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Commit 1c92eece authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
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move updated gauss_flow example to the correct folder

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The input script in.GD is an example simulation using Gaussian dynamics (GD).
The simulation is of a simple 2d Lennard-Jones fluid flowing through a pipe.
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.
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.
2) create box
3) set up potential
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.
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.
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).
examples/USER/flow_gauss/in.GD deleted 100644 → 0
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#LAMMPS input script
#in.GD
#see README for details
###############################################################################
#initialize variables
clear
#frequency for outputting info (timesteps)
variable dump_rate equal 50
variable thermo_rate equal 10
#equilibration time (timesteps)
variable equil equal 1000
#stabilization time (timesteps to reach steady-state)
variable stabil equal 1000
#data collection time (timesteps)
variable run equal 2000
#length of pipe
variable L equal 30
#width of pipe
variable d equal 20
#flux (mass/sigma*tau)
variable J equal 0.1
#simulation box dimensions
variable Lx equal 100
variable Ly equal 40
#bulk fluid density
variable dens equal 0.8
#lattice spacing for wall atoms
variable aWall equal 1.0 #1.7472
#timestep
variable ts equal 0.001
#temperature
variable T equal 2.0
#thermostat damping constant
variable tdamp equal ${ts}*100
units lj
dimension 2
atom_style atomic
###############################################################################
#create box
#create lattice with the spacing aWall
variable rhoWall equal ${aWall}^(-2)
lattice sq ${rhoWall}
#modify input dimensions to be multiples of aWall
variable L1 equal round($L/${aWall})*${aWall}
variable d1 equal round($d/${aWall})*${aWall}
variable Ly1 equal round(${Ly}/${aWall})*${aWall}
variable Lx1 equal round(${Lx}/${aWall})*${aWall}
#create simulation box
variable lx2 equal ${Lx1}/2
variable ly2 equal ${Ly1}/2
region simbox block -${lx2} ${lx2} -${ly2} ${ly2} 0 0.1 units box
create_box 2 simbox
#####################################################################
#set up potential
mass 1 1.0 #fluid atoms
mass 2 1.0 #wall atoms
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
neigh_modify exclude type 2 2
timestep ${ts}
#####################################################################
#create atoms
#create wall atoms everywhere
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
#remove wall atoms outside wall region
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
#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}
#choose x lattice const to give correct density
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
#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
#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
region bulk union 3 left pipe right
create_atoms 1 region bulk
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
neigh_modify exclude group wall wall
velocity bulk create $T 78915 dist gaussian rot yes mom yes loop geom
#####################################################################
#set up PUT
#see Evans and Morriss, Phys. Rev. Lett. 56(20) 1986, p. 2172
#average number of particles per box, Evans and Morriss used 2.0
variable NperBox equal 8.0
#calculate box sizes
variable boxSide equal sqrt(${NperBox}/${dens})
variable nX equal round(lx/${boxSide})
variable nY equal round(ly/${boxSide})
variable dX equal lx/${nX}
variable dY equal ly/${nY}
#temperature of fluid (excluding wall)
compute myT bulk temp
#profile-unbiased temperature of fluid
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
#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
#####################################################################
#equilibrate without GD
fix nvt bulk nvt temp $T $T ${tdamp}
fix_modify nvt temp myTp
fix 2 bulk enforce2d
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)
#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
fix GD bulk flow/gauss 1 0 0 #energy yes
#fix_modify GD energy yes
run ${stabil}
#####################################################################
#collect data
#print the applied force and total flux to ensure conservation of Jx
variable Fapp equal f_GD[1]
compute vxBulk bulk reduce sum vx
compute vyBulk bulk reduce sum vy
variable invVol equal 1.0/(lx*ly)
variable jx equal c_vxBulk*${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
#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
#for the pressure profile, use the same grid as the PUT
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
#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
#full trajectory
# dump 7 bulk custom ${dump_rate} bulk.lammpstrj id type x y z
# dump_modify 7 sort id
run ${run}
examples/USER/misc/flow_gauss/README
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The input script in.GD is an example simulation using Gaussian dynamics (GD). The input script in.GD is an example simulation using Gaussian dynamics (GD).
The simulation is of a simple 2d Lennard-Jones fluid flowing through a pipe. 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. 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. Note that the run times and box size are chosen to allow a fast example run.
They are not adequate for a real simulation. They are not adequate for a real simulation.
The script has the following parts: The script has the following parts:
1) initialize variables 1) initialize variables
These can be modified to customize the simulation. Note that if the These can be modified to customize the simulation. Note that if the
pipe dimensions L or d are changed, the geometry should be checked pipe dimensions L or d are changed, the geometry should be checked
by visualizing the coordinates in all.init.lammpstrj. by visualizing the coordinates in all.init.lammpstrj.
2) create box 2) create box
3) set up potential 3) set up potential
4) create atoms 4) create atoms
5) set up profile-unbiased thermostat (PUT) 5) set up profile-unbiased thermostat (PUT)
see Evans and Morriss, Phys. Rev. Lett. 56(20) 1986, p. 2172 see Evans and Morriss, Phys. Rev. Lett. 56(20) 1986, p. 2172
By default, this uses boxes which contain on average 8 molecules. By default, this uses boxes which contain on average 8 molecules.
6) equilibrate without GD 6) equilibrate without GD
7) initialize the center-of-mass velocity and run to achieve steady-state 7) initialize the center-of-mass velocity and run to achieve steady-state
The system is initialized with a uniform velocity profile, which The system is initialized with a uniform velocity profile, which
relaxes over the course of the simulation. relaxes over the course of the simulation.
8) collect data 8) collect data
The data is output in several files: The data is output in several files:
GD.out contains the force that GD applies, and the flux in the x- and 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 y- directions. The output Jx should be equal to the value of
J set in section 1, which is 0.1 by default. J set in section 1, which is 0.1 by default.
x_profiles contains the velocity, density, and pressure profiles in x_profiles contains the velocity, density, and pressure profiles in
the x-direction. The pressure profile is given by the x-direction. The pressure profile is given by
(-1/2V)*(c_spa[1] + c_spa[2]), where V is the volume of a (-1/2V)*(c_spa[1] + c_spa[2]), where V is the volume of a
slice. The pressure profile is computed with IK1, see slice. The pressure profile is computed with IK1, see
Todd, Evans, and Davis, Phys. Rev. E 52(2) 1995, p. 1627. Todd, Evans, and Davis, Phys. Rev. E 52(2) 1995, p. 1627.
Note that to compare with the pump method, or to Note that to compare with the pump method, or to
compute a pressure drop, you must correct this pressure compute a pressure drop, you must correct this pressure
profile as described in Strong 2016 above. profile as described in Strong 2016 above.
Vy_profile is the velocity profile inside the pipe along the Vy_profile is the velocity profile inside the pipe along the
y-direction, u_x(y). y-direction, u_x(y).
examples/USER/misc/flow_gauss/in.GD 100755 → 100644
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...@@ -7,83 +7,85 @@ ...@@ -7,83 +7,85 @@
clear clear
#frequency for outputting info (timesteps) #frequency for outputting info (timesteps)
variable dump_rate equal 50 variable dump_rate equal 50
variable thermo_rate equal 10 variable thermo_rate equal 10
#equilibration time (timesteps) #equilibration time (timesteps)
variable equil equal 1000 variable equil equal 1000
#stabilization time (timesteps to reach steady-state) #stabilization time (timesteps to reach steady-state)
variable stabil equal 1000 variable stabil equal 1000
#data collection time (timesteps) #data collection time (timesteps)
variable run equal 2000 variable run equal 2000
#length of pipe #length of pipe
variable L equal 30 variable L equal 30
#width of pipe #width of pipe
variable d equal 20 variable d equal 20
#flux (mass/sigma*tau) #flux (mass/sigma*tau)
variable J equal 0.1 variable J equal 0.1
#simulation box dimensions #simulation box dimensions
variable Lx equal 100 variable Lx equal 100
variable Ly equal 40 variable Ly equal 40
#bulk fluid density #bulk fluid density
variable dens equal 0.8 variable dens equal 0.8
#lattice spacing for wall atoms #lattice spacing for wall atoms
variable aWall equal 1.0 #1.7472 variable aWall equal 1.0 #1.7472
#timestep #timestep
variable ts equal 0.001 variable ts equal 0.001
#temperature #temperature
variable T equal 2.0 variable T equal 2.0
#thermostat damping constant #thermostat damping constant
variable tdamp equal ${ts}*100 variable tdamp equal ${ts}*100
units lj units lj
dimension 2 dimension 2
atom_style atomic atom_style atomic
############################################################################### ###############################################################################
#create box #create box
#create lattice with the spacing aWall #create lattice with the spacing aWall
variable rhoWall equal ${aWall}^(-2) variable rhoWall equal ${aWall}^(-2)
lattice sq ${rhoWall} lattice sq ${rhoWall}
#modify input dimensions to be multiples of aWall #modify input dimensions to be multiples of aWall
variable L1 equal round($L/${aWall})*${aWall} variable L1 equal round($L/${aWall})*${aWall}
variable d1 equal round($d/${aWall})*${aWall} variable d1 equal round($d/${aWall})*${aWall}
variable Ly1 equal round(${Ly}/${aWall})*${aWall} variable Ly1 equal round(${Ly}/${aWall})*${aWall}
variable Lx1 equal round(${Lx}/${aWall})*${aWall} variable Lx1 equal round(${Lx}/${aWall})*${aWall}
#create simulation box #create simulation box
variable lx2 equal ${Lx1}/2 variable lx2 equal ${Lx1}/2
variable ly2 equal ${Ly1}/2 variable ly2 equal ${Ly1}/2
region simbox block -${lx2} ${lx2} -${ly2} ${ly2} 0 0.1 units box region simbox block -${lx2} ${lx2} -${ly2} ${ly2} 0 0.1 units box
create_box 2 simbox create_box 2 simbox
##################################################################### #####################################################################
#set up potential #set up potential
mass 1 1.0 #fluid atoms mass 1 1.0 #fluid atoms
mass 2 1.0 #wall atoms mass 2 1.0 #wall atoms
pair_style lj/cut 2.5 pair_style lj/cut 2.5
pair_modify shift yes pair_modify shift yes
pair_coeff 1 1 1.0 1.0 2.5 pair_coeff 1 1 1.0 1.0 2.5
pair_coeff 1 2 1.0 1.0 1.12246 pair_coeff 1 2 1.0 1.0 1.12246
pair_coeff 2 2 0.0 0.0 0.0 pair_coeff 2 2 0.0 0.0
timestep ${ts} neigh_modify exclude type 2 2
timestep ${ts}
##################################################################### #####################################################################
#create atoms #create atoms
...@@ -92,167 +94,169 @@ timestep ${ts} ...@@ -92,167 +94,169 @@ timestep ${ts}
create_atoms 2 box create_atoms 2 box
#define region which is "walled off" #define region which is "walled off"
variable dhalf equal ${d1}/2 variable dhalf equal ${d1}/2
variable Lhalf equal ${L1}/2 variable Lhalf equal ${L1}/2
region walltop block -${Lhalf} ${Lhalf} ${dhalf} EDGE -0.1 0.1 & region walltop block -${Lhalf} ${Lhalf} ${dhalf} EDGE -0.1 0.1 &
units box units box
region wallbot block -${Lhalf} ${Lhalf} EDGE -${dhalf} -0.1 0.1 & region wallbot block -${Lhalf} ${Lhalf} EDGE -${dhalf} -0.1 0.1 &
units box units box
region outsidewall union 2 walltop wallbot side out region outsidewall union 2 walltop wallbot side out
#remove wall atoms outside wall region #remove wall atoms outside wall region
group outside region outsidewall group outside region outsidewall
delete_atoms group outside delete_atoms group outside
#remove wall atoms that aren't on edge of wall region #remove wall atoms that aren't on edge of wall region
variable x1 equal ${Lhalf}-${aWall} variable x1 equal ${Lhalf}-${aWall}
variable y1 equal ${dhalf}+${aWall} variable y1 equal ${dhalf}+${aWall}
region insideTop block -${x1} ${x1} ${y1} EDGE -0.1 0.1 units box region insideTop block -${x1} ${x1} ${y1} EDGE -0.1 0.1 units box
region insideBot block -${x1} ${x1} EDGE -${y1} -0.1 0.1 units box region insideBot block -${x1} ${x1} EDGE -${y1} -0.1 0.1 units box
region insideWall union 2 insideTop insideBot region insideWall union 2 insideTop insideBot
group insideWall region insideWall group insideWall region insideWall
delete_atoms group insideWall delete_atoms group insideWall
#define new lattice, to give correct fluid density #define new lattice, to give correct fluid density
#y lattice const must be a multiple of aWall #y lattice const must be a multiple of aWall
variable atrue equal ${dens}^(-1/2) variable atrue equal ${dens}^(-1/2)
variable ay equal round(${atrue}/${aWall})*${aWall} variable ay equal round(${atrue}/${aWall})*${aWall}
#choose x lattice const to give correct density #choose x lattice const to give correct density
variable ax equal (${ay}*${dens})^(-1) variable ax equal (${ay}*${dens})^(-1)
#change Lx to be multiple of ax #change Lx to be multiple of ax
variable Lx1 equal round(${Lx}/${ax})*${ax} variable Lx1 equal round(${Lx}/${ax})*${ax}
variable lx2 equal ${Lx1}/2 variable lx2 equal ${Lx1}/2
change_box all x final -${lx2} ${lx2} units box change_box all x final -${lx2} ${lx2} units box
#define new lattice #define new lattice
lattice custom ${dens} & lattice custom ${dens} &
a1 ${ax} 0.0 0.0 a2 0.0 ${ay} 0.0 a3 0.0 0.0 1.0 & 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 basis 0.0 0.0 0.0
#fill in rest of box with bulk particles #fill in rest of box with bulk particles
variable delta equal 0.001 variable delta equal 0.001
variable Ldelt equal ${Lhalf}+${delta} variable Ldelt equal ${Lhalf}+${delta}
variable dDelt equal ${dhalf}-${delta} variable dDelt equal ${dhalf}-${delta}
region left block EDGE -${Ldelt} EDGE EDGE -0.1 0.1 units box region left block EDGE -${Ldelt} EDGE EDGE -0.1 0.1 units box
region right block ${Ldelt} EDGE EDGE EDGE -0.1 0.1 units box region right block ${Ldelt} EDGE EDGE EDGE -0.1 0.1 units box
region pipe block -${Ldelt} ${Ldelt} -${dDelt} ${dDelt} -0.1 0.1 & region pipe block -${Ldelt} ${Ldelt} -${dDelt} ${dDelt} -0.1 0.1 &
units box units box
region bulk union 3 left pipe right region bulk union 3 left pipe right
create_atoms 1 region bulk create_atoms 1 region bulk
group bulk type 1 group bulk type 1
group wall type 2 group wall type 2
#remove atoms that are too close to wall #remove atoms that are too close to wall
delete_atoms overlap 0.9 bulk wall delete_atoms overlap 0.9 bulk wall
neighbor 0.3 bin neighbor 0.3 bin
neigh_modify delay 0 every 1 check yes neigh_modify delay 0 every 1 check yes
neigh_modify exclude group wall wall neigh_modify exclude group wall wall
velocity bulk create $T 78915 dist gaussian rot yes mom yes loop geom velocity bulk create $T 78915 dist gaussian rot yes mom yes loop geom
##################################################################### #####################################################################
#set up PUT #set up PUT
#see Evans and Morriss, Phys. Rev. Lett. 56(20) 1986, p. 2172 #see Evans and Morriss, Phys. Rev. Lett. 56(20) 1986, p. 2172
#average number of particles per box, Evans and Morriss used 2.0 #average number of particles per box, Evans and Morriss used 2.0
variable NperBox equal 8.0 variable NperBox equal 8.0
#calculate box sizes #calculate box sizes
variable boxSide equal sqrt(${NperBox}/${dens}) variable boxSide equal sqrt(${NperBox}/${dens})
variable nX equal round(lx/${boxSide}) variable nX equal round(lx/${boxSide})
variable nY equal round(ly/${boxSide}) variable nY equal round(ly/${boxSide})
variable dX equal lx/${nX} variable dX equal lx/${nX}
variable dY equal ly/${nY} variable dY equal ly/${nY}
#temperature of fluid (excluding wall) #temperature of fluid (excluding wall)
compute myT bulk temp compute myT bulk temp
#profile-unbiased temperature of fluid #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 setup
thermo ${thermo_rate} thermo ${thermo_rate}
thermo_style custom step c_myT c_myTp etotal press thermo_style custom step c_myT c_myTp etotal press
#dump initial configuration #dump initial configuration
dump 55 all custom 1 all.init.lammpstrj id type x y z vx vy vz # 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 56 wall custom 1 wall.init.lammpstrj id type x y z
dump_modify 55 sort id # dump_modify 55 sort id
dump_modify 56 sort id # dump_modify 56 sort id
run 0 run 0
undump 55 # undump 55
undump 56 # undump 56
##################################################################### #####################################################################
#equilibrate without GD #equilibrate without GD
fix nvt bulk nvt temp $T $T ${tdamp} fix nvt bulk nvt temp $T $T ${tdamp}
fix_modify nvt temp myTp fix_modify nvt temp myTp
fix 2 bulk enforce2d fix 2 bulk enforce2d
run ${equil} run ${equil}
##################################################################### #####################################################################
#initialize the COM velocity and run to achieve steady-state #initialize the COM velocity and run to achieve steady-state
#calculate velocity to add: V=J/rho_total #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 #first remove any COM velocity, then add back the streaming velocity
velocity bulk zero linear 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 GD bulk flow/gauss 1 0 0 #energy yes
#fix_modify GD energy yes #fix_modify GD energy yes
run ${stabil} run ${stabil}
##################################################################### #####################################################################
#collect data #collect data
#print the applied force and total flux to ensure conservation of Jx #print the applied force and total flux to ensure conservation of Jx
variable Fapp equal f_GD[1] variable Fapp equal f_GD[1]
compute vxBulk bulk reduce sum vx compute vxBulk bulk reduce sum vx
compute vyBulk bulk reduce sum vy compute vyBulk bulk reduce sum vy
variable invVol equal 1.0/(lx*ly) variable invVol equal 1.0/(lx*ly)
variable jx equal c_vxBulk*${invVol} variable jx equal c_vxBulk*${invVol}
variable jy equal c_vyBulk*${invVol} variable jy equal c_vyBulk*${invVol}
variable curr_step equal step variable curr_step equal step
fix print_vCOM all print ${dump_rate} & variable p_Fapp format Fapp %.3f
"${curr_step} ${Fapp} ${jx} ${jy}" file GD.out screen no & variable p_jx format jx %.5g
title "timestep Fapp Jx Jy" variable p_jy format jy %.5g
fix print_vCOM all print ${dump_rate} &
#compute IK1 pressure profile "${curr_step} ${p_Fapp} ${p_jx} ${p_jy}" file GD.out screen no &
title "timestep Fapp Jx Jy"
#compute IK1 pressure profile
#see Todd, Evans, and Davis, Phys. Rev. E 52(2) 1995, p. 1627 #see Todd, Evans, and Davis, Phys. Rev. E 52(2) 1995, p. 1627
#use profile-unbiased temperature to remove the streaming velocity #use profile-unbiased temperature to remove the streaming velocity
#from the kinetic part of the pressure #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 #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 #output pressure profile and other profiles
#the pressure profile is (-1/2V)*(c_spa[1] + c_spa[2]), where #the pressure profile is (-1/2V)*(c_spa[1] + c_spa[2]), where
#V is the volume of a slice #V is the volume of a slice
fix profiles bulk ave/chunk 1 1 ${dump_rate} chunkX & fix profiles bulk ave/chunk 1 1 ${dump_rate} chunkX &
vx density/mass c_spa[1] c_spa[2] & vx density/mass c_spa[1] c_spa[2] &
file x_profiles ave running overwrite file x_profiles ave running overwrite
#compute velocity profile across the pipe with a finer grid #compute velocity profile across the pipe with a finer grid
variable dYnew equal ${dY}/10 variable dYnew equal ${dY}/10
compute chunkY bulk chunk/atom bin/1d y center ${dYnew} units box & compute chunkY bulk chunk/atom bin/1d y center ${dYnew} units box &
region pipe region pipe
fix velYprof bulk ave/chunk 1 1 ${dump_rate} chunkY & fix velYprof bulk ave/chunk 1 1 ${dump_rate} chunkY &
vx file Vy_profile ave running overwrite vx file Vy_profile ave running overwrite
#full trajectory #full trajectory
dump 7 bulk custom ${dump_rate} bulk.lammpstrj & # dump 7 bulk custom ${dump_rate} bulk.lammpstrj id type x y z
id type x y z # dump_modify 7 sort id
dump_modify 7 sort id
run ${run} run ${run}
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