[Developers] libraries of functions
Mark Maunder
mmaunder at iattc.org
Fri Aug 15 10:33:41 PDT 2014
John,
What I can find for atan2 is the following.
dvector atan2 (const dvector &t1, const dvector &t2)
dvector atan2 (const dvector &t1, double t2)
dvector atan2 (double t1, const dvector &t2)
dvar_vector atan2 (const dvar_vector &t1, const dvar_vector &t2)
dvar_vector atan2 (const dvar_vector &t1, double t2)
dvar_vector atan2 (double t1, const dvar_vector &t2)
In the source code I find in fvar_fn1.cpp
prevariable & atan2 (const prevariable &v1, const prevariable &v2)
Description not yet available.
prevariable & atan2 (const prevariable &v1, const double v2)
Description not yet available.
prevariable & atan2 (const double v1, const prevariable &v2)
Description not yet available.
It's more like a field of rabbit holes. That's why I am reluctant to change the core code and would like to work with user defined libraries. I was advised to use templates and traits, but my experience with those was not very gratifying. Going back to multiple overloads using dvariables and prevariables looks like the best approach.
Why would a copy constructor defined for a double to a prevariable be dangerous since there is already one from a double to a dvariable? This would eliminate a whole set of overloaded functions that would need to be created.
Mark
-----Original Message-----
From: John Sibert [mailto:sibert at hawaii.edu]
Sent: Thursday, August 14, 2014 12:57 PM
To: Mark Maunder; William Stockhausen - NOAA Federal
Cc: developers at admb-project.org
Subject: Re: [Developers] libraries of functions
You guys are headed down a rabbit hole.
There are plenty of examples in admb of functions defined to take double, dvariable, dvar_vector, and ... arguments. Have a look at some of those (eg atan2(...) )before you start writing dangerous and useless constructors and casts.
John Sibert
Emeritus Researcher, SOEST
University of Hawaii at Manoa
Honolulu HI (GMT-10)
808-294-3842 (mobile)
Visit the ADMB project http://admb-project.org/
On 08/13/2014 12:26 PM, Mark Maunder wrote:
>
> So we need a copy constructor defined for a double to a prevariable.
> We probably also need a copy constructor defined for an int to a
> prevariable
>
> What about a dvector[1], an ivector[1], or higher dimensions to a
> prevariable?
>
> Then we could define the library functions as prevariables. Are there
> any disadvantages to this?
>
> Mark
>
> *From:*William Stockhausen - NOAA Federal
> [mailto:william.stockhausen at noaa.gov]
> *Sent:* Wednesday, August 13, 2014 1:46 PM
> *To:* Mark Maunder
> *Cc:* Steve Martell; developers at admb-project.org
> *Subject:* Re: [Developers] libraries of functions
>
> I think dvariable works with a double because it has a "copy
> constructor" defined for a double (so you can do something like
> "dvariable dv(0.124);" in your code. The compiler knows how to convert
> a double to a dvariable when you pass a double as the 1st input to
> Richards(const dvariable&,...) [note that your code calling this
> function w/ a double wouldn't compile if you didn't have the "const"
> there because c++ only constructs temporary variables (the resulting
> dvariable) when they are declared consts (and thus don't modify them
> in the function body)]. Passing a double as 1st input to
> Richards(const prevariable&,...) wouldn't work because prevariable
> doesn't have a copy constructor defined for a double, so the compiler
> doesn't know how to convert a double to a temporary prevariable&.
> Passing a dvariable to the latter function is no problem because a
> dvariable is already a prevariable because it's a derived class of
> prevariable.
>
> Where you'll get in trouble with Richards(const dvariable&,...) is
> when you try Richards(dvarvector[1],...) where dvarvector is a
> dvar_vector, because the operation dvarvector[1] returns a
> prevariable, not a dvariable! You're also out of luck with
> dvar3_array(i,j) [returns a prevariable] and I suspect most/all of the
> dvar array operations that return a single element.
>
> Buck
>
>
> ***************************************************
> * Dr. William T. Stockhausen *
> ***************************************************
> * Resource Ecology and Fisheries Management *
> * Alaska Fisheries Science Center *
> * National Marine Fisheries Service *
> * National Oceanic and Atmospheric Administration *
> * 7600 Sand Point Way N.E. *
> * Seattle, Washington 98115-6349 *
> ***************************************************
> * email: William.Stockhausen at noaa.gov
> <mailto:William.Stockhausen at noaa.gov> *
> * voice: 206-526-4241 fax: 206-526-6723 *
> * web : http://www.afsc.noaa.gov *
> ***************************************************
> All models are wrong, some are useful.--G.E.P. Box
> Beware of geeks bearing equations. --W. Buffett
> ***************************************************
> Disclaimer: The opinions expressed above are personal and do not
> necessarily reflect official NOAA policy.
>
> On Wed, Aug 13, 2014 at 9:45 AM, Mark Maunder <mmaunder at iattc.org
> <mailto:mmaunder at iattc.org>> wrote:
>
> Thanks Buck.
>
> However dvariable works for a double but a prevariable does not (nor
> does a named_dvariable, whatever that is). The error I get using
> prevariables is
>
> no matching function for call to 'Richards(double&, named_dvariable&,
> named_dvariable&, param_init_number&, named_dvariable&)
>
> *From:*William Stockhausen - NOAA Federal
> [mailto:william.stockhausen at noaa.gov
> <mailto:william.stockhausen at noaa.gov>]
> *Sent:* Tuesday, August 12, 2014 1:59 PM
> *To:* Mark Maunder
> *Cc:* Steve Martell; developers at admb-project.org
> <mailto:developers at admb-project.org>
>
>
> *Subject:* Re: [Developers] libraries of functions
>
> If you redefine all the dvariables in the function signature as
> prevariables, you may be ok (as long as you don't try passing in a
> double, which the last error in your error output seems to be
> indicating). This is because (if I followed things correctly in the
> online documentation):
>
> param_init_number inherits from named_dvariable, which inherits
> from dvariable, which inherits from prevariable.
>
> which you can partly see from the "Class Hierarchy" entry regarding
> prevariable on the online documentation (although param_init_number is
> missing). It would be a nice feature in the documentation if you could
> see the class hierarchy tree starting from the most-derived
> (param_init_number, in this case) to the base class(es).
>
> Buck
>
>
> ***************************************************
> * Dr. William T. Stockhausen *
> ***************************************************
> * Resource Ecology and Fisheries Management *
> * Alaska Fisheries Science Center *
> * National Marine Fisheries Service *
> * National Oceanic and Atmospheric Administration *
> * 7600 Sand Point Way N.E. *
> * Seattle, Washington 98115-6349 *
> ***************************************************
> * email: William.Stockhausen at noaa.gov
> <mailto:William.Stockhausen at noaa.gov> *
> * voice: 206-526-4241 <tel:206-526-4241> fax: 206-526-6723
> <tel:206-526-6723> *
> * web : http://www.afsc.noaa.gov *
> ***************************************************
> All models are wrong, some are useful.--G.E.P. Box
> Beware of geeks bearing equations. --W. Buffett
> ***************************************************
> Disclaimer: The opinions expressed above are personal and do not
> necessarily reflect official NOAA policy.
>
> On Tue, Aug 12, 2014 at 12:51 PM, Mark Maunder <mmaunder at iattc.org
> <mailto:mmaunder at iattc.org>> wrote:
>
> Any comments on the use of templates messing up the various forms of
> dvariable and the automatic translation between the different forms of
> dvariable (sorry for not using the right terminology). I think the
> beneficial use of templates for functions in ADMB might be a redherring.
>
> Mark
>
> *From:*developers-bounces at admb-project.org
> <mailto:developers-bounces at admb-project.org>
> [mailto:developers-bounces at admb-project.org
> <mailto:developers-bounces at admb-project.org>] *On Behalf Of *Steve
> Martell
> *Sent:* Tuesday, August 12, 2014 12:46 PM
> *To:* William Stockhausen - NOAA Federal
> *Cc:* developers at admb-project.org <mailto:developers at admb-project.org>
>
>
> *Subject:* Re: [Developers] libraries of functions
>
> My bad
>
> Should have been
>
> FUNCTION dvariable Richards(...)
>
> S
>
> On Aug 12, 2014, at 12:40 PM, William Stockhausen - NOAA Federal
> <william.stockhausen at noaa.gov <mailto:william.stockhausen at noaa.gov>>
> wrote:
>
> I don't think your suggestion will work, Steve (he said without having
> tried it). If I understand things correctly (going out on a looong
> limb here), "FUNCTION" is an identifier to the tpl2cpp translator that
> what follows is a function that 1) whose signature should be added to
> the model_parameters class declaration in tpl_name.htp and 2) whose
> implementation should be added to tpl_name.cpp.
>
> A nice (but probably tough to implement) feature in tpl2cpp would be
> the ability to put the following:
>
> FUNCTION dvariable model_parameters::Richards(const dvariable &age,
> const dvariable &Linf, const dvariable &K, const dvariable &t0, const
> dvariable &p)
>
> dvariable Length=Linf*pow((1+(1/p)*exp(-K*(age-t0))),-p);
>
> return(Length);
>
> into a file (functions.cxx, say) and be able to "include" that text in
> the tpl you're converting to cpp at a stage in the process before
> FUNCTIONs get converted to cpp equivalents. If such a feature is
> currently available, I haven't found it.
>
> Buck
>
> On Mon, Aug 11, 2014 at 3:59 PM, Steve Martell
> <martell.steve at gmail.com <mailto:martell.steve at gmail.com>> wrote:
>
> Try:
>
> FUNCTION dvariable model_parameters::Richards(const dvariable
> &age, const dvariable &Linf, const dvariable &K, const
> dvariable &t0, const dvariable &p)
>
> {
>
> {
>
> dvariable Length=Linf*pow((1+(1/p)*exp(-K*(age-t0))),-p);
>
> return(Length);
>
> }
>
> }
>
> On Aug 11, 2014, at 3:49 PM, Mark Maunder <mmaunder at iattc.org
> <mailto:mmaunder at iattc.org>> wrote:
>
> Why do I get an error if I put the following function in the file
> CAPAM_Growth.hpp and include it using #include<CAPAM_Growth.hpp>
> but if I put it in the tpl using the FUNCTION section I do not?
> The translator appears to just put it in the cpp with no changes
>
> dvariable model_parameters::Richards(const dvariable &age, const
> dvariable &Linf, const dvariable &K, const dvariable &t0, const
> dvariable &p)
>
> {
>
> {
>
> dvariable Length=Linf*pow((1+(1/p)*exp(-K*(age-t0))),-p);
>
> return(Length);
>
> }
>
> }
>
> The errors I get are
>
> In file included from igm.cpp:3:0:
>
> ./CAPAM_Growth.hpp:130:142: error: invalid use of incomplete type
> 'struct model_parameters'
>
> c:/ADMB/admb101-gcc452-win32\include/admodel.h:107:9: error:
> forward declaration of 'struct model_parameters'
>
> igm.cpp: In member function 'virtual void
> model_parameters::userfunction()':
>
> igm.cpp:127:46: error: no matching function for call to
> 'Richards(prevariable, named_dvariable&, named_dvariable&,
> param_init_number&, named_dvariable&)'
>
> igm.cpp:128:58: error: no matching function for call to
> 'Richards(prevariable&, named_dvariable&, named_dvariable&,
> param_init_number&, named_dvariable&)'
>
> igm.cpp:139:49: error: no matching function for call to
> 'Richards(double&, named_dvariable&, named_dvariable&,
> param_init_number&, named_dvariable&)'
>
> The selectivity special issue of the journal Fisheries Research is
> now published
>
> http://www.sciencedirect.com/science/journal/01657836/158/supp/C
>
> The Stock Synthesis special issue of the journal Fisheries
> Research
>
> http://www.sciencedirect.com/science/journal/01657836/142
>
> Mark Maunder
>
> Head of the Stock Assessment Program
>
> Inter-American Tropical Tuna Commission
>
> 8901 La Jolla Shores Dr.
>
> La Jolla, CA 92037-1508, USA
>
> Tel: (858) 546-7027 <tel:%28858%29%20546-7027>
>
> Fax: (858) 546-7133 <tel:%28858%29%20546-7133>
>
> mmaunder at iattc.org <mailto:mmaunder at iattc.org>
>
>
> http://www.fisheriesstockassessment.com/TikiWiki/tiki-index.php?page=M
> ark+Maunder
>
> Visit the Center for the Advancement of Population Assessment
> Methodology at
>
> http://www.capamresearch.org/
>
> Visit the AD Model Builder project at
>
> http://admb-project.org/
>
> See the following website for information on fisheries stock
> assessment http://www.fisheriesstockassessment.com/
>
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