From Command Line
In this tutorial, all calculations are performed via the command line.
Starting from version 1.1.6,
horton-part only supports input files in yaml format to run its programs.Below is a simple example of an input file,
sample_input.yaml:part-gen:
inputs:
- ./data/h2o.fchk
outputs:
- h2o_dens.npz
part-dens:
inputs:
- h2o_dens.npz
outputs:
- h2o_part.npz
This input file specifies the inputs and outputs for two sub-programs: part-gen and part-dens.
The
inputsofpart-genspecify the file used to generate the molecular density and molecular grids, which are stored in the path defined in theoutputssection ofpart-gen.The
outputsofpart-genbecome theinputsfor thepart-denssub-program, which partitions the molecular density into atomic contributions using various methods. The default method isaLISA.
To run the calculation in the terminal, use the following command:
part sample_input.yaml
If you prefer to run it in a Jupyter notebook, you will need to use the os module to execute the command.
[1]:
import os
Then, one can execute command through calling os.system function. The result is restored in h2o_part.npz that is a Numpy npz file.
[2]:
os.system("part sample_input.yaml")
/Library/Frameworks/Python.framework/Versions/3.10/lib/python3.10/site-packages/grid/molgrid.py:436: RuntimeWarning: Sizes are used for making the angular grids, degrees are ignored!
AtomGrid(rad_grid, degrees=None, sizes=[size], center=atcoord, rotate=rotate)
****************************************************************************************************
Settings for part-dens program with Horton-Part 0.0.post1
****************************************************************************************************
input : h2o_dens.npz
output : h2o_part.npz
basis_func : gauss
func_file : None
maxiter : 1000
threshold : 1e-06
inner_threshold : 1e-08
lmax : 3
log_level : INFO
solver : sc
part_job_type : do_partitioning
grid_type : 1
log_file : None
----------------------------------------------------------------------------------------------------
Load grid and density data from h2o_dens.npz ...
Load data done!
Time usage 0.000 s
Create molecular grid ...
Create molecular grid done!
Time usage 0.011 s
****************************************************************************************************
Partitioning
****************************************************************************************************
================================================================================
Information of integral grids.
--------------------------------------------------------------------------------
Grid size of molecular grid: 87300
************************************ Atom 0 ************************************
|-- Radial grid size: 150
|-- Angular grid sizes:
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194
************************************ Atom 1 ************************************
|-- Radial grid size: 150
|-- Angular grid sizes:
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194
************************************ Atom 2 ************************************
|-- Radial grid size: 150
|-- Angular grid sizes:
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194 194
194 194 194 194 194 194 194 194 194 194
--------------------------------------------------------------------------------
================================================================================
Performing a density-based AIM analysis with a wavefunction as input.
Molecular grid : MolGrid
Using local grids : True
Scheme : Linear Iterative Stockholder
Outer loop convergence threshold : 1.0e-06
Inner loop convergence threshold : 1.0e-08
Using global ISA : False
Maximum outer iterations : 1000
lmax : 3
Solver : SC
Basis function type : GAUSS
Grid type : 1
Load GAUSS basis functions
Iteration Change Entropy
1 1.22830e-01 2.11417e-01
2 2.65479e-02 1.08527e-01
3 1.49456e-02 7.83538e-02
4 9.42839e-03 6.32378e-02
5 6.28105e-03 5.46797e-02
6 4.36137e-03 4.95400e-02
7 3.13626e-03 4.63304e-02
8 2.32400e-03 4.42673e-02
9 1.76667e-03 4.29100e-02
10 1.37210e-03 4.19998e-02
11 1.08474e-03 4.13791e-02
12 8.70173e-04 4.09497e-02
13 7.06459e-04 4.06488e-02
/Users/runner/work/horton-part/horton-part/src/horton_part/scripts/partition_density.py:82: RuntimeWarning: Sizes are used for making the angular grids, degrees are ignored!
atgrid = AtomGrid(rgrid, sizes=sizes, center=atcoords[iatom], rotate=0)
14 5.79228e-04 4.04355e-02
15 4.78820e-04 4.02828e-02
16 3.98549e-04 4.01724e-02
17 3.33684e-04 4.00920e-02
18 2.80795e-04 4.00330e-02
19 2.37335e-04 3.99894e-02
20 2.01390e-04 3.99570e-02
21 1.71490e-04 3.99327e-02
22 1.46498e-04 3.99145e-02
23 1.25513e-04 3.99007e-02
24 1.07823e-04 3.98903e-02
25 9.28565e-05 3.98823e-02
26 8.01521e-05 3.98763e-02
27 6.93374e-05 3.98716e-02
28 6.01030e-05 3.98680e-02
29 5.21975e-05 3.98653e-02
30 4.54125e-05 3.98631e-02
31 3.95753e-05 3.98615e-02
32 3.45423e-05 3.98602e-02
33 3.01945e-05 3.98592e-02
34 2.64284e-05 3.98584e-02
35 2.31618e-05 3.98578e-02
36 2.03229e-05 3.98574e-02
37 1.78516e-05 3.98570e-02
38 1.56966e-05 3.98567e-02
39 1.38148e-05 3.98565e-02
40 1.21691e-05 3.98563e-02
41 1.07281e-05 3.98562e-02
42 9.46461e-06 3.98561e-02
43 8.35637e-06 3.98560e-02
44 7.38135e-06 3.98559e-02
45 6.52413e-06 3.98558e-02
46 5.76940e-06 3.98558e-02
47 5.10437e-06 3.98558e-02
48 4.52132e-06 3.98557e-02
49 4.00077e-06 3.98557e-02
50 3.54375e-06 3.98557e-02
51 3.13992e-06 3.98557e-02
52 2.78363e-06 3.98557e-02
53 2.46740e-06 3.98557e-02
54 2.18796e-06 3.98557e-02
55 1.94125e-06 3.98557e-02
56 1.72164e-06 3.98557e-02
57 1.52537e-06 3.98557e-02
58 1.35548e-06 3.98557e-02
59 1.20377e-06 3.98557e-02
60 1.06879e-06 3.98557e-02
61 9.47255e-07 3.98557e-02
****************************************************************************************************
Basis functions
****************************************************************************************************
Exponential order Exponents coefficients Initials values
----------------- ---------------------- ---------------
Atom H
2.0 5.672000 0.042900
2.0 1.505000 0.263900
2.0 0.530800 0.479000
2.0 0.220400 0.212700
Atom O
2.0 220.100000 0.186900
2.0 65.660000 0.657600
2.0 25.980000 0.975100
2.0 1.685000 3.065700
2.0 0.686000 2.562200
2.0 0.231100 0.552800
----------------------------------------------------------------------------------------------------
****************************************************************************************************
The modified initial propars
****************************************************************************************************
Propars of No. 1 atom O:
0.18689323
0.65757616
0.97506466
3.06558888
2.56210713
0.55277996
Propars of No. 2 atom H:
0.04296450
0.26429678
0.47972018
0.21301980
Propars of No. 3 atom H:
0.04296450
0.26429678
0.47972018
0.21301980
----------------------------------------------------------------------------------------------------
****************************************************************************************************
Results
****************************************************************************************************
Atomic charges [a.u.]:
O : -0.88081213
H : 0.44056855
H : 0.44056855
----------------------------------------------------------------------------------------------------
****************************************************************************************************
Optimized pro-atom parameters
****************************************************************************************************
Propars of No. 1 atom O:
0.19790820
0.63334631
0.98351828
2.93953329
3.29297763
0.83352841
Propars of No. 2 atom H:
0.07132704
0.34987871
0.12994288
0.00828282
Propars of No. 3 atom H:
0.07132704
0.34987871
0.12994288
0.00828282
----------------------------------------------------------------------------------------------------
****************************************************************************************************
Time usage
****************************************************************************************************
Do Partitioning : 0.89 s
Update Weights : 0.42 s
Update Atomic Parameters (iter*N_atom) : 0.39 s
----------------------------------------------------------------------------------------------------
[2]:
0
[3]:
# remove cache files
for f in ["h2o_dens.npz", "h2o_part.npz"]:
if os.path.exists(f):
os.remove(f)
[ ]: