sith.g09_stretching.from_extreme package

Submodules

sith.g09_stretching.from_extreme.info_from_opt.continuous_e2e(pattern, index1, index2, dir_output='e2e_continuous')

From a set of configurations in xyz files with pattern <all><pattern><all>.xyz, it guarantees that consecutive changes in the distance between the atoms with index1 and index2 are lower than 0.2A.

Parameters:

• pattern (str) – pattern of the input files. All the files with <all><pattern><all>.xyz will be read.

• index1 (int) – index of the first atom to align in the x axis. 1-base indexing.

• index2 (int) – index of the second atom to align in the x axis. 1-base indexing.

• dir_output (str. Default='e2e_continuous') – directory where to save the output files.

Returns:

• (ase.Atoms) new trajectory with continuous distance between index1 and

• index2. It creates the xyz files in dir_output.

sith.g09_stretching.from_extreme.info_from_opt.delta_angles_continuous(d_ij, nrs)

Make the difference of the angles continuous considering the periodicity of them.

Parameters:

• d_ij (numpy.Array) – set of delta dofs with form [structure][DOF]

• nrs (int) – Number of distances.

Return type:

(numpy.Array) new set of delta DOFs with delta angles continuous.

Note

Here, it is assumed that the first <nrs> DOFs in d_ij are distances and the rest are angles.

sith.g09_stretching.from_extreme.info_from_opt.info_from_opt(logfile, pattern)

Extracts configurations from a gaussian optimization trajectory and removes the structures that are outliers in the total energy.

Parameters:

• logfile (str) – gaussian log file.

• pattern (str) – pattern of the output. The results are xyz files called <pattern><i>.xyz

Returns:

• (ase.Atoms) new trajectory without the outliers. It creates the xyz files

• in between.

Note

You can use sith.g09_stretching.from_extreme.info_from_opt.reduce_struct() to make the DOFs of output trajectory continuous.

sith.g09_stretching.from_extreme.info_from_opt.reduce_structs(dir, pattern, print_reduced=False)

Check all the <all>-dofs.dat files and remove those files that represent irrelevant changes. It creates intermedias to guarantee continuous dofs.

Parameters:

• dir (str) – path to the directory containing all the <all>-dofs.dat files.

• pattern (str) – pattern for the output files, all of them will be then <pattern><i>.dat

Returns:

• (numpy.array) new set of DOFs [structure][DOF], which are reduced. In

• between, it also creates all <pattern><i>,dat.

Module contents

continuous_path

[script] sith/g09_stretching/from_extreme/continuous_path.sh

Creates the com files from the a set of xyz structures, and submit the jobs

with :bashscript: (-S here

refers to these subjobs)

-c Use this flag to run in a cluster. When -p is not defined, and you run in

a slurm job manager system, the number of processors is equal to the

number of cores asked in the submission of the job.

-i <index1,index2> indexes of the atoms used for constraining the distance

of the intermedia structures when optimizing. If this flag is not used

and a pdb is given through flag ‘-t’, indexes 1 and 2 will correspond to

the CH3 atoms in ACE and NME residues defined in the pdb if they exist.

-l <xc,base=”bmk,6-31+g”> level of DFT theory.

-n <name> this script will collect all the <name>.xyz files sorted in

alphabetic order as initial path. If this is a directory, this script

will create a subdirectory there called ‘conopt’ and copy the

<name>.xyz files to that subdirectory first.

-p <processors=1> number of processors per gaussian job. See description of

flag -c.

-S <job_options=’’> options for submitting a new job. This flag only makes

sense in slurm cluster. Please, do not include a name (-J), nor the

number of cores (-n, use -p for this). The input should be as in the next

example: "–partition=cpu –nice".

-t <template.pdb> pdb file used to read the indexes if -i is not

used.

-v verbose

-h prints this message.

workflow_from_extreme

[script] sith/g09_stretching/from_extreme/workflow_from_extreme.sh

This tool creates the files to do the sith analysis by optimizing a molecule,

then takes the intermedia steps and prepares a constrained optimization of each

one of them with :bashscript:

after creating intermedias states that guarantee continuity in the degrees of

freedom. This script submits in parallel each one of those optimizations with

:bashscript: (-S here refers

to these subjobs).

-a <alias> new name of the xyz file and subsequent files in directory

‘from_extreme’.

-c Use this flag to run in a cluster. When -p is not defined, and you run in

a slurm job manager system, the number of processors is equal to the

number of cores asked in the submission of the job.

-i <index1,index2> indexes of the atoms used for constraining the distance

of the intermedia structures when optimizing. If this flag is not used

but a pdb file is given (-t), indexes 1 and 2 will correspond to the CH3

atoms in ACE and NME residues defined in the pdb if they exist.

-l <xc,base=”bmk,6-31+g”> level of DFT theory.

-m <molecule> directory or coordinates file of configuration to be relaxed.

For example, "./AAA/" a trialanine configuration (‘last’ after

organizing all xyz files alphabetically all AAA*.xyz files in ./AAA/).

-p <processors=1> number of processors per gaussian job. See description of

flag -c.

-r Use it to restart, in which case no directory will be created and the new

<molecule>-optext.log is assumed to exist in the working directory.

-S <job_options=’’> options for submitting a new job. This flag only makes

sense in slurm cluster. Please, do not include a name (-J), nor the

number of cores (-n, use -p for this). The input should be as in the next

example: "–partition=cpu –nice".

-t <template.pdb> template pdb file to define indexes if -i is not used.

-v verbose.

-h prints this message.

Note

—-

The outputs are stored in a directory called ‘from_extreme’/

This tool requires gaussian and sklearn.

opt_and_forces

[script] sith/g09_stretching/from_extreme/opt_and_forces.sh

This code submits a gaussian job (typically an optimization) and uses the

output to compute the forces.

-c Use this flag to run in a cluster. When -p is not defined, and you run in

a slurm job manager system, the number of processors is equal to the

number of cores asked in the submission of the job.

-f <com file> name of the gaussian input file without extension (.com). The

output is has the same name, but .log extension.

-F use this flag fo AVIOD force calculation after optimization.

-p <processors=1> number of processors per gaussian job. See description of

flag -c.

-P <pattern=’conopt’> pattern to be replaced by ‘forces’ in the name of the

output files of the optimization when submitting the forces.

-S <job_options=’’> options for submitting a new job. This flag only makes

sense in slurm cluster. Please, do not include a name and add the options

as in the next example: “–partition=cpu –nice”.

-r if the optimization did not converge, restart it from the last

geometry.

-v verbose.

-h prints this message.

extr_dofs

[script] sith/g09_stretching/from_extreme/extr_dofs.sh

This tool extract the dofs of a set of xyz files using the gaussian tool

‘newzmat’. The ouput are files called <xyz file with pattern>-dofs.dat, where

pattern comes from -f flag.

-f <xyz files pattern>. The code will look for <pattern>.xyz

-h prints this message.