Difference between revisions of "Design of crystolecules"
m (added link to Mechanosynthesis page) |
(added notes about equilibration method - created molecular dynamics chapter) |
||
| Line 9: | Line 9: | ||
Too much oxygen must not be brought in direct bonding contact with carbon atoms since this may practically represent solid CO<sub>2</sub> which will likely behave like an explosive. The same goes for other combinations that are known to be highly energetic from normal cemistry. | Too much oxygen must not be brought in direct bonding contact with carbon atoms since this may practically represent solid CO<sub>2</sub> which will likely behave like an explosive. The same goes for other combinations that are known to be highly energetic from normal cemistry. | ||
Some examples: room temperature solid nitrogen (in sp3 hybridisation), oxygen chains, ... | Some examples: room temperature solid nitrogen (in sp3 hybridisation), oxygen chains, ... | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
=== avoid too high interface pressure in sleeve bearings === | === avoid too high interface pressure in sleeve bearings === | ||
| Line 24: | Line 18: | ||
Concave edges passivated with hydrogen sometimes causes the hydrogen atoms to massively overlap. | Concave edges passivated with hydrogen sometimes causes the hydrogen atoms to massively overlap. | ||
Sometimes two hydrogens can be replaced by a oxygen bridge but this introduces tension that may detrimentally deform the crystolecule. | Sometimes two hydrogens can be replaced by a oxygen bridge but this introduces tension that may detrimentally deform the crystolecule. | ||
| − | Alternating with oxygen with its bigger cousin | + | Alternating with oxygen with its bigger cousin sulfur or nitrogen with phosphor might help in some cases. |
Since passivation atoms add thickness it can be tricky to create parts complementary in shape. | Since passivation atoms add thickness it can be tricky to create parts complementary in shape. | ||
['''todo:''' collect some tricks here how this can be made easier] | ['''todo:''' collect some tricks here how this can be made easier] | ||
| + | |||
| + | == Regarding molecular dynamics == | ||
| + | |||
| + | === avoid elements left of the carbon group (at least for now) === | ||
| + | |||
| + | Electron deficiency bonds are misrepresented nanoengineer-1's current force field models. | ||
| + | A nitrogen atom adjacent to a boron atom embedded in a diamond crystal shouldn't strongly repel each other but instead behave almost like carbon atoms since the boron has the space for the nitrogens excess electron. Since aluminium is to an electron deficient element it is likely to misbehave the same way as boron does in the nanoengineer-1 model. | ||
| + | A safe way to go is to not use them yet in crystolecule designs. | ||
| + | |||
| + | === Equilibration method === | ||
| + | |||
| + | Nanoenginer-1 {{todo|version?|add latest nanoengineer-1 version 2015}} seems to use a rather naive force field equilibration method of just iteratively equilibrating all the atoms one after another and applying the changes all at once (not sure if this is the case - {{todo|check code|look into nanoengineer-1 code and check out the used equilibration method - is there documentation beside the code?}}) | ||
| + | that does not scale well. | ||
| + | A self adapting {{todo|add implementation ideas}} 6D space Fourier space deformation method might be implementable to speed up equilibration massively. | ||
| + | {{todo|IIRC there where news of a new faster equilibration method - find it and link it here}} | ||
== Related == | == Related == | ||
At any time the accessible crystolecule structures are given by the available capabilities of [[Mechanosynthesis]]. | At any time the accessible crystolecule structures are given by the available capabilities of [[Mechanosynthesis]]. | ||
| + | * molecular dynamics: {{WikipediaLink|https://en.wikipedia.org/wiki/Molecular_dynamics}} | ||
Revision as of 07:27, 2 October 2015
This page is about issues with the design of crystolecules / DMEs.
For a definition of what they are see here: "What are crystolecules DMEs?"
Some things to take care of
avoid quartz like solid CO2 or the like
Too much oxygen must not be brought in direct bonding contact with carbon atoms since this may practically represent solid CO2 which will likely behave like an explosive. The same goes for other combinations that are known to be highly energetic from normal cemistry. Some examples: room temperature solid nitrogen (in sp3 hybridisation), oxygen chains, ...
avoid too high interface pressure in sleeve bearings
If the fit gets too tight the atom "teeth" may jump without energy recuperation and it will work as friction unit instead.
check for too strained spots in auto-generated passivation layers
Concave edges passivated with hydrogen sometimes causes the hydrogen atoms to massively overlap. Sometimes two hydrogens can be replaced by a oxygen bridge but this introduces tension that may detrimentally deform the crystolecule. Alternating with oxygen with its bigger cousin sulfur or nitrogen with phosphor might help in some cases.
Since passivation atoms add thickness it can be tricky to create parts complementary in shape. [todo: collect some tricks here how this can be made easier]
Regarding molecular dynamics
avoid elements left of the carbon group (at least for now)
Electron deficiency bonds are misrepresented nanoengineer-1's current force field models. A nitrogen atom adjacent to a boron atom embedded in a diamond crystal shouldn't strongly repel each other but instead behave almost like carbon atoms since the boron has the space for the nitrogens excess electron. Since aluminium is to an electron deficient element it is likely to misbehave the same way as boron does in the nanoengineer-1 model. A safe way to go is to not use them yet in crystolecule designs.
Equilibration method
Nanoenginer-1 (TODO: version?) seems to use a rather naive force field equilibration method of just iteratively equilibrating all the atoms one after another and applying the changes all at once (not sure if this is the case - (TODO: check code)) that does not scale well. A self adapting (TODO: add implementation ideas) 6D space Fourier space deformation method might be implementable to speed up equilibration massively. (TODO: IIRC there where news of a new faster equilibration method - find it and link it here)
Related
At any time the accessible crystolecule structures are given by the available capabilities of Mechanosynthesis.
- molecular dynamics: (leave to Wikipedia - please come back again)
