git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6616 f3b2605a-c512-4ea7-a41b-209d697bcdaa

examples/USER/imd/README

@@ -5,12 +5,17 @@ initialization it will stop and wait for an IMD client to
 connect. Then launch VMD on the same machine with the respective
 script to connect and visualize the running simulation.  For example:
 
-mpirun -np 4 lmp_linux -in in.melt_imd
+mpirun -np 4 lmp_linux -log none -in in.melt_imd &
 vmd -e melt_imd-demo.vmd
 
-When exiting VMD, the simulation will wait for a new connection.  To
+When exiting VMD, the simulation will either continue or wait
-terminate the LAMMPS simulation, type "imd kill" into the VMD command
+for a new connection depending on whether the "nowait" flag was
-line prompt.
+activated or not.  To terminate the LAMMPS simulation, 
+type "imd kill" into the VMD command line prompt.
+
+To combine interactive MD with force feedback using a
+Novint Falcon game controller, have a look at:
+http://sites.google.com/site/akohlmey/software/vrpn-icms
 
 Examples:
 
@@ -28,6 +33,15 @@ Examples:
        representation again to re-enable the rest of
        the atoms and watch the blue atom move.
 
+bucky-plus-cnt:
+       this is "the buckyball challenge". a demo that
+       is very popular to demonstrate the use of IMD
+       with force feedback. The system is a SWCNT with
+       some atoms fixed in space and five C60 fullerenes
+       in a reflecting wall box. The challenge is to
+       push all five buckyballs into the nanotube and
+       have them stay inside.
+
  deca-ala-solv:
        a solvated deca alanin helix. The mouse mode is
        preset to move residues instead of individual
@@ -37,8 +51,8 @@ Examples:
  deca-ala:
        this is the same system as the previous, but 
        the fix is only applied to the peptide and thus
-       the corresponding vmd script needs a different
+       the corresponding VMD script needs a different
        topology file with the matching number of atoms
        to visualize it and receive the IMD data.
 
-In case of problems, contact <axel.kohlmeyer@temple.edu>.
+In case of problems, contact <akohlmey@gmail.com>.

examples/USER/imd/bucky_cnt_imd.vmd

@@ -0,0 +1,43 @@
+#!/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 {
+ global env
+ set env(VMDFULLSCREEN) 1
+ display resize 1200 900
+ rotate x by -5
+ rotate y by -5
+ axes location off
+}

examples/USER/imd/falcon.tcl

@@ -0,0 +1,10 @@
+#!/usr/local/bin/vmd
+ menu tool on
+ tool create tug falcon0 fbuttons0 ffeedback0
+ tool scale 50.0 0
+# tool scaleforce 50.0 0
+# tool scalespring 35.0
+ tool scaleforce 15.0 0
+ tool scalespring 15.0
+ tool rep 0 -1 -1
+

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

@@ -0,0 +1,59 @@
+# stick a buckyball into a nanotube
+units           real
+dimension       3
+boundary       f f f
+atom_style      molecular
+newton          on off
+
+processors * * 1
+
+# read topology 
+read_data       data.bucky-plus-cnt
+
+pair_style  lj/cut  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     1.4
+angle_coeff    1   40.000 120.00   35.00   2.41620
+dihedral_coeff 1    3.100   2     180   0.0
+
+neighbor        4.0 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
+#fix  comm       all imd 6789 unwrap on trate 10 nowait on
+
+# 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-gpu

@@ -0,0 +1,62 @@
+# stick a buckyball into a nanotube
+units           real
+dimension       3
+boundary       f f f
+atom_style      molecular
+newton          off
+
+processors * * 1
+
+# read topology 
+read_data       data.bucky-plus-cnt
+
+pair_style  lj/cut/gpu  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     1.4
+angle_coeff    1   40.000 120.00   35.00   2.41620
+dihedral_coeff 1    3.100   2     180   0.0
+
+neighbor        2.0 bin
+neigh_modify    delay 0 every 1 check yes
+
+timestep        2.0
+
+# required for GPU acceleration
+fix   gpu  all      gpu  force 0 0 1.0
+
+# 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
+#fix  comm       all imd 6789 unwrap on trate 10 nowait on
+
+# 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.deca-ala-solv-filter_imd

@@ -0,0 +1,33 @@
+# 
+units           real
+neighbor        2.5 bin
+neigh_modify    delay 1 every 1 
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+
+pair_style      lj/charmm/coul/long 8 10
+pair_modify     mix arithmetic
+special_bonds   charmm
+read_data       data.deca-ala-solv
+
+
+group peptide   id <= 103
+fix             rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23
+
+thermo          100
+thermo_style    multi
+timestep        2.0
+kspace_style    pppm 1e-5
+
+fix             ensemble all npt temp 300.0 300.0 100.0 aniso 1.0 1.0 1000.0 drag 0.2
+
+# IMD setup.
+fix  comm       all imd 5678 unwrap on trate 10 filter 20 2
+
+run 5000000
+
+

examples/USER/imd/in.deca-ala-solv_imd

@@ -23,11 +23,11 @@ thermo_style    multi
 timestep        2.0
 kspace_style    pppm 1e-5
 
-fix             ensemble all npt 300.0 300.0 100.0 xyz 1.0 1.0 1000.0 drag 0.2
+fix             ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2
 
 # IMD setup.
-fix  comm       all imd 5678 unwrap on trate 5
+fix  comm       all imd 5678 unwrap on trate 10
 
-run 5000
+run 5000000
 
 

examples/USER/imd/in.deca-ala_imd

@@ -23,11 +23,11 @@ thermo_style    multi
 timestep        2.0
 kspace_style    pppm 1e-5
 
-fix             ensemble all npt 300.0 300.0 100.0 xyz 1.0 1.0 1000.0 drag 0.2
+fix             ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2
 
 # IMD setup.
-fix  comm       peptide imd 5678 unwrap on trate 5
+fix  comm       peptide imd 5678 unwrap on trate 10
 
-run 5000
+run 5000000
 
 

examples/USER/imd/in.deca-ala_imd-gpu

@@ -0,0 +1,35 @@
+# 
+units           real
+neighbor        2.5 bin
+neigh_modify    delay 1 every 1 
+newton          off
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+
+pair_style      lj/charmm/coul/long/gpu 8 10
+pair_modify     mix arithmetic
+special_bonds   charmm
+read_data       data.deca-ala-solv
+
+fix             0 all gpu force/neigh 0 0 1.0    
+
+group peptide   id <= 103
+fix             rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23
+
+thermo          100
+thermo_style    multi
+timestep        2.0
+kspace_style    pppm/gpu 1e-5
+
+fix             ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2
+
+# IMD setup.
+fix  comm       peptide imd 5678 unwrap on trate 10
+
+run 5000000
+
+

examples/USER/imd/in.melt_imd

@@ -15,12 +15,14 @@ pair_style	lj/cut 2.5
 pair_coeff	1 1 1.0 1.0 2.5
 
 neighbor	0.3 bin
-neigh_modify	every 20 delay 0 check no
+neigh_modify	every 5 delay 10 check yes
+
+thermo_style    custom step pe ke spcpu
 
 fix		1 all nve
 
 # IMD setup.
-fix  comm       all imd 5678 unwrap off fscale 20.0 trate 10
+fix  comm       all imd 5678 unwrap off fscale 20.0 trate 10 nowait on
 
 thermo		500
-run		500000
+run		5000000

examples/USER/imd/in.melt_imd-gpu

@@ -0,0 +1,30 @@
+# 3d Lennard-Jones melt
+
+units		lj
+atom_style	atomic
+newton      off
+
+lattice		fcc 0.8442
+region		box block 0 10 0 10 0 10
+create_box	1 box
+create_atoms	1 box
+mass		1 1.0
+
+velocity	all create 3.0 87287
+
+pair_style	lj/cut/gpu 2.5
+pair_coeff	1 1 1.0 1.0 2.5
+
+neighbor	0.3 bin
+neigh_modify	every 5 delay 10 check yes
+
+thermo_style    custom step pe ke spcpu
+
+fix     0 all gpu force/neigh 0 0 1.0
+fix		1 all nve
+
+# IMD setup.
+fix  comm       all imd 5678 unwrap off fscale 20.0 trate 20 nowait on
+
+thermo		500
+run		5000000