conflicts before coffee 2

crystal_diffusion/data/parse_lammps.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+EXP_DIR="lammps_scripts/Si/si-custom/"
+DUMP_FILENAME="dump.si-300-1.yaml"
+THERMO_FILENAME="thermo_log.yaml"
+OUTPUT_NAME="demo.parquet"
+
+python crystal_diffusion/data/parse_lammps_outputs.py \
+    --dump_file  ${EXP_DIR}/${DUMP_FILENAME} \
+    --thermo_file ${EXP_DIR}/${THERMO_FILENAME} \
+    --output_name ${EXP_DIR}/${OUTPUT_NAME}

crystal_diffusion/data/parse_lammps_outputs.py

@@ -30,6 +30,7 @@ def parse_lammps_output(lammps_dump: str, lammps_thermo_log: str, output_name: s
             if 'id' not in doc['keywords']:  # sanity check
                 raise ValueError('id should be in LAMMPS dump file')
             atoms_info = defaultdict(list) # store information on atoms positions and forces here
+
             for data in doc['data']:  # loop over the atoms to get their positions and forces
                 for key, v in zip(doc['keywords'], data):
                     if key not in ['id', 'type', 'x', 'y', 'z', 'fx', 'fy', 'fz']:

data/run_lammps_example.sh

@@ -3,7 +3,11 @@
 TEMPERATURE=300
 BOX_SIZE=1
 
+<<<<<<< HEAD
 lmp < lammps_input_example.lammps -v STEP 10 -v T $TEMPERATURE -v S $BOX_SIZE
 
 # extract the thermodynamic outputs in a yaml file
-egrep  '^(keywords:|data:$|---$|\.\.\.$|  - \[)' log.lammps > log.yaml
+egrep  '^(keywords:|data:$|---$|\.\.\.$|  - \[)' log.lammps > log.yaml
+=======
+lmp < lammps_input_example.lammps -v STEP 10 -v T $TEMPERATURE -v S $BOX_SIZE
+>>>>>>> 5927511b163780d0be25d5db4a0eb8868b12f8b2