Andrew WildmanIn this example we will compute the most simple and straightforward job using ChronusQ, computing the Hartree-Fock Self-Consistent-Field single point ground state energy. Additionally, we will outline the anatomy of a ChronusQ output file.
Input file
For this example, let's use a familiar molecule: H2O. Below is our ChronusQ input file named water.inp
[Molecule]
charge = 0
mult = 1
geom:
O 0.0 -0.076 0.0
H 0.867 0.601 0.0
H -0.867 0.601 0.0
[QM]
reference = Real RHF
job = SCF
[BASIS]
basis = 6-31G(d)
[MISC]
nsmp = 1
mem = 100 MBAs we can see above, we have the charge neutral, singlet water molecule geometry defined in the [Molecule] section. In the [QM] section we request a real arithmetic restricted Hartree-Fock reference for our water molecule using reference = Real RHF, and to only compute the single point energy we request that job = SCF.
Next, we decide the use the 6-31g(d) Pople basis set in the [BASIS] section.
Finally, we define the resources we want to use in the [MISC] section. Since this is a small system, we only use a single cpu core nsmp = 1 and 100 megabytes of memory, mem = 100 MB. (By default 256 MB of memory is requested)
Now we are ready to run this job using ChronusQ. For more details on the input file format please visit the Input Sections wiki page.
Running ChronusQ
As explained in the Running ChronusQ wiki page, we can run this job from in the command line with
./chronusq water.inpBy default, ChronusQ will create 2 new files implicitly, water.bin and water.out where the .bin extension is the HDF5 formatted binary file, and the .out file is the standard output file in plain text format.
Output File Format
Now that our job has finished we can take a look at the output file. Let's break it down into a few separate sections.
1. Header and Input File Information
This section is pretty straightforward. The start time, banner and release version are displayed at the top, followed by the current author list. Right below, the input file used for the job is printed for clarity.
ChronusQ Job Started: Wed Sep 16 13:50:34 2020
______ __ ____
/ ____// /_ _____ ____ ____ __ __ _____ / __ \
/ / / __ \ / ___// __ \ / __ \ / / / // ___// / / /
/ /___ / / / // / / /_/ // / / // /_/ /(__ )/ /_/ /
\____//_/ /_//_/ \____//_/ /_/ \__,_//____/ \___\_\
Release Version: 0.3.3
Contributors List:
================================================================================
Name Institution
--------------------------------------------------------
Xiaosong Li University of Washington
David Williams-Young Lawrence Berkeley National Lab
Edward Valeev Virginia Tech
Alessio Petrone University of Washington
Shichao Sun University of Washington
Torin Stetina University of Washington
Andrew Wildman University of Washington
Joshua Goings University of Washington
Joseph Kasper University of Washington
Feizhi Ding University of Washington
Patrick Lestrange University of Washington
Hongbin Liu University of Washington
--------------------------------------------------------
Input File:
================================================================================
[Molecule]
charge = 0
mult = 1
geom:
O 0.0 -0.076 0.0
H 0.867 0.601 0.0
H -0.867 0.601 0.0
[QM]
reference = Real RHF
job = SCF
[BASIS]
basis = 6-31G(d)
[MISC]
nsmp = 1
mem = 100 MB
================================================================================
2. Compute Resources and Molecular System Data
In the first section, the amount of memory, number of cores used (OpenMP threads), and the number of MPI processes are displayed. Next, the molecular information section gives number of atoms, number of electrons, nuclear repulsion energy, and more. Finally, the basis set information is displayed including total number of functions and primitives, max angular momenta and shell information.
*** Allocating 100 MB ***
*** ChronusQ will use 1 OpenMP threads ***
*** ChronusQ will use 1 MPI Processes ***
Molecular Information:
================================================================================
NAtoms 3
Total Electrons 10
Charge 0 electrons
Nuclear Repulsion Energy 8.00224299e+00 Eh
Center of Mass { 0.00000e+00 ,-4.41498e-04 ,0.00000e+00 }
Center of Charges { 0.00000e+00 ,1.12250e-01 ,0.00000e+00 }
Moment of Inertia { 2.92985e+00 ,0.00000e+00 ,0.00000e+00 ,
0.00000e+00 ,5.41067e+00 ,0.00000e+00 ,
0.00000e+00 ,0.00000e+00 ,8.34052e+00 }
Geometry:
----------------------------------------------------------------------------
Element Charge Mass (AMU) X (Bohr) Y (Bohr) Z (Bohr)
O-16 8 1.59949e+01 0.00000e+00 -1.43619e-01 0.00000e+00
H-1 1 1.00783e+00 1.63839e+00 1.13573e+00 0.00000e+00
H-1 1 1.00783e+00 -1.63839e+00 1.13573e+00 0.00000e+00
================================================================================
*** Reading Basis Set from /home/torins/devel/chronusq_dev/basis/6-31g*.gbs ***
Basis Set Information:
================================================================================
NBasis 18
NPrimitive 35
NShell 10
Max Primitive 6
Max L 2
Shell Information:
----------------------------------------------------------------------------
# L Exponents Normalized Contraction
0 0 5.4847e+03 8.3174e-01
8.2523e+02 1.5308e+00
1.8805e+02 2.4771e+00
5.2965e+01 3.2563e+00
1.6898e+01 2.7929e+00
5.7996e+00 9.5494e-01
1 0 1.5540e+01 -6.1793e-01
3.5999e+00 -2.7572e-01
1.0138e+00 8.1421e-01
2 1 1.5540e+01 3.1169e+00
3.5999e+00 2.4014e+00
1.0138e+00 1.0544e+00
3 0 2.7001e-01 2.6696e-01
4 1 2.7001e-01 2.7743e-01
5 2 8.0000e-01 1.1138e+00
6 0 1.8731e+01 2.1494e-01
2.8254e+00 3.6457e-01
6.4012e-01 4.1505e-01
7 0 1.6128e-01 1.8138e-01
8 0 1.8731e+01 2.1494e-01
2.8254e+00 3.6457e-01
6.4012e-01 4.1505e-01
9 0 1.6128e-01 1.8138e-01
================================================================================
3. Integral and Hamiltonian Settings
In this section integral and property information is displayed. Specifically which types of property integrals (i.e. dipole, quadrupole, etc.) computed is displayed, along with the algorithm for computing the electron repulsion integral (ERI) tensor. By default, ERIs are computed using a direct, low memory usage, algorithm with a screening factor of 1.0e-12.
Property Integrals:
* Will Compute Length Gauge Electric Multipoles up to Octupole
* Will Compute Velocity Gauge Electric Multipoles up to Octupole
* Will Compute Magnetic Multipoles up to Quadrupole
Electron repulsion integral:
Contraction Algorithm:DIRECT
* Schwartz Screening Threshold = 1.0000e-12
================================================================================
*** Parsing QM.REFERENCE options ***
4. SCF Guess and Settings
In this section, a simplified output from the SAD guess procedure is displayed, where two atomic SCF calculations are run. (A doublet H atom, and a triple O atom in this case). Next, all of the main SCF procedural settings are displayed. These can be modified in the input file directly using the [SCF] section header.
*** Forming Initial Guess Density for SCF Procedure ***
* Forming the Superposition of Atomic Densities Guess (SAD)
*** Found 2 unique Atoms in Molecule Specification ***
*** Running 2 Atomic SCF calculations for SAD Guess ***
* Running AtomZ = 1 as a Doublet
* Running AtomZ = 8 as a Triplet
*** Forming Initial Fock Matrix from SAD Density ***
================================================================================
Self Consistent Field (SCF) Settings:
Reference: Real Restricted Hartree-Fock
Density Convergence Tolerence: 1.000000e-08
Energy Convergence Tolerence: 1.000000e-10
Maximum Number of SCF Cycles: 128
SCF Algorithm: Conventional SCF
Static Damping Factor: 7.000000e-01
Damping Error: 1.000000e-03
DIIS Extrapolation Algorithm: CDIIS
* DIIS will track up to 10 previous iterations
--------------------------------------------------------------------------------
5. Main SCF Output
In this section, the results per SCF iteration are displayed first until the final step that reaches convergence. The 2 most right columns display the change in energy and the change in density from the previous iteration respectively. After convergence, the orbital energies are displayed below. Lowest to highest energy orbitals are displayed from the top left, to the bottom right in each occupied and virtual block.
SCF Iteration Energy (Eh) ΔE (Eh) |ΔP(S)|
------------- ----------- ------- -------
SCFIt: 0 -76.8195753229
SCFIt: 1 -74.9896154092 1.8299599e+00 2.4981031e-02
SCFIt: 2 -76.5629923118 -1.5733769e+00 1.4300781e-02
SCFIt: 3 -75.7461640754 8.1682824e-01 4.9341074e-03
SCFIt: 4 -76.0028181628 -2.5665409e-01 2.1062649e-03
SCFIt: 5 -75.9806481414 2.2170021e-02 6.1569014e-04
SCFIt: 6 -75.9704381652 1.0209976e-02 1.3698133e-04
SCFIt: 7 -75.9747098884 -4.2717232e-03 5.2824313e-05
SCFIt: 8 -75.9734579910 1.2518974e-03 9.0155536e-06
*** Damping Disabled - Energy Difference Fell Below 1.0000000e-03 ***
SCFIt: 9 -75.9736898224 -2.3183139e-04 2.0607797e-06
SCFIt: 10 -75.9736681935 2.1628880e-05 7.2106100e-07
SCFIt: 11 -75.9736733327 -5.1391842e-06 9.1176185e-07
SCFIt: 12 -75.9736708513 2.4814145e-06 1.5668061e-07
SCFIt: 13 -75.9737320579 -6.1206663e-05 5.4235814e-06
SCFIt: 14 -75.9736304344 1.0162357e-04 6.5974681e-06
SCFIt: 15 -75.9736926756 -6.2241262e-05 5.8093502e-06
SCFIt: 16 -75.9736701198 2.2555821e-05 3.3917217e-06
SCFIt: 17 -75.9736606351 9.4847574e-06 8.0454338e-07
SCFIt: 18 -75.9736606145 2.0517746e-08 6.8077667e-07
SCFIt: 19 -75.9736697679 -9.1533343e-06 1.8012792e-07
SCFIt: 20 -75.9736722272 -2.4593662e-06 5.8290943e-10
SCFIt: 21 -75.9736722272 2.1074698e-11 5.3621408e-10
SCF Completed: E(R-RHF) = -75.9736722272 Eh after 21 SCF Iterations
================================================================================
SCF Results:
================================================================================
Orbital Eigenenergies (Alpha) / Eh
--------------------------------------------------------------------------------
Occupied:
-2.0583e+01 -1.2809e+00 -6.3527e-01 -5.4586e-01 -4.9106e-01
Virtual:
1.7831e-01 2.6050e-01 9.6640e-01 1.0178e+00 1.1677e+00
1.2166e+00 1.3553e+00 1.6405e+00 2.0516e+00 2.0647e+00
2.0891e+00 2.4650e+00 2.7049e+00
--------------------------------------------------------------------------------6. Multipole Integrals In this section, the multipole property integrals are printed in Debye/Angstrom units.
Multipole Information:
--------------------------------------------------------------------------------
Electric Dipole Moment (Debye)
X= -0.0000000003 Y= 2.3165901386 Z= 0.0000000011
Electric Quadrupole Moment (Debye-Å)
XX= -3.8498060251 XY= 0.0000000001 XZ= 0.0000000002
YX= 0.0000000001 YY= -5.6935069164 YZ= 0.0000000002
ZX= 0.0000000002 ZY= 0.0000000002 ZZ= -7.5181196032
Electric Octupole Moment (Debye-Ų)
XXX= -0.0000000007 XXY= 1.6252269574 XXZ= 0.0000000010
XYX= 1.6252269574 XYY= -0.0000000002 XYZ= 0.0000000000
XZX= 0.0000000010 XZY= 0.0000000000 XZZ= -0.0000000001
YXX= 1.6252269574 YXY= -0.0000000002 YXZ= 0.0000000000
YYX= -0.0000000002 YYY= 0.3085897554 YYZ= 0.0000000008
YZX= 0.0000000000 YZY= 0.0000000008 YZZ= -0.1698352376
ZXX= 0.0000000010 ZXY= 0.0000000000 ZXZ= -0.0000000001
ZYX= 0.0000000000 ZYY= 0.0000000008 ZYZ= -0.1698352376
ZZX= -0.0000000001 ZZY= -0.1698352376 ZZZ= 0.0000000017
--------------------------------------------------------------------------------7. Spin Information In this section, spin expectation values like <Sz> and <S2> are displayed. For our case, this is pretty boring since we have a spin restricted system.
Spin Information:
--------------------------------------------------------------------------------
<Sx> = 0.00000
<Sy> = 0.00000
<Sz> = 0.00000
<S²> = 0.00000
--------------------------------------------------------------------------------8. Charge Analysis Finally, the Mulliken and Lowdin charges are displayed for each atom in the system. The output file then ends with the wall clock time when it exited the program.
Charge Analysis:
--------------------------------------------------------------------------------
Atom Mulliken Charges Lowdin Charges
----------------------------------------------------------------------------
O-16 -0.84359 -0.65339
H-1 0.42179 0.32669
H-1 0.42179 0.32669
--------------------------------------------------------------------------------
ChronusQ Job Ended: Wed Sep 16 13:50:35 2020