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
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
//! The clap command tree for the CLI.
use clap::Subcommand;
use crate::analysis_commands::AnalysisAction;
use crate::ff_commands::FfAction;
use crate::format::StructureFormat;
use crate::mof_commands::MofAction;
use crate::powder_commands::PowderAction;
use crate::spacegroup;
use crate::symmetry::SymmetryAction;
use crate::build_structures;
#[derive(Debug, Subcommand)]
pub(crate) enum ProjectAction {
/// Pack a structure into a `.xtalproj` archive.
Pack {
/// Input structure path.
path: String,
/// Output archive path.
out: String,
},
/// Print the parts of a project archive.
Info {
/// Archive path.
path: String,
},
/// Extract a project into a directory.
Extract {
/// Archive path.
path: String,
/// Destination directory.
dir: String,
},
}
#[derive(Debug, Subcommand)]
pub(crate) enum Command {
/// Print the xtalforge version.
Version,
/// Add the hydrogens an X-ray structure is missing.
Hydrogens {
/// Input path, or `-` for standard input.
path: String,
/// X-H distance in Angstrom.
#[arg(long, default_value_t = 1.09)]
distance: f64,
/// Output path; defaults to standard output.
#[arg(long, value_name = "PATH")]
out: Option<String>,
/// Output format; defaults to the output extension or CIF.
#[arg(long, value_enum)]
format: Option<StructureFormat>,
},
/// Powder refinement: indexing, Le Bail/Pawley, Rietveld and cells.
Powder {
#[command(subcommand)]
action: PowderAction,
},
/// MOF topologies, blocks and framework assembly.
Mof {
#[command(subcommand)]
action: MofAction,
},
/// Porosity, nets and Zeo++ analysis.
Analysis {
#[command(subcommand)]
action: AnalysisAction,
},
/// Force-field energies, optimizers, charges and vibrations.
Ff {
#[command(subcommand)]
action: FfAction,
},
/// List the format registry.
Formats,
/// List parameter presets or print one schema.
Params {
/// Preset name; omit to list the presets.
name: Option<String>,
},
/// Pack, inspect or extract a project archive.
Project {
#[command(subcommand)]
action: ProjectAction,
},
/// Inspect or convert a multi-frame trajectory.
Trajectory {
/// Input path, or `-` for standard input.
path: String,
/// Frame index to write as a structure.
#[arg(long)]
frame: Option<usize>,
/// Output path; defaults to standard output.
#[arg(long, value_name = "PATH")]
out: Option<String>,
/// Output format; defaults to the output extension or CIF.
#[arg(long, value_enum)]
format: Option<StructureFormat>,
},
/// Apply a JSON command list to a structure.
Script {
/// Script path.
path: String,
},
/// Print reference data for an element.
Element {
/// Element symbol or atomic number.
input: String,
},
/// Print a summary of a structure or structure JSON document.
Info {
/// Input path, or `-` for standard input.
path: String,
},
/// Build a cell from its six parameters.
Cell {
/// a, b, c in Angstrom and alpha, beta, gamma in degrees.
#[arg(long, num_args = 6, value_names = ["a", "b", "c", "alpha", "beta", "gamma"])]
params: Vec<f64>,
},
/// Compute the volume of a cell from its six parameters.
CellVolume {
/// Cell length a in Angstrom.
a: f64,
/// Cell length b in Angstrom.
b: f64,
/// Cell length c in Angstrom.
c: f64,
/// Angle alpha in degrees.
alpha: f64,
/// Angle beta in degrees.
beta: f64,
/// Angle gamma in degrees.
gamma: f64,
},
/// Convert a structure between CIF, POSCAR and XYZ.
Convert {
/// Input path, or `-` for standard input.
path: String,
/// Output format.
#[arg(long, value_enum)]
format: StructureFormat,
/// Output path, or `-` for standard output.
#[arg(long, value_name = "PATH")]
out: Option<String>,
},
/// Calculate a PXRD pattern.
Pxrd {
/// Input path, or `-` for standard input.
path: String,
/// Radiation: cu-ka, cu-ka1, mo-ka, co-ka, fe-ka, cr-ka or ag-ka.
#[arg(long, default_value = "cu-ka")]
radiation: String,
/// Highest 2-theta in degrees.
#[arg(long, default_value_t = 80.0)]
max_two_theta: f64,
/// Step in degrees.
#[arg(long, default_value_t = 0.02)]
step: f64,
/// Output path; defaults to standard output.
#[arg(long, value_name = "PATH")]
out: Option<String>,
},
/// Build graphene or a nanotube.
Build {
#[command(subcommand)]
action: build_structures::BuildAction,
},
/// Build a printable STL mesh.
Mesh {
/// Input path, or `-` for standard input.
path: String,
/// Draw style: ball-stick, space-fill, wireframe or sticks.
#[arg(long, default_value = "ball-stick")]
style: String,
/// Atom radius multiplier.
#[arg(long, default_value_t = 1.0)]
scale: f64,
/// Output path; defaults to standard output.
#[arg(long, value_name = "PATH")]
out: Option<String>,
},
/// Build an na x nb x nc supercell.
Supercell {
/// Input path, or `-` for standard input.
path: String,
/// Repeats along a.
na: u32,
/// Repeats along b.
nb: u32,
/// Repeats along c.
nc: u32,
/// Output path; defaults to standard output.
#[arg(long, value_name = "PATH")]
out: Option<String>,
/// Output format; defaults to the output extension or CIF.
#[arg(long, value_enum)]
format: Option<StructureFormat>,
},
/// Cut a slab along the (h k l) plane.
Slab {
/// Input path, or `-` for standard input.
path: String,
/// First Miller index.
h: i32,
/// Second Miller index.
k: i32,
/// Third Miller index.
l: i32,
/// Number of layers.
#[arg(long, value_name = "N")]
layers: u32,
/// Vacuum above the slab in Angstrom.
#[arg(long, value_name = "A")]
vacuum: f64,
/// Output path; defaults to standard output.
#[arg(long, value_name = "PATH")]
out: Option<String>,
/// Output format; defaults to the output extension or CIF.
#[arg(long, value_enum)]
format: Option<StructureFormat>,
},
/// List the perceived bonds of the P1 cell.
Bonds {
/// Input path, or `-` for standard input.
path: String,
},
/// List the chordless rings of the P1 cell.
Rings {
/// Input path, or `-` for standard input.
path: String,
/// Largest ring size in atoms.
#[arg(long, value_name = "N", default_value_t = 6)]
max_size: usize,
},
/// List the matched functional groups.
Groups {
/// Input path, or `-` for standard input.
path: String,
},
/// List the periodic neighbors within a cutoff.
Neighbors {
/// Input path, or `-` for standard input.
path: String,
/// Cutoff radius in Angstrom.
#[arg(long, value_name = "A")]
cutoff: f64,
},
/// Minimum-image distance between two P1 atoms.
Distance {
/// Input path, or `-` for standard input.
path: String,
/// First atom index.
i: usize,
/// Second atom index.
j: usize,
},
/// Angle i-j-k in degrees.
Angle {
/// Input path, or `-` for standard input.
path: String,
/// First atom index.
i: usize,
/// Pivot atom index.
j: usize,
/// Third atom index.
k: usize,
},
/// Browse the space-group catalogue.
Spacegroup {
#[command(subcommand)]
action: spacegroup::SpacegroupAction,
},
/// Detect the space group and Wyckoff positions.
Symmetry {
#[command(subcommand)]
action: SymmetryAction,
},
/// Torsion i-j-k-l in degrees.
Torsion {
/// Input path, or `-` for standard input.
path: String,
/// First atom index.
i: usize,
/// Second atom index.
j: usize,
/// Third atom index.
k: usize,
/// Fourth atom index.
l: usize,
},
}