Summary
Semi Empirical Calculations
DebiChem - pakiety semiempiryczne
Ten metapakiet zainstaluje pakiety semiempiryczne, które mogą okazać się
użyteczne dla chemików.
Description
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DebiChem Semi Empirical Calculations packages
Official Debian packages with high relevance
cp2k
Ab Initio Molecular Dynamics
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Versions of package cp2k |
Release | Version | Architectures |
sid | 2023.2-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,s390x |
bookworm | 2023.1-2 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
bullseye | 8.1-9 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 6.1-2 | amd64,arm64,armhf,i386 |
stretch | 4.1-1 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 2.5.1-3 | amd64,armel,armhf,i386 |
upstream | 2024.3 |
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License: DFSG free
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CP2K is a program to perform simulations of solid state, liquid, molecular and
biological systems. It is especially aimed at massively parallel and linear
scaling electronic structure methods and state-of-the-art ab-initio molecular
dynamics (AIMD) simulations.
CP2K is optimized for the mixed Gaussian and Plane-Waves (GPW) method based on
pseudopotentials, but is able to run all-electron or pure plane-wave/Gaussian
calculations as well. Features include:
Ab-initio Electronic Structure Theory Methods using the QUICKSTEP module:
- Density-Functional Theory (DFT) energies and forces
- Hartree-Fock (HF) energies and forces
- Moeller-Plesset 2nd order perturbation theory (MP2) energies and forces
- Random Phase Approximation (RPA) energies
- Gas phase or Periodic boundary conditions (PBC)
- Basis sets include various standard Gaussian-Type Orbitals (GTOs), Pseudo-
potential plane-waves (PW), and a mixed Gaussian and (augmented) plane wave
approach (GPW/GAPW)
- Norm-conserving, seperable Goedecker-Teter-Hutter (GTH) and non-linear core
corrected (NLCC) pseudopotentials, or all-electron calculations
- Local Density Approximation (LDA) XC functionals including SVWN3, SVWN5,
PW92 and PADE
- Gradient-corrected (GGA) XC functionals including BLYP, BP86, PW91, PBE and
HCTH120 as well as the meta-GGA XC functional TPSS
- Hybrid XC functionals with exact Hartree-Fock Exchange (HFX) including
B3LYP, PBE0 and MCY3
- Double-hybrid XC functionals including B2PLYP and B2GPPLYP
- Additional XC functionals via LibXC
- Dispersion corrections via DFT-D2 and DFT-D3 pair-potential models
- Non-local van der Waals corrections for XC functionals including B88-vdW,
PBE-vdW and B97X-D
- DFT+U (Hubbard) correction
- Density-Fitting for DFT via Bloechl or Density Derived Atomic Point Charges
(DDAPC) charges, for HFX via Auxiliary Density Matrix Methods (ADMM) and
for MP2/RPA via Resolution-of-identity (RI)
- Sparse matrix and prescreening techniques for linear-scaling Kohn-Sham (KS)
matrix computation
- Orbital Transformation (OT) or Direct Inversion of the iterative subspace
(DIIS) self-consistent field (SCF) minimizer
- Local Resolution-of-Identity Projector Augmented Wave method (LRIGPW)
- Absolutely Localized Molecular Orbitals SCF (ALMO-SCF) energies for linear
scaling of molecular systems
- Excited states via time-dependent density-functional perturbation theory
(TDDFPT)
Ab-initio Molecular Dynamics:
- Born-Oppenheimer Molecular Dynamics (BOMD)
- Ehrenfest Molecular Dynamics (EMD)
- PS extrapolation of initial wavefunction
- Time-reversible Always Stable Predictor-Corrector (ASPC) integrator
- Approximate Car-Parrinello like Langevin Born-Oppenheimer Molecular Dynamics
(Second-Generation Car-Parrinello Molecular Dynamics (SGCP))
Mixed quantum-classical (QM/MM) simulations:
- Real-space multigrid approach for the evaluation of the Coulomb
interactions between the QM and the MM part
- Linear-scaling electrostatic coupling treating of periodic boundary
conditions
- Adaptive QM/MM
Further Features include:
- Single-point energies, geometry optimizations and frequency calculations
- Several nudged-elastic band (NEB) algorithms (B-NEB, IT-NEB, CI-NEB, D-NEB)
for minimum energy path (MEP) calculations
- Global optimization of geometries
- Solvation via the Self-Consistent Continuum Solvation (SCCS) model
- Semi-Empirical calculations including the AM1, RM1, PM3, MNDO, MNDO-d, PNNL
and PM6 parametrizations, density-functional tight-binding (DFTB) and
self-consistent-polarization tight-binding (SCP-TB), with or without
periodic boundary conditions
- Classical Molecular Dynamics (MD) simulations in microcanonical ensemble
(NVE) or canonical ensmble (NVT) with Nose-Hover and canonical sampling
through velocity rescaling (CSVR) thermostats
- Metadynamics including well-tempered Metadynamics for Free Energy
calculations
- Classical Force-Field (MM) simulations
- Monte-Carlo (MC) KS-DFT simulations
- Static (e.g. spectra) and dynamical (e.g. diffusion) properties
- ATOM code for pseudopotential generation
- Integrated molecular basis set optimization
CP2K does not implement conventional Car-Parrinello Molecular Dynamics (CPMD).
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molds
Półempiryczna struktura elektroniczna i dynamika molekularna
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Versions of package molds |
Release | Version | Architectures |
sid | 0.3.1-2 | amd64,arm64,armhf,i386,mips64el,ppc64el,riscv64,s390x |
jessie | 0.3.1-1 | amd64,armhf,i386 |
stretch | 0.3.1-1 | amd64,arm64,armhf,i386,mips64el,ppc64el |
buster | 0.3.1-1 | amd64,arm64,armhf,i386 |
bullseye | 0.3.1-1 | amd64,arm64,armhf,i386,mips64el,ppc64el,s390x |
bookworm | 0.3.1-1 | amd64,arm64,armhf,i386,mips64el,ppc64el,s390x |
trixie | 0.3.1-2 | amd64,arm64,armhf,i386,mips64el,ppc64el,riscv64,s390x |
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License: DFSG free
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MolDS jest półempiryczną strukturą elektroniczną i pakietem dynamiki molekularnej.
Udostępnia następujące funkcje:
- Metody półempiryczne CNDO2, INDO, ZINDO/S, MNDO, AM1 i PM3
- Stany wzbudzone poprzez interakcję pojedynczej konfiguracji (CIS)
- Korekty dyspersji dla AM1 (AM1-D) i PM3 (PM3-D)
- Korekcję parowania Gaussa (PDDG) w stosunku do PM3
- Jednopunktową, optymalizację geometrii, obliczenia typu Dynamika
molekularna (MD), Monte-Carlo (MC) i dynamikę polimerową (RPMD)
Obecnie MolDS dostarcza parametry dla elementów H, C, N, O i S.
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mopac
Molecular Orbital PACkage (MOPAC)
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Versions of package mopac |
Release | Version | Architectures |
trixie | 22.1.1-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 22.0.6+dfsg-1 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
sid | 22.1.1-2 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 23.0.3 |
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License: DFSG free
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MOPAC is a general-purpose semiempirical molecular orbital package for the
study of solid state and molecular structures and reactions.
The semiempirical Hamiltonians MNDO, AM1, PM3, PM6, RM1, MNDO-d and PM7 are
used in the electronic part of the calculation to obtain molecular orbitals,
the heat of formation and its derivative with respect to molecular geometry.
Using these results MOPAC calculates the vibrational spectra, thermodynamic
quantities, isotopic substitution effects and force constants for molecules,
radicals, ions, and polymers. For studying chemical reactions, a transition
state location routine and two transition state optimizing routines are
available. For users to get the most out of the program, they must understand
how the program works, how to enter data, how to interpret the results, and
what to do when things go wrong.
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mopac7-bin
Półempiryczna biblioteka chemii kwantowej (pliki binarne)
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Versions of package mopac7-bin |
Release | Version | Architectures |
bullseye | 1.15-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
buster | 1.15-6 | amd64,arm64,armhf,i386 |
sid | 1.15-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 1.15-7 | amd64,arm64,armel,armhf,i386,mips64el,ppc64el,riscv64,s390x |
bookworm | 1.15-6 | amd64,arm64,armel,armhf,i386,mips64el,mipsel,ppc64el,s390x |
stretch | 1.15-6 | amd64,arm64,armel,armhf,i386,mips,mips64el,mipsel,ppc64el,s390x |
jessie | 1.15-6 | amd64,armel,armhf,i386 |
Debtags of package mopac7-bin: |
field | chemistry |
role | program |
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License: DFSG free
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MOPAC zapewnia procedury rozwiązywania struktury elektronowej cząsteczek
na poziomie półempirycznym. Dostępne metody obejmują: MNDO, MINDO/3, AM1
i PM3.
Pakiet zawiera pliki binarne MOPAC7.
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xtb
semiempirical extended tight-binding program package
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Versions of package xtb |
Release | Version | Architectures |
bookworm | 6.5.1-3 | amd64,arm64,i386,mips64el,ppc64el,s390x |
sid | 6.7.0-1 | amd64,arm64,armhf,i386,mips64el,ppc64el,riscv64,s390x |
trixie | 6.7.0-1 | amd64,arm64,armhf,i386,mips64el,ppc64el,riscv64,s390x |
upstream | 6.7.1 |
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License: DFSG free
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xtb program performs semiempirical quantummechanical calculations. The
underlying effective Hamiltonian is derived from density functional tight
binding (DFTB). This implementation of the xTB Hamiltonian is currently
compatible with the zeroth, first and second level parametrisation for
geometries, frequencies and non-covalent interactions (GFN) as well as with
the ionisation potential and electron affinity (IPEA) parametrisation of the
GFN1 Hamiltonian. The generalized born (GB) model with solvent accessable
surface area (SASA) is also available available in this version. Ground state
calculations for the simplified Tamm-Danceoff approximation (sTDA) with the
vTB model are currently not implemented.
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