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#73 uncomment ts search following de_gsm
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joshkamm committed Jun 19, 2024
1 parent f286a56 commit a43c3c5
Showing 1 changed file with 16 additions and 13 deletions.
29 changes: 16 additions & 13 deletions src/conformational_sampling/gsm.py
Original file line number Diff line number Diff line change
@@ -6,6 +6,7 @@

import pyGSM

from conformational_sampling.analyze import ts_node
from conformational_sampling.main import load_stk_mol_list

# workaround for issue with pyGSM installation
@@ -527,19 +528,21 @@ def stk_de_gsm(config: Config):

# TS-Optimization following DE-GSM run

# ts_node_energy = ts_node(de_gsm.energies)[1]
# ts_node_index = de_gsm.energies.index(ts_node_energy)
# ts_node_geom = de_gsm.nodes[ts_node_index]
ts_node_energy = ts_node(de_gsm.energies)[1]
ts_node_index = de_gsm.energies.index(ts_node_energy)
ts_node_geom = de_gsm.nodes[ts_node_index]

# nifty.printcool("Optimizing TS node")
# optimizer.optimize(
# molecule=ts_node_geom,
# refE=de_gsm.energies[0],
# opt_steps=OPT_STEPS,
# opt_type="TS",
# ictan=de_gsm.ictan[ts_node_index],
# )

# de_gsm.nodes[ts_node_index] = ts_node_geom
nifty.printcool('Optimizing TS node')
geoms, energies = optimizer.optimize(
molecule=ts_node_geom,
refE=de_gsm.energies[0],
opt_steps=OPT_STEPS,
opt_type='TS',
ictan=de_gsm.ictan[ts_node_index],
)
manage_xyz.write_std_multixyz('ts_opt.xyz', geoms, energies, gradrms=None, dEs=None)
de_gsm.nodes[ts_node_index] = (
ts_node_geom # has ts_node_geom actually been updated during optimize?
)

gsm_plot(de_gsm.energies, x=range(len(de_gsm.energies)), title=1)

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