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All calculations on a moleculeΒΆ
[1]:
import qcportal as ptl
client = ptl.FractalClient()
mol = client.query_molecules(2)[0]
mol
You appear to be running in JupyterLab (or JavaScript failed to load for some other reason). You need to install the 3dmol extension:
jupyter labextension install jupyterlab_3dmol
[1]:
<Molecule(name='H6N2 ((1,),[])' formula='H3N' hash='5ad632d')>
Query the results table for all calculations performed on the molecule:
[2]:
ret = client.query_results(molecule=mol.id)
ret
[2]:
[<ResultRecord(id='735838' status='COMPLETE')>,
<ResultRecord(id='735899' status='COMPLETE')>,
<ResultRecord(id='970453' status='COMPLETE')>,
<ResultRecord(id='970514' status='COMPLETE')>,
<ResultRecord(id='608545' status='COMPLETE')>,
<ResultRecord(id='735599' status='COMPLETE')>,
<ResultRecord(id='735489' status='COMPLETE')>,
<ResultRecord(id='735550' status='COMPLETE')>,
<ResultRecord(id='1847216' status='COMPLETE')>,
<ResultRecord(id='1847316' status='COMPLETE')>,
<ResultRecord(id='624' status='COMPLETE')>,
<ResultRecord(id='663' status='COMPLETE')>,
<ResultRecord(id='1846816' status='COMPLETE')>,
<ResultRecord(id='1846916' status='COMPLETE')>,
<ResultRecord(id='468' status='COMPLETE')>,
<ResultRecord(id='507' status='COMPLETE')>,
<ResultRecord(id='63' status='COMPLETE')>,
<ResultRecord(id='208187' status='COMPLETE')>,
<ResultRecord(id='208287' status='COMPLETE')>,
<ResultRecord(id='1764410' status='COMPLETE')>,
<ResultRecord(id='1819425' status='COMPLETE')>,
<ResultRecord(id='1847016' status='COMPLETE')>,
<ResultRecord(id='1847116' status='COMPLETE')>,
<ResultRecord(id='546' status='COMPLETE')>,
<ResultRecord(id='585' status='COMPLETE')>,
<ResultRecord(id='618857' status='COMPLETE')>,
<ResultRecord(id='618957' status='COMPLETE')>,
<ResultRecord(id='621598' status='COMPLETE')>,
<ResultRecord(id='621698' status='COMPLETE')>]
Inspect one of the results:
[3]:
r = ret[9]
print(f"Program: {r.program}\nMethod: {r.method}\nBasis: {r.basis}")
Program: psi4
Method: b2plyp
Basis: aug-cc-pvtz
View the output file:
[5]:
print(r.get_stdout())
Memory set to 60.800 GiB by Python driver.
*** tstart() called on ca131
*** at Fri Jul 12 22:18:51 2019
=> Loading Basis Set <=
Name: AUG-CC-PVTZ
Role: ORBITAL
Keyword: BASIS
atoms 1 entry N line 281 file /home/lnaden/miniconda3/envs/qca/share/psi4/basis/aug-cc-pvtz.gbs
atoms 2-4 entry H line 36 file /home/lnaden/miniconda3/envs/qca/share/psi4/basis/aug-cc-pvtz.gbs
---------------------------------------------------------
SCF
by Justin Turney, Rob Parrish, Andy Simmonett
and Daniel G. A. Smith
RKS Reference
16 Threads, 62259 MiB Core
---------------------------------------------------------
==> Geometry <==
Molecular point group: cs
Full point group: Cs
Geometry (in Bohr), charge = 0, multiplicity = 1:
Center X Y Z Mass
------------ ----------------- ----------------- ----------------- -----------------
N 0.000538830000 0.000000000000 0.129095460000 14.003074004430
H -0.890229660000 1.529856130000 -0.596877300000 1.007825032230
H 1.772972570000 0.000000000000 -0.599942880000 1.007825032230
H -0.890229660000 -1.529856130000 -0.596877300000 1.007825032230
Running in cs symmetry.
Rotational constants: A = 9.98044 B = 9.90180 C = 6.34817 [cm^-1]
Rotational constants: A = 299206.07647 B = 296848.42896 C = 190313.28552 [MHz]
Nuclear repulsion = 11.947431780818354
Charge = 0
Multiplicity = 1
Electrons = 10
Nalpha = 5
Nbeta = 5
==> Algorithm <==
SCF Algorithm Type is DF.
DIIS enabled.
MOM disabled.
Fractional occupation disabled.
Guess Type is SAD.
Energy threshold = 1.00e-08
Density threshold = 1.00e-08
Integral threshold = 0.00e+00
==> Primary Basis <==
Basis Set: AUG-CC-PVTZ
Blend: AUG-CC-PVTZ
Number of shells: 41
Number of basis function: 115
Number of Cartesian functions: 130
Spherical Harmonics?: true
Max angular momentum: 3
==> DFT Potential <==
=> Composite Functional: B2PLYP <=
B2PLYP Double Hybrid Exchange-Correlation Functional
S. Grimme, J. Chem. Phys., 124, 034108, 2006
Deriv = 1
GGA = TRUE
Meta = FALSE
Exchange Hybrid = TRUE
MP2 Hybrid = TRUE
=> Exchange Functionals <=
0.4700 XC_GGA_X_B88
=> Exact (HF) Exchange <=
0.5300 HF
=> Correlation Functionals <=
0.7300 XC_GGA_C_LYP
=> MP2 Correlation <=
0.2700 MP2
=> Molecular Quadrature <=
Radial Scheme = TREUTLER
Pruning Scheme = FLAT
Nuclear Scheme = TREUTLER
BS radius alpha = 1
Pruning alpha = 1
Radial Points = 100
Spherical Points = 302
Total Points = 120800
Total Blocks = 962
Max Points = 256
Max Functions = 115
=> Loading Basis Set <=
Name: (AUG-CC-PVTZ AUX)
Role: JKFIT
Keyword: DF_BASIS_SCF
atoms 1 entry N line 224 file /home/lnaden/miniconda3/envs/qca/share/psi4/basis/aug-cc-pvtz-jkfit.gbs
atoms 2-4 entry H line 70 file /home/lnaden/miniconda3/envs/qca/share/psi4/basis/aug-cc-pvtz-jkfit.gbs
==> Pre-Iterations <==
-------------------------------------------------------
Irrep Nso Nmo Nalpha Nbeta Ndocc Nsocc
-------------------------------------------------------
A' 69 69 0 0 0 0
A" 46 46 0 0 0 0
-------------------------------------------------------
Total 115 115 5 5 5 0
-------------------------------------------------------
==> Integral Setup <==
DFHelper Memory: AOs need 0.029 GiB; user supplied 45.214 GiB. Using in-core AOs.
==> MemDFJK: Density-Fitted J/K Matrices <==
J tasked: Yes
K tasked: Yes
wK tasked: No
OpenMP threads: 16
Memory [MiB]: 46299
Algorithm: Core
Schwarz Cutoff: 1E-12
Mask sparsity (%): 0.0000
Fitting Condition: 1E-10
=> Auxiliary Basis Set <=
Basis Set: (AUG-CC-PVTZ AUX)
Blend: AUG-CC-PVTZ-JKFIT
Number of shells: 72
Number of basis function: 242
Number of Cartesian functions: 296
Spherical Harmonics?: true
Max angular momentum: 4
Cached 100.0% of DFT collocation blocks in 0.386 [GiB].
Minimum eigenvalue in the overlap matrix is 2.7046565184E-04.
Using Symmetric Orthogonalization.
SCF Guess: Superposition of Atomic Densities via on-the-fly atomic UHF.
==> Iterations <==
Total Energy Delta E RMS |[F,P]|
@DF-RKS iter SAD: -55.95900007653938 -5.59590e+01 0.00000e+00
@DF-RKS iter 1: -56.28269366355451 -3.23694e-01 7.97409e-03 DIIS
@DF-RKS iter 2: -56.25795337003415 2.47403e-02 8.17064e-03 DIIS
@DF-RKS iter 3: -56.46021265743074 -2.02259e-01 3.01786e-04 DIIS
@DF-RKS iter 4: -56.46058235120474 -3.69694e-04 4.20726e-05 DIIS
@DF-RKS iter 5: -56.46059082137342 -8.47017e-06 5.25979e-06 DIIS
@DF-RKS iter 6: -56.46059098813920 -1.66766e-07 8.96776e-07 DIIS
@DF-RKS iter 7: -56.46059099415442 -6.01521e-09 1.68815e-07 DIIS
@DF-RKS iter 8: -56.46059099435612 -2.01709e-10 1.85779e-08 DIIS
@DF-RKS iter 9: -56.46059099435834 -2.21689e-12 1.47837e-09 DIIS
Energy and wave function converged.
==> Post-Iterations <==
Orbital Energies [Eh]
---------------------
Doubly Occupied:
1Ap -14.819149 2Ap -0.976248 3Ap -0.534045
1App -0.533186 4Ap -0.339638
Virtual:
5Ap 0.005072 6Ap 0.034962 2App 0.035036
7Ap 0.089759 8Ap 0.113558 3App 0.134620
9Ap 0.134671 10Ap 0.169461 4App 0.169498
11Ap 0.193429 5App 0.193675 12Ap 0.207388
13Ap 0.306696 6App 0.319665 14Ap 0.330115
7App 0.330183 15Ap 0.372804 16Ap 0.394143
8App 0.394171 9App 0.426433 17Ap 0.426544
18Ap 0.496383 19Ap 0.530978 10App 0.531450
20Ap 0.658333 11App 0.692667 21Ap 0.692961
22Ap 0.725184 23Ap 0.787072 12App 0.828871
24Ap 0.837552 13App 0.838044 25Ap 0.891859
14App 0.892131 26Ap 0.948626 15App 0.954762
27Ap 0.954986 16App 1.004354 28Ap 1.020553
17App 1.020716 29Ap 1.059845 18App 1.060092
30Ap 1.097281 31Ap 1.134872 19App 1.135737
32Ap 1.217908 33Ap 1.256436 20App 1.257636
34Ap 1.496074 35Ap 1.634208 21App 1.635259
22App 1.645091 36Ap 1.726835 37Ap 1.734060
23App 1.734740 38Ap 1.869625 24App 1.894604
39Ap 1.895043 25App 1.922060 40Ap 1.922836
41Ap 2.121233 26App 2.214693 27App 2.232937
42Ap 2.233925 28App 2.288278 43Ap 2.288892
44Ap 2.313244 45Ap 3.184724 46Ap 3.357067
29App 3.358506 47Ap 3.788945 30App 3.791293
48Ap 3.804931 49Ap 3.957783 31App 3.958851
32App 4.008523 33App 4.044058 50Ap 4.050021
34App 4.052268 51Ap 4.134546 52Ap 4.153090
35App 4.153732 53Ap 4.281663 54Ap 4.326653
36App 4.328826 55Ap 4.479902 37App 4.535739
56Ap 4.537064 57Ap 4.758429 38App 4.761317
39App 4.806924 58Ap 4.846585 40App 4.847183
59Ap 4.852472 60Ap 5.024442 41App 5.425674
61Ap 5.428564 62Ap 5.493979 42App 5.650005
63Ap 5.656241 64Ap 5.792429 43App 6.095473
65Ap 6.100774 44App 6.175525 66Ap 6.371456
45App 6.689084 67Ap 6.689587 68Ap 7.415202
46App 7.422249 69Ap 16.716513
Final Occupation by Irrep:
Ap App
DOCC [ 4, 1 ]
@DF-RKS Final Energy: -56.46059099435834
=> Energetics <=
Nuclear Repulsion Energy = 11.9474317808183539
One-Electron Energy = -99.6482974230888345
Two-Electron Energy = 35.0831019748610800
DFT Exchange-Correlation Energy = -3.8428273269489335
Empirical Dispersion Energy = 0.0000000000000000
VV10 Nonlocal Energy = 0.0000000000000000
Total Energy = -56.4605909943583413
Computation Completed
Properties will be evaluated at 0.000000, 0.000000, 0.000000 [a0]
Properties computed using the SCF density matrix
Nuclear Dipole Moment: [e a0]
X: -0.0037 Y: 0.0000 Z: -0.8900
Electronic Dipole Moment: [e a0]
X: 0.0018 Y: 0.0000 Z: 0.2704
Dipole Moment: [e a0]
X: -0.0020 Y: 0.0000 Z: -0.6196 Total: 0.6196
Dipole Moment: [D]
X: -0.0050 Y: 0.0000 Z: -1.5749 Total: 1.5749
*** tstop() called on ca131 at Fri Jul 12 22:18:54 2019
Module time:
user time = 30.17 seconds = 0.50 minutes
system time = 1.14 seconds = 0.02 minutes
total time = 3 seconds = 0.05 minutes
Total time:
user time = 30.17 seconds = 0.50 minutes
system time = 1.14 seconds = 0.02 minutes
total time = 3 seconds = 0.05 minutes
*** tstart() called on ca131
*** at Fri Jul 12 22:18:54 2019
=> Loading Basis Set <=
Name: (AUG-CC-PVTZ AUX)
Role: RIFIT
Keyword: DF_BASIS_MP2
atoms 1 entry N line 206 file /home/lnaden/miniconda3/envs/qca/share/psi4/basis/aug-cc-pvtz-ri.gbs
atoms 2-4 entry H line 30 file /home/lnaden/miniconda3/envs/qca/share/psi4/basis/aug-cc-pvtz-ri.gbs
--------------------------------------------------------
DF-MP2
2nd-Order Density-Fitted Moller-Plesset Theory
RMP2 Wavefunction, 16 Threads
Rob Parrish, Justin Turney, Andy Simmonett,
Ed Hohenstein, and C. David Sherrill
--------------------------------------------------------
=> Auxiliary Basis Set <=
Basis Set: (AUG-CC-PVTZ AUX)
Blend: AUG-CC-PVTZ-RI
Number of shells: 70
Number of basis function: 244
Number of Cartesian functions: 301
Spherical Harmonics?: true
Max angular momentum: 4
--------------------------------------------------------
NBF = 115, NAUX = 244
--------------------------------------------------------
CLASS FOCC OCC AOCC AVIR VIR FVIR
PAIRS 1 5 4 110 110 0
--------------------------------------------------------
-----------------------------------------------------------
==================> DF-MP2 Energies <====================
-----------------------------------------------------------
Reference Energy = -56.4605909943583413 [Eh]
Singles Energy = -0.0000000000000000 [Eh]
Same-Spin Energy = -0.0643396155609966 [Eh]
Opposite-Spin Energy = -0.2226985414819575 [Eh]
Correlation Energy = -0.2870381570429541 [Eh]
Total Energy = -56.7476291514012985 [Eh]
-----------------------------------------------------------
================> DF-SCS-MP2 Energies <==================
-----------------------------------------------------------
SCS Same-Spin Scale = 0.3333333333333333 [-]
SCS Opposite-Spin Scale = 1.2000000000000000 [-]
SCS Same-Spin Energy = -0.0214465385203322 [Eh]
SCS Opposite-Spin Energy = -0.2672382497783490 [Eh]
SCS Correlation Energy = -0.2886847882986812 [Eh]
SCS Total Energy = -56.7492757826570227 [Eh]
-----------------------------------------------------------
B2PLYP Energy Summary
---------------------
DFT Reference Energy = -56.4605909943583413
Scaled MP2 Correlation = -0.0775003024015976
@Final double-hybrid DFT total energy = -56.5380912967599372
*** tstop() called on ca131 at Fri Jul 12 22:18:54 2019
Module time:
user time = 6.88 seconds = 0.11 minutes
system time = 0.01 seconds = 0.00 minutes
total time = 0 seconds = 0.00 minutes
Total time:
user time = 37.07 seconds = 0.62 minutes
system time = 1.15 seconds = 0.02 minutes
total time = 3 seconds = 0.05 minutes
[ ]: