merge with Axel changes
This commit is contained in:
Steve Plimpton
@ -34,9 +34,9 @@ details for HIPPO are in this paper: :ref:`(Rackers)
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.. math::
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U & = U_{intermolecular} + U_{intramolecular) \\
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U_{intermolecular} & = U_{hal} + U_{repulsion} + U_{dispersion} + U_{multipole} + U_{polar} + U_{qxfer} \\
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U_{intramolecular} & = U_{bond} + U_{angle} + U_{torsion} + U_{oop} + U_{b\theta} + U_{UB} + U_{pitorsion} + U_{bitorsion}
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U & = U_{intermolecular} + U_{intramolecular} \\
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U_{intermolecular} & = U_{hal} + U_{repulsion} + U_{dispersion} + U_{multipole} + U_{polar} + U_{qxfer} \\
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U_{intramolecular} & = U_{bond} + U_{angle} + U_{torsion} + U_{oop} + U_{b\theta} + U_{UB} + U_{pitorsion} + U_{bitorsion}
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For intermolecular terms, the AMOEBA force field includes only the
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:math:`U_{hal}`, :math:`U_{multipole}`, :math:`U_{polar}` terms. The
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@ -55,12 +55,12 @@ for a Urey-Bradley bond contribution between the I,K atoms in the IJK
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angle.
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The :math:`U_{pitorsion}` term is computed by the :doc:`fix
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amoeba/pitorsion <fix_pitorsion>` command. It computes 6-body
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amoeba/pitorsion <fix_amoeba_pitorsion>` command. It computes 6-body
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interaction between a pair of bonded atoms which each have 2
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additional bond partners.
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The :math:`U_{bitorsion}` term is computed by the :doc:`fix
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amoeba/bitorsion <fix_bitorsion>` command. It computes 5-body
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amoeba/bitorsion <fix_amoeba_bitorsion>` command. It computes 5-body
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interaction between two 4-body torsions (dihedrals) which overlap,
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having 3 atoms in common.
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@ -72,8 +72,8 @@ compute:
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* :doc:`angle_style amoeba <angle_amoeba>`
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* :doc:`dihedral_style fourier <dihedral_fourier>`
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* :doc:`improper_style amoeba <improper_amoeba>`
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* :doc:`fix amoeba/pitorsion <fix_pitorsion>`
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* :doc:`fix amoeba/bitorsion <fix_bitorsion>`
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* :doc:`fix amoeba/pitorsion <fix_amoeba_pitorsion>`
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* :doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>`
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----------
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@ -94,14 +94,14 @@ and HIPPO.
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improper_style amoeba
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# required per-atom data
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fix amtype all property/atom i_amtype ghost yes
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fix extra all property/atom &
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fix extra all property/atom &
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i_amgroup i_ired i_xaxis i_yaxis i_zaxis d_pval ghost yes
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fix polaxe all property/atom i_polaxe
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fix pit all amoeba/pitorsion # PiTorsion terms in FF
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fix_modify pit energy yes
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# Bitorsion terms in FF
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fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
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fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
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fix_modify bit energy yes
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read_data data.ubiquitin fix amtype NULL "Tinker Types" &
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@ -127,7 +127,7 @@ In the example above the fix ID is *amtype*.
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Similarly, if the system you are simulating defines AMOEBA/HIPPO
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pitorsion or bitorsion interactions, there will be entries in the data
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file for those interactions. They require a :doc:`fix
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amoeba/pitortion <fix_amoeba_pitortion>` and :doc:`fix
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amoeba/pitortion <fix_amoeba_pitorsion>` and :doc:`fix
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amoeba/bitorsion <fix_amoeba_bitorsion>` command be defined. In the
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example above, the IDs for these two fixes are *pit* and *bit*.
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@ -263,7 +263,7 @@ Switches and their arguments may be specified in any order.
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The -xyz switch is required and specifies an input XYZ file as an
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argument. The format of this file is an extended XYZ format used by
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Tinker for its input. Example *.xyz files are in the examples/amoeba
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Tinker for its input. Example \*.xyz files are in the examples/amoeba
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directory. The file lists the atoms in the system. Each atom has the
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following information: Tinker species name (ignored by LAMMPS), xyz
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coordinates, Tinker numeric type, and a list of atom IDs the atom is
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@ -27,6 +27,7 @@ page gives those details.
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:columns: 6
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* :ref:`ADIOS <PKG-ADIOS>`
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* :ref:`AMOEBA <PKG-AMOEBA>`
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* :ref:`ASPHERE <PKG-ASPHERE>`
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* :ref:`ATC <PKG-ATC>`
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* :ref:`AWPMD <PKG-AWPMD>`
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@ -148,6 +149,24 @@ This package has :ref:`specific installation instructions <adios>` on the :doc:`
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----------
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.. _PKG-AMOEBA:
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AMOEBA package
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---------------
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**Contents:**
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TODO
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**Supporting info:**
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* src/AMOEBA: filenames -> commands
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* :doc:`AMOEBA and HIPPO howto <Howto_amoeba>`
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* examples/amoeba
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* TODO
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----------
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.. _PKG-ASPHERE:
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ASPHERE package
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@ -33,6 +33,11 @@ whether an extra library is needed to build and use the package:
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- :doc:`dump adios <dump_adios>`
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- PACKAGES/adios
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- ext
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* - :ref:`AMOEBA <PKG-AMOEBA>`
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- AMOEBA and HIPPO force fields
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- :doc:`AMOEBA and HIPPO howto <Howto_amoeba>`
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- amoeba
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- no
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* - :ref:`ASPHERE <PKG-ASPHERE>`
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- aspherical particle models
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- :doc:`Howto spherical <Howto_spherical>`
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@ -29,9 +29,9 @@ The *amoeba* angle style uses the potential
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.. math::
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E & = E_a + E_{ba} + E_{ub} \\
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E_a = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6
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E_{ba} & = N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2(r_{jk} - r_2)(\theta - \theta_0)
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E_{UB} & = K_{ub} (r_{ik} - r_{ub})^2)
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E_a & = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6 \\
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E_{ba} & = N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2(r_{jk} - r_2)(\theta - \theta_0) \\
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E_{UB} & = K_{ub} (r_{ik} - r_{ub})^2
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where :math:`E_a` is the angle term, :math:`E_{ba}` is a bond-angle
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term, :math:`E_{UB}` is a Urey-Bradley bond term, :math:`\theta_0` is
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@ -45,7 +45,7 @@ calculations for the AMOEBA and HIPPO force fields. See the
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the implemention of AMOEBA and HIPPO in LAMMPS.
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Note that the :math:`E_a` and :math:`E_{ba}` formulas are identical to
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those used for the :doc:`angle_style class2/p6 <angle_class2_p6>`
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those used for the :doc:`angle_style class2/p6 <angle_class2>`
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command, however there is no bond-bond cross term formula for
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:math:`E_{bb}`. Additionally, there is a :math:`E_{UB}` term for a
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Urey-Bradley bond. It is effectively a harmonic bond between the I
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@ -1,7 +1,7 @@
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.. index:: fix amoeba/bitorsion
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fix amoeba/bitorsion command
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================
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============================
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Syntax
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""""""
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@ -1,7 +1,7 @@
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.. index:: fix amoeba/pitorsion
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fix amoeba/pitorsion command
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================
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============================
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Syntax
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""""""
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@ -86,7 +86,7 @@ the pitorsion 5-atom tuples; it is ignored by LAMMPS. The second
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column is the "type" of the interaction; it is an index into the
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PiTorsion Coeffs. The remaining 5 columns are the atom IDs of the
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atoms in the two 4-atom dihedrals that overlap to create the pitorsion
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5-body interaction.
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5-body interaction.
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Note that the *pitorsion types* and *pitorsions* and *PiTorsion
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Coeffs* and *PiTorsions* keywords for the header and body sections of
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@ -5,7 +5,7 @@ pair_style amoeba command
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=========================
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pair_style hippo command
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=========================
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========================
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Syntax
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""""""
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@ -36,8 +36,8 @@ Additional info
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* :doc:`Howto amoeba <howto_ameoba>`
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* examples/amoeba
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* tools/amoeba
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* potentials/*.amoeba
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* potentials/*.hippo
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* potentials/\*.amoeba
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* potentials/\*.hippo
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Description
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"""""""""""
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@ -72,7 +72,7 @@ while the HIPPO force field contains these terms:
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U_{hippo} = U_{repulsion} + U_{dispersion} + U_{multipole} + U_{polar} + U_{qxfer}
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Conceptually, these terms compute the following interactions:
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* :math:`U_{hal}` = buffered 14-7 van der Waals with offsets applied to hydrogen atoms
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* :math:`U_{repulsion}` = Pauli repulsion due to rearrangement of electron density
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* :math:`U_{dispersion}` = dispersion between correlated, instantaneous induced dipole moments
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@ -114,12 +114,12 @@ Only a single pair_coeff command is used with either the *amoeba* and
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pair_coeff * * ../potentials/water.prm.hippo ../potentials/water.key.hippo
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Examples of the PRM files are in the potentials directory with an
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*.amoeba or *.hippo suffix. The examples/amoeba directory has
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\*.amoeba or \*.hippo suffix. The examples/amoeba directory has
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examples of both PRM and KEY files.
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A Tinker PRM file is composed of sections, each of which has multiple
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lines. A Tinker KEY file is composed of lines, each of which has a
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keyword, followed by zero or more parameters.
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keyword followed by zero or more parameters.
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The list of PRM sections and KEY keywords which LAMMPS recognizes are
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listed on the :doc:`Howto amoeba <howto_ameoba>` doc page. If not
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@ -165,8 +165,8 @@ can only use these pair styles with real units.
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These potentials do not yet calculate per-atom energy or virial
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contributions.
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As explained on the :doc:`Howto amoeba <howto_ameoba>` doc page, use
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of these pair styles to run a simulation with the AMOEBA or HIPPO
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As explained on the :doc:`AMOEBA and HIPPO howto <Howto_amoeba>` page,
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use of these pair styles to run a simulation with the AMOEBA or HIPPO
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force fields requires several things.
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The first is a data file generated by the tools/tinker/tinker2lmp.py
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@ -186,18 +186,23 @@ commands for intramolecular interactions may also be required:
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* :doc:`angle_style amoeba <angle_amoeba>`
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* :doc:`dihedral_style fourier <dihedral_fourier>`
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* :doc:`improper_style amoeba <improper_amoeba>`
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* :doc:`fix amoeba/pitorsion <fix_pitorsion>`
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* :doc:`fix amoeba/bitorsion <fix_bitorsion>`
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* :doc:`fix amoeba/pitorsion <fix_amoeba_pitorsion>`
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* :doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>`
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----------
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Related commands
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""""""""""""""""
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:doc:`atom_style amoeba <atom_style>`, `bond_style amoeba
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:doc:<bond_amoeba>`, `angle_style amoeba <angle_amoeba>`,
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:doc:`dihedral_style amoeba <dihedral_amoeba>`, `special_bonds
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:doc:one/five <special_bonds>`
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:doc:`atom_style amoeba <atom_style>`,
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:doc:`bond_style class2 <bond_class2>`,
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:doc:`angle_style amoeba <angle_amoeba>`,
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:doc:`dihedral_style fourier <dihedral_fourier>`,
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:doc:`improper_style amoeba <improper_amoeba>`,
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:doc:`fix amoeba/pitorsion <fix_amoeba_pitorsion>`,
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:doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>`,
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:doc:`special_bonds one/five <special_bonds>`,
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:doc:`fix property/atom <fix_property_atom>`
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Default
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"""""""
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@ -116,6 +116,7 @@ accelerated styles exist.
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* :doc:`agni <pair_agni>` - AGNI machine-learning potential
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* :doc:`airebo <pair_airebo>` - AIREBO potential of Stuart
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* :doc:`airebo/morse <pair_airebo>` - AIREBO with Morse instead of LJ
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* :doc:`amoeba <pair_amoeba>` -
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* :doc:`atm <pair_atm>` - Axilrod-Teller-Muto potential
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* :doc:`awpmd/cut <pair_awpmd>` - Antisymmetrized Wave Packet MD potential for atoms and electrons
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* :doc:`beck <pair_beck>` - Beck potential
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@ -202,6 +203,7 @@ accelerated styles exist.
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* :doc:`hbond/dreiding/lj <pair_hbond_dreiding>` - DREIDING hydrogen bonding LJ potential
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* :doc:`hbond/dreiding/morse <pair_hbond_dreiding>` - DREIDING hydrogen bonding Morse potential
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* :doc:`hdnnp <pair_hdnnp>` - High-dimensional neural network potential
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* :doc:`hippo <pair_amoeba>` -
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* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>` - registry-dependent interlayer potential (ILP)
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* :doc:`ilp/tmd <pair_ilp_tmd>` - interlayer potential (ILP) potential for transition metal dichalcogenides (TMD)
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* :doc:`kim <pair_kim>` - interface to potentials provided by KIM project
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