Merge branch 'sam_dev' into atom_mapping_2023

BlauGroup · Nov 2, 2023 · 19b9df9 · 19b9df9
2 parents 0d0b02d + d1eff6d
commit 19b9df9
Show file tree

Hide file tree

Showing 116 changed files with 6,803 additions and 4,359 deletions.
diff --git a/HiPRGen/initial_state.py b/HiPRGen/initial_state.py
@@ -65,6 +65,22 @@ def find_mol_entry_by_entry_id(mol_entries, entry_id):
     );
 """
 
+create_interrupt_state_table = """
+    CREATE TABLE interrupt_state (
+            seed                   INTEGER NOT NULL,
+            species_id             INTEGER NOT NULL,
+            count                  INTEGER NOT NULL
+    );
+"""
+
+create_interrupt_cutoff_table = """
+    CREATE TABLE interrupt_cutoff (
+            seed                   INTEGER NOT NULL,
+            step                   INTEGER NOT NULL,
+            time                   INTEGER NOT NULL
+    );
+"""
+
 
 def insert_initial_state(
         initial_state,
@@ -83,6 +99,8 @@ def insert_initial_state(
     rn_cur.execute(create_initial_state_table)
     rn_cur.execute(create_trajectories_table)
     rn_cur.execute(create_factors_table)
+    rn_cur.execute(create_interrupt_state_table)
+    rn_cur.execute(create_interrupt_cutoff_table)
     rn_con.commit()
 
     rn_cur.execute(

diff --git a/HiPRGen/species_filter.py b/HiPRGen/species_filter.py
@@ -228,7 +228,7 @@ def add_electron_species(
     mol_entries, mol_entries_pickle_location, electron_free_energy
 ):
     e_site = Site(
-        DummySpecies("E", oxidation_state=None, properties=None), [0.0, 0.0, 0.0]
+        DummySpecies("E", oxidation_state=None), [0.0, 0.0, 0.0]
     )
     e_mol = Molecule.from_sites([e_site])
     e_mol.set_charge_and_spin(-1, 2)

diff --git a/euvl_phase1_test/.DS_Store b/euvl_phase1_test/.DS_Store
diff --git a/euvl_phase1_test/buckets.sqlite b/euvl_phase1_test/buckets.sqlite
diff --git a/euvl_phase1_test/dummy.tex b/euvl_phase1_test/dummy.tex
@@ -0,0 +1,7 @@
+\documentclass{article}
+\usepackage{graphicx}
+\usepackage[margin=1cm]{geometry}
+\usepackage{amsmath}
+\pagenumbering{gobble}
+\begin{document}
+\setlength\parindent{0pt}