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benchmark, direct scf, and improvement #38

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benchmark, direct scf, and improvement
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3 changes: 2 additions & 1 deletion .vscode/settings.json
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{
"C_Cpp.errorSquiggles": "disabled"
"C_Cpp.errorSquiggles": "disabled",
"cmake.sourceDirectory": "/mlx_devbox/users/xiaojie.wu/playground/gpu4pyscf/build/lib.linux-x86_64-cpython-39/gpu4pyscf/lib"
}
47 changes: 30 additions & 17 deletions README.md
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Expand Up @@ -24,33 +24,46 @@ python -m cupyx.tools.install_library --cuda 11.x --library cutensor

Features
--------
Density fitting scheme
- SCF, analytical Gradient, and analytical Hessian calculations for Hartree-Fock and DFT
- LDA, GGA, mGGA without density laplacian, hybrid, and range-separated functionals
- Geometry optimization and transition state search via [geomeTRIC](https://geometric.readthedocs.io/en/latest/)
- Dispersion corrections via [DFT3](https://github.com/dftd3/simple-dftd3) and [DFT4](https://github.com/dftd4/dftd4)
- Nonlocal functional correction (vv10) for SCF and gradient
- ECP is supported and calculated on CPU

Direct SCF scheme (experimental)
- SCF for Hartree-Fock and DFT
- LDA, GGA, mGGA without density laplacian, hybrid, and range-separated functionals
- Dispersion corrections via [DFT3](https://github.com/dftd3/simple-dftd3) and [DFT4](https://github.com/dftd4/dftd4)
- Nonlocal functional correction (vv10) for SCF and gradient
- ECP is supported and calculated on CPU
- Density fitting scheme and direct SCF scheme;
- SCF, analytical Gradient, and analytical Hessian calculations for Hartree-Fock and DFT;
- LDA, GGA, mGGA, hybrid, and range-separated functionals via [libXC](https://gitlab.com/libxc/libxc/-/tree/master/);
- Geometry optimization and transition state search via [geomeTRIC](https://geometric.readthedocs.io/en/latest/);
- Dispersion corrections via [DFT3](https://github.com/dftd3/simple-dftd3) and [DFT4](https://github.com/dftd4/dftd4);
- Nonlocal functional correction (vv10) for SCF and gradient;
- ECP is supported and calculated on CPU;

Limitations
--------
- Rys roots up to 8 for density fitting scheme;
- Rys roots up to 9 for direct scf scheme;
- Atomic basis up to g orbitals;
- Auxiliary basis up to h orbitals;
- Up to ~100 atoms with def2-tzvpd basis, consuming a large amount of CPU memory;
- Gradient, Hessian and Geometry optimization are unavailable for Direct SCF yet;
- Up to ~168 atoms with def2-tzvpd basis, consuming a large amount of CPU memory;
- Hessian is unavailable for Direct SCF yet;
- meta-GGA without density laplacian;


Examples
--------
Find examples in gpu4pyscf/examples

Benchmarks
--------
Speedup with GPU4PySCF v0.6.0 over Q-Chem 6.1 (Desity fitting, SCF, def2-tzvpp, def2-universal-jkfit, (99,590))

| mol | natm | LDA | PBE | B3LYP | M06 | wB97m-v |
|:------------------|-------:|-------:|-------:|--------:|-------:|----------:|
| 020_Vitamin_C | 20 | 2.86 | 6.09 | 13.11 | 11.58 | 17.46 |
| 031_Inosine | 31 | 13.14 | 15.87 | 16.57 | 25.89 | 26.14 |
| 033_Bisphenol_A | 33 | 12.31 | 16.88 | 16.54 | 28.45 | 28.82 |
| 037_Mg_Porphin | 37 | 13.85 | 19.03 | 20.53 | 28.31 | 30.27 |
| 042_Penicillin_V | 42 | 10.34 | 13.35 | 15.34 | 22.01 | 24.2 |
| 045_Ochratoxin_A | 45 | 13.34 | 15.3 | 19.66 | 27.08 | 25.41 |
| 052_Cetirizine | 52 | 17.79 | 17.44 | 19 | 24.41 | 25.87 |
| 057_Tamoxifen | 57 | 14.7 | 16.57 | 18.4 | 24.86 | 25.47 |
| 066_Raffinose | 66 | 13.77 | 14.2 | 20.47 | 22.94 | 25.35 |
| 084_Sphingomyelin | 84 | 14.24 | 12.82 | 15.96 | 22.11 | 24.46 |
| 095_Azadirachtin | 95 | 5.58 | 7.72 | 24.18 | 26.84 | 25.21 |
| 113_Taxol | 113 | 5.44 | 6.81 | 24.58 | 29.14 | nan |

Find more benchmarks in gpu4pyscf/benchmarks

204 changes: 204 additions & 0 deletions benchmarks/README.md
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# Benchmark details

Two types of machines for the following benchmarks
- A100-SXM4-80G with Intel(R) Xeon(R) Platinum 8336C CPU @ 2.30GHz
- V100-SXM4-32G with Intel(R) Xeon(R) Platinum 8260 CPU @ 2.40GHz

CUDA and GPU driver
- Driver Version: 450.191.01
- CUDA Version: 11.7

Q-Chem is running on Intel(R) Xeon(R) Platinum 8336C CPU @ 2.30GHz

'nan' indicates failed jobs with Q-Chem.

negative value indicates failed jobs with GPU4PySCF.

Raw data for density fitting can be found `benchmarks/df/organic`

Raw data for direct SCF can be found in `benchmarks/scf/water_clusters`

# Density fitting SCF single-point energy (v0.6.0)

## GPU4PySCF v0.6.0 on Nvidia A100-SXM4-80G vs Q-Chem 6.1 on 32 CPU threads

B3LYP with different basis

| mol | natm | sto-3g | 6-31g | def2-svp | def2-tzvpp | def2-tzvpd |
|:------------------|-------:|---------:|--------:|-----------:|-------------:|-------------:|
| 020_Vitamin_C | 20 | 0.92 | 1.5 | 2.13 | 5.94 | 8.36 |
| 031_Inosine | 31 | 4.74 | 7.12 | 10.98 | 17.02 | 21.17 |
| 033_Bisphenol_A | 33 | 4.53 | 6.24 | 7 | 16.55 | 20.96 |
| 037_Mg_Porphin | 37 | 7.38 | 9.9 | 13.88 | 16.9 | 23.39 |
| 042_Penicillin_V | 42 | 5.9 | 8.19 | 11.43 | 16.41 | 20.11 |
| 045_Ochratoxin_A | 45 | 6.94 | 10.06 | 12.9 | 15.33 | 21.62 |
| 052_Cetirizine | 52 | 7.15 | 9.86 | 13.85 | 17.34 | 23.24 |
| 057_Tamoxifen | 57 | 7.48 | 8.95 | 13.19 | 19.26 | 24.22 |
| 066_Raffinose | 66 | 8.22 | 10.12 | 14.98 | 15.28 | 16.1 |
| 084_Sphingomyelin | 84 | nan | 9.69 | 14.83 | 17.82 | 20.33 |
| 095_Azadirachtin | 95 | 16.06 | 17.18 | 24.22 | 23.29 | nan |
| 113_Taxol | 113 | 20.11 | 18.04 | 23.38 | 24 | nan |
| 168_Valinomycin | 168 | 23.43 | 19.41 | nan | nan | nan |

def2-tzvpp with different xc functionals

| mol | natm | LDA | PBE | B3LYP | M06 | wB97m-v |
|:------------------|-------:|-------:|-------:|--------:|-------:|----------:|
| 020_Vitamin_C | 20 | 2.86 | 6.09 | 13.11 | 11.58 | 17.46 |
| 031_Inosine | 31 | 13.14 | 15.87 | 16.57 | 25.89 | 26.14 |
| 033_Bisphenol_A | 33 | 12.31 | 16.88 | 16.54 | 28.45 | 28.82 |
| 037_Mg_Porphin | 37 | 13.85 | 19.03 | 20.53 | 28.31 | 30.27 |
| 042_Penicillin_V | 42 | 10.34 | 13.35 | 15.34 | 22.01 | 24.2 |
| 045_Ochratoxin_A | 45 | 13.34 | 15.3 | 19.66 | 27.08 | 25.41 |
| 052_Cetirizine | 52 | 17.79 | 17.44 | 19 | 24.41 | 25.87 |
| 057_Tamoxifen | 57 | 14.7 | 16.57 | 18.4 | 24.86 | 25.47 |
| 066_Raffinose | 66 | 13.77 | 14.2 | 20.47 | 22.94 | 25.35 |
| 084_Sphingomyelin | 84 | 14.24 | 12.82 | 15.96 | 22.11 | 24.46 |
| 095_Azadirachtin | 95 | 5.58 | 7.72 | 24.18 | 26.84 | 25.21 |
| 113_Taxol | 113 | 5.44 | 6.81 | 24.58 | 29.14 | nan |
| 168_Valinomycin | 168 | nan | nan | nan | nan | nan |

## GPU4PySCF v0.6.0 on Nvidia V100-SXM4-32G vs Q-Chem 6.1 on 32 CPU threads
B3LYP with different basis

| mol | natm | sto-3g | 6-31g | def2-svp | def2-tzvpp | def2-tzvpd |
|:------------------|-------:|---------:|--------:|-----------:|-------------:|-------------:|
| 020_Vitamin_C | 20 | 0.52 | 0.93 | 1.23 | 3.98 | 4.88 |
| 031_Inosine | 31 | 0.97 | 1.92 | 3.03 | 6.79 | 8.19 |
| 033_Bisphenol_A | 33 | 1.16 | 1.89 | 2.09 | 6.72 | 8.31 |
| 037_Mg_Porphin | 37 | 1.79 | 3.55 | 4.49 | 7.64 | 10.55 |
| 042_Penicillin_V | 42 | 1.37 | 2.62 | 3.63 | 7.69 | 9.24 |
| 045_Ochratoxin_A | 45 | 1.58 | 3.23 | 4.12 | 7.27 | 9.88 |
| 052_Cetirizine | 52 | 1.83 | 3.61 | 4.72 | 8.63 | 11.32 |
| 057_Tamoxifen | 57 | 1.92 | 3.3 | 4.59 | 9.72 | 7.87 |
| 066_Raffinose | 66 | 2.31 | 4.04 | 5.75 | 6.09 | 5.54 |
| 084_Sphingomyelin | 84 | nan | 3.29 | 4.92 | 7.32 | 8 |
| 095_Azadirachtin | 95 | 4.63 | 8.46 | 10.55 | 13.83 | nan |
| 113_Taxol | 113 | 6.55 | 10.1 | 9.43 | 12.31 | nan |
| 168_Valinomycin | 168 | 9.23 | 11.66 | nan | nan | nan |

def2-tzvpp with different xc functionals

| mol | natm | LDA | PBE | B3LYP | M06 | wB97m-v |
|:------------------|-------:|------:|------:|--------:|------:|----------:|
| 020_Vitamin_C | 20 | 1.89 | 3.3 | 8.18 | 5.95 | 10.58 |
| 031_Inosine | 31 | 4.64 | 5.95 | 6.41 | 9.48 | 13.15 |
| 033_Bisphenol_A | 33 | 4.85 | 6.64 | 6.58 | 11.04 | 14.72 |
| 037_Mg_Porphin | 37 | 5.61 | 8.6 | 9.01 | 12.34 | 16.56 |
| 042_Penicillin_V | 42 | 4.36 | 6.17 | 7.09 | 10.62 | 14.28 |
| 045_Ochratoxin_A | 45 | 5.47 | 6.97 | 8.74 | 12.05 | 14.14 |
| 052_Cetirizine | 52 | 8.43 | 8.51 | 9.16 | 12.44 | 15.37 |
| 057_Tamoxifen | 57 | 6.79 | 8.41 | 9.98 | 13.44 | 15.67 |
| 066_Raffinose | 66 | 3.22 | 4.31 | 8.11 | 10.58 | 13.22 |
| 084_Sphingomyelin | 84 | 3.34 | 3.97 | 6.52 | 8.63 | 12.11 |
| 095_Azadirachtin | 95 | 3.35 | 4.74 | 14.29 | 16.52 | 15.05 |
| 113_Taxol | 113 | 3.12 | 4.1 | 12.59 | 15.74 | nan |
# Density fitting gradient (v0.6.0)

## GPU4PySCF v0.6.0 on Nvidia A100-SXM4-80G vs Q-Chem 6.1 on 32 CPU threads

B3LYP with different basis

| mol | natm | sto-3g | 6-31g | def2-svp | def2-tzvpp | def2-tzvpd |
|:------------------|-------:|---------:|--------:|-----------:|-------------:|-------------:|
| 020_Vitamin_C | 20 | 3.13 | 4.12 | 5.98 | 9.71 | 10.7 |
| 031_Inosine | 31 | 11.42 | 9.82 | 13.23 | 16.47 | 16.16 |
| 033_Bisphenol_A | 33 | 13.28 | 10.3 | 11.94 | 16.08 | 16.02 |
| 037_Mg_Porphin | 37 | 13.75 | 10.54 | 15.87 | 18.33 | 19.89 |
| 042_Penicillin_V | 42 | 13.3 | 10.7 | 14.07 | 17.2 | 18.81 |
| 045_Ochratoxin_A | 45 | 14.68 | 11.33 | 16.28 | 19.79 | 20.94 |
| 052_Cetirizine | 52 | 21.46 | 14.62 | 19.55 | 20.51 | 21.93 |
| 057_Tamoxifen | 57 | 20.97 | 16.37 | 18.78 | 20.27 | 21.96 |
| 066_Raffinose | 66 | 25.4 | 17.78 | 25.71 | 23.88 | 22.38 |
| 084_Sphingomyelin | 84 | nan | 17.46 | 20.9 | 23.64 | 26.52 |
| 095_Azadirachtin | 95 | 39.13 | 32.27 | 40.78 | 39.94 | nan |
| 113_Taxol | 113 | 48.57 | 42.77 | 51.57 | 49.03 | nan |
| 168_Valinomycin | 168 | 87.81 | 72.58 | nan | nan | nan |

def2-tzvpp with different xc functionals

| mol | natm | LDA | PBE | B3LYP | M06 | wB97m-v |
|:------------------|-------:|-------:|-------:|--------:|-------:|----------:|
| 020_Vitamin_C | 20 | 5.02 | 7.04 | 10.55 | 9.28 | 11.11 |
| 031_Inosine | 31 | 7.3 | 10.03 | 15.12 | 12.62 | 13.9 |
| 033_Bisphenol_A | 33 | 7.58 | 11.1 | 15.55 | 12.64 | 14 |
| 037_Mg_Porphin | 37 | 7.47 | 11.34 | 18.05 | 15.81 | 14.85 |
| 042_Penicillin_V | 42 | 6.03 | 8.96 | 17.4 | 14.47 | 13.81 |
| 045_Ochratoxin_A | 45 | 7.51 | 9.33 | 19.51 | 17.2 | 14.55 |
| 052_Cetirizine | 52 | 8.32 | 9.7 | 20.8 | 16.46 | 15.7 |
| 057_Tamoxifen | 57 | 8.91 | 9.61 | 20.61 | 16.2 | 15 |
| 066_Raffinose | 66 | 8.52 | 9.46 | 24.2 | 18.63 | 17.13 |
| 084_Sphingomyelin | 84 | 8.51 | 9.49 | 23.62 | 21.63 | 17.66 |
| 095_Azadirachtin | 95 | 7.69 | 9.48 | 42.24 | 34.01 | 23.93 |
| 113_Taxol | 113 | 8.08 | 9.05 | 51.03 | 40.13 | nan |
| 168_Valinomycin | 168 | nan | nan | nan | nan | nan |

## GPU4PySCF v0.6.0 on Nvidia V100-SXM4-32G vs Q-Chem 6.1 on 32 CPU threads

B3LYP with different basis

| mol | natm | sto-3g | 6-31g | def2-svp | def2-tzvpp | def2-tzvpd |
|:------------------|-------:|---------:|--------:|-----------:|-------------:|-------------:|
| 020_Vitamin_C | 20 | 1.43 | 2.4 | 3.3 | 5.46 | 5.54 |
| 031_Inosine | 31 | 3.01 | 4.22 | 5.14 | 7.06 | 6.84 |
| 033_Bisphenol_A | 33 | 3.31 | 4.18 | 4.38 | 6.75 | 6.89 |
| 037_Mg_Porphin | 37 | 4.13 | 5.08 | 6.42 | 7.89 | 8.54 |
| 042_Penicillin_V | 42 | 4.05 | 5.06 | 5.89 | 7.88 | 8.39 |
| 045_Ochratoxin_A | 45 | 4.59 | 5.42 | 6.8 | 8.6 | 8.93 |
| 052_Cetirizine | 52 | 6.11 | 7.04 | 7.97 | 9.13 | 9.53 |
| 057_Tamoxifen | 57 | 6.17 | 8.05 | 7.74 | 9.3 | 9.22 |
| 066_Raffinose | 66 | 7.9 | 9.49 | 10.82 | 10.51 | 9.58 |
| 084_Sphingomyelin | 84 | nan | 7.64 | 7.99 | 9.56 | 10.39 |
| 095_Azadirachtin | 95 | 13.3 | 17.59 | 16.25 | 17.93 | nan |
| 113_Taxol | 113 | 17.55 | 23.43 | 20.81 | 21.54 | nan |
| 168_Valinomycin | 168 | 31.21 | 38.79 | nan | nan | nan |

def2-tzvpp with different xc functionals

| mol | natm | LDA | PBE | B3LYP | M06 | wB97m-v |
|:------------------|-------:|------:|------:|--------:|------:|----------:|
| 020_Vitamin_C | 20 | 3.19 | 4.28 | 5.9 | 4.82 | 5.84 |
| 031_Inosine | 31 | 3.21 | 4.5 | 6.55 | 5.52 | 6.39 |
| 033_Bisphenol_A | 33 | 3.55 | 4.87 | 6.61 | 5.51 | 6.48 |
| 037_Mg_Porphin | 37 | 3.19 | 5.2 | 8.32 | 7.26 | 6.81 |
| 042_Penicillin_V | 42 | 3.15 | 4.35 | 8.11 | 7.23 | 6.97 |
| 045_Ochratoxin_A | 45 | 3.32 | 4.29 | 8.99 | 8.04 | 6.92 |
| 052_Cetirizine | 52 | 3.51 | 4.6 | 9.41 | 8.18 | 7.57 |
| 057_Tamoxifen | 57 | 3.86 | 4.66 | 9.56 | 8.4 | 7.51 |
| 066_Raffinose | 66 | 3.4 | 4.32 | 10.94 | 9.4 | 8.29 |
| 084_Sphingomyelin | 84 | 3.15 | 3.81 | 9.66 | 8.97 | 8.03 |
| 095_Azadirachtin | 95 | 3.32 | 4.37 | 18.47 | 16.01 | 1.68 |
| 113_Taxol | 113 | 3.12 | 1.19 | 22.53 | 16.94 | nan |

# Density fitting hessian (v0.6.0)

coming soon..

# Direct SCF single-point energy (v0.6.0)
def2-tzvpp with different xc functionals

| mol | natm | LDA | PBE | B3LYP | M06 | wB97m-v |
|------:|-------:|-------:|-------:|--------:|-------:|----------:|
| 2 | 3 | 0.22 | 0.32 | 0.27 | 0.25 | 0.69 |
| 3 | 15 | 0.68 | 0.25 | 1.58 | 2.61 | 4.84 |
| 4 | 30 | 1.59 | 2.63 | 4.09 | 6.93 | 8.17 |
| 5 | 60 | 2.86 | 3.64 | 7.15 | 8.44 | 9.44 |
| 6 | 96 | 4.34 | 4.39 | 7.75 | 10.58 | 9.87 |
| 7 | 141 | 4.07 | 4.1 | 8.87 | 10.47 | 10.13 |
| 8 | 228 | 4.34 | 4.58 | 9.39 | 10.48 | 9.36 |
| 9 | 300 | 5.05 | 5.21 | 9.35 | 11.36 | nan |
| 10 | 417 | 4.91 | nan | nan | nan | nan |

# Direct SCF gradient (v0.6.0)
def2-tzvpp with different xc functionals

| mol | natm | LDA | PBE | B3LYP | M06 | wB97m-v |
|------:|-------:|-------:|-------:|--------:|-------:|----------:|
| 2 | 3 | 0.82 | 0.89 | 0.75 | 0.82 | 0.6 |
| 3 | 15 | 0.39 | 0.19 | 1.46 | 1.52 | 1.47 |
| 4 | 30 | 0.56 | 1.04 | 2.07 | 2.25 | 1.89 |
| 5 | 60 | 0.54 | 0.87 | 2.42 | 2.4 | 1.77 |
| 6 | 96 | 0.6 | 0.87 | 2.36 | 2.51 | 1.53 |
| 7 | 141 | 0.93 | 1.1 | 2.61 | 2.59 | 1.55 |
| 8 | 228 | 1.92 | 1.9 | 3.37 | 3.39 | 1.83 |
| 9 | 300 | 2.26 | 2.02 | 3.06 | 3.59 | nan |
| 10 | 417 | 2.46 | nan | nan | nan | nan |
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