readcon-core 0.14.2

An oxidized single and multiple CON file reader and writer with FFI bindings for ergonomic C/C++ usage.
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

{
  "$schema": "https://json-schema.org/draft/2020-12/schema",
  "$id": "https://lode-org.github.io/readcon-core/schema/con-metadata.schema.json",
  "title": "CON frame metadata (line 2)",
  "description": "JSON metadata object carried on line 2 of a CON frame, spec versions 2 and 3. Unrecognized keys are permitted and MUST be preserved by parsers.",
  "type": "object",
  "required": ["con_spec_version"],
  "properties": {
    "con_spec_version": {
      "type": "integer",
      "minimum": 2,
      "maximum": 3,
      "description": "Spec version of this frame. Files without JSON metadata are implicit version 1."
    },
    "sections": {
      "type": "array",
      "items": { "type": "string", "minLength": 1 },
      "uniqueItems": true,
      "description": "Declared per-atom sections following the coordinate blocks."
    },
    "validate": {
      "type": "boolean",
      "description": "Enable strict validation of declared sections."
    },
    "generator": {
      "type": "string",
      "description": "Tool name and version that wrote the frame."
    },
    "units": {
      "type": "object",
      "description": "Unit system, metatomic-style expressions. Required at version 3 with non-empty length and energy.",
      "properties": {
        "length": { "type": "string", "minLength": 1 },
        "energy": { "type": "string", "minLength": 1 },
        "mass": { "type": "string", "minLength": 1 },
        "time": { "type": "string", "minLength": 1 },
        "velocity": { "type": "string", "minLength": 1 },
        "force": { "type": "string", "minLength": 1 }
      },
      "additionalProperties": { "type": "string" }
    },
    "pbc": {
      "type": "array",
      "items": { "type": "boolean" },
      "minItems": 3,
      "maxItems": 3,
      "description": "Periodicity of the three cell directions."
    },
    "lattice_vectors": {
      "type": "array",
      "minItems": 3,
      "maxItems": 3,
      "items": {
        "type": "array",
        "minItems": 3,
        "maxItems": 3,
        "items": { "type": "number" }
      },
      "description": "Exact 3x3 cell matrix as row vectors."
    },
    "energy": { "type": "number", "description": "Per-frame total energy." },
    "potential": { "type": "object", "description": "Potential/calculator description." },
    "frame_index": { "type": "integer", "minimum": 0 },
    "time": { "type": "number" },
    "timestep": { "type": "number" },
    "neb_bead": { "type": "integer", "minimum": 0 },
    "neb_band": { "type": "integer", "minimum": 0 },
    "convergence_fmax": { "type": "number" },
    "convergence_energy": { "type": "number" },
    "converged": { "type": "boolean" },
    "fmax": { "type": "number" },
    "bonds": {
      "type": "array",
      "description": "Optional frame topology: [i, j] index pairs (0-based atom_data order) or objects with i, j, and optional order.",
      "items": {
        "oneOf": [
          {
            "type": "array",
            "minItems": 2,
            "maxItems": 2,
            "items": { "type": "integer", "minimum": 0 }
          },
          {
            "type": "object",
            "required": ["i", "j"],
            "properties": {
              "i": { "type": "integer", "minimum": 0 },
              "j": { "type": "integer", "minimum": 0 },
              "order": { "type": "number" }
            },
            "additionalProperties": true
          }
        ]
      }
    },
    "storage_dtypes": {
      "type": "object",
      "description": "In-memory element types after parsing; does not change on-disk text encoding.",
      "properties": {
        "positions": { "$ref": "#/$defs/hostedDtype" },
        "velocities": { "$ref": "#/$defs/hostedDtype" },
        "forces": { "$ref": "#/$defs/hostedDtype" },
        "energies": { "$ref": "#/$defs/hostedDtype" },
        "masses": { "$ref": "#/$defs/hostedDtype" },
        "atom_ids": { "$ref": "#/$defs/integerDtype" }
      },
      "additionalProperties": false
    },
    "chemfiles_atom_names": {
      "type": "array",
      "items": { "type": "string" },
      "description": "Display names sidecar from chemfiles import, chemfiles atom order."
    },
    "chemfiles_atom_types": {
      "type": "array",
      "items": { "type": "string" },
      "description": "Atomic types sidecar from chemfiles import, chemfiles atom order."
    },
    "chemfiles_atom_properties": {
      "description": "Per-atom property sidecar from chemfiles import.",
      "type": ["array", "object"]
    }
  },
  "allOf": [
    {
      "if": {
        "properties": { "con_spec_version": { "const": 3 } }
      },
      "then": {
        "required": ["units"],
        "properties": {
          "units": { "required": ["length", "energy"] }
        }
      }
    }
  ],
  "additionalProperties": true,
  "$defs": {
    "hostedDtype": {
      "type": "string",
      "enum": [
        "float16", "float32", "float64",
        "int8", "int16", "int32", "int64",
        "uint8", "uint16", "uint32", "uint64",
        "bool", "complex64", "complex128"
      ]
    },
    "integerDtype": {
      "type": "string",
      "enum": [
        "int8", "int16", "int32", "int64",
        "uint8", "uint16", "uint32", "uint64"
      ]
    }
  }
}