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JQuante is a basic Java QM toolkit, written in Java, that is inspired by PyQuante.

Java 100.00%

chemistry java quantum-mechanics

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mjbvz chrinide

jquante's Issues

Implement LCIIS

See: http://dx.doi.org/10.1021/acs.jctc.6b00666

RysTwoElectronTerm class is incomplete

Make use of existing linear algebra libraries

Interesting benchmarks here

Looks like EJML could be good

+ Active development
+ Maven artefact
+ Fast
- May not support everything
- Single threaded

Implement mixed ERIs as a function of angular momenta

See Efficient Calculation of Molecular Integrals over London Atomic Orbitals

Shellpair support

Work started here: 53f7fad

Wavefunction convergence is poor in comparision to other tools

With 2e5da8 and jquante-jmh 5cf53d

H2O HF/cc-pVTZ Single Point

NWChem:

              iter       energy          gnorm     gmax       time
             ----- ------------------- --------- --------- --------
                 1      -76.0215778847  8.47D-01  2.91D-01      0.3
                 2      -76.0544048507  1.97D-01  5.88D-02      0.3
                 3      -76.0566218348  1.63D-02  5.94D-03      0.3
                 4      -76.0566456310  7.11D-05  3.00D-05      0.4

PySCF

cycle= 1 E= -76.0189103739337  delta_E= -0.162  |g|= 0.444  |ddm|= 0.999
cycle= 2 E= -76.0459442465136  delta_E= -0.027  |g|= 0.257  |ddm|= 0.317
cycle= 3 E= -76.0558603448014  delta_E= -0.00992  |g|= 0.0325  |ddm|= 0.103
cycle= 4 E= -76.0560776210976  delta_E= -0.000217  |g|= 0.0061  |ddm|= 0.0193
cycle= 5 E= -76.0560945080452  delta_E= -1.69e-05  |g|= 0.00109  |ddm|= 0.00874
cycle= 6 E= -76.0560952210263  delta_E= -7.13e-07  |g|= 0.000188  |ddm|= 0.00148
cycle= 7 E= -76.0560952423026  delta_E= -2.13e-08  |g|= 2.5e-05  |ddm|= 0.000277
cycle= 8 E= -76.0560952425745  delta_E= -2.72e-10  |g|= 2.45e-06  |ddm|= 3.83e-05

Jquante

#!bash
DEBUG - SCF iteration: 0	Energy is : -61.317658101524195	delta_E: 61.317658101524195
DEBUG - SCF iteration: 1	Energy is : -66.43889101307678	delta_E: 5.121232911552589
DEBUG - SCF iteration: 2	Energy is : -71.62299993037095	delta_E: 5.184108917294168
DEBUG - SCF iteration: 3	Energy is : -69.93987931720403	delta_E: 1.6831206131669205
DEBUG - SCF iteration: 4	Energy is : -72.96860313203896	delta_E: 3.028723814834933
DEBUG - SCF iteration: 5	Energy is : -72.6646080594117	delta_E: 0.30399507262725933
DEBUG - SCF iteration: 6	Energy is : -74.1670563297645	delta_E: 1.5024482703528008
DEBUG - SCF iteration: 7	Energy is : -74.89817559308625	delta_E: 0.7311192633217445
DEBUG - SCF iteration: 8	Energy is : -75.51558713379177	delta_E: 0.6174115407055183
DEBUG - SCF iteration: 9	Energy is : -75.80248814745667	delta_E: 0.2869010136649024
DEBUG - SCF iteration: 10	Energy is : -75.94958686192496	delta_E: 0.14709871446828515
DEBUG - SCF iteration: 11	Energy is : -76.01124902578428	delta_E: 0.06166216385932444
DEBUG - SCF iteration: 12	Energy is : -76.03806868559914	delta_E: 0.026819659814862007
DEBUG - SCF iteration: 13	Energy is : -76.0489817829164	delta_E: 0.01091309731725687
DEBUG - SCF iteration: 14	Energy is : -76.05352062292408	delta_E: 0.00453884000768312
DEBUG - SCF iteration: 15	Energy is : -76.05536523112619	delta_E: 0.0018446082021057464
DEBUG - SCF iteration: 16	Energy is : -76.05612303985978	delta_E: 7.578087335957662E-4
DEBUG - SCF iteration: 17	Energy is : -76.05643170567717	delta_E: 3.086658173856449E-4
DEBUG - SCF iteration: 18	Energy is : -76.05655803380259	delta_E: 1.2632812541824023E-4
DEBUG - SCF iteration: 19	Energy is : -76.0566095637233	delta_E: 5.152992071089102E-5
223.032 s/op

Extract Shells from basis set

Add Schwarz inequality prescreening

See section 7 for a nice overview.

Use commons-math interpolators

Replace name.mjw.jquante.math.interpolater with org.apache.commons.math3.analysis.interpolation

Sort shells using LibInt ordering

Implement SAD for initial DM guess

Implement Superposition of Atomic Densities (SAD)

See: http://dx.doi.org/10.1002/jcc.20393

DIISFockExtrapolator might be broken

The DIISFockExtrapolator never seems to kick in, hence the number of SCF cycles in comparison to other QM is higher.

errorThreshold is never set and the line at

jquante/src/main/java/name/mjw/jquante/math/qm/DIISFockExtrapolator.java

Line 59 in c1af1b8

if (mxerr < errorThreshold && !isDiisStarted) {

is strange.

Support for B3LYP

What is needed:

Grid integration Scheme
Lebedev quadrature
Exchange functional: B3
LSDA
B88
HF
Correlation functional: LYP
LSDA
GGA

Experimental Valhalla branch

Creating a testing and benchmarking branch for the upcoming Project Valhalla features to see if there is an improvement in speed. Good starting example might be here.

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