forked from lijiext/lammps
move updated gauss_flow example to the correct folder
This commit is contained in:
Axel Kohlmeyer
parent
a04711b21f
commit
1c92eecea7
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@ -1,45 +0,0 @@
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The input script in.GD is an example simulation using Gaussian dynamics (GD).
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The simulation is of a simple 2d Lennard-Jones fluid flowing through a pipe.
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For details see online LAMMPS documentation and
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Strong and Eaves, J. Phys. Chem. Lett. 7(10) 2016, p. 1907.
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Note that the run times and box size are chosen to allow a fast example run.
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They are not adequate for a real simulation.
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The script has the following parts:
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1) initialize variables
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These can be modified to customize the simulation. Note that if the
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pipe dimensions L or d are changed, the geometry should be checked
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by visualizing the coordinates in all.init.lammpstrj.
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2) create box
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3) set up potential
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4) create atoms
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5) set up profile-unbiased thermostat (PUT)
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see Evans and Morriss, Phys. Rev. Lett. 56(20) 1986, p. 2172
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By default, this uses boxes which contain on average 8 molecules.
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6) equilibrate without GD
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7) initialize the center-of-mass velocity and run to achieve steady-state
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The system is initialized with a uniform velocity profile, which
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relaxes over the course of the simulation.
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8) collect data
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The data is output in several files:
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GD.out contains the force that GD applies, and the flux in the x- and
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y- directions. The output Jx should be equal to the value of
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J set in section 1, which is 0.1 by default.
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x_profiles contains the velocity, density, and pressure profiles in
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the x-direction. The pressure profile is given by
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(-1/2V)*(c_spa[1] + c_spa[2]), where V is the volume of a
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slice. The pressure profile is computed with IK1, see
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Todd, Evans, and Davis, Phys. Rev. E 52(2) 1995, p. 1627.
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Note that to compare with the pump method, or to
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compute a pressure drop, you must correct this pressure
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profile as described in Strong 2016 above.
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Vy_profile is the velocity profile inside the pipe along the
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y-direction, u_x(y).
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@ -1,262 +0,0 @@
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#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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@ -1,45 +1,45 @@
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The input script in.GD is an example simulation using Gaussian dynamics (GD).
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The simulation is of a simple 2d Lennard-Jones fluid flowing through a pipe.
|
||||
For details see online LAMMPS documentation and
|
||||
For details see online LAMMPS documentation and
|
||||
Strong and Eaves, J. Phys. Chem. Lett. 7(10) 2016, p. 1907.
|
||||
|
||||
Note that the run times and box size are chosen to allow a fast example run.
|
||||
They are not adequate for a real simulation.
|
||||
Note that the run times and box size are chosen to allow a fast example run.
|
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They are not adequate for a real simulation.
|
||||
|
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The script has the following parts:
|
||||
1) initialize variables
|
||||
These can be modified to customize the simulation. Note that if the
|
||||
pipe dimensions L or d are changed, the geometry should be checked
|
||||
by visualizing the coordinates in all.init.lammpstrj.
|
||||
These can be modified to customize the simulation. Note that if the
|
||||
pipe dimensions L or d are changed, the geometry should be checked
|
||||
by visualizing the coordinates in all.init.lammpstrj.
|
||||
|
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2) create box
|
||||
|
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|
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3) set up potential
|
||||
|
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4) create atoms
|
||||
|
||||
5) set up profile-unbiased thermostat (PUT)
|
||||
see Evans and Morriss, Phys. Rev. Lett. 56(20) 1986, p. 2172
|
||||
By default, this uses boxes which contain on average 8 molecules.
|
||||
see Evans and Morriss, Phys. Rev. Lett. 56(20) 1986, p. 2172
|
||||
By default, this uses boxes which contain on average 8 molecules.
|
||||
|
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6) equilibrate without GD
|
||||
|
||||
|
||||
7) initialize the center-of-mass velocity and run to achieve steady-state
|
||||
The system is initialized with a uniform velocity profile, which
|
||||
relaxes over the course of the simulation.
|
||||
The system is initialized with a uniform velocity profile, which
|
||||
relaxes over the course of the simulation.
|
||||
|
||||
8) collect data
|
||||
The data is output in several files:
|
||||
GD.out contains the force that GD applies, and the flux in the x- and
|
||||
y- directions. The output Jx should be equal to the value of
|
||||
J set in section 1, which is 0.1 by default.
|
||||
x_profiles contains the velocity, density, and pressure profiles in
|
||||
the x-direction. The pressure profile is given by
|
||||
(-1/2V)*(c_spa[1] + c_spa[2]), where V is the volume of a
|
||||
slice. The pressure profile is computed with IK1, see
|
||||
Todd, Evans, and Davis, Phys. Rev. E 52(2) 1995, p. 1627.
|
||||
Note that to compare with the pump method, or to
|
||||
compute a pressure drop, you must correct this pressure
|
||||
profile as described in Strong 2016 above.
|
||||
Vy_profile is the velocity profile inside the pipe along the
|
||||
y-direction, u_x(y).
|
||||
The data is output in several files:
|
||||
GD.out contains the force that GD applies, and the flux in the x- and
|
||||
y- directions. The output Jx should be equal to the value of
|
||||
J set in section 1, which is 0.1 by default.
|
||||
x_profiles contains the velocity, density, and pressure profiles in
|
||||
the x-direction. The pressure profile is given by
|
||||
(-1/2V)*(c_spa[1] + c_spa[2]), where V is the volume of a
|
||||
slice. The pressure profile is computed with IK1, see
|
||||
Todd, Evans, and Davis, Phys. Rev. E 52(2) 1995, p. 1627.
|
||||
Note that to compare with the pump method, or to
|
||||
compute a pressure drop, you must correct this pressure
|
||||
profile as described in Strong 2016 above.
|
||||
Vy_profile is the velocity profile inside the pipe along the
|
||||
y-direction, u_x(y).
|
||||
|
|
|
|||
|
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@ -7,83 +7,85 @@
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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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variable dump_rate equal 50
|
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variable thermo_rate equal 10
|
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|
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#equilibration time (timesteps)
|
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variable equil equal 1000
|
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variable equil equal 1000
|
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|
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#stabilization time (timesteps to reach steady-state)
|
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variable stabil equal 1000
|
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variable stabil equal 1000
|
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|
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#data collection time (timesteps)
|
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variable run equal 2000
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variable run equal 2000
|
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|
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#length of pipe
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variable L equal 30
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variable L equal 30
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|
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#width of pipe
|
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variable d equal 20
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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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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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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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variable dens equal 0.8
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|
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#lattice spacing for wall atoms
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variable aWall equal 1.0 #1.7472
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variable aWall equal 1.0 #1.7472
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|
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#timestep
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variable ts equal 0.001
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variable ts equal 0.001
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|
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#temperature
|
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variable T equal 2.0
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variable T equal 2.0
|
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|
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#thermostat damping constant
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variable tdamp equal ${ts}*100
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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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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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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})*${aWall}
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variable L1 equal round($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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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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||||
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mass 1 1.0 #fluid atoms
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||||
mass 2 1.0 #wall atoms
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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
|
||||
pair_modify shift yes
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 1.12246
|
||||
pair_coeff 2 2 0.0 0.0 0.0
|
||||
pair_style lj/cut 2.5
|
||||
pair_modify shift yes
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 1.12246
|
||||
pair_coeff 2 2 0.0 0.0
|
||||
|
||||
timestep ${ts}
|
||||
neigh_modify exclude type 2 2
|
||||
|
||||
timestep ${ts}
|
||||
|
||||
#####################################################################
|
||||
#create atoms
|
||||
|
|
@ -92,167 +94,169 @@ timestep ${ts}
|
|||
create_atoms 2 box
|
||||
|
||||
#define region which is "walled off"
|
||||
variable dhalf equal ${d1}/2
|
||||
variable Lhalf equal ${L1}/2
|
||||
region walltop block -${Lhalf} ${Lhalf} ${dhalf} EDGE -0.1 0.1 &
|
||||
units box
|
||||
region wallbot block -${Lhalf} ${Lhalf} EDGE -${dhalf} -0.1 0.1 &
|
||||
units box
|
||||
region outsidewall union 2 walltop wallbot side out
|
||||
variable dhalf equal ${d1}/2
|
||||
variable Lhalf equal ${L1}/2
|
||||
region walltop block -${Lhalf} ${Lhalf} ${dhalf} EDGE -0.1 0.1 &
|
||||
units box
|
||||
region wallbot block -${Lhalf} ${Lhalf} EDGE -${dhalf} -0.1 0.1 &
|
||||
units box
|
||||
region outsidewall union 2 walltop wallbot side out
|
||||
|
||||
#remove wall atoms outside wall region
|
||||
group outside region outsidewall
|
||||
delete_atoms group outside
|
||||
group outside region outsidewall
|
||||
delete_atoms group outside
|
||||
|
||||
#remove wall atoms that aren't on edge of wall region
|
||||
variable x1 equal ${Lhalf}-${aWall}
|
||||
variable y1 equal ${dhalf}+${aWall}
|
||||
region insideTop block -${x1} ${x1} ${y1} EDGE -0.1 0.1 units box
|
||||
region insideBot block -${x1} ${x1} EDGE -${y1} -0.1 0.1 units box
|
||||
region insideWall union 2 insideTop insideBot
|
||||
group insideWall region insideWall
|
||||
delete_atoms group insideWall
|
||||
variable x1 equal ${Lhalf}-${aWall}
|
||||
variable y1 equal ${dhalf}+${aWall}
|
||||
region insideTop block -${x1} ${x1} ${y1} EDGE -0.1 0.1 units box
|
||||
region insideBot block -${x1} ${x1} EDGE -${y1} -0.1 0.1 units box
|
||||
region insideWall union 2 insideTop insideBot
|
||||
group insideWall region insideWall
|
||||
delete_atoms group insideWall
|
||||
|
||||
#define new lattice, to give correct fluid density
|
||||
#y lattice const must be a multiple of aWall
|
||||
variable atrue equal ${dens}^(-1/2)
|
||||
variable ay equal round(${atrue}/${aWall})*${aWall}
|
||||
variable atrue equal ${dens}^(-1/2)
|
||||
variable ay equal round(${atrue}/${aWall})*${aWall}
|
||||
|
||||
#choose x lattice const to give correct density
|
||||
variable ax equal (${ay}*${dens})^(-1)
|
||||
variable ax equal (${ay}*${dens})^(-1)
|
||||
|
||||
#change Lx to be multiple of ax
|
||||
variable Lx1 equal round(${Lx}/${ax})*${ax}
|
||||
variable lx2 equal ${Lx1}/2
|
||||
change_box all x final -${lx2} ${lx2} units box
|
||||
variable Lx1 equal round(${Lx}/${ax})*${ax}
|
||||
variable lx2 equal ${Lx1}/2
|
||||
change_box all x final -${lx2} ${lx2} units box
|
||||
|
||||
#define new lattice
|
||||
lattice custom ${dens} &
|
||||
a1 ${ax} 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 &
|
||||
basis 0.0 0.0 0.0
|
||||
lattice custom ${dens} &
|
||||
a1 ${ax} 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 &
|
||||
basis 0.0 0.0 0.0
|
||||
|
||||
#fill in rest of box with bulk particles
|
||||
variable delta equal 0.001
|
||||
variable Ldelt equal ${Lhalf}+${delta}
|
||||
variable dDelt equal ${dhalf}-${delta}
|
||||
region left block EDGE -${Ldelt} EDGE EDGE -0.1 0.1 units box
|
||||
region right block ${Ldelt} EDGE EDGE EDGE -0.1 0.1 units box
|
||||
region pipe block -${Ldelt} ${Ldelt} -${dDelt} ${dDelt} -0.1 0.1 &
|
||||
units box
|
||||
variable delta equal 0.001
|
||||
variable Ldelt equal ${Lhalf}+${delta}
|
||||
variable dDelt equal ${dhalf}-${delta}
|
||||
region left block EDGE -${Ldelt} EDGE EDGE -0.1 0.1 units box
|
||||
region right block ${Ldelt} EDGE EDGE EDGE -0.1 0.1 units box
|
||||
region pipe block -${Ldelt} ${Ldelt} -${dDelt} ${dDelt} -0.1 0.1 &
|
||||
units box
|
||||
|
||||
region bulk union 3 left pipe right
|
||||
create_atoms 1 region bulk
|
||||
region bulk union 3 left pipe right
|
||||
create_atoms 1 region bulk
|
||||
|
||||
group bulk type 1
|
||||
group wall type 2
|
||||
group bulk type 1
|
||||
group wall type 2
|
||||
|
||||
#remove atoms that are too close to wall
|
||||
delete_atoms overlap 0.9 bulk wall
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
neigh_modify exclude group wall wall
|
||||
|
||||
velocity bulk create $T 78915 dist gaussian rot yes mom yes loop geom
|
||||
velocity bulk create $T 78915 dist gaussian rot yes mom yes loop geom
|
||||
|
||||
#####################################################################
|
||||
#set up PUT
|
||||
#see Evans and Morriss, Phys. Rev. Lett. 56(20) 1986, p. 2172
|
||||
|
||||
#average number of particles per box, Evans and Morriss used 2.0
|
||||
variable NperBox equal 8.0
|
||||
variable NperBox equal 8.0
|
||||
|
||||
#calculate box sizes
|
||||
variable boxSide equal sqrt(${NperBox}/${dens})
|
||||
variable nX equal round(lx/${boxSide})
|
||||
variable nY equal round(ly/${boxSide})
|
||||
variable dX equal lx/${nX}
|
||||
variable dY equal ly/${nY}
|
||||
variable boxSide equal sqrt(${NperBox}/${dens})
|
||||
variable nX equal round(lx/${boxSide})
|
||||
variable nY equal round(ly/${boxSide})
|
||||
variable dX equal lx/${nX}
|
||||
variable dY equal ly/${nY}
|
||||
|
||||
#temperature of fluid (excluding wall)
|
||||
compute myT bulk temp
|
||||
compute myT bulk temp
|
||||
|
||||
#profile-unbiased temperature of fluid
|
||||
compute myTp bulk temp/profile 1 1 0 xy ${nX} ${nY}
|
||||
compute myTp bulk temp/profile 1 1 0 xy ${nX} ${nY}
|
||||
|
||||
#thermo setup
|
||||
thermo ${thermo_rate}
|
||||
thermo_style custom step c_myT c_myTp etotal press
|
||||
thermo ${thermo_rate}
|
||||
thermo_style custom step c_myT c_myTp etotal press
|
||||
|
||||
#dump initial configuration
|
||||
dump 55 all custom 1 all.init.lammpstrj id type x y z vx vy vz
|
||||
dump 56 wall custom 1 wall.init.lammpstrj id type x y z
|
||||
dump_modify 55 sort id
|
||||
dump_modify 56 sort id
|
||||
run 0
|
||||
undump 55
|
||||
undump 56
|
||||
# dump 55 all custom 1 all.init.lammpstrj id type x y z vx vy vz
|
||||
# dump 56 wall custom 1 wall.init.lammpstrj id type x y z
|
||||
# dump_modify 55 sort id
|
||||
# dump_modify 56 sort id
|
||||
run 0
|
||||
# undump 55
|
||||
# undump 56
|
||||
|
||||
#####################################################################
|
||||
#equilibrate without GD
|
||||
|
||||
fix nvt bulk nvt temp $T $T ${tdamp}
|
||||
fix_modify nvt temp myTp
|
||||
fix 2 bulk enforce2d
|
||||
fix nvt bulk nvt temp $T $T ${tdamp}
|
||||
fix_modify nvt temp myTp
|
||||
fix 2 bulk enforce2d
|
||||
|
||||
run ${equil}
|
||||
run ${equil}
|
||||
|
||||
#####################################################################
|
||||
#initialize the COM velocity and run to achieve steady-state
|
||||
|
||||
#calculate velocity to add: V=J/rho_total
|
||||
variable Vadd equal $J*lx*ly/count(bulk)
|
||||
variable Vadd equal $J*lx*ly/count(bulk)
|
||||
|
||||
#first remove any COM velocity, then add back the streaming velocity
|
||||
velocity bulk zero linear
|
||||
velocity bulk set ${Vadd} 0.0 0.0 units box sum yes mom no
|
||||
velocity bulk set ${Vadd} 0.0 0.0 units box sum yes mom no
|
||||
|
||||
fix GD bulk flow/gauss 1 0 0 #energy yes
|
||||
#fix_modify GD energy yes
|
||||
fix GD bulk flow/gauss 1 0 0 #energy yes
|
||||
#fix_modify GD energy yes
|
||||
|
||||
run ${stabil}
|
||||
run ${stabil}
|
||||
|
||||
#####################################################################
|
||||
#collect data
|
||||
|
||||
#print the applied force and total flux to ensure conservation of Jx
|
||||
variable Fapp equal f_GD[1]
|
||||
compute vxBulk bulk reduce sum vx
|
||||
compute vyBulk bulk reduce sum vy
|
||||
variable Fapp equal f_GD[1]
|
||||
compute vxBulk bulk reduce sum vx
|
||||
compute vyBulk bulk reduce sum vy
|
||||
variable invVol equal 1.0/(lx*ly)
|
||||
variable jx equal c_vxBulk*${invVol}
|
||||
variable jy equal c_vyBulk*${invVol}
|
||||
variable curr_step equal step
|
||||
fix print_vCOM all print ${dump_rate} &
|
||||
"${curr_step} ${Fapp} ${jx} ${jy}" file GD.out screen no &
|
||||
title "timestep Fapp Jx Jy"
|
||||
variable jx equal c_vxBulk*${invVol}
|
||||
variable jy equal c_vyBulk*${invVol}
|
||||
variable curr_step equal step
|
||||
variable p_Fapp format Fapp %.3f
|
||||
variable p_jx format jx %.5g
|
||||
variable p_jy format jy %.5g
|
||||
fix print_vCOM all print ${dump_rate} &
|
||||
"${curr_step} ${p_Fapp} ${p_jx} ${p_jy}" file GD.out screen no &
|
||||
title "timestep Fapp Jx Jy"
|
||||
|
||||
#compute IK1 pressure profile
|
||||
#compute IK1 pressure profile
|
||||
#see Todd, Evans, and Davis, Phys. Rev. E 52(2) 1995, p. 1627
|
||||
#use profile-unbiased temperature to remove the streaming velocity
|
||||
#from the kinetic part of the pressure
|
||||
compute spa bulk stress/atom myTp
|
||||
compute spa bulk stress/atom myTp
|
||||
|
||||
#for the pressure profile, use the same grid as the PUT
|
||||
compute chunkX bulk chunk/atom bin/1d x lower ${dX} units box
|
||||
compute chunkX bulk chunk/atom bin/1d x lower ${dX} units box
|
||||
|
||||
#output pressure profile and other profiles
|
||||
#the pressure profile is (-1/2V)*(c_spa[1] + c_spa[2]), where
|
||||
#V is the volume of a slice
|
||||
fix profiles bulk ave/chunk 1 1 ${dump_rate} chunkX &
|
||||
vx density/mass c_spa[1] c_spa[2] &
|
||||
file x_profiles ave running overwrite
|
||||
fix profiles bulk ave/chunk 1 1 ${dump_rate} chunkX &
|
||||
vx density/mass c_spa[1] c_spa[2] &
|
||||
file x_profiles ave running overwrite
|
||||
|
||||
#compute velocity profile across the pipe with a finer grid
|
||||
variable dYnew equal ${dY}/10
|
||||
compute chunkY bulk chunk/atom bin/1d y center ${dYnew} units box &
|
||||
region pipe
|
||||
fix velYprof bulk ave/chunk 1 1 ${dump_rate} chunkY &
|
||||
vx file Vy_profile ave running overwrite
|
||||
variable dYnew equal ${dY}/10
|
||||
compute chunkY bulk chunk/atom bin/1d y center ${dYnew} units box &
|
||||
region pipe
|
||||
fix velYprof bulk ave/chunk 1 1 ${dump_rate} chunkY &
|
||||
vx file Vy_profile ave running overwrite
|
||||
|
||||
#full trajectory
|
||||
dump 7 bulk custom ${dump_rate} bulk.lammpstrj &
|
||||
id type x y z
|
||||
dump_modify 7 sort id
|
||||
# dump 7 bulk custom ${dump_rate} bulk.lammpstrj id type x y z
|
||||
# dump_modify 7 sort id
|
||||
|
||||
run ${run}
|
||||
run ${run}
|
||||
|
|
|
|||
Loading…
Reference in New Issue