Coordination number

Functions for calculating the coordination numbers.

Example

>>> import torch
>>> import tad_mctc as mctc
>>>
>>> # S22 system 4: formamide dimer
>>> numbers = mctc.batch.pack((
...     mctc.utils.to_number("C C N N H H H H H H O O".split()),
...     mctc.utils.to_number("C O N H H H".split()),
... ))
>>>
>>> # coordinates in Bohr
>>> positions = mctc.batch.pack((
...     torch.tensor([
...         [-3.81469488143921, +0.09993441402912, 0.00000000000000],
...         [+3.81469488143921, -0.09993441402912, 0.00000000000000],
...         [-2.66030049324036, -2.15898251533508, 0.00000000000000],
...         [+2.66030049324036, +2.15898251533508, 0.00000000000000],
...         [-0.73178529739380, -2.28237795829773, 0.00000000000000],
...         [-5.89039325714111, -0.02589114569128, 0.00000000000000],
...         [-3.71254944801331, -3.73605775833130, 0.00000000000000],
...         [+3.71254944801331, +3.73605775833130, 0.00000000000000],
...         [+0.73178529739380, +2.28237795829773, 0.00000000000000],
...         [+5.89039325714111, +0.02589114569128, 0.00000000000000],
...         [-2.74426102638245, +2.16115570068359, 0.00000000000000],
...         [+2.74426102638245, -2.16115570068359, 0.00000000000000],
...     ]),
...     torch.tensor([
...         [-0.55569743203406, +1.09030425468557, 0.00000000000000],
...         [+0.51473634678469, +3.15152550263611, 0.00000000000000],
...         [+0.59869690244446, -1.16861263789477, 0.00000000000000],
...         [-0.45355203669134, -2.74568780438064, 0.00000000000000],
...         [+2.52721209544999, -1.29200800956867, 0.00000000000000],
...         [-2.63139587595376, +0.96447869452240, 0.00000000000000],
...     ]),
... ))
>>>
>>> torch.set_printoptions(precision=7)
>>> print(mctc.cn_d4(numbers, positions))
tensor([[2.6886456, 2.6886456, 2.6314170, 2.6314168, 0.8594539, 0.9231414,
         0.8605307, 0.8605307, 0.8594539, 0.9231414, 0.8568342, 0.8568342],
        [2.6886456, 0.8568335, 2.6314168, 0.8605307, 0.8594532, 0.9231415,
         0.0000000, 0.0000000, 0.0000000, 0.0000000, 0.0000000, 0.0000000]])

• Coordination number: Common helpers
• coordination_number()
• cut_coordination_number()
• Coordination number: Counting functions
• derf_count()
• dexp_count()
• dgfn2_count()
• erf_count()
• exp_count()
• gfn2_count()
• Coordination number: DFT-D3
• cn_d3()
• cn_d3_gradient()
• Coordination number: DFT-D4
• cn_d4()
• Coordination number: Defaults
• CUTOFF_D3
• CUTOFF_D4
• CUTOFF_EEQ
• CUTOFF_EEQBC
• CUTOFF_EEQ_MAX
• CUTOFF_GFN2
• D4_K4
• D4_K5
• D4_K6
• KA
• KB
• KCN_D3
• KCN_D4
• KCN_EEQ
• KCN_EEQ_EN
• R_SHIFT
• Coordination number: EEQ
• cn_eeq()
• cn_eeq_en()
• cut_coordination_number()
• Coordination number: GFN2-xTB
• cn_gfn2()