Merge remote-tracking branch 'github/develop' into howto-bulk-to-slab
This commit is contained in:
Axel Kohlmeyer
47
.github/release_steps.md
vendored
47
.github/release_steps.md
vendored
@ -216,7 +216,7 @@ and using the CMake settings:
|
||||
|
||||
``` sh
|
||||
-D CMAKE_OSX_ARCHITECTURES=arm64;x86_64
|
||||
-D CMAKE_OSX_DEPLOYMENT_TARGER=11.0
|
||||
-D CMAKE_OSX_DEPLOYMENT_TARGET=11.0
|
||||
```
|
||||
|
||||
This will add the compiler flags `-arch arm64 -arch x86_64
|
||||
@ -324,6 +324,47 @@ At this point it should be possible to do a fast-forward merge of
|
||||
|
||||
### Push branches and tags
|
||||
|
||||
|
||||
|
||||
## LAMMPS Stable Update Release
|
||||
|
||||
After making a stable release, bugfixes from the 'develop' branch
|
||||
are selectively backported to the 'maintenance' branch. This is
|
||||
done with "git cherry-pick \<commit hash\>' wherever possible.
|
||||
The LAMMPS\_UPDATE define in "src/version.h" is set to "Maintenance".
|
||||
|
||||
### Prerequesites
|
||||
|
||||
When a sufficient number of bugfixes has accumulated or an urgent
|
||||
or important bugfix needs to be distributed a new stable update
|
||||
release is made. To make this publicly visible a pull request
|
||||
is submitted that will merge 'maintenance' into 'stable'. Before
|
||||
merging, set LAMMPS\_UPDATE in "src/version.h" to "Update #" with
|
||||
"#" indicating the update count (1, 2, and so on).
|
||||
Also draft suitable release notes under https://github.com/lammps/lammps/releases
|
||||
|
||||
### Fast-forward merge of 'maintenance' into 'stable', apply tag, and publish
|
||||
|
||||
Do a fast-forward merge of 'maintenance' to 'stable' and then
|
||||
apply the stable\_DMmmYYYY\_update# tag and push branch and tag
|
||||
to GitHub. The corresponding pull request will be automatically
|
||||
closed. Example:
|
||||
|
||||
```
|
||||
git checkout maintenance
|
||||
git pull
|
||||
git checkout stable
|
||||
git pull
|
||||
git merge --ff-only maintenance
|
||||
git tag -s -m 'Update 2 for Stable LAMMPS version 29 August 2024' stable_29Aug2024_update2
|
||||
git push git@github.com:lammps/lammps.git --tags maintenance stable
|
||||
```
|
||||
|
||||
Associate draft release notes with new tag and publish as "latest release".
|
||||
|
||||
On https://ci.lammps.org/ go to "dev", "stable" and manually execute
|
||||
the "update\_release" task. This will update https://docs.lammps.org/stable
|
||||
and prepare a stable tarball.
|
||||
|
||||
### Build and upload binary packages and source tarball to GitHub
|
||||
|
||||
The build procedure is the same as for the feature releases, only
|
||||
that packages are built from the 'stable' branch.
|
||||
|
||||
@ -431,8 +431,8 @@ else()
|
||||
target_link_libraries(lammps PUBLIC mpi_stubs)
|
||||
endif()
|
||||
|
||||
set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
|
||||
set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
|
||||
set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
|
||||
set(LAMMPS_SIZES_VALUES smallbig bigbig)
|
||||
set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
|
||||
validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
|
||||
string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
|
||||
|
||||
@ -260,8 +260,8 @@ endif()
|
||||
|
||||
################
|
||||
# integer size selection
|
||||
set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
|
||||
set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
|
||||
set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
|
||||
set(LAMMPS_SIZES_VALUES smallbig bigbig)
|
||||
set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
|
||||
validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
|
||||
string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
|
||||
|
||||
@ -119,6 +119,13 @@ configured) and additional files like LAMMPS API headers, manpages,
|
||||
potential and force field files. The location of the installation tree
|
||||
defaults to ``${HOME}/.local``.
|
||||
|
||||
.. note::
|
||||
|
||||
If you have set `-D CMAKE_INSTALL_PREFIX` to install LAMMPS into a
|
||||
system location on a Linux machine , you may also have to run (as
|
||||
root) the `ldconfig` program to update the cache file for fast lookup
|
||||
of system shared libraries.
|
||||
|
||||
.. _cmake_options:
|
||||
|
||||
Configuration and build options
|
||||
|
||||
@ -255,11 +255,10 @@ Traditional make
|
||||
|
||||
Before building LAMMPS, you must build the GPU library in ``lib/gpu``\ .
|
||||
You can do this manually if you prefer; follow the instructions in
|
||||
``lib/gpu/README``. Note that the GPU library uses MPI calls, so you must
|
||||
use the same MPI library (or the STUBS library) settings as the main
|
||||
LAMMPS code. This also applies to the ``-DLAMMPS_BIGBIG``\ ,
|
||||
``-DLAMMPS_SMALLBIG``\ , or ``-DLAMMPS_SMALLSMALL`` settings in whichever
|
||||
Makefile you use.
|
||||
``lib/gpu/README``. Note that the GPU library uses MPI calls, so you
|
||||
must use the same MPI library (or the STUBS library) settings as the
|
||||
main LAMMPS code. This also applies to the ``-DLAMMPS_BIGBIG`` or
|
||||
``-DLAMMPS_SMALLBIG`` settings in whichever Makefile you use.
|
||||
|
||||
You can also build the library in one step from the ``lammps/src`` dir,
|
||||
using a command like these, which simply invokes the ``lib/gpu/Install.py``
|
||||
|
||||
@ -221,9 +221,10 @@ HTML as a quick-n-dirty way of checking your manual page.
|
||||
|
||||
This translation uses `Pandoc <https://pandoc.org>`_ instead of Sphinx
|
||||
and thus all special Sphinx features (cross-references, advanced tables,
|
||||
embedding of Python docstring and doxygen documentation, and so on) will
|
||||
not render correctly. But this is a **very fast** way to check the content
|
||||
as HTML while writing the documentation.
|
||||
embedding of Python docstrings or doxygen documentation, and so on) will
|
||||
not render correctly. Most embedded math should render correctly. This
|
||||
is a **very fast** way to check the syntax and layout of a documentation
|
||||
file translated to HTML while writing it.
|
||||
|
||||
To translate **all** manual pages, you can type ``make fasthtml`` at the
|
||||
command line. The translated HTML files are then in the ``fasthtml``
|
||||
|
||||
@ -13,7 +13,8 @@ explains how to do this for building both with CMake and make.
|
||||
* `Size of LAMMPS integer types and size limits`_
|
||||
* `Read or write compressed files`_
|
||||
* `Output of JPEG, PNG, and movie files`_ via the :doc:`dump image <dump_image>` or :doc:`dump movie <dump_image>` commands
|
||||
* `Support for downloading files`_
|
||||
* `Support for downloading files from the input`_
|
||||
* `Prevent download of large potential files`_
|
||||
* `Memory allocation alignment`_
|
||||
* `Workaround for long long integers`_
|
||||
* `Exception handling when using LAMMPS as a library`_ to capture errors
|
||||
@ -315,7 +316,7 @@ large counters can become before "rolling over". The default setting of
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
-D LAMMPS_SIZES=value # smallbig (default) or bigbig or smallsmall
|
||||
-D LAMMPS_SIZES=value # smallbig (default) or bigbig
|
||||
|
||||
If the variable is not set explicitly, "smallbig" is used.
|
||||
|
||||
@ -326,7 +327,7 @@ large counters can become before "rolling over". The default setting of
|
||||
|
||||
.. code-block:: make
|
||||
|
||||
LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG or -DLAMMPS_SMALLSMALL
|
||||
LMP_INC = -DLAMMPS_SMALLBIG # or -DLAMMPS_BIGBIG
|
||||
|
||||
The default setting is ``-DLAMMPS_SMALLBIG`` if nothing is specified
|
||||
|
||||
@ -335,34 +336,27 @@ LAMMPS system size restrictions
|
||||
|
||||
.. list-table::
|
||||
:header-rows: 1
|
||||
:widths: 18 27 28 27
|
||||
:widths: 27 36 37
|
||||
:align: center
|
||||
|
||||
* -
|
||||
- smallbig
|
||||
- bigbig
|
||||
- smallsmall
|
||||
* - Total atom count
|
||||
- :math:`2^{63}` atoms (= :math:`9.223 \cdot 10^{18}`)
|
||||
- :math:`2^{63}` atoms (= :math:`9.223 \cdot 10^{18}`)
|
||||
- :math:`2^{31}` atoms (= :math:`2.147 \cdot 10^9`)
|
||||
* - Total timesteps
|
||||
- :math:`2^{63}` steps (= :math:`9.223 \cdot 10^{18}`)
|
||||
- :math:`2^{63}` steps (= :math:`9.223 \cdot 10^{18}`)
|
||||
- :math:`2^{31}` steps (= :math:`2.147 \cdot 10^9`)
|
||||
* - Atom ID values
|
||||
- :math:`1 \le i \le 2^{31} (= 2.147 \cdot 10^9)`
|
||||
- :math:`1 \le i \le 2^{63} (= 9.223 \cdot 10^{18})`
|
||||
- :math:`1 \le i \le 2^{31} (= 2.147 \cdot 10^9)`
|
||||
* - Image flag values
|
||||
- :math:`-512 \le i \le 511`
|
||||
- :math:`- 1\,048\,576 \le i \le 1\,048\,575`
|
||||
- :math:`-512 \le i \le 511`
|
||||
|
||||
The "bigbig" setting increases the size of image flags and atom IDs over
|
||||
"smallbig" and the "smallsmall" setting is only needed if your machine
|
||||
does not support 64-bit integers or incurs performance penalties when
|
||||
using them.
|
||||
the default "smallbig" setting.
|
||||
|
||||
These are limits for the core of the LAMMPS code, specific features or
|
||||
some styles may impose additional limits. The :ref:`ATC
|
||||
@ -516,8 +510,8 @@ during a run.
|
||||
|
||||
.. _libcurl:
|
||||
|
||||
Support for downloading files
|
||||
-----------------------------
|
||||
Support for downloading files from the input
|
||||
--------------------------------------------
|
||||
|
||||
.. versionadded:: 29Aug2024
|
||||
|
||||
@ -560,6 +554,25 @@ LAMMPS is compiled accordingly which needs the following settings:
|
||||
|
||||
----------
|
||||
|
||||
.. _download_pot:
|
||||
|
||||
Prevent download of large potential files
|
||||
-----------------------------------------
|
||||
|
||||
.. versionadded:: 8Feb2023
|
||||
|
||||
LAMMPS bundles a selection of potential files in the ``potentials``
|
||||
folder as examples of how those kinds of potential files look like and
|
||||
for use with the provided input examples in the ``examples`` tree. To
|
||||
keep the size of the distributed LAMMPS source package small, very large
|
||||
potential files (> 5 MBytes) are not bundled, but only downloaded on
|
||||
demand when the :doc:`corresponding package <Packages_list>` is
|
||||
installed. This automatic download can be prevented when :doc:`building
|
||||
LAMMPS with CMake <Build_cmake>` by adding the setting `-D
|
||||
DOWNLOAD_POTENTIALS=off` when configuring.
|
||||
|
||||
----------
|
||||
|
||||
.. _align:
|
||||
|
||||
Memory allocation alignment
|
||||
|
||||
@ -6233,8 +6233,9 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
|
||||
Atom IDs must be positive integers.
|
||||
|
||||
*One or more atom IDs is too big*
|
||||
The limit on atom IDs is set by the SMALLBIG, BIGBIG, SMALLSMALL
|
||||
setting in your LAMMPS build. See the :doc:`Build settings <Build_settings>` page for more info.
|
||||
The limit on atom IDs is set by the SMALLBIG, BIGBIG
|
||||
setting in your LAMMPS build. See the
|
||||
:doc:`Build settings <Build_settings>` page for more info.
|
||||
|
||||
*One or more atom IDs is zero*
|
||||
Either all atoms IDs must be zero or none of them.
|
||||
|
||||
@ -2773,8 +2773,7 @@ Procedures Bound to the :f:type:`lammps` Derived Type
|
||||
END SUBROUTINE external_callback
|
||||
END INTERFACE
|
||||
|
||||
where ``c_bigint`` is ``c_int`` if ``-DLAMMPS_SMALLSMALL`` was used and
|
||||
``c_int64_t`` otherwise; and ``c_tagint`` is ``c_int64_t`` if
|
||||
where ``c_bigint`` is ``c_int64_t`` and ``c_tagint`` is ``c_int64_t`` if
|
||||
``-DLAMMPS_BIGBIG`` was used and ``c_int`` otherwise.
|
||||
|
||||
The argument *caller* to :f:subr:`set_fix_external_callback` is unlimited
|
||||
|
||||
@ -2,14 +2,18 @@ Moltemplate Tutorial
|
||||
====================
|
||||
|
||||
In this tutorial, we are going to use the tool :ref:`Moltemplate
|
||||
<moltemplate>` to set up a classical molecular dynamic simulation using
|
||||
the :ref:`OPLS-AA force field <OPLSAA96>`. The first
|
||||
task is to describe an organic compound and create a complete input deck
|
||||
for LAMMPS. The second task is to map the OPLS-AA force field to a
|
||||
molecular sample created with an external tool, e.g. PACKMOL, and
|
||||
exported as a PDB file. The files used in this tutorial can be found
|
||||
in the ``tools/moltemplate/tutorial-files`` folder of the LAMMPS
|
||||
source code distribution.
|
||||
<Moltemplate1>` from https://moltemplate.org/ to set up a classical
|
||||
molecular dynamic simulation using the :ref:`OPLS-AA force field
|
||||
<oplsaa2024>`. The first task is to describe an organic compound and
|
||||
create a complete input deck for LAMMPS. The second task is to use
|
||||
moltemplate to build a polymer. The third task is to map the OPLS-AA
|
||||
force field to a molecular sample created with an external tool,
|
||||
e.g. PACKMOL, and exported as a PDB file. The files used in this
|
||||
tutorial can be found in the ``tools/moltemplate/tutorial-files`` folder
|
||||
of the LAMMPS source code distribution.
|
||||
|
||||
Many more examples can be found here: https://moltemplate.org/examples.html
|
||||
|
||||
|
||||
Simulating an organic solvent
|
||||
"""""""""""""""""""""""""""""
|
||||
@ -17,14 +21,13 @@ Simulating an organic solvent
|
||||
This example aims to create a cubic box of the organic solvent
|
||||
formamide.
|
||||
|
||||
The first step is to create a molecular topology in the
|
||||
LAMMPS-template (LT) file format representing a single molecule, which
|
||||
will be stored in a Moltemplate object called ``_FAM inherits OPLSAA {}``.
|
||||
The first step is to create a molecular topology in the LAMMPS-template
|
||||
(LT) file format representing a single molecule, which will be
|
||||
stored in a Moltemplate object called ``_FAM inherits OPLSAA {}``.
|
||||
This command states that the object ``_FAM`` is based on an existing
|
||||
object called ``OPLSAA``, which contains OPLS-AA parameters, atom type
|
||||
definitions, partial charges, masses and bond-angle rules for many organic
|
||||
and biological compounds.
|
||||
|
||||
The atomic structure is the starting point to populate the command
|
||||
``write('Data Atoms') {}``, which will write the ``Atoms`` section in the
|
||||
LAMMPS data file. The OPLS-AA force field uses the ``atom_style full``,
|
||||
@ -36,21 +39,23 @@ to the ``molID``, except that the same variable is used for the whole
|
||||
molecule. The atom types are assigned using ``@``-type variables. The
|
||||
assignment of atom types (e.g. ``@atom:177``, ``@atom:178``) is done using
|
||||
the OPLS-AA atom types defined in the "In Charges" section of the file
|
||||
``oplsaa.lt``, looking for a reasonable match with the description of the atom.
|
||||
``oplsaa2024.lt``, looking for a reasonable match with the description of the atom.
|
||||
The resulting file (``formamide.lt``) follows:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt # defines OPLSAA
|
||||
|
||||
_FAM inherits OPLSAA {
|
||||
|
||||
# atomID molID atomType charge coordX coordY coordZ
|
||||
write('Data Atoms') {
|
||||
$atom:C00 $mol @atom:177 0.00 0.100 0.490 0.0
|
||||
$atom:O01 $mol @atom:178 0.00 1.091 -0.250 0.0
|
||||
$atom:N02 $mol @atom:179 0.00 -1.121 -0.181 0.0
|
||||
$atom:H03 $mol @atom:182 0.00 -2.013 0.272 0.0
|
||||
$atom:H04 $mol @atom:182 0.00 -1.056 -1.190 0.0
|
||||
$atom:H05 $mol @atom:221 0.00 0.144 1.570 0.0
|
||||
$atom:C00 $mol @atom:235 0.00 0.100 0.490 0.0
|
||||
$atom:O01 $mol @atom:236 0.00 1.091 -0.250 0.0
|
||||
$atom:N02 $mol @atom:237 0.00 -1.121 -0.181 0.0
|
||||
$atom:H03 $mol @atom:240 0.00 -2.013 0.272 0.0
|
||||
$atom:H04 $mol @atom:240 0.00 -1.056 -1.190 0.0
|
||||
$atom:H05 $mol @atom:279 0.00 0.144 1.570 0.0
|
||||
}
|
||||
|
||||
# A list of the bonds in the molecule:
|
||||
@ -64,16 +69,17 @@ The resulting file (``formamide.lt``) follows:
|
||||
}
|
||||
}
|
||||
|
||||
You don't have to specify the charge in this example because they will
|
||||
be assigned according to the atom type. Analogously, only a
|
||||
"Data Bond List" section is needed as the atom type will determine the
|
||||
bond type. The other bonded interactions (e.g. angles,
|
||||
dihedrals, and impropers) will be automatically generated by
|
||||
You don't have to specify the charge in this example because the OPLSAA
|
||||
force-field assigns charge according to the atom type. (This is not true
|
||||
when using other force fields.) A "Data Bond List" section is needed as
|
||||
the atom type will determine the bond type. The other bonded interactions
|
||||
(e.g. angles, dihedrals, and impropers) will be automatically generated by
|
||||
Moltemplate.
|
||||
|
||||
If the simulation is non-neutral, or Moltemplate complains that you have
|
||||
missing bond, angle, or dihedral types, this means at least one of your
|
||||
atom types is incorrect.
|
||||
If the simulation is not charge-neutral, or Moltemplate complains that
|
||||
you have missing bond, angle, or dihedral types, this probably means that
|
||||
at least one of your atom types is incorrect (or that perhaps there is no
|
||||
suitable atom type currently defined in the ``oplsaa2024.lt`` file).
|
||||
|
||||
The second step is to create a master file with instructions to build a
|
||||
starting structure and the LAMMPS commands to run an NPT simulation. The
|
||||
@ -81,11 +87,9 @@ master file (``solv_01.lt``) follows:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
# Import the force field.
|
||||
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa.lt
|
||||
import formamide.lt # after oplsaa.lt, as it depends on it.
|
||||
import formamide.lt # Defines "_FAM" and OPLSAA
|
||||
|
||||
# Create the input sample.
|
||||
# Distribute the molecules on a 5x5x5 cubic grid with spacing 4.6
|
||||
solv = new _FAM [5].move( 4.6, 0, 0)
|
||||
[5].move( 0, 4.6, 0)
|
||||
[5].move( 0, 0, 4.6)
|
||||
@ -98,8 +102,11 @@ master file (``solv_01.lt``) follows:
|
||||
-11.5 11.5 zlo zhi
|
||||
}
|
||||
|
||||
# Create an input deck for LAMMPS.
|
||||
write_once("In Init"){
|
||||
# Note: The lines below in the "In Run" section are often omitted.
|
||||
|
||||
write_once("In Run"){
|
||||
# Create an input deck for LAMMPS.
|
||||
# Run an NPT simulation.
|
||||
# Input variables.
|
||||
variable run string solv_01 # output name
|
||||
variable ts equal 1 # timestep
|
||||
@ -109,12 +116,6 @@ master file (``solv_01.lt``) follows:
|
||||
variable equi equal 5000 # Equilibration steps
|
||||
variable prod equal 30000 # Production steps
|
||||
|
||||
# PBC (set them before the creation of the box).
|
||||
boundary p p p
|
||||
}
|
||||
|
||||
# Run an NPT simulation.
|
||||
write_once("In Run"){
|
||||
# Derived variables.
|
||||
variable tcouple equal \$\{ts\}*100
|
||||
variable pcouple equal \$\{ts\}*1000
|
||||
@ -143,7 +144,7 @@ master file (``solv_01.lt``) follows:
|
||||
unfix NPT
|
||||
}
|
||||
|
||||
The first two commands insert the content of files ``oplsaa.lt`` and
|
||||
The first two commands insert the content of files ``oplsaa2024.lt`` and
|
||||
``formamide.lt`` into the master file. At this point, we can use the
|
||||
command ``solv = new _FAM [N]`` to create N copies of a molecule of type
|
||||
``_FAM``. In this case, we create an array of 5*5*5 molecules on a cubic
|
||||
@ -153,21 +154,37 @@ the sample was created from scratch, we also specify the simulation box
|
||||
size in the "Data Boundary" section.
|
||||
|
||||
The LAMMPS setting for the force field are specified in the file
|
||||
``oplsaa.lt`` and are written automatically in the input deck. We also
|
||||
``oplsaa2024.lt`` and are written automatically in the input deck. We also
|
||||
specify the boundary conditions and a set of variables in
|
||||
the "In Init" section. The remaining commands to run an NPT simulation
|
||||
the "In Init" section.
|
||||
|
||||
The remaining commands to run an NPT simulation
|
||||
are written in the "In Run" section. Note that in this script, LAMMPS
|
||||
variables are protected with the escape character ``\`` to distinguish
|
||||
them from Moltemplate variables, e.g. ``\$\{run\}`` is a LAMMPS
|
||||
variable that is written in the input deck as ``${run}``.
|
||||
|
||||
(Note: Moltemplate can be slow to run, so you need to change you run
|
||||
settings frequently, I recommended moving those commands (from "In Run")
|
||||
out of your .lt files and into a separate file. Moltemplate creates a
|
||||
file named ``run.in.EXAMPLE`` for this purpose. You can put your run
|
||||
settings and fixes that file and then invoke LAMMPS using
|
||||
``mpirun -np 4 lmp -in run.in.EXAMPLE`` instead.)
|
||||
|
||||
|
||||
Compile the master file with:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
moltemplate.sh -overlay-all solv_01.lt
|
||||
moltemplate.sh solv_01.lt
|
||||
cleanup_moltemplate.sh # <-- optional: see below
|
||||
|
||||
And execute the simulation with the following:
|
||||
(Note: The optional "cleanup_moltemplate.sh" command deletes
|
||||
unused atom types, which sometimes makes LAMMPS run faster.
|
||||
But it does not work with many-body pair styles or dreiding-style h-bonds.
|
||||
Fortunately most force fields, including OPLSAA, don't use those features.)
|
||||
|
||||
Then execute the simulation with the following:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -180,15 +197,116 @@ And execute the simulation with the following:
|
||||
Snapshot of the sample at the beginning and end of the simulation.
|
||||
Rendered with Ovito.
|
||||
|
||||
|
||||
Building a simple polymer
|
||||
"""""""""""""""""""""""""
|
||||
Moltemplate is particularly useful for building polymers (and other molecules
|
||||
with sub-units). As an simple example, consider butane:
|
||||
|
||||
.. figure:: JPG/butane.jpg
|
||||
|
||||
The ``butane.lt`` file below defines Butane as a polymer containing
|
||||
4 monomers (of type ``CH3``, ``CH2``, ``CH2``, ``CH3``).
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt # defines OPLSAA
|
||||
|
||||
CH3 inherits OPLSAA {
|
||||
|
||||
# atomID molID atomType charge coordX coordY coordZ
|
||||
write("Data Atoms") {
|
||||
$atom:c $mol:... @atom:54 0.0 0.000000 0.4431163 0.000000
|
||||
$atom:h1 $mol:... @atom:60 0.0 0.000000 1.0741603 0.892431
|
||||
$atom:h2 $mol:... @atom:60 0.0 0.000000 1.0741603 -0.892431
|
||||
$atom:h3 $mol:... @atom:60 0.0 -0.892431 -0.1879277 0.000000
|
||||
}
|
||||
# (Using "$mol:..." indicates this object ("CH3") is part of a larger
|
||||
# molecule. Moltemplate will share the molecule-ID with that molecule.)
|
||||
|
||||
# A list of the bonds within the "CH3" molecular sub-unit:
|
||||
# BondID AtomID1 AtomID2
|
||||
write('Data Bond List') {
|
||||
$bond:ch1 $atom:c $atom:h1
|
||||
$bond:ch2 $atom:c $atom:h2
|
||||
$bond:ch3 $atom:c $atom:h3
|
||||
}
|
||||
}
|
||||
|
||||
CH2 inherits OPLSAA {
|
||||
|
||||
# atomID molID atomType charge coordX coordY coordZ
|
||||
write("Data Atoms") {
|
||||
$atom:c $mol:... @atom:57 0.0 0.000000 0.4431163 0.000000
|
||||
$atom:h1 $mol:... @atom:60 0.0 0.000000 1.0741603 0.892431
|
||||
$atom:h2 $mol:... @atom:60 0.0 0.000000 1.0741603 -0.892431
|
||||
}
|
||||
|
||||
# A list of the bonds within the "CH2" molecular sub-unit:
|
||||
# BondID AtomID1 AtomID2
|
||||
write('Data Bond List') {
|
||||
$bond:ch1 $atom:c $atom:h1
|
||||
$bond:ch2 $atom:c $atom:h2
|
||||
}
|
||||
}
|
||||
|
||||
Butane inherits OPLSAA {
|
||||
|
||||
create_var {$mol} # optional:force all monomers to share the same molecule-ID
|
||||
|
||||
# - Create 4 monomers
|
||||
# - Move them along the X axis using ".move()",
|
||||
# - Rotate them 180 degrees with respect to the previous monomer
|
||||
monomer1 = new CH3
|
||||
monomer2 = new CH2.rot(180,1,0,0).move(1.2533223,0,0)
|
||||
monomer3 = new CH2.move(2.5066446,0,0)
|
||||
monomer4 = new CH3.rot(180,0,0,1).move(3.7599669,0,0)
|
||||
|
||||
# A list of the bonds connecting different monomers together:
|
||||
write('Data Bond List') {
|
||||
$bond:b1 $atom:monomer1/c $atom:monomer2/c
|
||||
$bond:b2 $atom:monomer2/c $atom:monomer3/c
|
||||
$bond:b3 $atom:monomer3/c $atom:monomer4/c
|
||||
}
|
||||
}
|
||||
|
||||
Again, you don't have to specify the charge in this example because OPLSAA
|
||||
assigns charges according to the atom type.
|
||||
|
||||
This ``Butane`` object is a molecule which can be used anywhere other molecules
|
||||
can be used. (You can arrange ``Butane`` molecules on a lattice, as we did previously.
|
||||
You can also modify individual butane molecules by adding or deleting atoms or bonds.
|
||||
You can add bonds between specific butane molecules or use ``Butane`` as a
|
||||
subunit to define even larger molecules. See the moltemplate manual for details.)
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
How to build a complex polymer
|
||||
""""""""""""""""""""""""""""""""""""""""""
|
||||
A similar procedure can be used to create more complicated polymers,
|
||||
such as the NIPAM polymer example shown below. For details, see:
|
||||
|
||||
https://github.com/jewettaij/moltemplate/tree/master/examples/all_atom/force_field_OPLSAA/NIPAM_polymer+water+ions
|
||||
|
||||
|
||||
|
||||
|
||||
Mapping an existing structure
|
||||
"""""""""""""""""""""""""""""
|
||||
|
||||
Another helpful way to use Moltemplate is mapping an existing molecular
|
||||
sample to a force field. This is useful when a complex sample is
|
||||
assembled from different simulations or created with specialized
|
||||
software (e.g. PACKMOL). As in the previous example, all molecular
|
||||
species in the sample must be defined using single-molecule Moltemplate
|
||||
objects. For this example, we use a short polymer in a box containing
|
||||
sample to a force field. This is useful when a complex sample is assembled
|
||||
from different simulations or created with specialized software (e.g. PACKMOL).
|
||||
(Note: The previous link shows how to build this entire system from scratch
|
||||
using only moltemplate. However here we will assume instead that we obtained
|
||||
a PDB file for this system using PACKMOL.)
|
||||
|
||||
As in the previous examples, all molecular species in the sample
|
||||
are defined using single-molecule Moltemplate objects.
|
||||
For this example, we use a short polymer in a box containing
|
||||
water molecules and ions in the PDB file ``model.pdb``.
|
||||
|
||||
It is essential to understand that the order of atoms in the PDB file
|
||||
@ -246,25 +364,25 @@ The resulting master LT file defining short annealing at a fixed volume
|
||||
.. code-block:: bash
|
||||
|
||||
# Use the OPLS-AA force field for all species.
|
||||
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa.lt
|
||||
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt
|
||||
import PolyNIPAM.lt
|
||||
|
||||
# Define the SPC water and ions as in the OPLS-AA
|
||||
Ca inherits OPLSAA {
|
||||
write("Data Atoms"){
|
||||
$atom:a1 $mol:. @atom:354 0.0 0.00000 0.00000 0.000000
|
||||
$atom:a1 $mol:. @atom:412 0.0 0.00000 0.00000 0.000000
|
||||
}
|
||||
}
|
||||
Cl inherits OPLSAA {
|
||||
write("Data Atoms"){
|
||||
$atom:a1 $mol:. @atom:344 0.0 0.00000 0.00000 0.000000
|
||||
$atom:a1 $mol:. @atom:401 0.0 0.00000 0.00000 0.000000
|
||||
}
|
||||
}
|
||||
SPC inherits OPLSAA {
|
||||
write("Data Atoms"){
|
||||
$atom:O $mol:. @atom:76 0. 0.0000000 0.00000 0.000000
|
||||
$atom:H1 $mol:. @atom:77 0. 0.8164904 0.00000 0.5773590
|
||||
$atom:H2 $mol:. @atom:77 0. -0.8164904 0.00000 0.5773590
|
||||
$atom:O $mol:. @atom:9991 0. 0.0000000 0.00000 0.0000000
|
||||
$atom:H1 $mol:. @atom:9990 0. 0.8164904 0.00000 0.5773590
|
||||
$atom:H2 $mol:. @atom:9990 0. -0.8164904 0.00000 0.5773590
|
||||
}
|
||||
write("Data Bond List") {
|
||||
$bond:OH1 $atom:O $atom:H1
|
||||
@ -285,8 +403,15 @@ The resulting master LT file defining short annealing at a fixed volume
|
||||
0 26 zlo zhi
|
||||
}
|
||||
|
||||
# Define the input variables.
|
||||
write_once("In Init"){
|
||||
boundary p p p # "p p p" is the default. This line is optional.
|
||||
neighbor 3 bin # (This line is also optional in this example.)
|
||||
}
|
||||
|
||||
# Note: The lines below in the "In Run" section are often omitted.
|
||||
|
||||
# Run an NVT simulation.
|
||||
write_once("In Run"){
|
||||
# Input variables.
|
||||
variable run string sample01 # output name
|
||||
variable ts equal 2 # timestep
|
||||
@ -294,13 +419,6 @@ The resulting master LT file defining short annealing at a fixed volume
|
||||
variable p equal 1. # equilibrium pressure
|
||||
variable equi equal 30000 # equilibration steps
|
||||
|
||||
# PBC (set them before the creation of the box).
|
||||
boundary p p p
|
||||
neighbor 3 bin
|
||||
}
|
||||
|
||||
# Run an NVT simulation.
|
||||
write_once("In Run"){
|
||||
# Set the output.
|
||||
thermo 1000
|
||||
thermo_style custom step etotal evdwl ecoul elong ebond eangle &
|
||||
@ -314,8 +432,8 @@ The resulting master LT file defining short annealing at a fixed volume
|
||||
write_data \$\{run\}.min
|
||||
|
||||
# Set the constrains.
|
||||
group watergroup type @atom:76 @atom:77
|
||||
fix 0 watergroup shake 0.0001 10 0 b @bond:042_043 a @angle:043_042_043
|
||||
group watergroup type @atom:9991 @atom:9990
|
||||
fix 0 watergroup shake 0.0001 10 0 b @bond:spcO_spcH a @angle:spcH_spcO_spcH
|
||||
|
||||
# Short annealing.
|
||||
timestep \$\{ts\}
|
||||
@ -327,7 +445,7 @@ The resulting master LT file defining short annealing at a fixed volume
|
||||
|
||||
|
||||
In this example, the water model is SPC and it is defined in the
|
||||
``oplsaa.lt`` file with atom types ``@atom:76`` and ``@atom:77``. For
|
||||
``oplsaa2024.lt`` file with atom types ``@atom:9991`` and ``@atom:9990``. For
|
||||
water we also use the ``group`` and ``fix shake`` commands with
|
||||
Moltemplate ``@``-type variables, to ensure consistency with the
|
||||
numerical values assigned during compilation. To identify the bond and
|
||||
@ -336,19 +454,20 @@ are:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
replace{ @atom:76 @atom:76_b042_a042_d042_i042 }
|
||||
replace{ @atom:77 @atom:77_b043_a043_d043_i043 }
|
||||
replace{ @atom:9991 @atom:9991_bspcO_aspcO_dspcO_ispcO }
|
||||
replace{ @atom:9990 @atom:9990_bspcH_aspcH_dspcH_ispcH }
|
||||
|
||||
From which we can identify the following "Data Bonds By Type":
|
||||
``@bond:042_043 @atom:*_b042*_a*_d*_i* @atom:*_b043*_a*_d*_i*`` and
|
||||
"Data Angles By Type": ``@angle:043_042_043 @atom:*_b*_a043*_d*_i*
|
||||
@atom:*_b*_a042*_d*_i* @atom:*_b*_a043*_d*_i*``
|
||||
``@bond:spcO_spcH @atom:*_bspcO*_a*_d*_i* @atom:*_bspcH*_a*_d*_i*``
|
||||
and "Data Angles By Type":
|
||||
``@angle:spcH_spcO_spcH @atom:*_b*_aspcH*_d*_i* @atom:*_b*_aspcO*_d*_i* @atom:*_b*_aspcH*_d*_i*``
|
||||
|
||||
Compile the master file with:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
moltemplate.sh -overlay-all -pdb model.pdb sample01.lt
|
||||
moltemplate.sh -pdb model.pdb sample01.lt
|
||||
cleanup_moltemplate.sh
|
||||
|
||||
And execute the simulation with the following:
|
||||
|
||||
@ -363,8 +482,13 @@ And execute the simulation with the following:
|
||||
Sample visualized with Ovito loading the trajectory into the DATA
|
||||
file written after minimization.
|
||||
|
||||
|
||||
------------
|
||||
|
||||
.. _OPLSAA96:
|
||||
.. _oplsaa2024:
|
||||
|
||||
**(OPLS-AA)** Jorgensen, Maxwell, Tirado-Rives, J Am Chem Soc, 118(45), 11225-11236 (1996).
|
||||
**(OPLS-AA)** Jorgensen, W.L., Ghahremanpour, M.M., Saar, A., Tirado-Rives, J., J. Phys. Chem. B, 128(1), 250-262 (2024).
|
||||
|
||||
.. _Moltemplate1:
|
||||
|
||||
**(Moltemplate)** Jewett et al., J. Mol. Biol., 433(11), 166841 (2021)
|
||||
|
||||
@ -62,17 +62,17 @@ with :ref:`PNG, JPEG and FFMPEG output support <graphics>` enabled.
|
||||
|
||||
cd $LAMMPS_DIR/src
|
||||
|
||||
# add packages if necessary
|
||||
# add LAMMPS packages if necessary
|
||||
make yes-MOLECULE
|
||||
make yes-PYTHON
|
||||
|
||||
# compile shared library using Makefile
|
||||
make mpi mode=shlib LMP_INC="-DLAMMPS_PNG -DLAMMPS_JPEG -DLAMMPS_FFMPEG" JPG_LIB="-lpng -ljpeg"
|
||||
|
||||
Step 2: Installing the LAMMPS Python package
|
||||
""""""""""""""""""""""""""""""""""""""""""""
|
||||
Step 2: Installing the LAMMPS Python module
|
||||
"""""""""""""""""""""""""""""""""""""""""""
|
||||
|
||||
Next install the LAMMPS Python package into your current Python installation with:
|
||||
Next install the LAMMPS Python module into your current Python installation with:
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
@ -89,6 +89,29 @@ privileges) or into your personal Python module folder.
|
||||
Recompiling the shared library requires re-installing the Python
|
||||
package.
|
||||
|
||||
.. _externally_managed:
|
||||
|
||||
.. admonition:: Handling an "externally-managed-environment" Error
|
||||
:class: Hint
|
||||
|
||||
Some Python installations made through Linux distributions
|
||||
(e.g. Ubuntu 24.04LTS or later) will prevent installing the LAMMPS
|
||||
Python module into a system folder or a corresponding folder of the
|
||||
individual user as attempted by ``make install-python`` with an error
|
||||
stating that an *externally managed* python installation must be only
|
||||
managed by the same package package management tool. This is an
|
||||
optional setting, so not all Linux distributions follow it currently
|
||||
(Spring 2025). The reasoning and explanations for this error can be
|
||||
found in the `Python Packaging User Guide
|
||||
<https://packaging.python.org/en/latest/specifications/externally-managed-environments/>`_
|
||||
|
||||
These guidelines suggest to create a virtual environment and install
|
||||
the LAMMPS Python module there (see below). This is generally a good
|
||||
idea and the LAMMPS developers recommend this, too. If, however, you
|
||||
want to proceed and install the LAMMPS Python module regardless, you
|
||||
can install the "wheel" file (see above) manually with the ``pip``
|
||||
command by adding the ``--break-system-packages`` flag.
|
||||
|
||||
Installation inside of a virtual environment
|
||||
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
|
||||
|
||||
|
||||
Binary file not shown.
|
Before Width: | Height: | Size: 40 KiB After Width: | Height: | Size: 94 KiB |
BIN
doc/src/JPG/butane.jpg
Normal file
BIN
doc/src/JPG/butane.jpg
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 22 KiB |
@ -19,9 +19,9 @@ there are now a few requirements for including new changes or extensions.
|
||||
be added.
|
||||
- New features should also be implemented and documented not just
|
||||
for the C interface, but also the Python and Fortran interfaces.
|
||||
- All additions should work and be compatible with ``-DLAMMPS_BIGBIG``,
|
||||
``-DLAMMPS_SMALLBIG``, ``-DLAMMPS_SMALLSMALL`` as well as when
|
||||
compiling with and without MPI support.
|
||||
- All additions should work and be compatible with
|
||||
``-DLAMMPS_BIGBIG``, ``-DLAMMPS_SMALLBIG`` as well as when compiling
|
||||
with and without MPI support.
|
||||
- The ``library.h`` file should be kept compatible to C code at
|
||||
a level similar to C89. Its interfaces may not reference any
|
||||
custom data types (e.g. ``bigint``, ``tagint``, and so on) that
|
||||
|
||||
@ -110,13 +110,16 @@ folder that the dynamic loader searches or inside of the installed
|
||||
|
||||
.. code-block:: bash
|
||||
|
||||
python install.py -p <python package> -l <shared library> -v <version.h file> [-n]
|
||||
python install.py -p <python package> -l <shared library> -v <version.h file> [-n] [-f]
|
||||
|
||||
* The ``-p`` flag points to the ``lammps`` Python package folder to be installed,
|
||||
* the ``-l`` flag points to the LAMMPS shared library file to be installed,
|
||||
* the ``-v`` flag points to the LAMMPS version header file to extract the version date,
|
||||
* and the optional ``-n`` instructs the script to only build a wheel file
|
||||
but not attempt to install it.
|
||||
* the optional ``-n`` instructs the script to only build a wheel file but not attempt
|
||||
to install it,
|
||||
* and the optional ``-f`` argument instructs the script to force installation even if
|
||||
pip would otherwise refuse installation with an
|
||||
:ref:`error about externally managed environments <externally_managed>`.
|
||||
|
||||
.. tab:: Virtual environment
|
||||
|
||||
@ -198,6 +201,10 @@ folder that the dynamic loader searches or inside of the installed
|
||||
|
||||
The ``PYTHONPATH`` needs to point to the parent folder that contains the ``lammps`` package!
|
||||
|
||||
In case you run into an "externally-managed-environment" error when
|
||||
trying to install the LAMMPS Python module, please refer to
|
||||
:ref:`corresponding paragraph <externally_managed>` in the Python HOWTO
|
||||
page to learn about options for handling this error.
|
||||
|
||||
To verify if LAMMPS can be successfully started from Python, start the
|
||||
Python interpreter, load the ``lammps`` Python module and create a
|
||||
|
||||
@ -930,7 +930,7 @@ dependencies and redirects the download to the local cache.
|
||||
|
||||
mkdir build
|
||||
cd build
|
||||
cmake -D LAMMPS_DOWNLOADS_URL=${HTTP_CACHE_URL} -C "${LAMMPS_HTTP_CACHE_CONFIG}" -C ../cmake/presets/most.cmake ../cmake
|
||||
cmake -D LAMMPS_DOWNLOADS_URL=${HTTP_CACHE_URL} -C "${LAMMPS_HTTP_CACHE_CONFIG}" -C ../cmake/presets/most.cmake -D DOWNLOAD_POTENTIALS=off ../cmake
|
||||
make -j 8
|
||||
|
||||
deactivate_caches
|
||||
|
||||
BIN
doc/utils/sphinx-config/_static/up.png
Normal file
BIN
doc/utils/sphinx-config/_static/up.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 203 B |
@ -137,6 +137,7 @@
|
||||
{# the master_doc variable was renamed to root_doc in Sphinx 4 (master_doc still exists in later Sphinx versions) #}
|
||||
{%- set _logo_url = logo_url|default(pathto('_static/' + (logo or ""), 1)) %}
|
||||
{%- set _root_doc = root_doc|default(master_doc) %}
|
||||
<div id="sidebar-top-target"></div>
|
||||
<a href="{{ pathto(_root_doc) }}"{% if not theme_logo_only %} class="icon icon-home"{% endif %}>
|
||||
{% if not theme_logo_only %}{{ project }}{% endif %}
|
||||
{%- if logo or logo_url %}
|
||||
@ -172,6 +173,15 @@
|
||||
</div>
|
||||
{%- endblock %}
|
||||
</div>
|
||||
<!-- <div style="padding: 4px;">
|
||||
<center>
|
||||
<a href="#sidebar-top-target"><img src="_static/up.png" alt="(Up)"/> Go to top</a>
|
||||
</center>
|
||||
</div>
|
||||
-->
|
||||
<div style="position: fixed; bottom: 0px; width: 300px; height: 64px; padding: 4px; background-color: #272525; text-align: center">
|
||||
<a href="#sidebar-top-target" class="fa fa-caret-up" style="color: white"> Go to top</a>
|
||||
</div>
|
||||
</nav>
|
||||
|
||||
<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
|
||||
|
||||
@ -856,6 +856,7 @@ DNi
|
||||
Dobnikar
|
||||
Dobson
|
||||
docenv
|
||||
docstrings
|
||||
Dodds
|
||||
dodgerblue
|
||||
dof
|
||||
@ -1336,6 +1337,7 @@ Gflop
|
||||
gfortran
|
||||
ghostneigh
|
||||
ghostwhite
|
||||
Ghahremanpour
|
||||
Giacomo
|
||||
GiB
|
||||
gif
|
||||
@ -3262,6 +3264,7 @@ resquared
|
||||
REsquared
|
||||
restartfile
|
||||
restartinfo
|
||||
reStructuredText
|
||||
Restrepo
|
||||
rethrowing
|
||||
Revenga
|
||||
|
||||
@ -24,7 +24,7 @@
|
||||
* Follow the behavior of regular LAMMPS compilation and assume
|
||||
* -DLAMMPS_SMALLBIG when no define is set.
|
||||
*/
|
||||
#if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG) && !defined(LAMMPS_SMALLSMALL)
|
||||
#if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG)
|
||||
#define LAMMPS_SMALLBIG
|
||||
#endif
|
||||
|
||||
@ -100,8 +100,6 @@ extern "C" {
|
||||
|
||||
#if defined(LAMMPS_BIGBIG)
|
||||
typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **);
|
||||
#elif defined(LAMMPS_SMALLSMALL)
|
||||
typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **);
|
||||
#else
|
||||
typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **);
|
||||
#endif
|
||||
|
||||
@ -15,12 +15,12 @@ Masses
|
||||
|
||||
PairIJ Coeffs # dpd/coul/slater/long
|
||||
|
||||
1 1 78 4.5 yes 1
|
||||
1 2 78 4.5 yes 1
|
||||
1 3 78 4.5 yes 1
|
||||
2 2 78 4.5 no 1
|
||||
2 3 78 4.5 no 1
|
||||
3 3 78 4.5 no 1
|
||||
1 1 78 4.5 no 1
|
||||
1 2 78 4.5 no 1
|
||||
1 3 78 4.5 no 1
|
||||
2 2 78 4.5 yes 1
|
||||
2 3 78 4.5 yes 1
|
||||
3 3 78 4.5 yes 1
|
||||
|
||||
Atoms # full
|
||||
|
||||
|
||||
@ -10,49 +10,47 @@ variable cut_coul equal 2.0
|
||||
# Initialize LAMMPS run for 3-d periodic
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
units lj
|
||||
boundary p p p # periodic at all axes
|
||||
atom_style full
|
||||
dimension 3
|
||||
units lj
|
||||
boundary p p p # periodic at all axes
|
||||
atom_style full
|
||||
dimension 3
|
||||
|
||||
bond_style none
|
||||
angle_style none
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
bond_style none
|
||||
angle_style none
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
newton on
|
||||
comm_modify vel yes # store info of ghost atoms btw processors
|
||||
newton on
|
||||
comm_modify vel yes # store info of ghost atoms btw processors
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Box creation and configuration
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
# Define pair style and coefficients
|
||||
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
|
||||
read_data data.dpd_coul_slater_long
|
||||
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
|
||||
# Enable long range electrostatics solver
|
||||
kspace_style pppm 1e-04
|
||||
kspace_style pppm 1e-04
|
||||
|
||||
read_data data.dpd_coul_slater_long
|
||||
|
||||
# Construct neighbors every steps
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Run the simulation
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
|
||||
thermo_modify norm no
|
||||
thermo 100
|
||||
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
|
||||
thermo_modify norm no
|
||||
thermo 100
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
fix 1 all nve
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
|
||||
unfix 1
|
||||
run 1000
|
||||
|
||||
|
||||
@ -1,147 +0,0 @@
|
||||
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-262-g0aff26705c-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# DPD Ionic Fluid
|
||||
|
||||
variable T equal 1.0
|
||||
variable cut_DPD equal 1.0
|
||||
variable seed equal 165412
|
||||
variable lambda equal 0.25
|
||||
variable cut_coul equal 2.0
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Initialize LAMMPS run for 3-d periodic
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
units lj
|
||||
boundary p p p # periodic at all axes
|
||||
atom_style full
|
||||
dimension 3
|
||||
|
||||
bond_style none
|
||||
angle_style none
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
newton on
|
||||
comm_modify vel yes # store info of ghost atoms btw processors
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Box creation and configuration
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
# Define pair style and coefficients
|
||||
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 0.25 2
|
||||
|
||||
read_data data.dpd_coul_slater_long
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (5 5 5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
375 atoms
|
||||
reading velocities ...
|
||||
375 velocities
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
# Enable long range electrostatics solver
|
||||
kspace_style pppm 1e-04
|
||||
|
||||
# Construct neighbors every steps
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Run the simulation
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
|
||||
thermo_modify norm no
|
||||
thermo 100
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 1.4828454
|
||||
grid = 20 20 20
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 7.7240141e-05
|
||||
estimated relative force accuracy = 7.7240141e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 24389 8000
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3
|
||||
ghost atom cutoff = 3
|
||||
binsize = 1.5, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair dpd/coul/slater/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.359 | 8.359 | 8.359 Mbytes
|
||||
Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
|
||||
0 0.9849949 69.271905 125 4673.0443 0 -30.365103 4642.6792 552.58214 646.76798 65.851035
|
||||
100 1.0614027 69.794624 125 4659.0139 0 -31.906319 4627.1075 595.44692 612.94396 60.338653
|
||||
200 0.9422517 68.721098 125 4687.8862 0 -33.81531 4654.0709 528.6032 620.25627 62.726994
|
||||
300 0.8956649 69.323482 125 4721.0824 0 -33.854275 4687.2281 502.46801 670.22699 73.087908
|
||||
400 0.99584547 69.670416 125 4713.9086 0 -30.783633 4683.125 558.66931 607.65881 59.224652
|
||||
500 1.0565931 69.497816 125 4701.2584 0 -26.80545 4674.4529 592.74873 646.18907 71.398122
|
||||
600 1.0071523 70.26222 125 4659.2061 0 -29.98909 4629.217 565.01243 630.00244 58.264115
|
||||
700 1.0507355 67.920078 125 4695.255 0 -32.649209 4662.6058 589.46259 651.80459 70.573524
|
||||
800 0.98561942 68.279591 125 4745.7603 0 -28.98491 4716.7754 552.9325 627.14371 67.196483
|
||||
900 0.96470105 70.742864 125 4706.3605 0 -30.271633 4676.0889 541.19729 644.43036 79.474998
|
||||
1000 1.0204819 70.164419 125 4654.6077 0 -27.797433 4626.8103 572.49035 624.19728 71.825307
|
||||
Loop time of 2.10153 on 1 procs for 1000 steps with 375 atoms
|
||||
|
||||
Performance: 411128.483 tau/day, 475.843 timesteps/s, 178.441 katom-step/s
|
||||
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.1779 | 1.1779 | 1.1779 | 0.0 | 56.05
|
||||
Bond | 6.507e-05 | 6.507e-05 | 6.507e-05 | 0.0 | 0.00
|
||||
Kspace | 0.74636 | 0.74636 | 0.74636 | 0.0 | 35.51
|
||||
Neigh | 0.12903 | 0.12903 | 0.12903 | 0.0 | 6.14
|
||||
Comm | 0.039726 | 0.039726 | 0.039726 | 0.0 | 1.89
|
||||
Output | 0.00027587 | 0.00027587 | 0.00027587 | 0.0 | 0.01
|
||||
Modify | 0.0037596 | 0.0037596 | 0.0037596 | 0.0 | 0.18
|
||||
Other | | 0.004451 | | | 0.21
|
||||
|
||||
Nlocal: 375 ave 375 max 375 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3613 ave 3613 max 3613 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 62354 ave 62354 max 62354 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 62354
|
||||
Ave neighs/atom = 166.27733
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 65
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
|
||||
Total wall time: 0:00:02
|
||||
@ -1,147 +0,0 @@
|
||||
LAMMPS (17 Apr 2024 - Development - patch_17Apr2024-262-g0aff26705c-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# DPD Ionic Fluid
|
||||
|
||||
variable T equal 1.0
|
||||
variable cut_DPD equal 1.0
|
||||
variable seed equal 165412
|
||||
variable lambda equal 0.25
|
||||
variable cut_coul equal 2.0
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Initialize LAMMPS run for 3-d periodic
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
units lj
|
||||
boundary p p p # periodic at all axes
|
||||
atom_style full
|
||||
dimension 3
|
||||
|
||||
bond_style none
|
||||
angle_style none
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
newton on
|
||||
comm_modify vel yes # store info of ghost atoms btw processors
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Box creation and configuration
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
# Define pair style and coefficients
|
||||
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 0.25 2
|
||||
|
||||
read_data data.dpd_coul_slater_long
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (5 5 5)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
375 atoms
|
||||
reading velocities ...
|
||||
375 velocities
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.003 seconds
|
||||
|
||||
# Enable long range electrostatics solver
|
||||
kspace_style pppm 1e-04
|
||||
|
||||
# Construct neighbors every steps
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Run the simulation
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
|
||||
thermo_modify norm no
|
||||
thermo 100
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 1.4828454
|
||||
grid = 20 20 20
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 7.7240141e-05
|
||||
estimated relative force accuracy = 7.7240141e-05
|
||||
using double precision FFTW3
|
||||
3d grid and FFT values/proc = 10469 2000
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3
|
||||
ghost atom cutoff = 3
|
||||
binsize = 1.5, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair dpd/coul/slater/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.208 | 7.208 | 7.209 Mbytes
|
||||
Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
|
||||
0 0.9849949 69.076433 125 4673.0443 0 -30.365103 4642.6792 552.58214 613.18374 70.700582
|
||||
100 0.95374867 69.110009 125 4681.1097 0 -31.260804 4649.8489 535.053 629.95109 62.05418
|
||||
200 1.0076152 69.824904 125 4670.7458 0 -28.382203 4642.3636 565.27213 656.8501 72.049813
|
||||
300 1.0014752 69.666331 125 4696.454 0 -26.943577 4669.5105 561.8276 631.49861 74.737274
|
||||
400 0.98863876 69.731774 125 4700.7552 0 -23.816077 4676.9391 554.62634 637.74742 68.928573
|
||||
500 0.95782852 68.588075 125 4698.588 0 -29.249543 4669.3385 537.3418 646.31897 68.800569
|
||||
600 0.97443232 70.864079 125 4674.8821 0 -26.415644 4648.4664 546.65653 606.50755 78.664429
|
||||
700 0.98783988 68.908299 125 4692.5536 0 -28.092022 4664.4616 554.17817 638.98401 69.691814
|
||||
800 0.98000145 69.83977 125 4706.6365 0 -29.648365 4676.9881 549.78082 626.84362 73.133934
|
||||
900 1.0526251 69.466078 125 4671.9648 0 -30.941117 4641.0237 590.52269 618.1049 62.333546
|
||||
1000 0.98340746 69.527121 125 4728.2894 0 -31.869907 4696.4195 551.69159 630.14208 61.392611
|
||||
Loop time of 0.928543 on 4 procs for 1000 steps with 375 atoms
|
||||
|
||||
Performance: 930490.137 tau/day, 1076.956 timesteps/s, 403.859 katom-step/s
|
||||
98.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.30761 | 0.34974 | 0.38864 | 4.9 | 37.67
|
||||
Bond | 8.4633e-05 | 9.0539e-05 | 9.9184e-05 | 0.0 | 0.01
|
||||
Kspace | 0.39038 | 0.42976 | 0.47215 | 4.4 | 46.28
|
||||
Neigh | 0.033986 | 0.035576 | 0.036791 | 0.5 | 3.83
|
||||
Comm | 0.10247 | 0.10324 | 0.10481 | 0.3 | 11.12
|
||||
Output | 0.00024145 | 0.00027404 | 0.00036867 | 0.0 | 0.03
|
||||
Modify | 0.0022402 | 0.0025068 | 0.0026343 | 0.3 | 0.27
|
||||
Other | | 0.007356 | | | 0.79
|
||||
|
||||
Nlocal: 93.75 ave 96 max 93 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 2289.75 ave 2317 max 2271 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
Neighs: 15590.2 ave 16765 max 14540 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 62361
|
||||
Ave neighs/atom = 166.296
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 64
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1,145 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-468-gd830412228-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# DPD Ionic Fluid
|
||||
|
||||
variable T equal 1.0
|
||||
variable cut_DPD equal 1.0
|
||||
variable seed equal 165412
|
||||
variable lambda equal 0.25
|
||||
variable cut_coul equal 2.0
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Initialize LAMMPS run for 3-d periodic
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
units lj
|
||||
boundary p p p # periodic at all axes
|
||||
atom_style full
|
||||
dimension 3
|
||||
|
||||
bond_style none
|
||||
angle_style none
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
newton on
|
||||
comm_modify vel yes # store info of ghost atoms btw processors
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Box creation and configuration
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
# Define pair style and coefficients
|
||||
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 0.25 2
|
||||
|
||||
# Enable long range electrostatics solver
|
||||
kspace_style pppm 1e-04
|
||||
|
||||
read_data data.dpd_coul_slater_long
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (5 5 5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
375 atoms
|
||||
reading velocities ...
|
||||
375 velocities
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.001 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
# Construct neighbors every steps
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Run the simulation
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
|
||||
thermo_modify norm no
|
||||
thermo 100
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 1.4828454
|
||||
grid = 20 20 20
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 7.7240141e-05
|
||||
estimated relative force accuracy = 7.7240141e-05
|
||||
using double precision KISS FFT
|
||||
3d grid and FFT values/proc = 24389 8000
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3
|
||||
ghost atom cutoff = 3
|
||||
binsize = 1.5, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair dpd/coul/slater/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 8.359 | 8.359 | 8.359 Mbytes
|
||||
Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
|
||||
0 0.9849949 69.242343 125 4673.0443 -3.2653869 -30.365103 4639.4138 552.58214 646.89929 65.851035
|
||||
100 1.023885 69.716134 125 4676.9465 -4.9878506 -34.092864 4637.8658 574.39949 663.35845 94.350026
|
||||
200 1.0286646 69.674249 125 4636.201 -4.6314926 -33.406897 4598.1626 577.08087 614.52805 62.295431
|
||||
300 0.9745797 69.689534 125 4679.9157 -4.3964184 -30.560567 4644.9588 546.73921 603.46282 60.56253
|
||||
400 0.99487931 69.17085 125 4678.0362 -4.9518269 -34.446596 4638.6378 558.12729 656.99738 88.090014
|
||||
500 0.97732377 69.551562 125 4684.3709 -5.0851581 -33.863212 4645.4226 548.27864 647.12533 75.851935
|
||||
600 0.95396337 68.358297 125 4706.824 -4.269168 -33.634096 4668.9207 535.17345 604.31276 63.41042
|
||||
700 0.99397324 68.365109 125 4669.1062 -4.700146 -35.014001 4629.3921 557.61899 633.29262 74.300913
|
||||
800 1.0157864 69.263686 125 4664.1398 -4.0142381 -34.372669 4625.7529 569.85616 595.81462 67.046561
|
||||
900 0.9925779 70.008922 125 4652.3023 -2.7845751 -33.095293 4616.4224 556.8362 620.13154 82.785317
|
||||
1000 0.97336501 68.973657 125 4688.8002 -5.5239266 -36.42345 4646.8529 546.05777 625.66451 64.948859
|
||||
Loop time of 0.755094 on 1 procs for 1000 steps with 375 atoms
|
||||
|
||||
Performance: 1144228.093 tau/day, 1324.338 timesteps/s, 496.627 katom-step/s
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.14421 | 0.14421 | 0.14421 | 0.0 | 19.10
|
||||
Bond | 3.8885e-05 | 3.8885e-05 | 3.8885e-05 | 0.0 | 0.01
|
||||
Kspace | 0.53292 | 0.53292 | 0.53292 | 0.0 | 70.58
|
||||
Neigh | 0.056741 | 0.056741 | 0.056741 | 0.0 | 7.51
|
||||
Comm | 0.017676 | 0.017676 | 0.017676 | 0.0 | 2.34
|
||||
Output | 0.00024925 | 0.00024925 | 0.00024925 | 0.0 | 0.03
|
||||
Modify | 0.0016688 | 0.0016688 | 0.0016688 | 0.0 | 0.22
|
||||
Other | | 0.001588 | | | 0.21
|
||||
|
||||
Nlocal: 375 ave 375 max 375 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3570 ave 3570 max 3570 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19729 ave 19729 max 19729 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 19729
|
||||
Ave neighs/atom = 52.610667
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 66
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -0,0 +1,145 @@
|
||||
LAMMPS (4 Feb 2025 - Development - patch_4Feb2025-468-gd830412228-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:99)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# DPD Ionic Fluid
|
||||
|
||||
variable T equal 1.0
|
||||
variable cut_DPD equal 1.0
|
||||
variable seed equal 165412
|
||||
variable lambda equal 0.25
|
||||
variable cut_coul equal 2.0
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Initialize LAMMPS run for 3-d periodic
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
units lj
|
||||
boundary p p p # periodic at all axes
|
||||
atom_style full
|
||||
dimension 3
|
||||
|
||||
bond_style none
|
||||
angle_style none
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
newton on
|
||||
comm_modify vel yes # store info of ghost atoms btw processors
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Box creation and configuration
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
# Define pair style and coefficients
|
||||
pair_style dpd/coul/slater/long ${T} ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 ${cut_DPD} ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 ${seed} ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 ${lambda} ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 0.25 ${cut_coul}
|
||||
pair_style dpd/coul/slater/long 1 1 165412 0.25 2
|
||||
|
||||
# Enable long range electrostatics solver
|
||||
kspace_style pppm 1e-04
|
||||
|
||||
read_data data.dpd_coul_slater_long
|
||||
Reading data file ...
|
||||
orthogonal box = (0 0 0) to (5 5 5)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
375 atoms
|
||||
reading velocities ...
|
||||
375 velocities
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
0 = max # of 1-2 neighbors
|
||||
0 = max # of 1-3 neighbors
|
||||
0 = max # of 1-4 neighbors
|
||||
1 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
|
||||
# Construct neighbors every steps
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
#-------------------------------------------------------------------------------
|
||||
# Run the simulation
|
||||
#-------------------------------------------------------------------------------
|
||||
|
||||
thermo_style custom step temp press vol evdwl ecoul elong pe ke fnorm fmax
|
||||
thermo_modify norm no
|
||||
thermo 100
|
||||
|
||||
timestep 0.01
|
||||
run_style verlet
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
|
||||
G vector (1/distance) = 1.4828454
|
||||
grid = 20 20 20
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 7.7240141e-05
|
||||
estimated relative force accuracy = 7.7240141e-05
|
||||
using double precision KISS FFT
|
||||
3d grid and FFT values/proc = 10469 2000
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 3
|
||||
ghost atom cutoff = 3
|
||||
binsize = 1.5, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair dpd/coul/slater/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.208 | 7.208 | 7.209 Mbytes
|
||||
Step Temp Press Volume E_vdwl E_coul E_long PotEng KinEng Fnorm Fmax
|
||||
0 0.9849949 69.04687 125 4673.0443 -3.2653869 -30.365103 4639.4138 552.58214 613.14254 70.700582
|
||||
100 1.0206537 69.308834 125 4676.3153 -4.5693306 -33.647673 4638.0983 572.58672 630.70953 76.020236
|
||||
200 0.99990746 68.572978 125 4707.1556 -3.4977853 -33.275671 4670.3821 560.94809 633.00167 77.040049
|
||||
300 0.91055241 69.390592 125 4685.5268 -2.9764038 -29.986737 4652.5637 510.8199 614.61006 62.799933
|
||||
400 1.0080135 69.442971 125 4677.3078 -4.8740989 -32.908722 4639.525 565.49557 649.20121 61.033612
|
||||
500 0.99500653 68.275189 125 4718.6774 -4.2475783 -35.206868 4679.223 558.19867 657.3073 74.738502
|
||||
600 1.052925 70.601712 125 4703.6749 -2.8511316 -34.085418 4666.7383 590.69094 641.70441 59.043346
|
||||
700 0.96467445 69.502018 125 4720.4257 -4.3345734 -34.310005 4681.7811 541.18237 656.24965 72.433637
|
||||
800 1.0657358 70.960958 125 4685.5637 -5.8903418 -35.207202 4644.4661 597.87781 595.54446 61.462159
|
||||
900 1.0273388 68.735518 125 4693.5106 -2.4175829 -28.602387 4662.4906 576.33707 598.80294 71.747886
|
||||
1000 0.9702835 69.885576 125 4701.4385 -3.6513555 -29.487331 4668.2999 544.32904 666.55262 73.231425
|
||||
Loop time of 0.270344 on 4 procs for 1000 steps with 375 atoms
|
||||
|
||||
Performance: 3195929.791 tau/day, 3698.993 timesteps/s, 1.387 Matom-step/s
|
||||
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.031268 | 0.035485 | 0.039491 | 1.6 | 13.13
|
||||
Bond | 3.3378e-05 | 3.4848e-05 | 3.5667e-05 | 0.0 | 0.01
|
||||
Kspace | 0.18632 | 0.19083 | 0.19556 | 0.8 | 70.59
|
||||
Neigh | 0.012413 | 0.012991 | 0.013598 | 0.4 | 4.81
|
||||
Comm | 0.028195 | 0.028407 | 0.028626 | 0.1 | 10.51
|
||||
Output | 0.00013369 | 0.00015738 | 0.00022498 | 0.0 | 0.06
|
||||
Modify | 0.00055373 | 0.00059062 | 0.00068807 | 0.0 | 0.22
|
||||
Other | | 0.001846 | | | 0.68
|
||||
|
||||
Nlocal: 93.75 ave 95 max 92 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Nghost: 2286 ave 2307 max 2269 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
Neighs: 4945 ave 5443 max 4513 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 19780
|
||||
Ave neighs/atom = 52.746667
|
||||
Ave special neighs/atom = 0
|
||||
Neighbor list builds = 66
|
||||
Dangerous builds = 0
|
||||
|
||||
Total wall time: 0:00:00
|
||||
@ -131,8 +131,8 @@ endif()
|
||||
|
||||
################
|
||||
# integer size selection
|
||||
set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallsmall: all 32-bit, smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
|
||||
set(LAMMPS_SIZES_VALUES smallbig bigbig smallsmall)
|
||||
set(LAMMPS_SIZES "smallbig" CACHE STRING "LAMMPS integer sizes (smallbig: 64-bit #atoms #timesteps, bigbig: also 64-bit imageint, 64-bit atom ids)")
|
||||
set(LAMMPS_SIZES_VALUES smallbig bigbig)
|
||||
set_property(CACHE LAMMPS_SIZES PROPERTY STRINGS ${LAMMPS_SIZES_VALUES})
|
||||
validate_option(LAMMPS_SIZES LAMMPS_SIZES_VALUES)
|
||||
string(TOUPPER ${LAMMPS_SIZES} LAMMPS_SIZES)
|
||||
|
||||
@ -334,14 +334,6 @@ MODULE LIBLAMMPS
|
||||
|
||||
! Interface templates for fix external callbacks
|
||||
ABSTRACT INTERFACE
|
||||
SUBROUTINE external_callback_smallsmall(caller, timestep, ids, x, fexternal)
|
||||
IMPORT :: c_int, c_double
|
||||
CLASS(*), INTENT(INOUT) :: caller
|
||||
INTEGER(c_int), INTENT(IN) :: timestep
|
||||
INTEGER(c_int), DIMENSION(:), INTENT(IN) :: ids
|
||||
REAL(c_double), DIMENSION(:,:), INTENT(IN) :: x
|
||||
REAL(c_double), DIMENSION(:,:), INTENT(OUT) :: fexternal
|
||||
END SUBROUTINE external_callback_smallsmall
|
||||
SUBROUTINE external_callback_smallbig(caller, timestep, ids, x, fexternal)
|
||||
IMPORT :: c_int, c_double, c_int64_t
|
||||
CLASS(*), INTENT(INOUT) :: caller
|
||||
@ -363,8 +355,6 @@ MODULE LIBLAMMPS
|
||||
! Derived type for fix external callback data
|
||||
TYPE fix_external_data
|
||||
CHARACTER(LEN=:), ALLOCATABLE :: id
|
||||
PROCEDURE(external_callback_smallsmall), NOPASS, POINTER :: &
|
||||
callback_smallsmall => NULL()
|
||||
PROCEDURE(external_callback_smallbig), NOPASS, POINTER :: &
|
||||
callback_smallbig => NULL()
|
||||
PROCEDURE(external_callback_bigbig), NOPASS, POINTER :: &
|
||||
@ -2262,7 +2252,7 @@ CONTAINS
|
||||
CALL lammps_free(Cname)
|
||||
END SUBROUTINE lmp_scatter_atoms_subset_double
|
||||
|
||||
! equivalent function to lammps_gather_bonds (LAMMPS_SMALLSMALL or SMALLBIG)
|
||||
! equivalent function to lammps_gather_bonds (LAMMPS_SMALLBIG)
|
||||
SUBROUTINE lmp_gather_bonds_small(self, data)
|
||||
CLASS(lammps), INTENT(IN) :: self
|
||||
INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET, INTENT(OUT) :: data
|
||||
@ -2304,7 +2294,7 @@ CONTAINS
|
||||
CALL lammps_gather_bonds(self%handle, Cdata)
|
||||
END SUBROUTINE lmp_gather_bonds_big
|
||||
|
||||
! equivalent function to lammps_gather_angles (LAMMPS_SMALLSMALL or SMALLBIG)
|
||||
! equivalent function to lammps_gather_angles (LAMMPS_SMALLBIG)
|
||||
SUBROUTINE lmp_gather_angles_small(self, data)
|
||||
CLASS(lammps), INTENT(IN) :: self
|
||||
INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET, INTENT(OUT) :: data
|
||||
@ -2346,7 +2336,7 @@ CONTAINS
|
||||
CALL lammps_gather_angles(self%handle, Cdata)
|
||||
END SUBROUTINE lmp_gather_angles_big
|
||||
|
||||
! equivalent function to lammps_gather_dihedrals (LAMMPS_SMALLSMALL or SMALLBIG)
|
||||
! equivalent function to lammps_gather_dihedrals (LAMMPS_SMALLBIG)
|
||||
SUBROUTINE lmp_gather_dihedrals_small(self, data)
|
||||
CLASS(lammps), INTENT(IN) :: self
|
||||
INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET, INTENT(OUT) :: data
|
||||
@ -2388,7 +2378,7 @@ CONTAINS
|
||||
CALL lammps_gather_dihedrals(self%handle, Cdata)
|
||||
END SUBROUTINE lmp_gather_dihedrals_big
|
||||
|
||||
! equivalent function to lammps_gather_impropers (LAMMPS_SMALLSMALL or SMALLBIG)
|
||||
! equivalent function to lammps_gather_impropers (LAMMPS_SMALLBIG)
|
||||
SUBROUTINE lmp_gather_impropers_small(self, data)
|
||||
CLASS(lammps), INTENT(IN) :: self
|
||||
INTEGER(c_int), DIMENSION(:), ALLOCATABLE, TARGET, INTENT(OUT) :: data
|
||||
@ -2763,7 +2753,7 @@ CONTAINS
|
||||
IF (tagint_size /= 4_c_int .AND. (PRESENT(id) .OR. PRESENT(image))) THEN
|
||||
CALL lmp_error(self, LMP_ERROR_ALL + LMP_ERROR_WORLD, &
|
||||
'Unable to create_atoms; your id/image array types are incompatible&
|
||||
& with LAMMPS_SMALLBIG and LAMMPS_SMALLSMALL [Fortran/create_atoms]')
|
||||
& with LAMMPS_SMALLBIG [Fortran/create_atoms]')
|
||||
END IF
|
||||
n = SIZE(type, KIND=c_int)
|
||||
IF (PRESENT(bexpand)) THEN
|
||||
@ -3360,7 +3350,7 @@ CONTAINS
|
||||
construct_fix_external_data%id = ' '
|
||||
END FUNCTION construct_fix_external_data
|
||||
|
||||
! equivalent function to lammps_set_fix_external_callback for -DSMALLSMALL
|
||||
! equivalent function to lammps_set_fix_external_callback
|
||||
! note that "caller" is wrapped into a fix_external_data derived type along
|
||||
! with the fix id and the Fortran calling function.
|
||||
SUBROUTINE lmp_set_fix_external_callback(self, id, callback, caller)
|
||||
@ -3394,11 +3384,7 @@ CONTAINS
|
||||
ext_data(this_fix)%id = id
|
||||
ext_data(this_fix)%lammps_instance => self
|
||||
|
||||
IF (SIZE_TAGINT == 4_c_int .AND. SIZE_BIGINT == 4_c_int) THEN
|
||||
! -DSMALLSMALL
|
||||
c_callback = C_FUNLOC(callback_wrapper_smallsmall)
|
||||
CALL set_fix_external_callback_smallsmall(this_fix, callback)
|
||||
ELSE IF (SIZE_TAGINT == 8_c_int .AND. SIZE_BIGINT == 8_c_int) THEN
|
||||
IF (SIZE_TAGINT == 8_c_int .AND. SIZE_BIGINT == 8_c_int) THEN
|
||||
! -DBIGBIG
|
||||
c_callback = C_FUNLOC(callback_wrapper_bigbig)
|
||||
CALL set_fix_external_callback_bigbig(this_fix, callback)
|
||||
@ -3420,12 +3406,6 @@ CONTAINS
|
||||
END SUBROUTINE lmp_set_fix_external_callback
|
||||
|
||||
! Wrappers to assign callback pointers with explicit interfaces
|
||||
SUBROUTINE set_fix_external_callback_smallsmall(id, callback)
|
||||
INTEGER, INTENT(IN) :: id
|
||||
PROCEDURE(external_callback_smallsmall) :: callback
|
||||
|
||||
ext_data(id)%callback_smallsmall => callback
|
||||
END SUBROUTINE set_fix_external_callback_smallsmall
|
||||
|
||||
SUBROUTINE set_fix_external_callback_smallbig(id, callback)
|
||||
INTEGER, INTENT(IN) :: id
|
||||
@ -3450,9 +3430,7 @@ CONTAINS
|
||||
DO i = 1, SIZE(ext_data) - 1
|
||||
c_id = f2c_string(ext_data(i)%id)
|
||||
c_caller = C_LOC(ext_data(i))
|
||||
IF (SIZE_TAGINT == 4_c_int .AND. SIZE_BIGINT == 4_c_int) THEN
|
||||
c_callback = C_FUNLOC(callback_wrapper_smallsmall)
|
||||
ELSE IF (SIZE_TAGINT == 8_c_int .AND. SIZE_BIGINT == 8_c_int) THEN
|
||||
IF (SIZE_TAGINT == 8_c_int .AND. SIZE_BIGINT == 8_c_int) THEN
|
||||
c_callback = C_FUNLOC(callback_wrapper_bigbig)
|
||||
ELSE
|
||||
c_callback = C_FUNLOC(callback_wrapper_smallbig)
|
||||
@ -3464,34 +3442,6 @@ CONTAINS
|
||||
END SUBROUTINE rebind_external_callback_data
|
||||
|
||||
! companions to lmp_set_fix_external_callback to change interface
|
||||
SUBROUTINE callback_wrapper_smallsmall(caller, timestep, nlocal, ids, x, &
|
||||
fexternal) BIND(C)
|
||||
TYPE(c_ptr), INTENT(IN), VALUE :: caller
|
||||
INTEGER(c_int), INTENT(IN), VALUE :: timestep
|
||||
INTEGER(c_int), INTENT(IN), VALUE :: nlocal
|
||||
TYPE(c_ptr), INTENT(IN), VALUE :: ids, x, fexternal
|
||||
TYPE(c_ptr), DIMENSION(:), POINTER :: x0, f0
|
||||
INTEGER(c_int), DIMENSION(:), POINTER :: f_ids => NULL()
|
||||
REAL(c_double), DIMENSION(:,:), POINTER :: f_x => NULL(), &
|
||||
f_fexternal => NULL()
|
||||
TYPE(fix_external_data), POINTER :: f_caller => NULL()
|
||||
|
||||
CALL C_F_POINTER(ids, f_ids, [nlocal])
|
||||
CALL C_F_POINTER(x, x0, [nlocal])
|
||||
CALL C_F_POINTER(x0(1), f_x, [3, nlocal])
|
||||
CALL C_F_POINTER(fexternal, f0, [nlocal])
|
||||
CALL C_F_POINTER(f0(1), f_fexternal, [3, nlocal])
|
||||
IF (C_ASSOCIATED(caller)) THEN
|
||||
CALL C_F_POINTER(caller, f_caller)
|
||||
CALL f_caller%callback_smallsmall(f_caller%caller, timestep, f_ids, &
|
||||
f_x, f_fexternal)
|
||||
ELSE
|
||||
CALL lmp_error(f_caller%lammps_instance, &
|
||||
LMP_ERROR_ALL + LMP_ERROR_WORLD, &
|
||||
'Got null pointer from "caller"; this should never happen;&
|
||||
& please report a bug')
|
||||
END IF
|
||||
END SUBROUTINE callback_wrapper_smallsmall
|
||||
|
||||
SUBROUTINE callback_wrapper_smallbig(caller, timestep, nlocal, ids, x, &
|
||||
fexternal) BIND(C)
|
||||
|
||||
@ -11,8 +11,8 @@ EXTRAMAKE = Makefile.lammps.opencl
|
||||
# OCL_TUNE = -DCYPRESS_OCL # -- Uncomment for AMD Cypress
|
||||
OCL_TUNE = -DGENERIC_OCL # -- Uncomment for generic device
|
||||
|
||||
# this setting should match LAMMPS Makefile
|
||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||
# this setting should match the LAMMPS Makefile
|
||||
# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG
|
||||
|
||||
LMP_INC = -DLAMMPS_SMALLBIG
|
||||
|
||||
|
||||
@ -11,8 +11,8 @@ ifeq ($(CUDA_HOME),)
|
||||
CUDA_HOME = /usr/local/cuda
|
||||
endif
|
||||
|
||||
# this setting should match LAMMPS Makefile
|
||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||
# this setting should match the LAMMPS Makefile
|
||||
# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG
|
||||
|
||||
LMP_INC = -DLAMMPS_SMALLBIG
|
||||
|
||||
|
||||
@ -11,8 +11,8 @@ ifeq ($(CUDA_HOME),)
|
||||
CUDA_HOME = /usr/local/cuda
|
||||
endif
|
||||
|
||||
# this setting should match LAMMPS Makefile
|
||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||
# this setting should match the LAMMPS Makefile
|
||||
# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG
|
||||
|
||||
LMP_INC = -DLAMMPS_SMALLBIG
|
||||
|
||||
|
||||
@ -7,8 +7,8 @@
|
||||
# - change HIP_ARCH for your GPU
|
||||
# ------------------------------------------------------------------------- */
|
||||
|
||||
# this setting should match LAMMPS Makefile
|
||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||
# this setting should match the LAMMPS Makefile
|
||||
# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG
|
||||
|
||||
LMP_INC = -DLAMMPS_SMALLBIG
|
||||
|
||||
|
||||
@ -51,8 +51,8 @@ CUDA_ARCH = -arch=sm_60
|
||||
# Hopper hardware
|
||||
#CUDA_ARCH = -arch=sm_90
|
||||
|
||||
# this setting should match LAMMPS Makefile
|
||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||
# this setting should match the LAMMPS Makefile
|
||||
# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG
|
||||
|
||||
LMP_INC = -DLAMMPS_SMALLBIG
|
||||
|
||||
|
||||
@ -51,8 +51,8 @@ CUDA_CODE = -gencode arch=compute_50,code=[sm_50,compute_50] -gencode arch=compu
|
||||
|
||||
CUDA_ARCH += $(CUDA_CODE)
|
||||
|
||||
# this setting should match LAMMPS Makefile
|
||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||
# this setting should match the LAMMPS Makefile
|
||||
# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG
|
||||
|
||||
LMP_INC = -DLAMMPS_SMALLBIG
|
||||
|
||||
|
||||
@ -6,8 +6,8 @@
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.opencl
|
||||
|
||||
# this setting should match LAMMPS Makefile
|
||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||
# this setting should match the LAMMPS Makefile
|
||||
# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG
|
||||
|
||||
LMP_INC = -DLAMMPS_SMALLBIG
|
||||
|
||||
|
||||
@ -6,8 +6,8 @@
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.opencl
|
||||
|
||||
# this setting should match LAMMPS Makefile
|
||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||
# this setting should match the LAMMPS Makefile
|
||||
# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG
|
||||
|
||||
LMP_INC = -DLAMMPS_SMALLBIG
|
||||
|
||||
|
||||
@ -6,8 +6,8 @@
|
||||
|
||||
EXTRAMAKE = Makefile.lammps.opencl
|
||||
|
||||
# this setting should match LAMMPS Makefile
|
||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||
# this setting should match the LAMMPS Makefile
|
||||
# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG
|
||||
|
||||
LMP_INC = -DLAMMPS_SMALLBIG
|
||||
|
||||
|
||||
@ -45,8 +45,8 @@ CUDA_ARCH = -arch=sm_60
|
||||
#CUDA_ARCH = -arch=sm_80
|
||||
#CUDA_ARCH = -arch=sm_86
|
||||
|
||||
# this setting should match LAMMPS Makefile
|
||||
# one of LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG and LAMMPS_SMALLSMALL
|
||||
# this setting should match the LAMMPS Makefile
|
||||
# either LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG
|
||||
|
||||
LMP_INC = -DLAMMPS_SMALLBIG
|
||||
|
||||
|
||||
@ -136,10 +136,10 @@ IMPORTANT: If you re-build the library, e.g. for a different precision
|
||||
Makefile.linux clean, to ensure all previous derived files are removed
|
||||
before the new build is done.
|
||||
|
||||
NOTE: The system-specific setting LAMMPS_SMALLBIG (default), LAMMPS_BIGBIG,
|
||||
or LAMMPS_SMALLSMALL if specified when building LAMMPS (i.e. in
|
||||
src/MAKE/Makefile.foo) should be consistent with that specified
|
||||
when building libgpu.a (i.e. by LMP_INC in the lib/gpu/Makefile.bar).
|
||||
NOTE: The system-specific setting LAMMPS_SMALLBIG (default) or LAMMPS_BIGBIG
|
||||
- if specified when building LAMMPS (i.e. in src/MAKE/Makefile.foo) -
|
||||
should be consistent with that specified when building libgpu.a (i.e.
|
||||
by LMP_INC in the lib/gpu/Makefile.bar).
|
||||
|
||||
|
||||
------------------------------------------------------------------------------
|
||||
|
||||
@ -23,9 +23,6 @@
|
||||
#include "inttypes.h"
|
||||
#define tagint int64_t
|
||||
#endif
|
||||
#ifdef LAMMPS_SMALLSMALL
|
||||
#define tagint int
|
||||
#endif
|
||||
#ifndef _DOUBLE_DOUBLE
|
||||
_texture( pos_tex,float4);
|
||||
_texture( q_tex,float);
|
||||
@ -43,9 +40,6 @@ _texture( q_tex,int2);
|
||||
#ifdef LAMMPS_BIGBIG
|
||||
#define tagint long
|
||||
#endif
|
||||
#ifdef LAMMPS_SMALLSMALL
|
||||
#define tagint int
|
||||
#endif
|
||||
|
||||
#endif // defined(NV_KERNEL) || defined(USE_HIP)
|
||||
|
||||
|
||||
@ -287,16 +287,16 @@ __kernel void k_dpd_coul_slater_long(const __global numtyp4 *restrict x_,
|
||||
|
||||
// apply Slater electrostatic force if distance below Slater cutoff
|
||||
// and the two species have a slater coeff
|
||||
// cutsq[mtype].z -> Coulombic squared cutoff
|
||||
if ( cutsq[mtype].z != 0.0 && rsq < cutsq[mtype].z){
|
||||
// cutsq[mtype].z -> Slater cutoff
|
||||
// extra[j].x -> q[j] ; particle j charge
|
||||
if ( rsq < cutsq[mtype].z ){
|
||||
numtyp r2inv=ucl_recip(rsq);
|
||||
numtyp _erfc;
|
||||
numtyp grij = g_ewald * r;
|
||||
numtyp expm2 = ucl_exp(-grij*grij);
|
||||
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
|
||||
_erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
||||
numtyp prefactor = extra[j].x;
|
||||
prefactor *= qqrd2e * cutsq[mtype].z * qtmp/r;
|
||||
numtyp prefactor = qqrd2e * extra[j].x * 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)));
|
||||
@ -306,9 +306,9 @@ __kernel void k_dpd_coul_slater_long(const __global numtyp4 *restrict x_,
|
||||
|
||||
if (EVFLAG && eflag) {
|
||||
numtyp e_slater = ((numtyp)1.0 + rlamdainv)*exprlmdainv;
|
||||
numtyp e = prefactor*(_erfc-e_slater);
|
||||
if (factor_coul > (numtyp)0) e -= factor_coul*prefactor*((numtyp)1.0 - e_slater);
|
||||
e_coul += e;
|
||||
numtyp e_sf = prefactor*(_erfc-e_slater);
|
||||
if (factor_coul > (numtyp)0) e_sf -= factor_coul*prefactor*((numtyp)1.0 - e_slater);
|
||||
e_coul += e_sf;
|
||||
}
|
||||
} // if cut_coulsq
|
||||
|
||||
@ -471,16 +471,16 @@ __kernel void k_dpd_coul_slater_long_fast(const __global numtyp4 *restrict x_,
|
||||
|
||||
// apply Slater electrostatic force if distance below Slater cutoff
|
||||
// and the two species have a slater coeff
|
||||
// cutsq[mtype].z -> Coulombic squared cutoff
|
||||
if ( cutsq[mtype].z != 0.0 && rsq < cutsq[mtype].z){
|
||||
// cutsq[mtype].z -> Slater cutoff
|
||||
// extra[j].x -> q[j] ; particle j charge
|
||||
if ( rsq < cutsq[mtype].z ){
|
||||
numtyp r2inv=ucl_recip(rsq);
|
||||
numtyp _erfc;
|
||||
numtyp grij = g_ewald * r;
|
||||
numtyp expm2 = ucl_exp(-grij*grij);
|
||||
numtyp t = ucl_recip((numtyp)1.0 + EWALD_P*grij);
|
||||
_erfc = t * (A1+t*(A2+t*(A3+t*(A4+t*A5)))) * expm2;
|
||||
numtyp prefactor = extra[j].x;
|
||||
prefactor *= qqrd2e * cutsq[mtype].z * qtmp/r;
|
||||
numtyp prefactor = qqrd2e * extra[j].x * 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)));
|
||||
|
||||
@ -65,7 +65,7 @@ class DPDCoulSlaterLong : public BaseDPD<numtyp, acctyp> {
|
||||
/// coeff.x = a0, coeff.y = gamma, coeff.z = sigma, coeff.w = cut_dpd
|
||||
UCL_D_Vec<numtyp4> coeff;
|
||||
|
||||
/// cutsq.x = cutsq, cutsq.y = cut_dpdsq, cutsq.w = cut_slatersq
|
||||
/// cutsq.x = cutsq, cutsq.y = cut_dpdsq, cutsq.z = cut_slatersq
|
||||
UCL_D_Vec<numtyp4> cutsq;
|
||||
|
||||
/// Special LJ values
|
||||
|
||||
@ -23,9 +23,6 @@
|
||||
#include "inttypes.h"
|
||||
#define tagint int64_t
|
||||
#endif
|
||||
#ifdef LAMMPS_SMALLSMALL
|
||||
#define tagint int
|
||||
#endif
|
||||
#ifndef _DOUBLE_DOUBLE
|
||||
_texture( pos_tex,float4);
|
||||
_texture( q_tex,float);
|
||||
@ -43,9 +40,6 @@ _texture( q_tex,int2);
|
||||
#ifdef LAMMPS_BIGBIG
|
||||
#define tagint long
|
||||
#endif
|
||||
#ifdef LAMMPS_SMALLSMALL
|
||||
#define tagint int
|
||||
#endif
|
||||
|
||||
#endif // defined(NV_KERNEL) || defined(USE_HIP)
|
||||
|
||||
|
||||
@ -27,9 +27,6 @@
|
||||
#define tagint int64_t
|
||||
#endif
|
||||
#endif
|
||||
#ifdef LAMMPS_SMALLSMALL
|
||||
#define tagint int
|
||||
#endif
|
||||
#ifndef _DOUBLE_DOUBLE
|
||||
_texture( pos_tex,float4);
|
||||
_texture( q_tex,float);
|
||||
@ -50,9 +47,6 @@ _texture( q_tex,int2);
|
||||
#define tagint int64_t
|
||||
#endif
|
||||
#endif
|
||||
#ifdef LAMMPS_SMALLSMALL
|
||||
#define tagint int
|
||||
#endif
|
||||
#define pos_tex x_
|
||||
#define q_tex q_
|
||||
#endif
|
||||
|
||||
@ -28,9 +28,6 @@
|
||||
#define tagint int64_t
|
||||
#endif
|
||||
#endif
|
||||
#ifdef LAMMPS_SMALLSMALL
|
||||
#define tagint int
|
||||
#endif
|
||||
#ifndef _DOUBLE_DOUBLE
|
||||
_texture( pos_tex,float4);
|
||||
#else
|
||||
@ -140,9 +137,6 @@ __kernel void kernel_calc_cell_counts(const unsigned *restrict cell_id,
|
||||
#ifdef LAMMPS_BIGBIG
|
||||
#define tagint long
|
||||
#endif
|
||||
#ifdef LAMMPS_SMALLSMALL
|
||||
#define tagint int
|
||||
#endif
|
||||
#endif
|
||||
|
||||
__kernel void transpose(__global tagint *restrict out,
|
||||
|
||||
@ -150,8 +150,7 @@ enum{SPHERE_SPHERE,SPHERE_ELLIPSE,ELLIPSE_SPHERE,ELLIPSE_ELLIPSE};
|
||||
|
||||
// default to 32-bit smallint and other ints, 64-bit bigint:
|
||||
// same as defined in src/lmptype.h
|
||||
#if !defined(LAMMPS_SMALLSMALL) && !defined(LAMMPS_BIGBIG) && \
|
||||
!defined(LAMMPS_SMALLBIG)
|
||||
#if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG)
|
||||
#define LAMMPS_SMALLBIG
|
||||
#endif
|
||||
|
||||
@ -164,9 +163,5 @@ typedef int tagint;
|
||||
typedef int64_t tagint;
|
||||
#define OCL_INT_TYPE "-DLAMMPS_BIGBIG"
|
||||
#endif
|
||||
#ifdef LAMMPS_SMALLSMALL
|
||||
typedef int tagint;
|
||||
#define OCL_INT_TYPE "-DLAMMPS_SMALLSMALL"
|
||||
#endif
|
||||
|
||||
#endif // LAL_PRECISION_H
|
||||
|
||||
@ -406,7 +406,6 @@ ucl_inline int sbmask15(int j) { return j >> SBBITS15 & 7; };
|
||||
|
||||
// default to 32-bit smallint and other ints, 64-bit bigint:
|
||||
// same as defined in src/lmptype.h
|
||||
#if !defined(LAMMPS_SMALLSMALL) && !defined(LAMMPS_BIGBIG) && \
|
||||
!defined(LAMMPS_SMALLBIG)
|
||||
#if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG)
|
||||
#define LAMMPS_SMALLBIG
|
||||
#endif
|
||||
|
||||
@ -27,6 +27,8 @@ parser.add_argument("-w", "--wheeldir", required=False,
|
||||
help="path to a directory where the created wheel will be stored")
|
||||
parser.add_argument("-v", "--versionfile", required=True,
|
||||
help="path to the LAMMPS version.h source file")
|
||||
parser.add_argument("-f", "--force", action="store_true", required=False, default=False,
|
||||
help="force installation of LAMMPS Python package")
|
||||
|
||||
args = parser.parse_args()
|
||||
|
||||
@ -145,7 +147,10 @@ else:
|
||||
py_exe = sys.executable
|
||||
|
||||
try:
|
||||
txt = subprocess.check_output([py_exe, '-m', 'pip', 'install', '--force-reinstall', wheel], stderr=subprocess.STDOUT, shell=False)
|
||||
if args.force:
|
||||
txt = subprocess.check_output([py_exe, '-m', 'pip', 'install', '--force-reinstall', '--break-system-packages', wheel], stderr=subprocess.STDOUT, shell=False)
|
||||
else:
|
||||
txt = subprocess.check_output([py_exe, '-m', 'pip', 'install', '--force-reinstall', wheel], stderr=subprocess.STDOUT, shell=False)
|
||||
print(txt.decode('UTF-8'))
|
||||
sys.exit(0)
|
||||
except subprocess.CalledProcessError as err:
|
||||
@ -154,7 +159,10 @@ except subprocess.CalledProcessError as err:
|
||||
sys.exit(errmsg + "You need to uninstall the LAMMPS python module manually first.\n")
|
||||
try:
|
||||
print('Installing wheel into system site-packages folder failed. Trying user folder now')
|
||||
txt = subprocess.check_output([sys.executable, '-m', 'pip', 'install', '--user', '--force-reinstall', wheel], stderr=subprocess.STDOUT, shell=False)
|
||||
if args.force:
|
||||
txt = subprocess.check_output([sys.executable, '-m', 'pip', 'install', '--user', '--force-reinstall', '--break-system-packages', wheel], stderr=subprocess.STDOUT, shell=False)
|
||||
else:
|
||||
txt = subprocess.check_output([sys.executable, '-m', 'pip', 'install', '--user', '--force-reinstall', wheel], stderr=subprocess.STDOUT, shell=False)
|
||||
print(txt.decode('UTF-8'))
|
||||
except:
|
||||
sys.exit('Failed to install wheel ' + wheel)
|
||||
|
||||
@ -440,7 +440,7 @@ double BondBPMSpringPlastic::single(int type, double rsq, int i, int j, double &
|
||||
|
||||
double r = sqrt(rsq);
|
||||
double rinv = 1.0 / r;
|
||||
double e = (r - r0) / r0;
|
||||
double e = (r0 != 0.0) ? (r - r0) / r0 : 0.0;
|
||||
|
||||
if (normalize_flag)
|
||||
fforce = -k[type] * (e - ep);
|
||||
@ -460,7 +460,7 @@ double BondBPMSpringPlastic::single(int type, double rsq, int i, int j, double &
|
||||
fforce *= rinv;
|
||||
|
||||
if (smooth_flag) {
|
||||
double smooth = (r - r0) / (r0 * ecrit[type]);
|
||||
double smooth = (r0 != 0.0) ? (r - r0) / (r0 * ecrit[type]) : 0.0;
|
||||
smooth *= smooth;
|
||||
smooth *= smooth;
|
||||
smooth *= smooth;
|
||||
|
||||
@ -473,7 +473,8 @@ void PairDPDCoulSlaterLong::read_restart_settings(FILE *fp)
|
||||
void PairDPDCoulSlaterLong::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
fprintf(fp,"%d %g %g\n",i,a0[i][i],gamma[i][i]);
|
||||
fprintf(fp,"%d %g %g %s %g\n",i,a0[i][i],gamma[i][i],
|
||||
(cut_slatersq[i][i] == 0.0) ? "no" : "yes", cut_dpd[i][i]);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
@ -485,7 +486,7 @@ void PairDPDCoulSlaterLong::write_data_all(FILE *fp)
|
||||
for (int i = 1; i <= atom->ntypes; i++)
|
||||
for (int j = i; j <= atom->ntypes; j++)
|
||||
fprintf(fp,"%d %d %g %g %s %g\n",i,j,a0[i][j],gamma[i][j],
|
||||
(cut_slatersq[i][j] == 0.0) ? "yes" : "no", cut_dpd[i][j]);
|
||||
(cut_slatersq[i][j] == 0.0) ? "no" : "yes", cut_dpd[i][j]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -882,7 +882,7 @@ void ComputeStressMop::compute_dihedrals()
|
||||
double x_atom_4[3] = {0.0, 0.0, 0.0};
|
||||
|
||||
// initialization
|
||||
for (int i = 0; i < nvalues; i++) { dihedral_local[i] = 0.0; }
|
||||
for (int i = 0; i < nvalues; i++) dihedral_local[i] = 0.0;
|
||||
double local_contribution[3] = {0.0, 0.0, 0.0};
|
||||
|
||||
for (atom2 = 0; atom2 < nlocal; atom2++) {
|
||||
@ -1118,10 +1118,6 @@ void ComputeStressMop::compute_dihedrals()
|
||||
df[2] = sgn * (f1[2] + f3[2]);
|
||||
}
|
||||
|
||||
// no if matches
|
||||
else {
|
||||
df[0] = df[1] = df[2] = 0.0;
|
||||
}
|
||||
local_contribution[0] += df[0] / area * nktv2p;
|
||||
local_contribution[1] += df[1] / area * nktv2p;
|
||||
local_contribution[2] += df[2] / area * nktv2p;
|
||||
|
||||
@ -2301,7 +2301,7 @@ void Atom::first_reorder()
|
||||
// nfirst = index of first atom not in firstgroup
|
||||
// when find firstgroup atom out of place, swap it with atom nfirst
|
||||
|
||||
int bitmask = group->bitmask[firstgroup];
|
||||
const int bitmask = group->get_bitmask_by_id(FLERR, firstgroupname, "Atom::first_reorder");
|
||||
nfirst = 0;
|
||||
while (nfirst < nlocal && mask[nfirst] & bitmask) nfirst++;
|
||||
|
||||
|
||||
@ -52,9 +52,7 @@ void ChangeBox::command(int narg, char **arg)
|
||||
|
||||
// group
|
||||
|
||||
int igroup = group->find(arg[0]);
|
||||
if (igroup == -1) error->all(FLERR,"Could not find change_box group ID {}", arg[0]);
|
||||
int groupbit = group->bitmask[igroup];
|
||||
int groupbit = group->get_bitmask_by_id(FLERR, arg[0], "change_box");
|
||||
|
||||
// parse operation arguments
|
||||
// allocate ops to max possible length
|
||||
|
||||
@ -48,11 +48,11 @@ Compute::Compute(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
id = utils::strdup(arg[0]);
|
||||
if (!utils::is_id(id))
|
||||
error->all(FLERR,"Compute ID must be alphanumeric or underscore characters");
|
||||
error->all(FLERR,"Compute ID {} must only have alphanumeric or underscore characters", id);
|
||||
|
||||
groupbit = group->get_bitmask_by_id(FLERR, arg[1], fmt::format("compute {}", arg[2]));
|
||||
igroup = group->find(arg[1]);
|
||||
if (igroup == -1) error->all(FLERR,"Could not find compute group ID");
|
||||
groupbit = group->bitmask[igroup];
|
||||
if (igroup == -1) error->all(FLERR,"Could not find compute group ID {}", arg[1]);
|
||||
|
||||
style = utils::strdup(arg[2]);
|
||||
|
||||
|
||||
@ -39,8 +39,7 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
{
|
||||
if (narg < 5) error->all(FLERR, "Illegal compute coord/atom command");
|
||||
|
||||
jgroup = group->find("all");
|
||||
jgroupbit = group->bitmask[jgroup];
|
||||
jgroupbit = group->get_bitmask_by_id(FLERR, "all", "compute coord/atom");
|
||||
cstyle = NONE;
|
||||
|
||||
if (strcmp(arg[3], "cutoff") == 0) {
|
||||
@ -50,11 +49,10 @@ ComputeCoordAtom::ComputeCoordAtom(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
int iarg = 5;
|
||||
if ((narg > 6) && (strcmp(arg[5], "group") == 0)) {
|
||||
delete[] group2;
|
||||
group2 = utils::strdup(arg[6]);
|
||||
iarg += 2;
|
||||
jgroup = group->find(group2);
|
||||
if (jgroup == -1) error->all(FLERR, "Compute coord/atom group2 ID does not exist");
|
||||
jgroupbit = group->bitmask[jgroup];
|
||||
jgroupbit = group->get_bitmask_by_id(FLERR, group2, "compute coord/atom");
|
||||
}
|
||||
|
||||
ncol = narg - iarg + 1;
|
||||
|
||||
@ -46,7 +46,7 @@ class ComputeCoordAtom : public Compute {
|
||||
double **carray;
|
||||
|
||||
char *group2;
|
||||
int jgroup, jgroupbit;
|
||||
int jgroupbit;
|
||||
|
||||
class ComputeOrientOrderAtom *c_orientorder;
|
||||
char *id_orientorder;
|
||||
|
||||
@ -54,9 +54,7 @@ ComputeGroupGroup::ComputeGroupGroup(LAMMPS *lmp, int narg, char **arg) :
|
||||
extvector = 1;
|
||||
|
||||
group2 = utils::strdup(arg[3]);
|
||||
jgroup = group->find(group2);
|
||||
if (jgroup == -1) error->all(FLERR, "Compute group/group group ID does not exist");
|
||||
jgroupbit = group->bitmask[jgroup];
|
||||
jgroupbit = group->get_bitmask_by_id(FLERR, group2, "compute group/group");
|
||||
|
||||
pairflag = 1;
|
||||
kspaceflag = 0;
|
||||
@ -147,9 +145,7 @@ void ComputeGroupGroup::init()
|
||||
|
||||
// recheck that group 2 has not been deleted
|
||||
|
||||
jgroup = group->find(group2);
|
||||
if (jgroup == -1) error->all(FLERR, "Compute group/group group ID does not exist");
|
||||
jgroupbit = group->bitmask[jgroup];
|
||||
jgroupbit = group->get_bitmask_by_id(FLERR, group2, "compute group/group");
|
||||
|
||||
// need an occasional half neighbor list
|
||||
|
||||
|
||||
@ -35,7 +35,7 @@ class ComputeGroupGroup : public Compute {
|
||||
|
||||
private:
|
||||
char *group2;
|
||||
int jgroup, jgroupbit, othergroupbit;
|
||||
int jgroupbit;
|
||||
double **cutsq;
|
||||
double e_self, e_correction;
|
||||
int pairflag, kspaceflag, boundaryflag, molflag;
|
||||
|
||||
@ -59,12 +59,8 @@ void CreateBonds::command(int narg, char **arg)
|
||||
if (strcmp(arg[0], "many") == 0) {
|
||||
style = MANY;
|
||||
if (narg != 6) error->all(FLERR, "No optional keywords allowed with create_bonds many");
|
||||
igroup = group->find(arg[1]);
|
||||
if (igroup == -1) error->all(FLERR, "Cannot find create_bonds first group ID {}", arg[1]);
|
||||
group1bit = group->bitmask[igroup];
|
||||
igroup = group->find(arg[2]);
|
||||
if (igroup == -1) error->all(FLERR, "Cannot find create_bonds second group ID {}", arg[2]);
|
||||
group2bit = group->bitmask[igroup];
|
||||
group1bit = group->get_bitmask_by_id(FLERR, arg[1], "create_bonds");
|
||||
group2bit = group->get_bitmask_by_id(FLERR, arg[2], "create_bonds");
|
||||
btype = utils::inumeric(FLERR, arg[3], false, lmp);
|
||||
rmin = utils::numeric(FLERR, arg[4], false, lmp);
|
||||
rmax = utils::numeric(FLERR, arg[5], false, lmp);
|
||||
|
||||
@ -30,7 +30,7 @@ class CreateBonds : public Command {
|
||||
void command(int, char **) override;
|
||||
|
||||
private:
|
||||
int igroup, group1bit, group2bit;
|
||||
int group1bit, group2bit;
|
||||
int btype, atype, dtype;
|
||||
tagint batom1, batom2, aatom1, aatom2, aatom3, datom1, datom2, datom3, datom4;
|
||||
double rmin, rmax;
|
||||
|
||||
@ -87,8 +87,8 @@ void DeleteAtoms::command(int narg, char **arg)
|
||||
error->all(FLERR, "Unknown delete_atoms sub-command: {}", arg[0]);
|
||||
|
||||
if (allflag) {
|
||||
int igroup = group->find("all");
|
||||
if ((igroup >= 0) && modify->check_rigid_group_overlap(group->bitmask[igroup]))
|
||||
int igroupbit = group->get_bitmask_by_id(FLERR, "all", "delete_atoms");
|
||||
if (modify->check_rigid_group_overlap(igroupbit))
|
||||
error->warning(FLERR, "Attempting to delete atoms in rigid bodies");
|
||||
} else {
|
||||
if (modify->check_rigid_list_overlap(dlist))
|
||||
@ -216,8 +216,7 @@ void DeleteAtoms::delete_group(int narg, char **arg)
|
||||
{
|
||||
if (narg < 2) utils::missing_cmd_args(FLERR, "delete_atoms group", error);
|
||||
|
||||
int igroup = group->find(arg[1]);
|
||||
if (igroup == -1) error->all(FLERR, "Could not find delete_atoms group ID {}", arg[1]);
|
||||
int groupbit = group->get_bitmask_by_id(FLERR, arg[1], "delete_atoms");
|
||||
options(narg - 2, &arg[2]);
|
||||
|
||||
// check for special case of group = all
|
||||
@ -234,8 +233,6 @@ void DeleteAtoms::delete_group(int narg, char **arg)
|
||||
for (int i = 0; i < nlocal; i++) dlist[i] = 0;
|
||||
|
||||
int *mask = atom->mask;
|
||||
int groupbit = group->bitmask[igroup];
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) dlist[i] = 1;
|
||||
}
|
||||
@ -281,18 +278,11 @@ void DeleteAtoms::delete_overlap(int narg, char **arg)
|
||||
|
||||
const double cut = utils::numeric(FLERR, arg[1], false, lmp);
|
||||
const double cutsq = cut * cut;
|
||||
const int group1bit = group->get_bitmask_by_id(FLERR, arg[2], "delete_atoms");
|
||||
const int group2bit = group->get_bitmask_by_id(FLERR, arg[3], "delete_atoms");
|
||||
|
||||
int igroup1 = group->find(arg[2]);
|
||||
if (igroup1 < 0)
|
||||
error->all(FLERR, "Could not find delete_atoms overlap first group ID {}", arg[2]);
|
||||
int igroup2 = group->find(arg[3]);
|
||||
if (igroup2 < 0)
|
||||
error->all(FLERR, "Could not find delete_atoms overlap second group ID {}", arg[3]);
|
||||
options(narg - 4, &arg[4]);
|
||||
|
||||
const int group1bit = group->bitmask[igroup1];
|
||||
const int group2bit = group->bitmask[igroup2];
|
||||
|
||||
if (comm->me == 0) utils::logmesg(lmp, "System init for delete_atoms ...\n");
|
||||
|
||||
// request a full neighbor list for use by this command
|
||||
@ -454,9 +444,7 @@ void DeleteAtoms::delete_random(int narg, char **arg)
|
||||
error->all(FLERR, "Unknown delete_atoms random style: {}", arg[1]);
|
||||
}
|
||||
|
||||
int igroup = group->find(arg[4]);
|
||||
if (igroup == -1) error->all(FLERR, "Could not find delete_atoms random group ID {}", arg[4]);
|
||||
|
||||
int groupbit = group->get_bitmask_by_id(FLERR, arg[4], "delete_atoms");
|
||||
auto region = domain->get_region_by_id(arg[5]);
|
||||
if (!region && (strcmp(arg[5], "NULL") != 0))
|
||||
error->all(FLERR, "Could not find delete_atoms random region ID {}", arg[5]);
|
||||
@ -477,7 +465,6 @@ void DeleteAtoms::delete_random(int narg, char **arg)
|
||||
double **x = atom->x;
|
||||
int *mask = atom->mask;
|
||||
|
||||
int groupbit = group->bitmask[igroup];
|
||||
if (region) region->prematch();
|
||||
|
||||
// delete approximate fraction of atoms in both group and region
|
||||
|
||||
@ -56,11 +56,9 @@ void DeleteBonds::command(int narg, char **arg)
|
||||
|
||||
if (comm->me == 0) utils::logmesg(lmp,"Deleting bonds ...\n");
|
||||
|
||||
// identify group
|
||||
// get group bitmask
|
||||
|
||||
int igroup = group->find(arg[0]);
|
||||
if (igroup == -1) error->all(FLERR,"Cannot find delete_bonds group ID");
|
||||
int groupbit = group->bitmask[igroup];
|
||||
int groupbit = group->get_bitmask_by_id(FLERR, arg[0], "delete_bonds");
|
||||
|
||||
// set style and which = type value
|
||||
|
||||
|
||||
@ -74,8 +74,7 @@ void DisplaceAtoms::command(int narg, char **arg)
|
||||
// group and style
|
||||
|
||||
igroup = group->find(arg[0]);
|
||||
if (igroup == -1) error->all(FLERR,"Could not find displace_atoms group ID");
|
||||
groupbit = group->bitmask[igroup];
|
||||
groupbit = group->get_bitmask_by_id(FLERR, arg[0], "displace_atoms");
|
||||
|
||||
if (modify->check_rigid_group_overlap(groupbit))
|
||||
error->warning(FLERR,"Attempting to displace atoms in rigid bodies");
|
||||
|
||||
@ -58,7 +58,7 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) :
|
||||
id = utils::strdup(arg[0]);
|
||||
|
||||
igroup = group->find(arg[1]);
|
||||
groupbit = group->bitmask[igroup];
|
||||
groupbit = group->get_bitmask_by_id(FLERR, arg[1], fmt::format("dump {}", arg[2]));
|
||||
|
||||
style = utils::strdup(arg[2]);
|
||||
|
||||
@ -311,6 +311,7 @@ void Dump::init()
|
||||
|
||||
int Dump::count()
|
||||
{
|
||||
// group all
|
||||
if (igroup == 0) return atom->nlocal;
|
||||
|
||||
int *mask = atom->mask;
|
||||
|
||||
@ -48,8 +48,8 @@ Fix::Fix(LAMMPS *lmp, int /*narg*/, char **arg) :
|
||||
error->all(FLERR,"Fix ID must be alphanumeric or underscore characters");
|
||||
|
||||
igroup = group->find(arg[1]);
|
||||
if (igroup == -1) error->all(FLERR,"Could not find fix group ID");
|
||||
groupbit = group->bitmask[igroup];
|
||||
if (igroup == -1) error->all(FLERR,"Could not find fix {} group ID {}", arg[2], arg[1]);
|
||||
groupbit = group->get_bitmask_by_id(FLERR, arg[1], fmt::format("fix {}",arg[2]));
|
||||
|
||||
style = utils::strdup(arg[2]);
|
||||
|
||||
|
||||
@ -294,6 +294,7 @@ void FixHalt::end_of_step()
|
||||
for (int i = 0; i < universe->nworlds; ++i) {
|
||||
if (universe->me == universe->root_proc[i]) continue;
|
||||
MPI_Wait(req + i, MPI_STATUS_IGNORE);
|
||||
MPI_Request_free(req + i);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@ -271,7 +271,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) :
|
||||
delete[] id_dilate;
|
||||
id_dilate = utils::strdup(arg[iarg+1]);
|
||||
int idilate = group->find(id_dilate);
|
||||
if (idilate == -1)
|
||||
if (idilate < 0)
|
||||
error->all(FLERR,"Fix {} dilate group ID {} does not exist", style, id_dilate);
|
||||
}
|
||||
iarg += 2;
|
||||
@ -629,12 +629,8 @@ void FixNH::init()
|
||||
{
|
||||
// recheck that dilate group has not been deleted
|
||||
|
||||
if (allremap == 0) {
|
||||
int idilate = group->find(id_dilate);
|
||||
if (idilate == -1)
|
||||
error->all(FLERR,"Fix {} dilate group ID {} does not exist", style, id_dilate);
|
||||
dilate_group_bit = group->bitmask[idilate];
|
||||
}
|
||||
if (allremap == 0)
|
||||
dilate_group_bit = group->get_bitmask_by_id(FLERR, id_dilate, fmt::format("fix {}", style));
|
||||
|
||||
// ensure no conflict with fix deform
|
||||
|
||||
|
||||
@ -41,7 +41,7 @@ enum{BOX,LATTICE,FRACTION};
|
||||
FixRecenter::FixRecenter(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg)
|
||||
{
|
||||
if (narg < 6) error->all(FLERR,"Illegal fix recenter command");
|
||||
if (narg < 6) utils::missing_cmd_args(FLERR,"fix recenter", error);
|
||||
|
||||
xcom = ycom = zcom = 0.0;
|
||||
xflag = yflag = zflag = 1;
|
||||
@ -74,17 +74,15 @@ FixRecenter::FixRecenter(LAMMPS *lmp, int narg, char **arg) :
|
||||
int iarg = 6;
|
||||
while (iarg < narg) {
|
||||
if (strcmp(arg[iarg],"shift") == 0) {
|
||||
int igroup2 = group->find(arg[iarg+1]);
|
||||
if (igroup2 < 0) error->all(FLERR,"Could not find fix recenter group ID");
|
||||
group2bit = group->bitmask[igroup2];
|
||||
group2bit = group->get_bitmask_by_id(FLERR, arg[iarg+1], "fix recenter");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"units") == 0) {
|
||||
if (strcmp(arg[iarg+1],"box") == 0) scaleflag = BOX;
|
||||
else if (strcmp(arg[iarg+1],"lattice") == 0) scaleflag = LATTICE;
|
||||
else if (strcmp(arg[iarg+1],"fraction") == 0) scaleflag = FRACTION;
|
||||
else error->all(FLERR,"Illegal fix recenter command");
|
||||
else error->all(FLERR,"Unknown fix recenter units argument {}", arg[iarg+1]);
|
||||
iarg += 2;
|
||||
} else error->all(FLERR,"Illegal fix recenter command");
|
||||
} else error->all(FLERR,"Unknown fix recenter keyword {}", arg[iarg]);
|
||||
}
|
||||
|
||||
// scale xcom,ycom,zcom
|
||||
@ -103,8 +101,7 @@ FixRecenter::FixRecenter(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
// cannot have 0 atoms in group
|
||||
|
||||
if (group->count(igroup) == 0)
|
||||
error->all(FLERR,"Fix recenter group has no atoms");
|
||||
if (group->count(igroup) == 0) error->all(FLERR,"Fix recenter group {} has no atoms", arg[1]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
@ -73,11 +73,9 @@ FixSpring::FixSpring(LAMMPS *lmp, int narg, char **arg) :
|
||||
|
||||
group2 = utils::strdup(arg[4]);
|
||||
igroup2 = group->find(arg[4]);
|
||||
if (igroup2 == -1)
|
||||
error->all(FLERR,"Fix spring couple group ID does not exist");
|
||||
if (igroup2 == igroup)
|
||||
error->all(FLERR,"Two groups cannot be the same in fix spring couple");
|
||||
group2bit = group->bitmask[igroup2];
|
||||
error->all(FLERR,"The two groups cannot be the same in fix spring couple");
|
||||
group2bit = group->get_bitmask_by_id(FLERR, arg[4], "fix spring");
|
||||
|
||||
k_spring = utils::numeric(FLERR,arg[5],false,lmp);
|
||||
xflag = yflag = zflag = 1;
|
||||
@ -121,9 +119,7 @@ void FixSpring::init()
|
||||
|
||||
if (group2) {
|
||||
igroup2 = group->find(group2);
|
||||
if (igroup2 == -1)
|
||||
error->all(FLERR,"Fix spring couple group ID does not exist");
|
||||
group2bit = group->bitmask[igroup2];
|
||||
group2bit = group->get_bitmask_by_id(FLERR, group2, "fix spring");
|
||||
}
|
||||
|
||||
masstotal = group->mass(igroup);
|
||||
|
||||
@ -649,6 +649,19 @@ int Group::find_unused()
|
||||
return -1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
return group bitmask for given group id. Error out if group is not found.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
int Group::get_bitmask_by_id(const std::string &file, int line, const std::string &name,
|
||||
const std::string &caller)
|
||||
{
|
||||
int igroup = find(name);
|
||||
if (igroup < 0)
|
||||
error->all(file, line, "Group ID {} requested by {} does not exist", name, caller);
|
||||
return bitmask[igroup];
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
add atoms to group that are in same molecules as atoms already in group
|
||||
do not include molID = 0
|
||||
|
||||
@ -31,11 +31,13 @@ class Group : protected Pointers {
|
||||
|
||||
Group(class LAMMPS *);
|
||||
~Group() override;
|
||||
|
||||
void assign(int, char **); // assign atoms to a group
|
||||
void assign(const std::string &); // convenience function
|
||||
void create(const std::string &, int *); // add flagged atoms to a group
|
||||
int find(const std::string &); // lookup name in list of groups
|
||||
int find_or_create(const char *); // lookup name or create new group
|
||||
int get_bitmask_by_id(const std::string &, int, const std::string &, const std::string &);
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
|
||||
|
||||
@ -304,8 +304,6 @@ void Info::command(int narg, char **arg)
|
||||
fputs("-DLAMMPS_BIGBIG\n",out);
|
||||
#elif defined(LAMMPS_SMALLBIG)
|
||||
fputs("-DLAMMPS_SMALLBIG\n",out);
|
||||
#else // defined(LAMMPS_SMALLSMALL)
|
||||
fputs("-DLAMMPS_SMALLSMALL\n",out);
|
||||
#endif
|
||||
if (has_gzip_support()) utils::print(out,"\n{}\n",platform::compress_info());
|
||||
|
||||
|
||||
@ -694,11 +694,6 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
|
||||
sizeof(tagint) != 8 || sizeof(bigint) != 8)
|
||||
error->all(FLERR,"Small to big integers are not sized correctly");
|
||||
#endif
|
||||
#ifdef LAMMPS_SMALLSMALL
|
||||
if (sizeof(smallint) != 4 || sizeof(imageint) != 4 ||
|
||||
sizeof(tagint) != 4 || sizeof(bigint) != 4)
|
||||
error->all(FLERR,"Small to big integers are not sized correctly");
|
||||
#endif
|
||||
|
||||
// create Kokkos class if KOKKOS installed, unless explicitly switched off
|
||||
// instantiation creates dummy Kokkos class if KOKKOS is not installed
|
||||
@ -1487,8 +1482,6 @@ void LAMMPS::print_config(FILE *fp)
|
||||
fputs("-DLAMMPS_BIGBIG\n",fp);
|
||||
#elif defined(LAMMPS_SMALLBIG)
|
||||
fputs("-DLAMMPS_SMALLBIG\n",fp);
|
||||
#else // defined(LAMMPS_SMALLSMALL)
|
||||
fputs("-DLAMMPS_SMALLSMALL\n",fp);
|
||||
#endif
|
||||
|
||||
utils::print(fp,"sizeof(smallint): {}-bit\n"
|
||||
|
||||
@ -24,7 +24,7 @@
|
||||
/* We follow the behavior of regular LAMMPS compilation and assume
|
||||
* -DLAMMPS_SMALLBIG when no define is set. */
|
||||
|
||||
#if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG) && !defined(LAMMPS_SMALLSMALL)
|
||||
#if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG)
|
||||
#define LAMMPS_SMALLBIG
|
||||
#endif
|
||||
|
||||
|
||||
@ -80,10 +80,16 @@ static constexpr uint32_t MEMCPYMASK = (static_cast<uint32_t>(1) << 31) - 1U;
|
||||
|
||||
// default to 32-bit smallint and other ints, 64-bit bigint
|
||||
|
||||
#if !defined(LAMMPS_SMALLSMALL) && !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG)
|
||||
#if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG)
|
||||
#define LAMMPS_SMALLBIG
|
||||
#endif
|
||||
|
||||
// we no longer support LAMMPS_SMALLSMALL
|
||||
|
||||
#if defined(LAMMPS_SMALLSMALL)
|
||||
#error LAMMPS no longer supports -DLAMMPS_SMALLSMALL
|
||||
#endif
|
||||
|
||||
// allow user override of LONGLONG to LONG, necessary for some machines/MPI
|
||||
|
||||
#ifdef LAMMPS_LONGLONG_TO_LONG
|
||||
@ -162,40 +168,6 @@ typedef int64_t bigint;
|
||||
|
||||
#endif
|
||||
|
||||
// for machines that do not support 64-bit ints
|
||||
// 32-bit smallint/imageint/tagint/bigint
|
||||
|
||||
#ifdef LAMMPS_SMALLSMALL
|
||||
|
||||
typedef int smallint;
|
||||
typedef int imageint;
|
||||
typedef int tagint;
|
||||
typedef int bigint;
|
||||
|
||||
#define MAXSMALLINT INT_MAX
|
||||
#define MAXTAGINT INT_MAX
|
||||
#define MAXBIGINT INT_MAX
|
||||
#define MAXDOUBLEINT INT_MAX
|
||||
|
||||
#define MPI_LMP_TAGINT MPI_INT
|
||||
#define MPI_LMP_IMAGEINT MPI_INT
|
||||
#define MPI_LMP_BIGINT MPI_INT
|
||||
|
||||
#define TAGINT_FORMAT "%d"
|
||||
#define BIGINT_FORMAT "%d"
|
||||
|
||||
#define LAMMPS_TAGINT LAMMPS_INT
|
||||
#define LAMMPS_TAGINT_2D LAMMPS_INT_2D
|
||||
#define LAMMPS_BIGINT LAMMPS_INT
|
||||
#define LAMMPS_BIGINT_2D LAMMPS_INT_2D
|
||||
|
||||
#define IMGMASK 1023
|
||||
#define IMGMAX 512
|
||||
#define IMGBITS 10
|
||||
#define IMG2BITS 20
|
||||
|
||||
#endif
|
||||
|
||||
/** Data structure for packing 32-bit and 64-bit integers
|
||||
* into double (communication) buffers
|
||||
*
|
||||
|
||||
@ -272,16 +272,18 @@ void utils::print(FILE *fp, const std::string &mesg)
|
||||
|
||||
void utils::fmtargs_print(FILE *fp, fmt::string_view format, fmt::format_args args)
|
||||
{
|
||||
try {
|
||||
print(fp, fmt::vformat(format, args));
|
||||
} catch (fmt::format_error &) {
|
||||
; // do nothing
|
||||
}
|
||||
print(fp, fmt::vformat(format, args));
|
||||
}
|
||||
|
||||
std::string utils::errorurl(int errorcode)
|
||||
{
|
||||
return fmt::format("\nFor more information see https://docs.lammps.org/err{:04d}", errorcode);
|
||||
std::string url;
|
||||
try {
|
||||
url = fmt::format("\nFor more information see https://docs.lammps.org/err{:04d}", errorcode);
|
||||
} catch (std::exception &) {
|
||||
url = std::string("\nFor more information see https://docs.lammps.org/Errors_details.html");
|
||||
}
|
||||
return url;
|
||||
}
|
||||
|
||||
void utils::flush_buffers(LAMMPS *lmp)
|
||||
|
||||
@ -23,7 +23,7 @@
|
||||
#include <cstring>
|
||||
|
||||
// these must match settings in src/lmptype.h which builds LAMMPS with
|
||||
// -DLAMMPS_SMALLBIG (the default), -DLAMMPS_BIGBIG, or -DLAMMPS_SMALLSMALL
|
||||
// -DLAMMPS_SMALLBIG (the default) or -DLAMMPS_BIGBIG
|
||||
// you can edit the tools/Makefile to enforce the same setting
|
||||
// for the build of binary2txt, e.g.
|
||||
// g++ -g -DLAMMPS_BIGBIG binarytxt.o -o binary2txt
|
||||
@ -36,7 +36,7 @@
|
||||
#define PRId64 "ld"
|
||||
#endif
|
||||
|
||||
#if !defined(LAMMPS_SMALLSMALL) && !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG)
|
||||
#if !defined(LAMMPS_BIGBIG) && !defined(LAMMPS_SMALLBIG)
|
||||
#define LAMMPS_SMALLBIG
|
||||
#endif
|
||||
|
||||
@ -44,10 +44,6 @@
|
||||
typedef int tagint;
|
||||
typedef int64_t bigint;
|
||||
#define BIGINT_FORMAT "%" PRId64
|
||||
#elif defined(LAMMPS_SMALLSMALL)
|
||||
typedef int tagint;
|
||||
typedef int bigint;
|
||||
#define BIGINT_FORMAT "%d"
|
||||
#else /* LAMMPS_BIGBIG */
|
||||
typedef int64_t tagint;
|
||||
typedef int64_t bigint;
|
||||
|
||||
@ -94,8 +94,8 @@ endif()
|
||||
|
||||
option(BUILD_WHAM "Download and compile WHAM executable from Grossfield Lab" YES)
|
||||
if(BUILD_WHAM)
|
||||
set(WHAM_URL "http://membrane.urmc.rochester.edu/sites/default/files/wham/wham-release-2.0.11.tgz" CACHE STRING "URL for WHAM tarball")
|
||||
set(WHAM_MD5 "f56751ac71a8d1c485b9ebd4ccff8dbe" CACHE STRING "MD5 checksum of WHAM tarball")
|
||||
set(WHAM_URL "http://membrane.urmc.rochester.edu/sites/default/files/wham/wham-release-2.1.0.tgz" CACHE STRING "URL for WHAM tarball")
|
||||
set(WHAM_MD5 "4ed6e24254925ec124f44bb381c3b87f" CACHE STRING "MD5 checksum of WHAM tarball")
|
||||
mark_as_advanced(WHAM_URL)
|
||||
mark_as_advanced(WHAM_MD5)
|
||||
|
||||
@ -122,7 +122,7 @@ if(BUILD_WHAM)
|
||||
if(PATCH_FOUND)
|
||||
message(STATUS "Apply patch to customize WHAM using ${Patch_EXECUTABLE}")
|
||||
execute_process(
|
||||
COMMAND ${Patch_EXECUTABLE} -p1 -i ${CMAKE_CURRENT_SOURCE_DIR}/update-wham-2.0.11.patch
|
||||
COMMAND ${Patch_EXECUTABLE} -p1 -i ${CMAKE_CURRENT_SOURCE_DIR}/update-wham-2.1.0.patch
|
||||
WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/_deps/src/wham/
|
||||
)
|
||||
endif()
|
||||
|
||||
@ -61,7 +61,6 @@
|
||||
Highlight warnings and error messages in Output window
|
||||
Make Tutorial wizards more compact
|
||||
Include download and compilation of WHAM software from Alan Grossfield
|
||||
Add dialog to run WHAM directly from LAMMPS-GUI
|
||||
Add entry to Run menu to restart the LAMMPS instance
|
||||
Use mutex to avoid corruption of thermo data
|
||||
</description>
|
||||
|
||||
@ -1,73 +1,29 @@
|
||||
diff --git a/.gitignore b/.gitignore
|
||||
index 28ac6ef..a401160 100644
|
||||
--- a/.gitignore
|
||||
+++ b/.gitignore
|
||||
@@ -6,6 +6,8 @@ doc.toc
|
||||
wham-dist.tar.gz
|
||||
|
||||
*.o
|
||||
+*~
|
||||
|
||||
wham/wham
|
||||
wham-2d/wham-2d
|
||||
+/build
|
||||
diff --git a/CMakeLists.txt b/CMakeLists.txt
|
||||
new file mode 100644
|
||||
index 0000000..b4f0fe6
|
||||
--- /dev/null
|
||||
index b4f0fe6..a61cec8 100644
|
||||
--- a/CMakeLists.txt
|
||||
+++ b/CMakeLists.txt
|
||||
@@ -0,0 +1,38 @@
|
||||
+# Custom minimal -*- CMake -*- file for wham
|
||||
+
|
||||
+cmake_minimum_required(VERSION 3.16)
|
||||
+project(wham VERSION 2.0.11
|
||||
+ DESCRIPTION "WHAM: a fast, memory efficient implementation of the Weighted Histogram Analysis Method"
|
||||
+ LANGUAGES C
|
||||
+ HOMEPAGE_URL http://membrane.urmc.rochester.edu/content/wham/)
|
||||
+
|
||||
+include(GNUInstallDirs)
|
||||
+
|
||||
+add_executable(wham
|
||||
+ nr/ran2.c
|
||||
+ nr/locate.c
|
||||
+ wham/wham.c
|
||||
+ wham/file_read.c
|
||||
+ wham/histogram.c
|
||||
+ wham/bootstrap.c
|
||||
+)
|
||||
+target_include_directories(wham PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/wham)
|
||||
+target_link_libraries(wham PRIVATE m)
|
||||
+install(TARGETS wham DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||
+
|
||||
+add_executable(wham-2d
|
||||
+ nr/ran2.c
|
||||
+ nr/locate.c
|
||||
+ wham-2d/wham-2d.c
|
||||
+ wham-2d/file_read.c
|
||||
+ wham-2d/histogram.c
|
||||
+ wham/bootstrap.c
|
||||
+)
|
||||
+target_include_directories(wham-2d PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/wham)
|
||||
+target_link_libraries(wham-2d PRIVATE m)
|
||||
+install(TARGETS wham-2d DESTINATION ${CMAKE_INSTALL_BINDIR})
|
||||
+
|
||||
+install(FILES doc/doc.pdf
|
||||
+ TYPE DOC
|
||||
+ PERMISSIONS OWNER_READ GROUP_READ WORLD_READ
|
||||
+)
|
||||
diff --git a/nr/locate.c b/nr/locate.c
|
||||
index 9f92dc0..f3bf294 100644
|
||||
--- a/nr/locate.c
|
||||
+++ b/nr/locate.c
|
||||
@@ -11,7 +11,7 @@ void locate(double xx[], int n, double x, int *j)
|
||||
ascnd=(xx[n] > xx[0]); // I think this makes it zero based
|
||||
while (ju-jl > 1) {
|
||||
jm=(ju+jl) >> 1;
|
||||
- if (x > xx[jm] == ascnd)
|
||||
+ if ((x > xx[jm]) == ascnd)
|
||||
jl=jm;
|
||||
else
|
||||
ju=jm;
|
||||
@@ -1,7 +1,7 @@
|
||||
# Custom minimal -*- CMake -*- file for wham
|
||||
|
||||
cmake_minimum_required(VERSION 3.16)
|
||||
-project(wham VERSION 2.0.11
|
||||
+project(wham VERSION 2.1.0
|
||||
DESCRIPTION "WHAM: a fast, memory efficient implementation of the Weighted Histogram Analysis Method"
|
||||
LANGUAGES C
|
||||
HOMEPAGE_URL http://membrane.urmc.rochester.edu/content/wham/)
|
||||
diff --git a/doc/doc.tex b/doc/doc.tex
|
||||
index cf36616..84ee891 100644
|
||||
--- a/doc/doc.tex
|
||||
+++ b/doc/doc.tex
|
||||
@@ -53,7 +53,7 @@ Suggestions and patches are welcome.
|
||||
|
||||
|
||||
\subsection{New in release 2.1.0}
|
||||
-Two changes, both contributed by Alex Kohlmeyer. First, we switched from old
|
||||
+Two changes, both contributed by Axel Kohlmeyer. First, we switched from old
|
||||
make to CMake for the build. Second, we changed how energy units are set; where
|
||||
it used to be a compile-time option, now it is set on the command line.
|
||||
|
||||
diff --git a/wham-2d/histogram.c b/wham-2d/histogram.c
|
||||
index 1bd1329..b5d1c01 100644
|
||||
--- a/wham-2d/histogram.c
|
||||
@ -127,99 +83,10 @@ index 1bd1329..b5d1c01 100644
|
||||
-
|
||||
-
|
||||
diff --git a/wham-2d/wham-2d.c b/wham-2d/wham-2d.c
|
||||
index fb6e059..a6b8483 100644
|
||||
index 76389ac..05fe7cf 100644
|
||||
--- a/wham-2d/wham-2d.c
|
||||
+++ b/wham-2d/wham-2d.c
|
||||
@@ -25,7 +25,7 @@
|
||||
#include <time.h>
|
||||
#include "wham-2d.h"
|
||||
|
||||
-#define COMMAND_LINE "Command line: wham-2d Px[=0|pi|val] hist_min_x hist_max_x num_bins_x Py[=0|pi|val] hist_min_y hist_max_y num_bins_y tol temperature numpad metadatafile freefile use_mask\n"
|
||||
+#define COMMAND_LINE "Command line: wham-2d [units <real|metal|lj|...>] Px[=0|pi|val] hist_min_x hist_max_x num_bins_x Py[=0|pi|val] hist_min_y hist_max_y num_bins_y tol temperature numpad metadatafile freefile use_mask\n"
|
||||
double HIST_MAXx,HIST_MINx,BIN_WIDTHx;
|
||||
double HIST_MAXy,HIST_MINy,BIN_WIDTHy;
|
||||
double TOL;
|
||||
@@ -35,7 +35,7 @@ int NUM_BINSx, NUM_BINSy;
|
||||
int PERIODICx, PERIODICy;
|
||||
double PERIODx, PERIODy;
|
||||
double *data1,**num,***bias;
|
||||
-
|
||||
+double k_B = k_B_DEFAULT;
|
||||
|
||||
int main(int argc, char *argv[])
|
||||
{
|
||||
@@ -57,7 +57,7 @@ double sum;
|
||||
int iteration;
|
||||
int max_iteration = 100000;
|
||||
int numpad;
|
||||
-int **mask;
|
||||
+int **mask = NULL;
|
||||
int use_mask;
|
||||
|
||||
cpu1 = ((double) clock())/CLOCKS_PER_SEC;
|
||||
@@ -76,6 +76,61 @@ for (i=0; i<argc; i++)
|
||||
}
|
||||
printf("\n");
|
||||
|
||||
+// set k_B according to LAMMPS units settings
|
||||
+if (strcmp(argv[1],"units") == 0)
|
||||
+ {
|
||||
+ if (argc < 3)
|
||||
+ {
|
||||
+ printf( COMMAND_LINE );
|
||||
+ exit(-1);
|
||||
+ }
|
||||
+
|
||||
+ if (strcmp(argv[2], "lj") == 0)
|
||||
+ {
|
||||
+ k_B = 1.0;
|
||||
+ }
|
||||
+ else if (strcmp(argv[2], "real") == 0)
|
||||
+ {
|
||||
+ k_B = 0.0019872067;
|
||||
+ }
|
||||
+ else if (strcmp(argv[2], "metal") == 0)
|
||||
+ {
|
||||
+ k_B = 8.617343e-5;
|
||||
+ }
|
||||
+ else if (strcmp(argv[2], "si") == 0)
|
||||
+ {
|
||||
+ k_B = 1.3806504e-23;
|
||||
+ }
|
||||
+ else if (strcmp(argv[2], "cgs") == 0)
|
||||
+ {
|
||||
+ k_B = 1.3806504e-16;
|
||||
+ }
|
||||
+ else if (strcmp(argv[2], "electron") == 0)
|
||||
+ {
|
||||
+ k_B = 3.16681534e-6;
|
||||
+ }
|
||||
+ else if (strcmp(argv[2], "micro") == 0)
|
||||
+ {
|
||||
+ k_B = 1.3806504e-8;
|
||||
+ }
|
||||
+ else if (strcmp(argv[2], "nano") == 0)
|
||||
+ {
|
||||
+ k_B = 0.013806504;
|
||||
+ }
|
||||
+ else if (strcmp(argv[2], "default") == 0)
|
||||
+ {
|
||||
+ k_B = k_B_DEFAULT;
|
||||
+ }
|
||||
+ else
|
||||
+ {
|
||||
+ printf("Unknown unit style: %s\n%s", argv[2], COMMAND_LINE);
|
||||
+ exit(-1);
|
||||
+ }
|
||||
+ printf("# Setting value of k_B to = %.15g\n", k_B);
|
||||
+ argc -= 2;
|
||||
+ argv += 2;
|
||||
+ }
|
||||
+
|
||||
PERIODICx = parse_periodic(argv[1], &PERIODx);
|
||||
if (PERIODICx)
|
||||
{
|
||||
@@ -360,8 +415,8 @@ while ( ! iConverged || first)
|
||||
@@ -417,8 +417,8 @@ while ( ! iConverged || first)
|
||||
for (j=0; j< NUM_BINSy; j++)
|
||||
{
|
||||
calc_coor(i,j,coor);
|
||||
@ -230,7 +97,7 @@ index fb6e059..a6b8483 100644
|
||||
}
|
||||
}
|
||||
|
||||
@@ -444,8 +499,9 @@ if (!FREEFILE)
|
||||
@@ -501,8 +501,9 @@ if (!FREEFILE)
|
||||
for (j=0; j< NUM_BINSy; j++)
|
||||
{
|
||||
calc_coor(i,j,coor);
|
||||
@ -242,7 +109,7 @@ index fb6e059..a6b8483 100644
|
||||
}
|
||||
}
|
||||
exit(errno);
|
||||
@@ -461,25 +517,28 @@ else
|
||||
@@ -518,25 +519,28 @@ else
|
||||
for (j=-numpad; j<0; j++)
|
||||
{
|
||||
calc_coor(i,j,coor);
|
||||
@ -280,7 +147,7 @@ index fb6e059..a6b8483 100644
|
||||
}
|
||||
fprintf(FREEFILE, "\n");
|
||||
}
|
||||
@@ -490,25 +549,28 @@ else
|
||||
@@ -547,25 +551,28 @@ else
|
||||
for (j=-numpad; j<0; j++)
|
||||
{
|
||||
calc_coor(i,j,coor);
|
||||
@ -318,7 +185,7 @@ index fb6e059..a6b8483 100644
|
||||
}
|
||||
fprintf(FREEFILE, "\n");
|
||||
}
|
||||
@@ -519,25 +581,28 @@ else
|
||||
@@ -576,25 +583,28 @@ else
|
||||
for (j=-numpad; j<0; j++)
|
||||
{
|
||||
calc_coor(NUM_BINSx+i,j,coor);
|
||||
@ -356,30 +223,6 @@ index fb6e059..a6b8483 100644
|
||||
}
|
||||
fprintf(FREEFILE, "\n");
|
||||
}
|
||||
diff --git a/wham-2d/wham-2d.h b/wham-2d/wham-2d.h
|
||||
index b17e4bd..5fc17ff 100644
|
||||
--- a/wham-2d/wham-2d.h
|
||||
+++ b/wham-2d/wham-2d.h
|
||||
@@ -20,15 +20,15 @@ extern int NUM_BINSy;
|
||||
|
||||
extern int PERIODICx,PERIODICy; // flags to turn on periodicity
|
||||
extern double PERIODx, PERIODy; // flags to control periodic interval
|
||||
+extern double k_B;
|
||||
|
||||
// A couple of predefined periodic units
|
||||
#define DEGREES 360.0
|
||||
#define RADIANS 6.28318530717959
|
||||
|
||||
-#define k_B 0.001982923700 // Boltzmann's constant in kcal/mol K
|
||||
-//#define k_B 0.0083144621 // Boltzmann's constant kJ/mol-K
|
||||
-//#define k_B 1.0 // Boltzmann's constant in reduced units
|
||||
-
|
||||
+#define k_B_DEFAULT 0.001982923700 // Boltzmann's constant in kcal/mol K
|
||||
+//#define k_B_DEFAULT 0.0083144621 // Boltzmann's constant kJ/mol-K
|
||||
+//#define k_B_DEFAULT 1.0 // Boltzmann's constant in reduced units
|
||||
|
||||
|
||||
// Value inserted for the free energy of masked values
|
||||
diff --git a/wham/histogram.c b/wham/histogram.c
|
||||
index bc52d74..635b39f 100644
|
||||
--- a/wham/histogram.c
|
||||
@ -432,7 +275,7 @@ index bc52d74..635b39f 100644
|
||||
+return HIST_MIN + BIN_WIDTH*((double)i+0.5);
|
||||
}
|
||||
diff --git a/wham/wham.c b/wham/wham.c
|
||||
index 487871b..edb8125 100644
|
||||
index 19cf695..7bdbce1 100644
|
||||
--- a/wham/wham.c
|
||||
+++ b/wham/wham.c
|
||||
@@ -1,4 +1,4 @@
|
||||
@ -441,25 +284,11 @@ index 487871b..edb8125 100644
|
||||
* WHAM -- Weighted Histogram Analysis Method
|
||||
*
|
||||
* Reference 1: Computer Physics Communications, 91(1995) 275-282, Benoit Roux
|
||||
@@ -21,7 +21,7 @@
|
||||
#include "wham.h"
|
||||
|
||||
|
||||
-#define COMMAND_LINE "Command line: wham [P|Ppi|Pval] hist_min hist_max num_bins tol temperature numpad metadatafile freefile [num_MC_trials randSeed]\n"
|
||||
+#define COMMAND_LINE "Command line: wham [units <real|metal|lj|...>] [P|Ppi|Pval] hist_min hist_max num_bins tol temperature numpad metadatafile freefile [num_MC_trials randSeed]\n"
|
||||
|
||||
double HIST_MAX,HIST_MIN,BIN_WIDTH,TOL;
|
||||
double *HISTOGRAM;
|
||||
@@ -29,6 +29,7 @@ double kT;
|
||||
int NUM_BINS;
|
||||
int PERIODIC;
|
||||
double PERIOD;
|
||||
+double k_B = k_B_DEFAULT;
|
||||
|
||||
int main(int argc, char *argv[])
|
||||
{
|
||||
@@ -41,7 +42,7 @@ int first;
|
||||
int bin_min;
|
||||
@@ -39,10 +39,9 @@ double kT; // temperature
|
||||
int i,j;
|
||||
int len;
|
||||
int first;
|
||||
-int bin_min;
|
||||
int have_energy;
|
||||
char *freefile;
|
||||
-FILE *METAFILE, *FREEFILE;
|
||||
@ -467,69 +296,7 @@ index 487871b..edb8125 100644
|
||||
struct hist_group *hist_group;
|
||||
struct histogram *hp;
|
||||
double coor;
|
||||
@@ -82,6 +83,61 @@ for (i=0; i<argc; i++)
|
||||
}
|
||||
printf("\n");
|
||||
|
||||
+// set k_B according to LAMMPS units settings
|
||||
+if (strcmp(argv[1],"units") == 0)
|
||||
+ {
|
||||
+ if (argc < 3)
|
||||
+ {
|
||||
+ printf( COMMAND_LINE );
|
||||
+ exit(-1);
|
||||
+ }
|
||||
+
|
||||
+ if (strcmp(argv[2], "lj") == 0)
|
||||
+ {
|
||||
+ k_B = 1.0;
|
||||
+ }
|
||||
+ else if (strcmp(argv[2], "real") == 0)
|
||||
+ {
|
||||
+ k_B = 0.0019872067;
|
||||
+ }
|
||||
+ else if (strcmp(argv[2], "metal") == 0)
|
||||
+ {
|
||||
+ k_B = 8.617343e-5;
|
||||
+ }
|
||||
+ else if (strcmp(argv[2], "si") == 0)
|
||||
+ {
|
||||
+ k_B = 1.3806504e-23;
|
||||
+ }
|
||||
+ else if (strcmp(argv[2], "cgs") == 0)
|
||||
+ {
|
||||
+ k_B = 1.3806504e-16;
|
||||
+ }
|
||||
+ else if (strcmp(argv[2], "electron") == 0)
|
||||
+ {
|
||||
+ k_B = 3.16681534e-6;
|
||||
+ }
|
||||
+ else if (strcmp(argv[2], "micro") == 0)
|
||||
+ {
|
||||
+ k_B = 1.3806504e-8;
|
||||
+ }
|
||||
+ else if (strcmp(argv[2], "nano") == 0)
|
||||
+ {
|
||||
+ k_B = 0.013806504;
|
||||
+ }
|
||||
+ else if (strcmp(argv[2], "default") == 0)
|
||||
+ {
|
||||
+ k_B = k_B_DEFAULT;
|
||||
+ }
|
||||
+ else
|
||||
+ {
|
||||
+ printf("Unknown unit style: %s\n%s", argv[2], COMMAND_LINE);
|
||||
+ exit(-1);
|
||||
+ }
|
||||
+ printf("# Setting value of k_B to = %.15g\n", k_B);
|
||||
+ argc -= 2;
|
||||
+ argv += 2;
|
||||
+ }
|
||||
+
|
||||
if (toupper(argv[1][0]) == 'P')
|
||||
{
|
||||
PERIODIC = 1;
|
||||
@@ -123,7 +179,7 @@ if (argc != 9 && argc !=11)
|
||||
@@ -179,7 +178,7 @@ if (argc != 9 && argc !=11)
|
||||
printf( COMMAND_LINE );
|
||||
exit(-1);
|
||||
}
|
||||
@ -538,7 +305,7 @@ index 487871b..edb8125 100644
|
||||
HIST_MIN = atof(argv[1]);
|
||||
HIST_MAX = atof(argv[2]);
|
||||
NUM_BINS = atoi(argv[3]);
|
||||
@@ -213,13 +269,13 @@ if (!ave_pdf2)
|
||||
@@ -269,13 +268,13 @@ if (!ave_pdf2)
|
||||
printf("couldn't allocate space for ave_pdf2: %s\n", strerror(errno));
|
||||
exit(errno);
|
||||
}
|
||||
@ -554,7 +321,7 @@ index 487871b..edb8125 100644
|
||||
|
||||
i = get_numwindows(METAFILE);
|
||||
printf("#Number of windows = %d\n", i);
|
||||
@@ -248,7 +304,7 @@ assert(i == hist_group->num_windows);
|
||||
@@ -304,7 +303,7 @@ assert(i == hist_group->num_windows);
|
||||
// Figure out if we have trajectories at different temperatures.
|
||||
// Missing temperatures are set to -1 in read_metadata, and
|
||||
// since we require that either all trajectories specify a temperature
|
||||
@ -563,7 +330,7 @@ index 487871b..edb8125 100644
|
||||
// have to check one of them
|
||||
if (hist_group->kT[0] > 0)
|
||||
{
|
||||
@@ -257,7 +313,7 @@ if (hist_group->kT[0] > 0)
|
||||
@@ -313,7 +312,7 @@ if (hist_group->kT[0] > 0)
|
||||
else
|
||||
{
|
||||
have_energy = 0;
|
||||
@ -572,7 +339,7 @@ index 487871b..edb8125 100644
|
||||
{
|
||||
hist_group->kT[i] = kT;
|
||||
}
|
||||
@@ -269,7 +325,7 @@ if (!final_f)
|
||||
@@ -325,7 +324,7 @@ if (!final_f)
|
||||
{
|
||||
printf("couldn't allocate space for final_f: %s\n", strerror(errno));
|
||||
exit(errno);
|
||||
@ -581,7 +348,7 @@ index 487871b..edb8125 100644
|
||||
|
||||
free(HISTOGRAM);
|
||||
|
||||
@@ -305,7 +361,8 @@ while (! is_converged(hist_group) || first )
|
||||
@@ -361,7 +360,8 @@ while (! is_converged(hist_group) || first )
|
||||
for (i=0; i< NUM_BINS; i++)
|
||||
{
|
||||
coor = calc_coor(i);
|
||||
@ -591,7 +358,7 @@ index 487871b..edb8125 100644
|
||||
}
|
||||
printf("\n");
|
||||
|
||||
@@ -319,7 +376,7 @@ while (! is_converged(hist_group) || first )
|
||||
@@ -375,7 +375,7 @@ while (! is_converged(hist_group) || first )
|
||||
}
|
||||
}
|
||||
// Cheesy bailout if we're going on too long
|
||||
@ -600,7 +367,16 @@ index 487871b..edb8125 100644
|
||||
{
|
||||
printf("Too many iterations: %d\n", iteration);
|
||||
break;
|
||||
@@ -383,11 +440,11 @@ for (i=0; i< num_mc_runs; i++)
|
||||
@@ -408,7 +408,7 @@ for (i=0; i < NUM_BINS; i++)
|
||||
}
|
||||
|
||||
// Compute the free energy from the normalized probability
|
||||
-bin_min = calc_free(free_ene, prob,kT);
|
||||
+ calc_free(free_ene, prob,kT);
|
||||
|
||||
// Do the requested number of bootstrap monte carlo error analysis runs.
|
||||
if (num_mc_runs <= 0)
|
||||
@@ -439,11 +439,11 @@ for (i=0; i< num_mc_runs; i++)
|
||||
//printf("Faking %d: %d %d\n", i,j,hp->num_points);
|
||||
num_used = hp->last - hp->first + 1;
|
||||
mk_new_hist(hp->cum, hp->data, num_used, hp->num_mc_samples, &idum);
|
||||
@ -614,7 +390,7 @@ index 487871b..edb8125 100644
|
||||
// perform WHAM iterations on the fake data sets
|
||||
iteration = 0;
|
||||
first = 1;
|
||||
@@ -403,7 +460,7 @@ for (i=0; i< num_mc_runs; i++)
|
||||
@@ -459,7 +459,7 @@ for (i=0; i< num_mc_runs; i++)
|
||||
printf("Too many iterations: %d\n", iteration);
|
||||
break;
|
||||
}
|
||||
@ -623,7 +399,7 @@ index 487871b..edb8125 100644
|
||||
printf("#MC trial %d: %d iterations\n", i, iteration);
|
||||
printf("#PMF values\n");
|
||||
// accumulate the average and stdev of the resulting probabilities
|
||||
@@ -419,18 +476,19 @@ for (i=0; i< num_mc_runs; i++)
|
||||
@@ -475,18 +475,19 @@ for (i=0; i< num_mc_runs; i++)
|
||||
for (j=0; j < NUM_BINS; j++)
|
||||
{
|
||||
pdf = -kT*log(prob[j]);
|
||||
@ -647,7 +423,7 @@ index 487871b..edb8125 100644
|
||||
for (i=0; i < NUM_BINS; i++)
|
||||
{
|
||||
ave_p[i] /= (double)num_mc_runs;
|
||||
@@ -457,12 +515,12 @@ if (!FREEFILE)
|
||||
@@ -513,12 +514,12 @@ if (!FREEFILE)
|
||||
for (i=0; i< NUM_BINS; i++)
|
||||
{
|
||||
coor = calc_coor(i);
|
||||
@ -663,7 +439,7 @@ index 487871b..edb8125 100644
|
||||
}
|
||||
|
||||
exit(errno);
|
||||
@@ -470,38 +528,37 @@ if (!FREEFILE)
|
||||
@@ -526,38 +527,37 @@ if (!FREEFILE)
|
||||
else
|
||||
{
|
||||
// write out header
|
||||
@ -714,7 +490,7 @@ index 487871b..edb8125 100644
|
||||
}
|
||||
}
|
||||
|
||||
@@ -515,7 +572,7 @@ exit(0);
|
||||
@@ -571,7 +571,7 @@ exit(0);
|
||||
/*
|
||||
* Perform a single WHAM iteration
|
||||
*/
|
||||
@ -723,7 +499,7 @@ index 487871b..edb8125 100644
|
||||
int have_energy)
|
||||
{
|
||||
int i,j;
|
||||
@@ -535,9 +592,9 @@ for (i=0; i<NUM_BINS; i++)
|
||||
@@ -591,9 +591,9 @@ for (i=0; i<NUM_BINS; i++)
|
||||
num += (double) get_histval( &(hist_group->hists[j]),i);
|
||||
bias = calc_bias(hist_group,j,coor);
|
||||
bf = exp((hist_group->F_old[j] - bias) / hist_group->kT[j]);
|
||||
@ -736,27 +512,3 @@ index 487871b..edb8125 100644
|
||||
* number of points.
|
||||
*/
|
||||
if (have_energy)
|
||||
diff --git a/wham/wham.h b/wham/wham.h
|
||||
index aacc1e8..7d509f2 100644
|
||||
--- a/wham/wham.h
|
||||
+++ b/wham/wham.h
|
||||
@@ -15,14 +15,16 @@ extern double kT;
|
||||
extern int NUM_BINS;
|
||||
extern int PERIODIC;
|
||||
extern double PERIOD;
|
||||
+extern double k_B;
|
||||
+
|
||||
|
||||
// Some predefined periodic units
|
||||
#define DEGREES 360.0
|
||||
#define RADIANS 6.28318530717959
|
||||
|
||||
-#define k_B 0.001982923700 // Boltzmann's constant in kcal/mol K
|
||||
-//#define k_B 0.0083144621 // Boltzmann's constant kJ/mol-K
|
||||
-//#define k_B 1.0 // Boltzmann's constant in reduced units
|
||||
+#define k_B_DEFAULT 0.001982923700 // Boltzmann's constant in kcal/mol K
|
||||
+//#define k_B_DEFAULT 0.0083144621 // Boltzmann's constant kJ/mol-K
|
||||
+//#define k_B_DEFAULT 1.0 // Boltzmann's constant in reduced units
|
||||
|
||||
|
||||
// global (untrimmed) histogram, global to prevent reallocation
|
||||
@ -1,393 +1,419 @@
|
||||
# The oplsaa2023.lt file contains force-field parameters, atom type definitions,
|
||||
# partial charges, masses and bond-angle rules for the atoms in your system.
|
||||
|
||||
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt
|
||||
|
||||
# It defines these atom types:
|
||||
# atom-type charge mass btype epsilon sigma description
|
||||
# @atom:54 -0.18 12.011 CT 0.066 3.5 "n-CH3 all-atom C: alkanes"
|
||||
# @atom:57 -0.12 12.011 CT 0.066 3.51 "CH2 all-atom C: alkanes"
|
||||
# @atom:58 -0.06 12.011 CT 0.066 3.50 "CH all-atom C: alkanes"
|
||||
# @atom:60 0.06 1.008 HC 0.026 2.48 "H all-atom H: alkanes"
|
||||
# @atom:229 0.14 12.011 CT 0.066 3.50 "C on N: secondary N-CHR2 amide"
|
||||
# @atom:235 0.5 12.011 C~ 0.105 3.75 "C: C=O in amide. Acyl R in amides"
|
||||
# @atom:236 -0.5 15.999 O~ 0.21 2.96 "O: C=O in amide. is neutral - use"
|
||||
# @atom:238 -0.5 14.007 N~ 0.17 3.25 "N: secondary amide 279 for formyl H"
|
||||
# @atom:241 0.3 1.008 H~ 0 0 "H on N: secondary amide"
|
||||
# (Note: Future versions of OPLSAA might use different @atom type numbers.)
|
||||
|
||||
|
||||
|
||||
PolyNIPAM inherits OPLSAA {
|
||||
|
||||
# Charges will be overwritten.
|
||||
write("Data Atoms") {
|
||||
$atom:81_1 $mol @atom:81 0.0 -2.357 -0.245 0.629
|
||||
$atom:81_2 $mol @atom:81 0.0 -1.194 0.752 0.778
|
||||
$atom:85_1 $mol @atom:85 0.0 -2.027 -1.242 0.957
|
||||
$atom:177_1 $mol @atom:177 0.0 -1.743 2.168 0.640
|
||||
$atom:85_2 $mol @atom:85 0.0 -0.366 0.490 0.103
|
||||
$atom:180_1 $mol @atom:180 0.0 -1.147 2.943 -0.274
|
||||
$atom:178_1 $mol @atom:178 0.0 -2.700 2.545 1.293
|
||||
$atom:171_1 $mol @atom:171 0.0 -1.602 4.322 -0.446
|
||||
$atom:183_1 $mol @atom:183 0.0 -0.241 2.724 -0.647
|
||||
$atom:80_1 $mol @atom:80 0.0 -2.662 4.430 -1.547
|
||||
$atom:80_2 $mol @atom:80 0.0 -0.400 5.227 -0.741
|
||||
$atom:85_3 $mol @atom:85 0.0 -2.053 4.672 0.501
|
||||
$atom:85_4 $mol @atom:85 0.0 -3.539 3.796 -1.342
|
||||
$atom:85_5 $mol @atom:85 0.0 -2.245 4.148 -2.526
|
||||
$atom:85_6 $mol @atom:85 0.0 -3.006 5.475 -1.612
|
||||
$atom:85_7 $mol @atom:85 0.0 0.080 4.944 -1.690
|
||||
$atom:85_8 $mol @atom:85 0.0 0.355 5.185 0.060
|
||||
$atom:85_9 $mol @atom:85 0.0 -0.737 6.273 -0.826
|
||||
$atom:85_10 $mol @atom:85 0.0 -3.156 0.050 1.336
|
||||
$atom:85_11 $mol @atom:85 0.0 -0.808 0.718 1.811
|
||||
$atom:81_3 $mol @atom:81 0.0 -4.482 -0.662 -0.732
|
||||
$atom:82_1 $mol @atom:82 0.0 -2.984 -0.308 -0.783
|
||||
$atom:85_12 $mol @atom:85 0.0 -4.918 0.018 0.014
|
||||
$atom:177_2 $mol @atom:177 0.0 -2.344 -1.080 -1.873
|
||||
$atom:180_2 $mol @atom:180 0.0 -1.131 -1.604 -1.620
|
||||
$atom:178_2 $mol @atom:178 0.0 -2.876 -1.219 -2.965
|
||||
$atom:171_2 $mol @atom:171 0.0 -0.391 -2.304 -2.661
|
||||
$atom:183_2 $mol @atom:183 0.0 -0.690 -1.494 -0.727
|
||||
$atom:80_3 $mol @atom:80 0.0 0.802 -3.029 -2.033
|
||||
$atom:80_4 $mol @atom:80 0.0 0.094 -1.373 -3.777
|
||||
$atom:85_13 $mol @atom:85 0.0 -1.054 -3.067 -3.111
|
||||
$atom:85_14 $mol @atom:85 0.0 0.481 -3.774 -1.288
|
||||
$atom:85_15 $mol @atom:85 0.0 1.485 -2.319 -1.542
|
||||
$atom:85_16 $mol @atom:85 0.0 1.368 -3.558 -2.817
|
||||
$atom:85_17 $mol @atom:85 0.0 0.761 -0.594 -3.382
|
||||
$atom:85_18 $mol @atom:85 0.0 -0.738 -0.879 -4.300
|
||||
$atom:85_19 $mol @atom:85 0.0 0.653 -1.964 -4.521
|
||||
$atom:85_20 $mol @atom:85 0.0 -4.937 -0.363 -1.697
|
||||
$atom:85_21 $mol @atom:85 0.0 -2.967 0.717 -1.203
|
||||
$atom:81_4 $mol @atom:81 0.0 -6.422 -2.235 -0.754
|
||||
$atom:82_2 $mol @atom:82 0.0 -4.928 -2.114 -0.469
|
||||
$atom:85_22 $mol @atom:85 0.0 -6.565 -1.832 -1.770
|
||||
$atom:177_3 $mol @atom:177 0.0 -4.663 -2.569 0.992
|
||||
$atom:180_3 $mol @atom:180 0.0 -3.960 -3.716 1.081
|
||||
$atom:178_3 $mol @atom:178 0.0 -4.967 -1.904 1.963
|
||||
$atom:171_3 $mol @atom:171 0.0 -3.354 -4.204 2.319
|
||||
$atom:183_3 $mol @atom:183 0.0 -4.127 -4.397 0.356
|
||||
$atom:80_5 $mol @atom:80 0.0 -4.295 -4.572 3.473
|
||||
$atom:80_6 $mol @atom:80 0.0 -2.271 -3.244 2.828
|
||||
$atom:85_23 $mol @atom:85 0.0 -2.826 -5.135 2.038
|
||||
$atom:85_24 $mol @atom:85 0.0 -4.973 -5.396 3.211
|
||||
$atom:85_25 $mol @atom:85 0.0 -4.909 -3.718 3.794
|
||||
$atom:85_26 $mol @atom:85 0.0 -3.683 -4.896 4.331
|
||||
$atom:85_27 $mol @atom:85 0.0 -2.695 -2.272 3.123
|
||||
$atom:85_28 $mol @atom:85 0.0 -1.484 -3.073 2.079
|
||||
$atom:85_29 $mol @atom:85 0.0 -1.791 -3.686 3.717
|
||||
$atom:85_30 $mol @atom:85 0.0 -6.661 -3.312 -0.799
|
||||
$atom:85_31 $mol @atom:85 0.0 -4.422 -2.764 -1.206
|
||||
$atom:81_5 $mol @atom:81 0.0 -8.861 -2.101 -0.226
|
||||
$atom:82_3 $mol @atom:82 0.0 -7.457 -1.604 0.194
|
||||
$atom:85_32 $mol @atom:85 0.0 -8.826 -3.186 -0.048
|
||||
$atom:177_4 $mol @atom:177 0.0 -7.425 -0.036 0.256
|
||||
$atom:180_4 $mol @atom:180 0.0 -6.870 0.431 1.405
|
||||
$atom:178_4 $mol @atom:178 0.0 -8.004 0.653 -0.558
|
||||
$atom:171_4 $mol @atom:171 0.0 -7.168 1.765 1.912
|
||||
$atom:183_4 $mol @atom:183 0.0 -6.797 -0.317 2.080
|
||||
$atom:80_7 $mol @atom:80 0.0 -8.664 2.017 2.147
|
||||
$atom:80_8 $mol @atom:80 0.0 -6.545 2.857 1.036
|
||||
$atom:85_33 $mol @atom:85 0.0 -6.669 1.831 2.899
|
||||
$atom:85_34 $mol @atom:85 0.0 -9.114 1.252 2.800
|
||||
$atom:85_35 $mol @atom:85 0.0 -9.236 2.024 1.205
|
||||
$atom:85_36 $mol @atom:85 0.0 -8.786 3.001 2.625
|
||||
$atom:85_37 $mol @atom:85 0.0 -7.002 2.900 0.037
|
||||
$atom:85_38 $mol @atom:85 0.0 -5.460 2.706 0.913
|
||||
$atom:85_39 $mol @atom:85 0.0 -6.693 3.836 1.521
|
||||
$atom:85_40 $mol @atom:85 0.0 -9.602 -1.708 0.496
|
||||
$atom:85_41 $mol @atom:85 0.0 -7.328 -2.030 1.207
|
||||
$atom:81_6 $mol @atom:81 0.0 -10.877 -2.392 -1.741
|
||||
$atom:82_4 $mol @atom:82 0.0 -9.440 -1.848 -1.636
|
||||
$atom:85_42 $mol @atom:85 0.0 -11.441 -2.051 -0.857
|
||||
$atom:177_5 $mol @atom:177 0.0 -8.631 -2.553 -2.770
|
||||
$atom:180_5 $mol @atom:180 0.0 -8.499 -1.785 -3.863
|
||||
$atom:178_5 $mol @atom:178 0.0 -8.181 -3.684 -2.688
|
||||
$atom:171_5 $mol @atom:171 0.0 -7.938 -2.258 -5.119
|
||||
$atom:183_5 $mol @atom:183 0.0 -9.049 -0.943 -3.902
|
||||
$atom:80_9 $mol @atom:80 0.0 -8.792 -3.342 -5.780
|
||||
$atom:80_10 $mol @atom:80 0.0 -6.470 -2.687 -5.003
|
||||
$atom:85_43 $mol @atom:85 0.0 -7.963 -1.383 -5.795
|
||||
$atom:85_44 $mol @atom:85 0.0 -9.825 -2.995 -5.943
|
||||
$atom:85_45 $mol @atom:85 0.0 -8.838 -4.264 -5.179
|
||||
$atom:85_46 $mol @atom:85 0.0 -8.360 -3.594 -6.761
|
||||
$atom:85_47 $mol @atom:85 0.0 -6.361 -3.605 -4.407
|
||||
$atom:85_48 $mol @atom:85 0.0 -5.850 -1.903 -4.541
|
||||
$atom:85_49 $mol @atom:85 0.0 -6.071 -2.887 -6.011
|
||||
$atom:85_50 $mol @atom:85 0.0 -11.356 -1.921 -2.619
|
||||
$atom:85_51 $mol @atom:85 0.0 -9.494 -0.756 -1.795
|
||||
$atom:81_7 $mol @atom:81 0.0 -12.476 -4.326 -2.296
|
||||
$atom:82_5 $mol @atom:82 0.0 -11.042 -3.918 -1.914
|
||||
$atom:85_52 $mol @atom:85 0.0 -12.606 -4.028 -3.347
|
||||
$atom:177_6 $mol @atom:177 0.0 -10.631 -4.675 -0.614
|
||||
$atom:180_6 $mol @atom:180 0.0 -9.796 -5.703 -0.861
|
||||
$atom:178_6 $mol @atom:178 0.0 -11.127 -4.453 0.474
|
||||
$atom:171_6 $mol @atom:171 0.0 -9.186 -6.529 0.183
|
||||
$atom:183_6 $mol @atom:183 0.0 -9.206 -5.554 -1.669
|
||||
$atom:80_11 $mol @atom:80 0.0 -10.225 -7.315 0.995
|
||||
$atom:80_12 $mol @atom:80 0.0 -8.204 -5.783 1.100
|
||||
$atom:85_53 $mol @atom:85 0.0 -8.602 -7.290 -0.368
|
||||
$atom:85_54 $mol @atom:85 0.0 -10.889 -7.898 0.339
|
||||
$atom:85_55 $mol @atom:85 0.0 -10.843 -6.658 1.625
|
||||
$atom:85_56 $mol @atom:85 0.0 -9.699 -8.020 1.659
|
||||
$atom:85_57 $mol @atom:85 0.0 -8.739 -5.060 1.735
|
||||
$atom:85_58 $mol @atom:85 0.0 -7.431 -5.245 0.530
|
||||
$atom:85_59 $mol @atom:85 0.0 -7.700 -6.510 1.757
|
||||
$atom:85_60 $mol @atom:85 0.0 -12.525 -5.430 -2.285
|
||||
$atom:85_61 $mol @atom:85 0.0 -10.438 -4.244 -2.777
|
||||
$atom:81_8 $mol @atom:81 0.0 -14.920 -4.584 -1.600
|
||||
$atom:82_6 $mol @atom:82 0.0 -13.632 -3.752 -1.465
|
||||
$atom:85_62 $mol @atom:85 0.0 -14.649 -5.586 -1.247
|
||||
$atom:177_7 $mol @atom:177 0.0 -13.893 -2.285 -1.914
|
||||
$atom:180_7 $mol @atom:180 0.0 -13.965 -1.422 -0.889
|
||||
$atom:178_7 $mol @atom:178 0.0 -13.974 -1.956 -3.082
|
||||
$atom:171_7 $mol @atom:171 0.0 -14.239 0.001 -1.025
|
||||
$atom:183_7 $mol @atom:183 0.0 -13.577 -1.708 -0.004
|
||||
$atom:80_13 $mol @atom:80 0.0 -15.680 0.246 -1.480
|
||||
$atom:80_14 $mol @atom:80 0.0 -13.267 0.807 -1.893
|
||||
$atom:85_63 $mol @atom:85 0.0 -14.156 0.414 -0.002
|
||||
$atom:85_64 $mol @atom:85 0.0 -16.408 -0.251 -0.821
|
||||
$atom:85_65 $mol @atom:85 0.0 -15.849 -0.114 -2.507
|
||||
$atom:85_66 $mol @atom:85 0.0 -15.890 1.327 -1.461
|
||||
$atom:85_67 $mol @atom:85 0.0 -13.268 0.469 -2.940
|
||||
$atom:85_68 $mol @atom:85 0.0 -12.239 0.760 -1.513
|
||||
$atom:85_69 $mol @atom:85 0.0 -13.597 1.859 -1.881
|
||||
$atom:85_70 $mol @atom:85 0.0 -15.637 -4.195 -0.859
|
||||
$atom:85_71 $mol @atom:85 0.0 -13.362 -3.817 -0.395
|
||||
$atom:81_9 $mol @atom:81 0.0 -17.064 -5.395 -2.685
|
||||
$atom:82_7 $mol @atom:82 0.0 -15.684 -4.733 -2.934
|
||||
$atom:85_72 $mol @atom:85 0.0 -17.540 -4.759 -1.921
|
||||
$atom:177_8 $mol @atom:177 0.0 -14.870 -5.540 -3.996
|
||||
$atom:180_8 $mol @atom:180 0.0 -14.373 -4.756 -4.977
|
||||
$atom:178_8 $mol @atom:178 0.0 -14.748 -6.750 -3.981
|
||||
$atom:171_8 $mol @atom:171 0.0 -13.393 -5.268 -5.940
|
||||
$atom:183_8 $mol @atom:183 0.0 -14.174 -3.807 -4.679
|
||||
$atom:80_15 $mol @atom:80 0.0 -14.106 -6.091 -7.020
|
||||
$atom:80_16 $mol @atom:80 0.0 -12.175 -6.042 -5.407
|
||||
$atom:85_73 $mol @atom:85 0.0 -12.988 -4.367 -6.439
|
||||
$atom:85_74 $mol @atom:85 0.0 -14.926 -5.528 -7.494
|
||||
$atom:85_75 $mol @atom:85 0.0 -14.530 -7.019 -6.606
|
||||
$atom:85_76 $mol @atom:85 0.0 -13.392 -6.372 -7.812
|
||||
$atom:85_77 $mol @atom:85 0.0 -12.467 -7.007 -4.964
|
||||
$atom:85_78 $mol @atom:85 0.0 -11.600 -5.477 -4.663
|
||||
$atom:85_79 $mol @atom:85 0.0 -11.507 -6.251 -6.259
|
||||
$atom:85_80 $mol @atom:85 0.0 -17.675 -5.258 -3.598
|
||||
$atom:85_81 $mol @atom:85 0.0 -15.938 -3.724 -3.313
|
||||
$atom:81_10 $mol @atom:81 0.0 -18.749 -7.194 -2.096
|
||||
$atom:82_8 $mol @atom:82 0.0 -17.248 -6.883 -2.287
|
||||
$atom:85_82 $mol @atom:85 0.0 -19.267 -6.796 -2.989
|
||||
$atom:177_9 $mol @atom:177 0.0 -16.454 -7.269 -0.999
|
||||
$atom:180_9 $mol @atom:180 0.0 -15.335 -7.967 -1.254
|
||||
$atom:178_9 $mol @atom:178 0.0 -16.762 -6.899 0.120
|
||||
$atom:171_9 $mol @atom:171 0.0 -14.367 -8.387 -0.248
|
||||
$atom:183_9 $mol @atom:183 0.0 -15.240 -8.331 -2.192
|
||||
$atom:80_17 $mol @atom:80 0.0 -14.904 -9.451 0.715
|
||||
$atom:80_18 $mol @atom:80 0.0 -13.725 -7.242 0.549
|
||||
$atom:85_83 $mol @atom:85 0.0 -13.545 -8.861 -0.817
|
||||
$atom:85_84 $mol @atom:85 0.0 -15.290 -10.333 0.182
|
||||
$atom:85_85 $mol @atom:85 0.0 -15.717 -9.064 1.350
|
||||
$atom:85_86 $mol @atom:85 0.0 -14.087 -9.788 1.373
|
||||
$atom:85_87 $mol @atom:85 0.0 -14.468 -6.647 1.100
|
||||
$atom:85_88 $mol @atom:85 0.0 -13.139 -6.565 -0.089
|
||||
$atom:85_89 $mol @atom:85 0.0 -13.036 -7.679 1.290
|
||||
$atom:85_90 $mol @atom:85 0.0 -18.877 -8.292 -2.150
|
||||
$atom:85_91 $mol @atom:85 0.0 -16.939 -7.505 -3.147
|
||||
$atom:80_19 $mol @atom:80 0.0 -20.999 -7.206 -1.036
|
||||
$atom:82_9 $mol @atom:82 0.0 -19.540 -6.757 -0.843
|
||||
$atom:85_92 $mol @atom:85 0.0 -21.046 -8.300 -1.156
|
||||
$atom:85_93 $mol @atom:85 0.0 -21.439 -6.747 -1.936
|
||||
$atom:177_10 $mol @atom:177 0.0 -19.578 -5.207 -0.628
|
||||
$atom:180_10 $mol @atom:180 0.0 -19.061 -4.828 0.557
|
||||
$atom:178_10 $mol @atom:178 0.0 -20.185 -4.465 -1.375
|
||||
$atom:171_10 $mol @atom:171 0.0 -18.878 -3.426 0.994
|
||||
$atom:183_10 $mol @atom:183 0.0 -18.342 -5.450 0.901
|
||||
$atom:80_20 $mol @atom:80 0.0 -19.984 -2.451 0.558
|
||||
$atom:80_21 $mol @atom:80 0.0 -17.509 -2.857 0.610
|
||||
$atom:85_94 $mol @atom:85 0.0 -18.906 -3.470 2.099
|
||||
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||||
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||||
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||||
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||||
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|
||||
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||||
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|
||||
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||||
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||||
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|
||||
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|
||||
$atom:235_1 $mol:. @atom:235 0.0 -1.743 2.168 0.640
|
||||
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|
||||
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|
||||
$atom:236_1 $mol:. @atom:236 0.0 -2.700 2.545 1.293
|
||||
$atom:229_1 $mol:. @atom:229 0.0 -1.602 4.322 -0.446
|
||||
$atom:241_1 $mol:. @atom:241 0.0 -0.241 2.724 -0.647
|
||||
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|
||||
$atom:54_2 $mol:. @atom:54 0.0 -0.400 5.227 -0.741
|
||||
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|
||||
$atom:60_4 $mol:. @atom:60 0.0 -3.539 3.796 -1.342
|
||||
$atom:60_5 $mol:. @atom:60 0.0 -2.245 4.148 -2.526
|
||||
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|
||||
$atom:60_7 $mol:. @atom:60 0.0 0.080 4.944 -1.690
|
||||
$atom:60_8 $mol:. @atom:60 0.0 0.355 5.185 0.060
|
||||
$atom:60_9 $mol:. @atom:60 0.0 -0.737 6.273 -0.826
|
||||
$atom:60_10 $mol:. @atom:60 0.0 -3.156 0.050 1.336
|
||||
$atom:60_11 $mol:. @atom:60 0.0 -0.808 0.718 1.811
|
||||
$atom:57_3 $mol:. @atom:57 0.0 -4.482 -0.662 -0.732
|
||||
$atom:58_1 $mol:. @atom:58 0.0 -2.984 -0.308 -0.783
|
||||
$atom:60_12 $mol:. @atom:60 0.0 -4.918 0.018 0.014
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
$atom:241_2 $mol:. @atom:241 0.0 -0.690 -1.494 -0.727
|
||||
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|
||||
$atom:54_4 $mol:. @atom:54 0.0 0.094 -1.373 -3.777
|
||||
$atom:60_13 $mol:. @atom:60 0.0 -1.054 -3.067 -3.111
|
||||
$atom:60_14 $mol:. @atom:60 0.0 0.481 -3.774 -1.288
|
||||
$atom:60_15 $mol:. @atom:60 0.0 1.485 -2.319 -1.542
|
||||
$atom:60_16 $mol:. @atom:60 0.0 1.368 -3.558 -2.817
|
||||
$atom:60_17 $mol:. @atom:60 0.0 0.761 -0.594 -3.382
|
||||
$atom:60_18 $mol:. @atom:60 0.0 -0.738 -0.879 -4.300
|
||||
$atom:60_19 $mol:. @atom:60 0.0 0.653 -1.964 -4.521
|
||||
$atom:60_20 $mol:. @atom:60 0.0 -4.937 -0.363 -1.697
|
||||
$atom:60_21 $mol:. @atom:60 0.0 -2.967 0.717 -1.203
|
||||
$atom:57_4 $mol:. @atom:57 0.0 -6.422 -2.235 -0.754
|
||||
$atom:58_2 $mol:. @atom:58 0.0 -4.928 -2.114 -0.469
|
||||
$atom:60_22 $mol:. @atom:60 0.0 -6.565 -1.832 -1.770
|
||||
$atom:235_3 $mol:. @atom:235 0.0 -4.663 -2.569 0.992
|
||||
$atom:238_3 $mol:. @atom:238 0.0 -3.960 -3.716 1.081
|
||||
$atom:236_3 $mol:. @atom:236 0.0 -4.967 -1.904 1.963
|
||||
$atom:229_3 $mol:. @atom:229 0.0 -3.354 -4.204 2.319
|
||||
$atom:241_3 $mol:. @atom:241 0.0 -4.127 -4.397 0.356
|
||||
$atom:54_5 $mol:. @atom:54 0.0 -4.295 -4.572 3.473
|
||||
$atom:54_6 $mol:. @atom:54 0.0 -2.271 -3.244 2.828
|
||||
$atom:60_23 $mol:. @atom:60 0.0 -2.826 -5.135 2.038
|
||||
$atom:60_24 $mol:. @atom:60 0.0 -4.973 -5.396 3.211
|
||||
$atom:60_25 $mol:. @atom:60 0.0 -4.909 -3.718 3.794
|
||||
$atom:60_26 $mol:. @atom:60 0.0 -3.683 -4.896 4.331
|
||||
$atom:60_27 $mol:. @atom:60 0.0 -2.695 -2.272 3.123
|
||||
$atom:60_28 $mol:. @atom:60 0.0 -1.484 -3.073 2.079
|
||||
$atom:60_29 $mol:. @atom:60 0.0 -1.791 -3.686 3.717
|
||||
$atom:60_30 $mol:. @atom:60 0.0 -6.661 -3.312 -0.799
|
||||
$atom:60_31 $mol:. @atom:60 0.0 -4.422 -2.764 -1.206
|
||||
$atom:57_5 $mol:. @atom:57 0.0 -8.861 -2.101 -0.226
|
||||
$atom:58_3 $mol:. @atom:58 0.0 -7.457 -1.604 0.194
|
||||
$atom:60_32 $mol:. @atom:60 0.0 -8.826 -3.186 -0.048
|
||||
$atom:235_4 $mol:. @atom:235 0.0 -7.425 -0.036 0.256
|
||||
$atom:238_4 $mol:. @atom:238 0.0 -6.870 0.431 1.405
|
||||
$atom:236_4 $mol:. @atom:236 0.0 -8.004 0.653 -0.558
|
||||
$atom:229_4 $mol:. @atom:229 0.0 -7.168 1.765 1.912
|
||||
$atom:241_4 $mol:. @atom:241 0.0 -6.797 -0.317 2.080
|
||||
$atom:54_7 $mol:. @atom:54 0.0 -8.664 2.017 2.147
|
||||
$atom:54_8 $mol:. @atom:54 0.0 -6.545 2.857 1.036
|
||||
$atom:60_33 $mol:. @atom:60 0.0 -6.669 1.831 2.899
|
||||
$atom:60_34 $mol:. @atom:60 0.0 -9.114 1.252 2.800
|
||||
$atom:60_35 $mol:. @atom:60 0.0 -9.236 2.024 1.205
|
||||
$atom:60_36 $mol:. @atom:60 0.0 -8.786 3.001 2.625
|
||||
$atom:60_37 $mol:. @atom:60 0.0 -7.002 2.900 0.037
|
||||
$atom:60_38 $mol:. @atom:60 0.0 -5.460 2.706 0.913
|
||||
$atom:60_39 $mol:. @atom:60 0.0 -6.693 3.836 1.521
|
||||
$atom:60_40 $mol:. @atom:60 0.0 -9.602 -1.708 0.496
|
||||
$atom:60_41 $mol:. @atom:60 0.0 -7.328 -2.030 1.207
|
||||
$atom:57_6 $mol:. @atom:57 0.0 -10.877 -2.392 -1.741
|
||||
$atom:58_4 $mol:. @atom:58 0.0 -9.440 -1.848 -1.636
|
||||
$atom:60_42 $mol:. @atom:60 0.0 -11.441 -2.051 -0.857
|
||||
$atom:235_5 $mol:. @atom:235 0.0 -8.631 -2.553 -2.770
|
||||
$atom:238_5 $mol:. @atom:238 0.0 -8.499 -1.785 -3.863
|
||||
$atom:236_5 $mol:. @atom:236 0.0 -8.181 -3.684 -2.688
|
||||
$atom:229_5 $mol:. @atom:229 0.0 -7.938 -2.258 -5.119
|
||||
$atom:241_5 $mol:. @atom:241 0.0 -9.049 -0.943 -3.902
|
||||
$atom:54_9 $mol:. @atom:54 0.0 -8.792 -3.342 -5.780
|
||||
$atom:54_10 $mol:. @atom:54 0.0 -6.470 -2.687 -5.003
|
||||
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|
||||
$atom:60_44 $mol:. @atom:60 0.0 -9.825 -2.995 -5.943
|
||||
$atom:60_45 $mol:. @atom:60 0.0 -8.838 -4.264 -5.179
|
||||
$atom:60_46 $mol:. @atom:60 0.0 -8.360 -3.594 -6.761
|
||||
$atom:60_47 $mol:. @atom:60 0.0 -6.361 -3.605 -4.407
|
||||
$atom:60_48 $mol:. @atom:60 0.0 -5.850 -1.903 -4.541
|
||||
$atom:60_49 $mol:. @atom:60 0.0 -6.071 -2.887 -6.011
|
||||
$atom:60_50 $mol:. @atom:60 0.0 -11.356 -1.921 -2.619
|
||||
$atom:60_51 $mol:. @atom:60 0.0 -9.494 -0.756 -1.795
|
||||
$atom:57_7 $mol:. @atom:57 0.0 -12.476 -4.326 -2.296
|
||||
$atom:58_5 $mol:. @atom:58 0.0 -11.042 -3.918 -1.914
|
||||
$atom:60_52 $mol:. @atom:60 0.0 -12.606 -4.028 -3.347
|
||||
$atom:235_6 $mol:. @atom:235 0.0 -10.631 -4.675 -0.614
|
||||
$atom:238_6 $mol:. @atom:238 0.0 -9.796 -5.703 -0.861
|
||||
$atom:236_6 $mol:. @atom:236 0.0 -11.127 -4.453 0.474
|
||||
$atom:229_6 $mol:. @atom:229 0.0 -9.186 -6.529 0.183
|
||||
$atom:241_6 $mol:. @atom:241 0.0 -9.206 -5.554 -1.669
|
||||
$atom:54_11 $mol:. @atom:54 0.0 -10.225 -7.315 0.995
|
||||
$atom:54_12 $mol:. @atom:54 0.0 -8.204 -5.783 1.100
|
||||
$atom:60_53 $mol:. @atom:60 0.0 -8.602 -7.290 -0.368
|
||||
$atom:60_54 $mol:. @atom:60 0.0 -10.889 -7.898 0.339
|
||||
$atom:60_55 $mol:. @atom:60 0.0 -10.843 -6.658 1.625
|
||||
$atom:60_56 $mol:. @atom:60 0.0 -9.699 -8.020 1.659
|
||||
$atom:60_57 $mol:. @atom:60 0.0 -8.739 -5.060 1.735
|
||||
$atom:60_58 $mol:. @atom:60 0.0 -7.431 -5.245 0.530
|
||||
$atom:60_59 $mol:. @atom:60 0.0 -7.700 -6.510 1.757
|
||||
$atom:60_60 $mol:. @atom:60 0.0 -12.525 -5.430 -2.285
|
||||
$atom:60_61 $mol:. @atom:60 0.0 -10.438 -4.244 -2.777
|
||||
$atom:57_8 $mol:. @atom:57 0.0 -14.920 -4.584 -1.600
|
||||
$atom:58_6 $mol:. @atom:58 0.0 -13.632 -3.752 -1.465
|
||||
$atom:60_62 $mol:. @atom:60 0.0 -14.649 -5.586 -1.247
|
||||
$atom:235_7 $mol:. @atom:235 0.0 -13.893 -2.285 -1.914
|
||||
$atom:238_7 $mol:. @atom:238 0.0 -13.965 -1.422 -0.889
|
||||
$atom:236_7 $mol:. @atom:236 0.0 -13.974 -1.956 -3.082
|
||||
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|
||||
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|
||||
$atom:54_13 $mol:. @atom:54 0.0 -15.680 0.246 -1.480
|
||||
$atom:54_14 $mol:. @atom:54 0.0 -13.267 0.807 -1.893
|
||||
$atom:60_63 $mol:. @atom:60 0.0 -14.156 0.414 -0.002
|
||||
$atom:60_64 $mol:. @atom:60 0.0 -16.408 -0.251 -0.821
|
||||
$atom:60_65 $mol:. @atom:60 0.0 -15.849 -0.114 -2.507
|
||||
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|
||||
$atom:60_67 $mol:. @atom:60 0.0 -13.268 0.469 -2.940
|
||||
$atom:60_68 $mol:. @atom:60 0.0 -12.239 0.760 -1.513
|
||||
$atom:60_69 $mol:. @atom:60 0.0 -13.597 1.859 -1.881
|
||||
$atom:60_70 $mol:. @atom:60 0.0 -15.637 -4.195 -0.859
|
||||
$atom:60_71 $mol:. @atom:60 0.0 -13.362 -3.817 -0.395
|
||||
$atom:57_9 $mol:. @atom:57 0.0 -17.064 -5.395 -2.685
|
||||
$atom:58_7 $mol:. @atom:58 0.0 -15.684 -4.733 -2.934
|
||||
$atom:60_72 $mol:. @atom:60 0.0 -17.540 -4.759 -1.921
|
||||
$atom:235_8 $mol:. @atom:235 0.0 -14.870 -5.540 -3.996
|
||||
$atom:238_8 $mol:. @atom:238 0.0 -14.373 -4.756 -4.977
|
||||
$atom:236_8 $mol:. @atom:236 0.0 -14.748 -6.750 -3.981
|
||||
$atom:229_8 $mol:. @atom:229 0.0 -13.393 -5.268 -5.940
|
||||
$atom:241_8 $mol:. @atom:241 0.0 -14.174 -3.807 -4.679
|
||||
$atom:54_15 $mol:. @atom:54 0.0 -14.106 -6.091 -7.020
|
||||
$atom:54_16 $mol:. @atom:54 0.0 -12.175 -6.042 -5.407
|
||||
$atom:60_73 $mol:. @atom:60 0.0 -12.988 -4.367 -6.439
|
||||
$atom:60_74 $mol:. @atom:60 0.0 -14.926 -5.528 -7.494
|
||||
$atom:60_75 $mol:. @atom:60 0.0 -14.530 -7.019 -6.606
|
||||
$atom:60_76 $mol:. @atom:60 0.0 -13.392 -6.372 -7.812
|
||||
$atom:60_77 $mol:. @atom:60 0.0 -12.467 -7.007 -4.964
|
||||
$atom:60_78 $mol:. @atom:60 0.0 -11.600 -5.477 -4.663
|
||||
$atom:60_79 $mol:. @atom:60 0.0 -11.507 -6.251 -6.259
|
||||
$atom:60_80 $mol:. @atom:60 0.0 -17.675 -5.258 -3.598
|
||||
$atom:60_81 $mol:. @atom:60 0.0 -15.938 -3.724 -3.313
|
||||
$atom:57_10 $mol:. @atom:57 0.0 -18.749 -7.194 -2.096
|
||||
$atom:58_8 $mol:. @atom:58 0.0 -17.248 -6.883 -2.287
|
||||
$atom:60_82 $mol:. @atom:60 0.0 -19.267 -6.796 -2.989
|
||||
$atom:235_9 $mol:. @atom:235 0.0 -16.454 -7.269 -0.999
|
||||
$atom:238_9 $mol:. @atom:238 0.0 -15.335 -7.967 -1.254
|
||||
$atom:236_9 $mol:. @atom:236 0.0 -16.762 -6.899 0.120
|
||||
$atom:229_9 $mol:. @atom:229 0.0 -14.367 -8.387 -0.248
|
||||
$atom:241_9 $mol:. @atom:241 0.0 -15.240 -8.331 -2.192
|
||||
$atom:54_17 $mol:. @atom:54 0.0 -14.904 -9.451 0.715
|
||||
$atom:54_18 $mol:. @atom:54 0.0 -13.725 -7.242 0.549
|
||||
$atom:60_83 $mol:. @atom:60 0.0 -13.545 -8.861 -0.817
|
||||
$atom:60_84 $mol:. @atom:60 0.0 -15.290 -10.333 0.182
|
||||
$atom:60_85 $mol:. @atom:60 0.0 -15.717 -9.064 1.350
|
||||
$atom:60_86 $mol:. @atom:60 0.0 -14.087 -9.788 1.373
|
||||
$atom:60_87 $mol:. @atom:60 0.0 -14.468 -6.647 1.100
|
||||
$atom:60_88 $mol:. @atom:60 0.0 -13.139 -6.565 -0.089
|
||||
$atom:60_89 $mol:. @atom:60 0.0 -13.036 -7.679 1.290
|
||||
$atom:60_90 $mol:. @atom:60 0.0 -18.877 -8.292 -2.150
|
||||
$atom:60_91 $mol:. @atom:60 0.0 -16.939 -7.505 -3.147
|
||||
$atom:54_19 $mol:. @atom:54 0.0 -20.999 -7.206 -1.036
|
||||
$atom:58_9 $mol:. @atom:58 0.0 -19.540 -6.757 -0.843
|
||||
$atom:60_92 $mol:. @atom:60 0.0 -21.046 -8.300 -1.156
|
||||
$atom:60_93 $mol:. @atom:60 0.0 -21.439 -6.747 -1.936
|
||||
$atom:235_10 $mol:. @atom:235 0.0 -19.578 -5.207 -0.628
|
||||
$atom:238_10 $mol:. @atom:238 0.0 -19.061 -4.828 0.557
|
||||
$atom:236_10 $mol:. @atom:236 0.0 -20.185 -4.465 -1.375
|
||||
$atom:229_10 $mol:. @atom:229 0.0 -18.878 -3.426 0.994
|
||||
$atom:241_10 $mol:. @atom:241 0.0 -18.342 -5.450 0.901
|
||||
$atom:54_20 $mol:. @atom:54 0.0 -19.984 -2.451 0.558
|
||||
$atom:54_21 $mol:. @atom:54 0.0 -17.509 -2.857 0.610
|
||||
$atom:60_94 $mol:. @atom:60 0.0 -18.906 -3.470 2.099
|
||||
$atom:60_95 $mol:. @atom:60 0.0 -20.991 -2.887 0.651
|
||||
$atom:60_96 $mol:. @atom:60 0.0 -19.829 -2.132 -0.485
|
||||
$atom:60_97 $mol:. @atom:60 0.0 -19.955 -1.550 1.193
|
||||
$atom:60_98 $mol:. @atom:60 0.0 -17.405 -2.773 -0.482
|
||||
$atom:60_99 $mol:. @atom:60 0.0 -16.684 -3.475 0.993
|
||||
$atom:60_100 $mol:. @atom:60 0.0 -17.407 -1.849 1.043
|
||||
$atom:60_101 $mol:. @atom:60 0.0 -21.621 -6.939 -0.168
|
||||
$atom:60_102 $mol:. @atom:60 0.0 -19.160 -7.294 0.044
|
||||
}
|
||||
|
||||
# Note: You don't have to specify the charge in this example because we are
|
||||
# using the OPLSAA force-field which assigns charge according to
|
||||
# atom-type. Just leave these numbers as 0.00 for now.
|
||||
# Note: LAMMPS expects an integer in the 2nd column (the Molecule-ID number).
|
||||
# If we put "$mol:." there, moltemplate will generate this integer for you
|
||||
|
||||
write("Data Bond List") {
|
||||
$bond:id1 $atom:81_1 $atom:81_2
|
||||
$bond:id2 $atom:81_1 $atom:85_1
|
||||
$bond:id3 $atom:81_1 $atom:85_10
|
||||
$bond:id4 $atom:81_1 $atom:82_1
|
||||
$bond:id5 $atom:81_2 $atom:177_1
|
||||
$bond:id6 $atom:81_2 $atom:85_2
|
||||
$bond:id7 $atom:81_2 $atom:85_11
|
||||
$bond:id8 $atom:177_1 $atom:180_1
|
||||
$bond:id9 $atom:177_1 $atom:178_1
|
||||
$bond:id10 $atom:180_1 $atom:171_1
|
||||
$bond:id11 $atom:180_1 $atom:183_1
|
||||
$bond:id12 $atom:171_1 $atom:80_1
|
||||
$bond:id13 $atom:171_1 $atom:80_2
|
||||
$bond:id14 $atom:85_3 $atom:171_1
|
||||
$bond:id15 $atom:85_4 $atom:80_1
|
||||
$bond:id16 $atom:85_5 $atom:80_1
|
||||
$bond:id17 $atom:85_6 $atom:80_1
|
||||
$bond:id18 $atom:85_7 $atom:80_2
|
||||
$bond:id19 $atom:85_8 $atom:80_2
|
||||
$bond:id20 $atom:85_9 $atom:80_2
|
||||
$bond:id21 $atom:81_3 $atom:82_1
|
||||
$bond:id22 $atom:81_3 $atom:85_12
|
||||
$bond:id23 $atom:81_3 $atom:85_20
|
||||
$bond:id24 $atom:81_3 $atom:82_2
|
||||
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||||
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
$bond:id148 $atom:60_74 $atom:54_15
|
||||
$bond:id149 $atom:60_75 $atom:54_15
|
||||
$bond:id150 $atom:60_76 $atom:54_15
|
||||
$bond:id151 $atom:60_77 $atom:54_16
|
||||
$bond:id152 $atom:60_78 $atom:54_16
|
||||
$bond:id153 $atom:60_79 $atom:54_16
|
||||
$bond:id154 $atom:57_10 $atom:58_8
|
||||
$bond:id155 $atom:57_10 $atom:60_82
|
||||
$bond:id156 $atom:57_10 $atom:60_90
|
||||
$bond:id157 $atom:57_10 $atom:58_9
|
||||
$bond:id158 $atom:235_9 $atom:58_8
|
||||
$bond:id159 $atom:60_91 $atom:58_8
|
||||
$bond:id160 $atom:235_9 $atom:238_9
|
||||
$bond:id161 $atom:235_9 $atom:236_9
|
||||
$bond:id162 $atom:238_9 $atom:229_9
|
||||
$bond:id163 $atom:238_9 $atom:241_9
|
||||
$bond:id164 $atom:229_9 $atom:54_17
|
||||
$bond:id165 $atom:229_9 $atom:54_18
|
||||
$bond:id166 $atom:60_83 $atom:229_9
|
||||
$bond:id167 $atom:60_84 $atom:54_17
|
||||
$bond:id168 $atom:60_85 $atom:54_17
|
||||
$bond:id169 $atom:60_86 $atom:54_17
|
||||
$bond:id170 $atom:60_87 $atom:54_18
|
||||
$bond:id171 $atom:60_88 $atom:54_18
|
||||
$bond:id172 $atom:60_89 $atom:54_18
|
||||
$bond:id173 $atom:54_19 $atom:58_9
|
||||
$bond:id174 $atom:60_92 $atom:54_19
|
||||
$bond:id175 $atom:60_93 $atom:54_19
|
||||
$bond:id176 $atom:60_101 $atom:54_19
|
||||
$bond:id177 $atom:235_10 $atom:58_9
|
||||
$bond:id178 $atom:60_102 $atom:58_9
|
||||
$bond:id179 $atom:235_10 $atom:238_10
|
||||
$bond:id180 $atom:235_10 $atom:236_10
|
||||
$bond:id181 $atom:238_10 $atom:229_10
|
||||
$bond:id182 $atom:238_10 $atom:241_10
|
||||
$bond:id183 $atom:229_10 $atom:54_20
|
||||
$bond:id184 $atom:229_10 $atom:54_21
|
||||
$bond:id185 $atom:60_94 $atom:229_10
|
||||
$bond:id186 $atom:60_95 $atom:54_20
|
||||
$bond:id187 $atom:60_96 $atom:54_20
|
||||
$bond:id188 $atom:60_97 $atom:54_20
|
||||
$bond:id189 $atom:60_98 $atom:54_21
|
||||
$bond:id190 $atom:60_99 $atom:54_21
|
||||
$bond:id191 $atom:60_100 $atom:54_21
|
||||
}
|
||||
|
||||
} # end of "PolyNIPAM inherits OPLSAA" type definition
|
||||
|
||||
@ -1,24 +1,35 @@
|
||||
# The "oplsaa.lt" file contains force-field parameters, atom type definitions,
|
||||
# The oplsaa2024.lt file contains force-field parameters, atom type definitions,
|
||||
# partial charges, masses and bond-angle rules for the atoms in your system.
|
||||
|
||||
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt
|
||||
|
||||
# It defines these atom types:
|
||||
# atom-type charge mass btype epsilon sigma description
|
||||
# @atom:235 0.5 12.011 C~ 0.105 3.75 "C: C=O in amide. Acyl R in amides"
|
||||
# @atom:236 -0.5 15.999 O~ 0.21 2.96 "O: C=O in amide. is neutral - use"
|
||||
# @atom:237 -0.76 14.007 N~ 0.17 3.25 "N: primary amide. alkane params"
|
||||
# @atom:240 0.38 1.008 H~ 0 0 "H on N: primary amide"
|
||||
# @atom:279 0 1.008 HC 0.03 2.42 "AA H-alpha in aldehyde & formamide"
|
||||
# (Note: Future versions of OPLSAA might use different @atom type numbers.)
|
||||
|
||||
|
||||
_FAM inherits OPLSAA {
|
||||
|
||||
# atom-id mol-id atom-type charge X Y Z # comment
|
||||
|
||||
# atomID molID atomType charge coordX coordY coordZ
|
||||
write('Data Atoms') {
|
||||
$atom:C00 $mol @atom:177 0.00 0.100014490 0.490422099 0.0
|
||||
$atom:O01 $mol @atom:178 0.00 1.091153187 -0.250749643 0.0
|
||||
$atom:N02 $mol @atom:179 0.00 -1.121616690 -0.181085754 0.0
|
||||
$atom:H03 $mol @atom:182 0.00 -2.013715893 0.272535813 0.0
|
||||
$atom:H04 $mol @atom:182 0.00 -1.056768463 -1.190185868 0.0
|
||||
$atom:H05 $mol @atom:221 0.00 0.144676387 1.570292021 0.0
|
||||
$atom:C00 $mol @atom:235 0.00 0.100014490 0.490422099 0.0
|
||||
$atom:O01 $mol @atom:236 0.00 1.091153187 -0.250749643 0.0
|
||||
$atom:N02 $mol @atom:237 0.00 -1.121616690 -0.181085754 0.0
|
||||
$atom:H03 $mol @atom:240 0.00 -2.013715893 0.272535813 0.0
|
||||
$atom:H04 $mol @atom:240 0.00 -1.056768463 -1.190185868 0.0
|
||||
$atom:H05 $mol @atom:279 0.00 0.144676387 1.570292021 0.0
|
||||
}
|
||||
|
||||
# Note: You don't have to specify the charge in this example because we are
|
||||
# using the OPLSAA force-field which assigns charge according to
|
||||
# atom-type. Just leave these numbers as 0.00 for now.
|
||||
# Note: LAMMPS expects an integer in the 2nd column (the Molecule-ID number).
|
||||
# If we put "$mol" there, moltemplate will generate this integer for you
|
||||
# If we put "$mol" there, moltemplate will generate this integer for you
|
||||
|
||||
# A list of the bonds in the molecule:
|
||||
# BondID AtomID1 AtomID2
|
||||
@ -32,6 +43,6 @@ _FAM inherits OPLSAA {
|
||||
}
|
||||
|
||||
# In the "Data Bond List" section we don't have to specify the bond type.
|
||||
# The bond-type will be determined by the atom type (according to "oplsaa.lt")
|
||||
# Bond types will be determined by the atom type (according to oplsaa2024.lt).
|
||||
|
||||
}
|
||||
|
||||
@ -1,23 +1,25 @@
|
||||
# Use the OPLS-AA force field for all species.
|
||||
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa.lt
|
||||
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa2024.lt
|
||||
import PolyNIPAM.lt
|
||||
|
||||
# Define the SPC water and ions as in the OPLS-AA
|
||||
Ca inherits OPLSAA {
|
||||
write("Data Atoms"){
|
||||
$atom:a1 $mol:. @atom:354 0.0 0.00000 0.00000 0.000000
|
||||
$atom:a1 $mol:. @atom:412 0.0 0.00000 0.00000 0.000000
|
||||
}
|
||||
}
|
||||
|
||||
Cl inherits OPLSAA {
|
||||
write("Data Atoms"){
|
||||
$atom:a1 $mol:. @atom:344 0.0 0.00000 0.00000 0.000000
|
||||
$atom:a1 $mol:. @atom:401 0.0 0.00000 0.00000 0.000000
|
||||
}
|
||||
}
|
||||
|
||||
SPC inherits OPLSAA {
|
||||
write("Data Atoms"){
|
||||
$atom:O $mol:. @atom:76 0. 0.0000000 0.00000 0.000000
|
||||
$atom:H1 $mol:. @atom:77 0. 0.8164904 0.00000 0.5773590
|
||||
$atom:H2 $mol:. @atom:77 0. -0.8164904 0.00000 0.5773590
|
||||
$atom:O $mol:. @atom:9991 0. 0.0000000 0.00000 0.000000
|
||||
$atom:H1 $mol:. @atom:9990 0. 0.8164904 0.00000 0.5773590
|
||||
$atom:H2 $mol:. @atom:9990 0. -0.8164904 0.00000 0.5773590
|
||||
}
|
||||
write("Data Bond List") {
|
||||
$bond:OH1 $atom:O $atom:H1
|
||||
@ -38,37 +40,38 @@ write_once("Data Boundary"){
|
||||
0 26 zlo zhi
|
||||
}
|
||||
|
||||
# Define the input variables.
|
||||
write_once("In Init"){
|
||||
boundary p p p # "p p p" is the default. This line is optional.
|
||||
neighbor 3 bin # (This line is also optional in this example.)
|
||||
}
|
||||
|
||||
# Note: The lines below in the "In Run" section are often omitted.
|
||||
|
||||
# Run an NVT simulation.
|
||||
write_once("In Run"){
|
||||
# Input variables.
|
||||
variable run string sample01 # output name
|
||||
variable ts equal 2 # timestep
|
||||
variable temp equal 298.15 # equilibrium temperature
|
||||
variable p equal 1. # equilibrium pressure
|
||||
variable equi equal 30000 # equilibration steps
|
||||
|
||||
# PBC (set them before the creation of the box).
|
||||
boundary p p p
|
||||
neighbor 3 bin
|
||||
}
|
||||
|
||||
# Run an NVT simulation.
|
||||
write_once("In Run"){
|
||||
# Set the output.
|
||||
thermo 1000
|
||||
thermo_style custom step etotal evdwl ecoul elong ebond eangle edihed eimp pe ke temp press atoms vol density cpu
|
||||
thermo_style custom step etotal evdwl ecoul elong ebond eangle &
|
||||
edihed eimp pe ke temp press atoms vol density cpu
|
||||
thermo_modify flush yes
|
||||
compute pe1 all pe/atom pair
|
||||
dump TRJ all custom 100 \$\{run\}.dump id xu yu zu c_pe1
|
||||
|
||||
|
||||
# Minimise the input structure, just in case.
|
||||
minimize .01 .001 1000 100000
|
||||
write_data \$\{run\}.min
|
||||
|
||||
|
||||
# Set the constrains.
|
||||
group watergroup type @atom:76 @atom:77
|
||||
fix 0 watergroup shake 0.0001 10 0 b @bond:042_043 a @angle:043_042_043
|
||||
|
||||
group watergroup type @atom:9991 @atom:9990
|
||||
fix 0 watergroup shake 0.0001 10 0 b @bond:spcO_spcH a @angle:spcH_spcO_spcH
|
||||
|
||||
# Short annealing.
|
||||
timestep \$\{ts\}
|
||||
fix 1 all nvt temp \$\{temp\} \$\{temp\} \$(100*dt)
|
||||
@ -76,3 +79,4 @@ write_once("In Run"){
|
||||
run \$\{equi\}
|
||||
unfix 1
|
||||
}
|
||||
|
||||
|
||||
@ -1,8 +1,6 @@
|
||||
# Import the force field.
|
||||
import /usr/local/moltemplate/moltemplate/force_fields/oplsaa.lt
|
||||
import formamide.lt # after oplsaa.lt, as it depends on it.
|
||||
import formamide.lt # Defines "_FAM" and OPLSAA
|
||||
|
||||
# Create the input sample.
|
||||
# Distribute the molecules on a 5x5x5 cubic grid with spacing 4.6
|
||||
solv = new _FAM [5].move( 4.6, 0, 0)
|
||||
[5].move( 0, 4.6, 0)
|
||||
[5].move( 0, 0, 4.6)
|
||||
@ -15,8 +13,11 @@ write_once("Data Boundary") {
|
||||
-11.5 11.5 zlo zhi
|
||||
}
|
||||
|
||||
# Create an input deck for LAMMPS.
|
||||
write_once("In Init"){
|
||||
# Note: The lines below in the "In Run" section are often omitted.
|
||||
|
||||
write_once("In Run"){
|
||||
# Create an input deck for LAMMPS.
|
||||
# Run an NPT simulation.
|
||||
# Input variables.
|
||||
variable run string solv_01 # output name
|
||||
variable ts equal 1 # timestep
|
||||
@ -26,26 +27,20 @@ write_once("In Init"){
|
||||
variable equi equal 5000 # Equilibration steps
|
||||
variable prod equal 30000 # Production steps
|
||||
|
||||
# PBC (set them before the creation of the box).
|
||||
boundary p p p
|
||||
}
|
||||
|
||||
# Run an NPT simulation.
|
||||
write_once("In Run"){
|
||||
# Derived variables.
|
||||
variable tcouple equal \$\{ts\}*100
|
||||
variable pcouple equal \$\{ts\}*1000
|
||||
|
||||
# Output.
|
||||
thermo \$d
|
||||
thermo_style custom step etotal evdwl ecoul elong ebond eangle edihed eimp &
|
||||
ke pe temp press vol density cpu
|
||||
thermo_style custom step etotal evdwl ecoul elong ebond eangle &
|
||||
edihed eimp ke pe temp press vol density cpu
|
||||
thermo_modify flush yes
|
||||
|
||||
|
||||
# Trajectory.
|
||||
dump TRJ all dcd \$d \$\{run\}.dcd
|
||||
dump_modify TRJ unwrap yes
|
||||
|
||||
|
||||
# Thermalisation and relaxation, NPT ensemble.
|
||||
timestep \$\{ts\}
|
||||
fix NPT all npt temp \$\{temp\} \$\{temp\} \$\{tcouple\} iso \$p \$p \$\{pcouple\}
|
||||
@ -59,3 +54,4 @@ write_once("In Run"){
|
||||
run \$\{prod\}
|
||||
unfix NPT
|
||||
}
|
||||
|
||||
|
||||
@ -14,10 +14,7 @@ using ::testing::HasSubstr;
|
||||
using ::testing::StartsWith;
|
||||
|
||||
extern "C" {
|
||||
#ifdef LAMMPS_SMALLSMALL
|
||||
typedef int32_t step_t;
|
||||
typedef int32_t tag_t;
|
||||
#elif LAMMPS_SMALLBIG
|
||||
#if LAMMPS_SMALLBIG
|
||||
using step_t = int64_t;
|
||||
using tag_t = int32_t;
|
||||
#else
|
||||
|
||||
@ -127,15 +127,9 @@ TEST_F(LibraryProperties, thermo)
|
||||
const char *key = (const char *)lammps_last_thermo(lmp, "keyword", 0);
|
||||
EXPECT_THAT(key, StrEq("Step"));
|
||||
ival = *(int *)lammps_last_thermo(lmp, "type", 0);
|
||||
#if defined(LAMMPS_SMALLSMALL)
|
||||
EXPECT_EQ(ival, LAMMPS_INT);
|
||||
ival = *(int *)lammps_last_thermo(lmp, "data", 0);
|
||||
EXPECT_EQ(ival, 2);
|
||||
#else
|
||||
EXPECT_EQ(ival, LAMMPS_INT64);
|
||||
bval = *(bigint *)lammps_last_thermo(lmp, "data", 0);
|
||||
EXPECT_EQ(bval, 2);
|
||||
#endif
|
||||
|
||||
key = (const char *)lammps_last_thermo(lmp, "keyword", 1);
|
||||
EXPECT_THAT(key, StrEq("Temp"));
|
||||
@ -253,11 +247,7 @@ TEST_F(LibraryProperties, box)
|
||||
|
||||
TEST_F(LibraryProperties, setting)
|
||||
{
|
||||
#if defined(LAMMPS_SMALLSMALL)
|
||||
EXPECT_EQ(lammps_extract_setting(lmp, "bigint"), 4);
|
||||
#else
|
||||
EXPECT_EQ(lammps_extract_setting(lmp, "bigint"), 8);
|
||||
#endif
|
||||
#if defined(LAMMPS_BIGBIG)
|
||||
EXPECT_EQ(lammps_extract_setting(lmp, "tagint"), 8);
|
||||
EXPECT_EQ(lammps_extract_setting(lmp, "imageint"), 8);
|
||||
@ -375,15 +365,9 @@ TEST_F(LibraryProperties, global)
|
||||
char *c_ptr = (char *)lammps_extract_global(lmp, "units");
|
||||
EXPECT_THAT(c_ptr, StrEq("real"));
|
||||
|
||||
#if defined(LAMMPS_SMALLSMALL)
|
||||
EXPECT_EQ(lammps_extract_global_datatype(lmp, "ntimestep"), LAMMPS_INT);
|
||||
int *i_ptr = (int *)lammps_extract_global(lmp, "ntimestep");
|
||||
EXPECT_EQ((*i_ptr), 2);
|
||||
#else
|
||||
EXPECT_EQ(lammps_extract_global_datatype(lmp, "ntimestep"), LAMMPS_INT64);
|
||||
auto *b_ptr = (int64_t *)lammps_extract_global(lmp, "ntimestep");
|
||||
EXPECT_EQ((*b_ptr), 2);
|
||||
#endif
|
||||
|
||||
EXPECT_EQ(lammps_extract_global_datatype(lmp, "dt"), LAMMPS_DOUBLE);
|
||||
auto *d_ptr = (double *)lammps_extract_global(lmp, "dt");
|
||||
|
||||
@ -256,6 +256,41 @@ TEST_F(GroupTest, Molecular)
|
||||
command("group three include xxx"););
|
||||
}
|
||||
|
||||
TEST_F(GroupTest, Bitmap)
|
||||
{
|
||||
atomic_system();
|
||||
|
||||
BEGIN_HIDE_OUTPUT();
|
||||
command("group one region left");
|
||||
command("group two region right");
|
||||
command("group three empty");
|
||||
command("group four region left");
|
||||
command("group four region right");
|
||||
command("group six subtract four one");
|
||||
END_HIDE_OUTPUT();
|
||||
|
||||
int bm_one = group->get_bitmask_by_id(FLERR, "one", "unittest 1");
|
||||
int bm_two = group->get_bitmask_by_id(FLERR, "two", "unittest 2");
|
||||
int bm_three = group->get_bitmask_by_id(FLERR, "three", "unittest 3");
|
||||
int bm_four = group->get_bitmask_by_id(FLERR, "four", "unittest 4");
|
||||
int bm_six = group->get_bitmask_by_id(FLERR, "six", "unittest 6");
|
||||
int nlocal = lmp->atom->natoms;
|
||||
auto mask = lmp->atom->mask;
|
||||
|
||||
for (int i = 0; i < nlocal; ++i) {
|
||||
if ((mask[i] & bm_one) && (mask[i] & bm_two)) {
|
||||
EXPECT_NE((mask[i] & bm_four), 0);
|
||||
}
|
||||
if (mask[i] & bm_two) {
|
||||
EXPECT_NE((mask[i] & bm_six), 0);
|
||||
}
|
||||
EXPECT_EQ((mask[i] & bm_three), 0);
|
||||
}
|
||||
|
||||
TEST_FAILURE(".*ERROR: Group ID five requested by unittest 5 does not exist.*",
|
||||
group->get_bitmask_by_id(FLERR, "five", "unittest 5"););
|
||||
}
|
||||
|
||||
TEST_F(GroupTest, Dynamic)
|
||||
{
|
||||
atomic_system();
|
||||
|
||||
@ -2,7 +2,7 @@
|
||||
lammps_version: 17 Feb 2022
|
||||
tags: unstable
|
||||
date_generated: Fri Mar 18 22:17:36 2022
|
||||
epsilon: 2.5e-13
|
||||
epsilon: 1.0e-11
|
||||
skip_tests:
|
||||
prerequisites: ! |
|
||||
atom full
|
||||
|
||||
@ -85,11 +85,7 @@ TEST_F(LAMMPS_extract_global, units)
|
||||
TEST_F(LAMMPS_extract_global, ntimestep)
|
||||
{
|
||||
f_lammps_setup_extract_global();
|
||||
#ifdef LAMMPS_SMALLSMALL
|
||||
EXPECT_EQ(f_lammps_extract_global_ntimestep(), 0);
|
||||
#else
|
||||
EXPECT_EQ(f_lammps_extract_global_ntimestep_big(), 0l);
|
||||
#endif
|
||||
};
|
||||
|
||||
TEST_F(LAMMPS_extract_global, dt)
|
||||
@ -134,17 +130,10 @@ TEST_F(LAMMPS_extract_global, boxprops)
|
||||
TEST_F(LAMMPS_extract_global, atomprops)
|
||||
{
|
||||
f_lammps_setup_extract_global();
|
||||
#ifdef LAMMPS_SMALLSMALL
|
||||
EXPECT_EQ(f_lammps_extract_global_natoms(), 2);
|
||||
EXPECT_EQ(f_lammps_extract_global_nbonds(), 0);
|
||||
EXPECT_EQ(f_lammps_extract_global_nangles(), 0);
|
||||
EXPECT_EQ(f_lammps_extract_global_ndihedrals(), 0);
|
||||
#else
|
||||
EXPECT_EQ(f_lammps_extract_global_natoms_big(), 2l);
|
||||
EXPECT_EQ(f_lammps_extract_global_nbonds_big(), 0l);
|
||||
EXPECT_EQ(f_lammps_extract_global_nangles_big(), 0l);
|
||||
EXPECT_EQ(f_lammps_extract_global_ndihedrals_big(), 0l);
|
||||
#endif
|
||||
|
||||
EXPECT_EQ(f_lammps_extract_global_ntypes(), 1);
|
||||
EXPECT_EQ(f_lammps_extract_global_nlocal(), 2);
|
||||
@ -163,15 +152,8 @@ TEST_F(LAMMPS_extract_global, fullprops)
|
||||
if (!lammps_has_style(lmp, "atom", "full")) GTEST_SKIP();
|
||||
// This is not currently the world's most convincing test....
|
||||
f_lammps_setup_full_extract_global();
|
||||
#ifdef LAMMPS_SMALLSMALL
|
||||
EXPECT_EQ(f_lammps_extract_global_natoms(), 2);
|
||||
EXPECT_EQ(f_lammps_extract_global_nbonds(), 0);
|
||||
EXPECT_EQ(f_lammps_extract_global_nangles(), 0);
|
||||
EXPECT_EQ(f_lammps_extract_global_ndihedrals(), 0);
|
||||
#else
|
||||
EXPECT_EQ(f_lammps_extract_global_natoms_big(), 2l);
|
||||
EXPECT_EQ(f_lammps_extract_global_nbonds_big(), 0l);
|
||||
EXPECT_EQ(f_lammps_extract_global_nangles_big(), 0l);
|
||||
EXPECT_EQ(f_lammps_extract_global_ndihedrals_big(), 0l);
|
||||
#endif
|
||||
}
|
||||
|
||||
@ -98,11 +98,7 @@ TEST_F(LAMMPS_thermo, last_thermo)
|
||||
thermostr = (char *)f_lammps_last_thermo_string(6);
|
||||
EXPECT_STREQ(thermostr, "Press");
|
||||
free(thermostr);
|
||||
#if defined(LAMMPS_SMALLSMALL)
|
||||
EXPECT_EQ(f_lammps_last_thermo_type(1), multitype::LAMMPS_INT);
|
||||
#else
|
||||
EXPECT_EQ(f_lammps_last_thermo_type(1), multitype::LAMMPS_INT64);
|
||||
#endif
|
||||
EXPECT_EQ(f_lammps_last_thermo_int(1), 15);
|
||||
EXPECT_EQ(f_lammps_last_thermo_type(2), multitype::LAMMPS_DOUBLE);
|
||||
EXPECT_EQ(f_lammps_last_thermo_type(3), multitype::LAMMPS_DOUBLE);
|
||||
|
||||
@ -77,11 +77,7 @@ TEST_F(LAMMPS_properties, get_mpi_comm)
|
||||
|
||||
TEST_F(LAMMPS_properties, extract_setting)
|
||||
{
|
||||
#if defined(LAMMPS_SMALLSMALL)
|
||||
EXPECT_EQ(f_lammps_extract_setting("bigint"), 4);
|
||||
#else
|
||||
EXPECT_EQ(f_lammps_extract_setting("bigint"), 8);
|
||||
#endif
|
||||
#if defined(LAMMPS_BIGBIG)
|
||||
EXPECT_EQ(f_lammps_extract_setting("tagint"), 8);
|
||||
EXPECT_EQ(f_lammps_extract_setting("imageint"), 8);
|
||||
|
||||
@ -25,11 +25,7 @@ TEST(Types, ubuf)
|
||||
double buf[3];
|
||||
double d1 = 0.1;
|
||||
int i1 = -10;
|
||||
#if defined(LAMMPS_SMALLSMALL)
|
||||
bigint b1 = 2048;
|
||||
#else
|
||||
bigint b1 = (1L << 58) + (1L << 50);
|
||||
#endif
|
||||
buf[0] = d1;
|
||||
buf[1] = ubuf(i1).d;
|
||||
buf[2] = ubuf(b1).d;
|
||||
@ -58,11 +54,7 @@ TEST(Types, multitype)
|
||||
EXPECT_EQ(m[1].type, multitype::LAMMPS_INT);
|
||||
EXPECT_EQ(m[2].type, multitype::LAMMPS_DOUBLE);
|
||||
|
||||
#if defined(LAMMPS_SMALLSMALL)
|
||||
EXPECT_EQ(m[3].type, multitype::LAMMPS_INT);
|
||||
#else
|
||||
EXPECT_EQ(m[3].type, multitype::LAMMPS_INT64);
|
||||
#endif
|
||||
EXPECT_EQ(m[4].type, multitype::LAMMPS_INT);
|
||||
EXPECT_EQ(m[5].type, multitype::LAMMPS_DOUBLE);
|
||||
EXPECT_EQ(m[6].type, multitype::LAMMPS_NONE);
|
||||
@ -71,9 +63,7 @@ TEST(Types, multitype)
|
||||
EXPECT_EQ(m[1].data.i, i1);
|
||||
EXPECT_EQ(m[2].data.d, d1);
|
||||
|
||||
#if !defined(LAMMPS_SMALLSMALL)
|
||||
EXPECT_EQ(m[3].data.b, -((1L << 40) + (1L << 50)));
|
||||
#endif
|
||||
EXPECT_EQ(m[4].data.i, -1023);
|
||||
EXPECT_EQ(m[5].data.d, -2.225);
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user