142 lines
6.5 KiB
Plaintext
142 lines
6.5 KiB
Plaintext
#===========================================================================#
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# single particle drag tests #
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# #
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# Run consists of a colloidal particle being dragged with a constant force #
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# through an LB-fluid. The colloidal particle could be single atom or #
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# be a composite particle. Composite particles could be bonded or just #
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# rigidly constrained to stay together. You can set flags in the script to #
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# change these. #
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# #
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# Sample output from this run can be found in the files with "log." #
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# located in the same directory. #
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#===========================================================================#
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units nano
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dimension 3
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boundary p p f
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atom_style molecular
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region mydomain block -24.0 24.0 -24.0 24.0 -24.0 24.0
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#----------------------------------------------------------------------------
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# Set up particles with n_nodes and decide if bonded or rigid
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#----------------------------------------------------------------------------
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variable n_nodes equal 4 # 1, 4, 6 are options with definitions below
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variable is_bonded equal 0 # 0 or 1 (1 only if n_nodes > 1,
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# bond parameters set for n_node = 4 case)
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variable stpts equal 3 # 2, 3, 4 number of stencil points in any direction.
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variable tstep equal 0.00025
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if "${is_bonded} == 1" then &
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"create_box 1 mydomain bond/types 1 extra/bond/per/atom 6" &
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else &
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"create_box 1 mydomain"
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if "${n_nodes} == 1" then &
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"create_atoms 1 single 0.0 0.0 0.0" &
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elif "${n_nodes} == 4" &
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"create_atoms 1 single 0.0 0.0 0.204124" &
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"create_atoms 1 single -0.096225 -0.166667 -0.0680414" &
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"create_atoms 1 single -0.096225 0.166667 -0.0680414" &
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"create_atoms 1 single 0.19245 0. -0.0680414" &
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elif "${n_nodes} == 6" &
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"create_atoms 1 single 0.204124 0.0000000 0.0000000" &
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"create_atoms 1 single -0.204124 0.0000000 0.0000000" &
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"create_atoms 1 single 0.0000000 0.204124 0.0000000" &
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"create_atoms 1 single 0.0000000 -0.204124 0.0000000" &
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"create_atoms 1 single 0.0000000 0.0000000 0.204124" &
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"create_atoms 1 single 0.0000000 0.0000000 -0.204124"
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#----------------------------------------------------------------------------
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# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
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# to ensure that the particles belonging to a given processor remain inside
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# that processors lattice-Boltzmann grid.
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# The arguments for neigh_modify have been set to "delay 0 every 1", again
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# to ensure that the particles belonging to a given processor remain inside
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# that processors lattice-Boltzmann grid. However, these values can likely
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# be somewhat increased without issue. If a problem does arise (a particle
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# is outside of its processors LB grid) an error message is printed and
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# the simulation is terminated.
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#----------------------------------------------------------------------------
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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comm_modify cutoff 2.5 # cutoff for communcation shoud be at least 2 dx
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#----------------------------------------------------------------------------
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# Implement a hard-sphere interactions between particles & create bonds
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#----------------------------------------------------------------------------
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pair_style lj/cut 5.88
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pair_coeff * * 0.0 0.0 5.88
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variable total_mass equal 0.002398 # particle mass
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variable node_mass equal "v_total_mass / v_n_nodes"
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mass * ${node_mass}
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if "${is_bonded} == 1" then &
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"bond_style harmonic" &
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"bond_coeff 1 1.0 0.333333333" &
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"create_bonds many all all 1 0.3 0.35"
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#velocity all set 0.02 0.0 0.0
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#----------------------------------------------------------------------------
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# Define external forces (SHOULD COME BEFORE lb/fluid and lb/viscous FIXes)
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# to drag particles through the fluid.
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#----------------------------------------------------------------------------
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variable total_force equal 1.0 # total external force on the particle
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variable node_force equal "v_total_force / v_n_nodes"
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variable oscillateY equal cos(step*0.0005)/(-0.03+400*v_tstep)/v_n_nodes
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variable oscillateZ equal cos(step*0.0003)/(-0.03+400*v_tstep)/v_n_nodes
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fix drag all addforce ${node_force} v_oscillateY v_oscillateZ
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#---------------------------------------------------------------------------
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# Create a lattice-Boltzmann fluid covering the simulation domain.
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# This fluid feels a force due to the particle (group all here)
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# (however, this fix does not explicity apply a force back on to these
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# particles...this is accomplished through the use of the lb/viscous fix).
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# Use a fluid viscosity = 1.0, fluid density= 0.0009982071,(i.e. water) and
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# lattice spacing dx=1.2.
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# Different ".log" files in this directory show the output with the stencil
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# option being stencil 2, stencil 3, and stencil 4 (triliner, IBM, Key's).
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#----------------------------------------------------------------------------
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timestep ${tstep}
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fix FL all lb/fluid 1 1.0 0.0009982071 stencil ${stpts} dx 1.2
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#dumpxdmf 1000 fflow
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#----------------------------------------------------------------------------
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# Apply the force from the fluid to the particles, and integrate their
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# motion, constraining them to move and rotate together as a single rigid
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# spherical object or an elastically bonded object
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#----------------------------------------------------------------------------
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fix 2 all lb/viscous
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if "${n_nodes} == 1 || ${is_bonded} == 1" then &
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"fix 3 all nve" &
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else &
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"fix 3 all rigid group 1 all"
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#----------------------------------------------------------------------------
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# Create variables containing the positions/velocity of the colloids center
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# of mass.
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#----------------------------------------------------------------------------
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variable cmx equal xcm(all,x)
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variable cmy equal xcm(all,y)
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variable cmz equal xcm(all,z)
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variable vcmx equal vcm(all,x)
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variable vcmy equal vcm(all,y)
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variable vcmz equal vcm(all,z)
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if "${is_bonded} == 1" then &
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"variable comdatafile string drag_nb${n_nodes}_st${stpts}_dt${tstep}.out" &
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else &
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"variable comdatafile string drag_n${n_nodes}_st${stpts}_dt${tstep}.out"
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#fix printCM all print 100 "$(step) ${cmx} ${cmy} ${cmz} ${vcmx} ${vcmy} ${vcmz}" file ${comdatafile} screen no
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run 10000
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#run 100000
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