new tests

Author: ljwoods2

imdclient/tests/hpc_testing/lammps/lammps.md

@@ -44,4 +44,22 @@ pytest -s ../../test_manual.py \
     --topol_arg topology_after_min.data \
     --traj_arg lammps_trj.h5md \
     --first_frame_arg 1
+```
+
+```bash
+./lmp < /Users/ljwoods2/workspace/imdclient/imdclient/tests/hpc_testing/lammps/lammps_v3.in 
+
+```
+
+
+```bash 
+module load mamba
+# Environment containing IMDClient
+source activate imdclient-test
+
+pytest -s imdclient/tests/test_manual.py \
+    --topol_path_arg imdclient/tests/hpc_testing/topology_after_min.data \
+    --traj_path_arg imdclient/tests/hpc_testing/ \
+    --first_frame_arg <first traj frame to compare to IMD>
+
 ```

imdclient/tests/hpc_testing/lammps/lammps_v3_imd.in imdclient/tests/hpc_testing/lammps/lammps_v3.in

@@ -42,13 +42,19 @@ velocity all create 300 102939 dist gaussian mom yes rot yes
 # this is equlibration process.
 fix 1 all nve 
 
+## H5MD settings
+dump h5md1 all h5md 1 lammps_trj.h5md position velocity force box yes
+dump_modify h5md1 unwrap no
+
 ## IMD settings
 # https://docs.lammps.org/fix_imd.html
 fix 2 all imd 8888 version 3 unwrap off nowait off
 
 ## Run MD sim
 run 100
 
+undump h5md1 
+
 # Unfix the NVE. Additional lines if any will assume that this fix is off.
 unfix 1