coordinate value 1.0 is out of bin space in dimension 0 Error

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amami...@gmail.com

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Aug 27, 2020, 4:56:15 PM8/27/20
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I'm using westpa to probe the exchange rate of my system.
The init.sh seems to work fine.

Updating system with the options from the configuration file
Creating HDF5 file '/data/biggin/grte2001/KDEL/west.h5'
1 target state(s) present
Calculating progress coordinate values for basis states.
1 basis state(s) present
Preparing initial states


Total bins: 51
Initial replicas: 5 in 1 bins, total weight = 1
Total target replicas: 755

Simulation prepared.
1 of 151 (0.662252%) active bins are populated
per-bin minimum non-zero probability: 1
per-bin maximum probability: 1
per-bin probability dynamic range (kT): 0
per-segment minimum non-zero probability: 0.2
per-segment maximum non-zero probability: 0.2
per-segment probability dynamic range (kT): 0
norm = 1, error in norm = 0 (0*epsilon)

However, when I start running "$WEST_ROOT/bin/w_run --work-manager serial  --n-workers 1 "$@" "
I got

Updating system with the options from the configuration file
Maximum wallclock time: 4 days, 14:00:00

Thu Aug 27 21:51:13 2020
Iteration 1 (100 requested)
exception caught; shutting down
-- ERROR    [w_run] -- Traceback (most recent call last):
  File "/home/grte2001/.conda/envs/westpa/westpa-2020.03/lib/cmds/w_run.py", line 49, in <module>
    sim_manager.run()
  File "/home/grte2001/.conda/envs/westpa/westpa-2020.03/src/west/sim_manager.py", line 622, in run
    self.prepare_iteration()
  File "/home/grte2001/.conda/envs/westpa/westpa-2020.03/src/west/sim_manager.py", line 327, in prepare_iteration
    self.we_driver.new_iteration(target_states=target_states, new_weights= new_weights)
  File "/home/grte2001/.conda/envs/westpa/westpa-2020.03/src/west/we_driver.py", line 232, in new_iteration
    tstate_assignment = self.bin_mapper.assign([tstate.pcoord])[0]
  File "/home/grte2001/.conda/envs/westpa/westpa-2020.03/lib/west_tools/westpa/binning/assign.py", line 170, in assign
    rectilinear_assign(coords, mask, output, self.boundaries, self._boundlens)
  File "westpa/binning/_assign.pyx", line 44, in westpa.binning._assign.rectilinear_assign
  File "westpa/binning/_assign.pyx", line 97, in westpa.binning._assign.rectilinear_assign
ValueError: coordinate value 1.0 is out of bin space in dimension 0

It seems that there is nothing in the traj_segs and seg_logs.
There are only some new files in the istates/1, where there are five repeats of the initial configuration.
I have executed line by line of the get_pcoord.sh and runseg.sh and can verify that they are set up correctly and there shouldn't be any collective variable which is "1.0".

I wonder if I can get some help, please? Thank you.
Kind regards,
Zhiyi Wu

Anthony Bogetti

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Aug 27, 2020, 5:08:04 PM8/27/20
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Hello,

 

In the past, I’ve seen this error occur when the progress coordinate value does not fall into the user-defined bin-spacing.  For instance, if your binning scheme was defined as: [0, 5, 10, 100] and your progress coordinate ended up being 101, you would get that error because there are no “bounded” bins after 100, you would have to add ‘inf’ after 100 to get that to work.

 

Let’s check two things:

  1. Your binning scheme.  Can you send this along?  Where is it defined?
  2. Your progress coordinate value after one iteration.  What is your initial progress coordinate value and what do you expect it to be after one iteration?  It is a little strange you aren’t seeing anything in the traj_segs or seg_logs… If you manually run one segment using your dynamics input, do you get output files?  Is the structure reasonable?  Check this out and let me know.

 

We can start with those things and then look closer and see what is going on.

 

Anthony

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Amami Haruka

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Aug 27, 2020, 5:45:14 PM8/27/20
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Hi Anthony,
Thank you for the email.
The binning scheme is 
1. The CV is expected to went from 1.8 to 3.3 and potentially inf
west:
  system:
    driver: west.WESTSystem
    system_options:
      # Dimensionality of your progress coordinate
      pcoord_ndim: 1
      # Number of data points per iteration
      pcoord_len: 51
      # Data type for your progress coordinate
      pcoord_dtype: !!python/name:numpy.float32
      bins:
        type: RectilinearBinMapper
        # The edges of the bins
        boundaries:
          -  [ 1.7, 1.8 , 1.81, 1.82, 1.83, 1.84, 1.85, 1.86, 1.87, 1.88, 1.89, 1.9 ,
       1.91, 1.92, 1.93, 1.94, 1.95, 1.96, 1.97, 1.98, 1.99, 2.  , 2.01,
       2.02, 2.03, 2.04, 2.05, 2.06, 2.07, 2.08, 2.09, 2.1 , 2.11, 2.12,
       2.13, 2.14, 2.15, 2.16, 2.17, 2.18, 2.19, 2.2 , 2.21, 2.22, 2.23,
       2.24, 2.25, 2.26, 2.27, 2.28, 2.29, 2.3 , 2.31, 2.32, 2.33, 2.34,
       2.35, 2.36, 2.37, 2.38, 2.39, 2.4 , 2.41, 2.42, 2.43, 2.44, 2.45,
       2.46, 2.47, 2.48, 2.49, 2.5 , 2.51, 2.52, 2.53, 2.54, 2.55, 2.56,
       2.57, 2.58, 2.59, 2.6 , 2.61, 2.62, 2.63, 2.64, 2.65, 2.66, 2.67,
       2.68, 2.69, 2.7 , 2.71, 2.72, 2.73, 2.74, 2.75, 2.76, 2.77, 2.78,
       2.79, 2.8 , 2.81, 2.82, 2.83, 2.84, 2.85, 2.86, 2.87, 2.88, 2.89,
       2.9 , 2.91, 2.92, 2.93, 2.94, 2.95, 2.96, 2.97, 2.98, 2.99, 3.  ,
       3.01, 3.02, 3.03, 3.04, 3.05, 3.06, 3.07, 3.08, 3.09, 3.1 , 3.11,
       3.12, 3.13, 3.14, 3.15, 3.16, 3.17, 3.18, 3.19, 3.2 , 3.21, 3.22,
       3.23, 3.24, 3.25, 3.26, 3.27, 3.28, 3.29, 3.3, 'inf']
      # Number walkers per bin
      bin_target_counts: 5

2. The first iteration haven’t started.
If I manually run get_pcoord.sh, I would get 1.822664 for $WEST_PCOORD_RETURN.
If I manually run runseg.sh, I would get the same result and the WEST_PCOORD_RETURN is going between 1.8 and 1.85.
I think no evaluation has been performed when this error occurs, I have twicked the get_pcoord.sh and runseg.sh such that they will write something before evaluation and it seems that nothing is written out.
Kind regards,
Zhiyi Wu

Anthony Bogetti

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Aug 27, 2020, 5:49:33 PM8/27/20
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Hi Zhiyi,

 

Can you try adding a zero to the start of your bin definition?  Like this: [0, 1.7, 1.8, etc.].  Let me know what happens then.  Perhaps there is a value below 1.7 occurring, in which case it would throw that error.  I’ll think a little more about this, but give this a try for now.

 

Best,

Anthony

Amami Haruka

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Aug 27, 2020, 6:14:18 PM8/27/20
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Hi Anthony,
Adding zero seems to be working and the simulations are running. However, from the cv collected it doesn’t seems that the cv is reaching below 1.8.
Kind regards,
Zhiyi Wu

Anthony Bogetti

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Aug 28, 2020, 4:54:53 PM8/28/20
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Hi Zhiyi,

 

I’m glad to hear that it is now running.  Let us know if you run into any further errors.

 

Are you using multiple basis states for your simulation?  And do you have gen_istates turned on in the west.cfg?  I’m trying to think of why you would get that error, since it shouldn’t matter if you have a 0 there or not if your cv does not reach below 1.7.  Do you see any cv values below 1.7 after your simulation has run for some time?

Amami Haruka

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Aug 28, 2020, 5:01:07 PM8/28/20
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Hi Anthony,
Thank you for the help.

Are you using multiple basis states for your simulation?
I don’t think so. I have 0 1 unbound > bstates.txt
And do you have gen_istates turned on in the west.cfg?
Yes, I have gen_istates:          true
Do you see any cv values below 1.7 after your simulation has run for some time?
No the cv is protein-ligand distance and below 1.8 would mean ligand crashed into the protein.
Kind regards,
Zhiyi Wu

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