git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15050 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
1
examples/USER/manifold/diffusion/README
Normal file
1
examples/USER/manifold/diffusion/README
Normal file
@ -0,0 +1 @@
|
||||
This example uses fix nve/manifold/rattle and a Langevin thermostat to generate Brownian motion on a few manifolds. A plotting script is included to plot the mean squared displacement against theoretical expectation.
|
||||
4018
examples/USER/manifold/diffusion/msd.cyl.data
Normal file
4018
examples/USER/manifold/diffusion/msd.cyl.data
Normal file
File diff suppressed because it is too large
Load Diff
30
examples/USER/manifold/diffusion/msd.cyl.in
Normal file
30
examples/USER/manifold/diffusion/msd.cyl.in
Normal file
@ -0,0 +1,30 @@
|
||||
dimension 3
|
||||
units lj
|
||||
boundary f f p
|
||||
|
||||
read_data msd.cyl.data
|
||||
mass 1 1.0
|
||||
|
||||
pair_style none
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
variable R equal 5
|
||||
fix step all nve/manifold/rattle 1e-10 100 cylinder $R
|
||||
fix temp all langevin 1.0 1.0 1.0 12321 gjf yes
|
||||
velocity all create 1.0 1283
|
||||
run 25000
|
||||
compute dx2 all msd
|
||||
|
||||
variable D equal "1.0"
|
||||
variable t equal time
|
||||
variable my_msd equal "2*v_D*(v_t-125)+ 2*v_R*v_R*(1.0 - exp(-(v_t-125)*v_D/(v_R*v_R)) )"
|
||||
variable msd equal c_dx2[4]
|
||||
|
||||
dump traj all custom 100 msd.cyl.gz id type x y zu
|
||||
|
||||
fix msd_out all print 250 "$t ${msd} ${my_msd}" file msd.cyl.dat screen no
|
||||
|
||||
thermo_style custom time step pe ke etotal temp c_dx2[4] v_my_msd
|
||||
thermo 1000
|
||||
run 25000
|
||||
|
||||
BIN
examples/USER/manifold/diffusion/msd.pdf
Normal file
BIN
examples/USER/manifold/diffusion/msd.pdf
Normal file
Binary file not shown.
2016
examples/USER/manifold/diffusion/msd.plane.data
Normal file
2016
examples/USER/manifold/diffusion/msd.plane.data
Normal file
File diff suppressed because it is too large
Load Diff
29
examples/USER/manifold/diffusion/msd.plane.in
Normal file
29
examples/USER/manifold/diffusion/msd.plane.in
Normal file
@ -0,0 +1,29 @@
|
||||
dimension 3
|
||||
units lj
|
||||
boundary p p f
|
||||
|
||||
read_data msd.plane.data
|
||||
mass 1 1.0
|
||||
|
||||
pair_style none
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
variable R equal 8
|
||||
fix step all nve/manifold/rattle 1e-4 4 plane 0 0 1 0 0 0
|
||||
fix temp all langevin 1.0 1.0 1.0 12321 gjf yes
|
||||
|
||||
velocity all create 1.0 1283
|
||||
run 25000
|
||||
|
||||
compute dx2 all msd
|
||||
|
||||
variable D equal "1.0"
|
||||
variable t equal time
|
||||
variable my_msd equal "4*(v_t - 125)*v_D"
|
||||
variable msd equal c_dx2[4]
|
||||
|
||||
fix msd_out all print 250 "$t ${msd} ${my_msd}" file msd.plane.dat screen no
|
||||
|
||||
thermo_style custom time step pe ke etotal temp c_dx2[4] v_my_msd
|
||||
thermo 1000
|
||||
run 25000
|
||||
2016
examples/USER/manifold/diffusion/msd.sphere.data
Normal file
2016
examples/USER/manifold/diffusion/msd.sphere.data
Normal file
File diff suppressed because it is too large
Load Diff
27
examples/USER/manifold/diffusion/msd.sphere.in
Normal file
27
examples/USER/manifold/diffusion/msd.sphere.in
Normal file
@ -0,0 +1,27 @@
|
||||
dimension 3
|
||||
units lj
|
||||
boundary f f f
|
||||
|
||||
read_data msd.sphere.data
|
||||
mass 1 1.0
|
||||
|
||||
pair_style none
|
||||
atom_modify sort 0 1.0
|
||||
|
||||
variable R equal 8
|
||||
fix step all nve/manifold/rattle 1e-4 4 sphere $R
|
||||
fix temp all langevin 1.0 1.0 1.0 12321 gjf yes
|
||||
velocity all create 1.0 1283
|
||||
run 25000
|
||||
compute dx2 all msd
|
||||
|
||||
variable D equal "1.0"
|
||||
variable t equal time
|
||||
variable my_msd equal "2*v_R*v_R*(1.0 - exp(-2*(v_t-125)*v_D/(v_R*v_R)) )"
|
||||
variable msd equal c_dx2[4]
|
||||
|
||||
fix msd_out all print 250 "$t ${msd} ${my_msd}" file msd.sphere.dat screen no
|
||||
|
||||
thermo_style custom time step pe ke etotal temp c_dx2[4] v_my_msd
|
||||
thermo 1000
|
||||
run 25000
|
||||
BIN
examples/USER/manifold/diffusion/msd_plot2.pdf
Normal file
BIN
examples/USER/manifold/diffusion/msd_plot2.pdf
Normal file
Binary file not shown.
63
examples/USER/manifold/diffusion/plot_msd.gpl
Normal file
63
examples/USER/manifold/diffusion/plot_msd.gpl
Normal file
@ -0,0 +1,63 @@
|
||||
# Plots the observed and expected MSDs.
|
||||
#
|
||||
set term epslatex standalone size 12cm,8cm color dashed
|
||||
set output 'msd_plot2.tex'
|
||||
|
||||
msd_s(t,R,D) = 2*R*R*( 1 - exp(-2*D*t/(R*R)) )
|
||||
msd_c(t,R,D) = 2*D*t + 2*R*R*( 1 - exp(-D*t/(R*R)) )
|
||||
msd_p(t,D) = 4*D*t
|
||||
|
||||
set key bottom right box opaque maxrow 3 samplen 1 width -5
|
||||
|
||||
|
||||
set title 'Mean Squared Displacements on curved surfaces'
|
||||
set xlabel 'Time / $\tau$' offset 0,0.5
|
||||
set ylabel 'Mean squared displacement $\left<\delta x^2\right>$'
|
||||
|
||||
|
||||
set multiplot
|
||||
set size 1,1
|
||||
set origin 0,0
|
||||
|
||||
set xrange[0:130]
|
||||
set yrange[-80:520]
|
||||
|
||||
set style line 1 lc rgb '#000000' lw 6.0 dt 2
|
||||
set style line 2 lc rgb '#000000' lw 6.0 dt 3
|
||||
set style line 3 lc rgb '#000000' lw 3.0 dt 1
|
||||
|
||||
set grid
|
||||
|
||||
plot 'msd.plane.dat' u ($1-125):2 w p pt 4 ps 2.0 lw 2 lc rgb '#00AA00' ti 'Plane, data' \
|
||||
, 'msd.cyl.dat' u ($1-125):2 w p pt 6 ps 2.0 lw 2 lc rgb '#AA0000' ti 'Cylinder, data' \
|
||||
, 'msd.sphere.dat' u ($1-125):2 w p pt 8 ps 2.0 lw 2 lc rgb '#0000CC' ti 'Sphere, data' \
|
||||
, msd_p(x, 1.0) w l ls 1 ti 'Plane, theory' \
|
||||
, msd_c(x, 5, 1.0) w l ls 2 ti 'Cylinder, theory' \
|
||||
, msd_s(x, 8, 1.0) w l ls 3 ti 'Sphere, theory'
|
||||
|
||||
|
||||
|
||||
set origin 0.12,0.46
|
||||
set size 0.4,0.42
|
||||
|
||||
# Hack to remove old grid from inset:
|
||||
set object 1 rectangle from graph 0,0 to graph 1,1 fillcolor rgb "white" behind
|
||||
|
||||
|
||||
unset key
|
||||
set grid front
|
||||
|
||||
set title 'Short time behaviour' offset 0,-0.8
|
||||
set ylabel ''
|
||||
set xrange[0:10]
|
||||
set yrange[0:40]
|
||||
set ytics 10
|
||||
set xtics 2
|
||||
plot 'msd.plane.dat' u ($1-125):2 w p pt 4 ps 2.0 lw 2 lc rgb '#00AA00' ti 'Plane, data' \
|
||||
, 'msd.cyl.dat' u ($1-125):2 w p pt 6 ps 2.0 lw 2 lc rgb '#AA0000' ti 'Cylinder, data' \
|
||||
, 'msd.sphere.dat' u ($1-125):2 w p pt 8 ps 2.0 lw 2 lc rgb '#0000CC' ti 'Sphere, data' \
|
||||
, msd_p(x, 1.0) w l ls 1 ti 'plane, theory' \
|
||||
, msd_c(x, 5, 1.0) w l ls 2 ti 'cylinder, theory' \
|
||||
, msd_s(x, 8, 1.0) w l ls 3 ti 'sphere, theory'
|
||||
unset multiplot
|
||||
|
||||
3
examples/USER/manifold/energy/README
Normal file
3
examples/USER/manifold/energy/README
Normal file
@ -0,0 +1,3 @@
|
||||
This example runs an NVE simulation on various manifolds and checks for energy conservation.
|
||||
The script "energy.sh" automates the running of LAMMPS for the different manifolds, and if gnuplot is installed, it makes a nice plot.
|
||||
|
||||
1018
examples/USER/manifold/energy/cylinder.data
Normal file
1018
examples/USER/manifold/energy/cylinder.data
Normal file
File diff suppressed because it is too large
Load Diff
3
examples/USER/manifold/energy/cylinder.setup
Normal file
3
examples/USER/manifold/energy/cylinder.setup
Normal file
@ -0,0 +1,3 @@
|
||||
boundary f f p
|
||||
read_data cylinder.data
|
||||
variable manifold_params string "6.0"
|
||||
28
examples/USER/manifold/energy/energy.in
Normal file
28
examples/USER/manifold/energy/energy.in
Normal file
@ -0,0 +1,28 @@
|
||||
units lj
|
||||
dimension 3
|
||||
|
||||
include ${manifold}.setup
|
||||
|
||||
fix step all nve/manifold/rattle 1e-6 10 ${manifold} ${manifold_params}
|
||||
pair_style lj/smooth/linear 2.5
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_modify shift yes
|
||||
|
||||
# Rebalance:
|
||||
fix load all balance 1000 1.0 shift "xyz" 10 1.05
|
||||
|
||||
timestep 0.0005
|
||||
|
||||
variable t equal time
|
||||
variable U equal pe
|
||||
variable K equal ke
|
||||
variable E equal "v_U + v_K"
|
||||
|
||||
fix therm all print 25000 "$t $U $K $E" file thermo.${manifold}.dat screen no
|
||||
|
||||
dump traj all custom 1000000 dump.${manifold}.gz id type x y z
|
||||
|
||||
thermo_style custom time step temp pe ke etotal
|
||||
thermo 10000
|
||||
run ${STEPS}
|
||||
|
||||
27
examples/USER/manifold/energy/energy.plane.in
Normal file
27
examples/USER/manifold/energy/energy.plane.in
Normal file
@ -0,0 +1,27 @@
|
||||
units lj
|
||||
dimension 2
|
||||
|
||||
read_data plane.data
|
||||
|
||||
fix step all nve
|
||||
fix twod all enforce2d
|
||||
|
||||
pair_style lj/smooth/linear 2.5
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_modify shift yes
|
||||
|
||||
timestep 0.0005
|
||||
|
||||
variable t equal time
|
||||
variable U equal pe
|
||||
variable K equal ke
|
||||
variable E equal "v_U + v_K"
|
||||
|
||||
fix therm all print 25000 "$t $U $K $E" file thermo.plane.dat screen no
|
||||
|
||||
dump traj all custom 1000000 dump.plane.gz id type x y z
|
||||
|
||||
thermo_style custom time step temp pe ke etotal
|
||||
thermo 10000
|
||||
run ${STEPS}
|
||||
|
||||
39
examples/USER/manifold/energy/energy.sh
Normal file
39
examples/USER/manifold/energy/energy.sh
Normal file
@ -0,0 +1,39 @@
|
||||
#!/bin/bash
|
||||
#
|
||||
# Runs the various tests.
|
||||
#
|
||||
|
||||
# Set this to your lammps executable
|
||||
LMP="mpirun -np 2 lmp"
|
||||
|
||||
NO_GNUPLOT=$( command -v gnuplot >/dev/null 2>&1 )
|
||||
NSTEPS=100000000
|
||||
if [ $# -ge 1 ]; then
|
||||
NSTEPS=$1
|
||||
fi
|
||||
for MANIFOLD in torus sphere cylinder
|
||||
do
|
||||
echo "+=== Running example on "$MANIFOLD" ===+"
|
||||
DATE=$(date | awk '{ print $3$2substr($6,3) }')
|
||||
LOG=$MANIFOLD".energy."$DATE".log"
|
||||
$LMP -in energy.in -var manifold $MANIFOLD -log $MANIFOLD".energy.log" -var STEPS $NSTEPS
|
||||
echo "+======================================+"
|
||||
echo ""
|
||||
done
|
||||
# 2D plane for verification:
|
||||
$LMP -in energy.plane.in -log energy.plane.log -var STEPS $NSTEPS
|
||||
|
||||
|
||||
if [ $NO_GNUPLOT ]
|
||||
then
|
||||
echo "No Gnuplot found, not plotting."
|
||||
exit 0
|
||||
fi
|
||||
|
||||
E0S=$( head -n 2 thermo.sphere.dat | tail -n 1 | awk '{ print $4 }' )
|
||||
E0C=$( head -n 2 thermo.cylinder.dat | tail -n 1 | awk '{ print $4 }' )
|
||||
E0T=$( head -n 2 thermo.torus.dat | tail -n 1 | awk '{ print $4 }' )
|
||||
E0P=$( head -n 2 thermo.plane.dat | tail -n 1 | awk '{ print $4 }' )
|
||||
|
||||
echo "Plotting using Gnuplot"
|
||||
gnuplot -e "E0S="$E0S -e "E0C="$E0C -e "E0T="$E0T -e "E0P="$E0P plot_energies.gpl
|
||||
BIN
examples/USER/manifold/energy/energy_conservation.pdf
Normal file
BIN
examples/USER/manifold/energy/energy_conservation.pdf
Normal file
Binary file not shown.
BIN
examples/USER/manifold/energy/energy_conservation.png
Normal file
BIN
examples/USER/manifold/energy/energy_conservation.png
Normal file
Binary file not shown.
|
After Width: | Height: | Size: 84 KiB |
1022
examples/USER/manifold/energy/plane.anneal.data
Normal file
1022
examples/USER/manifold/energy/plane.anneal.data
Normal file
File diff suppressed because it is too large
Load Diff
1018
examples/USER/manifold/energy/plane.data
Normal file
1018
examples/USER/manifold/energy/plane.data
Normal file
File diff suppressed because it is too large
Load Diff
78
examples/USER/manifold/energy/plot_energies.gpl
Normal file
78
examples/USER/manifold/energy/plot_energies.gpl
Normal file
@ -0,0 +1,78 @@
|
||||
# Gnuplot script to plot the energies.
|
||||
#
|
||||
|
||||
#set term pngcairo size 800,600 solid color
|
||||
#set output 'energy_conservation.png'
|
||||
|
||||
set term epslatex size 14cm,10cm standalone color
|
||||
set output 'energy_conservation.tex'
|
||||
|
||||
E0S = 0.263720171785176
|
||||
E0C = 0.680969247210183
|
||||
E0T = 0.393139981206627
|
||||
E0P = -1.16336568585219
|
||||
E1S = 0.168915271276422
|
||||
E1C = 0.615216219988708
|
||||
E1T = 0.318731094092091
|
||||
E1P = -1.29808304730092
|
||||
|
||||
set grid
|
||||
set xlabel 'Time (LJ units)'
|
||||
set ylabel 'Relative energy deviation $(\mathcal{H}(t) - \mathcal{H}(0))/\mathcal{H}(0)$'
|
||||
set title 'Energy drift for RATTLE-M on various surfaces'
|
||||
|
||||
set key opaque box top left
|
||||
|
||||
set log x
|
||||
|
||||
col_S = '#CC0000'
|
||||
col_C = '#00CC00'
|
||||
col_T = '#0000CC'
|
||||
col_P = '#000000'
|
||||
|
||||
set multiplot
|
||||
|
||||
set xrange[10:5e6]
|
||||
set yrange[-0.02:0.02]
|
||||
|
||||
set ytics ( "$-2.0~10^{-2}$" -2e-2, "$-1.5~10^{-2}$" -1.5e-2, "$-1.0~10^{-2}$" -1e-2 \
|
||||
, "$-0.5~10^{-2}$" -0.5e-2, "$0$" 0, "$0.5~10^{-2}$" 0.5e-2, "$1.0~10^{-2}$" 1e-2 \
|
||||
, "$1.5~10^{-2}$" 1.5e-2, "$2.0~10^{-2}$" 2e-2 )
|
||||
|
||||
plot 'long_run_lj_cut/thermo.sphere.dat' u 1:($4/E1S-1) w l lw 2 lc rgb col_S ti 'S, Truncated' \
|
||||
, 'long_run_lj_cut/thermo.cylinder.dat' u 1:($4/E1C-1) w l lw 2 lc rgb col_C ti 'C, Truncated' \
|
||||
, 'long_run_lj_cut/thermo.torus.dat' u 1:($4/E1T-1) w l lw 2 lc rgb col_T ti 'T, Truncated' \
|
||||
, 'long_run_lj_cut/thermo.plane.dat' u 1:($4/E1P-1) w l lw 2 lc rgb col_P ti 'P, Truncated' \
|
||||
, 'thermo.sphere.dat' u 1:($4/E0S-1) w p pt 2 ps 1 lc rgb col_S ti 'S, Smoothed' \
|
||||
, 'thermo.cylinder.dat' u 1:($4/E0C-1) w p pt 4 ps 1 lc rgb col_C ti 'C, Smoothed' \
|
||||
, 'thermo.torus.dat' u 1:($4/E0T-1) w p pt 6 ps 1 lc rgb col_T ti 'T, Smoothed' \
|
||||
, 'thermo.plane.dat' u 1:($4/E0P-1) w p pt 8 ps 1 lc rgb col_P ti 'P, Smoothed'
|
||||
|
||||
set origin 0.285,0.106
|
||||
set size 0.55,0.4
|
||||
|
||||
set object 1 rectangle from graph 0,0 to graph 1,1 fillcolor rgb "white" behind
|
||||
|
||||
set xlabel ''
|
||||
set ylabel ''
|
||||
set title ''
|
||||
set xrange[10:500000]
|
||||
set yrange[-1.5e-5:1.5e-5]
|
||||
set ytics
|
||||
set format y "%0.1t 10^{%T}"
|
||||
set grid
|
||||
unset key
|
||||
|
||||
#set ytics ( "$-1.5~10^{-5}$" -1.5e-5, "$-1.0~10^{-5}$" -1e-5, "$-0.5~10^{-5}$" -0.5e-5, \
|
||||
# "$0$" 0, "$0.5~10^{-5}$" 0.5e-5, "$1.0~10^{-5}$" 1.0e-5, "$1.5~10^{-5}$" 1.5e-5 )
|
||||
|
||||
set ytics ( "$-1.8~10^{-5}$" -1.8e-5, "$-1.2~10^{-5}$" -1.2e-5, "$-0.6~10^{-5}$" -0.6e-5, \
|
||||
"$0$" 0, "$0.6~10^{-5}$" 0.6e-5, "$1.2~10^{-5}$" 1.2e-5, "$1.8~10^{-5}$" 1.8e-5 )
|
||||
|
||||
set title 'Smoothed only' offset 0,-0.5
|
||||
plot 'thermo.sphere.dat' u 1:($4/E0S - 1) w p pt 2 ps 1 lc rgb col_S \
|
||||
, 'thermo.cylinder.dat' u 1:($4/E0C - 1) w p pt 4 ps 1 lc rgb col_C \
|
||||
, 'thermo.torus.dat' u 1:($4/E0T - 1) w p pt 6 ps 1 lc rgb col_T \
|
||||
, 'thermo.plane.dat' u 1:($4/E0P - 1) w p pt 8 ps 1 lc rgb col_P
|
||||
|
||||
unset multiplot
|
||||
1018
examples/USER/manifold/energy/sphere.data
Normal file
1018
examples/USER/manifold/energy/sphere.data
Normal file
File diff suppressed because it is too large
Load Diff
3
examples/USER/manifold/energy/sphere.setup
Normal file
3
examples/USER/manifold/energy/sphere.setup
Normal file
@ -0,0 +1,3 @@
|
||||
boundary f f f
|
||||
read_data sphere.data
|
||||
variable manifold_params string "10.0"
|
||||
1018
examples/USER/manifold/energy/torus.data
Normal file
1018
examples/USER/manifold/energy/torus.data
Normal file
File diff suppressed because it is too large
Load Diff
3
examples/USER/manifold/energy/torus.setup
Normal file
3
examples/USER/manifold/energy/torus.setup
Normal file
@ -0,0 +1,3 @@
|
||||
boundary f f f
|
||||
read_data torus.data
|
||||
variable manifold_params string "10.0 4.0"
|
||||
1
examples/USER/manifold/thylakoid/README
Normal file
1
examples/USER/manifold/thylakoid/README
Normal file
@ -0,0 +1 @@
|
||||
This example simulates particles on a complex manifold that consists of pieces of cylinder, plane and sphere. By keeping track of when the blue particles reach the other compartment, information about mean escape times can be obtained.
|
||||
8026
examples/USER/manifold/thylakoid/thylakoid.data
Normal file
8026
examples/USER/manifold/thylakoid/thylakoid.data
Normal file
File diff suppressed because it is too large
Load Diff
33
examples/USER/manifold/thylakoid/thylakoid.in
Normal file
33
examples/USER/manifold/thylakoid/thylakoid.in
Normal file
@ -0,0 +1,33 @@
|
||||
units lj
|
||||
dimension 3
|
||||
boundary f f p
|
||||
|
||||
pair_style lj/cut 1.1225
|
||||
read_data thylakoid.data
|
||||
|
||||
pair_coeff * * 1.0 1.0
|
||||
pair_modify shift yes
|
||||
|
||||
# Makes about 100 particles type 2:
|
||||
region make_two sphere -29 0 0 6.25
|
||||
region everywhere block -25 25 -25 25 -25 25
|
||||
group two region make_two
|
||||
set group two type 2
|
||||
|
||||
# And deletes some of type 1 to allow more movement:
|
||||
group one type 1
|
||||
set group one type 1
|
||||
delete_atoms porosity everywhere 0.2 123
|
||||
|
||||
|
||||
# Start run
|
||||
variable wB equal 5.0
|
||||
variable LB equal 10.0
|
||||
variable lB equal 3.0
|
||||
fix step all nve/manifold/rattle 1e-4 10 thylakoid ${wB} ${LB} ${lB}
|
||||
|
||||
thermo_style custom time step pe ke etotal temp
|
||||
thermo 2500
|
||||
dump traj all custom 10000 thylakoid.dump id type x y z
|
||||
run 25000000
|
||||
|
||||
1
examples/USER/manifold/vir/README
Normal file
1
examples/USER/manifold/vir/README
Normal file
@ -0,0 +1 @@
|
||||
This example simulates some coarse-grained capsomere model attached to a slowly shrinking spherical surface.
|
||||
704
examples/USER/manifold/vir/init.data
Normal file
704
examples/USER/manifold/vir/init.data
Normal file
@ -0,0 +1,704 @@
|
||||
LAMMPS data file with capsid model
|
||||
|
||||
288 atoms
|
||||
4 atom types
|
||||
216 bonds
|
||||
3 bond types
|
||||
144 angles
|
||||
1 angle types
|
||||
|
||||
|
||||
-8 8 xlo xhi
|
||||
-8 8 ylo yhi
|
||||
-8 8 zlo zhi
|
||||
|
||||
|
||||
Masses
|
||||
|
||||
1 1.0
|
||||
2 1.1.728
|
||||
3 2.744
|
||||
4 1.0
|
||||
|
||||
Pair Coeffs # lj/cut
|
||||
|
||||
1 1 1 1.1225
|
||||
2 1 1.35 4
|
||||
3 1 2.1 4
|
||||
4 1 1 1.1225
|
||||
|
||||
PairIJ Coeffs # lj/cut
|
||||
|
||||
1 1 1 1 1.1225
|
||||
1 2 1 1.175 1.31894
|
||||
1 3 1 1.55 1.73988
|
||||
1 4 1 1 1.1225
|
||||
2 2 1 1.35 4
|
||||
2 3 1 1.725 1.93631
|
||||
2 4 1 1.175 1.31894
|
||||
3 3 1 2.1 4
|
||||
3 4 1 1.55 1.73988
|
||||
4 4 1 1 1.1225
|
||||
|
||||
Bond Coeffs # harmonic
|
||||
|
||||
1 50 0.659469
|
||||
2 50 0.855906
|
||||
3 50 0.659469
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 1 -0.701084 3.93343 0.19124
|
||||
2 1 2 -0.816669 4.58193 0.222769
|
||||
3 1 3 -0.966685 5.42359 0.263689
|
||||
4 1 4 -1.08227 6.07209 0.295219
|
||||
5 2 1 0.0618129 0.850751 3.90799
|
||||
6 2 2 0.0720038 0.991012 4.55229
|
||||
7 2 3 0.0852304 1.17305 5.38851
|
||||
8 2 4 0.0954213 1.31331 6.03281
|
||||
9 3 1 3.30064 -0.413296 -2.22148
|
||||
10 3 2 3.8448 -0.481435 -2.58773
|
||||
11 3 3 4.55106 -0.569871 -3.06307
|
||||
12 3 4 5.09523 -0.638009 -3.42932
|
||||
13 4 1 -1.59122 -1.3139 -3.42661
|
||||
14 4 2 -1.85356 -1.53052 -3.99155
|
||||
15 4 3 -2.19405 -1.81166 -4.72477
|
||||
16 4 4 -2.45639 -2.02828 -5.2897
|
||||
17 5 1 -3.9047 -0.80606 -0.32184
|
||||
18 5 2 -4.54846 -0.938953 -0.374901
|
||||
19 5 3 -5.38397 -1.11143 -0.443767
|
||||
20 5 4 -6.02773 -1.24432 -0.496828
|
||||
21 6 1 1.01166 3.7639 -0.899789
|
||||
22 6 2 1.17845 4.38444 -1.04813
|
||||
23 6 3 1.39492 5.18983 -1.24067
|
||||
24 6 4 1.56171 5.81037 -1.38901
|
||||
25 7 1 -1.05538 3.74967 -0.908937
|
||||
26 7 2 -1.22938 4.36786 -1.05879
|
||||
27 7 3 -1.45521 5.1702 -1.25328
|
||||
28 7 4 -1.62921 5.7884 -1.40314
|
||||
29 8 1 -1.51588 -2.46782 2.75898
|
||||
30 8 2 -1.76579 -2.87469 3.21385
|
||||
31 8 3 -2.09016 -3.40274 3.8042
|
||||
32 8 4 -2.34007 -3.8096 4.25907
|
||||
33 9 1 -2.25141 0.367776 3.28571
|
||||
34 9 2 -2.62259 0.42841 3.82742
|
||||
35 9 3 -3.10434 0.507105 4.53048
|
||||
36 9 4 -3.47552 0.56774 5.07219
|
||||
37 10 1 1.67684 1.52227 3.2971
|
||||
38 10 2 1.9533 1.77324 3.84069
|
||||
39 10 3 2.31211 2.09897 4.54619
|
||||
40 10 4 2.58856 2.34994 5.08978
|
||||
41 11 1 -3.25052 2.13047 -0.94615
|
||||
42 11 2 -3.78643 2.48171 -1.10214
|
||||
43 11 3 -4.48196 2.93758 -1.30459
|
||||
44 11 4 -5.01787 3.28883 -1.46058
|
||||
45 12 1 0.0676891 -0.567005 3.95903
|
||||
46 12 2 0.0788488 -0.660486 4.61174
|
||||
47 12 3 0.0933327 -0.781812 5.45888
|
||||
48 12 4 0.104492 -0.875292 6.1116
|
||||
49 13 1 1.59585 -1.27299 3.43988
|
||||
50 13 2 1.85895 -1.48286 4.007
|
||||
51 13 3 2.20043 -1.75525 4.74306
|
||||
52 13 4 2.46353 -1.96512 5.31018
|
||||
53 14 1 -1.40854 2.22169 -3.01332
|
||||
54 14 2 -1.64076 2.58797 -3.51012
|
||||
55 14 3 -1.94215 3.06336 -4.1549
|
||||
56 14 4 -2.17438 3.42964 -4.6517
|
||||
57 15 1 1.7153 -2.87555 -2.18838
|
||||
58 15 2 1.99809 -3.34963 -2.54917
|
||||
59 15 3 2.36513 -3.96493 -3.01743
|
||||
60 15 4 2.64792 -4.43901 -3.37822
|
||||
61 16 1 -2.22107 -2.07058 -2.60376
|
||||
62 16 2 -2.58725 -2.41195 -3.03303
|
||||
63 16 3 -3.06251 -2.85501 -3.59017
|
||||
64 16 4 -3.42869 -3.19638 -4.01945
|
||||
65 17 1 2.2192 1.29232 -3.06677
|
||||
66 17 2 2.58507 1.50538 -3.57238
|
||||
67 17 3 3.05993 1.7819 -4.2286
|
||||
68 17 4 3.4258 1.99496 -4.73421
|
||||
69 18 1 -2.03962 2.69954 -2.13364
|
||||
70 18 2 -2.37588 3.14461 -2.48541
|
||||
71 18 3 -2.81231 3.72225 -2.94196
|
||||
72 18 4 -3.14858 4.16731 -3.29373
|
||||
73 19 1 -3.49737 -0.254473 1.92449
|
||||
74 19 2 -4.07397 -0.296428 2.24178
|
||||
75 19 3 -4.82232 -0.350879 2.65357
|
||||
76 19 4 -5.39892 -0.392833 2.97086
|
||||
77 20 1 3.50808 -1.84615 0.533931
|
||||
78 20 2 4.08645 -2.15052 0.621959
|
||||
79 20 3 4.8371 -2.54555 0.736207
|
||||
80 20 4 5.41547 -2.84992 0.824235
|
||||
81 21 1 -0.325119 3.30809 2.22505
|
||||
82 21 2 -0.378721 3.85349 2.59188
|
||||
83 21 3 -0.448289 4.56134 3.06799
|
||||
84 21 4 -0.50189 5.10674 3.43483
|
||||
85 22 1 0.662812 0.0220505 -3.94464
|
||||
86 22 2 0.772088 0.0256859 -4.59498
|
||||
87 22 3 0.913914 0.0304042 -5.43904
|
||||
88 22 4 1.02319 0.0340396 -6.08939
|
||||
89 23 1 3.23422 -1.85295 -1.45135
|
||||
90 23 2 3.76744 -2.15844 -1.69062
|
||||
91 23 3 4.45949 -2.55492 -2.00118
|
||||
92 23 4 4.9927 -2.86041 -2.24046
|
||||
93 24 1 -3.96042 -0.0236549 0.560805
|
||||
94 24 2 -4.61337 -0.0275549 0.653263
|
||||
95 24 3 -5.4608 -0.0326165 0.773262
|
||||
96 24 4 -6.11375 -0.0365164 0.865721
|
||||
97 25 1 -0.68153 -3.49389 -1.82434
|
||||
98 25 2 -0.793892 -4.06992 -2.12512
|
||||
99 25 3 -0.939723 -4.81753 -2.51548
|
||||
100 25 4 -1.05208 -5.39356 -2.81626
|
||||
101 26 1 0.487017 3.94319 0.462684
|
||||
102 26 2 0.56731 4.59329 0.538966
|
||||
103 26 3 0.671521 5.43704 0.63797
|
||||
104 26 4 0.751814 6.08714 0.714251
|
||||
105 27 1 3.01581 -0.475516 2.58434
|
||||
106 27 2 3.51301 -0.553913 3.01041
|
||||
107 27 3 4.15833 -0.655663 3.5634
|
||||
108 27 4 4.65553 -0.73406 3.98947
|
||||
109 28 1 -0.782228 -0.526685 -3.88725
|
||||
110 28 2 -0.911192 -0.613518 -4.52813
|
||||
111 28 3 -1.07857 -0.726216 -5.35991
|
||||
112 28 4 -1.20753 -0.813049 -6.00079
|
||||
113 29 1 -2.59565 -0.97452 2.88321
|
||||
114 29 2 -3.02359 -1.13519 3.35856
|
||||
115 29 3 -3.579 -1.34371 3.97549
|
||||
116 29 4 -4.00694 -1.50438 4.45084
|
||||
117 30 1 1.7976 -0.409766 -3.54975
|
||||
118 30 2 2.09396 -0.477322 -4.13499
|
||||
119 30 3 2.4786 -0.565003 -4.89455
|
||||
120 30 4 2.77497 -0.63256 -5.47979
|
||||
121 31 1 1.32145 -3.66441 -0.908779
|
||||
122 31 2 1.53931 -4.26855 -1.05861
|
||||
123 31 3 1.82207 -5.05265 -1.25306
|
||||
124 31 4 2.03993 -5.65679 -1.40289
|
||||
125 32 1 0.541532 2.8122 2.79254
|
||||
126 32 2 0.630813 3.27584 3.25294
|
||||
127 32 3 0.746688 3.87758 3.85048
|
||||
128 32 4 0.835969 4.34122 4.31088
|
||||
129 33 1 0.85239 -2.98497 2.52257
|
||||
130 33 2 0.992921 -3.4771 2.93846
|
||||
131 33 3 1.17531 -4.11581 3.47823
|
||||
132 33 4 1.31584 -4.60794 3.89412
|
||||
133 34 1 2.3452 3.20727 0.46198
|
||||
134 34 2 2.73185 3.73605 0.538145
|
||||
135 34 3 3.23366 4.42233 0.636998
|
||||
136 34 4 3.62031 4.9511 0.713164
|
||||
137 35 1 -0.487077 -3.85764 0.938818
|
||||
138 35 2 -0.56738 -4.49364 1.0936
|
||||
139 35 3 -0.671604 -5.31908 1.29448
|
||||
140 35 4 -0.751907 -5.95508 1.44926
|
||||
141 36 1 2.5761 1.56047 2.63223
|
||||
142 36 2 3.00081 1.81774 3.0662
|
||||
143 36 3 3.55204 2.15164 3.62944
|
||||
144 36 4 3.97675 2.40892 4.06341
|
||||
145 37 1 1.1532 -1.61546 -3.47281
|
||||
146 37 2 1.34333 -1.8818 -4.04536
|
||||
147 37 3 1.59008 -2.22747 -4.78846
|
||||
148 37 4 1.78021 -2.49381 -5.36101
|
||||
149 38 1 3.80441 1.23346 -0.0709251
|
||||
150 38 2 4.43164 1.43681 -0.0826184
|
||||
151 38 3 5.24569 1.70074 -0.0977947
|
||||
152 38 4 5.87291 1.9041 -0.109488
|
||||
153 39 1 -0.831367 -1.75837 3.49528
|
||||
154 39 2 -0.968432 -2.04827 4.07153
|
||||
155 39 3 -1.14632 -2.42452 4.81944
|
||||
156 39 4 -1.28339 -2.71442 5.39569
|
||||
157 40 1 -3.35775 -2.00673 -0.835774
|
||||
158 40 2 -3.91134 -2.33757 -0.973565
|
||||
159 40 3 -4.62982 -2.76697 -1.1524
|
||||
160 40 4 -5.1834 -3.09781 -1.29019
|
||||
161 41 1 -2.20432 1.30999 -3.07
|
||||
162 41 2 -2.56774 1.52596 -3.57614
|
||||
163 41 3 -3.03942 1.80627 -4.23305
|
||||
164 41 4 -3.40284 2.02224 -4.73919
|
||||
165 42 1 1.09288 -3.66612 1.16842
|
||||
166 42 2 1.27306 -4.27054 1.36105
|
||||
167 42 3 1.50691 -5.055 1.61106
|
||||
168 42 4 1.68709 -5.65943 1.8037
|
||||
169 43 1 -3.07386 0.781288 2.43741
|
||||
170 43 2 -3.58064 0.910097 2.83926
|
||||
171 43 3 -4.23837 1.07727 3.36081
|
||||
172 43 4 -4.74515 1.20608 3.76266
|
||||
173 44 1 -3.15076 -2.10328 1.28411
|
||||
174 44 2 -3.67021 -2.45004 1.49582
|
||||
175 44 3 -4.3444 -2.90009 1.77059
|
||||
176 44 4 -4.86386 -3.24686 1.9823
|
||||
177 45 1 1.83257 3.15105 -1.64698
|
||||
178 45 2 2.1347 3.67056 -1.91852
|
||||
179 45 3 2.52683 4.34481 -2.27093
|
||||
180 45 4 2.82896 4.86431 -2.54247
|
||||
181 46 1 3.03229 2.44072 0.920939
|
||||
182 46 2 3.53221 2.84312 1.07277
|
||||
183 46 3 4.18105 3.36537 1.26983
|
||||
184 46 4 4.68097 3.76777 1.42166
|
||||
185 47 1 -0.685148 -2.46174 -3.0774
|
||||
186 47 2 -0.798106 -2.8676 -3.58476
|
||||
187 47 3 -0.944712 -3.39436 -4.24326
|
||||
188 47 4 -1.05767 -3.80022 -4.75062
|
||||
189 48 1 1.86019 2.48267 2.52509
|
||||
190 48 2 2.16687 2.89198 2.94139
|
||||
191 48 3 2.5649 3.42321 3.4817
|
||||
192 48 4 2.87159 3.83252 3.898
|
||||
193 49 1 3.92074 -0.28145 -0.740678
|
||||
194 49 2 4.56714 -0.327852 -0.862792
|
||||
195 49 3 5.40608 -0.388076 -1.02128
|
||||
196 49 4 6.05249 -0.434478 -1.14339
|
||||
197 50 1 -2.4331 -3.17132 -0.150833
|
||||
198 50 2 -2.83424 -3.69417 -0.1757
|
||||
199 50 3 -3.35486 -4.37276 -0.207975
|
||||
200 50 4 -3.756 -4.8956 -0.232842
|
||||
201 51 1 -2.9946 1.69085 -2.04289
|
||||
202 51 2 -3.48831 1.96961 -2.3797
|
||||
203 51 3 -4.12908 2.33142 -2.81683
|
||||
204 51 4 -4.62279 2.61018 -3.15364
|
||||
205 52 1 0.954769 3.56359 1.54571
|
||||
206 52 2 1.11218 4.15111 1.80055
|
||||
207 52 3 1.31648 4.91364 2.13129
|
||||
208 52 4 1.47389 5.50116 2.38613
|
||||
209 53 1 -0.000383688 3.35883 -2.17216
|
||||
210 53 2 -0.000446945 3.91259 -2.53028
|
||||
211 53 3 -0.000529046 4.6313 -2.99507
|
||||
212 53 4 -0.000592303 5.18506 -3.35318
|
||||
213 54 1 -1.13409 2.01537 3.26376
|
||||
214 54 2 -1.32106 2.34763 3.80185
|
||||
215 54 3 -1.56373 2.77887 4.50022
|
||||
216 54 4 -1.7507 3.11114 5.03831
|
||||
217 55 1 -0.18323 1.16707 -3.82157
|
||||
218 55 2 -0.213438 1.35949 -4.45162
|
||||
219 55 3 -0.252645 1.60921 -5.26934
|
||||
220 55 4 -0.282854 1.80162 -5.89939
|
||||
221 56 1 -3.16152 -1.58871 -1.86569
|
||||
222 56 2 -3.68275 -1.85063 -2.17328
|
||||
223 56 3 -4.35924 -2.19058 -2.57249
|
||||
224 56 4 -4.88048 -2.4525 -2.88008
|
||||
225 57 1 0.32697 -3.16727 -2.42105
|
||||
226 57 2 0.380876 -3.68945 -2.82021
|
||||
227 57 3 0.45084 -4.36717 -3.33825
|
||||
228 57 4 0.504746 -4.88935 -3.73741
|
||||
229 58 1 -2.57648 2.36979 1.93542
|
||||
230 58 2 -3.00126 2.76049 2.25451
|
||||
231 58 3 -3.55256 3.26756 2.66865
|
||||
232 58 4 -3.97734 3.65826 2.98773
|
||||
233 59 1 -1.84228 -3.2137 1.50934
|
||||
234 59 2 -2.14601 -3.74354 1.75819
|
||||
235 59 3 -2.54021 -4.4312 2.08115
|
||||
236 59 4 -2.84394 -4.96103 2.32999
|
||||
237 60 1 2.06726 -2.51456 2.32453
|
||||
238 60 2 2.40808 -2.92913 2.70777
|
||||
239 60 3 2.85043 -3.46718 3.20516
|
||||
240 60 4 3.19125 -3.88175 3.5884
|
||||
241 61 1 3.30924 -1.38831 1.76679
|
||||
242 61 2 3.85482 -1.6172 2.05807
|
||||
243 61 3 4.56292 -1.91427 2.43612
|
||||
244 61 4 5.10851 -2.14315 2.72741
|
||||
245 62 1 0.0662913 -3.53779 1.86538
|
||||
246 62 2 0.0772206 -4.12106 2.17292
|
||||
247 62 3 0.0914054 -4.87806 2.57206
|
||||
248 62 4 0.102335 -5.46133 2.8796
|
||||
249 63 1 -0.984186 3.66087 1.27648
|
||||
250 63 2 -1.14645 4.26443 1.48693
|
||||
251 63 3 -1.35704 5.04777 1.76007
|
||||
252 63 4 -1.5193 5.65133 1.97052
|
||||
253 64 1 -2.57041 2.98875 -0.678513
|
||||
254 64 2 -2.99419 3.48149 -0.790377
|
||||
255 64 3 -3.54419 4.12102 -0.935563
|
||||
256 64 4 -3.96797 4.61376 -1.04743
|
||||
257 65 1 -0.127433 -3.91751 -0.798032
|
||||
258 65 2 -0.148443 -4.56338 -0.929602
|
||||
259 65 3 -0.175711 -5.40164 -1.10036
|
||||
260 65 4 -0.19672 -6.04751 -1.23193
|
||||
261 66 1 -3.68506 0.947699 1.23377
|
||||
262 66 2 -4.29261 1.10394 1.43718
|
||||
263 66 3 -5.08112 1.30673 1.70118
|
||||
264 66 4 -5.68867 1.46297 1.90459
|
||||
265 67 1 -2.16602 -2.87045 -1.75181
|
||||
266 67 2 -2.52313 -3.3437 -2.04062
|
||||
267 67 3 -2.98661 -3.95791 -2.41547
|
||||
268 67 4 -3.34371 -4.43115 -2.70429
|
||||
269 68 1 -0.969111 0.140347 3.87829
|
||||
270 68 2 -1.12889 0.163486 4.51769
|
||||
271 68 3 -1.33625 0.193517 5.34755
|
||||
272 68 4 -1.49603 0.216656 5.98696
|
||||
273 69 1 3.55906 0.798001 -1.64203
|
||||
274 69 2 4.14584 0.929565 -1.91275
|
||||
275 69 3 4.90739 1.10032 -2.2641
|
||||
276 69 4 5.49417 1.23188 -2.53482
|
||||
277 70 1 -3.40994 -0.202713 -2.08115
|
||||
278 70 2 -3.97213 -0.236134 -2.42427
|
||||
279 70 3 -4.70178 -0.279509 -2.86958
|
||||
280 70 4 -5.26397 -0.31293 -3.2127
|
||||
281 71 1 2.62812 -1.82176 -2.40295
|
||||
282 71 2 3.06141 -2.12211 -2.79912
|
||||
283 71 3 3.62377 -2.51192 -3.31329
|
||||
284 71 4 4.05706 -2.81227 -3.70946
|
||||
285 72 1 -3.82746 0.847616 -0.795064
|
||||
286 72 2 -4.45848 0.98736 -0.926144
|
||||
287 72 3 -5.27746 1.16873 -1.09627
|
||||
288 72 4 -5.90849 1.30847 -1.22735
|
||||
|
||||
Bonds
|
||||
|
||||
1 1 1 2
|
||||
2 2 2 3
|
||||
3 3 3 4
|
||||
4 1 5 6
|
||||
5 2 6 7
|
||||
6 3 7 8
|
||||
7 1 9 10
|
||||
8 2 10 11
|
||||
9 3 11 12
|
||||
10 1 13 14
|
||||
11 2 14 15
|
||||
12 3 15 16
|
||||
13 1 17 18
|
||||
14 2 18 19
|
||||
15 3 19 20
|
||||
16 1 21 22
|
||||
17 2 22 23
|
||||
18 3 23 24
|
||||
19 1 25 26
|
||||
20 2 26 27
|
||||
21 3 27 28
|
||||
22 1 29 30
|
||||
23 2 30 31
|
||||
24 3 31 32
|
||||
25 1 33 34
|
||||
26 2 34 35
|
||||
27 3 35 36
|
||||
28 1 37 38
|
||||
29 2 38 39
|
||||
30 3 39 40
|
||||
31 1 41 42
|
||||
32 2 42 43
|
||||
33 3 43 44
|
||||
34 1 45 46
|
||||
35 2 46 47
|
||||
36 3 47 48
|
||||
37 1 49 50
|
||||
38 2 50 51
|
||||
39 3 51 52
|
||||
40 1 53 54
|
||||
41 2 54 55
|
||||
42 3 55 56
|
||||
43 1 57 58
|
||||
44 2 58 59
|
||||
45 3 59 60
|
||||
46 1 61 62
|
||||
47 2 62 63
|
||||
48 3 63 64
|
||||
49 1 65 66
|
||||
50 2 66 67
|
||||
51 3 67 68
|
||||
52 1 69 70
|
||||
53 2 70 71
|
||||
54 3 71 72
|
||||
55 1 73 74
|
||||
56 2 74 75
|
||||
57 3 75 76
|
||||
58 1 77 78
|
||||
59 2 78 79
|
||||
60 3 79 80
|
||||
61 1 81 82
|
||||
62 2 82 83
|
||||
63 3 83 84
|
||||
64 1 85 86
|
||||
65 2 86 87
|
||||
66 3 87 88
|
||||
67 1 89 90
|
||||
68 2 90 91
|
||||
69 3 91 92
|
||||
70 1 93 94
|
||||
71 2 94 95
|
||||
72 3 95 96
|
||||
73 1 97 98
|
||||
74 2 98 99
|
||||
75 3 99 100
|
||||
76 1 101 102
|
||||
77 2 102 103
|
||||
78 3 103 104
|
||||
79 1 105 106
|
||||
80 2 106 107
|
||||
81 3 107 108
|
||||
82 1 109 110
|
||||
83 2 110 111
|
||||
84 3 111 112
|
||||
85 1 113 114
|
||||
86 2 114 115
|
||||
87 3 115 116
|
||||
88 1 117 118
|
||||
89 2 118 119
|
||||
90 3 119 120
|
||||
91 1 121 122
|
||||
92 2 122 123
|
||||
93 3 123 124
|
||||
94 1 125 126
|
||||
95 2 126 127
|
||||
96 3 127 128
|
||||
97 1 129 130
|
||||
98 2 130 131
|
||||
99 3 131 132
|
||||
100 1 133 134
|
||||
101 2 134 135
|
||||
102 3 135 136
|
||||
103 1 137 138
|
||||
104 2 138 139
|
||||
105 3 139 140
|
||||
106 1 141 142
|
||||
107 2 142 143
|
||||
108 3 143 144
|
||||
109 1 145 146
|
||||
110 2 146 147
|
||||
111 3 147 148
|
||||
112 1 149 150
|
||||
113 2 150 151
|
||||
114 3 151 152
|
||||
115 1 153 154
|
||||
116 2 154 155
|
||||
117 3 155 156
|
||||
118 1 157 158
|
||||
119 2 158 159
|
||||
120 3 159 160
|
||||
121 1 161 162
|
||||
122 2 162 163
|
||||
123 3 163 164
|
||||
124 1 165 166
|
||||
125 2 166 167
|
||||
126 3 167 168
|
||||
127 1 169 170
|
||||
128 2 170 171
|
||||
129 3 171 172
|
||||
130 1 173 174
|
||||
131 2 174 175
|
||||
132 3 175 176
|
||||
133 1 177 178
|
||||
134 2 178 179
|
||||
135 3 179 180
|
||||
136 1 181 182
|
||||
137 2 182 183
|
||||
138 3 183 184
|
||||
139 1 185 186
|
||||
140 2 186 187
|
||||
141 3 187 188
|
||||
142 1 189 190
|
||||
143 2 190 191
|
||||
144 3 191 192
|
||||
145 1 193 194
|
||||
146 2 194 195
|
||||
147 3 195 196
|
||||
148 1 197 198
|
||||
149 2 198 199
|
||||
150 3 199 200
|
||||
151 1 201 202
|
||||
152 2 202 203
|
||||
153 3 203 204
|
||||
154 1 205 206
|
||||
155 2 206 207
|
||||
156 3 207 208
|
||||
157 1 209 210
|
||||
158 2 210 211
|
||||
159 3 211 212
|
||||
160 1 213 214
|
||||
161 2 214 215
|
||||
162 3 215 216
|
||||
163 1 217 218
|
||||
164 2 218 219
|
||||
165 3 219 220
|
||||
166 1 221 222
|
||||
167 2 222 223
|
||||
168 3 223 224
|
||||
169 1 225 226
|
||||
170 2 226 227
|
||||
171 3 227 228
|
||||
172 1 229 230
|
||||
173 2 230 231
|
||||
174 3 231 232
|
||||
175 1 233 234
|
||||
176 2 234 235
|
||||
177 3 235 236
|
||||
178 1 237 238
|
||||
179 2 238 239
|
||||
180 3 239 240
|
||||
181 1 241 242
|
||||
182 2 242 243
|
||||
183 3 243 244
|
||||
184 1 245 246
|
||||
185 2 246 247
|
||||
186 3 247 248
|
||||
187 1 249 250
|
||||
188 2 250 251
|
||||
189 3 251 252
|
||||
190 1 253 254
|
||||
191 2 254 255
|
||||
192 3 255 256
|
||||
193 1 257 258
|
||||
194 2 258 259
|
||||
195 3 259 260
|
||||
196 1 261 262
|
||||
197 2 262 263
|
||||
198 3 263 264
|
||||
199 1 265 266
|
||||
200 2 266 267
|
||||
201 3 267 268
|
||||
202 1 269 270
|
||||
203 2 270 271
|
||||
204 3 271 272
|
||||
205 1 273 274
|
||||
206 2 274 275
|
||||
207 3 275 276
|
||||
208 1 277 278
|
||||
209 2 278 279
|
||||
210 3 279 280
|
||||
211 1 281 282
|
||||
212 2 282 283
|
||||
213 3 283 284
|
||||
214 1 285 286
|
||||
215 2 286 287
|
||||
216 3 287 288
|
||||
|
||||
Angles
|
||||
|
||||
1 1 1 2 3
|
||||
2 1 2 3 4
|
||||
3 1 5 6 7
|
||||
4 1 6 7 8
|
||||
5 1 9 10 11
|
||||
6 1 10 11 12
|
||||
7 1 13 14 15
|
||||
8 1 14 15 16
|
||||
9 1 17 18 19
|
||||
10 1 18 19 20
|
||||
11 1 21 22 23
|
||||
12 1 22 23 24
|
||||
13 1 25 26 27
|
||||
14 1 26 27 28
|
||||
15 1 29 30 31
|
||||
16 1 30 31 32
|
||||
17 1 33 34 35
|
||||
18 1 34 35 36
|
||||
19 1 37 38 39
|
||||
20 1 38 39 40
|
||||
21 1 41 42 43
|
||||
22 1 42 43 44
|
||||
23 1 45 46 47
|
||||
24 1 46 47 48
|
||||
25 1 49 50 51
|
||||
26 1 50 51 52
|
||||
27 1 53 54 55
|
||||
28 1 54 55 56
|
||||
29 1 57 58 59
|
||||
30 1 58 59 60
|
||||
31 1 61 62 63
|
||||
32 1 62 63 64
|
||||
33 1 65 66 67
|
||||
34 1 66 67 68
|
||||
35 1 69 70 71
|
||||
36 1 70 71 72
|
||||
37 1 73 74 75
|
||||
38 1 74 75 76
|
||||
39 1 77 78 79
|
||||
40 1 78 79 80
|
||||
41 1 81 82 83
|
||||
42 1 82 83 84
|
||||
43 1 85 86 87
|
||||
44 1 86 87 88
|
||||
45 1 89 90 91
|
||||
46 1 90 91 92
|
||||
47 1 93 94 95
|
||||
48 1 94 95 96
|
||||
49 1 97 98 99
|
||||
50 1 98 99 100
|
||||
51 1 101 102 103
|
||||
52 1 102 103 104
|
||||
53 1 105 106 107
|
||||
54 1 106 107 108
|
||||
55 1 109 110 111
|
||||
56 1 110 111 112
|
||||
57 1 113 114 115
|
||||
58 1 114 115 116
|
||||
59 1 117 118 119
|
||||
60 1 118 119 120
|
||||
61 1 121 122 123
|
||||
62 1 122 123 124
|
||||
63 1 125 126 127
|
||||
64 1 126 127 128
|
||||
65 1 129 130 131
|
||||
66 1 130 131 132
|
||||
67 1 133 134 135
|
||||
68 1 134 135 136
|
||||
69 1 137 138 139
|
||||
70 1 138 139 140
|
||||
71 1 141 142 143
|
||||
72 1 142 143 144
|
||||
73 1 145 146 147
|
||||
74 1 146 147 148
|
||||
75 1 149 150 151
|
||||
76 1 150 151 152
|
||||
77 1 153 154 155
|
||||
78 1 154 155 156
|
||||
79 1 157 158 159
|
||||
80 1 158 159 160
|
||||
81 1 161 162 163
|
||||
82 1 162 163 164
|
||||
83 1 165 166 167
|
||||
84 1 166 167 168
|
||||
85 1 169 170 171
|
||||
86 1 170 171 172
|
||||
87 1 173 174 175
|
||||
88 1 174 175 176
|
||||
89 1 177 178 179
|
||||
90 1 178 179 180
|
||||
91 1 181 182 183
|
||||
92 1 182 183 184
|
||||
93 1 185 186 187
|
||||
94 1 186 187 188
|
||||
95 1 189 190 191
|
||||
96 1 190 191 192
|
||||
97 1 193 194 195
|
||||
98 1 194 195 196
|
||||
99 1 197 198 199
|
||||
100 1 198 199 200
|
||||
101 1 201 202 203
|
||||
102 1 202 203 204
|
||||
103 1 205 206 207
|
||||
104 1 206 207 208
|
||||
105 1 209 210 211
|
||||
106 1 210 211 212
|
||||
107 1 213 214 215
|
||||
108 1 214 215 216
|
||||
109 1 217 218 219
|
||||
110 1 218 219 220
|
||||
111 1 221 222 223
|
||||
112 1 222 223 224
|
||||
113 1 225 226 227
|
||||
114 1 226 227 228
|
||||
115 1 229 230 231
|
||||
116 1 230 231 232
|
||||
117 1 233 234 235
|
||||
118 1 234 235 236
|
||||
119 1 237 238 239
|
||||
120 1 238 239 240
|
||||
121 1 241 242 243
|
||||
122 1 242 243 244
|
||||
123 1 245 246 247
|
||||
124 1 246 247 248
|
||||
125 1 249 250 251
|
||||
126 1 250 251 252
|
||||
127 1 253 254 255
|
||||
128 1 254 255 256
|
||||
129 1 257 258 259
|
||||
130 1 258 259 260
|
||||
131 1 261 262 263
|
||||
132 1 262 263 264
|
||||
133 1 265 266 267
|
||||
134 1 266 267 268
|
||||
135 1 269 270 271
|
||||
136 1 270 271 272
|
||||
137 1 273 274 275
|
||||
138 1 274 275 276
|
||||
139 1 277 278 279
|
||||
140 1 278 279 280
|
||||
141 1 281 282 283
|
||||
142 1 282 283 284
|
||||
143 1 285 286 287
|
||||
144 1 286 287 288
|
||||
75
examples/USER/manifold/vir/vir.in
Normal file
75
examples/USER/manifold/vir/vir.in
Normal file
@ -0,0 +1,75 @@
|
||||
# Simple virus model.
|
||||
#
|
||||
|
||||
units lj
|
||||
dimension 3
|
||||
boundary f f f
|
||||
|
||||
atom_style angle
|
||||
pair_style lj/cut 4.0
|
||||
pair_modify shift yes
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
|
||||
neigh_modify binsize 5.0
|
||||
|
||||
read_data init.data
|
||||
|
||||
group NC type 1
|
||||
group rest type 2 3 4
|
||||
group CA type 3
|
||||
|
||||
|
||||
timestep 0.0001
|
||||
variable R equal "ramp(v_R0,v_R1)"
|
||||
|
||||
variable RF equal ${R1}
|
||||
variable Rw equal "v_RF - 0.5"
|
||||
|
||||
print "**** R scales from ${R0} to ${R1} and wall is at ${Rw} ****"
|
||||
|
||||
variable rr atom "sqrt( x*x + y*y + z*z )"
|
||||
compute ravg CA reduce ave v_rr
|
||||
|
||||
region my_sphere sphere 0 0 0 v_Rw side out
|
||||
fix wall all wall/region my_sphere lj126 1.0 1.0 1.1225
|
||||
|
||||
|
||||
variable U equal pe
|
||||
variable epair equal epair
|
||||
fix U all ave/time 2000 1 2000 v_U v_R v_epair
|
||||
variable t equal time
|
||||
variable ravg equal c_ravg
|
||||
|
||||
variable T equal 0.25
|
||||
|
||||
variable pU equal f_U[1]
|
||||
variable pE equal f_U[3]
|
||||
|
||||
fix out all print 2000 "$t ${pU} $R ${ravg} ${pE}" file thermo.${DATA}.dat screen no
|
||||
|
||||
fix step1 rest nvt temp $T $T 1.0
|
||||
fix step2 NC nvt/manifold/rattle 1e-4 10 sphere v_R temp $T $T 1.0
|
||||
|
||||
special_bonds lj 0 0 0
|
||||
|
||||
angle_coeff 1 250.0 180.0
|
||||
|
||||
thermo_style custom time step pe v_pU ke etotal epair temp v_R
|
||||
thermo 10000
|
||||
|
||||
|
||||
|
||||
compute pe all pe/atom
|
||||
fix pe_avg all ave/atom 100 50 5000 c_pe
|
||||
|
||||
|
||||
dump traj_all all custom 5000 virus.dump id type x y z f_pe_avg
|
||||
|
||||
run 2500000
|
||||
unfix out
|
||||
|
||||
fix step1 rest nvt temp $T $T 1.0
|
||||
fix step2 NC nvt/manifold/rattle 1e-4 10 sphere ${R1} temp $T $T 1.0
|
||||
|
||||
run 1000000
|
||||
Reference in New Issue
Block a user