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Merge branch 'master' into fix-ttm-grid

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Axel Kohlmeyer
2021-08-27 19:56:42 -04:00
parent e93ae9ba12 4d1a6cbd73
commit a66f3dfbdd
129 changed files with 4023 additions and 3006 deletions
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10
cmake/Modules/Tools.cmake
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@ -9,14 +9,16 @@ if(BUILD_TOOLS)
check_language(Fortran)
if(CMAKE_Fortran_COMPILER)
enable_language(Fortran)
add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f)
add_executable(chain.x ${LAMMPS_TOOLS_DIR}/chain.f90)
target_link_libraries(chain.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
install(TARGETS chain.x DESTINATION ${CMAKE_INSTALL_BINDIR})
add_executable(micelle2d.x ${LAMMPS_TOOLS_DIR}/micelle2d.f90)
target_link_libraries(micelle2d.x PRIVATE ${CMAKE_Fortran_IMPLICIT_LINK_LIBRARIES})
install(TARGETS chain.x micelle2d.x DESTINATION ${CMAKE_INSTALL_BINDIR})
else()
message(WARNING "No suitable Fortran compiler found, skipping build of 'chain.x'")
message(WARNING "No suitable Fortran compiler found, skipping build of 'chain.x' and 'micelle2d.x'")
endif()
else()
message(WARNING "CMake build doesn't support fortran, skipping build of 'chain.x'")
message(WARNING "CMake build doesn't support Fortran, skipping build of 'chain.x' and 'micelle2d.x'")
endif()
enable_language(C)

6
cmake/presets/clang.cmake
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@ -10,9 +10,9 @@ set(CMAKE_Fortran_COMPILER ${CLANG_FORTRAN} CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f95" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f95" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f95" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -Wextra -g -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_DEBUG "-Wall -Wextra -g" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELWITHDEBINFO "-Wall -Wextra -g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)

8
cmake/presets/gcc.cmake
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@ -1,4 +1,4 @@
# preset that will restore gcc/g++ with support for MPI and OpenMP (on Linux boxes)
# preset that will explicitly request gcc/g++ compilers with support for MPI and OpenMP
set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE)
set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
@ -15,9 +15,9 @@ set(CMAKE_C_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_C_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(MPI_Fortran "gfortran" CACHE STRING "" FORCE)
set(MPI_Fortran_COMPILER "mpifort" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -g" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_DEBUG "-Wall -g -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELWITHDEBINFO "-g -O2 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -std=f2003" CACHE STRING "" FORCE)
unset(HAVE_OMP_H_INCLUDE CACHE)
set(OpenMP_C "gcc" CACHE STRING "" FORCE)

1
doc/src/Build.rst
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@ -22,4 +22,5 @@ page.
Build_extras
Build_manual
Build_windows
Build_diskspace
Build_development

45
doc/src/Build_diskspace.rst Normal file
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@ -0,0 +1,45 @@
Notes for saving disk space when building LAMMPS from source
------------------------------------------------------------
LAMMPS is a large software project with a large number of source files,
extensive documentation, and a large collection of example files.
When downloading LAMMPS by cloning the
`git repository from GitHub <https://github.com/lammps/lammps>`_ this
will by default also download the entire commit history since September 2006.
Compiling LAMMPS will add the storage requirements of the compiled object
files and libraries to the tally.
In a user account on an HPC cluster with filesystem quotas or in other
environments with restricted disk space capacity it may be needed to
reduce the storage requirements. Here are some suggestions:
- Create a so-called shallow repository by cloning only the last commit
instead of the full project history by using ``git clone git@github.com:lammps/lammps --depth=1 --branch=master``.
This reduces the downloaded size to about half. With ``--depth=1`` it is not possible to check out different
versions/branches of LAMMPS, using ``--depth=1000`` will make multiple recent versions available at little
extra storage needs (the entire git history had nearly 30,000 commits in fall 2021).
- Download a tar archive from either the `download section on the LAMMPS homepage <https://www.lammps.org/download.html>`_
or from the `LAMMPS releases page on GitHub <https://github.com/lammps/lammps/releases>`_ these will not
contain the git history at all.
- Build LAMMPS without the debug flag (remove ``-g`` from the machine makefile or use ``-DCMAKE_BUILD_TYPE=Release``)
or use the ``strip`` command on the LAMMPS executable when no more debugging would be needed. The strip command
may also be applied to the LAMMPS shared library. The static library may be deleted entirely.
- Delete compiled object files and libraries after copying the LAMMPS executable to a permanent location.
When using the traditional build process, one may use ``make clean-<machine>`` or ``make clean-all``
to delete object files in the src folder. For CMake based builds, one may use ``make clean`` or just
delete the entire build folder.
- The folders containing the documentation tree (doc), the examples (examples) are not needed to build and
run LAMMPS and can be safely deleted. Some files in the potentials folder are large and may be deleted,
if not needed. The largest of those files (occupying about 120 MBytes combined) will only be downloaded on
demand, when the corresponding package is installed.
- When using the CMake build procedure, the compilation can be done on a (local) scratch storage that will not
count toward the quota. A local scratch file system may offer the additional benefit of speeding up creating
object files and linking with libraries compared to a networked file system. Also with CMake (and unlike with
the traditional make) it is possible to compile LAMMPS executables with different settings and packages included
from the same source tree since all the configuration information is stored in the build folder. So it is
not necessary to have multiple copies of LAMMPS.

5
doc/src/Intro_authors.rst
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@ -29,7 +29,7 @@ The following folks deserve special recognition. Many of the packages
they have written are unique for an MD code and LAMMPS would not be as
general-purpose as it is without their expertise and efforts.
* Metin Aktulga (MSU), REAXFF package for C version of ReaxFF
* Metin Aktulga (MSU), REAXFF package for C/C++ version of ReaxFF
* Mike Brown (Intel), GPU and INTEL packages
* Colin Denniston (U Western Ontario), LATBOLTZ package
* Georg Ganzenmuller (EMI), MACHDYN and SPH packages
@ -37,9 +37,10 @@ general-purpose as it is without their expertise and efforts.
* Reese Jones (Sandia) and colleagues, ATC package for atom/continuum coupling
* Christoph Kloss (DCS Computing), LIGGGHTS code for granular materials, built on top of LAMMPS
* Rudra Mukherjee (JPL), POEMS package for articulated rigid body motion
* Trung Ngyuen (Northwestern U), GPU and RIGID and BODY packages
* Trung Ngyuen (Northwestern U), GPU, RIGID, BODY, and DIELECTRIC packages
* Mike Parks (Sandia), PERI package for Peridynamics
* Roy Pollock (LLNL), Ewald and PPPM solvers
* Julien Tranchida (Sandia), SPIN package
* Christian Trott (Sandia), CUDA and KOKKOS packages
* Ilya Valuev (JIHT), AWPMD package for wave packet MD
* Greg Wagner (Northwestern U), MEAM package for MEAM potential

58
doc/src/Intro_features.rst
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@ -27,19 +27,19 @@ General features
* distributed memory message-passing parallelism (MPI)
* shared memory multi-threading parallelism (OpenMP)
* spatial decomposition of simulation domain for MPI parallelism
* particle decomposition inside of spatial decomposition for OpenMP parallelism
* particle decomposition inside of spatial decomposition for OpenMP and GPU parallelism
* GPLv2 licensed open-source distribution
* highly portable C++-11
* modular code with most functionality in optional packages
* only depends on MPI library for basic parallel functionality
* only depends on MPI library for basic parallel functionality, MPI stub for serial compilation
* other libraries are optional and only required for specific packages
* GPU (CUDA and OpenCL), Intel Xeon Phi, and OpenMP support for many code features
* GPU (CUDA, OpenCL, HIP, SYCL), Intel Xeon Phi, and OpenMP support for many code features
* easy to extend with new features and functionality
* runs from an input script
* syntax for defining and using variables and formulas
* syntax for looping over runs and breaking out of loops
* run one or multiple simulations simultaneously (in parallel) from one script
* build as library, invoke LAMMPS through library interface or provided Python wrapper
* build as library, invoke LAMMPS through library interface or provided Python wrapper or SWIG based wrappers
* couple with other codes: LAMMPS calls other code, other code calls LAMMPS, umbrella code calls both
.. _particle:
@ -57,9 +57,11 @@ Particle and model types
* granular materials
* coarse-grained mesoscale models
* finite-size spherical and ellipsoidal particles
* finite-size line segment (2d) and triangle (3d) particles
* finite-size line segment (2d) and triangle (3d) particles
* finite-size rounded polygons (2d) and polyhedra (3d) particles
* point dipole particles
* rigid collections of particles
* particles with magnetic spin
* rigid collections of n particles
* hybrid combinations of these
.. _ff:
@ -74,24 +76,28 @@ commands)
* pairwise potentials: Lennard-Jones, Buckingham, Morse, Born-Mayer-Huggins, Yukawa, soft, class 2 (COMPASS), hydrogen bond, tabulated
* charged pairwise potentials: Coulombic, point-dipole
* many-body potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB, SNAP, Streitz-Mintmire, 3-body polymorphic
* long-range interactions for charge, point-dipoles, and LJ dispersion: Ewald, Wolf, PPPM (similar to particle-mesh Ewald)
* many-body potentials: EAM, Finnis/Sinclair EAM, modified EAM (MEAM), embedded ion method (EIM), EDIP, ADP, Stillinger-Weber, Tersoff, REBO, AIREBO, ReaxFF, COMB, Streitz-Mintmire, 3-body polymorphic, BOP, Vashishta
* machine learning potentials: SNAP, GAP, ACE, N2P2, RANN, AGNI
* long-range interactions for charge, point-dipoles, and LJ dispersion: Ewald, Wolf, PPPM (similar to particle-mesh Ewald), MSM
* polarization models: :doc:`QEq <fix_qeq>`, :doc:`core/shell model <Howto_coreshell>`, :doc:`Drude dipole model <Howto_drude>`
* charge equilibration (QEq via dynamic, point, shielded, Slater methods)
* coarse-grained potentials: DPD, GayBerne, REsquared, colloidal, DLVO
* mesoscopic potentials: granular, Peridynamics, SPH
* mesoscopic potentials: granular, Peridynamics, SPH, mesoscopic tubular potential (MESONT)
* semi-empirical potentials: multi-ion generalized pseudopotential theory (MGPT), second moment tight binding + QEq (SMTB-Q), density functional tight-binding (LATTE)
* electron force field (eFF, AWPMD)
* bond potentials: harmonic, FENE, Morse, nonlinear, class 2, quartic (breakable)
* angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, class 2 (COMPASS)
* dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS
* improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS)
* bond potentials: harmonic, FENE, Morse, nonlinear, class 2, quartic (breakable), tabulated
* angle potentials: harmonic, CHARMM, cosine, cosine/squared, cosine/periodic, class 2 (COMPASS), tabulated
* dihedral potentials: harmonic, CHARMM, multi-harmonic, helix, class 2 (COMPASS), OPLS, tabulated
* improper potentials: harmonic, cvff, umbrella, class 2 (COMPASS), tabulated
* polymer potentials: all-atom, united-atom, bead-spring, breakable
* water potentials: TIP3P, TIP4P, SPC
* water potentials: TIP3P, TIP4P, SPC, SPC/E and variants
* interlayer potentials for graphene and analogues
* metal-organic framework potentials (QuickFF, MO-FF)
* implicit solvent potentials: hydrodynamic lubrication, Debye
* force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options
* force-field compatibility with common CHARMM, AMBER, DREIDING, OPLS, GROMACS, COMPASS options
* access to the `OpenKIM Repository <http://openkim.org>`_ of potentials via :doc:`kim command <kim_commands>`
* hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
* overlaid potentials: superposition of multiple pair potentials
* hybrid potentials: multiple pair, bond, angle, dihedral, improper potentials can be used in one simulation
* overlaid potentials: superposition of multiple pair potentials (including many-body) with optional scale factor
.. _create:
@ -124,9 +130,10 @@ Ensembles, constraints, and boundary conditions
* harmonic (umbrella) constraint forces
* rigid body constraints
* SHAKE bond and angle constraints
* Monte Carlo bond breaking, formation, swapping
* motion constraints to manifold surfaces
* Monte Carlo bond breaking, formation, swapping, template based reaction modeling
* atom/molecule insertion and deletion
* walls of various kinds
* walls of various kinds, static and moving
* non-equilibrium molecular dynamics (NEMD)
* variety of additional boundary conditions and constraints
@ -150,6 +157,7 @@ Diagnostics
^^^^^^^^^^^
* see various flavors of the :doc:`fix <fix>` and :doc:`compute <compute>` commands
* introspection command for system, simulation, and compile time settings and configurations
.. _output:
@ -164,8 +172,9 @@ Output
* parallel I/O of dump and restart files
* per-atom quantities (energy, stress, centro-symmetry parameter, CNA, etc)
* user-defined system-wide (log file) or per-atom (dump file) calculations
* spatial and time averaging of per-atom quantities
* time averaging of system-wide quantities
* custom partitioning (chunks) for binning, and static or dynamic grouping of atoms for analysis
* spatial, time, and per-chunk averaging of per-atom quantities
* time averaging and histogramming of system-wide quantities
* atom snapshots in native, XYZ, XTC, DCD, CFG formats
.. _replica1:
@ -178,7 +187,7 @@ Multi-replica models
* :doc:`parallel replica dynamics <prd>`
* :doc:`temperature accelerated dynamics <tad>`
* :doc:`parallel tempering <temper>`
* :doc:`path-integral MD <fix_pimd>`
* path-integral MD: `first variant <fix_pimd>`, `second variant <fix_ipi>`
* multi-walker collective variables with :doc:`Colvars <fix_colvars>` and :doc:`Plumed <fix_plumed>`
.. _prepost:
@ -210,11 +219,12 @@ page for details.
These are LAMMPS capabilities which you may not think of as typical
classical MD options:
* :doc:`static <balance>` and :doc:`dynamic load-balancing <fix_balance>`
* :doc:`static <balance>` and :doc:`dynamic load-balancing <fix_balance>`, optional with recursive bisectioning decomposition
* :doc:`generalized aspherical particles <Howto_body>`
* :doc:`stochastic rotation dynamics (SRD) <fix_srd>`
* :doc:`real-time visualization and interactive MD <fix_imd>`
* :doc:`real-time visualization and interactive MD <fix_imd>`, :doc:`built-in renderer for images and movies <dump_image>`
* calculate :doc:`virtual diffraction patterns <compute_xrd>`
* calculate :doc:`finite temperature phonon dispersion <fix_phonon>` and the :doc:`dynamical matrix of minimized structures <dynamical_matrix>`
* :doc:`atom-to-continuum coupling <fix_atc>` with finite elements
* coupled rigid body integration via the :doc:`POEMS <fix_poems>` library
* :doc:`QM/MM coupling <fix_qmmm>`

55
doc/src/Intro_opensource.rst
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@ -1,40 +1,61 @@
LAMMPS open-source license
--------------------------
LAMMPS is a freely-available open-source code, distributed under the
terms of the `GNU Public License Version 2 <gpl_>`_, which means you can
use or modify the code however you wish for your own purposes, but have
to adhere to certain rules when redistributing it or software derived
GPL version of LAMMPS
^^^^^^^^^^^^^^^^^^^^^
LAMMPS is an open-source code, available free-of-charge, and distributed
under the terms of the `GNU Public License Version 2 <gpl_>`_ (GPLv2),
which means you can use or modify the code however you wish for your own
purposes, but have to adhere to certain rules when redistributing it -
specifically in binary form - or are distributing software derived
from it or that includes parts of it.
LAMMPS comes with no warranty of any kind. As each source file states
in its header, it is a copyrighted code that is distributed free-of-
charge, under the terms of the `GNU Public License Version 2 <gpl_>`_
(GPLv2). This is often referred to as open-source distribution - see
`www.gnu.org <gnuorg_>`_ or `www.opensource.org <opensource_>`_. The
legal text of the GPL is in the LICENSE file included in the LAMMPS
distribution.
LAMMPS comes with no warranty of any kind.
As each source file states in its header, it is a copyrighted code, and
thus not in the public domain. For more information about open-source
software and open-source distribution, see `www.gnu.org <gnuorg_>`_
or `www.opensource.org <opensource_>`_. The legal text of the GPL as it
applies to LAMMPS is in the LICENSE file included in the LAMMPS distribution.
.. _gpl: https://github.com/lammps/lammps/blob/master/LICENSE
.. _lgpl: https://www.gnu.org/licenses/old-licenses/lgpl-2.1.html
.. _gnuorg: http://www.gnu.org
.. _opensource: http://www.opensource.org
Here is a summary of what the GPL means for LAMMPS users:
Here is a more specific summary of what the GPL means for LAMMPS users:
(1) Anyone is free to use, modify, or extend LAMMPS in any way they
(1) Anyone is free to use, copy, modify, or extend LAMMPS in any way they
choose, including for commercial purposes.
(2) If you **distribute** a modified version of LAMMPS, it must remain
open-source, meaning you distribute **all** of it under the terms of
the GPL. You should clearly annotate such a code as a derivative version
of LAMMPS.
open-source, meaning you are required to distribute **all** of it under
the terms of the GPL. You should clearly annotate such a modified code
as a derivative version of LAMMPS.
(3) If you release any code that includes or uses LAMMPS source code,
then it must also be open-sourced, meaning you distribute it under
the terms of the GPL.
the terms of the GPL. You may write code that interfaces LAMMPS to
a differently licensed library. In that case the code that provides
the interface must be licensed GPL, but not necessarily that library
unless you are distributing binaries that require the library to run.
(4) If you give LAMMPS files to someone else, the GPL LICENSE file and
source file headers (including the copyright and GPL notices) should
remain part of the code.
LGPL version of LAMMPS
^^^^^^^^^^^^^^^^^^^^^^
We occasionally make stable LAMMPS releases available under the `GNU
Lesser Public License v2.1 <lgpl_>`_. This is on request only and with
non-LGPL compliant files removed. This allows uses linking non-GPL
compatible software with the (otherwise unmodified) LAMMPS library
or loading it dynamically at runtime. Any **modifications** to
the LAMMPS code however, even with the LGPL licensed version, must still
be made available under the same open source terms as LAMMPS itself.

27
doc/src/Intro_overview.rst
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@ -10,24 +10,26 @@ conditions. It can model 2d or 3d systems with only a few particles
up to millions or billions.
LAMMPS can be built and run on a laptop or desktop machine, but is
designed for parallel computers. It will run on any parallel machine
that supports the `MPI <mpi_>`_ message-passing library. This includes
shared-memory boxes and distributed-memory clusters and
supercomputers.
designed for parallel computers. It will run in serial and on any
parallel machine that supports the `MPI <mpi_>`_ message-passing
library. This includes shared-memory boxes and distributed-memory
clusters and supercomputers. Parts of LAMMPS also support
`OpenMP multi-threading <omp_>`_, vectorization and GPU acceleration.
.. _mpi: https://en.wikipedia.org/wiki/Message_Passing_Interface
.. _lws: https://www.lammps.org
.. _omp: https://www.openmp.org
LAMMPS is written in C++ and requires a compiler that is at least
compatible with the C++-11 standard.
Earlier versions were written in F77 and F90. See the `History page
compatible with the C++-11 standard. Earlier versions were written in
F77, F90, and C++-98. See the `History page
<https://www.lammps.org/history.html>`_ of the website for details. All
versions can be downloaded from the `LAMMPS website <lws_>`_.
versions can be downloaded as source code from the `LAMMPS website
<lws_>`_.
LAMMPS is designed to be easy to modify or extend with new
capabilities, such as new force fields, atom types, boundary
conditions, or diagnostics. See the :doc:`Modify <Modify>` page for
more details.
LAMMPS is designed to be easy to modify or extend with new capabilities,
such as new force fields, atom types, boundary conditions, or
diagnostics. See the :doc:`Modify <Modify>` page for more details.
In the most general sense, LAMMPS integrates Newton's equations of
motion for a collection of interacting particles. A single particle
@ -47,4 +49,5 @@ MPI parallelization to partition the simulation domain into small
sub-domains of equal computational cost, one of which is assigned to
each processor. Processors communicate and store "ghost" atom
information for atoms that border their sub-domain. Multi-threading
parallelization with with particle-decomposition can be used in addition.
parallelization and GPU acceleration with with particle-decomposition
can be used in addition.

21
doc/src/Manual_version.rst
View File

@ -2,12 +2,21 @@ What does a LAMMPS version mean
-------------------------------
The LAMMPS "version" is the date when it was released, such as 1 May
2014. LAMMPS is updated continuously. Whenever we fix a bug or add a
feature, we release it in the next *patch* release, which are
typically made every couple of weeks. Info on patch releases are on
`this website page <https://www.lammps.org/bug.html>`_. Every few
months, the latest patch release is subjected to more thorough testing
and labeled as a *stable* version.
2014. LAMMPS is updated continuously and we aim to keep it working
correctly and reliably at all times. You can follow its development
in a public `git repository on GitHub <https://github.com/lammps/lammps>`_.
Whenever we fix a bug or update or add a feature, it will be merged into
the `master` branch of the git repository. When a sufficient number of
changes have accumulated *and* the software passes a set of automated
tests, we release it in the next *patch* release, which are made every
few weeks. Info on patch releases are on `this website page
<https://www.lammps.org/bug.html>`_.
Once or twice a year, only bug fixes and small, non-intrusive changes are
included for a period of time, and the code is subjected to more detailed
and thorough testing than the default automated testing. The latest
patch release after such a period is then labeled as a *stable* version.
Each version of LAMMPS contains all the features and bug-fixes up to
and including its version date.

2
doc/src/Tools.rst
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@ -172,7 +172,7 @@ Chris Lorenz (chris.lorenz at kcl.ac.uk), King's College London.
chain tool
----------------------
The file chain.f creates a LAMMPS data file containing bead-spring
The file chain.f90 creates a LAMMPS data file containing bead-spring
polymer chains and/or monomer solvent atoms. It uses a text file
containing chain definition parameters as an input. The created
chains and solvent atoms can strongly overlap, so LAMMPS needs to run

4
doc/src/fix_halt.rst
View File

@ -19,7 +19,7 @@ Syntax
bondmax = length of longest bond in the system (in length units)
tlimit = elapsed CPU time (in seconds)
diskfree = free disk space (in megabytes)
diskfree = free disk space (in MBytes)
v_name = name of :doc:`equal-style variable <variable>`
* operator = "<" or "<=" or ">" or ">=" or "==" or "!=" or "\|\^"
@ -81,7 +81,7 @@ the timer frequently across a large number of processors may be
non-negligible.
The *diskfree* attribute will check for available disk space (in
megabytes) on supported operating systems. By default it will
MBytes) on supported operating systems. By default it will
check the file system of the current working directory. This
can be changed with the optional *path* keyword, which will take
the path to a file or folder on the file system to be checked

2
doc/src/fix_qtb.rst
View File

@ -128,7 +128,7 @@ spectrum while consumes more memory. With fixed *f_max* and
:math:`\gamma`, *N_f* should be big enough to converge the classical
temperature :math:`T^{cl}` as a function of target quantum bath
temperature. Memory usage per processor could be from 10 to 100
Mbytes.
MBytes.
.. note::

5
doc/src/pair_airebo.rst
View File

@ -229,6 +229,11 @@ but you would need to create your own AIREBO or AIREBO-M potential file
with coefficients listed in the appropriate units, if your simulation
does not use "metal" units.
The pair styles provided here **only** support potential files parameterized
for the elements carbon and hydrogen (designated with "C" and "H" in the
*pair_coeff* command. Using potential files for other elements will trigger
an error.
Related commands
""""""""""""""""

23
doc/src/pair_snap.rst
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@ -135,7 +135,7 @@ with #) anywhere. Each non-blank non-comment line must contain one
keyword/value pair. The required keywords are *rcutfac* and
*twojmax*\ . Optional keywords are *rfac0*, *rmin0*,
*switchflag*, *bzeroflag*, *quadraticflag*, *chemflag*,
*bnormflag*, *wselfallflag*, and *chunksize*\ .
*bnormflag*, *wselfallflag*, *chunksize*, and *parallelthresh*\ .
The default values for these keywords are
@ -147,7 +147,8 @@ The default values for these keywords are
* *chemflag* = 0
* *bnormflag* = 0
* *wselfallflag* = 0
* *chunksize* = 4096
* *chunksize* = 32768
* *parallelthresh* = 8192
If *quadraticflag* is set to 1, then the SNAP energy expression includes
additional quadratic terms that have been shown to increase the overall
@ -188,14 +189,24 @@ corresponding *K*-vector of linear coefficients for element
which must equal the number of unique elements appearing in the LAMMPS
pair_coeff command, to avoid ambiguity in the number of coefficients.
The keyword *chunksize* is only applicable when using the
pair style *snap* with the KOKKOS package and is ignored otherwise.
This keyword controls
The keywords *chunksize* and *parallelthresh* are only applicable when
using the pair style *snap* with the KOKKOS package on GPUs and are
ignored otherwise.
The *chunksize* keyword controls
the number of atoms in each pass used to compute the bispectrum
components and is used to avoid running out of memory. For example
if there are 8192 atoms in the simulation and the *chunksize*
is set to 4096, the bispectrum calculation will be broken up
into two passes.
into two passes (running on a single GPU).
The *parallelthresh* keyword controls
a crossover threshold for performing extra parallelism. For
small systems, exposing additional parallism can be beneficial when
there is not enough work to fully saturate the GPU threads otherwise.
However, the extra parallelism also leads to more divergence
and can hurt performance when the system is already large enough to
saturate the GPU threads. Extra parallelism will be performed if the
*chunksize* (or total number of atoms per GPU) is smaller than
*parallelthresh*.
Detailed definitions for all the other keywords
are given on the :doc:`compute sna/atom <compute_sna_atom>` doc page.

3
doc/utils/sphinx-config/false_positives.txt
View File

@ -1174,6 +1174,7 @@ googletest
Gordan
Goudeau
GPa
GPL
gpu
gpuID
gpus
@ -1689,6 +1690,7 @@ Lett
Leuven
Leven
Lewy
LGPL
lgvdw
Liang
libatc
@ -1889,7 +1891,6 @@ maxX
Mayergoyz
Mayoral
mbt
Mbytes
MBytes
mc
McLachlan

1
lib/gpu/geryon/ocl_timer.h
View File

@ -139,7 +139,6 @@ class UCL_Timer {
cl_event start_event, stop_event;
cl_command_queue _cq;
double _total_time;
double t_factor;
bool _initialized;
bool has_measured_time;
};

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

@ -39,7 +39,7 @@ class UCL_D_Vec : public UCL_BaseMat {
};
typedef numtyp data_type;
UCL_D_Vec() : _cols(0), _row_bytes(0) {}
UCL_D_Vec() : _row_bytes(0), _cols(0) {}
~UCL_D_Vec() { _device_free(*this); }
/// Construct with n columns

12
lib/gpu/lal_lj_tip4p_long.cu
View File

@ -20,9 +20,13 @@
#define tagint int
#endif
#ifdef LAMMPS_BIGBIG
#include "inttypes.h"
#ifdef USE_OPENCL
#define tagint long
#else
#include "stdint.h"
#define tagint int64_t
#endif
#endif
#ifdef LAMMPS_SMALLSMALL
#define tagint int
#endif
@ -39,9 +43,13 @@ _texture( q_tex,int2);
#define tagint int
#endif
#ifdef LAMMPS_BIGBIG
#include "inttypes.h"
#ifdef USE_OPENCL
#define tagint long
#else
#include "stdint.h"
#define tagint int64_t
#endif
#endif
#ifdef LAMMPS_SMALLSMALL
#define tagint int
#endif

6
lib/gpu/lal_neighbor_gpu.cu
View File

@ -21,9 +21,13 @@
#define tagint int
#endif
#ifdef LAMMPS_BIGBIG
#include "inttypes.h"
#ifdef USE_OPENCL
#define tagint long
#else
#include "stdint.h"
#define tagint int64_t
#endif
#endif
#ifdef LAMMPS_SMALLSMALL
#define tagint int
#endif

2
lib/gpu/lal_precision.h
View File

@ -136,7 +136,7 @@ typedef int tagint;
#define OCL_INT_TYPE "-DLAMMPS_SMALLBIG"
#endif
#ifdef LAMMPS_BIGBIG
#include "inttypes.h"
#include "stdint.h"
typedef int64_t tagint;
#define OCL_INT_TYPE "-DLAMMPS_BIGBIG"
#endif

182
lib/mesont/CNTPot.f90
View File

@ -9,9 +9,9 @@
! the GNU General Public License.
!
! See the README file in the top-level LAMMPS directory.
!
!
! Contributing author: Alexey N. Volkov, UA, avolkov1@ua.edu
!-------------------------------------------------------------------------
!-------------------------------------------------------------------------
module CNTPot !*************************************************************************************
!
@ -21,34 +21,34 @@ module CNTPot !*****************************************************************
!
! Carbon nanotubes internal potentials:
! CNTSTRH0, harmonic stretching potential of type 0 with constant Young's modulus
! CNTSTRH1, harmonic stretching potential of type 1 with variable Young's modulus
! CNTSTRH1, harmonic stretching potential of type 1 with variable Young's modulus
! CNTSTRNH0, non-harmonic stretching with fracture potential of type 0
! CNTSTRNH1, non-harmonic stretching with fracture potential of type 1
! CNTBNDH, harmonic bending potential
! CNTBNDHB, harmonic bending-buckling potential
! CNTBNDHBF, harmonic bending-buckling potential with fracture
! CNTBNDHBF, harmonic bending-buckling potential with fracture
! CNTTRS, torsion potential
! CNTBRT, breathing potential
!
! The functional form and force constants of harmonic stretching, bending and
! torsion potentials are taken from:
! torsion potentials are taken from:
! L.V. Zhigilei, Ch. Wei, D. Srivastava, Phys. Rev. B 71, 165417 (2005)
!
! The model of stress-strain curve for the non-harmonic potential with fracture
! The model of stress-strain curve for the non-harmonic potential with fracture
! is developed and parameterized using the following constants
! -- Young's modulus
! -- Young's modulus
! -- maximum linear strain (only for the NH potential of type 1)
! -- tensile strength (or fracture strain)
! -- strain at failure (or fracture strain)
! -- maximum strain.
! All these parameters are assumed to be independent of CNT radius or chriality type.
! In this model, the true strain at failure CNTSTREft and true tensile strength
! In this model, the true strain at failure CNTSTREft and true tensile strength
! CNTSTRSft are slightly different from the imposed values CNTSTREf and CNTSTRSf.
!
! The non-harmonic stretching potentials of types 0 and 1 are different from
! The non-harmonic stretching potentials of types 0 and 1 are different from
! each other by the functional form of the stress-strain curve
!
! Different parameterizations of CNTSTRH0, CNTSTRNH0 and CNTSTRNH1 potentials can be chosen,
! Different parameterizations of CNTSTRH0, CNTSTRNH0 and CNTSTRNH1 potentials can be chosen,
! see subroutine CNTSTRSetParameterization
!
!---------------------------------------------------------------------------------------------------
@ -75,47 +75,47 @@ implicit none
integer(c_int), parameter :: CNTPOT_BFRACTURE = 5
! Harmonic stretching model (constant Young's modulus)
integer(c_int), parameter :: CNTSTRMODEL_H0 = 0
integer(c_int), parameter :: CNTSTRMODEL_H0 = 0
! Harmonic stretching model (Young's modulus depends on radius)
integer(c_int), parameter :: CNTSTRMODEL_H1 = 1
integer(c_int), parameter :: CNTSTRMODEL_H1 = 1
! Non-harmonic stretching with fracture, potential of type 0
integer(c_int), parameter :: CNTSTRMODEL_NH0F = 2
integer(c_int), parameter :: CNTSTRMODEL_NH0F = 2
! Non-harmonic stretching without fracture, potential of type 1
integer(c_int), parameter :: CNTSTRMODEL_NH1 = 3
integer(c_int), parameter :: CNTSTRMODEL_NH1 = 3
! Non-harmonic stretching with fracture, potential of type 1
integer(c_int), parameter :: CNTSTRMODEL_NH1F = 4
! Harmonic stretching model + axial buckling
integer(c_int), parameter :: CNTSTRMODEL_H1B = 5
integer(c_int), parameter :: CNTSTRMODEL_NH1F = 4
! Harmonic stretching model + axial buckling
integer(c_int), parameter :: CNTSTRMODEL_H1B = 5
! Harmonic stretching model + axial buckling + hysteresis
integer(c_int), parameter :: CNTSTRMODEL_H1BH = 6
integer(c_int), parameter :: CNTSTRMODEL_H1BH = 6
integer(c_int), parameter :: CNTBNDMODEL_H = 0 ! Harmonic bending model
integer(c_int), parameter :: CNTBNDMODEL_HB = 1 ! Harmonic bending - buckling model
integer(c_int), parameter :: CNTBNDMODEL_HBF = 2 ! Harmonic bending - buckling - fracture model
integer(c_int), parameter :: CNTBNDMODEL_HBH = 3 ! Harmonic bending - buckling + Hysteresis
integer(c_int), parameter :: CNTPOTNMAX = 4000 ! Maximum number of points in the interpolation tables
!---------------------------------------------------------------------------------------------------
! Parameters of potentials
!---------------------------------------------------------------------------------------------------
! Stretching potential
! Type of the bending model
integer(c_int) :: CNTSTRModel = CNTSTRMODEL_H1
! Type of parameterization
integer(c_int) :: CNTSTRParams = 0
integer(c_int) :: CNTSTRParams = 0
! Type of dependence of the Young's modulus on tube radius
integer(c_int) :: CNTSTRYMT = 0
integer(c_int) :: CNTSTRYMT = 0
! Parameters of non-harmonic potential and fracture model
real(c_double) :: CNTSTRR0 = 6.8d+00 ! Reference radius of nanotubes (A)
! (this parameter is not used for the model
! parametrization, but only for calculation of the
real(c_double) :: CNTSTRR0 = 6.8d+00 ! Reference radius of nanotubes (A)
! (this parameter is not used for the model
! parametrization, but only for calculation of the
! force constant in eV/A)
real(c_double) :: CNTSTRD0 = 3.4d+00 ! CNT wall thickness (A)
real(c_double) :: CNTSTREmin = -0.4d+00 ! Minimum strain in tabulated potential
real(c_double) :: CNTSTRD0 = 3.4d+00 ! CNT wall thickness (A)
real(c_double) :: CNTSTREmin = -0.4d+00 ! Minimum strain in tabulated potential
real(c_double) :: CNTSTREmax = 0.13d+00 ! Maximum strain in tabulated potential.
! Simultaneously, U=0 if E> CNTSTREmax
real(c_double) :: CNTSTREl = 5.0d-02 ! Maximum linear strain
@ -129,17 +129,17 @@ implicit none
real(c_double) :: CNTSTRSi ! Maximum stress (not used in the model) (Pa)
real(c_double) :: CNTSTRDf ! dF/dE at failure
real(c_double) :: CNTSTRAA, CNTSTRBB !
real(c_double) :: CNTSTRAA, CNTSTRBB !
real(c_double) :: CNTSTRAAA, CNTSTRBBB ! Auxiliary constants
real(c_double) :: CNTSTRUl, CNTSTRUf !
real(c_double) :: CNTSTRUl, CNTSTRUf !
! Axial buckling - hysteresis approach
real(c_double) :: CNTSTREc = -0.0142d+00 ! The minimum buckling strain
real(c_double) :: CNTSTREc1 = -0.04d+00 ! Critical axial buckling strain
real(c_double) :: CNTSTREc = -0.0142d+00 ! The minimum buckling strain
real(c_double) :: CNTSTREc1 = -0.04d+00 ! Critical axial buckling strain
real(c_double) :: CNTSTREc2 = -0.45d+00 ! Maximum buckling strain
! Bending potential
integer(c_int) :: CNTBNDModel = CNTBNDMODEL_H ! Type of the bending model
! Buckling model parameters
real(c_double) :: CNTBNDN = 1.0d+00 ! Buckling exponent
@ -149,9 +149,9 @@ implicit none
real(c_double) :: CNTBNDTF = M_PI * 120.0d+00 / 180.0d+00 ! Fracture buckling angle (rad)
real(c_double) :: CNTBNDN1
real(c_double) :: CNTBNDC2
contains !******************************************************************************************
!---------------------------------------------------------------------------------------------------
! Stretching potential
!---------------------------------------------------------------------------------------------------
@ -167,7 +167,7 @@ contains !**********************************************************************
!-------------------------------------------------------------------------------------------
integer(c_int), intent(in) :: PType
!-------------------------------------------------------------------------------------------
select case ( PType )
select case ( PType )
case ( 0 ) ! This parametrization is based on averaged exp. data of Ref. [1]
CNTSTRR0 = 6.8d+00 ! Ref. [1]
CNTSTRD0 = 3.4d+00 ! Ref. [1]
@ -180,7 +180,7 @@ contains !**********************************************************************
case ( 1 ) ! This parameterization is taken from Ref. [2] for (10,10) CNTs.
! These values are obtained in MD simulations with REBO potential.
! Values of Young's modulus, tensile strength and stress here
! are close to those obtained in Ref. [3] for pristine (defectless)
! are close to those obtained in Ref. [3] for pristine (defectless)
! (5,5) CNT in semi-empirical QM calculations based on PM3 model
CNTSTRR0 = 6.785d+00 ! Calculated with the usual formula for (10,10) CNT
CNTSTRD0 = 3.35d+00 ! Ref. [2]
@ -190,7 +190,7 @@ contains !**********************************************************************
CNTSTREf = 27.9d-02 ! Corresponds to maximum strain in Ref. [2]
CNTSTRS0 = 1.031e+12 ! Ref. [2]
CNTSTRSf = 148.5d+09 ! Corresponds to tensile strength in Ref. [2]
case ( 2 ) ! This parametrization is taken from Ref. [3] for (5,5) CNTs
case ( 2 ) ! This parametrization is taken from Ref. [3] for (5,5) CNTs
! with one atom vacancy defect obtained with the semi-empirical QM PM3 model
CNTSTRR0 = 3.43d+00 ! Ref. [3]
CNTSTRD0 = 3.4d+00 ! Ref. [3]
@ -246,14 +246,14 @@ contains !**********************************************************************
!
! Stretching without fracture, harmonic potential, with axial buckling without hysteresis
!
integer(c_int) function CNTSTRH1BCalc ( U, dUdL, L, R0, L0 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function CNTSTRH1BCalc ( U, dUdL, L, R0, L0 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! Young's modulus depends on R, see [4].
! Axial buckling without hysteresis.
!-------------------------------------------------------------------------------------------
!-------------------------------------------------------------------------------------------
real(c_double), intent(out) :: U, dUdL
real(c_double), intent(in) :: L, R0, L0
real(c_double) :: E, K, Kbcl, dUbcl, d, ud
real(c_double) :: E, K, Kbcl, dUbcl, d, ud
!-------------------------------------------------------------------------------------------
E = ( L - L0 ) / L0
K = 86.64d+00 + 100.56d+00 * R0
@ -266,7 +266,7 @@ contains !**********************************************************************
dUbcl = 0.5d+00 * L0 * K * CNTSTREc * CNTSTREc - Kbcl * CNTSTREc
U = Kbcl * E + dUbcl
dUdL = Kbcl / L0
CNTSTRH1BCalc = CNTPOT_STRETCHING
CNTSTRH1BCalc = CNTPOT_STRETCHING
else ! Return to harmonic potential
d = -0.0142794
dUdL = K * ( d + E - CNTSTREc2 )
@ -274,7 +274,7 @@ contains !**********************************************************************
Ud = 0.5d+00 * L0 * K * d * d
U = 0.5d+00 * L0 * (d+E-CNTSTREc2) * dUdL + dUbcl - Ud
CNTSTRH1BCalc = CNTPOT_STRETCHING
end if
end if
end function CNTSTRH1BCalc !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
@ -290,7 +290,7 @@ contains !**********************************************************************
!-------------------------------------------------------------------------------------------
real(c_double) :: E, K, dUbcl, Ebcl, Kbcl, Edu
real(c_double) :: C, DE, t
!-------------------------------------------------------------------------------------------
!-------------------------------------------------------------------------------------------
E = ( L - L0 ) / L0
K = 86.64d+00 + 100.56d+00 * R0
Kbcl = -10.98d+00 * L0
@ -319,7 +319,7 @@ contains !**********************************************************************
dUdL = Kbcl / L0
CNTSTRH1BHCalc = CNTPOT_SBUCKLING
Ebuc = 0.5d+00 * L0 * K * CNTSTREc1 * CNTSTREc1 - Kbcl * CNTSTREc1 - dUbcl
else ! Already buckled
else ! Already buckled
dUbcl = 0.5d+00 * L0 * K * CNTSTREc * CNTSTREc - Kbcl * CNTSTREc
U = Kbcl * E + dUbcl
dUdL = Kbcl / L0
@ -331,7 +331,7 @@ contains !**********************************************************************
U = 0.5d+00 * L0 * E * dUdL
CNTSTRH1BHCalc = CNTPOT_STRETCHING
Ebuc = 0.0d+00
end if
end if
end function CNTSTRH1BHCalc !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
@ -345,26 +345,26 @@ contains !**********************************************************************
!-------------------------------------------------------------------------------------------
E = ( L - L0 ) / L0
if ( E < CNTSTREf ) then
dUdL = ( CNTSTRAA - CNTSTRBB * E ) * E
dUdL = ( CNTSTRAA - CNTSTRBB * E ) * E
U = ( CNTSTRAAA - CNTSTRBBB * E ) * E * E
CNTSTRNH0FCalc = CNTPOT_STRETCHING
else
else
dUdL = 0.0d+00
U = 0.0d+00
CNTSTRNH0FCalc = CNTPOT_SFRACTURE
end if
U = L0 * R0 * U
dUdL = R0 * dUdL
dUdL = R0 * dUdL
end function CNTSTRNH0FCalc !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine CNTSTRNH0Init () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double) :: S
!-------------------------------------------------------------------------------------------
S = M_2PI * CNTSTRD0 * 1.0e-20 / K_MDFU
CNTSTRSl = CNTSTRS0 * CNTSTREl
CNTSTRF0 = CNTSTRS0 * S
CNTSTRFl = CNTSTRSl * S
CNTSTRFf = CNTSTRSf * S
CNTSTRF0 = CNTSTRS0 * S
CNTSTRFl = CNTSTRSl * S
CNTSTRFf = CNTSTRSf * S
CNTSTRAA = CNTSTRF0
CNTSTRBB = ( CNTSTRF0 * CNTSTREf - CNTSTRFf ) / ( CNTSTREf * CNTSTREf )
CNTSTRAAA= CNTSTRAA / 2.0d+00
@ -375,11 +375,11 @@ contains !**********************************************************************
CNTSTRSi = 0.0d+00
CNTSTRDf = 0.0d+00
end subroutine CNTSTRNH0Init !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! Stretching without fracture, non-harmonic potential of type 1
!
integer(c_int) function CNTSTRNH1Calc ( U, dUdL, L, R0, L0 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(out) :: U, dUdL
real(c_double), intent(in) :: L, R0, L0
@ -390,7 +390,7 @@ contains !**********************************************************************
dUdL = CNTSTRF0 * E
U = 0.5d+00 * E * dUdL
CNTSTRNH1Calc = CNTPOT_STRETCHING
else
else
DE = E - CNTSTREl
C = 1.0 + CNTSTRBB * DE
dUdL = CNTSTRFl + CNTSTRAA * ( 1.0d+00 - 1.0d+00 / C )
@ -398,13 +398,13 @@ contains !**********************************************************************
end if
CNTSTRNH1Calc = CNTPOT_STRETCHING
U = L0 * R0 * U
dUdL = R0 * dUdL
dUdL = R0 * dUdL
end function CNTSTRNH1Calc !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! Stretching with fracture, non-harmonic potential of type 1
!
integer(c_int) function CNTSTRNH1FCalc ( U, dUdL, L, R0, L0 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(out) :: U, dUdL
real(c_double), intent(in) :: L, R0, L0
@ -421,24 +421,24 @@ contains !**********************************************************************
dUdL = CNTSTRFl + CNTSTRAA * ( 1.0d+00 - 1.0d+00 / C )
U = CNTSTRUl + CNTSTRAAA * DE - CNTSTRBBB * dlog ( C )
CNTSTRNH1FCalc = CNTPOT_STRETCHING
else
else
dUdL = 0.0d+00
U = 0.0d+00
CNTSTRNH1FCalc = CNTPOT_SFRACTURE
end if
U = L0 * R0 * U
dUdL = R0 * dUdL
dUdL = R0 * dUdL
end function CNTSTRNH1FCalc !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine CNTSTRNH1Init () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double) :: S, C, E, t
integer(c_int) :: i, CaseID
!-------------------------------------------------------------------------------------------
S = M_2PI * CNTSTRD0 * 1.0e-20 / K_MDFU
CNTSTRSl = CNTSTRS0 * CNTSTREl
CNTSTRF0 = CNTSTRS0 * S
CNTSTRFl = CNTSTRSl * S
CNTSTRFf = CNTSTRSf * S
CNTSTRF0 = CNTSTRS0 * S
CNTSTRFl = CNTSTRSl * S
CNTSTRFf = CNTSTRSf * S
CNTSTRAA = ( CNTSTRFf - CNTSTRFl ) * ( CNTSTREf * CNTSTRF0 - CNTSTRFl ) / ( CNTSTREf * CNTSTRF0 - CNTSTRFf )
CNTSTRBB = CNTSTRF0 / CNTSTRAA
CNTSTRAAA= CNTSTRFl + CNTSTRAA
@ -449,7 +449,7 @@ contains !**********************************************************************
CNTSTRUl = 0.5d+00 * CNTSTRFl * CNTSTREl
CNTSTRUf = CNTSTRUl + ( CNTSTRFl + CNTSTRAA ) * ( CNTSTREf - CNTSTREl ) - CNTSTRAA * dlog ( C ) / CNTSTRBB
end subroutine CNTSTRNH1Init !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! General
!
@ -477,7 +477,7 @@ contains !**********************************************************************
CNTSTRCalc = CNTSTRH1BHCalc ( U, dUdL, L, R0, L0, ABF, Ebuc )
end select
end function CNTSTRCalc !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine CNTSTRInit ( STRModel, STRParams, YMType, Rref ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int), intent(in) :: STRModel, STRParams, YMType
real(c_double), intent(in) :: Rref
@ -498,13 +498,13 @@ contains !**********************************************************************
else
call CNTSTRNH1Init ()
end if
end if
end if
end subroutine CNTSTRInit !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!---------------------------------------------------------------------------------------------------
! Bending potentials
!---------------------------------------------------------------------------------------------------
subroutine BendingGradients ( K, G0, G1, G2, R0, R1, R2 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(inout) :: K
real(c_double), dimension(0:2), intent(inout) :: G0, G1, G2
@ -525,7 +525,7 @@ contains !**********************************************************************
G2 = G2 / L2
G1 = - ( G0 + G2 )
end subroutine BendingGradients !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function CNTBNDHCalc ( U, dUdC, C, R0, L0 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! Bending model of type 0:Harmonic bending potential.
!-------------------------------------------------------------------------------------------
@ -554,10 +554,10 @@ contains !**********************************************************************
! Check the condition for buckling
if ( C2 .ge. CNTBNDC2 ) then ! Buckling takes place
Theta= M_PI - acos ( C )
Kbnd = 63.8d+00 * R0**2.93d+00
Kbnd = 63.8d+00 * R0**2.93d+00
Kbcl = CNTBNDB * Kbnd / CNTBNDR
DUbcl= Kbnd * ( CNTBNDB * ( M_PI - 2.0d+00 * atan ( 2.0 * CNTBNDR / L0 ) ) - 0.5d+00 * L0 / CNTBNDR ) &
/ CNTBNDR
DUbcl= Kbnd * ( CNTBNDB * ( M_PI - 2.0d+00 * atan ( 2.0 * CNTBNDR / L0 ) ) - 0.5d+00 * L0 / CNTBNDR ) &
/ CNTBNDR
U = Kbcl * abs( Theta )**CNTBNDN - DUbcl
dUdC = Kbcl * CNTBNDN * abs( Theta )**CNTBNDN1 / sqrt ( 1.0d+00 - C * C )
CNTBNDHBCalc = CNTPOT_BBUCKLING
@ -568,7 +568,7 @@ contains !**********************************************************************
CNTBNDHBCalc = CNTPOT_BENDING
end if
end function CNTBNDHBCalc !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function CNTBNDHBFCalc ( U, dUdC, C, R0, L0 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(out) :: U, dUdC
real(c_double), intent(in) :: C, R0, L0
@ -586,10 +586,10 @@ contains !**********************************************************************
dUdC = 0.0d+00
CNTBNDHBFCalc = CNTPOT_BFRACTURE
else
Kbnd = 63.8d+00 * R0**2.93d+00
Kbnd = 63.8d+00 * R0**2.93d+00
Kbcl = CNTBNDB * Kbnd / CNTBNDR
DUbcl= Kbnd * ( CNTBNDB * ( M_PI - 2.0d+00 * atan ( 2.0 * CNTBNDR / L0 ) ) - &
0.5d+00 * L0 / CNTBNDR ) / CNTBNDR
0.5d+00 * L0 / CNTBNDR ) / CNTBNDR
U = Kbcl * abs ( Theta )**CNTBNDN - DUbcl
dUdC = Kbcl * CNTBNDN * abs ( Theta )**CNTBNDN1 / sqrt ( 1.0d+00 - C * C )
CNTBNDHBFCalc = CNTPOT_BBUCKLING
@ -601,7 +601,7 @@ contains !**********************************************************************
CNTBNDHBFCalc = CNTPOT_BENDING
end if
end function CNTBNDHBFCalc !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function CNTBNDHBHCalc ( U, dUdC, C, R0, L0, BBF, Ebuc ) !!!!!!!!!!!!!!!!!!!!
! Bending model of type 1: Harmonic bending potential with buckling with hysteresis approach.
!-------------------------------------------------------------------------------------------
@ -611,16 +611,16 @@ contains !**********************************************************************
real(c_double) :: E1, E2, C2, Kbnd, Kbcl,Theta,DUbcl, Ubcl, Cmin,Rmax
!-------------------------------------------------------------------------------------------
Rmax = 340.0d+00
Cmin = 1.0/(Rmax*Rmax)
Cmin = 1.0/(Rmax*Rmax)
E1 = 1.0d+00 - C
E2 = 1.0d+00 + C
E2 = 1.0d+00 + C
! Calculate the square of curvature
C2 = 4.0d+00 * E2 / ( L0 * L0 * E1 )
Theta = M_PI - acos ( C )
if ( C2 .lt. Cmin ) then ! Harmonic bending
if ( C2 .lt. Cmin ) then ! Harmonic bending
Kbnd = 2.0d+00 * ( 63.8d+00 * R0**2.93d+00 ) / L0
U = Kbnd * E2 / E1
dUdC = 2.0d+00 * Kbnd / ( E1 * E1 )
dUdC = 2.0d+00 * Kbnd / ( E1 * E1 )
CNTBNDHBHCalc = CNTPOT_BENDING
Ebuc = 0.0
else if ( C2 .ge. Cmin .and. C2 .lt. CNTBNDC2 ) then ! Potential depends on buckling flag of a node
@ -640,7 +640,7 @@ contains !**********************************************************************
dUdC = Kbcl * CNTBNDN * abs( Theta )**CNTBNDN1 / sqrt ( 1.0d+00 - C * C )
Ebuc = 0.0d+00
CNTBNDHBHCalc = CNTPOT_BBUCKLING
end if
end if
else ! Greater than buckling critical point
if ( BBF .eq. 1 ) then ! Already buckled
Theta= M_PI - acos ( C )
@ -653,7 +653,7 @@ contains !**********************************************************************
Ebuc = 0.0d00
CNTBNDHBHCalc = CNTPOT_BBUCKLING
else ! Newly buckled
Theta= M_PI - acos ( C )
Theta= M_PI - acos ( C )
Kbnd = 63.8d+00 * R0**2.93d+00
Kbcl = CNTBNDB * Kbnd / CNTBNDR
DUbcl= 2.0d+00*Kbnd * &
@ -666,11 +666,11 @@ contains !**********************************************************************
end if
end if
end function CNTBNDHBHCalc !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! General
!
integer(c_int) function CNTBNDCalc ( U, dUdC, C, R0, L0, BBF, Ebuc ) !!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(out) :: U, dUdC, Ebuc
real(c_double), intent(in) :: C, R0, L0
@ -688,7 +688,7 @@ contains !**********************************************************************
CNTBNDCalc = CNTBNDHBHCalc ( U, dUdC, C, R0, L0, BBF, Ebuc )
end select
end function CNTBNDCalc !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine CNTBNDInit ( BNDModel ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int), intent(in) :: BNDModel
real(c_double) :: A, E
@ -710,5 +710,5 @@ contains !**********************************************************************
call CNTSTRInit ( STRModel, STRParams, YMType, Rref )
call CNTBNDInit ( BNDModel )
end subroutine InitCNTPotModule !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
end module CNTPot !*********************************************************************************

100
lib/mesont/ExportCNT.f90
View File

@ -9,9 +9,9 @@
! the GNU General Public License.
!
! See the README file in the top-level LAMMPS directory.
!
!
! Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
!-------------------------------------------------------------------------
!-------------------------------------------------------------------------
module ExportCNT !**********************************************************************************
@ -28,122 +28,122 @@ contains
bind(c, name = "mesont_lib_InitCNTPotModule")
integer(c_int), intent(in) :: STRModel, STRParams, YMType, BNDModel
real(c_double), intent(in) :: Rref
call InitCNTPotModule(STRModel, STRParams, YMType, BNDModel, Rref)
endsubroutine
subroutine TPBInit_() &
bind(c, name = "mesont_lib_TPBInit")
call TPBInit()
endsubroutine
subroutine TPMInit_(M, N) &
bind(c, name = "mesont_lib_TPMInit")
integer(c_int), intent(in) :: M, N
call TPMInit(M, N)
endsubroutine
subroutine SetTablePath_(TPMFile_, N) &
bind(c, name = "mesont_lib_SetTablePath")
integer(c_int), intent(in) :: N
character(c_char), intent(in), dimension(N) :: TPMFile_
integer :: i
do i = 1, len(TPMFile)
if (i <= N) then
TPMFile(i:i) = TPMFile_(i)
else
else
TPMFile(i:i) = ' '
endif
enddo
endsubroutine
function get_R_ () &
bind(c, name = "mesont_lib_get_R")
real(c_double) :: get_R_
get_R_ = TPMR1
return
endfunction
subroutine TubeStretchingForceField_(U1, U2, F1, F2, S1, S2, X1, X2, R12, L12) &
bind(c, name = "mesont_lib_TubeStretchingForceField")
! Interaction energies associated with nodes X1 and X2
real(c_double), intent(inout) :: U1, U2
! Interaction energies associated with nodes X1 and X2
real(c_double), intent(inout) :: U1, U2
! Forces exerted on nodes X1 and X2
real(c_double), intent(inout), dimension(0:2) :: F1, F2
real(c_double), intent(inout), dimension(0:2) :: F1, F2
! Contributions of nodes X1 and X2 to the virial stress tensor
real(c_double), intent(inout), dimension(0:2,0:2) :: S1, S2
! Coordinates of the segment nodes
real(c_double), intent(in), dimension(0:2) :: X1, X2
real(c_double), intent(inout), dimension(0:2,0:2) :: S1, S2
! Coordinates of the segment nodes
real(c_double), intent(in), dimension(0:2) :: X1, X2
! Radius of a nanotube the segment (X1,X2) belongs to
real(c_double), intent(in) :: R12
real(c_double), intent(in) :: R12
! Equilibrium length of segment (X1,X2)
real(c_double), intent(in) :: L12
real(c_double), intent(in) :: L12
call TubeStretchingForceField(U1, U2, F1, F2, S1, S2, X1, X2, R12, L12)
endsubroutine
subroutine TubeBendingForceField_(U1, U2, U3, F1, F2, F3, S1, S2, S3, X1, X2, X3, R123, L123, BBF2) &
bind(c, name = "mesont_lib_TubeBendingForceField")
! Interaction energies associated with nodes X1, X2, and X3
real(c_double), intent(inout) :: U1, U2, U3
real(c_double), intent(inout) :: U1, U2, U3
! Forces exerted on nodes X1, X2, and X3
real(c_double), intent(inout), dimension(0:2) :: F1, F2, F3
real(c_double), intent(inout), dimension(0:2) :: F1, F2, F3
! Contributions of nodes X1, X2, and X3 to the virial stress tensor
real(c_double), intent(inout), dimension(0:2,0:2) :: S1, S2, S3
! Coordinates of nodes
real(c_double), intent(in), dimension(0:2) :: X1, X2, X3
real(c_double), intent(inout), dimension(0:2,0:2) :: S1, S2, S3
! Coordinates of nodes
real(c_double), intent(in), dimension(0:2) :: X1, X2, X3
! Radius of nanotube the segment (X1,X2) belongs to
real(c_double), intent(in) :: R123
real(c_double), intent(in) :: R123
! Equilibrium length of segment (X1,X2) and (X2,X3) (It is assumed to be the same for both segments)
real(c_double), intent(in) :: L123
real(c_double), intent(in) :: L123
integer(c_int), intent(inout) :: BBF2
call TubeBendingForceField(U1, U2, U3, F1, F2, F3, S1, S2, S3, X1, X2, X3, R123, L123, BBF2 )
endsubroutine
subroutine SegmentTubeForceField_(U1,U2,U,F1,F2,F,Fe,S1,S2,S,Se,X1,X2,R12,N,X,Xe,BBF,R,E1,E2,Ee,TPMType)&
bind(c, name = "mesont_lib_SegmentTubeForceField")
! Number of nodes in array X
integer(c_int), intent(in) :: N
integer(c_int), intent(in) :: N
! Interaction energies associated with nodes X1 and X2
real(c_double), intent(inout) :: U1, U2
real(c_double), intent(inout) :: U1, U2
! Interaction energies associated with nodes X
real(c_double), intent(inout), dimension(0:N-1) :: U
real(c_double), intent(inout), dimension(0:N-1) :: U
! Forces exerted on nodes X1 and X2
real(c_double), intent(inout), dimension(0:2) :: F1, F2
real(c_double), intent(inout), dimension(0:2) :: F1, F2
! Forces exerted on nodes X
real(c_double), intent(inout), dimension(0:2,0:N-1) :: F
real(c_double), intent(inout), dimension(0:2,0:N-1) :: F
! Force exerted on node Xe (can be updated only if Ee > 0)
real(c_double), intent(inout), dimension(0:2) :: Fe
real(c_double), intent(inout), dimension(0:2) :: Fe
! Contributions of nodes X1 and X2 to the virial stress tensor
real(c_double), intent(inout), dimension(0:2,0:2) :: S1, S2
real(c_double), intent(inout), dimension(0:2,0:2) :: S1, S2
! Contributions of nodes X to the virial stress tensor
real(c_double), intent(inout), dimension(0:2,0:2,0:N-1) :: S
real(c_double), intent(inout), dimension(0:2,0:2,0:N-1) :: S
! Contributions of node Xe to the virial stress tensor (can be updated only if Ee > 0)
real(c_double), intent(inout), dimension(0:2,0:2) :: Se
! Coordinates of the segment nodes
real(c_double), intent(in), dimension(0:2) :: X1, X2
real(c_double), intent(inout), dimension(0:2,0:2) :: Se
! Coordinates of the segment nodes
real(c_double), intent(in), dimension(0:2) :: X1, X2
! Radius of nanotube the segment (X1,X2) belongs to
real(c_double), intent(in) :: R12
real(c_double), intent(in) :: R12
! Coordinates of the nanotube nodes
real(c_double), intent(in), dimension(0:2,0:N-1) :: X
real(c_double), intent(in), dimension(0:2,0:N-1) :: X
! Additional node of the extended chain if Ee > 0
real(c_double), intent(in), dimension(0:2) :: Xe
! Bending buckling flags (BBF(i) = 1 in a case of buckling in node i)
integer(c_int), intent(in), dimension(0:N-1) :: BBF
real(c_double), intent(in), dimension(0:2) :: Xe
! Bending buckling flags (BBF(i) = 1 in a case of buckling in node i)
integer(c_int), intent(in), dimension(0:N-1) :: BBF
! Radius of nanotube X
real(c_double), intent(in) :: R
! E1 = 1 if the chain node 0 is a CNT end; E2 = 1 if the chain node N-1 is a CNT end;
integer(c_int), intent(in) :: E1, E2
real(c_double), intent(in) :: R
! E1 = 1 if the chain node 0 is a CNT end; E2 = 1 if the chain node N-1 is a CNT end;
integer(c_int), intent(in) :: E1, E2
! Parameter defining the type of the extended chain (0,1,2)
integer(c_int), intent(in) :: Ee
integer(c_int), intent(in) :: Ee
! Type of the tubular potential (0 or 1)
integer(c_int), intent(in) :: TPMType
integer(c_int), intent(in) :: TPMType
call SegmentTubeForceField(U1, U2, U, F1, F2, F, Fe, S1, S2, S, Se, X1, X2, R12, N, X, Xe, BBF, R, E1, E2, Ee, TPMType)
endsubroutine

20
lib/mesont/LinFun2.f90
View File

@ -9,9 +9,9 @@
! the GNU General Public License.
!
! See the README file in the top-level LAMMPS directory.
!
!
! Contributing author: Alexey N. Volkov, UA, avolkov1@ua.edu
!-------------------------------------------------------------------------
!-------------------------------------------------------------------------
module LinFun2 !************************************************************************************
!
@ -26,7 +26,7 @@ module LinFun2 !****************************************************************
!***************************************************************************************************
use iso_c_binding, only : c_int, c_double, c_char
implicit none
contains !******************************************************************************************
real(c_double) function CalcLinFun1_0 ( i, X, N, P, F ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@ -42,7 +42,7 @@ contains !**********************************************************************
A = 1.0d+00 - A0
CalcLinFun1_0 = A0 * F(i1) + A * F(i)
end function CalcLinFun1_0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine CalcLinFun1_1 ( S, Sx1, i, X, N, P, F, Fx ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(out) :: S, Sx1
integer(c_int), intent(in) :: i, N
@ -78,7 +78,7 @@ contains !**********************************************************************
G0 = B0 * F(i1,j1) + B * F(i1,j)
CalcLinFun2_0 = A0 * G0 + A * G
end function CalcLinFun2_0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine CalcLinFun2_1 ( S, Sx1, Sy1, i, j, X, Y, N1, N2, P1, P2, F, Fx, Fy ) !!!!!!!!!!!!
real(c_double), intent(out) :: S, Sx1, Sy1
integer(c_int), intent(in) :: i, j, N1, N2
@ -95,19 +95,19 @@ contains !**********************************************************************
A = 1.0d+00 - A0
B0 = ( P2(j) - Y ) / ( P2(j) - P2(j1) )
B = 1.0d+00 - B0
G = B0 * F(i,j1) + B * F(i,j)
G0 = B0 * F(i1,j1) + B * F(i1,j)
S = A0 * G0 + A * G
G = B0 * Fx(i,j1) + B * Fx(i,j)
G0 = B0 * Fx(i1,j1) + B * Fx(i1,j)
Sx1 = A0 * G0 + A * G
G = B0 * Fy(i,j1) + B * Fy(i,j)
G0 = B0 * Fy(i1,j1) + B * Fy(i1,j)
Sy1 = A0 * G0 + A * G
end subroutine CalcLinFun2_1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
end module LinFun2 !********************************************************************************

30
lib/mesont/Spline1.f90
View File

@ -9,9 +9,9 @@
! the GNU General Public License.
!
! See the README file in the top-level LAMMPS directory.
!
!
! Contributing author: Alexey N. Volkov, UA, avolkov1@ua.edu
!-------------------------------------------------------------------------
!-------------------------------------------------------------------------
module Spline1 !************************************************************************************
!
@ -64,7 +64,7 @@ contains !**********************************************************************
!-------------------------------------------------------------------------------------------
X(0) = F(0) / K1(0)
F(0) = - K2(0) / K1(0)
do i = 1, N - 1
do i = 1, N - 1
D = - ( K1(i) + F(i-1) * K0(i) )
X(i) = ( K0(i) * X(i-1) - F(i) ) / D
F(i) = K2(i) / D
@ -85,8 +85,8 @@ contains !**********************************************************************
K0(i) = P(i) - P(i-1)
K1(i) = ( F(i) - F(i-1) ) / K0(i)
end do
select case ( CL )
case (1)
select case ( CL )
case (1)
K1(0) = 2.0d+00 / 3.0d+00
K2(0) = 1.0d+00 / 3.0d+00
D (0) = 2 * ( K1(1) - M(0) ) / K0(1)
@ -98,14 +98,14 @@ contains !**********************************************************************
K1(0) = 1.0d+00
K2(0) = 0.0d+00
D(0) = 0.0d+00
end select
end select
Z = K1(N-1)
do i = 1, N - 2
do i = 1, N - 2
D(i) = 6.0d+00 * ( K1(i+1) - K1(i) )
K2(i) = K0(i+1)
K1(i) = 2.0d+00 * ( K2(i) + K0(i) )
end do
select case ( CR )
select case ( CR )
case (1)
D(N-1) = 2.0d+00 * ( M(N-1) - Z ) / K0(N-1)
K1(N-1) = 2.0d+00 / 3.0d+00
@ -118,14 +118,14 @@ contains !**********************************************************************
K1(N-1) = 1.0d+00
K0(N-1) = 0.0d+00
D(N-1) = 0.0d+00
end select
end select
call sprogonka3 ( N, K0, K1, K2, D, M )
end subroutine CreateSpline1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double) function CalcSpline1_0 ( i, X, N, P, F, M ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int), intent(in) :: i, N
real(c_double), intent(in) :: X
real(c_double), dimension(0:N-1), intent(in) :: P, F, M
real(c_double), dimension(0:N-1), intent(in) :: P, F, M
integer(c_int) :: j
real(c_double) :: HL, HR, H, H6, H26, HR2, HL2, HRH, HLH
!-------------------------------------------------------------------------------------------
@ -147,7 +147,7 @@ contains !**********************************************************************
real(c_double), intent(out) :: S, S1
integer(c_int), intent(in) :: i, N
real(c_double), intent(in) :: X
real(c_double), dimension(0:N-1), intent(in) :: P, F, M
real(c_double), dimension(0:N-1), intent(in) :: P, F, M
integer(c_int) :: j
real(c_double) :: HL, HR, H, H6, H26, HR2, HL2, HRH, HLH
!-------------------------------------------------------------------------------------------
@ -169,7 +169,7 @@ contains !**********************************************************************
real(c_double), intent(out) :: S, S1, S2
integer(c_int), intent(in) :: i, N
real(c_double), intent(in) :: X
real(c_double), dimension(0:N-1), intent(in) :: P, F, M
real(c_double), dimension(0:N-1), intent(in) :: P, F, M
integer(c_int) :: j
real(c_double) :: HL, HR, H, H6, H26, HR2, HL2, HRH, HLH
!-------------------------------------------------------------------------------------------
@ -185,7 +185,7 @@ contains !**********************************************************************
HRH = HR / H
S = ( M(j) * HR2 * HRH + M(i) * HL2 * HLH ) / 6.0d+00 + ( F(j) - M(j) * H26 ) * HRH + ( F(i) - M(i) * H26 ) * HLH
S1 = ( ( M(i) * HL2 - M(j) * HR2 ) / 2.0d+00 + F(i) - F(j) ) / H - H6 * ( M(i) - M(j) )
S2 = M(j) * HRH + M(i) * HLH
S2 = M(j) * HRH + M(i) * HLH
end subroutine CalcSpline1_2 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
end module Spline1 !********************************************************************************

26
lib/mesont/Spline2.f90
View File

@ -9,9 +9,9 @@
! the GNU General Public License.
!
! See the README file in the top-level LAMMPS directory.
!
!
! Contributing author: Alexey N. Volkov, UA, avolkov1@ua.edu
!-------------------------------------------------------------------------
!-------------------------------------------------------------------------
module Spline2 !************************************************************************************
!
@ -79,7 +79,7 @@ contains !**********************************************************************
Fxx = 0.0d+00
Fyy = 0.0d+00
Fxxyy = 0.0d+00
do II = 0, N2A
FF(0:N1-1) = F(0:N1-1,II)
MM(0) = Fxx(0,II)
@ -87,7 +87,7 @@ contains !**********************************************************************
call CreateSpline1 ( CL, CR, N1, P1, FF, MM, DD, K0, K1, K2 )
Fxx(0:N1-1,II) = MM(0:N1-1)
end do
do II = N2A + 1, N2 - 1
FF(0:N1-N1A-1) = F(N1A:N1-1,II)
MM(0) = Fxx(N1A,II)
@ -103,7 +103,7 @@ contains !**********************************************************************
call CreateSpline1 ( CD, CU, N2A + 1, P2, FF, MM, DD, K0, K1, K2 )
Fyy(II,0:N2A) = MM(0:N2A)
end do
do II = N1A, N1 - 1
MM(0) = Fyy(II,0)
MM(N-1) = Fyy(II,N2-1)
@ -111,19 +111,19 @@ contains !**********************************************************************
call CreateSpline1 ( CD, CU, N2, P2, FF, MM, DD, K0, K1, K2 )
Fyy(II,0:N2-1) = MM(0:N2-1)
end do
FF(0:N1-1) = Fyy(0:N1-1,0)
call CreateSpline1 ( 3, 3, N1, P1, FF, MM, DD, K0, K1, K2 )
Fxxyy(0:N1-1,0) = MM(0:N1-1)
FF(0:N1A) = Fyy(0:N1A,N2A)
call CreateSpline1 ( 3, 3, N1A + 1, P1, FF, MM, DD, K0, K1, K2 )
Fxxyy(0:N1A,N2A) = MM(0:N1A)
FF(0:N1-N1A-1) = Fyy(N1A:N1-1,N2-1 )
call CreateSpline1 ( 3, 3, N1-N1A, P1, FF, MM, DD, K0, K1, K2 )
Fxxyy(N1A:N1-1,N2-1) = MM(0:N1-N1A-1)
do II = 1, N1A
MM(0) = Fxxyy(II,0)
MM(N2A) = Fxxyy(II,N2A)
@ -131,7 +131,7 @@ contains !**********************************************************************
call CreateSpline1 ( 2 , 2, N2A + 1, P2, FF, MM, DD, K0, K1, K2 )
Fxxyy(II,0:N2A) = MM(0:N2A)
end do
do II = N1A + 1, N1 - 2
MM(0) = Fxxyy(II,0)
MM(N-1) = Fxxyy(II,N2-1)
@ -139,9 +139,9 @@ contains !**********************************************************************
call CreateSpline1 ( 2 , 2, N2, P2, FF, MM, DD, K0, K1, K2 )
Fxxyy(II,0:N2-1) = MM(0:N2-1)
end do
end subroutine CreateSpline2Ext !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double) function CalcSpline2_0 ( i, j, X, Y, N1, N2, P1, P2, F, Fxx, Fyy, Fxxyy ) !!!
integer(c_int), intent(in) :: i, j, N1, N2
real(c_double), intent(in) :: X, Y
@ -182,5 +182,5 @@ contains !**********************************************************************
call ValueSpline1_1 ( S, Sx1, X, P1(i), P1(i1), Gy_0, Gy_1,Gxxy_0, Gxxy_1, P1(i) - P1(i1) )
Sy1 = ValueSpline1_0 ( X, P1(i), P1(i1), Gyy_0, Gyy_1,Gxxyy_0, Gxxyy_1, P1(i) - P1(i1) )
end subroutine CalcSpline2_1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
end module Spline2 !********************************************************************************

140
lib/mesont/TPMForceField.f90
View File

@ -9,9 +9,9 @@
! the GNU General Public License.
!
! See the README file in the top-level LAMMPS directory.
!
!
! Contributing author: Alexey N. Volkov, UA, avolkov1@ua.edu
!-------------------------------------------------------------------------
!-------------------------------------------------------------------------
module TPMForceField !******************************************************************************
!
@ -32,32 +32,32 @@ use iso_c_binding, only : c_int, c_double, c_char
implicit none
contains !******************************************************************************************
subroutine TubeStretchingForceField ( U1, U2, F1, F2, S1, S2, X1, X2, R12, L12 ) !!!!!!!!!!!
! Interaction energies associated with nodes X1 and X2
real(c_double), intent(inout) :: U1, U2
real(c_double), intent(inout) :: U1, U2
! Forces exerted on nodes X1 and X2
real(c_double), intent(inout), dimension(0:2) :: F1, F2
real(c_double), intent(inout), dimension(0:2) :: F1, F2
! Contributions of nodes X1 and X2 to the virial stress tensor
real(c_double), intent(inout), dimension(0:2,0:2) :: S1, S2
! Coordinates of the segment nodes
real(c_double), intent(in), dimension(0:2) :: X1, X2
real(c_double), intent(inout), dimension(0:2,0:2) :: S1, S2
! Coordinates of the segment nodes
real(c_double), intent(in), dimension(0:2) :: X1, X2
! Radius of a nanotube the segment (X1,X2) belongs to
real(c_double), intent(in) :: R12
real(c_double), intent(in) :: R12
! Equilibrium length of segment (X1,X2)
real(c_double), intent(in) :: L12
real(c_double), intent(in) :: L12
!-------------------------------------------------------------------------------------------
integer(c_int) :: ii, jj, Event
real(c_double) :: U, F, LL, S, Ubcl
real(c_double), dimension(0:2) :: DX, FF
!-------------------------------------------------------------------------------------------
DX = X2 - X1
DX = X2 - X1
LL = S_V3norm3 ( DX )
Event = CNTSTRCalc ( U, F, LL, R12, L12, 0, Ubcl )
U = U / 2.0d+00
FF = DX * F / LL
F1 = F1 + FF
U1 = U1 + U
@ -68,25 +68,25 @@ contains !**********************************************************************
do ii = 0, 2
do jj = 0, 2
S = - 0.5d+00 * DX(ii) * FF(jj)
S1(ii,jj) = S1(ii,jj) + S
S2(ii,jj) = S2(ii,jj) + S
S1(ii,jj) = S1(ii,jj) + S
S2(ii,jj) = S2(ii,jj) + S
end do
end do
end subroutine TubeStretchingForceField !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine TubeBendingForceField ( U1, U2, U3, F1, F2, F3, S1, S2, S3, X1, X2, X3, R123, L123, BBF2 )
subroutine TubeBendingForceField ( U1, U2, U3, F1, F2, F3, S1, S2, S3, X1, X2, X3, R123, L123, BBF2 )
! Interaction energies associated with nodes X1, X2, and X3
real(c_double), intent(inout) :: U1, U2, U3
real(c_double), intent(inout) :: U1, U2, U3
! Forces exerted on nodes X1, X2, and X3
real(c_double), intent(inout), dimension(0:2) :: F1, F2, F3
real(c_double), intent(inout), dimension(0:2) :: F1, F2, F3
! Contributions of nodes X1, X2, and X3 to the virial stress tensor
real(c_double), intent(inout), dimension(0:2,0:2) :: S1, S2, S3
! Coordinates of nodes
real(c_double), intent(in), dimension(0:2) :: X1, X2, X3
real(c_double), intent(inout), dimension(0:2,0:2) :: S1, S2, S3
! Coordinates of nodes
real(c_double), intent(in), dimension(0:2) :: X1, X2, X3
! Radius of nanotube the segment (X1,X2) belongs to
real(c_double), intent(in) :: R123
real(c_double), intent(in) :: R123
! Equilibrium length of segment (X1,X2) and (X2,X3) (It is assumed to be the same for both segments)
real(c_double), intent(in) :: L123
real(c_double), intent(in) :: L123
integer(c_int), intent(inout) :: BBF2
!-------------------------------------------------------------------------------------------
integer(c_int) :: ii, jj, Event
@ -105,9 +105,9 @@ contains !**********************************************************************
U = U / 4.0d+00
F = - F
F1 = F1 + G0 * F
F2 = F2 + G1 * F
F3 = F3 + G2 * F
F1 = F1 + G0 * F
F2 = F2 + G1 * F
F3 = F3 + G2 * F
U1 = U1 + U
U2 = U2 + 2.0d+00 * U
@ -117,16 +117,16 @@ contains !**********************************************************************
do ii = 0, 2
do jj = 0, 2
S = 0.5d+00 * ( X1(ii) - X2(ii) ) * G0(jj)
S1(ii,jj) = S1(ii,jj) + S
S2(ii,jj) = S2(ii,jj) + S
S1(ii,jj) = S1(ii,jj) + S
S2(ii,jj) = S2(ii,jj) + S
S = 0.5d+00 * ( X3(ii) - X2(ii) ) * G2(jj)
S3(ii,jj) = S3(ii,jj) + S
S2(ii,jj) = S2(ii,jj) + S
S3(ii,jj) = S3(ii,jj) + S
S2(ii,jj) = S2(ii,jj) + S
end do
end do
end subroutine TubeBendingForceField !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! The purpose of subroutine SegmentTubeForceField is to calculate interaction forces
! The purpose of subroutine SegmentTubeForceField is to calculate interaction forces
! (as well potential energies and components of the virial stress tensor) between a segment
! (X1,X2) and a sequence of segments which belongs to a single CNT.
@ -134,7 +134,7 @@ contains !**********************************************************************
! neighbor list of segment (X1,X2).
! The nodes in X are assumed to be ordered according to their physical appearance in the nanotube.
! It means that (X(i),X(i+1)) are either correspond to a real segment or divided by segments
! It means that (X(i),X(i+1)) are either correspond to a real segment or divided by segments
! that do not belong to a nanotube.
! Concept of the extended chain:
@ -143,45 +143,45 @@ contains !**********************************************************************
! If node Xe follows XN and Xe is the nanotube end, then the extended chain is (X1,...,XN,Xe) and Ee = 2.
! In all other cases, the extended chain coincides with (X1,...,XN) and Ee = 0.
! If the extended chain contains additional node, then non-zero force is exerted on this node.
subroutine SegmentTubeForceField ( U1, U2, U, F1, F2, F, Fe, S1, S2, S, Se, X1, X2, R12, N, X, Xe,&
BBF, R, E1, E2, Ee, TPMType )
BBF, R, E1, E2, Ee, TPMType )
! Number of nodes in array X
integer(c_int), intent(in) :: N
! Interaction energies associated with nodes X1 and X2
real(c_double), intent(inout) :: U1, U2
integer(c_int), intent(in) :: N
! Interaction energies associated with nodes X1 and X2
real(c_double), intent(inout) :: U1, U2
! Interaction energies associated with nodes X
real(c_double), intent(inout), dimension(0:N-1) :: U
real(c_double), intent(inout), dimension(0:N-1) :: U
! Forces exerted on nodes X1 and X2
real(c_double), intent(inout), dimension(0:2) :: F1, F2
real(c_double), intent(inout), dimension(0:2) :: F1, F2
! Forces exerted on nodes X
real(c_double), intent(inout), dimension(0:2,0:N-1) :: F
real(c_double), intent(inout), dimension(0:2,0:N-1) :: F
! Force exerted on node Xe (can be updated only if Ee > 0)
real(c_double), intent(inout), dimension(0:2) :: Fe
real(c_double), intent(inout), dimension(0:2) :: Fe
! Contributions of nodes X1 and X2 to the virial stress tensor
real(c_double), intent(inout), dimension(0:2,0:2) :: S1, S2
real(c_double), intent(inout), dimension(0:2,0:2) :: S1, S2
! Contributions of nodes X to the virial stress tensor
real(c_double), intent(inout), dimension(0:2,0:2,0:N-1) :: S
real(c_double), intent(inout), dimension(0:2,0:2,0:N-1) :: S
! Contributions of node Xe to the virial stress tensor (can be updated only if Ee > 0)
real(c_double), intent(inout), dimension(0:2,0:2) :: Se
! Coordinates of the segment nodes
real(c_double), intent(in), dimension(0:2) :: X1, X2
real(c_double), intent(inout), dimension(0:2,0:2) :: Se
! Coordinates of the segment nodes
real(c_double), intent(in), dimension(0:2) :: X1, X2
! Radius of a nanotube the segment (X1,X2) belongs to
real(c_double), intent(in) :: R12
real(c_double), intent(in) :: R12
! Coordinates of the nanotube nodes
real(c_double), intent(in), dimension(0:2,0:N-1) :: X
real(c_double), intent(in), dimension(0:2,0:N-1) :: X
! Additional node of the extended chain if Ee > 0
real(c_double), intent(in), dimension(0:2) :: Xe
real(c_double), intent(in), dimension(0:2) :: Xe
! Bending buckling flags (BBF(i) = 1 in a case of buckling in node i)
integer(c_int), intent(in), dimension(0:N-1) :: BBF
integer(c_int), intent(in), dimension(0:N-1) :: BBF
! Radius of nanotube X
real(c_double), intent(in) :: R
real(c_double), intent(in) :: R
! E1 = 1 if the chain node 0 is a CNT end; E1 = 2 if the chain node N-1 is a CNT end
integer(c_int), intent(in) :: E1, E2
integer(c_int), intent(in) :: E1, E2
! Parameter defining the type of the extended chain (0,1,2)
integer(c_int), intent(in) :: Ee
integer(c_int), intent(in) :: Ee
! Type of the tubular potential (0 or 1)
integer(c_int), intent(in) :: TPMType
integer(c_int), intent(in) :: TPMType
!-------------------------------------------------------------------------------------------
integer(c_int) :: k, ii, jj, IntSign
integer(c_int) :: BType, EType, LocalTPMType
@ -191,18 +191,18 @@ contains !**********************************************************************
real(c_double), dimension(0:2) :: G, DG, DQ, XX
real(c_double) :: UT, DR, DS, DS1
! Interaction energies associated with nodes X1 and X2
real(c_double) :: xU1, xU2
real(c_double) :: xU1, xU2
! Interaction energies associated with nodes X
real(c_double), dimension(0:N-1) :: xU
real(c_double), dimension(0:N-1) :: xU
! Forces exerted on nodes X1 and X2
real(c_double), dimension(0:2) :: xF1, xF2
real(c_double), dimension(0:2) :: xF1, xF2
! Forces exerted on nodes X
real(c_double), dimension(0:2,0:N-1) :: xF
real(c_double), dimension(0:2,0:N-1) :: xF
! Force exerted on node Xe (can be updated only if Ee > 0)
real(c_double), dimension(0:2) :: xFe
real(c_double), dimension(0:2) :: xFe
!-------------------------------------------------------------------------------------------
! Looking for a buckling point
! Looking for a buckling point
BType = 0
do k = 0, N - 1
if ( BBF(k) == 1 ) then
@ -212,7 +212,7 @@ contains !**********************************************************************
end do
! Choosing the LocalTPMType and Etype.
! LocalTPMType is set to 0 if both ends of the chain are nanotube ends or the chain contains a buckling point.
! LocalTPMType is set to 0 if both ends of the chain are nanotube ends or the chain contains a buckling point.
! Overwise, LocalTPMType = TPMType.
if ( BType == 1 ) then
LocalTPMType = 0
@ -231,7 +231,7 @@ contains !**********************************************************************
if ( EType1 .and. EType2 ) then
LocalTPMType = 0
else
LocalTPMType = TPMType
LocalTPMType = TPMType
if ( EType1 ) then
EType = 1
else if ( EType2 ) then
@ -241,7 +241,7 @@ contains !**********************************************************************
end if
end if
end if
if ( LocalTPMType == 0 ) then
IntSign = TPMInteractionFW0 ( QQ, UT, xU1, xU2, xU, xF1, xF2, xF, G1, G2, X1, X2, N, N, X )
else
@ -263,10 +263,10 @@ contains !**********************************************************************
! Contributions to the virial stresses tensor
do ii = 0, 2
DR = 0.125d+00 * ( X2(ii) - X1(ii) )
DR = 0.125d+00 * ( X2(ii) - X1(ii) )
do jj = 0, 2
DS = DR * ( xF2(jj) - xF1(jj) )
S1(ii,jj) = S1(ii,jj) + DS
S1(ii,jj) = S1(ii,jj) + DS
S2(ii,jj) = S2(ii,jj) + DS
end do
end do
@ -278,24 +278,24 @@ contains !**********************************************************************
do ii = 0, 2
do jj = 0, 2
DS = DQ(ii) * xFe(jj)
S1(ii,jj) = S1(ii,jj) + DS
S1(ii,jj) = S1(ii,jj) + DS
S2(ii,jj) = S1(ii,jj) + DS
Se(ii,jj) = Se(ii,jj) + DS
end do
end do
end if
do k = 0, N - 2
DQ = 0.5d+00 * ( X(0:2,k+1) + X(0:2,k) ) - XX
DQ = 0.5d+00 * ( X(0:2,k+1) + X(0:2,k) ) - XX
call ApplyPeriodicBC ( DQ )
DQ = 0.125d+00 * DQ
G = G1(0:2,k+1) + G2(0:2,k)
DQ = 0.125d+00 * DQ
G = G1(0:2,k+1) + G2(0:2,k)
DG = G1(0:2,k+1) - G2(0:2,k)
do ii = 0, 2
DR = 0.125d+00 * ( X(ii,k+1) - X(ii,k) )
DR = 0.125d+00 * ( X(ii,k+1) - X(ii,k) )
do jj = 0, 2
DS = DQ(ii) * G(jj)
DS1 = DS + DR * DG(jj)
S1(ii,jj) = S1(ii,jj) + DS
S1(ii,jj) = S1(ii,jj) + DS
S2(ii,jj) = S2(ii,jj) + DS
S(ii,jj,k) = S(ii,jj,k) + DS1
S(ii,jj,k+1) = S(ii,jj,k+1) + DS1

18
lib/mesont/TPMGeom.f90
View File

@ -9,9 +9,9 @@
! the GNU General Public License.
!
! See the README file in the top-level LAMMPS directory.
!
!
! Contributing author: Alexey N. Volkov, UA, avolkov1@ua.edu
!-------------------------------------------------------------------------
!-------------------------------------------------------------------------
module TPMGeom !************************************************************************************
!
@ -39,20 +39,20 @@ implicit none
!---------------------------------------------------------------------------------------------------
! Global variables
!---------------------------------------------------------------------------------------------------
! Coordinates of the whole domain
real(c_double) :: DomXmin, DomXmax, DomYmin, DomYmax, DomZmin, DomZmax
real(c_double) :: DomLX, DomLY, DomLZ
real(c_double) :: DomLXhalf, DomLYhalf, DomLZhalf
! Boundary conditions
! Boundary conditions
integer(c_int) :: BC_X = 0
integer(c_int) :: BC_Y = 0
integer(c_int) :: BC_Z = 0
! Skin parameter in NBL and related algorithms
real(c_double) :: Rskin = 1.0d+00
contains !******************************************************************************************
subroutine ApplyPeriodicBC ( R ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@ -111,12 +111,12 @@ contains !**********************************************************************
! cosA, cosine of the angle between lines.
! D1, D2, displacements.
! L12, unit vector directed along the closest distance.
!-------------------------------------------------------------------------------------------
!-------------------------------------------------------------------------------------------
real(c_double), intent(inout) :: H, cosA, D1, D2
real(c_double), dimension(0:2), intent(out) :: L12
real(c_double), dimension(0:2), intent(in) :: R1, L1, R2, L2
!-------------------------------------------------------------------------------------------
real(c_double), intent(in) :: Prec
real(c_double), intent(in) :: Prec
real(c_double), dimension(0:2) :: Q1, Q2, R
real(c_double) :: C, DD1, DD2, C1, C2
!-------------------------------------------------------------------------------------------
@ -151,5 +151,5 @@ contains !**********************************************************************
L12 = L12 / H
end if
end function LineLine !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
end module TPMGeom !********************************************************************************

18
lib/mesont/TPMLib.f90
View File

@ -9,9 +9,9 @@
! the GNU General Public License.
!
! See the README file in the top-level LAMMPS directory.
!
!
! Contributing author: Alexey N. Volkov, UA, avolkov1@ua.edu
!-------------------------------------------------------------------------
!-------------------------------------------------------------------------
module TPMLib !*************************************************************************************
!
@ -61,7 +61,7 @@ contains !**********************************************************************
!---------------------------------------------------------------------------------------------------
! Simple mathematical functions
!---------------------------------------------------------------------------------------------------
real(c_double) function rad ( X ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(in) :: X
!-------------------------------------------------------------------------------------------
@ -76,7 +76,7 @@ contains !**********************************************************************
integer(c_int) function signum ( X ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(in) :: X
!-------------------------------------------------------------------------------------------
!-------------------------------------------------------------------------------------------
if ( X > 0 ) then
signum = 1
else if ( X < 0 ) then
@ -111,7 +111,7 @@ contains !**********************************************************************
subroutine V3_ort ( V ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), dimension(0:2), intent(inout) :: V
!-------------------------------------------------------------------------------------------
real(c_double) :: Vabs
real(c_double) :: Vabs
!-------------------------------------------------------------------------------------------
Vabs = S_V3norm3 ( V )
V(0) = V(0) / Vabs
@ -131,7 +131,7 @@ contains !**********************************************************************
!---------------------------------------------------------------------------------------------------
! Handling of spherical and Euler angles
!---------------------------------------------------------------------------------------------------
subroutine RotationMatrix3 ( M, Psi, Tet, Phi ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! Ksi, Tet and Phi are Euler angles
!-------------------------------------------------------------------------------------------
@ -156,7 +156,7 @@ contains !**********************************************************************
M(2,1) = - sT * cK
M(2,2) = cT
end subroutine RotationMatrix3 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine EulerAngles ( Psi, Tet, L ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(out) :: Tet, Psi
real(c_double), dimension(0:2), intent(in) :: L
@ -165,7 +165,7 @@ contains !**********************************************************************
Psi = atan2 ( L(1), L(0) )
if ( Psi > M_3PI_2 ) then
Psi = Psi - M_3PI_2
else
else
Psi = Psi + M_PI_2
end if
end subroutine EulerAngles !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@ -211,5 +211,5 @@ contains !**********************************************************************
close ( unit = Fuid )
Fuid = -1
end subroutine CloseFile !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
end module TPMLib !*********************************************************************************

34
lib/mesont/TPMM0.f90
View File

@ -9,9 +9,9 @@
! the GNU General Public License.
!
! See the README file in the top-level LAMMPS directory.
!
!
! Contributing author: Alexey N. Volkov, UA, avolkov1@ua.edu
!-------------------------------------------------------------------------
!-------------------------------------------------------------------------
module TPMM0 !**************************************************************************************
!
@ -32,7 +32,7 @@ use iso_c_binding, only : c_int, c_double, c_char
implicit none
contains !******************************************************************************************
integer(c_int) function TPMInteractionFSS ( Q, U, F1_1, F1_2, F2_1, F2_2, R1_1, R1_2, R2_1, R2_2, EType )
real(c_double), intent(inout) :: Q, U
real(c_double), dimension(0:2), intent(inout) :: F1_1, F1_2, F2_1, F2_2
@ -48,9 +48,9 @@ contains !**********************************************************************
L2 = S_V3norm3 ( Laxis2 )
Laxis2 = Laxis2 / L2
if ( EType < 2 ) then
TPMInteractionFSS = TPMInteractionF ( Q, U, F1_1, F1_2, F2_1, F2_2, Fd, R1_1, R1_2, R2_1, R2_2, 1 )
TPMInteractionFSS = TPMInteractionF ( Q, U, F1_1, F1_2, F2_1, F2_2, Fd, R1_1, R1_2, R2_1, R2_2, 1 )
R2_3 = R2_2 + R2_2 - R2_1
IntSign = TPMInteractionF ( Qa, Ua, F1_1a, F1_2a, F2_1a, F2_2a, Fd, R1_1, R1_2, R2_2, R2_3, 1 )
IntSign = TPMInteractionF ( Qa, Ua, F1_1a, F1_2a, F2_1a, F2_2a, Fd, R1_1, R1_2, R2_2, R2_3, 1 )
if ( IntSign > 0 ) then
TPMInteractionFSS = 1
call TPMSegmentForces ( F2_1a, F2_2a, F1_1a, F1_2a, R1_1, R1_2, R2, Laxis2, L2 )
@ -59,7 +59,7 @@ contains !**********************************************************************
F2_1a = F2_1a - F
end if
else
TPMInteractionFSS = TPMInteractionF ( Q, U, F1_1, F1_2, F2_1, F2_2, Fd, R1_1, R1_2, R2_1, R2_2, 2 )
TPMInteractionFSS = TPMInteractionF ( Q, U, F1_1, F1_2, F2_1, F2_2, Fd, R1_1, R1_2, R2_1, R2_2, 2 )
R2_3 = R2_1 + R2_1 - R2_2
IntSign = TPMInteractionF ( Qa, Ua, F1_1a, F1_2a, F2_1a, F2_2a, Fd, R1_1, R1_2, R2_1, R2_3, 1 )
if ( IntSign > 0 ) then
@ -74,13 +74,13 @@ contains !**********************************************************************
Q = Q - Qa
if ( Q < 0.0d+00 ) Q = 0.0d+00
U = U - Ua
F2_1 = F2_1 - F2_1a
F2_2 = F2_2 - F2_2a
F2_1 = F2_1 - F2_1a
F2_2 = F2_2 - F2_2a
F1_1 = F1_1 - F1_1a
F1_2 = F1_2 - F1_2a
end if
end function TPMInteractionFSS !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function TPMInteractionFW0 ( QQ, U, U1, U2, UU, F1, F2, F, G1, G2, R1, R2, N, NMAX, R )
real(c_double), intent(inout) :: U, U1, U2
integer(c_int), intent(in) :: N, NMAX
@ -142,7 +142,7 @@ contains !**********************************************************************
if ( D < Dmina ) Dmina = D
end if
end if
DR = R1 - R(0:2,i+1)
call ApplyPeriodicBC ( DR )
Dminb = sqr ( DR(0) ) + sqr ( DR(1) ) + sqr ( DR(2) )
@ -165,20 +165,20 @@ contains !**********************************************************************
if ( D < Dminb ) Dminb = D
end if
end if
if ( Dmina < Dminb ) then
EType = 1
else
EType = 2
end if
if ( TPMInteractionFSS ( QQ(i), Ua, F1_1a, F1_2a, F2_1a, F2_2a, R1, R2, R(0:2,i), R(0:2,i+1), &
if ( TPMInteractionFSS ( QQ(i), Ua, F1_1a, F1_2a, F2_1a, F2_2a, R1, R2, R(0:2,i), R(0:2,i+1), &
EType ) > 0 ) then
TPMInteractionFW0 = 1
U = U + Ua
Ua = 0.25d+00 * Ua
U1 = U1 + Ua
U2 = U2 + Ua
Ua = 0.25d+00 * Ua
U1 = U1 + Ua
U2 = U2 + Ua
UU(i) = UU(i) + Ua
UU(i+1) = UU(i+1) + Ua
F1 = F1 + F1_1a
@ -190,5 +190,5 @@ contains !**********************************************************************
end if
end do
end function TPMInteractionFW0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
end module TPMM0 !**********************************************************************************

62
lib/mesont/TPMM1.f90
View File

@ -9,9 +9,9 @@
! the GNU General Public License.
!
! See the README file in the top-level LAMMPS directory.
!
!
! Contributing author: Alexey N. Volkov, UA, avolkov1@ua.edu
!-------------------------------------------------------------------------
!-------------------------------------------------------------------------
module TPMM1 !**************************************************************************************
!
@ -56,9 +56,9 @@ implicit none
real(c_double), dimension(0:TPM_MAX_CHAIN-1) :: W, C
real(c_double), dimension(0:2) :: RR, E10
real(c_double) :: L10, D10
contains !******************************************************************************************
subroutine PairWeight1 ( W, E1_1, E1_2, E2_1, E2_2, R2_1, R2_2 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(out) :: W
real(c_double), dimension(0:2), intent(out) :: E1_1, E1_2, E2_1, E2_2
@ -78,7 +78,7 @@ contains !**********************************************************************
E2_2 = 0.0d+00
return
end if
E20 = 0.5d+00 * ( R2_2 - R2_1 )
E20 = 0.5d+00 * ( R2_2 - R2_1 )
L20 = sqrt ( S_V3xx ( E20 ) + sqr ( TPMR2 ) )
D20 = L10 + L20 + TPBRcutoff + RSkin
if ( D > D20 * D20 ) then
@ -96,12 +96,12 @@ contains !**********************************************************************
t = ( D - D10 ) / D20
W = 1.0d+00 - t * t * ( 3.0d+00 - 2.0d+00 * t )
dWdD = 3.0d+00 * t * ( t - 1.0d+00 ) / D20
E1_1 = dWdD * ( t * E10 - E )
E1_2 = dWdD * ( - t * E10 - E )
E2_1 = dWdD * ( E + t * E20 )
E2_2 = dWdD * ( E - t * E20 )
E1_1 = dWdD * ( t * E10 - E )
E1_2 = dWdD * ( - t * E10 - E )
E2_1 = dWdD * ( E + t * E20 )
E2_2 = dWdD * ( E - t * E20 )
end subroutine PairWeight1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function EndWeight1 ( W, E1_1, E1_2, E2_1, E2_2, R1_1, R1_2, R2_1, R2_2 ) !!!
real(c_double), intent(out) :: W
real(c_double), dimension(0:2), intent(out) :: E1_1, E1_2, E2_1, E2_2
@ -114,7 +114,7 @@ contains !**********************************************************************
E = 0.5d+00 * ( R2_1 + R2_2 - ( R1_1 + R1_2 ) )
call ApplyPeriodicBC ( E )
D = S_V3norm3 ( E )
E20 = 0.5d+00 * ( R2_2 - R2_1 )
E20 = 0.5d+00 * ( R2_2 - R2_1 )
L20 = sqrt ( S_V3xx ( E20 ) + sqr ( TPMR2 ) )
D1 = L10 + L20 + TPBRcutoff + RSkin
if ( D < D1 ) then
@ -126,7 +126,7 @@ contains !**********************************************************************
E2_2 = 0.0d+00
return
end if
D2 = D1 + TPMC3
D2 = D1 + TPMC3
if ( D > D2 ) then
EndWeight1 = 2
W = 0.0d+00
@ -142,13 +142,13 @@ contains !**********************************************************************
t = ( D - D1 ) / TPMC3
W = 1.0d+00 - t * t * ( 3.0d+00 - 2.0d+00 * t )
dWdD = 3.0d+00 * t * ( t - 1.0d+00 ) / TPMC3
E1_1 = dWdD * ( E10 - E )
E1_2 = dWdD * ( - E10 - E )
E2_1 = dWdD * ( E + E20 )
E2_2 = dWdD * ( E - E20 )
E1_1 = dWdD * ( E10 - E )
E1_2 = dWdD * ( - E10 - E )
E2_1 = dWdD * ( E + E20 )
E2_2 = dWdD * ( E - E20 )
end function EndWeight1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function TPMInteractionFC1 ( Q, U, F1, F2, P1, P2, Pe, Pe1, R1, R2, Q1, Q2, Qe, Qe1, EType )
integer(c_int) function TPMInteractionFC1 ( Q, U, F1, F2, P1, P2, Pe, Pe1, R1, R2, Q1, Q2, Qe, Qe1, EType )
real(c_double), intent(out) :: Q, U
real(c_double), dimension(0:2), intent(out) :: F1, F2, P1, P2, Pe, Pe1
real(c_double), dimension(0:2), intent(in) :: R1, R2, Q1, Q2, Qe, Qe1
@ -196,11 +196,11 @@ contains !**********************************************************************
end if
call TPMSegmentForces ( P1a, P2a, F1a, F2a, R1, R2, QX, M, L )
end if
if ( CaseID > 0 ) then
IntSignb = TPMInteractionF ( Qb, Ub, F1b, F2b, P1b, P2b, Peeb, R1, R2, Q1, Q2, 0 )
end if
if ( CaseID == 0 ) then
TPMInteractionFC1 = IntSigna
Q = Qa
@ -226,7 +226,7 @@ contains !**********************************************************************
TPMInteractionFC1 = 0
if ( IntSigna > 0 .or. IntSignb > 0 ) TPMInteractionFC1 = 1
W1 = 1.0d+00 - W
DU = Ub - Ua
DU = Ub - Ua
Q = W * Qa + W1 * Qb
U = W * Ua + W1 * Ub
Pe = ( W * Peea / D ) * Me
@ -240,7 +240,7 @@ contains !**********************************************************************
end if
end if
end function TPMInteractionFC1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function TPMInteractionFW1 ( QQ, U, U1, U2, UU, F1, F2, F, Fe, G1, G2, R1, R2, N, NMAX, R, Re, EType )
real(c_double), intent(out) :: U, U1, U2
integer(c_int), intent(in) :: N, NMAX, EType
@ -251,7 +251,7 @@ contains !**********************************************************************
real(c_double), dimension(0:2,0:NMAX-1), intent(in) :: R
!-------------------------------------------------------------------------------------------
integer(c_int) :: i, j
real(c_double) :: Q, WW, DD
real(c_double) :: Q, WW, DD
!-------------------------------------------------------------------------------------------
Q1 = 0.0d+00
Q2 = 0.0d+00
@ -259,7 +259,7 @@ contains !**********************************************************************
Z1 = 0.0d+00
Z2 = 0.0d+00
TPMInteractionFW1 = 0
E10 = 0.5d+00 * ( R2 - R1 )
E10 = 0.5d+00 * ( R2 - R1 )
L10 = sqrt ( S_V3xx ( E10 ) + sqr ( TPMR1 ) )
D10 = TPMR1 + TPMR2 + TPMC123 * TPBRcutoff + RSkin
E10 = E10 / L10
@ -293,10 +293,10 @@ contains !**********************************************************************
Qe = 0.0d+00
Qe1 = 0.0d+00
end if
TPMInteractionFW1 = TPMInteractionFC1 ( Q, U, F1, F2, S1, S2, Pe, Pe1, R1, R2, Q1, Q2, Qe, Qe1, EType )
TPMInteractionFW1 = TPMInteractionFC1 ( Q, U, F1, F2, S1, S2, Pe, Pe1, R1, R2, Q1, Q2, Qe, Qe1, EType )
if ( TPMInteractionFW1 == 0 ) return
W(0:N-2) = W(0:N-2) / WW
E1(0:2,0:N-2) = E1(0:2,0:N-2) / WW
E2(0:2,0:N-2) = E2(0:2,0:N-2) / WW
@ -322,7 +322,7 @@ contains !**********************************************************************
do j = 0, N - 2
if ( j == 0 ) then
DR = EE1(0:2,0) * ( 1.0d+00 - W(0) )
else
else
DR = - W(j) * EE1(0:2,0)
end if
F(0:2,0) = F(0:2,0) + C(j) * DR
@ -337,8 +337,8 @@ contains !**********************************************************************
else if ( j == i - 1 ) then
G1(0:2,i) = G1(0:2,i) + C(j) * ( EE2(0:2,j) - W(j) * EE2(0:2,i-1) )
G2(0:2,i) = G2(0:2,i) - C(j) * W(j) * EE1(0:2,i)
else
G1(0:2,i) = G1(0:2,i) - C(j) * W(j) * EE2(0:2,i-1)
else
G1(0:2,i) = G1(0:2,i) - C(j) * W(j) * EE2(0:2,i-1)
G2(0:2,i) = G2(0:2,i) - C(j) * W(j) * EE1(0:2,i)
end if
end do
@ -348,7 +348,7 @@ contains !**********************************************************************
do j = 0, N - 2
if ( j == N - 2 ) then
DR = EE2(0:2,N-2) * ( 1.0d+00 - W(N-2) )
else
else
DR = - W(j) * EE2(0:2,N-2)
end if
F(0:2,N-1) = F(0:2,N-1) + C(j) * DR
@ -368,5 +368,5 @@ contains !**********************************************************************
G1(0:2,N-1) = F(0:2,N-1)
G2(0:2,0) = F(0:2,0)
end function TPMInteractionFW1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
end module TPMM1 !**********************************************************************************

88
lib/mesont/TubePotBase.f90
View File

@ -9,9 +9,9 @@
! the GNU General Public License.
!
! See the README file in the top-level LAMMPS directory.
!
!
! Contributing author: Alexey N. Volkov, UA, avolkov1@ua.edu
!-------------------------------------------------------------------------
!-------------------------------------------------------------------------
module TubePotBase !********************************************************************************
!
@ -25,10 +25,10 @@ module TubePotBase !************************************************************
!
!---------------------------------------------------------------------------------------------------
!
! This module contains basic parameters for all modules involved into calculations of tubular
! This module contains basic parameters for all modules involved into calculations of tubular
! potentials.
!
! It includes definitions of
!
! It includes definitions of
! -- TPBU, Lennard-Jones (12-6) potential
! -- TPBQ, Transfer function
!
@ -43,7 +43,7 @@ implicit none
!---------------------------------------------------------------------------------------------------
! Constants
!---------------------------------------------------------------------------------------------------
! Types of the potential with respect to the breathing mode
integer(c_int), parameter :: TP_POT_MONO_R = 0
integer(c_int), parameter :: TP_POT_POLY_R = 1
@ -56,7 +56,7 @@ implicit none
! Mass of C atom
real(c_double), parameter :: TPBMc = 12.0107d+00 ! (Da)
! Parameters of the Van der Waals interaction between carbon atoms in graphene sheets, see
! Stuart S.J., Tutein A.B., Harrison J.A., J. Chem. Phys. 112(14), 2000
real(c_double), parameter :: TPBEcc = 0.00284d+00 ! (eV)
@ -66,73 +66,73 @@ implicit none
! Dresselhaus et al, Carbon 33(7), 1995
real(c_double), parameter :: TPBAcc = 1.421d+00 ! (A)
real(c_double), parameter :: TPBDcc = 4.0d+00 / ( TPBConstD * TPBAcc * TPBAcc ) ! (1/A^2)
! Specific heat of carbon nanotubes
real(c_double), parameter :: TPBSHcc = 600.0d+00 / K_MDCU ! (eV/(Da*K))
! Cutoff distances for the interactomic potential and transfer function.
! Changes in these parameters can result in necessity to change some numerical parameters too.
real(c_double), parameter :: TPBRmincc = 0.001d+00 * TPBScc ! (A)
real(c_double), parameter :: TPBRcutoffcc = 3.0d+00 * TPBScc ! (A)
real(c_double), parameter :: TPBRcutoff1cc = 2.16d+00 * TPBScc ! (A)
! Parameters of the transfer function for non-bonded interaction between carbon atoms
real(c_double), parameter :: TPBQScc = 7.0d+00 ! (A)
real(c_double), parameter :: TPBQRcutoff1cc = 8.0d+00 ! (A)
!---------------------------------------------------------------------------------------------------
! Global variables
!---------------------------------------------------------------------------------------------------
! Set to .true. to generate diagnostic and warning messages
logical :: TPErrCheck = .true.
character*512 :: TPErrMsg = ''
real(c_double) :: TPGeomPrec = 1.0d-06 ! Geometric precision, see TPInt
logical :: TPErrCheck = .true.
character*512 :: TPErrMsg = ''
real(c_double) :: TPGeomPrec = 1.0d-06 ! Geometric precision, see TPInt
integer(c_int) :: TPPotType = TP_POT_MONO_R ! Type of the potential with respect to the breathing mode
! Parameters of the interatomic potential and atoms distribution at the surface
! of the tube
real(c_double) :: TPBM = TPBMc ! Mass of an atom (Da)
real(c_double) :: TPBE = TPBEcc ! Depth of the energy well in (12-6) LJ interatomic potential (eV)
real(c_double) :: TPBS = TPBScc ! Sigma parameter of (12-6) LJ interatomic potential (A)
real(c_double) :: TPBD = TPBDcc ! Numerical density of atoms at the tube surface (1/A^2)
real(c_double) :: TPBSH = TPBSHcc ! Specific heat (eV/(Da*K))
real(c_double) :: TPBRmin = TPBRmincc ! (A)
real(c_double) :: TPBRcutoff = TPBRcutoffcc ! (A)
real(c_double) :: TPBRcutoff1 = TPBRcutoff1cc ! (A)
! Parameters of the transfer function
real(c_double) :: TPBQS = TPBQScc ! Sigma parameter of the transfer function (A)
real(c_double) :: TPBQRcutoff1 = TPBQRcutoff1cc! (A)
! Auxiliary variables
real(c_double) :: TPBE4, TPBE24, TPBDRcutoff, TPBQDRcutoff
real(c_double) :: TPBQR0 ! Constant-value distance for the transfer function (A)
! Table of inter-particle potential, force, and transfer function
integer(c_int) :: TPBN = TPBNMAX
real(c_double) :: TPBDR
real(c_double), dimension(0:TPBNMAX-1) :: TPBQ
real(c_double), dimension(0:TPBNMAX-1) :: TPBU, TPBdUdR
contains !******************************************************************************************
integer(c_int) function TPBsizeof () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
TPBsizeof = 8 * ( size ( TPBQ ) + size ( TPBU ) + size ( TPBdUdR ) )
end function TPBsizeof !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!---------------------------------------------------------------------------------------------------
! Interpolation
!---------------------------------------------------------------------------------------------------
real(c_double) function TPBQInt0 ( R ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(in) :: R
real(c_double), intent(in) :: R
!-------------------------------------------------------------------------------------------
real(c_double) :: Z, RR
integer(c_int) :: i
@ -140,7 +140,7 @@ contains !**********************************************************************
if ( R < TPBRmin ) then
!call PrintStdLogMsg ( TPErrMsg )
!write ( TPErrMsg, '(a,e20.10,a,e20.10)' ) ': R < Rmin: R=', R, ', Rmin=', TPBRmin
!call Error ( 'TPBQInt0', TPErrMsg )
!call Error ( 'TPBQInt0', TPErrMsg )
elseif ( R > TPBRcutoff ) then
TPBQInt0 = 0.0d+00
return
@ -149,11 +149,11 @@ contains !**********************************************************************
i = int ( RR )
RR = RR - i
Z = 1.0d+00 - RR
TPBQInt0 = TPBQ(i) * Z + TPBQ(i+1) * RR
TPBQInt0 = TPBQ(i) * Z + TPBQ(i+1) * RR
end function TPBQInt0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double) function TPBUInt0 ( R ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(in) :: R
real(c_double), intent(in) :: R
!-------------------------------------------------------------------------------------------
real(c_double) :: Z, RR
integer(c_int) :: i
@ -161,7 +161,7 @@ contains !**********************************************************************
if ( R < TPBRmin ) then
!call PrintStdLogMsg ( TPErrMsg )
!write ( TPErrMsg, '(a,e20.10,a,e20.10)' ) ': R < Rmin: R=', R, ', Rmin=', TPBRmin
!call Error ( 'TPBUInt0', TPErrMsg )
!call Error ( 'TPBUInt0', TPErrMsg )
elseif ( R > TPBRcutoff ) then
TPBUInt0 = 0.0d+00
return
@ -170,12 +170,12 @@ contains !**********************************************************************
i = int ( RR )
RR = RR - i
Z = 1.0d+00 - RR
TPBUInt0 = TPBU(i) * Z + TPBU(i+1) * RR
TPBUInt0 = TPBU(i) * Z + TPBU(i+1) * RR
end function TPBUInt0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine TPBUInt1 ( U, dUdR, R ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(out) :: U, dUdR
real(c_double), intent(in) :: R
real(c_double), intent(in) :: R
!-------------------------------------------------------------------------------------------
real(c_double) :: Z, RR
integer(c_int) :: i
@ -183,7 +183,7 @@ contains !**********************************************************************
if ( R < TPBRmin ) then
!call PrintStdLogMsg ( TPErrMsg )
!write ( TPErrMsg, '(a,e20.10,a,e20.10)' ) ': R < Rmin: R=', R, ', Rmin=', TPBRmin
!call Error ( 'TPBUInt1', TPErrMsg )
!call Error ( 'TPBUInt1', TPErrMsg )
elseif ( R > TPBRcutoff ) then
TPBU = 0.0d+00
TPBdUdR = 0.0d+00
@ -193,14 +193,14 @@ contains !**********************************************************************
i = int ( RR )
RR = RR - i
Z = 1.0d+00 - RR
U = TPBU(i) * Z + TPBU(i+1) * RR
U = TPBU(i) * Z + TPBU(i+1) * RR
dUdR = TPBdUdR(i) * Z + TPBdUdR(i+1) * RR
end subroutine TPBUInt1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!---------------------------------------------------------------------------------------------------
! Calculation
!---------------------------------------------------------------------------------------------------
real(c_double) function TPBQCalc0 ( R ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(in) :: R
!-------------------------------------------------------------------------------------------
@ -210,7 +210,7 @@ contains !**********************************************************************
TPBQCalc0 = 0.0d+00
else if ( R < TPBQR0 ) then
TPBQCalc0 = 1.0d+00
else
else
Z = TPBQS / R
Z = Z * Z * Z
Z = Z * Z
@ -222,7 +222,7 @@ contains !**********************************************************************
endif
endif
end function TPBQCalc0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double) function TPBUCalc0 ( R ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(in) :: R
!-------------------------------------------------------------------------------------------
@ -230,7 +230,7 @@ contains !**********************************************************************
!-------------------------------------------------------------------------------------------
if ( R > TPBRcutoff ) then
TPBUCalc0 = 0.0d+00
else
else
Z = TPBS / R
Z = Z * Z * Z
Z = Z * Z
@ -251,7 +251,7 @@ contains !**********************************************************************
if ( R > TPBRcutoff ) then
U = 0.0d+00
dUdR = 0.0d+00
else
else
Z = TPBS / R
Z = Z * Z * Z
Z = Z * Z
@ -266,7 +266,7 @@ contains !**********************************************************************
endif
endif
end subroutine TPBUCalc1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine TPBSegmentForces ( F1, F2, F, M, Laxis, L ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), dimension(0:2), intent(out) :: F1, F2
real(c_double), dimension(0:2), intent(in) :: F, M, Laxis
@ -284,7 +284,7 @@ contains !**********************************************************************
!---------------------------------------------------------------------------------------------------
! Initialization
!---------------------------------------------------------------------------------------------------
subroutine TPBInit () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double) :: R
integer(c_int) :: i

353
lib/mesont/TubePotMono.f90
View File

@ -9,9 +9,9 @@
! the GNU General Public License.
!
! See the README file in the top-level LAMMPS directory.
!
!
! Contributing author: Alexey N. Volkov, UA, avolkov1@ua.edu
!-------------------------------------------------------------------------
!-------------------------------------------------------------------------
module TubePotMono !********************************************************************************
!
@ -27,22 +27,22 @@ module TubePotMono !************************************************************
!
! Four potentials and transfer functions are calculated in this module:
!
! 1. SSTP (segment - semi-infinite tube parallel): Linear density of the potential along
! the segment axis which is produced by a parallel semi-infinite tube. 2D tables for this potential
! 1. SSTP (segment - semi-infinite tube parallel): Linear density of the potential along
! the segment axis which is produced by a parallel semi-infinite tube. 2D tables for this potential
! are generated at initialization or can be loaded from a file.
!
! 2. STP (segment - tube parallel): Linear density of the potential along the segment axis
! which is produced by a parallel infinite tubes. This is only a particular case of the SSTP potential,
! but it is considered separately for computational efficiency. 1D tables of this potential are taken
! 2. STP (segment - tube parallel): Linear density of the potential along the segment axis
! which is produced by a parallel infinite tubes. This is only a particular case of the SSTP potential,
! but it is considered separately for computational efficiency. 1D tables of this potential are taken
! from 2D tables of SSTP potential.
!
! 3. SST (segment - semi-infinite tube): Potential for a segment produced by an arbitrary-
! oriented semi-infinite tube. This potential can not be kept in 2D tables, therefore, all
! data are calculated 'on fly' with the help of SSTP potential and numerical integration along the
! oriented semi-infinite tube. This potential can not be kept in 2D tables, therefore, all
! data are calculated 'on fly' with the help of SSTP potential and numerical integration along the
! segment axis
!
! 4. ST (segment - tube): Potential for a segment produced by an arbitrary-oriented
! infinitely long tube. 2D tables for this potential are generated at initialization or can be
! 4. ST (segment - tube): Potential for a segment produced by an arbitrary-oriented
! infinitely long tube. 2D tables for this potential are generated at initialization or can be
! loaded from a file.
!
!***************************************************************************************************
@ -62,77 +62,77 @@ implicit none
integer(c_int), parameter :: TPMNZMAX = 129
integer(c_int), parameter :: TPMNEMAX = 128
integer(c_int), parameter :: TPMNHMAX = 1001
integer(c_int), parameter :: TPMNXMAX = 1001
integer(c_int), parameter :: TPMNMAX = 1001
integer(c_int), parameter :: TPMNHMAX = 1001
integer(c_int), parameter :: TPMNXMAX = 1001
integer(c_int), parameter :: TPMNMAX = 1001
!---------------------------------------------------------------------------------------------------
! Global variables
!---------------------------------------------------------------------------------------------------
integer(c_int) :: TPMStartMode = 1
character*512 :: TPMFile = 'MESONT-TABTP.xrs'
character(len=512) :: TPMFile = 'MESONT-TABTP.xrs'
integer(c_int) :: TPMUnitID ! Unit for the tabulated potential file
integer(c_int) :: TPMNZ = TPMNZMAX
integer(c_int) :: TPMNZ1 = TPMNZMAX - 1
integer(c_int) :: TPMNE = TPMNEMAX
integer(c_int) :: TPMNE1 = TPMNEMAX - 1
integer(c_int) :: TPMNH = TPMNHMAX
integer(c_int) :: TPMNH1 = TPMNHMAX - 1
integer(c_int) :: TPMNX = TPMNXMAX
integer(c_int) :: TPMNX1 = TPMNXMAX - 1
integer :: TPMChiIndM ! Chirality index M
integer :: TPMChiIndM ! Chirality index M
integer :: TPMChiIndN ! Chirality index N
real(c_double) :: TPMR1
real(c_double) :: TPMR2
real(c_double) :: TPMHmax
real(c_double) :: TPMDH
! Parameters of empirical correction functions
integer(c_int) :: TPMAN = 20
real(c_double) :: TPMAHmin
real(c_double) :: TPMAHmax
real(c_double) :: TPMADH
real(c_double), dimension(0:TPMNHMAX-1) :: TPMAH, TPMAF, TPMAFxx
! Fitting parameters that depend on the SWCNT chirality
real(c_double) :: TPMCaA = 0.22d+00 ! 0.22 for (10,10) CNTs
real(c_double) :: TPMCeA = 0.35d+00 ! 0.35 for (10,10) CNTs
real(c_double) :: TPMAHmin0 = 10.0d+00 ! 10.0 A for (10,10) CNTs
! Parameters of SSTP integrator
real(c_double) :: TPMDE
real(c_double), dimension(0:TPMNEMAX-1) :: TPMCE, TPMSE
! Additional parameters for SSTP potential
real(c_double) :: TPMSSTPDelta = 0.25d+00
integer(c_int) :: TPMSSTPNH
integer(c_int) :: TPMSSTPNX
real(c_double) :: TPMSSTPX1
real(c_double) :: TPMSSTPXmax
real(c_double) :: TPMSSTPDX
real(c_double), dimension(0:TPMNHMAX-1,0:TPMNXMAX-1) :: TPMSSTPG
real(c_double), dimension(0:TPMNHMAX-1,0:TPMNXMAX-1) :: TPMSSTPF, TPMSSTPFxx, TPMSSTPFyy, TPMSSTPFxxyy
real(c_double), dimension(0:TPMNHMAX-1) :: TPMSSTPH
real(c_double), dimension(0:TPMNXMAX-1) :: TPMSSTPX
! Additional parameters for STP potential
! In calculations of this potential, some parameters of SSTP potential are also used.
! In particular, STP potential has no its own integrator. All data comes from SSTP integrator.
! It does not result in any computational inefficiency unless the STP potential is used without SSTP one.
integer(c_int) :: TPMNN = 10
real(c_double), dimension(0:TPMNHMAX-1) :: TPMSTPG
real(c_double), dimension(0:TPMNHMAX-1) :: TPMSTPF, TPMSTPFxx
@ -140,25 +140,25 @@ implicit none
! Parameters for ST potential
! Minimum gap dh for ST-potential
real(c_double) :: TPMSTDelta = 1.0d+00
real(c_double) :: TPMSTDelta = 1.0d+00
! Number of subdivisions for every grid step in ST-integrator
integer(c_int) :: TPMSTNXS = 10
integer(c_int) :: TPMSTNXS = 10
real(c_double) :: TPMSTXmax
real(c_double) :: TPMSTH1
real(c_double) :: TPMSTH2
real(c_double) :: TPMSTDH12
real(c_double), dimension(0:TPMNHMAX-1,0:TPMNXMAX-1) :: TPMSTG
real(c_double), dimension(0:TPMNHMAX-1,0:TPMNXMAX-1) :: TPMSTF, TPMSTFxx, TPMSTFyy, TPMSTFxxyy
real(c_double), dimension(0:TPMNHMAX-1) :: TPMSTH
real(c_double), dimension(0:TPMNXMAX-1) :: TPMSTX
! Switching parameters
! Height switch (at H=0 in SST-potential)
integer(c_int) :: TPMHSwitch = 0 ! 1, use h-switch; 0, do not use the switch
real(c_double) :: TPMHS = 3.0d+00 ! Switch height, Angstrom
! Angle switch
integer(c_int) :: TPMASwitch = 0 ! 1, use a-switch; 0, do not use the switch
real(c_double) :: TPMAS = 3.0d+00 ! Switch angle, degree
@ -220,7 +220,7 @@ contains !**********************************************************************
R2Y = TPMR1 * TPMSE(j)
R2Z = Zmin - D
do k = 0, TPMNZ1 ! Integration over the length of the second tube
R = sqr ( R2X - R1X ) + sqr ( R2Y - R1Y ) + sqr ( R2Z )
R = sqr ( R2X - R1X ) + sqr ( R2Y - R1Y ) + sqr ( R2Z )
if ( R < Rcutoff2 ) then
R = dsqrt ( R )
if ( k == 0 .or. k == TPMNZ1 ) then
@ -239,7 +239,7 @@ contains !**********************************************************************
Q = Q * C
U = U * sqr ( TPBD ) * C
end subroutine TPMSSTPIntegrator !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function TPMSSTPInt0 ( Q, U, H, X ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! This function returns the transfer function Q and potential U for the SSTP potential
! calculated by interpolation in the table without switch.
@ -253,7 +253,7 @@ contains !**********************************************************************
i = 1 + int ( H / TPMDH )
j = 1 + int ( ( X + TPMSSTPXMax ) / TPMSSTPDX )
if ( ( i < TPMSSTPNH ) .and. ( j > TPMSSTPNX ) ) then
!call PrintTPErrMsg ()
!call PrintTPErrMsg ()
!!call PrintStdLogMsg (TPErrMsg )
!write ( TPErrMsg, '(a,e20.10,a,e20.10)' ) 'Tubes intersect each other: H=', H, ', X=', X
!call Error ( 'TPMSSTPInt0', TPErrMsg )
@ -273,7 +273,7 @@ contains !**********************************************************************
else
XX = X
end if
Q = CalcLinFun2_0 ( i, j, H, XX, TPMNH, TPMNX, TPMSSTPH, TPMSSTPX, TPMSSTPG )
Q = CalcLinFun2_0 ( i, j, H, XX, TPMNH, TPMNX, TPMSSTPH, TPMSSTPX, TPMSSTPG )
U = CalcSpline2_0 ( i, j, H, XX, TPMNH, TPMNX, TPMSSTPH, TPMSSTPX, TPMSSTPF, TPMSSTPFxx, TPMSSTPFyy, TPMSSTPFxxyy )
TPMSSTPInt0 = 1
end function TPMSSTPInt0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@ -303,7 +303,7 @@ contains !**********************************************************************
end if
end if
end function TPMSSTPInt0S !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function TPMSSTPInt1 ( Q, U, Uh, Ux, H, X ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! This function returns the transfer function Q, potential U, and derivatives Uh=dU/dH and
! Ux=dU/dX for the SSTP potential calculated by interpolation in the table without switch
@ -317,7 +317,7 @@ contains !**********************************************************************
i = 1 + int ( H / TPMDH )
j = 1 + int ( ( X + TPMSSTPXMax ) / TPMSSTPDX )
if ( ( i < TPMSSTPNH ) .and. ( j > TPMSSTPNX ) ) then
!call PrintTPErrMsg ()
!call PrintTPErrMsg ()
!!call PrintStdLogMsg ( TPErrMsg )
!write ( TPErrMsg, '(a,e20.10,a,e20.10)' ) 'Tubes intersect each other: H=', H, ', X=', X
!call Error ( 'TPMSSTPInt1', TPErrMsg )
@ -339,15 +339,15 @@ contains !**********************************************************************
else
XX = X
end if
Q = CalcLinFun2_0 ( i, j, H, XX, TPMNH, TPMNX, TPMSSTPH, TPMSSTPX, TPMSSTPG )
Q = CalcLinFun2_0 ( i, j, H, XX, TPMNH, TPMNX, TPMSSTPH, TPMSSTPX, TPMSSTPG )
call CalcSpline2_1 ( U, Uh, Ux, i, j, H, XX, TPMNH, TPMNX, TPMSSTPH, TPMSSTPX, TPMSSTPF, &
TPMSSTPFxx, TPMSSTPFyy, TPMSSTPFxxyy )
TPMSSTPFxx, TPMSSTPFyy, TPMSSTPFxxyy )
TPMSSTPInt1 = 1
end function TPMSSTPInt1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function TPMSSTPInt1S ( Q, U, Uh, Ux, H, X ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! This function returns the transfer function Q, potential U, and derivatives Uh=dU/dH and
! Ux=dU/dX for the SSTP potential calculated by interpolation in the table and switch to
! Ux=dU/dX for the SSTP potential calculated by interpolation in the table and switch to
! the case of zero H.
!-------------------------------------------------------------------------------------------
real(c_double), intent(out) :: Q, U, Uh, Ux
@ -375,7 +375,7 @@ contains !**********************************************************************
end if
end if
end function TPMSSTPInt1S !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine TPMSSTPWrite () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! This function writes the table of the SSTP potential to a disk file.
!-------------------------------------------------------------------------------------------
@ -412,7 +412,7 @@ contains !**********************************************************************
end do
end do
end subroutine TPMSSTPRead !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine TPMSSTPInit () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! This function calculates the table of the SSTP potential.
!-------------------------------------------------------------------------------------------
@ -424,7 +424,7 @@ contains !**********************************************************************
TPMDE = M_2PI / TPMNE
E = 0.0d+00
do i = 0, TPMNE1
TPMCE(i) = cos ( E )
TPMCE(i) = cos ( E )
TPMSE(i) = sin ( E )
E = E + TPMDE
end do
@ -444,7 +444,7 @@ contains !**********************************************************************
do j = 0, TPMNX1
if ( ( i .ge. TPMSSTPNH ) .or. ( j .le. TPMSSTPNX ) ) then
call TPMSSTPIntegrator ( TPMSSTPG(i,j), TPMSSTPF(i,j), TPMSSTPH(i), TPMSSTPX(j) )
print '(2i5,a,e20.10,a,e20.10,a,e20.10,a,e20.10)', i, j, ' H=', TPMSSTPH(i), &
print '(2i5,a,e20.10,a,e20.10,a,e20.10,a,e20.10)', i, j, ' H=', TPMSSTPH(i), &
', X=', TPMSSTPX(j), ', Q=', TPMSSTPG(i,j), ', U=', TPMSSTPF(i,j)
end if
end do
@ -454,11 +454,11 @@ contains !**********************************************************************
call TPMSSTPRead ()
end if
call CreateSpline2Ext ( 3, 3, 3, 3, TPMNH, TPMSSTPNH, TPMNX, TPMSSTPNX, TPMNMAX, TPMSSTPH, TPMSSTPX, &
TPMSSTPF, TPMSSTPFxx, TPMSSTPFyy, TPMSSTPFxxyy, FF, MM, DD, K0, K1, K2 )
TPMSSTPF, TPMSSTPFxx, TPMSSTPFyy, TPMSSTPFxxyy, FF, MM, DD, K0, K1, K2 )
end subroutine TPMSSTPInit !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!---------------------------------------------------------------------------------------------------
! STP potential for an infinite tube interacting with a parallel segment. No actual initialization
! STP potential for an infinite tube interacting with a parallel segment. No actual initialization
! is necessary for this potential, since the data are taken from the table for the SSTP potential.
!---------------------------------------------------------------------------------------------------
@ -473,7 +473,7 @@ contains !**********************************************************************
!-------------------------------------------------------------------------------------------
i = 1 + int ( H / TPMDH )
if ( i < TPMSSTPNH ) then
!call PrintTPErrMsg ()
!call PrintTPErrMsg ()
!!call PrintStdLogMsg ( TPErrMsg )
!write ( TPErrMsg, '(a,e20.10)' ) 'Tubes intersect each other: H=', H
!call Error ( 'TPMSTPInt0', TPErrMsg )
@ -485,13 +485,13 @@ contains !**********************************************************************
return
end if
if ( i == TPMNH ) i = TPMNH - 1
Q = CalcLinFun1_0 ( i, H, TPMNH, TPMSSTPH, TPMSTPG )
U = CalcSpline1_0 ( i, H, TPMNH, TPMSSTPH, TPMSTPF, TPMSTPFxx )
Q = CalcLinFun1_0 ( i, H, TPMNH, TPMSSTPH, TPMSTPG )
U = CalcSpline1_0 ( i, H, TPMNH, TPMSSTPH, TPMSTPF, TPMSTPFxx )
TPMSTPInt0 = 1
end function TPMSTPInt0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function TPMSTPInt1 ( Q, U, dUdH, H ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! This function returns the transfer function Q, potential U, and derivative dUdH for
! This function returns the transfer function Q, potential U, and derivative dUdH for
! the STP potential calculated by interpolation in the table.
!-------------------------------------------------------------------------------------------
real(c_double), intent(out) :: Q, U, dUdH
@ -500,7 +500,7 @@ contains !**********************************************************************
!-------------------------------------------------------------------------------------------
i = 1 + int ( H / TPMDH )
if ( i < TPMSSTPNH ) then
!call PrintTPErrMsg ()
!call PrintTPErrMsg ()
!!call PrintStdLogMsg ( TPErrMsg )
!write ( TPErrMsg, '(a,e20.10)' ) 'Tubes intersect each other: H=', H
!call Error ( 'TPMSTPInt0', TPErrMsg )
@ -512,11 +512,11 @@ contains !**********************************************************************
TPMSTPInt1 = 0
return
end if
Q = CalcLinFun1_0 ( i, H, TPMNH, TPMSSTPH, TPMSTPG )
call CalcSpline1_1 ( U, dUdH, i, H, TPMNH, TPMSSTPH, TPMSTPF, TPMSTPFxx )
Q = CalcLinFun1_0 ( i, H, TPMNH, TPMSSTPH, TPMSTPG )
call CalcSpline1_1 ( U, dUdH, i, H, TPMNH, TPMSSTPH, TPMSTPF, TPMSTPFxx )
TPMSTPInt1 = 1
end function TPMSTPInt1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine TPMSTPInit () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! This function initializes the table of the STP potential
!-------------------------------------------------------------------------------------------
@ -524,7 +524,7 @@ contains !**********************************************************************
TPMSTPF(0:TPMNH1) = TPMSSTPF(0:TPMNH1,TPMNX1)
TPMSTPFxx(0:TPMNH1) = TPMSSTPFxx(0:TPMNH1,TPMNX1)
end subroutine TPMSTPInit !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!---------------------------------------------------------------------------------------------------
! Fitting functions for the SST and ST potentials.
! This correction functions are chosen empirically to improve accuracy of the SST and ST potentials.
@ -567,14 +567,14 @@ contains !**********************************************************************
X = - ( X1_2 - X1_1 ) / 2.0d+00
do j = 0, ( TPTNXMAX - 1 ) / 2
HH = sqrt ( TPMAH(i) * TPMAH(i) + sqr ( X * sin ( M_PI_2 ) ) )
IntSign = TPMSTPInt0 ( Qb, Ub, HH )
IntSign = TPMSTPInt0 ( Qb, Ub, HH )
call TPTSetSegPosition2 ( TPTSeg1, R1_1, R1_2 )
call TPTSetSegPosition2 ( TPTSeg2, R2_1, R2_2 )
IntSign = TPTSectionPotential ( Qa, Ua, Fa, Ma, TPTSeg1, j, TPTSeg2 )
IntSign = TPTSectionPotential ( Qa, Ua, Fa, Ma, TPTSeg1, j, TPTSeg2 )
if ( j == 0 ) then
Uamin = Ua
Ubmin = Ub
else
else
if ( Ua < Uamin ) then
Uamin = Ua
end if
@ -614,7 +614,7 @@ contains !**********************************************************************
return
end if
i = 1 + int ( ( H - TPMAHmin ) / TPMADH )
TPMA0 = CalcSpline1_0 ( i, H, TPMAN, TPMAH, TPMAF, TPMAFxx )
TPMA0 = CalcSpline1_0 ( i, H, TPMAN, TPMAH, TPMAF, TPMAFxx )
end function TPMA0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine TPMA1 ( A, Ah, H ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@ -646,9 +646,9 @@ contains !**********************************************************************
i = 1 + int ( ( H - TPMAHmin ) / TPMADH )
call CalcSpline1_1 ( A, Ah, i, H, TPMAN, TPMAH, TPMAF, TPMAFxx )
end subroutine TPMA1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double) function TPMCu0 ( H, cosA, sinA ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! This function returns the correction function for the magnitude of the potential.
! This function returns the correction function for the magnitude of the potential.
!-------------------------------------------------------------------------------------------
real(c_double), intent(in) :: H, cosA, sinA
!-------------------------------------------------------------------------------------------
@ -656,7 +656,7 @@ contains !**********************************************************************
end function TPMCu0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine TPMCu1 ( Cu, CuH, CuA, H, cosA, sinA ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! The subroutine calculates the correction function Cu for the magnitude of the potential and
! The subroutine calculates the correction function Cu for the magnitude of the potential and
! its derivatives CuH and CuA.
!-------------------------------------------------------------------------------------------
real(c_double), intent(ouT) :: Cu, CuH, CuA
@ -664,7 +664,7 @@ contains !**********************************************************************
real(c_double) :: AA, AAh, D
!-------------------------------------------------------------------------------------------
call TPMA1 ( AA, AAh, H )
D = sqr ( sinA )
D = sqr ( sinA )
AA = AA - 1.0d+00
Cu = 1.0d+00 + AA * D
CuH = AAh * D
@ -672,7 +672,7 @@ contains !**********************************************************************
end subroutine TPMCu1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double) function TPMCa0 ( cosA, sinA ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! This function returns the correction function for the argument of the potential.
! This function returns the correction function for the argument of the potential.
! If correction is not necessary, it should return sinA.
!-------------------------------------------------------------------------------------------
real(c_double), intent(in) :: cosA, sinA
@ -681,21 +681,21 @@ contains !**********************************************************************
end function TPMCa0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine TPMCa1 ( Ca, CaA, Ka, KaA, cosA, sinA ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! This subroutine calculates the correction function Cu for the depth of the potential well
! and its derivatives CuH and CuA. If correction is not necessary, it returns Ca = sinA
! This subroutine calculates the correction function Cu for the depth of the potential well
! and its derivatives CuH and CuA. If correction is not necessary, it returns Ca = sinA
! and CaA = cosA.
!-------------------------------------------------------------------------------------------
real(c_double), intent(out) :: Ca, CaA, Ka, KaA
real(c_double), intent(in) :: cosA, sinA
!-------------------------------------------------------------------------------------------
Ka = 1.0d+00 / ( 1.0d+00 - TPMCaA * sqr ( sinA ) )
Ca = sinA * Ka
Ca = sinA * Ka
KaA = 2.0d+00 * TPMCaA * sinA * cosA * sqr ( Ka )
CaA = cosA * Ka + sinA * KaA
end subroutine TPMCa1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double) function TPMCe0 ( sinA ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! This function returns the correction function for the argument of the potential.
! This function returns the correction function for the argument of the potential.
! If correction is not necessary, it returns sinA.
!-------------------------------------------------------------------------------------------
real(c_double), intent(in) :: sinA
@ -713,19 +713,19 @@ contains !**********************************************************************
CeA = - 2.0d+00 * TPMCeA * sinA * cosA
Ke = TPMCeA
end subroutine TPMCe1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!---------------------------------------------------------------------------------------------------
! SST potential for the semi-infinite tube interacting with segment.
! This potential does not need any initialization. All necessary data is taken from tables of the
! SST potential for the semi-infinite tube interacting with segment.
! This potential does not need any initialization. All necessary data is taken from tables of the
! SSTP potential.
!---------------------------------------------------------------------------------------------------
integer(c_int) function TPMSSTPotential ( Q, U, X1, X2, H, cosA, D, N ) !!!!!!!!!!!!!!!!!!!!
! This function calculates the transfer function Q and potential U applied to a segment
! from a semi-infinite tube based on the numerical integration (trapezoidal rule) along the segment
! axis for non-parallel objects.
! This function calculates the transfer function Q and potential U applied to a segment
! from a semi-infinite tube based on the numerical integration (trapezoidal rule) along the segment
! axis for non-parallel objects.
! Relative position of the nanotube and segment is given by axial positions of the segment
! ends X1 and X2, height H, cosA= cos(A), where A is the cross-axis angle, and the displacement
! ends X1 and X2, height H, cosA= cos(A), where A is the cross-axis angle, and the displacement
! D of a nanotube end.
!-------------------------------------------------------------------------------------------
real(c_double), intent(out) :: Q, U
@ -761,7 +761,7 @@ contains !**********************************************************************
end function TPMSSTPotential !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function TPMSSTPotentialPar ( Q, U, R1_1, Laxis1, R2_1, Laxis2, L1, N ) !!!!!
! Potential for a segment and a semi-infinite tube is calculated by the numerical
! Potential for a segment and a semi-infinite tube is calculated by the numerical
! integration (trapezoidal rule) along the segment axis for parallel objects.
!-------------------------------------------------------------------------------------------
real(c_double), intent(out) :: Q, U
@ -799,9 +799,9 @@ contains !**********************************************************************
Q = Q * DX
U = U * DX
end function TPMSSTPotentialPar !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function TPMSSTForces ( Q, U, F1, F2, Fd, X1, X2, H, cosA, D, N ) !!!!!!!!!!!
! Potential and forces applied to the segment from a semi-infinite tube are calculated
! Potential and forces applied to the segment from a semi-infinite tube are calculated
! by the numerical integration (trapezoidal rule) along the segment axis.
! Non-parallel case.
!-------------------------------------------------------------------------------------------
@ -859,7 +859,7 @@ contains !**********************************************************************
X = X + DX
end do
if ( TPMSSTForces == 0 ) return
C = DX * Cu
I0 = I0 * C
Ih = Ih * C
@ -868,7 +868,7 @@ contains !**********************************************************************
Ix = Ix * C
Ix1 = Ix1 * C
DX = X2 - X1
DX = X2 - X1
Q = Q * C
U = I0
@ -877,23 +877,23 @@ contains !**********************************************************************
C1 = Ka * Ka * Ih1
C = h * ( C1 + cosA * Ke * Ix ) / DX
F1(0) = X2 * Uh - C
F1(0) = X2 * Uh - C
F2(0) = C - X1 * Uh
C = ( cosA * sinA * C1 + ( Ke * sinA - sinA ) * Ix ) / DX
F1(1) = Ua - X2 * C
F1(1) = Ua - X2 * C
F2(1) = X1 * C - Ua
C1 = Ca * Ca * Ih1 + cosA * Ix
C2 = Ca * Ca * Ih2 + cosA * Ix1
F1(2) = ( U - X2 * C1 + C2 ) / DX
F2(2) = ( X1 * C1 - C2 - U ) / DX
Fd = Ce * Ix
end function TPMSSTForces !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function TPMSSTForcesPar ( Q, U, F1, F2, Fd, R1_1, Laxis1, R2_1, Laxis2, L1, N )
! Potential and forces applied to the segment from a semi-infinite tube are calculated by
integer(c_int) function TPMSSTForcesPar ( Q, U, F1, F2, Fd, R1_1, Laxis1, R2_1, Laxis2, L1, N )
! Potential and forces applied to the segment from a semi-infinite tube are calculated by
! the numerical integration (trapezoidal rule) along the segment axis.
! Parallel case
!-------------------------------------------------------------------------------------------
@ -942,8 +942,8 @@ contains !**********************************************************************
U = U + Us
Fd = Fd + Usx
end if
F1 = F1 + Gamma * Fs
F2 = F2 + Beta * Fs
F1 = F1 + Gamma * Fs
F2 = F2 + Beta * Fs
end if
X = X + DX
end do
@ -954,15 +954,15 @@ contains !**********************************************************************
F1 = DX * F1 + Fs
F2 = DX * F2 - Fs
end function TPMSSTForcesPar !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!---------------------------------------------------------------------------------------------------
! ST: Potential for a infinite tube interacting with a segment
!--------------------------------------------------------------------------------------------------
!
! These functions are used to smooth boundaries in (H,X) domain for ST potential
!
real(c_double) function TPMSTXMin0 ( H ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(in) :: H
!-------------------------------------------------------------------------------------------
@ -979,7 +979,7 @@ contains !**********************************************************************
TPMSTXMin0 = sqrt ( TPMSTH2 * TPMSTH2 - H * H ) &
* ( 1.0d+00 - X * X * X * ( 3.0d+00 * X * ( 2.0d+00 * X - 5.0d+00 ) + 10.0d+00 ) )
end function TPMSTXMin0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double) function TPMSTXMax0 ( H ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(in) :: H
!-------------------------------------------------------------------------------------------
@ -1005,11 +1005,11 @@ contains !**********************************************************************
F = 1.0d+00 - X * X * X * ( 3.0d+00 * X * ( 2.0d+00 * X - 5.0d+00 ) + 10.0d+00 )
X = X * ( X - 1.0d+00 )
dFdX = - 30.0d+00 * X * X
XMin = sqrt ( TPMSTH2 * TPMSTH2 - H * H )
XMin = sqrt ( TPMSTH2 * TPMSTH2 - H * H )
dXMindH = - H * F / XMin + XMin * dFdX / TPMSTDH12
XMin = XMin * F
end subroutine TPMSTXMin1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine TPMSTXMax1 ( XMax, dXMaxdH, H ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(out) :: XMax, dXMaxdH
real(c_double), intent(in) :: H
@ -1017,11 +1017,11 @@ contains !**********************************************************************
XMax = sqrt ( TPMSTXMax * TPMSTXMax - H * H )
dXMaxdH = - H / XMax
end subroutine TPMSTXMax1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!
! ST (segment-tube) table
!
subroutine TPMSTIntegrator ( G, F, Q, U, H, X, DX ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(inout) :: G, F, Q, U
real(c_double), intent(in) :: H, X, DX
@ -1036,7 +1036,7 @@ contains !**********************************************************************
U = 0.0d+00
HH = dsqrt ( sqr ( H ) + sqr ( X ) )
if ( HH > TPMHmax ) return
IntSign = TPMSTPInt0 ( Q, U, HH )
IntSign = TPMSTPInt0 ( Q, U, HH )
if ( IntSign == 1 ) then
G = G + Q * DDX
F = F + U * DDX
@ -1059,10 +1059,10 @@ contains !**********************************************************************
G = 0.0d+00
F = 0.0d+00
TPMSTInt0 = 2
!call PrintTPErrMsg ()
!call PrintTPErrMsg ()
!!call PrintStdLogMsg ( TPErrMsg )
!all Error ( 'TPMSTInt0', 'H < 0' )
!!return
!!return
end if
S = signum ( X )
XA = dabs ( X )
@ -1074,7 +1074,7 @@ contains !**********************************************************************
if ( XXX < 0.0d+00 ) then
j = 1
XXXX = 0.0d+00
!call PrintTPErrMsg ()
!call PrintTPErrMsg ()
!write ( TPErrMsg, '(a,e20.10,a,e20.10,a,e20.10)' ) 'X < XMin, X=', XA, ', XMin=', XMin, ', H=', H
!call Error ( 'TPMSTInt0', TPErrMsg )
else if ( XXX .ge. 1.0d+00 ) then
@ -1084,8 +1084,8 @@ contains !**********************************************************************
XXXX = XXX
j = 1 + int ( XXXX * TPMNX1 )
end if
G = S * CalcLinFun2_0 ( i, j, H, XXXX, TPMNH, TPMNX, TPMSTH, TPMSTX, TPMSTG )
F = S * CalcSpline2_0 ( i, j, H, XXXX, TPMNH, TPMNX, TPMSTH, TPMSTX, TPMSTF, TPMSTFxx, TPMSTFyy, TPMSTFxxyy )
G = S * CalcLinFun2_0 ( i, j, H, XXXX, TPMNH, TPMNX, TPMSTH, TPMSTX, TPMSTG )
F = S * CalcSpline2_0 ( i, j, H, XXXX, TPMNH, TPMNX, TPMSTH, TPMSTX, TPMSTF, TPMSTFxx, TPMSTFyy, TPMSTFxxyy )
TPMSTInt0 = 1
end function TPMSTInt0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@ -1109,10 +1109,10 @@ contains !**********************************************************************
Fh = 0.0d+00
Fx = 0.0d+00
TPMSTInt1 = 2
!call PrintTPErrMsg ()
!call PrintTPErrMsg ()
!!call PrintStdLogMsg ( trim ( TPErrMsg ) )
!call Error ( 'TPMSTInt1', 'H < 0' )
!!return
!!return
end if
S = signum ( X )
XA = dabs ( X )
@ -1126,7 +1126,7 @@ contains !**********************************************************************
j = 1
XXX = 0.0d+00
XXXX = 0.0d+00
!call PrintTPErrMsg ()
!call PrintTPErrMsg ()
!write ( TPErrMsg, '(a,e20.10,a,e20.10,a,e20.10)' ) 'X < XMin, X=', XA, ', XMin=', XMin, ', H=', H
!call Error ( 'TPMSTInt', TPErrMsg )
else if ( XXX .ge. 1.0d+00 ) then
@ -1134,19 +1134,19 @@ contains !**********************************************************************
XXX = 1.0d+00
XXXX = 1.0d+00
else
XXXX = XXX
XXXX = XXX
j = 1 + int ( XXXX * TPMNX1 )
end if
G = S * CalcLinFun2_0 ( i, j, H, XXXX, TPMNH, TPMNX, TPMSTH, TPMSTX, TPMSTG )
G = S * CalcLinFun2_0 ( i, j, H, XXXX, TPMNH, TPMNX, TPMSTH, TPMSTX, TPMSTG )
call CalcSpline2_1 ( F, Fh, Fx, i, j, H, XXXX, TPMNH, TPMNX, TPMSTH, TPMSTX, &
TPMSTF, TPMSTFxx, TPMSTFyy, TPMSTFxxyy )
TPMSTF, TPMSTFxx, TPMSTFyy, TPMSTFxxyy )
Fx = Fx / DX
Fh = Fh - Fx * ( dXMaxdH * XXX + dXMindH * ( 1.0d+00 - XXX ) )
F = F * S
Fh = Fh * S
TPMSTInt1 = 1
end function TPMSTInt1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function TPMSTPotential ( Q, U, X1, X2, H, cosA, CaseID ) !!!!!!!!!!!!!!!!!!!
real(c_double), intent(out) :: Q, U
real(c_double), intent(in) :: X1, X2, H, cosA
@ -1157,7 +1157,7 @@ contains !**********************************************************************
if ( CaseID == MD_LINES_PAR ) then
TPMSTPotential = TPMSTPInt0 ( Q, U, H )
U = U * ( X2 - X1 )
return
return
end if
TPMSTPotential = 0
sinA = dsqrt ( 1.0d+00 - cosA * cosA )
@ -1192,12 +1192,12 @@ contains !**********************************************************************
F2(2) = - U
Q = Q * DX
U = U * DX
return
return
end if
sinA = dsqrt ( 1.0d+00 - cosA * cosA )
call TPMCa1 ( Ca, CaA, Ka, KaA, cosA, sinA )
IntSign1 = TPMSTInt1 ( GG1, FF1, Fh1, Fx1, H, X1 * Ca )
IntSign1 = TPMSTInt1 ( GG1, FF1, Fh1, Fx1, H, X1 * Ca )
IntSign2 = TPMSTInt1 ( GG2, FF2, Fh2, Fx2, H, X2 * Ca )
if ( ( IntSign1 .ne. 1 ) .and. ( IntSign2 .ne. 1 ) ) then
Q = 0.0d+00
@ -1205,11 +1205,11 @@ contains !**********************************************************************
F1 = 0.0d+00
F2 = 0.0d+00
TPMSTForces = 0
return
return
end if
call TPMCu1 ( Cu, CuH, CuA, H, cosA, sinA )
Q = Cu * ( GG2 - GG1 ) / Ca
U = Cu * ( FF2 - FF1 ) / Ca
@ -1218,19 +1218,19 @@ contains !**********************************************************************
D = CuH * U / Cu + Cu * ( Fh2 - Fh1 ) / Ca
F1(0) = ( X2 * D - C ) / DX
F2(0) = ( C - X1 * D ) / DX
C = cosA * B
D = ( CuA / Cu - CaA / Ca ) * U + CaA * Cu * ( X2 * Fx2 - X1 * Fx1 ) / Ca
F1(1) = ( D - X2 * C ) / DX
F2(1) = ( X1 * C - D ) / DX
F1(2) = Cu * Fx1
F2(2) = - Cu * Fx2
TPMSTForces = 1
end function TPMSTForces !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function TPMSTForceTorque( Qi, Ui, Fi, Ti, Q, U, F, T, Psi, PsiA, Cap, L, H, cosA, CaseID )
integer(c_int) function TPMSTForceTorque( Qi, Ui, Fi, Ti, Q, U, F, T, Psi, PsiA, Cap, L, H, cosA, CaseID )
real(c_double), intent(out) :: Qi, Ui, Fi, Ti, Q, U, F, T, Psi, PsiA, Cap
real(c_double), intent(in) :: L, H, cosA
integer(c_int), intent(in) :: CaseID
@ -1254,14 +1254,14 @@ contains !**********************************************************************
Psi = 0.0d+00
PsiA = 0.0d+00
Cap = 0.0d+00
return
return
end if
L2 = 0.5d+00 * L
sinA = dsqrt ( 1.0d+00 - cosA * cosA )
call TPMCa1 ( Ca, CaA, Ka, KaA, cosA, sinA )
IntSign = TPMSTInt1 ( GG, FF, Fh, Fx, H, L2 * Ca )
IntSign = TPMSTInt1 ( GGi, FFi, Fhi, Fxi, H, TPMSTXmax )
IntSign = TPMSTInt1 ( GG, FF, Fh, Fx, H, L2 * Ca )
IntSign = TPMSTInt1 ( GGi, FFi, Fhi, Fxi, H, TPMSTXmax )
if ( IntSign .ne. 1 ) then
Qi = 0.0d+00
Ui = 0.0d+00
@ -1275,11 +1275,11 @@ contains !**********************************************************************
PsiA = 0.0d+00
Cap = 0.0d+00
TPMSTForceTorque = 0
return
return
end if
call TPMCu1 ( Cu, CuH, CuA, H, cosA, sinA )
Psi = Cu / Ca
PsiA = ( CuA * Ca - Cu * CaA ) / Ca / Ca
Cap = CuA / Cu - KaA / Ka - cosA / sinA
@ -1287,16 +1287,16 @@ contains !**********************************************************************
Ui = 2.0d+00 * Psi * FFi
Fi = - 2.0d+00 * ( CuH * FFi / Ca + Psi * Fhi )
Ti = - Cap * Ui
Q = 2.0d+00 * Cu * GG / Ca
U = 2.0d+00 * Cu * FF / Ca
F = - 2.0d+00 * ( CuH * FF / Ca + Psi * Fh )
T = - 2.0d+00 * ( ( CuA * Ka - Cu * KaA ) / ( Ka * Ka * sinA ) - Cu * cosA / ( Ka * sinA * sinA ) ) * FF &
- 2.0d+00 * Cu / ( Ka * sinA ) * Fx * L2 * ( KaA * sinA + Ka * cosA )
TPMSTForceTorque = 1
end function TPMSTForceTorque !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine TPMSTInit () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double) :: X, Q, U, DX, DDX, XMin, XMax
integer(c_int) :: i, j, k
@ -1307,7 +1307,7 @@ contains !**********************************************************************
TPMSTDH12 = TPMSTH2 - TPMSTH1
TPMSTXmax = TPMHMax + TPMSTDelta
DX = 1.0 / TPMNX1
do j = 0, TPMNX1
do j = 0, TPMNX1
TPMSTX(j) = DX * j
end do
do i = 0, TPMNH1
@ -1323,7 +1323,7 @@ contains !**********************************************************************
TPMSTF(i,0) = 0.0d+00
TPMSTFyy(i,0) = U
TPMSTFyy(i,TPMNX1) = 0.0d+00
do j = 1, TPMNX1
do j = 1, TPMNX1
TPMSTG(i,j) = TPMSTG(i,j-1)
TPMSTF(i,j) = TPMSTF(i,j-1)
do k = 0, TPMSTNXS - 1
@ -1334,18 +1334,18 @@ contains !**********************************************************************
end do
end do
call CreateSpline2 ( 3, 3, 3, 3, TPMNH, TPMNX, TPMNMAX, TPMSTH, TPMSTX, TPMSTF, TPMSTFxx, &
TPMSTFyy, TPMSTFxxyy, FF, MM, DD, K0, K1, K2 )
TPMSTFyy, TPMSTFxxyy, FF, MM, DD, K0, K1, K2 )
end subroutine TPMSTInit !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!---------------------------------------------------------------------------------------------------
! Interaction functions: They can be used for calculation of the potential and forces between a
! Interaction functions: They can be used for calculation of the potential and forces between a
! segment and an infinite or semi-infinite nanotube.
!---------------------------------------------------------------------------------------------------
subroutine TPMSegmentForces ( F2_1, F2_2, F1_1, F1_2, R1_1, R1_2, R2, Laxis2, L2 ) !!!!!!!!!
real(c_double), dimension(0:2), intent(out) :: F2_1, F2_2
real(c_double), dimension(0:2), intent(in) :: F1_1, F1_2, R1_1, R1_2, R2, Laxis2
real(c_double), intent(in) :: L2
real(c_double), intent(in) :: L2
!-------------------------------------------------------------------------------------------
real(c_double), dimension(0:2) :: F, M, RR
!-------------------------------------------------------------------------------------------
@ -1389,11 +1389,11 @@ contains !**********************************************************************
L2 = S_V3norm3 ( Laxis2 )
Laxis1 = Laxis1 / L1
Laxis2 = Laxis2 / L2
L1 = 0.5d+00 * L1
L1 = 0.5d+00 * L1
L2 = 0.5d+00 * L2
if ( SType2 == 2 ) Laxis2 = - Laxis2
GeomID = LineLine ( H, cosA, D1, D2, L12, R1, Laxis1, R2, Laxis2, TPGeomPrec )
! Angle switch
if ( TPMASwitch == 0 ) then
if ( GeomID == MD_LINES_PAR ) then
@ -1414,7 +1414,7 @@ contains !**********************************************************************
SwitchID = 1
end if
end if
if ( SwitchID < 2 ) then
D2 = D2 - L2
if ( SType2 == 0 ) then
@ -1429,14 +1429,14 @@ contains !**********************************************************************
Ly = Ly * S
if ( IntSigna > 0 ) then
F1_1a = F1(0) * L12 + F1(1) * Ly + F1(2) * Laxis1
F1_2a = F2(0) * L12 + F2(1) * Ly + F2(2) * Laxis1
F1_2a = F2(0) * L12 + F2(1) * Ly + F2(2) * Laxis1
else
F1_1a = 0.0d+00
F1_2a = 0.0d+00
end if
end if
if ( SwitchID > 0 ) then
if ( SwitchID > 0 ) then
if ( SType2 == 0 ) then
call LinePoint ( H, L12, R2, Laxis2, R1 )
L12 = L12 - R1
@ -1451,7 +1451,7 @@ contains !**********************************************************************
else
L12 = L12 / H
F1_1b = F1(0) * L12 + F1(2) * Laxis1
F1_2b = F2(0) * L12 + F2(2) * Laxis1
F1_2b = F2(0) * L12 + F2(2) * Laxis1
end if
else
F1_1b = 0.0d+00
@ -1480,7 +1480,7 @@ contains !**********************************************************************
F1_2 = F1_2b
Fd = Fdb
TPMInteractionF = IntSignb
else
else
W1 = 1.0d+00 - W
Q = W * Qa + W1 * Qb
U = W * Ua + W1 * Ub
@ -1490,7 +1490,7 @@ contains !**********************************************************************
Fd = W * Fda + W1 * Fdb
TPMInteractionF = 0
if ( IntSigna > 0 .or. IntSignb > 0 ) TPMInteractionF = 1
end if
end if
! Calculation of forces for the complimentary tube
if ( SType2 == 2 ) Laxis2 = - Laxis2
@ -1510,7 +1510,7 @@ contains !**********************************************************************
F2_1 = F2_1 - DR
end if
end function TPMInteractionF !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function TPMInteractionU ( Q, U, R1_1, R1_2, R2_1, R2_2, SType2 ) !!!!!!!!!!!
real(c_double), intent(inout) :: Q, U
real(c_double), dimension(0:2), intent(in) :: R1_1, R1_2, R2_1, R2_2
@ -1560,7 +1560,7 @@ contains !**********************************************************************
IntSigna = TPMSSTPotential ( Qa, Ua, D1 - L1, D1 + L1, H, cosA, D2 - L2, TPMNN )
end if
end if
if ( SwitchID > 0 ) then
if ( Stype2 == 0 ) then
call LinePoint ( H, L12, R2, Laxis2, R1 )
@ -1573,7 +1573,7 @@ contains !**********************************************************************
IntSignb = TPMSSTPotentialPar ( Qb, Ub, R1_1, Laxis1, R2_2, Laxis2, 2.0d+00 * L1, TPMNN )
end if
end if
if ( SwitchID == 0 ) then
Q = Qa
U = Ua
@ -1612,14 +1612,14 @@ contains !**********************************************************************
D2 = 2.0d+00 * Delta
do i = 0, 2
DD = - Delta
do j = 0 , 1
RR = R1_1
do j = 0 , 1
RR = R1_1
RR(i) = RR(i) + DD
IntSign = TPMInteractionU ( QQ, U1_1(j,i), RR, R1_2, R2_1, R2_2, SType2 )
RR = R1_2
RR = R1_2
RR(i) = RR(i) + DD
IntSign = TPMInteractionU ( QQ, U1_2(j,i), R1_1, RR, R2_1, R2_2, SType2 )
RR = R2_1
RR = R2_1
RR(i) = RR(i) + DD;
IntSign = TPMInteractionU ( QQ, U2_1(j,i), R1_1, R1_2, RR, R2_2, SType2 )
RR = R2_2
@ -1635,7 +1635,7 @@ contains !**********************************************************************
F2_2(i) = ( U2_2(0,i) - U2_2(1,i) ) / D2
end do
end function TPMInteractionFNum !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!---------------------------------------------------------------------------------------------------
! Initialization
!---------------------------------------------------------------------------------------------------
@ -1643,10 +1643,10 @@ contains !**********************************************************************
subroutine TPMInit ( ChiIndM, ChiIndN ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int), intent(in) :: ChiIndM, ChiIndN
real(c_double) :: RT, DX
character*512 :: PDate
character(len=512) :: PDate
!-------------------------------------------------------------------------------------------
TPPotType = TP_POT_MONO_R
! Here we calculate the radius of nanotubes
RT = TPBAcc * sqrt ( 3.0d+00 * ( ChiIndM * ChiIndM + ChiIndN * ChiIndN + ChiIndM * ChiIndN ) ) / M_2PI
@ -1661,7 +1661,7 @@ contains !**********************************************************************
TPMHmax = TPMR1 + TPMR2 + TPBRcutoff
TPMDH = TPMHmax / TPMNH1
! Parameters of the angle switch
TPMASMin = sqr ( cos ( rad ( TPMAS ) ) )
TPMASMax = 1.0d+00 - TPGeomPrec
@ -1669,30 +1669,29 @@ contains !**********************************************************************
if ( TPMStartMode == 1 ) then
TPMUnitID = OpenFile ( TPMFile, 'rt', '' )
read ( unit = TPMUnitID, fmt = '()' )
read ( unit = TPMUnitID, fmt = '()' )
read ( unit = TPMUnitID, fmt = '()' )
read ( unit = TPMUnitID, fmt = '()' )
read ( unit = TPMUnitID, fmt = '()' )
read ( unit = TPMUnitID, fmt = '()' )
else
TPMUnitID = OpenFile ( TPMFile, 'wt', '' )
call fdate( PDate )
write ( unit = TPMUnitID, fmt = '(a,a)' ) 'DATE ', PDate
write ( unit = TPMUnitID, fmt = '(a,a)' ) 'DATE (unknown)'
write ( unit = TPMUnitID, fmt = '(a,i3,a,i3,a)' ) &
'Tabulated data of the tubular potential for (', ChiIndM, ',', ChiIndN, ') CNTs'
write ( unit = TPMUnitID, fmt = '(a)' ) &
'A. N. Volkov, L. V. Zhigilei, J. Phys. Chem. C 114, 5513-5531, 2010. doi: 10.1021/jp906142h'
end if
call TPMSSTPInit ()
call TPMSTPInit ()
DX = TPMR1 + TPMR2 + TPBRcutoff
call TPMAInit ( - DX, DX, - DX, DX )
call TPMAInit ( - DX, DX, - DX, DX )
call TPMSTInit ()
call CloseFile ( TPMUnitID )
end subroutine TPMInit !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
end module TubePotMono !****************************************************************************

60
lib/mesont/TubePotTrue.f90
View File

@ -9,9 +9,9 @@
! the GNU General Public License.
!
! See the README file in the top-level LAMMPS directory.
!
!
! Contributing author: Alexey N. Volkov, UA, avolkov1@ua.edu
!-------------------------------------------------------------------------
!-------------------------------------------------------------------------
module TubePotTrue !********************************************************************************
!
@ -25,8 +25,8 @@ module TubePotTrue !************************************************************
!
!---------------------------------------------------------------------------------------------------
!
! This module implements calculation of the true potential and transfer functions for interaction
! between two cylinder segments of nanotubes by direct integration over the surfaces of both
! This module implements calculation of the true potential and transfer functions for interaction
! between two cylinder segments of nanotubes by direct integration over the surfaces of both
! segments.
!
!***************************************************************************************************
@ -55,15 +55,15 @@ implicit none
integer(c_int) :: NX, NE ! Number of nodes for numerical integration
real(c_double) :: DX, DE ! Spacings
real(c_double), dimension(0:2,0:2) :: M ! Transformation matrix
real(c_double), dimension(0:TPTNXMAX-1,0:TPTNXMAX-1,0:2) :: Rtab! Node coordinates
real(c_double), dimension(0:TPTNXMAX-1,0:TPTNXMAX-1,0:2) :: Rtab! Node coordinates
end type TPTSEG !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!---------------------------------------------------------------------------------------------------
! Global variables
!---------------------------------------------------------------------------------------------------
type(TPTSEG) :: TPTSeg1, TPTSeg2 ! Two segments
contains !******************************************************************************************
subroutine TPTSegAxisVector ( S, Laxis ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
@ -96,11 +96,11 @@ contains !**********************************************************************
!-------------------------------------------------------------------------------------------
call TPTSegAxisVector ( S, Laxis )
call TPTSegRadVector ( S, Lrad, Eps )
R(0) = S%X + X * Laxis(0) + S%R * Lrad(0)
R(0) = S%X + X * Laxis(0) + S%R * Lrad(0)
R(1) = S%Y + X * Laxis(1) + S%R * Lrad(1)
R(2) = S%Z + X * Laxis(2) + S%R * Lrad(2)
end subroutine TPTRadiusVector !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine TPTCalcSegNodeTable ( S ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
type(TPTSEG), intent(inout) :: S
!-------------------------------------------------------------------------------------------
@ -111,7 +111,7 @@ contains !**********************************************************************
call RotationMatrix3 ( S%M, S%Psi, S%Theta, S%Phi )
do i = 0, S%NX - 1
Eps = 0.0d+00
do j = 0, S%NE - 1
do j = 0, S%NE - 1
call TPTRadiusVector ( S, S%Rtab(i,j,0:2), X, Eps )
Eps = Eps + S%DE
end do
@ -133,12 +133,12 @@ contains !**********************************************************************
S%Z = Rcenter(2)
call TPTCalcSegNodeTable ( S )
end subroutine TPTSetSegPosition1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
subroutine TPTSetSegPosition2 ( S, R1, R2 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
type(TPTSEG), intent(inout) :: S
real(c_double), dimension(0:2), intent(in) :: R1, R2
!-------------------------------------------------------------------------------------------
real(c_double), dimension(0:2) :: R, Laxis
real(c_double), dimension(0:2) :: R, Laxis
real(c_double) :: L
!-------------------------------------------------------------------------------------------
R = 0.5 * ( R1 + R2 )
@ -147,7 +147,7 @@ contains !**********************************************************************
Laxis = Laxis / L
call TPTSetSegPosition1 ( S, R, Laxis, L )
end subroutine TPTSetSegPosition2 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function TPTCheckIntersection ( S1, S2 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
type(TPTSEG), intent(in) :: S1, S2
!-------------------------------------------------------------------------------------------
@ -193,7 +193,7 @@ contains !**********************************************************************
Xmin = 0.0d+00
Xmax = 0.0d+00
TPTCalcPointRange = 0
return
return
end if
Distance = sqrt ( TPBRcutoff * TPBRcutoff - Distance * Distance )
Xmin = Displacement - Distance
@ -218,13 +218,13 @@ contains !**********************************************************************
R2_2(1) = - X2_2 * sin ( A )
R2_2(2) = X2_2 * cos ( A )
end subroutine TPTGetEnds !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!---------------------------------------------------------------------------------------------------
! Tubular potential
!---------------------------------------------------------------------------------------------------
integer(c_int) function TPTPointPotential ( Q, U, F, R, S ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
! This function returns the potential U and force F applied to an atom in position R and
! This function returns the potential U and force F applied to an atom in position R and
! produced by the segment S.
!-------------------------------------------------------------------------------------------
real(c_double), intent(out) :: Q, U
@ -243,7 +243,7 @@ contains !**********************************************************************
F = 0.0d+00
if ( TPTCalcPointRange ( S, Xmin, Xmax, R ) == 0 ) return
X = - S%L / 2.0
do i = 0, S%NX - 1
do i = 0, S%NX - 1
if ( X > Xmin .and. X < Xmax ) then
QQ = 0.0d+00
UU = 0.0d+00
@ -264,7 +264,7 @@ contains !**********************************************************************
Q = Q + 0.5d+00 * QQ
U = U + 0.5d+00 * UU
F = F + 0.5d+00 * FF
else
else
Q = Q + QQ
U = U + UU
F = F + FF
@ -279,7 +279,7 @@ contains !**********************************************************************
end function TPTPointPotential !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function TPTSectionPotential ( Q, U, F, M, S, i, Ssource ) !!!!!!!!!!!!!!!!!!
! This function returns the potential U, force F and torque M produced by the segment Ssource
! This function returns the potential U, force F and torque M produced by the segment Ssource
! and applied to the i-th circular cross-section of the segment S.
!-------------------------------------------------------------------------------------------
real(c_double), intent(out) :: Q, U
@ -290,7 +290,7 @@ contains !**********************************************************************
integer(c_int) :: j
real(c_double), dimension(0:2) :: R, Fp, Mp, Lrad
real(c_double) :: Qp, Up, Eps
real(c_double) :: Coeff
real(c_double) :: Coeff
!-------------------------------------------------------------------------------------------
TPTSectionPotential = 0
Q = 0.0d+00
@ -321,7 +321,7 @@ contains !**********************************************************************
end function TPTSectionPotential !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function TPTSegmentPotential ( Q, U, F, M, S, Ssource ) !!!!!!!!!!!!!!!!!!!!!!
! This function returns the potential U, force F and torque M produced by the segment
! This function returns the potential U, force F and torque M produced by the segment
! Ssource and applied to the segment S.
!-------------------------------------------------------------------------------------------
real(c_double), intent(out) :: Q, U
@ -340,7 +340,7 @@ contains !**********************************************************************
TPTSegmentPotential = 2
return
end if
do i = 0, S%NX - 1
do i = 0, S%NX - 1
if ( TPTSectionPotential ( Qc, Uc, Fc, Mc, S, i, Ssource ) == 1 ) then
if ( i == 0 .or. i == S%NX - 1 ) then
Q = Q + 0.5d+00 * Qc
@ -355,17 +355,17 @@ contains !**********************************************************************
end if
TPTSegmentPotential = 1
end if
end do
end do
Q = Q * S%DX
U = U * S%DX
F = F * S%DX
M = M * S%DX
end function TPTSegmentPotential !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!---------------------------------------------------------------------------------------------------
! Forces
!---------------------------------------------------------------------------------------------------
subroutine TPTSegmentForces ( F1, F2, F, M, Laxis, L ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), dimension(0:2), intent(out) :: F1, F2
real(c_double), dimension(0:2), intent(in) :: F, M, Laxis
@ -376,10 +376,10 @@ contains !**********************************************************************
FF = 0.5d+00 * F
MM = M / L
call V3_V3xxV3 ( FFF, MM, Laxis )
F1 = FF - FFF
F2 = FF + FFF
F1 = FF - FFF
F2 = FF + FFF
end subroutine TPTSegmentForces !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
integer(c_int) function TPTInteractionF ( Q, U, F1_1, F1_2, F2_1, F2_2, R1_1, R1_2, R2_1, R2_2 )
! This function returns the potential and forces applied to the ends of segments.
!-------------------------------------------------------------------------------------------
@ -413,7 +413,7 @@ contains !**********************************************************************
!---------------------------------------------------------------------------------------------------
! Initialization
!---------------------------------------------------------------------------------------------------
subroutine TPTInit ( R1, R2, NX, NE ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
real(c_double), intent(in) :: R1, R2
integer(c_int), intent(in) :: NX, NE

13
src/INTERLAYER/pair_ilp_graphene_hbn.cpp
View File

@ -47,6 +47,7 @@ using namespace InterLayer;
#define PGDELTA 1
static const char cite_ilp[] =
"ilp/graphene/hbn potential doi:10.1021/acs.nanolett.8b02848\n"
"@Article{Ouyang2018\n"
" author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},\n"
" title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},\n"
@ -482,7 +483,7 @@ void PairILPGrapheneHBN::calc_FRep(int eflag, int /* vflag */)
double dprodnorm1[3] = {0.0, 0.0, 0.0};
double fp1[3] = {0.0, 0.0, 0.0};
double fprod1[3] = {0.0, 0.0, 0.0};
double delkj[3] = {0.0, 0.0, 0.0};
double delki[3] = {0.0, 0.0, 0.0};
double fk[3] = {0.0, 0.0, 0.0};
inum = list->inum;
@ -588,12 +589,12 @@ void PairILPGrapheneHBN::calc_FRep(int eflag, int /* vflag */)
f[k][0] += fk[0];
f[k][1] += fk[1];
f[k][2] += fk[2];
delkj[0] = x[k][0] - x[j][0];
delkj[1] = x[k][1] - x[j][1];
delkj[2] = x[k][2] - x[j][2];
delki[0] = x[k][0] - x[i][0];
delki[1] = x[k][1] - x[i][1];
delki[2] = x[k][2] - x[i][2];
if (evflag)
ev_tally_xyz(k, j, nlocal, newton_pair, 0.0, 0.0, fk[0], fk[1], fk[2], delkj[0],
delkj[1], delkj[2]);
ev_tally_xyz(k, i, nlocal, newton_pair, 0.0, 0.0, fk[0], fk[1], fk[2], delki[0],
delki[1], delki[2]);
}
if (eflag) pvector[1] += evdwl = Tap * Vilp;

13
src/INTERLAYER/pair_kolmogorov_crespi_full.cpp
View File

@ -47,6 +47,7 @@ using namespace InterLayer;
#define PGDELTA 1
static const char cite_kc[] =
"kolmogorov/crespi/full potential doi:10.1021/acs.nanolett.8b02848\n"
"@Article{Ouyang2018\n"
" author = {W. Ouyang, D. Mandelli, M. Urbakh, and O. Hod},\n"
" title = {Nanoserpents: Graphene Nanoribbon Motion on Two-Dimensional Hexagonal Materials},\n"
@ -478,7 +479,7 @@ void PairKolmogorovCrespiFull::calc_FRep(int eflag, int /* vflag */)
double dprodnorm1[3] = {0.0, 0.0, 0.0};
double fp1[3] = {0.0, 0.0, 0.0};
double fprod1[3] = {0.0, 0.0, 0.0};
double delkj[3] = {0.0, 0.0, 0.0};
double delki[3] = {0.0, 0.0, 0.0};
double fk[3] = {0.0, 0.0, 0.0};
inum = list->inum;
@ -585,12 +586,12 @@ void PairKolmogorovCrespiFull::calc_FRep(int eflag, int /* vflag */)
f[k][0] += fk[0];
f[k][1] += fk[1];
f[k][2] += fk[2];
delkj[0] = x[k][0] - x[j][0];
delkj[1] = x[k][1] - x[j][1];
delkj[2] = x[k][2] - x[j][2];
delki[0] = x[k][0] - x[i][0];
delki[1] = x[k][1] - x[i][1];
delki[2] = x[k][2] - x[i][2];
if (evflag)
ev_tally_xyz(k, j, nlocal, newton_pair, 0.0, 0.0, fk[0], fk[1], fk[2], delkj[0],
delkj[1], delkj[2]);
ev_tally_xyz(k, j, nlocal, newton_pair, 0.0, 0.0, fk[0], fk[1], fk[2], delki[0],
delki[1], delki[2]);
}
if (eflag) {

26
src/INTERLAYER/pair_kolmogorov_crespi_z.cpp
View File

@ -28,6 +28,7 @@
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "potential_file_reader.h"
#include "tokenizer.h"
@ -158,7 +159,18 @@ void PairKolmogorovCrespiZ::compute(int eflag, int vflag)
if (eflag) { evdwl = -p.A * p.z06 / r6 + exp1 * sumCff - offset[itype][jtype]; }
if (evflag) {
ev_tally_xyz(i, j, nlocal, newton_pair, evdwl, 0, fsum, fsum, fpair, delx, dely, delz);
ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz);
if (vflag_either) {
double fi[3],fj[3];
fi[0] = delx * fpair1;
fi[1] = dely * fpair1;
fi[2] = 0;
fj[0] = -delx * fpair1;
fj[1] = -dely * fpair1;
fj[2] = 0;
v_tally2_newton(i,fi,x[i]);
v_tally2_newton(j,fj,x[j]);
}
}
}
}
@ -228,6 +240,18 @@ void PairKolmogorovCrespiZ::coeff(int narg, char **arg)
if (count == 0) error->all(FLERR, "Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairKolmogorovCrespiZ::init_style()
{
if (force->newton_pair == 0)
error->all(FLERR,"Pair style kolmogorov/crespi/z requires newton pair on");
neighbor->request(this,instance_me);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */

1
src/INTERLAYER/pair_kolmogorov_crespi_z.h
View File

@ -32,6 +32,7 @@ class PairKolmogorovCrespiZ : public Pair {
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
void init_style();
double init_one(int, int);
static constexpr int NPARAMS_PER_LINE = 11;

43
src/INTERLAYER/pair_lebedeva_z.cpp
View File

@ -30,6 +30,7 @@
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "potential_file_reader.h"
#include "tokenizer.h"
@ -137,16 +138,16 @@ void PairLebedevaZ::compute(int eflag, int vflag)
// derivatives
fpair = -6.0*p.A*p.z06/r8+p.B*p.alpha*exp1/r; // used for x,y,z
der = p.D1+2*p.D2*rhosq-p.lambda1*sumD; // used for x,y
fxy = fpair - 2*p.C*exp2*exp3*der;
fz = fpair + 2*p.C*p.lambda2*sumD*exp2*exp3;
fxy = 2*p.C*exp2*exp3*der;
fz = 2*p.C*p.lambda2*sumD*exp2*exp3;
f[i][0] += delx*fxy;
f[i][1] += dely*fxy;
f[i][2] += delz*fz;
f[i][0] += delx*(fpair-fxy);
f[i][1] += dely*(fpair-fxy);
f[i][2] += delz*(fpair+fz);
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fxy;
f[j][1] -= dely*fxy;
f[j][2] -= delz*fz;
f[j][0] -= delx*(fpair-fxy);
f[j][1] -= dely*(fpair-fxy);
f[j][2] -= delz*(fpair+fz);
}
if (eflag) {
@ -154,8 +155,18 @@ void PairLebedevaZ::compute(int eflag, int vflag)
}
if (evflag) {
ev_tally_xyz(i,j,nlocal,newton_pair,evdwl,0,
-fxy,-fxy,-fz,delx,dely,delz);
ev_tally(i, j, nlocal, newton_pair, evdwl, 0.0, fpair, delx, dely, delz);
if (vflag_either) {
double fi[3],fj[3];
fi[0] = -delx * fxy;
fi[1] = -dely * fxy;
fi[2] = delz * fz;
fj[0] = delx * fxy;
fj[1] = dely * fxy;
fj[2] = -delz * fz;
v_tally2_newton(i,fi,x[i]);
v_tally2_newton(j,fj,x[j]);
}
}
}
}
@ -226,6 +237,18 @@ void PairLebedevaZ::coeff(int narg, char **arg)
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLebedevaZ::init_style()
{
if (force->newton_pair == 0)
error->all(FLERR,"Pair style lebedeva/z requires newton pair on");
neighbor->request(this,instance_me);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */

1
src/INTERLAYER/pair_lebedeva_z.h
View File

@ -32,6 +32,7 @@ class PairLebedevaZ : public Pair {
virtual void compute(int, int);
void settings(int, char **);
void coeff(int, char **);
void init_style();
double init_one(int, int);
static constexpr int NPARAMS_PER_LINE = 12;

18
src/KOKKOS/pair_snap_kokkos.h
View File

@ -44,7 +44,8 @@ struct TagPairSNAPComputeForce{};
struct TagPairSNAPComputeNeigh{};
struct TagPairSNAPComputeCayleyKlein{};
struct TagPairSNAPPreUi{};
struct TagPairSNAPComputeUi{};
struct TagPairSNAPComputeUiSmall{}; // more parallelism, more divergence
struct TagPairSNAPComputeUiLarge{}; // less parallelism, no divergence
struct TagPairSNAPTransformUi{}; // re-order ulisttot from SoA to AoSoA, zero ylist
struct TagPairSNAPComputeZi{};
struct TagPairSNAPBeta{};
@ -53,7 +54,9 @@ struct TagPairSNAPTransformBi{}; // re-order blist from AoSoA to AoS
struct TagPairSNAPComputeYi{};
struct TagPairSNAPComputeYiWithZlist{};
template<int dir>
struct TagPairSNAPComputeFusedDeidrj{};
struct TagPairSNAPComputeFusedDeidrjSmall{}; // more parallelism, more divergence
template<int dir>
struct TagPairSNAPComputeFusedDeidrjLarge{}; // less parallelism, no divergence
// CPU backend only
struct TagPairSNAPComputeNeighCPU{};
@ -143,7 +146,10 @@ public:
void operator() (TagPairSNAPPreUi,const int iatom_mod, const int j, const int iatom_div) const;
KOKKOS_INLINE_FUNCTION
void operator() (TagPairSNAPComputeUi,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUi>::member_type& team) const;
void operator() (TagPairSNAPComputeUiSmall,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUiSmall>::member_type& team) const;
KOKKOS_INLINE_FUNCTION
void operator() (TagPairSNAPComputeUiLarge,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeUiLarge>::member_type& team) const;
KOKKOS_INLINE_FUNCTION
void operator() (TagPairSNAPTransformUi,const int iatom_mod, const int j, const int iatom_div) const;
@ -168,7 +174,11 @@ public:
template<int dir>
KOKKOS_INLINE_FUNCTION
void operator() (TagPairSNAPComputeFusedDeidrj<dir>,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeFusedDeidrj<dir> >::member_type& team) const;
void operator() (TagPairSNAPComputeFusedDeidrjSmall<dir>,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeFusedDeidrjSmall<dir> >::member_type& team) const;
template<int dir>
KOKKOS_INLINE_FUNCTION
void operator() (TagPairSNAPComputeFusedDeidrjLarge<dir>,const typename Kokkos::TeamPolicy<DeviceType, TagPairSNAPComputeFusedDeidrjLarge<dir> >::member_type& team) const;
// CPU backend only
KOKKOS_INLINE_FUNCTION

162
src/KOKKOS/pair_snap_kokkos_impl.h
View File

@ -341,18 +341,32 @@ void PairSNAPKokkos<DeviceType, real_type, vector_length>::compute(int eflag_in,
// ComputeUi w/vector parallelism, shared memory, direct atomicAdd into ulisttot
{
// team_size_compute_ui is defined in `pair_snap_kokkos.h`
// scratch size: 32 atoms * (twojmax+1) cached values, no double buffer
const int tile_size = vector_length * (twojmax + 1);
const int scratch_size = scratch_size_helper<complex>(team_size_compute_ui * tile_size);
// total number of teams needed: (natoms / 32) * (max_neighs) * ("bend" locations)
const int n_teams = chunk_size_div * max_neighs * (twojmax + 1);
const int n_teams_div = (n_teams + team_size_compute_ui - 1) / team_size_compute_ui;
if (chunk_size < parallel_thresh)
{
// Version with parallelism over j_bend
SnapAoSoATeamPolicy<DeviceType, team_size_compute_ui, TagPairSNAPComputeUi> policy_ui(n_teams_div, team_size_compute_ui, vector_length);
policy_ui = policy_ui.set_scratch_size(0, Kokkos::PerTeam(scratch_size));
Kokkos::parallel_for("ComputeUi",policy_ui,*this);
// total number of teams needed: (natoms / 32) * (max_neighs) * ("bend" locations)
const int n_teams = chunk_size_div * max_neighs * (twojmax + 1);
const int n_teams_div = (n_teams + team_size_compute_ui - 1) / team_size_compute_ui;
SnapAoSoATeamPolicy<DeviceType, team_size_compute_ui, TagPairSNAPComputeUiSmall> policy_ui(n_teams_div, team_size_compute_ui, vector_length);
policy_ui = policy_ui.set_scratch_size(0, Kokkos::PerTeam(scratch_size));
Kokkos::parallel_for("ComputeUiSmall",policy_ui,*this);
} else {
// Version w/out parallelism over j_bend
// total number of teams needed: (natoms / 32) * (max_neighs)
const int n_teams = chunk_size_div * max_neighs;
const int n_teams_div = (n_teams + team_size_compute_ui - 1) / team_size_compute_ui;
SnapAoSoATeamPolicy<DeviceType, team_size_compute_ui, TagPairSNAPComputeUiLarge> policy_ui(n_teams_div, team_size_compute_ui, vector_length);
policy_ui = policy_ui.set_scratch_size(0, Kokkos::PerTeam(scratch_size));
Kokkos::parallel_for("ComputeUiLarge",policy_ui,*this);
}
}
//TransformUi: un-"fold" ulisttot, zero ylist
@ -412,25 +426,51 @@ void PairSNAPKokkos<DeviceType, real_type, vector_length>::compute(int eflag_in,
const int tile_size = vector_length * (twojmax + 1);
const int scratch_size = scratch_size_helper<complex>(2 * team_size_compute_fused_deidrj * tile_size);
// total number of teams needed: (natoms / 32) * (max_neighs) * ("bend" locations)
const int n_teams = chunk_size_div * max_neighs * (twojmax + 1);
const int n_teams_div = (n_teams + team_size_compute_fused_deidrj - 1) / team_size_compute_fused_deidrj;
if (chunk_size < parallel_thresh)
{
// Version with parallelism over j_bend
// x direction
SnapAoSoATeamPolicy<DeviceType, team_size_compute_fused_deidrj, TagPairSNAPComputeFusedDeidrj<0> > policy_fused_deidrj_x(n_teams_div,team_size_compute_fused_deidrj,vector_length);
policy_fused_deidrj_x = policy_fused_deidrj_x.set_scratch_size(0, Kokkos::PerTeam(scratch_size));
Kokkos::parallel_for("ComputeFusedDeidrj<0>",policy_fused_deidrj_x,*this);
// total number of teams needed: (natoms / 32) * (max_neighs) * ("bend" locations)
const int n_teams = chunk_size_div * max_neighs * (twojmax + 1);
const int n_teams_div = (n_teams + team_size_compute_fused_deidrj - 1) / team_size_compute_fused_deidrj;
// y direction
SnapAoSoATeamPolicy<DeviceType, team_size_compute_fused_deidrj, TagPairSNAPComputeFusedDeidrj<1> > policy_fused_deidrj_y(n_teams_div,team_size_compute_fused_deidrj,vector_length);
policy_fused_deidrj_y = policy_fused_deidrj_y.set_scratch_size(0, Kokkos::PerTeam(scratch_size));
Kokkos::parallel_for("ComputeFusedDeidrj<1>",policy_fused_deidrj_y,*this);
// x direction
SnapAoSoATeamPolicy<DeviceType, team_size_compute_fused_deidrj, TagPairSNAPComputeFusedDeidrjSmall<0> > policy_fused_deidrj_x(n_teams_div,team_size_compute_fused_deidrj,vector_length);
policy_fused_deidrj_x = policy_fused_deidrj_x.set_scratch_size(0, Kokkos::PerTeam(scratch_size));
Kokkos::parallel_for("ComputeFusedDeidrjSmall<0>",policy_fused_deidrj_x,*this);
// z direction
SnapAoSoATeamPolicy<DeviceType, team_size_compute_fused_deidrj, TagPairSNAPComputeFusedDeidrj<2> > policy_fused_deidrj_z(n_teams_div,team_size_compute_fused_deidrj,vector_length);
policy_fused_deidrj_z = policy_fused_deidrj_z.set_scratch_size(0, Kokkos::PerTeam(scratch_size));
Kokkos::parallel_for("ComputeFusedDeidrj<2>",policy_fused_deidrj_z,*this);
// y direction
SnapAoSoATeamPolicy<DeviceType, team_size_compute_fused_deidrj, TagPairSNAPComputeFusedDeidrjSmall<1> > policy_fused_deidrj_y(n_teams_div,team_size_compute_fused_deidrj,vector_length);
policy_fused_deidrj_y = policy_fused_deidrj_y.set_scratch_size(0, Kokkos::PerTeam(scratch_size));
Kokkos::parallel_for("ComputeFusedDeidrjSmall<1>",policy_fused_deidrj_y,*this);
// z direction
SnapAoSoATeamPolicy<DeviceType, team_size_compute_fused_deidrj, TagPairSNAPComputeFusedDeidrjSmall<2> > policy_fused_deidrj_z(n_teams_div,team_size_compute_fused_deidrj,vector_length);
policy_fused_deidrj_z = policy_fused_deidrj_z.set_scratch_size(0, Kokkos::PerTeam(scratch_size));
Kokkos::parallel_for("ComputeFusedDeidrjSmall<2>",policy_fused_deidrj_z,*this);
} else {
// Version w/out parallelism over j_bend
// total number of teams needed: (natoms / 32) * (max_neighs)
const int n_teams = chunk_size_div * max_neighs;
const int n_teams_div = (n_teams + team_size_compute_fused_deidrj - 1) / team_size_compute_fused_deidrj;
// x direction
SnapAoSoATeamPolicy<DeviceType, team_size_compute_fused_deidrj, TagPairSNAPComputeFusedDeidrjLarge<0> > policy_fused_deidrj_x(n_teams_div,team_size_compute_fused_deidrj,vector_length);
policy_fused_deidrj_x = policy_fused_deidrj_x.set_scratch_size(0, Kokkos::PerTeam(scratch_size));
Kokkos::parallel_for("ComputeFusedDeidrjLarge<0>",policy_fused_deidrj_x,*this);
// y direction
SnapAoSoATeamPolicy<DeviceType, team_size_compute_fused_deidrj, TagPairSNAPComputeFusedDeidrjLarge<1> > policy_fused_deidrj_y(n_teams_div,team_size_compute_fused_deidrj,vector_length);
policy_fused_deidrj_y = policy_fused_deidrj_y.set_scratch_size(0, Kokkos::PerTeam(scratch_size));
Kokkos::parallel_for("ComputeFusedDeidrjLarge<1>",policy_fused_deidrj_y,*this);
// z direction
SnapAoSoATeamPolicy<DeviceType, team_size_compute_fused_deidrj, TagPairSNAPComputeFusedDeidrjLarge<2> > policy_fused_deidrj_z(n_teams_div,team_size_compute_fused_deidrj,vector_length);
policy_fused_deidrj_z = policy_fused_deidrj_z.set_scratch_size(0, Kokkos::PerTeam(scratch_size));
Kokkos::parallel_for("ComputeFusedDeidrjLarge<2>",policy_fused_deidrj_z,*this);
}
}
#endif // LMP_KOKKOS_GPU
@ -603,13 +643,13 @@ void PairSNAPKokkos<DeviceType, real_type, vector_length>::operator() (TagPairSN
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
const auto idxb = icoeff % idxb_max;
const auto idx_chem = icoeff / idxb_max;
auto bveci = my_sna.blist(idxb, idx_chem, ii);
real_type bveci = my_sna.blist(ii, idx_chem, idxb);
d_beta_pack(iatom_mod,icoeff,iatom_div) += d_coeffi[k]*bveci;
k++;
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
const auto jdxb = jcoeff % idxb_max;
const auto jdx_chem = jcoeff / idxb_max;
real_type bvecj = my_sna.blist(jdxb, jdx_chem, ii);
real_type bvecj = my_sna.blist(ii, jdx_chem, jdxb);
d_beta_pack(iatom_mod,icoeff,iatom_div) += d_coeffi[k]*bvecj;
d_beta_pack(iatom_mod,jcoeff,iatom_div) += d_coeffi[k]*bveci;
k++;
@ -736,7 +776,7 @@ void PairSNAPKokkos<DeviceType, real_type, vector_length>::operator() (TagPairSN
template<class DeviceType, typename real_type, int vector_length>
KOKKOS_INLINE_FUNCTION
void PairSNAPKokkos<DeviceType, real_type, vector_length>::operator() (TagPairSNAPComputeUi,const typename Kokkos::TeamPolicy<DeviceType,TagPairSNAPComputeUi>::member_type& team) const {
void PairSNAPKokkos<DeviceType, real_type, vector_length>::operator() (TagPairSNAPComputeUiSmall,const typename Kokkos::TeamPolicy<DeviceType,TagPairSNAPComputeUiSmall>::member_type& team) const {
SNAKokkos<DeviceType, real_type, vector_length> my_sna = snaKK;
// extract flattened atom_div / neighbor number / bend location
@ -756,11 +796,37 @@ void PairSNAPKokkos<DeviceType, real_type, vector_length>::operator() (TagPairSN
const int ninside = d_ninside(ii);
if (jj >= ninside) return;
my_sna.compute_ui(team,iatom_mod, jbend, jj, iatom_div);
my_sna.compute_ui_small(team, iatom_mod, jbend, jj, iatom_div);
});
}
template<class DeviceType, typename real_type, int vector_length>
KOKKOS_INLINE_FUNCTION
void PairSNAPKokkos<DeviceType, real_type, vector_length>::operator() (TagPairSNAPComputeUiLarge,const typename Kokkos::TeamPolicy<DeviceType,TagPairSNAPComputeUiLarge>::member_type& team) const {
SNAKokkos<DeviceType, real_type, vector_length> my_sna = snaKK;
// extract flattened atom_div / neighbor number / bend location
int flattened_idx = team.team_rank() + team.league_rank() * team_size_compute_ui;
// extract neighbor index, iatom_div
int iatom_div = flattened_idx / max_neighs; // removed "const" to work around GCC 7 bug
int jj = flattened_idx - iatom_div * max_neighs;
Kokkos::parallel_for(Kokkos::ThreadVectorRange(team, vector_length),
[&] (const int iatom_mod) {
const int ii = iatom_mod + vector_length * iatom_div;
if (ii >= chunk_size) return;
const int ninside = d_ninside(ii);
if (jj >= ninside) return;
my_sna.compute_ui_large(team,iatom_mod, jj, iatom_div);
});
}
template<class DeviceType, typename real_type, int vector_length>
KOKKOS_INLINE_FUNCTION
void PairSNAPKokkos<DeviceType, real_type, vector_length>::operator() (TagPairSNAPTransformUi,const int iatom_mod, const int idxu, const int iatom_div) const {
@ -861,9 +927,9 @@ void PairSNAPKokkos<DeviceType, real_type, vector_length>::operator() (TagPairSN
for (int itriple = 0; itriple < ntriples; itriple++) {
const auto blocal = my_sna.blist_pack(iatom_mod, idxb, itriple, iatom_div);
const real_type blocal = my_sna.blist_pack(iatom_mod, idxb, itriple, iatom_div);
my_sna.blist(idxb, itriple, iatom) = blocal;
my_sna.blist(iatom, itriple, idxb) = blocal;
}
}
@ -871,7 +937,7 @@ void PairSNAPKokkos<DeviceType, real_type, vector_length>::operator() (TagPairSN
template<class DeviceType, typename real_type, int vector_length>
template<int dir>
KOKKOS_INLINE_FUNCTION
void PairSNAPKokkos<DeviceType, real_type, vector_length>::operator() (TagPairSNAPComputeFusedDeidrj<dir>,const typename Kokkos::TeamPolicy<DeviceType,TagPairSNAPComputeFusedDeidrj<dir> >::member_type& team) const {
void PairSNAPKokkos<DeviceType, real_type, vector_length>::operator() (TagPairSNAPComputeFusedDeidrjSmall<dir>,const typename Kokkos::TeamPolicy<DeviceType,TagPairSNAPComputeFusedDeidrjSmall<dir> >::member_type& team) const {
SNAKokkos<DeviceType, real_type, vector_length> my_sna = snaKK;
// extract flattened atom_div / neighbor number / bend location
@ -891,12 +957,38 @@ void PairSNAPKokkos<DeviceType, real_type, vector_length>::operator() (TagPairSN
const int ninside = d_ninside(ii);
if (jj >= ninside) return;
my_sna.template compute_fused_deidrj<dir>(team, iatom_mod, jbend, jj, iatom_div);
my_sna.template compute_fused_deidrj_small<dir>(team, iatom_mod, jbend, jj, iatom_div);
});
}
template<class DeviceType, typename real_type, int vector_length>
template<int dir>
KOKKOS_INLINE_FUNCTION
void PairSNAPKokkos<DeviceType, real_type, vector_length>::operator() (TagPairSNAPComputeFusedDeidrjLarge<dir>,const typename Kokkos::TeamPolicy<DeviceType,TagPairSNAPComputeFusedDeidrjLarge<dir> >::member_type& team) const {
SNAKokkos<DeviceType, real_type, vector_length> my_sna = snaKK;
// extract flattened atom_div / neighbor number / bend location
int flattened_idx = team.team_rank() + team.league_rank() * team_size_compute_fused_deidrj;
// extract neighbor index, iatom_div
int iatom_div = flattened_idx / max_neighs; // removed "const" to work around GCC 7 bug
int jj = flattened_idx - max_neighs * iatom_div;
Kokkos::parallel_for(Kokkos::ThreadVectorRange(team, vector_length),
[&] (const int iatom_mod) {
const int ii = iatom_mod + vector_length * iatom_div;
if (ii >= chunk_size) return;
const int ninside = d_ninside(ii);
if (jj >= ninside) return;
my_sna.template compute_fused_deidrj_large<dir>(team, iatom_mod, jj, iatom_div);
});
}
/* ----------------------------------------------------------------------
Begin routines that are unique to the CPU codepath. These do not take
advantage of AoSoA data layouts, but that could be a good point of
@ -925,13 +1017,13 @@ void PairSNAPKokkos<DeviceType, real_type, vector_length>::operator() (TagPairSN
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
const auto idxb = icoeff % idxb_max;
const auto idx_chem = icoeff / idxb_max;
auto bveci = my_sna.blist(idxb,idx_chem,ii);
real_type bveci = my_sna.blist(ii,idx_chem,idxb);
d_beta(icoeff,ii) += d_coeffi[k]*bveci;
k++;
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
const auto jdxb = jcoeff % idxb_max;
const auto jdx_chem = jcoeff / idxb_max;
auto bvecj = my_sna.blist(jdxb,jdx_chem,ii);
real_type bvecj = my_sna.blist(ii,jdx_chem,jdxb);
d_beta(icoeff,ii) += d_coeffi[k]*bvecj;
d_beta(jcoeff,ii) += d_coeffi[k]*bveci;
k++;
@ -1221,7 +1313,7 @@ void PairSNAPKokkos<DeviceType, real_type, vector_length>::operator() (TagPairSN
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
const auto idxb = icoeff % idxb_max;
const auto idx_chem = icoeff / idxb_max;
evdwl += d_coeffi[icoeff+1]*my_sna.blist(idxb,idx_chem,ii);
evdwl += d_coeffi[icoeff+1]*my_sna.blist(ii,idx_chem,idxb);
}
// quadratic contributions
@ -1230,12 +1322,12 @@ void PairSNAPKokkos<DeviceType, real_type, vector_length>::operator() (TagPairSN
for (int icoeff = 0; icoeff < ncoeff; icoeff++) {
const auto idxb = icoeff % idxb_max;
const auto idx_chem = icoeff / idxb_max;
auto bveci = my_sna.blist(idxb,idx_chem,ii);
real_type bveci = my_sna.blist(ii,idx_chem,idxb);
evdwl += 0.5*d_coeffi[k++]*bveci*bveci;
for (int jcoeff = icoeff+1; jcoeff < ncoeff; jcoeff++) {
auto jdxb = jcoeff % idxb_max;
auto jdx_chem = jcoeff / idxb_max;
auto bvecj = my_sna.blist(jdxb,jdx_chem,ii);
auto bvecj = my_sna.blist(ii,jdx_chem,jdxb);
evdwl += d_coeffi[k++]*bveci*bvecj;
}
}

65
src/KOKKOS/sna_kokkos.h
View File

@ -45,12 +45,12 @@ struct WignerWrapper {
{ ; }
KOKKOS_INLINE_FUNCTION
complex get(const int& ma) {
complex get(const int& ma) const {
return complex(buffer[offset + 2 * vector_length * ma], buffer[offset + vector_length + 2 * vector_length * ma]);
}
KOKKOS_INLINE_FUNCTION
void set(const int& ma, const complex& store) {
void set(const int& ma, const complex& store) const {
buffer[offset + 2 * vector_length * ma] = store.re;
buffer[offset + vector_length + 2 * vector_length * ma] = store.im;
}
@ -122,8 +122,14 @@ inline
void compute_cayley_klein(const int&, const int&, const int&);
KOKKOS_INLINE_FUNCTION
void pre_ui(const int&, const int&, const int&, const int&); // ForceSNAP
// version of the code with parallelism over j_bend
KOKKOS_INLINE_FUNCTION
void compute_ui(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, const int, const int, const int, const int); // ForceSNAP
void compute_ui_small(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, const int, const int, const int, const int); // ForceSNAP
// version of the code without parallelism over j_bend
KOKKOS_INLINE_FUNCTION
void compute_ui_large(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, const int, const int, const int); // ForceSNAP
KOKKOS_INLINE_FUNCTION
void compute_zi(const int&, const int&, const int&); // ForceSNAP
KOKKOS_INLINE_FUNCTION
@ -135,6 +141,35 @@ inline
KOKKOS_INLINE_FUNCTION
void compute_bi(const int&, const int&, const int&); // ForceSNAP
// functions for derivatives, GPU only
// version of the code with parallelism over j_bend
template<int dir>
KOKKOS_INLINE_FUNCTION
void compute_fused_deidrj_small(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, const int, const int, const int, const int); //ForceSNAP
// version of the code without parallelism over j_bend
template<int dir>
KOKKOS_INLINE_FUNCTION
void compute_fused_deidrj_large(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, const int, const int, const int); //ForceSNAP
// core "evaluation" functions that get plugged into "compute" functions
// plugged into compute_ui_small, compute_ui_large
KOKKOS_FORCEINLINE_FUNCTION
void evaluate_ui_jbend(const WignerWrapper<real_type, vector_length>&, const complex&, const complex&, const real_type&, const int&,
const int&, const int&, const int&);
// plugged into compute_zi, compute_yi
KOKKOS_FORCEINLINE_FUNCTION
complex evaluate_zi(const int&, const int&, const int&, const int&, const int&, const int&, const int&, const int&, const int&,
const int&, const int&, const int&, const int&, const real_type*);
// plugged into compute_yi, compute_yi_with_zlist
KOKKOS_FORCEINLINE_FUNCTION
real_type evaluate_beta_scaled(const int&, const int&, const int&, const int&, const int&, const int&, const int&, const int&,
const Kokkos::View<real_type***, Kokkos::LayoutLeft, DeviceType> &);
// plugged into compute_fused_deidrj_small, compute_fused_deidrj_large
KOKKOS_FORCEINLINE_FUNCTION
real_type evaluate_duidrj_jbend(const WignerWrapper<real_type, vector_length>&, const complex&, const complex&, const real_type&,
const WignerWrapper<real_type, vector_length>&, const complex&, const complex&, const real_type&,
const int&, const int&, const int&, const int&);
// functions for bispectrum coefficients, CPU only
KOKKOS_INLINE_FUNCTION
void pre_ui_cpu(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team,const int&,const int&); // ForceSNAP
@ -148,11 +183,6 @@ inline
KOKKOS_INLINE_FUNCTION
void compute_bi_cpu(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int); // ForceSNAP
// functions for derivatives, GPU only
template<int dir>
KOKKOS_INLINE_FUNCTION
void compute_fused_deidrj(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, const int, const int, const int, const int); //ForceSNAP
// functions for derivatives, CPU only
KOKKOS_INLINE_FUNCTION
void compute_duidrj_cpu(const typename Kokkos::TeamPolicy<DeviceType>::member_type& team, int, int); //ForceSNAP
@ -168,23 +198,6 @@ inline
KOKKOS_INLINE_FUNCTION
void compute_s_dsfac(const real_type, const real_type, real_type&, real_type&); // compute_cayley_klein
static KOKKOS_FORCEINLINE_FUNCTION
void sincos_wrapper(double x, double* sin_, double *cos_) {
#ifdef __SYCL_DEVICE_ONLY__
*sin_ = sycl::sincos(x, cos_);
#else
sincos(x, sin_, cos_);
#endif
}
static KOKKOS_FORCEINLINE_FUNCTION
void sincos_wrapper(float x, float* sin_, float *cos_) {
#ifdef __SYCL_DEVICE_ONLY__
*sin_ = sycl::sincos(x, cos_);
#else
sincosf(x, sin_, cos_);
#endif
}
#ifdef TIMING_INFO
double* timers;
timespec starttime, endtime;
@ -207,7 +220,7 @@ inline
int twojmax, diagonalstyle;
t_sna_3d_ll blist;
t_sna_3d blist;
t_sna_3c_ll ulisttot;
t_sna_3c_ll ulisttot_full; // un-folded ulisttot, cpu only
t_sna_3c_ll zlist;

855
src/KOKKOS/sna_kokkos_impl.h
View File

File diff suppressed because it is too large Load Diff

1
src/MC/fix_atom_swap.cpp
View File

@ -516,7 +516,6 @@ double FixAtomSwap::energy_full()
if (force->kspace) force->kspace->compute(eflag,vflag);
if (modify->n_post_force) modify->post_force(vflag);
if (modify->n_end_of_step) modify->end_of_step();
update->eflag_global = update->ntimestep;
double total_energy = c_pe->compute_scalar();

2
src/MC/fix_charge_regulation.cpp
View File

@ -1108,7 +1108,7 @@ double FixChargeRegulation::energy_full() {
if (modify->n_pre_reverse) modify->pre_reverse(eflag,vflag);
if (modify->n_post_force) modify->post_force(vflag);
if (modify->n_end_of_step) modify->end_of_step();
update->eflag_global = update->ntimestep;
double total_energy = c_pe->compute_scalar();
return total_energy;

3
src/MC/fix_gcmc.cpp
View File

@ -2319,10 +2319,9 @@ double FixGCMC::energy_full()
if (modify->n_pre_reverse) modify->pre_reverse(eflag,vflag);
if (modify->n_post_force) modify->post_force(vflag);
if (modify->n_end_of_step) modify->end_of_step();
// NOTE: all fixes with energy_global_flag set and which
// operate at pre_force() or post_force() or end_of_step()
// operate at pre_force() or post_force()
// and which user has enabled via fix_modify energy yes,
// will contribute to total MC energy via pe->compute_scalar()

3
src/MC/fix_widom.cpp
View File

@ -1053,10 +1053,9 @@ double FixWidom::energy_full()
if (modify->n_pre_reverse) modify->pre_reverse(eflag,vflag);
if (modify->n_pre_force) modify->pre_force(vflag);
if (modify->n_end_of_step) modify->end_of_step();
// NOTE: all fixes with energy_global_flag set and which
// operate at pre_force() or post_force() or end_of_step()
// operate at pre_force() or post_force()
// and which user has enabled via fix_modify energy yes,
// will contribute to total MC energy via pe->compute_scalar()

5
src/ML-SNAP/pair_snap.cpp
View File

@ -628,7 +628,8 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
chemflag = 0;
bnormflag = 0;
wselfallflag = 0;
chunksize = 4096;
chunksize = 32768;
parallel_thresh = 8192;
// open SNAP parameter file on proc 0
@ -696,6 +697,8 @@ void PairSNAP::read_files(char *coefffilename, char *paramfilename)
wselfallflag = utils::inumeric(FLERR,keyval.c_str(),false,lmp);
else if (keywd == "chunksize")
chunksize = utils::inumeric(FLERR,keyval.c_str(),false,lmp);
else if (keywd == "parallelthresh")
parallel_thresh = utils::inumeric(FLERR,keyval.c_str(),false,lmp);
else
error->all(FLERR,"Unknown parameter '{}' in SNAP "
"parameter file", keywd);

2
src/ML-SNAP/pair_snap.h
View File

@ -59,7 +59,7 @@ class PairSNAP : public Pair {
double **scale; // for thermodynamic integration
int twojmax, switchflag, bzeroflag, bnormflag;
int chemflag, wselfallflag;
int chunksize;
int chunksize,parallel_thresh;
double rfac0, rmin0, wj1, wj2;
int rcutfacflag, twojmaxflag; // flags for required parameters
int beta_max; // length of beta

2
src/MOFFF/README
View File

@ -20,7 +20,7 @@ charges (dsf and long-range treatment of charges)
out-of-plane angle
See the file doc/drude_tutorial.html for getting started.
See the doc pages for "pair_style buck6d/coul/gauss", "anlge_style class2",
See the doc pages for "pair_style buck6d/coul/gauss", "angle_style class2",
"angle_style cosine/buck6d", and "improper_style inversion/harmonic"
commands to get started. Also see the above mentioned website and
literature for further documentation about the force field.

64
src/OPENMP/domain_omp.cpp
View File

@ -1,4 +1,3 @@
// clang-format off
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
@ -16,13 +15,16 @@
Contributing author : Axel Kohlmeyer (Temple U)
------------------------------------------------------------------------- */
#include "omp_compat.h"
#include "accelerator_omp.h"
#include "atom.h"
#include "error.h"
#include "omp_compat.h"
using namespace LAMMPS_NS;
typedef struct { double x,y,z; } dbl3_t;
typedef struct {
double x, y, z;
} dbl3_t;
/* ----------------------------------------------------------------------
enforce PBC and modify box image flags for each atom
@ -37,20 +39,35 @@ typedef struct { double x,y,z; } dbl3_t;
void DomainOMP::pbc()
{
dbl3_t * _noalias const x = (dbl3_t *)&atom->x[0][0];
dbl3_t * _noalias const v = (dbl3_t *)&atom->v[0][0];
const double * _noalias const lo = (triclinic == 0) ? boxlo : boxlo_lamda;
const double * _noalias const hi = (triclinic == 0) ? boxhi : boxhi_lamda;
const double * _noalias const period = (triclinic == 0) ? prd : prd_lamda;
const int * _noalias const mask = atom->mask;
imageint * _noalias const image = atom->image;
const int nlocal = atom->nlocal;
if (!nlocal) return;
// verify owned atoms have valid numerical coords
// may not if computed pairwise force between 2 atoms at same location
const double *_noalias const coord = &atom->x[0][0];
const int n3 = 3 * nlocal;
int flag = 0;
#if defined(_OPENMP) // clang-format off
#pragma omp parallel for LMP_DEFAULT_NONE schedule(static) reduction(+:flag)
#endif // clang-format on
for (int i = 0; i < n3; i++)
if (!std::isfinite(coord[i])) flag = 1;
if (flag) error->one(FLERR, "Non-numeric atom coords - simulation unstable");
dbl3_t *_noalias const x = (dbl3_t *) &atom->x[0][0];
dbl3_t *_noalias const v = (dbl3_t *) &atom->v[0][0];
const double *_noalias const lo = (triclinic == 0) ? boxlo : boxlo_lamda;
const double *_noalias const hi = (triclinic == 0) ? boxhi : boxhi_lamda;
const double *_noalias const period = (triclinic == 0) ? prd : prd_lamda;
const int *_noalias const mask = atom->mask;
imageint *_noalias const image = atom->image;
#if defined(_OPENMP)
#pragma omp parallel for LMP_DEFAULT_NONE schedule(static)
#endif
for (int i = 0; i < nlocal; i++) {
imageint idim,otherdims;
imageint idim, otherdims;
if (xperiodic) {
if (x[i].x < lo[0]) {
@ -64,7 +81,7 @@ void DomainOMP::pbc()
}
if (x[i].x >= hi[0]) {
x[i].x -= period[0];
x[i].x = MAX(x[i].x,lo[0]);
x[i].x = MAX(x[i].x, lo[0]);
if (deform_vremap && mask[i] & deform_groupbit) v[i].x -= h_rate[0];
idim = image[i] & IMGMASK;
otherdims = image[i] ^ idim;
@ -89,7 +106,7 @@ void DomainOMP::pbc()
}
if (x[i].y >= hi[1]) {
x[i].y -= period[1];
x[i].y = MAX(x[i].y,lo[1]);
x[i].y = MAX(x[i].y, lo[1]);
if (deform_vremap && mask[i] & deform_groupbit) {
v[i].x -= h_rate[5];
v[i].y -= h_rate[1];
@ -118,7 +135,7 @@ void DomainOMP::pbc()
}
if (x[i].z >= hi[2]) {
x[i].z -= period[2];
x[i].z = MAX(x[i].z,lo[2]);
x[i].z = MAX(x[i].z, lo[2]);
if (deform_vremap && mask[i] & deform_groupbit) {
v[i].x -= h_rate[4];
v[i].y -= h_rate[3];
@ -141,16 +158,17 @@ void DomainOMP::pbc()
void DomainOMP::lamda2x(int n)
{
dbl3_t * _noalias const x = (dbl3_t *)&atom->x[0][0];
const int num = n;
if (!n) return;
dbl3_t *_noalias const x = (dbl3_t *) &atom->x[0][0];
#if defined(_OPENMP)
#pragma omp parallel for LMP_DEFAULT_NONE schedule(static)
#endif
for (int i = 0; i < num; i++) {
x[i].x = h[0]*x[i].x + h[5]*x[i].y + h[4]*x[i].z + boxlo[0];
x[i].y = h[1]*x[i].y + h[3]*x[i].z + boxlo[1];
x[i].z = h[2]*x[i].z + boxlo[2];
x[i].x = h[0] * x[i].x + h[5] * x[i].y + h[4] * x[i].z + boxlo[0];
x[i].y = h[1] * x[i].y + h[3] * x[i].z + boxlo[1];
x[i].z = h[2] * x[i].z + boxlo[2];
}
}
@ -161,8 +179,9 @@ void DomainOMP::lamda2x(int n)
void DomainOMP::x2lamda(int n)
{
dbl3_t * _noalias const x = (dbl3_t *)&atom->x[0][0];
const int num = n;
if (!n) return;
dbl3_t *_noalias const x = (dbl3_t *) &atom->x[0][0];
#if defined(_OPENMP)
#pragma omp parallel for LMP_DEFAULT_NONE schedule(static)
@ -172,9 +191,8 @@ void DomainOMP::x2lamda(int n)
double delta1 = x[i].y - boxlo[1];
double delta2 = x[i].z - boxlo[2];
x[i].x = h_inv[0]*delta0 + h_inv[5]*delta1 + h_inv[4]*delta2;
x[i].y = h_inv[1]*delta1 + h_inv[3]*delta2;
x[i].z = h_inv[2]*delta2;
x[i].x = h_inv[0] * delta0 + h_inv[5] * delta1 + h_inv[4] * delta2;
x[i].y = h_inv[1] * delta1 + h_inv[3] * delta2;
x[i].z = h_inv[2] * delta2;
}
}

187
src/REACTION/fix_bond_react.cpp
View File

@ -140,6 +140,7 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
rxnfunclist[0] = "rxnsum";
rxnfunclist[1] = "rxnave";
nvvec = 0;
ncustomvars = 0;
vvec = nullptr;
nxspecial = nullptr;
@ -232,7 +233,6 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
memory->create(molecule_keyword,nreacts,"bond/react:molecule_keyword");
memory->create(nconstraints,nreacts,"bond/react:nconstraints");
memory->create(constraintstr,nreacts,MAXLINE,"bond/react:constraintstr");
memory->create(constraints,0,nreacts,"bond/react:constraints");
memory->create(var_flag,NUMVARVALS,nreacts,"bond/react:var_flag");
memory->create(var_id,NUMVARVALS,nreacts,"bond/react:var_id");
memory->create(iatomtype,nreacts,"bond/react:iatomtype");
@ -488,6 +488,9 @@ FixBondReact::FixBondReact(LAMMPS *lmp, int narg, char **arg) :
if (custom_charges_fragid[i] >= 0) CustomCharges(custom_charges_fragid[i],i);
}
// get the names of per-atom variables needed by 'rxn' functions of custom constraint
customvarnames();
// initialize Marsaglia RNG with processor-unique seed (Arrhenius prob)
rrhandom = new RanMars*[narrhenius];
@ -617,7 +620,6 @@ FixBondReact::~FixBondReact()
memory->destroy(stabilize_steps_flag);
memory->destroy(custom_charges_fragid);
memory->destroy(molecule_keyword);
memory->destroy(constraints);
memory->destroy(nconstraints);
memory->destroy(constraintstr);
memory->destroy(create_atoms_flag);
@ -1020,6 +1022,11 @@ void FixBondReact::post_integrate()
return;
}
// evaluate custom constraint variable values here and forward_comm
get_customvars();
commflag = 1;
comm->forward_comm_fix(this,ncustomvars);
// run through the superimpose algorithm
// this checks if simulation topology matches unreacted mol template
superimpose_algorithm();
@ -2086,6 +2093,100 @@ double FixBondReact::get_temperature(tagint **myglove, int row_offset, int col)
return t;
}
/* ----------------------------------------------------------------------
get per-atom variable names used by custom constraint
------------------------------------------------------------------------- */
void FixBondReact::customvarnames()
{
int pos,pos1,pos2,pos3,prev3;
std::string varstr,argstr,varid;
// search all constraints' varstr for special 'rxn' functions
// add variable names to customvarstrs
// add values to customvars
for (rxnID = 0; rxnID < nreacts; rxnID++) {
for (int i = 0; i < nconstraints[rxnID]; i++) {
if (constraints[i][rxnID].type == CUSTOM) {
varstr = constraints[i][rxnID].str;
prev3 = -1;
while (true) {
// find next reaction special function occurrence
pos1 = INT_MAX;
for (int i = 0; i < nrxnfunction; i++) {
pos = varstr.find(rxnfunclist[i],prev3+1);
if (pos == std::string::npos) continue;
if (pos < pos1) pos1 = pos;
}
if (pos1 == INT_MAX) break;
pos2 = varstr.find("(",pos1);
pos3 = varstr.find(")",pos2);
if (pos2 == std::string::npos || pos3 == std::string::npos)
error->all(FLERR,"Bond/react: Illegal rxn function syntax\n");
prev3 = pos3;
argstr = varstr.substr(pos2+1,pos3-pos2-1);
argstr.erase(remove_if(argstr.begin(), argstr.end(), isspace), argstr.end()); // remove whitespace
pos2 = argstr.find(",");
if (pos2 != std::string::npos) varid = argstr.substr(0,pos2);
else varid = argstr;
// check if we already know about this variable
int varidflag = 0;
for (int j = 0; j < ncustomvars; j++) {
if (customvarstrs[j] == varid) {
varidflag = 1;
break;
}
}
if (!varidflag) {
customvarstrs.resize(ncustomvars+1);
customvarstrs[ncustomvars++] = varid;
}
}
}
}
}
}
/* ----------------------------------------------------------------------
evaluate per-atom variables needed for custom constraint
------------------------------------------------------------------------- */
void FixBondReact::get_customvars()
{
double *tempvvec;
std::string varid;
int nall = atom->nlocal + atom->nghost;
memory->create(tempvvec,nall,"bond/react:tempvvec");
if (vvec == nullptr) {
memory->create(vvec,nall,ncustomvars,"bond/react:vvec");
nvvec = nall;
}
if (nvvec < nall) {
memory->grow(vvec,nall,ncustomvars,"bond/react:vvec");
nvvec = nall;
}
for (int i = 0; i < ncustomvars; i++) {
varid = customvarstrs[i];
if (varid.substr(0,2) != "v_") error->all(FLERR,"Bond/react: Reaction special function variable "
"name should begin with 'v_'");
varid = varid.substr(2);
int ivar = input->variable->find(varid.c_str());
if (ivar < 0)
error->all(FLERR,"Bond/react: Reaction special function variable "
"name does not exist");
if (!input->variable->atomstyle(ivar))
error->all(FLERR,"Bond/react: Reaction special function must "
"reference an atom-style variable");
input->variable->compute_atom(ivar,igroup,tempvvec,1,0);
for (int j = 0; j < nall; j++) vvec[j][i] = tempvvec[j];
}
memory->destroy(tempvvec);
}
/* ----------------------------------------------------------------------
evaulate expression for variable constraint
------------------------------------------------------------------------- */
@ -2120,6 +2221,7 @@ double FixBondReact::custom_constraint(std::string varstr)
evlstr.push_back(varstr.substr(prev3+1,pos1-(prev3+1)));
prev3 = pos3;
argstr = varstr.substr(pos2+1,pos3-pos2-1);
argstr.erase(remove_if(argstr.begin(), argstr.end(), isspace), argstr.end()); // remove whitespace
pos2 = argstr.find(",");
if (pos2 != std::string::npos) {
varid = argstr.substr(0,pos2);
@ -2145,25 +2247,19 @@ currently two 'rxn' functions: rxnsum and rxnave
double FixBondReact::rxnfunction(std::string rxnfunc, std::string varid,
std::string fragid)
{
if (varid.substr(0,2) != "v_") error->one(FLERR,"Bond/react: Reaction special function variable "
"name should begin with 'v_'");
varid = varid.substr(2);
int ivar = input->variable->find(varid.c_str());
int ivar = -1;
for (int i = 0; i < ncustomvars; i++) {
if (varid == customvarstrs[i]) {
ivar = i;
break;
}
}
// variable name should always be found, at this point
// however, let's double check for completeness
if (ivar < 0)
error->one(FLERR,"Bond/react: Reaction special function variable "
"name does not exist");
if (!input->variable->atomstyle(ivar))
error->one(FLERR,"Bond/react: Reaction special function must "
"reference an atom-style variable");
if (vvec == nullptr) {
memory->create(vvec,atom->nlocal,"bond/react:vvec");
nvvec = atom->nlocal;
}
if (nvvec < atom->nlocal) {
memory->grow(vvec,atom->nlocal,"bond/react:vvec");
nvvec = atom->nlocal;
}
input->variable->compute_atom(ivar,igroup,vvec,1,0);
int ifrag = -1;
if (fragid != "all") {
ifrag = onemol->findfragment(fragid.c_str());
@ -2178,14 +2274,14 @@ double FixBondReact::rxnfunction(std::string rxnfunc, std::string varid,
if (fragid == "all") {
for (int i = 0; i < onemol->natoms; i++) {
iatom = atom->map(glove[i][1]);
sumvvec += vvec[iatom];
sumvvec += vvec[iatom][ivar];
}
nsum = onemol->natoms;
} else {
for (int i = 0; i < onemol->natoms; i++) {
if (onemol->fragmentmask[ifrag][i]) {
iatom = atom->map(glove[i][1]);
sumvvec += vvec[iatom];
sumvvec += vvec[iatom][ivar];
nsum++;
}
}
@ -2830,6 +2926,19 @@ void FixBondReact::update_everything()
rxnID = local_mega_glove[0][i];
// reactions already shuffled from dedup procedure, so can skip first N
if (iskip[rxnID]++ < nlocalskips[rxnID]) continue;
// atoms inserted here for serial MPI_STUBS build only
if (create_atoms_flag[rxnID] == 1) {
onemol = atom->molecules[unreacted_mol[rxnID]];
twomol = atom->molecules[reacted_mol[rxnID]];
if (insert_atoms(local_mega_glove,i)) {
inserted_atoms_flag = 1;
} else { // create aborted
reaction_count_total[rxnID]--;
continue;
}
}
for (int j = 0; j < max_natoms+1; j++)
update_mega_glove[j][update_num_mega] = local_mega_glove[j][i];
update_num_mega++;
@ -2842,7 +2951,7 @@ void FixBondReact::update_everything()
// we can insert atoms here, now that reactions are finalized
// can't do it any earlier, due to skipped reactions (max_rxn)
// reactions that create atoms are always treated as 'global'
// for MPI build, reactions that create atoms are always treated as 'global'
if (create_atoms_flag[rxnID] == 1) {
onemol = atom->molecules[unreacted_mol[rxnID]];
twomol = atom->molecules[reacted_mol[rxnID]];
@ -2858,17 +2967,18 @@ void FixBondReact::update_everything()
update_mega_glove[j][update_num_mega] = global_mega_glove[j][i];
update_num_mega++;
}
// if inserted atoms and global map exists, reset map now instead
// of waiting for comm since other pre-exchange fixes may use it
// invoke map_init() b/c atom count has grown
// do this once after all atom insertions
if (inserted_atoms_flag == 1 && atom->map_style != Atom::MAP_NONE) {
atom->map_init();
atom->map_set();
}
}
delete [] iskip;
// if inserted atoms and global map exists, reset map now instead
// of waiting for comm since other pre-exchange fixes may use it
// invoke map_init() b/c atom count has grown
// do this once after all atom insertions
if (inserted_atoms_flag == 1 && atom->map_style != Atom::MAP_NONE) {
atom->map_init();
atom->map_set();
}
// mark to-delete atoms
nlocal = atom->nlocal;
if (nlocal > nmark) {
@ -3668,7 +3778,7 @@ void FixBondReact::read(int myrxn)
else if (strstr(line,"constraints")) {
sscanf(line,"%d",&nconstraints[myrxn]);
if (maxnconstraints < nconstraints[myrxn]) maxnconstraints = nconstraints[myrxn];
memory->grow(constraints,maxnconstraints,nreacts,"bond/react:constraints");
constraints.resize(maxnconstraints, std::vector<Constraint>(nreacts));
} else break;
}
@ -4027,6 +4137,15 @@ int FixBondReact::pack_forward_comm(int n, int *list, double *buf,
m = 0;
if (commflag == 1) {
for (i = 0; i < n; i++) {
j = list[i];
for (k = 0; k < ncustomvars; k++)
buf[m++] = vvec[j][k];
}
return m;
}
if (commflag == 2) {
for (i = 0; i < n; i++) {
j = list[i];
@ -4051,12 +4170,16 @@ int FixBondReact::pack_forward_comm(int n, int *list, double *buf,
void FixBondReact::unpack_forward_comm(int n, int first, double *buf)
{
int i,j,m,ns,last;
int i,j,k,m,ns,last;
m = 0;
last = first + n;
if (commflag == 2) {
if (commflag == 1) {
for (i = first; i < last; i++)
for (k = 0; k < ncustomvars; k++)
vvec[i][k] = buf[m++];
} else if (commflag == 2) {
for (i = first; i < last; i++)
partner[i] = (tagint) ubuf(buf[m++]).i;
} else {

20
src/REACTION/fix_bond_react.h
View File

@ -139,8 +139,6 @@ class FixBondReact : public Fix {
int **delete_atoms; // atoms in pre-reacted templates to delete
int **create_atoms; // atoms in post-reacted templates to create
int ***chiral_atoms; // pre-react chiral atoms. 1) flag 2) orientation 3-4) ordered atom types
int nvvec;
double *vvec; // per-atom vector to store variable constraint atom-style variable values
int **nxspecial, **onemol_nxspecial, **twomol_nxspecial; // full number of 1-4 neighbors
tagint **xspecial, **onemol_xspecial, **twomol_xspecial; // full 1-4 neighbor list
@ -151,14 +149,12 @@ class FixBondReact : public Fix {
// for all mega_gloves and global_mega_glove: first row is the ID of bond/react
tagint **local_mega_glove; // consolidation local of reaction instances
tagint **ghostly_mega_glove; // consolidation nonlocal of reaction instances
tagint *
*global_mega_glove; // consolidation (inter-processor) of gloves containing nonlocal atoms
tagint **global_mega_glove; // consolidation (inter-processor) of gloves containing nonlocal atoms
int *localsendlist; // indicates ghosts of other procs
int local_num_mega; // num of local reaction instances
int ghostly_num_mega; // num of ghostly reaction instances
int global_megasize; // num of reaction instances in global_mega_glove
int *
pioneers; // during Superimpose Algorithm, atoms which have been assigned, but whose first neighbors haven't
int *pioneers; // during Superimpose Algorithm, atoms which have been assigned, but whose first neighbors haven't
int glove_counter; // used to determine when to terminate Superimpose Algorithm
void read(int);
@ -180,8 +176,10 @@ class FixBondReact : public Fix {
int check_constraints();
void get_IDcoords(int, int, double *);
double get_temperature(tagint **, int, int);
double custom_constraint(std::string);
double rxnfunction(std::string, std::string, std::string);
void customvarnames(); // get per-atom variables names used by custom constraint
void get_customvars(); // evaluate local values for variables names used by custom constraint
double custom_constraint(std::string); // evaulate expression for custom constraint
double rxnfunction(std::string, std::string, std::string); // eval rxn_sum and rxn_ave
int get_chirality(double[12]); // get handedness given an ordered set of coordinates
void open(char *);
@ -216,7 +214,11 @@ class FixBondReact : public Fix {
double par[MAXCONPAR];
std::string str;
};
Constraint **constraints;
int ncustomvars;
std::vector<std::string> customvarstrs;
int nvvec;
double **vvec; // per-atom vector to store variable constraint atom-style variable values
std::vector<std::vector<Constraint>> constraints;
// DEBUG

5
src/atom.cpp
View File

@ -2471,7 +2471,7 @@ This function is called, e.g. from :doc:`fix property/atom <fix_property_atom>`.
*/
int Atom::add_custom(const char *name, int flag, int cols)
{
int index;
int index = -1;
if ((flag == 0) && (cols == 0)) {
index = nivector;
@ -2511,7 +2511,8 @@ int Atom::add_custom(const char *name, int flag, int cols)
dcols = (int *) memory->srealloc(dcols,ndarray*sizeof(int),"atom:dcols");
dcols[index] = cols;
}
if (index < 0)
error->all(FLERR,"Invalid call to Atom::add_custom()");
return index;
}

5
src/domain.cpp
View File

@ -528,10 +528,11 @@ void Domain::reset_box()
void Domain::pbc()
{
int nlocal = atom->nlocal;
if (!nlocal) return;
int i;
imageint idim,otherdims;
double *lo,*hi,*period;
int nlocal = atom->nlocal;
double **x = atom->x;
double **v = atom->v;
int *mask = atom->mask;
@ -542,7 +543,7 @@ void Domain::pbc()
double *coord;
int n3 = 3*nlocal;
coord = &x[0][0]; // note: x is always initialized to at least one element.
coord = &x[0][0];
int flag = 0;
for (i = 0; i < n3; i++)
if (!std::isfinite(*coord++)) flag = 1;

2
src/dump.cpp
View File

@ -100,7 +100,7 @@ Dump::Dump(LAMMPS *lmp, int /*narg*/, char **arg) : Pointers(lmp)
maxsbuf = 0;
sbuf = nullptr;
maxpbc = 0;
maxpbc = -1;
xpbc = vpbc = nullptr;
imagepbc = nullptr;

230
src/fix_property_atom.cpp
View File

@ -31,7 +31,7 @@ enum{MOLECULE,CHARGE,RMASS,IVEC,DVEC,IARRAY,DARRAY};
FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
nvalue(0), style(nullptr), index(nullptr), astyle(nullptr)
nvalue(0), styles(nullptr), index(nullptr), astyle(nullptr)
{
if (narg < 4) error->all(FLERR,"Illegal fix property/atom command");
@ -40,7 +40,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
int iarg = 3;
nvalue = narg-iarg;
style = new int[nvalue];
styles = new int[nvalue];
cols = new int[nvalue];
index = new int[nvalue];
@ -58,7 +58,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
"already has molecule attribute");
if (molecule_flag)
error->all(FLERR,"Fix property/atom cannot specify mol twice");
style[nvalue] = MOLECULE;
styles[nvalue] = MOLECULE;
cols[nvalue] = 0;
atom->molecule_flag = molecule_flag = 1;
values_peratom++;
@ -69,7 +69,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Fix property/atom q when atom_style already has charge attribute");
if (q_flag)
error->all(FLERR,"Fix property/atom cannot specify q twice");
style[nvalue] = CHARGE;
styles[nvalue] = CHARGE;
cols[nvalue] = 0;
atom->q_flag = q_flag = 1;
values_peratom++;
@ -80,7 +80,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
error->all(FLERR,"Fix property/atom rmass when atom_style already has rmass attribute");
if (rmass_flag)
error->all(FLERR,"Fix property/atom cannot specify rmass twice");
style[nvalue] = RMASS;
styles[nvalue] = RMASS;
cols[nvalue] = 0;
atom->rmass_flag = rmass_flag = 1;
values_peratom++;
@ -90,7 +90,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
// custom atom vector
} else if (utils::strmatch(arg[iarg],"^i_")) {
style[nvalue] = IVEC;
styles[nvalue] = IVEC;
int flag,ncols;
index[nvalue] = atom->find_custom(&arg[iarg][2],flag,ncols);
if (index[nvalue] >= 0)
@ -102,7 +102,7 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
iarg++;
} else if (utils::strmatch(arg[iarg],"^d_")) {
style[nvalue] = DVEC;
styles[nvalue] = DVEC;
int flag,ncols;
index[nvalue] = atom->find_custom(&arg[iarg][2],flag,ncols);
if (index[nvalue] >= 0)
@ -129,10 +129,10 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
if (arg[iarg][0] == 'i') {
which = 0;
style[nvalue] = IARRAY;
styles[nvalue] = IARRAY;
} else {
which = 1;
style[nvalue] = DARRAY;
styles[nvalue] = DARRAY;
}
index[nvalue] = atom->add_custom(&arg[iarg][3],which,ncols);
cols[nvalue] = ncols;
@ -165,9 +165,9 @@ FixPropertyAtom::FixPropertyAtom(LAMMPS *lmp, int narg, char **arg) :
if (border == 0) {
int flag = 0;
for (int i = 0; i < nvalue; i++)
if (style[i] == MOLECULE
|| style[i] == CHARGE
|| style[i] == RMASS) flag = 1;
if (styles[i] == MOLECULE
|| styles[i] == CHARGE
|| styles[i] == RMASS) flag = 1;
if (flag && comm->me == 0)
error->warning(FLERR,"Fix property/atom mol or charge or rmass "
"w/out ghost communication");
@ -201,30 +201,30 @@ FixPropertyAtom::~FixPropertyAtom()
// set ptrs to a null pointer, so they no longer exist for Atom class
for (int nv = 0; nv < nvalue; nv++) {
if (style[nv] == MOLECULE) {
if (styles[nv] == MOLECULE) {
atom->molecule_flag = 0;
memory->destroy(atom->molecule);
atom->molecule = nullptr;
} else if (style[nv] == CHARGE) {
} else if (styles[nv] == CHARGE) {
atom->q_flag = 0;
memory->destroy(atom->q);
atom->q = nullptr;
} else if (style[nv] == RMASS) {
} else if (styles[nv] == RMASS) {
atom->rmass_flag = 0;
memory->destroy(atom->rmass);
atom->rmass = nullptr;
} else if (style[nv] == IVEC) {
} else if (styles[nv] == IVEC) {
atom->remove_custom(index[nv],0,cols[nv]);
} else if (style[nv] == DVEC) {
} else if (styles[nv] == DVEC) {
atom->remove_custom(index[nv],1,cols[nv]);
} else if (style[nv] == IARRAY) {
} else if (styles[nv] == IARRAY) {
atom->remove_custom(index[nv],0,cols[nv]);
} else if (style[nv] == DARRAY) {
} else if (styles[nv] == DARRAY) {
atom->remove_custom(index[nv],1,cols[nv]);
}
}
delete [] style;
delete [] styles;
delete [] cols;
delete [] index;
delete [] astyle;
@ -291,21 +291,21 @@ void FixPropertyAtom::read_data_section(char *keyword, int n, char *buf, tagint
if ((m = atom->map(itag)) >= 0) {
for (j = 0; j < nvalue; j++) {
if (style[j] == MOLECULE) {
if (styles[j] == MOLECULE) {
atom->molecule[m] = values.next_tagint();
} else if (style[j] == CHARGE) {
} else if (styles[j] == CHARGE) {
atom->q[m] = values.next_double();
} else if (style[j] == RMASS) {
} else if (styles[j] == RMASS) {
atom->rmass[m] = values.next_double();
} else if (style[j] == IVEC) {
} else if (styles[j] == IVEC) {
atom->ivector[index[j]][m] = values.next_int();
} else if (style[j] == DVEC) {
} else if (styles[j] == DVEC) {
atom->dvector[index[j]][m] = values.next_double();
} else if (style[j] == IARRAY) {
} else if (styles[j] == IARRAY) {
ncol = cols[j];
for (k = 0; k < ncol; k++)
atom->iarray[index[j]][m][k] = values.next_int();
} else if (style[j] == DARRAY) {
} else if (styles[j] == DARRAY) {
ncol = cols[j];
for (k = 0; k < ncol; k++)
atom->darray[index[j]][m][k] = values.next_double();
@ -365,34 +365,34 @@ void FixPropertyAtom::write_data_section_pack(int /*mth*/, double **buf)
int icol = 1;
for (int nv = 0; nv < nvalue; nv++) {
if (style[nv] == MOLECULE) {
if (styles[nv] == MOLECULE) {
tagint *molecule = atom->molecule;
for (i = 0; i < nlocal; i++) buf[i][icol] = ubuf(molecule[i]).d;
icol++;
} else if (style[nv] == CHARGE) {
} else if (styles[nv] == CHARGE) {
double *q = atom->q;
for (i = 0; i < nlocal; i++) buf[i][icol] = q[i];
icol++;
} else if (style[nv] == RMASS) {
} else if (styles[nv] == RMASS) {
double *rmass = atom->rmass;
for (i = 0; i < nlocal; i++) buf[i][icol] = rmass[i];
icol++;
} else if (style[nv] == IVEC) {
} else if (styles[nv] == IVEC) {
int *ivec = atom->ivector[index[nv]];
for (i = 0; i < nlocal; i++) buf[i][icol] = ubuf(ivec[i]).d;
icol++;
} else if (style[nv] == DVEC) {
} else if (styles[nv] == DVEC) {
double *dvec = atom->dvector[index[nv]];
for (i = 0; i < nlocal; i++) buf[i][icol] = dvec[i];
icol++;
} else if (style[nv] == IARRAY) {
} else if (styles[nv] == IARRAY) {
int **iarray = atom->iarray[index[nv]];
ncol = cols[nv];
for (i = 0; i < nlocal; i++)
for (k = 0; k < ncol; k++)
buf[i][icol+k] = ubuf(iarray[i][k]).d;
icol += ncol;
} else if (style[nv] == DARRAY) {
} else if (styles[nv] == DARRAY) {
double **darray = atom->darray[index[nv]];
ncol = cols[nv];
for (i = 0; i < nlocal; i++)
@ -412,19 +412,19 @@ void FixPropertyAtom::write_data_section_pack(int /*mth*/, double **buf)
void FixPropertyAtom::write_data_section_keyword(int /*mth*/, FILE *fp)
{
if (nvalue == 1 && style[0] == MOLECULE) fprintf(fp,"\nMolecules\n\n");
else if (nvalue == 1 && style[0] == CHARGE) fprintf(fp,"\nCharges\n\n");
if (nvalue == 1 && styles[0] == MOLECULE) fprintf(fp,"\nMolecules\n\n");
else if (nvalue == 1 && styles[0] == CHARGE) fprintf(fp,"\nCharges\n\n");
else {
fprintf(fp,"\n%s #",id);
// write column hint as comment
for (int i = 0; i < nvalue; ++i) {
if (style[i] == MOLECULE) fputs(" mol",fp);
else if (style[i] == CHARGE) fputs(" q",fp);
else if (style[i] == RMASS) fputs(" rmass",fp);
else if (style[i] == IVEC) fprintf(fp," i_%s", atom->ivname[index[i]]);
else if (style[i] == DVEC) fprintf(fp, " d_%s", atom->dvname[index[i]]);
else if (style[i] == IARRAY) fprintf(fp, " i_%s", atom->ianame[index[i]]);
else if (style[i] == DARRAY) fprintf(fp, " d_%s", atom->daname[index[i]]);
if (styles[i] == MOLECULE) fputs(" mol",fp);
else if (styles[i] == CHARGE) fputs(" q",fp);
else if (styles[i] == RMASS) fputs(" rmass",fp);
else if (styles[i] == IVEC) fprintf(fp," i_%s", atom->ivname[index[i]]);
else if (styles[i] == DVEC) fprintf(fp, " d_%s", atom->dvname[index[i]]);
else if (styles[i] == IARRAY) fprintf(fp, " i_%s", atom->ianame[index[i]]);
else if (styles[i] == DARRAY) fprintf(fp, " d_%s", atom->daname[index[i]]);
}
fputs("\n\n",fp);
}
@ -446,22 +446,22 @@ void FixPropertyAtom::write_data_section(int /*mth*/, FILE *fp,
fprintf(fp,TAGINT_FORMAT,(tagint) ubuf(buf[i][0]).i);
icol = 1;
for (nv = 0; nv < nvalue; nv++) {
if (style[nv] == MOLECULE)
if (styles[nv] == MOLECULE)
fprintf(fp," " TAGINT_FORMAT,(tagint) ubuf(buf[i][icol++]).i);
else if (style[nv] == CHARGE)
else if (styles[nv] == CHARGE)
fprintf(fp," %g",buf[i][icol++]);
else if (style[nv] == RMASS)
else if (styles[nv] == RMASS)
fprintf(fp," %g",buf[i][icol++]);
else if (style[nv] == IVEC)
else if (styles[nv] == IVEC)
fprintf(fp," %d",(int) ubuf(buf[i][icol++]).i);
else if (style[nv] == DVEC)
else if (styles[nv] == DVEC)
fprintf(fp," %g",buf[i][icol++]);
else if (style[nv] == IARRAY) {
else if (styles[nv] == IARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++)
fprintf(fp," %d",(int) ubuf(buf[i][icol+k]).i);
icol += ncol;
} else if (style[nv] == DARRAY) {
} else if (styles[nv] == DARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++)
fprintf(fp," %g",buf[i][icol+k]);
@ -480,13 +480,13 @@ double FixPropertyAtom::memory_usage()
{
double bytes = 0.0;
for (int m = 0; m < nvalue; m++) {
if (style[m] == MOLECULE) bytes = atom->nmax * sizeof(tagint);
else if (style[m] == CHARGE) bytes = atom->nmax * sizeof(double);
else if (style[m] == RMASS) bytes = atom->nmax * sizeof(double);
else if (style[m] == IVEC) bytes = atom->nmax * sizeof(int);
else if (style[m] == DVEC) bytes = atom->nmax * sizeof(double);
else if (style[m] == IARRAY) bytes = atom->nmax * cols[m] * sizeof(int);
else if (style[m] == DARRAY) bytes = atom->nmax * cols[m] * sizeof(double);
if (styles[m] == MOLECULE) bytes = atom->nmax * sizeof(tagint);
else if (styles[m] == CHARGE) bytes = atom->nmax * sizeof(double);
else if (styles[m] == RMASS) bytes = atom->nmax * sizeof(double);
else if (styles[m] == IVEC) bytes = atom->nmax * sizeof(int);
else if (styles[m] == DVEC) bytes = atom->nmax * sizeof(double);
else if (styles[m] == IARRAY) bytes = (size_t) atom->nmax * cols[m] * sizeof(int);
else if (styles[m] == DARRAY) bytes = (size_t) atom->nmax * cols[m] * sizeof(double);
}
return bytes;
}
@ -501,33 +501,33 @@ double FixPropertyAtom::memory_usage()
void FixPropertyAtom::grow_arrays(int nmax)
{
for (int nv = 0; nv < nvalue; nv++) {
if (style[nv] == MOLECULE) {
if (styles[nv] == MOLECULE) {
memory->grow(atom->molecule,nmax,"atom:molecule");
size_t nbytes = (nmax-nmax_old) * sizeof(tagint);
memset(&atom->molecule[nmax_old],0,nbytes);
} else if (style[nv] == CHARGE) {
} else if (styles[nv] == CHARGE) {
memory->grow(atom->q,nmax,"atom:q");
size_t nbytes = (nmax-nmax_old) * sizeof(double);
memset(&atom->q[nmax_old],0,nbytes);
} else if (style[nv] == RMASS) {
} else if (styles[nv] == RMASS) {
memory->grow(atom->rmass,nmax,"atom:rmass");
size_t nbytes = (nmax-nmax_old) * sizeof(double);
memset(&atom->rmass[nmax_old],0,nbytes);
} else if (style[nv] == IVEC) {
} else if (styles[nv] == IVEC) {
memory->grow(atom->ivector[index[nv]],nmax,"atom:ivector");
size_t nbytes = (nmax-nmax_old) * sizeof(int);
memset(&atom->ivector[index[nv]][nmax_old],0,nbytes);
} else if (style[nv] == DVEC) {
} else if (styles[nv] == DVEC) {
memory->grow(atom->dvector[index[nv]],nmax,"atom:dvector");
size_t nbytes = (nmax-nmax_old) * sizeof(double);
memset(&atom->dvector[index[nv]][nmax_old],0,nbytes);
} else if (style[nv] == IARRAY) {
} else if (styles[nv] == IARRAY) {
memory->grow(atom->iarray[index[nv]],nmax,cols[nv],"atom:iarray");
size_t nbytes = (nmax-nmax_old) * cols[nv] * sizeof(int);
size_t nbytes = (size_t) (nmax-nmax_old) * cols[nv] * sizeof(int);
if (nbytes) memset(&atom->iarray[index[nv]][nmax_old][0],0,nbytes);
} else if (style[nv] == DARRAY) {
} else if (styles[nv] == DARRAY) {
memory->grow(atom->darray[index[nv]],nmax,cols[nv],"atom:darray");
size_t nbytes = (nmax-nmax_old) * cols[nv] * sizeof(double);
size_t nbytes = (size_t) (nmax-nmax_old) * cols[nv] * sizeof(double);
if (nbytes) memset(&atom->darray[index[nv]][nmax_old][0],0,nbytes);
}
}
@ -544,21 +544,21 @@ void FixPropertyAtom::copy_arrays(int i, int j, int /*delflag*/)
int k,ncol;
for (int nv = 0; nv < nvalue; nv++) {
if (style[nv] == MOLECULE)
if (styles[nv] == MOLECULE)
atom->molecule[j] = atom->molecule[i];
else if (style[nv] == CHARGE)
else if (styles[nv] == CHARGE)
atom->q[j] = atom->q[i];
else if (style[nv] == RMASS)
else if (styles[nv] == RMASS)
atom->rmass[j] = atom->rmass[i];
else if (style[nv] == IVEC)
else if (styles[nv] == IVEC)
atom->ivector[index[nv]][j] = atom->ivector[index[nv]][i];
else if (style[nv] == DVEC)
else if (styles[nv] == DVEC)
atom->dvector[index[nv]][j] = atom->dvector[index[nv]][i];
else if (style[nv] == IARRAY) {
else if (styles[nv] == IARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++)
atom->iarray[index[nv]][j][k] = atom->iarray[index[nv]][i][k];
} else if (style[nv] == DARRAY) {
} else if (styles[nv] == DARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++)
atom->darray[index[nv]][j][k] = atom->darray[index[nv]][i][k];
@ -576,37 +576,37 @@ int FixPropertyAtom::pack_border(int n, int *list, double *buf)
int m = 0;
for (int nv = 0; nv < nvalue; nv++) {
if (style[nv] == MOLECULE) {
if (styles[nv] == MOLECULE) {
tagint *molecule = atom->molecule;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(molecule[j]).d;
}
} else if (style[nv] == CHARGE) {
} else if (styles[nv] == CHARGE) {
double *q = atom->q;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = q[j];
}
} else if (style[nv] == RMASS) {
} else if (styles[nv] == RMASS) {
double *rmass = atom->rmass;
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = rmass[j];
}
} else if (style[nv] == IVEC) {
} else if (styles[nv] == IVEC) {
int *ivector = atom->ivector[index[nv]];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = ubuf(ivector[j]).d;
}
} else if (style[nv] == DVEC) {
} else if (styles[nv] == DVEC) {
double *dvector = atom->dvector[index[nv]];
for (i = 0; i < n; i++) {
j = list[i];
buf[m++] = dvector[j];
}
} else if (style[nv] == IARRAY) {
} else if (styles[nv] == IARRAY) {
int **iarray = atom->iarray[index[nv]];
ncol = cols[nv];
for (i = 0; i < n; i++) {
@ -614,7 +614,7 @@ int FixPropertyAtom::pack_border(int n, int *list, double *buf)
for (k = 0; k < ncol; k++)
buf[m++] = ubuf(iarray[j][k]).d;
}
} else if (style[nv] == DARRAY) {
} else if (styles[nv] == DARRAY) {
double **darray = atom->darray[index[nv]];
ncol = cols[nv];
for (i = 0; i < n; i++) {
@ -638,39 +638,39 @@ int FixPropertyAtom::unpack_border(int n, int first, double *buf)
int m = 0;
for (int nv = 0; nv < nvalue; nv++) {
if (style[nv] == MOLECULE) {
if (styles[nv] == MOLECULE) {
tagint *molecule = atom->molecule;
last = first + n;
for (i = first; i < last; i++)
molecule[i] = (tagint) ubuf(buf[m++]).i;
} else if (style[nv] == CHARGE) {
} else if (styles[nv] == CHARGE) {
double *q = atom->q;
last = first + n;
for (i = first; i < last; i++)
q[i] = buf[m++];
} else if (style[nv] == RMASS) {
} else if (styles[nv] == RMASS) {
double *rmass = atom->rmass;
last = first + n;
for (i = first; i < last; i++)
rmass[i] = buf[m++];
} else if (style[nv] == IVEC) {
} else if (styles[nv] == IVEC) {
int *ivector = atom->ivector[index[nv]];
last = first + n;
for (i = first; i < last; i++)
ivector[i] = (int) ubuf(buf[m++]).i;
} else if (style[nv] == DVEC) {
} else if (styles[nv] == DVEC) {
double *dvector = atom->dvector[index[nv]];
last = first + n;
for (i = first; i < last; i++)
dvector[i] = buf[m++];
} else if (style[nv] == IARRAY) {
} else if (styles[nv] == IARRAY) {
int **iarray = atom->iarray[index[nv]];
ncol = cols[nv];
last = first + n;
for (i = first; i < last; i++)
for (k = 0; k < ncol; k++)
iarray[i][k] = (int) ubuf(buf[m++]).i;
} else if (style[nv] == DARRAY) {
} else if (styles[nv] == DARRAY) {
double **darray = atom->darray[index[nv]];
ncol = cols[nv];
last = first + n;
@ -693,16 +693,16 @@ int FixPropertyAtom::pack_exchange(int i, double *buf)
int m = 0;
for (int nv = 0; nv < nvalue; nv++) {
if (style[nv] == MOLECULE) buf[m++] = ubuf(atom->molecule[i]).d;
else if (style[nv] == CHARGE) buf[m++] = atom->q[i];
else if (style[nv] == RMASS) buf[m++] = atom->rmass[i];
else if (style[nv] == IVEC) buf[m++] = ubuf(atom->ivector[index[nv]][i]).d;
else if (style[nv] == DVEC) buf[m++] = atom->dvector[index[nv]][i];
else if (style[nv] == IARRAY) {
if (styles[nv] == MOLECULE) buf[m++] = ubuf(atom->molecule[i]).d;
else if (styles[nv] == CHARGE) buf[m++] = atom->q[i];
else if (styles[nv] == RMASS) buf[m++] = atom->rmass[i];
else if (styles[nv] == IVEC) buf[m++] = ubuf(atom->ivector[index[nv]][i]).d;
else if (styles[nv] == DVEC) buf[m++] = atom->dvector[index[nv]][i];
else if (styles[nv] == IARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++)
buf[m++] = ubuf(atom->iarray[index[nv]][i][k]).d;
} else if (style[nv] == DARRAY) {
} else if (styles[nv] == DARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++)
buf[m++] = atom->darray[index[nv]][i][k];
@ -722,21 +722,21 @@ int FixPropertyAtom::unpack_exchange(int nlocal, double *buf)
int m = 0;
for (int nv = 0; nv < nvalue; nv++) {
if (style[nv] == MOLECULE)
if (styles[nv] == MOLECULE)
atom->molecule[nlocal] = (tagint) ubuf(buf[m++]).i;
else if (style[nv] == CHARGE)
else if (styles[nv] == CHARGE)
atom->q[nlocal] = buf[m++];
else if (style[nv] == RMASS)
else if (styles[nv] == RMASS)
atom->rmass[nlocal] = buf[m++];
else if (style[nv] == IVEC)
else if (styles[nv] == IVEC)
atom->ivector[index[nv]][nlocal] = (int) ubuf(buf[m++]).i;
else if (style[nv] == DVEC)
else if (styles[nv] == DVEC)
atom->dvector[index[nv]][nlocal] = buf[m++];
else if (style[nv] == IARRAY) {
else if (styles[nv] == IARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++)
atom->iarray[index[nv]][nlocal][k] = (int) ubuf(buf[m++]).i;
} else if (style[nv] == DARRAY) {
} else if (styles[nv] == DARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++)
atom->darray[index[nv]][nlocal][k] = buf[m++];
@ -760,16 +760,16 @@ int FixPropertyAtom::pack_restart(int i, double *buf)
int m = 1;
for (int nv = 0; nv < nvalue; nv++) {
if (style[nv] == MOLECULE) buf[m++] = ubuf(atom->molecule[i]).d;
else if (style[nv] == CHARGE) buf[m++] = atom->q[i];
else if (style[nv] == RMASS) buf[m++] = atom->rmass[i];
else if (style[nv] == IVEC) buf[m++] = ubuf(atom->ivector[index[nv]][i]).d;
else if (style[nv] == DVEC) buf[m++] = atom->dvector[index[nv]][i];
else if (style[nv] == IARRAY) {
if (styles[nv] == MOLECULE) buf[m++] = ubuf(atom->molecule[i]).d;
else if (styles[nv] == CHARGE) buf[m++] = atom->q[i];
else if (styles[nv] == RMASS) buf[m++] = atom->rmass[i];
else if (styles[nv] == IVEC) buf[m++] = ubuf(atom->ivector[index[nv]][i]).d;
else if (styles[nv] == DVEC) buf[m++] = atom->dvector[index[nv]][i];
else if (styles[nv] == IARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++)
buf[m++] = ubuf(atom->iarray[index[nv]][i][k]).d;
} else if (style[nv] == DARRAY) {
} else if (styles[nv] == DARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++)
buf[m++] = atom->darray[index[nv]][i][k];
@ -796,21 +796,21 @@ void FixPropertyAtom::unpack_restart(int nlocal, int nth)
m++;
for (int nv = 0; nv < nvalue; nv++) {
if (style[nv] == MOLECULE)
if (styles[nv] == MOLECULE)
atom->molecule[nlocal] = (tagint) ubuf(extra[nlocal][m++]).i;
else if (style[nv] == CHARGE)
else if (styles[nv] == CHARGE)
atom->q[nlocal] = extra[nlocal][m++];
else if (style[nv] == RMASS)
else if (styles[nv] == RMASS)
atom->rmass[nlocal] = extra[nlocal][m++];
else if (style[nv] == IVEC)
else if (styles[nv] == IVEC)
atom->ivector[index[nv]][nlocal] = (int) ubuf(extra[nlocal][m++]).i;
else if (style[nv] == DVEC)
else if (styles[nv] == DVEC)
atom->dvector[index[nv]][nlocal] = extra[nlocal][m++];
else if (style[nv] == IARRAY) {
else if (styles[nv] == IARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++)
atom->iarray[index[nv]][nlocal][k] = (int) ubuf(extra[nlocal][m++]).i;
} else if (style[nv] == DARRAY) {
} else if (styles[nv] == DARRAY) {
ncol = cols[nv];
for (k = 0; k < ncol; k++)
atom->darray[index[nv]][nlocal][k] = extra[nlocal][m++];

2
src/fix_property_atom.h
View File

@ -53,7 +53,7 @@ class FixPropertyAtom : public Fix {
protected:
int nvalue, border;
int molecule_flag, q_flag, rmass_flag; // flags for specific fields
int *style; // style of each value, see enum
int *styles; // style of each value, see enum
int *index; // indices into atom custom data structs
int *cols; // columns per value, for arrays
char *astyle; // atom style at instantiation

6
src/info.cpp
View File

@ -1356,8 +1356,10 @@ std::string Info::get_openmp_info()
// Supported OpenMP version corresponds to the release date of the
// specifications as posted at https://www.openmp.org/specifications/
#if _OPENMP > 201811
return "OpenMP newer than version 5.0";
#if _OPENMP > 202011
return "OpenMP newer than version 5.1";
#elif _OPENMP == 202011
return "OpenMP 5.1";
#elif _OPENMP == 201811
return "OpenMP 5.0";
#elif _OPENMP == 201611

2
src/library.cpp
View File

@ -2712,7 +2712,7 @@ Below is a brief C code demonstrating accessing this collected bond information.
#include <stdio.h>
#include <stdlib.h>
#include <inttypes.h>
#include <stdint.h>
#include "library.h"
int main(int argc, char **argv)

2
src/library.h
View File

@ -35,7 +35,7 @@
#endif
#if defined(LAMMPS_BIGBIG) || defined(LAMMPS_SMALLBIG)
#include <inttypes.h> /* for int64_t */
#include <stdint.h> /* for int64_t */
#endif
/** Data type constants for extracting data from atoms, computes and fixes

110
src/memory.h
View File

@ -27,7 +27,7 @@ class Memory : protected Pointers {
void sfree(void *);
void fail(const char *);
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
create/grow/destroy vecs and multidim arrays with contiguous memory blocks
only use with primitive data types, e.g. 1d vec of ints, 2d array of doubles
fail() prevents use with pointers,
@ -36,12 +36,15 @@ class Memory : protected Pointers {
for these other cases, use smalloc/srealloc/sfree directly
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
create a 1d array
------------------------------------------------------------------------- */
template <typename TYPE> TYPE *create(TYPE *&array, int n, const char *name)
{
// POSSIBLE future change
//if (n <= 0) return nullptr;
bigint nbytes = ((bigint) sizeof(TYPE)) * n;
array = (TYPE *) smalloc(nbytes, name);
return array;
@ -53,12 +56,18 @@ class Memory : protected Pointers {
return nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
grow or shrink 1d array
------------------------------------------------------------------------- */
template <typename TYPE> TYPE *grow(TYPE *&array, int n, const char *name)
{
// POSSIBLE future change
//if (n <= 0) {
// destroy(array);
// return nullptr;
// }
if (array == nullptr) return create(array, n, name);
bigint nbytes = ((bigint) sizeof(TYPE)) * n;
@ -72,7 +81,7 @@ class Memory : protected Pointers {
return nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
destroy a 1d array
------------------------------------------------------------------------- */
@ -82,13 +91,16 @@ class Memory : protected Pointers {
array = nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
create a 1d array with index from nlo to nhi inclusive
cannot grow it
------------------------------------------------------------------------- */
template <typename TYPE> TYPE *create1d_offset(TYPE *&array, int nlo, int nhi, const char *name)
{
// POSSIBLE future change
// if (nlo > nhi) return nullptr;
bigint nbytes = ((bigint) sizeof(TYPE)) * (nhi - nlo + 1);
array = (TYPE *) smalloc(nbytes, name);
array -= nlo;
@ -102,7 +114,7 @@ class Memory : protected Pointers {
return nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
destroy a 1d array with index offset
------------------------------------------------------------------------- */
@ -112,12 +124,15 @@ class Memory : protected Pointers {
array = nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
create a 2d array
------------------------------------------------------------------------- */
template <typename TYPE> TYPE **create(TYPE **&array, int n1, int n2, const char *name)
{
// POSSIBLE future change
//if (n1 <= 0 || n2 <= 0) return nullptr;
bigint nbytes = ((bigint) sizeof(TYPE)) * n1 * n2;
TYPE *data = (TYPE *) smalloc(nbytes, name);
nbytes = ((bigint) sizeof(TYPE *)) * n1;
@ -138,13 +153,19 @@ class Memory : protected Pointers {
return nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
grow or shrink 1st dim of a 2d array
last dim must stay the same
------------------------------------------------------------------------- */
template <typename TYPE> TYPE **grow(TYPE **&array, int n1, int n2, const char *name)
{
// POSSIBLE future change
//if (n1 <= 0 || n2 <= 0) {
// destroy(array);
// return nullptr;
// }
if (array == nullptr) return create(array, n1, n2, name);
bigint nbytes = ((bigint) sizeof(TYPE)) * n1 * n2;
@ -167,7 +188,7 @@ class Memory : protected Pointers {
return nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
destroy a 2d array
------------------------------------------------------------------------- */
@ -179,12 +200,15 @@ class Memory : protected Pointers {
array = nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
create a 2d array with a ragged 2nd dimension
------------------------------------------------------------------------- */
template <typename TYPE> TYPE **create_ragged(TYPE **&array, int n1, int *n2, const char *name)
{
// POSSIBLE future change
//if (n1 <= 0) return nullptr;
bigint n2sum = 0;
for (int i = 0; i < n1; i++) n2sum += n2[i];
@ -208,7 +232,7 @@ class Memory : protected Pointers {
return nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
create a 2d array with 2nd index from n2lo to n2hi inclusive
cannot grow it
------------------------------------------------------------------------- */
@ -216,6 +240,9 @@ class Memory : protected Pointers {
template <typename TYPE>
TYPE **create2d_offset(TYPE **&array, int n1, int n2lo, int n2hi, const char *name)
{
// POSSIBLE future change
//if (n1 <= 0 || n2lo > n2hi) return nullptr;
int n2 = n2hi - n2lo + 1;
create(array, n1, n2, name);
for (int i = 0; i < n1; i++) array[i] -= n2lo;
@ -230,7 +257,7 @@ class Memory : protected Pointers {
return nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
destroy a 2d array with 2nd index offset
------------------------------------------------------------------------- */
@ -242,12 +269,15 @@ class Memory : protected Pointers {
array = nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
create a 3d array
------------------------------------------------------------------------- */
template <typename TYPE> TYPE ***create(TYPE ***&array, int n1, int n2, int n3, const char *name)
{
// POSSIBLE future change
//if (n1 <= 0 || n2 <= 0 || n3 <= 0) return nullptr;
bigint nbytes = ((bigint) sizeof(TYPE)) * n1 * n2 * n3;
TYPE *data = (TYPE *) smalloc(nbytes, name);
nbytes = ((bigint) sizeof(TYPE *)) * n1 * n2;
@ -276,13 +306,19 @@ class Memory : protected Pointers {
return nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
grow or shrink 1st dim of a 3d array
last 2 dims must stay the same
------------------------------------------------------------------------- */
template <typename TYPE> TYPE ***grow(TYPE ***&array, int n1, int n2, int n3, const char *name)
{
// POSSIBLE future change
//if (n1 <= 0 || n2 <= 0 || n3 <= 0) {
// destroy(array);
// return nullptr;
//};
if (array == nullptr) return create(array, n1, n2, n3, name);
bigint nbytes = ((bigint) sizeof(TYPE)) * n1 * n2 * n3;
@ -313,7 +349,7 @@ class Memory : protected Pointers {
return nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
destroy a 3d array
------------------------------------------------------------------------- */
@ -326,7 +362,7 @@ class Memory : protected Pointers {
array = nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
create a 3d array with 1st index from n1lo to n1hi inclusive
cannot grow it
------------------------------------------------------------------------- */
@ -334,6 +370,8 @@ class Memory : protected Pointers {
template <typename TYPE>
TYPE ***create3d_offset(TYPE ***&array, int n1lo, int n1hi, int n2, int n3, const char *name)
{
if (n1lo > n1hi || n2 <= 0 || n3 <= 0) return nullptr;
int n1 = n1hi - n1lo + 1;
create(array, n1, n2, n3, name);
array -= n1lo;
@ -348,7 +386,7 @@ class Memory : protected Pointers {
return nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
free a 3d array with 1st index offset
------------------------------------------------------------------------- */
@ -361,7 +399,7 @@ class Memory : protected Pointers {
array = nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
create a 3d array with
1st index from n1lo to n1hi inclusive,
2nd index from n2lo to n2hi inclusive,
@ -373,6 +411,8 @@ class Memory : protected Pointers {
TYPE ***create3d_offset(TYPE ***&array, int n1lo, int n1hi, int n2lo, int n2hi, int n3lo,
int n3hi, const char *name)
{
if (n1lo > n1hi || n2lo > n2hi || n3lo > n3hi) return nullptr;
int n1 = n1hi - n1lo + 1;
int n2 = n2hi - n2lo + 1;
int n3 = n3hi - n3lo + 1;
@ -393,7 +433,7 @@ class Memory : protected Pointers {
return nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
free a 3d array with all 3 indices offset
------------------------------------------------------------------------- */
@ -407,13 +447,16 @@ class Memory : protected Pointers {
array = nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
create a 4d array
------------------------------------------------------------------------- */
template <typename TYPE>
TYPE ****create(TYPE ****&array, int n1, int n2, int n3, int n4, const char *name)
{
// POSSIBLE future change
//if (n1 <= 0 || n2 <= 0 || n3 <= 0 || n4 <= 0) return nullptr;
bigint nbytes = ((bigint) sizeof(TYPE)) * n1 * n2 * n3 * n4;
TYPE *data = (TYPE *) smalloc(nbytes, name);
nbytes = ((bigint) sizeof(TYPE *)) * n1 * n2 * n3;
@ -451,7 +494,7 @@ class Memory : protected Pointers {
return nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
grow or shrink 1st dim of a 4d array
last 3 dims must stay the same
------------------------------------------------------------------------- */
@ -459,6 +502,12 @@ class Memory : protected Pointers {
template <typename TYPE>
TYPE ****grow(TYPE ****&array, int n1, int n2, int n3, int n4, const char *name)
{
// POSSIBLE future change
//if (n1 <= 0 || n2 <= 0 || n3 <= 0 || n4 <= 0) {
// destroy(array);
// return nullptr;
// }
if (array == nullptr) return create(array, n1, n2, n3, n4, name);
bigint nbytes = ((bigint) sizeof(TYPE)) * n1 * n2 * n3 * n4;
@ -498,7 +547,7 @@ class Memory : protected Pointers {
return nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
destroy a 4d array
------------------------------------------------------------------------- */
@ -512,7 +561,7 @@ class Memory : protected Pointers {
array = nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
create a 4d array with indices
2nd index from n2lo to n2hi inclusive
3rd index from n3lo to n3hi inclusive
@ -524,6 +573,8 @@ class Memory : protected Pointers {
TYPE ****create4d_offset(TYPE ****&array, int n1, int n2lo, int n2hi, int n3lo, int n3hi,
int n4lo, int n4hi, const char *name)
{
if (n1 <= 0 || n2lo > n2hi || n3lo > n3hi || n4lo > n4hi) return nullptr;
int n2 = n2hi - n2lo + 1;
int n3 = n3hi - n3lo + 1;
int n4 = n4hi - n4lo + 1;
@ -545,8 +596,8 @@ class Memory : protected Pointers {
return nullptr;
}
/* ----------------------------------------------------------------------
free a 4d array with indices 2,3, and 4 offset
/* ----------------------------------------------------------------------
free a 4d array with indices 2,3,4 offset
------------------------------------------------------------------------- */
template <typename TYPE>
@ -560,13 +611,16 @@ class Memory : protected Pointers {
array = nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
create a 5d array
------------------------------------------------------------------------- */
template <typename TYPE>
TYPE *****create(TYPE *****&array, int n1, int n2, int n3, int n4, int n5, const char *name)
{
// POSSIBLE future change
//if (n1 <= 0 || n2 <= 0 || n3 <= 0 || n4 <= 0 || n5 <= 0) return nullptr;
bigint nbytes = ((bigint) sizeof(TYPE)) * n1 * n2 * n3 * n4 * n5;
TYPE *data = (TYPE *) smalloc(nbytes, name);
nbytes = ((bigint) sizeof(TYPE *)) * n1 * n2 * n3 * n4;
@ -611,7 +665,7 @@ class Memory : protected Pointers {
return nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
destroy a 5d array
------------------------------------------------------------------------- */
@ -626,7 +680,7 @@ class Memory : protected Pointers {
array = nullptr;
}
/* ----------------------------------------------------------------------
/* ----------------------------------------------------------------------
memory usage of arrays, including pointers
------------------------------------------------------------------------- */

6
src/molecule.cpp
View File

@ -148,13 +148,15 @@ Molecule::Molecule(LAMMPS *lmp, int narg, char **arg, int &index) :
if (me == 0)
utils::logmesg(lmp,"Read molecule template {}:\n {} molecules\n"
" {} fragments\n"
" {} atoms with max type {}\n"
" {} bonds with max type {}\n"
" {} angles with max type {}\n"
" {} dihedrals with max type {}\n"
" {} impropers with max type {}\n", id,nmolecules,
natoms,ntypes,nbonds,nbondtypes,nangles,nangletypes,
ndihedrals,ndihedraltypes,nimpropers,nimpropertypes);
nfragments,natoms,ntypes,nbonds,nbondtypes,nangles,
nangletypes,ndihedrals,ndihedraltypes,nimpropers,
nimpropertypes);
}
/* ---------------------------------------------------------------------- */

605
src/pair_table.cpp
View File

File diff suppressed because it is too large Load Diff

138
tools/binary2txt.cpp
View File

@ -19,8 +19,8 @@
// Syntax: binary2txt file1 file2 ...
// Creates: file1.txt file2.txt ...
#include <stdio.h>
#include <string.h>
#include <cstdio>
#include <cstring>
// these must match settings in src/lmptype.h which builds LAMMPS with
// -DLAMMPS_SMALLBIG (the default), -DLAMMPS_BIGBIG, or -DLAMMPS_SMALLSMALL
@ -57,10 +57,10 @@ typedef int64_t bigint;
int main(int narg, char **arg)
{
int i,j,k,m,n;
bigint ntimestep,natoms;
int size_one,nchunk,triclinic;
double xlo,xhi,ylo,yhi,zlo,zhi,xy,xz,yz;
int i, j, k, m, n;
bigint ntimestep, natoms;
int size_one, nchunk, triclinic;
double xlo, xhi, ylo, yhi, zlo, zhi, xy, xz, yz;
int boundary[3][2];
char boundstr[9];
@ -75,25 +75,25 @@ int main(int narg, char **arg)
// loop over files
for (int iarg = 1; iarg < narg; iarg++) {
printf("%s:",arg[iarg]);
printf("%s:", arg[iarg]);
fflush(stdout);
FILE *fp = fopen(arg[iarg],"rb");
FILE *fp = fopen(arg[iarg], "rb");
if (!fp) {
printf("ERROR: Could not open %s\n",arg[iarg]);
printf("ERROR: Could not open %s\n", arg[iarg]);
return 1;
}
n = strlen(arg[iarg]) + 1 + 4;
char *filetxt = new char[n];
strcpy(filetxt,arg[iarg]);
strcat(filetxt,".txt");
FILE *fptxt = fopen(filetxt,"w");
delete [] filetxt;
strcpy(filetxt, arg[iarg]);
strcat(filetxt, ".txt");
FILE *fptxt = fopen(filetxt, "w");
delete[] filetxt;
// detect newer format
char * magic_string = nullptr;
char * columns = nullptr;
char * unit_style = nullptr;
char *magic_string = nullptr;
char *columns = nullptr;
char *unit_style = nullptr;
// loop over snapshots in file
@ -101,7 +101,7 @@ int main(int narg, char **arg)
int endian = 0x0001;
int revision = 0x0001;
fread(&ntimestep,sizeof(bigint),1,fp);
fread(&ntimestep, sizeof(bigint), 1, fp);
// detect end-of-file
@ -116,7 +116,7 @@ int main(int narg, char **arg)
// first bigint encodes negative format name length
bigint magic_string_len = -ntimestep;
delete [] magic_string;
delete[] magic_string;
magic_string = new char[magic_string_len + 1];
fread(magic_string, sizeof(char), magic_string_len, fp);
magic_string[magic_string_len] = '\0';
@ -128,24 +128,24 @@ int main(int narg, char **arg)
fread(&revision, sizeof(int), 1, fp);
// read the real ntimestep
fread(&ntimestep,sizeof(bigint),1,fp);
fread(&ntimestep, sizeof(bigint), 1, fp);
}
fread(&natoms,sizeof(bigint),1,fp);
fread(&triclinic,sizeof(int),1,fp);
fread(&boundary[0][0],6*sizeof(int),1,fp);
fread(&xlo,sizeof(double),1,fp);
fread(&xhi,sizeof(double),1,fp);
fread(&ylo,sizeof(double),1,fp);
fread(&yhi,sizeof(double),1,fp);
fread(&zlo,sizeof(double),1,fp);
fread(&zhi,sizeof(double),1,fp);
fread(&natoms, sizeof(bigint), 1, fp);
fread(&triclinic, sizeof(int), 1, fp);
fread(&boundary[0][0], 6 * sizeof(int), 1, fp);
fread(&xlo, sizeof(double), 1, fp);
fread(&xhi, sizeof(double), 1, fp);
fread(&ylo, sizeof(double), 1, fp);
fread(&yhi, sizeof(double), 1, fp);
fread(&zlo, sizeof(double), 1, fp);
fread(&zhi, sizeof(double), 1, fp);
if (triclinic) {
fread(&xy,sizeof(double),1,fp);
fread(&xz,sizeof(double),1,fp);
fread(&yz,sizeof(double),1,fp);
fread(&xy, sizeof(double), 1, fp);
fread(&xz, sizeof(double), 1, fp);
fread(&yz, sizeof(double), 1, fp);
}
fread(&size_one,sizeof(int),1,fp);
fread(&size_one, sizeof(int), 1, fp);
if (magic_string && revision > 0x0001) {
// newer format includes units string, columns string
@ -155,8 +155,8 @@ int main(int narg, char **arg)
if (len > 0) {
// has units
delete [] unit_style;
unit_style = new char[len+1];
delete[] unit_style;
unit_style = new char[len + 1];
fread(unit_style, sizeof(char), len, fp);
unit_style[len] = '\0';
fprintf(fptxt, "ITEM: UNITS\n");
@ -173,90 +173,94 @@ int main(int narg, char **arg)
}
fread(&len, sizeof(int), 1, fp);
delete [] columns;
columns = new char[len+1];
delete[] columns;
columns = new char[len + 1];
fread(columns, sizeof(char), len, fp);
columns[len] = '\0';
}
fread(&nchunk,sizeof(int),1,fp);
fread(&nchunk, sizeof(int), 1, fp);
fprintf(fptxt,"ITEM: TIMESTEP\n");
fprintf(fptxt,BIGINT_FORMAT "\n",ntimestep);
fprintf(fptxt,"ITEM: NUMBER OF ATOMS\n");
fprintf(fptxt,BIGINT_FORMAT "\n",natoms);
fprintf(fptxt, "ITEM: TIMESTEP\n");
fprintf(fptxt, BIGINT_FORMAT "\n", ntimestep);
fprintf(fptxt, "ITEM: NUMBER OF ATOMS\n");
fprintf(fptxt, BIGINT_FORMAT "\n", natoms);
m = 0;
for (int idim = 0; idim < 3; idim++) {
for (int iside = 0; iside < 2; iside++) {
if (boundary[idim][iside] == 0) boundstr[m++] = 'p';
else if (boundary[idim][iside] == 1) boundstr[m++] = 'f';
else if (boundary[idim][iside] == 2) boundstr[m++] = 's';
else if (boundary[idim][iside] == 3) boundstr[m++] = 'm';
if (boundary[idim][iside] == 0)
boundstr[m++] = 'p';
else if (boundary[idim][iside] == 1)
boundstr[m++] = 'f';
else if (boundary[idim][iside] == 2)
boundstr[m++] = 's';
else if (boundary[idim][iside] == 3)
boundstr[m++] = 'm';
}
boundstr[m++] = ' ';
}
boundstr[8] = '\0';
if (!triclinic) {
fprintf(fptxt,"ITEM: BOX BOUNDS %s\n",boundstr);
fprintf(fptxt,"%-1.16e %-1.16e\n",xlo,xhi);
fprintf(fptxt,"%-1.16e %-1.16e\n",ylo,yhi);
fprintf(fptxt,"%-1.16e %-1.16e\n",zlo,zhi);
fprintf(fptxt, "ITEM: BOX BOUNDS %s\n", boundstr);
fprintf(fptxt, "%-1.16e %-1.16e\n", xlo, xhi);
fprintf(fptxt, "%-1.16e %-1.16e\n", ylo, yhi);
fprintf(fptxt, "%-1.16e %-1.16e\n", zlo, zhi);
} else {
fprintf(fptxt,"ITEM: BOX BOUNDS xy xz yz %s\n",boundstr);
fprintf(fptxt,"%-1.16e %-1.16e %-1.16e\n",xlo,xhi,xy);
fprintf(fptxt,"%-1.16e %-1.16e %-1.16e\n",ylo,yhi,xz);
fprintf(fptxt,"%-1.16e %-1.16e %-1.16e\n",zlo,zhi,yz);
fprintf(fptxt, "ITEM: BOX BOUNDS xy xz yz %s\n", boundstr);
fprintf(fptxt, "%-1.16e %-1.16e %-1.16e\n", xlo, xhi, xy);
fprintf(fptxt, "%-1.16e %-1.16e %-1.16e\n", ylo, yhi, xz);
fprintf(fptxt, "%-1.16e %-1.16e %-1.16e\n", zlo, zhi, yz);
}
if (columns)
fprintf(fptxt,"ITEM: ATOMS %s\n", columns);
fprintf(fptxt, "ITEM: ATOMS %s\n", columns);
else
fprintf(fptxt,"ITEM: ATOMS\n");
fprintf(fptxt, "ITEM: ATOMS\n");
// loop over processor chunks in file
for (i = 0; i < nchunk; i++) {
fread(&n,sizeof(int),1,fp);
fread(&n, sizeof(int), 1, fp);
// extend buffer to fit chunk size
if (n > maxbuf) {
if (buf) delete [] buf;
if (buf) delete[] buf;
buf = new double[n];
maxbuf = n;
}
// read chunk and write as size_one values per line
fread(buf,sizeof(double),n,fp);
fread(buf, sizeof(double), n, fp);
n /= size_one;
m = 0;
for (j = 0; j < n; j++) {
for (k = 0; k < size_one; k++) {
if(k+1 < size_one) {
fprintf(fptxt,"%g ",buf[m++]);
if (k + 1 < size_one) {
fprintf(fptxt, "%g ", buf[m++]);
} else {
fprintf(fptxt,"%g",buf[m++]);
fprintf(fptxt, "%g", buf[m++]);
}
}
fprintf(fptxt,"\n");
fprintf(fptxt, "\n");
}
}
printf(" " BIGINT_FORMAT,ntimestep);
printf(" " BIGINT_FORMAT, ntimestep);
fflush(stdout);
}
printf("\n");
delete [] columns;
delete [] magic_string;
delete [] unit_style;
delete[] columns;
delete[] magic_string;
delete[] unit_style;
columns = nullptr;
magic_string = nullptr;
unit_style = nullptr;
}
if (buf) delete [] buf;
if (buf) delete[] buf;
return 0;
}

321
tools/chain.f
View File

@ -1,321 +0,0 @@
c Create LAMMPS data file for collection of
c polymer bead-spring chains of various lengths and bead sizes
c Syntax: chain < def.chain > data.file
c def.chain is input file that specifies the chains
c data.file is output file that will be input for LAMMPS
c includes image flags in data file so chains can be unraveled later
program chain
integer swaptype
integer, allocatable :: nchain(:),nmonomer(:)
integer, allocatable :: ntype(:),nbondtype(:)
integer, allocatable :: type(:),molecule(:)
integer, allocatable :: imagex(:),imagey(:),imagez(:)
real*8, allocatable :: x(:),y(:),z(:)
real*8, allocatable :: bondlength(:),restrict(:)
common xprd,yprd,zprd,xboundlo,xboundhi,
$ yboundlo,yboundhi,zboundlo,zboundhi
real*8 random
900 format(a)
901 format(2f15.6,a)
902 format(i3,f5.1)
903 format(i10,i8,i8,3f10.4,3i4)
904 format(i9,i3,2i9)
c read chain definitions
read (5,*)
read (5,*)
read (5,*) rhostar
read (5,*) iseed
read (5,*) nsets
read (5,*) swaptype
allocate(nchain(nsets))
allocate(nmonomer(nsets))
allocate(ntype(nsets))
allocate(nbondtype(nsets))
allocate(bondlength(nsets))
allocate(restrict(nsets))
do iset = 1,nsets
read (5,*)
read (5,*) nchain(iset)
read (5,*) nmonomer(iset)
read (5,*) ntype(iset)
read (5,*) nbondtype(iset)
read (5,*) bondlength(iset)
read (5,*) restrict(iset)
enddo
c natoms = total # of monomers
natoms = 0
do iset = 1,nsets
natoms = natoms + nchain(iset)*nmonomer(iset)
enddo
allocate(x(natoms))
allocate(y(natoms))
allocate(z(natoms))
allocate(type(natoms))
allocate(molecule(natoms))
allocate(imagex(natoms))
allocate(imagey(natoms))
allocate(imagez(natoms))
c setup box size (sigma = 1.0)
volume = natoms/rhostar
xprd = volume**(1.0/3.0)
yprd = xprd
zprd = xprd
xboundlo = -xprd/2.0
xboundhi = -xboundlo
yboundlo = xboundlo
yboundhi = xboundhi
zboundlo = xboundlo
zboundhi = xboundhi
c generate random chains
c loop over sets and chains in each set
n = 0
nmolecule = 0
do iset = 1,nsets
do ichain = 1,nchain(iset)
nmolecule = nmolecule + 1
c random starting point for the chain in the box
x1 = 0.0
y1 = 0.0
z1 = 0.0
x2 = xboundlo + random(iseed)*xprd
y2 = yboundlo + random(iseed)*yprd
z2 = zboundlo + random(iseed)*zprd
c store 1st monomer of chain
c 1st monomer is always in original box (image = 0)
call pbc(x2,y2,z2)
n = n + 1
x(n) = x2
y(n) = y2
z(n) = z2
type(n) = ntype(iset)
imagex(n) = 0
imagey(n) = 0
imagez(n) = 0
if (swaptype == 0) then
molecule(n) = nmolecule
else
molecule(n) = 1
endif
c generate rest of monomers in this chain
do imonomer = 2,nmonomer(iset)
x0 = x1
y0 = y1
z0 = z1
x1 = x2
y1 = y2
z1 = z2
c random point inside sphere of unit radius
10 xinner = 2.0*random(iseed) - 1.0
yinner = 2.0*random(iseed) - 1.0
zinner = 2.0*random(iseed) - 1.0
rsq = xinner*xinner + yinner*yinner + zinner*zinner
if (rsq > 1.0) goto 10
c project point to surface of sphere of unit radius
r = sqrt(rsq)
xsurf = xinner/r
ysurf = yinner/r
zsurf = zinner/r
c create new point by scaling unit offsets by bondlength (sigma = 1.0)
x2 = x1 + xsurf*bondlength(iset)
y2 = y1 + ysurf*bondlength(iset)
z2 = z1 + zsurf*bondlength(iset)
c check that new point meets restriction requirement
c only for 3rd monomer and beyond
dx = x2 - x0
dy = y2 - y0
dz = z2 - z0
r = sqrt(dx*dx + dy*dy + dz*dz)
if (imonomer > 2 .and. r <= restrict(iset)) goto 10
c store new point
c if delta to previous bead is large, then increment/decrement image flag
call pbc(x2,y2,z2)
n = n + 1
x(n) = x2
y(n) = y2
z(n) = z2
type(n) = ntype(iset)
if (abs(x(n)-x(n-1)) < 2.0*bondlength(iset)) then
imagex(n) = imagex(n-1)
else if (x(n) - x(n-1) < 0.0) then
imagex(n) = imagex(n-1) + 1
else if (x(n) - x(n-1) > 0.0) then
imagex(n) = imagex(n-1) - 1
endif
if (abs(y(n)-y(n-1)) < 2.0*bondlength(iset)) then
imagey(n) = imagey(n-1)
else if (y(n) - y(n-1) < 0.0) then
imagey(n) = imagey(n-1) + 1
else if (y(n) - y(n-1) > 0.0) then
imagey(n) = imagey(n-1) - 1
endif
if (abs(z(n)-z(n-1)) < 2.0*bondlength(iset)) then
imagez(n) = imagez(n-1)
else if (z(n) - z(n-1) < 0.0) then
imagez(n) = imagez(n-1) + 1
else if (z(n) - z(n-1) > 0.0) then
imagez(n) = imagez(n-1) - 1
endif
if (swaptype == 0) then
molecule(n) = nmolecule
else if (swaptype == 1) then
molecule(n) = imonomer
else if (swaptype == 2) then
if (imonomer <= nmonomer(iset)/2) then
molecule(n) = imonomer
else
molecule(n) = nmonomer(iset)+1-imonomer
endif
endif
enddo
enddo
enddo
c compute quantities needed for LAMMPS file
nbonds = 0
ntypes = 0
nbondtypes = 0
do iset = 1,nsets
nbonds = nbonds + nchain(iset)*(nmonomer(iset)-1)
if (ntype(iset) > ntypes) ntypes = ntype(iset)
if (nbondtype(iset) > nbondtypes)
$ nbondtypes = nbondtype(iset)
enddo
c write out LAMMPS file
write (6,900) 'LAMMPS FENE chain data file'
write (6,*)
write (6,*) natoms,' atoms'
write (6,*) nbonds,' bonds'
write (6,*) 0,' angles'
write (6,*) 0,' dihedrals'
write (6,*) 0,' impropers'
write (6,*)
write (6,*) ntypes,' atom types'
write (6,*) nbondtypes,' bond types'
write (6,*) 0,' angle types'
write (6,*) 0,' dihedral types'
write (6,*) 0,' improper types'
write (6,*)
write (6,901) xboundlo,xboundhi,' xlo xhi'
write (6,901) yboundlo,yboundhi,' ylo yhi'
write (6,901) zboundlo,zboundhi,' zlo zhi'
write (6,*)
write (6,900) 'Masses'
write (6,*)
do i = 1,ntypes
write (6,902) i,1.0
enddo
write (6,*)
write (6,900) 'Atoms'
write (6,*)
do i = 1,natoms
write (6,903) i,molecule(i),type(i),x(i),y(i),z(i),
$ imagex(i),imagey(i),imagez(i)
enddo
if (nbonds > 0) then
write (6,*)
write (6,900) 'Bonds'
write (6,*)
n = 0
m = 0
do iset = 1,nsets
do ichain = 1,nchain(iset)
do imonomer = 1,nmonomer(iset)
n = n + 1
if (imonomer /= nmonomer(iset)) then
m = m + 1
write (6,904) m,nbondtype(iset),n,n+1
endif
enddo
enddo
enddo
endif
end
c ************
c Subroutines
c ************
c periodic boundary conditions - map atom back into periodic box
subroutine pbc(x,y,z)
common xprd,yprd,zprd,xboundlo,xboundhi,
$ yboundlo,yboundhi,zboundlo,zboundhi
if (x < xboundlo) x = x + xprd
if (x >= xboundhi) x = x - xprd
if (y < yboundlo) y = y + yprd
if (y >= yboundhi) y = y - yprd
if (z < zboundlo) z = z + zprd
if (z >= zboundhi) z = z - zprd
return
end
c RNG from Numerical Recipes
real*8 function random(iseed)
real*8 aa,mm,sseed
parameter (aa=16807.0D0,mm=2147483647.0D0)
sseed = iseed
sseed = mod(aa*sseed,mm)
random = sseed/mm
iseed = sseed
return
end

333
tools/chain.f90 Normal file
View File

@ -0,0 +1,333 @@
! Create LAMMPS data file for collection of
! polymer bead-spring chains of various lengths and bead sizes
! Syntax: chain < def.chain > data.file
! def.chain is input file that specifies the chains
! data.file is output file that will be input for LAMMPS
! includes image flags in data file so chains can be unraveled later
MODULE boxchain
IMPLICIT NONE
PUBLIC
REAL(KIND=8) :: xprd,yprd,zprd,xboundlo,xboundhi,yboundlo,yboundhi,zboundlo,zboundhi
CONTAINS
! periodic boundary conditions - map atom back into periodic box
SUBROUTINE pbc(x,y,z)
REAL(KIND=8), INTENT(inout) :: x,y,z
IF (x < xboundlo) x = x + xprd
IF (x >= xboundhi) x = x - xprd
IF (y < yboundlo) y = y + yprd
IF (y >= yboundhi) y = y - yprd
IF (z < zboundlo) z = z + zprd
IF (z >= zboundhi) z = z - zprd
END SUBROUTINE pbc
END MODULE boxchain
MODULE rngchain
IMPLICIT NONE
CONTAINS
! *very* minimal random number generator
REAL(KIND=8) FUNCTION random(iseed)
IMPLICIT NONE
INTEGER, INTENT(inout) :: iseed
REAL(KIND=8), PARAMETER :: aa=16807.0_8, mm=2147483647.0_8
REAL(KIND=8) :: sseed
sseed = REAL(iseed)
sseed = MOD(aa*sseed,mm)
random = sseed/mm
iseed = INT(sseed)
END FUNCTION random
END MODULE rngchain
PROGRAM chain
USE boxchain
USE rngchain
IMPLICIT NONE
INTEGER, ALLOCATABLE :: nchain(:),nmonomer(:)
INTEGER, ALLOCATABLE :: ntype(:),nbondtype(:)
INTEGER, ALLOCATABLE :: atomtype(:),molecule(:)
INTEGER, ALLOCATABLE :: imagex(:),imagey(:),imagez(:)
REAL(KIND=8), ALLOCATABLE :: x(:),y(:),z(:)
REAL(KIND=8), ALLOCATABLE :: bondlength(:),restrict(:)
INTEGER :: i, n, m, nmolecule, natoms, ntypes, nbonds, nbondtypes
INTEGER :: swaptype, iseed, nsets, iset, ichain, imonomer
REAL(KIND=8) :: r, rhostar, volume, rsq, xinner, yinner, zinner, xsurf, ysurf, zsurf
REAL(KIND=8) :: x0, y0, z0, x1, y1, z1, x2, y2, z2, dx, dy, dz
LOGICAL :: again
! read chain definitions
READ (5,*)
READ (5,*)
READ (5,*) rhostar
READ (5,*) iseed
READ (5,*) nsets
READ (5,*) swaptype
ALLOCATE(nchain(nsets))
ALLOCATE(nmonomer(nsets))
ALLOCATE(ntype(nsets))
ALLOCATE(nbondtype(nsets))
ALLOCATE(bondlength(nsets))
ALLOCATE(restrict(nsets))
DO iset = 1,nsets
READ (5,*)
READ (5,*) nchain(iset)
READ (5,*) nmonomer(iset)
READ (5,*) ntype(iset)
READ (5,*) nbondtype(iset)
READ (5,*) bondlength(iset)
READ (5,*) restrict(iset)
ENDDO
! natoms = total # of monomers
natoms = 0
DO iset = 1,nsets
natoms = natoms + nchain(iset)*nmonomer(iset)
ENDDO
ALLOCATE(x(natoms))
ALLOCATE(y(natoms))
ALLOCATE(z(natoms))
ALLOCATE(atomtype(natoms))
ALLOCATE(molecule(natoms))
ALLOCATE(imagex(natoms))
ALLOCATE(imagey(natoms))
ALLOCATE(imagez(natoms))
! setup box size (sigma = 1.0)
volume = natoms/rhostar
xprd = volume**(1.0/3.0)
yprd = xprd
zprd = xprd
xboundlo = -xprd/2.0
xboundhi = -xboundlo
yboundlo = xboundlo
yboundhi = xboundhi
zboundlo = xboundlo
zboundhi = xboundhi
! generate random chains
! loop over sets and chains in each set
n = 0
nmolecule = 0
DO iset = 1,nsets
DO ichain = 1,nchain(iset)
nmolecule = nmolecule + 1
! random starting point for the chain in the box
x1 = 0.0
y1 = 0.0
z1 = 0.0
x2 = xboundlo + random(iseed)*xprd
y2 = yboundlo + random(iseed)*yprd
z2 = zboundlo + random(iseed)*zprd
! store 1st monomer of chain
! 1st monomer is always in original box (image = 0)
CALL pbc(x2,y2,z2)
n = n + 1
x(n) = x2
y(n) = y2
z(n) = z2
atomtype(n) = ntype(iset)
imagex(n) = 0
imagey(n) = 0
imagez(n) = 0
IF (swaptype == 0) THEN
molecule(n) = nmolecule
ELSE
molecule(n) = 1
END IF
! generate rest of monomers in this chain
DO imonomer = 2, nmonomer(iset)
x0 = x1
y0 = y1
z0 = z1
x1 = x2
y1 = y2
z1 = z2
again = .TRUE.
DO WHILE (again)
! random point inside sphere of unit radius
xinner = 2.0*random(iseed) - 1.0
yinner = 2.0*random(iseed) - 1.0
zinner = 2.0*random(iseed) - 1.0
rsq = xinner*xinner + yinner*yinner + zinner*zinner
IF (rsq > 1.0) CYCLE
! project point to surface of sphere of unit radius
r = SQRT(rsq)
xsurf = xinner/r
ysurf = yinner/r
zsurf = zinner/r
! create new point by scaling unit offsets by bondlength (sigma = 1.0)
x2 = x1 + xsurf*bondlength(iset)
y2 = y1 + ysurf*bondlength(iset)
z2 = z1 + zsurf*bondlength(iset)
! check that new point meets restriction requirement
! only for 3rd monomer and beyond
dx = x2 - x0
dy = y2 - y0
dz = z2 - z0
r = SQRT(dx*dx + dy*dy + dz*dz)
IF (imonomer > 2 .AND. r <= restrict(iset)) CYCLE
! store new point
again = .FALSE.
! if delta to previous bead is large, then increment/decrement image flag
CALL pbc(x2,y2,z2)
n = n + 1
x(n) = x2
y(n) = y2
z(n) = z2
atomtype(n) = ntype(iset)
IF (ABS(x(n)-x(n-1)) < 2.0*bondlength(iset)) THEN
imagex(n) = imagex(n-1)
ELSE IF (x(n) - x(n-1) < 0.0) THEN
imagex(n) = imagex(n-1) + 1
ELSE IF (x(n) - x(n-1) > 0.0) THEN
imagex(n) = imagex(n-1) - 1
ENDIF
IF (ABS(y(n)-y(n-1)) < 2.0*bondlength(iset)) THEN
imagey(n) = imagey(n-1)
ELSE IF (y(n) - y(n-1) < 0.0) THEN
imagey(n) = imagey(n-1) + 1
ELSE IF (y(n) - y(n-1) > 0.0) THEN
imagey(n) = imagey(n-1) - 1
ENDIF
IF (ABS(z(n)-z(n-1)) < 2.0*bondlength(iset)) THEN
imagez(n) = imagez(n-1)
ELSE IF (z(n) - z(n-1) < 0.0) THEN
imagez(n) = imagez(n-1) + 1
ELSE IF (z(n) - z(n-1) > 0.0) THEN
imagez(n) = imagez(n-1) - 1
ENDIF
IF (swaptype == 0) THEN
molecule(n) = nmolecule
ELSE IF (swaptype == 1) THEN
molecule(n) = imonomer
ELSE IF (swaptype == 2) THEN
IF (imonomer <= nmonomer(iset)/2) THEN
molecule(n) = imonomer
ELSE
molecule(n) = nmonomer(iset)+1-imonomer
ENDIF
ENDIF
ENDDO
ENDDO
ENDDO
ENDDO
! compute quantities needed for LAMMPS file
nbonds = 0
ntypes = 0
nbondtypes = 0
DO iset = 1,nsets
nbonds = nbonds + nchain(iset)*(nmonomer(iset)-1)
IF (ntype(iset) > ntypes) ntypes = ntype(iset)
IF (nbondtype(iset) > nbondtypes) nbondtypes = nbondtype(iset)
ENDDO
! write out LAMMPS file
WRITE (6,*) 'LAMMPS FENE chain data file'
WRITE (6,*)
WRITE (6,*) natoms,' atoms'
WRITE (6,*) nbonds,' bonds'
WRITE (6,*) 0,' angles'
WRITE (6,*) 0,' dihedrals'
WRITE (6,*) 0,' impropers'
WRITE (6,*)
WRITE (6,*) ntypes,' atom types'
WRITE (6,*) nbondtypes,' bond types'
WRITE (6,*) 0,' angle types'
WRITE (6,*) 0,' dihedral types'
WRITE (6,*) 0,' improper types'
WRITE (6,*)
WRITE (6,'(2F15.6,A)') xboundlo,xboundhi,' xlo xhi'
WRITE (6,'(2F15.6,A)') yboundlo,yboundhi,' ylo yhi'
WRITE (6,'(2F15.6,A)') zboundlo,zboundhi,' zlo zhi'
WRITE (6,*)
WRITE (6,*) 'Masses'
WRITE (6,*)
DO i = 1,ntypes
WRITE (6,'(i3,f5.1)') i,1.0
ENDDO
WRITE (6,*)
WRITE (6,*) 'Atoms # molecular'
WRITE (6,*)
DO i = 1,natoms
WRITE (6,'(I10,I8,I8,3F10.4,3I4)') i,molecule(i),atomtype(i),x(i),y(i),z(i), &
imagex(i),imagey(i),imagez(i)
ENDDO
IF (nbonds > 0) THEN
WRITE (6,*)
WRITE (6,*) 'Bonds'
WRITE (6,*)
n = 0
m = 0
DO iset = 1,nsets
DO ichain = 1,nchain(iset)
DO imonomer = 1,nmonomer(iset)
n = n + 1
IF (imonomer /= nmonomer(iset)) THEN
m = m + 1
WRITE (6,'(i9,i3,2i9)') m,nbondtype(iset),n,n+1
ENDIF
ENDDO
ENDDO
ENDDO
ENDIF
DEALLOCATE(nchain, nmonomer, ntype, nbondtype, bondlength, restrict)
DEALLOCATE(x, y, z, atomtype, molecule, imagex, imagey, imagez)
END PROGRAM chain

3
tools/coding_standard/whitespace.py
View File

@ -34,6 +34,7 @@ exclude:
- lib/hdnnp
- lib/kim
- lib/kokkos
- lib/latte
- lib/machdyn
- lib/mdi
- lib/mscg
@ -41,6 +42,7 @@ exclude:
- lib/plumed
- lib/quip
- lib/scafacos
- lib/voronoi
- src/Make.sh
patterns:
- "*.c"
@ -51,6 +53,7 @@ patterns:
- "*.py"
- "*.rst"
- "*.sh"
- "*.f90"
- ".gitignore"
- "README"
- "requirements.txt"

233
tools/micelle2d.f
View File

@ -1,233 +0,0 @@
c Create LAMMPS 2003 input file for 2d LJ simulation of micelles
c
c Syntax: micelle2d < def.micelle2d > data.file
c
c def file contains size of system and number to turn into surfactants
c attaches a random surfactant tail(s) to random head
c if nonflag is set, will attach 2nd-neighbor bonds in surfactant
c solvent atoms = type 1
c micelle heads = type 2
c micelle tails = type 3,4,5,etc.
program micelle2d
parameter (maxatom=100000,maxbond=10000)
real*4 x(2,maxatom)
integer type(maxatom),molecule(maxatom)
integer bondatom(2,maxbond),bondtype(maxbond)
common xprd,yprd,zprd,xboundlo,xboundhi,yboundlo,yboundhi,
$ zboundlo,zboundhi
999 format (3i7,3f8.3)
998 format (4i7)
read (5,*)
read (5,*)
read (5,*) rhostar
read (5,*) iseed
read (5,*) nx,ny
read (5,*) nsurf
read (5,*) r0
read (5,*) ntails
read (5,*) nonflag
natoms = nx*ny
if (natoms+nsurf*ntails.gt.maxatom) then
write (6,*) 'Too many atoms - boost maxatom'
call exit(0)
endif
nbonds = nsurf*ntails
if (nonflag.eq.1) nbonds = nbonds + nsurf*(ntails-1)
if (nbonds.gt.maxbond) then
write (6,*) 'Too many surfactants - boost maxbond'
call exit(0)
endif
c box size
rlattice = (1.0/rhostar) ** 0.5
xboundlo = 0.0
xboundhi = nx*rlattice
yboundlo = 0.0
yboundhi = ny*rlattice
zboundlo = -0.1
zboundhi = 0.1
sigma = 1.0
xprd = xboundhi - xboundlo
yprd = yboundhi - yboundlo
zprd = zboundhi - zboundlo
c initial square lattice of solvents
m = 0
do j = 1,ny
do i = 1,nx
m = m + 1
x(1,m) = xboundlo + (i-1)*rlattice
x(2,m) = yboundlo + (j-1)*rlattice
molecule(m) = 0
type(m) = 1
enddo
enddo
c turn some into surfactants with molecule ID
c head changes to type 2
c create ntails for each head of types 3,4,...
c each tail is at distance r0 away in straight line with random orientation
do i = 1,nsurf
10 m = random(iseed)*natoms + 1
if (m.gt.natoms) m = natoms
if (molecule(m) .ne. 0) goto 10
molecule(m) = i
type(m) = 2
angle = random(iseed)*2.0*3.1415926
do j = 1,ntails
k = (i-1)*ntails + j
x(1,natoms+k) = x(1,m) + cos(angle)*j*r0*sigma
x(2,natoms+k) = x(2,m) + sin(angle)*j*r0*sigma
molecule(natoms+k) = i
type(natoms+k) = 2+j
call pbc(x(1,natoms+k),x(2,natoms+k))
if (j.eq.1) bondatom(1,k) = m
if (j.ne.1) bondatom(1,k) = natoms+k-1
bondatom(2,k) = natoms+k
bondtype(k) = 1
enddo
enddo
c if nonflag is set, add (ntails-1) 2nd nearest neighbor bonds to end
c of bond list
c k = location in bondatom list where nearest neighbor bonds for
c this surfactant are stored
if (nonflag.eq.1) then
nbonds = nsurf*ntails
do i = 1,nsurf
do j = 1,ntails-1
k = (i-1)*ntails + j
nbonds = nbonds + 1
bondatom(1,nbonds) = bondatom(1,k)
bondatom(2,nbonds) = bondatom(2,k+1)
bondtype(nbonds) = 2
enddo
enddo
endif
c write LAMMPS data file
natoms = natoms + nsurf*ntails
nbonds = nsurf*ntails
if (nonflag.eq.1) nbonds = nbonds + nsurf*(ntails-1)
ntypes = 2 + ntails
nbondtypes = 1
if (nonflag.eq.1) nbondtypes = 2
if (nsurf.eq.0) then
ntypes = 1
nbondtypes = 0
endif
write (6,*) 'LAMMPS 2d micelle data file'
write (6,*)
write (6,*) natoms,' atoms'
write (6,*) nbonds,' bonds'
write (6,*) 0,' angles'
write (6,*) 0,' dihedrals'
write (6,*) 0,' impropers'
write (6,*)
write (6,*) ntypes,' atom types'
write (6,*) nbondtypes,' bond types'
write (6,*) 0,' angle types'
write (6,*) 0,' dihedral types'
write (6,*) 0,' improper types'
write (6,*)
write (6,*) xboundlo,xboundhi,' xlo xhi'
write (6,*) yboundlo,yboundhi,' ylo yhi'
write (6,*) zboundlo,zboundhi,' zlo zhi'
write (6,*)
write (6,*) 'Masses'
write (6,*)
do i = 1,ntypes
write (6,*) i,1.0
enddo
write (6,*)
write (6,*) 'Atoms'
write (6,*)
do i = 1,natoms
write (6,999) i,molecule(i),type(i),x(1,i),x(2,i),0.0
enddo
if (nsurf.gt.0) then
write (6,*)
write (6,*) 'Bonds'
write (6,*)
do i = 1,nbonds
write (6,998) i,bondtype(i),bondatom(1,i),bondatom(2,i)
enddo
endif
c write Xmovie bond geometry file
open(1,file='bond.micelle')
write (1,*) 'ITEM: BONDS'
do i = 1,nbonds
write (1,*) bondtype(i),bondatom(1,i),bondatom(2,i)
enddo
close(1)
end
c ************
c Subroutines
c ************
c periodic boundary conditions - map atom back into periodic box
subroutine pbc(x,y)
common xprd,yprd,zprd,xboundlo,xboundhi,yboundlo,yboundhi,
$ zboundlo,zboundhi
if (x.lt.xboundlo) x = x + xprd
if (x.ge.xboundhi) x = x - xprd
if (y.lt.yboundlo) y = y + yprd
if (y.ge.yboundhi) y = y - yprd
return
end
c RNG - compute in double precision, return single
real*4 function random(iseed)
real*8 aa,mm,sseed
parameter (aa=16807.0D0,mm=2147483647.0D0)
sseed = iseed
sseed = mod(aa*sseed,mm)
random = sseed/mm
iseed = sseed
return
end

231
tools/micelle2d.f90 Normal file
View File

@ -0,0 +1,231 @@
! Create LAMMPS data file for 2d LJ simulation of micelles
!
! Syntax: micelle2d < def.micelle2d > data.file
!
! def file contains size of system and number to turn into surfactants
! attaches a random surfactant tail(s) to random head
! if nonflag is set, will attach 2nd-neighbor bonds in surfactant
! solvent atoms = type 1
! micelle heads = type 2
! micelle tails = type 3,4,5,etc.
MODULE boxmicelle
IMPLICIT NONE
PUBLIC
REAL(KIND=8) :: xprd,yprd,zprd,xboundlo,xboundhi,yboundlo,yboundhi,zboundlo,zboundhi
CONTAINS
! periodic boundary conditions - map atom back into periodic box
SUBROUTINE pbc(x,y)
REAL(KIND=8), INTENT(inout) :: x,y
IF (x < xboundlo) x = x + xprd
IF (x >= xboundhi) x = x - xprd
IF (y < yboundlo) y = y + yprd
IF (y >= yboundhi) y = y - yprd
END SUBROUTINE pbc
END MODULE boxmicelle
MODULE rngmicelle
IMPLICIT NONE
CONTAINS
! *very* minimal random number generator
REAL(KIND=8) FUNCTION random(iseed)
IMPLICIT NONE
INTEGER, INTENT(inout) :: iseed
REAL(KIND=8), PARAMETER :: aa=16807.0_8, mm=2147483647.0_8
REAL(KIND=8) :: sseed
sseed = REAL(iseed)
sseed = MOD(aa*sseed,mm)
random = sseed/mm
iseed = INT(sseed)
END FUNCTION random
END MODULE rngmicelle
PROGRAM micelle2d
USE boxmicelle
USE rngmicelle
IMPLICIT NONE
REAL(kind=8), ALLOCATABLE :: x(:,:)
INTEGER, ALLOCATABLE :: atomtype(:), molecule(:)
INTEGER, ALLOCATABLE :: bondatom(:,:),bondtype(:)
INTEGER :: natoms, maxatom, ntypes, nbonds, nbondtypes, iseed
INTEGER :: i, j, k, m, nx, ny, nsurf, ntails, nonflag
REAL(kind=8) :: rhostar, rlattice, sigma, angle,r0
REAL(kind=8), parameter :: pi = 3.14159265358979323846_8
LOGICAL :: again
READ(5,*)
READ(5,*)
READ(5,*) rhostar
READ(5,*) iseed
READ(5,*) nx,ny
READ(5,*) nsurf
READ(5,*) r0
READ(5,*) ntails
READ(5,*) nonflag
natoms = nx*ny
maxatom = natoms + nsurf*ntails
ALLOCATE(x(2,maxatom), molecule(maxatom), atomtype(maxatom))
nbonds = nsurf*ntails
IF (nonflag.EQ.1) nbonds = nbonds + nsurf*(ntails-1)
ALLOCATE(bondatom(2,nbonds), bondtype(nbonds))
! box size
rlattice = (1.0_8/rhostar) ** 0.5_8
xboundlo = 0.0_8
xboundhi = nx*rlattice
yboundlo = 0.0_8
yboundhi = ny*rlattice
zboundlo = -0.1_8
zboundhi = 0.1_8
sigma = 1.0_8
xprd = xboundhi - xboundlo
yprd = yboundhi - yboundlo
zprd = zboundhi - zboundlo
! initial square lattice of solvents
m = 0
DO j = 1,ny
DO i = 1,nx
m = m + 1
x(1,m) = xboundlo + (i-1)*rlattice
x(2,m) = yboundlo + (j-1)*rlattice
molecule(m) = 0
atomtype(m) = 1
ENDDO
ENDDO
! turn some into surfactants with molecule ID
! head changes to type 2
! create ntails for each head of types 3,4,...
! each tail is at distance r0 away in straight line with random orientation
DO i = 1,nsurf
again = .TRUE.
DO WHILE(again)
m = INT(random(iseed)*natoms + 1)
IF (m > natoms) m = natoms
IF (molecule(m) /= 0) CYCLE
again = .FALSE.
END DO
molecule(m) = i
atomtype(m) = 2
angle = random(iseed)*2.0_8*pi
DO j = 1,ntails
k = (i-1)*ntails + j
x(1,natoms+k) = x(1,m) + COS(angle)*j*r0*sigma
x(2,natoms+k) = x(2,m) + SIN(angle)*j*r0*sigma
molecule(natoms+k) = i
atomtype(natoms+k) = 2+j
CALL pbc(x(1,natoms+k),x(2,natoms+k))
IF (j == 1) bondatom(1,k) = m
IF (j /= 1) bondatom(1,k) = natoms+k-1
bondatom(2,k) = natoms+k
bondtype(k) = 1
ENDDO
ENDDO
! if nonflag is set, add (ntails-1) 2nd nearest neighbor bonds to end
! of bond list
! k = location in bondatom list where nearest neighbor bonds for
! this surfactant are stored
IF (nonflag == 1) THEN
nbonds = nsurf*ntails
DO i = 1,nsurf
DO j = 1,ntails-1
k = (i-1)*ntails + j
nbonds = nbonds + 1
bondatom(1,nbonds) = bondatom(1,k)
bondatom(2,nbonds) = bondatom(2,k+1)
bondtype(nbonds) = 2
ENDDO
ENDDO
ENDIF
! write LAMMPS data file
natoms = natoms + nsurf*ntails
nbonds = nsurf*ntails
IF (nonflag == 1) nbonds = nbonds + nsurf*(ntails-1)
ntypes = 2 + ntails
nbondtypes = 1
IF (nonflag == 1) nbondtypes = 2
IF (nsurf == 0) THEN
ntypes = 1
nbondtypes = 0
ENDIF
WRITE (6,*) 'LAMMPS 2d micelle data file'
WRITE (6,*)
WRITE (6,*) natoms,' atoms'
WRITE (6,*) nbonds,' bonds'
WRITE (6,*) 0,' angles'
WRITE (6,*) 0,' dihedrals'
WRITE (6,*) 0,' impropers'
WRITE (6,*)
WRITE (6,*) ntypes,' atom types'
WRITE (6,*) nbondtypes,' bond types'
WRITE (6,*) 0,' angle types'
WRITE (6,*) 0,' dihedral types'
WRITE (6,*) 0,' improper types'
WRITE (6,*)
WRITE (6,*) xboundlo,xboundhi,' xlo xhi'
WRITE (6,*) yboundlo,yboundhi,' ylo yhi'
WRITE (6,*) zboundlo,zboundhi,' zlo zhi'
WRITE (6,*)
WRITE (6,*) 'Masses'
WRITE (6,*)
DO i = 1,ntypes
WRITE (6,*) i,1.0
ENDDO
WRITE (6,*)
WRITE (6,*) 'Atoms # molecular'
WRITE (6,*)
DO i = 1,natoms
WRITE (6,'(3I7,3F8.3)') i,molecule(i),atomtype(i),x(1,i),x(2,i),0.0
ENDDO
IF (nsurf > 0) THEN
WRITE (6,*)
WRITE (6,*) 'Bonds'
WRITE (6,*)
DO i = 1,nbonds
WRITE (6,'(4I7)') i,bondtype(i),bondatom(1,i),bondatom(2,i)
ENDDO
ENDIF
DEALLOCATE(x,molecule,atomtype,bondtype,bondatom)
END PROGRAM micelle2d

2
unittest/force-styles/tests/atomic-pair-meam.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 10 Feb 2021
date_generated: Fri Feb 26 23:09:03 2021
epsilon: 5e-13
epsilon: 2.5e-12
prerequisites: ! |
pair meam
pre_commands: ! |

2
unittest/force-styles/tests/atomic-pair-meam_spline.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 10 Feb 2021
date_generated: Fri Feb 26 23:09:03 2021
epsilon: 1e-14
epsilon: 5e-14
prerequisites: ! |
pair meam/spline
pre_commands: ! |

2
unittest/force-styles/tests/atomic-pair-polymorphic_eam.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 10 Feb 2021
date_generated: Fri Feb 26 23:09:04 2021
epsilon: 5e-14
epsilon: 7.5e-14
prerequisites: ! |
pair polymorphic
pre_commands: ! |

2
unittest/force-styles/tests/bond-class2.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 10 Feb 2021
date_generated: Fri Feb 26 23:09:21 2021
epsilon: 1e-13
epsilon: 4e-13
prerequisites: ! |
atom full
bond class2

128
unittest/force-styles/tests/data.bilayer
View File

@ -1,72 +1,66 @@
LAMMPS data file. CGCMM style. atom_style full generated by VMD/TopoTools v1.8 on Sun Aug 15 17:12:56 EDT 2021
48 atoms
0 bonds
0 angles
0 dihedrals
0 impropers
3 atom types
0 bond types
0 angle types
0 dihedral types
0 improper types
0 7.38 xlo xhi
0 8.58 ylo yhi
0 10.0 zlo zhi
LAMMPS data file via write_data, version 30 Jul 2021, timestep = 0
Masses
48 atoms
3 atom types
1 11.000000 # 1
2 14.000000 # 2
3 12.000000 # 3
0 7.38 xlo xhi
0 8.58 ylo yhi
-0.010057298274271795 10 zlo zhi
Atoms # full
Masses
1 1 2 -0.420000 0.000000 0.715000 0.000000 # 2
2 1 1 0.420000 0.000000 2.145000 0.000000 # 1
3 1 2 -0.420000 1.238416 2.860000 0.000000 # 2
4 1 1 0.420000 1.238416 4.290000 0.000000 # 1
5 1 2 -0.420000 0.000000 5.005000 0.000000 # 2
6 1 1 0.420000 0.000000 6.435000 0.000000 # 1
7 1 2 -0.420000 1.238416 7.150000 0.000000 # 2
8 1 1 0.420000 1.238416 8.580000 0.000000 # 1
9 1 2 -0.420000 2.476833 0.715000 0.000000 # 2
10 1 1 0.420000 2.476833 2.145000 0.000000 # 1
11 1 2 -0.420000 3.715249 2.860000 0.000000 # 2
12 1 1 0.420000 3.715249 4.290000 0.000000 # 1
13 1 2 -0.420000 2.476833 5.005000 0.000000 # 2
14 1 1 0.420000 2.476833 6.435000 0.000000 # 1
15 1 2 -0.420000 3.715249 7.150000 0.000000 # 2
16 1 1 0.420000 3.715249 8.580000 0.000000 # 1
17 1 2 -0.420000 4.953665 0.715000 0.000000 # 2
18 1 1 0.420000 4.953665 2.145000 0.000000 # 1
19 1 2 -0.420000 6.192081 2.860000 0.000000 # 2
20 1 1 0.420000 6.192081 4.290000 0.000000 # 1
21 1 2 -0.420000 4.953665 5.005000 0.000000 # 2
22 1 1 0.420000 4.953665 6.435000 0.000000 # 1
23 1 2 -0.420000 6.192081 7.150000 0.000000 # 2
24 1 1 0.420000 6.192081 8.580000 0.000000 # 1
25 2 3 0.000000 1.238416 1.430000 3.330000 # 3
26 2 3 0.000000 0.000000 2.145000 3.330000 # 3
27 2 3 0.000000 0.000000 3.575000 3.330000 # 3
28 2 3 0.000000 1.238416 4.290000 3.330000 # 3
29 2 3 0.000000 1.238416 5.720000 3.330000 # 3
30 2 3 0.000000 0.000000 6.435000 3.330000 # 3
31 2 3 0.000000 0.000000 7.865000 3.330000 # 3
32 2 3 0.000000 1.238416 8.580000 3.330000 # 3
33 2 3 0.000000 3.715249 1.430000 3.330000 # 3
34 2 3 0.000000 2.476833 2.145000 3.330000 # 3
35 2 3 0.000000 2.476833 3.575000 3.330000 # 3
36 2 3 0.000000 3.715249 4.290000 3.330000 # 3
37 2 3 0.000000 3.715249 5.720000 3.330000 # 3
38 2 3 0.000000 2.476833 6.435000 3.330000 # 3
39 2 3 0.000000 2.476833 7.865000 3.330000 # 3
40 2 3 0.000000 3.715249 8.580000 3.330000 # 3
41 2 3 0.000000 6.192081 1.430000 3.330000 # 3
42 2 3 0.000000 4.953665 2.145000 3.330000 # 3
43 2 3 0.000000 4.953665 3.575000 3.330000 # 3
44 2 3 0.000000 6.192081 4.290000 3.330000 # 3
45 2 3 0.000000 6.192081 5.720000 3.330000 # 3
46 2 3 0.000000 4.953665 6.435000 3.330000 # 3
47 2 3 0.000000 4.953665 7.865000 3.330000 # 3
48 2 3 0.000000 6.192081 8.580000 3.330000 # 3
1 11
2 14
3 12
Atoms # full
1 1 2 -0.42 7.377582386921897 0.7221769963191714 0.0037771363154878545 -1 0 0
2 1 1 0.42 7.378315948261095 2.1411424242268047 0.005723979908844447 -1 0 0
3 1 2 -0.42 1.2447887970776952 2.8676004848245533 0.001348446268284902 0 0 0
4 1 1 0.42 1.2414656689644874 4.28578628613883 0.00011113531427045186 0 0 0
5 1 2 -0.42 0.002474815180746286 4.9992187428028405 -0.005589712651255407 0 0 0
6 1 1 0.42 7.379979983665971 6.4385854739759045 0.0010611130348691324 -1 0 0
7 1 2 -0.42 1.2317585840471603 7.158810080624563 -0.008974942974268898 0 0 0
8 1 1 0.42 1.2352508770341066 0.0037783122313107898 0.002093671640424837 0 1 0
9 1 2 -0.42 2.4773332782542727 0.7231766195586773 0.004444922690486966 0 0 0
10 1 1 0.42 2.4830271537615816 2.1501422709017723 0.006147046087378192 0 0 0
11 1 2 -0.42 3.709595948985172 2.8691715937849 0.006976742817543793 0 0 0
12 1 1 0.42 3.7240167199015244 4.289068384919813 0.002345347298470022 0 0 0
13 1 2 -0.42 2.4712325868621394 4.998856391973726 0.004379902423536359 0 0 0
14 1 1 0.42 2.474562437522464 6.433656440055303 -0.0012119905144032052 0 0 0
15 1 2 -0.42 3.725038325222275 7.159189010774339 -0.0002959156829379106 0 0 0
16 1 1 0.42 3.706133972373436 0.0037306803342563467 0.0015443778464311643 0 1 0
17 1 2 -0.42 4.956689237720773 0.7233633730273523 0.0032104707105134024 0 0 0
18 1 1 0.42 4.962115477057346 2.152167902820356 -0.009057298274271795 0 0 0
19 1 2 -0.42 6.184281256484653 2.869710737578436 0.008366480776279456 0 0 0
20 1 1 0.42 6.188803450864838 4.284231685327474 -0.008064701146476297 0 0 0
21 1 2 -0.42 4.949812422011079 5.0147217402047115 -0.006712379416782586 0 0 0
22 1 1 0.42 4.948281204520974 6.429549384016799 -0.00850282965158244 0 0 0
23 1 2 -0.42 6.194837058886999 7.1510817137970974 0.0003637878086249291 0 0 0
24 1 1 0.42 6.197894966950315 8.5753425339448 0.0019680102504640875 0 0 0
25 2 3 0 1.2443079194694104 1.4354905223825436 3.3292096834113867 0 0 0
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2
unittest/force-styles/tests/dihedral-multi_harmonic.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 10 Feb 2021
date_generated: Fri Feb 26 23:09:35 2021
epsilon: 2.5e-13
epsilon: 5e-13
prerequisites: ! |
atom full
dihedral multi/harmonic

2
unittest/force-styles/tests/dihedral-quadratic.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 10 Feb 2021
date_generated: Fri Feb 26 23:09:35 2021
epsilon: 2.5e-13
epsilon: 1e-12
prerequisites: ! |
atom full
dihedral quadratic

2
unittest/force-styles/tests/dihedral-spherical.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 30 Jul 2021
date_generated: Sun Aug 22 10:57:54 2021
epsilon: 2.5e-14
epsilon: 5e-14
skip_tests:
prerequisites: ! |
atom full

2
unittest/force-styles/tests/dihedral-table_cut_linear.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 10 Mar 2021
date_generated: Tue Mar 23 08:05:02 202
epsilon: 2e-14
epsilon: 5e-14
prerequisites: ! |
atom full
dihedral table/cut

2
unittest/force-styles/tests/dihedral-table_cut_spline.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 10 Mar 2021
date_generated: Tue Mar 23 08:06:45 202
epsilon: 2e-14
epsilon: 2.5e-13
prerequisites: ! |
atom full
dihedral table/cut

2
unittest/force-styles/tests/dihedral-table_linear.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 10 Mar 2021
date_generated: Mon Mar 22 21:19:05 202
epsilon: 1e-14
epsilon: 7.5e-14
prerequisites: ! |
atom full
dihedral table

2
unittest/force-styles/tests/dihedral-table_spline.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 10 Mar 2021
date_generated: Mon Mar 22 21:19:05 202
epsilon: 1e-14
epsilon: 1e-13
prerequisites: ! |
atom full
dihedral table

2
unittest/force-styles/tests/fix-timestep-addtorque_const.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 30 Jul 2021
date_generated: Sun Aug 22 14:22:56 2021
epsilon: 9e-12
epsilon: 2.5e-11
skip_tests:
prerequisites: ! |
atom full

2
unittest/force-styles/tests/fix-timestep-momentum_chunk.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 10 Feb 2021
date_generated: Fri Feb 26 23:09:54 2021
epsilon: 2e-14
epsilon: 1e-13
prerequisites: ! |
atom full
fix momentum/chunk

2
unittest/force-styles/tests/fix-timestep-nph_sphere.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 30 Jul 2021
date_generated: Sun Aug 22 14:13:03 2021
epsilon: 5e-14
epsilon: 2e-13
skip_tests:
prerequisites: ! |
atom full

2
unittest/force-styles/tests/fix-timestep-npt_sphere_aniso.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 30 Jul 2021
date_generated: Sun Aug 22 14:10:26 2021
epsilon: 1e-13
epsilon: 4e-13
skip_tests:
prerequisites: ! |
atom full

2
unittest/force-styles/tests/fix-timestep-npt_sphere_iso.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 30 Jul 2021
date_generated: Sun Aug 22 14:07:35 2021
epsilon: 5e-14
epsilon: 2e-13
skip_tests:
prerequisites: ! |
atom full

2
unittest/force-styles/tests/fix-timestep-npt_sphere_tri.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 30 Jul 2021
date_generated: Sun Aug 22 14:15:09 2021
epsilon: 2e-13
epsilon: 5e-13
skip_tests:
prerequisites: ! |
atom full

2
unittest/force-styles/tests/fix-timestep-oneway.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 10 Feb 2021
date_generated: Fri Feb 26 23:09:55 2021
epsilon: 4e-14
epsilon: 7.5e-14
prerequisites: ! |
atom full
fix oneway

2
unittest/force-styles/tests/fix-timestep-rattle_bond.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 10 Feb 2021
date_generated: Fri Feb 26 23:09:55 2021
epsilon: 1e-10
epsilon: 1.5e-10
prerequisites: ! |
atom full
fix rattle

2
unittest/force-styles/tests/fix-timestep-shake_bond.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 10 Feb 2021
date_generated: Fri Feb 26 23:09:58 2021
epsilon: 3.5e-11
epsilon: 5e-11
prerequisites: ! |
atom full
fix shake

2
unittest/force-styles/tests/fix-timestep-wall_harmonic_const.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 10 Feb 2021
date_generated: Fri Feb 26 23:09:59 2021
epsilon: 3e-14
epsilon: 4e-14
prerequisites: ! |
atom full
fix wall/harmonic

2
unittest/force-styles/tests/improper-harmonic.yaml
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@ -1,7 +1,7 @@
---
lammps_version: 10 Feb 2021
date_generated: Wed Feb 24 19:35:15 202
epsilon: 1e-11
epsilon: 2e-11
prerequisites: ! |
atom full
improper harmonic

94
unittest/force-styles/tests/kspace-ewald_tilted.yaml Normal file
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@ -0,0 +1,94 @@
---
lammps_version: 30 Jul 2021
date_generated: Tue Aug 24 16:00:03 2021
epsilon: 8.5e-14
skip_tests:
prerequisites: ! |
atom full
pair coul/long
kspace ewald
pre_commands: ! ""
post_commands: ! |
pair_modify mix arithmetic
pair_modify table 0
pair_modify compute no
group none empty
change_box all triclinic
change_box none xy final 0.5 xz final 0.5 yz final 0.5
kspace_style ewald 1.0e-6
kspace_modify gewald 0.3
input_file: in.fourmol
pair_style: coul/long 8.0
pair_coeff: ! |
* *
extract: ! ""
natoms: 29
init_vdwl: 0
init_coul: 0
init_stress: ! |2-
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init_forces: ! |2
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...

92
unittest/force-styles/tests/kspace-pppm_tilted.yaml Normal file
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@ -0,0 +1,92 @@
---
lammps_version: 30 Jul 2021
date_generated: Tue Aug 24 15:57:51 2021
epsilon: 1e-13
skip_tests: gpu
prerequisites: ! |
atom full
pair coul/long
kspace pppm
pre_commands: ! ""
post_commands: ! |
pair_modify compute no
group none empty
change_box all triclinic
change_box none xy final 0.5 xz final 0.5 yz final 0.5
kspace_style pppm 1.0e-6
kspace_modify gewald 0.3
input_file: in.fourmol
pair_style: coul/long 8.0
pair_coeff: ! |
* *
extract: ! ""
natoms: 29
init_vdwl: 0
init_coul: 0
init_stress: ! |2-
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
init_forces: ! |2
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29 4.2151929760224643e-01 -7.9119072040766358e-01 4.4262080871675447e-01
run_vdwl: 0
run_coul: 0
run_stress: ! |2-
0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00 0.0000000000000000e+00
run_forces: ! |2
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27 -8.6411178235841868e-01 1.6207327144466275e+00 -9.2534662609109775e-01
28 5.6960687175236380e-01 -9.0819316709272491e-01 5.3155039440194063e-01
29 4.2192140517923227e-01 -7.9125996757091022e-01 4.3997061496410916e-01
...

2
unittest/force-styles/tests/kspace-pppm_tip4p_ad.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 10 Feb 2021
date_generated: Fri Feb 26 23:09:34 2021
epsilon: 3e-13
epsilon: 4e-13
prerequisites: ! |
atom full
pair tip4p/long

2
unittest/force-styles/tests/manybody-pair-bop.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 8 Apr 2021
date_generated: Wed May 5 11:50:15 2021
epsilon: 2e-13
epsilon: 5e-13
prerequisites: ! |
pair bop
pre_commands: ! |

2
unittest/force-styles/tests/manybody-pair-bop_save.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 8 Apr 2021
date_generated: Wed May 5 11:50:24 2021
epsilon: 2e-14
epsilon: 9e-13
prerequisites: ! |
pair bop
pre_commands: ! |

204
unittest/force-styles/tests/manybody-pair-drip.yaml
View File

@ -1,7 +1,7 @@
---
lammps_version: 30 Jul 2021
date_generated: Tue Aug 17 15:09:48 2021
epsilon: 5e-14
date_generated: Tue Aug 24 15:36:39 2021
epsilon: 2e-13
skip_tests: single
prerequisites: ! |
pair drip
@ -16,110 +16,110 @@ pair_coeff: ! |
* * drip C.drip C C C
extract: ! ""
natoms: 48
init_vdwl: -1.1171061429439093
init_vdwl: -1.1165820288113353
init_coul: 0
init_stress: ! |-
-6.9372049706365035e-01 -6.9064113154966333e-01 1.1515233668963607e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.4292420626121039e-02
-6.9202029395419495e-01 -6.8748326656871916e-01 1.1598469113436700e+00 -8.7520222366446450e-04 -7.4904268268328076e-03 -4.8018384975223698e-03
init_forces: ! |2
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2 8.0767187286290179e-04 1.0588928659053852e-03 -3.1123566690577253e-02
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48 -8.0767953495988081e-04 -1.0588933379665191e-03 3.1123564482200175e-02
run_vdwl: -1.117107802396835
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48 -1.0286699191962320e-03 -1.5188666002277826e-03 3.1020493014426428e-02
run_vdwl: -1.116583686929748
run_coul: 0
run_stress: ! |-
-6.9372331738514981e-01 -6.9064389597684106e-01 1.1514755915204005e+00 0.0000000000000000e+00 0.0000000000000000e+00 -1.4292266024218578e-02
-6.9202313126699333e-01 -6.8748607721639632e-01 1.1597991092003139e+00 -8.7520711561815342e-04 -7.4903484534890319e-03 -4.8017742857855358e-03
run_forces: ! |2
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2 8.0765258918550525e-04 1.0588876993623385e-03 -3.1122680612106914e-02
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33 7.8802353059772515e-04 6.3186818726301624e-04 1.1208113889006823e-02
34 -4.4157767037679690e-04 -5.9159130843379026e-05 3.0896068470685031e-02
35 1.4552473121265397e-06 5.5777693731219765e-04 1.0463857570582444e-02
36 7.5305807476735965e-04 6.4063119252587969e-04 2.9445714727166269e-02
37 -5.1527886711158206e-04 4.5022029011034236e-04 1.0102553591648427e-02
38 -2.3334071714133271e-04 5.5981947321851779e-04 2.9312019903716846e-02
39 -8.4029973392166224e-04 -8.2857530655882402e-04 9.9596391825485173e-03
40 3.1175727776466388e-04 1.5729483520098114e-04 2.9567298942710162e-02
41 -2.2701903109886260e-03 -1.0402124774515768e-04 1.2320885381156934e-02
42 -1.6831498396996131e-04 -3.1136792853859915e-04 3.0274601848989606e-02
43 5.5664724581996916e-05 1.9307476178885243e-04 1.1909723052594356e-02
44 -9.5046209166255765e-04 -6.3004473120715018e-05 3.0132966879057418e-02
45 -1.4273207846817208e-03 -8.2385448535969076e-04 1.1604140080847982e-02
46 3.2400780661911109e-04 2.8806285981541469e-05 2.9005364916792991e-02
47 4.4459996506777412e-04 2.0256574589517135e-04 1.0421645129745381e-02
48 -1.0286493798823708e-03 -1.5188527673106898e-03 3.1019644299872643e-02
...

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