To read all data for an AMON, say ni1/AZ7_00001.json, do this
import json
with open('ni1/AZ7_00001.json') as fid:
dt = json.load(fid)To recover the cartesian coordinates of atoms (coords)
coords = dt['coords'].reshape( (-1,3) )Similarly, to get the reduced normal coordinates (rnc)
rn = dt['rn']
na = dt['na'] # total number of atoms
rnc = rn.reshape( (-1,na,3) )Bond order matrix is also available, and can be obtained through
bo = dt['bo'].reshape((na,na))| Key | Property | Note |
|---|---|---|
| id | molecular identity | e.g., AZ7_00001 |
| zs | a list of nuclear charges | |
| symbols | atomic symbols | |
| coords | atomic coordinates | in Angstrom (Ang) |
| smi | canonical SMILES string (or can) |
OEChem format |
| na | number of total atoms | |
| ni | number of heavy atoms | |
| ne/ne_up/ne_down | number of total, spin up & down electrons | |
| r2 | electronic spatial extent | in Bohr^2 |
| et | B3LYP/cc-pVTZ total energy | in Hartree |
| e_ne | nuclei-electron interaction energy | in Hartree |
| e_k | kinetic energy | in Hartree |
| e_nn | nuclear repulsion energy | in Hartree |
| e_disp | D3 dispersion energy (xc=b3lyp) |
in Hartree |
| mu | dipole moment | in Debye |
| mu_{a} | dipole components, a={x,y,z} |
in Debye |
| mu_{ab} | quadrupole moment components, b={x,y,z} |
in Debye-Ang |
| mu_{abc} | Octapole moment components, c={x,y,z} |
in Debye-Ang^2 |
| mu_{abcd} | Hexadecapole moment components, d={x,y,z} |
in Debye-Ang^3 |
| qa | Mulliken atomic charge | |
| homo | Highest occupied molecular orbital (MO) energy | in Hartree |
| lumo | Lowest unoccupied MO energy | in Hartree |
| gap | gap between HOMO and LUMO | in Hartree |
| eigs | MO energies | in Hartree |
| omega | harmonic frequencies | in cm^{-1} |
| omega0 | highest harmonic frequency | in cm^{-1} |
| ma | atomic masses | in Dalton |
| fc | force constants | in mDyne/Ang |
| mr | reduce masses | Dalton |
| ir | IR intensity | in km/mol |
| rn | reduced normal coordinates | within [0,1] |
| A,B,C | rotational constants | in GHz |
| alpha | isotropic polarizability | in Bohr^3 |
| alpha_{ab} | polarizability components | in Bohr^3 |
| P | pressure | in atm |
| T | temperature | in Kelvin (K) |
| zpe | zero point energy | in Hartree |
| U0 | internal energy at 0 K | in Hartree |
| U | internal energy at 298.15 K | in Hartree |
| H | enthalpy at 298.15 K | in Hartree |
| G | free energy at 298.15 K | in Hartree |
| S | entropy at 298.15 K | in Hartree/K |
| Cv | heat capacity at 298.15 K | in Hartree/K |