Mercurial > hg > octave-nkf
changeset 5694:95d90f781ca8
[project @ 2006-03-20 18:29:20 by jwe]
author | jwe |
---|---|
date | Mon, 20 Mar 2006 18:30:21 +0000 |
parents | 446b28529300 |
children | f6ddb906e30f |
files | src/ChangeLog src/DLD-FUNCTIONS/dasrt.cc src/DLD-FUNCTIONS/dassl.cc src/DLD-FUNCTIONS/lsode.cc src/DLD-FUNCTIONS/odessa.cc |
diffstat | 5 files changed, 6 insertions(+), 614 deletions(-) [+] |
line wrap: on
line diff
--- a/src/ChangeLog +++ b/src/ChangeLog @@ -175,10 +175,9 @@ DLD-FUNCTIONS/fft.cc, DLD-FUNCTIONS/fft2.cc, DLD-FUNCTIONS/fftn.cc, DLD-FUNCTIONS/fftw_wisdom.cc, DLD-FUNCTIONS/gammainc.cc, DLD-FUNCTIONS/gcd.cc, - DLD-FUNCTIONS/luinc.cc, DLD-FUNCTIONS/odessa.cc, - DLD-FUNCTIONS/sparse.cc, DLD-FUNCTIONS/spchol.cc, - DLD-FUNCTIONS/splu.cc, DLD-FUNCTIONS/spqr.cc, - DLD-FUNCTIONS/sqrtm.cc: + DLD-FUNCTIONS/luinc.cc, DLD-FUNCTIONS/sparse.cc, + DLD-FUNCTIONS/spchol.cc, DLD-FUNCTIONS/splu.cc, + DLD-FUNCTIONS/spqr.cc, DLD-FUNCTIONS/sqrtm.cc: Move @seealso inside @defXXX macro. Remove "and" from @seealso. 2006-03-04 John W. Eaton <jwe@octave.org>
--- a/src/DLD-FUNCTIONS/dasrt.cc +++ b/src/DLD-FUNCTIONS/dasrt.cc @@ -339,7 +339,7 @@ \n\ You can use the function @code{dasrt_options} to set optional\n\ parameters for @code{dasrt}.\n\ -@seealso{daspk, dasrt, lsode, odessa}\n\ +@seealso{daspk, dasrt, lsode}\n\ @end deftypefn") { octave_value_list retval;
--- a/src/DLD-FUNCTIONS/dassl.cc +++ b/src/DLD-FUNCTIONS/dassl.cc @@ -271,7 +271,7 @@ \n\ You can use the function @code{dassl_options} to set optional\n\ parameters for @code{dassl}.\n\ -@seealso{daspk, dasrt, lsode, odessa}\n\ +@seealso{daspk, dasrt, lsode}\n\ @end deftypefn") { octave_value_list retval;
--- a/src/DLD-FUNCTIONS/lsode.cc +++ b/src/DLD-FUNCTIONS/lsode.cc @@ -266,7 +266,7 @@ \n\ You can use the function @code{lsode_options} to set optional\n\ parameters for @code{lsode}.\n\ -@seealso{daspk, dassl, dasrt, odessa}\n\ +@seealso{daspk, dassl, dasrt}\n\ @end deftypefn") { octave_value_list retval;
deleted file mode 100644 --- a/src/DLD-FUNCTIONS/odessa.cc +++ /dev/null @@ -1,607 +0,0 @@ -/* - -Copyright (C) 2002 John W. Eaton - -This file is part of Octave. - -Octave 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, or (at your option) any -later version. - -Octave 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 Octave; see the file COPYING. If not, write to the Free -Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA -02110-1301, USA. - -*/ - -#ifdef HAVE_CONFIG_H -#include <config.h> -#endif - -#include <string> - -#include <iomanip> -#include <iostream> - -#include "ODESSA.h" -#include "lo-mappers.h" - -#include "defun-dld.h" -#include "error.h" -#include "gripes.h" -#include "oct-obj.h" -#include "ov-fcn.h" -#include "pager.h" -#include "pr-output.h" -#include "unwind-prot.h" -#include "utils.h" -#include "variables.h" -#include "parse.h" - -#include "ODESSA-opts.cc" - -// Global pointer for user defined function required by odessa. -static octave_function *odessa_f; -static octave_function *odessa_j; -static octave_function *odessa_b; - -// Have we warned about imaginary values returned from user function? -static bool warned_fcn_imaginary = false; -static bool warned_jac_imaginary = false; -static bool warned_b_imaginary = false; - -// Is this a recursive call? -static int call_depth = 0; - -static ColumnVector -odessa_user_f (const ColumnVector& x, double t, const ColumnVector& theta) -{ - ColumnVector retval; - - octave_value_list args; - - int n = x.length (); - int npar = theta.length (); - - if (npar > 1) - args(2) = theta; - else if (npar == 1) - args(2) = theta(0); - else - args(2) = Matrix (); - - args(1) = t; - - if (n > 1) - args(0) = x; - else if (n == 1) - args(0) = x(0); - else - args(0) = Matrix (); - - if (odessa_f) - { - octave_value_list tmp = odessa_f->do_multi_index_op (1, args); - - if (error_state) - { - gripe_user_supplied_eval ("odessa"); - return retval; - } - - if (tmp.length () > 0 && tmp(0).is_defined ()) - { - if (! warned_fcn_imaginary && tmp(0).is_complex_type ()) - { - warning ("odessa: ignoring imaginary part returned from user-supplied function"); - warned_fcn_imaginary = true; - } - - retval = ColumnVector (tmp(0).vector_value ()); - - if (error_state || retval.length () == 0) - gripe_user_supplied_eval ("odessa"); - } - else - gripe_user_supplied_eval ("odessa"); - } - - return retval; -} - -static Matrix -odessa_user_j (const ColumnVector& x, double t, const ColumnVector& theta) -{ - Matrix retval; - - if (odessa_j) - { - octave_value_list args; - - int n = x.length (); - int npar = theta.length (); - - if (npar > 1) - args(2) = theta; - else if (npar == 1) - args(2) = theta(0); - else - args(2) = Matrix (); - - args(1) = t; - - if (n > 1) - args(0) = x; - else if (n == 1) - args(0) = x(0); - else - args(0) = Matrix (); - - octave_value_list tmp = odessa_j->do_multi_index_op (1, args); - - if (error_state) - { - gripe_user_supplied_eval ("odessa"); - return retval; - } - - if (tmp.length () > 0 && tmp(0).is_defined ()) - { - if (! warned_jac_imaginary && tmp(0).is_complex_type ()) - { - warning ("odessa: ignoring imaginary part returned from user-supplied jacobian function"); - warned_jac_imaginary = true; - } - - retval = tmp(0).matrix_value (); - - if (error_state || retval.length () == 0) - gripe_user_supplied_eval ("odessa"); - } - else - gripe_user_supplied_eval ("odessa"); - } - - return retval; -} - -static ColumnVector -odessa_user_b (const ColumnVector& x, double t, - const ColumnVector& theta, int column) -{ - ColumnVector retval; - - if (odessa_b) - { - octave_value_list args; - - int n = x.length (); - int npar = theta.length (); - - args(3) = static_cast<double> (column); - - if (npar > 1) - args(2) = theta; - else if (npar == 1) - args(2) = theta(0); - else - args(2) = Matrix (); - - args(1) = t; - - if (n > 1) - args(0) = x; - else if (n == 1) - args(0) = x(0); - else - args(0) = Matrix (); - - octave_value_list tmp = odessa_b->do_multi_index_op (1, args); - - if (error_state) - { - gripe_user_supplied_eval ("odessa"); - return retval; - } - - if (tmp.length () > 0 && tmp(0).is_defined ()) - { - if (! warned_b_imaginary && tmp(0).is_complex_type ()) - { - warning ("odessa: ignoring imaginary part returned from user-supplied inhomogeneity function"); - warned_b_imaginary = true; - } - - retval = ColumnVector (tmp(0).vector_value ()); - - if (error_state || retval.length () == 0) - gripe_user_supplied_eval ("odessa"); - } - else - gripe_user_supplied_eval ("odessa"); - } - - return retval; -} - -static octave_value -make_list (const Array<Matrix>& m_array) -{ - octave_value_list retval; - - int len = m_array.length (); - - retval.resize (len); - - for (int i = 0; i < len; i++) - retval(i) = m_array(i); - - return octave_value (retval); -} - -#define ODESSA_ABORT() \ - do \ - { \ - unwind_protect::run_frame ("Fodessa"); \ - return retval; \ - } \ - while (0) - -#define ODESSA_ABORT1(msg) \ - do \ - { \ - ::error ("odessa: " msg); \ - ODESSA_ABORT (); \ - } \ - while (0) - -#define ODESSA_ABORT2(fmt, arg) \ - do \ - { \ - ::error ("odessa: " fmt, arg); \ - ODESSA_ABORT (); \ - } \ - while (0) - -DEFUN_DLD (odessa, args, nargout, - "-*- texinfo -*-\n\ -@deftypefn {Loadable Function} {[@var{x}, @var{sx}, @var{istate}, @var{msg}]} odessa (@var{fcn}, @var{x_0}, @var{p}, @var{sx_0}, @var{t}, @var{t_crit})\n\ -Solve the set of differential equations\n\ -@tex\n\ -$$ {dx \\over dt} = f (x, t; p) $$\n\ -with\n\ -$$ x(t_0) = x_0 $$\n\ -@end tex\n\ -@ifinfo\n\ -\n\ -@example\n\ -dx\n\ --- = f(x, t; p)\n\ -dt\n\ -@end example\n\ -\n\ -with\n\ -\n\ -@example\n\ -x(t_0) = x_0\n\ -@end example\n\ -\n\ -@end ifinfo\n\ -and simultaneously compute the first-order sensitivity coefficients\n\ -given by\n\ -\n\ -@example\n\ -s'(t) = j(t)*s(t) + df/dp\n\ -@end example\n\ -\n\ -in which\n\ -\n\ -@example\n\ -s(t) = dx(t)/dp (sensitivity functions)\n\ -s'(t) = d(dx(t)/dp)/dt\n\ -j(t) = df(x,t;p)/dx(t) (Jacobian matrix)\n\ -df/dp = df(x,t;p)/dp (inhomogeneity matrix)\n\ -@end example\n\ -\n\ -The solution is returned in the matrix @var{x}, with each row\n\ -corresponding to an element of the vector @var{t}. The first element\n\ -of @var{t} should be @math{t_0} and should correspond to the initial\n\ -state of the system @var{x_0}, so that the first row of the output\n\ -is @var{x_0}.\n\ -\n\ -The sensitivities are returned in a list of matrices, @var{sx},\n\ -with each element of the list corresponding to an element of the\n\ -vector @var{t}.\n\ -\n\ -The first argument, @var{fcn}, is a string that names the function to\n\ -call to compute the vector of right hand sides for the set of equations.\n\ -The function must have the form\n\ -\n\ -@example\n\ -@var{xdot} = f (@var{x}, @var{t}, @var{p})\n\ -@end example\n\ -\n\ -@noindent\n\ -in which @var{xdot} and @var{x} are vectors and @var{t} is a scalar.\n\ -\n\ -The variable @var{p} is a vector of parameters.\n\ -\n\ -The @var{fcn} argument may also be an array of strings\n\ -\n\ -@example\n\ -[\"f\"; \"j\"; \"b\"]\n\ -@end example\n\ -\n\ -in which the first element names the function @math{f} described\n\ -above, the second element names a function to compute the Jacobian\n\ -of @math{f}, and the third element names a function to compute the\n\ -inhomogeneity matrix.\n\ -\n\ -The Jacobian function must have the form\n\ -\n\ -@example\n\ -@var{jac} = j (@var{x}, @var{t}, @var{p})\n\ -@end example\n\ -\n\ -in which @var{x}, @var{t}, and @var{p} have the same meanings as\n\ -above for the function @var{f}, and @var{jac} is the matrix of\n\ -partial derivatives\n\ -@tex\n\ -$$ J = {\\partial f_i \\over \\partial x_j} $$\n\ -@end tex\n\ -@ifinfo\n\ -\n\ -@example\n\ - df_i\n\ -jac = ----\n\ - dx_j\n\ -@end example\n\ -\n\ -@end ifinfo\n\ -\n\ -The function @var{b} must have the form\n\ -\n\ -@example\n\ -@var{dfdp} = b (@var{x}, @var{t}, @var{p}, @var{c})\n\ -@end example\n\ -\n\ -in which @var{x}, @var{t}, and @var{p} have the same meanings as\n\ -above for the function @var{f}, @var{c} indicates which partial\n\ -derivatives to return in @var{dfdp}. For example, if @var{c} is 2,\n\ -you should return the vector\n\ -\n\ -@example\n\ - df_i\n\ -dfdp = ----, i = 1:length(x)\n\ - dp_2\n\ -@end example\n\ -\n\ -The second argument, @var{x_0}, specifies the intial state of the system.\n\ -\n\ -The third argument, @var{p}, specifies the set of parameters.\n\ -\n\ -The fourth argument, @var{sx_0} specifies the initial values of the\n\ -sensitivities.\n\ -\n\ -The sixth argument is optional, and may be used to specify a set of\n\ -times that the ODE solver should not integrate past. It is useful for\n\ -avoiding difficulties with singularities and points where there is a\n\ -discontinuity in the derivative.\n\ -\n\ -After a successful computation, the value of @var{istate} will be 2\n\ -(consistent with the Fortran version of @sc{Odessa}).\n\ -\n\ -If the computation is not successful, @var{istate} will be something\n\ -other than 2 and @var{msg} will contain additional information.\n\ -\n\ -You can use the function @code{odessa_options} to set optional\n\ -parameters for @code{odessa}.\n\ -@seealso{daspk, dassl, dasrt, lsode}\n\ -@end deftypefn") -{ - octave_value_list retval; - - warned_fcn_imaginary = false; - warned_jac_imaginary = false; - warned_b_imaginary = false; - - unwind_protect::begin_frame ("Fodessa"); - - unwind_protect_int (call_depth); - call_depth++; - - if (call_depth > 1) - ODESSA_ABORT1 ("invalid recursive call"); - - int nargin = args.length (); - - if (nargin < 5 || nargin > 6) - { - print_usage ("odessa"); - unwind_protect::run_frame ("Fodessa"); - return retval; - } - - odessa_f = 0; - odessa_j = 0; - odessa_b = 0; - - octave_value f_arg = args(0); - - int nr = f_arg.rows (); - - if (nr == 1) - { - odessa_f = extract_function - (f_arg, "odessa", "__odessa_fcn__", - "function xdot = __odessa_fcn__ (x, t, p) xdot = ", - "; endfunction"); - } - else if (nr == 2 || nr == 3) - { - string_vector tmp = f_arg.all_strings (); - - if (! error_state) - { - odessa_f = extract_function - (tmp(0), "odessa", "__odessa_fcn__", - "function xdot = __odessa_fcn__ (x, t, p) xdot = ", - "; endfunction"); - - if (odessa_f) - { - odessa_j = extract_function - (tmp(1), "odessa", "__odessa_jac__", - "function xdot = __odessa_jac__ (x, t, p) jac = ", - "; endfunction"); - - if (odessa_j && nr == 3) - { - odessa_b = extract_function - (tmp(2), "odessa", "__odessa_b__", - "function dfdp = __odessa_b__ (x, t, p, c) dfdp = ", - "; endfunction"); - - if (! odessa_b) - odessa_j = 0; - } - - if (! odessa_j) - odessa_f = 0; - } - } - } - - if (error_state || ! odessa_f) - ODESSA_ABORT1 - ("expecting function name as argument 1"); - - ColumnVector state (args(1).vector_value ()); - - if (error_state) - ODESSA_ABORT1 ("expecting state vector as argument 2"); - - bool have_parameters = false; - - ColumnVector theta; - Matrix sensitivity_guess; - - if (nargin == 5 || nargin == 6) - { - octave_value theta_arg = args(2); - - if (! theta_arg.is_empty ()) - { - theta = ColumnVector (theta_arg.vector_value ()); - - if (error_state) - ODESSA_ABORT1 - ("expecting parameter vector as argument 3"); - } - - have_parameters = (theta.length () > 0); - - if (have_parameters) - { - sensitivity_guess = args(3).matrix_value (); - - if (error_state) - ODESSA_ABORT1 - ("expecting sensitivity guess as argument 4"); - - if (sensitivity_guess.rows () != state.length () - || sensitivity_guess.columns () != theta.length ()) - ODESSA_ABORT1 - ("incorrect dimension for sensitivity guess"); - } - } - - ColumnVector out_times (args(4).vector_value ()); - - if (error_state) - ODESSA_ABORT1 - ("expecting output time vector as %s argument 5"); - - ColumnVector crit_times; - - bool crit_times_set = false; - - if (nargin == 6) - { - crit_times = ColumnVector (args(5).vector_value ()); - - if (error_state) - ODESSA_ABORT1 - ("expecting critical time vector as argument 6"); - - crit_times_set = true; - } - - ODESFunc func (odessa_user_f); - - if (odessa_j) - func.set_jsub_function (odessa_user_j); - - if (odessa_b) - func.set_bsub_function (odessa_user_b); - - double tzero = out_times (0); - - ODESSA_result output; - - ODESSA ode = have_parameters - ? ODESSA (state, theta, sensitivity_guess, tzero, func) - : ODESSA (state, tzero, func); - - ode.set_options (odessa_opts); - - if (crit_times_set) - output = ode.integrate (out_times, crit_times); - else - output = ode.integrate (out_times); - - if (! error_state) - { - int k = have_parameters ? 3 : 2; - - std::string msg = ode.error_message (); - - retval(k--) = msg; - retval(k--) = static_cast<double> (ode.integration_state ()); - - if (ode.integration_ok ()) - { - if (have_parameters) - retval(1) = make_list (output.state_sensitivity ()); - - retval(0) = output.state (); - } - else - { - if (have_parameters) - retval(1) = Matrix (); - - retval(0) = Matrix (); - - if ((have_parameters && nargout < 3) || nargout < 2) - error ("odessa: %s", msg.c_str ()); - } - } - - unwind_protect::run_frame ("Fodessa"); - - return retval; -} - -/* -;;; Local Variables: *** -;;; mode: C++ *** -;;; End: *** -*/