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Merge remote-tracking branch 'upstream/develop' into develop

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This commit is contained in:
Aidan Thompson
2022-07-15 16:40:56 -06:00
parent c1ae5d0ce1 151a7f7039
commit b5c079ff91
263 changed files with 94995 additions and 1565 deletions
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4
cmake/CMakeLists.txt
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@ -194,6 +194,7 @@ option(CMAKE_VERBOSE_MAKEFILE "Generate verbose Makefiles" OFF)
set(STANDARD_PACKAGES
ADIOS
AMOEBA
ASPHERE
ATC
AWPMD
@ -202,7 +203,7 @@ set(STANDARD_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS
@ -358,6 +359,7 @@ pkg_depends(MPIIO MPI)
pkg_depends(ATC MANYBODY)
pkg_depends(LATBOLTZ MPI)
pkg_depends(SCAFACOS MPI)
pkg_depends(AMOEBA KSPACE)
pkg_depends(DIELECTRIC KSPACE)
pkg_depends(DIELECTRIC EXTRA-PAIR)
pkg_depends(CG-DNA MOLECULE)

3
cmake/presets/all_off.cmake
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@ -3,6 +3,7 @@
set(ALL_PACKAGES
ADIOS
AMOEBA
ASPHERE
ATC
AWPMD
@ -11,7 +12,7 @@ set(ALL_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS

3
cmake/presets/all_on.cmake
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@ -5,6 +5,7 @@
set(ALL_PACKAGES
ADIOS
AMOEBA
ASPHERE
ATC
AWPMD
@ -13,7 +14,7 @@ set(ALL_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS

3
cmake/presets/mingw-cross.cmake
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@ -1,4 +1,5 @@
set(WIN_PACKAGES
AMOEBA
ASPHERE
ATC
AWPMD
@ -7,7 +8,7 @@ set(WIN_PACKAGES
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS

3
cmake/presets/most.cmake
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@ -3,13 +3,14 @@
# are removed. The resulting binary should be able to run most inputs.
set(ALL_PACKAGES
AMOEBA
ASPHERE
BOCS
BODY
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS

3
cmake/presets/windows.cmake
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@ -1,11 +1,12 @@
set(WIN_PACKAGES
AMOEBA
ASPHERE
BOCS
BODY
BPM
BROWNIAN
CG-DNA
CG-SDK
CG-SPICA
CLASS2
COLLOID
COLVARS

4
doc/src/Commands_bond.rst
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@ -74,6 +74,7 @@ OPT.
*
*
*
* :doc:`amoeba <angle_amoeba>`
* :doc:`charmm (iko) <angle_charmm>`
* :doc:`class2 (ko) <angle_class2>`
* :doc:`class2/p6 <angle_class2>`
@ -92,7 +93,7 @@ OPT.
* :doc:`harmonic (iko) <angle_harmonic>`
* :doc:`mm3 <angle_mm3>`
* :doc:`quartic (o) <angle_quartic>`
* :doc:`sdk (o) <angle_sdk>`
* :doc:`spica (o) <angle_spica>`
* :doc:`table (o) <angle_table>`
.. _dihedral:
@ -152,6 +153,7 @@ OPT.
*
*
*
* :doc:`amoeba <improper_amoeba>`
* :doc:`class2 (ko) <improper_class2>`
* :doc:`cossq (o) <improper_cossq>`
* :doc:`cvff (io) <improper_cvff>`

2
doc/src/Commands_fix.rst
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@ -28,6 +28,8 @@ OPT.
* :doc:`adapt/fep <fix_adapt_fep>`
* :doc:`addforce <fix_addforce>`
* :doc:`addtorque <fix_addtorque>`
* :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>`
* :doc:`amoeba/pitorsion <fix_amoeba_pitorsion>`
* :doc:`append/atoms <fix_append_atoms>`
* :doc:`atc <fix_atc>`
* :doc:`atom/swap <fix_atom_swap>`

8
doc/src/Commands_pair.rst
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@ -38,6 +38,7 @@ OPT.
* :doc:`agni (o) <pair_agni>`
* :doc:`airebo (io) <pair_airebo>`
* :doc:`airebo/morse (io) <pair_airebo>`
* :doc:`amoeba <pair_amoeba>`
* :doc:`atm <pair_atm>`
* :doc:`awpmd/cut <pair_awpmd>`
* :doc:`beck (go) <pair_beck>`
@ -124,6 +125,7 @@ OPT.
* :doc:`hbond/dreiding/lj (o) <pair_hbond_dreiding>`
* :doc:`hbond/dreiding/morse (o) <pair_hbond_dreiding>`
* :doc:`hdnnp <pair_hdnnp>`
* :doc:`hippo <pair_amoeba>`
* :doc:`ilp/graphene/hbn (t) <pair_ilp_graphene_hbn>`
* :doc:`ilp/tmd (t) <pair_ilp_tmd>`
* :doc:`kolmogorov/crespi/full <pair_kolmogorov_crespi_full>`
@ -179,9 +181,9 @@ OPT.
* :doc:`lj/long/tip4p/long (o) <pair_lj_long>`
* :doc:`lj/mdf <pair_mdf>`
* :doc:`lj/relres (o) <pair_lj_relres>`
* :doc:`lj/sdk (gko) <pair_sdk>`
* :doc:`lj/sdk/coul/long (go) <pair_sdk>`
* :doc:`lj/sdk/coul/msm (o) <pair_sdk>`
* :doc:`lj/spica (gko) <pair_spica>`
* :doc:`lj/spica/coul/long (go) <pair_spica>`
* :doc:`lj/spica/coul/msm (o) <pair_spica>`
* :doc:`lj/sf/dipole/sf (go) <pair_dipole>`
* :doc:`lj/smooth (go) <pair_lj_smooth>`
* :doc:`lj/smooth/linear (o) <pair_lj_smooth_linear>`

3
doc/src/Developer_utils.rst
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@ -154,6 +154,9 @@ and parsing files or arguments.
.. doxygenfunction:: trim_and_count_words
:project: progguide
.. doxygenfunction:: join_words
:project: progguide
.. doxygenfunction:: split_words
:project: progguide

126
doc/src/Errors_messages.rst
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@ -476,65 +476,6 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Bonds defined but no bond types*
The data file header lists bonds but no bond types.
*Bond/react: Cannot use fix bond/react with non-molecular systems*
Only systems with bonds that can be changed can be used. Atom_style
template does not qualify.
*Bond/react: Invalid template atom ID in map file*
Atom IDs in molecule templates range from 1 to the number of atoms in the template.
*Bond/react: Rmax cutoff is longer than pairwise cutoff*
This is not allowed because bond creation is done using the pairwise
neighbor list.
*Bond/react: Molecule template ID for fix bond/react does not exist*
A valid molecule template must have been created with the molecule
command.
*Bond/react: Reaction templates must contain the same number of atoms*
There should be a one-to-one correspondence between atoms in the
pre-reacted and post-reacted templates, as specified by the map file.
*Bond/react: Unknown section in map file*
Please ensure reaction map files are properly formatted.
*Bond/react: Atom/Bond type affected by reaction too close to template edge*
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the map
file. This could cause incorrect assignment of bonds, angle, etc.
Generally, this means you must include more atoms in your templates,
such that there are at least two atoms between each atom involved in
the reaction and an edge atom.
*Bond/react: Fix bond/react needs ghost atoms from farther away*
This is because a processor needs to map the entire unreacted
molecule template onto simulation atoms it knows about. The
comm_modify cutoff command can be used to extend the communication
range.
*Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted*
Self-explanatory.
*Bond/react: First neighbors of chiral atoms must be of mutually different types*
Self-explanatory.
*Bond/react: Chiral atoms must have exactly four first neighbors*
Self-explanatory.
*Bond/react: Molecule template 'Coords' section required for chiralIDs keyword*
The coordinates of atoms in the pre-reacted template are used to determine
chirality.
*Bond/react special bond generation overflow*
The number of special bonds per-atom created by a reaction exceeds the
system setting. See the read_data or create_box command for how to
specify this value.
*Bond/react topology/atom exceed system topology/atom*
The number of bonds, angles etc per-atom created by a reaction exceeds
the system setting. See the read_data or create_box command for how to
specify this value.
*Both restart files must use % or neither*
Self-explanatory.
@ -1291,7 +1232,7 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Cannot use chosen neighbor list style with lj/gromacs/kk*
Self-explanatory.
*Cannot use chosen neighbor list style with lj/sdk/kk*
*Cannot use chosen neighbor list style with lj/spica/kk*
That style is not supported by Kokkos.
*Cannot use chosen neighbor list style with pair eam/kk*
@ -1659,10 +1600,10 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Cannot use newton pair with lj/gromacs/gpu pair style*
Self-explanatory.
*Cannot use newton pair with lj/sdk/coul/long/gpu pair style*
*Cannot use newton pair with lj/spica/coul/long/gpu pair style*
Self-explanatory.
*Cannot use newton pair with lj/sdk/gpu pair style*
*Cannot use newton pair with lj/spica/gpu pair style*
Self-explanatory.
*Cannot use newton pair with lj96/cut/gpu pair style*
@ -3521,6 +3462,65 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
acquire needed info, The comm_modify cutoff command can be used to
extend the communication range.
*Fix bond/react: Cannot use fix bond/react with non-molecular systems*
Only systems with bonds that can be changed can be used. Atom_style
template does not qualify.
*Fix bond/react: Invalid template atom ID in map file*
Atom IDs in molecule templates range from 1 to the number of atoms in the template.
*Fix bond/react: Rmax cutoff is longer than pairwise cutoff*
This is not allowed because bond creation is done using the pairwise
neighbor list.
*Fix bond/react: Molecule template ID for fix bond/react does not exist*
A valid molecule template must have been created with the molecule
command.
*Fix bond/react: Reaction templates must contain the same number of atoms*
There should be a one-to-one correspondence between atoms in the
pre-reacted and post-reacted templates, as specified by the map file.
*Fix bond/react: Unknown section in map file*
Please ensure reaction map files are properly formatted.
*Fix bond/react: Atom/Bond type affected by reaction too close to template edge*
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the map
file. This could cause incorrect assignment of bonds, angle, etc.
Generally, this means you must include more atoms in your templates,
such that there are at least two atoms between each atom involved in
the reaction and an edge atom.
*Fix bond/react: Fix bond/react needs ghost atoms from farther away*
This is because a processor needs to map the entire unreacted
molecule template onto simulation atoms it knows about. The
comm_modify cutoff command can be used to extend the communication
range.
*Fix bond/react: A deleted atom cannot remain bonded to an atom that is not deleted*
Self-explanatory.
*Fix bond/react: First neighbors of chiral atoms must be of mutually different types*
Self-explanatory.
*Fix bond/react: Chiral atoms must have exactly four first neighbors*
Self-explanatory.
*Fix bond/react: Molecule template 'Coords' section required for chiralIDs keyword*
The coordinates of atoms in the pre-reacted template are used to determine
chirality.
*Fix bond/react special bond generation overflow*
The number of special bonds per-atom created by a reaction exceeds the
system setting. See the read_data or create_box command for how to
specify this value.
*Fix bond/react topology/atom exceed system topology/atom*
The number of bonds, angles etc per-atom created by a reaction exceeds
the system setting. See the read_data or create_box command for how to
specify this value.
*Fix bond/swap cannot use dihedral or improper styles*
These styles cannot be defined when using this fix.
@ -6782,7 +6782,7 @@ keyword to allow for additional bonds to be formed
This is because the computation of constraint forces within a water
molecule adds forces to atoms owned by other processors.
*Pair style lj/sdk/coul/long/gpu requires atom attribute q*
*Pair style lj/spica/coul/long/gpu requires atom attribute q*
The atom style defined does not have this attribute.
*Pair style nb3b/harmonic requires atom IDs*

19
doc/src/Errors_warnings.rst
View File

@ -68,14 +68,6 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
length, multiplying by the number of bonds in the interaction (e.g. 3
for a dihedral) and adding a small amount of stretch.
*Bond/react: Atom affected by reaction too close to template edge*
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the superimpose
file. This could cause incorrect assignment of bonds, angle, etc.
Generally, this means you must include more atoms in your templates,
such that there are at least two atoms between each atom involved in
the reaction and an edge atom.
*Both groups in compute group/group have a net charge; the Kspace boundary correction to energy will be non-zero*
Self-explanatory.
@ -206,12 +198,20 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
*Fix SRD walls overlap but fix srd overlap not set*
You likely want to set this in your input script.
* Fix bond/create is used multiple times or with fix bond/break - may not work as expected*
*Fix bond/create is used multiple times or with fix bond/break - may not work as expected*
When using fix bond/create multiple times or in combination with
fix bond/break, the individual fix instances do not share information
about changes they made at the same time step and thus it may result
in unexpected behavior.
*Fix bond/react: Atom affected by reaction too close to template edge*
This means an atom which changes type or connectivity during the
reaction is too close to an 'edge' atom defined in the superimpose
file. This could cause incorrect assignment of bonds, angle, etc.
Generally, this means you must include more atoms in your templates,
such that there are at least two atoms between each atom involved in
the reaction and an edge atom.
*Fix bond/swap will ignore defined angles*
See the page for fix bond/swap for more info on this
restriction.
@ -810,4 +810,3 @@ This will most likely cause errors in kinetic fluctuations.
*Using pair tail corrections with pair_modify compute no*
The tail corrections will thus not be computed.

1
doc/src/Howto.rst
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@ -65,6 +65,7 @@ Force fields howto
:maxdepth: 1
Howto_bioFF
Howto_amoeba
Howto_tip3p
Howto_tip4p
Howto_spc

324
doc/src/Howto_amoeba.rst Normal file
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@ -0,0 +1,324 @@
AMOEBA and HIPPO force fields
=============================
The AMOEBA and HIPPO polarizable force fields were developed by Jay
Ponder's group at the U Washington at St Louis. Their implementation
in LAMMPS was done using F90 code provided by the Ponder group from
their `Tinker MD code <https://dasher.wustl.edu/tinker/>`_.
The current implementation (July 2022) of AMOEBA in LAMMPS matches the
version discussed in :ref:`(Ponder) <amoeba-Ponder>`, :ref:`(Ren)
<amoeba-Ren>`, and :ref:`(Shi) <amoeba-Shi>`. Likewise the current
implementation of HIPPO in LAMMPS matches the version discussed in
:ref:`(Rackers) <amoeba-Rackers>`.
These force fields can be used when polarization effects are desired
in simulations of water, organic molecules, and biomolecules including
proteins, provided that parameterizations (Tinker PRM force field
files) are available for the systems you are interested in. Files in
the LAMMPS potentials directory with a "amoeba" or "hippo" suffix can
be used. The Tinker distribution and website have additional force
field files as well:
`https://github.com/TinkerTools/tinker/tree/release/params
<https://github.com/TinkerTools/tinker/tree/release/params>`_.
Note that currently, HIPPO can only be used for water systems, but
HIPPO files for a variety of small organic and biomolecules are in
preparation by the Ponder group. Those force field files will be
included in the LAMMPS distribution when available.
To use the AMOEBA or HIPPO force fields, a simulation must be 3d, and
fully periodic or fully non-periodic, and use an orthogonal (not
triclinic) simulation box.
----------
The AMOEBA and HIPPO force fields contain the following terms in their
energy (U) computation. Further details for AMOEBA equations are in
:ref:`(Ponder) <amoeba-Ponder>`, further details for the HIPPO
equations are in :ref:`(Rackers) <amoeba-Rackers>`.
.. math::
U & = U_{intermolecular} + U_{intramolecular} \\
U_{intermolecular} & = U_{hal} + U_{repulsion} + U_{dispersion} + U_{multipole} + U_{polar} + U_{qxfer} \\
U_{intramolecular} & = U_{bond} + U_{angle} + U_{torsion} + U_{oop} + U_{b\theta} + U_{UB} + U_{pitorsion} + U_{bitorsion}
For intermolecular terms, the AMOEBA force field includes only the
:math:`U_{hal}`, :math:`U_{multipole}`, :math:`U_{polar}` terms. The
HIPPO force field includes all but the :math:`U_{hal}` term. In
LAMMPS, these are all computed by the :doc:`pair_style amoeba or hippo
<pair_style>` command. Note that the :math:`U_{multipole}` and
:math:`U_{polar}` terms in this formula are not the same for the
AMOEBA and HIPPO force fields.
For intramolecular terms, the :math:`U_{bond}`, :math:`U_{angle}`,
:math:`U_{torsion}`, :math:`U_{oop}` terms are computed by the
:doc:`bond_style class2 <bond_class2>` :doc:`angle_style amoeba
<angle_amoeba>`, :doc:`dihedral_style fourier <dihedral_fourier>`, and
:doc:`improper_style amoeba <improper_amoeba>` commands respectively.
The :doc:`angle_style amoeba <angle_amoeba>` command includes the
:math:`U_{b\theta}` bond-angle cross term, and the :math:`U_{UB}` term
for a Urey-Bradley bond contribution between the I,K atoms in the IJK
angle.
The :math:`U_{pitorsion}` term is computed by the :doc:`fix
amoeba/pitorsion <fix_amoeba_pitorsion>` command. It computes 6-body
interaction between a pair of bonded atoms which each have 2
additional bond partners.
The :math:`U_{bitorsion}` term is computed by the :doc:`fix
amoeba/bitorsion <fix_amoeba_bitorsion>` command. It computes 5-body
interaction between two 4-body torsions (dihedrals) which overlap,
having 3 atoms in common.
These command doc pages have additional details on the terms they
compute:
* :doc:`pair_style amoeba or hippo <pair_amoeba>`
* :doc:`bond_style class2 <bond_class2>`
* :doc:`angle_style amoeba <angle_amoeba>`
* :doc:`dihedral_style fourier <dihedral_fourier>`
* :doc:`improper_style amoeba <improper_amoeba>`
* :doc:`fix amoeba/pitorsion <fix_amoeba_pitorsion>`
* :doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>`
----------
To use the AMOEBA or HIPPO force fields in LAMMPS, use commands like
the following appropriately in your input script. The only change
needed for AMOEBA vs HIPPO simulation is for the :doc:`pair_style
<pair_style>` and :doc:`pair_coeff <pair_coeff>` commands, as shown
below. See examples/amoeba for example input scripts for both AMOEBA
and HIPPO.
.. code-block:: LAMMPS
units real # required
atom_style amoeba
bond_style class2 # CLASS2 package
angle_style amoeba
dihedral_style fourier # EXTRA-MOLECULE package
improper_style amoeba
# required per-atom data
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 polaxe all property/atom i_polaxe
fix pit all amoeba/pitorsion # PiTorsion terms in FF
fix_modify pit energy yes
# Bitorsion terms in FF
fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
fix_modify bit energy yes
read_data data.ubiquitin fix amtype NULL "Tinker Types" &
fix pit "pitorsion types" "PiTorsion Coeffs" &
fix pit pitorsions PiTorsions &
fix bit bitorsions BiTorsions
pair_style amoeba # AMOEBA FF
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
pair_style hippo # HIPPO FF
pair_coeff * * hippo_water.prm hippo_water.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes # 1-5 neighbors
The data file read by the :doc:`read_data <read_data>` command should
be created by the tools/tinker/tinker2lmp.py conversion program
described below. It will create a section in the data file with the
header "Tinker Types". A :doc:`fix property/atom <fix_property_atom>`
command for the data must be specified before the read_data command.
In the example above the fix ID is *amtype*.
Similarly, if the system you are simulating defines AMOEBA/HIPPO
pitorsion or bitorsion interactions, there will be entries in the data
file for those interactions. They require a :doc:`fix
amoeba/pitortion <fix_amoeba_pitorsion>` and :doc:`fix
amoeba/bitorsion <fix_amoeba_bitorsion>` command be defined. In the
example above, the IDs for these two fixes are *pit* and *bit*.
Of course, if the system being modeled does not have one or more of
the following -- bond, angle, dihedral, improper, pitorsion,
bitorsion interactions -- then the corresponding style and fix
commands above do not need to be used. See the example scripts in
examples/amoeba for water systems as examples; they are simpler than
what is listed above.
The two :doc:`fix property/atom <fix_property_atom>` commands with IDs
(in the example above) *extra* and *polaxe* are also needed to define
internal per-atom quantities used by the AMOEBA and HIPPO force
fields.
The :doc:`pair_coeff <pair_coeff>` command used for either the AMOEBA
or HIPPO force field takes two arguments for Tinker force field files,
namely a PRM and KEY file. The keyfile can be specified as NULL and
default values for a various settings will be used. Note that these 2
files are meant to allow use of native Tinker files as-is. However
LAMMPS does not support all the options which can be included
in a Tinker PRM or KEY file. See specifics below.
A :doc:`special_bonds <special_bonds>` command with the *one/five*
option is required, since the AMOEBA/HIPPO force fields define
weighting factors for not only 1-2, 1-3, 1-4 interactions, but also
1-5 interactions. This command will trigger a per-atom list of 1-5
neighbors to be generated. The AMOEBA and HIPPO force fields define
their own custom weighting factors for all the 1-2, 1-3, 1-4, 1-5
terms which in the Tinker PRM and KEY files; they can be different for
different terms in the force field.
In addition to the list above, these command doc pages have additional
details:
* :doc:`atom_style amoeba <atom_style>`
* :doc:`fix property/atom <fix_property_atom>`
* :doc:`special_bonds <special_bonds>`
----------
Tinker PRM and KEY files
A Tinker PRM file is composed of sections, each of which has multiple
lines. This is the list of PRM sections LAMMPS knows how to parse and
use. Any other sections are skipped:
* Angle Bending Parameters
* Atom Type Definitions
* Atomic Multipole Parameters
* Bond Stretching Parameters
* Charge Penetration Parameters
* Charge Transfer Parameters
* Dipole Polarizability Parameters
* Dispersion Parameters
* Force Field Definition
* Literature References
* Out-of-Plane Bend Parameters
* Pauli Repulsion Parameters
* Pi-Torsion Parameters
* Stretch-Bend Parameters
* Torsion-Torsion Parameters
* Torsional Parameters
* Urey-Bradley Parameters
* Van der Waals Pair Parameters
* Van der Waals Parameters
A Tinker KEY file is composed of lines, each of which has a keyword
followed by zero or more parameters. This is the list of keywords
LAMMPS knows how to parse and use in the same manner Tinker does. Any
other keywords are skipped. The value in parenthesis is the default
value for the keyword if it is not specified, or if the keyfile in the
:doc:`pair_coeff <pair_coeff>` command is specified as NULL:
* a-axis (0.0)
* b-axis (0.0)
* c-axis (0.0)
* ctrn-cutoff (6.0)
* ctrn-taper (0.9 * ctrn-cutoff)
* cutoff
* delta-halgren (0.07)
* dewald (no long-range dispersion unless specified)
* dewald-alpha (0.4)
* dewald-cutoff (7.0)
* dispersion-cutoff (9.0)
* dispersion-taper (9.0 * dispersion-cutoff)
* dpme-grid
* dpme-order (4)
* ewald (no long-range electrostatics unless specified)
* ewald-alpha (0.4)
* ewald-cutoff (7.0)
* gamma-halgren (0.12)
* mpole-cutoff (9.0)
* mpole-taper (0.65 * mpole-cutoff)
* pcg-guess (enabled by default)
* pcg-noguess (disable pcg-guess if specified)
* pcg-noprecond (disable pcg-precond if specified)
* pcg-peek (1.0)
* pcg-precond (enabled by default)
* pewald-alpha (0.4)
* pme-grid
* pme-order (5)
* polar-eps (1.0e-6)
* polar-iter (100)
* polar-predict (no prediction operation unless specified)
* ppme-order (5)
* repulsion-cutoff (6.0)
* repulsion-taper (0.9 * repulsion-cutoff)
* taper
* usolve-cutoff (4.5)
* usolve-diag (2.0)
* vdw-cutoff (9.0)
* vdw-taper (0.9 * vdw-cutoff)
----------
Tinker2lmp.py tool
This conversion tool is found in the tools/tinker directory.
As shown in examples/amoeba/README, these commands produce
the data files found in examples/amoeba, and also illustrate
all the options available to use with the tinker2lmp.py script:
.. code-block:: bash
% python tinker2lmp.py -xyz water_dimer.xyz -amoeba amoeba_water.prm -data data.water_dimer.amoeba # AMOEBA non-periodic system
% python tinker2lmp.py -xyz water_dimer.xyz -hippo hippo_water.prm -data data.water_dimer.hippo # HIPPO non-periodic system
% python tinker2lmp.py -xyz water_box.xyz -amoeba amoeba_water.prm -data data.water_box.amoeba -pbc 18.643 18.643 18.643 # AMOEBA periodic system
% python tinker2lmp.py -xyz water_box.xyz -hippo hippo_water.prm -data data.water_box.hippo -pbc 18.643 18.643 18.643 # HIPPO periodic system
% python tinker2lmp.py -xyz ubiquitin.xyz -amoeba amoeba_ubiquitin.prm -data data.ubiquitin.new -pbc 54.99 41.91 41.91 -bitorsion bitorsion.ubiquitin.data.new # system with bitorsions
Switches and their arguments may be specified in any order.
The -xyz switch is required and specifies an input XYZ file as an
argument. The format of this file is an extended XYZ format defined
and used by Tinker for its input. Example \*.xyz files are in the
examples/amoeba directory. The file lists the atoms in the system.
Each atom has the following information: Tinker species name (ignored
by LAMMPS), xyz coordinates, Tinker numeric type, and a list of atom
IDs the atom is bonded to.
Here is more information about the extended XYZ format defined and
used by Tinker, and links to programs that convert standard PDB files
to the extended XYZ format:
* `http://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html <http://openbabel.org/docs/current/FileFormats/Tinker_XYZ_format.html>`_
* `https://github.com/emleddin/pdbxyz-xyzpdb <https://github.com/emleddin/pdbxyz-xyzpdb>`_
* `https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f <https://github.com/TinkerTools/tinker/blob/release/source/pdbxyz.f>`_
The -amoeba or -hippo switch is required. It specifies an input
AMOEBA or HIPPO PRM force field file as an argument. This should be
the same file used by the :doc:`pair_style <pair_style>` command in
the input script.
The -data switch is required. It specifies an output file name for
the LAMMPS data file that will be produced.
For periodic systems, the -pbc switch is required. It specifies the
periodic box size for each dimension (x,y,z). For a Tinker simulation
these are specified in the KEY file.
The -bitorsion switch is only needed if the system contains Tinker
bitorsion interactions. The data for each type of bitorsion
interaction will be written to the specified file, and read by the
:doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>` command. The data
includes 2d arrays of values to which splines are fit, and thus is not
compatible with the LAMMPS data file format.
----------
.. _howto-Ponder:
**(Ponder)** Ponder, Wu, Ren, Pande, Chodera, Schnieders, Haque, Mobley, Lambrecht, DiStasio Jr, M. Head-Gordon, Clark, Johnson, T. Head-Gordon, J Phys Chem B, 114, 2549-2564 (2010).
.. _howto-Rackers:
**(Rackers)** Rackers, Silva, Wang, Ponder, J Chem Theory Comput, 17, 7056-7084 (2021).
.. _howto-Ren:
**(Ren)** Ren and Ponder, J Phys Chem B, 107, 5933 (2003).
.. _howto-Shi:
**(Shi)** Shi, Xia, Zhang, Best, Wu, Ponder, Ren, J Chem Theory Comp, 9, 4046, 2013.

45
doc/src/Packages_details.rst
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@ -27,6 +27,7 @@ page gives those details.
:columns: 6
* :ref:`ADIOS <PKG-ADIOS>`
* :ref:`AMOEBA <PKG-AMOEBA>`
* :ref:`ASPHERE <PKG-ASPHERE>`
* :ref:`ATC <PKG-ATC>`
* :ref:`AWPMD <PKG-AWPMD>`
@ -35,7 +36,7 @@ page gives those details.
* :ref:`BPM <PKG-BPM>`
* :ref:`BROWNIAN <PKG-BROWNIAN>`
* :ref:`CG-DNA <PKG-CG-DNA>`
* :ref:`CG-SDK <PKG-CG-SDK>`
* :ref:`CG-SPICA <PKG-CG-SPICA>`
* :ref:`CLASS2 <PKG-CLASS2>`
* :ref:`COLLOID <PKG-COLLOID>`
* :ref:`COLVARS <PKG-COLVARS>`
@ -149,6 +150,24 @@ This package has :ref:`specific installation instructions <adios>` on the :doc:`
----------
.. _PKG-AMOEBA:
AMOEBA package
---------------
**Contents:**
TODO
**Supporting info:**
* src/AMOEBA: filenames -> commands
* :doc:`AMOEBA and HIPPO howto <Howto_amoeba>`
* examples/amoeba
* TODO
----------
.. _PKG-ASPHERE:
ASPHERE package
@ -365,28 +384,30 @@ The CG-DNA package requires that also the `MOLECULE <PKG-MOLECULE>`_ and
----------
.. _PKG-CG-SDK:
.. _PKG-CG-SPICA:
CG-SDK package
CG-SPICA package
------------------
**Contents:**
Several pair styles and an angle style which implement the
coarse-grained SDK model of Shinoda, DeVane, and Klein which enables
simulation of ionic liquids, electrolytes, lipids and charged amino
acids.
coarse-grained SPICA (formerly called SDK) model which enables
simulation of biological or soft material systems.
**Author:** Axel Kohlmeyer (Temple U).
**Original Author:** Axel Kohlmeyer (Temple U).
**Maintainers:** Yusuke Miyazaki and Wataru Shinoda (Okayama U).
**Supporting info:**
* src/CG-SDK: filenames -> commands
* src/CG-SDK/README
* :doc:`pair_style lj/sdk/\* <pair_sdk>`
* :doc:`angle_style sdk <angle_sdk>`
* examples/PACKAGES/cgsdk
* src/CG-SPICA: filenames -> commands
* src/CG-SPICA/README
* :doc:`pair_style lj/spica/\* <pair_spica>`
* :doc:`angle_style spica <angle_spica>`
* examples/PACKAGES/cgspica
* https://www.lammps.org/pictures.html#cg
* https://www.spica-ff.org/
----------

13
doc/src/Packages_list.rst
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@ -33,6 +33,11 @@ whether an extra library is needed to build and use the package:
- :doc:`dump adios <dump_adios>`
- PACKAGES/adios
- ext
* - :ref:`AMOEBA <PKG-AMOEBA>`
- AMOEBA and HIPPO force fields
- :doc:`AMOEBA and HIPPO howto <Howto_amoeba>`
- amoeba
- no
* - :ref:`ASPHERE <PKG-ASPHERE>`
- aspherical particle models
- :doc:`Howto spherical <Howto_spherical>`
@ -73,10 +78,10 @@ whether an extra library is needed to build and use the package:
- src/CG-DNA/README
- PACKAGES/cgdna
- no
* - :ref:`CG-SDK <PKG-CG-SDK>`
- SDK coarse-graining model
- :doc:`pair_style lj/sdk <pair_sdk>`
- PACKAGES/cgsdk
* - :ref:`CG-SPICA <PKG-CG-SPICA>`
- SPICA (SDK) coarse-graining model
- :doc:`pair_style lj/spica <pair_spica>`
- PACKAGES/cgspica
- no
* - :ref:`CLASS2 <PKG-CLASS2>`
- class 2 force fields

138
doc/src/angle_amoeba.rst Normal file
View File

@ -0,0 +1,138 @@
.. index:: angle_style amoeba
angle_style amoeba command
==========================
Syntax
""""""
.. code-block:: LAMMPS
angle_style amoeba
Examples
""""""""
.. code-block:: LAMMPS
angle_style amoeba
angle_coeff * 75.0 -25.0 1.0 0.3 0.02 0.003
angle_coeff * ba 3.6551 24.895 1.0119 1.5228
angle_coeff * ub -7.6 1.5537
Description
"""""""""""
The *amoeba* angle style uses the potential
.. math::
E & = E_a + E_{ba} + E_{ub} \\
E_a & = K_2\left(\theta - \theta_0\right)^2 + K_3\left(\theta - \theta_0\right)^3 + K_4\left(\theta - \theta_0\right)^4 + K_5\left(\theta - \theta_0\right)^5 + K_6\left(\theta - \theta_0\right)^6 \\
E_{ba} & = N_1 (r_{ij} - r_1) (\theta - \theta_0) + N_2(r_{jk} - r_2)(\theta - \theta_0) \\
E_{UB} & = K_{ub} (r_{ik} - r_{ub})^2
where :math:`E_a` is the angle term, :math:`E_{ba}` is a bond-angle
term, :math:`E_{UB}` is a Urey-Bradley bond term, :math:`\theta_0` is
the equilibrium angle, :math:`r_1` and :math:`r_2` are the equilibrium
bond lengths, and :math:`r_{ub}` is the equilibrium Urey-Bradley bond
length.
These formulas match how the Tinker MD code performs its angle
calculations for the AMOEBA and HIPPO force fields. See the
:doc:`Howto amoeba <Howto_amoeba>` page for more information about
the implementation of AMOEBA and HIPPO in LAMMPS.
Note that the :math:`E_a` and :math:`E_{ba}` formulas are identical to
those used for the :doc:`angle_style class2/p6 <angle_class2>`
command, however there is no bond-bond cross term formula for
:math:`E_{bb}`. Additionally, there is a :math:`E_{UB}` term for a
Urey-Bradley bond. It is effectively a harmonic bond between the I
and K atoms of angle IJK, even though that bond is not enumerated in
the "Bonds" section of the data file.
There are also two ways that Tinker computes the angle :math:`\theta`
in the :math:`E_a` formula. The first is the standard way of treating
IJK as an "in-plane" angle. The second is an "out-of-plane" method
which Tinker may use if the center atom J in the angle is bonded to
one additional atom in addition to I and K. In this case, all 4 atoms
are used to compute the :math:`E_a` formula, resulting in forces on
all 4 atoms. In the Tinker PRM file, these 2 options are denoted by
*angle* versus *anglep* entries in the "Angle Bending Parameters"
section of the PRM force field file. The *pflag* coefficient
described below selects between the 2 options.
----------
Coefficients for the :math:`E_a`, :math:`E_{bb}`, and :math:`E_{ub}`
formulas must be defined for each angle type via the :doc:`angle_coeff
<angle_coeff>` command as in the example above, or in the data file or
restart files read by the :doc:`read_data <read_data>` or
:doc:`read_restart <read_restart>` commands.
These are the 8 coefficients for the :math:`E_a` formula:
* pflag = 0 or 1
* ubflag = 0 or 1
* :math:`\theta_0` (degrees)
* :math:`K_2` (energy)
* :math:`K_3` (energy)
* :math:`K_4` (energy)
* :math:`K_5` (energy)
* :math:`K_6` (energy)
A pflag value of 0 vs 1 selects between the "in-plane" and
"out-of-plane" options described above. Ubflag is 1 if there is a
Urey-Bradley term associated with this angle type, else it is 0.
:math:`\theta_0` is specified in degrees, but LAMMPS converts it to
radians internally; hence the various :math:`K` values are effectively
energy per radian\^2 or radian\^3 or radian\^4 or radian\^5 or
radian\^6.
For the :math:`E_{ba}` formula, each line in a :doc:`angle_coeff
<angle_coeff>` command in the input script lists 5 coefficients, the
first of which is "ba" to indicate they are BondAngle coefficients.
In a data file, these coefficients should be listed under a "BondAngle
Coeffs" heading and you must leave out the "ba", i.e. only list 4
coefficients after the angle type.
* ba
* :math:`N_1` (energy/distance\^2)
* :math:`N_2` (energy/distance\^2)
* :math:`r_1` (distance)
* :math:`r_2` (distance)
The :math:`\theta_0` value in the :math:`E_{ba}` formula is not specified,
since it is the same value from the :math:`E_a` formula.
For the :math:`E_{ub}` formula, each line in a :doc:`angle_coeff
<angle_coeff>` command in the input script lists 3 coefficients, the
first of which is "ub" to indicate they are UreyBradley coefficients.
In a data file, these coefficients should be listed under a
"UreyBradley Coeffs" heading and you must leave out the "ub",
i.e. only list 2 coefficients after the angle type.
* ub
* :math:`K_{ub}` (energy/distance\^2)
* :math:`r_{ub}` (distance)
----------
Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the AMOEBA
package. See the :doc:`Build package <Build_package>` doc page for
more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`
Default
"""""""
none

2
doc/src/angle_class2.rst
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@ -24,7 +24,7 @@ Examples
.. code-block:: LAMMPS
angle_style class2
angle_coeff * 75.0
angle_coeff * 75.0 25.0 0.3 0.002
angle_coeff 1 bb 10.5872 1.0119 1.5228
angle_coeff * ba 3.6551 24.895 1.0119 1.5228

37
doc/src/angle_sdk.rst → doc/src/angle_spica.rst
View File

@ -1,32 +1,32 @@
.. index:: angle_style sdk
.. index:: angle_style sdk/omp
.. index:: angle_style spica
.. index:: angle_style spica/omp
angle_style sdk command
=======================
angle_style spica command
=========================
Accelerator Variants: *sdk/omp*
Accelerator Variants: *spica/omp*
Syntax
""""""
.. code-block:: LAMMPS
angle_style sdk
angle_style spica
angle_style sdk/omp
angle_style spica/omp
Examples
""""""""
.. code-block:: LAMMPS
angle_style sdk
angle_style spica
angle_coeff 1 300.0 107.0
Description
"""""""""""
The *sdk* angle style is a combination of the harmonic angle potential,
The *spica* angle style is a combination of the harmonic angle potential,
.. math::
@ -34,10 +34,10 @@ The *sdk* angle style is a combination of the harmonic angle potential,
where :math:`\theta_0` is the equilibrium value of the angle and
:math:`K` a prefactor, with the *repulsive* part of the non-bonded
*lj/sdk* pair style between the atoms 1 and 3. This angle potential is
intended for coarse grained MD simulations with the CMM parameterization
using the :doc:`pair_style lj/sdk <pair_sdk>`. Relative to the
pair_style *lj/sdk*, however, the energy is shifted by
*lj/spica* pair style between the atoms 1 and 3. This angle potential is
intended for coarse grained MD simulations with the SPICA (formerly called SDK) parameterization
using the :doc:`pair_style lj/spica <pair_spica>`. Relative to the
pair_style *lj/spica*, however, the energy is shifted by
:math:`\epsilon`, to avoid sudden jumps. Note that the usual 1/2 factor
is included in :math:`K`.
@ -51,9 +51,12 @@ The following coefficients must be defined for each angle type via the
radians internally; hence :math:`K` is effectively energy per
radian\^2.
The required *lj/sdk* parameters are extracted automatically from the
The required *lj/spica* parameters are extracted automatically from the
pair_style.
Style *sdk*, the original implementation of style *spica*, is available
for backward compatibility.
----------
.. include:: accel_styles.rst
@ -64,14 +67,14 @@ Restrictions
""""""""""""
This angle style can only be used if LAMMPS was built with the
CG-SDK package. See the :doc:`Build package <Build_package>` doc
CG-SPICA package. See the :doc:`Build package <Build_package>` doc
page for more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style harmonic <angle_harmonic>`, :doc:`pair_style lj/sdk <pair_sdk>`,
:doc:`pair_style lj/sdk/coul/long <pair_sdk>`
:doc:`angle_coeff <angle_coeff>`, :doc:`angle_style harmonic <angle_harmonic>`, :doc:`pair_style lj/spica <pair_spica>`,
:doc:`pair_style lj/spica/coul/long <pair_spica>`
Default
"""""""

3
doc/src/angle_style.rst
View File

@ -73,6 +73,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
* :doc:`zero <angle_zero>` - topology but no interactions
* :doc:`hybrid <angle_hybrid>` - define multiple styles of angle interactions
* :doc:`amoeba <angle_amoeba>` - AMOEBA angle
* :doc:`charmm <angle_charmm>` - CHARMM angle
* :doc:`class2 <angle_class2>` - COMPASS (class 2) angle
* :doc:`class2/p6 <angle_class2>` - COMPASS (class 2) angle expanded to 6th order
@ -91,7 +92,7 @@ of (g,i,k,o,t) to indicate which accelerated styles exist.
* :doc:`harmonic <angle_harmonic>` - harmonic angle
* :doc:`mm3 <angle_mm3>` - anharmonic angle
* :doc:`quartic <angle_quartic>` - angle with cubic and quartic terms
* :doc:`sdk <angle_sdk>` - harmonic angle with repulsive SDK pair style between 1-3 atoms
* :doc:`spica <angle_spica>` - harmonic angle with repulsive SPICA pair style between 1-3 atoms
* :doc:`table <angle_table>` - tabulated by angle
----------

94
doc/src/atom_style.rst
View File

@ -10,7 +10,7 @@ Syntax
atom_style style args
* style = *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *hybrid*
* style = *amoeba* or *angle* or *atomic* or *body* or *bond* or *charge* or *dipole* or *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *hybrid*
.. parsed-literal::
@ -78,6 +78,8 @@ coordinates, velocities, atom IDs and types. See the
:doc:`set <set>` commands for info on how to set these various
quantities.
+--------------+-----------------------------------------------------+--------------------------------------+
| *amoeba* | molecular + charge + 1/5 neighbors | AMOEBA/HIPPO polarized force fields |
+--------------+-----------------------------------------------------+--------------------------------------+
| *angle* | bonds and angles | bead-spring polymers with stiffness |
+--------------+-----------------------------------------------------+--------------------------------------+
@ -137,11 +139,13 @@ quantities.
.. note::
It is possible to add some attributes, such as a molecule ID, to
atom styles that do not have them via the :doc:`fix property/atom <fix_property_atom>` command. This command also
allows new custom attributes consisting of extra integer or
floating-point values to be added to atoms. See the :doc:`fix property/atom <fix_property_atom>` page for examples of cases
where this is useful and details on how to initialize, access, and
output the custom values.
atom styles that do not have them via the :doc:`fix property/atom
<fix_property_atom>` command. This command also allows new custom
attributes consisting of extra integer or floating-point values to
be added to atoms. See the :doc:`fix property/atom
<fix_property_atom>` page for examples of cases where this is
useful and details on how to initialize, access, and output the
custom values.
All of the above styles define point particles, except the *sphere*,
*bpm/sphere*, *ellipsoid*, *electron*, *peri*, *wavepacket*, *line*,
@ -154,19 +158,20 @@ per-type basis, using the :doc:`mass <mass>` command, The finite-size
particle styles assign mass to individual particles on a per-particle
basis.
For the *sphere* and *bpm/sphere* styles, the particles are spheres and each stores a
per-particle diameter and mass. If the diameter > 0.0, the particle
is a finite-size sphere. If the diameter = 0.0, it is a point
particle. Note that by use of the *disc* keyword with the :doc:`fix
nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere <fix_nvt_sphere>`,
:doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix npt/sphere
<fix_npt_sphere>` commands for the *sphere* style, spheres can be effectively treated as 2d
discs for a 2d simulation if desired. See also the :doc:`set
density/disc <set>` command. The *sphere* and *bpm/sphere* styles take an optional 0
or 1 argument. A value of 0 means the radius of each sphere is
constant for the duration of the simulation. A value of 1 means the
radii may vary dynamically during the simulation, e.g. due to use of
the :doc:`fix adapt <fix_adapt>` command.
For the *sphere* and *bpm/sphere* styles, the particles are spheres
and each stores a per-particle diameter and mass. If the diameter >
0.0, the particle is a finite-size sphere. If the diameter = 0.0, it
is a point particle. Note that by use of the *disc* keyword with the
:doc:`fix nve/sphere <fix_nve_sphere>`, :doc:`fix nvt/sphere
<fix_nvt_sphere>`, :doc:`fix nph/sphere <fix_nph_sphere>`, :doc:`fix
npt/sphere <fix_npt_sphere>` commands for the *sphere* style, spheres
can be effectively treated as 2d discs for a 2d simulation if desired.
See also the :doc:`set density/disc <set>` command. The *sphere* and
*bpm/sphere* styles take an optional 0 or 1 argument. A value of 0
means the radius of each sphere is constant for the duration of the
simulation. A value of 1 means the radii may vary dynamically during
the simulation, e.g. due to use of the :doc:`fix adapt <fix_adapt>`
command.
For the *ellipsoid* style, the particles are ellipsoids and each
stores a flag which indicates whether it is a finite-size ellipsoid or
@ -175,15 +180,16 @@ vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
with its orientation.
For the *dielectric* style, each particle can be either a physical
particle (e.g. an ion), or an interface particle representing a boundary
element. For physical particles, the per-particle properties are
the same as atom_style full. For interface particles, in addition to
these properties, each particle also has an area, a normal unit vector,
a mean local curvature, the mean and difference of the dielectric constants
of two sides of the interface, and the local dielectric constant at the
boundary element. The distinction between the physical and interface
particles is only meaningful when :doc:`fix polarize <fix_polarize>`
commands are applied to the interface particles.
particle (e.g. an ion), or an interface particle representing a
boundary element. For physical particles, the per-particle properties
are the same as atom_style full. For interface particles, in addition
to these properties, each particle also has an area, a normal unit
vector, a mean local curvature, the mean and difference of the
dielectric constants of two sides of the interface, and the local
dielectric constant at the boundary element. The distinction between
the physical and interface particles is only meaningful when :doc:`fix
polarize <fix_polarize>` commands are applied to the interface
particles.
For the *dipole* style, a point dipole is defined for each point
particle. Note that if you wish the particles to be finite-size
@ -272,16 +278,17 @@ showing the use of the *template* atom style versus *molecular*.
.. note::
When using the *template* style with a :doc:`molecule template <molecule>` that contains multiple molecules, you should
insure the atom types, bond types, angle_types, etc in all the
molecules are consistent. E.g. if one molecule represents H2O and
another CO2, then you probably do not want each molecule file to
define 2 atom types and a single bond type, because they will conflict
with each other when a mixture system of H2O and CO2 molecules is
defined, e.g. by the :doc:`read_data <read_data>` command. Rather the
H2O molecule should define atom types 1 and 2, and bond type 1. And
the CO2 molecule should define atom types 3 and 4 (or atom types 3 and
2 if a single oxygen type is desired), and bond type 2.
When using the *template* style with a :doc:`molecule template
<molecule>` that contains multiple molecules, you should insure the
atom types, bond types, angle_types, etc in all the molecules are
consistent. E.g. if one molecule represents H2O and another CO2,
then you probably do not want each molecule file to define 2 atom
types and a single bond type, because they will conflict with each
other when a mixture system of H2O and CO2 molecules is defined,
e.g. by the :doc:`read_data <read_data>` command. Rather the H2O
molecule should define atom types 1 and 2, and bond type 1. And
the CO2 molecule should define atom types 3 and 4 (or atom types 3
and 2 if a single oxygen type is desired), and bond type 2.
For the *body* style, the particles are arbitrary bodies with internal
attributes defined by the "style" of the bodies, which is specified by
@ -339,6 +346,8 @@ Many of the styles listed above are only enabled if LAMMPS was built
with a specific package, as listed below. See the :doc:`Build package
<Build_package>` page for more info.
The *amoeba* style is part of the AMOEBA package.
The *angle*, *bond*, *full*, *molecular*, and *template* styles are
part of the MOLECULE package.
@ -350,9 +359,11 @@ The *dipole* style is part of the DIPOLE package.
The *peri* style is part of the PERI package for Peridynamics.
The *oxdna* style is part of the CG-DNA package for coarse-grained simulation of DNA and RNA.
The *oxdna* style is part of the CG-DNA package for coarse-grained
simulation of DNA and RNA.
The *electron* style is part of the EFF package for :doc:`electronic force fields <pair_eff>`.
The *electron* style is part of the EFF package for :doc:`electronic
force fields <pair_eff>`.
The *dpd* style is part of the DPD-REACT package for dissipative
particle dynamics (DPD).
@ -363,7 +374,8 @@ dissipative particle dynamics (mDPD), and transport dissipative particle
dynamics (tDPD), respectively.
The *sph* style is part of the SPH package for smoothed particle
hydrodynamics (SPH). See `this PDF guide <PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
hydrodynamics (SPH). See `this PDF guide
<PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
The *mesont* style is part of the MESONT package.

10
doc/src/compute_contact_atom.rst
View File

@ -8,10 +8,11 @@ Syntax
.. parsed-literal::
compute ID group-ID contact/atom
compute ID group-ID contact/atom group2-ID
* ID, group-ID are documented in :doc:`compute <compute>` command
* contact/atom = style name of this compute command
* group2-ID = optional argument to restrict which atoms to consider for contacts (see below)
Examples
""""""""
@ -19,6 +20,7 @@ Examples
.. code-block:: LAMMPS
compute 1 all contact/atom
compute 1 all contact/atom mygroup
Description
"""""""""""
@ -45,6 +47,9 @@ overview of LAMMPS output options.
The per-atom vector values will be a number >= 0.0, as explained
above.
The optional *group2-ID* argument allows to specify from which group atoms
contribute to the coordination number. Default setting is group 'all'.
Restrictions
""""""""""""
@ -63,4 +68,7 @@ Related commands
Default
"""""""
*group2-ID* = all
none

86
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@ -45,7 +45,7 @@ Syntax
* w_1, w_2,... = list of neighbor weights, one for each type
* nx, ny, nz = number of grid points in x, y, and z directions (positive integer)
* zero or more keyword/value pairs may be appended
* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag* or *switchinnerflag* or *sinner* or *dinner*
* keyword = *rmin0* or *switchflag* or *bzeroflag* or *quadraticflag* or *chem* or *bnormflag* or *wselfallflag* or *bikflag* or *switchinnerflag* or *sinner* or *dinner* or *dgradflag*
.. parsed-literal::
@ -68,9 +68,6 @@ Syntax
*wselfallflag* value = *0* or *1*
*0* = self-contribution only for element of central atom
*1* = self-contribution for all elements
*bikflag* value = *0* or *1* (only implemented for compute snap)
*0* = per-atom bispectrum descriptors are summed over atoms
*1* = per-atom bispectrum descriptors are not summed over atoms
*switchinnerflag* value = *0* or *1*
*0* = do not use inner switching function
*1* = use inner switching function
@ -78,6 +75,12 @@ Syntax
*sinnerlist* = *ntypes* values of *Sinner* (distance units)
*dinner* values = *dinnerlist*
*dinnerlist* = *ntypes* values of *Dinner* (distance units)
*bikflag* value = *0* or *1* (only implemented for compute snap)
*0* = descriptors are summed over atoms of each type
*1* = descriptors are listed separately for each atom
*dgradflag* value = *0* or *1* (only implemented for compute snap)
*0* = descriptor gradients are summed over atoms of each type
*1* = descriptor gradients are listed separately for each atom pair
Examples
""""""""
@ -360,15 +363,6 @@ This option is typically used in conjunction with the *chem* keyword,
and LAMMPS will generate a warning if both *chem* and *bnormflag*
are not both set or not both unset.
The keyword *bikflag* determines whether or not to expand the bispectrum
rows of the global array returned by compute snap. If *bikflag* is set
to *1* then the bispectrum row, which is typically the per-atom bispectrum
descriptors :math:`B_{i,k}` summed over all atoms *i* to produce
:math:`B_k`, becomes bispectrum rows equal to the number of atoms. Thus,
the resulting bispectrum rows are :math:`B_{i,k}` instead of just
:math:`B_k`. In this case, the entries in the final column for these rows
are set to zero.
The keyword *switchinnerflag* with value 1
activates an additional radial switching
function similar to :math:`f_c(r)` above, but acting to switch off
@ -393,6 +387,36 @@ When the central atom and the neighbor atom have different types,
the values of :math:`S_{inner}` and :math:`D_{inner}` are
the arithmetic means of the values for both types.
The keywords *bikflag* and *dgradflag* are only used by compute *snap*.
The keyword *bikflag* determines whether or not to list the descriptors
of each atom separately, or sum them together and list in a single row.
If *bikflag* is set
to *0* then a single bispectrum row is used, which contains the per-atom bispectrum
descriptors :math:`B_{i,k}` summed over all atoms *i* to produce
:math:`B_k`. If *bikflag* is set
to *1* this is replaced by a separate per-atom bispectrum row for each atom.
In this case, the entries in the final column for these rows
are set to zero.
The keyword *dgradflag* determines whether to sum atom gradients or list
them separately. If *dgradflag* is set to 0, the bispectrum
descriptor gradients w.r.t. atom *j* are summed over all atoms *i'*
of type *I* (similar to *snad/atom* above).
If *dgradflag* is set to 1, gradients are listed separately for each pair of atoms.
Each row corresponds
to a single term :math:`\frac{\partial {B_{i,k} }}{\partial {r}^a_j}`
where :math:`{r}^a_j` is the *a-th* position coordinate of the atom with global
index *j*. This also changes
the number of columns to be equal to the number of bispectrum components, with 3
additional columns representing the indices :math:`i`, :math:`j`, and :math:`a`,
as explained more in the Output info section below. The option *dgradflag=1*
requires that *bikflag=1*.
.. note::
Using *dgradflag* = 1 produces a global array with :math:`N + 3N^2 + 1` rows
which becomes expensive for systems with more than 1000 atoms.
.. note::
If you have a bonded system, then the settings of :doc:`special_bonds
@ -503,6 +527,42 @@ components. For the purposes of handling contributions to force, virial,
and quadratic combinations, these :math:`N_{elem}^3` sub-blocks are
treated as a single block of :math:`K N_{elem}^3` columns.
If the *bik* keyword is set to 1, the structure of the snap array is expanded.
The first :math:`N` rows of the snap array
correspond to :math:`B_{i,k}` instead of a single row summed over atoms :math:`i`.
In this case, the entries in the final column for these rows
are set to zero. Also, each row contains only non-zero entries for the
columns corresponding to the type of that atom. This is not true in the case
of *dgradflag* keyword = 1 (see below).
If the *dgradflag* keyword is set to 1, this changes the structure of the
global array completely.
Here the *snad/atom* quantities are replaced with rows corresponding to
descriptor gradient components on single atoms:
.. math::
\frac{\partial {B_{i,k} }}{\partial {r}^a_j}
where :math:`{r}^a_j` is the *a-th* position coordinate of the atom with global
index *j*. The rows are
organized in chunks, where each chunk corresponds to an atom with global index
:math:`j`. The rows in an atom :math:`j` chunk correspond to
atoms with global index :math:`i`. The total number of rows for
these descriptor gradients is therefore :math:`3N^2`.
The number of columns is equal to the number of bispectrum components,
plus 3 additional left-most columns representing the global atom indices
:math:`i`, :math:`j`,
and Cartesian direction :math:`a` (0, 1, 2, for x, y, z).
The first 3 columns of the first :math:`N` rows belong to the reference
potential force components. The remaining K columns contain the
:math:`B_{i,k}` per-atom descriptors corresponding to the non-zero entries
obtained when *bikflag* = 1.
The first column of the last row, after the first
:math:`N + 3N^2` rows, contains the reference potential
energy. The virial components are not used with this option. The total number of
rows is therefore :math:`N + 3N^2 + 1` and the number of columns is :math:`K + 3`.
These values can be accessed by any command that uses per-atom values
from a compute as input. See the :doc:`Howto output <Howto_output>` doc
page for an overview of LAMMPS output options. To see how this command

5
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@ -783,6 +783,11 @@ To write gzipped dump files, you must either compile LAMMPS with the
-DLAMMPS_GZIP option or use the styles from the COMPRESS package.
See the :doc:`Build settings <Build_settings>` page for details.
While a dump command is active (i.e. has not been stopped by using
the undump command), no commands may be used that will change the
timestep (e.g. :doc:`reset_timestep <reset_timestep>`). LAMMPS
will terminate with an error otherwise.
The *atom/gz*, *cfg/gz*, *custom/gz*, and *xyz/gz* styles are part of
the COMPRESS package. They are only enabled if LAMMPS was built with
that package. See the :doc:`Build package <Build_package>` page for

4
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@ -171,6 +171,8 @@ accelerated styles exist.
* :doc:`adapt/fep <fix_adapt_fep>` - enhanced version of fix adapt
* :doc:`addforce <fix_addforce>` - add a force to each atom
* :doc:`addtorque <fix_addtorque>` - add a torque to a group of atoms
* :doc:`amoeba/bitorsion <fix_amoeba_bitorsion>` - torsion/torsion terms in AMOEBA force field
* :doc:`amoeba/pitorsion <fix_amoeba_pitorsion>` - 6-body terms in AMOEBA force field
* :doc:`append/atoms <fix_append_atoms>` - append atoms to a running simulation
* :doc:`atc <fix_atc>` - initiates a coupled MD/FE simulation
* :doc:`atom/swap <fix_atom_swap>` - Monte Carlo atom type swapping
@ -194,7 +196,7 @@ accelerated styles exist.
* :doc:`bond/swap <fix_bond_swap>` - Monte Carlo bond swapping
* :doc:`box/relax <fix_box_relax>` - relax box size during energy minimization
* :doc:`charge/regulation <fix_charge_regulation>` - Monte Carlo sampling of charge regulation
* :doc:`cmap <fix_cmap>` - enables CMAP cross-terms of the CHARMM force field
* :doc:`cmap <fix_cmap>` - CMAP torsion/torsion terms in CHARMM force field
* :doc:`colvars <fix_colvars>` - interface to the collective variables "Colvars" library
* :doc:`controller <fix_controller>` - apply control loop feedback mechanism
* :doc:`damping/cundall <fix_damping_cundall>` - Cundall non-viscous damping for granular simulations

166
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@ -0,0 +1,166 @@
.. index:: fix amoeba/bitorsion
fix amoeba/bitorsion command
============================
Syntax
""""""
.. parsed-literal::
fix ID group-ID ameoba/bitorsion filename
* ID, group-ID are documented in :doc:`fix <fix>` command
* amoeba/bitorsion = style name of this fix command
* filename = force-field file with AMOEBA bitorsion coefficients
Examples
""""""""
.. code-block:: LAMMPS
fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
read_data proteinX.data fix bit bitorsions BiTorsions
fix_modify bit energy yes
Description
"""""""""""
This command enables 5-body torsion/torsion interactions to be added
to simulations which use the AMOEBA and HIPPO force fields. It
matches how the Tinker MD code computes its torsion/torsion
interactions for the AMOEBA and HIPPO force fields. See the
:doc:`Howto amoeba <Howto_amoeba>` doc page for more information about
the implementation of AMOEBA and HIPPO in LAMMPS.
Bitorsion interactions add additional potential energy contributions
to pairs of overlapping phi-psi dihedrals of amino-acids, which are
important to properly represent their conformational behavior.
The examples/amoeba directory has a sample input script and data file
for ubiquitin, which illustrates use of the fix amoeba/bitorsion
command.
As in the example above, this fix should be used before reading a data
file that contains a listing of bitorsion interactions. The
*filename* specified should contain the bitorsion parameters for the
AMOEBA or HIPPO force field.
The data file read by the :doc:`read_data <read_data>` command must
contain the topology of all the bitorsion interactions, similar to the
topology data for bonds, angles, dihedrals, etc. Specifically it
should have a line like this in its header section:
.. parsed-literal::
N bitorsions
where N is the number of bitorsion 5-body interactions. It should
also have a section in the body of the data file like this with N
lines:
.. parsed-literal::
BiTorsions
1 1 8 10 12 18 20
2 5 18 20 22 25 27
[...]
N 3 314 315 317 318 330
The first column is an index from 1 to N to enumerate the bitorsion
5-atom tuples; it is ignored by LAMMPS. The second column is the
*type* of the interaction; it is an index into the bitorsion force
field file. The remaining 5 columns are the atom IDs of the atoms in
the two 4-atom dihedrals that overlap to create the bitorsion 5-body
interaction. Note that the *bitorsions* and *BiTorsions* keywords for
the header and body sections match those specified in the
:doc:`read_data <read_data>` command following the data file name.
The data file should be generated by using the
tools/tinker/tinker2lmp.py conversion script which creates a LAMMPS
data file from Tinker input files, including its PRM file which
contains the parameters necessary for computing bitorsion
interactions. The script must be invoked with the optional
"-bitorsion" flag to do this; see the example for the ubiquitin system
in the tools/tinker/README file. The same conversion script also
creates the file of bitorsion coefficient data which is read by this
command.
The potential energy associated with bitorsion interactions can be
output as described below. It can also be included in the total
potential energy of the system, as output by the :doc:`thermo_style
<thermo_style>` command, if the :doc:`fix_modify energy <fix_modify>`
command is used, as in the example above. See the note below about
how to include the bitorsion energy when performing an :doc:`energy
minimization <minimize>`.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix writes the list of bitorsion interactions to :doc:`binary
restart files <restart>`. See the :doc:`read_restart <read_restart>`
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
this fix to add the potential energy of the bitorsion interactions to
both the global potential energy and peratom potential energies of the
system as part of :doc:`thermodynamic output <thermo_style>` or output
by the :doc:`compute pe/atom <compute_pe_atom>` command. The default
setting for this fix is :doc:`fix_modify energy yes <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the bitorsion interactions to
both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute
stress/atom <compute_stress_atom>` commands. The former can be
accessed by :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the potential
energy discussed above. The scalar value calculated by this fix is
"extensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.
The forces due to this fix are imposed during an energy minimization,
invoked by the :doc:`minimize <minimize>` command.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA
<run_style>` integrator the fix is adding its forces. Default is the
outermost level.
.. note::
For energy minimization, if you want the potential energy
associated with the bitorsion terms forces to be included in the
total potential energy of the system (the quantity being
minimized), you MUST not disable the :doc:`fix_modify <fix_modify>`
*energy* option for this fix.
Restrictions
""""""""""""
To function as expected this fix command must be issued *before* a
:doc:`read_data <read_data>` command but *after* a :doc:`read_restart
<read_restart>` command.
This fix can only be used if LAMMPS was built with the AMOEBA package.
See the :doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`fix_modify <fix_modify>`, :doc:`read_data <read_data>`
Default
"""""""
none

178
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@ -0,0 +1,178 @@
.. index:: fix amoeba/pitorsion
fix amoeba/pitorsion command
============================
Syntax
""""""
.. parsed-literal::
fix ID group-ID ameoba/pitorsion
* ID, group-ID are documented in :doc:`fix <fix>` command
* amoeba/pitorsion = style name of this fix command
Examples
""""""""
.. code-block:: LAMMPS
fix pit all amoeba/pitorsion
read_data proteinX.data fix pit "pitorsion types" "PiTorsion Coeffs" &
fix pit pitorsions PiTorsions
fix_modify pit energy yes
Description
"""""""""""
This command enables 6-body pitorsion interactions to be added to
simulations which use the AMOEBA and HIPPO force fields. It matches
how the Tinker MD code computes its pitorsion interactions for the
AMOEBA and HIPPO force fields. See the :doc:`Howto amoeba
<Howto_amoeba>` doc page for more information about the implementation
of AMOEBA and HIPPO in LAMMPS.
Pitorsion interactions add additional potential energy contributions
to 6-tuples of atoms IJKLMN which have a bond between atoms K and L,
where both K and L are additionally bonded to exactly two other atoms.
Namely K is also bonded to I and J. And L is also bonded to M and N.
The examples/amoeba directory has a sample input script and data file
for ubiquitin, which illustrates use of the fix amoeba/pitorsion
command.
As in the example above, this fix should be used before reading a data
file that contains a listing of pitorsion interactions.
The data file read by the :doc:`read_data <read_data>` command must
contain the topology of all the pitorsion interactions, similar to the
topology data for bonds, angles, dihedrals, etc. Specifically it
should have two lines like these in its header section:
.. parsed-literal::
M pitorsion types
N pitorsions
where N is the number of pitorsion 5-body interactions and M is the
number of pitorsion types. It should also have two sections in the body
of the data file like these with M and N lines each:
.. parsed-literal::
PiTorsion Coeffs
1 6.85
2 10.2
[...]
M 6.85
.. parsed-literal::
PiTorsions
1 1 8 10 12 18 20
2 5 18 20 22 25 27
[...]
N 3 314 315 317 318 330
For PiTorsion Coeffs, the first column is an index from 1 to M to
enumerate the pitorsion types. The second column is the single
prefactor coefficient needed for each type.
For PiTorsions, the first column is an index from 1 to N to enumerate
the pitorsion 5-atom tuples; it is ignored by LAMMPS. The second
column is the "type" of the interaction; it is an index into the
PiTorsion Coeffs. The remaining 5 columns are the atom IDs of the
atoms in the two 4-atom dihedrals that overlap to create the pitorsion
5-body interaction.
Note that the *pitorsion types* and *pitorsions* and *PiTorsion
Coeffs* and *PiTorsions* keywords for the header and body sections of
the data file match those specified in the :doc:`read_data
<read_data>` command following the data file name.
The data file should be generated by using the
tools/tinker/tinker2lmp.py conversion script which creates a LAMMPS
data file from Tinker input files, including its PRM file which
contains the parameters necessary for computing pitorsion
interactions.
The potential energy associated with pitorsion interactions can be
output as described below. It can also be included in the total
potential energy of the system, as output by the :doc:`thermo_style
<thermo_style>` command, if the :doc:`fix_modify energy <fix_modify>`
command is used, as in the example above. See the note below about
how to include the pitorsion energy when performing an :doc:`energy
minimization <minimize>`.
----------
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
This fix writes the list of pitorsion interactions to :doc:`binary
restart files <restart>`. See the :doc:`read_restart <read_restart>`
command for info on how to re-specify a fix in an input script that
reads a restart file, so that the operation of the fix continues in an
uninterrupted fashion.
The :doc:`fix_modify <fix_modify>` *energy* option is supported by
this fix to add the potential energy of the pitorsion interactions to
both the global potential energy and peratom potential energies of the
system as part of :doc:`thermodynamic output <thermo_style>` or output
by the :doc:`compute pe/atom <compute_pe_atom>` command. The default
setting for this fix is :doc:`fix_modify energy yes <fix_modify>`.
The :doc:`fix_modify <fix_modify>` *virial* option is supported by
this fix to add the contribution due to the pitorsion interactions to
both the global pressure and per-atom stress of the system via the
:doc:`compute pressure <compute_pressure>` and :doc:`compute
stress/atom <compute_stress_atom>` commands. The former can be
accessed by :doc:`thermodynamic output <thermo_style>`. The default
setting for this fix is :doc:`fix_modify virial yes <fix_modify>`.
This fix computes a global scalar which can be accessed by various
:doc:`output commands <Howto_output>`. The scalar is the potential
energy discussed above. The scalar value calculated by this fix is
"extensive".
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.
The forces due to this fix are imposed during an energy minimization,
invoked by the :doc:`minimize <minimize>` command.
The :doc:`fix_modify <fix_modify>` *respa* option is supported by this
fix. This allows to set at which level of the :doc:`r-RESPA
<run_style>` integrator the fix is adding its forces. Default is the
outermost level.
.. note::
For energy minimization, if you want the potential energy
associated with the pitorsion terms forces to be included in the
total potential energy of the system (the quantity being
minimized), you MUST not disable the :doc:`fix_modify <fix_modify>`
*energy* option for this fix.
Restrictions
""""""""""""
To function as expected this fix command must be issued *before* a
:doc:`read_data <read_data>` command but *after* a :doc:`read_restart
<read_restart>` command.
This fix can only be used if LAMMPS was built with the AMOEBA package.
See the :doc:`Build package <Build_package>` page for more info.
Related commands
""""""""""""""""
:doc:`fix_modify <fix_modify>`, :doc:`read_data <read_data>`
Default
"""""""
none

66
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@ -26,13 +26,13 @@ Examples
Description
"""""""""""
This command enables CMAP cross-terms to be added to simulations which
use the CHARMM force field. These are relevant for any CHARMM model
of a peptide or protein sequences that is 3 or more amino-acid
residues long; see :ref:`(Buck) <Buck>` and :ref:`(Brooks) <Brooks2>`
for details, including the analytic energy expressions for CMAP
interactions. The CMAP cross-terms add additional potential energy
contributions to pairs of overlapping phi-psi dihedrals of
This command enables CMAP 5-body interactions to be added to
simulations which use the CHARMM force field. These are relevant for
any CHARMM model of a peptide or protein sequences that is 3 or more
amino-acid residues long; see :ref:`(Buck) <Buck>` and :ref:`(Brooks)
<Brooks2>` for details, including the analytic energy expressions for
CMAP interactions. The CMAP 5-body terms add additional potential
energy contributions to pairs of overlapping phi-psi dihedrals of
amino-acids, which are important to properly represent their
conformational behavior.
@ -47,15 +47,15 @@ lammps/potentials directory: charmm22.cmap and charmm36.cmap.
The data file read by the "read_data" must contain the topology of all
the CMAP interactions, similar to the topology data for bonds, angles,
dihedrals, etc. Specially it should have a line like this
in its header section:
dihedrals, etc. Specially it should have a line like this in its
header section:
.. parsed-literal::
N crossterms
where N is the number of CMAP cross-terms. It should also have a section
in the body of the data file like this with N lines:
where N is the number of CMAP 5-body interactions. It should also
have a section in the body of the data file like this with N lines:
.. parsed-literal::
@ -66,28 +66,29 @@ in the body of the data file like this with N lines:
[...]
N 3 314 315 317 318 330
The first column is an index from 1 to N to enumerate the CMAP terms;
it is ignored by LAMMPS. The second column is the "type" of the
interaction; it is an index into the CMAP force field file. The
The first column is an index from 1 to N to enumerate the CMAP 5-atom
tuples; it is ignored by LAMMPS. The second column is the "type" of
the interaction; it is an index into the CMAP force field file. The
remaining 5 columns are the atom IDs of the atoms in the two 4-atom
dihedrals that overlap to create the CMAP 5-body interaction. Note
that the "crossterm" and "CMAP" keywords for the header and body
sections match those specified in the read_data command following the
data file name; see the :doc:`read_data <read_data>` page for
more details.
dihedrals that overlap to create the CMAP interaction. Note that the
"crossterm" and "CMAP" keywords for the header and body sections match
those specified in the read_data command following the data file name;
see the :doc:`read_data <read_data>` page for more details.
A data file containing CMAP cross-terms can be generated from a PDB
file using the charmm2lammps.pl script in the tools/ch2lmp directory
of the LAMMPS distribution. The script must be invoked with the
optional "-cmap" flag to do this; see the tools/ch2lmp/README file for
more information.
A data file containing CMAP 5-body interactions can be generated from
a PDB file using the charmm2lammps.pl script in the tools/ch2lmp
directory of the LAMMPS distribution. The script must be invoked with
the optional "-cmap" flag to do this; see the tools/ch2lmp/README file
for more information. The same conversion script also creates the
file of CMAP coefficient data which is read by this command.
The potential energy associated with CMAP interactions can be output
as described below. It can also be included in the total potential
energy of the system, as output by the
:doc:`thermo_style <thermo_style>` command, if the :doc:`fix_modify energy <fix_modify>` command is used, as in the example above. See
the note below about how to include the CMAP energy when performing an
:doc:`energy minimization <minimize>`.
energy of the system, as output by the :doc:`thermo_style
<thermo_style>` command, if the :doc:`fix_modify energy <fix_modify>`
command is used, as in the example above. See the note below about
how to include the CMAP energy when performing an :doc:`energy
minimization <minimize>`.
----------
@ -134,10 +135,11 @@ outermost level.
.. note::
If you want the potential energy associated with the CMAP terms
forces to be included in the total potential energy of the system
(the quantity being minimized), you MUST not disable the
:doc:`fix_modify <fix_modify>` *energy* option for this fix.
For energy minimization, if you want the potential energy
associated with the CMAP terms forces to be included in the total
potential energy of the system (the quantity being minimized), you
MUST not disable the :doc:`fix_modify <fix_modify>` *energy* option
for this fix.
Restrictions
""""""""""""

54
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@ -20,7 +20,7 @@ Syntax
* Nfreq = calculate average bond-order every this many timesteps
* filename = name of output file
* zero or more keyword/value pairs may be appended
* keyword = *cutoff* or *element* or *position*
* keyword = *cutoff* or *element* or *position* or *delete*
.. parsed-literal::
@ -31,6 +31,14 @@ Syntax
*position* value = posfreq filepos
posfreq = write position files every this many timestep
filepos = name of position output file
*delete* value = filedel keyword value
filedel = name of delete species output file
keyword = *specieslist* or *masslimit*
*specieslist* value = Nspecies Species1 Species2 ...
Nspecies = number of species in list
*masslimit* value = massmin massmax
massmin = minimum molecular weight of species to delete
massmax = maximum molecular weight of species to delete
Examples
""""""""
@ -40,6 +48,7 @@ Examples
fix 1 all reaxff/species 10 10 100 species.out
fix 1 all reaxff/species 1 2 20 species.out cutoff 1 1 0.40 cutoff 1 2 0.55
fix 1 all reaxff/species 1 100 100 species.out element Au O H position 1000 AuOH.pos
fix 1 all reaxff/species 1 100 100 species.out delete species.del masslimit 0 50
Description
"""""""""""
@ -59,13 +68,18 @@ the first line.
.. warning::
In order to compute averaged data, it is required that there are no
neighbor list rebuilds between the *Nfreq* steps. For that reason, fix
*reaxff/species* may change your neighbor list settings. There will
be a warning message showing the new settings. Having an *Nfreq*
setting that is larger than what is required for correct computation
of the ReaxFF force field interactions can thus lead to incorrect
results. For typical ReaxFF calculations a value of 100 is already
quite large.
neighbor list rebuilds for at least Nrepeat\*Nevery steps preceding
each *Nfreq* step. For that reason, fix *reaxff/species* may
change your neighbor list settings. Reneighboring will occur no
more frequently than every Nrepeat\*Nevery timesteps, and will
occur less frequently if *Nfreq* is not a multiple of
Nrepeat\*Nevery. There will be a warning message showing the new
settings. Having a *Nfreq* setting that is larger than what is
required for correct computation of the ReaxFF force field
interactions, in combination with certain *Nrepeat* and *Nevery*
settings, can thus lead to incorrect results. For typical ReaxFF
calculations, reneighboring only every 100 steps is already quite a
low frequency.
If the filename ends with ".gz", the output file is written in gzipped
format. A gzipped dump file will be about 3x smaller than the text version,
@ -104,6 +118,30 @@ character appears in *filepos*, then one file per snapshot is written
at *posfreq* and the "\*" character is replaced with the timestep
value. For example, AuO.pos.\* becomes AuO.pos.0, AuO.pos.1000, etc.
The optional keyword *delete* enables the periodic removal of
molecules from the system. Criteria for deletion can be either a list
of specific chemical formulae or a range of molecular weights.
Molecules are deleted every *Nfreq* timesteps, and bond connectivity
is determined using the *Nevery* and *Nrepeat* keywords. The
*filedel* argument is the name of the output file that records the
species that are removed from the system. The *specieslist* keyword
permits specific chemical species to be deleted. The *Nspecies*
argument specifies how many species are eligible for deletion and is
followed by a list of chemical formulae, whose strings are compared to
species identified by this fix. For example, "specieslist 2 CO CO2"
deletes molecules that are identified as "CO" and "CO2" in the species
output file. When using the *specieslist* keyword, the *filedel* file
has the following format: the first line lists the chemical formulae
eligible for deletion, and each additional line contains the timestep
on which a molecule deletion occurs and the number of each species
deleted on that timestep. The *masslimit* keyword permits deletion of
molecules with molecular weights between *massmin* and *massmax*.
When using the *masslimit* keyword, each line of the *filedel* file
contains the timestep on which deletions occurs, followed by how many
of each species are deleted (with quantities preceding chemical
formulae). The *specieslist* and *masslimit* keywords cannot both be
used in the same *reaxff/species* fix.
----------
The *Nevery*, *Nrepeat*, and *Nfreq* arguments specify on what

77
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@ -0,0 +1,77 @@
.. index:: improper_style amoeba
improper_style harmonic command
===============================
Syntax
""""""
.. code-block:: LAMMPS
improper_style amoeba
Examples
""""""""
.. code-block:: LAMMPS
improper_style amoeba
improper_coeff 1 49.6
Description
"""""""""""
The *amoeba* improper style uses the potential
.. math::
E = K (\chi)^2
where :math:`\chi` is the improper angle and :math:`K` is a prefactor.
Note that the usual 1/2 factor is included in :math:`K`.
This formula seems like a simplified version of the formula for the
:doc:`improper_style harmonic <improper_harmonic>` command with
:math:`\chi_0` = 0.0. However the computation of the angle
:math:`\chi` is done differently to match how the Tinker MD code
computes its out-of-plane improper for the AMOEBA and HIPPO force
fields. See the :doc:`Howto amoeba <Howto_amoeba>` doc page for more
information about the implementation of AMOEBA and HIPPO in LAMMPS.
If the 4 atoms in an improper quadruplet (listed in the data file read
by the :doc:`read_data <read_data>` command are ordered I,J,K,L then
atoms I,K,L are considered to lie in a plane and atom J is
out-of-place. The angle :math:`\chi_0` is computed as the Allinger
angle which is defined as the angle between the plane of I,K,L, and
the vector from atom I to atom J.
The following coefficient must be defined for each improper type via
the :doc:`improper_coeff <improper_coeff>` command as in the example
above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands:
* :math:`K` (energy)
Note that the angle :math:`\chi` is computed in radians; hence
:math:`K` is effectively energy per radian\^2.
----------
Restrictions
""""""""""""
This improper style can only be used if LAMMPS was built with the
AMOEBA package. See the :doc:`Build package <Build_package>` doc page
for more info.
Related commands
""""""""""""""""
:doc:`improper_coeff <improper_coeff>`, `improper_harmonic
:doc:<improper_harmonic>`
Default
"""""""
none

1
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@ -77,6 +77,7 @@ more of (g,i,k,o,t) to indicate which accelerated styles exist.
* :doc:`zero <improper_zero>` - topology but no interactions
* :doc:`hybrid <improper_hybrid>` - define multiple styles of improper interactions
* :doc:`amoeba <improper_amoeba>` - AMOEBA out-of-plane improper
* :doc:`class2 <improper_class2>` - COMPASS (class 2) improper
* :doc:`cossq <improper_cossq>` - improper with a cosine squared term
* :doc:`cvff <improper_cvff>` - CVFF improper

17
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@ -29,15 +29,16 @@ Examples
Description
"""""""""""
The *kim command* includes a set of sub-commands that allow LAMMPS users to use
interatomic models (IM) (potentials and force fields) and their predictions for
various physical properties archived in the
`Open Knowledgebase of Interatomic Models (OpenKIM) <https://openkim.org>`_
repository.
The *kim command* includes a set of sub-commands that allow LAMMPS
users to use interatomic models (IM) (potentials and force fields) and
their predictions for various physical properties archived in the
`Open Knowledgebase of Interatomic Models (OpenKIM)
<https://openkim.org>`_ repository.
Using OpenKIM provides LAMMPS users with immediate access to a large number of
verified IMs and their predictions. OpenKIM IMs have multiple benefits including
`reliability, reproducibility and convenience <https://openkim.org/doc/overview/kim-features/>`_.
Using OpenKIM provides LAMMPS users with immediate access to a large
number of verified IMs and their predictions. OpenKIM IMs have
multiple benefits including `reliability, reproducibility and
convenience <https://openkim.org/doc/overview/kim-features/>`_.
.. _IM_types:

50
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@ -49,29 +49,27 @@ sometimes be faster. Either style should give the same answers.
The *multi* style is a modified binning algorithm that is useful for
systems with a wide range of cutoff distances, e.g. due to different
size particles. For granular pair styles, cutoffs are set to the
sum of the maximum atomic radii for each atom type.
For the *bin* style, the bin size is set to 1/2 of
the largest cutoff distance between any pair of atom types and a
single set of bins is defined to search over for all atom types. This
can be inefficient if one pair of types has a very long cutoff, but
other type pairs have a much shorter cutoff. The *multi* style uses
different sized bins for collections of different sized particles, where
"size" may mean the physical size of the particle or its cutoff
distance for interacting with other particles. Different
size particles. For granular pair styles, cutoffs are set to the sum of
the maximum atomic radii for each atom type. For the *bin* style, the
bin size is set to 1/2 of the largest cutoff distance between any pair
of atom types and a single set of bins is defined to search over for all
atom types. This can be inefficient if one pair of types has a very
long cutoff, but other type pairs have a much shorter cutoff. The
*multi* style uses different sized bins for collections of different
sized particles, where "size" may mean the physical size of the particle
or its cutoff distance for interacting with other particles. Different
sets of bins are then used to construct the neighbor lists as as further
described by Shire, Hanley, and Stratford :ref:`(Shire) <bytype-Shire>`.
This imposes some extra setup overhead, but the searches themselves
may be much faster. By default, each atom type defines a separate
collection of particles. For systems where two or more atom types
have the same size (either physical size or cutoff distance), the
definition of collections can be customized, which can result in less
overhead and faster performance. See the :doc:`neigh_modify <neigh_modify>`
command for how to define custom collections. Whether the collection
definition is customized or not, also see the
:doc:`comm_modify mode multi <comm_modify>` command for communication
options that further improve performance in a manner consistent with
neighbor style multi.
This imposes some extra setup overhead, but the searches themselves may
be much faster. By default, each atom type defines a separate collection
of particles. For systems where two or more atom types have the same
size (either physical size or cutoff distance), the definition of
collections can be customized, which can result in less overhead and
faster performance. See the :doc:`neigh_modify <neigh_modify>` command
for how to define custom collections. Whether the collection definition
is customized or not, also see the :doc:`comm_modify mode multi
<comm_modify>` command for communication options that further improve
performance in a manner consistent with neighbor style multi.
An alternate style, *multi/old*, sets the bin size to 1/2 of the shortest
cutoff distance and multiple sets of bins are defined to search over for
@ -80,6 +78,16 @@ algorithm in LAMMPS but was found to be significantly slower than the new
approach. For now we are keeping the old option in case there are use cases
where multi/old outperforms the new multi style.
.. note::
If there are multiple sub-styles in a :doc:`hybrid/overlay pair style
<pair_hybrid>` that cover the same atom types, but have significantly
different cutoffs, the *multi* style does not apply. Instead, the
:doc:`pair_modify neigh/trim <pair_modify>` setting applies (which is
*yes* by default). Please check the neighbor list summary printed at
the beginning of a calculation to verify that the desired set of
neighbor list builds is performed.
The :doc:`neigh_modify <neigh_modify>` command has additional options
that control how often neighbor lists are built and which pairs are

253
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@ -0,0 +1,253 @@
.. index:: pair_style amoeba
.. index:: pair_style hippo
pair_style amoeba command
=========================
pair_style hippo command
========================
Syntax
""""""
.. code-block:: LAMMPS
pair_style style
* style = *amoeba* or *hippo*
Examples
""""""""
.. code-block:: LAMMPS
pair_style amoeba
pair_coeff * * protein.prm.amoeba protein.key.amoeba
.. code-block:: LAMMPS
pair_style hippo
pair_coeff * * water.prm.hippo water.key.hippo
Additional info
"""""""""""""""
* :doc:`Howto amoeba <Howto_amoeba>`
* examples/amoeba
* tools/amoeba
* potentials/\*.amoeba
* potentials/\*.hippo
Description
"""""""""""
The *amoeba* style computes the AMOEBA polarizable field formulated
by Jay Ponder's group at the U Washington at St Louis :ref:`(Ren)
<amoeba-Ren>`, :ref:`(Shi) <amoeba-Shi>`. The *hippo* style computes
the HIPPO polarizable force field, an extension to AMOEBA, formulated
by Josh Rackers and collaborators in the Ponder group :ref:`(Rackers)
<amoeba-Rackers>`.
These force fields can be used when polarization effects are desired
in simulations of water, organic molecules, and biomolecules including
proteins, provided that parameterizations (Tinker PRM force field
files) are available for the systems you are interested in. Files in
the LAMMPS potentials directory with a "amoeba" or "hippo" suffix can
be used. The Tinker distribution and website have additional force
field files as well.
As discussed on the :doc:`Howto amoeba <Howto_amoeba>` doc page, the
intermolecular (non-bonded) portion of the AMOEBA force field contains
these terms:
.. math::
U_{amoeba} = U_{multipole} + U_{polar} + U_{hal}
while the HIPPO force field contains these terms:
.. math::
U_{hippo} = U_{multipole} + U_{polar} + U_{qxfer} + U_{repulsion} + U_{dispersion}
Conceptually, these terms compute the following interactions:
* :math:`U_{hal}` = buffered 14-7 van der Waals with offsets applied to hydrogen atoms
* :math:`U_{repulsion}` = Pauli repulsion due to rearrangement of electron density
* :math:`U_{dispersion}` = dispersion between correlated, instantaneous induced dipole moments
* :math:`U_{multipole}` = electrostatics between permanent point charges, dipoles, and quadrupoles
* :math:`U_{polar}` = electronic polarization between induced point dipoles
* :math:`U_{qxfer}` = charge transfer effects
Note that the AMOEBA versus HIPPO force fields typically compute the
same term differently using their own formulas. The references on
this doc page give full details for both force fields.
The formulas for the AMOEBA energy terms are:
.. math::
U_{hal} = \epsilon_{ij} \left( \frac{1.07}{\rho_{ij} + 0.07} \right)^7 \left( \frac{1.12}{\rho_{ij}^7 + 0.12} - 2 \right)
U_{multipole} = \vec{M_i}\bold{T_{ij}}\vec{M_j}
\vec{M} = \left( q, \vec{\mu_{perm}}, \bold{\Theta} \right)
U_{polar} = \frac{1}{2}\vec{\mu_i}^{ind} \vec{E_i}^{perm}
The formulas for the HIPPO energy terms are:
.. math::
U_{multipole} = Z_i \frac{1}{r_{ij}} Z_j + Z_i T_{ij}^{damp} \vec{M_j} + Z_j T_{ji}^{damp} \vec{M_i} + \vec{M_i} T_{ij}^{damp} \vec{M_j}
\vec{M} = \left( Q, \vec{\mu_{perm}}, \bold{\Theta} \right)
U_{polar} = \frac{1}{2}\vec{\mu_i}^{ind} \vec{E_i}^{perm}
U_{qxfer} = \epsilon_i e^{-\eta_j r_{ij}} + \epsilon_j e^{-\eta_i r_{ij}}
U_{repulsion} = \frac{K_i K_j}{r_{ij}} S^2
S^2 = \left( \int{\phi_i \phi_j} dv \right)^2 = \vec{M_i}\bold{T_{ij}^{repulsion}}\vec{M_j}
U_{dispersion} = -\frac{C_6^iC_6^j}{r_{ij}^6} \left( f_{damp}^{dispersion} \right)_{ij}^2
.. note::
The AMOEBA and HIPPO force fields compute long-range charge, dipole,
and quadrupole interactions as well as long-range dispersion
effects. However, unlike other models with long-range interactions
in LAMMPS, this does not require use of a KSpace style via the
:doc:`kspace_style <kspace_style>` command. That is because for
AMOEBA and HIPPO the long-range computations are intertwined with
the pairwise computations. So these pair style include both short-
and long-range computations. This means the energy and virial
computed by the pair style as well as the "Pair" timing reported by
LAMMPS will include the long-range calculations.
The implementation of the AMOEBA and HIPPO force fields in LAMMPS was
done using F90 code provided by the Ponder group from their `Tinker MD
code <https://dasher.wustl.edu/tinker/>`_.
The current implementation (July 2022) of AMOEBA in LAMMPS matches the
version discussed in :ref:`(Ponder) <amoeba-Ponder>`, :ref:`(Ren)
<amoeba-Ren>`, and :ref:`(Shi) <amoeba-Shi>`. Likewise the current
implementation of HIPPO in LAMMPS matches the version discussed in
:ref:`(Rackers) <amoeba-Rackers>`.
----------
Only a single pair_coeff command is used with either the *amoeba* and
*hippo* styles which specifies two Tinker files, a PRM and KEY file.
.. code-block:: LAMMPS
pair_coeff * * ../potentials/protein.prm.amoeba ../potentials/protein.key.amoeba
pair_coeff * * ../potentials/water.prm.hippo ../potentials/water.key.hippo
Examples of the PRM files are in the potentials directory with an
\*.amoeba or \*.hippo suffix. The examples/amoeba directory has
examples of both PRM and KEY files.
A Tinker PRM file is composed of sections, each of which has multiple
lines. A Tinker KEY file is composed of lines, each of which has a
keyword followed by zero or more parameters.
The list of PRM sections and KEY keywords which LAMMPS recognizes are
listed on the :doc:`Howto amoeba <Howto_amoeba>` doc page. If not
recognized, the section or keyword is skipped.
Note that if the KEY file is specified as NULL, then no file is
required; default values for various AMOEBA/HIPPO settings are used.
The :doc:`Howto amoeba <Howto_amoeba>` doc page also gives the default
settings.
----------
Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
These pair styles do not support the :doc:`pair_modify <pair_modify>`
mix, shift, table, and tail options.
These pair styles do not write their information to :doc:`binary
restart files <restart>`, since it is stored in potential files.
Thus, you need to re-specify the pair_style and pair_coeff commands in
an input script that reads a restart file.
These pair styles can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. They do not support the
*inner*\ , *middle*\ , *outer* keywords.
----------
Restrictions
""""""""""""
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 and examples/amoeba directories are Tinker
files parameterized for Tinker units. Their numeric parameters are
converted by LAMMPS to its real units :doc:`units <units>`. Thus you
can only use these pair styles with real units.
These potentials do not yet calculate per-atom energy or virial
contributions.
As explained on the :doc:`AMOEBA and HIPPO howto <Howto_amoeba>` page,
use of these pair styles to run a simulation with the AMOEBA or HIPPO
force fields requires several things.
The first is a data file generated by the tools/tinker/tinker2lmp.py
conversion script which uses Tinker file force field file input to
create a data file compatible with LAMMPS.
The second is use of these commands:
* :doc:`atom_style amoeba <atom_style>`
* :doc:`fix property/atom <fix_property_atom>`
* :doc:`special_bonds one/five <special_bonds>`
And third, depending on the model being simulated, these
commands for intramolecular interactions may also be required:
* :doc:`bond_style class2 <bond_class2>`
* :doc:`angle_style amoeba <angle_amoeba>`
* :doc:`dihedral_style fourier <dihedral_fourier>`
* :doc:`improper_style amoeba <improper_amoeba>`
* :doc:`fix amoeba/pitorsion <fix_amoeba_pitorsion>`
* :doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>`
----------
Related commands
""""""""""""""""
:doc:`atom_style amoeba <atom_style>`,
:doc:`bond_style class2 <bond_class2>`,
:doc:`angle_style amoeba <angle_amoeba>`,
:doc:`dihedral_style fourier <dihedral_fourier>`,
:doc:`improper_style amoeba <improper_amoeba>`,
:doc:`fix amoeba/pitorsion <fix_amoeba_pitorsion>`,
:doc:`fix amoeba/bitorsion <fix_amoeba_bitorsion>`,
:doc:`special_bonds one/five <special_bonds>`,
:doc:`fix property/atom <fix_property_atom>`
Default
"""""""
none
----------
.. _amoeba-Ponder:
**(Ponder)** Ponder, Wu, Ren, Pande, Chodera, Schnieders, Haque, Mobley, Lambrecht, DiStasio Jr, M. Head-Gordon, Clark, Johnson, T. Head-Gordon, J Phys Chem B, 114, 2549-2564 (2010).
.. _amoeba-Rackers:
**(Rackers)** Rackers, Silva, Wang, Ponder, J Chem Theory Comput, 17, 7056-7084 (2021).
.. _amoeba-Ren:
**(Ren)** Ren and Ponder, J Phys Chem B, 107, 5933 (2003).
.. _amoeba-Shi:
**(Shi)** Shi, Xia, Zhang, Best, Wu, Ponder, Ren, J Chem Theory Comp, 9, 4046, 2013.

32
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@ -13,7 +13,7 @@ Syntax
* one or more keyword/value pairs may be listed
* keyword = *pair* or *shift* or *mix* or *table* or *table/disp* or *tabinner*
or *tabinner/disp* or *tail* or *compute* or *nofdotr* or *special* or
*compute/tally*
*compute/tally* or *neigh/trim*
.. parsed-literal::
@ -37,6 +37,7 @@ Syntax
which = *lj/coul* or *lj* or *coul*
w1,w2,w3 = 1-2, 1-3, 1-4 weights from 0.0 to 1.0 inclusive
*compute/tally* value = *yes* or *no*
*neigh/trim* value = *yes* or *no*
Examples
""""""""
@ -283,6 +284,31 @@ the *pair* keyword. Use *no* to disable, or *yes* to enable.
The "pair_modify pair compute/tally" command must be issued
**before** the corresponding compute style is defined.
The *neigh/trim* keyword controls whether an explicit cutoff is set for
each neighbor list request issued by individual pair sub-styles when
using :doc:`pair hybrid/overlay <pair_hybrid>`. When this keyword is
set to *no*, then the cutoff of each pair sub-style neighbor list will
be set equal to the largest cutoff, even if a shorter cutoff is
specified for a particular sub-style. If possible the neighbor list
will be copied directly from another list. When this keyword is set to
*yes* then the cutoff of the neighbor list will be explicitly set to the
value requested by the pair sub-style, and if possible the list will be
created by trimming neighbors from another list with a longer cutoff,
otherwise a new neighbor list will be created with the specified cutoff.
The *yes* option can be faster when there are multiple pair styles with
different cutoffs since the number of pair-wise distance checks between
neighbors is reduced (but the time required to build the neighbor lists
is increased). The *no* option could be faster when two or more neighbor
lists have similar (but not exactly the same) cutoffs.
.. note::
The "pair_modify neigh/trim" command *only* applies when there are
multiple pair sub-styles for the same atoms with different cutoffs,
i.e. when using pair style hybrid/overlay. If you have different
cutoffs for different pairs for atoms type, the :doc:`neighbor style
multi <neighbor>` should be used to create optimized neighbor lists.
----------
Restrictions
@ -298,13 +324,13 @@ Related commands
:doc:`pair_style <pair_style>`, :doc:`pair_style hybrid <pair_hybrid>`,
:doc:`pair_coeff <pair_coeff>`, :doc:`thermo_style <thermo_style>`,
:doc:`compute \*/tally <compute_tally>`
:doc:`compute \*/tally <compute_tally>`, :doc:`neighbor multi <neighbor>`
Default
"""""""
The option defaults are mix = geometric, shift = no, table = 12,
tabinner = sqrt(2.0), tail = no, and compute = yes.
tabinner = sqrt(2.0), tail = no, compute = yes, and neigh/trim yes.
Note that some pair styles perform mixing, but only a certain style of
mixing. See the doc pages for individual pair styles for details.

100
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@ -1,27 +1,27 @@
.. index:: pair_style lj/sdk
.. index:: pair_style lj/sdk/gpu
.. index:: pair_style lj/sdk/kk
.. index:: pair_style lj/sdk/omp
.. index:: pair_style lj/sdk/coul/long
.. index:: pair_style lj/sdk/coul/long/gpu
.. index:: pair_style lj/sdk/coul/long/omp
.. index:: pair_style lj/sdk/coul/msm
.. index:: pair_style lj/sdk/coul/msm/omp
.. index:: pair_style lj/spica
.. index:: pair_style lj/spica/gpu
.. index:: pair_style lj/spica/kk
.. index:: pair_style lj/spica/omp
.. index:: pair_style lj/spica/coul/long
.. index:: pair_style lj/spica/coul/long/gpu
.. index:: pair_style lj/spica/coul/long/omp
.. index:: pair_style lj/spica/coul/msm
.. index:: pair_style lj/spica/coul/msm/omp
pair_style lj/sdk command
=========================
pair_style lj/spica command
===========================
Accelerator Variants: *lj/sdk/gpu*, *lj/sdk/kk*, *lj/sdk/omp*
Accelerator Variants: *lj/spica/gpu*, *lj/spica/kk*, *lj/spica/omp*
pair_style lj/sdk/coul/long command
===================================
pair_style lj/spica/coul/long command
=====================================
Accelerator Variants: *lj/sdk/coul/long/gpu*, *lj/sdk/coul/long/omp*
Accelerator Variants: *lj/spica/coul/long/gpu*, *lj/spica/coul/long/omp*
pair_style lj/sdk/coul/msm command
==================================
pair_style lj/spica/coul/msm command
====================================
Accelerator Variants: *lj/sdk/coul/msm/omp*
Accelerator Variants: *lj/spica/coul/msm/omp*
Syntax
""""""
@ -30,14 +30,14 @@ Syntax
pair_style style args
* style = *lj/sdk* or *lj/sdk/coul/long*
* style = *lj/spica* or *lj/spica/coul/long*
* args = list of arguments for a particular style
.. parsed-literal::
*lj/sdk* args = cutoff
*lj/spica* args = cutoff
cutoff = global cutoff for Lennard Jones interactions (distance units)
*lj/sdk/coul/long* args = cutoff (cutoff2)
*lj/spica/coul/long* args = cutoff (cutoff2)
cutoff = global cutoff for LJ (and Coulombic if only 1 arg) (distance units)
cutoff2 = global cutoff for Coulombic (optional) (distance units)
@ -46,21 +46,21 @@ Examples
.. code-block:: LAMMPS
pair_style lj/sdk 2.5
pair_style lj/spica 2.5
pair_coeff 1 1 lj12_6 1 1.1 2.8
pair_style lj/sdk/coul/long 10.0
pair_style lj/sdk/coul/long 10.0 12.0
pair_style lj/spica/coul/long 10.0
pair_style lj/spica/coul/long 10.0 12.0
pair_coeff 1 1 lj9_6 100.0 3.5 12.0
pair_style lj/sdk/coul/msm 10.0
pair_style lj/sdk/coul/msm 10.0 12.0
pair_style lj/spica/coul/msm 10.0
pair_style lj/spica/coul/msm 10.0 12.0
pair_coeff 1 1 lj9_6 100.0 3.5 12.0
Description
"""""""""""
The *lj/sdk* styles compute a 9/6, 12/4, or 12/6 Lennard-Jones potential,
The *lj/spica* styles compute a 9/6, 12/4, 12/5, or 12/6 Lennard-Jones potential,
given by
.. math::
@ -71,14 +71,20 @@ given by
E = & \frac{3\sqrt{3}}{2} \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^4 \right]
\qquad r < r_c \\
E = & \frac{12}{7}\left(\frac{12}{5}\right)^{\left(\frac{5}{7}\right)} \epsilon
\left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^5 \right]
\qquad r < r_c \\
E = & 4 \epsilon \left[ \left(\frac{\sigma}{r}\right)^{12} -
\left(\frac{\sigma}{r}\right)^6 \right]
\qquad r < r_c
as required for the SDK Coarse-grained MD parameterization discussed in
:ref:`(Shinoda) <Shinoda3>` and :ref:`(DeVane) <DeVane>`. Rc is the cutoff.
as required for the SPICA (formerly called SDK) and the pSPICA Coarse-grained MD parameterization discussed in
:ref:`(Shinoda) <Shinoda3>`, :ref:`(DeVane) <DeVane>`, :ref:`(Seo) <Seo>`, and :ref:`(Miyazaki) <Miyazaki>`.
Rc is the cutoff.
Summary information on these force fields can be found at https://www.spica-ff.org
Style *lj/sdk/coul/long* computes the adds Coulombic interactions
Style *lj/spica/coul/long* computes the adds Coulombic interactions
with an additional damping factor applied so it can be used in
conjunction with the :doc:`kspace_style <kspace_style>` command and
its *ewald* or *pppm* or *pppm/cg* option. The Coulombic cutoff
@ -92,7 +98,7 @@ above, or in the data file or restart files read by the
:doc:`read_data <read_data>` or :doc:`read_restart <read_restart>`
commands, or by mixing as described below:
* cg_type (lj9_6, lj12_4, or lj12_6)
* cg_type (lj9_6, lj12_4, lj12_5, or lj12_6)
* epsilon (energy units)
* sigma (distance units)
* cutoff1 (distance units)
@ -108,11 +114,15 @@ and Coulombic interactions for this type pair. If both coefficients
are specified, they are used as the LJ and Coulombic cutoffs for this
type pair.
For *lj/sdk/coul/long* and *lj/sdk/coul/msm* only the LJ cutoff can be
For *lj/spica/coul/long* and *lj/spica/coul/msm* only the LJ cutoff can be
specified since a Coulombic cutoff cannot be specified for an
individual I,J type pair. All type pairs use the same global
Coulombic cutoff specified in the pair_style command.
The original implementation of the above styles are
style *lj/sdk*, *lj/sdk/coul/long*, and *lj/sdk/coul/msm*,
and available for backward compatibility.
----------
.. include:: accel_styles.rst
@ -123,24 +133,24 @@ Mixing, shift, table, tail correction, restart, rRESPA info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
For atom type pairs I,J and I != J, the epsilon and sigma coefficients
and cutoff distance for all of the lj/sdk pair styles *cannot* be mixed,
and cutoff distance for all of the lj/spica pair styles *cannot* be mixed,
since different pairs may have different exponents. So all parameters
for all pairs have to be specified explicitly through the "pair_coeff"
command. Defining then in a data file is also not supported, due to
limitations of that file format.
All of the lj/sdk pair styles support the
All of the lj/spica pair styles support the
:doc:`pair_modify <pair_modify>` shift option for the energy of the
Lennard-Jones portion of the pair interaction.
The *lj/sdk/coul/long* pair styles support the
The *lj/spica/coul/long* pair styles support the
:doc:`pair_modify <pair_modify>` table option since they can tabulate
the short-range portion of the long-range Coulombic interaction.
All of the lj/sdk pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do
All of the lj/spica pair styles write their information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do
not need to be specified in an input script that reads a restart file.
The lj/sdk and lj/cut/coul/long pair styles do not support
The lj/spica and lj/cut/coul/long pair styles do not support
the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style respa <run_style>` command.
----------
@ -148,8 +158,8 @@ the use of the *inner*, *middle*, and *outer* keywords of the :doc:`run_style re
Restrictions
""""""""""""
All of the lj/sdk pair styles are part of the CG-SDK package. The
*lj/sdk/coul/long* style also requires the KSPACE package to be built
All of the lj/spica pair styles are part of the CG-SPICA package. The
*lj/spica/coul/long* style also requires the KSPACE package to be built
(which is enabled by default). They are only enabled if LAMMPS was
built with that package. See the :doc:`Build package <Build_package>`
doc page for more info.
@ -157,7 +167,7 @@ doc page for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`angle_style sdk <angle_sdk>`
:doc:`pair_coeff <pair_coeff>`, :doc:`angle_style spica <angle_spica>`
Default
"""""""
@ -168,8 +178,16 @@ none
.. _Shinoda3:
**(Shinoda)** Shinoda, DeVane, Klein, Mol Sim, 33, 27 (2007).
**(Shinoda)** Shinoda, DeVane, Klein, Mol Sim, 33, 27-36 (2007).
.. _DeVane:
**(DeVane)** Shinoda, DeVane, Klein, Soft Matter, 4, 2453-2462 (2008).
.. _Seo:
**(Seo)** Seo, Shinoda, J Chem Theory Comput, 15, 762-774 (2019).
.. _Miyazaki:
**(Miyazaki)** Miyazaki, Okazaki, Shinoda, J Chem Theory Comput, 16, 782-793 (2020).

8
doc/src/pair_style.rst
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@ -116,6 +116,7 @@ accelerated styles exist.
* :doc:`agni <pair_agni>` - AGNI machine-learning potential
* :doc:`airebo <pair_airebo>` - AIREBO potential of Stuart
* :doc:`airebo/morse <pair_airebo>` - AIREBO with Morse instead of LJ
* :doc:`amoeba <pair_amoeba>` -
* :doc:`atm <pair_atm>` - Axilrod-Teller-Muto potential
* :doc:`awpmd/cut <pair_awpmd>` - Antisymmetrized Wave Packet MD potential for atoms and electrons
* :doc:`beck <pair_beck>` - Beck potential
@ -202,6 +203,7 @@ accelerated styles exist.
* :doc:`hbond/dreiding/lj <pair_hbond_dreiding>` - DREIDING hydrogen bonding LJ potential
* :doc:`hbond/dreiding/morse <pair_hbond_dreiding>` - DREIDING hydrogen bonding Morse potential
* :doc:`hdnnp <pair_hdnnp>` - High-dimensional neural network potential
* :doc:`hippo <pair_amoeba>` -
* :doc:`ilp/graphene/hbn <pair_ilp_graphene_hbn>` - registry-dependent interlayer potential (ILP)
* :doc:`ilp/tmd <pair_ilp_tmd>` - interlayer potential (ILP) potential for transition metal dichalcogenides (TMD)
* :doc:`kim <pair_kim>` - interface to potentials provided by KIM project
@ -258,9 +260,9 @@ accelerated styles exist.
* :doc:`lj/long/tip4p/long <pair_lj_long>` - long-range LJ and long-range Coulomb for TIP4P water
* :doc:`lj/mdf <pair_mdf>` - LJ potential with a taper function
* :doc:`lj/relres <pair_lj_relres>` - LJ using multiscale Relative Resolution (RelRes) methodology :ref:`(Chaimovich) <Chaimovich2>`.
* :doc:`lj/sdk <pair_sdk>` - LJ for SDK coarse-graining
* :doc:`lj/sdk/coul/long <pair_sdk>` - LJ for SDK coarse-graining with long-range Coulomb
* :doc:`lj/sdk/coul/msm <pair_sdk>` - LJ for SDK coarse-graining with long-range Coulomb via MSM
* :doc:`lj/spica <pair_spica>` - LJ for SPICA coarse-graining
* :doc:`lj/spica/coul/long <pair_spica>` - LJ for SPICA coarse-graining with long-range Coulomb
* :doc:`lj/spica/coul/msm <pair_spica>` - LJ for SPICA coarse-graining with long-range Coulomb via MSM
* :doc:`lj/sf/dipole/sf <pair_dipole>` - LJ with dipole interaction with shifted forces
* :doc:`lj/smooth <pair_lj_smooth>` - smoothed Lennard-Jones potential
* :doc:`lj/smooth/linear <pair_lj_smooth_linear>` - linear smoothed LJ potential

141
doc/src/pair_sw.rst
View File

@ -24,13 +24,16 @@ Syntax
pair_style style keyword values
* style = *sw* or *sw/mod*
* keyword = *maxdelcs*
* keyword = *maxdelcs* or *threebody*
.. parsed-literal::
*maxdelcs* value = delta1 delta2 (optional)
*maxdelcs* value = delta1 delta2 (optional, sw/mod only)
delta1 = The minimum thershold for the variation of cosine of three-body angle
delta2 = The maximum threshold for the variation of cosine of three-body angle
*threebody* value = *on* or *off* (optional, sw only)
on (default) = Compute both the three-body and two-body terms of the potential
off = Compute only the two-body term of the potential
Examples
""""""""
@ -44,6 +47,11 @@ Examples
pair_style sw/mod maxdelcs 0.25 0.35
pair_coeff * * tmd.sw.mod Mo S S
pair_style hybrid sw threebody on sw threebody off
pair_coeff * * sw 1 mW_xL.sw mW NULL
pair_coeff 1 2 sw 2 mW_xL.sw mW xL
pair_coeff 2 2 sw 2 mW_xL.sw mW xL
Description
"""""""""""
@ -68,22 +76,25 @@ three-body term. The summations in the formula are over all neighbors J
and K of atom I within a cutoff distance :math:`a `\sigma`.
The *sw/mod* style is designed for simulations of materials when
distinguishing three-body angles are necessary, such as borophene
and transition metal dichalcogenides, which cannot be described
by the original code for the Stillinger-Weber potential.
For instance, there are several types of angles around each Mo atom in `MoS_2`,
and some unnecessary angle types should be excluded in the three-body interaction.
Such exclusion may be realized by selecting proper angle types directly.
The exclusion of unnecessary angles is achieved here by the cut-off function (`f_C(\delta)`),
which induces only minimum modifications for LAMMPS.
distinguishing three-body angles are necessary, such as borophene and
transition metal dichalcogenides, which cannot be described by the
original code for the Stillinger-Weber potential. For instance, there
are several types of angles around each Mo atom in `MoS_2`, and some
unnecessary angle types should be excluded in the three-body
interaction. Such exclusion may be realized by selecting proper angle
types directly. The exclusion of unnecessary angles is achieved here by
the cut-off function (`f_C(\delta)`), which induces only minimum
modifications for LAMMPS.
Validation, benchmark tests, and applications of the *sw/mod* style
can be found in :ref:`(Jiang2) <Jiang2>` and :ref:`(Jiang3) <Jiang3>`.
The *sw/mod* style computes the energy E of a system of atoms, whose potential
function is mostly the same as the Stillinger-Weber potential. The only modification
is in the three-body term, where the value of :math:`\delta = \cos \theta_{ijk} - \cos \theta_{0ijk}`
used in the original energy and force expression is scaled by a switching factor :math:`f_C(\delta)`:
The *sw/mod* style computes the energy E of a system of atoms, whose
potential function is mostly the same as the Stillinger-Weber
potential. The only modification is in the three-body term, where the
value of :math:`\delta = \cos \theta_{ijk} - \cos \theta_{0ijk}` used in
the original energy and force expression is scaled by a switching factor
:math:`f_C(\delta)`:
.. math::
@ -94,28 +105,46 @@ used in the original energy and force expression is scaled by a switching factor
0 & \left| \delta \right| > \delta_2
\end{array} \right. \\
This cut-off function decreases smoothly from 1 to 0 over the range :math:`[\delta_1, \delta_2]`.
This smoothly turns off the energy and force contributions for :math:`\left| \delta \right| > \delta_2`.
It is suggested that :math:`\delta 1` and :math:`\delta_2` to be the value around
:math:`0.5 \left| \cos \theta_1 - \cos \theta_2 \right|`, with
:math:`\theta_1` and :math:`\theta_2` as the different types of angles around an atom.
For borophene and transition metal dichalcogenides, :math:`\delta_1 = 0.25` and :math:`\delta_2 = 0.35`.
This value enables the cut-off function to exclude unnecessary angles in the three-body SW terms.
This cut-off function decreases smoothly from 1 to 0 over the range
:math:`[\delta_1, \delta_2]`. This smoothly turns off the energy and
force contributions for :math:`\left| \delta \right| > \delta_2`. It is
suggested that :math:`\delta 1` and :math:`\delta_2` to be the value
around :math:`0.5 \left| \cos \theta_1 - \cos \theta_2 \right|`, with
:math:`\theta_1` and :math:`\theta_2` as the different types of angles
around an atom. For borophene and transition metal dichalcogenides,
:math:`\delta_1 = 0.25` and :math:`\delta_2 = 0.35`. This value enables
the cut-off function to exclude unnecessary angles in the three-body SW
terms.
.. note::
The cut-off function is just to be used as a technique to exclude some unnecessary angles,
and it has no physical meaning. It should be noted that the force and potential are inconsistent
with each other in the decaying range of the cut-off function, as the angle dependence for the
cut-off function is not implemented in the force (first derivation of potential).
However, the angle variation is much smaller than the given threshold value for actual simulations,
so the inconsistency between potential and force can be neglected in actual simulations.
The cut-off function is just to be used as a technique to exclude
some unnecessary angles, and it has no physical meaning. It should be
noted that the force and potential are inconsistent with each other
in the decaying range of the cut-off function, as the angle
dependence for the cut-off function is not implemented in the force
(first derivation of potential). However, the angle variation is
much smaller than the given threshold value for actual simulations,
so the inconsistency between potential and force can be neglected in
actual simulations.
Only a single pair_coeff command is used with the *sw* and *sw/mod* styles
which specifies a Stillinger-Weber potential file with parameters for all
needed elements. These are mapped to LAMMPS atom types by specifying
N additional arguments after the filename in the pair_coeff command,
where N is the number of LAMMPS atom types:
The *threebody* keyword is optional and determines whether or not the
three-body term of the potential is calculated. The default value is
"on" and it is only available for the plain *sw* pair style variants,
but not available for the *sw/mod* and :doc:`sw/angle/table
<pair_sw_angle_table>` pair style variants. To turn off the threebody
contributions all :math:`\lambda_{ijk}` parameters from the potential
file are forcibly set to 0. In addition the pair style implementation
may employ code optimizations for the *threebody off* setting that can
result in significant speedups versus the default. These code optimizations
are currently only available for the MANYBODY and OPENMP packages.
Only a single pair_coeff command is used with the *sw* and *sw/mod*
styles which specifies a Stillinger-Weber potential file with parameters
for all needed elements, except for when the *threebody off* setting is
used (see note below). These are mapped to LAMMPS atom types by
specifying N additional arguments after the filename in the pair_coeff
command, where N is the number of LAMMPS atom types:
* filename
* N element names = mapping of SW elements to atom types
@ -130,16 +159,22 @@ pair_coeff command:
.. code-block:: LAMMPS
pair_style sw
pair_coeff * * SiC.sw Si Si Si C
The first 2 arguments must be \* \* so as to span all LAMMPS atom types.
The first three Si arguments map LAMMPS atom types 1,2,3 to the Si
element in the SW file. The final C argument maps LAMMPS atom type 4
to the C element in the SW file. If a mapping value is specified as
NULL, the mapping is not performed. This can be used when a *sw*
The first three Si arguments map LAMMPS atom types 1, 2, and 3 to the Si
element in the SW file. The final C argument maps LAMMPS atom type 4 to
the C element in the SW file. If an argument value is specified as
NULL, the mapping is not performed. This can be used when an *sw*
potential is used as part of the *hybrid* pair style. The NULL values
are placeholders for atom types that will be used with other
potentials.
are placeholders for atom types that will be used with other potentials.
.. note::
When the *threebody off* keyword is used, multiple pair_coeff commands may
be used to specific the pairs of atoms which don't require three-body term.
In these cases, the first 2 arguments are not required to be \* \*.
Stillinger-Weber files in the *potentials* directory of the LAMMPS
distribution have a ".sw" suffix. Lines that are not blank or
@ -243,30 +278,39 @@ described above from values in the potential file.
This pair style does not support the :doc:`pair_modify <pair_modify>`
shift, table, and tail options.
This pair style does not write its information to :doc:`binary restart files <restart>`, since it is stored in potential files. Thus, you
need to re-specify the pair_style and pair_coeff commands in an input
script that reads a restart file.
This pair style does not write its information to :doc:`binary restart
files <restart>`, since it is stored in potential files. Thus, you need
to re-specify the pair_style and pair_coeff commands in an input script
that reads a restart file.
This pair style can only be used via the *pair* keyword of the
:doc:`run_style respa <run_style>` command. It does not support the
*inner*, *middle*, *outer* keywords.
The single() function of the *sw* pair style is only enabled and
supported for the case of the *threebody off* setting.
----------
Restrictions
""""""""""""
This pair style is part of the MANYBODY package. It is only enabled
if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
This pair style is part of the MANYBODY package. It is only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
This pair style requires the :doc:`newton <newton>` setting to be "on"
for pair interactions.
The Stillinger-Weber potential files provided with LAMMPS (see the
potentials directory) are parameterized for metal :doc:`units <units>`.
You can use the SW potential with any LAMMPS units, but you would need
to create your own SW potential file with coefficients listed in the
appropriate units if your simulation does not use "metal" units.
You can use the sw or sw/mod pair styles with any LAMMPS units, but you
would need to create your own SW potential file with coefficients listed
in the appropriate units if your simulation does not use "metal" units.
If the potential file contains a 'UNITS:' metadata tag in the first line
of the potential file, then LAMMPS can convert it transparently between
"metal" and "real" units.
Related commands
""""""""""""""""
@ -276,8 +320,9 @@ Related commands
Default
"""""""
The default values for the *maxdelcs* setting of the *sw/mod* pair
style are *delta1* = 0.25 and *delta2* = 0.35`.
The default value for the *threebody* setting of the "sw" pair style is
"on", the default values for the "*maxdelcs* setting of the *sw/mod*
pair style are *delta1* = 0.25 and *delta2* = 0.35`.
----------

3
doc/src/pair_sw_angle_table.rst
View File

@ -296,7 +296,8 @@ for pair interactions.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style sw <pair_sw>`, :doc:`pair_style threebody/table <pair_threebody_table>`
:doc:`pair_coeff <pair_coeff>`, :doc:`pair_style sw <pair_sw>`,
:doc:`pair_style threebody/table <pair_threebody_table>`
----------

35
doc/src/read_dump.rst
View File

@ -24,12 +24,13 @@ Syntax
*fx*,\ *fy*,\ *fz* = force components
* zero or more keyword/value pairs may be appended
* keyword = *nfile* or *box* or *replace* or *purge* or *trim* or *add* or *label* or *scaled* or *wrapped* or *format*
* keyword = *nfile* or *box* or *timestep* or *replace* or *purge* or *trim* or *add* or *label* or *scaled* or *wrapped* or *format*
.. parsed-literal::
*nfile* value = Nfiles = how many parallel dump files exist
*box* value = *yes* or *no* = replace simulation box with dump box
*timestep* value = *yes* or *no* = reset simulation timestep with dump timestep
*replace* value = *yes* or *no* = overwrite atoms with dump atoms
*purge* value = *yes* or *no* = delete all atoms before adding dump atoms
*trim* value = *yes* or *no* = trim atoms not in dump snapshot
@ -60,6 +61,7 @@ Examples
read_dump dump.dcd 0 x y z box yes format molfile dcd
read_dump dump.file 1000 x y z vx vy vz box yes format molfile lammpstrj /usr/local/lib/vmd/plugins/LINUXAMD64/plugins/molfile
read_dump dump.file 5000 x y vx vy trim yes
read_dump dump.file 5000 x y vx vy add yes box no timestep no
read_dump ../run7/dump.file.gz 10000 x y z box yes
read_dump dump.xyz 10 x y z box no format molfile xyz ../plugins
read_dump dump.dcd 0 x y z format molfile dcd
@ -71,9 +73,9 @@ Description
"""""""""""
Read atom information from a dump file to overwrite the current atom
coordinates, and optionally the atom velocities and image flags and
the simulation box dimensions. This is useful for restarting a run
from a particular snapshot in a dump file. See the
coordinates, and optionally the atom velocities and image flags, the
simulation timestep, and the simulation box dimensions. This is useful
for restarting a run from a particular snapshot in a dump file. See the
:doc:`read_restart <read_restart>` and :doc:`read_data <read_data>`
commands for alternative methods to do this. Also see the
:doc:`rerun <rerun>` command for a means of reading multiple snapshots
@ -89,9 +91,9 @@ Also note that reading per-atom information from a dump snapshot is
limited to the atom coordinates, velocities and image flags, as
explained below. Other atom properties, which may be necessary to run
a valid simulation, such as atom charge, or bond topology information
for a molecular system, are not read from (or even contained in) dump
files. Thus this auxiliary information should be defined in the usual
way, e.g. in a data file read in by a :doc:`read_data <read_data>`
for a molecular system, are not read from (or may not even be contained
in) dump files. Thus this auxiliary information should be defined in
the usual way, e.g. in a data file read in by a :doc:`read_data <read_data>`
command, before using the read_dump command, or by the :doc:`set <set>`
command, after the dump snapshot is read.
@ -165,11 +167,10 @@ variable *ntimestep*:
uint64_t ntimestep 5*scalar
(0) 0 50 100 150 200
Note that the *xyz*
and *molfile* formats do not store the timestep. For these formats,
timesteps are numbered logically, in a sequential manner, starting
from 0. Thus to access the 10th snapshot in an *xyz* or *mofile*
formatted dump file, use *Nstep* = 9.
Note that the *xyz* and *molfile* formats do not store the timestep.
For these formats, timesteps are numbered logically, in a sequential
manner, starting from 0. Thus to access the 10th snapshot in an *xyz*
or *mofile* formatted dump file, use *Nstep* = 9.
The dimensions of the simulation box for the selected snapshot are
also read; see the *box* keyword discussion below. For the *native*
@ -266,8 +267,10 @@ for how this is done, determined by the specified fields and optional
keywords.
The timestep of the snapshot becomes the current timestep for the
simulation. See the :doc:`reset_timestep <reset_timestep>` command if
you wish to change this after the dump snapshot is read.
simulation unless the *timestep* keyword is specified with a *no* value
(default setting is *yes*). See the :doc:`reset_timestep <reset_timestep>`
command if you wish to change this to a different value after the dump
snapshot is read.
If the *box* keyword is specified with a *yes* value, then the current
simulation box dimensions are replaced by the dump snapshot box
@ -391,7 +394,7 @@ Related commands
Default
"""""""
The option defaults are box = yes, replace = yes, purge = no, trim =
no, add = no, scaled = no, wrapped = yes, and format = native.
The option defaults are box = yes, timestep = yes, replace = yes, purge = no,
trim = no, add = no, scaled = no, wrapped = yes, and format = native.
.. _vmd: http://www.ks.uiuc.edu/Research/vmd

104
doc/src/special_bonds.rst
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@ -11,7 +11,7 @@ Syntax
special_bonds keyword values ...
* one or more keyword/value pairs may be appended
* keyword = *amber* or *charmm* or *dreiding* or *fene* or *lj/coul* or *lj* or *coul* or *angle* or *dihedral*
* keyword = *amber* or *charmm* or *dreiding* or *fene* or *lj/coul* or *lj* or *coul* or *angle* or *dihedral* or *one/five*
.. parsed-literal::
@ -27,6 +27,7 @@ Syntax
w1,w2,w3 = weights (0.0 to 1.0) on pairwise Coulombic interactions
*angle* value = *yes* or *no*
*dihedral* value = *yes* or *no*
*one/five* value = *yes* or *no*
Examples
""""""""
@ -45,10 +46,10 @@ Description
Set weighting coefficients for pairwise energy and force contributions
between pairs of atoms that are also permanently bonded to each other,
either directly or via one or two intermediate bonds. These weighting
factors are used by nearly all :doc:`pair styles <pair_style>` in LAMMPS
that compute simple pairwise interactions. Permanent bonds between
atoms are specified by defining the bond topology in the data file
read by the :doc:`read_data <read_data>` command. Typically a
factors are used by nearly all :doc:`pair styles <pair_style>` in
LAMMPS that compute simple pairwise interactions. Permanent bonds
between atoms are specified by defining the bond topology in the data
file read by the :doc:`read_data <read_data>` command. Typically a
:doc:`bond_style <bond_style>` command is also used to define a bond
potential. The rationale for using these weighting factors is that
the interaction between a pair of bonded atoms is all (or mostly)
@ -58,31 +59,34 @@ atoms should be excluded (or reduced by a weighting factor).
.. note::
These weighting factors are NOT used by :doc:`pair styles <pair_style>` that compute many-body interactions, since the
"bonds" that result from such interactions are not permanent, but are
created and broken dynamically as atom conformations change. Examples
of pair styles in this category are EAM, MEAM, Stillinger-Weber,
Tersoff, COMB, AIREBO, and ReaxFF. In fact, it generally makes no
sense to define permanent bonds between atoms that interact via these
potentials, though such bonds may exist elsewhere in your system,
e.g. when using the :doc:`pair_style hybrid <pair_hybrid>` command.
Thus LAMMPS ignores special_bonds settings when many-body potentials
are calculated. Please note, that the existence of explicit bonds
for atoms that are described by a many-body potential will alter the
neighbor list and thus can render the computation of those interactions
invalid, since those pairs are not only used to determine direct
pairwise interactions but also neighbors of neighbors and more.
The recommended course of action is to remove such bonds, or - if
that is not possible - use a special bonds setting of 1.0 1.0 1.0.
These weighting factors are NOT used by :doc:`pair styles
<pair_style>` that compute many-body interactions, since the
"bonds" that result from such interactions are not permanent, but
are created and broken dynamically as atom conformations change.
Examples of pair styles in this category are EAM, MEAM,
Stillinger-Weber, Tersoff, COMB, AIREBO, and ReaxFF. In fact, it
generally makes no sense to define permanent bonds between atoms
that interact via these potentials, though such bonds may exist
elsewhere in your system, e.g. when using the :doc:`pair_style
hybrid <pair_hybrid>` command. Thus LAMMPS ignores special_bonds
settings when many-body potentials are calculated. Please note,
that the existence of explicit bonds for atoms that are described
by a many-body potential will alter the neighbor list and thus can
render the computation of those interactions invalid, since those
pairs are not only used to determine direct pairwise interactions
but also neighbors of neighbors and more. The recommended course
of action is to remove such bonds, or - if that is not possible -
use a special bonds setting of 1.0 1.0 1.0.
.. note::
Unlike some commands in LAMMPS, you cannot use this command
multiple times in an incremental fashion: e.g. to first set the LJ
settings and then the Coulombic ones. Each time you use this command
it sets all the coefficients to default values and only overrides the
one you specify, so you should set all the options you need each time
you use it. See more details at the bottom of this page.
settings and then the Coulombic ones. Each time you use this
command it sets all the coefficients to default values and only
overrides the one you specify, so you should set all the options
you need each time you use it. See more details at the bottom of
this page.
The Coulomb factors are applied to any Coulomb (charge interaction)
term that the potential calculates. The LJ factors are applied to the
@ -94,14 +98,14 @@ exclude it completely.
The first of the 3 coefficients (LJ or Coulombic) is the weighting
factor on 1-2 atom pairs, which are pairs of atoms directly bonded to
each other. The second coefficient is the weighting factor on 1-3 atom
pairs which are those separated by 2 bonds (e.g. the two H atoms in a
water molecule). The third coefficient is the weighting factor on 1-4
atom pairs which are those separated by 3 bonds (e.g. the first and fourth
atoms in a dihedral interaction). Thus if the 1-2 coefficient is set
to 0.0, then the pairwise interaction is effectively turned off for
all pairs of atoms bonded to each other. If it is set to 1.0, then
that interaction will be at full strength.
each other. The second coefficient is the weighting factor on 1-3
atom pairs which are those separated by 2 bonds (e.g. the two H atoms
in a water molecule). The third coefficient is the weighting factor
on 1-4 atom pairs which are those separated by 3 bonds (e.g. the first
and fourth atoms in a dihedral interaction). Thus if the 1-2
coefficient is set to 0.0, then the pairwise interaction is
effectively turned off for all pairs of atoms bonded to each other.
If it is set to 1.0, then that interaction will be at full strength.
.. note::
@ -184,21 +188,27 @@ interaction between atoms 2 and 5 will be unaffected (full weighting
of 1.0). If the *dihedral* keyword is specified as *no* which is the
default, then the 2,5 interaction will also be weighted by 0.5.
The *one/five* keyword enable calculation and storage of a list of 1-5
neighbors in the molecular topology for each atom. It is required by
some pair styles, such as :doc:`pair_style amoeba <pair_style>` and
:doc:`pair_style hippo <pair_style>`.
----------
.. note::
LAMMPS stores and maintains a data structure with a list of the
first, second, and third neighbors of each atom (within the bond topology of
the system). If new bonds are created (or molecules added containing
atoms with more special neighbors), the size of this list needs to
grow. Note that adding a single bond always adds a new first neighbor
but may also induce \*many\* new second and third neighbors, depending on the
molecular topology of your system. Using the *extra/special/per/atom*
keyword to either :doc:`read_data <read_data>` or :doc:`create_box <create_box>`
reserves empty space in the list for this N additional first, second, or third
neighbors to be added. If you do not do this, you may get an error
when bonds (or molecules) are added.
first, second, and third neighbors of each atom (within the bond
topology of the system). If new bonds are created (or molecules
added containing atoms with more special neighbors), the size of
this list needs to grow. Note that adding a single bond always
adds a new first neighbor but may also induce \*many\* new second
and third neighbors, depending on the molecular topology of your
system. Using the *extra/special/per/atom* keyword to either
:doc:`read_data <read_data>` or :doc:`create_box <create_box>`
reserves empty space in the list for this N additional first,
second, or third neighbors to be added. If you do not do this, you
may get an error when bonds (or molecules) are added.
----------
@ -226,16 +236,16 @@ In the first case you end up with (after the second command):
LJ: 0.0 0.0 0.0
Coul: 0.0 0.0 1.0
while only in the second case, you get the desired settings of:
while only in the second case do you get the desired settings of:
.. parsed-literal::
LJ: 0.0 1.0 1.0
Coul: 0.0 0.0 1.0
This happens because the LJ (and Coul) settings are reset to
their default values before modifying them, each time the
*special_bonds* command is issued.
This happens because the LJ (and Coul) settings are reset to their
default values before modifying them, each time the *special_bonds*
command is issued.
Restrictions
""""""""""""

11
doc/utils/check-styles.py
View File

@ -254,8 +254,9 @@ for command_type, entries in index.items():
print("Total number of style index entries:", total_index)
skip_angle = ('sdk')
skip_fix = ('python', 'NEIGH_HISTORY/omp','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species')
skip_pair = ('meam/c','lj/sf','reax/c')
skip_pair = ('meam/c','lj/sf','reax/c','lj/sdk','lj/sdk/coul/long','lj/sdk/coul/msm')
skip_compute = ('pressure/cylinder')
counter = 0
@ -269,8 +270,8 @@ counter += check_style('Commands_pair.rst', doc_dir, ":doc:`(.+) <pair.+>`",pair
counter += check_style('pair_style.rst', doc_dir, ":doc:`(.+) <pair.+>` -",pair,'Pair',skip=skip_pair,suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <bond.+>`",bond,'Bond',suffix=True)
counter += check_style('bond_style.rst', doc_dir, ":doc:`(.+) <bond.+>` -",bond,'Bond',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <angle.+>`",angle,'Angle',suffix=True)
counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) <angle.+>` -",angle,'Angle',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <angle.+>`",angle,'Angle',skip=skip_angle,suffix=True)
counter += check_style('angle_style.rst', doc_dir, ":doc:`(.+) <angle.+>` -",angle,'Angle',skip=skip_angle,suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <dihedral.+>`",dihedral,'Dihedral',suffix=True)
counter += check_style('dihedral_style.rst', doc_dir, ":doc:`(.+) <dihedral.+>` -",dihedral,'Dihedral',suffix=False)
counter += check_style('Commands_bond.rst', doc_dir, ":doc:`(.+) <improper.+>`",improper,'Improper',suffix=True)
@ -284,12 +285,12 @@ counter = 0
counter += check_style_index("compute", compute, index["compute"], skip=['pressure/cylinder'])
counter += check_style_index("fix", fix, index["fix"], skip=['python','acks2/reax','qeq/reax','reax/c/bonds','reax/c/species'])
counter += check_style_index("angle_style", angle, index["angle_style"])
counter += check_style_index("angle_style", angle, index["angle_style"], skip=['sdk'])
counter += check_style_index("bond_style", bond, index["bond_style"])
counter += check_style_index("dihedral_style", dihedral, index["dihedral_style"])
counter += check_style_index("improper_style", improper, index["improper_style"])
counter += check_style_index("kspace_style", kspace, index["kspace_style"])
counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c', 'lj/sf','reax/c'])
counter += check_style_index("pair_style", pair, index["pair_style"], skip=['meam/c','lj/sf','reax/c','lj/sdk','lj/sdk/coul/long','lj/sdk/coul/msm'])
if counter:
print(f"Found {counter} issue(s) with style index")

44
doc/utils/sphinx-config/false_positives.txt
View File

@ -269,6 +269,7 @@ binutils
biomolecular
biomolecule
Biomolecules
biomolecules
Biophys
Biosym
biquadratic
@ -278,6 +279,7 @@ Bispectrum
bitbucket
bitmapped
bitmask
bitorsion
bitrate
bitrates
Bitzek
@ -421,6 +423,8 @@ CGDNA
cgs
cgsdk
CGSDK
cgspica
CGSPICA
Chaimovich
Chalopin
Champaign
@ -443,6 +447,7 @@ chiralIDs
ChiralIDs
chirality
Cho
Chodera
ChooseOffset
chris
Christoph
@ -577,6 +582,7 @@ cstring
cstyle
csvr
ctrl
ctrn
ctypes
Ctypes
cuda
@ -697,6 +703,7 @@ devel
Devemy
deviatoric
Devine
dewald
df
dfftw
DFT
@ -774,6 +781,7 @@ DPD
dpdTheta
dphi
DPhil
dpme
dr
dR
dragforce
@ -1277,6 +1285,7 @@ gzipped
Haak
Hafskjold
halfstepback
halgren
Halperin
Halver
Hamaker
@ -1284,6 +1293,7 @@ Hamel
Hammerschmidt
Hanley
haptic
Haque
Hara
Harpertown
Harting
@ -1627,6 +1637,7 @@ Kemper
kepler
keV
Keyes
keyfile
Khersonskii
Khrapak
Khvostov
@ -1702,6 +1713,7 @@ Ladd
lagrangian
lambdai
LambdaLanczos
Lambrecht
lamda
lammps
Lammps
@ -2076,6 +2088,7 @@ Mishin
Mishra
mistyped
mistyrose
Miyazaki
Mj
mK
mkdir
@ -2087,6 +2100,7 @@ mlparks
Mniszewski
mnt
mobi
Mobley
modc
Modell
modelled
@ -2137,6 +2151,7 @@ mpiexec
mpiio
mpirun
mplayer
mpole
mps
mradius
Mrovec
@ -2171,6 +2186,7 @@ multicore
multielectron
multinode
multiphysics
Multipole
multiscale
multisectioning
multithreading
@ -2358,6 +2374,7 @@ nodesets
Noehring
Noffset
noforce
noguess
Noid
nolib
nonequilibrium
@ -2366,6 +2383,7 @@ nonGaussian
nonlocal
Nonlocal
Noordhoek
noprecond
nopreliminary
Nord
norder
@ -2471,6 +2489,7 @@ ohenrich
ok
Okabe
Okamoto
Okazaki
O'Keefe
OKeefe
oldlace
@ -2542,6 +2561,7 @@ palegreen
paleturquoise
palevioletred
Panagiotopoulos
Pande
Pandit
Papaconstantopoulos
papayawhip
@ -2576,6 +2596,7 @@ Pavia
Paxton
pbc
pc
pcg
pchain
Pchain
pcmoves
@ -2609,7 +2630,9 @@ Persp
peru
Peskin
Pettifor
pewald
pfactor
pflag
pgi
ph
Philipp
@ -2642,6 +2665,7 @@ pIp
Pisarev
Pishevar
Pitera
pitorsion
pj
pjintve
pKa
@ -2657,6 +2681,7 @@ plt
plumedfile
pmb
pmcmoves
pme
Pmolrotate
Pmoltrans
pN
@ -2681,6 +2706,7 @@ polyelectrolyte
polyhedra
Polym
polymorphism
Ponder
popen
Popoola
Popov
@ -2699,6 +2725,7 @@ potin
Pourtois
powderblue
PowerShell
ppme
ppn
pppm
Prakash
@ -2708,6 +2735,7 @@ pre
Pre
prec
precession
precond
prefactor
prefactors
prepend
@ -2729,6 +2757,7 @@ pscrozi
pseudodynamics
pseudopotential
pSp
pSPICA
Pstart
Pstop
pstyle
@ -2802,6 +2831,8 @@ Qsb
qtb
quadratically
quadrupolar
quadrupole
quadrupoles
Quant
quartic
quat
@ -2818,6 +2849,7 @@ qw
qx
qy
qz
Rackers
radialscreened
radialscreenedspin
radialspin
@ -3057,6 +3089,7 @@ Schimansky
Schiotz
Schlitter
Schmid
Schnieders
Schoen
Schotte
Schratt
@ -3087,6 +3120,7 @@ semiaxes
semimetals
Semin
Sensable
Seo
Sep
seqdep
Serpico
@ -3191,12 +3225,15 @@ Souza
sp
spacings
Spearot
specieslist
specular
spellcheck
Spellmeyer
Speybroeck
sph
SPH
spica
SPICA
Spickermann
splined
spparks
@ -3513,6 +3550,9 @@ Tz
Tzou
ub
Uberuaga
ubflag
Ubflag
ubiquitin
uca
uChem
uCond
@ -3566,12 +3606,14 @@ upenn
upto
Urbakh
Urbana
UreyBradley
Usabiaga
usec
uSemiParallel
userguide
username
usleep
usolve
usr
util
utils
@ -3605,6 +3647,7 @@ Vcm
vdfmax
vdim
vdisplace
vdw
vdW
vdwl
vec
@ -3758,6 +3801,7 @@ Xeon
xflag
xhi
xHost
Xia
Xiaohu
Xiaowang
Xie

11
examples/PACKAGES/cgsdk/README → examples/PACKAGES/cgspica/README
View File

@ -1,7 +1,8 @@
LAMMPS CG-SDK example problems
LAMMPS CG-SPICA example problems
Each of these sub-directories contains a sample problem for the SDK
coarse grained MD potentials that you can run with LAMMPS.
Each of these sub-directories contains a sample problem for
the SPICA (formerly called SDK) coarse grained MD potentials
that you can run with LAMMPS.
These are the two sample systems
@ -9,11 +10,11 @@ peg-verlet: coarse grained PEG surfactant/water mixture lamella
verlet version
this example uses the plain LJ term only, no charges.
two variants are provided regular harmonic angles and
the SDK variant that includes 1-3 LJ repulsion.
the SPICA variant that includes 1-3 LJ repulsion.
sds-monolayer: coarse grained SDS surfactant monolayers at water/vapor
interface.
this example uses the SDK LJ term with coulomb and shows
this example uses the SPICA LJ term with coulomb and shows
how to use the combined coulomb style vs. hybrid/overlay
with possible optimizations due to the small number of
charged particles in this system

0
examples/PACKAGES/cgsdk/peg-verlet/data.pegc12e8.gz → examples/PACKAGES/cgspica/peg-verlet/data.pegc12e8.gz
View File

2
examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8 → examples/PACKAGES/cgspica/peg-verlet/in.pegc12e8
View File

@ -9,7 +9,7 @@ atom_style angle
processors * * 1
# read topology and force field
pair_style lj/sdk 15.0
pair_style lj/sdk 15.0 # compatible with "lj/spica"
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 1.0

4
examples/PACKAGES/cgsdk/peg-verlet/in.pegc12e8-angle → examples/PACKAGES/cgspica/peg-verlet/in.pegc12e8-angle
View File

@ -9,9 +9,9 @@ atom_style angle
processors * * 1
# read topology and force field
pair_style lj/sdk 15.0
pair_style lj/sdk 15.0 # compatible with "lj/spica"
bond_style harmonic
angle_style sdk
angle_style sdk # compatible with "spica"
special_bonds lj/coul 0.0 0.0 1.0
read_data data.pegc12e8.gz

0
examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1 → examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8-angle.g++.1
View File

0
examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4 → examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8-angle.g++.4
View File

0
examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.1 → examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8.g++.1
View File

0
examples/PACKAGES/cgsdk/peg-verlet/log.27Nov18.pegc12e8.g++.4 → examples/PACKAGES/cgspica/peg-verlet/log.27Nov18.pegc12e8.g++.4
View File

0
examples/PACKAGES/cgsdk/sds-monolayer/data.sds.gz → examples/PACKAGES/cgspica/sds-monolayer/data.sds.gz
View File

4
examples/PACKAGES/cgsdk/sds-monolayer/in.sds-hybrid → examples/PACKAGES/cgspica/sds-monolayer/in.sds-hybrid
View File

@ -5,9 +5,9 @@ dimension 3
atom_style full
processors * * 1
pair_style hybrid/overlay lj/sdk 15.0 coul/long 26.5
pair_style hybrid/overlay lj/sdk 15.0 coul/long 26.5 # "lj/sdk" is compatible with "lj/spica"
bond_style harmonic
angle_style sdk
angle_style sdk # compatible with "spica"
special_bonds lj/coul 0.0 0.0 1.0
read_data data.sds.gz

4
examples/PACKAGES/cgsdk/sds-monolayer/in.sds-regular → examples/PACKAGES/cgspica/sds-monolayer/in.sds-regular
View File

@ -5,9 +5,9 @@ dimension 3
atom_style full
processors * * 1
pair_style lj/sdk/coul/long 15.0
pair_style lj/sdk/coul/long 15.0 # compatible with "lj/spica/coul/long"
bond_style harmonic
angle_style sdk
angle_style sdk # compatible with "spica"
special_bonds lj/coul 0.0 0.0 1.0
read_data data.sds.gz

0
examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.1 → examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-hybrid.g++.1
View File

0
examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-hybrid.g++.4 → examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-hybrid.g++.4
View File

0
examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.1 → examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-regular.g++.1
View File

0
examples/PACKAGES/cgsdk/sds-monolayer/log.27Nov18.sds-regular.g++.4 → examples/PACKAGES/cgspica/sds-monolayer/log.27Nov18.sds-regular.g++.4
View File

1
examples/README
View File

@ -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

24
examples/amoeba/README Normal file
View File

@ -0,0 +1,24 @@
Data files in this directory were created using the
tools/tinker/tinker2lmp.py script as follows:
** water_dimer:
% python tinker2lmp.py -xyz water_dimer.xyz -amoeba amoeba_water.prm -data data.water_dimer.amoeba
% python tinker2lmp.py -xyz water_dimer.xyz -hippo hippo_water.prm -data data.water_dimer.hippo
** water_hexamer:
% python tinker2lmp.py -xyz water_hexamer.xyz -amoeba amoeba_water.prm -data data.water_hexamer.amoeba
% python tinker2lmp.py -xyz water_hexamer.xyz -hippo hippo_water.prm -data data.water_hexamer.hippo
** water_box:
% python tinker2lmp.py -xyz water_box.xyz -amoeba amoeba_water.prm -data data.water_box.amoeba -pbc 18.643 18.643 18.643
% python tinker2lmp.py -xyz water_box.xyz -hippo hippo_water.prm -data data.water_box.hippo -pbc 18.643 18.643 18.643
** ubiquitin:
% python tinker2lmp.py -xyz ubiquitin.xyz -amoeba amoeba_ubiquitin.prm -data data.ubiquitin -pbc 54.99 41.91 41.91 -bitorsion bitorsion.ubiquitin.data

18
examples/amoeba/amoeba_ubiquitin.key Normal file
View File

@ -0,0 +1,18 @@
!! DATE: 2022-07-05 UNITS: real
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

11584
examples/amoeba/amoeba_ubiquitin.prm Normal file
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File diff suppressed because it is too large Load Diff

10
examples/amoeba/amoeba_water.key Normal file
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@ -0,0 +1,10 @@
!! DATE: 2022-07-05 UNITS: real
parameters ./amoeba.prm
digits 8
cutoff 10
taper 8
polar-eps 1e-5
usolve-diag 1.0

160
examples/amoeba/amoeba_water.prm Normal file
View File

@ -0,0 +1,160 @@
!! DATE: 2022-07-05 UNITS: real
##############################
## ##
## 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

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!! DATE: 2022-07-05 UNITS: real
parameters ./amoeba.prm
digits 10
openmp-threads 1
ewald
ewald-alpha 0.4
pewald-alpha 0.5
pme-grid 24 24 24
neighbor-list
a-axis 18.643
cutoff 7
taper 6
polar-eps 1e-5
usolve-diag 1.0

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1988
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1988
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LAMMPS data file created from Tinker water_dimer.xyz and amoeba_water.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 0.9572 556.85 -1419.9675 2112.20165625
Angle Coeffs
1 0 1 108.5 48.7 -39.064262472 8.95286947775 -6.41202044508 11.5462823034
BondAngle Coeffs
1 0.0 0.0 0.0 0.0
UreyBradley Coeffs
1 -7.6 1.5537
Tinker Types
1 1
2 2
3 2
4 1
5 2
6 2

62
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LAMMPS data file created from Tinker water_dimer.xyz and hippo_water.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 0.9572 556.85 -1419.9675 2112.20165625
Angle Coeffs
1 0 0 107.7 48.7 -39.064262472 8.95286947775 -6.41202044508 11.5462823034
BondAngle Coeffs
1 0.0 0.0 0.0 0.0
UreyBradley Coeffs
1 0.0 0.0
Tinker Types
1 1
2 2
3 2
4 1
5 2
6 2

98
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LAMMPS data file created from Tinker water_hexamer.xyz and amoeba_water.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 0.9572 556.85 -1419.9675 2112.20165625
Angle Coeffs
1 0 1 108.5 48.7 -39.064262472 8.95286947775 -6.41202044508 11.5462823034
BondAngle Coeffs
1 0.0 0.0 0.0 0.0
UreyBradley Coeffs
1 -7.6 1.5537
Tinker Types
1 1
2 2
3 2
4 1
5 2
6 2
7 1
8 2
9 2
10 1
11 2
12 2
13 1
14 2
15 2
16 1
17 2
18 2

98
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LAMMPS data file created from Tinker water_hexamer.xyz and hippo_water.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 0.9572 556.85 -1419.9675 2112.20165625
Angle Coeffs
1 0 0 107.7 48.7 -39.064262472 8.95286947775 -6.41202044508 11.5462823034
BondAngle Coeffs
1 0.0 0.0 0.0 0.0
UreyBradley Coeffs
1 0.0 0.0
Tinker Types
1 1
2 2
3 2
4 1
5 2
6 2
7 1
8 2
9 2
10 1
11 2
12 2
13 1
14 2
15 2
16 1
17 2
18 2

10
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!! DATE: 2022-07-05 UNITS: real
parameters ./hippo.prm
digits 8
cutoff 10
taper 8
polar-eps 1e-5
usolve-diag 1.0

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!! DATE: 2022-07-05 UNITS: real
##############################
## ##
## 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

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!! DATE: 2022-07-05 UNITS: real
parameters ./hippo.prm
digits 8
verbose
ewald
ewald-alpha 0.4
pewald-alpha 0.5
dewald
dewald-alpha 0.45
dpme-grid 16 16 16
neighbor-list
a-axis 18.643
cutoff 7
taper 6
polar-eps 1e-5
usolve-diag 1.0

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# solvated ubiquitin molecule with AMOEBA force field
units real
boundary p p p
atom_modify sort 0 0.0
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style fourier
improper_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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
fix pit all amoeba/pitorsion
fix_modify pit energy yes
fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
fix_modify bit energy yes
# read data file
read_data data.ubiquitin fix amtype NULL "Tinker Types" &
fix pit "pitorsion types" "PiTorsion Coeffs" &
fix pit pitorsions PiTorsions &
fix bit bitorsions BiTorsions
pair_style amoeba
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
#dump 1 all custom 10 dump.ubiquitin id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 1
run 10

43
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# replicate water box with AMOEBA or HIPPO
units real
boundary p p p
atom_style amoeba
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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_box.amoeba fix amtype NULL "Tinker Types"
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water_box.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_box id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 10
run 100

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# water box with AMOEBA or HIPPO
units real
boundary p p p
atom_style amoeba
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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_box.hippo fix amtype NULL "Tinker Types"
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water_box.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_box id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 10
run 100

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# water dimer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_dimer.amoeba fix amtype NULL "Tinker Types"
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 10
run 100

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# water dimer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_dimer.hippo fix amtype NULL "Tinker Types"
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 10
run 100

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# water hexamer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_hexamer.amoeba fix amtype NULL "Tinker Types"
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 10
run 100

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# water hexamer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_hexamer.hippo fix amtype NULL "Tinker Types"
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water.key
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp &
emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 10
run 100

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LAMMPS (23 Jun 2022)
# solvated ubiquitin molecule with AMOEBA force field
units real
boundary p p p
atom_modify sort 0 0.0
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style fourier
improper_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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
fix pit all amoeba/pitorsion
fix_modify pit energy yes
fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
fix_modify bit energy yes
# read data file
read_data data.ubiquitin fix amtype NULL "Tinker Types" fix pit "pitorsion types" "PiTorsion Coeffs" fix pit pitorsions PiTorsions fix bit bitorsions BiTorsions
Reading data file ...
orthogonal box = (0 0 0) to (54.99 41.91 41.91)
1 by 1 by 1 MPI processor grid
reading atoms ...
9737 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
3 = max impropers/atom
reading bonds ...
6908 bonds
reading angles ...
5094 angles
reading dihedrals ...
3297 dihedrals
reading impropers ...
651 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
9 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
21 = max # of special neighbors
special bonds CPU = 0.004 seconds
read_data CPU = 0.091 seconds
pair_style amoeba
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
Reading potential file amoeba_ubiquitin.prm with DATE: 2022-07-05
Skipping section: AMOEBA Protein Force Field Atom Classes
Skipping section: Torsion-Torsion Parameters
Skipping section: Biopolymer Atom Type Conversions
Reading potential file amoeba_ubiquitin.key with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
4 = max # of 1-2 neighbors
9 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
58 = max # of 1-5 neighbors
21 = max # of special neighbors
special bonds CPU = 0.007 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
#dump 1 all custom 10 dump.ubiquitin id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 1
run 10
AMOEBA force field settings
hal: cut 12 taper 10.8 vscale 0 0 1 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 60 48 48 mscale 0 0 0.4 1
polar: cut 7 aewald 0.5 bsorder 5 FFT 60 48 48
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 8 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair amoeba, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
AMOEBA group count: 3196
Per MPI rank memory allocation (min/avg/max) = 258.3 | 258.3 | 258.3 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -35338.057 2856.5938 1955.5431 224.37609 65.00809 5101.5211 -30247.585 -6336.5196 -5795.4272 -6329.8149 -6884.3167 349.52657 77.164877 652.41925
1 29.61379 -35356.153 2037.3541 1840.7883 223.90217 64.293945 4166.3385 -30341.522 -6486.773 -6452.8463 -6841.5982 -7386.1106 311.38025 120.72605 545.35513
2 78.518242 -35383.65 825.39919 1538.3909 222.55095 62.191009 2648.5321 -30467.814 -5502.9841 -6410.2998 -6396.1829 -6937.8137 217.3515 210.76948 294.28051
3 88.8921 -35402.11 938.99299 1162.2914 220.5271 58.832521 2380.644 -30453.516 -1929.5417 -3331.1291 -2769.7218 -3350.5733 117.32302 279.72705 31.237776
4 68.740402 -35477.589 2048.0659 858.03795 218.14277 54.460022 3178.7066 -30316.325 2041.1138 594.25938 1665.7799 1030.8539 66.230421 304.28296 -155.80224
5 76.267862 -35707.869 2206.6534 736.37385 215.75693 49.401674 3208.1859 -30299.377 2276.9276 536.21124 1893.4621 1258.492 92.097191 299.65604 -228.58369
6 118.24373 -36092.77 1166.179 815.59206 213.67399 44.022297 2239.4673 -30435.629 -1677.8051 -3988.2428 -2669.6848 -3247.7207 197.42472 285.87129 -162.35459
7 137.7204 -36521.444 782.87113 1026.745 212.04289 38.686259 2060.3452 -30479.082 -5987.83 -8386.8104 -7363.188 -7888.261 357.00835 253.66346 32.827786
8 112.66452 -36897.181 1750.0569 1269.152 210.83571 33.742799 3263.7874 -30379.432 -7886.4081 -9703.2601 -9043.015 -9555.2908 490.76046 182.31259 278.727
9 88.237359 -37209.906 2695.1766 1454.55 209.91331 29.503458 4389.1434 -30276.565 -8202.16 -9492.368 -9110.7037 -9639.2288 502.55699 107.82333 443.6705
10 108.86756 -37474.988 2240.4603 1523.7936 209.10313 26.208515 3999.5656 -30333.279 -8468.4347 -9956.923 -9709.5874 -10224.682 365.98214 95.262991 425.12746
Loop time of 24.2102 on 1 procs for 10 steps with 9737 atoms
Performance: 0.036 ns/day, 672.507 hours/ns, 0.413 timesteps/s
97.8% CPU use with 1 MPI tasks x no OpenMP threads
AMOEBA timing breakdown:
Init time: 0.0401664 0.17%
Hal time: 7.62094 31.51%
Mpole time: 2.44622 10.12%
Induce time: 9.28925 38.41%
Polar time: 4.78631 19.79%
Total time: 24.1829
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 24.183 | 24.183 | 24.183 | 0.0 | 99.89
Bond | 0.016031 | 0.016031 | 0.016031 | 0.0 | 0.07
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.004396 | 0.004396 | 0.004396 | 0.0 | 0.02
Output | 0.0011692 | 0.0011692 | 0.0011692 | 0.0 | 0.00
Modify | 0.0044765 | 0.0044765 | 0.0044765 | 0.0 | 0.02
Other | | 0.001194 | | | 0.00
Nlocal: 9737 ave 9737 max 9737 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 31511 ave 31511 max 31511 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 5.6393e+06 ave 5.6393e+06 max 5.6393e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 5639296
Ave neighs/atom = 579.16155
Ave special neighs/atom = 3.1364897
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:27

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LAMMPS (23 Jun 2022)
# solvated ubiquitin molecule with AMOEBA force field
units real
boundary p p p
atom_modify sort 0 0.0
atom_style amoeba
bond_style class2
angle_style amoeba
dihedral_style fourier
improper_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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
fix pit all amoeba/pitorsion
fix_modify pit energy yes
fix bit all amoeba/bitorsion bitorsion.ubiquitin.data
fix_modify bit energy yes
# read data file
read_data data.ubiquitin fix amtype NULL "Tinker Types" fix pit "pitorsion types" "PiTorsion Coeffs" fix pit pitorsions PiTorsions fix bit bitorsions BiTorsions
Reading data file ...
orthogonal box = (0 0 0) to (54.99 41.91 41.91)
2 by 1 by 2 MPI processor grid
reading atoms ...
9737 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
18 = max dihedrals/atom
scanning impropers ...
3 = max impropers/atom
reading bonds ...
6908 bonds
reading angles ...
5094 angles
reading dihedrals ...
3297 dihedrals
reading impropers ...
651 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
9 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
21 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.072 seconds
pair_style amoeba
pair_coeff * * amoeba_ubiquitin.prm amoeba_ubiquitin.key
Reading potential file amoeba_ubiquitin.prm with DATE: 2022-07-05
Skipping section: AMOEBA Protein Force Field Atom Classes
Skipping section: Torsion-Torsion Parameters
Skipping section: Biopolymer Atom Type Conversions
Reading potential file amoeba_ubiquitin.key with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
4 = max # of 1-2 neighbors
9 = max # of 1-3 neighbors
19 = max # of 1-4 neighbors
58 = max # of 1-5 neighbors
21 = max # of special neighbors
special bonds CPU = 0.002 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
#dump 1 all custom 10 dump.ubiquitin id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 1
run 10
AMOEBA force field settings
hal: cut 12 taper 10.8 vscale 0 0 1 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 60 48 48 mscale 0 0 0.4 1
polar: cut 7 aewald 0.5 bsorder 5 FFT 60 48 48
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 15 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 8 6 6
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair amoeba, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
AMOEBA group count: 3196
Per MPI rank memory allocation (min/avg/max) = 144.2 | 144.7 | 145.4 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -35338.057 2856.5938 1955.5431 224.37609 65.00809 5101.5211 -30247.585 -6336.5196 -5795.4272 -6329.8149 -6884.3167 349.52657 77.164877 652.41925
1 29.61379 -35356.153 2037.3541 1840.7883 223.90217 64.293945 4166.3385 -30341.522 -6486.773 -6452.8463 -6841.5982 -7386.1106 311.38025 120.72605 545.35513
2 78.518242 -35383.65 825.39919 1538.3909 222.55095 62.191009 2648.5321 -30467.814 -5502.9841 -6410.2998 -6396.1829 -6937.8137 217.3515 210.76948 294.28051
3 88.8921 -35402.11 938.99299 1162.2914 220.5271 58.832521 2380.644 -30453.516 -1929.5417 -3331.1291 -2769.7218 -3350.5733 117.32302 279.72705 31.237776
4 68.740402 -35477.589 2048.0659 858.03795 218.14277 54.460022 3178.7066 -30316.325 2041.1138 594.25938 1665.7799 1030.8539 66.230421 304.28296 -155.80224
5 76.267862 -35707.869 2206.6534 736.37385 215.75693 49.401674 3208.1859 -30299.377 2276.9276 536.21124 1893.4621 1258.492 92.097191 299.65604 -228.58369
6 118.24373 -36092.77 1166.179 815.59206 213.67399 44.022297 2239.4673 -30435.629 -1677.8051 -3988.2428 -2669.6848 -3247.7207 197.42472 285.87129 -162.35459
7 137.7204 -36521.444 782.87113 1026.745 212.04289 38.686259 2060.3452 -30479.082 -5987.83 -8386.8104 -7363.188 -7888.261 357.00835 253.66346 32.827786
8 112.66452 -36897.181 1750.0569 1269.152 210.83571 33.742799 3263.7874 -30379.432 -7886.4081 -9703.2601 -9043.015 -9555.2908 490.76046 182.31259 278.727
9 88.237359 -37209.906 2695.1766 1454.55 209.91331 29.503458 4389.1434 -30276.565 -8202.16 -9492.368 -9110.7037 -9639.2288 502.55699 107.82333 443.6705
10 108.86756 -37474.988 2240.4603 1523.7936 209.10313 26.208515 3999.5656 -30333.279 -8468.4347 -9956.923 -9709.5874 -10224.682 365.98214 95.262991 425.12746
Loop time of 6.03244 on 4 procs for 10 steps with 9737 atoms
Performance: 0.143 ns/day, 167.568 hours/ns, 1.658 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
AMOEBA timing breakdown:
Init time: 0.0192504 0.32%
Hal time: 1.86975 31.05%
Mpole time: 0.633256 10.52%
Induce time: 2.26029 37.54%
Polar time: 1.23884 20.57%
Total time: 6.02139
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 6.0202 | 6.0215 | 6.0228 | 0.0 | 99.82
Bond | 0.0029895 | 0.0033805 | 0.0036579 | 0.4 | 0.06
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0044978 | 0.0059188 | 0.0070446 | 1.5 | 0.10
Output | 0.00055049 | 0.00062352 | 0.00079826 | 0.0 | 0.01
Modify | 0.00067451 | 0.00071394 | 0.00074612 | 0.0 | 0.01
Other | | 0.0003294 | | | 0.01
Nlocal: 2434.25 ave 2498 max 2390 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Nghost: 16683.2 ave 16765 max 16568 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Neighs: 1.40982e+06 ave 1.52088e+06 max 1.30717e+06 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 5639296
Ave neighs/atom = 579.16155
Ave special neighs/atom = 3.1364897
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:07

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LAMMPS (23 Jun 2022)
# replicate water box with AMOEBA or HIPPO
units real
boundary p p p
atom_style amoeba
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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_box.amoeba fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (0 0 0) to (18.643 18.643 18.643)
1 by 1 by 1 MPI processor grid
reading atoms ...
648 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
432 bonds
reading angles ...
216 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.010 seconds
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water_box.key
Reading potential file amoeba_water.prm with DATE: 2022-07-05
Reading potential file amoeba_water_box.key with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_box id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 10
run 100
AMOEBA force field settings
hal: cut 7 taper 6 vscale 0 0 1 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9
ghost atom cutoff = 9
binsize = 4.5, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair amoeba, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
AMOEBA group count: 216
Per MPI rank memory allocation (min/avg/max) = 56.94 | 56.94 | 56.94 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -2172.0637 166.82637 83.732524 0 0 250.5589 -1921.5048 -6181.4178 -4772.1682 -6954.8414 -6817.2437 -272.19967 3173.3481 2229.9454
10 105.50186 -2373.7036 136.67877 106.86833 0 0 243.5471 -1926.6873 -8440.8076 -10450.396 -9513.7369 -9664.6007 -301.7395 322.28511 1917.0314
20 143.89822 -2358.363 70.950306 76.775658 0 0 147.72596 -1933.1172 -7370.2083 -7728.5515 -11580.39 -8675.2341 -806.78779 780.67516 2096.34
30 157.22465 -2375.4739 50.393531 87.108003 0 0 137.50153 -1934.7514 -4449.577 -6946.7795 -7865.2165 -4954.2358 -417.69587 -1004.2877 -36.388669
40 150.92481 -2354.1892 78.482464 53.798462 0 0 132.28093 -1930.8371 353.42948 -939.14353 -4636.5062 475.58057 -1073.8523 -1583.9471 -574.21807
50 153.0181 -2388.7322 100.20232 65.813823 0 0 166.01614 -1927.6078 3975.1981 1368.1361 425.64533 3886.0124 -1806.8586 -2534.5272 -2118.2395
60 155.01494 -2364.3168 92.946192 44.248949 0 0 137.19514 -1928.1623 5793.7546 3524.7523 1420.4096 6108.7958 -1536.5261 -2558.8204 -1501.5292
70 166.70755 -2383.503 76.491199 55.01988 0 0 131.51108 -1930.4824 4744.1583 1919.3954 2838.7666 2669.745 -169.21643 -188.08678 -2256.4142
80 171.83506 -2388.0612 76.465932 49.1299 0 0 125.59583 -1931.067 2210.3658 -318.23867 330.74353 -395.26693 -43.142216 252.53012 -1987.0412
90 175.73401 -2423.8154 90.786573 63.719496 0 0 154.50607 -1930.3915 -916.91571 -3942.3954 -2566.5361 -3414.8202 199.82369 2365.9443 -266.38604
100 173.72684 -2422.367 99.75941 57.294464 0 0 157.05387 -1930.2663 -3585.8356 -5734.1341 -5882.0146 -6232.4353 -227.79935 959.68225 404.47924
Loop time of 14.5572 on 1 procs for 100 steps with 648 atoms
Performance: 0.594 ns/day, 40.437 hours/ns, 6.869 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
AMOEBA timing breakdown:
Init time: 0.0224497 0.15%
Hal time: 1.00248 6.90%
Mpole time: 1.42229 9.78%
Induce time: 9.23983 63.55%
Polar time: 2.8515 19.61%
Total time: 14.5386
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.539 | 14.539 | 14.539 | 0.0 | 99.87
Bond | 0.0029302 | 0.0029302 | 0.0029302 | 0.0 | 0.02
Neigh | 0.010789 | 0.010789 | 0.010789 | 0.0 | 0.07
Comm | 0.0027888 | 0.0027888 | 0.0027888 | 0.0 | 0.02
Output | 0.00040039 | 0.00040039 | 0.00040039 | 0.0 | 0.00
Modify | 0.0007305 | 0.0007305 | 0.0007305 | 0.0 | 0.01
Other | | 0.0008703 | | | 0.01
Nlocal: 648 ave 648 max 648 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4290 ave 4290 max 4290 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 98545 ave 98545 max 98545 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 98545
Ave neighs/atom = 152.07562
Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:14

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LAMMPS (23 Jun 2022)
# replicate water box with AMOEBA or HIPPO
units real
boundary p p p
atom_style amoeba
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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_box.amoeba fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (0 0 0) to (18.643 18.643 18.643)
1 by 2 by 2 MPI processor grid
reading atoms ...
648 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
432 bonds
reading angles ...
216 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.011 seconds
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water_box.key
Reading potential file amoeba_water.prm with DATE: 2022-07-05
Reading potential file amoeba_water_box.key with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_box id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 10
run 100
AMOEBA force field settings
hal: cut 7 taper 6 vscale 0 0 1 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9
ghost atom cutoff = 9
binsize = 4.5, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair amoeba, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
AMOEBA group count: 216
Per MPI rank memory allocation (min/avg/max) = 56.38 | 56.38 | 56.38 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -2172.0637 166.82637 83.732524 0 0 250.5589 -1921.5048 -6181.4178 -4772.1682 -6954.8414 -6817.2437 -272.19967 3173.3481 2229.9454
10 105.50186 -2373.7036 136.67877 106.86833 0 0 243.5471 -1926.6873 -8440.8076 -10450.396 -9513.7369 -9664.6007 -301.7395 322.28511 1917.0314
20 143.89822 -2358.363 70.950306 76.775658 0 0 147.72596 -1933.1172 -7370.2083 -7728.5515 -11580.39 -8675.2341 -806.78779 780.67516 2096.34
30 157.22465 -2375.4739 50.393531 87.108003 0 0 137.50153 -1934.7514 -4449.577 -6946.7795 -7865.2165 -4954.2358 -417.69587 -1004.2877 -36.388669
40 150.92481 -2354.1892 78.482464 53.798462 0 0 132.28093 -1930.8371 353.42948 -939.14353 -4636.5062 475.58057 -1073.8523 -1583.9471 -574.21807
50 153.0181 -2388.7322 100.20232 65.813823 0 0 166.01614 -1927.6078 3975.1981 1368.1361 425.64533 3886.0124 -1806.8586 -2534.5272 -2118.2395
60 155.01494 -2364.3168 92.946192 44.248949 0 0 137.19514 -1928.1623 5793.7546 3524.7523 1420.4096 6108.7958 -1536.5261 -2558.8204 -1501.5292
70 166.70755 -2383.503 76.491199 55.01988 0 0 131.51108 -1930.4824 4744.1583 1919.3954 2838.7666 2669.745 -169.21643 -188.08678 -2256.4142
80 171.83506 -2388.0612 76.465932 49.1299 0 0 125.59583 -1931.067 2210.3658 -318.23867 330.74353 -395.26693 -43.142216 252.53012 -1987.0412
90 175.73401 -2423.8154 90.786573 63.719496 0 0 154.50607 -1930.3915 -916.91571 -3942.3954 -2566.5361 -3414.8202 199.82369 2365.9443 -266.38604
100 173.72684 -2422.367 99.75941 57.294464 0 0 157.05387 -1930.2663 -3585.8356 -5734.1341 -5882.0146 -6232.4353 -227.79935 959.68225 404.47924
Loop time of 5.22237 on 4 procs for 100 steps with 648 atoms
Performance: 1.654 ns/day, 14.507 hours/ns, 19.148 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
AMOEBA timing breakdown:
Init time: 0.0217547 0.42%
Hal time: 0.246901 4.74%
Mpole time: 0.489975 9.41%
Induce time: 3.54999 68.15%
Polar time: 0.900374 17.28%
Total time: 5.20901
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 5.2084 | 5.2093 | 5.2114 | 0.1 | 99.75
Bond | 0.00074127 | 0.00080769 | 0.00084525 | 0.0 | 0.02
Neigh | 0.0014801 | 0.001481 | 0.0014832 | 0.0 | 0.03
Comm | 0.007438 | 0.0095884 | 0.010526 | 1.3 | 0.18
Output | 0.00028866 | 0.00033051 | 0.00044509 | 0.0 | 0.01
Modify | 0.00020399 | 0.00020969 | 0.00021248 | 0.0 | 0.00
Other | | 0.000658 | | | 0.01
Nlocal: 162 ave 164 max 159 min
Histogram: 1 0 0 0 0 0 1 0 1 1
Nghost: 2568.5 ave 2585 max 2544 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Neighs: 24636.2 ave 25226 max 23891 min
Histogram: 1 0 0 0 0 0 2 0 0 1
Total # of neighbors = 98545
Ave neighs/atom = 152.07562
Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:05

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LAMMPS (23 Jun 2022)
# water box with AMOEBA or HIPPO
units real
boundary p p p
atom_style amoeba
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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_box.hippo fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (0 0 0) to (18.643 18.643 18.643)
1 by 1 by 1 MPI processor grid
reading atoms ...
648 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
432 bonds
reading angles ...
216 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.011 seconds
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water_box.key
Reading potential file hippo_water.prm with DATE: 2022-07-05
Reading potential file hippo_water_box.key with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_box id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 10
run 100
HIPPO force field settings
repulsion: cut 7 taper 6 rscale 0 0 1 1
qxfer: cut 7 taper 6 mscale 0 0 0.4 1
dispersion: cut 7 aewald 0.45 bsorder 4 FFT 16 16 16 dspscale 0 0 0.4 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9
ghost atom cutoff = 9
binsize = 4.5, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair hippo, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
HIPPO group count: 216
Per MPI rank memory allocation (min/avg/max) = 56.46 | 56.46 | 56.46 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -2188.594 166.82637 77.478353 0 0 244.30473 -1944.2893 -10859.589 -9285.4645 -11598.049 -11695.254 -282.7072 3164.4148 2495.2578
10 100.94691 -2350.192 116.13156 88.56605 0 0 204.69761 -1950.8098 -11480.919 -13574.139 -12190.797 -12798.212 -263.77028 280.62864 1974.1486
20 153.91622 -2358.3058 36.396961 66.22466 0 0 102.62162 -1958.8438 -7778.4529 -8492.3868 -11999.431 -9125.9998 -917.99962 589.09064 1788.2094
30 145.5951 -2343.9956 39.651541 65.833248 0 0 105.48479 -1957.7184 -288.79965 -2574.4466 -3820.4824 -414.28285 -347.51491 -1147.3995 -126.71025
40 126.87801 -2340.2623 102.93951 43.896946 0 0 146.83646 -1948.7309 6766.15 5908.7048 1280.0961 7930.8191 -1085.6811 -1596.6859 -714.82888
50 134.52078 -2358.9232 107.49288 44.253826 0 0 151.74671 -1947.7419 8762.4348 6023.4661 5377.0189 9396.0316 -1629.1364 -1663.1666 -2381.51
60 173.10181 -2374.3854 51.097314 33.03646 0 0 84.133774 -1956.4102 4614.2907 1719.1989 505.79149 4552.3167 -1661.1714 -587.92108 -1380.6732
70 184.86849 -2391.6106 39.916931 35.978152 0 0 75.895083 -1959.1811 -2146.9339 -4993.4021 -4095.6729 -4897.5768 -833.09046 1542.411 -1539.5266
80 164.75795 -2406.3017 101.94229 33.067832 0 0 135.01013 -1953.542 -8779.3265 -10545.409 -10418.702 -12098.858 -1319.194 1750.3511 -275.1272
90 151.17491 -2434.6876 152.21826 41.301673 0 0 193.51993 -1949.6141 -13330.691 -15436.505 -13791.461 -16934.674 149.25497 2289.1026 976.14333
100 166.99163 -2452.5298 143.57768 35.341459 0 0 178.91914 -1951.5533 -14918.51 -16077.49 -17353.738 -18140.466 19.009088 1487.0469 1084.0231
Loop time of 9.10254 on 1 procs for 100 steps with 648 atoms
Performance: 0.949 ns/day, 25.285 hours/ns, 10.986 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
HIPPO timing breakdown:
Init time: 0.0131104 0.14%
Repulse time: 1.06663 11.73%
Disp time: 0.585678 6.44%
Mpole time: 1.7162 18.88%
Induce time: 3.27504 36.03%
Polar time: 2.14366 23.58%
Qxfer time: 0.289804 3.19%
Total time: 9.09012
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.0902 | 9.0902 | 9.0902 | 0.0 | 99.86
Bond | 0.0024561 | 0.0024561 | 0.0024561 | 0.0 | 0.03
Neigh | 0.005878 | 0.005878 | 0.005878 | 0.0 | 0.06
Comm | 0.0023344 | 0.0023344 | 0.0023344 | 0.0 | 0.03
Output | 0.00036107 | 0.00036107 | 0.00036107 | 0.0 | 0.00
Modify | 0.00062368 | 0.00062368 | 0.00062368 | 0.0 | 0.01
Other | | 0.0006736 | | | 0.01
Nlocal: 648 ave 648 max 648 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 4282 ave 4282 max 4282 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 98490 ave 98490 max 98490 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 98490
Ave neighs/atom = 151.99074
Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:09

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LAMMPS (23 Jun 2022)
# water box with AMOEBA or HIPPO
units real
boundary p p p
atom_style amoeba
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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_box.hippo fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (0 0 0) to (18.643 18.643 18.643)
1 by 2 by 2 MPI processor grid
reading atoms ...
648 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
432 bonds
reading angles ...
216 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_data CPU = 0.013 seconds
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water_box.key
Reading potential file hippo_water.prm with DATE: 2022-07-05
Reading potential file hippo_water_box.key with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_box id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 10
run 100
HIPPO force field settings
repulsion: cut 7 taper 6 rscale 0 0 1 1
qxfer: cut 7 taper 6 mscale 0 0 0.4 1
dispersion: cut 7 aewald 0.45 bsorder 4 FFT 16 16 16 dspscale 0 0 0.4 1
multipole: cut 7 aewald 0.4 bsorder 5 FFT 24 24 24 mscale 0 0 0.4 1
polar: cut 7 aewald 0.5 bsorder 5 FFT 24 24 24
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 9
ghost atom cutoff = 9
binsize = 4.5, bins = 5 5 5
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair hippo, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
HIPPO group count: 216
Per MPI rank memory allocation (min/avg/max) = 55.94 | 55.94 | 55.94 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -2188.594 166.82637 77.478353 0 0 244.30473 -1944.2893 -10859.589 -9285.4645 -11598.049 -11695.254 -282.7072 3164.4148 2495.2578
10 100.94691 -2350.192 116.13156 88.56605 0 0 204.69761 -1950.8098 -11480.919 -13574.139 -12190.797 -12798.212 -263.77028 280.62864 1974.1486
20 153.91622 -2358.3058 36.396961 66.22466 0 0 102.62162 -1958.8438 -7778.4529 -8492.3868 -11999.431 -9125.9998 -917.99962 589.09064 1788.2094
30 145.5951 -2343.9956 39.651541 65.833248 0 0 105.48479 -1957.7184 -288.79965 -2574.4466 -3820.4824 -414.28285 -347.51491 -1147.3995 -126.71025
40 126.87801 -2340.2623 102.93951 43.896946 0 0 146.83646 -1948.7309 6766.15 5908.7048 1280.0961 7930.8191 -1085.6811 -1596.6859 -714.82888
50 134.52078 -2358.9232 107.49288 44.253826 0 0 151.74671 -1947.7419 8762.4348 6023.4661 5377.0189 9396.0316 -1629.1364 -1663.1666 -2381.51
60 173.10181 -2374.3854 51.097314 33.03646 0 0 84.133774 -1956.4102 4614.2907 1719.1989 505.79149 4552.3167 -1661.1714 -587.92108 -1380.6732
70 184.86849 -2391.6106 39.916931 35.978152 0 0 75.895083 -1959.1811 -2146.9339 -4993.4021 -4095.6729 -4897.5768 -833.09046 1542.411 -1539.5266
80 164.75795 -2406.3017 101.94229 33.067832 0 0 135.01013 -1953.542 -8779.3265 -10545.409 -10418.702 -12098.858 -1319.194 1750.3511 -275.1272
90 151.17491 -2434.6876 152.21826 41.301673 0 0 193.51993 -1949.6141 -13330.691 -15436.505 -13791.461 -16934.674 149.25497 2289.1026 976.14333
100 166.99163 -2452.5298 143.57768 35.341459 0 0 178.91914 -1951.5533 -14918.51 -16077.49 -17353.738 -18140.466 19.009088 1487.0469 1084.0231
Loop time of 3.60321 on 4 procs for 100 steps with 648 atoms
Performance: 2.398 ns/day, 10.009 hours/ns, 27.753 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
HIPPO timing breakdown:
Init time: 0.0162772 0.45%
Repulse time: 0.329178 9.19%
Disp time: 0.244602 6.83%
Mpole time: 0.640969 17.89%
Induce time: 1.44984 40.47%
Polar time: 0.821061 22.92%
Qxfer time: 0.0804381 2.25%
Total time: 3.58237
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.5752 | 3.5827 | 3.59 | 0.4 | 99.43
Bond | 0.00065212 | 0.00072305 | 0.00075673 | 0.0 | 0.02
Neigh | 0.0015663 | 0.0015681 | 0.00157 | 0.0 | 0.04
Comm | 0.0097453 | 0.017024 | 0.024558 | 5.5 | 0.47
Output | 0.00030331 | 0.0003444 | 0.00045896 | 0.0 | 0.01
Modify | 0.00018335 | 0.00020346 | 0.00021611 | 0.0 | 0.01
Other | | 0.0006822 | | | 0.02
Nlocal: 162 ave 166 max 160 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Nghost: 2563.25 ave 2589 max 2535 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Neighs: 24622.5 ave 25210 max 24056 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Total # of neighbors = 98490
Ave neighs/atom = 151.99074
Ave special neighs/atom = 2
Neighbor list builds = 2
Dangerous builds = 0
Total wall time: 0:00:03

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LAMMPS (23 Jun 2022)
# water dimer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_dimer.amoeba fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934)
1 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
4 bonds
reading angles ...
2 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water.key
Reading potential file amoeba_water.prm with DATE: 2022-07-05
Reading potential file amoeba_water.key with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 10
run 100
AMOEBA force field settings
hal: cut 10 taper 8 vscale 0 0 1 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair amoeba, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
AMOEBA group count: 2
Per MPI rank memory allocation (min/avg/max) = 48.33 | 48.33 | 48.33 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -5.1627563 0.025695395 0.71581114 0 0 0.74150653 -4.4212497 -12260.522 -43226.042 39448.214 -33003.739 -85.160886 -28101.905 -72.971988
10 1.1174766 -4.7928792 0.045080327 0.30848527 0 0 0.35356559 -4.4226587 -14728.416 11456.119 -52592.829 -3262.8454 70.868937 29494.268 57.977562
20 3.0821934 -5.1387316 0.013108182 0.65694692 0 0 0.6700551 -4.4227393 3007.4148 -25925.326 49641.41 -15284.933 -79.726771 -29005.234 -68.530079
30 3.461967 -4.8079248 0.013888863 0.31895667 0 0 0.33284554 -4.423482 8616.211 40027.877 -31134.295 16291.126 72.510013 23088.238 51.407946
40 4.2181367 -5.0535921 0.0099009766 0.55796811 0 0 0.56786908 -4.4228557 24239.885 -5761.6967 62095.735 15576.675 -76.240192 -33057.385 -58.850871
50 5.216657 -4.8012751 0.0053003148 0.29489399 0 0 0.30019431 -4.4233315 17728.056 44785.731 -21215.714 28613.715 66.24671 20292.137 51.010856
60 9.45101 -5.0818046 0.0043357361 0.5118733 0 0 0.51620903 -4.4247372 16893.135 -15068.961 50111.11 13824.77 -75.966047 -34809.168 -52.83183
70 10.385926 -4.8250769 0.022572262 0.22235766 0 0 0.24492992 -4.4253547 -1117.3665 19070.918 -36063.612 11648.813 61.067533 25754.59 53.919881
80 12.797691 -5.123735 0.023756795 0.48275385 0 0 0.50651065 -4.4264869 -6491.9826 -28436.037 20681.908 -14176.121 -64.024669 -35737.052 -52.583533
90 12.569481 -4.8303379 0.060369422 0.15670502 0 0 0.21707444 -4.4259273 -16762.536 1720.5855 -47624.986 -6793.7441 59.966729 30024.566 52.339671
100 17.750788 -5.1195235 0.039885925 0.38711474 0 0 0.42700067 -4.4279642 -10817.92 -21833.456 4186.8301 -18211.329 -43.11086 -32664.671 -41.508916
Loop time of 0.00539351 on 1 procs for 100 steps with 6 atoms
Performance: 1601.925 ns/day, 0.015 hours/ns, 18540.802 timesteps/s
97.1% CPU use with 1 MPI tasks x no OpenMP threads
AMOEBA timing breakdown:
Init time: 0.000111932 2.32%
Hal time: 0.00045057 9.33%
Mpole time: 0.00055958 11.59%
Induce time: 0.00238881 49.46%
Polar time: 0.0013042 27.00%
Total time: 0.00482974
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0048575 | 0.0048575 | 0.0048575 | 0.0 | 90.06
Bond | 9.4036e-05 | 9.4036e-05 | 9.4036e-05 | 0.0 | 1.74
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.3435e-05 | 1.3435e-05 | 1.3435e-05 | 0.0 | 0.25
Output | 0.00034323 | 0.00034323 | 0.00034323 | 0.0 | 6.36
Modify | 3.5435e-05 | 3.5435e-05 | 3.5435e-05 | 0.0 | 0.66
Other | | 4.986e-05 | | | 0.92
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 15 ave 15 max 15 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15
Ave neighs/atom = 2.5
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (23 Jun 2022)
# water dimer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_dimer.amoeba fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934)
2 by 1 by 2 MPI processor grid
reading atoms ...
6 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
4 bonds
reading angles ...
2 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.009 seconds
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water.key
Reading potential file amoeba_water.prm with DATE: 2022-07-05
Reading potential file amoeba_water.key with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 10
run 100
AMOEBA force field settings
hal: cut 10 taper 8 vscale 0 0 1 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair amoeba, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
AMOEBA group count: 2
Per MPI rank memory allocation (min/avg/max) = 48.35 | 48.48 | 48.62 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -5.1627563 0.025695395 0.71581114 0 0 0.74150653 -4.4212497 -12260.522 -43226.042 39448.214 -33003.739 -85.160886 -28101.905 -72.971988
10 1.1174766 -4.7928792 0.045080327 0.30848527 0 0 0.35356559 -4.4226587 -14728.416 11456.119 -52592.829 -3262.8454 70.868937 29494.268 57.977562
20 3.0821934 -5.1387316 0.013108182 0.65694692 0 0 0.6700551 -4.4227393 3007.4148 -25925.326 49641.41 -15284.933 -79.726771 -29005.234 -68.530079
30 3.461967 -4.8079248 0.013888863 0.31895667 0 0 0.33284554 -4.423482 8616.211 40027.877 -31134.295 16291.126 72.510013 23088.238 51.407946
40 4.2181367 -5.0535921 0.0099009766 0.55796811 0 0 0.56786908 -4.4228557 24239.885 -5761.6967 62095.735 15576.675 -76.240192 -33057.385 -58.850871
50 5.216657 -4.8012751 0.0053003148 0.29489399 0 0 0.30019431 -4.4233315 17728.056 44785.731 -21215.714 28613.715 66.24671 20292.137 51.010856
60 9.45101 -5.0818046 0.0043357361 0.5118733 0 0 0.51620903 -4.4247372 16893.135 -15068.961 50111.11 13824.77 -75.966047 -34809.168 -52.83183
70 10.385926 -4.8250769 0.022572262 0.22235766 0 0 0.24492992 -4.4253547 -1117.3665 19070.918 -36063.612 11648.813 61.067533 25754.59 53.919881
80 12.797691 -5.123735 0.023756795 0.48275385 0 0 0.50651065 -4.4264869 -6491.9826 -28436.037 20681.908 -14176.121 -64.024669 -35737.052 -52.583533
90 12.569481 -4.8303379 0.060369422 0.15670502 0 0 0.21707444 -4.4259273 -16762.536 1720.5855 -47624.986 -6793.7441 59.966729 30024.566 52.339671
100 17.750788 -5.1195235 0.039885925 0.38711474 0 0 0.42700067 -4.4279642 -10817.92 -21833.456 4186.8301 -18211.329 -43.11086 -32664.671 -41.508916
Loop time of 0.0160927 on 4 procs for 100 steps with 6 atoms
Performance: 536.891 ns/day, 0.045 hours/ns, 6214.012 timesteps/s
99.7% CPU use with 4 MPI tasks x no OpenMP threads
AMOEBA timing breakdown:
Init time: 0.000643833 4.58%
Hal time: 0.000105979 0.75%
Mpole time: 0.00070704 5.03%
Induce time: 0.0115637 82.32%
Polar time: 0.00101148 7.20%
Total time: 0.0140469
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.014163 | 0.014289 | 0.01443 | 0.1 | 88.79
Bond | 1.3072e-05 | 4.8341e-05 | 8.4206e-05 | 0.0 | 0.30
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00071242 | 0.00081499 | 0.0010064 | 0.0 | 5.06
Output | 0.00041395 | 0.00049646 | 0.0005516 | 0.0 | 3.08
Modify | 2.5768e-05 | 3.3385e-05 | 4.7843e-05 | 0.0 | 0.21
Other | | 0.0004106 | | | 2.55
Nlocal: 1.5 ave 3 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 4.5 ave 6 max 3 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 3.75 ave 12 max 0 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Total # of neighbors = 15
Ave neighs/atom = 2.5
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (23 Jun 2022)
# water dimer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_dimer.hippo fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934)
1 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
4 bonds
reading angles ...
2 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water.key
Reading potential file hippo_water.prm with DATE: 2022-07-05
Reading potential file hippo_water.key with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 10
run 100
HIPPO force field settings
repulsion: cut 10 taper 8 rscale 0 0 1 1
qxfer: cut 10 taper 8 mscale 0 0 0.4 1
dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair hippo, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 47.9 | 47.9 | 47.9 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -5.0101954 0.025695395 0.51472748 0 0 0.54042288 -4.4697726 -11875.159 -38149.178 29162.678 -26638.977 -70.63422 -24614.614 -58.505595
10 0.75132894 -4.7952077 0.028216017 0.28494196 0 0 0.31315798 -4.4708519 -13243.822 12661.254 -49613.657 -2923.1497 69.449413 29456.684 56.087663
20 2.1716525 -5.0036265 0.011809223 0.48875837 0 0 0.50056759 -4.4706925 4371.5298 -22102.532 47044.297 -12243.648 -74.588915 -28903.762 -64.48154
30 2.9930198 -4.8261906 0.0091463366 0.30162756 0 0 0.3107739 -4.4708086 9992.4549 41973.539 -20985.339 8415.1715 67.458145 25027.414 40.261795
40 3.312268 -4.9802484 0.010400667 0.45076258 0 0 0.46116325 -4.4697189 21565.307 -11602.414 65186.215 10476.902 -83.374203 -33222.094 -64.700001
50 4.3187397 -4.8535614 0.0060313545 0.31244652 0 0 0.31847788 -4.4707168 11344.244 45839.35 -21073.749 8438.8954 73.345039 29422.636 43.897876
60 4.9127902 -5.0035271 0.0070589202 0.45246538 0 0 0.4595243 -4.4707824 6529.9354 -37107.891 46740.24 9015.2973 -90.41111 -34402.095 -53.57079
70 5.3145827 -4.8748857 0.025797484 0.29875503 0 0 0.32455252 -4.4711244 -10208.876 26324.134 -49272.688 -8697.2875 84.479942 36185.667 57.000355
80 3.8409793 -5.0262066 0.027669388 0.47104466 0 0 0.49871405 -4.4702464 -9777.1809 -52088.554 28053.855 -6033.4555 -94.607853 -44638.417 -59.108505
90 3.0683704 -4.8369716 0.035455716 0.28466932 0 0 0.32012503 -4.4711155 -10626.245 31066.635 -49425.925 -14107.889 87.765958 34632.905 52.101981
100 3.5262799 -4.9906817 0.016687539 0.45011301 0 0 0.46680055 -4.4713252 5216.7691 -34991.221 43883.163 6082.1058 -95.830393 -48645.129 -64.784334
Loop time of 0.00554871 on 1 procs for 100 steps with 6 atoms
Performance: 1557.118 ns/day, 0.015 hours/ns, 18022.197 timesteps/s
98.4% CPU use with 1 MPI tasks x no OpenMP threads
HIPPO timing breakdown:
Init time: 0.000115545 2.34%
Repulse time: 0.000625219 12.67%
Disp time: 0.000296056 6.00%
Mpole time: 0.000954451 19.35%
Induce time: 0.00169706 34.40%
Polar time: 0.001079 21.87%
Qxfer time: 0.000160858 3.26%
Total time: 0.0049333
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0049642 | 0.0049642 | 0.0049642 | 0.0 | 89.47
Bond | 8.7687e-05 | 8.7687e-05 | 8.7687e-05 | 0.0 | 1.58
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.8012e-05 | 1.8012e-05 | 1.8012e-05 | 0.0 | 0.32
Output | 0.00037567 | 0.00037567 | 0.00037567 | 0.0 | 6.77
Modify | 4.1717e-05 | 4.1717e-05 | 4.1717e-05 | 0.0 | 0.75
Other | | 6.144e-05 | | | 1.11
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 15 ave 15 max 15 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 15
Ave neighs/atom = 2.5
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (23 Jun 2022)
# water dimer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_dimer.hippo fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (-1.463996 -0.756549 -0.009705) to (0.933234 0.75612 2.935934)
2 by 1 by 2 MPI processor grid
reading atoms ...
6 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
4 bonds
reading angles ...
2 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.008 seconds
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water.key
Reading potential file hippo_water.prm with DATE: 2022-07-05
Reading potential file hippo_water.key with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_dimer id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 10
run 100
HIPPO force field settings
repulsion: cut 10 taper 8 rscale 0 0 1 1
qxfer: cut 10 taper 8 mscale 0 0 0.4 1
dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair hippo, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
HIPPO group count: 2
Per MPI rank memory allocation (min/avg/max) = 47.91 | 48.04 | 48.18 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -5.0101954 0.025695395 0.51472748 0 0 0.54042288 -4.4697726 -11875.159 -38149.178 29162.678 -26638.977 -70.63422 -24614.614 -58.505595
10 0.75132894 -4.7952077 0.028216017 0.28494196 0 0 0.31315798 -4.4708519 -13243.822 12661.254 -49613.657 -2923.1497 69.449413 29456.684 56.087663
20 2.1716525 -5.0036265 0.011809223 0.48875837 0 0 0.50056759 -4.4706925 4371.5298 -22102.532 47044.297 -12243.648 -74.588915 -28903.762 -64.48154
30 2.9930198 -4.8261906 0.0091463366 0.30162756 0 0 0.3107739 -4.4708086 9992.4549 41973.539 -20985.339 8415.1715 67.458145 25027.414 40.261795
40 3.312268 -4.9802484 0.010400667 0.45076258 0 0 0.46116325 -4.4697189 21565.307 -11602.414 65186.215 10476.902 -83.374203 -33222.094 -64.700001
50 4.3187397 -4.8535614 0.0060313545 0.31244652 0 0 0.31847788 -4.4707168 11344.244 45839.35 -21073.749 8438.8954 73.345039 29422.636 43.897876
60 4.9127902 -5.0035271 0.0070589202 0.45246538 0 0 0.4595243 -4.4707824 6529.9354 -37107.891 46740.24 9015.2973 -90.41111 -34402.095 -53.57079
70 5.3145827 -4.8748857 0.025797484 0.29875503 0 0 0.32455252 -4.4711244 -10208.876 26324.134 -49272.688 -8697.2875 84.479942 36185.667 57.000355
80 3.8409793 -5.0262066 0.027669388 0.47104466 0 0 0.49871405 -4.4702464 -9777.1809 -52088.554 28053.855 -6033.4555 -94.607853 -44638.417 -59.108505
90 3.0683704 -4.8369716 0.035455716 0.28466932 0 0 0.32012503 -4.4711155 -10626.245 31066.635 -49425.925 -14107.889 87.765958 34632.905 52.101981
100 3.5262799 -4.9906817 0.016687539 0.45011301 0 0 0.46680055 -4.4713252 5216.7691 -34991.221 43883.163 6082.1058 -95.830393 -48645.129 -64.784334
Loop time of 0.0121417 on 4 procs for 100 steps with 6 atoms
Performance: 711.596 ns/day, 0.034 hours/ns, 8236.062 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
HIPPO timing breakdown:
Init time: 0.000597179 5.89%
Repulse time: 0.000498881 4.92%
Disp time: 8.8931e-05 0.88%
Mpole time: 0.000837487 8.26%
Induce time: 0.00727381 71.77%
Polar time: 0.000785393 7.75%
Qxfer time: 4.87313e-05 0.48%
Total time: 0.0101354
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.010257 | 0.010374 | 0.01049 | 0.1 | 85.44
Bond | 1.2833e-05 | 4.7018e-05 | 8.6931e-05 | 0.0 | 0.39
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0006916 | 0.00076578 | 0.00092404 | 0.0 | 6.31
Output | 0.00040685 | 0.00049547 | 0.00057258 | 0.0 | 4.08
Modify | 3.3096e-05 | 3.6004e-05 | 4.4046e-05 | 0.0 | 0.30
Other | | 0.0004238 | | | 3.49
Nlocal: 1.5 ave 3 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Nghost: 4.5 ave 6 max 3 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 3.75 ave 12 max 0 min
Histogram: 2 0 1 0 0 0 0 0 0 1
Total # of neighbors = 15
Ave neighs/atom = 2.5
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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# water hexamer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_hexamer.amoeba fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847)
1 by 1 by 1 MPI processor grid
reading atoms ...
18 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
12 bonds
reading angles ...
6 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water.key
Reading potential file amoeba_water.prm with DATE: 2022-07-05
Reading potential file amoeba_water.key with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 10
run 100
AMOEBA force field settings
hal: cut 10 taper 8 vscale 0 0 1 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair amoeba, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
AMOEBA group count: 6
Per MPI rank memory allocation (min/avg/max) = 48.28 | 48.28 | 48.28 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -48.469664 1.9820353 2.2499329 0 0 4.2319683 -44.237696 -26322.671 -28303.103 -27669.614 -22995.296 1312.6688 2624.8394 4042.0489
10 6.3616471 -46.626437 1.7910812 0.25704063 0 0 2.0481218 -44.255947 -23813.06 -24671.886 -17167.34 -30208.043 -474.208 -8339.5934 -5278.359
20 15.149798 -48.177533 1.1130818 2.007499 0 0 3.1205807 -44.289255 -16468.855 -20150.975 -18596.629 -12107.083 885.52697 6320.1867 3064.949
30 17.896968 -45.959274 0.54802739 0.19519937 0 0 0.74322676 -44.309141 -4749.0624 -9053.7792 -182.37209 -6721.7499 -2003.7641 -627.56998 -1658.1301
40 16.203813 -46.840973 0.1371751 1.5793326 0 0 1.7165077 -44.303357 9267.4858 6108.7966 4116.4548 16028.336 380.03787 8468.0648 4492.3331
50 11.584975 -45.166711 0.017120512 0.28622888 0 0 0.30334939 -44.276308 22189.511 21453.083 22339.471 21668.607 150.93139 1059.5253 200.0668
60 10.002055 -45.994946 0.037889337 1.1987062 0 0 1.2365956 -44.251509 30944.004 35801.925 19832.696 36241.326 2042.3054 2320.5193 1660.0834
70 11.272241 -45.411622 0.07431614 0.51778317 0 0 0.59209931 -44.248316 32055.564 39306.193 30181.52 25601.501 1373.4778 -4501.0686 -2570.4767
80 14.011502 -46.081444 0.089688317 1.006928 0 0 1.0966163 -44.274812 25661.838 38836.598 12603.734 24205.867 -867.36437 -4211.9639 -2820.6725
90 17.659498 -46.247295 0.21744649 0.82687716 0 0 1.0443237 -44.308098 12101.207 19426.995 14142.311 1046.299 -2157.5418 -2141.2454 -2621.456
100 17.630532 -46.788272 0.61811601 0.9654966 0 0 1.5836126 -44.311254 -4455.3587 3961.5737 -11554.095 -7458.8012 -3120.9771 -1532.1706 -1499.0117
Loop time of 0.0418011 on 1 procs for 100 steps with 18 atoms
Performance: 206.693 ns/day, 0.116 hours/ns, 2392.284 timesteps/s
99.4% CPU use with 1 MPI tasks x no OpenMP threads
AMOEBA timing breakdown:
Init time: 0.000326312 0.80%
Hal time: 0.0050371 12.28%
Mpole time: 0.00454501 11.08%
Induce time: 0.0200157 48.79%
Polar time: 0.0110863 27.02%
Total time: 0.0410272
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.041065 | 0.041065 | 0.041065 | 0.0 | 98.24
Bond | 0.00019979 | 0.00019979 | 0.00019979 | 0.0 | 0.48
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 1.5617e-05 | 1.5617e-05 | 1.5617e-05 | 0.0 | 0.04
Output | 0.00037937 | 0.00037937 | 0.00037937 | 0.0 | 0.91
Modify | 6.5901e-05 | 6.5901e-05 | 6.5901e-05 | 0.0 | 0.16
Other | | 7.527e-05 | | | 0.18
Nlocal: 18 ave 18 max 18 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 153 ave 153 max 153 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 153
Ave neighs/atom = 8.5
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (23 Jun 2022)
# water hexamer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_hexamer.amoeba fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847)
2 by 1 by 2 MPI processor grid
reading atoms ...
18 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
12 bonds
reading angles ...
6 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.008 seconds
# force field
pair_style amoeba
pair_coeff * * amoeba_water.prm amoeba_water.key
Reading potential file amoeba_water.prm with DATE: 2022-07-05
Reading potential file amoeba_water.key with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 10
run 100
AMOEBA force field settings
hal: cut 10 taper 8 vscale 0 0 1 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 1 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair amoeba, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
AMOEBA group count: 6
Per MPI rank memory allocation (min/avg/max) = 48.3 | 48.3 | 48.3 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -48.469664 1.9820353 2.2499329 0 0 4.2319683 -44.237696 -26322.671 -28303.103 -27669.614 -22995.296 1312.6688 2624.8394 4042.0489
10 6.3616471 -46.626437 1.7910812 0.25704063 0 0 2.0481218 -44.255947 -23813.06 -24671.886 -17167.34 -30208.043 -474.208 -8339.5934 -5278.359
20 15.149798 -48.177533 1.1130818 2.007499 0 0 3.1205807 -44.289255 -16468.855 -20150.975 -18596.629 -12107.083 885.52697 6320.1867 3064.949
30 17.896968 -45.959274 0.54802739 0.19519937 0 0 0.74322676 -44.309141 -4749.0624 -9053.7792 -182.37209 -6721.7499 -2003.7641 -627.56998 -1658.1301
40 16.203813 -46.840973 0.1371751 1.5793326 0 0 1.7165077 -44.303357 9267.4858 6108.7966 4116.4548 16028.336 380.03787 8468.0648 4492.3331
50 11.584975 -45.166711 0.017120512 0.28622888 0 0 0.30334939 -44.276308 22189.511 21453.083 22339.471 21668.607 150.93139 1059.5253 200.0668
60 10.002055 -45.994946 0.037889337 1.1987062 0 0 1.2365956 -44.251509 30944.004 35801.925 19832.696 36241.326 2042.3054 2320.5193 1660.0834
70 11.272241 -45.411622 0.07431614 0.51778317 0 0 0.59209931 -44.248316 32055.564 39306.193 30181.52 25601.501 1373.4778 -4501.0686 -2570.4767
80 14.011502 -46.081444 0.089688317 1.006928 0 0 1.0966163 -44.274812 25661.838 38836.598 12603.734 24205.867 -867.36437 -4211.9639 -2820.6725
90 17.659498 -46.247295 0.21744649 0.82687716 0 0 1.0443237 -44.308098 12101.207 19426.995 14142.311 1046.299 -2157.5418 -2141.2454 -2621.456
100 17.630532 -46.788272 0.61811601 0.9654966 0 0 1.5836126 -44.311254 -4455.3587 3961.5737 -11554.095 -7458.8012 -3120.9771 -1532.1706 -1499.0117
Loop time of 0.0397428 on 4 procs for 100 steps with 18 atoms
Performance: 217.398 ns/day, 0.110 hours/ns, 2516.180 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
AMOEBA timing breakdown:
Init time: 0.000772875 2.05%
Hal time: 0.00114925 3.04%
Mpole time: 0.00316129 8.37%
Induce time: 0.0278156 73.61%
Polar time: 0.0048762 12.90%
Total time: 0.0377876
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.03793 | 0.038002 | 0.038115 | 0.0 | 95.62
Bond | 6.3821e-05 | 8.0969e-05 | 9.9652e-05 | 0.0 | 0.20
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00067584 | 0.00085989 | 0.0009896 | 0.0 | 2.16
Output | 0.00035407 | 0.00040202 | 0.00051789 | 0.0 | 1.01
Modify | 3.6589e-05 | 4.0916e-05 | 4.417e-05 | 0.0 | 0.10
Other | | 0.0003569 | | | 0.90
Nlocal: 4.5 ave 6 max 3 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 13.5 ave 15 max 12 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 38.25 ave 77 max 9 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 153
Ave neighs/atom = 8.5
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

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LAMMPS (23 Jun 2022)
# water hexamer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_hexamer.hippo fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847)
1 by 1 by 1 MPI processor grid
reading atoms ...
18 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
12 bonds
reading angles ...
6 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water.key
Reading potential file hippo_water.prm with DATE: 2022-07-05
Reading potential file hippo_water.key with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 10
run 100
HIPPO force field settings
repulsion: cut 10 taper 8 rscale 0 0 1 1
qxfer: cut 10 taper 8 mscale 0 0 0.4 1
dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair hippo, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 47.84 | 47.84 | 47.84 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -47.362156 1.9820353 1.6634749 0 0 3.6455102 -43.716646 -34513.768 -42206.078 -31383.641 -29951.584 2850.1184 3579.9253 5768.3698
10 11.52238 -45.959856 1.53397 0.085100522 0 0 1.6190706 -43.756903 -28644.676 -34867.94 -19324.955 -32842.522 -370.63233 -6452.0859 -4002.3535
20 20.237283 -46.772008 0.54762833 1.3835192 0 0 1.9311476 -43.815361 -10546.356 -10116.359 -17063.425 -6393.701 -1166.7608 4243.6327 3493.9596
30 20.666374 -45.011106 0.086797459 0.071122604 0 0 0.15792006 -43.805943 13150.762 15882.022 10964.553 10630.278 -6754.7642 -432.29165 -3783.115
40 10.639014 -45.430939 0.18926921 0.96410995 0 0 1.1533792 -43.738441 33402.664 41252.58 19726.586 38211.875 -6166.03 6081.5692 1815.7739
50 10.992432 -44.741108 0.19575431 0.25851128 0 0 0.45426559 -43.729815 37696.923 41572.466 33299.43 37168.141 -3254.5134 2.9639226 -1017.3669
60 19.748633 -45.461264 0.035287281 0.63217389 0 0 0.66746117 -43.793065 26212.839 28825.788 16048.096 31876.925 3504.5461 135.3505 420.28566
70 26.129957 -46.022729 0.30434543 0.56770169 0 0 0.87204711 -43.826579 3919.9866 -2755.6905 11500.428 517.54333 5626.9543 -2238.5786 86.305984
80 17.768494 -46.309777 1.1680612 0.45551823 0 0 1.6235794 -43.785801 -18335.898 -22168.789 -14488.992 -20048.346 7343.173 -2646.2196 -2525.6625
90 8.3822494 -47.063502 2.0182644 0.88875358 0 0 2.9070179 -43.731724 -33693.203 -43487.996 -15178.35 -43214.494 2412.6411 1993.0113 1780.7512
100 8.6486333 -46.517402 1.9551958 0.38696887 0 0 2.3421647 -43.736979 -34734.97 -34372.659 -28372.146 -42286.799 226.18821 40.353457 -755.93912
Loop time of 0.0384281 on 1 procs for 100 steps with 18 atoms
Performance: 224.836 ns/day, 0.107 hours/ns, 2602.266 timesteps/s
99.7% CPU use with 1 MPI tasks x no OpenMP threads
HIPPO timing breakdown:
Init time: 0.000296169 0.79%
Repulse time: 0.00605807 16.08%
Disp time: 0.00222186 5.90%
Mpole time: 0.00734879 19.51%
Induce time: 0.0128126 34.02%
Polar time: 0.00749189 19.89%
Qxfer time: 0.00142542 3.78%
Total time: 0.0376635
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.037703 | 0.037703 | 0.037703 | 0.0 | 98.11
Bond | 0.00016755 | 0.00016755 | 0.00016755 | 0.0 | 0.44
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 2.4711e-05 | 2.4711e-05 | 2.4711e-05 | 0.0 | 0.06
Output | 0.00038288 | 0.00038288 | 0.00038288 | 0.0 | 1.00
Modify | 6.4863e-05 | 6.4863e-05 | 6.4863e-05 | 0.0 | 0.17
Other | | 8.521e-05 | | | 0.22
Nlocal: 18 ave 18 max 18 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 153 ave 153 max 153 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 153
Ave neighs/atom = 8.5
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

151
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LAMMPS (23 Jun 2022)
# water hexamer with AMOEBA or HIPPO
units real
boundary s s s
atom_style amoeba
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 d_redID d_pval ghost yes
fix extra2 all property/atom i_polaxe d2_xyzaxis 3
# read data file
read_data data.water_hexamer.hippo fix amtype NULL "Tinker Types"
Reading data file ...
orthogonal box = (-2.517835 -1.523041 -1.734766) to (2.675716 2.01883 2.220847)
2 by 1 by 2 MPI processor grid
reading atoms ...
18 atoms
scanning bonds ...
2 = max bonds/atom
scanning angles ...
1 = max angles/atom
reading bonds ...
12 bonds
reading angles ...
6 angles
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.008 seconds
# force field
pair_style hippo
pair_coeff * * hippo_water.prm hippo_water.key
Reading potential file hippo_water.prm with DATE: 2022-07-05
Reading potential file hippo_water.key with DATE: 2022-07-05
special_bonds lj/coul 0.5 0.5 0.5 one/five yes
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.5 0.5 0.5
special bond factors coul: 0.5 0.5 0.5
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
1 = max # of 1-4 neighbors
2 = max # of 1-5 neighbors
2 = max # of special neighbors
special bonds CPU = 0.001 seconds
# thermo output
compute virial all pressure NULL virial
thermo_style custom step temp epair ebond eangle edihed eimp emol etotal press c_virial[*]
#dump 1 all custom 10 dump.water_hexamer id type x y z fx fy fz
#dump_modify 1 sort id
# dynamics
fix 1 all nve
thermo 10
run 100
HIPPO force field settings
repulsion: cut 10 taper 8 rscale 0 0 1 1
qxfer: cut 10 taper 8 mscale 0 0 0.4 1
dispersion: cut 10 aewald 0 dspscale 0 0 0.4 1
multipole: cut 10 aewald 0 mscale 0 0 0.4 1
polar: cut 10 aewald 0
pscale 0 0 1 1 piscale 0 0 0.5 1 wscale 0.2 1 1 1 d/u scale 0 1
precondition: cut 4.5
Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 1 1 1
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair hippo, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
WARNING: Proc sub-domain size < neighbor skin, could lead to lost atoms (../domain.cpp:970)
HIPPO group count: 6
Per MPI rank memory allocation (min/avg/max) = 47.86 | 47.86 | 47.86 Mbytes
Step Temp E_pair E_bond E_angle E_dihed E_impro E_mol TotEng Press c_virial[1] c_virial[2] c_virial[3] c_virial[4] c_virial[5] c_virial[6]
0 0 -47.362156 1.9820353 1.6634749 0 0 3.6455102 -43.716646 -34513.768 -42206.078 -31383.641 -29951.584 2850.1184 3579.9253 5768.3698
10 11.52238 -45.959856 1.53397 0.085100522 0 0 1.6190706 -43.756903 -28644.676 -34867.94 -19324.955 -32842.522 -370.63233 -6452.0859 -4002.3535
20 20.237283 -46.772008 0.54762833 1.3835192 0 0 1.9311476 -43.815361 -10546.356 -10116.359 -17063.425 -6393.701 -1166.7608 4243.6327 3493.9596
30 20.666374 -45.011106 0.086797459 0.071122604 0 0 0.15792006 -43.805943 13150.762 15882.022 10964.553 10630.278 -6754.7642 -432.29165 -3783.115
40 10.639014 -45.430939 0.18926921 0.96410995 0 0 1.1533792 -43.738441 33402.664 41252.58 19726.586 38211.875 -6166.03 6081.5692 1815.7739
50 10.992432 -44.741108 0.19575431 0.25851128 0 0 0.45426559 -43.729815 37696.923 41572.466 33299.43 37168.141 -3254.5134 2.9639226 -1017.3669
60 19.748633 -45.461264 0.035287281 0.63217389 0 0 0.66746117 -43.793065 26212.839 28825.788 16048.096 31876.925 3504.5461 135.3505 420.28566
70 26.129957 -46.022729 0.30434543 0.56770169 0 0 0.87204711 -43.826579 3919.9866 -2755.6905 11500.428 517.54333 5626.9543 -2238.5786 86.305984
80 17.768494 -46.309777 1.1680612 0.45551823 0 0 1.6235794 -43.785801 -18335.898 -22168.789 -14488.992 -20048.346 7343.173 -2646.2196 -2525.6625
90 8.3822494 -47.063502 2.0182644 0.88875358 0 0 2.9070179 -43.731724 -33693.203 -43487.996 -15178.35 -43214.494 2412.6411 1993.0113 1780.7512
100 8.6486333 -46.517402 1.9551958 0.38696887 0 0 2.3421647 -43.736979 -34734.97 -34372.659 -28372.146 -42286.799 226.18821 40.353457 -755.93912
Loop time of 0.0332539 on 4 procs for 100 steps with 18 atoms
Performance: 259.819 ns/day, 0.092 hours/ns, 3007.165 timesteps/s
99.4% CPU use with 4 MPI tasks x no OpenMP threads
HIPPO timing breakdown:
Init time: 0.000776397 2.52%
Repulse time: 0.00298646 9.69%
Disp time: 0.000570048 1.85%
Mpole time: 0.00370735 12.02%
Induce time: 0.0186844 60.59%
Polar time: 0.00372843 12.09%
Qxfer time: 0.000377474 1.22%
Total time: 0.0308356
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.030832 | 0.031056 | 0.031379 | 0.1 | 93.39
Bond | 7.9467e-05 | 9.2634e-05 | 0.00010651 | 0.0 | 0.28
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.00073586 | 0.0011119 | 0.001379 | 0.8 | 3.34
Output | 0.00045718 | 0.00052546 | 0.00061508 | 0.0 | 1.58
Modify | 3.7723e-05 | 5.1869e-05 | 6.5238e-05 | 0.0 | 0.16
Other | | 0.000416 | | | 1.25
Nlocal: 4.5 ave 6 max 3 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Nghost: 13.5 ave 15 max 12 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 38.25 ave 77 max 9 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 153
Ave neighs/atom = 8.5
Ave special neighs/atom = 2
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:00

9738
examples/amoeba/ubiquitin.xyz Normal file
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649
examples/amoeba/water_box.xyz Normal file
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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
167 H 0.110320 -0.665826 5.311239 2 166
168 H 0.420366 -2.216367 5.267301 2 166
169 O 1.100526 1.019490 -9.255318 1 170 171
170 H 1.460815 0.575286 -8.484128 2 169
171 H 0.265613 0.594128 -9.297750 2 169
172 O -1.842348 2.327827 -5.355326 1 173 174
173 H -1.572941 2.573139 -6.288125 2 172
174 H -2.216679 1.439934 -5.361006 2 172
175 O 2.452307 -2.814686 -6.448759 1 176 177
176 H 2.862295 -3.091668 -5.589336 2 175
177 H 2.913920 -3.262923 -7.181510 2 175
178 O -2.207998 -3.112007 5.945795 1 179 180
179 H -1.262203 -3.125339 6.205467 2 178
180 H -2.228269 -2.421858 5.220629 2 178
181 O 5.845471 5.020556 -6.836491 1 182 183
182 H 5.557986 5.913737 -6.753889 2 181
183 H 5.089998 4.459153 -6.661079 2 181
184 O -3.421643 4.865553 0.731755 1 185 186
185 H -3.965419 4.458452 1.478214 2 184
186 H -3.973445 4.958338 -0.044430 2 184
187 O -2.302950 -2.349717 2.112168 1 188 189
188 H -2.576438 -1.873492 2.873191 2 187
189 H -1.882868 -1.715106 1.503782 2 187
190 O 0.305885 4.878766 3.791182 1 191 192
191 H 0.299338 5.855407 4.097578 2 190
192 H 1.169911 4.563497 4.030616 2 190
193 O 2.925008 -3.664845 -3.607450 1 194 195
194 H 3.015896 -3.916618 -2.644267 2 193
195 H 2.353923 -2.889459 -3.518284 2 193
196 O 1.111505 -4.070255 -9.085693 1 197 198
197 H 2.084905 -4.227348 -9.180249 2 196
198 H 0.897072 -4.902218 -8.740523 2 196
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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
View 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

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