def test_water_pp_pb(self): """ This is for initializing with SIESTA radial orbitals """ from numpy import einsum, array import os dname = os.path.dirname(os.path.abspath(__file__)) sv = mf(label='water', cd=dname) sv.diag_check() self.assertTrue(abs(sv.ucell).sum()>0) pb = sv.pb self.assertEqual(sv.norbs, 23) self.assertEqual(len(pb.bp2info), 3) vden = pb.get_ac_vertex_array() ccden = pb.get_da2cc_den() moms = pb.comp_moments() oref = sv.overlap_coo().toarray() over = einsum('lab,l->ab', vden, moms[0]) dcoo = sv.dipole_coo() dref = array([dc.toarray() for dc in dcoo]) dipo = einsum('lab,lx->xab', vden, moms[1]) emean = (abs(oref-over).sum()/(oref.size)) emax = (abs(oref-over).max()) self.assertAlmostEqual(emean, 0.000102115844911, 4) self.assertAlmostEqual(emax, 0.00182562129245, 4) emean = (abs(dref-dipo).sum()/(dref.size)) emax = (abs(dref-dipo).max()) self.assertAlmostEqual(emean, 0.000618731257284, 4) self.assertAlmostEqual(emax, 0.0140744946617, 4)
def test_dens_elec(self): """ Compute density in coordinate space with scf, integrate and compare with number of electrons """ from timeit import default_timer as timer sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__))) dm = sv.make_rdm1() #dm = sv.comp_dm() #print(sv.get_occupations()) #print(dir(sv.ao_log) ) #print((sv.ao_log.psi_log[0][0]**2 *sv.ao_log.rr**3 * np.log(sv.ao_log.rr[1]/sv.ao_log.rr[0])).sum()) #print((sv.ao_log.psi_log[0][1]**2 *sv.ao_log.rr**3 * np.log(sv.ao_log.rr[1]/sv.ao_log.rr[0])).sum()) #print((sv.ao_log.psi_log[0][2]**2 *sv.ao_log.rr**3 * np.log(sv.ao_log.rr[1]/sv.ao_log.rr[0])).sum()) #print((sv.ao_log.psi_log[0][3]**2 *sv.ao_log.rr**3 * np.log(sv.ao_log.rr[1]/sv.ao_log.rr[0])).sum()) #print((sv.ao_log.psi_log[0][4]**2 *sv.ao_log.rr**3 * np.log(sv.ao_log.rr[1]/sv.ao_log.rr[0])).sum()) # #print((sv.ao_log.psi_log[1][0]**2 *sv.ao_log.rr**3 * np.log(sv.ao_log.rr[1]/sv.ao_log.rr[0])).sum()) #print((sv.ao_log.psi_log[1][1]**2 *sv.ao_log.rr**3 * np.log(sv.ao_log.rr[1]/sv.ao_log.rr[0])).sum()) #print((sv.ao_log.psi_log[1][2]**2 *sv.ao_log.rr**3 * np.log(sv.ao_log.rr[1]/sv.ao_log.rr[0])).sum()) grid = sv.build_3dgrid_pp(level=5) #t1 = timer() #dens1 = sv.dens_elec_vec(grid.coords, dm) #t2 = timer(); print(t2-t1); t1 = timer() t1 = timer() dens = sv.dens_elec(grid.coords, dm) #t2 = timer(); print(t2-t1); t1 = timer() nelec = np.einsum("is,i", dens, grid.weights)[0] #t2 = timer(); print(t2-t1, nelec, sv.hsx.nelec, dens.shape); t1 = timer() self.assertAlmostEqual(nelec, sv.hsx.nelec, 2)
def test_aos_libnao(self): """ Computing of the atomic orbitals """ sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__))) cc = Cube(sv, nx=20, ny=20, nz=20) aos = sv.comp_aos_den(cc.get_coords()) self.assertEqual(aos.shape[0], cc.nx*cc.ny*cc.nz) self.assertEqual(aos.shape[1], sv.norbs)
def test_aos_libnao(self): """ Computing of the atomic orbitals """ sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__))) cc = Cube(sv, nx=20, ny=20, nz=20) aos = sv.comp_aos_den(cc.get_coords()) self.assertEqual(aos.shape[0], cc.nx * cc.ny * cc.nz) self.assertEqual(aos.shape[1], sv.norbs)
def test_sv_after_gpaw(self): """ init ao_log_c with it radial orbitals from GPAW """ if calc is None: return self.assertTrue(hasattr(calc, 'setups')) sv = mf(gpaw=calc) self.assertEqual(sv.ao_log.nr, 1024)
def test_sv_after_gpaw(self): """ init ao_log_c with it radial orbitals from GPAW """ if calc is None: return self.assertTrue(hasattr(calc, 'setups')) sv = mf(gpaw=calc) self.assertEqual(sv.ao_log.nr, 1024)
def test_exc(self): """ Compute exchange-correlation energy """ from timeit import default_timer as timer sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__))) dm = sv.make_rdm1() exc = sv.exc(dm, xc_code='1.0*LDA,1.0*PZ', level=4) #self.assertAlmostEqual(exc, -4.1422234271159333) ? redone water? self.assertAlmostEqual(exc, -4.1422239276270201)
def test_mo_cube_libnao(self): """ Computing of the atomic orbitals """ sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__))) cc = Cube(sv, nx=40, ny=40, nz=40) co2val = sv.comp_aos_den(cc.get_coords()) nocc_0t = int(sv.nelectron / 2) c2orb = np.dot(co2val, sv.wfsx.x[0,0,nocc_0t,:,0]).reshape((cc.nx, cc.ny, cc.nz)) cc.write(c2orb, "water_mo.cube", comment='H**O')
def test_sv_after_gpaw(self): """ init ao_log_c with it radial orbitals from GPAW """ if calc is None: return self.assertTrue(hasattr(calc, 'setups')) sv = mf(gpaw=calc) self.assertEqual(sv.ao_log.nr, 1024) over = sv.overlap_coo().toarray() error = sv.hsx.check_overlaps(over) self.assertLess(error, 1e-4)
def test_mo_cube_libnao(self): """ Computing of the atomic orbitals """ sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__))) cc = Cube(sv, nx=40, ny=40, nz=40) co2val = sv.comp_aos_den(cc.get_coords()) nocc_0t = int(sv.nelectron / 2) c2orb = np.dot(co2val, sv.wfsx.x[0, 0, nocc_0t, :, 0]).reshape( (cc.nx, cc.ny, cc.nz)) cc.write(c2orb, "water_mo.cube", comment='H**O')
def test_137_h2o_rks_nonin_pb(self): """ This """ mol = gto.M(verbose=1, atom='O 0 0 0; H 0 0.489 1.074; H 0 0.489 -1.074', basis='cc-pvdz') gto_mf = dft.RKS(mol) gto_mf.kernel() nao_mf = mf(gto=mol, mf=gto_mf, gen_pb=False) comega = np.arange(0.0, 2.0, 0.01) + 1j * 0.03 pnonin = -nao_mf.polariz_nonin_ave_matelem(comega).imag data = np.array([comega.real * HARTREE2EV, pnonin]) np.savetxt('test_137_h2o_rks_nonin_pb.txt', data.T, fmt=['%f', '%f']) data_ref = np.loadtxt('test_137_h2o_rks_nonin_pb.txt-ref').T self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3))
def test_dens_elec(self): """ Compute density in coordinate space with scf, integrate and compare with number of electrons """ from timeit import default_timer as timer gto_mf = scf_gto.RKS(mol) gto_mf.kernel() sv = mf(mf=gto_mf, gto=mol) dm = sv.make_rdm1() grid = sv.build_3dgrid_pp(level=5) dens = sv.dens_elec(grid.coords, dm) nelec = np.einsum("is,i", dens, grid.weights)[0] self.assertAlmostEqual(nelec, sv.nelectron, 6)
def test_siesta2sv_df(self): import subprocess import os siesta_fdf = """ xml.write .true. PAO.EnergyShift 100 meV %block ChemicalSpeciesLabel 1 11 Na %endblock ChemicalSpeciesLabel NumberOfAtoms 2 NumberOfSpecies 1 %block AtomicCoordinatesAndAtomicSpecies 0.77573521 0.00000000 0.00000000 1 -0.77573521 0.00000000 0.00000000 1 %endblock AtomicCoordinatesAndAtomicSpecies MD.NumCGsteps 0 COOP.Write .true. WriteDenchar .true. """ label = 'siesta' fi = open(label + '.fdf', 'w') print(siesta_fdf, file=fi) fi.close() for sp in ['Na']: try: os.remove(sp + '.psf') except: pass try: pppath = get_pseudo(sp) except: print('get_pseudo( ' + sp + ' ) is not working--> skip siesta run') return os.symlink(pppath, sp + '.psf') errorcode = subprocess.call(get_siesta_command(label), shell=True) if errorcode: raise RuntimeError( 'siesta returned an error: {0}'.format(errorcode)) # run test system_vars from pyscf.nao import mf sv = mf(label=label) self.assertEqual(sv.norbs, 10) self.assertTrue(sv.diag_check()) self.assertTrue(sv.overlap_check())
def test_vrtx_cc_apairs(self): """ This is to test a batch generation vertices for bilocal atomic pairs. """ from numpy import allclose dname = os.path.dirname(os.path.abspath(__file__)) sv = mf(label='water', cd=dname) pbb = sv.pb pba = prod_basis(sv) for a,b in zip(pba.bp2info,pbb.bp2info): for a1,a2 in zip(a.atoms,b.atoms): self.assertEqual(a1,a2) for a1,a2 in zip(a.cc2a, b.cc2a): self.assertEqual(a1,a2) self.assertTrue(allclose(a.vrtx, b.vrtx)) self.assertTrue(allclose(a.cc, b.cc)) self.assertLess(abs(pbb.get_da2cc_sparse().tocsr()-pba.get_da2cc_sparse().tocsr()).sum(), 1e-9) self.assertLess(abs(pbb.get_dp_vertex_sparse().tocsr()-pba.get_dp_vertex_sparse().tocsr()).sum(), 1e-10)
def test_siesta2sv_df(self): import subprocess import os siesta_fdf = """ xml.write .true. PAO.EnergyShift 100 meV %block ChemicalSpeciesLabel 1 11 Na %endblock ChemicalSpeciesLabel NumberOfAtoms 2 NumberOfSpecies 1 %block AtomicCoordinatesAndAtomicSpecies 0.77573521 0.00000000 0.00000000 1 -0.77573521 0.00000000 0.00000000 1 %endblock AtomicCoordinatesAndAtomicSpecies MD.NumCGsteps 0 COOP.Write .true. WriteDenchar .true. """ label = 'siesta' fi = open(label+'.fdf', 'w') print(siesta_fdf, file=fi) fi.close() for sp in ['Na']: try: os.remove(sp+'.psf') except : pass try: pppath = get_pseudo(sp) except: print('get_pseudo( '+sp+' ) is not working--> skip siesta run' ) return os.symlink(pppath, sp+'.psf') errorcode = subprocess.call(get_siesta_command(label), shell=True) if errorcode: raise RuntimeError('siesta returned an error: {0}'.format(errorcode)) # run test system_vars from pyscf.nao import mf sv = mf(label=label) self.assertEqual(sv.norbs, 10) self.assertTrue( sv.diag_check() ) self.assertTrue( sv.overlap_check())
def test_vrtx_cc_apairs(self): """ This is to test a batch generation vertices for bilocal atomic pairs. """ from numpy import allclose dname = os.path.dirname(os.path.abspath(__file__)) sv = mf(label='water', cd=dname) pbb = sv.pb pba = prod_basis(sv) for a, b in zip(pba.bp2info, pbb.bp2info): for a1, a2 in zip(a.atoms, b.atoms): self.assertEqual(a1, a2) for a1, a2 in zip(a.cc2a, b.cc2a): self.assertEqual(a1, a2) self.assertTrue(allclose(a.vrtx, b.vrtx)) self.assertTrue(allclose(a.cc, b.cc)) self.assertLess( abs(pbb.get_da2cc_sparse().tocsr() - pba.get_da2cc_sparse().tocsr()).sum(), 1e-9) self.assertLess( abs(pbb.get_dp_vertex_sparse().tocsr() - pba.get_dp_vertex_sparse().tocsr()).sum(), 1e-10)
def test_read_siesta_bulk_spin(self): """ Test reading of bulk, spin-resolved SIESTA calculation """ chdir = os.path.dirname(os.path.abspath(__file__)) + '/ice' sv = mf(label='siesta', cd=chdir) sv.diag_check()
def test_fireball(self): """ Test computation of matrix elements of overlap after fireball """ sv = mf(fireball="fireball.out", gen_pb=False) s_ref = sv.hsx.s4_csr.toarray() s = sv.overlap_coo().toarray()
def test_dft_sv(self): """ Try to compute the xc potential """ sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__))) vxc = sv.vxc_lil()
def test_sf_gw_res_corr(self): """ This is choice of wmin and wmax in GW """ mol = gto.M( verbose = 1, atom = '''H 0 0 0; H 0.17 0.7 0.587''', basis = 'cc-pvdz',) gto_mf = scf.RHF(mol) gto_mf.kernel() s = mf(mf=gto_mf, gto=mol)
from __future__ import print_function, division import os,unittest,numpy as np from pyscf.nao import mf dname = os.path.dirname(os.path.abspath(__file__)) dft = mf(label='water', cd=dname) class KnowValues(unittest.TestCase): def test_dos(self): """ This is DoS with the KS eigenvalues """ omegas = np.linspace(-1.0,1.0,500)+1j*0.01 dos = dft.dos(omegas) data = np.array([27.2114*omegas.real, dos]) np.savetxt('water.dos.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt(dname+'/water.dos.txt-ref') self.assertTrue(np.allclose(data_ref,data.T, rtol=1.0, atol=1e-05)) def test_pdos(self): """ This is PDoS with SIESTA starting point """ omegas = np.linspace(-1.0,1.0,500)+1j*0.01 pdos = dft.pdos(omegas) data = np.array([27.2114*omegas.real, pdos[0], pdos[1], pdos[2]]) np.savetxt('water.pdos.txt', data.T) data_ref = np.loadtxt(dname+'/water.pdos.txt-ref') self.assertTrue(np.allclose(data_ref,data.T, rtol=1.0, atol=1e-05)) if __name__ == "__main__": unittest.main()
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. from __future__ import print_function, division import os,unittest from pyscf.nao import mf sv = mf(label='water', cd=os.path.dirname(os.path.abspath(__file__))) class KnowValues(unittest.TestCase): def test_init_sv_libnao(self): """ Init system variables on libnao's site """ sv.init_libnao() if __name__ == "__main__": unittest.main()
def test_read_siesta_bulk_spin(self): """ Test reading of bulk, spin-resolved SIESTA calculation """ chdir = os.path.dirname(os.path.abspath(__file__))+'/ice' sv = mf(label='siesta', cd=chdir) sv.diag_check()
s = np.sqrt(ss + 0.25) - 0.5 return ss, s * 2 + 1 # # Example of reading pySCF mean-field calculation. # if __name__ == "__main__": from pyscf import gto, scf as scf_gto from pyscf.nao import nao, mf """ Interpreting small Gaussian calculation """ mol = gto.M(atom='O 0 0 0; H 0 0 1; H 0 1 0; Be 1 0 0', basis='ccpvdz') # coordinates in Angstrom! dft = scf_gto.RKS(mol) dft.kernel() sv = mf(mf=dft, gto=dft.mol, rcut_tol=1e-9, nr=512, rmin=1e-6) print(sv.ao_log.sp2norbs) print(sv.ao_log.sp2nmult) print(sv.ao_log.sp2rcut) print(sv.ao_log.sp_mu2rcut) print(sv.ao_log.nr) print(sv.ao_log.rr[0:4], sv.ao_log.rr[-1:-5:-1]) print(sv.ao_log.psi_log[0].shape, sv.ao_log.psi_log_rl[0].shape) print(dir(sv.pb)) print(sv.pb.norbs) print(sv.pb.npdp) print(sv.pb.c2s[-1])
def test_fireball(self): """ Test computation of matrix elements of overlap after fireball """ sv = mf(fireball="fireball.out", gen_pb=False) s_ref = sv.hsx.s4_csr.toarray() s = sv.overlap_coo().toarray() print(abs(s-s_ref).sum())
ax.grid(True, which='both') ax.axhline(y=0, color='k') ax.axvline(x=0, color='k') plt.ylim(-3.0,3.0) plt.show() # # Example of reading pySCF mean-field calculation. # if __name__=="__main__": from pyscf import gto, scf as scf_gto from pyscf.nao import nao, mf """ Interpreting small Gaussian calculation """ mol = gto.M(atom='O 0 0 0; H 0 0 1; H 0 1 0; Be 1 0 0', basis='ccpvdz') # coordinates in Angstrom! dft = scf_gto.RKS(mol) dft.kernel() sv = mf(mf=dft, gto=dft.mol, rcut_tol=1e-9, nr=512, rmin=1e-6) print(sv.ao_log.sp2norbs) print(sv.ao_log.sp2nmult) print(sv.ao_log.sp2rcut) print(sv.ao_log.sp_mu2rcut) print(sv.ao_log.nr) print(sv.ao_log.rr[0:4], sv.ao_log.rr[-1:-5:-1]) print(sv.ao_log.psi_log[0].shape, sv.ao_log.psi_log_rl[0].shape) print(dir(sv.pb)) print(sv.pb.norbs) print(sv.pb.npdp) print(sv.pb.c2s[-1])
from __future__ import print_function, division import os, unittest, numpy as np from pyscf.nao import mf dname = os.path.dirname(os.path.abspath(__file__)) dft = mf(label='water', cd=dname) class KnowValues(unittest.TestCase): def test_dos(self): """ This is DoS with the KS eigenvalues """ omegas = np.linspace(-1.0, 1.0, 500) + 1j * 0.01 dos = dft.dos(omegas) data = np.array([27.2114 * omegas.real, dos]) np.savetxt('water.dos.txt', data.T, fmt=['%f', '%f']) data_ref = np.loadtxt(dname + '/water.dos.txt-ref') self.assertTrue(np.allclose(data_ref, data.T, rtol=1.0, atol=1e-05)) def test_pdos(self): """ This is PDoS with SIESTA starting point """ omegas = np.linspace(-1.0, 1.0, 500) + 1j * 0.01 pdos = dft.pdos(omegas) data = np.array([27.2114 * omegas.real, pdos[0], pdos[1], pdos[2]]) np.savetxt('water.pdos.txt', data.T) data_ref = np.loadtxt(dname + '/water.pdos.txt-ref') self.assertTrue(np.allclose(data_ref, data.T, rtol=1.0, atol=1e-05)) if __name__ == "__main__": unittest.main()
# You may obtain a copy of the License at # # http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. from __future__ import print_function, division from os.path import abspath, dirname from pyscf.nao import mf import unittest, numpy as np sv = mf(label='water', cd=dirname(abspath(__file__))) pb = sv.pb vab_arr_ref = pb.get_dp_vertex_array() class KnowValues(unittest.TestCase): def test_pb_doubly_sparse(self): """ This is to test generation of a doubly sparse format. """ self.assertEqual(len(vab_arr_ref.shape), 3) self.assertEqual(vab_arr_ref.shape, (pb.npdp,pb.norbs,pb.norbs)) vab_ds = pb.get_dp_vertex_doubly_sparse(axis=2) vab_arr = vab_ds.toarray() self.assertLess(abs(vab_arr-vab_arr_ref).sum()/vab_arr.size, 1e-15) def test_pb_sparse(self): """ This is to test generation of a doubly sparse format. """