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a | |
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acf (Unix, Windows) |
This module implements the functionality to compute Autocorrelation Functions (ACF)
and do some transformations of them
The assumption is that data are provided in a matrix form - not vectors, so we can handle the
data of arbitrary dimensionality |
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autoconnect (Unix, Windows) |
This module implements functions to determine the connectivity
matrix in molecular systems. |
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b | |
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build (Unix, Windows) |
This module implements functions for building molecular structures |
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c | |
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compute_hprime (Unix, Windows) |
This module computes the transition dipole moments in the basis of KS
orbitals extracted from QE |
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CP2K_methods (Unix, Windows) |
This module implements functions for processing the CP2K inputs and outputs. |
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cube_file_methods (Unix, Windows) |
This module implements functions for processing with cube files |
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d | |
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data_conv (Unix, Windows) |
This module implements various functions for data conversions and data transformations |
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data_outs (Unix, Windows) |
This module implements various functions for printing out data |
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data_read (Unix, Windows) |
This module implements various functions for getting data from files |
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data_stat (Unix, Windows) |
This module implements various functions for data analysis |
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decoherence_times (Unix, Windows) |
This module implements functions to compute decoherence times and relevant quantities |
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DFTB_methods (Unix, Windows) |
This module implements functions for dealing with the outputs from DFTB+ package |
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e | |
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ERGO_methods (Unix, Windows) |
This module implements functions for dealing with the outputs of the ErgoSCF package |
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f | |
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fgr_py (Unix, Windows) |
This module implements the auxiliary Python functions for dealing with
various kinds of FGR calculations (as implemented in C++) |
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fit (Unix, Windows) |
This module implements a linear regression method and several pre-defined fit functions |
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fix_motion (Unix, Windows) |
This module implements functions for removing translation of CM and
rotation around it |
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ft (Unix, Windows) |
This module implements the functionality to compute Fourier Transforms |
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g | |
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Gaussian_methods (Unix, Windows) |
This module implements functions for processing the Gaussian inputs and outputs. |
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h | |
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hpc_utils (Unix, Windows) |
This module implements the functionality to run distributed calculations
on the HPC |
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i | |
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influence_spectrum (Unix, Windows) |
This module implements functions to compute the autocorrelation functions
and their Fourier spectra (influence spectra) of the time-series of matrices (e.g.
of the "vibronic" Hamiltonian data sampled along the MD trajectories) |
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init_ensembles (Unix, Windows) |
This module implements functions that allocate memory for ensembles of trajectories |
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init_system (Unix, Windows) |
This module implements functions to initialize System() objects |
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l | |
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LAMMPS_methods (Unix, Windows) |
This module implements various functions for computing with LAMMPS |
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libra_py |
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libra_py.acf |
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libra_py.autoconnect |
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libra_py.build |
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libra_py.CP2K_methods |
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libra_py.cube_file_methods |
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libra_py.data_conv |
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libra_py.data_outs |
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libra_py.data_read |
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libra_py.data_stat |
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libra_py.DFTB_methods |
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libra_py.dynamics.exact.save |
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libra_py.dynamics.heom.plot |
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libra_py.ERGO_methods |
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libra_py.fgr_py |
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libra_py.fit |
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libra_py.fix_motion |
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libra_py.ft |
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libra_py.Gaussian_methods |
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libra_py.hpc_utils |
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libra_py.hungarian |
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libra_py.influence_spectrum |
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libra_py.init_ensembles |
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libra_py.init_system |
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libra_py.LAMMPS_methods |
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libra_py.LoadGAFF |
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libra_py.LoadMMFF94 |
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libra_py.LoadMolecule |
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libra_py.LoadPT |
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libra_py.LoadTRIPOS |
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libra_py.LoadUFF |
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libra_py.models.Faist_Levine |
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libra_py.models.Henon_Heiles |
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libra_py.models.Holstein |
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libra_py.models.Libra |
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libra_py.models.LVC |
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libra_py.models.Martens |
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libra_py.models.SSY |
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libra_py.models.Tully |
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libra_py.namd |
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libra_py.normal_modes |
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libra_py.nve_md |
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libra_py.parse_gamess |
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libra_py.pdos |
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libra_py.probabilities |
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libra_py.QE_methods |
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libra_py.QE_utils |
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libra_py.regexlib |
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libra_py.scan |
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libra_py.scf |
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libra_py.tsh |
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libra_py.tsh_stat |
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libra_py.unavoided |
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libra_py.units |
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libra_py.vesta2qe |
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libra_py.workflows.nbra.compute_hprime |
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libra_py.workflows.nbra.compute_properties |
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libra_py.workflows.nbra.decoherence_times |
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libra_py.workflows.nbra.lz |
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libra_py.workflows.nbra.mapping |
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libra_py.workflows.nbra.qsh |
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libra_py.workflows.nbra.step2 |
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libra_py.workflows.nbra.step2_analysis |
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libra_py.workflows.nbra.step2_dftb |
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libra_py.workflows.nbra.step2_ergoscf |
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libra_py.workflows.nbra.step2_many_body |
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libra_py.workflows.nbra.step3 |
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libra_py.workflows.nbra.step4 |
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LoadMolecule (Unix, Windows) |
This module implements functions for loading data into a Chemobject
objects - by reading formatted data files. |
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m | |
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mapping (Unix, Windows) |
This module implements the methods to map single-electron properties (e.g. KS basis)
to many-electron ones (e.g. Slater Determinat basis) |
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models_Faist_Levine (Unix, Windows) |
This module implements the 1D, 2-level models of Faist and Levine |
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models_Henon_Heiles (Unix, Windows) |
This module implements the Henon-Heiles model potential |
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models_Holstein (Unix, Windows) |
This module implements the Henon-Heiles Hamiltonians |
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models_Libra (Unix, Windows) |
The Libra models - well, they are not necessarily introduced here for the
first time (the special cases might have been already used in different context),
but these are the models we define for the internal test purposes |
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models_LVC (Unix, Windows) |
This module implements Linear Vibronic Coupling (LVC) Hamiltonian |
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models_Martens (Unix, Windows) |
This module implements Eckart barrier potentials as used by Martens |
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models_SSY (Unix, Windows) |
This module implements the 2D, 2-level model of Shenvi-Subotnik-Yang |
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models_Tully (Unix, Windows) |
This module implements 3 Tully models for testing NA-MD dynamics |
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n | |
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namd (Unix, Windows) |
This module implements functions for running NA-MD |
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nve_md (Unix, Windows) |
This module implements a number of auxiliary functions for simpler
implementation of classical MD simulations |
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p | |
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pdos (Unix, Windows) |
This module implements functions for computing Projected (Partial)
Densities of States (pDOS) from various outputs |
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probabilities (Unix, Windows) |
This module aims to implement the probabilities to find system in a given state |
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q | |
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QE_methods (Unix, Windows) |
This module implements functions for dealing with the outputs from QE (Quantum Espresso) package.
This package contains the following functions:
* cryst2cart(a1,a2,a3,r)
* read_qe_schema(filename, verbose=0)
* read_qe_index(filename, orb_list, verbose=0)
* read_qe_wfc_info(filename, verbose=0)
* read_qe_wfc_grid(filename, verbose=0)
* read_qe_wfc(filename, orb_list, verbose=0)
* read_md_data(filename)
* read_md_data_xyz(filename, PT, dt)
* read_md_data_xyz2(filename, PT)
* read_md_data_cell(filename)
* out2inp(out_filename,templ_filename,wd,prefix,t0,tmax,dt)
* out2pdb(out_filename,T,dt,pdb_prefix)
* out2xyz(out_filename,T,dt,xyz_filename)
* xyz2inp(out_filename,templ_filename,wd,prefix,t0,tmax,dt)
* get_QE_normal_modes(filename, verbosity=0)
* run_qe(params, t, dirname0, dirname1)
* read_info(params)
* read_all(params)
* read_wfc_grid(params) |
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qsh (Unix, Windows) |
Implementation of the QuasiStochastic Hamiltonian method
Akimov, J. Phys. Chem. Lett. 2017, 8, 5190 |
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s | |
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scan (Unix, Windows) |
This module implements functions for
performing various types of calculations related to PES scans |
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step2 (Unix, Windows) |
This module implements functions for doing NAC calculaitons in the 1-electron
basis of KS orbitals, withe the QE package |
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step2_analysis (Unix, Windows) |
This module implements functions for postprocessing the data generated by the
step2 module functions |
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step2_dftb (Unix, Windows) |
This module implements functions for doing NAC calculaitons in the 1-electron
basis of KS orbitals, with the DFTB+ package. It also implements functions for obtaining
TD-DFTB energies with the DFTB+ package. |
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step2_ergoscf (Unix, Windows) |
This module implements functions for doing NAC calculaitons in the 1-electron
basis of MOs, with the ErgoSCF package |
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step2_many_body (Unix, Windows) |
This module implements functions for computing the overlap and nonadiabatic couplings matrices. |
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t | |
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tsh (Unix, Windows) |
This module implements the generic function for TSH calculations as well as some
customized versions of TSH recipes |
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tsh_stat (Unix, Windows) |
This module implements various functions for analysis of the statistics
in the TSH calculations |
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u | |
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units (Unix, Windows) |
This module defines the units conversion factors and implements the
functions for unit conversion |