Merge pull request #1841 from phankl/stable
Mesoscopic potential for carbon nanotubes
This commit is contained in:
Axel Kohlmeyer
@ -174,6 +174,7 @@ OPT.
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* :doc:`meam/c <pair_meamc>`
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* :doc:`meam/c <pair_meamc>`
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* :doc:`meam/spline (o) <pair_meam_spline>`
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* :doc:`meam/spline (o) <pair_meam_spline>`
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* :doc:`meam/sw/spline <pair_meam_sw_spline>`
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* :doc:`meam/sw/spline <pair_meam_sw_spline>`
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* :doc:`mesocnt <pair_mesocnt>`
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* :doc:`mgpt <pair_mgpt>`
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* :doc:`mgpt <pair_mgpt>`
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* :doc:`mie/cut (g) <pair_mie>`
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* :doc:`mie/cut (g) <pair_mie>`
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* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
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* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>`
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@ -257,4 +258,3 @@ OPT.
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* :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
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* :doc:`yukawa/colloid (go) <pair_yukawa_colloid>`
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* :doc:`zbl (gko) <pair_zbl>`
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* :doc:`zbl (gko) <pair_zbl>`
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*
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*
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*
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161
doc/src/pair_mesocnt.rst
Normal file
161
doc/src/pair_mesocnt.rst
Normal file
@ -0,0 +1,161 @@
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.. index:: pair\_style mesocnt
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pair\_style mesocnt command
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===========================
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Syntax
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""""""
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.. parsed-literal::
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pair_style mesocnt
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Examples
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""""""""
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.. parsed-literal::
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pair_style mesocnt
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pair_coeff \* \* 10_10.cnt
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Description
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"""""""""""
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Style *mesocnt* implements a mesoscopic potential
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for the interaction of carbon nanotubes (CNTs). In this potential,
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CNTs are modelled as chains of cylindrical segments in which
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each infinitesimal surface element interacts with all other
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CNT surface elements with the Lennard-Jones (LJ) term adopted from
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the :doc:`airebo <pair_airebo>` style. The interaction energy
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is then computed by integrating over the surfaces of all interacting
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CNTs.
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The potential is based on interactions between one cylindrical
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segment and infinitely or semi-infinitely long CNTs as described
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in :ref:`(Volkov1) <Volkov1>`. Chains of segments are
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converted to these (semi-)infinite CNTs bases on an approximate
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chain approach outlined in :ref:`(Volkov2) <Volkov2>`.
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This allows to simplify the computation of the interactions
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significantly and reduces the computational times to the
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same order of magnitude as for regular bead spring models
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where beads interact with the standard :doc:`pair_lj/cut <pair_lj>`
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potential.
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In LAMMPS, cylindrical segments are represented by bonds. Each
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segment is defined by its two end points ("nodes") which correspond
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to atoms in LAMMPS. For the exact functional form of the potential
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and implementation details, the reader is referred to the
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original papers :ref:`(Volkov1) <Volkov1>` and
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:ref:`(Volkov2) <Volkov2>`.
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The potential requires tabulated data provided in a single ASCII
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text file specified in the :doc:`pair\_coeff <pair_coeff>` command.
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The first line of the file provides a time stamp and
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general information. The second line lists four integers giving
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the number of data points provided in the subsequent four
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data tables. The third line lists four floating point numbers:
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the CNT radius R, the LJ parameter sigma and two numerical
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parameters delta1 and delta2. These four parameters are given
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in Angstroms. This is followed by four data tables each separated
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by a single empty line. The first two tables have two columns
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and list the parameters uInfParallel and Gamma respectively.
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The last two tables have three columns giving data on a quadratic
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array and list the parameters Phi and uSemiParallel respectively.
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uInfParallel and uSemiParallel are given in eV/Angstrom, Phi is
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given in eV and Gamma is unitless.
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Potential files for CNTs can be readily generated using the freely
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available code provided on
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.. parsed-literal::
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https://github.com/phankl/cntpot
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Using the same approach, it should also be possible to
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generate potential files for other 1D systems such as
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boron nitride nanotubes.
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.. note::
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LAMMPS comes with one *mesocnt* style potential file
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where the default number of data points per table is 1001.
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This is sufficient for NVT simulations. For proper energy
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conservation, we recommend using a potential file where
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the resolution for Phi is at least 2001 data points.
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.. note::
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The *mesocnt* style requires CNTs to be represented
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as a chain of atoms connected by bonds. Atoms need
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to be numbered consecutively within one chain.
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Atoms belonging to different CNTs need to be assigned
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different molecule IDs.
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A full summary of the method and LAMMPS implementation details
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is expected to soon become available in Computer Physics
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Communications.
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----------
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**Mixing, shift, table, tail correction, restart, rRESPA info**\ :
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This pair style does not support mixing.
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This pair style does not support the :doc:`pair\_modify <pair_modify>`
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shift, table, and tail options.
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The *mesocnt* pair style do not write their information to :doc:`binary restart files <restart>`,
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since it is stored in tabulated potential files.
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Thus, you need to re-specify the pair\_style and pair\_coeff commands in
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an input script that reads a restart file.
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This pair style can only be used via the *pair* keyword of the
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:doc:`run\_style respa <run_style>` command. They do not support the
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*inner*\ , *middle*\ , *outer* keywords.
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----------
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Restrictions
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""""""""""""
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This style is part of the USER-MISC package. It is only
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enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` doc page for more info.
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This pair potential requires the :doc:`newton <newton>` setting to be
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"on" for pair interactions.
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Related commands
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""""""""""""""""
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:doc:`pair\_coeff <pair_coeff>`
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**Default:** none
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----------
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.. _Volkov1:
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**(Volkov1)** Volkov and Zhigilei, J Phys Chem C, 114, 5513 (2010).
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.. _Volkov2:
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**(Volkov2)** Volkov, Simov and Zhigilei, APS Meeting Abstracts,
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Q31.013 (2008).
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.. _lws: http://lammps.sandia.gov
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.. _ld: Manual.html
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.. _lc: Commands_all.html
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@ -244,6 +244,7 @@ accelerated styles exist.
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* :doc:`meam/c <pair_meamc>` - modified embedded atom method (MEAM) in C
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* :doc:`meam/c <pair_meamc>` - modified embedded atom method (MEAM) in C
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* :doc:`meam/spline <pair_meam_spline>` - splined version of MEAM
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* :doc:`meam/spline <pair_meam_spline>` - splined version of MEAM
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* :doc:`meam/sw/spline <pair_meam_sw_spline>` - splined version of MEAM with a Stillinger-Weber term
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* :doc:`meam/sw/spline <pair_meam_sw_spline>` - splined version of MEAM with a Stillinger-Weber term
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* :doc:`mesocnt <pair_mesocnt>` - mesoscale model for (carbon) nanotubes
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* :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
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* :doc:`mgpt <pair_mgpt>` - simplified model generalized pseudopotential theory (MGPT) potential
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* :doc:`mie/cut <pair_mie>` - Mie potential
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* :doc:`mie/cut <pair_mie>` - Mie potential
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* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
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* :doc:`mm3/switch3/coulgauss/long <pair_mm3_switch3_coulgauss_long>` - smoothed MM3 vdW potential with Gaussian electrostatics
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@ -1673,6 +1673,7 @@ Mersenne
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Merz
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Merz
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meshless
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meshless
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meso
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meso
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mesocnt
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mesoparticle
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mesoparticle
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mesoscale
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mesoscale
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mesoscopic
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mesoscopic
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@ -2587,6 +2588,7 @@ Sikandar
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Silbert
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Silbert
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Silling
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Silling
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Sim
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Sim
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Simov
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Simul
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Simul
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simulations
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simulations
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Sinnott
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Sinnott
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@ -2921,6 +2923,7 @@ UEF
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ufm
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ufm
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Uhlenbeck
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Uhlenbeck
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Ui
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Ui
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uInfParallel
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uk
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uk
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ul
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ul
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ulb
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ulb
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@ -2961,6 +2964,7 @@ upto
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Urbakh
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Urbakh
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Urbana
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Urbana
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usec
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usec
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uSemiParallel
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userguide
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userguide
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username
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username
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usr
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usr
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@ -3028,6 +3032,7 @@ VMDHOME
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vn
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vn
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Voigt
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Voigt
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volfactor
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volfactor
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Volkov
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Volpe
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Volpe
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volpress
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volpress
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volumetric
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volumetric
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@ -3180,6 +3185,7 @@ zflag
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Zhang
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Zhang
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Zhen
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Zhen
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zhi
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zhi
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Zhigilei
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Zhou
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Zhou
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Zhu
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Zhu
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zi
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zi
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1
examples/USER/misc/mesocnt/C_10_10.mesocnt
Symbolic link
1
examples/USER/misc/mesocnt/C_10_10.mesocnt
Symbolic link
@ -0,0 +1 @@
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../../../../potentials/C_10_10.mesocnt
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1521
examples/USER/misc/mesocnt/cnt.data
Normal file
1521
examples/USER/misc/mesocnt/cnt.data
Normal file
File diff suppressed because it is too large
Load Diff
38
examples/USER/misc/mesocnt/in.cnt
Normal file
38
examples/USER/misc/mesocnt/in.cnt
Normal file
@ -0,0 +1,38 @@
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#Initialisation
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units nano
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dimension 3
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boundary p p p
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atom_style full
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comm_modify cutoff 11.0
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neighbor 7.80 bin
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newton on
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#Read data
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read_data cnt.data
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replicate 1 2 2
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#Force field
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bond_style harmonic
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bond_coeff 1 268896.77 2.0
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angle_style harmonic
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angle_coeff 1 46562.17 180.0
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pair_style mesocnt
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pair_coeff * * C_10_10.mesocnt
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#Output
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thermo 1000
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dump xyz all xyz 1000 cnt.xyz
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#Simulation setup
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timestep 1.0e-05
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#Nose-Hoover thermostat
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fix nvt all nvt temp 300 300 0.001
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run 10000
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126
examples/USER/misc/mesocnt/log.9Jan20.cnt.g++.1
Normal file
126
examples/USER/misc/mesocnt/log.9Jan20.cnt.g++.1
Normal file
@ -0,0 +1,126 @@
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LAMMPS (09 Jan 2020)
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#Initialisation
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units nano
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dimension 3
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boundary p p p
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atom_style full
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comm_modify cutoff 11.0
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neighbor 7.80 bin
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newton on
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#Read data
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read_data cnt.data
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orthogonal box = (0 0 0) to (600 600 60)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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500 atoms
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scanning bonds ...
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1 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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498 bonds
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reading angles ...
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|
496 angles
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|
2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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|
4 = max # of 1-4 neighbors
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|
6 = max # of special neighbors
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|
special bonds CPU = 0.000180006 secs
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|
read_data CPU = 0.00125766 secs
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|
replicate 1 2 2
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|
orthogonal box = (0 0 0) to (600 1200 120)
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|
1 by 1 by 1 MPI processor grid
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|
2000 atoms
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||||||
|
1992 bonds
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||||||
|
1984 angles
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|
2 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
4 = max # of 1-4 neighbors
|
||||||
|
6 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.00054121 secs
|
||||||
|
replicate CPU = 0.000902414 secs
|
||||||
|
|
||||||
|
#Force field
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
bond_coeff 1 268896.77 2.0
|
||||||
|
|
||||||
|
angle_style harmonic
|
||||||
|
angle_coeff 1 46562.17 180.0
|
||||||
|
|
||||||
|
pair_style mesocnt
|
||||||
|
pair_coeff * * 10_10.cnt
|
||||||
|
Reading potential file 10_10.cnt with DATE: 2020-01-13
|
||||||
|
|
||||||
|
#Output
|
||||||
|
|
||||||
|
thermo 1000
|
||||||
|
dump xyz all xyz 1000 cnt.xyz
|
||||||
|
|
||||||
|
#Simulation setup
|
||||||
|
|
||||||
|
timestep 1.0e-05
|
||||||
|
|
||||||
|
#Nose-Hoover thermostat
|
||||||
|
fix nvt all nvt temp 300 300 0.001
|
||||||
|
run 10000
|
||||||
|
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:226)
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 10.177
|
||||||
|
ghost atom cutoff = 11
|
||||||
|
binsize = 5.0885, bins = 118 236 24
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair mesocnt, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 11.21 | 11.21 | 11.21 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -4632.0136 5.7939238e-17 -4632.0136 -0.00015032304
|
||||||
|
1000 298.82235 -19950.274 13208.089 5628.7024 -0.0056205182
|
||||||
|
2000 300.43933 -28320.212 11980.296 -3902.0877 -0.0045324757
|
||||||
|
3000 300.4263 -36049.855 11338.405 -12274.161 -0.0018833539
|
||||||
|
4000 299.13368 -43471.21 11926.882 -19160.553 -0.00043030866
|
||||||
|
5000 293.77858 -50083.893 12334.927 -25586.884 -0.0015653738
|
||||||
|
6000 296.4851 -56330.135 12325.63 -31730.376 -0.0012795986
|
||||||
|
7000 298.20879 -62120.359 12582.297 -37192.574 -0.0013845796
|
||||||
|
8000 299.45547 -67881.692 13058.926 -42425.669 -0.00021100885
|
||||||
|
9000 301.82622 -73333.698 13598.257 -47240.197 -0.0006009197
|
||||||
|
10000 307.16873 -78292.306 13818.929 -51756.96 -0.0005609903
|
||||||
|
Loop time of 4.0316 on 1 procs for 10000 steps with 2000 atoms
|
||||||
|
|
||||||
|
Performance: 2143.072 ns/day, 0.011 hours/ns, 2480.408 timesteps/s
|
||||||
|
99.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 2.5955 | 2.5955 | 2.5955 | 0.0 | 64.38
|
||||||
|
Bond | 1.1516 | 1.1516 | 1.1516 | 0.0 | 28.57
|
||||||
|
Neigh | 0.001163 | 0.001163 | 0.001163 | 0.0 | 0.03
|
||||||
|
Comm | 0.0019577 | 0.0019577 | 0.0019577 | 0.0 | 0.05
|
||||||
|
Output | 0.020854 | 0.020854 | 0.020854 | 0.0 | 0.52
|
||||||
|
Modify | 0.21637 | 0.21637 | 0.21637 | 0.0 | 5.37
|
||||||
|
Other | | 0.04409 | | | 1.09
|
||||||
|
|
||||||
|
Nlocal: 2000 ave 2000 max 2000 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0 ave 0 max 0 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: 13320 ave 13320 max 13320 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 13320
|
||||||
|
Ave neighs/atom = 6.66
|
||||||
|
Ave special neighs/atom = 5.952
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:05
|
||||||
126
examples/USER/misc/mesocnt/log.9Jan20.cnt.g++.4
Normal file
126
examples/USER/misc/mesocnt/log.9Jan20.cnt.g++.4
Normal file
@ -0,0 +1,126 @@
|
|||||||
|
LAMMPS (09 Jan 2020)
|
||||||
|
#Initialisation
|
||||||
|
|
||||||
|
units nano
|
||||||
|
dimension 3
|
||||||
|
boundary p p p
|
||||||
|
atom_style full
|
||||||
|
comm_modify cutoff 11.0
|
||||||
|
neighbor 7.80 bin
|
||||||
|
newton on
|
||||||
|
|
||||||
|
#Read data
|
||||||
|
|
||||||
|
read_data cnt.data
|
||||||
|
orthogonal box = (0 0 0) to (600 600 60)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
500 atoms
|
||||||
|
scanning bonds ...
|
||||||
|
1 = max bonds/atom
|
||||||
|
scanning angles ...
|
||||||
|
1 = max angles/atom
|
||||||
|
reading bonds ...
|
||||||
|
498 bonds
|
||||||
|
reading angles ...
|
||||||
|
496 angles
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
4 = max # of 1-4 neighbors
|
||||||
|
6 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.000354767 secs
|
||||||
|
read_data CPU = 0.00286365 secs
|
||||||
|
replicate 1 2 2
|
||||||
|
orthogonal box = (0 0 0) to (600 1200 120)
|
||||||
|
1 by 4 by 1 MPI processor grid
|
||||||
|
2000 atoms
|
||||||
|
1992 bonds
|
||||||
|
1984 angles
|
||||||
|
2 = max # of 1-2 neighbors
|
||||||
|
2 = max # of 1-3 neighbors
|
||||||
|
4 = max # of 1-4 neighbors
|
||||||
|
6 = max # of special neighbors
|
||||||
|
special bonds CPU = 0.00019598 secs
|
||||||
|
replicate CPU = 0.00055337 secs
|
||||||
|
|
||||||
|
#Force field
|
||||||
|
|
||||||
|
bond_style harmonic
|
||||||
|
bond_coeff 1 268896.77 2.0
|
||||||
|
|
||||||
|
angle_style harmonic
|
||||||
|
angle_coeff 1 46562.17 180.0
|
||||||
|
|
||||||
|
pair_style mesocnt
|
||||||
|
pair_coeff * * 10_10.cnt
|
||||||
|
Reading potential file 10_10.cnt with DATE: 2020-01-13
|
||||||
|
|
||||||
|
#Output
|
||||||
|
|
||||||
|
thermo 1000
|
||||||
|
dump xyz all xyz 1000 cnt.xyz
|
||||||
|
|
||||||
|
#Simulation setup
|
||||||
|
|
||||||
|
timestep 1.0e-05
|
||||||
|
|
||||||
|
#Nose-Hoover thermostat
|
||||||
|
fix nvt all nvt temp 300 300 0.001
|
||||||
|
run 10000
|
||||||
|
WARNING: Using a manybody potential with bonds/angles/dihedrals and special_bond exclusions (src/pair.cpp:226)
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 10.177
|
||||||
|
ghost atom cutoff = 11
|
||||||
|
binsize = 5.0885, bins = 118 236 24
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair mesocnt, perpetual
|
||||||
|
attributes: full, newton on
|
||||||
|
pair build: full/bin
|
||||||
|
stencil: full/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 2.725 | 2.725 | 2.725 Mbytes
|
||||||
|
Step Temp E_pair E_mol TotEng Press
|
||||||
|
0 0 -4632.0136 5.7939238e-17 -4632.0136 -0.00015032304
|
||||||
|
1000 298.82235 -19950.274 13208.089 5628.7024 -0.0056205182
|
||||||
|
2000 300.43861 -28320.205 11980.287 -3902.1202 -0.0045324738
|
||||||
|
3000 300.41076 -36049.308 11339.149 -12273.513 -0.0018848513
|
||||||
|
4000 299.13326 -43471.424 11927.668 -19159.998 -0.00042845101
|
||||||
|
5000 293.78857 -50083.216 12333.969 -25586.752 -0.0015664633
|
||||||
|
6000 296.45482 -56329.621 12326.419 -31730.328 -0.0012773686
|
||||||
|
7000 298.19097 -62119.086 12581.4 -37192.937 -0.0013862831
|
||||||
|
8000 299.46424 -67880.989 13057.62 -42425.908 -0.00020874264
|
||||||
|
9000 301.80677 -73332.208 13597.237 -47240.532 -0.00060074773
|
||||||
|
10000 307.17104 -78292.912 13818.889 -51757.51 -0.00056148282
|
||||||
|
Loop time of 1.23665 on 4 procs for 10000 steps with 2000 atoms
|
||||||
|
|
||||||
|
Performance: 6986.607 ns/day, 0.003 hours/ns, 8086.351 timesteps/s
|
||||||
|
96.1% CPU use with 4 MPI tasks x no OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 0.66321 | 0.68439 | 0.71413 | 2.5 | 55.34
|
||||||
|
Bond | 0.28561 | 0.29434 | 0.30976 | 1.7 | 23.80
|
||||||
|
Neigh | 0.00043321 | 0.00043637 | 0.00043917 | 0.0 | 0.04
|
||||||
|
Comm | 0.026656 | 0.05346 | 0.097228 | 12.7 | 4.32
|
||||||
|
Output | 0.0070224 | 0.0073031 | 0.0081415 | 0.6 | 0.59
|
||||||
|
Modify | 0.12769 | 0.15394 | 0.18743 | 6.5 | 12.45
|
||||||
|
Other | | 0.04279 | | | 3.46
|
||||||
|
|
||||||
|
Nlocal: 500 ave 504 max 496 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Nghost: 22 ave 24 max 20 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
Neighs: 0 ave 0 max 0 min
|
||||||
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||||
|
FullNghs: 3330 ave 3368 max 3292 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||||
|
|
||||||
|
Total # of neighbors = 13320
|
||||||
|
Ave neighs/atom = 6.66
|
||||||
|
Ave special neighs/atom = 5.952
|
||||||
|
Neighbor list builds = 1
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:02
|
||||||
2006011
potentials/C_10_10.mesocnt
Normal file
2006011
potentials/C_10_10.mesocnt
Normal file
File diff suppressed because it is too large
Load Diff
@ -89,6 +89,7 @@ lcbop LCBOP long-range bond-order potential
|
|||||||
meam modified EAM (MEAM) library and individual elements/alloys
|
meam modified EAM (MEAM) library and individual elements/alloys
|
||||||
meam.spline modified EAM (MEAM) spline potential
|
meam.spline modified EAM (MEAM) spline potential
|
||||||
meam.sw.spline modified EAM (MEAM) Stillinger-Weber spline potential
|
meam.sw.spline modified EAM (MEAM) Stillinger-Weber spline potential
|
||||||
|
mesocnt mesoscopic carbon nanotube (CNT) potential
|
||||||
mgpt model generalized pseudopotential theory (MGPT) potential
|
mgpt model generalized pseudopotential theory (MGPT) potential
|
||||||
nb3b.harmonic nonbonded 3-body harmonic potential
|
nb3b.harmonic nonbonded 3-body harmonic potential
|
||||||
poly polymorphic 3-body potential
|
poly polymorphic 3-body potential
|
||||||
|
|||||||
@ -91,6 +91,7 @@ pair_style kolmogorov/crespi/full, Wengen Ouyang (Tel Aviv University), w.g.ouya
|
|||||||
pair_style kolmogorov/crespi/z, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Feb 17
|
pair_style kolmogorov/crespi/z, Jaap Kroes (Radboud U), jaapkroes at gmail dot com, 28 Feb 17
|
||||||
pair_style meam/spline, Alexander Stukowski (LLNL), alex at stukowski.com, 1 Feb 12
|
pair_style meam/spline, Alexander Stukowski (LLNL), alex at stukowski.com, 1 Feb 12
|
||||||
pair_style meam/sw/spline, Robert Rudd (LLNL), robert.rudd at llnl.gov, 1 Oct 12
|
pair_style meam/sw/spline, Robert Rudd (LLNL), robert.rudd at llnl.gov, 1 Oct 12
|
||||||
|
pair_style mesocnt, Philipp Kloza (U Cambridge), pak37 at cam.ac.uk, 15 Jan 20
|
||||||
pair_style morse/smooth/linear, Stefan Paquay (TU Eindhoven), stefanpaquay at gmail.com, 29 Feb 16
|
pair_style morse/smooth/linear, Stefan Paquay (TU Eindhoven), stefanpaquay at gmail.com, 29 Feb 16
|
||||||
pair_style srp, Tim Sirk, tim.sirk at us.army.mil, 21 Nov 14
|
pair_style srp, Tim Sirk, tim.sirk at us.army.mil, 21 Nov 14
|
||||||
pair_style tersoff/table, Luca Ferraro, luca.ferraro@caspur.it, 1 Dec 11
|
pair_style tersoff/table, Luca Ferraro, luca.ferraro@caspur.it, 1 Dec 11
|
||||||
|
|||||||
1837
src/USER-MISC/pair_mesocnt.cpp
Normal file
1837
src/USER-MISC/pair_mesocnt.cpp
Normal file
File diff suppressed because it is too large
Load Diff
170
src/USER-MISC/pair_mesocnt.h
Normal file
170
src/USER-MISC/pair_mesocnt.h
Normal file
@ -0,0 +1,170 @@
|
|||||||
|
#ifdef PAIR_CLASS
|
||||||
|
|
||||||
|
PairStyle(mesocnt, PairMesoCNT)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_PAIR_MESOCNT_H
|
||||||
|
#define LMP_PAIR_MESOCNT_H
|
||||||
|
|
||||||
|
#include "pair.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class PairMesoCNT : public Pair {
|
||||||
|
public:
|
||||||
|
PairMesoCNT(class LAMMPS *);
|
||||||
|
~PairMesoCNT();
|
||||||
|
void compute(int, int);
|
||||||
|
void settings(int, char **);
|
||||||
|
void coeff(int, char **);
|
||||||
|
void init_style();
|
||||||
|
double init_one(int, int);
|
||||||
|
|
||||||
|
protected:
|
||||||
|
int uinf_points,gamma_points,phi_points,usemi_points;
|
||||||
|
int nlocal_size,reduced_neigh_size;
|
||||||
|
int *reduced_nlist,*numchainlist;
|
||||||
|
int **reduced_neighlist,**nchainlist,**endlist;
|
||||||
|
int ***chainlist;
|
||||||
|
|
||||||
|
double ang,ang_inv,eunit,funit;
|
||||||
|
double delta1,delta2;
|
||||||
|
double r,rsq,d,rc,rcsq,rc0,cutoff,cutoffsq;
|
||||||
|
double r_ang,rsq_ang,d_ang,rc_ang,rcsq_ang,cutoff_ang,cutoffsq_ang;
|
||||||
|
double sig,sig_ang,comega,ctheta;
|
||||||
|
double hstart_uinf,hstart_gamma,
|
||||||
|
hstart_phi,psistart_phi,hstart_usemi,xistart_usemi;
|
||||||
|
double delh_uinf,delh_gamma,delh_phi,delpsi_phi,delh_usemi,delxi_usemi;
|
||||||
|
|
||||||
|
double p1[3],p2[3],p[3],m[3];
|
||||||
|
double *param,*w,*wnode;
|
||||||
|
double **dq_w;
|
||||||
|
double ***q1_dq_w,***q2_dq_w;
|
||||||
|
double *uinf_data,*gamma_data,**phi_data,**usemi_data;
|
||||||
|
double **uinf_coeff,**gamma_coeff,****phi_coeff,****usemi_coeff;
|
||||||
|
double **flocal,**fglobal,**basis;
|
||||||
|
|
||||||
|
char *file;
|
||||||
|
|
||||||
|
void allocate();
|
||||||
|
void bond_neigh();
|
||||||
|
void neigh_common(int, int, int &, int *);
|
||||||
|
void chain_split(int *, int, int &, int **, int *, int *);
|
||||||
|
void sort(int *, int);
|
||||||
|
void read_file();
|
||||||
|
void read_data(FILE *, double *, double &, double &, int);
|
||||||
|
void read_data(FILE *, double **, double &, double &,
|
||||||
|
double &, double &, int);
|
||||||
|
|
||||||
|
void spline_coeff(double *, double **, double, int);
|
||||||
|
void spline_coeff(double **, double ****, double, double, int);
|
||||||
|
|
||||||
|
double spline(double, double, double, double **, int);
|
||||||
|
double dspline(double, double, double, double **, int);
|
||||||
|
double spline(double, double, double, double, double, double,
|
||||||
|
double ****, int);
|
||||||
|
double dxspline(double, double, double, double, double, double,
|
||||||
|
double ****, int);
|
||||||
|
double dyspline(double, double, double, double, double, double,
|
||||||
|
double ****, int);
|
||||||
|
|
||||||
|
void geometry(const double *, const double *, const double *,
|
||||||
|
const double *, const double *,
|
||||||
|
double *, double *, double *, double **);
|
||||||
|
void weight(const double *, const double *, const double *,
|
||||||
|
const double *, double &, double *, double *,
|
||||||
|
double *, double *);
|
||||||
|
|
||||||
|
void finf(const double *, double &, double **);
|
||||||
|
void fsemi(const double *, double &, double &, double **);
|
||||||
|
|
||||||
|
// inlined functions for efficiency
|
||||||
|
|
||||||
|
inline double heaviside(double x) {
|
||||||
|
if (x > 0) return 1.0;
|
||||||
|
else return 0.0;
|
||||||
|
}
|
||||||
|
|
||||||
|
inline double s(double x) {
|
||||||
|
return heaviside(-x) + heaviside(x)*heaviside(1-x)*(1 - x*x*(3 - 2*x));
|
||||||
|
}
|
||||||
|
|
||||||
|
inline double ds(double x) {
|
||||||
|
return 6 * heaviside(x) * heaviside(1-x) * x * (x-1);
|
||||||
|
}
|
||||||
|
|
||||||
|
inline double s5(double x) {
|
||||||
|
double x2 = x * x;
|
||||||
|
return heaviside(-x)
|
||||||
|
+ heaviside(x)*heaviside(1-x)*(1 - x2*x*(6*x2 - 15*x + 10));
|
||||||
|
}
|
||||||
|
|
||||||
|
inline double ds5(double x) {
|
||||||
|
double x2 = x * x;
|
||||||
|
return -30 * heaviside(x) * heaviside(1-x) * x2 * (x2 - 2*x + 1);
|
||||||
|
}
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Illegal ... command
|
||||||
|
|
||||||
|
Self-explanatory. Check the input script syntax and compare to the
|
||||||
|
documentation for the command. You can use -echo screen as a
|
||||||
|
command-line option when running LAMMPS to see the offending line.
|
||||||
|
|
||||||
|
E: Incorrect args for pair coefficients
|
||||||
|
|
||||||
|
Self-explanatory. Check the input script or data file.
|
||||||
|
|
||||||
|
E: Pair style mesocnt does not support lj units
|
||||||
|
|
||||||
|
Self-explanatory. Specify different unit system using the units
|
||||||
|
command.
|
||||||
|
|
||||||
|
E: Pair style mesocnt requires atom IDs
|
||||||
|
|
||||||
|
Self-explanatory. Turn on atom IDs using the atom_modify command.
|
||||||
|
|
||||||
|
E: Pair style mesocnt requires newton pair on
|
||||||
|
|
||||||
|
Self-explanatory. Turn on Newton's third law with the newton command.
|
||||||
|
|
||||||
|
E: Cannot open mesocnt file %s
|
||||||
|
|
||||||
|
The specified mesocnt potential file cannot be opened. Check that the
|
||||||
|
path and name are correct.
|
||||||
|
|
||||||
|
E: Premature end of file in pair table %s
|
||||||
|
|
||||||
|
The specified mesocnt potential file is shorter than specified. Check
|
||||||
|
if the correct file is being used and the right number of data points
|
||||||
|
was specified in the pair_style
|
||||||
|
|
||||||
|
W: %d of %d lines were incomplete or could not be parsed completely
|
||||||
|
in pair table %s
|
||||||
|
|
||||||
|
A number of lines in the specified mesocnt potential file is incomplete
|
||||||
|
or in the wrong format. Check the file for errors and missing data.
|
||||||
|
|
||||||
|
W: %d spacings in the first column were different from the first spacing
|
||||||
|
in the pair table %s
|
||||||
|
|
||||||
|
The spacings between x coordinates in the first column of the specified
|
||||||
|
mesocnt potential file vary throughout the file. Use a potential file
|
||||||
|
with higher precision.
|
||||||
|
|
||||||
|
W: %d spacings in second column were different from first
|
||||||
|
spacing in pair table %s
|
||||||
|
|
||||||
|
The spacings between y coordinates in the second column of the specified
|
||||||
|
mesocnt potential file vary throughout the file. Use a potential file
|
||||||
|
with higher precision.
|
||||||
|
|
||||||
|
*/
|
||||||
@ -43,6 +43,9 @@ namespace MathExtra {
|
|||||||
|
|
||||||
// 3x3 matrix operations
|
// 3x3 matrix operations
|
||||||
|
|
||||||
|
inline void zeromat3(double m[3][3]);
|
||||||
|
inline void zeromat3(double **m);
|
||||||
|
|
||||||
inline void col2mat(const double *ex, const double *ey, const double *ez,
|
inline void col2mat(const double *ex, const double *ey, const double *ez,
|
||||||
double m[3][3]);
|
double m[3][3]);
|
||||||
inline double det3(const double mat[3][3]);
|
inline double det3(const double mat[3][3]);
|
||||||
@ -52,6 +55,12 @@ namespace MathExtra {
|
|||||||
double ans[3][3]);
|
double ans[3][3]);
|
||||||
inline void plus3(const double m[3][3], const double m2[3][3],
|
inline void plus3(const double m[3][3], const double m2[3][3],
|
||||||
double ans[3][3]);
|
double ans[3][3]);
|
||||||
|
inline void plus3(const double m[3][3], double **m2, double **ans);
|
||||||
|
inline void minus3(const double m[3][3], const double m2[3][3],
|
||||||
|
double ans[3][3]);
|
||||||
|
inline void minus3(double **m, const double m2[3][3],
|
||||||
|
double ans[3][3]);
|
||||||
|
|
||||||
inline void times3(const double m[3][3], const double m2[3][3],
|
inline void times3(const double m[3][3], const double m2[3][3],
|
||||||
double ans[3][3]);
|
double ans[3][3]);
|
||||||
inline void transpose_times3(const double m[3][3], const double m2[3][3],
|
inline void transpose_times3(const double m[3][3], const double m2[3][3],
|
||||||
@ -71,6 +80,8 @@ namespace MathExtra {
|
|||||||
double ans[3][3]);
|
double ans[3][3]);
|
||||||
inline void vecmat(const double *v, const double m[3][3], double *ans);
|
inline void vecmat(const double *v, const double m[3][3], double *ans);
|
||||||
inline void scalar_times3(const double f, double m[3][3]);
|
inline void scalar_times3(const double f, double m[3][3]);
|
||||||
|
inline void outer3(const double *v1, const double *v2,
|
||||||
|
double ans[3][3]);
|
||||||
|
|
||||||
void write3(const double mat[3][3]);
|
void write3(const double mat[3][3]);
|
||||||
int mldivide3(const double mat[3][3], const double *vec, double *ans);
|
int mldivide3(const double mat[3][3], const double *vec, double *ans);
|
||||||
@ -707,4 +718,76 @@ inline void MathExtra::rotation_generator_z(const double m[3][3],
|
|||||||
ans[2][2] = 0;
|
ans[2][2] = 0;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
// set matrix to zero
|
||||||
|
|
||||||
|
inline void MathExtra::zeromat3(double m[3][3])
|
||||||
|
{
|
||||||
|
m[0][0] = m[0][1] = m[0][2] = 0.0;
|
||||||
|
m[1][0] = m[1][1] = m[1][2] = 0.0;
|
||||||
|
m[2][0] = m[2][1] = m[2][2] = 0.0;
|
||||||
|
}
|
||||||
|
|
||||||
|
inline void MathExtra::zeromat3(double **m)
|
||||||
|
{
|
||||||
|
m[0][0] = m[0][1] = m[0][2] = 0.0;
|
||||||
|
m[1][0] = m[1][1] = m[1][2] = 0.0;
|
||||||
|
m[2][0] = m[2][1] = m[2][2] = 0.0;
|
||||||
|
}
|
||||||
|
|
||||||
|
// add two matrices
|
||||||
|
|
||||||
|
inline void MathExtra::plus3(const double m[3][3], double **m2,
|
||||||
|
double **ans)
|
||||||
|
{
|
||||||
|
ans[0][0] = m[0][0]+m2[0][0];
|
||||||
|
ans[0][1] = m[0][1]+m2[0][1];
|
||||||
|
ans[0][2] = m[0][2]+m2[0][2];
|
||||||
|
ans[1][0] = m[1][0]+m2[1][0];
|
||||||
|
ans[1][1] = m[1][1]+m2[1][1];
|
||||||
|
ans[1][2] = m[1][2]+m2[1][2];
|
||||||
|
ans[2][0] = m[2][0]+m2[2][0];
|
||||||
|
ans[2][1] = m[2][1]+m2[2][1];
|
||||||
|
ans[2][2] = m[2][2]+m2[2][2];
|
||||||
|
}
|
||||||
|
|
||||||
|
// subtract two matrices
|
||||||
|
|
||||||
|
inline void MathExtra::minus3(const double m[3][3], const double m2[3][3],
|
||||||
|
double ans[3][3])
|
||||||
|
{
|
||||||
|
ans[0][0] = m[0][0]-m2[0][0];
|
||||||
|
ans[0][1] = m[0][1]-m2[0][1];
|
||||||
|
ans[0][2] = m[0][2]-m2[0][2];
|
||||||
|
ans[1][0] = m[1][0]-m2[1][0];
|
||||||
|
ans[1][1] = m[1][1]-m2[1][1];
|
||||||
|
ans[1][2] = m[1][2]-m2[1][2];
|
||||||
|
ans[2][0] = m[2][0]-m2[2][0];
|
||||||
|
ans[2][1] = m[2][1]-m2[2][1];
|
||||||
|
ans[2][2] = m[2][2]-m2[2][2];
|
||||||
|
}
|
||||||
|
|
||||||
|
inline void MathExtra::minus3(double **m, const double m2[3][3],
|
||||||
|
double ans[3][3])
|
||||||
|
{
|
||||||
|
ans[0][0] = m[0][0]-m2[0][0];
|
||||||
|
ans[0][1] = m[0][1]-m2[0][1];
|
||||||
|
ans[0][2] = m[0][2]-m2[0][2];
|
||||||
|
ans[1][0] = m[1][0]-m2[1][0];
|
||||||
|
ans[1][1] = m[1][1]-m2[1][1];
|
||||||
|
ans[1][2] = m[1][2]-m2[1][2];
|
||||||
|
ans[2][0] = m[2][0]-m2[2][0];
|
||||||
|
ans[2][1] = m[2][1]-m2[2][1];
|
||||||
|
ans[2][2] = m[2][2]-m2[2][2];
|
||||||
|
}
|
||||||
|
|
||||||
|
// compute outer product of two vectors
|
||||||
|
|
||||||
|
inline void MathExtra::outer3(const double *v1, const double *v2,
|
||||||
|
double ans[3][3])
|
||||||
|
{
|
||||||
|
ans[0][0] = v1[0]*v2[0]; ans[0][1] = v1[0]*v2[1]; ans[0][2] = v1[0]*v2[2];
|
||||||
|
ans[1][0] = v1[1]*v2[0]; ans[1][1] = v1[1]*v2[1]; ans[1][2] = v1[1]*v2[2];
|
||||||
|
ans[2][0] = v1[2]*v2[0]; ans[2][1] = v1[2]*v2[1]; ans[2][2] = v1[2]*v2[2];
|
||||||
|
}
|
||||||
|
|
||||||
#endif
|
#endif
|
||||||
|
|||||||
Reference in New Issue
Block a user