From dfe2e03b3da4d13e74c4b94a0481caaad1f1810d Mon Sep 17 00:00:00 2001 From: Juncheng E Date: Tue, 17 Sep 2019 21:38:04 +0200 Subject: [PATCH] add MD extension - add missed scopes, coordinate attribute - correct description of the triclinic simulation box - remove irrelevant simex and lammps references --- EXT_MD.md | 132 ++++++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 132 insertions(+) create mode 100644 EXT_MD.md diff --git a/EXT_MD.md b/EXT_MD.md new file mode 100644 index 0000000..427cfd6 --- /dev/null +++ b/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`