INitial commit of CAC code

docs/Commands/boundary.md

@@ -0,0 +1,22 @@
+# boundary
+
+```sh
+boundary xyz
+```
+
+## Inputs
+
+`xyz` - string describing the boundary conditions in which `x`, `y`, and `z` can have values of either `p` for periodic or `s` for shrink-wrapped.
+
+## Examples
+
+```sh
+boundary ppp
+boundary sps
+```
+
+## Description 
+
+Boundary sets the boundary conditions of the model being either periodic or shrink-wrapped. 
+Because boundary data is included within the restart file format, this command is not strictly required.
+If included this command will override the boundary conditions defined within the data file.

docs/Commands/dump.md

@@ -0,0 +1,23 @@
+# dump
+
+```sh
+dump id group style n fname
+```
+
+## Inputs
+
+`id` - id for dump command
+
+`group` - group to be dumped
+
+`style` - dump style, currently only accepts `out`
+
+`n` - dump every `n` steps. If `n` is `0` then the dump file is only written at the beginning and end of a minimize or run.
+
+`fname` - file name to write to. Will strip extensions and replace with the timestep and .out. 
+
+## Example
+
+```
+
+```

docs/Commands/group.md

@@ -0,0 +1,52 @@
+# group
+
+```sh
+group id selection shape ...
+```
+
+## Inputs 
+
+`id` - assigned id for the group.
+
+`selection` - either `atoms`, `elements`, or `all`. 
+
+`shape` - either `block`, `sphere`, or `type`.
+
+**Additional arguments depend on the group shape passed and are listed below:** 
+
+```sh
+group id selection block xlo xhi ylo yhi zlo zhi
+```
+where `{x,y,z}lo` are the lower bounds along `x,y,z` and `{x,y,z}hi` are the upper bounds along `x,y,z`.
+
+```sh
+group id selection sphere x y z r
+```
+where `x y z` define the centroid of the sphere and `r` defines the radius of the sphere.
+
+```sh
+group id selection type n
+```
+where `n` is a number which selects the `n`th atom type.
+
+## Examples
+```sh
+group tophalf all block -inf inf -inf inf inf*0.5 inf
+group precip atoms sphere 100 78 78 10
+group Ni atoms type 2
+```
+
+## Description
+
+The group option is used in conjunction with other commands which require a group input. 
+**A default `all` group is defined which contains all atoms and elements.**
+A subsection of all atoms or elements can be selected using the group command.
+`id` is used to refer to the group in other commands.
+`selection` determines which element types are selected within the group. 
+A group can be defined containing only `atoms`, `elements`, or `both`. 
+If element types are within the bounds of the group but are not specified with `selection` they are not defined as members of the group.
+
+All positions for the group command can be specified using position specifications described [here](../Misc/position.md).
+
+
+

docs/Commands/min_style.md

@@ -0,0 +1,25 @@
+# min_style
+
+```sh
+min_style minimizer
+```
+
+## Inputs
+
+`minimizer` - Either `fire` or `cg`.
+
+## Examples
+
+```sh
+min_style fire
+min_style cg
+```
+
+## Description
+
+This code sets the minimizer for future `minimize` commands.
+Currently CAC has implemented both conjugate gradient minimization, `cg`, and the fast inertial relaxation engine [1], `fire`. 
+
+## References
+
+[1] Guénolé, Julien et al. "Assessment and optimization of the fast inertial relaxation engine (fire) for energy minimization in atomistic simulations and its implementation in lammps" Computational Materials Science (2020)

docs/Commands/minimize.md

@@ -0,0 +1,31 @@
+# minimize 
+
+```sh
+minimize ftol etol max_iter
+```
+
+## Inputs
+
+`ftol` - force tolerance
+
+`etol` - energy tolerance
+
+`max_iter` - maximum number of iterations to calculate before exiting.
+
+## Examples
+
+```sh
+minimize 10d-10 10d-10 10000
+```
+
+## Description
+
+The minimize command is used to perform energy minimization on the CAC model. 
+The minimization method is chosen by the [min_style](./min_style.md) command. 
+Minimization is considered to be complete under the following conditions:
+
+1. \( \frac{(E_i - E_{i-1})}{E_i} < etol \), where \( i \) is the current iteration.
+2. No atom has a force component greater than `ftol`
+3. The number of iterations is greater than `max_iter`
+
+

docs/Commands/neighbor.md

@@ -0,0 +1,21 @@
+# neighbor
+
+```sh
+neighbor skin
+```
+
+## Inputs
+
+`skin` - The skin distance in angstrom added to the cutoff radius for construction of verlet lists.
+
+## Examples
+
+```sh
+neighbor 1.5
+```
+
+## Description
+
+This command specifies the additional skin distance which is used when constructing the verlet neighbor lists.
+When an atom has moved greater than the half of the skin distance, then the neighbor lists are reconstructed.
+

docs/Commands/potential.md

@@ -0,0 +1,29 @@
+# potential
+
+```sh
+potential pot_type file elements ...
+```
+
+## Inputs
+
+`pot_type` - Potential type, currently accepts either "eam" for setfl formatted eam/alloy potentials, or "fs" for eam finnis sinclair style potentials.
+`file` - Potential file, currently only accepts .eam.alloy style potential files
+
+`elements ...` - List of atomic elements mapping the atom type number to atomic species. Can be excluded resulting in mapping atomic types based on ordering within the potential file.
+
+## Examples
+
+```sh
+potential CuNi.eam.alloy Ni Cu
+potential Cu_mishin1.eam.alloy 
+```
+
+## Description
+
+This command specifies the potential information.
+**Currently only .eam.alloy style potentials are accepted.** 
+The `elements ...` portion of the code is used to map the numeric atom type to the potential file.
+For the first example, `Ni Cu` maps atoms with type 1 to Ni and atoms with type 2 to Cu.
+Inputting `Cu Ni` would instead reverse the order and map atoms with type 1 to Cu and vice-versa.
+This can be excluded, as in the second example.
+If the CuNi.eam.alloy file is ordered with Ni first and Cu second, then `potential CuNi.eam.alloy Ni Cu` is equivalent to `potential CuNi.eam.alloy`.

docs/Commands/read_data.md

@@ -0,0 +1,24 @@
+# read_data
+
+```
+read_data filename
+```
+
+## Inputs 
+
+`filename` - Input file to be read in restart format.
+
+## Examples 
+
+```sh
+read_data model_1.restart
+```
+
+## Description
+
+Model building capabilities are not included into the CAC simulation tool. 
+Instead the [CAC model builder (CACmb)](https://gitlab.com/aselimov/cacmb) must be used to create models in the .restart format.
+The read_data command reads in one .restart formatted data file and distributes the model across all processors.
+
+
+

docs/Commands/run.md

@@ -0,0 +1,10 @@
+# run 
+```sh
+run ensemble timesteps
+```
+
+## Inputs
+
+`ensemble` - currently either `nve` or `qd`.
+
+`timesteps` - The number of timesteps to run of dynamics

docs/Commands/setforce.md

@@ -0,0 +1,9 @@
+# setforce
+
+```
+setforce group_id fx fy fz
+```
+
+## Inputs
+
+`group_id` - id for student

docs/Commands/temp.md

@@ -0,0 +1,26 @@
+# temp
+
+```sh
+temp command group_id args
+```
+
+## Inputs
+
+`command`  - Command for temp option, either `create` or `control`.
+
+`group_id` - Group id to apply temperature control to 
+
+**Additional arguments depend on the command passed and are listed below** 
+
+```sh
+temp create group_id T_target
+```
+
+- `T_target` - Target temperature
+
+```sh
+temp control group_id T_target time_constant
+```
+
+- `T_target` - Target temperature 
+- `time_constant` - time constant 

docs/Commands/thermo.md

@@ -0,0 +1,22 @@
+# thermo
+
+```sh
+thermo step
+```
+
+## Inputs
+
+`step` - Output every `step` steps.
+
+## Examples
+
+```
+thermo 50
+```
+
+## Descriptions
+
+Currently the thermo output is fixed. 
+For energy minimization, the thermo output contains only the energy and second norm of the global force vector.
+For dynamics, the thermo output also contains the kinetic energy and the temperature.
+

docs/Commands/thermo_style.md

@@ -0,0 +1,32 @@
+# thermo_style
+
+```sh
+thermo_style args
+```
+
+## Inputs
+
+`args` - List of thermo_style options. Acceptable options are listed below:
+
+## Examples
+
+```
+thermo 50
+```
+
+## Descriptions
+
+The `thermo_style` command sets the thermo output for CAC. 
+By default the thermostyle command only outputs the potential energy and the global force norm.
+Acceptable options for thermo_style are listed below:
+
+- `pe`: potential energy
+- `fnorm`: global force norm
+- `temp`: temperature
+- `temp_c`: temperature in CG 
+- `temp_a`: temperature in atoms
+- `ke`: kinetic energy
+- `ke_c`: kinetic energy in CG 
+- `ke_a`: kinetic energy in atoms
+- `lx`, `ly`, `lz`: Box dimensions in x, y, z respectively
+- `px`, `py`, `pz`: Box pressure in x, y, z respectively