diff --git a/examples/USER/flow_gauss/README b/examples/USER/flow_gauss/README
deleted file mode 100644
index ef7cc82d961fc056b16fd127b8dda5dfb5b38220..0000000000000000000000000000000000000000
--- a/examples/USER/flow_gauss/README
+++ /dev/null
@@ -1,45 +0,0 @@
-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).
diff --git a/examples/USER/flow_gauss/in.GD b/examples/USER/flow_gauss/in.GD
deleted file mode 100644
index bcff4d4c57bba23b014b7c3dae942884be8c84a2..0000000000000000000000000000000000000000
--- a/examples/USER/flow_gauss/in.GD
+++ /dev/null
@@ -1,262 +0,0 @@
-#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}
diff --git a/examples/USER/misc/flow_gauss/README b/examples/USER/misc/flow_gauss/README
index 4966cd2dc919eee2bd33f3970da1cb1a0d075eba..ef7cc82d961fc056b16fd127b8dda5dfb5b38220 100644
--- a/examples/USER/misc/flow_gauss/README
+++ b/examples/USER/misc/flow_gauss/README
@@ -1,45 +1,45 @@
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
+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.
+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.
+ 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.
+ 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.
+ 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).
diff --git a/examples/USER/misc/flow_gauss/in.GD b/examples/USER/misc/flow_gauss/in.GD
old mode 100755
new mode 100644
index 8117715c12705752c4efacaa04d6b562aef5e716..bcff4d4c57bba23b014b7c3dae942884be8c84a2
--- a/examples/USER/misc/flow_gauss/in.GD
+++ b/examples/USER/misc/flow_gauss/in.GD
@@ -7,83 +7,85 @@
clear
#frequency for outputting info (timesteps)
-variable dump_rate equal 50
-variable thermo_rate equal 10
+variable dump_rate equal 50
+variable thermo_rate equal 10
#equilibration time (timesteps)
-variable equil equal 1000
+variable equil equal 1000
#stabilization time (timesteps to reach steady-state)
-variable stabil equal 1000
+variable stabil equal 1000
#data collection time (timesteps)
-variable run equal 2000
+variable run equal 2000
#length of pipe
-variable L equal 30
+variable L equal 30
#width of pipe
-variable d equal 20
+variable d equal 20
#flux (mass/sigma*tau)
-variable J equal 0.1
+variable J equal 0.1
#simulation box dimensions
-variable Lx equal 100
-variable Ly equal 40
+variable Lx equal 100
+variable Ly equal 40
#bulk fluid density
-variable dens equal 0.8
+variable dens equal 0.8
#lattice spacing for wall atoms
-variable aWall equal 1.0 #1.7472
+variable aWall equal 1.0 #1.7472
#timestep
-variable ts equal 0.001
+variable ts equal 0.001
#temperature
-variable T equal 2.0
+variable T equal 2.0
#thermostat damping constant
-variable tdamp equal ${ts}*100
+variable tdamp equal ${ts}*100
-units lj
-dimension 2
-atom_style atomic
+units lj
+dimension 2
+atom_style atomic
###############################################################################
#create box
#create lattice with the spacing aWall
-variable rhoWall equal ${aWall}^(-2)
-lattice sq ${rhoWall}
+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})*${aWall}
+variable L1 equal round($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
+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
+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 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} ${jy}" file GD.out screen no &
- title "timestep Fapp Jx Jy"
-
-#compute IK1 pressure profile
+variable jx equal c_vxBulk*${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
+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}
diff --git a/examples/USER/flow_gauss/log.6Jul17.GD.g++.1 b/examples/USER/misc/flow_gauss/log.6Jul17.GD.g++.1
similarity index 100%
rename from examples/USER/flow_gauss/log.6Jul17.GD.g++.1
rename to examples/USER/misc/flow_gauss/log.6Jul17.GD.g++.1
diff --git a/examples/USER/flow_gauss/log.6Jul17.GD.g++.4 b/examples/USER/misc/flow_gauss/log.6Jul17.GD.g++.4
similarity index 100%
rename from examples/USER/flow_gauss/log.6Jul17.GD.g++.4
rename to examples/USER/misc/flow_gauss/log.6Jul17.GD.g++.4
diff --git a/examples/USER/flow_gauss/output-files/GD.out b/examples/USER/misc/flow_gauss/output-files/GD.out
similarity index 100%
rename from examples/USER/flow_gauss/output-files/GD.out
rename to examples/USER/misc/flow_gauss/output-files/GD.out
diff --git a/examples/USER/flow_gauss/output-files/Vy_profile b/examples/USER/misc/flow_gauss/output-files/Vy_profile
similarity index 100%
rename from examples/USER/flow_gauss/output-files/Vy_profile
rename to examples/USER/misc/flow_gauss/output-files/Vy_profile
diff --git a/examples/USER/flow_gauss/output-files/x_profiles b/examples/USER/misc/flow_gauss/output-files/x_profiles
similarity index 100%
rename from examples/USER/flow_gauss/output-files/x_profiles
rename to examples/USER/misc/flow_gauss/output-files/x_profiles