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parameters.rs
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use feos_core::joback::JobackRecord;
use feos_core::parameter::{Parameter, PureRecord};
use ndarray::{Array, Array1, Array2};
use num_traits::Zero;
use serde::{Deserialize, Serialize};
use std::collections::HashMap;
use std::fmt::Write;
/// PeTS parameter set.
#[derive(Serialize, Deserialize, Debug, Clone, Default)]
pub struct PetsRecord {
/// Segment diameter in units of Angstrom
pub sigma: f64,
/// Energetic parameter in units of Kelvin
pub epsilon_k: f64,
/// Entropy scaling parameters for viscosity
#[serde(skip_serializing_if = "Option::is_none")]
pub viscosity: Option<[f64; 4]>,
/// Entropy scaling parameters for self-diffusion coefficient
#[serde(skip_serializing_if = "Option::is_none")]
pub diffusion: Option<[f64; 5]>,
/// Entropy scaling parameters for thermal conductivity
#[serde(skip_serializing_if = "Option::is_none")]
pub thermal_conductivity: Option<[f64; 4]>,
}
impl std::fmt::Display for PetsRecord {
fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
write!(f, "PetsRecord(sigma={}", self.sigma)?;
write!(f, ", epsilon_k={}", self.epsilon_k)?;
if let Some(n) = &self.viscosity {
write!(f, ", viscosity={:?}", n)?;
}
if let Some(n) = &self.diffusion {
write!(f, ", diffusion={:?}", n)?;
}
if let Some(n) = &self.thermal_conductivity {
write!(f, ", thermal_conductivity={:?}", n)?;
}
write!(f, ")")
}
}
impl PetsRecord {
pub fn new(
sigma: f64,
epsilon_k: f64,
viscosity: Option<[f64; 4]>,
diffusion: Option<[f64; 5]>,
thermal_conductivity: Option<[f64; 4]>,
) -> PetsRecord {
PetsRecord {
sigma,
epsilon_k,
viscosity,
diffusion,
thermal_conductivity,
}
}
}
#[derive(Serialize, Deserialize, Clone, Default, Debug)]
pub struct PetsBinaryRecord {
k_ij: f64,
}
impl From<f64> for PetsBinaryRecord {
fn from(k_ij: f64) -> Self {
Self { k_ij }
}
}
#[derive(Serialize, Deserialize, Debug, Clone, Default)]
pub struct PetsParameters {
pub molarweight: Array1<f64>,
pub sigma: Array1<f64>,
pub epsilon_k: Array1<f64>,
pub k_ij: Array2<f64>,
pub sigma_ij: Array2<f64>,
pub epsilon_k_ij: Array2<f64>,
pub e_k_ij: Array2<f64>,
pub viscosity: Option<Array2<f64>>,
pub diffusion: Option<Array2<f64>>,
pub thermal_conductivity: Option<Array2<f64>>,
pub pure_records: Vec<PureRecord<PetsRecord, JobackRecord>>,
pub joback_records: Option<Vec<JobackRecord>>,
pub binary_records: Array2<PetsBinaryRecord>,
}
impl Parameter for PetsParameters {
type Pure = PetsRecord;
type IdealGas = JobackRecord;
type Binary = PetsBinaryRecord;
fn from_records(
pure_records: Vec<PureRecord<Self::Pure, Self::IdealGas>>,
binary_records: Array2<PetsBinaryRecord>,
) -> Self {
let n = pure_records.len();
let mut molarweight = Array::zeros(n);
let mut sigma = Array::zeros(n);
let mut epsilon_k = Array::zeros(n);
let mut viscosity = Vec::with_capacity(n);
let mut diffusion = Vec::with_capacity(n);
let mut thermal_conductivity = Vec::with_capacity(n);
let mut component_index = HashMap::with_capacity(n);
for (i, record) in pure_records.iter().enumerate() {
component_index.insert(record.identifier.clone(), i);
let r = &record.model_record;
sigma[i] = r.sigma;
epsilon_k[i] = r.epsilon_k;
viscosity.push(r.viscosity);
diffusion.push(r.diffusion);
thermal_conductivity.push(r.thermal_conductivity);
molarweight[i] = record.molarweight;
}
let k_ij = binary_records.map(|br| br.k_ij);
let mut epsilon_k_ij = Array::zeros((n, n));
let mut sigma_ij = Array::zeros((n, n));
let mut e_k_ij = Array::zeros((n, n));
for i in 0..n {
for j in 0..n {
e_k_ij[[i, j]] = (epsilon_k[i] * epsilon_k[j]).sqrt();
epsilon_k_ij[[i, j]] = (1.0 - k_ij[[i, j]]) * e_k_ij[[i, j]];
sigma_ij[[i, j]] = 0.5 * (sigma[i] + sigma[j]);
}
}
let viscosity_coefficients = if viscosity.iter().any(|v| v.is_none()) {
None
} else {
let mut v = Array2::zeros((4, viscosity.len()));
for (i, vi) in viscosity.iter().enumerate() {
v.column_mut(i).assign(&Array1::from(vi.unwrap().to_vec()));
}
Some(v)
};
let diffusion_coefficients = if diffusion.iter().any(|v| v.is_none()) {
None
} else {
let mut v = Array2::zeros((5, diffusion.len()));
for (i, vi) in diffusion.iter().enumerate() {
v.column_mut(i).assign(&Array1::from(vi.unwrap().to_vec()));
}
Some(v)
};
let thermal_conductivity_coefficients = if thermal_conductivity.iter().any(|v| v.is_none())
{
None
} else {
let mut v = Array2::zeros((4, thermal_conductivity.len()));
for (i, vi) in thermal_conductivity.iter().enumerate() {
v.column_mut(i).assign(&Array1::from(vi.unwrap().to_vec()));
}
Some(v)
};
let joback_records = pure_records
.iter()
.map(|r| r.ideal_gas_record.clone())
.collect();
Self {
molarweight,
sigma,
epsilon_k,
k_ij,
sigma_ij,
epsilon_k_ij,
e_k_ij,
viscosity: viscosity_coefficients,
diffusion: diffusion_coefficients,
thermal_conductivity: thermal_conductivity_coefficients,
pure_records,
joback_records,
binary_records,
}
}
fn records(
&self,
) -> (
&[PureRecord<PetsRecord, JobackRecord>],
&Array2<PetsBinaryRecord>,
) {
(&self.pure_records, &self.binary_records)
}
}
impl PetsParameters {
pub fn to_markdown(&self) -> String {
let mut output = String::new();
let o = &mut output;
write!(
o,
"|component|molarweight|$\\sigma$|$\\varepsilon$|\n|-|-|-|-|"
)
.unwrap();
for i in 0..self.sigma.len() {
let component = self.pure_records[i].identifier.name.clone();
let component = component.unwrap_or(format!("Component {}", i + 1));
write!(
o,
"\n|{}|{}|{}|{}|",
component, self.molarweight[i], self.sigma[i], self.epsilon_k[i],
)
.unwrap();
}
output
}
}
impl std::fmt::Display for PetsParameters {
fn fmt(&self, f: &mut std::fmt::Formatter<'_>) -> std::fmt::Result {
write!(f, "PetsParameters(")?;
write!(f, "\n\tmolarweight={}", self.molarweight)?;
write!(f, "\n\tsigma={}", self.sigma)?;
write!(f, "\n\tepsilon_k={}", self.epsilon_k)?;
if !self.k_ij.iter().all(|k| k.is_zero()) {
write!(f, "\n\tk_ij=\n{}", self.k_ij)?;
}
write!(f, "\n)")
}
}
#[cfg(test)]
pub mod utils {
use super::*;
use feos_core::joback::JobackRecord;
use std::rc::Rc;
pub fn argon_parameters() -> Rc<PetsParameters> {
let argon_json = r#"
{
"identifier": {
"cas": "7440-37-1",
"name": "argon",
"iupac_name": "argon",
"smiles": "[Ar]",
"inchi": "InChI=1/Ar",
"formula": "Ar"
},
"model_record": {
"sigma": 3.4050,
"epsilon_k": 119.8,
"viscosity": [0.0, 0.0, 0.0, 0.0],
"thermal_conductivity": [0.0, 0.0, 0.0, 0.0],
"diffusion": [0.0, 0.0, 0.0, 0.0, 0.0]
},
"molarweight": 39.948
}"#;
let argon_record: PureRecord<PetsRecord, JobackRecord> =
serde_json::from_str(argon_json).expect("Unable to parse json.");
Rc::new(PetsParameters::new_pure(argon_record))
}
pub fn krypton_parameters() -> Rc<PetsParameters> {
let krypton_json = r#"
{
"identifier": {
"cas": "7439-90-9",
"name": "krypton",
"iupac_name": "krypton",
"smiles": "[Kr]",
"inchi": "InChI=1S/Kr",
"formula": "Kr"
},
"model_record": {
"sigma": 3.6300,
"epsilon_k": 163.10
},
"molarweight": 83.798
}"#;
let krypton_record: PureRecord<PetsRecord, JobackRecord> =
serde_json::from_str(krypton_json).expect("Unable to parse json.");
Rc::new(PetsParameters::new_pure(krypton_record))
}
pub fn argon_krypton_parameters() -> Rc<PetsParameters> {
let binary_json = r#"[
{
"identifier": {
"cas": "7440-37-1",
"name": "argon",
"iupac_name": "argon",
"smiles": "[Ar]",
"inchi": "1/Ar",
"formula": "Ar"
},
"model_record": {
"sigma": 3.4050,
"epsilon_k": 119.8,
"viscosity": [0.0, 0.0, 0.0, 0.0],
"thermal_conductivity": [0.0, 0.0, 0.0, 0.0],
"diffusion": [0.0, 0.0, 0.0, 0.0, 0.0]
},
"molarweight": 39.948
},
{
"identifier": {
"cas": "7439-90-9",
"name": "krypton",
"iupac_name": "krypton",
"smiles": "[Kr]",
"inchi": "InChI=1S/Kr",
"formula": "Kr"
},
"model_record": {
"sigma": 3.6300,
"epsilon_k": 163.10,
"viscosity": [0.0, 0.0, 0.0, 0.0],
"thermal_conductivity": [0.0, 0.0, 0.0, 0.0],
"diffusion": [0.0, 0.0, 0.0, 0.0, 0.0]
},
"molarweight": 83.798
}
]"#;
let binary_record: Vec<PureRecord<PetsRecord, JobackRecord>> =
serde_json::from_str(binary_json).expect("Unable to parse json.");
Rc::new(PetsParameters::new_binary(binary_record, None))
}
}