MD Extension updates

[JunCEEE]

For the discussion in openPMD/openPMD-standard#218

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}
 +-- method: <string>[] {["lj/cut 3.0","eam/alloy"]}
 +-- methodParameters: <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}            
            /-- box
             +-- boundary: <string>[3] {["periodic","periodic","periodic"]}
             +-- dimension: <unit32>[1] {3}
                /-- origin: <float64>[2] {[0., 0., 0.]}
                /-- vectors: <float64>[3][3] {[[3,0,0],[0,3,0],[0,0,10]]}
                 +-- unitSI: <float64>[1] {1.0e-10}
            /-- particles
                /-- Cu
                    /-- id: <uint64>[108]
                    /-- 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]
                    /-- 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]