bio_files 0.5.1

Save and load common biology file formats
Documentation 
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185

//! [Self-Consistent-Field (SCF)](https://www.faccts.de/docs/orca/6.1/manual/contents/essentialelements/scf.html)

use super::make_inp_block;

/// [Convergence Tolerances](https://www.faccts.de/docs/orca/6.1/manual/contents/essentialelements/scf.html#convergence-tolerances)
#[derive(Clone, Copy, PartialEq, Debug, Default)]
pub enum ScfConvergenceTolerance {
    /// Between medium and strong
    #[default]
    None,
    Sloppy,
    Loose,
    Medium,
    Strong,
    Tight,
    VeryTight,
    Extreme,
}

impl ScfConvergenceTolerance {
    pub fn keyword(self) -> String {
        match self {
            Self::None => "",
            Self::Sloppy => "Sloppy",
            Self::Loose => "Loose",
            Self::Medium => "Medium",
            Self::Strong => "Strong",
            Self::Tight => "Tight",
            Self::VeryTight => "VeryTight",
            Self::Extreme => "Extreme",
        }
        .to_string()
    }
}

#[derive(Clone, Copy, PartialEq, Debug, Default)]
pub enum ScfMode {
    /// Direct is the ORCA default if not specified.
    #[default]
    Direct,
    Conventional,
}

impl ScfMode {
    pub fn keyword(self) -> String {
        match self {
            Self::Direct => "Direct",
            Self::Conventional => "Conventional",
        }
        .to_string()
    }
}

/// [Choice of Initial Guess](https://www.faccts.de/docs/orca/6.1/manual/contents/essentialelements/initialguess.html)
#[derive(Clone, Copy, PartialEq, Debug)]
pub enum ScfGuess {
    HCore,
    Hueckel,
    PAtom,
    PModel,
    MORead,
}

impl ScfGuess {
    pub fn keyword(self) -> String {
        match self {
            Self::HCore => "HCore",
            Self::Hueckel => "Hueckel",
            Self::PAtom => "PAtom",
            Self::PModel => "PModel",
            Self::MORead => "MORead",
        }
        .to_owned()
    }
}

/// [Choice of Initial Guess](https://www.faccts.de/docs/orca/6.1/manual/contents/essentialelements/initialguess.html)
#[derive(Clone, Copy, PartialEq, Debug)]
pub enum ScfGuessMode {
    FMatrix,
    CMatrix,
}

impl ScfGuessMode {
    pub fn keyword(self) -> String {
        match self {
            Self::FMatrix => "FMatrix",
            Self::CMatrix => "CMatrix",
        }
        .to_owned()
    }
}

/// [Wavefunction Types](https://www.faccts.de/docs/orca/6.1/manual/contents/modelchemistries/hftype.html#wavefunction-types-rhf-rks-uhf-uks-roks-and-more)
#[derive(Clone, Copy, PartialEq, Debug)]
// todo: Add more config releatd to this A/R. Maybe wrapped variants.
pub enum WaveFunctionType {
    /// closed-shell (RKS for DFT)
    Rhf,
    /// unrestricted open-shell (UKS for DFT)
    Uhf,
    /// restricted open-shell (ROKS for DFT)
    Rohf,
    /// complete active space SCF
    Casscf,
}

impl WaveFunctionType {
    pub fn keyword(self) -> String {
        match self {
            Self::Rhf => "RHF",
            Self::Uhf => "UHF",
            Self::Rohf => "ROHF",
            Self::Casscf => "CASSCF",
        }
        .to_string()
    }
}

/// [Self-Consistent-Field](https://www.faccts.de/docs/orca/6.1/manual/contents/essentialelements/scf.html)
/// [Integral  Handling](ttps://www.faccts.de/docs/orca/6.1/manual/contents/essentialelements/integralhandling.html)
#[derive(Clone, Debug)]
pub struct Scf {
    // todo: Damping, level shifting etc. Lots more features to implement
    pub convergence_tolerance: ScfConvergenceTolerance,
    pub mode: ScfMode,
    pub wave_function_type: Option<WaveFunctionType>,
    pub thresh: Option<f32>,
    pub t_cut: Option<f32>,
    pub direct_reset_freq: Option<u16>,
    pub max_disk: Option<u16>,
    pub max_int_mem: Option<u16>,
    /// [Dipolar Electric Fields](https://www.faccts.de/docs/orca/6.1/manual/contents/essentialelements/finEfield.html#dipolar-electric-fields)
    pub e_field: Option<[f32; 3]>,
    /// [Quadrupolar Electric Fields](https://www.faccts.de/docs/orca/6.1/manual/contents/essentialelements/finEfield.html#quadrupolar-electric-fields)
    pub q_field: Option<[f32; 6]>, // todo: Allow custom values. See https://www.faccts.de/docs/orca/6.1/manual/contents/essentialelements/scf.html Table 2.9
    pub guess: Option<ScfGuess>,
    pub guess_mode: Option<ScfGuessMode>,
}

impl Scf {
    pub fn make_inp(&self) -> String {
        let mut contents = vec![
            ("Convergence", self.convergence_tolerance.keyword()),
            ("SCFMode", self.mode.keyword()),
        ];

        if let Some(v) = self.wave_function_type {
            contents.push(("HFType", v.keyword()));
        }

        if let Some(v) = self.thresh {
            contents.push(("Thresh", format!("{v:.6}")));
        }
        if let Some(v) = self.t_cut {
            contents.push(("TCut", format!("{v:.6}")));
        }
        if let Some(v) = self.thresh {
            contents.push(("Thresh", format!("{v}")));
        }
        if let Some(v) = self.max_disk {
            contents.push(("MaxDisk", format!("{v}")));
        }
        if let Some(v) = self.max_int_mem {
            contents.push(("MaxIntMem", format!("{v}")));
        }
        if let Some([x, y, z]) = self.e_field {
            contents.push(("EField", format!("{x:.6} {y:.6} {z:.6}")))
        }
        if let Some([xx, yy, zz, xy, xz, yz]) = self.q_field {
            contents.push((
                "QField",
                format!("{xx:.6} {yy:.6} {zz:.6} {xy:.6} {xz:.6} {yz:.6}"),
            ))
        }
        if let Some(v) = self.guess {
            contents.push(("Guess", v.keyword()));
        }
        if let Some(v) = self.guess_mode {
            contents.push(("GuessMode", v.keyword()));
        }

        make_inp_block("scf", &contents, &[])
    }
}