[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-08-20 Thread Arham Amouei
Follow-up Comment #19, task #15348 (project administration):

Mature people accept their failures and see the reality as it is, not as one
wishes it to be. The GNU project, though very helpful, was only partially
successful. Now there is no OS that can be called GNU.

Thanks for the review.

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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-08-20 Thread Ineiev
Update of task #15348 (project administration):

  Status: In Progress => Cancelled  
 Open/Closed:Open => Closed 

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Follow-up Comment #18:

> Respect doesn't justify using misnomers and seeing the reality in a
distorted way. I also have respect for the developers of LibreOffice, X11,
Firefox, etc. But should I include these in the name of the whole system? As
you know, a distribution like Ubuntu or CentOS includes software from
different origins.
> 
> Informed people use the name "Linux distribution" for these Desktop systems
not because Linux makes up the biggest part of the system, but because it is
the heart of the system, the most vital single module. If you are worried that
people may think that the whole system is originated from Mr Torvalds, I will
explain the meaning of the term "Linux distribution" in the documentation,
which is not written yet.

All these points are addressed in the GNU/Linux FAQ
.

> You are right that the phrase "Operating Systems with Linux kernel" includes
Android which is not the target of this package. Adding the modifier "Desktop"
at the beginning may solve it but makes the phrase a little too long!

This also reminds me the argument where the OP said, "a two-legged animal
without feathers and with broad flat nails."

I believe the further discussion is pointless.  We've clearly established that
you don't agree with Savannah hosting requirements.

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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-08-20 Thread Arham Amouei
Follow-up Comment #17, task #15348 (project administration):

Thanks for the reply.

Okay. So the only remaining point is the system name.

>  "GNU+Linux" will do; if your respect is so great, you could call it just
"GNU". 

Respect doesn't justify using misnomers and seeing the reality in a distorted
way. I also have respect for the developers of LibreOffice, X11, Firefox, etc.
But should I include these in the name of the whole system? As you know, a
distribution like Ubuntu or CentOS includes software from different origins.

Informed people use the name "Linux distribution" for these Desktop systems
not because Linux makes up the biggest part of the system, but because it is
the heart of the system, the most vital single module. If you are worried that
people may think that the whole system is originated from Mr Torvalds, I will
explain the meaning of the term "Linux distribution" in the documentation,
which is not written yet.

You are right that the phrase "Operating Systems with Linux kernel" includes
Android which is not the target of this package. Adding the modifier "Desktop"
at the beginning may solve it but makes the phrase a little too long!

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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-08-20 Thread Ineiev
Follow-up Comment #16, task #15348 (project administration):

> Actually I'm paying great attention to the notices, thanks to what I've
learned from people like you. But README and the example files do not
constitute the main part of this project. It's very unlikely that one day we
face a dispute over who their exact copyright holders are

Lightning strikes are also very unlikely; however, in certain cases lightning
rods are mandatory, even though they don't always protect from lightning.

> (even if that happens the records in the git repository will settle that).

The records in the git repository typically don't contain the names of
copyright holders.  They record committers and authors (if the committer cares
to write them down), no copyright holders.  Also, the records of the
repository won't help at the point where the repository isn't available.

> I won't insist on using the phrase "The authors of FMD" in the notices of
those files, but it would look awkward if, for example, the names of 10 people
are listed in a short readme file because each of them added one paragraph or
so.

If people made a small addition, copyright notices needn't mention them
 ("In that
case, you should always include a copyright notice in the name of main
copyright holder of the file."); moreover, contributions of 5-6 lines are not
copyrightable at all.

> Two final remarks:
> 1. Despite my really great respect and debt to people who have worked on
GNU, I don't like the term GNU/Linux.

"GNU+Linux" will do; if your respect is so great, you could call it just
"GNU".

> I'm going to use phrases like "Operating Systems with Linux kernel"

Does your package really depend on Linux more than on GNU?  I guess, the users
would have less issues with running it on top of GNU/kFreeBSD or maybe even
GNU/Hurd than on top of Android, wouldn't they?

> 2. We may have more than one host for this project (2 hosts are enough). I
hope this isn't against your rules. The git repositories on all hosts will
always be up-to-date.

Yes, using additional external facilities is up to you.

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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-08-18 Thread Arham Amouei
Follow-up Comment #15, task #15348 (project administration):

Thanks for the reply.

> What actually matters is whether the maintainers of the package basically
understand where these parts of copyright notices come from, and whether they
have a commitment to maintain the notices.

Actually I'm paying great attention to the notices, thanks to what I've
learned from people like you. But README and the example files do not
constitute the main part of this project. It's very unlikely that one day we
face a dispute over who their exact copyright holders are (even if that
happens the records in the git repository will settle that). I won't insist on
using the phrase "The authors of FMD" in the notices of those files, but it
would look awkward if, for example, the names of 10 people are listed in a
short readme file because each of them added one paragraph or so. Please
inform me of your final judgment about the usage of the phrase "The authors of
FMD" in the mentioned files. I'll prepare the files according to that.

Two final remarks:
1. Despite my really great respect and debt to people who have worked on GNU,
I don't like the term GNU/Linux. I'm going to use phrases like "Operating
Systems with Linux kernel" or, more generally, "Unix-like systems" instead.
2. We may have more than one host for this project (2 hosts are enough). I
hope this isn't against your rules. The git repositories on all hosts will
always be up-to-date.

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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-08-18 Thread Ineiev
Follow-up Comment #14, task #15348 (project administration):

> But if you are not familiar with the legal aspects enough, how can you
decide if the copyright notices in a package are "valid" or not?

The copyright notices should have the established form and list the right
years and copyright holders.  Of course, in most cases I hardly can tell who
is the real copyright holder of the files I wasn't involved in writing (as
opposed to the files I write myself).  However, this isn't essential.

What actually matters is whether the maintainers of the package basically
understand where these parts of copyright notices come from, and whether they
have a commitment to maintain the notices; so far, I'm getting an impression
you haven't.

> Some projects use...

It also doesn't matter what other people do.  You and me are not responsible
for their actions.

> And I see that even many GNU projects does NOT abide by all the things you
say. Just for an example, the files ChangeLog and THANKS of the latest gzip
torball doesn't have notices.

Thank you!  Please file a bug report against gzip and make sure the issue is
fixed.

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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-08-16 Thread Arham Amouei
Follow-up Comment #13, task #15348 (project administration):

Thanks for the reply. But if you are not familiar with the legal aspects
enough, how can you decide if the copyright notices in a package are "valid"
or not? Some projects use collective copyright notices like

Copyright © 2016-2018 The TokTok team.
Copyright © 2013 Tox project.

(URL: https://github.com/TokTok/c-toxcore)

Maybe you should consult with a lawyer in FSF about this because of your job
and responsibility.

And I see that even many GNU projects does NOT abide by all the things you
say. Just for an example, the files ChangeLog and THANKS of the latest gzip
torball doesn't have notices.

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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-08-15 Thread Ineiev
Follow-up Comment #12, task #15348 (project administration):

> Is there a way that we declare all the contributors (including
> those in the future) as writers/copyright holders of some files?

I'm not a lawyer, but as far as I know, assigning copyright needs some kind of
paperwork from the current copyright holders.  Every time you add a
contributor, you would need signed papers from every previous contributor.

> It is not important to us who the exact authors of some files are.

Having valid copyright notices is important for the users of your package.  If
you have no real commitment to maintain these records carefully, let us not
register your package on Savannah.

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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-08-13 Thread Arham Amouei
Follow-up Comment #11, task #15348 (project administration):

I'm learning from you and I'm thankful for that.

> In README.txt, the copyright note refers to AUTHORS; this
> is too easy to get wrong when AUTHORS is edited.  I'd
> suggest writing down the actual authors instead.

Is there a way that we declare all the contributors (including 
those in the future) as writers/copyright holders of some files?
It is not important to us who the exact authors of some files are.

We may add new names to AUTHORS but no name will be removed.

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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-08-13 Thread Ineiev
Follow-up Comment #10, task #15348 (project administration):

Thank you!

In README.txt, the copyright note refers to AUTHORS; this
is too easy to get wrong when AUTHORS is edited.  I'd
suggest writing down the actual authors instead.

Likewise, Python files in examples/ refer to AUTHORS
instead of explicitly listing them.  These files also
say that a copy of CC0 should be provided with them,
but no copy of CC0 is included.

(If you add a copy of CC0, please note that the text
of it has no copyright and license notices, you'll
need to add them like in task #15279.)

Files like examples/log.lammps.argon.morse have no notices.

Please check other files as well.

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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-08-11 Thread Arham Amouei
Additional Item Attachment, task #15348 (project administration):

File name: fmd-2019-aug-11.tar.gz Size:78 KB




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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-08-11 Thread Arham Amouei
Follow-up Comment #9, task #15348 (project administration):

To facilitate the process, I have also made the following changes to the
package:

* added copyright and license notices to src/makefile
* added copyright and license notices to setup.py
* added copyright and license notices to tests/test_molframe.py
* changed README.md to README.txt and added copyright and license notices (GNU
All-Permissive License)
* deleted the file inside potentials directory, because wasn't sure about its
license (I've written to its author to see if it can be distributed with a
GPL-licensed software -- but it's not an essential part of the package)
* dedicated examples/*.c & examples/*.py & examples/in.lammps.argon to public
domain by including related notices

The two files examples/log.lammps.argon.lj and examples/log.lammps.argon.morse
are log files produced by the free software LAMMPS, when it processes the
input script file examples/in.lammps.argon. We have included them so that the
user can easily compare the results of our software with the output of the
famous LAMMPS.

Please see the updated tarball.

Thanks,
Arham

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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-08-10 Thread Arham Amouei
Follow-up Comment #8, task #15348 (project administration):

Now I understand free licenses and the meaning of compatibility with GPL much
better.

Here is an updated list of the dependencies:

*GNU Scientific Library*:

License: GPL v3 or later
URL: https://savannah.gnu.org/projects/gsl

*Message Passing Interface (MPI)*

There are different implementations of MPI, some of which are free software.
For example, Open MPI uses "3-clause BSD license" (Modified BSD license).
URL: https://www.open-mpi.org/community/license.php

*NumPy*

License: 3-clause BSD license (Modified BSD license)
URL: https://numpy.org/index.html

*ASE*

License: LGPL v2.1 or later
URL: https://wiki.fysik.dtu.dk/ase/about.html

*periodictable*

License: Public Domain
URL: https://pypi.org/project/periodictable/

*mpi4py*

License: FreeBSD license (2-clause BSD license)
URL: https://pypi.org/project/mpi4py/


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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-08-06 Thread Arham Amouei
Follow-up Comment #7, task #15348 (project administration):

I see. I think within a week I can learn what I need to know about free
licenses.

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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-08-06 Thread Ineiev
Update of task #15348 (project administration):

 Should Start On: Thu 01 Aug 2019 12:00:00 AM UTC => Mon 29 Jul 2019
12:00:00 AM UTC
   Should be Finished on: Thu 01 Aug 2019 12:00:00 AM UTC => Thu 08 Aug 2019
12:00:00 AM UTC

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Follow-up Comment #6:

We have no resources to continually check all hosted packages for compliance.
The GNU project does provide a set of licensing-related pages like
https://www.gnu.org/licenses/license-list.html
https://www.gnu.org/licenses/gpl-faq.html
https://www.gnu.org/licenses/gpl-howto.html, but in general, we have to rely
on the ability of package maintainers to tell whether licenses are compatible
and whether they are free.


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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-08-01 Thread Arham Amouei
Follow-up Comment #5, task #15348 (project administration):

I am sorry for my mistake about the license of ASE. In the following updated
list, I have used the license names as mentioned by the authors/maintainers
themselves. Honestly, I do not have detailed knowledge about free licenses
available, so I should leave it to you to judge if the licenses of NumPy and
mpi4py are GPL-compatible.

The dependencies include:

*GNU Scientific Library*

License: GPL
URL: https://www.gnu.org/software/gsl

*Message Passing Interface (MPI)*

There are different implementations of MPI, some of which are free software.
For example, Open MPI uses "3-clause BSD license".
URL: https://www.open-mpi.org/community/license.php

*NumPy*

License: BSD
URL: https://numpy.org/index.html

*ASE*

License: LGPL 2.1 or any later version
URL: https://wiki.fysik.dtu.dk/ase/about.html

*periodictable*

License: Public Domain
URL: https://pypi.org/project/periodictable/

*mpi4py*

License: BSD
URL: https://pypi.org/project/mpi4py/ 

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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-08-01 Thread Ineiev
Update of task #15348 (project administration):

 Should Start On: Mon 29 Jul 2019 12:00:00 AM UTC => Thu 01 Aug 2019
12:00:00 AM UTC
   Should be Finished on: Thu 08 Aug 2019 12:00:00 AM UTC => Thu 01 Aug 2019
12:00:00 AM UTC

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Follow-up Comment #4:

https://wiki.fysik.dtu.dk/ase/about.html says "LGPL 2.1 or later", not "GPL";
also, the wording "BSD-like" is too vague to define a license.  It includes at
least one GPL-incompatible license
, which is
unacceptable for Savannah.

Could you rewrite this list more carefully?

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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-07-31 Thread Arham Amouei
Follow-up Comment #3, task #15348 (project administration):

The dependencies include:

* GNU Scientific Library
License: GPL
URL: https://www.gnu.org/software/gsl

* Message Passing Interface (MPI)
There are different implementations of MPI, some of which are free software.
For example MPICH, a very widely used one, uses a BSD-like license.
URL: https://www.mpich.org/downloads/

* NumPy
License: BSD-like
URL: https://numpy.org/license.html

* ASE
License: GPL
URL: https://wiki.fysik.dtu.dk/ase/about.html

* periodictable
License: Public Domain
URL: https://pypi.org/project/periodictable/

* mpi4py
License: BSD
URL: https://pypi.org/project/mpi4py/

One part of the code needs Python to run.

We like the name "fmd", but if you insist "fmdlib" is also acceptable to us.
:)

I also attached a tarball. Please let me know if anything else should be done
as well. Thank you.

(file #47280)
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Additional Item Attachment:

File name: fmd.tar.gz Size:552 KB




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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-07-31 Thread Arham Amouei
Follow-up Comment #2, task #15348 (project administration):


[comment #1 comment #1:]
> Please list all your dependencies with links to their licensing terms; also,
please provide a tarball of your package.
> 
> Also, it would be nice if the System Name were longer and more descriptive;
could you suggest a new one?

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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-07-30 Thread Ineiev
Update of task #15348 (project administration):

  Status:None => In Progress
 Assigned to:None => ineiev 

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Follow-up Comment #1:

Please list all your dependencies with links to their licensing terms; also,
please provide a tarball of your package.

Also, it would be nice if the System Name were longer and more descriptive;
could you suggest a new one?

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[Savannah-register-public] [task #15348] Submission of Free Molecular Dynamics

2019-07-29 Thread Arham Amouei
URL:
  

 Summary: Submission of Free Molecular Dynamics
 Project: Savannah Administration
Submitted by: a_amouei
Submitted on: Mon 29 Jul 2019 03:02:31 PM UTC
 Should Start On: Mon 29 Jul 2019 12:00:00 AM UTC
   Should be Finished on: Thu 08 Aug 2019 12:00:00 AM UTC
Category: Project Approval
Priority: 5 - Normal
  Status: None
 Privacy: Public
Percent Complete: 0%
 Assigned to: None
 Open/Closed: Open
 Discussion Lock: Any
  Effort: 0.00

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Details:

A new project has been registered at Savannah
This project account will remain inactive until a site admin approves
or discards the registration.


= Registration Administration =

While this item will be useful to track the registration process,
*approving or discarding the registration must be done using the specific
Group Administration
 page*,
accessible only to site administrators,
effectively *logged as site administrators* (superuser):

* Group Administration



= Registration Details =

* Name: *Free Molecular Dynamics*
* System Name:  *fmd*
* Type: non-GNU software and documentation
* License: GNU General Public License v3 or later



== Description: ==
Free Molecular Dynamics (FMD) is a library for performing classical molecular
dynamics (MD) simulations on different kinds of computers, from laptops to
computer clusters. Its core part, which particularly executes all
computationally expensive operations, is written in C for efficiency. Another
part of FMD, written in Python and named PyFMD, adds features which are
essential for many, if not most, simulations. PyFMD also provides Python
programmers with an object-oriented interface for interacting with the core
part of FMD within Python programs.


== Other Software Required: ==
GNU Scientific Library
Message-Passing Interface (MPI)


== Tarball URL: ==
https://github.com/a-amouei/fmd






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