ppap4lmp  0.7.2
pro_radial_distribution_function.h
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1 
9 #ifndef PRO_RADIAL_DISTRIBUTION_FUNCTION_H
10 #define PRO_RADIAL_DISTRIBUTION_FUNCTION_H
11 
12 #include <processors/processor.h>
13 
37 class ProRadialDistributionFunction : public Processor {
38  protected:
45  int n_bins = 1;
52  double bin_width = 1.0;
59  bool bin_from_r = false;
68  bool beyond_half = false;
72  ArrayXd rdf;
77  Vec<ArrayXd> rdf_traj;
82  Vec<int> number_traj;
87  Vec<double> volume_traj;
94  Vec<ArrayXi> counts_traj;
101  virtual void run_impl(
102  const int index) override;
103  public:
152  ProRadialDistributionFunction(
153  const ElPtr &targets,
154  const ElPtr &box);
201  ProRadialDistributionFunction(
202  const Vec<std::pair<ElPtr,ElPtr>> &pairs);
203  virtual ~ProRadialDistributionFunction() = default;
208  virtual void prepare() override;
219  virtual void finish() override;
239  void set_bin(
240  double bin_width_,
241  int n_bins_);
257  void bin_from_r_to_r_plus_dr(
258  bool bin_from_r_ = true);
273  void beyond_half_box_length(
274  bool beyond_half_ = true);
281  const ArrayXd get_r_axis();
288  const ArrayXd &get_rdf();
295  const Vec<ArrayXd> &get_rdf_traj();
296 };
297 
298 #endif
ProRadialDistributionFunction::get_rdf_traj
const Vec< ArrayXd > & get_rdf_traj()
Get a sequence of radial distribution functions as list of one-dimensional arrays.
Definition: pro_radial_distribution_function.cpp:275
ElPtr
ShPtr< Element > ElPtr
An alias for a shared pointer of Element class.
Definition: element.h:378
ProRadialDistributionFunction::run_impl
virtual void run_impl(const int index) override
Implementation of analysis using an element of generators.
Definition: pro_radial_distribution_function.cpp:46
ProRadialDistributionFunction::ProRadialDistributionFunction
ProRadialDistributionFunction(const ElPtr &targets, const ElPtr &box)
Constructor of ProRadialDistributionFunction class for a snapshot of simulation.
Definition: pro_radial_distribution_function.cpp:20
ProRadialDistributionFunction::finish
virtual void finish() override
Compute rdf and rdf_traj from number_traj, volume_traj and counts_traj.
Definition: pro_radial_distribution_function.cpp:172
ProRadialDistributionFunction::get_rdf
const ArrayXd & get_rdf()
Get the radial distribution function as a one-dimensional array.
Definition: pro_radial_distribution_function.cpp:268
ProRadialDistributionFunction::bin_from_r_to_r_plus_dr
void bin_from_r_to_r_plus_dr(bool bin_from_r_=true)
By default, the bins are [0, 0.5*dr), [0.5*dr, 1.5*dr), ... . If this method is called without a para...
Definition: pro_radial_distribution_function.cpp:238
Vec
std::vector< T > Vec
Vec is an alias for vector (same as list in Python).
Definition: std.h:27
ProRadialDistributionFunction::prepare
virtual void prepare() override
Resize number_traj, volume_traj and counts_traj.
Definition: pro_radial_distribution_function.cpp:163
ProRadialDistributionFunction::get_r_axis
const ArrayXd get_r_axis()
Get a one-dimensional array of distance, [0, dr, 2*dr, ... ], where dr is width of a bin...
Definition: pro_radial_distribution_function.cpp:254
processor.h
This file has a definition of Processor class, where an analysis process is programmed.
Processor
Processor analyzes data contained in one or more Generator objects.
Definition: processor.h:18
ProRadialDistributionFunction
ProRadialDistributionFunction computes radial distribution function (RDF).
Definition: pro_radial_distribution_function.h:37
ProRadialDistributionFunction::beyond_half_box_length
void beyond_half_box_length(bool beyond_half_=true)
Use a sample including particles of which distance from a reference particle are larger than half the...
Definition: pro_radial_distribution_function.cpp:246
ArrayXd
Eigen::Array< double, Eigen::Dynamic, 1 > ArrayXd
ArrayXd is an alias for a column array of float numbers.
Definition: eigen.h:42
ProRadialDistributionFunction::set_bin
void set_bin(double bin_width_, int n_bins_)
Set width and number of bins in the distance axis. Each bin is a spherical shell of which center is p...
Definition: pro_radial_distribution_function.cpp:228