Python numpy.savetxt() Examples
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Example #1
Source File: test_0082_bse_gw_gto_be.py From pyscf with Apache License 2.0 | 6 votes |
def test_bse_gto_vs_nao_inter_0082(self): """ Interacting case """ #dm1 = gto_mf.make_rdm1() #o1 = gto_mf.get_ovlp() #print(__name__, 'dm1*o1', (dm1*o1).sum()) nao_td = bse_iter(mf=gto_mf, gto=mol, verbosity=0, xc_code='GW', perform_gw=True) #dm2 = nao_td.make_rdm1() #o2 = nao_td.get_ovlp() #n = nao_td.norbs #print(__name__, 'dm2*o2', (dm2.reshape((n,n))*o2).sum()) omegas = np.linspace(0.0,2.0,450)+1j*0.04 p_iter = -nao_td.comp_polariz_inter_ave(omegas).imag data = np.array([omegas.real*27.2114, p_iter]) np.savetxt('be.bse_iter.omega.inter.ave.txt', data.T, fmt=['%f','%f'])
Example #2
Source File: test_0150_bse_h2o_uhf_rpa.py From pyscf with Apache License 2.0 | 6 votes |
def test_0150_bse_h2o_uhf_rpa(self): """ Interacting case """ mol=gto.M(verbose=0,atom='O 0 0 0;H 0 0.489 1.074;H 0 0.489 -1.074',basis='cc-pvdz',) gto_mf = scf.UKS(mol) gto_mf.xc = 'hf' gto_mf.kernel() gto_td = tddft.dRPA(gto_mf) gto_td.nstates = 95 gto_td.kernel() omegas = np.arange(0.0, 2.0, 0.01) + 1j*0.03 p_ave = -polariz_freq_osc_strength(gto_td.e, gto_td.oscillator_strength(), omegas).imag data = np.array([omegas.real*HARTREE2EV, p_ave]) np.savetxt('test_0150_bse_h2o_uhf_rpa_pyscf.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt('test_0150_bse_h2o_uhf_rpa_pyscf.txt-ref').T self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3)) nao_td = bse_iter(mf=gto_mf, gto=mol, verbosity=0, xc_code='RPA') polariz = -nao_td.comp_polariz_inter_ave(omegas).imag data = np.array([omegas.real*HARTREE2EV, polariz]) np.savetxt('test_0150_bse_h2o_uhf_rpa_nao.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt('test_0150_bse_h2o_uhf_rpa_nao.txt-ref').T self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3))
Example #3
Source File: test_0151_bse_h2b_uhf_rpa.py From pyscf with Apache License 2.0 | 6 votes |
def test_151_bse_h2b_uhf_rpa(self): """ This """ mol = gto.M(verbose=1,atom='B 0 0 0; H 0 0.489 1.074; H 0 0.489 -1.074',basis='cc-pvdz',spin=3) gto_mf = scf.UKS(mol) gto_mf.xc = 'hf' gto_mf.kernel() gto_td = tddft.dRPA(gto_mf) gto_td.nstates = 190 gto_td.kernel() omegas = np.arange(0.0, 2.0, 0.01) + 1j*0.03 p_ave = -polariz_freq_osc_strength(gto_td.e, gto_td.oscillator_strength(), omegas).imag data = np.array([omegas.real*HARTREE2EV, p_ave]) np.savetxt('test_0151_bse_h2b_uhf_rpa_pyscf.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt('test_0151_bse_h2b_uhf_rpa_pyscf.txt-ref').T self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3)) nao_td = bse_iter(mf=gto_mf, gto=mol, verbosity=0, xc_code='RPA') polariz = -nao_td.comp_polariz_inter_ave(omegas).imag data = np.array([omegas.real*HARTREE2EV, polariz]) np.savetxt('test_0151_bse_h2b_uhf_rpa_nao.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt('test_0151_bse_h2b_uhf_rpa_nao.txt-ref').T self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3))
Example #4
Source File: test_0096_h2_ae_qchem_irf.py From pyscf with Apache License 2.0 | 6 votes |
def test_qchem_irf(self): """ Test """ gto_hf = dft.RKS(mol) gto_hf.kernel() nocc = mol.nelectron//2 nmo = gto_hf.mo_energy.size nvir = nmo-nocc gto_td = tddft.dRPA(gto_hf) gto_td.nstates = min(100, nocc*nvir) gto_td.kernel() gto_gw = GW(gto_hf, gto_td) gto_gw.kernel() nao_td = tddft_iter(mf=gto_hf, gto=mol, xc_code='RPA') eps = 0.02 omegas = np.arange(0.0,2.0,eps/2.0)+1j*eps p_iter = -nao_td.comp_polariz_inter_ave(omegas).imag data = np.array([omegas.real*27.2114, p_iter]) np.savetxt('NH.tddft_iter_rpa.omega.inter.pav.txt', data.T, fmt=['%f','%f']) np.set_printoptions(linewidth=180) #qrf = qchem_inter_rf(mf=gto_hf, gto=mol, pb_algorithm='fp', verbosity=1)
Example #5
Source File: utils.py From dynamic-training-with-apache-mxnet-on-aws with Apache License 2.0 | 6 votes |
def pred_test(testing_data, exe, param_list=None, save_path=""): ret = numpy.zeros((testing_data.shape[0], 2)) if param_list is None: for i in range(testing_data.shape[0]): exe.arg_dict['data'][:] = testing_data[i, 0] exe.forward(is_train=False) ret[i, 0] = exe.outputs[0].asnumpy() ret[i, 1] = numpy.exp(exe.outputs[1].asnumpy()) numpy.savetxt(save_path, ret) else: for i in range(testing_data.shape[0]): pred = numpy.zeros((len(param_list),)) for j in range(len(param_list)): exe.copy_params_from(param_list[j]) exe.arg_dict['data'][:] = testing_data[i, 0] exe.forward(is_train=False) pred[j] = exe.outputs[0].asnumpy() ret[i, 0] = pred.mean() ret[i, 1] = pred.std()**2 numpy.savetxt(save_path, ret) mse = numpy.square(ret[:, 0] - testing_data[:, 0] **3).mean() return mse, ret
Example #6
Source File: test_0013_gpaw_overlap_nao.py From pyscf with Apache License 2.0 | 6 votes |
def test_sv_after_gpaw(self): """ init ao_log with radial orbitals from GPAW """ if calc is None: return self.assertTrue(hasattr(calc, 'setups')) sv = mf(gpaw=calc, gen_pb=False) self.assertEqual(sv.ao_log.nr, 1024) over = sv.overlap_coo().toarray() error = sv.hsx.check_overlaps(over) self.assertLess(error, 1e-4) #print("overlap error: ", error/over.size) #print("Pyscf gpaw") #for py, gp in zip(over[:, 0], sv.wfsx.overlaps[:, 0]): # print("{0:.5f} {1:.5f}".format(py, gp)) #np.savetxt("Pyscf.overlaps", over) #np.savetxt("gpaw.overlaps", sv.wfsx.overlaps,)
Example #7
Source File: gap.py From mlearn with BSD 3-Clause "New" or "Revised" License | 6 votes |
def write_param(self, xml_filename='gap.xml'): """ Write xml file to perform lammps calculation. Args: xml_filename (str): Filename to store xml formatted parameters. """ if not self.param: raise RuntimeError("The xml and parameters should be provided.") tree = self.param.get('xml') root = tree.getroot() gpcoordinates = list(root.iter('gpCoordinates'))[0] param_filename = "{}.soapparam".format(self.name) gpcoordinates.set('sparseX_filename', param_filename) np.savetxt(param_filename, self.param.get('param'), fmt='%.20e') tree.write(xml_filename) pair_coeff = self.pair_coeff.format(xml_filename, '\"Potential xml_label={}\"'. format(self.param.get('potential_label')), self.specie.Z) ff_settings = [self.pair_style, pair_coeff] return ff_settings
Example #8
Source File: utils.py From pruning_yolov3 with GNU General Public License v3.0 | 6 votes |
def print_mutation(hyp, results, bucket=''): # Print mutation results to evolve.txt (for use with train.py --evolve) a = '%10s' * len(hyp) % tuple(hyp.keys()) # hyperparam keys b = '%10.3g' * len(hyp) % tuple(hyp.values()) # hyperparam values c = '%10.3g' * len(results) % results # results (P, R, mAP, F1, test_loss) print('\n%s\n%s\nEvolved fitness: %s\n' % (a, b, c)) if bucket: os.system('gsutil cp gs://%s/evolve.txt .' % bucket) # download evolve.txt with open('evolve.txt', 'a') as f: # append result f.write(c + b + '\n') x = np.unique(np.loadtxt('evolve.txt', ndmin=2), axis=0) # load unique rows np.savetxt('evolve.txt', x[np.argsort(-fitness(x))], '%10.3g') # save sort by fitness if bucket: os.system('gsutil cp evolve.txt gs://%s' % bucket) # upload evolve.txt
Example #9
Source File: ingest_flower102.py From ArtGAN with BSD 3-Clause "New" or "Revised" License | 6 votes |
def run(self): """ resize images then write manifest files to disk. """ self.write_label() self.collectdata() records = [(fname, tgt) for fname, tgt in self.trainpairlist.items()] np.savetxt(self.manifests['train'], records, fmt='%s,%s') records = [(fname, tgt) for fname, tgt in self.valpairlist.items()] np.savetxt(self.manifests['val'], records, fmt='%s,%s') records = [(fname, tgt) for fname, tgt in self.testpairlist.items()] np.savetxt(self.manifests['test'], records, fmt='%s,%s')
Example #10
Source File: main.py From transferlearning with MIT License | 6 votes |
def extract_feature(model, dataloader, save_path, load_from_disk=True, model_path=''): if load_from_disk: model = models.Network(base_net=args.model_name, n_class=args.num_class) model.load_state_dict(torch.load(model_path)) model = model.to(DEVICE) model.eval() correct = 0 fea_all = torch.zeros(1,1+model.base_network.output_num()).to(DEVICE) with torch.no_grad(): for inputs, labels in dataloader: inputs, labels = inputs.to(DEVICE), labels.to(DEVICE) feas = model.get_features(inputs) labels = labels.view(labels.size(0), 1).float() x = torch.cat((feas, labels), dim=1) fea_all = torch.cat((fea_all, x), dim=0) outputs = model(inputs) preds = torch.max(outputs, 1)[1] correct += torch.sum(preds == labels.data.long()) test_acc = correct.double() / len(dataloader.dataset) fea_numpy = fea_all.cpu().numpy() np.savetxt(save_path, fea_numpy[1:], fmt='%.6f', delimiter=',') print('Test acc: %f' % test_acc) # You may want to classify with 1nn after getting features
Example #11
Source File: test_0139_h2o_uks_nonin_pb.py From pyscf with Apache License 2.0 | 6 votes |
def test_139_h2o_uks_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.UKS(mol) gto_mf.kernel() nao_mf = bse_iter(gto=mol, mf=gto_mf) 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_139_h2o_uks_nonin_matelem.txt', data.T, fmt=['%f','%f']) #data_ref = np.loadtxt('test_139_h2o_uks_nonin_matelem.txt-ref').T #self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3)) pnonin = -nao_mf.comp_polariz_nonin_ave(comega).imag data = np.array([comega.real*HARTREE2EV, pnonin]) np.savetxt('test_139_h2o_uks_nonin_nao.txt', data.T, fmt=['%f','%f']) #data_ref = np.loadtxt('test_139_h2o_uks_nonin_nao.txt-ref').T #self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3))
Example #12
Source File: test_0152_bse_h2b_uks_pz.py From pyscf with Apache License 2.0 | 6 votes |
def test_152_bse_h2b_uks_pz(self): """ This """ mol = gto.M(verbose=1,atom='B 0 0 0; H 0 0.489 1.074; H 0 0.489 -1.074',basis='cc-pvdz',spin=3) gto_mf = scf.UKS(mol) gto_mf.kernel() gto_td = tddft.TDDFT(gto_mf) gto_td.nstates = 190 gto_td.kernel() omegas = np.arange(0.0, 2.0, 0.01) + 1j*0.03 p_ave = -polariz_freq_osc_strength(gto_td.e, gto_td.oscillator_strength(), omegas).imag data = np.array([omegas.real*HARTREE2EV, p_ave]) np.savetxt('test_0152_bse_h2b_uks_pz_pyscf.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt('test_0152_bse_h2b_uks_pz_pyscf.txt-ref').T self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3)) nao_td = bse_iter(mf=gto_mf, gto=mol, verbosity=0) polariz = -nao_td.comp_polariz_inter_ave(omegas).imag data = np.array([omegas.real*HARTREE2EV, polariz]) np.savetxt('test_0152_bse_h2b_uks_pz_nao.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt('test_0152_bse_h2b_uks_pz_nao.txt-ref').T self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3))
Example #13
Source File: test_0035_bse_nonin_nao.py From pyscf with Apache License 2.0 | 6 votes |
def test_bse_iter_nonin(self): """ Compute polarization with LDA TDDFT """ from timeit import default_timer as timer dname = os.path.dirname(os.path.abspath(__file__)) bse = bse_iter(label='water', cd=dname, iter_broadening=1e-2, xc_code='RPA', verbosity=0) omegas = np.linspace(0.0,2.0,500)+1j*bse.eps pxx = np.zeros(len(omegas)) for iw,omega in enumerate(omegas): for ixyz in range(1): vab = bse.apply_l0(bse.dip_ab[ixyz], omega) pxx[iw] = pxx[iw] - (vab.imag*bse.dip_ab[ixyz].reshape(-1)).sum() data = np.array([omegas.real*27.2114, pxx]) np.savetxt('water.bse_iter_rpa.omega.nonin.pxx.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt(dname+'/water.bse_iter_rpa.omega.nonin.pxx.txt-ref') #print(' bse.l0_ncalls ', bse.l0_ncalls) self.assertTrue(np.allclose(data_ref,data.T, rtol=1.0, atol=1e-05))
Example #14
Source File: test_0146_bse_h2o_rhf_rpa.py From pyscf with Apache License 2.0 | 6 votes |
def test_0146_bse_h2o_rhf_rpa(self): """ Interacting case """ mol=gto.M(verbose=0,atom='O 0 0 0;H 0 0.489 1.074;H 0 0.489 -1.074',basis='cc-pvdz',) gto_hf = scf.RKS(mol) gto_hf.xc = 'hf' gto_hf.kernel() gto_td = tddft.dRPA(gto_hf) gto_td.nstates = 95 gto_td.kernel() omegas = np.arange(0.0, 2.0, 0.01) + 1j*0.03 #p_ave = -polariz_inter_ave(gto_hf, mol, gto_td, omegas).imag p_ave = -polariz_freq_osc_strength(gto_td.e, gto_td.oscillator_strength(), omegas).imag data = np.array([omegas.real*HARTREE2EV, p_ave]) np.savetxt('test_0146_bse_h2o_rhf_rpa_pyscf.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt('test_0146_bse_h2o_rhf_rpa_pyscf.txt-ref').T self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3)) nao_td = bse_iter(mf=gto_hf, gto=mol, verbosity=0, xc_code='RPA') p_iter = -nao_td.comp_polariz_inter_ave(omegas).imag data = np.array([omegas.real*HARTREE2EV, p_iter]) np.savetxt('test_0146_bse_h2o_rhf_rpa_nao.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt('test_0146_bse_h2o_rhf_rpa_nao.txt-ref').T self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3))
Example #15
Source File: test_0083_gw_bse_h2_ae.py From pyscf with Apache License 2.0 | 6 votes |
def test_gw(self): """ This is GW """ mol = gto.M( verbose = 1, atom = '''H 0 0 0; H 0.17 0.7 0.587''', basis = 'cc-pvdz',) #mol = gto.M( verbose = 0, atom = '''H 0.0 0.0 -0.3707; H 0.0 0.0 0.3707''', basis = 'cc-pvdz',) gto_mf = scf.RHF(mol) gto_mf.kernel() #print('gto_mf.mo_energy:', gto_mf.mo_energy) b = bse_iter(mf=gto_mf, gto=mol, perform_gw=True, xc_code='GW', verbosity=0, nvrt=4) #self.assertAlmostEqual(b.mo_energy[0], -0.5967647) #self.assertAlmostEqual(b.mo_energy[1], 0.19072719) omegas = np.linspace(0.0,2.0,450)+1j*0.04 p_iter = -b.comp_polariz_inter_ave(omegas).imag data = np.array([omegas.real*27.2114, p_iter]) np.savetxt('h2_gw_bse_iter.omega.inter.ave.txt', data.T) data_ref = np.loadtxt('h2_gw_bse_iter.omega.inter.ave.txt-ref').T #print(__name__, abs(data_ref-data).sum()/data.size) self.assertTrue(np.allclose(data_ref, data, 5)) p_iter = -b.comp_polariz_nonin_ave(omegas).imag data = np.array([omegas.real*27.2114, p_iter]) np.savetxt('h2_gw_bse_iter.omega.nonin.ave.txt', data.T)
Example #16
Source File: test_0040_bse_rpa_nao.py From pyscf with Apache License 2.0 | 6 votes |
def test_0040_bse_rpa_nao(self): """ Compute polarization with RPA via 2-point non-local potentials (BSE solver) """ from timeit import default_timer as timer dname = os.path.dirname(os.path.abspath(__file__)) bse = bse_iter(label='water', cd=dname, xc_code='RPA', verbosity=0) omegas = np.linspace(0.0,2.0,150)+1j*0.01 #print(__name__, omegas.shape) pxx = np.zeros(len(omegas)) for iw,omega in enumerate(omegas): for ixyz in range(1): dip = bse.dip_ab[ixyz] vab = bse.apply_l(dip, omega) pxx[iw] = pxx[iw] - (vab.imag*dip.reshape(-1)).sum() data = np.array([omegas.real*27.2114, pxx]) np.savetxt('water.bse_iter_rpa.omega.inter.pxx.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt(dname+'/water.bse_iter_rpa.omega.inter.pxx.txt-ref') #print(' bse.l0_ncalls ', bse.l0_ncalls) self.assertTrue(np.allclose(data_ref,data.T, rtol=1.0, atol=1e-05))
Example #17
Source File: test_0162_bse_h2o_spin2_uhf_cis.py From pyscf with Apache License 2.0 | 6 votes |
def test_0162_bse_h2o_spin2_uhf_cis(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',spin=2) gto_mf = scf.UHF(mol) gto_mf.kernel() gto_td = tddft.TDDFT(gto_mf) gto_td.nstates = 190 gto_td.kernel() omegas = np.arange(0.0, 2.0, 0.01) + 1j*0.03 p_ave = -polariz_freq_osc_strength(gto_td.e, gto_td.oscillator_strength(), omegas).imag data = np.array([omegas.real*HARTREE2EV, p_ave]) np.savetxt('test_0162_bse_h2o_spin2_uhf_cis_pyscf.txt', data.T, fmt=['%f','%f']) #data_ref = np.loadtxt('test_0162_bse_h2o_spin2_uhf_cis_pyscf.txt-ref').T #self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3)) nao_td = bse_iter(mf=gto_mf, gto=mol, verbosity=0, xc_code='CIS') polariz = -nao_td.comp_polariz_inter_ave(omegas).imag data = np.array([omegas.real*HARTREE2EV, polariz]) np.savetxt('test_0162_bse_h2o_spin2_uhf_cis_nao.txt', data.T, fmt=['%f','%f']) #data_ref = np.loadtxt('test_0162_bse_h2o_spin2_uhf_cis_nao.txt-ref').T #self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3), \ # msg="{}".format(abs(data_ref-data).sum()/data.size))
Example #18
Source File: test_0091_tddft_x_zip_na20.py From pyscf with Apache License 2.0 | 6 votes |
def test_x_zip_feature_na20_chain(self): """ This a test for compression of the eigenvectos at higher energies """ dname = dirname(abspath(__file__)) siesd = dname+'/sodium_20' x = td_c(label='siesta', cd=siesd,x_zip=True, x_zip_emax=0.25,x_zip_eps=0.05,jcutoff=7,xc_code='RPA',nr=128, fermi_energy=-0.0913346431431985) eps = 0.005 ww = np.arange(0.0, 0.5, eps/2.0)+1j*eps data = np.array([ww.real*27.2114, -x.comp_polariz_inter_ave(ww).imag]) fname = 'na20_chain.tddft_iter_rpa.omega.inter.ave.x_zip.txt' np.savetxt(fname, data.T, fmt=['%f','%f']) #print(__file__, fname) data_ref = np.loadtxt(dname+'/'+fname+'-ref') #print(' x.rf0_ncalls ', x.rf0_ncalls) #print(' x.matvec_ncalls ', x.matvec_ncalls) self.assertTrue(np.allclose(data_ref,data.T, rtol=1.0e-1, atol=1e-06))
Example #19
Source File: confusionMatrix.py From Chinese-Character-and-Calligraphic-Image-Processing with MIT License | 6 votes |
def get_predict_labels(): inputs = tf.placeholder("float", [None, 64, 64, 1]) is_training = tf.placeholder("bool") prediction, _ = googlenet(inputs, is_training) predict_labels = tf.argmax(prediction, 1) sess = tf.Session() sess.run(tf.global_variables_initializer()) saver = tf.train.Saver() data = sio.loadmat("../data/dataset.mat") testdata = data["test"] / 127.5 - 1.0 testlabel = data["testlabels"] saver.restore(sess, "../save_para/.\\model.ckpt") nums_test = testlabel.shape[1] PREDICT_LABELS = np.zeros([nums_test]) for i in range(nums_test // BATCH_SIZE): PREDICT_LABELS[i * BATCH_SIZE:i * BATCH_SIZE + BATCH_SIZE] = sess.run(predict_labels, feed_dict={inputs: testdata[i * BATCH_SIZE:i * BATCH_SIZE + BATCH_SIZE], is_training: False}) PREDICT_LABELS[(nums_test // BATCH_SIZE - 1) * BATCH_SIZE + BATCH_SIZE:] = sess.run(predict_labels, feed_dict={inputs: testdata[(nums_test // BATCH_SIZE - 1) * BATCH_SIZE + BATCH_SIZE:], is_training: False}) np.savetxt("../data/predict_labels.txt", PREDICT_LABELS)
Example #20
Source File: test_0161_bse_h2b_spin1_uhf_cis.py From pyscf with Apache License 2.0 | 6 votes |
def test_161_bse_h2b_spin1_uhf_cis(self): """ This """ mol = gto.M(verbose=1,atom='B 0 0 0; H 0 0.489 1.074; H 0 0.489 -1.074',basis='cc-pvdz',spin=1) gto_mf = scf.UHF(mol) gto_mf.kernel() gto_td = tddft.TDHF(gto_mf) gto_td.nstates = 150 gto_td.kernel() omegas = np.arange(0.0, 2.0, 0.01) + 1j*0.03 p_ave = -polariz_freq_osc_strength(gto_td.e, gto_td.oscillator_strength(), omegas).imag data = np.array([omegas.real*HARTREE2EV, p_ave]) np.savetxt('test_0161_bse_h2b_spin1_uhf_cis_pyscf.txt', data.T, fmt=['%f','%f']) #data_ref = np.loadtxt('test_0159_bse_h2b_uhf_cis_pyscf.txt-ref').T #self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3)) nao_td = bse_iter(mf=gto_mf, gto=mol, verbosity=0, xc_code='CIS') polariz = -nao_td.comp_polariz_inter_ave(omegas).imag data = np.array([omegas.real*HARTREE2EV, polariz]) np.savetxt('test_0161_bse_h2b_spin1_uhf_cis_nao.txt', data.T, fmt=['%f','%f']) #data_ref = np.loadtxt('test_0161_bse_h2b_spin1_uhf_cis_nao.txt-ref').T #self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3))
Example #21
Source File: generate.py From pymoo with Apache License 2.0 | 6 votes |
def generate_test_data(): for str_problem in ["osy"]: problem = get_problem(str_problem) X = [] # define a callback function that prints the X and F value of the best individual def my_callback(algorithm): pop = algorithm.pop _X = pop.get("X")[np.random.permutation(len(pop))[:10]] X.append(_X) minimize(problem, method='nsga2', method_args={'pop_size': 100}, termination=('n_gen', 100), callback=my_callback, pf=problem.pareto_front(), disp=True, seed=1) np.savetxt("%s.x" % str_problem, np.concatenate(X, axis=0), delimiter=",")
Example #22
Source File: test_0157_bse_h2o_rhf_cis.py From pyscf with Apache License 2.0 | 6 votes |
def test_157_bse_h2o_rhf_cis(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 = scf.RHF(mol) gto_mf.kernel() gto_td = tddft.TDDFT(gto_mf) gto_td.nstates = 190 gto_td.kernel() omegas = np.arange(0.0, 2.0, 0.01) + 1j*0.03 p_ave = -polariz_freq_osc_strength(gto_td.e, gto_td.oscillator_strength(), omegas).imag data = np.array([omegas.real*HARTREE2EV, p_ave]) np.savetxt('test_0157_bse_h2o_rhf_cis_pyscf.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt('test_0157_bse_h2o_rhf_cis_pyscf.txt-ref').T self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3)) nao_td = bse_iter(mf=gto_mf, gto=mol, verbosity=0, xc_code='CIS') polariz = -nao_td.comp_polariz_inter_ave(omegas).imag data = np.array([omegas.real*HARTREE2EV, polariz]) np.savetxt('test_0157_bse_h2o_rhf_cis_nao.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt('test_0157_bse_h2o_rhf_cis_nao.txt-ref').T self.assertTrue(np.allclose(data_ref, data, atol=5e-5, rtol=5e-2), msg="{}".format(abs(data_ref-data).sum()/data.size ) )
Example #23
Source File: generate_rotations.py From pointnet-registration-framework with MIT License | 6 votes |
def main(args): # dataset testset = get_datasets(args) batch_size = len(testset) amp = args.deg * math.pi / 180.0 w = torch.randn(batch_size, 3) w = w / w.norm(p=2, dim=1, keepdim=True) * amp t = torch.rand(batch_size, 3) * args.max_trans if args.format == 'wv': # the output: twist vectors. R = ptlk.so3.exp(w) # (N, 3) --> (N, 3, 3) G = torch.zeros(batch_size, 4, 4) G[:, 3, 3] = 1 G[:, 0:3, 0:3] = R G[:, 0:3, 3] = t x = ptlk.se3.log(G) # --> (N, 6) else: # rotation-vector and translation-vector x = torch.cat((w, t), dim=1) numpy.savetxt(args.outfile, x, delimiter=',')
Example #24
Source File: test_0163_bse_h2o_spin2_uhf_rpa.py From pyscf with Apache License 2.0 | 5 votes |
def test_0163_bse_h2o_spin2_uhf_rpa(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',spin=2) gto_mf = scf.UKS(mol) gto_mf.xc = 'hf' gto_mf.kernel() gto_td = tddft.dRPA(gto_mf) gto_td.nstates = 190 gto_td.kernel() omegas = np.arange(0.0, 2.0, 0.01) + 1j*0.03 p_ave = -polariz_freq_osc_strength(gto_td.e, gto_td.oscillator_strength(), omegas).imag data = np.array([omegas.real*HARTREE2EV, p_ave]) np.savetxt('test_0163_bse_h2o_spin2_uhf_rpa_pyscf.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt('test_0163_bse_h2o_spin2_uhf_rpa_pyscf.txt-ref').T self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3)) nao_td = bse_iter(mf=gto_mf, gto=mol, verbosity=0, xc_code='RPA') polariz = -nao_td.comp_polariz_inter_ave(omegas).imag data = np.array([omegas.real*HARTREE2EV, polariz]) np.savetxt('test_0163_bse_h2o_spin2_uhf_rpa_nao.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt('test_0163_bse_h2o_spin2_uhf_rpa_nao.txt-ref').T self.assertTrue(np.allclose(data_ref, data, atol=1e-5, rtol=1e-3), \ msg="{}".format(abs(data_ref-data).sum()/data.size))
Example #25
Source File: test_0070_tddft_upkc.py From pyscf with Apache License 2.0 | 5 votes |
def test_tddft_upkc(self): """ This is a comparison of two equivalent ways of computing the polarizability for water molecule """ td = tddft_iter_2ord(label='water', cd=dirname(abspath(__file__)),jcutoff=7,xc_code='RPA',verbosity=0) omegas = np.arange(0.0,1.0,0.005)+1j*0.01 pxx1 = -td.comp_polariz_nonin_xx(omegas).imag data1 = np.array([omegas.real*27.2114, pxx1]) np.savetxt('water.tddft_iter_nonin.txt', data1.T) #print(' td.rf0_ncalls ', td.rf0_ncalls) #print(' td.matvec_ncalls ', td.matvec_ncalls) pxx1 = -td.comp_polariz_inter_xx(omegas).imag data1 = np.array([omegas.real*27.2114, pxx1]) np.savetxt('water.tddft_iter_unit.txt', data1.T) #print(' td.rf0_ncalls ', td.rf0_ncalls) #print(' td.matvec_ncalls ', td.matvec_ncalls) pxx2 = td.polariz_upkc(omegas) wp = np.zeros((2*pxx2.shape[1]+1,pxx2.shape[0])) wp[0,:] = omegas.real*27.2114 wp[1:pxx2.shape[1]+1,:] = pxx2.real.T wp[pxx2.shape[1]+1:,:] = pxx2.imag.T np.savetxt('water.tddft_iter_upkc.txt', wp.T) #print(' td.rf0_ncalls ', td.rf0_ncalls) #print(' td.matvec_ncalls ', td.matvec_ncalls) pxx3 = -td.polariz_dckcd(omegas).imag data1 = np.array([omegas.real*27.2114, pxx3]) np.savetxt('water.tddft_iter_dckcd.txt', data1.T) #print(' td.rf0_ncalls ', td.rf0_ncalls) #print(' td.matvec_ncalls ', td.matvec_ncalls)
Example #26
Source File: test_0138_h2o_rks_pz_pb.py From pyscf with Apache License 2.0 | 5 votes |
def test_138_h2o_rks_rpa_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 = tddft_iter(gto=mol, mf=gto_mf) comega = np.arange(0.0, 2.0, 0.01) + 1j*0.03 pnonin = -nao_mf.comp_polariz_inter_ave(comega, verbosity=0).imag data = np.array([comega.real*HARTREE2EV, pnonin]) np.savetxt('test_138_h2o_rks_pz_pb.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt('test_138_h2o_rks_pz_pb.txt-ref').T self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3))
Example #27
Source File: test_0156_bse_h2b_uhf_nonin.py From pyscf with Apache License 2.0 | 5 votes |
def test_156_bse_h2b_uks_nonin(self): """ This example is with discrepancies... """ mol = gto.M(verbose=1,atom='B 0 0 0; H 0 0.489 1.074; H 0 0.489 -1.074',basis='cc-pvdz',spin=3) gto_mf = scf.UHF(mol) gto_mf.kernel() omegas = np.arange(0.0, 2.0, 0.01) + 1j*0.03 p_ave = -polariz_nonin_ave(gto_mf, mol, omegas).imag data = np.array([omegas.real*HARTREE2EV, p_ave]) np.savetxt('test_0156_bse_h2b_uhf_nonin_pyscf.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt('test_0156_bse_h2b_uhf_nonin_pyscf.txt-ref').T self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3)) nao_td = bse_iter(mf=gto_mf, gto=mol, verbosity=0, xc_code='RPA') polariz = -nao_td.polariz_nonin_ave_matelem(omegas).imag data = np.array([omegas.real*HARTREE2EV, polariz]) np.savetxt('test_0156_bse_h2b_uhf_nonin_matelem.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt('test_0156_bse_h2b_uhf_nonin_matelem.txt-ref').T self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3)) polariz = -nao_td.comp_polariz_nonin_ave(omegas).imag data = np.array([omegas.real*HARTREE2EV, polariz]) np.savetxt('test_0156_bse_h2b_uhf_nonin_nao.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt('test_0156_bse_h2b_uhf_nonin_nao.txt-ref').T self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3))
Example #28
Source File: test_0132_h2o_uhf_nonin_pb.py From pyscf with Apache License 2.0 | 5 votes |
def test_132_h2o_uhf_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',spin=0) gto_mf = scf.UHF(mol) gto_mf.kernel() nao_mf = chi0_matvec(gto=mol, mf=gto_mf, tol_loc=1e-5, tol_biloc=1e-7) comega = np.arange(0.0, 2.0, 0.01) + 1j*0.03 pnonin = -nao_mf.comp_polariz_nonin_ave(comega, verbosity=1).imag data = np.array([comega.real*HARTREE2EV, pnonin]) np.savetxt('test_132_h2o_uhf_nonin_pb.txt', data.T, fmt=['%f','%f']) data_ref = np.loadtxt('test_132_h2o_uhf_nonin_pb.txt-ref').T self.assertTrue(np.allclose(data_ref, data, atol=1e-6, rtol=1e-3))
Example #29
Source File: test_0081_bse_nonin_gto_be.py From pyscf with Apache License 2.0 | 5 votes |
def test_bse_gto_vs_nao_nonin_0081(self): """ Non-interacting case """ #print(__name__, 'gto.mo_energy', gto_mf.mo_energy) nao_td = bse_iter(mf=gto_mf, gto=mol, verbosity=0, perform_gw=True) omegas = np.linspace(0.0,2.0,450)+1j*0.04 p_iter = -nao_td.comp_polariz_nonin_ave(omegas).imag data = np.array([omegas.real*27.2114, p_iter]) np.savetxt('be.bse_iter.omega.nonin.ave.txt', data.T, fmt=['%f','%f'])
Example #30
Source File: test_0066_gw_al_atom.py From pyscf with Apache License 2.0 | 5 votes |
def test_0066_al_atom(self): """ Spin-resolved case GW procedure. """ gw = gw_c(mf=gto_mf, gto=mol, verbosity=0, niter_max_ev=16, nocc=3, nvrt=3) self.assertEqual(gw.nspin, 2) gw.kernel_gw() #gw.report() np.savetxt('eigvals_g0w0_pyscf_rescf_al_0066.txt', gw.mo_energy_gw[0,:,:].T) #ev_ref = np.loadtxt('eigvals_g0w0_pyscf_rescf_al_0066.txt-ref').T #for n2e,n2r in zip(gw.mo_energy_gw[0], ev_ref): # for e,r in zip(n2e,n2r): self.assertAlmostEqual(e, r)