New pair-style ylz added to ASPHERE package
This commit is contained in:
mehdibghk
114
doc/src/pair_ylz.rst
Executable file
114
doc/src/pair_ylz.rst
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.. index:: pair_style ylz
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.. index:: pair_style ylz/gpu
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.. index:: pair_style ylz/intel
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.. index:: pair_style ylz/omp
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pair_style ylc command
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===========================
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Accelerator Variants: *ylz/gpu*, *ylz/intel*, *ylz/omp*
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Syntax
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""""""
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.. code-block:: LAMMPS
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pair_style ylz cutoff
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* cutoff = global cutoff for interactions (distance units)
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Examples
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""""""""
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.. code-block:: LAMMPS
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pair_style ylz 2.6
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pair_coeff * * 1.0 1.0 4 3 0.0 2.6
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Description
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"""""""""""
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The *ylz* (Yuan-Li-Zhang)
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:ref:`(Yuan) <Yuan>` style computes anisotropic interactions between pairs of particles considering the relative particle orientations via the formulas
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.. math::
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U ( \mathbf{r}_{ij}, \mathbf{n}_i, \mathbf{n}_j ) =\left\{\begin{matrix} \mathbf{u}_R(r)+\left [ 1-\phi (\mathbf{r\hat{}}_{ij}, \mathbf{n}_i, \mathbf{n}_j ) \right ]\epsilon, ~~ r<\mathbf{r}_{min} \\ \mathbf{u}_A(r)\phi (\mathbf{r\hat{}}_{ij}, \mathbf{n}_i, \mathbf{n}_j ),~~ \mathbf{r}_{min}<r<\mathbf{r}_{c} \\ \end{matrix}\right.\\\\ \phi (\mathbf{r\hat{}}_{ij}, \mathbf{n}_i, \mathbf{n}_j )=1+\mu (a(\mathbf{r\hat{}}_{ij}, \mathbf{n}_i, \mathbf{n}_j )-1) \\\\ a(\mathbf{r\hat{}}_{ij}, \mathbf{n}_i, \mathbf{n}_j )=(\mathbf{n}_i\times\mathbf{r\hat{}}_{ij} )\cdot (\mathbf{n}_j\times\mathbf{r\hat{}}_{ij} )+sin\mathbf{\theta}_0(\mathbf{n}_i-\mathbf{n}_j)\cdot \mathbf{r\hat{}}_{ij}\\\\ \mathbf{u}_R(r)=\epsilon \left [ \left ( \frac{{r}_{min}}{r} \right )^{4}-2\left ( \frac{{r}_{min}}{r}\right )^{2} \right ] \\\\ \mathbf{u}_A(r)=-\epsilon\;cos^{2\zeta }\left ( \frac{\pi}{2}\frac{\left ( {r}-{r}_{min} \right )}{\left ( {r}_{c}-{r}_{min} \right )} \right ) \\
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where :math:`r_{i}` and :math:`r_{j}` are the center position vectors of particles i and j, respectively, :math:`r_{ij}=r_{i}-r_{j}` is the inter-particle distance vector, :math:`r=\left|r_{ij} \right|` and :math:`{r\hat{}}_{ij}=\mathbf{r}_{ij}/r`. The unit vectors :math:`n_{i}` and :math:`n_{j}` represent the axes of symmetry of particles i and j, respectively. :math:`u_R` and :math:`u_A` are the repulsive and attractive potentials. :math:`\phi` is an angular function which depends on the relative orientation between pair particles. :math:`\mu` is the parameter related to bending rigidity, :math:`\theta_{0}` is the parameter related to the spontaneous curvature, and :math:`\epsilon` is the energy unit, respectively. The :math:`\zeta` controls the slope of the attractive branch and :math:`{r}_{c}`is the cutoff radius. :math:`r_{min}` is the distance which minimizes the potential energy :math:`u_{A}(r)`and :math:`r_{min}=2^{1/6}\sigma`, where :math:`\sigma` is the length unit.
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Use of this pair style requires the NVE, NVT, or NPT fixes with the *asphere* extension (e.g. :doc:`fix nve/asphere <fix_nve_asphere>`) in order to integrate particle rotation. Additionally, :doc:`atom_style ellipsoid <atom_style>` should be used since it defines the rotational state of each particle.
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The following coefficients must be defined for each pair of atoms types via the :doc:`pair_coeff <pair_coeff>` command as in the examples above, or in the data file or restart files read by the :doc:`read_data <read_data>` or :doc:`read_restart <read_restart>` commands, or by mixing as described below:
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* :math:`\epsilon` = well depth (energy units)
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* :math:`\sigma` = minimum effective particle radii (distance units)
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* :math:`\zeta` = tune parameter for the slope of the attractive branch
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* :math:`\mu` = parameter related to bending rigidity
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* :math:`\sin(\theta _{0})` is the sine of parameter related to the spontaneous curvature
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* cutoff (distance units)
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The last coefficient is optional. If not specified, the global
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cutoff specified in the pair_style command is used.
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----------
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.. include:: accel_styles.rst
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----------
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Mixing, shift, table, tail correction, restart, rRESPA info
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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For atom type pairs I,J and I != J, the epsilon and sigma coefficients and cutoff distance for this pair style can be mixed. The default mix value is *geometric*\ . See the "pair_modify" command for details.
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The :doc:`pair_modify <pair_modify>` table option is not relevant for this pair style.
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This pair style does not support the :doc:`pair_modify <pair_modify>` tail option for adding long-range tail corrections to energy and pressure.
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This pair style writes its information to :doc:`binary restart files <restart>`, so pair_style and pair_coeff commands do not need to be specified in 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 :doc:`run_style respa <run_style>` command. It does 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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The *ylz* style is part of the ASPHERE package. It is only enabled if LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
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These pair styles require that atoms store torque and a quaternion to represent their orientation, as defined by the :doc:`atom_style <atom_style>`. It also require they store a per-type :doc:`shape <set>`. The particles cannot store a per-particle diameter.
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This pair style requires that atoms be ellipsoids as defined by the
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:doc:`atom_style ellipsoid <atom_style>` command.
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Particles acted on by the potential can be finite-size aspherical or
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spherical particles, or point particles. Spherical particles have all
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3 of their shape parameters equal to each other. Point particles have
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all 3 of their shape parameters equal to 0.0.
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Related commands
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""""""""""""""""
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:doc:`pair_coeff <pair_coeff>`, :doc:`fix nve/asphere <fix_nve_asphere>`,
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:doc:`compute temp/asphere <compute_temp_asphere>`, :doc:`pair_style resquared <pair_resquared>`, :doc:`pair_style gayberne <pair_resquared>`
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Default
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"""""""
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none
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----------
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.. _Yuan:
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**(Yuan)** Yuan, Huang, Li, Lykotrafitis, Zhang, Phys. Rev. E, 82, 011905(2010).
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55
examples/ASPHERE/flat_membrane/in_flat_membrane
Executable file
55
examples/ASPHERE/flat_membrane/in_flat_membrane
Executable file
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# flat membrane demo
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variable r0 equal 0.97
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variable d1 equal ${r0}
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variable d2 equal sqrt(3.0)*${r0}
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variable d3 equal 3.0*${r0}
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variable ro equal 2./${d1}/${d2}/${d3}
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variable T equal 0.23
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variable LD equal 1.0
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units lj
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atom_style ellipsoid
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boundary p p p
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lattice custom ${ro} a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 &
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a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
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region box block 0 40 0 24 -20 20
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create_box 1 box
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region membrane block 0 40 0 24 -0.5 0.5
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create_atoms 1 region membrane
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group membrane region membrane
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set type 1 mass 1.0
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set type 1 shape 1 1 1
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set group all quat 0 -1 0 90
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#compute memb all temp/com
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#compute rot all temp/asphere bias memb
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velocity all create ${T} 87287 loop geom
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pair_style ylz 2.6
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pair_coeff * * 1.0 1.0 4 3 0.0 2.6
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neighbor 1.0 bin
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thermo_style custom step temp press pxx pyy
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thermo 200
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timestep 0.01
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dump 1 all atom 10 dump_onlymembrane.lammpstrj
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fix 1 all langevin ${T} ${T} ${LD} 48279
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fix 2 all nve/asphere
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run 3000
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161
examples/ASPHERE/flat_membrane/log.lammps
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161
examples/ASPHERE/flat_membrane/log.lammps
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LAMMPS (29 Sep 2021 - Update 3)
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# only membrane
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variable r0 equal 0.97
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variable d1 equal ${r0}
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variable d1 equal 0.97
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variable d2 equal sqrt(3.0)*${r0}
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variable d2 equal sqrt(3.0)*0.97
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variable d3 equal 3.0*${r0}
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variable d3 equal 3.0*0.97
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variable ro equal 2./${d1}/${d2}/${d3}
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variable ro equal 2./0.97/${d2}/${d3}
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variable ro equal 2./0.97/1.68008928334181/${d3}
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variable ro equal 2./0.97/1.68008928334181/2.91
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variable T equal 0.23
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variable LD equal 1.0
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units lj
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atom_style ellipsoid
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boundary p p p
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lattice custom ${ro} a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
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lattice custom 0.421728460751825 a1 ${d1} 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
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lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 ${d2} 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
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lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 ${d3} basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
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lattice custom 0.421728460751825 a1 0.97 0.0 0.0 a2 0.0 1.68008928334181 0.0 a3 0.0 0.0 2.91 basis 0.0 0.0 0.0 basis 0.5 0.5 0.0
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Lattice spacing in x,y,z = 0.97000000 1.6800893 2.9100000
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region box block 0 40 0 24 -20 20
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create_box 1 box
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Created orthogonal box = (0.0000000 0.0000000 -58.200000) to (38.800000 40.322143 58.200000)
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1 by 1 by 1 MPI processor grid
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region membrane block 0 40 0 24 -0.5 0.5
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create_atoms 1 region membrane
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Created 1920 atoms
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using lattice units in orthogonal box = (0.0000000 0.0000000 -58.200000) to (38.800000 40.322143 58.200000)
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create_atoms CPU = 0.000 seconds
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group membrane region membrane
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1920 atoms in group membrane
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set type 1 mass 1.0
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Setting atom values ...
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1920 settings made for mass
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set type 1 shape 1 1 1
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Setting atom values ...
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1920 settings made for shape
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set group all quat 0 -1 0 90
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Setting atom values ...
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1920 settings made for quat
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compute memb all temp/com
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compute rot all temp/asphere bias memb
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velocity all create ${T} 87287 loop geom
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velocity all create 0.23 87287 loop geom
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pair_style ylz 2.6
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pair_coeff * * 1.0 1.0 4 3 0.0 2.6
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neighbor 1.0 bin
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thermo_style custom step temp press pxx pyy
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thermo 200
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timestep 0.01
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dump 1 all atom 10 dump_onlymembrane.lammpstrj
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fix 1 all langevin ${T} ${T} ${LD} 48279
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fix 1 all langevin 0.23 ${T} ${LD} 48279
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fix 1 all langevin 0.23 0.23 ${LD} 48279
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fix 1 all langevin 0.23 0.23 1 48279
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fix 2 all nve/asphere
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run 3000
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Your simulation uses code contributions which should be cited:
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- pair ylz command:
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@Article{Yuan10,
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author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
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title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
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journal = {Phys. Rev. E},
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year = 2010,
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volume = 82,
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pages = {011905}
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}
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CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
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Neighbor list info ...
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update every 1 steps, delay 10 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 3.6
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ghost atom cutoff = 3.6
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binsize = 1.8, bins = 22 23 65
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair ylz, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 6.097 | 6.097 | 6.097 Mbytes
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Step Temp Press Pxx Pyy
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0 0.23 -0.0073508785 -0.012283389 -0.012234574
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200 0.20903886 -0.0010605951 -0.0011885957 -0.00198842
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400 0.21898026 -0.00069250685 -0.0013217981 -0.00073225707
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600 0.22689361 -0.00057919328 -0.00076880503 -0.0010242283
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800 0.22983221 -0.00032145682 -0.00051928834 -0.00059337525
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1000 0.23819392 -0.00027969126 -0.00088082301 -5.2666567e-05
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1200 0.22053795 -0.00029571329 -0.0004446455 -0.00035529929
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1400 0.22285021 -0.0002690371 -0.00068896571 -3.6258442e-05
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1600 0.22687044 2.8599875e-05 -0.00032651798 0.0004056081
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1800 0.23356905 -2.28742e-05 -0.00027073251 0.00025081131
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2000 0.22499821 8.8230586e-06 -7.5750159e-05 0.0001988705
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2200 0.23162995 -9.026855e-05 -0.00025832535 5.4904927e-05
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2400 0.22920223 0.00016700455 3.5283125e-05 0.00034955857
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2600 0.2260299 5.3095557e-05 0.00025691786 0.00013353467
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2800 0.2296401 0.00043234854 0.00058344966 0.00063645193
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3000 0.22564577 2.6423111e-05 8.9918406e-05 0.00022146229
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Loop time of 5.08921 on 1 procs for 3000 steps with 1920 atoms
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Performance: 509312.653 tau/day, 589.482 timesteps/s
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99.7% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 4.2251 | 4.2251 | 4.2251 | 0.0 | 83.02
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Neigh | 0.07599 | 0.07599 | 0.07599 | 0.0 | 1.49
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Comm | 0.026195 | 0.026195 | 0.026195 | 0.0 | 0.51
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Output | 0.21176 | 0.21176 | 0.21176 | 0.0 | 4.16
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Modify | 0.53849 | 0.53849 | 0.53849 | 0.0 | 10.58
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Other | | 0.01168 | | | 0.23
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Nlocal: 1920.00 ave 1920 max 1920 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 772.000 ave 772 max 772 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 46804.0 ave 46804 max 46804 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 46804
|
||||||
|
Ave neighs/atom = 24.377083
|
||||||
|
Neighbor list builds = 99
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
|
||||||
|
# notes-1: for npt control, t_start,p_start don't need to be the same as real staring value, moreover, it can cause problem.
|
||||||
|
# notes-2: drag=0.2 is effective for control pressure, pressure reach desired value too slow if no drag
|
||||||
|
# notes-3: pressure reach equilibrium much quicker than temperature
|
||||||
|
Total wall time: 0:00:05
|
||||||
35
examples/ASPHERE/vesicle/in.vesicle
Normal file
35
examples/ASPHERE/vesicle/in.vesicle
Normal file
@ -0,0 +1,35 @@
|
|||||||
|
# Vesicle demo
|
||||||
|
|
||||||
|
variable T equal 0.2
|
||||||
|
variable LD equal 1.0
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style ellipsoid
|
||||||
|
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
read_data read_data.vesicle1026
|
||||||
|
|
||||||
|
compute ali all temp/com
|
||||||
|
compute rott all temp/asphere bias ali
|
||||||
|
|
||||||
|
velocity all create ${T} 87287 loop geom
|
||||||
|
|
||||||
|
pair_style ylz 2.6
|
||||||
|
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
|
||||||
|
neighbor 1.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step temp press pxx pyy
|
||||||
|
thermo 200
|
||||||
|
|
||||||
|
timestep 0.001
|
||||||
|
|
||||||
|
dump 1 all atom 10 onlymembrane2.lammpstrj
|
||||||
|
|
||||||
|
fix 1 all langevin ${T} ${T} ${LD} 48279
|
||||||
|
|
||||||
|
|
||||||
|
fix 2 all nve/asphere
|
||||||
|
|
||||||
|
run 3000
|
||||||
|
|
||||||
124
examples/ASPHERE/vesicle/log.lammps
Normal file
124
examples/ASPHERE/vesicle/log.lammps
Normal file
@ -0,0 +1,124 @@
|
|||||||
|
LAMMPS (29 Sep 2021 - Update 3)
|
||||||
|
variable T equal 0.2
|
||||||
|
variable LD equal 1.0
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style ellipsoid
|
||||||
|
|
||||||
|
boundary p p p
|
||||||
|
|
||||||
|
read_data read_data.vesicle1026
|
||||||
|
Reading data file ...
|
||||||
|
orthogonal box = (-35.000000 -35.000000 -35.000000) to (35.000000 35.000000 35.000000)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
2938 atoms
|
||||||
|
2938 ellipsoids
|
||||||
|
read_data CPU = 0.008 seconds
|
||||||
|
|
||||||
|
compute ali all temp/com
|
||||||
|
compute rott all temp/asphere bias ali
|
||||||
|
|
||||||
|
velocity all create ${T} 87287 loop geom
|
||||||
|
velocity all create 0.2 87287 loop geom
|
||||||
|
|
||||||
|
pair_style ylz 2.6
|
||||||
|
pair_coeff * * 1.0 1.0 4 3 0.0 2.6
|
||||||
|
neighbor 1.0 bin
|
||||||
|
|
||||||
|
thermo_style custom step temp press pxx pyy
|
||||||
|
thermo 200
|
||||||
|
|
||||||
|
timestep 0.001
|
||||||
|
|
||||||
|
dump 1 all atom 10 onlymembrane2.lammpstrj
|
||||||
|
|
||||||
|
fix 1 all langevin ${T} ${T} ${LD} 48279
|
||||||
|
fix 1 all langevin 0.2 ${T} ${LD} 48279
|
||||||
|
fix 1 all langevin 0.2 0.2 ${LD} 48279
|
||||||
|
fix 1 all langevin 0.2 0.2 1 48279
|
||||||
|
|
||||||
|
|
||||||
|
fix 2 all nve/asphere
|
||||||
|
|
||||||
|
run 3000
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Your simulation uses code contributions which should be cited:
|
||||||
|
|
||||||
|
- pair ylz command:
|
||||||
|
|
||||||
|
@Article{Yuan10,
|
||||||
|
author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},
|
||||||
|
title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},
|
||||||
|
journal = {Phys. Rev. E},
|
||||||
|
year = 2010,
|
||||||
|
volume = 82,
|
||||||
|
pages = {011905}
|
||||||
|
}
|
||||||
|
|
||||||
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||||
|
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 10 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 3.6
|
||||||
|
ghost atom cutoff = 3.6
|
||||||
|
binsize = 1.8, bins = 39 39 39
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair ylz, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/bin/atomonly/newton
|
||||||
|
stencil: half/bin/3d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 6.203 | 6.203 | 6.203 Mbytes
|
||||||
|
Step Temp Press Pxx Pyy
|
||||||
|
0 0.2 -0.0054891414 -0.0052713616 -0.0053641136
|
||||||
|
200 0.12816247 -0.0051288861 -0.0048542514 -0.0049847561
|
||||||
|
400 0.1377632 -0.0048071582 -0.0045651263 -0.0048444087
|
||||||
|
600 0.14983781 -0.0045305725 -0.0043305994 -0.0046127777
|
||||||
|
800 0.16205271 -0.0041176346 -0.0040534483 -0.0041351779
|
||||||
|
1000 0.17462122 -0.0037000069 -0.0034938539 -0.0037915494
|
||||||
|
1200 0.18335448 -0.0032674318 -0.0032790248 -0.0031967931
|
||||||
|
1400 0.19195613 -0.0029332101 -0.0030823703 -0.0028287799
|
||||||
|
1600 0.19261762 -0.0025263447 -0.0025152249 -0.0026205398
|
||||||
|
1800 0.19758674 -0.0021087725 -0.001981333 -0.002309048
|
||||||
|
2000 0.19748896 -0.0017662369 -0.0019316344 -0.0016696035
|
||||||
|
2200 0.20196986 -0.0013363214 -0.0015581191 -0.0013384961
|
||||||
|
2400 0.20109248 -0.0009190831 -0.0010331417 -0.0010664316
|
||||||
|
2600 0.20228664 -0.00053590675 -0.00071808747 -0.00050218533
|
||||||
|
2800 0.20512955 -0.00030845899 -0.00016244901 -0.00047877516
|
||||||
|
3000 0.19855941 -7.9520073e-05 -0.00014969215 -5.4724226e-06
|
||||||
|
Loop time of 7.2222 on 1 procs for 3000 steps with 2938 atoms
|
||||||
|
|
||||||
|
Performance: 35889.329 tau/day, 415.386 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 | 6.0158 | 6.0158 | 6.0158 | 0.0 | 83.30
|
||||||
|
Neigh | 0.034308 | 0.034308 | 0.034308 | 0.0 | 0.48
|
||||||
|
Comm | 0.0015149 | 0.0015149 | 0.0015149 | 0.0 | 0.02
|
||||||
|
Output | 0.31567 | 0.31567 | 0.31567 | 0.0 | 4.37
|
||||||
|
Modify | 0.83787 | 0.83787 | 0.83787 | 0.0 | 11.60
|
||||||
|
Other | | 0.01702 | | | 0.24
|
||||||
|
|
||||||
|
Nlocal: 2938.00 ave 2938 max 2938 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 0.00000 ave 0 max 0 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 73242.0 ave 73242 max 73242 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 73242
|
||||||
|
Ave neighs/atom = 24.929204
|
||||||
|
Neighbor list builds = 26
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
|
||||||
|
# notes-1: for npt control, t_start,p_start don't need to be the same as real staring value, moreover, it can cause problem.
|
||||||
|
# notes-2: drag=0.2 is effective for control pressure, pressure reach desired value too slow if no drag
|
||||||
|
# notes-3: pressure reach equilibrium much quicker than temperature
|
||||||
|
Total wall time: 0:00:07
|
||||||
887047
examples/ASPHERE/vesicle/onlymembrane2.lammpstrj
Normal file
887047
examples/ASPHERE/vesicle/onlymembrane2.lammpstrj
Normal file
File diff suppressed because it is too large
Load Diff
5894
examples/ASPHERE/vesicle/read_data.vesicle1026
Executable file
5894
examples/ASPHERE/vesicle/read_data.vesicle1026
Executable file
File diff suppressed because it is too large
Load Diff
551
src/ASPHERE/pair_ylz.cpp
Executable file
551
src/ASPHERE/pair_ylz.cpp
Executable file
@ -0,0 +1,551 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://www.lammps.org/, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
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: Mehdi Baghaee (SUSTech)
|
||||||
|
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#include "pair_ylz.h"
|
||||||
|
|
||||||
|
#include <cmath>
|
||||||
|
#include "math_extra.h"
|
||||||
|
#include "atom.h"
|
||||||
|
#include "atom_vec_ellipsoid.h"
|
||||||
|
#include "comm.h"
|
||||||
|
#include "force.h"
|
||||||
|
#include "neighbor.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
#include "citeme.h"
|
||||||
|
#include "memory.h"
|
||||||
|
#include "error.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
static const char cite_pair_ylz[] =
|
||||||
|
"pair ylz command:\n\n"
|
||||||
|
"@Article{Yuan10,\n"
|
||||||
|
" author = {H. Yuan, C. Huang, J. Li, G. Lykotrafitis, and S. Zhang},\n"
|
||||||
|
" title = {One-particle-thick, solvent-free, coarse-grained model for biological and biomimetic fluid membranes},\n"
|
||||||
|
" journal = {Phys. Rev. E},\n"
|
||||||
|
" year = 2010,\n"
|
||||||
|
" volume = 82,\n"
|
||||||
|
" pages = {011905}\n"
|
||||||
|
"}\n\n";
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
PairYLZ::PairYLZ(LAMMPS *lmp) : Pair(lmp)
|
||||||
|
{
|
||||||
|
if (lmp->citeme) lmp->citeme->add(cite_pair_ylz);
|
||||||
|
|
||||||
|
single_enable = 0;
|
||||||
|
writedata = 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
free all arrays
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
PairYLZ::~PairYLZ()
|
||||||
|
{
|
||||||
|
if (allocated) {
|
||||||
|
memory->destroy(setflag);
|
||||||
|
memory->destroy(cutsq);
|
||||||
|
|
||||||
|
memory->destroy(epsilon);
|
||||||
|
memory->destroy(sigma);
|
||||||
|
memory->destroy(cut);
|
||||||
|
memory->destroy(zeta);
|
||||||
|
memory->destroy(mu);
|
||||||
|
memory->destroy(beta);
|
||||||
|
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairYLZ::compute(int eflag, int vflag)
|
||||||
|
{
|
||||||
|
int i,j,ii,jj,inum,jnum,itype,jtype;
|
||||||
|
double evdwl,one_eng,rsq,forcelj,factor_lj;
|
||||||
|
double fforce[3],ttor[3],rtor[3],r12[3];
|
||||||
|
double a1[3][3],a2[3][3];
|
||||||
|
int *ilist,*jlist,*numneigh,**firstneigh;
|
||||||
|
double *iquat,*jquat;
|
||||||
|
|
||||||
|
evdwl = 0.0;
|
||||||
|
ev_init(eflag , vflag);
|
||||||
|
|
||||||
|
AtomVecEllipsoid::Bonus *bonus = avec->bonus;
|
||||||
|
int *ellipsoid = atom->ellipsoid;
|
||||||
|
double **x = atom->x;
|
||||||
|
double **f = atom->f;
|
||||||
|
double **tor = atom->torque;
|
||||||
|
int *type = atom->type;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
double *special_lj = force->special_lj;
|
||||||
|
int newton_pair = force->newton_pair;
|
||||||
|
|
||||||
|
inum = list->inum;
|
||||||
|
ilist = list->ilist;
|
||||||
|
numneigh = list->numneigh;
|
||||||
|
firstneigh = list->firstneigh;
|
||||||
|
|
||||||
|
// loop over neighbors of my atoms
|
||||||
|
|
||||||
|
for (ii = 0; ii < inum; ii++) {
|
||||||
|
i = ilist[ii];
|
||||||
|
itype = type[i];
|
||||||
|
|
||||||
|
iquat = bonus[ellipsoid[i]].quat;
|
||||||
|
MathExtra::quat_to_mat_trans(iquat,a1);
|
||||||
|
|
||||||
|
|
||||||
|
jlist = firstneigh[i];
|
||||||
|
jnum = numneigh[i];
|
||||||
|
|
||||||
|
for (jj = 0; jj < jnum; jj++) {
|
||||||
|
j = jlist[jj];
|
||||||
|
factor_lj = special_lj[sbmask(j)];
|
||||||
|
j &= NEIGHMASK;
|
||||||
|
|
||||||
|
// r12 = center to center vector
|
||||||
|
|
||||||
|
r12[0] = x[j][0]-x[i][0];
|
||||||
|
r12[1] = x[j][1]-x[i][1];
|
||||||
|
r12[2] = x[j][2]-x[i][2];
|
||||||
|
rsq = MathExtra::dot3(r12,r12);
|
||||||
|
jtype = type[j];
|
||||||
|
|
||||||
|
// compute if less than cutoff
|
||||||
|
|
||||||
|
if (rsq < cutsq[itype][jtype]) {
|
||||||
|
|
||||||
|
jquat = bonus[ellipsoid[j]].quat;
|
||||||
|
MathExtra::quat_to_mat_trans(jquat,a2);
|
||||||
|
one_eng = ylz_analytic(i,j,a1,a2,r12,rsq,fforce,ttor,rtor);
|
||||||
|
|
||||||
|
fforce[0] *= factor_lj;
|
||||||
|
fforce[1] *= factor_lj;
|
||||||
|
fforce[2] *= factor_lj;
|
||||||
|
ttor[0] *= factor_lj;
|
||||||
|
ttor[1] *= factor_lj;
|
||||||
|
ttor[2] *= factor_lj;
|
||||||
|
|
||||||
|
f[i][0] += fforce[0];
|
||||||
|
f[i][1] += fforce[1];
|
||||||
|
f[i][2] += fforce[2];
|
||||||
|
tor[i][0] += ttor[0];
|
||||||
|
tor[i][1] += ttor[1];
|
||||||
|
tor[i][2] += ttor[2];
|
||||||
|
|
||||||
|
if (newton_pair || j < nlocal) {
|
||||||
|
rtor[0] *= factor_lj;
|
||||||
|
rtor[1] *= factor_lj;
|
||||||
|
rtor[2] *= factor_lj;
|
||||||
|
f[j][0] -= fforce[0];
|
||||||
|
f[j][1] -= fforce[1];
|
||||||
|
f[j][2] -= fforce[2];
|
||||||
|
tor[j][0] += rtor[0];
|
||||||
|
tor[j][1] += rtor[1];
|
||||||
|
tor[j][2] += rtor[2];
|
||||||
|
}
|
||||||
|
|
||||||
|
if (eflag) evdwl = factor_lj*one_eng;
|
||||||
|
|
||||||
|
if (evflag) ev_tally_xyz(i,j,nlocal,newton_pair,
|
||||||
|
evdwl,0.0,fforce[0],fforce[1],fforce[2],
|
||||||
|
-r12[0],-r12[1],-r12[2]);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (vflag_fdotr) virial_fdotr_compute();
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
allocate all arrays
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairYLZ::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(epsilon,n+1,n+1,"pair:epsilon");
|
||||||
|
memory->create(sigma,n+1,n+1,"pair:sigma");
|
||||||
|
memory->create(cut,n+1,n+1,"pair:cut");
|
||||||
|
memory->create(zeta,n+1,n+1,"pair:zeta");
|
||||||
|
memory->create(mu,n+1,n+1,"pair:mu");
|
||||||
|
memory->create(beta,n+1,n+1,"pair:beta");
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
global settings
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairYLZ::settings(int narg, char **arg)
|
||||||
|
{
|
||||||
|
if (narg != 1) error->all(FLERR,"Illegal pair_style command");
|
||||||
|
|
||||||
|
cut_global = utils::numeric(FLERR,arg[0],false, lmp);
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
set coeffs for one or more type pairs
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairYLZ::coeff(int narg, char **arg)
|
||||||
|
{
|
||||||
|
if (narg < 8 || narg > 8)
|
||||||
|
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 epsilon_one = utils::numeric(FLERR,arg[2], false, lmp);
|
||||||
|
double sigma_one = utils::numeric(FLERR,arg[3], false, lmp);
|
||||||
|
double zeta_one = utils::numeric(FLERR,arg[4], false, lmp);
|
||||||
|
double mu_one = utils::numeric(FLERR,arg[5], false, lmp);
|
||||||
|
double beta_one = utils::numeric(FLERR,arg[6], false, lmp);
|
||||||
|
double cut_one = utils::numeric(FLERR,arg[7], false, lmp);
|
||||||
|
|
||||||
|
int count = 0;
|
||||||
|
for (int i = ilo; i <= ihi; i++) {
|
||||||
|
for (int j = MAX(jlo,i); j <= jhi; j++) {
|
||||||
|
epsilon[i][j] = epsilon_one;
|
||||||
|
sigma[i][j] = sigma_one;
|
||||||
|
cut[i][j] = cut_one;
|
||||||
|
zeta[i][j] = zeta_one;
|
||||||
|
mu[i][j] = mu_one;
|
||||||
|
beta[i][j] = beta_one;
|
||||||
|
|
||||||
|
setflag[i][j] = 1;
|
||||||
|
count++;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
init specific to this pair style
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairYLZ::init_style()
|
||||||
|
{
|
||||||
|
avec = (AtomVecEllipsoid *) atom->style_match("ellipsoid");
|
||||||
|
if (!avec) error->all(FLERR,"Pair YLZ requires atom style ellipsoid");
|
||||||
|
|
||||||
|
neighbor->request(this,instance_me);
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
init for one type pair i,j and corresponding j,i
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
double PairYLZ::init_one(int i, int j)
|
||||||
|
{
|
||||||
|
|
||||||
|
if (setflag[i][j] == 0) {
|
||||||
|
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
|
||||||
|
sigma[i][i],sigma[j][j]);
|
||||||
|
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
|
||||||
|
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
epsilon[j][i] = epsilon[i][j];
|
||||||
|
sigma[j][i] = sigma[i][j];
|
||||||
|
zeta[j][i] = zeta[i][j];
|
||||||
|
mu[j][i] = mu[i][j];
|
||||||
|
beta[j][i] = beta[i][j];
|
||||||
|
|
||||||
|
return cut[i][j];
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
proc 0 writes to restart file
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairYLZ::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(&epsilon[i][j],sizeof(double),1,fp);
|
||||||
|
fwrite(&sigma[i][j],sizeof(double),1,fp);
|
||||||
|
fwrite(&cut[i][j],sizeof(double),1,fp);
|
||||||
|
fwrite(&zeta[i][j],sizeof(double),1,fp);
|
||||||
|
fwrite(&mu[i][j],sizeof(double),1,fp);
|
||||||
|
fwrite(&beta[i][j],sizeof(double),1,fp);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
proc 0 reads from restart file, bcasts
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairYLZ::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) utils::sfread(FLERR, &setflag[i][j],sizeof(int),1,fp, nullptr, error);
|
||||||
|
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
|
||||||
|
if (setflag[i][j]) {
|
||||||
|
if (me == 0) {
|
||||||
|
utils::sfread(FLERR, &epsilon[i][j],sizeof(double),1,fp, nullptr, error);
|
||||||
|
utils::sfread(FLERR, &sigma[i][j],sizeof(double),1,fp, nullptr, error);
|
||||||
|
utils::sfread(FLERR, &cut[i][j],sizeof(double),1,fp, nullptr, error);
|
||||||
|
utils::sfread(FLERR, &zeta[i][j],sizeof(double),1,fp, nullptr, error);
|
||||||
|
utils::sfread(FLERR, &mu[i][j],sizeof(double),1,fp, nullptr, error);
|
||||||
|
utils::sfread(FLERR, &beta[i][j],sizeof(double),1,fp, nullptr, error);
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
|
||||||
|
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
|
||||||
|
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
|
||||||
|
MPI_Bcast(&zeta[i][j],1,MPI_DOUBLE,0,world);
|
||||||
|
MPI_Bcast(&mu[i][j],1,MPI_DOUBLE,0,world);
|
||||||
|
MPI_Bcast(&beta[i][j],1,MPI_DOUBLE,0,world);
|
||||||
|
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
proc 0 writes to restart file
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairYLZ::write_restart_settings(FILE *fp)
|
||||||
|
{
|
||||||
|
//fwrite(&model_type,sizeof(int),1,fp);
|
||||||
|
fwrite(&cut_global,sizeof(double),1,fp);
|
||||||
|
fwrite(&offset_flag,sizeof(int),1,fp);
|
||||||
|
fwrite(&mix_flag,sizeof(int),1,fp);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
proc 0 reads from restart file, bcasts
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairYLZ::read_restart_settings(FILE *fp)
|
||||||
|
{
|
||||||
|
int me = comm->me;
|
||||||
|
if (me == 0) {
|
||||||
|
|
||||||
|
// utils::sfread(FLERR, &model_type,sizeof(int),1,fp, nullptr, error);
|
||||||
|
utils::sfread(FLERR, &cut_global,sizeof(double),1,fp, nullptr, error);
|
||||||
|
utils::sfread(FLERR, &offset_flag,sizeof(int),1,fp, nullptr, error);
|
||||||
|
utils::sfread(FLERR, &mix_flag,sizeof(int),1,fp, nullptr, error);
|
||||||
|
}
|
||||||
|
|
||||||
|
//MPI_Bcast(&model_type,1,MPI_DOUBLE,0,world);
|
||||||
|
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
|
||||||
|
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
|
||||||
|
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
proc 0 writes to data file
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairYLZ::write_data(FILE *fp)
|
||||||
|
{
|
||||||
|
for (int i = 1; i <= atom->ntypes; i++)
|
||||||
|
fprintf(fp,"%d %g %g %g %g %g %g\n",i,
|
||||||
|
epsilon[i][i],sigma[i][i],cut[i][i],zeta[i][i],mu[i][i], beta[i][i]);
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
proc 0 writes all pairs to data file
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void PairYLZ::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 %g %g %g %g %g\n",i,j,
|
||||||
|
epsilon[i][i],sigma[i][i],cut[i][j],zeta[i][j],mu[i][j], beta[i][j]);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
compute analytic energy, force (fforce), and torque (ttor & rtor)
|
||||||
|
based on rotation matrices a
|
||||||
|
if newton is off, rtor is not calculated for ghost atoms
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
double PairYLZ::ylz_analytic(const int i,const int j,double a1[3][3],
|
||||||
|
double a2[3][3], double *r12,
|
||||||
|
const double rsq, double *fforce,
|
||||||
|
double *ttor, double *rtor)
|
||||||
|
|
||||||
|
{
|
||||||
|
int *type = atom->type;
|
||||||
|
int newton_pair = force->newton_pair;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
|
||||||
|
double r12hat[3];
|
||||||
|
MathExtra::normalize3(r12,r12hat);
|
||||||
|
double r = sqrt(rsq);
|
||||||
|
|
||||||
|
|
||||||
|
double ni1[3],nj1[3],dphi_drhat[3],dUdrhat[3],dUdni1[3],dUdnj1[3],dphi_dni1[3],dphi_dnj1[3] ;
|
||||||
|
double t,t1,t2,t4,cos_t,U,uR,uA,dUdr,dUdphi;
|
||||||
|
double pi = 3.141592653589793, pow2_1by6 = 1.122462048309373;
|
||||||
|
|
||||||
|
double energy_well = epsilon[type[i]][type[j]];
|
||||||
|
double rmin = pow2_1by6*sigma[type[i]][type[j]];
|
||||||
|
double rcut = cut[type[i]][type[j]];
|
||||||
|
double zt = zeta[type[i]][type[j]];
|
||||||
|
double muu = mu[type[i]][type[j]];
|
||||||
|
double sint = beta[type[i]][type[j]];
|
||||||
|
|
||||||
|
ni1[0]=a1[0][0];
|
||||||
|
ni1[1]=a1[0][1];
|
||||||
|
ni1[2]=a1[0][2];
|
||||||
|
|
||||||
|
nj1[0]=a2[0][0];
|
||||||
|
nj1[1]=a2[0][1];
|
||||||
|
nj1[2]=a2[0][2];
|
||||||
|
|
||||||
|
double ninj = MathExtra::dot3(ni1,nj1);
|
||||||
|
double ni1rhat = MathExtra::dot3(ni1,r12hat);
|
||||||
|
double nj1rhat = MathExtra::dot3(nj1,r12hat);
|
||||||
|
|
||||||
|
double a = ninj + (sint-ni1rhat)*(sint+nj1rhat) - 2.0*sint*sint;
|
||||||
|
double phi = 1.0 + (a-1.0)*muu;
|
||||||
|
|
||||||
|
dphi_drhat[0] = muu*( (sint-ni1rhat)*nj1[0]-ni1[0]*(sint+nj1rhat) );
|
||||||
|
dphi_drhat[1] = muu*( (sint-ni1rhat)*nj1[1]-ni1[1]*(sint+nj1rhat) );
|
||||||
|
dphi_drhat[2] = muu*( (sint-ni1rhat)*nj1[2]-ni1[2]*(sint+nj1rhat) );
|
||||||
|
|
||||||
|
dphi_dni1[0] = muu*(nj1[0]-r12hat[0]*(sint+nj1rhat));
|
||||||
|
dphi_dni1[1] = muu*(nj1[1]-r12hat[1]*(sint+nj1rhat));
|
||||||
|
dphi_dni1[2] = muu*(nj1[2]-r12hat[2]*(sint+nj1rhat));
|
||||||
|
|
||||||
|
dphi_dnj1[0] = muu*(ni1[0]+r12hat[0]*(sint-ni1rhat));
|
||||||
|
dphi_dnj1[1] = muu*(ni1[1]+r12hat[1]*(sint-ni1rhat));
|
||||||
|
dphi_dnj1[2] = muu*(ni1[2]+r12hat[2]*(sint-ni1rhat));
|
||||||
|
|
||||||
|
if (r < rmin)
|
||||||
|
{
|
||||||
|
t = rmin/r;
|
||||||
|
t2=t*t;
|
||||||
|
t4=t2*t2;
|
||||||
|
uR = (t4 - 2.0*t2)*energy_well;
|
||||||
|
|
||||||
|
U = uR +(1.0 - phi)*energy_well;
|
||||||
|
|
||||||
|
dUdr = 4.0*(t2-t4)/r*energy_well;
|
||||||
|
|
||||||
|
dUdphi = -energy_well;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
else
|
||||||
|
{
|
||||||
|
|
||||||
|
t = pi/2.0*(r-rmin)/(rcut-rmin);
|
||||||
|
cos_t = cos(t);
|
||||||
|
t1=cos_t;
|
||||||
|
|
||||||
|
for (int k = 1; k <= 2*zt-2; k++) {t1 *= cos_t;} // get cos()^(2zt-1)
|
||||||
|
|
||||||
|
uA = -energy_well*t1*cos_t;
|
||||||
|
|
||||||
|
U = uA*phi;
|
||||||
|
|
||||||
|
dUdr = 4.0*pi/(rcut-rmin)*(t1)*sin(t)*phi*energy_well;
|
||||||
|
|
||||||
|
dUdphi = uA;
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
dUdrhat[0] = dUdphi*dphi_drhat[0];
|
||||||
|
dUdrhat[1] = dUdphi*dphi_drhat[1];
|
||||||
|
dUdrhat[2] = dUdphi*dphi_drhat[2];
|
||||||
|
|
||||||
|
double dUdrhatrhat = MathExtra::dot3(dUdrhat,r12hat);
|
||||||
|
|
||||||
|
fforce[0] = dUdr*r12hat[0] + (dUdrhat[0]-dUdrhatrhat*r12hat[0])/r;
|
||||||
|
fforce[1] = dUdr*r12hat[1] + (dUdrhat[1]-dUdrhatrhat*r12hat[1])/r;
|
||||||
|
fforce[2] = dUdr*r12hat[2] + (dUdrhat[2]-dUdrhatrhat*r12hat[2])/r;
|
||||||
|
|
||||||
|
// torque i
|
||||||
|
dUdni1[0] = dUdphi*dphi_dni1[0];
|
||||||
|
dUdni1[1] = dUdphi*dphi_dni1[1];
|
||||||
|
dUdni1[2] = dUdphi*dphi_dni1[2];
|
||||||
|
|
||||||
|
MathExtra::cross3(dUdni1,ni1,ttor); //minus sign is replace by swapping ni1 and dUdni1
|
||||||
|
|
||||||
|
if (newton_pair || j < nlocal) {
|
||||||
|
|
||||||
|
dUdnj1[0] = dUdphi*dphi_dnj1[0];
|
||||||
|
dUdnj1[1] = dUdphi*dphi_dnj1[1];
|
||||||
|
dUdnj1[2] = dUdphi*dphi_dnj1[2];
|
||||||
|
|
||||||
|
MathExtra::cross3(dUdnj1,nj1,rtor); //minus sign is replace by swapping ni1 and dUdni1
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
// output energy, force, torque, only for the in_two_particles input file, for checking the model implementation
|
||||||
|
/*
|
||||||
|
fprintf(screen,"energy = %f \n",U);
|
||||||
|
fprintf(screen,"force_i = %f %f %f \n",fforce[0],fforce[1],fforce[2]);
|
||||||
|
fprintf(screen,"torque_i = %f %f %f \n",ttor[0],ttor[1],ttor[2]);
|
||||||
|
fprintf(screen,"torque_j = %f %f %f \n",rtor[0],rtor[1],rtor[2]);
|
||||||
|
*/
|
||||||
|
|
||||||
|
return U;
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
83
src/ASPHERE/pair_ylz.h
Executable file
83
src/ASPHERE/pair_ylz.h
Executable file
@ -0,0 +1,83 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
http://lammps.sandia.gov, Sandia National Laboratories
|
||||||
|
Steve Plimpton, sjplimp@sandia.gov
|
||||||
|
|
||||||
|
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.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef PAIR_CLASS
|
||||||
|
|
||||||
|
PairStyle(ylz,PairYLZ);
|
||||||
|
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_PAIR_YLZ_H
|
||||||
|
#define LMP_PAIR_YLZ_H
|
||||||
|
|
||||||
|
#include "pair.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class PairYLZ : public Pair {
|
||||||
|
public:
|
||||||
|
PairYLZ(LAMMPS *lmp);
|
||||||
|
virtual ~PairYLZ();
|
||||||
|
virtual void compute(int, int);
|
||||||
|
virtual void settings(int, char **);
|
||||||
|
void coeff(int, char **);
|
||||||
|
virtual void init_style();
|
||||||
|
double init_one(int, int);
|
||||||
|
void write_restart(FILE *);
|
||||||
|
void read_restart(FILE *);
|
||||||
|
void write_restart_settings(FILE *);
|
||||||
|
void read_restart_settings(FILE *);
|
||||||
|
void write_data(FILE *);
|
||||||
|
void write_data_all(FILE *);
|
||||||
|
|
||||||
|
|
||||||
|
protected:
|
||||||
|
|
||||||
|
double cut_global;
|
||||||
|
|
||||||
|
double **epsilon,**sigma,**cut,**zeta,**mu,**beta; // model parameter values for atom-type pairs
|
||||||
|
|
||||||
|
class AtomVecEllipsoid *avec;
|
||||||
|
|
||||||
|
void allocate();
|
||||||
|
double ylz_analytic(const int i, const int j, double a1[3][3],
|
||||||
|
double a2[3][3], double *r12,
|
||||||
|
const double rsq, double *fforce, double *ttor,
|
||||||
|
double *rtor);
|
||||||
|
|
||||||
|
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
#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 ylz requires atom style ellipsoid
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
|
*/
|
||||||
|
|
||||||
Reference in New Issue
Block a user