add SWCNT plus buckyball demo for fix imd.

examples/USER/imd/bucky_cnt_imd.vmd

@@ -0,0 +1,41 @@
+#!/usr/local/bin/vmd
+# Display settings
+display projection Perspective
+
+mol new bucky-plus-cnt-mol.psf type psf first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
+mol delrep 0 top
+mol representation Licorice 0.3 10.0 10.0
+mol color ColorID 7
+mol selection {index >= 300}
+mol addrep top
+mol selection {index < 300}
+mol color ColorID 23
+mol material Glossy
+mol representation VDW 0.600000 15.000000
+mol addrep top
+
+mol rename top {Put the balls into the tube}
+
+draw delete all
+draw material AOChalky
+draw color gray
+draw triangle {-36.0 -31.0  -7.0} { 46.0 -31.0  -7.0} { 46.0  31.0  -7.0}
+draw triangle {-36.0 -31.0  -7.0} {-36.0  31.0  -7.0} { 46.0  31.0  -7.0}
+draw color red
+draw triangle {-36.0 -31.0  -7.0} {-36.0 -31.0   7.0} {-36.0  31.0   7.0}
+draw triangle {-36.0 -31.0  -7.0} {-36.0  31.0  -7.0} {-36.0  31.0   7.0}
+draw triangle { 46.0 -31.0  -7.0} { 46.0 -31.0   7.0} { 46.0  31.0   7.0}
+draw triangle { 46.0 -31.0  -7.0} { 46.0  31.0  -7.0} { 46.0  31.0   7.0}
+draw triangle {-36.0 -31.0  -7.0} {-36.0 -31.0   7.0} { 46.0 -31.0   7.0}
+draw triangle {-36.0 -31.0  -7.0} { 46.0 -31.0  -7.0} { 46.0 -31.0   7.0}
+draw triangle {-36.0  31.0  -7.0} {-36.0  31.0   7.0} { 46.0  31.0   7.0}
+draw triangle {-36.0  31.0  -7.0} { 46.0  31.0  -7.0} { 46.0  31.0   7.0}
+
+
+imd connect localhost 6789
+after idle {
+ display resize 1200 900
+ rotate x by -5
+ rotate y by -5
+ axes location off
+}

examples/USER/imd/in.bucky-plus-cnt

@@ -0,0 +1,60 @@
+# stick a buckyball into a nanotube
+units           real
+dimension       3
+boundary       f f f
+atom_style      molecular
+newton          on off
+
+#
+#processors     3 2 1
+processors * * *
+
+# read topology 
+read_data       data.bucky-plus-cnt
+
+pair_style  lj/cut/opt  10.0
+bond_style  harmonic
+angle_style charmm
+dihedral_style charmm
+
+special_bonds lj/coul 0.0 0.0 0.0
+
+pair_coeff  1  1    0.07    3.55
+pair_coeff  1  2    0.07    3.55
+pair_coeff  2  2    0.07    3.55
+bond_coeff     1  305.0     1.375
+angle_coeff    1   40.000 120.00   35.00   2.41620
+dihedral_coeff 1    3.100   2     180   0.0
+
+neighbor        5.0 bin
+neigh_modify    delay 0 every 1 check yes
+
+timestep        2.0
+
+# we only move some atoms.
+group mobile type 1
+
+# have balls bounce off the walls
+fix     walls       mobile wall/reflect xlo EDGE ylo EDGE zlo EDGE xhi EDGE yhi EDGE zhi EDGE
+
+velocity mobile create 303.0 46659 mom yes rot yes dist gaussian
+
+# take some potential energy out of the system
+minimize 1.0e-4 1.0e-6 100 1000
+
+reset_timestep 0
+
+fix     integrate   mobile nve
+fix     thermostat  mobile langevin 300.0 300.0 2000.0 234624
+
+# IMD setup.
+fix  comm       all imd 6789 unwrap on trate 10
+
+# temperature is based on mobile atoms only
+compute mobtemp mobile temp
+thermo_style    custom step pe ke evdwl emol c_mobtemp spcpu
+thermo          1000
+thermo_modify   norm yes
+thermo_modify   temp mobtemp
+
+run             100000000

examples/USER/imd/in.bucky-plus-cnt-filter

@@ -0,0 +1,60 @@
+# stick a buckyball into a nanotube
+units           real
+dimension       3
+boundary       f f f
+atom_style      molecular
+newton          on off
+
+#
+#processors     3 2 1
+processors * * *
+
+# read topology 
+read_data       data.bucky-plus-cnt
+
+pair_style  lj/cut/opt  10.0
+bond_style  harmonic
+angle_style charmm
+dihedral_style charmm
+
+special_bonds lj/coul 0.0 0.0 0.0
+
+pair_coeff  1  1    0.07    3.55
+pair_coeff  1  2    0.07    3.55
+pair_coeff  2  2    0.07    3.55
+bond_coeff     1  305.0     1.375
+angle_coeff    1   40.000 120.00   35.00   2.41620
+dihedral_coeff 1    3.100   2     180   0.0
+
+neighbor        5.0 bin
+neigh_modify    delay 0 every 1 check yes
+
+timestep        2.0
+
+# we only move some atoms.
+group mobile type 1
+
+# have balls bounce off the walls
+fix     walls       mobile wall/reflect xlo EDGE ylo EDGE zlo EDGE xhi EDGE yhi EDGE zhi EDGE
+
+velocity mobile create 303.0 46659 mom yes rot yes dist gaussian
+
+# take some potential energy out of the system
+minimize 1.0e-4 1.0e-6 100 1000
+
+reset_timestep 0
+
+fix     integrate   mobile nve
+fix     thermostat  mobile langevin 300.0 300.0 2000.0 234624
+
+# IMD setup.
+fix  comm       all imd 6789 unwrap on trate 10 filter 20 3
+
+# temperature is based on mobile atoms only
+compute mobtemp mobile temp
+thermo_style    custom step pe ke evdwl emol c_mobtemp spcpu
+thermo          1000
+thermo_modify   norm yes
+thermo_modify   temp mobtemp
+
+run             100000000

src/USER-IMD/fix_imd.cpp

@@ -992,7 +992,7 @@ void FixIMD::ioworker()
         float *recvcoord = (float *) (msgdata+IMDHEADERSIZE);
         filter_coordinates(recvcoord);
       }
-      
+
       /* send coordinate data, if client is able to accept */
       if (clientsock && imdsock_selwrite(clientsock,0)) {
         imd_writen(clientsock, msgdata, msglen);