update

  endif()

endforeach()

if(PKG_USER-MESONT)

  enable_language(Fortran)

  string(REGEX REPLACE "^USER-" "" PKG_LIB "USER-MESONT")

  string(TOLOWER "${PKG_LIB}" PKG_LIB)

  file(GLOB_RECURSE ${PKG_LIB}_SOURCES

    ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB}/[^.]*.f90)

  add_library(${PKG_LIB} STATIC ${${PKG_LIB}_SOURCES})

  list(APPEND LAMMPS_LINK_LIBS ${PKG_LIB})

  target_include_directories(${PKG_LIB} PUBLIC ${LAMMPS_LIB_SOURCE_DIR}/${PKG_LIB})

  #include(Packages/USER-MESONT)

  #list(APPEND DEFAULT_PACKAGES "USER-MESONT")

  set(USER-MESONT_SOURCES_DIR ${LAMMPS_SOURCE_DIR}/USER-MESONT)

  file(GLOB USER-MESONT_SOURCES ${USER-MESONT_SOURCES_DIR}/[^.]*.cpp)

  file(GLOB USER-MESONT_HEADERS ${USER-MESONT_SOURCES_DIR}/[^.]*.h)

  DetectBuildSystemConflict(${LAMMPS_SOURCE_DIR} ${USER-MESONT_SOURCES} ${USER-MESONT_HEADERS})

  RegisterStyles(${USER-MESONT_SOURCES_DIR})

  list(APPEND LIB_SOURCES ${USER-MESONT_SOURCES})

  include_directories(${USER-MESONT_SOURCES_DIR})

endif()

if(PKG_USER-AWPMD)

  target_link_libraries(awpmd ${LAPACK_LIBRARIES})

endif()

* ID, group-ID are documented in :doc:`compute <compute>` command

* mesont = style name of the compute command

* mode = one of estretch, ebend, etube, stretch_tot, ebend_tot, and etube_tot (see details below)

* mode = one of estretch, ebend, etube (see details below)

Examples

""""""""

Description

"""""""""""

These computes define computations for the per-node stretching (estretch),

bending (ebend), and intertube (etube) energies, as well as the total 

stretching (estretch_tot), bending (ebend_tot), and intertube (etube_tot) 

energies for each atom (node) in a group. The evaluated value is selected by 

a parameter passed to the compute: estretch, ebend, etube, estretch_tot, 

ebend_tot, and etube_tot.

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 a parameter passed to the compute: estretch, 

ebend, etube.

**Output info:**

These computes calculate per-node (per-atom) vectors (estretch, ebend, etube), 

which can be accessed by any command that uses per-atom values from a 

compute as input, and global scalars (stretch_tot, ebend_tot, and etube_tot). 

See the :doc:`Howto output <Howto_output>` doc page for an overview of LAMMPS 

output options.

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>` doc page for an overview of 

LAMMPS output options.

The per-atom vector values will be in energy :doc:`units <units>`.

The computed values are provided in energy :doc:`units <units>`.

Restrictions

""""""""""""

**Default:** none

.. _lws: http://lammps.sandia.gov

.. _ld: Manual.html

.. _lc: Commands_all.html

   pair_style mesont/tpm cut table_path BendingMode TPMType 

* cut = the cutoff distance

* table_path = the path to the potential table, the default value is ./

* BendingMode = the parameter defining the type of the bending potential for nanotubes: 0 - harmonic bending :ref:`[1] <Srivastava>`, 1 - anharmonic potential of bending and bending-buckling :ref:`[2] <Zhigilei1>`

* TPMType = the parameter determining the type of the inter-tube interaction term: 0 - segment-segment approach, 1 - segment-chain approach :ref:`[3 <Zhigilei2>`, :ref:`4] <Zhigilei3>`

* 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.

.. parsed-literal::

   pair_style mesont/tpm 25.0 ./ 0 0

   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:`[1] <Srivastava>`.

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

   U = U_{str} + U_{bnd} + U_{vdW}

where :math:`U_{str}`  is the harmonic potential describing the stretching of nanotube

:ref:`[1] <Srivastava>`, :math:`U_{bnd}`  is the potential for nanotube bending

:ref:`[1] <Srivastava>` and bending-buckling :ref:`[2] <Zhigilei1>`, and

: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:`[3 <Zhigilei2>`, :ref:`4] <Zhigilei3>`. The stretching energy, :math:`U_{str}` ,

: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:`[3] <Zhigilei2>`.

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:`[4] <Zhigilei3>`. This potential approximates the results of direct

: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

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,

CNT\_10\_10, is tabulated for (10,10) nanotubes.

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

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:`[3] <Zhigilei2>`. Finally, 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

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:`[2 <Zhigilei1>`, :ref:`4] <Zhigilei3>`.

:ref:`(Zhigilei1 <Zhigilei1>`, :ref:`Zhigilei3) <Zhigilei3>`.

----------

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:`[2 <Zhigilei1>`, :ref:`4 <Zhigilei3>` - :ref:`7] <Zhigilei6>`. With

: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:`[8 <Zhigilei7>` - :ref:`10] <Zhigilei9>`. The methods for modeling of

: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:`[11] <Zhigilei10>` and mesoscopic description of covalent cross-links

between nanotubes :ref:`[12] <Banna>` have also been developed but are not

: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 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.

segments. Because of the use of extended chain concept at CNT ends, the recommended 

cutoff is 3L.

The TPMSSTP.xrs and TPMA.xrs potential files provided with LAMMPS (see the

potentials directory) are parameterized for metal :doc:`units <units>`.

The MESONT-TABTP_10_10.xrs potential file provided with LAMMPS (see the

potentials directory) 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 TPMSSTP.xrs and TPMA.xrs potential files

with coefficients listed in appropriate units, if your simulation

.. _Srivastava:

**[1]** Zhigilei, Wei, Srivastava, Phys. Rev. B 71, 165417 (2005).

**(Srivastava)** Zhigilei, Wei, Srivastava, Phys. Rev. B 71, 165417 (2005).

.. _Zhigilei1:

**[2]** Volkov and Zhigilei, ACS Nano 4, 6187 (2010).

**(Zhigilei1)** Volkov and Zhigilei, ACS Nano 4, 6187 (2010).

.. _Zhigilei2:

**[3]** Volkov, Simov, Zhigilei, ASME paper IMECE2008, 68021 (2008).

**(Zhigilei2)** Volkov, Simov, Zhigilei, ASME paper IMECE2008, 68021 (2008).

.. _Zhigilei3:

**[4]** Volkov, Zhigilei, J. Phys. Chem. C 114, 5513 (2010).

**(Zhigilei3)** Volkov, Zhigilei, J. Phys. Chem. C 114, 5513 (2010).

.. _Zhigilei4:

**[5]** Wittmaack, Banna, Volkov, Zhigilei, Carbon 130, 69 (2018).

**(Zhigilei4)** Wittmaack, Banna, Volkov, Zhigilei, Carbon 130, 69 (2018).

.. _Zhigilei5:

**[6]** Wittmaack, Volkov, Zhigilei, Compos. Sci. Technol. 166, 66 (2018).

**(Zhigilei5)** Wittmaack, Volkov, Zhigilei, Compos. Sci. Technol. 166, 66 (2018).

.. _Zhigilei6:

**[7]** Wittmaack, Volkov, Zhigilei, Carbon 143, 587 (2019).

**(Zhigilei6)** Wittmaack, Volkov, Zhigilei, Carbon 143, 587 (2019).

.. _Zhigilei7:

**[8]** Volkov, Zhigilei, Phys. Rev. Lett. 104, 215902 (2010).

**(Zhigilei7)** Volkov, Zhigilei, Phys. Rev. Lett. 104, 215902 (2010).

.. _Zhigilei8:

**[9]** Volkov, Shiga, Nicholson, Shiomi, Zhigilei, J. Appl. Phys. 111, 053501 (2012).

**(Zhigilei8)** Volkov, Shiga, Nicholson, Shiomi, Zhigilei, J. Appl. Phys. 111, 053501 (2012).

.. _Zhigilei9:

**[10]** Volkov, Zhigilei, Appl. Phys. Lett. 101, 043113 (2012).

**(Zhigilei9)** Volkov, Zhigilei, Appl. Phys. Lett. 101, 043113 (2012).

.. _Zhigilei10:

**[11]** Jacobs, Nicholson, Zemer, Volkov, Zhigilei, Phys. Rev. B 86, 165414 (2012).

**(Zhigilei10)** Jacobs, Nicholson, Zemer, Volkov, Zhigilei, Phys. Rev. B 86, 165414 (2012).

.. _Banna:

**[12]** Volkov, Banna, Comp. Mater. Sci. 176, 109410 (2020).

**(Banna)** Volkov, Banna, Comp. Mater. Sci. 176, 109410 (2020).

.. _lws: http://lammps.sandia.gov

.. _ld: Manual.html

.. _lc: Commands_all.html

"film" is an example with a film composed of 396 200-nm-long 

  nanotubes (79596 nodes).

processors      1 1 *

newton          on

units           metal

lattice         sc 1.0

atom_style      mesont

#               cut, path, BendingMode, TPMType

pair_style      mesont/tpm 45.0 ../../../potentials/CNT_10_10 0 0

pair_style      mesont/tpm 45.0 ../../../potentials/MESONT-TABTP_10_10.xrs 0 0

read_data       data.bundle

pair_coeff      * *

compute         Eb all mesont ebend

compute         Et all mesont etube

compute         B all property/atom buckling

compute         Es_tot all mesont estretch_tot

compute         Eb_tot all mesont ebend_tot

compute         Et_tot all mesont etube_tot

thermo_style    custom step time temp etotal ke pe c_Es_tot c_Eb_tot c_Et_tot

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