From owner-chemistry@ccl.net Fri Dec 8 04:43:00 2023 From: "Grigoriy Zhurko reg_zhurko%%chemcraftprog.com" To: CCL Subject: CCL: Calculation of Gibbs energies of molecules with small frequencies Message-Id: <-55053-231208032901-24889-TRiUE5FHM0T1ABrHYi2fSA*_*server.ccl.net> X-Original-From: Grigoriy Zhurko Content-Type: multipart/mixed; boundary="----------0690421002E5522D1" Date: Fri, 8 Dec 2023 11:28:34 +0300 MIME-Version: 1.0 Sent to CCL by: Grigoriy Zhurko [reg_zhurko/./chemcraftprog.com] ------------0690421002E5522D1 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit I have one more question concerning the msRRHO. If this approach implies the attached formula, it works improperly when the computation has negative frequencies. Such frequencies are sometimes produced as a result of numerical noise (I got a lot of them for a system with PCM water solvation model and explicit water molecules). Did anyone suggest to make the negative frequencies zero or e.g 100 cm-1 in such cases? According to my experience, it is difficult and CPU-consuming to get rid of the negative frequencies in such cases, and possibly not necessary, if we simply make small frequencies bigger. Grigoriy Zhurko. ------------0690421002E5522D1 Content-Type: image/png; name="form_msrrho_prakht.png" Content-transfer-encoding: base64 Content-Disposition: attachment; filename="form_msrrho_prakht.png" iVBORw0KGgoAAAANSUhEUgAAATIAAABvCAIAAADgw9sPAAAAAXNSR0IArs4c6QAAAARnQU1B AACxjwv8YQUAAAAJcEhZcwAADsMAAA7DAcdvqGQAABXySURBVHhe7Z1/TBtXnsDnz/vDuhW6 /eMsFQkJIaETEqoQf4BQBX+QTYQWUHIcSxJZEDUyURqRHwok3QJR1yRKnG4PlF0nbX0JPpp1 rviSrcviELtpTIXT4mvNgUUciFk7wSkYJ/gMwmDzuHnjsWNgZjy2x+Ox8z5/Zaaumfn6feb9 mPfeF9tCIBACA2mJQAgOpCUCITiQlgiE4EBaIhCCA2mJQAgOpCUCITiQlgiE4EBaIhCCA2mJ QAgOpCUzfpep/6PG2trDLdLWs7IvBr74UDG6Asj/mBkI6hayIJ58gLRkAKxa+qpF+xXWFeJo efL64Zw6lT2TShFvt7BifzzljvG1WRBPnkBaMrBmUzZgolaNK0CecN09o5gMkgcZAW+34NRI e83hP0JDFsSTJ5CWDGz6TJdKsZzSjmFXgHikrzmsc8STPmPg7RbYaJkF8eQJpCUjYHlKebQA ExU035rypf+xDnzOCTMdP9vcfvJz0fB0C2y0FFw8BQvSMhasStKKTXdbrQlx775lgSifNCe/ 6VcNDqqVd0zuNbfpjlI9OKjq/8ZGVBqBBYv2WnvzBzKV0U71t4DbMkR+4W6GzS4qLXH4kIGd 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In our codes we us -50cm^-1 as the threshold for inversion. This works well for the numerical issues you describe. For larger imaginary modes one has to be cautious, these indicate transition states or saddle points on the energy surface. best wishes, Philipp On 08.12.23 08:28, Grigoriy Zhurko reg_zhurko%%chemcraftprog.com wrote: > I have one more question concerning the msRRHO. If this approach implies the attached formula, it works improperly when the computation has negative frequencies. Such frequencies are sometimes produced as a result of numerical noise (I got a lot of them for a system with PCM water solvation model and explicit water molecules). Did anyone suggest to make the negative frequencies zero or e.g 100 cm-1 in such cases? According to my experience, it is difficult and CPU-consuming to get rid of the negative frequencies in such cases, and possibly not necessary, if we simply make small frequencies bigger. > Grigoriy Zhurko. -- Dr. Philipp Pracht (pp555]~[cam.ac.uk) Yusuf Hamied Department of Chemistry University of Cambridge Lensfield Road, Cambridge CB2 1EW United Kingdom From owner-chemistry@ccl.net Fri Dec 8 08:08:01 2023 From: "Stefan Grimme grimme * thch.uni-bonn.de" To: CCL Subject: CCL: Calculation of Gibbs energies of molecules with small frequencies Message-Id: <-55055-231208080547-6616-bWGleKKGhXoRgQY2yaBbuQ#,#server.ccl.net> X-Original-From: "Stefan Grimme" Date: Fri, 8 Dec 2023 08:05:43 -0500 Sent to CCL by: "Stefan Grimme" [grimme~!~thch.uni-bonn.de] Dear Grigoriy, our practice is to make (small) imaginary frequency values real and include them in mRRHO. Imaginary modes caused by numerical issues (often methyl rotations) usually correspond to small valued real ones. Because mRRHO effectively damps their effect, this is much less a problem than in RRHO where such modes (even if they are just neglected) can cause large errors. However, modes with values e.g. larger than i50-100 cm-1 should be explicitly treated. For a reference see Angew. Chem. Int. Ed., (2022), 61, e202205735. DOI: 10.1002/anie.202205735 Best Stefan From owner-chemistry@ccl.net Fri Dec 8 19:49:01 2023 From: "Prasanta Bandyopadhyay mailprasanta88~~gmail.com" To: CCL Subject: CCL:G: Start post-Hartree Fock calculation from Localized orbitals in PySCF Message-Id: <-55056-231208190550-18524-eDAy5arUVRUdMo0s1jdFiw:_:server.ccl.net> X-Original-From: "Prasanta Bandyopadhyay" Date: Fri, 8 Dec 2023 19:05:49 -0500 Sent to CCL by: "Prasanta Bandyopadhyay" [mailprasanta88=gmail.com] Hello everyone. This is my first message to the community. It is known that the Localized Molecular Orbitals can do CCSD calculations in less time. After a canonical HF calculation, I am trying to do Boys Localization and feed the localized orbitals to start the CCSD calculation in PySCF. I did not find any such references or examples. So, my input may also be erroneous. If my inputs are correct, then there may be some problems with CCSD convergence. I have run a sample code in ipython notebook and sharing the input/output. Please help. Python 3.10.11 | packaged by conda-forge | (main, May 10 2023, 18:58:44) [GCC 11.3.0] Type 'copyright', 'credits' or 'license' for more information IPython 8.15.0 -- An enhanced Interactive Python. Type '?' for help. ...: atom = [ ...: [ 'H' , 0.000000 , 0.000000 , 0.100000], ...: [ 'H1' , 0.000000 , 0.000000 , 0.860000], ...: [ 'H' , 2.000000 , 0.000000 , 0.100000], ...: [ 'H1' , 2.000000 , 0.000000 , 0.860000]], ...: basis = {'H': gto.parse(''' ...: H S ...: 0.9000000000D+00 0.1000000000D+01 ...: H S ...: 0.3000000000D+00 0.1000000000D+01 ...: '''),'H1': gto.parse(''' ...: H S ...: 0.9900000000D+00 0.1000000000D+01 ...: H S ...: 0.3900000000D+00 0.1000000000D+01 ...: ''') ...: }, ...: cart=True ...: ) ...: mf=scf.RHF(mol) ...: mf.kernel() ...: # Canonical CCSD calculation ...: ccsd_can = cc.CCSD(mf) ...: ccsd_can.kernel() System: uname_result(system='Linux', node='prasanta', release='6.2.0-37-generic', version='#38~22.04.1-Ubuntu SMP PREEMPT_DYNAMIC Thu Nov 2 18:01:13 UTC 2', machine='x86_64') Threads 6 Python 3.10.11 | packaged by conda-forge | (main, May 10 2023, 18:58:44) [GCC 11.3.0] numpy 1.24.3 scipy 1.10.1 Date: Fri Dec 8 23:45:32 2023 PySCF version 2.3.0 PySCF path /home/pro/psi4conda/lib/python3.10/site-packages/pyscf [CONFIG] conf_file None [INPUT] verbose = 4 [INPUT] num. atoms = 4 [INPUT] num. electrons = 4 [INPUT] charge = 0 [INPUT] spin (= nelec alpha-beta = 2S) = 0 [INPUT] symmetry False subgroup None [INPUT] Mole.unit = angstrom [INPUT] Cartesian GTO integrals (6d 10f) [INPUT] Symbol X Y Z unit X Y Z unit Magmom [INPUT] 1 H 0.000000000000 0.000000000000 0.100000000000 AA 0.000000000000 0.000000000000 0.188972612457 Bohr 0.0 [INPUT] 2 H1 0.000000000000 0.000000000000 0.860000000000 AA 0.000000000000 0.000000000000 1.625164467126 Bohr 0.0 [INPUT] 3 H 2.000000000000 0.000000000000 0.100000000000 AA 3.779452249130 0.000000000000 0.188972612457 Bohr 0.0 [INPUT] 4 H1 2.000000000000 0.000000000000 0.860000000000 AA 3.779452249130 0.000000000000 1.625164467126 Bohr 0.0 nuclear repulsion = 2.41641498659376 number of shells = 8 number of NR pGTOs = 8 number of NR cGTOs = 8 basis = {'H': [[0, [0.9, 1.0]], [0, [0.3, 1.0]]], 'H1': [[0, [0.99, 1.0]], [0, [0.39, 1.0]]]} ecp = {} CPU time: 0.76 ******** ******** method = RHF initial guess = minao damping factor = 0 level_shift factor = 0 DIIS = diis_start_cycle = 1 diis_space = 8 SCF conv_tol = 1e-09 SCF conv_tol_grad = None SCF max_cycles = 50 direct_scf = True direct_scf_tol = 1e-13 chkfile to save SCF result = /home/pro/tmpho51b2t8 max_memory 4000 MB (current use 133 MB) Set gradient conv threshold to 3.16228e-05 Initial guess from minao. init E= -1.39106822755651 HOMO = -0.433617041428962 LUMO = 0.282308074774963 cycle= 1 E= -2.06295523982167 delta_E= -0.672 |g|= 0.0727 |ddm|= 0.799 HOMO = -0.473556403806346 LUMO = 0.412321896221053 cycle= 2 E= -2.06454743844608 delta_E= -0.00159 |g|= 0.0118 |ddm|= 0.0747 HOMO = -0.469582406635784 LUMO = 0.416563705787143 cycle= 3 E= -2.06459105895304 delta_E= -4.36e-05 |g|= 0.000111 |ddm|= 0.0144 HOMO = -0.469553180529867 LUMO = 0.416580776242043 cycle= 4 E= -2.06459106222831 delta_E= -3.28e-09 |g|= 6.29e-06 |ddm|= 0.000152 HOMO = -0.469554412248582 LUMO = 0.4165811859113 cycle= 5 E= -2.06459106224563 delta_E= -1.73e-11 |g|= 3.17e-07 |ddm|= 1.39e-05 HOMO = -0.469554206106277 LUMO = 0.416581169256107 Extra cycle E= -2.06459106224566 delta_E= -3.73e-14 |g|= 5.96e-08 |ddm|= 3.61e-07 converged SCF energy = -2.06459106224566 ******** ******** CC2 = 0 CCSD nocc = 2, nmo = 8 max_cycle = 50 direct = 0 conv_tol = 1e-07 conv_tol_normt = 1e-05 diis_space = 6 diis_start_cycle = 0 diis_start_energy_diff = 1e+09 max_memory 4000 MB (current use 141 MB) Init t2, MP2 energy = -2.09735912778898 E_corr(MP2) -0.0327680655433131 Init E_corr(CCSD) = -0.0327680655433144 cycle = 1 E_corr(CCSD) = -0.0433288723433739 dE = -0.0105608068 norm(t1,t2) = 0.0338082 cycle = 2 E_corr(CCSD) = -0.0469749314685062 dE = -0.00364605913 norm(t1,t2) = 0.0129309 cycle = 3 E_corr(CCSD) = -0.0491424777892665 dE = -0.00216754632 norm(t1,t2) = 0.00506568 cycle = 4 E_corr(CCSD) = -0.0491155494004375 dE = 2.69283888e-05 norm(t1,t2) = 0.000214851 cycle = 5 E_corr(CCSD) = -0.0491166716803206 dE = -1.12227988e-06 norm(t1,t2) = 2.73751e-05 cycle = 6 E_corr(CCSD) = -0.0491164004888309 dE = 2.7119149e-07 norm(t1,t2) = 7.07441e-06 cycle = 7 E_corr(CCSD) = -0.0491163959830784 dE = 4.50575245e-09 norm(t1,t2) = 2.03493e-06 CCSD converged E(CCSD) = -2.113707458228743 E_corr = -0.04911639598307844 Out[1]: (-0.04911639598307844, array([[ 9.66395727e-04, -7.15861468e-17, 3.73379105e-03, 2.44065462e-18, -1.57904882e-03, -1.32952145e-16], [ 2.00856366e-16, -1.07204164e-03, 2.38841448e-16, 3.31332992e-03, 8.65144493e-17, -1.87163682e-03]]), array([[[[-5.54907257e-02, -6.98304215e-17, 4.96365459e-03, 6.15454933e-17, 1.62904246e-02, 2.35860458e-16], [-6.98304215e-17, -4.32600566e-02, -1.46096206e-17, -6.18073805e-03, 2.82455911e-16, -1.38761644e-02], [ 4.96365459e-03, -1.46096206e-17, -1.76383333e-02, 3.47288702e-17, -7.08184505e-04, -3.53184896e-18], [ 6.15454933e-17, -6.18073805e-03, 3.47288702e-17, -1.34470086e-02, 2.46462720e-17, -7.67761587e-04], [ 1.62904246e-02, 2.82455911e-16, -7.08184505e-04, 2.46462720e-17, -1.08204284e-02, -1.05483455e-17], [ 2.35860458e-16, -1.38761644e-02, -3.53184896e-18, -7.67761587e-04, -1.05483455e-17, -9.06019104e-03]], [[-2.71717382e-16, 5.62101570e-02, 8.10011333e-17, 7.13198951e-03, -2.29155940e-16, 1.58849468e-02], [ 4.83892195e-02, 2.06293400e-16, -5.44502289e-03, -2.97797424e-17, -1.81692514e-02, -2.42204538e-16], [ 5.75513408e-17, -5.73018600e-03, 4.25602864e-17, -1.63495118e-02, -1.40076323e-18, 5.15636384e-04], [ 6.22957127e-03, -3.83416194e-17, -1.65269939e-02, -6.88327791e-18, -1.97040906e-03, -2.58176270e-17], [-2.00659956e-16, -1.75761121e-02, 4.95767349e-18, -2.03951127e-03, 3.50784025e-16, -1.06212681e-02], [ 1.48299958e-02, -2.38310658e-16, 4.72373240e-04, -2.78193986e-17, -1.06327588e-02, -3.40485550e-16]]], [[[-2.71717382e-16, 4.83892195e-02, 5.75513408e-17, 6.22957127e-03, -2.00659956e-16, 1.48299958e-02], [ 5.62101570e-02, 2.06293400e-16, -5.73018600e-03, -3.83416194e-17, -1.75761121e-02, -2.38310658e-16], [ 8.10011333e-17, -5.44502289e-03, 4.25602864e-17, -1.65269939e-02, 4.95767349e-18, 4.72373240e-04], [ 7.13198951e-03, -2.97797424e-17, -1.63495118e-02, -6.88327791e-18, -2.03951127e-03, -2.78193986e-17], [-2.29155940e-16, -1.81692514e-02, -1.40076323e-18, -1.97040906e-03, 3.50784025e-16, -1.06327588e-02], [ 1.58849468e-02, -2.42204538e-16, 5.15636384e-04, -2.58176270e-17, -1.06212681e-02, -3.40485550e-16]], [[-5.46358905e-02, 1.30287310e-16, 5.13339295e-03, 8.49872253e-17, 1.95471507e-02, 3.66679032e-16], [ 1.30287310e-16, -5.74430970e-02, -5.56956115e-17, -7.49341692e-03, 2.84447125e-16, -1.68101818e-02], [ 5.13339295e-03, -5.56956115e-17, -2.14792869e-02, -1.04757120e-17, -6.44811716e-04, -1.83577455e-18], [ 8.49872253e-17, -7.49341692e-03, -1.04757120e-17, -1.65366923e-02, 1.87452778e-17, -7.38305129e-04], [ 1.95471507e-02, 2.84447125e-16, -6.44811716e-04, 1.87452778e-17, -1.26396619e-02, -4.00584700e-17], [ 3.66679032e-16, -1.68101818e-02, -1.83577455e-18, -7.38305129e-04, -4.00584700e-17, -1.06101681e-02]]]])) In [2]: In [2]: localization_method = 'boys' # You can choose 'boys', 'iao', 'pipek', e ...: tc. ...: mo_coeff_localized = lo.orth.orth_ao(mol, localization_method) ...: ...: mo_occ_localized = mf.mo_occ /home/pro/psi4conda/lib/python3.10/site-packages/pyscf/dft/libxc.py:772: UserWarning: Since PySCF-2.3, B3LYP (and B3P86) are changed to the VWN-RPA variant, the same to the B3LYP functional in Gaussian and ORCA (issue 1480). To restore the VWN5 definition, you can put the setting "B3LYP_WITH_VWN5 = True" in pyscf_conf.py warnings.warn('Since PySCF-2.3, B3LYP (and B3P86) are changed to the VWN-RPA variant, ' In [3]: ccsd_localized = cc.CCSD(mf) ...: ccsd_localized.mo_coeff = mo_coeff_localized ...: mo_occ_localized = mf.mo_occ ...: ccsd_localized.mo_occ = mo_occ_localized ...: ccsd_localized.kernel() ******** ******** CC2 = 0 CCSD nocc = 2, nmo = 8 max_cycle = 50 direct = 0 conv_tol = 1e-07 conv_tol_normt = 1e-05 diis_space = 6 diis_start_cycle = 0 diis_start_energy_diff = 1e+09 max_memory 4000 MB (current use 150 MB) Init t2, MP2 energy = 3.27530080154194 E_corr(MP2) -0.00569411069633339 Init E_corr(CCSD) = 0.216714827164018 cycle = 1 E_corr(CCSD) = -3.04461060576688 dE = -3.26132543 norm(t1,t2) = 36.1895 cycle = 2 E_corr(CCSD) = -19.1686545365852 dE = -16.1240439 norm(t1,t2) = 2491.19 cycle = 3 E_corr(CCSD) = 19.8047923107763 dE = 38.9734468 norm(t1,t2) = 2.68056e+06 cycle = 4 E_corr(CCSD) = 25.879418175191 dE = 6.07462586 norm(t1,t2) = 1.40707e+06 cycle = 5 E_corr(CCSD) = 27.2766254838092 dE = 1.39720731 norm(t1,t2) = 329057 cycle = 6 E_corr(CCSD) = -2.01780064492512 dE = -29.2944261 norm(t1,t2) = 364817 cycle = 7 E_corr(CCSD) = -2.97753280814283 dE = -0.959732163 norm(t1,t2) = 47972.5 cycle = 8 E_corr(CCSD) = -1817.22134315427 dE = -1814.24381 norm(t1,t2) = 109750 cycle = 9 E_corr(CCSD) = 0 dE = 1817.22134 norm(t1,t2) = 6.03432e+10 cycle = 10 E_corr(CCSD) = 0 dE = 0 norm(t1,t2) = 2.2255 cycle = 11 E_corr(CCSD) = 0 dE = 0 norm(t1,t2) = 2.2255 cycle = 12 E_corr(CCSD) = 0 dE = 0 norm(t1,t2) = 2.2255 cycle = 13 E_corr(CCSD) = 0 dE = 0 norm(t1,t2) = 2.2255 cycle = 14 E_corr(CCSD) = 0 dE = 0 norm(t1,t2) = 2.2255 cycle = 15 E_corr(CCSD) = 0.216714827164027 dE = 0.216714827 norm(t1,t2) = 2.2255 cycle = 16 E_corr(CCSD) = 0.108084643542402 dE = -0.108630184 norm(t1,t2) = 36.1895 cycle = 17 E_corr(CCSD) = -0.170149619083507 dE = -0.278234263 norm(t1,t2) = 35.9229 WARN: diis singular, eigh(h) [-3.72002754e-01 -1.08414679e-13 -2.85868422e-14 4.94132623e+00 2.12412279e+01 4.71628680e+01 2.69791993e+03] --------------------------------------------------------------------------- LinAlgError Traceback (most recent call last) Cell In[3], line 5 3 mo_occ_localized = mf.mo_occ 4 ccsd_localized.mo_occ = mo_occ_localized ----> 5 ccsd_localized.kernel() File ~/psi4conda/lib/python3.10/site-packages/pyscf/cc/ccsd.py:1076, in CCSD.kernel(self, t1, t2, eris) 1075 def kernel(self, t1=None, t2=None, eris=None): -> 1076 return self.ccsd(t1, t2, eris) File ~/psi4conda/lib/python3.10/site-packages/pyscf/cc/ccsd.py:1091, in CCSD.ccsd(self, t1, t2, eris) 1087 if eris is None: 1088 eris = self.ao2mo(self.mo_coeff) 1090 self.converged, self.e_corr, self.t1, self.t2 = \ -> 1091 kernel(self, eris, t1, t2, max_cycle=self.max_cycle, 1092 tol=self.conv_tol, tolnormt=self.conv_tol_normt, 1093 verbose=self.verbose, callback=self.callback) 1094 self._finalize() 1095 return self.e_corr, self.t1, self.t2 File ~/psi4conda/lib/python3.10/site-packages/pyscf/cc/ccsd.py:83, in kernel(mycc, eris, t1, t2, max_cycle, tol, tolnormt, verbose, callback) 81 t1, t2 = t1new, t2new 82 t1new = t2new = None ---> 83 t1, t2 = mycc.run_diis(t1, t2, istep, normt, eccsd-eold, adiis) 84 eold, eccsd = eccsd, mycc.energy(t1, t2, eris) 85 log.info('cycle = %d E_corr(CCSD) = %.15g dE = %.9g norm(t1,t2) = %.6g', 86 istep+1, eccsd, eccsd - eold, normt) File ~/psi4conda/lib/python3.10/site-packages/pyscf/cc/ccsd.py:1243, in CCSD.run_diis(self, t1, t2, istep, normt, de, adiis) 1239 if (adiis and 1240 istep >= self.diis_start_cycle and 1241 abs(de) < self.diis_start_energy_diff): 1242 vec = self.amplitudes_to_vector(t1, t2) -> 1243 t1, t2 = self.vector_to_amplitudes(adiis.update(vec)) 1244 logger.debug1(self, 'DIIS for step %d', istep) 1245 return t1, t2 File ~/psi4conda/lib/python3.10/site-packages/pyscf/lib/diis.py:237, in DIIS.update(self, x, xerr) 235 else: 236 self._xprev = None # release memory first --> 237 self._xprev = xnew = self.extrapolate(nd) 239 self._store('xprev', xnew) 240 if 'xprev' not in self._buffer: # not incore File ~/psi4conda/lib/python3.10/site-packages/pyscf/lib/diis.py:264, in DIIS.extrapolate(self, nd) 262 except numpy.linalg.linalg.LinAlgError as e: 263 logger.warn(self, ' diis singular, eigh(h) %s', w) --> 264 raise e 265 logger.debug1(self, 'diis-c %s', c) 267 xnew = None File ~/psi4conda/lib/python3.10/site-packages/pyscf/lib/diis.py:261, in DIIS.extrapolate(self, nd) 259 else: 260 try: --> 261 c = numpy.linalg.solve(h, g) 262 except numpy.linalg.linalg.LinAlgError as e: 263 logger.warn(self, ' diis singular, eigh(h) %s', w) File <__array_function__ internals>:200, in solve(*args, **kwargs) File ~/psi4conda/lib/python3.10/site-packages/numpy/linalg/linalg.py:386, in solve(a, b) 384 signature = 'DD->D' if isComplexType(t) else 'dd->d' 385 extobj = get_linalg_error_extobj(_raise_linalgerror_singular) --> 386 r = gufunc(a, b, signature=signature, extobj=extobj) 388 return wrap(r.astype(result_t, copy=False)) File ~/psi4conda/lib/python3.10/site-packages/numpy/linalg/linalg.py:89, in _raise_linalgerror_singular(err, flag) 88 def _raise_linalgerror_singular(err, flag): ---> 89 raise LinAlgError("Singular matrix") LinAlgError: Singular matrix