/-- item Either a dataset or a group, indented by 4 spaces to its parent group.
+-- attribute An attribute, indented by 1 space to its relateed group or dataset.
/-- dataset: <type>[dim1][dim2] {value} A dataset with a [dim1 x dim2] array and of type <type>. The value of the data is {value}.
This example is conforming to openPMD MD extension (draft), and can be written with openPMD-api directly without observables.
Root
+-- openPMD: <string>[] {1.1.0}
+-- openPMDextension: <unit64>[1] {2}
+-- author: <string>[] {Juncheng E <[email protected]>}
+-- basePath: <string>[] {/data/%T/}
+-- particlesPath: <string>[] {particles/}
+-- date: <string>[] {2019-09-05 20:45:02 +0200}
+-- iterationEncoding: <string>[] {groupBased}
+-- interationFormat: <string>[] {/data/%T}
+-- software: <string>[] {LAMMPS}
+-- softwareVersion: <string>[] {7 Aug 2019}
+-- forceField: <string>[] {["lj/cut 3.0","eam/alloy"]}
+-- forceFieldParameter: <string>[] {["pair_coeff * * 1 1","pair_coeff 1 1 Cu_mishin1.eam.alloy Cu"]}
+-- comment: <string>[] {"NPT, temperature was reduced by 100 K every 5000 steps."}
/-- data
/-- 0
+-- dt: <float64>[1] {1.0}
+-- time: <float32>[1] {0.0}
+-- timeUnitSI: <float64>[1] {1.0e-12}
/-- observables <optional, openPMD API incompatible>
/-- temprerature: <float64>[1] {300}
+-- unitSI: <float64>[1] {1.0}
/-- volume: <float64>[1] {27}
+-- unitSI: <float64>[1] {1.0e-24}
/-- pressure: <float64>[1] {200}
+-- unitSI: <float64>[1] {1e6}
/-- particles
/-- Cu
/-- id: <uint64>[108]
/-- box <optional>
+-- boundary: <string>[3] {["periodic","periodic","periodic"]}
+-- dimension: <unit32>[1] {3}
/-- edge: <float64>[3][3] {[[1,0,0],[0,1,0],[0,0,1]]}
/-- limit: <float64>[3][2] {[[0,300],[0,300],[0,300]]}
+-- unitSI: <float64>[1] {1.0e-10}
/-- position
+-- timeOffset: <float64>[1] {0.0}
+-- unitDimension: <float64>[7] {[1,0,0,0,0,0,0]}
+-- coordinate: <string>[] {absolute}
/-- x: <float64>[108]
+-- unitSI: <float64>[1.0e-10]
/-- y: <float64>[108]
+-- unitSI: <float64>[1.0e-10]
/-- z: <float64>[108]
+-- unitSI: <float64>[1.0e-10]
/-- velocity
+-- timeOffset: <float64>[1] {0.0}
+-- unitDimension: <float64>[7] {[1,0,0,0,0,0,0]}
/-- x: <float64>[108]
+-- unitSI: <float64>[1.0e-10]
/-- y: <float64>[108]
+-- unitSI: <float64>[1.0e-10]
/-- z: <float64>[108]
+-- unitSI: <float64>[1.0e-10]
/-- C
/-- id: <uint64>[108]
/-- box
+-- boundary: <string>[3] {["periodic","periodic","periodic"]}
+-- dimension: <unit32>[1] {3}
/-- edge: <float64>[3][3] {[[1,0,0],[0,1,0],[0,0,1]]}
/-- limit: <float64>[3][2] {[[0,300],[0,300],[0,300]]}
+-- unitSI: <float64>[1] {1.0e-10}
/-- position
+-- timeOffset: <float64>[1] {0.0}
+-- unitDimension: <float64>[7] {[1,0,0,0,0,0,0]}
+-- coordinate: <string>[] {absolute}
/-- x: <float64>[108]
+-- unitSI: <float64>[1.0e-10]
/-- y: <float64>[108]
+-- unitSI: <float64>[1.0e-10]
/-- z: <float64>[108]
+-- unitSI: <float64>[1.0e-10]
/-- velocity
+-- timeOffset: <float64>[1] {0.0}
+-- unitDimension: <float64>[7] {[1,0,0,0,0,0,0]}
/-- x: <float64>[108]
+-- unitSI: <float64>[1.0e-10]
/-- y: <float64>[108]
+-- unitSI: <float64>[1.0e-10]
/-- z: <float64>[108]
+-- unitSI: <float64>[1.0e-10]
- LAMMPS h5md dump https://lammps.sandia.gov/doc/dump_h5md.html
- LAMMPS triclinic simulation box https://lammps.sandia.gov/doc/Howto_triclinic.html
- h5md webpage https://nongnu.org/h5md/
- h5md paper de Buyl, Colberg and Hofling, H5MD: A structured, efficient, and portable file format for molecular data, Comp. Phys. Comm. 185(6), 1546-1553 (2014)
- Atomeye cfg standard http://li.mit.edu/Archive/Graphics/A/#extended_CFG
- Interatomic potentials (Force Fields) https://www.ctcms.nist.gov/potentials/ https://en.wikipedia.org/wiki/Force_field_(chemistry) https://www.sciencedirect.com/science/article/pii/S1359028613000788