Add example and documentation for multiple coordinate sets (3dSets)

README.md

@@ -21,3 +21,10 @@ represntations for chemistry, and to document those representations more
 formally than has been done in the past.
 
 [Chemical_JSON]: http://wiki.openchemistry.org/Chemical_JSON
+
+## Documentation
+
+Project documentation is available in the [docs directory](./docs).
+This content is migrated from the archived Open Chemistry wiki and
+serves as a centralized reference until a dedicated documentation
+site is available.

and examples links clickable in documentation

@@ -0,0 +1,25 @@
+diff --git a/README.md b/README.md
+index 0d32498..2f670cd 100644
+--- a/README.md
++++ b/README.md
+@@ -25,7 +25,7 @@ formally than has been done in the past.
+ 
+ ## Documentation
+ 
+-Project documentation is available in the `docs/` directory.  
++Project documentation is available in the [docs/](docs/) directory. 
+ This content is migrated from the archived Open Chemistry wiki and will
+ serve as a centralized reference until a dedicated documentation site
+ is available.
+diff --git a/docs/overview.md b/docs/overview.md
+index 8eb64d2..dbac41e 100644
+--- a/docs/overview.md
++++ b/docs/overview.md
+@@ -28,6 +28,5 @@ The format is designed to be extensible, allowing new properties to be
+ added without breaking existing tools.
+ 
+ ## Example
+-
+-See the `examples/` directory in this repository for concrete examples
++See the [examples/](../examples/) directory in this repository for concrete examples
+ of ChemicalJSON files, including small molecules and periodic systems.

docs/coordinate-sets.md

@@ -0,0 +1,18 @@
+## Multiple Coordinate Sets (3dSets)
+
+ChemicalJSON supports multiple coordinate sets using `coords.3dSets`, represented as an array of coordinate arrays.
+
+Each entry in `3dSets` contains a complete set of Cartesian coordinates for all atoms in the system. This can be used to represent conformers, geometry optimization steps, or simple animations.
+
+### Example
+
+See `examples/multiple-coordinate-sets.json` for a minimal example demonstrating two coordinate frames.
+
+### Current Limitations
+
+The current format does not standardize:
+- time steps for coordinate series (e.g., molecular dynamics)
+- per-frame energies or forces
+- an explicit default coordinate set index
+
+Consumers typically interpret the first entry in `3dSets` as the initial frame, but this behavior is not formally defined.

docs/overview.md

@@ -0,0 +1,24 @@
+# ChemicalJSON
+
+## Purpose
+
+ChemicalJSON is a JSON-based format for representing chemical data
+in a structured and machine-readable way. It is designed to support
+storage, exchange, and processing of chemical information across
+different tools and programming languages.
+
+## Basic Structure
+
+A ChemicalJSON document typically includes:
+
+- Metadata such as molecule name and formula
+- Atomic information (elements, coordinates)
+- Optional properties such as unit cells, energies, or orbitals
+
+The format is designed to be extensible, allowing new properties
+to be added without breaking existing tools.
+
+## Examples
+
+See the [examples directory](../examples) for concrete examples of
+ChemicalJSON files, including small molecules and periodic systems.

examples/multiple-coordinate-sets.json

@@ -0,0 +1,21 @@
+{
+    "chemicalJson": 1,
+    "atoms": {
+      "elements": { "number": [8, 1, 1] }
+    },
+    "coords": {
+      "3dSets": [
+        [
+          [0.000, 0.000, 0.000],
+          [0.957, 0.000, 0.000],
+          [-0.239, 0.927, 0.000]
+        ],
+        [
+          [0.000, 0.000, 0.010],
+          [0.957, 0.000, 0.010],
+          [-0.239, 0.927, 0.010]
+        ]
+      ]
+    }
+  }
+