263 lines
8.2 KiB
GDScript
263 lines
8.2 KiB
GDScript
#LAMMPS input script
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#in.GD
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#see README for details
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###############################################################################
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#initialize variables
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clear
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#frequency for outputting info (timesteps)
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variable dump_rate equal 50
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variable thermo_rate equal 10
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#equilibration time (timesteps)
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variable equil equal 1000
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#stabilization time (timesteps to reach steady-state)
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variable stabil equal 1000
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#data collection time (timesteps)
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variable run equal 2000
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#length of pipe
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variable L equal 30
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#width of pipe
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variable d equal 20
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#flux (mass/sigma*tau)
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variable J equal 0.1
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#simulation box dimensions
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variable Lx equal 100
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variable Ly equal 40
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#bulk fluid density
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variable dens equal 0.8
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#lattice spacing for wall atoms
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variable aWall equal 1.0 #1.7472
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#timestep
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variable ts equal 0.001
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#temperature
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variable T equal 2.0
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#thermostat damping constant
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variable tdamp equal ${ts}*100
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units lj
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dimension 2
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atom_style atomic
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###############################################################################
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#create box
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#create lattice with the spacing aWall
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variable rhoWall equal ${aWall}^(-2)
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lattice sq ${rhoWall}
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#modify input dimensions to be multiples of aWall
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variable L1 equal round($L/${aWall})*${aWall}
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variable d1 equal round($d/${aWall})*${aWall}
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variable Ly1 equal round(${Ly}/${aWall})*${aWall}
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variable Lx1 equal round(${Lx}/${aWall})*${aWall}
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#create simulation box
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variable lx2 equal ${Lx1}/2
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variable ly2 equal ${Ly1}/2
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region simbox block -${lx2} ${lx2} -${ly2} ${ly2} 0 0.1 units box
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create_box 2 simbox
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#####################################################################
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#set up potential
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mass 1 1.0 #fluid atoms
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mass 2 1.0 #wall atoms
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pair_style lj/cut 2.5
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pair_modify shift yes
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pair_coeff 1 1 1.0 1.0 2.5
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pair_coeff 1 2 1.0 1.0 1.12246
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pair_coeff 2 2 0.0 0.0
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neigh_modify exclude type 2 2
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timestep ${ts}
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#####################################################################
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#create atoms
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#create wall atoms everywhere
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create_atoms 2 box
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#define region which is "walled off"
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variable dhalf equal ${d1}/2
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variable Lhalf equal ${L1}/2
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region walltop block -${Lhalf} ${Lhalf} ${dhalf} EDGE -0.1 0.1 &
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units box
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region wallbot block -${Lhalf} ${Lhalf} EDGE -${dhalf} -0.1 0.1 &
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units box
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region outsidewall union 2 walltop wallbot side out
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#remove wall atoms outside wall region
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group outside region outsidewall
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delete_atoms group outside
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#remove wall atoms that aren't on edge of wall region
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variable x1 equal ${Lhalf}-${aWall}
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variable y1 equal ${dhalf}+${aWall}
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region insideTop block -${x1} ${x1} ${y1} EDGE -0.1 0.1 units box
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region insideBot block -${x1} ${x1} EDGE -${y1} -0.1 0.1 units box
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region insideWall union 2 insideTop insideBot
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group insideWall region insideWall
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delete_atoms group insideWall
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#define new lattice, to give correct fluid density
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#y lattice const must be a multiple of aWall
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variable atrue equal ${dens}^(-1/2)
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variable ay equal round(${atrue}/${aWall})*${aWall}
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#choose x lattice const to give correct density
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variable ax equal (${ay}*${dens})^(-1)
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#change Lx to be multiple of ax
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variable Lx1 equal round(${Lx}/${ax})*${ax}
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variable lx2 equal ${Lx1}/2
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change_box all x final -${lx2} ${lx2} units box
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#define new lattice
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lattice custom ${dens} &
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a1 ${ax} 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 &
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basis 0.0 0.0 0.0
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#fill in rest of box with bulk particles
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variable delta equal 0.001
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variable Ldelt equal ${Lhalf}+${delta}
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variable dDelt equal ${dhalf}-${delta}
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region left block EDGE -${Ldelt} EDGE EDGE -0.1 0.1 units box
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region right block ${Ldelt} EDGE EDGE EDGE -0.1 0.1 units box
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region pipe block -${Ldelt} ${Ldelt} -${dDelt} ${dDelt} -0.1 0.1 &
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units box
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region bulk union 3 left pipe right
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create_atoms 1 region bulk
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group bulk type 1
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group wall type 2
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#remove atoms that are too close to wall
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delete_atoms overlap 0.9 bulk wall
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neighbor 0.3 bin
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neigh_modify delay 0 every 1 check yes
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neigh_modify exclude group wall wall
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velocity bulk create $T 78915 dist gaussian rot yes mom yes loop geom
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#####################################################################
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#set up PUT
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#see Evans and Morriss, Phys. Rev. Lett. 56(20) 1986, p. 2172
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#average number of particles per box, Evans and Morriss used 2.0
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variable NperBox equal 8.0
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#calculate box sizes
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variable boxSide equal sqrt(${NperBox}/${dens})
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variable nX equal round(lx/${boxSide})
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variable nY equal round(ly/${boxSide})
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variable dX equal lx/${nX}
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variable dY equal ly/${nY}
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#temperature of fluid (excluding wall)
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compute myT bulk temp
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#profile-unbiased temperature of fluid
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compute myTp bulk temp/profile 1 1 0 xy ${nX} ${nY}
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#thermo setup
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thermo ${thermo_rate}
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thermo_style custom step c_myT c_myTp etotal press
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#dump initial configuration
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# dump 55 all custom 1 all.init.lammpstrj id type x y z vx vy vz
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# dump 56 wall custom 1 wall.init.lammpstrj id type x y z
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# dump_modify 55 sort id
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# dump_modify 56 sort id
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run 0
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# undump 55
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# undump 56
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#####################################################################
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#equilibrate without GD
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fix nvt bulk nvt temp $T $T ${tdamp}
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fix_modify nvt temp myTp
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fix 2 bulk enforce2d
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run ${equil}
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#####################################################################
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#initialize the COM velocity and run to achieve steady-state
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#calculate velocity to add: V=J/rho_total
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variable Vadd equal $J*lx*ly/count(bulk)
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#first remove any COM velocity, then add back the streaming velocity
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velocity bulk zero linear
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velocity bulk set ${Vadd} 0.0 0.0 units box sum yes mom no
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fix GD bulk flow/gauss 1 0 0 #energy yes
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#fix_modify GD energy yes
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run ${stabil}
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#####################################################################
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#collect data
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#print the applied force and total flux to ensure conservation of Jx
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variable Fapp equal f_GD[1]
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compute vxBulk bulk reduce sum vx
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compute vyBulk bulk reduce sum vy
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variable invVol equal 1.0/(lx*ly)
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variable jx equal c_vxBulk*${invVol}
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variable jy equal c_vyBulk*${invVol}
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variable curr_step equal step
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variable p_Fapp format Fapp %.3f
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variable p_jx format jx %.5g
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variable p_jy format jy %.5g
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fix print_vCOM all print ${dump_rate} &
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"${curr_step} ${p_Fapp} ${p_jx} ${p_jy}" file GD.out screen no &
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title "timestep Fapp Jx Jy"
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#compute IK1 pressure profile
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#see Todd, Evans, and Davis, Phys. Rev. E 52(2) 1995, p. 1627
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#use profile-unbiased temperature to remove the streaming velocity
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#from the kinetic part of the pressure
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compute spa bulk stress/atom myTp
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#for the pressure profile, use the same grid as the PUT
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compute chunkX bulk chunk/atom bin/1d x lower ${dX} units box
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#output pressure profile and other profiles
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#the pressure profile is (-1/2V)*(c_spa[1] + c_spa[2]), where
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#V is the volume of a slice
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fix profiles bulk ave/chunk 1 1 ${dump_rate} chunkX &
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vx density/mass c_spa[1] c_spa[2] &
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file x_profiles ave running overwrite
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#compute velocity profile across the pipe with a finer grid
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variable dYnew equal ${dY}/10
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compute chunkY bulk chunk/atom bin/1d y center ${dYnew} units box &
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region pipe
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fix velYprof bulk ave/chunk 1 1 ${dump_rate} chunkY &
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vx file Vy_profile ave running overwrite
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#full trajectory
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# dump 7 bulk custom ${dump_rate} bulk.lammpstrj id type x y z
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# dump_modify 7 sort id
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run ${run}
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