Greetings,
I am having difficulties getting a region to "move".first, I select a
region as a part of the data file then moving it toward rest part and
pass through it. my input file and part of the data file are at
following. when I watch the image result it was an expanding system
not moving.
another try was using remap for the cylindrical region but there was
an error about putting remap it does not allow to between two-run.
I would appreciate you helping out for this simulation.
regard
---------- Initialize Simulation ---------------------
clear
units real
dimension 3
boundary p p p
atom_style full
bond_style class2
angle_style class2
dihedral_style class2
improper_style class2
------ Interatomic Potential --------------------
pair_style lj/class2/coul/long 9.35 3.272
read_data hntpu5.data
kspace_style pppm 1.0e-5
pair_modify mix arithmetic
neighbor 0.0001 bin
neigh_modify delay 0 every 1 check yes page 500000 one 50000
special_bonds charmm
---------- define variables ---------------------
variable stemperature equal 5 # temperature in kelvin
variable alattice equal 70.520 # lattice constant (unit A)
variable myseed equal 12345 # the value seed for the velocity
variable xmax equal 90.000000000 # size in the x-direction
variable ymax equal 35.870779246 # size in the y-direction
variable zmax equal 35.907677103 # size in the z-direction
variable xmin equal -90.000000000 # size in the x-direction
variable ymin equal -35.870779246 # size in the y-direction
variable zmin equal -35.907677103 # size in the z-direction
variable time_step equal 0.00001 # time step in pico seconds
variable time_eq equal 10 # time steps for the equlibration part
variable time_shock equal 150 # time steps for the piston
variable vpiston equal 1.300 # piston speed in (km/s) multiply by ten
to obtain (A/ps)
variable Nevery equal 10 # use input values every this many timesteps
variable Nrepeat equal 5 # number of times to use input values for calculating
variable Nfreq equal 100 # calculate averages every this many timesteps
variable deltaz equal 3 # thickness of spatial bins in dim (distance units)
variable atomrate equal 100 # the rate in timestep that atoms are dump as CFG
variable tdamp equal "v_time_step100" # DO NOT CHANGE
variable pdamp equal "v_time_step1000" # DO NOT CHANGE
variable Up equal "10*v_vpiston" # DO NOT CHANGE
timestep ${time_step}
reset_timestep 0
define size of the simulation box
region sim_box block \{xmin\} {xmax} \{ymin\} {ymax} \{zmin\} {zmax}
##################define a group for the atom_box region
region atom_box block \{xmin\} {xmax} \{ymin\} {ymax} \{zmin\} {zmax}
group atom_box region atom_box
############ define atoms in a small region
variable dx equal -2.0
region piston cylinder x 7.79706494 9.26983933 20 98.6837835 171.5844725
region bulk block \{xmin\} 98\.6737835 {ymin} \{ymax\} {zmin} ${zmax}
group piston region piston
group bulk region bulk
set group piston type 1
set group bulk type 2
---------- Define Settings ---------------------
compute eng all pe/atom
compute peratom all pe/atom
compute pe all reduce sum c_peratom
## Compute stress information for Atomeye visualization
compute myKE bulk ke/atom
compute myPE bulk pe/atom
compute myCOM bulk com
compute 1 all chunk/atom type
compute vz bulk property/atom vz
compute s all stress/atom NULL
compute s1 all reduce sum c_s[1]
compute s2 all reduce sum c_s[2]
compute s3 all reduce sum c_s[3]
compute p all reduce sum c_s[1] c_s[2] c_s[3]
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
------------ Equilibrate --------------------------
velocity atom_box create \{stemperature\} {myseed} rot yes dist gaussian
fix equilibration all npt temp \{stemperature\} {stemperature}
\{tdamp\} iso 0 0 {pdamp} drag 1
variable pp1 equal "step"
variable pp2 equal "pxx/10000"
variable pp3 equal "pyy/10000"
variable pp4 equal "pzz/10000"
variable pp5 equal "lx"
variable pp6 equal "ly"
variable pp7 equal "lz"
variable pp8 equal "temp"
variable pp9 equal "c_myCOM[3]"
variable pp10 equal "epair"
variable pp11 equal "ebond"
variable pp12 equal "eangle"
variable pp13 equal "edihed"
variable V equal -10.0
variable x equal vdisplace(0.0,$V)
fix 3 piston move variable v_x NULL NULL v_V NULL NULL
fix output1 all print 100 "\{pp1\} {pp2} \{pp3\} {pp4} \{pp5\} {pp6}
\{pp7\} {pp8} \{pp10\} {pp11} \{pp12\} {pp13} c_s1 c_s2 c_s3 vz v_Up "
file run.${stemperature}K.out screen no
dump d2 piston image 10 img-*.jpg type type zoom 0.75 adiam 1.2 size 640 480
dump m1 all movie 10 movie.avi type type size 640 480
dump apf all custom 10 atom_position.dat id type x y z ix iy iz
dump trjfile all custom 1000 dump.lammpstrj id mol type x y z ix iy iz
thermo_style custom step temp pxx pyy pzz lx ly lz epair ebond eangle
edihed press v_press c_s1 c_s2 c_s3
thermo 10
timestep 0.000001
run 1000000
unfix equilibration
unfix output1
print "All done"
LAMMPS data file. msi2lmp v3.9.9 / 05 Nov 2018 for
C:\Users\heida\OneDrive\Desktop\lammps\HNTPU\5percent\new5\final\7\hntpu5
28630 atoms
31242 bonds
57249 angles
92665 dihedrals
30208 impropers
16 atom types
22 bond types
41 angle types
53 dihedral types
34 improper types
-90.000000000 90.000000000 xlo xhi
-35.870779246 35.870779246 ylo yhi
-35.907677103 35.907677103 zlo zhi
-0.142492172 0.056278336 0.058395694 xy xz yz
Masses
1 12.011150
2 14.006700
3 1.007970
4 1.007970
5 12.011150
6 14.006700
7 12.011150
8 15.999400
9 15.999400
10 12.011150
11 26.982000
12 28.086000
13 1.007970
14 15.999400
15 15.999400
16 15.999400
Pair Coeffs
1 0.0620000000 3.8540000000
2 0.1500000000 3.7200000000
3 0.0230000000 2.8780000000
4 0.0216000000 1.4210000000
5 0.0680000000 3.9150000000
6 0.3330000000 3.5290000000
7 0.0640000000 3.9000000000
8 0.1200000000 3.3000000000
9 0.0670000000 3.3600000000
10 0.1080000000 3.8700000000
11 0.0680000000 2.9150000000
12 0.1310000000 4.2900000000
13 0.0080000000 1.0870000000
14 0.0800000000 3.3000000000
15 0.0800000000 3.3000000000
16 0.1920000000 3.4300000000
Bond Coeffs
1 1.4000 350.0000 0.0000 0.0000
2 1.1010 345.0000 -691.8900 844.6000
3 1.5300 299.6700 -501.7700 679.8100
4 0.0000 0.0000 0.0000 0.0000
5 1.5010 321.9021 -521.8208 572.1628
6 1.4170 470.8361 -627.6179 1327.6345
7 1.0982 372.8251 -803.4526 894.3173
8 0.0000 0.0000 0.0000 0.0000
9 0.0000 0.0000 0.0000 0.0000
10 1.3750 368.7309 -832.4784 1274.0231
11 1.2160 823.7948 -1878.7939 2303.5310
12 1.4200 400.3954 -835.1951 1313.0142
13 1.5010 321.9021 -521.8208 572.1628
14 1.1010 345.0000 -691.8900 844.6000
15 1.5300 299.6700 -501.7700 679.8100
16 1.5300 299.6700 -501.7700 679.8100
17 0.0000 0.0000 0.0000 0.0000
18 0.0000 0.0000 0.0000 0.0000
19 0.0000 0.0000 0.0000 0.0000
20 0.0000 0.0000 0.0000 0.0000
21 1.6400 350.1232 -517.3424 673.7067
22 0.0000 0.0000 0.0000 0.0000
Angle Coeffs
1 0.0000 0.0000 0.0000 0.0000
2 0.0000 0.0000 0.0000 0.0000
3 107.6600 39.6410 -12.9210 -2.4318
4 110.7700 41.4530 -10.6040 5.1290
5 0.0000 0.0000 0.0000 0.0000
6 0.0000 0.0000 0.0000 0.0000
7 111.0000 44.3234 -9.4454 0.0000
8 0.0000 0.0000 0.0000 0.0000
9 111.0000 44.3234 -9.4454 0.0000
10 120.0500 44.7148 -22.7352 0.0000
11 117.9400 35.1558 -12.4682 0.0000
12 0.0000 0.0000 0.0000 0.0000
13 118.9000 61.0226 -34.9931 0.0000
14 0.0000 0.0000 0.0000 0.0000
15 0.0000 0.0000 0.0000 0.0000
16 0.0000 0.0000 0.0000 0.0000
17 0.0000 0.0000 0.0000 0.0000
18 118.9855 98.6813 -22.2485 10.3673
19 109.0000 38.9739 -6.2595 -8.1710
20 0.0000 0.0000 0.0000 0.0000
21 108.7280 58.5446 -10.8088 -12.4006
22 111.0000 44.3234 -9.4454 0.0000
23 107.6600 39.6410 -12.9210 -2.4318
24 111.2700 54.5381 -8.3642 -13.0838
25 110.7700 41.4530 -10.6040 5.1290
26 0.0000 0.0000 0.0000 0.0000
27 110.7700 41.4530 -10.6040 5.1290
28 111.2700 54.5381 -8.3642 -13.0838
29 110.7700 41.4530 -10.6040 5.1290
30 0.0000 0.0000 0.0000 0.0000
31 0.0000 0.0000 0.0000 0.0000
32 0.0000 0.0000 0.0000 0.0000
33 0.0000 0.0000 0.0000 0.0000
34 0.0000 0.0000 0.0000 0.0000
35 0.0000 0.0000 0.0000 0.0000
36 0.0000 0.0000 0.0000 0.0000
37 0.0000 0.0000 0.0000 0.0000
38 0.0000 0.0000 0.0000 0.0000
39 0.0000 0.0000 0.0000 0.0000
40 110.7000 70.3069 -6.9375 0.0000
41 0.0000 0.0000 0.0000 0.0000
Dihedral Coeffs
1 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
2 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
3 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
4 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000