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 doc/src/angle_mm3.rst +8 −6 Original line number Diff line number Diff line Loading @@ -28,20 +28,22 @@ as defined in :ref:`(Allinger) <mm3-allinger1989>` E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right] where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a prefactor. The anharmonic prefactors have units :math:`\deg^{-n}`, for example :math:`-0.014 \deg^{-1}`, :math:`5.6 \cdot 10^{-5} \deg^{-2}`, ... where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a prefactor. The anharmonic prefactors have units :math:`\deg^{-n}`, for example :math:`-0.014 \deg^{-1}`, :math:`5.6 \cdot 10^{-5} \deg^{-2}`, ... The following coefficients 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: * :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. Restrictions """""""""""" Loading 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
doc/src/angle_mm3.rst +8 −6 Original line number Diff line number Diff line Loading @@ -28,20 +28,22 @@ as defined in :ref:`(Allinger) <mm3-allinger1989>` E = K (\theta - \theta_0)^2 \left[ 1 - 0.014(\theta - \theta_0) + 5.6(10)^{-5} (\theta - \theta_0)^2 - 7.0(10)^{-7} (\theta - \theta_0)^3 + 9(10)^{-10} (\theta - \theta_0)^4 \right] where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a prefactor. The anharmonic prefactors have units :math:`\deg^{-n}`, for example :math:`-0.014 \deg^{-1}`, :math:`5.6 \cdot 10^{-5} \deg^{-2}`, ... where :math:`\theta_0` is the equilibrium value of the angle, and :math:`K` is a prefactor. The anharmonic prefactors have units :math:`\deg^{-n}`, for example :math:`-0.014 \deg^{-1}`, :math:`5.6 \cdot 10^{-5} \deg^{-2}`, ... The following coefficients 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: * :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. Restrictions """""""""""" Loading
