Adding spring bondstyle
This commit is contained in:
Joel Thomas Clemmer
@ -59,7 +59,7 @@ neighbors are included in the neighbor list. All bonded neighbors must be includ
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in neighbor lists as they could become unbonded at any timestep.
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Currently there are two types of bonds included in this package. The first
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bond style, :doc:`bond bpm/simple <bond_bpm_simple>`, only applies pairwise,
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bond style, :doc:`bond bpm/spring <bond_bpm_spring>`, only applies pairwise,
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central body forces. Point particles must have :doc:`bond atom style <atom_style>`
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and may be thought of as nodes in a spring network. Alternatively,
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the second bond style, :doc:`bond bpm/rotational <bond_bpm_rotational>`,
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@ -304,6 +304,7 @@ models for mesoscale simulations of solids and fracture. See the
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* :doc:`Howto_bpm <Howto_bpm>`
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* :doc:`atom_style sphere/bpm <atom_style>`
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* :doc:`bond_style bpm/rotational <bond_bpm_rotational>`
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* :doc:`bond_style bpm/spring <bond_bpm_spring>`
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* :doc:`compute nbonds/atom <compute_nbonds_atom>`
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* :doc:`fix nve/sphere/bpm <fix_nve_sphere_bpm>`
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* :doc:`fix update/special/bonds <fix_update_special_bonds>`
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@ -28,7 +28,7 @@ Examples
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.. code-block:: LAMMPS
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bond_style bpm/rotational
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bond_coeff 1
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bond_coeff 1 1.0 0.2 0.02 0.02 0.20 0.04 0.04 0.04 0.1 0.02 0.002 0.002
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bond_style bpm/rotational myfix time id1 id2
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fix myfix all store/local 1000 3
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143
doc/src/bond_bpm_spring.rst
Normal file
143
doc/src/bond_bpm_spring.rst
Normal file
@ -0,0 +1,143 @@
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.. index:: bond_style bpm/spring
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bond_style bpm/spring command
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==========================
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Syntax
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""""""
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.. code-block:: LAMMPS
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bond_style bpm/spring keyword value attribute1 attribute2 ...
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* optional keyword = *store/local*
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.. parsed-literal::
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*store/local* values = ID of associated fix store/local followed by one or more attributes
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*id1, id2* = IDs of 2 atoms in the bond
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*time* = the time the bond broke
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*x, y, z* = the center of mass position of the 2 atoms when the bond broke
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*x/ref, y/ref, z/ref* = the inintial center of mass position of the 2 atoms
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Examples
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""""""""
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.. code-block:: LAMMPS
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bond_style bpm/spring
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bond_coeff 1 1.0 0.05 0.1
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bond_style bpm/spring myfix time id1 id2
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fix myfix all store/local 1000 3
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dump 1 all local 1000 dump.broken f_myfix[1] f_myfix[2] f_myfix[3]
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dump_modify 1 write_header no
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Description
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"""""""""""
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The *bpm/spring* bond style computes forces and torques based
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on deviations from the initial reference state of the two atoms.
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The reference state is stored by each bond when it is first computed
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in the setup of a run. Data is then preserved across run commands and
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is written to :doc:`binary restart files <restart>` such that restarting
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the system will not reset the reference state of a bond.
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This bond style only applies central-body forces which conserve the translational
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and rotational degrees of freedom of a bonded set of particles. The force
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has a magnitude of
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.. math::
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f = k (r - r_0) w
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where :math:`k_r` is a stiffness, :math:`r` is the current distance and
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:math:`r_0` is the initial distance between the two particles, and :math:`w`
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is a smoothing factor.
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Bonds will break at a strain of :math:`\epsilon_c`.
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This is done by setting by setting its type to 0 such that forces are
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no longer computed.
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The smoothing factor :math:`w` is constructed such that forces smoothly
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go to zero, avoiding discontinuities, as bonds approach the critical strain
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.. math::
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w = 1.0 - \left( \frac{r - r_0}{r_0 \epsilon_c} \right^4 .
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Finally, additional damping forces and torques are applied to the two
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particles. A force is applied proportional to the difference in the
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normal velocity of particles using a similar construction as
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dissipative particle dynamics (:ref:`(Groot) <Groot1>`):
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.. math::
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F_D = - \gamma_n w (\hat{r} \bullet \vec{v})
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where :math:`\gamma_n` is the damping strength, :math:`\hat{r}` is the
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radial normal vector, and :math:`\vec{v}` is the velocity difference
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between the two particles.
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The following coefficients must be defined for each bond type via the
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:doc:`bond_coeff <bond_coeff>` command as in the example above, or in
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the data file or restart files read by the :doc:`read_data <read_data>`
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or :doc:`read_restart <read_restart>` commands:
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* :math:`k` (force/distance units)
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* :math:`\epsilon_c` (unit less)
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* :math:`\gamma` (force/velocity units)
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As bonds can be broken between neighbor list builds, particular
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:doc:`special_bonds <special_bonds>` are required. See the `:doc: how to <Howto_BPM>`
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page on BPMs or `:doc: fix update/special/bonds <fix_update_special_bonds>`
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for details.
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This bond style tracks broken bonds and can record them using an instance of
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:doc:`fix store/local <fix_store_local>` if the *store/local* keyword is
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used followed by the ID of the fix and then a series of bond attributes.
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Note that when bonds are dumped to a file via the :doc:`dump local <dump>`
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command, bonds with type 0 (broken bonds) are not included. The
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:doc:`delete_bonds <delete_bonds>` command can also be used to query the
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status of broken bonds or permanently delete them, e.g.:
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.. code-block:: LAMMPS
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delete_bonds all stats
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delete_bonds all bond 0 remove
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----------
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Restart
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"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
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This bond style writes the reference state of each bond to
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:doc:`binary restart files <restart>`. Loading a restart
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file will properly resume bonds.
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Restrictions
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""""""""""""
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This bond style can only be used if LAMMPS was built with the BPM
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package. See the :doc:`Build package <Build_package>` doc page for more
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info.
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The *bpm/spring* style requires 1-3 and 1-4 :doc:`special_bonds <special_bonds>`
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be turned off using the :doc:`special_bonds <special_bonds>` command.
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Related commands
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""""""""""""""""
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:doc:`bond_coeff <bond_coeff>`, :doc:`fix store/local <fix_store_local>`
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Default
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"""""""
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none
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.. _Groot1:
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**(Groot)** Groot and Warren, J Chem Phys, 107, 4423-35 (1997).
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@ -1,12 +1,12 @@
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units lj
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dimension 3
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boundary m m m
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boundary f f f
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atom_style sphere/bpm
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special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
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newton on off
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comm_modify vel yes cutoff 2.6
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lattice fcc 1.0
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region box block -5 15 -20 20 -20 20
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region box block -25 15 -22 22 -22 22
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create_box 1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
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region disk cylinder x 0.0 0.0 20.0 -0.5 0.5
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@ -32,7 +32,6 @@ fix 3 all update/special/bonds
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create_bonds many plate plate 1 0.0 1.5
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create_bonds many projectile projectile 2 0.0 1.5
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change_box all boundary s s s
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neighbor 0.3 bin
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special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
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@ -44,9 +43,10 @@ compute tbond all reduce sum c_nbond
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timestep 0.05
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thermo_style custom step ke pe pxx pyy pzz c_tbond
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thermo 100
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thermo_modify lost ignore lost/bond ignore
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#dump 1 all custom 100 atomDump id radius x y z c_nbond
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dump 2 all local 100 brokenDump f_2[1] f_2[2] f_2[3]
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dump_modify 2 header no
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run 10000
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run 7500
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54
examples/bpm/impact/impact_spring_bpm.lmp
Normal file
54
examples/bpm/impact/impact_spring_bpm.lmp
Normal file
@ -0,0 +1,54 @@
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units lj
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dimension 3
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boundary f f f
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atom_style bond
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special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
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newton on off
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comm_modify vel yes cutoff 2.6
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lattice fcc 1.0
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region box block -25 15 -22 22 -22 22
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create_box 1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
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region disk cylinder x 0.0 0.0 20.0 -0.5 0.5
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create_atoms 1 region disk
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group plate region disk
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region ball sphere 8.0 0.0 0.0 6.0
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create_atoms 1 region ball
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group projectile region ball
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displace_atoms all random 0.1 0.1 0.1 134598738
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mass 1 1.0
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neighbor 1.0 bin
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pair_style lj/cut 1.0
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bond_style bpm/spring store/local 2 time id1 id2
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pair_coeff 1 1 $(1/(18*PI)) $(2^(-1/6)) 1.0
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bond_coeff 1 1.0 0.04 1.0
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bond_coeff 2 1.0 0.20 1.0
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fix 1 all nve
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fix 2 all store/local 100 3
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fix 3 all update/special/bonds
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create_bonds many plate plate 1 0.0 1.5
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create_bonds many projectile projectile 2 0.0 1.5
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neighbor 0.3 bin
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special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
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velocity projectile set -0.05 0.0 0.0
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compute nbond all nbond/atom
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compute tbond all reduce sum c_nbond
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timestep 0.1
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thermo_style custom step ke pe pxx pyy pzz c_tbond
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thermo 100
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thermo_modify lost ignore lost/bond ignore
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#dump 1 all custom 100 atomDump id x y z c_nbond
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dump 2 all local 100 brokenDump f_2[1] f_2[2] f_2[3]
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dump_modify 2 header no
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run 7500
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215
examples/bpm/impact/log.30Jul2021.impact_rotational.g++1.4
Normal file
215
examples/bpm/impact/log.30Jul2021.impact_rotational.g++1.4
Normal file
@ -0,0 +1,215 @@
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LAMMPS (30 Jul 2021)
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units lj
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dimension 3
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boundary f f f
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atom_style sphere/bpm
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special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
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newton on off
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comm_modify vel yes cutoff 2.6
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lattice fcc 1.0
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Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
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region box block -25 15 -22 22 -22 22
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create_box 1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
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Created orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
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1 by 1 by 1 MPI processor grid
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region disk cylinder x 0.0 0.0 20.0 -0.5 0.5
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create_atoms 1 region disk
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Created 7529 atoms
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using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
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create_atoms CPU = 0.004 seconds
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group plate region disk
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7529 atoms in group plate
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region ball sphere 8.0 0.0 0.0 6.0
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create_atoms 1 region ball
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Created 3589 atoms
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using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
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create_atoms CPU = 0.002 seconds
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group projectile region ball
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3589 atoms in group projectile
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displace_atoms all random 0.1 0.1 0.1 134598738
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Displacing atoms ...
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neighbor 1.0 bin
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pair_style gran/hooke/history 1.0 NULL 0.5 NULL 0.1 1
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bond_style bpm/rotational store/local 2 time id1 id2
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pair_coeff 1 1
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bond_coeff 1 1.0 0.2 0.02 0.02 0.05 0.01 0.01 0.01 0.1 0.02 0.002 0.002
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bond_coeff 2 1.0 0.2 0.02 0.02 0.20 0.04 0.04 0.04 0.1 0.02 0.002 0.002
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fix 1 all nve/sphere/bpm
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fix 2 all store/local 100 3
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fix 3 all update/special/bonds
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create_bonds many plate plate 1 0.0 1.5
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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 = 2
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ghost atom cutoff = 2.6
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binsize = 1, bins = 64 70 70
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2 neighbor lists, perpetual/occasional/extra = 1 1 0
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(1) command create_bonds, occasional
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attributes: full, newton on
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pair build: full/bin
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stencil: full/bin/3d
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bin: standard
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(2) pair gran/hooke/history, perpetual
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attributes: half, newton on, size, history
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pair build: half/size/bin/newton
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stencil: half/bin/3d
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bin: standard
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Added 38559 bonds, new total = 38559
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 1 1
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special bond factors coul: 0 1 1
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15 = max # of 1-2 neighbors
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101 = max # of special neighbors
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special bonds CPU = 0.007 seconds
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create_bonds many projectile projectile 2 0.0 1.5
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Added 21869 bonds, new total = 60428
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 1 1
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special bond factors coul: 0 1 1
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16 = max # of 1-2 neighbors
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101 = max # of special neighbors
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special bonds CPU = 0.010 seconds
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neighbor 0.3 bin
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special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
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velocity projectile set -0.05 0.0 0.0
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compute nbond all nbond/atom
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compute tbond all reduce sum c_nbond
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timestep 0.05
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thermo_style custom step ke pe pxx pyy pzz c_tbond
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thermo 100
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thermo_modify lost ignore lost/bond ignore
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#dump 1 all custom 100 atomDump id radius x y z c_nbond
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dump 2 all local 100 brokenDump f_2[1] f_2[2] f_2[3]
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dump_modify 2 header no
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run 7500
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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 = 1.3
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ghost atom cutoff = 2.6
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binsize = 0.65, bins = 98 108 108
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair gran/hooke/history, perpetual
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attributes: half, newton on, size, history
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pair build: half/size/bin/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) = 39.18 | 39.18 | 39.18 Mbytes
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Step KinEng PotEng Pxx Pyy Pzz c_tbond
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0 0.00053238861 0 3.8217307e-05 0 0 10.8703
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100 0.00053238861 0 3.8217307e-05 3.7024766e-13 -2.6107956e-13 10.8703
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200 0.00053238861 0 3.8217307e-05 -4.6764996e-13 5.7734804e-13 10.8703
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300 0.00053238861 0 3.8217308e-05 -6.6404932e-13 -1.4463201e-13 10.8703
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400 0.00053238861 0 3.8217307e-05 -1.5842255e-13 3.2646699e-14 10.8703
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500 0.00053102307 0 3.6857657e-05 -5.0613842e-07 -4.5464639e-07 10.8703
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600 0.00051549565 0 1.5836226e-05 -6.6250357e-06 -7.1458399e-06 10.868322
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700 0.00050120381 0 -1.9467767e-05 -7.7209878e-06 -1.121158e-05 10.850333
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800 0.00049861454 0 1.5365076e-05 5.214591e-06 2.7950985e-06 10.803742
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900 0.00049582022 0 5.7445368e-05 -2.1846154e-05 -2.3927093e-05 10.738082
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1000 0.00049342915 0 4.9596969e-05 -8.1907786e-06 -1.3269952e-05 10.688433
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1100 0.00048639213 0 1.0822487e-05 3.9352339e-05 4.0409565e-05 10.667026
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1200 0.000483091 0 3.8492853e-06 2.2015581e-05 3.1490077e-05 10.646159
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1300 0.00047987023 0 5.8429983e-05 -7.8096854e-06 3.9318833e-06 10.631229
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1400 0.00048104927 0 4.6603937e-05 -1.2320299e-05 -1.010841e-05 10.619536
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1500 0.00047270384 0 -1.622772e-06 1.5996657e-05 1.5652658e-05 10.606944
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1600 0.00045720595 0 1.64434e-06 1.0627449e-05 7.2901589e-06 10.597949
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1700 0.00044826095 0 3.3113848e-05 -3.1886382e-05 -4.1076437e-05 10.584458
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1800 0.00044859158 0 3.8589858e-05 -3.217135e-05 -4.4394932e-05 10.554236
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1900 0.00044410417 0 1.6071124e-06 3.469787e-06 -1.172431e-05 10.528153
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2000 0.00043690537 0 1.8298385e-05 3.2800463e-05 2.3766026e-05 10.49955
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2100 0.00043113053 0 5.5169319e-05 1.0337577e-05 6.8334001e-06 10.449541
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2200 0.00042795839 0 3.3555532e-05 -7.8682107e-06 1.4501739e-06 10.40277
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2300 0.0004240013 0 8.8868452e-06 1.8196289e-06 2.755748e-05 10.362115
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2400 0.00042426888 0 2.3953861e-05 1.7614888e-05 4.2827512e-05 10.340529
|
||||
2500 0.00041903776 0 5.1969184e-05 2.5725967e-05 4.2229194e-05 10.324879
|
||||
2600 0.00042070944 0 4.0633614e-05 2.6089786e-05 3.2212886e-05 10.313006
|
||||
2700 0.00041907255 0 1.0826647e-05 2.7725133e-05 3.3535626e-05 10.301673
|
||||
2800 0.00041823551 0 2.7757924e-05 1.462054e-05 1.629062e-05 10.288001
|
||||
2900 0.00041833009 0 5.016926e-05 2.1116657e-06 -9.0474367e-06 10.276129
|
||||
3000 0.0004200714 0 2.9312093e-05 8.0995894e-06 -1.427634e-05 10.266954
|
||||
3100 0.00041930877 0 8.2905585e-06 2.5106255e-06 -6.0475079e-06 10.259039
|
||||
3200 0.00042002824 0 2.7415565e-05 -2.5467008e-05 -1.1758229e-05 10.249146
|
||||
3300 0.00041772304 0 4.7010143e-05 -3.2166248e-05 -2.3740064e-05 10.245728
|
||||
3400 0.00041567147 0 2.265559e-05 -1.4994351e-05 -1.4387458e-05 10.244828
|
||||
3500 0.00041264993 0 9.4675076e-06 -1.2940542e-05 -2.6164909e-06 10.243929
|
||||
3600 0.00041296772 0 3.2135436e-05 -2.3723233e-05 -1.1358132e-05 10.243029
|
||||
3700 0.00041218299 0 4.3546104e-05 -1.6744403e-05 -2.1466737e-05 10.240871
|
||||
3800 0.00041196427 0 2.4626877e-05 8.2428335e-06 -9.6621514e-06 10.236913
|
||||
3900 0.00041061174 0 1.5527454e-05 1.4796165e-05 8.5041818e-06 10.229718
|
||||
4000 0.00041008163 0 3.6758236e-05 -4.1693239e-06 -2.3638032e-07 10.221083
|
||||
4100 0.00040807476 0 4.2903311e-05 -8.7361319e-06 -9.2843568e-06 10.211909
|
||||
4200 0.00040749974 0 2.1764542e-05 -1.5964475e-07 1.1116464e-06 10.205972
|
||||
4300 0.00040585168 0 1.6398189e-05 -6.2081757e-07 1.4245018e-05 10.203454
|
||||
4400 0.00040614156 0 3.8921994e-05 -1.0816449e-05 8.8070462e-06 10.198237
|
||||
4500 0.00040550623 0 4.1195875e-05 -4.4468565e-06 -4.5109048e-06 10.19356
|
||||
4600 0.00040471568 0 1.9924175e-05 8.0584659e-06 2.8014197e-06 10.186904
|
||||
4700 0.00040443998 0 2.0848233e-05 7.2219213e-06 8.5736771e-06 10.182947
|
||||
4800 0.00040411017 0 3.8995426e-05 -3.5139599e-06 -1.7346701e-06 10.17773
|
||||
4900 0.00040369283 0 3.8616558e-05 -3.8837458e-07 -6.5227651e-06 10.174492
|
||||
5000 0.00040347603 0 1.957792e-05 5.3591428e-06 5.0851337e-06 10.171074
|
||||
5100 0.00040318 0 2.0628515e-05 -6.133528e-06 8.9227218e-06 10.166217
|
||||
5200 0.00040396442 0 3.9097282e-05 -1.3317561e-05 -2.4599499e-06 10.158842
|
||||
5300 0.00040420662 0 3.5316538e-05 -1.4346009e-06 -5.7802302e-06 10.154704
|
||||
5400 0.00040419432 0 1.9706975e-05 6.6651292e-06 3.0821293e-06 10.148768
|
||||
5500 0.00040500025 0 2.2492943e-05 -8.2260426e-06 4.6721228e-06 10.14463
|
||||
5600 0.00040447185 0 3.8628198e-05 -8.844675e-06 -6.7043678e-07 10.143191
|
||||
5700 0.00040435949 0 3.5236357e-05 5.3512632e-06 -2.9663861e-07 10.141752
|
||||
5800 0.00040356839 0 1.8078404e-05 7.7468465e-06 4.1618489e-06 10.141045
|
||||
5900 0.00040255066 0 2.5803838e-05 9.5521231e-07 3.4211797e-06 10.14251
|
||||
6000 0.00040255799 0 3.8202776e-05 -3.5222942e-06 -7.4050996e-06 10.14233
|
||||
6100 0.00040280742 0 3.0004475e-05 2.0612828e-06 -7.0155478e-06 10.14197
|
||||
6200 0.00040180209 0 1.8453425e-05 2.5937959e-06 6.019204e-06 10.142703
|
||||
6300 0.00040159364 0 2.6608078e-05 -3.4326767e-06 6.5089502e-06 10.142163
|
||||
6400 0.00039963271 0 3.7746341e-05 -1.3954533e-06 -6.6816781e-06 10.143076
|
||||
6500 0.0003995975 0 2.7758521e-05 6.370558e-06 -8.535581e-06 10.143076
|
||||
6600 0.00039973428 0 1.8062746e-05 6.3493548e-06 1.2970441e-06 10.143076
|
||||
6700 0.00039987367 0 2.7872598e-05 2.9794629e-07 3.1449123e-06 10.143988
|
||||
6800 0.00039942046 0 3.6871697e-05 4.4181241e-07 -3.7266658e-06 10.146188
|
||||
6900 0.00039937936 0 2.73304e-05 6.4090146e-06 1.1834424e-06 10.147835
|
||||
7000 0.00039934517 0 2.0161434e-05 5.3875016e-06 1.141564e-05 10.147835
|
||||
7100 0.00039884824 0 3.0603701e-05 7.327098e-07 5.1369462e-06 10.148402
|
||||
7200 0.00039774709 0 3.5965545e-05 3.6906864e-06 -5.6506465e-06 10.148969
|
||||
7300 0.00039642146 0 2.4883695e-05 7.2866197e-06 -8.2009411e-07 10.151379
|
||||
7400 0.00039605388 0 2.0790699e-05 2.6616664e-06 1.1522615e-05 10.152321
|
||||
7500 0.00039471805 0 3.0911798e-05 -4.6441697e-06 5.9470361e-06 10.154748
|
||||
Loop time of 114.934 on 1 procs for 7500 steps with 11089 atoms
|
||||
|
||||
Performance: 281901.613 tau/day, 65.255 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 1.2383 | 1.2383 | 1.2383 | 0.0 | 1.08
|
||||
Bond | 101.4 | 101.4 | 101.4 | 0.0 | 88.22
|
||||
Neigh | 2.7723 | 2.7723 | 2.7723 | 0.0 | 2.41
|
||||
Comm | 0.075342 | 0.075342 | 0.075342 | 0.0 | 0.07
|
||||
Output | 0.06732 | 0.06732 | 0.06732 | 0.0 | 0.06
|
||||
Modify | 9.1154 | 9.1154 | 9.1154 | 0.0 | 7.93
|
||||
Other | | 0.2695 | | | 0.23
|
||||
|
||||
Nlocal: 11089.0 ave 11089 max 11089 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: 45554.0 ave 45554 max 45554 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 45554
|
||||
Ave neighs/atom = 4.1080350
|
||||
Ave special neighs/atom = 10.156101
|
||||
Neighbor list builds = 467
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:55
|
||||
220
examples/bpm/impact/log.30Jul2021.impact_simple.g++1.4
Normal file
220
examples/bpm/impact/log.30Jul2021.impact_simple.g++1.4
Normal file
@ -0,0 +1,220 @@
|
||||
LAMMPS (30 Jul 2021)
|
||||
units lj
|
||||
dimension 3
|
||||
boundary f f f
|
||||
atom_style bond
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
newton on off
|
||||
comm_modify vel yes cutoff 2.6
|
||||
lattice fcc 1.0
|
||||
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||
region box block -25 15 -22 22 -22 22
|
||||
create_box 1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
|
||||
Created orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
region disk cylinder x 0.0 0.0 20.0 -0.5 0.5
|
||||
create_atoms 1 region disk
|
||||
Created 7529 atoms
|
||||
using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
|
||||
create_atoms CPU = 0.003 seconds
|
||||
group plate region disk
|
||||
7529 atoms in group plate
|
||||
|
||||
region ball sphere 8.0 0.0 0.0 6.0
|
||||
create_atoms 1 region ball
|
||||
Created 3589 atoms
|
||||
using lattice units in orthogonal box = (-39.685026 -34.922823 -34.922823) to (23.811016 34.922823 34.922823)
|
||||
create_atoms CPU = 0.002 seconds
|
||||
group projectile region ball
|
||||
3589 atoms in group projectile
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 134598738
|
||||
Displacing atoms ...
|
||||
|
||||
mass 1 1.0
|
||||
|
||||
neighbor 1.0 bin
|
||||
pair_style lj/cut 1.0
|
||||
bond_style bpm/spring store/local 2 time id1 id2
|
||||
pair_coeff 1 1 $(1/(18*PI)) $(2^(-1/6)) 1.0
|
||||
pair_coeff 1 1 0.017683882565766150669 $(2^(-1/6)) 1.0
|
||||
pair_coeff 1 1 0.017683882565766150669 0.89089871814033927411 1.0
|
||||
bond_coeff 1 1.0 0.04 1.0
|
||||
bond_coeff 2 1.0 0.20 1.0
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all store/local 100 3
|
||||
fix 3 all update/special/bonds
|
||||
|
||||
create_bonds many plate plate 1 0.0 1.5
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2.6
|
||||
binsize = 1, bins = 64 70 70
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command create_bonds, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Added 38559 bonds, new total = 38559
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
15 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.006 seconds
|
||||
create_bonds many projectile projectile 2 0.0 1.5
|
||||
WARNING: Communication cutoff 2.6 is shorter than a bond length based estimate of 2.799982026012842. This may lead to errors. (../comm.cpp:734)
|
||||
Added 21869 bonds, new total = 60428
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
16 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.008 seconds
|
||||
|
||||
neighbor 0.3 bin
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
velocity projectile set -0.05 0.0 0.0
|
||||
compute nbond all nbond/atom
|
||||
compute tbond all reduce sum c_nbond
|
||||
|
||||
timestep 0.1
|
||||
thermo_style custom step ke pe pxx pyy pzz c_tbond
|
||||
thermo 100
|
||||
thermo_modify lost ignore lost/bond ignore
|
||||
#dump 1 all custom 100 atomDump id x y z c_nbond
|
||||
|
||||
dump 2 all local 100 brokenDump f_2[1] f_2[2] f_2[3]
|
||||
dump_modify 2 header no
|
||||
|
||||
run 7500
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.3
|
||||
ghost atom cutoff = 2.6
|
||||
binsize = 0.65, bins = 98 108 108
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 22.50 | 22.50 | 22.50 Mbytes
|
||||
Step KinEng PotEng Pxx Pyy Pzz c_tbond
|
||||
0 0.0010167873 0 7.298968e-05 0 0 10.8703
|
||||
100 0.0010167873 0 7.298968e-05 -8.7429897e-20 -8.8470837e-20 10.8703
|
||||
200 0.0010167873 0 7.298968e-05 -7.2809565e-20 -8.0915788e-20 10.8703
|
||||
300 0.0010019973 -5.3291343e-05 0.00010093361 8.6373038e-06 9.8886169e-06 10.862565
|
||||
400 0.00096754254 -0.00013445443 0.00012114639 -1.0451037e-05 -1.3102312e-05 10.814535
|
||||
500 0.00098230681 -0.0001559819 8.1573507e-05 1.0019714e-05 6.6044989e-06 10.765785
|
||||
600 0.00099346016 -0.00021242987 7.8181991e-05 5.3246616e-06 6.7747639e-06 10.711999
|
||||
700 0.00097743083 -0.00022519088 9.2593451e-05 -1.3368324e-05 -9.1024741e-06 10.683037
|
||||
800 0.00097657062 -0.00025160598 7.6171833e-05 -3.6699488e-06 -3.156595e-06 10.648858
|
||||
900 0.00096573642 -0.00030010781 7.221088e-05 2.7980135e-06 8.3953748e-06 10.602806
|
||||
1000 0.00088967922 -0.00026225991 7.2273749e-05 -3.3180725e-06 1.7000133e-06 10.571429
|
||||
1100 0.00086637472 -0.00028264644 6.1827699e-05 -2.5263518e-06 -8.804488e-07 10.550198
|
||||
1200 0.00084322002 -0.00030067163 5.3193544e-05 -5.4186506e-06 -7.4414952e-07 10.528787
|
||||
1300 0.00082546285 -0.00029621074 5.8387607e-05 -5.4986846e-07 2.1039469e-06 10.507017
|
||||
1400 0.0008157657 -0.00031617563 5.8009972e-05 7.3256966e-06 4.560414e-06 10.481288
|
||||
1500 0.00083393604 -0.00030638038 5.2255981e-05 1.4804765e-05 9.4914663e-06 10.451961
|
||||
1600 0.00081285118 -0.00035496629 5.312358e-05 1.4502252e-05 1.3433953e-05 10.426849
|
||||
1700 0.00078740406 -0.00034224637 5.0152957e-05 1.0822543e-05 1.1601587e-05 10.406767
|
||||
1800 0.00076088167 -0.00039346684 5.0685628e-05 1.4591838e-05 6.8909935e-06 10.396831
|
||||
1900 0.00073852613 -0.00040295897 4.9940437e-05 2.2598772e-06 -1.0055633e-05 10.381741
|
||||
2000 0.00071844253 -0.00038465525 4.9242922e-05 -2.3157129e-05 -1.7381528e-05 10.36989
|
||||
2100 0.00070212224 -0.00039396945 4.380536e-05 -3.3139297e-05 -2.5812742e-05 10.359806
|
||||
2200 0.00068509947 -0.00038059464 4.1430464e-05 -2.8642858e-05 -3.0274798e-05 10.348131
|
||||
2300 0.00066204726 -0.00037290268 4.0755035e-05 -2.4099531e-05 -2.31417e-05 10.341529
|
||||
2400 0.00066390231 -0.00040132712 3.7909178e-05 -1.1313567e-05 -4.0596624e-06 10.325887
|
||||
2500 0.00067466471 -0.00036822838 3.3769672e-05 8.9955187e-06 7.2249524e-06 10.307692
|
||||
2600 0.00063522312 -0.00040169247 3.3473414e-05 1.7842262e-05 1.8667217e-05 10.294388
|
||||
2700 0.00071914116 -0.00044796394 4.069137e-05 2.9483289e-05 4.2250507e-05 10.234934
|
||||
2800 0.00070369013 -0.00044931969 3.1275752e-05 2.9033491e-05 3.9770684e-05 10.200721
|
||||
2900 0.00070512114 -0.00042845959 3.0186471e-05 2.5771984e-05 2.4348678e-05 10.177838
|
||||
3000 0.00069482317 -0.00044283829 3.3405984e-05 2.3415957e-05 2.2902999e-05 10.142896
|
||||
3100 0.00066723285 -0.00047945243 3.209325e-05 1.0654925e-05 2.0497587e-05 10.122195
|
||||
3200 0.00064836823 -0.00051480546 3.036046e-05 3.5029031e-06 1.1456758e-05 10.099135
|
||||
3300 0.00062844846 -0.0005036651 2.8409131e-05 -9.8098376e-06 -4.684996e-06 10.090311
|
||||
3400 0.00060808824 -0.00051335015 2.8585528e-05 -1.299304e-05 -1.042155e-05 10.085279
|
||||
3500 0.00060141771 -0.00053944948 3.3073003e-05 -1.4007198e-05 -1.4890004e-05 10.076632
|
||||
3600 0.00058955439 -0.00058831267 3.3193604e-05 -1.4717218e-05 -2.0169028e-05 10.067983
|
||||
3700 0.00057562588 -0.00053594395 3.1855934e-05 -1.2759241e-05 -1.778831e-05 10.06007
|
||||
3800 0.00056288488 -0.0005584841 3.0312862e-05 -9.7942798e-06 -1.5748733e-05 10.058818
|
||||
3900 0.0005587151 -0.00057123887 3.0257207e-05 -7.8343432e-06 -1.1945945e-05 10.056117
|
||||
4000 0.00055252357 -0.00056341012 3.0643644e-05 -3.5123196e-06 -7.6221264e-06 10.055766
|
||||
4100 0.00054746835 -0.0006001176 3.0871838e-05 3.1185521e-06 -2.7579162e-06 10.053254
|
||||
4200 0.00055406659 -0.00058858425 3.4129718e-05 1.0050578e-05 5.7346642e-06 10.040079
|
||||
4300 0.00055197755 -0.00060160199 3.2641549e-05 1.5817736e-05 9.4864214e-06 10.035028
|
||||
4400 0.00054566896 -0.00064016609 3.3944385e-05 2.157204e-05 6.1187523e-06 10.036121
|
||||
4500 0.00054060111 -0.00065952834 3.3119093e-05 2.4172484e-05 4.9459325e-06 10.03685
|
||||
4600 0.00054065729 -0.00066744113 3.223805e-05 2.3503537e-05 9.0427401e-06 10.035405
|
||||
4700 0.00054098427 -0.00064504776 3.2037001e-05 1.926565e-05 1.0546415e-05 10.034501
|
||||
4800 0.00054141253 -0.00068174982 3.1935667e-05 1.2727978e-05 8.8624733e-06 10.033418
|
||||
4900 0.00054027919 -0.00064378606 3.1759404e-05 7.3709768e-06 8.0812107e-06 10.035601
|
||||
5000 0.00053821803 -0.00064717177 3.1834908e-05 5.5119444e-06 5.2280812e-06 10.036692
|
||||
5100 0.00053536579 -0.00066007859 3.2403937e-05 4.0857527e-06 -1.5295741e-07 10.037419
|
||||
5200 0.00053648695 -0.00063942795 3.2383043e-05 1.6197156e-07 -4.7369656e-06 10.038326
|
||||
5300 0.00053622807 -0.00064591007 3.329864e-05 -1.7924131e-06 -6.7951652e-06 10.039233
|
||||
5400 0.00053960407 -0.0006173041 3.3993069e-05 -1.7932927e-06 -6.0531078e-06 10.03779
|
||||
5500 0.00053796949 -0.00063172209 3.4211179e-05 -3.0279549e-06 -6.3779479e-06 10.036344
|
||||
5600 0.00053754609 -0.00065574707 3.4750932e-05 -5.5906378e-06 -8.8682325e-06 10.03689
|
||||
5700 0.00053800964 -0.00067017804 3.4577555e-05 -8.2489481e-06 -1.0448862e-05 10.036528
|
||||
5800 0.00053783078 -0.00062551374 3.516311e-05 -9.7501091e-06 -1.0484624e-05 10.037074
|
||||
5900 0.00053771802 -0.00063683303 3.536403e-05 -1.0978806e-05 -1.1331075e-05 10.038889
|
||||
6000 0.00053818926 -0.0006480219 3.556216e-05 -1.1313579e-05 -1.2936664e-05 10.038889
|
||||
6100 0.00053847422 -0.0006368473 3.5618731e-05 -9.846739e-06 -1.2685058e-05 10.038709
|
||||
6200 0.00053845201 -0.00063840856 3.5837807e-05 -7.1875428e-06 -1.1762856e-05 10.038709
|
||||
6300 0.00053667612 -0.00066242577 3.6073709e-05 -4.7480116e-06 -1.1847933e-05 10.039616
|
||||
6400 0.00053622069 -0.00068157063 3.6102907e-05 -2.6083138e-06 -1.0659141e-05 10.039616
|
||||
6500 0.00053523267 -0.00069280776 3.6305856e-05 6.3043373e-07 -7.1642325e-06 10.041433
|
||||
6600 0.0005330839 -0.00066567528 3.6114434e-05 3.5272096e-06 -2.960556e-06 10.042888
|
||||
6700 0.00053197306 -0.00066248792 3.6043626e-05 5.2775896e-06 2.4477165e-07 10.043254
|
||||
6800 0.00053144495 -0.00069604723 3.6046963e-05 6.4421403e-06 5.1877078e-07 10.040901
|
||||
6900 0.00053079408 -0.00068001276 3.5639415e-05 7.9689078e-06 -4.083361e-07 10.040177
|
||||
7000 0.00053012176 -0.00068635527 3.5599595e-05 8.9040006e-06 -4.4296434e-07 10.039996
|
||||
7100 0.00052958544 -0.00067840066 3.5846725e-05 8.6942859e-06 2.6834024e-06 10.040543
|
||||
7200 0.00052858813 -0.00068968438 3.5554886e-05 6.0568352e-06 4.7776634e-06 10.041271
|
||||
7300 0.00052845993 -0.00070888583 3.5468591e-05 1.4110758e-06 5.6592858e-06 10.040909
|
||||
7400 0.00052678004 -0.00072652527 3.5417511e-05 -2.0145276e-06 6.3632678e-06 10.041818
|
||||
7500 0.00052676205 -0.00072008847 3.5601092e-05 -4.5673532e-06 7.3467401e-06 10.041455
|
||||
Loop time of 17.1712 on 1 procs for 7500 steps with 11048 atoms
|
||||
|
||||
Performance: 3773764.428 tau/day, 436.778 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 2.3271 | 2.3271 | 2.3271 | 0.0 | 13.55
|
||||
Bond | 5.8378 | 5.8378 | 5.8378 | 0.0 | 34.00
|
||||
Neigh | 4.42 | 4.42 | 4.42 | 0.0 | 25.74
|
||||
Comm | 0.07213 | 0.07213 | 0.07213 | 0.0 | 0.42
|
||||
Output | 0.064105 | 0.064105 | 0.064105 | 0.0 | 0.37
|
||||
Modify | 4.3202 | 4.3202 | 4.3202 | 0.0 | 25.16
|
||||
Other | | 0.1298 | | | 0.76
|
||||
|
||||
Nlocal: 11048.0 ave 11048 max 11048 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: 46555.0 ave 46555 max 46555 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 46555
|
||||
Ave neighs/atom = 4.2138849
|
||||
Ave special neighs/atom = 10.041455
|
||||
Neighbor list builds = 732
|
||||
Dangerous builds = 710
|
||||
Total wall time: 0:00:17
|
||||
@ -1,241 +0,0 @@
|
||||
LAMMPS (30 Jul 2021)
|
||||
units lj
|
||||
dimension 3
|
||||
boundary m m m
|
||||
atom_style sphere/bpm
|
||||
special_bonds lj 0.0 1.0 1.0 coul 0.0 1.0 1.0
|
||||
newton on off
|
||||
comm_modify vel yes cutoff 2.6
|
||||
lattice fcc 1.0
|
||||
Lattice spacing in x,y,z = 1.5874011 1.5874011 1.5874011
|
||||
region box block -5 15 -20 20 -20 20
|
||||
create_box 1 box bond/types 2 extra/bond/per/atom 20 extra/special/per/atom 50
|
||||
Created orthogonal box = (-7.9370053 -31.748021 -31.748021) to (23.811016 31.748021 31.748021)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
|
||||
region disk cylinder x 0.0 0.0 20.0 -0.5 0.5
|
||||
create_atoms 1 region disk
|
||||
Created 7527 atoms
|
||||
using lattice units in orthogonal box = (-7.9370053 -31.748021 -31.748021) to (23.811016 31.748021 31.748021)
|
||||
create_atoms CPU = 0.002 seconds
|
||||
group plate region disk
|
||||
7527 atoms in group plate
|
||||
|
||||
region ball sphere 8.0 0.0 0.0 6.0
|
||||
create_atoms 1 region ball
|
||||
Created 3589 atoms
|
||||
using lattice units in orthogonal box = (-7.9370053 -31.748021 -31.748021) to (23.811016 31.748021 31.748021)
|
||||
create_atoms CPU = 0.001 seconds
|
||||
group projectile region ball
|
||||
3589 atoms in group projectile
|
||||
|
||||
displace_atoms all random 0.1 0.1 0.1 134598738
|
||||
Displacing atoms ...
|
||||
|
||||
neighbor 1.0 bin
|
||||
pair_style gran/hooke/history 1.0 NULL 0.5 NULL 0.1 1
|
||||
bond_style bpm/rotational store/local 2 time id1 id2
|
||||
pair_coeff 1 1
|
||||
bond_coeff 1 1.0 0.2 0.02 0.02 0.05 0.01 0.01 0.01 0.1 0.02 0.002 0.002
|
||||
bond_coeff 2 1.0 0.2 0.02 0.02 0.20 0.04 0.04 0.04 0.1 0.02 0.002 0.002
|
||||
|
||||
fix 1 all nve/sphere/bpm
|
||||
fix 2 all store/local 100 3
|
||||
fix 3 all update/special/bonds
|
||||
|
||||
create_bonds many plate plate 1 0.0 1.5
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2
|
||||
ghost atom cutoff = 2.6
|
||||
binsize = 1, bins = 32 64 64
|
||||
2 neighbor lists, perpetual/occasional/extra = 1 1 0
|
||||
(1) command create_bonds, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
(2) pair gran/hooke/history, perpetual
|
||||
attributes: half, newton on, size, history
|
||||
pair build: half/size/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Added 38551 bonds, new total = 38551
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
15 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.002 seconds
|
||||
create_bonds many projectile projectile 2 0.0 1.5
|
||||
Added 21869 bonds, new total = 60420
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 1 1
|
||||
special bond factors coul: 0 1 1
|
||||
16 = max # of 1-2 neighbors
|
||||
101 = max # of special neighbors
|
||||
special bonds CPU = 0.002 seconds
|
||||
change_box all boundary s s s
|
||||
Changing box ...
|
||||
|
||||
neighbor 0.3 bin
|
||||
special_bonds lj 0.0 1.0 1.0 coul 1.0 1.0 1.0
|
||||
|
||||
velocity projectile set -0.05 0.0 0.0
|
||||
compute nbond all nbond/atom
|
||||
compute tbond all reduce sum c_nbond
|
||||
|
||||
timestep 0.05
|
||||
thermo_style custom step ke pe pxx pyy pzz c_tbond
|
||||
thermo 100
|
||||
dump 1 all custom 100 atomDump id radius x y z c_nbond
|
||||
|
||||
dump 2 all local 100 brokenDump f_2[1] f_2[2] f_2[3]
|
||||
dump_modify 2 header no
|
||||
|
||||
run 10000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.3
|
||||
ghost atom cutoff = 2.6
|
||||
binsize = 0.65, bins = 36 97 97
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair gran/hooke/history, perpetual
|
||||
attributes: half, newton on, size, history
|
||||
pair build: half/size/bin/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 34.27 | 34.28 | 34.28 Mbytes
|
||||
Step KinEng PotEng Pxx Pyy Pzz c_tbond
|
||||
0 0.00053248439 -5.4354084 0.00012848545 -1.0639387e-19 1.5819554e-19 10.870817
|
||||
100 0.00053248439 -5.4354084 0.00013017373 1.1334839e-12 1.784281e-12 10.870817
|
||||
200 0.00053248439 -5.4354084 0.00013279102 1.6787387e-12 5.4953548e-13 10.870817
|
||||
300 0.00053248439 -5.4354084 0.00013459514 3.0577302e-12 -1.2088316e-12 10.870817
|
||||
400 0.00053248439 -5.4354084 0.00013739515 9.7326931e-13 1.1562543e-12 10.870817
|
||||
500 0.00053111833 -5.4353812 0.00013532154 -1.8602155e-06 -1.6702711e-06 10.870817
|
||||
600 0.00051558884 -5.4335908 5.8899364e-05 -2.4651157e-05 -2.6584555e-05 10.868838
|
||||
700 0.0005013055 -5.4216397 -7.255462e-05 -2.8970044e-05 -4.1925574e-05 10.850846
|
||||
800 0.00049878634 -5.3947446 5.6196335e-05 1.8649508e-05 8.9976433e-06 10.803706
|
||||
900 0.00049589843 -5.3619596 0.00020821095 -7.7726675e-05 -8.6749853e-05 10.737855
|
||||
1000 0.00049487709 -5.3376233 0.00017638288 -2.8676423e-05 -4.5487748e-05 10.683879
|
||||
1100 0.00048720924 -5.3283688 4.0171402e-05 0.0001406456 0.00014483 10.662648
|
||||
1200 0.00048274004 -5.3195134 7.4824656e-06 7.4411513e-05 0.00010365246 10.643397
|
||||
1300 0.00047990668 -5.3127593 0.00018114159 -2.9205108e-05 1.1366149e-05 10.629723
|
||||
1400 0.00048034109 -5.3084824 0.000147425 -6.2432251e-05 -3.8277687e-05 10.620187
|
||||
1500 0.00047225373 -5.3024141 8.6252599e-07 2.4082822e-05 3.049023e-05 10.608492
|
||||
1600 0.00045698513 -5.2972292 1.0763242e-05 4.1148987e-05 2.83019e-05 10.599676
|
||||
1700 0.00044854655 -5.2896066 0.00010217014 -6.9430229e-05 -9.6661607e-05 10.587262
|
||||
1800 0.00044929529 -5.2775304 0.00010981512 -8.0553726e-05 -0.00011931185 10.562972
|
||||
1900 0.00044441992 -5.2650251 1.8882842e-05 1.0491309e-05 -3.879472e-05 10.540842
|
||||
2000 0.00043947002 -5.2484561 4.4869915e-05 6.8824059e-05 3.5808833e-05 10.511155
|
||||
2100 0.00043372382 -5.2265524 0.00013970367 1.6484426e-05 2.2785645e-05 10.469054
|
||||
2200 0.00043174768 -5.2069377 9.4662371e-05 2.2278647e-06 3.5962708e-05 10.427852
|
||||
2300 0.0004270123 -5.1924656 2.3188212e-05 6.1522399e-06 7.4262622e-05 10.396006
|
||||
2400 0.00042569191 -5.1848751 5.7811979e-05 2.7124197e-05 0.0001072424 10.378733
|
||||
2500 0.00042259717 -5.1758217 0.00013069307 3.3656662e-05 0.00010197635 10.359482
|
||||
2600 0.00042271375 -5.1700793 9.5183077e-05 5.3232578e-05 8.9912385e-05 10.347787
|
||||
2700 0.00042252395 -5.1628759 2.6305437e-05 6.7644983e-05 7.7095778e-05 10.332674
|
||||
2800 0.00042123755 -5.1549973 6.5875753e-05 2.8392569e-05 2.8079356e-05 10.315941
|
||||
2900 0.00042132346 -5.1508594 0.00011264272 6.3410829e-06 -2.1983564e-05 10.306405
|
||||
3000 0.00042343054 -5.1495182 7.3503612e-05 3.8773748e-05 -9.519275e-06 10.301547
|
||||
3100 0.00042220412 -5.1483831 2.5233575e-05 5.0076476e-05 3.938746e-06 10.299568
|
||||
3200 0.00042303815 -5.1466902 6.1939664e-05 -9.1346169e-06 -2.5920911e-05 10.29651
|
||||
3300 0.00042000178 -5.144782 9.8814555e-05 -4.04749e-05 -4.2876825e-05 10.292371
|
||||
3400 0.00041874209 -5.1416065 5.1246647e-05 -2.7877246e-05 -3.225052e-05 10.286254
|
||||
3500 0.00041582277 -5.1397016 2.0053694e-05 -3.5797833e-05 -1.536015e-05 10.282296
|
||||
3600 0.00041607097 -5.139236 6.0675623e-05 -5.7232123e-05 -3.1162791e-05 10.281036
|
||||
3700 0.00041445536 -5.1373913 8.7909083e-05 -4.1136114e-05 -5.2627526e-05 10.277978
|
||||
3800 0.0004147342 -5.1323122 4.6324048e-05 7.0253754e-06 -3.3511914e-05 10.268442
|
||||
3900 0.00041446917 -5.1294358 2.8646507e-05 1.5201733e-05 -1.13759e-05 10.262504
|
||||
4000 0.00041346205 -5.1250314 6.540586e-05 -1.17595e-05 -2.8050171e-05 10.254948
|
||||
4100 0.00041230785 -5.1219436 7.9364924e-05 -4.1504333e-06 -2.2530525e-05 10.248111
|
||||
4200 0.00041198555 -5.1177883 4.3515184e-05 1.5227343e-05 -6.3707934e-06 10.240014
|
||||
4300 0.0004111489 -5.1134893 2.8350236e-05 2.0718016e-06 1.2010375e-05 10.231558
|
||||
4400 0.00041090623 -5.1104369 6.2460747e-05 -2.5959985e-05 7.8242641e-07 10.224901
|
||||
4500 0.00040944466 -5.1085221 6.7135567e-05 -1.7699087e-05 -4.7022089e-06 10.220943
|
||||
4600 0.00040810594 -5.1065034 3.5212952e-05 1.3568365e-05 1.3875486e-05 10.217704
|
||||
4700 0.00040810646 -5.1039941 3.3409499e-05 1.7215022e-05 2.8204859e-05 10.212487
|
||||
4800 0.0004074837 -5.1015741 5.5792503e-05 1.9563116e-06 1.823506e-06 10.207089
|
||||
4900 0.00040677077 -5.0987121 5.6695901e-05 8.2729584e-06 -1.2713008e-05 10.201871
|
||||
5000 0.00040636045 -5.0961728 3.0704198e-05 2.2141861e-05 8.2099332e-06 10.196474
|
||||
5100 0.00040606831 -5.0947673 3.1281394e-05 7.0864149e-06 2.0262936e-05 10.193055
|
||||
5200 0.00040652265 -5.0940213 5.2610835e-05 -1.2888854e-05 3.0894446e-06 10.191076
|
||||
5300 0.00040642029 -5.0931407 4.6148958e-05 -9.5544284e-06 -6.047443e-06 10.189457
|
||||
5400 0.00040642806 -5.0915733 2.59528e-05 -3.3035524e-06 1.026995e-05 10.186038
|
||||
5500 0.00040686546 -5.0908 2.9026708e-05 -9.0382082e-06 1.4643294e-05 10.184059
|
||||
5600 0.0004064361 -5.0908057 4.6731327e-05 -1.2664731e-05 -2.6232887e-06 10.183339
|
||||
5700 0.00040629203 -5.0903044 4.0856223e-05 -1.2201759e-06 -1.3169401e-05 10.18262
|
||||
5800 0.00040637688 -5.0890571 2.2625249e-05 8.7645385e-06 -6.2486963e-06 10.180281
|
||||
5900 0.00040613721 -5.0874767 2.8382883e-05 2.4072343e-06 2.0419388e-07 10.176862
|
||||
6000 0.00040668084 -5.0865465 4.3602089e-05 -5.4962058e-06 -4.5087421e-06 10.174523
|
||||
6100 0.00040707325 -5.0865389 3.4958823e-05 -2.0750124e-06 -1.6708517e-06 10.174343
|
||||
6200 0.00040691768 -5.0863974 2.1602821e-05 3.1566836e-06 1.0526645e-05 10.174343
|
||||
6300 0.00040705673 -5.0862887 2.9412395e-05 9.2283412e-07 1.4273225e-05 10.173983
|
||||
6400 0.00040648035 -5.0860509 3.9684464e-05 -1.663237e-06 3.9771927e-06 10.173624
|
||||
6500 0.00040710623 -5.0861041 3.1078617e-05 1.732822e-06 3.4003409e-06 10.173624
|
||||
6600 0.00040665879 -5.0857907 2.0693771e-05 3.3053846e-06 1.2181329e-05 10.173264
|
||||
6700 0.00040650151 -5.0854203 2.8479998e-05 2.7244033e-06 9.7566436e-06 10.172364
|
||||
6800 0.00040635649 -5.0851816 3.5150661e-05 1.6906684e-06 -6.155957e-06 10.171644
|
||||
6900 0.00040670804 -5.0848974 2.4632227e-05 2.9367001e-06 -1.0691056e-05 10.171105
|
||||
7000 0.00040693354 -5.0843039 1.8740741e-05 6.024808e-06 4.2065619e-07 10.169665
|
||||
7100 0.00040728228 -5.0843393 2.7137965e-05 5.5506702e-06 5.5908974e-06 10.169665
|
||||
7200 0.0004074084 -5.0842875 3.0307934e-05 2.0170793e-06 -2.4296651e-06 10.169485
|
||||
7300 0.00040723509 -5.0843468 2.1465618e-05 1.9642493e-06 -3.6022271e-06 10.169485
|
||||
7400 0.00040756027 -5.0843623 1.6801323e-05 -1.9748948e-06 1.4205345e-06 10.169306
|
||||
7500 0.00040829979 -5.0843202 2.4772881e-05 -6.1251363e-06 2.0247483e-06 10.169126
|
||||
7600 0.00040822994 -5.0843182 2.7272667e-05 -3.0357928e-06 4.894101e-07 10.169126
|
||||
7700 0.00040831723 -5.0843052 1.9410405e-05 3.6094291e-06 1.5451381e-06 10.169126
|
||||
7800 0.00040868149 -5.0843706 1.6484224e-05 3.3901782e-06 3.9911363e-06 10.169126
|
||||
7900 0.00040872521 -5.0843735 2.2844838e-05 2.8813595e-06 1.4869802e-06 10.169126
|
||||
8000 0.00040853749 -5.0843239 2.3537039e-05 5.1951501e-06 -1.2448734e-06 10.169126
|
||||
8100 0.00040812899 -5.0842554 1.6947117e-05 7.5128919e-06 -1.0877933e-06 10.168946
|
||||
8200 0.00040812313 -5.0842813 1.5639254e-05 3.6719094e-06 -9.3497783e-07 10.168946
|
||||
8300 0.00040817027 -5.0842752 2.0634335e-05 2.5358492e-07 -3.2726598e-06 10.168946
|
||||
8400 0.00040774138 -5.084215 2.0224447e-05 1.3696075e-06 -3.3568279e-06 10.168766
|
||||
8500 0.00040760502 -5.0842 1.4541525e-05 9.3556598e-07 1.1823477e-06 10.168766
|
||||
8600 0.00040756971 -5.0841463 1.4460781e-05 -2.7822738e-06 4.3070092e-06 10.168766
|
||||
8700 0.00040706312 -5.0840255 1.8278276e-05 -5.20189e-06 1.0784628e-06 10.168766
|
||||
8800 0.00040670111 -5.0839094 1.7116511e-05 -9.4769204e-07 -3.2089738e-06 10.168586
|
||||
8900 0.00040617439 -5.0838164 1.3315166e-05 3.2313582e-06 -2.3144297e-06 10.168586
|
||||
9000 0.00040576758 -5.0837468 1.3898828e-05 1.5947021e-06 -2.0719014e-06 10.168586
|
||||
9100 0.00040577217 -5.0837244 1.6547097e-05 1.1667189e-06 -3.2056138e-06 10.168406
|
||||
9200 0.00040615545 -5.0837984 1.4946269e-05 4.3601683e-06 -2.1585248e-06 10.168406
|
||||
9300 0.00040638526 -5.083836 1.1737091e-05 5.1607613e-06 7.2161152e-07 10.168406
|
||||
9400 0.0004062125 -5.0838558 1.2486756e-05 1.9996225e-06 1.6192477e-06 10.168406
|
||||
9500 0.00040627984 -5.0839239 1.441806e-05 -6.6274154e-07 -2.9396969e-07 10.168406
|
||||
9600 0.0004065461 -5.0839109 1.3189089e-05 -5.1486848e-07 4.6653236e-07 10.168406
|
||||
9700 0.00040642188 -5.0838722 1.0626956e-05 -1.7580535e-06 2.8200944e-06 10.168226
|
||||
9800 0.0004061705 -5.0838326 1.1280802e-05 -3.4868266e-06 2.7287279e-06 10.168226
|
||||
9900 0.00040666798 -5.0835647 1.2432396e-05 -2.8727154e-06 1.4556152e-07 10.167686
|
||||
10000 0.00040675506 -5.0831833 1.0832242e-05 4.3061564e-07 -4.1422229e-07 10.166967
|
||||
Loop time of 48.2068 on 4 procs for 10000 steps with 11116 atoms
|
||||
|
||||
Performance: 896139.501 tau/day, 207.440 timesteps/s
|
||||
97.7% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.39096 | 0.42232 | 0.45519 | 4.6 | 0.88
|
||||
Bond | 30.522 | 33.954 | 38.166 | 51.7 | 70.43
|
||||
Neigh | 1.1822 | 1.1872 | 1.1915 | 0.3 | 2.46
|
||||
Comm | 3.4201 | 7.9545 | 11.664 | 115.6 | 16.50
|
||||
Output | 1.0078 | 1.0085 | 1.0099 | 0.1 | 2.09
|
||||
Modify | 3.0972 | 3.3841 | 3.7307 | 14.3 | 7.02
|
||||
Other | | 0.2958 | | | 0.61
|
||||
|
||||
Nlocal: 2779.00 ave 4159 max 1635 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Nghost: 1002.00 ave 1229 max 800 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Neighs: 11431.8 ave 18381 max 6059 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 45727
|
||||
Ave neighs/atom = 4.1136200
|
||||
Ave special neighs/atom = 10.166967
|
||||
Neighbor list builds = 637
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:48
|
||||
4
src/.gitignore
vendored
4
src/.gitignore
vendored
@ -257,8 +257,8 @@
|
||||
/bond_bpm.h
|
||||
/bond_bpm_rotational.cpp
|
||||
/bond_bpm_rotational.h
|
||||
/bond_bpm_simple.cpp
|
||||
/bond_bpm_simple.h
|
||||
/bond_bpm_spring.cpp
|
||||
/bond_bpm_spring.h
|
||||
/compute_nbond_atom.cpp
|
||||
/compute_nbond_atom.h
|
||||
/fix_bond_history.cpp
|
||||
|
||||
338
src/BPM/bond_bpm_spring.cpp
Normal file
338
src/BPM/bond_bpm_spring.cpp
Normal file
@ -0,0 +1,338 @@
|
||||
// clang-format off
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "bond_bpm_spring.h"
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "domain.h"
|
||||
#include "error.h"
|
||||
#include "fix_bond_history.h"
|
||||
#include "force.h"
|
||||
#include "math_const.h"
|
||||
#include "math_extra.h"
|
||||
#include "memory.h"
|
||||
#include "modify.h"
|
||||
#include "neighbor.h"
|
||||
#include "pair.h"
|
||||
|
||||
#include <mpi.h>
|
||||
#include <cmath>
|
||||
#include <cstring>
|
||||
|
||||
#define EPSILON 1e-10
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace MathExtra;
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondBPMSpring::BondBPMSpring(LAMMPS *lmp) : BondBPM(lmp)
|
||||
{
|
||||
partial_flag = 1;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
BondBPMSpring::~BondBPMSpring()
|
||||
{
|
||||
if (fix_bond_history) modify->delete_fix("BOND_HISTORY_BPM_SPRING");
|
||||
|
||||
if (allocated) {
|
||||
memory->destroy(setflag);
|
||||
memory->destroy(k);
|
||||
memory->destroy(ecrit);
|
||||
memory->destroy(gamma);
|
||||
}
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Store data for a single bond - if bond added after LAMMPS init (e.g. pour)
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
double BondBPMSpring::store_bond(int n,int i,int j)
|
||||
{
|
||||
int m,k;
|
||||
double delx, dely, delz, r;
|
||||
double **x = atom->x;
|
||||
double **bondstore = fix_bond_history->bondstore;
|
||||
tagint *tag = atom->tag;
|
||||
|
||||
delx = x[i][0] - x[j][0];
|
||||
dely = x[i][1] - x[j][1];
|
||||
delz = x[i][2] - x[j][2];
|
||||
|
||||
r = sqrt(delx*delx + dely*dely + delz*delz);
|
||||
bondstore[n][0] = r;
|
||||
|
||||
if (i < atom->nlocal) {
|
||||
for (m = 0; m < atom->num_bond[i]; m ++) {
|
||||
if (atom->bond_atom[i][m] == tag[j]) {
|
||||
fix_bond_history->update_atom_value(i, m, 0, r);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (j < atom->nlocal) {
|
||||
for (m = 0; m < atom->num_bond[j]; m ++) {
|
||||
if (atom->bond_atom[j][m] == tag[i]) {
|
||||
fix_bond_history->update_atom_value(j, m, 0, r);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return r;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Store data for all bonds called once
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMSpring::store_data()
|
||||
{
|
||||
int i, j, m, type;
|
||||
double delx, dely, delz, r;
|
||||
double **x = atom->x;
|
||||
int **bond_type = atom->bond_type;
|
||||
|
||||
for (i = 0; i < atom->nlocal; i ++) {
|
||||
for (m = 0; m < atom->num_bond[i]; m ++) {
|
||||
type = bond_type[i][m];
|
||||
|
||||
//Skip if bond was turned off
|
||||
if(type < 0)
|
||||
continue;
|
||||
|
||||
// map to find index n
|
||||
j = atom->map(atom->bond_atom[i][m]);
|
||||
if(j == -1) error->one(FLERR, "Atom missing in BPM bond");
|
||||
|
||||
delx = x[i][0] - x[j][0];
|
||||
dely = x[i][1] - x[j][1];
|
||||
delz = x[i][2] - x[j][2];
|
||||
|
||||
// Get closest image in case bonded with ghost
|
||||
domain->minimum_image(delx, dely, delz);
|
||||
r = sqrt(delx*delx + dely*dely + delz*delz);
|
||||
fix_bond_history->update_atom_value(i, m, 0, r);
|
||||
}
|
||||
}
|
||||
|
||||
fix_bond_history->post_neighbor();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMSpring::compute(int eflag, int vflag)
|
||||
{
|
||||
|
||||
if (! fix_bond_history->stored_flag) {
|
||||
fix_bond_history->stored_flag = true;
|
||||
store_data();
|
||||
}
|
||||
|
||||
int i1,i2,itmp,m,n,type,itype,jtype;
|
||||
double delx, dely, delz, delvx, delvy, delvz;
|
||||
double e, rsq, r, r0, rinv, smooth, fbond, dot;
|
||||
|
||||
ev_init(eflag,vflag);
|
||||
|
||||
if (vflag_global == 2)
|
||||
force->pair->vflag_either = force->pair->vflag_global = 1;
|
||||
|
||||
double **cutsq = force->pair->cutsq;
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
tagint *tag = atom->tag;
|
||||
int **bondlist = neighbor->bondlist;
|
||||
int nbondlist = neighbor->nbondlist;
|
||||
int nlocal = atom->nlocal;
|
||||
int newton_bond = force->newton_bond;
|
||||
|
||||
double **bondstore = fix_bond_history->bondstore;
|
||||
|
||||
for (n = 0; n < nbondlist; n++) {
|
||||
|
||||
// skip bond if already broken
|
||||
if (bondlist[n][2] <= 0) continue;
|
||||
|
||||
i1 = bondlist[n][0];
|
||||
i2 = bondlist[n][1];
|
||||
type = bondlist[n][2];
|
||||
r0 = bondstore[n][0];
|
||||
|
||||
delx = x[i1][0] - x[i2][0];
|
||||
dely = x[i1][1] - x[i2][1];
|
||||
delz = x[i1][2] - x[i2][2];
|
||||
|
||||
rsq = delx*delx + dely*dely + delz*delz;
|
||||
r = sqrt(rsq);
|
||||
e = (r - r0)/r0;
|
||||
|
||||
if (fabs(e) > ecrit[type]) {
|
||||
bondlist[n][2] = 0;
|
||||
process_broken(i1, i2);
|
||||
continue;
|
||||
}
|
||||
|
||||
rinv = 1.0/r;
|
||||
fbond = -k[type]*(r-r0);
|
||||
|
||||
delvx = v[i1][0] - v[i2][0];
|
||||
delvy = v[i1][1] - v[i2][1];
|
||||
delvz = v[i1][2] - v[i2][2];
|
||||
dot = delx*delvx + dely*delvy + delz*delvz;
|
||||
fbond -= gamma[type]*dot*rinv;
|
||||
|
||||
smooth = (r-r0)/(r0*ecrit[type]);
|
||||
smooth *= smooth;
|
||||
smooth *= smooth;
|
||||
smooth = 1 - smooth;
|
||||
|
||||
fbond *= rinv*smooth;
|
||||
|
||||
if (newton_bond || i1 < nlocal) {
|
||||
f[i1][0] += delx*fbond;
|
||||
f[i1][1] += dely*fbond;
|
||||
f[i1][2] += delz*fbond;
|
||||
}
|
||||
|
||||
if (newton_bond || i2 < nlocal) {
|
||||
f[i2][0] -= delx*fbond;
|
||||
f[i2][1] -= dely*fbond;
|
||||
f[i2][2] -= delz*fbond;
|
||||
}
|
||||
|
||||
if (evflag) ev_tally(i1,i2,nlocal,newton_bond,0.0,fbond,delx,dely,delz);
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMSpring::allocate()
|
||||
{
|
||||
allocated = 1;
|
||||
int n = atom->nbondtypes;
|
||||
|
||||
memory->create(k,n+1,"bond:k");
|
||||
memory->create(ecrit,n+1,"bond:ecrit");
|
||||
memory->create(gamma,n+1,"bond:gamma");
|
||||
|
||||
memory->create(setflag,n+1,"bond:setflag");
|
||||
for (int i = 1; i <= n; i++) setflag[i] = 0;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
set coeffs for one or more types
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMSpring::coeff(int narg, char **arg)
|
||||
{
|
||||
if (narg != 4) error->all(FLERR,"Incorrect args for bond coefficients");
|
||||
if (!allocated) allocate();
|
||||
|
||||
int ilo,ihi;
|
||||
utils::bounds(FLERR,arg[0],1,atom->nbondtypes,ilo,ihi,error);
|
||||
|
||||
double k_one = utils::numeric(FLERR,arg[1],false,lmp);
|
||||
double ecrit_one = utils::numeric(FLERR,arg[2],false,lmp);
|
||||
double gamma_one = utils::numeric(FLERR,arg[3],false,lmp);
|
||||
|
||||
int count = 0;
|
||||
for (int i = ilo; i <= ihi; i++) {
|
||||
k[i] = k_one;
|
||||
ecrit[i] = ecrit_one;
|
||||
gamma[i] = gamma_one;
|
||||
setflag[i] = 1;
|
||||
count++;
|
||||
|
||||
if (1.0+ecrit[i] > max_stretch) max_stretch = 1.0+ecrit[i];
|
||||
}
|
||||
|
||||
if (count == 0) error->all(FLERR,"Incorrect args for bond coefficients");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
check if pair defined and special_bond settings are valid
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMSpring::init_style()
|
||||
{
|
||||
BondBPM::init_style();
|
||||
|
||||
if (comm->ghost_velocity == 0)
|
||||
error->all(FLERR,"Bond bpm/spring requires ghost atoms store velocity");
|
||||
|
||||
if (!fix_bond_history)
|
||||
fix_bond_history = (FixBondHistory *) modify->add_fix(
|
||||
"BOND_HISTORY_BPM_SPRING all BOND_HISTORY 0 1");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes out coeffs to restart file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMSpring::write_restart(FILE *fp)
|
||||
{
|
||||
fwrite(&k[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&ecrit[1],sizeof(double),atom->nbondtypes,fp);
|
||||
fwrite(&gamma[1],sizeof(double),atom->nbondtypes,fp);
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 reads coeffs from restart file, bcasts them
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMSpring::read_restart(FILE *fp)
|
||||
{
|
||||
allocate();
|
||||
|
||||
if (comm->me == 0) {
|
||||
utils::sfread(FLERR,&k[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&ecrit[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
utils::sfread(FLERR,&gamma[1],sizeof(double),atom->nbondtypes,fp,nullptr,error);
|
||||
}
|
||||
MPI_Bcast(&k[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&ecrit[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
MPI_Bcast(&gamma[1],atom->nbondtypes,MPI_DOUBLE,0,world);
|
||||
|
||||
for (int i = 1; i <= atom->nbondtypes; i++) setflag[i] = 1;
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
proc 0 writes to data file
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
void BondBPMSpring::write_data(FILE *fp)
|
||||
{
|
||||
for (int i = 1; i <= atom->nbondtypes; i++)
|
||||
fprintf(fp,"%d %g %g %g\n", i,k[i],ecrit[i],gamma[i]);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
double BondBPMSpring::single(int type, double rsq, int i, int j,
|
||||
double &fforce)
|
||||
{
|
||||
// Not yet enabled
|
||||
if (type <= 0) return 0.0;
|
||||
|
||||
//double r0;
|
||||
//for (int n = 0; n < atom->num_bond[i]; n ++) {
|
||||
// if (atom->bond_atom[i][n] == atom->tag[j]) {
|
||||
// r0 = fix_bond_history->get_atom_value(i, n, 0);
|
||||
// }
|
||||
//}
|
||||
}
|
||||
74
src/BPM/bond_bpm_spring.h
Normal file
74
src/BPM/bond_bpm_spring.h
Normal file
@ -0,0 +1,74 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://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.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef BOND_CLASS
|
||||
// clang-format off
|
||||
BondStyle(bpm/spring,BondBPMSpring)
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_BOND_BPM_SPRING_H
|
||||
#define LMP_BOND_BPM_SPRING_H
|
||||
|
||||
#include "bond_bpm.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class BondBPMSpring : public BondBPM {
|
||||
public:
|
||||
BondBPMSpring(class LAMMPS *);
|
||||
virtual ~BondBPMSpring();
|
||||
virtual void compute(int, int);
|
||||
void coeff(int, char **);
|
||||
void init_style();
|
||||
void write_restart(FILE *);
|
||||
void read_restart(FILE *);
|
||||
void write_data(FILE *);
|
||||
double single(int, double, int, int, double &);
|
||||
|
||||
protected:
|
||||
double *k, *ecrit, *gamma;
|
||||
|
||||
void allocate();
|
||||
void store_data();
|
||||
double store_bond(int, int, int);
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Atom missing in BPM bond
|
||||
|
||||
Bonded atom cannot be found
|
||||
|
||||
E: Incorrect args for bond coefficients
|
||||
|
||||
Self-explanatory. Check the input script or data file.
|
||||
|
||||
E: Bond bpm/rotational requires atom style sphere/bpm
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Bond style bpm requires 1-3 and 1-4 special weights of 1.0
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
W: Bond style bpm/rotational not intended for 2d use, may be inefficient
|
||||
|
||||
This bond style will perform a lot of unnecessary calculations in 2d
|
||||
|
||||
*/
|
||||
Reference in New Issue
Block a user