update

doc/src/compute_mesont.rst

@@ -13,7 +13,7 @@ Syntax
 
 * 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
 """"""""
@@ -26,22 +26,19 @@ 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
 """"""""""""
@@ -57,7 +54,3 @@ Related commands
 
 **Default:** none
 
-
-.. _lws: http://lammps.sandia.gov
-.. _ld: Manual.html
-.. _lc: Commands_all.html

doc/src/pair_mesont_tpm.rst

@@ -12,9 +12,9 @@ Syntax
    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.
@@ -25,14 +25,14 @@ Examples
 
 .. 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
@@ -49,19 +49,19 @@ energy of the system:
    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
@@ -69,7 +69,7 @@ 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,
-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
@@ -88,7 +88,7 @@ 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:`[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
@@ -96,7 +96,7 @@ 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:`[2 <Zhigilei1>`, :ref:`4] <Zhigilei3>`.
+:ref:`(Zhigilei1 <Zhigilei1>`, :ref:`Zhigilei3) <Zhigilei3>`.
 
 
 ----------
@@ -106,15 +106,17 @@ 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:`[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.
 
@@ -142,10 +144,11 @@ 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.
+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
@@ -163,53 +166,49 @@ Related commands
 
 .. _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