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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14127 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2015-10-21 18:16:47 +00:00
parent b2c2e38ba3
commit ddfb996d8e
5 changed files with 274 additions and 20 deletions
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107
examples/USER/lb/polymer/in.polymer_default_gamma Executable file
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#===========================================================================#
# polymer test #
# #
# Run consists of a lone 32-bead coarse-grained polymer #
# undergoing Brownian motion in thermal lattice-Boltzmann fluid. #
# #
# Here, gamma (used in the calculation of the monomer-fluid interaction #
# force) is set by the user (gamma = 0.03 for this simulation...this #
# value has been calibrated a priori through simulations of the drag #
# force acting on a single particle of the same radius). #
# Sample output from this run can be found in the file: #
# 'dump.polymer.lammpstrj' #
# and viewed using, e.g., the VMD software. #
# #
#===========================================================================#
units nano
dimension 3
boundary p p p
atom_style hybrid molecular
special_bonds fene
read_data data.polymer
#----------------------------------------------------------------------------
# Need a neighbor bin size smaller than the lattice-Boltzmann grid spacing
# to ensure that the particles belonging to a given processor remain inside
# that processors lattice-Boltzmann grid.
#----------------------------------------------------------------------------
neighbor 0.5 bin
neigh_modify delay 0 every 1 check yes
neigh_modify exclude type 2 2
neigh_modify exclude type 2 1
#----------------------------------------------------------------------------
# Implement a hard-sphere interaction between the particles at the center of
# each monomer (use a truncated and shifted Lennard-Jones potential).
#----------------------------------------------------------------------------
bond_style fene
bond_coeff 1 60.0 2.25 4.14195 1.5
pair_style lj/cut 1.68369
pair_coeff 1 1 4.14195 1.5 1.68369
pair_coeff 1 2 4.14195 1.5 1.68369
pair_coeff 2 2 0 1.0
mass * 0.000000771064
timestep 0.00003
#----------------------------------------------------------------------------
# ForceAtoms are the particles at the center of each monomer which
# do not interact with the fluid, but are used to implement the hard-sphere
# interactions.
# FluidAtoms are the particles representing the surface of the monomer
# which do interact with the fluid. Monomer surface is shell of radius 0.7
#----------------------------------------------------------------------------
group ForceAtoms type 1
group FluidAtoms type 2
#---------------------------------------------------------------------------
# Create a lattice-Boltzmann fluid covering the simulation domain.
# This fluid feels a force due to the particles specified through FluidAtoms
# (however, this fix does not explicity apply a force back on to these
# particles. This is accomplished through the use of the lb/viscous
# fix).
# Uses the standard LB integration scheme, fluid viscosity = 0.023333333,
# fluid density= 0.0000166368, lattice spacing dx=1.0, and mass unit,
# dm=0.0000166368.
# Use the default method to calculate the interaction force between the
# particles and the fluid. This calculation requires the surface area
# of the composite object represented by each particle node. By default
# this area is assumed equal to dx*dx; however, since this is not the case
# here, it is input through the setArea keyword (i.e. particles of type 2
# correspond to a surface area of 0.2025=4 Pi R^2/N ).
# Use the trilinear interpolation stencil to distribute the force from
# a given particle onto the fluid mesh (results in a smaller hydrodynamic
# radius than if the Peskin stencil is used).
# Use a thermal lattice-Boltzmann fluid (temperature 300K, random number
# seed=15003). This enables the particles to undergo Brownian motion in
# the fluid.
#----------------------------------------------------------------------------
fix 1 FluidAtoms lb/fluid 3 1 0.023333333 0.0000166368 setArea 2 0.20525 dx 1.0 dm 0.0000166368 noise 300.0 15003
#----------------------------------------------------------------------------
# Apply the force from the fluid to the particles, and integrate their
# motion, constraining them to move and rotate together as a single rigid
# spherical object.
# Since both the ForceAtoms (central atoms), and the FluidAtoms (spherical
# shell) should move and rotate together, this fix is applied to all of
# the atoms in the system. However, since the central atoms should not
# feel a force due to the fluid, they are excluded from the fluid force
# calculation.
#----------------------------------------------------------------------------
fix 2 FluidAtoms lb/viscous
fix 3 all rigid molecule
#----------------------------------------------------------------------------
# To ensure that numerical errors do not lead to a buildup of momentum in the
# system, the momentum_lb fix is used every 10000 timesteps to zero out the
# total (particle plus fluid) momentum in the system.
#----------------------------------------------------------------------------
fix 4 all lb/momentum 10000 linear 1 1 1
#----------------------------------------------------------------------------
# Write position and velocity coordinates into a file every 2000 time steps.
#----------------------------------------------------------------------------
dump 1 ForceAtoms custom 2000 dump.polymer_default_gamma.lammpstrj id x y z vx vy vz
run 2000001

2
examples/USER/lb/polymer/in.polymer → examples/USER/lb/polymer/in.polymer_setgamma
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@ -101,5 +101,5 @@ fix 3 all lb/momentum 10000 linear 1 1 1
# Write position and velocity coordinates into a file every 2000 time steps.
#----------------------------------------------------------------------------
dump 1 ForceAtoms custom 2000 dump.polymer.lammpstrj id x y z vx vy vz
dump 1 ForceAtoms custom 2000 dump.polymer_setgamma.lammpstrj id x y z vx vy vz
run 2000001

19
examples/USER/lb/polymer/out.polymer
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@ -1,19 +0,0 @@
LAMMPS (22 Feb 2013)
Scanning data file ...
1 = max bonds/atom
Reading data file ...
orthogonal box = (0 0 0) to (40 40 40)
2 by 2 by 2 MPI processor grid
992 atoms
31 bonds
Finding 1-2 1-3 1-4 neighbors ...
2 = max # of 1-2 neighbors
2 = max # of special neighbors
32 atoms in group ForceAtoms
960 atoms in group FluidAtoms
Using a lattice-Boltzmann grid of 40 by 40 by 40 total grid points. (fix_lb_fluid.cpp:354)
32 rigid bodies with 992 atoms
Setting up run ...
Memory usage per processor = 0.539707 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8.2758489 2790.7741 2782.4982 1.8503717e-20

83
examples/USER/lb/polymer/out.polymer_default_gamma Normal file
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LAMMPS (10 Aug 2015)
Reading data file ...
orthogonal box = (0 0 0) to (40 40 40)
2 by 2 by 4 MPI processor grid
reading atoms ...
992 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
31 bonds
Finding 1-2 1-3 1-4 neighbors ...
Special bond factors lj: 0 1 1
Special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
32 atoms in group ForceAtoms
960 atoms in group FluidAtoms
Using a lattice-Boltzmann grid of 40 by 40 by 40 total grid points. (../fix_lb_fluid.cpp:385)
32 rigid bodies with 992 atoms
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 2.18369
ghost atom cutoff = 2.18369
Setting up Verlet run ...
Unit style : nano
Current step: 0
Time step : 3e-05
Memory usage per processor = 0.111926 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8.2758489 2790.7741 2782.4982 1.9081958e-20
2000001 4.3017148 0 2792.6037 2798.2163 -0.00077006865
Loop time of 51900 on 16 procs for 2000001 steps with 992 atoms
Pair time (%) = 4.33729 (0.00835701)
Bond time (%) = 3.33134 (0.00641876)
Neigh time (%) = 35.1247 (0.0676777)
Comm time (%) = 61.528 (0.118551)
Outpt time (%) = 0.361813 (0.000697135)
Other time (%) = 51795.3 (99.7983)
Nlocal: 62 ave 465 max 0 min
Histogram: 11 0 3 1 0 0 0 0 0 1
Nghost: 94.8125 ave 340 max 0 min
Histogram: 9 0 0 0 4 0 0 1 0 2
Neighs: 0.25 ave 2 max 0 min
Histogram: 13 0 0 0 0 2 0 0 0 1
Total # of neighbors = 4
Ave neighs/atom = 0.00403226
Ave special neighs/atom = 0.0625
Neighbor list builds = 23853
Dangerous builds = 0
------------------------------------------------------------
Sender: LSF System <lsfadmin@lsfhost.localdomain>
Subject: Job 883849: </opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer_default_gamma> Done
Job </opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer_default_gamma> was submitted from host <req770> by user <colin>.
Job was executed on host(s) <16*lsfhost.localdomain>, in queue <mpi>, as user <colin>.
</home/colin> was used as the home directory.
</home/colin/lammps-10Aug15/examples/USER/lb/tested/polymer_default> was used as the working directory.
Started at Mon Aug 24 11:13:12 2015
Results reported at Tue Aug 25 01:38:50 2015
Your job looked like:
------------------------------------------------------------
# LSBATCH: User input
/opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer_default_gamma
------------------------------------------------------------
Successfully completed.
Resource usage summary:
CPU time : 829343.88 sec.
Max Memory : 43 MB
Max Swap : 805 MB
The output (if any) is above this job summary.

83
examples/USER/lb/polymer/out.polymer_setgamma Normal file
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LAMMPS (10 Aug 2015)
Reading data file ...
orthogonal box = (0 0 0) to (40 40 40)
2 by 2 by 4 MPI processor grid
reading atoms ...
992 atoms
scanning bonds ...
1 = max bonds/atom
reading bonds ...
31 bonds
Finding 1-2 1-3 1-4 neighbors ...
Special bond factors lj: 0 1 1
Special bond factors coul: 0 1 1
2 = max # of 1-2 neighbors
2 = max # of special neighbors
32 atoms in group ForceAtoms
960 atoms in group FluidAtoms
Using a lattice-Boltzmann grid of 40 by 40 by 40 total grid points. (../fix_lb_fluid.cpp:385)
32 rigid bodies with 992 atoms
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 0 steps, check yes
master list distance cutoff = 2.18369
ghost atom cutoff = 2.18369
Setting up Verlet run ...
Unit style : nano
Current step: 0
Time step : 3e-05
Memory usage per processor = 0.108554 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -8.2758489 2790.7741 2782.4982 -0.00085093693
2000001 0.5548925 0 2792.3403 2803.7286 -0.0037777326
Loop time of 50862.3 on 16 procs for 2000001 steps with 992 atoms
Pair time (%) = 4.10128 (0.0080635)
Bond time (%) = 3.29621 (0.00648066)
Neigh time (%) = 40.0195 (0.0786822)
Comm time (%) = 89.3201 (0.175612)
Outpt time (%) = 1.05399 (0.00207224)
Other time (%) = 50724.5 (99.7291)
Nlocal: 62 ave 501 max 0 min
Histogram: 14 0 0 0 0 0 0 0 0 2
Nghost: 29 ave 259 max 0 min
Histogram: 14 0 0 0 0 0 0 1 0 1
Neighs: 0.375 ave 3 max 0 min
Histogram: 14 0 0 0 0 0 0 0 0 2
Total # of neighbors = 6
Ave neighs/atom = 0.00604839
Ave special neighs/atom = 0.0625
Neighbor list builds = 30671
Dangerous builds = 0
------------------------------------------------------------
Sender: LSF System <lsfadmin@lsfhost.localdomain>
Subject: Job 883848: </opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer> Done
Job </opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer> was submitted from host <req770> by user <colin>.
Job was executed on host(s) <16*lsfhost.localdomain>, in queue <mpi>, as user <colin>.
</home/colin> was used as the home directory.
</home/colin/lammps-10Aug15/examples/USER/lb/tested/polymer> was used as the working directory.
Started at Mon Aug 24 11:12:37 2015
Results reported at Tue Aug 25 01:20:46 2015
Your job looked like:
------------------------------------------------------------
# LSBATCH: User input
/opt/hpmpi/bin/mpirun -srun ./lmp_mpi -in in.polymer
------------------------------------------------------------
Successfully completed.
Resource usage summary:
CPU time : 812767.44 sec.
Max Memory : 44 MB
Max Swap : 812 MB
The output (if any) is above this job summary.