, r0, ...., r1, r1+1), and
 !!     (z0-2, z0-1, r0, ...., z1, z1+1), respectively.
 !!     rmax = r1 - r0 + 4 and zmax = z1 - z0 + 4.
 !!-----------------------------------------------
 ! subroutine cdr_advect_vec
 ! subroutine mat_efield_r
 ! subroutine mat_efield_z
 ! subroutine mat_cdr_f_ad_r
 ! subroutine mat_cdr_f_ad_z
 ! subroutine make_vecs_er
    subroutine cdr_advect_vec(mass,charge,dens_array,d_dens_array, &
                          er_array,ez_array,diffusion_coeff,dr,dz, &
                          sprite_module,r0,r1,z0,z1)
       implicit none
 !     ..
 !     .. Parameters ..
       double precision,parameter :: ONE  = 1.0D0
 !     ..
 !     .. Dummy Variables ..
       logical,intent(in)          :: sprite_module
       integer,intent(in)          :: r0,r1,z0,z1
       double precision,intent(in) :: charge,dr,dz,mass,diffusion_coeff
 !     ..
 !     .. Dummy Arrays ..
       double precision,dimension(r0-2:r1+1,z0-2:z1+1),intent(in)  :: &
                        dens_array,er_array,ez_array
       double precision,dimension(r0-2:r1+1,z0-2:z1+1),intent(out) :: &
                        d_dens_array
 !     ..
 !     .. Local Variables ..
       integer          :: ir,ishift
       double precision :: cm0,cm,gdz_inv,d_iso0,d_iso
 !     ..
 !     .. Local arrays ..
       double precision,dimension(r0:r1-1)             :: er_min
       double precision,dimension(r0+1:r1)             :: er
       double precision,dimension(z1-z0)               :: d_iso_r
       double precision,dimension(z1-z0+1)             :: d_iso_z
       double precision,dimension(r1-r0+1,z1-z0  )     :: mat_r
       double precision,dimension(r1-r0  ,z1-z0+1)     :: mat_z
       double precision,dimension(r1-r0+1,z1-z0  )     :: efield_r
       double precision,dimension(r0:r1-1,z0-1:z1-1)   :: efield_z
 !     ..
 !     .. External subroutines ..
       external :: mat_efield_r,mat_efield_z,mat_cdr_f_ad_r,mat_cdr_f_ad_z
 !     ..
       if (mass <= 0) return
       ! <ISOTROPIC DIFFUSSION>
       d_iso0 = diffusion_coeff / mass
       ! </ISOTROPIC DIFFUSION>
       gdz_inv = ONE / dz
       cm0 = charge / mass
       if (.not.sprite_module) then
         cm = cm0
         d_iso = d_iso0
       end if
 !-----------------------------------------------
 !     Increase the values r0, r1, z0 and z1 with 3:
 !     because of 2 buffer cells at the left side and to compensate the C 0
 !-----------------------------------------------
       ishift = 3
       ! Compute the electric field in radial direction
       call mat_efield_r(er_array(r0-1:r1-1,z0:z1-1), &
                         efield_r,d_iso_r,cm0,d_iso0, &
                         r0,r1,dz,z0,z1,ishift,dr,sprite_module)
       ! Calculate the radial advection from left and right
       call mat_cdr_f_ad_r(dens_array(r0-2:r1+1,z0:z1-1), &
                           efield_r(1:r1-r0+1,1:z1-z0),d_iso_r, &
                           mat_r,r0,r1,z0,z1)
       ! Add the radial advection
       call  make_vecs_er (er_min,er,r0,r1,dr)
       do ir = r0,r1-1
          d_dens_array(ir,z0:z1-1) = d_dens_array(ir,z0:z1-1) + &
                                     er_min(ir) * mat_r(ir-r0+1,1:z1-z0) - &
                                     er(ir+1)   * mat_r(ir-r0+2,1:z1-z0)
       end do
       ! Compute the electric field in axial direction
       call mat_efield_z(ez_array(r0  :r1-1,z0-1:z1-1), &
                         efield_z(r0:r1-1,z0-1:z1-1),d_iso_z,cm0,d_iso0, &
                         r0,r1,dz,z0,z1,ishift,dz,sprite_module)
       ! Calculate the axial advection from the north and south
       call mat_cdr_f_ad_z(dens_array(r0  :r1-1,z0-2:z1+1), &
                           efield_z(r0:r1-1,z0-1:z1-1),d_iso_z, &
                           mat_z,r0,r1,z0,z1)
       ! Add the axial advection
       d_dens_array(r0:r1-1,z0:z1-1) = d_dens_array(r0:r1-1,z0:z1-1) + &
                                       gdz_inv * (mat_z(1:,1:z1-z0) - &
                                                  mat_z(1:,2:z1-z0+1))
    end subroutine cdr_advect_vec
    subroutine mat_efield_r(er_array,efield,d_iso,cm0,d_iso0, &
                            r0,r1,dz,z0,z1,z_shift,dx,sprite_module)
 !     ..
       implicit none
 !     ..
 !     .. Parameters ..
       double precision,parameter :: HALF = 0.5D0,ONE  = 1.0D0
 !     ..
 !     .. Dummy Variables ..
       logical,intent(in)          :: sprite_module
       integer,intent(in)          :: r0,r1,z0,z1,z_shift
       double precision,intent(in) :: cm0,d_iso0,dz,dx
 !     ..
 !     .. Dummy Arrays ..
       double precision,dimension(r1-r0+1,z1-z0),intent(in)  :: er_array
       double precision,dimension(r1-r0+1,z1-z0),intent(out) :: efield
       double precision,dimension(z1-z0),intent(out)         :: d_iso
 !     ..
 !     .. Local Variables ..
       integer                           :: iz
 !     ..
 !     .. Local arrays ..
       double precision,dimension(z1-z0) :: back_dens_inv,cm
 !-----------------------------------------------
       ! If the densities are varying...
       if (sprite_module) then
          do iz = z0,z1
             ! spr_density_at(iz) = (iz-z_shift + half) * dz
             ! back_dens_inv = ONE / spr_density_at
             back_dens_inv(iz-z0+1) = ONE / ((iz-z_shift + half) * dz)
          end do
          cm    = cm0 * back_dens_inv
          d_iso = d_iso0 * back_dens_inv
       else
          back_dens_inv = ONE
          cm            = cm0
          d_iso         = d_iso0
       end if
       d_iso = d_iso / dx
       ! efield = cm * er_array
       do iz = 1,z1-z0
          efield(:,iz) = cm(iz) * er_array(:,iz)
       end do
    end subroutine mat_efield_r
    subroutine mat_efield_z (ez_array,efield,d_iso,cm0,d_iso0, &
                             r0,r1,dz,z0,z1,z_shift,dx,sprite_module)
 !     ..
       implicit none
 !     ..
 !     .. Parameters ..
       double precision,parameter :: HALF = 0.5D0,ONE  = 1.0D0
 !     ..
 !     .. Dummy Variables ..
       logical,intent(in)          :: sprite_module
       integer,intent(in)          :: r0,r1,z0,z1,z_shift
       double precision,intent(in) :: cm0,d_iso0,dz,dx
 !     ..
 !     .. Dummy Arrays ..
       double precision,dimension(r0:r1-1,z0-1:z1-1),intent(in)  :: ez_array
       double precision,dimension(r0:r1-1,z0-1:z1-1),intent(out) :: efield
       double precision,dimension(z0-1:z1-1),intent(out)     :: d_iso
 !     ..
 !     .. Local Variables ..
       integer                               :: iz
 !     ..
 !     .. Local arrays ..
       double precision,dimension(z0-1:z1-1) :: back_dens_inv,cm
 !     ..
 !-----------------------------------------------
       ! If the densities are varying...
       if (sprite_module) then
          do iz = z0-1,z1+1
             ! spr_density_at(iz) = (iz-z_shift + half) * dz
             ! back_dens_inv = ONE / spr_density_at
             back_dens_inv(iz) = ONE / ((iz-z_shift - half) * dz)
          end do
          cm    = cm0 * back_dens_inv
          d_iso = d_iso0 * back_dens_inv
       else
          back_dens_inv = ONE
          cm            = cm0
          d_iso         = d_iso0
       end if
       d_iso = d_iso / dx
       ! efield = cm * ez_array
       do iz = z0-1,z1-1
          efield(:,iz) = cm(iz) * ez_array(:,iz)
       end do
    end subroutine mat_efield_z
    subroutine mat_cdr_f_ad_r(data_array,efield,d_iso,mat_r,r0,r1,z0,z1)
 !     ..
       implicit none
 !     ..
 !     .. Parameters ..
       double precision,parameter :: ZERO = 0.0D0,HALF = 0.5D0, &
                                     ONE  = 1.0D0,THREE = 3.0D0, &
                                     verysmall = 1.0e-20
 !     ..
 !     .. Dummy Variables ..
       integer,intent(in) :: r0,r1,z0,z1
 !     ..
 !     .. Dummy Arrays ..
       double precision,dimension(z1-z0),intent(in)          :: d_iso
       double precision,dimension(r1-r0+1,z1-z0),intent(in)  :: efield
       double precision,dimension(r1-r0+4,z1-z0),intent(in)  :: data_array
       double precision,dimension(r1-r0+1,z1-z0),intent(out) :: mat_r
 !     ..
 !     .. Local Variables ..
       integer            :: iz,length
 !     ..
 !     .. Local arrays ..
       double precision,dimension(r1-r0+1,z1-z0) :: aux,psi_p
       double precision,dimension(r1-r0+3,z1-z0) :: mat_diff
 !     ..
 !-----------------------------------------------
       length = r1 - r0 + 1
       mat_diff(1:length+2,:) = data_array(2:length+3,:) - &
                                data_array(1:length+2,:)
       where (abs(mat_diff(2:length+1,:)) > verysmall)
           where (efield>=ZERO)
             ! p_min  =data_array(ir-k1,iz-k2)
             ! p      =data_array(ir,iz)
             ! p_plus =data_array(ir+k1,iz+k2)
              psi_p = mat_diff(1:length,:) / mat_diff(2:length+1,:)
          elsewhere (efield<ZERO)
             ! p       =data_array(ir,iz)
             ! p_plus  =data_array(ir+  k1,iz+  k2)
             ! p_2plus =data_array(ir+2*k1,iz+2*k2)
              psi_p = mat_diff(3:length+2,:) / mat_diff(2:length+1,:)
          end where
          where (psi_p <= ZERO)
             ! psi_p = psi_MN (psi_p)
             psi_p = ZERO
          elsewhere (psi_p >= 4)
             psi_p = ONE
          elsewhere (psi_p >= 0.4)
             psi_p = (ONE + HALF * psi_p) / THREE
          end where
       elsewhere  ! abs(mat_diff(2:length+1,:)) < verysmall
          psi_p = -ONE
       end where
       ! sigmasigma is (sigma_{i+1,j} - sigma_{i,j})*/
       ! sigmasigma = p - p_plus
       aux = psi_p * mat_diff(2:length+1,:)
       ! aux = p + psi_p * sigmasigma
       where (efield>=ZERO)
          aux = data_array(2:length+1,:) + aux
       elsewhere
          aux = data_array(3:length+2,:) - aux
       end where
       ! aux = efield * (p + psi_p * sigmasigma)
       aux = aux * efield
       do iz = 1,z1-z0
          ! mat_r = d_iso * sigmasigma
          mat_r(1:length,iz) = d_iso(iz) * mat_diff(2:length+1,iz)
       end do
       ! mat_r =  efield * (p + psi_p * sigmasigma) + d_iso * sigmasigma
       mat_r = aux - mat_r
    end subroutine mat_cdr_f_ad_r
    subroutine mat_cdr_f_ad_z(data_array,efield,d_iso,mat_z,r0,r1,z0,z1)
 !     ..
       implicit none
 !     ..
 !     .. Parameters ..
       double precision,parameter :: ZERO = 0.0D0,HALF = 0.5D0, &
                                     ONE  = 1.0D0,THREE = 3.0D0, &
                                     verysmall = 1.0e-20
 !     ..
 !     .. Dummy Variables ..
       integer,intent(in)          :: r0,r1,z0,z1
 !     ..
 !     .. Dummy Arrays ..
       double precision,dimension(z1-z0+1),intent(in)           :: d_iso
       double precision,dimension(r0:r1-1,z0-1:z1-1),intent(in) :: efield
       double precision,dimension(r1-r0,z1-z0+4),intent(in)     :: data_array
       double precision,dimension(r1-r0,z1-z0+1),intent(out)    :: mat_z
 !     ..
 !     .. Local Variables ..
       integer          :: iz,length
 !     ..
 !     .. Local Arrays ..
       double precision,dimension(r1-r0,z1-z0+1) :: aux,psi_p,pij
       double precision,dimension(r1-r0,z1-z0+3) :: mat_diff
 !-----------------------------------------------
       length = z1 - z0 + 1
       mat_diff(:,1:length+2) = data_array(:,2:length+3) - &
                                data_array(:,1:length+2)
       where (abs(mat_diff(:,2:length+1)) > verysmall)
          ! psi_p = (p - p_min) / (p_plus- p)
          where (efield>ZERO)
             ! p_min  =data_array(ir-k1,iz-k2)
             ! p      =data_array(ir,iz)
             ! p_plus =data_array(ir+k1,iz+k2)
             psi_p = mat_diff(:,1:length) / mat_diff(:,2:length+1)
          elsewhere ! efield=<ZERO
             ! p       =data_array(ir,iz)
             ! p_plus  =data_array(ir+  k1,iz+  k2)
             ! p_2plus =data_array(ir+2*k1,iz+2*k2)
             psi_p = mat_diff(:,3:length+2) / mat_diff(:,2:length+1)
          end where
          ! psi_p = psi_MN (psi_p)
          pij   = psi_p
          where ((psi_p > 0.4) .and. (psi_p < 4))
             pij =  (ONE + HALF * psi_p) / THREE
          elsewhere (psi_p >= 4)
             pij = ONE
          else where (psi_p <= ZERO)
             pij = ZERO
          end where
       elsewhere ! abs(mat_diff(:,2:length+1)) < verysmall
          pij = ONE
       end where
       ! sigmasigma is (sigma_{i+1,j} - sigma_{i,j})*/
       ! sigmasigma = p - p_plus
       aux = pij * mat_diff(:,2:length+1)
       ! aux = p + pij * sigmasigma
       where (efield>=0)
          aux = data_array(:,2:length+1) + aux
       elsewhere
          aux = data_array(:,3:length+2) - aux
       end where
       ! aux = efield * (p + pij * sigmasigma)
       aux = aux * efield
       do iz = 1,length
          ! mat_z = d_iso * sigmasigma
          mat_z(:,iz) = d_iso(iz) * mat_diff(:,iz+1)
       end do
       ! mat_z =  efield * (p + pij * sigmasigma) + d_iso * sigmasigma
       mat_z = aux - mat_z
    end subroutine mat_cdr_f_ad_z
    subroutine make_vecs_er (er_min,er,r0,r1,dr)
 !     ..
       implicit none
+!
 !     .. Parameters ..
       double precision,parameter :: HALF = 0.5D0,ONE  = 1.0D0
 !     ..
 !     .. Dummy Variables ..
       integer,intent(in)                              :: r0,r1
       double precision,intent(in)                     :: dr
 !     ..
 !     .. Dummy Arrays ..
       double precision,dimension(r0:r1-1),intent(out) :: er_min
       double precision,dimension(r0+1:r1),intent(out) :: er
 !     ..
 !     .. Local Variables ..
       integer          :: ir
       double precision :: r_inv
 !     ..
 ! .............................................................
       do ir = r0,r1-1
          r_inv = ONE / ((ir+ HALF) * dr)
          er_min(ir) = ir * r_inv
          er(ir+1)   = (ir+1) * r_inv
       end do
    end subroutine make_vecs_er

arcos_f90/src/cdr_advect_diffu_wrap.c

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@@ new file 100644 @@
 /** @file cdr_advect_diffu_wrap.c
 *   @brief Wrapper function for the cdr_advect_diffu function.
+*
 *   This function makes it possible to call the Fortran routine cdr_advect_vec
 *   a c function. The c routine is named arcos_cdr_advect_vec.
+*
 *   @author Margreet Nool - 2009
 */
 #include "stdlib.h"
 #include "stdio.h"
 #include "math.h"
 int number_cdr=0;
 /* cdr_advect: vectorized fortran90 routine; see f90/src/cdr_advect_vec.f90 */
 void cdr_advect_vec_(double *mass,double *charge,double *dens_array,
                  double *d_dens_array,double *er_array,double *ez_array,
 		 double *diffusion_coeff,double *dr,double *dz,
 		 int *sprite_module,int *r0,int *r1,int *z0,int *z1);
 /* Calls hstcrt and checks for errors. If an error occurs, prints the
  corresponding message and exists. */
 void
 arcos_cdr_advect_vec(double mass,double charge,double *dens_array,
                  double *d_dens_array,double *er_array,int er_len,
 		 double *ez_array,int ez_len,double diffusion_coeff,
                  double dr,double dz,int sprite_module,
                  int r0,int r1,int z0,int z1)
+{
   if ( number_cdr % 1000 == 0 ) {
      fprintf(stdout, "wrap:# calls cdr_advec_vec       =%d\n",number_cdr);
+  }
   cdr_advect_vec_(&mass,&charge,dens_array,d_dens_array,er_array,ez_array,
               &diffusion_coeff,&dr,&dz,&sprite_module,&r0,&r1,&z0,&z1);
   number_cdr += 1;
+}

doc/README

➞

Show inline comments

		new file 100644
		Use jannis versie van doxygen:

		/ufs/teunisse/progs/doxygen-1.8.2/bin/doxygen

doc/doxygen_config_file

➞

Show inline comments

@@ new file 100644 @@
 # Doxyfile 1.7.5
 # This file describes the settings to be used by the documentation system
 # doxygen (www.doxygen.org) for a project
+#
 # All text after a hash (#) is considered a comment and will be ignored
 # The format is:
 #       TAG = value [value, ...]
 # For lists items can also be appended using:
 #       TAG += value [value, ...]
 # Values that contain spaces should be placed between quotes (" ")
 #---------------------------------------------------------------------------
 # Project related configuration options
 #---------------------------------------------------------------------------
 # This tag specifies the encoding used for all characters in the config file
 # that follow. The default is UTF-8 which is also the encoding used for all
 # text before the first occurrence of this tag. Doxygen uses libiconv (or the
 # iconv built into libc) for the transcoding. See
 # http://www.gnu.org/software/libiconv for the list of possible encodings.
 DOXYFILE_ENCODING      = UTF-8
 # The PROJECT_NAME tag is a single word (or a sequence of words surrounded
 # by quotes) that should identify the project.
 PROJECT_NAME           = "Streamer fluid modeling - An overview of ARCoS"
 # The PRO4JECT_NUMBER tag can be used to enter a project or revision number.
 # This could be handy for archiving the generated documentation or
 # if some version control system is used.
 PROJECT_NUMBER         = 1.0
 # The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute)
 # base path where the generated documentation will be put.
 # If a relative path is entered, it will be relative to the location
 # where doxygen was started. If left blank the current directory will be used.
 OUTPUT_DIRECTORY       = documentation
 # If the CREATE_SUBDIRS tag is set to YES, then doxygen will create
 # 4096 sub-directories (in 2 levels) under the output directory of each output
 # format and will distribute the generated files over these directories.
 # Enabling this option can be useful when feeding doxygen a huge amount of
 # source files, where putting all generated files in the same directory would
 # otherwise cause performance problems for the file system.
 CREATE_SUBDIRS         = NO
 # The OUTPUT_LANGUAGE tag is used to specify the language in which all
 # documentation generated by doxygen is written. Doxygen will use this
 # information to generate all constant output in the proper language.
 # The default language is English, other supported languages are:
 # Afrikaans, Arabic, Brazilian, Catalan, Chinese, Chinese-Traditional,
 # Croatian, Czech, Danish, Dutch, Esperanto, Farsi, Finnish, French, German,
 # Greek, Hungarian, Italian, Japanese, Japanese-en (Japanese with English
 # messages), Korean, Korean-en, Lithuanian, Norwegian, Macedonian, Persian,
 # Polish, Portuguese, Romanian, Russian, Serbian, Serbian-Cyrilic, Slovak,
 # Slovene, Spanish, Swedish, Ukrainian, and Vietnamese.
 OUTPUT_LANGUAGE        = English
 # If the BRIEF_MEMBER_DESC tag is set to YES (the default) Doxygen will
 # include brief member descriptions after the members that are listed in
 # the file and class documentation (similar to JavaDoc).
 # Set to NO to disable this.
 BRIEF_MEMBER_DESC      = YES
 # If the REPEAT_BRIEF tag is set to YES (the default) Doxygen will prepend
 # the brief description of a member or function before the detailed description.
 # Note: if both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the
 # brief descriptions will be completely suppressed.
 REPEAT_BRIEF           = YES
 # This tag implements a quasi-intelligent brief description abbreviator
 # that is used to form the text in various listings. Each string
 # in this list, if found as the leading text of the brief description, will be
 # stripped from the text and the result after processing the whole list, is
 # used as the annotated text. Otherwise, the brief description is used as-is.
 # If left blank, the following values are used ("$name" is automatically
 # replaced with the name of the entity): "The $name class" "The $name widget"
 # "The $name file" "is" "provides" "specifies" "contains"
 # "represents" "a" "an" "the"
 ABBREVIATE_BRIEF       =
 # If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then
 # Doxygen will generate a detailed section even if there is only a brief
 # description.
 ALWAYS_DETAILED_SEC    = NO
 # If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all
 # inherited members of a class in the documentation of that class as if those
 # members were ordinary class members. Constructors, destructors and assignment
 # operators of the base classes will not be shown.
 INLINE_INHERITED_MEMB  = NO
 # If the FULL_PATH_NAMES tag is set to YES then Doxygen will prepend the full
 # path before files name in the file list and in the header files. If set
 # to NO the shortest path that makes the file name unique will be used.
 FULL_PATH_NAMES        = NO
 # If the FULL_PATH_NAMES tag is set to YES then the STRIP_FROM_PATH tag
 # can be used to strip a user-defined part of the path. Stripping is
 # only done if one of the specified strings matches the left-hand part of
 # the path. The tag can be used to show relative paths in the file list.
 # If left blank the directory from which doxygen is run is used as the
 # path to strip.
 STRIP_FROM_PATH        =
 # The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of
 # the path mentioned in the documentation of a class, which tells
 # the reader which header file to include in order to use a class.
 # If left blank only the name of the header file containing the class
 # definition is used. Otherwise one should specify the include paths that
 # are normally passed to the compiler using the -I flag.
 STRIP_FROM_INC_PATH    =
 # If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter
 # (but less readable) file names. This can be useful is your file systems
 # doesn't support long names like on DOS, Mac, or CD-ROM.
 SHORT_NAMES            = NO
 # If the JAVADOC_AUTOBRIEF tag is set to YES then Doxygen
 # will interpret the first line (until the first dot) of a JavaDoc-style
 # comment as the brief description. If set to NO, the JavaDoc
 # comments will behave just like regular Qt-style comments
 # (thus requiring an explicit @brief command for a brief description.)
 JAVADOC_AUTOBRIEF      = NO
 # If the QT_AUTOBRIEF tag is set to YES then Doxygen will
 # interpret the first line (until the first dot) of a Qt-style
 # comment as the brief description. If set to NO, the comments
 # will behave just like regular Qt-style comments (thus requiring
 # an explicit \brief command for a brief description.)
 QT_AUTOBRIEF           = NO
 # The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make Doxygen
 # treat a multi-line C++ special comment block (i.e. a block of //! or ///
 # comments) as a brief description. This used to be the default behaviour.
 # The new default is to treat a multi-line C++ comment block as a detailed
 # description. Set this tag to YES if you prefer the old behaviour instead.
 MULTILINE_CPP_IS_BRIEF = NO
 # If the INHERIT_DOCS tag is set to YES (the default) then an undocumented
 # member inherits the documentation from any documented member that it
 # re-implements.
 INHERIT_DOCS           = YES
 # If the SEPARATE_MEMBER_PAGES tag is set to YES, then doxygen will produce
 # a new page for each member. If set to NO, the documentation of a member will
 # be part of the file/class/namespace that contains it.
 SEPARATE_MEMBER_PAGES  = NO
 # The TAB_SIZE tag can be used to set the number of spaces in a tab.
 # Doxygen uses this value to replace tabs by spaces in code fragments.
 TAB_SIZE               = 3
 # This tag can be used to specify a number of aliases that acts
 # as commands in the documentation. An alias has the form "name=value".
 # For example adding "sideeffect=\par Side Effects:\n" will allow you to
 # put the command \sideeffect (or @sideeffect) in the documentation, which
 # will result in a user-defined paragraph with heading "Side Effects:".
 # You can put \n's in the value part of an alias to insert newlines.
 ALIASES                =
 # Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C
 # sources only. Doxygen will then generate output that is more tailored for C.
 # For instance, some of the names that are used will be different. The list
 # of all members will be omitted, etc.
 OPTIMIZE_OUTPUT_FOR_C  = NO
 # Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java
 # sources only. Doxygen will then generate output that is more tailored for
 # Java. For instance, namespaces will be presented as packages, qualified
 # scopes will look different, etc.
 OPTIMIZE_OUTPUT_JAVA   = NO
 # Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran
 # sources only. Doxygen will then generate output that is more tailored for
 # Fortran.
 OPTIMIZE_FOR_FORTRAN   = YES
 # Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL
 # sources. Doxygen will then generate output that is tailored for
 # VHDL.
 OPTIMIZE_OUTPUT_VHDL   = NO
 # Doxygen selects the parser to use depending on the extension of the files it
 # parses. With this tag you can assign which parser to use for a given extension.
 # Doxygen has a built-in mapping, but you can override or extend it using this
 # tag. The format is ext=language, where ext is a file extension, and language
 # is one of the parsers supported by doxygen: IDL, Java, Javascript, CSharp, C,
 # C++, D, PHP, Objective-C, Python, Fortran, VHDL, C, C++. For instance to make
 # doxygen treat .inc files as Fortran files (default is PHP), and .f files as C
 # (default is Fortran), use: inc=Fortran f=C. Note that for custom extensions
 # you also need to set FILE_PATTERNS otherwise the files are not read by doxygen.
 EXTENSION_MAPPING      = *.F
 # If you use STL classes (i.e. std::string, std::vector, etc.) but do not want
 # to include (a tag file for) the STL sources as input, then you should
 # set this tag to YES in order to let doxygen match functions declarations and
 # definitions whose arguments contain STL classes (e.g. func(std::string); v.s.
 # func(std::string) {}). This also make the inheritance and collaboration
 # diagrams that involve STL classes more complete and accurate.
 #BUILTIN_STL_SUPPORT    = NO
 BUILTIN_STL_SUPPORT    = YES
 # If you use Microsoft's C++/CLI language, you should set this option to YES to
 # enable parsing support.
 CPP_CLI_SUPPORT        = NO
 # Set the SIP_SUPPORT tag to YES if your project consists of sip sources only.
 # Doxygen will parse them like normal C++ but will assume all classes use public
 # instead of private inheritance when no explicit protection keyword is present.
 SIP_SUPPORT            = NO
 # For Microsoft's IDL there are propget and propput attributes to indicate getter
 # and setter methods for a property. Setting this option to YES (the default)
 # will make doxygen to replace the get and set methods by a property in the
 # documentation. This will only work if the methods are indeed getting or
 # setting a simple type. If this is not the case, or you want to show the
 # methods anyway, you should set this option to NO.
 IDL_PROPERTY_SUPPORT   = YES
 # If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC
 # tag is set to YES, then doxygen will reuse the documentation of the first
 # member in the group (if any) for the other members of the group. By default
 # all members of a group must be documented explicitly.
 DISTRIBUTE_GROUP_DOC   = NO
 # Set the SUBGROUPING tag to YES (the default) to allow class member groups of
 # the same type (for instance a group of public functions) to be put as a
 # subgroup of that type (e.g. under the Public Functions section). Set it to
 # NO to prevent subgrouping. Alternatively, this can be done per class using
 # the \nosubgrouping command.
 SUBGROUPING            = YES
 # When TYPEDEF_HIDES_STRUCT is enabled, a typedef of a struct, union, or enum
 # is documented as struct, union, or enum with the name of the typedef. So
 # typedef struct TypeS {} TypeT, will appear in the documentation as a struct
 # with name TypeT. When disabled the typedef will appear as a member of a file,
 # namespace, or class. And the struct will be named TypeS. This can typically
 # be useful for C code in case the coding convention dictates that all compound
 # types are typedef'ed and only the typedef is referenced, never the tag name.
 TYPEDEF_HIDES_STRUCT   = NO
 # The SYMBOL_CACHE_SIZE determines the size of the internal cache use to
 # determine which symbols to keep in memory and which to flush to disk.
 # When the cache is full, less often used symbols will be written to disk.
 # For small to medium size projects (<1000 input files) the default value is
 # probably good enough. For larger projects a too small cache size can cause
 # doxygen to be busy swapping symbols to and from disk most of the time
 # causing a significant performance penality.
 # If the system has enough physical memory increasing the cache will improve the
 # performance by keeping more symbols in memory. Note that the value works on
 # a logarithmic scale so increasing the size by one will rougly double the
 # memory usage. The cache size is given by this formula:
 # 2^(16+SYMBOL_CACHE_SIZE). The valid range is 0..9, the default is 0,
 # corresponding to a cache size of 2^16 = 65536 symbols
 SYMBOL_CACHE_SIZE      = 0
 #---------------------------------------------------------------------------
 # Build related configuration options
 #---------------------------------------------------------------------------
 # If the EXTRACT_ALL tag is set to YES doxygen will assume all entities in
 # documentation are documented, even if no documentation was available.
 # Private class members and static file members will be hidden unless
 # the EXTRACT_PRIVATE and EXTRACT_STATIC tags are set to YES
 EXTRACT_ALL            = YES
 # If the EXTRACT_PRIVATE tag is set to YES all private members of a class
 # will be included in the documentation.
 EXTRACT_PRIVATE        = YES
 # If the EXTRACT_STATIC tag is set to YES all static members of a file
 # will be included in the documentation.
 EXTRACT_STATIC         = YES
 # If the EXTRACT_LOCAL_CLASSES tag is set to YES classes (and structs)
 # defined locally in source files will be included in the documentation.
 # If set to NO only classes defined in header files are included.
 EXTRACT_LOCAL_CLASSES  = YES
 # This flag is only useful for Objective-C code. When set to YES local
 # methods, which are defined in the implementation section but not in
 # the interface are included in the documentation.
 # If set to NO (the default) only methods in the interface are included.
 EXTRACT_LOCAL_METHODS  = YES
 # If this flag is set to YES, the members of anonymous namespaces will be
 # extracted and appear in the documentation as a namespace called
 # 'anonymous_namespace{file}', where file will be replaced with the base
 # name of the file that contains the anonymous namespace. By default
 # anonymous namespace are hidden.
 EXTRACT_ANON_NSPACES   = NO
 # If the HIDE_UNDOC_MEMBERS tag is set to YES, Doxygen will hide all
 # undocumented members of documented classes, files or namespaces.
 # If set to NO (the default) these members will be included in the
 # various overviews, but no documentation section is generated.
 # This option has no effect if EXTRACT_ALL is enabled.
 HIDE_UNDOC_MEMBERS     = NO
 # If the HIDE_UNDOC_CLASSES tag is set to YES, Doxygen will hide all
 # undocumented classes that are normally visible in the class hierarchy.
 # If set to NO (the default) these classes will be included in the various
 # overviews. This option has no effect if EXTRACT_ALL is enabled.
 HIDE_UNDOC_CLASSES     = NO
 # If the HIDE_FRIEND_COMPOUNDS tag is set to YES, Doxygen will hide all
 # friend (class|struct|union) declarations.
 # If set to NO (the default) these declarations will be included in the
 # documentation.
 HIDE_FRIEND_COMPOUNDS  = NO
 # If the HIDE_IN_BODY_DOCS tag is set to YES, Doxygen will hide any
 # documentation blocks found inside the body of a function.
 # If set to NO (the default) these blocks will be appended to the
 # function's detailed documentation block.
 HIDE_IN_BODY_DOCS      = NO
 # The INTERNAL_DOCS tag determines if documentation
 # that is typed after a \internal command is included. If the tag is set
 # to NO (the default) then the documentation will be excluded.
 # Set it to YES to include the internal documentation.
 INTERNAL_DOCS          = NO
 # If the CASE_SENSE_NAMES tag is set to NO then Doxygen will only generate
 # file names in lower-case letters. If set to YES upper-case letters are also
 # allowed. This is useful if you have classes or files whose names only differ
 # in case and if your file system supports case sensitive file names. Windows
 # and Mac users are advised to set this option to NO.
 CASE_SENSE_NAMES       =  YES
 # If the HIDE_SCOPE_NAMES tag is set to NO (the default) then Doxygen
 # will show members with their full class and namespace scopes in the
 # documentation. If set to YES the scope will be hidden.
 HIDE_SCOPE_NAMES       = NO
 # If the SHOW_INCLUDE_FILES tag is set to YES (the default) then Doxygen
 # will put a list of the files that are included by a file in the documentation
 # of that file.
 SHOW_INCLUDE_FILES     = YES
 # If the FORCE_LOCAL_INCLUDES tag is set to YES then Doxygen
 # will list include files with double quotes in the documentation
 # rather than with sharp brackets.
 FORCE_LOCAL_INCLUDES   = NO
 # If the INLINE_INFO tag is set to YES (the default) then a tag [inline]
 # is inserted in the documentation for inline members.
 INLINE_INFO            = YES
 # If the SORT_MEMBER_DOCS tag is set to YES (the default) then doxygen
 # will sort the (detailed) documentation of file and class members
 # alphabetically by member name. If set to NO the members will appear in
 # declaration order.
 #SORT_MEMBER_DOCS       = YES
 SORT_MEMBER_DOCS       = NO
 # If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the
 # brief documentation of file, namespace and class members alphabetically
 # by member name. If set to NO (the default) the members will appear in
 # declaration order.
 SORT_BRIEF_DOCS        = NO
 # If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen
 # will sort the (brief and detailed) documentation of class members so that
 # constructors and destructors are listed first. If set to NO (the default)
 # the constructors will appear in the respective orders defined by
 # SORT_MEMBER_DOCS and SORT_BRIEF_DOCS.
 # This tag will be ignored for brief docs if SORT_BRIEF_DOCS is set to NO
 # and ignored for detailed docs if SORT_MEMBER_DOCS is set to NO.
 SORT_MEMBERS_CTORS_1ST = NO
 # If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the
 # hierarchy of group names into alphabetical order. If set to NO (the default)
 # the group names will appear in their defined order.
 SORT_GROUP_NAMES       = NO
 # If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be
 # sorted by fully-qualified names, including namespaces. If set to
 # NO (the default), the class list will be sorted only by class name,
 # not including the namespace part.
 # Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES.
 # Note: This option applies only to the class list, not to the
 # alphabetical list.
 SORT_BY_SCOPE_NAME     = NO
 # The GENERATE_TODOLIST tag can be used to enable (YES) or
 # disable (NO) the todo list. This list is created by putting \todo
 # commands in the documentation.
 GENERATE_TODOLIST      = YES
 # The GENERATE_TESTLIST tag can be used to enable (YES) or
 # disable (NO) the test list. This list is created by putting \test
 # commands in the documentation.
 GENERATE_TESTLIST      = YES
 # The GENERATE_BUGLIST tag can be used to enable (YES) or
 # disable (NO) the bug list. This list is created by putting \bug
 # commands in the documentation.
 GENERATE_BUGLIST       = YES
 # The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or
 # disable (NO) the deprecated list. This list is created by putting
 # \deprecated commands in the documentation.
 GENERATE_DEPRECATEDLIST= YES
 # The ENABLED_SECTIONS tag can be used to enable conditional
 # documentation sections, marked by \if sectionname ... \endif.
 ENABLED_SECTIONS       =
 # The MAX_INITIALIZER_LINES tag determines the maximum number of lines
 # the initial value of a variable or define consists of for it to appear in
 # the documentation. If the initializer consists of more lines than specified
 # here it will be hidden. Use a value of 0 to hide initializers completely.
 # The appearance of the initializer of individual variables and defines in the
 # documentation can be controlled using \showinitializer or \hideinitializer
 # command in the documentation regardless of this setting.
 MAX_INITIALIZER_LINES  = 30
 # Set the SHOW_USED_FILES tag to NO to disable the list of files generated
 # at the bottom of the documentation of classes and structs. If set to YES the
 # list will mention the files that were used to generate the documentation.
 SHOW_USED_FILES        = YES
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the
 # Folder Tree View (if specified). The default is YES.
 SHOW_FILES             = YES
 # Set the SHOW_NAMESPACES tag to NO to disable the generation of the
 # Namespaces page.
 # This will remove the Namespaces entry from the Quick Index
 # and from the Folder Tree View (if specified). The default is YES.
 SHOW_NAMESPACES        = YES
 # The FILE_VERSION_FILTER tag can be used to specify a program or script that
 # doxygen should invoke to get the current version for each file (typically from
 # the version control system). Doxygen will invoke the program by executing (via
 # popen()) the command <command> <input-file>, where <command> is the value of
 # the FILE_VERSION_FILTER tag, and <input-file> is the name of an input file
 # provided by doxygen. Whatever the program writes to standard output
 # is used as the file version. See the manual for examples.
 FILE_VERSION_FILTER    =
 # The LAYOUT_FILE tag can be used to specify a layout file which will be parsed
 # by doxygen. The layout file controls the global structure of the generated
 # output files in an output format independent way. The create the layout file
 # that represents doxygen's defaults, run doxygen with the -l option.
 # You can optionally specify a file name after the option, if omitted
 # DoxygenLayout.xml will be used as the name of the layout file.
 LAYOUT_FILE            =
 #---------------------------------------------------------------------------
 # configuration options related to warning and progress messages
 #---------------------------------------------------------------------------
 # The QUIET tag can be used to turn on/off the messages that are generated
 # by doxygen. Possible values are YES and NO. If left blank NO is used.
 QUIET                  = NO
 # The WARNINGS tag can be used to turn on/off the warning messages that are
 # generated by doxygen. Possible values are YES and NO. If left blank
 # NO is used.
 WARNINGS               = YES
 # If WARN_IF_UNDOCUMENTED is set to YES, then doxygen will generate warnings
 # for undocumented members. If EXTRACT_ALL is set to YES then this flag will
 # automatically be disabled.
 WARN_IF_UNDOCUMENTED   = YES
 # If WARN_IF_DOC_ERROR is set to YES, doxygen will generate warnings for
 # potential errors in the documentation, such as not documenting some
 # parameters in a documented function, or documenting parameters that
 # don't exist or using markup commands wrongly.
 WARN_IF_DOC_ERROR      = YES
 # This WARN_NO_PARAMDOC option can be abled to get warnings for
 # functions that are documented, but have no documentation for their parameters
 # or return value. If set to NO (the default) doxygen will only warn about
 # wrong or incomplete parameter documentation, but not about the absence of
 # documentation.
 WARN_NO_PARAMDOC       = NO
 # The WARN_FORMAT tag determines the format of the warning messages that
 # doxygen can produce. The string should contain the $file, $line, and $text
 # tags, which will be replaced by the file and line number from which the
 # warning originated and the warning text. Optionally the format may contain
 # $version, which will be replaced by the version of the file (if it could
 # be obtained via FILE_VERSION_FILTER)
 WARN_FORMAT            = "$file:$line: $text"
 # The WARN_LOGFILE tag can be used to specify a file to which warning
 # and error messages should be written. If left blank the output is written
 # to stderr.
 WARN_LOGFILE           =
 #---------------------------------------------------------------------------
 # configuration options related to the input files
 #---------------------------------------------------------------------------
 # The INPUT tag can be used to specify the files and/or directories that contain
 # documented source files. You may enter file names like "myfile.cpp" or
 # directories like "/usr/src/myproject". Separate the files or directories
 # with spaces.
 INPUT                  =  ../src ../include ../input markdown ../arcos_f90/src
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding, which is
 # also the default input encoding. Doxygen uses libiconv (or the iconv built
 # into libc) for the transcoding. See http://www.gnu.org/software/libiconv for
 # the list of possible encodings.
 INPUT_ENCODING         = UTF-8
 # If the value of the INPUT tag contains directories, you can use the
 # FILE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
 # and *.h) to filter out the source-files in the directories. If left
 # blank the following patterns are tested:
 # *.c *.cc *.cxx *.cpp *.c++ *.java *.ii *.ixx *.ipp *.i++ *.inl *.h *.hh *.hxx
 # *.hpp *.h++ *.idl *.odl *.cs *.php *.php3 *.inc *.m *.mm *.py *.f90
 FILE_PATTERNS          = *.c *.h MA*.md *.eps *.bib *.cfg *f90
 #FILE_PATTERNS          = MA*.md *.eps *.bib
 # The RECURSIVE tag can be used to turn specify whether or not subdirectories
 # should be searched for input files as well. Possible values are YES and NO.
 # If left blank NO is used.
 RECURSIVE              = NO
 # The EXCLUDE tag can be used to specify files and/or directories that should
 # excluded from the INPUT source files. This way you can easily exclude a
 # subdirectory from a directory tree whose root is specified with the INPUT tag.
 EXCLUDE                =
 # The EXCLUDE_SYMLINKS tag can be used select whether or not files or
 # directories that are symbolic links (a Unix filesystem feature) are excluded
 # from the input.
 EXCLUDE_SYMLINKS       = NO
 # If the value of the INPUT tag contains directories, you can use the
 # EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude
 # certain files from those directories. Note that the wildcards are matched
 # against the file with absolute path, so to exclude all test directories
 # for example use the pattern */test/*
 EXCLUDE_PATTERNS       = *.f
 # The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names
 # (namespaces, classes, functions, etc.) that should be excluded from the
 # output. The symbol name can be a fully qualified name, a word, or if the
 # wildcard * is used, a substring. Examples: ANamespace, AClass,
 # AClass::ANamespace, ANamespace::*Test
 EXCLUDE_SYMBOLS        =
 # The EXAMPLE_PATH tag can be used to specify one or more files or
 # directories that contain example code fragments that are included (see
 # the \include command).
 EXAMPLE_PATH           =
 # If the value of the EXAMPLE_PATH tag contains directories, you can use the
 # EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp
 # and *.h) to filter out the source-files in the directories. If left
 # blank all files are included.
 EXAMPLE_PATTERNS       =
 # If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be
 # searched for input files to be used with the \include or \dontinclude
 # commands irrespective of the value of the RECURSIVE tag.
 # Possible values are YES and NO. If left blank NO is used.
 EXAMPLE_RECURSIVE      = NO
 # The IMAGE_PATH tag can be used to specify one or more files or
 # directories that contain image that are included in the documentation (see
 # the \image command).
 IMAGE_PATH             = figures
 # The INPUT_FILTER tag can be used to specify a program that doxygen should
 # invoke to filter for each input file. Doxygen will invoke the filter program
 # by executing (via popen()) the command <filter> <input-file>, where <filter>
 # is the value of the INPUT_FILTER tag, and <input-file> is the name of an
 # input file. Doxygen will then use the output that the filter program writes
 # to standard output.
 # If FILTER_PATTERNS is specified, this tag will be
 # ignored.
 INPUT_FILTER           =
 # The FILTER_PATTERNS tag can be used to specify filters on a per file pattern
 # basis.
 # Doxygen will compare the file name with each pattern and apply the
 # filter if there is a match.
 # The filters are a list of the form:
 # pattern=filter (like *.cpp=my_cpp_filter). See INPUT_FILTER for further
 # info on how filters are used. If FILTER_PATTERNS is empty, INPUT_FILTER
 # is applied to all files.
 FILTER_PATTERNS        =
 # If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using
 # INPUT_FILTER) will be used to filter the input files when producing source
 # files to browse (i.e. when SOURCE_BROWSER is set to YES).
 FILTER_SOURCE_FILES    = NO
 #---------------------------------------------------------------------------
 # configuration options related to source browsing
 #---------------------------------------------------------------------------
 # If the SOURCE_BROWSER tag is set to YES then a list of source files will
 # be generated. Documented entities will be cross-referenced with these sources.
 # Note: To get rid of all source code in the generated output, make sure also
 # VERBATIM_HEADERS is set to NO.
 #SOURCE_BROWSER         = NO
 SOURCE_BROWSER         = YES
 # Setting the INLINE_SOURCES tag to YES will include the body
 # of functions and classes directly in the documentation.
 INLINE_SOURCES         = NO
 # Setting the STRIP_CODE_COMMENTS tag to YES (the default) will instruct
 # doxygen to hide any special comment blocks from generated source code
 # fragments. Normal C and C++ comments will always remain visible.
 STRIP_CODE_COMMENTS    = YES
 # If the REFERENCED_BY_RELATION tag is set to YES
 # then for each documented function all documented
 # functions referencing it will be listed.
 REFERENCED_BY_RELATION = NO
 # If the REFERENCES_RELATION tag is set to YES
 # then for each documented function all documented entities
 # called/used by that function will be listed.
 REFERENCES_RELATION    = NO
 # If the REFERENCES_LINK_SOURCE tag is set to YES (the default)
 # and SOURCE_BROWSER tag is set to YES, then the hyperlinks from
 # functions in REFERENCES_RELATION and REFERENCED_BY_RELATION lists will
 # link to the source code.
 # Otherwise they will link to the documentation.
 REFERENCES_LINK_SOURCE = YES
 # If the USE_HTAGS tag is set to YES then the references to source code
 # will point to the HTML generated by the htags(1) tool instead of doxygen
 # built-in source browser. The htags tool is part of GNU's global source
 # tagging system (see http://www.gnu.org/software/global/global.html). You
 # will need version 4.8.6 or higher.
 USE_HTAGS              = NO
 # If the VERBATIM_HEADERS tag is set to YES (the default) then Doxygen
 # will generate a verbatim copy of the header file for each class for
 # which an include is specified. Set to NO to disable this.
 VERBATIM_HEADERS       = YES
 #---------------------------------------------------------------------------
 # configuration options related to the alphabetical class index
 #---------------------------------------------------------------------------
 # If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index
 # of all compounds will be generated. Enable this if the project
 # contains a lot of classes, structs, unions or interfaces.
 ALPHABETICAL_INDEX     = NO
 # If the alphabetical index is enabled (see ALPHABETICAL_INDEX) then
 # the COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns
 # in which this list will be split (can be a number in the range [1..20])
 COLS_IN_ALPHA_INDEX    = 5
 # In case all classes in a project start with a common prefix, all
 # classes will be put under the same header in the alphabetical index.
 # The IGNORE_PREFIX tag can be used to specify one or more prefixes that
 # should be ignored while generating the index headers.
 IGNORE_PREFIX          =
 #---------------------------------------------------------------------------
 # configuration options related to the HTML output
 #---------------------------------------------------------------------------
 # If the GENERATE_HTML tag is set to YES (the default) Doxygen will
 # generate HTML output.
 GENERATE_HTML          = YES
 # The HTML_OUTPUT tag is used to specify where the HTML docs will be put.
 # If a relative path is entered the value of OUTPUT_DIRECTORY will be
 # put in front of it. If left blank `html' will be used as the default path.
 HTML_OUTPUT            = html
 # The HTML_FILE_EXTENSION tag can be used to specify the file extension for
 # each generated HTML page (for example: .htm,.php,.asp). If it is left blank
 # doxygen will generate files with .html extension.
 HTML_FILE_EXTENSION    = .html
 # The HTML_HEADER tag can be used to specify a personal HTML header for
 # each generated HTML page. If it is left blank doxygen will generate a
 # standard header.
 HTML_HEADER            =
 # The HTML_FOOTER tag can be used to specify a personal HTML footer for
 # each generated HTML page. If it is left blank doxygen will generate a
 # standard footer.
 HTML_FOOTER            =
 # The HTML_STYLESHEET tag can be used to specify a user-defined cascading
 # style sheet that is used by each HTML page. It can be used to
 # fine-tune the look of the HTML output. If the tag is left blank doxygen
 # will generate a default style sheet. Note that doxygen will try to copy
 # the style sheet file to the HTML output directory, so don't put your own
 # stylesheet in the HTML output directory as well, or it will be erased!
 HTML_STYLESHEET        =
 # The HTML_COLORSTYLE_HUE tag controls the color of the HTML output.
 # Doxygen will adjust the colors in the stylesheet and background images
 # according to this color. Hue is specified as an angle on a colorwheel,
 # see http://en.wikipedia.org/wiki/Hue for more information.
 # For instance the value 0 represents red, 60 is yellow, 120 is green,
 # 180 is cyan, 240 is blue, 300 purple, and 360 is red again.
 # The allowed range is 0 to 359.
 HTML_COLORSTYLE_HUE    = 220
 # The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of
 # the colors in the HTML output. For a value of 0 the output will use
 # grayscales only. A value of 255 will produce the most vivid colors.
 HTML_COLORSTYLE_SAT    = 100
 # The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to
 # the luminance component of the colors in the HTML output. Values below
 # 100 gradually make the output lighter, whereas values above 100 make
 # the output darker. The value divided by 100 is the actual gamma applied,
 # so 80 represents a gamma of 0.8, The value 220 represents a gamma of 2.2,
 # and 100 does not change the gamma.
 HTML_COLORSTYLE_GAMMA  = 80
 # If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML
 # page will contain the date and time when the page was generated. Setting
 # this to NO can help when comparing the output of multiple runs.
 HTML_TIMESTAMP         = YES
 # If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML
 # documentation will contain sections that can be hidden and shown after the
 # page has loaded. For this to work a browser that supports
 # JavaScript and DHTML is required (for instance Mozilla 1.0+, Firefox
 # Netscape 6.0+, Internet explorer 5.0+, Konqueror, or Safari).
 HTML_DYNAMIC_SECTIONS  = NO
 # If the GENERATE_DOCSET tag is set to YES, additional index files
 # will be generated that can be used as input for Apple's Xcode 3
 # integrated development environment, introduced with OSX 10.5 (Leopard).
 # To create a documentation set, doxygen will generate a Makefile in the
 # HTML output directory. Running make will produce the docset in that
 # directory and running "make install" will install the docset in
 # ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find
 # it at startup.
 # See http://developer.apple.com/tools/creatingdocsetswithdoxygen.html
 # for more information.
 GENERATE_DOCSET        = NO
 # When GENERATE_DOCSET tag is set to YES, this tag determines the name of the
 # feed. A documentation feed provides an umbrella under which multiple
 # documentation sets from a single provider (such as a company or product suite)
 # can be grouped.
 DOCSET_FEEDNAME        = "Doxygen generated docs 1.7.4"
 # When GENERATE_DOCSET tag is set to YES, this tag specifies a string that
 # should uniquely identify the documentation set bundle. This should be a
 # reverse domain-name style string, e.g. com.mycompany.MyDocSet. Doxygen
 # will append .docset to the name.
 DOCSET_BUNDLE_ID       = org.doxygen.Project
 # When GENERATE_PUBLISHER_ID tag specifies a string that should uniquely identify
 # the documentation publisher. This should be a reverse domain-name style
 # string, e.g. com.mycompany.MyDocSet.documentation.
 DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
 # The GENERATE_PUBLISHER_NAME tag identifies the documentation publisher.
 DOCSET_PUBLISHER_NAME  = Publisher
 # If the GENERATE_HTMLHELP tag is set to YES, additional index files
 # will be generated that can be used as input for tools like the
 # Microsoft HTML help workshop to generate a compiled HTML help file (.chm)
 # of the generated HTML documentation.
 GENERATE_HTMLHELP      = NO
 # If the GENERATE_HTMLHELP tag is set to YES, the CHM_FILE tag can
 # be used to specify the file name of the resulting .chm file. You
 # can add a path in front of the file if the result should not be
 # written to the html output directory.
 CHM_FILE               =
 # If the GENERATE_HTMLHELP tag is set to YES, the HHC_LOCATION tag can
 # be used to specify the location (absolute path including file name) of
 # the HTML help compiler (hhc.exe). If non-empty doxygen will try to run
 # the HTML help compiler on the generated index.hhp.
 HHC_LOCATION           =
 # If the GENERATE_HTMLHELP tag is set to YES, the GENERATE_CHI flag
 # controls if a separate .chi index file is generated (YES) or that
 # it should be included in the master .chm file (NO).
 GENERATE_CHI           = NO
 # If the GENERATE_HTMLHELP tag is set to YES, the CHM_INDEX_ENCODING
 # is used to encode HtmlHelp index (hhk), content (hhc) and project file
 # content.
 CHM_INDEX_ENCODING     =
 # If the GENERATE_HTMLHELP tag is set to YES, the BINARY_TOC flag
 # controls whether a binary table of contents is generated (YES) or a
 # normal table of contents (NO) in the .chm file.
 BINARY_TOC             = NO
 # The TOC_EXPAND flag can be set to YES to add extra items for group members
 # to the contents of the HTML help documentation and to the tree view.
 TOC_EXPAND             = NO
 # If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and
 # QHP_VIRTUAL_FOLDER are set, an additional index file will be generated
 # that can be used as input for Qt's qhelpgenerator to generate a
 # Qt Compressed Help (.qch) of the generated HTML documentation.
 GENERATE_QHP           = NO
 # If the QHG_LOCATION tag is specified, the QCH_FILE tag can
 # be used to specify the file name of the resulting .qch file.
 # The path specified is relative to the HTML output folder.
 QCH_FILE               =
 # The QHP_NAMESPACE tag specifies the namespace to use when generating
 # Qt Help Project output. For more information please see
 # http://doc.trolltech.com/qthelpproject.html#namespace
 QHP_NAMESPACE          = org.doxygen.Project
 # The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating
 # Qt Help Project output. For more information please see
 # http://doc.trolltech.com/qthelpproject.html#virtual-folders
 QHP_VIRTUAL_FOLDER     = doc
 # If QHP_CUST_FILTER_NAME is set, it specifies the name of a custom filter to
 # add. For more information please see
 # http://doc.trolltech.com/qthelpproject.html#custom-filters
 QHP_CUST_FILTER_NAME   =
 # The QHP_CUST_FILT_ATTRS tag specifies the list of the attributes of the
 # custom filter to add. For more information please see
 # <a href="http://doc.trolltech.com/qthelpproject.html#custom-filters">
 # Qt Help Project / Custom Filters</a>.
 QHP_CUST_FILTER_ATTRS  =
 # The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this
 # project's
 # filter section matches.
 # <a href="http://doc.trolltech.com/qthelpproject.html#filter-attributes">
 # Qt Help Project / Filter Attributes</a>.
 QHP_SECT_FILTER_ATTRS  =
 # If the GENERATE_QHP tag is set to YES, the QHG_LOCATION tag can
 # be used to specify the location of Qt's qhelpgenerator.
 # If non-empty doxygen will try to run qhelpgenerator on the generated
 # .qhp file.
 QHG_LOCATION           =
 # If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files
 #  will be generated, which together with the HTML files, form an Eclipse help
 # plugin. To install this plugin and make it available under the help contents
 # menu in Eclipse, the contents of the directory containing the HTML and XML
 # files needs to be copied into the plugins directory of eclipse. The name of
 # the directory within the plugins directory should be the same as
 # the ECLIPSE_DOC_ID value. After copying Eclipse needs to be restarted before
 # the help appears.
 GENERATE_ECLIPSEHELP   = NO
 # A unique identifier for the eclipse help plugin. When installing the plugin
 # the directory name containing the HTML and XML files should also have
 # this name.
 ECLIPSE_DOC_ID         = org.doxygen.Project
 # The DISABLE_INDEX tag can be used to turn on/off the condensed index at
 # top of each HTML page. The value NO (the default) enables the index and
 # the value YES disables it.
 DISABLE_INDEX          = NO
 # This tag can be used to set the number of enum values (range [1..20])
 # that doxygen will group on one line in the generated HTML documentation.
 ENUM_VALUES_PER_LINE   = 4
 # The GENERATE_TREEVIEW tag is used to specify whether a tree-like index
 # structure should be generated to display hierarchical information.
 # If the tag value is set to YES, a side panel will be generated
 # containing a tree-like index structure (just like the one that
 # is generated for HTML Help). For this to work a browser that supports
 # JavaScript, DHTML, CSS and frames is required (i.e. any modern browser).
 # Windows users are probably better off using the HTML help feature.
 GENERATE_TREEVIEW      = NO
 # If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be
 # used to set the initial width (in pixels) of the frame in which the tree
 # is shown.
 TREEVIEW_WIDTH         = 250
 # When the EXT_LINKS_IN_WINDOW option is set to YES doxygen will open
 # links to external symbols imported via tag files in a separate window.
 EXT_LINKS_IN_WINDOW    = NO
 # Use this tag to change the font size of Latex formulas included
 # as images in the HTML documentation. The default is 10. Note that
 # when you change the font size after a successful doxygen run you need
 # to manually remove any form_*.png images from the HTML output directory
 # to force them to be regenerated.
 FORMULA_FONTSIZE       = 10
 # Use the FORMULA_TRANPARENT tag to determine whether or not the images
 # generated for formulas are transparent PNGs. Transparent PNGs are
 # not supported properly for IE 6.0, but are supported on all modern browsers.
 # Note that when changing this option you need to delete any form_*.png files
 # in the HTML output before the changes have effect.
 FORMULA_TRANSPARENT    = YES
 # When the SEARCHENGINE tag is enabled doxygen will generate a search box
 # for the HTML output. The underlying search engine uses javascript
 # and DHTML and should work on any modern browser. Note that when using
 # HTML help (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets
 # (GENERATE_DOCSET) there is already a search function so this one should
 # typically be disabled. For large projects the javascript based search engine
 # can be slow, then enabling SERVER_BASED_SEARCH may provide a better solution.
 SEARCHENGINE           = YES
 # When the SERVER_BASED_SEARCH tag is enabled the search engine will be
 # implemented using a PHP enabled web server instead of at the web client
 # using Javascript. Doxygen will generate the search PHP script and index
 # file to put on the web server. The advantage of the server
 # based approach is that it scales better to large projects and allows
 # full text search. The disadvances is that it is more difficult to setup
 # and does not have live searching capabilities.
 SERVER_BASED_SEARCH    = NO
 #---------------------------------------------------------------------------
 # configuration options related to the LaTeX output
 #---------------------------------------------------------------------------
 # If the GENERATE_LATEX tag is set to YES (the default) Doxygen will
 # generate Latex output.
 #GENERATE_LATEX         = YES
 GENERATE_LATEX         = NO
 # The LATEX_OUTPUT tag is used to specify where the LaTeX docs will be put.
 # If a relative path is entered the value of OUTPUT_DIRECTORY will be
 # put in front of it. If left blank `latex' will be used as the default path.
 LATEX_OUTPUT           = latex
 # The LATEX_CMD_NAME tag can be used to specify the LaTeX command name to be
 # invoked. If left blank `latex' will be used as the default command name.
 # Note that when enabling USE_PDFLATEX this option is only used for
 # generating bitmaps for formulas in the HTML output, but not in the
 # Makefile that is written to the output directory.
 LATEX_CMD_NAME         = latex
 # The MAKEINDEX_CMD_NAME tag can be used to specify the command name to
 # generate index for LaTeX. If left blank `makeindex' will be used as the
 # default command name.
 MAKEINDEX_CMD_NAME     = makeindex
 # If the COMPACT_LATEX tag is set to YES Doxygen generates more compact
 # LaTeX documents. This may be useful for small projects and may help to
 # save some trees in general.
 COMPACT_LATEX          = NO
 # The PAPER_TYPE tag can be used to set the paper type that is used
 # by the printer. Possible values are: a4, a4wide, letter, legal and
 # executive. If left blank a4wide will be used.
 PAPER_TYPE             = a4wide
 # The EXTRA_PACKAGES tag can be to specify one or more names of LaTeX
 # packages that should be included in the LaTeX output.
 EXTRA_PACKAGES         =
 # The LATEX_HEADER tag can be used to specify a personal LaTeX header for
 # the generated latex document. The header should contain everything until
 # the first chapter. If it is left blank doxygen will generate a
 # standard header. Notice: only use this tag if you know what you are doing!
 LATEX_HEADER           =
 # If the PDF_HYPERLINKS tag is set to YES, the LaTeX that is generated
 # is prepared for conversion to pdf (using ps2pdf). The pdf file will
 # contain links (just like the HTML output) instead of page references
 # This makes the output suitable for online browsing using a pdf viewer.
 PDF_HYPERLINKS         = YES
 # If the USE_PDFLATEX tag is set to YES, pdflatex will be used instead of
 # plain latex in the generated Makefile. Set this option to YES to get a
 # higher quality PDF documentation.
 USE_PDFLATEX           = YES
 # If the LATEX_BATCHMODE tag is set to YES, doxygen will add the \\batchmode.
 # command to the generated LaTeX files. This will instruct LaTeX to keep
 # running if errors occur, instead of asking the user for help.
 # This option is also used when generating formulas in HTML.
 LATEX_BATCHMODE        = NO
 # If LATEX_HIDE_INDICES is set to YES then doxygen will not
 # include the index chapters (such as File Index, Compound Index, etc.)
 # in the output.
 LATEX_HIDE_INDICES     = NO
 # If LATEX_SOURCE_CODE is set to YES then doxygen will include
 # source code with syntax highlighting in the LaTeX output.
 # Note that which sources are shown also depends on other settings
 # such as SOURCE_BROWSER.
 LATEX_SOURCE_CODE      = NO
 #---------------------------------------------------------------------------
 # configuration options related to the RTF output
 #---------------------------------------------------------------------------
 # If the GENERATE_RTF tag is set to YES Doxygen will generate RTF output
 # The RTF output is optimized for Word 97 and may not look very pretty with
 # other RTF readers or editors.
 GENERATE_RTF           = NO
 # The RTF_OUTPUT tag is used to specify where the RTF docs will be put.
 # If a relative path is entered the value of OUTPUT_DIRECTORY will be
 # put in front of it. If left blank `rtf' will be used as the default path.
 RTF_OUTPUT             = rtf
 # If the COMPACT_RTF tag is set to YES Doxygen generates more compact
 # RTF documents. This may be useful for small projects and may help to
 # save some trees in general.
 COMPACT_RTF            = NO
 # If the RTF_HYPERLINKS tag is set to YES, the RTF that is generated
 # will contain hyperlink fields. The RTF file will
 # contain links (just like the HTML output) instead of page references.
 # This makes the output suitable for online browsing using WORD or other
 # programs which support those fields.
 # Note: wordpad (write) and others do not support links.
 RTF_HYPERLINKS         = NO
 # Load stylesheet definitions from file. Syntax is similar to doxygen's
 # config file, i.e. a series of assignments. You only have to provide
 # replacements, missing definitions are set to their default value.
 RTF_STYLESHEET_FILE    =
 # Set optional variables used in the generation of an rtf document.
 # Syntax is similar to doxygen's config file.
 RTF_EXTENSIONS_FILE    =
 #---------------------------------------------------------------------------
 # configuration options related to the man page output
 #---------------------------------------------------------------------------
 # If the GENERATE_MAN tag is set to YES (the default) Doxygen will
 # generate man pages
 GENERATE_MAN           = NO
 # The MAN_OUTPUT tag is used to specify where the man pages will be put.
 # If a relative path is entered the value of OUTPUT_DIRECTORY will be
 # put in front of it. If left blank `man' will be used as the default path.
 MAN_OUTPUT             = man
 # The MAN_EXTENSION tag determines the extension that is added to
 # the generated man pages (default is the subroutine's section .3)
 MAN_EXTENSION          = .3
 # If the MAN_LINKS tag is set to YES and Doxygen generates man output,
 # then it will generate one additional man file for each entity
 # documented in the real man page(s). These additional files
 # only source the real man page, but without them the man command
 # would be unable to find the correct page. The default is NO.
 MAN_LINKS              = NO
 #---------------------------------------------------------------------------
 # configuration options related to the XML output
 #---------------------------------------------------------------------------
 # If the GENERATE_XML tag is set to YES Doxygen will
 # generate an XML file that captures the structure of
 # the code including all documentation.
 GENERATE_XML           = NO
 # The XML_OUTPUT tag is used to specify where the XML pages will be put.
 # If a relative path is entered the value of OUTPUT_DIRECTORY will be
 # put in front of it. If left blank `xml' will be used as the default path.
 XML_OUTPUT             = xml
 # The XML_SCHEMA tag can be used to specify an XML schema,
 # which can be used by a validating XML parser to check the
 # syntax of the XML files.
 XML_SCHEMA             =
 # The XML_DTD tag can be used to specify an XML DTD,
 # which can be used by a validating XML parser to check the
 # syntax of the XML files.
 XML_DTD                =
 # If the XML_PROGRAMLISTING tag is set to YES Doxygen will
 # dump the program listings (including syntax highlighting
 # and cross-referencing information) to the XML output. Note that
 # enabling this will significantly increase the size of the XML output.
 XML_PROGRAMLISTING     = YES
 #---------------------------------------------------------------------------
 # configuration options for the AutoGen Definitions output
 #---------------------------------------------------------------------------
 # If the GENERATE_AUTOGEN_DEF tag is set to YES Doxygen will
 # generate an AutoGen Definitions (see autogen.sf.net) file
 # that captures the structure of the code including all
 # documentation. Note that this feature is still experimental
 # and incomplete at the moment.
 GENERATE_AUTOGEN_DEF   = NO
 #---------------------------------------------------------------------------
 # configuration options related to the Perl module output
 #---------------------------------------------------------------------------
 # If the GENERATE_PERLMOD tag is set to YES Doxygen will
 # generate a Perl module file that captures the structure of
 # the code including all documentation. Note that this
 # feature is still experimental and incomplete at the
 # moment.
 GENERATE_PERLMOD       = NO
 # If the PERLMOD_LATEX tag is set to YES Doxygen will generate
 # the necessary Makefile rules, Perl scripts and LaTeX code to be able
 # to generate PDF and DVI output from the Perl module output.
 PERLMOD_LATEX          = NO
 # If the PERLMOD_PRETTY tag is set to YES the Perl module output will be
 # nicely formatted so it can be parsed by a human reader.
 # This is useful
 # if you want to understand what is going on.
 # On the other hand, if this
 # tag is set to NO the size of the Perl module output will be much smaller
 # and Perl will parse it just the same.
 PERLMOD_PRETTY         = YES
 # The names of the make variables in the generated doxyrules.make file
 # are prefixed with the string contained in PERLMOD_MAKEVAR_PREFIX.
 # This is useful so different doxyrules.make files included by the same
 # Makefile don't overwrite each other's variables.
 PERLMOD_MAKEVAR_PREFIX =
 #---------------------------------------------------------------------------
 # Configuration options related to the preprocessor
 #---------------------------------------------------------------------------
 # If the ENABLE_PREPROCESSING tag is set to YES (the default) Doxygen will
 # evaluate all C-preprocessor directives found in the sources and include
 # files.
 ENABLE_PREPROCESSING   = YES
 # If the MACRO_EXPANSION tag is set to YES Doxygen will expand all macro
 # names in the source code. If set to NO (the default) only conditional
 # compilation will be performed. Macro expansion can be done in a controlled
 # way by setting EXPAND_ONLY_PREDEF to YES.
 MACRO_EXPANSION        = YES
 # If the EXPAND_ONLY_PREDEF and MACRO_EXPANSION tags are both set to YES
 # then the macro expansion is limited to the macros specified with the
 # PREDEFINED and EXPAND_AS_DEFINED tags.
 EXPAND_ONLY_PREDEF     = YES
 # If the SEARCH_INCLUDES tag is set to YES (the default) the includes files
 # in the INCLUDE_PATH (see below) will be search if a #include is found.
 SEARCH_INCLUDES        = YES
 # The INCLUDE_PATH tag can be used to specify one or more directories that
 # contain include files that are not input files but should be processed by
 # the preprocessor.
 INCLUDE_PATH           =
 # You can use the INCLUDE_FILE_PATTERNS tag to specify one or more wildcard
 # patterns (like *.h and *.hpp) to filter out the header-files in the
 # directories. If left blank, the patterns specified with FILE_PATTERNS will
 # be used.
 INCLUDE_FILE_PATTERNS  = *.h
 # The PREDEFINED tag can be used to specify one or more macro names that
 # are defined before the preprocessor is started (similar to the -D option of
 # gcc). The argument of the tag is a list of macros of the form: name
 # or name=definition (no spaces). If the definition and the = are
 # omitted =1 is assumed. To prevent a macro definition from being
 # undefined via #undef or recursively expanded use the := operator
 # instead of the = operator.
 PREDEFINED             = decl_param()=
 # If the MACRO_EXPANSION and EXPAND_ONLY_PREDEF tags are set to YES then
 # this tag can be used to specify a list of macro names that should be expanded.
 # The macro definition that is found in the sources will be used.
 # Use the PREDEFINED tag if you want to use a different macro definition.
 EXPAND_AS_DEFINED      =
 # If the SKIP_FUNCTION_MACROS tag is set to YES (the default) then
 # doxygen's preprocessor will remove all function-like macros that are alone
 # on a line, have an all uppercase name, and do not end with a semicolon. Such
 # function macros are typically used for boiler-plate code, and will confuse
 # the parser if not removed.
 SKIP_FUNCTION_MACROS   = YES
 #---------------------------------------------------------------------------
 # Configuration::additions related to external references
 #---------------------------------------------------------------------------
 # The TAGFILES option can be used to specify one or more tagfiles.
 # Optionally an initial location of the external documentation
 # can be added for each tagfile. The format of a tag file without
 # this location is as follows:
+#
 # TAGFILES = file1 file2 ...
 # Adding location for the tag files is done as follows:
+#
 # TAGFILES = file1=loc1 "file2 = loc2" ...
 # where "loc1" and "loc2" can be relative or absolute paths or
 # URLs. If a location is present for each tag, the installdox tool
 # does not have to be run to correct the links.
 # Note that each tag file must have a unique name
 # (where the name does NOT include the path)
 # If a tag file is not located in the directory in which doxygen
 # is run, you must also specify the path to the tagfile here.
 TAGFILES               =
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 %%EndResource
 /F9_0 /CMR7 1 1
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 pdfMakeFont
 %%BeginResource: font CMMI10
 %!PS-AdobeFont-1.0: CMMI10 003.002
 %%Title: CMMI10
 %Version: 003.002
 %%CreationDate: Mon Jul 13 16:17:00 2009
 %%Creator: David M. Jones
 %Copyright: Copyright (c) 1997, 2009 American Mathematical Society
 %Copyright:  (<http://www.ams.org>), with Reserved Font Name CMMI10.
 % This Font Software is licensed under the SIL Open Font License, Version 1.1.
 % This license is in the accompanying file OFL.txt, and is also
 % available with a FAQ at: http://scripts.sil.org/OFL.
 %%EndComments
 FontDirectory/CMMI10 known{/CMMI10 findfont dup/UniqueID known{dup
 /UniqueID get 5087385 eq exch/FontType get 1 eq and}{pop false}ifelse
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 dict begin
 /FontType 1 def
 /FontMatrix [0.001 0 0 0.001 0 0 ]readonly def
 /FontName /CMMI10 def
 /FontBBox {-32 -250 1048 750 }readonly def
 /PaintType 0 def
 /FontInfo 10 dict dup begin
 /version (003.002) readonly def
 /Notice (Copyright \050c\051 1997, 2009 American Mathematical Society \050<http://www.ams.org>\051, with Reserved Font Name CMMI10.) readonly def
 /FullName (CMMI10) readonly def
 /FamilyName (Computer Modern) readonly def
 /Weight (Medium) readonly def
 /ItalicAngle -14.04 def
 /isFixedPitch false def
 /UnderlinePosition -100 def
 /UnderlineThickness 50 def
 /ascent 750 def
 end readonly def
 /Encoding 256 array
 1 255 { 1 index exch /.notdef put} for
 dup 30 /phi put
 dup 76 /L put
 dup 80 /P put
 dup 81 /Q put
 dup 82 /R put
 dup 193 /phi put
 readonly def
 currentdict end
 currentfile eexec
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 pdfMakeFont
 %%BeginResource: font CMR10
 %!PS-AdobeFont-1.0: CMR10 003.002
 %%Title: CMR10
 %Version: 003.002
 %%CreationDate: Mon Jul 13 16:17:00 2009
 %%Creator: David M. Jones
 %Copyright: Copyright (c) 1997, 2009 American Mathematical Society
 %Copyright:  (<http://www.ams.org>), with Reserved Font Name CMR10.
 % This Font Software is licensed under the SIL Open Font License, Version 1.1.
 % This license is in the accompanying file OFL.txt, and is also
 % available with a FAQ at: http://scripts.sil.org/OFL.
 %%EndComments
 FontDirectory/CMR10 known{/CMR10 findfont dup/UniqueID known{dup
 /UniqueID get 5000793 eq exch/FontType get 1 eq and}{pop false}ifelse
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 dict begin
 /FontType 1 def
 /FontMatrix [0.001 0 0 0.001 0 0 ]readonly def
 /FontName /CMR10 def
 /FontBBox {-40 -250 1009 750 }readonly def
 /PaintType 0 def
 /FontInfo 9 dict dup begin
 /version (003.002) readonly def
 /Notice (Copyright \050c\051 1997, 2009 American Mathematical Society \050<http://www.ams.org>\051, with Reserved Font Name CMR10.) readonly def
 /FullName (CMR10) readonly def
 /FamilyName (Computer Modern) readonly def
 /Weight (Medium) readonly def
 /ItalicAngle 0 def
 /isFixedPitch false def
 /UnderlinePosition -100 def
 /UnderlineThickness 50 def
 end readonly def
 /Encoding 256 array
 1 255 { 1 index exch /.notdef put} for
 dup 48 /zero put
 dup 61 /equal put
 readonly def
 currentdict end
 currentfile eexec
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 %%EndResource
 /F6_0 /CMR10 1 1
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 pdfMakeFont
 %%BeginResource: font CMMI7
 %!PS-AdobeFont-1.0: CMMI7 003.002
 %%Title: CMMI7
 %Version: 003.002
 %%CreationDate: Mon Jul 13 16:17:00 2009
 %%Creator: David M. Jones
 %Copyright: Copyright (c) 1997, 2009 American Mathematical Society
 %Copyright:  (<http://www.ams.org>), with Reserved Font Name CMMI7.
 % This Font Software is licensed under the SIL Open Font License, Version 1.1.
 % This license is in the accompanying file OFL.txt, and is also
 % available with a FAQ at: http://scripts.sil.org/OFL.
 %%EndComments
 FontDirectory/CMMI7 known{/CMMI7 findfont dup/UniqueID known{dup
 /UniqueID get 5087382 eq exch/FontType get 1 eq and}{pop false}ifelse
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 dict begin
 /FontType 1 def
 /FontMatrix [0.001 0 0 0.001 0 0 ]readonly def
 /FontName /CMMI7 def
 /FontBBox {-1 -250 1171 750 }readonly def
 /PaintType 0 def
 /FontInfo 10 dict dup begin
 /version (003.002) readonly def
 /Notice (Copyright \050c\051 1997, 2009 American Mathematical Society \050<http://www.ams.org>\051, with Reserved Font Name CMMI7.) readonly def
 /FullName (CMMI7) readonly def
 /FamilyName (Computer Modern) readonly def
 /Weight (Medium) readonly def
 /ItalicAngle -14.04 def
 /isFixedPitch false def
 /UnderlinePosition -100 def
 /UnderlineThickness 50 def
 /ascent 750 def
 end readonly def
 /Encoding 256 array
 1 255 { 1 index exch /.notdef put} for
 dup 100 /d put
 dup 101 /e put
 dup 108 /l put
 dup 110 /n put
 readonly def
 currentdict end
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 % Polyline
  [60] 0 sd
 n 3600 7800 m
 7800 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 3600 8400 m
 8400 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 3600 9000 m
 9000 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 3600 9600 m
 9600 l gs col1 s gr  [] 0 sd
 % Polyline
 .000 slw
 n 3600 600 m 9600 600 l 9600 10200 l 3600 10200 l
  cp gs col0 s gr
 % Polyline
 n 4800 4200 m 8400 4200 l 8400 7200 l 4800 7200 l
  cp gs col0 s gr
 % Polyline
 .500 slw
  [60] 0 sd
 n 4200 600 m
 10200 l gs col1 s gr  [] 0 sd
 % Polyline
 .000 slw
 n 5400 1500 m 7800 1500 l 7800 2700 l 5400 2700 l
  cp gs col0 s gr
 % Polyline
 .500 slw
  [60] 0 sd
 n 6300 1200 m
 4200 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 6900 1200 m
 4200 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 8700 1200 m
 4200 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 5100 4200 m
 7200 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 5700 4200 m
 7200 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 6300 4200 m
 7200 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 6900 4200 m
 7200 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 7500 4200 m
 7200 l gs col1 s gr  [] 0 sd
 % Polyline
 n 8546 3900 m 8554 3900 l gs col0 s gr
 % Polyline
  [60] 0 sd
 n 8100 1200 m
 4200 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 4200 3300 m
 3300 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 4200 2100 m
 2100 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 8700 1200 m
 4200 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 4200 1500 m
 1500 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 8100 4200 m
 7200 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 4800 5100 m
 5100 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 3600 5400 m
 5400 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 4800 5700 m
 5700 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 4800 6300 m
 6300 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 4875 6900 m
 6900 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 4800 4500 m
 4500 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 5400 600 m
 10200 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 4800 600 m
 10200 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 7500 1200 m
 4200 l gs col1 s gr  [] 0 sd
 % Polyline
 .000 slw
 n 7800 1800 m 8400 1800 l 8400 3000 l 7800 3000 l
  cp gs col0 s gr
 % Polyline
 .500 slw
  [60] 0 sd
 n 8400 600 m
 10200 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 4800 1950 m
 1950 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 4800 2250 m
 2250 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 4800 2550 m
 2550 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 5100 1200 m
 4200 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 7800 2850 m
 2850 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 5400 1650 m
 1650 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 3600 1800 m
 1800 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 4200 2700 m
 2700 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 5700 1200 m
 4200 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 4200 3900 m
 3900 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 4500 1200 m
 4200 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 3600 2400 m
 2400 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 3600 3000 m
 3000 l gs col1 s gr  [] 0 sd
 % Polyline
 .000 slw
 n 5400 1800 m 4800 1800 l 4800 3000 l 5400 3000 l
  cp gs col0 s gr
 % Polyline
 .500 slw
  [60] 0 sd
 n 4800 2850 m
 2850 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 4950 1800 m
 3000 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 5250 1800 m
 3000 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 7950 1800 m
 3000 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 8250 1800 m
 3000 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 7650 1500 m
 2700 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 7050 1500 m
 2700 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 6750 1500 m
 2700 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 6450 1500 m
 2700 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 6150 1500 m
 2700 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 5850 1500 m
 2700 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 5550 1500 m
 2700 l gs col1 s gr  [] 0 sd
 % Polyline
  [60] 0 sd
 n 7350 1500 m
 2700 l gs col1 s gr  [] 0 sd
 /Times-Roman ff 300.00 scf sf
 9975 m
 gs 1 -1 sc (a) col0 sh gr
 /Times-Roman ff 300.00 scf sf
 6600 m
 gs 1 -1 sc (ab) col0 sh gr
 /Times-Roman ff 300.00 scf sf
 3825 m
 gs 1 -1 sc (ac) col0 sh gr
 /Times-Roman ff 300.00 scf sf
 2775 m
 gs 1 -1 sc (aca) col0 sh gr
 /Times-Roman ff 300.00 scf sf
 2400 m
 gs 1 -1 sc (acb) col0 sh gr
 /Times-Roman ff 300.00 scf sf
 2775 m
 gs 1 -1 sc (acc) col0 sh gr
 % here ends figure;
 pagefooter
 showpage
 %%Trailer
 %EOF

doc/figures/grids.fig

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@@ new file 100644 @@
 #FIG 3.2  Produced by xfig version 3.2.5b
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 .00
 Single
 -2
 2
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 600 6000 10200
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 600 7200 10200
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 600 9000 10200
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 600 4200 10200
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 4200 7500 7200
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 3900
 1 1 1 1 7 50 -1 -1 4.000 0 0 -1 0 0 2
 1200 8100 4200
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 3300 9000 3300
 1 1 1 1 7 50 -1 -1 4.000 0 0 -1 0 0 2
 2100 9000 2100
 1 1 1 1 7 50 -1 -1 4.000 0 0 -1 0 0 2
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 1500 9000 1500
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 4200 8100 7200
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 5100 8400 5100
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 5700 8400 5700
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 6300 8400 6300
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 6900 8475 6900
 1 1 1 1 7 50 -1 -1 4.000 0 0 -1 0 0 2
 4500 8400 4500
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 600 4800 10200
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 600 8400 10200
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 2550 8400 2550
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 2850 8400 2850
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 3900 9000 3900
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 0 0 50 -1 0 18 0.0000 2 135 375 7850 2775 acc\001

doc/figures/grids.png

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