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Friction example
Substitute (twice):
region lo-asperity sphere 32 7 0 8
region lo-asperity tri 26 7 32 14 38 7
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#2 - Molecule size/shape
Stick-slip  owoncorrugatedsurfaces
Nikolai Priezjev group at Michigan State U
Niavarani and Priezjev, J Chem Phys, 129, 144902 (2008)
Flow is function ofcorrugationwavelength andchainlength
Monitorshape and motion of chains
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Compute gyration/molecule for R
g
of each polymer chain
Input script:
compute id all gyration/molecule ftensorg
compute
vector()method(40lines,onevalue/molecule):
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) f
imol = molecule[i];
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - comall[imol][0];
dy = unwrap[1] - comall[imol][1];
dz = unwrap[2] - comall[imol][2];
massone = mass[type[i]];
rg[imol] += (dx*dx + + dy*dy y + + dz*dz) ) * * massone;
g
MPI
Allreduce(rg,vector,nmolecules,...);
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Compute gyration/molecule for R
g
of each polymer chain
Input script:
compute id all gyration/molecule ftensorg
compute
vector()method(40lines,onevalue/molecule):
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit) f
imol = molecule[i];
domain->unmap(x[i],image[i],unwrap);
dx = unwrap[0] - comall[imol][0];
dy = unwrap[1] - comall[imol][1];
dz = unwrap[2] - comall[imol][2];
massone = mass[type[i]];
rg[imol] += (dx*dx + + dy*dy y + + dz*dz) ) * * massone;
g
MPI
Allreduce(rg,vector,nmolecules,...);
For shape,computeinertia/molecule is similar logic
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#3 - Solvent evaporation
Nanoparticle orderinginpolymersw/solventevaporation
SCheng & G Grest, J Chem Phys, 138, 064701 (2013)
Spring MRS meeting, 2013
Evaporate solventatcontrolledrateaboveL/Vinterface
Ordering is function ofNP/polymerinteractionstrength
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Fix evaporate removes solvent at specied rate
Input script:
fix id solvent evaporate
N M topbox 38277 fmolecule yesg
pre
exchange()method
identify atoms in region volume
pick random subset (consistent across procs)
delete from system
also remove molecules the deleted particles are in
200 lines of code (molecules add some complexity)
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#4 - Grain boundary migration
KJanssens, et al, Nature Materials, 5, 124 (2006)
Addsyntheticenergy/force as function of mis-orientation
Drives atoms near boundary from orientation I to J
#4 - Grain boundary migration
KJanssens, et al, Nature Materials, 5, 124 (2006)
Addsyntheticenergy/force as function of mis-orientation
Drives atoms near boundary from orientation I to J
Mobility / migration velocity / driving force
Extract accurate mobility fromshortsimulation
Build a bi-crystal
Input script commands:
region lower box x EDGE EDGE E EDGE EDGE E EDGE 20.0
region upper box x EDGE EDGE E EDGE EDGE E 20.0 EDGE
lattice fcc 4.04 origin n 0 0 20 0 orient x -3 3 1 1 0 ...
create
atoms 1 region n lower
lattice fcc 4.04 origin n 0 0 20 0 orient x 3 1 0 0 ...
create
atoms 1 region n upper
delete
atoms overlap 0.5 5 all l all
Fix orient/fcc to impose driving force
2les: src/x
orient
fcc.cpp and x
orient
fcc.h
Requestfullneighborlist, every timestep:
int irequest = neighbor->request((void *) this);
neighbor->requests[irequest]->pair = 0;
neighbor->requests[irequest]->fix = 1;
neighbor->requests[irequest]->half = 0;
neighbor->requests[irequest]->full = 1;
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