[cig-commits] r5059 - in mc/3D/CitcomS/trunk: . bin doc lib module
tests visual
leif at geodynamics.org
leif at geodynamics.org
Tue Oct 17 02:18:16 PDT 2006
Author: leif
Date: 2006-10-17 02:18:15 -0700 (Tue, 17 Oct 2006)
New Revision: 5059
Added:
mc/3D/CitcomS/trunk/Citcom.c
mc/3D/CitcomS/trunk/CitcomSFull.c
mc/3D/CitcomS/trunk/CitcomSRegional.c
mc/3D/CitcomS/trunk/project.cfg
Removed:
mc/3D/CitcomS/trunk/bin/Citcom.c
mc/3D/CitcomS/trunk/doc/CitComS.doxyconf
Modified:
mc/3D/CitcomS/trunk/
mc/3D/CitcomS/trunk/Makefile.am
mc/3D/CitcomS/trunk/configure.ac
mc/3D/CitcomS/trunk/lib/Pan_problem_misc_functions.c
mc/3D/CitcomS/trunk/lib/Tracer_advection.c
mc/3D/CitcomS/trunk/module/CitcomSmodule.c
mc/3D/CitcomS/trunk/module/Makefile.am
mc/3D/CitcomS/trunk/module/Regionalmodule.c
mc/3D/CitcomS/trunk/module/advdiffu.c
mc/3D/CitcomS/trunk/module/bindings.c
mc/3D/CitcomS/trunk/module/exceptions.c
mc/3D/CitcomS/trunk/module/initial_conditions.c
mc/3D/CitcomS/trunk/module/mesher.c
mc/3D/CitcomS/trunk/module/misc.c
mc/3D/CitcomS/trunk/module/outputs.c
mc/3D/CitcomS/trunk/module/setProperties.c
mc/3D/CitcomS/trunk/module/stokes_solver.c
mc/3D/CitcomS/trunk/setup.py
mc/3D/CitcomS/trunk/tests/Makefile.am
mc/3D/CitcomS/trunk/visual/Makefile.am
Log:
Transitioning to Merlin. (Warning: still under construction.)
Property changes on: mc/3D/CitcomS/trunk
___________________________________________________________________
Name: svn:externals
- m4 http://geodynamics.org/svn/cig/cs/autoconf/trunk
Copied: mc/3D/CitcomS/trunk/Citcom.c (from rev 4957, mc/3D/CitcomS/trunk/bin/Citcom.c)
===================================================================
--- mc/3D/CitcomS/trunk/bin/Citcom.c 2006-10-12 14:48:43 UTC (rev 4957)
+++ mc/3D/CitcomS/trunk/Citcom.c 2006-10-17 09:18:15 UTC (rev 5059)
@@ -0,0 +1,201 @@
+/*
+ *~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ *
+ *<LicenseText>
+ *
+ * CitcomS by Louis Moresi, Shijie Zhong, Lijie Han, Eh Tan,
+ * Clint Conrad, Michael Gurnis, and Eun-seo Choi.
+ * Copyright (C) 1994-2005, California Institute of Technology.
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ *
+ *</LicenseText>
+ *
+ *~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ */
+#include <mpi.h>
+
+#include <math.h>
+#include <sys/types.h>
+
+#include "element_definitions.h"
+#include "global_defs.h"
+#include "citcom_init.h"
+#include "output.h"
+#include "parallel_related.h"
+
+extern int Emergency_stop;
+
+void solver_init(struct All_variables *E);
+
+int main(argc,argv)
+ int argc;
+ char **argv;
+
+{ /* Functions called by main*/
+ void general_stokes_solver();
+ void general_stokes_solver_pseudo_surf();
+ void read_instructions();
+ void solve_constrained_flow();
+ void solve_derived_velocities();
+ void process_temp_field();
+ void post_processing();
+ void vcopy();
+ void construct_mat_group();
+ void read_velocity_boundary_from_file();
+ void read_mat_from_file();
+ void open_time();
+ void output_finalize();
+
+ float dot();
+ float cpu_time_on_vp_it;
+
+ int cpu_total_seconds,k, *temp;
+ double CPU_time0(),time,initial_time,start_time,avaimem();
+
+ struct All_variables *E;
+ MPI_Comm world;
+
+ MPI_Init(&argc,&argv); /* added here to allow command-line input */
+
+ if (argc < 2) {
+ fprintf(stderr,"Usage: %s PARAMETERFILE\n", argv[0]);
+ parallel_process_termination();
+ }
+
+ world = MPI_COMM_WORLD;
+ E = citcom_init(&world); /* allocate global E and do initializaion here */
+
+ solver_init(E);
+
+ start_time = time = CPU_time0();
+ read_instructions(E, argv[1]);
+
+ cpu_time_on_vp_it = CPU_time0();
+ initial_time = cpu_time_on_vp_it - time;
+ if (E->parallel.me == 0) {
+ fprintf(stderr,"Input parameters taken from file '%s'\n",argv[1]);
+ fprintf(stderr,"Initialization complete after %g seconds\n\n",initial_time);
+ fprintf(E->fp,"Initialization complete after %g seconds\n\n",initial_time);
+ fflush(E->fp);
+ }
+
+ if (E->control.post_p) {
+ post_processing(E);
+ parallel_process_termination();
+ }
+
+ if(E->control.pseudo_free_surf) {
+ if(E->mesh.topvbc == 2)
+ general_stokes_solver_pseudo_surf(E);
+ else
+ assert(0);
+ }
+ else
+ general_stokes_solver(E);
+
+ (E->problem_output)(E, E->monitor.solution_cycles);
+
+ /* information about simulation time and wall clock time */
+ output_time(E, E->monitor.solution_cycles);
+
+
+ if (E->control.stokes) {
+
+ if(E->control.tracer==1)
+ (E->problem_tracer_advection)(E);
+
+ parallel_process_termination();
+ }
+
+ while ( E->control.keep_going && (Emergency_stop == 0) ) {
+ E->monitor.solution_cycles++;
+ if(E->monitor.solution_cycles>E->control.print_convergence)
+ E->control.print_convergence=1;
+
+ (E->next_buoyancy_field)(E);
+
+ if(((E->advection.total_timesteps < E->advection.max_total_timesteps) &&
+ (E->advection.timesteps < E->advection.max_timesteps)) ||
+ (E->advection.total_timesteps < E->advection.min_timesteps) )
+ E->control.keep_going = 1;
+ else
+ E->control.keep_going = 0;
+
+ cpu_total_seconds = CPU_time0()-start_time;
+ if (cpu_total_seconds > E->control.record_all_until) {
+ E->control.keep_going = 0;
+ }
+
+ if (E->monitor.T_interior>1.5) {
+ fprintf(E->fp,"quit due to maxT = %.4e sub_iteration%d\n",E->monitor.T_interior,E->advection.last_sub_iterations);
+ parallel_process_termination();
+ }
+
+ general_stokes_solver(E);
+
+ if(E->control.tracer==1)
+ (E->problem_tracer_advection)(E);
+
+ if ((E->monitor.solution_cycles % E->control.record_every)==0) {
+ (E->problem_output)(E, E->monitor.solution_cycles);
+ }
+
+ /* information about simulation time and wall clock time */
+ output_time(E, E->monitor.solution_cycles);
+
+ if(E->control.mat_control==1)
+ read_mat_from_file(E);
+ /*
+ else
+ construct_mat_group(E);
+ */
+
+ if(E->control.vbcs_file==1)
+ read_velocity_boundary_from_file(E);
+ /*
+ else
+ renew_top_velocity_boundary(E);
+ */
+
+
+
+ if (E->parallel.me == 0) {
+ fprintf(E->fp,"CPU total = %g & CPU = %g for step %d time = %.4e dt = %.4e maxT = %.4e sub_iteration%d\n",CPU_time0()-start_time,CPU_time0()-time,E->monitor.solution_cycles,E->monitor.elapsed_time,E->advection.timestep,E->monitor.T_interior,E->advection.last_sub_iterations);
+
+ time = CPU_time0();
+ }
+
+ }
+
+
+
+
+ if (E->parallel.me == 0) {
+ fprintf(stderr,"cycles=%d\n",E->monitor.solution_cycles);
+ cpu_time_on_vp_it=CPU_time0()-cpu_time_on_vp_it;
+ fprintf(stderr,"Average cpu time taken for velocity step = %f\n",
+ cpu_time_on_vp_it/((float)(E->monitor.solution_cycles-E->control.restart)));
+ fprintf(E->fp,"Initialization overhead = %f\n",initial_time);
+ fprintf(E->fp,"Average cpu time taken for velocity step = %f\n",
+ cpu_time_on_vp_it/((float)(E->monitor.solution_cycles-E->control.restart)));
+ }
+
+ output_finalize(E);
+ parallel_process_termination();
+
+ return(0);
+
+}
Added: mc/3D/CitcomS/trunk/CitcomSFull.c
===================================================================
--- mc/3D/CitcomS/trunk/CitcomSFull.c 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/CitcomSFull.c 2006-10-17 09:18:15 UTC (rev 5059)
@@ -0,0 +1,38 @@
+/*
+ *~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ *
+ *<LicenseText>
+ *
+ * CitcomS by Louis Moresi, Shijie Zhong, Lijie Han, Eh Tan,
+ * Clint Conrad, Michael Gurnis, and Eun-seo Choi.
+ * Copyright (C) 1994-2005, California Institute of Technology.
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ *
+ *</LicenseText>
+ *
+ *~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ */
+
+struct All_variables;
+
+void full_solver_init(struct All_variables *E);
+
+void solver_init(struct All_variables *E)
+{
+ full_solver_init(E);
+}
+
+/* end of file */
Added: mc/3D/CitcomS/trunk/CitcomSRegional.c
===================================================================
--- mc/3D/CitcomS/trunk/CitcomSRegional.c 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/CitcomSRegional.c 2006-10-17 09:18:15 UTC (rev 5059)
@@ -0,0 +1,38 @@
+/*
+ *~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ *
+ *<LicenseText>
+ *
+ * CitcomS by Louis Moresi, Shijie Zhong, Lijie Han, Eh Tan,
+ * Clint Conrad, Michael Gurnis, and Eun-seo Choi.
+ * Copyright (C) 1994-2005, California Institute of Technology.
+ *
+ * This program is free software; you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation; either version 2 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
+ *
+ *</LicenseText>
+ *
+ *~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+ */
+
+struct All_variables;
+
+void regional_solver_init(struct All_variables *E);
+
+void solver_init(struct All_variables *E)
+{
+ regional_solver_init(E);
+}
+
+/* end of file */
Modified: mc/3D/CitcomS/trunk/Makefile.am
===================================================================
--- mc/3D/CitcomS/trunk/Makefile.am 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/Makefile.am 2006-10-17 09:18:15 UTC (rev 5059)
@@ -23,19 +23,95 @@
# $Id$
-ACLOCAL_AMFLAGS = -I ./m4
+SUBDIRS =
+DIST_SUBDIRS = examples tests visual
+MERLIN_SUBDIRS = module
-if COND_PYRE
- MAYBE_PYRE = CitcomS etc examples module tests visual
-endif
+bin_PROGRAMS = CitcomSFull CitcomSRegional
-SUBDIRS = $(MAYBE_PYTHIA) $(MAYBE_EXCHANGER) lib $(MAYBE_PYRE) bin
-DIST_SUBDIRS = \
- $(MAYBE_DIST_PYTHIA) $(MAYBE_DIST_EXCHANGER) \
- lib bin \
- CitcomS etc examples module tests visual
+CitcomSFull_SOURCES = Citcom.c CitcomSFull.c
+CitcomSFull_LDADD = libCitcomS.a
+CitcomSRegional_SOURCES = Citcom.c CitcomSRegional.c
+CitcomSRegional_LDADD = libCitcomS.a
+
+noinst_LIBRARIES = libCitcomS.a
+
+libCitcomS_a_CPPFLAGS = -I$(top_srcdir)/lib
+libCitcomS_a_SOURCES = \
+ lib/Advection_diffusion.c \
+ lib/advection_diffusion.h \
+ lib/advection.h \
+ lib/BC_util.c \
+ lib/Citcom_init.c \
+ lib/citcom_init.h \
+ lib/Construct_arrays.c \
+ lib/Convection.c \
+ lib/convection_variables.h \
+ lib/Drive_solvers.c \
+ lib/drive_solvers.h \
+ lib/Element_calculations.c \
+ lib/element_definitions.h \
+ lib/General_matrix_functions.c \
+ lib/global_defs.h \
+ lib/Global_operations.c \
+ lib/hdf5_related.h \
+ lib/Initial_temperature.c \
+ lib/initial_temperature.h \
+ lib/Instructions.c \
+ lib/Interuption.c \
+ lib/interuption.h \
+ lib/lith_age.h \
+ lib/Lith_age.c \
+ lib/Nodal_mesh.c \
+ lib/Output.c \
+ lib/output.h \
+ lib/Output_h5.c \
+ lib/output_h5.h \
+ lib/Pan_problem_misc_functions.c \
+ lib/parallel_related.h \
+ lib/Parallel_util.c \
+ lib/Parsing.c \
+ lib/parsing.h \
+ lib/Phase_change.c \
+ lib/phase_change.h \
+ lib/Problem_related.c \
+ lib/Process_buoyancy.c \
+ lib/Shape_functions.c \
+ lib/Size_does_matter.c \
+ lib/Solver_conj_grad.c \
+ lib/Solver_multigrid.c \
+ lib/solver.h \
+ lib/sphere_communication.h \
+ lib/Sphere_harmonics.c \
+ lib/Sphere_util.c \
+ lib/Stokes_flow_Incomp.c \
+ lib/temperature_descriptions.h \
+ lib/Topo_gravity.c \
+ lib/Tracer_advection.c \
+ lib/tracer_defs.h \
+ lib/viscosity_descriptions.h \
+ lib/Viscosity_structures.c \
+ lib/Full_boundary_conditions.c \
+ lib/Full_geometry_cartesian.c \
+ lib/Full_lith_age_read_files.c \
+ lib/Full_parallel_related.c \
+ lib/Full_read_input_from_files.c \
+ lib/Full_solver.c \
+ lib/Full_sphere_related.c \
+ lib/Full_version_dependent.c \
+ lib/Regional_boundary_conditions.c \
+ lib/Regional_geometry_cartesian.c \
+ lib/Regional_lith_age_read_files.c \
+ lib/Regional_parallel_related.c \
+ lib/Regional_read_input_from_files.c \
+ lib/Regional_solver.c \
+ lib/Regional_sphere_related.c \
+ lib/Regional_version_dependent.c
+
EXTRA_DIST = \
- doc/CitComS.doxyconf
+ lib/Obsolete.c \
+ lib/Full_obsolete.c \
+ lib/Regional_obsolete.c
## end of Makefile.am
Deleted: mc/3D/CitcomS/trunk/bin/Citcom.c
===================================================================
--- mc/3D/CitcomS/trunk/bin/Citcom.c 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/bin/Citcom.c 2006-10-17 09:18:15 UTC (rev 5059)
@@ -1,206 +0,0 @@
-/*
- *~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- *
- *<LicenseText>
- *
- * CitcomS by Louis Moresi, Shijie Zhong, Lijie Han, Eh Tan,
- * Clint Conrad, Michael Gurnis, and Eun-seo Choi.
- * Copyright (C) 1994-2005, California Institute of Technology.
- *
- * This program is free software; you can redistribute it and/or modify
- * it under the terms of the GNU General Public License as published by
- * the Free Software Foundation; either version 2 of the License, or
- * (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
- *
- *</LicenseText>
- *
- *~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- */
-#include <mpi.h>
-
-#include <math.h>
-#include <sys/types.h>
-
-#include "element_definitions.h"
-#include "global_defs.h"
-#include "citcom_init.h"
-#include "output.h"
-#include "parallel_related.h"
-
-extern int Emergency_stop;
-
-void full_solver_init(struct All_variables *E);
-void regional_solver_init(struct All_variables *E);
-
-int main(argc,argv)
- int argc;
- char **argv;
-
-{ /* Functions called by main*/
- void general_stokes_solver();
- void general_stokes_solver_pseudo_surf();
- void read_instructions();
- void solve_constrained_flow();
- void solve_derived_velocities();
- void process_temp_field();
- void post_processing();
- void vcopy();
- void construct_mat_group();
- void read_velocity_boundary_from_file();
- void read_mat_from_file();
- void open_time();
- void output_finalize();
-
- float dot();
- float cpu_time_on_vp_it;
-
- int cpu_total_seconds,k, *temp;
- double CPU_time0(),time,initial_time,start_time,avaimem();
-
- struct All_variables *E;
- MPI_Comm world;
-
- MPI_Init(&argc,&argv); /* added here to allow command-line input */
-
- if (argc < 2) {
- fprintf(stderr,"Usage: %s PARAMETERFILE\n", argv[0]);
- parallel_process_termination();
- }
-
- world = MPI_COMM_WORLD;
- E = citcom_init(&world); /* allocate global E and do initializaion here */
-
-#ifdef CITCOMS_SOLVER_FULL
- full_solver_init(E);
-#else
- regional_solver_init(E);
-#endif
-
- start_time = time = CPU_time0();
- read_instructions(E, argv[1]);
-
- cpu_time_on_vp_it = CPU_time0();
- initial_time = cpu_time_on_vp_it - time;
- if (E->parallel.me == 0) {
- fprintf(stderr,"Input parameters taken from file '%s'\n",argv[1]);
- fprintf(stderr,"Initialization complete after %g seconds\n\n",initial_time);
- fprintf(E->fp,"Initialization complete after %g seconds\n\n",initial_time);
- fflush(E->fp);
- }
-
- if (E->control.post_p) {
- post_processing(E);
- parallel_process_termination();
- }
-
- if(E->control.pseudo_free_surf) {
- if(E->mesh.topvbc == 2)
- general_stokes_solver_pseudo_surf(E);
- else
- assert(0);
- }
- else
- general_stokes_solver(E);
-
- (E->problem_output)(E, E->monitor.solution_cycles);
-
- /* information about simulation time and wall clock time */
- output_time(E, E->monitor.solution_cycles);
-
-
- if (E->control.stokes) {
-
- if(E->control.tracer==1)
- (E->problem_tracer_advection)(E);
-
- parallel_process_termination();
- }
-
- while ( E->control.keep_going && (Emergency_stop == 0) ) {
- E->monitor.solution_cycles++;
- if(E->monitor.solution_cycles>E->control.print_convergence)
- E->control.print_convergence=1;
-
- (E->next_buoyancy_field)(E);
-
- if(((E->advection.total_timesteps < E->advection.max_total_timesteps) &&
- (E->advection.timesteps < E->advection.max_timesteps)) ||
- (E->advection.total_timesteps < E->advection.min_timesteps) )
- E->control.keep_going = 1;
- else
- E->control.keep_going = 0;
-
- cpu_total_seconds = CPU_time0()-start_time;
- if (cpu_total_seconds > E->control.record_all_until) {
- E->control.keep_going = 0;
- }
-
- if (E->monitor.T_interior>1.5) {
- fprintf(E->fp,"quit due to maxT = %.4e sub_iteration%d\n",E->monitor.T_interior,E->advection.last_sub_iterations);
- parallel_process_termination();
- }
-
- general_stokes_solver(E);
-
- if(E->control.tracer==1)
- (E->problem_tracer_advection)(E);
-
- if ((E->monitor.solution_cycles % E->control.record_every)==0) {
- (E->problem_output)(E, E->monitor.solution_cycles);
- }
-
- /* information about simulation time and wall clock time */
- output_time(E, E->monitor.solution_cycles);
-
- if(E->control.mat_control==1)
- read_mat_from_file(E);
- /*
- else
- construct_mat_group(E);
- */
-
- if(E->control.vbcs_file==1)
- read_velocity_boundary_from_file(E);
- /*
- else
- renew_top_velocity_boundary(E);
- */
-
-
-
- if (E->parallel.me == 0) {
- fprintf(E->fp,"CPU total = %g & CPU = %g for step %d time = %.4e dt = %.4e maxT = %.4e sub_iteration%d\n",CPU_time0()-start_time,CPU_time0()-time,E->monitor.solution_cycles,E->monitor.elapsed_time,E->advection.timestep,E->monitor.T_interior,E->advection.last_sub_iterations);
-
- time = CPU_time0();
- }
-
- }
-
-
-
-
- if (E->parallel.me == 0) {
- fprintf(stderr,"cycles=%d\n",E->monitor.solution_cycles);
- cpu_time_on_vp_it=CPU_time0()-cpu_time_on_vp_it;
- fprintf(stderr,"Average cpu time taken for velocity step = %f\n",
- cpu_time_on_vp_it/((float)(E->monitor.solution_cycles-E->control.restart)));
- fprintf(E->fp,"Initialization overhead = %f\n",initial_time);
- fprintf(E->fp,"Average cpu time taken for velocity step = %f\n",
- cpu_time_on_vp_it/((float)(E->monitor.solution_cycles-E->control.restart)));
- }
-
- output_finalize(E);
- parallel_process_termination();
-
- return(0);
-
-}
Modified: mc/3D/CitcomS/trunk/configure.ac
===================================================================
--- mc/3D/CitcomS/trunk/configure.ac 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/configure.ac 2006-10-17 09:18:15 UTC (rev 5059)
@@ -26,196 +26,35 @@
AC_PREREQ(2.59)
AC_INIT([CitcomS], [2.1.0], [cig-mc at geodynamics.org], [CitcomS])
-AC_CONFIG_AUX_DIR([./aux-config])
-AC_CONFIG_SRCDIR([bin/Citcom.c])
-AC_CONFIG_HEADER([portinfo])
-AC_CONFIG_MACRO_DIR([m4])
+AC_CONFIG_SRCDIR([Citcom.c])
+AC_CONFIG_HEADER([config.h])
AM_INIT_AUTOMAKE([foreign])
-# 'configure' options
-AC_ARG_VAR(PYTHON, [Python interpreter])
-AC_ARG_VAR(PYTHONPATH, [Python module search path])
-AC_ARG_VAR(PHDF5_HOME, [home path to parallel HDF5 library])
-AC_ARG_WITH([pyre],
- [AC_HELP_STRING([--with-pyre],
- [build Pyre modules @<:@default=yes@:>@])],
- [want_pyre="$withval"],
- [want_pyre=yes])
-AM_CONDITIONAL([COND_PYRE], [test "$want_pyre" = yes])
-AC_ARG_WITH([exchanger],
- [AC_HELP_STRING([--with-exchanger],
- [use Exchanger @<:@default=auto@:>@])],
- [want_exchanger="$withval"],
- [want_exchanger=auto])
-AC_ARG_WITH([hdf5],
- [AC_HELP_STRING([--with-hdf5],
- [enable HDF5 output @<:@default=auto@:>@])],
- [want_hdf5="$withval"],
- [want_hdf5=auto])
-AC_ARG_ENABLE([embedding],
- [AC_HELP_STRING([--enable-embedding],
- [embed Python with CitcomS in a single executable @<:@default=yes@:>@])],
- [want_embedding="$enableval"],
- [want_embedding=yes])
-AM_CONDITIONAL([COND_EMBEDDING], [test "$want_embedding" = yes])
-
-if test "$want_pyre" = yes; then
- # Check for Python.
- AM_PATH_PYTHON([2.3])
- CIT_PYTHON_SYSCONFIG
-
- # Checks for Python modules and packages.
- CIT_CHECK_PYTHON_EGG([pythia >= 0.8.1.0b2, < 0.8-2.0a])
- if test "$want_exchanger" != no; then
- CIT_CHECK_PYTHON_EGG([Exchanger >= 1.0, < 2.0a],
- [ # found
- if test "$want_exchanger" = auto; then
- want_exchanger=yes
- fi
- ], [ # not found
- if test "$want_exchanger" = auto; then
- want_exchanger=no
- AC_MSG_WARN(['Exchanger' package not found; disabling Exchanger support])
- else
- AC_MSG_ERROR(['Exchanger' package not found])
- fi
- ])
- fi
- CIT_PYTHON_EGG_FLAGS
-else
- want_exchanger=no
-fi
-AM_CONDITIONAL([COND_EXCHANGER], [test "$want_exchanger" = yes])
-
# Checks for programs.
-CIT_PROG_MPICC
-CIT_PROG_MPICXX
-CC=$MPICC
-CXX=$MPICXX
-if test "$want_pyre" = yes; then
- CIT_PROG_PYCONFIG
- AC_SUBST([pkgsysconfdir], [\${sysconfdir}/$PACKAGE])
-fi
-# We don't need Fortran.
-AC_PROVIDE([AC_PROG_F77])
-AC_PROG_LIBTOOL
-AC_LANG(C)
+AC_PROG_CC([mpicc hcc mpcc mpcc_r mpxlc cmpicc gcc cc cl icc ecc pgcc xlc xlc_r])
+AC_PROG_RANLIB
# Checks for libraries.
-if test "$want_exchanger" = yes; then
- AC_LANG_PUSH(C++)
- CIT_CHECK_LIB_MPI
- AC_LANG_POP(C++)
-else
- CIT_CHECK_LIB_MPI
-fi
+AC_SEARCH_LIBS([MPI_Init], [mpi mpich])
+AC_SEARCH_LIBS([sqrt], [m])
# Checks for header files.
-if test "$want_exchanger" = yes; then
- AC_LANG_PUSH(C++)
- CIT_HEADER_MPI
- AC_LANG_POP(C++)
-else
- CIT_HEADER_MPI
-fi
-if test "$want_hdf5" != no; then
- if test "$PHDF5_HOME"; then
- CPPFLAGS="-I$PHDF5_HOME/include $CPPFLAGS"
- fi
- AC_CHECK_HEADERS([hdf5.h], [AC_DEFINE([HAVE_HDF5_H])], [HDF5NOTFOUND=1])
- if test "$HDF5NOTFOUND"; then
- if test "$want_hdf5" = auto; then
- want_hdf5=no
- AC_MSG_WARN([Cannot find hdf5.h, disabling HDF5 support])
- else
- AC_MSG_ERROR([HDF5 header file "hdf5.h" not found!])
- fi
- fi
-fi
+AC_CHECK_HEADER([mpi.h])
AC_CHECK_HEADERS([malloc.h])
# Checks for typedefs, structures, and compiler characteristics.
# Checks for library functions.
-AC_ARG_VAR(LIBM, [math library])
-if test -z "$LIBM"; then
- AC_CHECK_FUNC(sqrt, , [
- AC_CHECK_LIB(m, sqrt, [
- LIBM="-lm"
- ], [
- AC_MSG_ERROR([math library not found; try setting LIBM])
- ])
- ])
-fi
-AC_SUBST(LIBM)
-if test "$want_hdf5" != no; then
- if test "$PHDF5_HOME"; then
- LDFLAGS="-L$PHDF5_HOME/lib $LDFLAGS"
- fi
- # Checks for basic HDF5 function
- AC_CHECK_FUNC(H5Fopen, , [
- AC_CHECK_LIB(hdf5, H5Fopen, [LIBHDF5="-lhdf5"], [HDF5NOTFOUND=1])
- ])
- if test "$HDF5NOTFOUND"; then
- if test "$want_hdf5" = auto; then
- want_hdf5=no
- AC_MSG_WARN([Cannot find HDF5 library, disabling HDF5 support])
- else
- AC_MSG_ERROR([HDF5 library not found; try setting PHDF5_HOME])
- fi
- fi
-fi
-if test "$want_hdf5" != no; then
- # Checks for HDF5 parallel-IO function
- AC_CHECK_LIB(hdf5, H5Pset_dxpl_mpio, [have_phdf5="yes"], [HDF5NOTFOUND=1])
- if test "$HDF5NOTFOUND"; then
- if test "$want_hdf5" = auto; then
- want_hdf5=no
- AC_MSG_WARN([Cannot find parallel HDF5 library, disabling HDF5 support])
- else
- AC_MSG_ERROR([Need Parallel HDF5; try compiling HDF5 with --enable-parallel])
- fi
- fi
- if test "$want_hdf5" = auto; then
- want_hdf5=yes
- fi
-fi
-AM_CONDITIONAL([COND_HDF5], [test "$want_hdf5" = yes])
-AC_SUBST(LIBHDF5)
-
AC_CONFIG_FILES([Makefile
- bin/Makefile
- CitcomS/Makefile
- etc/Makefile
examples/Makefile
- lib/Makefile
- module/Makefile
- module/Exchanger/Makefile
tests/Makefile
visual/Makefile
visual/OpenDXMacro/Makefile])
AC_OUTPUT
-# report configuration summary
-echo -e "\n\n"
-echo "================ Configuration Summary ================"
-echo -e "\t PYTHON: " $PYTHON
-echo -e "\t PYTHONPATH: " $PYTHONPATH
-echo -e "\t MPICC: " $MPICC
-if test "$want_exchanger" = yes; then
- echo -e "\t MPICXX: " $MPICXX
-fi
-echo -e "\t CFLAGS: " $CFLAGS
-echo -e "\t CPPFLAGS: " $CPPFLAGS
-echo -e "\t LDFLAGS: " $LDFLAGS
-if test "$want_exchanger" = yes; then
- echo -e "\t CXXFLAGS: " $CXXFLAGS
-fi
-echo -e "\t with-pyre: " $want_pyre
-echo -e "\t with-exchanger: " $want_exchanger
-echo -e "\t with-hdf5: " $want_hdf5
-echo
+# Warning!
+AC_MSG_WARN([to build the Pyrized version, run 'merlin configure' instead])
dnl end of configure.ac
Deleted: mc/3D/CitcomS/trunk/doc/CitComS.doxyconf
===================================================================
--- mc/3D/CitcomS/trunk/doc/CitComS.doxyconf 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/doc/CitComS.doxyconf 2006-10-17 09:18:15 UTC (rev 5059)
@@ -1,1098 +0,0 @@
-# Doxyfile 1.3.5
-
-# 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
-#---------------------------------------------------------------------------
-
-# The PROJECT_NAME tag is a single word (or a sequence of words surrounded
-# by quotes) that should identify the project.
-
-PROJECT_NAME = CitComS-pyre
-
-# The PROJECT_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 =
-
-# 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 = ./doc
-
-# 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:
-# Brazilian, Catalan, Chinese, Chinese-Traditional, Croatian, Czech, Danish, Dutch,
-# Finnish, French, German, Greek, Hungarian, Italian, Japanese, Japanese-en
-# (Japanese with English messages), Korean, Norwegian, Polish, Portuguese,
-# Romanian, Russian, Serbian, Slovak, Slovene, Spanish, Swedish, and Ukrainian.
-
-OUTPUT_LANGUAGE = English
-
-# This tag can be used to specify the encoding used in the generated output.
-# The encoding is not always determined by the language that is chosen,
-# but also whether or not the output is meant for Windows or non-Windows users.
-# In case there is a difference, setting the USE_WINDOWS_ENCODING tag to YES
-# forces the Windows encoding (this is the default for the Windows binary),
-# whereas setting the tag to NO uses a Unix-style encoding (the default for
-# all platforms other than Windows).
-
-USE_WINDOWS_ENCODING = NO
-
-# 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. It is allowed to use relative paths in the argument list.
-
-STRIP_FROM_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 the Qt-style comments (thus requiring an
-# explicit @brief command for a brief description.
-
-JAVADOC_AUTOBRIEF = YES
-
-# 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 DETAILS_AT_TOP tag is set to YES then Doxygen
-# will output the detailed description near the top, like JavaDoc.
-# If set to NO, the detailed description appears after the member
-# documentation.
-
-DETAILS_AT_TOP = 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 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
-
-# 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 = 4
-
-# 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 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
-
-#---------------------------------------------------------------------------
-# 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
-
-# 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
-# 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 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
-
-# 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 = NO
-
-# 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 = NO
-
-# 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 = NO
-
-# 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
-
-#---------------------------------------------------------------------------
-# 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
-
-# The WARN_FORMAT tag determines the format of the warning messages that
-# doxygen can produce. The string should contain the $file, $line, and $text
-# tags, which will be replaced by the file and line number from which the
-# warning originated and the warning text.
-
-WARN_FORMAT = "$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 = module/Exchanger
-
-# 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
-
-FILE_PATTERNS =
-
-# 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 = YES
-
-# 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.
-
-EXCLUDE_PATTERNS =
-
-# 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 =
-
-# 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.
-
-INPUT_FILTER =
-
-# 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 = 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 (the default)
-# then for each documented function all documented
-# functions referencing it will be listed.
-
-REFERENCED_BY_RELATION = YES
-
-# If the REFERENCES_RELATION tag is set to YES (the default)
-# then for each documented function all documented entities
-# called/used by that function will be listed.
-
-REFERENCES_RELATION = YES
-
-# 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 = YES
-
-# 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 = 3
-
-# 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 =
-
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes,
-# files or namespaces will be aligned in HTML using tables. If set to
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS = YES
-
-# 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 compressed 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 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
-
-# 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
-
-# If the GENERATE_TREEVIEW tag 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 (for instance Mozilla 1.0+,
-# Netscape 6.0+, Internet explorer 5.0+, or Konqueror). Windows users are
-# probably better off using the HTML help feature.
-
-GENERATE_TREEVIEW = YES
-
-# 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
-
-#---------------------------------------------------------------------------
-# 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
-
-# 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.
-
-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
-
-#---------------------------------------------------------------------------
-# 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_PREDEFINED tags.
-
-EXPAND_ONLY_PREDEF = NO
-
-# 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 =
-
-# 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.
-
-PREDEFINED = DEBUG
-
-# 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::addtions 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 = ../Exchanger/Exchanger.tag=../../../Exchanger/doc/html
-
-# When a file name is specified after GENERATE_TAGFILE, doxygen will create
-# a tag file that is based on the input files it reads.
-
-GENERATE_TAGFILE =
-
-# If the ALLEXTERNALS tag is set to YES all external classes will be listed
-# in the class index. If set to NO only the inherited external classes
-# will be listed.
-
-ALLEXTERNALS = NO
-
-# If the EXTERNAL_GROUPS tag is set to YES all external groups will be listed
-# in the modules index. If set to NO, only the current project's groups will
-# be listed.
-
-EXTERNAL_GROUPS = YES
-
-# The PERL_PATH should be the absolute path and name of the perl script
-# interpreter (i.e. the result of `which perl').
-
-PERL_PATH = /usr/bin/perl
-
-#---------------------------------------------------------------------------
-# Configuration options related to the dot tool
-#---------------------------------------------------------------------------
-
-# If the CLASS_DIAGRAMS tag is set to YES (the default) Doxygen will
-# generate a inheritance diagram (in HTML, RTF and LaTeX) for classes with base or
-# super classes. Setting the tag to NO turns the diagrams off. Note that this
-# option is superseded by the HAVE_DOT option below. This is only a fallback. It is
-# recommended to install and use dot, since it yields more powerful graphs.
-
-CLASS_DIAGRAMS = YES
-
-# If set to YES, the inheritance and collaboration graphs will hide
-# inheritance and usage relations if the target is undocumented
-# or is not a class.
-
-HIDE_UNDOC_RELATIONS = YES
-
-# If you set the HAVE_DOT tag to YES then doxygen will assume the dot tool is
-# available from the path. This tool is part of Graphviz, a graph visualization
-# toolkit from AT&T and Lucent Bell Labs. The other options in this section
-# have no effect if this option is set to NO (the default)
-
-HAVE_DOT = YES
-
-# If the CLASS_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect inheritance relations. Setting this tag to YES will force the
-# the CLASS_DIAGRAMS tag to NO.
-
-CLASS_GRAPH = YES
-
-# If the COLLABORATION_GRAPH and HAVE_DOT tags are set to YES then doxygen
-# will generate a graph for each documented class showing the direct and
-# indirect implementation dependencies (inheritance, containment, and
-# class references variables) of the class with other documented classes.
-
-COLLABORATION_GRAPH = YES
-
-# If the UML_LOOK tag is set to YES doxygen will generate inheritance and
-# collaboration diagrams in a style similar to the OMG's Unified Modeling
-# Language.
-
-UML_LOOK = YES
-
-# If set to YES, the inheritance and collaboration graphs will show the
-# relations between templates and their instances.
-
-TEMPLATE_RELATIONS = NO
-
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDE_GRAPH, and HAVE_DOT
-# tags are set to YES then doxygen will generate a graph for each documented
-# file showing the direct and indirect include dependencies of the file with
-# other documented files.
-
-INCLUDE_GRAPH = YES
-
-# If the ENABLE_PREPROCESSING, SEARCH_INCLUDES, INCLUDED_BY_GRAPH, and
-# HAVE_DOT tags are set to YES then doxygen will generate a graph for each
-# documented header file showing the documented files that directly or
-# indirectly include this file.
-
-INCLUDED_BY_GRAPH = YES
-
-# If the CALL_GRAPH and HAVE_DOT tags are set to YES then doxygen will
-# generate a call dependency graph for every global function or class method.
-# Note that enabling this option will significantly increase the time of a run.
-# So in most cases it will be better to enable call graphs for selected
-# functions only using the \callgraph command.
-
-CALL_GRAPH = YES
-
-# If the GRAPHICAL_HIERARCHY and HAVE_DOT tags are set to YES then doxygen
-# will graphical hierarchy of all classes instead of a textual one.
-
-GRAPHICAL_HIERARCHY = YES
-
-# The DOT_IMAGE_FORMAT tag can be used to set the image format of the images
-# generated by dot. Possible values are png, jpg, or gif
-# If left blank png will be used.
-
-DOT_IMAGE_FORMAT = png
-
-# The tag DOT_PATH can be used to specify the path where the dot tool can be
-# found. If left blank, it is assumed the dot tool can be found on the path.
-
-DOT_PATH =
-
-# The DOTFILE_DIRS tag can be used to specify one or more directories that
-# contain dot files that are included in the documentation (see the
-# \dotfile command).
-
-DOTFILE_DIRS =
-
-# The MAX_DOT_GRAPH_WIDTH tag can be used to set the maximum allowed width
-# (in pixels) of the graphs generated by dot. If a graph becomes larger than
-# this value, doxygen will try to truncate the graph, so that it fits within
-# the specified constraint. Beware that most browsers cannot cope with very
-# large images.
-
-MAX_DOT_GRAPH_WIDTH = 600
-
-# The MAX_DOT_GRAPH_HEIGHT tag can be used to set the maximum allows height
-# (in pixels) of the graphs generated by dot. If a graph becomes larger than
-# this value, doxygen will try to truncate the graph, so that it fits within
-# the specified constraint. Beware that most browsers cannot cope with very
-# large images.
-
-MAX_DOT_GRAPH_HEIGHT = 800
-
-# The MAX_DOT_GRAPH_DEPTH tag can be used to set the maximum depth of the
-# graphs generated by dot. A depth value of 3 means that only nodes reachable
-# from the root by following a path via at most 3 edges will be shown. Nodes that
-# lay further from the root node will be omitted. Note that setting this option to
-# 1 or 2 may greatly reduce the computation time needed for large code bases. Also
-# note that a graph may be further truncated if the graph's image dimensions are
-# not sufficient to fit the graph (see MAX_DOT_GRAPH_WIDTH and MAX_DOT_GRAPH_HEIGHT).
-# If 0 is used for the depth value (the default), the graph is not depth-constrained.
-
-MAX_DOT_GRAPH_DEPTH = 2
-
-# If the GENERATE_LEGEND tag is set to YES (the default) Doxygen will
-# generate a legend page explaining the meaning of the various boxes and
-# arrows in the dot generated graphs.
-
-GENERATE_LEGEND = YES
-
-# If the DOT_CLEANUP tag is set to YES (the default) Doxygen will
-# remove the intermediate dot files that are used to generate
-# the various graphs.
-
-DOT_CLEANUP = YES
-
-#---------------------------------------------------------------------------
-# Configuration::addtions related to the search engine
-#---------------------------------------------------------------------------
-
-# The SEARCHENGINE tag specifies whether or not a search engine should be
-# used. If set to NO the values of all tags below this one will be ignored.
-
-SEARCHENGINE = NO
Modified: mc/3D/CitcomS/trunk/lib/Pan_problem_misc_functions.c
===================================================================
--- mc/3D/CitcomS/trunk/lib/Pan_problem_misc_functions.c 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/lib/Pan_problem_misc_functions.c 2006-10-17 09:18:15 UTC (rev 5059)
@@ -26,6 +26,10 @@
*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
#include "element_definitions.h"
#include "global_defs.h"
Modified: mc/3D/CitcomS/trunk/lib/Tracer_advection.c
===================================================================
--- mc/3D/CitcomS/trunk/lib/Tracer_advection.c 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/lib/Tracer_advection.c 2006-10-17 09:18:15 UTC (rev 5059)
@@ -37,6 +37,9 @@
*/
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
#include <mpi.h>
#include <math.h>
Modified: mc/3D/CitcomS/trunk/module/CitcomSmodule.c
===================================================================
--- mc/3D/CitcomS/trunk/module/CitcomSmodule.c 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/module/CitcomSmodule.c 2006-10-17 09:18:15 UTC (rev 5059)
@@ -25,7 +25,6 @@
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-#include <portinfo>
#include <Python.h>
#include "CitcomSmodule.h"
Modified: mc/3D/CitcomS/trunk/module/Makefile.am
===================================================================
--- mc/3D/CitcomS/trunk/module/Makefile.am 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/module/Makefile.am 2006-10-17 09:18:15 UTC (rev 5059)
@@ -23,53 +23,11 @@
# $Id$
-if COND_EXCHANGER
- MAYBE_EXCHANGER = Exchanger
-endif
-SUBDIRS = $(MAYBE_EXCHANGER)
+noinst_LIBRARIES = libCitcomSLib.a
-noinst_LIBRARIES =
-pyexec_LTLIBRARIES =
+CitcomSLib_a_CPPFLAGS = -I$(top_srcdir)/lib
-if COND_EMBEDDING
- # static library
- noinst_LIBRARIES += libCitcomSLibmodule.a
-else
- # extension module (libtool)
- pyexec_LTLIBRARIES += CitcomSLibmodule.la
-endif
-
-# static libraries
-
-libCitcomSLibmodule_a_CFLAGS = $(AM_CFLAGS) # hack for automake
-libCitcomSLibmodule_a_SOURCES = $(sources)
-
-if COND_HDF5
- libCitcomSLibmodule_a_CFLAGS += -DUSE_HDF5
-endif
-
-# extension modules (libtool)
-
-CitcomSLibmodule_la_LDFLAGS = -module -release $(VERSION)
-CitcomSLibmodule_la_LIBADD = \
- $(top_builddir)/lib/libCitcomS.la \
- $(PYTHON_EGG_LDFLAGS) \
- $(MPILIBS)
-CitcomSLibmodule_la_SOURCES = $(sources)
-
-# compiler settings
-
-CC = $(MPICC)
-INCLUDES = \
- -I$(top_srcdir)/module/Regional \
- -I$(top_srcdir)/lib \
- $(PYTHON_EGG_CPPFLAGS) \
- -I$(PYTHON_INCDIR) \
- $(MPIINCLUDES)
-
-# sources
-
-sources = \
+CitcomSLib_a_SOURCES = \
CitcomSmodule.c \
CitcomSmodule.h \
advdiffu.c \
Modified: mc/3D/CitcomS/trunk/module/Regionalmodule.c
===================================================================
--- mc/3D/CitcomS/trunk/module/Regionalmodule.c 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/module/Regionalmodule.c 2006-10-17 09:18:15 UTC (rev 5059)
@@ -26,7 +26,6 @@
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
//
-#include <portinfo>
#include <Python.h>
#include "exceptions.h"
Modified: mc/3D/CitcomS/trunk/module/advdiffu.c
===================================================================
--- mc/3D/CitcomS/trunk/module/advdiffu.c 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/module/advdiffu.c 2006-10-17 09:18:15 UTC (rev 5059)
@@ -25,7 +25,6 @@
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-#include <portinfo>
#include <Python.h>
#include <stdio.h>
Modified: mc/3D/CitcomS/trunk/module/bindings.c
===================================================================
--- mc/3D/CitcomS/trunk/module/bindings.c 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/module/bindings.c 2006-10-17 09:18:15 UTC (rev 5059)
@@ -25,7 +25,6 @@
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-#include <portinfo>
#include <Python.h>
#include "bindings.h"
Modified: mc/3D/CitcomS/trunk/module/exceptions.c
===================================================================
--- mc/3D/CitcomS/trunk/module/exceptions.c 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/module/exceptions.c 2006-10-17 09:18:15 UTC (rev 5059)
@@ -25,7 +25,6 @@
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-#include <portinfo>
#include <Python.h>
PyObject *pyCitcom_runtimeError = 0;
Modified: mc/3D/CitcomS/trunk/module/initial_conditions.c
===================================================================
--- mc/3D/CitcomS/trunk/module/initial_conditions.c 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/module/initial_conditions.c 2006-10-17 09:18:15 UTC (rev 5059)
@@ -25,7 +25,6 @@
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-#include <portinfo>
#include <Python.h>
#include "exceptions.h"
#include "initial_conditions.h"
Modified: mc/3D/CitcomS/trunk/module/mesher.c
===================================================================
--- mc/3D/CitcomS/trunk/module/mesher.c 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/module/mesher.c 2006-10-17 09:18:15 UTC (rev 5059)
@@ -25,7 +25,6 @@
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-#include <portinfo>
#include <Python.h>
#include "exceptions.h"
Modified: mc/3D/CitcomS/trunk/module/misc.c
===================================================================
--- mc/3D/CitcomS/trunk/module/misc.c 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/module/misc.c 2006-10-17 09:18:15 UTC (rev 5059)
@@ -25,7 +25,6 @@
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-#include <portinfo>
#include <Python.h>
Modified: mc/3D/CitcomS/trunk/module/outputs.c
===================================================================
--- mc/3D/CitcomS/trunk/module/outputs.c 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/module/outputs.c 2006-10-17 09:18:15 UTC (rev 5059)
@@ -25,7 +25,6 @@
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-#include <portinfo>
#include <Python.h>
#include <stdio.h>
Modified: mc/3D/CitcomS/trunk/module/setProperties.c
===================================================================
--- mc/3D/CitcomS/trunk/module/setProperties.c 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/module/setProperties.c 2006-10-17 09:18:15 UTC (rev 5059)
@@ -25,7 +25,6 @@
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-#include <portinfo>
#include <Python.h>
#include <stddef.h>
#include <stdio.h>
Modified: mc/3D/CitcomS/trunk/module/stokes_solver.c
===================================================================
--- mc/3D/CitcomS/trunk/module/stokes_solver.c 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/module/stokes_solver.c 2006-10-17 09:18:15 UTC (rev 5059)
@@ -25,7 +25,6 @@
//~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
-#include <portinfo>
#include <Python.h>
Added: mc/3D/CitcomS/trunk/project.cfg
===================================================================
--- mc/3D/CitcomS/trunk/project.cfg 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/project.cfg 2006-10-17 09:18:15 UTC (rev 5059)
@@ -0,0 +1,132 @@
+[merlin.spells.thisfile.metadata]
+format.version = '1'
+
+
+[projects.CitcomS]
+
+version = '2.1'
+
+summary = """A finite element mantle convection code."""
+
+description = """
+ CitcomS is a finite element code designed to solve thermal convection
+ problems relevant to Earth's mantle. Written in C, the code runs on a
+ variety of parallel processing computers, including shared and
+ distributed memory platforms."""
+
+license = licenses.GPL
+homepage = 'http://www.geodynamics.org/cig/software/packages/citcoms/'
+contact = mailingLists.cigMC
+
+
+# actions
+
+
+[projects.CitcomS.actions.run]
+requires = [libraries.CitcomS]
+entryPoint = libraries.CitcomS.SimpleApp
+
+
+# components
+
+
+[projects.CitcomS.components.hdf]
+modifiers = [optional]
+requires = [libraries.HDFLib]
+
+
+[projects.CitcomS.components.exchanger]
+modifiers = [experimental]
+requires = [libraries.ExchangerLib]
+
+
+# programs (legacy)
+
+
+[projects.CitcomS.programs.CitcomSFull]
+modifiers = [legacy, primitive]
+requires = [libraries.libCitcomS]
+source.files = ['Citcom.c', 'CitcomSFull.c']
+
+
+[projects.CitcomS.programs.CitcomSRegional]
+modifiers = [legacy, primitive]
+requires = [libraries.libCitcomS]
+source.files = ['Citcom.c', 'CitcomSRegional.c']
+
+
+# libraries
+
+
+[projects.CitcomS.libraries.CitcomS]
+authors = [tan2, ces74, puru]
+modifiers = [scriptable]
+requires = [libraries.CitcomSLib, imports.pythia]
+
+
+[projects.CitcomS.libraries.CitcomSLib]
+modifiers = [private, native]
+source.directory = module
+requires = [libraries.libCitcomS]
+
+
+[projects.CitcomS.libraries.libCitcomS]
+authors = [moresi, szhong, han, tan2, conrad, gurnis]
+modifiers = [private, primitive]
+source.directory = lib
+requires = [imports.libm, imports.MPI]
+
+
+[projects.CitcomS.libraries.ExchangerLib]
+modifiers = [private, native]
+requires = [imports.Exchanger]
+
+
+[projects.CitcomS.libraries.HDFLib]
+modifiers = [private, native]
+requires = [imports.HDF]
+
+
+# authors of CitcomS & CitcomSLib
+
+[people]
+
+tan2.name = 'Eh Tan'
+tan2.modifiers = [author]
+
+ces74.name = 'Eun-seo Choi'
+ces74.modifiers = [author]
+
+puru.name = 'Pururav Thoutireddy'
+puru.modifiers = [author]
+
+
+# authors of libCitcomS
+
+[people]
+
+moresi.name = 'Louis Moresi'
+moresi.modifiers = [original author]
+
+szhong.name = 'Shijie Zhong'
+szhong.modifiers = [author]
+
+han.name = 'Lijie Han'
+han.modifiers = [author]
+
+# tan2 (listed above)
+
+conrad.name = 'Clint Conrad'
+conrad.modifiers = [author]
+
+gurnis.name = 'Michael Gurnis'
+gurnis.modifiers = [author]
+
+# ces74 (listed above)
+
+
+[mailingLists.cig.mc]
+postAddress = 'cig-mc at geodynamics.org'
+
+
+# end of file
Modified: mc/3D/CitcomS/trunk/setup.py
===================================================================
--- mc/3D/CitcomS/trunk/setup.py 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/setup.py 2006-10-17 09:18:15 UTC (rev 5059)
@@ -1,33 +1,6 @@
-from ez_setup import use_setuptools
-use_setuptools()
+from imports.merlin import use_merlin
+use_merlin()
-from setuptools import setup, find_packages
-
-setup(
-
- name = 'CitcomS',
- version = '2.1',
-
- zip_safe = False,
- packages = find_packages(),
-
- #setup_requires = [
- #'merlin',
- #],
- install_requires = [
- 'pythia[pyre,mpi] >= 0.8.1.0b2, < 0.8-2.0a, == dev',
- ],
- extras_require = {
- 'Exchanger': ['Exchanger >= 1.0, < 2.0a'],
- },
-
- author = 'Louis Moresi, et al.',
- author_email = 'cig-mc at geodynamics.org',
- description = """A finite element mantle convection code.""",
- long_description = """CitcomS is a finite element code designed to solve thermal convection problems relevant to Earth's mantle. Written in C, the code runs on a variety of parallel processing computers, including shared and distributed memory platforms.""",
- license = 'GPL',
- url = 'http://www.geodynamics.org/cig/software/packages/citcoms/',
- download_url = 'http://crust.geodynamics.org/~leif/shipping/', # temporary
-
-)
+from merlin import setup
+setup()
Modified: mc/3D/CitcomS/trunk/tests/Makefile.am
===================================================================
--- mc/3D/CitcomS/trunk/tests/Makefile.am 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/tests/Makefile.am 2006-10-17 09:18:15 UTC (rev 5059)
@@ -23,23 +23,8 @@
# $Id$
-# C++ tests
-TESTS = $(EXTRA_PROGRAMS)
-INSTALL_TESTS = $(EXTRA_PROGRAMS)
-EXTRA_PROGRAMS = array2d
-array2d_SOURCES = array2d.cc
-PYTHON_BLDLIBRARY = -lpython$(PYTHON_VERSION)
-INCLUDES = \
- -I$(top_srcdir)/lib/Common \
- $(MPIINCLUDES)
-LDADD = \
- -lExchanger \
- -l_mpimodule -ljournal \
- $(PYTHON_BLDLIBRARY) \
- $(MPILIBS)
-CC = $(MPICC)
-
EXTRA_DIST = \
+ array2d.cc \
asap.py \
exchange.py \
hrothgar.py \
Modified: mc/3D/CitcomS/trunk/visual/Makefile.am
===================================================================
--- mc/3D/CitcomS/trunk/visual/Makefile.am 2006-10-17 09:11:50 UTC (rev 5058)
+++ mc/3D/CitcomS/trunk/visual/Makefile.am 2006-10-17 09:18:15 UTC (rev 5059)
@@ -109,14 +109,15 @@
chmod 644 "$(DESTDIR)$(visualdir)/$$f"; \
done
-if COND_HDF5
- bin_PROGRAMS = h5tocap h5steps
- h5tocap_SOURCES = h5tocap.c
- h5tocap_LDADD = $(LIBHDF5)
- h5steps_SOURCES = h5steps.c
- h5steps_LDADD = $(LIBHDF5)
-endif
+# if COND_HDF5
+# bin_PROGRAMS = h5tocap h5steps
+# h5tocap_SOURCES = h5tocap.c
+# h5tocap_LDADD = $(LIBHDF5)
+# h5steps_SOURCES = h5steps.c
+# h5steps_LDADD = $(LIBHDF5)
+# endif
CLEANFILES = $(nodist_visual_DATA)
EXTRA_DIST = $(visual_templates)
+
## end of Makefile.am
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