Loading doc/src/Install_linux.rst +19 −13 Original line number Diff line number Diff line Loading @@ -21,8 +21,14 @@ Pre-built Ubuntu Linux executables A pre-built LAMMPS executable suitable for running on the latest Ubuntu Linux versions, can be downloaded as a Debian package. This allows you to install LAMMPS with a single command, and stay up-to-date with the current version of LAMMPS by simply updating your operating system. up-to-date with the current stable version of LAMMPS by simply updating your operating system. Please note, that the repository below offers two LAMMPS packages, ``lammps-daily`` and ``lammps-stable``. The LAMMPS developers recommend to use the ``lammps-stable`` package for any production simulations. The ``lammps-daily`` package is built from the LAMMPS development sources, and those versions may have known issues and bugs when new features are added and the software has not undergone full release testing. To install the appropriate personal-package archives (PPAs), do the following once: Loading @@ -37,16 +43,16 @@ To install LAMMPS do the following once: .. code-block:: bash $ sudo apt-get install lammps-daily $ sudo apt-get install lammps-stable This downloads an executable named ``lmp_daily`` to your box, which This downloads an executable named ``lmp_stable`` to your box, which can then be used in the usual way to run input scripts: .. code-block:: bash $ lmp_daily -in in.lj $ lmp_stable -in in.lj To update LAMMPS to the most current version, do the following: To update LAMMPS to the most current stable version, do the following: .. code-block:: bash Loading @@ -58,25 +64,25 @@ To get a copy of the current documentation and examples: .. code-block:: bash $ sudo apt-get install lammps-daily-doc $ sudo apt-get install lammps-stable-doc which will download the doc files in ``/usr/share/doc/lammps-daily-doc/doc`` and example problems in ``/usr/share/doc/lammps-stable-doc/doc`` and example problems in ``/usr/share/doc/lammps-doc/examples``. To get a copy of the current potentials files: .. code-block:: bash $ sudo apt-get install lammps-daily-data $ sudo apt-get install lammps-stable-data which will download the potentials files to ``/usr/share/lammps-daily/potentials``. The ``lmp_daily`` binary is ``/usr/share/lammps-stable/potentials``. The ``lmp_stable`` binary is hard-coded to look for potential files in this directory (it does not use the `LAMMPS_POTENTIALS` environment variable, as described in :doc:`pair_coeff <pair_coeff>` command). The ``lmp_daily`` binary is built with the :ref:`KIM package <kim>` which The ``lmp_stable`` binary is built with the :ref:`KIM package <kim>` which results in the above command also installing the `kim-api` binaries when LAMMPS is installed. In order to use potentials from `openkim.org <openkim_>`_, you can install the `openkim-models` package Loading @@ -89,9 +95,9 @@ To un-install LAMMPS, do the following: .. code-block:: bash $ sudo apt-get remove lammps-daily $ sudo apt-get remove lammps-stable Please use ``lmp_daily -help`` to see which compilation options, packages, Please use ``lmp_stable -help`` to see which compilation options, packages, and styles are included in the binary. Thanks to Anton Gladky (gladky.anton at gmail.com) for setting up this Loading doc/src/angle_charmm.rst +4 −3 Original line number Diff line number Diff line Loading @@ -49,13 +49,14 @@ The following coefficients must be defined for each angle type via the the data file or restart files read by the :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` commands: * :math:`K` (energy/radian\^2) * :math:`K` (energy) * :math:`\theta_0` (degrees) * :math:`K_{ub}` (energy/distance\^2) * :math:`r_{ub}` (distance) :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence the units of :math:`K` are in energy/radian\^2. :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence :math:`K` is effectively energy per radian\^2. ---------- Loading doc/src/angle_class2.rst +24 −18 Original line number Diff line number Diff line Loading @@ -41,27 +41,29 @@ The *class2* angle style uses the potential E_{bb} & = M (r_{ij} - r_1) (r_{jk} - r_2) \\ E_{ba} & = N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2(r_{jk} - r_2)(\theta - \theta_0) where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond term, and :math:`E_{ba}` is a bond-angle term. :math:`\theta_0` is the equilibrium angle and :math:`r_1` and :math:`r_2` are the equilibrium bond lengths. where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond term, and :math:`E_{ba}` is a bond-angle term. :math:`\theta_0` is the equilibrium angle and :math:`r_1` and :math:`r_2` are the equilibrium bond lengths. See :ref:`(Sun) <angle-Sun>` for a description of the COMPASS class2 force field. Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ba}` formulas must be defined for each angle type via the :doc:`angle_coeff <angle_coeff>` command as in the example above, or in the data file or restart files read by the :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` commands. Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ba}` formulas must be defined for each angle type via the :doc:`angle_coeff <angle_coeff>` command as in the example above, or in the data file or restart files read by the :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` commands. These are the 4 coefficients for the :math:`E_a` formula: * :math:`\theta_0` (degrees) * :math:`K_2` (energy/radian\^2) * :math:`K_3` (energy/radian\^3) * :math:`K_4` (energy/radian\^4) * :math:`K_2` (energy) * :math:`K_3` (energy) * :math:`K_4` (energy) :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence the units of the various :math:`K` are in per-radian. :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence the various :math:`K` are effectively energy per radian\^2 or radian\^3 or radian\^4. For the :math:`E_{bb}` formula, each line in a :doc:`angle_coeff <angle_coeff>` command in the input script lists 4 coefficients, the first of which Loading Loading @@ -122,11 +124,15 @@ The *class2/p6* angle style uses the *class2* potential expanded to sixth order: In this expanded term 6 coefficients for the :math:`E_a` formula need to be set: * :math:`\theta_0` (degrees) * :math:`K_2` (energy/radian\^2) * :math:`K_3` (energy/radian\^3) * :math:`K_4` (energy/radian\^4) * :math:`K_5` (energy/radian\^5) * :math:`K_6` (energy/radian\^6) * :math:`K_2` (energy) * :math:`K_3` (energy) * :math:`K_4` (energy) * :math:`K_5` (energy) * :math:`K_6` (energy) :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence the various :math:`K` are effectively energy per radian\^2 or radian\^3 or radian\^4 or radian\^5 or radian\^6. The bond-bond and bond-angle terms remain unchanged. Loading doc/src/angle_cross.rst +5 −4 Original line number Diff line number Diff line Loading @@ -40,14 +40,15 @@ the data file or restart files read by the :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` commands: * :math:`K_{SS}` (energy/distance\^2) * :math:`K_{BS0}` (energy/distance/rad) * :math:`K_{BS1}` (energy/distance/rad) * :math:`K_{BS0}` (energy/distance) * :math:`K_{BS1}` (energy/distance) * :math:`r_{12,0}` (distance) * :math:`r_{32,0}` (distance) * :math:`\theta_0` (degrees) :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence the units of :math:`K_{BS0}` and :math:`K_{BS1}` are in energy/distance/radian. :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence the :math:`K_{BS0}` and :math:`K_{BS1}` are effectively energy/distance per radian. Restrictions """""""""""" Loading doc/src/angle_harmonic.rst +9 −6 Original line number Diff line number Diff line Loading @@ -44,11 +44,12 @@ The following coefficients must be defined for each angle type via the the data file or restart files read by the :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` commands: * :math:`K` (energy/radian\^2) * :math:`K` (energy) * :math:`\theta_0` (degrees) :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence the units of :math:`K` are in energy/radian\^2. :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence :math:`K` is effectively energy per radian\^2. ---------- Loading @@ -61,11 +62,13 @@ produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info. LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the :doc:`suffix <suffix>` command in your input script. by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the :doc:`suffix <suffix>` command in your input script. See the :doc:`Speed packages <Speed_packages>` doc page for more instructions on how to use the accelerated styles effectively. Loading Loading
doc/src/Install_linux.rst +19 −13 Original line number Diff line number Diff line Loading @@ -21,8 +21,14 @@ Pre-built Ubuntu Linux executables A pre-built LAMMPS executable suitable for running on the latest Ubuntu Linux versions, can be downloaded as a Debian package. This allows you to install LAMMPS with a single command, and stay up-to-date with the current version of LAMMPS by simply updating your operating system. up-to-date with the current stable version of LAMMPS by simply updating your operating system. Please note, that the repository below offers two LAMMPS packages, ``lammps-daily`` and ``lammps-stable``. The LAMMPS developers recommend to use the ``lammps-stable`` package for any production simulations. The ``lammps-daily`` package is built from the LAMMPS development sources, and those versions may have known issues and bugs when new features are added and the software has not undergone full release testing. To install the appropriate personal-package archives (PPAs), do the following once: Loading @@ -37,16 +43,16 @@ To install LAMMPS do the following once: .. code-block:: bash $ sudo apt-get install lammps-daily $ sudo apt-get install lammps-stable This downloads an executable named ``lmp_daily`` to your box, which This downloads an executable named ``lmp_stable`` to your box, which can then be used in the usual way to run input scripts: .. code-block:: bash $ lmp_daily -in in.lj $ lmp_stable -in in.lj To update LAMMPS to the most current version, do the following: To update LAMMPS to the most current stable version, do the following: .. code-block:: bash Loading @@ -58,25 +64,25 @@ To get a copy of the current documentation and examples: .. code-block:: bash $ sudo apt-get install lammps-daily-doc $ sudo apt-get install lammps-stable-doc which will download the doc files in ``/usr/share/doc/lammps-daily-doc/doc`` and example problems in ``/usr/share/doc/lammps-stable-doc/doc`` and example problems in ``/usr/share/doc/lammps-doc/examples``. To get a copy of the current potentials files: .. code-block:: bash $ sudo apt-get install lammps-daily-data $ sudo apt-get install lammps-stable-data which will download the potentials files to ``/usr/share/lammps-daily/potentials``. The ``lmp_daily`` binary is ``/usr/share/lammps-stable/potentials``. The ``lmp_stable`` binary is hard-coded to look for potential files in this directory (it does not use the `LAMMPS_POTENTIALS` environment variable, as described in :doc:`pair_coeff <pair_coeff>` command). The ``lmp_daily`` binary is built with the :ref:`KIM package <kim>` which The ``lmp_stable`` binary is built with the :ref:`KIM package <kim>` which results in the above command also installing the `kim-api` binaries when LAMMPS is installed. In order to use potentials from `openkim.org <openkim_>`_, you can install the `openkim-models` package Loading @@ -89,9 +95,9 @@ To un-install LAMMPS, do the following: .. code-block:: bash $ sudo apt-get remove lammps-daily $ sudo apt-get remove lammps-stable Please use ``lmp_daily -help`` to see which compilation options, packages, Please use ``lmp_stable -help`` to see which compilation options, packages, and styles are included in the binary. Thanks to Anton Gladky (gladky.anton at gmail.com) for setting up this Loading
doc/src/angle_charmm.rst +4 −3 Original line number Diff line number Diff line Loading @@ -49,13 +49,14 @@ The following coefficients must be defined for each angle type via the the data file or restart files read by the :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` commands: * :math:`K` (energy/radian\^2) * :math:`K` (energy) * :math:`\theta_0` (degrees) * :math:`K_{ub}` (energy/distance\^2) * :math:`r_{ub}` (distance) :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence the units of :math:`K` are in energy/radian\^2. :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence :math:`K` is effectively energy per radian\^2. ---------- Loading
doc/src/angle_class2.rst +24 −18 Original line number Diff line number Diff line Loading @@ -41,27 +41,29 @@ The *class2* angle style uses the potential E_{bb} & = M (r_{ij} - r_1) (r_{jk} - r_2) \\ E_{ba} & = N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2(r_{jk} - r_2)(\theta - \theta_0) where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond term, and :math:`E_{ba}` is a bond-angle term. :math:`\theta_0` is the equilibrium angle and :math:`r_1` and :math:`r_2` are the equilibrium bond lengths. where :math:`E_a` is the angle term, :math:`E_{bb}` is a bond-bond term, and :math:`E_{ba}` is a bond-angle term. :math:`\theta_0` is the equilibrium angle and :math:`r_1` and :math:`r_2` are the equilibrium bond lengths. See :ref:`(Sun) <angle-Sun>` for a description of the COMPASS class2 force field. Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ba}` formulas must be defined for each angle type via the :doc:`angle_coeff <angle_coeff>` command as in the example above, or in the data file or restart files read by the :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` commands. Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ba}` formulas must be defined for each angle type via the :doc:`angle_coeff <angle_coeff>` command as in the example above, or in the data file or restart files read by the :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` commands. These are the 4 coefficients for the :math:`E_a` formula: * :math:`\theta_0` (degrees) * :math:`K_2` (energy/radian\^2) * :math:`K_3` (energy/radian\^3) * :math:`K_4` (energy/radian\^4) * :math:`K_2` (energy) * :math:`K_3` (energy) * :math:`K_4` (energy) :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence the units of the various :math:`K` are in per-radian. :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence the various :math:`K` are effectively energy per radian\^2 or radian\^3 or radian\^4. For the :math:`E_{bb}` formula, each line in a :doc:`angle_coeff <angle_coeff>` command in the input script lists 4 coefficients, the first of which Loading Loading @@ -122,11 +124,15 @@ The *class2/p6* angle style uses the *class2* potential expanded to sixth order: In this expanded term 6 coefficients for the :math:`E_a` formula need to be set: * :math:`\theta_0` (degrees) * :math:`K_2` (energy/radian\^2) * :math:`K_3` (energy/radian\^3) * :math:`K_4` (energy/radian\^4) * :math:`K_5` (energy/radian\^5) * :math:`K_6` (energy/radian\^6) * :math:`K_2` (energy) * :math:`K_3` (energy) * :math:`K_4` (energy) * :math:`K_5` (energy) * :math:`K_6` (energy) :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence the various :math:`K` are effectively energy per radian\^2 or radian\^3 or radian\^4 or radian\^5 or radian\^6. The bond-bond and bond-angle terms remain unchanged. Loading
doc/src/angle_cross.rst +5 −4 Original line number Diff line number Diff line Loading @@ -40,14 +40,15 @@ the data file or restart files read by the :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` commands: * :math:`K_{SS}` (energy/distance\^2) * :math:`K_{BS0}` (energy/distance/rad) * :math:`K_{BS1}` (energy/distance/rad) * :math:`K_{BS0}` (energy/distance) * :math:`K_{BS1}` (energy/distance) * :math:`r_{12,0}` (distance) * :math:`r_{32,0}` (distance) * :math:`\theta_0` (degrees) :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence the units of :math:`K_{BS0}` and :math:`K_{BS1}` are in energy/distance/radian. :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence the :math:`K_{BS0}` and :math:`K_{BS1}` are effectively energy/distance per radian. Restrictions """""""""""" Loading
doc/src/angle_harmonic.rst +9 −6 Original line number Diff line number Diff line Loading @@ -44,11 +44,12 @@ The following coefficients must be defined for each angle type via the the data file or restart files read by the :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` commands: * :math:`K` (energy/radian\^2) * :math:`K` (energy) * :math:`\theta_0` (degrees) :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence the units of :math:`K` are in energy/radian\^2. :math:`\theta_0` is specified in degrees, but LAMMPS converts it to radians internally; hence :math:`K` is effectively energy per radian\^2. ---------- Loading @@ -61,11 +62,13 @@ produce the same results, except for round-off and precision issues. These accelerated styles are part of the GPU, USER-INTEL, KOKKOS, USER-OMP and OPT packages, respectively. They are only enabled if LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info. LAMMPS was built with those packages. See the :doc:`Build package <Build_package>` doc page for more info. You can specify the accelerated styles explicitly in your input script by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the :doc:`suffix <suffix>` command in your input script. by including their suffix, or you can use the :doc:`-suffix command-line switch <Run_options>` when you invoke LAMMPS, or you can use the :doc:`suffix <suffix>` command in your input script. See the :doc:`Speed packages <Speed_packages>` doc page for more instructions on how to use the accelerated styles effectively. Loading
