### Meson Build Setup and Install

Source: https://github.com/crest-lab/crest/blob/master/README.md

Set Fortran and C compilers, set the installation prefix, and then set up and install the build using Meson. This is primarily tested with Intel compilers.

```bash
export FC=ifort CC=icc
Meson setup _build --prefix=$PWD/_dist
Meson install -C _build
```

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

### Install Project Include Directory

Source: https://github.com/crest-lab/crest/blob/master/CMakeLists.txt

Installs the project's source include directory to the installation prefix.

```cmake
install(
  DIRECTORY
  "${CMAKE_CURRENT_SOURCE_DIR}/include/"
  DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}"
)
```

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

### Execute CREST Example Script

Source: https://github.com/crest-lab/crest/blob/master/examples/README.md

To run any of the example scripts, navigate to the respective directory and execute the 'run.sh' script from the command line. Ensure that 'xtb' and 'crest' binaries are in your PATH.

```bash
./run.sh
```

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

### Install Build Include Directory

Source: https://github.com/crest-lab/crest/blob/master/CMakeLists.txt

Installs the project's build include directory to the installation prefix, with a subdirectory based on 'module-dir'.

```cmake
install(
  DIRECTORY
  "${CMAKE_CURRENT_BINARY_DIR}/include/"
  DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}/${module-dir}"
)
```

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

### Install Targets (with Shared Library)

Source: https://github.com/crest-lab/crest/blob/master/CMakeLists.txt

Installs the static library, shared library, and executable targets, along with their associated export files and include directories.

```cmake
install(
      TARGETS
      "lib-${PROJECT_NAME}-static"
#      "lib-${PROJECT_NAME}-shared"
      "${PROJECT_NAME}-exe"
      EXPORT "${PROJECT_NAME}-targets"
      LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}"
      ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}"
      RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}"
      INCLUDES DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}"
   )
```

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

### Install Package License Files

Source: https://github.com/crest-lab/crest/blob/master/CMakeLists.txt

Installs license files to the specified destination directory. Ensure the destination path is correctly defined.

```cmake
install(
  FILES
  "COPYING"
  "COPYING.LESSER"
  DESTINATION "${CMAKE_INSTALL_DATADIR}/licenses/${PROJECT_NAME}"
)
```

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

### Build CREST from Source (Meson/Intel)

Source: https://context7.com/crest-lab/crest/llms.txt

Build CREST from source using Meson with Intel compilers. Specify the installation prefix.

```bash
export FC=ifort CC=icc
meson setup _build --prefix=$PWD/_dist
meson install -C _build
```

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

### CMake Build Setup

Source: https://github.com/crest-lab/crest/blob/master/README.md

Set Fortran and C compilers and configure the CMake build directory. Ensure LAPACK and OpenMP shared libraries are in the library path.

```bash
export FC=gfortran CC=gcc
cmake -B _build
```

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

### Install CREST using Precompiled Binary (Intel)

Source: https://context7.com/crest-lab/crest/llms.txt

Download and unpack the statically linked Intel build of CREST. Ensure the executable is added to your PATH.

```bash
wget https://github.com/crest-lab/crest/releases/download/latest/crest-intel-2023.1.0-ubuntu-latest.tar.xz
tar -xf crest-intel-2023.1.0-ubuntu-latest.tar.xz
export PATH=$PWD:$PATH
```

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

### Solvated Conformational Search Workflow

Source: https://context7.com/crest-lab/crest/llms.txt

An end-to-end example of a conformational search for 1-propanol in water, followed by re-sorting with CREGEN.

```bash
# 1. Run conformational search (GFN2-xTB, ALPB water, 8 threads)
crest struc.xyz -gfn2 -alpb h2o -T 8 -ewin 6.0

# 2. Re-sort the ensemble with tighter thresholds using CREGEN standalone
crest struc.xyz -cregen crest_conformers.xyz -ewin 4.0 -rthr 0.10 -ethr 0.03

# 3. Inspect the number of unique conformers
grep -c '^\s*[0-9]' crest_ensemble.xyz || wc -l < crest_ensemble.xyz

# 4. Split ensemble into individual directories for downstream QM refinement
crest -splitfile crest_ensemble.xyz

# Result structure:
# ./SPLIT/
#   STRUC1/  ... STRUCN/   <- one directory per conformer

```

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

### Install Targets (without Shared Library)

Source: https://github.com/crest-lab/crest/blob/master/CMakeLists.txt

Installs the static library and executable targets, along with their associated export files and include directories, when shared library is not built.

```cmake
install(
      TARGETS
      "lib-${PROJECT_NAME}-static"
      "${PROJECT_NAME}-exe"
      EXPORT "${PROJECT_NAME}-targets"
      ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}"
      RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}"
      INCLUDES DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}"
   )
```

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

### Install CREST using Precompiled Binary (GNU)

Source: https://context7.com/crest-lab/crest/llms.txt

Download and unpack the statically linked GNU build of CREST. Ensure the executable is added to your PATH.

```bash
wget https://github.com/crest-lab/crest/releases/download/latest/crest-gnu-12-ubuntu-latest.tar.xz
tar -xf crest-gnu-12-ubuntu-latest.tar.xz
export PATH=$PWD:$PATH
```

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

### Install Exported Targets

Source: https://github.com/crest-lab/crest/blob/master/CMakeLists.txt

Installs the CMake export file for the project targets, defining a namespace for imported targets.

```cmake
install(
  EXPORT
  "${PROJECT_NAME}-targets"
  NAMESPACE
  "${PROJECT_NAME}::"
  DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/${PROJECT_NAME}"
)
```

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

### Xmol .xyz Input Format Example

Source: https://context7.com/crest-lab/crest/llms.txt

Example of the Xmol `.xyz` format for input structures. The first line is the atom count, the second is an optional comment, and subsequent lines specify element and coordinates.

```xyz
12

C          1.00510       -0.04436        0.07729
C          2.52196       -0.10014        0.05638
C          3.03386       -1.52959       -0.04885
O          4.45512       -1.53382       -0.04957
H          0.66450        0.99293        0.15400
H          0.60392       -0.59767        0.93240
H          0.58435       -0.47325       -0.83778
H          2.92490        0.36854        0.96213
H          2.90338        0.49174       -0.78421
H          2.68484       -2.01184       -0.96764
H          2.69552       -2.12845        0.80244
H          4.74911       -1.01511       -0.81774
```

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

### Tautomer Screening in Solution Workflow

Source: https://context7.com/crest-lab/crest/llms.txt

Example workflow for screening guanine tautomers in implicit water, followed by sorting and RMSD calculation.

```bash
# 1. Screen guanine tautomers in implicit water solvent
crest guanine.xyz -tautomerize -alpb h2o -ewin 10.0 -T 4

# 2. Sort the tautomers further
crest guanine.xyz -cregen tautomers.xyz -ewin 10.0 -notopo

# 3. Calculate RMSD between the canonical tautomer and all others
for i in $(seq 2 5); do
  crest -rmsd guanine.xyz SPLIT/STRUC${i}/struc.xyz
done

# Output: tautomers.xyz (5 structures within 10 kcal/mol for guanine)

```

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

### Unpack Precompiled Binary (Intel)

Source: https://github.com/crest-lab/crest/blob/master/README.md

Use this command to unpack the Intel build of the CREST binary. Ensure you have `tar` installed.

```bash
tar -xf crest-intel-2023.1.0-ubuntu-latest.tar.xz
```

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

### Example tblite TOML Parameter File

Source: https://context7.com/crest-lab/crest/llms.txt

An excerpt from a tblite TOML parameter file, defining Hamiltonian and dispersion parameters for GFN2-xTB.

```toml
# Example: excerpt from assets/tblite/gfn2.toml
[meta]
name = "GFN2-xTB"
reference = "C. Bannwarth, S. Ehlert and S. Grimme., J. Chem. Theory Comput., 2019, 15, 1652-1671."
version = 1
format = 1

[hamiltonian.xtb]
wexp = 5.0e-1      # weighting exponent
kpol = 2.0e0       # polarization constant
enscale = 2.0e-2   # energy scaling

[dispersion.d4]
s6 = 1.0e0
s8 = 2.7e0
a1 = 5.2e-1
a2 = 5.0e0

[element.C]
shells = [ "2s", "2p" ]
levels = [ -1.397e+01, -1.006e+01 ]
slater = [ 2.096e+00, 1.800e+00 ]
gam = 5.380e-01
zeff = 4.231e+00
en = 2.55

```

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

### Install CREST using Conda

Source: https://context7.com/crest-lab/crest/llms.txt

Install CREST via conda. It is recommended to set OPENBLAS_NUM_THREADS to 1 to avoid threading conflicts.

```bash
conda install conda-forge::crest
# Recommended: avoid OpenBLAS threading conflicts
export OPENBLAS_NUM_THREADS=1
```

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

### Unpack Precompiled Binary (GNU)

Source: https://github.com/crest-lab/crest/blob/master/README.md

Use this command to unpack the GNU build of the CREST binary. Ensure you have `tar` installed.

```bash
tar -xf crest-gnu-12-ubuntu-latest.tar.xz
```

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

### Install CREST via Conda

Source: https://github.com/crest-lab/crest/blob/master/README.md

Install CREST from the conda-forge channel using the conda package manager. This method provides a dynamically linked CMake/GNU build.

```bash
conda install conda-forge::crest
```

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

### Define Static Library Include Directories

Source: https://github.com/crest-lab/crest/blob/master/CMakeLists.txt

Specifies include directories for the static library, differentiating between build and install interfaces.

```cmake
target_include_directories(
  "lib-${PROJECT_NAME}-static"
  PUBLIC
  $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>
  $<BUILD_INTERFACE:${PROJECT_BINARY_DIR}/include>
  $<INSTALL_INTERFACE:$<INSTALL_PREFIX>/${CMAKE_INSTALL_INCLUDEDIR}>
)
```

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

### Default Conformational Search (iMTD-GC)

Source: https://context7.com/crest-lab/crest/llms.txt

Execute the default iMTD-GC workflow for conformational searching. This produces unique conformers and all degenerate structures. Examples show basic usage, solvent inclusion, and different GFN levels.

```bash
# Basic run: 1-propanol in gas phase, 2 kcal/mol energy window
crest struc.xyz -ewin 2.0

# With GFN2-xTB in implicit H2O solvent, using 4 CPU threads
crest struc.xyz -ewin 2.0 -g h2o -gfn2 -T 4

# Use GFN1-xTB instead of default GFN2-xTB
crest struc.xyz -gfn1

# Use GFN-FF (force-field level, fast)
crest struc.xyz -gfnff

# Composite GFN2-xTB//GFN-FF (single-point GFN2 on GFN-FF geometries)
crest struc.xyz -gfn2//gfnff

# Outputs:
#   crest_conformers.xyz  — unique conformers within -ewin window

```

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

### Configure OpenBLAS for Conda Installation

Source: https://github.com/crest-lab/crest/blob/master/README.md

If using OpenBLAS as a shared library backend with CREST installed via Conda, set this environment variable to 1 to avoid potential warnings in concurrent parallel code sections.

```bash
export OPENBLAS_NUM_THREADS=1
```

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

### Define Shared Library Include Directories

Source: https://github.com/crest-lab/crest/blob/master/CMakeLists.txt

Specifies include directories for the shared library, differentiating between build and install interfaces.

```cmake
target_include_directories(
      "lib-${PROJECT_NAME}-shared"
      PUBLIC
      $<BUILD_INTERFACE:${PROJECT_SOURCE_DIR}/include>
      $<BUILD_INTERFACE:${PROJECT_BINARY_DIR}/include>
      $<INSTALL_INTERFACE:$<INSTALL_PREFIX>/${CMAKE_INSTALL_INCLUDEDIR}>
   )
```

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

### Set Unpaired Electrons (Spin) in CREST

Source: https://context7.com/crest-lab/crest/llms.txt

Specify the number of unpaired electrons using the -uhf option for radical species. For example, -uhf 1 sets a doublet radical.

```bash
crest struc.xyz -uhf 1
```

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

### Meson Build with GNU Compilers

Source: https://github.com/crest-lab/crest/blob/master/README.md

When building with gfortran and gcc using Meson, specify the MKL backend. Compatibility with GNU compilers may be limited.

```bash
meson setup _build --prefix=$PWD/_dist -Dla_backend=mkl
```

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

### Dry Run: Inspect Settings Without Calculation

Source: https://context7.com/crest-lab/crest/llms.txt

Perform a dry run to preview settings and check for the `xtb` binary without executing any calculations. This is useful for verifying configurations.

```bash
# Usage: crest <input> -dry
crest struc.xyz -dry

# With a custom xtb binary name
crest struc.xyz -dry -xnam xtb6.4

# Expected output (truncated):
#  -------------------------------------------------------
#  Starting z-matrix sorting algorithm
#  CREST ensemble generation
#  ...
#  *No* calculation will be performed (dry run).

```

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

### Build CREST from Source (CMake)

Source: https://context7.com/crest-lab/crest/llms.txt

Clone the CREST repository, initialize and update submodules, then build using CMake with GNU compilers. An optional static build and test execution are also shown.

```bash
# Clone and initialize subprojects (tblite, gfnff, gfn0, etc.)
git clone https://github.com/crest-lab/crest.git
cd crest
git submodule init
git submodule update

# Build with GNU compilers
export FC=gfortran CC=gcc
cmake -B _build
make -C _build

# Optional: static build
cmake -B _build -DSTATICBUILD=true
make -C _build

# Optional: run tests
make test -C _build
```

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

### CMake Build and Test

Source: https://github.com/crest-lab/crest/blob/master/README.md

Build the CREST binary using make and optionally run tests. This command assumes the CMake build directory has been configured.

```bash
make -C _build
```

```bash
make test -C _build
```

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

### Configure CREGEN Thresholds

Source: https://context7.com/crest-lab/crest/llms.txt

Fine-tune CREGEN's ensemble comparison using energy window (-ewin), RMSD (-rthr), energy (-ethr), rotational constant (-bthr), and population (-pthr) thresholds. Options -notopo and -nowr disable topology checks and writing new files, respectively.

```bash
crest struc.xyz -cregen ensemble.xyz -ewin 4.0
```

```bash
crest struc.xyz -cregen ensemble.xyz -rthr 0.200
```

```bash
crest struc.xyz -cregen ensemble.xyz -ethr 0.10
```

```bash
crest struc.xyz -cregen ensemble.xyz -bthr 0.02
```

```bash
crest struc.xyz -cregen ensemble.xyz -pthr 0.10
```

```bash
crest struc.xyz -cregen ensemble.xyz -notopo
```

```bash
crest struc.xyz -cregen ensemble.xyz -nowr
```

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

### Meson Static Build Default

Source: https://github.com/crest-lab/crest/blob/master/README.md

The Meson build by default creates a statically linked binary. No specific flag is needed for static linking.

```bash
meson setup _build --prefix=$PWD/_dist
```

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

### Initialize Git Submodules

Source: https://github.com/crest-lab/crest/blob/master/README.md

Initialize and update git submodules before compiling. This is a prerequisite for building from source.

```bash
git submodule init
git submodule update
```

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

### Initialize and Update Git Submodules

Source: https://github.com/crest-lab/crest/blob/master/subprojects/README.md

Use these commands to initialize and update external projects managed as git submodules.

```bash
git submodule init
git submodule update
```

```bash
git submodule update --remote
```

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

### Tautomer Sampling with CREST

Source: https://context7.com/crest-lab/crest/llms.txt

Generate prototropic tautomers by combining protonation and deprotonation steps. Control the energy window, iteration count, and solvent model.

```bash
# Tautomer screening of guanine with 10 kcal/mol window
crest struc.xyz -tautomerize -ewin 10.0
# Output: tautomers.xyz  (5 tautomers within 10 kcal/mol for guanine at GFN2-xTB)
```

```bash
# Reverse order: deprotonate first, then protonate
crest struc.xyz -tautomerize -trev
```

```bash
# Set number of protonation/deprotonation cycles (default 2)
crest struc.xyz -tautomerize -iter 3
```

```bash
# In implicit solvent
crest struc.xyz -tautomerize -alpb h2o -ewin 15.0
```

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

### Structural Analysis Utilities with CREST

Source: https://context7.com/crest-lab/crest/llms.txt

Standalone tools for RMSD calculations, topology analysis, z-matrix sorting, thermochemical data, and file splitting. Use '-constrain' to write a sample constraint file.

```bash
# Calculate RMSD between two structures (Angstroms)
crest -rmsd struct1.xyz struct2.xyz
```

```bash
# Calculate heavy-atom RMSD only
crest -rmsdheavy struct1.xyz struct2.xyz
```

```bash
# Analyze topology of a structure (connectivity, bond orders, etc.)
crest -testtopo struc.xyz
```

```bash
# Sort z-matrix of input structure
crest -zsort struc.xyz
```

```bash
# Calculate thermochemical data for a single structure
# (requires 'vibspectrum' file with vibrational frequencies in TM format)
crest -thermo struc.xyz
```

```bash
# Split a multi-structure ensemble into separate directories under ./SPLIT/
crest -splitfile ensemble.xyz
```

```bash
# Split only structures 5 through 20
crest -splitfile ensemble.xyz 5 20
```

```bash
# Write sample constraint file for atoms 2,5,7 without running search
crest -constrain 2,5,7
```

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

### Protonation Site Sampling with CREST

Source: https://context7.com/crest-lab/crest/llms.txt

Enumerate protonation sites (protomers) of a molecule using LMO approach. Specify custom energy windows or create metal/ion adducts using '-swel'.

```bash
# Protonation of uracil (gas phase, GFN2-xTB)
crest struc.xyz -protonate
# Output: protonated.xyz  (default energy window: 30 kcal/mol)
```

```bash
# With a custom energy window
crest struc.xyz -protonate -ewin 20.0
```

```bash
# Create metal/ion adducts instead of protonation (e.g., Cs+)
crest struc.xyz -protonate -swel Cs+
```

```bash
# Other examples of -swel:
crest struc.xyz -protonate -swel Na+
crest struc.xyz -protonate -swel Ca2+
crest struc.xyz -protonate -swel Li+
```

```bash
# Deprotonation site sampling
crest struc.xyz -deprotonate
# Output: deprotonated.xyz
```

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

### Perform Quick Conformational Search in CREST

Source: https://context7.com/crest-lab/crest/llms.txt

The -quick option performs a reduced conformational search for a faster, rough ensemble.

```bash
crest struc.xyz -quick
```

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

### Set Executable Properties

Source: https://github.com/crest-lab/crest/blob/master/CMakeLists.txt

Configures properties for the executable, including Fortran module directory, runtime output directory, and output name.

```cmake
set_target_properties(
  ${PROJECT_NAME}-exe
  PROPERTIES
  Fortran_MODULE_DIRECTORY ${PROJECT_BINARY_DIR}/include
  RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}
  OUTPUT_NAME "${PROJECT_NAME}"
)
```

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

### MSREACT: Mass Spectra Fragment Generator with CREST

Source: https://context7.com/crest-lab/crest/llms.txt

Generate fragmentation products for mass spectrometry simulation by applying repulsive potentials. Control attractive potentials, shifts, bond distances, and output filtering.

```bash
# Start MSREACT mode on an input structure
crest struc.xyz -msreact
```

```bash
# Disable attractive H–LMO potential
crest struc.xyz -msreact -msnoattrh
```

```bash
# Perform 10 optimizations with randomly shifted atom positions
crest struc.xyz -msreact -msnshifts 10
```

```bash
# Maximum bond distance for repulsive potential (default 3 bonds)
crest struc.xyz -msreact -msnbonds 2
```

```bash
# Print only 50 random fragments
crest struc.xyz -msreact -msnfrag 50
```

```bash
# Print only non-dissociated structures (isomers only)
crest struc.xyz -msreact -msiso
```

```bash
# Print only dissociated structures (no isomers)
crest struc.xyz -msreact -msnoiso
```

```bash
# Deduplicate by InChI codes (requires obabel in PATH)
crest struc.xyz -msreact -msinchi
```

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

### Apply Cartesian Constraints in CREST

Source: https://context7.com/crest-lab/crest/llms.txt

Generate a sample constraint file using -constrain, then run the constrained search with -cinp. Custom force constants can be set with -fc.

```bash
crest struc.xyz -constrain 1-4
# Creates: .xcontrol.sample
```

```bash
crest struc.xyz -cinp .xcontrol.sample
```

```bash
# The .xcontrol.sample file looks like:
# $constrain
#   atoms: 1-4
#   force constant=0.5
# $end
```

```bash
crest struc.xyz -cinp .xcontrol.sample -fc 1.0
```

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

### Enable Unit Tests

Source: https://github.com/crest-lab/crest/blob/master/CMakeLists.txt

Configures and enables unit testing if the WITH_TESTS option is set. This typically involves adding a subdirectory for test sources.

```cmake
if (WITH_TESTS)
  enable_testing()
  add_subdirectory("test")
endif()
```

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

### Use CREST v4 iMTD-sMTD Workflow

Source: https://context7.com/crest-lab/crest/llms.txt

The -v4 flag enables the iMTD-sMTD workflow, serving as an alternative to the default iMTD-GC method.

```bash
crest struc.xyz -v4
```

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

### Define Executable Include Directories

Source: https://github.com/crest-lab/crest/blob/master/CMakeLists.txt

Specifies include directories for the executable, differentiating between private and build interfaces.

```cmake
target_include_directories(
   ${PROJECT_NAME}-exe 
   PRIVATE 
   ${PROJECT_SOURCE_DIR}/include
   $<BUILD_INTERFACE:${PROJECT_BINARY_DIR}/include>
)
```

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

### CMake Static Build Option

Source: https://github.com/crest-lab/crest/blob/master/README.md

Configure a static build with CMake by setting the STATICBUILD option to true. This is an alternative to the default dynamic build.

```bash
cmake -B _build -DSTATICBUILD=true
```

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

### Set Energy Window for Fragment Sorting

Source: https://context7.com/crest-lab/crest/llms.txt

Adjust the energy window for fragment sorting. The default is 200 kcal/mol.

```bash
crest struc.xyz -msreact -ewin 150.0
```

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

### Configure Parallel Execution and MD Time Step in CREST

Source: https://context7.com/crest-lab/crest/llms.txt

Use -T to set the number of threads for parallel execution and -tstep to define the MD time step in femtoseconds.

```bash
crest struc.xyz -T 8 -tstep 5
```

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

### Create Test Executable in CMake

Source: https://github.com/crest-lab/crest/blob/master/test/CMakeLists.txt

Adds an executable target for running tests. It compiles the specified test source files and links them against the project's static library and the test-drive library.

```cmake
add_executable(
  "${PROJECT_NAME}-tester"
  "${test-srcs}"
)
target_link_libraries(
  "${PROJECT_NAME}-tester"
  PRIVATE
  "lib-${PROJECT_NAME}-static"
  "test-drive::test-drive"
)
```

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

### Set Static Library Properties

Source: https://github.com/crest-lab/crest/blob/master/CMakeLists.txt

Configures properties for the static library, such as the Fortran module directory, archive output location, and position-independent code.

```cmake
set_target_properties(
   "lib-${PROJECT_NAME}-static"
   PROPERTIES
   Fortran_MODULE_DIRECTORY "${PROJECT_BINARY_DIR}/include"
   ARCHIVE_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}"
   POSITION_INDEPENDENT_CODE ON
   OUTPUT_NAME "${PROJECT_NAME}"
 )
```

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

### Optimize Trajectory Frames with CREST

Source: https://context7.com/crest-lab/crest/llms.txt

Optimize every structure in an existing MD trajectory or ensemble file without performing a new conformational search. Use '-screen' for multilevel optimization with progressive thresholds and sorting.

```bash
# Optimize every frame in a trajectory (no sorting)
crest -mdopt xtb.trj
# Output: crest_ensemble.xyz (optimized frames, unsorted)
```

```bash
# Multilevel optimization with progressive thresholds + sorting after each step
crest -screen ensemble.xyz
# Output: crest_ensemble.xyz (sorted, deduplicated)
```

```bash
# With a custom xtb binary
crest -mdopt xtb.trj -xnam xtb6.4
```

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

### Ensemble Comparison with CREST

Source: https://context7.com/crest-lab/crest/llms.txt

Compare two independently generated ensembles to quantify overlap and equivalences. Ensure structures have the same atom ordering. Limit comparison to a specific number of conformers.

```bash
# Compare ensemble1.xyz and ensemble2.xyz (must have same atom ordering)
crest struc.xyz -compare ensemble1.xyz ensemble2.xyz
```

```bash
# Limit comparison to the 5 lowest conformers from each ensemble
crest struc.xyz -compare ensemble1.xyz ensemble2.xyz -maxcomp 5
```

```bash
# Compare NMR-equivalent nuclei in a rotamer ensemble
crest struc.xyz -eqv
crest struc.xyz -nmr
```

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

### Configure Static Library Linking

Source: https://github.com/crest-lab/crest/blob/master/CMakeLists.txt

Defines linking for the static library, including OpenMP support and conditional linking of various optional libraries based on build flags.

```cmake
set(LINK_OpenMP FALSE)
if(WITH_OpenMP AND NOT STATICBUILD)
  set(LINK_OpenMP TRUE)
endif()

target_link_libraries(
   "lib-${PROJECT_NAME}-static"
   PUBLIC
   ${BLAS_LIBRARIES}
   ${LAPACK_LIBRARIES}
   $<$<BOOL:${LINK_OpenMP}>:OpenMP::OpenMP_Fortran>
   $<$<BOOL:${WITH_TBLITE}>:tblite::tblite>
   $<$<BOOL:${WITH_GFN0}>:gfn0::gfn0>
   $<$<BOOL:${WITH_GFNFF}>:gfnff::gfnff>
   $<$<BOOL:${WITH_LIBPVOL}>:pvol::pvol>
   $<$<BOOL:${WITH_TOMLF}>:toml-f::toml-f>
   $<$<BOOL:${WITH_LWONIOM}>:lwoniom::lwoniom>
   $<$<BOOL:${STATICBUILD}>:-static>
)
```

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

### Link Executable to Static Library

Source: https://github.com/crest-lab/crest/blob/master/CMakeLists.txt

Links the executable target to the static library and conditionally links the '-static' flag.

```cmake
target_link_libraries(
   ${PROJECT_NAME}-exe
   PRIVATE
   "lib-${PROJECT_NAME}-static"
   $<$<BOOL:${STATICBUILD}>:-static>
)
```

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

### Apply Implicit Solvation in CREST

Source: https://context7.com/crest-lab/crest/llms.txt

Use -g for GBSA solvation (e.g., chloroform) or -alpb for ALPB solvation (e.g., water), which is generally more accurate.

```bash
crest struc.xyz -g chcl3
```

```bash
crest struc.xyz -alpb h2o
```

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

### Set Geometry Optimization Level in CREST

Source: https://context7.com/crest-lab/crest/llms.txt

Control the optimization level for xTB calculations using the -opt flag. Available options include vloose, loose, normal, tight, and vtight (default).

```bash
crest struc.xyz -opt tight
```

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

### Deduplicate by MolBar Codes

Source: https://context7.com/crest-lab/crest/llms.txt

Use this command to deduplicate structures based on MolBar codes. Requires molbar to be in the system's PATH.

```bash
crest struc.xyz -msreact -msmolbar
```

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

### Apply Automatic Bond Constraints in CREST

Source: https://context7.com/crest-lab/crest/llms.txt

Use -cbonds to apply automatic bond constraints derived from the topology, useful for GFN-FF. Use -nocbonds to disable this feature.

```bash
crest struc.xyz -cbonds
```

```bash
crest struc.xyz -nocbonds
```

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

### Conformational Entropy Calculation with CREST

Source: https://context7.com/crest-lab/crest/llms.txt

Compute conformational entropy and molecular heat capacity using the msRRHO approximation. Adjust temperature range, frequency scaling, and thresholds for accuracy.

```bash
# Entropy calculation using the iMTD-sMTD workflow
crest struc.xyz -entropy
```

```bash
# Temperature range for entropy evaluation (default: 280-380 K in 10 K steps)
crest struc.xyz -entropy -trange 250 400 10
```

```bash
# Frequency scaling factor (default 1.0)
crest struc.xyz -entropy -fscal 0.9
```

```bash
# Vibrational/rotational entropy interpolation threshold (default 25.0 cm^-1)
crest struc.xyz -entropy -sthr 30.0
```

```bash
# Imaginary mode inversion cutoff (default -50.0 cm^-1)
crest struc.xyz -entropy -ithr -100.0
```

```bash
# Population coverage threshold for msRRHO average (default 0.9 = 90%)
crest struc.xyz -entropy -ptot 0.95
```

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

### Sort Ensemble with CREGEN

Source: https://context7.com/crest-lab/crest/llms.txt

Use CREGEN to deduplicate and rank ensembles or MD trajectories. Specify the reference structure, trajectory file, and optionally energy window, RMSD, and energy thresholds.

```bash
crest struc.xyz -cregen xtb.trj -ewin 100.0
```

```bash
crest struc.xyz -cregen ensemble.xyz
```

```bash
crest struc.xyz -cregen ensemble.xyz -rthr 0.125 -ethr 0.05
```

```bash
crest struc.xyz -cregen ensemble.xyz -temp 298.15
```

```bash
crest struc.xyz -cregen ensemble.xyz -cluster 5
```

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

### Set Shared Library Properties

Source: https://github.com/crest-lab/crest/blob/master/CMakeLists.txt

Configures properties for the shared library, such as module directory, library output location, versioning, and output name.

```cmake
set_target_properties(
      "lib-${PROJECT_NAME}-shared"
      PROPERTIES
      Fortran_MODULE_DIRECTORY "${PROJECT_BINARY_DIR}/include"
      LIBRARY_OUTPUT_DIRECTORY "${PROJECT_BINARY_DIR}"
      OUTPUT_NAME "${PROJECT_NAME}"
      VERSION "${PROJECT_VERSION}"
      SOVERSION "${PROJECT_VERSION_MAJOR}"
   )
```

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

### Define Executable Target

Source: https://github.com/crest-lab/crest/blob/master/CMakeLists.txt

Adds an executable target to the build, specifying its source files.

```cmake
add_executable(
  ${PROJECT_NAME}-exe
  ${prog}
)
```

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

### Configure Shared Library Linking

Source: https://github.com/crest-lab/crest/blob/master/CMakeLists.txt

Defines linking for the shared library, including OpenMP support and conditional linking of various optional libraries.

```cmake
target_link_libraries(
      "lib-${PROJECT_NAME}-shared"
      PUBLIC
      ${BLAS_LIBRARIES}
      ${LAPACK_LIBRARIES}
      $<$<BOOL:${WITH_OpenMP}>:OpenMP::OpenMP_Fortran>
      $<$<BOOL:${WITH_TBLITE}>:tblite::tblite>
      $<$<BOOL:${WITH_GFN0}>:gfn0::gfn0>
      $<$<BOOL:${WITH_GFNFF}>:gfnff::gfnff>
      $<$<BOOL:${WITH_LIBPVOL}>:pvol::pvol>
      $<$<BOOL:${WITH_TOMLF}>:toml-f::toml-f>
      $<$<BOOL:${WITH_LWONIOM}>:lwoniom::lwoniom>
   )
```

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

### Set Molecular Dynamics Length in CREST

Source: https://context7.com/crest-lab/crest/llms.txt

Control the total length of the MD simulation using -mdlen. It can be set to a specific value in picoseconds or as a multiplier of the default.

```bash
crest struc.xyz -mdlen 10
```

```bash
crest struc.xyz -mdlen x1.5
```

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

### Perform NCI Sampling in CREST

Source: https://context7.com/crest-lab/crest/llms.txt

The -nci flag initiates Non-Covalent Interaction sampling for complexes. The -wscal option scales the ellipsoidal wall potential.

```bash
crest struc.xyz -nci
```

```bash
crest struc.xyz -nci -wscal 1.2
```

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

### Control Parallel Threads in CREST

Source: https://context7.com/crest-lab/crest/llms.txt

Set the total number of threads for OpenMP parallelism using the -T option or the OMP_NUM_THREADS environment variable. For OpenBLAS builds, set OPENBLAS_NUM_THREADS to 1 to prevent conflicts.

```bash
crest struc.xyz -T 16
```

```bash
export OMP_NUM_THREADS=16
crest struc.xyz
```

```bash
export OPENBLAS_NUM_THREADS=1
crest struc.xyz -T 8
```

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

### Set Molecular Charge in CREST

Source: https://context7.com/crest-lab/crest/llms.txt

Use the -chrg option to specify the molecular charge for calculations. This is useful for ionic species.

```bash
crest struc.xyz -chrg 1
```

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

### Add Tests to CTest in CMake

Source: https://github.com/crest-lab/crest/blob/master/test/CMakeLists.txt

Registers each defined test with CTest. This allows tests to be discovered and run using the CTest command-line tool.

```cmake
foreach(t IN LISTS tests)
  add_test("${PROJECT_NAME}/${t}" "${PROJECT_NAME}-tester" "${t}")
endforeach()
```

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

### Define Test Names in CMake

Source: https://github.com/crest-lab/crest/blob/master/test/CMakeLists.txt

Sets a list of test names that will be used to generate test executables and CTest entries. These names are converted to C identifiers for use in the build system.

```cmake
set(
  tests
  "tblite"
  "gfnff"
  "gfn0"
  "gfn0occ"
  "CN"
  "optimization"
)
set(
  test-srcs
  "testmol.f90"
  "helpers.f90"
  "main.f90"
)
foreach(t IN LISTS tests)
  string(MAKE_C_IDENTIFIER ${t} t) 
  list(APPEND test-srcs "test_${t}.F90")
endforeach()
```

=== COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.