diff --git a/_sources/observables.md.txt b/_sources/observables.md.txt index 1b09d6389..26a4d292d 100644 --- a/_sources/observables.md.txt +++ b/_sources/observables.md.txt @@ -171,6 +171,13 @@ Print the energy associated to all (or a subset of) the external forces acting o * `type = force_energy`: the observable type. * `[print_group = ]`: limit the energy computation to the forces belonging to a specific group of forces. This can be set by adding a `group_name` option to the [desired external forces](forces.md#common-options). If not set, all external forces will be considered. +## External force acting on particle(s) + +Print the force vector acting on all (or a subset of all) particles due to external forces. This observable supports the `update_every` option. + +* `type = external_force`: the observable type. +* `particles`: list of comma-separated particle indexes whose force vectors should be printed. + ## Configuration Print an [oxDNA configuration](configurations.md#configuration-file). diff --git a/index.html b/index.html index 7f147d0ea..fc1fbd32d 100644 --- a/index.html +++ b/index.html @@ -185,6 +185,7 @@

oxDNA
  • Interaction energy between pairs of particles
  • Stretched bonds
  • Energy associated to the external forces
    • +
  • External force acting on particle(s)
  • Configuration
  • Pressure
  • Stress autocorrelation
    • diff --git a/oat/api.html b/oat/api.html index a0b6c8f12..9bbc950f4 100644 --- a/oat/api.html +++ b/oat/api.html @@ -328,7 +328,7 @@

    Clustering

    oxDNA_analysis_tools.clustering.get_centroid

    -

    Takes the output from DBSCAN and produces the trajectory and centroid from each cluster.

    +

    Takes the output from DBSCAN and finds the centroid of each cluster.

    oxDNA_analysis_tools.clustering.perform_DBSCAN

    Use the DBSCAN algorithm to identify clusters of configurations based on a given order parameter.

    @@ -352,16 +352,16 @@

    Clustering
    -oxDNA_analysis_tools.clustering.get_centroid(points, metric_name, labs, traj_info, top_info) → List[int]
    -

    Takes the output from DBSCAN and produces the trajectory and centroid from each cluster.

    +oxDNA_analysis_tools.clustering.get_centroid(points: ndarray, metric_name: str, labs: ndarray, traj_info: TrajInfo, top_info: TopInfo) → List[int] +

    Takes the output from DBSCAN and finds the centroid of each cluster.

    Parameters:

    • points (numpy.array) – The points fed to the clstering algorithm.

      • -

    • metric_name (str) – The type of data the points represent.

      • +

    • metric_name (str) – The type of data the points represent (‘euclidean’ or ‘precomputed’).

    • labs (numpy.array) – The cluster each point belongs to.

    • traj_info (TrajInfo) – Trajectory metadata.

      • -

    • tpo_file (TopInfo) – Topology metadata.

      • +

    • top_info (TopInfo) – Topology metadata.

    @@ -369,17 +369,20 @@

    Clustering
    -oxDNA_analysis_tools.clustering.perform_DBSCAN(traj_info: TrajInfo, top_info: TopInfo, op: ndarray, metric: str, eps: float, min_samples: int)
    +oxDNA_analysis_tools.clustering.perform_DBSCAN(traj_info: TrajInfo, top_info: TopInfo, op: ndarray, metric: str, eps: float, min_samples: int, op_names: List[str] = [], no_traj: bool = False, interactive_plot: bool = False, min_clusters: int = -1) → ndarray

    Use the DBSCAN algorithm to identify clusters of configurations based on a given order parameter.

    Parameters:

    • traj_info (TrajInfo) – Information about the trajectory

    • top_info (TopInfo) – Information about the topology

      • -

    • op (np.ndarray) – The order parameter(s) to use

      • +

    • op (np.ndarray) – The order parameter(s) to use (shape = n_confs x n_op for metric=euclidean, n_confs x n_confs for metric=precomputed)

    • metric (str) – Either ‘euclidean’ or ‘precomputed’ for whether the distance needs to be calculated

    • eps (float) – The maximum distance between two points to be considered in the same neighborhood

    • min_samples (int) – The minimum number of points to be considered a neighborhood

      • +

    • no_traj (bool) – If True, skip splitting the trajectory (these are slow)

      • +

    • interactive_plot (bool) – If True, show plot interactivley instead of saving as an animation

      • +

    • min_clusters (int) – If less than min_clusters are found, return and don’t do further calculations

    diff --git a/oat/cli.html b/oat/cli.html index 07f4a3ece..98774712a 100644 --- a/oat/cli.html +++ b/oat/cli.html @@ -460,9 +460,10 @@

    Named Arguments

    Finds the ensemble of distances between any two particles in the system

    -
    usage: oat distance [-h] [-i input [input ...]] [-o output_file]
-                    [-f <histogram/trajectory/both>] [-d data_file]
-                    [-n names [names ...]] [-p num_cpus] [-c]
+
    usage: oat distance [-h]
+                    [-i input p1 p2 p1 p2...) [input p1 p2 (p1 p2... ...]]
+                    [-o output_file] [-f <histogram/trajectory/both>]
+                    [-d data_file] [-n names [names ...]] [-p num_cpus] [-c]
 
    
 
    
 
    
@@ -973,7 +974,7 @@ 
    Named Arguments
    
 
    Extracts parts of a structure into separate trajectories
    
 
    
-
    usage: oat subset_trajectory [-h] [-i index index] [-p num_cpus] [-f]
+
    usage: oat subset_trajectory [-h] [-i index outfile] [-p num_cpus] [-f]
                              trajectory topology
 
    
 
    
@@ -1008,7 +1009,9 @@ 
    Named Arguments
    
 
    superimposes one or more structures sharing a topology to a reference structure
    
 
    
-
    usage: oat superimpose [-h] [-i index_file] reference victims [victims ...]
+
    usage: oat superimpose [-h] [-i index_file]
+                       [-o output_names [output_names ...]]
+                       reference victims [victims ...]
 
    
 
    
 
    
@@ -1028,6 +1031,9 @@ 
    Named Arguments
      
 
    • traj_info (TrajInfo) – The trajectory info
      • 
 
    • top_info (TopInfo) – The topology info
      • 
-
    • ntopart (int) – The number of confs to read at a time
      • 
+
    • chunk_size (int) – The number of confs to read at a time.  Defaults to config.get_chunk_size()
      •
    Returns:
    diff --git a/observables.html b/observables.html index f713d7d89..368b98802 100644 --- a/observables.html +++ b/observables.html @@ -70,6 +70,7 @@
  • Interaction energy between pairs of particles
  • Stretched bonds
  • Energy associated to the external forces
    • +
  • External force acting on particle(s)
  • Configuration
  • Pressure
  • Stress autocorrelation
    • @@ -296,6 +297,14 @@

    Energy associated to the external forces[print_group = <string>]: limit the energy computation to the forces belonging to a specific group of forces. This can be set by adding a group_name option to the desired external forces. If not set, all external forces will be considered.

    +
    +

    External force acting on particle(s)

    +

    Print the force vector acting on all (or a subset of all) particles due to external forces. This observable supports the update_every option.

    +
      +

    • type = external_force: the observable type.

      • +

    • particles: list of comma-separated particle indexes whose force vectors should be printed.

      • +
    +

    Configuration

    Print an oxDNA configuration.

    diff --git a/searchindex.js b/searchindex.js index 3e03b3d1f..77d0e32de 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"docnames": ["configurations", "events", "ffs", "forces", "index", "input", "install", "oat/api", "oat/cli", "oat/forces", "oat/index", "oat/utils", "observables", "oxpy/extending/forces", "oxpy/extending/observables", "oxpy/index", "oxpy/modules/analysis", "oxpy/modules/core/core", "oxpy/modules/core/forces", "oxpy/modules/core/observables", "oxpy/modules/utils", "performance", "relaxation", "scaling", "umbrella_sampling", "usage"], "filenames": ["configurations.md", "events.md", "ffs.md", "forces.md", "index.md", "input.md", "install.md", "oat/api.md", "oat/cli.md", "oat/forces.md", "oat/index.md", "oat/utils.md", "observables.md", "oxpy/extending/forces.md", "oxpy/extending/observables.md", "oxpy/index.md", "oxpy/modules/analysis.md", "oxpy/modules/core/core.md", "oxpy/modules/core/forces.md", "oxpy/modules/core/observables.md", 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"oxDNA_analysis_tools.distance.min_image"]], "minify() (in module oxdna_analysis_tools.minify)": [[7, "oxDNA_analysis_tools.minify.minify"]], "multidimensional_scaling_mean() (in module oxdna_analysis_tools.multidimensional_scaling_mean)": [[7, "oxDNA_analysis_tools.multidimensional_scaling_mean.multidimensional_scaling_mean"]], "output() (in module oxdna_analysis_tools.deviations)": [[7, "oxDNA_analysis_tools.deviations.output"]], "output_bonds() (in module oxdna_analysis_tools.output_bonds)": [[7, "oxDNA_analysis_tools.output_bonds.output_bonds"]], "parse_dot_bracket() (in module oxdna_analysis_tools.db_to_force)": [[7, "oxDNA_analysis_tools.db_to_force.parse_dot_bracket"]], "pca() (in module oxdna_analysis_tools.pca)": [[7, "oxDNA_analysis_tools.pca.pca"]], "perform_dbscan() (in module oxdna_analysis_tools.clustering)": [[7, "oxDNA_analysis_tools.clustering.perform_DBSCAN"]], "persistence_length() (in module oxdna_analysis_tools.persistence_length)": [[7, "oxDNA_analysis_tools.persistence_length.persistence_length"]], "pos (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.pos"]], "set_chunk_size() (in module oxdna_analysis_tools.config)": [[7, "oxDNA_analysis_tools.config.set_chunk_size"]], "split_trajectory() (in module oxdna_analysis_tools.clustering)": [[7, "oxDNA_analysis_tools.clustering.split_trajectory"]], "start1 (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.start1"]], "start2 (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.start2"]], "subset() (in module oxdna_analysis_tools.subset_trajectory)": [[7, "oxDNA_analysis_tools.subset_trajectory.subset"]], "superimpose() (in module oxdna_analysis_tools.superimpose)": [[7, "oxDNA_analysis_tools.superimpose.superimpose"]], "svd_align() (in module oxdna_analysis_tools.align)": [[7, "oxDNA_analysis_tools.align.svd_align"]], "time (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.time"]], "vectorized_min_image() (in module oxdna_analysis_tools.distance)": [[7, "oxDNA_analysis_tools.distance.vectorized_min_image"]], "harmonic_trap() (in module oxdna_analysis_tools.external_force_utils.forces)": [[9, "oxDNA_analysis_tools.external_force_utils.forces.harmonic_trap"]], "mutual_trap() (in module oxdna_analysis_tools.external_force_utils.forces)": [[9, "oxDNA_analysis_tools.external_force_utils.forces.mutual_trap"]], "read_force_file() (in module oxdna_analysis_tools.external_force_utils.force_reader)": [[9, "oxDNA_analysis_tools.external_force_utils.force_reader.read_force_file"]], "repulsion_plane() (in module oxdna_analysis_tools.external_force_utils.forces)": [[9, "oxDNA_analysis_tools.external_force_utils.forces.repulsion_plane"]], "repulsion_sphere() (in module oxdna_analysis_tools.external_force_utils.forces)": 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module oxdna_analysis_tools.utils.ryereader)": [[11, "oxDNA_analysis_tools.UTILS.RyeReader.describe"]], "display_files() (in module oxdna_analysis_tools.utils.oxview)": [[11, "oxDNA_analysis_tools.UTILS.oxview.display_files"]], "energy (oxdna_analysis_tools.utils.data_structures.configuration attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Configuration.energy"]], "file_size (oxdna_analysis_tools.utils.data_structures.chunk attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Chunk.file_size"]], "fit_plane() (in module oxdna_analysis_tools.utils.geom)": [[11, "oxDNA_analysis_tools.UTILS.geom.fit_plane"]], "flro_patchy_conf() (in module oxdna_analysis_tools.utils.oxview)": [[11, "oxDNA_analysis_tools.UTILS.oxview.flro_patchy_conf"]], "from_path() (in module oxdna_analysis_tools.utils.oxview)": [[11, "oxDNA_analysis_tools.UTILS.oxview.from_path"]], "get_dna_axis() (in module oxdna_analysis_tools.utils.geom)": [[11, 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module": [[16, "the-analysis-module"]], "The core module": [[17, "the-core-module"]], "The core.forces module": [[18, "the-core-forces-module"]], "The core.observables module": [[19, "the-core-observables-module"]], "The utils module": [[20, "the-utils-module"]], "Improving performance": [[21, "improving-performance"]], "Molecular dynamics": [[21, "molecular-dynamics"]], "GPU simulations": [[21, "gpu-simulations"]], "Monte Carlo": [[21, "monte-carlo"]], "Relaxing initial configurations": [[22, "relaxing-initial-configurations"]], "First stage: Monte Carlo relaxation": [[22, "first-stage-monte-carlo-relaxation"]], "Second stage: molecular dynamics relaxation": [[22, "second-stage-molecular-dynamics-relaxation"]], "Efficient GPU usage": [[23, "efficient-gpu-usage"]], "Simulation performance on GPU classes": [[23, "simulation-performance-on-gpu-classes"]], "Increasing simulation throughput with multi-process service": [[23, "increasing-simulation-throughput-with-multi-process-service"]], "Umbrella sampling": [[24, "umbrella-sampling"]], "Setting the order parameters and weights": [[24, "setting-the-order-parameters-and-weights"]], "Data evaluation and estimation of the melting temperature": [[24, "data-evaluation-and-estimation-of-the-melting-temperature"]], "Usage": [[25, "usage"]], "DNAnalysis": [[25, "dnanalysis"]], "confGenerator": [[25, "confgenerator"]]}, "indexentries": {"duplex (class in oxdna_analysis_tools.duplex_finder)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex"]], "align() (in module oxdna_analysis_tools.align)": [[7, "oxDNA_analysis_tools.align.align"]], "align_positions() (in module oxdna_analysis_tools.pca)": [[7, "oxDNA_analysis_tools.pca.align_positions"]], "anm_parameterize() (in module oxdna_analysis_tools.anm_parameterize)": [[7, "oxDNA_analysis_tools.anm_parameterize.anm_parameterize"]], "axis (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.axis"]], "backbone_flexibility() (in module oxdna_analysis_tools.backbone_flexibility)": [[7, "oxDNA_analysis_tools.backbone_flexibility.backbone_flexibility"]], "bond_analysis() (in module oxdna_analysis_tools.bond_analysis)": [[7, "oxDNA_analysis_tools.bond_analysis.bond_analysis"]], "centroid() (in module oxdna_analysis_tools.centroid)": [[7, "oxDNA_analysis_tools.centroid.centroid"]], "check() (in module oxdna_analysis_tools.config)": [[7, "oxDNA_analysis_tools.config.check"]], "contact_map() (in module oxdna_analysis_tools.contact_map)": [[7, "oxDNA_analysis_tools.contact_map.contact_map"]], "db_to_forcelist() (in module oxdna_analysis_tools.db_to_force)": [[7, "oxDNA_analysis_tools.db_to_force.db_to_forcelist"]], "decimate() (in module oxdna_analysis_tools.decimate)": [[7, "oxDNA_analysis_tools.decimate.decimate"]], "deviations() (in module oxdna_analysis_tools.deviations)": [[7, "oxDNA_analysis_tools.deviations.deviations"]], "distance() (in module oxdna_analysis_tools.distance)": [[7, "oxDNA_analysis_tools.distance.distance"]], "distance_deviations() (in module oxdna_analysis_tools.multidimensional_scaling_mean)": [[7, "oxDNA_analysis_tools.multidimensional_scaling_mean.distance_deviations"]], "duplex_finder() (in module oxdna_analysis_tools.duplex_finder)": [[7, "oxDNA_analysis_tools.duplex_finder.duplex_finder"]], "end1 (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.end1"]], "end2 (oxdna_analysis_tools.duplex_finder.duplex attribute)": [[7, "oxDNA_analysis_tools.duplex_finder.Duplex.end2"]], "file_info() (in module oxdna_analysis_tools.file_info)": [[7, "oxDNA_analysis_tools.file_info.file_info"]], "find_duplex() (in module oxdna_analysis_tools.duplex_finder)": [[7, "oxDNA_analysis_tools.duplex_finder.find_duplex"]], "fit_pl() (in module oxdna_analysis_tools.persistence_length)": [[7, "oxDNA_analysis_tools.persistence_length.fit_PL"]], "get_angle_between() (in module 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"minify() (in module oxdna_analysis_tools.minify)": [[7, "oxDNA_analysis_tools.minify.minify"]], "multidimensional_scaling_mean() (in module oxdna_analysis_tools.multidimensional_scaling_mean)": [[7, "oxDNA_analysis_tools.multidimensional_scaling_mean.multidimensional_scaling_mean"]], "output() (in module oxdna_analysis_tools.deviations)": [[7, "oxDNA_analysis_tools.deviations.output"]], "output_bonds() (in module oxdna_analysis_tools.output_bonds)": [[7, "oxDNA_analysis_tools.output_bonds.output_bonds"]], "parse_dot_bracket() (in module oxdna_analysis_tools.db_to_force)": [[7, "oxDNA_analysis_tools.db_to_force.parse_dot_bracket"]], "pca() (in module oxdna_analysis_tools.pca)": [[7, "oxDNA_analysis_tools.pca.pca"]], "perform_dbscan() (in module oxdna_analysis_tools.clustering)": [[7, "oxDNA_analysis_tools.clustering.perform_DBSCAN"]], "persistence_length() (in module oxdna_analysis_tools.persistence_length)": [[7, "oxDNA_analysis_tools.persistence_length.persistence_length"]], "pos 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"oxDNA_analysis_tools.duplex_finder.Duplex.time"]], "vectorized_min_image() (in module oxdna_analysis_tools.distance)": [[7, "oxDNA_analysis_tools.distance.vectorized_min_image"]], "harmonic_trap() (in module oxdna_analysis_tools.external_force_utils.forces)": [[9, "oxDNA_analysis_tools.external_force_utils.forces.harmonic_trap"]], "mutual_trap() (in module oxdna_analysis_tools.external_force_utils.forces)": [[9, "oxDNA_analysis_tools.external_force_utils.forces.mutual_trap"]], "read_force_file() (in module oxdna_analysis_tools.external_force_utils.force_reader)": [[9, "oxDNA_analysis_tools.external_force_utils.force_reader.read_force_file"]], "repulsion_plane() (in module oxdna_analysis_tools.external_force_utils.forces)": [[9, "oxDNA_analysis_tools.external_force_utils.forces.repulsion_plane"]], "repulsion_sphere() (in module oxdna_analysis_tools.external_force_utils.forces)": [[9, "oxDNA_analysis_tools.external_force_utils.forces.repulsion_sphere"]], "rotating_harmonic_trap() (in 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"oxDNA_analysis_tools.UTILS.RyeReader.describe"]], "display_files() (in module oxdna_analysis_tools.utils.oxview)": [[11, "oxDNA_analysis_tools.UTILS.oxview.display_files"]], "energy (oxdna_analysis_tools.utils.data_structures.configuration attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Configuration.energy"]], "file_size (oxdna_analysis_tools.utils.data_structures.chunk attribute)": [[11, "oxDNA_analysis_tools.UTILS.data_structures.Chunk.file_size"]], "fit_plane() (in module oxdna_analysis_tools.utils.geom)": [[11, "oxDNA_analysis_tools.UTILS.geom.fit_plane"]], "flro_patchy_conf() (in module oxdna_analysis_tools.utils.oxview)": [[11, "oxDNA_analysis_tools.UTILS.oxview.flro_patchy_conf"]], "from_path() (in module oxdna_analysis_tools.utils.oxview)": [[11, "oxDNA_analysis_tools.UTILS.oxview.from_path"]], "get_dna_axis() (in module oxdna_analysis_tools.utils.geom)": [[11, "oxDNA_analysis_tools.UTILS.geom.get_DNA_axis"]], "get_rna_axis() (in module 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