xmds-user — All topics related to XMDS that are relevant to the entire user base.

[xmds-user] xmds installation fails

[Angela W. <ang...@gm...>]

Hello,

I'm having trouble installing xmds, I think the issue is that it can't find
h5cc, even though I point to where it is...  and have checked it is where I
point to (installation command and output copied below). Unless its an
issue with h5cc itself.  Anyone else come across this issue and know how to
resolve it?

Thanks for your help,
Angela.

xmds2 --reconfigure --include-path
/opt/homebrew/Cellar/hdf5/1.14.3_1/include/ --lib-path
/opt/homebrew/Cellar/hdf5/1.14.3_1/lib/
/opt/homebrew/bin/xmds2:4: DeprecationWarning: pkg_resources is deprecated
as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  __import__('pkg_resources').require('xmds2==3.1.0')
xmds2 version 3.1.0 "My kingdom for a tentacle" (r3121)
Copyright 2000-2019 Graham Dennis, Joseph Hope, Mattias Johnsson
                    and the xmds team

Configuring for single-process scripts...
Checking for 'clang++' (C++ compiler)    : /usr/bin/clang++
Checking whether the compiler works      : yes
Checking that we have a C++ compiler     : yes
Checking whether we are cross-compiling  : no
Trying to make compiler optimise for this machine : yes
Trying to make compiler tune for this machine     : yes
Checking for compiler flags -O3                   : yes
Checking for compiler flags -ffast-math           : yes
Checking for compiler flags -funroll-all-loops    : yes
Checking for compiler flags -fomit-frame-pointer  : yes
Checking for compiler flags -falign-loops         : yes
Checking for compiler flags -fstrict-aliasing     : yes
Checking for compiler flags -momit-leaf-frame-pointer : yes
Checking for cautious math flags                      : yes
Checking for Autovectorisation                        : yes
Checking for OpenMP                                   : no
Checking for pthreads                                 : yes
Checking for compiler debug flags                     : yes
Checking for srandomdev                               : yes
Checking for /dev/urandom                             : yes
Checking for program 'h5cc'                           :
/opt/homebrew/bin/h5cc
Traceback (most recent call last):
  File "/opt/homebrew/bin/xmds2", line 7, in <module>
    exec(compile(f.read(), __file__, 'exec'))
  File "/Applications/xmds-3.1.0/bin/xmds2", line 4, in <module>
    sys.exit(parser2.main())
             ^^^^^^^^^^^^^^
  File "/Applications/xmds-3.1.0/xpdeint/parser2.py", line 219, in main
    return Configuration.run_reconfig(includePaths, libPaths)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/xmds-3.1.0/xpdeint/Configuration.py", line 145, in
run_reconfig
    return run_config(includePaths = includePaths, libPaths = libPaths)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/xmds-3.1.0/xpdeint/Configuration.py", line 119, in
run_config
    ret = ctx.execute()
          ^^^^^^^^^^^^^
  File "/Applications/xmds-3.1.0/xpdeint/waf/waflib/Configure.py", line
159, in execute
    super(ConfigurationContext, self).execute()
  File "/Applications/xmds-3.1.0/xpdeint/waf/waflib/Context.py", line 204,
in execute
    self.recurse([os.path.dirname(g_module.root_path)])
  File "/Applications/xmds-3.1.0/xpdeint/Configuration.py", line 56, in
<lambda>
    lambda x, y: getattr(Context.g_module, x.cmd or x.fun, Utils.nada)(x)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/xmds-3.1.0/xpdeint/Configuration.py", line 85, in _
    return f(ctx, *args, **kw)
           ^^^^^^^^^^^^^^^^^^^
  File "/Applications/xmds-3.1.0/xpdeint/support/wscript", line 747, in
configure
    configure_compiler()
  File "/Applications/xmds-3.1.0/xpdeint/support/wscript", line 401, in
configure_compiler
    h5cc_shared_flags = conf.cmd_and_log([conf.env['H5CC'][0], '-show',
'-shlib'])

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Applications/xmds-3.1.0/xpdeint/waf/waflib/Context.py", line 461,
in cmd_and_log
    raise e
waflib.Errors.WafError: Command ['/opt/homebrew/bin/h5cc', '-show',
'-shlib'] returned 1

[xmds-user] About convergence tolerance

[Gerardo O. U. <ger...@ci...>]

Hello,

I´m learning to use XMDS2. I have already performed some simulations.
Right now, I am interested in solving the nonlinear Schrödinger equation to get the groundstate by using imaginary time.
I have already been able to do that. But I would like to know if there is a way to set the change in energy/wavefunction as a convergence parameter instead of only evolving the equation in time?

Thank you for your time

Best regards,

Gerardo


________________________________

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[xmds-user] MPI in XMDS2

[Weinberger, H. <har...@uc...>]

Dear Developers,

I am trying to run an XMDS2 script with the MPI framework.

I can see in the documentation for 2.2.2 that you have the <driver name="mpi-multi-path" paths="8" /> for distributing a set of processes over a machine in parallel.

I need a bit more control over the output (I want each process to be outputted to its own file in the format of output_$(mpi_comm_rank).h5) and so I can also initialise each of the processes with a random seed associated with its mpi_comm_rank (to initialise Wiener noise). Do you have any functionality to allow this in XMDS2?

Thank you for your help,

Best
Harvey

Re: [xmds-user] Looping the Simulation with a changed parameter

[Matthew D. <md...@ph...>]

Hi all,

It is possible to pass variables to xmds executable from the command line.  This example shows you how:

http://www.xmds.org/worked_examples.html?highlight=argument#wignerarguments

I write a shell script to loop over the variable of interest, create a unique directory for each, put the correct files in it, and execute xmds2 from there.

HTH,
Matt.

========================================================================
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Professor of Physics
Chair of SMP Equity, Diversity, and Inclusion committee

School of Mathematics and Physics
The University of Queensland
Brisbane Qld 4072 Australia

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From: Craig Chisholm via xmds-user <xmd...@li...>
Date: Thursday, 3 August 2023 at 8:37 pm
To: xmd...@li... <xmd...@li...>
Subject: Re: [xmds-user] Looping the Simulation with a changed parameter
Hi Khush Dave,

I don't know how to do what you want in xmds2 but I can share my alternative workflow.

In the xmds2 script, I define the variable to loop over as a command line argument then, I use a python script to call the program with subprocess.
For example, if we have a script called program.xmds with <name>program</name> and a command line argument called variable then I could have a Python script that goes

import subprocess

#compile the program
subprocess.run(['xmds2',program+'.xmds'])

#loop variable from 0 to 9
for i in range(10):
    subprocess.run('./'+program,'--variable',str(i)])

The output files are always named program.h5 and prgram.xsil so I usually also move the outputs to a subdirectory as part of the loop other wise they get overwritten each time and you only keep the last one.

I also use this if I need to run multiple programs where one program is initialised with the break point of the previous program.

I hope this helps you even if it doesn't answer your question.

Best,

Craig
________________________________
From: Dave Khush Keyur 19096 via xmds-user <xmd...@li...>
Sent: 01 August 2023 16:05
To: xmd...@li... <xmd...@li...>
Subject: [xmds-user] Looping the Simulation with a changed parameter

CAUTION: This email originated from outside the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.
Hey there,

I understand this may sound silly.

I wish to run my XMDS2 simulation over and over again with one constant parameter being changed every iteration. I also wish to produce the output for each iteration and then initialize all vectors to the initial condition. The cycle option in <sequence> does not allow me to do these two steps which are required for my work. I tried using a general for loop in C++ format but that does not compile with the software. Is there a way you can help me with this?

--
Regards,
Khush Dave.
[Image removed by sender.]

Re: [xmds-user] Looping the Simulation with a changed parameter

[Craig C. <Cra...@ic...>]

Hi Khush Dave,

I don't know how to do what you want in xmds2 but I can share my alternative workflow.

In the xmds2 script, I define the variable to loop over as a command line argument then, I use a python script to call the program with subprocess.
For example, if we have a script called program.xmds with <name>program</name> and a command line argument called variable then I could have a Python script that goes

import subprocess

#compile the program
subprocess.run(['xmds2',program+'.xmds'])

#loop variable from 0 to 9
for i in range(10):
    subprocess.run('./'+program,'--variable',str(i)])

The output files are always named program.h5 and prgram.xsil so I usually also move the outputs to a subdirectory as part of the loop other wise they get overwritten each time and you only keep the last one.

I also use this if I need to run multiple programs where one program is initialised with the break point of the previous program.

I hope this helps you even if it doesn't answer your question.

Best,

Craig
________________________________
From: Dave Khush Keyur 19096 via xmds-user <xmd...@li...>
Sent: 01 August 2023 16:05
To: xmd...@li... <xmd...@li...>
Subject: [xmds-user] Looping the Simulation with a changed parameter

CAUTION: This email originated from outside the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.
Hey there,

I understand this may sound silly.

I wish to run my XMDS2 simulation over and over again with one constant parameter being changed every iteration. I also wish to produce the output for each iteration and then initialize all vectors to the initial condition. The cycle option in <sequence> does not allow me to do these two steps which are required for my work. I tried using a general for loop in C++ format but that does not compile with the software. Is there a way you can help me with this?

--
Regards,
Khush Dave.

[xmds-user] Looping the Simulation with a changed parameter

[Dave K. K. 1. <kh...@ii...>]

Hey there,

I understand this may sound silly.

I wish to run my XMDS2 simulation over and over again with one constant
parameter being changed every iteration. I also wish to produce the output
for each iteration and then initialize all vectors to the initial
condition. The cycle option in <sequence> does not allow me to do these two
steps which are required for my work. I tried using a general for loop in
C++ format but that does not compile with the software. Is there a way you
can help me with this?

-- 
Regards,
Khush Dave.

Re: [xmds-user] Using mode index to initialize a vector

[Mattias J. <mat...@mq...>]

Hi Ghislain,

Since you're clearly capable and willing to engage in C hackery that accesses the underlying variable names, here's something you could try.

Add a comment before the if statement like

   // Ghislan
   if (kx_index % 2 == 0){
   ...

and then run xmds2 on the script. This will generate a C++ file with a .cc extension. Open that file and search for "Ghislan". You will then see the loop that is doing the intialization, and you will be able to see what the loop variable is called. You can then use that in your xmds script.

Cheers,
Mattias
________________________________
From: Ghislain de Labbey <ghi...@co...>
Sent: Tuesday, 18 April 2023 8:46 PM
To: xmd...@li... <xmd...@li...>
Subject: [xmds-user] Using mode index to initialize a vector

Hi,

I'm trying to initialize a vector in the spectral basis, using DCT
transform. For example, let's say that I want a triangular potential,
only modes of even index contribute :

<vector name="potential" dimensions="x" type="real" initial_basis="kx">
    <components> V </components>
    <initialisation>
        <![CDATA[
            if (kx_index % 2 == 0){
            V = pow(1./kx, 2);
            }
        ]]>
    </initialisation>

</vector>

However, I get the error "use of undeclared identifier 'kx_index' ". Is
there a way to get the index of the mode and not the wavenumber at
initialization ?

Maybe I could use some trick like int(kx*_max_x/M_PI) to get the index
but I don't know how safe it is.

Cheers,

Ghislain



_______________________________________________
xmds-user mailing list
xmd...@li...
https://lists.sourceforge.net/lists/listinfo/xmds-user<https://lists.sourceforge.net/lists/listinfo/xmds-user>

[xmds-user] Using mode index to initialize a vector

[Ghislain de L. <ghi...@co...>]

Hi,

I'm trying to initialize a vector in the spectral basis, using DCT 
transform. For example, let's say that I want a triangular potential, 
only modes of even index contribute :

<vector name="potential" dimensions="x" type="real" initial_basis="kx">
     <components> V </components>
     <initialisation>
         <![CDATA[
             if (kx_index % 2 == 0){
             V = pow(1./kx, 2);
             }
         ]]>
     </initialisation>

</vector>

However, I get the error "use of undeclared identifier 'kx_index' ". Is 
there a way to get the index of the mode and not the wavenumber at 
initialization ?

Maybe I could use some trick like int(kx*_max_x/M_PI) to get the index 
but I don't know how safe it is.

Cheers,

Ghislain

Re: [xmds-user] Bessel cylindrical coordinates normalisation

[Craig C. <Cra...@ic...>]

I see,

I was surprised by this because I never saw it working that way using FFT and the filter segment looked the same but I suppose it could be that it's placed subtly differently and I just need to inspect the script more carefully or that it is related to step size.

Thank you for the help.

Best,

Craig
________________________________
From: Mattias Johnsson <mat...@mq...>
Sent: 11 February 2022 11:53
To: Craig Chisholm <Cra...@ic...>; Craig Chisholm via xmds-user <xmd...@li...>
Subject: Re: [xmds-user] Bessel cylindrical coordinates normalisation

CAUTION: This email originated from outside the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.
I guess it would depend on where the filter was applied relative to the evolution step and the sampling. If it happens just before the sampling it should be exactly normalized, otherwise not. Regardless, as you make the timesteps smaller the deviation from perfect normalization should approach zero.

________________________________
From: Craig Chisholm <Cra...@ic...>
Sent: Friday, 11 February 2022 7:29 PM
To: Mattias Johnsson <mat...@mq...>; Craig Chisholm via xmds-user <xmd...@li...>
Subject: Re: [xmds-user] Bessel cylindrical coordinates normalisation

Hi Matthias and Matthew,

Thank you for the explanation, indeed I didn't know how the normalisation worked, my mistake.

Regarding using the sampling_group: indeed, I tried this before trapz and I was confused that it takes time to converge to the correct number because I thought that the

<filter>
  <dependencies>wavefunction normalisation</dependencies>
  <![CDATA[
    // Correct normalisation of the wavefunction
    phi *= sqrt(Nparticles/Ncalc);
  ]]>
</filter>

part should enforce that the normalisation is 1 on each step even if the correct shape has not been found yet. Is there something else here which I am not understanding?

Best,

Craig
________________________________
From: Mattias Johnsson <mat...@mq...>
Sent: 11 February 2022 03:48
To: Craig Chisholm via xmds-user <xmd...@li...>; Craig Chisholm <Cra...@ic...>
Subject: Re: [xmds-user] Bessel cylindrical coordinates normalisation

Hi Craig,

> Thank you for the answers. If I understand correctly, if I would choose a higher order
> Bessel transform I would get sampling at r = 0 but also angular momentum in the
> form -m^2/r^2, or is there some way to remove that contribution? As I see from Blair's
>  email, it should be possible to put any grid, but does XMDS2 have this feature implemented?

Honestly, I have very little knowledge of how the Bessel basis works in XMDS2. But I believe there is no way to specify grid points explicitly; you have to take what XMDS2 gives you. They are fixed due to transformation properties, the need for quadrature integration to work etc.

Also I note that the contribution -m^2/r^2 diverges at r=0, suggesting that point might be wise to ignore anyway.

> With regards to the normalisation, I have been testing with the script bessel_cosine_groundstate.xmds
> from the examples folder. The results are the same as it is or if I modify it to use dft instead of
> dct on the z axis. I see that numerical integration > doesn't work properly when 0 is not
> included in the axis. As an example, I take f = (2/sigma^2)*exp(-r^2/sigma^2) integrating
> this with rdr as the 'volume' element gives 1. In Python (numpy.trapz), when I take the grid
>  from the example script and sigma = 1e-6 I get 0.9338052073724259. If I append 0 to the
> start of the grid, I get 0.9855312028781402 which tells me that the missing contribution
>  between 0 and the first point is important. If I increase the number of grid points the
> answer tends to 1. So, I already see that the numerical integration is not working on this grid.
> Independently of that, I am still surprised that the norm changes during the calculation since
> the filter segment should be forcing it to 1 at each step regardless of how good or bad the integration is.

Your integration example is irrelevant in this case: for cylindrical coordinates the area element goes as (r dθ), which goes to zero as r -> 0. So missing out the zero point has asymptotically no weight. But yes, on any grid naive integration will have an error; the question is whether that error goes to zero as the number of grid points goes to infinity.

But more importantly, keep in mind XMDS2 isn't "missing out" the zero point - it's using a basis transform where it doesn't exist, so it's perfectly consistent. It's not like it chose a grid, then removed the zero point. Which does mean, of course, the norm should be preserved under unitary evolution.

So, regarding the norm in that example, it looks fine to me. You can look at it by adding

      <sampling_group basis="r(0) z(0)" initial_sample="no">
        <moments>norm</moments>
        <dependencies>wavefunction</dependencies>
        <![CDATA[
          norm = mod2(phi);
        ]]>
      </sampling_group>

as an output moment group. The norm starts off at about 49000 (remember we specified 5e5 particles), then asymptotically approaches 50000 as you'd expect. Remember this is a ground state finder, which is not​ unitary evolution. It works by evolving the system in imaginary time, which makes all states decay according to their energy. So you run it for a step, let the population decay, then renormalize. Rinse and repeat. In the end you're only left with the lowest energy state, which is the ground state, and that state will be left with the correct normalization (e.g. 50000 particles).

Cheers,
Mattias

Re: [xmds-user] Bessel cylindrical coordinates normalisation

[Craig C. <Cra...@ic...>]

Hi Matthias and Matthew,

Thank you for the explanation, indeed I didn't know how the normalisation worked, my mistake.

Regarding using the sampling_group: indeed, I tried this before trapz and I was confused that it takes time to converge to the correct number because I thought that the

<filter>
  <dependencies>wavefunction normalisation</dependencies>
  <![CDATA[
    // Correct normalisation of the wavefunction
    phi *= sqrt(Nparticles/Ncalc);
  ]]>
</filter>

part should enforce that the normalisation is 1 on each step even if the correct shape has not been found yet. Is there something else here which I am not understanding?

Best,

Craig
________________________________
From: Mattias Johnsson <mat...@mq...>
Sent: 11 February 2022 03:48
To: Craig Chisholm via xmds-user <xmd...@li...>; Craig Chisholm <Cra...@ic...>
Subject: Re: [xmds-user] Bessel cylindrical coordinates normalisation

Hi Craig,

> Thank you for the answers. If I understand correctly, if I would choose a higher order
> Bessel transform I would get sampling at r = 0 but also angular momentum in the
> form -m^2/r^2, or is there some way to remove that contribution? As I see from Blair's
>  email, it should be possible to put any grid, but does XMDS2 have this feature implemented?

Honestly, I have very little knowledge of how the Bessel basis works in XMDS2. But I believe there is no way to specify grid points explicitly; you have to take what XMDS2 gives you. They are fixed due to transformation properties, the need for quadrature integration to work etc.

Also I note that the contribution -m^2/r^2 diverges at r=0, suggesting that point might be wise to ignore anyway.

> With regards to the normalisation, I have been testing with the script bessel_cosine_groundstate.xmds
> from the examples folder. The results are the same as it is or if I modify it to use dft instead of
> dct on the z axis. I see that numerical integration > doesn't work properly when 0 is not
> included in the axis. As an example, I take f = (2/sigma^2)*exp(-r^2/sigma^2) integrating
> this with rdr as the 'volume' element gives 1. In Python (numpy.trapz), when I take the grid
>  from the example script and sigma = 1e-6 I get 0.9338052073724259. If I append 0 to the
> start of the grid, I get 0.9855312028781402 which tells me that the missing contribution
>  between 0 and the first point is important. If I increase the number of grid points the
> answer tends to 1. So, I already see that the numerical integration is not working on this grid.
> Independently of that, I am still surprised that the norm changes during the calculation since
> the filter segment should be forcing it to 1 at each step regardless of how good or bad the integration is.

Your integration example is irrelevant in this case: for cylindrical coordinates the area element goes as (r dθ), which goes to zero as r -> 0. So missing out the zero point has asymptotically no weight. But yes, on any grid naive integration will have an error; the question is whether that error goes to zero as the number of grid points goes to infinity.

But more importantly, keep in mind XMDS2 isn't "missing out" the zero point - it's using a basis transform where it doesn't exist, so it's perfectly consistent. It's not like it chose a grid, then removed the zero point. Which does mean, of course, the norm should be preserved under unitary evolution.

So, regarding the norm in that example, it looks fine to me. You can look at it by adding

      <sampling_group basis="r(0) z(0)" initial_sample="no">
        <moments>norm</moments>
        <dependencies>wavefunction</dependencies>
        <![CDATA[
          norm = mod2(phi);
        ]]>
      </sampling_group>

as an output moment group. The norm starts off at about 49000 (remember we specified 5e5 particles), then asymptotically approaches 50000 as you'd expect. Remember this is a ground state finder, which is not​ unitary evolution. It works by evolving the system in imaginary time, which makes all states decay according to their energy. So you run it for a step, let the population decay, then renormalize. Rinse and repeat. In the end you're only left with the lowest energy state, which is the ground state, and that state will be left with the correct normalization (e.g. 50000 particles).

Cheers,
Mattias

________________________________
From: Craig Chisholm via xmds-user <xmd...@li...>
Sent: Friday, 11 February 2022 3:34 AM
To: Craig Chisholm via xmds-user <xmd...@li...>
Subject: Re: [xmds-user] Bessel cylindrical coordinates normalisation

Hi Mattias and Blair,

Thank you for the answers. If I understand correctly, if I would choose a higher order Bessel transform I would get sampling at r = 0 but also angular momentum in the form -m^2/r^2, or is there some way to remove that contribution? As I see from Blair's email, it should be possible to put any grid, but does XMDS2 have this feature implemented?

With regards to the normalisation, I have been testing with the script bessel_cosine_groundstate.xmds from the examples folder. The results are the same as it is or if I modify it to use dft instead of dct on the z axis. I see that numerical integration doesn't work properly when 0 is not included in the axis.
As an example, I take f = (2/sigma^2)*exp(-r^2/sigma^2) integrating this with rdr as the 'volume' element gives 1. In Python (numpy.trapz), when I take the grid from the example script and sigma = 1e-6 I get 0.9338052073724259. If I append 0 to the start of the grid, I get 0.9855312028781402 which tells me that the missing contribution between 0 and the first point is important. If I increase the number of grid points the answer tends to 1. So, I already see that the numerical integration is not working on this grid. Independently of that, I am still surprised that the norm changes during the calculation since the filter segment should be forcing it to 1 at each step regardless of how good or bad the integration is.

Best,

Craig

P.S. Apologies to Blair for spam, I accidentally replied to you instead of the list.

________________________________
From: Blair Blakie <bla...@ot...>
Sent: 10 February 2022 10:19
To: Craig Chisholm <Cra...@ic...>
Subject: Re: [xmds-user] Bessel cylindrical coordinates normalisation

CAUTION: This email originated from outside the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.

Hi Craig



I hope you are well.



I’m on the XMDS mailing list so I saw your message. I actually don’t use XMDS but I do use Bessel methods a lot (e.g. see https://journals.aps.org/prresearch/pdf/10.1103/PhysRevResearch.3.013283 ).

Because it is a spectral method you can always output the result to any grid, including one that has a zero point. I could find a reference if you need it. The loss of norm is concerning -  the Bessel methods should be extremely conserving.



BB



From: Mattias Johnsson <mat...@mq...>
Date: Thursday, 10 February 2022 at 12:10 PM
To: "xmd...@li..." <xmd...@li...>, Craig Chisholm <Cra...@ic...>
Subject: Re: [xmds-user] Bessel cylindrical coordinates normalisation



Hi Chris,



I'm not very familiar with the Bessel transform, but after having a quick look at XMDS2's code, here's what I can tell you.



Regarding including the r=0 point: When using the Bessel transform, the position of the grid points are given by the zeroes of the Bessel function (multiplied by a scaling factor).



From the documentation: http://www.xmds.org/reference_elements.html#the-bessel-and-bessel-neumann-transforms "The order m of the transform is defined by the order attribute in the <dimension> element, which must be assigned as a non-negative integer. If the order is not specified, it defaults to zero which corresponds to the solution being independent of the angular coordinate θ."



So if you're choosing the default order, it's a Bessel function of the first kind with m=0, which doesn't have a zero at the origin.



Regarding your normalisation issue, I'm afraid I have no idea what the problem is.



Cheers,

Mattias

________________________________

From: Craig Chisholm via xmds-user <xmd...@li...>
Sent: Tuesday, 8 February 2022 9:26 PM
To: xmd...@li... <xmd...@li...>
Subject: [xmds-user] Bessel cylindrical coordinates normalisation



Hello,



I am having trouble with using the Bessel transform in cylindrical coordinates. Specifically, I have two problems:

  1.  I see that the normalisation of the wavefunction is evolving over time in spite of using continuous normalisation.
  2.  I would like to have r = 0 as part of the grid for the output but I haven't found a way to do this.

I'm using xmds2 version 2.2.3 "It came from the deep" (Debian package 2.2.3+dfsg-5) on Ubuntu 18.04 LTS and Linux Mint 19.3 and XMDS2 version 2.2.2 "XMDS2 is a game of two halves" on Ubuntu 16.04 LTS. On all three systems it's the same.



Please let me know if I should be providing additional information or diagnostics.



Thank you,



Craig Chisholm

PhD Student

ICFO - The Institute of Photonic Sciences

Av. Carl Friedrich Gauss, 3

08860 Castelldefels

Barcelona, Spain

Research Group: Ultracold Quantum Gases

Office Telephone:          +34 935542304

Laboratory Telephone: +34 935542263

Re: [xmds-user] Bessel cylindrical coordinates normalisation

[Mattias J. <mat...@mq...>]

I guess it would depend on where the filter was applied relative to the evolution step and the sampling. If it happens just before the sampling it should be exactly normalized, otherwise not. Regardless, as you make the timesteps smaller the deviation from perfect normalization should approach zero.

________________________________
From: Craig Chisholm <Cra...@ic...>
Sent: Friday, 11 February 2022 7:29 PM
To: Mattias Johnsson <mat...@mq...>; Craig Chisholm via xmds-user <xmd...@li...>
Subject: Re: [xmds-user] Bessel cylindrical coordinates normalisation

Hi Matthias and Matthew,

Thank you for the explanation, indeed I didn't know how the normalisation worked, my mistake.

Regarding using the sampling_group: indeed, I tried this before trapz and I was confused that it takes time to converge to the correct number because I thought that the

<filter>
  <dependencies>wavefunction normalisation</dependencies>
  <![CDATA[
    // Correct normalisation of the wavefunction
    phi *= sqrt(Nparticles/Ncalc);
  ]]>
</filter>

part should enforce that the normalisation is 1 on each step even if the correct shape has not been found yet. Is there something else here which I am not understanding?

Best,

Craig
________________________________
From: Mattias Johnsson <mat...@mq...>
Sent: 11 February 2022 03:48
To: Craig Chisholm via xmds-user <xmd...@li...>; Craig Chisholm <Cra...@ic...>
Subject: Re: [xmds-user] Bessel cylindrical coordinates normalisation

Hi Craig,

> Thank you for the answers. If I understand correctly, if I would choose a higher order
> Bessel transform I would get sampling at r = 0 but also angular momentum in the
> form -m^2/r^2, or is there some way to remove that contribution? As I see from Blair's
>  email, it should be possible to put any grid, but does XMDS2 have this feature implemented?

Honestly, I have very little knowledge of how the Bessel basis works in XMDS2. But I believe there is no way to specify grid points explicitly; you have to take what XMDS2 gives you. They are fixed due to transformation properties, the need for quadrature integration to work etc.

Also I note that the contribution -m^2/r^2 diverges at r=0, suggesting that point might be wise to ignore anyway.

> With regards to the normalisation, I have been testing with the script bessel_cosine_groundstate.xmds
> from the examples folder. The results are the same as it is or if I modify it to use dft instead of
> dct on the z axis. I see that numerical integration > doesn't work properly when 0 is not
> included in the axis. As an example, I take f = (2/sigma^2)*exp(-r^2/sigma^2) integrating
> this with rdr as the 'volume' element gives 1. In Python (numpy.trapz), when I take the grid
>  from the example script and sigma = 1e-6 I get 0.9338052073724259. If I append 0 to the
> start of the grid, I get 0.9855312028781402 which tells me that the missing contribution
>  between 0 and the first point is important. If I increase the number of grid points the
> answer tends to 1. So, I already see that the numerical integration is not working on this grid.
> Independently of that, I am still surprised that the norm changes during the calculation since
> the filter segment should be forcing it to 1 at each step regardless of how good or bad the integration is.

Your integration example is irrelevant in this case: for cylindrical coordinates the area element goes as (r dθ), which goes to zero as r -> 0. So missing out the zero point has asymptotically no weight. But yes, on any grid naive integration will have an error; the question is whether that error goes to zero as the number of grid points goes to infinity.

But more importantly, keep in mind XMDS2 isn't "missing out" the zero point - it's using a basis transform where it doesn't exist, so it's perfectly consistent. It's not like it chose a grid, then removed the zero point. Which does mean, of course, the norm should be preserved under unitary evolution.

So, regarding the norm in that example, it looks fine to me. You can look at it by adding

      <sampling_group basis="r(0) z(0)" initial_sample="no">
        <moments>norm</moments>
        <dependencies>wavefunction</dependencies>
        <![CDATA[
          norm = mod2(phi);
        ]]>
      </sampling_group>

as an output moment group. The norm starts off at about 49000 (remember we specified 5e5 particles), then asymptotically approaches 50000 as you'd expect. Remember this is a ground state finder, which is not​ unitary evolution. It works by evolving the system in imaginary time, which makes all states decay according to their energy. So you run it for a step, let the population decay, then renormalize. Rinse and repeat. In the end you're only left with the lowest energy state, which is the ground state, and that state will be left with the correct normalization (e.g. 50000 particles).

Cheers,
Mattias

Re: [xmds-user] Bessel cylindrical coordinates normalisation

[Mattias J. <mat...@mq...>]

I guess it would depend on where the filter was applied relative to the evolution step and the sampling. If it happens just before the sampling it should be exactly normalized, otherwise not. Regardless, as you make the timesteps smaller the deviation from normalization should approach zero.
________________________________
From: Craig Chisholm <Cra...@ic...>
Sent: Friday, 11 February 2022 7:29 PM
To: Mattias Johnsson <mat...@mq...>; Craig Chisholm via xmds-user <xmd...@li...>
Subject: Re: [xmds-user] Bessel cylindrical coordinates normalisation

Hi Matthias and Matthew,

Thank you for the explanation, indeed I didn't know how the normalisation worked, my mistake.

Regarding using the sampling_group: indeed, I tried this before trapz and I was confused that it takes time to converge to the correct number because I thought that the

<filter>
  <dependencies>wavefunction normalisation</dependencies>
  <![CDATA[
    // Correct normalisation of the wavefunction
    phi *= sqrt(Nparticles/Ncalc);
  ]]>
</filter>

part should enforce that the normalisation is 1 on each step even if the correct shape has not been found yet. Is there something else here which I am not understanding?

Best,

Craig
________________________________
From: Mattias Johnsson <mat...@mq...>
Sent: 11 February 2022 03:48
To: Craig Chisholm via xmds-user <xmd...@li...>; Craig Chisholm <Cra...@ic...>
Subject: Re: [xmds-user] Bessel cylindrical coordinates normalisation

Hi Craig,

> Thank you for the answers. If I understand correctly, if I would choose a higher order
> Bessel transform I would get sampling at r = 0 but also angular momentum in the
> form -m^2/r^2, or is there some way to remove that contribution? As I see from Blair's
>  email, it should be possible to put any grid, but does XMDS2 have this feature implemented?

Honestly, I have very little knowledge of how the Bessel basis works in XMDS2. But I believe there is no way to specify grid points explicitly; you have to take what XMDS2 gives you. They are fixed due to transformation properties, the need for quadrature integration to work etc.

Also I note that the contribution -m^2/r^2 diverges at r=0, suggesting that point might be wise to ignore anyway.

> With regards to the normalisation, I have been testing with the script bessel_cosine_groundstate.xmds
> from the examples folder. The results are the same as it is or if I modify it to use dft instead of
> dct on the z axis. I see that numerical integration > doesn't work properly when 0 is not
> included in the axis. As an example, I take f = (2/sigma^2)*exp(-r^2/sigma^2) integrating
> this with rdr as the 'volume' element gives 1. In Python (numpy.trapz), when I take the grid
>  from the example script and sigma = 1e-6 I get 0.9338052073724259. If I append 0 to the
> start of the grid, I get 0.9855312028781402 which tells me that the missing contribution
>  between 0 and the first point is important. If I increase the number of grid points the
> answer tends to 1. So, I already see that the numerical integration is not working on this grid.
> Independently of that, I am still surprised that the norm changes during the calculation since
> the filter segment should be forcing it to 1 at each step regardless of how good or bad the integration is.

Your integration example is irrelevant in this case: for cylindrical coordinates the area element goes as (r dθ), which goes to zero as r -> 0. So missing out the zero point has asymptotically no weight. But yes, on any grid naive integration will have an error; the question is whether that error goes to zero as the number of grid points goes to infinity.

But more importantly, keep in mind XMDS2 isn't "missing out" the zero point - it's using a basis transform where it doesn't exist, so it's perfectly consistent. It's not like it chose a grid, then removed the zero point. Which does mean, of course, the norm should be preserved under unitary evolution.

So, regarding the norm in that example, it looks fine to me. You can look at it by adding

      <sampling_group basis="r(0) z(0)" initial_sample="no">
        <moments>norm</moments>
        <dependencies>wavefunction</dependencies>
        <![CDATA[
          norm = mod2(phi);
        ]]>
      </sampling_group>

as an output moment group. The norm starts off at about 49000 (remember we specified 5e5 particles), then asymptotically approaches 50000 as you'd expect. Remember this is a ground state finder, which is not​ unitary evolution. It works by evolving the system in imaginary time, which makes all states decay according to their energy. So you run it for a step, let the population decay, then renormalize. Rinse and repeat. In the end you're only left with the lowest energy state, which is the ground state, and that state will be left with the correct normalization (e.g. 50000 particles).

Cheers,
Mattias

________________________________
From: Craig Chisholm via xmds-user <xmd...@li...>
Sent: Friday, 11 February 2022 3:34 AM
To: Craig Chisholm via xmds-user <xmd...@li...>
Subject: Re: [xmds-user] Bessel cylindrical coordinates normalisation

Hi Mattias and Blair,

Thank you for the answers. If I understand correctly, if I would choose a higher order Bessel transform I would get sampling at r = 0 but also angular momentum in the form -m^2/r^2, or is there some way to remove that contribution? As I see from Blair's email, it should be possible to put any grid, but does XMDS2 have this feature implemented?

With regards to the normalisation, I have been testing with the script bessel_cosine_groundstate.xmds from the examples folder. The results are the same as it is or if I modify it to use dft instead of dct on the z axis. I see that numerical integration doesn't work properly when 0 is not included in the axis.
As an example, I take f = (2/sigma^2)*exp(-r^2/sigma^2) integrating this with rdr as the 'volume' element gives 1. In Python (numpy.trapz), when I take the grid from the example script and sigma = 1e-6 I get 0.9338052073724259. If I append 0 to the start of the grid, I get 0.9855312028781402 which tells me that the missing contribution between 0 and the first point is important. If I increase the number of grid points the answer tends to 1. So, I already see that the numerical integration is not working on this grid. Independently of that, I am still surprised that the norm changes during the calculation since the filter segment should be forcing it to 1 at each step regardless of how good or bad the integration is.

Best,

Craig

P.S. Apologies to Blair for spam, I accidentally replied to you instead of the list.

________________________________
From: Blair Blakie <bla...@ot...>
Sent: 10 February 2022 10:19
To: Craig Chisholm <Cra...@ic...>
Subject: Re: [xmds-user] Bessel cylindrical coordinates normalisation

CAUTION: This email originated from outside the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.

Hi Craig



I hope you are well.



I’m on the XMDS mailing list so I saw your message. I actually don’t use XMDS but I do use Bessel methods a lot (e.g. see https://journals.aps.org/prresearch/pdf/10.1103/PhysRevResearch.3.013283<https://journals.aps.org/prresearch/pdf/10.1103/PhysRevResearch.3.013283> ).

Because it is a spectral method you can always output the result to any grid, including one that has a zero point. I could find a reference if you need it. The loss of norm is concerning -  the Bessel methods should be extremely conserving.



BB



From: Mattias Johnsson <mat...@mq...>
Date: Thursday, 10 February 2022 at 12:10 PM
To: "xmd...@li..." <xmd...@li...>, Craig Chisholm <Cra...@ic...>
Subject: Re: [xmds-user] Bessel cylindrical coordinates normalisation



Hi Chris,



I'm not very familiar with the Bessel transform, but after having a quick look at XMDS2's code, here's what I can tell you.



Regarding including the r=0 point: When using the Bessel transform, the position of the grid points are given by the zeroes of the Bessel function (multiplied by a scaling factor).



From the documentation: http://www.xmds.org/reference_elements.html#the-bessel-and-bessel-neumann-transforms<http://www.xmds.org/reference_elements.html#the-bessel-and-bessel-neumann-transforms> "The order m of the transform is defined by the order attribute in the <dimension> element, which must be assigned as a non-negative integer. If the order is not specified, it defaults to zero which corresponds to the solution being independent of the angular coordinate θ."



So if you're choosing the default order, it's a Bessel function of the first kind with m=0, which doesn't have a zero at the origin.



Regarding your normalisation issue, I'm afraid I have no idea what the problem is.



Cheers,

Mattias

________________________________

From: Craig Chisholm via xmds-user <xmd...@li...>
Sent: Tuesday, 8 February 2022 9:26 PM
To: xmd...@li... <xmd...@li...>
Subject: [xmds-user] Bessel cylindrical coordinates normalisation



Hello,



I am having trouble with using the Bessel transform in cylindrical coordinates. Specifically, I have two problems:

  1.  I see that the normalisation of the wavefunction is evolving over time in spite of using continuous normalisation.
  2.  I would like to have r = 0 as part of the grid for the output but I haven't found a way to do this.

I'm using xmds2 version 2.2.3 "It came from the deep" (Debian package 2.2.3+dfsg-5) on Ubuntu 18.04 LTS and Linux Mint 19.3 and XMDS2 version 2.2.2 "XMDS2 is a game of two halves" on Ubuntu 16.04 LTS. On all three systems it's the same.



Please let me know if I should be providing additional information or diagnostics.



Thank you,



Craig Chisholm

PhD Student

ICFO - The Institute of Photonic Sciences

Av. Carl Friedrich Gauss, 3

08860 Castelldefels

Barcelona, Spain

Research Group: Ultracold Quantum Gases

Office Telephone:          +34 935542304

Laboratory Telephone: +34 935542263

Re: [xmds-user] Bessel cylindrical coordinates normalisation

[Mattias J. <mat...@mq...>]

Hi Craig,

> Thank you for the answers. If I understand correctly, if I would choose a higher order
> Bessel transform I would get sampling at r = 0 but also angular momentum in the
> form -m^2/r^2, or is there some way to remove that contribution? As I see from Blair's
>  email, it should be possible to put any grid, but does XMDS2 have this feature implemented?

Honestly, I have very little knowledge of how the Bessel basis works in XMDS2. But I believe there is no way to specify grid points explicitly; you have to take what XMDS2 gives you. They are fixed due to transformation properties, the need for quadrature integration to work etc.

Also I note that the contribution -m^2/r^2 diverges at r=0, suggesting that point might be wise to ignore anyway.

> With regards to the normalisation, I have been testing with the script bessel_cosine_groundstate.xmds
> from the examples folder. The results are the same as it is or if I modify it to use dft instead of
> dct on the z axis. I see that numerical integration > doesn't work properly when 0 is not
> included in the axis. As an example, I take f = (2/sigma^2)*exp(-r^2/sigma^2) integrating
> this with rdr as the 'volume' element gives 1. In Python (numpy.trapz), when I take the grid
>  from the example script and sigma = 1e-6 I get 0.9338052073724259. If I append 0 to the
> start of the grid, I get 0.9855312028781402 which tells me that the missing contribution
>  between 0 and the first point is important. If I increase the number of grid points the
> answer tends to 1. So, I already see that the numerical integration is not working on this grid.
> Independently of that, I am still surprised that the norm changes during the calculation since
> the filter segment should be forcing it to 1 at each step regardless of how good or bad the integration is.

Your integration example is irrelevant in this case: for cylindrical coordinates the area element goes as (r dθ), which goes to zero as r -> 0. So missing out the zero point has asymptotically no weight. But yes, on any grid naive integration will have an error; the question is whether that error goes to zero as the number of grid points goes to infinity.

But more importantly, keep in mind XMDS2 isn't "missing out" the zero point - it's using a basis transform where it doesn't exist, so it's perfectly consistent. It's not like it chose a grid, then removed the zero point. Which does mean, of course, the norm should be preserved under unitary evolution.

So, regarding the norm in that example, it looks fine to me. You can look at it by adding

      <sampling_group basis="r(0) z(0)" initial_sample="no">
        <moments>norm</moments>
        <dependencies>wavefunction</dependencies>
        <![CDATA[
          norm = mod2(phi);
        ]]>
      </sampling_group>

as an output moment group. The norm starts off at about 49000 (remember we specified 5e5 particles), then asymptotically approaches 50000 as you'd expect. Remember this is a ground state finder, which is not? unitary evolution. It works by evolving the system in imaginary time, which makes all states decay according to their energy. So you run it for a step, let the population decay, then renormalize. Rinse and repeat. In the end you're only left with the lowest energy state, which is the ground state, and that state will be left with the correct normalization (e.g. 50000 particles).

Cheers,
Mattias

________________________________
From: Craig Chisholm via xmds-user <xmd...@li...>
Sent: Friday, 11 February 2022 3:34 AM
To: Craig Chisholm via xmds-user <xmd...@li...>
Subject: Re: [xmds-user] Bessel cylindrical coordinates normalisation

Hi Mattias and Blair,

Thank you for the answers. If I understand correctly, if I would choose a higher order Bessel transform I would get sampling at r = 0 but also angular momentum in the form -m^2/r^2, or is there some way to remove that contribution? As I see from Blair's email, it should be possible to put any grid, but does XMDS2 have this feature implemented?

With regards to the normalisation, I have been testing with the script bessel_cosine_groundstate.xmds from the examples folder. The results are the same as it is or if I modify it to use dft instead of dct on the z axis. I see that numerical integration doesn't work properly when 0 is not included in the axis.
As an example, I take f = (2/sigma^2)*exp(-r^2/sigma^2) integrating this with rdr as the 'volume' element gives 1. In Python (numpy.trapz), when I take the grid from the example script and sigma = 1e-6 I get 0.9338052073724259. If I append 0 to the start of the grid, I get 0.9855312028781402 which tells me that the missing contribution between 0 and the first point is important. If I increase the number of grid points the answer tends to 1. So, I already see that the numerical integration is not working on this grid. Independently of that, I am still surprised that the norm changes during the calculation since the filter segment should be forcing it to 1 at each step regardless of how good or bad the integration is.

Best,

Craig

P.S. Apologies to Blair for spam, I accidentally replied to you instead of the list.

________________________________
From: Blair Blakie <bla...@ot...>
Sent: 10 February 2022 10:19
To: Craig Chisholm <Cra...@ic...>
Subject: Re: [xmds-user] Bessel cylindrical coordinates normalisation

CAUTION: This email originated from outside the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.

Hi Craig



I hope you are well.



I’m on the XMDS mailing list so I saw your message. I actually don’t use XMDS but I do use Bessel methods a lot (e.g. see https://journals.aps.org/prresearch/pdf/10.1103/PhysRevResearch.3.013283<https://journals.aps.org/prresearch/pdf/10.1103/PhysRevResearch.3.013283> ).

Because it is a spectral method you can always output the result to any grid, including one that has a zero point. I could find a reference if you need it. The loss of norm is concerning -  the Bessel methods should be extremely conserving.



BB



From: Mattias Johnsson <mat...@mq...>
Date: Thursday, 10 February 2022 at 12:10 PM
To: "xmd...@li..." <xmd...@li...>, Craig Chisholm <Cra...@ic...>
Subject: Re: [xmds-user] Bessel cylindrical coordinates normalisation



Hi Chris,



I'm not very familiar with the Bessel transform, but after having a quick look at XMDS2's code, here's what I can tell you.



Regarding including the r=0 point: When using the Bessel transform, the position of the grid points are given by the zeroes of the Bessel function (multiplied by a scaling factor).



>From the documentation: http://www.xmds.org/reference_elements.html#the-bessel-and-bessel-neumann-transforms<http://www.xmds.org/reference_elements.html#the-bessel-and-bessel-neumann-transforms> "The order m of the transform is defined by the order attribute in the <dimension> element, which must be assigned as a non-negative integer. If the order is not specified, it defaults to zero which corresponds to the solution being independent of the angular coordinate θ."



So if you're choosing the default order, it's a Bessel function of the first kind with m=0, which doesn't have a zero at the origin.



Regarding your normalisation issue, I'm afraid I have no idea what the problem is.



Cheers,

Mattias

________________________________

From: Craig Chisholm via xmds-user <xmd...@li...>
Sent: Tuesday, 8 February 2022 9:26 PM
To: xmd...@li... <xmd...@li...>
Subject: [xmds-user] Bessel cylindrical coordinates normalisation



Hello,



I am having trouble with using the Bessel transform in cylindrical coordinates. Specifically, I have two problems:

  1.  I see that the normalisation of the wavefunction is evolving over time in spite of using continuous normalisation.
  2.  I would like to have r = 0 as part of the grid for the output but I haven't found a way to do this.

I'm using xmds2 version 2.2.3 "It came from the deep" (Debian package 2.2.3+dfsg-5) on Ubuntu 18.04 LTS and Linux Mint 19.3 and XMDS2 version 2.2.2 "XMDS2 is a game of two halves" on Ubuntu 16.04 LTS. On all three systems it's the same.



Please let me know if I should be providing additional information or diagnostics.



Thank you,



Craig Chisholm

PhD Student

ICFO - The Institute of Photonic Sciences

Av. Carl Friedrich Gauss, 3

08860 Castelldefels

Barcelona, Spain

Research Group: Ultracold Quantum Gases

Office Telephone:          +34 935542304

Laboratory Telephone: +34 935542263

Re: [xmds-user] Bessel cylindrical coordinates normalisation

[Craig C. <Cra...@ic...>]

Hi Mattias and Blair,

Thank you for the answers. If I understand correctly, if I would choose a higher order Bessel transform I would get sampling at r = 0 but also angular momentum in the form -m^2/r^2, or is there some way to remove that contribution? As I see from Blair's email, it should be possible to put any grid, but does XMDS2 have this feature implemented?

With regards to the normalisation, I have been testing with the script bessel_cosine_groundstate.xmds from the examples folder. The results are the same as it is or if I modify it to use dft instead of dct on the z axis. I see that numerical integration doesn't work properly when 0 is not included in the axis.
As an example, I take f = (2/sigma^2)*exp(-r^2/sigma^2) integrating this with rdr as the 'volume' element gives 1. In Python (numpy.trapz), when I take the grid from the example script and sigma = 1e-6 I get 0.9338052073724259. If I append 0 to the start of the grid, I get 0.9855312028781402 which tells me that the missing contribution between 0 and the first point is important. If I increase the number of grid points the answer tends to 1. So, I already see that the numerical integration is not working on this grid. Independently of that, I am still surprised that the norm changes during the calculation since the filter segment should be forcing it to 1 at each step regardless of how good or bad the integration is.

Best,

Craig

P.S. Apologies to Blair for spam, I accidentally replied to you instead of the list.

________________________________
From: Blair Blakie <bla...@ot...>
Sent: 10 February 2022 10:19
To: Craig Chisholm <Cra...@ic...>
Subject: Re: [xmds-user] Bessel cylindrical coordinates normalisation

CAUTION: This email originated from outside the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe.

Hi Craig



I hope you are well.



I’m on the XMDS mailing list so I saw your message. I actually don’t use XMDS but I do use Bessel methods a lot (e.g. see https://journals.aps.org/prresearch/pdf/10.1103/PhysRevResearch.3.013283 ).

Because it is a spectral method you can always output the result to any grid, including one that has a zero point. I could find a reference if you need it. The loss of norm is concerning -  the Bessel methods should be extremely conserving.



BB



From: Mattias Johnsson <mat...@mq...>
Date: Thursday, 10 February 2022 at 12:10 PM
To: "xmd...@li..." <xmd...@li...>, Craig Chisholm <Cra...@ic...>
Subject: Re: [xmds-user] Bessel cylindrical coordinates normalisation



Hi Chris,



I'm not very familiar with the Bessel transform, but after having a quick look at XMDS2's code, here's what I can tell you.



Regarding including the r=0 point: When using the Bessel transform, the position of the grid points are given by the zeroes of the Bessel function (multiplied by a scaling factor).



>From the documentation: http://www.xmds.org/reference_elements.html#the-bessel-and-bessel-neumann-transforms: "The order m of the transform is defined by the order attribute in the <dimension> element, which must be assigned as a non-negative integer. If the order is not specified, it defaults to zero which corresponds to the solution being independent of the angular coordinate θ."



So if you're choosing the default order, it's a Bessel function of the first kind with m=0, which doesn't have a zero at the origin.



Regarding your normalisation issue, I'm afraid I have no idea what the problem is.



Cheers,

Mattias

________________________________

From: Craig Chisholm via xmds-user <xmd...@li...>
Sent: Tuesday, 8 February 2022 9:26 PM
To: xmd...@li... <xmd...@li...>
Subject: [xmds-user] Bessel cylindrical coordinates normalisation



Hello,



I am having trouble with using the Bessel transform in cylindrical coordinates. Specifically, I have two problems:

  1.  I see that the normalisation of the wavefunction is evolving over time in spite of using continuous normalisation.
  2.  I would like to have r = 0 as part of the grid for the output but I haven't found a way to do this.

I'm using xmds2 version 2.2.3 "It came from the deep" (Debian package 2.2.3+dfsg-5) on Ubuntu 18.04 LTS and Linux Mint 19.3 and XMDS2 version 2.2.2 "XMDS2 is a game of two halves" on Ubuntu 16.04 LTS. On all three systems it's the same.



Please let me know if I should be providing additional information or diagnostics.



Thank you,



Craig Chisholm

PhD Student

ICFO - The Institute of Photonic Sciences

Av. Carl Friedrich Gauss, 3

08860 Castelldefels

Barcelona, Spain

Research Group: Ultracold Quantum Gases

Office Telephone:          +34 935542304

Laboratory Telephone: +34 935542263

Re: [xmds-user] Bessel cylindrical coordinates normalisation

[Mattias J. <mat...@mq...>]

Hi Chris,

I'm not very familiar with the Bessel transform, but after having a quick look at XMDS2's code, here's what I can tell you.

Regarding including the r=0 point: When using the Bessel transform, the position of the grid points are given by the zeroes of the Bessel function (multiplied by a scaling factor).

>From the documentation: http://www.xmds.org/reference_elements.html#the-bessel-and-bessel-neumann-transforms: "The order m of the transform is defined by the order attribute in the <dimension> element, which must be assigned as a non-negative integer. If the order is not specified, it defaults to zero which corresponds to the solution being independent of the angular coordinate θ."

So if you're choosing the default order, it's a Bessel function of the first kind with m=0, which doesn't have a zero at the origin.

Regarding your normalisation issue, I'm afraid I have no idea what the problem is.

Cheers,
Mattias
________________________________
From: Craig Chisholm via xmds-user <xmd...@li...>
Sent: Tuesday, 8 February 2022 9:26 PM
To: xmd...@li... <xmd...@li...>
Subject: [xmds-user] Bessel cylindrical coordinates normalisation

Hello,

I am having trouble with using the Bessel transform in cylindrical coordinates. Specifically, I have two problems:

  1.  I see that the normalisation of the wavefunction is evolving over time in spite of using continuous normalisation.
  2.  I would like to have r = 0 as part of the grid for the output but I haven't found a way to do this.

I'm using xmds2 version 2.2.3 "It came from the deep" (Debian package 2.2.3+dfsg-5) on Ubuntu 18.04 LTS and Linux Mint 19.3 and XMDS2 version 2.2.2 "XMDS2 is a game of two halves" on Ubuntu 16.04 LTS. On all three systems it's the same.

Please let me know if I should be providing additional information or diagnostics.

Thank you,


Craig Chisholm

PhD Student
ICFO - The Institute of Photonic Sciences
Av. Carl Friedrich Gauss, 3
08860 Castelldefels
Barcelona, Spain
Research Group: Ultracold Quantum Gases
Office Telephone:          +34 935542304
Laboratory Telephone: +34 935542263

[xmds-user] Importing an output from Julia to xmds

[rodrigo b. <bru...@gm...>]

Hi all,

Does anybody have experience passing a .h5 file generated by the package
hdf5.jl in julia to xmds?

Regards,
Bruni

[xmds-user] Bessel cylindrical coordinates normalisation

[Craig C. <Cra...@ic...>]

Hello,

I am having trouble with using the Bessel transform in cylindrical coordinates. Specifically, I have two problems:

  1.  I see that the normalisation of the wavefunction is evolving over time in spite of using continuous normalisation.
  2.  I would like to have r = 0 as part of the grid for the output but I haven't found a way to do this.

I'm using xmds2 version 2.2.3 "It came from the deep" (Debian package 2.2.3+dfsg-5) on Ubuntu 18.04 LTS and Linux Mint 19.3 and XMDS2 version 2.2.2 "XMDS2 is a game of two halves" on Ubuntu 16.04 LTS. On all three systems it's the same.

Please let me know if I should be providing additional information or diagnostics.

Thank you,


Craig Chisholm

PhD Student
ICFO - The Institute of Photonic Sciences
Av. Carl Friedrich Gauss, 3
08860 Castelldefels
Barcelona, Spain
Research Group: Ultracold Quantum Gases
Office Telephone:          +34 935542304
Laboratory Telephone: +34 935542263

Re: [xmds-user] Is Github not monitored? And... installation fail

[Mattias J. <mat...@mq...>]

Hi Thomas,

Apologies for the lack of response to issues on the GitHub page. The XMDS2 GitHub currently only exists to host the Mac Homebrew installer, as the main codebase is under SVN on SourceForge.

The situation is that currently we have no maintainer for the Mac version of XMDS2, or even someone with a modern version of the OS and hardware who's willing to test things. I'm the linux guy, and don't have a Mac. This means that the current Homebrew installer may or may not work in many situations. I'm glad you managed to install manually, as that should always work.

That said, I have heard from some Mac users that some numerical Python packages like numpy haven't been fully ported to the M1 yet, and may have some issues. Perhaps that is a contributer to the problems.

Honestly, if there's anyone out there with any experience with the Homebrew package manager and Python who would be interested in testing / fixing the Homebrew installer (it should be publicly accessible from the GitHub page, and is very simple) we would be very grateful.

Cheers,
Mattias


________________________________
From: Thomas Sturges <stu...@gm...>
Sent: Thursday, 20 January 2022 9:14 PM
To: xmd...@li... <xmd...@li...>
Subject: [xmds-user] Is Github not monitored? And... installation fail

Hello,

Is the Github page not being monitored?
There has been an open issue there since March 2021 with no reply.
On the other hand I have received great responses from this mailing list in the past.
I am having trouble running xmds2 on an M1 mac.
I'm sure it was working before, but now I get error messages:


(base) tomsturges@Toms-MacBook-Air XMDS2 % xmds2

Traceback (most recent call last):

  File "/opt/homebrew/bin/xmds2", line 4, in <module>

    __import__('pkg_resources').require('xmds2==3.0.0')

  File "/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line 3267, in <module>

    def _initialize_master_working_set():

  File "/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line 3241, in _call_aside

    f(*args, **kwargs)

  File "/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line 3279, in _initialize_master_working_set

    working_set = WorkingSet._build_master()

  File "/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line 573, in _build_master

    ws.require(__requires__)

  File "/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line 891, in require

    needed = self.resolve(parse_requirements(requirements))

  File "/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line 777, in resolve

    raise DistributionNotFound(req, requirers)

pkg_resources.DistributionNotFound: The 'xmds2==3.0.0' distribution was not found and is required by the application

So I also tried reinstalling with homebrew and get more error messages:



Thanks,
Tom

Re: [xmds-user] Is Github not monitored? And... installation fail

[Mattias J. <mat...@mq...>]

Hi Thomas,

Sorry about the lack of response to issues on the GitHub page. The XMDS2 GitHub currently only exists to host the Mac Homebrew installer, as the main codebase is under SVN on SourceForge.

The situation is that currently we have no maintainer for the Mac version of XMDS2, or even someone with a modern version of the OS and hardware who's willing to test things. I'm the linux guy, and don't have a Mac. This means that the current Homebrew installer may or may not work in many situations. I'm glad you managed to install manually, as that should always work.

That said, I have heard from some Mac users that some numerical Python packages like numpy haven't been fully ported to the M1 yet, and may have some issues. Perhaps that is a contributer to the problems.

Honestly, if there's anyone out there with any experience with the Homebrew package manager and Python who would be interested in testing / fixing the Homebrew installer (it should be publicly accessible from the GitHub page, and is very simple) we would be very grateful.

Cheers,
Mattias


________________________________
From: Thomas Sturges <stu...@gm...>
Sent: Thursday, 20 January 2022 9:57 PM
To: xmd...@li... <xmd...@li...>
Subject: Re: [xmds-user] Is Github not monitored? And... installation fail

I have now installed xmds from source instead, and it seems to be working.
But perhaps it is useful to know about these errors associated with homebrew anyway.
Also I am unable to uninstall the homebrew version with `brew uninstall xmds2`:


(base) tomsturges@Toms-MacBook-Air XMDS2 % brew uninstall xmds2

Error: No such keg: /opt/homebrew/Cellar/xmds2


Instead I did the following which seemed to work:


(base) tomsturges@Toms-MacBook-Air XMDS2 % brew uninstall --force xmds2

(base) tomsturges@Toms-MacBook-Air XMDS2 % brew cleanup -s xmds2

Removing: /Users/tomsturges/Library/Caches/Homebrew/xmds2--3.1.0.tar.gz... (30.2MB)

Removing: /Users/tomsturges/Library/Caches/Homebrew/xmds2--numpy--1.16.0.zip... (4.8MB)

Removing: /Users/tomsturges/Library/Caches/Homebrew/xmds2--pyparsing--2.2.0.tar.tar.gz... (1.2MB)

Removing: /Users/tomsturges/Library/Caches/Homebrew/xmds2--lxml--4.3.0.tar.gz... (2.4MB)

Removing: /Users/tomsturges/Library/Caches/Homebrew/xmds2--mpmath--1.0.0.tar.tar.gz... (499.4KB)

Removing: /Users/tomsturges/Library/Caches/Homebrew/xmds2--Cheetah3--3.0.0.tar.tar.gz... (853.7KB)



On Thu, Jan 20, 2022 at 11:14 AM Thomas Sturges <stu...@gm...<mailto:stu...@gm...>> wrote:
Hello,

Is the Github page not being monitored?
There has been an open issue there since March 2021 with no reply.
On the other hand I have received great responses from this mailing list in the past.
I am having trouble running xmds2 on an M1 mac.
I'm sure it was working before, but now I get error messages:


(base) tomsturges@Toms-MacBook-Air XMDS2 % xmds2

Traceback (most recent call last):

  File "/opt/homebrew/bin/xmds2", line 4, in <module>

    __import__('pkg_resources').require('xmds2==3.0.0')

  File "/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line 3267, in <module>

    def _initialize_master_working_set():

  File "/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line 3241, in _call_aside

    f(*args, **kwargs)

  File "/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line 3279, in _initialize_master_working_set

    working_set = WorkingSet._build_master()

  File "/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line 573, in _build_master

    ws.require(__requires__)

  File "/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line 891, in require

    needed = self.resolve(parse_requirements(requirements))

  File "/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line 777, in resolve

    raise DistributionNotFound(req, requirers)

pkg_resources.DistributionNotFound: The 'xmds2==3.0.0' distribution was not found and is required by the application

So I also tried reinstalling with homebrew and get more error messages:


(base) tomsturges@Toms-MacBook-Air XMDS2 % brew install xmds2/xmds2/xmds2


Running `brew update --preinstall`...

==> Auto-updated Homebrew!

Updated 1 tap (homebrew/core).

==> New Formulae

libadwaita

==> Updated Formulae

Updated 1 formula.


==> Downloading https://pypi.python.org/packages/5b/22/0238132792f3600717fad9647<https://pypi.python.org/packages/5b/22/0238132792f3600717fad9647>

Already downloaded: /Users/tomsturges/Library/Caches/Homebrew/downloads/3eabdae732c49317c1f7ac784a949262efb6dd0e5908a898b91a6e4a54875e4e--Cheetah3-3.0.0.tar.gz

==> Downloading https://pypi.python.org/packages/3c/ec/a94f8cf7274ea60b5413df054<https://pypi.python.org/packages/3c/ec/a94f8cf7274ea60b5413df054>

Already downloaded: /Users/tomsturges/Library/Caches/Homebrew/downloads/135d9c7d19095f975f8a7cb80d7a0972497fdd79ce2aed989d28ac0681dd39d5--pyparsing-2.2.0.tar.gz

==> Downloading https://pypi.python.org/packages/7a/05/b3d1472885d8dc0606936ea5d<https://pypi.python.org/packages/7a/05/b3d1472885d8dc0606936ea5d>

Already downloaded: /Users/tomsturges/Library/Caches/Homebrew/downloads/8d0f1a905bc5e03b81965cf11aa6f468a52fcd07a0356ea92ed5efa2a7826e06--mpmath-1.0.0.tar.gz

==> Downloading https://pypi.python.org/packages/04/b6/d7faa70a3e3eac39f943cc6a6<https://pypi.python.org/packages/04/b6/d7faa70a3e3eac39f943cc6a6>

Already downloaded: /Users/tomsturges/Library/Caches/Homebrew/downloads/132d8b361b397f783d2a122472fce69e77ea705d75289ecc3dcde77bce88d140--numpy-1.16.0.zip

==> Downloading https://pypi.python.org/packages/16/4a/b085a04d6dad79aa5c00c65c9<https://pypi.python.org/packages/16/4a/b085a04d6dad79aa5c00c65c9>

Already downloaded: /Users/tomsturges/Library/Caches/Homebrew/downloads/04c66558491da327f74c9499f7876ac42409a0d12bd5d3e9b264d2715114bdb9--lxml-4.3.0.tar.gz

==> Downloading https://sourceforge.net/projects/xmds/files/xmds-3.1.0.tar.gz<https://sourceforge.net/projects/xmds/files/xmds-3.1.0.tar.gz>

Already downloaded: /Users/tomsturges/Library/Caches/Homebrew/downloads/e3a2dd653106178cb5c79a499a3d119d15091f14ed90e6dba8096e7e0ab1b2ad--xmds-3.1.0.tar.gz

==> Installing xmds2 from xmds2/xmds2

==> python3 -m venv --system-site-packages /opt/homebrew/Cellar/xmds2/3.1.0/libe

==> /opt/homebrew/Cellar/xmds2/3.1.0/libexec/bin/pip install -v --no-deps --no-b

==> /opt/homebrew/Cellar/xmds2/3.1.0/libexec/bin/pip install -v --no-deps --no-b

==> /opt/homebrew/Cellar/xmds2/3.1.0/libexec/bin/pip install -v --no-deps --no-b

==> /opt/homebrew/Cellar/xmds2/3.1.0/libexec/bin/pip install -v --no-deps --no-b

Last 15 lines from /Users/tomsturges/Library/Logs/Homebrew/xmds2/05.pip:

      File "/private/tmp/xmds2--numpy-20220120-1711-s6r7lk/numpy-1.16.0/numpy/distutils/fcompiler/environment.py", line 53, in _get_var

        var = self._hook_handler(name, hook)

      File "/private/tmp/xmds2--numpy-20220120-1711-s6r7lk/numpy-1.16.0/numpy/distutils/fcompiler/__init__.py", line 709, in _environment_hook

        return hook()

      File "/private/tmp/xmds2--numpy-20220120-1711-s6r7lk/numpy-1.16.0/numpy/distutils/fcompiler/gnu.py", line 350, in get_flags_linker_so

        flags = GnuFCompiler.get_flags_linker_so(self)

      File "/private/tmp/xmds2--numpy-20220120-1711-s6r7lk/numpy-1.16.0/numpy/distutils/fcompiler/gnu.py", line 144, in get_flags_linker_so

        os.environ['MACOSX_DEPLOYMENT_TARGET'] = target

      File "/opt/homebrew/Cellar/python@3.9/3.9.10/Frameworks/Python.framework/Versions/3.9/lib/python3.9/os.py", line 684, in __setitem__

        value = self.encodevalue(value)

      File "/opt/homebrew/Cellar/python@3.9/3.9.10/Frameworks/Python.framework/Versions/3.9/lib/python3.9/os.py", line 756, in encode

        raise TypeError("str expected, not %s" % type(value).__name__)

    TypeError: str expected, not int

    Running setup.py install for numpy: finished with status 'error'

ERROR: Command errored out with exit status 1: /opt/homebrew/Cellar/xmds2/3.1.0/libexec/bin/python3.9 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/tmp/xmds2--numpy-20220120-1711-s6r7lk/numpy-1.16.0/setup.py'"'"'; __file__='"'"'/private/tmp/xmds2--numpy-20220120-1711-s6r7lk/numpy-1.16.0/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/tmp/pip-record-9pntciym/install-record.txt --single-version-externally-managed --compile --install-headers /opt/homebrew/Cellar/xmds2/3.1.0/libexec/include/site/python3.9/numpy Check the logs for full command output.


If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):

  https://github.com/xmds2/homebrew-xmds2/issues<https://aus01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fxmds2%2Fhomebrew-xmds2%2Fissues&data=04%7C01%7Cmattias.johnsson%40mq.edu.au%7C06842cbe1c8445e0a58c08d9dc03bab0%7C82c514c1a7174087be06d40d2070ad52%7C0%7C0%7C637782732027625830%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=42crVf%2BVHNM%2Flmzf8vgrybWxUbp%2BqtpKGheCFoxiVos%3D&reserved=0>


Thanks,
Tom

Re: [xmds-user] Is Github not monitored? And... installation fail

[Thomas S. <stu...@gm...>]

I have now installed xmds from source instead, and it seems to be working.
But perhaps it is useful to know about these errors associated with
homebrew anyway.
Also I am unable to uninstall the homebrew version with `brew uninstall
xmds2`:

(base) tomsturges@Toms-MacBook-Air XMDS2 % brew uninstall xmds2

Error: No such keg: /opt/homebrew/Cellar/xmds2


Instead I did the following which seemed to work:


(base) tomsturges@Toms-MacBook-Air XMDS2 % brew uninstall --force xmds2

(base) tomsturges@Toms-MacBook-Air XMDS2 % brew cleanup -s xmds2

Removing: /Users/tomsturges/Library/Caches/Homebrew/xmds2--3.1.0.tar.gz...
(30.2MB)

Removing:
/Users/tomsturges/Library/Caches/Homebrew/xmds2--numpy--1.16.0.zip...
(4.8MB)

Removing:
/Users/tomsturges/Library/Caches/Homebrew/xmds2--pyparsing--2.2.0.tar.tar.gz...
(1.2MB)

Removing:
/Users/tomsturges/Library/Caches/Homebrew/xmds2--lxml--4.3.0.tar.gz...
(2.4MB)

Removing:
/Users/tomsturges/Library/Caches/Homebrew/xmds2--mpmath--1.0.0.tar.tar.gz...
(499.4KB)

Removing:
/Users/tomsturges/Library/Caches/Homebrew/xmds2--Cheetah3--3.0.0.tar.tar.gz...
(853.7KB)



On Thu, Jan 20, 2022 at 11:14 AM Thomas Sturges <stu...@gm...>
wrote:

> Hello,
>
> Is the Github page not being monitored?
> There has been an open issue there since March 2021 with no reply.
> On the other hand I have received great responses from this mailing list
> in the past.
> I am having trouble running xmds2 on an M1 mac.
> I'm sure it was working before, but now I get error messages:
>
> (base) tomsturges@Toms-MacBook-Air XMDS2 % xmds2
>
> Traceback (most recent call last):
>
>   File "/opt/homebrew/bin/xmds2", line 4, in <module>
>
>     __import__('pkg_resources').require('xmds2==3.0.0')
>
>   File
> "/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line
> 3267, in <module>
>
>     def _initialize_master_working_set():
>
>   File
> "/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line
> 3241, in _call_aside
>
>     f(*args, **kwargs)
>
>   File
> "/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line
> 3279, in _initialize_master_working_set
>
>     working_set = WorkingSet._build_master()
>
>   File
> "/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line
> 573, in _build_master
>
>     ws.require(__requires__)
>
>   File
> "/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line
> 891, in require
>
>     needed = self.resolve(parse_requirements(requirements))
>
>   File
> "/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line
> 777, in resolve
>
>     raise DistributionNotFound(req, requirers)
>
> pkg_resources.DistributionNotFound: The 'xmds2==3.0.0' distribution was
> not found and is required by the application
>
> So I also tried reinstalling with homebrew and get more error messages:
>
> (base) tomsturges@Toms-MacBook-Air XMDS2 % brew install xmds2/xmds2/xmds2
>
>
> Running `brew update --preinstall`...
>
> ==> *Auto-updated Homebrew!*
>
> Updated 1 tap (homebrew/core).
>
> ==> *New Formulae*
>
> libadwaita
>
> ==> *Updated Formulae*
>
> Updated 1 formula.
>
>
> ==> *Downloading
> https://pypi.python.org/packages/5b/22/0238132792f3600717fad9647
> <https://pypi.python.org/packages/5b/22/0238132792f3600717fad9647>*
>
> Already downloaded:
> /Users/tomsturges/Library/Caches/Homebrew/downloads/3eabdae732c49317c1f7ac784a949262efb6dd0e5908a898b91a6e4a54875e4e--Cheetah3-3.0.0.tar.gz
>
> ==> *Downloading
> https://pypi.python.org/packages/3c/ec/a94f8cf7274ea60b5413df054
> <https://pypi.python.org/packages/3c/ec/a94f8cf7274ea60b5413df054>*
>
> Already downloaded:
> /Users/tomsturges/Library/Caches/Homebrew/downloads/135d9c7d19095f975f8a7cb80d7a0972497fdd79ce2aed989d28ac0681dd39d5--pyparsing-2.2.0.tar.gz
>
> ==> *Downloading
> https://pypi.python.org/packages/7a/05/b3d1472885d8dc0606936ea5d
> <https://pypi.python.org/packages/7a/05/b3d1472885d8dc0606936ea5d>*
>
> Already downloaded:
> /Users/tomsturges/Library/Caches/Homebrew/downloads/8d0f1a905bc5e03b81965cf11aa6f468a52fcd07a0356ea92ed5efa2a7826e06--mpmath-1.0.0.tar.gz
>
> ==> *Downloading
> https://pypi.python.org/packages/04/b6/d7faa70a3e3eac39f943cc6a6
> <https://pypi.python.org/packages/04/b6/d7faa70a3e3eac39f943cc6a6>*
>
> Already downloaded:
> /Users/tomsturges/Library/Caches/Homebrew/downloads/132d8b361b397f783d2a122472fce69e77ea705d75289ecc3dcde77bce88d140--numpy-1.16.0.zip
>
> ==> *Downloading
> https://pypi.python.org/packages/16/4a/b085a04d6dad79aa5c00c65c9
> <https://pypi.python.org/packages/16/4a/b085a04d6dad79aa5c00c65c9>*
>
> Already downloaded:
> /Users/tomsturges/Library/Caches/Homebrew/downloads/04c66558491da327f74c9499f7876ac42409a0d12bd5d3e9b264d2715114bdb9--lxml-4.3.0.tar.gz
>
> ==> *Downloading
> https://sourceforge.net/projects/xmds/files/xmds-3.1.0.tar.gz
> <https://sourceforge.net/projects/xmds/files/xmds-3.1.0.tar.gz>*
>
> Already downloaded:
> /Users/tomsturges/Library/Caches/Homebrew/downloads/e3a2dd653106178cb5c79a499a3d119d15091f14ed90e6dba8096e7e0ab1b2ad--xmds-3.1.0.tar.gz
>
> ==> *Installing xmds2 from xmds2/xmds2*
>
> ==> *python3 -m venv --system-site-packages
> /opt/homebrew/Cellar/xmds2/3.1.0/libe*
>
> ==> */opt/homebrew/Cellar/xmds2/3.1.0/libexec/bin/pip install -v
> --no-deps --no-b*
>
> ==> */opt/homebrew/Cellar/xmds2/3.1.0/libexec/bin/pip install -v
> --no-deps --no-b*
>
> ==> */opt/homebrew/Cellar/xmds2/3.1.0/libexec/bin/pip install -v
> --no-deps --no-b*
>
> ==> */opt/homebrew/Cellar/xmds2/3.1.0/libexec/bin/pip install -v
> --no-deps --no-b*
>
> Last 15 lines from /Users/tomsturges/Library/Logs/Homebrew/xmds2/05.pip:
>
>       File
> "/private/tmp/xmds2--numpy-20220120-1711-s6r7lk/numpy-1.16.0/numpy/distutils/fcompiler/environment.py",
> line 53, in _get_var
>
>         var = self._hook_handler(name, hook)
>
>       File
> "/private/tmp/xmds2--numpy-20220120-1711-s6r7lk/numpy-1.16.0/numpy/distutils/fcompiler/__init__.py",
> line 709, in _environment_hook
>
>         return hook()
>
>       File
> "/private/tmp/xmds2--numpy-20220120-1711-s6r7lk/numpy-1.16.0/numpy/distutils/fcompiler/gnu.py",
> line 350, in get_flags_linker_so
>
>         flags = GnuFCompiler.get_flags_linker_so(self)
>
>       File
> "/private/tmp/xmds2--numpy-20220120-1711-s6r7lk/numpy-1.16.0/numpy/distutils/fcompiler/gnu.py",
> line 144, in get_flags_linker_so
>
>         os.environ['MACOSX_DEPLOYMENT_TARGET'] = target
>
>       File "/opt/homebrew/Cellar/python@3.9/3.9.10/Frameworks/Python.framework/Versions/3.9/lib/python3.9/os.py",
> line 684, in __setitem__
>
>         value = self.encodevalue(value)
>
>       File "/opt/homebrew/Cellar/python@3.9/3.9.10/Frameworks/Python.framework/Versions/3.9/lib/python3.9/os.py",
> line 756, in encode
>
>         raise TypeError("str expected, not %s" % type(value).__name__)
>
>     TypeError: str expected, not int
>
>     Running setup.py install for numpy: finished with status 'error'
>
> ERROR: Command errored out with exit status 1:
> /opt/homebrew/Cellar/xmds2/3.1.0/libexec/bin/python3.9 -u -c 'import io,
> os, sys, setuptools, tokenize; sys.argv[0] =
> '"'"'/private/tmp/xmds2--numpy-20220120-1711-s6r7lk/numpy-1.16.0/setup.py'"'"';
> __file__='"'"'/private/tmp/xmds2--numpy-20220120-1711-s6r7lk/numpy-1.16.0/setup.py'"'"';f
> = getattr(tokenize, '"'"'open'"'"', open)(__file__) if
> os.path.exists(__file__) else io.StringIO('"'"'from setuptools import
> setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"',
> '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))'
> install --record /private/tmp/pip-record-9pntciym/install-record.txt
> --single-version-externally-managed --compile --install-headers
> /opt/homebrew/Cellar/xmds2/3.1.0/libexec/include/site/python3.9/numpy Check
> the logs for full command output.
>
>
> If reporting this issue please do so at (not Homebrew/brew or
> Homebrew/core):
>
>   https://github.com/xmds2/homebrew-xmds2/issues
>
>
> Thanks,
> Tom
>

[xmds-user] Is Github not monitored? And... installation fail

[Thomas S. <stu...@gm...>]

Hello,

Is the Github page not being monitored?
There has been an open issue there since March 2021 with no reply.
On the other hand I have received great responses from this mailing list in
the past.
I am having trouble running xmds2 on an M1 mac.
I'm sure it was working before, but now I get error messages:

(base) tomsturges@Toms-MacBook-Air XMDS2 % xmds2

Traceback (most recent call last):

  File "/opt/homebrew/bin/xmds2", line 4, in <module>

    __import__('pkg_resources').require('xmds2==3.0.0')

  File
"/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line
3267, in <module>

    def _initialize_master_working_set():

  File
"/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line
3241, in _call_aside

    f(*args, **kwargs)

  File
"/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line
3279, in _initialize_master_working_set

    working_set = WorkingSet._build_master()

  File
"/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line
573, in _build_master

    ws.require(__requires__)

  File
"/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line
891, in require

    needed = self.resolve(parse_requirements(requirements))

  File
"/opt/homebrew/lib/python3.9/site-packages/pkg_resources/__init__.py", line
777, in resolve

    raise DistributionNotFound(req, requirers)

pkg_resources.DistributionNotFound: The 'xmds2==3.0.0' distribution was not
found and is required by the application

So I also tried reinstalling with homebrew and get more error messages:

(base) tomsturges@Toms-MacBook-Air XMDS2 % brew install xmds2/xmds2/xmds2


Running `brew update --preinstall`...

==> *Auto-updated Homebrew!*

Updated 1 tap (homebrew/core).

==> *New Formulae*

libadwaita

==> *Updated Formulae*

Updated 1 formula.


==> *Downloading
https://pypi.python.org/packages/5b/22/0238132792f3600717fad9647
<https://pypi.python.org/packages/5b/22/0238132792f3600717fad9647>*

Already downloaded:
/Users/tomsturges/Library/Caches/Homebrew/downloads/3eabdae732c49317c1f7ac784a949262efb6dd0e5908a898b91a6e4a54875e4e--Cheetah3-3.0.0.tar.gz

==> *Downloading
https://pypi.python.org/packages/3c/ec/a94f8cf7274ea60b5413df054
<https://pypi.python.org/packages/3c/ec/a94f8cf7274ea60b5413df054>*

Already downloaded:
/Users/tomsturges/Library/Caches/Homebrew/downloads/135d9c7d19095f975f8a7cb80d7a0972497fdd79ce2aed989d28ac0681dd39d5--pyparsing-2.2.0.tar.gz

==> *Downloading
https://pypi.python.org/packages/7a/05/b3d1472885d8dc0606936ea5d
<https://pypi.python.org/packages/7a/05/b3d1472885d8dc0606936ea5d>*

Already downloaded:
/Users/tomsturges/Library/Caches/Homebrew/downloads/8d0f1a905bc5e03b81965cf11aa6f468a52fcd07a0356ea92ed5efa2a7826e06--mpmath-1.0.0.tar.gz

==> *Downloading
https://pypi.python.org/packages/04/b6/d7faa70a3e3eac39f943cc6a6
<https://pypi.python.org/packages/04/b6/d7faa70a3e3eac39f943cc6a6>*

Already downloaded:
/Users/tomsturges/Library/Caches/Homebrew/downloads/132d8b361b397f783d2a122472fce69e77ea705d75289ecc3dcde77bce88d140--numpy-1.16.0.zip

==> *Downloading
https://pypi.python.org/packages/16/4a/b085a04d6dad79aa5c00c65c9
<https://pypi.python.org/packages/16/4a/b085a04d6dad79aa5c00c65c9>*

Already downloaded:
/Users/tomsturges/Library/Caches/Homebrew/downloads/04c66558491da327f74c9499f7876ac42409a0d12bd5d3e9b264d2715114bdb9--lxml-4.3.0.tar.gz

==> *Downloading
https://sourceforge.net/projects/xmds/files/xmds-3.1.0.tar.gz
<https://sourceforge.net/projects/xmds/files/xmds-3.1.0.tar.gz>*

Already downloaded:
/Users/tomsturges/Library/Caches/Homebrew/downloads/e3a2dd653106178cb5c79a499a3d119d15091f14ed90e6dba8096e7e0ab1b2ad--xmds-3.1.0.tar.gz

==> *Installing xmds2 from xmds2/xmds2*

==> *python3 -m venv --system-site-packages
/opt/homebrew/Cellar/xmds2/3.1.0/libe*

==> */opt/homebrew/Cellar/xmds2/3.1.0/libexec/bin/pip install -v --no-deps
--no-b*

==> */opt/homebrew/Cellar/xmds2/3.1.0/libexec/bin/pip install -v --no-deps
--no-b*

==> */opt/homebrew/Cellar/xmds2/3.1.0/libexec/bin/pip install -v --no-deps
--no-b*

==> */opt/homebrew/Cellar/xmds2/3.1.0/libexec/bin/pip install -v --no-deps
--no-b*

Last 15 lines from /Users/tomsturges/Library/Logs/Homebrew/xmds2/05.pip:

      File
"/private/tmp/xmds2--numpy-20220120-1711-s6r7lk/numpy-1.16.0/numpy/distutils/fcompiler/environment.py",
line 53, in _get_var

        var = self._hook_handler(name, hook)

      File
"/private/tmp/xmds2--numpy-20220120-1711-s6r7lk/numpy-1.16.0/numpy/distutils/fcompiler/__init__.py",
line 709, in _environment_hook

        return hook()

      File
"/private/tmp/xmds2--numpy-20220120-1711-s6r7lk/numpy-1.16.0/numpy/distutils/fcompiler/gnu.py",
line 350, in get_flags_linker_so

        flags = GnuFCompiler.get_flags_linker_so(self)

      File
"/private/tmp/xmds2--numpy-20220120-1711-s6r7lk/numpy-1.16.0/numpy/distutils/fcompiler/gnu.py",
line 144, in get_flags_linker_so

        os.environ['MACOSX_DEPLOYMENT_TARGET'] = target

      File "/opt/homebrew/Cellar/python@3.9/3.9.10/Frameworks/Python.framework/Versions/3.9/lib/python3.9/os.py",
line 684, in __setitem__

        value = self.encodevalue(value)

      File "/opt/homebrew/Cellar/python@3.9/3.9.10/Frameworks/Python.framework/Versions/3.9/lib/python3.9/os.py",
line 756, in encode

        raise TypeError("str expected, not %s" % type(value).__name__)

    TypeError: str expected, not int

    Running setup.py install for numpy: finished with status 'error'

ERROR: Command errored out with exit status 1:
/opt/homebrew/Cellar/xmds2/3.1.0/libexec/bin/python3.9 -u -c 'import io,
os, sys, setuptools, tokenize; sys.argv[0] =
'"'"'/private/tmp/xmds2--numpy-20220120-1711-s6r7lk/numpy-1.16.0/setup.py'"'"';
__file__='"'"'/private/tmp/xmds2--numpy-20220120-1711-s6r7lk/numpy-1.16.0/setup.py'"'"';f
= getattr(tokenize, '"'"'open'"'"', open)(__file__) if
os.path.exists(__file__) else io.StringIO('"'"'from setuptools import
setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"',
'"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))'
install --record /private/tmp/pip-record-9pntciym/install-record.txt
--single-version-externally-managed --compile --install-headers
/opt/homebrew/Cellar/xmds2/3.1.0/libexec/include/site/python3.9/numpy Check
the logs for full command output.


If reporting this issue please do so at (not Homebrew/brew or
Homebrew/core):

  https://github.com/xmds2/homebrew-xmds2/issues


Thanks,
Tom

Re: [xmds-user] Integration over a subdomain

[Mattias J. <mat...@mq...>]

Hi Heitor,

I think the issue is the following: when you create your truncated field psiRED, you take the original wave function psi and set it to zero from a radius r > rcrit.

The problem with this is that you now have a very fast change in the wave function at r = rcrit and since momentum is given by  dpsi/dx, you get very high kinetic energies. You can see this by noting if double the grid points from 128 -> 256, the energy discrepancy nearly doubles, because you've now doubled the value of dpsi/dx (twice the spatial resolution means the drop off is twice as fast).

So the result is physically reasonable.

Remember momentum is the Fourier transform of position, so asking about the kinetic energy in a restricted spatial region is a bit of a dodgy question.

Cheers,
Mattias

________________________________
From: Heitor da Silva <he...@fi...>
Sent: Tuesday, 21 December 2021 7:48 AM
To: xmd...@li... <xmd...@li...>
Subject: [xmds-user] Integration over a subdomain

Hi all,

I am using xmds2 to solve an NLSE in which I add an imaginary potential to account for absorbing boundary conditions as proposed in the thread How to implement absorbing boundary layer method<https://sourceforge.net/p/xmds/mailman/message/34775082/>.

Later, I will have to calculate relevant quantities of the system up to the critical value of r where this potential starts to be valid. To see if I'm doing things right, I took the example of a harmonic oscillator whose ground-state solution is known to compare to numerical results but for this case, without using the imaginary potential.

I filtered the wavefunction over the subdomain as follows

<computed_vector name="varRED" dimensions="r" type="complex">
    <components> psiRED </components>
    <evaluation>
      <dependencies basis="r">wavefunction</dependencies>
      <![CDATA[
        if (r < rcrit) {
          psiRED = psi ;
        }
      ]]>
    </evaluation>
  </computed_vector>

and then tried to evaluate the potential and kinetic energy over it. For the former, I am getting the correct results but it is not working for the kinetic term. In the code I wrote these quantities as

  <computed_vector name="pot_energyR" dimensions="" type="real">
    <components> en_potR </components>
    <evaluation>
      <dependencies basis="r">varRED</dependencies>
      <![CDATA[
        // Calculate the potential energy.
        en_potR = 0.5*(r*r)*mod2(psiRED);
      ]]>
    </evaluation>
  </computed_vector>

<computed_vector name="kin_energyR" dimensions="" type="real">
    <components> en_kinR </components>
    <evaluation>
      <dependencies basis="kr">varRED</dependencies>
      <![CDATA[
        // Calculate the potential energy.
        en_kinR = 0.5*kr*kr*mod2(psiRED); //kinetic energy
      ]]>
    </evaluation>
  </computed_vector>

For example, for a critical value rcrit = 1.5 (of a domain r -> (0,3)), the integration of the analytical expression of the ground-state for the 2D harmonic oscillator yields ~ 0.328726 for each of the energy contributions but I am getting a value around 10 for the kinetic contribution from xmds2 simulation. I would say that the problem is in the corresponding Fourier space of this subdomain. So my question is how to define it correctly? Also, I wonder if there is another way to tackle this problem in xmds2 different from the one I adopted. I mean an alternative when an integration over a subdomain is needed.

Please find the code attached.

Thanks in advance.

--
Heitor da Silva

PhD Student in Quantum Optics - Universidade Federal do Rio Grande do Norte<https://www.ufrn.br>

Mobile: +55 11 97267 7782
Skype: heitorgalacian
Institutional e-mail: he...@fi...<mailto:he...@fi...>
Personal e-mail: hei...@gm...<mailto:hei...@gm...>

[xmds-user] Integration over a subdomain

[Heitor da S. <he...@fi...>]

Hi all,

I am using xmds2 to solve an NLSE in which I add an imaginary potential to
account for absorbing boundary conditions as proposed in the thread *How to
implement absorbing boundary layer method
<https://sourceforge.net/p/xmds/mailman/message/34775082/>. *

Later, I will have to calculate relevant quantities of the system up to the
critical value of r where this potential starts to be valid. To see if I'm
doing things right, I took the example of a harmonic oscillator whose
ground-state solution is known to compare to numerical results but for this
case, without using the imaginary potential.

I filtered the wavefunction over the subdomain as follows

<computed_vector name="varRED" dimensions="r" type="complex">
    <components> psiRED </components>
    <evaluation>
      <dependencies basis="r">wavefunction</dependencies>
      <![CDATA[
        if (r < rcrit) {
          psiRED = psi ;
        }
      ]]>
    </evaluation>
  </computed_vector>

and then tried to evaluate the potential and kinetic energy over it. For
the former, I am getting the correct results but it is not working for the
kinetic term. In the code I wrote these quantities as

  <computed_vector name="pot_energyR" dimensions="" type="real">
    <components> en_potR </components>
    <evaluation>
      <dependencies basis="r">varRED</dependencies>
      <![CDATA[
        // Calculate the potential energy.
        en_potR = 0.5*(r*r)*mod2(psiRED);
      ]]>
    </evaluation>
  </computed_vector>

<computed_vector name="kin_energyR" dimensions="" type="real">
    <components> en_kinR </components>
    <evaluation>
      <dependencies basis="kr">varRED</dependencies>
      <![CDATA[
        // Calculate the potential energy.
        en_kinR = 0.5*kr*kr*mod2(psiRED); //kinetic energy
      ]]>
    </evaluation>
  </computed_vector>

For example, for a critical value rcrit = 1.5 (of a domain r -> (0,3)), the
integration of the analytical expression of the ground-state for the 2D
harmonic oscillator yields ~ 0.328726 for each of the energy contributions
but I am getting a value around 10 for the kinetic contribution from xmds2
simulation. I would say that the problem is in the corresponding Fourier
space of this subdomain. So my question is how to define it correctly?
Also, I wonder if there is another way to tackle this problem in xmds2
different from the one I adopted. I mean an alternative when an integration
over a subdomain is needed.

Please find the code attached.

Thanks in advance.

-- 
*Heitor da Silva*

PhD Student in Quantum Optics - Universidade Federal do Rio Grande do Norte
<https://www.ufrn.br>

*Mobile: *+55 11 97267 7782
*Skype:* heitorgalacian
*Institutional e-mail: *he...@fi...
*Personal e-mail:* hei...@gm...

[xmds-user] Initial state from imported data

[Mark M. <mar...@gm...>]

Hi all.

I am solving a cubic-quintic NLSE using imaginary time to study its
groundstate. Next, I would like to collect the groundstate solution
obtained and use it as initial state for the same equation but running the
simulation in real time.
Previously, I searched here in the forum whether someone had already dealt
with this problem of importing data from a wavefunction and use it as
initial state. I tried to follow the steps described in
https://sourceforge.net/p/xmds/mailman/message/31964254/ but I haven't
succeeded yet in running the simulation in real time.

For the script in imaginary time, I have the following sample group for the
wavefunction

<sampling_group initial_sample="yes" basis="r">
        <dependencies> wavefunction </dependencies>
        <moments> psireal psiimag </moments>
        <![CDATA[
          psireal = Re(psi);
          psiimag = Im(psi);
      ]]>
 </sampling_group>

Here cqnlse_imag.h5 is the name of the output from the script run in
imaginary time. For this output, the keys are 4: 1 for the energy I
compute, 1 for the density as a function of r, 3 for the normalization and
4 for the values of r, the time and the real and imaginary components of
the wavefunction (psireal, psiimag).

Then I am trying to import this data to my script in real time as follows:

.....
<geometry>
    <propagation_dimension> t </propagation_dimension>
    <transverse_dimensions>
      <dimension name="r" lattice="512" domain="(0, 1)" transform="bessel"
volume_prefactor="2*M_PI" />
    </transverse_dimensions>
</geometry>

<vector name="psi_INT" initial_basis="r" type="complex">
    <components> psireal psiimag </components>
    <initialisation kind="hdf5">
      <filename>
          cqnlse_imag.h5
      </filename>
    </initialisation>
</vector>

<vector name="wavefunction" type="complex" initial_basis="r">
    <components>
      psi
    </components>
    <initialisation>
    <dependencies basis="r">psi_INT</dependencies>
      <![CDATA[
         psi = psireal + i*psiimag;
       ]]>
    </initialisation>
  </vector>

....

When I run the script, it returns the following error:

cq_nlse_real.cc:1049: Error: Unable to find dimension 'r' in HDF5 file.

cq_nlse_real is the name I chose for the script in real time. I did not get
how I import the values of the wavefunction groundstate correctly.
Can any one shine some light on how I can make it?

Thanks in advance.
Mark.

Re: [xmds-user] XMDS2 workaround to install fail on OSX Big Sur

[Karen K. <kar...@uq...>]

Hi Santiago, I tried that before trying Stuart's hack, and I have tried it again now. I am getting this:

=========================================================================

==> Installing xmds2 from xmds2/xmds2
==> Downloading https://pypi.python.org/packages/5b/22/0238132792f3600717fad9647072486e2c15b7b45f845b52cc484b9af024/Cheetah3-3.0.0.
Already downloaded: /Users/karen/Library/Caches/Homebrew/downloads/3eabdae732c49317c1f7ac784a949262efb6dd0e5908a898b91a6e4a54875e4e--Cheetah3-3.0.0.tar.gz
==> Downloading https://pypi.python.org/packages/3c/ec/a94f8cf7274ea60b5413df054f82a8980523efd712ec55a59e7c3357cf7c/pyparsing-2.2.0
Already downloaded: /Users/karen/Library/Caches/Homebrew/downloads/135d9c7d19095f975f8a7cb80d7a0972497fdd79ce2aed989d28ac0681dd39d5--pyparsing-2.2.0.tar.gz
==> Downloading https://pypi.python.org/packages/7a/05/b3d1472885d8dc0606936ea5da0ccb1b4785682e78ab15e34ada24aea8d5/mpmath-1.0.0.ta
Already downloaded: /Users/karen/Library/Caches/Homebrew/downloads/8d0f1a905bc5e03b81965cf11aa6f468a52fcd07a0356ea92ed5efa2a7826e06--mpmath-1.0.0.tar.gz
==> Downloading https://pypi.python.org/packages/04/b6/d7faa70a3e3eac39f943cc6a6a64ce378259677de516bd899dd9eb8f9b32/numpy-1.16.0.zi
Already downloaded: /Users/karen/Library/Caches/Homebrew/downloads/132d8b361b397f783d2a122472fce69e77ea705d75289ecc3dcde77bce88d140--numpy-1.16.0.zip
==> Downloading https://pypi.python.org/packages/16/4a/b085a04d6dad79aa5c00c65c9b2bbcb2c6c22e5ac341e7968e0ad2c57e2f/lxml-4.3.0.tar.
Already downloaded: /Users/karen/Library/Caches/Homebrew/downloads/04c66558491da327f74c9499f7876ac42409a0d12bd5d3e9b264d2715114bdb9--lxml-4.3.0.tar.gz
==> Downloading https://downloads.sourceforge.net/project/xmds/xmds-3.0.0.tar.gz
Already downloaded: /Users/karen/Library/Caches/Homebrew/downloads/8556906122d6bb7f96062f3a0afb9aece97d15d2ad4f0ca6a57557f0e2982589--xmds-3.0.0.tar.gz
==> python3 -m venv --system-site-packages /usr/local/Cellar/xmds2/3.0.0/libexec
==> /usr/local/Cellar/xmds2/3.0.0/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /private/tmp/xmds2--Che
==> /usr/local/Cellar/xmds2/3.0.0/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /private/tmp/xmds2--pyp
==> /usr/local/Cellar/xmds2/3.0.0/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /private/tmp/xmds2--mpm
==> /usr/local/Cellar/xmds2/3.0.0/libexec/bin/pip install -v --no-deps --no-binary :all: --ignore-installed /private/tmp/xmds2--num
Last 15 lines from /Users/karen/Library/Logs/Homebrew/xmds2/05.pip:
    installed = install_given_reqs(
  File "/usr/local/Cellar/xmds2/3.0.0/libexec/lib/python3.9/site-packages/pip/_internal/req/__init__.py", line 77, in install_given_reqs
    requirement.install(
  File "/usr/local/Cellar/xmds2/3.0.0/libexec/lib/python3.9/site-packages/pip/_internal/req/req_install.py", line 829, in install
    six.reraise(*exc.parent)
  File "/usr/local/Cellar/xmds2/3.0.0/libexec/lib/python3.9/site-packages/pip/_vendor/six.py", line 703, in reraise
    raise value
  File "/usr/local/Cellar/xmds2/3.0.0/libexec/lib/python3.9/site-packages/pip/_internal/operations/install/legacy.py", line 69, in install
    runner(
  File "/usr/local/Cellar/xmds2/3.0.0/libexec/lib/python3.9/site-packages/pip/_internal/utils/subprocess.py", line 274, in runner
    call_subprocess(
  File "/usr/local/Cellar/xmds2/3.0.0/libexec/lib/python3.9/site-packages/pip/_internal/utils/subprocess.py", line 244, in call_subprocess
    raise InstallationSubprocessError(proc.returncode, command_desc)
pip._internal.exceptions.InstallationSubprocessError: Command errored out with exit status 1: /usr/local/Cellar/xmds2/3.0.0/libexec/bin/python3.9 -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/private/tmp/pip-req-build-q9mqax3n/setup.py'"'"'; __file__='"'"'/private/tmp/pip-req-build-q9mqax3n/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /private/tmp/pip-record-fxn_5zr_/install-record.txt --single-version-externally-managed --compile --install-headers /usr/local/Cellar/xmds2/3.0.0/libexec/include/site/python3.9/numpy Check the logs for full command output.
Removed build tracker: '/private/tmp/pip-req-tracker-p812pw8c'

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
  https://github.com/xmds2/homebrew-xmds2/issues

================================================================================================

-??

Thanks,

Karen
--
Karen Kheruntsyan
Professor of Theoretical Physics
School of Mathematics and Physics
The University of Queensland
Brisbane QLD 4072
AUSTRALIA

Phone: +61 - (0)7 - 33653420
Fax:   +61 - (0)7 - 33651242
E-mail: kar...@uq...<mailto:kar...@uq...>
URL: https://people.smp.uq.edu.au/KarenKheruntsyan

On 10 Jul 2021, at 9:07 pm, Santiago Francisco Caballero Benitez <san...@gm...<mailto:san...@gm...>> wrote:

Hi Karen,

I installed via brew and it works like that. The current installer from the page doesn’t work.

brew install xmds2/xmds2/xmds2

I hope this helps,

Cheers,

Santiago


On 10 Jul 2021, at 5:41 am, Karen Kheruntsyan <kar...@uq...<mailto:kar...@uq...>> wrote:

Hi Stuart, others,

So, I am trying to install xmds3 under Big Sur, but so far unsuccessfully. I downloaded xmds-3.0.0; it was in my Downloads folder. I moved that entire folder into the Applications folder. I went into the directory ../Applications/xmds-3.0.0 in the terminal window and typed "sudo ./setup.py develop" as suggested by Stuart. But I am getting the following error:

RuntimeError: Running cythonize failed!

The last few lines from the terminal window are:
    ...
    ...
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 193, in setup_context
    yield
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 254, in run_setup
    _execfile(setup_script, ns)
  File "/usr/local/lib/python3.9/site-packages/setuptools/sandbox.py", line 43, in _execfile
    exec(code, globals, locals)
  File "/tmp/easy_install-5x0b0flm/numpy-1.21.0/setup.py", line 447, in <module>
  File "/tmp/easy_install-5x0b0flm/numpy-1.21.0/setup.py", line 429, in setup_package
  File "/tmp/easy_install-5x0b0flm/numpy-1.21.0/setup.py", line 235, in generate_cython
RuntimeError: Running cythonize failed!

So, is there any workaround?

Thanks,

Karen
--
Karen Kheruntsyan
Professor of Theoretical Physics
School of Mathematics and Physics
The University of Queensland
Brisbane QLD 4072
AUSTRALIA

Phone: +61 - (0)7 - 33653420
Fax:   +61 - (0)7 - 33651242
E-mail: kar...@uq...<mailto:kar...@uq...>
URL: https://people.smp.uq.edu.au/KarenKheruntsyan

On 19 Apr 2021, at 4:58 pm, Stuart Szigeti <stu...@an...<mailto:stu...@an...>> wrote:

A few users have been experiencing issues with the home brew installer for MacOS X Big Sur.

However, since it is failing on the final step (the installation of XMDS2 itself), I managed this workaround:

1. Download the XMDS2 source from: https://sourceforge.net/projects/xmds/

2. Follow steps (6) and (7) of the source installation instructions (http://www.xmds.org/installation.html). Specifically, in the xmds-3.0.0/ directory, type "sudo ./setup.py develop" followed by "xmds2 --reconfigure".

Dr Stuart Szigeti
Australian Research Council DECRA Fellow
Department of Quantum Science
Research School of Physics
Room 108, 38A Science Road  | The Australian National University | ACT 2601 Australia
E: stu...@an...<mailto:stu...@an...>

PhB(Sci)(Hons), PhD(Theor Phys), GCertHEd
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