error in na cl association (while parsing a flow node did not find expected node content)

[Ibrahim Mohamed]

i am trying to do the na cl association tutorial in gromacs but it produces this error.

/lfs01/workdirs/cairo029u1/1PHD/WESTPA/trial/nacl_gromacs/gromacs/westpa_files

westpa_files

Traceback (most recent call last):

  File "/home/cairo029u1/.local/bin/w_init", line 8, in <module>

    sys.exit(entry_point())

  File "/home/cairo029u1/.local/lib/python3.9/site-packages/westpa/cli/core/w_init.py", line 109, in entry_point

    westpa.rc.process_args(args)

  File "/home/cairo029u1/.local/lib/python3.9/site-packages/westpa/core/_rc.py", line 223, in process_args

    self.read_config()

  File "/home/cairo029u1/.local/lib/python3.9/site-packages/westpa/core/_rc.py", line 249, in read_config

    self.config.update_from_file(self.rcfile)

  File "/home/cairo029u1/.local/lib/python3.9/site-packages/westpa/core/yamlcfg.py", line 107, in update_from_file

    self._data.update(yaml.load(file, Loader=YLoader))

  File "/home/cairo029u1/.local/lib/python3.9/site-packages/yaml/__init__.py", line 81, in load

    return loader.get_single_data()

  File "/home/cairo029u1/.local/lib/python3.9/site-packages/yaml/constructor.py", line 49, in get_single_data

    node = self.get_single_node()

  File "yaml/_yaml.pyx", line 673, in yaml._yaml.CParser.get_single_node

  File "yaml/_yaml.pyx", line 687, in yaml._yaml.CParser._compose_document

  File "yaml/_yaml.pyx", line 731, in yaml._yaml.CParser._compose_node

  File "yaml/_yaml.pyx", line 845, in yaml._yaml.CParser._compose_mapping_node

  File "yaml/_yaml.pyx", line 731, in yaml._yaml.CParser._compose_node

  File "yaml/_yaml.pyx", line 845, in yaml._yaml.CParser._compose_mapping_node

  File "yaml/_yaml.pyx", line 731, in yaml._yaml.CParser._compose_node

  File "yaml/_yaml.pyx", line 845, in yaml._yaml.CParser._compose_mapping_node

  File "yaml/_yaml.pyx", line 731, in yaml._yaml.CParser._compose_node

  File "yaml/_yaml.pyx", line 845, in yaml._yaml.CParser._compose_mapping_node

  File "yaml/_yaml.pyx", line 731, in yaml._yaml.CParser._compose_node

  File "yaml/_yaml.pyx", line 845, in yaml._yaml.CParser._compose_mapping_node

  File "yaml/_yaml.pyx", line 729, in yaml._yaml.CParser._compose_node

  File "yaml/_yaml.pyx", line 806, in yaml._yaml.CParser._compose_sequence_node

  File "yaml/_yaml.pyx", line 729, in yaml._yaml.CParser._compose_node

  File "yaml/_yaml.pyx", line 808, in yaml._yaml.CParser._compose_sequence_node

  File "yaml/_yaml.pyx", line 860, in yaml._yaml.CParser._parse_next_event

yaml.parser.ParserError: while parsing a flow node

did not find expected node content

  in "west.cfg", line 22, column 46

this is the west.cfg file:

# The master WEST configuration file for a simulation.

# vi: set filetype=yaml :

---

west:

  system:

    driver: westpa.core.systems.WESTSystem

    system_options:

      # Dimensionality of your progress coordinate

      pcoord_ndim: 1

      # Number of data points per iteration

      # Needs to be pcoord_len >= 2 (minimum of parent, last frame) to work with most analysis tools

      # number of frames outpputted from MD ENGINE

      pcoord_len: 51

      # Data type for your progress coordinate

      pcoord_dtype: !!python/name:numpy.float32

      bins:

        type: RectilinearBinMapper

        # The edges of the bins

        boundaries:

          -  [ 0.00, 2.60, 2.80, 3.00, 3.20, 3.40, 3.60, 3.80,

               4.00, 4.50, 5.00, 5.50, 6.00, 7.00, 8.0, 9.0, 10.0,

               11.0, 12.0, 13.0, 14.0, 15.0, ,16.0, 17.0, 18.0, 19.0, 20.0, 'inf']

      # bins:

      #   type: RecursiveBinMapper

      #   base:

      #     type: RectilinearBinMapper

      #     boundaries:

      #       - [-inf, 0., 15., inf]

      #   mappers:

      #     - type: MABBinMapper

      #       nbins: [20]

      #       at: [0]

      # Number walkers per bin

      bin_target_counts: 2

  propagation:

    max_total_iterations: 2

    max_run_wallclock:    72:00:00

    propagator:           executable

    gen_istates:          true

  data:

    west_data_file: west.h5

    datasets:

      - name:        pcoord

        scaleoffset: 4

    data_refs:

      iteration:     $WEST_SIM_ROOT/traj_segs/iter_{n_iter:06d}.h5

      segment:       $WEST_SIM_ROOT/traj_segs/{segment.n_iter:06d}/{segment.seg_id:06d}

      basis_state:   $WEST_SIM_ROOT/bstates/{basis_state.auxref}

      initial_state: $WEST_SIM_ROOT/istates/{initial_state.iter_created}/{initial_state.state_id}.xml

  plugins:

  executable:

    environ:

      PROPAGATION_DEBUG: 1

    propagator:

      executable: $WEST_SIM_ROOT/westpa_scripts/runseg.sh

      stdout:     $WEST_SIM_ROOT/seg_logs/{segment.n_iter:06d}-{segment.seg_id:06d}.log

      stderr:     stdout

      stdin:      null

      cwd:        null

      environ:

        SEG_DEBUG: 1

    get_pcoord:

      executable: $WEST_SIM_ROOT/westpa_scripts/get_pcoord.sh

      stdout:     $WEST_SIM_ROOT/get_pcoord.log

      stderr:     stdout

    gen_istate:

      executable: $WEST_SIM_ROOT/westpa_scripts/gen_istate.sh

      stdout:     /dev/null

      stderr:     stdout

    post_iteration:

      enabled:    true

      executable: $WEST_SIM_ROOT/westpa_scripts/post_iter.sh

      stderr:     stdout

    pre_iteration:

      enabled:    false

      executable: $WEST_SIM_ROOT/westpa_scripts/pre_iter.sh

      stderr:     stdout

  # Settings for w_ipa, an interactive analysis program that can also automate analysis.

  analysis:

     directory: ANALYSIS                # specify the directory all analysis files should exist in.

     kinetics:                          # general options for both kinetics routines.

       step_iter: 1

       evolution: cumulative

       extra: [ 'disable-correl' ]

     analysis_schemes:                  # Analysis schemes.  Required: name (TEST), states, and bins

       TEST:

         enabled: True

         bins:

           - type: RectilinearBinMapper

             boundaries:

               - [0.0,2.6,12.0,'inf']

         states:

           - label: bound

             coords:

               - [0]

           - label: unbound

             coords:

               - [12.1]

[Leung, Jeremy]

Hi Ibrahim,

This is a classic error when there are typos in your west.cfg. If you look closely at your boundaries, you have two commas in a row between 15.0 and 16.0.

-- JL

---
Jeremy M. G. Leung
PhD Candidate, Chemistry
Graduate Student Researcher, Chemistry (Chong Lab)
University of Pittsburgh | 219 Parkman Avenue, Pittsburgh, PA 15260
jml...@pitt.edu | [He, Him, His]

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[hollowic...@gmail.com]

Yes thank you for your help

Sent from Yahoo Mail on Android

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