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Merge branch 'develop' into test-fix-numdiff

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This commit is contained in:
Axel Kohlmeyer
2024-01-26 23:21:44 -05:00
parent b6b2c029b6 7d53f8d1c5
commit 75c20aa5a5
649 changed files with 6975 additions and 4491 deletions
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2
.github/workflows/coverity.yml vendored
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@ -25,7 +25,7 @@ jobs:
- name: Cache Coverity
id: cache-coverity
uses: actions/cache@v3
uses: actions/cache@v4
with:
path: ./download/
key: ${{ runner.os }}-download-${{ hashFiles('**/coverity_tool.*') }}

2
.github/workflows/unittest-macos.yml vendored
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@ -32,7 +32,7 @@ jobs:
run: mkdir build
- name: Set up ccache
uses: actions/cache@v3
uses: actions/cache@v4
with:
path: ${{ env.CCACHE_DIR }}
key: macos-ccache-${{ github.sha }}

7
cmake/Modules/Packages/GPU.cmake
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@ -1,3 +1,10 @@
# Silence CMake warnings about FindCUDA being obsolete.
# We may need to eventually rewrite this section to use enable_language(CUDA)
if(POLICY CMP0146)
cmake_policy(SET CMP0146 OLD)
endif()
set(GPU_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/GPU)
set(GPU_SOURCES ${GPU_SOURCES_DIR}/gpu_extra.h
${GPU_SOURCES_DIR}/fix_gpu.h

4
cmake/Modules/Packages/MDI.cmake
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@ -8,8 +8,8 @@ option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an al
if(DOWNLOAD_MDI)
message(STATUS "MDI download requested - we will build our own")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.16.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "407db44e2d79447ab5c1233af1965f65" CACHE STRING "MD5 checksum for MDI tarball")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.26.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "3124bb85259471e2a53a891f04bf697a" CACHE STRING "MD5 checksum for MDI tarball")
mark_as_advanced(MDI_URL)
mark_as_advanced(MDI_MD5)
GetFallbackURL(MDI_URL MDI_FALLBACK)

3
doc/Makefile
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@ -100,6 +100,7 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
echo "############################################" ;\
deactivate ;\
@ -182,6 +183,7 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst ;\
env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst ;\
$(PYTHON) utils/check-styles.py -s ../src -d src ;\
echo "############################################" ;\
deactivate ;\
@ -231,6 +233,7 @@ role_check :
@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
@( env LC_ALL=C grep -n ':\(ref\|doc\):[^`]' $(RSTDIR)/*.rst && exit 1 || : )
@( env LC_ALL=C grep -n '\(ref\|doc\)`[^`]' $(RSTDIR)/*.rst && exit 1 || : )
link_check : $(VENV) html
@(\

2
doc/src/Commands_bond.rst
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@ -124,7 +124,7 @@ OPT.
*
*
* :doc:`charmm (iko) <dihedral_charmm>`
* :doc:`charmmfsw <dihedral_charmm>`
* :doc:`charmmfsw (k) <dihedral_charmm>`
* :doc:`class2 (ko) <dihedral_class2>`
* :doc:`cosine/shift/exp (o) <dihedral_cosine_shift_exp>`
* :doc:`fourier (io) <dihedral_fourier>`

2
doc/src/Commands_pair.rst
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@ -146,7 +146,7 @@ OPT.
* :doc:`lj/charmm/coul/long/soft (o) <pair_fep_soft>`
* :doc:`lj/charmm/coul/msm (o) <pair_charmm>`
* :doc:`lj/charmmfsw/coul/charmmfsh <pair_charmm>`
* :doc:`lj/charmmfsw/coul/long <pair_charmm>`
* :doc:`lj/charmmfsw/coul/long (k) <pair_charmm>`
* :doc:`lj/class2 (gko) <pair_class2>`
* :doc:`lj/class2/coul/cut (ko) <pair_class2>`
* :doc:`lj/class2/coul/cut/soft <pair_fep_soft>`

66
doc/src/Developer_updating.rst
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@ -20,6 +20,7 @@ Available topics in mostly chronological order are:
- `Use ev_init() to initialize variables derived from eflag and vflag`_
- `Use utils::numeric() functions instead of force->numeric()`_
- `Use utils::open_potential() function to open potential files`_
- `Use symbolic Atom and AtomVec constants instead of numerical values`_
- `Simplify customized error messages`_
- `Use of "override" instead of "virtual"`_
- `Simplified and more compact neighbor list requests`_
@ -196,6 +197,71 @@ New:
fp = utils::open_potential(filename, lmp);
Use symbolic Atom and AtomVec constants instead of numerical values
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. versionchanged:: 18Sep2020
Properties in LAMMPS that were represented by integer values (0, 1,
2, 3) to indicate settings in the ``Atom`` and ``AtomVec`` classes (or
classes derived from it) (and its derived classes) have been converted
to use scoped enumerators instead.
.. list-table::
:header-rows: 1
:widths: auto
* - Symbolic Constant
- Value
- Symbolic Constant
- Value
* - Atom::GROW
- 0
- Atom::MAP_NONE
- 0
* - Atom::RESTART
- 1
- Atom::MAP_ARRAY
- 1
* - Atom::BORDER
- 2
- Atom::MAP_HASH
- 2
* - Atom::ATOMIC
- 0
- Atom::MAP_YES
- 3
* - Atom::MOLECULAR
- 1
- AtomVec::PER_ATOM
- 0
* - Atom::TEMPLATE
- 2
- AtomVec::PER_TYPE
- 1
Old:
.. code-block:: c++
molecular = 0;
mass_type = 1;
if (atom->molecular == 2)
if (atom->map_style == 2)
atom->add_callback(0);
atom->delete_callback(id,1);
New:
.. code-block:: c++
molecular = Atom::ATOMIC;
mass_type = AtomVec::PER_TYPE;
if (atom->molecular == Atom::TEMPLATE)
if (atom->map_style == Atom::MAP_HASH)
atom->add_callback(Atom::GROW);
atom->delete_callback(id,Atom::RESTART);
Simplify customized error messages
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

45
doc/src/Fortran.rst
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@ -315,6 +315,10 @@ of the contents of the :f:mod:`LIBLAMMPS` Fortran interface to LAMMPS.
:ftype extract_variable: function
:f set_variable: :f:subr:`set_variable`
:ftype set_variable: subroutine
:f set_string_variable: :f:subr:`set_set_string_variable`
:ftype set_string_variable: subroutine
:f set_internal_variable: :f:subr:`set_internal_variable`
:ftype set_internal_variable: subroutine
:f gather_atoms: :f:subr:`gather_atoms`
:ftype gather_atoms: subroutine
:f gather_atoms_concat: :f:subr:`gather_atoms_concat`
@ -1398,7 +1402,28 @@ Procedures Bound to the :f:type:`lammps` Derived Type
Set the value of a string-style variable.
.. versionadded:: 3Nov2022
.. deprecated:: TBD
This function assigns a new value from the string *str* to the string-style
variable *name*\ . If *name* does not exist or is not a string-style
variable, an error is generated.
.. warning::
This subroutine is deprecated and :f:subr:`set_string_variable`
should be used instead.
:p character(len=*) name: name of the variable
:p character(len=*) str: new value to assign to the variable
:to: :cpp:func:`lammps_set_variable`
--------
.. f:subroutine:: set_string_variable(name, str)
Set the value of a string-style variable.
.. versionadded:: TBD
This function assigns a new value from the string *str* to the string-style
variable *name*\ . If *name* does not exist or is not a string-style
@ -1406,7 +1431,23 @@ Procedures Bound to the :f:type:`lammps` Derived Type
:p character(len=*) name: name of the variable
:p character(len=*) str: new value to assign to the variable
:to: :cpp:func:`lammps_set_variable`
:to: :cpp:func:`lammps_set_string_variable`
--------
.. f:subroutine:: set_internal_variable(name, val)
Set the value of a internal-style variable.
.. versionadded:: TBD
This function assigns a new value from the floating-point number *val* to
the internal-style variable *name*\ . If *name* does not exist or is not
an internal-style variable, an error is generated.
:p character(len=*) name: name of the variable
:p read(c_double) val: new value to assign to the variable
:to: :cpp:func:`lammps_set_internal_variable`
--------

12
doc/src/Library_objects.rst
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@ -9,6 +9,8 @@ fixes, or variables in LAMMPS using the following functions:
- :cpp:func:`lammps_extract_variable_datatype`
- :cpp:func:`lammps_extract_variable`
- :cpp:func:`lammps_set_variable`
- :cpp:func:`lammps_set_string_variable`
- :cpp:func:`lammps_set_internal_variable`
- :cpp:func:`lammps_variable_info`
-----------------------
@ -38,6 +40,16 @@ fixes, or variables in LAMMPS using the following functions:
-----------------------
.. doxygenfunction:: lammps_set_string_variable
:project: progguide
-----------------------
.. doxygenfunction:: lammps_set_internal_variable
:project: progguide
-----------------------
.. doxygenfunction:: lammps_variable_info
:project: progguide

4
doc/src/angle_charmm.rst
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@ -70,7 +70,9 @@ for more info.
Related commands
""""""""""""""""
:doc:`angle_coeff <angle_coeff>`
:doc:`angle_coeff <angle_coeff>`, :doc:`pair_style lj/charmm variants <pair_charmm>`,
:doc:`dihedral_style charmm <dihedral_charmm>`,
:doc:`dihedral_style charmmfsw <dihedral_charmm>`, :doc:`fix cmap <fix_cmap>`
Default
"""""""

19
doc/src/angle_lepton.rst
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@ -11,7 +11,16 @@ Syntax
.. code-block:: LAMMPS
angle_style lepton
angle_style style args
* style = *lepton*
* args = optional arguments
.. parsed-literal::
args = *auto_offset* or *no_offset*
*auto_offset* = offset the potential energy so that the value at theta0 is 0.0 (default)
*no_offset* = do not offset the potential energy
Examples
""""""""
@ -19,6 +28,7 @@ Examples
.. code-block:: LAMMPS
angle_style lepton
angle_style lepton no_offset
angle_coeff 1 120.0 "k*theta^2; k=250.0"
angle_coeff 2 90.0 "k2*theta^2 + k3*theta^3 + k4*theta^4; k2=300.0; k3=-100.0; k4=50.0"
@ -41,6 +51,13 @@ angle coefficient. For example `"200.0*theta^2"` represents a
U_{angle,i} = K (\theta_i - \theta_0)^2 = K \theta^2 \qquad \theta = \theta_i - \theta_0
.. versionchanged:: TBD
By default the potential energy U is shifted so that the value U is 0.0
for $theta = theta_0$. This is equivalent to using the optional keyword
*auto_offset*. When using the keyword *no_offset* instead, the
potential energy is not shifted.
The `Lepton library <https://simtk.org/projects/lepton>`_, that the
*lepton* angle style interfaces with, evaluates this expression string
at run time to compute the pairwise energy. It also creates an

614
doc/src/atom_style.rst
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@ -49,248 +49,221 @@ Examples
Description
"""""""""""
Define what style of atoms to use in a simulation. This determines
what attributes are associated with the atoms. This command must be
used before a simulation is setup via a :doc:`read_data <read_data>`,
:doc:`read_restart <read_restart>`, or :doc:`create_box <create_box>`
command.
The *atom_style* command selects which per-atom attributes are
associated with atoms in a LAMMPS simulation and thus stored and
communicated with those atoms as well as read from and stored in data
and restart files. Different models (e.g. :doc:`pair styles
<pair_style>`) require access to specific per-atom attributes and thus
require a specific atom style. For example, to compute Coulomb
interactions, the atom must have a "charge" (aka "q") attribute.
A number of distinct atom styles exist that combine attributes. Some
atom styles are a superset of other atom styles. Further attributes
may be added to atoms either via using a hybrid style which provides a
union of the attributes of the sub-styles, or via the :doc:`fix
property/atom <fix_property_atom>` command. The *atom_style* command
must be used before a simulation is setup via a :doc:`read_data
<read_data>`, :doc:`read_restart <read_restart>`, or :doc:`create_box
<create_box>` command.
.. note::
Many of the atom styles discussed here are only enabled if
LAMMPS was built with a specific package, as listed below in the
Restrictions section.
Many of the atom styles discussed here are only enabled if LAMMPS was
built with a specific package, as listed below in the Restrictions
section.
Once a style is assigned, it cannot be changed, so use a style general
enough to encompass all attributes. E.g. with style *bond*, angular
terms cannot be used or added later to the model. It is OK to use a
style more general than needed, though it may be slightly inefficient.
Once a style is selected and the simulation box defined, it cannot be
changed but only augmented with the :doc:`fix property/atom
<fix_property_atom>` command. So one should select an atom style
general enough to encompass all attributes required. E.g. with atom
style *bond*, it is not possible to define angles and use angle styles.
The choice of style affects what quantities are stored by each atom,
what quantities are communicated between processors to enable forces
to be computed, and what quantities are listed in the data file read
by the :doc:`read_data <read_data>` command.
It is OK to use a style more general than needed, though it may be
slightly inefficient because it will allocate and communicate
additional unused data.
These are the additional attributes of each style and the typical
kinds of physical systems they are used to model. All styles store
coordinates, velocities, atom IDs and types. See the
Atom style attributes
"""""""""""""""""""""
The atom style *atomic* has the minimum subset of per-atom attributes
and is also the default setting. It encompasses the following per-atom
attributes (name of the vector or array in the :doc:`Atom class
<Classes_atom>` is given in parenthesis): atom-ID (tag), type (type),
position (x), velocities (v), forces (f), image flags (image), group
membership (mask). Since all atom styles are a superset of atom style
*atomic*\ , they all include these attributes.
This table lists all the available atom styles, which attributes they
provide, which :doc:`package <Packages>` is required to use them, and
what the typical applications are that use them. See the
:doc:`read_data <read_data>`, :doc:`create_atoms <create_atoms>`, and
:doc:`set <set>` commands for info on how to set these various
quantities.
:doc:`set <set>` commands for details on how to set these various
quantities. More information about many of the styles is provided in
the Additional Information section below.
+--------------+-----------------------------------------------------+--------------------------------------+
| *amoeba* | molecular + charge + 1/5 neighbors | AMOEBA/HIPPO polarized force fields |
+--------------+-----------------------------------------------------+--------------------------------------+
| *angle* | bonds and angles | bead-spring polymers with stiffness |
+--------------+-----------------------------------------------------+--------------------------------------+
| *atomic* | only the default values | coarse-grain liquids, solids, metals |
+--------------+-----------------------------------------------------+--------------------------------------+
| *body* | mass, inertia moments, quaternion, angular momentum | arbitrary bodies |
+--------------+-----------------------------------------------------+--------------------------------------+
| *bond* | bonds | bead-spring polymers |
+--------------+-----------------------------------------------------+--------------------------------------+
| *charge* | charge | atomic system with charges |
+--------------+-----------------------------------------------------+--------------------------------------+
| *dielectric* | normx normy normz area/patch ed em epsilon curv | system with surface polarization |
+--------------+-----------------------------------------------------+--------------------------------------+
| *dipole* | charge and dipole moment | system with dipolar particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *dpd* | internal temperature and internal energies | DPD particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *edpd* | temperature and heat capacity | eDPD particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *electron* | charge and spin and eradius | electronic force field |
+--------------+-----------------------------------------------------+--------------------------------------+
| *ellipsoid* | shape, quaternion, angular momentum | aspherical particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *full* | molecular + charge | bio-molecules |
+--------------+-----------------------------------------------------+--------------------------------------+
| *line* | end points, angular velocity | rigid bodies |
+--------------+-----------------------------------------------------+--------------------------------------+
| *mdpd* | density | mDPD particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *molecular* | bonds, angles, dihedrals, impropers | uncharged molecules |
+--------------+-----------------------------------------------------+--------------------------------------+
| *oxdna* | nucleotide polarity | coarse-grained DNA and RNA models |
+--------------+-----------------------------------------------------+--------------------------------------+
| *peri* | mass, volume | mesoscopic Peridynamic models |
+--------------+-----------------------------------------------------+--------------------------------------+
| *smd* | volume, kernel diameter, contact radius, mass | solid and fluid SPH particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *sph* | rho, esph, cv | SPH particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *sphere* | diameter, mass, angular velocity | granular models |
+--------------+-----------------------------------------------------+--------------------------------------+
| *bpm/sphere* | diameter, mass, angular velocity, quaternion | granular bonded particle models (BPM)|
+--------------+-----------------------------------------------------+--------------------------------------+
| *spin* | magnetic moment | system with magnetic particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *tdpd* | chemical concentration | tDPD particles |
+--------------+-----------------------------------------------------+--------------------------------------+
| *template* | template index, template atom | small molecules with fixed topology |
+--------------+-----------------------------------------------------+--------------------------------------+
| *tri* | corner points, angular momentum | rigid bodies |
+--------------+-----------------------------------------------------+--------------------------------------+
| *wavepacket* | charge, spin, eradius, etag, cs_re, cs_im | AWPMD |
+--------------+-----------------------------------------------------+--------------------------------------+
.. list-table::
:header-rows: 1
:widths: auto
* - Atom style
- Attributes
- Required package
- Applications
* - *amoeba*
- *full* + "1-5 special neighbor data"
- :ref:`AMOEBA <PKG-AMOEBA>`
- AMOEBA/HIPPO force fields
* - *angle*
- *bond* + "angle data"
- :ref:`MOLECULE <PKG-MOLECULE>`
- bead-spring polymers with stiffness
* - *atomic*
- tag, type, x, v, f, image, mask
-
- atomic liquids, solids, metals
* - *body*
- *atomic* + radius, rmass, angmom, torque, body
- :ref:`BODY <PKG-BODY>`
- arbitrary bodies, see :doc:`body howto <Howto_body>`
* - *bond*
- *atomic* + molecule, nspecial, special + "bond data"
- :ref:`MOLECULE <PKG-MOLECULE>`
- bead-spring polymers
* - *bpm/sphere*
- *bond* + radius, rmass, omega, torque, quat
- :ref:`BPM <PKG-BPM>`
- granular bonded particle models, see :doc:`BPM howto <Howto_bpm>`
* - *charge*
- *atomic* + q
-
- atomic systems with charges
* - *dielectric*
- *full* + mu, area, ed, em, epsilon, curvature, q_scaled
- :ref:`DIELECTRIC <PKG-DIELECTRIC>`
- systems with surface polarization
* - *dipole*
- *charge* + mu
- :ref:`DIPOLE <PKG-DIPOLE>`
- atomic systems with charges and point dipoles
* - *dpd*
- *atomic* + rho + "reactive DPD data"
- :ref:`DPD-REACT <PKG-DPD-REACT>`
- reactive DPD
* - *edpd*
- *atomic* + "eDPD data"
- :ref:`DPD-MESO <PKG-DPD-MESO>`
- Energy conservative DPD (eDPD)
* - *electron*
- *charge* + espin, eradius, ervel, erforce
- :ref:`EFF <PKG-EFF>`
- Electron force field systems
* - *ellipsoid*
- *atomic* + rmass, angmom, torque, ellipsoid
-
- aspherical particles
* - *full*
- *molecular* + q
- :ref:`MOLECULE <PKG-MOLECULE>`
- molecular force fields
* - *line*
- *atomic* + molecule, radius, rmass, omega, torque, line
-
- 2-d rigid body particles
* - *mdpd*
- *atomic* + rho, drho, vest
- :ref:`DPD-MESO <PKG-DPD-MESO>`
- Many-body DPD (mDPD)
* - *molecular*
- *angle* + "dihedral and improper data"
- :ref:`MOLECULE <PKG-MOLECULE>`
- apolar and uncharged molecules
* - *oxdna*
- *atomic* + id5p
- :ref:`CG-DNA <PKG-CG-DNA>`
- coarse-grained DNA and RNA models
* - *peri*
- *atomic* + rmass, vfrac, s0, x0
- :ref:`PERI <PKG-PERI>`
- mesoscopic Peridynamics models
* - *smd*
- *atomic* + molecule, radius, rmass + "smd data"
- :ref:`MACHDYN <PKG-MACHDYN>`
- Smooth Mach Dynamics models
* - *sph*
- *atomic* + "sph data"
- :ref:`SPH <PKG-SPH>`
- Smoothed particle hydrodynamics models
* - *sphere*
- *atomic* + radius, rmass, omega, torque
-
- finite size spherical particles, e.g. granular models
* - *spin*
- *atomic* + "magnetic moment data"
- :ref:`SPIN <PKG-SPIN>`
- magnetic particles
* - *tdpd*
- *atomic* + cc, cc_flux, vest
- :ref:`DPD-MESO <PKG-DPD-MESO>`
- Transport DPD (tDPD)
* - *template*
- *atomic* + molecule, molindex, molatom
- :ref:`MOLECULE <PKG-MOLECULE>`
- molecular systems where attributes are taken from :doc:`molecule files <molecule>`
* - *tri*
- *sphere* + molecule, angmom, tri
-
- 3-d triangulated rigid body LJ particles
* - *wavepacket*
- *charge* + "wavepacket data"
- :ref:`AWPMD <PKG-AWPMD>`
- Antisymmetrized wave packet MD
.. 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.
It is possible to add some attributes, such as a molecule ID and
charge, to atom styles that do not have them built in using the
:doc:`fix property/atom <fix_property_atom>` command. This command
also allows new custom-named attributes consisting of extra integer
or floating-point values or vectors 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 these custom values.
All of the above styles define point particles, except the *sphere*,
*bpm/sphere*, *ellipsoid*, *electron*, *peri*, *wavepacket*, *line*,
*tri*, and *body* styles, which define finite-size particles. See the
:doc:`Howto spherical <Howto_spherical>` page for an overview of using
finite-size particle models with LAMMPS.
----------
All of the point-particle styles assign mass to particles on a
per-type basis, using the :doc:`mass <mass>` command, The finite-size
particle styles assign mass to individual particles on a per-particle
basis.
Particle size and mass
""""""""""""""""""""""
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. These
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.
All of the atom styles define point particles unless they (1) define
finite-size spherical particles via the *radius* attribute, or (2)
define finite-size aspherical particles (e.g. the *body*, *ellipsoid*,
*line*, and *tri* styles). Most of these styles can also be used with
mixtures of point and finite-size particles.
For the *ellipsoid* style, the particles are ellipsoids and each
stores a flag which indicates whether it is a finite-size ellipsoid or
a point particle. If it is an ellipsoid, it also stores a shape
vector with the 3 diameters of the ellipsoid and a quaternion 4-vector
with its orientation.
Note that the *radius* property may need to be provided as a
*diameter* (e.g. in :doc:`molecule files <molecule>` or :doc:`data
files <read_data>`). See the :doc:`Howto spherical <Howto_spherical>`
page for an overview of using finite-size spherical and aspherical
particle models with LAMMPS.
For the *dielectric* style, each particle can be either a physical
particle (e.g. an ion), or an interface particle representing a boundary
element between two regions of different dielectric constant. For
interface particles, in addition to the properties associated with
atom_style full, each particle also should be assigned a normal unit
vector (defined by normx, normy, normz), an area (area/patch), the
difference and mean of the dielectric constants of two sides of the
interface along the direction of the normal vector (ed and em), the
local dielectric constant at the boundary element (epsilon), and a mean
local curvature (curv). Physical particles must be assigned these
values, as well, but only their local dielectric constants will be used;
see documentation for associated :doc:`pair styles <pair_dielectric>`
and :doc:`fixes <fix_polarize>`. The distinction between the physical
and interface particles is only meaningful when :doc:`fix polarize
<fix_polarize>` commands are applied to the interface particles. This
style is part of the DIELECTRIC package.
Unless an atom style defines the per-atom *rmass* attribute, particle
masses are defined on a per-type basis, using the :doc:`mass <mass>`
command. This means each particle's mass is indexed by its atom
*type*.
For the *dipole* style, a point dipole is defined for each point
particle. Note that if you wish the particles to be finite-size
spheres as in a Stockmayer potential for a dipolar fluid, so that the
particles can rotate due to dipole-dipole interactions, then you need
to use atom_style hybrid sphere dipole, which will assign both a
diameter and dipole moment to each particle.
A few styles define the per-atom *rmass* attribute which can also be
added using the :doc:`fix property/atom <fix_property_atom>` command.
In this case each particle stores its own mass. Atom styles that have
a per-atom rmass may define it indirectly through setting particle
diameter and density on a per-particle basis. If both per-type mass
and per-atom *rmass* are defined (e.g. in a hybrid style), the
per-atom mass will take precedence in any operation which which works
with both flavors of mass.
For the *electron* style, the particles representing electrons are 3d
Gaussians with a specified position and bandwidth or uncertainty in
position, which is represented by the eradius = electron size.
----------
For the *peri* style, the particles are spherical and each stores a
per-particle mass and volume.
The *bpm/sphere* style is part of the BPM package.
The *oxdna* style is for coarse-grained nucleotides and stores the
3'-to-5' polarity of the nucleotide strand, which is set through
the bond topology in the data file. The first (second) atom in a
bond definition is understood to point towards the 3'-end (5'-end)
of the strand. Note that this style is part of the CG-DNA package.
The *dpd* style is for dissipative particle dynamics (DPD) particles.
Note that it is part of the DPD-REACT package, and is not for use with
the :doc:`pair_style dpd or dpd/stat <pair_dpd>` commands, which can
simply use atom_style atomic. Atom_style dpd extends DPD particle
properties with internal temperature (dpdTheta), internal conductive
energy (uCond), internal mechanical energy (uMech), and internal
chemical energy (uChem).
The *edpd* style is for energy-conserving dissipative particle
dynamics (eDPD) particles which store a temperature (edpd_temp), and
heat capacity(edpd_cv).
The *mdpd* style is for many-body dissipative particle dynamics (mDPD)
particles which store a density (rho) for considering
density-dependent many-body interactions.
The *tdpd* style is for transport dissipative particle dynamics (tDPD)
particles which store a set of chemical concentration. An integer
"cc_species" is required to specify the number of chemical species
involved in a tDPD system.
The *sph* style is for smoothed particle hydrodynamics (SPH)
particles which store a density (rho), energy (esph), and heat capacity
(cv).
The *smd* style is for a general formulation of Smooth Particle
Hydrodynamics. Both fluids and solids can be modeled. Particles
store the mass and volume of an integration point, a kernel diameter
used for calculating the field variables (e.g. stress and deformation)
and a contact radius for calculating repulsive forces which prevent
individual physical bodies from penetrating each other.
For the *spin* style, a magnetic spin is associated to each atom.
Those spins have a norm (their magnetic moment) and a direction.
The *wavepacket* style is similar to *electron*, but the electrons may
consist of several Gaussian wave packets, summed up with coefficients
cs= (cs_re,cs_im). Each of the wave packets is treated as a separate
particle in LAMMPS, wave packets belonging to the same electron must
have identical *etag* values.
For the *line* style, the particles are idealized line segments and
each stores a per-particle mass and length and orientation (i.e. the
end points of the line segment).
For the *tri* style, the particles are planar triangles and each
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle).
The *template* style allows molecular topology (bonds,angles,etc) to be
defined via a molecule template using the :doc:`molecule <molecule>`
command. The template stores one or more molecules with a single copy
of the topology info (bonds,angles,etc) of each. Individual atoms
only store a template index and template atom to identify which
molecule and which atom-within-the-molecule they represent. Using the
*template* style instead of the *bond*, *angle*, *molecular* styles
can save memory for systems comprised of a large number of small
molecules, all of a single type (or small number of types). See the
paper by Grime and Voth, in :ref:`(Grime) <Grime>`, for examples of how this
can be advantageous for large-scale coarse-grained systems.
The ``examples/template`` directory has a few demo inputs and examples
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 ensure 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.
Additional information about specific atom styles
"""""""""""""""""""""""""""""""""""""""""""""""""
For the *body* style, the particles are arbitrary bodies with internal
attributes defined by the "style" of the bodies, which is specified by
@ -309,6 +282,148 @@ Note that there may be additional arguments required along with the
*bstyle* specification, in the atom_style body command. These
arguments are described on the :doc:`Howto body <Howto_body>` doc page.
For the *dielectric* style, each particle can be either a physical
particle (e.g. an ion), or an interface particle representing a boundary
element between two regions of different dielectric constant. For
interface particles, in addition to the properties associated with
atom_style full, each particle also should be assigned a normal unit
vector (defined by normx, normy, normz), an area (area/patch), the
difference and mean of the dielectric constants of two sides of the
interface along the direction of the normal vector (ed and em), the
local dielectric constant at the boundary element (epsilon), and a mean
local curvature (curv). Physical particles must be assigned these
values, as well, but only their local dielectric constants will be used;
see documentation for associated :doc:`pair styles <pair_dielectric>`
and :doc:`fixes <fix_polarize>`. The distinction between the physical
and interface particles is only meaningful when :doc:`fix polarize
<fix_polarize>` commands are applied to the interface particles. This
style is part of the DIELECTRIC package.
For the *dipole* style, a point dipole vector mu is defined for each
point particle. Note that if you wish the particles to be finite-size
spheres as in a Stockmayer potential for a dipolar fluid, so that the
particles can rotate due to dipole-dipole interactions, then you need
to use the command `atom_style hybrid sphere dipole`, which will
assign both a diameter and dipole moment to each particle. This also
requires using an integrator with a "/sphere" suffix like :doc:`fix
nve/sphere <fix_nve_sphere>` or :doc:`fix nvt/sphere <fix_nvt_sphere>`
and the "update dipole" or "update dlm" parameters to the fix
commands.
The *dpd* style is for reactive dissipative particle dynamics (DPD)
particles. Note that it is part of the DPD-REACT package, and is not
required for use with the :doc:`pair_style dpd or dpd/stat <pair_dpd>`
commands, which only require the attributes from atom_style *atomic*.
Atom_style *dpd* extends DPD particle properties with internal
temperature (dpdTheta), internal conductive energy (uCond), internal
mechanical energy (uMech), and internal chemical energy (uChem).
The *edpd* style is for energy-conserving dissipative particle
dynamics (eDPD) particles which store a temperature (edpd_temp), and
heat capacity (edpd_cv).
For the *electron* style, the particles representing electrons are 3d
Gaussians with a specified position and bandwidth or uncertainty in
position, which is represented by the eradius = electron size.
For the *ellipsoid* style, particles can be ellipsoids which each
stores a shape vector with the 3 diameters of the ellipsoid and a
quaternion 4-vector with its orientation. Each particle stores a flag
in the ellipsoid vector which indicates whether it is an ellipsoid (1)
or a point particle (0).
For the *line* style, particles can be are idealized line segments
which store a per-particle mass and length and orientation (i.e. the
end points of the line segment). Each particle stores a flag in the
line vector which indicates whether it is a line segment (1) or a
point particle (0).
The *mdpd* style is for many-body dissipative particle dynamics (mDPD)
particles which store a density (rho) for considering density-dependent
many-body interactions.
The *oxdna* style is for coarse-grained nucleotides and stores the
3'-to-5' polarity of the nucleotide strand, which is set through
the bond topology in the data file. The first (second) atom in a
bond definition is understood to point towards the 3'-end (5'-end)
of the strand.
For the *peri* style, the particles are spherical and each stores a
per-particle mass and volume.
The *smd* style is for Smooth Particle Mach dynamics. Both fluids and
solids can be modeled. Particles store the mass and volume of an
integration point, a kernel diameter used for calculating the field
variables (e.g. stress and deformation) and a contact radius for
calculating repulsive forces which prevent individual physical bodies
from penetrating each other.
The *sph* style is for smoothed particle hydrodynamics (SPH) particles
which store a density (rho), energy (esph), and heat capacity (cv).
For the *spin* style, a magnetic spin is associated with each atom.
Those spins have a norm (their magnetic moment) and a direction.
The *tdpd* style is for transport dissipative particle dynamics (tDPD)
particles which store a set of chemical concentration. An integer
"cc_species" is required to specify the number of chemical species
involved in a tDPD system.
The *wavepacket* style is similar to the *electron* style, but the
electrons may consist of several Gaussian wave packets, summed up with
coefficients cs= (cs_re,cs_im). Each of the wave packets is treated
as a separate particle in LAMMPS, wave packets belonging to the same
electron must have identical *etag* values.
The *sphere* and *bpm/sphere* styles allow particles to be either point
particles or finite-size particles. If the *radius* attribute is >
0.0, the particle is a finite-size sphere. If the diameter = 0.0, it
is a point particle. Note that by using 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. These styles also
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 (this is
the default). 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.
The *template* style allows molecular topology (bonds,angles,etc) to be
defined via a molecule template using the :doc:`molecule <molecule>`
command. The template stores one or more molecules with a single copy
of the topology info (bonds,angles,etc) of each. Individual atoms only
store a template index and template atom to identify which molecule and
which atom-within-the-molecule they represent. Using the *template*
style instead of the *bond*, *angle*, *molecular* styles can save memory
for systems comprised of a large number of small molecules, all of a
single type (or small number of types). See the paper by Grime and
Voth, in :ref:`(Grime) <Grime>`, for examples of how this can be
advantageous for large-scale coarse-grained systems. The
``examples/template`` directory has a few demo inputs and examples
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 ensure 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 *tri* style, particles can be planar triangles which each
stores a per-particle mass and size and orientation (i.e. the corner
points of the triangle). Each particle stores a flag in the tri
vector which indicates whether it is a triangle (1) or a point
particle (0).
----------
Typically, simulations require only a single (non-hybrid) atom style.
@ -326,11 +441,12 @@ dipole". When a hybrid style is used, atoms store and communicate the
union of all quantities implied by the individual styles.
When using the *hybrid* style, you cannot combine the *template* style
with another molecular style that stores bond,angle,etc info on a
with another molecular style that stores bond, angle, etc info on a
per-atom basis.
LAMMPS can be extended with new atom styles as well as new body
styles; see the :doc:`Modify <Modify>` doc page.
LAMMPS can be extended with new atom styles as well as new body styles;
see the corresponding manual page on :doc:`modifying & extending LAMMPS
<Modify_atom>`.
----------
@ -346,54 +462,20 @@ This command cannot be used after the simulation box is defined by a
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.
The *line* and *tri* styles are part of the ASPHERE package.
The *body* style is part of the BODY package.
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 *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).
The *edpd*, *mdpd*, and *tdpd* styles are part of the DPD-MESO package
for energy-conserving dissipative particle dynamics (eDPD), many-body
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.
The *spin* style is part of the SPIN package.
The *wavepacket* style is part of the AWPMD package for the
:doc:`antisymmetrized wave packet MD method <pair_awpmd>`.
<Build_package>` page for more info. The table above lists which package
is required for individual atom styles.
Related commands
""""""""""""""""
:doc:`read_data <read_data>`, :doc:`pair_style <pair_style>`
:doc:`read_data <read_data>`, :doc:`pair_style <pair_style>`,
:doc:`fix property/atom <fix_property_atom>`, :doc:`set <set>`
Default
"""""""
The default atom style is atomic. If atom_style sphere is used its
default argument is 0.
The default atom style is *atomic*. If atom_style *sphere* or
*bpm/sphere* is used, its default argument is 0.
----------

19
doc/src/bond_lepton.rst
View File

@ -11,7 +11,16 @@ Syntax
.. code-block:: LAMMPS
bond_style lepton
bond_style style args
* style = *lepton*
* args = optional arguments
.. parsed-literal::
args = *auto_offset* or *no_offset*
*auto_offset* = offset the potential energy so that the value at r0 is 0.0 (default)
*no_offset* = do not offset the potential energy
Examples
""""""""
@ -19,6 +28,7 @@ Examples
.. code-block:: LAMMPS
bond_style lepton
bond_style lepton no_offset
bond_coeff 1 1.5 "k*r^2; k=250.0"
bond_coeff 2 1.1 "k2*r^2 + k3*r^3 + k4*r^4; k2=300.0; k3=-100.0; k4=50.0"
@ -40,6 +50,13 @@ constant *K* of 200.0 energy units:
U_{bond,i} = K (r_i - r_0)^2 = K r^2 \qquad r = r_i - r_0
.. versionchanged:: TBD
By default the potential energy U is shifted so that he value U is 0.0
for $r = r_0$. This is equivalent to using the optional keyword
*auto_offset*. When using the keyword *no_offset* instead, the
potential energy is not shifted.
The `Lepton library <https://simtk.org/projects/lepton>`_, that the
*lepton* bond style interfaces with, evaluates this expression string at
run time to compute the pairwise energy. It also creates an analytical

7
doc/src/dihedral_charmm.rst
View File

@ -3,6 +3,7 @@
.. index:: dihedral_style charmm/kk
.. index:: dihedral_style charmm/omp
.. index:: dihedral_style charmmfsw
.. index:: dihedral_style charmmfsw/kk
dihedral_style charmm command
=============================
@ -12,6 +13,8 @@ Accelerator Variants: *charmm/intel*, *charmm/kk*, *charmm/omp*
dihedral_style charmmfsw command
================================
Accelerator Variants: *charmmfsw/kk*
Syntax
""""""
@ -144,7 +147,9 @@ for more info.
Related commands
""""""""""""""""
:doc:`dihedral_coeff <dihedral_coeff>`
:doc:`dihedral_coeff <dihedral_coeff>`,
:doc:`pair_style lj/charmm variants <pair_charmm>`,
:doc:`angle_style charmm <angle_charmm>`, :doc:`fix cmap <fix_cmap>`
Default
"""""""

96
doc/src/fix_neb.rst
View File

@ -109,7 +109,7 @@ Note that in this case the specified *Kspring* is in
force/distance units.
With a value of *ideal*, the spring force is computed as suggested in
ref`(WeinanE) <WeinanE>`
:ref:`(WeinanE) <WeinanE>`
.. math::
@ -120,18 +120,18 @@ and :math:`RD_{ideal}` is the ideal *RD* for which all the images are
equally spaced. I.e. :math:`RD_{ideal} = (i-1) \cdot meanDist` when the
climbing replica is off, where *i* is the replica number). The
*meanDist* is the average distance between replicas. Note that in this
case the specified *Kspring* is in force units. When the climbing replica
is on, :math:`RD_{ideal}` and :math:`meanDist` are calculated separately
each side of the climbing image. Note that the *ideal* form of nudging
can often be more effective at keeping the replicas equally spaced before
climbing, then equally spaced either side of the climbing image whilst
climbing.
case the specified *Kspring* is in force units. When the climbing
replica is on, :math:`RD_{ideal}` and :math:`meanDist` are calculated
separately each side of the climbing image. Note that the *ideal* form
of nudging can often be more effective at keeping the replicas equally
spaced before climbing, then equally spaced either side of the climbing
image whilst climbing.
With a value of *equal* the spring force is computed as for *ideal*
when the climbing replica is off, promoting equidistance. When the climbing
With a value of *equal* the spring force is computed as for *ideal* when
the climbing replica is off, promoting equidistance. When the climbing
replica is on, the spring force is computed to promote equidistant
absolute differences in energy, rather than distance, each side of
the climbing image:
absolute differences in energy, rather than distance, each side of the
climbing image:
.. math::
@ -143,23 +143,22 @@ where *ED* is the cumulative sum of absolute energy differences:
ED = \sum_{i<N} \left|E(R_{i+1}) - E(R_i)\right|,
*meanEdist* is the average absolute energy difference between
replicas up to the climbing image or from the climbing image
to the final image, for images before or after the climbing
image respectively. :math:`ED_{ideal}` is the corresponding
cumulative sum of average absolute energy differences in
each case, in close analogy to *ideal*. This form of nudging
is to aid schemes which integrate forces along, or near to,
NEB pathways such as :doc:`fix_pafi <fix_pafi>`.
*meanEdist* is the average absolute energy difference between replicas
up to the climbing image or from the climbing image to the final image,
for images before or after the climbing image
respectively. :math:`ED_{ideal}` is the corresponding cumulative sum of
average absolute energy differences in each case, in close analogy to
*ideal*. This form of nudging is to aid schemes which integrate forces
along, or near to, NEB pathways such as :doc:`fix_pafi <fix_pafi>`.
----------
The keyword *perp* specifies if and how a perpendicular nudging force
is computed. It adds a spring force perpendicular to the path in
order to prevent the path from becoming too strongly kinked. It can
The keyword *perp* specifies if and how a perpendicular nudging force is
computed. It adds a spring force perpendicular to the path in order to
prevent the path from becoming too strongly kinked. It can
significantly improve the convergence of the NEB calculation when the
resolution is poor. I.e. when few replicas are used; see
:ref:`(Maras) <Maras1>` for details.
resolution is poor. I.e. when few replicas are used; see :ref:`(Maras)
<Maras1>` for details.
The perpendicular spring force is given by
@ -181,10 +180,10 @@ force is added.
By default, no additional forces act on the first and last replicas
during the NEB relaxation, so these replicas simply relax toward their
respective local minima. By using the key word *end*, additional
forces can be applied to the first and/or last replicas, to enable
them to relax toward a MEP while constraining their energy E to the
target energy ETarget.
respective local minima. By using the key word *end*, additional forces
can be applied to the first and/or last replicas, to enable them to
relax toward a MEP while constraining their energy E to the target
energy ETarget.
If :math:`E_{Target} > E`, the interatomic force :math:`F_i` for the
specified replica becomes:
@ -197,33 +196,33 @@ specified replica becomes:
The "spring" constant on the difference in energies is the specified
*Kspring3* value.
When *estyle* is specified as *first*, the force is applied to the
first replica. When *estyle* is specified as *last*, the force is
applied to the last replica. Note that the *end* keyword can be used
twice to add forces to both the first and last replicas.
When *estyle* is specified as *first*, the force is applied to the first
replica. When *estyle* is specified as *last*, the force is applied to
the last replica. Note that the *end* keyword can be used twice to add
forces to both the first and last replicas.
For both these *estyle* settings, the target energy *ETarget* is set
to the initial energy of the replica (at the start of the NEB
calculation).
If the *estyle* is specified as *last/efirst* or *last/efirst/middle*,
force is applied to the last replica, but the target energy *ETarget*
is continuously set to the energy of the first replica, as it evolves
force is applied to the last replica, but the target energy *ETarget* is
continuously set to the energy of the first replica, as it evolves
during the NEB relaxation.
The difference between these two *estyle* options is as follows. When
*estyle* is specified as *last/efirst*, no change is made to the
inter-replica force applied to the intermediate replicas (neither
first or last). If the initial path is too far from the MEP, an
intermediate replica may relax "faster" and reach a lower energy than
the last replica. In this case the intermediate replica will be
relaxing toward its own local minima. This behavior can be prevented
by specifying *estyle* as *last/efirst/middle* which will alter the
inter-replica force applied to intermediate replicas by removing the
contribution of the gradient to the inter-replica force. This will
only be done if a particular intermediate replica has a lower energy
than the first replica. This should effectively prevent the
intermediate replicas from over-relaxing.
inter-replica force applied to the intermediate replicas (neither first
or last). If the initial path is too far from the MEP, an intermediate
replica may relax "faster" and reach a lower energy than the last
replica. In this case the intermediate replica will be relaxing toward
its own local minima. This behavior can be prevented by specifying
*estyle* as *last/efirst/middle* which will alter the inter-replica
force applied to intermediate replicas by removing the contribution of
the gradient to the inter-replica force. This will only be done if a
particular intermediate replica has a lower energy than the first
replica. This should effectively prevent the intermediate replicas from
over-relaxing.
After converging a NEB calculation using an *estyle* of
*last/efirst/middle*, you should check that all intermediate replicas
@ -237,9 +236,10 @@ target energy.
Restart, fix_modify, output, run start/stop, minimize info
"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
No information about this fix is written to :doc:`binary restart files <restart>`. None of the :doc:`fix_modify <fix_modify>` options
are relevant to this fix. No global or per-atom quantities are stored
by this fix for access by various :doc:`output commands <Howto_output>`.
No information about this fix is written to :doc:`binary restart files
<restart>`. None of the :doc:`fix_modify <fix_modify>` options are
relevant to this fix. No global or per-atom quantities are stored by
this fix for access by various :doc:`output commands <Howto_output>`.
No parameter of this fix can be used with the *start/stop* keywords of
the :doc:`run <run>` command.

2
doc/src/fix_qeq.rst
View File

@ -232,8 +232,6 @@ These fixes are part of the QEQ package. They are only enabled if
LAMMPS was built with that package. See the :doc:`Build package
<Build_package>` page for more info.
These qeq fixes are not compatible with the GPU and USER-INTEL packages.
These qeq fixes will ignore electric field contributions from
:doc:`fix efield <fix_efield>`.

138
doc/src/molecule.rst
View File

@ -126,14 +126,50 @@ molecule (header keyword = inertia).
Format of a molecule file
"""""""""""""""""""""""""
The format of an individual molecule file is similar but
(not identical) to the data file read by the :doc:`read_data <read_data>`
commands, and is as follows.
The format of an individual molecule file looks similar but is
different than that of a data file read by the :doc:`read_data <read_data>`
commands. Here is a simple example for a TIP3P water molecule:
.. code-block::
# Water molecule. TIP3P geometry
# header section:
3 atoms
2 bonds
1 angles
# body section:
Coords
1 0.00000 -0.06556 0.00000
2 0.75695 0.52032 0.00000
3 -0.75695 0.52032 0.00000
Types
1 1 # O
2 2 # H
3 2 # H
Charges
1 -0.834
2 0.417
3 0.417
Bonds
1 1 1 2
2 1 1 3
Angles
1 1 2 1 3
A molecule file has a header and a body. The header appears first. The
first line of the header and thus of the molecule file is *always* skipped;
it typically contains a description of the file or a comment from the software
that created the file.
first line of the header and thus of the molecule file is *always*
skipped; it typically contains a description of the file or a comment
from the software that created the file.
Then lines are read one line at a time. Lines can have a trailing
comment starting with '#' that is ignored. There *must* be at least one
@ -158,25 +194,62 @@ appear if the value(s) are different than the default, except when
defining a *body* particle, which requires setting the number of
*atoms* to 1, and setting the *inertia* in a specific section (see below).
* N *atoms* = # of atoms N in molecule, default = 0
* Nb *bonds* = # of bonds Nb in molecule, default = 0
* Na *angles* = # of angles Na in molecule, default = 0
* Nd *dihedrals* = # of dihedrals Nd in molecule, default = 0
* Ni *impropers* = # of impropers Ni in molecule, default = 0
* Nf *fragments* = # of fragments Nf in molecule, default = 0
* Ninteger Ndouble *body* = # of integer and floating-point values
in body particle, default = 0
* Mtotal *mass* = total mass of molecule
* Xc Yc Zc *com* = coordinates of center-of-mass of molecule
* Ixx Iyy Izz Ixy Ixz Iyz *inertia* = 6 components of inertia tensor of molecule
.. list-table::
:header-rows: 1
:widths: auto
For *mass*, *com*, and *inertia*, the default is for LAMMPS to
calculate this quantity itself if needed, assuming the molecules
consist of a set of point particles or finite-size particles (with a
non-zero diameter) that do not overlap. If finite-size particles in
the molecule do overlap, LAMMPS will not account for the overlap
effects when calculating any of these 3 quantities, so you should
pre-compute them yourself and list the values in the file.
* - Number(s)
- Keyword
- Meaning
- Default Value
* - N
- atoms
- # of atoms N in molecule
- 0
* - Nb
- bonds
- # of bonds Nb in molecule
- 0
* - Na
- angles
- # of angles Na in molecule
- 0
* - Nd
- dihedrals
- # of dihedrals Nd in molecule
- 0
* - Ni
- impropers
- # of impropers Ni in molecule
- 0
* - Nf
- fragments
- # of fragments Nf in molecule
- 0
* - Ninteger Ndouble
- body
- # of integer and floating-point values in body particle
- 0
* - Mtotal
- mass
- total mass of molecule
- computed
* - Xc Yc Zc
- com
- coordinates of center-of-mass of molecule
- computed
* - Ixx Iyy Izz Ixy Ixz Iyz
- inertia
- 6 components of inertia tensor of molecule
- computed
For *mass*, *com*, and *inertia*, the default is for LAMMPS to calculate
this quantity itself if needed, assuming the molecules consist of a set
of point particles or finite-size particles (with a non-zero diameter)
that do **not** overlap. If finite-size particles in the molecule
**do** overlap, LAMMPS will not account for the overlap effects when
calculating any of these 3 quantities, so you should pre-compute them
yourself and list the values in the file.
The mass and center-of-mass coordinates (Xc,Yc,Zc) are
self-explanatory. The 6 moments of inertia (ixx,iyy,izz,ixy,ixz,iyz)
@ -188,7 +261,7 @@ internally.
These are the allowed section keywords for the body of the file.
* *Coords, Types, Molecules, Fragments, Charges, Diameters, Masses* = atom-property sections
* *Coords, Types, Molecules, Fragments, Charges, Diameters, Dipoles, Masses* = atom-property sections
* *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
* *Special Bond Counts, Special Bonds* = special neighbor info
* *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
@ -303,6 +376,21 @@ not listed, the default diameter of each atom in the molecule is 1.0.
----------
.. versionadded:: TBD
*Dipoles* section:
* one line per atom
* line syntax: ID mux muy muz
* mux,muy,muz = x-, y-, and z-component of point dipole vector of atom
This section is only allowed for :doc:`atom styles <atom_style>` that
support particles with point dipoles, e.g. atom_style dipole. If not
listed, the default dipole component of each atom in the molecule is set
to 0.0.
----------
*Masses* section:
* one line per atom

13
doc/src/neb.rst
View File

@ -10,7 +10,7 @@ Syntax
neb etol ftol N1 N2 Nevery file-style arg keyword values
* etol = stopping tolerance for energy (energy units)
* etol = stopping tolerance for energy (dimensionless)
* ftol = stopping tolerance for force (force units)
* N1 = max # of iterations (timesteps) to run initial NEB
* N2 = max # of iterations (timesteps) to run barrier-climbing NEB
@ -89,10 +89,11 @@ potentials, and the starting configuration when the neb command is
issued should be the same for every replica.
In a NEB calculation each replica is connected to other replicas by
inter-replica nudging forces. These forces are imposed by the :doc:`fix neb <fix_neb>` command, which must be used in conjunction with the
neb command. The group used to define the fix neb command defines the
NEB atoms which are the only ones that inter-replica springs are
applied to. If the group does not include all atoms, then non-NEB
inter-replica nudging forces. These forces are imposed by the
:doc:`fix neb <fix_neb>` command, which must be used in conjunction
with the neb command. The group used to define the fix neb command
defines the NEB atoms which are the only ones that inter-replica springs
are applied to. If the group does not include all atoms, then non-NEB
atoms have no inter-replica springs and the forces they feel and their
motion is computed in the usual way due only to other atoms within
their replica. Conceptually, the non-NEB atoms provide a background
@ -445,7 +446,7 @@ Related commands
""""""""""""""""
:doc:`prd <prd>`, :doc:`temper <temper>`, :doc:`fix langevin <fix_langevin>`,
:doc:`fix viscous <fix_viscous>`
:doc:`fix viscous <fix_viscous>`, :doc:`fix neb <fix_neb>`
Default
"""""""

7
doc/src/pair_charmm.rst
View File

@ -16,6 +16,7 @@
.. index:: pair_style lj/charmm/coul/msm/omp
.. index:: pair_style lj/charmmfsw/coul/charmmfsh
.. index:: pair_style lj/charmmfsw/coul/long
.. index:: pair_style lj/charmmfsw/coul/long/kk
pair_style lj/charmm/coul/charmm command
========================================
@ -43,6 +44,8 @@ pair_style lj/charmmfsw/coul/charmmfsh command
pair_style lj/charmmfsw/coul/long command
=========================================
Accelerator Variants: *lj/charmmfsw/coul/long/kk*
Syntax
""""""
@ -281,7 +284,9 @@ page for more info.
Related commands
""""""""""""""""
:doc:`pair_coeff <pair_coeff>`
:doc:`pair_coeff <pair_coeff>`, :doc:`angle_style charmm <angle_charmm>`,
:doc:`dihedral_style charmm <dihedral_charmm>`,
:doc:`dihedral_style charmmfsw <dihedral_charmm>`, :doc:`fix cmap <fix_cmap>`
Default
"""""""

6
doc/src/pair_lepton.rst
View File

@ -72,7 +72,7 @@ interactions between particles which depend on the distance and have a
cutoff. The potential function must be provided as an expression string
using "r" as the distance variable. With pair style *lepton/coul* one
may additionally reference the charges of the two atoms of the pair with
"qi" and "qj", respectively. With pair style *lepton/coul* one may
"qi" and "qj", respectively. With pair style *lepton/sphere* one may
instead reference the radii of the two atoms of the pair with "radi" and
"radj", respectively; this is half of the diameter that can be set in
:doc:`data files <read_data>` or the :doc:`set command <set>`.
@ -166,8 +166,8 @@ mixing. Thus, expressions for *all* I,J pairs must be specified
explicitly.
Only pair style *lepton* supports the :doc:`pair_modify shift <pair_modify>`
option for shifting the energy of the pair interaction so that it is
0 at the cutoff, pair styles *lepton/coul* and *lepton/sphere* do *not*.
option for shifting the potential energy of the pair interaction so that
it is 0 at the cutoff, pair styles *lepton/coul* and *lepton/sphere* do *not*.
The :doc:`pair_modify table <pair_modify>` options are not relevant for
the these pair styles.

8
doc/utils/sphinx-config/false_positives.txt
View File

@ -125,6 +125,7 @@ antisymmetry
anton
Antonelli
api
apolar
Apoorva
Appl
Appshaw
@ -151,6 +152,7 @@ asphericity
Asq
assignee
assively
associativity
Asta
Astart
Astop
@ -798,6 +800,7 @@ dlabel
dlambda
DLAMMPS
dll
dlm
dlopen
dm
dmax
@ -1015,6 +1018,7 @@ Ercolessi
Erdmann
erf
erfc
erforce
Erhart
erorate
erose
@ -2235,8 +2239,10 @@ Mohd
Mohles
mol
Mol
molatom
molfile
Molfile
molindex
MolPairStyle
moltemplate
momb
@ -2569,6 +2575,7 @@ ns
Ns
Nsample
Nskip
nspecial
Nspecies
nsq
Nstart
@ -3877,6 +3884,7 @@ versa
Verstraelen
ves
vflag
vfrac
vhi
vibrational
Vij

2
examples/COUPLE/plugin/liblammpsplugin.c
View File

@ -110,6 +110,8 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
ADDSYM(extract_variable);
ADDSYM(extract_variable_datatype);
ADDSYM(set_variable);
ADDSYM(set_string_variable);
ADDSYM(set_internal_variable);
ADDSYM(variable_info);
ADDSYM(gather_atoms);

6
examples/COUPLE/plugin/liblammpsplugin.h
View File

@ -152,9 +152,11 @@ struct _liblammpsplugin {
void *(*extract_compute)(void *, const char *, int, int);
void *(*extract_fix)(void *, const char *, int, int, int, int);
void *(*extract_variable)(void *, const char *, char *);
void *(*extract_variable)(void *, const char *, const char *);
int (*extract_variable_datatype)(void *, const char *);
int (*set_variable)(void *, char *, char *);
int (*set_variable)(void *, const char *, const char *);
int (*set_string_variable)(void *, const char *, const char *);
int (*set_internal_variable)(void *, const char *, double);
int (*variable_info)(void *, int, char *, int);
void (*gather_atoms)(void *, const char *, int, int, void *);

369
examples/PACKAGES/cgdna/util/generate.py
View File

@ -22,22 +22,26 @@
"""
Import basic modules
"""
# for python2/3 compatibility
from __future__ import print_function
import sys, os, timeit
from timeit import default_timer as timer
start_time = timer()
"""
Try to import numpy; if failed, import a local version mynumpy
Try to import numpy; if failed, import a local version mynumpy
which needs to be provided
"""
try:
import numpy as np
except:
print >> sys.stderr, "numpy not found. Exiting."
print("numpy not found. Exiting.", file=sys.stderr)
sys.exit(1)
"""
Check that the required arguments (box offset and size in simulation units
Check that the required arguments (box offset and size in simulation units
and the sequence file were provided
"""
try:
@ -45,8 +49,8 @@ try:
box_length = float(sys.argv[2])
infile = sys.argv[3]
except:
print >> sys.stderr, "Usage: %s <%s> <%s> <%s>" % (sys.argv[0], \
"box offset", "box length", "file with sequences")
print( "Usage: %s <%s> <%s> <%s>" % (sys.argv[0], \
"box offset", "box length", "file with sequences"), file=sys.stderr)
sys.exit(1)
box = np.array ([box_length, box_length, box_length])
@ -57,8 +61,7 @@ try:
inp = open (infile, 'r')
inp.close()
except:
print >> sys.stderr, "Could not open file '%s' for reading. \
Aborting." % infile
print( "Could not open file '%s' for reading. Aborting." % infile, file=sys.stderr)
sys.exit(2)
# return parts of a string
@ -86,7 +89,7 @@ Define auxiliary variables for the construction of a helix
# center of the double strand
CM_CENTER_DS = POS_BASE + 0.2
# ideal distance between base sites of two nucleotides
# ideal distance between base sites of two nucleotides
# which are to be base paired in a duplex
BASE_BASE = 0.3897628551303122
@ -118,7 +121,7 @@ strandnum = []
bonds = []
"""
"""
Convert local body frame to quaternion DOF
"""
def exyz_to_quat (mya1, mya3):
@ -135,25 +138,25 @@ def exyz_to_quat (mya1, mya3):
# compute other components from it
if q0sq >= 0.25:
myquat[0] = np.sqrt(q0sq)
myquat[1] = (mya2[2] - mya3[1]) / (4.0*myquat[0])
myquat[2] = (mya3[0] - mya1[2]) / (4.0*myquat[0])
myquat[3] = (mya1[1] - mya2[0]) / (4.0*myquat[0])
myquat[0] = np.sqrt(q0sq)
myquat[1] = (mya2[2] - mya3[1]) / (4.0*myquat[0])
myquat[2] = (mya3[0] - mya1[2]) / (4.0*myquat[0])
myquat[3] = (mya1[1] - mya2[0]) / (4.0*myquat[0])
elif q1sq >= 0.25:
myquat[1] = np.sqrt(q1sq)
myquat[0] = (mya2[2] - mya3[1]) / (4.0*myquat[1])
myquat[2] = (mya2[0] + mya1[1]) / (4.0*myquat[1])
myquat[3] = (mya1[2] + mya3[0]) / (4.0*myquat[1])
myquat[1] = np.sqrt(q1sq)
myquat[0] = (mya2[2] - mya3[1]) / (4.0*myquat[1])
myquat[2] = (mya2[0] + mya1[1]) / (4.0*myquat[1])
myquat[3] = (mya1[2] + mya3[0]) / (4.0*myquat[1])
elif q2sq >= 0.25:
myquat[2] = np.sqrt(q2sq)
myquat[0] = (mya3[0] - mya1[2]) / (4.0*myquat[2])
myquat[1] = (mya2[0] + mya1[1]) / (4.0*myquat[2])
myquat[3] = (mya3[1] + mya2[2]) / (4.0*myquat[2])
myquat[2] = np.sqrt(q2sq)
myquat[0] = (mya3[0] - mya1[2]) / (4.0*myquat[2])
myquat[1] = (mya2[0] + mya1[1]) / (4.0*myquat[2])
myquat[3] = (mya3[1] + mya2[2]) / (4.0*myquat[2])
elif q3sq >= 0.25:
myquat[3] = np.sqrt(q3sq)
myquat[0] = (mya1[1] - mya2[0]) / (4.0*myquat[3])
myquat[1] = (mya3[0] + mya1[2]) / (4.0*myquat[3])
myquat[2] = (mya3[1] + mya2[2]) / (4.0*myquat[3])
myquat[3] = np.sqrt(q3sq)
myquat[0] = (mya1[1] - mya2[0]) / (4.0*myquat[3])
myquat[1] = (mya3[0] + mya1[2]) / (4.0*myquat[3])
myquat[2] = (mya3[1] + mya2[2]) / (4.0*myquat[3])
norm = 1.0/np.sqrt(myquat[0]*myquat[0] + myquat[1]*myquat[1] + \
myquat[2]*myquat[2] + myquat[3]*myquat[3])
@ -169,62 +172,62 @@ Adds a strand to the system by appending it to the array of previous strands
"""
def add_strands (mynewpositions, mynewa1s, mynewa3s):
overlap = False
# This is a simple check for each of the particles where for previously
# placed particles i we check whether it overlaps with any of the
# This is a simple check for each of the particles where for previously
# placed particles i we check whether it overlaps with any of the
# newly created particles j
print >> sys.stdout, "## Checking for overlaps"
print( "## Checking for overlaps", file=sys.stdout)
for i in xrange(len(positions)):
for i in range(len(positions)):
p = positions[i]
pa1 = a1s[i]
p = positions[i]
pa1 = a1s[i]
for j in xrange (len(mynewpositions)):
for j in range (len(mynewpositions)):
q = mynewpositions[j]
qa1 = mynewa1s[j]
q = mynewpositions[j]
qa1 = mynewa1s[j]
# skip particles that are anyway too far away
dr = p - q
dr -= box * np.rint (dr / box)
if np.dot(dr, dr) > RC2:
continue
# skip particles that are anyway too far away
dr = p - q
dr -= box * np.rint(dr / box)
if np.dot(dr, dr) > RC2:
continue
# base site and backbone site of the two particles
# base site and backbone site of the two particles
p_pos_back = p + pa1 * POS_BACK
p_pos_base = p + pa1 * POS_BASE
q_pos_back = q + qa1 * POS_BACK
q_pos_base = q + qa1 * POS_BASE
# check for no overlap between the two backbone sites
# check for no overlap between the two backbone sites
dr = p_pos_back - q_pos_back
dr -= box * np.rint (dr / box)
dr -= box * np.rint(dr / box)
if np.dot(dr, dr) < RC2_BACK:
overlap = True
# check for no overlap between the two base sites
# check for no overlap between the two base sites
dr = p_pos_base - q_pos_base
dr -= box * np.rint (dr / box)
dr -= box * np.rint(dr / box)
if np.dot(dr, dr) < RC2_BASE:
overlap = True
# check for no overlap between backbone site of particle p
# with base site of particle q
# check for no overlap between backbone site of particle p
# with base site of particle q
dr = p_pos_back - q_pos_base
dr -= box * np.rint (dr / box)
if np.dot(dr, dr) < RC2_BACK_BASE:
overlap = True
# check for no overlap between base site of particle p and
# backbone site of particle q
# check for no overlap between base site of particle p and
# backbone site of particle q
dr = p_pos_base - q_pos_back
dr -= box * np.rint (dr / box)
if np.dot(dr, dr) < RC2_BACK_BASE:
overlap = True
# exit if there is an overlap
# exit if there is an overlap
if overlap:
return False
@ -237,10 +240,10 @@ def add_strands (mynewpositions, mynewa1s, mynewa3s):
a1s.append (p)
for p in mynewa3s:
a3s.append (p)
# calculate quaternion from local body frame and append
for ia in xrange(len(mynewpositions)):
mynewquaternions = exyz_to_quat(mynewa1s[ia],mynewa3s[ia])
quaternions.append(mynewquaternions)
# calculate quaternion from local body frame and append
for ia in range(len(mynewpositions)):
mynewquaternions = exyz_to_quat(mynewa1s[ia],mynewa3s[ia])
quaternions.append(mynewquaternions)
return True
@ -281,7 +284,7 @@ def get_rotation_matrix(axis, anglest):
[olc*x*z-st*y, olc*y*z+st*x, olc*z*z+ct]])
"""
Generates the position and orientation vectors of a
Generates the position and orientation vectors of a
(single or double) strand from a sequence string
"""
def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \
@ -295,76 +298,75 @@ def generate_strand(bp, sequence=None, start_pos=np.array([0, 0, 0]), \
# overall direction of the helix
dir = np.array(dir, dtype=float)
if sequence == None:
sequence = np.random.randint(1, 5, bp)
sequence = np.random.randint(1, 5, bp)
# the elseif here is most likely redundant
# the elseif here is most likely redundant
elif len(sequence) != bp:
n = bp - len(sequence)
sequence += np.random.randint(1, 5, n)
print >> sys.stderr, "sequence is too short, adding %d random bases" % n
n = bp - len(sequence)
sequence += np.random.randint(1, 5, n)
print( "sequence is too short, adding %d random bases" % n, file=sys.stderr)
# normalize direction
dir_norm = np.sqrt(np.dot(dir,dir))
if dir_norm < 1e-10:
print >> sys.stderr, "direction must be a valid vector, \
defaulting to (0, 0, 1)"
dir = np.array([0, 0, 1])
print( "direction must be a valid vector, defaulting to (0, 0, 1)", file=sys.stderr)
dir = np.array([0, 0, 1])
else: dir /= dir_norm
# find a vector orthogonal to dir to act as helix direction,
# if not provided switch off random orientation
if perp is None or perp is False:
v1 = np.random.random_sample(3)
v1 -= dir * (np.dot(dir, v1))
v1 /= np.sqrt(sum(v1*v1))
v1 = np.random.random_sample(3)
v1 -= dir * (np.dot(dir, v1))
v1 /= np.sqrt(sum(v1*v1))
else:
v1 = perp;
v1 = perp;
# generate rotational matrix representing the overall rotation of the helix
R0 = get_rotation_matrix(dir, rot)
# rotation matrix corresponding to one step along the helix
R = get_rotation_matrix(dir, [1, "bp"])
# set the vector a1 (backbone to base) to v1
# set the vector a1 (backbone to base) to v1
a1 = v1
# apply the global rotation to a1
# apply the global rotation to a1
a1 = np.dot(R0, a1)
# set the position of the fist backbone site to start_pos
rb = np.array(start_pos)
# set a3 to the direction of the helix
a3 = dir
for i in range(bp):
# work out the position of the centre of mass of the nucleotide
rcdm = rb - CM_CENTER_DS * a1
# append to newpositions
mynewpositions.append(rcdm)
mynewa1s.append(a1)
mynewa3s.append(a3)
# if we are not at the end of the helix, we work out a1 and rb for the
# next nucleotide along the helix
if i != bp - 1:
a1 = np.dot(R, a1)
rb += a3 * BASE_BASE
rcdm = rb - CM_CENTER_DS * a1
# if we are working on a double strand, we do a cycle similar
# append to newpositions
mynewpositions.append(rcdm)
mynewa1s.append(a1)
mynewa3s.append(a3)
# if we are not at the end of the helix, we work out a1 and rb for the
# next nucleotide along the helix
if i != bp - 1:
a1 = np.dot(R, a1)
rb += a3 * BASE_BASE
# if we are working on a double strand, we do a cycle similar
# to the previous one but backwards
if double == True:
a1 = -a1
a3 = -dir
R = R.transpose()
for i in range(bp):
rcdm = rb - CM_CENTER_DS * a1
mynewpositions.append (rcdm)
mynewa1s.append (a1)
mynewa3s.append (a3)
a1 = np.dot(R, a1)
rb += a3 * BASE_BASE
a1 = -a1
a3 = -dir
R = R.transpose()
for i in range(bp):
rcdm = rb - CM_CENTER_DS * a1
mynewpositions.append (rcdm)
mynewa1s.append (a1)
mynewa3s.append (a3)
a1 = np.dot(R, a1)
rb += a3 * BASE_BASE
assert (len (mynewpositions) > 0)
@ -391,10 +393,10 @@ def read_strands(filename):
try:
infile = open (filename)
except:
print >> sys.stderr, "Could not open file '%s'. Aborting." % filename
print( "Could not open file '%s'. Aborting." % filename, file=sys.stderr )
sys.exit(2)
# This block works out the number of nucleotides and strands by reading
# This block works out the number of nucleotides and strands by reading
# the number of non-empty lines in the input file and the number of letters,
# taking the possible DOUBLE keyword into account.
nstrands, nnucl, nbonds = 0, 0, 0
@ -406,30 +408,29 @@ def read_strands(filename):
if line[:6] == 'DOUBLE':
line = line.split()[1]
length = len(line)
print >> sys.stdout, "## Found duplex of %i base pairs" % length
print( "## Found duplex of %i base pairs" % length, file=sys.stdout)
nnucl += 2*length
nstrands += 2
nbonds += (2*length-2)
nbonds += (2*length-2)
else:
line = line.split()[0]
length = len(line)
print >> sys.stdout, \
"## Found single strand of %i bases" % length
print( "## Found single strand of %i bases" % length, file=sys.stdout)
nnucl += length
nstrands += 1
nbonds += length-1
nbonds += length-1
# rewind the sequence input file
infile.seek(0)
print >> sys.stdout, "## nstrands, nnucl = ", nstrands, nnucl
print( "## nstrands, nnucl = ", nstrands, nnucl, file=sys.stdout)
# generate the data file in LAMMPS format
try:
out = open ("data.oxdna", "w")
except:
print >> sys.stderr, "Could not open data file for writing. Aborting."
print( "Could not open data file for writing. Aborting.", file=sys.stderr)
sys.exit(2)
lines = infile.readlines()
nlines = len(lines)
i = 1
@ -440,115 +441,114 @@ def read_strands(filename):
line = line.upper().strip()
# skip empty lines
if len(line) == 0:
i += 1
continue
if len(line) == 0:
i += 1
continue
# block for duplexes: last argument of the generate function
# is set to 'True'
# block for duplexes: last argument of the generate function
# is set to 'True'
if line[:6] == 'DOUBLE':
line = line.split()[1]
length = len(line)
seq = [(base_to_number[x]) for x in line]
myns += 1
for b in xrange(length):
basetype.append(seq[b])
strandnum.append(myns)
myns += 1
for b in range(length):
basetype.append(seq[b])
strandnum.append(myns)
for b in xrange(length-1):
bondpair = [noffset + b, noffset + b + 1]
bonds.append(bondpair)
noffset += length
for b in range(length-1):
bondpair = [noffset + b, noffset + b + 1]
bonds.append(bondpair)
noffset += length
# create the sequence of the second strand as made of
# complementary bases
seq2 = [5-s for s in seq]
seq2.reverse()
# create the sequence of the second strand as made of
# complementary bases
seq2 = [5-s for s in seq]
seq2.reverse()
myns += 1
for b in xrange(length):
basetype.append(seq2[b])
strandnum.append(myns)
myns += 1
for b in range(length):
basetype.append(seq2[b])
strandnum.append(myns)
for b in xrange(length-1):
bondpair = [noffset + b, noffset + b + 1]
bonds.append(bondpair)
noffset += length
print >> sys.stdout, "## Created duplex of %i bases" % (2*length)
for b in range(length-1):
bondpair = [noffset + b, noffset + b + 1]
bonds.append(bondpair)
noffset += length
# generate random position of the first nucleotide
print( "## Created duplex of %i bases" % (2*length), file=sys.stdout)
# generate random position of the first nucleotide
cdm = box_offset + np.random.random_sample(3) * box
# generate the random direction of the helix
# generate the random direction of the helix
axis = np.random.random_sample(3)
axis /= np.sqrt(np.dot(axis, axis))
# use the generate function defined above to create
# the position and orientation vector of the strand
# use the generate function defined above to create
# the position and orientation vector of the strand
newpositions, newa1s, newa3s = generate_strand(len(line), \
sequence=seq, dir=axis, start_pos=cdm, double=True)
sequence=seq, dir=axis, start_pos=cdm, double=True)
# generate a new position for the strand until it does not overlap
# with anything already present
start = timer()
# with anything already present
start = timer()
while not add_strands(newpositions, newa1s, newa3s):
cdm = box_offset + np.random.random_sample(3) * box
axis = np.random.random_sample(3)
axis /= np.sqrt(np.dot(axis, axis))
newpositions, newa1s, newa3s = generate_strand(len(line), \
sequence=seq, dir=axis, start_pos=cdm, double=True)
print >> sys.stdout, "## Trying %i" % i
end = timer()
print >> sys.stdout, "## Added duplex of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
(2*length, i, nlines, end-start, len(positions), nnucl)
sequence=seq, dir=axis, start_pos=cdm, double=True)
print( "## Trying %i" % i, file=sys.stdout)
end = timer()
print( "## Added duplex of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
(2*length, i, nlines, end-start, len(positions), nnucl), file=sys.stdout)
# block for single strands: last argument of the generate function
# is set to 'False'
# block for single strands: last argument of the generate function
# is set to 'False'
else:
length = len(line)
seq = [(base_to_number[x]) for x in line]
myns += 1
for b in xrange(length):
basetype.append(seq[b])
strandnum.append(myns)
myns += 1
for b in range(length):
basetype.append(seq[b])
strandnum.append(myns)
for b in xrange(length-1):
bondpair = [noffset + b, noffset + b + 1]
bonds.append(bondpair)
noffset += length
for b in range(length-1):
bondpair = [noffset + b, noffset + b + 1]
bonds.append(bondpair)
noffset += length
# generate random position of the first nucleotide
# generate random position of the first nucleotide
cdm = box_offset + np.random.random_sample(3) * box
# generate the random direction of the helix
# generate the random direction of the helix
axis = np.random.random_sample(3)
axis /= np.sqrt(np.dot(axis, axis))
print >> sys.stdout, \
"## Created single strand of %i bases" % length
print("## Created single strand of %i bases" % length, file=sys.stdout)
newpositions, newa1s, newa3s = generate_strand(length, \
sequence=seq, dir=axis, start_pos=cdm, double=False)
start = timer()
start = timer()
while not add_strands(newpositions, newa1s, newa3s):
cdm = box_offset + np.random.random_sample(3) * box
axis = np.random.random_sample(3)
axis /= np.sqrt(np.dot(axis, axis))
axis /= np.sqrt(np.dot(axis, axis))
newpositions, newa1s, newa3s = generate_strand(length, \
sequence=seq, dir=axis, start_pos=cdm, double=False)
sequence=seq, dir=axis, start_pos=cdm, double=False)
print >> sys.stdout, "## Trying %i" % (i)
end = timer()
print >> sys.stdout, "## Added single strand of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
(length, i, nlines, end-start,len(positions), nnucl)
end = timer()
print( "## Added single strand of %i bases (line %i/%i) in %.2fs, now at %i/%i" % \
(length, i, nlines, end-start,len(positions), nnucl), file=sys.stdout)
i += 1
# sanity check
if not len(positions) == nnucl:
print len(positions), nnucl
print( len(positions), nnucl )
raise AssertionError
out.write('# LAMMPS data file\n')
@ -580,44 +580,41 @@ def read_strands(filename):
out.write('Atoms\n')
out.write('\n')
for i in xrange(nnucl):
out.write('%d %d %22.15le %22.15le %22.15le %d 1 1\n' \
% (i+1, basetype[i], \
positions[i][0], positions[i][1], positions[i][2], \
strandnum[i]))
for i in range(nnucl):
out.write('%d %d %22.15le %22.15le %22.15le %d 1 1\n' \
% (i+1, basetype[i], positions[i][0], positions[i][1], positions[i][2], strandnum[i]))
out.write('\n')
out.write('# Atom-ID, translational, rotational velocity\n')
out.write('Velocities\n')
out.write('\n')
for i in xrange(nnucl):
out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
% (i+1,0.0,0.0,0.0,0.0,0.0,0.0))
for i in range(nnucl):
out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
% (i+1,0.0,0.0,0.0,0.0,0.0,0.0))
out.write('\n')
out.write('# Atom-ID, shape, quaternion\n')
out.write('Ellipsoids\n')
out.write('\n')
for i in xrange(nnucl):
out.write(\
"%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
% (i+1,1.1739845031423408,1.1739845031423408,1.1739845031423408, \
quaternions[i][0],quaternions[i][1], quaternions[i][2],quaternions[i][3]))
for i in range(nnucl):
out.write("%d %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le %22.15le\n" \
% (i+1,1.1739845031423408,1.1739845031423408,1.1739845031423408, \
quaternions[i][0],quaternions[i][1], quaternions[i][2],quaternions[i][3]))
out.write('\n')
out.write('# Bond topology\n')
out.write('Bonds\n')
out.write('\n')
for i in xrange(nbonds):
out.write("%d %d %d %d\n" % (i+1,1,bonds[i][0],bonds[i][1]))
for i in range(nbonds):
out.write("%d %d %d %d\n" % (i+1,1,bonds[i][0],bonds[i][1]))
out.close()
print >> sys.stdout, "## Wrote data to 'data.oxdna'"
print >> sys.stdout, "## DONE"
print("## Wrote data to 'data.oxdna'", file=sys.stdout)
print("## DONE", file=sys.stdout)
# call the above main() function, which executes the program
read_strands (infile)
@ -627,4 +624,6 @@ runtime = end_time-start_time
hours = runtime/3600
minutes = (runtime-np.rint(hours)*3600)/60
seconds = (runtime-np.rint(hours)*3600-np.rint(minutes)*60)%60
print >> sys.stdout, "## Total runtime %ih:%im:%.2fs" % (hours,minutes,seconds)
print( "## Total runtime %ih:%im:%.2fs" % (hours,minutes,seconds), file=sys.stdout)

75
examples/PACKAGES/cgdna/util/generate_simple.py
View File

@ -1,5 +1,8 @@
# Setup tool for oxDNA input in LAMMPS format.
# for python2/3 compatibility
from __future__ import print_function
import math,numpy as np,sys,os
# system size
@ -250,59 +253,59 @@ def duplex_array():
qrot3=math.sin(0.5*twist)
for letter in strand[2]:
temp1=[]
temp2=[]
temp1=[]
temp2=[]
temp1.append(nt2num[letter])
temp2.append(compnt2num[letter])
temp1.append(nt2num[letter])
temp2.append(compnt2num[letter])
temp1.append([posx1,posy1,posz1])
temp2.append([posx2,posy2,posz2])
temp1.append([posx1,posy1,posz1])
temp2.append([posx2,posy2,posz2])
vel=[0,0,0,0,0,0]
temp1.append(vel)
temp2.append(vel)
vel=[0,0,0,0,0,0]
temp1.append(vel)
temp2.append(vel)
temp1.append(shape)
temp2.append(shape)
temp1.append(shape)
temp2.append(shape)
temp1.append(quat1)
temp2.append(quat2)
temp1.append(quat1)
temp2.append(quat2)
quat1_0 = quat1[0]*qrot0 - quat1[1]*qrot1 - quat1[2]*qrot2 - quat1[3]*qrot3
quat1_1 = quat1[0]*qrot1 + quat1[1]*qrot0 + quat1[2]*qrot3 - quat1[3]*qrot2
quat1_2 = quat1[0]*qrot2 + quat1[2]*qrot0 + quat1[3]*qrot1 - quat1[1]*qrot3
quat1_3 = quat1[0]*qrot3 + quat1[3]*qrot0 + quat1[1]*qrot2 + quat1[2]*qrot1
quat1_0 = quat1[0]*qrot0 - quat1[1]*qrot1 - quat1[2]*qrot2 - quat1[3]*qrot3
quat1_1 = quat1[0]*qrot1 + quat1[1]*qrot0 + quat1[2]*qrot3 - quat1[3]*qrot2
quat1_2 = quat1[0]*qrot2 + quat1[2]*qrot0 + quat1[3]*qrot1 - quat1[1]*qrot3
quat1_3 = quat1[0]*qrot3 + quat1[3]*qrot0 + quat1[1]*qrot2 + quat1[2]*qrot1
quat1 = [quat1_0,quat1_1,quat1_2,quat1_3]
quat1 = [quat1_0,quat1_1,quat1_2,quat1_3]
posx1=axisx - dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
posy1=axisy - dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
posz1=posz1+risez
posx1=axisx - dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
posy1=axisy - dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
posz1=posz1+risez
quat2_0 = quat2[0]*qrot0 - quat2[1]*qrot1 - quat2[2]*qrot2 + quat2[3]*qrot3
quat2_1 = quat2[0]*qrot1 + quat2[1]*qrot0 - quat2[2]*qrot3 - quat2[3]*qrot2
quat2_2 = quat2[0]*qrot2 + quat2[2]*qrot0 + quat2[3]*qrot1 + quat2[1]*qrot3
quat2_3 =-quat2[0]*qrot3 + quat2[3]*qrot0 + quat2[1]*qrot2 + quat2[2]*qrot1
quat2_0 = quat2[0]*qrot0 - quat2[1]*qrot1 - quat2[2]*qrot2 + quat2[3]*qrot3
quat2_1 = quat2[0]*qrot1 + quat2[1]*qrot0 - quat2[2]*qrot3 - quat2[3]*qrot2
quat2_2 = quat2[0]*qrot2 + quat2[2]*qrot0 + quat2[3]*qrot1 + quat2[1]*qrot3
quat2_3 =-quat2[0]*qrot3 + quat2[3]*qrot0 + quat2[1]*qrot2 + quat2[2]*qrot1
quat2 = [quat2_0,quat2_1,quat2_2,quat2_3]
quat2 = [quat2_0,quat2_1,quat2_2,quat2_3]
posx2=axisx + dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
posy2=axisy + dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
posz2=posz1
posx2=axisx + dcomh*(quat1[0]**2+quat1[1]**2-quat1[2]**2-quat1[3]**2)
posy2=axisy + dcomh*(2*(quat1[1]*quat1[2]+quat1[0]*quat1[3]))
posz2=posz1
if (len(nucleotide)+1 > strandstart):
topology.append([1,len(nucleotide),len(nucleotide)+1])
comptopo.append([1,len(nucleotide)+len(strand[2]),len(nucleotide)+len(strand[2])+1])
if (len(nucleotide)+1 > strandstart):
topology.append([1,len(nucleotide),len(nucleotide)+1])
comptopo.append([1,len(nucleotide)+len(strand[2]),len(nucleotide)+len(strand[2])+1])
nucleotide.append(temp1)
compstrand.append(temp2)
nucleotide.append(temp1)
compstrand.append(temp2)
for ib in range(len(compstrand)):
nucleotide.append(compstrand[len(compstrand)-1-ib])
nucleotide.append(compstrand[len(compstrand)-1-ib])
for ib in range(len(comptopo)):
topology.append(comptopo[ib])
topology.append(comptopo[ib])
return

2
examples/PACKAGES/reaction/create_atoms_polystyrene/in.grow_styrene
View File

@ -40,7 +40,7 @@ fix 1 statted_grp_REACT nvt temp $T $T 100
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
thermo_style custom step temp press density f_myrxns[1]
thermo_style custom step temp press density f_myrxns[*]
thermo 100

4
examples/PACKAGES/reaction/nylon,6-6_melt/in.large_nylon_melt
View File

@ -26,7 +26,7 @@ read_data large_nylon_melt.data.gz &
extra/angle/per/atom 15 &
extra/dihedral/per/atom 15 &
extra/improper/per/atom 25 &
extra/special/per/atom 25
extra/special/per/atom 25
velocity all create 800.0 4928459 dist gaussian
@ -50,7 +50,7 @@ fix 1 statted_grp_REACT nvt temp 800 800 100
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
thermo_style custom step temp press density f_myrxns[*] # cumulative reaction counts
# restart 100 restart1 restart2

5
examples/PACKAGES/reaction/tiny_epoxy/in.tiny_epoxy.stabilized
View File

@ -20,7 +20,8 @@ improper_style class2
special_bonds lj/coul 0 0 1
pair_modify tail yes mix sixthpower
read_data tiny_epoxy.data
read_data tiny_epoxy.data &
extra/special/per/atom 25
velocity all create 300.0 4928459 dist gaussian
@ -44,7 +45,7 @@ fix rxns all bond/react stabilization yes statted_grp .03 &
fix 1 statted_grp_REACT nvt temp 300 300 100
thermo_style custom step temp f_rxns[1] f_rxns[2] f_rxns[3] f_rxns[4]
thermo_style custom step temp f_rxns[*]
run 2000

2
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized
View File

@ -50,7 +50,7 @@ fix 1 statted_grp_REACT nvt temp 300 300 100
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
thermo_style custom step temp press density f_myrxns[*]
# restart 100 restart1 restart2

2
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.stabilized_variable_probability
View File

@ -54,7 +54,7 @@ fix 1 statted_grp_REACT nvt temp 300 300 100
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[1] f_myrxns[2]
thermo_style custom step temp press density v_prob1 v_prob2 f_myrxns[*]
# restart 100 restart1 restart2

2
examples/PACKAGES/reaction/tiny_nylon/in.tiny_nylon.unstabilized
View File

@ -47,7 +47,7 @@ fix myrxns all bond/react stabilization no &
fix 1 all nve/limit .03
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
thermo_style custom step temp press density f_myrxns[*]
# restart 100 restart1 restart2

2
examples/PACKAGES/reaction/tiny_polystyrene/in.tiny_polystyrene.stabilized
View File

@ -51,7 +51,7 @@ fix 1 statted_grp_REACT nvt temp $T $T 100
fix 4 bond_react_MASTER_group temp/rescale 1 $T $T 1 1
thermo_style custom step temp press density f_rxn1[1] f_rxn1[2] f_rxn1[3]
thermo_style custom step temp press density f_rxn1[*]
run 10000

54
fortran/lammps.f90
View File

@ -118,6 +118,8 @@ MODULE LIBLAMMPS
PROCEDURE :: extract_fix => lmp_extract_fix
PROCEDURE :: extract_variable => lmp_extract_variable
PROCEDURE :: set_variable => lmp_set_variable
PROCEDURE :: set_string_variable => lmp_set_string_variable
PROCEDURE :: set_internal_variable => lmp_set_internal_variable
PROCEDURE, PRIVATE :: lmp_gather_atoms_int
PROCEDURE, PRIVATE :: lmp_gather_atoms_double
GENERIC :: gather_atoms => lmp_gather_atoms_int, &
@ -557,6 +559,21 @@ MODULE LIBLAMMPS
INTEGER(c_int) :: lammps_set_variable
END FUNCTION lammps_set_variable
FUNCTION lammps_set_string_variable(handle, name, str) BIND(C)
IMPORT :: c_int, c_ptr
IMPLICIT NONE
TYPE(c_ptr), VALUE :: handle, name, str
INTEGER(c_int) :: lammps_set_string_variable
END FUNCTION lammps_set_string_variable
FUNCTION lammps_set_internal_variable(handle, name, val) BIND(C)
IMPORT :: c_int, c_ptr, c_double
IMPLICIT NONE
TYPE(c_ptr), VALUE :: handle, name
REAL(c_double), VALUE :: val
INTEGER(c_int) :: lammps_set_internal_variable
END FUNCTION lammps_set_internal_variable
SUBROUTINE lammps_gather_atoms(handle, name, type, count, data) BIND(C)
IMPORT :: c_int, c_ptr
IMPLICIT NONE
@ -1631,6 +1648,43 @@ CONTAINS
END IF
END SUBROUTINE lmp_set_variable
! equivalent function to lammps_set_string_variable
SUBROUTINE lmp_set_string_variable(self, name, str)
CLASS(lammps), INTENT(IN) :: self
CHARACTER(LEN=*), INTENT(IN) :: name, str
INTEGER :: err
TYPE(c_ptr) :: Cstr, Cname
Cstr = f2c_string(str)
Cname = f2c_string(name)
err = lammps_set_string_variable(self%handle, Cname, Cstr)
CALL lammps_free(Cname)
CALL lammps_free(Cstr)
IF (err /= 0) THEN
CALL lmp_error(self, LMP_ERROR_WARNING + LMP_ERROR_WORLD, &
'WARNING: unable to set string variable "' // name &
// '" [Fortran/set_variable]')
END IF
END SUBROUTINE lmp_set_string_variable
! equivalent function to lammps_set_internal_variable
SUBROUTINE lmp_set_internal_variable(self, name, val)
CLASS(lammps), INTENT(IN) :: self
CHARACTER(LEN=*), INTENT(IN) :: name
REAL(KIND=c_double), INTENT(IN) :: val
INTEGER :: err
TYPE(c_ptr) :: Cstr, Cname
Cname = f2c_string(name)
err = lammps_set_internal_variable(self%handle, Cname, val)
CALL lammps_free(Cname)
IF (err /= 0) THEN
CALL lmp_error(self, LMP_ERROR_WARNING + LMP_ERROR_WORLD, &
'WARNING: unable to set internal variable "' // name &
// '" [Fortran/set_variable]')
END IF
END SUBROUTINE lmp_set_internal_variable
! equivalent function to lammps_gather_atoms (for integers)
SUBROUTINE lmp_gather_atoms_int(self, name, count, data)
CLASS(lammps), INTENT(IN) :: self

4
lib/gpu/Makefile.cuda
View File

@ -134,11 +134,11 @@ $(OBJ_DIR)/scan_app.cu_o: cudpp_mini/scan_app.cu
$(GPU_LIB): $(OBJS) $(CUDPP)
$(AR) -crusv $(GPU_LIB) $(OBJS) $(CUDPP)
@cp $(EXTRAMAKE) Makefile.lammps
# test app for querying device info
$(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
clean:
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CUHS) *.linkinfo

4
lib/gpu/Makefile.cuda_mps
View File

@ -133,11 +133,11 @@ $(OBJ_DIR)/scan_app.cu_o: cudpp_mini/scan_app.cu
$(GPU_LIB): $(OBJS) $(CUDPP)
$(AR) -crusv $(GPU_LIB) $(OBJS) $(CUDPP)
@cp $(EXTRAMAKE) Makefile.lammps
# test app for querying device info
$(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
clean:
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CUHS) *.linkinfo

4
lib/gpu/Makefile.hip
View File

@ -98,10 +98,10 @@ HIP_GPU_OPTS += $(HIP_OPTS) -I./
ifeq (spirv,$(HIP_PLATFORM))
HIP_HOST_OPTS += -fPIC
HIP_GPU_CC = $(HIP_PATH)/bin/hipcc -c
HIP_GPU_OPTS_S =
HIP_GPU_OPTS_S =
HIP_GPU_OPTS_E =
HIP_KERNEL_SUFFIX = .cpp
HIP_LIBS_TARGET =
HIP_LIBS_TARGET =
export HCC_AMDGPU_TARGET := $(HIP_ARCH)
else ifeq (clang,$(HIP_COMPILER))
HIP_HOST_OPTS += -fPIC

2
lib/gpu/Makefile.lammps.mac_ocl
View File

@ -2,4 +2,4 @@
gpu_SYSINC = -DFFT_SINGLE
gpu_SYSLIB = -framework OpenCL
gpu_SYSPATH =
gpu_SYSPATH =

2
lib/gpu/Makefile.lammps.mingw-cross
View File

@ -2,5 +2,5 @@
# settings for OpenCL builds
gpu_SYSINC =
gpu_SYSLIB = -Wl,--enable-stdcall-fixup -L../../tools/mingw-cross$(LIBOBJDIR) -Wl,-Bdynamic,-lOpenCL,-Bstatic
gpu_SYSPATH =
gpu_SYSPATH =

2
lib/gpu/Makefile.lammps.opencl
View File

@ -2,4 +2,4 @@
gpu_SYSINC =
gpu_SYSLIB = -lOpenCL
gpu_SYSPATH =
gpu_SYSPATH =

2
lib/gpu/Makefile.linux
View File

@ -1,4 +1,4 @@
# /* ----------------------------------------------------------------------
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for CUDA
# - Change CUDA_ARCH for your GPU
# ------------------------------------------------------------------------- */

2
lib/gpu/Makefile.linux_multi
View File

@ -1,4 +1,4 @@
# /* ----------------------------------------------------------------------
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for CUDA complied for multiple compute capabilities
# - Add your GPU to CUDA_CODE
# ------------------------------------------------------------------------- */

4
lib/gpu/Makefile.linux_opencl
View File

@ -1,4 +1,4 @@
# /* ----------------------------------------------------------------------
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for OpenCL - Mixed precision
# ------------------------------------------------------------------------- */
@ -11,7 +11,7 @@ EXTRAMAKE = Makefile.lammps.opencl
LMP_INC = -DLAMMPS_SMALLBIG
OCL_INC =
OCL_INC =
OCL_CPP = mpic++ -std=c++11 -O3 -DMPICH_IGNORE_CXX_SEEK $(LMP_INC) $(OCL_INC)
OCL_LINK = -lOpenCL
OCL_PREC = -D_SINGLE_DOUBLE

2
lib/gpu/Makefile.mac_opencl
View File

@ -1,4 +1,4 @@
# /* ----------------------------------------------------------------------
# /* ----------------------------------------------------------------------
# Generic Mac Makefile for OpenCL - Single precision with FFT_SINGLE
# ------------------------------------------------------------------------- */

2
lib/gpu/Makefile.mac_opencl_mpi
View File

@ -1,4 +1,4 @@
# /* ----------------------------------------------------------------------
# /* ----------------------------------------------------------------------
# Generic Mac Makefile for OpenCL - Single precision with FFT_SINGLE
# ------------------------------------------------------------------------- */

2
lib/gpu/Makefile.oneapi
View File

@ -1,4 +1,4 @@
# /* ----------------------------------------------------------------------
# /* ----------------------------------------------------------------------
# Linux Makefile for Intel oneAPI - Mixed precision
# ------------------------------------------------------------------------- */

2
lib/gpu/Makefile.oneapi_prof
View File

@ -1,4 +1,4 @@
# /* ----------------------------------------------------------------------
# /* ----------------------------------------------------------------------
# Linux Makefile for Intel oneAPI - Mixed precision (with timing enabled)
# ------------------------------------------------------------------------- */

2
lib/gpu/Makefile.serial
View File

@ -1,4 +1,4 @@
# /* ----------------------------------------------------------------------
# /* ----------------------------------------------------------------------
# Generic Linux Makefile for CUDA without MPI libraries
# - Change CUDA_ARCH for your GPU
# ------------------------------------------------------------------------- */

4
lib/gpu/Nvidia.makefile
View File

@ -11,7 +11,7 @@ HOST_H = lal_answer.h lal_atom.h lal_balance.h lal_base_atomic.h lal_base_amoeba
lal_base_charge.h lal_base_dipole.h lal_base_dpd.h \
lal_base_ellipsoid.h lal_base_three.h lal_device.h lal_neighbor.h \
lal_neighbor_shared.h lal_pre_ocl_config.h $(NVD_H)
# Source files
SRCS := $(wildcard ./lal_*.cpp)
OBJS := $(subst ./,$(OBJ_DIR)/,$(SRCS:%.cpp=%.o))
@ -127,7 +127,7 @@ $(GPU_LIB): $(OBJS) $(CUDPP)
# test app for querying device info
$(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
clean:
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CUHS) *.cubin *.linkinfo

2
lib/gpu/Nvidia.makefile_multi
View File

@ -89,7 +89,7 @@ $(GPU_LIB): $(OBJS) $(CUDPP)
# test app for querying device info
$(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda
clean:
-rm -f $(EXECS) $(GPU_LIB) $(OBJS) $(CUDPP) $(CUHS) *.linkinfo

6
lib/gpu/geryon/nvd_device.h
View File

@ -138,7 +138,7 @@ class UCL_Device {
/** \note You cannot delete the default stream **/
inline void pop_command_queue() {
if (_cq.size()<2) return;
CU_SAFE_CALL_NS(cuStreamDestroy(_cq.back()));
cuStreamDestroy(_cq.back());
_cq.pop_back();
}
@ -426,8 +426,8 @@ void UCL_Device::clear() {
if (_device>-1) {
for (int i=1; i<num_queues(); i++) pop_command_queue();
#if GERYON_NVD_PRIMARY_CONTEXT
CU_SAFE_CALL_NS(cuCtxSetCurrent(_old_context));
CU_SAFE_CALL_NS(cuDevicePrimaryCtxRelease(_cu_device));
cuCtxSetCurrent(_old_context);
cuDevicePrimaryCtxRelease(_cu_device);
#else
cuCtxDestroy(_context);
#endif

2
lib/gpu/geryon/ocl_memory.h
View File

@ -108,7 +108,7 @@ inline int _host_alloc(mat_type &mat, copy_type &cm, const size_t n,
return UCL_MEMORY_ERROR;
*mat.host_ptr() = (typename mat_type::data_type*)
clEnqueueMapBuffer(cm.cq(),mat.cbegin(),CL_TRUE,
map_perm,0,n,0,NULL,NULL,NULL);
map_perm,0,n,0,NULL,NULL,NULL);
mat.cq()=cm.cq();
CL_SAFE_CALL(clRetainCommandQueue(mat.cq()));

6
lib/gpu/lal_amoeba.cu
View File

@ -2033,13 +2033,13 @@ __kernel void k_amoeba_special15(__global int * dev_nbor,
const __global tagint *restrict special15,
const int inum, const int nall, const int nbor_pitch,
const int t_per_atom) {
int tid, ii, offset, n_stride, i;
int tid, ii, offset, n_stride, j;
atom_info(t_per_atom,ii,tid,offset);
if (ii<inum) {
int numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,j,numj,
n_stride,nbor_end,nbor);
int n15 = nspecial15[ii];
@ -2048,7 +2048,7 @@ __kernel void k_amoeba_special15(__global int * dev_nbor,
int sj=dev_packed[nbor];
int which = sj >> SBBITS & 3;
int j = sj & NEIGHMASK;
j = sj & NEIGHMASK;
tagint jtag = tag[j];
if (!which) {

2
lib/gpu/lal_base_sph.cpp
View File

@ -195,7 +195,7 @@ void BaseSPHT::compute(const int f_ago, const int inum_full, const int nall,
int **firstneigh, const bool eflag_in, const bool vflag_in,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *tag,
double **host_v, const int nlocal) {
double **host_v) {
acc_timers();
int eflag, vflag;
if (eatom) eflag=2;

4
lib/gpu/lal_base_sph.h
View File

@ -15,7 +15,7 @@
***************************************************************************/
#ifndef LAL_BASE_SPH_H
#define LAL_BASE_DPD_H
#define LAL_BASE_SPH_H
#include "lal_device.h"
#include "lal_balance.h"
@ -132,7 +132,7 @@ class BaseSPH {
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *tag,
double **v, const int nlocal);
double **v);
/// Pair loop with device neighboring
int** compute(const int ago, const int inum_full, const int nall,

1
lib/gpu/lal_coul_slater_long.cu
View File

@ -102,6 +102,7 @@ __kernel void k_coul_slater_long(const __global numtyp4 *restrict x_,
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
_erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
fetch(prefactor,j,q_tex);
prefactor *= qqrd2e * scale[mtype] * qtmp/r;
numtyp rlamdainv = r * lamdainv;
numtyp exprlmdainv = ucl_exp((numtyp)-2.0*rlamdainv);
numtyp slater_term = exprlmdainv*((numtyp)1.0 + ((numtyp)2.0*rlamdainv*((numtyp)1.0+rlamdainv)));

4
lib/gpu/lal_coul_slater_long.h
View File

@ -13,8 +13,8 @@
email : ndactrung@gmail.com
***************************************************************************/
#ifndef LAL_Coul_Slater_Long_H
#define LAL_Coul_Slater_Long_H
#ifndef LAL_COUL_SLATER_LONG_H
#define LAL_COUL_SLATER_LONG_H
#include "lal_base_charge.h"

6
lib/gpu/lal_eam.cpp
View File

@ -303,7 +303,7 @@ double EAMT::host_memory_usage() const {
}
// ---------------------------------------------------------------------------
// Copy nbor list from host if necessary and then compute atom energies/forces
// Copy nbor list from host if necessary and then compute per-atom fp
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void EAMT::compute(const int f_ago, const int inum_full, const int nlocal,
@ -379,7 +379,7 @@ void EAMT::compute(const int f_ago, const int inum_full, const int nlocal,
}
// ---------------------------------------------------------------------------
// Reneighbor on GPU and then compute per-atom densities
// Reneighbor on GPU and then compute per-atom fp
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
int** EAMT::compute(const int ago, const int inum_full, const int nall,
@ -461,7 +461,7 @@ int** EAMT::compute(const int ago, const int inum_full, const int nall,
}
// ---------------------------------------------------------------------------
// Copy nbor list from host if necessary and then calculate forces, virials,..
// Update per-atom fp, and then calculate forces, virials,..
// ---------------------------------------------------------------------------
template <class numtyp, class acctyp>
void EAMT::compute2(int *ilist, const bool eflag, const bool vflag,

12
lib/gpu/lal_edpd.cu
View File

@ -324,8 +324,8 @@ __kernel void k_edpd(const __global numtyp4 *restrict x_,
f.z+=delz*force;
// heat transfer
if (r < coeff2w) {
if (r < coeff2w) {
numtyp wrT = (numtyp)1.0 - r/coeff2w;
wrT = MAX((numtyp)0.0,MIN((numtyp)1.0,wrT));
wrT = ucl_pow(wrT, (numtyp)0.5*coeff2z); // powerT[itype][jtype]
@ -401,10 +401,8 @@ __kernel void k_edpd_fast(const __global numtyp4 *restrict x_,
__local numtyp4 sc[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp4 kc[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp sp_lj[4];
__local numtyp sp_sqrt[4];
if (tid<4) {
sp_lj[tid]=sp_lj_in[tid];
sp_sqrt[tid]=sp_sqrt_in[tid];
}
if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
coeff[tid]=coeff_in[tid];
@ -567,7 +565,7 @@ __kernel void k_edpd_fast(const __global numtyp4 *restrict x_,
// heat transfer
if (r < coeff2w) {
if (r < coeff2w) {
numtyp wrT = (numtyp)1.0 - r/coeff2w;
wrT = MAX((numtyp)0.0,MIN((numtyp)1.0,wrT));
wrT = ucl_pow(wrT, (numtyp)0.5*coeff2z); // powerT[itype][jtype]
@ -581,10 +579,10 @@ __kernel void k_edpd_fast(const __global numtyp4 *restrict x_,
factor += kcx*T_pow.x + kcy*T_pow.y + kcz*T_pow.z + kcw*T_pow.w;
kappaT *= factor;
}
numtyp kij = cvi*cvj*kappaT * T_ij*T_ij;
numtyp alphaij = ucl_sqrt((numtyp)2.0*kboltz*kij);
numtyp dQc = kij * wrT*wrT * (Tj - Ti )/(Ti*Tj);
numtyp dQd = wr*wr*( GammaIJ * vijeij*vijeij - SigmaIJ*SigmaIJ/mass_itype ) - SigmaIJ * wr *vijeij *randnum;
dQd /= (cvi+cvj);

10
lib/gpu/lal_hippo.cu
View File

@ -1225,7 +1225,9 @@ __kernel void k_hippo_udirect2b(const __global numtyp4 *restrict x_,
atom_info(t_per_atom,ii,tid,offset);
int n_stride;
#if (SHUFFLE_AVAIL == 0)
local_allocate_store_charge();
#endif
acctyp _fieldp[6];
for (int l=0; l<6; l++) _fieldp[l]=(acctyp)0;
@ -1410,7 +1412,9 @@ __kernel void k_hippo_umutual2b(const __global numtyp4 *restrict x_,
atom_info(t_per_atom,ii,tid,offset);
int n_stride;
#if (SHUFFLE_AVAIL == 0)
local_allocate_store_charge();
#endif
acctyp _fieldp[6];
for (int l=0; l<6; l++) _fieldp[l]=(acctyp)0;
@ -2452,13 +2456,13 @@ __kernel void k_hippo_special15(__global int * dev_nbor,
const __global tagint *restrict special15,
const int inum, const int nall, const int nbor_pitch,
const int t_per_atom) {
int tid, ii, offset, n_stride, i;
int tid, ii, offset, n_stride, j;
atom_info(t_per_atom,ii,tid,offset);
if (ii<inum) {
int numj, nbor, nbor_end;
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,i,numj,
nbor_info(dev_nbor,dev_packed,nbor_pitch,t_per_atom,ii,offset,j,numj,
n_stride,nbor_end,nbor);
int n15 = nspecial15[ii];
@ -2467,7 +2471,7 @@ __kernel void k_hippo_special15(__global int * dev_nbor,
int sj=dev_packed[nbor];
int which = sj >> SBBITS & 3;
int j = sj & NEIGHMASK;
j = sj & NEIGHMASK;
tagint jtag = tag[j];
if (!which) {

16
lib/gpu/lal_mdpd.cu
View File

@ -210,13 +210,12 @@ __kernel void k_mdpd(const __global numtyp4 *restrict x_,
const numtyp rhoi = extra[i].x;
numtyp factor_dpd, factor_sqrt;
numtyp factor_dpd;
for ( ; nbor<nbor_end; nbor+=n_stride) {
ucl_prefetch(dev_packed+nbor+n_stride);
int j=dev_packed[nbor];
factor_dpd = sp_lj[sbmask(j)];
factor_sqrt = sp_sqrt[sbmask(j)];
j &= NEIGHMASK;
numtyp4 jx; fetch4(jx,j,pos_tex); //x_[j];
@ -240,22 +239,21 @@ __kernel void k_mdpd(const __global numtyp4 *restrict x_,
numtyp delvy = iv.y - jv.y;
numtyp delvz = iv.z - jv.z;
numtyp dot = delx*delvx + dely*delvy + delz*delvz;
numtyp A_attij = coeff[mtype].x;
numtyp B_repij = coeff[mtype].y;
numtyp gammaij = coeff[mtype].z;
numtyp sigmaij = coeff[mtype].w;
numtyp cutij = coeff2[mtype].x;
numtyp cut_rij = coeff2[mtype].y;
numtyp cutsqij = coeff2[mtype].z;
numtyp wc = (numtyp)1.0 - r/cutij;
numtyp wc_r = (numtyp)1.0 - r/cut_rij;
wc_r = MAX(wc_r,(numtyp)0.0);
numtyp wr = wc;
const numtyp rhoj = extra[j].x;
unsigned int tag1=itag, tag2=jtag;
if (tag1 > tag2) {
tag1 = jtag; tag2 = itag;
@ -322,10 +320,8 @@ __kernel void k_mdpd_fast(const __global numtyp4 *restrict x_,
__local numtyp4 coeff[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp4 coeff2[MAX_SHARED_TYPES*MAX_SHARED_TYPES];
__local numtyp sp_lj[4];
__local numtyp sp_sqrt[4];
if (tid<4) {
sp_lj[tid]=sp_lj_in[tid];
sp_sqrt[tid]=sp_sqrt_in[tid];
}
if (tid<MAX_SHARED_TYPES*MAX_SHARED_TYPES) {
coeff[tid]=coeff_in[tid];
@ -339,7 +335,6 @@ __kernel void k_mdpd_fast(const __global numtyp4 *restrict x_,
const numtyp sigmaij=coeff_in[ONETYPE].w;
const numtyp cutij=coeff2_in[ONETYPE].x;
const numtyp cut_rij=coeff2_in[ONETYPE].y;
const numtyp cutsqij=coeff2_in[ONETYPE].z;
const numtyp cutsq_p=cutsq[ONETYPE];
#endif
@ -412,7 +407,6 @@ __kernel void k_mdpd_fast(const __global numtyp4 *restrict x_,
numtyp sigmaij = coeff[mtype].w;
numtyp cutij = coeff2[mtype].x;
numtyp cut_rij = coeff2[mtype].y;
numtyp cutsqij = coeff2[mtype].z;
#endif
numtyp wc = (numtyp)1.0 - r/cutij;
@ -421,7 +415,7 @@ __kernel void k_mdpd_fast(const __global numtyp4 *restrict x_,
numtyp wr = wc;
const numtyp rhoj = extra[j].x;
unsigned int tag1=itag, tag2=jtag;
if (tag1 > tag2) {
tag1 = jtag; tag2 = itag;

6
lib/gpu/lal_sph_heatconduction.cu
View File

@ -70,7 +70,9 @@ __kernel void k_sph_heatconduction(const __global numtyp4 *restrict x_,
atom_info(t_per_atom,ii,tid,offset);
int n_stride;
#if (SHUFFLE_AVAIL == 0)
local_allocate_store_pair();
#endif
acctyp dEacc = (acctyp)0;
@ -171,7 +173,9 @@ __kernel void k_sph_heatconduction_fast(const __global numtyp4 *restrict x_,
#endif
int n_stride;
#if (SHUFFLE_AVAIL == 0)
local_allocate_store_pair();
#endif
acctyp dEacc = (acctyp)0;
@ -234,7 +238,7 @@ __kernel void k_sph_heatconduction_fast(const __global numtyp4 *restrict x_,
// Lucy Kernel, 2d
wfd = (numtyp)-19.098593171027440292 * wfd * wfd * ihsq * ihsq * ihsq;
}
// total thermal energy increment
numtyp D = coeffx; // alpha[itype][jtype] diffusion coefficient
numtyp deltaE = (numtyp)2.0 * mass_itype * mass_jtype / (mass_itype + mass_jtype);

4
lib/gpu/lal_sph_heatconduction.h
View File

@ -13,8 +13,8 @@
email : ndactrung@gmail.com
***************************************************************************/
#ifndef LAL_SPH_LJ_H
#define LAL_SPH_LJ_H
#ifndef LAL_SPH_HEATCONDUCTION_H
#define LAL_SPH_HEATCONDUCTION_H
#include "lal_base_sph.h"

4
lib/gpu/lal_sph_heatconduction_ext.cpp
View File

@ -110,10 +110,10 @@ void sph_heatconduction_gpu_compute(const int ago, const int inum_full, const in
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *host_tag,
double **host_v, const int nlocal) {
double **host_v) {
SPHHeatConductionMF.compute(ago, inum_full, nall, host_x, host_type, ilist, numj,
firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success,
host_tag, host_v, nlocal);
host_tag, host_v);
}
void sph_heatconduction_gpu_get_extra_data(double *host_rho, double *host_esph) {

4
lib/gpu/lal_sph_lj.cu
View File

@ -362,7 +362,7 @@ __kernel void k_sph_lj_fast(const __global numtyp4 *restrict x_,
// Lucy Kernel, 2d
wfd = (numtyp)-19.098593171027440292 * wfd * wfd * ihsq * ihsq * ihsq;
}
// function call to LJ EOS
numtyp fcj[2];
LJEOS2(rhoj, esphj, cvj, fcj);
@ -404,7 +404,7 @@ __kernel void k_sph_lj_fast(const __global numtyp4 *restrict x_,
drhoEacc.y += deltaE;
if (EVFLAG && eflag) {
numtyp e = (numtyp)0;
numtyp e = (numtyp)0;
energy+=e;
}
if (EVFLAG && vflag) {

4
lib/gpu/lal_sph_lj_ext.cpp
View File

@ -110,10 +110,10 @@ void sph_lj_gpu_compute(const int ago, const int inum_full, const int nall,
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *host_tag,
double **host_v, const int nlocal) {
double **host_v) {
SPHLJMF.compute(ago, inum_full, nall, host_x, host_type, ilist, numj,
firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success,
host_tag, host_v, nlocal);
host_tag, host_v);
}
void sph_lj_gpu_get_extra_data(double *host_rho, double *host_esph, double *host_cv) {

8
lib/gpu/lal_sph_taitwater.cu
View File

@ -145,9 +145,9 @@ __kernel void k_sph_taitwater(const __global numtyp4 *restrict x_,
// Lucy Kernel, 2d
wfd = (numtyp)-19.098593171027440292 * wfd * wfd * ihsq * ihsq * ihsq;
}
// compute pressure of atom j with Tait EOS
numtyp tmp = rhoj / rho0_jtype;
numtyp fj = tmp * tmp * tmp;
fj = B_jtype * (fj * fj * tmp - (numtyp)1.0);
@ -321,7 +321,7 @@ __kernel void k_sph_taitwater_fast(const __global numtyp4 *restrict x_,
wfd = (numtyp)-19.098593171027440292 * wfd * wfd * ihsq * ihsq * ihsq;
}
// compute pressure of atom j with Tait EOS
// compute pressure of atom j with Tait EOS
numtyp tmp = rhoj / rho0_jtype;
numtyp fj = tmp * tmp * tmp;
fj = B_jtype * (fj * fj * tmp - (numtyp)1.0);
@ -356,7 +356,7 @@ __kernel void k_sph_taitwater_fast(const __global numtyp4 *restrict x_,
drhoEacc.y += deltaE;
if (EVFLAG && eflag) {
numtyp e = (numtyp)0;
numtyp e = (numtyp)0;
energy+=e;
}
if (EVFLAG && vflag) {

4
lib/gpu/lal_sph_taitwater_ext.cpp
View File

@ -114,10 +114,10 @@ void sph_taitwater_gpu_compute(const int ago, const int inum_full, const int nal
int **firstneigh, const bool eflag, const bool vflag,
const bool eatom, const bool vatom, int &host_start,
const double cpu_time, bool &success, tagint *host_tag,
double **host_v, const int nlocal) {
double **host_v) {
SPHTaitwaterMF.compute(ago, inum_full, nall, host_x, host_type, ilist, numj,
firstneigh, eflag, vflag, eatom, vatom, host_start, cpu_time, success,
host_tag, host_v, nlocal);
host_tag, host_v);
}
void sph_taitwater_gpu_get_extra_data(double *host_rho) {

3
lib/mdi/Install.py
View File

@ -32,7 +32,7 @@ make lib-mdi args="-m mpi" # build MDI lib with same settings as in the mpi Make
# settings
version = "1.4.16"
version = "1.4.26"
url = "https://github.com/MolSSI-MDI/MDI_Library/archive/v%s.tar.gz" % version
# known checksums for different MDI versions. used to validate the download.
@ -41,6 +41,7 @@ checksums = { \
'1.4.12' : '7a222353ae8e03961d5365e6cd48baee', \
'1.4.14' : '7a059bb12535360fdcb7de8402f9a0fc', \
'1.4.16' : '407db44e2d79447ab5c1233af1965f65', \
'1.4.26' : '3124bb85259471e2a53a891f04bf697a', \
}
# print error message or help

50
python/lammps/core.py
View File

@ -282,6 +282,8 @@ class lammps(object):
self.lib.lammps_config_accelerator.argtypes = [c_char_p, c_char_p, c_char_p]
self.lib.lammps_set_variable.argtypes = [c_void_p, c_char_p, c_char_p]
self.lib.lammps_set_string_variable.argtypes = [c_void_p, c_char_p, c_char_p]
self.lib.lammps_set_internal_variable.argtypes = [c_void_p, c_char_p, c_double]
self.lib.lammps_has_style.argtypes = [c_void_p, c_char_p, c_char_p]
@ -1252,6 +1254,8 @@ class lammps(object):
def set_variable(self,name,value):
"""Set a new value for a LAMMPS string style variable
.. deprecated:: TBD
This is a wrapper around the :cpp:func:`lammps_set_variable`
function of the C-library interface.
@ -1271,6 +1275,52 @@ class lammps(object):
# -------------------------------------------------------------------------
def set_string_variable(self,name,value):
"""Set a new value for a LAMMPS string style variable
.. versionadded:: TBD
This is a wrapper around the :cpp:func:`lammps_set_string_variable`
function of the C-library interface.
:param name: name of the variable
:type name: string
:param value: new variable value
:type value: any. will be converted to a string
:return: either 0 on success or -1 on failure
:rtype: int
"""
if name: name = name.encode()
else: return -1
if value: value = str(value).encode()
else: return -1
with ExceptionCheck(self):
return self.lib.lammps_set_string_variable(self.lmp,name,value)
# -------------------------------------------------------------------------
def set_internal_variable(self,name,value):
"""Set a new value for a LAMMPS internal style variable
.. versionadded:: TBD
This is a wrapper around the :cpp:func:`lammps_set_internal_variable`
function of the C-library interface.
:param name: name of the variable
:type name: string
:param value: new variable value
:type value: float or compatible. will be converted to float
:return: either 0 on success or -1 on failure
:rtype: int
"""
if name: name = name.encode()
else: return -1
with ExceptionCheck(self):
return self.lib.lammps_set_internal_variable(self.lmp,name,value)
# -------------------------------------------------------------------------
# return vector of atom properties gathered across procs
# 3 variants to match src/library.cpp
# name = atom property recognized by LAMMPS in atom->extract()

2
src/.gitignore vendored
View File

@ -346,8 +346,6 @@
/bond_bpm_spring.h
/compute_nbond_atom.cpp
/compute_nbond_atom.h
/fix_bond_history.cpp
/fix_bond_history.h
/fix_nve_bpm_sphere.cpp
/fix_nve_bpm_sphere.h
/fix_update_special_bonds.cpp

2
src/ADIOS/reader_adios.cpp
View File

@ -30,7 +30,7 @@
using namespace LAMMPS_NS;
#define SMALL 1.0e-6
static constexpr double SMALL = 1.0e-6;
namespace LAMMPS_NS {
class ReadADIOSInternal {

9
src/AMOEBA/amoeba_convolution.cpp
View File

@ -47,13 +47,8 @@ enum{MPOLE_GRID,POLAR_GRID,POLAR_GRIDC,DISP_GRID,INDUCE_GRID,INDUCE_GRIDC};
//#define SCALE 1
#define SCALE 0
#ifdef FFT_SINGLE
#define ZEROF 0.0f
#define ONEF 1.0f
#else
#define ZEROF 0.0
#define ONEF 1.0
#endif
static constexpr FFT_SCALAR ZEROF = 0.0;
static constexpr FFT_SCALAR ONEF = 1.0;
/* ----------------------------------------------------------------------
partition an FFT grid across processors

35
src/AMOEBA/amoeba_file.cpp
View File

@ -25,23 +25,23 @@
using namespace LAMMPS_NS;
enum{UNKNOWN,FFIELD,LITERATURE,ATOMTYPE,VDWL,VDWLPAIR,BSTRETCH,SBEND,ABEND,
PAULI,DISPERSION,UB,OUTPLANE,TORSION,PITORSION,ATOMMULT,
QPENETRATION,DIPPOLAR,QTRANSFER,END_OF_FILE};
enum{ALLINGER,BUFFERED_14_7};
enum{ARITHMETIC,GEOMETRIC,CUBIC_MEAN,R_MIN,SIGMA,DIAMETER,HARMONIC,HHG,W_H};
enum{MUTUAL,OPT,TCG,DIRECT};
enum{NOFRAME,ZONLY,ZTHENX,BISECTOR,ZBISECT,THREEFOLD};
enum{GEAR,ASPC,LSQR};
enum { UNKNOWN, FFIELD, LITERATURE, ATOMTYPE, VDWL, VDWLPAIR, BSTRETCH, SBEND, ABEND,
PAULI, DISPERSION, UB, OUTPLANE, TORSION, PITORSION, ATOMMULT, QPENETRATION, DIPPOLAR,
QTRANSFER, END_OF_FILE };
enum { ALLINGER, BUFFERED_14_7 };
enum { ARITHMETIC, GEOMETRIC, CUBIC_MEAN, R_MIN, SIGMA, DIAMETER, HARMONIC, HHG, W_H };
enum { MUTUAL, OPT, TCG, DIRECT };
enum { NOFRAME, ZONLY, ZTHENX, BISECTOR, ZBISECT, THREEFOLD };
enum { GEAR, ASPC, LSQR };
#define MAXLINE 65536 // crazy big for TORSION-TORSION section
#define MAX_TYPE_PER_GROUP 6 // max types per AMOEBA group
#define MAX_FRAME_PER_TYPE 32 // max multipole frames for any AMOEBA type
static constexpr int MAXLINE = 65536; // crazy big for TORSION-TORSION section
static constexpr int MAX_TYPE_PER_GROUP = 6; // max types per AMOEBA group
static constexpr int MAX_FRAME_PER_TYPE = 32; // max multipole frames for any AMOEBA type
#define DELTA_TYPE_CLASS 32
#define DELTA_VDWL_PAIR 16
static constexpr int DELTA_TYPE_CLASS = 32;
static constexpr int DELTA_VDWL_PAIR = 16;
#define BOHR 0.52917721067 // Bohr in Angstroms
static constexpr double BOHR = 0.52917721067; // Bohr in Angstroms
// methods to read, parse, and store info from force field file
@ -79,7 +79,7 @@ void PairAmoeba::read_prmfile(char *filename)
int me = comm->me;
FILE *fptr;
char line[MAXLINE];
char line[MAXLINE] = {'\0'};
if (me == 0) {
fptr = utils::open_potential(filename, lmp, nullptr);
@ -179,8 +179,7 @@ void PairAmoeba::read_prmfile(char *filename)
for (int i = 1; i <= n_amtype; i++) nmultiframe[i] = 0;
}
char next[MAXLINE];
next[0] = '\0';
char next[MAXLINE] = {'\0'};
bool has_next = false;
int n;
while (true) {
@ -381,7 +380,7 @@ void PairAmoeba::read_keyfile(char *filename)
int me = comm->me;
FILE *fptr;
char line[MAXLINE];
char line[MAXLINE] = {'\0'};
if (me == 0) {
fptr = utils::open_potential(filename, lmp, nullptr);
if (fptr == nullptr)

2
src/AMOEBA/amoeba_induce.cpp
View File

@ -41,7 +41,7 @@ enum{GEAR,ASPC,LSQR};
enum{BUILD,APPLY};
enum{GORDON1,GORDON2};
#define DEBYE 4.80321 // conversion factor from q-Angs (real units) to Debye
static constexpr double DEBYE = 4.80321; // conversion factor from q-Angs (real units) to Debye
/* ----------------------------------------------------------------------
induce = induced dipole moments via pre-conditioned CG solver

8
src/AMOEBA/amoeba_multipole.cpp
View File

@ -35,11 +35,11 @@ enum{FIELD,ZRSD,TORQUE,UFLD}; // reverse comm
enum{VDWL,REPULSE,QFER,DISP,MPOLE,POLAR,USOLV,DISP_LONG,MPOLE_LONG,POLAR_LONG};
#ifdef FFT_SINGLE
#define ZEROF 0.0f
#define ONEF 1.0f
static constexpr FFT_SCALAR ZEROF = 0.0f;
static constexpr FFT_SCALAR ONEF = 1.0f;
#else
#define ZEROF 0.0
#define ONEF 1.0
static constexpr FFT_SCALAR ZEROF = 0.0;
static constexpr FFT_SCALAR ONEF = 1.0;
#endif
/* ----------------------------------------------------------------------

2
src/AMOEBA/angle_amoeba.cpp
View File

@ -30,7 +30,7 @@
using namespace LAMMPS_NS;
using namespace MathConst;
#define SMALL 0.001
static constexpr double SMALL = 0.001;
/* ---------------------------------------------------------------------- */

10
src/AMOEBA/fix_amoeba_bitorsion.cpp
View File

@ -32,10 +32,10 @@ using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
#define BITORSIONMAX 6 // max # of BiTorsion terms stored by one atom
#define LISTDELTA 10000
#define LB_FACTOR 1.5
#define MAXLINE 1024
static constexpr int BITORSIONMAX = 6; // max # of BiTorsion terms stored by one atom
static constexpr int LISTDELTA = 10000;
static constexpr double LB_FACTOR = 1.5;
static constexpr int MAXLINE = 1024;
// spline weighting factors
@ -724,7 +724,7 @@ double FixAmoebaBiTorsion::compute_scalar()
void FixAmoebaBiTorsion::read_grid_data(char *bitorsion_file)
{
char line[MAXLINE];
char line[MAXLINE] = {'\0'};
char *eof;
FILE *fp = nullptr;

6
src/AMOEBA/fix_amoeba_pitorsion.cpp
View File

@ -32,9 +32,9 @@ using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
#define PITORSIONMAX 6 // max # of PiTorsion terms stored by one atom
#define LISTDELTA 8196
#define LB_FACTOR 1.5
static constexpr int PITORSIONMAX = 6; // max # of PiTorsion terms stored by one atom
static constexpr int LISTDELTA = 8196;
static constexpr double LB_FACTOR = 1.5;
/* ---------------------------------------------------------------------- */

4
src/AMOEBA/improper_amoeba.cpp
View File

@ -28,8 +28,8 @@
using namespace LAMMPS_NS;
using namespace MathConst;
#define TOLERANCE 0.05
#define SMALL 0.001
static constexpr double TOLERANCE = 0.05;
static constexpr double SMALL = 0.001;
/* ---------------------------------------------------------------------- */

2
src/AMOEBA/pair_amoeba.cpp
View File

@ -47,7 +47,7 @@ enum{MPOLE_GRID,POLAR_GRID,POLAR_GRIDC,DISP_GRID,INDUCE_GRID,INDUCE_GRIDC};
enum{MUTUAL,OPT,TCG,DIRECT};
enum{GEAR,ASPC,LSQR};
#define DELTASTACK 16
static constexpr int DELTASTACK = 16;
#define DEBUG_AMOEBA 0
/* ---------------------------------------------------------------------- */

2
src/ASPHERE/compute_temp_asphere.cpp
View File

@ -33,7 +33,7 @@ using namespace LAMMPS_NS;
enum{ROTATE,ALL};
#define INERTIA 0.2 // moment of inertia prefactor for ellipsoid
static constexpr double INERTIA = 0.2; // moment of inertia prefactor for ellipsoid
/* ---------------------------------------------------------------------- */

2
src/ASPHERE/fix_nve_asphere.cpp
View File

@ -26,7 +26,7 @@
using namespace LAMMPS_NS;
using namespace FixConst;
#define INERTIA 0.2 // moment of inertia prefactor for ellipsoid
static constexpr double INERTIA = 0.2; // moment of inertia prefactor for ellipsoid
/* ---------------------------------------------------------------------- */

2
src/ASPHERE/fix_nve_line.cpp
View File

@ -23,7 +23,7 @@ using namespace LAMMPS_NS;
using namespace FixConst;
using namespace MathConst;
#define INERTIA (1.0/12.0) // moment of inertia prefactor for line segment
static constexpr double INERTIA = (1.0/12.0); // moment of inertia prefactor for line segment
/* ---------------------------------------------------------------------- */

2
src/ASPHERE/pair_line_lj.cpp
View File

@ -25,7 +25,7 @@
using namespace LAMMPS_NS;
#define DELTA 10000
static constexpr int DELTA = 10000;
/* ---------------------------------------------------------------------- */

2
src/ASPHERE/pair_tri_lj.cpp
View File

@ -26,7 +26,7 @@
using namespace LAMMPS_NS;
#define DELTA 20
static constexpr int DELTA = 20;
/* ---------------------------------------------------------------------- */

104
src/BOCS/fix_bocs.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -42,31 +41,30 @@ using namespace LAMMPS_NS;
using namespace FixConst;
static const char cite_user_bocs_package[] =
"BOCS package: doi:10.1021/acs.jpcb.7b09993\n\n"
"@Article{Dunn2018,\n"
" author = {N. J. H. Dunn and K. M. Lebold and M. R. {DeLyser} and\n"
" J. F. Rudzinski and W. G. Noid},\n"
" title = {{BOCS}: Bottom-Up Open-Source Coarse-Graining Software},\n"
" journal = {J.~Phys.\\ Chem.~B},\n"
" year = 2018,\n"
" volume = 122,\n"
" number = 13,\n"
" pages = {3363--3377}\n"
"}\n\n";
"BOCS package: doi:10.1021/acs.jpcb.7b09993\n\n"
"@Article{Dunn2018,\n"
" author = {N. J. H. Dunn and K. M. Lebold and M. R. {DeLyser} and\n"
" J. F. Rudzinski and W. G. Noid},\n"
" title = {{BOCS}: Bottom-Up Open-Source Coarse-Graining Software},\n"
" journal = {J.~Phys.\\ Chem.~B},\n"
" year = 2018,\n"
" volume = 122,\n"
" number = 13,\n"
" pages = {3363--3377}\n"
"}\n\n";
static constexpr double DELTAFLIP = 0.1;
static constexpr double TILTMAX = 1.5;
static constexpr int NUM_INPUT_DATA_COLUMNS = 2; // columns in the pressure correction file
#define DELTAFLIP 0.1
#define TILTMAX 1.5
enum{NOBIAS,BIAS};
enum{NONE,XYZ,XY,YZ,XZ};
enum{ISO,ANISO,TRICLINIC};
const int NUM_INPUT_DATA_COLUMNS = 2; // columns in the pressure correction file
enum { NOBIAS, BIAS };
enum { NONE, XYZ, XY, YZ, XZ };
enum { ISO, ANISO, TRICLINIC };
/* ----------------------------------------------------------------------
NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion
---------------------------------------------------------------------- */
// clang-format off
FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), id_dilate(nullptr), irregular(nullptr), id_temp(nullptr),
@ -75,7 +73,7 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
{
if (lmp->citeme) lmp->citeme->add(cite_user_bocs_package);
if (narg < 4) error->all(FLERR,"Illegal fix bocs command");
if (narg < 4) utils::missing_cmd_args(FLERR,"fix bocs",error);
restart_global = 1;
dynamic_group_allow = 1;
@ -102,8 +100,6 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
omega_mass_flag = 0;
etap_mass_flag = 0;
flipflag = 1;
dipole_flag = 0;
dlm_flag = 0;
tcomputeflag = 0;
pcomputeflag = 0;
@ -266,13 +262,6 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
if (p_flag[2] && domain->zperiodic == 0)
error->all(FLERR,"Cannot use fix bocs on a non-periodic dimension");
if (dipole_flag) {
if (!atom->sphere_flag)
error->all(FLERR,"Using update dipole flag requires atom style sphere");
if (!atom->mu_flag)
error->all(FLERR,"Using update dipole flag requires atom attribute mu");
}
if ((tstat_flag && t_period <= 0.0) ||
(p_flag[0] && p_period[0] <= 0.0) ||
(p_flag[1] && p_period[1] <= 0.0) ||
@ -616,8 +605,8 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
// Data file lines hold two floating point numbers.
// Line length we allocate should be long enough without being too long.
// 128 seems safe for a line we expect to be < 30 chars.
const int MAX_F_TABLE_LINE_LENGTH = 128;
char line[MAX_F_TABLE_LINE_LENGTH];
constexpr int MAX_F_TABLE_LINE_LENGTH = 128;
char line[MAX_F_TABLE_LINE_LENGTH] = {'\0'};
std::vector<std::string> inputLines;
while (fgets(line, MAX_F_TABLE_LINE_LENGTH, fpi)) {
inputLines.emplace_back(line);
@ -649,17 +638,13 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
for (int i = 0; i < (int)inputLines.size(); ++i) {
lineNum++; // count each line processed now so lineNum messages can be 1-based
test_sscanf = sscanf(inputLines.at(i).c_str()," %f , %f ",&f1, &f2);
if (test_sscanf == 2)
{
if (test_sscanf == 2) {
data[VOLUME][i] = (double)f1;
data[PRESSURE_CORRECTION][i] = (double)f2;
if (i == 1)
{
if (i == 1) {
// second entry is used to compute the validation interval used below
stdVolumeInterval = data[VOLUME][i] - data[VOLUME][i-1];
}
else if (i > 1)
{
} else if (i > 1) {
// after second entry, all intervals are validated
currVolumeInterval = data[VOLUME][i] - data[VOLUME][i-1];
if (fabs(currVolumeInterval - stdVolumeInterval) > volumeIntervalTolerance) {
@ -673,17 +658,14 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
}
// no concluding else is intentional: i = 0, first line, no interval to validate
}
}
else
{
} else {
if (comm->me == 0)
error->warning(FLERR,"Bad input format: did not find 2 comma separated numeric"
" values in line {} of file {}\nWARNING:\tline: {}",
lineNum, filename, inputLines.at(i));
badInput = true;
}
if (badInput)
{
if (badInput) {
numBadVolumeIntervals++;
}
}
@ -700,18 +682,13 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
error->warning(FLERR,"Bad volume / pressure-correction data: {}\nSee details above", filename);
}
if (p_basis_type == BASIS_LINEAR_SPLINE)
{
if (p_basis_type == BASIS_LINEAR_SPLINE) {
spline_length = numEntries;
numEntries = build_linear_splines(data);
}
else if (p_basis_type == BASIS_CUBIC_SPLINE)
{
} else if (p_basis_type == BASIS_CUBIC_SPLINE) {
spline_length = numEntries;
numEntries = build_cubic_splines(data);
}
else
{
} else {
error->all(FLERR,"ERROR: invalid p_basis_type value of {} in read_F_table", p_basis_type);
}
@ -724,8 +701,7 @@ int FixBocs::build_linear_splines(double **data) {
splines[VOLUME] = (double *) calloc(spline_length,sizeof(double));
splines[PRESSURE_CORRECTION] = (double *) calloc(spline_length,sizeof(double));
for (int i = 0; i < spline_length; ++i)
{
for (int i = 0; i < spline_length; ++i) {
splines[VOLUME][i] = data[VOLUME][i];
splines[PRESSURE_CORRECTION][i] = data[PRESSURE_CORRECTION][i];
}
@ -758,18 +734,15 @@ int FixBocs::build_cubic_splines(double **data)
memory->create(mu, n, "mu");
memory->create(z, n, "z");
for (int i=0; i<n; i++)
{
for (int i=0; i<n; i++) {
a[i] = data[1][i];
b[i] = 0.0;
d[i] = 0.0;
if (i<(n-1))
{
if (i<(n-1)) {
h[i] = (data[0][i+1] - data[0][i]);
}
double alpha_i;
if (i>1 && i<(n-1))
{
if (i>1 && i<(n-1)) {
alpha_i = (3.0 / h[i]) * ( data[1][i+1] - data[1][i]) - (3.0 / h[i-1] )
* ( data[1][i] - data[1][i-1] );
alpha[i-1] = alpha_i;
@ -779,8 +752,7 @@ int FixBocs::build_cubic_splines(double **data)
mu[0] = 0.0;
z[0] = 0.0;
for (int i=1; i<n-1; i++)
{
for (int i=1; i<n-1; i++) {
l[i] = 2*(data[0][i+1] - data[0][i-1]) - h[i-1] * mu[i-1];
mu[i] = h[i]/l[i];
z[i] = (alpha[i] - h[i-1] * z[i-1]) / l[i];
@ -797,19 +769,15 @@ int FixBocs::build_cubic_splines(double **data)
c[n] = 0.0;
d[n] = 0.0;
for (int j=n-1; j>=0; j--)
{
for (int j=n-1; j>=0; j--) {
c[j] = z[j] - mu[j]*c[j+1];
b[j] = (a[j+1]-a[j])/h[j] - h[j]*(c[j+1] + 2.0 * c[j])/3.0;
d[j] = (c[j+1]-c[j])/(3.0 * h[j]);
}
int numSplines = n - 1;
memory->create(splines, NUM_CUBIC_SPLINE_COLUMNS, numSplines, "splines");
for (int idx = 0; idx < numSplines; ++idx)
{
for (int idx = 0; idx < numSplines; ++idx) {
splines[0][idx] = data[0][idx];
splines[1][idx] = a[idx];
splines[2][idx] = b[idx];

2
src/BOCS/fix_bocs.h
View File

@ -129,8 +129,6 @@ class FixBocs : public Fix {
int eta_mass_flag; // 1 if eta_mass updated, 0 if not.
int omega_mass_flag; // 1 if omega_mass updated, 0 if not.
int etap_mass_flag; // 1 if etap_mass updated, 0 if not.
int dipole_flag; // 1 if dipole is updated, 0 if not.
int dlm_flag; // 1 if using the DLM rotational integrator, 0 if not
int scaleyz; // 1 if yz scaled with lz
int scalexz; // 1 if xz scaled with lz

2
src/BODY/body_nparticle.cpp
View File

@ -26,7 +26,7 @@
using namespace LAMMPS_NS;
#define EPSILON 1.0e-7
static constexpr double EPSILON = 1.0e-7;
enum{SPHERE,LINE,TRI}; // also in DumpImage
/* ---------------------------------------------------------------------- */

2
src/BODY/body_rounded_polygon.cpp
View File

@ -32,7 +32,7 @@
using namespace LAMMPS_NS;
#define EPSILON 1.0e-7
static constexpr double EPSILON = 1.0e-7;
enum{SPHERE,LINE}; // also in DumpImage
/* ---------------------------------------------------------------------- */

2
src/BODY/body_rounded_polyhedron.cpp
View File

@ -31,7 +31,7 @@
using namespace LAMMPS_NS;
#define EPSILON 1.0e-7
static constexpr double EPSILON = 1.0e-7;
#define MAX_FACE_SIZE 4 // maximum number of vertices per face (for now)
enum{SPHERE,LINE}; // also in DumpImage

2
src/BODY/compute_body_local.cpp
View File

@ -25,7 +25,7 @@
using namespace LAMMPS_NS;
#define DELTA 10000
static constexpr int DELTA = 10000;
enum{ID,TYPE,INDEX};

6
src/BODY/fix_wall_body_polygon.cpp
View File

@ -43,9 +43,9 @@ enum {INVALID=0,NONE=1,VERTEX=2};
enum {FAR=0,XLO,XHI,YLO,YHI};
//#define _POLYGON_DEBUG
#define DELTA 10000
#define EPSILON 1e-2 // dimensionless threshold (dot products, end point checks, contact checks)
#define BIG 1.0e20
static constexpr int DELTA = 10000;
static constexpr double EPSILON = 1e-2; // dimensionless threshold (dot products, end point checks, contact checks)
static constexpr double BIG = 1.0e20;
#define MAX_CONTACTS 4 // maximum number of contacts for 2D models
#define EFF_CONTACTS 2 // effective contacts for 2D models

6
src/BODY/fix_wall_body_polyhedron.cpp
View File

@ -43,9 +43,9 @@ enum {INVALID=0,NONE=1,VERTEX=2};
enum {FAR=0,XLO,XHI,YLO,YHI,ZLO,ZHI};
//#define _POLYHEDRON_DEBUG
#define DELTA 10000
#define EPSILON 1e-3 // dimensionless threshold (dot products, end point checks)
#define BIG 1.0e20
static constexpr int DELTA = 10000;
static constexpr double EPSILON = 1e-3; // dimensionless threshold (dot products, end point checks)
static constexpr double BIG = 1.0e20;
#define MAX_CONTACTS 4 // maximum number of contacts for 2D models
#define EFF_CONTACTS 2 // effective contacts for 2D models

2
src/BODY/pair_body_nparticle.cpp
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@ -29,7 +29,7 @@
using namespace LAMMPS_NS;
#define DELTA 10000
static constexpr int DELTA = 10000;
/* ---------------------------------------------------------------------- */

4
src/BODY/pair_body_rounded_polygon.cpp
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@ -39,8 +39,8 @@
using namespace LAMMPS_NS;
#define DELTA 10000
#define EPSILON 1e-3 // dimensionless threshold (dot products, end point checks, contact checks)
static constexpr int DELTA = 10000;
static constexpr double EPSILON = 1e-3; // dimensionless threshold (dot products, end point checks, contact checks)
#define MAX_CONTACTS 4 // maximum number of contacts for 2D models
#define EFF_CONTACTS 2 // effective contacts for 2D models

4
src/BODY/pair_body_rounded_polyhedron.cpp
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@ -43,8 +43,8 @@
using namespace LAMMPS_NS;
using namespace MathConst;
#define DELTA 10000
#define EPSILON 1e-3 // dimensionless threshold (dot products, end point checks, contact checks)
static constexpr int DELTA = 10000;
static constexpr double EPSILON = 1e-3; // dimensionless threshold (dot products, end point checks, contact checks)
#define MAX_FACE_SIZE 4 // maximum number of vertices per face (same as BodyRoundedPolyhedron)
#define MAX_CONTACTS 32 // for 3D models (including duplicated counts)

1
src/BPM/atom_vec_bpm_sphere.cpp
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@ -35,7 +35,6 @@ AtomVecBPMSphere::AtomVecBPMSphere(LAMMPS *_lmp) : AtomVec(_lmp)
radvary = 0;
atom->molecule_flag = 1;
atom->sphere_flag = 1;
atom->radius_flag = atom->rmass_flag = atom->omega_flag = atom->torque_flag = atom->quat_flag = 1;
// strings with peratom variables to include in each AtomVec method

4
src/BPM/bond_bpm_rotational.cpp
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@ -28,7 +28,7 @@
#include <cmath>
#include <cstring>
#define EPSILON 1e-10
static constexpr double EPSILON = 1e-10;
using namespace LAMMPS_NS;
using MathConst::MY_SQRT2;
@ -645,7 +645,7 @@ void BondBPMRotational::init_style()
{
BondBPM::init_style();
if (!atom->quat_flag || !atom->sphere_flag)
if (!atom->quat_flag || !atom->radius_flag || !atom->omega_flag)
error->all(FLERR, "Bond bpm/rotational requires atom style bpm/sphere");
if (comm->ghost_velocity == 0)
error->all(FLERR, "Bond bpm/rotational requires ghost atoms store velocity");

2
src/BPM/bond_bpm_spring.cpp
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@ -26,7 +26,7 @@
#include <cmath>
#include <cstring>
#define EPSILON 1e-10
static constexpr double EPSILON = 1e-10;
using namespace LAMMPS_NS;

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