RHF/UHF code written in in Julia (with integrals provided by libcint via GaussianBasis.jl). Primarily written to to be a simple, but general and easy-to-understand RHF/UHF code without being horribly slow. Might one day turn into something useful.
- 1 and 2-electron integrals via GaussianBasis.jl and libcint.
- Conventional RHF and UHF algorithm using 2-el integrals as full rank-4 tensor (4c) or sparse version (sparse4c)
- Fock matrix speedup (4c) via LoopVectorization.jl
- Mulliken population analysis (RHF and UHF)
- Mayer bond orders (RHF and UHF)
- SCF convergence aids: DIIS, levelshifting, static damping
- Basis sets:
- Support for all internal basis sets in GaussianBasis.jl.
- Support for reading in external basis set in ORCA format.
- Improving speed:
- Further fine-tuning of Fock code for sparse 2el-integral version.
- Density fitting
- Improving SCF convergence:
- Dynamic damping
- Better guess than Hcore
- DFT support:
- interface to LibXC
- DFT grids
- hybrid-DFT
- Support broken-symmetry guess
- Simple electric properties (dipole, EFG)
- Hirshfeld population analysis
- Direct SCF algorithm ?
- Noncollinear HF/DFT
- Read-in basis set: Normalize contraction coefficients. Code currently assumes normalization.
- GaussianBasis.jl (1 and 2-electron integrals)
- Molecules.jl (helper program with GaussianBasis.jl)
- LoopVectorization.jl (only to speed up Fock when using full 4-rank TEIs )
- PrettyTables.jl (pretty output)
- Crayons.jl (pretty output)
Option 1. Manual setup:
First clone or download the Jotunn source-code. Make package available to Julia by setting the environment variable:
export JULIA_LOAD_PATH=/path/to/Jotunn/src:$JULIA_LOAD_PATH
#copy-paste in Unix shell to make Jotunn package available to JuliaOption 2. Install package:
Launch a Julia session and copy-paste the line below into Julia REPL. This will install Jotunn as a Julia package:
using Pkg; Pkg.add(url="https://github.com/RagnarB83/Jotunn.jl")create_fragment (a function to create a Jotunn molecule fragment object)
function create_fragment(;coords_string=nothing,xyzfile=nothing,pdbfile=nothing,fragfile=nothing, coords=nothing,
elems=nothing, calc_connectivity=false, label=nothing, charge=nothing, mult=nothing)jSCF (a function to run the Jotunn RHF/UHF code).
function jSCF(fragment, basisset="sto-3g"; WFtype::String="RHF", guess::String="hcore", basisfile::String="none", maxiter::Int64=120,
print_final_matrices::Bool=false, rmsDP_threshold::Float64=5e-9, maxDP_threshold::Float64=1e-7, tei_type::String="sparse4c",
energythreshold::Float64=1e-8, debugprint::Bool=false, fock_algorithm::String="loop",
levelshift::Bool=false, levelshift_val::Float64=0.10, lshift_thresh::Float64=0.01,
damping::Bool=true, damping_val::Float64=0.4, damping_thresh::Float64=0.01,
diis::Bool=false, diis_size::Int64=7, diis_thresh::Float64=0.01,
printlevel::Int64=1)Option 1: Launch an interactive julia session:
juliaThen within Julia REPL, import Jotunn, create a molecule fragment and call jSCF :
using Jotunn
H2 = create_fragment(coords_string="""
H 0.0 0.0 0.0
H 0.0 0.0 0.74
""", charge=0, mult=1)
jSCF(H2, "sto-3g")Option 2: Create a Julia script (e.g. test.jl)
test.jl:
using Jotunn
H2 = create_fragment(coords_string="""
H 0.0 0.0 0.0
H 0.0 0.0 0.74
""", charge=0, mult=1)Run inputscript like this:
julia test.jlExample inputfiles below can all be found in examples directory
See GaussianBasis/lib directory for list of available basis-sets.
simple-input.jl:
using Jotunn
# Create molecular fragments
H2 = create_fragment(coords_string="""
H 0.0 0.0 0.0
H 0.0 0.0 0.74
""", charge=0, mult=1)
#Simple call
result= jSCF(H2, "sto-3g")
println("Result dictionary from Jotunn: $result")
println("Energy: $(result["energy"]) Eh")moreoptions-input.jl:
using Jotunn
H2O = create_fragment(xyzfile="h2o.xyz", charge=0, mult=1)
#More keywords
result= jSCF(H2O, "sto-3g"; maxiter=200, fock_algorithm="turbo", printlevel=2,
WFtype="RHF", levelshift=2.0, lshift_thresh=1e-4, tei_type="4c",
print_final_matrices=true, debugprint=true)alloptions-input.jl:
using Jotunn
H2O = create_fragment(xyzfile="h2o.xyz", charge=0, mult=1)
#All features
result = jSCF(H2O, basisset="STO-3G"; WFtype="RHF", guess="hcore", basisfile="none", maxiter=120,
print_final_matrices=false, rmsDP_threshold=5e-9, maxDP_threshold=1e-7, tei_type="4c",
energythreshold=1e-8, debugprint=false, fock_algorithm="turbo",
levelshift=false, levelshift_val=0.10, lshift_thresh=0.01,
damping=true, damping_val=0.4, damping_thresh=0.01,
printlevel=1)
==================================================
JOTUNN
a simple quantum chemistry program in Julia
==================================================
jSCF module: a RHF/UHF program
SYSTEM
========================= =================
Number of atoms 3
Molecule formula OHH
Charge 0
Spin multiplicity 1
No. electrons 10
No. unpaired electrons 0
Nuclear repulsion 9.11937991
========================= =================
Integrals provided via GaussianBasis.jl library
Creating basis set object
Calculating 1-electron integrals
Calculating 2-electron integrals
2.461401 seconds (3.59 M allocations: 169.377 MiB, 3.08% gc time, 98.97% compilation time)
Choosing Fock algorithm.
Small system (Basis dim: 24). Choosing loop Fock.
Providing guess for density matrix
Energy of guess: 9.119379905339786 Eh
CALCULATION SETTINGS
========================= =================
HF type RHF
Basis set def2-svp
No. basis functions 24
Guess hcore
2-electron type 4c
Fock algorithm loop
S lowest eigenvalue 0.0281
Levelshift false
Levelshift parameter 0.1000
Lshift-turnoff thresh. 0.0100
Damping true
Damping parameter 0.4000
Damp-turnoff thresh. 0.0100
DIIS false
DIIS vec size 7
DIIS thresh. 0.0100
========================= =================
Beginning SCF iterations
Iter Energy deltaE RMS-DP Max-DP Lshift Damp DIIS
1 -126.165023244 -126.165023244 0.422360951 0.766341001 false true false
2 -90.891462805 35.273560439 0.144192193 0.976274234 false true false
3 -77.074577330 13.816885475 0.177725075 1.918743295 false true false
4 -76.127629367 0.946947963 0.073956975 0.835446553 false true false
5 -76.010001447 0.117627920 0.029057353 0.340558595 false true false
6 -75.972851329 0.037150118 0.011633177 0.141278309 false true false
7 -75.962058521 0.010792808 0.004814077 0.060224092 false true false
8 -75.957733508 0.004325013 0.000795942 0.004387088 false false false
9 -75.959936967 -0.002203459 0.000275068 0.002149001 false false false
10 -75.960270463 -0.000333496 0.000103929 0.000945157 false false false
11 -75.960395859 -0.000125396 0.000040334 0.000397913 false false false
12 -75.960425046 -0.000029186 0.000015887 0.000166315 false false false
13 -75.960441935 -0.000016889 0.000006333 0.000067903 false false false
14 -75.960444414 -0.000002479 0.000002553 0.000028294 false false false
15 -75.960447558 -0.000003143 0.000001038 0.000011428 false false false
16 -75.960447455 0.000000103 0.000000427 0.000004844 false false false
17 -75.960448170 -0.000000715 0.000000177 0.000001934 false false false
18 -75.960447999 0.000000171 0.000000075 0.000000849 false false false
19 -75.960448191 -0.000000192 0.000000032 0.000000330 false false false
20 -75.960448113 0.000000078 0.000000014 0.000000154 false false false
21 -75.960448171 -0.000000058 0.000000006 0.000000057 false false false
22 -75.960448141 0.000000030 0.000000003 0.000000029 false false false
23 -75.960448160 -0.000000019 0.000000001 0.000000010 false false false
24 -75.960448150 0.000000010 0.000000001 0.000000006 false false false
25 -75.960448156 -0.000000006 0.000000000 0.000000002 false false false
SCF converged in 25 iterations! Hell yeah! 🎉
┌──────────────────────┬────────────────┐
│ Energy contributions │ E(Eh) │
├──────────────────────┼────────────────┤
│ Total energy │ -75.96044816 │
│ Nuclear repulsion │ 9.11937991 │
│ Electronic energy │ -85.07982806 │
│ 1-electron energy │ -122.90608315 │
│ 2-electron energy │ 37.82625508 │
│ Kinetic energy │ 75.74591703 │
│ Potential energy │ -151.70636519 │
├──────────────────────┼────────────────┤
│ Virial ratio │ 2.00283225 │
└──────────────────────┴────────────────┘
1.332684 seconds (1.72 M allocations: 90.361 MiB, 2.09% gc time, 94.01% compilation time)
MO Energies (closed-shell)
┌────┬──────┬──────────────┬──────────────┐
│ MO │ Occ. │ E(Eh) │ E(eV) │
├────┼──────┼──────────────┼──────────────┤
│ 1 │ 2.0 │ -20.5475 │ -559.1252 │
│ 2 │ 2.0 │ -1.3154 │ -35.7944 │
│ 3 │ 2.0 │ -0.6979 │ -18.9900 │
│ 4 │ 2.0 │ -0.5683 │ -15.4630 │
│ 5 │ 2.0 │ -0.4978 │ -13.5452 │
│ 6 │ 0.0 │ 0.1748 │ 4.7574 │
│ 7 │ 0.0 │ 0.2542 │ 6.9167 │
│ 8 │ 0.0 │ 0.7862 │ 21.3927 │
│ 9 │ 0.0 │ 0.8642 │ 23.5149 │
│ 10 │ 0.0 │ 1.1852 │ 32.2514 │
│ 11 │ 0.0 │ 1.2017 │ 32.7013 │
│ 12 │ 0.0 │ 1.2705 │ 34.5727 │
│ 13 │ 0.0 │ 1.3419 │ 36.5163 │
│ 14 │ 0.0 │ 1.5981 │ 43.4873 │
│ 15 │ 0.0 │ 1.6553 │ 45.0430 │
│ 16 │ 0.0 │ 1.8029 │ 49.0589 │
│ 17 │ 0.0 │ 2.0563 │ 55.9553 │
│ 18 │ 0.0 │ 2.5418 │ 69.1649 │
│ 19 │ 0.0 │ 2.5863 │ 70.3762 │
│ 20 │ 0.0 │ 3.3239 │ 90.4486 │
│ 21 │ 0.0 │ 3.3739 │ 91.8083 │
│ 22 │ 0.0 │ 3.5635 │ 96.9678 │
│ 23 │ 0.0 │ 3.8870 │ 105.7716 │
│ 24 │ 0.0 │ 4.2295 │ 115.0902 │
└────┴──────┴──────────────┴──────────────┘
Mulliken Population Analysis (closed-shell)
┌──────┬─────────┬────────────┐
│ Atom │ Element │ Charge │
├──────┼─────────┼────────────┤
│ 1 │ O │ -0.353914 │
│ 2 │ H │ 0.176957 │
│ 3 │ H │ 0.176957 │
└──────┴─────────┴────────────┘
Sum of charges: 0.0000
Mayer bond orders
Threshold: 0.01
┌─────────┬────────┐
│ Bond │ MBO │
├─────────┼────────┤
│ O1 - H2 │ 0.9947 │
│ O1 - H3 │ 0.9947 │
└─────────┴────────┘
FINAL RESULTS
====================== =================
Final HF energy -75.96044816
Molecule formula OHH
Number of electrons 10
Basis set def2-svp
HF type RHF
Fock algorithm loop
SCF iterations 25
====================== =================