git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15017 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
@ -5,7 +5,7 @@
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LAMMPS Documentation
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====================
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10 May 2016 version
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11 May 2016 version
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-------------------
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Version info:
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@ -1509,65 +1509,67 @@ User packages
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The current list of user-contributed packages is as follows:
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| Package | Description | Author(s) | Doc page | Example | Pic/movie | Library |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-ATC <USER-ATC>` | atom-to-continuum coupling | Jones & Templeton & Zimmerman (1) | :doc:`fix atc <fix_atc>` | USER/atc | `atc <atc_>`_ | lib/atc |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-AWPMD <USER-AWPMD>` | wave-packet MD | Ilya Valuev (JIHT) | :doc:`pair_style awpmd/cut <pair_awpmd>` | USER/awpmd | - | lib/awpmd |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-CG-CMM <USER-CG-CMM>` | coarse-graining model | Axel Kohlmeyer (Temple U) | :doc:`pair_style lj/sdk <pair_sdk>` | USER/cg-cmm | `cg <cg_>`_ | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-COLVARS <USER-COLVARS>` | collective variables | Fiorin & Henin & Kohlmeyer (2) | :doc:`fix colvars <fix_colvars>` | USER/colvars | `colvars <colvars>`_ | lib/colvars |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-CUDA <USER-CUDA>` | NVIDIA GPU styles | Christian Trott (U Tech Ilmenau) | :doc:`Section accelerate <accelerate_cuda>` | USER/cuda | - | lib/cuda |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-DIFFRACTION <USER-DIFFRACTION>` | virutal x-ray and electron diffraction | Shawn Coleman (ARL) | :doc:`compute xrd <compute_xrd>` | USER/diffraction | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-DPD <USER-DPD>` | dissipative particle dynamics (DPD) | Larentzos & Mattox & Brennan (5) | src/USER-DPD/README | USER/dpd | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-DRUDE <USER-DRUDE>` | Drude oscillators | Dequidt & Devemy & Padua (3) | :doc:`tutorial <tutorial_drude>` | USER/drude | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-EFF <USER-EFF>` | electron force field | Andres Jaramillo-Botero (Caltech) | :doc:`pair_style eff/cut <pair_eff>` | USER/eff | `eff <eff_>`_ | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-FEP <USER-FEP>` | free energy perturbation | Agilio Padua (U Blaise Pascal Clermont-Ferrand) | :doc:`compute fep <compute_fep>` | USER/fep | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-H5MD <USER-H5MD>` | dump output via HDF5 | Pierre de Buyl (KU Leuven) | :doc:`dump h5md <dump_h5md>` | - | - | lib/h5md |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-INTEL <USER-INTEL>` | Vectorized CPU and Intel(R) coprocessor styles | W. Michael Brown (Intel) | :doc:`Section accelerate <accelerate_intel>` | examples/intel | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-LB <USER-LB>` | Lattice Boltzmann fluid | Colin Denniston (U Western Ontario) | :doc:`fix lb/fluid <fix_lb_fluid>` | USER/lb | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-MGPT <USER-MGPT>` | fast MGPT multi-ion potentials | Tomas Oppelstrup & John Moriarty (LLNL) | :doc:`pair_style mgpt <pair_mgpt>` | USER/mgpt | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-MISC <USER-MISC>` | single-file contributions | USER-MISC/README | USER-MISC/README | - | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-MOLFILE <USER-MOLFILE>` | `VMD <VMD_>`_ molfile plug-ins | Axel Kohlmeyer (Temple U) | :doc:`dump molfile <dump_molfile>` | - | - | VMD-MOLFILE |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-OMP <USER-OMP>` | OpenMP threaded styles | Axel Kohlmeyer (Temple U) | :doc:`Section accelerate <accelerate_omp>` | - | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-PHONON <USER-PHONON>` | phonon dynamical matrix | Ling-Ti Kong (Shanghai Jiao Tong U) | :doc:`fix phonon <fix_phonon>` | USER/phonon | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-QMMM <USER-QMMM>` | QM/MM coupling | Axel Kohlmeyer (Temple U) | :doc:`fix qmmm <fix_qmmm>` | USER/qmmm | - | lib/qmmm |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-QTB <USER-QTB>` | quantum nuclear effects | Yuan Shen (Stanford) | :doc:`fix qtb <fix_qtb>` :doc:`fix qbmsst <fix_qbmsst>` | qtb | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-QUIP <USER-QUIP>` | QUIP/libatoms interface | Albert Bartok-Partay (U Cambridge) | :doc:`pair_style quip <pair_quip>` | USER/quip | - | lib/quip |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-REAXC <USER-REAXC>` | C version of ReaxFF | Metin Aktulga (LBNL) | :doc:`pair_style reaxc <pair_reax_c>` | reax | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-SMD <USER-SMD>` | smoothed Mach dynamics | Georg Ganzenmuller (EMI) | `userguide.pdf <PDF/SMD_LAMMPS_userguide.pdf>`_ | USER/smd | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-SMTBQ <USER-SMTBQ>` | Second Moment Tight Binding - QEq potential | Salles & Maras & Politano & Tetot (4) | :doc:`pair_style smtbq <pair_smtbq>` | USER/smtbq | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-SPH <USER-SPH>` | smoothed particle hydrodynamics | Georg Ganzenmuller (EMI) | `userguide.pdf <PDF/SPH_LAMMPS_userguide.pdf>`_ | USER/sph | `sph <sph_>`_ | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-TALLY <USER-TALLY>` | Pairwise tallied computes | Axel Kohlmeyer (Temple U) | :doc:`compute <...>/tally <compute_tally>` | USER/tally | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| :ref:`USER-VTK <USER-VTK>` | VTK-style dumps | Berger and Queteschiner (6) | :doc:`compute custom/vtk <compute_custom_vtk>` | - | - | lib/vtk |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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| | | | | | | |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+----------------------+-------------+
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| Package | Description | Author(s) | Doc page | Example | Pic/movie | Library |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-ATC <USER-ATC>` | atom-to-continuum coupling | Jones & Templeton & Zimmerman (1) | :doc:`fix atc <fix_atc>` | USER/atc | `atc <atc_>`_ | lib/atc |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-AWPMD <USER-AWPMD>` | wave-packet MD | Ilya Valuev (JIHT) | :doc:`pair_style awpmd/cut <pair_awpmd>` | USER/awpmd | - | lib/awpmd |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-CG-CMM <USER-CG-CMM>` | coarse-graining model | Axel Kohlmeyer (Temple U) | :doc:`pair_style lj/sdk <pair_sdk>` | USER/cg-cmm | `cg <cg_>`_ | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-COLVARS <USER-COLVARS>` | collective variables | Fiorin & Henin & Kohlmeyer (2) | :doc:`fix colvars <fix_colvars>` | USER/colvars | `colvars <colvars>`_ | lib/colvars |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-CUDA <USER-CUDA>` | NVIDIA GPU styles | Christian Trott (U Tech Ilmenau) | :doc:`Section accelerate <accelerate_cuda>` | USER/cuda | - | lib/cuda |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-DIFFRACTION <USER-DIFFRACTION>` | virutal x-ray and electron diffraction | Shawn Coleman (ARL) | :doc:`compute xrd <compute_xrd>` | USER/diffraction | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-DPD <USER-DPD>` | dissipative particle dynamics (DPD) | Larentzos & Mattox & Brennan (5) | src/USER-DPD/README | USER/dpd | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-DRUDE <USER-DRUDE>` | Drude oscillators | Dequidt & Devemy & Padua (3) | :doc:`tutorial <tutorial_drude>` | USER/drude | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-EFF <USER-EFF>` | electron force field | Andres Jaramillo-Botero (Caltech) | :doc:`pair_style eff/cut <pair_eff>` | USER/eff | `eff <eff_>`_ | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-FEP <USER-FEP>` | free energy perturbation | Agilio Padua (U Blaise Pascal Clermont-Ferrand) | :doc:`compute fep <compute_fep>` | USER/fep | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-H5MD <USER-H5MD>` | dump output via HDF5 | Pierre de Buyl (KU Leuven) | :doc:`dump h5md <dump_h5md>` | - | - | lib/h5md |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-INTEL <USER-INTEL>` | Vectorized CPU and Intel(R) coprocessor styles | W. Michael Brown (Intel) | :doc:`Section accelerate <accelerate_intel>` | examples/intel | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-LB <USER-LB>` | Lattice Boltzmann fluid | Colin Denniston (U Western Ontario) | :doc:`fix lb/fluid <fix_lb_fluid>` | USER/lb | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-MGPT <USER-MGPT>` | fast MGPT multi-ion potentials | Tomas Oppelstrup & John Moriarty (LLNL) | :doc:`pair_style mgpt <pair_mgpt>` | USER/mgpt | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-MISC <USER-MISC>` | single-file contributions | USER-MISC/README | USER-MISC/README | - | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-MANIFOLD <USER-MANIFOLD>` | motion on 2d surface | Stefan Paquay (Eindhoven U of Technology) | :doc:`fix manifoldforce <fix_manifoldforce>` | - | `manifold <manifold_>`_ | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-MOLFILE <USER-MOLFILE>` | `VMD <VMD_>`_ molfile plug-ins | Axel Kohlmeyer (Temple U) | :doc:`dump molfile <dump_molfile>` | - | - | VMD-MOLFILE |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-OMP <USER-OMP>` | OpenMP threaded styles | Axel Kohlmeyer (Temple U) | :doc:`Section accelerate <accelerate_omp>` | - | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-PHONON <USER-PHONON>` | phonon dynamical matrix | Ling-Ti Kong (Shanghai Jiao Tong U) | :doc:`fix phonon <fix_phonon>` | USER/phonon | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-QMMM <USER-QMMM>` | QM/MM coupling | Axel Kohlmeyer (Temple U) | :doc:`fix qmmm <fix_qmmm>` | USER/qmmm | - | lib/qmmm |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-QTB <USER-QTB>` | quantum nuclear effects | Yuan Shen (Stanford) | :doc:`fix qtb <fix_qtb>` :doc:`fix qbmsst <fix_qbmsst>` | qtb | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-QUIP <USER-QUIP>` | QUIP/libatoms interface | Albert Bartok-Partay (U Cambridge) | :doc:`pair_style quip <pair_quip>` | USER/quip | - | lib/quip |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-REAXC <USER-REAXC>` | C version of ReaxFF | Metin Aktulga (LBNL) | :doc:`pair_style reaxc <pair_reax_c>` | reax | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-SMD <USER-SMD>` | smoothed Mach dynamics | Georg Ganzenmuller (EMI) | `userguide.pdf <PDF/SMD_LAMMPS_userguide.pdf>`_ | USER/smd | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-SMTBQ <USER-SMTBQ>` | Second Moment Tight Binding - QEq potential | Salles & Maras & Politano & Tetot (4) | :doc:`pair_style smtbq <pair_smtbq>` | USER/smtbq | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-SPH <USER-SPH>` | smoothed particle hydrodynamics | Georg Ganzenmuller (EMI) | `userguide.pdf <PDF/SPH_LAMMPS_userguide.pdf>`_ | USER/sph | `sph <sph_>`_ | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-TALLY <USER-TALLY>` | Pairwise tallied computes | Axel Kohlmeyer (Temple U) | :doc:`compute <...>/tally <compute_tally>` | USER/tally | - | - |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| :ref:`USER-VTK <USER-VTK>` | VTK-style dumps | Berger and Queteschiner (6) | :doc:`compute custom/vtk <compute_custom_vtk>` | - | - | lib/vtk |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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| | | | | | | |
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+--------------------------------------------+------------------------------------------------+-------------------------------------------------+---------------------------------------------------------+------------------+-------------------------+-------------+
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.. _atc: http://lammps.sandia.gov/pictures.html#atc
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@ -1581,6 +1583,10 @@ The current list of user-contributed packages is as follows:
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.. _manifold: http://lammps.sandia.gov/movies.html#manifold
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.. _sph: http://lammps.sandia.gov/movies.html#sph
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@ -2064,6 +2070,37 @@ Examples: examples/USER/misc
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----------
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.. _USER-MANIFOLD:
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USER-MANIFOLD package
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^^^^^^^^^^^^^^^^^^^^^
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Supporting info:
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This package contains a dump molfile command which uses molfile
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plugins that are bundled with the
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`VMD <http://www.ks.uiuc.edu/Research/vmd>`_ molecular visualization and
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analysis program, to enable LAMMPS to dump its information in formats
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compatible with various molecular simulation tools.
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This package allows LAMMPS to perform MD simulations of particles
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constrained on a manifold (i.e., a 2D subspace of the 3D simulation
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box). It achieves this using the RATTLE constraint algorithm applied
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to single-particle constraint functions g(xi,yi,zi) = 0 and their
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derivative (i.e. the normal of the manifold) n = grad(g).
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See this doc page to get started:
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:doc:`fix manifoldforce <fix_manifoldforce>`
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The person who created this package is Stefan Paquay, at the Eindhoven
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University of Technology (TU/e), The Netherlands (s.paquay at tue.nl).
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Contact him directly if you have questions.
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----------
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.. _USER-MOLFILE:
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USER-MOLFILE package
|
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Reference in New Issue
Block a user