Document the new LAMMPS trajectories

MDANSE/Src/MDANSE/Framework/Configurators/ConfigFileConfigurator.py

@@ -122,7 +122,7 @@ def parse(self):
                 for j in range(1, self["n_atom_types"] + 1):
                     data_line = (
                         lines[i + j].strip().split("#")[0]
-                    )  # Remove commentary if any
+                    )  # Remove comments, if present
                     idx, mass = data_line.split()[0:2]
                     idx = int(idx)
                     mass = float(mass)

MDANSE/Tests/UnitTests/Data/mo.lmp

@@ -0,0 +1,54 @@
+
+# This is the input file which created the following test files:
+# lammps_moly_custom.txt
+# lammps_moly_h5md.h5
+# lammps_moly_xyz.txt
+# It requires the starting structure defined in:
+# structure_moly.lammps
+# The important information needed for correct reading of the files
+# is that unit system is 'electron' and time step is 0.5 time units.
+
+# Intialization
+units          electron
+dimension      3
+boundary       p p p
+atom_style     full
+
+atom_modify map array sort 100 2.0
+
+# Atom Definition
+read_data      structure_moly.lammps
+replicate      8 8 8
+
+pair_style mgpt
+pair_coeff * * Mo5.2.mgpt.parmin Mo5.2.mgpt.potin 108.0
+
+neighbor        0.5 bin
+neigh_modify    every 10 delay 0 check no
+
+# for electron units, time is given in fs
+timestep       0.5
+compute 1 all pressure thermo_temp
+
+thermo_style   custom step temp etotal c_1[*]
+thermo         100
+
+minimize 1.0e-4 1.0e-6 3 5
+
+velocity       all create 2500.00 4928459 rot yes mom yes dist gaussian
+fix            1 all nvt temp 2500.0 2500.0 100.0 tchain 1
+# fix            2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
+
+# Settings
+
+
+# Output
+dump             dumpXYZ all xyz 1 lammps_moly_xyz.txt
+dump             dumpPos all custom 1 lammps_moly_custom.txt id type x y z
+dump h5md1 all h5md 1 lammps_moly_h5md.h5 position image velocity force
+write_dump all h5md lammps_moly_h5md.h5 file_from h5md1 species
+# dump           dumpCharge all custom 1 dump.charges id type x y z q
+
+# Run the simulation
+run            10
+