mirror of https://github.com/lammps/lammps.git
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@6616 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
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@ -5,12 +5,17 @@ initialization it will stop and wait for an IMD client to
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connect. Then launch VMD on the same machine with the respective
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script to connect and visualize the running simulation. For example:
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mpirun -np 4 lmp_linux -in in.melt_imd
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mpirun -np 4 lmp_linux -log none -in in.melt_imd &
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vmd -e melt_imd-demo.vmd
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When exiting VMD, the simulation will wait for a new connection. To
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terminate the LAMMPS simulation, type "imd kill" into the VMD command
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line prompt.
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When exiting VMD, the simulation will either continue or wait
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for a new connection depending on whether the "nowait" flag was
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activated or not. To terminate the LAMMPS simulation,
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type "imd kill" into the VMD command line prompt.
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To combine interactive MD with force feedback using a
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Novint Falcon game controller, have a look at:
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http://sites.google.com/site/akohlmey/software/vrpn-icms
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Examples:
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@ -28,6 +33,15 @@ Examples:
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representation again to re-enable the rest of
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the atoms and watch the blue atom move.
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bucky-plus-cnt:
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this is "the buckyball challenge". a demo that
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is very popular to demonstrate the use of IMD
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with force feedback. The system is a SWCNT with
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some atoms fixed in space and five C60 fullerenes
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in a reflecting wall box. The challenge is to
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push all five buckyballs into the nanotube and
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have them stay inside.
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deca-ala-solv:
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a solvated deca alanin helix. The mouse mode is
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preset to move residues instead of individual
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@ -37,8 +51,8 @@ Examples:
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deca-ala:
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this is the same system as the previous, but
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the fix is only applied to the peptide and thus
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the corresponding vmd script needs a different
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the corresponding VMD script needs a different
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topology file with the matching number of atoms
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to visualize it and receive the IMD data.
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In case of problems, contact <axel.kohlmeyer@temple.edu>.
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In case of problems, contact <akohlmey@gmail.com>.
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,43 @@
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#!/usr/local/bin/vmd
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# Display settings
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display projection Perspective
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mol new bucky-plus-cnt-mol.psf type psf first 0 last -1 step 1 filebonds 1 autobonds 1 waitfor all
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mol delrep 0 top
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mol representation Licorice 0.3 10.0 10.0
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mol color ColorID 7
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mol selection {index >= 300}
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mol addrep top
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mol selection {index < 300}
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mol color ColorID 23
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mol material Glossy
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mol representation VDW 0.600000 15.000000
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mol addrep top
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mol rename top {Put the balls into the tube}
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draw delete all
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draw material AOChalky
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draw color gray
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draw triangle {-36.0 -31.0 -7.0} { 46.0 -31.0 -7.0} { 46.0 31.0 -7.0}
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draw triangle {-36.0 -31.0 -7.0} {-36.0 31.0 -7.0} { 46.0 31.0 -7.0}
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draw color red
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draw triangle {-36.0 -31.0 -7.0} {-36.0 -31.0 7.0} {-36.0 31.0 7.0}
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draw triangle {-36.0 -31.0 -7.0} {-36.0 31.0 -7.0} {-36.0 31.0 7.0}
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draw triangle { 46.0 -31.0 -7.0} { 46.0 -31.0 7.0} { 46.0 31.0 7.0}
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draw triangle { 46.0 -31.0 -7.0} { 46.0 31.0 -7.0} { 46.0 31.0 7.0}
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draw triangle {-36.0 -31.0 -7.0} {-36.0 -31.0 7.0} { 46.0 -31.0 7.0}
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draw triangle {-36.0 -31.0 -7.0} { 46.0 -31.0 -7.0} { 46.0 -31.0 7.0}
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draw triangle {-36.0 31.0 -7.0} {-36.0 31.0 7.0} { 46.0 31.0 7.0}
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draw triangle {-36.0 31.0 -7.0} { 46.0 31.0 -7.0} { 46.0 31.0 7.0}
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imd connect localhost 6789
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after idle {
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global env
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set env(VMDFULLSCREEN) 1
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display resize 1200 900
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rotate x by -5
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rotate y by -5
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axes location off
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}
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,10 @@
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#!/usr/local/bin/vmd
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menu tool on
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tool create tug falcon0 fbuttons0 ffeedback0
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tool scale 50.0 0
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# tool scaleforce 50.0 0
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# tool scalespring 35.0
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tool scaleforce 15.0 0
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tool scalespring 15.0
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tool rep 0 -1 -1
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@ -0,0 +1,59 @@
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# stick a buckyball into a nanotube
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units real
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dimension 3
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boundary f f f
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atom_style molecular
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newton on off
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processors * * 1
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# read topology
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read_data data.bucky-plus-cnt
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pair_style lj/cut 10.0
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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special_bonds lj/coul 0.0 0.0 0.0
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pair_coeff 1 1 0.07 3.55
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pair_coeff 1 2 0.07 3.55
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pair_coeff 2 2 0.07 3.55
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bond_coeff 1 305.0 1.4
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angle_coeff 1 40.000 120.00 35.00 2.41620
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dihedral_coeff 1 3.100 2 180 0.0
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neighbor 4.0 bin
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neigh_modify delay 0 every 1 check yes
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timestep 2.0
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# we only move some atoms.
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group mobile type 1
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# have balls bounce off the walls
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fix walls mobile wall/reflect xlo EDGE ylo EDGE zlo EDGE xhi EDGE yhi EDGE zhi EDGE
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velocity mobile create 303.0 46659 mom yes rot yes dist gaussian
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# take some potential energy out of the system
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minimize 1.0e-4 1.0e-6 100 1000
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reset_timestep 0
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fix integrate mobile nve
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fix thermostat mobile langevin 300.0 300.0 2000.0 234624
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# IMD setup.
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fix comm all imd 6789 unwrap on trate 10
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#fix comm all imd 6789 unwrap on trate 10 nowait on
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# temperature is based on mobile atoms only
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compute mobtemp mobile temp
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thermo_style custom step pe ke evdwl emol c_mobtemp spcpu
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thermo 1000
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thermo_modify norm yes
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thermo_modify temp mobtemp
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run 100000000
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@ -0,0 +1,62 @@
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# stick a buckyball into a nanotube
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units real
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dimension 3
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boundary f f f
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atom_style molecular
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newton off
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processors * * 1
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# read topology
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read_data data.bucky-plus-cnt
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pair_style lj/cut/gpu 10.0
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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special_bonds lj/coul 0.0 0.0 0.0
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pair_coeff 1 1 0.07 3.55
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pair_coeff 1 2 0.07 3.55
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pair_coeff 2 2 0.07 3.55
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bond_coeff 1 305.0 1.4
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angle_coeff 1 40.000 120.00 35.00 2.41620
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dihedral_coeff 1 3.100 2 180 0.0
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neighbor 2.0 bin
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neigh_modify delay 0 every 1 check yes
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timestep 2.0
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# required for GPU acceleration
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fix gpu all gpu force 0 0 1.0
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# we only move some atoms.
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group mobile type 1
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# have balls bounce off the walls
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fix walls mobile wall/reflect xlo EDGE ylo EDGE zlo EDGE xhi EDGE yhi EDGE zhi EDGE
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velocity mobile create 303.0 46659 mom yes rot yes dist gaussian
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# take some potential energy out of the system
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minimize 1.0e-4 1.0e-6 100 1000
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reset_timestep 0
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fix integrate mobile nve
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fix thermostat mobile langevin 300.0 300.0 2000.0 234624
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# IMD setup.
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fix comm all imd 6789 unwrap on trate 10
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#fix comm all imd 6789 unwrap on trate 10 nowait on
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# temperature is based on mobile atoms only
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compute mobtemp mobile temp
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thermo_style custom step pe ke evdwl emol c_mobtemp spcpu
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thermo 1000
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thermo_modify norm yes
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thermo_modify temp mobtemp
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run 100000000
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@ -0,0 +1,33 @@
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#
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units real
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neighbor 2.5 bin
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neigh_modify delay 1 every 1
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atom_style full
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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pair_style lj/charmm/coul/long 8 10
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pair_modify mix arithmetic
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special_bonds charmm
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read_data data.deca-ala-solv
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group peptide id <= 103
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fix rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23
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thermo 100
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thermo_style multi
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timestep 2.0
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kspace_style pppm 1e-5
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fix ensemble all npt temp 300.0 300.0 100.0 aniso 1.0 1.0 1000.0 drag 0.2
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# IMD setup.
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fix comm all imd 5678 unwrap on trate 10 filter 20 2
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run 5000000
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@ -23,11 +23,11 @@ thermo_style multi
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timestep 2.0
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kspace_style pppm 1e-5
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fix ensemble all npt 300.0 300.0 100.0 xyz 1.0 1.0 1000.0 drag 0.2
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fix ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2
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# IMD setup.
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fix comm all imd 5678 unwrap on trate 5
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fix comm all imd 5678 unwrap on trate 10
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run 5000
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run 5000000
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@ -23,11 +23,11 @@ thermo_style multi
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timestep 2.0
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kspace_style pppm 1e-5
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fix ensemble all npt 300.0 300.0 100.0 xyz 1.0 1.0 1000.0 drag 0.2
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fix ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2
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# IMD setup.
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fix comm peptide imd 5678 unwrap on trate 5
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fix comm peptide imd 5678 unwrap on trate 10
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run 5000
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run 5000000
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@ -0,0 +1,35 @@
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#
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units real
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neighbor 2.5 bin
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neigh_modify delay 1 every 1
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newton off
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atom_style full
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bond_style harmonic
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angle_style charmm
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dihedral_style charmm
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improper_style harmonic
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pair_style lj/charmm/coul/long/gpu 8 10
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pair_modify mix arithmetic
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special_bonds charmm
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read_data data.deca-ala-solv
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fix 0 all gpu force/neigh 0 0 1.0
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group peptide id <= 103
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fix rigidh all shake 1e-6 100 1000 t 1 2 3 4 5 a 23
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thermo 100
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thermo_style multi
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timestep 2.0
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kspace_style pppm/gpu 1e-5
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fix ensemble all npt temp 300.0 300.0 100.0 iso 1.0 1.0 1000.0 drag 0.2
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# IMD setup.
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fix comm peptide imd 5678 unwrap on trate 10
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run 5000000
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@ -15,12 +15,14 @@ pair_style lj/cut 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify every 20 delay 0 check no
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neigh_modify every 5 delay 10 check yes
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thermo_style custom step pe ke spcpu
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fix 1 all nve
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# IMD setup.
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fix comm all imd 5678 unwrap off fscale 20.0 trate 10
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fix comm all imd 5678 unwrap off fscale 20.0 trate 10 nowait on
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thermo 500
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run 500000
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run 5000000
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@ -0,0 +1,30 @@
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# 3d Lennard-Jones melt
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units lj
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atom_style atomic
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newton off
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lattice fcc 0.8442
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region box block 0 10 0 10 0 10
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create_box 1 box
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create_atoms 1 box
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mass 1 1.0
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velocity all create 3.0 87287
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pair_style lj/cut/gpu 2.5
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pair_coeff 1 1 1.0 1.0 2.5
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neighbor 0.3 bin
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neigh_modify every 5 delay 10 check yes
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thermo_style custom step pe ke spcpu
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fix 0 all gpu force/neigh 0 0 1.0
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fix 1 all nve
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# IMD setup.
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fix comm all imd 5678 unwrap off fscale 20.0 trate 20 nowait on
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thermo 500
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run 5000000
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