Merge branch 'develop' into collected-small-changes
This commit is contained in:
Axel Kohlmeyer
@ -265,6 +265,7 @@ set(STANDARD_PACKAGES
|
|||||||
MC
|
MC
|
||||||
MDI
|
MDI
|
||||||
MEAM
|
MEAM
|
||||||
|
MESONT
|
||||||
MGPT
|
MGPT
|
||||||
MISC
|
MISC
|
||||||
ML-HDNNP
|
ML-HDNNP
|
||||||
@ -308,9 +309,8 @@ set(STANDARD_PACKAGES
|
|||||||
YAFF)
|
YAFF)
|
||||||
|
|
||||||
set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT INTEL OPENMP)
|
set(SUFFIX_PACKAGES CORESHELL GPU KOKKOS OPT INTEL OPENMP)
|
||||||
set(EXTRA_PACKAGES MESONT)
|
|
||||||
|
|
||||||
foreach(PKG ${STANDARD_PACKAGES} ${EXTRA_PACKAGES} ${SUFFIX_PACKAGES})
|
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
|
||||||
option(PKG_${PKG} "Build ${PKG} Package" OFF)
|
option(PKG_${PKG} "Build ${PKG} Package" OFF)
|
||||||
endforeach()
|
endforeach()
|
||||||
|
|
||||||
@ -520,7 +520,7 @@ else()
|
|||||||
set(CUDA_REQUEST_PIC)
|
set(CUDA_REQUEST_PIC)
|
||||||
endif()
|
endif()
|
||||||
|
|
||||||
foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE MESONT NETCDF
|
foreach(PKG_WITH_INCL KSPACE PYTHON ML-IAP VORONOI COLVARS ML-HDNNP MDI MOLFILE NETCDF
|
||||||
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM LATTE MSCG COMPRESS ML-PACE LEPTON)
|
PLUMED QMMM ML-QUIP SCAFACOS MACHDYN VTK KIM LATTE MSCG COMPRESS ML-PACE LEPTON)
|
||||||
if(PKG_${PKG_WITH_INCL})
|
if(PKG_${PKG_WITH_INCL})
|
||||||
include(Packages/${PKG_WITH_INCL})
|
include(Packages/${PKG_WITH_INCL})
|
||||||
@ -568,7 +568,7 @@ RegisterStyles(${LAMMPS_SOURCE_DIR})
|
|||||||
########################################################
|
########################################################
|
||||||
option(DOWNLOAD_POTENTIALS "Automatically download large potential files" ON)
|
option(DOWNLOAD_POTENTIALS "Automatically download large potential files" ON)
|
||||||
mark_as_advanced(DOWNLOAD_POTENTIALS)
|
mark_as_advanced(DOWNLOAD_POTENTIALS)
|
||||||
foreach(PKG ${STANDARD_PACKAGES} ${EXTRA_PACKAGES} ${SUFFIX_PACKAGES})
|
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
|
||||||
if(PKG_${PKG})
|
if(PKG_${PKG})
|
||||||
FetchPotentials(${LAMMPS_SOURCE_DIR}/${PKG} ${LAMMPS_POTENTIALS_DIR})
|
FetchPotentials(${LAMMPS_SOURCE_DIR}/${PKG} ${LAMMPS_POTENTIALS_DIR})
|
||||||
endif()
|
endif()
|
||||||
@ -708,7 +708,7 @@ target_include_directories(lammps PRIVATE ${LAMMPS_STYLE_HEADERS_DIR})
|
|||||||
######################################
|
######################################
|
||||||
set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n")
|
set(temp "#ifndef LMP_INSTALLED_PKGS_H\n#define LMP_INSTALLED_PKGS_H\n")
|
||||||
set(temp "${temp}const char * LAMMPS_NS::LAMMPS::installed_packages[] = {\n")
|
set(temp "${temp}const char * LAMMPS_NS::LAMMPS::installed_packages[] = {\n")
|
||||||
set(temp_PKG_LIST ${STANDARD_PACKAGES} ${EXTRA_PACKAGES} ${SUFFIX_PACKAGES})
|
set(temp_PKG_LIST ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
|
||||||
list(SORT temp_PKG_LIST)
|
list(SORT temp_PKG_LIST)
|
||||||
foreach(PKG ${temp_PKG_LIST})
|
foreach(PKG ${temp_PKG_LIST})
|
||||||
if(PKG_${PKG})
|
if(PKG_${PKG})
|
||||||
@ -929,7 +929,7 @@ message(STATUS "<<< Build configuration >>>
|
|||||||
# Print package summary
|
# Print package summary
|
||||||
###############################################################################
|
###############################################################################
|
||||||
set(ENABLED_PACKAGES)
|
set(ENABLED_PACKAGES)
|
||||||
foreach(PKG ${STANDARD_PACKAGES} ${EXTRA_PACKAGES} ${SUFFIX_PACKAGES})
|
foreach(PKG ${STANDARD_PACKAGES} ${SUFFIX_PACKAGES})
|
||||||
if(PKG_${PKG})
|
if(PKG_${PKG})
|
||||||
list(APPEND ENABLED_PACKAGES ${PKG})
|
list(APPEND ENABLED_PACKAGES ${PKG})
|
||||||
endif()
|
endif()
|
||||||
|
|||||||
@ -1,73 +0,0 @@
|
|||||||
|
|
||||||
|
|
||||||
set(MESONT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/MESONT)
|
|
||||||
include(StyleHeaderUtils)
|
|
||||||
include(CheckLanguage)
|
|
||||||
|
|
||||||
# always include C++-only sources
|
|
||||||
file(GLOB MESONT_SOURCES ${CONFIGURE_DEPENDS} ${MESONT_SOURCES_DIR}/[^.]*mesocnt*.cpp)
|
|
||||||
file(GLOB MESONT_HEADERS ${CONFIGURE_DEPENDS} ${MESONT_SOURCES_DIR}/[^.]*mesocnt*.h)
|
|
||||||
# remove derived class when base class is not available
|
|
||||||
if(NOT PKG_MOLECULE)
|
|
||||||
list(REMOVE_ITEM MESONT_SOURCES ${MESONT_SOURCES_DIR}/bond_mesocnt.cpp)
|
|
||||||
list(REMOVE_ITEM MESONT_HEADERS ${MESONT_SOURCES_DIR}/bond_mesocnt.h)
|
|
||||||
endif()
|
|
||||||
|
|
||||||
# include styles dependent on Fortran library only when Fortran is available.
|
|
||||||
check_language(Fortran)
|
|
||||||
if(CMAKE_Fortran_COMPILER)
|
|
||||||
enable_language(Fortran)
|
|
||||||
file(GLOB MESONT_LIB_SOURCES ${CONFIGURE_DEPENDS} ${LAMMPS_LIB_SOURCE_DIR}/mesont/[^.]*.f90)
|
|
||||||
add_library(mesont STATIC ${MESONT_LIB_SOURCES})
|
|
||||||
set_target_properties(mesont PROPERTIES OUTPUT_NAME lammps_mesont${LAMMPS_MACHINE})
|
|
||||||
target_link_libraries(lammps PRIVATE mesont)
|
|
||||||
|
|
||||||
list(APPEND MESONT_SOURCES ${MESONT_SOURCES_DIR}/pair_mesont_tpm.cpp)
|
|
||||||
list(APPEND MESONT_SOURCES ${MESONT_SOURCES_DIR}/atom_vec_mesont.cpp)
|
|
||||||
list(APPEND MESONT_SOURCES ${MESONT_SOURCES_DIR}/compute_mesont.cpp)
|
|
||||||
list(APPEND MESONT_HEADERS ${MESONT_SOURCES_DIR}/pair_mesont_tpm.h)
|
|
||||||
list(APPEND MESONT_HEADERS ${MESONT_SOURCES_DIR}/atom_vec_mesont.h)
|
|
||||||
list(APPEND MESONT_HEADERS ${MESONT_SOURCES_DIR}/compute_mesont.h)
|
|
||||||
endif()
|
|
||||||
|
|
||||||
# check for package files in src directory due to old make system
|
|
||||||
DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${MESONT_SOURCES} ${MESONT_HEADERS})
|
|
||||||
|
|
||||||
# manually register style headers
|
|
||||||
get_property(alist GLOBAL PROPERTY ANGLE)
|
|
||||||
get_property(blist GLOBAL PROPERTY BOND)
|
|
||||||
get_property(clist GLOBAL PROPERTY COMPUTE)
|
|
||||||
get_property(plist GLOBAL PROPERTY PAIR)
|
|
||||||
get_property(vlist GLOBAL PROPERTY ATOM_VEC)
|
|
||||||
foreach(fname ${MESONT_HEADERS})
|
|
||||||
file(STRINGS ${fname} is_style LIMIT_COUNT 1 REGEX ANGLE_CLASS)
|
|
||||||
if(is_style)
|
|
||||||
list(APPEND alist ${fname})
|
|
||||||
endif()
|
|
||||||
file(STRINGS ${fname} is_style LIMIT_COUNT 1 REGEX BOND_CLASS)
|
|
||||||
if(is_style)
|
|
||||||
list(APPEND blist ${fname})
|
|
||||||
endif()
|
|
||||||
file(STRINGS ${fname} is_style LIMIT_COUNT 1 REGEX COMPUTE_CLASS)
|
|
||||||
if(is_style)
|
|
||||||
list(APPEND clist ${fname})
|
|
||||||
endif()
|
|
||||||
file(STRINGS ${fname} is_style LIMIT_COUNT 1 REGEX PAIR_CLASS)
|
|
||||||
if(is_style)
|
|
||||||
list(APPEND plist ${fname})
|
|
||||||
endif()
|
|
||||||
file(STRINGS ${fname} is_style LIMIT_COUNT 1 REGEX ATOM_CLASS)
|
|
||||||
if(is_style)
|
|
||||||
list(APPEND vlist ${fname})
|
|
||||||
endif()
|
|
||||||
endforeach()
|
|
||||||
set_property(GLOBAL PROPERTY ANGLE "${alist}")
|
|
||||||
set_property(GLOBAL PROPERTY BOND "${blist}")
|
|
||||||
set_property(GLOBAL PROPERTY COMPUTE "${clist}")
|
|
||||||
set_property(GLOBAL PROPERTY PAIR "${plist}")
|
|
||||||
set_property(GLOBAL PROPERTY ATOM_VEC "${vlist}")
|
|
||||||
|
|
||||||
target_sources(lammps PRIVATE ${MESONT_SOURCES})
|
|
||||||
target_include_directories(lammps PRIVATE ${MESONT_SOURCES_DIR})
|
|
||||||
|
|
||||||
RegisterPackages(${MESONT_SOURCES_DIR})
|
|
||||||
@ -40,6 +40,7 @@ set(ALL_PACKAGES
|
|||||||
MANYBODY
|
MANYBODY
|
||||||
MC
|
MC
|
||||||
MEAM
|
MEAM
|
||||||
|
MESONT
|
||||||
MISC
|
MISC
|
||||||
ML-IAP
|
ML-IAP
|
||||||
ML-POD
|
ML-POD
|
||||||
|
|||||||
@ -16,7 +16,6 @@ set(PACKAGES_WITH_LIB
|
|||||||
LEPTON
|
LEPTON
|
||||||
MACHDYN
|
MACHDYN
|
||||||
MDI
|
MDI
|
||||||
MESONT
|
|
||||||
ML-HDNNP
|
ML-HDNNP
|
||||||
ML-PACE
|
ML-PACE
|
||||||
ML-QUIP
|
ML-QUIP
|
||||||
|
|||||||
@ -36,6 +36,7 @@ set(WIN_PACKAGES
|
|||||||
MANYBODY
|
MANYBODY
|
||||||
MC
|
MC
|
||||||
MEAM
|
MEAM
|
||||||
|
MESONT
|
||||||
MISC
|
MISC
|
||||||
ML-IAP
|
ML-IAP
|
||||||
ML-POD
|
ML-POD
|
||||||
|
|||||||
@ -47,7 +47,6 @@ This is the list of packages that may require additional steps.
|
|||||||
* :ref:`LEPTON <lepton>`
|
* :ref:`LEPTON <lepton>`
|
||||||
* :ref:`MACHDYN <machdyn>`
|
* :ref:`MACHDYN <machdyn>`
|
||||||
* :ref:`MDI <mdi>`
|
* :ref:`MDI <mdi>`
|
||||||
* :ref:`MESONT <mesont>`
|
|
||||||
* :ref:`ML-HDNNP <ml-hdnnp>`
|
* :ref:`ML-HDNNP <ml-hdnnp>`
|
||||||
* :ref:`ML-IAP <mliap>`
|
* :ref:`ML-IAP <mliap>`
|
||||||
* :ref:`ML-PACE <ml-pace>`
|
* :ref:`ML-PACE <ml-pace>`
|
||||||
@ -1852,48 +1851,6 @@ MDI package
|
|||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
.. _mesont:
|
|
||||||
|
|
||||||
MESONT package
|
|
||||||
-------------------------
|
|
||||||
|
|
||||||
This package includes a library written in Fortran 90 in the
|
|
||||||
``lib/mesont`` folder, so a working Fortran 90 compiler is required to
|
|
||||||
compile it. Also, the files with the force field data for running the
|
|
||||||
bundled examples are not included in the source distribution. Instead
|
|
||||||
they will be downloaded the first time this package is installed.
|
|
||||||
|
|
||||||
.. tabs::
|
|
||||||
|
|
||||||
.. tab:: CMake build
|
|
||||||
|
|
||||||
No additional settings are needed besides ``-D PKG_MESONT=yes``
|
|
||||||
|
|
||||||
.. tab:: Traditional make
|
|
||||||
|
|
||||||
Before building LAMMPS, you must build the *mesont* library in
|
|
||||||
``lib/mesont``\ . You can also do it in one step from the
|
|
||||||
``lammps/src`` dir, using a command like these, which simply
|
|
||||||
invokes the ``lib/mesont/Install.py`` script with the specified
|
|
||||||
args:
|
|
||||||
|
|
||||||
.. code-block:: bash
|
|
||||||
|
|
||||||
make lib-mesont # print help message
|
|
||||||
make lib-mesont args="-m gfortran" # build with GNU g++ compiler (settings as with "make serial")
|
|
||||||
make lib-mesont args="-m ifort" # build with Intel icc compiler
|
|
||||||
|
|
||||||
The build should produce two files: ``lib/mesont/libmesont.a`` and
|
|
||||||
``lib/mesont/Makefile.lammps``\ . The latter is copied from an
|
|
||||||
existing ``Makefile.lammps.\*`` and has settings needed to build
|
|
||||||
LAMMPS with the *mesont* library (though typically the settings
|
|
||||||
contain only the Fortran runtime library). If necessary, you can
|
|
||||||
edit/create a new ``lib/mesont/Makefile.machine`` file for your
|
|
||||||
system, which should define an ``EXTRAMAKE`` variable to specify a
|
|
||||||
corresponding ``Makefile.lammps.machine`` file.
|
|
||||||
|
|
||||||
----------
|
|
||||||
|
|
||||||
.. _molfile:
|
.. _molfile:
|
||||||
|
|
||||||
MOLFILE package
|
MOLFILE package
|
||||||
|
|||||||
@ -50,7 +50,6 @@ packages:
|
|||||||
* :ref:`LEPTON <lepton>`
|
* :ref:`LEPTON <lepton>`
|
||||||
* :ref:`MACHDYN <machdyn>`
|
* :ref:`MACHDYN <machdyn>`
|
||||||
* :ref:`MDI <mdi>`
|
* :ref:`MDI <mdi>`
|
||||||
* :ref:`MESONT <mesont>`
|
|
||||||
* :ref:`ML-HDNNP <ml-hdnnp>`
|
* :ref:`ML-HDNNP <ml-hdnnp>`
|
||||||
* :ref:`ML-IAP <mliap>`
|
* :ref:`ML-IAP <mliap>`
|
||||||
* :ref:`ML-PACE <ml-pace>`
|
* :ref:`ML-PACE <ml-pace>`
|
||||||
|
|||||||
@ -88,7 +88,6 @@ KOKKOS, o = OPENMP, t = OPT.
|
|||||||
* :doc:`ke/atom/eff <compute_ke_atom_eff>`
|
* :doc:`ke/atom/eff <compute_ke_atom_eff>`
|
||||||
* :doc:`ke/eff <compute_ke_eff>`
|
* :doc:`ke/eff <compute_ke_eff>`
|
||||||
* :doc:`ke/rigid <compute_ke_rigid>`
|
* :doc:`ke/rigid <compute_ke_rigid>`
|
||||||
* :doc:`mesont <compute_mesont>`
|
|
||||||
* :doc:`mliap <compute_mliap>`
|
* :doc:`mliap <compute_mliap>`
|
||||||
* :doc:`momentum <compute_momentum>`
|
* :doc:`momentum <compute_momentum>`
|
||||||
* :doc:`msd <compute_msd>`
|
* :doc:`msd <compute_msd>`
|
||||||
|
|||||||
@ -204,7 +204,6 @@ OPT.
|
|||||||
* :doc:`meam/sw/spline <pair_meam_sw_spline>`
|
* :doc:`meam/sw/spline <pair_meam_sw_spline>`
|
||||||
* :doc:`mesocnt <pair_mesocnt>`
|
* :doc:`mesocnt <pair_mesocnt>`
|
||||||
* :doc:`mesocnt/viscous <pair_mesocnt>`
|
* :doc:`mesocnt/viscous <pair_mesocnt>`
|
||||||
* :doc:`mesont/tpm <pair_mesont_tpm>`
|
|
||||||
* :doc:`mgpt <pair_mgpt>`
|
* :doc:`mgpt <pair_mgpt>`
|
||||||
* :doc:`mie/cut (g) <pair_mie>`
|
* :doc:`mie/cut (g) <pair_mie>`
|
||||||
* :doc:`mliap (k) <pair_mliap>`
|
* :doc:`mliap (k) <pair_mliap>`
|
||||||
|
|||||||
@ -59,6 +59,17 @@ Minimize style *fire/old* has been removed. Its functionality can be
|
|||||||
reproduced with *fire* with specific options. Please see the
|
reproduced with *fire* with specific options. Please see the
|
||||||
:doc:`min_modify command <min_modify>` documentation for details.
|
:doc:`min_modify command <min_modify>` documentation for details.
|
||||||
|
|
||||||
|
Pair style mesont/tpm, compute style mesont, atom style mesont
|
||||||
|
--------------------------------------------------------------
|
||||||
|
|
||||||
|
.. deprecated:: TBD
|
||||||
|
|
||||||
|
Pair style *mesont/tpm*, compute style *mesont*, and atom style
|
||||||
|
*mesont* have been removed from the :ref:`MESONT package <PKG-MESONT>`.
|
||||||
|
The same functionality is available through
|
||||||
|
:doc:`pair style mesocnt <pair_mesocnt>`,
|
||||||
|
:doc:`bond style mesocnt <bond_mesocnt>` and
|
||||||
|
:doc:`angle style mesocnt <angle_mesocnt>`.
|
||||||
|
|
||||||
REAX package
|
REAX package
|
||||||
------------
|
------------
|
||||||
|
|||||||
@ -1621,25 +1621,23 @@ MESONT package
|
|||||||
**Contents:**
|
**Contents:**
|
||||||
|
|
||||||
MESONT is a LAMMPS package for simulation of nanomechanics of nanotubes
|
MESONT is a LAMMPS package for simulation of nanomechanics of nanotubes
|
||||||
(NTs). The model is based on a coarse-grained representation of NTs as
|
(NTs). The model is based on a coarse-grained representation of NTs as
|
||||||
"flexible cylinders" consisting of a variable number of
|
"flexible cylinders" consisting of a variable number of
|
||||||
segments. Internal interactions within a NT and the van der Waals
|
segments. Internal interactions within a NT and the van der Waals
|
||||||
interaction between the tubes are described by a mesoscopic force field
|
interaction between the tubes are described by a mesoscopic force field
|
||||||
designed and parameterized based on the results of atomic-level
|
designed and parameterized based on the results of atomic-level
|
||||||
molecular dynamics simulations. The description of the force field is
|
molecular dynamics simulations. The description of the force field is
|
||||||
provided in the papers listed below.
|
provided in the papers listed in ``src/MESONT/README``.
|
||||||
|
|
||||||
This package contains two independent implementations of this model:
|
This package used to have two independent implementations of this model:
|
||||||
:doc:`pair_style mesont/tpm <pair_mesont_tpm>` is the original
|
the original implementation using a Fortran library written by the
|
||||||
implementation of the model based on a Fortran library in the
|
developers of the model and a second implementation written in C++ by
|
||||||
``lib/mesont`` folder. The second implementation is provided by the
|
Philipp Kloza (U Cambridge). Since the C++ implementation offers the
|
||||||
mesocnt styles (:doc:`bond_style mesocnt <bond_mesocnt>`,
|
same features as the original implementation with the addition of
|
||||||
:doc:`angle_style mesocnt <angle_mesocnt>` and :doc:`pair_style mesocnt
|
friction, is typically faster, and easier to compile/install, the
|
||||||
<pair_mesocnt>`). The mesocnt implementation has the same features as
|
Fortran library based implementation has since been obsoleted and
|
||||||
the original implementation with the addition of friction, but is
|
removed from the distribution. You have to download and compile
|
||||||
directly implemented in C++, interfaces more cleanly with general LAMMPS
|
an older version of LAMMPS if you want to use those.
|
||||||
functionality, and is typically faster. It also does not require its own
|
|
||||||
atom style and can be installed without any external libraries.
|
|
||||||
|
|
||||||
**Download of potential files:**
|
**Download of potential files:**
|
||||||
|
|
||||||
@ -1648,12 +1646,14 @@ not included in the regular downloaded packages of LAMMPS or the git
|
|||||||
repositories. Instead, they will be automatically downloaded from a web
|
repositories. Instead, they will be automatically downloaded from a web
|
||||||
server when the package is installed for the first time.
|
server when the package is installed for the first time.
|
||||||
|
|
||||||
**Authors of the *mesont* styles:**
|
**Authors of the obsoleted *mesont* styles:**
|
||||||
|
|
||||||
Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University
|
Maxim V. Shugaev (University of Virginia), Alexey N. Volkov (University
|
||||||
of Alabama), Leonid V. Zhigilei (University of Virginia)
|
of Alabama), Leonid V. Zhigilei (University of Virginia)
|
||||||
|
|
||||||
**Author of the *mesocnt* styles:**
|
.. deprecated:: TBD
|
||||||
|
|
||||||
|
**Author of the C++ styles:**
|
||||||
Philipp Kloza (U Cambridge)
|
Philipp Kloza (U Cambridge)
|
||||||
|
|
||||||
.. versionadded:: 15Jun2020
|
.. versionadded:: 15Jun2020
|
||||||
@ -1662,14 +1662,10 @@ Philipp Kloza (U Cambridge)
|
|||||||
|
|
||||||
* src/MESONT: filenames -> commands
|
* src/MESONT: filenames -> commands
|
||||||
* src/MESONT/README
|
* src/MESONT/README
|
||||||
* :doc:`atom_style mesont <atom_style>`
|
|
||||||
* :doc:`pair_style mesont/tpm <pair_mesont_tpm>`
|
|
||||||
* :doc:`compute mesont <compute_mesont>`
|
|
||||||
* :doc:`bond_style mesocnt <bond_mesocnt>`
|
* :doc:`bond_style mesocnt <bond_mesocnt>`
|
||||||
* :doc:`angle_style mesocnt <angle_mesocnt>`
|
* :doc:`angle_style mesocnt <angle_mesocnt>`
|
||||||
* :doc:`pair_style mesocnt <pair_mesocnt>`
|
* :doc:`pair_style mesocnt <pair_mesocnt>`
|
||||||
* examples/PACKAGES/mesont
|
* examples/PACKAGES/mesont
|
||||||
* tools/mesont
|
|
||||||
|
|
||||||
----------
|
----------
|
||||||
|
|
||||||
|
|||||||
@ -275,9 +275,9 @@ whether an extra library is needed to build and use the package:
|
|||||||
- no
|
- no
|
||||||
* - :ref:`MESONT <PKG-MESONT>`
|
* - :ref:`MESONT <PKG-MESONT>`
|
||||||
- mesoscopic tubular potential model
|
- mesoscopic tubular potential model
|
||||||
- pair styles :doc:`mesont/tpm <pair_mesont_tpm>`, :doc:`mesocnt <pair_mesocnt>`
|
- pair styles :doc:`mesocnt <pair_mesocnt>`
|
||||||
- PACKAGES/mesont
|
- PACKAGES/mesont
|
||||||
- int
|
- no
|
||||||
* - :ref:`MGPT <PKG-MGPT>`
|
* - :ref:`MGPT <PKG-MGPT>`
|
||||||
- fast MGPT multi-ion potentials
|
- fast MGPT multi-ion potentials
|
||||||
- :doc:`pair_style mgpt <pair_mgpt>`
|
- :doc:`pair_style mgpt <pair_mgpt>`
|
||||||
|
|||||||
@ -10,7 +10,7 @@ Syntax
|
|||||||
|
|
||||||
atom_style style args
|
atom_style style args
|
||||||
|
|
||||||
* style = *amoeba* or *angle* or *atomic* or *body* or *bond* or *charge* or *dielectric* or *dipole* or *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *mesont* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *wavepacket* or *hybrid*
|
* style = *amoeba* or *angle* or *atomic* or *body* or *bond* or *charge* or *dielectric* or *dipole* or *dpd* or *edpd* or *electron* or *ellipsoid* or *full* or *line* or *mdpd* or *molecular* or *oxdna* or *peri* or *smd* or *sph* or *sphere* or *bpm/sphere* or *spin* or *tdpd* or *tri* or *template* or *wavepacket* or *hybrid*
|
||||||
|
|
||||||
.. parsed-literal::
|
.. parsed-literal::
|
||||||
|
|
||||||
@ -109,8 +109,6 @@ quantities.
|
|||||||
+--------------+-----------------------------------------------------+--------------------------------------+
|
+--------------+-----------------------------------------------------+--------------------------------------+
|
||||||
| *mdpd* | density | mDPD particles |
|
| *mdpd* | density | mDPD particles |
|
||||||
+--------------+-----------------------------------------------------+--------------------------------------+
|
+--------------+-----------------------------------------------------+--------------------------------------+
|
||||||
| *mesont* | mass, radius, length, buckling, connections, tube id| mesoscopic nanotubes |
|
|
||||||
+--------------+-----------------------------------------------------+--------------------------------------+
|
|
||||||
| *molecular* | bonds, angles, dihedrals, impropers | uncharged molecules |
|
| *molecular* | bonds, angles, dihedrals, impropers | uncharged molecules |
|
||||||
+--------------+-----------------------------------------------------+--------------------------------------+
|
+--------------+-----------------------------------------------------+--------------------------------------+
|
||||||
| *oxdna* | nucleotide polarity | coarse-grained DNA and RNA models |
|
| *oxdna* | nucleotide polarity | coarse-grained DNA and RNA models |
|
||||||
@ -382,8 +380,6 @@ The *sph* style is part of the SPH package for smoothed particle
|
|||||||
hydrodynamics (SPH). See `this PDF guide
|
hydrodynamics (SPH). See `this PDF guide
|
||||||
<PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
|
<PDF/SPH_LAMMPS_userguide.pdf>`_ to using SPH in LAMMPS.
|
||||||
|
|
||||||
The *mesont* style is part of the MESONT package.
|
|
||||||
|
|
||||||
The *spin* style is part of the SPIN package.
|
The *spin* style is part of the SPIN package.
|
||||||
|
|
||||||
The *wavepacket* style is part of the AWPMD package for the
|
The *wavepacket* style is part of the AWPMD package for the
|
||||||
|
|||||||
@ -254,7 +254,6 @@ The individual style names on the :doc:`Commands compute <Commands_compute>` pag
|
|||||||
* :doc:`pair/local <compute_pair_local>` - distance/energy/force of each pairwise interaction
|
* :doc:`pair/local <compute_pair_local>` - distance/energy/force of each pairwise interaction
|
||||||
* :doc:`pe <compute_pe>` - potential energy
|
* :doc:`pe <compute_pe>` - potential energy
|
||||||
* :doc:`pe/atom <compute_pe_atom>` - potential energy for each atom
|
* :doc:`pe/atom <compute_pe_atom>` - potential energy for each atom
|
||||||
* :doc:`mesont <compute_mesont>` - Nanotube bending,stretching, and intertube energies
|
|
||||||
* :doc:`pe/mol/tally <compute_tally>` - potential energy between two groups of atoms separated into intermolecular and intramolecular components via the tally callback mechanism
|
* :doc:`pe/mol/tally <compute_tally>` - potential energy between two groups of atoms separated into intermolecular and intramolecular components via the tally callback mechanism
|
||||||
* :doc:`pe/tally <compute_tally>` - potential energy between two groups of atoms via the tally callback mechanism
|
* :doc:`pe/tally <compute_tally>` - potential energy between two groups of atoms via the tally callback mechanism
|
||||||
* :doc:`plasticity/atom <compute_plasticity_atom>` - Peridynamic plasticity for each atom
|
* :doc:`plasticity/atom <compute_plasticity_atom>` - Peridynamic plasticity for each atom
|
||||||
|
|||||||
@ -1,59 +0,0 @@
|
|||||||
.. index:: compute mesont
|
|
||||||
|
|
||||||
compute mesont command
|
|
||||||
======================
|
|
||||||
|
|
||||||
Syntax
|
|
||||||
""""""
|
|
||||||
|
|
||||||
.. code-block:: LAMMPS
|
|
||||||
|
|
||||||
compute ID group-ID mesont style
|
|
||||||
|
|
||||||
* ID, group-ID are documented in :doc:`compute <compute>` command
|
|
||||||
* mesont = style name of the compute command
|
|
||||||
* style = *estretch* or *ebend* or *etube*
|
|
||||||
|
|
||||||
Examples
|
|
||||||
""""""""
|
|
||||||
|
|
||||||
|
|
||||||
.. code-block:: LAMMPS
|
|
||||||
|
|
||||||
compute 1 all mesont estretch
|
|
||||||
|
|
||||||
Description
|
|
||||||
"""""""""""
|
|
||||||
|
|
||||||
These computes define computations for the stretching (*estretch*), bending
|
|
||||||
(*ebend*), and intertube (*etube*) per-node (atom) and total energies. The
|
|
||||||
evaluated value is selected by the style parameter passed to the compute
|
|
||||||
(*estretch*, *ebend*,or *etube*).
|
|
||||||
|
|
||||||
Output info
|
|
||||||
"""""""""""
|
|
||||||
|
|
||||||
These computes calculate per-node (per-atom) vectors, which can be accessed by
|
|
||||||
any command that uses per-atom values from a compute as input, and global
|
|
||||||
scalars. See the :doc:`Howto output <Howto_output>` page for an overview of
|
|
||||||
LAMMPS output options.
|
|
||||||
|
|
||||||
The computed values are provided in energy :doc:`units <units>`.
|
|
||||||
|
|
||||||
Restrictions
|
|
||||||
""""""""""""
|
|
||||||
These computes are part of the MESONT package. They are only enabled if
|
|
||||||
LAMMPS is built with that package. See the :doc:`Build package <Build_package>`
|
|
||||||
doc page for more info. In addition, :doc:`mesont pair_style <pair_style>`
|
|
||||||
must be used.
|
|
||||||
|
|
||||||
Related commands
|
|
||||||
""""""""""""""""
|
|
||||||
|
|
||||||
:doc:`dump custom <dump>`
|
|
||||||
|
|
||||||
Default
|
|
||||||
"""""""
|
|
||||||
|
|
||||||
none
|
|
||||||
|
|
||||||
@ -90,11 +90,6 @@ Syntax
|
|||||||
de = change in thermal energy
|
de = change in thermal energy
|
||||||
cv = heat capacity
|
cv = heat capacity
|
||||||
|
|
||||||
.. parsed-literal::
|
|
||||||
|
|
||||||
MESONT package per-atom properties:
|
|
||||||
buckling = buckling flag used in mesoscopic simulation of nanotubes
|
|
||||||
|
|
||||||
Examples
|
Examples
|
||||||
""""""""
|
""""""""
|
||||||
|
|
||||||
|
|||||||
@ -216,9 +216,8 @@ LAMMPS was built with that package. See the :doc:`Build package
|
|||||||
These pair styles require the :doc:`newton <newton>` setting to be
|
These pair styles require the :doc:`newton <newton>` setting to be
|
||||||
"on" for pair interactions.
|
"on" for pair interactions.
|
||||||
|
|
||||||
These pair styles require all 3 :doc:`special_bonds lj
|
These pair styles require all 3 :doc:`special_bonds lj <special_bonds>`
|
||||||
<special_bonds>` settings to be non-zero for proper neighbor list
|
settings to be non-zero for proper neighbor list construction.
|
||||||
construction.
|
|
||||||
|
|
||||||
Pair style *mesocnt/viscous* requires you to use the :doc:`comm_modify
|
Pair style *mesocnt/viscous* requires you to use the :doc:`comm_modify
|
||||||
vel yes <comm_modify>` command so that velocities are stored by ghost
|
vel yes <comm_modify>` command so that velocities are stored by ghost
|
||||||
@ -227,7 +226,9 @@ atoms.
|
|||||||
Related commands
|
Related commands
|
||||||
""""""""""""""""
|
""""""""""""""""
|
||||||
|
|
||||||
:doc:`pair_coeff <pair_coeff>`
|
:doc:`pair_coeff <pair_coeff>`,
|
||||||
|
:doc:`bond_style mesocnt <bond_mesocnt>`,
|
||||||
|
:doc:`angle_style mesocnt <angle_mesocnt>`
|
||||||
|
|
||||||
Default
|
Default
|
||||||
"""""""
|
"""""""
|
||||||
|
|||||||
@ -1,219 +0,0 @@
|
|||||||
.. index:: pair_style mesont/tpm
|
|
||||||
|
|
||||||
pair_style mesont/tpm command
|
|
||||||
=============================
|
|
||||||
|
|
||||||
Syntax
|
|
||||||
""""""
|
|
||||||
|
|
||||||
|
|
||||||
.. parsed-literal::
|
|
||||||
|
|
||||||
pair_style mesont/tpm cut table_path BendingMode TPMType
|
|
||||||
|
|
||||||
* cut = the cutoff distance
|
|
||||||
* table_path = the path to the potential table
|
|
||||||
* BendingMode = the parameter defining the type of the bending potential for nanotubes: 0 - harmonic bending :ref:`(Srivastava) <Srivastava>`, 1 - anharmonic potential of bending and bending-buckling :ref:`(Zhigilei1) <Zhigilei1>`
|
|
||||||
* TPMType = the parameter determining the type of the inter-tube interaction term: 0 - segment-segment approach, 1 - segment-chain approach :ref:`(Zhigilei2 <Zhigilei2>`, :ref:`Zhigilei3) <Zhigilei3>`
|
|
||||||
|
|
||||||
The segment-segment approach is approximately 5 times slower than segment-chain approximation.
|
|
||||||
The parameter BendingMode also affects the calculation of the inter-tube interaction term when TPMType = 1. In this case, when BendingMode = 1, each continuous chain of segments is additionally replaced by a number of sub-chains divided by bending buckling kinks.
|
|
||||||
|
|
||||||
Examples
|
|
||||||
""""""""
|
|
||||||
|
|
||||||
|
|
||||||
.. parsed-literal::
|
|
||||||
|
|
||||||
pair_style mesont/tpm 30.0 MESONT-TABTP_10_10.xrs 0 0
|
|
||||||
|
|
||||||
Description
|
|
||||||
"""""""""""
|
|
||||||
|
|
||||||
The tubular potential model (TPM) force field is designed for mesoscopic
|
|
||||||
simulations of interacting flexible nanotubes. The force field is based on the
|
|
||||||
mesoscopic computational model suggested in Ref. :ref:`(Srivastava) <Srivastava>`.
|
|
||||||
In this model, each nanotube is represented by a chain of mesoscopic elements
|
|
||||||
in the form of stretchable cylindrical segments, where each segment consists
|
|
||||||
of multiple atoms. Each nanotube is divided into segments by a sequence of
|
|
||||||
nodes placed on the nanotube centerline. This sequence of nodes determines the
|
|
||||||
spatial position of the cylindrical segments and defines the configuration of
|
|
||||||
the entire tube.
|
|
||||||
|
|
||||||
The potential force field that controls the dynamic behavior of a system of
|
|
||||||
interacting nanotubes is given by the following equation defining the potential
|
|
||||||
energy of the system:
|
|
||||||
|
|
||||||
.. math::
|
|
||||||
|
|
||||||
U = U_{str} + U_{bnd} + U_{vdW}
|
|
||||||
|
|
||||||
where :math:`U_{str}` is the harmonic potential describing the stretching of nanotube
|
|
||||||
:ref:`(Srivastava) <Srivastava>`, :math:`U_{bnd}` is the potential for nanotube bending
|
|
||||||
:ref:`(Srivastava) <Srivastava>` and bending-buckling :ref:`(Zhigilei1) <Zhigilei1>`, and
|
|
||||||
:math:`U_{vdW}` is the potential describing van-der Waals interaction between nanotubes
|
|
||||||
:ref:`(Zhigilei2 <Zhigilei2>`, :ref:`Zhigilei3) <Zhigilei3>`. The stretching energy, :math:`U_{str}` ,
|
|
||||||
is given by the sum of stretching energies of individual nanotube segments.
|
|
||||||
The bending energy, :math:`U_{bnd}` , is given by the sum of bending energies in all
|
|
||||||
internal nanotube nodes. The tube-tube interaction energy, :math:`U_{vdW}` , is calculated
|
|
||||||
based on the tubular potential method suggested in Ref. :ref:`(Zhigilei2) <Zhigilei2>`.
|
|
||||||
The tubular potential method is briefly described below.
|
|
||||||
|
|
||||||
The interaction between two straight nanotubes of arbitrary length and
|
|
||||||
orientation is described by the approximate tubular potential developed in
|
|
||||||
:ref:`(Zhigilei3) <Zhigilei3>`. This potential approximates the results of direct
|
|
||||||
integration of carbon-carbon interatomic potential over the surfaces of the
|
|
||||||
interacting nanotubes, with the force sources homogeneously distributed over
|
|
||||||
the nanotube surfaces. The input data for calculation of tubular potentials
|
|
||||||
are partially tabulated. For single-walled CNTs of arbitrary chirality, the
|
|
||||||
tabulated potential data can be generated in the form of ASCII files
|
|
||||||
TPMSSTP.xrs and TPMA.xrs by the stand-alone code TMDPotGen included in the
|
|
||||||
tool directory of LAMMPS release. The potential provided with LAMMPS release,
|
|
||||||
MESONT-TABTP_10_10.xrs, is tabulated for (10,10) nanotubes.
|
|
||||||
|
|
||||||
Calculations of the interaction between curved or bent nanotubes are performed
|
|
||||||
on either segment-segment or segment-chain basis. In the first case, activated
|
|
||||||
when parameter TPMType is equal to 0, the tubular potential is calculated for
|
|
||||||
each pair of interacting mesoscopic segments. In this case, however, small
|
|
||||||
potential barriers for inter-tube sliding are introduced. While relatively
|
|
||||||
small, these barriers are still larger than the ones that originate from the
|
|
||||||
atomic-scale corrugation in atomistic modeling of inter-tube interaction. The
|
|
||||||
latter are too weak to prevent room-temperature rearrangements of defect-free
|
|
||||||
CNT, while the artificial mesoscopic barriers due to the segment-segment
|
|
||||||
interaction can impede sliding of nanotubes with respect to each other and
|
|
||||||
affect the kinetics of structural rearrangements in a system of nanotubes at
|
|
||||||
moderate mesoscopic temperatures. In the second case, activated when parameter
|
|
||||||
TPMType is equal to 1, the inter-tube interaction term is calculated based on
|
|
||||||
the segment-chain approach. In this case, for each NT segment, the list of its
|
|
||||||
neighboring segments is divided into short continuous chains of segments
|
|
||||||
belonging to individual nanotubes. For each pair of a segment and a chain, the
|
|
||||||
curved chain is approximated by a straight equivalent nanotube based on the
|
|
||||||
weighted approach suggested in Ref. :ref:`(Zhigilei2) <Zhigilei2>`. Finally, the
|
|
||||||
interaction between the segment and straight equivalent chain is calculated
|
|
||||||
based on the tubular potential. In this case, and in the absence of bending
|
|
||||||
buckling (i.e., when parameter BendingMode is equal to 0), the tubular
|
|
||||||
potential method ensures the absence of corrugation of the effective inter-tube
|
|
||||||
interaction potential for curved nanotubes and eliminates any barriers for the
|
|
||||||
inter-tube sliding. As a result, the tubular potential method can describe the
|
|
||||||
spontaneous self-assembly of nanotubes into continuous networks of bundles
|
|
||||||
:ref:`(Zhigilei1 <Zhigilei1>`, :ref:`Zhigilei3) <Zhigilei3>`.
|
|
||||||
|
|
||||||
|
|
||||||
----------
|
|
||||||
|
|
||||||
|
|
||||||
The TMD force field has been used for generation of nanotube films, fibers,
|
|
||||||
and vertically aligned forests of nanotubes. Mesoscopic dynamic simulations
|
|
||||||
were used to prepare realistic structures of continuous networks of nanotube
|
|
||||||
bundles and to study their structural and mechanical properties
|
|
||||||
:ref:`(Zhigilei1 <Zhigilei1>`, :ref:`Zhigilei3 <Zhigilei3>`, :ref:`Zhigilei4 <Zhigilei4>`,
|
|
||||||
:ref:`Zhigilei5 <Zhigilei5>`, :ref:`Zhigilei6) <Zhigilei6>`. With
|
|
||||||
additional models for heat transfer, this force filed was also used to
|
|
||||||
study the thermal transport properties of carbon nanotube films
|
|
||||||
:ref:`(Zhigilei7 <Zhigilei7>`, :ref:`Zhigilei8 <Zhigilei8>`, :ref:`Zhigilei8) <Zhigilei8>`.
|
|
||||||
The methods for modeling of
|
|
||||||
the mechanical energy dissipation into heat (energy exchange between the
|
|
||||||
dynamic degrees of freedom of the mesoscopic model and the energy of atomic
|
|
||||||
vibrations that are not explicitly represented in the model)
|
|
||||||
:ref:`(Zhigilei10) <Zhigilei10>` and mesoscopic description of covalent cross-links
|
|
||||||
between nanotubes :ref:`(Banna) <Banna>` have also been developed but are not
|
|
||||||
included in this first release of the LAMMPS implementation of the force field.
|
|
||||||
Further details can be found in references provided below.
|
|
||||||
|
|
||||||
The MESONT package also provides TMDGen code designed to generate initial samples
|
|
||||||
composed of straight and dispersed nanotubes of given chirality and length at a
|
|
||||||
given material density, which is available in tools directory. In the generated
|
|
||||||
samples, nanotubes are distributed with random positions and orientations. Both
|
|
||||||
periodic and free boundary conditions are available along each axis of the
|
|
||||||
system of coordinates. All parameters in the sample files generated with TMDGen
|
|
||||||
are given in metal :doc:`units <units>`.
|
|
||||||
|
|
||||||
Restrictions
|
|
||||||
""""""""""""
|
|
||||||
|
|
||||||
|
|
||||||
This pair style is a part of the MSEONT package, and it is only enabled if
|
|
||||||
LAMMPS is built with that package. See the :doc:`Build package <Build_package>`
|
|
||||||
doc page for more information.
|
|
||||||
|
|
||||||
This pair potential requires use of :doc:`mesont atomic style <atom_style>`.
|
|
||||||
|
|
||||||
This pair potential requires the :doc:`newton <newton>` setting to be "on" for
|
|
||||||
pair interactions.
|
|
||||||
|
|
||||||
The cutoff distance should be set to be at least :math:`max\left[2L,\sqrt{L^2/2+(2R+T_{cut})^2}\right]` ,
|
|
||||||
where L is the maximum segment length, R is the maximum tube radius, and
|
|
||||||
:math:`T_{cut}` = 10.2 A is the maximum distance between the surfaces of interacting
|
|
||||||
segments. Because of the use of extended chain concept at CNT ends, the recommended
|
|
||||||
cutoff is 3L.
|
|
||||||
|
|
||||||
.. note::
|
|
||||||
|
|
||||||
Because of their size, *mesont* style potential files
|
|
||||||
are not bundled with LAMMPS. When compiling LAMMPS from
|
|
||||||
source code, the file ``TABTP_10_10.mesont`` should be downloaded
|
|
||||||
transparently from `https://download.lammps.org/potentials/TABTP_10_10.mesont <https://download.lammps.org/potentials/TABTP_10_10.mesont>`_
|
|
||||||
|
|
||||||
The ``TABTP_10_10.mesont`` potential file is parameterized for metal :doc:`units <units>`.
|
|
||||||
You can use the carbon nanotube mesoscopic force field with any LAMMPS units,
|
|
||||||
but you would need to create your own potential files with coefficients listed in
|
|
||||||
appropriate units, if your simulation does not use "metal" units.
|
|
||||||
|
|
||||||
The chirality parameters set during system generation must match the values
|
|
||||||
specified during generation of the potential tables.
|
|
||||||
|
|
||||||
Related commands
|
|
||||||
""""""""""""""""
|
|
||||||
|
|
||||||
:doc:`pair_coeff <pair_coeff>`
|
|
||||||
|
|
||||||
----------
|
|
||||||
|
|
||||||
.. _Srivastava:
|
|
||||||
|
|
||||||
**(Srivastava)** Zhigilei, Wei, Srivastava, Phys. Rev. B 71, 165417 (2005).
|
|
||||||
|
|
||||||
.. _Zhigilei1:
|
|
||||||
|
|
||||||
**(Zhigilei1)** Volkov and Zhigilei, ACS Nano 4, 6187 (2010).
|
|
||||||
|
|
||||||
.. _Zhigilei2:
|
|
||||||
|
|
||||||
**(Zhigilei2)** Volkov, Simov, Zhigilei, ASME paper IMECE2008, 68021 (2008).
|
|
||||||
|
|
||||||
.. _Zhigilei3:
|
|
||||||
|
|
||||||
**(Zhigilei3)** Volkov, Zhigilei, J. Phys. Chem. C 114, 5513 (2010).
|
|
||||||
|
|
||||||
.. _Zhigilei4:
|
|
||||||
|
|
||||||
**(Zhigilei4)** Wittmaack, Banna, Volkov, Zhigilei, Carbon 130, 69 (2018).
|
|
||||||
|
|
||||||
.. _Zhigilei5:
|
|
||||||
|
|
||||||
**(Zhigilei5)** Wittmaack, Volkov, Zhigilei, Compos. Sci. Technol. 166, 66 (2018).
|
|
||||||
|
|
||||||
.. _Zhigilei6:
|
|
||||||
|
|
||||||
**(Zhigilei6)** Wittmaack, Volkov, Zhigilei, Carbon 143, 587 (2019).
|
|
||||||
|
|
||||||
.. _Zhigilei7:
|
|
||||||
|
|
||||||
**(Zhigilei7)** Volkov, Zhigilei, Phys. Rev. Lett. 104, 215902 (2010).
|
|
||||||
|
|
||||||
.. _Zhigilei8:
|
|
||||||
|
|
||||||
**(Zhigilei8)** Volkov, Shiga, Nicholson, Shiomi, Zhigilei, J. Appl. Phys. 111, 053501 (2012).
|
|
||||||
|
|
||||||
.. _Zhigilei9:
|
|
||||||
|
|
||||||
**(Zhigilei9)** Volkov, Zhigilei, Appl. Phys. Lett. 101, 043113 (2012).
|
|
||||||
|
|
||||||
.. _Zhigilei10:
|
|
||||||
|
|
||||||
**(Zhigilei10)** Jacobs, Nicholson, Zemer, Volkov, Zhigilei, Phys. Rev. B 86, 165414 (2012).
|
|
||||||
|
|
||||||
.. _Banna:
|
|
||||||
|
|
||||||
**(Banna)** Volkov, Banna, Comp. Mater. Sci. 176, 109410 (2020).
|
|
||||||
|
|
||||||
@ -283,7 +283,6 @@ accelerated styles exist.
|
|||||||
* :doc:`mesocnt <pair_mesocnt>` - mesoscopic vdW potential for (carbon) nanotubes
|
* :doc:`mesocnt <pair_mesocnt>` - mesoscopic vdW potential for (carbon) nanotubes
|
||||||
* :doc:`mesocnt/viscous <pair_mesocnt>` - mesoscopic vdW potential for (carbon) nanotubes with friction
|
* :doc:`mesocnt/viscous <pair_mesocnt>` - mesoscopic vdW potential for (carbon) nanotubes with friction
|
||||||
* :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
|
* :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
|
||||||
* :doc:`mesont/tpm <pair_mesont_tpm>` - nanotubes mesoscopic force field
|
|
||||||
* :doc:`mie/cut <pair_mie>` - Mie potential
|
* :doc:`mie/cut <pair_mie>` - Mie potential
|
||||||
* :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
|
* :doc:`mm3/switch3/coulgauss/long <pair_lj_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
|
||||||
* :doc:`momb <pair_momb>` - Many-Body Metal-Organic (MOMB) force field
|
* :doc:`momb <pair_momb>` - Many-Body Metal-Organic (MOMB) force field
|
||||||
|
|||||||
@ -710,8 +710,6 @@ of analysis.
|
|||||||
- atom-ID molecule-ID atom-type lineflag density x y z
|
- atom-ID molecule-ID atom-type lineflag density x y z
|
||||||
* - mdpd
|
* - mdpd
|
||||||
- atom-ID atom-type rho x y z
|
- atom-ID atom-type rho x y z
|
||||||
* - mesont
|
|
||||||
- atom-ID molecule-ID atom-type bond_nt mass mradius mlength buckling x y z
|
|
||||||
* - molecular
|
* - molecular
|
||||||
- atom-ID molecule-ID atom-type x y z
|
- atom-ID molecule-ID atom-type x y z
|
||||||
* - peri
|
* - peri
|
||||||
@ -742,8 +740,6 @@ The per-atom values have these meanings and units, listed alphabetically:
|
|||||||
* atom-ID = integer ID of atom
|
* atom-ID = integer ID of atom
|
||||||
* atom-type = type of atom (1-Ntype, or type label)
|
* atom-type = type of atom (1-Ntype, or type label)
|
||||||
* bodyflag = 1 for body particles, 0 for point particles
|
* bodyflag = 1 for body particles, 0 for point particles
|
||||||
* bond_nt = bond NT factor for MESONT particles (?? units)
|
|
||||||
* buckling = buckling factor for MESONT particles (?? units)
|
|
||||||
* ccN = chemical concentration for tDPD particles for each species (mole/volume units)
|
* ccN = chemical concentration for tDPD particles for each species (mole/volume units)
|
||||||
* cradius = contact radius for SMD particles (distance units)
|
* cradius = contact radius for SMD particles (distance units)
|
||||||
* cs_re,cs_im = real/imaginary parts of wave packet coefficients
|
* cs_re,cs_im = real/imaginary parts of wave packet coefficients
|
||||||
@ -760,9 +756,7 @@ The per-atom values have these meanings and units, listed alphabetically:
|
|||||||
* kradius = kernel radius for SMD particles (distance units)
|
* kradius = kernel radius for SMD particles (distance units)
|
||||||
* lineflag = 1 for line segment particles, 0 for point or spherical particles
|
* lineflag = 1 for line segment particles, 0 for point or spherical particles
|
||||||
* mass = mass of particle (mass units)
|
* mass = mass of particle (mass units)
|
||||||
* mlength = ?? length for MESONT particles (distance units)
|
|
||||||
* molecule-ID = integer ID of molecule the atom belongs to
|
* molecule-ID = integer ID of molecule the atom belongs to
|
||||||
* mradius = ?? radius for MESONT particles (distance units)
|
|
||||||
* mux,muy,muz = components of dipole moment of atom (dipole units)
|
* mux,muy,muz = components of dipole moment of atom (dipole units)
|
||||||
* q = charge on atom (charge units)
|
* q = charge on atom (charge units)
|
||||||
* rho = density (need units) for SPH particles
|
* rho = density (need units) for SPH particles
|
||||||
|
|||||||
@ -4,16 +4,7 @@
|
|||||||
The files in this folder provide examples of using the CNT
|
The files in this folder provide examples of using the CNT
|
||||||
mesoscopic force field (MESONT).
|
mesoscopic force field (MESONT).
|
||||||
|
|
||||||
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
|
|
||||||
|
|
||||||
"bundle" is an example with a single bundle composed of 7 nanotubes
|
|
||||||
using the mesont/tpm pair style
|
|
||||||
|
|
||||||
"film" is an example with a film composed of 396 200-nm-long
|
|
||||||
nanotubes (79596 nodes) using the mesont/tpm pair style
|
|
||||||
|
|
||||||
|
|
||||||
Contributing author: Philipp Kloza (U Cambridge), pak37@cam.ac.uk
|
Contributing author: Philipp Kloza (U Cambridge), pak37@cam.ac.uk
|
||||||
|
|
||||||
"cnt" is an example showing CNT aerogel formation
|
"film_mesocnt" is an example showing CNT aerogel formation
|
||||||
using the mesocnt pair style
|
using the mesocnt pair style
|
||||||
|
|||||||
@ -1 +0,0 @@
|
|||||||
../../../potentials/TABTP_10_10.mesont
|
|
||||||
@ -1,93 +0,0 @@
|
|||||||
|
|
||||||
|
|
||||||
77 atoms
|
|
||||||
|
|
||||||
1 atom types
|
|
||||||
|
|
||||||
-143.89 143.89 xlo xhi
|
|
||||||
-143.89 143.89 ylo yhi
|
|
||||||
0 220 zlo zhi
|
|
||||||
|
|
||||||
Masses
|
|
||||||
|
|
||||||
1 1.0
|
|
||||||
|
|
||||||
Atoms
|
|
||||||
|
|
||||||
1 1 1 11 2 5860.43 6.785 20 0 0 0 0 0 0 0
|
|
||||||
2 1 1 1 3 5860.43 6.785 20 0 0 0 20 0 0 0
|
|
||||||
3 1 1 2 4 5860.43 6.785 20 0 0 0 40 0 0 0
|
|
||||||
4 1 1 3 5 5860.43 6.785 20 0 0 0 60 0 0 0
|
|
||||||
5 1 1 4 6 5860.43 6.785 20 0 0 0 80 0 0 0
|
|
||||||
6 1 1 5 7 5860.43 6.785 20 0 0 0 100 0 0 0
|
|
||||||
7 1 1 6 8 5860.43 6.785 20 0 0 0 120 0 0 0
|
|
||||||
8 1 1 7 9 5860.43 6.785 20 0 0 0 140 0 0 0
|
|
||||||
9 1 1 8 10 5860.43 6.785 20 0 0 0 160 0 0 0
|
|
||||||
10 1 1 9 11 5860.43 6.785 20 0 0 0 180 0 0 0
|
|
||||||
11 1 1 10 1 5860.43 6.785 20 0 0 0 200 0 0 0
|
|
||||||
12 2 1 22 13 5860.43 6.785 20 0 16.6992 0 0 0 0 0
|
|
||||||
13 2 1 12 14 5860.43 6.785 20 0 16.6992 0 20 0 0 0
|
|
||||||
14 2 1 13 15 5860.43 6.785 20 0 16.6992 0 40 0 0 0
|
|
||||||
15 2 1 14 16 5860.43 6.785 20 0 16.6992 0 60 0 0 0
|
|
||||||
16 2 1 15 17 5860.43 6.785 20 0 16.6992 0 80 0 0 0
|
|
||||||
17 2 1 16 18 5860.43 6.785 20 0 16.6992 0 100 0 0 0
|
|
||||||
18 2 1 17 19 5860.43 6.785 20 0 16.6992 0 120 0 0 0
|
|
||||||
19 2 1 18 20 5860.43 6.785 20 0 16.6992 0 140 0 0 0
|
|
||||||
20 2 1 19 21 5860.43 6.785 20 0 16.6992 0 160 0 0 0
|
|
||||||
21 2 1 20 22 5860.43 6.785 20 0 16.6992 0 180 0 0 0
|
|
||||||
22 2 1 21 12 5860.43 6.785 20 0 16.6992 0 200 0 0 0
|
|
||||||
23 3 1 33 24 5860.43 6.785 20 0 8.3496 14.4619 0 0 0 0
|
|
||||||
24 3 1 23 25 5860.43 6.785 20 0 8.3496 14.4619 20 0 0 0
|
|
||||||
25 3 1 24 26 5860.43 6.785 20 0 8.3496 14.4619 40 0 0 0
|
|
||||||
26 3 1 25 27 5860.43 6.785 20 0 8.3496 14.4619 60 0 0 0
|
|
||||||
27 3 1 26 28 5860.43 6.785 20 0 8.3496 14.4619 80 0 0 0
|
|
||||||
28 3 1 27 29 5860.43 6.785 20 0 8.3496 14.4619 100 0 0 0
|
|
||||||
29 3 1 28 30 5860.43 6.785 20 0 8.3496 14.4619 120 0 0 0
|
|
||||||
30 3 1 29 31 5860.43 6.785 20 0 8.3496 14.4619 140 0 0 0
|
|
||||||
31 3 1 30 32 5860.43 6.785 20 0 8.3496 14.4619 160 0 0 0
|
|
||||||
32 3 1 31 33 5860.43 6.785 20 0 8.3496 14.4619 180 0 0 0
|
|
||||||
33 3 1 32 23 5860.43 6.785 20 0 8.3496 14.4619 200 0 0 0
|
|
||||||
34 4 1 44 35 5860.43 6.785 20 0 -8.3496 14.4619 0 0 0 0
|
|
||||||
35 4 1 34 36 5860.43 6.785 20 0 -8.3496 14.4619 20 0 0 0
|
|
||||||
36 4 1 35 37 5860.43 6.785 20 0 -8.3496 14.4619 40 0 0 0
|
|
||||||
37 4 1 36 38 5860.43 6.785 20 0 -8.3496 14.4619 60 0 0 0
|
|
||||||
38 4 1 37 39 5860.43 6.785 20 0 -8.3496 14.4619 80 0 0 0
|
|
||||||
39 4 1 38 40 5860.43 6.785 20 0 -8.3496 14.4619 100 0 0 0
|
|
||||||
40 4 1 39 41 5860.43 6.785 20 0 -8.3496 14.4619 120 0 0 0
|
|
||||||
41 4 1 40 42 5860.43 6.785 20 0 -8.3496 14.4619 140 0 0 0
|
|
||||||
42 4 1 41 43 5860.43 6.785 20 0 -8.3496 14.4619 160 0 0 0
|
|
||||||
43 4 1 42 44 5860.43 6.785 20 0 -8.3496 14.4619 180 0 0 0
|
|
||||||
44 4 1 43 34 5860.43 6.785 20 0 -8.3496 14.4619 200 0 0 0
|
|
||||||
45 5 1 55 46 5860.43 6.785 20 0 -16.6992 0 0 0 0 0
|
|
||||||
46 5 1 45 47 5860.43 6.785 20 0 -16.6992 0 20 0 0 0
|
|
||||||
47 5 1 46 48 5860.43 6.785 20 0 -16.6992 0 40 0 0 0
|
|
||||||
48 5 1 47 49 5860.43 6.785 20 0 -16.6992 0 60 0 0 0
|
|
||||||
49 5 1 48 50 5860.43 6.785 20 0 -16.6992 0 80 0 0 0
|
|
||||||
50 5 1 49 51 5860.43 6.785 20 0 -16.6992 0 100 0 0 0
|
|
||||||
51 5 1 50 52 5860.43 6.785 20 0 -16.6992 0 120 0 0 0
|
|
||||||
52 5 1 51 53 5860.43 6.785 20 0 -16.6992 0 140 0 0 0
|
|
||||||
53 5 1 52 54 5860.43 6.785 20 0 -16.6992 0 160 0 0 0
|
|
||||||
54 5 1 53 55 5860.43 6.785 20 0 -16.6992 0 180 0 0 0
|
|
||||||
55 5 1 54 45 5860.43 6.785 20 0 -16.6992 0 200 0 0 0
|
|
||||||
56 6 1 66 57 5860.43 6.785 20 0 -8.3496 -14.4619 0 0 0 0
|
|
||||||
57 6 1 56 58 5860.43 6.785 20 0 -8.3496 -14.4619 20 0 0 0
|
|
||||||
58 6 1 57 59 5860.43 6.785 20 0 -8.3496 -14.4619 40 0 0 0
|
|
||||||
59 6 1 58 60 5860.43 6.785 20 0 -8.3496 -14.4619 60 0 0 0
|
|
||||||
60 6 1 59 61 5860.43 6.785 20 0 -8.3496 -14.4619 80 0 0 0
|
|
||||||
61 6 1 60 62 5860.43 6.785 20 0 -8.3496 -14.4619 100 0 0 0
|
|
||||||
62 6 1 61 63 5860.43 6.785 20 0 -8.3496 -14.4619 120 0 0 0
|
|
||||||
63 6 1 62 64 5860.43 6.785 20 0 -8.3496 -14.4619 140 0 0 0
|
|
||||||
64 6 1 63 65 5860.43 6.785 20 0 -8.3496 -14.4619 160 0 0 0
|
|
||||||
65 6 1 64 66 5860.43 6.785 20 0 -8.3496 -14.4619 180 0 0 0
|
|
||||||
66 6 1 65 56 5860.43 6.785 20 0 -8.3496 -14.4619 200 0 0 0
|
|
||||||
67 7 1 77 68 5860.43 6.785 20 0 8.3496 -14.4619 0 0 0 0
|
|
||||||
68 7 1 67 69 5860.43 6.785 20 0 8.3496 -14.4619 20 0 0 0
|
|
||||||
69 7 1 68 70 5860.43 6.785 20 0 8.3496 -14.4619 40 0 0 0
|
|
||||||
70 7 1 69 71 5860.43 6.785 20 0 8.3496 -14.4619 60 0 0 0
|
|
||||||
71 7 1 70 72 5860.43 6.785 20 0 8.3496 -14.4619 80 0 0 0
|
|
||||||
72 7 1 71 73 5860.43 6.785 20 0 8.3496 -14.4619 100 0 0 0
|
|
||||||
73 7 1 72 74 5860.43 6.785 20 0 8.3496 -14.4619 120 0 0 0
|
|
||||||
74 7 1 73 75 5860.43 6.785 20 0 8.3496 -14.4619 140 0 0 0
|
|
||||||
75 7 1 74 76 5860.43 6.785 20 0 8.3496 -14.4619 160 0 0 0
|
|
||||||
76 7 1 75 77 5860.43 6.785 20 0 8.3496 -14.4619 180 0 0 0
|
|
||||||
77 7 1 76 67 5860.43 6.785 20 0 8.3496 -14.4619 200 0 0 0
|
|
||||||
File diff suppressed because it is too large
Load Diff
@ -1,29 +0,0 @@
|
|||||||
processors 1 1 *
|
|
||||||
newton on
|
|
||||||
units metal
|
|
||||||
lattice sc 1.0
|
|
||||||
boundary fs fs p
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 5 delay 0 check yes
|
|
||||||
|
|
||||||
atom_style mesont
|
|
||||||
# cut, path, BendingMode, TPMType
|
|
||||||
pair_style mesont/tpm 45.0 MESONT-TABTP_10_10.xrs 0 0
|
|
||||||
read_data data.bundle
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
velocity all create 6000.0 2019
|
|
||||||
timestep 0.005
|
|
||||||
fix 1 all nve
|
|
||||||
thermo 10
|
|
||||||
reset_timestep 0
|
|
||||||
|
|
||||||
compute Es all mesont estretch
|
|
||||||
compute Eb all mesont ebend
|
|
||||||
compute Et all mesont etube
|
|
||||||
compute B all property/atom buckling
|
|
||||||
|
|
||||||
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
|
|
||||||
#dump out_dump all custom 50 dump.bundle id type x y z c_Es c_Eb c_Et c_B ix iy iz
|
|
||||||
|
|
||||||
run 100
|
|
||||||
@ -1,28 +0,0 @@
|
|||||||
newton on
|
|
||||||
units metal
|
|
||||||
lattice sc 1.0
|
|
||||||
boundary p p fs
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 5 delay 0 check yes
|
|
||||||
|
|
||||||
atom_style mesont
|
|
||||||
# cut, path, BendingMode, TPMType
|
|
||||||
pair_style mesont/tpm 30.0 MESONT-TABTP_10_10.xrs 1 0
|
|
||||||
read_data data.film
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
velocity all create 600.0 2019
|
|
||||||
timestep 0.01
|
|
||||||
fix 1 all nve
|
|
||||||
thermo 10
|
|
||||||
reset_timestep 0
|
|
||||||
|
|
||||||
compute Es all mesont estretch
|
|
||||||
compute Eb all mesont ebend
|
|
||||||
compute Et all mesont etube
|
|
||||||
compute B all property/atom buckling
|
|
||||||
|
|
||||||
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
|
|
||||||
#dump out_dump all custom 10 dump.film id type x y z c_Es c_Eb c_Et c_B ix iy iz
|
|
||||||
|
|
||||||
run 20
|
|
||||||
@ -1,90 +0,0 @@
|
|||||||
LAMMPS (5 May 2020)
|
|
||||||
processors 1 1 *
|
|
||||||
newton on
|
|
||||||
units metal
|
|
||||||
lattice sc 1.0
|
|
||||||
Lattice spacing in x,y,z = 1 1 1
|
|
||||||
boundary fs fs p
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 5 delay 0 check yes
|
|
||||||
|
|
||||||
atom_style mesont
|
|
||||||
# cut, path, BendingMode, TPMType
|
|
||||||
pair_style mesont/tpm 45.0 MESONT-TABTP_10_10.xrs 0 0
|
|
||||||
read_data data.bundle
|
|
||||||
orthogonal box = (-143.89 -143.89 0) to (143.89 143.89 220)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
77 atoms
|
|
||||||
read_data CPU = 0.000613213 secs
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
velocity all create 6000.0 2019
|
|
||||||
timestep 0.005
|
|
||||||
fix 1 all nve
|
|
||||||
thermo 10
|
|
||||||
reset_timestep 0
|
|
||||||
|
|
||||||
compute Es all mesont estretch
|
|
||||||
compute Eb all mesont ebend
|
|
||||||
compute Et all mesont etube
|
|
||||||
compute B all property/atom buckling
|
|
||||||
|
|
||||||
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
|
|
||||||
#dump out_dump all custom 50 dump.bundle id type x y z c_Es c_Eb c_Et c_B ix iy iz
|
|
||||||
|
|
||||||
run 100
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 5 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 46
|
|
||||||
ghost atom cutoff = 46
|
|
||||||
binsize = 23, bins = 7 7 10
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair mesont/tpm, perpetual
|
|
||||||
attributes: full, newton on, ghost
|
|
||||||
pair build: full/bin/ghost
|
|
||||||
stencil: full/ghost/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 4.675 | 4.675 | 4.675 Mbytes
|
|
||||||
Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
|
|
||||||
0 0 6000 -201.86935 58.942626 -260.81198 0 0 -260.81198
|
|
||||||
10 0.05 5114.1875 -201.86234 50.240607 -252.10295 4.8334861 2.3998206 -259.33626
|
|
||||||
20 0.1 3437.2958 -201.8522 33.767207 -235.61941 11.42384 8.3426957 -255.38594
|
|
||||||
30 0.15 2430.6571 -201.85242 23.878219 -225.73064 10.346152 14.72688 -250.80367
|
|
||||||
40 0.2 2154.4755 -201.85683 21.165074 -223.0219 6.8146112 18.325709 -248.16222
|
|
||||||
50 0.25 2021.7899 -201.85503 19.861601 -221.71663 9.2972022 17.644143 -248.65798
|
|
||||||
60 0.3 2234.553 -201.85193 21.951737 -223.80367 13.541921 13.673721 -251.01931
|
|
||||||
70 0.35 3099.6503 -201.85721 30.450255 -232.30747 11.833679 9.0583807 -253.19953
|
|
||||||
80 0.4 3849.9855 -201.8635 37.821376 -239.68487 7.9899173 6.4332848 -254.10807
|
|
||||||
90 0.45 3618.1311 -201.85967 35.543692 -237.40336 9.2616931 7.0452637 -253.71032
|
|
||||||
100 0.5 2866.2722 -201.85273 28.157602 -230.01033 12.204916 10.284525 -252.49977
|
|
||||||
Loop time of 0.419735 on 1 procs for 100 steps with 77 atoms
|
|
||||||
|
|
||||||
Performance: 102.922 ns/day, 0.233 hours/ns, 238.245 timesteps/s
|
|
||||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.41922 | 0.41922 | 0.41922 | 0.0 | 99.88
|
|
||||||
Neigh | 5.8174e-05 | 5.8174e-05 | 5.8174e-05 | 0.0 | 0.01
|
|
||||||
Comm | 7.0333e-05 | 7.0333e-05 | 7.0333e-05 | 0.0 | 0.02
|
|
||||||
Output | 0.00017667 | 0.00017667 | 0.00017667 | 0.0 | 0.04
|
|
||||||
Modify | 0.00011945 | 0.00011945 | 0.00011945 | 0.0 | 0.03
|
|
||||||
Other | | 8.702e-05 | | | 0.02
|
|
||||||
|
|
||||||
Nlocal: 77 ave 77 max 77 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 35 ave 35 max 35 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 2222 ave 2222 max 2222 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 2222
|
|
||||||
Ave neighs/atom = 28.8571
|
|
||||||
Neighbor list builds = 1
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:01
|
|
||||||
@ -1,90 +0,0 @@
|
|||||||
LAMMPS (5 May 2020)
|
|
||||||
processors 1 1 *
|
|
||||||
newton on
|
|
||||||
units metal
|
|
||||||
lattice sc 1.0
|
|
||||||
Lattice spacing in x,y,z = 1 1 1
|
|
||||||
boundary fs fs p
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 5 delay 0 check yes
|
|
||||||
|
|
||||||
atom_style mesont
|
|
||||||
# cut, path, BendingMode, TPMType
|
|
||||||
pair_style mesont/tpm 45.0 MESONT-TABTP_10_10.xrs 0 0
|
|
||||||
read_data data.bundle
|
|
||||||
orthogonal box = (-143.89 -143.89 0) to (143.89 143.89 220)
|
|
||||||
1 by 1 by 4 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
77 atoms
|
|
||||||
read_data CPU = 0.000590563 secs
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
velocity all create 6000.0 2019
|
|
||||||
timestep 0.005
|
|
||||||
fix 1 all nve
|
|
||||||
thermo 10
|
|
||||||
reset_timestep 0
|
|
||||||
|
|
||||||
compute Es all mesont estretch
|
|
||||||
compute Eb all mesont ebend
|
|
||||||
compute Et all mesont etube
|
|
||||||
compute B all property/atom buckling
|
|
||||||
|
|
||||||
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
|
|
||||||
#dump out_dump all custom 50 dump.bundle id type x y z c_Es c_Eb c_Et c_B ix iy iz
|
|
||||||
|
|
||||||
run 100
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 5 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 46
|
|
||||||
ghost atom cutoff = 46
|
|
||||||
binsize = 23, bins = 7 7 10
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair mesont/tpm, perpetual
|
|
||||||
attributes: full, newton on, ghost
|
|
||||||
pair build: full/bin/ghost
|
|
||||||
stencil: full/ghost/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 4.671 | 4.671 | 4.671 Mbytes
|
|
||||||
Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
|
|
||||||
0 0 6000 -201.86935 58.942626 -260.81198 0 0 -260.81198
|
|
||||||
10 0.05 5114.1875 -201.86234 50.240607 -252.10295 4.8334861 2.3998206 -259.33626
|
|
||||||
20 0.1 3437.2958 -201.8522 33.767207 -235.61941 11.42384 8.3426957 -255.38594
|
|
||||||
30 0.15 2430.6571 -201.85242 23.878219 -225.73064 10.346152 14.72688 -250.80367
|
|
||||||
40 0.2 2154.4755 -201.85683 21.165074 -223.0219 6.8146112 18.325709 -248.16222
|
|
||||||
50 0.25 2021.7899 -201.85503 19.861601 -221.71663 9.2972022 17.644143 -248.65798
|
|
||||||
60 0.3 2234.553 -201.85193 21.951737 -223.80367 13.541921 13.673721 -251.01931
|
|
||||||
70 0.35 3099.6503 -201.85721 30.450255 -232.30747 11.833679 9.0583807 -253.19953
|
|
||||||
80 0.4 3849.9855 -201.8635 37.821376 -239.68487 7.9899173 6.4332848 -254.10807
|
|
||||||
90 0.45 3618.1311 -201.85967 35.543692 -237.40336 9.2616931 7.0452637 -253.71032
|
|
||||||
100 0.5 2866.2722 -201.85273 28.157602 -230.01033 12.204916 10.284525 -252.49977
|
|
||||||
Loop time of 0.145545 on 4 procs for 100 steps with 77 atoms
|
|
||||||
|
|
||||||
Performance: 296.815 ns/day, 0.081 hours/ns, 687.071 timesteps/s
|
|
||||||
95.9% CPU use with 4 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.046723 | 0.097529 | 0.14388 | 11.0 | 67.01
|
|
||||||
Neigh | 2.5511e-05 | 2.8729e-05 | 3.171e-05 | 0.0 | 0.02
|
|
||||||
Comm | 0.00058556 | 0.045174 | 0.098462 | 16.5 | 31.04
|
|
||||||
Output | 0.0001483 | 0.0010182 | 0.002851 | 3.5 | 0.70
|
|
||||||
Modify | 3.8147e-05 | 4.065e-05 | 4.4107e-05 | 0.0 | 0.03
|
|
||||||
Other | | 0.001755 | | | 1.21
|
|
||||||
|
|
||||||
Nlocal: 19.25 ave 21 max 16 min
|
|
||||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
|
||||||
Nghost: 33.25 ave 40 max 28 min
|
|
||||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 555.5 ave 606 max 460 min
|
|
||||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
|
||||||
|
|
||||||
Total # of neighbors = 2222
|
|
||||||
Ave neighs/atom = 28.8571
|
|
||||||
Neighbor list builds = 1
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:01
|
|
||||||
@ -1,81 +0,0 @@
|
|||||||
LAMMPS (5 May 2020)
|
|
||||||
newton on
|
|
||||||
units metal
|
|
||||||
lattice sc 1.0
|
|
||||||
Lattice spacing in x,y,z = 1 1 1
|
|
||||||
boundary p p fs
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 5 delay 0 check yes
|
|
||||||
|
|
||||||
atom_style mesont
|
|
||||||
# cut, path, BendingMode, TPMType
|
|
||||||
pair_style mesont/tpm 30.0 MESONT-TABTP_10_10.xrs 1 0
|
|
||||||
read_data data.film
|
|
||||||
orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
79596 atoms
|
|
||||||
read_data CPU = 0.0860629 secs
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
velocity all create 600.0 2019
|
|
||||||
timestep 0.01
|
|
||||||
fix 1 all nve
|
|
||||||
thermo 10
|
|
||||||
reset_timestep 0
|
|
||||||
|
|
||||||
compute Es all mesont estretch
|
|
||||||
compute Eb all mesont ebend
|
|
||||||
compute Et all mesont etube
|
|
||||||
compute B all property/atom buckling
|
|
||||||
|
|
||||||
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
|
|
||||||
#dump out_dump all custom 10 dump.film id type x y z c_Es c_Eb c_Et c_B ix iy iz
|
|
||||||
|
|
||||||
run 20
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 5 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 31
|
|
||||||
ghost atom cutoff = 31
|
|
||||||
binsize = 15.5, bins = 323 323 26
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair mesont/tpm, perpetual
|
|
||||||
attributes: full, newton on, ghost
|
|
||||||
pair build: full/bin/ghost
|
|
||||||
stencil: full/ghost/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 37.43 | 37.43 | 37.43 Mbytes
|
|
||||||
Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
|
|
||||||
0 0 600 1347.2158 6173.0767 -4825.8609 28.669574 21.29406 -4875.8245
|
|
||||||
10 0.1 389.40755 1373.7864 4006.4045 -2632.6181 848.00267 1404.4323 -4885.053
|
|
||||||
20 0.2 313.65714 1399.9427 3227.0494 -1827.1067 1201.1732 1882.1342 -4910.4141
|
|
||||||
Loop time of 10.2438 on 1 procs for 20 steps with 79596 atoms
|
|
||||||
|
|
||||||
Performance: 1.687 ns/day, 14.228 hours/ns, 1.952 timesteps/s
|
|
||||||
99.0% CPU use with 1 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 10.226 | 10.226 | 10.226 | 0.0 | 99.82
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.00081086 | 0.00081086 | 0.00081086 | 0.0 | 0.01
|
|
||||||
Output | 0.00046563 | 0.00046563 | 0.00046563 | 0.0 | 0.00
|
|
||||||
Modify | 0.015165 | 0.015165 | 0.015165 | 0.0 | 0.15
|
|
||||||
Other | | 0.001869 | | | 0.02
|
|
||||||
|
|
||||||
Nlocal: 79596 ave 79596 max 79596 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 1879 ave 1879 max 1879 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 642270 ave 642270 max 642270 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 642270
|
|
||||||
Ave neighs/atom = 8.06912
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:11
|
|
||||||
@ -1,81 +0,0 @@
|
|||||||
LAMMPS (5 May 2020)
|
|
||||||
newton on
|
|
||||||
units metal
|
|
||||||
lattice sc 1.0
|
|
||||||
Lattice spacing in x,y,z = 1 1 1
|
|
||||||
boundary p p fs
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 5 delay 0 check yes
|
|
||||||
|
|
||||||
atom_style mesont
|
|
||||||
# cut, path, BendingMode, TPMType
|
|
||||||
pair_style mesont/tpm 30.0 MESONT-TABTP_10_10.xrs 1 0
|
|
||||||
read_data data.film
|
|
||||||
orthogonal box = (-2500 -2500 -300) to (2500 2500 402.42)
|
|
||||||
2 by 2 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
79596 atoms
|
|
||||||
read_data CPU = 0.0704217 secs
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
velocity all create 600.0 2019
|
|
||||||
timestep 0.01
|
|
||||||
fix 1 all nve
|
|
||||||
thermo 10
|
|
||||||
reset_timestep 0
|
|
||||||
|
|
||||||
compute Es all mesont estretch
|
|
||||||
compute Eb all mesont ebend
|
|
||||||
compute Et all mesont etube
|
|
||||||
compute B all property/atom buckling
|
|
||||||
|
|
||||||
thermo_style custom step time temp etotal ke pe c_Es c_Eb c_Et
|
|
||||||
#dump out_dump all custom 10 dump.film id type x y z c_Es c_Eb c_Et c_B ix iy iz
|
|
||||||
|
|
||||||
run 20
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 5 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 31
|
|
||||||
ghost atom cutoff = 31
|
|
||||||
binsize = 15.5, bins = 323 323 26
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair mesont/tpm, perpetual
|
|
||||||
attributes: full, newton on, ghost
|
|
||||||
pair build: full/bin/ghost
|
|
||||||
stencil: full/ghost/bin/3d
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 12.81 | 12.81 | 12.83 Mbytes
|
|
||||||
Step Time Temp TotEng KinEng PotEng c_Es c_Eb c_Et
|
|
||||||
0 0 600 1347.2158 6173.0767 -4825.8609 28.669574 21.29406 -4875.8245
|
|
||||||
10 0.1 389.40755 1373.7864 4006.4045 -2632.6181 848.00267 1404.4323 -4885.053
|
|
||||||
20 0.2 313.65714 1399.9427 3227.0494 -1827.1067 1201.1732 1882.1342 -4910.4141
|
|
||||||
Loop time of 3.67186 on 4 procs for 20 steps with 79596 atoms
|
|
||||||
|
|
||||||
Performance: 4.706 ns/day, 5.100 hours/ns, 5.447 timesteps/s
|
|
||||||
95.8% CPU use with 4 MPI tasks x no OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 2.7317 | 3.1286 | 3.6556 | 18.8 | 85.20
|
|
||||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
||||||
Comm | 0.0036943 | 0.53094 | 0.92822 | 45.8 | 14.46
|
|
||||||
Output | 0.00026512 | 0.00035298 | 0.00055647 | 0.0 | 0.01
|
|
||||||
Modify | 0.010463 | 0.010884 | 0.011153 | 0.3 | 0.30
|
|
||||||
Other | | 0.001109 | | | 0.03
|
|
||||||
|
|
||||||
Nlocal: 19899 ave 21951 max 18667 min
|
|
||||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
|
||||||
Nghost: 970.75 ave 1031 max 920 min
|
|
||||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
|
||||||
Neighs: 0 ave 0 max 0 min
|
|
||||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
||||||
FullNghs: 160568 ave 181723 max 147382 min
|
|
||||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 642270
|
|
||||||
Ave neighs/atom = 8.06912
|
|
||||||
Neighbor list builds = 0
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:04
|
|
||||||
@ -1,13 +0,0 @@
|
|||||||
CNTPot.o: CNTPot.f90 TPMLib.o
|
|
||||||
ExportCNT.o: ExportCNT.f90 CNTPot.o TPMLib.o TubePotMono.o TPMForceField.o
|
|
||||||
LinFun2.o: LinFun2.f90
|
|
||||||
Spline1.o: Spline1.f90
|
|
||||||
Spline2.o: Spline2.f90 Spline1.o
|
|
||||||
TPMForceField.o: TPMForceField.f90 CNTPot.o TPMM0.o TPMM1.o
|
|
||||||
TPMGeom.o: TPMGeom.f90 TPMLib.o
|
|
||||||
TPMLib.o: TPMLib.f90
|
|
||||||
TPMM0.o: TPMM0.f90 TubePotMono.o
|
|
||||||
TPMM1.o: TPMM1.f90 TubePotMono.o
|
|
||||||
TubePotBase.o: TubePotBase.f90 TPMLib.o
|
|
||||||
TubePotMono.o: TubePotMono.f90 TPMLib.o TPMGeom.o TubePotBase.o TubePotTrue.o LinFun2.o Spline2.o
|
|
||||||
TubePotTrue.o: TubePotTrue.f90 TPMGeom.o TubePotBase.o
|
|
||||||
1
lib/mesont/.gitignore
vendored
1
lib/mesont/.gitignore
vendored
@ -1 +0,0 @@
|
|||||||
*.mod
|
|
||||||
@ -1,714 +0,0 @@
|
|||||||
! ------------ ----------------------------------------------------------
|
|
||||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
! https://www.lammps.org/ Sandia National Laboratories
|
|
||||||
! LAMMPS development team: developers@lammps.org
|
|
||||||
!
|
|
||||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
! certain rights in this software. This software is distributed under
|
|
||||||
! 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 !*************************************************************************************
|
|
||||||
!
|
|
||||||
! Mesoscopic potential for internal modes in CNTs.
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! 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
|
|
||||||
! 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
|
|
||||||
! CNTTRS, torsion potential
|
|
||||||
! CNTBRT, breathing potential
|
|
||||||
!
|
|
||||||
! The functional form and force constants of harmonic stretching, bending and
|
|
||||||
! 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
|
|
||||||
! is developed and parameterized using the following constants
|
|
||||||
! -- 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
|
|
||||||
! CNTSTRSft are slightly different from the imposed values CNTSTREf and CNTSTRSf.
|
|
||||||
!
|
|
||||||
! 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,
|
|
||||||
! see subroutine CNTSTRSetParameterization
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 13.00, 2020
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
|
|
||||||
use TPMLib
|
|
||||||
use iso_c_binding, only : c_int, c_double, c_char
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Constants
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
integer(c_int), parameter :: CNTPOT_STRETCHING = 0
|
|
||||||
integer(c_int), parameter :: CNTPOT_SBUCKLING = 1
|
|
||||||
integer(c_int), parameter :: CNTPOT_SFRACTURE = 2
|
|
||||||
|
|
||||||
integer(c_int), parameter :: CNTPOT_BENDING = 3
|
|
||||||
integer(c_int), parameter :: CNTPOT_BBUCKLING = 4
|
|
||||||
integer(c_int), parameter :: CNTPOT_BFRACTURE = 5
|
|
||||||
|
|
||||||
! Harmonic stretching model (constant Young's modulus)
|
|
||||||
integer(c_int), parameter :: CNTSTRMODEL_H0 = 0
|
|
||||||
! Harmonic stretching model (Young's modulus depends on radius)
|
|
||||||
integer(c_int), parameter :: CNTSTRMODEL_H1 = 1
|
|
||||||
! Non-harmonic stretching with fracture, potential of type 0
|
|
||||||
integer(c_int), parameter :: CNTSTRMODEL_NH0F = 2
|
|
||||||
! Non-harmonic stretching without fracture, potential of type 1
|
|
||||||
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
|
|
||||||
! Harmonic stretching model + axial buckling + hysteresis
|
|
||||||
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
|
|
||||||
! Type of dependence of the Young's modulus on tube radius
|
|
||||||
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
|
|
||||||
! 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) :: 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
|
|
||||||
real(c_double) :: CNTSTREf = 12.0d-02 ! Strain at failure
|
|
||||||
real(c_double) :: CNTSTRS0 = 0.850e+12 ! Young's modulus (Pa)
|
|
||||||
real(c_double) :: CNTSTRSl ! Maximum linear stress (Pa)
|
|
||||||
real(c_double) :: CNTSTRSf = 75.0d+09 ! Tensile strength (Pa)
|
|
||||||
real(c_double) :: CNTSTRF0 ! Elastic force constant (eV/A**2)
|
|
||||||
real(c_double) :: CNTSTRFl ! Maximal linear force, (eV/A**2)
|
|
||||||
real(c_double) :: CNTSTRFf ! Tensile force at failure (eV/A**2)
|
|
||||||
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) :: CNTSTRAAA, CNTSTRBBB ! Auxiliary constants
|
|
||||||
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) :: 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
|
|
||||||
real(c_double) :: CNTBNDB = 0.68d+00 ! Buckling number
|
|
||||||
real(c_double) :: CNTBNDR = 275.0d+00 ! Critical radius of curvature (A)
|
|
||||||
! This is the mean value for (10,10) SWCNT
|
|
||||||
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
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
subroutine CNTSTRSetParameterization ( PType ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This subroutine setups parameters for further parameterization of stretching models
|
|
||||||
! References:
|
|
||||||
! [1] Yu M.-F. et al., Phys. Rev. Lett. 84(24), 5552 (2000)
|
|
||||||
! [2] Liew K.M. et al., Acta Materialia 52, 2521 (2004)
|
|
||||||
! [3] Mielke S.L. et al., Chem. Phys. Lett. 390, 413 (2004)
|
|
||||||
! [4] Zhigilei L.V. et al., Phys. Rev. B 71, 165417 (2005)
|
|
||||||
! [5] Kelly B.T., Physics of graphite, 1981
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer(c_int), intent(in) :: 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]
|
|
||||||
CNTSTREmin = -0.4d+00 ! Chosen arbitrary
|
|
||||||
CNTSTREmax = 3.64d-02 ! = CNTSTREf + 0.005
|
|
||||||
CNTSTREl = 2.0d-02 ! Chosen arbitrary
|
|
||||||
CNTSTREf = 3.14d-02 ! Ref. [1]
|
|
||||||
CNTSTRS0 = 1.002e+12 ! Ref. [1]
|
|
||||||
CNTSTRSf = 30.0d+09 ! Ref. [1]
|
|
||||||
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)
|
|
||||||
! (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]
|
|
||||||
CNTSTREmin = -0.4d+00 ! Chosen arbitrary
|
|
||||||
CNTSTREmax = 28.4d-02 ! = CNTSTREf + 0.005
|
|
||||||
CNTSTREl = 5.94d-02 ! Ref. [2]
|
|
||||||
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
|
|
||||||
! 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]
|
|
||||||
CNTSTREmin = -0.4d+00 ! Chosen arbitrary
|
|
||||||
CNTSTREmax = 15.8d-02 ! = CNTSTREf + 0.005
|
|
||||||
CNTSTREl = 6.00d-02 ! Chosen similar to Ref. [2]
|
|
||||||
CNTSTREf = 15.3d-02 ! Ref. [3]
|
|
||||||
CNTSTRS0 = 1.100e+12 ! Ref. [3]
|
|
||||||
CNTSTRSf = 100.0d+09 ! Ref. [3]
|
|
||||||
case ( 3 ) ! This special parameterization changes only the value of Young's modulus
|
|
||||||
! in accordance with the stretching constant in Ref. [4]
|
|
||||||
CNTSTRS0 = ( 86.64d+00 + 100.56d+00 * CNTSTRR0 ) * K_MDFU &
|
|
||||||
/ ( M_2PI * CNTSTRR0 * CNTSTRD0 * 1.0d-20 ) ! Ref. [4]
|
|
||||||
case ( 4 ) ! This special parameterization changes only the value of Young's modulus
|
|
||||||
! making it equal to the in-plane Young's modulus of graphite
|
|
||||||
CNTSTRR0 = 6.785d+00 ! Calculated with the usual formula for (10,10) CNT
|
|
||||||
CNTSTRD0 = 3.4d+00 ! Ref. [1]
|
|
||||||
CNTSTRS0 = 1.06e+12 ! Ref. [5]
|
|
||||||
end select
|
|
||||||
end subroutine CNTSTRSetParameterization !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!
|
|
||||||
! Stretching without fracture, harmonic potential
|
|
||||||
!
|
|
||||||
|
|
||||||
integer(c_int) function CNTSTRH0Calc ( U, dUdL, L, R0, L0 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! Young's modulus is independent of R.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double), intent(out) :: U, dUdL
|
|
||||||
real(c_double), intent(in) :: L, R0, L0
|
|
||||||
real(c_double) :: E
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
E = ( L - L0 ) / L0
|
|
||||||
dUdL = R0 * CNTSTRF0 * E
|
|
||||||
U = 0.5d+00 * L0 * E * dUdL
|
|
||||||
CNTSTRH0Calc = CNTPOT_STRETCHING
|
|
||||||
end function CNTSTRH0Calc !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
integer(c_int) function CNTSTRH1Calc ( U, dUdL, L, R0, L0 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! Young's modulus depends on R, see [4].
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double), intent(out) :: U, dUdL
|
|
||||||
real(c_double), intent(in) :: L, R0, L0
|
|
||||||
real(c_double) :: E, K
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
E = ( L - L0 ) / L0
|
|
||||||
K = 86.64d+00 + 100.56d+00 * R0
|
|
||||||
dUdL = K * E
|
|
||||||
U = 0.5d+00 * L0 * E * dUdL
|
|
||||||
CNTSTRH1Calc = CNTPOT_STRETCHING
|
|
||||||
end function CNTSTRH1Calc !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!
|
|
||||||
! Stretching without fracture, harmonic potential, with axial buckling without hysteresis
|
|
||||||
!
|
|
||||||
|
|
||||||
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
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
E = ( L - L0 ) / L0
|
|
||||||
K = 86.64d+00 + 100.56d+00 * R0
|
|
||||||
Kbcl = -10.98d+00 * L0
|
|
||||||
if ( E .gt. CNTSTREc ) then ! Harmonic stretching
|
|
||||||
dUdL = K * E
|
|
||||||
U = 0.5d+00 * L0 * E * dUdL
|
|
||||||
CNTSTRH1BCalc = CNTPOT_STRETCHING
|
|
||||||
else if ( E .gt. CNTSTREc2 ) then ! Axial buckling
|
|
||||||
dUbcl = 0.5d+00 * L0 * K * CNTSTREc * CNTSTREc - Kbcl * CNTSTREc
|
|
||||||
U = Kbcl * E + dUbcl
|
|
||||||
dUdL = Kbcl / L0
|
|
||||||
CNTSTRH1BCalc = CNTPOT_STRETCHING
|
|
||||||
else ! Return to harmonic potential
|
|
||||||
d = -0.0142794
|
|
||||||
dUdL = K * ( d + E - CNTSTREc2 )
|
|
||||||
dUbcl = 0.5d+00 * L0 * K * CNTSTREc * CNTSTREc - Kbcl * CNTSTREc + Kbcl * CNTSTREc2
|
|
||||||
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 function CNTSTRH1BCalc !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!
|
|
||||||
! Stretching without fracture, harmonic potential, with axial buckling with hysteresis
|
|
||||||
!
|
|
||||||
|
|
||||||
integer(c_int) function CNTSTRH1BHCalc ( U, dUdL, L, R0, L0, ABF, Ebuc ) !!!!!!!!!!!!!!!!!!!
|
|
||||||
! Young's modulus depends on R, see [4]
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double), intent(out) :: U, dUdL, Ebuc
|
|
||||||
real(c_double), intent(in) :: L, R0, L0
|
|
||||||
integer(c_int), intent(in) :: ABF
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
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
|
|
||||||
if ( E .gt. CNTSTREc ) then ! Harmonic potential - no buckling
|
|
||||||
dUdL = K * E
|
|
||||||
U = 0.5d+00 * L0 * E * dUdL
|
|
||||||
CNTSTRH1BHCalc = CNTPOT_STRETCHING
|
|
||||||
Ebuc = 0.0d+00
|
|
||||||
else if ( E .gt. CNTSTREc1 ) then ! Above minimal buckling strain, but not at critical strain
|
|
||||||
if ( ABF .eq. 0 ) then ! Not buckled. Continue harmonic potential
|
|
||||||
dUdL = K * E
|
|
||||||
U = 0.5d+00 * L0 * E * dUdL
|
|
||||||
CNTSTRH1BHCalc = CNTPOT_STRETCHING
|
|
||||||
Ebuc = 0.0d+00
|
|
||||||
else ! Relaxing from buckled state. Use buckling potential
|
|
||||||
dUbcl = 0.5d+00 * L0 * K * CNTSTREc * CNTSTREc - Kbcl * CNTSTREc
|
|
||||||
U = Kbcl * E + dUbcl
|
|
||||||
dUdL = Kbcl / L0
|
|
||||||
CNTSTRH1BHCalc = CNTPOT_SBUCKLING
|
|
||||||
Ebuc = 0.0d+00
|
|
||||||
end if
|
|
||||||
else if( E .gt. CNTSTREc2 ) then ! Axial buckling strain region
|
|
||||||
if ( ABF .eq. 0 ) then ! Newly buckled
|
|
||||||
dUbcl = 0.5d+00 * L0 * K * CNTSTREc * CNTSTREc - Kbcl * CNTSTREc
|
|
||||||
U = Kbcl * E + dUbcl
|
|
||||||
dUdL = Kbcl / L0
|
|
||||||
CNTSTRH1BHCalc = CNTPOT_SBUCKLING
|
|
||||||
Ebuc = 0.5d+00 * L0 * K * CNTSTREc1 * CNTSTREc1 - Kbcl * CNTSTREc1 - dUbcl
|
|
||||||
else ! Already buckled
|
|
||||||
dUbcl = 0.5d+00 * L0 * K * CNTSTREc * CNTSTREc - Kbcl * CNTSTREc
|
|
||||||
U = Kbcl * E + dUbcl
|
|
||||||
dUdL = Kbcl / L0
|
|
||||||
CNTSTRH1BHCalc = CNTPOT_SBUCKLING
|
|
||||||
Ebuc = 0.0d+00
|
|
||||||
end if
|
|
||||||
else ! Maximum strain and return to harmonic potential
|
|
||||||
dUdL = K * E
|
|
||||||
U = 0.5d+00 * L0 * E * dUdL
|
|
||||||
CNTSTRH1BHCalc = CNTPOT_STRETCHING
|
|
||||||
Ebuc = 0.0d+00
|
|
||||||
end if
|
|
||||||
end function CNTSTRH1BHCalc !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!
|
|
||||||
! Stretching with fracture, non-harmonic potential of type 0
|
|
||||||
!
|
|
||||||
|
|
||||||
integer(c_int) function CNTSTRNH0FCalc ( U, dUdL, L, R0, L0 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real(c_double), intent(out) :: U, dUdL
|
|
||||||
real(c_double), intent(in) :: L, R0, L0
|
|
||||||
real(c_double) :: E, DE, t
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
E = ( L - L0 ) / L0
|
|
||||||
if ( E < CNTSTREf ) then
|
|
||||||
dUdL = ( CNTSTRAA - CNTSTRBB * E ) * E
|
|
||||||
U = ( CNTSTRAAA - CNTSTRBBB * E ) * E * E
|
|
||||||
CNTSTRNH0FCalc = CNTPOT_STRETCHING
|
|
||||||
else
|
|
||||||
dUdL = 0.0d+00
|
|
||||||
U = 0.0d+00
|
|
||||||
CNTSTRNH0FCalc = CNTPOT_SFRACTURE
|
|
||||||
end if
|
|
||||||
U = L0 * R0 * U
|
|
||||||
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
|
|
||||||
CNTSTRAA = CNTSTRF0
|
|
||||||
CNTSTRBB = ( CNTSTRF0 * CNTSTREf - CNTSTRFf ) / ( CNTSTREf * CNTSTREf )
|
|
||||||
CNTSTRAAA= CNTSTRAA / 2.0d+00
|
|
||||||
CNTSTRBBB= CNTSTRAA / 3.0d+00
|
|
||||||
CNTSTRUl = 0.0d+00
|
|
||||||
CNTSTRUf = ( CNTSTRAAA - CNTSTRBBB * CNTSTREf ) * CNTSTREf * CNTSTREf
|
|
||||||
! These two values are not defined yet
|
|
||||||
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
|
|
||||||
real(c_double) :: E, C, DE, t
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
E = ( L - L0 ) / L0
|
|
||||||
if ( E < CNTSTREl ) then
|
|
||||||
dUdL = CNTSTRF0 * E
|
|
||||||
U = 0.5d+00 * E * dUdL
|
|
||||||
CNTSTRNH1Calc = CNTPOT_STRETCHING
|
|
||||||
else
|
|
||||||
DE = E - CNTSTREl
|
|
||||||
C = 1.0 + CNTSTRBB * DE
|
|
||||||
dUdL = CNTSTRFl + CNTSTRAA * ( 1.0d+00 - 1.0d+00 / C )
|
|
||||||
U = CNTSTRUl + CNTSTRAAA * DE - CNTSTRBBB * dlog ( C )
|
|
||||||
end if
|
|
||||||
CNTSTRNH1Calc = CNTPOT_STRETCHING
|
|
||||||
U = L0 * R0 * U
|
|
||||||
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
|
|
||||||
real(c_double) :: E, C, DE, t
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
E = ( L - L0 ) / L0
|
|
||||||
if ( E < CNTSTREl ) then
|
|
||||||
dUdL = CNTSTRF0 * E
|
|
||||||
U = 0.5d+00 * E * dUdL
|
|
||||||
CNTSTRNH1FCalc = CNTPOT_STRETCHING
|
|
||||||
else if ( E < CNTSTREf ) then
|
|
||||||
DE = E - CNTSTREl
|
|
||||||
C = 1.0 + CNTSTRBB * DE
|
|
||||||
dUdL = CNTSTRFl + CNTSTRAA * ( 1.0d+00 - 1.0d+00 / C )
|
|
||||||
U = CNTSTRUl + CNTSTRAAA * DE - CNTSTRBBB * dlog ( C )
|
|
||||||
CNTSTRNH1FCalc = CNTPOT_STRETCHING
|
|
||||||
else
|
|
||||||
dUdL = 0.0d+00
|
|
||||||
U = 0.0d+00
|
|
||||||
CNTSTRNH1FCalc = CNTPOT_SFRACTURE
|
|
||||||
end if
|
|
||||||
U = L0 * R0 * U
|
|
||||||
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
|
|
||||||
CNTSTRAA = ( CNTSTRFf - CNTSTRFl ) * ( CNTSTREf * CNTSTRF0 - CNTSTRFl ) / ( CNTSTREf * CNTSTRF0 - CNTSTRFf )
|
|
||||||
CNTSTRBB = CNTSTRF0 / CNTSTRAA
|
|
||||||
CNTSTRAAA= CNTSTRFl + CNTSTRAA
|
|
||||||
CNTSTRBBB= CNTSTRAA / CNTSTRBB
|
|
||||||
CNTSTRSi = CNTSTRSl + CNTSTRAA / S
|
|
||||||
C = 1.0 + CNTSTRBB * ( CNTSTREf - CNTSTREl )
|
|
||||||
CNTSTRDf = CNTSTRF0 / C / C
|
|
||||||
CNTSTRUl = 0.5d+00 * CNTSTRFl * CNTSTREl
|
|
||||||
CNTSTRUf = CNTSTRUl + ( CNTSTRFl + CNTSTRAA ) * ( CNTSTREf - CNTSTREl ) - CNTSTRAA * dlog ( C ) / CNTSTRBB
|
|
||||||
end subroutine CNTSTRNH1Init !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!
|
|
||||||
! General
|
|
||||||
!
|
|
||||||
|
|
||||||
integer(c_int) function CNTSTRCalc ( U, dUdL, L, R0, L0 , ABF, Ebuc ) !!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real(c_double), intent(out) :: U, dUdL, Ebuc
|
|
||||||
real(c_double), intent(in) :: L, R0, L0
|
|
||||||
integer(c_int), intent(in) :: ABF
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Ebuc = 0.0d+00
|
|
||||||
select case ( CNTSTRModel )
|
|
||||||
case ( CNTSTRMODEL_H0 )
|
|
||||||
CNTSTRCalc = CNTSTRH0Calc ( U, dUdL, L, R0, L0 )
|
|
||||||
case ( CNTSTRMODEL_H1 )
|
|
||||||
CNTSTRCalc = CNTSTRH1Calc ( U, dUdL, L, R0, L0 )
|
|
||||||
case ( CNTSTRMODEL_NH0F )
|
|
||||||
CNTSTRCalc = CNTSTRNH0FCalc ( U, dUdL, L, R0, L0 )
|
|
||||||
case ( CNTSTRMODEL_NH1 )
|
|
||||||
CNTSTRCalc = CNTSTRNH1Calc ( U, dUdL, L, R0, L0 )
|
|
||||||
case ( CNTSTRMODEL_NH1F )
|
|
||||||
CNTSTRCalc = CNTSTRNH1FCalc ( U, dUdL, L, R0, L0 )
|
|
||||||
case ( CNTSTRMODEL_H1B )
|
|
||||||
CNTSTRCalc = CNTSTRH1BCalc ( U, dUdL, L, R0, L0 )
|
|
||||||
case ( CNTSTRMODEL_H1BH )
|
|
||||||
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
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
CNTSTRModel = STRModel
|
|
||||||
CNTSTRParams = STRParams
|
|
||||||
CNTSTRYMT = YMType
|
|
||||||
if ( STRModel .ne. CNTSTRMODEL_H1 ) then
|
|
||||||
call CNTSTRSetParameterization ( STRParams )
|
|
||||||
if ( YMType == 2 ) then
|
|
||||||
call CNTSTRSetParameterization ( 4 )
|
|
||||||
else if ( YMType == 1 ) then
|
|
||||||
CNTSTRR0 = Rref
|
|
||||||
call CNTSTRSetParameterization ( 3 )
|
|
||||||
end if
|
|
||||||
if ( STRModel == CNTSTRMODEL_NH0F ) then
|
|
||||||
call CNTSTRNH0Init ()
|
|
||||||
else
|
|
||||||
call CNTSTRNH1Init ()
|
|
||||||
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
|
|
||||||
real(c_double), dimension(0:2), intent(in) :: R0, R1, R2
|
|
||||||
real(c_double), dimension(0:2) :: DR0, DR2
|
|
||||||
real(c_double) :: L0, L2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
DR0 = R0 - R1
|
|
||||||
DR2 = R2 - R1
|
|
||||||
L0 = S_V3norm3 ( DR0 )
|
|
||||||
L2 = S_V3norm3 ( DR2 )
|
|
||||||
DR0 = DR0 / L0
|
|
||||||
DR2 = DR2 / L2
|
|
||||||
K = S_V3xV3 ( DR0, DR2 )
|
|
||||||
G0 = DR2 - K * DR0
|
|
||||||
G2 = DR0 - K * DR2
|
|
||||||
G0 = G0 / L0
|
|
||||||
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.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double), intent(out) :: U, dUdC
|
|
||||||
real(c_double), intent(in) :: C, R0, L0
|
|
||||||
real(c_double) :: E, K
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
E = 1.0d+00 - C
|
|
||||||
K = 2.0d+00 * ( 63.8d+00 * R0**2.93d+00 ) / L0
|
|
||||||
U = K * ( 1.0d+00 + C ) / E
|
|
||||||
dUdC = 2.0d+00 * K / ( E * E )
|
|
||||||
CNTBNDHCalc = CNTPOT_BENDING
|
|
||||||
end function CNTBNDHCalc !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
integer(c_int) function CNTBNDHBCalc ( U, dUdC, C, R0, L0 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! Bending model of type 1: Harmonic bending potential with buckling.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double), intent(out) :: U, dUdC
|
|
||||||
real(c_double), intent(in) :: C, R0, L0
|
|
||||||
real(c_double) :: E1, E2, C2, Kbnd, Kbcl, Theta, DUbcl
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
E1 = 1.0d+00 - C
|
|
||||||
E2 = 1.0d+00 + C
|
|
||||||
! Calculate the square of curvature
|
|
||||||
C2 = 4.0d+00 * E2 / ( L0 * L0 * E1 )
|
|
||||||
! 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
|
|
||||||
Kbcl = CNTBNDB * Kbnd / 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
|
|
||||||
else ! 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 )
|
|
||||||
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
|
|
||||||
real(c_double) :: E1, E2, C2, Kbnd, Kbcl, Theta, DUbcl
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
E1 = 1.0d+00 - C
|
|
||||||
E2 = 1.0d+00 + C
|
|
||||||
! Calculate the square of curvature
|
|
||||||
C2 = 4.0d+00 * E2 / ( L0 * L0 * E1 )
|
|
||||||
! Check the condition for buckling
|
|
||||||
if ( C2 .ge. CNTBNDC2 ) then ! Buckling takes place
|
|
||||||
Theta= M_PI - acos ( C )
|
|
||||||
if ( Theta > CNTBNDTF ) then ! Fracture takes place
|
|
||||||
U = 0.0d+00
|
|
||||||
dUdC = 0.0d+00
|
|
||||||
CNTBNDHBFCalc = CNTPOT_BFRACTURE
|
|
||||||
else
|
|
||||||
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
|
|
||||||
U = Kbcl * abs ( Theta )**CNTBNDN - DUbcl
|
|
||||||
dUdC = Kbcl * CNTBNDN * abs ( Theta )**CNTBNDN1 / sqrt ( 1.0d+00 - C * C )
|
|
||||||
CNTBNDHBFCalc = CNTPOT_BBUCKLING
|
|
||||||
end if
|
|
||||||
else ! 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 )
|
|
||||||
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.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double), intent(out) :: U, dUdC, Ebuc
|
|
||||||
real(c_double), intent(in) :: C , R0, L0
|
|
||||||
integer(c_int), intent(in) :: BBF
|
|
||||||
real(c_double) :: E1, E2, C2, Kbnd, Kbcl,Theta,DUbcl, Ubcl, Cmin,Rmax
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Rmax = 340.0d+00
|
|
||||||
Cmin = 1.0/(Rmax*Rmax)
|
|
||||||
E1 = 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
|
|
||||||
Kbnd = 2.0d+00 * ( 63.8d+00 * R0**2.93d+00 ) / L0
|
|
||||||
U = Kbnd * E2 / 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
|
|
||||||
if ( BBF .eq. 0 ) then ! Not buckled yet. Continue 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 )
|
|
||||||
CNTBNDHBHCalc = CNTPOT_BENDING
|
|
||||||
Ebuc = 0.0d+00
|
|
||||||
else ! Already has been buckled or is buckled. Use buckling potential until Cmin.
|
|
||||||
Theta= M_PI - acos ( C )
|
|
||||||
Kbnd = 63.8d+00 * R0**2.93d+00
|
|
||||||
Kbcl = CNTBNDB * Kbnd / CNTBNDR
|
|
||||||
DUbcl= 2.0d+00*Kbnd * &
|
|
||||||
(1.0d+00+cos(l0/Rmax+M_PI))/(1.0d+00-cos(l0/Rmax+M_PI))/L0-Kbcl*abs(l0/Rmax)**CNTBNDN
|
|
||||||
U = Kbcl * abs( Theta )**CNTBNDN + DUbcl
|
|
||||||
dUdC = Kbcl * CNTBNDN * abs( Theta )**CNTBNDN1 / sqrt ( 1.0d+00 - C * C )
|
|
||||||
Ebuc = 0.0d+00
|
|
||||||
CNTBNDHBHCalc = CNTPOT_BBUCKLING
|
|
||||||
end if
|
|
||||||
else ! Greater than buckling critical point
|
|
||||||
if ( BBF .eq. 1 ) then ! Already buckled
|
|
||||||
Theta= M_PI - acos ( C )
|
|
||||||
Kbnd = 63.8d+00 * R0**2.93d+00
|
|
||||||
Kbcl = CNTBNDB * Kbnd / CNTBNDR
|
|
||||||
DUbcl= 2.0d+00*Kbnd * &
|
|
||||||
(1.0d+00+cos(l0/Rmax+M_PI))/(1.0d+00-cos(l0/Rmax+M_PI))/L0-Kbcl*abs(l0/Rmax)**CNTBNDN
|
|
||||||
U = Kbcl * abs( Theta )**CNTBNDN + DUbcl
|
|
||||||
dUdC = Kbcl * CNTBNDN * abs( Theta )**CNTBNDN1 / sqrt ( 1.0d+00 - C * C )
|
|
||||||
Ebuc = 0.0d00
|
|
||||||
CNTBNDHBHCalc = CNTPOT_BBUCKLING
|
|
||||||
else ! Newly buckled
|
|
||||||
Theta= M_PI - acos ( C )
|
|
||||||
Kbnd = 63.8d+00 * R0**2.93d+00
|
|
||||||
Kbcl = CNTBNDB * Kbnd / CNTBNDR
|
|
||||||
DUbcl= 2.0d+00*Kbnd * &
|
|
||||||
(1.0d+00+cos(l0/Rmax+M_PI))/(1.0d+00-cos(l0/Rmax+M_PI))/L0-Kbcl*abs(l0/Rmax)**CNTBNDN
|
|
||||||
U = Kbcl * abs( Theta )**CNTBNDN + DUbcl
|
|
||||||
dUdC = Kbcl * CNTBNDN * abs( Theta )**CNTBNDN1 / sqrt ( 1.0d+00 - C * C )
|
|
||||||
Ebuc = 2.0d+00*Kbnd * (1.0d+00+cos(l0/CNTBNDR+M_PI)) / (1.0d+00-cos(l0/CNTBNDR+M_PI))/L0 &
|
|
||||||
- Kbcl * abs ( l0 / CNTBNDR ) ** CNTBNDN - dUbcl
|
|
||||||
CNTBNDHBHCalc = CNTPOT_BBUCKLING
|
|
||||||
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
|
|
||||||
integer(c_int), intent(in) :: BBF
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Ebuc = 0.0d+00
|
|
||||||
select case ( CNTBNDModel )
|
|
||||||
case ( CNTBNDMODEL_H )
|
|
||||||
CNTBNDCalc = CNTBNDHCalc ( U, dUdC, C, R0, L0 )
|
|
||||||
case ( CNTBNDMODEL_HB )
|
|
||||||
CNTBNDCalc = CNTBNDHBCalc ( U, dUdC, C, R0, L0 )
|
|
||||||
case ( CNTBNDMODEL_HBF )
|
|
||||||
CNTBNDCalc = CNTBNDHBFCalc ( U, dUdC, C, R0, L0 )
|
|
||||||
case ( CNTBNDMODEL_HBH )
|
|
||||||
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
|
|
||||||
integer(c_int) :: i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
CNTBNDModel= BNDModel
|
|
||||||
CNTBNDN1 = CNTBNDN - 1.0d+00
|
|
||||||
CNTBNDC2 = 1.0d+00 / ( CNTBNDR * CNTBNDR )
|
|
||||||
end subroutine CNTBNDInit !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Module initialization
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
subroutine InitCNTPotModule ( STRModel, STRParams, YMType, BNDModel, Rref ) !!!!!!!!!!!!!!!!
|
|
||||||
integer(c_int), intent(in) :: STRModel, STRParams, YMType, BNDModel
|
|
||||||
real(c_double), intent(in) :: Rref
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
call CNTSTRInit ( STRModel, STRParams, YMType, Rref )
|
|
||||||
call CNTBNDInit ( BNDModel )
|
|
||||||
end subroutine InitCNTPotModule !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end module CNTPot !*********************************************************************************
|
|
||||||
@ -1,150 +0,0 @@
|
|||||||
! ------------ ----------------------------------------------------------
|
|
||||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
! https://www.lammps.org/ Sandia National Laboratories
|
|
||||||
! LAMMPS development team: developers@lammps.org
|
|
||||||
!
|
|
||||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
! certain rights in this software. This software is distributed under
|
|
||||||
! 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 !**********************************************************************************
|
|
||||||
|
|
||||||
use iso_c_binding
|
|
||||||
use CNTPot
|
|
||||||
use TPMLib
|
|
||||||
use TubePotMono
|
|
||||||
use TPMForceField
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
contains
|
|
||||||
|
|
||||||
subroutine InitCNTPotModule_(STRModel, STRParams, YMType, BNDModel, Rref) &
|
|
||||||
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
|
|
||||||
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
|
|
||||||
! Forces exerted on nodes X1 and X2
|
|
||||||
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
|
|
||||||
! Radius of a nanotube the segment (X1,X2) belongs to
|
|
||||||
real(c_double), intent(in) :: R12
|
|
||||||
! Equilibrium length of segment (X1,X2)
|
|
||||||
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
|
|
||||||
! Forces exerted on nodes X1, X2, and X3
|
|
||||||
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
|
|
||||||
! Radius of nanotube the segment (X1,X2) belongs to
|
|
||||||
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
|
|
||||||
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
|
|
||||||
! 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
|
|
||||||
! Forces exerted on nodes X1 and X2
|
|
||||||
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
|
|
||||||
! Force exerted on node Xe (can be updated only if Ee > 0)
|
|
||||||
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
|
|
||||||
! Contributions of nodes X to the virial stress tensor
|
|
||||||
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
|
|
||||||
! Radius of nanotube the segment (X1,X2) belongs to
|
|
||||||
real(c_double), intent(in) :: R12
|
|
||||||
! Coordinates of the nanotube nodes
|
|
||||||
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
|
|
||||||
! 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
|
|
||||||
! Parameter defining the type of the extended chain (0,1,2)
|
|
||||||
integer(c_int), intent(in) :: Ee
|
|
||||||
! Type of the tubular potential (0 or 1)
|
|
||||||
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
|
|
||||||
|
|
||||||
endmodule ExportCNT !*******************************************************************************
|
|
||||||
@ -1,97 +0,0 @@
|
|||||||
#!/usr/bin/env python
|
|
||||||
|
|
||||||
"""
|
|
||||||
Install.py tool to do a generic build of a library
|
|
||||||
soft linked to by many of the lib/Install.py files
|
|
||||||
used to automate the steps described in the corresponding lib/README
|
|
||||||
"""
|
|
||||||
|
|
||||||
from __future__ import print_function
|
|
||||||
import sys, os, subprocess
|
|
||||||
from argparse import ArgumentParser
|
|
||||||
|
|
||||||
sys.path.append('..')
|
|
||||||
from install_helpers import get_cpus, fullpath
|
|
||||||
|
|
||||||
parser = ArgumentParser(prog='Install.py',
|
|
||||||
description="LAMMPS library build wrapper script")
|
|
||||||
|
|
||||||
HELP = """
|
|
||||||
Syntax from src dir: make lib-libname args="-m machine -e suffix"
|
|
||||||
Syntax from lib dir: python Install.py -m machine -e suffix
|
|
||||||
|
|
||||||
libname = name of lib dir (e.g. atc, h5md, meam, poems, etc)
|
|
||||||
specify -m and optionally -e, order does not matter
|
|
||||||
|
|
||||||
Examples:
|
|
||||||
|
|
||||||
make lib-poems args="-m serial" # build POEMS lib with same settings as in the serial Makefile in src
|
|
||||||
make lib-colvars args="-m mpi" # build COLVARS lib with same settings as in the mpi Makefile in src
|
|
||||||
make lib-meam args="-m ifort" # build MEAM lib with custom Makefile.ifort (using Intel Fortran)
|
|
||||||
"""
|
|
||||||
|
|
||||||
# parse and process arguments
|
|
||||||
|
|
||||||
parser.add_argument("-m", "--machine",
|
|
||||||
help="suffix of a <libname>/Makefile.* file used for compiling this library")
|
|
||||||
parser.add_argument("-e", "--extramake",
|
|
||||||
help="set EXTRAMAKE variable in <libname>/Makefile.<machine> to Makefile.lammps.<extramake>")
|
|
||||||
|
|
||||||
args = parser.parse_args()
|
|
||||||
|
|
||||||
# print help message and exit, if neither build nor path options are given
|
|
||||||
if not args.machine and not args.extramake:
|
|
||||||
parser.print_help()
|
|
||||||
sys.exit(HELP)
|
|
||||||
|
|
||||||
machine = args.machine
|
|
||||||
extraflag = args.extramake
|
|
||||||
if extraflag:
|
|
||||||
suffix = args.extramake
|
|
||||||
else:
|
|
||||||
suffix = 'empty'
|
|
||||||
|
|
||||||
# set lib from working dir
|
|
||||||
|
|
||||||
cwd = fullpath('.')
|
|
||||||
lib = os.path.basename(cwd)
|
|
||||||
|
|
||||||
# create Makefile.auto as copy of Makefile.machine
|
|
||||||
# reset EXTRAMAKE if requested
|
|
||||||
|
|
||||||
if not os.path.exists("Makefile.%s" % machine):
|
|
||||||
sys.exit("lib/%s/Makefile.%s does not exist" % (lib, machine))
|
|
||||||
|
|
||||||
lines = open("Makefile.%s" % machine, 'r').readlines()
|
|
||||||
fp = open("Makefile.auto", 'w')
|
|
||||||
|
|
||||||
has_extramake = False
|
|
||||||
for line in lines:
|
|
||||||
words = line.split()
|
|
||||||
if len(words) == 3 and words[0] == "EXTRAMAKE" and words[1] == '=':
|
|
||||||
has_extramake = True
|
|
||||||
if extraflag:
|
|
||||||
line = line.replace(words[2], "Makefile.lammps.%s" % suffix)
|
|
||||||
fp.write(line)
|
|
||||||
|
|
||||||
fp.close()
|
|
||||||
|
|
||||||
# make the library via Makefile.auto optionally with parallel make
|
|
||||||
n_cpus = get_cpus()
|
|
||||||
|
|
||||||
print("Building lib%s.a ..." % lib)
|
|
||||||
cmd = "make -f Makefile.auto clean; make -f Makefile.auto -j%d" % n_cpus
|
|
||||||
try:
|
|
||||||
txt = subprocess.check_output(cmd, shell=True, stderr=subprocess.STDOUT)
|
|
||||||
print(txt.decode('UTF-8'))
|
|
||||||
except subprocess.CalledProcessError as e:
|
|
||||||
print("Make failed with:\n %s" % e.output.decode('UTF-8'))
|
|
||||||
sys.exit(1)
|
|
||||||
|
|
||||||
if os.path.exists("lib%s.a" % lib):
|
|
||||||
print("Build was successful")
|
|
||||||
else:
|
|
||||||
sys.exit("Build of lib/%s/lib%s.a was NOT successful" % (lib, lib))
|
|
||||||
|
|
||||||
if has_extramake and not os.path.exists("Makefile.lammps"):
|
|
||||||
print("WARNING: lib/%s/Makefile.lammps was NOT created" % lib)
|
|
||||||
@ -1,113 +0,0 @@
|
|||||||
! ------------ ----------------------------------------------------------
|
|
||||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
! https://www.lammps.org/ Sandia National Laboratories
|
|
||||||
! LAMMPS development team: developers@lammps.org
|
|
||||||
!
|
|
||||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
! certain rights in this software. This software is distributed under
|
|
||||||
! 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 !************************************************************************************
|
|
||||||
!
|
|
||||||
! Bi-linear functions and their derivatives.
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 09.01, 2017
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
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 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
integer(c_int), intent(in) :: i, N
|
|
||||||
real(c_double), intent(in) :: X
|
|
||||||
real(c_double), dimension(0:N-1), intent(in) :: P
|
|
||||||
real(c_double), dimension(0:N-1), intent(inout) :: F
|
|
||||||
integer(c_int) :: i1
|
|
||||||
real(c_double) :: A, A0
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
i1 = i - 1
|
|
||||||
A0 = ( P(i) - X ) / ( P(i) - P(i1) )
|
|
||||||
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
|
|
||||||
real(c_double), intent(in) :: X
|
|
||||||
real(c_double), dimension(0:N-1), intent(in) :: P
|
|
||||||
real(c_double), dimension(0:N-1), intent(inout) :: F, Fx
|
|
||||||
integer(c_int) :: i1
|
|
||||||
real(c_double) :: A, A0
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
i1 = i - 1
|
|
||||||
A0 = ( P(i) - X ) / ( P(i) - P(i1) )
|
|
||||||
A = 1.0d+00 - A0
|
|
||||||
S = A0 * F(i1) + A * F(i)
|
|
||||||
Sx1 = A0 * Fx(i1) + A * Fx(i)
|
|
||||||
end subroutine CalcLinFun1_1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
real(c_double) function CalcLinFun2_0 ( i, j, X, Y, N1, N2, P1, P2, F ) !!
|
|
||||||
integer(c_int), intent(in) :: i, j, N1, N2
|
|
||||||
real(c_double), intent(in) :: X, Y
|
|
||||||
real(c_double), dimension(0:N1-1), intent(in) :: P1
|
|
||||||
real(c_double), dimension(0:N2-1), intent(in) :: P2
|
|
||||||
real(c_double), dimension(0:N1-1,0:N2-1), intent(inout) :: F
|
|
||||||
integer(c_int) :: i1, j1
|
|
||||||
real(c_double) :: A, A0, B, B0, G, G0
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
i1 = i - 1
|
|
||||||
j1 = j - 1
|
|
||||||
A0 = ( P1(i) - X ) / ( P1(i) - P1(i1) )
|
|
||||||
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)
|
|
||||||
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
|
|
||||||
real(c_double), intent(in) :: X, Y
|
|
||||||
real(c_double), dimension(0:N1-1), intent(in) :: P1
|
|
||||||
real(c_double), dimension(0:N2-1), intent(in) :: P2
|
|
||||||
real(c_double), dimension(0:N1-1,0:N2-1), intent(inout) :: F, Fx, Fy
|
|
||||||
integer(c_int) :: i1, j1
|
|
||||||
real(c_double) :: A, A0, B, B0, G, G0
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
i1 = i - 1
|
|
||||||
j1 = j - 1
|
|
||||||
A0 = ( P1(i) - X ) / ( P1(i) - P1(i1) )
|
|
||||||
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 !********************************************************************************
|
|
||||||
@ -1,46 +0,0 @@
|
|||||||
SHELL = /bin/sh
|
|
||||||
|
|
||||||
# which file will be copied to Makefile.lammps
|
|
||||||
|
|
||||||
EXTRAMAKE = Makefile.lammps.gfortran
|
|
||||||
|
|
||||||
# ------ FILES ------
|
|
||||||
|
|
||||||
SRC = LinFun2.f90 Spline1.f90 Spline2.f90 TPMLib.f90 TPMGeom.f90 TubePotBase.f90 TubePotTrue.f90 \
|
|
||||||
TubePotMono.f90 TPMM0.f90 TPMM1.f90 CNTPot.f90 TPMForceField.f90 ExportCNT.f90
|
|
||||||
|
|
||||||
FILES = $(SRC) Makefile
|
|
||||||
|
|
||||||
# ------ DEFINITIONS ------
|
|
||||||
|
|
||||||
LIB = libmesont.a
|
|
||||||
OBJ = $(SRC:.f90=.o)
|
|
||||||
|
|
||||||
# ------ SETTINGS ------
|
|
||||||
|
|
||||||
F90 = gfortran
|
|
||||||
F90FLAGS = -O3 -fPIC -ftree-vectorize -g
|
|
||||||
ARCHIVE = ar
|
|
||||||
ARCHFLAG = -rc
|
|
||||||
USRLIB =
|
|
||||||
SYSLIB =
|
|
||||||
|
|
||||||
# ------ MAKE PROCEDURE ------
|
|
||||||
|
|
||||||
lib: $(OBJ)
|
|
||||||
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
|
|
||||||
@cp $(EXTRAMAKE) Makefile.lammps
|
|
||||||
|
|
||||||
# ------ COMPILE RULES ------
|
|
||||||
|
|
||||||
%.o:%.f90
|
|
||||||
$(F90) $(F90FLAGS) -c $<
|
|
||||||
|
|
||||||
include .depend
|
|
||||||
# ------ CLEAN ------
|
|
||||||
|
|
||||||
clean:
|
|
||||||
-rm *.o *.mod $(LIB)
|
|
||||||
|
|
||||||
tar:
|
|
||||||
-tar -cvf ../MESONT.tar $(FILES)
|
|
||||||
@ -1,46 +0,0 @@
|
|||||||
SHELL = /bin/sh
|
|
||||||
|
|
||||||
# which file will be copied to Makefile.lammps
|
|
||||||
|
|
||||||
EXTRAMAKE = Makefile.lammps.ifort
|
|
||||||
|
|
||||||
# ------ FILES ------
|
|
||||||
|
|
||||||
SRC = LinFun2.f90 Spline1.f90 Spline2.f90 TPMLib.f90 TPMGeom.f90 TubePotBase.f90 TubePotTrue.f90 \
|
|
||||||
TubePotMono.f90 TPMM0.f90 TPMM1.f90 CNTPot.f90 TPMForceField.f90 ExportCNT.f90
|
|
||||||
|
|
||||||
FILES = $(SRC) Makefile
|
|
||||||
|
|
||||||
# ------ DEFINITIONS ------
|
|
||||||
|
|
||||||
LIB = libmesont.a
|
|
||||||
OBJ = $(SRC:.f90=.o)
|
|
||||||
|
|
||||||
# ------ SETTINGS ------
|
|
||||||
|
|
||||||
F90 = ifort
|
|
||||||
F90FLAGS = -O3 -fPIC -g
|
|
||||||
ARCHIVE = ar
|
|
||||||
ARCHFLAG = -rc
|
|
||||||
USRLIB =
|
|
||||||
SYSLIB =
|
|
||||||
|
|
||||||
# ------ MAKE PROCEDURE ------
|
|
||||||
|
|
||||||
lib: $(OBJ)
|
|
||||||
$(ARCHIVE) $(ARFLAGS) $(LIB) $(OBJ)
|
|
||||||
@cp $(EXTRAMAKE) Makefile.lammps
|
|
||||||
|
|
||||||
# ------ COMPILE RULES ------
|
|
||||||
|
|
||||||
%.o:%.f90
|
|
||||||
$(F90) $(F90FLAGS) -c $<
|
|
||||||
|
|
||||||
include .depend
|
|
||||||
# ------ CLEAN ------
|
|
||||||
|
|
||||||
clean:
|
|
||||||
-rm *.o *.mod $(LIB)
|
|
||||||
|
|
||||||
tar:
|
|
||||||
-tar -cvf ../MESONT.tar $(FILES)
|
|
||||||
@ -1,5 +0,0 @@
|
|||||||
# Settings that the LAMMPS build will import when this package library is used
|
|
||||||
|
|
||||||
mesont_SYSINC =
|
|
||||||
mesont_SYSLIB = -lgfortran
|
|
||||||
mesont_SYSPATH =
|
|
||||||
@ -1,5 +0,0 @@
|
|||||||
# Settings that the LAMMPS build will import when this package library is used
|
|
||||||
|
|
||||||
mesont_SYSINC =
|
|
||||||
mesont_SYSLIB = -lifcore -lsvml -limf -ldl -lstdc++
|
|
||||||
mesont_SYSPATH =
|
|
||||||
@ -1 +0,0 @@
|
|||||||
Makefile.gfortran
|
|
||||||
@ -1,67 +0,0 @@
|
|||||||
MESONT is a LAMMPS package for simulation of nanomechanics of carbon
|
|
||||||
nanotubes (CNTs). The model is based on a coarse-grained representation
|
|
||||||
of CNTs as "flexible cylinders" consisting of a variable number of
|
|
||||||
segments. Internal interactions within a CNT and the van der Waals
|
|
||||||
interaction between the tubes are described by a mesoscopic force
|
|
||||||
field designed and parameterized based on the results of atomic-level
|
|
||||||
molecular dynamics simulations. The description of the force field
|
|
||||||
is provided in the papers listed below.
|
|
||||||
|
|
||||||
This folder contains a Fortran library implementing basic level functions
|
|
||||||
describing stretching, bending, and intertube components of the CNT tubular
|
|
||||||
potential model (TPM) mesoscopic force field.
|
|
||||||
|
|
||||||
This library was created by Alexey N. Volkov, University of Alabama,
|
|
||||||
avolkov1@ua.edu.
|
|
||||||
|
|
||||||
--
|
|
||||||
|
|
||||||
References:
|
|
||||||
|
|
||||||
L. V. Zhigilei, C. Wei, and D. Srivastava, Mesoscopic model for dynamic
|
|
||||||
simulations of carbon nanotubes, Phys. Rev. B 71, 165417, 2005.
|
|
||||||
|
|
||||||
A. N. Volkov and L. V. Zhigilei, Structural stability of carbon nanotube
|
|
||||||
films: The role of bending buckling, ACS Nano 4, 6187-6195, 2010.
|
|
||||||
|
|
||||||
A. N. Volkov, K. R. Simov, and L. V. Zhigilei, Mesoscopic model for simulation
|
|
||||||
of CNT-based materials, Proceedings of the ASME International Mechanical
|
|
||||||
Engineering Congress and Exposition (IMECE2008), ASME paper IMECE2008-68021,
|
|
||||||
2008.
|
|
||||||
|
|
||||||
A. N. Volkov and L. V. Zhigilei, Mesoscopic interaction potential for carbon
|
|
||||||
nanotubes of arbitrary length and orientation, J. Phys. Chem. C 114, 5513-5531,
|
|
||||||
2010.
|
|
||||||
|
|
||||||
B. K. Wittmaack, A. H. Banna, A. N. Volkov, L. V. Zhigilei, Mesoscopic
|
|
||||||
modeling of structural self-organization of carbon nanotubes into vertically
|
|
||||||
aligned networks of nanotube bundles, Carbon 130, 69-86, 2018.
|
|
||||||
|
|
||||||
B. K. Wittmaack, A. N. Volkov, L. V. Zhigilei, Mesoscopic modeling of the
|
|
||||||
uniaxial compression and recovery of vertically aligned carbon nanotube
|
|
||||||
forests, Compos. Sci. Technol. 166, 66-85, 2018.
|
|
||||||
|
|
||||||
B. K. Wittmaack, A. N. Volkov, L. V. Zhigilei, Phase transformation as the
|
|
||||||
mechanism of mechanical deformation of vertically aligned carbon nanotube
|
|
||||||
arrays: Insights from mesoscopic modeling, Carbon 143, 587-597, 2019.
|
|
||||||
|
|
||||||
A. N. Volkov and L. V. Zhigilei, Scaling laws and mesoscopic modeling of
|
|
||||||
thermal conductivity in carbon nanotube materials, Phys. Rev. Lett. 104,
|
|
||||||
215902, 2010.
|
|
||||||
|
|
||||||
A. N. Volkov, T. Shiga, D. Nicholson, J. Shiomi, and L. V. Zhigilei, Effect
|
|
||||||
of bending buckling of carbon nanotubes on thermal conductivity of carbon
|
|
||||||
nanotube materials, J. Appl. Phys. 111, 053501, 2012.
|
|
||||||
|
|
||||||
A. N. Volkov and L. V. Zhigilei, Heat conduction in carbon nanotube materials:
|
|
||||||
Strong effect of intrinsic thermal conductivity of carbon nanotubes, Appl.
|
|
||||||
Phys. Lett. 101, 043113, 2012.
|
|
||||||
|
|
||||||
W. M. Jacobs, D. A. Nicholson, H. Zemer, A. N. Volkov, and L. V. Zhigilei,
|
|
||||||
Acoustic energy dissipation and thermalization in carbon nanotubes: Atomistic
|
|
||||||
modeling and mesoscopic description, Phys. Rev. B 86, 165414, 2012.
|
|
||||||
|
|
||||||
A. N. Volkov and A. H. Banna, Mesoscopic computational model of covalent
|
|
||||||
cross-links and mechanisms of load transfer in cross-linked carbon nanotube
|
|
||||||
films with continuous networks of bundles, Comp. Mater. Sci. 176, 109410, 2020.
|
|
||||||
|
|
||||||
@ -1,191 +0,0 @@
|
|||||||
! ------------ ----------------------------------------------------------
|
|
||||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
! https://www.lammps.org/ Sandia National Laboratories
|
|
||||||
! LAMMPS development team: developers@lammps.org
|
|
||||||
!
|
|
||||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
! certain rights in this software. This software is distributed under
|
|
||||||
! 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 !************************************************************************************
|
|
||||||
!
|
|
||||||
! One-dimensional cubic spline function.
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 09.01, 2017
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
use iso_c_binding, only : c_int, c_double, c_char
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
contains !******************************************************************************************
|
|
||||||
|
|
||||||
real(c_double) function ValueSpline1_0 ( X, Xi, Xi_1, Yi, Yi_1, Mi, Mi_1, Hi_1 ) !!!!!!!!!!!!
|
|
||||||
real(c_double), intent(in) :: X, Xi, Xi_1, Yi, Yi_1, Mi, Mi_1, Hi_1
|
|
||||||
real(c_double) :: H26, HL, HR
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
H26 = Hi_1 * Hi_1 / 6.0
|
|
||||||
Hl = X - Xi_1
|
|
||||||
Hr = Xi - X
|
|
||||||
ValueSpline1_0 = ( ( Mi_1 * Hr * Hr * Hr + Mi * Hl * Hl * Hl ) / 6.0 + ( Yi_1 - Mi_1 * H26 ) * Hr &
|
|
||||||
+ ( Yi - Mi * H26 ) * Hl ) / Hi_1
|
|
||||||
end function ValueSpline1_0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine ValueSpline1_1 ( S, S1, X, Xi, Xi_1, Yi, Yi_1, Mi, Mi_1, Hi_1 ) !!!!!!!!!!!!!!!!!
|
|
||||||
real(c_double), intent(out) :: S, S1
|
|
||||||
real(c_double), intent(in) :: X, Xi, Xi_1, Yi, Yi_1, Mi, Mi_1, Hi_1
|
|
||||||
real(c_double) :: H6, H26, HL, HR, HL2, HR2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
H6 = Hi_1 / 6.0d+00
|
|
||||||
H26 = Hi_1 * H6
|
|
||||||
HL = X - Xi_1
|
|
||||||
HR = Xi - X
|
|
||||||
HL2 = HL * HL
|
|
||||||
HR2 = HR * HR
|
|
||||||
S = ( ( Mi_1 * HR2 * Hr + Mi * HL2 * Hl ) / 6.0 + ( Yi_1 - Mi_1 * H26 ) * HR + ( Yi - Mi * H26 ) * HL ) / Hi_1
|
|
||||||
S1 = ( ( Mi * HL2 - Mi_1 * HR2 ) / 2.0d+00 + Yi - Yi_1 ) / Hi_1 - H6 * ( Mi - Mi_1 )
|
|
||||||
end subroutine ValueSpline1_1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine sprogonka3 ( N, K0, K1, K2, F, X ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
integer(c_int), intent(in) :: N
|
|
||||||
real(c_double), dimension(0:N-1), intent(in) :: K0, K1, K2
|
|
||||||
real(c_double), dimension(0:N-1), intent(inout) :: F, X
|
|
||||||
real(c_double) :: D
|
|
||||||
integer(c_int) :: i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
X(0) = F(0) / K1(0)
|
|
||||||
F(0) = - K2(0) / K1(0)
|
|
||||||
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
|
|
||||||
end do
|
|
||||||
do i = N - 2, 0, -1
|
|
||||||
X(i) = X(i) + F(i) * X(i+1)
|
|
||||||
end do
|
|
||||||
end subroutine sprogonka3 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine CreateSpline1 ( CL, CR, N, P, F, M, D, K0, K1, K2 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
integer(c_int), intent(in) :: CL, CR, N
|
|
||||||
real(c_double), dimension (0:N-1), intent(in) :: P, F
|
|
||||||
real(c_double), dimension (0:N-1), intent(inout):: M, D, K0, K1, K2
|
|
||||||
integer(c_int) :: i
|
|
||||||
real(c_double) :: Z
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
do i = 1, N - 1
|
|
||||||
K0(i) = P(i) - P(i-1)
|
|
||||||
K1(i) = ( F(i) - F(i-1) ) / K0(i)
|
|
||||||
end do
|
|
||||||
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)
|
|
||||||
case (2)
|
|
||||||
K1(0) = 1.0d+00
|
|
||||||
K2(0) = 0.0d+00
|
|
||||||
D(0) = M(0)
|
|
||||||
case (3)
|
|
||||||
K1(0) = 1.0d+00
|
|
||||||
K2(0) = 0.0d+00
|
|
||||||
D(0) = 0.0d+00
|
|
||||||
end select
|
|
||||||
Z = K1(N-1)
|
|
||||||
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 )
|
|
||||||
case (1)
|
|
||||||
D(N-1) = 2.0d+00 * ( M(N-1) - Z ) / K0(N-1)
|
|
||||||
K1(N-1) = 2.0d+00 / 3.0d+00
|
|
||||||
K0(N-1) = 1.0d+00 / 3.0d+00
|
|
||||||
case (2)
|
|
||||||
K1(N-1) = 1.0d+00
|
|
||||||
K0(N-1) = 0.0d+00
|
|
||||||
D(N-1) = M(N-1)
|
|
||||||
case (3)
|
|
||||||
K1(N-1) = 1.0d+00
|
|
||||||
K0(N-1) = 0.0d+00
|
|
||||||
D(N-1) = 0.0d+00
|
|
||||||
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
|
|
||||||
integer(c_int) :: j
|
|
||||||
real(c_double) :: HL, HR, H, H6, H26, HR2, HL2, HRH, HLH
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
j = i - 1
|
|
||||||
HL = X - P(j)
|
|
||||||
HR = P(i) - X
|
|
||||||
H = P(i) - P(j)
|
|
||||||
H6 = H / 6.0d+00
|
|
||||||
H26 = H * H6
|
|
||||||
HL2 = HL * HL
|
|
||||||
HR2 = HR * HR
|
|
||||||
HLH = HL / H
|
|
||||||
HRH = HR / H
|
|
||||||
CalcSpline1_0 = ( M(j) * HR2 * HRH + M(i) * HL2 * HLH ) / 6.0d+00 + ( F(j) - M(j) * H26 ) * HRH &
|
|
||||||
+ ( F(i) - M(i) * H26 ) * HLH
|
|
||||||
end function CalcSpline1_0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine CalcSpline1_1 ( S, S1, i, X, N, P, F, M ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
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
|
|
||||||
integer(c_int) :: j
|
|
||||||
real(c_double) :: HL, HR, H, H6, H26, HR2, HL2, HRH, HLH
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
j = i - 1
|
|
||||||
HL = X - P(j)
|
|
||||||
HR = P(i) - X
|
|
||||||
H = P(i) - P(j)
|
|
||||||
H6 = H / 6.0d+00
|
|
||||||
H26 = H * H6
|
|
||||||
HL2 = HL * HL
|
|
||||||
HR2 = HR * HR
|
|
||||||
HLH = HL / H
|
|
||||||
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) )
|
|
||||||
end subroutine CalcSpline1_1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine CalcSpline1_2 ( S, S1, S2, i, X, N, P, F, M ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
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
|
|
||||||
integer(c_int) :: j
|
|
||||||
real(c_double) :: HL, HR, H, H6, H26, HR2, HL2, HRH, HLH
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
j = i - 1
|
|
||||||
HL = X - P(j)
|
|
||||||
HR = P(i) - X
|
|
||||||
H = P(i) - P(j)
|
|
||||||
H6 = H / 6.0d+00
|
|
||||||
H26 = H * H6
|
|
||||||
HL2 = HL * HL
|
|
||||||
HR2 = HR * HR
|
|
||||||
HLH = HL / H
|
|
||||||
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
|
|
||||||
end subroutine CalcSpline1_2 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end module Spline1 !********************************************************************************
|
|
||||||
@ -1,186 +0,0 @@
|
|||||||
! ------------ ----------------------------------------------------------
|
|
||||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
! https://www.lammps.org/ Sandia National Laboratories
|
|
||||||
! LAMMPS development team: developers@lammps.org
|
|
||||||
!
|
|
||||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
! certain rights in this software. This software is distributed under
|
|
||||||
! 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 !************************************************************************************
|
|
||||||
!
|
|
||||||
! Two-dimensional cubic spline function.
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 09.01, 2017
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
|
|
||||||
use Spline1
|
|
||||||
use iso_c_binding, only : c_int, c_double, c_char
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
contains !******************************************************************************************
|
|
||||||
|
|
||||||
subroutine CreateSpline2 ( CL, CD, CR, CU, N1, N2, N, P1, P2, F, Fxx, Fyy, Fxxyy, FF, MM, DD, K0, K1, K2 )
|
|
||||||
integer(c_int), intent(in) :: CL, CD, CR, CU, N1, N2, N
|
|
||||||
real(c_double), dimension(0:N1-1), intent(in) :: P1
|
|
||||||
real(c_double), dimension(0:N2-1), intent(in) :: P2
|
|
||||||
real(c_double), dimension(0:N1-1,0:N2-1), intent(inout) :: F, Fxx, Fyy, Fxxyy
|
|
||||||
real(c_double), dimension(0:N-1), intent(inout) :: FF, MM, DD, K0, K1, K2
|
|
||||||
integer(c_int) :: II
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
do II = 0, N2 - 1
|
|
||||||
FF(0:N1-1) = F(0:N1-1,II)
|
|
||||||
MM(0) = Fxx(0,II)
|
|
||||||
MM(N1-1) = Fxx(N1-1,II)
|
|
||||||
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 = 0, N1 - 1
|
|
||||||
MM(0) = Fyy(II,0)
|
|
||||||
MM(N-1) = Fyy(II,N2-1)
|
|
||||||
FF(0:N2-1) = F(II,0:N2-1)
|
|
||||||
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:N1-1) = Fyy(0:N1-1,N2-1 )
|
|
||||||
call CreateSpline1 ( 3, 3, N1, P1, FF, MM, DD, K0, K1, k2 )
|
|
||||||
Fxxyy(0:N1-1,N2-1) = MM(0:N1-1)
|
|
||||||
do II = 1, N1 - 2
|
|
||||||
MM(0) = Fxxyy(II,0)
|
|
||||||
MM(N-1) = Fxxyy(II,N2-1)
|
|
||||||
FF(0:N2-1) = Fxx(II,0:N2-1)
|
|
||||||
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 CreateSpline2 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine CreateSpline2Ext ( CL, CD, CR, CU, N1, N1A, N2, N2A, N, P1, P2, F, Fxx, Fyy, Fxxyy, FF, MM, DD, K0, K1, K2 )
|
|
||||||
integer(c_int), intent(in) :: CL, CD, CR, CU, N1, N1A, N2, N2A, N
|
|
||||||
real(c_double), dimension(0:N1-1), intent(in) :: P1
|
|
||||||
real(c_double), dimension(0:N2-1), intent(in) :: P2
|
|
||||||
real(c_double), dimension(0:N1-1,0:N2-1), intent(inout) :: F, Fxx, Fyy, Fxxyy
|
|
||||||
real(c_double), dimension(0:N-1), intent(inout) :: FF, MM, DD, K0, K1, K2
|
|
||||||
integer(c_int) :: II
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
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)
|
|
||||||
MM(N1-1) = Fxx(N1-1,II)
|
|
||||||
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)
|
|
||||||
MM(N1-N1A-1) = Fxx(N1-1,II)
|
|
||||||
call CreateSpline1 ( CL, CR, N1 - N1A, P1, FF, MM, DD, K0, K1, K2 )
|
|
||||||
Fxx(N1A:N1-1,II) = MM(0:N1-N1A-1)
|
|
||||||
end do
|
|
||||||
|
|
||||||
do II = 0, N1A - 1
|
|
||||||
MM(0) = Fyy(II,0)
|
|
||||||
MM(N2A) = Fyy(II,N2A)
|
|
||||||
FF(0:N2A) = F(II,0:N2A)
|
|
||||||
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)
|
|
||||||
FF(0:N2-1) = F(II,0:N2-1)
|
|
||||||
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)
|
|
||||||
FF(0:N2A) = Fxx(II,0:N2A)
|
|
||||||
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)
|
|
||||||
FF(0:N2-1) = Fxx(II,0:N2-1)
|
|
||||||
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
|
|
||||||
real(c_double), dimension(0:N1-1), intent(in) :: P1
|
|
||||||
real(c_double), dimension(0:N2-1), intent(in) :: P2
|
|
||||||
real(c_double), dimension(0:N1-1,0:N2-1), intent(inout) :: F, Fxx, Fyy, Fxxyy
|
|
||||||
integer(c_int) :: i1, j1
|
|
||||||
real(c_double) :: T, Gy_0, Gy_1, Gxxy_0, Gxxy_1
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
i1 = i - 1
|
|
||||||
j1 = j - 1
|
|
||||||
T = P2(j) - P2(j1)
|
|
||||||
Gy_0 = ValueSpline1_0 ( Y, P2(j), P2(j1), F(i,j), F(i,j1), Fyy(i,j), Fyy(i,j1), T )
|
|
||||||
Gy_1 = ValueSpline1_0 ( Y, P2(j), P2(j1), F(i1,j), F(i1,j1), Fyy(i1,j), Fyy(i1,j1), T )
|
|
||||||
Gxxy_0 = ValueSpline1_0 ( Y, P2(j), P2(j1), Fxx(i,j), Fxx(i,j1), Fxxyy(i,j), Fxxyy(i,j1), T )
|
|
||||||
Gxxy_1 = ValueSpline1_0 ( Y, P2(j), P2(j1), Fxx(i1,j), Fxx(i1,j1), Fxxyy(i1,j), Fxxyy(i1,j1), T )
|
|
||||||
CalcSpline2_0 = ValueSpline1_0 ( X, P1(i), P1(i1), Gy_0, Gy_1,Gxxy_0, Gxxy_1, P1(i) - P1(i1) )
|
|
||||||
end function CalcSpline2_0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine CalcSpline2_1 ( S, Sx1, Sy1, i, j, X, Y, N1, N2, P1, P2, F, Fxx, Fyy, Fxxyy ) !!!
|
|
||||||
real(c_double), intent(out) :: S, Sx1, Sy1
|
|
||||||
integer(c_int), intent(in) :: i, j, N1, N2
|
|
||||||
real(c_double), intent(in) :: X, Y
|
|
||||||
real(c_double), dimension(0:N1-1), intent(in) :: P1
|
|
||||||
real(c_double), dimension(0:N2-1), intent(in) :: P2
|
|
||||||
real(c_double), dimension(0:N1-1,0:N2-1), intent(inout) :: F, Fxx, Fyy, Fxxyy
|
|
||||||
integer(c_int) :: i1, j1
|
|
||||||
real(c_double) :: T, Gy_0, Gy_1, Gxxy_0, Gxxy_1
|
|
||||||
real(c_double) :: Gyy_0, Gyy_1, Gxxyy_0, Gxxyy_1
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
i1 = i - 1
|
|
||||||
j1 = j - 1
|
|
||||||
T = P2(j) - P2(j1)
|
|
||||||
call ValueSpline1_1 ( Gy_0, Gyy_0, Y, P2(j), P2(j1), F(i,j), F(i,j1), Fyy(i,j), Fyy(i,j1), T )
|
|
||||||
call ValueSpline1_1 ( Gy_1, Gyy_1, Y, P2(j), P2(j1), F(i1,j), F(i1,j1), Fyy(i1,j), Fyy(i1,j1), T )
|
|
||||||
call ValueSpline1_1 ( Gxxy_0, Gxxyy_0, Y, P2(j), P2(j1), Fxx(i,j), Fxx(i,j1), Fxxyy(i,j), Fxxyy(i,j1), T )
|
|
||||||
call ValueSpline1_1 ( Gxxy_1, Gxxyy_1, Y, P2(j), P2(j1), Fxx(i1,j), Fxx(i1,j1), Fxxyy(i1,j), Fxxyy(i1,j1), T )
|
|
||||||
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 !********************************************************************************
|
|
||||||
@ -1,316 +0,0 @@
|
|||||||
! ------------ ----------------------------------------------------------
|
|
||||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
! https://www.lammps.org/ Sandia National Laboratories
|
|
||||||
! LAMMPS development team: developers@lammps.org
|
|
||||||
!
|
|
||||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
! certain rights in this software. This software is distributed under
|
|
||||||
! 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 !******************************************************************************
|
|
||||||
!
|
|
||||||
! Calculation of the TMD force field
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! PGI Fortran, Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, version 09.01, 2020
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
|
|
||||||
use CNTPot
|
|
||||||
use TPMM0
|
|
||||||
use TPMM1
|
|
||||||
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
|
|
||||||
! Forces exerted on nodes X1 and X2
|
|
||||||
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
|
|
||||||
! Radius of a nanotube the segment (X1,X2) belongs to
|
|
||||||
real(c_double), intent(in) :: R12
|
|
||||||
! Equilibrium length of segment (X1,X2)
|
|
||||||
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
|
|
||||||
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
|
|
||||||
|
|
||||||
F2 = F2 - FF
|
|
||||||
U2 = U2 + U
|
|
||||||
|
|
||||||
! Stress
|
|
||||||
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
|
|
||||||
end do
|
|
||||||
end do
|
|
||||||
end subroutine TubeStretchingForceField !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
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
|
|
||||||
! Forces exerted on nodes X1, X2, and X3
|
|
||||||
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
|
|
||||||
! Radius of nanotube the segment (X1,X2) belongs to
|
|
||||||
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
|
|
||||||
integer(c_int), intent(inout) :: BBF2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer(c_int) :: ii, jj, Event
|
|
||||||
real(c_double) :: U, F, K, S, Ubcl
|
|
||||||
real(c_double), dimension(0:2) :: G0, G1, G2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
call BendingGradients ( K, G0, G1, G2, X1, X2, X3 )
|
|
||||||
Event = CNTBNDCalc ( U, F, K, R123, L123, BBF2, Ubcl )
|
|
||||||
|
|
||||||
if ( Event == CNTPOT_BBUCKLING ) then
|
|
||||||
BBF2 = 1
|
|
||||||
else
|
|
||||||
BBF2 = 0
|
|
||||||
end if
|
|
||||||
|
|
||||||
U = U / 4.0d+00
|
|
||||||
F = - F
|
|
||||||
|
|
||||||
F1 = F1 + G0 * F
|
|
||||||
F2 = F2 + G1 * F
|
|
||||||
F3 = F3 + G2 * F
|
|
||||||
|
|
||||||
U1 = U1 + U
|
|
||||||
U2 = U2 + 2.0d+00 * U
|
|
||||||
U3 = U3 + U
|
|
||||||
|
|
||||||
! Stress
|
|
||||||
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
|
|
||||||
S = 0.5d+00 * ( X3(ii) - X2(ii) ) * G2(jj)
|
|
||||||
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
|
|
||||||
! (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.
|
|
||||||
|
|
||||||
! It is assumed that X contains ALL nodes of a single CNT that are included into the
|
|
||||||
! 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
|
|
||||||
! that do not belong to a nanotube.
|
|
||||||
|
|
||||||
! Concept of the extended chain:
|
|
||||||
! Let's consider a sequence of nodes (X1,X2,...,XN) forming continuous part of a nanotube.
|
|
||||||
! If node Xe precedes X1 and Xe is the nanotube end, then the extended chain is (Xe,X1,...,XN) and Ee = 1.
|
|
||||||
! 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 )
|
|
||||||
! 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
|
|
||||||
! Interaction energies associated with nodes X
|
|
||||||
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
|
|
||||||
! Forces exerted on nodes X
|
|
||||||
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
|
|
||||||
! Contributions of nodes X1 and X2 to the virial stress tensor
|
|
||||||
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
|
|
||||||
! 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
|
|
||||||
! Radius of a nanotube the segment (X1,X2) belongs to
|
|
||||||
real(c_double), intent(in) :: R12
|
|
||||||
! Coordinates of the nanotube nodes
|
|
||||||
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
|
|
||||||
! Radius of nanotube X
|
|
||||||
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
|
|
||||||
! Parameter defining the type of the extended chain (0,1,2)
|
|
||||||
integer(c_int), intent(in) :: Ee
|
|
||||||
! Type of the tubular potential (0 or 1)
|
|
||||||
integer(c_int), intent(in) :: TPMType
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer(c_int) :: k, ii, jj, IntSign
|
|
||||||
integer(c_int) :: BType, EType, LocalTPMType
|
|
||||||
real(c_double), dimension(0:2,0:N-1) :: G1, G2
|
|
||||||
real(c_double), dimension(0:N-1) :: QQ
|
|
||||||
logical :: EType1, EType2
|
|
||||||
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
|
|
||||||
! Interaction energies associated with nodes X
|
|
||||||
real(c_double), dimension(0:N-1) :: xU
|
|
||||||
! Forces exerted on nodes X1 and X2
|
|
||||||
real(c_double), dimension(0:2) :: xF1, xF2
|
|
||||||
! Forces exerted on nodes X
|
|
||||||
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
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
! Looking for a buckling point
|
|
||||||
BType = 0
|
|
||||||
do k = 0, N - 1
|
|
||||||
if ( BBF(k) == 1 ) then
|
|
||||||
BType = 1
|
|
||||||
exit
|
|
||||||
end if
|
|
||||||
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.
|
|
||||||
! Overwise, LocalTPMType = TPMType.
|
|
||||||
if ( BType == 1 ) then
|
|
||||||
LocalTPMType = 0
|
|
||||||
EType = 0
|
|
||||||
else
|
|
||||||
if ( E1 == 1 ) then ! The first node in the chain is the tube end
|
|
||||||
EType1 = .true.
|
|
||||||
else
|
|
||||||
EType1 = .false.
|
|
||||||
end if
|
|
||||||
if ( E2 == 1 ) then ! The last node in the chain is the tube end
|
|
||||||
EType2 = .true.
|
|
||||||
else
|
|
||||||
EType2 = .false.
|
|
||||||
end if
|
|
||||||
if ( EType1 .and. EType2 ) then
|
|
||||||
LocalTPMType = 0
|
|
||||||
else
|
|
||||||
LocalTPMType = TPMType
|
|
||||||
if ( EType1 ) then
|
|
||||||
EType = 1
|
|
||||||
else if ( EType2 ) then
|
|
||||||
EType = 2
|
|
||||||
else ! No tube ends in the chain
|
|
||||||
EType = 0
|
|
||||||
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
|
|
||||||
if ( EType == 0 ) then
|
|
||||||
if ( Ee == 1 ) then ! The first node in the extended chain is the tube end
|
|
||||||
EType = 3
|
|
||||||
else if ( Ee == 2 ) then ! The last node in the extended chain is the tube end
|
|
||||||
EType = 4
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
IntSign = TPMInteractionFW1 ( QQ, UT, xU1, xU2, xU, xF1, xF2, xF, xFe, G1, G2, X1, X2, N, N, X, Xe, EType )
|
|
||||||
end if
|
|
||||||
if ( IntSign == 0 ) return ! No interaction
|
|
||||||
|
|
||||||
! Final potential energies
|
|
||||||
U1 = U1 + 0.5d+00 * xU1
|
|
||||||
U2 = U2 + 0.5d+00 * xU2
|
|
||||||
U(0:N-1) = U(0:N-1) + 0.5d+00 * xU(0:N-1)
|
|
||||||
|
|
||||||
! Contributions to the virial stresses tensor
|
|
||||||
do ii = 0, 2
|
|
||||||
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
|
|
||||||
S2(ii,jj) = S2(ii,jj) + DS
|
|
||||||
end do
|
|
||||||
end do
|
|
||||||
XX = 0.5d+00 * ( X2 + X1 )
|
|
||||||
if ( EType > 2 ) then
|
|
||||||
DQ = Xe - XX
|
|
||||||
call ApplyPeriodicBC ( DQ )
|
|
||||||
DQ = DQ / 6.0d+00
|
|
||||||
do ii = 0, 2
|
|
||||||
do jj = 0, 2
|
|
||||||
DS = DQ(ii) * xFe(jj)
|
|
||||||
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
|
|
||||||
call ApplyPeriodicBC ( DQ )
|
|
||||||
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) )
|
|
||||||
do jj = 0, 2
|
|
||||||
DS = DQ(ii) * G(jj)
|
|
||||||
DS1 = DS + DR * DG(jj)
|
|
||||||
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
|
|
||||||
end do
|
|
||||||
end do
|
|
||||||
end do
|
|
||||||
|
|
||||||
! Final forces
|
|
||||||
F1 = F1 + 0.5d+00 * xF1
|
|
||||||
F2 = F2 + 0.5d+00 * xF2
|
|
||||||
F(0:2,0:N-1) = F(0:2,0:N-1) + 0.5d+00 * xF(0:2,0:N-1)
|
|
||||||
if ( EType > 2 ) then
|
|
||||||
Fe = Fe + 0.5d+00 * xFe
|
|
||||||
end if
|
|
||||||
|
|
||||||
end subroutine SegmentTubeForceField !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end module TPMForceField !**************************************************************************
|
|
||||||
@ -1,155 +0,0 @@
|
|||||||
! ------------ ----------------------------------------------------------
|
|
||||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
! https://www.lammps.org/ Sandia National Laboratories
|
|
||||||
! LAMMPS development team: developers@lammps.org
|
|
||||||
!
|
|
||||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
! certain rights in this software. This software is distributed under
|
|
||||||
! 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 !************************************************************************************
|
|
||||||
!
|
|
||||||
! Geometry functions.
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 09.01, 2017
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
|
|
||||||
use TPMLib
|
|
||||||
use iso_c_binding, only : c_int, c_double, c_char
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Constants
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
integer(c_int), parameter :: MD_LINES_NONPAR = 0
|
|
||||||
integer(c_int), parameter :: MD_LINES_PAR = 1
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! 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
|
|
||||||
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 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This subroutine changes coordinates of the point according to the periodic boundary conditions
|
|
||||||
! it order to make sure that the point is inside the computational cell,
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double), dimension(0:2), intent(inout) :: R
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
if ( BC_X == 1 ) then
|
|
||||||
if ( R(0) .GT. DomLXHalf ) then
|
|
||||||
R(0) = R(0) - DomLX
|
|
||||||
else if ( R(0) .LT. - DomLXHalf ) then
|
|
||||||
R(0) = R(0) + DomLX
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
if ( BC_Y == 1 ) then
|
|
||||||
if ( R(1) .GT. DomLYHalf ) then
|
|
||||||
R(1) = R(1) - DomLY
|
|
||||||
else if ( R(1) .LT. - DomLYHalf ) then
|
|
||||||
R(1) = R(1) + DomLY
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
if ( BC_Z == 1 ) then
|
|
||||||
if ( R(2) .GT. DomLZHalf ) then
|
|
||||||
R(2) = R(2) - DomLZ
|
|
||||||
else if ( R(2) .LT. - DomLZHalf ) then
|
|
||||||
R(2) = R(2) + DomLZ
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
end subroutine ApplyPeriodicBC !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine LinePoint ( Displacement, Q, R1, L1, R0 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function calculates the point Q of projection of point R0 onto line (R1,L1).
|
|
||||||
! Q = R1 + Displacement * L1.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double), intent(inout) :: Displacement
|
|
||||||
real(c_double), dimension(0:2), intent(inout) :: Q
|
|
||||||
real(c_double), dimension(0:2), intent(in) :: R1, L1, R0
|
|
||||||
!--------------------------------------------------------------------------------------------
|
|
||||||
Q = R0 - R1
|
|
||||||
! Here we take into account periodic boundaries
|
|
||||||
call ApplyPeriodicBC ( Q )
|
|
||||||
Displacement = S_V3xV3 ( Q, L1 )
|
|
||||||
Q = R1 + Displacement * L1
|
|
||||||
end subroutine LinePoint !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
integer(c_int) function LineLine ( H, cosA, D1, D2, L12, R1, L1, R2, L2, Prec ) !!!!!!!!!!!!
|
|
||||||
! This function determines the smallest distance H between two lines (R1,L1) and (R2,L2).
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
! Input values:
|
|
||||||
! R1, L1, point and direction of line 1.
|
|
||||||
! R2, L2, point and direction of line 2.
|
|
||||||
! Prec, precision for the case L1 * L2 = 0 (parallel lines).
|
|
||||||
! Return values:
|
|
||||||
! H, minimum distance between lines.
|
|
||||||
! 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), dimension(0:2) :: Q1, Q2, R
|
|
||||||
real(c_double) :: C, DD1, DD2, C1, C2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
cosA = S_V3xV3 ( L1, L2 )
|
|
||||||
C = 1.0 - sqr ( cosA )
|
|
||||||
if ( C < Prec ) then ! Lines are parallel to each other
|
|
||||||
LineLine = MD_LINES_PAR
|
|
||||||
return
|
|
||||||
end if
|
|
||||||
LineLine = MD_LINES_NONPAR
|
|
||||||
R = R2 - R1
|
|
||||||
! Here we take into account periodic boundary conditions
|
|
||||||
call ApplyPeriodicBC ( R )
|
|
||||||
DD1 = S_V3xV3 ( R, L1 )
|
|
||||||
DD2 = S_V3xV3 ( R, L2 )
|
|
||||||
D1 = ( cosA * DD2 - DD1 ) / C
|
|
||||||
D2 = ( DD2 - cosA * DD1 ) / C
|
|
||||||
Q1 = R1 - D1 * L1
|
|
||||||
Q2 = R2 - D2 * L2
|
|
||||||
L12 = Q2 - Q1
|
|
||||||
! Here we take into account periodic boundary conditions
|
|
||||||
call ApplyPeriodicBC ( L12 )
|
|
||||||
H = S_V3norm3 ( L12 )
|
|
||||||
if ( H < Prec ) then ! Lines intersect each other
|
|
||||||
C1 = signum ( D1 )
|
|
||||||
C2 = signum ( D1 ) * signum ( cosA )
|
|
||||||
Q1 = C1 * L1
|
|
||||||
Q2 = C2 * L2
|
|
||||||
call V3_V3xxV3 ( L12, Q1, Q2 )
|
|
||||||
call V3_ort ( L12 )
|
|
||||||
else ! No intersection
|
|
||||||
L12 = L12 / H
|
|
||||||
end if
|
|
||||||
end function LineLine !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end module TPMGeom !********************************************************************************
|
|
||||||
@ -1,215 +0,0 @@
|
|||||||
! ------------ ----------------------------------------------------------
|
|
||||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
! https://www.lammps.org/ Sandia National Laboratories
|
|
||||||
! LAMMPS development team: developers@lammps.org
|
|
||||||
!
|
|
||||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
! certain rights in this software. This software is distributed under
|
|
||||||
! 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 !*************************************************************************************
|
|
||||||
!
|
|
||||||
! Basic constants, types, and mathematical functions.
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 09.01, 2017
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
use iso_c_binding, only : c_int, c_double, c_char
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Mathematical constants
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
real(c_double), parameter :: M_PI_2 = 1.57079632679489661923
|
|
||||||
real(c_double), parameter :: M_PI = 3.14159265358979323846
|
|
||||||
real(c_double), parameter :: M_3PI_2 = 4.71238898038468985769
|
|
||||||
real(c_double), parameter :: M_2PI = 6.28318530717958647692
|
|
||||||
real(c_double), parameter :: M_PI_180 = 0.017453292519943295769
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Physical unit constants
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
real(c_double), parameter :: K_AMU = 1.66056E-27 ! a.m.u. (atomic mass unit, Dalton)
|
|
||||||
real(c_double), parameter :: K_EV = 1.60217646e-19 ! eV (electron-volt)
|
|
||||||
|
|
||||||
real(c_double), parameter :: K_MDLU = 1.0E-10 ! MD length unit (m)
|
|
||||||
real(c_double), parameter :: K_MDEU = K_EV ! MD energy unit (J)
|
|
||||||
real(c_double), parameter :: K_MDMU = K_AMU ! MD mass unit (kg)
|
|
||||||
real(c_double), parameter :: K_MDFU = K_MDEU / K_MDLU ! MD force unit (N)
|
|
||||||
real(c_double), parameter :: K_MDCU = K_MDEU / K_MDMU ! MD specific heat unit (J/(kg*K))
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Global variables
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
integer(c_int) :: StdUID = 31
|
|
||||||
|
|
||||||
contains !******************************************************************************************
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Simple mathematical functions
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
real(c_double) function rad ( X ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real(c_double), intent(in) :: X
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
rad = X * M_PI_180
|
|
||||||
end function rad !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
real(c_double) function sqr ( X ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real(c_double), intent(in) :: X
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
sqr = X * X
|
|
||||||
end function sqr !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
integer(c_int) function signum ( X ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real(c_double), intent(in) :: X
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
if ( X > 0 ) then
|
|
||||||
signum = 1
|
|
||||||
else if ( X < 0 ) then
|
|
||||||
signum = -1
|
|
||||||
else
|
|
||||||
signum = 0
|
|
||||||
end if
|
|
||||||
end function signum !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Vector & matrix functions
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
real(c_double) function S_V3xx ( V ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real(c_double), dimension(0:2), intent(in) :: V
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
S_V3xx = V(0) * V(0) + V(1) * V(1) + V(2) * V(2)
|
|
||||||
end function S_V3xx !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
real(c_double) function S_V3xV3 ( V1, V2 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real(c_double), dimension(0:2), intent(in) :: V1, V2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
S_V3xV3 = V1(0) * V2(0) + V1(1) * V2(1) + V1(2) * V2(2)
|
|
||||||
end function S_V3xV3 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
real(c_double) function S_V3norm3 ( V ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real(c_double), dimension(0:2), intent(in) :: V
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
S_V3norm3 = dsqrt ( V(0) * V(0) + V(1) * V(1) + V(2) * V(2) )
|
|
||||||
end function S_V3norm3 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine V3_ort ( V ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real(c_double), dimension(0:2), intent(inout) :: V
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double) :: Vabs
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Vabs = S_V3norm3 ( V )
|
|
||||||
V(0) = V(0) / Vabs
|
|
||||||
V(1) = V(1) / Vabs
|
|
||||||
V(2) = V(2) / Vabs
|
|
||||||
end subroutine V3_ort !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine V3_V3xxV3 ( V, V1, V2 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real(c_double), dimension(0:2), intent(out) :: V
|
|
||||||
real(c_double), dimension(0:2), intent(in) :: V1, V2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
V(0) = V1(1) * V2(2) - V1(2) * V2(1)
|
|
||||||
V(1) = V1(2) * V2(0) - V1(0) * V2(2)
|
|
||||||
V(2) = V1(0) * V2(1) - V1(1) * V2(0)
|
|
||||||
end subroutine V3_V3xxV3 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Handling of spherical and Euler angles
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
subroutine RotationMatrix3 ( M, Psi, Tet, Phi ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! Ksi, Tet and Phi are Euler angles
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double), dimension(0:2,0:2), intent(out) :: M
|
|
||||||
real(c_double), intent(in) :: Psi, Tet, Phi
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double) :: cK, sK, cT, sT, cP, sP
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
cK = dcos ( Psi )
|
|
||||||
sK = dsin ( Psi )
|
|
||||||
cT = dcos ( Tet )
|
|
||||||
sT = dsin ( Tet )
|
|
||||||
cP = dcos ( Phi )
|
|
||||||
sP = dsin ( Phi )
|
|
||||||
M(0,0) = cP * cK - sK * sP * cT
|
|
||||||
M(0,1) = cP * sK + sP * cT * cK
|
|
||||||
M(0,2) = sP * sT
|
|
||||||
M(1,0) = - sP * cK - cP * cT * sK
|
|
||||||
M(1,1) = - sP * sK + cP * cT * cK
|
|
||||||
M(1,2) = cP * sT
|
|
||||||
M(2,0) = sT * sK
|
|
||||||
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
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Tet = acos ( L(2) )
|
|
||||||
Psi = atan2 ( L(1), L(0) )
|
|
||||||
if ( Psi > M_3PI_2 ) then
|
|
||||||
Psi = Psi - M_3PI_2
|
|
||||||
else
|
|
||||||
Psi = Psi + M_PI_2
|
|
||||||
end if
|
|
||||||
end subroutine EulerAngles !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! File input and output
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
integer(c_int) function OpenFile ( Name, Params, Path ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
character*(*), intent(in) :: Name, Params, Path
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer(c_int) :: Fuid
|
|
||||||
character*512 :: FullName, Msg, Name1, Action1, Status1, Form1, Position1
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
OpenFile = StdUID + 1
|
|
||||||
if ( Params(1:1) == 'r' ) then
|
|
||||||
Action1 = 'read'
|
|
||||||
Status1 = 'old'
|
|
||||||
Position1 = 'rewind'
|
|
||||||
else if ( Params(1:1) == 'w' ) then
|
|
||||||
Action1 = 'write'
|
|
||||||
Status1 = 'replace'
|
|
||||||
Position1 = 'rewind'
|
|
||||||
else if ( Params(1:1) == 'a' ) then
|
|
||||||
Action1 = 'write'
|
|
||||||
Status1 = 'old'
|
|
||||||
Position1 = 'append'
|
|
||||||
endif
|
|
||||||
if ( Params(2:2) == 'b' ) then
|
|
||||||
Form1 = 'binary'
|
|
||||||
else
|
|
||||||
Form1 = 'formatted'
|
|
||||||
endif
|
|
||||||
open ( unit = OpenFile, file = Name, form = Form1, action = Action1, status = Status1, position = Position1 )
|
|
||||||
StdUID = StdUID + 1
|
|
||||||
return
|
|
||||||
end function OpenFile !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine CloseFile ( Fuid ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
integer(c_int), intent(inout) :: Fuid
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
if ( Fuid < 0 ) return
|
|
||||||
close ( unit = Fuid )
|
|
||||||
Fuid = -1
|
|
||||||
end subroutine CloseFile !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end module TPMLib !*********************************************************************************
|
|
||||||
@ -1,194 +0,0 @@
|
|||||||
! ------------ ----------------------------------------------------------
|
|
||||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
! https://www.lammps.org/ Sandia National Laboratories
|
|
||||||
! LAMMPS development team: developers@lammps.org
|
|
||||||
!
|
|
||||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
! certain rights in this software. This software is distributed under
|
|
||||||
! 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 !**************************************************************************************
|
|
||||||
!
|
|
||||||
! Combined/Weighted TPM potential of type 0.
|
|
||||||
!
|
|
||||||
! Direct application of SST potential to calculation of segment-segment interaction.
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 09.01, 2017
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
|
|
||||||
use TubePotMono
|
|
||||||
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
|
|
||||||
real(c_double), dimension(0:2), intent(in) :: R1_1, R1_2, R2_1, R2_2
|
|
||||||
integer(c_int), intent(in) :: EType
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double) :: Qa, Ua, Fd, L2
|
|
||||||
real(c_double), dimension(0:2) :: F1_1a, F1_2a, F2_1a, F2_2a, R2_3, R2, Laxis2, F
|
|
||||||
integer(c_int) :: IntSign
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
R2 = 0.5d+00 * ( R2_1 + R2_2 )
|
|
||||||
Laxis2 = R2_2 - R2_1
|
|
||||||
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 )
|
|
||||||
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 )
|
|
||||||
if ( IntSign > 0 ) then
|
|
||||||
TPMInteractionFSS = 1
|
|
||||||
call TPMSegmentForces ( F2_1a, F2_2a, F1_1a, F1_2a, R1_1, R1_2, R2, Laxis2, L2 )
|
|
||||||
F = ( Fd - S_V3xV3 ( F2_2a, Laxis2 ) ) * Laxis2
|
|
||||||
F2_2a = F2_2a + F
|
|
||||||
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 )
|
|
||||||
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
|
|
||||||
TPMInteractionFSS = 1
|
|
||||||
call TPMSegmentForces ( F2_1a, F2_2a, F1_1a, F1_2a, R1_1, R1_2, R2, Laxis2, L2 )
|
|
||||||
F = ( - Fd - S_V3xV3 ( F2_1a, Laxis2 ) ) * Laxis2
|
|
||||||
F2_1a = F2_1a + F
|
|
||||||
F2_2a = F2_2a - F
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
if ( IntSign > 0 ) then
|
|
||||||
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
|
|
||||||
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
|
|
||||||
real(c_double), dimension(0:NMAX-1), intent(out) :: QQ, UU
|
|
||||||
real(c_double), dimension(0:2), intent(out) :: F1, F2
|
|
||||||
real(c_double), dimension(0:2,0:NMAX-1), intent(out) :: F, G1, G2
|
|
||||||
real(c_double), dimension(0:2), intent(in) :: R1, R2
|
|
||||||
real(c_double), dimension(0:2,0:NMAX-1), intent(in) :: R
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer(c_int) :: i, SType2, GeomID, EType
|
|
||||||
real(c_double) :: Ua
|
|
||||||
real(c_double), dimension(0:2) :: F1_1a, F1_2a, F2_1a, F2_2a
|
|
||||||
real(c_double), dimension(0:2) :: R1a, R2a, Laxis1, Laxis2, L12, DR
|
|
||||||
real(c_double) :: L1, L2, D1, D2, H, cosA, D, Dmina, Dminb
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
QQ = 0.0d+00
|
|
||||||
U = 0.0d+00
|
|
||||||
U1 = 0.0d+00
|
|
||||||
U2 = 0.0d+00
|
|
||||||
UU = 0.0d+00
|
|
||||||
F1 = 0.0d+00
|
|
||||||
F2 = 0.0d+00
|
|
||||||
F = 0.0d+00
|
|
||||||
G1 = 0.0d+00
|
|
||||||
G2 = 0.0d+00
|
|
||||||
TPMInteractionFW0 = 0
|
|
||||||
do i = 0, N - 2
|
|
||||||
R1a = 0.5d+00 * ( R1 + R2 )
|
|
||||||
R2a = 0.5d+00 * ( R(0:2,i+1) + R(0:2,i) )
|
|
||||||
Laxis1 = R2 - R1
|
|
||||||
Laxis2 = R(0:2,i+1) - R(0:2,i)
|
|
||||||
L1 = S_V3norm3 ( Laxis1 )
|
|
||||||
L2 = S_V3norm3 ( Laxis2 )
|
|
||||||
Laxis1 = Laxis1 / L1
|
|
||||||
Laxis2 = Laxis2 / L2
|
|
||||||
L2 = 0.5d+00 * L2
|
|
||||||
L1 = 0.5d+00 * L1
|
|
||||||
GeomID = LineLine ( H, cosA, D1, D2, L12, R1a, Laxis1, R2a, Laxis2, TPGeomPrec )
|
|
||||||
|
|
||||||
DR = R1 - R(0:2,i)
|
|
||||||
call ApplyPeriodicBC ( DR )
|
|
||||||
Dmina = sqr ( DR(0) ) + sqr ( DR(1) ) + sqr ( DR(2) )
|
|
||||||
DR = R2 - R(0:2,i)
|
|
||||||
call ApplyPeriodicBC ( DR )
|
|
||||||
D = sqr ( DR(0) ) + sqr ( DR(1) ) + sqr ( DR(2) )
|
|
||||||
if ( D < Dmina ) Dmina = D
|
|
||||||
if ( GeomID == MD_LINES_NONPAR ) then
|
|
||||||
D = ( D2 - L2 ) * cosA
|
|
||||||
if ( D > D1 - L1 .and. D < D1 + L1 ) then
|
|
||||||
D = sqr ( D2 - L2 ) * ( 1.0d+00 - sqr ( cosA ) ) + sqr ( H )
|
|
||||||
if ( D < Dmina ) Dmina = D
|
|
||||||
end if
|
|
||||||
else
|
|
||||||
call LinePoint ( D, DR, R1, Laxis1, R(0:2,i) )
|
|
||||||
if ( D > 0.0d+00 .and. D < 2.0d+00 * L1 ) then
|
|
||||||
DR = DR - R(0:2,i)
|
|
||||||
call ApplyPeriodicBC ( DR )
|
|
||||||
D = sqr ( DR(0) ) + sqr ( DR(1) ) + sqr ( DR(2) )
|
|
||||||
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) )
|
|
||||||
DR = R2 - R(0:2,i+1)
|
|
||||||
call ApplyPeriodicBC ( DR )
|
|
||||||
D = sqr ( DR(0) ) + sqr ( DR(1) ) + sqr ( DR(2) )
|
|
||||||
if ( D < Dminb ) Dminb = D
|
|
||||||
if ( GeomID == MD_LINES_NONPAR ) then
|
|
||||||
D = ( D2 + L2 ) * cosA
|
|
||||||
if ( D > D1 - L1 .and. D < D1 + L1 ) then
|
|
||||||
D = sqr ( D2 + L2 ) * ( 1.0d+00 - sqr ( cosA ) ) + sqr ( H )
|
|
||||||
if ( D < Dminb ) Dminb = D
|
|
||||||
end if
|
|
||||||
else
|
|
||||||
call LinePoint ( D, DR, R1, Laxis1, R(0:2,i+1) )
|
|
||||||
if ( D > 0.0d+00 .and. D < 2.0d+00 * L1 ) then
|
|
||||||
DR = DR - R(0:2,i+1)
|
|
||||||
call ApplyPeriodicBC ( DR )
|
|
||||||
D = sqr ( DR(0) ) + sqr ( DR(1) ) + sqr ( DR(2) )
|
|
||||||
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), &
|
|
||||||
EType ) > 0 ) then
|
|
||||||
TPMInteractionFW0 = 1
|
|
||||||
U = U + 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
|
|
||||||
F2 = F2 + F1_2a
|
|
||||||
F(0:2,i) = F(0:2,i) + F2_1a
|
|
||||||
F(0:2,i+1) = F(0:2,i+1) + F2_2a
|
|
||||||
G2(0:2,i) = F2_1a
|
|
||||||
G1(0:2,i+1) = F2_2a
|
|
||||||
end if
|
|
||||||
end do
|
|
||||||
end function TPMInteractionFW0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end module TPMM0 !**********************************************************************************
|
|
||||||
@ -1,372 +0,0 @@
|
|||||||
! ------------ ----------------------------------------------------------
|
|
||||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
! https://www.lammps.org/ Sandia National Laboratories
|
|
||||||
! LAMMPS development team: developers@lammps.org
|
|
||||||
!
|
|
||||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
! certain rights in this software. This software is distributed under
|
|
||||||
! 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 !**************************************************************************************
|
|
||||||
!
|
|
||||||
! Combined/Weighted potential of type 1.
|
|
||||||
!
|
|
||||||
! Calculation of the combined potential is based on the 'extended' chain.
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran.
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 09.01, 2017
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
|
|
||||||
use TubePotMono
|
|
||||||
use iso_c_binding, only : c_int, c_double, c_char
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Constants
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
! Maximum length of a segment chain
|
|
||||||
integer(c_int), parameter :: TPM_MAX_CHAIN = 100
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Numerical parameters
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
! Switching parameters
|
|
||||||
real(c_double) :: TPMC123 = 1.0d+00 ! Non-dimensional
|
|
||||||
real(c_double) :: TPMC3 = 10.0d+00 ! (A)
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Global variables
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
! These global variables are used to speedup calculations
|
|
||||||
real(c_double), dimension(0:2,0:TPM_MAX_CHAIN-1) :: E1, E2, EE1, EE2
|
|
||||||
real(c_double), dimension(0:2) :: Q1, Q2, Qe, Qe1, DR, Z1, Z2, S1, S2, Pe, Pe1
|
|
||||||
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
|
|
||||||
real(c_double), dimension(0:2), intent(in) :: R2_1, R2_2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double) :: D, L20, D20, t, dWdD
|
|
||||||
real(c_double), dimension(0:2) :: E, E20
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
E = 0.5d+00 * ( R2_1 + R2_2 ) - RR
|
|
||||||
call ApplyPeriodicBC ( E )
|
|
||||||
D = E(0) * E(0) + E(1) * E(1) + E(2) * E(2)
|
|
||||||
if ( D < D10 * D10 ) then
|
|
||||||
W = 1.0d+00
|
|
||||||
E1_1 = 0.0d+00
|
|
||||||
E1_2 = 0.0d+00
|
|
||||||
E2_1 = 0.0d+00
|
|
||||||
E2_2 = 0.0d+00
|
|
||||||
return
|
|
||||||
end if
|
|
||||||
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
|
|
||||||
W = 0.0d+00
|
|
||||||
E1_1 = 0.0d+00
|
|
||||||
E1_2 = 0.0d+00
|
|
||||||
E2_1 = 0.0d+00
|
|
||||||
E2_2 = 0.0d+00
|
|
||||||
return
|
|
||||||
end if
|
|
||||||
D = sqrt ( D )
|
|
||||||
E = E / D
|
|
||||||
E20 = E20 / L20
|
|
||||||
D20 = D20 - D10
|
|
||||||
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 )
|
|
||||||
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
|
|
||||||
real(c_double), dimension(0:2), intent(in) :: R1_1, R1_2, R2_1, R2_2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double) :: D, L20
|
|
||||||
real(c_double) :: D1, D2, t, dWdD
|
|
||||||
real(c_double), dimension(0:2) :: RR, E, E20
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
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 )
|
|
||||||
L20 = sqrt ( S_V3xx ( E20 ) + sqr ( TPMR2 ) )
|
|
||||||
D1 = L10 + L20 + TPBRcutoff + RSkin
|
|
||||||
if ( D < D1 ) then
|
|
||||||
EndWeight1 = 0
|
|
||||||
W = 1.0d+00
|
|
||||||
E1_1 = 0.0d+00
|
|
||||||
E1_2 = 0.0d+00
|
|
||||||
E2_1 = 0.0d+00
|
|
||||||
E2_2 = 0.0d+00
|
|
||||||
return
|
|
||||||
end if
|
|
||||||
D2 = D1 + TPMC3
|
|
||||||
if ( D > D2 ) then
|
|
||||||
EndWeight1 = 2
|
|
||||||
W = 0.0d+00
|
|
||||||
E1_1 = 0.0d+00
|
|
||||||
E1_2 = 0.0d+00
|
|
||||||
E2_1 = 0.0d+00
|
|
||||||
E2_2 = 0.0d+00
|
|
||||||
return
|
|
||||||
end if
|
|
||||||
EndWeight1 = 1
|
|
||||||
E = E / D
|
|
||||||
E20 = E20 / L20
|
|
||||||
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 )
|
|
||||||
end function EndWeight1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
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
|
|
||||||
integer(c_int), intent(in) :: EType
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double), dimension(0:2) :: M, QX, Me, F1a, F2a, P1a, P2a, F1b, F2b, P1b, P2b, ER1, ER2, EQe, EQe1
|
|
||||||
real(c_double) :: W, W1, D, Qa, Qb, Ua, Ub, L, Pee, Peea, Peeb, DU
|
|
||||||
integer(c_int) :: IntSigna, IntSignb, CaseID
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
if ( EType == 0 ) then
|
|
||||||
TPMInteractionFC1 = TPMInteractionF ( Q, U, F1, F2, P1, P2, Pee, R1, R2, Q1, Q2, 0 )
|
|
||||||
Pe = 0.0d+00
|
|
||||||
Pe1 = 0.0d+00
|
|
||||||
else if ( EType < 3 ) then
|
|
||||||
QX = 0.5d+00 * ( Q1 + Q2 )
|
|
||||||
M = Q2 - Q1
|
|
||||||
L = S_V3norm3 ( M )
|
|
||||||
M = M / L
|
|
||||||
Me = Qe - QX
|
|
||||||
D = S_V3norm3 ( Me )
|
|
||||||
if ( EType == 1 ) then
|
|
||||||
TPMInteractionFC1 = TPMInteractionF ( Q, U, F1, F2, P1, P2, Pee, R1, R2, QX - D * M, QX, 1 )
|
|
||||||
else
|
|
||||||
TPMInteractionFC1 = TPMInteractionF ( Q, U, F1, F2, P1, P2, Pee, R1, R2, QX, QX + D * M, 2 )
|
|
||||||
end if
|
|
||||||
call TPMSegmentForces ( P1, P2, F1, F2, R1, R2, QX, M, L )
|
|
||||||
Pe = ( Pee / D ) * Me
|
|
||||||
Pe1 = 0.0d+00
|
|
||||||
QX = 0.5d+00 * Pe
|
|
||||||
P1 = P1 + QX
|
|
||||||
P2 = P2 + QX
|
|
||||||
else
|
|
||||||
CaseID = EndWeight1 ( W, ER1, ER2, EQe, Eqe1, R1, R2, Qe, Qe1 )
|
|
||||||
if ( CaseID < 2 ) then
|
|
||||||
QX = 0.5d+00 * ( Q1 + Q2 )
|
|
||||||
M = Q2 - Q1
|
|
||||||
L = S_V3norm3 ( M )
|
|
||||||
M = M / L
|
|
||||||
Me = Qe - QX
|
|
||||||
D = S_V3norm3 ( Me )
|
|
||||||
if ( EType == 3 ) then
|
|
||||||
IntSigna = TPMInteractionF ( Qa, Ua, F1a, F2a, P1a, P2a, Peea, R1, R2, QX - D * M, QX, 1 )
|
|
||||||
else
|
|
||||||
IntSigna = TPMInteractionF ( Qa, Ua, F1a, F2a, P1a, P2a, Peea, R1, R2, QX, QX + D * M, 2 )
|
|
||||||
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
|
|
||||||
U = Ua
|
|
||||||
F1 = F1a
|
|
||||||
F2 = F2a
|
|
||||||
Pe = ( Peea / D ) * Me
|
|
||||||
Pe1 = 0.0d+00
|
|
||||||
QX = 0.5d+00 * Pe
|
|
||||||
P1 = P1a + QX
|
|
||||||
P2 = P2a + QX
|
|
||||||
else if ( CaseID == 2 ) then
|
|
||||||
TPMInteractionFC1 = IntSignb
|
|
||||||
Q = Qb
|
|
||||||
U = Ub
|
|
||||||
F1 = F1b
|
|
||||||
F2 = F2b
|
|
||||||
P1 = P1b
|
|
||||||
P2 = P2b
|
|
||||||
Pe = 0.0d+00
|
|
||||||
Pe1 = 0.0d+00
|
|
||||||
else
|
|
||||||
TPMInteractionFC1 = 0
|
|
||||||
if ( IntSigna > 0 .or. IntSignb > 0 ) TPMInteractionFC1 = 1
|
|
||||||
W1 = 1.0d+00 - W
|
|
||||||
DU = Ub - Ua
|
|
||||||
Q = W * Qa + W1 * Qb
|
|
||||||
U = W * Ua + W1 * Ub
|
|
||||||
Pe = ( W * Peea / D ) * Me
|
|
||||||
QX = 0.5d+00 * Pe
|
|
||||||
F1 = W * F1a + W1 * F1b + DU * ER1
|
|
||||||
F2 = W * F2a + W1 * F2b + DU * ER2
|
|
||||||
P1 = W * P1a + W1 * P1b + QX
|
|
||||||
P2 = W * P2a + W1 * P2b + QX
|
|
||||||
Pe = Pe - DU * EQe
|
|
||||||
Pe1 = - DU * EQe1
|
|
||||||
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
|
|
||||||
real(c_double), dimension(0:NMAX-1), intent(out) :: QQ, UU
|
|
||||||
real(c_double), dimension(0:2), intent(out) :: F1, F2, Fe
|
|
||||||
real(c_double), dimension(0:2,0:NMAX-1), intent(out) :: F, G1, G2
|
|
||||||
real(c_double), dimension(0:2), intent(in) :: R1, R2, Re
|
|
||||||
real(c_double), dimension(0:2,0:NMAX-1), intent(in) :: R
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer(c_int) :: i, j
|
|
||||||
real(c_double) :: Q, WW, DD
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Q1 = 0.0d+00
|
|
||||||
Q2 = 0.0d+00
|
|
||||||
WW = 0.0d+00
|
|
||||||
Z1 = 0.0d+00
|
|
||||||
Z2 = 0.0d+00
|
|
||||||
TPMInteractionFW1 = 0
|
|
||||||
E10 = 0.5d+00 * ( R2 - R1 )
|
|
||||||
L10 = sqrt ( S_V3xx ( E10 ) + sqr ( TPMR1 ) )
|
|
||||||
D10 = TPMR1 + TPMR2 + TPMC123 * TPBRcutoff + RSkin
|
|
||||||
E10 = E10 / L10
|
|
||||||
RR = 0.5d+00 * ( R1 + R2 )
|
|
||||||
do i = 0, N - 2
|
|
||||||
call PairWeight1 ( W(i), E1(0:2,i), E2(0:2,i), EE1(0:2,i), EE2(0:2,i), R(0:2,i), R(0:2,i+1) )
|
|
||||||
Q1 = Q1 + W(i) * R(0:2,i)
|
|
||||||
Q2 = Q2 + W(i) * R(0:2,i+1)
|
|
||||||
WW = WW + W(i)
|
|
||||||
Z1 = Z1 + E1(0:2,i)
|
|
||||||
Z2 = Z2 + E2(0:2,i)
|
|
||||||
end do
|
|
||||||
if ( WW .le. TPGeomPrec ) return
|
|
||||||
Q1 = Q1 / WW
|
|
||||||
Q2 = Q2 / WW
|
|
||||||
Z1 = Z1 / WW
|
|
||||||
Z2 = Z2 / WW
|
|
||||||
if ( EType == 1 ) then
|
|
||||||
Qe = R(0:2,0)
|
|
||||||
Qe1 = R(0:2,1)
|
|
||||||
else if ( EType == 2 ) then
|
|
||||||
Qe = R(0:2,N-1)
|
|
||||||
Qe1 = R(0:2,N-2)
|
|
||||||
else if ( EType == 3 ) then
|
|
||||||
Qe = Re
|
|
||||||
Qe1 = R(0:2,0)
|
|
||||||
else if ( EType == 4 ) then
|
|
||||||
Qe = Re
|
|
||||||
Qe1 = R(0:2,N-1)
|
|
||||||
else
|
|
||||||
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 )
|
|
||||||
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
|
|
||||||
EE1(0:2,0:N-2) = EE1(0:2,0:N-2) / WW
|
|
||||||
EE2(0:2,0:N-2) = EE2(0:2,0:N-2) / WW
|
|
||||||
G1(0:2,0:N-1) = 0.0d+00
|
|
||||||
G2(0:2,0:N-1) = 0.0d+00
|
|
||||||
U1 = 0.25d+00 * U
|
|
||||||
U2 = U1
|
|
||||||
UU = 0.0d+00
|
|
||||||
do i = 0, N - 2
|
|
||||||
QQ(i) = W(i) * Q
|
|
||||||
DD = W(i) * U1
|
|
||||||
UU(i) = UU(i) + DD
|
|
||||||
UU(i+1) = UU(i+1) + DD
|
|
||||||
end do
|
|
||||||
do i = 0, N - 2
|
|
||||||
C(i) = S_V3xV3 ( S1, R(0:2,i) ) + S_V3xV3 ( S2, R(0:2,i+1) )
|
|
||||||
F1 = F1 + C(i) * ( E1(0:2,i) - W(i) * Z1 )
|
|
||||||
F2 = F2 + C(i) * ( E2(0:2,i) - W(i) * Z2 )
|
|
||||||
end do
|
|
||||||
F(0:2,0) = W(0) * S1
|
|
||||||
do j = 0, N - 2
|
|
||||||
if ( j == 0 ) then
|
|
||||||
DR = EE1(0:2,0) * ( 1.0d+00 - W(0) )
|
|
||||||
else
|
|
||||||
DR = - W(j) * EE1(0:2,0)
|
|
||||||
end if
|
|
||||||
F(0:2,0) = F(0:2,0) + C(j) * DR
|
|
||||||
end do
|
|
||||||
do i = 1, N - 2
|
|
||||||
G1(0:2,i) = W(i-1) * S2
|
|
||||||
G2(0:2,i) = W(i) * S1
|
|
||||||
do j = 0, N - 2
|
|
||||||
if ( j == i ) then
|
|
||||||
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) * ( EE1(0:2,j) - W(j) * EE1(0:2,i) )
|
|
||||||
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)
|
|
||||||
G2(0:2,i) = G2(0:2,i) - C(j) * W(j) * EE1(0:2,i)
|
|
||||||
end if
|
|
||||||
end do
|
|
||||||
F(0:2,i) = G1(0:2,i) + G2(0:2,i)
|
|
||||||
end do
|
|
||||||
F(0:2,N-1) = W(N-2) * S2
|
|
||||||
do j = 0, N - 2
|
|
||||||
if ( j == N - 2 ) then
|
|
||||||
DR = EE2(0:2,N-2) * ( 1.0d+00 - W(N-2) )
|
|
||||||
else
|
|
||||||
DR = - W(j) * EE2(0:2,N-2)
|
|
||||||
end if
|
|
||||||
F(0:2,N-1) = F(0:2,N-1) + C(j) * DR
|
|
||||||
end do
|
|
||||||
Fe = 0.0d+00
|
|
||||||
if ( EType == 1 ) then
|
|
||||||
F(0:2,0) = F(0:2,0) - Pe
|
|
||||||
else if ( EType == 2 ) then
|
|
||||||
F(0:2,N-1) = F(0:2,N-1) - Pe
|
|
||||||
else if ( EType == 3 ) then
|
|
||||||
F(0:2,0) = F(0:2,0) - Pe1
|
|
||||||
Fe = - Pe
|
|
||||||
else if ( EType == 4 ) then
|
|
||||||
F(0:2,N-1) = F(0:2,N-1) - Pe1
|
|
||||||
Fe = - Pe
|
|
||||||
end if
|
|
||||||
G1(0:2,N-1) = F(0:2,N-1)
|
|
||||||
G2(0:2,0) = F(0:2,0)
|
|
||||||
end function TPMInteractionFW1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end module TPMM1 !**********************************************************************************
|
|
||||||
@ -1,306 +0,0 @@
|
|||||||
! ------------ ----------------------------------------------------------
|
|
||||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
! https://www.lammps.org/ Sandia National Laboratories
|
|
||||||
! LAMMPS development team: developers@lammps.org
|
|
||||||
!
|
|
||||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
! certain rights in this software. This software is distributed under
|
|
||||||
! 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 !********************************************************************************
|
|
||||||
!
|
|
||||||
! Non-bonded pair interaction potential and transfer functions for atoms composing nanotubes.
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 09.01, 2017
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! This module contains basic parameters for all modules involved into calculations of tubular
|
|
||||||
! potentials.
|
|
||||||
!
|
|
||||||
! It includes definitions of
|
|
||||||
! -- TPBU, Lennard-Jones (12-6) potential
|
|
||||||
! -- TPBQ, Transfer function
|
|
||||||
!
|
|
||||||
! All default values are adjusted for non-bonded carbon-carbon interaction in carbon nanotubes.
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
|
|
||||||
use TPMLib
|
|
||||||
use iso_c_binding, only : c_int, c_double, c_char
|
|
||||||
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
|
|
||||||
|
|
||||||
! Maximal number of elements in corresponding tables
|
|
||||||
integer(c_int), parameter :: TPBNMAX = 2001
|
|
||||||
|
|
||||||
! Numerical constants
|
|
||||||
real(c_double), parameter :: TPbConstD = 5.196152422706632d+00 ! = 3.0**1.5
|
|
||||||
|
|
||||||
! 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)
|
|
||||||
real(c_double), parameter :: TPBScc = 3.4d+00 ! (A)
|
|
||||||
|
|
||||||
! Lattice parameter and surface number density of atoms for a graphene sheet, see
|
|
||||||
! 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
|
|
||||||
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) :: Z, RR
|
|
||||||
integer(c_int) :: i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
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 )
|
|
||||||
elseif ( R > TPBRcutoff ) then
|
|
||||||
TPBQInt0 = 0.0d+00
|
|
||||||
return
|
|
||||||
endif
|
|
||||||
RR = ( R - TPBRmin ) / TPBDR
|
|
||||||
i = int ( RR )
|
|
||||||
RR = RR - i
|
|
||||||
Z = 1.0d+00 - 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) :: Z, RR
|
|
||||||
integer(c_int) :: i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
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 )
|
|
||||||
elseif ( R > TPBRcutoff ) then
|
|
||||||
TPBUInt0 = 0.0d+00
|
|
||||||
return
|
|
||||||
endif
|
|
||||||
RR = ( R - TPBRmin ) / TPBDR
|
|
||||||
i = int ( RR )
|
|
||||||
RR = RR - i
|
|
||||||
Z = 1.0d+00 - 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) :: Z, RR
|
|
||||||
integer(c_int) :: i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
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 )
|
|
||||||
elseif ( R > TPBRcutoff ) then
|
|
||||||
TPBU = 0.0d+00
|
|
||||||
TPBdUdR = 0.0d+00
|
|
||||||
return
|
|
||||||
endif
|
|
||||||
RR = ( R - TPBRmin ) / TPBDR
|
|
||||||
i = int ( RR )
|
|
||||||
RR = RR - i
|
|
||||||
Z = 1.0d+00 - 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
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double) :: Z, t, S
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
if ( R > TPBRcutoff ) then
|
|
||||||
TPBQCalc0 = 0.0d+00
|
|
||||||
else if ( R < TPBQR0 ) then
|
|
||||||
TPBQCalc0 = 1.0d+00
|
|
||||||
else
|
|
||||||
Z = TPBQS / R
|
|
||||||
Z = Z * Z * Z
|
|
||||||
Z = Z * Z
|
|
||||||
TPBQCalc0 = 4.0d+00 * ( 1.0d+00 - Z ) * Z
|
|
||||||
if ( R > TPBQRcutoff1 ) then
|
|
||||||
t = ( R - TPBQRcutoff1 ) / TPBQDRcutoff
|
|
||||||
S = 1.0d+00 - t * t * ( 3.0d+00 - 2.0d+00 * t )
|
|
||||||
TPBQCalc0 = TPBQCalc0 * S
|
|
||||||
endif
|
|
||||||
endif
|
|
||||||
end function TPBQCalc0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
real(c_double) function TPBUCalc0 ( R ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real(c_double), intent(in) :: R
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double) :: Z, t, S
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
if ( R > TPBRcutoff ) then
|
|
||||||
TPBUCalc0 = 0.0d+00
|
|
||||||
else
|
|
||||||
Z = TPBS / R
|
|
||||||
Z = Z * Z * Z
|
|
||||||
Z = Z * Z
|
|
||||||
TPBUCalc0 = TPBE4 * ( Z - 1.0d+00 ) * Z
|
|
||||||
if ( R > TPBRcutoff1 ) then
|
|
||||||
t = ( R - TPBRcutoff1 ) / TPBDRcutoff
|
|
||||||
S = 1.0d+00 - t * t * ( 3.0d+00 - 2.0d+00 * t )
|
|
||||||
TPBUCalc0 = TPBUCalc0 * S
|
|
||||||
endif
|
|
||||||
endif
|
|
||||||
end function TPBUCalc0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine TPBUCalc1 ( U, dUdR, R ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real(c_double), intent(out) :: U, dUdR
|
|
||||||
real(c_double), intent(in) :: R
|
|
||||||
real(c_double) :: Z, t, S, dSdR
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
if ( R > TPBRcutoff ) then
|
|
||||||
U = 0.0d+00
|
|
||||||
dUdR = 0.0d+00
|
|
||||||
else
|
|
||||||
Z = TPBS / R
|
|
||||||
Z = Z * Z * Z
|
|
||||||
Z = Z * Z
|
|
||||||
U = TPBE4 * ( Z - 1.0d+00 ) * Z
|
|
||||||
dUdR = TPBE24 * ( 2.0d+00 * Z - 1.0d+00 ) * Z / R
|
|
||||||
if ( R > TPBRcutoff1 ) then
|
|
||||||
t = ( R - TPBRcutoff1 ) / TPBDRcutoff
|
|
||||||
S = 1.0d+00 - t * t * ( 3.0d+00 - 2.0d+00 * t )
|
|
||||||
dSdR = 6.0d+00 * t * ( t - 1.0d+00 ) / TPBDRcutoff
|
|
||||||
dUdR = dUdR * S + U * dSdR
|
|
||||||
U = U * S
|
|
||||||
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
|
|
||||||
real(c_double), intent(in) :: L
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double), dimension(0:2) :: FF, MM, FFF
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
FF = 0.5d+00 * F
|
|
||||||
MM = M / L
|
|
||||||
call V3_V3xxV3 ( FFF, MM, Laxis )
|
|
||||||
F1 = FF - FFF
|
|
||||||
F2 = FF + FFF
|
|
||||||
end subroutine TPBSegmentForces !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Initialization
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
subroutine TPBInit () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real(c_double) :: R
|
|
||||||
integer(c_int) :: i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
TPBE4 = 4.0d+00 * TPBE
|
|
||||||
TPBE24 = - 24.0d+00 * TPBE
|
|
||||||
TPBDRcutoff = TPBRcutoff - TPBRcutoff1
|
|
||||||
TPBQDRcutoff = TPBRcutoff - TPBQRcutoff1
|
|
||||||
TPBQR0 = TPBQS * 2.0d+00 ** ( 1.0d+00 / 6.0d+00 )
|
|
||||||
TPBDR = ( TPBRcutoff - TPBRmin ) / ( TPBN - 1 )
|
|
||||||
R = TPBRmin
|
|
||||||
do i = 0, TPBN - 1
|
|
||||||
TPBQ(i) = TPBQCalc0 ( R )
|
|
||||||
call TPBUCalc1 ( TPBU(i), TPBdUdR(i), R )
|
|
||||||
R = R + TPBDR
|
|
||||||
enddo
|
|
||||||
end subroutine TPBInit !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end module TubePotBase !****************************************************************************
|
|
||||||
File diff suppressed because it is too large
Load Diff
@ -1,443 +0,0 @@
|
|||||||
! ------------ ----------------------------------------------------------
|
|
||||||
! LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
! https://www.lammps.org/ Sandia National Laboratories
|
|
||||||
! LAMMPS development team: developers@lammps.org
|
|
||||||
!
|
|
||||||
! Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
! DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
! certain rights in this software. This software is distributed under
|
|
||||||
! 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 !********************************************************************************
|
|
||||||
!
|
|
||||||
! TMD Library: True tubular potential and transfer function
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 09.01, 2017
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! 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.
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
|
|
||||||
use TPMGeom
|
|
||||||
use TubePotBase
|
|
||||||
use iso_c_binding, only : c_int, c_double, c_char
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Constants
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
integer(c_int), parameter :: TPTNXMAX = 257
|
|
||||||
integer(c_int), parameter :: TPTNEMAX = 128
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Types
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
type TPTSEG !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real(c_double) :: X, Y, Z
|
|
||||||
real(c_double) :: Psi, Theta, Phi ! Euler's angles
|
|
||||||
real(c_double) :: R ! Segment radius
|
|
||||||
real(c_double) :: L ! Segment length
|
|
||||||
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
|
|
||||||
end type TPTSEG !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Global variables
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
type(TPTSEG) :: TPTSeg1, TPTSeg2 ! Two segments
|
|
||||||
|
|
||||||
contains !******************************************************************************************
|
|
||||||
|
|
||||||
subroutine TPTSegAxisVector ( S, Laxis ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
type(TPTSEG), intent(in) :: S
|
|
||||||
real(c_double), dimension(0:2), intent(out) :: Laxis
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Laxis(0:2) = S%M(2,0:2)
|
|
||||||
end subroutine TPTSegAxisVector !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine TPTSegRadVector ( S, Lrad, Eps ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
type(TPTSEG), intent(in) :: S
|
|
||||||
real(c_double), dimension(0:2), intent(out) :: Lrad
|
|
||||||
real(c_double), intent(in) :: Eps
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double) :: Ce, Se
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Ce = cos ( Eps )
|
|
||||||
Se = sin ( Eps )
|
|
||||||
Lrad(0) = Ce * S%M(0,0) + Se * S%M(1,0)
|
|
||||||
Lrad(1) = Ce * S%M(0,1) + Se * S%M(1,1)
|
|
||||||
Lrad(2) = Ce * S%M(0,2) + Se * S%M(1,2)
|
|
||||||
end subroutine TPTSegRadVector !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine TPTRadiusVector ( S, R, X, Eps ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
type(TPTSEG), intent(in) :: S
|
|
||||||
real(c_double), dimension(0:2), intent(out) :: R
|
|
||||||
real(c_double), intent(in) :: X, Eps
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double), dimension(0:2) :: Laxis, Lrad
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
call TPTSegAxisVector ( S, Laxis )
|
|
||||||
call TPTSegRadVector ( S, Lrad, Eps )
|
|
||||||
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
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double) :: X, Eps
|
|
||||||
integer(c_int) :: i, j
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
X = - S%L / 2.0
|
|
||||||
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
|
|
||||||
call TPTRadiusVector ( S, S%Rtab(i,j,0:2), X, Eps )
|
|
||||||
Eps = Eps + S%DE
|
|
||||||
end do
|
|
||||||
X = X + S%DX
|
|
||||||
end do
|
|
||||||
end subroutine TPTCalcSegNodeTable !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine TPTSetSegPosition1 ( S, Rcenter, Laxis, L ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
type(TPTSEG), intent(inout) :: S
|
|
||||||
real(c_double), dimension(0:2), intent(in) :: Rcenter, Laxis
|
|
||||||
real(c_double), intent(in) :: L
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
S%L = L
|
|
||||||
S%DX = L / ( S%NX - 1 )
|
|
||||||
call EulerAngles ( S%Psi, S%Theta, Laxis )
|
|
||||||
S%Phi= 0.0d+00
|
|
||||||
S%X = Rcenter(0)
|
|
||||||
S%Y = Rcenter(1)
|
|
||||||
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) :: L
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
R = 0.5 * ( R1 + R2 )
|
|
||||||
Laxis = R2 - R1
|
|
||||||
L = S_V3norm3 ( Laxis )
|
|
||||||
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
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer(c_int) :: i, j
|
|
||||||
real(c_double) :: L1, L2, Displacement, D
|
|
||||||
real(c_double), dimension(0:2) :: Laxis, Q, R
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
L2 = S1%L / 2.0
|
|
||||||
L1 = - L2
|
|
||||||
call TPTSegAxisVector ( S1, Laxis )
|
|
||||||
R(0) = S1%X
|
|
||||||
R(1) = S1%Y
|
|
||||||
R(2) = S1%Z
|
|
||||||
do i = 0, S2%NX - 1
|
|
||||||
do j = 0, S2%NE - 1
|
|
||||||
call LinePoint ( Displacement, Q, R, Laxis, S2%Rtab(i,j,0:2) )
|
|
||||||
D = sqrt ( sqr ( Q(0) - S2%Rtab(i,j,0) ) + sqr ( Q(1) - S2%Rtab(i,j,1) ) &
|
|
||||||
+ sqr ( Q(2) - S2%Rtab(i,j,2) ) )
|
|
||||||
if ( Displacement > L1 .and. Displacement < L2 .and. D < S1%R ) then
|
|
||||||
TPTCheckIntersection = 1
|
|
||||||
return
|
|
||||||
end if
|
|
||||||
end do
|
|
||||||
end do
|
|
||||||
TPTCheckIntersection = 0
|
|
||||||
end function TPTCheckIntersection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
integer(c_int) function TPTCalcPointRange ( S, Xmin, Xmax, Re ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
type(TPTSEG), intent(in) :: S
|
|
||||||
real(c_double), intent(out) :: Xmin, Xmax
|
|
||||||
real(c_double), dimension(0:2), intent(in) :: Re
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double) :: Displacement, Distance
|
|
||||||
real(c_double), dimension(0:2) :: Laxis, Q, R
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
call TPTSegAxisVector ( S, Laxis )
|
|
||||||
R(0) = S%X
|
|
||||||
R(1) = S%Y
|
|
||||||
R(2) = S%Z
|
|
||||||
call LinePoint ( Displacement, Q, R, Laxis, Re )
|
|
||||||
Distance = sqrt ( sqr ( Q(0) - Re(0) ) + sqr ( Q(1) - Re(1) ) + sqr ( Q(2) - Re(2) ) ) - S%R
|
|
||||||
if ( TPBRcutoff < Distance ) then
|
|
||||||
Xmin = 0.0d+00
|
|
||||||
Xmax = 0.0d+00
|
|
||||||
TPTCalcPointRange = 0
|
|
||||||
return
|
|
||||||
end if
|
|
||||||
Distance = sqrt ( TPBRcutoff * TPBRcutoff - Distance * Distance )
|
|
||||||
Xmin = Displacement - Distance
|
|
||||||
Xmax = Displacement + Distance
|
|
||||||
TPTCalcPointRange = 1
|
|
||||||
end function TPTCalcPointRange !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine TPTGetEnds ( R1_1, R1_2, R2_1, R2_2, X1_1, X1_2, X2_1, X2_2, H, A ) !!!!!!!!!!!!!
|
|
||||||
real(c_double), dimension(0:2), intent(out) :: R1_1, R1_2, R2_1, R2_2
|
|
||||||
real(c_double), intent(in) :: X1_1, X1_2, X2_1, X2_2, H, A
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
R1_1(0) = 0.0d+00
|
|
||||||
R1_1(1) = 0.0d+00
|
|
||||||
R1_1(2) = X1_1
|
|
||||||
R1_2(0) = 0.0d+00
|
|
||||||
R1_2(1) = 0.0d+00
|
|
||||||
R1_2(2) = X1_2
|
|
||||||
R2_1(0) = H
|
|
||||||
R2_1(1) = - X2_1 * sin ( A )
|
|
||||||
R2_1(2) = X2_1 * cos ( A )
|
|
||||||
R2_2(0) = H
|
|
||||||
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
|
|
||||||
! produced by the segment S.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double), intent(out) :: Q, U
|
|
||||||
real(c_double), dimension(0:2), intent(out) :: F
|
|
||||||
real(c_double), dimension(0:2), intent(in) :: R
|
|
||||||
type(TPTSEG), intent(in) :: S
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer(c_int) :: i, j
|
|
||||||
real(c_double), dimension(0:2) :: RR, FF
|
|
||||||
real(c_double) :: QQ, UU, UUU, FFF, Rabs
|
|
||||||
real(c_double) :: Coeff, Xmin, Xmax, X
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
TPTPointPotential = 0
|
|
||||||
Q = 0.0d+00
|
|
||||||
U = 0.0d+00
|
|
||||||
F = 0.0d+00
|
|
||||||
if ( TPTCalcPointRange ( S, Xmin, Xmax, R ) == 0 ) return
|
|
||||||
X = - S%L / 2.0
|
|
||||||
do i = 0, S%NX - 1
|
|
||||||
if ( X > Xmin .and. X < Xmax ) then
|
|
||||||
QQ = 0.0d+00
|
|
||||||
UU = 0.0d+00
|
|
||||||
FF = 0.0d+00
|
|
||||||
do j = 0, S%NE - 1
|
|
||||||
RR(0:2) = S%Rtab(i,j,0:2) - R(0:2)
|
|
||||||
Rabs = S_V3norm3 ( RR )
|
|
||||||
if ( Rabs < TPBRcutoff ) then
|
|
||||||
QQ = QQ + TPBQCalc0 ( Rabs )
|
|
||||||
call TPBUCalc1 ( UUU, FFF, Rabs )
|
|
||||||
UU = UU + UUU
|
|
||||||
FFF = FFF / Rabs
|
|
||||||
FF = FF + FFF * RR
|
|
||||||
TPTPointPotential = 1
|
|
||||||
end if
|
|
||||||
end do
|
|
||||||
if ( i == 0 .or. i == S%NX - 1 ) then
|
|
||||||
Q = Q + 0.5d+00 * QQ
|
|
||||||
U = U + 0.5d+00 * UU
|
|
||||||
F = F + 0.5d+00 * FF
|
|
||||||
else
|
|
||||||
Q = Q + QQ
|
|
||||||
U = U + UU
|
|
||||||
F = F + FF
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
X = X + S%DX
|
|
||||||
end do
|
|
||||||
Coeff = TPBD * S%DX * S%R * S%DE
|
|
||||||
Q = Q * S%DX * S%R * S%DE
|
|
||||||
U = U * Coeff
|
|
||||||
F = F * Coeff
|
|
||||||
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
|
|
||||||
! and applied to the i-th circular cross-section of the segment S.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double), intent(out) :: Q, U
|
|
||||||
real(c_double), dimension(0:2), intent(out) :: F, M
|
|
||||||
type(TPTSEG), intent(in) :: S, Ssource
|
|
||||||
integer(c_int), intent(in) :: i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer(c_int) :: j
|
|
||||||
real(c_double), dimension(0:2) :: R, Fp, Mp, Lrad
|
|
||||||
real(c_double) :: Qp, Up, Eps
|
|
||||||
real(c_double) :: Coeff
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
TPTSectionPotential = 0
|
|
||||||
Q = 0.0d+00
|
|
||||||
U = 0.0d+00
|
|
||||||
F = 0.0d+00
|
|
||||||
M = 0.0d+00
|
|
||||||
Eps = 0.0d+00
|
|
||||||
do j = 0, S%NE - 1
|
|
||||||
call TPTSegRadVector ( S, Lrad, Eps )
|
|
||||||
if ( TPTPointPotential ( Qp, Up, Fp, S%Rtab(i,j,0:2), Ssource ) == 1 ) then
|
|
||||||
Q = Q + Qp
|
|
||||||
U = U + Up
|
|
||||||
F = F + Fp
|
|
||||||
R(0) = S%Rtab(i,j,0) - S%X
|
|
||||||
R(1) = S%Rtab(i,j,1) - S%Y
|
|
||||||
R(2) = S%Rtab(i,j,2) - S%Z
|
|
||||||
call V3_V3xxV3 ( Mp, R, Fp )
|
|
||||||
M = M + Mp
|
|
||||||
TPTSectionPotential = 1
|
|
||||||
end if
|
|
||||||
Eps = Eps + S%DE
|
|
||||||
end do
|
|
||||||
Coeff = TPBD * S%R * S%DE
|
|
||||||
Q = Q * S%R * S%DE
|
|
||||||
U = U * Coeff
|
|
||||||
F = F * Coeff
|
|
||||||
M = M * Coeff
|
|
||||||
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
|
|
||||||
! Ssource and applied to the segment S.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double), intent(out) :: Q, U
|
|
||||||
real(c_double), dimension(0:2), intent(out) :: F, M
|
|
||||||
type(TPTSEG), intent(in) :: S, Ssource
|
|
||||||
integer(c_int) :: i
|
|
||||||
real(c_double), dimension(0:2) :: Fc, Mc
|
|
||||||
real(c_double) :: Qc, Uc
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
TPTSegmentPotential = 0
|
|
||||||
Q = 0.0d+00
|
|
||||||
U = 0.0d+00
|
|
||||||
F = 0.0d+00
|
|
||||||
M = 0.0d+00
|
|
||||||
if ( TPTCheckIntersection ( S, Ssource ) == 1 ) then
|
|
||||||
TPTSegmentPotential = 2
|
|
||||||
return
|
|
||||||
end if
|
|
||||||
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
|
|
||||||
U = U + 0.5d+00 * Uc
|
|
||||||
F = F + 0.5d+00 * Fc
|
|
||||||
M = M + 0.5d+00 * Mc
|
|
||||||
else
|
|
||||||
Q = Q + Qc
|
|
||||||
U = U + Uc
|
|
||||||
F = F + Fc
|
|
||||||
M = M + Mc
|
|
||||||
end if
|
|
||||||
TPTSegmentPotential = 1
|
|
||||||
end if
|
|
||||||
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
|
|
||||||
real(c_double), intent(in) :: L
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double), dimension(0:2) :: MM, FF, FFF
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
FF = 0.5d+00 * F
|
|
||||||
MM = M / L
|
|
||||||
call V3_V3xxV3 ( FFF, MM, Laxis )
|
|
||||||
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.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double), intent(out) :: Q, U
|
|
||||||
real(c_double), dimension(0:2), intent(out) :: F1_1, F1_2, F2_1, F2_2
|
|
||||||
real(c_double), dimension(0:2), intent(in) :: R1_1, R1_2, R2_1, R2_2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real(c_double), dimension(0:2) :: R1, R2, Laxis1, Laxis2, DR, F1, M1, F2, M2
|
|
||||||
real(c_double) :: L1, L2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
R1 = 0.5 * ( R1_1 + R1_2 )
|
|
||||||
R2 = 0.5 * ( R2_1 + R2_2 )
|
|
||||||
Laxis1 = R1_2 - R1_1
|
|
||||||
Laxis2 = R2_2 - R2_1
|
|
||||||
L1 = S_V3norm3 ( Laxis1 )
|
|
||||||
L2 = S_V3norm3 ( Laxis2 )
|
|
||||||
Laxis1 = Laxis1 / L1
|
|
||||||
Laxis2 = Laxis2 / L2
|
|
||||||
DR = R2 - R1
|
|
||||||
call TPTSetSegPosition1 ( TPTSeg1, R1, Laxis1, L1 )
|
|
||||||
call TPTSetSegPosition1 ( TPTSeg2, R2, Laxis2, L2 )
|
|
||||||
TPTInteractionF = TPTSegmentPotential ( Q, U, F1, M1, TPTSeg1, TPTSeg2 )
|
|
||||||
if ( TPTInteractionF .ne. 1 ) return
|
|
||||||
call V3_V3xxV3 ( M2, DR, F1 )
|
|
||||||
F2 = - F1
|
|
||||||
M2 = - M1 - M2
|
|
||||||
call TPTSegmentForces ( F1_1, F1_2, F1, M1, Laxis1, L1 )
|
|
||||||
call TPTSegmentForces ( F2_1, F2_2, F2, M2, Laxis2, L2 )
|
|
||||||
end function TPTInteractionF !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Initialization
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
subroutine TPTInit ( R1, R2, NX, NE ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real(c_double), intent(in) :: R1, R2
|
|
||||||
integer(c_int), intent(in) :: NX, NE
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
TPTSeg1%X = 0.0d+00
|
|
||||||
TPTSeg1%Y = 0.0d+00
|
|
||||||
TPTSeg1%Z = 0.0d+00
|
|
||||||
TPTSeg1%Psi = 0.0d+00
|
|
||||||
TPTSeg1%Theta = 0.0d+00
|
|
||||||
TPTSeg1%Phi = 0.0d+00
|
|
||||||
TPTSeg1%R = R1
|
|
||||||
TPTSeg1%NX = NX
|
|
||||||
TPTSeg1%NE = NE
|
|
||||||
TPTSeg1%DE = M_2PI / NE
|
|
||||||
TPTSeg2%X = 0.0d+00
|
|
||||||
TPTSeg2%Y = 0.0d+00
|
|
||||||
TPTSeg2%Z = 0.0d+00
|
|
||||||
TPTSeg2%Psi = 0.0d+00
|
|
||||||
TPTSeg2%Theta = 0.0d+00
|
|
||||||
TPTSeg2%Phi = 0.0d+00
|
|
||||||
TPTSeg2%R = R2
|
|
||||||
TPTSeg2%NX = NX
|
|
||||||
TPTSeg2%NE = NE
|
|
||||||
TPTSeg2%DE = M_2PI / NE
|
|
||||||
end subroutine TPTInit !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end module TubePotTrue !****************************************************************************
|
|
||||||
@ -1,79 +0,0 @@
|
|||||||
# Install/unInstall package files in LAMMPS
|
|
||||||
# mode = 0/1/2 for uninstall/install/update
|
|
||||||
|
|
||||||
mode=$1
|
|
||||||
|
|
||||||
# enforce using portable C locale
|
|
||||||
LC_ALL=C
|
|
||||||
export LC_ALL
|
|
||||||
|
|
||||||
# arg1 = file, arg2 = file it depends on
|
|
||||||
|
|
||||||
action () {
|
|
||||||
if (test $mode = 0) then
|
|
||||||
rm -f ../$1
|
|
||||||
elif (! cmp -s $1 ../$1) then
|
|
||||||
if (test -z "$2" || test -e ../$2) then
|
|
||||||
cp $1 ..
|
|
||||||
if (test $mode = 2) then
|
|
||||||
echo " updating src/$1"
|
|
||||||
fi
|
|
||||||
fi
|
|
||||||
elif (test -n "$2") then
|
|
||||||
if (test ! -e ../$2) then
|
|
||||||
rm -f ../$1
|
|
||||||
fi
|
|
||||||
fi
|
|
||||||
}
|
|
||||||
|
|
||||||
# list of files with optional dependencies
|
|
||||||
action angle_mesocnt.cpp
|
|
||||||
action angle_mesocnt.h
|
|
||||||
action bond_mesocnt.cpp bond_harmonic.cpp
|
|
||||||
action bond_mesocnt.h bond_harmonic.h
|
|
||||||
action compute_mesont.cpp
|
|
||||||
action compute_mesont.h
|
|
||||||
action pair_mesocnt.cpp
|
|
||||||
action pair_mesocnt.h
|
|
||||||
action pair_mesocnt_viscous.cpp
|
|
||||||
action pair_mesocnt_viscous.h
|
|
||||||
|
|
||||||
action export_mesont.h
|
|
||||||
action atom_vec_mesont.cpp
|
|
||||||
action atom_vec_mesont.h
|
|
||||||
action pair_mesont_tpm.cpp
|
|
||||||
action pair_mesont_tpm.h
|
|
||||||
|
|
||||||
# edit 2 Makefile.package files to include/exclude package info
|
|
||||||
|
|
||||||
if (test $1 = 1) then
|
|
||||||
|
|
||||||
if (test -e ../Makefile.package) then
|
|
||||||
sed -i -e 's/[^ \t]*mesont[^ \t]* //' ../Makefile.package
|
|
||||||
sed -i -e 's|^PKG_INC =[ \t]*|&-I../../lib/mesont |' ../Makefile.package
|
|
||||||
sed -i -e 's|^PKG_PATH =[ \t]*|&-L../../lib/mesont |' ../Makefile.package
|
|
||||||
sed -i -e 's|^PKG_LIB =[ \t]*|&-lmesont |' ../Makefile.package
|
|
||||||
sed -i -e 's|^PKG_SYSINC =[ \t]*|&$(mesont_SYSINC) |' ../Makefile.package
|
|
||||||
sed -i -e 's|^PKG_SYSLIB =[ \t]*|&$(mesont_SYSLIB) |' ../Makefile.package
|
|
||||||
sed -i -e 's|^PKG_SYSPATH =[ \t]*|&$(mesont_SYSPATH) |' ../Makefile.package
|
|
||||||
fi
|
|
||||||
|
|
||||||
if (test -e ../Makefile.package.settings) then
|
|
||||||
sed -i -e '/^[ \t]*include.*mesont.*$/d' ../Makefile.package.settings
|
|
||||||
# multiline form needed for BSD sed on Macs
|
|
||||||
sed -i -e '4 i \
|
|
||||||
include ..\/..\/lib\/mesont\/Makefile.lammps
|
|
||||||
' ../Makefile.package.settings
|
|
||||||
fi
|
|
||||||
|
|
||||||
elif (test $1 = 0) then
|
|
||||||
|
|
||||||
if (test -e ../Makefile.package) then
|
|
||||||
sed -i -e 's/[^ \t]*mesont[^ \t]* //' ../Makefile.package
|
|
||||||
fi
|
|
||||||
|
|
||||||
if (test -e ../Makefile.package.settings) then
|
|
||||||
sed -i -e '/^[ \t]*include.*mesont.*$/d' ../Makefile.package.settings
|
|
||||||
fi
|
|
||||||
|
|
||||||
fi
|
|
||||||
@ -9,33 +9,20 @@ is provided in the papers listed below.
|
|||||||
|
|
||||||
--
|
--
|
||||||
|
|
||||||
This package was created by Maxim Shugaev (mvs9t@virginia.edu)
|
This package was originally created by Maxim Shugaev (mvs9t@virginia.edu)
|
||||||
at the University of Virginia.
|
at the University of Virginia.
|
||||||
The Fortran library implementing basic level functions describing stretching,
|
The Fortran library implementing basic level functions describing stretching,
|
||||||
bending, and intertube components of the mesoscopic CNT force field, used
|
bending, and intertube components of the mesoscopic CNT force field, used
|
||||||
by this package is developed by Alexey N. Volkov (avolkov1@ua.edu)
|
by this package was developed by Alexey N. Volkov (avolkov1@ua.edu)
|
||||||
at the University of Alabama.
|
at the University of Alabama.
|
||||||
|
|
||||||
--
|
Since then the functionality has been re-implemented in C++ by
|
||||||
|
Philipp Kloza (U Cambridge) with some additions and the Fortran
|
||||||
|
implementation was removed in early 2023 since C++ version is
|
||||||
|
faster and easier to compile and maintain.
|
||||||
|
|
||||||
The following commands are contained in this package:
|
Please see the LAMMPS manual for more information about this package
|
||||||
|
and how to install and use it.
|
||||||
atom_style mesont
|
|
||||||
This command enables mesont atom_style containing variables used for
|
|
||||||
further commands in MESONT.
|
|
||||||
|
|
||||||
pair_style mesont/tpm cut table_path BendingMode TPMType
|
|
||||||
This command activates a pair_style describing CNT mesoscopic tubular
|
|
||||||
potential model (TPM) force field. "cut" is cutoff distance that should
|
|
||||||
be set to be at least max(2.0*L, sqrt(L^2/2 + (2.0*R + Tcut)^2)),
|
|
||||||
where L is the maximum segment length, R is the maximum tube radius,
|
|
||||||
and Tcut = 10.2 A is the maximum distance between surfaces of interacting
|
|
||||||
segments. However, the recommended cutoff is 3L.
|
|
||||||
|
|
||||||
compute mesont
|
|
||||||
This command allows evaluation of per atom and total values of stretching,
|
|
||||||
bending, and intertube interaction components of energies. Use the following
|
|
||||||
flags: 'estretch', 'ebend', 'etube'.
|
|
||||||
|
|
||||||
--
|
--
|
||||||
|
|
||||||
|
|||||||
@ -1,47 +0,0 @@
|
|||||||
/* ----------------------------------------------------------------------
|
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
|
||||||
LAMMPS development team: developers@lammps.org
|
|
||||||
|
|
||||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
certain rights in this software. This software is distributed under
|
|
||||||
the GNU General Public License.
|
|
||||||
|
|
||||||
See the README file in the top-level LAMMPS directory.
|
|
||||||
|
|
||||||
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
#include "atom_vec_mesont.h"
|
|
||||||
#include "atom.h"
|
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
AtomVecMesoNT::AtomVecMesoNT(LAMMPS *lmp) : AtomVec(lmp)
|
|
||||||
{
|
|
||||||
molecular = Atom::ATOMIC;
|
|
||||||
mass_type = PER_TYPE;
|
|
||||||
|
|
||||||
atom->mesont_flag = 1;
|
|
||||||
|
|
||||||
// strings with peratom variables to include in each AtomVec method
|
|
||||||
// strings cannot contain fields in corresponding AtomVec default strings
|
|
||||||
// order of fields in a string does not matter
|
|
||||||
// except: fields_data_atom & fields_data_vel must match data file
|
|
||||||
|
|
||||||
fields_grow = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
|
|
||||||
fields_copy = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
|
|
||||||
fields_border = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
|
|
||||||
fields_border_vel = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
|
|
||||||
fields_exchange = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
|
|
||||||
fields_restart = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
|
|
||||||
fields_create = {"rmass", "radius", "length", "buckling", "bond_nt", "molecule"};
|
|
||||||
fields_data_atom = {"id", "molecule", "type", "bond_nt", "rmass",
|
|
||||||
"radius", "length", "buckling", "x"};
|
|
||||||
fields_data_vel = {"id", "v"};
|
|
||||||
|
|
||||||
setup_fields();
|
|
||||||
}
|
|
||||||
@ -1,37 +0,0 @@
|
|||||||
/* -*- c++ -*- ----------------------------------------------------------
|
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
|
||||||
LAMMPS development team: developers@lammps.org
|
|
||||||
|
|
||||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
certain rights in this software. This software is distributed under
|
|
||||||
the GNU General Public License.
|
|
||||||
|
|
||||||
See the README file in the top-level LAMMPS directory.
|
|
||||||
|
|
||||||
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
#ifdef ATOM_CLASS
|
|
||||||
// clang-format off
|
|
||||||
AtomStyle(mesont,AtomVecMesoNT);
|
|
||||||
// clang-format on
|
|
||||||
#else
|
|
||||||
|
|
||||||
#ifndef LMP_ATOM_VEC_MESONT_H
|
|
||||||
#define LMP_ATOM_VEC_MESONT_H
|
|
||||||
|
|
||||||
#include "atom_vec.h"
|
|
||||||
|
|
||||||
namespace LAMMPS_NS {
|
|
||||||
|
|
||||||
class AtomVecMesoNT : virtual public AtomVec {
|
|
||||||
public:
|
|
||||||
AtomVecMesoNT(class LAMMPS *);
|
|
||||||
};
|
|
||||||
|
|
||||||
} // namespace LAMMPS_NS
|
|
||||||
|
|
||||||
#endif
|
|
||||||
#endif
|
|
||||||
@ -1,156 +0,0 @@
|
|||||||
// clang-format off
|
|
||||||
/* -*- c++ -*- ----------------------------------------------------------
|
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
|
||||||
LAMMPS development team: developers@lammps.org
|
|
||||||
|
|
||||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
certain rights in this software. This software is distributed under
|
|
||||||
the GNU General Public License.
|
|
||||||
|
|
||||||
See the README file in the top-level LAMMPS directory.
|
|
||||||
|
|
||||||
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
#include "compute_mesont.h"
|
|
||||||
|
|
||||||
#include "atom.h"
|
|
||||||
#include "comm.h"
|
|
||||||
#include "error.h"
|
|
||||||
#include "force.h"
|
|
||||||
#include "memory.h"
|
|
||||||
#include "pair.h"
|
|
||||||
#include "update.h"
|
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
ComputeMesoNT::ComputeMesoNT(LAMMPS *lmp, int narg, char **arg) :
|
|
||||||
Compute(lmp, narg, arg), energy(nullptr) {
|
|
||||||
if (narg != 4) error->all(FLERR,"Illegal compute mesont command");
|
|
||||||
|
|
||||||
std::string ctype = arg[3];
|
|
||||||
if (ctype == "estretch") compute_type = ES;
|
|
||||||
else if (ctype == "ebend") compute_type = EB;
|
|
||||||
else if (ctype == "etube") compute_type = ET;
|
|
||||||
else error->all(FLERR,"Illegal compute mesont command");
|
|
||||||
|
|
||||||
peratom_flag = 1;
|
|
||||||
size_peratom_cols = 0;
|
|
||||||
peatomflag = 1;
|
|
||||||
timeflag = 1;
|
|
||||||
comm_reverse = 1;
|
|
||||||
extscalar = 1;
|
|
||||||
scalar_flag = 1;
|
|
||||||
nmax = 0;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
ComputeMesoNT::~ComputeMesoNT() {
|
|
||||||
memory->destroy(energy);
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
double ComputeMesoNT::compute_scalar() {
|
|
||||||
invoked_scalar = update->ntimestep;
|
|
||||||
if (update->eflag_global != invoked_scalar)
|
|
||||||
error->all(FLERR,"Energy was not tallied on needed timestep");
|
|
||||||
|
|
||||||
int i;
|
|
||||||
double* ptr = nullptr;
|
|
||||||
if (compute_type == ES)
|
|
||||||
ptr = static_cast<double*>(force->pair->extract("mesonttpm_Es_tot",i));
|
|
||||||
else if (compute_type == EB)
|
|
||||||
ptr = static_cast<double*>(force->pair->extract("mesonttpm_Eb_tot",i));
|
|
||||||
else if (compute_type == ET)
|
|
||||||
ptr = static_cast<double*>(force->pair->extract("mesonttpm_Et_tot",i));
|
|
||||||
else error->all(FLERR,"Illegal compute mesont command");
|
|
||||||
|
|
||||||
if (!ptr) error->all(FLERR,
|
|
||||||
"compute mesont is allowed only with mesont/tpm pair style");
|
|
||||||
MPI_Allreduce(ptr,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
|
|
||||||
|
|
||||||
return scalar;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void ComputeMesoNT::compute_peratom() {
|
|
||||||
invoked_peratom = update->ntimestep;
|
|
||||||
if (update->eflag_atom != invoked_peratom)
|
|
||||||
error->all(FLERR,"Per-atom energy was not tallied on needed timestep");
|
|
||||||
|
|
||||||
// grow local energy array if necessary
|
|
||||||
// needs to be atom->nmax in length
|
|
||||||
if (atom->nmax > nmax) {
|
|
||||||
memory->destroy(energy);
|
|
||||||
nmax = atom->nmax;
|
|
||||||
memory->create(energy,nmax,"mesont_Eb:energy");
|
|
||||||
vector_atom = energy;
|
|
||||||
}
|
|
||||||
|
|
||||||
// npair includes ghosts if newton_bond is set
|
|
||||||
// ntotal includes ghosts if either newton flag is set
|
|
||||||
int nlocal = atom->nlocal;
|
|
||||||
int npair = nlocal;
|
|
||||||
if (force->newton) npair += atom->nghost;
|
|
||||||
int ntotal = nlocal;
|
|
||||||
if (force->newton) ntotal += atom->nghost;
|
|
||||||
int i;
|
|
||||||
// clear local energy array
|
|
||||||
for (int i = 0; i < ntotal; i++) energy[i] = 0.0;
|
|
||||||
double* ptr = nullptr;
|
|
||||||
if (compute_type == ES)
|
|
||||||
ptr = static_cast<double*>(force->pair->extract("mesonttpm_Es",i));
|
|
||||||
else if (compute_type == EB)
|
|
||||||
ptr = static_cast<double*>(force->pair->extract("mesonttpm_Eb",i));
|
|
||||||
else if (compute_type == ET)
|
|
||||||
ptr = static_cast<double*>(force->pair->extract("mesonttpm_Et",i));
|
|
||||||
else error->all(FLERR,"Illegal compute mesont command");
|
|
||||||
|
|
||||||
if (ptr) for (i = 0; i < npair; i++) energy[i] += ptr[i];
|
|
||||||
else error->all(FLERR,
|
|
||||||
"compute mesont is allowed only with mesont/tpm pair style");
|
|
||||||
|
|
||||||
// communicate ghost energy between neighbor procs
|
|
||||||
if (force->newton) comm->reverse_comm(this);
|
|
||||||
|
|
||||||
// zero energy of atoms not in group
|
|
||||||
// only do this after comm since ghost contributions must be included
|
|
||||||
int *mask = atom->mask;
|
|
||||||
for (int i = 0; i < nlocal; i++)
|
|
||||||
if (!(mask[i] & groupbit)) energy[i] = 0.0;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
int ComputeMesoNT::pack_reverse_comm(int n, int first, double *buf) {
|
|
||||||
int m = 0;
|
|
||||||
int last = first + n;
|
|
||||||
for (int i = first; i < last; i++) buf[m++] = energy[i];
|
|
||||||
return m;
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void ComputeMesoNT::unpack_reverse_comm(int n, int *list, double *buf) {
|
|
||||||
int m = 0;
|
|
||||||
for (int i = 0; i < n; i++) {
|
|
||||||
int j = list[i];
|
|
||||||
energy[j] += buf[m++];
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
memory usage of local atom-based array
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
double ComputeMesoNT::memory_usage() {
|
|
||||||
double bytes = (double)nmax * sizeof(double);
|
|
||||||
return bytes;
|
|
||||||
}
|
|
||||||
@ -1,51 +0,0 @@
|
|||||||
/* -*- c++ -*- ----------------------------------------------------------
|
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
|
||||||
LAMMPS development team: developers@lammps.org
|
|
||||||
|
|
||||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
certain rights in this software. This software is distributed under
|
|
||||||
the GNU General Public License.
|
|
||||||
|
|
||||||
See the README file in the top-level LAMMPS directory.
|
|
||||||
|
|
||||||
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
#ifdef COMPUTE_CLASS
|
|
||||||
// clang-format off
|
|
||||||
ComputeStyle(mesont,ComputeMesoNT);
|
|
||||||
// clang-format on
|
|
||||||
#else
|
|
||||||
|
|
||||||
#ifndef LMP_COMPUTE_MESONT_ATOM_H
|
|
||||||
#define LMP_COMPUTE_MESONT_ATOM_H
|
|
||||||
|
|
||||||
#include "compute.h"
|
|
||||||
|
|
||||||
namespace LAMMPS_NS {
|
|
||||||
|
|
||||||
class ComputeMesoNT : public Compute {
|
|
||||||
public:
|
|
||||||
ComputeMesoNT(class LAMMPS *, int, char **);
|
|
||||||
~ComputeMesoNT() override;
|
|
||||||
void init() override {}
|
|
||||||
void compute_peratom() override;
|
|
||||||
double compute_scalar() override;
|
|
||||||
int pack_reverse_comm(int, int, double *) override;
|
|
||||||
void unpack_reverse_comm(int, int *, double *) override;
|
|
||||||
double memory_usage() override;
|
|
||||||
|
|
||||||
private:
|
|
||||||
int nmax;
|
|
||||||
double *energy;
|
|
||||||
|
|
||||||
enum ComputeType { ES, EB, ET };
|
|
||||||
ComputeType compute_type;
|
|
||||||
};
|
|
||||||
|
|
||||||
} // namespace LAMMPS_NS
|
|
||||||
|
|
||||||
#endif
|
|
||||||
#endif
|
|
||||||
@ -1,48 +0,0 @@
|
|||||||
/* -*- c++ -*- ----------------------------------------------------------
|
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
|
||||||
LAMMPS development team: developers@lammps.org
|
|
||||||
|
|
||||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
certain rights in this software. This software is distributed under
|
|
||||||
the GNU General Public License.
|
|
||||||
|
|
||||||
See the README file in the top-level LAMMPS directory.
|
|
||||||
|
|
||||||
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
#ifdef __cplusplus
|
|
||||||
extern "C" {
|
|
||||||
#endif
|
|
||||||
// see ExportCNT.f90 in lib/mesont for function details
|
|
||||||
void mesont_lib_TPBInit();
|
|
||||||
void mesont_lib_TPMInit(const int &M, const int &N);
|
|
||||||
void mesont_lib_SetTablePath(const char *TPMFile, const int &N);
|
|
||||||
|
|
||||||
void mesont_lib_InitCNTPotModule(const int &STRModel, const int &STRParams, const int &YMType,
|
|
||||||
const int &BNDModel, const double &Rref);
|
|
||||||
|
|
||||||
double mesont_lib_get_R();
|
|
||||||
|
|
||||||
void mesont_lib_TubeStretchingForceField(double &U1, double &U2, double *F1, double *F2, double *S1,
|
|
||||||
double *S2, const double *X1, const double *X2,
|
|
||||||
const double &R12, const double &L12);
|
|
||||||
|
|
||||||
void mesont_lib_TubeBendingForceField(double &U1, double &U2, double &U3, double *F1, double *F2,
|
|
||||||
double *F3, double *S1, double *S2, double *S3,
|
|
||||||
const double *X1, const double *X2, const double *X3,
|
|
||||||
const double &R123, const double &L123, int &BBF2);
|
|
||||||
|
|
||||||
void mesont_lib_SegmentTubeForceField(double &U1, double &U2, double *U, double *F1, double *F2,
|
|
||||||
double *F, double *Fe, double *S1, double *S2, double *S,
|
|
||||||
double *Se, const double *X1, const double *X2,
|
|
||||||
const double &R12, const int &N, const double *X,
|
|
||||||
const double *Xe, const int *BBF, const double &R,
|
|
||||||
const int &E1, const int &E2, const int &Ee,
|
|
||||||
const int &TPMType);
|
|
||||||
|
|
||||||
#ifdef __cplusplus
|
|
||||||
}
|
|
||||||
#endif
|
|
||||||
@ -1371,7 +1371,7 @@ void PairMesoCNT::chain_split(int *redlist, int numred, int *nchain, int **chain
|
|||||||
|
|
||||||
tagint *tag = atom->tag;
|
tagint *tag = atom->tag;
|
||||||
tagint *mol = atom->molecule;
|
tagint *mol = atom->molecule;
|
||||||
tagint *type = atom->type;
|
int *type = atom->type;
|
||||||
int clen = 0;
|
int clen = 0;
|
||||||
int cid = 0;
|
int cid = 0;
|
||||||
|
|
||||||
|
|||||||
@ -1,777 +0,0 @@
|
|||||||
// clang-format off
|
|
||||||
/* -*- c++ -*- ----------------------------------------------------------
|
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
|
||||||
LAMMPS development team: developers@lammps.org
|
|
||||||
|
|
||||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
certain rights in this software. This software is distributed under
|
|
||||||
the GNU General Public License.
|
|
||||||
|
|
||||||
See the README file in the top-level LAMMPS directory.
|
|
||||||
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
#include "pair_mesont_tpm.h"
|
|
||||||
#include "export_mesont.h"
|
|
||||||
|
|
||||||
#include "atom.h"
|
|
||||||
#include "comm.h"
|
|
||||||
#include "force.h"
|
|
||||||
#include "memory.h"
|
|
||||||
#include "error.h"
|
|
||||||
#include "neighbor.h"
|
|
||||||
#include "neigh_list.h"
|
|
||||||
|
|
||||||
#include <cstring>
|
|
||||||
#include <cmath>
|
|
||||||
|
|
||||||
#include <array>
|
|
||||||
#include <fstream>
|
|
||||||
#include <algorithm>
|
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
|
||||||
|
|
||||||
class MESONTList {
|
|
||||||
public:
|
|
||||||
MESONTList(const Atom* atom, const NeighList* nblist);
|
|
||||||
~MESONTList() = default;;
|
|
||||||
//list of segments
|
|
||||||
const std::vector<std::array<int,2>>& get_segments() const;
|
|
||||||
//list of triplets
|
|
||||||
const std::vector<std::array<int,3>>& get_triplets() const;
|
|
||||||
//list of neighbor chains [start,end] for segments
|
|
||||||
//(use idx() to get real indexes)
|
|
||||||
const std::vector<std::vector<std::array<int,2>>>& get_nbs() const;
|
|
||||||
//convert idx from sorted representation to real idx
|
|
||||||
int get_idx(int idx) const;
|
|
||||||
//return list of indexes for conversion from sorted representation
|
|
||||||
const std::vector<int>& get_idx_list() const;
|
|
||||||
//convert idx from real idx to sorted representation
|
|
||||||
int get_idxb(int idx) const;
|
|
||||||
//return list of indexes for conversion to sorted representation
|
|
||||||
const std::vector<int>& get_idxb_list() const;
|
|
||||||
//check if the node is the end of the tube
|
|
||||||
bool is_end(int idx) const;
|
|
||||||
|
|
||||||
std::array<int,2> get_segment(int idx) const;
|
|
||||||
std::array<int,3> get_triplet(int idx) const;
|
|
||||||
|
|
||||||
static const int cnt_end = -1;
|
|
||||||
static const int domain_end = -2;
|
|
||||||
static const int not_cnt = -3;
|
|
||||||
private:
|
|
||||||
std::vector<std::array<int,2>> chain_list, segments;
|
|
||||||
std::vector<std::array<int,3>> triplets;
|
|
||||||
std::vector<std::vector<std::array<int,2>>> nb_chains;
|
|
||||||
std::vector<int> index_list, index_list_b;
|
|
||||||
};
|
|
||||||
|
|
||||||
//=============================================================================
|
|
||||||
|
|
||||||
inline const std::vector<std::vector<std::array<int,2>>> &
|
|
||||||
MESONTList::get_nbs() const {
|
|
||||||
return nb_chains;
|
|
||||||
}
|
|
||||||
|
|
||||||
inline int MESONTList::get_idx(int idx) const {
|
|
||||||
return index_list[idx];
|
|
||||||
}
|
|
||||||
|
|
||||||
inline const std::vector<int>& MESONTList::get_idx_list() const {
|
|
||||||
return index_list;
|
|
||||||
};
|
|
||||||
|
|
||||||
|
|
||||||
inline int MESONTList::get_idxb(int idx) const {
|
|
||||||
return index_list_b[idx];
|
|
||||||
}
|
|
||||||
|
|
||||||
inline const std::vector<int>& MESONTList::get_idxb_list() const {
|
|
||||||
return index_list_b;
|
|
||||||
};
|
|
||||||
|
|
||||||
inline const std::vector<std::array<int,2>> & MESONTList::get_segments()
|
|
||||||
const {
|
|
||||||
return segments;
|
|
||||||
}
|
|
||||||
|
|
||||||
inline const std::vector<std::array<int,3>> & MESONTList::get_triplets()
|
|
||||||
const {
|
|
||||||
return triplets;
|
|
||||||
}
|
|
||||||
|
|
||||||
inline std::array<int,2> MESONTList::get_segment(int idx) const {
|
|
||||||
std::array<int,2> result;
|
|
||||||
result[0] = chain_list[idx][0];
|
|
||||||
result[1] = idx;
|
|
||||||
return result;
|
|
||||||
}
|
|
||||||
|
|
||||||
inline std::array<int,3> MESONTList::get_triplet(int idx) const {
|
|
||||||
std::array<int,3> result;
|
|
||||||
result[0] = chain_list[idx][0];
|
|
||||||
result[1] = idx;
|
|
||||||
result[2] = chain_list[idx][1];
|
|
||||||
return result;
|
|
||||||
}
|
|
||||||
|
|
||||||
inline bool MESONTList::is_end(int idx) const {
|
|
||||||
return chain_list[idx][0] == cnt_end || chain_list[idx][1] == cnt_end;
|
|
||||||
};
|
|
||||||
|
|
||||||
template<typename T>
|
|
||||||
void vector_union(std::vector<T>& v1, std::vector<T>& v2,
|
|
||||||
std::vector<T>& merged) {
|
|
||||||
std::sort(v1.begin(), v1.end());
|
|
||||||
std::sort(v2.begin(), v2.end());
|
|
||||||
merged.reserve(v1.size() + v2.size());
|
|
||||||
typename std::vector<T>::iterator it1 = v1.begin();
|
|
||||||
typename std::vector<T>::iterator it2 = v2.begin();
|
|
||||||
|
|
||||||
while (it1 != v1.end() && it2 != v2.end()) {
|
|
||||||
if (*it1 < *it2) {
|
|
||||||
if (merged.empty() || merged.back() < *it1) merged.push_back(*it1);
|
|
||||||
++it1;
|
|
||||||
}
|
|
||||||
else {
|
|
||||||
if (merged.empty() || merged.back() < *it2) merged.push_back(*it2);
|
|
||||||
++it2;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
while (it1 != v1.end()) {
|
|
||||||
if (merged.empty() || merged.back() < *it1) merged.push_back(*it1);
|
|
||||||
++it1;
|
|
||||||
}
|
|
||||||
|
|
||||||
while (it2 != v2.end()) {
|
|
||||||
if (merged.empty() || merged.back() < *it2) merged.push_back(*it2);
|
|
||||||
++it2;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
MESONTList::MESONTList(const Atom* atom, const NeighList* nblist) {
|
|
||||||
if (atom == nullptr || nblist == nullptr) return;
|
|
||||||
//number of local atoms at the node
|
|
||||||
int nlocal = atom->nlocal;
|
|
||||||
//total number of atoms in the node and ghost shell treated as NTs
|
|
||||||
int nall = nblist->inum + nblist->gnum;
|
|
||||||
//total number of atoms in the node and ghost shell
|
|
||||||
int ntot = atom->nlocal + atom->nghost;
|
|
||||||
tagint* const g_id = atom->tag;
|
|
||||||
tagint** const bonds = atom->bond_nt;
|
|
||||||
tagint* const chain_id = atom->molecule;
|
|
||||||
int* ilist = nblist->ilist;
|
|
||||||
|
|
||||||
//convert bonds to local id representation
|
|
||||||
chain_list.resize(ntot, {not_cnt,not_cnt});
|
|
||||||
for (int ii = 0; ii < nall; ii++) {
|
|
||||||
int i = ilist[ii];
|
|
||||||
chain_list[i][0] = domain_end;
|
|
||||||
chain_list[i][1] = domain_end;
|
|
||||||
}
|
|
||||||
for (int ii = 0; ii < nall; ii++) {
|
|
||||||
int i = ilist[ii];
|
|
||||||
int nnb = nblist->numneigh[i];
|
|
||||||
for (int m = 0; m < 2; m++)
|
|
||||||
if (bonds[i][m] == cnt_end) chain_list[i][m] = cnt_end;
|
|
||||||
for (int j = 0; j < nnb; j++) {
|
|
||||||
int nb = nblist->firstneigh[i][j];
|
|
||||||
if (bonds[i][0] == g_id[nb]) {
|
|
||||||
chain_list[i][0] = nb;
|
|
||||||
chain_list[nb][1] = i;
|
|
||||||
break;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
//reorder chains: index list
|
|
||||||
//list of indexes for conversion FROM reordered representation
|
|
||||||
index_list.reserve(nall);
|
|
||||||
index_list_b.resize(ntot, -1); // convert index TO reordered representation
|
|
||||||
for (int i = 0; i < ntot; i++) {
|
|
||||||
if (chain_list[i][0] == cnt_end || chain_list[i][0] == domain_end) {
|
|
||||||
index_list.push_back(i);
|
|
||||||
index_list_b[i] = index_list.size() - 1;
|
|
||||||
int idx = i;
|
|
||||||
while (true) {
|
|
||||||
idx = chain_list[idx][1];
|
|
||||||
if (idx == cnt_end || idx == domain_end) break;
|
|
||||||
else index_list.push_back(idx);
|
|
||||||
index_list_b[idx] = index_list.size() - 1;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
//segment list
|
|
||||||
for (int i = 0; i < nlocal; i++) {
|
|
||||||
if (chain_list[i][0] == not_cnt) continue;
|
|
||||||
if (chain_list[i][0] != cnt_end && chain_list[i][0] != domain_end &&
|
|
||||||
g_id[i] < g_id[chain_list[i][0]])
|
|
||||||
segments.push_back({i,chain_list[i][0]});
|
|
||||||
if (chain_list[i][1] != cnt_end && chain_list[i][1] != domain_end &&
|
|
||||||
g_id[i] < g_id[chain_list[i][1]])
|
|
||||||
segments.push_back({i,chain_list[i][1]});
|
|
||||||
}
|
|
||||||
int nbonds = segments.size();
|
|
||||||
|
|
||||||
//triplets
|
|
||||||
for (int i = 0; i < nlocal; i++) {
|
|
||||||
if (chain_list[i][0] == not_cnt) continue;
|
|
||||||
if (chain_list[i][0] != cnt_end && chain_list[i][0] != domain_end &&
|
|
||||||
chain_list[i][1] != cnt_end && chain_list[i][1] != domain_end)
|
|
||||||
triplets.push_back(get_triplet(i));
|
|
||||||
}
|
|
||||||
|
|
||||||
//segment neighbor list
|
|
||||||
nb_chains.resize(nbonds);
|
|
||||||
std::vector<int> nb_list_i[2], nb_list;
|
|
||||||
for (int i = 0; i < nbonds; i++) {
|
|
||||||
//union of nb lists
|
|
||||||
for (int m = 0; m < 2; m++) {
|
|
||||||
nb_list_i[m].resize(0);
|
|
||||||
int idx = segments[i][m];
|
|
||||||
if (idx >= nlocal) continue;
|
|
||||||
int nnb = nblist->numneigh[idx];
|
|
||||||
for (int j = 0; j < nnb; j++) {
|
|
||||||
int jdx = nblist->firstneigh[idx][j];
|
|
||||||
//no self interactions for nbs within the same tube
|
|
||||||
if (chain_id[jdx] == chain_id[idx] &&
|
|
||||||
std::abs(index_list_b[idx] - index_list_b[jdx]) <= 5) continue;
|
|
||||||
nb_list_i[m].push_back(index_list_b[jdx]);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
vector_union(nb_list_i[0], nb_list_i[1], nb_list);
|
|
||||||
|
|
||||||
int nnb = nb_list.size();
|
|
||||||
if (nnb > 0) {
|
|
||||||
int idx_s = nb_list[0];
|
|
||||||
for (int j = 0; j < nnb; j++) {
|
|
||||||
//if nodes are not continuous in the sorted representation
|
|
||||||
//or represent chain ends, create a new neighbor chain
|
|
||||||
int idx_next = chain_list[index_list[nb_list[j]]][1];
|
|
||||||
if ((j == nnb - 1) || (nb_list[j] + 1 != nb_list[j+1]) ||
|
|
||||||
(idx_next == cnt_end) || (idx_next == domain_end)) {
|
|
||||||
std::array<int,2> chain;
|
|
||||||
chain[0] = idx_s;
|
|
||||||
chain[1] = nb_list[j];
|
|
||||||
//make sure that segments having at least one node
|
|
||||||
//in the neighbor list are included
|
|
||||||
int idx0 = index_list[chain[0]]; // real id of the ends
|
|
||||||
int idx1 = index_list[chain[1]];
|
|
||||||
if (chain_list[idx0][0] != cnt_end &&
|
|
||||||
chain_list[idx0][0] != domain_end) chain[0] -= 1;
|
|
||||||
if (chain_list[idx1][1] != cnt_end &&
|
|
||||||
chain_list[idx1][1] != domain_end) chain[1] += 1;
|
|
||||||
if (chain[0] != chain[1]) nb_chains[i].push_back(chain);
|
|
||||||
idx_s = (j == nnb - 1) ? -1 : nb_list[j + 1];
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
nb_list.resize(0);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
// the cutoff distance between walls of tubes
|
|
||||||
static const double TPBRcutoff = 3.0*3.4;
|
|
||||||
int PairMESONTTPM::instance_count = 0;
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
PairMESONTTPM::PairMESONTTPM(LAMMPS *lmp) : Pair(lmp) {
|
|
||||||
writedata=1;
|
|
||||||
BendingMode = 0; // Harmonic bending model
|
|
||||||
TPMType = 0; // Inter-tube segment-segment interaction
|
|
||||||
tab_path = nullptr;
|
|
||||||
tab_path_length = 0;
|
|
||||||
|
|
||||||
eatom_s = nullptr;
|
|
||||||
eatom_b = nullptr;
|
|
||||||
eatom_t = nullptr;
|
|
||||||
nmax = 0;
|
|
||||||
instance_count++;
|
|
||||||
if (instance_count > 1) error->all(FLERR,
|
|
||||||
"only a single instance of mesont/tpm pair style can be created");
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
PairMESONTTPM::~PairMESONTTPM()
|
|
||||||
{
|
|
||||||
if (allocated) {
|
|
||||||
memory->destroy(setflag);
|
|
||||||
memory->destroy(cutsq);
|
|
||||||
memory->destroy(cut);
|
|
||||||
|
|
||||||
memory->destroy(eatom_s);
|
|
||||||
memory->destroy(eatom_b);
|
|
||||||
memory->destroy(eatom_t);
|
|
||||||
}
|
|
||||||
instance_count--;
|
|
||||||
if (tab_path != nullptr) memory->destroy(tab_path);
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void PairMESONTTPM::compute(int eflag, int vflag) {
|
|
||||||
// set per atom values and accumulators
|
|
||||||
// reallocate per-atom arrays if necessary
|
|
||||||
ev_init(eflag,vflag);
|
|
||||||
if (atom->nmax > nmax && eflag_atom) {
|
|
||||||
memory->destroy(eatom_s);
|
|
||||||
memory->create(eatom_s,comm->nthreads*maxeatom,"pair:eatom_s");
|
|
||||||
memory->destroy(eatom_b);
|
|
||||||
memory->create(eatom_b,comm->nthreads*maxeatom,"pair:eatom_b");
|
|
||||||
memory->destroy(eatom_t);
|
|
||||||
memory->create(eatom_t,comm->nthreads*maxeatom,"pair:eatom_t");
|
|
||||||
nmax = atom->nmax;
|
|
||||||
}
|
|
||||||
//total number of atoms in the node and ghost shell treated as NTs
|
|
||||||
int nall = list->inum + list->gnum;
|
|
||||||
//total number of atoms in the node and ghost shell
|
|
||||||
int ntot = atom->nlocal + atom->nghost;
|
|
||||||
int newton_pair = force->newton_pair;
|
|
||||||
if (!newton_pair)
|
|
||||||
error->all(FLERR,"Pair style mesont/tpm requires newton pair on");
|
|
||||||
|
|
||||||
double **x = atom->x;
|
|
||||||
double **f = atom->f;
|
|
||||||
double *r = atom->radius;
|
|
||||||
double *l = atom->length;
|
|
||||||
int *buckling = atom->buckling;
|
|
||||||
tagint *g_id = atom->tag;
|
|
||||||
|
|
||||||
//check if cutoff is chosen correctly
|
|
||||||
double RT = mesont_lib_get_R();
|
|
||||||
double Lmax = 0.0;
|
|
||||||
for (int ii = 0; ii < list->inum; ii++) {
|
|
||||||
int i = list->ilist[ii];
|
|
||||||
if (Lmax < l[i]) Lmax = l[i];
|
|
||||||
}
|
|
||||||
double Rcut_min = std::max(2.0*Lmax, std::sqrt(0.5*Lmax*Lmax + std::pow((2.0*RT + TPBRcutoff),2)));
|
|
||||||
if (cut_global < Rcut_min) {
|
|
||||||
error->all(FLERR, "The selected cutoff is too small for the current system : "
|
|
||||||
"L_max = {:.8}, R_max = {:.8}, Rc = {:.8}, Rcut_min = {:.8}",
|
|
||||||
Lmax, RT, cut_global, Rcut_min);
|
|
||||||
}
|
|
||||||
|
|
||||||
//generate bonds and chain nblist
|
|
||||||
MESONTList ntlist(atom, list);
|
|
||||||
|
|
||||||
//reorder data to make it contiguous within tubes
|
|
||||||
//and compatible with Fortran functions
|
|
||||||
std::vector<double> x_sort(3*nall), f_sort(3*nall), s_sort(9*nall);
|
|
||||||
std::vector<double> u_ts_sort(nall), u_tb_sort(nall), u_tt_sort(nall);
|
|
||||||
std::vector<int> b_sort(nall);
|
|
||||||
for (int i = 0; i < nall; i++) {
|
|
||||||
int idx = ntlist.get_idx(i);
|
|
||||||
for (int j = 0; j < 3; j++) x_sort[3*i+j] = x[idx][j];
|
|
||||||
b_sort[i] = buckling[idx];
|
|
||||||
}
|
|
||||||
|
|
||||||
//bending potential
|
|
||||||
int n_triplets = ntlist.get_triplets().size();
|
|
||||||
for (int i = 0; i < n_triplets; i++) {
|
|
||||||
const std::array<int,3>& t = ntlist.get_triplets()[i];
|
|
||||||
//idx of nodes of a triplet in sorted representation
|
|
||||||
int idx_s0 = ntlist.get_idxb(t[0]);
|
|
||||||
int idx_s1 = ntlist.get_idxb(t[1]);
|
|
||||||
int idx_s2 = ntlist.get_idxb(t[2]);
|
|
||||||
|
|
||||||
double* X1 = &(x_sort[3*idx_s0]);
|
|
||||||
double* X2 = &(x_sort[3*idx_s1]);
|
|
||||||
double* X3 = &(x_sort[3*idx_s2]);
|
|
||||||
double& U1b = u_tb_sort[idx_s0];
|
|
||||||
double& U2b = u_tb_sort[idx_s1];
|
|
||||||
double& U3b = u_tb_sort[idx_s2];
|
|
||||||
double* F1 = &(f_sort[3*idx_s0]);
|
|
||||||
double* F2 = &(f_sort[3*idx_s1]);
|
|
||||||
double* F3 = &(f_sort[3*idx_s2]);
|
|
||||||
double* S1 = &(s_sort[9*idx_s0]);
|
|
||||||
double* S2 = &(s_sort[9*idx_s1]);
|
|
||||||
double* S3 = &(s_sort[9*idx_s2]);
|
|
||||||
double& R123 = r[t[1]];
|
|
||||||
double& L123 = l[t[1]];
|
|
||||||
int& BBF2 = b_sort[idx_s1];
|
|
||||||
|
|
||||||
mesont_lib_TubeBendingForceField(U1b, U2b, U3b, F1, F2, F3, S1, S2, S3,
|
|
||||||
X1, X2, X3, R123, L123, BBF2);
|
|
||||||
}
|
|
||||||
|
|
||||||
//share new values of buckling
|
|
||||||
if (BendingMode == 1) {
|
|
||||||
for (int i = 0; i < nall; i++) {
|
|
||||||
int idx = ntlist.get_idx(i);
|
|
||||||
buckling[idx] = b_sort[i];
|
|
||||||
}
|
|
||||||
comm->forward_comm(this);
|
|
||||||
for (int i = 0; i < nall; i++) {
|
|
||||||
int idx = ntlist.get_idx(i);
|
|
||||||
b_sort[i] = buckling[idx];
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
//segment-segment and segment-tube interactions
|
|
||||||
int n_segments = ntlist.get_segments().size();
|
|
||||||
double Rmax = 0.0;
|
|
||||||
Lmax = 0.0;
|
|
||||||
for (int i = 0; i < n_segments; i++) {
|
|
||||||
const std::array<int,2>& s = ntlist.get_segments()[i];
|
|
||||||
//idx of a segment end 1 in sorted representation
|
|
||||||
int idx_s0 = ntlist.get_idxb(s[0]);
|
|
||||||
//idx of a segment end 2 in sorted representation
|
|
||||||
int idx_s1 = ntlist.get_idxb(s[1]);
|
|
||||||
double* X1 = &(x_sort[3*idx_s0]);
|
|
||||||
double* X2 = &(x_sort[3*idx_s1]);
|
|
||||||
double length = std::sqrt(std::pow(X1[0]-X2[0],2) +
|
|
||||||
std::pow(X1[1]-X2[1],2) + std::pow(X1[2]-X2[2],2));
|
|
||||||
if (length > Lmax) Lmax = length;
|
|
||||||
double& U1t = u_tt_sort[idx_s0];
|
|
||||||
double& U2t = u_tt_sort[idx_s1];
|
|
||||||
double& U1s = u_ts_sort[idx_s0];
|
|
||||||
double& U2s = u_ts_sort[idx_s1];
|
|
||||||
double* F1 = &(f_sort[3*idx_s0]);
|
|
||||||
double* F2 = &(f_sort[3*idx_s1]);
|
|
||||||
double* S1 = &(s_sort[9*idx_s0]);
|
|
||||||
double* S2 = &(s_sort[9*idx_s1]);
|
|
||||||
double R12 = r[s[0]]; if (R12 > Rmax) Rmax = R12;
|
|
||||||
if (std::abs(R12 - RT) > 1e-3)
|
|
||||||
error->all(FLERR,"Inconsistent input and potential table");
|
|
||||||
//assume that the length of the segment is defined by the node with
|
|
||||||
//smallest global id
|
|
||||||
double L12 = (g_id[s[0]] > g_id[s[1]]) ? l[s[1]] : l[s[0]];
|
|
||||||
mesont_lib_TubeStretchingForceField(U1s, U2s, F1, F2, S1, S2, X1, X2,
|
|
||||||
R12, L12);
|
|
||||||
|
|
||||||
for (int nc = 0; nc < (int)ntlist.get_nbs()[i].size(); nc++) {
|
|
||||||
//id of the beginning and end of the chain in the sorted representation
|
|
||||||
const std::array<int,2>& chain = ntlist.get_nbs()[i][nc];
|
|
||||||
int N = chain[1] - chain[0] + 1; //number of elements in the chain
|
|
||||||
int end1 = ntlist.get_idx(chain[0]); //chain ends (real representation)
|
|
||||||
int end2 = ntlist.get_idx(chain[1]);
|
|
||||||
double* X = &(x_sort[3*chain[0]]);
|
|
||||||
double* Ut = &(u_tt_sort[chain[0]]);
|
|
||||||
double* F = &(f_sort[3*chain[0]]);
|
|
||||||
double* S = &(s_sort[9*chain[0]]);
|
|
||||||
double R = r[end1];
|
|
||||||
int* BBF = &(b_sort[chain[0]]);
|
|
||||||
int E1 = ntlist.is_end(end1);
|
|
||||||
int E2 = ntlist.is_end(end2);
|
|
||||||
|
|
||||||
int Ee = 0;
|
|
||||||
double* Xe = X; double* Fe = F; double* Se = S;
|
|
||||||
if (!E1 && ntlist.get_triplet(end1)[0] != MESONTList::domain_end &&
|
|
||||||
ntlist.get_triplet(ntlist.get_triplet(end1)[0])[0] ==
|
|
||||||
MESONTList::cnt_end) {
|
|
||||||
Ee = 1;
|
|
||||||
int idx = ntlist.get_idxb(ntlist.get_triplet(end1)[0]);
|
|
||||||
Xe = &(x_sort[3*idx]);
|
|
||||||
Fe = &(f_sort[3*idx]);
|
|
||||||
Se = &(s_sort[9*idx]);
|
|
||||||
}
|
|
||||||
else if (!E2 && ntlist.get_triplet(end2)[2] != MESONTList::domain_end &&
|
|
||||||
ntlist.get_triplet(ntlist.get_triplet(end2)[2])[2] ==
|
|
||||||
MESONTList::cnt_end) {
|
|
||||||
Ee = 2;
|
|
||||||
int idx = ntlist.get_idxb(ntlist.get_triplet(end2)[2]);
|
|
||||||
Xe = &(x_sort[3*idx]);
|
|
||||||
Fe = &(f_sort[3*idx]);
|
|
||||||
Se = &(s_sort[9*idx]);
|
|
||||||
}
|
|
||||||
|
|
||||||
mesont_lib_SegmentTubeForceField(U1t, U2t, Ut, F1, F2, F, Fe, S1, S2, S,
|
|
||||||
Se, X1, X2, R12, N, X, Xe, BBF, R, E1, E2, Ee, TPMType);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
//check if cutoff is chosen correctly
|
|
||||||
Rcut_min = std::max(2.0*Lmax, std::sqrt(0.5*Lmax*Lmax + std::pow((2.0*Rmax + TPBRcutoff),2)));
|
|
||||||
if (cut_global < Rcut_min) {
|
|
||||||
error->all(FLERR, "The selected cutoff is too small for the current system : "
|
|
||||||
"L_max = {:.8}, R_max = {:.8}, Rc = {:.8}, Rcut_min = {:.8}",
|
|
||||||
Lmax, RT, cut_global, Rcut_min);
|
|
||||||
}
|
|
||||||
|
|
||||||
//convert from sorted representation
|
|
||||||
for (int i = 0; i < nall; i++) {
|
|
||||||
int idx = ntlist.get_idx(i);
|
|
||||||
for (int j = 0; j < 3; j++) f[idx][j] += f_sort[3*i+j];
|
|
||||||
buckling[idx] = b_sort[i];
|
|
||||||
}
|
|
||||||
if (eflag_global) {
|
|
||||||
energy_s = energy_b = energy_t = 0.0;
|
|
||||||
for (int i = 0; i < nall; i++) {
|
|
||||||
energy_s += u_ts_sort[i];
|
|
||||||
energy_b += u_tb_sort[i];
|
|
||||||
energy_t += u_tt_sort[i];
|
|
||||||
}
|
|
||||||
eng_vdwl += energy_s + energy_b + energy_t;
|
|
||||||
}
|
|
||||||
if (eflag_atom) {
|
|
||||||
for (int i = 0; i < ntot; i++)
|
|
||||||
eatom_s[i] = eatom_b[i] = eatom_t[i] = 0.0;
|
|
||||||
|
|
||||||
for (int i = 0; i < nall; i++) {
|
|
||||||
int idx = ntlist.get_idx(i);
|
|
||||||
eatom_s[idx] += u_ts_sort[i];
|
|
||||||
eatom_b[idx] += u_tb_sort[i];
|
|
||||||
eatom_t[idx] += u_tt_sort[i];
|
|
||||||
eatom[idx] += u_ts_sort[i] + u_tb_sort[i] + u_tt_sort[i];
|
|
||||||
}
|
|
||||||
}
|
|
||||||
if (vflag_global) {
|
|
||||||
for (int i = 0; i < nall; i++) {
|
|
||||||
virial[0] += s_sort[9*i+0]; //xx
|
|
||||||
virial[1] += s_sort[9*i+4]; //yy
|
|
||||||
virial[2] += s_sort[9*i+8]; //zz
|
|
||||||
virial[3] += s_sort[9*i+1]; //xy
|
|
||||||
virial[4] += s_sort[9*i+2]; //xz
|
|
||||||
virial[5] += s_sort[9*i+5]; //yz
|
|
||||||
}
|
|
||||||
}
|
|
||||||
if (vflag_atom) {
|
|
||||||
for (int i = 0; i < nall; i++) {
|
|
||||||
int idx = ntlist.get_idx(i);
|
|
||||||
vatom[idx][0] += s_sort[9*i+0]; //xx
|
|
||||||
vatom[idx][1] += s_sort[9*i+4]; //yy
|
|
||||||
vatom[idx][2] += s_sort[9*i+8]; //zz
|
|
||||||
vatom[idx][3] += s_sort[9*i+1]; //xy
|
|
||||||
vatom[idx][4] += s_sort[9*i+2]; //xz
|
|
||||||
vatom[idx][5] += s_sort[9*i+5]; //yz
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
allocate all arrays
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void PairMESONTTPM::allocate() {
|
|
||||||
allocated = 1;
|
|
||||||
int n = atom->ntypes;
|
|
||||||
|
|
||||||
memory->create(setflag,n+1,n+1,"pair:setflag");
|
|
||||||
for (int i = 1; i <= n; i++)
|
|
||||||
for (int j = i; j <= n; j++)
|
|
||||||
setflag[i][j] = 0;
|
|
||||||
|
|
||||||
memory->create(cutsq,n+1,n+1,"pair:cutsq");
|
|
||||||
memory->create(cut,n+1,n+1,"pair:cut");
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
global settings
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void PairMESONTTPM::settings(int narg, char **arg) {
|
|
||||||
if ((narg == 0) || (narg > 4))
|
|
||||||
error->all(FLERR,"Illegal pair_style command");
|
|
||||||
cut_global = utils::numeric(FLERR,arg[0],false,lmp);
|
|
||||||
|
|
||||||
// reset cutoffs that have been explicitly set
|
|
||||||
if (allocated) {
|
|
||||||
int i,j;
|
|
||||||
for (i = 1; i <= atom->ntypes; i++)
|
|
||||||
for (j = i+1; j <= atom->ntypes; j++)
|
|
||||||
cut[i][j] = cut_global;
|
|
||||||
}
|
|
||||||
std::string TPMAFile = (narg > 1) ? arg[1] : "MESONT-TABTP.xrs";
|
|
||||||
tab_path_length = TPMAFile.length();
|
|
||||||
if (tab_path != nullptr) memory->destroy(tab_path);
|
|
||||||
//c_str returns '\0' terminated string
|
|
||||||
memory->create(tab_path,tab_path_length+1,"pair:path");
|
|
||||||
std::memcpy(tab_path, TPMAFile.c_str(), tab_path_length+1);
|
|
||||||
mesont_lib_SetTablePath(tab_path, tab_path_length);
|
|
||||||
|
|
||||||
if (narg > 2) {
|
|
||||||
BendingMode = utils::numeric(FLERR,arg[2],false,lmp);
|
|
||||||
if ((BendingMode < 0) || (BendingMode > 1))
|
|
||||||
error->all(FLERR,"Incorrect BendingMode");
|
|
||||||
}
|
|
||||||
if (narg > 3) {
|
|
||||||
TPMType = utils::numeric(FLERR,arg[3],false,lmp);
|
|
||||||
if ((TPMType < 0) || (TPMType > 1))
|
|
||||||
error->all(FLERR,"Incorrect TPMType");
|
|
||||||
}
|
|
||||||
|
|
||||||
mesont_lib_TPBInit();
|
|
||||||
int M, N;
|
|
||||||
std::ifstream in(TPMAFile);
|
|
||||||
if (!in.is_open()) error->all(FLERR,"Incorrect table path");
|
|
||||||
std::string tmp;
|
|
||||||
std::getline(in,tmp);
|
|
||||||
std::getline(in,tmp);
|
|
||||||
std::getline(in,tmp);
|
|
||||||
in >> M >> N;
|
|
||||||
in.close();
|
|
||||||
mesont_lib_TPMInit(M, N);
|
|
||||||
mesont_lib_InitCNTPotModule(1, 3, 0, BendingMode, mesont_lib_get_R());
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
set coeffs for one or more type pairs
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void PairMESONTTPM::coeff(int narg, char **arg) {
|
|
||||||
if ((narg < 2) || (narg > 3))
|
|
||||||
error->all(FLERR,"Incorrect args for pair coefficients");
|
|
||||||
|
|
||||||
if (!allocated) allocate();
|
|
||||||
|
|
||||||
int ilo,ihi,jlo,jhi;
|
|
||||||
utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
|
|
||||||
utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
|
|
||||||
|
|
||||||
double cut_one = cut_global;
|
|
||||||
if (narg == 3) cut_one = utils::numeric(FLERR,arg[2],false,lmp);
|
|
||||||
|
|
||||||
int count = 0;
|
|
||||||
for (int i = ilo; i <= ihi; i++) {
|
|
||||||
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
|
||||||
cut[i][j] = cut_one;
|
|
||||||
setflag[i][j] = 1;
|
|
||||||
count++;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
init for one type pair i,j and corresponding j,i
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
double PairMESONTTPM::init_one(int i, int j) {
|
|
||||||
if (setflag[i][j] == 0) {
|
|
||||||
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
|
|
||||||
}
|
|
||||||
|
|
||||||
return cut[i][j];
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
proc 0 writes to restart file
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void PairMESONTTPM::write_restart(FILE *fp) {
|
|
||||||
write_restart_settings(fp);
|
|
||||||
|
|
||||||
int i,j;
|
|
||||||
for (i = 1; i <= atom->ntypes; i++)
|
|
||||||
for (j = i; j <= atom->ntypes; j++) {
|
|
||||||
fwrite(&setflag[i][j],sizeof(int),1,fp);
|
|
||||||
if (setflag[i][j]) {
|
|
||||||
fwrite(&cut[i][j],sizeof(double),1,fp);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
proc 0 reads from restart file, bcasts
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void PairMESONTTPM::read_restart(FILE *fp) {
|
|
||||||
read_restart_settings(fp);
|
|
||||||
allocate();
|
|
||||||
|
|
||||||
int i,j;
|
|
||||||
int me = comm->me;
|
|
||||||
for (i = 1; i <= atom->ntypes; i++)
|
|
||||||
for (j = i; j <= atom->ntypes; j++) {
|
|
||||||
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
|
|
||||||
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
|
|
||||||
if (setflag[i][j]) {
|
|
||||||
if (me == 0) {
|
|
||||||
fread(&cut[i][j],sizeof(double),1,fp);
|
|
||||||
}
|
|
||||||
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
proc 0 writes to restart file
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void PairMESONTTPM::write_restart_settings(FILE *fp) {
|
|
||||||
fwrite(&BendingMode,sizeof(int),1,fp);
|
|
||||||
fwrite(&TPMType,sizeof(int),1,fp);
|
|
||||||
fwrite(&cut_global,sizeof(double),1,fp);
|
|
||||||
fwrite(&tab_path_length,sizeof(int),1,fp);
|
|
||||||
fwrite(tab_path,tab_path_length+1,1,fp);
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
proc 0 reads from restart file, bcasts
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void PairMESONTTPM::read_restart_settings(FILE *fp) {
|
|
||||||
int me = comm->me;
|
|
||||||
if (me == 0) {
|
|
||||||
fread(&BendingMode,sizeof(int),1,fp);
|
|
||||||
fread(&TPMType,sizeof(int),1,fp);
|
|
||||||
fread(&cut_global,sizeof(double),1,fp);
|
|
||||||
fread(&tab_path_length,sizeof(int),1,fp);
|
|
||||||
}
|
|
||||||
MPI_Bcast(&BendingMode,1,MPI_INT,0,world);
|
|
||||||
MPI_Bcast(&TPMType,1,MPI_INT,0,world);
|
|
||||||
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
|
|
||||||
MPI_Bcast(&tab_path_length,1,MPI_INT,0,world);
|
|
||||||
|
|
||||||
if (tab_path != nullptr) memory->destroy(tab_path);
|
|
||||||
memory->create(tab_path,tab_path_length+1,"pair:path");
|
|
||||||
if (me == 0) fread(tab_path,tab_path_length+1,1,fp);
|
|
||||||
MPI_Bcast(tab_path,tab_path_length+1,MPI_CHAR,0,world);
|
|
||||||
mesont_lib_SetTablePath(tab_path,tab_path_length);
|
|
||||||
mesont_lib_TPBInit();
|
|
||||||
int M, N;
|
|
||||||
std::ifstream in(tab_path);
|
|
||||||
if (!in.is_open()) error->all(FLERR,"Incorrect table path");
|
|
||||||
std::string tmp;
|
|
||||||
std::getline(in,tmp);
|
|
||||||
std::getline(in,tmp);
|
|
||||||
std::getline(in,tmp);
|
|
||||||
in >> M >> N;
|
|
||||||
in.close();
|
|
||||||
mesont_lib_TPMInit(M, N);
|
|
||||||
mesont_lib_InitCNTPotModule(1, 3, 0, BendingMode, mesont_lib_get_R());
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
proc 0 writes to data file
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void PairMESONTTPM::write_data(FILE *fp) {
|
|
||||||
for (int i = 1; i <= atom->ntypes; i++)
|
|
||||||
fprintf(fp,"%d\n",i);
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
proc 0 writes all pairs to data file
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void PairMESONTTPM::write_data_all(FILE *fp) {
|
|
||||||
for (int i = 1; i <= atom->ntypes; i++)
|
|
||||||
for (int j = i; j <= atom->ntypes; j++)
|
|
||||||
fprintf(fp,"%d %d %g\n",i,j,cut[i][j]);
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void PairMESONTTPM::init_style() {
|
|
||||||
//make sure that a full list is created (including ghost nodes)
|
|
||||||
neighbor->add_request(this, NeighConst::REQ_FULL | NeighConst::REQ_GHOST);
|
|
||||||
}
|
|
||||||
|
|
||||||
void* PairMESONTTPM::extract(const char *str, int &) {
|
|
||||||
if (strcmp(str,"mesonttpm_Es_tot") == 0) return &energy_s;
|
|
||||||
else if (strcmp(str,"mesonttpm_Eb_tot") == 0) return &energy_b;
|
|
||||||
else if (strcmp(str,"mesonttpm_Et_tot") == 0) return &energy_t;
|
|
||||||
else if (strcmp(str,"mesonttpm_Es") == 0) return eatom_s;
|
|
||||||
else if (strcmp(str,"mesonttpm_Eb") == 0) return eatom_b;
|
|
||||||
else if (strcmp(str,"mesonttpm_Et") == 0) return eatom_t;
|
|
||||||
else return nullptr;
|
|
||||||
};
|
|
||||||
@ -1,66 +0,0 @@
|
|||||||
/* -*- c++ -*- ----------------------------------------------------------
|
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
|
||||||
LAMMPS development team: developers@lammps.org
|
|
||||||
|
|
||||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
certain rights in this software. This software is distributed under
|
|
||||||
the GNU General Public License.
|
|
||||||
|
|
||||||
See the README file in the top-level LAMMPS directory.
|
|
||||||
|
|
||||||
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
#ifdef PAIR_CLASS
|
|
||||||
// clang-format off
|
|
||||||
PairStyle(mesont/tpm,PairMESONTTPM);
|
|
||||||
// clang-format on
|
|
||||||
#else
|
|
||||||
|
|
||||||
#ifndef LMP_PAIR_MESONT_TPM_H
|
|
||||||
#define LMP_PAIR_MESONT_TPM_H
|
|
||||||
|
|
||||||
#include "pair.h"
|
|
||||||
|
|
||||||
namespace LAMMPS_NS {
|
|
||||||
|
|
||||||
class PairMESONTTPM : public Pair {
|
|
||||||
public:
|
|
||||||
PairMESONTTPM(class LAMMPS *);
|
|
||||||
~PairMESONTTPM() override;
|
|
||||||
void compute(int, int) override;
|
|
||||||
void settings(int, char **) override;
|
|
||||||
void coeff(int, char **) override;
|
|
||||||
double init_one(int, int) override;
|
|
||||||
void write_restart(FILE *) override;
|
|
||||||
void read_restart(FILE *) override;
|
|
||||||
void write_restart_settings(FILE *) override;
|
|
||||||
void read_restart_settings(FILE *) override;
|
|
||||||
void write_data(FILE *) override;
|
|
||||||
void write_data_all(FILE *) override;
|
|
||||||
void init_style() override;
|
|
||||||
|
|
||||||
double energy_s; // accumulated energies for stretching
|
|
||||||
double energy_b; // accumulated energies for bending
|
|
||||||
double energy_t; // accumulated energies for tube-tube interaction
|
|
||||||
double *eatom_s, *eatom_b, *eatom_t; // accumulated per-atom values
|
|
||||||
|
|
||||||
protected:
|
|
||||||
int BendingMode, TPMType;
|
|
||||||
char *tab_path;
|
|
||||||
int tab_path_length;
|
|
||||||
double cut_global;
|
|
||||||
double **cut;
|
|
||||||
static int instance_count;
|
|
||||||
int nmax;
|
|
||||||
|
|
||||||
virtual void allocate();
|
|
||||||
void *extract(const char *, int &) override;
|
|
||||||
};
|
|
||||||
|
|
||||||
} // namespace LAMMPS_NS
|
|
||||||
|
|
||||||
#endif
|
|
||||||
#endif
|
|
||||||
@ -1,4 +1,3 @@
|
|||||||
# list of potential files to be fetched when this package is installed
|
# list of potential files to be fetched when this package is installed
|
||||||
# potential file md5sum
|
# potential file md5sum
|
||||||
C_10_10.mesocnt 68b5ca26283968fd9889aa0a37f7b7fb
|
C_10_10.mesocnt 68b5ca26283968fd9889aa0a37f7b7fb
|
||||||
TABTP_10_10.mesont 744a739da49ad5e78492c1fc9fd9f8c1
|
|
||||||
|
|||||||
@ -154,7 +154,7 @@ PACKMOST = \
|
|||||||
bocs \
|
bocs \
|
||||||
body \
|
body \
|
||||||
bpm \
|
bpm \
|
||||||
brownian \
|
brownian \
|
||||||
cg-dna \
|
cg-dna \
|
||||||
cg-spica \
|
cg-spica \
|
||||||
class2 \
|
class2 \
|
||||||
@ -180,6 +180,7 @@ PACKMOST = \
|
|||||||
manybody \
|
manybody \
|
||||||
mc \
|
mc \
|
||||||
meam \
|
meam \
|
||||||
|
mesont \
|
||||||
misc \
|
misc \
|
||||||
ml-snap \
|
ml-snap \
|
||||||
mofff \
|
mofff \
|
||||||
@ -228,7 +229,6 @@ PACKLIB = \
|
|||||||
latboltz \
|
latboltz \
|
||||||
lepton \
|
lepton \
|
||||||
mdi \
|
mdi \
|
||||||
mesont \
|
|
||||||
molfile \
|
molfile \
|
||||||
netcdf \
|
netcdf \
|
||||||
ml-pace \
|
ml-pace \
|
||||||
@ -243,7 +243,7 @@ PACKLIB = \
|
|||||||
|
|
||||||
PACKSYS = compress latboltz mpiio python
|
PACKSYS = compress latboltz mpiio python
|
||||||
|
|
||||||
PACKINT = atc awpmd colvars electrode gpu kokkos lepton mesont ml-pod poems
|
PACKINT = atc awpmd colvars electrode gpu kokkos lepton ml-pod poems
|
||||||
|
|
||||||
PACKEXT = \
|
PACKEXT = \
|
||||||
adios \
|
adios \
|
||||||
|
|||||||
@ -51,7 +51,15 @@ lmpinstalledpkgs.h
|
|||||||
lmpgitversion.h
|
lmpgitversion.h
|
||||||
mliap_model_python_couple.cpp
|
mliap_model_python_couple.cpp
|
||||||
mliap_model_python_couple.h
|
mliap_model_python_couple.h
|
||||||
# removed on 11 January 2022
|
# removed on 20 January 2023
|
||||||
|
atom_vec_mesont.cpp
|
||||||
|
atom_vec_mesont.h
|
||||||
|
compute_mesont.cpp
|
||||||
|
compute_mesont.h
|
||||||
|
export_mesont.h
|
||||||
|
pair_mesont_tpm.cpp
|
||||||
|
pair_mesont_tpm.h
|
||||||
|
# removed on 11 January 2023
|
||||||
min_fire_old.cpp
|
min_fire_old.cpp
|
||||||
min_fire_old.h
|
min_fire_old.h
|
||||||
# renamed on 11 July 2022
|
# renamed on 11 July 2022
|
||||||
|
|||||||
24
src/atom.cpp
24
src/atom.cpp
@ -186,12 +186,6 @@ Atom::Atom(LAMMPS *_lmp) : Pointers(_lmp)
|
|||||||
cc = cc_flux = nullptr;
|
cc = cc_flux = nullptr;
|
||||||
edpd_temp = edpd_flux = edpd_cv = nullptr;
|
edpd_temp = edpd_flux = edpd_cv = nullptr;
|
||||||
|
|
||||||
// MESONT package
|
|
||||||
|
|
||||||
length = nullptr;
|
|
||||||
buckling = nullptr;
|
|
||||||
bond_nt = nullptr;
|
|
||||||
|
|
||||||
// MACHDYN package
|
// MACHDYN package
|
||||||
|
|
||||||
contact_radius = nullptr;
|
contact_radius = nullptr;
|
||||||
@ -527,12 +521,6 @@ void Atom::peratom_create()
|
|||||||
add_peratom("cc",&cc,DOUBLE,1);
|
add_peratom("cc",&cc,DOUBLE,1);
|
||||||
add_peratom("cc_flux",&cc_flux,DOUBLE,1,1); // set per-thread flag
|
add_peratom("cc_flux",&cc_flux,DOUBLE,1,1); // set per-thread flag
|
||||||
|
|
||||||
// MESONT package
|
|
||||||
|
|
||||||
add_peratom("length",&length,DOUBLE,0);
|
|
||||||
add_peratom("buckling",&buckling,INT,0);
|
|
||||||
add_peratom("bond_nt",&bond_nt,tagintsize,2);
|
|
||||||
|
|
||||||
// SPH package
|
// SPH package
|
||||||
|
|
||||||
add_peratom("rho",&rho,DOUBLE,0);
|
add_peratom("rho",&rho,DOUBLE,0);
|
||||||
@ -2919,12 +2907,6 @@ void *Atom::extract(const char *name)
|
|||||||
if (strcmp(name,"cv") == 0) return (void *) cv;
|
if (strcmp(name,"cv") == 0) return (void *) cv;
|
||||||
if (strcmp(name,"vest") == 0) return (void *) vest;
|
if (strcmp(name,"vest") == 0) return (void *) vest;
|
||||||
|
|
||||||
// MESONT package
|
|
||||||
|
|
||||||
if (strcmp(name,"length") == 0) return (void *) length;
|
|
||||||
if (strcmp(name,"buckling") == 0) return (void *) buckling;
|
|
||||||
if (strcmp(name,"bond_nt") == 0) return (void *) bond_nt;
|
|
||||||
|
|
||||||
// MACHDYN package
|
// MACHDYN package
|
||||||
|
|
||||||
if (strcmp(name, "contact_radius") == 0) return (void *) contact_radius;
|
if (strcmp(name, "contact_radius") == 0) return (void *) contact_radius;
|
||||||
@ -3043,12 +3025,6 @@ int Atom::extract_datatype(const char *name)
|
|||||||
if (strcmp(name,"cv") == 0) return LAMMPS_DOUBLE;
|
if (strcmp(name,"cv") == 0) return LAMMPS_DOUBLE;
|
||||||
if (strcmp(name,"vest") == 0) return LAMMPS_DOUBLE_2D;
|
if (strcmp(name,"vest") == 0) return LAMMPS_DOUBLE_2D;
|
||||||
|
|
||||||
// MESONT package
|
|
||||||
|
|
||||||
if (strcmp(name,"length") == 0) return LAMMPS_DOUBLE;
|
|
||||||
if (strcmp(name,"buckling") == 0) return LAMMPS_INT;
|
|
||||||
if (strcmp(name,"bond_nt") == 0) return LAMMPS_TAGINT_2D;
|
|
||||||
|
|
||||||
// MACHDYN package
|
// MACHDYN package
|
||||||
|
|
||||||
if (strcmp(name, "contact_radius") == 0) return LAMMPS_DOUBLE;
|
if (strcmp(name, "contact_radius") == 0) return LAMMPS_DOUBLE;
|
||||||
|
|||||||
@ -145,12 +145,6 @@ class Atom : protected Pointers {
|
|||||||
double *edpd_cv; // heat capacity
|
double *edpd_cv; // heat capacity
|
||||||
int cc_species;
|
int cc_species;
|
||||||
|
|
||||||
// MESONT package
|
|
||||||
|
|
||||||
double *length;
|
|
||||||
int *buckling;
|
|
||||||
tagint **bond_nt;
|
|
||||||
|
|
||||||
// MACHDYN package
|
// MACHDYN package
|
||||||
|
|
||||||
double *contact_radius;
|
double *contact_radius;
|
||||||
|
|||||||
@ -28,6 +28,11 @@ ComputeDeprecated::ComputeDeprecated(LAMMPS *lmp, int narg, char **arg) : Comput
|
|||||||
if (lmp->comm->me == 0)
|
if (lmp->comm->me == 0)
|
||||||
utils::logmesg(lmp, "\nCompute style 'DEPRECATED' is a dummy style\n\n");
|
utils::logmesg(lmp, "\nCompute style 'DEPRECATED' is a dummy style\n\n");
|
||||||
return;
|
return;
|
||||||
|
} else if (my_style == "mesont") {
|
||||||
|
if (lmp->comm->me == 0)
|
||||||
|
utils::logmesg(lmp,
|
||||||
|
"\nCompute style 'mesont' and the associated pair style have been "
|
||||||
|
"removed. Please use pair style 'mesocnt' instead.\n\n");
|
||||||
}
|
}
|
||||||
error->all(FLERR, "This compute style is no longer available");
|
error->all(FLERR, "This compute style is no longer available");
|
||||||
}
|
}
|
||||||
|
|||||||
@ -15,6 +15,7 @@
|
|||||||
// clang-format off
|
// clang-format off
|
||||||
// list all deprecated and removed compute styles here
|
// list all deprecated and removed compute styles here
|
||||||
ComputeStyle(DEPRECATED,ComputeDeprecated);
|
ComputeStyle(DEPRECATED,ComputeDeprecated);
|
||||||
|
ComputeStyle(mesont,ComputeDeprecated);
|
||||||
// clang-format on
|
// clang-format on
|
||||||
#else
|
#else
|
||||||
|
|
||||||
@ -30,8 +31,6 @@ class ComputeDeprecated : public Compute {
|
|||||||
ComputeDeprecated(class LAMMPS *, int, char **);
|
ComputeDeprecated(class LAMMPS *, int, char **);
|
||||||
void init() override {}
|
void init() override {}
|
||||||
};
|
};
|
||||||
|
|
||||||
} // namespace LAMMPS_NS
|
} // namespace LAMMPS_NS
|
||||||
|
|
||||||
#endif
|
#endif
|
||||||
#endif
|
#endif
|
||||||
|
|||||||
@ -48,6 +48,11 @@ void PairDeprecated::settings(int, char **)
|
|||||||
utils::logmesg(lmp,
|
utils::logmesg(lmp,
|
||||||
"\nPair style 'reax' has been removed from LAMMPS "
|
"\nPair style 'reax' has been removed from LAMMPS "
|
||||||
"after the 12 December 2018 version\n\n");
|
"after the 12 December 2018 version\n\n");
|
||||||
|
} else if (my_style == "mesont/tpm") {
|
||||||
|
if (lmp->comm->me == 0)
|
||||||
|
utils::logmesg(lmp,
|
||||||
|
"\nPair style 'mesont/tpm' has been removed from LAMMPS. "
|
||||||
|
"Please use pair style 'mesocnt' instead\n\n");
|
||||||
}
|
}
|
||||||
error->all(FLERR, "This pair style is no longer available");
|
error->all(FLERR, "This pair style is no longer available");
|
||||||
}
|
}
|
||||||
|
|||||||
@ -15,6 +15,7 @@
|
|||||||
// clang-format off
|
// clang-format off
|
||||||
PairStyle(DEPRECATED,PairDeprecated);
|
PairStyle(DEPRECATED,PairDeprecated);
|
||||||
PairStyle(reax,PairDeprecated);
|
PairStyle(reax,PairDeprecated);
|
||||||
|
PairStyle(mesont/tpm,PairDeprecated);
|
||||||
// clang-format on
|
// clang-format on
|
||||||
#else
|
#else
|
||||||
|
|
||||||
|
|||||||
@ -33,7 +33,6 @@ lmp2arc convert LAMMPS output to Accelrys Insight format
|
|||||||
lmp2cfg convert LAMMPS output to CFG files for AtomEye viz
|
lmp2cfg convert LAMMPS output to CFG files for AtomEye viz
|
||||||
magic patterns to detect LAMMPS files with the file(1) command
|
magic patterns to detect LAMMPS files with the file(1) command
|
||||||
matlab MatLab scripts for post-processing LAMMPS output
|
matlab MatLab scripts for post-processing LAMMPS output
|
||||||
mesont Tools for use with the MESONT package
|
|
||||||
micelle2d create a data file of small lipid chains in solvent
|
micelle2d create a data file of small lipid chains in solvent
|
||||||
moltemplate Instructions for installing the Moltemplate builder program
|
moltemplate Instructions for installing the Moltemplate builder program
|
||||||
msi2lmp use Accelrys Insight code to setup LAMMPS input
|
msi2lmp use Accelrys Insight code to setup LAMMPS input
|
||||||
|
|||||||
@ -1,58 +0,0 @@
|
|||||||
=== MESONT tools ===
|
|
||||||
===============================
|
|
||||||
|
|
||||||
The programs in this folder can be used to analyze the
|
|
||||||
output of simulations using the CNT mesoscopic force
|
|
||||||
field (MESONT).
|
|
||||||
|
|
||||||
dump2vtk.cpp converts output written in *.dump format (the
|
|
||||||
sequence of columns must be "ATOMS id type x y z Es Eb Et
|
|
||||||
Ek ix iy iz", the same as in the examples at examples\USER\mesont)
|
|
||||||
into VTK format that can be visualized as a set of tubes in
|
|
||||||
Paraview (or other packages). The executable takes 3 parameters:
|
|
||||||
system.init - an input file with information about connections
|
|
||||||
between cnt nodes, config.dump - LAMMPS output with snapshots,
|
|
||||||
out - output folder for writing VTK files (must exist).
|
|
||||||
|
|
||||||
Code TMDPotGen is designed to generate ASCII text files TPMSSTP.xrs
|
|
||||||
and TPMA.xrs containing tabulated tubular potentials for
|
|
||||||
single-walled CNTs with a given chirality (m,n). The input
|
|
||||||
parameters for the code must be provided in the form of an ASCII
|
|
||||||
text file TMDPotGen.xdt. The output of the code are files TPMSSTP.xrs
|
|
||||||
and TPMA.xrs. All parameters in the tables are given in metal units.
|
|
||||||
The generation of the tables takes approximately 4 hours.
|
|
||||||
|
|
||||||
Code TMDGen is designed to generate initial samples composed of
|
|
||||||
straight and dispersed nanotubes of given chirality and length at
|
|
||||||
a given material density. In the generated samples, nanotubes are
|
|
||||||
distributed with random positions and orientations. Both periodic
|
|
||||||
and free boundary conditions are available along each axis of the
|
|
||||||
system. The input parameters for the code must be provided in form
|
|
||||||
of an ASCII text file TMDGen.xdt and include the following:
|
|
||||||
LS0: sample size along z- and y-directions (A)
|
|
||||||
HS0: sample size along z-direction (A)
|
|
||||||
DS0: material density (g/cm^3)
|
|
||||||
BC_X0: Type of boundary conditions along x-direction (0, Free; 1, Periodic)
|
|
||||||
BC_Y0: Type of boundary conditions along y-direction (0, Free; 1, Periodic)
|
|
||||||
BC_Z0: Type of boundary conditions along z-direction (0, Free; 1, Periodic)
|
|
||||||
ChiIndM: First chirality index of nanotubes
|
|
||||||
ChiIndN: Second chirality index of nanotubes
|
|
||||||
LT0: Nanotube length (A)
|
|
||||||
SegType: Parameter that defines how a nanotubes will be divided into
|
|
||||||
segments(0, NSeg0 will be used; 1, LSeg0 will be used)
|
|
||||||
NSeg0: Number of segments in every nanotube. Used if SegType = 0. Then
|
|
||||||
LSeg0 = LT0 / NSeg0
|
|
||||||
LSeg0: Length of segments in every nanotube. Used if SegType = 1. Then
|
|
||||||
NSeg0 = [ LT0 / LSeg0 ]
|
|
||||||
DeltaT: Minimum gap between nanotube walls in the generated sample (A)
|
|
||||||
NAmax: Maximum number of attempts to add new nanotube to the sample
|
|
||||||
GeomPrec: Precision of calculations (dimensionless).
|
|
||||||
The output of the code is an ASCII text file TMDSample.init written in the
|
|
||||||
LAMMPS format compatible with cnt atomic style. All parameters in the sample
|
|
||||||
files generated with TMDGen are given in metal units.
|
|
||||||
|
|
||||||
|
|
||||||
This packages were created by Maxim Shugaev (mvs9t@virginia.edu)
|
|
||||||
at the University of Virginia and by Alexey N. Volkov (avolkov1@ua.edu)
|
|
||||||
at the University of Alabama.
|
|
||||||
|
|
||||||
@ -1,33 +0,0 @@
|
|||||||
#---------------------------------------------------------------------------------------------------
|
|
||||||
#
|
|
||||||
# This is Makefile for builing the executable TMDGen
|
|
||||||
#
|
|
||||||
# Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, 2020, Version 13.00
|
|
||||||
#
|
|
||||||
#---------------------------------------------------------------------------------------------------
|
|
||||||
EXEPATH = .
|
|
||||||
|
|
||||||
F90 = ifort
|
|
||||||
F90FLAGS = -O3 -ipo
|
|
||||||
LDFLAGS =
|
|
||||||
|
|
||||||
OBJS = TPMLib.o TPMGeom.o TMDGenData.o TMDGen3D.o TMDGen.o
|
|
||||||
EXE = $(EXEPATH)/TMDGen
|
|
||||||
|
|
||||||
# compile and load
|
|
||||||
default:
|
|
||||||
@echo " "
|
|
||||||
@echo "Compiling Code of Program TMDGen"
|
|
||||||
@echo "FORTRAN 90"
|
|
||||||
$(MAKE) $(EXE)
|
|
||||||
|
|
||||||
$(EXE): $(OBJS)
|
|
||||||
$(F90) $(F90FLAGS) $(LDFLAGS) -o $(EXE) $(OBJS)
|
|
||||||
|
|
||||||
.SUFFIXES: .f90 .o
|
|
||||||
.f90.o:
|
|
||||||
$(F90) $(F90FLAGS) -c $*.f90
|
|
||||||
|
|
||||||
clean:
|
|
||||||
rm -f *.o
|
|
||||||
|
|
||||||
@ -1,267 +0,0 @@
|
|||||||
program TMDGen !************************************************************************************
|
|
||||||
!
|
|
||||||
! Stand-alone generator of 3D CNT samples.
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, 2020, Version 13.00
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
|
|
||||||
use TMDGen3D
|
|
||||||
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Global variables
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
integer*4 :: Nseg, Nnode
|
|
||||||
real*8 :: DS00
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Body
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
print *, 'TMD generator of 3D CNT samples, v. 13.00'
|
|
||||||
print '(a34,a,i10)', 'Maximum number of nanotubes', ' : ', MAX_TUBE
|
|
||||||
|
|
||||||
call SetRandomSeed ()
|
|
||||||
|
|
||||||
! Reading and printing of governing parameters
|
|
||||||
call LoadGoverningParameters ()
|
|
||||||
call PrintGoverningParameters ()
|
|
||||||
|
|
||||||
! Here we calculate the radius of nanotubes
|
|
||||||
RT0 = TPBA * sqrt ( 3.0d+00 * ( ChiIndM * ChiIndM + ChiIndN * ChiIndN + ChiIndM * ChiIndN ) ) / M_2PI;
|
|
||||||
|
|
||||||
! Here we calculate parameters of the desired sample
|
|
||||||
call InitSample ()
|
|
||||||
DS0 = DS0 * ( K_MDDU / 1.0d+03 )
|
|
||||||
call PrintSampleParameters ( 'Desired' )
|
|
||||||
DS00 = DS0
|
|
||||||
DS0 = DS0 / ( K_MDDU / 1.0d+03 )
|
|
||||||
|
|
||||||
call Generator3D ()
|
|
||||||
|
|
||||||
! Here we write the major output file with the sample
|
|
||||||
!call WriteOutputFile_old_format ()
|
|
||||||
!call WriteOutputFile ()
|
|
||||||
|
|
||||||
! Here we write an auxiliary Tecplot file to visualize the initial sample
|
|
||||||
!PrintTecplotFile ()
|
|
||||||
call WriteLAMMPSFile()
|
|
||||||
|
|
||||||
! Here we print parameters of the final sample
|
|
||||||
call PrintSampleParameters ( 'Final' )
|
|
||||||
print '(a34,a,f15.4,a)', 'Nanotube radius ', ' : ', RT0, ' a'
|
|
||||||
print '(a34,a,f15.4,a)', 'Nanotube length ', ' : ', LT0, ' a'
|
|
||||||
print '(a34,a,f15.4,a)', 'Nanotube mass ', ' : ', M_2PI * RT0 * LT0 * TPBM * TPBD, ' Da'
|
|
||||||
if ( SegType == 0 ) then
|
|
||||||
LSeg0 = LT0 / NSeg0
|
|
||||||
else
|
|
||||||
NSeg0 = int ( LT0 / LSeg0 ) + 1
|
|
||||||
LSeg0 = LT0 / NSeg0
|
|
||||||
end if
|
|
||||||
print '(a34,a,f15.4,a)', 'Nanotube segment length ', ' : ', LSeg0, ' a'
|
|
||||||
print '(a34,a,f15.4,a)', 'Nanotube segment mass ', ' : ', M_2PI * RT0 * LSeg0 * TPBM * TPBD, ' Da'
|
|
||||||
print '(a34,a,f15.4)', 'Desired / Real densities ', ' : ', DS00 / DS0
|
|
||||||
print '(a34,a,i10)', 'Real number of tubes', ' : ', NT
|
|
||||||
print '(a34,a,i10)', 'Real number of segments', ' : ', Nseg
|
|
||||||
print '(a34,a,i10)', 'Real number of nodes', ' : ', Nnode
|
|
||||||
|
|
||||||
contains !******************************************************************************************
|
|
||||||
|
|
||||||
subroutine DiscretizeTube ( X0, DL, NS, i ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function calculaats geometrical parameters that are necessary to represent straight
|
|
||||||
! tube i as a sequence of segments.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, dimension(0:2), intent(out) :: X0
|
|
||||||
real*8, intent(out) :: DL
|
|
||||||
integer*4, intent(out) :: NS
|
|
||||||
integer*4, intent(in) :: i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, dimension(0:2) :: X1
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
call GetTubeEnds ( X0, X1, i )
|
|
||||||
if ( SegType == 0 ) then
|
|
||||||
NS = NSeg0
|
|
||||||
else
|
|
||||||
NS = int ( LT(i) / LSeg0 ) + 1
|
|
||||||
end if
|
|
||||||
DL = LT(i) / NS
|
|
||||||
end subroutine DiscretizeTube !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine WriteOutputFile_old_format () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function writes a dat file (version 2) with the initial nanotube sample.
|
|
||||||
! This file is used by TMD/TMDMPI to start a new simulation.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer*4 :: Fuid, i, j, NTS, Prop
|
|
||||||
real*8 :: DL, L, L00, M00, I00, J00, C00, LL00, MM00, II00, JJ00, CC00
|
|
||||||
real*8, dimension(0:2) :: X, X0
|
|
||||||
logical*4 :: PrintNode
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Fuid = OpenFile ( 'TMDGen_old.dat', "wt", "" )
|
|
||||||
write ( unit = Fuid, fmt = '(i12)' ) 3
|
|
||||||
write ( unit = Fuid, fmt = '(2i4,4e20.12)' ) ChiIndM, ChiIndN, RT0, TPBA, TPBD, TPBM
|
|
||||||
write ( unit = Fuid, fmt = '(3e20.12)' ) DomXmin, DomYmin, DomZmin
|
|
||||||
write ( unit = Fuid, fmt = '(3e20.12)' ) DomXmax, DomYmax, DomZmax
|
|
||||||
write ( unit = Fuid, fmt = '(3i12)' ) BC_X, BC_Y, BC_Z
|
|
||||||
write ( unit = Fuid, fmt = '(i12)' ) NT
|
|
||||||
Nseg = 0
|
|
||||||
Nnode = 0
|
|
||||||
do i = 0, NT - 1
|
|
||||||
call DiscretizeTube ( X0, DL, NTS, i )
|
|
||||||
L00 = LT(i) / NTS
|
|
||||||
M00 = TubeMass ( i ) / NTS
|
|
||||||
I00 = 0.0d+00
|
|
||||||
J00 = M00 * sqr ( RT(i) )
|
|
||||||
C00 = M00 * TubeSpecificHeat ( i )
|
|
||||||
Nseg = Nseg + NTS
|
|
||||||
write ( unit = Fuid, fmt = '(i12)' ) NTS + 1
|
|
||||||
Nnode = Nnode + NTS + 1
|
|
||||||
L = 0.0d+00
|
|
||||||
do j = 0, NTS
|
|
||||||
X = X0 + L * DT(i,0:2)
|
|
||||||
MM00 = M00
|
|
||||||
II00 = I00
|
|
||||||
JJ00 = J00
|
|
||||||
CC00 = C00
|
|
||||||
LL00 = L00
|
|
||||||
if ( j == 0 .or. j == NTS ) then
|
|
||||||
MM00 = 0.5d+00 * M00
|
|
||||||
II00 = 0.5d+00 * I00
|
|
||||||
JJ00 = 0.5d+00 * J00
|
|
||||||
CC00 = 0.5d+00 * C00
|
|
||||||
end if
|
|
||||||
if ( j == NTS ) LL00 = 0.0d+00
|
|
||||||
Prop = 0
|
|
||||||
write ( unit = Fuid, fmt = '(i2,6e20.12)' ) Prop, RT(0), LL00, MM00, II00, JJ00, CC00
|
|
||||||
write ( unit = Fuid, fmt = '(6e20.12)' ) X, RT(i), 0.0d+00, 300.0d+00
|
|
||||||
L = L + DL
|
|
||||||
end do
|
|
||||||
end do
|
|
||||||
write ( unit = Fuid, fmt = '(i12)' ) 0
|
|
||||||
write ( unit = Fuid, fmt = '(i12)' ) 0
|
|
||||||
call CloseFile ( Fuid )
|
|
||||||
end subroutine WriteOutputFile_old_format !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine WriteOutputFile () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function writes a dat file (version 2) with the initial nanotube sample.
|
|
||||||
! This file is used by TMD/TMDMPI to start a new simulation.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer*4 :: Fuid, i, j, NTS
|
|
||||||
real*8 :: DL, L, L00, M00, LL00, MM00
|
|
||||||
real*8, dimension(0:2) :: X, X0
|
|
||||||
logical*4 :: PrintNode
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Fuid = OpenFile ( 'TMDGen.dat', "wt", "" )
|
|
||||||
write ( unit = Fuid, fmt = '(2i4,4e20.12)' ) ChiIndM, ChiIndN, RT0, TPBA, TPBD, TPBM
|
|
||||||
write ( unit = Fuid, fmt = '(3e20.12)' ) DomXmin, DomYmin, DomZmin
|
|
||||||
write ( unit = Fuid, fmt = '(3e20.12)' ) DomXmax, DomYmax, DomZmax
|
|
||||||
write ( unit = Fuid, fmt = '(3i12)' ) BC_X, BC_Y, BC_Z
|
|
||||||
write ( unit = Fuid, fmt = '(i12)' ) NT
|
|
||||||
Nseg = 0
|
|
||||||
Nnode = 0
|
|
||||||
do i = 0, NT - 1
|
|
||||||
call DiscretizeTube ( X0, DL, NTS, i )
|
|
||||||
L00 = LT(i) / NTS
|
|
||||||
M00 = TubeMass ( i ) / NTS
|
|
||||||
Nseg = Nseg + NTS
|
|
||||||
write ( unit = Fuid, fmt = '(i12)' ) NTS + 1
|
|
||||||
Nnode = Nnode + NTS + 1
|
|
||||||
L = 0.0d+00
|
|
||||||
do j = 0, NTS
|
|
||||||
X = X0 + L * DT(i,0:2)
|
|
||||||
MM00 = M00
|
|
||||||
LL00 = L00
|
|
||||||
if ( j == 0 .or. j == NTS ) MM00 = 0.5d+00 * M00
|
|
||||||
if ( j == NTS ) LL00 = 0.0d+00
|
|
||||||
write ( unit = Fuid, fmt = '(5e20.12)' ) X, LL00, MM00
|
|
||||||
L = L + DL
|
|
||||||
end do
|
|
||||||
end do
|
|
||||||
call CloseFile ( Fuid )
|
|
||||||
end subroutine WriteOutputFile !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine PrintTecplotFile () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function prints Tecplot file to visualize the generated sample
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer*4 :: Fuid, i
|
|
||||||
real*8 :: LT2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Fuid = OpenFile ( 'TMDGen.plt', "wt", "" )
|
|
||||||
write ( unit = Fuid, fmt = '(a)' ) 'VARIABLES="X" "Y" "Z"'
|
|
||||||
do i = 0, NT - 1
|
|
||||||
write ( unit = Fuid, fmt = '(a,i,a)' ) 'ZONE T="T', i, '"'
|
|
||||||
LT2 = 0.5d+00 * LT(i)
|
|
||||||
write ( unit = Fuid, fmt = '(3e20.12)' ) CT(i,0:2) - LT2 * DT(i,0:2)
|
|
||||||
write ( unit = Fuid, fmt = '(3e20.12)' ) CT(i,0:2) + LT2 * DT(i,0:2)
|
|
||||||
end do
|
|
||||||
call CloseFile ( Fuid )
|
|
||||||
end subroutine PrintTecplotFile !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
|
|
||||||
subroutine WriteLAMMPSFile () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function writes a dat file (version 2) with the initial nanotube sample.
|
|
||||||
! This file is used by TMD/TMDMPI to start a new simulation.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer*4 :: file_id, i, j, NTS, node_id, b1, b2
|
|
||||||
real*8 :: DL, L, L00, M00, LL00, MM00
|
|
||||||
real*8, dimension(0:2) :: X, X0
|
|
||||||
logical*4 :: PrintNode
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
open(newunit = file_id, file = 'TMDSample.init')
|
|
||||||
write(file_id,*)
|
|
||||||
write(file_id,*)
|
|
||||||
!count the number of nodes and segments
|
|
||||||
Nseg = 0
|
|
||||||
Nnode = 0
|
|
||||||
do i = 0, NT - 1
|
|
||||||
call DiscretizeTube (X0, DL, NTS, i)
|
|
||||||
Nseg = Nseg + NTS
|
|
||||||
Nnode = Nnode + NTS + 1
|
|
||||||
enddo
|
|
||||||
write(file_id,'(i9,a)') Nnode, " atoms"
|
|
||||||
write(file_id,*)
|
|
||||||
write(file_id,*) "1 atom types"
|
|
||||||
write(file_id,*)
|
|
||||||
write(file_id,'(2e20.12,2a)') DomXmin, DomXmax, " xlo xhi"
|
|
||||||
write(file_id,'(2e20.12,2a)') DomYmin, DomYmax, " ylo yhi"
|
|
||||||
write(file_id,'(2e20.12,2a)') DomZmin, DomZmax, " zlo zhi"
|
|
||||||
write(file_id,*)
|
|
||||||
write(file_id,*) "Masses"
|
|
||||||
write(file_id,*)
|
|
||||||
write(file_id,*) "1 1.0"
|
|
||||||
write(file_id,*)
|
|
||||||
write(file_id,*) "Atoms"
|
|
||||||
write(file_id,*)
|
|
||||||
|
|
||||||
node_id = 1
|
|
||||||
do i = 0, NT - 1
|
|
||||||
call DiscretizeTube(X0, DL, NTS, i)
|
|
||||||
L00 = LT(i) / NTS
|
|
||||||
M00 = TubeMass (i) / NTS
|
|
||||||
|
|
||||||
b1 = -1
|
|
||||||
L = 0.0d+00
|
|
||||||
do j = 0, NTS
|
|
||||||
b2 = node_id + 1
|
|
||||||
if (j == NTS) b2 = -1
|
|
||||||
MM00 = M00
|
|
||||||
LL00 = L00
|
|
||||||
if (j == 0 .or. j == NTS) MM00 = 0.5d+00 * M00
|
|
||||||
if (j == NTS) LL00 = 0.0d+00
|
|
||||||
X = X0 + L * DT(i,0:2)
|
|
||||||
write(file_id,'(2i9,a,2i9,3e14.7,a,3e20.12,a)') node_id, i, " 1 ", b1, b2, MM00, RT(i), LL00, " 0 ", X, " 0 0 0"
|
|
||||||
b1 = node_id
|
|
||||||
node_id = node_id + 1
|
|
||||||
L = L + DL
|
|
||||||
enddo
|
|
||||||
enddo
|
|
||||||
close(file_id)
|
|
||||||
end subroutine !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end program TMDGen !********************************************************************************
|
|
||||||
@ -1,15 +0,0 @@
|
|||||||
0.400000000000E+04 : LS0, A
|
|
||||||
0.400000000000E+04 : HS0, A
|
|
||||||
0.010000000000E+00 : DS0, Density g/cm^3
|
|
||||||
1 : BC_X0, periodic along X
|
|
||||||
1 : BC_Y0, periodic along Y
|
|
||||||
0 : BC_Z0, periodic along Z
|
|
||||||
10 : ChiIndM, tube chirality M
|
|
||||||
10 : ChiIndN, tube chirality N
|
|
||||||
0.200000000000E+04 : LT0, A
|
|
||||||
0 : SegType
|
|
||||||
100 : NSeg0
|
|
||||||
0.200000000000E+02 : LSeg0
|
|
||||||
0.500000000000E+01 : DeltaT, A
|
|
||||||
1000000 : NAmax
|
|
||||||
0.100000000000E-06 : GeomPrec
|
|
||||||
@ -1,231 +0,0 @@
|
|||||||
module TMDGen3D !***********************************************************************************
|
|
||||||
!
|
|
||||||
! Generator of 3D CNT samples for TPM force field
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 13.00, 2020
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
use TMDGenData
|
|
||||||
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
contains !******************************************************************************************
|
|
||||||
|
|
||||||
real*8 function MinimalDistance3D ( S1, S2, H, cosA, P, Q ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function returns the minimum distance between two line segments in 3D
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, intent(out) :: S1, S2
|
|
||||||
real*8, intent(in) :: H, cosA
|
|
||||||
real*8, dimension(0:1), intent(in) :: P, Q
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8 :: H2, cosA2, D
|
|
||||||
real*8, dimension(0:1) :: P1, Q1
|
|
||||||
integer*4, dimension(0:1,0:1) :: KA
|
|
||||||
integer*4 :: i, j, K
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
if ( ( P(0) * P(1) .le. 0.0d+00 ) .and. ( Q(0) * Q(1) .le. 0.0d+00 ) ) then
|
|
||||||
MinimalDistance3D = H
|
|
||||||
S1 = 0.5d+00 * ( P(0) + P(1) )
|
|
||||||
S2 = 0.5d+00 * ( Q(0) + Q(1) )
|
|
||||||
return
|
|
||||||
end if
|
|
||||||
do i = 0, 1
|
|
||||||
P1(i) = P(i) * cosA
|
|
||||||
Q1(i) = Q(i) * cosA
|
|
||||||
end do
|
|
||||||
KA = 1
|
|
||||||
K = 0
|
|
||||||
do i = 0, 1
|
|
||||||
if ( ( Q1(i) .ge. P(0) ) .and. ( Q1(i) .le. P(1) ) ) then
|
|
||||||
D = sqr ( Q(i) )
|
|
||||||
if ( K == 0 ) then
|
|
||||||
MinimalDistance3D = D
|
|
||||||
S1 = Q1(i)
|
|
||||||
S2 = Q(i)
|
|
||||||
K = 1
|
|
||||||
else if ( D < MinimalDistance3D ) then
|
|
||||||
MinimalDistance3D = D
|
|
||||||
S1 = Q1(i)
|
|
||||||
S2 = Q(i)
|
|
||||||
end if
|
|
||||||
KA(0,i) = 0
|
|
||||||
KA(1,i) = 0
|
|
||||||
end if
|
|
||||||
if ( ( P1(i) .ge. Q(0) ) .and. ( P1(i) .le. Q(1) ) ) then
|
|
||||||
D = sqr ( P(i) )
|
|
||||||
if ( K == 0 ) then
|
|
||||||
MinimalDistance3D = D
|
|
||||||
S1 = P(i)
|
|
||||||
S2 = P1(i)
|
|
||||||
K = 1
|
|
||||||
else if ( D < MinimalDistance3D ) then
|
|
||||||
MinimalDistance3D = D
|
|
||||||
S1 = P(i)
|
|
||||||
S2 = P1(i)
|
|
||||||
end if
|
|
||||||
KA(i,0) = 0
|
|
||||||
KA(i,1) = 0
|
|
||||||
end if
|
|
||||||
end do
|
|
||||||
H2 = sqr ( H )
|
|
||||||
cosA2 = 2.0d+00 * cosA
|
|
||||||
if ( K == 1 ) MinimalDistance3D = H2 + MinimalDistance3D * ( 1.0d+00 - sqr ( cosA ) )
|
|
||||||
do i = 0, 1
|
|
||||||
do j = 0, 1
|
|
||||||
if ( KA(i,j) == 1 ) then
|
|
||||||
D = H2 + sqr ( P(i) ) + sqr ( Q(j) ) - P(i) * Q(j) * cosA2
|
|
||||||
if ( K == 0 ) then
|
|
||||||
MinimalDistance3D = D
|
|
||||||
S1 = P(i)
|
|
||||||
S2 = Q(j)
|
|
||||||
K = 1
|
|
||||||
else if ( D < MinimalDistance3D ) then
|
|
||||||
MinimalDistance3D = D
|
|
||||||
S1 = P(i)
|
|
||||||
S2 = Q(j)
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
end do
|
|
||||||
end do
|
|
||||||
MinimalDistance3D = dsqrt ( MinimalDistance3D )
|
|
||||||
end function MinimalDistance3D !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine RandTube3D ( X, L ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This subroutine generates a random tube in an isotropic 3D sample
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, dimension(0:2), intent(out) :: X, L
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8 :: CT, ST, E
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
if ( BC_X0 == 0 ) then
|
|
||||||
X(0)= LS0 * randnumber ()
|
|
||||||
else
|
|
||||||
X(0)= LS0 * ( 0.5d+00 - 1.0d+00 * randnumber () )
|
|
||||||
end if
|
|
||||||
if ( BC_Y0 == 0 ) then
|
|
||||||
X(1)= LS0 * randnumber ()
|
|
||||||
else
|
|
||||||
X(1)= LS0 * ( 0.5d+00 - 1.0d+00 * randnumber () )
|
|
||||||
end if
|
|
||||||
if ( BC_Z0 == 0 ) then
|
|
||||||
X(2)= HS0 *randnumber ()
|
|
||||||
else
|
|
||||||
X(2)= HS0 * ( 0.5d+00 - 1.0d+00 * randnumber () )
|
|
||||||
end if
|
|
||||||
CT = 1.0d+00 - 2.0d+00 * randnumber ()
|
|
||||||
ST = sqrt ( 1.0d+00 - sqr ( CT ) )
|
|
||||||
E = M_2PI * randnumber ()
|
|
||||||
L(0)= CT
|
|
||||||
L(1)= ST * cos ( E )
|
|
||||||
L(2)= ST * sin ( E )
|
|
||||||
end subroutine RandTube3D !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
logical function AddTubeToSample3D ( MS ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function adds the last generated tube to the existing sample, if possible.
|
|
||||||
! In a case of periodic boundaries, this version is valid only f the tube length is smaller
|
|
||||||
! than the half of the sample.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, intent(inout) :: MS
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer*4 :: i, m
|
|
||||||
real*8 :: Dmin, LT2, H, cosA, D1, D2, S1, S2
|
|
||||||
real*8, dimension(0:2) :: X, L12
|
|
||||||
real*8, dimension(0:1) :: P, Q
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
AddTubeToSample3D = .false.
|
|
||||||
if ( .not. IsTubeInside ( NT ) ) return
|
|
||||||
|
|
||||||
LT2 = 0.5d+00 * LT(NT)
|
|
||||||
do m = 0, NT - 1
|
|
||||||
X = CT(NT,0:2)
|
|
||||||
if ( LineLine ( H, cosA, D1, D2, L12, X, DT(NT,0:2), CT(m,0:2), DT(m,0:2), GeomPrec ) == MD_LINES_NONPAR ) then
|
|
||||||
P(0) = D1 - LT2
|
|
||||||
P(1) = D1 + LT2
|
|
||||||
Q(0) = D2 - 0.5d+00 * LT(m)
|
|
||||||
Q(1) = D2 + 0.5d+00 * LT(m)
|
|
||||||
Dmin = MinimalDistance3D ( S1, S2, H, cosA, P, Q )
|
|
||||||
else
|
|
||||||
call LinePoint ( H, L12, CT(m,0:2), DT(m,0:2), X )
|
|
||||||
L12 = L12 - X
|
|
||||||
call ApplyPeriodicBC ( L12 )
|
|
||||||
Dmin = S_V3norm3 ( L12 )
|
|
||||||
end if
|
|
||||||
if ( Dmin < RT(NT) + RT(m) + DeltaT ) return
|
|
||||||
end do
|
|
||||||
|
|
||||||
MS = MS + TubeMass ( NT )
|
|
||||||
NT = NT + 1
|
|
||||||
AddTubeToSample3D = .true.
|
|
||||||
end function AddTubeToSample3D !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine Generator3D () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This subroutine implements the whole fgenerator of 3D samples
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer*4 :: NA, NT0
|
|
||||||
real*8 :: MS
|
|
||||||
real*8 :: X1, X2, Y1, Y2, Z1, Z2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
NT = 0
|
|
||||||
MS = 0.0d+00
|
|
||||||
NT0 = int ( MS0 / ( M_2PI * RT0 * LT0 * TPBM * TPBD ) )
|
|
||||||
do
|
|
||||||
if ( NT == MAX_TUBE ) then
|
|
||||||
print *, 'Error in [Generator3D]: MAX_TUBE is too small'
|
|
||||||
stop
|
|
||||||
end if
|
|
||||||
if ( MS .ge. MS0 ) exit
|
|
||||||
NA = 0
|
|
||||||
! Trying to add the tube to the sample
|
|
||||||
! The maximal number of attempts is equal to NAmax
|
|
||||||
RT(NT) = RT0
|
|
||||||
LT(NT) = LT0
|
|
||||||
do
|
|
||||||
if ( NA == NAmax ) exit
|
|
||||||
call RandTube3D ( CT(NT,0:2), DT(NT,0:2) )
|
|
||||||
if ( AddTubeToSample3D ( MS ) ) then
|
|
||||||
print '(a,i10,a,i10,a,i10)', 'Tube ', NT, '(Appr.', NT0, ' total): Attempt ', NA
|
|
||||||
if ( BC_X0 == 0 ) then
|
|
||||||
X1 = CT(NT,0) - 0.5d+00 * LT(NT) * DT(NT,0)
|
|
||||||
X2 = CT(NT,0) + 0.5d+00 * LT(NT) * DT(NT,0)
|
|
||||||
if ( DomXmin > X1 ) DomXmin = X1
|
|
||||||
if ( DomXmin > X2 ) DomXmin = X2
|
|
||||||
if ( DomXmax < X1 ) DomXmax = X1
|
|
||||||
if ( DomXmax < X2 ) DomXmax = X2
|
|
||||||
end if
|
|
||||||
if ( BC_Y0 == 0 ) then
|
|
||||||
Y1 = CT(NT,1) - 0.5d+00 * LT(NT) * DT(NT,1)
|
|
||||||
Y2 = CT(NT,1) + 0.5d+00 * LT(NT) * DT(NT,1)
|
|
||||||
if ( DomYmin > Y1 ) DomYmin = Y1
|
|
||||||
if ( DomYmin > Y2 ) DomYmin = Y2
|
|
||||||
if ( DomYmax < Y1 ) DomYmax = Y1
|
|
||||||
if ( DomYmax < Y2 ) DomYmax = Y2
|
|
||||||
end if
|
|
||||||
if ( BC_Z0 == 0 ) then
|
|
||||||
Z1 = CT(NT,2) - 0.5d+00 * LT(NT) * DT(NT,2)
|
|
||||||
Z2 = CT(NT,2) + 0.5d+00 * LT(NT) * DT(NT,2)
|
|
||||||
if ( DomZmin > Z1 ) DomZmin = Z1
|
|
||||||
if ( DomZmin > Z2 ) DomZmin = Z2
|
|
||||||
if ( DomZmax < Z1 ) DomZmax = Z1
|
|
||||||
if ( DomZmax < Z2 ) DomZmax = Z2
|
|
||||||
end if
|
|
||||||
exit
|
|
||||||
end if
|
|
||||||
NA = NA + 1
|
|
||||||
end do
|
|
||||||
end do
|
|
||||||
MS0 = MS
|
|
||||||
|
|
||||||
if ( BC_X0 == 0 ) DomLX = DomXmax - DomXmin
|
|
||||||
if ( BC_Y0 == 0 ) DomLY = DomYmax - DomYmin
|
|
||||||
if ( BC_Z0 == 0 ) DomLZ = DomZmax - DomZmin
|
|
||||||
|
|
||||||
VS0 = ( DomXmax - DomXmin ) * ( DomYmax - DomYmin ) * ( DomZmax - DomZmin )
|
|
||||||
DS0 = MS0 / VS0 * ( K_MDDU / 1.0d+03 )
|
|
||||||
end subroutine Generator3D !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end module TMDGen3D !*******************************************************************************
|
|
||||||
@ -1,289 +0,0 @@
|
|||||||
module TMDGenData !*********************************************************************************
|
|
||||||
!
|
|
||||||
! Common data for TMDGen
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 13.00, 2020
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
use TPMGeom
|
|
||||||
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Constants
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
integer*4, parameter :: MAX_TUBE = 1000000 ! Maximum number of tubes in 3D
|
|
||||||
|
|
||||||
real*8, parameter :: K_MDDU = K_MDMU / K_MDLU / K_MDLU / K_MDLU ! MD density unit (kg/m**3)
|
|
||||||
|
|
||||||
!
|
|
||||||
! These parameters are specific for carbon nanotubes and taken from module TubePotBase
|
|
||||||
!
|
|
||||||
|
|
||||||
real*8, parameter :: TPbConstD = 5.196152422706632d+00 ! = 3.0**1.5
|
|
||||||
! Mass of C atom
|
|
||||||
real*8, parameter :: TPBM = 12.0107d+00 ! (a.m.u.)
|
|
||||||
! Lattice parameter and numerical density of atoms for a graphene sheet, see Dresselhaus et al, Carbon 33(7), 1995
|
|
||||||
real*8, parameter :: TPBA = 1.421d+00 ! (Angstrom)
|
|
||||||
real*8, parameter :: TPBD = 4.0d+00 / ( TPBConstD * TPBA * TPBA ) ! (1/Angstrom^2)
|
|
||||||
! Specific heat of carbon nanotubes
|
|
||||||
real*8, parameter :: TPBSH = 600.0d+00 / K_MDCU ! (eV/(Da*K))
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Governing parameters
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
! Parameters of the sample
|
|
||||||
|
|
||||||
real*8 :: LS0 = 4000.0 ! Sample size in x, y-directions (Angstrom)
|
|
||||||
real*8 :: HS0 = 4000.0 ! Sample size in z-direction (Angstrom)
|
|
||||||
real*8 :: DS0 = 0.01 ! Density (g/cm**3)
|
|
||||||
integer*4 :: BC_X0 = 1 ! Boundary conditions in x-direction: 0, free; 1, periodic
|
|
||||||
integer*4 :: BC_Y0 = 1 ! Boundary conditions in y-direction: 0, free; 1, periodic
|
|
||||||
integer*4 :: BC_Z0 = 1 ! Boundary conditions in z-direction: 0, free; 1, periodic
|
|
||||||
|
|
||||||
! Parameters of tubes
|
|
||||||
integer*4 :: ChiIndM = 10 ! Chirality index m of nanotubes
|
|
||||||
integer*4 :: ChiIndN = 10 ! Chirality index n of nanotubes
|
|
||||||
real*8 :: LT0 = 2000.0 ! Characterstic length of tubes (Angstrom)
|
|
||||||
integer*4 :: SegType = 0 ! 0, number of segments per tube is fixed
|
|
||||||
! 1, rounded length of segments is fixed
|
|
||||||
integer*4 :: NSeg0 = 100 ! Number of segments per tube
|
|
||||||
real*8 :: LSeg0 = 20.0d+00 ! Length of the segment (Angstrom)
|
|
||||||
|
|
||||||
|
|
||||||
! Parameters controlling the sample structure
|
|
||||||
|
|
||||||
real*8 :: DeltaT = 3.0 ! Minimal distance between tubes (Angstrom)
|
|
||||||
integer*4 :: NAmax = 50000 ! Maximal number of attempts (for SampleType = 4 it is used as an input paramtere for number of tubes)
|
|
||||||
real*8 :: GeomPrec = 1.0d-06 ! Geometrical precision
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Computed data
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
real*8 :: RT0 = 6.785 ! Radius of tubes (Angstrom)
|
|
||||||
|
|
||||||
real*8 :: VS0 ! Desired volume of the sample, Angstrom**3
|
|
||||||
real*8 :: MS0 ! Desired mass of the sample, Da (For SampleType = 4 it is the defined fixed mass- definition is given in TMDGen7T)
|
|
||||||
|
|
||||||
real*8 :: CTCD ! Center to center distance between any surrounding tube and center tube (used for SampleType == 4 only)
|
|
||||||
|
|
||||||
integer*4 :: NT ! Real number of tubes
|
|
||||||
real*8, dimension(0:MAX_TUBE-1) :: RT ! Radii of tubes, Angstrom
|
|
||||||
real*8, dimension(0:MAX_TUBE-1) :: LT ! Lengths of tubes, Angstrom
|
|
||||||
real*8, dimension(0:MAX_TUBE-1,0:2) :: CT ! Coordinates of tubes' centers, Angstrom
|
|
||||||
real*8, dimension(0:MAX_TUBE-1,0:2) :: DT ! Directions of tubes
|
|
||||||
integer*4, dimension(0:MAX_TUBE-1) :: AT ! Parent axes of tubes. It is used only in GeneratorBundle ()
|
|
||||||
|
|
||||||
contains !******************************************************************************************
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Pseudo-random number generator
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
real*8 function randnumber () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function returns a pseudo-random number with uniform distribution in [0,1]
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
call random_number ( randnumber )
|
|
||||||
end function randnumber !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine SetRandomSeed () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This subroutine sets random seed for the pseudo-random number generator
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer :: i, n, clock
|
|
||||||
integer, dimension(:), allocatable :: seed
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
call RANDOM_SEED ( size = n )
|
|
||||||
allocate ( seed(n) )
|
|
||||||
call SYSTEM_CLOCK ( COUNT = clock )
|
|
||||||
seed = clock + 37 * (/ (i - 1, i = 1, n) /)
|
|
||||||
call RANDOM_SEED ( PUT = seed )
|
|
||||||
deallocate ( seed )
|
|
||||||
end subroutine SetRandomSeed !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Generators for (random) properties of nanotubes
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
real*8 function TubeMass ( i ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function returns the mass of the tube in Da
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer*4, intent(in) :: i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
TubeMass = M_2PI * RT(i) * LT(i) * TPBM * TPBD
|
|
||||||
end function TubeMass !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
real*8 function TubeSpecificHeat ( i ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function returns the specific heat of the tube
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer*4, intent(in) :: i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
TubeSpecificHeat = TPBSH
|
|
||||||
end function TubeSpecificHeat !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Reading and printing of input parameters
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
subroutine LoadGoverningParameters () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function reads governing parameters from xdt file
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer*4 :: Fuid, i
|
|
||||||
character*512 :: Msg
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Fuid = OpenFile ( 'TMDGen.xdt', 'rt', '' )
|
|
||||||
read ( unit = Fuid, fmt = '(e22.12)' ) LS0
|
|
||||||
read ( unit = Fuid, fmt = '(e22.12)' ) HS0
|
|
||||||
read ( unit = Fuid, fmt = '(e22.12)' ) DS0
|
|
||||||
read ( unit = Fuid, fmt = '(i22)' ) BC_X0
|
|
||||||
read ( unit = Fuid, fmt = '(i22)' ) BC_Y0
|
|
||||||
read ( unit = Fuid, fmt = '(i22)' ) BC_Z0
|
|
||||||
read ( unit = Fuid, fmt = '(i22)' ) ChiIndM
|
|
||||||
read ( unit = Fuid, fmt = '(i22)' ) ChiIndN
|
|
||||||
read ( unit = Fuid, fmt = '(e22.12)' ) LT0
|
|
||||||
read ( unit = Fuid, fmt = '(i22)' ) SegType
|
|
||||||
read ( unit = Fuid, fmt = '(i22)' ) NSeg0
|
|
||||||
read ( unit = Fuid, fmt = '(e22.12)' ) LSeg0
|
|
||||||
read ( unit = Fuid, fmt = '(e22.12)' ) DeltaT
|
|
||||||
read ( unit = Fuid, fmt = '(i22)' ) NAmax
|
|
||||||
read ( unit = Fuid, fmt = '(e22.12)' ) GeomPrec
|
|
||||||
call CloseFile ( Fuid )
|
|
||||||
end subroutine LoadGoverningParameters !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine PrintGoverningParameters () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function prints governing parameters to xlg file
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer*4 :: Fuid, i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Fuid = OpenFile ( 'TMDGen.xlg', 'wt', '' )
|
|
||||||
write ( unit = Fuid, fmt = '(e22.12,a)' ) LS0, ' : LS0, Angstrom'
|
|
||||||
write ( unit = Fuid, fmt = '(e22.12,a)' ) HS0, ' : HS0, Angstrom'
|
|
||||||
write ( unit = Fuid, fmt = '(e22.12,a)' ) DS0, ' : DS0, g/cm**3'
|
|
||||||
write ( unit = Fuid, fmt = '(e22.12,a)' ) DS0, ' : SC0, 1/A**2'
|
|
||||||
write ( unit = Fuid, fmt = '(i22,a)' ) BC_X0, ' : BC_X0'
|
|
||||||
write ( unit = Fuid, fmt = '(i22,a)' ) BC_Y0, ' : BC_Y0'
|
|
||||||
write ( unit = Fuid, fmt = '(i22,a)' ) BC_Z0, ' : BC_Z0'
|
|
||||||
write ( unit = Fuid, fmt = '(i22,a)' ) ChiIndM, ' : ChiIndM'
|
|
||||||
write ( unit = Fuid, fmt = '(i22,a)' ) ChiIndN, ' : ChiIndN'
|
|
||||||
write ( unit = Fuid, fmt = '(e22.12,a)' ) LT0, ' : LT0, Angstrom'
|
|
||||||
write ( unit = Fuid, fmt = '(i22,a)' ) SegType, ' : SegType'
|
|
||||||
write ( unit = Fuid, fmt = '(i22,a)' ) NSeg0, ' : NSeg0'
|
|
||||||
write ( unit = Fuid, fmt = '(e22.12,a)' ) LSeg0, ' : LSeg0, Angstrom'
|
|
||||||
write ( unit = Fuid, fmt = '(e22.12,a)' ) DeltaT, ' : DeltaT'
|
|
||||||
write ( unit = Fuid, fmt = '(i22,a)' ) NAmax, ' : NAmax'
|
|
||||||
write ( unit = Fuid, fmt = '(e22.12,a)' ) GeomPrec, ' : GeomPrec'
|
|
||||||
call CloseFile ( Fuid )
|
|
||||||
end subroutine PrintGoverningParameters !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Printing of sample parameters
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
subroutine PrintSampleParameters ( ParType ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function prints the most imprtant parameters of the sample.
|
|
||||||
! In the code, it used twice to print parameters of the desired and really generated samples.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
character*(*), intent(in) :: ParType
|
|
||||||
real*8 :: MP, M, V
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
print '(a,a,a)', '*** ', trim(ParType), ' properties of the sample'
|
|
||||||
print '(a34,a,f15.4,a)', 'L', ' : ', LS0, ' A'
|
|
||||||
print '(a34,a,f15.4,a)', 'H', ' : ', HS0, ' A'
|
|
||||||
print '(a34,a,f15.4,a)', 'Density', ' : ', DS0, ' g/cm**3'
|
|
||||||
print '(a34,a,e15.8,a)', 'Volume', ' : ', VS0, ' A*3'
|
|
||||||
print '(a34,a,e15.8,a)', 'Mass', ' : ', MS0, ' Da'
|
|
||||||
print '(a34,a,i10)', 'BC_X', ' : ', BC_X0
|
|
||||||
print '(a34,a,i10)', 'BC_Y', ' : ', BC_Y0
|
|
||||||
print '(a34,a,i10)', 'BC_Z', ' : ', BC_Z0
|
|
||||||
end subroutine PrintSampleParameters !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Initializing of basic geometrical parameters of the generated sample
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
subroutine InitSample () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function initializes the geometrical parameters of the sample (sizes, etc.)
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
BC_X = BC_X0
|
|
||||||
BC_Y = BC_Y0
|
|
||||||
BC_Z = BC_Z0
|
|
||||||
DomXmin = - LS0 / 2.0d+00
|
|
||||||
DomXmax = LS0 / 2.0d+00
|
|
||||||
DomYmin = - LS0 / 2.0d+00
|
|
||||||
DomYmax = LS0 / 2.0d+00
|
|
||||||
DomZmin = - HS0 / 2.0d+00
|
|
||||||
DomZmax = HS0 / 2.0d+00
|
|
||||||
|
|
||||||
if ( BC_X0 == 0 ) then
|
|
||||||
DomXmin = 0.0d+00
|
|
||||||
DomXmax = LS0
|
|
||||||
end if
|
|
||||||
if ( BC_Y0 == 0 ) then
|
|
||||||
DomYmin = 0.0d+00
|
|
||||||
DomYmax = LS0
|
|
||||||
end if
|
|
||||||
if ( BC_Z0 == 0 ) then
|
|
||||||
DomZmin = 0.0d+00
|
|
||||||
DomZmax = HS0
|
|
||||||
end if
|
|
||||||
|
|
||||||
DomLX = DomXmax - DomXmin
|
|
||||||
DomLY = DomYmax - DomYmin
|
|
||||||
DomLZ = DomZmax - DomZmin
|
|
||||||
DomLXHalf = 0.5d+00 * DomLX
|
|
||||||
DomLYHalf = 0.5d+00 * DomLY
|
|
||||||
DomLZHalf = 0.5d+00 * DomLZ
|
|
||||||
|
|
||||||
DS0 = DS0 / ( K_MDDU / 1.0d+03 )
|
|
||||||
VS0 = LS0 * LS0 * HS0
|
|
||||||
MS0 = DS0 * VS0
|
|
||||||
end subroutine InitSample !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! A few auxiliary functions
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
subroutine GetTubeEnds ( X0, X1, i ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function calculates coordinates of two ends of nanotube i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, dimension(0:2), intent(out) :: X0, X1
|
|
||||||
integer*4, intent(in) :: i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8 :: LT2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
LT2 = 0.5d+00 * LT(i)
|
|
||||||
X0 = CT(i,0:2) - LT2 * DT(i,0:2)
|
|
||||||
X1 = CT(i,0:2) + LT2 * DT(i,0:2)
|
|
||||||
end subroutine GetTubeEnds !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
logical function IsTubeInside ( i ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function returns true if nanotube i lies inside the sample. Otherwise it returns false.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer*4, intent(in) :: i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer*4 :: n
|
|
||||||
real*8, dimension(0:2) :: X0, X1, Xmin, Xmax
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
IsTubeInside = .true.
|
|
||||||
if ( BC_X == 1 .and. BC_Y == 1 .and. BC_Z == 1 ) return
|
|
||||||
call GetTubeEnds ( X0, X1, i )
|
|
||||||
do n = 0, 2
|
|
||||||
Xmin(n) = min ( X0(n), X1(n) )
|
|
||||||
Xmax(n) = max ( X0(n), X1(n) )
|
|
||||||
end do
|
|
||||||
IsTubeInside = .false.
|
|
||||||
if ( BC_X == 0 .and. ( Xmin(0) < DomXmin .or. Xmax(0) > DomXmax ) ) return
|
|
||||||
if ( BC_Y == 0 .and. ( Xmin(1) < DomYmin .or. Xmax(1) > DomYmax ) ) return
|
|
||||||
if ( BC_Z == 0 .and. ( Xmin(2) < DomZmin .or. Xmax(2) > DomZmax ) ) return
|
|
||||||
IsTubeInside = .true.
|
|
||||||
end function IsTubeInside !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end module TMDGenData !*****************************************************************************
|
|
||||||
@ -1,45 +0,0 @@
|
|||||||
newton on
|
|
||||||
log cnt.log
|
|
||||||
echo both
|
|
||||||
units metal
|
|
||||||
lattice sc 1.0
|
|
||||||
boundary p p fs
|
|
||||||
neighbor 1.0 bin
|
|
||||||
neigh_modify every 5 delay 0 check yes
|
|
||||||
|
|
||||||
atom_style cnt
|
|
||||||
#cut, RT, STRMode, BendingMode, STRParams, YMType, TPMType, TPMSSTP.xrs, TPMA.xrs
|
|
||||||
pair_style cnt/cnt 45.0 6.785 1 0 3 0 0 ../../../potentials/TPMSSTP.xrs ../../../potentials/TPMA.xrs
|
|
||||||
read_data TMDSample.init
|
|
||||||
pair_coeff * *
|
|
||||||
|
|
||||||
velocity all create 600.0 2019
|
|
||||||
timestep 0.010
|
|
||||||
fix 1 all nve
|
|
||||||
#fix 1 all nvt temp 300.0 300.0 1.0
|
|
||||||
thermo_modify flush yes
|
|
||||||
thermo 1
|
|
||||||
reset_timestep 0
|
|
||||||
|
|
||||||
compute Es all cnt/Es
|
|
||||||
compute Eb all cnt/Eb
|
|
||||||
compute Et all cnt/Et
|
|
||||||
compute Ek all ke/atom
|
|
||||||
compute Es_tot all cnt/Es_tot
|
|
||||||
compute Eb_tot all cnt/Eb_tot
|
|
||||||
compute Et_tot all cnt/Et_tot
|
|
||||||
compute Ep_tot all pe
|
|
||||||
compute Ek_tot all ke
|
|
||||||
variable time_ equal time
|
|
||||||
variable Ep_ equal c_Ep_tot
|
|
||||||
variable Ek_ equal c_Ek_tot
|
|
||||||
variable Etot_ equal v_Ek_+v_Ep_
|
|
||||||
variable Es_ equal c_Es_tot
|
|
||||||
variable Eb_ equal c_Eb_tot
|
|
||||||
variable Et_ equal c_Et_tot
|
|
||||||
|
|
||||||
dump out_dump all custom 50 config_E.dump id type x y z c_Es c_Eb c_Et c_Ek ix iy iz
|
|
||||||
fix out_info all print 10 "${time_} ${Etot_} ${Ek_} ${Ep_} ${Es_} ${Eb_} ${Et_}" file "E.txt" screen no
|
|
||||||
|
|
||||||
run 50
|
|
||||||
write_data system_E.data
|
|
||||||
@ -1,144 +0,0 @@
|
|||||||
module TPMGeom !************************************************************************************
|
|
||||||
!
|
|
||||||
! Geometry functions for TPM force field
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, 2020, Version 13.00
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
|
|
||||||
use TPMLib
|
|
||||||
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Constants
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
integer*4, parameter :: MD_LINES_NONPAR = 0
|
|
||||||
integer*4, parameter :: MD_LINES_PAR = 1
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Global variables
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
! Coordinates of the whole domain
|
|
||||||
real*8 :: DomXmin, DomXmax, DomYmin, DomYmax, DomZmin, DomZmax
|
|
||||||
real*8 :: DomLX, DomLY, DomLZ
|
|
||||||
real*8 :: DomLXhalf, DomLYhalf, DomLZhalf
|
|
||||||
|
|
||||||
! Boundary conditions
|
|
||||||
integer*4 :: BC_X = 0
|
|
||||||
integer*4 :: BC_Y = 0
|
|
||||||
integer*4 :: BC_Z = 0
|
|
||||||
|
|
||||||
! Skin parameter in NBL and related algorithms
|
|
||||||
real*8 :: Rskin = 1.0d+00
|
|
||||||
|
|
||||||
contains !******************************************************************************************
|
|
||||||
|
|
||||||
subroutine ApplyPeriodicBC ( R ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This subroutine changes coortinates of the point accorning to periodic boundary conditions
|
|
||||||
! it order to makesure that the point is inside the computational cell
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, dimension(0:2), intent(inout) :: R
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
! These commented lines implemment the more general, but less efficient algorithm
|
|
||||||
!if ( BC_X == 1 ) R(0) = R(0) - DomLX * roundint ( R(0) / DomLX )
|
|
||||||
!if ( BC_Y == 1 ) R(1) = R(1) - DomLY * roundint ( R(1) / DomLY )
|
|
||||||
!if ( BC_Z == 1 ) R(2) = R(2) - DomLZ * roundint ( R(2) / DomLZ )
|
|
||||||
if ( BC_X == 1 ) then
|
|
||||||
if ( R(0) .GT. DomLXHalf ) then
|
|
||||||
R(0) = R(0) - DomLX
|
|
||||||
else if ( R(0) .LT. - DomLXHalf ) then
|
|
||||||
R(0) = R(0) + DomLX
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
if ( BC_Y == 1 ) then
|
|
||||||
if ( R(1) .GT. DomLYHalf ) then
|
|
||||||
R(1) = R(1) - DomLY
|
|
||||||
else if ( R(1) .LT. - DomLYHalf ) then
|
|
||||||
R(1) = R(1) + DomLY
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
if ( BC_Z == 1 ) then
|
|
||||||
if ( R(2) .GT. DomLZHalf ) then
|
|
||||||
R(2) = R(2) - DomLZ
|
|
||||||
else if ( R(2) .LT. - DomLZHalf ) then
|
|
||||||
R(2) = R(2) + DomLZ
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
end subroutine ApplyPeriodicBC !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine LinePoint ( Displacement, Q, R1, L1, R0 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function calculates the point Q of projection of point R0 on line (R1,L1)
|
|
||||||
! Q = R1 + Disaplacement * L1
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, intent(inout) :: Displacement
|
|
||||||
real*8, dimension(0:2), intent(inout) :: Q
|
|
||||||
real*8, dimension(0:2), intent(in) :: R1, L1, R0
|
|
||||||
!--------------------------------------------------------------------------------------------
|
|
||||||
Q = R0 - R1
|
|
||||||
! Here we take into account periodic boundaries
|
|
||||||
call ApplyPeriodicBC ( Q )
|
|
||||||
Displacement = S_V3xV3 ( Q, L1 )
|
|
||||||
Q = R1 + Displacement * L1
|
|
||||||
end subroutine LinePoint !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
integer*4 function LineLine ( H, cosA, D1, D2, L12, R1, L1, R2, L2, Prec ) !!!!!!!!!!!!!!!!!
|
|
||||||
! This function determines the neares distance H between two lines (R1,L1) and (R2,L2)
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
! Input values:
|
|
||||||
! R1, L1, point and direction of line 1
|
|
||||||
! R2, L2, point and direction of line 2
|
|
||||||
! Prec, precision for the case L1 * L2 = 0 (parallel lines)
|
|
||||||
! Return values:
|
|
||||||
! H, minimal distance between lines
|
|
||||||
! cosA, cosine of angle between lines
|
|
||||||
! D1, D2, displacemets
|
|
||||||
! L12, unit vector directed along the closes distance
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, intent(inout) :: H, cosA, D1, D2
|
|
||||||
real*8, dimension(0:2), intent(out) :: L12
|
|
||||||
real*8, dimension(0:2), intent(in) :: R1, L1, R2, L2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, intent(in) :: Prec
|
|
||||||
real*8, dimension(0:2) :: Q1, Q2, R
|
|
||||||
real*8 :: C, DD1, DD2, C1, C2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
cosA = S_V3xV3 ( L1, L2 )
|
|
||||||
C = 1.0 - sqr ( cosA )
|
|
||||||
if ( C < Prec ) then ! Lines are parallel to each other
|
|
||||||
LineLine = MD_LINES_PAR
|
|
||||||
return
|
|
||||||
end if
|
|
||||||
LineLine = MD_LINES_NONPAR
|
|
||||||
R = R2 - R1
|
|
||||||
! Here we take into account periodic boundaries
|
|
||||||
call ApplyPeriodicBC ( R )
|
|
||||||
DD1 = S_V3xV3 ( R, L1 )
|
|
||||||
DD2 = S_V3xV3 ( R, L2 )
|
|
||||||
D1 = ( cosA * DD2 - DD1 ) / C
|
|
||||||
D2 = ( DD2 - cosA * DD1 ) / C
|
|
||||||
Q1 = R1 - D1 * L1
|
|
||||||
Q2 = R2 - D2 * L2
|
|
||||||
L12 = Q2 - Q1
|
|
||||||
! Here we take into account periodic boundaries
|
|
||||||
call ApplyPeriodicBC ( L12 )
|
|
||||||
H = S_V3norm3 ( L12 )
|
|
||||||
if ( H < Prec ) then ! Lines intersect each other
|
|
||||||
C1 = signum ( D1 )
|
|
||||||
C2 = signum ( D1 ) * signum ( cosA )
|
|
||||||
Q1 = C1 * L1
|
|
||||||
Q2 = C2 * L2
|
|
||||||
call V3_V3xxV3 ( L12, Q1, Q2 )
|
|
||||||
call V3_ort ( L12 )
|
|
||||||
else ! No intersection
|
|
||||||
L12 = L12 / H
|
|
||||||
end if
|
|
||||||
end function LineLine !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end module TPMGeom !********************************************************************************
|
|
||||||
@ -1,205 +0,0 @@
|
|||||||
module TPMLib !*************************************************************************************
|
|
||||||
!
|
|
||||||
! Common constants, types, and functions for TPM force field
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, 2020, Version 13.00
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Mathematical constants
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
real*8, parameter :: M_PI_2 = 1.57079632679489661923
|
|
||||||
real*8, parameter :: M_PI = 3.14159265358979323846
|
|
||||||
real*8, parameter :: M_3PI_2 = 4.71238898038468985769
|
|
||||||
real*8, parameter :: M_2PI = 6.28318530717958647692
|
|
||||||
real*8, parameter :: M_PI_180 = 0.017453292519943295769
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Physical unit constants
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
real*8, parameter :: K_AMU = 1.66056E-27 ! a.m.u. (atomic mass unit, Dalton)
|
|
||||||
real*8, parameter :: K_EV = 1.60217646e-19 ! eV (electron-volt)
|
|
||||||
|
|
||||||
real*8, parameter :: K_MDLU = 1.0E-10 ! MD length unit (m)
|
|
||||||
real*8, parameter :: K_MDEU = K_EV ! MD energy unit (J)
|
|
||||||
real*8, parameter :: K_MDMU = K_AMU ! MD mass unit (kg)
|
|
||||||
real*8, parameter :: K_MDFU = K_MDEU / K_MDLU ! MD force unit (N)
|
|
||||||
real*8, parameter :: K_MDCU = K_MDEU / K_MDMU ! MD specific heat unit (J/(kg*K))
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Global variables
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
integer*4 :: StdUID = 31
|
|
||||||
|
|
||||||
contains !******************************************************************************************
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Simple mathematical functions
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
real*8 function rad ( X ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, intent(in) :: X
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
rad = X * M_PI_180
|
|
||||||
end function rad !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
real*8 function sqr ( X ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, intent(in) :: X
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
sqr = X * X
|
|
||||||
end function sqr !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
integer*4 function signum ( X ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, intent(in) :: X
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
if ( X > 0 ) then
|
|
||||||
signum = 1
|
|
||||||
else if ( X < 0 ) then
|
|
||||||
signum = -1
|
|
||||||
else
|
|
||||||
signum = 0
|
|
||||||
end if
|
|
||||||
end function signum !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Vector & matrix functions
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
real*8 function S_V3xx ( V ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, dimension(0:2), intent(in) :: V
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
S_V3xx = V(0) * V(0) + V(1) * V(1) + V(2) * V(2)
|
|
||||||
end function S_V3xx !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
real*8 function S_V3xV3 ( V1, V2 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, dimension(0:2), intent(in) :: V1, V2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
S_V3xV3 = V1(0) * V2(0) + V1(1) * V2(1) + V1(2) * V2(2)
|
|
||||||
end function S_V3xV3 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
real*8 function S_V3norm3 ( V ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, dimension(0:2), intent(in) :: V
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
S_V3norm3 = dsqrt ( V(0) * V(0) + V(1) * V(1) + V(2) * V(2) )
|
|
||||||
end function S_V3norm3 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine V3_ort ( V ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! Vector production
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, dimension(0:2), intent(inout) :: V
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8 :: Vabs
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Vabs = S_V3norm3 ( V )
|
|
||||||
V(0) = V(0) / Vabs
|
|
||||||
V(1) = V(1) / Vabs
|
|
||||||
V(2) = V(2) / Vabs
|
|
||||||
end subroutine V3_ort !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine V3_V3xxV3 ( V, V1, V2 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! Vector production
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, dimension(0:2), intent(out) :: V
|
|
||||||
real*8, dimension(0:2), intent(in) :: V1, V2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
V(0) = V1(1) * V2(2) - V1(2) * V2(1)
|
|
||||||
V(1) = V1(2) * V2(0) - V1(0) * V2(2)
|
|
||||||
V(2) = V1(0) * V2(1) - V1(1) * V2(0)
|
|
||||||
end subroutine V3_V3xxV3 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Handling of spherical and Euler angles
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
subroutine RotationMatrix3 ( M, Psi, Tet, Phi ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! Ksi, Tet and Phi are Euler angles
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, dimension(0:2,0:2), intent(out) :: M
|
|
||||||
real*8, intent(in) :: Psi, Tet, Phi
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8 :: cK, sK, cT, sT, cP, sP
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
cK = dcos ( Psi )
|
|
||||||
sK = dsin ( Psi )
|
|
||||||
cT = dcos ( Tet )
|
|
||||||
sT = dsin ( Tet )
|
|
||||||
cP = dcos ( Phi )
|
|
||||||
sP = dsin ( Phi )
|
|
||||||
M(0,0) = cP * cK - sK * sP * cT
|
|
||||||
M(0,1) = cP * sK + sP * cT * cK
|
|
||||||
M(0,2) = sP * sT
|
|
||||||
M(1,0) = - sP * cK - cP * cT * sK
|
|
||||||
M(1,1) = - sP * sK + cP * cT * cK
|
|
||||||
M(1,2) = cP * sT
|
|
||||||
M(2,0) = sT * sK
|
|
||||||
M(2,1) = - sT * cK
|
|
||||||
M(2,2) = cT
|
|
||||||
end subroutine RotationMatrix3 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine EulerAngles ( Psi, Tet, L ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, intent(out) :: Tet, Psi
|
|
||||||
real*8, dimension(0:2), intent(in) :: L
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Tet = acos ( L(2) )
|
|
||||||
Psi = atan2 ( L(1), L(0) )
|
|
||||||
if ( Psi > M_3PI_2 ) then
|
|
||||||
Psi = Psi - M_3PI_2
|
|
||||||
else
|
|
||||||
Psi = Psi + M_PI_2
|
|
||||||
end if
|
|
||||||
end subroutine EulerAngles !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! File inout and output
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
integer*4 function OpenFile ( Name, Params, Path ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
character*(*), intent(in) :: Name, Params, Path
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer*4 :: Fuid
|
|
||||||
character*512 :: FullName, Msg, Name1, Action1, Status1, Form1, Position1
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
OpenFile = StdUID + 1
|
|
||||||
if ( Params(1:1) == 'r' ) then
|
|
||||||
Action1 = 'read'
|
|
||||||
Status1 = 'old'
|
|
||||||
Position1 = 'rewind'
|
|
||||||
else if ( Params(1:1) == 'w' ) then
|
|
||||||
Action1 = 'write'
|
|
||||||
Status1 = 'replace'
|
|
||||||
Position1 = 'rewind'
|
|
||||||
else if ( Params(1:1) == 'a' ) then
|
|
||||||
Action1 = 'write'
|
|
||||||
Status1 = 'old'
|
|
||||||
Position1 = 'append'
|
|
||||||
endif
|
|
||||||
if ( Params(2:2) == 'b' ) then
|
|
||||||
Form1 = 'binary'
|
|
||||||
else
|
|
||||||
Form1 = 'formatted'
|
|
||||||
endif
|
|
||||||
open ( unit = OpenFile, file = Name, form = Form1, action = Action1, status = Status1, position = Position1 )
|
|
||||||
StdUID = StdUID + 1
|
|
||||||
return
|
|
||||||
end function OpenFile !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine CloseFile ( Fuid ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
integer*4, intent(inout) :: Fuid
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
if ( Fuid < 0 ) return
|
|
||||||
close ( unit = Fuid )
|
|
||||||
Fuid = -1
|
|
||||||
end subroutine CloseFile !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end module TPMLib !*********************************************************************************
|
|
||||||
|
|
||||||
@ -1,98 +0,0 @@
|
|||||||
module LinFun2 !************************************************************************************
|
|
||||||
!
|
|
||||||
! Bi-linear functions and their derivatives.
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 09.01, 2017
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
contains !******************************************************************************************
|
|
||||||
|
|
||||||
real*8 function CalcLinFun1_0 ( i, X, N, P, F ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
integer*4, intent(in) :: i, N
|
|
||||||
real*8, intent(in) :: X
|
|
||||||
real*8, dimension(0:N-1), intent(in) :: P
|
|
||||||
real*8, dimension(0:N-1), intent(inout) :: F
|
|
||||||
integer*4 :: i1
|
|
||||||
real*8 :: A, A0
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
i1 = i - 1
|
|
||||||
A0 = ( P(i) - X ) / ( P(i) - P(i1) )
|
|
||||||
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*8, intent(out) :: S, Sx1
|
|
||||||
integer*4, intent(in) :: i, N
|
|
||||||
real*8, intent(in) :: X
|
|
||||||
real*8, dimension(0:N-1), intent(in) :: P
|
|
||||||
real*8, dimension(0:N-1), intent(inout) :: F, Fx
|
|
||||||
integer*4 :: i1
|
|
||||||
real*8 :: A, A0
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
i1 = i - 1
|
|
||||||
A0 = ( P(i) - X ) / ( P(i) - P(i1) )
|
|
||||||
A = 1.0d+00 - A0
|
|
||||||
S = A0 * F(i1) + A * F(i)
|
|
||||||
Sx1 = A0 * Fx(i1) + A * Fx(i)
|
|
||||||
end subroutine CalcLinFun1_1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
real*8 function CalcLinFun2_0 ( i, j, X, Y, N1, N2, P1, P2, F ) !!
|
|
||||||
integer*4, intent(in) :: i, j, N1, N2
|
|
||||||
real*8, intent(in) :: X, Y
|
|
||||||
real*8, dimension(0:N1-1), intent(in) :: P1
|
|
||||||
real*8, dimension(0:N2-1), intent(in) :: P2
|
|
||||||
real*8, dimension(0:N1-1,0:N2-1), intent(inout) :: F
|
|
||||||
integer*4 :: i1, j1
|
|
||||||
real*8 :: A, A0, B, B0, G, G0
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
i1 = i - 1
|
|
||||||
j1 = j - 1
|
|
||||||
A0 = ( P1(i) - X ) / ( P1(i) - P1(i1) )
|
|
||||||
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)
|
|
||||||
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*8, intent(out) :: S, Sx1, Sy1
|
|
||||||
integer*4, intent(in) :: i, j, N1, N2
|
|
||||||
real*8, intent(in) :: X, Y
|
|
||||||
real*8, dimension(0:N1-1), intent(in) :: P1
|
|
||||||
real*8, dimension(0:N2-1), intent(in) :: P2
|
|
||||||
real*8, dimension(0:N1-1,0:N2-1), intent(inout) :: F, Fx, Fy
|
|
||||||
integer*4 :: i1, j1
|
|
||||||
real*8 :: A, A0, B, B0, G, G0
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
i1 = i - 1
|
|
||||||
j1 = j - 1
|
|
||||||
A0 = ( P1(i) - X ) / ( P1(i) - P1(i1) )
|
|
||||||
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 !********************************************************************************
|
|
||||||
@ -1,35 +0,0 @@
|
|||||||
#---------------------------------------------------------------------------------------------------
|
|
||||||
#
|
|
||||||
# This is Makefile for builing the executable TMDPotGen
|
|
||||||
#
|
|
||||||
# Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, 2020, Version 13.00
|
|
||||||
#
|
|
||||||
#---------------------------------------------------------------------------------------------------
|
|
||||||
EXEPATH = .
|
|
||||||
|
|
||||||
F90 = ifort
|
|
||||||
F90FLAGS = -Ofast -mcmodel=medium
|
|
||||||
#F90 = pgf90
|
|
||||||
#F90FLAGS = -fast -mcmodel=medium
|
|
||||||
LDFLAGS =
|
|
||||||
|
|
||||||
OBJS = TPMLib.o LinFun2.o Spline1.o Spline2.o TPMGeom.o TubePotBase.o TubePotTrue.o TubePotMono.o TMDPotGen.o
|
|
||||||
EXE = $(EXEPATH)/TMDPotGen
|
|
||||||
|
|
||||||
# compile and load
|
|
||||||
default:
|
|
||||||
@echo " "
|
|
||||||
@echo "Compiling Code of Program TMDPotGen"
|
|
||||||
@echo "FORTRAN 90"
|
|
||||||
$(MAKE) $(EXE)
|
|
||||||
|
|
||||||
$(EXE): $(OBJS)
|
|
||||||
$(F90) $(F90FLAGS) $(LDFLAGS) -o $(EXE) $(OBJS)
|
|
||||||
|
|
||||||
.SUFFIXES: .f90 .o
|
|
||||||
.f90.o:
|
|
||||||
$(F90) $(F90FLAGS) -c $*.f90
|
|
||||||
|
|
||||||
clean:
|
|
||||||
rm -f *.o
|
|
||||||
|
|
||||||
@ -1,177 +0,0 @@
|
|||||||
module Spline1 !************************************************************************************
|
|
||||||
!
|
|
||||||
! One-dimensional cubic spline function.
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 09.01, 2017
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
contains !******************************************************************************************
|
|
||||||
|
|
||||||
real*8 function ValueSpline1_0 ( X, Xi, Xi_1, Yi, Yi_1, Mi, Mi_1, Hi_1 ) !!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, intent(in) :: X, Xi, Xi_1, Yi, Yi_1, Mi, Mi_1, Hi_1
|
|
||||||
real*8 :: H26, HL, HR
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
H26 = Hi_1 * Hi_1 / 6.0
|
|
||||||
Hl = X - Xi_1
|
|
||||||
Hr = Xi - X
|
|
||||||
ValueSpline1_0 = ( ( Mi_1 * Hr * Hr * Hr + Mi * Hl * Hl * Hl ) / 6.0 + ( Yi_1 - Mi_1 * H26 ) * Hr &
|
|
||||||
+ ( Yi - Mi * H26 ) * Hl ) / Hi_1
|
|
||||||
end function ValueSpline1_0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine ValueSpline1_1 ( S, S1, X, Xi, Xi_1, Yi, Yi_1, Mi, Mi_1, Hi_1 ) !!!!!!!!!!!!!!!!!
|
|
||||||
real*8, intent(out) :: S, S1
|
|
||||||
real*8, intent(in) :: X, Xi, Xi_1, Yi, Yi_1, Mi, Mi_1, Hi_1
|
|
||||||
real*8 :: H6, H26, HL, HR, HL2, HR2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
H6 = Hi_1 / 6.0d+00
|
|
||||||
H26 = Hi_1 * H6
|
|
||||||
HL = X - Xi_1
|
|
||||||
HR = Xi - X
|
|
||||||
HL2 = HL * HL
|
|
||||||
HR2 = HR * HR
|
|
||||||
S = ( ( Mi_1 * HR2 * Hr + Mi * HL2 * Hl ) / 6.0 + ( Yi_1 - Mi_1 * H26 ) * HR + ( Yi - Mi * H26 ) * HL ) / Hi_1
|
|
||||||
S1 = ( ( Mi * HL2 - Mi_1 * HR2 ) / 2.0d+00 + Yi - Yi_1 ) / Hi_1 - H6 * ( Mi - Mi_1 )
|
|
||||||
end subroutine ValueSpline1_1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine sprogonka3 ( N, K0, K1, K2, F, X ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
integer*4, intent(in) :: N
|
|
||||||
real*8, dimension(0:N-1), intent(in) :: K0, K1, K2
|
|
||||||
real*8, dimension(0:N-1), intent(inout) :: F, X
|
|
||||||
real*8 :: D
|
|
||||||
integer*4 :: i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
X(0) = F(0) / K1(0)
|
|
||||||
F(0) = - K2(0) / K1(0)
|
|
||||||
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
|
|
||||||
end do
|
|
||||||
do i = N - 2, 0, -1
|
|
||||||
X(i) = X(i) + F(i) * X(i+1)
|
|
||||||
end do
|
|
||||||
end subroutine sprogonka3 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine CreateSpline1 ( CL, CR, N, P, F, M, D, K0, K1, K2 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
integer*4, intent(in) :: CL, CR, N
|
|
||||||
real*8, dimension (0:N-1), intent(in) :: P, F
|
|
||||||
real*8, dimension (0:N-1), intent(inout):: M, D, K0, K1, K2
|
|
||||||
integer*4 :: i
|
|
||||||
real*8 :: Z
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
do i = 1, N - 1
|
|
||||||
K0(i) = P(i) - P(i-1)
|
|
||||||
K1(i) = ( F(i) - F(i-1) ) / K0(i)
|
|
||||||
end do
|
|
||||||
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)
|
|
||||||
case (2)
|
|
||||||
K1(0) = 1.0d+00
|
|
||||||
K2(0) = 0.0d+00
|
|
||||||
D(0) = M(0)
|
|
||||||
case (3)
|
|
||||||
K1(0) = 1.0d+00
|
|
||||||
K2(0) = 0.0d+00
|
|
||||||
D(0) = 0.0d+00
|
|
||||||
end select
|
|
||||||
Z = K1(N-1)
|
|
||||||
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 )
|
|
||||||
case (1)
|
|
||||||
D(N-1) = 2.0d+00 * ( M(N-1) - Z ) / K0(N-1)
|
|
||||||
K1(N-1) = 2.0d+00 / 3.0d+00
|
|
||||||
K0(N-1) = 1.0d+00 / 3.0d+00
|
|
||||||
case (2)
|
|
||||||
K1(N-1) = 1.0d+00
|
|
||||||
K0(N-1) = 0.0d+00
|
|
||||||
D(N-1) = M(N-1)
|
|
||||||
case (3)
|
|
||||||
K1(N-1) = 1.0d+00
|
|
||||||
K0(N-1) = 0.0d+00
|
|
||||||
D(N-1) = 0.0d+00
|
|
||||||
end select
|
|
||||||
call sprogonka3 ( N, K0, K1, K2, D, M )
|
|
||||||
end subroutine CreateSpline1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
real*8 function CalcSpline1_0 ( i, X, N, P, F, M ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
integer*4, intent(in) :: i, N
|
|
||||||
real*8, intent(in) :: X
|
|
||||||
real*8, dimension(0:N-1), intent(in) :: P, F, M
|
|
||||||
integer*4 :: j
|
|
||||||
real*8 :: HL, HR, H, H6, H26, HR2, HL2, HRH, HLH
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
j = i - 1
|
|
||||||
HL = X - P(j)
|
|
||||||
HR = P(i) - X
|
|
||||||
H = P(i) - P(j)
|
|
||||||
H6 = H / 6.0d+00
|
|
||||||
H26 = H * H6
|
|
||||||
HL2 = HL * HL
|
|
||||||
HR2 = HR * HR
|
|
||||||
HLH = HL / H
|
|
||||||
HRH = HR / H
|
|
||||||
CalcSpline1_0 = ( M(j) * HR2 * HRH + M(i) * HL2 * HLH ) / 6.0d+00 + ( F(j) - M(j) * H26 ) * HRH &
|
|
||||||
+ ( F(i) - M(i) * H26 ) * HLH
|
|
||||||
end function CalcSpline1_0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine CalcSpline1_1 ( S, S1, i, X, N, P, F, M ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, intent(out) :: S, S1
|
|
||||||
integer*4, intent(in) :: i, N
|
|
||||||
real*8, intent(in) :: X
|
|
||||||
real*8, dimension(0:N-1), intent(in) :: P, F, M
|
|
||||||
integer*4 :: j
|
|
||||||
real*8 :: HL, HR, H, H6, H26, HR2, HL2, HRH, HLH
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
j = i - 1
|
|
||||||
HL = X - P(j)
|
|
||||||
HR = P(i) - X
|
|
||||||
H = P(i) - P(j)
|
|
||||||
H6 = H / 6.0d+00
|
|
||||||
H26 = H * H6
|
|
||||||
HL2 = HL * HL
|
|
||||||
HR2 = HR * HR
|
|
||||||
HLH = HL / H
|
|
||||||
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) )
|
|
||||||
end subroutine CalcSpline1_1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine CalcSpline1_2 ( S, S1, S2, i, X, N, P, F, M ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, intent(out) :: S, S1, S2
|
|
||||||
integer*4, intent(in) :: i, N
|
|
||||||
real*8, intent(in) :: X
|
|
||||||
real*8, dimension(0:N-1), intent(in) :: P, F, M
|
|
||||||
integer*4 :: j
|
|
||||||
real*8 :: HL, HR, H, H6, H26, HR2, HL2, HRH, HLH
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
j = i - 1
|
|
||||||
HL = X - P(j)
|
|
||||||
HR = P(i) - X
|
|
||||||
H = P(i) - P(j)
|
|
||||||
H6 = H / 6.0d+00
|
|
||||||
H26 = H * H6
|
|
||||||
HL2 = HL * HL
|
|
||||||
HR2 = HR * HR
|
|
||||||
HLH = HL / H
|
|
||||||
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
|
|
||||||
end subroutine CalcSpline1_2 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end module Spline1 !********************************************************************************
|
|
||||||
|
|
||||||
@ -1,171 +0,0 @@
|
|||||||
module Spline2 !************************************************************************************
|
|
||||||
!
|
|
||||||
! Two-dimensional cubic spline function.
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 09.01, 2017
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
|
|
||||||
use Spline1
|
|
||||||
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
contains !******************************************************************************************
|
|
||||||
|
|
||||||
subroutine CreateSpline2 ( CL, CD, CR, CU, N1, N2, N, P1, P2, F, Fxx, Fyy, Fxxyy, FF, MM, DD, K0, K1, K2 )
|
|
||||||
integer*4, intent(in) :: CL, CD, CR, CU, N1, N2, N
|
|
||||||
real*8, dimension(0:N1-1), intent(in) :: P1
|
|
||||||
real*8, dimension(0:N2-1), intent(in) :: P2
|
|
||||||
real*8, dimension(0:N1-1,0:N2-1), intent(inout) :: F, Fxx, Fyy, Fxxyy
|
|
||||||
real*8, dimension(0:N-1), intent(inout) :: FF, MM, DD, K0, K1, K2
|
|
||||||
integer*4 :: II
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
do II = 0, N2 - 1
|
|
||||||
FF(0:N1-1) = F(0:N1-1,II)
|
|
||||||
MM(0) = Fxx(0,II)
|
|
||||||
MM(N1-1) = Fxx(N1-1,II)
|
|
||||||
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 = 0, N1 - 1
|
|
||||||
MM(0) = Fyy(II,0)
|
|
||||||
MM(N-1) = Fyy(II,N2-1)
|
|
||||||
FF(0:N2-1) = F(II,0:N2-1)
|
|
||||||
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:N1-1) = Fyy(0:N1-1,N2-1 )
|
|
||||||
call CreateSpline1 ( 3, 3, N1, P1, FF, MM, DD, K0, K1, k2 )
|
|
||||||
Fxxyy(0:N1-1,N2-1) = MM(0:N1-1)
|
|
||||||
do II = 1, N1 - 2
|
|
||||||
MM(0) = Fxxyy(II,0)
|
|
||||||
MM(N-1) = Fxxyy(II,N2-1)
|
|
||||||
FF(0:N2-1) = Fxx(II,0:N2-1)
|
|
||||||
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 CreateSpline2 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine CreateSpline2Ext ( CL, CD, CR, CU, N1, N1A, N2, N2A, N, P1, P2, F, Fxx, Fyy, Fxxyy, FF, MM, DD, K0, K1, K2 )
|
|
||||||
integer*4, intent(in) :: CL, CD, CR, CU, N1, N1A, N2, N2A, N
|
|
||||||
real*8, dimension(0:N1-1), intent(in) :: P1
|
|
||||||
real*8, dimension(0:N2-1), intent(in) :: P2
|
|
||||||
real*8, dimension(0:N1-1,0:N2-1), intent(inout) :: F, Fxx, Fyy, Fxxyy
|
|
||||||
real*8, dimension(0:N-1), intent(inout) :: FF, MM, DD, K0, K1, K2
|
|
||||||
integer*4 :: II
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
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)
|
|
||||||
MM(N1-1) = Fxx(N1-1,II)
|
|
||||||
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)
|
|
||||||
MM(N1-N1A-1) = Fxx(N1-1,II)
|
|
||||||
call CreateSpline1 ( CL, CR, N1 - N1A, P1, FF, MM, DD, K0, K1, K2 )
|
|
||||||
Fxx(N1A:N1-1,II) = MM(0:N1-N1A-1)
|
|
||||||
end do
|
|
||||||
|
|
||||||
do II = 0, N1A - 1
|
|
||||||
MM(0) = Fyy(II,0)
|
|
||||||
MM(N2A) = Fyy(II,N2A)
|
|
||||||
FF(0:N2A) = F(II,0:N2A)
|
|
||||||
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)
|
|
||||||
FF(0:N2-1) = F(II,0:N2-1)
|
|
||||||
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)
|
|
||||||
FF(0:N2A) = Fxx(II,0:N2A)
|
|
||||||
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)
|
|
||||||
FF(0:N2-1) = Fxx(II,0:N2-1)
|
|
||||||
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*8 function CalcSpline2_0 ( i, j, X, Y, N1, N2, P1, P2, F, Fxx, Fyy, Fxxyy ) !!!!!!!!!!!
|
|
||||||
integer*4, intent(in) :: i, j, N1, N2
|
|
||||||
real*8, intent(in) :: X, Y
|
|
||||||
real*8, dimension(0:N1-1), intent(in) :: P1
|
|
||||||
real*8, dimension(0:N2-1), intent(in) :: P2
|
|
||||||
real*8, dimension(0:N1-1,0:N2-1), intent(inout) :: F, Fxx, Fyy, Fxxyy
|
|
||||||
integer*4 :: i1, j1
|
|
||||||
real*8 :: T, Gy_0, Gy_1, Gxxy_0, Gxxy_1
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
i1 = i - 1
|
|
||||||
j1 = j - 1
|
|
||||||
T = P2(j) - P2(j1)
|
|
||||||
Gy_0 = ValueSpline1_0 ( Y, P2(j), P2(j1), F(i,j), F(i,j1), Fyy(i,j), Fyy(i,j1), T )
|
|
||||||
Gy_1 = ValueSpline1_0 ( Y, P2(j), P2(j1), F(i1,j), F(i1,j1), Fyy(i1,j), Fyy(i1,j1), T )
|
|
||||||
Gxxy_0 = ValueSpline1_0 ( Y, P2(j), P2(j1), Fxx(i,j), Fxx(i,j1), Fxxyy(i,j), Fxxyy(i,j1), T )
|
|
||||||
Gxxy_1 = ValueSpline1_0 ( Y, P2(j), P2(j1), Fxx(i1,j), Fxx(i1,j1), Fxxyy(i1,j), Fxxyy(i1,j1), T )
|
|
||||||
CalcSpline2_0 = ValueSpline1_0 ( X, P1(i), P1(i1), Gy_0, Gy_1,Gxxy_0, Gxxy_1, P1(i) - P1(i1) )
|
|
||||||
end function CalcSpline2_0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine CalcSpline2_1 ( S, Sx1, Sy1, i, j, X, Y, N1, N2, P1, P2, F, Fxx, Fyy, Fxxyy ) !!!
|
|
||||||
real*8, intent(out) :: S, Sx1, Sy1
|
|
||||||
integer*4, intent(in) :: i, j, N1, N2
|
|
||||||
real*8, intent(in) :: X, Y
|
|
||||||
real*8, dimension(0:N1-1), intent(in) :: P1
|
|
||||||
real*8, dimension(0:N2-1), intent(in) :: P2
|
|
||||||
real*8, dimension(0:N1-1,0:N2-1), intent(inout) :: F, Fxx, Fyy, Fxxyy
|
|
||||||
integer*4 :: i1, j1
|
|
||||||
real*8 :: T, Gy_0, Gy_1, Gxxy_0, Gxxy_1
|
|
||||||
real*8 :: Gyy_0, Gyy_1, Gxxyy_0, Gxxyy_1
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
i1 = i - 1
|
|
||||||
j1 = j - 1
|
|
||||||
T = P2(j) - P2(j1)
|
|
||||||
call ValueSpline1_1 ( Gy_0, Gyy_0, Y, P2(j), P2(j1), F(i,j), F(i,j1), Fyy(i,j), Fyy(i,j1), T )
|
|
||||||
call ValueSpline1_1 ( Gy_1, Gyy_1, Y, P2(j), P2(j1), F(i1,j), F(i1,j1), Fyy(i1,j), Fyy(i1,j1), T )
|
|
||||||
call ValueSpline1_1 ( Gxxy_0, Gxxyy_0, Y, P2(j), P2(j1), Fxx(i,j), Fxx(i,j1), Fxxyy(i,j), Fxxyy(i,j1), T )
|
|
||||||
call ValueSpline1_1 ( Gxxy_1, Gxxyy_1, Y, P2(j), P2(j1), Fxx(i1,j), Fxx(i1,j1), Fxxyy(i1,j), Fxxyy(i1,j1), T )
|
|
||||||
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 !********************************************************************************
|
|
||||||
@ -1,62 +0,0 @@
|
|||||||
program TMDPotGen !*********************************************************************************
|
|
||||||
!
|
|
||||||
! Stand-alone generator of files containing tubular potential data for single-walled CNTs.
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 13.00, 2020
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
|
|
||||||
use TubePotMono
|
|
||||||
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Global variables
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
integer*4 :: ChiIndM = 10 ! Chirality index m of nanotubes
|
|
||||||
integer*4 :: ChiIndN = 10 ! Chirality index n of nanotubes
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Body
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
TPMStartMode = 0
|
|
||||||
|
|
||||||
! Reading and printing of governing parameters
|
|
||||||
call LoadGoverningParameters ()
|
|
||||||
call PrintGoverningParameters ()
|
|
||||||
|
|
||||||
call TPBInit ()
|
|
||||||
call TPMInit ( ChiIndM, ChiIndN )
|
|
||||||
|
|
||||||
contains !------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
subroutine LoadGoverningParameters () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function reads governing parameters from xdt file
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer*4 :: Fuid, i
|
|
||||||
character*512 :: Msg
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Fuid = OpenFile ( 'TMDPotGen.xdt', 'rt', '' )
|
|
||||||
read ( unit = Fuid, fmt = '(i22)' ) ChiIndM
|
|
||||||
read ( unit = Fuid, fmt = '(i22)' ) ChiIndN
|
|
||||||
call CloseFile ( Fuid )
|
|
||||||
end subroutine LoadGoverningParameters !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine PrintGoverningParameters () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function prints governing parameters to xlg file
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer*4 :: Fuid, i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Fuid = OpenFile ( 'TMDPotGen.xlg', 'wt', '' )
|
|
||||||
write ( unit = Fuid, fmt = '(i22,a)' ) ChiIndM, ' : ChiIndM'
|
|
||||||
write ( unit = Fuid, fmt = '(i22,a)' ) ChiIndN, ' : ChiIndN'
|
|
||||||
call CloseFile ( Fuid )
|
|
||||||
end subroutine PrintGoverningParameters !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end program TMDPotGen !*****************************************************************************
|
|
||||||
@ -1,2 +0,0 @@
|
|||||||
10 : ChiIndM
|
|
||||||
10 : ChiIndN
|
|
||||||
@ -1,144 +0,0 @@
|
|||||||
module TPMGeom !************************************************************************************
|
|
||||||
!
|
|
||||||
! Geometry functions for TPM force field.
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 13.00, 2020
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
|
|
||||||
use TPMLib
|
|
||||||
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Constants
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
integer*4, parameter :: MD_LINES_NONPAR = 0
|
|
||||||
integer*4, parameter :: MD_LINES_PAR = 1
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Global variables
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
! Coordinates of the whole domain
|
|
||||||
real*8 :: DomXmin, DomXmax, DomYmin, DomYmax, DomZmin, DomZmax
|
|
||||||
real*8 :: DomLX, DomLY, DomLZ
|
|
||||||
real*8 :: DomLXhalf, DomLYhalf, DomLZhalf
|
|
||||||
|
|
||||||
! Boundary conditions
|
|
||||||
integer*4 :: BC_X = 0
|
|
||||||
integer*4 :: BC_Y = 0
|
|
||||||
integer*4 :: BC_Z = 0
|
|
||||||
|
|
||||||
! Skin parameter in NBL and related algorithms
|
|
||||||
real*8 :: Rskin = 1.0d+00
|
|
||||||
|
|
||||||
contains !******************************************************************************************
|
|
||||||
|
|
||||||
subroutine ApplyPeriodicBC ( R ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This subroutine changes coordinates of the point according to periodic boundary conditions
|
|
||||||
! it order to make sure that the point is inside the computational cell
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, dimension(0:2), intent(inout) :: R
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
! These commented lines implement the more general, but less efficient algorithm
|
|
||||||
!if ( BC_X == 1 ) R(0) = R(0) - DomLX * roundint ( R(0) / DomLX )
|
|
||||||
!if ( BC_Y == 1 ) R(1) = R(1) - DomLY * roundint ( R(1) / DomLY )
|
|
||||||
!if ( BC_Z == 1 ) R(2) = R(2) - DomLZ * roundint ( R(2) / DomLZ )
|
|
||||||
if ( BC_X == 1 ) then
|
|
||||||
if ( R(0) .GT. DomLXHalf ) then
|
|
||||||
R(0) = R(0) - DomLX
|
|
||||||
else if ( R(0) .LT. - DomLXHalf ) then
|
|
||||||
R(0) = R(0) + DomLX
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
if ( BC_Y == 1 ) then
|
|
||||||
if ( R(1) .GT. DomLYHalf ) then
|
|
||||||
R(1) = R(1) - DomLY
|
|
||||||
else if ( R(1) .LT. - DomLYHalf ) then
|
|
||||||
R(1) = R(1) + DomLY
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
if ( BC_Z == 1 ) then
|
|
||||||
if ( R(2) .GT. DomLZHalf ) then
|
|
||||||
R(2) = R(2) - DomLZ
|
|
||||||
else if ( R(2) .LT. - DomLZHalf ) then
|
|
||||||
R(2) = R(2) + DomLZ
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
end subroutine ApplyPeriodicBC !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine LinePoint ( Displacement, Q, R1, L1, R0 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function calculates the point Q of projection of point R0 on line (R1,L1)
|
|
||||||
! Q = R1 + Disaplacement * L1
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, intent(inout) :: Displacement
|
|
||||||
real*8, dimension(0:2), intent(inout) :: Q
|
|
||||||
real*8, dimension(0:2), intent(in) :: R1, L1, R0
|
|
||||||
!--------------------------------------------------------------------------------------------
|
|
||||||
Q = R0 - R1
|
|
||||||
! Here we take into account periodic boundaries
|
|
||||||
call ApplyPeriodicBC ( Q )
|
|
||||||
Displacement = S_V3xV3 ( Q, L1 )
|
|
||||||
Q = R1 + Displacement * L1
|
|
||||||
end subroutine LinePoint !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
integer*4 function LineLine ( H, cosA, D1, D2, L12, R1, L1, R2, L2, Prec ) !!!!!!!!!!!!!!!!!
|
|
||||||
! This function determines the nearest distance H between two lines (R1,L1) and (R2,L2)
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
! Input values:
|
|
||||||
! R1, L1, point and direction of line 1
|
|
||||||
! R2, L2, point and direction of line 2
|
|
||||||
! Prec, precision for the case L1 * L2 = 0 (parallel lines)
|
|
||||||
! Return values:
|
|
||||||
! H, minimal distance between lines
|
|
||||||
! cosA, cosine of angle between lines
|
|
||||||
! D1, D2, displacements
|
|
||||||
! L12, unit vector directed along the closes distance
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, intent(inout) :: H, cosA, D1, D2
|
|
||||||
real*8, dimension(0:2), intent(out) :: L12
|
|
||||||
real*8, dimension(0:2), intent(in) :: R1, L1, R2, L2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, intent(in) :: Prec
|
|
||||||
real*8, dimension(0:2) :: Q1, Q2, R
|
|
||||||
real*8 :: C, DD1, DD2, C1, C2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
cosA = S_V3xV3 ( L1, L2 )
|
|
||||||
C = 1.0 - sqr ( cosA )
|
|
||||||
if ( C < Prec ) then ! Lines are parallel to each other
|
|
||||||
LineLine = MD_LINES_PAR
|
|
||||||
return
|
|
||||||
end if
|
|
||||||
LineLine = MD_LINES_NONPAR
|
|
||||||
R = R2 - R1
|
|
||||||
! Here we take into account periodic boundaries
|
|
||||||
call ApplyPeriodicBC ( R )
|
|
||||||
DD1 = S_V3xV3 ( R, L1 )
|
|
||||||
DD2 = S_V3xV3 ( R, L2 )
|
|
||||||
D1 = ( cosA * DD2 - DD1 ) / C
|
|
||||||
D2 = ( DD2 - cosA * DD1 ) / C
|
|
||||||
Q1 = R1 - D1 * L1
|
|
||||||
Q2 = R2 - D2 * L2
|
|
||||||
L12 = Q2 - Q1
|
|
||||||
! Here we take into account periodic boundaries
|
|
||||||
call ApplyPeriodicBC ( L12 )
|
|
||||||
H = S_V3norm3 ( L12 )
|
|
||||||
if ( H < Prec ) then ! Lines intersect each other
|
|
||||||
C1 = signum ( D1 )
|
|
||||||
C2 = signum ( D1 ) * signum ( cosA )
|
|
||||||
Q1 = C1 * L1
|
|
||||||
Q2 = C2 * L2
|
|
||||||
call V3_V3xxV3 ( L12, Q1, Q2 )
|
|
||||||
call V3_ort ( L12 )
|
|
||||||
else ! No intersection
|
|
||||||
L12 = L12 / H
|
|
||||||
end if
|
|
||||||
end function LineLine !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end module TPMGeom !********************************************************************************
|
|
||||||
@ -1,205 +0,0 @@
|
|||||||
module TPMLib !*************************************************************************************
|
|
||||||
!
|
|
||||||
! Common constants, types, and functions for TPM force field.
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 13.00, 2020
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Mathematical constants
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
real*8, parameter :: M_PI_2 = 1.57079632679489661923
|
|
||||||
real*8, parameter :: M_PI = 3.14159265358979323846
|
|
||||||
real*8, parameter :: M_3PI_2 = 4.71238898038468985769
|
|
||||||
real*8, parameter :: M_2PI = 6.28318530717958647692
|
|
||||||
real*8, parameter :: M_PI_180 = 0.017453292519943295769
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Physical unit constants
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
real*8, parameter :: K_AMU = 1.66056E-27 ! a.m.u. (atomic mass unit, Dalton)
|
|
||||||
real*8, parameter :: K_EV = 1.60217646e-19 ! eV (electron-volt)
|
|
||||||
|
|
||||||
real*8, parameter :: K_MDLU = 1.0E-10 ! MD length unit (m)
|
|
||||||
real*8, parameter :: K_MDEU = K_EV ! MD energy unit (J)
|
|
||||||
real*8, parameter :: K_MDMU = K_AMU ! MD mass unit (kg)
|
|
||||||
real*8, parameter :: K_MDFU = K_MDEU / K_MDLU ! MD force unit (N)
|
|
||||||
real*8, parameter :: K_MDCU = K_MDEU / K_MDMU ! MD specific heat unit (J/(kg*K))
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Global variables
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
integer*4 :: StdUID = 31
|
|
||||||
|
|
||||||
contains !******************************************************************************************
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Simple mathematical functions
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
real*8 function rad ( X ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, intent(in) :: X
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
rad = X * M_PI_180
|
|
||||||
end function rad !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
real*8 function sqr ( X ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, intent(in) :: X
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
sqr = X * X
|
|
||||||
end function sqr !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
integer*4 function signum ( X ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, intent(in) :: X
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
if ( X > 0 ) then
|
|
||||||
signum = 1
|
|
||||||
else if ( X < 0 ) then
|
|
||||||
signum = -1
|
|
||||||
else
|
|
||||||
signum = 0
|
|
||||||
end if
|
|
||||||
end function signum !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Vector & matrix functions
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
real*8 function S_V3xx ( V ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, dimension(0:2), intent(in) :: V
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
S_V3xx = V(0) * V(0) + V(1) * V(1) + V(2) * V(2)
|
|
||||||
end function S_V3xx !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
real*8 function S_V3xV3 ( V1, V2 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, dimension(0:2), intent(in) :: V1, V2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
S_V3xV3 = V1(0) * V2(0) + V1(1) * V2(1) + V1(2) * V2(2)
|
|
||||||
end function S_V3xV3 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
real*8 function S_V3norm3 ( V ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, dimension(0:2), intent(in) :: V
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
S_V3norm3 = dsqrt ( V(0) * V(0) + V(1) * V(1) + V(2) * V(2) )
|
|
||||||
end function S_V3norm3 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine V3_ort ( V ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! Vector production
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, dimension(0:2), intent(inout) :: V
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8 :: Vabs
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Vabs = S_V3norm3 ( V )
|
|
||||||
V(0) = V(0) / Vabs
|
|
||||||
V(1) = V(1) / Vabs
|
|
||||||
V(2) = V(2) / Vabs
|
|
||||||
end subroutine V3_ort !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine V3_V3xxV3 ( V, V1, V2 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! Vector production
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, dimension(0:2), intent(out) :: V
|
|
||||||
real*8, dimension(0:2), intent(in) :: V1, V2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
V(0) = V1(1) * V2(2) - V1(2) * V2(1)
|
|
||||||
V(1) = V1(2) * V2(0) - V1(0) * V2(2)
|
|
||||||
V(2) = V1(0) * V2(1) - V1(1) * V2(0)
|
|
||||||
end subroutine V3_V3xxV3 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Handling of spherical and Euler angles
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
subroutine RotationMatrix3 ( M, Psi, Tet, Phi ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! Ksi, Tet and Phi are Euler angles
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, dimension(0:2,0:2), intent(out) :: M
|
|
||||||
real*8, intent(in) :: Psi, Tet, Phi
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8 :: cK, sK, cT, sT, cP, sP
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
cK = dcos ( Psi )
|
|
||||||
sK = dsin ( Psi )
|
|
||||||
cT = dcos ( Tet )
|
|
||||||
sT = dsin ( Tet )
|
|
||||||
cP = dcos ( Phi )
|
|
||||||
sP = dsin ( Phi )
|
|
||||||
M(0,0) = cP * cK - sK * sP * cT
|
|
||||||
M(0,1) = cP * sK + sP * cT * cK
|
|
||||||
M(0,2) = sP * sT
|
|
||||||
M(1,0) = - sP * cK - cP * cT * sK
|
|
||||||
M(1,1) = - sP * sK + cP * cT * cK
|
|
||||||
M(1,2) = cP * sT
|
|
||||||
M(2,0) = sT * sK
|
|
||||||
M(2,1) = - sT * cK
|
|
||||||
M(2,2) = cT
|
|
||||||
end subroutine RotationMatrix3 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine EulerAngles ( Psi, Tet, L ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, intent(out) :: Tet, Psi
|
|
||||||
real*8, dimension(0:2), intent(in) :: L
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Tet = acos ( L(2) )
|
|
||||||
Psi = atan2 ( L(1), L(0) )
|
|
||||||
if ( Psi > M_3PI_2 ) then
|
|
||||||
Psi = Psi - M_3PI_2
|
|
||||||
else
|
|
||||||
Psi = Psi + M_PI_2
|
|
||||||
end if
|
|
||||||
end subroutine EulerAngles !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! File input and output
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
integer*4 function OpenFile ( Name, Params, Path ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
character*(*), intent(in) :: Name, Params, Path
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer*4 :: Fuid
|
|
||||||
character*512 :: FullName, Msg, Name1, Action1, Status1, Form1, Position1
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
OpenFile = StdUID + 1
|
|
||||||
if ( Params(1:1) == 'r' ) then
|
|
||||||
Action1 = 'read'
|
|
||||||
Status1 = 'old'
|
|
||||||
Position1 = 'rewind'
|
|
||||||
else if ( Params(1:1) == 'w' ) then
|
|
||||||
Action1 = 'write'
|
|
||||||
Status1 = 'replace'
|
|
||||||
Position1 = 'rewind'
|
|
||||||
else if ( Params(1:1) == 'a' ) then
|
|
||||||
Action1 = 'write'
|
|
||||||
Status1 = 'old'
|
|
||||||
Position1 = 'append'
|
|
||||||
endif
|
|
||||||
if ( Params(2:2) == 'b' ) then
|
|
||||||
Form1 = 'binary'
|
|
||||||
else
|
|
||||||
Form1 = 'formatted'
|
|
||||||
endif
|
|
||||||
open ( unit = OpenFile, file = Name, form = Form1, action = Action1, status = Status1, position = Position1 )
|
|
||||||
StdUID = StdUID + 1
|
|
||||||
return
|
|
||||||
end function OpenFile !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine CloseFile ( Fuid ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
integer*4, intent(inout) :: Fuid
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
if ( Fuid < 0 ) return
|
|
||||||
close ( unit = Fuid )
|
|
||||||
Fuid = -1
|
|
||||||
end subroutine CloseFile !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end module TPMLib !*********************************************************************************
|
|
||||||
|
|
||||||
@ -1,289 +0,0 @@
|
|||||||
module TubePotBase !********************************************************************************
|
|
||||||
!
|
|
||||||
! Non-Bonded pair interaction potential and transfer functions for atoms composing nanotubes.
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 13.00, 2020
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! This module contains basic parameters for all modules involved into calculations of tubular
|
|
||||||
! potentials.
|
|
||||||
!
|
|
||||||
! It includes definitions of
|
|
||||||
! -- TPBU, Lennard-Jones (12-6) potential;
|
|
||||||
! -- TPBQ, Transfer function,
|
|
||||||
!
|
|
||||||
! All default values are adjusted for non-bonded carbon-carbon interaction in carbon nanotubes.
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
|
|
||||||
use TPMLib
|
|
||||||
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Constants
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
! Types of the potential with respect to the breathing mode
|
|
||||||
integer*4, parameter :: TP_POT_MONO_R = 0
|
|
||||||
integer*4, parameter :: TP_POT_POLY_R = 1
|
|
||||||
|
|
||||||
! Maximum number of elements in corresponding tables
|
|
||||||
integer*4, parameter :: TPBNMAX = 2001
|
|
||||||
|
|
||||||
! Numerical constants
|
|
||||||
real*8, parameter :: TPbConstD = 5.196152422706632d+00 ! = 3.0**1.5
|
|
||||||
|
|
||||||
! Mass of C atom
|
|
||||||
real*8, 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*8, parameter :: TPBEcc = 0.00284d+00 ! (eV)
|
|
||||||
real*8, parameter :: TPBScc = 3.4d+00 ! (A)
|
|
||||||
|
|
||||||
! Lattice parameter and surface number density of atoms for a graphene sheet, see
|
|
||||||
! Dresselhaus et al, Carbon 33(7), 1995
|
|
||||||
real*8, parameter :: TPBAcc = 1.421d+00 ! (A)
|
|
||||||
real*8, parameter :: TPBDcc = 4.0d+00 / ( TPBConstD * TPBAcc * TPBAcc ) ! (1/A^2)
|
|
||||||
|
|
||||||
! Specific heat of carbon nanotubes
|
|
||||||
real*8, parameter :: TPBSHcc = 600.0d+00 / K_MDCU ! (eV/(Da*K))
|
|
||||||
|
|
||||||
! Cutoff distances for interactomic potential and transfer function.
|
|
||||||
! Changes in these parameters can result in necessity to change some numerical parameters too.
|
|
||||||
real*8, parameter :: TPBRmincc = 0.001d+00 * TPBScc ! (A)
|
|
||||||
real*8, parameter :: TPBRcutoffcc = 3.0d+00 * TPBScc ! (A)
|
|
||||||
real*8, parameter :: TPBRcutoff1cc = 2.16d+00 * TPBScc ! (A)
|
|
||||||
|
|
||||||
! Parameters of the transfer function for non-bonded interaction between carbon atoms
|
|
||||||
real*8, parameter :: TPBQScc = 7.0d+00 ! (A)
|
|
||||||
real*8, parameter :: TPBQRcutoff1cc = 8.0d+00 ! (A)
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Global variables
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
logical :: TPErrCheck = .true. ! Set to .true. to generate diagnostic and warning messages
|
|
||||||
character*512 :: TPErrMsg = ''
|
|
||||||
|
|
||||||
real*8 :: TPGeomPrec = 1.0d-06 ! Geometric precision, see TPInt
|
|
||||||
integer*4 :: 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 nanotube surface
|
|
||||||
|
|
||||||
real*8 :: TPBM = TPBMc ! Mass of an atom (Da)
|
|
||||||
real*8 :: TPBE = TPBEcc ! Depth of the energy well in (12-6) LJ interatomic potential (eV)
|
|
||||||
real*8 :: TPBS = TPBScc ! Sigma parameter of (12-6) LJ interatomic potential (A)
|
|
||||||
real*8 :: TPBD = TPBDcc ! Numerical density of atoms at the tube surface (1/A^2)
|
|
||||||
real*8 :: TPBSH = TPBSHcc ! Specific heat (eV/(Da*K))
|
|
||||||
|
|
||||||
real*8 :: TPBRmin = TPBRmincc ! (A)
|
|
||||||
real*8 :: TPBRcutoff = TPBRcutoffcc ! (A)
|
|
||||||
real*8 :: TPBRcutoff1 = TPBRcutoff1cc ! (A)
|
|
||||||
|
|
||||||
! Physical parameters of the transfer function
|
|
||||||
|
|
||||||
real*8 :: TPBQS = TPBQScc ! Sigma parameter of the transfer function (A)
|
|
||||||
real*8 :: TPBQRcutoff1 = TPBQRcutoff1cc ! (A)
|
|
||||||
|
|
||||||
! Auxiliary variables
|
|
||||||
|
|
||||||
real*8 :: TPBE4, TPBE24, TPBDRcutoff, TPBQDRcutoff
|
|
||||||
real*8 :: TPBQR0 ! Constant-value distance for the transfer function (A)
|
|
||||||
|
|
||||||
! Table of inter-particle potential, force, and transfer function
|
|
||||||
|
|
||||||
integer*4 :: TPBN = TPBNMAX
|
|
||||||
real*8 :: TPBDR
|
|
||||||
real*8, dimension(0:TPBNMAX-1) :: TPBQ
|
|
||||||
real*8, dimension(0:TPBNMAX-1) :: TPBU, TPBdUdR
|
|
||||||
|
|
||||||
contains !******************************************************************************************
|
|
||||||
|
|
||||||
integer*4 function TPBsizeof () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
TPBsizeof = 8 * ( size ( TPBQ ) + size ( TPBU ) + size ( TPBdUdR ) )
|
|
||||||
end function TPBsizeof !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Interpolation
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
real*8 function TPBQInt0 ( R ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, intent(in) :: R
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8 :: Z, RR
|
|
||||||
integer*4 :: i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
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 )
|
|
||||||
elseif ( R > TPBRcutoff ) then
|
|
||||||
TPBQInt0 = 0.0d+00
|
|
||||||
return
|
|
||||||
endif
|
|
||||||
RR = ( R - TPBRmin ) / TPBDR
|
|
||||||
i = int ( RR )
|
|
||||||
RR = RR - i
|
|
||||||
Z = 1.0d+00 - RR
|
|
||||||
TPBQInt0 = TPBQ(i) * Z + TPBQ(i+1) * RR
|
|
||||||
end function TPBQInt0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
real*8 function TPBUInt0 ( R ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, intent(in) :: R
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8 :: Z, RR
|
|
||||||
integer*4 :: i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
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 )
|
|
||||||
elseif ( R > TPBRcutoff ) then
|
|
||||||
TPBUInt0 = 0.0d+00
|
|
||||||
return
|
|
||||||
endif
|
|
||||||
RR = ( R - TPBRmin ) / TPBDR
|
|
||||||
i = int ( RR )
|
|
||||||
RR = RR - i
|
|
||||||
Z = 1.0d+00 - RR
|
|
||||||
TPBUInt0 = TPBU(i) * Z + TPBU(i+1) * RR
|
|
||||||
end function TPBUInt0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine TPBUInt1 ( U, dUdR, R ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, intent(out) :: U, dUdR
|
|
||||||
real*8, intent(in) :: R
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8 :: Z, RR
|
|
||||||
integer*4 :: i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
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 )
|
|
||||||
elseif ( R > TPBRcutoff ) then
|
|
||||||
TPBU = 0.0d+00
|
|
||||||
TPBdUdR = 0.0d+00
|
|
||||||
return
|
|
||||||
endif
|
|
||||||
RR = ( R - TPBRmin ) / TPBDR
|
|
||||||
i = int ( RR )
|
|
||||||
RR = RR - i
|
|
||||||
Z = 1.0d+00 - RR
|
|
||||||
U = TPBU(i) * Z + TPBU(i+1) * RR
|
|
||||||
dUdR = TPBdUdR(i) * Z + TPBdUdR(i+1) * RR
|
|
||||||
end subroutine TPBUInt1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Calculation
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
real*8 function TPBQCalc0 ( R ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, intent(in) :: R
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8 :: Z, t, S
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
if ( R > TPBRcutoff ) then
|
|
||||||
TPBQCalc0 = 0.0d+00
|
|
||||||
else if ( R < TPBQR0 ) then
|
|
||||||
TPBQCalc0 = 1.0d+00
|
|
||||||
else
|
|
||||||
Z = TPBQS / R
|
|
||||||
Z = Z * Z * Z
|
|
||||||
Z = Z * Z
|
|
||||||
TPBQCalc0 = 4.0d+00 * ( 1.0d+00 - Z ) * Z
|
|
||||||
if ( R > TPBQRcutoff1 ) then
|
|
||||||
t = ( R - TPBQRcutoff1 ) / TPBQDRcutoff
|
|
||||||
S = 1.0d+00 - t * t * ( 3.0d+00 - 2.0d+00 * t )
|
|
||||||
TPBQCalc0 = TPBQCalc0 * S
|
|
||||||
endif
|
|
||||||
endif
|
|
||||||
end function TPBQCalc0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
real*8 function TPBUCalc0 ( R ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, intent(in) :: R
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8 :: Z, t, S
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
if ( R > TPBRcutoff ) then
|
|
||||||
TPBUCalc0 = 0.0d+00
|
|
||||||
else
|
|
||||||
Z = TPBS / R
|
|
||||||
Z = Z * Z * Z
|
|
||||||
Z = Z * Z
|
|
||||||
TPBUCalc0 = TPBE4 * ( Z - 1.0d+00 ) * Z
|
|
||||||
if ( R > TPBRcutoff1 ) then
|
|
||||||
t = ( R - TPBRcutoff1 ) / TPBDRcutoff
|
|
||||||
S = 1.0d+00 - t * t * ( 3.0d+00 - 2.0d+00 * t )
|
|
||||||
TPBUCalc0 = TPBUCalc0 * S
|
|
||||||
endif
|
|
||||||
endif
|
|
||||||
end function TPBUCalc0 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine TPBUCalc1 ( U, dUdR, R ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, intent(out) :: U, dUdR
|
|
||||||
real*8, intent(in) :: R
|
|
||||||
real*8 :: Z, t, S, dSdR
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
if ( R > TPBRcutoff ) then
|
|
||||||
U = 0.0d+00
|
|
||||||
dUdR = 0.0d+00
|
|
||||||
else
|
|
||||||
Z = TPBS / R
|
|
||||||
Z = Z * Z * Z
|
|
||||||
Z = Z * Z
|
|
||||||
U = TPBE4 * ( Z - 1.0d+00 ) * Z
|
|
||||||
dUdR = TPBE24 * ( 2.0d+00 * Z - 1.0d+00 ) * Z / R
|
|
||||||
if ( R > TPBRcutoff1 ) then
|
|
||||||
t = ( R - TPBRcutoff1 ) / TPBDRcutoff
|
|
||||||
S = 1.0d+00 - t * t * ( 3.0d+00 - 2.0d+00 * t )
|
|
||||||
dSdR = 6.0d+00 * t * ( t - 1.0d+00 ) / TPBDRcutoff
|
|
||||||
dUdR = dUdR * S + U * dSdR
|
|
||||||
U = U * S
|
|
||||||
endif
|
|
||||||
endif
|
|
||||||
end subroutine TPBUCalc1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine TPBSegmentForces ( F1, F2, F, M, Laxis, L ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, dimension(0:2), intent(out) :: F1, F2
|
|
||||||
real*8, dimension(0:2), intent(in) :: F, M, Laxis
|
|
||||||
real*8, intent(in) :: L
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, dimension(0:2) :: FF, MM, FFF
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
FF = 0.5d+00 * F
|
|
||||||
MM = M / L
|
|
||||||
call V3_V3xxV3 ( FFF, MM, Laxis )
|
|
||||||
F1 = FF - FFF
|
|
||||||
F2 = FF + FFF
|
|
||||||
end subroutine TPBSegmentForces !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Initialization
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
subroutine TPBInit () !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8 :: R
|
|
||||||
integer*4 :: i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
TPBE4 = 4.0d+00 * TPBE
|
|
||||||
TPBE24 = - 24.0d+00 * TPBE
|
|
||||||
TPBDRcutoff = TPBRcutoff - TPBRcutoff1
|
|
||||||
TPBQDRcutoff = TPBRcutoff - TPBQRcutoff1
|
|
||||||
TPBQR0 = TPBQS * 2.0d+00 ** ( 1.0d+00 / 6.0d+00 )
|
|
||||||
TPBDR = ( TPBRcutoff - TPBRmin ) / ( TPBN - 1 )
|
|
||||||
R = TPBRmin
|
|
||||||
do i = 0, TPBN - 1
|
|
||||||
TPBQ(i) = TPBQCalc0 ( R )
|
|
||||||
call TPBUCalc1 ( TPBU(i), TPBdUdR(i), R )
|
|
||||||
R = R + TPBDR
|
|
||||||
enddo
|
|
||||||
end subroutine TPBInit !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end module TubePotBase !****************************************************************************
|
|
||||||
File diff suppressed because it is too large
Load Diff
@ -1,428 +0,0 @@
|
|||||||
module TubePotTrue !********************************************************************************
|
|
||||||
!
|
|
||||||
! True tubular potential and transfer function
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! This module implements calculation of true potential and transfer functions for interaction
|
|
||||||
! between two cylinder segments of nanotubes by direct integration over the surfaces of both
|
|
||||||
! segments.
|
|
||||||
!
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
!
|
|
||||||
! Intel Fortran
|
|
||||||
!
|
|
||||||
! Alexey N. Volkov, University of Alabama, avolkov1@ua.edu, Version 13.00, 2020
|
|
||||||
!
|
|
||||||
!***************************************************************************************************
|
|
||||||
|
|
||||||
use TPMGeom
|
|
||||||
use TubePotBase
|
|
||||||
|
|
||||||
implicit none
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Constants
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
integer*4, parameter :: TPTNXMAX = 257
|
|
||||||
integer*4, parameter :: TPTNEMAX = 128
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Types
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
type TPTSEG !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8 :: X, Y, Z
|
|
||||||
real*8 :: Psi, Theta, Phi ! Euler's angles
|
|
||||||
real*8 :: R ! Segment radius
|
|
||||||
real*8 :: L ! Segment length
|
|
||||||
integer*4 :: NX, NE ! Number of nodes for numerical integration
|
|
||||||
real*8 :: DX, DE ! Spacings
|
|
||||||
real*8, dimension(0:2,0:2) :: M ! Transformation matrix
|
|
||||||
real*8, 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 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
type(TPTSEG), intent(in) :: S
|
|
||||||
real*8, dimension(0:2), intent(out) :: Laxis
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Laxis(0:2) = S%M(2,0:2)
|
|
||||||
end subroutine TPTSegAxisVector !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine TPTSegRadVector ( S, Lrad, Eps ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
type(TPTSEG), intent(in) :: S
|
|
||||||
real*8, dimension(0:2), intent(out) :: Lrad
|
|
||||||
real*8, intent(in) :: Eps
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8 :: Ce, Se
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
Ce = cos ( Eps )
|
|
||||||
Se = sin ( Eps )
|
|
||||||
Lrad(0) = Ce * S%M(0,0) + Se * S%M(1,0)
|
|
||||||
Lrad(1) = Ce * S%M(0,1) + Se * S%M(1,1)
|
|
||||||
Lrad(2) = Ce * S%M(0,2) + Se * S%M(1,2)
|
|
||||||
end subroutine TPTSegRadVector !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine TPTRadiusVector ( S, R, X, Eps ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
type(TPTSEG), intent(in) :: S
|
|
||||||
real*8, dimension(0:2), intent(out) :: R
|
|
||||||
real*8, intent(in) :: X, Eps
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, dimension(0:2) :: Laxis, Lrad
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
call TPTSegAxisVector ( S, Laxis )
|
|
||||||
call TPTSegRadVector ( S, Lrad, Eps )
|
|
||||||
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
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8 :: X, Eps
|
|
||||||
integer*4 :: i, j
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
X = - S%L / 2.0
|
|
||||||
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
|
|
||||||
call TPTRadiusVector ( S, S%Rtab(i,j,0:2), X, Eps )
|
|
||||||
Eps = Eps + S%DE
|
|
||||||
end do
|
|
||||||
X = X + S%DX
|
|
||||||
end do
|
|
||||||
end subroutine TPTCalcSegNodeTable !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine TPTSetSegPosition1 ( S, Rcenter, Laxis, L ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
type(TPTSEG), intent(inout) :: S
|
|
||||||
real*8, dimension(0:2), intent(in) :: Rcenter, Laxis
|
|
||||||
real*8, intent(in) :: L
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
S%L = L
|
|
||||||
S%DX = L / ( S%NX - 1 )
|
|
||||||
call EulerAngles ( S%Psi, S%Theta, Laxis )
|
|
||||||
S%Phi= 0.0d+00
|
|
||||||
S%X = Rcenter(0)
|
|
||||||
S%Y = Rcenter(1)
|
|
||||||
S%Z = Rcenter(2)
|
|
||||||
call TPTCalcSegNodeTable ( S )
|
|
||||||
end subroutine TPTSetSegPosition1 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine TPTSetSegPosition2 ( S, R1, R2 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
type(TPTSEG), intent(inout) :: S
|
|
||||||
real*8, dimension(0:2), intent(in) :: R1, R2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, dimension(0:2) :: R, Laxis
|
|
||||||
real*8 :: L
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
R = 0.5 * ( R1 + R2 )
|
|
||||||
Laxis = R2 - R1
|
|
||||||
L = S_V3norm3 ( Laxis )
|
|
||||||
Laxis = Laxis / L
|
|
||||||
call TPTSetSegPosition1 ( S, R, Laxis, L )
|
|
||||||
end subroutine TPTSetSegPosition2 !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
integer*4 function TPTCheckIntersection ( S1, S2 ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
type(TPTSEG), intent(in) :: S1, S2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer*4 :: i, j
|
|
||||||
real*8 :: L1, L2, Displacement, D
|
|
||||||
real*8, dimension(0:2) :: Laxis, Q, R
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
L2 = S1%L / 2.0
|
|
||||||
L1 = - L2
|
|
||||||
call TPTSegAxisVector ( S1, Laxis )
|
|
||||||
R(0) = S1%X
|
|
||||||
R(1) = S1%Y
|
|
||||||
R(2) = S1%Z
|
|
||||||
do i = 0, S2%NX - 1
|
|
||||||
do j = 0, S2%NE - 1
|
|
||||||
call LinePoint ( Displacement, Q, R, Laxis, S2%Rtab(i,j,0:2) )
|
|
||||||
D = sqrt ( sqr ( Q(0) - S2%Rtab(i,j,0) ) + sqr ( Q(1) - S2%Rtab(i,j,1) ) &
|
|
||||||
+ sqr ( Q(2) - S2%Rtab(i,j,2) ) )
|
|
||||||
if ( Displacement > L1 .and. Displacement < L2 .and. D < S1%R ) then
|
|
||||||
TPTCheckIntersection = 1
|
|
||||||
return
|
|
||||||
end if
|
|
||||||
end do
|
|
||||||
end do
|
|
||||||
TPTCheckIntersection = 0
|
|
||||||
end function TPTCheckIntersection !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
integer*4 function TPTCalcPointRange ( S, Xmin, Xmax, Re ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
type(TPTSEG), intent(in) :: S
|
|
||||||
real*8, intent(out) :: Xmin, Xmax
|
|
||||||
real*8, dimension(0:2), intent(in) :: Re
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8 :: Displacement, Distance
|
|
||||||
real*8, dimension(0:2) :: Laxis, Q, R
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
call TPTSegAxisVector ( S, Laxis )
|
|
||||||
R(0) = S%X
|
|
||||||
R(1) = S%Y
|
|
||||||
R(2) = S%Z
|
|
||||||
call LinePoint ( Displacement, Q, R, Laxis, Re )
|
|
||||||
Distance = sqrt ( sqr ( Q(0) - Re(0) ) + sqr ( Q(1) - Re(1) ) + sqr ( Q(2) - Re(2) ) ) - S%R
|
|
||||||
if ( TPBRcutoff < Distance ) then
|
|
||||||
Xmin = 0.0d+00
|
|
||||||
Xmax = 0.0d+00
|
|
||||||
TPTCalcPointRange = 0
|
|
||||||
return
|
|
||||||
end if
|
|
||||||
Distance = sqrt ( TPBRcutoff * TPBRcutoff - Distance * Distance )
|
|
||||||
Xmin = Displacement - Distance
|
|
||||||
Xmax = Displacement + Distance
|
|
||||||
TPTCalcPointRange = 1
|
|
||||||
end function TPTCalcPointRange !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
subroutine TPTGetEnds ( R1_1, R1_2, R2_1, R2_2, X1_1, X1_2, X2_1, X2_2, H, A ) !!!!!!!!!!!!!
|
|
||||||
real*8, dimension(0:2), intent(out) :: R1_1, R1_2, R2_1, R2_2
|
|
||||||
real*8, intent(in) :: X1_1, X1_2, X2_1, X2_2, H, A
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
R1_1(0) = 0.0d+00
|
|
||||||
R1_1(1) = 0.0d+00
|
|
||||||
R1_1(2) = X1_1
|
|
||||||
R1_2(0) = 0.0d+00
|
|
||||||
R1_2(1) = 0.0d+00
|
|
||||||
R1_2(2) = X1_2
|
|
||||||
R2_1(0) = H
|
|
||||||
R2_1(1) = - X2_1 * sin ( A )
|
|
||||||
R2_1(2) = X2_1 * cos ( A )
|
|
||||||
R2_2(0) = H
|
|
||||||
R2_2(1) = - X2_2 * sin ( A )
|
|
||||||
R2_2(2) = X2_2 * cos ( A )
|
|
||||||
end subroutine TPTGetEnds !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Tubular potential
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
integer*4 function TPTPointPotential ( Q, U, F, R, S ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function returns the potential U and force F applied to the atom in position R and
|
|
||||||
! produced by the segment S.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, intent(out) :: Q, U
|
|
||||||
real*8, dimension(0:2), intent(out) :: F
|
|
||||||
real*8, dimension(0:2), intent(in) :: R
|
|
||||||
type(TPTSEG), intent(in) :: S
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer*4 :: i, j
|
|
||||||
real*8, dimension(0:2) :: RR, FF
|
|
||||||
real*8 :: QQ, UU, UUU, FFF, Rabs
|
|
||||||
real*8 :: Coeff, Xmin, Xmax, X
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
TPTPointPotential = 0
|
|
||||||
Q = 0.0d+00
|
|
||||||
U = 0.0d+00
|
|
||||||
F = 0.0d+00
|
|
||||||
if ( TPTCalcPointRange ( S, Xmin, Xmax, R ) == 0 ) return
|
|
||||||
X = - S%L / 2.0
|
|
||||||
do i = 0, S%NX - 1
|
|
||||||
if ( X > Xmin .and. X < Xmax ) then
|
|
||||||
QQ = 0.0d+00
|
|
||||||
UU = 0.0d+00
|
|
||||||
FF = 0.0d+00
|
|
||||||
do j = 0, S%NE - 1
|
|
||||||
RR(0:2) = S%Rtab(i,j,0:2) - R(0:2)
|
|
||||||
Rabs = S_V3norm3 ( RR )
|
|
||||||
if ( Rabs < TPBRcutoff ) then
|
|
||||||
QQ = QQ + TPBQCalc0 ( Rabs )
|
|
||||||
call TPBUCalc1 ( UUU, FFF, Rabs )
|
|
||||||
UU = UU + UUU
|
|
||||||
FFF = FFF / Rabs
|
|
||||||
FF = FF + FFF * RR
|
|
||||||
TPTPointPotential = 1
|
|
||||||
end if
|
|
||||||
end do
|
|
||||||
if ( i == 0 .or. i == S%NX - 1 ) then
|
|
||||||
Q = Q + 0.5d+00 * QQ
|
|
||||||
U = U + 0.5d+00 * UU
|
|
||||||
F = F + 0.5d+00 * FF
|
|
||||||
else
|
|
||||||
Q = Q + QQ
|
|
||||||
U = U + UU
|
|
||||||
F = F + FF
|
|
||||||
end if
|
|
||||||
end if
|
|
||||||
X = X + S%DX
|
|
||||||
end do
|
|
||||||
Coeff = TPBD * S%DX * S%R * S%DE
|
|
||||||
Q = Q * S%DX * S%R * S%DE
|
|
||||||
U = U * Coeff
|
|
||||||
F = F * Coeff
|
|
||||||
end function TPTPointPotential !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
integer*4 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
|
|
||||||
! and applied to the i-th circular cross-section of the segment S.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, intent(out) :: Q, U
|
|
||||||
real*8, dimension(0:2), intent(out) :: F, M
|
|
||||||
type(TPTSEG), intent(in) :: S, Ssource
|
|
||||||
integer*4, intent(in) :: i
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
integer*4 :: j
|
|
||||||
real*8, dimension(0:2) :: R, Fp, Mp, Lrad
|
|
||||||
real*8 :: Qp, Up, Eps
|
|
||||||
real*8 :: Coeff
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
TPTSectionPotential = 0
|
|
||||||
Q = 0.0d+00
|
|
||||||
U = 0.0d+00
|
|
||||||
F = 0.0d+00
|
|
||||||
M = 0.0d+00
|
|
||||||
Eps = 0.0d+00
|
|
||||||
do j = 0, S%NE - 1
|
|
||||||
call TPTSegRadVector ( S, Lrad, Eps )
|
|
||||||
if ( TPTPointPotential ( Qp, Up, Fp, S%Rtab(i,j,0:2), Ssource ) == 1 ) then
|
|
||||||
Q = Q + Qp
|
|
||||||
U = U + Up
|
|
||||||
F = F + Fp
|
|
||||||
R(0) = S%Rtab(i,j,0) - S%X
|
|
||||||
R(1) = S%Rtab(i,j,1) - S%Y
|
|
||||||
R(2) = S%Rtab(i,j,2) - S%Z
|
|
||||||
call V3_V3xxV3 ( Mp, R, Fp )
|
|
||||||
M = M + Mp
|
|
||||||
TPTSectionPotential = 1
|
|
||||||
end if
|
|
||||||
Eps = Eps + S%DE
|
|
||||||
end do
|
|
||||||
Coeff = TPBD * S%R * S%DE
|
|
||||||
Q = Q * S%R * S%DE
|
|
||||||
U = U * Coeff
|
|
||||||
F = F * Coeff
|
|
||||||
M = M * Coeff
|
|
||||||
end function TPTSectionPotential !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
integer*4 function TPTSegmentPotential ( Q, U, F, M, S, Ssource ) !!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
! This function returns the potential U, force F and torque M produced by the segment
|
|
||||||
! Ssource and applied to the segment S.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, intent(out) :: Q, U
|
|
||||||
real*8, dimension(0:2), intent(out) :: F, M
|
|
||||||
type(TPTSEG), intent(in) :: S, Ssource
|
|
||||||
integer*4 :: i
|
|
||||||
real*8, dimension(0:2) :: Fc, Mc
|
|
||||||
real*8 :: Qc, Uc
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
TPTSegmentPotential = 0
|
|
||||||
Q = 0.0d+00
|
|
||||||
U = 0.0d+00
|
|
||||||
F = 0.0d+00
|
|
||||||
M = 0.0d+00
|
|
||||||
if ( TPTCheckIntersection ( S, Ssource ) == 1 ) then
|
|
||||||
TPTSegmentPotential = 2
|
|
||||||
return
|
|
||||||
end if
|
|
||||||
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
|
|
||||||
U = U + 0.5d+00 * Uc
|
|
||||||
F = F + 0.5d+00 * Fc
|
|
||||||
M = M + 0.5d+00 * Mc
|
|
||||||
else
|
|
||||||
Q = Q + Qc
|
|
||||||
U = U + Uc
|
|
||||||
F = F + Fc
|
|
||||||
M = M + Mc
|
|
||||||
end if
|
|
||||||
TPTSegmentPotential = 1
|
|
||||||
end if
|
|
||||||
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*8, dimension(0:2), intent(out) :: F1, F2
|
|
||||||
real*8, dimension(0:2), intent(in) :: F, M, Laxis
|
|
||||||
real*8, intent(in) :: L
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, dimension(0:2) :: MM, FF, FFF
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
FF = 0.5d+00 * F
|
|
||||||
MM = M / L
|
|
||||||
call V3_V3xxV3 ( FFF, MM, Laxis )
|
|
||||||
F1 = FF - FFF
|
|
||||||
F2 = FF + FFF
|
|
||||||
end subroutine TPTSegmentForces !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
integer*4 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.
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, intent(out) :: Q, U
|
|
||||||
real*8, dimension(0:2), intent(out) :: F1_1, F1_2, F2_1, F2_2
|
|
||||||
real*8, dimension(0:2), intent(in) :: R1_1, R1_2, R2_1, R2_2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
real*8, dimension(0:2) :: R1, R2, Laxis1, Laxis2, DR, F1, M1, F2, M2
|
|
||||||
real*8 :: L1, L2
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
R1 = 0.5 * ( R1_1 + R1_2 )
|
|
||||||
R2 = 0.5 * ( R2_1 + R2_2 )
|
|
||||||
Laxis1 = R1_2 - R1_1
|
|
||||||
Laxis2 = R2_2 - R2_1
|
|
||||||
L1 = S_V3norm3 ( Laxis1 )
|
|
||||||
L2 = S_V3norm3 ( Laxis2 )
|
|
||||||
Laxis1 = Laxis1 / L1
|
|
||||||
Laxis2 = Laxis2 / L2
|
|
||||||
DR = R2 - R1
|
|
||||||
call TPTSetSegPosition1 ( TPTSeg1, R1, Laxis1, L1 )
|
|
||||||
call TPTSetSegPosition1 ( TPTSeg2, R2, Laxis2, L2 )
|
|
||||||
TPTInteractionF = TPTSegmentPotential ( Q, U, F1, M1, TPTSeg1, TPTSeg2 )
|
|
||||||
if ( TPTInteractionF .ne. 1 ) return
|
|
||||||
call V3_V3xxV3 ( M2, DR, F1 )
|
|
||||||
F2 = - F1
|
|
||||||
M2 = - M1 - M2
|
|
||||||
call TPTSegmentForces ( F1_1, F1_2, F1, M1, Laxis1, L1 )
|
|
||||||
call TPTSegmentForces ( F2_1, F2_2, F2, M2, Laxis2, L2 )
|
|
||||||
end function TPTInteractionF !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
! Initialization
|
|
||||||
!---------------------------------------------------------------------------------------------------
|
|
||||||
|
|
||||||
subroutine TPTInit ( R1, R2, NX, NE ) !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
real*8, intent(in) :: R1, R2
|
|
||||||
integer*4, intent(in) :: NX, NE
|
|
||||||
!-------------------------------------------------------------------------------------------
|
|
||||||
TPTSeg1%X = 0.0d+00
|
|
||||||
TPTSeg1%Y = 0.0d+00
|
|
||||||
TPTSeg1%Z = 0.0d+00
|
|
||||||
TPTSeg1%Psi = 0.0d+00
|
|
||||||
TPTSeg1%Theta = 0.0d+00
|
|
||||||
TPTSeg1%Phi = 0.0d+00
|
|
||||||
TPTSeg1%R = R1
|
|
||||||
TPTSeg1%NX = NX
|
|
||||||
TPTSeg1%NE = NE
|
|
||||||
TPTSeg1%DE = M_2PI / NE
|
|
||||||
TPTSeg2%X = 0.0d+00
|
|
||||||
TPTSeg2%Y = 0.0d+00
|
|
||||||
TPTSeg2%Z = 0.0d+00
|
|
||||||
TPTSeg2%Psi = 0.0d+00
|
|
||||||
TPTSeg2%Theta = 0.0d+00
|
|
||||||
TPTSeg2%Phi = 0.0d+00
|
|
||||||
TPTSeg2%R = R2
|
|
||||||
TPTSeg2%NX = NX
|
|
||||||
TPTSeg2%NE = NE
|
|
||||||
TPTSeg2%DE = M_2PI / NE
|
|
||||||
end subroutine TPTInit !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
|
|
||||||
|
|
||||||
end module TubePotTrue !****************************************************************************
|
|
||||||
@ -1,247 +0,0 @@
|
|||||||
/* -*- c++ -*- ----------------------------------------------------------
|
|
||||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
|
||||||
https://www.lammps.org/, Sandia National Laboratories
|
|
||||||
LAMMPS development team: developers@lammps.org
|
|
||||||
|
|
||||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
|
||||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
|
||||||
certain rights in this software. This software is distributed under
|
|
||||||
the GNU General Public License.
|
|
||||||
|
|
||||||
See the README file in the top-level LAMMPS directory.
|
|
||||||
|
|
||||||
Contributing author: Maxim Shugaev (UVA), mvs9t@virginia.edu
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
#include <iostream>
|
|
||||||
#include <cstdlib>
|
|
||||||
#include <fstream>
|
|
||||||
#include <string>
|
|
||||||
#include <string.h>
|
|
||||||
#include <vector>
|
|
||||||
#include <array>
|
|
||||||
#include <regex>
|
|
||||||
#include <string.h>
|
|
||||||
#include <cmath>
|
|
||||||
//#include <filesystem>
|
|
||||||
|
|
||||||
static const std::string data_file0 = "system.init";
|
|
||||||
static const std::string data_dump0 = "config.dump";
|
|
||||||
static const std::string out_dir0 = "out";
|
|
||||||
|
|
||||||
struct Particle {
|
|
||||||
double x, y, z, vx, vy, vz, Es, Eb, Et, Ep, Ek;
|
|
||||||
char type, nx, ny, nz;
|
|
||||||
};
|
|
||||||
|
|
||||||
class Lamps_base {
|
|
||||||
public:
|
|
||||||
Lamps_base() = default;
|
|
||||||
virtual ~Lamps_base() = default;
|
|
||||||
|
|
||||||
int open(const std::string& filename);
|
|
||||||
int next(); //get next snapshot from the opened file
|
|
||||||
virtual int write(const std::string& filename) const = 0;
|
|
||||||
|
|
||||||
inline double get_X1() const { return X1; };
|
|
||||||
inline double get_X2() const { return X2; };
|
|
||||||
inline double get_Y1() const { return Y1; };
|
|
||||||
inline double get_Y2() const { return Y2; };
|
|
||||||
inline double get_Z1() const { return Z1; };
|
|
||||||
inline double get_Z2() const { return Z2; };
|
|
||||||
inline int get_Natoms() const { return Natoms; };
|
|
||||||
inline int get_Nsteps() const { return Nsteps; };
|
|
||||||
inline int is_open() const { return open_stat; };
|
|
||||||
inline const Particle& get(int i) const { return particles[i]; };
|
|
||||||
inline Particle& get(int i) { return particles[i]; };
|
|
||||||
|
|
||||||
protected:
|
|
||||||
virtual int load() = 0;
|
|
||||||
|
|
||||||
int Nsteps, Natoms, open_stat;
|
|
||||||
double X1, X2, Y1, Y2, Z1, Z2;
|
|
||||||
std::vector<Particle> particles;
|
|
||||||
std::ifstream in;
|
|
||||||
};
|
|
||||||
|
|
||||||
class Lamps_dump : public Lamps_base {
|
|
||||||
public:
|
|
||||||
Lamps_dump() = default;
|
|
||||||
~Lamps_dump() = default;
|
|
||||||
|
|
||||||
virtual int write(const std::string& filename) const override;
|
|
||||||
private:
|
|
||||||
virtual int load() override;
|
|
||||||
};
|
|
||||||
|
|
||||||
int Lamps_base::open(const std::string& filename) {
|
|
||||||
in.open(filename); if (!in.is_open()) return EXIT_FAILURE;
|
|
||||||
return load();
|
|
||||||
}
|
|
||||||
|
|
||||||
int Lamps_base::next() {
|
|
||||||
return load();
|
|
||||||
}
|
|
||||||
|
|
||||||
int Lamps_dump::write(const std::string& filename) const {
|
|
||||||
return EXIT_FAILURE;
|
|
||||||
}
|
|
||||||
|
|
||||||
int Lamps_dump::load() {
|
|
||||||
std::string inbuf; char* tmp_cptr;
|
|
||||||
open_stat = 0;
|
|
||||||
|
|
||||||
if (!getline(in, inbuf)) return EXIT_FAILURE;
|
|
||||||
if (!getline(in, inbuf)) return EXIT_FAILURE;
|
|
||||||
Nsteps = std::stoi(inbuf);
|
|
||||||
if (!getline(in, inbuf)) return EXIT_FAILURE;
|
|
||||||
if (!getline(in, inbuf)) return EXIT_FAILURE;
|
|
||||||
Natoms = std::stoi(inbuf);
|
|
||||||
particles.resize(Natoms);
|
|
||||||
if (!getline(in, inbuf)) return EXIT_FAILURE;
|
|
||||||
|
|
||||||
if (!getline(in, inbuf)) return EXIT_FAILURE;
|
|
||||||
X1 = strtof(inbuf.c_str(), &tmp_cptr);
|
|
||||||
X2 = strtof(tmp_cptr + 1, &tmp_cptr);
|
|
||||||
|
|
||||||
if (!getline(in, inbuf)) return EXIT_FAILURE;
|
|
||||||
Y1 = strtof(inbuf.c_str(), &tmp_cptr);
|
|
||||||
Y2 = strtof(tmp_cptr + 1, &tmp_cptr);
|
|
||||||
|
|
||||||
if (!getline(in, inbuf)) return EXIT_FAILURE;
|
|
||||||
Z1 = strtof(inbuf.c_str(), &tmp_cptr);
|
|
||||||
Z2 = strtof(tmp_cptr + 1, &tmp_cptr);
|
|
||||||
|
|
||||||
if (!getline(in, inbuf)) return EXIT_FAILURE;
|
|
||||||
for (int i = 0; i < Natoms; i++) {
|
|
||||||
if (!getline(in, inbuf)) return EXIT_FAILURE;
|
|
||||||
int id = strtol(inbuf.c_str(), &tmp_cptr, 10) - 1; // modify based on a particular file format
|
|
||||||
particles[id].type = static_cast<char>(strtol(tmp_cptr + 1, &tmp_cptr, 10));
|
|
||||||
particles[id].x = strtof(tmp_cptr + 1, &tmp_cptr);
|
|
||||||
particles[id].y = strtof(tmp_cptr + 1, &tmp_cptr);
|
|
||||||
particles[id].z = strtof(tmp_cptr + 1, &tmp_cptr);
|
|
||||||
particles[id].Es = strtof(tmp_cptr + 1, &tmp_cptr);
|
|
||||||
particles[id].Eb = strtof(tmp_cptr + 1, &tmp_cptr);
|
|
||||||
particles[id].Et = strtof(tmp_cptr + 1, &tmp_cptr);
|
|
||||||
particles[id].Ep = particles[id].Es + particles[id].Eb + particles[id].Et;
|
|
||||||
particles[id].Ek = strtof(tmp_cptr + 1, &tmp_cptr);
|
|
||||||
}
|
|
||||||
open_stat = true;
|
|
||||||
|
|
||||||
return EXIT_SUCCESS;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
int main(int argc, char* argv[]) {
|
|
||||||
std::string data_file = (argc > 1) ? argv[1] : data_file0;
|
|
||||||
std::string data_dump = (argc > 2) ? argv[2] : data_dump0;
|
|
||||||
std::string out_dir = (argc > 3) ? argv[3] : out_dir0;
|
|
||||||
//std::filesystem::remove_all(out_dir);
|
|
||||||
//std::filesystem::create_directories(out_dir);
|
|
||||||
|
|
||||||
//list of bonds
|
|
||||||
std::ifstream in(data_file);
|
|
||||||
if (!in.is_open()) {
|
|
||||||
std::cout << "cannot open " << data_file << std::endl;
|
|
||||||
return EXIT_FAILURE;
|
|
||||||
}
|
|
||||||
std::string buf;
|
|
||||||
std::string atoms_l = "Atoms";
|
|
||||||
while (std::getline(in, buf)){
|
|
||||||
if (buf == atoms_l) break;
|
|
||||||
if (in.eof()) return EXIT_FAILURE;
|
|
||||||
}
|
|
||||||
std::getline(in, buf);
|
|
||||||
char* tmp_cptr;
|
|
||||||
std::vector<std::array<int, 2>> bonds;
|
|
||||||
while (std::getline(in, buf)) {
|
|
||||||
if (in.eof() || buf.size() == 0) break;
|
|
||||||
int idx = strtol(buf.c_str(), &tmp_cptr, 10);
|
|
||||||
int m_idx = strtol(tmp_cptr + 1, &tmp_cptr, 10);
|
|
||||||
int type = strtol(tmp_cptr + 1, &tmp_cptr, 10);
|
|
||||||
int id1 = strtol(tmp_cptr + 1, &tmp_cptr, 10);
|
|
||||||
int id2 = strtol(tmp_cptr + 1, &tmp_cptr, 10);
|
|
||||||
if(id1 >= 0 && id2 >= 0) bonds.push_back({id1 - 1, id2 - 1});
|
|
||||||
}
|
|
||||||
|
|
||||||
//dump
|
|
||||||
Lamps_dump dump;
|
|
||||||
dump.open(data_dump);
|
|
||||||
if (!dump.is_open()) {
|
|
||||||
std::cout << "cannot open " << data_dump << std::endl;
|
|
||||||
return EXIT_FAILURE;
|
|
||||||
}
|
|
||||||
double Lx = dump.get_X2() - dump.get_X1();
|
|
||||||
double Ly = dump.get_Y2() - dump.get_Y1();
|
|
||||||
double Lz = dump.get_Z2() - dump.get_Z1();
|
|
||||||
while (1) {
|
|
||||||
std::ofstream out(out_dir + "/cnt" + std::to_string(dump.get_Nsteps()) + ".vtk");
|
|
||||||
if (!out.is_open()) {
|
|
||||||
std::cout << "cannot create " << out_dir + "/cnt" + std::to_string(dump.get_Nsteps()) + ".vtk" << std::endl;
|
|
||||||
std::cout << "create the output directory \"" << out_dir << "\" manually" << std::endl;
|
|
||||||
return EXIT_FAILURE;
|
|
||||||
}
|
|
||||||
out << "# vtk DataFile Version 3.0\n# \nASCII\n\nDATASET UNSTRUCTURED_GRID\n";
|
|
||||||
out << "POINTS " << dump.get_Natoms() << " float\n";
|
|
||||||
for (int i = 0; i < dump.get_Natoms(); i++) {
|
|
||||||
out << dump.get(i).x << " " << dump.get(i).y << " " << dump.get(i).z << " " << "\n";
|
|
||||||
}
|
|
||||||
|
|
||||||
int bond_count = 0;
|
|
||||||
for (int i = 0; i < bonds.size(); i++) {
|
|
||||||
double f1 = std::fabs(dump.get(bonds[i][0]).x - dump.get(bonds[i][1]).x);
|
|
||||||
double f2 = std::fabs(dump.get(bonds[i][0]).y - dump.get(bonds[i][1]).y);
|
|
||||||
double f3 = std::fabs(dump.get(bonds[i][0]).z - dump.get(bonds[i][1]).z);
|
|
||||||
if ((std::fabs(dump.get(bonds[i][0]).x - dump.get(bonds[i][1]).x) < 0.5*Lx)
|
|
||||||
&& (std::fabs(dump.get(bonds[i][0]).y - dump.get(bonds[i][1]).y) < 0.5*Ly)
|
|
||||||
&& (std::fabs(dump.get(bonds[i][0]).z - dump.get(bonds[i][1]).z) < 0.5*Lz))
|
|
||||||
bond_count++;
|
|
||||||
}
|
|
||||||
out << "\nCELLS " << bond_count << " " << 3*bond_count << "\n";
|
|
||||||
for (int i = 0; i < bonds.size(); i++) {
|
|
||||||
if ((std::fabs(dump.get(bonds[i][0]).x - dump.get(bonds[i][1]).x) < 0.5 * Lx)
|
|
||||||
&& (std::fabs(dump.get(bonds[i][0]).y - dump.get(bonds[i][1]).y) < 0.5 * Ly)
|
|
||||||
&& (std::fabs(dump.get(bonds[i][0]).z - dump.get(bonds[i][1]).z) < 0.5 * Lz))
|
|
||||||
out << "2 " << bonds[i][0] << " " << bonds[i][1] << " " << "\n";
|
|
||||||
}
|
|
||||||
|
|
||||||
out << "\nCELL_TYPES " << bond_count << "\n";
|
|
||||||
for (int i = 0; i < bond_count; i++) {
|
|
||||||
out << "4\n";
|
|
||||||
}
|
|
||||||
|
|
||||||
out << "\nPOINT_DATA " << dump.get_Natoms() << "\n";
|
|
||||||
out << "SCALARS Ep float 1\n";
|
|
||||||
out << "LOOKUP_TABLE default\n";
|
|
||||||
for (int i = 0; i < dump.get_Natoms(); i++) {
|
|
||||||
out << dump.get(i).Ep << "\n";
|
|
||||||
}
|
|
||||||
|
|
||||||
out << "\nSCALARS Ek float 1\n";
|
|
||||||
out << "LOOKUP_TABLE default\n";
|
|
||||||
for (int i = 0; i < dump.get_Natoms(); i++) {
|
|
||||||
out << dump.get(i).Ek << "\n";
|
|
||||||
}
|
|
||||||
|
|
||||||
out << "\nSCALARS Es float 1\n";
|
|
||||||
out << "LOOKUP_TABLE default\n";
|
|
||||||
for (int i = 0; i < dump.get_Natoms(); i++) {
|
|
||||||
out << dump.get(i).Es << "\n";
|
|
||||||
}
|
|
||||||
|
|
||||||
out << "\nSCALARS Eb float 1\n";
|
|
||||||
out << "LOOKUP_TABLE default\n";
|
|
||||||
for (int i = 0; i < dump.get_Natoms(); i++) {
|
|
||||||
out << dump.get(i).Eb << "\n";
|
|
||||||
}
|
|
||||||
|
|
||||||
out << "\nSCALARS Et float 1\n";
|
|
||||||
out << "LOOKUP_TABLE default\n";
|
|
||||||
for (int i = 0; i < dump.get_Natoms(); i++) {
|
|
||||||
out << dump.get(i).Et << "\n";
|
|
||||||
}
|
|
||||||
|
|
||||||
if (dump.next() != EXIT_SUCCESS) break;
|
|
||||||
}
|
|
||||||
return EXIT_SUCCESS;
|
|
||||||
}
|
|
||||||
@ -422,9 +422,6 @@ void ASSERT_ATOM_STATE_EQ(Atom *atom, const AtomState &expected)
|
|||||||
ASSERT_ARRAY_ALLOCATED(atom->edpd_temp, false);
|
ASSERT_ARRAY_ALLOCATED(atom->edpd_temp, false);
|
||||||
ASSERT_ARRAY_ALLOCATED(atom->edpd_flux, false);
|
ASSERT_ARRAY_ALLOCATED(atom->edpd_flux, false);
|
||||||
ASSERT_ARRAY_ALLOCATED(atom->edpd_cv, false);
|
ASSERT_ARRAY_ALLOCATED(atom->edpd_cv, false);
|
||||||
ASSERT_ARRAY_ALLOCATED(atom->length, false);
|
|
||||||
ASSERT_ARRAY_ALLOCATED(atom->buckling, false);
|
|
||||||
ASSERT_ARRAY_ALLOCATED(atom->bond_nt, false);
|
|
||||||
ASSERT_ARRAY_ALLOCATED(atom->contact_radius, false);
|
ASSERT_ARRAY_ALLOCATED(atom->contact_radius, false);
|
||||||
ASSERT_ARRAY_ALLOCATED(atom->smd_data_9, false);
|
ASSERT_ARRAY_ALLOCATED(atom->smd_data_9, false);
|
||||||
ASSERT_ARRAY_ALLOCATED(atom->smd_stress, false);
|
ASSERT_ARRAY_ALLOCATED(atom->smd_stress, false);
|
||||||
|
|||||||
Reference in New Issue
Block a user