fix minor bugs for example code of DA in solvent (#77)

Correct parameters in examples of DA in the solvent. Closes #76
duartegroup · Dec 6, 2023 · 02bfbb1 · 02bfbb1
1 parent 4d4442c
commit 02bfbb1
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diff --git a/examples/DA_paper/2D_pes/pes.py b/examples/DA_paper/2D_pes/pes.py
@@ -296,7 +296,7 @@ def optimise_with_fix_solute(solute, configuration, fmax, mlp, constraint = True
     endo = mlt.potentials.ACE('endo_ace_wB97M_imwater', system)
 
     TS = mlt.ConfigurationSet()
-    TS.load_xyz(filename = 'cis_endo_TS_wB97M.xyz')
+    TS.load_xyz(filename = 'cis_endo_TS_wB97M.xyz', charge = 0, mult = 1)
     TS = TS[0]
     TS.box = Box([100, 100, 100])
     TS.charge = 0

diff --git a/examples/DA_paper/training/explicit/endo_ace_ex.py b/examples/DA_paper/training/explicit/endo_ace_ex.py
@@ -188,7 +188,7 @@ def generate_init_configs(n, bulk_water = True, TS = True):
         TS: whether to include the TS of the reaction in the system"""
     init_configs = mlt.ConfigurationSet()
     TS = mlt.ConfigurationSet()
-    TS.load_xyz(filename = 'cis_endo_TS_wB97M.xyz')
+    TS.load_xyz(filename = 'cis_endo_TS_wB97M.xyz', charge = 0, mult = 1)
     TS = TS[0]
     TS.box = Box([11, 11, 11])
     TS.charge = 0

diff --git a/examples/DA_paper/uphill/uphill.py b/examples/DA_paper/uphill/uphill.py
@@ -196,7 +196,7 @@ def traj_study(configs,  ml_potential,  init_md_time_fs = 500, max_time_fs = 300
     endo = mlt.potentials.ACE('endo_in_water_ace_wB97M', system)
 
     TS = mlt.ConfigurationSet()
-    TS.load_xyz(filename = 'cis_endo_TS_wB97M.xyz')
+    TS.load_xyz(filename = 'cis_endo_TS_wB97M.xyz', charge = 0, mult = 1)
     TS = TS[0]
     TS.box = Box([21.5, 21.5,21.5])
     TS.charge = 0