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From: Robert Dodier <robert.dodier@gm...>  20140409 22:25:08

Robert Dodier <robert.dodier <at> gmail.com> writes: > I invented a scheme to load documentation index files from share > directories so that any topics will be discoverable via ? and ??. > I put it on a branch; see branch multipletexinfodirsbranch, > specifically commit e4505c04f. As this problem seems to recur every now > and then, I think I'll merge it into master at some point. Just looked at this again  turns out that commit was merged some months ago. The code in that commit makes it possible to load perpackage maximaindex.lisp files. It is still necessary to run makeinfo and build_index.pl to generate the .info and the index, and to load the index in the Maxima session via load("foopackage/maximaindex.lisp") (i.e., indices are not discovered automatically). So automating all that stuff is a good job for a rainy day. best Robert Dodier 
From: Edwin Woollett <woollett@ch...>  20140409 20:28:02

feature request: stiff o.d.e. solvers for initial value problems in Maxima. Many advanced numerical algorithms that solve differential equations are available as (open source) computer codes, written in programming languages like FORTRAN or C, and available in repositories like GAMS (http://gams.nist.gov) or NETLIB (www.netlib.org). An example of what can be done to make this code available for work in modern interactive numerical environments is the work of Karline Soetaert and L.R. Petzold (and others) for the open source R numerical platform. Present ode solvers in the R package deSolve use adaptive step size control, some solvers control the order of the formula adaptively, or switch between different types of methods, depending on the local properties of the ode's to be solved. The R package deSolve includes methods to solve stiff and nonstiff problems, that deal with full, banded, or arbitrarily sparse Jacobians, etc. The implementation includes stiff and nonstiff integration routines based on the ODEPACK FORTRAN codes (Hindmarsh 1983). It also includes fixed and adaptive timestep explicit RungeKutta solvers, the Euler method, and the implicit RungeKutta method RADAU (Hairer and Wanner 2010). The default integration method, based on the FORTRAN code LSODA is one that switches automatically between stiff and nonstiff systems (Petzold 1983). This is a very robust method, but not necessarily the most efficient solver for one particular problem. See (Soetaert et al. 2010b) for more information about when to use which solver in deSolve. For most cases, the default solver, ode, and the default settings will do. One can optionally trigger specific available methods to override the default used by the deSolve wrapper ode. The explicit RungeKutta methods are de novo implementations in C, based on the Butcher tables (Butcher 1987). They comprise simple RungeKutta formulae (Euler's method euler, Heun's method rk2, the classical 4th order RungeKutta, rk4) and several RungeKutta pairs of order 3(2) to order 8(7). The embedded, explicit methods are according to Fehlberg (1967) (rk..f, ode45), Dormand and Prince (1980, 1981) (rk..dp.), Bogacki and Shampine (1989) (rk23bs, ode23) and Cash and Karp (1990) (rk45ck), where ode23 and ode45 are aliases for the popular methods rk23bs resp. rk45dp7. With the following statement all implemented rk methods are shown: > rkMethod() [1] "euler" "rk2" "rk4" "rk23" "rk23bs" "rk34f" [7] "rk45f" "rk45ck" "rk45e" "rk45dp6" "rk45dp7" "rk78dp" [13] "rk78f" "irk3r" "irk5r" "irk4hh" "irk6kb" "irk4l" [19] "irk6l" "ode23" "ode45" This list also contains implicit RungeKutta's (irk..), but they are not yet optimally coded. The only wellimplemented implicit RungeKutta is the radau method (Hairer and Wanner 2010).  References: Hairer E, Wanner G (2010). "Solving Ordinary Differential Equations II: Stiff and Differential Algebraic Problems. Second Revised Edition. SpringerVerlag, Heidelberg. Hindmarsh, AC (1983). "ODEPACK, a Systematized Collection of ODE Solvers." In R Stepleman (ed.), "Scientifc Computing, Vol. 1 of IMACS Transactions on Scientifc Computation," pp. 5564, IMACS / NorthHolland, Amsterdam. Petzold, LR (1983). "Automatic Selection of Methods for Solving Stiff and Nonstiff Systems of Ordinary Differential Equations." SIAM Journal on Scientifc and Statistical Computing, 4, 136148. Soetaert, Karline; Cash, Jeff; and Mazzia, Francesca: "Solving Differential Equations in R", 2012, SpringerVerlag.  Ted Woollett 
From: couraud <l.couraud@gm...>  20140409 20:19:24

On 20140406, David Billinghurst <dbmaxima@...> wrote: > OK. There is a new windows installer > http://billinghurst.customer.netspace.net.au/maxima5.33.0.1.exe Thanks, David. Works for me on Windows 8.1. Test suite runs without unexpected errors, plotting works, help works. Just 2 small detail: 1) Banner still display version 5.33.0 not 5.33.0.1 2) I saw Maxima installer for 5.33.0 is 37908 Kbytes but the 5.33.0.1 is only 33334 Kbytes. best Laurent Couraud   Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test & Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees _______________________________________________ Maximadiscuss mailing list Maximadiscuss@... https://lists.sourceforge.net/lists/listinfo/maximadiscuss 
From: Robert Dodier <robert.dodier@gm...>  20140409 18:25:31

On 20140406, David Billinghurst <dbmaxima@...> wrote: > OK. There is a new windows installer > http://billinghurst.customer.netspace.net.au/maxima5.33.0.1.exe Thanks, David. Works for me on Windows Vista. Test suite runs without unexpected errors, plotting works, help works. best Robert Dodier 
From: Raymond Toy <toy.raymond@gm...>  20140409 18:23:49

>>>>> "Leo" == Leo Butler <l_butler@...> writes: Leo> "Edwin Woollett" <woollett@...> writes: >> I wish someone with the appropriate skill set could add some >> numerical ode solvers related to the livermore solvers (lsoda, etc) >> which can handle stiff o.d.e.s. >> >> ted Leo> Ted, would you mind putting this on the sourceforge page, as a feature Leo> request, please. Leo> I know that Ray has done work on porting quadpack routines from fortran Leo> to common lisp. I wonder if an alternative approach, linking to the GSL In the f2cl distribution there is a working Lisp translation of lsoda. It could be added as another share library for maxima. This is straightforward but tedious mostly because a suitable user interface needs to be designed and then marshalling all of the data from maxima into something that the routine can use, and the returning the result to maxima in a meaningful way. Note that if you're expecting Fortranlike speeds from this, you'll probably be sad. Leo> (or other) libraries, would be feasible? I think we are still blocked on the lack of cffi working on all the lisps we support. At least for the "official" maxima. Users can do whatever they want, of course. Ray 
From: Leo Butler <l_butler@us...>  20140409 17:37:00

"Edwin Woollett" <woollett@...> writes: > I wish someone with the appropriate skill set could add some > numerical ode solvers related to the livermore solvers (lsoda, etc) > which can handle stiff o.d.e.s. > > ted Ted, would you mind putting this on the sourceforge page, as a feature request, please. I know that Ray has done work on porting quadpack routines from fortran to common lisp. I wonder if an alternative approach, linking to the GSL (or other) libraries, would be feasible? Leo  Leo Butler <l_butler@...> SDF Public Access UNIX System  http://sdf.lonestar.org 
From: Stavros Macrakis <macrakis@al...>  20140409 16:15:40

To copy ordering relations, this should work: copy_relations(var1,var2) := apply('assume,subst(var2,var1,facts(var1)))$ Unfortunately, declare(qq,integer) results in facts returning kind(qq,integer), but assume(kind(qq,integer)) gives an error.... s On Tue, Apr 8, 2014 at 7:13 PM, nijso beishuizen <nijso@...> wrote: > Hi, > > I would like to create a new variable b that inherits all properties from > variable a (at least the ones shown by facts(a)), but b is not a, so a+b > would not reduce to 2a. > > How can I do this? > > Best, > Nijso > > >  > Put Bad Developers to Shame > Dominate Development with Jenkins Continuous Integration > Continuously Automate Build, Test & Deployment > Start a new project now. Try Jenkins in the cloud. > http://p.sf.net/sfu/13600_Cloudbees > _______________________________________________ > Maximadiscuss mailing list > Maximadiscuss@... > https://lists.sourceforge.net/lists/listinfo/maximadiscuss > > 
From: Leo Butler <l_butler@us...>  20140409 12:04:49

"Edwin Woollett" <woollett@...> writes: > Yes, that cured the problem. > trunc_error = 0.0 for i = 39 loop trip. > > Ted I pushed a fix and updated the test file using your examples. You can download the updated rkf45.mac from https://sourceforge.net/p/maxima/code/ci/master/tree/share/contrib/rkf45/rkf45.mac?format=raw Leo >  >  Original Message  > From: Leo Butler > To: maximadiscuss@... > Sent: Tuesday, April 08, 2014 3:45 PM > Subject: Re: [Maximadiscuss] rkf45 can't cope with interpolating > functionpiece > > > "Edwin Woollett" <woollett@...> writes: > >> I had the wrong syntax calling rkf45 in the example >> code file I previously sent to the list, but >> after correcting the syntax to: >> >> soln_lin2 : rkf45( dydt, y, 1, [t , 0, 1]), >> >> in the code file driven1c.mac, I get exactly the same >> failure to cope (by rkf45) with the interpolating >> function piece. >>  >> (%i16) load(driven1c); >> fll(sL) = [1.0,1.0,51] >> fll(snL) = [0.90291,1.053531,51] >> noisy signal data >> fll(tsnL) = [[0,0.90291],[1.0,1.053531],51] >> slin(0.5) = 0.88955 >> soln using rk() >> fll(soln_lin) = [[0.0,1.0],[1.0,0.65303],101] >> soln using rkf45() >> expt: undefined: 0 to a negative exponent. >> #0: rkf45(odes=t*y+(11.96189*t+0.90291)*charfun(t < 0.02)+charfun(0.68 <= >> t >> and t < >> 0.7)*(22.40386*t15.82754)+cha...,funcs=y,initial=1,interval=[t,0,1],options=[])(myrkf45.mac >> line 186) > > Ted, the abovementioned line 186 should be > > h_optimal:min(max(0.84089641525371*(atol/trunc_error)^0.25,0.1),4)*h, > > Is that correct? I think the error is caused by trunc_error=0, so try > replacing that line with > > h_optimal:min(max(0.84089641525371*(atol/max(1e30,trunc_error))^0.25,0.1),4)*h, > > and tell me if that fixes the problem (it did for me). > > Leo > >>  an error. To debug this try: debugmode(true); >> >>  >> corrected code file driven1c.mac: >>  >> /* driven1c.mac : compare behavior of rk and rkf45 >> with an interpolating function */ >> >> /* create noisy signal points (tL, snL) */ >> >> (signal(t) := cos(2*%pi*t), >> tL : makelist(t,t,0,1,0.02), >> sL : float(map('signal, tL)), >> print(" fll(sL) = ",fll(sL)), >> s1 : make_random_state(2014), >> set_random_state(s1), >> snL : jitter(sL, 0.2), >> print(" fll(snL) = ",fll(snL)), >> >> /* create interpolating function slin(t) from >> noisy signal points */ >> >> load("interpol.mac"), >> tsnL : xyData(tL,snL), >> print(" noisy signal data "), >> print(" fll(tsnL) = ",fll(tsnL)), >> define(slin(x), linearinterpol(tsnL)), >> print(" slin(0.5) = ", slin(0.5)), >> >> /* use slin(t) interpolating function as >> a driving term in ode, and integrate >> o.d.e. with rk() */ >> >> print(" soln using rk() "), >> dydt : t*y + slin(t), >> soln_lin : rk(dydt,y,1,[t,0,1,0.01]), >> print(" fll(soln_lin) = ",fll(soln_lin)), >> >> /* try to integrate same ode with rkf45 */ >> >> print(" soln using rkf45() "), >> load("myrkf45.mac"), >> soln_lin2 : rkf45(dydt,y,1,[t,0,1]), >> print(" fll(soln_lin2) = ",fll(soln_lin2)))$ >>  >> >> homemade utility functions used: >> >> fll(x) := [first(x),last(x),length(x)]$ >> >> jitter1(val,amount) := val + amount*(random(2.0)  1.0)$ >> >> /* add random noise to a list of numbers */ >> >> jitter(aaL, amount) := ( >> if not listp(aaL) then return("first arg must be a list"), >> map('lambda([xx],jitter1(xx,amount)),aaL))$ >> >> xyData(uuL,vvL) := (makelist([uuL[kk],vvL[kk]],kk,1,length(uuL)))$ >>  >> >> Ted Woollett >> >> >> >> >> >> >>  >> Put Bad Developers to Shame >> Dominate Development with Jenkins Continuous Integration >> Continuously Automate Build, Test & Deployment >> Start a new project now. Try Jenkins in the cloud. >> http://p.sf.net/sfu/13600_Cloudbees  Leo Butler <l_butler@...> SDF Public Access UNIX System  http://sdf.lonestar.org 
From: Edwin Woollett <woollett@ch...>  20140409 00:05:29

Yes, that cured the problem. trunc_error = 0.0 for i = 39 loop trip. Ted   Original Message  From: Leo Butler To: maximadiscuss@... Sent: Tuesday, April 08, 2014 3:45 PM Subject: Re: [Maximadiscuss] rkf45 can't cope with interpolating functionpiece "Edwin Woollett" <woollett@...> writes: > I had the wrong syntax calling rkf45 in the example > code file I previously sent to the list, but > after correcting the syntax to: > > soln_lin2 : rkf45( dydt, y, 1, [t , 0, 1]), > > in the code file driven1c.mac, I get exactly the same > failure to cope (by rkf45) with the interpolating > function piece. >  > (%i16) load(driven1c); > fll(sL) = [1.0,1.0,51] > fll(snL) = [0.90291,1.053531,51] > noisy signal data > fll(tsnL) = [[0,0.90291],[1.0,1.053531],51] > slin(0.5) = 0.88955 > soln using rk() > fll(soln_lin) = [[0.0,1.0],[1.0,0.65303],101] > soln using rkf45() > expt: undefined: 0 to a negative exponent. > #0: rkf45(odes=t*y+(11.96189*t+0.90291)*charfun(t < 0.02)+charfun(0.68 <= > t > and t < > 0.7)*(22.40386*t15.82754)+cha...,funcs=y,initial=1,interval=[t,0,1],options=[])(myrkf45.mac > line 186) Ted, the abovementioned line 186 should be h_optimal:min(max(0.84089641525371*(atol/trunc_error)^0.25,0.1),4)*h, Is that correct? I think the error is caused by trunc_error=0, so try replacing that line with h_optimal:min(max(0.84089641525371*(atol/max(1e30,trunc_error))^0.25,0.1),4)*h, and tell me if that fixes the problem (it did for me). Leo >  an error. To debug this try: debugmode(true); > >  > corrected code file driven1c.mac: >  > /* driven1c.mac : compare behavior of rk and rkf45 > with an interpolating function */ > > /* create noisy signal points (tL, snL) */ > > (signal(t) := cos(2*%pi*t), > tL : makelist(t,t,0,1,0.02), > sL : float(map('signal, tL)), > print(" fll(sL) = ",fll(sL)), > s1 : make_random_state(2014), > set_random_state(s1), > snL : jitter(sL, 0.2), > print(" fll(snL) = ",fll(snL)), > > /* create interpolating function slin(t) from > noisy signal points */ > > load("interpol.mac"), > tsnL : xyData(tL,snL), > print(" noisy signal data "), > print(" fll(tsnL) = ",fll(tsnL)), > define(slin(x), linearinterpol(tsnL)), > print(" slin(0.5) = ", slin(0.5)), > > /* use slin(t) interpolating function as > a driving term in ode, and integrate > o.d.e. with rk() */ > > print(" soln using rk() "), > dydt : t*y + slin(t), > soln_lin : rk(dydt,y,1,[t,0,1,0.01]), > print(" fll(soln_lin) = ",fll(soln_lin)), > > /* try to integrate same ode with rkf45 */ > > print(" soln using rkf45() "), > load("myrkf45.mac"), > soln_lin2 : rkf45(dydt,y,1,[t,0,1]), > print(" fll(soln_lin2) = ",fll(soln_lin2)))$ >  > > homemade utility functions used: > > fll(x) := [first(x),last(x),length(x)]$ > > jitter1(val,amount) := val + amount*(random(2.0)  1.0)$ > > /* add random noise to a list of numbers */ > > jitter(aaL, amount) := ( > if not listp(aaL) then return("first arg must be a list"), > map('lambda([xx],jitter1(xx,amount)),aaL))$ > > xyData(uuL,vvL) := (makelist([uuL[kk],vvL[kk]],kk,1,length(uuL)))$ >  > > Ted Woollett > > > > > > >  > Put Bad Developers to Shame > Dominate Development with Jenkins Continuous Integration > Continuously Automate Build, Test & Deployment > Start a new project now. Try Jenkins in the cloud. > http://p.sf.net/sfu/13600_Cloudbees  Leo Butler <l_butler@...> SDF Public Access UNIX System  http://sdf.lonestar.org  Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test & Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees _______________________________________________ Maximadiscuss mailing list Maximadiscuss@... https://lists.sourceforge.net/lists/listinfo/maximadiscuss 