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glosim2 is not currently compatible with Python 3 or the most up-to-date version of Quippy. It would be helpful, at the minimum, to know what version of Quippy glosim2 has been tested for.

Hi, when I run GlobalSimilarity.py it seems to run but it just freezes and nothing happens, this is the output:

root@0f7ecc515774:~/glosim2# python GlobalSimilarity.py ../100.xyz --nocenters 1
 WARNING: libAtoms::Hello World: environment variable OMP_STACKSIZE not set explicitly. The default value - system and compiler dependent - may be too small for some applications.
_____/\\\\\\\\\\\\__/\\\\\\_____________________________________________________________/\\\\\\\\\_____        
 ___/\\\//////////__\////\\\___________________________________________________________/\\\///////\\\___       
  __/\\\________________\/\\\________________________________/\\\______________________\///______\//\\\__      
   _\/\\\____/\\\\\\\____\/\\\________/\\\\\_____/\\\\\\\\\\_\///_____/\\\\\__/\\\\\______________/\\\/___     
    _\/\\\___\/////\\\____\/\\\______/\\\///\\\__\/\\\//////___/\\\__/\\\///\\\\\///\\\_________/\\\//_____    
     _\/\\\_______\/\\\____\/\\\_____/\\\__\//\\\_\/\\\\\\\\\\_\/\\\_\/\\\_\//\\\__\/\\\______/\\\//________   
      _\/\\\_______\/\\\____\/\\\____\//\\\__/\\\__\////////\\\_\/\\\_\/\\\__\/\\\__\/\\\____/\\\/___________  
       _\//\\\\\\\\\\\\/___/\\\\\\\\\__\///\\\\\/____/\\\\\\\\\\_\/\\\_\/\\\__\/\\\__\/\\\___/\\\\\\\\\\\\\\\_ 
        __\////////////____\/////////_____\/////_____\//////////__\///__\///___\///___\///___\///////////////__
Sat Mar 17 08:33:35 2018
Start Computing the global average kernel of ../100.xyz
using output prefix = ../100-n8-l6-c3.5-g0.5-cw1.0-cotw0.5-average-zeta2-nonorm
Reading 100 input atomic structure from ../100.xyz: done 00:00:00 (h:m:s)
Compute soap and environmental kernels with a pool of 4 workers and 4 threads over 10 chunks: 00:00:00 (h:m:s)
listener  False
Env kernels:   0%|                                                                                                                                             | 0/5050 [00:00<?, ?it/s]

This is in the quippy docker and with 100.xyz contains 100 libatoms xyz crystal structures.

Do you maybe know what is going on?

Hi,

The GlobalSimilarity.py works well and seems very useful thanks! However, I have larger systems and would like to use your parallelised version GlobalSimilarity_cluster.py
When running it using:

python ../GlobalSimilarity_cluster.py small_molecules.xyz --xlim 0,11 --ylim 513661,21 -np 16 -sek

It terminates without any errors, but the pickle that should contain the Kernel is just empty? I tried using the example small_molecules.xyz too. What am I doing wrong?

By default this the global kernel is not normalized, but enabling it currently does not do the correct normalization:

def normalizeKernel(kernel):
    n,m = kernel.shape
    for it in range(n):
        for jt in range(m):
            kernel[it,jt] = kernel[it,jt] / np.sqrt(kernel[it,it]* kernel[jt,jt])
    return kernel

The problem is that kernel[it,jt] is in later loops used again as kernel[jt,jt]. This could be solved by keeping a copy of the diagonal.

GLOSIM2 doesn't support the latest version of tqdm package (4.2.1) but it works with older version (4.11.1).
Error message looks like:

/\\\\\\/\\\/\\\\_
/\//////////////\_/\///////\_
/\_/\_/\_/////\_
/\_/\\\_/\_/\\_/\\\\\////\\_/\\__________/\/
_/\_/////\_/\_/\///\_/\///////\__/\///\\///\_/\//
/\_/\_/\_/\_//\_/\\\\\/\_/\_//\_/\_/\//___
/\_/\_/\_//\_/\_////////\_/\_/\_/\_/\_/\/________
//\\\\\\//\\\\_///\\//\\\\\/\_/\_/\_/\_/\\\\\\\_
////////////____////////////////////////////////////_///////////////
Mon Apr 23 13:23:16 2018
Start Computing the global average kernel of mol-50.xyz
using output prefix = mol-50-n8-l6-c3.5-g0.5-cw1.0-cotw0.5-average-zeta2-nonorm
Reading 50 input atomic structure from mol-50.xyz: done 00:00:00 (h:m:s)
Compute soap and environmental kernels with a pool of 4 workers and 4 threads over 10 chunks: 00:00:00 (h:m:s)
listener False
SOAP vectors: 0%| | 0/12 [00:00<?, ?it/s]Exception KeyError: KeyError(<weakref at 0x7f371c7ff5d0; to 'tqdm' at 0x7f371c85d790>,) in <bound method tqdm.del of SOAP vectors: 0%| | 0/12 [00:00<?, ?it/s]> ignored
Traceback (most recent call last):
File "GlobalSimilarity.py", line 249, in
**soap_params)
File "GlobalSimilarity.py", line 114, in get_environmentalKernels
environmentalKernels = get_environmentalKernels_mt_mp_chunks(**kargs)
File "/home/maksimov/programs/glosim2/libmatch/environmental_kernel.py", line 658, in get_environmentalKernels_mt_mp_chunks
results = pool.run()
File "/home/maksimov/programs/glosim2/libmatch/environmental_kernel.py", line 526, in run
res = self.pool.map(self.func, self.chunks)
File "/home/maksimov/anaconda2/lib/python2.7/multiprocessing/pool.py", line 253, in map
return self.map_async(func, iterable, chunksize).get()
File "/home/maksimov/anaconda2/lib/python2.7/multiprocessing/pool.py", line 572, in get
raise self._value
AttributeError: NeighborList instance has no attribute 'build'
SOAP vectors: 0%| | 0/12 [00:00<?, ?it/s]Exception KeyError: KeyError(<weakref at 0x7f371c813680; to 'tqdm' at 0x7f371c7f54d0>,) in <bound method tqdm.del of SOAP vectors: 0%| | 0/12 [00:00<?, ?it/s]> ignored
SOAP vectors: 0%| | 0/12 [00:00<?, ?it/s]Exception KeyError: KeyError(<weakref at 0x7f371c813680; to 'tqdm' at 0x7f371c801b10>,) in <bound method tqdm.del of SOAP vectors: 0%| | 0/12 [00:00<?, ?it/s]> ignored
SOAP vectors: 0%| | 0/12 [00:00<?, ?it/s]Exception KeyError: KeyError(<weakref at 0x7f371c813940; to 'tqdm' at 0x7f371c817310>,) in <bound method tqdm.del of SOAP vectors: 0%| | 0/12 [00:00<?, ?it/s]> ignored
Exception KeyError: KeyError(<weakref at 0x7f3707fed6d8; to 'tqdm' at 0x7f3707ff1450>,) in <bound method tqdm.del of SOAP vectors: 0%| | 0/12 [00:00<?, ?it/s]> ignored
Exception KeyError: KeyError(<weakref at 0x7f3707fed7e0; to 'tqdm' at 0x7f3707f81210>,) in <bound method tqdm.del of SOAP vectors: 0%| | 0/12 [00:00<?, ?it/s]> ignored
Exception KeyError: KeyError(<weakref at 0x7f3707ff1b50; to 'tqdm' at 0x7f3707fe6f90>,) in <bound method tqdm.del of SOAP vectors: 0%| | 0/12 [00:00<?, ?it/s]> ignored
Exception KeyError: KeyError(<weakref at 0x7f3707fc9730; to 'tqdm' at 0x7f3707fe8390>,) in <bound method tqdm.del of SOAP vectors: 0%| | 0/12 [00:00<?, ?it/s]> ignored
Exception KeyError: KeyError(<weakref at 0x7f3707f89af8; to 'tqdm' at 0x7f3707f8bed0>,) in <bound method tqdm.del of SOAP vectors: 0%| | 0/12 [00:00<?, ?it/s]> ignored
Exception KeyError: KeyError(<weakref at 0x7f3707fedaa0; to 'tqdm' at 0x7f3707fc7890>,) in <bound method tqdm.del of SOAP vectors: 0%| | 0/14 [00:00<?, ?it/s]> ignored