def test_adc_parse():
CAPH = CAPHamiltonian(output=os.path.join(dest_dir, "adc.out"))
assert np.isclose(CAPH._W[0][0], -6.3724737e+01)
CAPH = CAPHamiltonian(output=os.path.join(dest_dir, "adc.out"),
onset="4000")
assert np.isclose(CAPH._W[0][0], -4.9669293e+01)
try:
CAPH = CAPHamiltonian(output=os.path.join(dest_dir, "adc.out"),
onset="1000")
except:
pass
def get_corrected_energy(pc):
CAPH = CAPHamiltonian(pc=pc)
eta_list = np.linspace(0, 5000, 101)
eta_list = np.around(eta_list * 1E-5, decimals=5)
CAPH.run_trajectory(eta_list)
traj = CAPH.track_state(1, tracking="energy")
corr_energy, corr_eta_opt = traj.find_eta_opt(corrected=True,
start_idx=10,
end_idx=-1,
ref_energy=ref_energy,
units="eV")
return corr_energy
def test_biorthogonalization():
CAPH = CAPHamiltonian(output=os.path.join(dest_dir, "n2_opencap.out"))
CAPH.run_trajectory([0.01])
roots = CAPH._all_roots[0]
ovlp = np.zeros((len(roots), len(roots)), dtype='complex_')
for i in range(0, len(roots)):
lr = roots[i].Leigvc
for j in range(0, len(roots)):
rr = roots[j].Reigvc
ovlp[i][j] = np.dot(lr, rr)
identity = np.identity(len(roots))
diff = np.sum(ovlp - identity)
assert np.isclose(diff, 0.0)
def test_roots():
CAPH = CAPHamiltonian(output=os.path.join(dest_dir, "n2_opencap.out"))
CAPH.run_trajectory(eta_list)
traj = CAPH.track_state(1)
E1, eta1, root1 = traj.find_eta_opt(corrected=True,
units="au",
return_root=True)
E2, root2 = traj.get_energy(eta1,
corrected=True,
units="au",
return_root=True)
assert root1 == root2
assert np.isclose(E1, E2)
def test_molcas():
sys = pyopencap.System(sys_dict)
pc = pyopencap.CAP(sys, cap_dict, 10)
pc.read_data(es_dict)
pc.compute_ao_cap(cap_dict)
pc.compute_projected_cap()
CAPH = CAPHamiltonian(pc=pc)
def test_eomcc_parse():
CAPH = CAPHamiltonian(output=os.path.join(dest_dir, "eomcc.out"))
assert np.isclose(CAPH._H0[0][0], -1.09353e+02)
CAPH = CAPHamiltonian(output=os.path.join(dest_dir, "eomcc.out"),
irrep="B2g")
assert np.isclose(CAPH._H0[0][0], -1.09313e+02)
CAPH = CAPHamiltonian(output=os.path.join(dest_dir, "eomcc_old.out"),
irrep="B2g")
assert np.isclose(CAPH._H0[0][0], -1.09313e+02)
CAPH = CAPHamiltonian(output=os.path.join(dest_dir, "eomcc.out"),
irrep="all")
assert len(CAPH._H0) == 10
try:
CAPH = CAPHamiltonian(output=os.path.join(dest_dir, "eomcc.out"),
irrep="B1g")
except:
pass
def test_qchem():
sys = pyopencap.System(sys_dict)
pc = pyopencap.CAP(sys, cap_dict, 5)
pc.read_data(es_dict)
pc.compute_ao_cap(cap_dict)
pc.compute_projected_cap()
W = pc.get_projected_cap()
pc.compute_ao_cap(cap_dict2)
pc.compute_projected_cap()
W2 = pc.get_projected_cap()
assert not W[0][0] == W2[0][0]
CAPH = CAPHamiltonian(pc=pc)
def test_eta_opt():
CAPH = CAPHamiltonian(output=os.path.join(dest_dir, "n2_opencap.out"))
CAPH.run_trajectory(eta_list)
traj = CAPH.track_state(1, tracking="overlap")
uc_energy_au, uc_eta = traj.find_eta_opt(units="au")
corr_energy_au, corr_eta = traj.find_eta_opt(corrected=True, units="au")
uc_energy_ev, uc_eta = traj.find_eta_opt(ref_energy=ref_energy, units="eV")
corr_energy_ev, corr_eta = traj.find_eta_opt(ref_energy=ref_energy,
corrected=True,
units="eV")
assert np.isclose(np.real(uc_energy_au), -109.265006)
assert np.isclose(np.real(corr_energy_au), -109.26652)
assert np.isclose(np.real(uc_energy_ev), 2.6381)
assert np.isclose(np.real(corr_energy_ev), 2.59686)
traj = CAPH.track_state(1, tracking="energy")
uc_energy_au = traj.get_energy(uc_eta)
corr_energy_au = traj.get_energy(corr_eta, corrected=True)
uc_energy_ev = traj.get_energy(uc_eta, ref_energy=ref_energy, units="eV")
corr_energy_ev = traj.get_energy(corr_eta,
ref_energy=ref_energy,
corrected=True,
units="eV")
assert np.isclose(np.real(uc_energy_au), -109.265006)
assert np.isclose(np.real(corr_energy_au), -109.26652)
assert np.isclose(np.real(uc_energy_ev), 2.6381)
assert np.isclose(np.real(corr_energy_ev), 2.59686)
def test_energies_ev():
CAPH = CAPHamiltonian(output=os.path.join(dest_dir, "n2_opencap.out"))
CAPH.run_trajectory(eta_list)
assert np.isclose(np.real(CAPH.energies_ev(ref_energy=ref_energy)[0]),
1.3174781)
traj = CAPH.track_state(1, tracking="overlap")
assert np.isclose(np.real(traj.energies_ev(ref_energy=ref_energy)[0]),
2.55378)
def test_correction():
CAPH = CAPHamiltonian(output=os.path.join(dest_dir, "n2_opencap.out"))
CAPH.run_trajectory(eta_list)
traj = CAPH.track_state(1, correction="density")
E1, eta1 = traj.find_eta_opt(corrected=True, units="au")
traj = CAPH.track_state(1, correction="derivative")
E2, eta2 = traj.find_eta_opt(corrected=True, units="au")
assert np.isclose(E1, E2)
assert np.isclose(eta1, eta2)
def test_tracking():
CAPH = CAPHamiltonian(output=os.path.join(dest_dir, "n2_opencap.out"))
CAPH.run_trajectory(eta_list)
traj = CAPH.track_state(1, tracking="overlap")
E1, eta1 = traj.find_eta_opt(corrected=True, units="au")
traj = CAPH.track_state(1, tracking="energy")
E2, eta2 = traj.find_eta_opt(corrected=True, units="au")
assert np.isclose(E1, E2)
assert np.isclose(eta1, eta2)
def test_energies_ev():
CAPH = CAPHamiltonian(output=os.path.join(dest_dir, "n2_opencap.out"))
CAPH.run_trajectory(eta_list)
traj = CAPH.track_state(1, tracking="overlap")
# fill density matrices
h0 = np.zeros((nstates, nstates))
for i in range(0, len(e)):
h0[i][i] = e[i]
# compute CAP
pc = pyopencap.CAP(s, cap_dict, nstates)
for i in range(0, len(fs.ci)):
for j in range(0, len(fs.ci)):
dm1 = fs.trans_rdm1(fs.ci[i], fs.ci[j], myhf.mo_coeff.shape[1],
mol.nelec)
dm1_ao = np.einsum('pi,ij,qj->pq', myhf.mo_coeff, dm1,
myhf.mo_coeff.conj())
pc.add_tdm(dm1_ao, i, j, "pyscf")
pc.compute_projected_cap()
W = pc.get_projected_cap()
from pyopencap.analysis import CAPHamiltonian as CAPH
my_CAPH = CAPH(H0=h0, W=W)
my_CAPH.export("H2_fci_opencap.out")
end = time.time()
print("Time:")
print(end - start)
import os
os.remove("molden_in.molden")
h0 = np.zeros((nstates, nstates))
for i in range(0, len(h0)):
h0[i][i] = E_0 + state.excitation_energy[i]
for i in range(0, nstates):
state2state = State2States(state, initial=i)
rdm = state.state_dm[i]
rdm_alpha, rdm_beta = rdm.to_ao_basis()
rdm_alpha = rdm_alpha.to_ndarray()
rdm_beta = rdm_beta.to_ndarray()
pc.add_tdms(rdm_alpha, rdm_beta, i, i, "psi4")
for j, tdm in enumerate(state2state.transition_dm):
tdm_alpha, tdm_beta = tdm.to_ao_basis()
tdm_alpha = tdm_alpha.to_ndarray()
tdm_beta = tdm_beta.to_ndarray()
pc.add_tdms(tdm_alpha, tdm_beta, i, i + j + 1, "psi4")
pc.add_tdms(tdm_alpha.conj().T,
tdm_beta.conj().T, i + j + 1, i, "psi4")
pc.compute_projected_cap()
W = pc.get_projected_cap()
from pyopencap.analysis import CAPHamiltonian as CAPH
my_CAPH = CAPH(H0=h0, W=W)
my_CAPH.export("n2_adc_opencap.out")
end = time.time()
print("Time:")
print(end - start)
'''
# Analyze OpenCAP output file, view eigenvalue trajectory
import pyopencap
from pyopencap.analysis import CAPHamiltonian
import numpy as np
import argparse
import matplotlib.pyplot as plt
parser = argparse.ArgumentParser(description='Process OpenCAP output file.')
parser.add_argument('output_file',help='OpenCAP output file')
args = parser.parse_args()
CAPH = CAPHamiltonian(output=args.output_file)
eta_list = np.linspace(0,5000,101)
eta_list = np.around(eta_list * 1E-5,decimals=5)
CAPH.run_trajectory(eta_list)
plt.plot(np.real(CAPH.total_energies),np.imag(CAPH.total_energies),'ro')
plt.show()
for i in range(0,CAPH.nstates):
traj = CAPH.track_state(i,tracking="overlap")
uc_energy, eta_opt = traj.find_eta_opt(start_idx=10)
corr_energy, corr_eta_opt = traj.find_eta_opt(corrected=True,start_idx=10)
plt.plot(np.real(traj.uncorrected_energies),np.imag(traj.uncorrected_energies),'-ro')
plt.plot(np.real(traj.corrected_energies),np.imag(traj.corrected_energies),'-bo')
plt.plot(np.real(corr_energy),np.imag(corr_energy),"g*",markersize=20)
plt.plot(np.real(uc_energy),np.imag(uc_energy),"g*",markersize=20)
plt.show()
es_dict = {
"package": "openmolcas",
"method": "ms-caspt2",
"molcas_output": OUTPUT_FILE,
"rassi_h5": RASSI_FILE,
}
s = pyopencap.System(sys_dict)
pc = pyopencap.CAP(s, cap_dict, 10)
pc.read_data(es_dict)
pc.compute_projected_cap()
W = pc.get_projected_cap()
h0 = pc.get_H()
CAPH = CAPHamiltonian(H0=h0, W=W)
eta_list = np.linspace(0, 5000, 101)
eta_list = np.around(eta_list * 1E-5, decimals=5)
CAPH.run_trajectory(eta_list)
ref_energy = -109.36219955
traj = CAPH.track_state(2, tracking="overlap")
# Find optimal value of eta
uc_energy, eta_opt = traj.find_eta_opt(start_idx=10,
ref_energy=ref_energy,
units="eV")
# start_idx and end_idx for search use python slice notation (i.e. [start_idx:end_idx]).
corr_energy, corr_eta_opt = traj.find_eta_opt(corrected=True,
start_idx=10,
end_idx=-1,
ref_energy=ref_energy,
units="eV")
def test_init_from_matrices():
CAPH = CAPHamiltonian(output=os.path.join(dest_dir, "eomcc.out"))
CAPH2 = CAPHamiltonian(H0=CAPH._H0, W=CAPH._W)
assert CAPH._nstates == CAPH2._nstates
def test_include_states():
CAPH = CAPHamiltonian(output=os.path.join(dest_dir, "n2_opencap.out"))
CAPH.run_trajectory(eta_list, include_states=[0, 1, 2, 4])
assert CAPH.H0.shape == CAPH.W.shape == (4, 4)
assert np.isclose(CAPH.H0[3][3], -1.089933e+02)
assert np.isclose(CAPH.W[3][3], -1.65280e+02)
def test_opencap_parse():
CAPH = CAPHamiltonian(output=os.path.join(dest_dir, "n2_opencap.out"))
assert np.isclose(CAPH._W[0][0], -4.28708660e+01)
def test_export():
CAPH = CAPHamiltonian(output=os.path.join(dest_dir, "n2_opencap.out"))
CAPH.export("test.out")
CAPH2 = CAPHamiltonian(output="test.out")
assert np.isclose(CAPH._H0[0][0], CAPH2._H0[0][0])
os.remove("test.out")
es_dict = {
"package": "qchem",
"method": "eom",
"qchem_output": "../../analysis/N2/ref_outputs/qc_inp.out",
"qchem_fchk": "../../analysis/N2/ref_outputs/qc_inp.fchk",
}
s = pyopencap.System(sys_dict)
pc = pyopencap.CAP(s, cap_dict, 5)
pc.read_data(es_dict)
pc.compute_projected_cap()
W = pc.get_projected_cap()
H0 = pc.get_H()
CAPH = CAPHamiltonian(pc=pc)
eta_list = np.linspace(0, 5000, 201)
eta_list = np.around(eta_list * 1E-5, decimals=5)
CAPH.run_trajectory(eta_list)
traj = CAPH.track_state(1, tracking="energy")
ref_energy = -109.36195558
# Find optimal value of eta
uc_energy, eta_opt = traj.find_eta_opt(start_idx=10,
ref_energy=ref_energy,
units="eV")
# start_idx and end_idx for search use python slice notation (i.e. [start_idx:end_idx]).
corr_energy, corr_eta_opt = traj.find_eta_opt(corrected=True,
start_idx=10,
end_idx=-1,
ref_energy=ref_energy,
units="eV")
mytd = tdscf.TDA(mf).run(nstates=nstates)
print(mytd.e_tot)
H0 = np.zeros((nstates, nstates))
for i in range(0, len(mytd.e_tot)):
H0[i][i] = mytd.e_tot[i]
for i in range(0, nstates):
for j in range(i, nstates):
dm1_alpha, dm1_beta = tda_density_matrix(mytd, i, j)
pc.add_tdms(dm1_alpha, dm1_beta, i, j, "pyscf")
if not i == j:
pc.add_tdms(dm1_alpha.conj().T, dm1_beta.conj().T, j, i, "pyscf")
pc.compute_projected_cap()
W = pc.get_projected_cap()
from pyopencap.analysis import CAPHamiltonian as CAPH
my_CAPH = CAPH(H0=H0, W=W)
my_CAPH.export("n2_tddft_opencap.out")
import os
os.remove("molden_in.molden")
os.remove('n2.chk')
end = time.time()
print("Time:")
print(end - start)