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working! want to clean up a bit, though

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This commit is contained in:
William Ball 2021-08-06 22:59:39 -04:00
parent 2c0a38ec9e
commit 8294f1c183
5 changed files with 122 additions and 121 deletions
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35
fractal_dimension/circle_counting_new/data/cube.txt
View file

@ -1,30 +1,9 @@
{{{1, 0, 0, 0, 0, 0, 0, 0}, {0, 1, 0, 0, 0, 0, 0, 0}, {2, 1, 0, 0, 0, 3, -1,
0}, {3, 0, 0, 0, 0, 3, -1, 0}, {1, -1, 0, 0, 0, 1, 0, 0}, {0, 0, 0, 0, 0, 1, 0,
0}, {2, 0, 0, 0, 0, 4, -1, 0}, {3, -1, 0, 0, 0, 4, -1, 0}}, {{1, 0, 0, 0, 0, 0,
0, 0}, {0, 1, 0, 0, 0, 0, 0, 0}, {0, 0, 1, 0, 0, 0, 0, 0}, {1, -1, 1, 0, 0, 0,
0, 0}, {3, 1, 2, 0, 0, -1, 0, 0}, {2, 2, 2, 0, 0, -1, 0, 0}, {2, 1, 3, 0, 0,
-1, 0, 0}, {3, 0, 3, 0, 0, -1, 0, 0}}, {{1, 0, 0, 0, 0, 0, 0, 0}, {3, 0, 0, 0,
0, 0, -1, 3}, {2, 0, 0, 1, 0, 0, -1, 3}, {0, 0, 0, 1, 0, 0, 0, 0}, {1, 0, 0,
-1, 0, 0, 0, 1}, {3, 0, 0, -1, 0, 0, -1, 4}, {2, 0, 0, 0, 0, 0, -1, 4}, {0, 0,
0, 0, 0, 0, 0, 1}}, {{-1, 4, 0, 0, 0, 0, 2, 0}, {0, 1, 0, 0, 0, 0, 0, 0}, {0,
1, 0, 0, 0, -1, 1, 0}, {-1, 4, 0, 0, 0, -1, 3, 0}, {-1, 3, 0, 0, 0, 1, 2, 0},
{0, 0, 0, 0, 0, 1, 0, 0}, {0, 0, 0, 0, 0, 0, 1, 0}, {-1, 3, 0, 0, 0, 0, 3, 0}},
{{0, 0, 0, 3, 0, -1, 3, 0}, {0, 0, 0, 3, 0, -1, 4, -1}, {0, 0, 0, 1, 0, 0, 1,
-1}, {0, 0, 0, 1, 0, 0, 0, 0}, {0, 0, 0, 2, 0, -1, 3, 1}, {0, 0, 0, 2, 0, -1,
4, 0}, {0, 0, 0, 0, 0, 0, 1, 0}, {0, 0, 0, 0, 0, 0, 0, 1}}, {{0, 0, 0, -1, 0,
3, -1, 4}, {0, 0, 0, -1, 0, 3, 0, 3}, {0, 0, 0, -1, 0, 2, 1, 3}, {0, 0, 0, -1,
0, 2, 0, 4}, {0, 0, 0, 0, 0, 1, -1, 1}, {0, 0, 0, 0, 0, 1, 0, 0}, {0, 0, 0, 0,
0, 0, 1, 0}, {0, 0, 0, 0, 0, 0, 0, 1}}}
{{0., 8.485281374238571, -1., 0.}, {0., -2.8284271247461903,
1., 0.}, {1.4142135623730951, 18.38477631085024, -5.,
1.4142135623730951}, {1.4142135623730951,
7.0710678118654755, -3.,
1.4142135623730951}, {1.4142135623730951,
18.38477631085024, -5., -1.4142135623730951},
{1.4142135623730951,
7.0710678118654755, -3., -1.4142135623730951},
{2.8284271247461903, 16.970562748477143, -7.,
0.}, {2.8284271247461903, 28.284271247461902, -9., 0.}}
{{1, -1, -3, -1, -1, -3, -5, -3}, {-1,
1, -1, -3, -3, -1, -3, -5}, {-3, -1,
1, -1, -5, -3, -1, -3}, {-1, -3, -1,
1, -3, -5, -3, -1}, {-1, -3, -5, -3,
1, -1, -3, -1}, {-3, -1, -3, -5, -1,
1, -1, -3}, {-5, -3, -1, -3, -3, -1,
1, -1}, {-3, -5, -3, -1, -1, -3, -1, 1}}
{{0, 1, 5, 4}, {0, 3, 2, 1}, {0, 4, 7, 3}, {1, 2, 6, 5}, {2, 3, 7, 6}, {4, 5, 6, 7}}

29
fractal_dimension/circle_counting_new/data/octahedron.txt
View file

@ -1,28 +1,5 @@
{{{1., 0., 0., 0., 0., 0.}, {0., 1., 0., 0., 0., 0.}, {4., 3., 0.,
3., -1., 0.}, {0., 0., 0., 1., 0., 0.}, {4., 2., 0., 4., -1.,
0.}, {3., 3., 0., 4., -1., 0.}}, {{1., 0., 0., 0., 0., 0.}, {0.,
1., 0., 0., 0., 0.}, {0., 0., 1., 0., 0., 0.}, {3., 4., 3., 0.,
0., -1.}, {3., 3., 4., 0., 0., -1.}, {2., 4., 4., 0.,
0., -1.}}, {{1., 0., 0., 0., 0., 0.}, {3., 0., 0., 4.,
3., -1.}, {3., 0., 0., 3., 4., -1.}, {0., 0., 0., 1., 0., 0.}, {0.,
0., 0., 0., 1., 0.}, {2., 0., 0., 4., 4., -1.}}, {{1., 0., 0., 0.,
0., 0.}, {3., 0., 4., 0., 3., -1.}, {0., 0., 1., 0., 0., 0.}, {3.,
0., 3., 0., 4., -1.}, {0., 0., 0., 0., 1., 0.}, {2., 0., 4., 0.,
4., -1.}}, {{-1., 4., 4., 0., 0., 2.}, {0., 1., 0., 0., 0.,
0.}, {0., 0., 1., 0., 0., 0.}, {-1., 4., 3., 0., 0., 3.}, {-1., 3.,
4., 0., 0., 3.}, {0., 0., 0., 0., 0., 1.}}, {{0., 3., 0., 4., -1.,
3.}, {0., 1., 0., 0., 0., 0.}, {0., 3., 0., 3., -1., 4.}, {0., 0.,
0., 1., 0., 0.}, {0., 2., 0., 4., -1., 4.}, {0., 0., 0., 0., 0.,
1.}}, {{-1., 0., 4., 0., 4., 2.}, {-1., 0., 4., 0., 3., 3.}, {0.,
0., 1., 0., 0., 0.}, {-1., 0., 3., 0., 4., 3.}, {0., 0., 0., 0.,
1., 0.}, {0., 0., 0., 0., 0., 1.}}, {{0., 0., -1., 3., 4.,
3.}, {0., 0., -1., 3., 3., 4.}, {0., 0., -1., 2., 4., 4.}, {0., 0.,
0., 1., 0., 0.}, {0., 0., 0., 0., 1., 0.}, {0., 0., 0., 0., 0.,
1.}}}
{{10., 8., -5.656854249492381, 7.}, {24.,
24., -16.970562748477143, 17.}, {8., 10., -5.656854249492381,
7.}, {12., 10., -8.485281374238571, 7.}, {-4., -4.,
2.8284271247461903, -3.}, {10., 12., -8.485281374238571, 7.}}
{{1, -1, -1, -1, -1, -3}, {-1, 1, -1, -1, -3, -1}, {-1, -1,
1, -3, -1, -1}, {-1, -1, -3, 1, -1, -1}, {-1, -3, -1, -1,
1, -1}, {-3, -1, -1, -1, -1, 1}}
{{0, 1, 3}, {0, 2, 1}, {0, 3, 4}, {0, 4, 2}, {1, 2, 5}, {1, 5, 3}, {2, 4, 5}, {3, 5, 4}}

13
fractal_dimension/circle_counting_new/data/tetrahedron.txt
View file

@ -1,9 +1,8 @@
{{{1., 0., 0., 0.}, {0., 1., 0., 0.}, {2., 2., -1., 2.}, {0., 0., 0.,
1.}}, {{1., 0., 0., 0.}, {0., 1., 0., 0.}, {0., 0., 1., 0.}, {2.,
2., 2., -1.}}, {{1., 0., 0., 0.}, {2., -1., 2., 2.}, {0., 0., 1.,
0.}, {0., 0., 0., 1.}}, {{-1., 2., 2., 2.}, {0., 1., 0., 0.}, {0.,
0., 1., 0.}, {0., 0., 0., 1.}}}
{{6., 4., -4., 3.}, {4., 4., -4., 1.}, {4., 6., -4., 3.}, {-2., -2., 2., -1.}}
{
{1.0, -1.0, -1.0, -1.0},
{-1.0, 1.0, -1.0, -1.0},
{-1.0, -1.0, 1.0, -1.0},
{-1.0, -1.0, -1.0, 1.0},
}
{{1, 2, 3}, {0, 2, 3}, {0, 1, 3}, {0, 1, 2}}

135
fractal_dimension/circle_counting_new/src/main.rs
View file

@ -1,6 +1,11 @@
#![allow(dead_code)]
use crate::{fractal::fractal_dimension, parser::read_file};
use crate::{
fractal::fractal_dimension,
gram_matrix::{algebraic_generators, geometric_generators, root_tuple},
parser::read_file,
};
use nalgebra::DVector;
use std::process;
use structopt::StructOpt;
@ -8,9 +13,9 @@ use ansi_term::Color::Yellow;
pub mod constants;
pub mod fractal;
pub mod gram_matrix;
pub mod parser;
pub mod search;
pub mod gram_matrix;
/// Compute fractal dimension of crystallographic packings via the circle counting method
#[derive(StructOpt)]
@ -53,11 +58,10 @@ fn main() {
let beginning = std::time::Instant::now();
let (mut generators, root, faces, orthogonal_generators) = read_file(&opt.data_file)
.unwrap_or_else(|err| {
eprintln!("{}", err);
process::exit(-1);
});
let (gram_matrix, faces) = read_file(&opt.data_file).unwrap_or_else(|err| {
eprintln!("{}", err);
process::exit(-1);
});
let after_parsing = std::time::Instant::now();
if time {
@ -82,52 +86,109 @@ fn main() {
);
}
if !opt.geometric {
let c = nalgebra::DMatrix::from_columns(&root);
let ct = c
.clone()
.pseudo_inverse(1e-5)
.expect(format!("Invalid root matrix {}", c).as_str());
println!("{}", c);
println!("{}", ct);
generators = generators
.iter()
.map(|sigma| &c * sigma.transpose() * &ct)
.collect();
}
if debug {
println!(
"{} (parsed from file {})",
Yellow.paint("Generators"),
opt.data_file
);
for generator in &generators {
println!("{}", generator);
}
println!(
"{} (parsed from file {}):",
Yellow.paint("Root Tuple"),
Yellow.paint("Gram Matrix"),
opt.data_file
);
for circle in &root {
println!("{}", circle);
}
println!("{}\n", gram_matrix);
println!(
"{} (parsed from file {}):",
Yellow.paint("Faces"),
opt.data_file
);
println!("{:?}\n", faces);
println!(
/* println!(
"{} (parsed from file {}):",
Yellow.paint("Orthogonal Generators"),
opt.data_file
);
println!("{:?}\n", orthogonal_generators);
println!("{:?}\n", orthogonal_generators); */
}
// finding a suitable root tuple
let mut root = None;
for face in faces.iter().skip(1) {
for vertex in face {
let mut valid = true;
for vertex2 in &faces[0] {
if *vertex == *vertex2 {
valid = false;
break;
}
}
if valid {
let temp = root_tuple(
&gram_matrix,
(faces[0][0], faces[0][1], faces[0][2]),
*vertex,
);
let mut valid = true;
let generators = geometric_generators(&gram_matrix, &faces, &temp);
for gen in generators {
if gen[(1, 0)].abs() <= 1e-8 {
valid = false;
break;
}
}
if valid {
root = Some(temp);
println!("{}\t{:?}", vertex, faces[0]);
break;
}
}
}
if root.is_some() {
break;
}
}
if root.is_none() {
panic!("Invalid face scheme!");
}
let root = root.unwrap();
let generators = geometric_generators(&gram_matrix, &faces, &root);
if debug {
println!(
"{} (computed using gram_matrix):",
Yellow.paint("Root Matrix")
);
println!("{}", root);
println!(
"{} (computed using gram_matrix and root):",
Yellow.paint("Geometric generators")
);
for generator in &generators {
println!("{}", generator);
}
let generators = algebraic_generators(&gram_matrix, &faces);
println!(
"{} (computed using gram_matrix and root):",
Yellow.paint("Algebraic generators")
);
for generator in &generators {
println!("{}", generator);
}
}
let mut temp = vec![];
for circle in root.column_iter() {
temp.push(DVector::from_iterator(
4,
circle.iter().map(|val| val.clone()),
));
}
let root = temp;
let delta = fractal_dimension(
generators,
root,
@ -136,7 +197,7 @@ fn main() {
debug,
depth,
faces,
orthogonal_generators,
vec![],
)
.unwrap();
let after_computing = std::time::Instant::now();

31
fractal_dimension/circle_counting_new/src/parser.rs
View file

@ -1,6 +1,6 @@
use std::fs;
use nalgebra::{DMatrix, DVector};
use nalgebra::DMatrix;
use ansi_term::Color::Red;
#[derive(Debug, PartialEq)]
@ -213,11 +213,9 @@ fn matrix_to_rust_value_flat(value: &Value) -> Result<Vec<f64>, String> {
Ok(result)
}
pub type Generator = DMatrix<f64>;
pub type Root = Vec<DVector<f64>>;
pub type Matrix = DMatrix<f64>;
pub type FaceList = Vec<Vec<usize>>;
pub type OrthogonalGenerators = Vec<Vec<usize>>;
pub type Data = (Vec<Generator>, Root, FaceList, OrthogonalGenerators);
pub type Data = (Matrix, FaceList);
pub fn read_file(filename: &str) -> Result<Data, String> {
let contents = match fs::read_to_string(filename) {
Ok(contents) => contents,
@ -226,28 +224,16 @@ pub fn read_file(filename: &str) -> Result<Data, String> {
let results = eval_full(contents)?;
let mut generators = vec![];
if let Value::List(gens) = &results[0] {
for val in gens {
let mat = matrix_to_rust_value(val)?;
let mat2 = matrix_to_rust_value_flat(val)?;
generators.push(DMatrix::from_row_slice(mat.len(), mat[0].len(), &mat2));
}
} else {
return Err(format!(
"Expected first value in file to be the generators; got {:?}",
results[0]
));
}
let n = matrix_to_rust_value(&results[0])?.len();
let gram_matrix = DMatrix::from_row_slice(n, n, &matrix_to_rust_value_flat(&results[0])?);
let root = matrix_to_rust_value(&results[1])?;
let faces = matrix_to_rust_value(&results[2])?;
let faces = matrix_to_rust_value(&results[1])?;
let faces = faces
.iter()
.map(|v| v.iter().map(|x| x.round() as usize).collect())
.collect();
let orthogonal_generators: Vec<Vec<usize>> = if results.len() < 4 {
let orthogonal_generators: Vec<Vec<usize>> = if results.len() < 3 {
vec![]
} else {
matrix_to_rust_value(&results[3])?
@ -263,8 +249,7 @@ pub fn read_file(filename: &str) -> Result<Data, String> {
}
}
let new_root = root.iter().map(|circ| DVector::from_column_slice(circ)).collect();
Ok((generators, new_root, faces, orthogonal_generators))
Ok((gram_matrix, faces))
}
#[cfg(test)]