Running calculations
After creating a System, and having initialized an engine or imported a wrapper function, we can actually start running calculations.
Generic calculations (engines)
Generic calculations are implemented as class methods in the various engines. The available options, the class method name, and the engines for which they have been implemented are:
Calculation type |
method name |
Engines implemented |
|---|---|---|
Single point energy |
|
xTB, Orca, DFTB+ |
Geometry optimisation + Frequency analysis |
|
xTB, Orca, DFTB+ |
Frequency analysis |
|
xTB, Orca |
Numerical frequency analysis |
|
Orca |
Relaxed surface scan |
|
Orca |
Transition state optimization |
|
Orca |
Transition state search via relaxed surface scan |
|
Orca |
Climbing Image Nudged Elastic Band method |
|
Orca |
Transition state search via Nudged Elastic Band method |
|
Orca |
NVT Molecular Dynamics |
|
DFTB+ |
Simulated annealing |
|
DFTB+ |
The only mandatory parameter to be passed is the System on which to run the calculation. To run the calculation, simply call the function. The output of a calculation is (usually) a System object which can be assigned to a new variable:
from spycci.systems import System
from spycci.engines.xtb import XtbInput
mol = System("water.xyz")
xtb = XtbInput()
mol_opt = xtb.opt(mol)
print(" ~~~ mol: ~~~")
print(mol)
print(" ~~~ mol_opt: ~~~")
print(mol_opt)
~~~ mol: ~~~
=========================================================
SYSTEM: water
=========================================================
Number of atoms: 3
Charge: 0
Spin multiplicity: 1
********************** GEOMETRY *************************
Total system mass: 18.0153 amu
----------------------------------------------
index atom x (Å) y (Å) z (Å)
----------------------------------------------
0 O 0.03595 2.78898 0.00000
1 H 1.00595 2.78898 0.00000
2 H -0.28738 2.19789 0.69783
----------------------------------------------
********************** PROPERTIES *************************
Geometry level of theory: None
Electronic level of theory: None
Vibronic level of theory: None
Electronic energy: None Eh
Vibronic energy: None Eh
Helmholtz free energy: None Eh
Gibbs free energy: None Eh
pKa: None
~~~ mol_opt: ~~~
=========================================================
SYSTEM: water
=========================================================
Number of atoms: 3
Charge: 0
Spin multiplicity: 1
********************** GEOMETRY *************************
Total system mass: 18.0153 amu
----------------------------------------------
index atom x (Å) y (Å) z (Å)
----------------------------------------------
0 O 0.00000 -0.37937 0.00000
1 H 0.77221 0.18968 -0.00000
2 H -0.77221 0.18969 0.00000
----------------------------------------------
********************** PROPERTIES *************************
Geometry level of theory: XtbInput || method: gfn2 | solvent: None
Electronic level of theory: XtbInput || method: gfn2 | solvent: None
Vibronic level of theory: XtbInput || method: gfn2 | solvent: None
Electronic energy: -5.070544446692 Eh
Vibronic energy: 0.002508973529 Eh
Helmholtz free energy: None Eh
Gibbs free energy: -5.068035473164 Eh
pKa: None
MULLIKEN ANALYSIS
----------------------------------------------
index atom charge spin
----------------------------------------------
0 O -0.56500 0.00000
1 H 0.28200 0.00000
2 H 0.28200 0.00000
Alternatively, you can directly update the input System with the inplace flag:
from spycci.systems import System
from spycci.engines.xtb import XtbInput
mol = System("water.xyz")
xtb = XtbInput()
print(" ~~~ mol before opt: ~~~ ")
print(mol)
xtb.opt(mol, inplace=True)
print(" ~~~ mol after opt: ~~~ ")
print(mol)
~~~ mol before opt: ~~~
=========================================================
SYSTEM: water
=========================================================
Number of atoms: 3
Charge: 0
Spin multiplicity: 1
********************** GEOMETRY *************************
Total system mass: 18.0153 amu
----------------------------------------------
index atom x (Å) y (Å) z (Å)
----------------------------------------------
0 O 0.03595 2.78898 0.00000
1 H 1.00595 2.78898 0.00000
2 H -0.28738 2.19789 0.69783
----------------------------------------------
********************** PROPERTIES *************************
Geometry level of theory: None
Electronic level of theory: None
Vibronic level of theory: None
Electronic energy: None Eh
Vibronic energy: None Eh
Helmholtz free energy: None Eh
Gibbs free energy: None Eh
pKa: None
~~~ mol after opt: ~~~
=========================================================
SYSTEM: water
=========================================================
Number of atoms: 3
Charge: 0
Spin multiplicity: 1
********************** GEOMETRY *************************
Total system mass: 18.0153 amu
----------------------------------------------
index atom x (Å) y (Å) z (Å)
----------------------------------------------
0 O 0.00000 -0.37937 0.00000
1 H 0.77221 0.18968 -0.00000
2 H -0.77221 0.18969 0.00000
----------------------------------------------
********************** PROPERTIES *************************
Geometry level of theory: XtbInput || method: gfn2 | solvent: None
Electronic level of theory: XtbInput || method: gfn2 | solvent: None
Vibronic level of theory: XtbInput || method: gfn2 | solvent: None
Electronic energy: -5.070544446692 Eh
Vibronic energy: 0.002508973529 Eh
Helmholtz free energy: None Eh
Gibbs free energy: -5.068035473164 Eh
pKa: None
MULLIKEN ANALYSIS
----------------------------------------------
index atom charge spin
----------------------------------------------
0 O -0.56500 0.00000
1 H 0.28200 0.00000
2 H 0.28200 0.00000
Special calculations (wrappers)
Some calculations are instead implemented as functions within the corresponding wrapper submodule, and work a little differently from the previous methods in the sense that they do not compute System properties but they usually generate other System objects (or collections thereof). While Engines are general-purpose tools which in theory allow the user to carry out similar calculations with different programs (e.g., geometry optimization via the opt function in OrcaInput or XtbInput are carried out in the same way), wrappers are much more program-specific and each wrapper allows to carry out different operations.
CREST
Calculation type |
method name |
|---|---|
Tautomer search |
|
Conformer search |
|
Deprotomer search |
|
Protomer search |
|
Quantum Cluster Growth |
|
Quantum Cluster Growth + ensemble evaluation |
|
These can be imported directly from the corresponding submodule. For more details on each specific function, please refer to the corresponding API page.
The CREST tautomer, conformer, deprotonation, and protonation routines all require a System object as input, and return a list of tautomer, conformers, deprotomers, and protomers, respectively, ordered by relative energy:
from spycci.systems import System
from spycci.wrappers.crest import conformer_search
mol = System("mymol.xyz")
conformers = conformer_search(mol)
lowest_energy_conformer = conformers[0]
The QCG routines are used to create an explicitly solvated cluster, surrounding a solute with a certain number of solvent molecules. By default, the program keeps adding solvent molecules until energy convergence is reached with respect to the addition of other molecules. For more details on how to customise this kind of calculation, please refer to the API page.
from spycci.systems import System
from spycci.wrappers.crest import qcg_grow
solute = System("solute.xyz")
solvent = System("solvent.xyz")
cluster = qcg_grow(solute, solvent)
Packmol
The Packmol wrapper allows for the construction of explicitly solvated systems, as a fast alternative to the QCG routines, useful for setting up MD calculations. The currently available functions are:
Calculation type |
method name |
|---|---|
Generation of explicit solvation cube |
|
Like the QCG routines, you need to provide a solute and a solvent System. The packmol_cube routine however allows you a finer degree of control, as you also need to provide two of the following three parameters:
nsolv: number of solvent molecules to put in the cubetarget_dens: target density of the solvated box, in g/Lcube_side: length of the simulation box, in Å
Given two of these parameters, the third will be calculated accordingly. For example, the following code generates a cubic solvation box with 50 solvent molecules and a target density of 997 g/L:
from spycci.systems import System
from spycci.wrappers.packmol import packmol_cube
solute = System("urea.xyz")
solvent = System("water.xyz")
solvated_cube = packmol_cube(solute, solvent, nsolv=50, target_dens=997)
print(solvated_cube)
=========================================================
SYSTEM: urea_50waters
=========================================================
Number of atoms: 158
Charge: 0
Spin multiplicity: 1
Periodic system with box size: 11.6968 Å
********************** GEOMETRY *************************
Total system mass: 960.8193 amu
----------------------------------------------
index atom x (Å) y (Å) z (Å)
----------------------------------------------
0 C 5.67500 5.59400 6.27900
1 N 5.71300 4.95300 5.03000
2 H 5.90100 3.95900 5.06700
3 H 6.17200 5.43600 4.26800
4 N 5.71500 6.99700 6.23800
5 H 6.16900 7.43100 5.44400
6 H 5.90800 7.44500 7.12600
7 O 5.53500 4.97100 7.33300
8 O 2.47400 9.08200 10.90000
9 H 3.23500 9.68300 10.87900
10 H 1.81500 9.37200 10.25000
11 O 10.78300 7.99900 10.76900
12 H 11.70800 7.70900 10.73400
13 H 10.49500 8.04700 11.69400
14 O 2.17100 11.77100 11.44600
15 H 1.70000 10.96300 11.70400
16 H 3.10000 11.70300 11.71400
17 O 9.93400 5.53200 5.55800
18 H 9.91300 6.50100 5.58600
19 H 10.36900 5.19500 6.35800
20 O 10.99800 5.21200 11.69500
21 H 10.22100 5.79300 11.68000
22 H 10.72600 4.30400 11.49000
23 O 10.85700 5.88700 1.00600
24 H 10.07800 5.55300 1.47800
25 H 11.63600 5.36900 1.26200
26 O 11.61800 1.74200 1.63700
27 H 11.69700 2.34600 2.39200
28 H 10.98200 2.10200 1.00000
29 O 5.06300 3.49700 8.90800
30 H 4.13400 3.77700 8.88100
31 H 5.11000 2.52900 8.88300
32 O 8.61600 10.41700 11.62500
33 H 9.27500 9.77700 11.31400
34 H 8.99600 11.30900 11.60200
35 O 1.74500 1.12200 9.39300
36 H 2.55100 1.00100 8.86700
37 H 1.06200 1.54000 8.84600
38 O 3.34600 5.04200 6.98500
39 H 2.56800 5.27900 7.51400
40 H 3.47600 5.70300 6.28800
41 O 1.31800 9.69100 3.75600
42 H 2.19300 9.66500 4.17300
43 H 1.34900 10.26600 2.97500
44 O 8.52200 5.14800 3.92300
45 H 8.27600 6.04300 4.20500
46 H 8.51700 5.10200 2.95400
47 O 1.70200 7.82300 7.62700
48 H 1.12000 7.07800 7.41100
49 H 2.47900 7.80500 7.04700
50 O 5.67500 10.96200 10.65500
51 H 5.02200 11.67900 10.65100
52 H 6.09300 10.91100 11.52900
53 O 10.90200 11.12500 7.60400
54 H 10.12200 11.69900 7.55800
55 H 11.69800 11.66900 7.71000
56 O 4.97500 4.77100 11.60400
57 H 4.02800 4.66900 11.42300
58 H 5.40300 3.90100 11.58200
59 O 4.15300 8.12600 8.44100
60 H 4.20000 7.15900 8.39500
61 H 3.53700 8.38700 9.14300
62 O 8.71900 2.92700 5.07200
63 H 9.65300 3.18900 5.11100
64 H 8.62300 2.02300 5.41100
65 O 11.57200 9.44900 5.69900
66 H 11.67400 8.60700 5.22800
67 H 11.65000 9.29600 6.65400
68 O 8.52400 4.57400 7.27900
69 H 8.31200 5.49400 7.05600
70 H 7.89500 3.98200 6.83800
71 O 11.62100 10.71500 1.88400
72 H 11.54200 9.91200 1.34500
73 H 10.80900 11.24000 1.80300
74 O 5.53900 10.74300 6.88500
75 H 5.41800 11.69500 7.02100
76 H 4.70200 10.34900 6.59200
77 O 1.62300 4.47100 9.31600
78 H 2.32600 4.37300 9.97700
79 H 1.00700 3.72500 9.38500
80 O 10.96000 11.13300 4.49800
81 H 11.69600 11.68400 4.80900
82 H 10.29800 11.69400 4.06400
83 O 4.75300 9.95800 3.51200
84 H 4.60500 9.01000 3.37400
85 H 4.47600 10.20200 4.40900
86 O 4.14300 7.75400 11.32000
87 H 4.73200 8.38100 11.76900
88 H 4.35300 6.85200 11.60700
89 O 1.79700 11.68700 5.82700
90 H 0.99500 11.28000 5.46300
91 H 2.54500 11.51200 5.23500
92 O 8.55900 1.56200 11.67000
93 H 8.87900 2.43900 11.40700
94 H 8.38300 1.03100 10.87800
95 O 8.48500 7.43200 8.05400
96 H 8.10400 8.23500 7.66600
97 H 9.03000 7.67000 8.82000
98 O 4.12100 3.00400 4.22900
99 H 4.05300 2.05000 4.07300
100 H 3.44200 3.27700 4.86600
101 O 2.42700 2.30300 6.61300
102 H 2.99500 2.53900 7.36300
103 H 2.11600 1.39000 6.71900
104 O 5.87600 7.49700 9.92000
105 H 6.32400 7.28500 10.75400
106 H 5.77900 8.45900 9.84100
107 O 10.75800 1.15400 10.42100
108 H 10.70300 1.23900 11.38600
109 H 11.68000 1.00000 10.16200
110 O 3.21800 2.66200 11.00900
111 H 3.15800 1.69400 10.97800
112 H 2.62000 3.00000 11.69400
113 O 11.00700 7.30500 7.30100
114 H 11.09200 7.59800 8.22200
115 H 11.75400 6.72900 7.07500
116 O 7.99000 10.93200 8.70000
117 H 7.10100 10.56800 8.83200
118 H 8.52100 10.30800 8.18200
119 O 11.42300 1.01000 7.65600
120 H 11.68500 1.43200 6.82300
121 H 10.63400 1.45100 8.00800
122 O 1.94600 7.16000 9.92400
123 H 1.03900 7.39600 9.67300
124 H 2.31400 6.54900 9.26800
125 O 11.13200 4.43200 4.08400
126 H 11.69600 3.64500 4.14600
127 H 11.68700 5.21900 3.97000
128 O 8.93500 8.62000 3.76600
129 H 8.38500 9.24600 4.26300
130 H 9.87100 8.84800 3.88700
131 O 11.60900 3.25900 8.27200
132 H 11.67900 4.04600 8.83400
133 H 11.35400 3.52500 7.37400
134 O 10.78200 11.05900 10.35900
135 H 11.71300 11.31800 10.44700
136 H 10.34100 11.65100 9.73000
137 O 1.98800 7.38900 2.56100
138 H 2.69800 8.04500 2.47400
139 H 2.16900 6.81800 3.32400
140 O 6.42500 1.80800 10.47800
141 H 6.39500 1.81500 11.44800
142 H 5.99100 1.00700 10.14700
143 O 6.69100 5.59300 9.40600
144 H 6.85800 6.05700 8.57100
145 H 7.48300 5.09600 9.66400
146 O 9.31200 1.00000 2.02900
147 H 8.87300 1.80800 1.71900
148 H 9.84100 1.20100 2.81600
149 O 1.36500 3.68100 4.28200
150 H 1.00300 3.16500 5.01900
151 H 1.29200 3.16800 3.46200
152 O 10.16100 5.51700 9.35700
153 H 9.98800 5.75600 8.43300
154 H 10.98000 5.94600 9.65300
155 O 1.74500 11.70100 9.19700
156 H 2.36700 11.00300 8.94000
157 H 0.99600 11.30700 9.67100
----------------------------------------------
********************** PROPERTIES *************************
Geometry level of theory: None
Electronic level of theory: None
Vibronic level of theory: None
Electronic energy: None Eh
Vibronic energy: None Eh
Helmholtz free energy: None Eh
Gibbs free energy: None Eh
pKa: None