pysoftk.htp_tools package
Submodules
pysoftk.htp_tools.calculator_htp module
- class pysoftk.htp_tools.calculator_htp.Htp(ending)[source]
Bases:
object- Class enabling High-throughput calculations in different
created folders for provided molecules.
- ending
Extension of the molecular format used to perform a search within many directories.
- Type:
str
- xtb_path
Path where the xtb executable is located.
- Type:
str
- xyz_geom
Name of the supplied molecule in .xyz format
- Type:
str
- init_dir
Path where the calculation is starting (optional)
- Type:
str
- num_cores
Number of cores which the GFN-XTB2 code will use.
- Type:
int, optional
- threshold
Level of geometry optimization required as defined in GFN-XTB2 code.
- Type:
str, optional
Note
This class requires tqdm, GFN-XTB and/or PYSCF semiempirical installation to be used.
- htp_xtb_ff(path_xtb, max_work, cores, threshold='crude')[source]
Function to perform a parallel concurrent calculation at the gfn-ff level of theory.
- Parameters:
path_xtb (str) – Path where the xtb executable is located.
max_work (int) – Number of maximum amount of workers in a concurrent job default is 1.
num_cores (int, optional) – Number of cores which the GFN-XTB2 code will use.
threshold (str, optional) – Level of geometry optimization required as defined in GFN-XTB2 code.
- Returns:
A relaxed structure as produced by the GFN-XTB2 code.
- Return type:
None
- htp_xtb_gfn(path_xtb, max_work, cores, threshold='crude')[source]
Function to perform a parallel concurrent calculation at the gfn-xtb level of theory.
- Parameters:
path_xtb (str) – Path where the xtb executable is located.
max_work (int) – Number of maximum amount of workers in a concurrent job default is 1.
num_cores (int, optional) – Number of cores which the GFN-XTB2 code will use.
threshold (str, optional) – Level of geometry optimization required as defined in GFN-XTB2 code.
- Returns:
A relaxed structure as produced by the GFN-XTB2 code.
- Return type:
None
- static xtb_ff(xtb_path, xyz_geom, init_dir, num_cores=None, threshold=None)[source]
Function invoking GFN-XTB Force-Field implementation for geometry optimization.
- Parameters:
xtb_path (str) – Path where the GFN-XTB2 executable is located
num_cores (int, optional) – Number of cores used by the GFN-XTB code.
threshold (str, optional) – Level of geometry optimization required as defined in GFN-XTB2 code.
xyz_geom (str) – Provided geometry to be relaxed.
init_dir (str) – Root path directory where folders containing the structures are found.
- Returns:
output – File name output.log containing the optimization process carried out by GFN-XTB2.
- Return type:
str
- static xtb_gfn(xtb_path, xyz_geom, init_dir, num_cores=None, threshold=None)[source]
Function invoking GFN-XTB Force-Field implementation for geometry optimization.
- Parameters:
xtb_path (str) – Path where the GFN-XTB2 executable is located
num_cores (int, optional) – Number of cores which the GFN-XTB2 code will use.
threshold (str, optional) – Level of geometry optimization required as defined in GFN-XTB2 code.
xyz_geom (str) – Provided geometry to be relaxed.
init_dir (str) – Root path directory where folders containing the structures are found.
- Returns:
output – File name output.log containing the optimization process carried out by GFN-XTB2.
- Return type:
str