initial version of AMOEBA/HIPPO force field files
This commit is contained in:
Steve Plimpton
126
doc/src/Howto_amoeba.rst
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126
doc/src/Howto_amoeba.rst
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AMOEBA and HIPPO force fields
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=============================
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The AMOEBA and HIPPO polarizable force fields were developed by Jay
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Ponder's group at U Washington at St Louis. Their implementation in
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LAMMPS was done using code provided by the Ponder group from their
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`Tinker MD code <https://dasher.wustl.edu/tinker/>`_ written in F90.
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NOTE: what version of AMOEBA and HIPPO does LAMMPS implement?
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These force fields can be used when polarization effects are desired
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in simulations of water, organic molecules, and biomolecules including
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proteins, provided that parameterizations (force field files) are
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available for the systems you are interested in. Files in the LAMMPS
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potentials with a "amoeba" or "hippo" suffix can be used. The Tinker
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distribution and website may have other such files.
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Note that currently, HIPPO can only be used for water systems, but
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HIPPO files for a variety of small organic and biomolecules are in
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preparation by the Ponder group. They will be included in the LAMMPS
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distribution when available.
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The :doc:`pair_style amoeba <pair_amoeba>` doc page gives a brief
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description of the AMOEBA and HIPPO force fields. Further details for
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AMOEBA are in these papers: :ref:`(Ren) <amoeba-Ren>`, :ref:`(Shi)
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<amoeba-Shi>`. Further details for HIPPO are in this paper:
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:ref:`(Rackers) <amoeba-Rackers>`.
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----------
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To use the AMOEBA force field in LAMMPS you should use these commands
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appropriately in your input script. The only change needed for a
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HIPPO simulation is for the pair_style and pair_coeff commands.
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See examples/amoeba for example input scripts.
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.. code-block:: LAMMPS
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units real # required
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atom_style hybrid full amoeba
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bond_style amoeba
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angle_style amoeba
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dihedral_style amoeba
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fix amtype all property/atom i_amtype ghost yes # fix ID matches read_data command
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fix amoeba1 all property/atom & # fix ID (amoeba12) does not matter
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i_amgroup i_ired i_xaxis i_yaxis i_zaxis d_pval ghost yes
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fix amoeba2 all property/atom i_polaxe
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read_data filename fix amtype NULL "Tinker Types" # fix ID matches fix command
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pair_coeff * * ../potentials/protein.prm.amoeba ../potentials/protein.key.amoeba # for AMOEBA
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pair_coeff * * ../potentials/water.prm.hippo ../potentials/water.key.hippo # for HIPPO
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special_bonds lj/coul 0.5 0.5 0.5 one/five yes
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Both AMOEBA and HIPPO use amoeba for bond/angle/dihedral styles,
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assuming the molecular system has bonds, angles, or dihedrals. These
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style commands must be be used before the data file is read, as the
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data file defines the coefficients for the various bond/angle/dihedral
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types. The pair_style command can come after the read_data command,
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as no pair coefficients are defined in the data file.
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The :doc:`fix property/atom <fix_property_atom>` commands are required
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to create per-atom data used by the AMOEBA/HIPPO force fields, some of
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which is defined in the LAMMPS data file. The LAMMPS data file should
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be produced as a pre-processing step by the tinker2lmp.py Python
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script in tools/amoeba with a command like one of the following.
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The tools/amoeba/README file has more details on using this tool.
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.. code-block:: bash
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% python tinker2lmp.py -xyz tinker.xyz -amoeba protein.prm.amoeba -data lmp.data # AMOEBA for non-periodic systems
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% python tinker2lmp.py -xyz tinker.xyz -amoeba protein.prm.amoeba -data lmp.data -pbc 10.0 20.0 15.0 # AMOEBA for periodic systems
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% python tinker2lmp.py -xyz tinker.xyz -hippo water.prm.hippo -data lmp.data # HIPPO for non-periodic systems
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% python tinker2lmp.py -xyz tinker.xyz -hippo water.prm.hippo -data lmp.data -pbc 10.0 20.0 15.0 # HIPPO for periodic systems
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Note that two input files are needed and a LAMMPS data file (lmp.data)
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is produced. The data file will have information on Tinker atom types
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and AMOEBA/HIPPO force field parameters for bonds, angles, and
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dihedrals.
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The first input is an XYZ file listing all the atoms in the
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system.
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NOTE: is this a Tinker-augmented-XYZ format or standard? In either
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case, how do we suggest LAMMPS users come up with these files?
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The second input is an AMOEBA or HIPPO PRM (force field) file. The
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format of these files is defined by Tinker. A few such files are
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provided in the LAMMPS potentials directory. Others may be available
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in the Tinker distribution or from the Ponder group.
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The pair_coeff command should specify the same PRM file, and
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optionally a Tinker-format KEY file. See the :doc:`pair_style amoeba
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<pair_amoeba>` doc page for more information about Tinker PRM and KEY
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files.
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Finally, the :doc:`special_bonds <special_bonds>` command is used to
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set all LJ and Coulombic 1-2, 1-3, 1-4 weighting factors to non-zero
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and non-unity values, and to generate a per-atom list of 1-5 neighbors
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as well. This is to insure all bond-topology neighbors are included
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in the neighbor lists used by AMOEBA/HIPPO. These force fields apply
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their own custom weighting factors to all these terms, including the
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1-5 neighbors.
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----------
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These command doc pages have additional details:
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* :doc:`pair_style amoeba or hippo <pair_ameoba>`
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* :doc:`bond_style amoeba <bond_amoeba>`
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* :doc:`angle_style amoeba <angle_charmm>`
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* :doc:`dihedral_style amoeba <dihedral_amoeba>`
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* :doc:`fix property/atom <fix_property_atom>`
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* :doc:`special_bonds <special_bonds>`
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----------
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.. _howto-Ren:
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**(Ren)** Ren and Ponder, J Phys Chem B, 107, 5933 (2003).
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.. _howto-Shi:
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**(Shi)** Shi, Xiz, Znahg, Best, Wu, Ponder, Ren, J Chem Theory Comp,
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9, 4046, 2013.
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.. _howto-Rackers:
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**(Rackers)** Rackers and Ponder, J Chem Phys, 150, 084104 (2010).
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223
doc/src/pair_amoeba.rst
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223
doc/src/pair_amoeba.rst
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@ -0,0 +1,223 @@
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.. index:: pair_style amoeba
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.. index:: pair_style hippo
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pair_style amoeba command
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=========================
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pair_style hippo command
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=========================
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Syntax
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""""""
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.. code-block:: LAMMPS
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pair_style style
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* style = *amoeba* or *hippo*
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Examples
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""""""""
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.. code-block:: LAMMPS
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pair_style amoeba
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pair_coeff * * protein.prm.amoeba protein.key.amoeba
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.. code-block:: LAMMPS
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pair_style hippo
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pair_coeff * * water.prm.hippo water.key.hippo
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Additional info
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"""""""""""""""
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doc:`Howto amoeba <howto_ameoba>`
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doc:`bond_style amoeba <bond_amoeba>`
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doc:`angle_style amoeba <angle_amoeba>`
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doc:`dihedral_style amoeba <dihedral_amoeba>`
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examples/amoeba
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tools/amoeba
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potentials/\*.prm.ameoba
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potentials/\*.key.ameoba
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potentials/\*.prm.hippo
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potentials/\*.key.hippo
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Description
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"""""""""""
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NOTE: edit this paragraph however you wish including adding or changing
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citations (see bottom of this file)
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The *amoeba* style computes the AMOEBA polarizeable field formulated
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by Jay Ponder's group at U Washington at St Louis :ref:`(Ren)
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<amoeba-Ren>`, :ref:`(Shi) <amoeba-Shi>`. The *hippo* style
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computes the HIPPO polarizeable force field , an extension to AMOEBA,
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formulated by Josh Rackers and collaborators in the Ponder group
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:ref:`(Rackers) <amoeba-Rackers>`.
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|
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These force fields can be used when polarization effects are desired
|
||||
in simulations of water, organic molecules, and biomolecules including
|
||||
proteins, provided that parameterizations (force field files) are
|
||||
available for the systems you are interested in. Files in the LAMMPS
|
||||
potentials with a "amoeba" or "hippo" suffix can be used. The Tinker
|
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distribution and website may have other such files.
|
||||
|
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NOTE: replace these LaTeX formulas with a list of AMOEBA and HIPPO
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terms in some simple notation. If desired, a more detailed
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mathematical expression for each term could also be included below
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the initial 2 formulas.
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The AMOEBA force field can be written as a collection of terms
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.. math::
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E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
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\left(\frac{\sigma}{r}\right)^6 \right]
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\qquad r < r_c
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:math:`r_c` is the cutoff, blah is the dipole, etc
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The HIPPO force field is similar but alters some of the terms
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.. math::
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E = 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
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\left(\frac{\sigma}{r}\right)^6 \right]
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\qquad r < r_c
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:math:`r_c` is the cutoff, blah is the dipole, etc
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NOTE: Add a sentence for each term to explain what physical effects
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the FFs are encoding. E.g. The polar term iteratively computes an
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induced dipole for each atom, then calculates dipole-dipole
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interactions ...
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See the AMOEBA and HIPPO papers for further details.
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.. note::
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The AMOEBA and HIPPO force fields compute long-range charge, dipole,
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and quadrupole interactions (NOTE: also long-range dispersion?).
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However, unlike other models with long-range interactions in LAMMPS,
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this does not require use of a KSpace style via the
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:doc:`kspace_style <kspace_style>` command. That is because for
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AMOEBA and HIPPO the long-range computations are intertwined with
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the pairwise compuations. So these pair style include both short-
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and long-range computations. This means the energy and virial
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computed by the pair style as well as the "Pair" timing reported by
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LAMMPS will include the long-range components.
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.. note::
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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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force fields requires your input script to use the :doc:`atom_style
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hybrid full amoeba <atom_style>` atom style, AMOEBA versions of
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bond/angle/dihedral styles, the :doc:`special_bonds one/five
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<special_bonds>` option, and the :doc:`fix property/atom one/five
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<fix_property>` command to define several additional per-atom
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properties. The latter requires a "Tinker Types" section be
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included in the LAMMPS data file. This can be auto-generated using
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the tools/amoeba/tinker2lmp.py Python script. See the :doc:`Howto
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amoeba <howto_ameoba>` doc page and tools/amoeba/README file for
|
||||
details on using that tool.
|
||||
|
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The implementation of the AMOEBA and HIPPO force fields in LAMMPS was
|
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done using code provided by the Ponder group from their `Tinker MD
|
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code <https://dasher.wustl.edu/tinker/>`_ written in F90.
|
||||
|
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NOTE: what version of AMOEBA and HIPPO does LAMMPS implement?
|
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|
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----------
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Only a single pair_coeff command is used with either the *amoeba* and
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*hippo* styles which specifies two Tinker files, a PRM and KEY file.
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.. code-block:: LAMMPS
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pair_coeff * * ../potentials/protein.prm.amoeba ../potentials/protein.key.amoeba
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pair_coeff * * ../potentials/water.prm.hippo ../potentials/water.key.hippo
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See examples of these files in the potentials directory.
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The format of a PRM file is a collection of sections, each with
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multiple lines. These are the sections which LAMMPS recognizes:
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NOTE: need to list these, possibly there are some LAMMPS skips
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or which need to be removed for LAMMPS to use the PRM file?
|
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The format of a KEY file is a series of lines, with one parameter and
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its value per line. These are the parameters which LAMMPS recognizes:
|
||||
|
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NOTE: need to list these, possibly there are some keywords LAMMPS skips
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or which need to be removed for LAMMPS to use the KEY file?
|
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|
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NOTE: Any other info about PRM and KEY files we should explain
|
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for LAMMPS users here?
|
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----------
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Mixing, shift, table, tail correction, restart, rRESPA info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
|
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These pair styles do not support the :doc:`pair_modify <pair_modify>`
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mix, shift, table, and tail options.
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|
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These pair styles do not write their information to :doc:`binary
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restart files <restart>`, since it is stored in potential files.
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Thus, you need to re-specify the pair_style and pair_coeff commands in
|
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an input script that reads a restart file.
|
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These pair styles can only be used via the *pair* keyword of the
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:doc:`run_style respa <run_style>` command. They do not support the
|
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*inner*\ , *middle*\ , *outer* keywords.
|
||||
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----------
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|
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Restrictions
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""""""""""""
|
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|
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These pair styles are part of the AMOEBA package. They are only
|
||||
enabled if LAMMPS was built with that package. See the :doc:`Build
|
||||
package <Build_package>` doc page for more info.
|
||||
|
||||
The AMOEBA and HIPPO potential (PRM) and KEY files provided with
|
||||
LAMMPS in the potentials directory are Tinker files parameterized for
|
||||
Tinker units. Their numeric parameters are converted by LAMMPS to its
|
||||
real units :doc:`units <units>`. You can only use these pair styles
|
||||
with real units.
|
||||
|
||||
These potentials do not yet calculate per-atom energy or virial
|
||||
contributions.
|
||||
|
||||
----------
|
||||
|
||||
Related commands
|
||||
""""""""""""""""
|
||||
|
||||
:doc:`atom_style amoeba <atom_style>`, `bond_style amoeba
|
||||
:doc:<bond_amoeba>`, `angle_style amoeba <angle_amoeba>`,
|
||||
:doc:`dihedral_style amoeba <dihedral_amoeba>`, `special_bonds
|
||||
:doc:one/five <special_bonds>`
|
||||
|
||||
Default
|
||||
"""""""
|
||||
|
||||
none
|
||||
|
||||
----------
|
||||
|
||||
.. _amoeba-Ren:
|
||||
|
||||
**(Ren)** Ren and Ponder, J Phys Chem B, 107, 5933 (2003).
|
||||
|
||||
.. _amoeba-Shi:
|
||||
|
||||
**(Shi)** Shi, Xiz, Znahg, Best, Wu, Ponder, Ren, J Chem Theory Comp,
|
||||
9, 4046, 2013.
|
||||
|
||||
.. _amoeba-Rackers:
|
||||
|
||||
**(Rackers)** Rackers and Ponder, J Chem Phys, 150, 084104 (2010).
|
||||
@ -59,6 +59,7 @@ sub-directories:
|
||||
|
||||
accelerate: use of all the various accelerator packages
|
||||
airebo: polyethylene with AIREBO potential
|
||||
amoeba: small water and bio models with AMOEBA and HIPPO potentials
|
||||
atm: Axilrod-Teller-Muto potential
|
||||
balance: dynamic load balancing, 2d system
|
||||
body: body particles, 2d system
|
||||
|
||||
17
examples/amoeba/amoeba_ubiquitin.key
Normal file
17
examples/amoeba/amoeba_ubiquitin.key
Normal file
@ -0,0 +1,17 @@
|
||||
parameters ./amoeba.prm
|
||||
verbose
|
||||
neighbor-list
|
||||
tau-temperature 1.0
|
||||
tau-pressure 2.0
|
||||
a-axis 54.99
|
||||
b-axis 41.91
|
||||
c-axis 41.91
|
||||
vdw-cutoff 12.0
|
||||
ewald
|
||||
ewald-alpha 0.4
|
||||
pewald-alpha 0.5
|
||||
ewald-cutoff 7.0
|
||||
#pme-grid 60 45 45
|
||||
pme-grid 60 48 48
|
||||
pme-order 5
|
||||
polar-eps 0.00001
|
||||
11583
examples/amoeba/amoeba_ubiquitin.prm
Normal file
11583
examples/amoeba/amoeba_ubiquitin.prm
Normal file
File diff suppressed because it is too large
Load Diff
9
examples/amoeba/amoeba_water.key
Normal file
9
examples/amoeba/amoeba_water.key
Normal file
@ -0,0 +1,9 @@
|
||||
parameters ./amoeba.prm
|
||||
|
||||
digits 8
|
||||
|
||||
cutoff 10
|
||||
taper 8
|
||||
|
||||
polar-eps 1e-5
|
||||
usolve-diag 1.0
|
||||
159
examples/amoeba/amoeba_water.prm
Normal file
159
examples/amoeba/amoeba_water.prm
Normal file
@ -0,0 +1,159 @@
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||||
|
||||
##############################
|
||||
## ##
|
||||
## Force Field Definition ##
|
||||
## ##
|
||||
##############################
|
||||
|
||||
|
||||
forcefield AMOEBA-WATER-2003
|
||||
|
||||
bond-cubic -2.55
|
||||
bond-quartic 3.793125
|
||||
angle-cubic -0.014
|
||||
angle-quartic 0.000056
|
||||
angle-pentic -0.0000007
|
||||
angle-sextic 0.000000022
|
||||
opbendtype ALLINGER
|
||||
opbend-cubic -0.014
|
||||
opbend-quartic 0.000056
|
||||
opbend-pentic -0.0000007
|
||||
opbend-sextic 0.000000022
|
||||
torsionunit 0.5
|
||||
vdwtype BUFFERED-14-7
|
||||
radiusrule CUBIC-MEAN
|
||||
radiustype R-MIN
|
||||
radiussize DIAMETER
|
||||
epsilonrule HHG
|
||||
dielectric 1.0
|
||||
polarization MUTUAL
|
||||
vdw-12-scale 0.0
|
||||
vdw-13-scale 0.0
|
||||
vdw-14-scale 1.0
|
||||
vdw-15-scale 1.0
|
||||
mpole-12-scale 0.0
|
||||
mpole-13-scale 0.0
|
||||
mpole-14-scale 0.4
|
||||
#mpole-15-scale 0.8
|
||||
polar-12-scale 0.0
|
||||
polar-13-scale 0.0
|
||||
polar-14-scale 1.0
|
||||
polar-15-scale 1.0
|
||||
polar-12-intra 0.0
|
||||
polar-13-intra 0.0
|
||||
polar-14-intra 0.5
|
||||
polar-15-intra 1.0
|
||||
direct-11-scale 0.0
|
||||
direct-12-scale 1.0
|
||||
direct-13-scale 1.0
|
||||
direct-14-scale 1.0
|
||||
mutual-11-scale 1.0
|
||||
mutual-12-scale 1.0
|
||||
mutual-13-scale 1.0
|
||||
mutual-14-scale 1.0
|
||||
|
||||
|
||||
#############################
|
||||
## ##
|
||||
## Literature References ##
|
||||
## ##
|
||||
#############################
|
||||
|
||||
|
||||
P. Ren and J. W. Ponder, "A Polarizable Atomic Multipole Water Model
|
||||
for Molecular Mechanics Simulation", J. Phys. Chem. B, 107, 5933-5947
|
||||
(2003)
|
||||
|
||||
Y. Kong, "Multipole Electrostatic Methods for Protein Modeling with
|
||||
Reaction Field Treatment", Ph.D. thesis, DBBS Program in Molecular
|
||||
Biophysics, Washington University, St. Louis, August, 1997 [available
|
||||
online from http://dasher.wustl.edu/ponder/]
|
||||
|
||||
alternative valence parameters to match symmetric and antisymmetric
|
||||
stretch frequencies by David Semrouni, Ecole Polytechnique, Paris
|
||||
|
||||
|
||||
#############################
|
||||
## ##
|
||||
## Atom Type Definitions ##
|
||||
## ##
|
||||
#############################
|
||||
|
||||
|
||||
atom 1 1 O "AMOEBA Water O" 8 15.995 2
|
||||
atom 2 2 H "AMOEBA Water H" 1 1.008 1
|
||||
|
||||
|
||||
################################
|
||||
## ##
|
||||
## Van der Waals Parameters ##
|
||||
## ##
|
||||
################################
|
||||
|
||||
|
||||
vdw 1 3.4050 0.1100
|
||||
vdw 2 2.6550 0.0135 0.910
|
||||
|
||||
|
||||
##################################
|
||||
## ##
|
||||
## Bond Stretching Parameters ##
|
||||
## ##
|
||||
##################################
|
||||
|
||||
|
||||
#bond 1 2 529.60 0.9572 !! original AMOEBA water
|
||||
bond 1 2 556.85 0.9572
|
||||
|
||||
|
||||
################################
|
||||
## ##
|
||||
## Angle Bending Parameters ##
|
||||
## ##
|
||||
################################
|
||||
|
||||
|
||||
#angle 2 1 2 34.05 108.50 !! original AMOEBA water
|
||||
angle 2 1 2 48.70 108.50
|
||||
|
||||
|
||||
###############################
|
||||
## ##
|
||||
## Urey-Bradley Parameters ##
|
||||
## ##
|
||||
###############################
|
||||
|
||||
|
||||
#ureybrad 2 1 2 38.25 1.5537 !! original AMOEBA water
|
||||
ureybrad 2 1 2 -7.60 1.5537
|
||||
|
||||
|
||||
###################################
|
||||
## ##
|
||||
## Atomic Multipole Parameters ##
|
||||
## ##
|
||||
###################################
|
||||
|
||||
|
||||
multipole 1 -2 -2 -0.51966
|
||||
0.00000 0.00000 0.14279
|
||||
0.37928
|
||||
0.00000 -0.41809
|
||||
0.00000 0.00000 0.03881
|
||||
|
||||
multipole 2 1 2 0.25983
|
||||
-0.03859 0.00000 -0.05818
|
||||
-0.03673
|
||||
0.00000 -0.10739
|
||||
-0.00203 0.00000 0.14412
|
||||
|
||||
|
||||
########################################
|
||||
## ##
|
||||
## Dipole Polarizability Parameters ##
|
||||
## ##
|
||||
########################################
|
||||
|
||||
|
||||
polarize 1 0.837 0.390 2
|
||||
polarize 2 0.496 0.390 1
|
||||
31673
examples/amoeba/data.ubiquitin
Normal file
31673
examples/amoeba/data.ubiquitin
Normal file
File diff suppressed because it is too large
Load Diff
1980
examples/amoeba/data.water_box
Normal file
1980
examples/amoeba/data.water_box
Normal file
File diff suppressed because it is too large
Load Diff
54
examples/amoeba/data.water_dimer.amoeba
Normal file
54
examples/amoeba/data.water_dimer.amoeba
Normal file
@ -0,0 +1,54 @@
|
||||
LAMMPS data file created from Tinker water_dimer.xyz and water03.prm files
|
||||
|
||||
6 atoms
|
||||
4 bonds
|
||||
2 angles
|
||||
2 atom types
|
||||
1 bond types
|
||||
1 angle types
|
||||
-1.463996 0.933234 xlo xhi
|
||||
-0.756549 0.75612 ylo yhi
|
||||
-0.009705 2.935934 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 15.995
|
||||
2 1.008
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 0 -0.024616 -0.001154 -0.003748
|
||||
2 1 2 0 -0.244211 -0.000666 0.933978
|
||||
3 1 2 0 0.932234 -0.000406 -0.008705
|
||||
4 2 1 0 -0.892721 0.000120 2.773674
|
||||
5 2 2 0 -1.462996 0.755120 2.933870
|
||||
6 2 2 0 -1.461809 -0.755549 2.934934
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 1 3
|
||||
3 1 4 5
|
||||
4 1 4 6
|
||||
|
||||
Angles
|
||||
|
||||
1 1 2 1 3
|
||||
2 1 5 4 6
|
||||
|
||||
Bond Coeffs
|
||||
|
||||
1 556.85 0.9572
|
||||
|
||||
Angle Coeffs
|
||||
|
||||
1 48.70 108.50
|
||||
|
||||
Tinker Types
|
||||
|
||||
1 1 1
|
||||
2 2 1
|
||||
3 2 1
|
||||
4 1 2
|
||||
5 2 2
|
||||
6 2 2
|
||||
54
examples/amoeba/data.water_dimer.hippo
Normal file
54
examples/amoeba/data.water_dimer.hippo
Normal file
@ -0,0 +1,54 @@
|
||||
LAMMPS data file created from Tinker water_dimer.xyz and water19.prm files
|
||||
|
||||
6 atoms
|
||||
4 bonds
|
||||
2 angles
|
||||
2 atom types
|
||||
1 bond types
|
||||
1 angle types
|
||||
-1.463996 0.933234 xlo xhi
|
||||
-0.756549 0.75612 ylo yhi
|
||||
-0.009705 2.935934 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 15.999
|
||||
2 1.008
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 0 -0.024616 -0.001154 -0.003748
|
||||
2 1 2 0 -0.244211 -0.000666 0.933978
|
||||
3 1 2 0 0.932234 -0.000406 -0.008705
|
||||
4 2 1 0 -0.892721 0.000120 2.773674
|
||||
5 2 2 0 -1.462996 0.755120 2.933870
|
||||
6 2 2 0 -1.461809 -0.755549 2.934934
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 1 3
|
||||
3 1 4 5
|
||||
4 1 4 6
|
||||
|
||||
Angles
|
||||
|
||||
1 1 2 1 3
|
||||
2 1 5 4 6
|
||||
|
||||
Bond Coeffs
|
||||
|
||||
1 556.85 0.9572
|
||||
|
||||
Angle Coeffs
|
||||
|
||||
1 48.70 107.70
|
||||
|
||||
Tinker Types
|
||||
|
||||
1 1 1
|
||||
2 2 1
|
||||
3 2 1
|
||||
4 1 2
|
||||
5 2 2
|
||||
6 2 2
|
||||
90
examples/amoeba/data.water_hexamer.amoeba
Normal file
90
examples/amoeba/data.water_hexamer.amoeba
Normal file
@ -0,0 +1,90 @@
|
||||
LAMMPS data file created from Tinker water_hexamer.xyz and water03.prm files
|
||||
|
||||
18 atoms
|
||||
12 bonds
|
||||
6 angles
|
||||
2 atom types
|
||||
1 bond types
|
||||
1 angle types
|
||||
-2.517835 2.675716 xlo xhi
|
||||
-1.523041 2.01883 ylo yhi
|
||||
-1.734766 2.220847 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 15.995
|
||||
2 1.008
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 0 -1.502169 -0.191359 1.434927
|
||||
2 1 2 0 -0.601054 -0.596972 1.553718
|
||||
3 1 2 0 -2.006698 -0.422327 2.219847
|
||||
4 2 1 0 -1.744575 -0.382348 -1.309144
|
||||
5 2 2 0 -1.888941 -0.479653 -0.347624
|
||||
6 2 2 0 -2.516835 -0.766765 -1.733766
|
||||
7 3 1 0 -0.560409 2.017830 -0.121984
|
||||
8 3 2 0 -0.947720 1.533567 0.625228
|
||||
9 3 2 0 -0.989831 1.592736 -0.877419
|
||||
10 4 1 0 0.964803 -1.165765 1.439987
|
||||
11 4 2 0 0.979557 -1.522041 0.527833
|
||||
12 4 2 0 1.542224 -0.393692 1.344373
|
||||
13 5 1 0 0.974705 -1.401503 -1.335970
|
||||
14 5 2 0 0.065161 -1.118951 -1.522886
|
||||
15 5 2 0 1.470709 -0.570933 -1.277710
|
||||
16 6 1 0 2.002280 1.057824 -0.124502
|
||||
17 6 2 0 1.141637 1.532266 -0.140121
|
||||
18 6 2 0 2.674716 1.735342 -0.237995
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 1 3
|
||||
3 1 4 5
|
||||
4 1 4 6
|
||||
5 1 7 8
|
||||
6 1 7 9
|
||||
7 1 10 11
|
||||
8 1 10 12
|
||||
9 1 13 14
|
||||
10 1 13 15
|
||||
11 1 16 17
|
||||
12 1 16 18
|
||||
|
||||
Angles
|
||||
|
||||
1 1 2 1 3
|
||||
2 1 5 4 6
|
||||
3 1 8 7 9
|
||||
4 1 11 10 12
|
||||
5 1 14 13 15
|
||||
6 1 17 16 18
|
||||
|
||||
Bond Coeffs
|
||||
|
||||
1 556.85 0.9572
|
||||
|
||||
Angle Coeffs
|
||||
|
||||
1 48.70 108.50
|
||||
|
||||
Tinker Types
|
||||
|
||||
1 1 1
|
||||
2 2 1
|
||||
3 2 1
|
||||
4 1 2
|
||||
5 2 2
|
||||
6 2 2
|
||||
7 1 3
|
||||
8 2 3
|
||||
9 2 3
|
||||
10 1 4
|
||||
11 2 4
|
||||
12 2 4
|
||||
13 1 5
|
||||
14 2 5
|
||||
15 2 5
|
||||
16 1 6
|
||||
17 2 6
|
||||
18 2 6
|
||||
90
examples/amoeba/data.water_hexamer.hippo
Normal file
90
examples/amoeba/data.water_hexamer.hippo
Normal file
@ -0,0 +1,90 @@
|
||||
LAMMPS data file created from Tinker water_hexamer.xyz and water19.prm files
|
||||
|
||||
18 atoms
|
||||
12 bonds
|
||||
6 angles
|
||||
2 atom types
|
||||
1 bond types
|
||||
1 angle types
|
||||
-2.517835 2.675716 xlo xhi
|
||||
-1.523041 2.01883 ylo yhi
|
||||
-1.734766 2.220847 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 15.999
|
||||
2 1.008
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 0 -1.502169 -0.191359 1.434927
|
||||
2 1 2 0 -0.601054 -0.596972 1.553718
|
||||
3 1 2 0 -2.006698 -0.422327 2.219847
|
||||
4 2 1 0 -1.744575 -0.382348 -1.309144
|
||||
5 2 2 0 -1.888941 -0.479653 -0.347624
|
||||
6 2 2 0 -2.516835 -0.766765 -1.733766
|
||||
7 3 1 0 -0.560409 2.017830 -0.121984
|
||||
8 3 2 0 -0.947720 1.533567 0.625228
|
||||
9 3 2 0 -0.989831 1.592736 -0.877419
|
||||
10 4 1 0 0.964803 -1.165765 1.439987
|
||||
11 4 2 0 0.979557 -1.522041 0.527833
|
||||
12 4 2 0 1.542224 -0.393692 1.344373
|
||||
13 5 1 0 0.974705 -1.401503 -1.335970
|
||||
14 5 2 0 0.065161 -1.118951 -1.522886
|
||||
15 5 2 0 1.470709 -0.570933 -1.277710
|
||||
16 6 1 0 2.002280 1.057824 -0.124502
|
||||
17 6 2 0 1.141637 1.532266 -0.140121
|
||||
18 6 2 0 2.674716 1.735342 -0.237995
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 1 1 3
|
||||
3 1 4 5
|
||||
4 1 4 6
|
||||
5 1 7 8
|
||||
6 1 7 9
|
||||
7 1 10 11
|
||||
8 1 10 12
|
||||
9 1 13 14
|
||||
10 1 13 15
|
||||
11 1 16 17
|
||||
12 1 16 18
|
||||
|
||||
Angles
|
||||
|
||||
1 1 2 1 3
|
||||
2 1 5 4 6
|
||||
3 1 8 7 9
|
||||
4 1 11 10 12
|
||||
5 1 14 13 15
|
||||
6 1 17 16 18
|
||||
|
||||
Bond Coeffs
|
||||
|
||||
1 556.85 0.9572
|
||||
|
||||
Angle Coeffs
|
||||
|
||||
1 48.70 107.70
|
||||
|
||||
Tinker Types
|
||||
|
||||
1 1 1
|
||||
2 2 1
|
||||
3 2 1
|
||||
4 1 2
|
||||
5 2 2
|
||||
6 2 2
|
||||
7 1 3
|
||||
8 2 3
|
||||
9 2 3
|
||||
10 1 4
|
||||
11 2 4
|
||||
12 2 4
|
||||
13 1 5
|
||||
14 2 5
|
||||
15 2 5
|
||||
16 1 6
|
||||
17 2 6
|
||||
18 2 6
|
||||
9
examples/amoeba/hippo_water.key
Normal file
9
examples/amoeba/hippo_water.key
Normal file
@ -0,0 +1,9 @@
|
||||
parameters ./hippo.prm
|
||||
|
||||
digits 8
|
||||
|
||||
cutoff 10
|
||||
taper 8
|
||||
|
||||
polar-eps 1e-5
|
||||
usolve-diag 1.0
|
||||
319
examples/amoeba/hippo_water.prm
Normal file
319
examples/amoeba/hippo_water.prm
Normal file
@ -0,0 +1,319 @@
|
||||
|
||||
##############################
|
||||
## ##
|
||||
## Force Field Definition ##
|
||||
## ##
|
||||
##############################
|
||||
|
||||
|
||||
forcefield HIPPO-WATER-2019
|
||||
|
||||
bond-cubic -2.55
|
||||
bond-quartic 3.793125
|
||||
angle-cubic -0.014
|
||||
angle-quartic 0.000056
|
||||
angle-pentic -0.0000007
|
||||
angle-sextic 0.000000022
|
||||
opbendtype ALLINGER
|
||||
opbend-cubic -0.014
|
||||
opbend-quartic 0.000056
|
||||
opbend-pentic -0.0000007
|
||||
opbend-sextic 0.000000022
|
||||
torsionunit 0.5
|
||||
dielectric 1.0
|
||||
polarization MUTUAL
|
||||
rep-12-scale 0.0
|
||||
rep-13-scale 0.0
|
||||
rep-14-scale 1.0
|
||||
rep-15-scale 1.0
|
||||
disp-12-scale 0.0
|
||||
disp-13-scale 0.0
|
||||
disp-14-scale 0.4
|
||||
#disp-15-scale 0.8
|
||||
mpole-12-scale 0.0
|
||||
mpole-13-scale 0.0
|
||||
mpole-14-scale 0.4
|
||||
#mpole-15-scale 0.8
|
||||
polar-12-scale 0.0
|
||||
polar-13-scale 0.0
|
||||
polar-14-scale 1.0
|
||||
polar-15-scale 1.0
|
||||
polar-12-intra 0.0
|
||||
polar-13-intra 0.0
|
||||
polar-14-intra 0.5
|
||||
polar-15-intra 1.0
|
||||
direct-11-scale 0.0
|
||||
direct-12-scale 1.0
|
||||
direct-13-scale 1.0
|
||||
direct-14-scale 1.0
|
||||
mutual-11-scale 1.0
|
||||
mutual-12-scale 1.0
|
||||
mutual-13-scale 1.0
|
||||
mutual-14-scale 1.0
|
||||
induce-12-scale 0.2
|
||||
induce-13-scale 1.0
|
||||
induce-14-scale 1.0
|
||||
induce-15-scale 1.0
|
||||
|
||||
|
||||
#############################
|
||||
## ##
|
||||
## Literature References ##
|
||||
## ##
|
||||
#############################
|
||||
|
||||
|
||||
This is a preliminary parameter set for water based on the HIPPO
|
||||
(Hydrogen-like Intermolecular Polarizable Potential) force field.
|
||||
It uses terms describing charge penetration, damped dispersion, and
|
||||
anisotropic repulsion as per the papers below. The parameters are as
|
||||
of 13 May 2019 and are from Roseane dos Reis Silva and Josh Rackers
|
||||
in the Ponder lab at Washington University. These parameter values
|
||||
are under development and are subject to change.
|
||||
|
||||
J. A. Rackers, Q. Wang, C. Liu, J.-P. Piquemal, P. Ren and J. W. Ponder,
|
||||
An Optimized Charge Penetration Model for Use with the AMOEBA Force Field,
|
||||
Physical Chemistry Chemical Physics, 19, 276-291 (2017)
|
||||
|
||||
J. A. Rackers, C. Liu, P. Ren and J. W. Ponder, A Physically Grounded
|
||||
Damped Dispersion Model with Particle Mesh Ewald Summation, Journal
|
||||
of Chemical Physics, 149, 084115 (2018)
|
||||
|
||||
J. A. Rackers and J. W. Ponder, Classical Pauli Repulsion: An Anisotropic,
|
||||
Atomic Multipole Model, Journal of Chemical Physics, 150, 084104 (2019)
|
||||
|
||||
|
||||
#############################
|
||||
## ##
|
||||
## Atom Type Definitions ##
|
||||
## ##
|
||||
#############################
|
||||
|
||||
|
||||
atom 1 1 O "HIPPO Water O" 8 15.999 2
|
||||
atom 2 2 H "HIPPO Water H" 1 1.008 1
|
||||
|
||||
|
||||
##################################
|
||||
## ##
|
||||
## Bond Stretching Parameters ##
|
||||
## ##
|
||||
##################################
|
||||
|
||||
|
||||
bond 1 2 556.85 0.9572 !! all
|
||||
|
||||
|
||||
################################
|
||||
## ##
|
||||
## Angle Bending Parameters ##
|
||||
## ##
|
||||
################################
|
||||
|
||||
|
||||
#angle 2 1 2 48.70 108.50 !! orig
|
||||
#angle 2 1 2 48.70 107.70 !! 13
|
||||
#angle 2 1 2 48.70 107.70 !! 12
|
||||
#angle 2 1 2 48.70 107.70 !! 16t-i2
|
||||
#angle 2 1 2 48.70 107.70 !! 16t-i6
|
||||
#angle 2 1 2 48.70 107.70 !! 17t-i3
|
||||
angle 2 1 2 48.70 107.70 !! 17t-i6
|
||||
|
||||
|
||||
##################################
|
||||
## ##
|
||||
## Pauli Repulsion Parameters ##
|
||||
## ##
|
||||
##################################
|
||||
|
||||
|
||||
#repulsion 1 2.8478 4.6069 3.3353 !! orig
|
||||
#repulsion 2 2.0560 4.8356 0.7423 !! orig
|
||||
#repulsion 1 2.7716 4.4097 3.3789 !! 13
|
||||
#repulsion 2 2.0410 4.8567 0.6592 !! 13
|
||||
#repulsion 1 2.7875 4.4310 3.3914 !! 12
|
||||
#repulsion 2 2.0510 4.8314 0.6557 !! 12
|
||||
#repulsion 1 2.8604 4.5590 3.3554 !! t16-i2
|
||||
#repulsion 2 2.0508 4.8497 0.7264 !! t16-i2
|
||||
#repulsion 1 2.8618 4.4770 3.3790 !! t16-i6
|
||||
#repulsion 2 2.0658 4.9052 0.6831 !! t16-i6
|
||||
#repulsion 1 2.8644 4.4964 3.3594 !! t17-i3
|
||||
#repulsion 2 2.0605 4.8965 0.6958 !! t17-i3
|
||||
repulsion 1 2.8758 4.4394 3.3883 !! t17-i6
|
||||
repulsion 2 2.0610 4.9367 0.6505 !! t17-i6
|
||||
|
||||
|
||||
#############################
|
||||
## ##
|
||||
## Dispersion Parameters ##
|
||||
## ##
|
||||
#############################
|
||||
|
||||
|
||||
#dispersion 1 16.4682 4.4288 !! orig
|
||||
#dispersion 2 2.9470 4.9751 !! orig
|
||||
#dispersion 1 17.0790 4.3977 !! 13
|
||||
#dispersion 2 4.2262 4.9255 !! 13
|
||||
#dispersion 1 17.0607 4.3872 !! 12
|
||||
#dispersion 2 4.2382 4.9542 !! 12
|
||||
#dispersion 1 16.6803 4.4470 !! t16-i2
|
||||
#dispersion 2 3.4415 4.9267 !! t16-i2
|
||||
#dispersion 1 16.7807 4.4427 !! t16-i6
|
||||
#dispersion 2 3.8508 4.9261 !! t16-i6
|
||||
#dispersion 1 16.6579 4.2763 !! t17-i3
|
||||
#dispersion 2 3.2999 4.9597 !! t17-i3
|
||||
dispersion 1 16.7190 4.3418 !! t17-i6
|
||||
dispersion 2 3.4239 4.9577 !! t17-i6
|
||||
|
||||
|
||||
###################################
|
||||
## ##
|
||||
## Atomic Multipole Parameters ##
|
||||
## ##
|
||||
###################################
|
||||
|
||||
|
||||
!! orig
|
||||
#multipole 1 -2 -2 -0.38280
|
||||
0.00000 0.00000 0.05477
|
||||
0.69866
|
||||
0.00000 -0.60471
|
||||
0.00000 0.00000 -0.09395
|
||||
#multipole 2 1 2 0.19140
|
||||
0.00000 0.00000 -0.20097
|
||||
0.03881
|
||||
0.00000 0.02214
|
||||
0.00000 0.00000 -0.06095
|
||||
!! 13
|
||||
#multipole 1 -2 -2 -0.38296
|
||||
0.00000 0.00000 0.05086
|
||||
0.70053
|
||||
0.00000 -0.61138
|
||||
0.00000 0.00000 -0.08915
|
||||
#multipole 2 1 2 0.19148
|
||||
0.00000 0.00000 -0.20142
|
||||
0.06672
|
||||
0.00000 0.04168
|
||||
0.01245 0.00000 -0.10840
|
||||
!! 12
|
||||
#multipole 1 -2 -2 -0.38468
|
||||
0.00000 0.00000 0.05069
|
||||
0.70076
|
||||
0.00000 -0.61593
|
||||
0.00000 0.00000 -0.08483
|
||||
#multipole 2 1 2 0.19234
|
||||
0.00000 0.00000 -0.20236
|
||||
0.06136
|
||||
0.00000 0.04166
|
||||
0.00591 0.00000 -0.10302
|
||||
!! t16-i2
|
||||
#multipole 1 -2 -2 -0.38236
|
||||
0.00000 0.00000 0.05488
|
||||
0.69693
|
||||
0.00000 -0.60514
|
||||
0.00000 0.00000 -0.09179
|
||||
#multipole 2 1 2 0.19118
|
||||
0.00000 0.00000 -0.20081
|
||||
0.04614
|
||||
0.00000 0.02258
|
||||
0.00000 0.00000 -0.07172
|
||||
!! t16-i6
|
||||
#multipole 1 -2 -2 -0.37854
|
||||
0.00000 0.00000 0.05439
|
||||
0.68442
|
||||
0.00000 -0.61857
|
||||
0.00000 0.00000 -0.06585
|
||||
#multipole 2 1 2 0.18927
|
||||
0.00000 0.00000 -0.19918
|
||||
0.05839
|
||||
0.00000 0.03699
|
||||
0.00683 0.00000 -0.09538
|
||||
!! t17-i3
|
||||
#multipole 1 -2 -2 -0.37944
|
||||
0.00000 0.00000 0.05496
|
||||
0.69091
|
||||
0.00000 -0.60566
|
||||
0.00000 0.00000 -0.08525
|
||||
#multipole 2 1 2 0.18972
|
||||
0.00000 0.00000 -0.20057
|
||||
0.05030
|
||||
0.00000 0.03290
|
||||
0.00187 0.00000 -0.08320
|
||||
!! t17-i6
|
||||
multipole 1 -2 -2 -0.37724
|
||||
0.00000 0.00000 0.05410
|
||||
0.68565
|
||||
0.00000 -0.60559
|
||||
0.00000 0.00000 -0.08006
|
||||
multipole 2 1 2 0.18862
|
||||
0.00000 0.00000 -0.19902
|
||||
0.06206
|
||||
0.00000 0.04341
|
||||
0.00709 0.00000 -0.10547
|
||||
|
||||
|
||||
#####################################
|
||||
## ##
|
||||
## Charge Penetration Parameters ##
|
||||
## ##
|
||||
#####################################
|
||||
|
||||
|
||||
#chgpen 1 6.0000 4.4288 !! orig
|
||||
#chgpen 2 1.0000 4.9751 !! orig
|
||||
#chgpen 1 6.0000 4.3977 !! 13
|
||||
#chgpen 2 1.0000 4.9255 !! 13
|
||||
#chgpen 1 6.0000 4.3872 !! 12
|
||||
#chgpen 2 1.0000 4.9542 !! 12
|
||||
#chgpen 1 6.0000 4.4470 !! t16-i2
|
||||
#chgpen 2 1.0000 4.9767 !! t16-i2
|
||||
#chgpen 1 6.0000 4.4427 !! t16-i6
|
||||
#chgpen 2 1.0000 4.9261 !! t16-i6
|
||||
#chgpen 1 6.0000 4.3763 !! t17-i3
|
||||
#chgpen 2 1.0000 4.9597 !! t17-i3
|
||||
chgpen 1 6.0000 4.3418 !! t17-i6
|
||||
chgpen 2 1.0000 4.9577 !! t17-i6
|
||||
|
||||
|
||||
########################################
|
||||
## ##
|
||||
## Dipole Polarizability Parameters ##
|
||||
## ##
|
||||
########################################
|
||||
|
||||
|
||||
#polarize 1 0.7482 2 !! orig
|
||||
#polarize 2 0.3703 1 !! orig
|
||||
#polarize 1 0.7448 2 !! 13
|
||||
#polarize 2 0.3897 1 !! 13
|
||||
#polarize 1 0.7442 2 !! 12
|
||||
#polarize 2 0.3874 1 !! 12
|
||||
#polarize 1 0.7499 2 !! t16-i2
|
||||
#polarize 2 0.3706 1 !! t16-i2
|
||||
#polarize 1 0.7403 2 !! t16-i6
|
||||
#polarize 2 0.3774 1 !! t16-i6
|
||||
#polarize 1 0.7416 2 !! t17-i3
|
||||
#polarize 2 0.3670 1 !! t17-i3
|
||||
polarize 1 0.7332 2 !! t17-i6
|
||||
polarize 2 0.3691 1 !! t17-i6
|
||||
|
||||
|
||||
##################################
|
||||
## ##
|
||||
## Charge Transfer Parameters ##
|
||||
## ##
|
||||
##################################
|
||||
|
||||
|
||||
#chgtrn 1 3.5788 0.0000 !! orig
|
||||
#chgtrn 2 0.0000 3.3292 !1 orig
|
||||
#chgtrn 1 3.5856 0.0000 !! 13
|
||||
#chgtrn 2 0.0000 3.3482 !! 13
|
||||
#chgtrn 1 3.5867 0.0000 !! t16-i2
|
||||
#chgtrn 2 0.0000 3.3105 !! t16-i2
|
||||
#chgtrn 1 3.5812 0.0000 !! t16-i6
|
||||
#chgtrn 2 0.0000 3.2909 !! t16-i6
|
||||
#chgtrn 1 3.5762 0.0000 !! t17-i3
|
||||
#chgtrn 2 0.0000 3.2881 !! t17-i3
|
||||
chgtrn 1 3.5551 0.0000 !! t17-i6
|
||||
chgtrn 2 0.0000 3.2812 !! t17-i6
|
||||
105
examples/amoeba/in.ubiquitin
Normal file
105
examples/amoeba/in.ubiquitin
Normal file
@ -0,0 +1,105 @@
|
||||
# default cmd-line variable settings
|
||||
|
||||
variable a index ""
|
||||
variable diff index 0
|
||||
|
||||
units real
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
comm_modify cutoff 5.0
|
||||
|
||||
atom_style amoeba
|
||||
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
|
||||
|
||||
bond_style class2
|
||||
angle_style amoeba
|
||||
#dihedral_style nharmonic
|
||||
dihedral_style none
|
||||
|
||||
# per-atom properties required by AMOEBA or HIPPO
|
||||
|
||||
fix amtype all property/atom i_amtype ghost yes
|
||||
fix extra all property/atom &
|
||||
i_amgroup i_ired i_xaxis i_yaxis i_zaxis d_pval ghost yes
|
||||
fix extra2 all property/atom i_polaxe
|
||||
|
||||
read_data data.${struc}.angles fix amtype NULL "Tinker Types"
|
||||
#read_data data.watersmall fix amtype NULL "Tinker Types"
|
||||
#read_data data.water_hexamer fix amtype NULL "Tinker Types"
|
||||
|
||||
# insure all 1-2,1-3,1-4,1-5 are in Tinker neigh list
|
||||
|
||||
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
|
||||
|
||||
# force field terms
|
||||
# depends on 2 command-line variables
|
||||
# ff = amoeba or hippo, a = args for pair_style
|
||||
|
||||
if "${ff} == amoeba" then &
|
||||
"pair_style amoeba $a" &
|
||||
"pair_coeff * * amoeba.prm amoeba.key"
|
||||
|
||||
if "${ff} == hippo" then &
|
||||
"pair_style hippo $a" &
|
||||
"pair_coeff * * hippo.prm hippo.key"
|
||||
|
||||
if "${ff} == amoeba_direct" then &
|
||||
"pair_style amoeba $a" &
|
||||
"pair_coeff * * amoeba_direct.prm amoeba_direct.key"
|
||||
|
||||
if "${ff} == hippo_direct" then &
|
||||
"pair_style hippo $a" &
|
||||
"pair_coeff * * hippo_direct.prm hippo_direct.key"
|
||||
|
||||
if "${ff} == amoeba_opt" then &
|
||||
"pair_style amoeba $a" &
|
||||
"pair_coeff * * amoeba.prm amoeba_opt.key"
|
||||
|
||||
if "${ff} == hippo_opt" then &
|
||||
"pair_style hippo $a" &
|
||||
"pair_coeff * * hippo.prm hippo_opt.key"
|
||||
|
||||
# optional turn off angle and dihedral
|
||||
|
||||
#angle_style none
|
||||
dihedral_style none
|
||||
|
||||
# numeric difference of forces
|
||||
|
||||
#compute nd all pe
|
||||
#fix nd all numdiff ${diff} 1.0e-5 nd
|
||||
#variable dx atom abs(fx+f_nd[1])
|
||||
#variable dy atom abs(fy+f_nd[2])
|
||||
#variable dz atom abs(fz+f_nd[3])
|
||||
#compute rd all reduce max v_dx v_dy v_dz
|
||||
|
||||
# setup force components this way so can dump them
|
||||
|
||||
fix fhal all store/state 0 fx fy fz
|
||||
fix frepulse all store/state 0 fx fy fz
|
||||
fix fdisp all store/state 0 fx fy fz
|
||||
fix fpolar all store/state 0 fx fy fz
|
||||
fix fmpole all store/state 0 fx fy fz
|
||||
fix fqxfer all store/state 0 fx fy fz
|
||||
|
||||
dump 1 all custom 1 ${dumpfile} id type x y z fx fy fz &
|
||||
# f_fhal[1] f_fhal[2] f_fhal[3] &
|
||||
# f_fdisp[1] f_fdisp[2] f_fdisp[3] &
|
||||
# f_frepulse[1] f_frepulse[2] f_frepulse[3] &
|
||||
# f_fpolar[1] f_fpolar[2] f_fpolar[3] &
|
||||
# f_fmpole[1] f_fmpole[2] f_fmpole[3] &
|
||||
# f_fqxfer[1] f_fqxfer[2] f_fqxfer[3]
|
||||
# f_nd[1] f_nd[2] f_nd[3]
|
||||
|
||||
dump_modify 1 format float "%20.16g" sort id
|
||||
|
||||
compute virial all pressure NULL virial
|
||||
|
||||
# thermo output
|
||||
|
||||
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*] #c_rd[*]
|
||||
thermo_modify format float "%20.16g"
|
||||
|
||||
# 0-step run
|
||||
|
||||
run 0
|
||||
106
examples/amoeba/in.water_box
Normal file
106
examples/amoeba/in.water_box
Normal file
@ -0,0 +1,106 @@
|
||||
# test of HIPPO water dimer system
|
||||
|
||||
# default cmd-line variable settings
|
||||
|
||||
variable a index ""
|
||||
variable diff index 0
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
atom_style amoeba
|
||||
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
|
||||
|
||||
bond_style class2
|
||||
angle_style amoeba
|
||||
|
||||
# per-atom properties required by AMOEBA or HIPPO
|
||||
|
||||
fix amtype all property/atom i_amtype ghost yes
|
||||
fix extra all property/atom &
|
||||
i_amgroup i_ired i_xaxis i_yaxis i_zaxis d_pval ghost yes
|
||||
fix extra2 all property/atom i_polaxe
|
||||
|
||||
read_data data.${struc}.angles fix amtype NULL "Tinker Types"
|
||||
#read_data data.watersmall fix amtype NULL "Tinker Types"
|
||||
#read_data data.water_hexamer fix amtype NULL "Tinker Types"
|
||||
|
||||
# insure all 1-2,1-3,1-4 are in Tinker neigh list
|
||||
|
||||
special_bonds lj/coul 0.5 0.5 0.5
|
||||
|
||||
# force field terms
|
||||
# depends on 2 command-line variables
|
||||
# ff = amoeba or hippo, a = args for pair_style
|
||||
|
||||
if "${ff} == amoeba" then &
|
||||
"pair_style amoeba $a" &
|
||||
"pair_coeff * * amoeba.prm amoeba.key"
|
||||
|
||||
if "${ff} == hippo" then &
|
||||
"pair_style hippo $a" &
|
||||
"pair_coeff * * hippo.prm hippo.key"
|
||||
|
||||
if "${ff} == amoeba_direct" then &
|
||||
"pair_style amoeba $a" &
|
||||
"pair_coeff * * amoeba_direct.prm amoeba_direct.key"
|
||||
|
||||
if "${ff} == hippo_direct" then &
|
||||
"pair_style hippo $a" &
|
||||
"pair_coeff * * hippo_direct.prm hippo_direct.key"
|
||||
|
||||
if "${ff} == amoeba_opt" then &
|
||||
"pair_style amoeba $a" &
|
||||
"pair_coeff * * amoeba.prm amoeba_opt.key"
|
||||
|
||||
if "${ff} == hippo_opt" then &
|
||||
"pair_style hippo $a" &
|
||||
"pair_coeff * * hippo.prm hippo_opt.key"
|
||||
|
||||
|
||||
# turn off bond/angle interactions for now
|
||||
|
||||
#bond_style none
|
||||
#angle_style none
|
||||
|
||||
# numeric difference of forces
|
||||
|
||||
#compute nd all pe
|
||||
#fix nd all numdiff ${diff} 1.0e-5 nd
|
||||
#variable dx atom abs(fx+f_nd[1])
|
||||
#variable dy atom abs(fy+f_nd[2])
|
||||
#variable dz atom abs(fz+f_nd[3])
|
||||
#compute rd all reduce max v_dx v_dy v_dz
|
||||
|
||||
# setup force components this way so can dump them
|
||||
|
||||
fix fhal all store/state 0 fx fy fz
|
||||
fix frepulse all store/state 0 fx fy fz
|
||||
fix fdisp all store/state 0 fx fy fz
|
||||
fix fpolar all store/state 0 fx fy fz
|
||||
fix fmpole all store/state 0 fx fy fz
|
||||
fix fqxfer all store/state 0 fx fy fz
|
||||
|
||||
dump 1 all custom 1 ${dumpfile} id type x y z fx fy fz &
|
||||
# f_fhal[1] f_fhal[2] f_fhal[3] &
|
||||
# f_fdisp[1] f_fdisp[2] f_fdisp[3] &
|
||||
# f_frepulse[1] f_frepulse[2] f_frepulse[3] &
|
||||
# f_fpolar[1] f_fpolar[2] f_fpolar[3] &
|
||||
# f_fmpole[1] f_fmpole[2] f_fmpole[3] &
|
||||
# f_fqxfer[1] f_fqxfer[2] f_fqxfer[3] &
|
||||
# f_nd[1] f_nd[2] f_nd[3]
|
||||
|
||||
dump_modify 1 format float "%15.10g" sort id
|
||||
|
||||
compute virial all pressure NULL virial
|
||||
|
||||
# thermo output
|
||||
|
||||
thermo_style custom step temp epair ebond eanble etotal press c_virial[*] #c_rd[*]
|
||||
thermo_modify format float "%15.10g"
|
||||
|
||||
# 0-step run
|
||||
|
||||
run 0
|
||||
104
examples/amoeba/in.water_dimer
Normal file
104
examples/amoeba/in.water_dimer
Normal file
@ -0,0 +1,104 @@
|
||||
# test of HIPPO water dimer system
|
||||
|
||||
# default cmd-line variable settings
|
||||
|
||||
variable a index ""
|
||||
variable diff index 0
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
boundary s s s
|
||||
|
||||
atom_style amoeba
|
||||
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
|
||||
|
||||
bond_style class2
|
||||
angle_style amoeba
|
||||
dihedral_style none
|
||||
|
||||
# per-atom properties required by AMOEBA or HIPPO
|
||||
|
||||
fix amtype all property/atom i_amtype ghost yes
|
||||
fix extra all property/atom &
|
||||
i_amgroup i_ired i_xaxis i_yaxis i_zaxis d_pval ghost yes
|
||||
fix extra2 all property/atom i_polaxe
|
||||
|
||||
read_data data.${struc}.bonds fix amtype NULL "Tinker Types"
|
||||
#read_data data.watersmall fix amtype NULL "Tinker Types"
|
||||
#read_data data.water_hexamer fix amtype NULL "Tinker Types"
|
||||
|
||||
# insure all 1-2,1-3,1-4 are in Tinker neigh list
|
||||
|
||||
special_bonds lj/coul 0.5 0.5 0.5
|
||||
|
||||
# force field terms
|
||||
# depends on 2 command-line variables
|
||||
# ff = amoeba or hippo, a = args for pair_style
|
||||
|
||||
if "${ff} == amoeba" then &
|
||||
"pair_style amoeba $a" &
|
||||
"pair_coeff * * amoeba.prm amoeba.key"
|
||||
|
||||
if "${ff} == hippo" then &
|
||||
"pair_style hippo $a" &
|
||||
"pair_coeff * * hippo.prm hippo.key"
|
||||
|
||||
if "${ff} == amoeba_direct" then &
|
||||
"pair_style amoeba $a" &
|
||||
"pair_coeff * * amoeba_direct.prm amoeba_direct.key"
|
||||
|
||||
if "${ff} == hippo_direct" then &
|
||||
"pair_style hippo $a" &
|
||||
"pair_coeff * * hippo_direct.prm hippo_direct.key"
|
||||
|
||||
if "${ff} == amoeba_opt" then &
|
||||
"pair_style amoeba $a" &
|
||||
"pair_coeff * * amoeba.prm amoeba_opt.key"
|
||||
|
||||
if "${ff} == hippo_opt" then &
|
||||
"pair_style hippo $a" &
|
||||
"pair_coeff * * hippo.prm hippo_opt.key"
|
||||
|
||||
|
||||
# turn off bond/angle interactions for now
|
||||
|
||||
#bond_style none
|
||||
#angle_style none
|
||||
|
||||
# numeric difference of forces
|
||||
|
||||
#compute nd all pe
|
||||
#fix nd all numdiff ${diff} 1.0e-5 nd
|
||||
#variable dx atom abs(fx+f_nd[1])
|
||||
#variable dy atom abs(fy+f_nd[2])
|
||||
#variable dz atom abs(fz+f_nd[3])
|
||||
#compute rd all reduce max v_dx v_dy v_dz
|
||||
|
||||
# setup force components this way so can dump them
|
||||
|
||||
fix fhal all store/state 0 fx fy fz
|
||||
fix frepulse all store/state 0 fx fy fz
|
||||
fix fdisp all store/state 0 fx fy fz
|
||||
fix fpolar all store/state 0 fx fy fz
|
||||
fix fmpole all store/state 0 fx fy fz
|
||||
fix fqxfer all store/state 0 fx fy fz
|
||||
|
||||
dump 1 all custom 1 ${dumpfile} id type fx fy fz &
|
||||
# f_fhal[1] f_fhal[2] f_fhal[3] &
|
||||
# f_fdisp[1] f_fdisp[2] f_fdisp[3] &
|
||||
# f_frepulse[1] f_frepulse[2] f_frepulse[3] &
|
||||
# f_fpolar[1] f_fpolar[2] f_fpolar[3] &
|
||||
# f_fmpole[1] f_fmpole[2] f_fmpole[3] &
|
||||
# f_fqxfer[1] f_fqxfer[2] f_fqxfer[3] &
|
||||
# f_nd[1] f_nd[2] f_nd[3]
|
||||
|
||||
dump_modify 1 format float "%15.10g" sort id
|
||||
|
||||
# thermo output
|
||||
|
||||
thermo_style custom step temp epair ebond eangle etotal press #c_rd[*]
|
||||
thermo_modify format float "%15.10g"
|
||||
|
||||
# 0-step run
|
||||
|
||||
run 0
|
||||
103
examples/amoeba/in.water_hexamer
Normal file
103
examples/amoeba/in.water_hexamer
Normal file
@ -0,0 +1,103 @@
|
||||
# test of HIPPO water dimer system
|
||||
|
||||
# default cmd-line variable settings
|
||||
|
||||
variable a index ""
|
||||
variable diff index 0
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
boundary s s s
|
||||
|
||||
atom_style amoeba
|
||||
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
# per-atom properties required by AMOEBA or HIPPO
|
||||
|
||||
fix amtype all property/atom i_amtype ghost yes
|
||||
fix extra all property/atom &
|
||||
i_amgroup i_ired i_xaxis i_yaxis i_zaxis d_pval ghost yes
|
||||
fix extra2 all property/atom i_polaxe
|
||||
|
||||
read_data data.${struc} fix amtype NULL "Tinker Types"
|
||||
#read_data data.watersmall fix amtype NULL "Tinker Types"
|
||||
#read_data data.water_hexamer fix amtype NULL "Tinker Types"
|
||||
|
||||
# insure all 1-2,1-3,1-4 are in Tinker neigh list
|
||||
|
||||
special_bonds lj/coul 0.5 0.5 0.5
|
||||
|
||||
# force field terms
|
||||
# depends on 2 command-line variables
|
||||
# ff = amoeba or hippo, a = args for pair_style
|
||||
|
||||
if "${ff} == amoeba" then &
|
||||
"pair_style amoeba $a" &
|
||||
"pair_coeff * * amoeba.prm amoeba.key"
|
||||
|
||||
if "${ff} == hippo" then &
|
||||
"pair_style hippo $a" &
|
||||
"pair_coeff * * hippo.prm hippo.key"
|
||||
|
||||
if "${ff} == amoeba_direct" then &
|
||||
"pair_style amoeba $a" &
|
||||
"pair_coeff * * amoeba_direct.prm amoeba_direct.key"
|
||||
|
||||
if "${ff} == hippo_direct" then &
|
||||
"pair_style hippo $a" &
|
||||
"pair_coeff * * hippo_direct.prm hippo_direct.key"
|
||||
|
||||
if "${ff} == amoeba_opt" then &
|
||||
"pair_style amoeba $a" &
|
||||
"pair_coeff * * amoeba.prm amoeba_opt.key"
|
||||
|
||||
if "${ff} == hippo_opt" then &
|
||||
"pair_style hippo $a" &
|
||||
"pair_coeff * * hippo.prm hippo_opt.key"
|
||||
|
||||
|
||||
# turn off bond/angle interactions for now
|
||||
|
||||
bond_style none
|
||||
angle_style none
|
||||
|
||||
# numeric difference of forces
|
||||
|
||||
#compute nd all pe
|
||||
#fix nd all numdiff ${diff} 1.0e-5 nd
|
||||
#variable dx atom abs(fx+f_nd[1])
|
||||
#variable dy atom abs(fy+f_nd[2])
|
||||
#variable dz atom abs(fz+f_nd[3])
|
||||
#compute rd all reduce max v_dx v_dy v_dz
|
||||
|
||||
# setup force components this way so can dump them
|
||||
|
||||
fix fhal all store/state 0 fx fy fz
|
||||
fix frepulse all store/state 0 fx fy fz
|
||||
fix fdisp all store/state 0 fx fy fz
|
||||
fix fpolar all store/state 0 fx fy fz
|
||||
fix fmpole all store/state 0 fx fy fz
|
||||
fix fqxfer all store/state 0 fx fy fz
|
||||
|
||||
dump 1 all custom 1 ${dumpfile} id type x y z fx fy fz &
|
||||
# f_fhal[1] f_fhal[2] f_fhal[3] &
|
||||
# f_fdisp[1] f_fdisp[2] f_fdisp[3] &
|
||||
# f_frepulse[1] f_frepulse[2] f_frepulse[3] &
|
||||
# f_fpolar[1] f_fpolar[2] f_fpolar[3] &
|
||||
# f_fmpole[1] f_fmpole[2] f_fmpole[3] &
|
||||
# f_fqxfer[1] f_fqxfer[2] f_fqxfer[3] &
|
||||
# f_nd[1] f_nd[2] f_nd[3]
|
||||
|
||||
dump_modify 1 format float "%15.10g" sort id
|
||||
|
||||
# thermo output
|
||||
|
||||
thermo_style custom step temp epair emol etotal press #c_rd[*]
|
||||
thermo_modify format float "%15.10g"
|
||||
|
||||
# 0-step run
|
||||
|
||||
run 0
|
||||
9738
examples/amoeba/ubiquitin.xyz
Normal file
9738
examples/amoeba/ubiquitin.xyz
Normal file
File diff suppressed because it is too large
Load Diff
649
examples/amoeba/water_box.xyz
Normal file
649
examples/amoeba/water_box.xyz
Normal file
@ -0,0 +1,649 @@
|
||||
648 Water Cubic Box (18.643 Ang, 216 AMOEBA)
|
||||
1 O 8.679662 7.087692 -0.696862 1 2 3
|
||||
2 H 7.809455 6.755792 -0.382259 2 1
|
||||
3 H 8.722232 6.814243 -1.617561 2 1
|
||||
4 O -0.117313 8.244447 6.837616 1 5 6
|
||||
5 H 0.216892 7.895445 6.050027 2 4
|
||||
6 H 0.444268 7.826013 7.530196 2 4
|
||||
7 O 8.379057 -0.092611 6.814631 1 8 9
|
||||
8 H 9.340423 0.098069 6.734062 2 7
|
||||
9 H 7.939619 0.573676 6.269838 2 7
|
||||
10 O 6.589952 1.844323 -6.923167 1 11 12
|
||||
11 H 5.885429 2.402305 -6.717934 2 10
|
||||
12 H 6.181533 1.062747 -7.273678 2 10
|
||||
13 O 7.146600 5.753582 2.331517 1 14 15
|
||||
14 H 6.368123 6.126035 2.862678 2 13
|
||||
15 H 7.025018 6.294645 1.518196 2 13
|
||||
16 O -2.426581 -8.504195 -2.504834 1 17 18
|
||||
17 H -1.692063 -8.368252 -3.058292 2 16
|
||||
18 H -2.793207 -7.602469 -2.403097 2 16
|
||||
19 O -8.038375 -3.605589 2.303691 1 20 21
|
||||
20 H -8.113753 -4.248127 3.018494 2 19
|
||||
21 H -7.619392 -2.863004 2.709622 2 19
|
||||
22 O -1.480631 8.244085 -8.272215 1 23 24
|
||||
23 H -2.090204 8.687978 -7.676996 2 22
|
||||
24 H -0.700878 8.823325 -8.322213 2 22
|
||||
25 O -3.741962 -2.777830 -2.326319 1 26 27
|
||||
26 H -4.620456 -2.444778 -2.390519 2 25
|
||||
27 H -3.728921 -3.160952 -1.433101 2 25
|
||||
28 O -6.467812 -5.265942 0.408263 1 29 30
|
||||
29 H -6.585076 -4.796537 -0.413008 2 28
|
||||
30 H -7.021252 -4.752640 1.007958 2 28
|
||||
31 O 9.273577 5.342431 4.055460 1 32 33
|
||||
32 H 8.645939 5.466500 4.837640 2 31
|
||||
33 H 8.741774 5.686149 3.302820 2 31
|
||||
34 O 1.830160 4.276731 -6.993499 1 35 36
|
||||
35 H 1.703275 5.223773 -6.703852 2 34
|
||||
36 H 2.408113 3.853447 -6.383339 2 34
|
||||
37 O 1.964382 6.832988 8.373101 1 38 39
|
||||
38 H 2.496135 7.215781 9.056298 2 37
|
||||
39 H 1.811283 5.905846 8.573539 2 37
|
||||
40 O 5.405568 4.388994 7.932737 1 41 42
|
||||
41 H 5.537380 3.438955 7.781311 2 40
|
||||
42 H 4.755156 4.734908 7.290617 2 40
|
||||
43 O 3.229998 2.928417 -1.090650 1 44 45
|
||||
44 H 3.931090 3.198265 -1.702769 2 43
|
||||
45 H 3.004438 3.708969 -0.493266 2 43
|
||||
46 O 7.462400 5.262829 6.131170 1 47 48
|
||||
47 H 8.025650 5.588493 6.881770 2 46
|
||||
48 H 6.935076 4.455766 6.325405 2 46
|
||||
49 O -8.864042 7.023845 -6.659632 1 50 51
|
||||
50 H -8.370939 6.372557 -7.141895 2 49
|
||||
51 H -9.489800 7.315873 -7.293125 2 49
|
||||
52 O -4.526299 3.549989 8.030031 1 53 54
|
||||
53 H -5.169770 4.224127 7.731323 2 52
|
||||
54 H -4.262096 3.801892 8.884875 2 52
|
||||
55 O 4.823286 -1.386218 4.038464 1 56 57
|
||||
56 H 5.493155 -0.669965 4.013081 2 55
|
||||
57 H 4.187463 -1.101832 3.338433 2 55
|
||||
58 O -2.151150 -2.017060 -8.593685 1 59 60
|
||||
59 H -2.475709 -2.320356 -7.783564 2 58
|
||||
60 H -2.650484 -2.434614 -9.307384 2 58
|
||||
61 O 1.944893 4.933226 0.497910 1 62 63
|
||||
62 H 2.553221 5.263352 1.205303 2 61
|
||||
63 H 2.082534 5.590999 -0.202171 2 61
|
||||
64 O -6.827006 -5.285917 -2.371899 1 65 66
|
||||
65 H -7.405873 -6.022738 -2.075913 2 64
|
||||
66 H -6.398443 -5.453726 -3.235054 2 64
|
||||
67 O -8.538047 -7.577917 -1.688532 1 68 69
|
||||
68 H -8.075591 -8.448260 -1.513455 2 67
|
||||
69 H -9.389507 -7.836271 -2.051835 2 67
|
||||
70 O -6.916556 -1.100882 -5.168782 1 71 72
|
||||
71 H -6.365888 -1.659366 -5.746210 2 70
|
||||
72 H -6.538885 -0.249374 -5.325993 2 70
|
||||
73 O 6.330290 -9.323893 -6.416630 1 74 75
|
||||
74 H 7.026026 -9.680578 -7.007727 2 73
|
||||
75 H 6.812488 -8.683594 -5.925799 2 73
|
||||
76 O -2.424345 -5.918126 2.701855 1 77 78
|
||||
77 H -1.613829 -5.486394 2.503024 2 76
|
||||
78 H -3.144797 -5.307275 2.618121 2 76
|
||||
79 O 0.637202 -6.080457 5.849135 1 80 81
|
||||
80 H 0.892312 -6.092342 4.907709 2 79
|
||||
81 H -0.339074 -5.838972 5.853292 2 79
|
||||
82 O 5.199216 -2.264918 -0.138343 1 83 84
|
||||
83 H 5.802838 -2.788698 -0.697536 2 82
|
||||
84 H 5.670340 -1.679393 0.462296 2 82
|
||||
85 O 0.510145 7.629450 4.054500 1 86 87
|
||||
86 H -0.071135 8.146563 3.452959 2 85
|
||||
87 H 1.464962 7.740819 3.669172 2 85
|
||||
88 O 3.146724 8.895843 6.526257 1 89 90
|
||||
89 H 3.506091 8.599906 7.352942 2 88
|
||||
90 H 2.145729 8.929622 6.682029 2 88
|
||||
91 O 7.308541 -8.339335 -2.471342 1 92 93
|
||||
92 H 6.562127 -8.180601 -3.062803 2 91
|
||||
93 H 6.993025 -8.364954 -1.531235 2 91
|
||||
94 O -7.530792 1.069683 4.989387 1 95 96
|
||||
95 H -7.565406 1.971422 4.648636 2 94
|
||||
96 H -7.938250 0.433547 4.370266 2 94
|
||||
97 O 4.452035 2.700609 -5.437815 1 98 99
|
||||
98 H 4.603326 3.058652 -4.551590 2 97
|
||||
99 H 4.386453 1.737004 -5.180419 2 97
|
||||
100 O 8.427922 -8.619286 1.784691 1 101 102
|
||||
101 H 8.340498 -8.005342 2.536225 2 100
|
||||
102 H 8.496720 -9.530562 2.174667 2 100
|
||||
103 O -8.109456 1.753830 -3.096997 1 104 105
|
||||
104 H -7.245287 1.827177 -2.721417 2 103
|
||||
105 H -8.082178 1.783171 -4.059329 2 103
|
||||
106 O 2.776933 -5.701955 7.748213 1 107 108
|
||||
107 H 3.287974 -5.069688 7.233816 2 106
|
||||
108 H 1.987041 -5.817355 7.200131 2 106
|
||||
109 O 3.635171 -6.953519 5.339628 1 110 111
|
||||
110 H 3.353851 -7.592789 6.031367 2 109
|
||||
111 H 2.875801 -6.787975 4.740576 2 109
|
||||
112 O 6.888027 -4.169023 -1.800190 1 113 114
|
||||
113 H 7.559735 -4.813701 -2.004669 2 112
|
||||
114 H 6.603805 -3.759237 -2.626496 2 112
|
||||
115 O -4.470837 -4.105640 3.415362 1 116 117
|
||||
116 H -4.991607 -3.358538 3.140956 2 115
|
||||
117 H -4.791764 -4.392214 4.254387 2 115
|
||||
118 O 8.282263 -0.462068 -2.560579 1 119 120
|
||||
119 H 8.776769 -1.293641 -2.335945 2 118
|
||||
120 H 8.760297 0.384816 -2.651128 2 118
|
||||
121 O 4.737236 1.616430 4.901115 1 122 123
|
||||
122 H 3.969692 2.168368 5.152631 2 121
|
||||
123 H 5.184651 2.148403 4.154746 2 121
|
||||
124 O -3.497332 -5.781436 -2.202713 1 125 126
|
||||
125 H -4.038857 -5.773824 -1.381680 2 124
|
||||
126 H -4.152970 -6.012265 -2.829379 2 124
|
||||
127 O -2.863989 -0.259334 -1.857006 1 128 129
|
||||
128 H -2.132201 -0.027953 -1.174211 2 127
|
||||
129 H -2.873625 -1.224425 -1.874253 2 127
|
||||
130 O 1.138300 1.133100 -2.085899 1 131 132
|
||||
131 H 1.965506 1.503520 -1.725316 2 130
|
||||
132 H 0.420521 1.534440 -1.551356 2 130
|
||||
133 O -0.561328 4.590705 -2.780017 1 134 135
|
||||
134 H -0.061173 3.919356 -3.294128 2 133
|
||||
135 H -0.082763 4.733898 -1.955602 2 133
|
||||
136 O -6.423002 -1.705204 -2.528225 1 137 138
|
||||
137 H -7.233989 -1.949552 -1.975418 2 136
|
||||
138 H -6.678416 -1.321413 -3.351278 2 136
|
||||
139 O -2.772100 2.552210 -0.672282 1 140 141
|
||||
140 H -2.907489 3.483552 -0.385605 2 139
|
||||
141 H -2.977127 2.592348 -1.635820 2 139
|
||||
142 O 6.708678 -4.852016 -8.379280 1 143 144
|
||||
143 H 6.593474 -5.094964 -7.447187 2 142
|
||||
144 H 6.582524 -5.591596 -8.966502 2 142
|
||||
145 O -8.497001 -0.440284 2.803721 1 146 147
|
||||
146 H -8.422350 0.331961 2.183451 2 145
|
||||
147 H -9.377295 -0.756160 2.677026 2 145
|
||||
148 O 2.975383 -0.894970 6.060783 1 149 150
|
||||
149 H 2.093991 -0.995700 5.670129 2 148
|
||||
150 H 3.458832 -0.759248 5.263958 2 148
|
||||
151 O -6.085023 -1.629620 7.970284 1 152 153
|
||||
152 H -6.685848 -2.391830 7.820849 2 151
|
||||
153 H -6.177296 -1.190584 8.835912 2 151
|
||||
154 O -3.763523 -3.356777 8.285436 1 155 156
|
||||
155 H -4.660650 -3.029414 8.406662 2 154
|
||||
156 H -3.411834 -3.178947 7.431180 2 154
|
||||
157 O -1.100120 -0.320162 0.375372 1 158 159
|
||||
158 H -0.527013 -1.012183 0.128652 2 157
|
||||
159 H -0.673226 0.288559 0.934677 2 157
|
||||
160 O 0.910209 -8.271802 1.411429 1 161 162
|
||||
161 H 0.158544 -8.759532 1.870895 2 160
|
||||
162 H 0.565924 -7.546113 0.944383 2 160
|
||||
163 O 1.554065 -6.468033 3.310872 1 164 165
|
||||
164 H 1.362455 -7.162802 2.722340 2 163
|
||||
165 H 1.616233 -5.622409 2.872854 2 163
|
||||
166 O 0.543127 -1.388652 4.886094 1 167 168
|
||||
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|
||||
452 H -1.918884 7.705593 6.804078 2 451
|
||||
453 H -1.975225 6.330832 6.121365 2 451
|
||||
454 O -3.440263 7.005018 9.111704 1 455 456
|
||||
455 H -2.633953 7.421761 9.465848 2 454
|
||||
456 H -3.654896 7.513753 8.256470 2 454
|
||||
457 O 6.452501 -5.478051 -5.722874 1 458 459
|
||||
458 H 7.297698 -5.914122 -5.586895 2 457
|
||||
459 H 6.253267 -4.919338 -4.937095 2 457
|
||||
460 O -6.528475 4.497861 -5.573636 1 461 462
|
||||
461 H -6.257840 4.684056 -4.656222 2 460
|
||||
462 H -7.247764 3.931701 -5.623068 2 460
|
||||
463 O -7.310706 8.183648 7.852201 1 464 465
|
||||
464 H -6.552879 7.735013 7.436342 2 463
|
||||
465 H -6.877865 8.451022 8.686616 2 463
|
||||
466 O -1.476441 -7.867001 7.421787 1 467 468
|
||||
467 H -0.852398 -8.570669 7.084405 2 466
|
||||
468 H -1.363740 -7.190554 6.737331 2 466
|
||||
469 O 5.228019 -0.495870 -7.592953 1 470 471
|
||||
470 H 4.737616 -0.538139 -6.742036 2 469
|
||||
471 H 4.625354 -0.901329 -8.269022 2 469
|
||||
472 O 7.566531 -1.006734 1.808213 1 473 474
|
||||
473 H 7.657411 -1.866188 1.428564 2 472
|
||||
474 H 7.358547 -0.388051 1.139943 2 472
|
||||
475 O 1.850924 -5.717449 -5.035416 1 476 477
|
||||
476 H 1.721040 -6.227449 -4.217213 2 475
|
||||
477 H 2.199319 -4.856378 -4.692892 2 475
|
||||
478 O -8.904325 6.791585 -3.842866 1 479 480
|
||||
479 H -8.690637 5.952112 -3.490118 2 478
|
||||
480 H -8.676001 6.844077 -4.770651 2 478
|
||||
481 O -3.434304 4.397198 -7.863568 1 482 483
|
||||
482 H -2.634777 3.892027 -7.779256 2 481
|
||||
483 H -3.432847 5.161485 -7.310788 2 481
|
||||
484 O -7.446738 6.124823 0.150068 1 485 486
|
||||
485 H -7.404893 5.207959 0.481504 2 484
|
||||
486 H -8.405563 6.215466 -0.024439 2 484
|
||||
487 O 0.195330 -7.307128 -3.501714 1 488 489
|
||||
488 H -0.240912 -6.769004 -4.243655 2 487
|
||||
489 H -0.194915 -6.981989 -2.679860 2 487
|
||||
490 O 7.068819 9.130323 7.260588 1 491 492
|
||||
491 H 6.559855 8.400987 7.699406 2 490
|
||||
492 H 7.972497 8.829223 7.213747 2 490
|
||||
493 O -0.185218 -3.192290 -6.289346 1 494 495
|
||||
494 H 0.776651 -3.073203 -6.391948 2 493
|
||||
495 H -0.497426 -2.964088 -7.170893 2 493
|
||||
496 O -2.073630 4.369672 5.251074 1 497 498
|
||||
497 H -1.868638 3.811508 6.060261 2 496
|
||||
498 H -1.253174 4.326708 4.781680 2 496
|
||||
499 O -0.855003 3.069108 -7.935226 1 500 501
|
||||
500 H 0.075758 3.132202 -7.617253 2 499
|
||||
501 H -1.009845 2.207487 -8.320426 2 499
|
||||
502 O -6.328833 0.064083 -8.467228 1 503 504
|
||||
503 H -7.268416 0.384648 -8.383978 2 502
|
||||
504 H -5.825246 0.919304 -8.320175 2 502
|
||||
505 O -8.276352 -8.809851 -6.344910 1 506 507
|
||||
506 H -7.541457 -8.792368 -5.688031 2 505
|
||||
507 H -8.510208 -9.731116 -6.353248 2 505
|
||||
508 O 0.463654 2.826776 7.018388 1 509 510
|
||||
509 H 0.875324 3.588447 7.482107 2 508
|
||||
510 H 0.770257 2.126646 7.583650 2 508
|
||||
511 O 0.478371 -3.407198 6.910039 1 512 513
|
||||
512 H 0.585298 -2.996750 7.756467 2 511
|
||||
513 H 0.556531 -4.390636 7.183527 2 511
|
||||
514 O -1.689559 7.002511 -3.303561 1 515 516
|
||||
515 H -1.009152 7.635432 -3.553133 2 514
|
||||
516 H -1.333699 6.195680 -2.919485 2 514
|
||||
517 O 9.000097 -6.227871 8.137681 1 518 519
|
||||
518 H 9.373858 -6.821152 7.497417 2 517
|
||||
519 H 8.024020 -6.011019 8.033727 2 517
|
||||
520 O 1.272378 1.954065 3.058033 1 521 522
|
||||
521 H 1.260842 2.615112 2.341207 2 520
|
||||
522 H 1.890312 2.223439 3.732934 2 520
|
||||
523 O 4.139066 -3.527427 -9.022609 1 524 525
|
||||
524 H 4.070028 -3.499117 -9.985525 2 523
|
||||
525 H 4.960292 -3.942364 -8.778433 2 523
|
||||
526 O 7.176276 2.178662 -4.075940 1 527 528
|
||||
527 H 6.995275 1.684022 -4.873223 2 526
|
||||
528 H 7.621313 2.984315 -4.393994 2 526
|
||||
529 O -0.034836 -3.929919 2.148095 1 530 531
|
||||
530 H 0.838003 -3.513346 2.259663 2 529
|
||||
531 H -0.654999 -3.288581 2.426748 2 529
|
||||
532 O -8.701616 2.795237 -5.700842 1 533 534
|
||||
533 H -8.848959 2.145603 -6.420186 2 532
|
||||
534 H -9.464654 3.362988 -5.610379 2 532
|
||||
535 O 2.804444 8.909551 -5.635389 1 536 537
|
||||
536 H 3.063615 9.805993 -5.770957 2 535
|
||||
537 H 3.512196 8.486179 -5.165468 2 535
|
||||
538 O 3.236002 8.357402 3.636639 1 539 540
|
||||
539 H 3.450854 9.071799 3.073263 2 538
|
||||
540 H 3.476445 8.586691 4.607935 2 538
|
||||
541 O 5.628532 7.185941 8.510937 1 542 543
|
||||
542 H 5.467837 6.318153 8.138885 2 541
|
||||
543 H 4.964153 7.477925 9.150467 2 541
|
||||
544 O -3.767261 1.260390 2.017681 1 545 546
|
||||
545 H -3.707734 2.019520 2.565591 2 544
|
||||
546 H -3.364602 1.609935 1.212351 2 544
|
||||
547 O 8.228917 -3.441761 0.850139 1 548 549
|
||||
548 H 9.022130 -3.709208 1.334881 2 547
|
||||
549 H 7.553662 -3.976731 1.276651 2 547
|
||||
550 O -3.004292 1.345869 7.236734 1 551 552
|
||||
551 H -3.715311 0.724731 6.912689 2 550
|
||||
552 H -3.525684 2.111901 7.538936 2 550
|
||||
553 O 4.901423 -5.547141 -0.119795 1 554 555
|
||||
554 H 5.327550 -5.560969 0.769770 2 553
|
||||
555 H 5.447642 -4.930752 -0.617088 2 553
|
||||
556 O -3.306210 8.469477 -0.495057 1 557 558
|
||||
557 H -2.836855 9.122642 -1.080706 2 556
|
||||
558 H -3.311215 8.916887 0.353875 2 556
|
||||
559 O -6.572180 3.018421 -0.262079 1 560 561
|
||||
560 H -6.711444 2.659956 0.606460 2 559
|
||||
561 H -6.040782 2.473886 -0.843542 2 559
|
||||
562 O -5.429147 -5.967833 5.177682 1 563 564
|
||||
563 H -4.896648 -6.608203 4.692534 2 562
|
||||
564 H -5.386594 -6.130690 6.117931 2 562
|
||||
565 O 6.054430 7.035601 0.031519 1 566 567
|
||||
566 H 5.939348 7.951184 -0.141094 2 565
|
||||
567 H 5.390949 6.866654 0.702638 2 565
|
||||
568 O -0.890229 -2.615376 -3.621726 1 569 570
|
||||
569 H -1.695442 -2.097314 -3.537976 2 568
|
||||
570 H -0.895128 -2.637531 -4.561712 2 568
|
||||
571 O -5.446979 0.994907 -2.106714 1 572 573
|
||||
572 H -4.494883 0.997912 -1.881595 2 571
|
||||
573 H -5.759736 0.094199 -1.919247 2 571
|
||||
574 O -7.517688 -4.078340 7.202707 1 575 576
|
||||
575 H -8.242348 -4.324693 7.729813 2 574
|
||||
576 H -6.924399 -4.817453 7.269430 2 574
|
||||
577 O -1.134884 8.628488 2.081069 1 578 579
|
||||
578 H -1.962897 8.634713 2.554947 2 577
|
||||
579 H -1.119731 7.882422 1.516003 2 577
|
||||
580 O -6.288317 8.011683 2.022129 1 581 582
|
||||
581 H -6.404647 8.858198 1.546109 2 580
|
||||
582 H -6.669138 7.315199 1.482614 2 580
|
||||
583 O -6.766934 -4.026505 -8.306645 1 584 585
|
||||
584 H -6.542552 -4.855702 -8.828363 2 583
|
||||
585 H -7.743726 -3.954163 -8.170031 2 583
|
||||
586 O 6.895244 7.052113 -3.031289 1 587 588
|
||||
587 H 7.810039 7.265357 -3.330751 2 586
|
||||
588 H 6.666757 7.541675 -2.202178 2 586
|
||||
589 O 8.003260 4.735929 -5.168656 1 590 591
|
||||
590 H 7.233375 4.730204 -5.685772 2 589
|
||||
591 H 8.406708 5.629580 -5.300038 2 589
|
||||
592 O -5.230160 -6.461196 -4.390836 1 593 594
|
||||
593 H -5.701559 -7.313756 -4.377348 2 592
|
||||
594 H -4.855545 -6.327970 -5.273444 2 592
|
||||
595 O -3.803496 -9.221115 7.305476 1 596 597
|
||||
596 H -2.934288 -8.877999 7.425047 2 595
|
||||
597 H -4.416066 -8.566250 7.573191 2 595
|
||||
598 O -5.990438 -1.574415 3.072521 1 599 600
|
||||
599 H -5.805447 -1.119293 3.933731 2 598
|
||||
600 H -6.651651 -0.947206 2.634773 2 598
|
||||
601 O 1.155451 7.138377 -1.178317 1 602 603
|
||||
602 H 0.330359 7.363227 -0.724568 2 601
|
||||
603 H 1.055145 7.478676 -2.100793 2 601
|
||||
604 O -5.886817 5.150957 -2.997276 1 605 606
|
||||
605 H -5.191777 4.556623 -2.611465 2 604
|
||||
606 H -5.401622 6.003350 -3.064194 2 604
|
||||
607 O 2.539927 3.387568 4.976180 1 608 609
|
||||
608 H 1.760904 3.182324 5.589217 2 607
|
||||
609 H 2.841539 4.315465 5.278853 2 607
|
||||
610 O 8.331859 -7.344673 -5.188191 1 611 612
|
||||
611 H 8.424401 -7.586778 -4.198621 2 610
|
||||
612 H 8.911675 -7.764424 -5.823267 2 610
|
||||
613 O -5.774081 1.315144 -5.304553 1 614 615
|
||||
614 H -5.222992 1.580336 -6.077077 2 613
|
||||
615 H -6.219878 2.178441 -5.093360 2 613
|
||||
616 O 6.340084 -4.926064 2.149626 1 617 618
|
||||
617 H 5.639784 -4.766017 2.829591 2 616
|
||||
618 H 6.883511 -5.598794 2.562820 2 616
|
||||
619 O -2.722394 6.614441 -5.843805 1 620 621
|
||||
620 H -2.332414 7.251953 -6.403722 2 619
|
||||
621 H -2.221682 6.596615 -5.034993 2 619
|
||||
622 O -1.813152 0.712824 -9.048176 1 623 624
|
||||
623 H -1.763921 -0.271744 -8.916841 2 622
|
||||
624 H -2.097796 0.860500 -9.970314 2 622
|
||||
625 O 6.146244 -6.879929 8.376712 1 626 627
|
||||
626 H 5.324465 -7.183905 8.841506 2 625
|
||||
627 H 6.642264 -7.749945 8.201756 2 625
|
||||
628 O 2.887544 8.612615 0.453821 1 629 630
|
||||
629 H 2.452117 8.047637 -0.251289 2 628
|
||||
630 H 2.348751 9.285636 0.895642 2 628
|
||||
631 O -8.475558 -8.180718 6.501232 1 632 633
|
||||
632 H -8.034310 -8.945692 6.891221 2 631
|
||||
633 H -8.173606 -8.179435 5.569319 2 631
|
||||
634 O 6.714205 -2.947903 6.551671 1 635 636
|
||||
635 H 7.143284 -2.459194 7.270891 2 634
|
||||
636 H 7.212365 -2.637046 5.791018 2 634
|
||||
637 O 6.445003 -5.462306 5.577966 1 638 639
|
||||
638 H 6.730099 -4.696457 6.073312 2 637
|
||||
639 H 6.099428 -6.099736 6.222859 2 637
|
||||
640 O -1.818761 -6.080111 -8.805420 1 641 642
|
||||
641 H -1.644534 -6.777931 -9.477669 2 640
|
||||
642 H -2.078582 -5.258591 -9.215838 2 640
|
||||
643 O 6.037377 2.950576 2.863541 1 644 645
|
||||
644 H 6.409766 3.757001 2.570754 2 643
|
||||
645 H 5.577033 2.617474 2.090587 2 643
|
||||
646 O -7.731645 3.337668 3.301121 1 647 648
|
||||
647 H -8.345957 4.027222 3.589257 2 646
|
||||
648 H -8.130328 2.845238 2.577949 2 646
|
||||
7
examples/amoeba/water_dimer.xyz
Normal file
7
examples/amoeba/water_dimer.xyz
Normal file
@ -0,0 +1,7 @@
|
||||
6 Schaefer Water Dimer 1
|
||||
1 O -0.024616 -0.001154 -0.003748 1 2 3
|
||||
2 H -0.244211 -0.000666 0.933978 2 1
|
||||
3 H 0.932234 -0.000406 -0.008705 2 1
|
||||
4 O -0.892721 0.000120 2.773674 1 5 6
|
||||
5 H -1.462996 0.755120 2.933870 2 4
|
||||
6 H -1.461809 -0.755549 2.934934 2 4
|
||||
19
examples/amoeba/water_hexamer.xyz
Normal file
19
examples/amoeba/water_hexamer.xyz
Normal file
@ -0,0 +1,19 @@
|
||||
18 TINKER Water Hexamer
|
||||
1 O -1.502169 -0.191359 1.434927 1 2 3
|
||||
2 H -0.601054 -0.596972 1.553718 2 1
|
||||
3 H -2.006698 -0.422327 2.219847 2 1
|
||||
4 O -1.744575 -0.382348 -1.309144 1 5 6
|
||||
5 H -1.888941 -0.479653 -0.347624 2 4
|
||||
6 H -2.516835 -0.766765 -1.733766 2 4
|
||||
7 O -0.560409 2.017830 -0.121984 1 8 9
|
||||
8 H -0.947720 1.533567 0.625228 2 7
|
||||
9 H -0.989831 1.592736 -0.877419 2 7
|
||||
10 O 0.964803 -1.165765 1.439987 1 11 12
|
||||
11 H 0.979557 -1.522041 0.527833 2 10
|
||||
12 H 1.542224 -0.393692 1.344373 2 10
|
||||
13 O 0.974705 -1.401503 -1.335970 1 14 15
|
||||
14 H 0.065161 -1.118951 -1.522886 2 13
|
||||
15 H 1.470709 -0.570933 -1.277710 2 13
|
||||
16 O 2.002280 1.057824 -0.124502 1 17 18
|
||||
17 H 1.141637 1.532266 -0.140121 2 16
|
||||
18 H 2.674716 1.735342 -0.237995 2 16
|
||||
@ -17,6 +17,7 @@
|
||||
#include "comm.h"
|
||||
#include "error.h"
|
||||
#include "irregular.h"
|
||||
#include "pair.h"
|
||||
#include "kspace.h"
|
||||
#include "memory.h"
|
||||
|
||||
@ -926,31 +927,41 @@ int GridComm::ghost_adjacent_tiled()
|
||||
forward comm of my owned cells to other's ghost cells
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void GridComm::forward_comm_kspace(KSpace *kspace, int nper, int nbyte, int which,
|
||||
void *buf1, void *buf2, MPI_Datatype datatype)
|
||||
void GridComm::forward_comm(KSpace *kspace, int nper, int nbyte, int which,
|
||||
void *buf1, void *buf2, MPI_Datatype datatype)
|
||||
{
|
||||
if (layout == REGULAR)
|
||||
forward_comm_kspace_regular(kspace,nper,nbyte,which,buf1,buf2,datatype);
|
||||
forward_comm_regular(kspace,nper,nbyte,which,buf1,buf2,datatype);
|
||||
else
|
||||
forward_comm_kspace_tiled(kspace,nper,nbyte,which,buf1,buf2,datatype);
|
||||
forward_comm_tiled(kspace,nper,nbyte,which,buf1,buf2,datatype);
|
||||
}
|
||||
|
||||
void GridComm::forward_comm(Pair *pair, int nper, int nbyte, int which,
|
||||
void *buf1, void *buf2, MPI_Datatype datatype)
|
||||
{
|
||||
if (layout == REGULAR)
|
||||
forward_comm_regular(pair,nper,nbyte,which,buf1,buf2,datatype);
|
||||
else
|
||||
forward_comm_tiled(pair,nper,nbyte,which,buf1,buf2,datatype);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
forward comm on regular grid of procs via list of swaps with 6 neighbor procs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
template <class T>
|
||||
void GridComm::
|
||||
forward_comm_kspace_regular(KSpace *kspace, int nper, int /*nbyte*/, int which,
|
||||
void *buf1, void *buf2, MPI_Datatype datatype)
|
||||
forward_comm_regular(T *caller, int nper, int /*nbyte*/, int which,
|
||||
void *buf1, void *buf2, MPI_Datatype datatype)
|
||||
{
|
||||
int m;
|
||||
MPI_Request request;
|
||||
|
||||
for (m = 0; m < nswap; m++) {
|
||||
if (swap[m].sendproc == me)
|
||||
kspace->pack_forward_grid(which,buf2,swap[m].npack,swap[m].packlist);
|
||||
caller->pack_forward_grid(which,buf2,swap[m].npack,swap[m].packlist);
|
||||
else
|
||||
kspace->pack_forward_grid(which,buf1,swap[m].npack,swap[m].packlist);
|
||||
caller->pack_forward_grid(which,buf1,swap[m].npack,swap[m].packlist);
|
||||
|
||||
if (swap[m].sendproc != me) {
|
||||
if (swap[m].nunpack) MPI_Irecv(buf2,nper*swap[m].nunpack,datatype,
|
||||
@ -960,7 +971,7 @@ forward_comm_kspace_regular(KSpace *kspace, int nper, int /*nbyte*/, int which,
|
||||
if (swap[m].nunpack) MPI_Wait(&request,MPI_STATUS_IGNORE);
|
||||
}
|
||||
|
||||
kspace->unpack_forward_grid(which,buf2,swap[m].nunpack,swap[m].unpacklist);
|
||||
caller->unpack_forward_grid(which,buf2,swap[m].nunpack,swap[m].unpacklist);
|
||||
}
|
||||
}
|
||||
|
||||
@ -968,9 +979,10 @@ forward_comm_kspace_regular(KSpace *kspace, int nper, int /*nbyte*/, int which,
|
||||
forward comm on tiled grid decomp via Send/Recv lists of each neighbor proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
template <class T>
|
||||
void GridComm::
|
||||
forward_comm_kspace_tiled(KSpace *kspace, int nper, int nbyte, int which,
|
||||
void *buf1, void *vbuf2, MPI_Datatype datatype)
|
||||
forward_comm_tiled(T *caller, int nper, int nbyte, int which,
|
||||
void *buf1, void *vbuf2, MPI_Datatype datatype)
|
||||
{
|
||||
int i,m,offset;
|
||||
|
||||
@ -987,15 +999,15 @@ forward_comm_kspace_tiled(KSpace *kspace, int nper, int nbyte, int which,
|
||||
// perform all sends to other procs
|
||||
|
||||
for (m = 0; m < nsend; m++) {
|
||||
kspace->pack_forward_grid(which,buf1,send[m].npack,send[m].packlist);
|
||||
caller->pack_forward_grid(which,buf1,send[m].npack,send[m].packlist);
|
||||
MPI_Send(buf1,nper*send[m].npack,datatype,send[m].proc,0,gridcomm);
|
||||
}
|
||||
|
||||
// perform all copies to self
|
||||
|
||||
for (m = 0; m < ncopy; m++) {
|
||||
kspace->pack_forward_grid(which,buf1,copy[m].npack,copy[m].packlist);
|
||||
kspace->unpack_forward_grid(which,buf1,copy[m].nunpack,copy[m].unpacklist);
|
||||
caller->pack_forward_grid(which,buf1,copy[m].npack,copy[m].packlist);
|
||||
caller->unpack_forward_grid(which,buf1,copy[m].nunpack,copy[m].unpacklist);
|
||||
}
|
||||
|
||||
// unpack all received data
|
||||
@ -1003,7 +1015,7 @@ forward_comm_kspace_tiled(KSpace *kspace, int nper, int nbyte, int which,
|
||||
for (i = 0; i < nrecv; i++) {
|
||||
MPI_Waitany(nrecv,requests,&m,MPI_STATUS_IGNORE);
|
||||
offset = nper * recv[m].offset * nbyte;
|
||||
kspace->unpack_forward_grid(which,(void *) &buf2[offset],
|
||||
caller->unpack_forward_grid(which,(void *) &buf2[offset],
|
||||
recv[m].nunpack,recv[m].unpacklist);
|
||||
}
|
||||
}
|
||||
@ -1012,31 +1024,41 @@ forward_comm_kspace_tiled(KSpace *kspace, int nper, int nbyte, int which,
|
||||
reverse comm of my ghost cells to sum to owner cells
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void GridComm::reverse_comm_kspace(KSpace *kspace, int nper, int nbyte, int which,
|
||||
void *buf1, void *buf2, MPI_Datatype datatype)
|
||||
void GridComm::reverse_comm(KSpace *kspace, int nper, int nbyte, int which,
|
||||
void *buf1, void *buf2, MPI_Datatype datatype)
|
||||
{
|
||||
if (layout == REGULAR)
|
||||
reverse_comm_kspace_regular(kspace,nper,nbyte,which,buf1,buf2,datatype);
|
||||
reverse_comm_regular(kspace,nper,nbyte,which,buf1,buf2,datatype);
|
||||
else
|
||||
reverse_comm_kspace_tiled(kspace,nper,nbyte,which,buf1,buf2,datatype);
|
||||
reverse_comm_tiled(kspace,nper,nbyte,which,buf1,buf2,datatype);
|
||||
}
|
||||
|
||||
void GridComm::reverse_comm(Pair *pair, int nper, int nbyte, int which,
|
||||
void *buf1, void *buf2, MPI_Datatype datatype)
|
||||
{
|
||||
if (layout == REGULAR)
|
||||
reverse_comm_regular(pair,nper,nbyte,which,buf1,buf2,datatype);
|
||||
else
|
||||
reverse_comm_tiled(pair,nper,nbyte,which,buf1,buf2,datatype);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
reverse comm on regular grid of procs via list of swaps with 6 neighbor procs
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
template <class T>
|
||||
void GridComm::
|
||||
reverse_comm_kspace_regular(KSpace *kspace, int nper, int /*nbyte*/, int which,
|
||||
void *buf1, void *buf2, MPI_Datatype datatype)
|
||||
reverse_comm_regular(T *caller, int nper, int /*nbyte*/, int which,
|
||||
void *buf1, void *buf2, MPI_Datatype datatype)
|
||||
{
|
||||
int m;
|
||||
MPI_Request request;
|
||||
|
||||
for (m = nswap-1; m >= 0; m--) {
|
||||
if (swap[m].recvproc == me)
|
||||
kspace->pack_reverse_grid(which,buf2,swap[m].nunpack,swap[m].unpacklist);
|
||||
caller->pack_reverse_grid(which,buf2,swap[m].nunpack,swap[m].unpacklist);
|
||||
else
|
||||
kspace->pack_reverse_grid(which,buf1,swap[m].nunpack,swap[m].unpacklist);
|
||||
caller->pack_reverse_grid(which,buf1,swap[m].nunpack,swap[m].unpacklist);
|
||||
|
||||
if (swap[m].recvproc != me) {
|
||||
if (swap[m].npack) MPI_Irecv(buf2,nper*swap[m].npack,datatype,
|
||||
@ -1046,7 +1068,7 @@ reverse_comm_kspace_regular(KSpace *kspace, int nper, int /*nbyte*/, int which,
|
||||
if (swap[m].npack) MPI_Wait(&request,MPI_STATUS_IGNORE);
|
||||
}
|
||||
|
||||
kspace->unpack_reverse_grid(which,buf2,swap[m].npack,swap[m].packlist);
|
||||
caller->unpack_reverse_grid(which,buf2,swap[m].npack,swap[m].packlist);
|
||||
}
|
||||
}
|
||||
|
||||
@ -1054,9 +1076,10 @@ reverse_comm_kspace_regular(KSpace *kspace, int nper, int /*nbyte*/, int which,
|
||||
reverse comm on tiled grid decomp via Send/Recv lists of each neighbor proc
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
template <class T>
|
||||
void GridComm::
|
||||
reverse_comm_kspace_tiled(KSpace *kspace, int nper, int nbyte, int which,
|
||||
void *buf1, void *vbuf2, MPI_Datatype datatype)
|
||||
reverse_comm_tiled(T *caller, int nper, int nbyte, int which,
|
||||
void *buf1, void *vbuf2, MPI_Datatype datatype)
|
||||
{
|
||||
int i,m,offset;
|
||||
|
||||
@ -1073,15 +1096,15 @@ reverse_comm_kspace_tiled(KSpace *kspace, int nper, int nbyte, int which,
|
||||
// perform all sends to other procs
|
||||
|
||||
for (m = 0; m < nrecv; m++) {
|
||||
kspace->pack_reverse_grid(which,buf1,recv[m].nunpack,recv[m].unpacklist);
|
||||
caller->pack_reverse_grid(which,buf1,recv[m].nunpack,recv[m].unpacklist);
|
||||
MPI_Send(buf1,nper*recv[m].nunpack,datatype,recv[m].proc,0,gridcomm);
|
||||
}
|
||||
|
||||
// perform all copies to self
|
||||
|
||||
for (m = 0; m < ncopy; m++) {
|
||||
kspace->pack_reverse_grid(which,buf1,copy[m].nunpack,copy[m].unpacklist);
|
||||
kspace->unpack_reverse_grid(which,buf1,copy[m].npack,copy[m].packlist);
|
||||
caller->pack_reverse_grid(which,buf1,copy[m].nunpack,copy[m].unpacklist);
|
||||
caller->unpack_reverse_grid(which,buf1,copy[m].npack,copy[m].packlist);
|
||||
}
|
||||
|
||||
// unpack all received data
|
||||
@ -1089,7 +1112,7 @@ reverse_comm_kspace_tiled(KSpace *kspace, int nper, int nbyte, int which,
|
||||
for (i = 0; i < nsend; i++) {
|
||||
MPI_Waitany(nsend,requests,&m,MPI_STATUS_IGNORE);
|
||||
offset = nper * send[m].offset * nbyte;
|
||||
kspace->unpack_reverse_grid(which,(void *) &buf2[offset],
|
||||
caller->unpack_reverse_grid(which,(void *) &buf2[offset],
|
||||
send[m].npack,send[m].packlist);
|
||||
}
|
||||
}
|
||||
|
||||
@ -27,8 +27,11 @@ class GridComm : protected Pointers {
|
||||
virtual ~GridComm();
|
||||
void setup(int &, int &);
|
||||
int ghost_adjacent();
|
||||
void forward_comm_kspace(class KSpace *, int, int, int, void *, void *, MPI_Datatype);
|
||||
void reverse_comm_kspace(class KSpace *, int, int, int, void *, void *, MPI_Datatype);
|
||||
|
||||
void forward_comm(class KSpace *, int, int, int, void *, void *, MPI_Datatype);
|
||||
void forward_comm(class Pair *, int, int, int, void *, void *, MPI_Datatype);
|
||||
void reverse_comm(class KSpace *, int, int, int, void *, void *, MPI_Datatype);
|
||||
void reverse_comm(class Pair *, int, int, int, void *, void *, MPI_Datatype);
|
||||
|
||||
protected:
|
||||
int me, nprocs;
|
||||
@ -181,10 +184,14 @@ class GridComm : protected Pointers {
|
||||
int ghost_adjacent_regular();
|
||||
int ghost_adjacent_tiled();
|
||||
|
||||
void forward_comm_kspace_regular(class KSpace *, int, int, int, void *, void *, MPI_Datatype);
|
||||
void forward_comm_kspace_tiled(class KSpace *, int, int, int, void *, void *, MPI_Datatype);
|
||||
void reverse_comm_kspace_regular(class KSpace *, int, int, int, void *, void *, MPI_Datatype);
|
||||
void reverse_comm_kspace_tiled(class KSpace *, int, int, int, void *, void *, MPI_Datatype);
|
||||
template <class T>
|
||||
void forward_comm_regular(T *, int, int, int, void *, void *, MPI_Datatype);
|
||||
template <class T>
|
||||
void forward_comm_tiled(T *, int, int, int, void *, void *, MPI_Datatype);
|
||||
template <class T>
|
||||
void reverse_comm_regular(T *, int, int, int, void *, void *, MPI_Datatype);
|
||||
template <class T>
|
||||
void reverse_comm_tiled(T *, int, int, int, void *, void *, MPI_Datatype);
|
||||
|
||||
virtual void grow_swap();
|
||||
void grow_overlap();
|
||||
|
||||
@ -465,8 +465,8 @@ void MSM::compute(int eflag, int vflag)
|
||||
// to fully sum contribution in their 3d grid
|
||||
|
||||
current_level = 0;
|
||||
gcall->reverse_comm_kspace(this,1,sizeof(double),REVERSE_RHO,
|
||||
gcall_buf1,gcall_buf2,MPI_DOUBLE);
|
||||
gcall->reverse_comm(this,1,sizeof(double),REVERSE_RHO,
|
||||
gcall_buf1,gcall_buf2,MPI_DOUBLE);
|
||||
|
||||
// forward communicate charge density values to fill ghost grid points
|
||||
// compute direct sum interaction and then restrict to coarser grid
|
||||
@ -474,8 +474,8 @@ void MSM::compute(int eflag, int vflag)
|
||||
for (int n=0; n<=levels-2; n++) {
|
||||
if (!active_flag[n]) continue;
|
||||
current_level = n;
|
||||
gc[n]->forward_comm_kspace(this,1,sizeof(double),FORWARD_RHO,
|
||||
gc_buf1[n],gc_buf2[n],MPI_DOUBLE);
|
||||
gc[n]->forward_comm(this,1,sizeof(double),FORWARD_RHO,
|
||||
gc_buf1[n],gc_buf2[n],MPI_DOUBLE);
|
||||
direct(n);
|
||||
restriction(n);
|
||||
}
|
||||
@ -487,16 +487,16 @@ void MSM::compute(int eflag, int vflag)
|
||||
if (domain->nonperiodic) {
|
||||
current_level = levels-1;
|
||||
gc[levels-1]->
|
||||
forward_comm_kspace(this,1,sizeof(double),FORWARD_RHO,
|
||||
gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);
|
||||
forward_comm(this,1,sizeof(double),FORWARD_RHO,
|
||||
gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);
|
||||
direct_top(levels-1);
|
||||
gc[levels-1]->
|
||||
reverse_comm_kspace(this,1,sizeof(double),REVERSE_AD,
|
||||
gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);
|
||||
reverse_comm(this,1,sizeof(double),REVERSE_AD,
|
||||
gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);
|
||||
if (vflag_atom)
|
||||
gc[levels-1]->
|
||||
reverse_comm_kspace(this,6,sizeof(double),REVERSE_AD_PERATOM,
|
||||
gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);
|
||||
reverse_comm(this,6,sizeof(double),REVERSE_AD_PERATOM,
|
||||
gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);
|
||||
|
||||
} else {
|
||||
// Here using MPI_Allreduce is cheaper than using commgrid
|
||||
@ -506,8 +506,8 @@ void MSM::compute(int eflag, int vflag)
|
||||
current_level = levels-1;
|
||||
if (vflag_atom)
|
||||
gc[levels-1]->
|
||||
reverse_comm_kspace(this,6,sizeof(double),REVERSE_AD_PERATOM,
|
||||
gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);
|
||||
reverse_comm(this,6,sizeof(double),REVERSE_AD_PERATOM,
|
||||
gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);
|
||||
}
|
||||
}
|
||||
|
||||
@ -519,28 +519,28 @@ void MSM::compute(int eflag, int vflag)
|
||||
prolongation(n);
|
||||
|
||||
current_level = n;
|
||||
gc[n]->reverse_comm_kspace(this,1,sizeof(double),REVERSE_AD,
|
||||
gc_buf1[n],gc_buf2[n],MPI_DOUBLE);
|
||||
gc[n]->reverse_comm(this,1,sizeof(double),REVERSE_AD,
|
||||
gc_buf1[n],gc_buf2[n],MPI_DOUBLE);
|
||||
|
||||
// extra per-atom virial communication
|
||||
|
||||
if (vflag_atom)
|
||||
gc[n]->reverse_comm_kspace(this,6,sizeof(double),REVERSE_AD_PERATOM,
|
||||
gc_buf1[n],gc_buf2[n],MPI_DOUBLE);
|
||||
gc[n]->reverse_comm(this,6,sizeof(double),REVERSE_AD_PERATOM,
|
||||
gc_buf1[n],gc_buf2[n],MPI_DOUBLE);
|
||||
}
|
||||
|
||||
// all procs communicate E-field values
|
||||
// to fill ghost cells surrounding their 3d bricks
|
||||
|
||||
current_level = 0;
|
||||
gcall->forward_comm_kspace(this,1,sizeof(double),FORWARD_AD,
|
||||
gcall_buf1,gcall_buf2,MPI_DOUBLE);
|
||||
gcall->forward_comm(this,1,sizeof(double),FORWARD_AD,
|
||||
gcall_buf1,gcall_buf2,MPI_DOUBLE);
|
||||
|
||||
// extra per-atom energy/virial communication
|
||||
|
||||
if (vflag_atom)
|
||||
gcall->forward_comm_kspace(this,6,sizeof(double),FORWARD_AD_PERATOM,
|
||||
gcall_buf1,gcall_buf2,MPI_DOUBLE);
|
||||
gcall->forward_comm(this,6,sizeof(double),FORWARD_AD_PERATOM,
|
||||
gcall_buf1,gcall_buf2,MPI_DOUBLE);
|
||||
|
||||
// calculate the force on my particles (interpolation)
|
||||
|
||||
|
||||
@ -160,8 +160,8 @@ void MSMCG::compute(int eflag, int vflag)
|
||||
// to fully sum contribution in their 3d grid
|
||||
|
||||
current_level = 0;
|
||||
gcall->reverse_comm_kspace(this,1,sizeof(double),REVERSE_RHO,
|
||||
gcall_buf1,gcall_buf2,MPI_DOUBLE);
|
||||
gcall->reverse_comm(this,1,sizeof(double),REVERSE_RHO,
|
||||
gcall_buf1,gcall_buf2,MPI_DOUBLE);
|
||||
|
||||
// forward communicate charge density values to fill ghost grid points
|
||||
// compute direct sum interaction and then restrict to coarser grid
|
||||
@ -169,8 +169,9 @@ void MSMCG::compute(int eflag, int vflag)
|
||||
for (n=0; n<=levels-2; n++) {
|
||||
if (!active_flag[n]) continue;
|
||||
current_level = n;
|
||||
gc[n]->forward_comm_kspace(this,1,sizeof(double),FORWARD_RHO,
|
||||
gc_buf1[n],gc_buf2[n],MPI_DOUBLE);
|
||||
gc[n]->forward_comm(this,1,sizeof(double),FORWARD_RHO,
|
||||
gc_buf1[n],gc_buf2[n],MPI_DOUBLE);
|
||||
|
||||
direct(n);
|
||||
restriction(n);
|
||||
}
|
||||
@ -182,16 +183,16 @@ void MSMCG::compute(int eflag, int vflag)
|
||||
if (domain->nonperiodic) {
|
||||
current_level = levels-1;
|
||||
gc[levels-1]->
|
||||
forward_comm_kspace(this,1,sizeof(double),FORWARD_RHO,
|
||||
gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);
|
||||
forward_comm(this,1,sizeof(double),FORWARD_RHO,
|
||||
gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);
|
||||
direct_top(levels-1);
|
||||
gc[levels-1]->
|
||||
reverse_comm_kspace(this,1,sizeof(double),REVERSE_AD,
|
||||
gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);
|
||||
reverse_comm(this,1,sizeof(double),REVERSE_AD,
|
||||
gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);
|
||||
if (vflag_atom)
|
||||
gc[levels-1]->
|
||||
reverse_comm_kspace(this,6,sizeof(double),REVERSE_AD_PERATOM,
|
||||
gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);
|
||||
gc[levels-1]->
|
||||
reverse_comm(this,6,sizeof(double),REVERSE_AD_PERATOM,
|
||||
gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);
|
||||
|
||||
} else {
|
||||
// Here using MPI_Allreduce is cheaper than using commgrid
|
||||
@ -200,9 +201,9 @@ void MSMCG::compute(int eflag, int vflag)
|
||||
grid_swap_reverse(levels-1,egrid[levels-1]);
|
||||
current_level = levels-1;
|
||||
if (vflag_atom)
|
||||
gc[levels-1]->
|
||||
reverse_comm_kspace(this,6,sizeof(double),REVERSE_AD_PERATOM,
|
||||
gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);
|
||||
gc[levels-1]->
|
||||
reverse_comm(this,6,sizeof(double),REVERSE_AD_PERATOM,
|
||||
gc_buf1[levels-1],gc_buf2[levels-1],MPI_DOUBLE);
|
||||
}
|
||||
}
|
||||
|
||||
@ -214,28 +215,28 @@ void MSMCG::compute(int eflag, int vflag)
|
||||
prolongation(n);
|
||||
|
||||
current_level = n;
|
||||
gc[n]->reverse_comm_kspace(this,1,sizeof(double),REVERSE_AD,
|
||||
gc_buf1[n],gc_buf2[n],MPI_DOUBLE);
|
||||
gc[n]->reverse_comm(this,1,sizeof(double),REVERSE_AD,
|
||||
gc_buf1[n],gc_buf2[n],MPI_DOUBLE);
|
||||
|
||||
// extra per-atom virial communication
|
||||
|
||||
if (vflag_atom)
|
||||
gc[n]->reverse_comm_kspace(this,6,sizeof(double),REVERSE_AD_PERATOM,
|
||||
gc_buf1[n],gc_buf2[n],MPI_DOUBLE);
|
||||
gc[n]->reverse_comm(this,6,sizeof(double),REVERSE_AD_PERATOM,
|
||||
gc_buf1[n],gc_buf2[n],MPI_DOUBLE);
|
||||
}
|
||||
|
||||
// all procs communicate E-field values
|
||||
// to fill ghost cells surrounding their 3d bricks
|
||||
|
||||
current_level = 0;
|
||||
gcall->forward_comm_kspace(this,1,sizeof(double),FORWARD_AD,
|
||||
gcall_buf1,gcall_buf2,MPI_DOUBLE);
|
||||
gcall->forward_comm(this,1,sizeof(double),FORWARD_AD,
|
||||
gcall_buf1,gcall_buf2,MPI_DOUBLE);
|
||||
|
||||
// extra per-atom energy/virial communication
|
||||
|
||||
if (vflag_atom)
|
||||
gcall->forward_comm_kspace(this,6,sizeof(double),FORWARD_AD_PERATOM,
|
||||
gcall_buf1,gcall_buf2,MPI_DOUBLE);
|
||||
gcall->forward_comm(this,6,sizeof(double),FORWARD_AD_PERATOM,
|
||||
gcall_buf1,gcall_buf2,MPI_DOUBLE);
|
||||
|
||||
// calculate the force on my particles (interpolation)
|
||||
|
||||
|
||||
@ -638,8 +638,8 @@ void PPPM::compute(int eflag, int vflag)
|
||||
// to fully sum contribution in their 3d bricks
|
||||
// remap from 3d decomposition to FFT decomposition
|
||||
|
||||
gc->reverse_comm_kspace(this,1,sizeof(FFT_SCALAR),REVERSE_RHO,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->reverse_comm(this,1,sizeof(FFT_SCALAR),REVERSE_RHO,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
brick2fft();
|
||||
|
||||
// compute potential gradient on my FFT grid and
|
||||
@ -653,21 +653,21 @@ void PPPM::compute(int eflag, int vflag)
|
||||
// to fill ghost cells surrounding their 3d bricks
|
||||
|
||||
if (differentiation_flag == 1)
|
||||
gc->forward_comm_kspace(this,1,sizeof(FFT_SCALAR),FORWARD_AD,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->forward_comm(this,1,sizeof(FFT_SCALAR),FORWARD_AD,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
else
|
||||
gc->forward_comm_kspace(this,3,sizeof(FFT_SCALAR),FORWARD_IK,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->forward_comm(this,3,sizeof(FFT_SCALAR),FORWARD_IK,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
// extra per-atom energy/virial communication
|
||||
|
||||
if (evflag_atom) {
|
||||
if (differentiation_flag == 1 && vflag_atom)
|
||||
gc->forward_comm_kspace(this,6,sizeof(FFT_SCALAR),FORWARD_AD_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->forward_comm(this,6,sizeof(FFT_SCALAR),FORWARD_AD_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
else if (differentiation_flag == 0)
|
||||
gc->forward_comm_kspace(this,7,sizeof(FFT_SCALAR),FORWARD_IK_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->forward_comm(this,7,sizeof(FFT_SCALAR),FORWARD_IK_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
}
|
||||
|
||||
// calculate the force on my particles
|
||||
@ -3119,8 +3119,8 @@ void PPPM::compute_group_group(int groupbit_A, int groupbit_B, int AA_flag)
|
||||
density_brick = density_A_brick;
|
||||
density_fft = density_A_fft;
|
||||
|
||||
gc->reverse_comm_kspace(this,1,sizeof(FFT_SCALAR),REVERSE_RHO,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->reverse_comm(this,1,sizeof(FFT_SCALAR),REVERSE_RHO,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
brick2fft();
|
||||
|
||||
// group B
|
||||
@ -3128,8 +3128,8 @@ void PPPM::compute_group_group(int groupbit_A, int groupbit_B, int AA_flag)
|
||||
density_brick = density_B_brick;
|
||||
density_fft = density_B_fft;
|
||||
|
||||
gc->reverse_comm_kspace(this,1,sizeof(FFT_SCALAR),REVERSE_RHO,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->reverse_comm(this,1,sizeof(FFT_SCALAR),REVERSE_RHO,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
brick2fft();
|
||||
|
||||
// switch back pointers
|
||||
|
||||
@ -177,8 +177,8 @@ void PPPMCG::compute(int eflag, int vflag)
|
||||
// to fully sum contribution in their 3d bricks
|
||||
// remap from 3d decomposition to FFT decomposition
|
||||
|
||||
gc->reverse_comm_kspace(this,1,sizeof(FFT_SCALAR),REVERSE_RHO,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->reverse_comm(this,1,sizeof(FFT_SCALAR),REVERSE_RHO,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
brick2fft();
|
||||
|
||||
// compute potential gradient on my FFT grid and
|
||||
@ -192,21 +192,21 @@ void PPPMCG::compute(int eflag, int vflag)
|
||||
// to fill ghost cells surrounding their 3d bricks
|
||||
|
||||
if (differentiation_flag == 1)
|
||||
gc->forward_comm_kspace(this,1,sizeof(FFT_SCALAR),FORWARD_AD,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->forward_comm(this,1,sizeof(FFT_SCALAR),FORWARD_AD,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
else
|
||||
gc->forward_comm_kspace(this,3,sizeof(FFT_SCALAR),FORWARD_IK,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->forward_comm(this,3,sizeof(FFT_SCALAR),FORWARD_IK,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
// extra per-atom energy/virial communication
|
||||
|
||||
if (evflag_atom) {
|
||||
if (differentiation_flag == 1 && vflag_atom)
|
||||
gc->forward_comm_kspace(this,6,sizeof(FFT_SCALAR),FORWARD_AD_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->forward_comm(this,6,sizeof(FFT_SCALAR),FORWARD_AD_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
else if (differentiation_flag == 0)
|
||||
gc->forward_comm_kspace(this,7,sizeof(FFT_SCALAR),FORWARD_IK_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->forward_comm(this,7,sizeof(FFT_SCALAR),FORWARD_IK_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
}
|
||||
|
||||
// calculate the force on my particles
|
||||
|
||||
@ -443,8 +443,8 @@ void PPPMDipole::compute(int eflag, int vflag)
|
||||
// to fully sum contribution in their 3d bricks
|
||||
// remap from 3d decomposition to FFT decomposition
|
||||
|
||||
gc_dipole->reverse_comm_kspace(this,3,sizeof(FFT_SCALAR),REVERSE_MU,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc_dipole->reverse_comm(this,3,sizeof(FFT_SCALAR),REVERSE_MU,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
brick2fft_dipole();
|
||||
|
||||
// compute potential gradient on my FFT grid and
|
||||
@ -457,14 +457,14 @@ void PPPMDipole::compute(int eflag, int vflag)
|
||||
// all procs communicate E-field values
|
||||
// to fill ghost cells surrounding their 3d bricks
|
||||
|
||||
gc_dipole->forward_comm_kspace(this,9,sizeof(FFT_SCALAR),FORWARD_MU,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc_dipole->forward_comm(this,9,sizeof(FFT_SCALAR),FORWARD_MU,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
// extra per-atom energy/virial communication
|
||||
|
||||
if (evflag_atom)
|
||||
gc_dipole->forward_comm_kspace(this,18,sizeof(FFT_SCALAR),FORWARD_MU_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc_dipole->forward_comm(this,18,sizeof(FFT_SCALAR),FORWARD_MU_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
// calculate the force on my particles
|
||||
|
||||
|
||||
@ -299,8 +299,8 @@ void PPPMDipoleSpin::compute(int eflag, int vflag)
|
||||
// to fully sum contribution in their 3d bricks
|
||||
// remap from 3d decomposition to FFT decomposition
|
||||
|
||||
gc_dipole->reverse_comm_kspace(this,3,sizeof(FFT_SCALAR),REVERSE_MU,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc_dipole->reverse_comm(this,3,sizeof(FFT_SCALAR),REVERSE_MU,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
brick2fft_dipole();
|
||||
|
||||
// compute potential gradient on my FFT grid and
|
||||
@ -313,14 +313,14 @@ void PPPMDipoleSpin::compute(int eflag, int vflag)
|
||||
// all procs communicate E-field values
|
||||
// to fill ghost cells surrounding their 3d bricks
|
||||
|
||||
gc_dipole->forward_comm_kspace(this,9,sizeof(FFT_SCALAR),FORWARD_MU,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc_dipole->forward_comm(this,9,sizeof(FFT_SCALAR),FORWARD_MU,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
// extra per-atom energy/virial communication
|
||||
|
||||
if (evflag_atom)
|
||||
gc->forward_comm_kspace(this,18,sizeof(FFT_SCALAR),FORWARD_MU_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->forward_comm(this,18,sizeof(FFT_SCALAR),FORWARD_MU_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
// calculate the force on my particles
|
||||
|
||||
|
||||
@ -930,8 +930,8 @@ void PPPMDisp::compute(int eflag, int vflag)
|
||||
|
||||
make_rho_c();
|
||||
|
||||
gc->reverse_comm_kspace(this,1,sizeof(FFT_SCALAR),REVERSE_RHO,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->reverse_comm(this,1,sizeof(FFT_SCALAR),REVERSE_RHO,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
brick2fft(nxlo_in,nylo_in,nzlo_in,nxhi_in,nyhi_in,nzhi_in,
|
||||
density_brick,density_fft,work1,remap);
|
||||
@ -945,14 +945,14 @@ void PPPMDisp::compute(int eflag, int vflag)
|
||||
virial_1,vg,vg2,
|
||||
u_brick,v0_brick,v1_brick,v2_brick,v3_brick,v4_brick,v5_brick);
|
||||
|
||||
gc->forward_comm_kspace(this,1,sizeof(FFT_SCALAR),FORWARD_AD,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->forward_comm(this,1,sizeof(FFT_SCALAR),FORWARD_AD,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
fieldforce_c_ad();
|
||||
|
||||
if (vflag_atom)
|
||||
gc->forward_comm_kspace(this,6,sizeof(FFT_SCALAR),FORWARD_AD_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->forward_comm(this,6,sizeof(FFT_SCALAR),FORWARD_AD_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
} else {
|
||||
poisson_ik(work1,work2,density_fft,fft1,fft2,
|
||||
@ -964,14 +964,14 @@ void PPPMDisp::compute(int eflag, int vflag)
|
||||
vdx_brick,vdy_brick,vdz_brick,virial_1,vg,vg2,
|
||||
u_brick,v0_brick,v1_brick,v2_brick,v3_brick,v4_brick,v5_brick);
|
||||
|
||||
gc->forward_comm_kspace(this,3,sizeof(FFT_SCALAR),FORWARD_IK,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->forward_comm(this,3,sizeof(FFT_SCALAR),FORWARD_IK,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
fieldforce_c_ik();
|
||||
|
||||
if (evflag_atom)
|
||||
gc->forward_comm_kspace(this,7,sizeof(FFT_SCALAR),FORWARD_IK_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->forward_comm(this,7,sizeof(FFT_SCALAR),FORWARD_IK_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
}
|
||||
|
||||
if (evflag_atom) fieldforce_c_peratom();
|
||||
@ -988,8 +988,8 @@ void PPPMDisp::compute(int eflag, int vflag)
|
||||
|
||||
make_rho_g();
|
||||
|
||||
gc6->reverse_comm_kspace(this,1,sizeof(FFT_SCALAR),REVERSE_RHO_GEOM,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
gc6->reverse_comm(this,1,sizeof(FFT_SCALAR),REVERSE_RHO_GEOM,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
brick2fft(nxlo_in_6,nylo_in_6,nzlo_in_6,nxhi_in_6,nyhi_in_6,nzhi_in_6,
|
||||
density_brick_g,density_fft_g,work1_6,remap_6);
|
||||
@ -1004,14 +1004,14 @@ void PPPMDisp::compute(int eflag, int vflag)
|
||||
u_brick_g,v0_brick_g,v1_brick_g,v2_brick_g,
|
||||
v3_brick_g,v4_brick_g,v5_brick_g);
|
||||
|
||||
gc6->forward_comm_kspace(this,1,sizeof(FFT_SCALAR),FORWARD_AD_GEOM,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
gc6->forward_comm(this,1,sizeof(FFT_SCALAR),FORWARD_AD_GEOM,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
fieldforce_g_ad();
|
||||
|
||||
if (vflag_atom)
|
||||
gc6->forward_comm_kspace(this,6,sizeof(FFT_SCALAR),FORWARD_AD_PERATOM_GEOM,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
gc6->forward_comm(this,6,sizeof(FFT_SCALAR),FORWARD_AD_PERATOM_GEOM,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
} else {
|
||||
poisson_ik(work1_6,work2_6,density_fft_g,fft1_6,fft2_6,
|
||||
@ -1024,14 +1024,14 @@ void PPPMDisp::compute(int eflag, int vflag)
|
||||
u_brick_g,v0_brick_g,v1_brick_g,v2_brick_g,
|
||||
v3_brick_g,v4_brick_g,v5_brick_g);
|
||||
|
||||
gc6->forward_comm_kspace(this,3,sizeof(FFT_SCALAR),FORWARD_IK_GEOM,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
gc6->forward_comm(this,3,sizeof(FFT_SCALAR),FORWARD_IK_GEOM,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
fieldforce_g_ik();
|
||||
|
||||
if (evflag_atom)
|
||||
gc6->forward_comm_kspace(this,7,sizeof(FFT_SCALAR),FORWARD_IK_PERATOM_GEOM,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
gc6->forward_comm(this,7,sizeof(FFT_SCALAR),FORWARD_IK_PERATOM_GEOM,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
}
|
||||
|
||||
if (evflag_atom) fieldforce_g_peratom();
|
||||
@ -1048,8 +1048,8 @@ void PPPMDisp::compute(int eflag, int vflag)
|
||||
|
||||
make_rho_a();
|
||||
|
||||
gc6->reverse_comm_kspace(this,7,sizeof(FFT_SCALAR),REVERSE_RHO_ARITH,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
gc6->reverse_comm(this,7,sizeof(FFT_SCALAR),REVERSE_RHO_ARITH,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
brick2fft_a();
|
||||
|
||||
@ -1078,14 +1078,14 @@ void PPPMDisp::compute(int eflag, int vflag)
|
||||
u_brick_a4,v0_brick_a4,v1_brick_a4,v2_brick_a4,
|
||||
v3_brick_a4,v4_brick_a4,v5_brick_a4);
|
||||
|
||||
gc6->forward_comm_kspace(this,7,sizeof(FFT_SCALAR),FORWARD_AD_ARITH,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
gc6->forward_comm(this,7,sizeof(FFT_SCALAR),FORWARD_AD_ARITH,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
fieldforce_a_ad();
|
||||
|
||||
if (evflag_atom)
|
||||
gc6->forward_comm_kspace(this,42,sizeof(FFT_SCALAR),FORWARD_AD_PERATOM_ARITH,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
gc6->forward_comm(this,42,sizeof(FFT_SCALAR),FORWARD_AD_PERATOM_ARITH,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
} else {
|
||||
poisson_ik(work1_6,work2_6,density_fft_a3,fft1_6,fft2_6,
|
||||
@ -1119,14 +1119,14 @@ void PPPMDisp::compute(int eflag, int vflag)
|
||||
u_brick_a4,v0_brick_a4,v1_brick_a4,v2_brick_a4,
|
||||
v3_brick_a4,v4_brick_a4,v5_brick_a4);
|
||||
|
||||
gc6->forward_comm_kspace(this,21,sizeof(FFT_SCALAR),FORWARD_IK_ARITH,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
gc6->forward_comm(this,21,sizeof(FFT_SCALAR),FORWARD_IK_ARITH,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
fieldforce_a_ik();
|
||||
|
||||
if (evflag_atom)
|
||||
gc6->forward_comm_kspace(this,49,sizeof(FFT_SCALAR),FORWARD_IK_PERATOM_ARITH,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
gc6->forward_comm(this,49,sizeof(FFT_SCALAR),FORWARD_IK_PERATOM_ARITH,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
}
|
||||
|
||||
if (evflag_atom) fieldforce_a_peratom();
|
||||
@ -1143,8 +1143,8 @@ void PPPMDisp::compute(int eflag, int vflag)
|
||||
|
||||
make_rho_none();
|
||||
|
||||
gc6->reverse_comm_kspace(this,nsplit_alloc,sizeof(FFT_SCALAR),REVERSE_RHO_NONE,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
gc6->reverse_comm(this,nsplit_alloc,sizeof(FFT_SCALAR),REVERSE_RHO_NONE,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
brick2fft_none();
|
||||
|
||||
@ -1158,16 +1158,16 @@ void PPPMDisp::compute(int eflag, int vflag)
|
||||
n += 2;
|
||||
}
|
||||
|
||||
gc6->forward_comm_kspace(this,1*nsplit_alloc,sizeof(FFT_SCALAR),
|
||||
FORWARD_AD_NONE,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
gc6->forward_comm(this,1*nsplit_alloc,sizeof(FFT_SCALAR),
|
||||
FORWARD_AD_NONE,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
fieldforce_none_ad();
|
||||
|
||||
if (vflag_atom)
|
||||
gc6->forward_comm_kspace(this,6*nsplit_alloc,sizeof(FFT_SCALAR),
|
||||
FORWARD_AD_PERATOM_NONE,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
gc6->forward_comm(this,6*nsplit_alloc,sizeof(FFT_SCALAR),
|
||||
FORWARD_AD_PERATOM_NONE,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
} else {
|
||||
int n = 0;
|
||||
@ -1180,16 +1180,16 @@ void PPPMDisp::compute(int eflag, int vflag)
|
||||
n += 2;
|
||||
}
|
||||
|
||||
gc6->forward_comm_kspace(this,3*nsplit_alloc,sizeof(FFT_SCALAR),
|
||||
FORWARD_IK_NONE,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
gc6->forward_comm(this,3*nsplit_alloc,sizeof(FFT_SCALAR),
|
||||
FORWARD_IK_NONE,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
fieldforce_none_ik();
|
||||
|
||||
if (evflag_atom)
|
||||
gc6->forward_comm_kspace(this,7*nsplit_alloc,sizeof(FFT_SCALAR),
|
||||
FORWARD_IK_PERATOM_NONE,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
gc6->forward_comm(this,7*nsplit_alloc,sizeof(FFT_SCALAR),
|
||||
FORWARD_IK_PERATOM_NONE,
|
||||
gc6_buf1,gc6_buf2,MPI_FFT_SCALAR);
|
||||
}
|
||||
|
||||
if (evflag_atom) fieldforce_none_peratom();
|
||||
|
||||
@ -157,8 +157,8 @@ void PPPMStagger::compute(int eflag, int vflag)
|
||||
// to fully sum contribution in their 3d bricks
|
||||
// remap from 3d decomposition to FFT decomposition
|
||||
|
||||
gc->reverse_comm_kspace(this,1,sizeof(FFT_SCALAR),REVERSE_RHO,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->reverse_comm(this,1,sizeof(FFT_SCALAR),REVERSE_RHO,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
brick2fft();
|
||||
|
||||
// compute potential gradient on my FFT grid and
|
||||
@ -172,21 +172,21 @@ void PPPMStagger::compute(int eflag, int vflag)
|
||||
// to fill ghost cells surrounding their 3d bricks
|
||||
|
||||
if (differentiation_flag == 1)
|
||||
gc->forward_comm_kspace(this,1,sizeof(FFT_SCALAR),FORWARD_AD,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->forward_comm(this,1,sizeof(FFT_SCALAR),FORWARD_AD,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
else
|
||||
gc->forward_comm_kspace(this,3,sizeof(FFT_SCALAR),FORWARD_IK,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->forward_comm(this,3,sizeof(FFT_SCALAR),FORWARD_IK,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
|
||||
// extra per-atom energy/virial communication
|
||||
|
||||
if (evflag_atom) {
|
||||
if (differentiation_flag == 1 && vflag_atom)
|
||||
gc->forward_comm_kspace(this,6,sizeof(FFT_SCALAR),FORWARD_AD_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->forward_comm(this,6,sizeof(FFT_SCALAR),FORWARD_AD_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
else if (differentiation_flag == 0)
|
||||
gc->forward_comm_kspace(this,7,sizeof(FFT_SCALAR),FORWARD_IK_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
gc->forward_comm(this,7,sizeof(FFT_SCALAR),FORWARD_IK_PERATOM,
|
||||
gc_buf1,gc_buf2,MPI_FFT_SCALAR);
|
||||
}
|
||||
|
||||
// calculate the force on my particles
|
||||
|
||||
@ -49,6 +49,7 @@ endif
|
||||
|
||||
PACKAGE = \
|
||||
adios \
|
||||
amoeba \
|
||||
asphere \
|
||||
awpmd \
|
||||
bocs \
|
||||
|
||||
138
src/angle.cpp
138
src/angle.cpp
@ -25,6 +25,8 @@
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathConst;
|
||||
|
||||
#define FOURTH 0.25
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
Angle::Angle(LAMMPS *lmp) : Pointers(lmp)
|
||||
@ -221,30 +223,16 @@ void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond,
|
||||
virial[4] += v[4];
|
||||
virial[5] += v[5];
|
||||
} else {
|
||||
if (i < nlocal) {
|
||||
virial[0] += THIRD*v[0];
|
||||
virial[1] += THIRD*v[1];
|
||||
virial[2] += THIRD*v[2];
|
||||
virial[3] += THIRD*v[3];
|
||||
virial[4] += THIRD*v[4];
|
||||
virial[5] += THIRD*v[5];
|
||||
}
|
||||
if (j < nlocal) {
|
||||
virial[0] += THIRD*v[0];
|
||||
virial[1] += THIRD*v[1];
|
||||
virial[2] += THIRD*v[2];
|
||||
virial[3] += THIRD*v[3];
|
||||
virial[4] += THIRD*v[4];
|
||||
virial[5] += THIRD*v[5];
|
||||
}
|
||||
if (k < nlocal) {
|
||||
virial[0] += THIRD*v[0];
|
||||
virial[1] += THIRD*v[1];
|
||||
virial[2] += THIRD*v[2];
|
||||
virial[3] += THIRD*v[3];
|
||||
virial[4] += THIRD*v[4];
|
||||
virial[5] += THIRD*v[5];
|
||||
}
|
||||
double prefactor = 0.0;
|
||||
if (i < nlocal) prefactor += 1.0;
|
||||
if (j < nlocal) prefactor += 1.0;
|
||||
if (k < nlocal) prefactor += 1.0;
|
||||
virial[0] += prefactor*THIRD*v[0];
|
||||
virial[1] += prefactor*THIRD*v[1];
|
||||
virial[2] += prefactor*THIRD*v[2];
|
||||
virial[3] += prefactor*THIRD*v[3];
|
||||
virial[4] += prefactor*THIRD*v[4];
|
||||
virial[5] += prefactor*THIRD*v[5];
|
||||
}
|
||||
}
|
||||
|
||||
@ -277,6 +265,7 @@ void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond,
|
||||
}
|
||||
|
||||
// per-atom centroid virial
|
||||
|
||||
if (cvflag_atom) {
|
||||
|
||||
// r0 = (r1+r2+r3)/3
|
||||
@ -303,6 +292,7 @@ void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond,
|
||||
cvatom[i][7] += a1[2]*f1[0];
|
||||
cvatom[i][8] += a1[2]*f1[1];
|
||||
}
|
||||
|
||||
if (newton_bond || j < nlocal) {
|
||||
double a2[3];
|
||||
double f2[3];
|
||||
@ -326,6 +316,7 @@ void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond,
|
||||
cvatom[j][7] += a2[2]*f2[0];
|
||||
cvatom[j][8] += a2[2]*f2[1];
|
||||
}
|
||||
|
||||
if (newton_bond || k < nlocal) {
|
||||
double a3[3];
|
||||
|
||||
@ -347,6 +338,105 @@ void Angle::ev_tally(int i, int j, int k, int nlocal, int newton_bond,
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
tally energy and virial into global and per-atom accumulators
|
||||
virial = r1F1 + r2F2 + r3F3 + r4F4
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Angle::ev_tally4(int i, int j, int k, int m, int nlocal, int newton_bond,
|
||||
double eangle,
|
||||
double *f1, double *f2, double *f3, double *f4)
|
||||
{
|
||||
double eanglefourth,v[6];
|
||||
|
||||
if (eflag_either) {
|
||||
if (eflag_global) {
|
||||
if (newton_bond) energy += eangle;
|
||||
else {
|
||||
eanglefourth = FOURTH*eangle;
|
||||
if (i < nlocal) energy += eanglefourth;
|
||||
if (j < nlocal) energy += eanglefourth;
|
||||
if (k < nlocal) energy += eanglefourth;
|
||||
}
|
||||
}
|
||||
if (eflag_atom) {
|
||||
eanglefourth = FOURTH*eangle;
|
||||
if (newton_bond || i < nlocal) eatom[i] += eanglefourth;
|
||||
if (newton_bond || j < nlocal) eatom[j] += eanglefourth;
|
||||
if (newton_bond || k < nlocal) eatom[k] += eanglefourth;
|
||||
if (newton_bond || m < nlocal) eatom[m] += eanglefourth;
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_either) {
|
||||
double **x = atom->x;
|
||||
v[0] = x[i][0]*f1[0] + x[j][0]*f2[0] + x[k][0]*f3[0] + x[m][0]*f4[0];
|
||||
v[1] = x[i][1]*f1[1] + x[j][1]*f2[1] + x[k][1]*f3[1] + x[m][1]*f4[1];
|
||||
v[2] = x[i][2]*f1[2] + x[j][2]*f2[2] + x[k][2]*f3[2] + x[m][2]*f4[2];
|
||||
v[3] = x[i][0]*f1[1] + x[j][0]*f2[1] + x[k][0]*f3[1] + x[m][0]*f4[1];
|
||||
v[4] = x[i][0]*f1[2] + x[j][0]*f2[2] + x[k][0]*f3[2] + x[m][0]*f4[2];
|
||||
v[5] = x[i][1]*f1[2] + x[j][1]*f2[2] + x[k][1]*f3[2] + x[m][1]*f4[2];
|
||||
|
||||
if (vflag_global) {
|
||||
if (newton_bond) {
|
||||
virial[0] += v[0];
|
||||
virial[1] += v[1];
|
||||
virial[2] += v[2];
|
||||
virial[3] += v[3];
|
||||
virial[4] += v[4];
|
||||
virial[5] += v[5];
|
||||
} else {
|
||||
double prefactor = 0.0;
|
||||
if (i < nlocal) prefactor += 1.0;
|
||||
if (j < nlocal) prefactor += 1.0;
|
||||
if (k < nlocal) prefactor += 1.0;
|
||||
if (m < nlocal) prefactor += 1.0;
|
||||
virial[0] += prefactor*FOURTH*v[0];
|
||||
virial[1] += prefactor*FOURTH*v[1];
|
||||
virial[2] += prefactor*FOURTH*v[2];
|
||||
virial[3] += prefactor*FOURTH*v[3];
|
||||
virial[4] += prefactor*FOURTH*v[4];
|
||||
virial[5] += prefactor*FOURTH*v[5];
|
||||
}
|
||||
}
|
||||
|
||||
if (vflag_atom) {
|
||||
if (newton_bond || i < nlocal) {
|
||||
vatom[i][0] += FOURTH*v[0];
|
||||
vatom[i][1] += FOURTH*v[1];
|
||||
vatom[i][2] += FOURTH*v[2];
|
||||
vatom[i][3] += FOURTH*v[3];
|
||||
vatom[i][4] += FOURTH*v[4];
|
||||
vatom[i][5] += FOURTH*v[5];
|
||||
}
|
||||
if (newton_bond || j < nlocal) {
|
||||
vatom[j][0] += FOURTH*v[0];
|
||||
vatom[j][1] += FOURTH*v[1];
|
||||
vatom[j][2] += FOURTH*v[2];
|
||||
vatom[j][3] += FOURTH*v[3];
|
||||
vatom[j][4] += FOURTH*v[4];
|
||||
vatom[j][5] += FOURTH*v[5];
|
||||
}
|
||||
if (newton_bond || k < nlocal) {
|
||||
vatom[k][0] += FOURTH*v[0];
|
||||
vatom[k][1] += FOURTH*v[1];
|
||||
vatom[k][2] += FOURTH*v[2];
|
||||
vatom[k][3] += FOURTH*v[3];
|
||||
vatom[k][4] += FOURTH*v[4];
|
||||
vatom[k][5] += FOURTH*v[5];
|
||||
}
|
||||
if (newton_bond || m < nlocal) {
|
||||
vatom[m][0] += FOURTH*v[0];
|
||||
vatom[m][1] += FOURTH*v[1];
|
||||
vatom[m][2] += FOURTH*v[2];
|
||||
vatom[m][3] += FOURTH*v[3];
|
||||
vatom[m][4] += FOURTH*v[4];
|
||||
vatom[m][5] += FOURTH*v[5];
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double Angle::memory_usage()
|
||||
|
||||
@ -77,6 +77,7 @@ class Angle : protected Pointers {
|
||||
void ev_setup(int, int, int alloc = 1);
|
||||
void ev_tally(int, int, int, int, int, double, double *, double *, double, double, double, double,
|
||||
double, double);
|
||||
void ev_tally4(int, int, int, int, int, int, double, double *, double *, double *, double *);
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
12
src/atom.cpp
12
src/atom.cpp
@ -203,6 +203,12 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
|
||||
rho = drho = esph = desph = cv = nullptr;
|
||||
vest = nullptr;
|
||||
|
||||
// AMOEBA package
|
||||
|
||||
maxspecial15 = 1;
|
||||
nspecial15 = nullptr;
|
||||
special15 = nullptr;
|
||||
|
||||
// DIELECTRIC package
|
||||
|
||||
area = ed = em = epsilon = curvature = q_unscaled = nullptr;
|
||||
@ -539,6 +545,11 @@ void Atom::peratom_create()
|
||||
add_peratom("eff_plastic_strain_rate",&eff_plastic_strain_rate,DOUBLE,0);
|
||||
add_peratom("damage",&damage,DOUBLE,0);
|
||||
|
||||
// AMOEBA package
|
||||
|
||||
add_peratom("nspecial15",&nspecial15,INT,0);
|
||||
add_peratom_vary("special15",&special15,tagintsize,&maxspecial15,&nspecial15,0);
|
||||
|
||||
// DIELECTRIC package
|
||||
|
||||
add_peratom("area",&area,DOUBLE,0);
|
||||
@ -654,6 +665,7 @@ void Atom::set_atomflag_defaults()
|
||||
mesont_flag = 0;
|
||||
contact_radius_flag = smd_data_9_flag = smd_stress_flag = 0;
|
||||
eff_plastic_strain_flag = eff_plastic_strain_rate_flag = 0;
|
||||
nspecial15_flag = 0;
|
||||
|
||||
pdscale = 1.0;
|
||||
}
|
||||
|
||||
10
src/atom.h
10
src/atom.h
@ -161,6 +161,12 @@ class Atom : protected Pointers {
|
||||
double *rho, *drho, *esph, *desph, *cv;
|
||||
double **vest;
|
||||
|
||||
// AMOEBA package
|
||||
|
||||
int *nspecial15; // # of 1-5 neighs
|
||||
tagint **special15; // IDs of 1-5 neighs of each atom
|
||||
int maxspecial15; // special15[nlocal][maxspecial15]
|
||||
|
||||
// DIELECTRIC package
|
||||
|
||||
double *area, *ed, *em, *epsilon, *curvature, *q_unscaled;
|
||||
@ -198,6 +204,10 @@ class Atom : protected Pointers {
|
||||
int contact_radius_flag, smd_data_9_flag, smd_stress_flag;
|
||||
int eff_plastic_strain_flag, eff_plastic_strain_rate_flag;
|
||||
|
||||
// AMOEBA package
|
||||
|
||||
int nspecial15_flag;
|
||||
|
||||
// Peridynamics scale factor, used by dump cfg
|
||||
|
||||
double pdscale;
|
||||
|
||||
@ -31,7 +31,7 @@ enum{MOLECULE,CHARGE,RMASS,IVEC,DVEC,IARRAY,DARRAY};
|
||||
|
||||
FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg),
|
||||
nvalue(0), style(nullptr), index(nullptr), astyle(nullptr)
|
||||
nvalue(0), styles(nullptr), index(nullptr), astyle(nullptr)
|
||||
{
|
||||
if (narg < 4) error->all(FLERR,"Illegal fix property/atom command");
|
||||
|
||||
@ -40,7 +40,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
int iarg = 3;
|
||||
nvalue = narg-iarg;
|
||||
style = new int[nvalue];
|
||||
styles = new int[nvalue];
|
||||
cols = new int[nvalue];
|
||||
index = new int[nvalue];
|
||||
|
||||
@ -58,7 +58,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
"already has molecule attribute");
|
||||
if (molecule_flag)
|
||||
error->all(FLERR,"Fix property/atom cannot specify mol twice");
|
||||
style[nvalue] = MOLECULE;
|
||||
styles[nvalue] = MOLECULE;
|
||||
cols[nvalue] = 0;
|
||||
atom->molecule_flag = molecule_flag = 1;
|
||||
values_peratom++;
|
||||
@ -69,7 +69,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
error->all(FLERR,"Fix property/atom q when atom_style already has charge attribute");
|
||||
if (q_flag)
|
||||
error->all(FLERR,"Fix property/atom cannot specify q twice");
|
||||
style[nvalue] = CHARGE;
|
||||
styles[nvalue] = CHARGE;
|
||||
cols[nvalue] = 0;
|
||||
atom->q_flag = q_flag = 1;
|
||||
values_peratom++;
|
||||
@ -80,7 +80,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
error->all(FLERR,"Fix property/atom rmass when atom_style already has rmass attribute");
|
||||
if (rmass_flag)
|
||||
error->all(FLERR,"Fix property/atom cannot specify rmass twice");
|
||||
style[nvalue] = RMASS;
|
||||
styles[nvalue] = RMASS;
|
||||
cols[nvalue] = 0;
|
||||
atom->rmass_flag = rmass_flag = 1;
|
||||
values_peratom++;
|
||||
@ -90,7 +90,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
// custom atom vector
|
||||
|
||||
} else if (utils::strmatch(arg[iarg],"^i_")) {
|
||||
style[nvalue] = IVEC;
|
||||
styles[nvalue] = IVEC;
|
||||
int flag,ncols;
|
||||
index[nvalue] = atom->find_custom(&arg[iarg][2],flag,ncols);
|
||||
if (index[nvalue] >= 0)
|
||||
@ -102,7 +102,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
iarg++;
|
||||
|
||||
} else if (utils::strmatch(arg[iarg],"^d_")) {
|
||||
style[nvalue] = DVEC;
|
||||
styles[nvalue] = DVEC;
|
||||
int flag,ncols;
|
||||
index[nvalue] = atom->find_custom(&arg[iarg][2],flag,ncols);
|
||||
if (index[nvalue] >= 0)
|
||||
@ -129,10 +129,10 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
if (arg[iarg][0] == 'i') {
|
||||
which = 0;
|
||||
style[nvalue] = IARRAY;
|
||||
styles[nvalue] = IARRAY;
|
||||
} else {
|
||||
which = 1;
|
||||
style[nvalue] = DARRAY;
|
||||
styles[nvalue] = DARRAY;
|
||||
}
|
||||
index[nvalue] = atom->add_custom(&arg[iarg][3],which,ncols);
|
||||
cols[nvalue] = ncols;
|
||||
@ -165,9 +165,8 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
if (border == 0) {
|
||||
int flag = 0;
|
||||
for (int i = 0; i < nvalue; i++)
|
||||
if (style[i] == MOLECULE
|
||||
|| style[i] == CHARGE
|
||||
|| style[i] == RMASS) flag = 1;
|
||||
if (styles[i] == MOLECULE || styles[i] == CHARGE || styles[i] == RMASS)
|
||||
flag = 1;
|
||||
if (flag && comm->me == 0)
|
||||
error->warning(FLERR,"Fix property/atom mol or charge or rmass "
|
||||
"w/out ghost communication");
|
||||
@ -201,25 +200,25 @@ FixPropertyAtom::~FixPropertyAtom()
|
||||
// set ptrs to a null pointer, so they no longer exist for Atom class
|
||||
|
||||
for (int nv = 0; nv < nvalue; nv++) {
|
||||
if (style[nv] == MOLECULE) {
|
||||
if (styles[nv] == MOLECULE) {
|
||||
atom->molecule_flag = 0;
|
||||
memory->destroy(atom->molecule);
|
||||
atom->molecule = nullptr;
|
||||
} else if (style[nv] == CHARGE) {
|
||||
} else if (styles[nv] == CHARGE) {
|
||||
atom->q_flag = 0;
|
||||
memory->destroy(atom->q);
|
||||
atom->q = nullptr;
|
||||
} else if (style[nv] == RMASS) {
|
||||
} else if (styles[nv] == RMASS) {
|
||||
atom->rmass_flag = 0;
|
||||
memory->destroy(atom->rmass);
|
||||
atom->rmass = nullptr;
|
||||
} else if (style[nv] == IVEC) {
|
||||
} else if (styles[nv] == IVEC) {
|
||||
atom->remove_custom(index[nv],0,cols[nv]);
|
||||
} else if (style[nv] == DVEC) {
|
||||
} else if (styles[nv] == DVEC) {
|
||||
atom->remove_custom(index[nv],1,cols[nv]);
|
||||
} else if (style[nv] == IARRAY) {
|
||||
} else if (styles[nv] == IARRAY) {
|
||||
atom->remove_custom(index[nv],0,cols[nv]);
|
||||
} else if (style[nv] == DARRAY) {
|
||||
} else if (styles[nv] == DARRAY) {
|
||||
atom->remove_custom(index[nv],1,cols[nv]);
|
||||
}
|
||||
}
|
||||
@ -291,21 +290,21 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, tagint
|
||||
|
||||
if ((m = atom->map(itag)) >= 0) {
|
||||
for (j = 0; j < nvalue; j++) {
|
||||
if (style[j] == MOLECULE) {
|
||||
if (styles[j] == MOLECULE) {
|
||||
atom->molecule[m] = values.next_tagint();
|
||||
} else if (style[j] == CHARGE) {
|
||||
} else if (styles[j] == CHARGE) {
|
||||
atom->q[m] = values.next_double();
|
||||
} else if (style[j] == RMASS) {
|
||||
} else if (styles[j] == RMASS) {
|
||||
atom->rmass[m] = values.next_double();
|
||||
} else if (style[j] == IVEC) {
|
||||
} else if (styles[j] == IVEC) {
|
||||
atom->ivector[index[j]][m] = values.next_int();
|
||||
} else if (style[j] == DVEC) {
|
||||
} else if (styles[j] == DVEC) {
|
||||
atom->dvector[index[j]][m] = values.next_double();
|
||||
} else if (style[j] == IARRAY) {
|
||||
} else if (styles[j] == IARRAY) {
|
||||
ncol = cols[j];
|
||||
for (k = 0; k < ncol; k++)
|
||||
atom->iarray[index[j]][m][k] = values.next_int();
|
||||
} else if (style[j] == DARRAY) {
|
||||
} else if (styles[j] == DARRAY) {
|
||||
ncol = cols[j];
|
||||
for (k = 0; k < ncol; k++)
|
||||
atom->darray[index[j]][m][k] = values.next_double();
|
||||
@ -365,34 +364,34 @@ void FixPropertyAtom::write_data_section_pack(int /*mth*/, double **buf)
|
||||
|
||||
int icol = 1;
|
||||
for (int nv = 0; nv < nvalue; nv++) {
|
||||
if (style[nv] == MOLECULE) {
|
||||
if (styles[nv] == MOLECULE) {
|
||||
tagint *molecule = atom->molecule;
|
||||
for (i = 0; i < nlocal; i++) buf[i][icol] = ubuf(molecule[i]).d;
|
||||
icol++;
|
||||
} else if (style[nv] == CHARGE) {
|
||||
} else if (styles[nv] == CHARGE) {
|
||||
double *q = atom->q;
|
||||
for (i = 0; i < nlocal; i++) buf[i][icol] = q[i];
|
||||
icol++;
|
||||
} else if (style[nv] == RMASS) {
|
||||
} else if (styles[nv] == RMASS) {
|
||||
double *rmass = atom->rmass;
|
||||
for (i = 0; i < nlocal; i++) buf[i][icol] = rmass[i];
|
||||
icol++;
|
||||
} else if (style[nv] == IVEC) {
|
||||
} else if (styles[nv] == IVEC) {
|
||||
int *ivec = atom->ivector[index[nv]];
|
||||
for (i = 0; i < nlocal; i++) buf[i][icol] = ubuf(ivec[i]).d;
|
||||
icol++;
|
||||
} else if (style[nv] == DVEC) {
|
||||
} else if (styles[nv] == DVEC) {
|
||||
double *dvec = atom->dvector[index[nv]];
|
||||
for (i = 0; i < nlocal; i++) buf[i][icol] = dvec[i];
|
||||
icol++;
|
||||
} else if (style[nv] == IARRAY) {
|
||||
} else if (styles[nv] == IARRAY) {
|
||||
int **iarray = atom->iarray[index[nv]];
|
||||
ncol = cols[nv];
|
||||
for (i = 0; i < nlocal; i++)
|
||||
for (k = 0; k < ncol; k++)
|
||||
buf[i][icol+k] = ubuf(iarray[i][k]).d;
|
||||
icol += ncol;
|
||||
} else if (style[nv] == DARRAY) {
|
||||
} else if (styles[nv] == DARRAY) {
|
||||
double **darray = atom->darray[index[nv]];
|
||||
ncol = cols[nv];
|
||||
for (i = 0; i < nlocal; i++)
|
||||
@ -412,19 +411,19 @@ void FixPropertyAtom::write_data_section_pack(int /*mth*/, double **buf)
|
||||
|
||||
void FixPropertyAtom::write_data_section_keyword(int /*mth*/, FILE *fp)
|
||||
{
|
||||
if (nvalue == 1 && style[0] == MOLECULE) fprintf(fp,"\nMolecules\n\n");
|
||||
else if (nvalue == 1 && style[0] == CHARGE) fprintf(fp,"\nCharges\n\n");
|
||||
if (nvalue == 1 && styles[0] == MOLECULE) fprintf(fp,"\nMolecules\n\n");
|
||||
else if (nvalue == 1 && styles[0] == CHARGE) fprintf(fp,"\nCharges\n\n");
|
||||
else {
|
||||
fprintf(fp,"\n%s #",id);
|
||||
// write column hint as comment
|
||||
for (int i = 0; i < nvalue; ++i) {
|
||||
if (style[i] == MOLECULE) fputs(" mol",fp);
|
||||
else if (style[i] == CHARGE) fputs(" q",fp);
|
||||
else if (style[i] == RMASS) fputs(" rmass",fp);
|
||||
else if (style[i] == IVEC) fprintf(fp," i_%s", atom->ivname[index[i]]);
|
||||
else if (style[i] == DVEC) fprintf(fp, " d_%s", atom->dvname[index[i]]);
|
||||
else if (style[i] == IARRAY) fprintf(fp, " i_%s", atom->ianame[index[i]]);
|
||||
else if (style[i] == DARRAY) fprintf(fp, " d_%s", atom->daname[index[i]]);
|
||||
if (styles[i] == MOLECULE) fputs(" mol",fp);
|
||||
else if (styles[i] == CHARGE) fputs(" q",fp);
|
||||
else if (styles[i] == RMASS) fputs(" rmass",fp);
|
||||
else if (styles[i] == IVEC) fprintf(fp," i_%s", atom->ivname[index[i]]);
|
||||
else if (styles[i] == DVEC) fprintf(fp, " d_%s", atom->dvname[index[i]]);
|
||||
else if (styles[i] == IARRAY) fprintf(fp, " i_%s", atom->ianame[index[i]]);
|
||||
else if (styles[i] == DARRAY) fprintf(fp, " d_%s", atom->daname[index[i]]);
|
||||
}
|
||||
fputs("\n\n",fp);
|
||||
}
|
||||
@ -446,22 +445,22 @@ void FixPropertyAtom::write_data_section(int /*mth*/, FILE *fp,
|
||||
fprintf(fp,TAGINT_FORMAT,(tagint) ubuf(buf[i][0]).i);
|
||||
icol = 1;
|
||||
for (nv = 0; nv < nvalue; nv++) {
|
||||
if (style[nv] == MOLECULE)
|
||||
if (styles[nv] == MOLECULE)
|
||||
fprintf(fp," " TAGINT_FORMAT,(tagint) ubuf(buf[i][icol++]).i);
|
||||
else if (style[nv] == CHARGE)
|
||||
else if (styles[nv] == CHARGE)
|
||||
fprintf(fp," %g",buf[i][icol++]);
|
||||
else if (style[nv] == RMASS)
|
||||
else if (styles[nv] == RMASS)
|
||||
fprintf(fp," %g",buf[i][icol++]);
|
||||
else if (style[nv] == IVEC)
|
||||
else if (styles[nv] == IVEC)
|
||||
fprintf(fp," %d",(int) ubuf(buf[i][icol++]).i);
|
||||
else if (style[nv] == DVEC)
|
||||
else if (styles[nv] == DVEC)
|
||||
fprintf(fp," %g",buf[i][icol++]);
|
||||
else if (style[nv] == IARRAY) {
|
||||
else if (styles[nv] == IARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
fprintf(fp," %d",(int) ubuf(buf[i][icol+k]).i);
|
||||
icol += ncol;
|
||||
} else if (style[nv] == DARRAY) {
|
||||
} else if (styles[nv] == DARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
fprintf(fp," %g",buf[i][icol+k]);
|
||||
@ -480,13 +479,13 @@ double FixPropertyAtom::memory_usage()
|
||||
{
|
||||
double bytes = 0.0;
|
||||
for (int m = 0; m < nvalue; m++) {
|
||||
if (style[m] == MOLECULE) bytes = atom->nmax * sizeof(tagint);
|
||||
else if (style[m] == CHARGE) bytes = atom->nmax * sizeof(double);
|
||||
else if (style[m] == RMASS) bytes = atom->nmax * sizeof(double);
|
||||
else if (style[m] == IVEC) bytes = atom->nmax * sizeof(int);
|
||||
else if (style[m] == DVEC) bytes = atom->nmax * sizeof(double);
|
||||
else if (style[m] == IARRAY) bytes = atom->nmax * cols[m] * sizeof(int);
|
||||
else if (style[m] == DARRAY) bytes = atom->nmax * cols[m] * sizeof(double);
|
||||
if (styles[m] == MOLECULE) bytes = atom->nmax * sizeof(tagint);
|
||||
else if (styles[m] == CHARGE) bytes = atom->nmax * sizeof(double);
|
||||
else if (styles[m] == RMASS) bytes = atom->nmax * sizeof(double);
|
||||
else if (styles[m] == IVEC) bytes = atom->nmax * sizeof(int);
|
||||
else if (styles[m] == DVEC) bytes = atom->nmax * sizeof(double);
|
||||
else if (styles[m] == IARRAY) bytes = atom->nmax * cols[m] * sizeof(int);
|
||||
else if (styles[m] == DARRAY) bytes = atom->nmax * cols[m] * sizeof(double);
|
||||
}
|
||||
return bytes;
|
||||
}
|
||||
@ -501,31 +500,31 @@ double FixPropertyAtom::memory_usage()
|
||||
void FixPropertyAtom::grow_arrays(int nmax)
|
||||
{
|
||||
for (int nv = 0; nv < nvalue; nv++) {
|
||||
if (style[nv] == MOLECULE) {
|
||||
if (styles[nv] == MOLECULE) {
|
||||
memory->grow(atom->molecule,nmax,"atom:molecule");
|
||||
size_t nbytes = (nmax-nmax_old) * sizeof(tagint);
|
||||
memset(&atom->molecule[nmax_old],0,nbytes);
|
||||
} else if (style[nv] == CHARGE) {
|
||||
} else if (styles[nv] == CHARGE) {
|
||||
memory->grow(atom->q,nmax,"atom:q");
|
||||
size_t nbytes = (nmax-nmax_old) * sizeof(double);
|
||||
memset(&atom->q[nmax_old],0,nbytes);
|
||||
} else if (style[nv] == RMASS) {
|
||||
} else if (styles[nv] == RMASS) {
|
||||
memory->grow(atom->rmass,nmax,"atom:rmass");
|
||||
size_t nbytes = (nmax-nmax_old) * sizeof(double);
|
||||
memset(&atom->rmass[nmax_old],0,nbytes);
|
||||
} else if (style[nv] == IVEC) {
|
||||
} else if (styles[nv] == IVEC) {
|
||||
memory->grow(atom->ivector[index[nv]],nmax,"atom:ivector");
|
||||
size_t nbytes = (nmax-nmax_old) * sizeof(int);
|
||||
memset(&atom->ivector[index[nv]][nmax_old],0,nbytes);
|
||||
} else if (style[nv] == DVEC) {
|
||||
} else if (styles[nv] == DVEC) {
|
||||
memory->grow(atom->dvector[index[nv]],nmax,"atom:dvector");
|
||||
size_t nbytes = (nmax-nmax_old) * sizeof(double);
|
||||
memset(&atom->dvector[index[nv]][nmax_old],0,nbytes);
|
||||
} else if (style[nv] == IARRAY) {
|
||||
} else if (styles[nv] == IARRAY) {
|
||||
memory->grow(atom->iarray[index[nv]],nmax,cols[nv],"atom:iarray");
|
||||
size_t nbytes = (nmax-nmax_old) * cols[nv] * sizeof(int);
|
||||
if (nbytes) memset(&atom->iarray[index[nv]][nmax_old][0],0,nbytes);
|
||||
} else if (style[nv] == DARRAY) {
|
||||
} else if (styles[nv] == DARRAY) {
|
||||
memory->grow(atom->darray[index[nv]],nmax,cols[nv],"atom:darray");
|
||||
size_t nbytes = (nmax-nmax_old) * cols[nv] * sizeof(double);
|
||||
if (nbytes) memset(&atom->darray[index[nv]][nmax_old][0],0,nbytes);
|
||||
@ -544,21 +543,21 @@ void FixPropertyAtom::copy_arrays(int i, int j, int /*delflag*/)
|
||||
int k,ncol;
|
||||
|
||||
for (int nv = 0; nv < nvalue; nv++) {
|
||||
if (style[nv] == MOLECULE)
|
||||
if (styles[nv] == MOLECULE)
|
||||
atom->molecule[j] = atom->molecule[i];
|
||||
else if (style[nv] == CHARGE)
|
||||
else if (styles[nv] == CHARGE)
|
||||
atom->q[j] = atom->q[i];
|
||||
else if (style[nv] == RMASS)
|
||||
else if (styles[nv] == RMASS)
|
||||
atom->rmass[j] = atom->rmass[i];
|
||||
else if (style[nv] == IVEC)
|
||||
else if (styles[nv] == IVEC)
|
||||
atom->ivector[index[nv]][j] = atom->ivector[index[nv]][i];
|
||||
else if (style[nv] == DVEC)
|
||||
else if (styles[nv] == DVEC)
|
||||
atom->dvector[index[nv]][j] = atom->dvector[index[nv]][i];
|
||||
else if (style[nv] == IARRAY) {
|
||||
else if (styles[nv] == IARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
atom->iarray[index[nv]][j][k] = atom->iarray[index[nv]][i][k];
|
||||
} else if (style[nv] == DARRAY) {
|
||||
} else if (styles[nv] == DARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
atom->darray[index[nv]][j][k] = atom->darray[index[nv]][i][k];
|
||||
@ -576,37 +575,37 @@ int FixPropertyAtom::pack_border(int n, int *list, double *buf)
|
||||
|
||||
int m = 0;
|
||||
for (int nv = 0; nv < nvalue; nv++) {
|
||||
if (style[nv] == MOLECULE) {
|
||||
if (styles[nv] == MOLECULE) {
|
||||
tagint *molecule = atom->molecule;
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
buf[m++] = ubuf(molecule[j]).d;
|
||||
}
|
||||
} else if (style[nv] == CHARGE) {
|
||||
} else if (styles[nv] == CHARGE) {
|
||||
double *q = atom->q;
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
buf[m++] = q[j];
|
||||
}
|
||||
} else if (style[nv] == RMASS) {
|
||||
} else if (styles[nv] == RMASS) {
|
||||
double *rmass = atom->rmass;
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
buf[m++] = rmass[j];
|
||||
}
|
||||
} else if (style[nv] == IVEC) {
|
||||
} else if (styles[nv] == IVEC) {
|
||||
int *ivector = atom->ivector[index[nv]];
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
buf[m++] = ubuf(ivector[j]).d;
|
||||
}
|
||||
} else if (style[nv] == DVEC) {
|
||||
} else if (styles[nv] == DVEC) {
|
||||
double *dvector = atom->dvector[index[nv]];
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
buf[m++] = dvector[j];
|
||||
}
|
||||
} else if (style[nv] == IARRAY) {
|
||||
} else if (styles[nv] == IARRAY) {
|
||||
int **iarray = atom->iarray[index[nv]];
|
||||
ncol = cols[nv];
|
||||
for (i = 0; i < n; i++) {
|
||||
@ -614,7 +613,7 @@ int FixPropertyAtom::pack_border(int n, int *list, double *buf)
|
||||
for (k = 0; k < ncol; k++)
|
||||
buf[m++] = ubuf(iarray[j][k]).d;
|
||||
}
|
||||
} else if (style[nv] == DARRAY) {
|
||||
} else if (styles[nv] == DARRAY) {
|
||||
double **darray = atom->darray[index[nv]];
|
||||
ncol = cols[nv];
|
||||
for (i = 0; i < n; i++) {
|
||||
@ -638,39 +637,39 @@ int FixPropertyAtom::unpack_border(int n, int first, double *buf)
|
||||
|
||||
int m = 0;
|
||||
for (int nv = 0; nv < nvalue; nv++) {
|
||||
if (style[nv] == MOLECULE) {
|
||||
if (styles[nv] == MOLECULE) {
|
||||
tagint *molecule = atom->molecule;
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++)
|
||||
molecule[i] = (tagint) ubuf(buf[m++]).i;
|
||||
} else if (style[nv] == CHARGE) {
|
||||
} else if (styles[nv] == CHARGE) {
|
||||
double *q = atom->q;
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++)
|
||||
q[i] = buf[m++];
|
||||
} else if (style[nv] == RMASS) {
|
||||
} else if (styles[nv] == RMASS) {
|
||||
double *rmass = atom->rmass;
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++)
|
||||
rmass[i] = buf[m++];
|
||||
} else if (style[nv] == IVEC) {
|
||||
} else if (styles[nv] == IVEC) {
|
||||
int *ivector = atom->ivector[index[nv]];
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++)
|
||||
ivector[i] = (int) ubuf(buf[m++]).i;
|
||||
} else if (style[nv] == DVEC) {
|
||||
} else if (styles[nv] == DVEC) {
|
||||
double *dvector = atom->dvector[index[nv]];
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++)
|
||||
dvector[i] = buf[m++];
|
||||
} else if (style[nv] == IARRAY) {
|
||||
} else if (styles[nv] == IARRAY) {
|
||||
int **iarray = atom->iarray[index[nv]];
|
||||
ncol = cols[nv];
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++)
|
||||
for (k = 0; k < ncol; k++)
|
||||
iarray[i][k] = (int) ubuf(buf[m++]).i;
|
||||
} else if (style[nv] == DARRAY) {
|
||||
} else if (styles[nv] == DARRAY) {
|
||||
double **darray = atom->darray[index[nv]];
|
||||
ncol = cols[nv];
|
||||
last = first + n;
|
||||
@ -693,16 +692,16 @@ int FixPropertyAtom::pack_exchange(int i, double *buf)
|
||||
|
||||
int m = 0;
|
||||
for (int nv = 0; nv < nvalue; nv++) {
|
||||
if (style[nv] == MOLECULE) buf[m++] = ubuf(atom->molecule[i]).d;
|
||||
else if (style[nv] == CHARGE) buf[m++] = atom->q[i];
|
||||
else if (style[nv] == RMASS) buf[m++] = atom->rmass[i];
|
||||
else if (style[nv] == IVEC) buf[m++] = ubuf(atom->ivector[index[nv]][i]).d;
|
||||
else if (style[nv] == DVEC) buf[m++] = atom->dvector[index[nv]][i];
|
||||
else if (style[nv] == IARRAY) {
|
||||
if (styles[nv] == MOLECULE) buf[m++] = ubuf(atom->molecule[i]).d;
|
||||
else if (styles[nv] == CHARGE) buf[m++] = atom->q[i];
|
||||
else if (styles[nv] == RMASS) buf[m++] = atom->rmass[i];
|
||||
else if (styles[nv] == IVEC) buf[m++] = ubuf(atom->ivector[index[nv]][i]).d;
|
||||
else if (styles[nv] == DVEC) buf[m++] = atom->dvector[index[nv]][i];
|
||||
else if (styles[nv] == IARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
buf[m++] = ubuf(atom->iarray[index[nv]][i][k]).d;
|
||||
} else if (style[nv] == DARRAY) {
|
||||
} else if (styles[nv] == DARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
buf[m++] = atom->darray[index[nv]][i][k];
|
||||
@ -722,21 +721,21 @@ int FixPropertyAtom::unpack_exchange(int nlocal, double *buf)
|
||||
|
||||
int m = 0;
|
||||
for (int nv = 0; nv < nvalue; nv++) {
|
||||
if (style[nv] == MOLECULE)
|
||||
if (styles[nv] == MOLECULE)
|
||||
atom->molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
|
||||
else if (style[nv] == CHARGE)
|
||||
else if (styles[nv] == CHARGE)
|
||||
atom->q[nlocal] = buf[m++];
|
||||
else if (style[nv] == RMASS)
|
||||
else if (styles[nv] == RMASS)
|
||||
atom->rmass[nlocal] = buf[m++];
|
||||
else if (style[nv] == IVEC)
|
||||
else if (styles[nv] == IVEC)
|
||||
atom->ivector[index[nv]][nlocal] = (int) ubuf(buf[m++]).i;
|
||||
else if (style[nv] == DVEC)
|
||||
else if (styles[nv] == DVEC)
|
||||
atom->dvector[index[nv]][nlocal] = buf[m++];
|
||||
else if (style[nv] == IARRAY) {
|
||||
else if (styles[nv] == IARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
atom->iarray[index[nv]][nlocal][k] = (int) ubuf(buf[m++]).i;
|
||||
} else if (style[nv] == DARRAY) {
|
||||
} else if (styles[nv] == DARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
atom->darray[index[nv]][nlocal][k] = buf[m++];
|
||||
@ -760,16 +759,16 @@ int FixPropertyAtom::pack_restart(int i, double *buf)
|
||||
|
||||
int m = 1;
|
||||
for (int nv = 0; nv < nvalue; nv++) {
|
||||
if (style[nv] == MOLECULE) buf[m++] = ubuf(atom->molecule[i]).d;
|
||||
else if (style[nv] == CHARGE) buf[m++] = atom->q[i];
|
||||
else if (style[nv] == RMASS) buf[m++] = atom->rmass[i];
|
||||
else if (style[nv] == IVEC) buf[m++] = ubuf(atom->ivector[index[nv]][i]).d;
|
||||
else if (style[nv] == DVEC) buf[m++] = atom->dvector[index[nv]][i];
|
||||
else if (style[nv] == IARRAY) {
|
||||
if (styles[nv] == MOLECULE) buf[m++] = ubuf(atom->molecule[i]).d;
|
||||
else if (styles[nv] == CHARGE) buf[m++] = atom->q[i];
|
||||
else if (styles[nv] == RMASS) buf[m++] = atom->rmass[i];
|
||||
else if (styles[nv] == IVEC) buf[m++] = ubuf(atom->ivector[index[nv]][i]).d;
|
||||
else if (styles[nv] == DVEC) buf[m++] = atom->dvector[index[nv]][i];
|
||||
else if (styles[nv] == IARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
buf[m++] = ubuf(atom->iarray[index[nv]][i][k]).d;
|
||||
} else if (style[nv] == DARRAY) {
|
||||
} else if (styles[nv] == DARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
buf[m++] = atom->darray[index[nv]][i][k];
|
||||
@ -796,21 +795,21 @@ void FixPropertyAtom::unpack_restart(int nlocal, int nth)
|
||||
m++;
|
||||
|
||||
for (int nv = 0; nv < nvalue; nv++) {
|
||||
if (style[nv] == MOLECULE)
|
||||
if (styles[nv] == MOLECULE)
|
||||
atom->molecule[nlocal] = (tagint) ubuf(extra[nlocal][m++]).i;
|
||||
else if (style[nv] == CHARGE)
|
||||
else if (styles[nv] == CHARGE)
|
||||
atom->q[nlocal] = extra[nlocal][m++];
|
||||
else if (style[nv] == RMASS)
|
||||
else if (styles[nv] == RMASS)
|
||||
atom->rmass[nlocal] = extra[nlocal][m++];
|
||||
else if (style[nv] == IVEC)
|
||||
else if (styles[nv] == IVEC)
|
||||
atom->ivector[index[nv]][nlocal] = (int) ubuf(extra[nlocal][m++]).i;
|
||||
else if (style[nv] == DVEC)
|
||||
else if (styles[nv] == DVEC)
|
||||
atom->dvector[index[nv]][nlocal] = extra[nlocal][m++];
|
||||
else if (style[nv] == IARRAY) {
|
||||
else if (styles[nv] == IARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
atom->iarray[index[nv]][nlocal][k] = (int) ubuf(extra[nlocal][m++]).i;
|
||||
} else if (style[nv] == DARRAY) {
|
||||
} else if (styles[nv] == DARRAY) {
|
||||
ncol = cols[nv];
|
||||
for (k = 0; k < ncol; k++)
|
||||
atom->darray[index[nv]][nlocal][k] = extra[nlocal][m++];
|
||||
|
||||
@ -53,7 +53,7 @@ class FixPropertyAtom : public Fix {
|
||||
protected:
|
||||
int nvalue, border;
|
||||
int molecule_flag, q_flag, rmass_flag; // flags for specific fields
|
||||
int *style; // style of each value, see enum
|
||||
int *styles; // style of each value, see enum
|
||||
int *index; // indices into atom custom data structs
|
||||
int *cols; // columns per value, for arrays
|
||||
char *astyle; // atom style at instantiation
|
||||
|
||||
@ -31,18 +31,17 @@ enum{UNKNOWN,GLOBAL,PERATOM};
|
||||
FixStore::FixStore(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
|
||||
vstore(nullptr), astore(nullptr), rbuf(nullptr)
|
||||
{
|
||||
if (narg != 6) error->all(FLERR,"Illegal fix store command");
|
||||
if (narg != 6 && narg != 7) error->all(FLERR,"Illegal fix store command");
|
||||
|
||||
// 4th arg determines GLOBAL vs PERATOM values
|
||||
// syntax: id group style global nrow ncol
|
||||
// Nrow by Ncol array of global values
|
||||
// Ncol = 1 is vector, Ncol > 1 is array
|
||||
// syntax: id group style peratom 0/1 nvalues
|
||||
// global syntax: id group style global n1 n2
|
||||
// N2 = 1 is vector, N2 > 1 is array, no tensor allowed (yet)
|
||||
// peratom syntax: id group style peratom 0/1 n1 n2 (n3), last arg optional
|
||||
// 0/1 flag = not-store or store peratom values in restart file
|
||||
// N2 = 1 and no n3 is vector, N2 > 1 and no n3 is array, N3 = tensor
|
||||
// nvalues = # of peratom values, N = 1 is vector, N > 1 is array
|
||||
|
||||
disable = 0;
|
||||
nvalues = vecflag = 0;
|
||||
flavor = UNKNOWN;
|
||||
|
||||
if (strcmp(arg[3],"global") == 0) flavor = GLOBAL;
|
||||
@ -52,35 +51,48 @@ vstore(nullptr), astore(nullptr), rbuf(nullptr)
|
||||
// GLOBAL values are always written to restart file
|
||||
// PERATOM restart_peratom is set by caller
|
||||
|
||||
vecflag = arrayflag = tensorflag = 0;
|
||||
|
||||
if (flavor == GLOBAL) {
|
||||
restart_global = 1;
|
||||
nrow = utils::inumeric(FLERR,arg[4],false,lmp);
|
||||
ncol = utils::inumeric(FLERR,arg[5],false,lmp);
|
||||
if (nrow <= 0 || ncol <= 0)
|
||||
error->all(FLERR,"Illegal fix store command");
|
||||
vecflag = 0;
|
||||
if (ncol == 1) vecflag = 1;
|
||||
n1 = utils::inumeric(FLERR,arg[4],false,lmp);
|
||||
n2 = utils::inumeric(FLERR,arg[5],false,lmp);
|
||||
if (narg == 7) error->all(FLERR,"Illegal fix store command");
|
||||
if (n1 <= 0 || n2 <= 0) error->all(FLERR,"Illegal fix store command");
|
||||
if (n2 == 1) vecflag = 1;
|
||||
else arrayflag = 1;
|
||||
nrow = n1;
|
||||
ncol = n2;
|
||||
}
|
||||
|
||||
if (flavor == PERATOM) {
|
||||
restart_peratom = utils::inumeric(FLERR,arg[4],false,lmp);
|
||||
nvalues = utils::inumeric(FLERR,arg[5],false,lmp);
|
||||
if (restart_peratom < 0 or restart_peratom > 1 || nvalues <= 0)
|
||||
n2 = utils::inumeric(FLERR,arg[5],false,lmp);
|
||||
if (narg == 7) n3 = utils::inumeric(FLERR,arg[6],false,lmp);
|
||||
else n3 = 1;
|
||||
if (restart_peratom < 0 || restart_peratom > 1)
|
||||
error->all(FLERR,"Illegal fix store command");
|
||||
vecflag = 0;
|
||||
if (nvalues == 1) vecflag = 1;
|
||||
if (n2 <= 0 || n3 <= 0) error->all(FLERR,"Illegal fix store command");
|
||||
if (n2 == 1 && narg == 6) vecflag = 1;
|
||||
else if (narg == 6) arrayflag = 1;
|
||||
else tensorflag = 1;
|
||||
nvalues = n2*n3;
|
||||
nbytes = n2*n3 * sizeof(double);
|
||||
}
|
||||
|
||||
vstore = nullptr;
|
||||
astore = nullptr;
|
||||
vstore = NULL;
|
||||
astore = NULL;
|
||||
tstore = NULL;
|
||||
|
||||
// allocate vector or array and restart buffer rbuf
|
||||
// allocate data struct and restart buffer rbuf
|
||||
// for PERATOM, register with Atom class
|
||||
|
||||
if (flavor == GLOBAL) {
|
||||
if (vecflag) memory->create(vstore,nrow,"fix/store:vstore");
|
||||
else memory->create(astore,nrow,ncol,"fix/store:astore");
|
||||
memory->create(rbuf,nrow*ncol+2,"fix/store:rbuf");
|
||||
if (vecflag) memory->create(vstore,n1,"fix/store:vstore");
|
||||
else if (arrayflag) memory->create(astore,n1,n2,"fix/store:astore");
|
||||
memory->create(rbuf,n1*n2+2,"fix/store:rbuf");
|
||||
}
|
||||
|
||||
if (flavor == PERATOM) {
|
||||
grow_arrays(atom->nmax);
|
||||
atom->add_callback(Atom::GROW);
|
||||
@ -92,21 +104,31 @@ vstore(nullptr), astore(nullptr), rbuf(nullptr)
|
||||
// PERATOM may be comm->exchanged before filled by caller
|
||||
|
||||
if (flavor == GLOBAL) {
|
||||
if (vecflag)
|
||||
for (int i = 0; i < nrow; i++) vstore[i] = 0.0;
|
||||
else
|
||||
for (int i = 0; i < nrow; i++)
|
||||
for (int j = 0; j < ncol; j++)
|
||||
if (vecflag) {
|
||||
for (int i = 0; i < n1; i++)
|
||||
vstore[i] = 0.0;
|
||||
} else if (arrayflag) {
|
||||
for (int i = 0; i < n1; i++)
|
||||
for (int j = 0; j < n2; j++)
|
||||
astore[i][j] = 0.0;
|
||||
}
|
||||
}
|
||||
|
||||
if (flavor == PERATOM) {
|
||||
int nlocal = atom->nlocal;
|
||||
if (vecflag)
|
||||
for (int i = 0; i < nlocal; i++) vstore[i] = 0.0;
|
||||
else
|
||||
if (vecflag) {
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
for (int j = 0; j < nvalues; j++)
|
||||
vstore[i] = 0.0;
|
||||
} else if (arrayflag) {
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
for (int j = 0; j < n2; j++)
|
||||
astore[i][j] = 0.0;
|
||||
} else if (tensorflag) {
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
for (int j = 0; j < n2; j++)
|
||||
for (int k = 0; k < n3; k++)
|
||||
tstore[i][j][k] = 0.0;
|
||||
}
|
||||
maxexchange = nvalues;
|
||||
}
|
||||
}
|
||||
@ -124,6 +146,7 @@ FixStore::~FixStore()
|
||||
|
||||
memory->destroy(vstore);
|
||||
memory->destroy(astore);
|
||||
memory->destroy(tstore);
|
||||
memory->destroy(rbuf);
|
||||
}
|
||||
|
||||
@ -141,7 +164,7 @@ int FixStore::setmask()
|
||||
caller will do subsequent initialization
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixStore::reset_global(int nrow_caller, int ncol_caller)
|
||||
void FixStore::reset_global(int n1_caller, int n2_caller)
|
||||
{
|
||||
memory->destroy(vstore);
|
||||
memory->destroy(astore);
|
||||
@ -149,29 +172,31 @@ void FixStore::reset_global(int nrow_caller, int ncol_caller)
|
||||
vstore = nullptr;
|
||||
astore = nullptr;
|
||||
|
||||
vecflag = 0;
|
||||
if (ncol_caller == 1) vecflag = 1;
|
||||
nrow = nrow_caller;
|
||||
ncol = ncol_caller;
|
||||
if (vecflag) memory->create(vstore,nrow,"fix/store:vstore");
|
||||
else memory->create(astore,nrow,ncol,"fix/store:astore");
|
||||
memory->create(rbuf,nrow*ncol+2,"fix/store:rbuf");
|
||||
vecflag = arrayflag = 0;
|
||||
if (n2_caller == 1) vecflag = 1;
|
||||
else arrayflag = 1;
|
||||
|
||||
n1 = n1_caller;
|
||||
n2 = n2_caller;
|
||||
if (vecflag) memory->create(vstore,n1,"fix/store:vstore");
|
||||
else if (arrayflag) memory->create(astore,n1,n2,"fix/store:astore");
|
||||
memory->create(rbuf,n1*n2+2,"fix/store:rbuf");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
write global array to restart file
|
||||
write global vector/array to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void FixStore::write_restart(FILE *fp)
|
||||
{
|
||||
// fill rbuf with size and vec/array values
|
||||
// fill rbuf with size and vector/array values
|
||||
|
||||
rbuf[0] = nrow;
|
||||
rbuf[1] = ncol;
|
||||
if (vecflag) memcpy(&rbuf[2],vstore,sizeof(double)*nrow);
|
||||
else memcpy(&rbuf[2],&astore[0][0],sizeof(double)*nrow*ncol);
|
||||
rbuf[0] = n1;
|
||||
rbuf[1] = n2;
|
||||
if (vecflag) memcpy(&rbuf[2],vstore,n1*sizeof(double));
|
||||
else if (arrayflag) memcpy(&rbuf[2],&astore[0][0],n1*n2*sizeof(double));
|
||||
|
||||
int n = nrow*ncol + 2;
|
||||
int n = n1*n2 + 2;
|
||||
if (comm->me == 0) {
|
||||
int size = n * sizeof(double);
|
||||
fwrite(&size,sizeof(int),1,fp);
|
||||
@ -188,33 +213,34 @@ void FixStore::restart(char *buf)
|
||||
// first 2 values in buf are vec/array sizes
|
||||
|
||||
double *dbuf = (double *) buf;
|
||||
int nrow_restart = dbuf[0];
|
||||
int ncol_restart = dbuf[1];
|
||||
int n1_restart = dbuf[0];
|
||||
int n2_restart = dbuf[1];
|
||||
|
||||
// if size of vec/array has changed,
|
||||
// means the restart file is setting size of vec or array and doing init
|
||||
// because caller did not know size at time this fix was instantiated
|
||||
// reallocate vstore or astore accordingly
|
||||
|
||||
if (nrow != nrow_restart || ncol != ncol_restart) {
|
||||
if (n1 != n1_restart || n2 != n2_restart) {
|
||||
memory->destroy(vstore);
|
||||
memory->destroy(astore);
|
||||
memory->destroy(rbuf);
|
||||
vstore = nullptr;
|
||||
astore = nullptr;
|
||||
|
||||
vecflag = 0;
|
||||
if (ncol_restart == 1) vecflag = 1;
|
||||
nrow = nrow_restart;
|
||||
ncol = ncol_restart;
|
||||
if (vecflag) memory->create(vstore,nrow,"fix/store:vstore");
|
||||
else memory->create(astore,nrow,ncol,"fix/store:astore");
|
||||
memory->create(rbuf,nrow*ncol+2,"fix/store:rbuf");
|
||||
vecflag = arrayflag = 0;
|
||||
if (n2_restart == 1) vecflag = 1;
|
||||
else arrayflag = 1;
|
||||
n1 = n1_restart;
|
||||
n2 = n2_restart;
|
||||
if (vecflag) memory->create(vstore,n1,"fix/store:vstore");
|
||||
else if (arrayflag) memory->create(astore,n1,n2,"fix/store:astore");
|
||||
memory->create(rbuf,n1*n2+2,"fix/store:rbuf");
|
||||
}
|
||||
|
||||
int n = nrow*ncol;
|
||||
int n = n1*n2;
|
||||
if (vecflag) memcpy(vstore,&dbuf[2],n*sizeof(double));
|
||||
else memcpy(&astore[0][0],&dbuf[2],n*sizeof(double));
|
||||
else if (arrayflag) memcpy(&astore[0][0],&dbuf[2],n*sizeof(double));
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -224,7 +250,8 @@ void FixStore::restart(char *buf)
|
||||
void FixStore::grow_arrays(int nmax)
|
||||
{
|
||||
if (vecflag) memory->grow(vstore,nmax,"store:vstore");
|
||||
else memory->grow(astore,nmax,nvalues,"store:astore");
|
||||
else if (arrayflag) memory->grow(astore,nmax,n2,"store:astore");
|
||||
else if (tensorflag) memory->grow(tstore,nmax,n2,n3,"store:tstore");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -235,10 +262,14 @@ void FixStore::copy_arrays(int i, int j, int /*delflag*/)
|
||||
{
|
||||
if (disable) return;
|
||||
|
||||
if (vecflag) vstore[j] = vstore[i];
|
||||
else
|
||||
if (vecflag) {
|
||||
vstore[j] = vstore[i];
|
||||
} else if (arrayflag) {
|
||||
for (int m = 0; m < nvalues; m++)
|
||||
astore[j][m] = astore[i][m];
|
||||
} else if (tensorflag) {
|
||||
memcpy(&tstore[j][0][0],&tstore[i][0][0],nbytes);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -249,10 +280,15 @@ int FixStore::pack_exchange(int i, double *buf)
|
||||
{
|
||||
if (disable) return 0;
|
||||
|
||||
if (vecflag) buf[0] = vstore[i];
|
||||
else
|
||||
if (vecflag) {
|
||||
buf[0] = vstore[i];
|
||||
} else if (arrayflag) {
|
||||
for (int m = 0; m < nvalues; m++)
|
||||
buf[m] = astore[i][m];
|
||||
} else if (tensorflag) {
|
||||
memcpy(buf,&tstore[i][0][0],nbytes);
|
||||
}
|
||||
|
||||
return nvalues;
|
||||
}
|
||||
|
||||
@ -264,10 +300,15 @@ int FixStore::unpack_exchange(int nlocal, double *buf)
|
||||
{
|
||||
if (disable) return 0;
|
||||
|
||||
if (vecflag) vstore[nlocal] = buf[0];
|
||||
else
|
||||
if (vecflag) {
|
||||
vstore[nlocal] = buf[0];
|
||||
} else if (arrayflag) {
|
||||
for (int m = 0; m < nvalues; m++)
|
||||
astore[nlocal][m] = buf[m];
|
||||
} else if (tensorflag) {
|
||||
memcpy(&tstore[nlocal][0][0],buf,nbytes);
|
||||
}
|
||||
|
||||
return nvalues;
|
||||
}
|
||||
|
||||
@ -284,10 +325,16 @@ int FixStore::pack_restart(int i, double *buf)
|
||||
|
||||
// pack buf[0] this way because other fixes unpack it
|
||||
buf[0] = nvalues+1;
|
||||
if (vecflag) buf[1] = vstore[i];
|
||||
else
|
||||
|
||||
if (vecflag) {
|
||||
buf[1] = vstore[i];
|
||||
} else if (arrayflag) {
|
||||
for (int m = 0; m < nvalues; m++)
|
||||
buf[m+1] = astore[i][m];
|
||||
} else if (tensorflag) {
|
||||
memcpy(&buf[1],&tstore[i][0][0],nbytes);
|
||||
}
|
||||
|
||||
return nvalues+1;
|
||||
}
|
||||
|
||||
@ -308,10 +355,14 @@ void FixStore::unpack_restart(int nlocal, int nth)
|
||||
for (int i = 0; i < nth; i++) m += static_cast<int> (extra[nlocal][m]);
|
||||
m++;
|
||||
|
||||
if (vecflag) vstore[nlocal] = extra[nlocal][m];
|
||||
else
|
||||
if (vecflag) {
|
||||
vstore[nlocal] = extra[nlocal][m];
|
||||
} else if (arrayflag) {
|
||||
for (int i = 0; i < nvalues; i++)
|
||||
astore[nlocal][i] = extra[nlocal][m++];
|
||||
} else if (tensorflag) {
|
||||
memcpy(&tstore[nlocal][0][0],&extra[nlocal][m],nbytes);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -335,13 +386,13 @@ int FixStore::size_restart(int /*nlocal*/)
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
memory usage of local atom-based array
|
||||
memory usage of global or peratom atom-based array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double FixStore::memory_usage()
|
||||
{
|
||||
double bytes = 0.0;
|
||||
if (flavor == GLOBAL) bytes += (double)nrow*ncol * sizeof(double);
|
||||
if (flavor == PERATOM) bytes += (double)atom->nmax*nvalues * sizeof(double);
|
||||
if (flavor == GLOBAL) bytes += n1*n2 * sizeof(double);
|
||||
if (flavor == PERATOM) bytes += atom->nmax*n2*n3 * sizeof(double);
|
||||
return bytes;
|
||||
}
|
||||
|
||||
@ -26,10 +26,10 @@ namespace LAMMPS_NS {
|
||||
|
||||
class FixStore : public Fix {
|
||||
public:
|
||||
int nrow, ncol; // size of global data array
|
||||
int nvalues; // number of per-atom values
|
||||
int nrow,ncol; // copy of n1,n2 for GLOBAL array for classes to access
|
||||
double *vstore; // vector storage for GLOBAL or PERATOM
|
||||
double **astore; // array storage for GLOBAL or PERATOM
|
||||
double ***tstore; // tensor (3d array) storage for PERATOM
|
||||
int disable; // 1 if operations (except grow) are currently disabled
|
||||
|
||||
FixStore(class LAMMPS *, int, char **);
|
||||
@ -52,10 +52,16 @@ class FixStore : public Fix {
|
||||
double memory_usage();
|
||||
|
||||
private:
|
||||
int flavor; // GLOBAL or PERATOM
|
||||
int vecflag; // 1 if ncol=1 or nvalues=1
|
||||
int flavor; // GLOBAL or PERATOM
|
||||
int vecflag; // 1 if ncol=1 or nvalues=1
|
||||
int arrayflag; // 1 if a 2d array (vector per atom)
|
||||
int tensorflag; // 1 if a 3d array (array per atom)
|
||||
|
||||
double *rbuf; // restart buffer for GLOBAL vec/array
|
||||
int n1,n2,n3; // size of 3d dims of data struct
|
||||
int nvalues; // number of per-atom values
|
||||
int nbytes; // number of per-atom bytes
|
||||
|
||||
double *rbuf; // restart buffer for GLOBAL vec/array/tensor
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
@ -47,6 +47,7 @@ Force::Force(LAMMPS *lmp) : Pointers(lmp)
|
||||
special_lj[1] = special_lj[2] = special_lj[3] = 0.0;
|
||||
special_coul[1] = special_coul[2] = special_coul[3] = 0.0;
|
||||
special_angle = special_dihedral = 0;
|
||||
special_onefive = 0;
|
||||
special_extra = 0;
|
||||
|
||||
dielectric = 1.0;
|
||||
@ -755,6 +756,7 @@ void Force::set_special(int narg, char **arg)
|
||||
special_lj[1] = special_lj[2] = special_lj[3] = 0.0;
|
||||
special_coul[1] = special_coul[2] = special_coul[3] = 0.0;
|
||||
special_angle = special_dihedral = 0;
|
||||
special_onefive = 0;
|
||||
|
||||
int iarg = 0;
|
||||
while (iarg < narg) {
|
||||
@ -824,6 +826,15 @@ void Force::set_special(int narg, char **arg)
|
||||
else if (strcmp(arg[iarg+1],"yes") == 0) special_dihedral = 1;
|
||||
else error->all(FLERR,"Illegal special_bonds command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"one/five") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR,"Illegal special_bonds command");
|
||||
if (strcmp(arg[iarg+1],"no") == 0) special_onefive = 0;
|
||||
else if (strcmp(arg[iarg+1],"yes") == 0) special_onefive = 1;
|
||||
else error->all(FLERR,"Illegal special_bonds command");
|
||||
if (special_onefive && atom->nspecial15_flag == 0)
|
||||
error->all(FLERR,"Cannot set special_bonds one/five if "
|
||||
"atom style does not support it");
|
||||
iarg += 2;
|
||||
} else error->all(FLERR,"Illegal special_bonds command");
|
||||
}
|
||||
|
||||
|
||||
@ -115,6 +115,7 @@ class Force : protected Pointers {
|
||||
int special_dihedral; // 0 if defined dihedrals are ignored
|
||||
// 1 if only weight 1,4 atoms if in a dihedral
|
||||
int special_extra; // extra space for added bonds
|
||||
int special_onefive; // 0 if 1-5 neighbors are not stored, 1 if yes
|
||||
|
||||
Force(class LAMMPS *);
|
||||
~Force();
|
||||
|
||||
@ -1815,6 +1815,7 @@ void Input::special_bonds()
|
||||
double lj3 = force->special_lj[3];
|
||||
double coul2 = force->special_coul[2];
|
||||
double coul3 = force->special_coul[3];
|
||||
int onefive = force->special_onefive;
|
||||
int angle = force->special_angle;
|
||||
int dihedral = force->special_dihedral;
|
||||
|
||||
@ -1825,6 +1826,7 @@ void Input::special_bonds()
|
||||
if (domain->box_exist && atom->molecular == Atom::MOLECULAR) {
|
||||
if (lj2 != force->special_lj[2] || lj3 != force->special_lj[3] ||
|
||||
coul2 != force->special_coul[2] || coul3 != force->special_coul[3] ||
|
||||
onefive != force->special_onefive ||
|
||||
angle != force->special_angle ||
|
||||
dihedral != force->special_dihedral) {
|
||||
Special special(lmp);
|
||||
|
||||
66
src/memory.h
66
src/memory.h
@ -361,10 +361,10 @@ class Memory : protected Pointers {
|
||||
array = nullptr;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
create a 3d array with
|
||||
1st index from n1lo to n1hi inclusive,
|
||||
2nd index from n2lo to n2hi inclusive,
|
||||
/* ----------------------------------------------------------------------
|
||||
create a 3d array with all 3 indices offset
|
||||
1st index from n1lo to n1hi inclusive
|
||||
2nd index from n2lo to n2hi inclusive
|
||||
3rd index from n3lo to n3hi inclusive
|
||||
cannot grow it
|
||||
------------------------------------------------------------------------- */
|
||||
@ -512,8 +512,8 @@ class Memory : protected Pointers {
|
||||
array = nullptr;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
create a 4d array with indices
|
||||
/* ----------------------------------------------------------------------
|
||||
create a 4d array with indices 2,3,4 offset
|
||||
2nd index from n2lo to n2hi inclusive
|
||||
3rd index from n3lo to n3hi inclusive
|
||||
4th index from n4lo to n4hi inclusive
|
||||
@ -545,8 +545,8 @@ class Memory : protected Pointers {
|
||||
return nullptr;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
free a 4d array with indices 2,3, and 4 offset
|
||||
/* ----------------------------------------------------------------------
|
||||
free a 4d array with indices 2,3,4 offset
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
template <typename TYPE>
|
||||
@ -560,7 +560,55 @@ class Memory : protected Pointers {
|
||||
array = nullptr;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
/* ----------------------------------------------------------------------
|
||||
create a 4d array with indices 1,2,3 offset
|
||||
1st index from n1lo to n2hi inclusive
|
||||
2nd index from n3lo to n3hi inclusive
|
||||
3rd index from n4lo to n4hi inclusive
|
||||
cannot grow it
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
template <typename TYPE>
|
||||
TYPE ****create4d_offset_last(TYPE ****&array, int n1lo, int n1hi,
|
||||
int n2lo, int n2hi, int n3lo, int n3hi, int n4,
|
||||
const char *name)
|
||||
{
|
||||
int n1 = n1hi - n1lo + 1;
|
||||
int n2 = n2hi - n2lo + 1;
|
||||
int n3 = n3hi - n3lo + 1;
|
||||
create(array,n1,n2,n3,n4,name);
|
||||
|
||||
bigint m = ((bigint) n1) * n2;
|
||||
for (bigint i = 0; i < m; i++) array[0][i] -= n3lo;
|
||||
for (int i = 0; i < n1; i++) array[i] -= n2lo;
|
||||
array -= n1lo;
|
||||
return array;
|
||||
}
|
||||
|
||||
template <typename TYPE>
|
||||
TYPE ****create4d_offset_last(TYPE *****& /*array*/, int /*n1lo*/, int /*n1hi*/,
|
||||
int /*n2lo*/, int /*n2hi*/,
|
||||
int /*n3lo*/, int /*n3hi*/, int /*n4*/,
|
||||
const char *name)
|
||||
{fail(name); return nullptr;}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
free a 4d array with indices 1,2,3 offset
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
template <typename TYPE>
|
||||
void destroy4d_offset_last(TYPE ****&array,
|
||||
int n1_offset, int n2_offset, int n3_offset)
|
||||
{
|
||||
if (array == nullptr) return;
|
||||
sfree(&array[n1_offset][n2_offset][n3_offset][0]);
|
||||
sfree(&array[n1_offset][n2_offset][n3_offset]);
|
||||
sfree(&array[n1_offset][n2_offset]);
|
||||
sfree(&array[n1_offset]);
|
||||
array = nullptr;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
create a 5d array
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
|
||||
@ -493,8 +493,8 @@ void Neighbor::init()
|
||||
// flag = 0 if both LJ/Coulomb special values are 0.0
|
||||
// flag = 1 if both LJ/Coulomb special values are 1.0
|
||||
// flag = 2 otherwise or if KSpace solver is enabled
|
||||
// pairwise portion of KSpace solver uses all 1-2,1-3,1-4 neighbors
|
||||
// or selected Coulomb-approixmation pair styles require it
|
||||
// b/c pairwise portion of KSpace solver uses all 1-2,1-3,1-4 neighbors
|
||||
// some Coulomb-approximation pair styles also require it (below)
|
||||
|
||||
if (force->special_lj[1] == 0.0 && force->special_coul[1] == 0.0)
|
||||
special_flag[1] = 0;
|
||||
@ -514,10 +514,10 @@ void Neighbor::init()
|
||||
special_flag[3] = 1;
|
||||
else special_flag[3] = 2;
|
||||
|
||||
// We cannot remove special neighbors with kspace or kspace-like pair styles
|
||||
// as the exclusion needs to remove the full coulomb and not the damped interaction.
|
||||
// Special treatment is required for hybrid pair styles since Force::pair_match()
|
||||
// will only return a non-null pointer if there is only one substyle of the kind.
|
||||
// cannot remove special neighbors with kspace or kspace-like pair styles
|
||||
// b/c exclusion needs to remove the full coulomb and not the damped interaction
|
||||
// special treatment required for hybrid pair styles since Force::pair_match()
|
||||
// will only return a non-NULL pointer if there is only one substyle of the kind
|
||||
|
||||
if (force->kspace) {
|
||||
special_flag[1] = special_flag[2] = special_flag[3] = 2;
|
||||
@ -526,7 +526,8 @@ void Neighbor::init()
|
||||
if (ph) {
|
||||
int flag=0;
|
||||
for (int isub=0; isub < ph->nstyles; ++isub) {
|
||||
if (force->pair_match("coul/wolf",0,isub)
|
||||
if (force->pair_match("amoeba",0,isub)
|
||||
|| force->pair_match("coul/wolf",0,isub)
|
||||
|| force->pair_match("coul/dsf",0,isub)
|
||||
|| force->pair_match("coul/exclude",0)
|
||||
|| force->pair_match("thole",0,isub))
|
||||
@ -535,7 +536,8 @@ void Neighbor::init()
|
||||
if (flag)
|
||||
special_flag[1] = special_flag[2] = special_flag[3] = 2;
|
||||
} else {
|
||||
if (force->pair_match("coul/wolf",0)
|
||||
if (force->pair_match("amoeba",0)
|
||||
|| force->pair_match("coul/wolf",0)
|
||||
|| force->pair_match("coul/dsf",0)
|
||||
|| force->pair_match("coul/exclude",0)
|
||||
|| force->pair_match("thole",0))
|
||||
|
||||
@ -190,6 +190,12 @@ class Pair : protected Pointers {
|
||||
virtual void unpack_forward_comm(int, int, double *) {}
|
||||
virtual int pack_reverse_comm(int, int, double *) { return 0; }
|
||||
virtual void unpack_reverse_comm(int, int *, double *) {}
|
||||
|
||||
virtual void pack_forward_grid(int, void *, int, int *) {}
|
||||
virtual void unpack_forward_grid(int, void *, int, int *) {}
|
||||
virtual void pack_reverse_grid(int, void *, int, int *) {}
|
||||
virtual void unpack_reverse_grid(int, void *, int, int *) {}
|
||||
|
||||
virtual double memory_usage();
|
||||
|
||||
void set_copymode(int value) { copymode = value; }
|
||||
|
||||
228
src/special.cpp
228
src/special.cpp
@ -35,7 +35,7 @@ Special::Special(LAMMPS *lmp) : Pointers(lmp)
|
||||
MPI_Comm_rank(world,&me);
|
||||
MPI_Comm_size(world,&nprocs);
|
||||
|
||||
onetwo = onethree = onefour = nullptr;
|
||||
onetwo = onethree = onefour = onefive = NULL;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
@ -45,12 +45,13 @@ Special::~Special()
|
||||
memory->destroy(onetwo);
|
||||
memory->destroy(onethree);
|
||||
memory->destroy(onefour);
|
||||
memory->destroy(onefive);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
create 1-2, 1-3, 1-4 lists of topology neighbors
|
||||
store in onetwo, onethree, onefour for each atom
|
||||
store 3 counters in nspecial[i]
|
||||
create 1-2, 1-3, 1-4 lists of topology neighbors, 1-5 list is optional
|
||||
store in onetwo, onethree, onefour, onefive for each atom
|
||||
store first 3 counters in nspecial[i], and 4th in nspecial15[i]
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Special::build()
|
||||
@ -69,9 +70,14 @@ void Special::build()
|
||||
utils::logmesg(lmp,mesg);
|
||||
}
|
||||
|
||||
// set onefive_flag if special_bonds command set it
|
||||
|
||||
onefive_flag = force->special_onefive;
|
||||
|
||||
// initialize nspecial counters to 0
|
||||
|
||||
int **nspecial = atom->nspecial;
|
||||
int *nspecial15 = atom->nspecial15;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
@ -80,6 +86,10 @@ void Special::build()
|
||||
nspecial[i][2] = 0;
|
||||
}
|
||||
|
||||
if (onefive_flag) {
|
||||
for (int i = 0; i < nlocal; i++) nspecial15[i] = 0;
|
||||
}
|
||||
|
||||
// setup atomIDs and procowner vectors in rendezvous decomposition
|
||||
|
||||
atom_owners();
|
||||
@ -96,8 +106,10 @@ void Special::build()
|
||||
utils::logmesg(lmp,"{:>6} = max # of 1-2 neighbors\n",maxall);
|
||||
|
||||
// done if special_bond weights for 1-3, 1-4 are set to 1.0
|
||||
// onefive_flag must also be off, else 1-4 is needed to create 1-5
|
||||
|
||||
if (force->special_lj[2] == 1.0 && force->special_coul[2] == 1.0 &&
|
||||
if (!onefive_flag &&
|
||||
force->special_lj[2] == 1.0 && force->special_coul[2] == 1.0 &&
|
||||
force->special_lj[3] == 1.0 && force->special_coul[3] == 1.0) {
|
||||
dedup();
|
||||
combine();
|
||||
@ -119,8 +131,10 @@ void Special::build()
|
||||
utils::logmesg(lmp,"{:>6} = max # of 1-3 neighbors\n",maxall);
|
||||
|
||||
// done if special_bond weights for 1-4 are set to 1.0
|
||||
// onefive_flag must also be off, else 1-4 is needed to create 1-5
|
||||
|
||||
if (force->special_lj[3] == 1.0 && force->special_coul[3] == 1.0) {
|
||||
if (!onefive_flag &&
|
||||
force->special_lj[3] == 1.0 && force->special_coul[3] == 1.0) {
|
||||
dedup();
|
||||
if (force->special_angle) angle_trim();
|
||||
combine();
|
||||
@ -141,7 +155,17 @@ void Special::build()
|
||||
if (me == 0)
|
||||
utils::logmesg(lmp,"{:>6} = max # of 1-4 neighbors\n",maxall);
|
||||
|
||||
// finish processing the onetwo, onethree, onefour lists
|
||||
// optionally store 1-5 neighbors
|
||||
// tally nspecial15[i] = # of 1-5 neighbors of atom i
|
||||
// create onefive[i] = list of 1-5 neighbors for atom i
|
||||
|
||||
if (onefive_flag) {
|
||||
onefive_build();
|
||||
if (me == 0)
|
||||
utils::logmesg(lmp,fmt::format("{:>6} = max # of 1-5 neighbors\n",maxall));
|
||||
}
|
||||
|
||||
// finish processing the onetwo, onethree, onefour, onefive lists
|
||||
|
||||
dedup();
|
||||
if (force->special_angle) angle_trim();
|
||||
@ -150,7 +174,6 @@ void Special::build()
|
||||
fix_alteration();
|
||||
memory->destroy(procowner);
|
||||
memory->destroy(atomIDs);
|
||||
|
||||
timer_output(time1);
|
||||
}
|
||||
|
||||
@ -450,7 +473,7 @@ void Special::onefour_build()
|
||||
// setup input buf to rendezvous comm
|
||||
// datums = pairs of onethree and onetwo partners where onethree is unknown
|
||||
// these pairs are onefour neighbors
|
||||
// datum = onetwo ID, onetwo ID
|
||||
// datum = onethree ID, onetwo ID
|
||||
// owning proc for each datum = onethree ID % nprocs
|
||||
|
||||
nsend = 0;
|
||||
@ -521,8 +544,113 @@ void Special::onefour_build()
|
||||
memory->sfree(outbuf);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
optional onefive build
|
||||
uses rendezvous comm
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Special::onefive_build()
|
||||
{
|
||||
int i,j,k,m,proc;
|
||||
|
||||
int **nspecial = atom->nspecial;
|
||||
int *nspecial15 = atom->nspecial15;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
// nsend = # of my datums to send
|
||||
|
||||
int nsend = 0;
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
for (j = 0; j < nspecial[i][2]; j++) {
|
||||
m = atom->map(onefour[i][j]);
|
||||
if (m < 0 || m >= nlocal) nsend += nspecial[i][0];
|
||||
}
|
||||
}
|
||||
|
||||
int *proclist;
|
||||
memory->create(proclist,nsend,"special:proclist");
|
||||
PairRvous *inbuf = (PairRvous *)
|
||||
memory->smalloc((bigint) nsend*sizeof(PairRvous),"special:inbuf");
|
||||
|
||||
// setup input buf to rendezvous comm
|
||||
// datums = pairs of onefour and onetwo partners where onefour is unknown
|
||||
// these pairs are onefive neighbors
|
||||
// datum = onefour ID, onetwo ID
|
||||
// owning proc for each datum = onefour ID % nprocs
|
||||
|
||||
nsend = 0;
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
for (j = 0; j < nspecial[i][2]; j++) {
|
||||
m = atom->map(onefour[i][j]);
|
||||
if (m >= 0 && m < nlocal) continue;
|
||||
proc = onefour[i][j] % nprocs;
|
||||
for (k = 0; k < nspecial[i][0]; k++) {
|
||||
proclist[nsend] = proc;
|
||||
inbuf[nsend].atomID = onefour[i][j];
|
||||
inbuf[nsend].partnerID = onetwo[i][k];
|
||||
nsend++;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
// perform rendezvous operation
|
||||
|
||||
char *buf;
|
||||
int nreturn = comm->rendezvous(RVOUS,nsend,(char *) inbuf,sizeof(PairRvous),
|
||||
0,proclist,
|
||||
rendezvous_pairs,0,buf,sizeof(PairRvous),
|
||||
(void *) this);
|
||||
PairRvous *outbuf = (PairRvous *) buf;
|
||||
|
||||
memory->destroy(proclist);
|
||||
memory->sfree(inbuf);
|
||||
|
||||
// set nspecial15 and onefive for all owned atoms
|
||||
// based on owned info plus rendezvous output info
|
||||
// output datums = pairs of atoms that are 1-5 neighbors
|
||||
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
for (j = 0; j < nspecial[i][2]; j++) {
|
||||
m = atom->map(onefour[i][j]);
|
||||
if (m >= 0 && m < nlocal) nspecial15[m] += nspecial[i][0];
|
||||
}
|
||||
}
|
||||
|
||||
for (m = 0; m < nreturn; m++) {
|
||||
i = atom->map(outbuf[m].atomID);
|
||||
nspecial15[i]++;
|
||||
}
|
||||
|
||||
int max = 0;
|
||||
for (i = 0; i < nlocal; i++)
|
||||
max = MAX(max,nspecial15[i]);
|
||||
|
||||
MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
|
||||
memory->create(onefive,nlocal,maxall,"special:onefive");
|
||||
|
||||
for (i = 0; i < nlocal; i++) nspecial15[i] = 0;
|
||||
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
for (j = 0; j < nspecial[i][2]; j++) {
|
||||
m = atom->map(onefour[i][j]);
|
||||
if (m < 0 || m >= nlocal) continue;
|
||||
for (k = 0; k < nspecial[i][0]; k++) {
|
||||
onefive[m][nspecial15[m]++] = onetwo[i][k];
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
for (m = 0; m < nreturn; m++) {
|
||||
i = atom->map(outbuf[m].atomID);
|
||||
onefive[i][nspecial15[i]++] = outbuf[m].partnerID;
|
||||
}
|
||||
|
||||
memory->sfree(outbuf);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
remove duplicates within each of onetwo, onethree, onefour individually
|
||||
also dedup onefive if enabled
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Special::dedup()
|
||||
@ -536,15 +664,18 @@ void Special::dedup()
|
||||
|
||||
// use map to cull duplicates
|
||||
// exclude original atom explicitly
|
||||
// adjust onetwo, onethree, onefour values to reflect removed duplicates
|
||||
// adjust onetwo, onethree, onefour, onefive values to remove duplicates
|
||||
// must unset map for each atom
|
||||
|
||||
int **nspecial = atom->nspecial;
|
||||
int *nspecial15 = atom->nspecial15;
|
||||
tagint *tag = atom->tag;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
int unique;
|
||||
|
||||
// dedup onetwo
|
||||
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
unique = 0;
|
||||
atom->map_one(tag[i],0);
|
||||
@ -560,6 +691,8 @@ void Special::dedup()
|
||||
for (j = 0; j < unique; j++) atom->map_one(onetwo[i][j],-1);
|
||||
}
|
||||
|
||||
// dedup onethree
|
||||
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
unique = 0;
|
||||
atom->map_one(tag[i],0);
|
||||
@ -575,6 +708,8 @@ void Special::dedup()
|
||||
for (j = 0; j < unique; j++) atom->map_one(onethree[i][j],-1);
|
||||
}
|
||||
|
||||
// dedup onefour
|
||||
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
unique = 0;
|
||||
atom->map_one(tag[i],0);
|
||||
@ -590,6 +725,25 @@ void Special::dedup()
|
||||
for (j = 0; j < unique; j++) atom->map_one(onefour[i][j],-1);
|
||||
}
|
||||
|
||||
// dedup onefive
|
||||
|
||||
if (onefive_flag) {
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
unique = 0;
|
||||
atom->map_one(tag[i],0);
|
||||
for (j = 0; j < nspecial15[i]; j++) {
|
||||
m = onefive[i][j];
|
||||
if (atom->map(m) < 0) {
|
||||
onefive[i][unique++] = m;
|
||||
atom->map_one(m,0);
|
||||
}
|
||||
}
|
||||
nspecial15[i] = unique;
|
||||
atom->map_one(tag[i],-1);
|
||||
for (j = 0; j < unique; j++) atom->map_one(onefive[i][j],-1);
|
||||
}
|
||||
}
|
||||
|
||||
// re-create map
|
||||
|
||||
atom->map_init(0);
|
||||
@ -601,6 +755,7 @@ void Special::dedup()
|
||||
concatenate onetwo, onethree, onefour into master atom->special list
|
||||
remove duplicates between 3 lists, leave dup in first list it appears in
|
||||
convert nspecial[0], nspecial[1], nspecial[2] into cumulative counters
|
||||
if 1-5 is enabled, reset nspecial15/special15 to remove dups with 1-2,1-3,1-4
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void Special::combine()
|
||||
@ -612,6 +767,7 @@ void Special::combine()
|
||||
MPI_Comm_rank(world,&me);
|
||||
|
||||
int **nspecial = atom->nspecial;
|
||||
int *nspecial15 = atom->nspecial15;
|
||||
tagint *tag = atom->tag;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
@ -624,12 +780,14 @@ void Special::combine()
|
||||
atom->map_clear();
|
||||
|
||||
// unique = # of unique nspecial neighbors of one atom
|
||||
// unique15 = ditto for 1-5 interactions
|
||||
// cull duplicates using map to check for them
|
||||
// exclude original atom explicitly
|
||||
// must unset map for each atom
|
||||
|
||||
int unique;
|
||||
int unique,unique15;
|
||||
int maxspecial = 0;
|
||||
int maxspecial15 = 0;
|
||||
|
||||
for (i = 0; i < nlocal; i++) {
|
||||
unique = 0;
|
||||
@ -659,15 +817,30 @@ void Special::combine()
|
||||
|
||||
maxspecial = MAX(maxspecial,unique);
|
||||
|
||||
if (onefive_flag) {
|
||||
unique15 = 0;
|
||||
for (j = 0; j < nspecial15[i]; j++) {
|
||||
m = onefive[i][j];
|
||||
if (atom->map(m) < 0) {
|
||||
unique15++;
|
||||
atom->map_one(m,0);
|
||||
}
|
||||
}
|
||||
maxspecial15 = MAX(maxspecial15,unique15);
|
||||
}
|
||||
|
||||
atom->map_one(tag[i],-1);
|
||||
for (j = 0; j < nspecial[i][0]; j++) atom->map_one(onetwo[i][j],-1);
|
||||
for (j = 0; j < nspecial[i][1]; j++) atom->map_one(onethree[i][j],-1);
|
||||
for (j = 0; j < nspecial[i][2]; j++) atom->map_one(onefour[i][j],-1);
|
||||
if (onefive_flag)
|
||||
for (j = 0; j < nspecial15[i]; j++) atom->map_one(onefive[i][j],-1);
|
||||
}
|
||||
|
||||
// if atom->maxspecial has been updated before, make certain
|
||||
// we do not reset it to a smaller value. Since atom->maxspecial
|
||||
// is initialized to 1, this ensures that it is larger than zero.
|
||||
// if atom->maxspecial has been updated before,
|
||||
// make certain it is not reset to a smaller value
|
||||
// since atom->maxspecial is initialized to 1,
|
||||
// this ensures that it stays larger than zero
|
||||
|
||||
maxspecial = MAX(atom->maxspecial,maxspecial);
|
||||
|
||||
@ -702,12 +875,23 @@ void Special::combine()
|
||||
memory->create(atom->special,atom->nmax,atom->maxspecial,"atom:special");
|
||||
}
|
||||
|
||||
tagint **special = atom->special;
|
||||
// if 1-5 is enabled, similarly compute global maxspecial15 and reallocate
|
||||
|
||||
if (onefive_flag) {
|
||||
maxspecial15 = MAX(atom->maxspecial15,maxspecial15);
|
||||
MPI_Allreduce(&maxspecial15,&atom->maxspecial15,1,MPI_INT,MPI_MAX,world);
|
||||
memory->destroy(atom->special15);
|
||||
memory->create(atom->special15,atom->nmax,atom->maxspecial15,"atom:special15");
|
||||
}
|
||||
|
||||
// ----------------------------------------------------
|
||||
// fill special array with 1-2, 1-3, 1-4 neighs for each atom
|
||||
// optionally fill special15 array with 1-5 neighs
|
||||
// ----------------------------------------------------
|
||||
|
||||
tagint **special = atom->special;
|
||||
tagint **special15 = atom->special15;
|
||||
|
||||
// again use map to cull duplicates
|
||||
// exclude original atom explicitly
|
||||
// adjust nspecial[i] values to reflect removed duplicates
|
||||
@ -744,8 +928,22 @@ void Special::combine()
|
||||
}
|
||||
nspecial[i][2] = unique;
|
||||
|
||||
if (onefive_flag) {
|
||||
unique15 = 0;
|
||||
for (j = 0; j < nspecial15[i]; j++) {
|
||||
m = onefive[i][j];
|
||||
if (atom->map(m) < 0) {
|
||||
special15[i][unique15++] = m;
|
||||
atom->map_one(m,0);
|
||||
}
|
||||
}
|
||||
nspecial15[i] = unique15;
|
||||
}
|
||||
|
||||
atom->map_one(tag[i],-1);
|
||||
for (j = 0; j < nspecial[i][2]; j++) atom->map_one(special[i][j],-1);
|
||||
if (onefive_flag)
|
||||
for (j = 0; j < nspecial15[i]; j++) atom->map_one(special15[i][j],-1);
|
||||
}
|
||||
|
||||
// re-create map
|
||||
|
||||
@ -27,7 +27,8 @@ class Special : protected Pointers {
|
||||
private:
|
||||
int me, nprocs;
|
||||
int maxall;
|
||||
tagint **onetwo, **onethree, **onefour;
|
||||
int onefive_flag;
|
||||
tagint **onetwo,**onethree,**onefour,**onefive;
|
||||
|
||||
// data used by rendezvous callback methods
|
||||
|
||||
@ -51,6 +52,7 @@ class Special : protected Pointers {
|
||||
void onetwo_build_newton_off();
|
||||
void onethree_build();
|
||||
void onefour_build();
|
||||
void onefive_build();
|
||||
|
||||
void dedup();
|
||||
void angle_trim();
|
||||
|
||||
@ -48,6 +48,7 @@ singularity Singularity container descriptions suitable for LAMMPS de
|
||||
smd convert Smooth Mach Dynamics triangles to VTK
|
||||
spin perform a cubic polynomial interpolation of a GNEB MEP
|
||||
swig Interface file and demo scripts for SWIG wrappers for the LAMMPS C library interface
|
||||
tinker2lmp.py convert Tinker input files to LAMMPS input files
|
||||
valgrind suppression files for use with valgrind's memcheck tool
|
||||
vim add-ons to VIM editor for editing LAMMPS input scripts
|
||||
xmgrace a collection of scripts to generate xmgrace plots
|
||||
|
||||
913
tools/tinker2lmp.py
Normal file
913
tools/tinker2lmp.py
Normal file
@ -0,0 +1,913 @@
|
||||
#!/bin/env python
|
||||
|
||||
# convert a Tinker XYZ file + PRM file to a LAMMPS data file
|
||||
|
||||
# Syntax: python tinker2lmp.py -switch args -switch args ...
|
||||
# -xyz file = Tinker XYZ file name (required)
|
||||
# -amoeba file = AMOEBA PRM force field file name (required, or hippo)
|
||||
# -hippo file = HIPPO PRM force field file name (required, or amoeba)
|
||||
# -data file = LAMMPS data file to output (required)
|
||||
# -nopbc = non-periodic system (default)
|
||||
# -pbc xhi yhi zhi = periodic system from 0 to hi in each dimension (optional)
|
||||
|
||||
import sys,os,math
|
||||
path = os.environ["LAMMPS_PYTHON_TOOLS"]
|
||||
sys.path.append(path)
|
||||
from data import data
|
||||
|
||||
BIG = 1.0e20
|
||||
DELTA = 0.001 # delta on LAMMPS shrink-wrap box size, in Angstroms
|
||||
|
||||
# ----------------------
|
||||
# methods and classes
|
||||
# ----------------------
|
||||
|
||||
# print an error message and exit
|
||||
|
||||
def error(txt=""):
|
||||
if not txt:
|
||||
print "Syntax: tinker2lmp.py -switch args ..."
|
||||
print " -xyz file"
|
||||
print " -amoeba file"
|
||||
print " -hippo file"
|
||||
print " -data file"
|
||||
print " -nopbc"
|
||||
print " -pbc xhi yhi zhi"
|
||||
else: print "ERROR:",txt
|
||||
sys.exit()
|
||||
|
||||
# read and store values from a Tinker xyz file
|
||||
|
||||
class XYZfile:
|
||||
def __init__(self,file):
|
||||
lines = open(file,'r').readlines()
|
||||
natoms = int(lines[0].split()[0])
|
||||
id = []
|
||||
type = []
|
||||
x = []
|
||||
y = []
|
||||
z = []
|
||||
bonds = []
|
||||
|
||||
for line in lines[1:natoms+1]:
|
||||
words = line.split()
|
||||
id.append(int(words[0]))
|
||||
x.append(words[2])
|
||||
y.append(words[3])
|
||||
z.append(words[4])
|
||||
type.append(int(words[5]))
|
||||
blist = words[6:]
|
||||
blist = [int(one) for one in blist]
|
||||
bonds.append(blist)
|
||||
|
||||
self.natoms = natoms
|
||||
self.id = id
|
||||
self.type = type
|
||||
self.x = x
|
||||
self.y = y
|
||||
self.z = z
|
||||
self.bonds = bonds
|
||||
|
||||
# triplet of atoms in an angle = atom 1,2,3
|
||||
# atom2 is center atom
|
||||
# nbonds = number of atoms which atom2 is bonded to
|
||||
# hcount = # of H atoms which atom2 is bonded to, excluding atom1 and atom3
|
||||
|
||||
def angle_hbond_count(self,atom1,atom2,atom3,lmptype,lmpmass):
|
||||
bondlist = self.bonds[atom2-1]
|
||||
nbonds = len(bondlist)
|
||||
|
||||
hcount = 0
|
||||
for bondID in bondlist:
|
||||
if atom1 == bondID: continue
|
||||
if atom3 == bondID: continue
|
||||
massone = lmpmass[lmptype[bondID-1]-1]
|
||||
if int(massone+0.5) == 1: hcount += 1
|
||||
|
||||
return nbonds,hcount
|
||||
|
||||
# read and store select values from a Tinker force field PRM file
|
||||
# ntypes = # of Tinker types
|
||||
# per-type values: class and mass
|
||||
# scalar force field params in Force Field Definition section
|
||||
# bond, angle, dihedral coeffs indexed by Tinker classes
|
||||
|
||||
class PRMfile:
|
||||
def __init__(self,file):
|
||||
lines = open(file,'r').readlines()
|
||||
self.nlines = len(lines)
|
||||
self.lines = lines
|
||||
|
||||
self.force_field_definition()
|
||||
self.classes,self.masses = self.peratom()
|
||||
self.polgroup = self.polarize()
|
||||
self.bondparams = self.bonds()
|
||||
self.angleparams = self.angles()
|
||||
self.bondangleparams = self.bondangles()
|
||||
self.torsionparams = self.torsions()
|
||||
self.ntypes = len(self.masses)
|
||||
|
||||
def force_field_definition(self):
|
||||
iline = self.find_section("Force Field Definition")
|
||||
iline += 3
|
||||
while iline < self.nlines:
|
||||
words = self.lines[iline].split()
|
||||
if len(words):
|
||||
if words[0].startswith("###########"): break
|
||||
if words[0] == "bond-cubic": self.bond_cubic = float(words[1])
|
||||
elif words[0] == "bond-quartic": self.bond_quartic = float(words[1])
|
||||
elif words[0] == "angle-cubic": self.angle_cubic = float(words[1])
|
||||
elif words[0] == "angle-quartic": self.angle_quartic = float(words[1])
|
||||
elif words[0] == "angle-pentic": self.angle_pentic = float(words[1])
|
||||
elif words[0] == "angle-sextic": self.angle_sextic = float(words[1])
|
||||
iline += 1
|
||||
|
||||
def peratom(self):
|
||||
classes = []
|
||||
masses = []
|
||||
iline = self.find_section("Atom Type Definitions")
|
||||
if iline < 0: return classes,masses
|
||||
iline += 3
|
||||
while iline < self.nlines:
|
||||
words = self.lines[iline].split()
|
||||
if len(words):
|
||||
if words[0].startswith("###########"): break
|
||||
# NOTE: assumes atom entries are numbered consecutively
|
||||
if words[0] == "atom":
|
||||
classes.append(int(words[2]))
|
||||
masses.append(float(words[-2]))
|
||||
iline += 1
|
||||
return classes,masses
|
||||
|
||||
def polarize(self):
|
||||
polgroup = []
|
||||
iline = self.find_section("Dipole Polarizability Parameters")
|
||||
if iline < 0: return polgroup
|
||||
iline += 3
|
||||
while iline < self.nlines:
|
||||
words = self.lines[iline].split()
|
||||
if len(words):
|
||||
if words[0].startswith("###########"): break
|
||||
# trim off any end-of-line comments
|
||||
if "!!" in words: words = words[:words.index("!!")]
|
||||
# NOTE: assumes polarize entries are numbered consecutively
|
||||
if words[0] == "polarize":
|
||||
if amoeba: bondtypes = words[4:]
|
||||
if hippo: bondtypes = words[3:]
|
||||
bondtypes = [int(one) for one in bondtypes]
|
||||
polgroup.append(bondtypes)
|
||||
iline += 1
|
||||
return polgroup
|
||||
|
||||
# convert PRMfile params to LAMMPS bond_style class2 params
|
||||
|
||||
def bonds(self):
|
||||
params = []
|
||||
iline = self.find_section("Bond Stretching Parameters")
|
||||
if iline < 0: return params
|
||||
iline += 3
|
||||
while iline < self.nlines:
|
||||
words = self.lines[iline].split()
|
||||
if len(words):
|
||||
if words[0].startswith("###########"): break
|
||||
if words[0] == "bond":
|
||||
class1 = int(words[1])
|
||||
class2 = int(words[2])
|
||||
value1 = float(words[3])
|
||||
value2 = float(words[4])
|
||||
lmp1 = value2
|
||||
lmp2 = value1
|
||||
lmp3 = self.bond_cubic * value1
|
||||
lmp4 = self.bond_quartic * value1
|
||||
params.append((class1,class2,lmp1,lmp2,lmp3,lmp4))
|
||||
iline += 1
|
||||
return params
|
||||
|
||||
# convert PRMfile params to LAMMPS angle_style class2/p6 params
|
||||
# line may have prefactor plus 1,2,3 angle0 params
|
||||
# save prefactor/angle0 pairs as option 1,2,3
|
||||
|
||||
def angles(self):
|
||||
r2d = 180.0 / math.pi
|
||||
params = []
|
||||
iline = self.find_section("Angle Bending Parameters")
|
||||
if iline < 0: return params
|
||||
iline += 3
|
||||
while iline < self.nlines:
|
||||
words = self.lines[iline].split()
|
||||
if len(words):
|
||||
if words[0].startswith("###########"): break
|
||||
if words[0] == "angle" or words[0] == "anglep":
|
||||
if words[0] == "angle": pflag = 0
|
||||
if words[0] == "anglep": pflag = 1
|
||||
|
||||
class1 = int(words[1])
|
||||
class2 = int(words[2])
|
||||
class3 = int(words[3])
|
||||
value1 = float(words[4])
|
||||
value2 = float(words[5])
|
||||
option1 = ()
|
||||
option2 = ()
|
||||
option3 = ()
|
||||
|
||||
lmp1 = value2
|
||||
lmp2 = value1
|
||||
lmp3 = self.angle_cubic * value1 * r2d
|
||||
lmp4 = self.angle_quartic * value1 * r2d*r2d
|
||||
lmp5 = self.angle_pentic * value1 * r2d*r2d*r2d
|
||||
lmp6 = self.angle_sextic * value1 * r2d*r2d*r2d*r2d
|
||||
|
||||
option1 = (pflag,lmp1,lmp2,lmp3,lmp4,lmp5,lmp6)
|
||||
|
||||
if len(words) >= 7:
|
||||
value3 = float(words[6])
|
||||
lmp1 = value3
|
||||
option2 = (pflag,lmp1,lmp2,lmp3,lmp4,lmp5,lmp6)
|
||||
|
||||
if len(words) == 8:
|
||||
value4 = float(words[7])
|
||||
lmp1 = value4
|
||||
option3 = (pflag,lmp1,lmp2,lmp3,lmp4,lmp5,lmp6)
|
||||
|
||||
if not option2 and not option3:
|
||||
params.append((class1,class2,class3,[option1]))
|
||||
elif not option3:
|
||||
params.append((class1,class2,class3,[option1,option2]))
|
||||
else:
|
||||
params.append((class1,class2,class3,[option1,option2,option3]))
|
||||
|
||||
iline += 1
|
||||
return params
|
||||
|
||||
# convert PRMfile params to LAMMPS angle_style class2/p6 bondangle params
|
||||
# lmp3,lmp4 = equilibrium bond lengths for 2 bonds in angle
|
||||
# need to find these values in self.bondparams
|
||||
# put them in a dictionary for efficient searching
|
||||
|
||||
def bondangles(self):
|
||||
params = []
|
||||
iline = self.find_section("Stretch Bend Parameters")
|
||||
if iline < 0: return params
|
||||
iline += 3
|
||||
|
||||
bdict = {}
|
||||
for m,params in enumerate(self.bondparams):
|
||||
bdict[(params[0],params[1])] = params[2]
|
||||
|
||||
while iline < self.nlines:
|
||||
words = self.lines[iline].split()
|
||||
if len(words):
|
||||
if words[0].startswith("###########"): break
|
||||
if words[0] == "strbnd":
|
||||
class1 = int(words[1])
|
||||
class2 = int(words[2])
|
||||
class3 = int(words[3])
|
||||
value1 = float(words[4])
|
||||
value2 = float(words[5])
|
||||
lmp1 = value1
|
||||
lmp2 = value2
|
||||
lmp3 = lmp4 = 0.0
|
||||
if (class2,class1) in bdict: lmp3 = bdict[(class2,class1)]
|
||||
if (class1,class2) in bdict: lmp3 = bdict[(class1,class2)]
|
||||
if (class2,class3) in bdict: lmp4 = bdict[(class2,class3)]
|
||||
if (class3,class2) in bdict: lmp4 = bdict[(class3,class2)]
|
||||
if lmp3 == 0.0 or lmp4 == 0.0:
|
||||
print "Bond in BondAngle term not found",class1,class2,class3
|
||||
sys.exit()
|
||||
params.append((class1,class2,class3,lmp1,lmp2,lmp3,lmp4))
|
||||
iline += 1
|
||||
return params
|
||||
|
||||
def torsions(self):
|
||||
params = []
|
||||
iline = self.find_section("Torsional Parameters")
|
||||
if iline < 0: return params
|
||||
iline += 3
|
||||
while iline < self.nlines:
|
||||
words = self.lines[iline].split()
|
||||
if len(words):
|
||||
if words[0].startswith("###########"): break
|
||||
if words[0] == "torsion":
|
||||
class1 = int(words[1])
|
||||
class2 = int(words[2])
|
||||
class3 = int(words[3])
|
||||
class4 = int(words[4])
|
||||
value1 = words[5]
|
||||
value2 = words[6]
|
||||
value3 = words[7]
|
||||
value4 = words[8]
|
||||
value5 = words[9]
|
||||
value6 = words[10]
|
||||
value7 = words[11]
|
||||
value8 = words[12]
|
||||
value9 = words[13]
|
||||
params.append((class1,class2,class3,class4,
|
||||
value1,value2,value3,value4,value5,
|
||||
value6,value7,value8,value9))
|
||||
iline += 1
|
||||
return params
|
||||
|
||||
def find_section(self,txt):
|
||||
txt = "## %s ##" % txt
|
||||
for iline,line in enumerate(self.lines):
|
||||
if txt in line: return iline
|
||||
return -1
|
||||
|
||||
# ----------------------------------------
|
||||
# main program
|
||||
# ----------------------------------------
|
||||
|
||||
args = sys.argv[1:]
|
||||
narg = len(args)
|
||||
|
||||
# process args
|
||||
|
||||
amoeba = hippo = 0
|
||||
xyzfile = ""
|
||||
prmfile = ""
|
||||
datafile = ""
|
||||
pbcflag = 0
|
||||
|
||||
iarg = 0
|
||||
while iarg < narg:
|
||||
if args[iarg] == "-xyz":
|
||||
if iarg + 2 > narg: error()
|
||||
xyzfile = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-amoeba":
|
||||
if iarg + 2 > narg: error()
|
||||
amoeba = 1
|
||||
prmfile = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-hippo":
|
||||
if iarg + 2 > narg: error()
|
||||
hippo = 1
|
||||
prmfile = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-data":
|
||||
if iarg + 2 > narg: error()
|
||||
datafile = args[iarg+1]
|
||||
iarg += 2
|
||||
elif args[iarg] == "-nopbc":
|
||||
pbcflag = 0
|
||||
iarg += 1
|
||||
elif args[iarg] == "-pbc":
|
||||
if iarg + 4 > narg: error()
|
||||
pbcflag = 1
|
||||
xhi = float(args[iarg+1])
|
||||
yhi = float(args[iarg+2])
|
||||
zhi = float(args[iarg+3])
|
||||
boxhi = [xhi,yhi,zhi]
|
||||
iarg += 4
|
||||
else: error()
|
||||
|
||||
# error check
|
||||
|
||||
if not xyzfile: error("xyzfile not specified")
|
||||
if not prmfile: error("prmfile not specified")
|
||||
if not datafile: error("datafile not specified")
|
||||
|
||||
# read Tinker xyz and prm files
|
||||
|
||||
xyz = XYZfile(xyzfile)
|
||||
prm = PRMfile(prmfile)
|
||||
|
||||
# create LAMMPS box bounds based on pbcflag
|
||||
|
||||
natoms = xyz.natoms
|
||||
x = xyz.x
|
||||
y = xyz.y
|
||||
z = xyz.z
|
||||
|
||||
if pbcflag:
|
||||
boxlo = [0,0,0]
|
||||
else:
|
||||
xlo = ylo = zlo = BIG
|
||||
xhi = yhi = zhi = -BIG
|
||||
for i in xrange(natoms):
|
||||
xlo = min(xlo,float(x[i]))
|
||||
ylo = min(ylo,float(y[i]))
|
||||
zlo = min(zlo,float(z[i]))
|
||||
xhi = max(xhi,float(x[i]))
|
||||
yhi = max(yhi,float(y[i]))
|
||||
zhi = max(zhi,float(z[i]))
|
||||
boxlo = [xlo-DELTA,ylo-DELTA,zlo-DELTA]
|
||||
boxhi = [xhi+DELTA,yhi+DELTA,zhi+DELTA]
|
||||
|
||||
# ----------------------------------------
|
||||
# create LAMMPS atom types for each unique Tinker per-type mass
|
||||
# NOTE: maybe should assign LAMMPS types in a different way,
|
||||
# e.g. one LAMMPS type for each used Tinker type
|
||||
# ----------------------------------------
|
||||
|
||||
# ntypes = # of LAMMPS atoms types = unique Tinker masses
|
||||
# lmptype = which LAMMPS type for each atom (1 to Ntypes)
|
||||
# lmpmass = list of per-type masses
|
||||
# ttype = list of Tinker types for each atom (1 to prm.ntypes)
|
||||
# tink2lmp = mapping of Tinker types to LAMMPS types
|
||||
|
||||
natoms = xyz.natoms
|
||||
ttype = xyz.type
|
||||
tmasses = prm.masses
|
||||
|
||||
ntypes = 0
|
||||
lmptype = []
|
||||
lmpmass = []
|
||||
tink2lmp = {}
|
||||
|
||||
for itype in ttype:
|
||||
if itype not in tink2lmp:
|
||||
mass = tmasses[itype-1]
|
||||
if mass not in lmpmass:
|
||||
ntypes += 1
|
||||
lmpmass.append(mass)
|
||||
jtype = ntypes
|
||||
else: jtype = lmpmass.index(mass) + 1
|
||||
tink2lmp[itype] = jtype
|
||||
lmptype.append(tink2lmp[itype])
|
||||
|
||||
# ----------------------------------------
|
||||
# identify molecules from Tinker bond connectivity
|
||||
# ----------------------------------------
|
||||
|
||||
# molID = which molecule each atom is in (1 to Nmol)
|
||||
# use stack to store IDs of atoms to recursively loop over
|
||||
|
||||
natoms = xyz.natoms
|
||||
id = xyz.id
|
||||
bonds = xyz.bonds
|
||||
|
||||
molID = natoms*[0]
|
||||
nmol = 0
|
||||
|
||||
for i in id:
|
||||
if molID[i-1] > 0: continue
|
||||
nmol += 1
|
||||
molID[i-1] = nmol
|
||||
stack = [i]
|
||||
while stack:
|
||||
j = stack.pop()
|
||||
for k in bonds[j-1]:
|
||||
if molID[k-1] == 0:
|
||||
molID[k-1] = nmol
|
||||
stack.append(k)
|
||||
|
||||
# ----------------------------------------
|
||||
# create lists of bonds, angles, dihedrals
|
||||
# ----------------------------------------
|
||||
|
||||
# create blist = list of bonds
|
||||
# avoid double counting by requiring atom1 < atom2
|
||||
|
||||
id = xyz.id
|
||||
type = xyz.type
|
||||
bonds = xyz.bonds
|
||||
|
||||
blist = []
|
||||
|
||||
for atom1 in id:
|
||||
for atom2 in bonds[atom1-1]:
|
||||
if atom1 < atom2:
|
||||
blist.append((atom1,atom2))
|
||||
|
||||
# create alist = list of angles
|
||||
# generate topology by double loop over bonds of center atom2
|
||||
# avoid double counting by requiring atom1 < atom3
|
||||
|
||||
id = xyz.id
|
||||
type = xyz.type
|
||||
bonds = xyz.bonds
|
||||
|
||||
alist = []
|
||||
|
||||
for atom2 in id:
|
||||
for atom1 in bonds[atom2-1]:
|
||||
for atom3 in bonds[atom2-1]:
|
||||
if atom3 == atom1: continue
|
||||
if atom1 < atom3:
|
||||
alist.append((atom1,atom2,atom3))
|
||||
|
||||
# create dlist = list of dihedrals
|
||||
# generate topology via triple loop over neighbors of dihedral atom2
|
||||
# double loop over bonds of atom2
|
||||
# additional loop over bonds of atom3
|
||||
# avoid double counting by requiring atom1 < atom3
|
||||
|
||||
id = xyz.id
|
||||
type = xyz.type
|
||||
bonds = xyz.bonds
|
||||
|
||||
dlist = []
|
||||
|
||||
for atom2 in id:
|
||||
for atom1 in bonds[atom2-1]:
|
||||
for atom3 in bonds[atom2-1]:
|
||||
if atom3 == atom1: continue
|
||||
for atom4 in bonds[atom3-1]:
|
||||
if atom4 == atom2 or atom4 == atom1: continue
|
||||
if atom1 < atom3:
|
||||
dlist.append((atom1,atom2,atom3,atom4))
|
||||
|
||||
# ----------------------------------------
|
||||
# create lists of bond/angle/dihedral types
|
||||
# ----------------------------------------
|
||||
|
||||
# generate btype = LAMMPS type of each bond
|
||||
# generate bparams = LAMMPS params for each bond type
|
||||
# flags[i] = which LAMMPS bond type (1-N) the Ith Tinker PRM file bond is
|
||||
# 0 = none
|
||||
# convert prm.bondparams to a dictionary for efficient searching
|
||||
# key = (class1,class2)
|
||||
# value = (M,params) where M is index into prm.bondparams
|
||||
|
||||
id = xyz.id
|
||||
type = xyz.type
|
||||
classes = prm.classes
|
||||
|
||||
bdict = {}
|
||||
for m,params in enumerate(prm.bondparams):
|
||||
bdict[(params[0],params[1])] = (m,params)
|
||||
|
||||
flags = len(prm.bondparams)*[0]
|
||||
btype = []
|
||||
bparams = []
|
||||
|
||||
for atom1,atom2 in blist:
|
||||
type1 = type[atom1-1]
|
||||
type2 = type[atom2-1]
|
||||
c1 = classes[type1-1]
|
||||
c2 = classes[type2-1]
|
||||
|
||||
if (c1,c2) in bdict: m,params = bdict[(c1,c2)]
|
||||
elif (c2,c1) in bdict: m,params = bdict[(c2,c1)]
|
||||
else:
|
||||
print "Bond not found",atom1,atom2,c1,c2
|
||||
sys.exit()
|
||||
|
||||
if not flags[m]:
|
||||
v1,v2,v3,v4 = params[2:]
|
||||
bparams.append((v1,v2,v3,v4))
|
||||
flags[m] = len(bparams)
|
||||
btype.append(flags[m])
|
||||
|
||||
# generate atype = LAMMPS type of each angle
|
||||
# generate aparams = LAMMPS params for each angle type
|
||||
# generate baparams = LAMMPS bond-angle params for each angle type
|
||||
# flags[i] = which LAMMPS angle type (1-N) the Tinker FF file angle I is
|
||||
# 0 = none
|
||||
# Tinker FF file angle entries can have 1, 2, or 3 options
|
||||
# noptions = total # of Tinker FF file entries with options included
|
||||
# convert prm.angleparams to a dictionary for efficient searching
|
||||
# key = (class1,class2)
|
||||
# value = (M,params) where M is index into prm.angleparams
|
||||
|
||||
id = xyz.id
|
||||
type = xyz.type
|
||||
classes = prm.classes
|
||||
|
||||
adict = {}
|
||||
noptions = 0
|
||||
for m,params in enumerate(prm.angleparams):
|
||||
adict[(params[0],params[1],params[2])] = (noptions,params)
|
||||
n = len(params[3])
|
||||
noptions += n
|
||||
|
||||
flags = noptions*[0]
|
||||
#baflags = len(baprm)*[0]
|
||||
atype = []
|
||||
aparams = []
|
||||
baparams = []
|
||||
|
||||
#DEBUG
|
||||
opcount = 0
|
||||
|
||||
for atom1,atom2,atom3 in alist:
|
||||
type1 = type[atom1-1]
|
||||
type2 = type[atom2-1]
|
||||
type3 = type[atom3-1]
|
||||
c1 = classes[type1-1]
|
||||
c2 = classes[type2-1]
|
||||
c3 = classes[type3-1]
|
||||
|
||||
if (c1,c2,c3) in adict or (c3,c2,c1) in adict:
|
||||
if (c1,c2,c3) in adict: m,params = adict[(c1,c2,c3)]
|
||||
if (c3,c2,c1) in adict: m,params = adict[(c3,c2,c1)]
|
||||
|
||||
# params is a sequence of 1 or 2 or 3 options
|
||||
# which = which of 1,2,3 options this atom triplet matches
|
||||
# for which = 2 or 3, increment m to index correct position in flags
|
||||
# how match is determined:
|
||||
# if 2 options:
|
||||
# require atom2 have 3 bond partners, including atom1 and atom3
|
||||
# option 1 if additional bond is not to an H atom
|
||||
# option 2 if additional bond is to an H atom
|
||||
# if 3 options:
|
||||
# require atom2 have 4 bond partners, including atom1 and atom3
|
||||
# option 1 if neither of 2 additional bonds is to an H atom
|
||||
# option 2 if one of 2 additional bonds is to an H atom
|
||||
# option 3 if both of 2 additional bonds is to an H atom
|
||||
|
||||
# DEBUG
|
||||
debugflag = 0
|
||||
|
||||
if len(params[3]) == 1:
|
||||
which = 1
|
||||
|
||||
elif len(params[3]) == 2:
|
||||
nbonds,hcount = xyz.angle_hbond_count(atom1,atom2,atom3,lmptype,lmpmass)
|
||||
|
||||
if nbonds != 3:
|
||||
print "Center angle atom has wrong bond count"
|
||||
print " angle atom IDs:",atom1,atom2,atom3
|
||||
print " angle atom classes:",c1,c2,c3
|
||||
print " Tinker FF file param options:",len(params[3])
|
||||
print " Nbonds and hydrogen count:",nbonds,hcount
|
||||
#sys.exit() // NOTE: allow this for now
|
||||
|
||||
if hcount == 0: which = 1
|
||||
elif hcount == 1:
|
||||
which = 2
|
||||
m += 1
|
||||
|
||||
print "3-bond angle"
|
||||
print " angle atom IDs:",atom1,atom2,atom3
|
||||
print " angle atom classes:",c1,c2,c3
|
||||
print " Tinker FF file param options:",len(params[3])
|
||||
print " Nbonds and hydrogen count:",nbonds,hcount
|
||||
print " which:",which,m
|
||||
|
||||
# DEBUG
|
||||
debugflag = 1
|
||||
opcount += 1
|
||||
|
||||
elif len(params[3]) == 3:
|
||||
nbonds,hcount = xyz.angle_hbond_count(atom1,atom2,atom3,lmptype,lmpmass)
|
||||
|
||||
if nbonds != 4:
|
||||
print "Center angle atom has wrong bond count"
|
||||
print " angle atom IDs:",atom1,atom2,atom3
|
||||
print " angle atom classes:",c1,c2,c3
|
||||
print " Tinker FF file param options:",len(params[3])
|
||||
print " Nbonds and hydrogen count:",nbonds,hcount
|
||||
#sys.exit() // NOTE: allow this for now
|
||||
|
||||
if hcount == 0: which = 1
|
||||
elif hcount == 1:
|
||||
which = 2
|
||||
m += 1
|
||||
elif hcount == 2:
|
||||
which = 3
|
||||
m += 2
|
||||
|
||||
print "4-bond angle"
|
||||
print " angle atom IDs:",atom1,atom2,atom3
|
||||
print " angle atom classes:",c1,c2,c3
|
||||
print " Tinker FF file param options:",len(params[3])
|
||||
print " Nbonds and hydrogen count:",nbonds,hcount
|
||||
print " which:",which,m
|
||||
|
||||
# DEBUG
|
||||
debugflag = 1
|
||||
opcount += 1
|
||||
|
||||
else:
|
||||
print "Angle not found",atom1,atom2,atom3,c1,c2,c3
|
||||
sys.exit()
|
||||
|
||||
if not flags[m]:
|
||||
pflag,v1,v2,v3,v4,v5,v6 = params[3][which-1]
|
||||
# DEBUG single line
|
||||
if debugflag: pflag = 2
|
||||
aparams.append((pflag,v1,v2,v3,v4,v5,v6))
|
||||
flags[m] = len(aparams)
|
||||
atype.append(flags[m])
|
||||
|
||||
print "OPTION angles",opcount
|
||||
|
||||
# NOTE: baparams may need to be flipped if match is 3,2,1 instead of 1,2,3
|
||||
|
||||
# NOTE: mismatch between angle and bondangle params may not be handled right
|
||||
# should be a new LAMMPS type if either angle or bondangle params do not match?
|
||||
#for m,params in enumerate(baprm):
|
||||
# c1,c2,c3,v1,v2,v3,v4 = params
|
||||
# if (c1 == class1 and c2 == class2 and c3 == class3) or \
|
||||
# (c1 == class3 and c2 == class2 and c3 == class1):
|
||||
# found += 1
|
||||
# if baflags[m]:
|
||||
# continue
|
||||
# #atype.append(baflags[m])
|
||||
# else:
|
||||
# baparams.append((v1,v2,v3,v4))
|
||||
# baflags[m] = len(baparams)
|
||||
# #atype.append(baflags[m])
|
||||
# break
|
||||
# if found != 1: print "Not found",atom1,atom2,atom3,class1,class2,class3
|
||||
|
||||
# generate dtype = LAMMPS type of each dihedral
|
||||
# generate dparams = LAMMPS params for each dihedral type
|
||||
# flags[i] = which LAMMPS dihedral type (1-N) the Tinker FF file dihedral I is
|
||||
# 0 = none
|
||||
# convert prm.torsionparams to a dictionary for efficient searching
|
||||
# key = (class1,class2)
|
||||
# value = (M,params) where M is index into prm.torsionparams
|
||||
|
||||
id = xyz.id
|
||||
type = xyz.type
|
||||
classes = prm.classes
|
||||
|
||||
ddict = {}
|
||||
for m,params in enumerate(prm.torsionparams):
|
||||
ddict[(params[0],params[1],params[2],params[3])] = (m,params)
|
||||
|
||||
flags = len(prm.torsionparams)*[0]
|
||||
dtype = []
|
||||
dparams = []
|
||||
|
||||
for atom1,atom2,atom3,atom4 in dlist:
|
||||
type1 = type[atom1-1]
|
||||
type2 = type[atom2-1]
|
||||
type3 = type[atom3-1]
|
||||
type4 = type[atom4-1]
|
||||
c1 = classes[type1-1]
|
||||
c2 = classes[type2-1]
|
||||
c3 = classes[type3-1]
|
||||
c4 = classes[type4-1]
|
||||
|
||||
if (c1,c2,c3,c4) in ddict: m,params = ddict[(c1,c2,c3,c4)]
|
||||
elif (c4,c3,c2,c1) in ddict: m,params = ddict[(c4,c3,c2,c1)]
|
||||
else:
|
||||
print "Dihedral not found",atom1,atom2,atom3,atom4,c1,c2,c3,c4
|
||||
sys.exit()
|
||||
|
||||
if not flags[m]:
|
||||
v1,v2,v3,v4,v5,v6,v7,v8,v9 = params[4:]
|
||||
dparams.append((v1,v2,v3,v4,v5,v6,v7,v8,v9))
|
||||
flags[m] = len(dparams)
|
||||
dtype.append(flags[m])
|
||||
|
||||
# ----------------------------------------
|
||||
# assign each atom to a Tinker group
|
||||
# NOTE: doing this inside LAMMPS now
|
||||
# comment out unless need to test
|
||||
# ----------------------------------------
|
||||
|
||||
# ngroup = # of groups
|
||||
# tgroup[i] = groupID (1 to Ngroups) for each atom
|
||||
# use stack to store IDs of atoms to recursively loop over
|
||||
# do not set tgroup for an atom if already assigned to a group
|
||||
# only add atoms J (bonded to M) to stack
|
||||
# whose Tinker type is in polgroup list for atom M's Tinker type
|
||||
|
||||
#natoms = xyz.natoms
|
||||
#id = xyz.id
|
||||
#bonds = xyz.bonds
|
||||
#ttype = xyz.type
|
||||
#polgroup = prm.polgroup
|
||||
|
||||
#tgroup = natoms*[0]
|
||||
#ngroups = 0
|
||||
|
||||
#for i in id:
|
||||
# if tgroup[i-1] > 0: continue
|
||||
#
|
||||
# ngroups += 1
|
||||
# groupID = ngroups
|
||||
# stack = [i]
|
||||
# while stack:
|
||||
# m = stack.pop()
|
||||
# if tgroup[m-1] > 0: continue
|
||||
# tgroup[m-1] = groupID
|
||||
# for j in bonds[m-1]:
|
||||
# if tgroup[j-1] > 0: continue
|
||||
# if ttype[j-1] not in polgroup[ttype[m-1]-1]: continue
|
||||
# stack.append(j)
|
||||
|
||||
# ----------------------------------------
|
||||
# write LAMMPS data file via Pizza.py data class
|
||||
# ----------------------------------------
|
||||
|
||||
d = data()
|
||||
|
||||
natoms = xyz.natoms
|
||||
id = xyz.id
|
||||
x = xyz.x
|
||||
y = xyz.y
|
||||
z = xyz.z
|
||||
ttype = xyz.type
|
||||
|
||||
nbonds = len(blist)
|
||||
nangles = len(alist)
|
||||
ndihedrals = len(dlist)
|
||||
|
||||
# data file header values
|
||||
|
||||
d.title = "LAMMPS data file created from Tinker %s and %s files\n" % \
|
||||
(xyzfile,prmfile)
|
||||
|
||||
d.headers["atoms"] = natoms
|
||||
d.headers["atom types"] = ntypes
|
||||
|
||||
d.headers["xlo xhi"] = (boxlo[0],boxhi[0])
|
||||
d.headers["ylo yhi"] = (boxlo[1],boxhi[1])
|
||||
d.headers["zlo zhi"] = (boxlo[2],boxhi[2])
|
||||
|
||||
# data file sections
|
||||
|
||||
lines = []
|
||||
for i,mass in enumerate(lmpmass):
|
||||
line = "%d %s" % (i+1,mass)
|
||||
lines.append(line+'\n')
|
||||
d.sections["Masses"] = lines
|
||||
|
||||
lines = []
|
||||
for i,one in enumerate(id):
|
||||
line = "%d %d %d %g %s %s %s" % (one,molID[i],lmptype[i],0.0,x[i],y[i],z[i])
|
||||
lines.append(line+'\n')
|
||||
d.sections["Atoms"] = lines
|
||||
|
||||
lines = []
|
||||
for i,one in enumerate(ttype):
|
||||
# comment out inclusion of Tinker group, now done by LAMMPS
|
||||
#line = "%d %d %d" % (id[i],one,tgroup[i])
|
||||
line = "%d %d" % (id[i],one)
|
||||
lines.append(line+'\n')
|
||||
d.sections["Tinker Types"] = lines
|
||||
|
||||
if nbonds:
|
||||
d.headers["bonds"] = len(blist)
|
||||
d.headers["bond types"] = len(bparams)
|
||||
|
||||
lines = []
|
||||
for i,one in enumerate(bparams):
|
||||
strone = [str(single) for single in one]
|
||||
line = "%d %s" % (i+1,' '.join(strone))
|
||||
lines.append(line+'\n')
|
||||
d.sections["Bond Coeffs"] = lines
|
||||
|
||||
lines = []
|
||||
for i,one in enumerate(blist):
|
||||
line = "%d %d %d %d" % (i+1,btype[i],one[0],one[1])
|
||||
lines.append(line+'\n')
|
||||
d.sections["Bonds"] = lines
|
||||
|
||||
if nangles:
|
||||
d.headers["angles"] = len(alist)
|
||||
d.headers["angle types"] = len(aparams)
|
||||
|
||||
lines = []
|
||||
for i,one in enumerate(aparams):
|
||||
strone = [str(single) for single in one]
|
||||
line = "%d %s" % (i+1,' '.join(strone))
|
||||
lines.append(line+'\n')
|
||||
d.sections["Angle Coeffs"] = lines
|
||||
|
||||
#lines = []
|
||||
#for i,one in enumerate(aparams):
|
||||
# line = "%d %g %g %g" % (i+1,0.0,0.0,0.0)
|
||||
# lines.append(line+'\n')
|
||||
#d.sections["BondBond Coeffs"] = lines
|
||||
|
||||
#lines = []
|
||||
#for i,one in enumerate(aparams):
|
||||
# line = "%d %g %g %g %g" % (i+1,0.0,0.0,0.0,0.0)
|
||||
# lines.append(line+'\n')
|
||||
# d.sections["BondAngle Coeffs"] = lines
|
||||
|
||||
lines = []
|
||||
for i,one in enumerate(alist):
|
||||
line = "%d %d %d %d %d" % (i+1,atype[i],one[0],one[1],one[2])
|
||||
lines.append(line+'\n')
|
||||
d.sections["Angles"] = lines
|
||||
|
||||
if ndihedrals:
|
||||
d.headers["dihedrals"] = len(dlist)
|
||||
d.headers["dihedral types"] = len(dparams)
|
||||
|
||||
lines = []
|
||||
for i,one in enumerate(dparams):
|
||||
line = "%d %s" % (i+1,' '.join(one))
|
||||
lines.append(line+'\n')
|
||||
d.sections["Dihedral Coeffs"] = lines
|
||||
|
||||
lines = []
|
||||
for i,one in enumerate(dlist):
|
||||
line = "%d %d %d %d %d %d" % (i+1,dtype[i],one[0],one[1],one[2],one[3])
|
||||
lines.append(line+'\n')
|
||||
d.sections["Dihedrals"] = lines
|
||||
|
||||
d.write(datafile)
|
||||
|
||||
# print stats to screen
|
||||
|
||||
print "Natoms =",natoms
|
||||
print "Ntypes =",ntypes
|
||||
print "Tinker XYZ types =",len(tink2lmp)
|
||||
print "Tinker PRM types =",prm.ntypes
|
||||
#print "Tinker groups =",ngroups
|
||||
print "Nmol =",nmol
|
||||
print "Nbonds =",len(blist)
|
||||
print "Nangles =",len(alist)
|
||||
print "Ndihedrals =",len(dlist)
|
||||
print "Nbondtypes =",len(bparams)
|
||||
print "Nangletypes =",len(aparams)
|
||||
print "Ndihedraltypes =",len(dparams)
|
||||
Reference in New Issue
Block a user