LAMMPS

https://docs.lammps.org/latest/
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### Hybrid Pair Style Setup Example

Source: https://docs.lammps.org/latest/pair_hybrid.html

Example of setting up a hybrid simulation with EAM/alloy, LJ/cut/Coul/cut, and LJ/cut potentials. This demonstrates how to assign coefficients for different atom types and interactions.

```lammps
pair_style hybrid eam/alloy lj/cut/coul/cut 10.0 lj/cut 8.0
pair_coeff * * eam/alloy nialhjea Ni Ni NULL
pair_coeff 3 3 lj/cut/coul/cut 1.0 1.0
pair_coeff 1*2 3 lj/cut 0.8 1.3
```

--------------------------------

### Example: hbond/dreiding/lj Pair Style Setup

Source: https://docs.lammps.org/latest/pair_hbond_dreiding.html

Sets up the hbond/dreiding/lj pair style with a hybrid overlay. This example demonstrates how to define the style and its parameters, including the power of cosine, distance cutoffs, and angle cutoff.

```bash
pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/lj 4 9.0 11.0 90.0
```

```bash
pair_coeff 1 2 hbond/dreiding/lj 3 i 9.5 2.75 4 9.0 11.0 90.0
```

--------------------------------

### Full Adaptive-Precision Potential Setup

Source: https://docs.lammps.org/latest/fix_lambda_apip.html

This comprehensive example shows the complete setup for an adaptive-precision potential, including hybrid pair styles, coefficients, and the lambda/apip fix.

```lammps
pair_style hybrid/overlay eam/fs/apip pace/precise/apip lambda/input/csp/apip fcc cutoff 5.0 lambda/zone/apip 12.0
pair_coeff * * eam/fs/apip Cu.eam.fs Cu
pair_coeff * * pace/precise/apip Cu_precise.yace Cu
pair_coeff * * lambda/input/csp/apip
pair_coeff * * lambda/zone/apip
fix 2 all lambda/apip 3.0 3.5 time_averaged_zone 4.0 12.0 110 110 min_delta_lambda 0.01
```

--------------------------------

### Example of compute ke/atom/eff

Source: https://docs.lammps.org/latest/compute_ke_atom_eff.html

A simple example demonstrating how to apply the compute ke/atom/eff command to all atoms in the system. This is useful for initial setup and testing.

```bash
compute 1 all ke/atom/eff
```

--------------------------------

### Example min_style Commands

Source: https://docs.lammps.org/latest/min_style.html

Provides examples of how to invoke different min_style commands. These examples demonstrate basic usage for conjugate gradient, fire, and spin minimization.

```bash
min_style cg
min_style fire
min_style spin
```

--------------------------------

### Example: peri/lps Pair Style and Coefficients

Source: https://docs.lammps.org/latest/pair_peri.html

Demonstrates the setup for the Peridynamic state-based linear peridynamic solid (LPS) model. Requires coefficients for bulk modulus, shear modulus, horizon, and bond breaking criteria.

```bash
pair_style peri/lps
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25
```

--------------------------------

### Example: peri/eps Pair Style and Coefficients

Source: https://docs.lammps.org/latest/pair_peri.html

Demonstrates the setup for the Peridynamic state-based elastic-plastic solid (EPS) model. Requires coefficients for moduli, horizon, bond breaking, and yield stress.

```bash
pair_style peri/eps
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 118.43
```

--------------------------------

### Example: peri/pmb Pair Style and Coefficients

Source: https://docs.lammps.org/latest/pair_peri.html

Demonstrates the setup for the Peridynamic bond-based prototype microelastic brittle (PMB) model. Requires coefficients for spring constant, horizon, and bond breaking criteria.

```bash
pair_style peri/pmb
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
```

--------------------------------

### Compute Pressure Examples

Source: https://docs.lammps.org/latest/compute_pressure.html

Examples demonstrating the usage of the compute pressure command. These examples show how to specify the temperature ID and different pressure components like pair, bond, and hybrid.

```bash
compute 1 all pressure thermo_temp

```

```bash
compute 1 all pressure NULL pair bond

```

```bash
compute 1 all pressure NULL pair/hybrid lj/cut

```

--------------------------------

### Compute composition/atom examples

Source: https://docs.lammps.org/latest/compute_composition_atom.html

Examples demonstrating the use of the compute composition/atom command. The first example uses default settings, while the second specifies a cutoff distance.

```bash
compute 1 all composition/atom
```

```bash
compute 1 all composition/atom cutoff 9.0
comm_modify cutoff 9.0
```

--------------------------------

### Example: peri/ves Pair Style and Coefficients

Source: https://docs.lammps.org/latest/pair_peri.html

Demonstrates the setup for the Peridynamic state-based linear peridynamic viscoelastic solid (VES) model. Includes coefficients for moduli, horizon, bond breaking, and viscoelastic relaxation parameters.

```bash
pair_style peri/ves
pair_coeff * * 14.9e9 14.9e9 0.0015001 0.0005 0.25 0.5 0.001
```

--------------------------------

### NPT/Sphere Examples

Source: https://docs.lammps.org/latest/fix_npt_sphere.html

Provides various examples of using the fix npt/sphere command with different settings for temperature, pressure, and particle behavior. These examples demonstrate common use cases and options.

```bash
fix 1 all npt/sphere temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
```

```bash
fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0
```

```bash
fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 disc
```

```bash
fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 drag 0.2
```

```bash
fix 2 all npt/sphere temp 300.0 300.0 100.0 x 5.0 5.0 1000.0 update dipole
```

```bash
fix 2 water npt/sphere temp 300.0 300.0 100.0 aniso 0.0 0.0 1000.0 dilate partial
```

--------------------------------

### Compute MSD Examples

Source: https://docs.lammps.org/latest/compute_msd.html

Provides examples of how to use the compute msd command. The first example is a basic usage, while the second demonstrates using the 'com' and 'average' options.

```bash
compute 1 all msd
```

```bash
compute 1 upper msd com yes average yes
```

--------------------------------

### Navigate to LAMMPS Example Directory

Source: https://docs.lammps.org/latest/Howto_wsl.html

Change the current directory to the 'melt' example folder within the LAMMPS installation.

```bash
cd ../examples/melt
```

--------------------------------

### Include Command Examples

Source: https://docs.lammps.org/latest/include.html

Examples demonstrating how to use the include command to switch to different input script files.

```bash
include newfile
```

```bash
include in.run2
```

--------------------------------

### Create Property Instance with Local File (Usage Example)

Source: https://docs.lammps.org/latest/kim_commands.html

Example showing how to create a property instance using a local file as the property definition.

```bash
kim property create 1 new-property.edn

```

--------------------------------

### Example temper command usage

Source: https://docs.lammps.org/latest/temper.html

Example usages of the temper command. The first example shows a basic setup, while the second includes an optional index for temperature assignment.

```lammps
temper 100000 100 $t tempfix 0 58728
```

```lammps
temper 40000 100 $t tempfix 0 32285 $w
```

--------------------------------

### Example: Compute fragment/atom (default)

Source: https://docs.lammps.org/latest/compute_cluster_atom.html

Example of using the compute fragment/atom command with default settings.

```bash
compute 1 all fragment/atom
```

--------------------------------

### DPD/ext Pair Style Examples

Source: https://docs.lammps.org/latest/pair_dpd_ext.html

Provides example commands for setting up the dpd/ext pair style and its coefficients.

```bash
pair_style dpd/ext 1.0 2.5 34387
pair_coeff 1 1 25.0 4.5 4.5 0.5 0.5 1.2
pair_coeff 1 2 40.0 4.5 4.5 0.5 0.5 1.2
```

```bash
pair_style hybrid/overlay lj/cut 2.5 dpd/ext/tstat 1.0 1.0 2.5 34387
pair_coeff * * lj/cut 1.0 1.0
pair_coeff * * 4.5 4.5 0.5 0.5 1.2
```

--------------------------------

### CMakeLists.txt for Using Installed LAMMPS

Source: https://docs.lammps.org/latest/Build_cmake.html

Example CMakeLists.txt file for a C++ project that uses the installed LAMMPS package. Ensure CMAKE_PREFIX_PATH is set correctly.

```cmake
cmake_minimum_required(VERSION 3.20)
project(simpleCC CXX)
# set this to the LAMMPS installation location
if(NOT CMAKE_PREFIX_PATH)
  set(CMAKE_PREFIX_PATH $ENV{HOME}/.local)
endif()
find_package(LAMMPS REQUIRED)
add_executable(simpleCC simple.cpp)
target_link_libraries(simpleCC PRIVATE LAMMPS::LAMMPS)

```

--------------------------------

### Basic pair_style bpm/spring Examples

Source: https://docs.lammps.org/latest/pair_bpm_spring.html

Provides examples of how to set up the bpm/spring pair style and its coefficients. The first example uses default settings, while the second includes an anharmonic term and a fourth coefficient.

```bash
pair_style bpm/spring
pair_coeff * * 1.0 1.0 1.0
```

```bash
pair_style bpm/spring anharmonic yes
pair_coeff 1 1 1.0 1.0 1.0 50.0
```

--------------------------------

### Example of 'start' and 'stop' with a fix

Source: https://docs.lammps.org/latest/run.html

Demonstrates how 'start' and 'stop' keywords in the run command can be used in conjunction with a fix command to apply changes over a series of runs.

```lammps
fix         1 all nvt 200.0 300.0 1.0
run         1000 start 0 stop 10000
run         1000 start 0 stop 10000
...
run         1000 start 0 stop 10000
```

--------------------------------

### Example Pair Style Configurations

Source: https://docs.lammps.org/latest/pair_thole.html

Demonstrates how to configure the 'hybrid/overlay' and 'lj/cut/thole/long' pair styles with specific parameters. These examples show setting up interactions with different atom types and cutoffs.

```bash
pair_style hybrid/overlay ... thole 2.6 12.0
```

```bash
pair_coeff 1 1 thole 1.0
```

```bash
pair_coeff 1 2 thole 1.0 2.6 10.0
```

```bash
pair_coeff * 2 thole 1.0 2.6
```

```bash
pair_style lj/cut/thole/long 2.6 12.0
```

--------------------------------

### Hybrid/Overlay EAM/FS and Coul/CTIP Example

Source: https://docs.lammps.org/latest/pair_coul.html

Example demonstrating the hybridization of EAM/FS and Coul/CTIP pair styles for complex material interactions. Includes charge equilibration setup.

```lammps
pair_style hybrid/overlay eam/fs coul/ctip 0.30 12.0
pair_coeff * * eam/fs NiO.eam.fs Ni O
pair_coeff * * coul/ctip NiO.ctip Ni O
fix 1 all qeq/ctip 1 12.0 1.0e-8 100 coul/ctip cdamp 0.30 maxrepeat 10
```

--------------------------------

### Example Usage of fix nve/asphere

Source: https://docs.lammps.org/latest/fix_nve_asphere.html

An example demonstrating how to apply the fix nve/asphere command to all particles in a group. This is a common starting point for simulations involving aspherical particles.

```bash
fix 1 all nve/asphere
```

--------------------------------

### Verify LAMMPS Python Module Installation

Source: https://docs.lammps.org/latest/Python_install.html

Starts the Python interpreter, imports the lammps module, and creates a LAMMPS instance to verify a successful installation. This should not produce any error messages.

```python
import lammps
lmp = lammps.lammps()

```

--------------------------------

### Example: SMTB-Q Pair Style Initialization and Coefficients for TiO2

Source: https://docs.lammps.org/latest/pair_smtbq.html

This example demonstrates how to set up the SMTB-Q pair style for a TiO2 system, specifying the potential file and mapping oxygen and titanium atom types.

```lammps
pair_coeff * * PathToLammps/potentials/ffield.smtbq.TiO2 O Ti
```

--------------------------------

### Example Hybrid Bond Style Configuration

Source: https://docs.lammps.org/latest/bond_hybrid.html

Demonstrates how to set up a hybrid bond style with harmonic and fene potentials for different bond types.

```bash
bond_style hybrid harmonic fene
bond_coeff 1 harmonic 80.0 1.2
bond_coeff 2* fene 30.0 1.5 1.0 1.0
```

--------------------------------

### Example: hbond/dreiding/morse Pair Style Setup

Source: https://docs.lammps.org/latest/pair_hbond_dreiding.html

Configures the hbond/dreiding/morse pair style using a hybrid overlay. This example shows the parameters for the Morse potential variant, including its specific coefficients and cutoffs.

```bash
pair_style hybrid/overlay lj/cut 10.0 hbond/dreiding/morse 2 9.0 11.0 90.0
```

```bash
pair_coeff 1 2 hbond/dreiding/morse 3 i 3.88 1.7241379 2.9 2 9.0 11.0 90.0
```

--------------------------------

### Plugin Command Examples

Source: https://docs.lammps.org/latest/plugin.html

Illustrates various ways to use the plugin command, including loading, unloading specific styles or commands, listing loaded plugins, clearing all plugins, and restoring them.

```text
plugin load morse2plugin.so
plugin unload pair morse2/omp
plugin unload command hello
plugin list
plugin clear
plugin restore
```

--------------------------------

### Compute POD/atom Command Examples

Source: https://docs.lammps.org/latest/compute_pod_atom.html

Illustrates the usage of compute pod/atom and its variants with parameter and coefficient files.

```bash
compute d all pod/atom Ta_param.pod
compute dd all podd/atom Ta_param.pod
compute ldd all pod/local Ta_param.pod
compute gdd all podd/global Ta_param.pod
compute d all pod/atom Ta_param.pod Ta_coefficients.pod
compute dd all podd/atom Ta_param.pod Ta_coefficients.pod
compute ldd all pod/local Ta_param.pod Ta_coefficients.pod
compute gdd all podd/global Ta_param.pod Ta_coefficients.pod
```

--------------------------------

### Example of Tersoff/ZBL Pair Style and Coefficients

Source: https://docs.lammps.org/latest/pair_tersoff_zbl.html

A complete example demonstrating the setup of the tersoff/zbl pair style followed by the assignment of potential coefficients, mapping Si and C elements to LAMMPS atom types.

```lammps
pair_style tersoff/zbl
pair_coeff * * SiC.tersoff.zbl Si C Si

```

--------------------------------

### Hybrid Overlay/Scaled Style Example

Source: https://docs.lammps.org/latest/pair_hybrid.html

Demonstrates equivalent configurations for hybrid/overlay styles, showing how to define LJ/cut interactions for all pairs and specific pairs.

```bash
pair_style lj/cut 2.5
pair_coeff * * 1.0 1.0
pair_coeff 2 2 1.5 0.8

pair_style hybrid/overlay lj/cut 2.5
pair_coeff * * lj/cut 1.0 1.0
pair_coeff 2 2 lj/cut 1.5 0.8
```

--------------------------------

### Basic Langevin Thermostatting Example

Source: https://docs.lammps.org/latest/fix_langevin.html

Applies Langevin dynamics to thermostat atoms with specified start and stop temperatures and damping.

```lammps
fix 3 boundary langevin 1.0 1.0 1000.0 699483

```

--------------------------------

### Basic Langevin thermostat example

Source: https://docs.lammps.org/latest/fix_langevin_eff.html

Applies a Langevin thermostat with specified start and stop temperatures, damping, and random seed.

```lammps
fix 3 boundary langevin/eff 1.0 1.0 10.0 699483
```

--------------------------------

### lammps_config_package_name

Source: https://docs.lammps.org/latest/Library_config.html

Retrieves the name of a package at a specific index in the list of installed packages. This function is used to get the name of a package given its index.

```APIDOC
## lammps_config_package_name

### Description
Gets the name of a package from the list of installed packages in the LAMMPS library. This function copies the name of the package with the specified index into a provided buffer.

### Method
int

### Parameters
#### Path Parameters
* **idx** (int) - Required - The index of the package in the list of included packages (0 <= idx < package count).
* **buffer** (char*) - Required - A string buffer to copy the name of the package to.
* **buf_size** (int) - Required - The size of the provided string buffer.

### Returns
1 if successful, otherwise 0. If the index is out of range, the function returns 0 and the buffer is set to an empty string. If the package name exceeds the buffer size, it will be truncated.
```

--------------------------------

### Examples for oxDNA/FENE Bond Styles (Real Units)

Source: https://docs.lammps.org/latest/bond_oxdna.html

Demonstrates setting bond coefficients for oxDNA/FENE, oxDNA2/FENE, oxDNA3/FENE, and oxRNA2/FENE using real units. Note that oxDNA3/FENE uses a potential file.

```bash
# Real units
bond_style oxdna/fene
bond_coeff * 11.92337812042065 2.1295 6.409795

bond_style oxdna2/fene
bond_coeff * 11.92337812042065 2.1295 6.4430152

bond_style oxdna3/fene
bond_coeff * oxdna3_real.cgdna

bond_style oxrna2/fene
bond_coeff * 11.92337812042065 2.1295 6.482800913
```

--------------------------------

### Example Usage of fix nve/dot

Source: https://docs.lammps.org/latest/fix_nve_dot.html

Demonstrates how to apply the nve/dot fix to all atoms in a simulation. This is a common starting point for NVE simulations using this integrator.

```text
fix 1 all nve/dot
```

--------------------------------

### Example: Compute Temperature Profile with Binning

Source: https://docs.lammps.org/latest/compute_temp_profile.html

Demonstrates how to use the compute temp/profile command to calculate temperature, including spatial binning and specifying the output format as 'bin'.

```lammps
compute myTemp flow temp/profile 1 1 1 x 10
compute myTemp flow temp/profile 1 1 1 x 10 out bin
compute myTemp flow temp/profile 0 1 1 xyz 20 20 20
```

--------------------------------

### Configure and Build LAMMPS with CMake

Source: https://docs.lammps.org/latest/Build_cmake.html

Example of configuring LAMMPS with a specific installation path and then building the project. It demonstrates how CMake detects MPI and OpenMP support.

```bash
cmake -S . -B build -D CMAKE_PREFIX_PATH=$HOME/Downloads/test-install
-- The CXX compiler identification is GNU 15.2.1
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/lib64/ccache/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found MPI_CXX: /usr/lib64/mpich/lib/libmpicxx.so (found version "4.1")
-- Found MPI: TRUE (found version "4.1") found components: CXX
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5") found components: CXX
-- Found LAMMPS: /home/akohlmey/Downloads/test-install/lib64/liblammps.so.0
-- Configuring done (0.9s)
-- Generating done (0.0s)
-- Build files have been written to: /home/akohlmey/Downloads/test-simple/build
cmake --build build
[ 50%] Building CXX object CMakeFiles/simpleCC.dir/simple.cpp.o
[100%] Linking CXX executable simpleCC
[100%] Built target simpleCC

```

--------------------------------

### Example: Initialize SW potential for Si

Source: https://docs.lammps.org/latest/kim_commands.html

Initializes the Stillinger-Weber potential for Silicon using metal units.

```bash
kim init SW_StillingerWeber_1985_Si__MO_405512056662_005 metal
kim interactions Si
```

--------------------------------

### Basic aip/water/2dm Usage

Source: https://docs.lammps.org/latest/pair_aip_water_2dm.html

This example shows a basic setup for the aip/water/2dm pair style with a specified cutoff and taper flag. It is typically used with the hybrid/overlay command.

```lammps
pair_style  hybrid/overlay aip/water/2dm 16.0 1
pair_coeff  * * aip/water/2dm  CBNOH.aip.water.2dm C Ow Hw
```

--------------------------------

### ComputeTemp setup() Method

Source: https://docs.lammps.org/latest/Developer_write_compute.html

Called at the start of each run, this method computes the degrees of freedom for temperature calculation. It determines if the degrees of freedom need to be re-computed dynamically.

```cpp
void ComputeTemp::setup()
{
  dynamic = 0;
  if (dynamic_user || group->dynamic[igroup]) dynamic = 1;
  dof_compute();
}
```

--------------------------------

### Examples of write_data Command Usage

Source: https://docs.lammps.org/latest/write_data.html

Illustrative examples demonstrating various ways to use the write_data command, including different filenames and options.

```bash
write_data data.polymer
```

```bash
write_data data.polymer.gz
```

```bash
write_data data.*
```

```bash
write_data data.solid triclinic/general
```

--------------------------------

### Basic balance command usage

Source: https://docs.lammps.org/latest/balance.html

These examples demonstrate basic usage of the balance command with different balancing strategies and parameters. They show how to adjust subdomain sizes based on atom count or specific weighting schemes.

```bash
balance 0.9 x uniform y 0.4 0.5 0.6
```

```bash
balance 1.2 shift xz 5 1.1
```

```bash
balance 1.0 shift xz 5 1.1
```

```bash
balance 1.1 rcb
```

```bash
balance 1.0 shift x 10 1.1 weight group 2 fast 0.5 slow 2.0
```

```bash
balance 1.0 shift x 10 1.1 weight time 0.8 weight neigh 0.5 weight store balance
```

```bash
balance 1.0 shift x 20 1.0 out tmp.balance
```

--------------------------------

### Run LAMMPS Example in Parallel with MPI

Source: https://docs.lammps.org/latest/Howto_wsl.html

Execute a LAMMPS input script in parallel using MPI with 4 processes. This requires an MPI implementation to be installed and configured.

```bash
mpirun -np 4 $LAMMPS_BUILD_DIR/lmp -in in.melt
```

--------------------------------

### Compute Stress/MOP/Profile Example

Source: https://docs.lammps.org/latest/compute_stress_mop.html

Calculates the stress profile in the x-direction, starting from the lower boundary with a plane separation of 0.1 distance units, including total stress contributions.

```lammps
compute 1 all stress/mop/profile x lower 0.1 total
```

--------------------------------

### Compute XRD Example with Manual Spacing

Source: https://docs.lammps.org/latest/compute_xrd.html

This example demonstrates the compute xrd command using manual spacing for reciprocal lattice points, along with 2Theta range, Lorentz-polarization factor, and specific 'c' parameters.

```bash
compute 2 all xrd 1.541838 Al O 2Theta 10 100 c 0.05 0.05 0.05 LP 1 manual
```

--------------------------------

### Setting up temperatures and thermostatting for temper

Source: https://docs.lammps.org/latest/temper.html

This example demonstrates how to define multiple temperatures using a 'variable' command and apply them to a thermostat fix. This setup is then used with the 'temper' command.

```lammps
variable t world 300.0 310.0 320.0 330.0
fix myfix all nvt temp $t $t 100.0
temper 100000 100 $t myfix 3847 58382
```

--------------------------------

### kim query Examples

Source: https://docs.lammps.org/latest/kim_commands.html

Illustrates basic usage of the kim query command for retrieving lattice constants and available models.

```text
kim query a0 get_lattice_constant_cubic crystal=[fcc] species=[Al] units=[angstrom]
```

```text
kim query model index get_available_models species=[Al] potential_type=[eam]
```

--------------------------------

### Hybrid Overlay with EAM, REBO, and saip/metal

Source: https://docs.lammps.org/latest/pair_saip_metal.html

This example illustrates a more complex hybrid/overlay setup involving EAM, REBO, and saip/metal pair styles. It specifies coefficients for each style.

```lammps
pair_style  hybrid/overlay eam rebo saip/metal 16.0
pair_coeff  1 1 eam  Au_u3.eam  Au NULL NULL
pair_coeff  * * rebo CH.rebo    NULL  C H
pair_coeff  * * saip/metal      CHAu.ILP  Au C H
```

--------------------------------

### Example: Fix external with pf/callback

Source: https://docs.lammps.org/latest/fix_external.html

Demonstrates using the 'pf/callback' mode. The first example applies callbacks every 1 step, and the second applies them every 100 steps.

```bash
fix 1 all external pf/callback 1 1
```

```bash
fix 1 all external pf/callback 100 1
```

--------------------------------

### Example Makefiles for Intel Compilation

Source: https://docs.lammps.org/latest/Speed_intel.html

These Makefiles are provided for building LAMMPS with Intel compilers and different MPI implementations. Select the appropriate file based on your MPI setup.

```makefile
Makefile.intel_cpu_intelmpi  # Intel Compiler, Intel MPI
Makefile.intel_cpu_mpich     # Intel Compiler, MPICH
Makefile.intel_cpu_openmpi   # Intel Compiler, OpenMPI
```

--------------------------------

### Detect LAMMPS Files with 'file' Command

Source: https://docs.lammps.org/latest/Tools.html

This example shows how the 'file' command, after installing LAMMPS magic patterns, can identify various LAMMPS file types and provide details about them.

```bash
$ file *.*
dihedral-quadratic.restart:   LAMMPS binary restart file (rev 2), Version 10 Mar 2021, Little Endian
mol-pair-wf_cut.restart:      LAMMPS binary restart file (rev 2), Version 24 Dec 2020, Little Endian
atom.bin:                     LAMMPS atom style binary dump (rev 2), Little Endian, First time step: 445570
custom.bin:                   LAMMPS custom style binary dump (rev 2), Little Endian, First time step: 100
bn1.lammpstrj:                LAMMPS text mode dump, First time step: 5000
data.fourmol:                 LAMMPS data file written by LAMMPS
pnc.data:                     LAMMPS data file written by msi2lmp
data.spce:                    LAMMPS data file written by TopoTools
B.data:                       LAMMPS data file written by OVITO
log.lammps:                   LAMMPS log file written by version 10 Feb 2021


```

--------------------------------

### Dump Image Examples

Source: https://docs.lammps.org/latest/dump_image.html

Examples of dumping simulation snapshots as images in different formats and with various styling options.

```bash
dump d0 all image 100 dump.*.jpg type type
```

```bash
dump d1 mobile image 500 snap.*.png element element ssao yes 4539 0.6
```

```bash
dump d2 all image 200 img-*.ppm type type zoom 2.5 adiam 1.5 size 1280 720
```

--------------------------------

### Initializing Buckled Property

Source: https://docs.lammps.org/latest/angle_mesocnt.html

This example shows how to initialize the 'i_buckled' atomic variable when CNTs are already buckled at the start of the simulation. A run 0 command is necessary before defining the pair_style.

```bash
angle_style mesocnt
angle_coeff 1 buckling C 10 10 20.0

run 0

pair_style mesocnt 60.0
pair_coeff * * C_10_10.mesocnt 1
```

--------------------------------

### aip/water/2dm with lj/cut/tip4p/long

Source: https://docs.lammps.org/latest/pair_aip_water_2dm.html

This example demonstrates using aip/water/2dm in conjunction with the lj/cut/tip4p/long pair style within a hybrid/overlay setup. It includes specific pair_coeff definitions for different atom types.

```lammps
pair_style  hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
pair_coeff  * *   aip/water/2dm        CBNOH.aip.water.2dm    C Ow Hw
pair_coeff  2 2   lj/cut/tip4p/long    8.0313e-3  3.1589      # O-O
pair_coeff  2 3   lj/cut/tip4p/long    0.0        0.0         # O-H
pair_coeff  3 3   lj/cut/tip4p/long    0.0        0.0         # H-H
```

--------------------------------

### Hybrid GCMC+MD Simulation Setup

Source: https://docs.lammps.org/latest/fix_gcmc.html

Example of setting up a hybrid GCMC and MD simulation using fix nvt. Ensures proper temperature calculation and dynamic updates for the reservoir.

```lammps
compute mdtemp mdatoms temp
compute_modify mdtemp dynamic/dof yes
fix mdnvt mdatoms nvt temp 300.0 300.0 10.0
fix_modify mdnvt temp mdtemp
```

--------------------------------

### REBO Pair Coefficient Setup

Source: https://docs.lammps.org/latest/pair_airebo.html

Demonstrates setting coefficients for the REBO pair style, specifying the potential file and element types.

```bash
pair_coeff * * ../potentials/CH.rebo H C
```

--------------------------------

### SRP/React Pair Style Example with Bond Creation

Source: https://docs.lammps.org/latest/pair_srp.html

Demonstrates the srp/react pair style in a hybrid setup, integrated with a 'fix bond/create' command. This is suitable for systems where bonds can form and break.

```bash
fix        create all bond/create   100  1  2  1.0 1 prob  0.2  19852
pair_style hybrid dpd 1.0 1.0 12345 srp/react 0.8 * min create exclude yes
pair_coeff 1 1 dpd 60.0 50 1.0
pair_coeff 1 2 none
pair_coeff 2 2 srp/react 40.0
```
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