# 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: 2 # Number of data points per iteration pcoord_len: 101 # Data type for your progress coordinate pcoord_dtype: !!python/name:numpy.float32 bins: type: RectilinearBinMapper # The edges of the bins boundaries: - [0.0, 1.8, 2.2, 2.6, 3.0, 3.5, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0, 11, 12, 14, 16, 18, 20, 'inf'] - [0, 2, 4, 6, 8, 10, 12, 14, 16, 18, 20, 21, 22, 23, 24, 25, 26, 'inf'] bin_target_counts: 4 propagation: max_total_iterations: 2 max_run_wallclock: 72:00:00 propagator: executable gen_istates: false data: west_data_file: west.h5 datasets: - name: pcoord # store progress coordinates with HDF5 scale/offset dtype: float32 scaleoffset: 4 # with 4 decimal places of precision - name: dihedral_2 # store progress coordinates with HDF5 scale/offset dtype: float32 scaleoffset: 4 # with 4 decimal places of precision - name: dihedral_3 # store progress coordinates with HDF5 scale/offset dtype: float32 scaleoffset: 4 # with 4 decimal places of precision - name: dihedral_4 # store progress coordinates with HDF5 scale/offset dtype: float32 scaleoffset: 4 # with 4 decimal places of precision - name: dihedral_5 # store progress coordinates with HDF5 scale/offset dtype: float32 scaleoffset: 4 # with 4 decimal places of precision - name: dihedral_6 # store progress coordinates with HDF5 scale/offset dtype: float32 scaleoffset: 4 # with 4 decimal places of precision - name: dihedral_7 # store progress coordinates with HDF5 scale/offset dtype: float32 scaleoffset: 4 # with 4 decimal places of precision - name: dihedral_8 # store progress coordinates with HDF5 scale/offset dtype: float32 scaleoffset: 4 # with 4 decimal places of precision - name: dihedral_9 # store progress coordinates with HDF5 scale/offset dtype: float32 scaleoffset: 4 # with 4 decimal places of precision - name: dihedral_10 # store progress coordinates with HDF5 scale/offset dtype: float32 scaleoffset: 4 # with 4 decimal places of precision - name: dihedral_11 # store progress coordinates with HDF5 scale/offset dtype: float32 scaleoffset: 4 # with 4 decimal places of precision - name: dihedral_12 # store progress coordinates with HDF5 scale/offset dtype: float32 scaleoffset: 4 # with 4 decimal places of precision - name: dihedral_13 # store progress coordinates with HDF5 scale/offset dtype: float32 scaleoffset: 4 # with 4 decimal places of precision - name: dihedral_14 # store progress coordinates with HDF5 scale/offset dtype: float32 scaleoffset: 4 # with 4 decimal places of precision - name: heavy_sc_rmsd_p53 dtype: float32 scaleoffset: 4 # with 4 decimal places of precision data_refs: 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}.rst plugins: - plugin: westext.wess.WESSDriver # must name Python object enabled: false # optional, implied by presence in plugins list do_reweighting: true window_size: 0.5 - plugin: westext.constantratio.TargetRatio # must name Python object enabled: false # optional, implied by presence in plugins list max_replicas: 504 state_definitions: None state_weights: [1] executable: environ: PROPAGATION_DEBUG: 1 datasets: - name: heavy_sc_rmsd_p53 enabled: true - name: dihedral_2 enabled: true - name: dihedral_3 enabled: true - name: dihedral_4 enabled: true - name: dihedral_5 enabled: true - name: dihedral_6 enabled: true - name: dihedral_7 enabled: true - name: dihedral_8 enabled: true - name: dihedral_9 enabled: true - name: dihedral_10 enabled: true - name: dihedral_11 enabled: true - name: dihedral_12 enabled: true - name: dihedral_13 enabled: true - name: dihedral_14 enabled: true 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: pcoord.log stderr: pcoord.err 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 stdout: post_iter.log stderr: stdout pre_iteration: enabled: false executable: $WEST_SIM_ROOT/westpa_scripts/pre_iter.sh stdout: pre_iter.log 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. #w_assign: # extra: [ 'subsample' ] kinetics: # general options for both kinetics routines. step_iter: 1 evolution: blocked extra: [ 'disable-correl' ] analysis_schemes: # Analysis schemes. Required: name (TEST), states, and bins ALL: enabled: True bins: - type: RectilinearBinMapper boundaries: - [0.0, 5.0, 'inf'] - [0.0, 5.0, 'inf'] states: - label: s0 coords: - [1.0, 1.0] - label: s1 coords: - [11.0, 1.0] - label: s2 coords: - [1.0, 11.0] - label: s3 coords: - [11.0, 11.0] T02: enabled: True bins: - type: RectilinearBinMapper boundaries: - [0.0, 5.0, 'inf'] - [0.0, 5.0, 'inf'] states: - label: s0 coords: - [1.0, 1.0] - label: s2 coords: - [1.0, 11.0] T12: enabled: True bins: - type: RectilinearBinMapper boundaries: - [0.0, 5.0, 'inf'] - [0.0, 5.0, 'inf'] states: - label: s1 coords: - [11.0, 1.0] - label: s2 coords: - [1.0, 11.0] T32: enabled: True bins: - type: RectilinearBinMapper boundaries: - [0.0, 5.0, 'inf'] - [0.0, 5.0, 'inf'] states: - label: s3 coords: - [11.0, 11.0] - label: s2 coords: - [1.0, 11.0]