def test_adv_plt_2dhistogram():
# Advanced: Combine wave functions from across 5 simulations
tot_cds = []
tot_dw = []
for sim_num in range(5):
temp_sim = pv.SimInfo(
f'pyvibdmc/sample_sim_data/tutorial_water_{sim_num}_sim_info.hdf5') # 5 independent DMC sims!
cds, dw = temp_sim.get_wfns([2500, 3500])
tot_cds.append(cds)
tot_dw.append(dw)
tot_cds = np.concatenate(tot_cds, axis=0)
tot_dw = np.concatenate(tot_dw)
# Advanced: 2D Histogram
analyzer = pv.AnalyzeWfn(tot_cds) # initialize analyzer object
bond_len_OH1 = analyzer.bond_length(0, 2)
bond_len_OH2 = analyzer.bond_length(1, 2)
# bond_angle = np.rad2deg(analyzer.bond_angle(atm1=0,atm_vert=2,atm3=1))
bins_x, bins_y, amp = analyzer.projection_2d(bond_len_OH1,
bond_len_OH2,
desc_weights=tot_dw,
bins=[15, 15],
range=[[0.5, 1.5], [0.5, 1.5]],
normalize=True)
pv.Plotter.plt_hist2d(binsx=bins_x,
binsy=bins_y,
hist_2d=amp,
xlabel="ROH 1 (Angstroms)",
ylabel="ROH 2 (Angstroms)",
save_name=f"{savefigpth}2d_histogram.png")
def test_zpe_std():
zpes = []
for sim_num in range(5):
test_sim = pv.SimInfo(
f'pyvibdmc/sample_sim_data/tutorial_water_{sim_num}_sim_info.hdf5') # 5 independent DMC sims!
this_zpe = test_sim.get_zpe(onwards=100)
zpes.append(this_zpe)
final_zpe = np.average(zpes)
final_std_dev = np.std(zpes)
def test_adv_plt_many_vrefs():
"""Plot lots of vrefs on top of each other"""
# My favorite plotting settings
params = {'text.usetex': False,
'mathtext.fontset': 'dejavusans',
'font.size': 14}
plt.rcParams.update(params)
# Time to plot!
fig, ax = plt.subplots()
for sim_num in range(5):
temp_sim = pv.SimInfo(
f'pyvibdmc/sample_sim_data/tutorial_water_{sim_num}_sim_info.hdf5') # 5 independent DMC sims!
this_vref = temp_sim.get_vref()
ax.plot(this_vref[:, 0], this_vref[:, 1])
ax.set_xlabel("Time Step")
ax.set_ylabel(r"Vref ($\rm{cm^{-1}}$)")
fig.savefig(f"{savefigpth}ManyVrefs.png", dpi=300, bbox_inches='tight')
plt.close()
def test_mass_increase_dmc():
potDir = os.path.join(os.path.dirname(__file__),
'../sample_potentials/PythonPots/')
pyFile = 'harmonicOscillator1D.py'
potFunc = 'oh_stretch_harm'
harm_pot = pv.Potential(potential_function=potFunc,
python_file=pyFile,
potential_directory=potDir,
num_cores=2)
myDMC = pv.DMC_Sim(
sim_name="harm_osc_cont",
output_folder=sim_ex_dir,
weighting='discrete',
num_walkers=5000,
num_timesteps=1000,
equil_steps=200,
chkpt_every=100,
wfn_every=500,
desc_wt_steps=499,
atoms=["X"],
delta_t=5,
potential=harm_pot,
log_every=50,
start_structures=np.zeros((1, 1, 1)),
cur_timestep=0,
# cont_wt_thresh=[0.002, 15],
masses=pv.Constants.reduced_mass('O-H') * 50,
DEBUG_mass_change={
'change_every': 100,
'factor_per_change': 0.5
})
myDMC.run()
sim = pv.SimInfo(f'{sim_ex_dir}/harm_osc_cont_sim_info.hdf5')
pv.Plotter.plt_vref_vs_tau(sim.get_vref())
pv.Plotter.plt_pop_vs_tau(sim.get_pop())
assert True
import numpy as np
import matplotlib.pyplot as plt
import pytest
import sys
import pyvibdmc as pv
test_sim = pv.SimInfo('pyvibdmc/sample_sim_data/tutorial_water_0_sim_info.hdf5')
savefigpth = 'pyvibdmc/tests/'
# Test writing and reading xyz coords from file
def test_write_xyz_file():
cds, dws = test_sim.get_wfns([2500, 3500]) # get two wave functions just for testing
atm_str_list = ["H", "H", "O"]
pv.XYZNPY.write_xyz(coords=cds, fname=f'{savefigpth}water_cds.xyz', atm_strings=atm_str_list,
cmt='from dmc simulation')
cds_back = pv.XYZNPY.extract_xyz(f'{savefigpth}water_cds.xyz', num_atoms=len(atm_str_list))
assert np.allclose(cds, cds_back)
def test_get_all_siminfo():
vref_vs_tau = test_sim.get_vref()
pop_vs_tau = test_sim.get_pop()
atom_nums = test_sim.get_atomic_nums()
atom_masses = test_sim.get_atom_masses()
# Basic SimInfoStuff
def test_sim_data_zpe():
zpe = test_sim.get_zpe(onwards=100)