restore gaussian flow example that was lost. tweak input to make it usable for comparing

examples/USER/flow_gauss/README

+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

+#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/flow_gauss/output-files/GD.out

+timestep Fapp Jx Jy
+2050 -215.835 0.1 -0.002562
+2100 -220.455 0.1 -0.0019705
+2150 55.212 0.1 -0.0028338
+2200 87.052 0.1 -0.0042335
+2250 -62.998 0.1 -0.0045646
+2300 71.630 0.1 -0.0039858
+2350 43.159 0.1 -0.0029771
+2400 109.930 0.1 -0.0018522
+2450 110.735 0.1 -0.0011188
+2500 107.071 0.1 0.0005978
+2550 335.449 0.1 0.0010164
+2600 159.694 0.1 -0.00015953
+2650 6.532 0.1 -0.0004907
+2700 65.524 0.1 -0.00093116
+2750 79.662 0.1 -0.0033425
+2800 69.846 0.1 -0.0055377
+2850 122.175 0.1 -0.00721
+2900 32.456 0.1 -0.0086166
+2950 -85.137 0.1 -0.01107
+3000 154.735 0.1 -0.011337
+3050 72.979 0.1 -0.0095316
+3100 -24.457 0.1 -0.0098708
+3150 -0.383 0.1 -0.0094961
+3200 132.434 0.1 -0.011524
+3250 48.222 0.1 -0.014966
+3300 -73.186 0.1 -0.016999
+3350 172.062 0.1 -0.018554
+3400 106.144 0.1 -0.021202
+3450 -22.860 0.1 -0.01949
+3500 22.120 0.1 -0.016033
+3550 -254.920 0.1 -0.012172
+3600 -147.218 0.1 -0.011162
+3650 -12.508 0.1 -0.010255
+3700 81.846 0.1 -0.0085117
+3750 -79.406 0.1 -0.0061294
+3800 -34.994 0.1 -0.0026239
+3850 94.992 0.1 -0.0015312
+3900 -0.345 0.1 -0.0011157
+3950 -88.693 0.1 -0.0018929
+4000 156.029 0.1 -0.0024547

examples/USER/flow_gauss/output-files/Vy_profile

+# Chunk-averaged data for fix velYprof and group file
+# Timestep Number-of-chunks Total-count
+# Chunk Coord1 Ncount vx
+4000 130 18774
+  1 -19.8462 0 0
+  2 -19.5385 0 0
+  3 -19.2308 0 0
+  4 -18.9231 0 0
+  5 -18.6154 0 0
+  6 -18.3077 0 0
+  7 -18 0 0
+  8 -17.6923 0 0
+  9 -17.3846 0 0
+  10 -17.0769 0 0
+  11 -16.7692 0 0
+  12 -16.4615 0 0
+  13 -16.1538 0 0
+  14 -15.8462 0 0
+  15 -15.5385 0 0
+  16 -15.2308 0 0
+  17 -14.9231 0 0
+  18 -14.6154 0 0
+  19 -14.3077 0 0
+  20 -14 0 0
+  21 -13.6923 0 0
+  22 -13.3846 0 0
+  23 -13.0769 0 0
+  24 -12.7692 0 0
+  25 -12.4615 0 0
+  26 -12.1538 0 0
+  27 -11.8462 0 0
+  28 -11.5385 0 0
+  29 -11.2308 0 0
+  30 -10.9231 0 0
+  31 -10.6154 0 0
+  32 -10.3077 0 0
+  33 -10 0 0
+  34 -9.69231 0 0
+  35 -9.38462 0 0
+  36 -9.07692 12.3415 0.126356
+  37 -8.76923 9.14634 0.119194
+  38 -8.46154 3.46341 0.0688559
+  39 -8.15385 7.26829 0.180935
+  40 -7.84615 9.97561 0.114685
+  41 -7.53846 6.14634 0.158317
+  42 -7.23077 7.17073 0.128092
+  43 -6.92308 8.56098 0.30356
+  44 -6.61538 7.7561 0.118822
+  45 -6.30769 6.04878 0.170019
+  46 -6 8.19512 0.146873
+  47 -5.69231 8.4878 0.258003
+  48 -5.38462 7.21951 0.0612577
+  49 -5.07692 7.14634 0.394221
+  50 -4.76923 7.34146 0.214609
+  51 -4.46154 7.90244 0.1583
+  52 -4.15385 6.36585 0.191919
+  53 -3.84615 8.04878 0.202891
+  54 -3.53846 7.2439 -0.00173288
+  55 -3.23077 7.53659 0.117062
+  56 -2.92308 6.41463 0.324614
+  57 -2.61538 7.60976 0.496272
+  58 -2.30769 8.39024 0.364642
+  59 -2 6.73171 0.292624
+  60 -1.69231 7.02439 0.517913
+  61 -1.38462 8.43902 0.534594
+  62 -1.07692 7.21951 0.497622
+  63 -0.769231 6.95122 0.303701
+  64 -0.461538 8.68293 0.406682
+  65 -0.153846 7.5122 0.218835
+  66 0.153846 6.82927 0.189413
+  67 0.461538 8.26829 0.228409
+  68 0.769231 7.2439 0.506845
+  69 1.07692 7.97561 0.154118
+  70 1.38462 8.26829 0.144882
+  71 1.69231 6.58537 0.192568
+  72 2 7.46341 0.360144
+  73 2.30769 8.95122 0.0112179
+  74 2.61538 6.58537 0.276061
+  75 2.92308 6.53659 0.114354
+  76 3.23077 8.46341 0.0386417
+  77 3.53846 8 0.0711626
+  78 3.84615 6.92683 0.203194
+  79 4.15385 8.4878 0.317789
+  80 4.46154 7.5122 0.268122
+  81 4.76923 6.58537 -0.112372
+  82 5.07692 9.02439 0.115702
+  83 5.38462 7.41463 -0.067424
+  84 5.69231 6.07317 0.0626918
+  85 6 8.34146 -0.0153977
+  86 6.30769 8.21951 0.281342
+  87 6.61538 6.29268 0.359939
+  88 6.92308 8.87805 0.110875
+  89 7.23077 6.09756 0.134999
+  90 7.53846 6.65854 0.0841478
+  91 7.84615 10.8537 0.144519
+  92 8.15385 5.58537 0.309331
+  93 8.46154 5.80488 0.103667
+  94 8.76923 7.60976 0.39288
+  95 9.07692 12.0244 0.462022
+  96 9.38462 0 0
+  97 9.69231 0 0
+  98 10 0 0
+  99 10.3077 0 0
+  100 10.6154 0 0
+  101 10.9231 0 0
+  102 11.2308 0 0
+  103 11.5385 0 0
+  104 11.8462 0 0
+  105 12.1538 0 0
+  106 12.4615 0 0
+  107 12.7692 0 0
+  108 13.0769 0 0
+  109 13.3846 0 0
+  110 13.6923 0 0
+  111 14 0 0
+  112 14.3077 0 0
+  113 14.6154 0 0
+  114 14.9231 0 0
+  115 15.2308 0 0
+  116 15.5385 0 0
+  117 15.8462 0 0
+  118 16.1538 0 0
+  119 16.4615 0 0
+  120 16.7692 0 0
+  121 17.0769 0 0
+  122 17.3846 0 0
+  123 17.6923 0 0
+  124 18 0 0
+  125 18.3077 0 0
+  126 18.6154 0 0
+  127 18.9231 0 0
+  128 19.2308 0 0
+  129 19.5385 0 0
+  130 19.8462 0 0

examples/USER/flow_gauss/output-files/x_profiles

+# Chunk-averaged data for fix profiles and group density/mass
+# Timestep Number-of-chunks Total-count
+# Chunk Coord1 Ncount vx density/mass c_spa[1] c_spa[2]
+4000 32 109675
+  1 -48.4375 97.7805 0.159561 0.782244 -9.17487 -8.9018
+  2 -45.3125 100.927 0.187846 0.807415 -9.24302 -9.92813
+  3 -42.1875 99.0976 0.227036 0.79278 -9.03415 -9.66032
+  4 -39.0625 101.146 0.243495 0.809171 -8.89515 -9.25314
+  5 -35.9375 98.7805 0.194616 0.790244 -9.13265 -8.52663
+  6 -32.8125 97.8049 0.165768 0.782439 -9.26009 -8.52446
+  7 -29.6875 100.195 0.0758064 0.801561 -9.02933 -8.50733
+  8 -26.5625 98.4878 0.054432 0.787902 -9.61672 -9.24963
+  9 -23.4375 99.9268 0.0740914 0.799415 -9.88959 -9.94984
+  10 -20.3125 99.7561 0.130294 0.798049 -10.2459 -9.39412
+  11 -17.1875 102.463 0.120168 0.819707 -10.6072 -10.254
+  12 -14.0625 47.6341 0.208545 0.381073 -9.85715 -10.0799
+  13 -10.9375 48.1951 0.238051 0.385561 -9.81349 -10.569
+  14 -7.8125 47.439 0.287107 0.379512 -10.0184 -9.63087
+  15 -4.6875 48.2439 0.22506 0.385951 -9.83794 -9.6963
+  16 -1.5625 48.4634 0.208869 0.387707 -9.29366 -10.0114
+  17 1.5625 46.4878 0.19447 0.371902 -10.2409 -9.84627
+  18 4.6875 47.2927 0.168034 0.378341 -10.1523 -11.908
+  19 7.8125 48.6829 0.145552 0.389463 -10.24 -11.0582
+  20 10.9375 48.8293 0.214036 0.390634 -9.27729 -10.1074
+  21 14.0625 46.9756 0.267083 0.375805 -9.24833 -9.83182
+  22 17.1875 97.2683 0.175404 0.778146 -9.64001 -8.61724
+  23 20.3125 101.146 0.10746 0.809171 -9.33416 -9.82308
+  24 23.4375 101.927 0.157503 0.815415 -9.76491 -10.1909
+  25 26.5625 101.024 0.179934 0.808195 -9.72775 -9.98559
+  26 29.6875 100.976 0.180631 0.807805 -9.33871 -10.0228
+  27 32.8125 96.4146 0.144418 0.771317 -9.74826 -9.79723
+  28 35.9375 101.244 0.117224 0.809951 -8.95584 -8.80226
+  29 39.0625 102 0.10507 0.816 -9.15563 -8.98232
+  30 42.1875 101.195 0.040236 0.809561 -9.1499 -8.95112
+  31 45.3125 96.9512 0.0312252 0.77561 -9.20475 -9.0005
+  32 48.4375 100.244 0.103032 0.801951 -9.16324 -8.77526