Soft matter scientist seeking hard matter expertise! I am wondering if anyone on the boards has experience with building either surfaces or bulk crystal structures in EMC using all-atom force fields, beyond the fcc, bcc, and diamond .esh examples present in the $emc_root/lib/ folder. For example: I am interested in building some structures that use \alpha-quartz as described in a paper with all of its force field parameters. This is known to crystallize in the P3_221 space group (no. 154) and I have an example LAMMPS .data file for its unit cell or a rectangular building block cell. a_quartz_unit_cell.lammps05 (5.1 KB) a_quartz_001_rectangular_cell.lammps05 (8.6 KB)
I have two questions:
One, could one build a bulk periodic crystal of this unit cell in EMC? I am imagining making a bulk cubic structure and then using the carve command to carve out a spherical nanoparticle from it.
Two, could one create a surface of this unit cell, where there is a different chemistry (decoration of O atoms with hydrogens) on the exposed surface?
The surface example included in EMC with the carbon diamond sandwiching decane has been helpful in learning some of these basics, but the united-atom representation of the surface has left me wondering if it is possible to use an all-atom chemistry where the very edge would have some different atoms on it. Additionally, I’m not entirely sure where to start in defining my own unit cell even after reading the manual. Any help would be appreciated!
Hi all -
I’ve been working on attempting to initialize a crystalline quartz unit cell using EMC scripting, following some guidance from the polyethylene.emc template and some of the other example files included in the distribution. I was able to put what I think are all of the atom types and force field parameters I will need into this file, as well as the coordinates in the unit cell.
However, I am getting stuck in trying to make this a crystal structure that can be repeated - I am not quite sure how to do this part, and am wondering if anyone who has used EMC for making crystalline structures could offer some input. As a side note, if I even try to add a script in the last several lines and use the put and lammps commands to generate a data file, I end up with an error which is either
Connection out of range for site 0.
or System out of range for site 0.
And it seems to be a coin flip which one pops up upon execution. This makes me think that I am fundamentally misunderstanding something about how EMC scripting is supposed to work (I have only really used EMC setup before this).
Following the surface and grafted nanoparticle examples, I think I will be able to accomplish the other goals I had outlined above once I get this part worked out.
In case anyone is reading this, I wanted to follow up. After spending some more time on this and carefully studying the fcc_bonded_8.emc and polyethylene.emc files included in the emc/v9.4.4/lib/ folder, as well as the build.emc for polyethylene that was present in the v9.4.2 distrubtion, I think I have (mostly) figured this out. I am attaching the two files I have generated based on these to build a bulk alpha-quartz structure based on a rectangular unit cell from the aforementioned paper. alpha_quartz_r.emc (8.7 KB) build.emc (2.2 KB)
alpha_quartz_r.emc is the file which describes the structure of the unit cell and minimal force field parameters for the bulk. build.emc is the file which constructs a ~roughly cubic crystal of the user’s choice and evaluates the initial forces. If you execute build.emc as written, it will build a nearly 5x5x5nm cube of silica in LAMMPS data file format. Visualized with OVITO:
As written the build script cannot yet handle dealing with the surface moieties, so my next task is to work on that. But I figured that, since there are not as many posts on the forums about how to use the crystal structure functionalities of EMC, I would post this as an example that will hopefully help somebody else in the future.
