Re: [votca] Hessian NOT a positive definite!

[Christoph Junghans]

On Thu, Jul 19, 2018 at 18:15 'Andrey Brukhno' via votca <
votca@googlegroups.com> wrote:

> Hello,
>
> I managed to run the RE iteration for a system with 10 non-bonded
> potentials (types).. well, the first iteration anyway, where it terminated
> after about an hour of running csg_reupdate with the following error:
>
> *Hessian NOT a positive definite! *
> This can be a result of poor initial guess or ill-suited CG potential
> settings or poor CG sampling.
>
> My understanding is, sometimes this might happen, but this was my second
> trial where I virtually doubled (44 -> 88) the number of knots and (in both
> cases) I use potentials derived from an earlier IBI iteration.
>
> I would really appreciate clues, hints or general advice as to how to
> alleviate the issue.
>
Sikandar will know more, but most likely you will need to throw away some
frames at the beginning of the trajectory and run the iterations for a bit
longer!

Christoph

>
> Thanks!
> Andrey
>
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Re: [votca] Re: csg_reupdate error: property not found: re.function

[Christoph Junghans]

On Thu, Jul 19, 2018 at 17:26 'Andrey Brukhno' via votca <
votca@googlegroups.com> wrote:

>
>
> On Thursday, July 19, 2018 at 7:57:57 PM UTC+1, Christoph Junghans wrote:
>
>> On Thu, Jul 19, 2018 at 10:44 AM, 'Andrey Brukhno' via votca
>>  wrote:
>> > I get:
>> >
>> > ...  ...
>> > Total number of parameters to optimize: 333
>> > an error occurred:
>> > property not found: scale
>> See here:
>>
>> https://github.com/votca/csg-tutorials/blob/master/spce/re/settings.xml#L69
>>
>> Christoph
>>
>>
> Actually, I am a bit confused not seeing re.traj tag for atomistic
> trajectory. I thought RE iteration requires recalculating CG averages in
> over atomistic ensemble (trajectory) for every new set of CG potentials?
>
> Also, what about the corresponding re.topology tag - specifying what?
>
Both options exist:
https://github.com/votca/csg/blob/master/share/scripts/inverse/update_re.sh#L30

Christoph


> Andrey
>
>
>>
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[votca] Hessian NOT a positive definite!

['Andrey Brukhno' via votca]

Hello,

I managed to run the RE iteration for a system with 10 non-bonded 
potentials (types).. well, the first iteration anyway, where it terminated 
after about an hour of running csg_reupdate with the following error:

*Hessian NOT a positive definite! *
This can be a result of poor initial guess or ill-suited CG potential 
settings or poor CG sampling.

My understanding is, sometimes this might happen, but this was my second 
trial where I virtually doubled (44 -> 88) the number of knots and (in both 
cases) I use potentials derived from an earlier IBI iteration. 

I would really appreciate clues, hints or general advice as to how to 
alleviate the issue.

Thanks!
Andrey

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Re: [votca] Re: csg_reupdate error: property not found: re.function

['Andrey Brukhno' via votca]

On Thursday, July 19, 2018 at 7:57:57 PM UTC+1, Christoph Junghans wrote:
>
> On Thu, Jul 19, 2018 at 10:44 AM, 'Andrey Brukhno' via votca 
> > wrote: 
> > I get: 
> > 
> > ...  ... 
> > Total number of parameters to optimize: 333 
> > an error occurred: 
> > property not found: scale 
> See here: 
> https://github.com/votca/csg-tutorials/blob/master/spce/re/settings.xml#L69 
>
> Christoph 
>
>
Actually, I am a bit confused not seeing re.traj tag for atomistic 
trajectory. I thought RE iteration requires recalculating CG averages in 
over atomistic ensemble (trajectory) for every new set of CG potentials? 

Also, what about the corresponding re.topology tag - specifying what? 

Andrey
 

>
>

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Re: [votca] Missing, not found Eigen3 during VOTCA installation

['Andrey Brukhno' via votca]

Ok, I will give it a try on my home PC.

Andrey

On Thursday, July 19, 2018 at 8:19:03 PM UTC+1, Christoph Junghans wrote:
>
> On Thu, Jul 19, 2018 at 10:57 AM, 'Andrey Brukhno' via votca 
> > wrote: 
> > 
> > 
> > On Thursday, July 19, 2018 at 4:48:14 PM UTC+1, Christoph Junghans 
> wrote: 
> >> 
> >> >> 
> >> >> > We recently fixed an issue in the Eigen3 detection: 
> >> >> > 
> >> >> > 
> >> >> > 
> https://github.com/votca/votca/commit/8fdcedae9b46e1739fa2ef8589cd5a8f6881d420
>  
> >> >> > which includes: 
> >> >> > 
> >> >> > 
> >> >> > 
> https://github.com/votca/tools/commit/3ee8b88e6022772b843f21a04f66a5bd8bfddd09
>  
> >> >> > 
> >> >> > 
> >> >> > 
> https://github.com/votca/csg/commit/c3f9b3e2841c4b5c0eac20e4d843f6b108750ecf 
> >> >> > Did you use that version? 
> >> > 
> >> > 
> >> > No, I have not tried any newer version yet. My aim was to get the 
> latest 
> >> > release installed, which spack did succeed to do (v1.4.1). 
> >> But then I don't understand your original error because votca-csg 
> >> 1.4.1 doesn't depend on Eigen3. 
> > 
> > 
> > I guess I meant (implicitly) that I tried to follow the instructions for 
> > installation using cmake found on one of the VOTCA's webpages, and 
> that's 
> > when I encountered the error message about eigen3 (not sure now what 
> version 
> > it was, but I think 1.5.1). But then I went the spack way and was 
> satisfied. 
> > Since then I have not tried cmake for any other version. But I may try 
> on my 
> > home PC soon. 
> I see, it is a bit confusing in the README of the new buildsystem, 
> hopefully that makes it more clear: 
>
> https://github.com/votca/votca/commit/40cbeb2daf4b4647292cf423e9755125cb7c3380
>  
>
> Christoph 
> > 
> >> 
> >> 
> >> > 
> >> > BTW, when I tried to install with apt-get nothing happened: no votca 
> >> > package 
> >> > found. Perhaps it would only work for 2016(+) Ubuntu? 
> >> Yes, only 2016.4 and later: 
> >> 
> >> 
> https://packages.ubuntu.com/search?keywords=votca-csg=names=all=all
>  
> >> and v1.4.1 only in Ubuntu 18.04! 
> >> 
> >> > 
> >> >> 
> >> >> > 
> >> >> >> 
> >> >> >> Not sure what went wrong, but I had to use alternative way of 
> >> >> >> installation 
> >> >> >> via spack, and it worked eventually, although it lloked like 
> spack 
> >> >> >> installed 
> >> >> >> ALL the dependencies along with VOTCA in a separate directory, 
> which 
> >> >> >> is 
> >> >> >> of 
> >> >> >> course an overkill. 
> >> >> > That is Spack's design, so don't complain to me! And yes we need 
> to 
> >> >> > update the dependencies of the VOTCA package in Spack. 
> >> >> https://github.com/spack/spack/pull/8757 
> >> > 
> >> > 
> >> > I see... Otherwise I also noticed that spack installs csg and tools 
> >> > separately in two directories beside each other. But then 
> VOTCARC.bash 
> >> > etc 
> >> > occur in the tools/bin and VOTCASHARE points at votca_tools/share 
> >> > instead of 
> >> > votca_csg/share, so the scripts/inverse are not found. I had to reset 
> >> > VOTCASHARE correctly in my .bashrc. 
> >> Good point I will have to think, how to fix that. I think the VOTCARC 
> >> file should get installed to start with as csg_inverse will 
> >> auto-detect the location (using csg_call in your PATH) if VOTCASHARE 
> >> isn't set. 
> >> 
> >> Christoph 
> >> 
> >> > 
> >> > I mentioned this for other users to be aware. 
> >> > 
> >> > Andrey 
> >> >> 
> >> >> 
> >> >> >> 
> >> >> >> I suppose this post is just to notify the current developers that 
> >> >> >> there 
> >> >> >> might be some issue with finding an exiasting Eigen3 dir. 
> >> >> > Thanks for letting us know, can you try if above versions fix the 
> >> >> > issue 
> >> >> > for you? 
> >> >> > 
> >> >> > Christoph 
> >> >> >> 
> >> >> >> Thanks 
> >> >> >> Andrey 
> >> >> >> 
> >> >> >> -- 
> >> >> >> You received this message because you are subscribed to the 
> Google 
> >> >> >> Groups 
> >> >> >> "votca" group. 
> >> >> >> To unsubscribe from this group and stop receiving emails from it, 
> >> >> >> send 
> >> >> >> an 
> >> >> >> email to votca+un...@googlegroups.com. 
> >> >> >> To post to this group, send email to vo...@googlegroups.com. 
> >> >> >> Visit this group at https://groups.google.com/group/votca. 
> >> >> >> For more options, visit https://groups.google.com/d/optout. 
> >> >> > 
> >> >> > 
> >> >> > 
> >> >> > -- 
> >> >> > Christoph Junghans 
> >> >> > Web: http://www.compphys.de 
> >> >> 
> >> >> 
> >> >> 
> >> >> -- 
> >> >> Christoph Junghans 
> >> >> Web: http://www.compphys.de 
> >> > 
> >> > -- 
> >> > You received this message because you are subscribed to the Google 
> >> > Groups 
> >> > "votca" group. 
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> send 
> >> > an 
> >> > email to votca+un...@googlegroups.com. 
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> >> > Visit this group at https://groups.google.com/group/votca. 
> >> > For more options, visit 

Re: [votca] Missing, not found Eigen3 during VOTCA installation

[Christoph Junghans]

On Thu, Jul 19, 2018 at 10:57 AM, 'Andrey Brukhno' via votca
 wrote:
>
>
> On Thursday, July 19, 2018 at 4:48:14 PM UTC+1, Christoph Junghans wrote:
>>
>> >>
>> >> > We recently fixed an issue in the Eigen3 detection:
>> >> >
>> >> >
>> >> > https://github.com/votca/votca/commit/8fdcedae9b46e1739fa2ef8589cd5a8f6881d420
>> >> > which includes:
>> >> >
>> >> >
>> >> > https://github.com/votca/tools/commit/3ee8b88e6022772b843f21a04f66a5bd8bfddd09
>> >> >
>> >> >
>> >> > https://github.com/votca/csg/commit/c3f9b3e2841c4b5c0eac20e4d843f6b108750ecf
>> >> > Did you use that version?
>> >
>> >
>> > No, I have not tried any newer version yet. My aim was to get the latest
>> > release installed, which spack did succeed to do (v1.4.1).
>> But then I don't understand your original error because votca-csg
>> 1.4.1 doesn't depend on Eigen3.
>
>
> I guess I meant (implicitly) that I tried to follow the instructions for
> installation using cmake found on one of the VOTCA's webpages, and that's
> when I encountered the error message about eigen3 (not sure now what version
> it was, but I think 1.5.1). But then I went the spack way and was satisfied.
> Since then I have not tried cmake for any other version. But I may try on my
> home PC soon.
I see, it is a bit confusing in the README of the new buildsystem,
hopefully that makes it more clear:
https://github.com/votca/votca/commit/40cbeb2daf4b4647292cf423e9755125cb7c3380

Christoph
>
>>
>>
>> >
>> > BTW, when I tried to install with apt-get nothing happened: no votca
>> > package
>> > found. Perhaps it would only work for 2016(+) Ubuntu?
>> Yes, only 2016.4 and later:
>>
>> https://packages.ubuntu.com/search?keywords=votca-csg=names=all=all
>> and v1.4.1 only in Ubuntu 18.04!
>>
>> >
>> >>
>> >> >
>> >> >>
>> >> >> Not sure what went wrong, but I had to use alternative way of
>> >> >> installation
>> >> >> via spack, and it worked eventually, although it lloked like spack
>> >> >> installed
>> >> >> ALL the dependencies along with VOTCA in a separate directory, which
>> >> >> is
>> >> >> of
>> >> >> course an overkill.
>> >> > That is Spack's design, so don't complain to me! And yes we need to
>> >> > update the dependencies of the VOTCA package in Spack.
>> >> https://github.com/spack/spack/pull/8757
>> >
>> >
>> > I see... Otherwise I also noticed that spack installs csg and tools
>> > separately in two directories beside each other. But then VOTCARC.bash
>> > etc
>> > occur in the tools/bin and VOTCASHARE points at votca_tools/share
>> > instead of
>> > votca_csg/share, so the scripts/inverse are not found. I had to reset
>> > VOTCASHARE correctly in my .bashrc.
>> Good point I will have to think, how to fix that. I think the VOTCARC
>> file should get installed to start with as csg_inverse will
>> auto-detect the location (using csg_call in your PATH) if VOTCASHARE
>> isn't set.
>>
>> Christoph
>>
>> >
>> > I mentioned this for other users to be aware.
>> >
>> > Andrey
>> >>
>> >>
>> >> >>
>> >> >> I suppose this post is just to notify the current developers that
>> >> >> there
>> >> >> might be some issue with finding an exiasting Eigen3 dir.
>> >> > Thanks for letting us know, can you try if above versions fix the
>> >> > issue
>> >> > for you?
>> >> >
>> >> > Christoph
>> >> >>
>> >> >> Thanks
>> >> >> Andrey
>> >> >>
>> >> >> --
>> >> >> You received this message because you are subscribed to the Google
>> >> >> Groups
>> >> >> "votca" group.
>> >> >> To unsubscribe from this group and stop receiving emails from it,
>> >> >> send
>> >> >> an
>> >> >> email to votca+un...@googlegroups.com.
>> >> >> To post to this group, send email to vo...@googlegroups.com.
>> >> >> Visit this group at https://groups.google.com/group/votca.
>> >> >> For more options, visit https://groups.google.com/d/optout.
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Christoph Junghans
>> >> > Web: http://www.compphys.de
>> >>
>> >>
>> >>
>> >> --
>> >> Christoph Junghans
>> >> Web: http://www.compphys.de
>> >
>> > --
>> > You received this message because you are subscribed to the Google
>> > Groups
>> > "votca" group.
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>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>
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Re: [votca] Re: csg_reupdate error: property not found: re.function

['Andrey Brukhno' via votca]

Thanks Christoph! 
That was helpful - I restarted iteration now.

On Thursday, July 19, 2018 at 7:57:57 PM UTC+1, Christoph Junghans wrote:
>
> On Thu, Jul 19, 2018 at 10:44 AM, 'Andrey Brukhno' via votca 
> > wrote: 
> > Hello again, 
> > 
> > By now, that the simulation for one iteration has finished 
> (successfully), I 
> > got a similar error during the analysis: 
> > 
> > # ERROR: 
> > # 
> > # critical: 'csg_reupdate --nt 8 --top topol.tpr --trj traj.xtc 
> --options 
> > settings.xml --begin 0 --first-frame 0' failed 
> > # 
> > # For details see the logfile 
> > 
> /home/andrey/Work/Models/DOPC-long-wtip4p-new/ire-Rc1.65nm-freeN-dihs_CG-fits1-151c/inverse.log
>  
>
> > 
> > Interestingly the error is not mirrored in inverse.log (which reports no 
> > error at all), but when I try to run: 
> > 
> > $ csg_reupdate --nt 8 --top topol.tpr --trj traj.xtc --options 
> settings.xml 
> > --begin 0 --first-frame 0 
> > 
> > I get: 
> > 
> > ...  ... 
> > Total number of parameters to optimize: 333 
> > an error occurred: 
> > property not found: scale 
> See here: 
> https://github.com/votca/csg-tutorials/blob/master/spce/re/settings.xml#L69 
>
> Christoph 
>
> > 
> > I am lost here, because my settings.xml file works with ibi and imc and 
> here 
> > is the output of `grep scale` for it: 
> > 
> >   scale smooth 
> > 0.10 
> >   scale smooth 
> > 0.10 
> >   scale smooth 
> > 0.10 
> >   scale smooth 
> > 0.10 
> >   scale smooth 
> > 0.10 
> >   scale smooth 
> > 0.10 
> >   scale smooth 
> > 0.10 
> >   scale smooth 
> > 0.10 
> >   scale smooth 
> > 0.10 
> >   scale smooth 
> > 0.10 
> > 
> > Did the location of scale tag change? Or is it some other scale tag that 
> is 
> > missing? 
> > 
> > Andrey 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups 
> > "votca" group. 
> > To unsubscribe from this group and stop receiving emails from it, send 
> an 
> > email to votca+un...@googlegroups.com . 
> > To post to this group, send email to vo...@googlegroups.com 
> . 
> > Visit this group at https://groups.google.com/group/votca. 
> > For more options, visit https://groups.google.com/d/optout. 
>
>
>
> -- 
> Christoph Junghans 
> Web: http://www.compphys.de 
>

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Re: [votca] Re: csg_reupdate error: property not found: re.function

[Christoph Junghans]

On Thu, Jul 19, 2018 at 10:44 AM, 'Andrey Brukhno' via votca
 wrote:
> Hello again,
>
> By now, that the simulation for one iteration has finished (successfully), I
> got a similar error during the analysis:
>
> # ERROR:
> #
> # critical: 'csg_reupdate --nt 8 --top topol.tpr --trj traj.xtc --options
> settings.xml --begin 0 --first-frame 0' failed
> #
> # For details see the logfile
> /home/andrey/Work/Models/DOPC-long-wtip4p-new/ire-Rc1.65nm-freeN-dihs_CG-fits1-151c/inverse.log
>
> Interestingly the error is not mirrored in inverse.log (which reports no
> error at all), but when I try to run:
>
> $ csg_reupdate --nt 8 --top topol.tpr --trj traj.xtc --options settings.xml
> --begin 0 --first-frame 0
>
> I get:
>
> ...  ...
> Total number of parameters to optimize: 333
> an error occurred:
> property not found: scale
See here:
https://github.com/votca/csg-tutorials/blob/master/spce/re/settings.xml#L69

Christoph

>
> I am lost here, because my settings.xml file works with ibi and imc and here
> is the output of `grep scale` for it:
>
>   scale smooth
> 0.10
>   scale smooth
> 0.10
>   scale smooth
> 0.10
>   scale smooth
> 0.10
>   scale smooth
> 0.10
>   scale smooth
> 0.10
>   scale smooth
> 0.10
>   scale smooth
> 0.10
>   scale smooth
> 0.10
>   scale smooth
> 0.10
>
> Did the location of scale tag change? Or is it some other scale tag that is
> missing?
>
> Andrey
>
> --
> You received this message because you are subscribed to the Google Groups
> "votca" group.
> To unsubscribe from this group and stop receiving emails from it, send an
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-- 
Christoph Junghans
Web: http://www.compphys.de

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Re: [votca] Missing, not found Eigen3 during VOTCA installation

['Andrey Brukhno' via votca]

On Thursday, July 19, 2018 at 4:48:14 PM UTC+1, Christoph Junghans wrote:
>
> >> 
> >> > We recently fixed an issue in the Eigen3 detection: 
> >> > 
> >> > 
> https://github.com/votca/votca/commit/8fdcedae9b46e1739fa2ef8589cd5a8f6881d420
>  
> >> > which includes: 
> >> > 
> >> > 
> https://github.com/votca/tools/commit/3ee8b88e6022772b843f21a04f66a5bd8bfddd09
>  
> >> > 
> >> > 
> https://github.com/votca/csg/commit/c3f9b3e2841c4b5c0eac20e4d843f6b108750ecf 
> >> > Did you use that version? 
> > 
> > 
> > No, I have not tried any newer version yet. My aim was to get the latest 
> > release installed, which spack did succeed to do (v1.4.1). 
> But then I don't understand your original error because votca-csg 
> 1.4.1 doesn't depend on Eigen3. 
>

I guess I meant (implicitly) that I tried to follow the instructions for 
installation using cmake found on one of the VOTCA's webpages, and that's 
when I encountered the error message about eigen3 (not sure now what 
version it was, but I think 1.5.1). But then I went the spack way and was 
satisfied. Since then I have not tried cmake for any other version. But I 
may try on my home PC soon.
 

>
> > 
> > BTW, when I tried to install with apt-get nothing happened: no votca 
> package 
> > found. Perhaps it would only work for 2016(+) Ubuntu? 
> Yes, only 2016.4 and later: 
>
> https://packages.ubuntu.com/search?keywords=votca-csg=names=all=all
>  
> and v1.4.1 only in Ubuntu 18.04! 
>
> > 
> >> 
> >> > 
> >> >> 
> >> >> Not sure what went wrong, but I had to use alternative way of 
> >> >> installation 
> >> >> via spack, and it worked eventually, although it lloked like spack 
> >> >> installed 
> >> >> ALL the dependencies along with VOTCA in a separate directory, which 
> is 
> >> >> of 
> >> >> course an overkill. 
> >> > That is Spack's design, so don't complain to me! And yes we need to 
> >> > update the dependencies of the VOTCA package in Spack. 
> >> https://github.com/spack/spack/pull/8757 
> > 
> > 
> > I see... Otherwise I also noticed that spack installs csg and tools 
> > separately in two directories beside each other. But then VOTCARC.bash 
> etc 
> > occur in the tools/bin and VOTCASHARE points at votca_tools/share 
> instead of 
> > votca_csg/share, so the scripts/inverse are not found. I had to reset 
> > VOTCASHARE correctly in my .bashrc. 
> Good point I will have to think, how to fix that. I think the VOTCARC 
> file should get installed to start with as csg_inverse will 
> auto-detect the location (using csg_call in your PATH) if VOTCASHARE 
> isn't set. 
>
> Christoph 
>
> > 
> > I mentioned this for other users to be aware. 
> > 
> > Andrey 
> >> 
> >> 
> >> >> 
> >> >> I suppose this post is just to notify the current developers that 
> there 
> >> >> might be some issue with finding an exiasting Eigen3 dir. 
> >> > Thanks for letting us know, can you try if above versions fix the 
> issue 
> >> > for you? 
> >> > 
> >> > Christoph 
> >> >> 
> >> >> Thanks 
> >> >> Andrey 
> >> >> 
> >> >> -- 
> >> >> You received this message because you are subscribed to the Google 
> >> >> Groups 
> >> >> "votca" group. 
> >> >> To unsubscribe from this group and stop receiving emails from it, 
> send 
> >> >> an 
> >> >> email to votca+un...@googlegroups.com. 
> >> >> To post to this group, send email to vo...@googlegroups.com. 
> >> >> Visit this group at https://groups.google.com/group/votca. 
> >> >> For more options, visit https://groups.google.com/d/optout. 
> >> > 
> >> > 
> >> > 
> >> > -- 
> >> > Christoph Junghans 
> >> > Web: http://www.compphys.de 
> >> 
> >> 
> >> 
> >> -- 
> >> Christoph Junghans 
> >> Web: http://www.compphys.de 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups 
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>
>
>
> -- 
> Christoph Junghans 
> Web: http://www.compphys.de 
>

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[votca] Re: csg_reupdate error: property not found: re.function

['Andrey Brukhno' via votca]

Hello again,

By now, that the simulation for one iteration has finished (successfully), 
I got a similar error during the analysis:

# ERROR:

#
# critical: 'csg_reupdate --nt 8 --top topol.tpr --trj traj.xtc --options 
settings.xml --begin 0 --first-frame 0' failed 
#
# For details see the logfile 
/home/andrey/Work/Models/DOPC-long-wtip4p-new/ire-Rc1.65nm-freeN-dihs_CG-fits1-151c/inverse.log
  
 

Interestingly the error is not mirrored in inverse.log (which reports no 
error at all), but when I try to run:

$ csg_reupdate --nt 8 --top topol.tpr --trj traj.xtc --options settings.xml 
--begin 0 --first-frame 0

I get:

...  ...
Total number of parameters to optimize: 333
an error occurred:
property not found: scale

I am lost here, because my settings.xml file works with ibi and imc and 
here is the output of `grep scale` for it:

  scale smooth
0.10
  scale smooth
0.10
  scale smooth
0.10
  scale smooth
0.10
  scale smooth
0.10
  scale smooth
0.10
  scale smooth
0.10
  scale smooth
0.10
  scale smooth
0.10
  scale smooth
0.10

Did the location of scale tag change? Or is it some other scale tag that is 
missing?

Andrey

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Re: [votca] Missing, not found Eigen3 during VOTCA installation

[Christoph Junghans]

On Thu, Jul 19, 2018 at 9:33 AM, 'Andrey Brukhno' via votca
 wrote:
>
>
> On Thursday, July 19, 2018 at 3:27:52 PM UTC+1, Christoph Junghans wrote:
>>
>> On Wed, Jul 18, 2018 at 12:20 PM, Christoph Junghans 
>> wrote:
>> > On Wed, Jul 18, 2018 at 12:04 PM, 'Andrey Brukhno' via votca
>> >  wrote:
>> >> Hello,
>> >>
>> >> The last time I was installing the CSG package in my Ubuntu (up-to-date
>> >> 2014
>> >> LTS) I got this error from cmake: eigen3 not found, with a suggestion
>> >> to
>> >> provide the path to it. I then downloaded the library from their
>> >> website,
>> >> installed it and added its include directory to both my $PATH and to
>> >> the
>> >> environment under the suggested name EIGEN3_INCLUDE_DIR. But cmake
>> >> still
>> >> complained and stopped with the same error, even when I fed it the
>> >> flag:
>> >> -DEIGEN3_INCLUDE_DIR=.
>> > Just a reminder that 2014 was already 4 years ago ;-)
>
>
> Thanks, up to now it did not hurt to stay with that version, but eventually
> yes an upgrade is pending. :)
>
>>
>> > We recently fixed an issue in the Eigen3 detection:
>> >
>> > https://github.com/votca/votca/commit/8fdcedae9b46e1739fa2ef8589cd5a8f6881d420
>> > which includes:
>> >
>> > https://github.com/votca/tools/commit/3ee8b88e6022772b843f21a04f66a5bd8bfddd09
>> >
>> > https://github.com/votca/csg/commit/c3f9b3e2841c4b5c0eac20e4d843f6b108750ecf
>> > Did you use that version?
>
>
> No, I have not tried any newer version yet. My aim was to get the latest
> release installed, which spack did succeed to do (v1.4.1).
But then I don't understand your original error because votca-csg
1.4.1 doesn't depend on Eigen3.

>
> BTW, when I tried to install with apt-get nothing happened: no votca package
> found. Perhaps it would only work for 2016(+) Ubuntu?
Yes, only 2016.4 and later:
https://packages.ubuntu.com/search?keywords=votca-csg=names=all=all
and v1.4.1 only in Ubuntu 18.04!

>
>>
>> >
>> >>
>> >> Not sure what went wrong, but I had to use alternative way of
>> >> installation
>> >> via spack, and it worked eventually, although it lloked like spack
>> >> installed
>> >> ALL the dependencies along with VOTCA in a separate directory, which is
>> >> of
>> >> course an overkill.
>> > That is Spack's design, so don't complain to me! And yes we need to
>> > update the dependencies of the VOTCA package in Spack.
>> https://github.com/spack/spack/pull/8757
>
>
> I see... Otherwise I also noticed that spack installs csg and tools
> separately in two directories beside each other. But then VOTCARC.bash etc
> occur in the tools/bin and VOTCASHARE points at votca_tools/share instead of
> votca_csg/share, so the scripts/inverse are not found. I had to reset
> VOTCASHARE correctly in my .bashrc.
Good point I will have to think, how to fix that. I think the VOTCARC
file should get installed to start with as csg_inverse will
auto-detect the location (using csg_call in your PATH) if VOTCASHARE
isn't set.

Christoph

>
> I mentioned this for other users to be aware.
>
> Andrey
>>
>>
>> >>
>> >> I suppose this post is just to notify the current developers that there
>> >> might be some issue with finding an exiasting Eigen3 dir.
>> > Thanks for letting us know, can you try if above versions fix the issue
>> > for you?
>> >
>> > Christoph
>> >>
>> >> Thanks
>> >> Andrey
>> >>
>> >> --
>> >> You received this message because you are subscribed to the Google
>> >> Groups
>> >> "votca" group.
>> >> To unsubscribe from this group and stop receiving emails from it, send
>> >> an
>> >> email to votca+un...@googlegroups.com.
>> >> To post to this group, send email to vo...@googlegroups.com.
>> >> Visit this group at https://groups.google.com/group/votca.
>> >> For more options, visit https://groups.google.com/d/optout.
>> >
>> >
>> >
>> > --
>> > Christoph Junghans
>> > Web: http://www.compphys.de
>>
>>
>>
>> --
>> Christoph Junghans
>> Web: http://www.compphys.de
>
> --
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-- 
Christoph Junghans
Web: http://www.compphys.de

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Re: [votca] Missing, not found Eigen3 during VOTCA installation

['Andrey Brukhno' via votca]

On Thursday, July 19, 2018 at 3:27:52 PM UTC+1, Christoph Junghans wrote:
>
> On Wed, Jul 18, 2018 at 12:20 PM, Christoph Junghans  > wrote: 
> > On Wed, Jul 18, 2018 at 12:04 PM, 'Andrey Brukhno' via votca 
> > > wrote: 
> >> Hello, 
> >> 
> >> The last time I was installing the CSG package in my Ubuntu (up-to-date 
> 2014 
> >> LTS) I got this error from cmake: eigen3 not found, with a suggestion 
> to 
> >> provide the path to it. I then downloaded the library from their 
> website, 
> >> installed it and added its include directory to both my $PATH and to 
> the 
> >> environment under the suggested name EIGEN3_INCLUDE_DIR. But cmake 
> still 
> >> complained and stopped with the same error, even when I fed it the 
> flag: 
> >> -DEIGEN3_INCLUDE_DIR=. 
> > Just a reminder that 2014 was already 4 years ago ;-) 
>

Thanks, up to now it did not hurt to stay with that version, but eventually 
yes an upgrade is pending. :)
 

> > We recently fixed an issue in the Eigen3 detection: 
> > 
> https://github.com/votca/votca/commit/8fdcedae9b46e1739fa2ef8589cd5a8f6881d420
>  
> > which includes: 
> > 
> https://github.com/votca/tools/commit/3ee8b88e6022772b843f21a04f66a5bd8bfddd09
>  
> > 
> https://github.com/votca/csg/commit/c3f9b3e2841c4b5c0eac20e4d843f6b108750ecf 
> > Did you use that version? 
>

No, I have not tried any newer version yet. My aim was to get the latest 
release installed, which spack did succeed to do (v1.4.1).

BTW, when I tried to install with apt-get nothing happened: no votca 
package found. Perhaps it would only work for 2016(+) Ubuntu?
 

> > 
> >> 
> >> Not sure what went wrong, but I had to use alternative way of 
> installation 
> >> via spack, and it worked eventually, although it lloked like spack 
> installed 
> >> ALL the dependencies along with VOTCA in a separate directory, which is 
> of 
> >> course an overkill. 
> > That is Spack's design, so don't complain to me! And yes we need to 
> > update the dependencies of the VOTCA package in Spack. 
> https://github.com/spack/spack/pull/8757 
>

I see... Otherwise I also noticed that spack installs csg and tools 
separately in two directories beside each other. But then VOTCARC.bash etc 
occur in the tools/bin and VOTCASHARE points at votca_tools/share instead 
of votca_csg/share, so the scripts/inverse are not found. I had to 
reset VOTCASHARE correctly in my .bashrc. 

I mentioned this for other users to be aware.
 
Andrey

>
> >> 
> >> I suppose this post is just to notify the current developers that there 
> >> might be some issue with finding an exiasting Eigen3 dir. 
> > Thanks for letting us know, can you try if above versions fix the issue 
> for you? 
> > 
> > Christoph 
> >> 
> >> Thanks 
> >> Andrey 
> >> 
> >> -- 
> >> You received this message because you are subscribed to the Google 
> Groups 
> >> "votca" group. 
> >> To unsubscribe from this group and stop receiving emails from it, send 
> an 
> >> email to votca+un...@googlegroups.com . 
> >> To post to this group, send email to vo...@googlegroups.com 
> . 
> >> Visit this group at https://groups.google.com/group/votca. 
> >> For more options, visit https://groups.google.com/d/optout. 
> > 
> > 
> > 
> > -- 
> > Christoph Junghans 
> > Web: http://www.compphys.de 
>
>
>
> -- 
> Christoph Junghans 
> Web: http://www.compphys.de 
>

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Re: [votca] csg_reupdate error: property not found: re.function

['Andrey Brukhno' via votca]

Hi Christoph,

On Thursday, July 19, 2018 at 4:01:48 PM UTC+1, Christoph Junghans wrote:
>
> On Thu, Jul 19, 2018 at 8:56 AM, 'Andrey Brukhno' via votca 
> > wrote: 
> > Hello, 
> > 
> > Anyone encountered this error? 
> > 
> > $ csg_reupdate --gentable true --param-in-ext param.new --options 
> > ./settings.xml -v 
> > an error occurred: 
> > property not found: re.function 
> > 
> > while the settings.xml file does contain the correctly formatted 
> subsection 
> > for each potential, like below 
> > 
> >
> >   cbspl 
> >
> > 
> > I would appreciate any clues. 
> Here is an working example: 
>
> https://github.com/votca/csg/blob/master/src/tools/references/spce/settings_re.xml
>  
> 
>  
> Maybe you put the block in the wrong location. 
>

This is from where I actually copy-pasted the re tag into my settings.xml 
file.
However, indeed, upon checking it again now it appeared that the re tag in 
the spce/re example is outside the inverse tag, unlike the tags for imc, 
for example. It is a bit confusing but alright I relocated it by now - and 
it works!

Thanks for the hint!

Andrey
 

>
> Christoph 
> > 
> > Andrey 
> > 
> > -- 
> > You received this message because you are subscribed to the Google 
> Groups 
> > "votca" group. 
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> an 
> > email to votca+un...@googlegroups.com . 
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> . 
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> > For more options, visit https://groups.google.com/d/optout. 
>
>
>
> -- 
> Christoph Junghans 
> Web: http://www.compphys.de 
>

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Re: [votca] csg_reupdate error: property not found: re.function

[Christoph Junghans]

On Thu, Jul 19, 2018 at 8:56 AM, 'Andrey Brukhno' via votca
 wrote:
> Hello,
>
> Anyone encountered this error?
>
> $ csg_reupdate --gentable true --param-in-ext param.new --options
> ./settings.xml -v
> an error occurred:
> property not found: re.function
>
> while the settings.xml file does contain the correctly formatted subsection
> for each potential, like below
>
>   
>   cbspl
>   
>
> I would appreciate any clues.
Here is an working example:
https://github.com/votca/csg/blob/master/src/tools/references/spce/settings_re.xml
Maybe you put the block in the wrong location.

Christoph
>
> Andrey
>
> --
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[votca] csg_reupdate error: property not found: re.function

['Andrey Brukhno' via votca]

Hello,

Anyone encountered this error?

$ csg_reupdate --gentable true --param-in-ext param.new --options 
./settings.xml -v
an error occurred:
property not found: re.function

while the settings.xml file does contain the correctly formatted subsection 
for each potential, like below

  
  cbspl
  

I would appreciate any clues.

Andrey

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Re: [votca] Missing, not found Eigen3 during VOTCA installation

[Christoph Junghans]

On Wed, Jul 18, 2018 at 12:20 PM, Christoph Junghans  wrote:
> On Wed, Jul 18, 2018 at 12:04 PM, 'Andrey Brukhno' via votca
>  wrote:
>> Hello,
>>
>> The last time I was installing the CSG package in my Ubuntu (up-to-date 2014
>> LTS) I got this error from cmake: eigen3 not found, with a suggestion to
>> provide the path to it. I then downloaded the library from their website,
>> installed it and added its include directory to both my $PATH and to the
>> environment under the suggested name EIGEN3_INCLUDE_DIR. But cmake still
>> complained and stopped with the same error, even when I fed it the flag:
>> -DEIGEN3_INCLUDE_DIR=.
> Just a reminder that 2014 was already 4 years ago ;-)
> We recently fixed an issue in the Eigen3 detection:
> https://github.com/votca/votca/commit/8fdcedae9b46e1739fa2ef8589cd5a8f6881d420
> which includes:
> https://github.com/votca/tools/commit/3ee8b88e6022772b843f21a04f66a5bd8bfddd09
> https://github.com/votca/csg/commit/c3f9b3e2841c4b5c0eac20e4d843f6b108750ecf
> Did you use that version?
>
>>
>> Not sure what went wrong, but I had to use alternative way of installation
>> via spack, and it worked eventually, although it lloked like spack installed
>> ALL the dependencies along with VOTCA in a separate directory, which is of
>> course an overkill.
> That is Spack's design, so don't complain to me! And yes we need to
> update the dependencies of the VOTCA package in Spack.
https://github.com/spack/spack/pull/8757

>>
>> I suppose this post is just to notify the current developers that there
>> might be some issue with finding an exiasting Eigen3 dir.
> Thanks for letting us know, can you try if above versions fix the issue for 
> you?
>
> Christoph
>>
>> Thanks
>> Andrey
>>
>> --
>> You received this message because you are subscribed to the Google Groups
>> "votca" group.
>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to votca+unsubscr...@googlegroups.com.
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>> Visit this group at https://groups.google.com/group/votca.
>> For more options, visit https://groups.google.com/d/optout.
>
>
>
> --
> Christoph Junghans
> Web: http://www.compphys.de



-- 
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Re: [votca] Re: Initial parameters for RE iteration with 10 potentials

['Andrey Brukhno' via votca]

Hi Sikandar,

Thanks for confirming my conclusion about the CG-CG.param.init file.

Would you be able to comment on my question regarding the Sci-Py class 
BSplines?

Best regards
Andrey

On Thursday, July 19, 2018 at 3:51:53 AM UTC+1, sikandar wrote:
>
> Hi Andrey,
>
> The initial parameter file *.param.init for the B-spline potential 
> function contains break-points in the first column and knot values in the 
> second column. 
>
> As you observed in csg-tutorial/spce/re/ example, the initial values for 
> the knot values can be set to the PMF obtained by inverting the target 
> RDFs, i.e., c_i = -kTlog(g(r_i)). I have found this approach of 
> initializing knot values work well in my RE coarse-graining experiments.
>
> Best,
> Sikandar
>
> On Wed, Jul 18, 2018 at 4:42 PM 'Andrey Brukhno' via votca <
> vo...@googlegroups.com > wrote:
>
>> Well, to reduce the burden on the developers' answering (probably obvious 
>> for them) questions, here is what I discovered by simply plotting the 
>> CG-CG.param.init file from the tutorial in csg-tutorials/spce/re/
>>
>> The CG-CG.param.init file appears to contain the -RT\ln(g_{target}(r)) 
>> data sampled at the spline knots, i.e. the first column is for the knot 
>> values (r) and the second column is the corresponding PMF in kJ/mol - see 
>> the attached plot. I am not sure what is the origin for the slight 
>> discrepancies that are seen in the graph (resampling artefacts?), but it 
>> seems that the mystery about this file has been cleared up.
>>
>> Andrey
>>
>> On Wednesday, July 18, 2018 at 10:23:27 PM UTC+1, Andrey Brukhno wrote:
>>>
>>> Wow, nobody can answer this straightaway? - I wonder: does this mean 
>>> that no non-associate of the VOTCA team ever used RE method for their 
>>> actual problem (i.e. not a tutorial case)?
>>>
>>> Anyway, may I ask those on the team now: in what relation VOTCA's 
>>> B-spline definition is with the corresponding Sci-Py class 
>>> (scipy.interpolate.BSpline)?
>>>
>>>
>>> https://docs.scipy.org/doc/scipy/reference/generated/scipy.interpolate.BSpline.html
>>>
>>> I also have another question: what is the actual format of the 
>>> .param.init file? - it is far from being clear in the manual, as the file 
>>> itself is never described.
>>>
>>> Thanks again.
>>>
>>> Andrey
>>>
>>> On Wednesday, July 18, 2018 at 6:51:44 PM UTC+1, Andrey Brukhno wrote:

 Hello,

 In an attempt to compare some data obtained with IBI to RE, I am trying 
 to start a relative entropy iteration for the same system. However, I do 
 not know how to generate the initial parameters (aka CG-CG.param.init 
 file) 
 for my system (which would comprise 10 different interaction types).

 Initially I thought VOTCA would be able to generate the necessary 
 *.param.init files based on my initial potentials provided as *.pot.in 
 (the IBI results) and/or distributions (*.dist.tgt). But it seems not to 
 be 
 the case, as it complaints in the inverse.log about missing *.param.init 
 files.

 Can anyone suggest a workaround? - I googled and searched here but did 
 not find anything regrading a practical way of creating those files (nor 
 in 
 the manual).

 Please note: my question is very practical - I know how fit numerical 
 data with regular cubic splines, say in Grace, but VOTCA is using 
 B-splines 
 which are more general (which is good!) but also more involved, so I guess 
 the coefficients of cubic splines cannot be used as initial "guess" for 
 the 
 RE iteration. 

 I essentially need to know what software could do that - ?

 Thanks in advance!

 Andrey

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