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49 lines
2.8 KiB
49 lines
2.8 KiB
4 years ago
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# Getting Started
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The CACmb tool separates commands into two general groups, modes and options.
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Modes are the main commands which conduct primary operations, these are listed below:
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* [Mode Convert](Modes/convert.md)
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* [Mode Create](Modes/create.md)
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* [Mode Merge](Modes/merge.md)
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To start a cacmb run, it is required to run one of the available modes and only one mode can be run at a time.
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Additionally one can use options in order to adjust the model during any of the mode runs and unlimited number of options may be used.
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While single line commands may be used satisfactorily to build a model, in order to build more complex models it is required to run multiple commands.
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Currently CACmb only supports rhombehedral FCC finite elements with faces aligned to {111} slip planes.
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This finite element is the primitive unit cell for the FCC crystal and is shown below:
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## Simple Example 1
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For example, to build a model with an atomistic region bound by a coarse-grained region the following commands should be run:
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```
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cacmb --create Cu fcc 3.615 15 duplicate 4 2 1 orient [112] [1-10] [11-1] Cu_cg.mb -ow
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cacmb --create Cu fcc 3.615 2 duplicate 30 15 2 orient [112] [1-10] [11-1] Cu_at.mb -ow
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cacmb --merge z 3 Cu_cg.mb Cu_at.mb Cu_cg.mb model.xyz -ow
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```
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When visualizing the model.xyz file using ovito we see our desired model (where the red atoms represent the element nodes and blue atoms are atomistic regions):
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**Important Note: In order to fully utilize the cacmb capabilites use the .mb format when running multiple model build steps**
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A description of each build step is below:
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1. Build a coarse grained model with elements that have 15 atoms per edge. Orientation is set to `[112] [1-10] [11-1]`. We save it to `Cu_cg.mb` and pass `-ow` which is the flag to overwrite existing files with that name.
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2. Build an atomistic model with the same dimensionsin the x and y directions as the coarse grained model. *A general way to match dimensions is by setting the duplicate value of the atoms to `esize*duplicate/2`. So for the x dimension we do `15*4/2` which is 30 and for the y dimension `15*2/2` which is 15.
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3. Merge the models by stacking the coarse-grained and atomistic models. We start the stacking sequence from the bottom so the first region is the `Cu_cg.mb`, followed by the `Cu_at.mb` model in the middle, followed by another `Cu_cg.mb` region. We output it to model.xyz which renders the atoms and nodes of the model for visualization.
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This whole process can be easily run as a shell script as long as cacmb is on your path.
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```sh
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#!/bin/sh
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cacmb --create Cu fcc 3.615 15 duplicate 4 2 1 orient [112] [1-10] [11-1] Cu_cg.mb -ow
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cacmb --create Cu fcc 3.615 2 duplicate 30 15 2 orient [112] [1-10] [11-1] Cu_at.mb -ow
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cacmb --merge z 3 Cu_cg.mb Cu_at.mb Cu_cg.mb model.xyz -ow
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```
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