add MD extension

- add missed scopes, coordinate attribute
- correct description of the triclinic simulation box
- remove irrelevant simex and lammps references

EXT_MD.md

@@ -0,0 +1,132 @@
+Domain-Specific Naming Conventions for Molecular Dynamics Simulation Codes
+=======================================================================
+
+openPMD extension name: `MD`
+
+VERSION: 0.0.3 (January 26th, 2020)
+
+Introduction
+------------
+
+This extension is specifically designed for the molecular dynamics simulation codes.
+
+The current version of this extension is suitable to allow the output of
+arbitrary simulation codes to be post-processed and compared with common
+tools and frameworks. Future versions will define a common set of required
+records and further attributes.
+
+The example data structure can be found [HERE](https://github.com/ejcjason/MDDomainExtension).
+
+Root Group
+---------------------------
+
+### Additional Attributes for the `Root` group
+
+The following additional attributes are defined in this extension.
+The individual requirement is given in `scope`.
+
+  - `forceField`
+    - type: 1-dimensional array of N (string) elements, where N is the number of force fields (interatomic potentials) implemented in the simulation.
+    - scope: *optional*
+    - description: the methods implemented in the simulation to describe the force fields (interatomic potentials). See [Interatomic Potentials Repository](https://www.ctcms.nist.gov/potentials/).
+    - example values:
+      - `eam/alloy`
+      - `lj/cut 3.0`
+      - ...
+  - `forceFieldParameters`
+    - type: 1-dimensional array of N (string) elements, where N is the number of force fields (interatomic potentials) implemented in the simulation.
+    - scope: *optional*
+    - description: the parameters specification for the `forceField` methods. See [Interatomic Potentials Repository](https://www.ctcms.nist.gov/potentials/).
+    - example values:
+      - `pair_coeff * * 1 1`
+      - `pair_coeff 1 1 Cu_mishin1.eam.alloy Cu`
+      - ...
+
+Observable Records
+---------------------------
+
+`observables` is an *optional* group that contains physical observables that are derived from the system state, i.e., thermodynamic information (e.g. temperature, energy, pressure).
+
+### Naming conventions
+
+The naming conventions conforming the naming conventions for [Scalar, Vector and Tensor Records](https://github.com/openPMD/openPMD-standard/blob/latest/STANDARD.md#naming-conventions) in [openPMD base standard](https://github.com/openPMD/openPMD-standard/blob/latest/STANDARD.md).
+
+- `scalar` record
+  - type: *(any type)*
+  - data set: `recordName` unique name in group `basePath` + `observables`
+  - examples:
+    - /data/observables/temperature
+    - /data/observables/pressure
+
+### Attributes for each `observable` record
+
+The attributes of unit system for records should be included as defined in [openPMD base standard](https://github.com/openPMD/openPMD-standard/blob/latest/STANDARD.md#unit-systems-and-dimensionality).
+
+
+Particle Records
+---------------------------
+
+### Additional attributes for each `position` record
+
+The following attributes are defined in this extension. The individual requirement is given in `scope`. 
+
+- `coordinate`
+    - type: *(string)*
+    - scope: *required*
+    - description: the representation of the stored position coordinates
+    - available values:
+      - `absolute` the unscaled coordinates
+      - `fractional` the coordinates that are scaled in the range of [0,1] relative to the length of each box edge; in this coordinate system, the `unitSI` of each position component should be `1.0`
+
+### Additional Sub-Group for each Particle Species
+
+`box` is an *optional* sub-group for each particle species to contain the information of the simulation box. 
+
+### Attributes for Sub-Group `box`
+
+The following attributes are defined in this extension.
+If the `box` sub-group exists, the following attributes within it are required.
+The individual requirement is given in `scope`. 
+
+  - `dimension`
+    - type: *(uint32)*
+    - scope: *required*, if `box` sub-group exists
+    - description: the spacial dimension **D** of the simulation box.
+    - example values:
+      - `2` 2D simulation box
+      - `3` 3D simulation box
+      - ...
+
+  - `boundary`
+    - type: array of *(string)* containing **D** elements, where **D** is the value of `dimension`.
+    - scope: *required*, if `box` sub-group exists
+    - description: the boundary condition of the box along each dimension. The allowed values in `boundary` are either **periodic** or **none**.
+    - example values:
+      - `["periodic","periodic","periodic"]`  periodic in all the three dimensions
+      - `["none","periodic","periodic"]` periodic in only *y* and *z* dimensions
+
+### Records for Sub-Group `box`
+
+The following records are defined in this extension.
+If the `box` sub-group exists, the following records within it are required.
+The individual requirement is given in `scope`. 
+  - `edge`
+    - type: DxD array of *(floatX)*, where **D** is the value of `dimension`.
+    - scope: *required*, if `box` sub-group exists
+    - description: the edge vector of the simulation box in each dimension.
+    - example values:
+      - `[[1.,0.,0.],[0.,1.,0.],[0.,0.,1.]]` 3D cubic simulation box, Ax = (1.,0.,0.), Ay = (0.,1.,0.), Az = (0.,0.,1.)
+      - `[[3.46,0.,0.],[1.73,2.997,0.],[0.,0.,10.]]` 3D triclinic simulation box, Ax = (3.46,0.,0.), Ay = (1.73,2.997,0.), Az = (0.,0.,10.)
+      - `[[1.,0.],[1.,1.]]` 2D rectangle simulation box, Ax = (1.,0.), Ay = (0.,1.)
+  - `limit`
+    - type: Dx2 array of *(floatX)*, where **D** is the value of `dimension`.
+    - scope: *required*, if `box` sub-group exists
+    - description: the starting and the ending of each edge vector.
+    - example values:
+      - `[[0.,300.],[0.,150.],[0.,180.]]`  A 3D box example: xlo = 0, xhi = 300, ylo = 0, yhi = 150, zlo = 0, zhi = 180 
+      - `[[0.,300.],[15.,280.]]` A 2D box example: xlo = 0, xhi = 300, ylo = 15, yhi = 280
+  - `unitSI`
+    - type: *(float64)*
+    - scope: *required*, if `box` sub-group exists
+    - description: unit-conversion factor to convert simulation unit to SI units
+    - example: `1.0e-10`