def test_anapot_growingstring_opt():
coords = (
(-1.05274, 1.02776, 0),
(1.94101, 3.85427, 0),
)
calc_getter = AnaPot
eps = .05
damp = .05
images = get_geoms(coords, calc_getter)
gs_kwargs = {
"max_nodes": 10,
"perp_thresh": 0.5,
# "perp_thresh": 1,
}
gs = GrowingString(images, calc_getter, reparam_every=1)
# from pysisyphus.optimizers.QuickMin import QuickMin
# opt = QuickMin(gs)
# self.coords = [c.reshape(-1, 3) for c in self.gs.coords_list]
# self.tangents = self.gs.tangent_list
# self.perp_forces = self.gs.perp_force_list
from pysisyphus.optimizers.SteepestDescent import SteepestDescent
# opt = SteepestDescent(gs, alpha=0.05, bt_disable=True, max_cycles=175)
opt = SteepestDescent(gs, alpha=0.05, bt_disable=True, max_cycles=70)
opt.run()
xlim = (-2, 2.5)
ylim = (0, 5)
levels = (-3, 4, 80)
ap = AnimPlot(AnaPot(), opt, xlim=xlim, ylim=ylim, levels=levels)
ap.animate()
def test_multi_run():
# NEB
geoms = AnaPot().get_path(10)
cos = NEB(geoms)
neb_kwargs = {
"dump": True,
"h5_group_name": "neb",
}
neb_opt = SteepestDescent(cos, **neb_kwargs)
neb_opt.run()
# GrowingString
geoms = AnaPot().get_path(10)
gsm = GrowingString(geoms, calc_getter=AnaPot, perp_thresh=0.25)
gsm_kwargs = {
"dump": True,
"h5_group_name": "gsm",
"stop_in_when_full": 0,
}
gsm_opt = StringOptimizer(gsm, **gsm_kwargs)
gsm_opt.run()
# calc = geoms[0].calculator
# calc.anim_opt(opt, show=True)
# Simple Optimization
geom = AnaPot().get_path(10)[5]
opt_kwargs = {
"dump": True,
"h5_group_name": "opt",
}
opt = RFOptimizer(geom, **opt_kwargs)
opt.run()
def test_neb_springs(neb_kwargs, ref_cycle):
calc = AnaPot()
geoms = calc.get_path(15)
neb = NEB(geoms, **neb_kwargs)
opt = SteepestDescent(neb)
opt.run()
# calc.anim_opt(opt, show=True)
assert (opt.is_converged)
assert (opt.cur_cycle == ref_cycle)
def test_wfo_ref():
in_path = THIS_DIR / "butadiene_twist"
geom = geom_from_xyz_file(in_path / "02_buta_twist.xyz")
turbo = Turbomole(in_path, track=True, wfo_basis="def2-svp")
geom.set_calculator(turbo)
opt_kwargs = {
"max_cycles": 2,
"dump": True,
}
opt = SteepestDescent(geom, **opt_kwargs)
opt.run()
def test_freeend_anapot():
calc = AnaPot()
geoms = calc.get_path(15)
geoms = geoms[3:11]
fe_neb = FreeEndNEB(geoms)
opt = SteepestDescent(fe_neb)
opt.run()
# calc.anim_opt(opt, show=True)
assert opt.is_converged
assert opt.cur_cycle == 31
def test_wfo_compare_sto3g():
in_path = THIS_DIR / "butadiene_twist_sto3g"
geom = geom_from_xyz_file(in_path / "02_buta_twist.xyz")
turbo = Turbomole(in_path, track=True, wfo_basis="sto-3g")
geom.set_calculator(turbo)
opt_kwargs = {
"max_cycles": 1,
"dump": True,
}
opt = SteepestDescent(geom, **opt_kwargs)
opt.run()
wfow = turbo.wfow
wfow.compare(wfow)
def test_wfo_compare_neon():
in_path = THIS_DIR / "neon"
geom = geom_from_xyz_file(in_path / "neon.xyz")
turbo = Turbomole(in_path, track=True, wfo_basis="def2-svp")
geom.set_calculator(turbo)
opt_kwargs = {
"max_cycles": 1,
"dump": True,
}
opt = SteepestDescent(geom, **opt_kwargs)
opt.run()
wfow = turbo.wfow
wfow.compare(wfow)
def test_freeend_freeendpot():
calc = FreeEndNEBPot()
geoms = calc.get_path(50)[:35]
kwargs = {
"k_min": 5,
"k_max": 10,
}
fe_neb = FreeEndNEB(geoms, **kwargs)
opt = SteepestDescent(fe_neb, max_cycles=100)
opt.run()
# calc.anim_opt(opt, show=True)
assert opt.is_converged
assert opt.cur_cycle == 93
def test_wfo_compare_neon_dimer():
in_path = THIS_DIR / "neon_dimer"
geom = geom_from_xyz_file(in_path / "neon_dimer.xyz")
turbo = Turbomole(in_path, track=True, wfo_basis="def2-svp")
geom.set_calculator(turbo)
opt_kwargs = {
"max_cycles": 5,
"dump": True,
"track": True,
# "convergence": {
# "max_force_thresh": 2.5e-8,
# }
}
opt = SteepestDescent(geom, **opt_kwargs)
#import pdb; pdb.set_trace()
opt.run()
def test_dask():
with LocalCluster(n_workers=2) as cluster:
address = cluster.scheduler_address
geoms = geom_from_library(
"ala_dipeptide_iso_b3lyp_631gd_10_images.trj")
for i, geom in enumerate(geoms):
calc = XTB(pal=1, calc_number=i)
geom.set_calculator(calc)
neb = NEB(geoms, scheduler=address)
max_cycles = 1
opt = SteepestDescent(neb, align=True, max_cycles=max_cycles)
opt.run()
assert opt.cur_cycle == (max_cycles - 1)
def test_fs():
from pysisyphus.calculators.XTB import XTB
from pysisyphus.cos.FreezingString import FreezingString
# educt = geom_from_library("ciscis_24hexadiene_xtbopt.xyz")
# product = geom_from_library("trans34dimethylcyclobutene.xyz")
educt = AnaPot.get_geom((-1.05274, 1.02776, 0))
product = AnaPot.get_geom((1.94101, 3.85427, 0))
images = (educt, product)
def calc_getter():
return AnaPot()
fs = FreezingString(images, calc_getter, max_nodes=10)
from pysisyphus.optimizers.SteepestDescent import SteepestDescent
sd = SteepestDescent(fs)
sd.run()
pot = AnaPot()
pot.plot()
crds = fs.allcoords.reshape(-1, 3)
# pot.ax.plot(c[:,0], c[:,1], "o-")
pot.ax.plot(*crds[:,:2].T, "o-")
plt.show()
from pysisyphus.optimizers.StringOptimizer import StringOptimizer
def test_mb_gs_opt():
coords = (
(0.614, 0.031, 0),
(-.563, 1.43, 0),
)
calc_getter = MullerBrownPot
# pot = calc_getter()
# pot.plot()
# plt.show()
images = get_geoms(coords, calc_getter)
gs_kwargs = {
"max_nodes": 16,
"perp_thresh": 50,
"fix_ends": True,
}
gs = GrowingString(images, calc_getter, **gs_kwargs)
from pysisyphus.optimizers.QuickMin import QuickMin
from pysisyphus.optimizers.SteepestDescent import SteepestDescent as SD
# opt = QuickMin(gs)
opt = SD(gs, alpha=0.4, bt_disable=True)
opt.run()
ap = AnimPlot(calc_getter(), opt)
ap.animate()
def test_dump_neb():
# NEB
geoms = AnaPot().get_path(10)
cos = NEB(geoms)
opt_kwargs = {
"dump": True,
# "rms_force": 1.0,
"h5_group_name": "neb",
}
opt = SteepestDescent(cos, **opt_kwargs)
# opt = SteepestDescent(geoms[7], **opt_kwargs)
opt.run()
# GrowingString
geoms = AnaPot().get_path(10)
gsm = GrowingString(geoms, calc_getter=AnaPot, perp_thresh=0.25)
opt_kwargs = {
"dump": True,
"h5_group_name": "gsm",
"gamma": 10.,
"stop_in_when_full": 0,
}
opt = StringOptimizer(gsm, **opt_kwargs)
opt.run()
calc = geoms[0].calculator
# calc.anim_opt(opt, show=True)
# # Simple Optimization
# geom = AnaPot().get_path(10)[5]
# opt_kwargs = {
# "dump": True,
# "h5_group_name": "opt",
# }
# opt = RFOptimizer(geom, **opt_kwargs)
# opt.run()
return
hei_coords, *_ = cos.get_splined_hei()
ts_geom = geoms[0].copy()
ts_geom.coords = hei_coords
ts_geom.set_calculator(AnaPot())
ts_opt_kwargs = {
# "dump": True,
"thresh": "gau_tight",
}
ts_opt = RSIRFOptimizer(ts_geom, **ts_opt_kwargs)
ts_opt.run()
def test_butadiene_track_opt():
in_path = THIS_DIR / "butadiene"
geom = geom_from_xyz_file(in_path / "butadiene_hf_sto3g.xyz")
turbo = Turbomole(in_path, track=True, wfo_basis="def2-svp")
geom.set_calculator(turbo)
#fn = "/scratch/programme/pysisyphus/tests/test_turbo_butadien_td_opt/wfo_backup.out"
#with open(fn) as handle:
# stdout = handle.read()
#wfo = turbo.wfow
#a = wfo.parse_wfoverlap_out(stdout)
#print(a)
#print(a.reshape(-1, 6))
opt_kwargs = {
"max_cycles": 10,
"dump": True,
}
opt = ConjugateGradient(geom, **opt_kwargs)
opt = SteepestDescent(geom, **opt_kwargs)
opt.run()