Added user-manifold package.
This commit is contained in:
Stefan Paquay
61
doc/fix_manifoldforce.txt
Normal file
61
doc/fix_manifoldforce.txt
Normal file
@ -0,0 +1,61 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix manifoldforce command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID manifoldforce manifold manifold-args ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
manifold = name of the manifold :l
|
||||
manifold-args = parameters for the manifold :l
|
||||
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix constrain all manifoldforce sphere 5.0
|
||||
|
||||
[Description:]
|
||||
|
||||
This fix subtracts each time step from the force the component along the normal of the specified manifold.
|
||||
This can be used in combination with "minimize"_minimize.html to remove overlap between particles while
|
||||
keeping them (roughly) constrained to the given manifold, e.g. to set up a run with "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html.
|
||||
I have found that only {hftn} and {quickmin} with a very small time step perform adequately though.
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix. No global or per-atom quantities are stored
|
||||
by this fix for access by various "output
|
||||
commands"_Section_howto.html#howto_15. No parameter of this fix can
|
||||
be used with the {start/stop} keywords of the "run"_run.html command.
|
||||
This fix is invoked during "energy minimization"_minimize.html.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
|
||||
was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
section for more info.
|
||||
|
||||
Only use this with {min_style hftn} or {min_style quickmin}. If not, the constraints
|
||||
will not be satisfied very well at all. A warning is generated if the {min_style} is
|
||||
incompatible but no error.
|
||||
|
||||
:line
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix nve/manifold/rattle"_fix_nve_manifold_rattle.html, "fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html
|
||||
|
||||
100
doc/fix_nve_manifold_rattle.txt
Normal file
100
doc/fix_nve_manifold_rattle.txt
Normal file
@ -0,0 +1,100 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix nve/manifold/rattle command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID nve/manifold/rattle tol maxit manifold manifold-args keyword value ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
nve/manifold/rattle = style name of this fix command :l
|
||||
tol = tolerance to which Newton iteration must converge :l
|
||||
maxit = maximum number of iterations to perform :l
|
||||
manifold = name of the manifold :l
|
||||
manifold-args = parameters for the manifold :l
|
||||
one or more keyword/value pairs may be appended :l
|
||||
keyword = {every}
|
||||
{every} values = N
|
||||
N = print info about iteration every N steps. N = 0 means no output :pre
|
||||
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all nve/manifold/rattle 1e-4 10 sphere 5.0
|
||||
fix step all nve/manifold/rattle 1e-8 100 ellipsoid 2.5 2.5 5.0 every 25 :pre
|
||||
|
||||
[Description:]
|
||||
|
||||
Perform constant NVE integration to update position and velocity for
|
||||
atoms constrained to a curved surface (manifold) in the group each timestep. The constraint
|
||||
is handled by RATTLE "(Andersen)"_#Andersen written out for the special case of
|
||||
single-particle constraints as explained in "(Paquay)"_#Paquay.
|
||||
V is volume; E is energy. This way, the dynamics of particles constrained to
|
||||
curved surfaces can be studied. If combined with "fix langevin"_fix_langevin.html, this generates
|
||||
Brownian motion of particles constrained to a curved surface. For a list of currently supported
|
||||
manifolds and their parameters, see "manifolds"_user_manifolds.html.
|
||||
|
||||
Note that the particles must initially be close to the manifold in question. If not, RATTLE will
|
||||
not be able to iterate until the constraint is satisfied, and an error is generated. For simple
|
||||
manifolds this can be achieved with {region} and {create_atoms} commands, but for more complex
|
||||
surfaces it might be more useful to write a script.
|
||||
|
||||
The manifold args may be equal-style variables, like so:
|
||||
|
||||
variable R equal "ramp(5.0,3.0)"
|
||||
fix shrink_sphere all nve/manifold/rattle 1e-4 10 sphere v_R :pre
|
||||
|
||||
In this case, the manifold parameter will change in time according to the variable.
|
||||
This is not a problem for the time integrator as long as the change of the manifold is slow with respect to the dynamics of the particles.
|
||||
Note that if the manifold has to exert work on the particles because of these changes, the total energy might not be conserved.
|
||||
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix. No global or per-atom quantities are stored
|
||||
by this fix for access by various "output
|
||||
commands"_Section_howto.html#howto_15. No parameter of this fix can
|
||||
be used with the {start/stop} keywords of the "run"_run.html command.
|
||||
This fix is not invoked during "energy minimization"_minimize.html.
|
||||
|
||||
:line
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
|
||||
was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
section for more info.
|
||||
|
||||
Only use this with {min_style hftn} or {min_style quickmin}. If not, the constraints
|
||||
will not be satisfied very well at all. A warning is generated if the {min_style} is
|
||||
incompatible but no error.
|
||||
|
||||
:line
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix nvt/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix manifoldforce"_fix_manifoldforce.html
|
||||
|
||||
[Default:] every = 0, tchain = 3
|
||||
|
||||
:line
|
||||
|
||||
:link(Andersen)
|
||||
[(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983).
|
||||
|
||||
:link(Paquay)
|
||||
[(Paquay)] Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
|
||||
preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/.
|
||||
|
||||
|
||||
85
doc/fix_nvt_manifold_rattle.txt
Normal file
85
doc/fix_nvt_manifold_rattle.txt
Normal file
@ -0,0 +1,85 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
fix nvt/manifold/rattle command :h3
|
||||
|
||||
[Syntax:]
|
||||
|
||||
fix ID group-ID nvt/manifold/rattle tol maxit manifold manifold-args keyword value ... :pre
|
||||
|
||||
ID, group-ID are documented in "fix"_fix.html command :ulb,l
|
||||
nvt/manifold/rattle = style name of this fix command :l
|
||||
tol = tolerance to which Newton iteration must converge :l
|
||||
maxit = maximum number of iterations to perform :l
|
||||
manifold = name of the manifold :l
|
||||
manifold-args = parameters for the manifold :l
|
||||
one or more keyword/value pairs may be appended :l
|
||||
keyword = {temp} or {tchain} or {every}
|
||||
{temp} values = Tstart Tstop Tdamp
|
||||
Tstart, Tstop = external temperature at start/end of run
|
||||
Tdamp = temperature damping parameter (time units)
|
||||
{tchain} value = N
|
||||
N = length of thermostat chain (1 = single thermostat)
|
||||
{every} value = N
|
||||
N = print info about iteration every N steps. N = 0 means no output :pre
|
||||
|
||||
|
||||
:ule
|
||||
|
||||
[Examples:]
|
||||
|
||||
fix 1 all nvt/manifold/rattle 1e-4 10 cylinder 3.0 temp 1.0 1.0 10.0
|
||||
|
||||
[Description:]
|
||||
|
||||
This fix combines the RATTLE-based "(Andersen)"_#Andersen time integrator of "fix nve/manifold/rattle"_fix_nve_manifold_rattle.html "(Paquay)"_#Paquay with a Nose-Hoover-chain thermostat to sample the
|
||||
canonical ensemble of particles constrained to a curved surface (manifold). This sampling does suffer from discretization bias of O(dt).
|
||||
For a list of currently supported manifolds and their parameters, see "manifolds"_user_manifolds.html
|
||||
|
||||
:line
|
||||
|
||||
[Restart, fix_modify, output, run start/stop, minimize info:]
|
||||
|
||||
No information about this fix is written to "binary restart
|
||||
files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix. No global or per-atom quantities are stored
|
||||
by this fix for access by various "output
|
||||
commands"_Section_howto.html#howto_15. No parameter of this fix can
|
||||
be used with the {start/stop} keywords of the "run"_run.html command.
|
||||
This fix is not invoked during "energy minimization"_minimize.html.
|
||||
|
||||
:line
|
||||
|
||||
|
||||
[Restrictions:]
|
||||
|
||||
This fix is part of the USER-MANIFOLD package. It is only enabled if LAMMPS
|
||||
was built with that package. See the "Making LAMMPS"_Section_start.html#start_3
|
||||
section for more info.
|
||||
|
||||
Only use this with {min_style hftn} or {min_style quickmin}. If not, the constraints
|
||||
will not be satisfied very well at all. A warning is generated if the {min_style} is
|
||||
incompatible but no error.
|
||||
|
||||
:line
|
||||
|
||||
|
||||
[Related commands:]
|
||||
|
||||
"fix nve/manifold/rattle"_fix_nvt_manifold_rattle.html, "fix manifoldforce"_fix_manifoldforce.html
|
||||
[Default:] every = 0
|
||||
|
||||
:line
|
||||
|
||||
:link(Andersen)
|
||||
[(Andersen)] Andersen, J. Comp. Phys. 52, 24, (1983).
|
||||
|
||||
:link(Paquay)
|
||||
[(Paquay)] Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
|
||||
preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/.
|
||||
|
||||
30
doc/user_manifolds.txt
Normal file
30
doc/user_manifolds.txt
Normal file
@ -0,0 +1,30 @@
|
||||
"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
|
||||
|
||||
:link(lws,http://lammps.sandia.gov)
|
||||
:link(ld,Manual.html)
|
||||
:link(lc,Section_commands.html#comm)
|
||||
|
||||
:line
|
||||
|
||||
[Description:]
|
||||
|
||||
Below is a list of currently supported manifolds, their parameters and a short description of them.
|
||||
The parameters listed here are in the same order as they should be passed to the relevant fixes.
|
||||
|
||||
|
||||
{manifold} || {parameters} || {equation} || {description}
|
||||
cylinder || R || x^2 + y^2 - R^2 = 0 || Cylinder along z-axis, axis going through (0,0,0)
|
||||
cylinder_dent || R l a || x^2 + y^2 - r(z)^2 = 0, r(x) = R if |z| > l, r(z) = R - a*(1 + cos(z/l))/2 otherwise || A cylinder with a dent around z = 0
|
||||
dumbbell || a A B c || -( x^2 + y^2 ) * (a^2 - z^2/c^2) * ( 1 + (A*sin(B*z^2))^4) = 0 || A dumbbell ||
|
||||
ellipsoid || a b c || (x/a)^2 + (y/b)^2 + (z/c)^2 = 0 || An ellipsoid
|
||||
plane || a b c x0 y0 z0 || a*(x-x0) + b*(y-y0) + c*(z-z0) = 0 || A plane with normal (a,b,c) going through point (x0,y0,z0)
|
||||
plane_wiggle || a w || z - a*sin(w*x) = 0 || A plane with a sinusoidal modulation on z along x.
|
||||
sphere || R || x^2 + y^2 + z^2 - R^2 = 0 || A sphere of radius R
|
||||
supersphere || R q || |x|^q + |y|^q + |z|^q - R^q = 0 || A supersphere of hyperradius R
|
||||
spine || a, A, B, B2, c || -(x^2 + y^2)*(a^2 - z^2/f(z)^2)*(1 + (A*sin(g(z)*z^2))^4), f(z) = c if z > 0, 1 otherwise; g(z) = B if z > 0, B2 otherwise || An approximation to a dendtritic spine
|
||||
thylakoid || wB LB lB || Various, see "(Paquay)"_#Paquay || A model grana thylakoid consisting of two block-like compartments connected by a bridge of width wB, length LB and taper length lB
|
||||
torus || R r || (R - sqrt( x^2 + y^2 ) )^2 + z^2 - r^2 || A torus with large radius R and small radius r, centered on (0,0,0) :tb(s=||)
|
||||
|
||||
:link(Paquay)
|
||||
[(Paquay)] Paquay and Kusters, Biophys. J., 110, ???, (2016), to be published,
|
||||
preprint available at "arXiv:1411.3019"_http://arxiv.org/abs/1411.3019/.
|
||||
4
examples/USER/manifold/diffusion/.directory
Normal file
4
examples/USER/manifold/diffusion/.directory
Normal file
@ -0,0 +1,4 @@
|
||||
[Dolphin]
|
||||
Timestamp=2016,3,2,16,8,35
|
||||
Version=3
|
||||
ViewMode=1
|
||||
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
|
||||
|
||||
4
examples/USER/manifold/energy/.directory
Normal file
4
examples/USER/manifold/energy/.directory
Normal file
@ -0,0 +1,4 @@
|
||||
[Dolphin]
|
||||
Timestamp=2016,3,2,16,6,15
|
||||
Version=3
|
||||
ViewMode=1
|
||||
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"
|
||||
4
examples/USER/manifold/thylakoid/.directory
Normal file
4
examples/USER/manifold/thylakoid/.directory
Normal file
@ -0,0 +1,4 @@
|
||||
[Dolphin]
|
||||
Timestamp=2016,3,2,16,13,51
|
||||
Version=3
|
||||
ViewMode=1
|
||||
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
|
||||
|
||||
4
examples/USER/manifold/virus/.directory
Normal file
4
examples/USER/manifold/virus/.directory
Normal file
@ -0,0 +1,4 @@
|
||||
[Dolphin]
|
||||
Timestamp=2016,3,2,16,11,43
|
||||
Version=3
|
||||
ViewMode=1
|
||||
1
examples/USER/manifold/virus/README
Normal file
1
examples/USER/manifold/virus/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/virus/init.data
Normal file
704
examples/USER/manifold/virus/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/virus/virus.in
Normal file
75
examples/USER/manifold/virus/virus.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
|
||||
35
src/USER-MANIFOLD/Install.sh
Normal file
35
src/USER-MANIFOLD/Install.sh
Normal file
@ -0,0 +1,35 @@
|
||||
# Install/unInstall package files in LAMMPS
|
||||
# mode = 0/1/2 for uninstall/install/update
|
||||
#
|
||||
# Copied from USER-MISC.
|
||||
#
|
||||
|
||||
mode=$1
|
||||
|
||||
# arg1 = file, arg2 = file it depends on
|
||||
|
||||
action () {
|
||||
if (test $mode = 0) then
|
||||
rm -f ../$1
|
||||
elif (! cmp -s $1 ../$1) then
|
||||
if (test -z "$2" || test -e ../$2) then
|
||||
cp $1 ..
|
||||
if (test $mode = 2) then
|
||||
echo " updating src/$1"
|
||||
fi
|
||||
fi
|
||||
elif (test ! -n "$2") then
|
||||
if (test ! -e ../$2) then
|
||||
rm -f ../$1
|
||||
fi
|
||||
fi
|
||||
}
|
||||
|
||||
# all package files
|
||||
# Factory needs to be remade after each modification/new manifold,
|
||||
# other than that it is all good.
|
||||
|
||||
for file in *.cpp *.h; do
|
||||
action $file
|
||||
# manifold_factory.cpp
|
||||
done
|
||||
89
src/USER-MANIFOLD/README
Normal file
89
src/USER-MANIFOLD/README
Normal file
@ -0,0 +1,89 @@
|
||||
+==============================================================================+
|
||||
This file is a part of the USER-MANIFOLD package.
|
||||
|
||||
This package allows LAMMPS to perform MD simulations of particles
|
||||
constrained on a manifold (i.e., a 2D subspace of the 3D simulation
|
||||
box). It achieves this using the RATTLE constraint algorithm applied
|
||||
to single-particle constraint functions g(xi,yi,zi) = 0 and their
|
||||
derivative (i.e. the normal of the manifold) n = grad(g).
|
||||
|
||||
Stefan Paquay, s.paquay@tue.nl
|
||||
Applied Physics/Theory of Polymers and Soft Matter,
|
||||
Eindhoven University of Technology (TU/e), The Netherlands
|
||||
|
||||
Thanks to Remy Kusters at TU/e for testing.
|
||||
|
||||
This software is distributed under the GNU General Public License.
|
||||
+==============================================================================+
|
||||
|
||||
|
||||
At the moment we have a few manifolds available, extending them is very easy:
|
||||
To add a new manifold, do the following in the "USER-MANIFOLD" directory:
|
||||
|
||||
0. Create a new pair of source/header files, and name them "manifold_*.cpp/h",
|
||||
where you should replace '*' with some (descriptive) name.
|
||||
1. In the header file, add the following:
|
||||
a. Include guards.
|
||||
b. Make sure you #include "manifold.h"
|
||||
c. In namespace LAMMPS_NS, add a new class that inherits publicly from manifold
|
||||
and protectedly from Pointers.
|
||||
d. The constructor has to take ( LAMMPS*, int, char ** ) as arguments,
|
||||
and should initialise Pointers.
|
||||
e. The header file has to contain somewhere the macro ManifoldStyle with as
|
||||
first argument the name of the manifold and as second argument the name
|
||||
of the class implementing this manifold. The macro expands into some code
|
||||
that registers the manifold during static initialisation, before main is
|
||||
entered.
|
||||
|
||||
|
||||
2. In the source file, make sure you implement the following (of course,
|
||||
you can also implement these in the header):
|
||||
+====================================+=========================================+
|
||||
| Function signature | Purpose |
|
||||
+====================================+=========================================+
|
||||
| destructor | Free space (can be empty) |
|
||||
| constructor | Has to take (LAMMPS *lmp, int, char **) |
|
||||
| | as arguments and has to initialise |
|
||||
| | Pointers with lmp. |
|
||||
| double g( double *x ) | A function that is 0 if the 3-vector |
|
||||
| | x is on the manifold. |
|
||||
| void n( double *x, double *n ) | Stores the normal of position x in the |
|
||||
| | 3-vector n. |
|
||||
| static const char *type() | Returns text that identifies the |
|
||||
| | manifold in LAMMPS input scripts. |
|
||||
| const char *id() | Should return whatever type() returns. |
|
||||
| static int expected_argc() | Returns the number of arguments needed |
|
||||
| | for the construction/initialisation of |
|
||||
| | your manifold. Example: Sphere only |
|
||||
| | needs a radius, so it returns 1. The |
|
||||
| | spine needs 5 parameters, so it |
|
||||
| | returns 5. |
|
||||
| int nparams() | Should return same as expected_argc() |
|
||||
+====================================+=========================================+
|
||||
|
||||
If the above instructions seem a bit intimidating, you can get by just fine
|
||||
by copying an existing manifold and modifying it. See e.g. manifold_sphere for
|
||||
a relatively simple manifold.
|
||||
|
||||
|
||||
|
||||
With those things in place, the install script should be able to add your
|
||||
manifold to LAMMPS without any extra work, so just running
|
||||
make yes-user-manifold
|
||||
make <your_architecture>
|
||||
should (re)compile LAMMPS with the manifolds added.
|
||||
|
||||
|
||||
+==============================================================================+
|
||||
Obviously, you need some parameters to represent the surface, such as the radius
|
||||
in the case of a sphere. These should be passed to the nve/manifold/rattle fix,
|
||||
with the following syntax:
|
||||
fix ID group-ID nve/manifold/rattle tol maxit manifold_style args
|
||||
|
||||
tol = tolerance to which RATTLE tries to satisfy the constraints
|
||||
maxit = maximum number of iterations RATTLE uses each time step
|
||||
manifold_style = manifold style, should equal what type() of the desired
|
||||
manifold returns
|
||||
args = parameters for the manifold, order is manifold-dependent.
|
||||
can be equal style variables
|
||||
+==============================================================================+
|
||||
184
src/USER-MANIFOLD/fix_manifoldforce.cpp
Normal file
184
src/USER-MANIFOLD/fix_manifoldforce.cpp
Normal file
@ -0,0 +1,184 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "math.h"
|
||||
#include "string.h"
|
||||
#include "stdlib.h"
|
||||
#include "atom.h"
|
||||
#include "update.h"
|
||||
#include "respa.h"
|
||||
#include "error.h"
|
||||
#include "force.h"
|
||||
|
||||
#include "manifold.h"
|
||||
#include "fix_manifoldforce.h" // For stuff
|
||||
#include "manifold_factory.h" // For constructing manifold
|
||||
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
|
||||
// Helper functions for parameters/equal style variables in input script
|
||||
inline bool was_var( const char *arg )
|
||||
{
|
||||
return strstr( arg, "v_" ) == arg;
|
||||
}
|
||||
|
||||
inline bool str_eq( const char *str1, const char *str2 )
|
||||
{
|
||||
return strcmp(str1,str2) == 0;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixManifoldForce::FixManifoldForce(LAMMPS *lmp, int narg, char **arg) :
|
||||
Fix(lmp, narg, arg)
|
||||
{
|
||||
int me = -1;
|
||||
MPI_Comm_rank(world,&me);
|
||||
|
||||
|
||||
// Check the min-style:
|
||||
int good_minner = str_eq(update->minimize_style,"hftn") |
|
||||
str_eq(update->minimize_style,"quickmin");
|
||||
if( !good_minner){
|
||||
error->warning(FLERR,"Minimizing with fix manifoldforce without hftn or quickmin is fishy");
|
||||
}
|
||||
|
||||
|
||||
// Command is given as
|
||||
// fix <name> <group> manifoldforce manifold_name manifold_args
|
||||
if( narg < 5 ){
|
||||
error->all(FLERR,"Illegal fix manifoldforce! No manifold given");
|
||||
}
|
||||
const char *m_name = arg[3];
|
||||
ptr_m = create_manifold(m_name,lmp,narg,arg);
|
||||
|
||||
// Construct manifold from factory:
|
||||
if( !ptr_m ){
|
||||
char msg[2048];
|
||||
snprintf(msg,2048,"Manifold pointer for manifold '%s' was NULL for some reason", arg[3]);
|
||||
error->all(FLERR,msg);
|
||||
}
|
||||
|
||||
|
||||
// After constructing the manifold, you can safely make
|
||||
// room for the parameters
|
||||
nvars = ptr_m->nparams();
|
||||
if( narg < nvars+4 ){
|
||||
char msg[2048];
|
||||
sprintf(msg,"Manifold %s needs at least %d argument(s)!",
|
||||
m_name, nvars);
|
||||
error->all(FLERR,msg);
|
||||
}
|
||||
|
||||
*(ptr_m->get_params()) = new double[nvars];
|
||||
if( ptr_m->get_params() == NULL ){
|
||||
error->all(FLERR,"Parameter pointer was NULL!");
|
||||
}
|
||||
|
||||
// This part here stores the names/text of each argument,
|
||||
// determines which params are equal-style variables,
|
||||
// and sets the values of those arguments that were _not_
|
||||
// equal style vars (so that they are not overwritten each time step).
|
||||
|
||||
double *params = *(ptr_m->get_params());
|
||||
for( int i = 0; i < nvars; ++i ){
|
||||
if( was_var( arg[i+4] ) )
|
||||
error->all(FLERR,"Equal-style variables not allowed with fix manifoldforce");
|
||||
|
||||
// Use force->numeric to trigger an error if arg is not a number.
|
||||
params[i] = force->numeric(FLERR,arg[i+4]);
|
||||
}
|
||||
|
||||
|
||||
// Perform any further initialisation for the manifold that depends on params:
|
||||
ptr_m->post_param_init();
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
int FixManifoldForce::setmask()
|
||||
{
|
||||
int mask = 0;
|
||||
mask |= POST_FORCE;
|
||||
mask |= POST_FORCE_RESPA;
|
||||
mask |= MIN_POST_FORCE;
|
||||
return mask;
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixManifoldForce::setup(int vflag)
|
||||
{
|
||||
if (strstr(update->integrate_style,"verlet"))
|
||||
post_force(vflag);
|
||||
else {
|
||||
int nlevels_respa = ((Respa *) update->integrate)->nlevels;
|
||||
for (int ilevel = 0; ilevel < nlevels_respa; ilevel++) {
|
||||
((Respa *) update->integrate)->copy_flevel_f(ilevel);
|
||||
post_force_respa(vflag,ilevel,0);
|
||||
((Respa *) update->integrate)->copy_f_flevel(ilevel);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixManifoldForce::min_setup(int vflag)
|
||||
{
|
||||
post_force(vflag);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixManifoldForce::post_force(int vflag)
|
||||
{
|
||||
double **x = atom->x;
|
||||
double **f = atom->f;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
double n[3];
|
||||
double invn2;
|
||||
double dot;
|
||||
for (int i = 0; i < nlocal; i++){
|
||||
if (mask[i] & groupbit) {
|
||||
// Determine normal of particle:
|
||||
ptr_m->n(x[i],n);
|
||||
|
||||
invn2 = 1.0 / ( n[0]*n[0] + n[1]*n[1] + n[2]*n[2] );
|
||||
dot = f[i][0]*n[0] + f[i][1]*n[1] + f[i][2]*n[2];
|
||||
|
||||
f[i][0] -= dot*n[0] * invn2;
|
||||
f[i][1] -= dot*n[1] * invn2;
|
||||
f[i][2] -= dot*n[2] * invn2;
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixManifoldForce::post_force_respa(int vflag, int ilevel, int iloop)
|
||||
{
|
||||
post_force(vflag);
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixManifoldForce::min_post_force(int vflag)
|
||||
{
|
||||
post_force(vflag);
|
||||
}
|
||||
81
src/USER-MANIFOLD/fix_manifoldforce.h
Normal file
81
src/USER-MANIFOLD/fix_manifoldforce.h
Normal file
@ -0,0 +1,81 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
-------------------------------------------------------------------------
|
||||
|
||||
This file is a part of the USER-MANIFOLD package.
|
||||
|
||||
Copyright (2013-2015) Stefan Paquay, Eindhoven University of Technology.
|
||||
License: GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
This file is part of the user-manifold package written by
|
||||
Stefan Paquay at the Eindhoven University of Technology.
|
||||
This module makes it possible to do MD with particles constrained
|
||||
to pretty arbitrary manifolds characterised by some constraint function
|
||||
g(x,y,z) = 0 and its normal grad(g). The number of manifolds available
|
||||
right now is limited but can be extended straightforwardly by making
|
||||
a new class that inherits from manifold and implements all pure virtual
|
||||
methods.
|
||||
|
||||
This fix subtracts force components that point out of the manifold,
|
||||
useful for minimisation on surfaces.
|
||||
|
||||
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(manifoldforce,FixManifoldForce)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_MANIFOLDFORCE_H
|
||||
#define LMP_FIX_MANIFOLDFORCE_H
|
||||
|
||||
#include "fix.h"
|
||||
#include "manifold.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixManifoldForce : public Fix {
|
||||
public:
|
||||
FixManifoldForce(class LAMMPS *, int, char **);
|
||||
int setmask();
|
||||
void setup(int);
|
||||
void min_setup(int);
|
||||
void post_force(int);
|
||||
void post_force_respa(int, int, int);
|
||||
void min_post_force(int);
|
||||
|
||||
|
||||
private:
|
||||
manifold *ptr_m;
|
||||
|
||||
// Stuff to store the parameters in.
|
||||
int nvars; // # of args after manifold name.
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
*/
|
||||
640
src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
Normal file
640
src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
Normal file
@ -0,0 +1,640 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
-----------------------------------------------------------------------
|
||||
|
||||
This file is a part of the USER-MANIFOLD package.
|
||||
|
||||
Copyright (2013-2014) Stefan Paquay, Eindhoven University of Technology.
|
||||
License: GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
This file is part of the user-manifold package written by
|
||||
Stefan Paquay at the Eindhoven University of Technology.
|
||||
This module makes it possible to do MD with particles constrained
|
||||
to pretty arbitrary manifolds characterised by some constraint function
|
||||
g(x,y,z) = 0 and its normal grad(g). The number of manifolds available
|
||||
right now is limited but can be extended straightforwardly by making
|
||||
a new class that inherits from manifold and implements all pure virtual
|
||||
methods.
|
||||
|
||||
Thanks to Remy Kusters for beta-testing!
|
||||
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
|
||||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "atom.h"
|
||||
#include "force.h"
|
||||
#include "update.h"
|
||||
#include "respa.h"
|
||||
#include "error.h"
|
||||
#include "group.h"
|
||||
#include "math.h"
|
||||
#include "input.h"
|
||||
#include "variable.h"
|
||||
#include "citeme.h"
|
||||
#include "memory.h"
|
||||
#include "comm.h"
|
||||
|
||||
|
||||
#include "fix_nve_manifold_rattle.h"
|
||||
#include "manifold_factory.h"
|
||||
#include "manifold.h"
|
||||
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
|
||||
enum { CONST, EQUAL }; // For treating the variables.
|
||||
|
||||
|
||||
static const char* cite_fix_nve_manifold_rattle =
|
||||
"fix nve/manifold/rattle command:\n\n"
|
||||
"@article{paquay-2016,\n"
|
||||
" author = {Paquay, Stefan and Kusters, Remy}, \n"
|
||||
" eprint = {arXiv:1411.3019}, \n"
|
||||
" title = {A method for molecular dynamics on curved surfaces}, \n"
|
||||
" url = {http://arxiv.org/abs/1411.3019}, \n"
|
||||
" year = 2016, \n"
|
||||
" journal = {Arxiv preprint, \\url{http://arxiv.org/abs/1411.3019}}, \n"
|
||||
" note = {To be published in Biophys. J.}, \n"
|
||||
"}\n\n";
|
||||
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
---------------------------------------------------------------------------*/
|
||||
FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg,
|
||||
int error_on_unknown_keyword )
|
||||
: Fix(lmp,narg,arg)
|
||||
{
|
||||
if( lmp->citeme) lmp->citeme->add(cite_fix_nve_manifold_rattle);
|
||||
if( narg < 6 ) error->all(FLERR, "Illegal fix nve/manifold/rattle command");
|
||||
|
||||
// Set all bits/settings:
|
||||
time_integrate = 1;
|
||||
dynamic_group_allow = 1;
|
||||
size_vector = 0;
|
||||
dof_flag = 1;
|
||||
|
||||
nevery = 0;
|
||||
dtv = dtf = 0;
|
||||
|
||||
tolerance = force->numeric( FLERR, arg[3] );
|
||||
max_iter = force->numeric( FLERR, arg[4] );
|
||||
|
||||
ptr_m = create_manifold(arg[5], lmp, narg, arg);
|
||||
if( !ptr_m ){
|
||||
error->all(FLERR,"Error creating manifold pointer");
|
||||
}
|
||||
|
||||
nvars = ptr_m->nparams();
|
||||
tstrs = new char*[nvars];
|
||||
tvars = new int[nvars];
|
||||
tstyle = new int[nvars];
|
||||
is_var = new int[nvars];
|
||||
|
||||
if( !tstrs || !tvars || !tstyle || !is_var ){
|
||||
error->all(FLERR, "Error creating manifold arg arrays");
|
||||
}
|
||||
|
||||
// Loop over manifold args:
|
||||
for( int i = 0; i < nvars; ++i ){
|
||||
int len = 0, offset = 0;
|
||||
if( was_var( arg[i+6] ) ){
|
||||
len = strlen(arg[i+6]) - 1; // -1 because -2 for v_, +1 for \0.
|
||||
is_var[i] = 1;
|
||||
offset = 2;
|
||||
}else{
|
||||
force->numeric(FLERR,arg[i+6]); // Check if legal number.
|
||||
len = strlen( arg[i+6] ) + 1; // +1 for \0.
|
||||
is_var[i] = 0;
|
||||
}
|
||||
tstrs[i] = new char[len];
|
||||
if( tstrs[i] == NULL ) error->all(FLERR,"Error allocating space for args.");
|
||||
strcpy( tstrs[i], arg[i+6] + offset );
|
||||
}
|
||||
|
||||
*ptr_m->get_params() = new double[nvars];
|
||||
if( !(*ptr_m->get_params()) ) error->all(FLERR,"Failed to allocate params!");
|
||||
for( int i = 0; i < nvars; ++i ){
|
||||
// If param i was variable type, it will be set later...
|
||||
(*ptr_m->get_params())[i] = is_var[i] ? 0.0 : force->numeric( FLERR, arg[i+6] );
|
||||
}
|
||||
ptr_m->post_param_init();
|
||||
|
||||
|
||||
// Loop over rest of args:
|
||||
int argi = 6 + nvars;
|
||||
while( argi < narg ){
|
||||
if( strcmp(arg[argi], "every") == 0 ){
|
||||
nevery = force->inumeric(FLERR,arg[argi+1]);
|
||||
argi += 2;
|
||||
}else if( error_on_unknown_keyword ){
|
||||
char msg[2048];
|
||||
sprintf(msg,"Error parsing arg \"%s\".\n", arg[argi]);
|
||||
error->all(FLERR, msg);
|
||||
}else{
|
||||
argi += 1;
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
---------------------------------------------------------------------------*/
|
||||
FixNVEManifoldRattle::~FixNVEManifoldRattle()
|
||||
{
|
||||
if( tstrs ){
|
||||
for( int i = 0; i < nvars; ++i ){
|
||||
delete [] tstrs[i];
|
||||
}
|
||||
delete [] tstrs;
|
||||
}
|
||||
|
||||
if( tvars ) delete [] tvars;
|
||||
if( tstyle ) delete [] tstyle;
|
||||
if( is_var ) delete [] is_var;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
---------------------------------------------------------------------------*/
|
||||
void FixNVEManifoldRattle::reset_dt()
|
||||
{
|
||||
dtv = update->dt;
|
||||
dtf = 0.5 * update->dt * force->ftm2v;
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
void FixNVEManifoldRattle::print_stats( const char *header )
|
||||
{
|
||||
double n = stats.natoms;
|
||||
if( n > 0 ){
|
||||
stats.x_iters_per_atom += stats.x_iters / n;
|
||||
stats.v_iters_per_atom += stats.v_iters / n;
|
||||
}
|
||||
|
||||
double x_iters = 0, v_iters = 0;
|
||||
bigint ntimestep = update->ntimestep;
|
||||
int me = -1;
|
||||
|
||||
|
||||
MPI_Comm_rank(world,&me);
|
||||
MPI_Allreduce(&stats.x_iters_per_atom,&x_iters,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
MPI_Allreduce(&stats.v_iters_per_atom,&v_iters,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
// Set iters back to zero:
|
||||
stats.x_iters_per_atom = stats.x_iters = 0;
|
||||
stats.v_iters_per_atom = stats.v_iters = 0;
|
||||
|
||||
|
||||
if( me == 0 ){
|
||||
double inv_tdiff = 1.0/( static_cast<double>(ntimestep) - stats.last_out );
|
||||
stats.last_out = ntimestep;
|
||||
|
||||
fprintf(screen, "%s stats for time step " BIGINT_FORMAT " on %d atoms:\n",
|
||||
header, ntimestep, stats.natoms);
|
||||
fprintf(screen, " iters/atom: x = %f, v = %f, dofs removed %d",
|
||||
x_iters * inv_tdiff, v_iters * inv_tdiff, stats.dofs_removed);
|
||||
fprintf(screen,"\n");
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
---------------------------------------------------------------------------*/
|
||||
int FixNVEManifoldRattle::was_var( const char *str )
|
||||
{
|
||||
if( strlen(str) > 2 ){
|
||||
return (str[0] == 'v') && (str[1] == '_');
|
||||
}else{
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
---------------------------------------------------------------------------*/
|
||||
int FixNVEManifoldRattle::setmask()
|
||||
{
|
||||
int mask = 0;
|
||||
mask |= INITIAL_INTEGRATE;
|
||||
mask |= FINAL_INTEGRATE;
|
||||
if( nevery > 0 ) mask |= END_OF_STEP;
|
||||
|
||||
return mask;
|
||||
}
|
||||
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
---------------------------------------------------------------------------*/
|
||||
void FixNVEManifoldRattle::init()
|
||||
{
|
||||
// Makes sure the manifold params are set initially.
|
||||
|
||||
update_var_params();
|
||||
reset_dt();
|
||||
}
|
||||
|
||||
|
||||
void FixNVEManifoldRattle::update_var_params()
|
||||
{
|
||||
if( nevery > 0 ){
|
||||
stats.x_iters = 0;
|
||||
stats.v_iters = 0;
|
||||
stats.natoms = 0;
|
||||
stats.x_iters_per_atom = 0.0;
|
||||
stats.v_iters_per_atom = 0.0;
|
||||
}
|
||||
|
||||
double **ptr_params = ptr_m->get_params();
|
||||
for( int i = 0; i < nvars; ++i ){
|
||||
if( is_var[i] ){
|
||||
tvars[i] = input->variable->find(tstrs[i]);
|
||||
if( tvars[i] < 0 ){
|
||||
error->all(FLERR,
|
||||
"Variable name for fix nve/manifold/rattle does not exist");
|
||||
}
|
||||
if( input->variable->equalstyle(tvars[i]) ){
|
||||
tstyle[i] = EQUAL;
|
||||
double new_val = input->variable->compute_equal(tvars[i]);
|
||||
// fprintf( stdout, "New value of var %d is now %f\n", i+1, new_val );
|
||||
*(ptr_params[i]) = new_val;
|
||||
}else{
|
||||
error->all(FLERR,
|
||||
"Variable for fix nve/manifold/rattle is invalid style");
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
---------------------------------------------------------------------------*/
|
||||
int FixNVEManifoldRattle::dof(int igroup)
|
||||
{
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
int natoms = 0;
|
||||
for( int i = 0; i < nlocal; ++i ){
|
||||
if(mask[i] & groupbit) ++natoms;
|
||||
}
|
||||
|
||||
int dofs;
|
||||
MPI_Allreduce( &natoms, &dofs, 1, MPI_INT, MPI_SUM, world );
|
||||
|
||||
// Make sure that, if there is just no or one atom, no dofs are subtracted,
|
||||
// since for the first atom already 3 dofs are subtracted because of the
|
||||
// centre of mass corrections:
|
||||
if( dofs <= 1 ) dofs = 0;
|
||||
stats.dofs_removed = dofs;
|
||||
|
||||
return dofs;
|
||||
}
|
||||
|
||||
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
---------------------------------------------------------------------------*/
|
||||
double FixNVEManifoldRattle::memory_usage()
|
||||
{
|
||||
double bytes = 0.0;
|
||||
|
||||
bytes += sizeof(statistics);
|
||||
bytes += sizeof(*ptr_m) + sizeof(ptr_m);
|
||||
bytes += nvars*sizeof(double) + sizeof(double*);
|
||||
bytes += nvars*( sizeof(char*) + 3*sizeof(int) );
|
||||
return bytes;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
---------------------------------------------------------------------------*/
|
||||
void FixNVEManifoldRattle::initial_integrate(int vflag)
|
||||
{
|
||||
update_var_params();
|
||||
nve_x_rattle(igroup, groupbit);
|
||||
}
|
||||
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
---------------------------------------------------------------------------*/
|
||||
void FixNVEManifoldRattle::final_integrate()
|
||||
{
|
||||
nve_v_rattle(igroup, groupbit);
|
||||
}
|
||||
|
||||
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
---------------------------------------------------------------------------*/
|
||||
void FixNVEManifoldRattle::end_of_step()
|
||||
{
|
||||
print_stats( "nve/manifold/rattle" );
|
||||
}
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
---------------------------------------------------------------------------*/
|
||||
void FixNVEManifoldRattle::nve_x_rattle(int igroup, int groupbit)
|
||||
{
|
||||
double dtfm;
|
||||
// update v and x of atoms in group
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double *rmass = atom->rmass;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
int natoms = 0;
|
||||
|
||||
if (igroup == atom->firstgroup){
|
||||
nlocal = atom->nfirst;
|
||||
}
|
||||
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++){
|
||||
if (mask[i] & groupbit){
|
||||
natoms++;
|
||||
dtfm = dtf / rmass[i];
|
||||
rattle_manifold_x( x[i], v[i], f[i], dtv, dtfm, atom->tag[i] );
|
||||
}
|
||||
}
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++){
|
||||
if (mask[i] & groupbit) {
|
||||
natoms++;
|
||||
dtfm = dtf / mass[type[i]];
|
||||
rattle_manifold_x( x[i], v[i], f[i], dtv, dtfm, atom->tag[i] );
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if( nevery > 0 ){
|
||||
// Count ALL atoms this fix works on:
|
||||
MPI_Allreduce(&natoms,&stats.natoms,1,MPI_INT,MPI_SUM,world);
|
||||
}
|
||||
}
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
---------------------------------------------------------------------------*/
|
||||
void FixNVEManifoldRattle::nve_v_rattle(int igroup, int groupbit)
|
||||
{
|
||||
double dtfm;
|
||||
|
||||
// update v of atoms in group
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double *rmass = atom->rmass;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / rmass[i];
|
||||
rattle_manifold_v( v[i], f[i], x[i], dtfm, atom->tag[i] );
|
||||
}
|
||||
}
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++){
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / mass[type[i]];
|
||||
rattle_manifold_v( v[i], f[i], x[i], dtfm, atom->tag[i] );
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
---------------------------------------------------------------------------*/
|
||||
void FixNVEManifoldRattle::rattle_manifold_x(double *x, double *v,
|
||||
double *f, double dtv,
|
||||
double dtfm, tagint tagi )
|
||||
{
|
||||
/*
|
||||
A RATTLE update for the position constraint.
|
||||
Original update is x += dtv * v_1/2
|
||||
Now you do
|
||||
v_1/2(lambda) = v_0 + dtfm * ( f + lambda*n_old )
|
||||
and solve
|
||||
xold - xnew + dtv * v_1/2(lambda) = 0
|
||||
g(xnew) = 0
|
||||
for x and lambda. The lambda you find then gives v_1/2 as well.
|
||||
*/
|
||||
double xo[3]; // Previous position to update from.
|
||||
double vo[3]; // Previous velocity to update from.
|
||||
double l = 0; // Lagrangian multiplier for constraint forces.
|
||||
double R[4]; // System that is 0.
|
||||
double dx[4]; // Update that follows from Newton iteration.
|
||||
double no[3]; // Normal at xo.
|
||||
double nn[3]; // Normal at x, the new position.
|
||||
double res; // Residual.
|
||||
int iters = 0; // Iterations used
|
||||
|
||||
double c = dtfm*dtv; // Used for iterating in the Newton loop:
|
||||
double no_nn, nn_R;
|
||||
|
||||
vo[0] = v[0];
|
||||
vo[1] = v[1];
|
||||
vo[2] = v[2];
|
||||
|
||||
xo[0] = x[0];
|
||||
xo[1] = x[1];
|
||||
xo[2] = x[2];
|
||||
|
||||
double gg = ptr_m->g_and_n(x,no);
|
||||
nn[0] = no[0];
|
||||
nn[1] = no[1];
|
||||
nn[2] = no[2];
|
||||
|
||||
double vt[3];
|
||||
vt[0] = vo[0] + dtfm*f[0];
|
||||
vt[1] = vo[1] + dtfm*f[1];
|
||||
vt[2] = vo[2] + dtfm*f[2];
|
||||
double no_dt[3];
|
||||
no_dt[0] = dtfm*no[0];
|
||||
no_dt[1] = dtfm*no[1];
|
||||
no_dt[2] = dtfm*no[2];
|
||||
|
||||
// Assume that no_nn is roughly constant during iteration:
|
||||
|
||||
const double c_inv = 1.0 / c;
|
||||
|
||||
|
||||
while ( 1 ) {
|
||||
v[0] = vt[0] - l*no_dt[0];
|
||||
v[1] = vt[1] - l*no_dt[1];
|
||||
v[2] = vt[2] - l*no_dt[2];
|
||||
|
||||
R[0] = xo[0] - x[0] + dtv * v[0];
|
||||
R[1] = xo[1] - x[1] + dtv * v[1];
|
||||
R[2] = xo[2] - x[2] + dtv * v[2];
|
||||
R[3] = gg;
|
||||
|
||||
// Analytic solution to system J*(dx,dy,dz,dl)^T = R
|
||||
// no_nn = no[0]*nn[0] + no[1]*nn[1] + no[2]*nn[2];
|
||||
nn_R = nn[0]*R[0] + nn[1]*R[1] + nn[2]*R[2];
|
||||
no_nn = no[0]*nn[0] + no[1]*nn[1] + no[2]*nn[2];
|
||||
double n_inv = 1.0 / no_nn;
|
||||
|
||||
// fprintf( screen, "nn_R = %f, no_nn = %f\n", nn_R, no_nn );
|
||||
|
||||
dx[3] = -nn_R - R[3];
|
||||
dx[3] *= n_inv;
|
||||
dx[0] = -R[0] - no[0]*dx[3];
|
||||
dx[1] = -R[1] - no[1]*dx[3];
|
||||
dx[2] = -R[2] - no[2]*dx[3];
|
||||
|
||||
dx[3] *= c_inv;
|
||||
|
||||
|
||||
x[0] -= dx[0];
|
||||
x[1] -= dx[1];
|
||||
x[2] -= dx[2];
|
||||
l -= dx[3];
|
||||
|
||||
res = infnorm<4>(R);
|
||||
++iters;
|
||||
|
||||
if( (res < tolerance) || (iters >= max_iter) ) break;
|
||||
|
||||
// Update nn and g.
|
||||
gg = ptr_m->g(x);
|
||||
ptr_m->n(x,nn);
|
||||
// gg = ptr_m->g(x);
|
||||
}
|
||||
|
||||
if( iters >= max_iter && res > tolerance ){
|
||||
char msg[2048];
|
||||
sprintf(msg,"Failed to constrain atom %d (x = (%f, %f, %f)! res = %e, iters = %d\n",
|
||||
tagi, x[0], x[1], x[2], res, iters);
|
||||
error->one(FLERR,msg);
|
||||
}
|
||||
|
||||
// "sync" x and v:
|
||||
v[0] = vt[0] - l*no_dt[0];
|
||||
v[1] = vt[1] - l*no_dt[1];
|
||||
v[2] = vt[2] - l*no_dt[2];
|
||||
|
||||
stats.x_iters += iters;
|
||||
}
|
||||
|
||||
|
||||
/* -----------------------------------------------------------------------------
|
||||
---------------------------------------------------------------------------*/
|
||||
void FixNVEManifoldRattle::rattle_manifold_v(double *v, double *f,
|
||||
double *x, double dtfm,
|
||||
tagint tagi )
|
||||
{
|
||||
/*
|
||||
The original update was
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
|
||||
Now you add the rattle-like update:
|
||||
vold - vnew + dtfm * F + mu * n_new = 0
|
||||
dot( vnew, n_new ) = 0
|
||||
*/
|
||||
double vo[3]; // V at t + 1/2 dt
|
||||
double l = 0; // Lagrangian multiplier for constraint forces.
|
||||
double R[4]; // System that is 0.
|
||||
double dv[4]; // Update that follows from Newton iteration.
|
||||
double n[3]; // Normal.
|
||||
double res; // Residual.
|
||||
int iters = 0; // Iterations used
|
||||
|
||||
double c = dtfm; // Used for iterating in the Newton loop:
|
||||
double nn2, nn_R;
|
||||
|
||||
vo[0] = v[0];
|
||||
vo[1] = v[1];
|
||||
vo[2] = v[2];
|
||||
|
||||
// Initial guess is unconstrained update:
|
||||
v[0] += dtfm*f[0];
|
||||
v[1] += dtfm*f[1];
|
||||
v[2] += dtfm*f[2];
|
||||
|
||||
ptr_m->n(x,n);
|
||||
|
||||
double vt[3];
|
||||
vt[0] = vo[0] + dtfm*f[0];
|
||||
vt[1] = vo[1] + dtfm*f[1];
|
||||
vt[2] = vo[2] + dtfm*f[2];
|
||||
double no_dt[3];
|
||||
no_dt[0] = dtfm*n[0];
|
||||
no_dt[1] = dtfm*n[1];
|
||||
no_dt[2] = dtfm*n[2];
|
||||
|
||||
nn2 = n[0]*n[0] + n[1]*n[1] + n[2]*n[2];
|
||||
|
||||
const double n_inv = 1.0 / nn2;
|
||||
const double c_inv = 1.0 / c;
|
||||
|
||||
do{
|
||||
R[0] = vt[0] - v[0] - l * no_dt[0];
|
||||
R[1] = vt[1] - v[1] - l * no_dt[1];
|
||||
R[2] = vt[2] - v[2] - l * no_dt[2];
|
||||
R[3] = v[0]*n[0] + v[1]*n[1] + v[2]*n[2];
|
||||
|
||||
// Analytic solution to system J*(dx,dy,dz,dl)^T = R
|
||||
nn_R = n[0]*R[0] + n[1]*R[1] + n[2]*R[2];
|
||||
|
||||
dv[3] = -nn_R - R[3];
|
||||
dv[3] *= n_inv;
|
||||
dv[0] = -n[0]*dv[3] - R[0];
|
||||
dv[1] = -n[1]*dv[3] - R[1];
|
||||
dv[2] = -n[2]*dv[3] - R[2];
|
||||
dv[3] *= c_inv;
|
||||
|
||||
v[0] -= dv[0];
|
||||
v[1] -= dv[1];
|
||||
v[2] -= dv[2];
|
||||
l -= dv[3];
|
||||
|
||||
res = infnorm<4>(R);
|
||||
++iters;
|
||||
}while( (res > tolerance) && (iters < max_iter) );
|
||||
|
||||
if( iters >= max_iter && res >= tolerance ){
|
||||
char msg[2048];
|
||||
sprintf(msg,"Failed to constrain atom %d (x = (%f, %f, %f)! res = %e, iters = %d\n",
|
||||
tagi, x[0], x[1], x[2], res, iters);
|
||||
error->all(FLERR,msg);
|
||||
}
|
||||
|
||||
stats.v_iters += iters;
|
||||
}
|
||||
170
src/USER-MANIFOLD/fix_nve_manifold_rattle.h
Executable file
170
src/USER-MANIFOLD/fix_nve_manifold_rattle.h
Executable file
@ -0,0 +1,170 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
-----------------------------------------------------------------------
|
||||
|
||||
This file is a part of the USER-MANIFOLD package.
|
||||
|
||||
Copyright (2013-2014) Stefan Paquay, Eindhoven University of Technology.
|
||||
License: GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
This file is part of the user-manifold package written by
|
||||
Stefan Paquay at the Eindhoven University of Technology.
|
||||
This module makes it possible to do MD with particles constrained
|
||||
to pretty arbitrary manifolds characterised by some constraint function
|
||||
g(x,y,z) = 0 and its normal grad(g). The number of manifolds available
|
||||
right now is limited but can be extended straightforwardly by making
|
||||
a new class that inherits from manifold and implements all pure virtual
|
||||
methods.
|
||||
|
||||
Thanks to Remy Kusters for beta-testing!
|
||||
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(nve/manifold/rattle,FixNVEManifoldRattle)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NVE_MANIFOLD_RATTLE_H
|
||||
#define LMP_FIX_NVE_MANIFOLD_RATTLE_H
|
||||
|
||||
#include "fix.h"
|
||||
#include "manifold.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixNVEManifoldRattle : public Fix {
|
||||
public:
|
||||
|
||||
struct statistics {
|
||||
|
||||
statistics() : x_iters(0), v_iters(0), x_iters_per_atom(0),
|
||||
v_iters_per_atom(0), natoms(0), dofs_removed(0),
|
||||
last_out(0) {}
|
||||
double x_iters, v_iters;
|
||||
double x_iters_per_atom;
|
||||
double v_iters_per_atom;
|
||||
int natoms;
|
||||
int dofs_removed;
|
||||
bigint last_out;
|
||||
};
|
||||
|
||||
FixNVEManifoldRattle(LAMMPS *, int &, char **, int = 1);
|
||||
virtual ~FixNVEManifoldRattle();
|
||||
// All this stuff is interface, so you DO need to implement them.
|
||||
// Just delegate them to the workhorse classes.
|
||||
virtual int setmask();
|
||||
virtual void initial_integrate(int);
|
||||
virtual void final_integrate();
|
||||
virtual void init();
|
||||
virtual void reset_dt();
|
||||
virtual void end_of_step();
|
||||
virtual int dof(int);
|
||||
virtual void setup(int){} // Not needed for fixNVE but is for fixNVT
|
||||
virtual double memory_usage();
|
||||
|
||||
protected:
|
||||
|
||||
int nevery;
|
||||
|
||||
double dtv, dtf;
|
||||
double tolerance;
|
||||
int max_iter;
|
||||
|
||||
char **tstrs;
|
||||
int *tvars;
|
||||
int *tstyle;
|
||||
int *is_var;
|
||||
|
||||
statistics stats;
|
||||
int update_style;
|
||||
int nvars;
|
||||
|
||||
manifold *ptr_m;
|
||||
|
||||
|
||||
void print_stats( const char * );
|
||||
|
||||
int was_var( const char * );
|
||||
|
||||
virtual void update_var_params();
|
||||
virtual void rattle_manifold_x( double *, double *, double *, double, double, tagint );
|
||||
virtual void rattle_manifold_v( double *, double *, double *, double, tagint );
|
||||
|
||||
virtual void nve_x_rattle(int, int);
|
||||
virtual void nve_v_rattle(int, int);
|
||||
};
|
||||
}
|
||||
|
||||
|
||||
|
||||
#endif // LMP_FIX_NVE_MANIFOLD_RATTLE_H
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: There is no manifold named ...
|
||||
|
||||
Self-explanatory. You requested a manifold whose name was not
|
||||
registered at the factory.
|
||||
|
||||
E: Manifold pointer was NULL for some reason!
|
||||
|
||||
This indicates a bug. The factory was unable to properly create
|
||||
the requested manifold even though it was registered. Send the
|
||||
maintainer an e-mail.
|
||||
|
||||
E: Manifold ... needs at least ... argument(s)!
|
||||
|
||||
Self-explanatory. Provide enough arguments for the proper
|
||||
creating of the requested manifold.
|
||||
|
||||
E: Parameter pointer was NULL!
|
||||
|
||||
This indicates a bug. The array that contains the parameters
|
||||
could not be allocated. Send the maintainer an e-mail.
|
||||
|
||||
E: Could not allocate space for arg!
|
||||
|
||||
One of the arguments provided was too long (it contained
|
||||
too many characters)
|
||||
|
||||
E: Option ... needs ... argument(s):
|
||||
|
||||
Self-explanatory. Read the documentation of this fix properly.
|
||||
|
||||
|
||||
E: Illegal fix nve/manifold/rattle command! Option ... not recognized!
|
||||
|
||||
Self-explanatory. The given option(s) do not exist.
|
||||
|
||||
E: Variable name for fix nve/manifold/rattle does not exist
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Variable for fix nve/manifold/rattle is invalid style
|
||||
|
||||
fix nve/manifold/rattle only supports equal style variables.
|
||||
|
||||
|
||||
|
||||
*/
|
||||
415
src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp
Normal file
415
src/USER-MANIFOLD/fix_nvt_manifold_rattle.cpp
Normal file
@ -0,0 +1,415 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
-----------------------------------------------------------------------
|
||||
|
||||
This file is a part of the USER-MANIFOLD package.
|
||||
|
||||
Copyright (2013-2014) Stefan Paquay, Eindhoven University of Technology.
|
||||
License: GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
This file is part of the user-manifold package written by
|
||||
Stefan Paquay at the Eindhoven University of Technology.
|
||||
This module makes it possible to do MD with particles constrained
|
||||
to pretty arbitrary manifolds characterised by some constraint function
|
||||
g(x,y,z) = 0 and its normal grad(g). The number of manifolds available
|
||||
right now is limited but can be extended straightforwardly by making
|
||||
a new class that inherits from manifold and implements all pure virtual
|
||||
methods.
|
||||
|
||||
Thanks to Remy Kusters for beta-testing!
|
||||
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
|
||||
#include "stdio.h"
|
||||
#include "stdlib.h"
|
||||
#include "string.h"
|
||||
#include "atom.h"
|
||||
#include "force.h"
|
||||
#include "update.h"
|
||||
#include "respa.h"
|
||||
#include "error.h"
|
||||
#include "group.h"
|
||||
#include "math.h"
|
||||
#include "input.h"
|
||||
#include "variable.h"
|
||||
#include "citeme.h"
|
||||
#include "memory.h"
|
||||
#include "comm.h"
|
||||
#include "modify.h"
|
||||
#include "compute.h"
|
||||
|
||||
#include "fix_nvt_manifold_rattle.h"
|
||||
#include "manifold.h"
|
||||
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
|
||||
enum {CONSTANT,EQUAL};
|
||||
enum {NOBIAS,BIAS};
|
||||
|
||||
|
||||
|
||||
|
||||
static const char* cite_fix_nvt_manifold_rattle =
|
||||
"fix nve/manifold/rattle command:\n\n"
|
||||
"@article{paquay-2016,\n"
|
||||
" author = {Paquay, Stefan and Kusters, Remy}, \n"
|
||||
" eprint = {arXiv:1411.3019}, \n"
|
||||
" title = {A method for molecular dynamics on curved surfaces}, \n"
|
||||
" url = {http://arxiv.org/abs/1411.3019}, \n"
|
||||
" year = 2016, \n"
|
||||
" journal = {Arxiv preprint, \\url{http://arxiv.org/abs/1411.3019}}, \n"
|
||||
" note = {To be published in Biophys. J.}, \n"
|
||||
"}\n\n";
|
||||
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixNVTManifoldRattle::FixNVTManifoldRattle(LAMMPS *lmp, int narg, char **arg,
|
||||
int error_on_unknown_keyword )
|
||||
: FixNVEManifoldRattle(lmp,narg,arg, 0)
|
||||
{
|
||||
if (lmp->citeme) lmp->citeme->add(cite_fix_nvt_manifold_rattle);
|
||||
|
||||
if( narg < 6 ) error->all(FLERR,"Illegal fix nvt/manifold/rattle command");
|
||||
|
||||
// Set all bits/settings:
|
||||
dof_flag = 1;
|
||||
dthalf = dt4 = dt8 = 0;
|
||||
|
||||
t_start = t_stop = t_period = t_current = t_target = ke_target = 0.0;
|
||||
t_freq = drag = tdrag_factor = 0;
|
||||
|
||||
boltz = force->boltz, nktv2p = force->nktv2p;
|
||||
tdof = 0;
|
||||
mtchain = 3;
|
||||
factor_eta = 0.0;
|
||||
which = got_temp = 0;
|
||||
|
||||
int argi = 6 + ptr_m->nparams();
|
||||
while( argi < narg )
|
||||
{
|
||||
if( strcmp( arg[argi], "temp") == 0 ){
|
||||
if( argi+3 >= narg )
|
||||
error->all(FLERR,"Keyword 'temp' needs 3 arguments");
|
||||
|
||||
t_start = force->numeric(FLERR, arg[argi+1]);
|
||||
t_stop = force->numeric(FLERR, arg[argi+2]);
|
||||
t_period = force->numeric(FLERR, arg[argi+3]);
|
||||
t_target = t_start;
|
||||
got_temp = 1;
|
||||
|
||||
argi += 4;
|
||||
}else if( strcmp( arg[argi], "tchain" ) == 0 ){
|
||||
if( argi+1 >= narg )
|
||||
error->all(FLERR,"Keyword 'tchain' needs 1 argument");
|
||||
|
||||
mtchain = force->inumeric(FLERR, arg[argi+1]);
|
||||
argi += 2;
|
||||
}else if( error_on_unknown_keyword ){
|
||||
char msg[2048];
|
||||
sprintf(msg,"Error parsing arg \"%s\".\n", arg[argi]);
|
||||
error->all(FLERR, msg);
|
||||
}else{
|
||||
argi += 1;
|
||||
}
|
||||
}
|
||||
|
||||
reset_dt();
|
||||
|
||||
if( !got_temp ) error->all(FLERR,"Fix nvt/manifold/rattle needs 'temp'!");
|
||||
|
||||
if( t_period < 0.0 ){
|
||||
error->all(FLERR,"Fix nvt/manifold/rattle damping parameter must be > 0.0");
|
||||
}
|
||||
|
||||
// Create temperature compute:
|
||||
const char *fix_id = arg[1];
|
||||
int n = strlen(fix_id)+6;
|
||||
id_temp = new char[n];
|
||||
strcpy(id_temp,fix_id);
|
||||
strcat(id_temp,"_temp");
|
||||
char **newarg = new char*[3];
|
||||
newarg[0] = id_temp;
|
||||
newarg[1] = group->names[igroup];
|
||||
newarg[2] = (char*) "temp";
|
||||
|
||||
|
||||
modify->add_compute(3,newarg);
|
||||
delete [] newarg;
|
||||
int icompute = modify->find_compute(id_temp);
|
||||
if( icompute < 0 ){
|
||||
error->all(FLERR,"Temperature ID for fix nvt/manifold/rattle "
|
||||
"does not exist");
|
||||
}
|
||||
temperature = modify->compute[icompute];
|
||||
if( temperature->tempbias ) which = BIAS;
|
||||
else which = NOBIAS;
|
||||
|
||||
// Set t_freq from t_period
|
||||
t_freq = 1.0 / t_period;
|
||||
|
||||
// Init Nosé-Hoover chain:
|
||||
eta = new double[mtchain];
|
||||
eta_dot = new double[mtchain+1];
|
||||
eta_dotdot = new double[mtchain];
|
||||
eta_mass = new double[mtchain];
|
||||
eta_dot[mtchain] = 0.0;
|
||||
|
||||
eta_dot[mtchain] = 0.0;
|
||||
for( int ich = 0; ich < mtchain; ++ich ){
|
||||
eta[ich] = eta_dot[ich] = eta_dotdot[ich] = 0.0;
|
||||
}
|
||||
|
||||
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
FixNVTManifoldRattle::~FixNVTManifoldRattle()
|
||||
{
|
||||
// Deallocate heap-allocated objects.
|
||||
if( eta ) delete[] eta;
|
||||
if( eta_dot ) delete[] eta_dot;
|
||||
if( eta_dotdot ) delete[] eta_dotdot;
|
||||
if( eta_mass ) delete[] eta_mass;
|
||||
|
||||
modify->delete_compute(id_temp);
|
||||
if( id_temp ) delete[] id_temp;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
int FixNVTManifoldRattle::setmask()
|
||||
{
|
||||
int mask = 0;
|
||||
mask |= INITIAL_INTEGRATE;
|
||||
mask |= FINAL_INTEGRATE;
|
||||
if( nevery > 0 ) mask |= END_OF_STEP;
|
||||
|
||||
return mask;
|
||||
}
|
||||
|
||||
|
||||
/* --------------------------------------------------------------------------
|
||||
Check that force modification happens before position and velocity update.
|
||||
Make sure respa is not used.
|
||||
------------------------------------------------------------------------- */
|
||||
void FixNVTManifoldRattle::init()
|
||||
{
|
||||
// Makes sure the manifold params are set initially.
|
||||
update_var_params();
|
||||
|
||||
int icompute = modify->find_compute(id_temp);
|
||||
if( icompute < 0 ){
|
||||
error->all(FLERR,"Temperature ID for fix nvt/manifold/rattle "
|
||||
"does not exist");
|
||||
}
|
||||
temperature = modify->compute[icompute];
|
||||
if( temperature->tempbias ) which = BIAS;
|
||||
else which = NOBIAS;
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
void FixNVTManifoldRattle::setup(int vflag)
|
||||
{
|
||||
compute_temp_target();
|
||||
|
||||
t_current = temperature->compute_scalar();
|
||||
tdof = temperature->dof;
|
||||
|
||||
// Compute/set eta-masses:
|
||||
double inv_t_freq2 = 1.0 / (t_freq*t_freq);
|
||||
eta_mass[0] = tdof * boltz * t_target * inv_t_freq2;
|
||||
for( int ich = 1; ich < mtchain; ++ich ){
|
||||
eta_mass[ich] = boltz * t_target * inv_t_freq2;
|
||||
}
|
||||
|
||||
for( int ich = 1; ich < mtchain; ++ich ){
|
||||
eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1] -
|
||||
boltz * t_target ) / eta_mass[ich];
|
||||
}
|
||||
}
|
||||
|
||||
void FixNVTManifoldRattle::compute_temp_target()
|
||||
{
|
||||
|
||||
t_current = temperature->compute_scalar();
|
||||
tdof = temperature->dof;
|
||||
|
||||
double delta = update->ntimestep - update->beginstep;
|
||||
if (delta != 0.0){
|
||||
delta /= update->endstep - update->beginstep;
|
||||
}
|
||||
|
||||
tdof = temperature->dof;
|
||||
t_target = t_start + delta * (t_stop-t_start);
|
||||
ke_target = tdof * boltz * t_target;
|
||||
}
|
||||
|
||||
void FixNVTManifoldRattle::nhc_temp_integrate()
|
||||
{
|
||||
int ich;
|
||||
// t_current = temperature->compute_scalar();
|
||||
// tdof = temperature->dof;
|
||||
compute_temp_target();
|
||||
|
||||
double expfac, kecurrent = tdof * boltz * t_current;
|
||||
double inv_t_freq2 = 1.0 / (t_freq*t_freq);
|
||||
eta_mass[0] = tdof * boltz * t_target * inv_t_freq2;
|
||||
for( int ich = 1; ich < mtchain; ++ich ){
|
||||
eta_mass[ich] = boltz * t_target * inv_t_freq2;
|
||||
}
|
||||
|
||||
if( eta_mass[0] > 0.0 ){
|
||||
eta_dotdot[0] = (kecurrent - ke_target)/eta_mass[0];
|
||||
}else{
|
||||
eta_dotdot[0] = 0;
|
||||
}
|
||||
|
||||
for( ich = mtchain-1; ich > 0; --ich ){
|
||||
expfac = exp(-dt8*eta_dot[ich+1]);
|
||||
eta_dot[ich] *= expfac;
|
||||
eta_dot[ich] += eta_dotdot[ich] * dt4;
|
||||
eta_dot[ich] *= tdrag_factor * expfac;
|
||||
|
||||
}
|
||||
|
||||
expfac = exp(-dt8*eta_dot[1]);
|
||||
eta_dot[0] *= expfac;
|
||||
eta_dot[0] += eta_dotdot[0] * dt4;
|
||||
eta_dot[0] *= tdrag_factor * expfac;
|
||||
|
||||
factor_eta = exp(-dthalf*eta_dot[0]);
|
||||
|
||||
if( factor_eta == 0 ){
|
||||
char msg[2048];
|
||||
sprintf(msg, "WTF, factor_eta is 0! dthalf = %f, eta_dot[0] = %f",
|
||||
dthalf, eta_dot[0]);
|
||||
error->all(FLERR,msg);
|
||||
}
|
||||
|
||||
nh_v_temp();
|
||||
|
||||
t_current *= factor_eta*factor_eta;
|
||||
kecurrent = tdof * boltz * t_current;
|
||||
|
||||
if( eta_mass[0] > 0.0 ){
|
||||
eta_dotdot[0] = (kecurrent - ke_target) / eta_mass[0];
|
||||
}else{
|
||||
eta_dotdot[0] = 0.0;
|
||||
}
|
||||
|
||||
for( int ich = 1; ich < mtchain; ++ich ){
|
||||
eta[ich] += dthalf*eta_dot[ich];
|
||||
}
|
||||
eta_dot[0] *= expfac;
|
||||
eta_dot[0] += eta_dotdot[0]*dt4;
|
||||
eta_dot[0] *= expfac;
|
||||
|
||||
for( int ich = 1; ich < mtchain; ++ich ){
|
||||
expfac = exp(-dt8*eta_dot[ich+1]);
|
||||
eta_dot[ich] *= expfac;
|
||||
eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1]
|
||||
- boltz*t_target) / eta_mass[ich];
|
||||
eta_dot[ich] *= eta_dotdot[ich] * dt4;
|
||||
eta_dot[ich] *= expfac;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
void FixNVTManifoldRattle::nh_v_temp()
|
||||
{
|
||||
double **v = atom->v;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if( igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
|
||||
|
||||
|
||||
if( which == NOBIAS ){
|
||||
for( int i = 0; i < nlocal; ++i ){
|
||||
if( mask[i] & groupbit ){
|
||||
v[i][0] *= factor_eta;
|
||||
v[i][1] *= factor_eta;
|
||||
v[i][2] *= factor_eta;
|
||||
}
|
||||
}
|
||||
}else if( which == BIAS ){
|
||||
for( int i = 0; i < nlocal; ++i ){
|
||||
if( mask[i] & groupbit ){
|
||||
temperature->remove_bias(i,v[i]);
|
||||
v[i][0] *= factor_eta;
|
||||
v[i][1] *= factor_eta;
|
||||
v[i][2] *= factor_eta;
|
||||
temperature->restore_bias(i,v[i]);
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
// Most of this logic is based on fix_nh:
|
||||
void FixNVTManifoldRattle::initial_integrate(int vflag)
|
||||
{
|
||||
|
||||
update_var_params();
|
||||
|
||||
compute_temp_target();
|
||||
nhc_temp_integrate();
|
||||
|
||||
nve_x_rattle(igroup, groupbit);
|
||||
}
|
||||
|
||||
void FixNVTManifoldRattle::final_integrate()
|
||||
{
|
||||
nve_v_rattle(igroup, groupbit);
|
||||
|
||||
nhc_temp_integrate();
|
||||
}
|
||||
|
||||
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
void FixNVTManifoldRattle::reset_dt()
|
||||
{
|
||||
FixNVEManifoldRattle::reset_dt();
|
||||
|
||||
dthalf = 0.5 * update->dt;
|
||||
dt4 = 0.25 * update->dt;
|
||||
dt8 = 0.125 * update->dt;
|
||||
tdrag_factor = 1.0 - (update->dt * t_freq * drag);
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
double FixNVTManifoldRattle::memory_usage()
|
||||
{
|
||||
double bytes = FixNVEManifoldRattle::memory_usage();
|
||||
bytes += (4*mtchain+1)*sizeof(double);
|
||||
|
||||
return bytes;
|
||||
}
|
||||
152
src/USER-MANIFOLD/fix_nvt_manifold_rattle.h
Normal file
152
src/USER-MANIFOLD/fix_nvt_manifold_rattle.h
Normal file
@ -0,0 +1,152 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
-----------------------------------------------------------------------
|
||||
|
||||
This file is a part of the USER-MANIFOLD package.
|
||||
|
||||
Copyright (2013-2014) Stefan Paquay, Eindhoven University of Technology.
|
||||
License: GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
This file is part of the user-manifold package written by
|
||||
Stefan Paquay at the Eindhoven University of Technology.
|
||||
This module makes it possible to do MD with particles constrained
|
||||
to pretty arbitrary manifolds characterised by some constraint function
|
||||
g(x,y,z) = 0 and its normal grad(g). The number of manifolds available
|
||||
right now is limited but can be extended straightforwardly by making
|
||||
a new class that inherits from manifold and implements all pure virtual
|
||||
methods.
|
||||
|
||||
Thanks to Remy Kusters for beta-testing!
|
||||
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
|
||||
#ifdef FIX_CLASS
|
||||
|
||||
FixStyle(nvt/manifold/rattle,FixNVTManifoldRattle)
|
||||
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NVT_MANIFOLD_RATTLE_H
|
||||
#define LMP_FIX_NVT_MANIFOLD_RATTLE_H
|
||||
|
||||
#include "fix_nve_manifold_rattle.h"
|
||||
|
||||
|
||||
|
||||
/*
|
||||
FixNVTManifoldRattle works by wrapping some Nose-Hoover thermostat routines
|
||||
around the time integration functions of FixNVEManifoldRattle.
|
||||
*/
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixNVTManifoldRattle : public FixNVEManifoldRattle {
|
||||
public:
|
||||
FixNVTManifoldRattle(LAMMPS *, int, char **, int = 1);
|
||||
virtual ~FixNVTManifoldRattle();
|
||||
|
||||
virtual void initial_integrate(int);
|
||||
virtual void final_integrate();
|
||||
virtual void init();
|
||||
virtual void reset_dt();
|
||||
virtual int setmask();
|
||||
virtual void setup(int); // Not needed for fixNVE but is for fixNVT
|
||||
virtual double memory_usage();
|
||||
|
||||
|
||||
|
||||
protected:
|
||||
|
||||
void compute_temp_target();
|
||||
void nhc_temp_integrate();
|
||||
void nh_v_temp();
|
||||
|
||||
double dthalf, dt4, dt8;
|
||||
|
||||
char *id_temp;
|
||||
class Compute* temperature;
|
||||
double t_start,t_stop, t_period;
|
||||
double t_current,t_target,ke_target;
|
||||
double t_freq, drag, tdrag_factor;
|
||||
double boltz,nktv2p,tdof;
|
||||
double *eta,*eta_dot;
|
||||
double *eta_dotdot;
|
||||
double *eta_mass;
|
||||
int mtchain;
|
||||
double factor_eta;
|
||||
int which, got_temp;
|
||||
|
||||
const char *fix_id;
|
||||
};
|
||||
}
|
||||
|
||||
|
||||
|
||||
#endif // LMP_FIX_NVE_MANIFOLD_RATTLE_H
|
||||
#endif
|
||||
|
||||
/* ERROR/WARNING messages:
|
||||
|
||||
E: Illegal ... command
|
||||
|
||||
Self-explanatory. Check the input script syntax and compare to the
|
||||
documentation for the command. You can use -echo screen as a
|
||||
command-line option when running LAMMPS to see the offending line.
|
||||
|
||||
E: There is no manifold named ...
|
||||
|
||||
Self-explanatory. You requested a manifold whose name was not
|
||||
registered at the factory.
|
||||
|
||||
E: Manifold pointer was NULL for some reason!
|
||||
|
||||
This indicates a bug. The factory was unable to properly create
|
||||
the requested manifold even though it was registered. Send the
|
||||
maintainer an e-mail.
|
||||
|
||||
E: Manifold ... needs at least ... argument(s)!
|
||||
|
||||
Self-explanatory. Provide enough arguments for the proper
|
||||
creating of the requested manifold.
|
||||
|
||||
E: Parameter pointer was NULL!
|
||||
|
||||
This indicates a bug. The array that contains the parameters
|
||||
could not be allocated. Send the maintainer an e-mail.
|
||||
|
||||
E: Could not allocate space for arg!
|
||||
|
||||
One of the arguments provided was too long (it contained
|
||||
too many characters)
|
||||
|
||||
E: Option ... needs ... argument(s):
|
||||
|
||||
Self-explanatory. Read the documentation of this fix properly.
|
||||
|
||||
|
||||
E: Illegal fix nve/manifold/rattle command! Option ... not recognized!
|
||||
|
||||
Self-explanatory. The given option(s) do not exist.
|
||||
|
||||
E: Variable name for fix nve/manifold/rattle does not exist
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Variable for fix nve/manifold/rattle is invalid style
|
||||
|
||||
fix nve/manifold/rattle only supports equal style variables.
|
||||
|
||||
|
||||
|
||||
*/
|
||||
101
src/USER-MANIFOLD/manifold.h
Normal file
101
src/USER-MANIFOLD/manifold.h
Normal file
@ -0,0 +1,101 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
-----------------------------------------------------------------------
|
||||
|
||||
This file is a part of the USER-MANIFOLD package.
|
||||
|
||||
This package allows LAMMPS to perform MD simulations of particles
|
||||
constrained on a manifold (i.e., a 2D subspace of the 3D simulation
|
||||
box). It achieves this using the RATTLE constraint algorithm applied
|
||||
to single-particle constraint functions g(xi,yi,zi) = 0 and their
|
||||
derivative (i.e. the normal of the manifold) n = grad(g).
|
||||
|
||||
It is very easy to add your own manifolds to the current zoo
|
||||
(we now have sphere, a dendritic spine approximation, a 2D plane (for
|
||||
testing purposes) and a wave-y plane.
|
||||
See the README file for more info.
|
||||
|
||||
Stefan Paquay, s.paquay@tue.nl
|
||||
Applied Physics/Theory of Polymers and Soft Matter,
|
||||
Eindhoven University of Technology (TU/e), The Netherlands
|
||||
|
||||
Thanks to Remy Kusters at TU/e for testing.
|
||||
|
||||
This software is distributed under the GNU General Public License.
|
||||
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef LMP_MANIFOLD_H
|
||||
#define LMP_MANIFOLD_H
|
||||
|
||||
#include "pointers.h"
|
||||
#include "error.h"
|
||||
#include "math.h"
|
||||
#include "string.h"
|
||||
#include "lmptype.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
// Abstract base class.
|
||||
class manifold {
|
||||
public:
|
||||
manifold() : params(NULL){ }
|
||||
virtual ~manifold(){ delete[] params; }
|
||||
virtual double g( const double * ) = 0;
|
||||
virtual void n( const double *, double * ) = 0;
|
||||
|
||||
|
||||
// Variant of g that computes n at the same time.
|
||||
virtual double g_and_n( const double *x, double *nn )
|
||||
{
|
||||
this->n(x,nn);
|
||||
return g(x);
|
||||
}
|
||||
|
||||
virtual const char *id() = 0;
|
||||
|
||||
virtual void set_atom_id( tagint a_id ){}
|
||||
virtual int nparams() = 0;
|
||||
double **get_params(){ return ¶ms; };
|
||||
|
||||
// Overload if any initialisation depends on params:
|
||||
virtual void post_param_init(){}
|
||||
virtual void checkup(){} // Some diagnostics...
|
||||
protected:
|
||||
double *params;
|
||||
};
|
||||
|
||||
|
||||
|
||||
// Some utility functions that are templated, so I implement them
|
||||
// here in the header.
|
||||
template< unsigned int size > inline
|
||||
double infnorm( double *vect )
|
||||
{
|
||||
double largest = fabs( vect[0] );
|
||||
for( unsigned int i = 1; i < size; ++i ){
|
||||
double c = fabs( vect[i] );
|
||||
largest = ( c > largest ) ? c : largest;
|
||||
}
|
||||
return largest;
|
||||
}
|
||||
|
||||
inline double dot( double *a, double *b ){
|
||||
return a[0]*b[0] + a[1]*b[1] + a[2]*b[2];
|
||||
}
|
||||
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
|
||||
|
||||
|
||||
#endif // LMP_MANIFOLD_H
|
||||
22
src/USER-MANIFOLD/manifold_cylinder.cpp
Normal file
22
src/USER-MANIFOLD/manifold_cylinder.cpp
Normal file
@ -0,0 +1,22 @@
|
||||
#include "manifold_cylinder.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
double manifold_cylinder::g( const double *x )
|
||||
{
|
||||
double R = params[0];
|
||||
double r2 = x[0]*x[0] + x[1]*x[1];
|
||||
return R*R - r2;
|
||||
}
|
||||
|
||||
void manifold_cylinder::n( const double *x, double *n )
|
||||
{
|
||||
n[0] = -2*x[0];
|
||||
n[1] = -2*x[1];
|
||||
n[2] = 0.0;
|
||||
}
|
||||
|
||||
|
||||
manifold_cylinder::manifold_cylinder( LAMMPS *lmp, int argc,
|
||||
char **argv ) : Pointers(lmp)
|
||||
{}
|
||||
26
src/USER-MANIFOLD/manifold_cylinder.h
Normal file
26
src/USER-MANIFOLD/manifold_cylinder.h
Normal file
@ -0,0 +1,26 @@
|
||||
#ifndef LMP_MANIFOLD_CYLINDER_H
|
||||
#define LMP_MANIFOLD_CYLINDER_H
|
||||
|
||||
#include "manifold.h"
|
||||
|
||||
// A normal cylinder
|
||||
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
class manifold_cylinder : public manifold, protected Pointers {
|
||||
public:
|
||||
enum { NPARAMS = 1 }; // Number of parameters.
|
||||
manifold_cylinder( LAMMPS *lmp, int, char ** );
|
||||
virtual ~manifold_cylinder(){}
|
||||
virtual double g( const double *x );
|
||||
virtual void n( const double *x, double *n );
|
||||
static const char *type(){ return "cylinder"; }
|
||||
virtual const char *id(){ return type(); }
|
||||
static int expected_argc(){ return NPARAMS; }
|
||||
virtual int nparams(){ return NPARAMS; }
|
||||
};
|
||||
}
|
||||
|
||||
|
||||
|
||||
#endif // LMP_MANIFOLD_CYLINDER_H
|
||||
42
src/USER-MANIFOLD/manifold_cylinder_dent.cpp
Normal file
42
src/USER-MANIFOLD/manifold_cylinder_dent.cpp
Normal file
@ -0,0 +1,42 @@
|
||||
#include "manifold_cylinder_dent.h"
|
||||
#include "math_const.h"
|
||||
|
||||
#include <math.h>
|
||||
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
manifold_cylinder_dent::manifold_cylinder_dent( LAMMPS *lmp, int argc,
|
||||
char **argv ) : Pointers(lmp)
|
||||
{}
|
||||
|
||||
|
||||
double manifold_cylinder_dent::g( const double *x )
|
||||
{
|
||||
double l = params[1], R = params[0], a = params[2];
|
||||
double r2 = x[1]*x[1] + x[0]*x[0];
|
||||
if( fabs(x[2]) < 0.5*l ){
|
||||
double k = MathConst::MY_2PI / l;
|
||||
double c = R - 0.5*a*( 1.0 + cos(k*x[2]) );
|
||||
return c*c - r2;
|
||||
}else{
|
||||
return R*R - r2;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
void manifold_cylinder_dent::n( const double *x, double *n )
|
||||
{
|
||||
double l = params[1], R = params[0], a = params[2];
|
||||
if( fabs(x[2]) < 0.5*l ){
|
||||
double k = MathConst::MY_2PI / l;
|
||||
double c = R - 0.5*a*(1.0 + cos(k*x[2]));
|
||||
n[0] = -2*x[0];
|
||||
n[1] = -2*x[1];
|
||||
n[2] = c*a*k*sin(k*x[2]);
|
||||
}else{
|
||||
n[0] = -2*x[0];
|
||||
n[1] = -2*x[1];
|
||||
n[2] = 0.0;
|
||||
}
|
||||
}
|
||||
24
src/USER-MANIFOLD/manifold_cylinder_dent.h
Normal file
24
src/USER-MANIFOLD/manifold_cylinder_dent.h
Normal file
@ -0,0 +1,24 @@
|
||||
#ifndef LMP_MANIFOLD_CYLINDER_DENT_H
|
||||
#define LMP_MANIFOLD_CYLINDER_DENT_H
|
||||
|
||||
#include "manifold.h"
|
||||
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
class manifold_cylinder_dent : public manifold, protected Pointers {
|
||||
public:
|
||||
manifold_cylinder_dent( LAMMPS *lmp, int, char ** );
|
||||
enum { NPARAMS = 3 }; // Number of parameters.
|
||||
virtual ~manifold_cylinder_dent(){}
|
||||
virtual double g( const double *x );
|
||||
virtual void n( const double *x, double *n );
|
||||
static const char *type(){ return "cylinder/dent"; }
|
||||
virtual const char *id(){ return type(); }
|
||||
static int expected_argc(){ return NPARAMS; }
|
||||
virtual int nparams(){ return NPARAMS; }
|
||||
};
|
||||
}
|
||||
|
||||
|
||||
|
||||
#endif // LMP_MANIFOLD_CYLINDER_DENT_H
|
||||
41
src/USER-MANIFOLD/manifold_dumbbell.cpp
Normal file
41
src/USER-MANIFOLD/manifold_dumbbell.cpp
Normal file
@ -0,0 +1,41 @@
|
||||
#include "manifold_dumbbell.h"
|
||||
|
||||
#include <math.h>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
manifold_dumbbell::manifold_dumbbell( LAMMPS *lmp, int argc, char **argv ) : Pointers(lmp)
|
||||
{}
|
||||
|
||||
|
||||
/*
|
||||
* Equation for dumbbell is:
|
||||
*
|
||||
* -x^2 - y^2 + (a^2 - (z/c)^2)*( 1 + A*sin(const(z) *z^2) )^4
|
||||
* const(z) = (z < 0) ? B2 : B
|
||||
* params[4] = { a, A, B, c }
|
||||
*/
|
||||
|
||||
|
||||
double manifold_dumbbell::g( const double *x )
|
||||
{
|
||||
double a = params[0];
|
||||
double A = params[1];
|
||||
double B = params[2];
|
||||
double c = params[3];
|
||||
return -1.0*(x[0]*x[0]+x[1]*x[1])+(a*a-x[2]*x[2]/(c*c))*(1.0+pow(A*sin(B *x[2]*x[2]),4));
|
||||
}
|
||||
|
||||
void manifold_dumbbell::n( const double *x, double *nn )
|
||||
{
|
||||
double a = params[0];
|
||||
double A = params[1];
|
||||
double B = params[2];
|
||||
double c = params[3];
|
||||
nn[0] = -2.0*x[0];
|
||||
nn[1] = -2.0*x[1];
|
||||
nn[2] = 8.0*A*A*A*A*B*x[2]*(a*a-(x[2]*x[2]/(c*c)))*cos(B*x[2]*x[2]) *
|
||||
pow(sin(B*x[2]*x[2]),3)-2*x[2]*(1+pow(A*sin(B*x[2]*x[2]),4))/(c*c);
|
||||
}
|
||||
|
||||
|
||||
28
src/USER-MANIFOLD/manifold_dumbbell.h
Normal file
28
src/USER-MANIFOLD/manifold_dumbbell.h
Normal file
@ -0,0 +1,28 @@
|
||||
#ifndef LMP_MANIFOLD_DUMBBELL_H
|
||||
#define LMP_MANIFOLD_DUMBBELL_H
|
||||
|
||||
#include "manifold.h"
|
||||
|
||||
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
// A dendritic dumbbell approximation:
|
||||
class manifold_dumbbell : public manifold, protected Pointers {
|
||||
public:
|
||||
enum { NPARAMS = 4 }; // Number of parameters.
|
||||
manifold_dumbbell( LAMMPS *lmp, int, char ** );
|
||||
virtual ~manifold_dumbbell(){}
|
||||
virtual double g ( const double *x );
|
||||
virtual void n ( const double *x, double *nn );
|
||||
|
||||
static const char* type(){ return "dumbbell"; }
|
||||
virtual const char *id(){ return type(); }
|
||||
|
||||
static int expected_argc(){ return NPARAMS; }
|
||||
virtual int nparams(){ return NPARAMS; }
|
||||
};
|
||||
}
|
||||
|
||||
|
||||
|
||||
#endif // LMP_MANIFOLD_DUMBBELL_H
|
||||
26
src/USER-MANIFOLD/manifold_ellipsoid.cpp
Normal file
26
src/USER-MANIFOLD/manifold_ellipsoid.cpp
Normal file
@ -0,0 +1,26 @@
|
||||
#include "manifold_ellipsoid.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
manifold_ellipsoid::manifold_ellipsoid( LAMMPS *lmp, int narg, char **argv ) : Pointers(lmp)
|
||||
{}
|
||||
|
||||
|
||||
double manifold_ellipsoid::g( const double *x )
|
||||
{
|
||||
const double ai = 1.0 / params[0];
|
||||
const double bi = 1.0 / params[1];
|
||||
const double ci = 1.0 / params[2];
|
||||
return x[0]*x[0]*ai*ai + x[1]*x[1]*bi*bi + x[2]*x[2]*ci*ci - 1.0;
|
||||
}
|
||||
|
||||
void manifold_ellipsoid::n( const double *x, double * n )
|
||||
{
|
||||
const double ai = 1.0 / params[0];
|
||||
const double bi = 1.0 / params[1];
|
||||
const double ci = 1.0 / params[2];
|
||||
n[0] = 2*x[0]*ai*ai;
|
||||
n[1] = 2*x[1]*bi*bi;
|
||||
n[2] = 2*x[2]*ci*ci;
|
||||
}
|
||||
|
||||
26
src/USER-MANIFOLD/manifold_ellipsoid.h
Normal file
26
src/USER-MANIFOLD/manifold_ellipsoid.h
Normal file
@ -0,0 +1,26 @@
|
||||
#ifndef LMP_MANIFOLD_ELLIPSOID_H
|
||||
#define LMP_MANIFOLD_ELLIPSOID_H
|
||||
|
||||
#include "manifold.h"
|
||||
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
// An ellipsoid:
|
||||
class manifold_ellipsoid : public manifold, protected Pointers {
|
||||
public:
|
||||
enum { NPARAMS = 3 };
|
||||
manifold_ellipsoid( LAMMPS *lmp, int, char ** );
|
||||
virtual ~manifold_ellipsoid(){}
|
||||
virtual double g( const double *x );
|
||||
virtual void n( const double *x, double *n );
|
||||
|
||||
static const char* type(){ return "ellipsoid"; }
|
||||
virtual const char *id(){ return type(); }
|
||||
static int expected_argc(){ return NPARAMS; }
|
||||
virtual int nparams(){ return NPARAMS; }
|
||||
};
|
||||
}
|
||||
|
||||
|
||||
|
||||
#endif // LMP_MANIFOLD_ELLIPSOID_H
|
||||
154
src/USER-MANIFOLD/manifold_factory.h
Normal file
154
src/USER-MANIFOLD/manifold_factory.h
Normal file
@ -0,0 +1,154 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
-----------------------------------------------------------------------
|
||||
|
||||
This file is a part of the USER-MANIFOLD package.
|
||||
|
||||
Copyright (2013-2014) Stefan Paquay, Eindhoven University of Technology.
|
||||
License: GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
This file is part of the user-manifold package written by
|
||||
Stefan Paquay at the Eindhoven University of Technology.
|
||||
This module makes it possible to do MD with particles constrained
|
||||
to pretty arbitrary manifolds characterised by some constraint function
|
||||
g(x,y,z) = 0 and its normal grad(g). The number of manifolds available
|
||||
right now is limited but can be extended straightforwardly by making
|
||||
a new class that inherits from manifold and implements all pure virtual
|
||||
methods.
|
||||
|
||||
Thanks to Remy Kusters for beta-testing!
|
||||
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
|
||||
#ifndef LMP_MANIFOLD_FACTORY_H
|
||||
#define LMP_MANIFOLD_FACTORY_H
|
||||
|
||||
|
||||
#include "manifold.h"
|
||||
#include "pointers.h"
|
||||
|
||||
#include <string>
|
||||
#include <map>
|
||||
|
||||
|
||||
#include "manifold_cylinder.h"
|
||||
#include "manifold_cylinder_dent.h"
|
||||
#include "manifold_dumbbell.h"
|
||||
#include "manifold_ellipsoid.h"
|
||||
#include "manifold_plane.h"
|
||||
#include "manifold_plane_wiggle.h"
|
||||
#include "manifold_sphere.h"
|
||||
#include "manifold_supersphere.h"
|
||||
#include "manifold_spine.h"
|
||||
#include "manifold_spine_opt.h"
|
||||
#include "manifold_thylakoid.h"
|
||||
#include "manifold_torus.h"
|
||||
|
||||
|
||||
inline int str_eql(const char *s1, const char *s2)
|
||||
{
|
||||
return strcmp(s1,s2) == 0;
|
||||
}
|
||||
|
||||
/*
|
||||
* Defining USE_PHONY_LAMMPS makes sure that none of the LAMMPS classes are
|
||||
* included/compiled. This is done in order to allow other programs to use
|
||||
* the manifold_factory without compiling all of LAMMPS itself. The relevant
|
||||
* classes/functions are replaced with dummy ones defined in this #ifdef-block:
|
||||
*/
|
||||
#ifdef USE_PHONY_LAMMPS
|
||||
# ifdef __GNUG__
|
||||
# warning Not compiling actual LAMMPS classes!
|
||||
# endif
|
||||
|
||||
|
||||
struct Error {
|
||||
void all(const char *fname, int line, const char* msg)
|
||||
{
|
||||
fprintf(stderr,"ERROR: %s (%s:%d)",msg,fname,line);
|
||||
std::terminate();
|
||||
}
|
||||
|
||||
void one(const char *fname, int line, const char* msg)
|
||||
{
|
||||
fprintf(stderr,"ERROR: %s (%s:%d)",msg,fname,line);
|
||||
std::terminate();
|
||||
}
|
||||
};
|
||||
|
||||
struct LAMMPS { };
|
||||
|
||||
struct Pointers
|
||||
{
|
||||
Pointers(LAMMPS *) : error( &e ){}
|
||||
Error e;
|
||||
Error *error;
|
||||
};
|
||||
|
||||
static FILE *screen = fopen("/dev/stdout","w");
|
||||
|
||||
#define FLERR __FILE__,__LINE__ // Equivalent to definition in pointers.h
|
||||
#endif // USE_PHONY_LAMMPS
|
||||
|
||||
|
||||
|
||||
// Macro to simplify the fix_impl creation:
|
||||
#define RETURN_MANIFOLD_IF(MNAME, MANIFOLD_TYPE) \
|
||||
do { \
|
||||
using namespace LAMMPS_NS; \
|
||||
if( strcmp( MNAME, MANIFOLD_TYPE::type() ) == 0 ) {\
|
||||
return new MANIFOLD_TYPE(lmp,narg,arg); \
|
||||
} \
|
||||
}while(0)
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
template <typename m_type>
|
||||
void make_manifold_if( manifold **man_ptr, const char *name,
|
||||
LAMMPS *lmp, int narg, char **arg )
|
||||
{
|
||||
if( strcmp( m_type::type(), name ) == 0 ){
|
||||
if( *man_ptr == NULL ){
|
||||
*man_ptr = new m_type(lmp, narg, arg);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
inline manifold* create_manifold(const char *mname, LAMMPS *lmp,
|
||||
int narg, char **arg )
|
||||
{
|
||||
using namespace LAMMPS_NS;
|
||||
manifold *man = NULL;
|
||||
make_manifold_if<manifold_cylinder> ( &man, mname, lmp, narg, arg );
|
||||
make_manifold_if<manifold_cylinder_dent>( &man, mname, lmp, narg, arg );
|
||||
make_manifold_if<manifold_dumbbell> ( &man, mname, lmp, narg, arg );
|
||||
make_manifold_if<manifold_ellipsoid> ( &man, mname, lmp, narg, arg );
|
||||
make_manifold_if<manifold_plane> ( &man, mname, lmp, narg, arg );
|
||||
make_manifold_if<manifold_plane_wiggle> ( &man, mname, lmp, narg, arg );
|
||||
make_manifold_if<manifold_sphere> ( &man, mname, lmp, narg, arg );
|
||||
make_manifold_if<manifold_supersphere> ( &man, mname, lmp, narg, arg );
|
||||
make_manifold_if<manifold_spine> ( &man, mname, lmp, narg, arg );
|
||||
// make_manifold_if<manifold_spine_opt> ( &man, mname, lmp, narg, arg );
|
||||
make_manifold_if<manifold_thylakoid> ( &man, mname, lmp, narg, arg );
|
||||
make_manifold_if<manifold_torus> ( &man, mname, lmp, narg, arg );
|
||||
|
||||
|
||||
return man;
|
||||
}
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
|
||||
#endif // LMP_MANIFOLD_FACTORY_H
|
||||
54
src/USER-MANIFOLD/manifold_hypersphere.h
Normal file
54
src/USER-MANIFOLD/manifold_hypersphere.h
Normal file
@ -0,0 +1,54 @@
|
||||
#ifndef LMP_MANIFOLD_SUPERSPHERE_H
|
||||
#define LMP_MANIFOLD_SUPERSPHERE_H
|
||||
|
||||
#include "manifold.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
// A supersphere:
|
||||
class manifold_supersphere : public manifold, protected Pointers {
|
||||
public:
|
||||
enum { NPARAMS = 2 };
|
||||
manifold_supersphere( LAMMPS *lmp, int, char ** ) : Pointers(lmp){}
|
||||
|
||||
virtual ~manifold_supersphere(){}
|
||||
|
||||
double my_sign( double a )
|
||||
{
|
||||
return (a > 0) - (a < 0);
|
||||
}
|
||||
|
||||
virtual double g( const double *x )
|
||||
{
|
||||
double R = params[0];
|
||||
double q = params[1];
|
||||
double xx = fabs(x[0]);
|
||||
double yy = fabs(x[1]);
|
||||
double zz = fabs(x[2]);
|
||||
|
||||
double rr = pow(xx,q) + pow(yy,q) + pow(zz,q);
|
||||
|
||||
return rr - pow(R,q);
|
||||
}
|
||||
|
||||
virtual void n( const double *x, double *nn )
|
||||
{
|
||||
double q = params[1];
|
||||
double xx = fabs(x[0]);
|
||||
double yy = fabs(x[1]);
|
||||
double zz = fabs(x[2]);
|
||||
|
||||
nn[0] = q * my_sign(x[0])*pow(xx,q-1);
|
||||
nn[1] = q * my_sign(x[1])*pow(yy,q-1);
|
||||
nn[2] = q * my_sign(x[2])*pow(zz,q-1);
|
||||
}
|
||||
|
||||
static const char* type(){ return "supersphere"; }
|
||||
virtual const char *id(){ return type(); }
|
||||
static int expected_argc(){ return NPARAMS; }
|
||||
virtual int nparams(){ return NPARAMS; }
|
||||
};
|
||||
}
|
||||
|
||||
|
||||
|
||||
#endif
|
||||
22
src/USER-MANIFOLD/manifold_plane.cpp
Normal file
22
src/USER-MANIFOLD/manifold_plane.cpp
Normal file
@ -0,0 +1,22 @@
|
||||
#include "manifold_plane.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
manifold_plane::manifold_plane( LAMMPS *lmp, int argc, char **argv ) :
|
||||
Pointers(lmp)
|
||||
{}
|
||||
|
||||
double manifold_plane::g( const double *x )
|
||||
{
|
||||
double a = params[0], b = params[1], c = params[2];
|
||||
double x0 = params[3], y0 = params[4], z0 = params[5];
|
||||
return a*(x[0] - x0) + b*(x[1] - y0) + c*(x[2] - z0);
|
||||
}
|
||||
|
||||
|
||||
void manifold_plane::n( const double *x, double *n )
|
||||
{
|
||||
n[0] = params[0];
|
||||
n[1] = params[1];
|
||||
n[2] = params[2];
|
||||
}
|
||||
25
src/USER-MANIFOLD/manifold_plane.h
Normal file
25
src/USER-MANIFOLD/manifold_plane.h
Normal file
@ -0,0 +1,25 @@
|
||||
#ifndef LMP_MANIFOLD_PLANE_H
|
||||
#define LMP_MANIFOLD_PLANE_H
|
||||
|
||||
#include "manifold.h"
|
||||
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
// A 2D plane
|
||||
class manifold_plane : public manifold, protected Pointers {
|
||||
public:
|
||||
enum { NPARAMS = 6 }; // Number of parameters.
|
||||
manifold_plane( LAMMPS *lmp, int, char ** );
|
||||
virtual ~manifold_plane(){}
|
||||
virtual double g( const double *x );
|
||||
virtual void n( const double *x, double *n );
|
||||
static const char *type(){ return "plane"; }
|
||||
virtual const char *id(){ return type(); }
|
||||
static int expected_argc(){ return NPARAMS; }
|
||||
virtual int nparams(){ return NPARAMS; }
|
||||
};
|
||||
}
|
||||
|
||||
|
||||
|
||||
#endif // LMP_MANIFOLD_PLANE_H
|
||||
27
src/USER-MANIFOLD/manifold_plane_wiggle.cpp
Normal file
27
src/USER-MANIFOLD/manifold_plane_wiggle.cpp
Normal file
@ -0,0 +1,27 @@
|
||||
#include "manifold_plane_wiggle.h"
|
||||
|
||||
#include <math.h>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
manifold_plane_wiggle::manifold_plane_wiggle( LAMMPS *lmp, int argc, char **argv ) :
|
||||
Pointers(lmp)
|
||||
{}
|
||||
|
||||
|
||||
double manifold_plane_wiggle::g( const double *x )
|
||||
{
|
||||
double a = params[0];
|
||||
double w = params[1];
|
||||
return x[2] - a*sin(w*x[0]);
|
||||
}
|
||||
|
||||
|
||||
void manifold_plane_wiggle::n( const double *x, double *n )
|
||||
{
|
||||
double a = params[0];
|
||||
double w = params[1];
|
||||
n[2] = 1;
|
||||
n[1] = 0.0;
|
||||
n[0] = -a*w*cos(x[0]);
|
||||
}
|
||||
25
src/USER-MANIFOLD/manifold_plane_wiggle.h
Normal file
25
src/USER-MANIFOLD/manifold_plane_wiggle.h
Normal file
@ -0,0 +1,25 @@
|
||||
#ifndef LMP_MANIFOLD_PLANE_WIGGLE_H
|
||||
#define LMP_MANIFOLD_PLANE_WIGGLE_H
|
||||
|
||||
#include "manifold.h"
|
||||
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
// A 2D wiggly/wave-y plane (Like z = A cos(kx))
|
||||
class manifold_plane_wiggle : public manifold, protected Pointers {
|
||||
public:
|
||||
enum { NPARAMS = 2 }; // Number of parameters.
|
||||
manifold_plane_wiggle( LAMMPS *lmp, int, char ** );
|
||||
virtual ~manifold_plane_wiggle(){}
|
||||
virtual double g( const double *x );
|
||||
virtual void n( const double *x, double *n );
|
||||
static const char *type(){ return "plane/wiggle"; }
|
||||
virtual const char *id(){ return type(); }
|
||||
static int expected_argc(){ return NPARAMS; }
|
||||
virtual int nparams(){ return NPARAMS; }
|
||||
};
|
||||
}
|
||||
|
||||
|
||||
|
||||
#endif // LMP_MANIFOLD_PLANE_WIGGLE_H
|
||||
695
src/USER-MANIFOLD/manifold_rattle_integrator.cpp
Normal file
695
src/USER-MANIFOLD/manifold_rattle_integrator.cpp
Normal file
@ -0,0 +1,695 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
-----------------------------------------------------------------------
|
||||
|
||||
This file is a part of the USER-MANIFOLD package.
|
||||
|
||||
Copyright (2013-2014) Stefan Paquay, Eindhoven University of Technology.
|
||||
License: GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
This file is part of the user-manifold package written by
|
||||
Stefan Paquay at the Eindhoven University of Technology.
|
||||
This module makes it possible to do MD with particles constrained
|
||||
to pretty arbitrary manifolds characterised by some constraint function
|
||||
g(x,y,z) = 0 and its normal grad(g). The number of manifolds available
|
||||
right now is limited but can be extended straightforwardly by making
|
||||
a new class that inherits from manifold and implements all pure virtual
|
||||
methods.
|
||||
|
||||
Thanks to Remy Kusters for beta-testing!
|
||||
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "force.h"
|
||||
#include "input.h"
|
||||
#include "manifold_factory.h"
|
||||
#include "update.h"
|
||||
#include "variable.h"
|
||||
|
||||
|
||||
#include "manifold_rattle_integrator.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
enum { CONST, EQUAL }; // For treating the variables.
|
||||
|
||||
inline int was_var( const char *str )
|
||||
{
|
||||
if( strlen(str) > 2 ){
|
||||
return (str[0] == 'v') && (str[1] == '_');
|
||||
}else{
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
|
||||
void LAMMPS_NS::shift_args_back( int argi, char ***arg_ptr, int delta, int &narg )
|
||||
{
|
||||
for( int i = argi; i < narg-delta; ++i ){
|
||||
(*arg_ptr)[i] = (*arg_ptr[i+delta]);
|
||||
}
|
||||
narg -= delta;
|
||||
}
|
||||
|
||||
|
||||
|
||||
/* -------------------------------------------------------------------------
|
||||
Integrator stuff. Constructor:
|
||||
------------------------------------------------------------------------ */
|
||||
ManifoldRattleIntegratorBase::ManifoldRattleIntegratorBase(LAMMPS *lmp, int &narg,
|
||||
char ***arg_ptr )
|
||||
: Pointers(lmp), tstrs(NULL), tvars(NULL), tstyle(NULL), is_var(NULL)
|
||||
{
|
||||
char **arg = *arg_ptr;
|
||||
|
||||
// Defaults for member variables:
|
||||
nevery = 0;
|
||||
dtv = dtf = 0;
|
||||
|
||||
tolerance = force->numeric( FLERR, arg[3] );
|
||||
max_iter = force->numeric( FLERR, arg[4] );
|
||||
|
||||
update_style = 1;
|
||||
|
||||
int argi = 6; // 6 for general args, + nvars for manifold vars.
|
||||
|
||||
|
||||
while( argi < narg ){
|
||||
if( comm->me == 0 ){
|
||||
fprintf(screen,"Parsing arg \"%s\"\n",arg[argi]);
|
||||
}
|
||||
if( is_legal_keyword( arg[argi] ) ){
|
||||
int status = parse_arg(argi, narg, arg_ptr);
|
||||
if( status ){
|
||||
char msg[256];
|
||||
sprintf(msg,"Error parsing arg \"%s\".\n", arg[argi]);
|
||||
error->all(FLERR, msg);
|
||||
}
|
||||
}else{
|
||||
++argi;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* -------------------------------------------------------------------------
|
||||
Destructor:
|
||||
------------------------------------------------------------------------ */
|
||||
ManifoldRattleIntegratorBase::~ManifoldRattleIntegratorBase()
|
||||
{
|
||||
if( tstrs ){
|
||||
for( int i = 0; i < nvars; ++i ){
|
||||
delete [] tstrs[i];
|
||||
}
|
||||
delete [] tstrs;
|
||||
}
|
||||
|
||||
if( tvars ) delete [] tvars;
|
||||
if( tstyle ) delete [] tstyle;
|
||||
if( is_var ) delete [] is_var;
|
||||
|
||||
}
|
||||
|
||||
|
||||
void ManifoldRattleIntegratorBase::init_manifold( int narg, char **arg,
|
||||
manifold *man_ptr )
|
||||
{
|
||||
if( !man_ptr ) error->all(FLERR,"manifold ptr was NULL");
|
||||
|
||||
tstrs = new char*[nvars];
|
||||
tvars = new int[nvars];
|
||||
tstyle = new int[nvars];
|
||||
is_var = new int[nvars];
|
||||
|
||||
if( !tstrs || !tvars || !tstyle || !is_var ){
|
||||
error->all(FLERR, "Error creating manifold arg arrays");
|
||||
}
|
||||
|
||||
|
||||
for( int i = 0; i < nvars; ++i ){
|
||||
int len = 0, offset = 0;
|
||||
if( was_var( arg[i+6] ) ){
|
||||
len = strlen(arg[i+6]) - 1; // -1 because -2 for v_, +1 for \0.
|
||||
is_var[i] = 1;
|
||||
offset = 2;
|
||||
}else{
|
||||
force->numeric(FLERR,arg[i+6]); // Check if legal number.
|
||||
len = strlen( arg[i+6] ) + 1; // +1 for \0.
|
||||
is_var[i] = 0;
|
||||
}
|
||||
tstrs[i] = new char[len];
|
||||
if( tstrs[i] == NULL ) error->all(FLERR,"Error allocating space for args.");
|
||||
strcpy( tstrs[i], arg[i+6] + offset );
|
||||
}
|
||||
|
||||
|
||||
*(man_ptr->get_params()) = new double[nvars];
|
||||
if( !(*man_ptr->get_params()) ) error->all(FLERR,"Failed to allocate params!");
|
||||
|
||||
|
||||
for( int i = 0; i < nvars; ++i ){
|
||||
// If param i was variable type, it will be set later...
|
||||
(*man_ptr->get_params())[i] = is_var[i] ? 0.0 : force->numeric( FLERR, arg[i+6] );
|
||||
}
|
||||
man_ptr->post_param_init();
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
void ManifoldRattleIntegratorBase::reset_dt()
|
||||
{
|
||||
dtv = update->dt;
|
||||
dtf = 0.5 * update->dt * force->ftm2v;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
// Identifies keyword in (*arg_ptr)[argi], handles it properly, and strips
|
||||
// the relevant args from (*arg_ptr) and subtracts the number of args handled
|
||||
// from narg (so that (*arg_ptr) contains narg elements again.
|
||||
// Returns 0 on success, -1 otherwise.
|
||||
int ManifoldRattleIntegratorBase::parse_arg( int argi, int &narg,
|
||||
char ***arg_ptr )
|
||||
{
|
||||
if( strcmp((*arg_ptr)[argi], "every") == 0 ){
|
||||
if( argi + 1 >= narg ){
|
||||
error->all(FLERR,"keyword every needs one argument");
|
||||
}
|
||||
nevery = force->inumeric(FLERR,(*arg_ptr)[argi+1]);
|
||||
shift_args_back( argi, arg_ptr, 2, narg );
|
||||
|
||||
return 0;
|
||||
}
|
||||
if( strcmp((*arg_ptr)[argi], "style") == 0 ){
|
||||
if( argi + 1 >= narg ){
|
||||
error->all(FLERR,"keyword every needs one argument");
|
||||
}
|
||||
update_style = force->inumeric(FLERR, (*arg_ptr)[argi+1]);
|
||||
if( update_style < 1 || update_style > 2 ){
|
||||
error->warning(FLERR,"update style not known, reverting to standard");
|
||||
}
|
||||
|
||||
shift_args_back( argi, arg_ptr, 2, narg );
|
||||
|
||||
return 0;
|
||||
}
|
||||
|
||||
return -1;
|
||||
}
|
||||
|
||||
|
||||
|
||||
int ManifoldRattleIntegratorBase::is_legal_keyword( const char *arg )
|
||||
{
|
||||
return strcmp(arg, "every") == 0;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
void ManifoldRattleIntegratorBase::print_stats(const char *header)
|
||||
{
|
||||
double n = stats.natoms;
|
||||
if( n > 0 ){
|
||||
stats.x_iters_per_atom += stats.x_iters / n;
|
||||
stats.v_iters_per_atom += stats.v_iters / n;
|
||||
}
|
||||
|
||||
double x_iters = 0, v_iters = 0;
|
||||
bigint ntimestep = update->ntimestep;
|
||||
int me = -1;
|
||||
|
||||
|
||||
MPI_Comm_rank(world,&me);
|
||||
MPI_Allreduce(&stats.x_iters_per_atom,&x_iters,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
MPI_Allreduce(&stats.v_iters_per_atom,&v_iters,1,MPI_DOUBLE,MPI_SUM,world);
|
||||
|
||||
// Set iters back to zero:
|
||||
stats.x_iters_per_atom = stats.x_iters = 0;
|
||||
stats.v_iters_per_atom = stats.v_iters = 0;
|
||||
|
||||
|
||||
if( me == 0 ){
|
||||
double inv_tdiff = 1.0/( static_cast<double>(ntimestep) - stats.last_out );
|
||||
stats.last_out = ntimestep;
|
||||
|
||||
fprintf(screen, "%s stats for time step " BIGINT_FORMAT " on %d atoms:\n",
|
||||
header, ntimestep, stats.natoms);
|
||||
fprintf(screen, " iters/atom: x = %f, v = %f, dofs removed %d",
|
||||
x_iters * inv_tdiff, v_iters * inv_tdiff, stats.dofs_removed);
|
||||
fprintf(screen,"\n");
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------------
|
||||
Modify the force so that the new positions remain approximately on manifold.
|
||||
Time step velocity (half-way) and position accordingly.
|
||||
-------------------------------------------------------------------------------- */
|
||||
void ManifoldRattleIntegratorBase::nve_x_rattle(int igroup, int groupbit)
|
||||
{
|
||||
double dtfm;
|
||||
// update v and x of atoms in group
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double *rmass = atom->rmass;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
int natoms = 0;
|
||||
|
||||
if (igroup == atom->firstgroup){
|
||||
nlocal = atom->nfirst;
|
||||
}
|
||||
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++){
|
||||
if (mask[i] & groupbit){
|
||||
natoms++;
|
||||
dtfm = dtf / rmass[i];
|
||||
rattle_manifold_x( x[i], v[i], f[i], dtv, dtfm, atom->tag[i] );
|
||||
}
|
||||
}
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++){
|
||||
if (mask[i] & groupbit) {
|
||||
natoms++;
|
||||
dtfm = dtf / mass[type[i]];
|
||||
rattle_manifold_x( x[i], v[i], f[i], dtv, dtfm, atom->tag[i] );
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if( nevery > 0 ){
|
||||
// Count ALL atoms this fix works on:
|
||||
MPI_Allreduce(&natoms,&stats.natoms,1,MPI_INT,MPI_SUM,world);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------------
|
||||
Time step (other half) the velocities so that they remain in manifold.
|
||||
-------------------------------------------------------------------------------- */
|
||||
void ManifoldRattleIntegratorBase::nve_v_rattle(int igroup, int groupbit)
|
||||
{
|
||||
double dtfm;
|
||||
|
||||
// update v of atoms in group
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double *rmass = atom->rmass;
|
||||
double *mass = atom->mass;
|
||||
int *type = atom->type;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
if (rmass) {
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / rmass[i];
|
||||
rattle_manifold_v( v[i], f[i], x[i], dtfm );
|
||||
}
|
||||
}
|
||||
} else {
|
||||
for (int i = 0; i < nlocal; i++){
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / mass[type[i]];
|
||||
rattle_manifold_v( v[i], f[i], x[i], dtfm );
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
/******************* ManifoldRattleIntegrator stuff. *****************/
|
||||
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Performs a rattle update for x
|
||||
------------------------------------------------------------------------- */
|
||||
void ManifoldRattleIntegrator::rattle_manifold_x(double *x, double *v,
|
||||
double *f, double dtv,
|
||||
double dtfm, int tagi )
|
||||
{
|
||||
/*
|
||||
A RATTLE update for the position constraint.
|
||||
Original update is x += dtv * v_1/2
|
||||
Now you do
|
||||
v_1/2(lambda) = v_0 + dtfm * ( f + lambda*n_old )
|
||||
and solve
|
||||
xold - xnew + dtv * v_1/2(lambda) = 0
|
||||
g(xnew) = 0
|
||||
for x and lambda. The lambda you find then gives v_1/2 as well.
|
||||
*/
|
||||
double xo[3]; // Previous position to update from.
|
||||
double vo[3]; // Previous velocity to update from.
|
||||
double l = 0; // Lagrangian multiplier for constraint forces.
|
||||
double R[4]; // System that is 0.
|
||||
double dx[4]; // Update that follows from Newton iteration.
|
||||
double no[3]; // Normal at xo.
|
||||
double nn[3]; // Normal at x, the new position.
|
||||
double res; // Residual.
|
||||
int iters = 0; // Iterations used
|
||||
|
||||
double c = dtfm*dtv; // Used for iterating in the Newton loop:
|
||||
double no_nn, nn_R;
|
||||
|
||||
vo[0] = v[0];
|
||||
vo[1] = v[1];
|
||||
vo[2] = v[2];
|
||||
|
||||
xo[0] = x[0];
|
||||
xo[1] = x[1];
|
||||
xo[2] = x[2];
|
||||
|
||||
double gg = ptr_m->g_and_n(x,no);
|
||||
nn[0] = no[0];
|
||||
nn[1] = no[1];
|
||||
nn[2] = no[2];
|
||||
|
||||
double vt[3];
|
||||
vt[0] = vo[0] + dtfm*f[0];
|
||||
vt[1] = vo[1] + dtfm*f[1];
|
||||
vt[2] = vo[2] + dtfm*f[2];
|
||||
double no_dt[3];
|
||||
no_dt[0] = dtfm*no[0];
|
||||
no_dt[1] = dtfm*no[1];
|
||||
no_dt[2] = dtfm*no[2];
|
||||
|
||||
// Assume that no_nn is roughly constant during iteration:
|
||||
|
||||
const double c_inv = 1.0 / c;
|
||||
|
||||
|
||||
while ( 1 ) {
|
||||
v[0] = vt[0] - l*no_dt[0];
|
||||
v[1] = vt[1] - l*no_dt[1];
|
||||
v[2] = vt[2] - l*no_dt[2];
|
||||
|
||||
R[0] = xo[0] - x[0] + dtv * v[0];
|
||||
R[1] = xo[1] - x[1] + dtv * v[1];
|
||||
R[2] = xo[2] - x[2] + dtv * v[2];
|
||||
R[3] = gg;
|
||||
|
||||
// Analytic solution to system J*(dx,dy,dz,dl)^T = R
|
||||
// no_nn = no[0]*nn[0] + no[1]*nn[1] + no[2]*nn[2];
|
||||
nn_R = nn[0]*R[0] + nn[1]*R[1] + nn[2]*R[2];
|
||||
no_nn = no[0]*nn[0] + no[1]*nn[1] + no[2]*nn[2];
|
||||
double n_inv = 1.0 / no_nn;
|
||||
|
||||
// fprintf( screen, "nn_R = %f, no_nn = %f\n", nn_R, no_nn );
|
||||
|
||||
dx[3] = -nn_R - R[3];
|
||||
dx[3] *= n_inv;
|
||||
dx[0] = -R[0] - no[0]*dx[3];
|
||||
dx[1] = -R[1] - no[1]*dx[3];
|
||||
dx[2] = -R[2] - no[2]*dx[3];
|
||||
|
||||
dx[3] *= c_inv;
|
||||
|
||||
|
||||
double smooth = 1.0; // / sqrt( 1.0 + res*res );
|
||||
x[0] -= smooth*dx[0];
|
||||
x[1] -= smooth*dx[1];
|
||||
x[2] -= smooth*dx[2];
|
||||
l -= smooth*dx[3];
|
||||
|
||||
/*
|
||||
fprintf( screen, "dx = (%e, %e, %e, %e), R = (%e, %e, %e, %e)\n",
|
||||
dx[0], dx[1], dx[2], dx[3], R[0], R[1], R[2], R[3] );
|
||||
fprintf( screen, "x = (%f, %f, %f, %f), n = (%f, %f, %f)\n",
|
||||
x[0], x[1], x[2], l, nn[0], nn[1], nn[2] );
|
||||
*/
|
||||
|
||||
res = infnorm<4>(R);
|
||||
++iters;
|
||||
|
||||
if( (res < tolerance) || (iters >= max_iter) ) break;
|
||||
|
||||
// Update nn and g.
|
||||
gg = ptr_m->g(x);
|
||||
ptr_m->n(x,nn);
|
||||
// gg = ptr_m->g(x);
|
||||
}
|
||||
|
||||
if( iters >= max_iter && res > tolerance ){
|
||||
char msg[2048];
|
||||
sprintf(msg,"Failed to constrain atom %d (x = (%f, %f, %f)! res = %e, iters = %d\n",
|
||||
tagi, x[0], x[1], x[2], res, iters);
|
||||
error->one(FLERR,msg);
|
||||
}
|
||||
|
||||
// "sync" x and v:
|
||||
v[0] = vt[0] - l*no_dt[0];
|
||||
v[1] = vt[1] - l*no_dt[1];
|
||||
v[2] = vt[2] - l*no_dt[2];
|
||||
|
||||
stats.x_iters += iters;
|
||||
}
|
||||
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
Performs a rattle update for v
|
||||
------------------------------------------------------------------------- */
|
||||
void ManifoldRattleIntegrator::rattle_manifold_v(double *v, double *f,
|
||||
double *x, double dtfm,
|
||||
int tagi )
|
||||
{
|
||||
/*
|
||||
The original update was
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
|
||||
Now you add the rattle-like update:
|
||||
vold - vnew + dtfm * F + mu * n_new = 0
|
||||
dot( vnew, n_new ) = 0
|
||||
*/
|
||||
double vo[3]; // V at t + 1/2 dt
|
||||
double l = 0; // Lagrangian multiplier for constraint forces.
|
||||
double R[4]; // System that is 0.
|
||||
double dv[4]; // Update that follows from Newton iteration.
|
||||
double n[3]; // Normal.
|
||||
double res; // Residual.
|
||||
int iters = 0; // Iterations used
|
||||
|
||||
double c = dtfm; // Used for iterating in the Newton loop:
|
||||
double nn2, nn_R;
|
||||
|
||||
vo[0] = v[0];
|
||||
vo[1] = v[1];
|
||||
vo[2] = v[2];
|
||||
|
||||
// Initial guess is unconstrained update:
|
||||
v[0] += dtfm*f[0];
|
||||
v[1] += dtfm*f[1];
|
||||
v[2] += dtfm*f[2];
|
||||
|
||||
ptr_m->n(x,n);
|
||||
|
||||
double vt[3];
|
||||
vt[0] = vo[0] + dtfm*f[0];
|
||||
vt[1] = vo[1] + dtfm*f[1];
|
||||
vt[2] = vo[2] + dtfm*f[2];
|
||||
double no_dt[3];
|
||||
no_dt[0] = dtfm*n[0];
|
||||
no_dt[1] = dtfm*n[1];
|
||||
no_dt[2] = dtfm*n[2];
|
||||
|
||||
nn2 = n[0]*n[0] + n[1]*n[1] + n[2]*n[2];
|
||||
|
||||
const double n_inv = 1.0 / nn2;
|
||||
const double c_inv = 1.0 / c;
|
||||
|
||||
switch( update_style ){
|
||||
default:
|
||||
case 1:
|
||||
do{
|
||||
R[0] = vt[0] - v[0] - l * no_dt[0];
|
||||
R[1] = vt[1] - v[1] - l * no_dt[1];
|
||||
R[2] = vt[2] - v[2] - l * no_dt[2];
|
||||
R[3] = v[0]*n[0] + v[1]*n[1] + v[2]*n[2];
|
||||
|
||||
// Analytic solution to system J*(dx,dy,dz,dl)^T = R
|
||||
nn_R = n[0]*R[0] + n[1]*R[1] + n[2]*R[2];
|
||||
|
||||
dv[3] = -nn_R - R[3];
|
||||
dv[3] *= n_inv;
|
||||
dv[0] = -n[0]*dv[3] - R[0];
|
||||
dv[1] = -n[1]*dv[3] - R[1];
|
||||
dv[2] = -n[2]*dv[3] - R[2];
|
||||
dv[3] *= c_inv;
|
||||
|
||||
v[0] -= dv[0];
|
||||
v[1] -= dv[1];
|
||||
v[2] -= dv[2];
|
||||
l -= dv[3];
|
||||
|
||||
res = infnorm<4>(R);
|
||||
++iters;
|
||||
}while( (res > tolerance) && (iters < max_iter) );
|
||||
|
||||
if( iters >= max_iter && res >= tolerance ){
|
||||
char msg[2048];
|
||||
sprintf(msg,"Failed to constrain atom %d (x = (%f, %f, %f)! res = %e, iters = %d\n",
|
||||
tagi, x[0], x[1], x[2], res, iters);
|
||||
error->all(FLERR,msg);
|
||||
}
|
||||
break;
|
||||
|
||||
case 2:{
|
||||
double mass = dtfm / update->dt;
|
||||
double vhnp = vo[0]*n[0] + vo[1]*n[1] + vo[2]*n[2];
|
||||
double fpnp = f[0]*n[0] + f[1]*n[1] + f[2]*n[2];
|
||||
double phnp = dtfm*vhnp / update->dt;
|
||||
|
||||
l = (2.0*mass/update->dt)*phnp + fpnp;
|
||||
v[0] += 0.5*dtv*f[0] - n[0]*(phnp + fpnp);
|
||||
v[1] += 0.5*dtv*f[1] - n[1]*(phnp + fpnp);
|
||||
v[2] += 0.5*dtv*f[2] - n[2]*(phnp + fpnp);
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
stats.v_iters += iters;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
int ManifoldRattleIntegratorBase::dof( int igroup, int groupbit )
|
||||
{
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
int natoms = 0;
|
||||
for( int i = 0; i < nlocal; ++i ){
|
||||
if(mask[i] & groupbit) ++natoms;
|
||||
}
|
||||
|
||||
int dofs;
|
||||
MPI_Allreduce( &natoms, &dofs, 1, MPI_INT, MPI_SUM, world );
|
||||
|
||||
// Make sure that, if there is just no or one atom, no dofs are subtracted,
|
||||
// since for the first atom already 3 dofs are subtracted because of the
|
||||
// centre of mass corrections:
|
||||
if( dofs <= 1 ) dofs = 0;
|
||||
stats.dofs_removed = dofs;
|
||||
|
||||
return dofs;
|
||||
}
|
||||
|
||||
|
||||
|
||||
ManifoldRattleIntegrator::ManifoldRattleIntegrator( LAMMPS *lmp, int &narg,
|
||||
char ***arg_ptr ) :
|
||||
ManifoldRattleIntegratorBase( lmp, narg, arg_ptr ), ptr_m(NULL)
|
||||
{
|
||||
char **arg = *arg_ptr;
|
||||
ptr_m = create_manifold(arg[5], lmp, narg, arg);
|
||||
if( !ptr_m ){
|
||||
char msg[2048];
|
||||
sprintf(msg,"Could not create manifold of type \"%s\"", arg[5]);
|
||||
error->all(FLERR,msg);
|
||||
}
|
||||
|
||||
nvars = ptr_m->nparams();
|
||||
|
||||
init_manifold( narg, arg, ptr_m );
|
||||
}
|
||||
|
||||
ManifoldRattleIntegrator::~ManifoldRattleIntegrator()
|
||||
{
|
||||
if( ptr_m ) delete ptr_m;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
void ManifoldRattleIntegrator::init()
|
||||
{
|
||||
// Makes sure the manifold params are set initially.
|
||||
update_var_params();
|
||||
|
||||
reset_dt();
|
||||
}
|
||||
|
||||
void ManifoldRattleIntegrator::update_params()
|
||||
{
|
||||
update_var_params();
|
||||
}
|
||||
|
||||
void ManifoldRattleIntegrator::update_var_params()
|
||||
{
|
||||
if( nevery > 0 ){
|
||||
stats.x_iters = 0;
|
||||
stats.v_iters = 0;
|
||||
stats.natoms = 0;
|
||||
stats.x_iters_per_atom = 0.0;
|
||||
stats.v_iters_per_atom = 0.0;
|
||||
}
|
||||
|
||||
double **ptr_params = ptr_m->get_params();
|
||||
for( int i = 0; i < nvars; ++i ){
|
||||
if( is_var[i] ){
|
||||
tvars[i] = input->variable->find(tstrs[i]);
|
||||
if( tvars[i] < 0 ){
|
||||
error->all(FLERR,
|
||||
"Variable name for fix nve/manifold/rattle does not exist");
|
||||
}
|
||||
if( input->variable->equalstyle(tvars[i]) ){
|
||||
tstyle[i] = EQUAL;
|
||||
double new_val = input->variable->compute_equal(tvars[i]);
|
||||
// fprintf( stdout, "New value of var %d is now %f\n", i+1, new_val );
|
||||
*(ptr_params[i]) = new_val;
|
||||
}else{
|
||||
error->all(FLERR,
|
||||
"Variable for fix nve/manifold/rattle is invalid style");
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
double ManifoldRattleIntegrator::memory_usage()
|
||||
{
|
||||
double bytes = 0.0;
|
||||
|
||||
bytes += sizeof(statistics);
|
||||
bytes += sizeof(*ptr_m) + sizeof(ptr_m);
|
||||
bytes += nvars*sizeof(double) + sizeof(double*);
|
||||
bytes += nvars*( sizeof(char*) + 3*sizeof(int) );
|
||||
return bytes;
|
||||
}
|
||||
|
||||
|
||||
131
src/USER-MANIFOLD/manifold_rattle_integrator.h
Normal file
131
src/USER-MANIFOLD/manifold_rattle_integrator.h
Normal file
@ -0,0 +1,131 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
-----------------------------------------------------------------------
|
||||
|
||||
This file is a part of the USER-MANIFOLD package.
|
||||
|
||||
Copyright (2013-2015) Stefan Paquay, Eindhoven University of Technology.
|
||||
License: GNU General Public License v.2
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
This file is part of the user-manifold package written by
|
||||
Stefan Paquay at the Eindhoven University of Technology.
|
||||
This module makes it possible to do MD with particles constrained
|
||||
to pretty arbitrary manifolds characterised by some constraint function
|
||||
g(x,y,z) = 0 and its normal grad(g). The number of manifolds available
|
||||
right now is limited but can be extended straightforwardly by making
|
||||
a new class that inherits from manifold and implements all pure virtual
|
||||
methods.
|
||||
|
||||
Thanks to Remy Kusters for beta-testing!
|
||||
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef LMP_MANIFOLD_RATTLE_INTEGRATOR_H
|
||||
#define LMP_MANIFOLD_RATTLE_INTEGRATOR_H
|
||||
|
||||
#include "manifold.h"
|
||||
#include "pointers.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
// A general util function for handling args.
|
||||
void shift_args_back( int argi, char ***arg_ptr, int delta, int &narg );
|
||||
|
||||
class ManifoldRattleIntegratorBase : public Pointers
|
||||
{
|
||||
public:
|
||||
|
||||
struct statistics {
|
||||
|
||||
statistics() : x_iters(0), v_iters(0), x_iters_per_atom(0),
|
||||
v_iters_per_atom(0), natoms(0), dofs_removed(0),
|
||||
last_out(0) {}
|
||||
double x_iters, v_iters;
|
||||
double x_iters_per_atom;
|
||||
double v_iters_per_atom;
|
||||
int natoms;
|
||||
int dofs_removed;
|
||||
bigint last_out;
|
||||
};
|
||||
|
||||
ManifoldRattleIntegratorBase( LAMMPS*, int &, char *** );
|
||||
~ManifoldRattleIntegratorBase();
|
||||
|
||||
virtual void init() = 0;
|
||||
virtual void update_params() = 0;
|
||||
virtual double memory_usage() = 0;
|
||||
|
||||
|
||||
virtual void nve_x_rattle(int, int);
|
||||
virtual void nve_v_rattle(int, int);
|
||||
virtual int nparams() = 0;
|
||||
|
||||
void init_manifold( int, char **, manifold * );
|
||||
|
||||
void print_stats( const char * );
|
||||
void reset_dt();
|
||||
|
||||
int parse_arg( int , int &, char *** );
|
||||
int is_legal_keyword( const char * );
|
||||
|
||||
int dof(int,int);
|
||||
|
||||
int nevery;
|
||||
|
||||
protected:
|
||||
double dtv, dtf;
|
||||
double tolerance;
|
||||
int max_iter;
|
||||
|
||||
char **tstrs;
|
||||
int *tvars;
|
||||
int *tstyle;
|
||||
int *is_var;
|
||||
|
||||
statistics stats;
|
||||
int update_style;
|
||||
int nvars;
|
||||
|
||||
private:
|
||||
virtual void rattle_manifold_x( double*, double*, double*, double, double, int = 0 ) = 0;
|
||||
virtual void rattle_manifold_v( double*, double*, double*, double, int = 0 ) = 0;
|
||||
};
|
||||
|
||||
|
||||
class ManifoldRattleIntegrator : public ManifoldRattleIntegratorBase
|
||||
{
|
||||
public:
|
||||
ManifoldRattleIntegrator(LAMMPS *, int&, char *** );
|
||||
virtual ~ManifoldRattleIntegrator();
|
||||
|
||||
virtual void init();
|
||||
virtual void update_params();
|
||||
virtual double memory_usage();
|
||||
|
||||
virtual int nparams(){ return ptr_m->nparams(); }
|
||||
|
||||
|
||||
private:
|
||||
void update_var_params();
|
||||
virtual void rattle_manifold_x( double*, double*, double*, double, double, int = 0 );
|
||||
virtual void rattle_manifold_v( double*, double*, double*, double, int = 0);
|
||||
|
||||
manifold *ptr_m;
|
||||
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
|
||||
#endif // LMP_MANIFOLD_RATTLE_INTEGRATOR_H
|
||||
54
src/USER-MANIFOLD/manifold_sphere.h
Normal file
54
src/USER-MANIFOLD/manifold_sphere.h
Normal file
@ -0,0 +1,54 @@
|
||||
#ifndef LMP_MANIFOLD_SPHERE_H
|
||||
#define LMP_MANIFOLD_SPHERE_H
|
||||
|
||||
#include "manifold.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
// A sphere:
|
||||
class manifold_sphere : public manifold, protected Pointers {
|
||||
public:
|
||||
enum { NPARAMS = 1 };
|
||||
manifold_sphere( LAMMPS *lmp, int, char ** ) : Pointers(lmp){}
|
||||
|
||||
virtual ~manifold_sphere(){}
|
||||
virtual double g( const double *x )
|
||||
{
|
||||
double R = params[0];
|
||||
double r2 = x[0]*x[0] + x[1]*x[1] + x[2]*x[2];
|
||||
return r2 - R*R;
|
||||
}
|
||||
|
||||
virtual double g_and_n( const double *x, double *nn )
|
||||
{
|
||||
double R = params[0];
|
||||
double r2 = x[0]*x[0] + x[1]*x[1] + x[2]*x[2];
|
||||
nn[0] = 2*x[0];
|
||||
nn[1] = 2*x[1];
|
||||
nn[2] = 2*x[2];
|
||||
|
||||
return r2 - R*R;
|
||||
}
|
||||
|
||||
virtual void n( const double *x, double *nn )
|
||||
{
|
||||
nn[0] = 2*x[0];
|
||||
nn[1] = 2*x[1];
|
||||
nn[2] = 2*x[2];
|
||||
}
|
||||
|
||||
virtual void H( double *x, double h[3][3] )
|
||||
{
|
||||
h[0][1] = h[0][2] = h[1][0] = h[1][2] = h[2][0] = h[2][1] = 0.0;
|
||||
h[0][0] = h[1][1] = h[2][2] = 2.0;
|
||||
}
|
||||
|
||||
static const char* type(){ return "sphere"; }
|
||||
virtual const char *id(){ return type(); }
|
||||
static int expected_argc(){ return NPARAMS; }
|
||||
virtual int nparams(){ return NPARAMS; }
|
||||
};
|
||||
}
|
||||
|
||||
|
||||
|
||||
#endif // LMP_MANIFOLD_SPHERE_H
|
||||
54
src/USER-MANIFOLD/manifold_spine.cpp
Normal file
54
src/USER-MANIFOLD/manifold_spine.cpp
Normal file
@ -0,0 +1,54 @@
|
||||
#include "manifold_spine.h"
|
||||
|
||||
#include <math.h>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
manifold_spine::manifold_spine( LAMMPS *lmp, int argc, char **argv ) : Pointers(lmp)
|
||||
{}
|
||||
|
||||
|
||||
/*
|
||||
* Equation for spine is:
|
||||
*
|
||||
* -x^2 - y^2 + (a^2 - (z/c)^2)*( 1 + A*sin(const(z) *z^2) )^4
|
||||
* const(z) = (z < 0) ? B2 : B
|
||||
* params[5] = { a, A, B, B2, c }
|
||||
*/
|
||||
|
||||
|
||||
double manifold_spine::g( const double *x )
|
||||
{
|
||||
double a = params[0];
|
||||
double A = params[1];
|
||||
double B = params[2];
|
||||
double B2 = params[3];
|
||||
double c = params[4];
|
||||
if (x[2]>0){
|
||||
return -1.0*(x[0]*x[0]+x[1]*x[1])+(a*a-x[2]*x[2]/(c*c))*(1.0+pow(A*sin(B *x[2]*x[2]),4));
|
||||
}else{
|
||||
return -1.0*(x[0]*x[0]+x[1]*x[1])+(a*a-x[2]*x[2]) *(1.0+pow(A*sin(B2*x[2]*x[2]),4));
|
||||
}
|
||||
}
|
||||
|
||||
void manifold_spine::n( const double *x, double *nn )
|
||||
{
|
||||
double a = params[0];
|
||||
double A = params[1];
|
||||
double B = params[2];
|
||||
double B2 = params[3];
|
||||
double c = params[4];
|
||||
if (x[2]>0){
|
||||
nn[0] = -2.0*x[0];
|
||||
nn[1] = -2.0*x[1];
|
||||
nn[2] = 8.0*A*A*A*A*B*x[2]*(a*a-(x[2]*x[2]/(c*c)))*cos(B*x[2]*x[2]) *
|
||||
pow(sin(B*x[2]*x[2]),3)-2*x[2]*(1+pow(A*sin(B*x[2]*x[2]),4))/(c*c);
|
||||
}else{
|
||||
nn[0] = -2.0*x[0];
|
||||
nn[1] = -2.0*x[1];
|
||||
nn[2] = 8.0*A*A*A*A*B2*x[2]*(a*a-x[2]*x[2])*cos(B2*x[2]*x[2]) *
|
||||
pow(sin(B2*x[2]*x[2]),3)-2*x[2]*(1+pow(A*sin(B2*x[2]*x[2]),4));
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
28
src/USER-MANIFOLD/manifold_spine.h
Normal file
28
src/USER-MANIFOLD/manifold_spine.h
Normal file
@ -0,0 +1,28 @@
|
||||
#ifndef LMP_MANIFOLD_SPINE_H
|
||||
#define LMP_MANIFOLD_SPINE_H
|
||||
|
||||
#include "manifold.h"
|
||||
|
||||
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
// A dendritic spine approximation:
|
||||
class manifold_spine : public manifold, protected Pointers {
|
||||
public:
|
||||
enum { NPARAMS = 5 }; // Number of parameters.
|
||||
manifold_spine( LAMMPS *lmp, int, char ** );
|
||||
virtual ~manifold_spine(){}
|
||||
virtual double g ( const double *x );
|
||||
virtual void n ( const double *x, double *nn );
|
||||
|
||||
static const char* type(){ return "spine"; }
|
||||
virtual const char *id(){ return type(); }
|
||||
|
||||
static int expected_argc(){ return NPARAMS; }
|
||||
virtual int nparams(){ return NPARAMS; }
|
||||
};
|
||||
}
|
||||
|
||||
|
||||
|
||||
#endif // LMP_MANIFOLD_SPINE_H
|
||||
171
src/USER-MANIFOLD/manifold_spine_opt.cpp
Normal file
171
src/USER-MANIFOLD/manifold_spine_opt.cpp
Normal file
@ -0,0 +1,171 @@
|
||||
#include "comm.h"
|
||||
#include "manifold_spine_opt.h"
|
||||
#include "math_const.h"
|
||||
|
||||
#include <math.h>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
using namespace MathConst;
|
||||
|
||||
manifold_spine_opt::manifold_spine_opt( LAMMPS *lmp, int argc, char **argv ) : Pointers(lmp), lu_table(2048)
|
||||
{
|
||||
}
|
||||
|
||||
|
||||
manifold_spine_opt::~manifold_spine_opt()
|
||||
{
|
||||
}
|
||||
|
||||
|
||||
/*
|
||||
* Equation for spine is:
|
||||
*
|
||||
* -x^2 - y^2 + (a^2 - (z/c)^2)*( 1 + A*sin(const(z) *z^2) )^4
|
||||
* const(z) = (z < 0) ? B2 : B
|
||||
* params[5] = { a, A, B, B2, c }
|
||||
*
|
||||
* These functions are however optimized quite a bit (but still slow =()
|
||||
*/
|
||||
|
||||
|
||||
double manifold_spine_opt::g( const double *x )
|
||||
{
|
||||
const double B = params[2];
|
||||
const double B2 = params[3];
|
||||
|
||||
const double x2 = x[0]*x[0];
|
||||
const double y2 = x[1]*x[1];
|
||||
const double z2 = x[2]*x[2];
|
||||
|
||||
// Delay branching up to here, compute everything that is used by both before.
|
||||
if( x[2] > 0 ){
|
||||
const double z2_c2 = inv_c2 * z2;
|
||||
|
||||
const double Bz2 = B * z2;
|
||||
const double s_Bz2 = lu_table.sin(Bz2);
|
||||
const double s2_Bz2 = s_Bz2*s_Bz2;
|
||||
const double s4_Bz2 = s2_Bz2*s2_Bz2;
|
||||
const double one_p_A4s4 = 1.0 + A4*s4_Bz2;
|
||||
const double a2_m_z2_c2 = a2 - z2_c2;
|
||||
|
||||
return -x2 - y2 + a2_m_z2_c2 * one_p_A4s4;
|
||||
|
||||
}else{
|
||||
const double Bz2 = B2 * z2;
|
||||
const double s_Bz2 = lu_table.sin(Bz2);
|
||||
const double s2_Bz2 = s_Bz2*s_Bz2;
|
||||
const double s3_Bz2 = s_Bz2*s2_Bz2;
|
||||
const double s4_Bz2 = s2_Bz2*s2_Bz2;
|
||||
const double one_p_A4s4 = (1.0 + A4*s4_Bz2);
|
||||
const double a2_m_z2 = a2 - z2;
|
||||
|
||||
return -x2 - y2 + a2_m_z2 * one_p_A4s4;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
void manifold_spine_opt::n( const double *x, double *nn )
|
||||
{
|
||||
const double B = params[2];
|
||||
const double B2 = params[3];
|
||||
|
||||
|
||||
nn[0] = -2*x[0];
|
||||
nn[1] = -2*x[1];
|
||||
|
||||
const double z2 = x[2]*x[2];
|
||||
|
||||
// Delay branching up to here, compute everything that is used by both before.
|
||||
if( x[2] > 0 ){
|
||||
const double z2_c2 = inv_c2 * z2;
|
||||
const double z_c2 = inv_c2 * x[2];
|
||||
|
||||
const double Bz2 = B * z2;
|
||||
const double c_Bz2 = lu_table.cos(Bz2);
|
||||
const double s_Bz2 = lu_table.sin(Bz2);
|
||||
const double s2_Bz2 = s_Bz2*s_Bz2;
|
||||
const double s3_Bz2 = s_Bz2*s2_Bz2;
|
||||
const double s4_Bz2 = s2_Bz2*s2_Bz2;
|
||||
const double one_p_A4s4 = 1.0 + A4*s4_Bz2;
|
||||
const double a2_m_z2_c2 = a2 - z2_c2;
|
||||
|
||||
|
||||
nn[2] = 8*A4*B*x[2] * a2_m_z2_c2 * c_Bz2 * s3_Bz2 - 2.0*z_c2 * one_p_A4s4;
|
||||
|
||||
}else{
|
||||
const double Bz2 = B2 * z2;
|
||||
const double c_Bz2 = lu_table.cos(Bz2);
|
||||
const double s_Bz2 = lu_table.sin(Bz2);
|
||||
const double s2_Bz2 = s_Bz2*s_Bz2;
|
||||
const double s3_Bz2 = s_Bz2*s2_Bz2;
|
||||
const double s4_Bz2 = s2_Bz2*s2_Bz2;
|
||||
const double one_p_A4s4 = (1.0 + A4*s4_Bz2);
|
||||
const double a2_m_z2 = a2 - z2;
|
||||
|
||||
|
||||
nn[2] = 8*A4*B2*x[2] * a2_m_z2 * c_Bz2 * s3_Bz2 - 2.0*x[2] * one_p_A4s4;
|
||||
}
|
||||
}
|
||||
|
||||
double manifold_spine_opt::g_and_n( const double *x, double *nn )
|
||||
{
|
||||
const double B = params[2];
|
||||
const double B2 = params[3];
|
||||
|
||||
nn[0] = -2*x[0];
|
||||
nn[1] = -2*x[1];
|
||||
|
||||
const double x2 = x[0]*x[0];
|
||||
const double y2 = x[1]*x[1];
|
||||
const double z2 = x[2]*x[2];
|
||||
|
||||
// Delay branching up to here, compute everything that is used by both before.
|
||||
if( x[2] > 0 ){
|
||||
const double z2_c2 = inv_c2 * z2;
|
||||
const double z_c2 = inv_c2 * x[2];
|
||||
|
||||
const double Bz2 = B * z2;
|
||||
const double c_Bz2 = lu_table.cos(Bz2);
|
||||
const double s_Bz2 = lu_table.sin(Bz2);
|
||||
const double s2_Bz2 = s_Bz2*s_Bz2;
|
||||
const double s3_Bz2 = s_Bz2*s2_Bz2;
|
||||
const double s4_Bz2 = s2_Bz2*s2_Bz2;
|
||||
const double one_p_A4s4 = 1.0 + A4*s4_Bz2;
|
||||
const double a2_m_z2_c2 = a2 - z2_c2;
|
||||
|
||||
|
||||
nn[2] = 8*A4*B*x[2] * a2_m_z2_c2 * c_Bz2 * s3_Bz2 - 2.0*z_c2 * one_p_A4s4;
|
||||
return -x2 - y2 + a2_m_z2_c2 * one_p_A4s4;
|
||||
|
||||
}else{
|
||||
const double Bz2 = B2 * z2;
|
||||
const double c_Bz2 = lu_table.cos(Bz2);
|
||||
const double s_Bz2 = lu_table.sin(Bz2);
|
||||
const double s2_Bz2 = s_Bz2*s_Bz2;
|
||||
const double s3_Bz2 = s_Bz2*s2_Bz2;
|
||||
const double s4_Bz2 = s2_Bz2*s2_Bz2;
|
||||
const double one_p_A4s4 = (1.0 + A4*s4_Bz2);
|
||||
const double a2_m_z2 = a2 - z2;
|
||||
|
||||
|
||||
nn[2] = 8*A4*B2*x[2] * a2_m_z2 * c_Bz2 * s3_Bz2 - 2.0*x[2] * one_p_A4s4;
|
||||
return -x2 - y2 + a2_m_z2 * one_p_A4s4;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
void manifold_spine_opt::post_param_init()
|
||||
{
|
||||
const double a = params[0];
|
||||
const double A = params[1];
|
||||
const double c = params[4];
|
||||
|
||||
c2 = c*c;
|
||||
inv_c2 = 1.0 / c2;
|
||||
a2 = a*a;
|
||||
const double A2 = A*A;
|
||||
A4 = A2*A2;
|
||||
}
|
||||
|
||||
35
src/USER-MANIFOLD/manifold_spine_opt.h
Normal file
35
src/USER-MANIFOLD/manifold_spine_opt.h
Normal file
@ -0,0 +1,35 @@
|
||||
#ifndef LMP_MANIFOLD_SPINE_OPT_H
|
||||
#define LMP_MANIFOLD_SPINE_OPT_H
|
||||
|
||||
#include "manifold.h"
|
||||
#include "sincos_lookup.h"
|
||||
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
// A dendritic spine approximation:
|
||||
class manifold_spine_opt : public manifold, protected Pointers {
|
||||
public:
|
||||
enum { NPARAMS = 5 }; // Number of parameters.
|
||||
manifold_spine_opt( LAMMPS *lmp, int, char ** );
|
||||
virtual ~manifold_spine_opt();
|
||||
virtual double g ( const double *x );
|
||||
virtual void n ( const double *x, double *nn );
|
||||
virtual double g_and_n( const double *x, double *nn );
|
||||
|
||||
|
||||
static const char* type(){ return "spine/opt"; }
|
||||
virtual const char *id(){ return type(); }
|
||||
|
||||
static int expected_argc(){ return NPARAMS; }
|
||||
virtual int nparams(){ return NPARAMS; }
|
||||
|
||||
virtual void post_param_init();
|
||||
private:
|
||||
double c2, inv_c2, a2, A4;
|
||||
|
||||
sincos_lookup lu_table;
|
||||
|
||||
};
|
||||
}
|
||||
|
||||
#endif // LMP_MANIFOLD_SPINE_OPT_H
|
||||
54
src/USER-MANIFOLD/manifold_supersphere.h
Normal file
54
src/USER-MANIFOLD/manifold_supersphere.h
Normal file
@ -0,0 +1,54 @@
|
||||
#ifndef LMP_MANIFOLD_SUPERSPHERE_H
|
||||
#define LMP_MANIFOLD_SUPERSPHERE_H
|
||||
|
||||
#include "manifold.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
// A sphere:
|
||||
class manifold_supersphere : public manifold, protected Pointers {
|
||||
public:
|
||||
enum { NPARAMS = 2 };
|
||||
manifold_supersphere( LAMMPS *lmp, int, char ** ) : Pointers(lmp){}
|
||||
|
||||
virtual ~manifold_supersphere(){}
|
||||
|
||||
double my_sign( double a )
|
||||
{
|
||||
return (a > 0) - (a < 0);
|
||||
}
|
||||
|
||||
virtual double g( const double *x )
|
||||
{
|
||||
double R = params[0];
|
||||
double q = params[1];
|
||||
double xx = fabs(x[0]);
|
||||
double yy = fabs(x[1]);
|
||||
double zz = fabs(x[2]);
|
||||
|
||||
double rr = pow(xx,q) + pow(yy,q) + pow(zz,q);
|
||||
|
||||
return rr - pow(R,q);
|
||||
}
|
||||
|
||||
virtual void n( const double *x, double *nn )
|
||||
{
|
||||
double q = params[1];
|
||||
double xx = fabs(x[0]);
|
||||
double yy = fabs(x[1]);
|
||||
double zz = fabs(x[2]);
|
||||
|
||||
nn[0] = q * my_sign(x[0])*pow(xx,q-1);
|
||||
nn[1] = q * my_sign(x[1])*pow(yy,q-1);
|
||||
nn[2] = q * my_sign(x[2])*pow(zz,q-1);
|
||||
}
|
||||
|
||||
static const char* type(){ return "supersphere"; }
|
||||
virtual const char *id(){ return type(); }
|
||||
static int expected_argc(){ return NPARAMS; }
|
||||
virtual int nparams(){ return NPARAMS; }
|
||||
};
|
||||
}
|
||||
|
||||
|
||||
|
||||
#endif
|
||||
382
src/USER-MANIFOLD/manifold_thermostat_nh.cpp
Normal file
382
src/USER-MANIFOLD/manifold_thermostat_nh.cpp
Normal file
@ -0,0 +1,382 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
-----------------------------------------------------------------------
|
||||
|
||||
This file is a part of the USER-MANIFOLD package.
|
||||
|
||||
Copyright (2013-2014) Stefan Paquay, Eindhoven University of Technology.
|
||||
License: GNU General Public License v.2.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
This file is part of the user-manifold package written by
|
||||
Stefan Paquay at the Eindhoven University of Technology.
|
||||
This module makes it possible to do MD with particles constrained
|
||||
to pretty arbitrary manifolds characterised by some constraint function
|
||||
g(x,y,z) = 0 and its normal grad(g). The number of manifolds available
|
||||
right now is limited but can be extended straightforwardly by making
|
||||
a new class that inherits from manifold and implements all pure virtual
|
||||
methods.
|
||||
|
||||
Thanks to Remy Kusters for beta-testing!
|
||||
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#include "atom.h"
|
||||
#include "comm.h"
|
||||
#include "compute.h"
|
||||
#include "error.h"
|
||||
#include "fix.h"
|
||||
#include "force.h"
|
||||
#include "group.h"
|
||||
#include "math.h"
|
||||
#include "modify.h"
|
||||
#include "neighbor.h"
|
||||
#include "update.h"
|
||||
|
||||
|
||||
#include "manifold_thermostat_nh.h"
|
||||
#include "manifold_rattle_integrator.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
||||
|
||||
enum {CONSTANT,EQUAL};
|
||||
enum {NOBIAS,BIAS};
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
ManifoldThermostatNH::ManifoldThermostatNH( LAMMPS *lmp, int &narg,
|
||||
char ***arg_ptr, const char *f_id,
|
||||
int argi, int igroup, int groupbit )
|
||||
: Pointers(lmp), id_temp(NULL), temperature(NULL), eta(NULL), eta_dot(NULL),
|
||||
eta_dotdot(NULL), eta_mass(NULL), fix_id(f_id),
|
||||
igroup(igroup), groupbit(groupbit)
|
||||
{
|
||||
dthalf = dt4 = dt8 = 0;
|
||||
|
||||
t_start = t_stop = t_period = t_current = t_target = ke_target = 0.0;
|
||||
t_freq = drag = tdrag_factor = 0;
|
||||
|
||||
boltz = force->boltz, nktv2p = force->nktv2p;
|
||||
tdof = 0;
|
||||
mtchain = 3;
|
||||
factor_eta = 0.0;
|
||||
which = got_temp = 0;
|
||||
|
||||
// argi is passed from somewhere else.
|
||||
while( argi < narg ){
|
||||
char **arg = *arg_ptr;
|
||||
if( comm->me == 0 ){
|
||||
fprintf(screen,"Parsing arg \"%s\"\n",arg[argi]);
|
||||
}
|
||||
if( is_legal_keyword( arg[argi] ) ){
|
||||
int status = parse_arg(argi, narg, arg_ptr);
|
||||
if( status ){
|
||||
char msg[256];
|
||||
sprintf(msg,"Error parsing arg \"%s\".\n", arg[argi]);
|
||||
error->all(FLERR, msg);
|
||||
}
|
||||
}else{
|
||||
++argi;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
if( !got_temp ) error->all(FLERR,"Fix nvt/manifold/rattle needs 'temp'!");
|
||||
|
||||
if( t_period < 0.0 ){
|
||||
error->all(FLERR,"Fix nvt/manifold/rattle damping parameter must be > 0.0");
|
||||
}
|
||||
|
||||
// Create temperature compute:
|
||||
int n = strlen(fix_id)+6;
|
||||
id_temp = new char[n];
|
||||
strcpy(id_temp,fix_id);
|
||||
strcat(id_temp,"_temp");
|
||||
char **newarg = new char*[3];
|
||||
newarg[0] = id_temp;
|
||||
newarg[1] = group->names[igroup];
|
||||
newarg[2] = (char*) "temp";
|
||||
modify->add_compute(3,newarg);
|
||||
delete [] newarg;
|
||||
int icompute = modify->find_compute(id_temp);
|
||||
if( icompute < 0 ){
|
||||
error->all(FLERR,"Temperature ID for fix nvt/manifold/rattle "
|
||||
"does not exist");
|
||||
}
|
||||
temperature = modify->compute[icompute];
|
||||
if( temperature->tempbias ) which = BIAS;
|
||||
else which = NOBIAS;
|
||||
|
||||
// Set t_freq from t_period
|
||||
t_freq = 1.0 / t_period;
|
||||
|
||||
// Init Nosé-Hoover chain:
|
||||
eta = new double[mtchain];
|
||||
eta_dot = new double[mtchain+1];
|
||||
eta_dotdot = new double[mtchain];
|
||||
eta_mass = new double[mtchain];
|
||||
eta_dot[mtchain] = 0.0;
|
||||
|
||||
eta_dot[mtchain] = 0.0;
|
||||
for( int ich = 0; ich < mtchain; ++ich ){
|
||||
eta[ich] = eta_dot[ich] = eta_dotdot[ich] = 0.0;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
ManifoldThermostatNH::~ManifoldThermostatNH()
|
||||
{
|
||||
// Deallocate heap-allocated objects.
|
||||
if( eta ) delete[] eta;
|
||||
if( eta_dot ) delete[] eta_dot;
|
||||
if( eta_dotdot ) delete[] eta_dotdot;
|
||||
if( eta_mass ) delete[] eta_mass;
|
||||
|
||||
modify->delete_compute(id_temp);
|
||||
if( id_temp ) delete[] id_temp;
|
||||
|
||||
}
|
||||
|
||||
int ManifoldThermostatNH::parse_arg( int argi, int &narg, char ***arg_ptr )
|
||||
{
|
||||
if( strcmp( (*arg_ptr)[argi], "temp") == 0 ){
|
||||
if( argi+3 >= narg )
|
||||
error->all(FLERR,"Keyword 'temp' needs 3 arguments");
|
||||
|
||||
t_start = force->numeric(FLERR,(*arg_ptr)[argi+1]);
|
||||
t_stop = force->numeric(FLERR,(*arg_ptr)[argi+2]);
|
||||
t_period = force->numeric(FLERR,(*arg_ptr)[argi+3]);
|
||||
t_target = t_start;
|
||||
got_temp = 1;
|
||||
|
||||
shift_args_back( argi, arg_ptr, 4, narg );
|
||||
|
||||
return 0;
|
||||
|
||||
}else if( strcmp( (*arg_ptr)[argi], "tchain" ) == 0 ){
|
||||
if( argi+1 >= narg )
|
||||
error->all(FLERR,"Keyword 'tchain' needs 1 argument");
|
||||
|
||||
mtchain = force->inumeric(FLERR, (*arg_ptr)[argi+1]);
|
||||
shift_args_back( argi, arg_ptr, 2, narg );
|
||||
|
||||
return 0;
|
||||
}
|
||||
return -1;
|
||||
}
|
||||
|
||||
|
||||
|
||||
int ManifoldThermostatNH::is_legal_keyword( const char *arg )
|
||||
{
|
||||
return (strcmp(arg, "temp") == 0) || (strcmp(arg, "tchain") == 0 );
|
||||
}
|
||||
|
||||
|
||||
void ManifoldThermostatNH::init()
|
||||
{
|
||||
int icompute = modify->find_compute(id_temp);
|
||||
if( icompute < 0 ){
|
||||
error->all(FLERR,"Temperature ID for fix nvt/manifold/rattle "
|
||||
"does not exist");
|
||||
}
|
||||
temperature = modify->compute[icompute];
|
||||
if( temperature->tempbias ) which = BIAS;
|
||||
else which = NOBIAS;
|
||||
}
|
||||
|
||||
|
||||
|
||||
double ManifoldThermostatNH::memory_usage()
|
||||
{
|
||||
double bytes = 0.0;
|
||||
|
||||
return bytes;
|
||||
}
|
||||
|
||||
|
||||
// All of this is copied/stolen from fix_nh:
|
||||
void ManifoldThermostatNH::setup(int vflag)
|
||||
{
|
||||
compute_temp_target();
|
||||
|
||||
t_current = temperature->compute_scalar();
|
||||
tdof = temperature->dof;
|
||||
|
||||
// Compute/set eta-masses:
|
||||
double inv_t_freq2 = 1.0 / (t_freq*t_freq);
|
||||
eta_mass[0] = tdof * boltz * t_target * inv_t_freq2;
|
||||
for( int ich = 1; ich < mtchain; ++ich ){
|
||||
eta_mass[ich] = boltz * t_target * inv_t_freq2;
|
||||
}
|
||||
for( int ich = 1; ich < mtchain; ++ich ){
|
||||
eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1] -
|
||||
boltz * t_target ) / eta_mass[ich];
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
void ManifoldThermostatNH::compute_temp_target()
|
||||
{
|
||||
t_current = temperature->compute_scalar();
|
||||
tdof = temperature->dof;
|
||||
|
||||
double delta = update->ntimestep - update->beginstep;
|
||||
if (delta != 0.0){
|
||||
delta /= update->endstep - update->beginstep;
|
||||
}
|
||||
|
||||
tdof = temperature->dof;
|
||||
t_target = t_start + delta * (t_stop-t_start);
|
||||
ke_target = tdof * boltz * t_target;
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
void ManifoldThermostatNH::nhc_temp_integrate()
|
||||
{
|
||||
int ich;
|
||||
// t_current = temperature->compute_scalar();
|
||||
// tdof = temperature->dof;
|
||||
compute_temp_target();
|
||||
|
||||
double expfac, kecurrent = tdof * boltz * t_current;
|
||||
double inv_t_freq2 = 1.0 / (t_freq*t_freq);
|
||||
eta_mass[0] = tdof * boltz * t_target * inv_t_freq2;
|
||||
for( int ich = 1; ich < mtchain; ++ich ){
|
||||
eta_mass[ich] = boltz * t_target * inv_t_freq2;
|
||||
}
|
||||
|
||||
if( eta_mass[0] > 0.0 ){
|
||||
eta_dotdot[0] = (kecurrent - ke_target)/eta_mass[0];
|
||||
}else{
|
||||
eta_dotdot[0] = 0;
|
||||
}
|
||||
|
||||
for( ich = mtchain-1; ich > 0; --ich ){
|
||||
expfac = exp(-dt8*eta_dot[ich+1]);
|
||||
eta_dot[ich] *= expfac;
|
||||
eta_dot[ich] += eta_dotdot[ich] * dt4;
|
||||
eta_dot[ich] *= tdrag_factor * expfac;
|
||||
|
||||
}
|
||||
|
||||
expfac = exp(-dt8*eta_dot[1]);
|
||||
eta_dot[0] *= expfac;
|
||||
eta_dot[0] += eta_dotdot[0] * dt4;
|
||||
eta_dot[0] *= tdrag_factor * expfac;
|
||||
|
||||
factor_eta = exp(-dthalf*eta_dot[0]);
|
||||
|
||||
|
||||
if( factor_eta == 0 ){
|
||||
char msg[2048];
|
||||
sprintf(msg, "WTF, factor_eta is 0! dthalf = %f, eta_dot[0] = %f",
|
||||
dthalf, eta_dot[0]);
|
||||
error->all(FLERR,msg);
|
||||
}
|
||||
|
||||
nh_v_temp();
|
||||
|
||||
t_current *= factor_eta*factor_eta;
|
||||
kecurrent = tdof * boltz * t_current;
|
||||
if( eta_mass[0] > 0.0 ){
|
||||
eta_dotdot[0] = (kecurrent - ke_target) / eta_mass[0];
|
||||
}else{
|
||||
eta_dotdot[0] = 0.0;
|
||||
}
|
||||
|
||||
for( int ich = 1; ich < mtchain; ++ich ){
|
||||
eta[ich] += dthalf*eta_dot[ich];
|
||||
}
|
||||
eta_dot[0] *= expfac;
|
||||
eta_dot[0] += eta_dotdot[0]*dt4;
|
||||
eta_dot[0] *= expfac;
|
||||
|
||||
for( int ich = 1; ich < mtchain; ++ich ){
|
||||
expfac = exp(-dt8*eta_dot[ich+1]);
|
||||
eta_dot[ich] *= expfac;
|
||||
eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1]
|
||||
- boltz*t_target) / eta_mass[ich];
|
||||
eta_dot[ich] *= eta_dotdot[ich] * dt4;
|
||||
eta_dot[ich] *= expfac;
|
||||
}
|
||||
}
|
||||
|
||||
void ManifoldThermostatNH::nh_v_temp()
|
||||
{
|
||||
double **v = atom->v;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if( igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
if( which == NOBIAS ){
|
||||
for( int i = 0; i < nlocal; ++i ){
|
||||
if( mask[i] & groupbit ){
|
||||
v[i][0] *= factor_eta;
|
||||
v[i][1] *= factor_eta;
|
||||
v[i][2] *= factor_eta;
|
||||
}
|
||||
}
|
||||
}else if( which == BIAS ){
|
||||
for( int i = 0; i < nlocal; ++i ){
|
||||
if( mask[i] & groupbit ){
|
||||
temperature->remove_bias(i,v[i]);
|
||||
v[i][0] *= factor_eta;
|
||||
v[i][1] *= factor_eta;
|
||||
v[i][2] *= factor_eta;
|
||||
temperature->restore_bias(i,v[i]);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
void ManifoldThermostatNH::print_stats( const char *header )
|
||||
{
|
||||
|
||||
}
|
||||
|
||||
|
||||
void ManifoldThermostatNH::reset_dt()
|
||||
{
|
||||
dthalf = 0.5 * update->dt;
|
||||
dt4 = 0.25 * update->dt;
|
||||
dt8 = 0.125 * update->dt;
|
||||
tdrag_factor = 1.0 - (update->dt * t_freq * drag);
|
||||
}
|
||||
|
||||
|
||||
void ManifoldThermostatNH::print_stuff()
|
||||
{
|
||||
if( comm->me != 0 ) return;
|
||||
fprintf(screen, "\n\n********* Thermostat settings ************\n");
|
||||
fprintf(screen, "Target temperature is %f\n", t_target);
|
||||
|
||||
fprintf(screen, "\n\n******************************************\n\n\n");
|
||||
}
|
||||
|
||||
void ManifoldThermostatNH::update_t_current()
|
||||
{
|
||||
if (which == BIAS && neighbor->ago == 0)
|
||||
t_current = temperature->compute_scalar();
|
||||
}
|
||||
91
src/USER-MANIFOLD/manifold_thermostat_nh.h
Normal file
91
src/USER-MANIFOLD/manifold_thermostat_nh.h
Normal file
@ -0,0 +1,91 @@
|
||||
/* ----------------------------------------------------------------------
|
||||
Lammps - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
http://lammps.sandia.gov, Sandia National Laboratories
|
||||
Steve Plimpton, sjplimp@sandia.gov
|
||||
|
||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
-----------------------------------------------------------------------
|
||||
|
||||
This file is a part of the USER-MANIFOLD package.
|
||||
|
||||
Copyright (2013-2015) Stefan Paquay, Eindhoven University of Technology.
|
||||
License: GNU General Public License v.2
|
||||
|
||||
See the README file in the top-level LAMMPS directory.
|
||||
|
||||
This file is part of the user-manifold package written by
|
||||
Stefan Paquay at the Eindhoven University of Technology.
|
||||
This module makes it possible to do MD with particles constrained
|
||||
to pretty arbitrary manifolds characterised by some constraint function
|
||||
g(x,y,z) = 0 and its normal grad(g). The number of manifolds available
|
||||
right now is limited but can be extended straightforwardly by making
|
||||
a new class that inherits from manifold and implements all pure virtual
|
||||
methods.
|
||||
|
||||
Thanks to Remy Kusters for beta-testing!
|
||||
|
||||
------------------------------------------------------------------------- */
|
||||
|
||||
#ifndef LMP_MANIFOLD_THERMOSTAT_NH_H
|
||||
#define LMP_MANIFOLD_THERMOSTAT_NH_H
|
||||
|
||||
#include "pointers.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class ManifoldThermostatNH : protected Pointers {
|
||||
public:
|
||||
|
||||
ManifoldThermostatNH(LAMMPS *, int&, char ***, const char *,
|
||||
int, int, int );
|
||||
~ManifoldThermostatNH();
|
||||
|
||||
int parse_arg( int , int &, char *** );
|
||||
int is_legal_keyword( const char * );
|
||||
double memory_usage();
|
||||
|
||||
void print_stats( const char * );
|
||||
void init();
|
||||
void setup(int);
|
||||
void compute_temp_target();
|
||||
void nhc_temp_integrate();
|
||||
void nh_v_temp();
|
||||
void reset_dt();
|
||||
|
||||
int nevery;
|
||||
|
||||
void print_stuff();
|
||||
void update_t_current();
|
||||
|
||||
private:
|
||||
// Fix NVT needs more params for Nose-Hoover chain
|
||||
double dthalf, dt4, dt8;
|
||||
|
||||
char *id_temp;
|
||||
class Compute* temperature;
|
||||
double t_start,t_stop, t_period;
|
||||
double t_current,t_target,ke_target;
|
||||
double t_freq, drag, tdrag_factor;
|
||||
double boltz,nktv2p,tdof;
|
||||
double *eta,*eta_dot;
|
||||
double *eta_dotdot;
|
||||
double *eta_mass;
|
||||
int mtchain;
|
||||
double factor_eta;
|
||||
int which, got_temp;
|
||||
|
||||
const char *fix_id;
|
||||
|
||||
int igroup, groupbit;
|
||||
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
|
||||
#endif // LMP_MANIFOLD_THERMOSTAT_NH_H
|
||||
619
src/USER-MANIFOLD/manifold_thylakoid.cpp
Normal file
619
src/USER-MANIFOLD/manifold_thylakoid.cpp
Normal file
@ -0,0 +1,619 @@
|
||||
#include "manifold_thylakoid.h"
|
||||
#include "math.h"
|
||||
|
||||
#include "comm.h"
|
||||
#include "domain.h" // For some checks regarding the simulation box.
|
||||
|
||||
|
||||
#define MANIFOLD_THYLAKOID_DEBUG
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
||||
manifold_thylakoid::manifold_thylakoid( LAMMPS *lmp, int narg, char ** arg)
|
||||
: Pointers(lmp)
|
||||
{
|
||||
// You can NOT depend on proper construction of the domains in
|
||||
// the constructor, because the params are set by the function that
|
||||
// calls the factory-construction method. Instead, the constructing
|
||||
// fix should call post_param_init();
|
||||
}
|
||||
|
||||
|
||||
|
||||
manifold_thylakoid::~manifold_thylakoid()
|
||||
{
|
||||
for( std::size_t i = 0; i < parts.size(); ++i ){
|
||||
delete parts[i];
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
void manifold_thylakoid::post_param_init()
|
||||
{
|
||||
// Set coefficients:
|
||||
lT = 3; // Radius of cylinder edges of stacks
|
||||
LT = 15; // Size of faces of cylinder stacks
|
||||
pad = 3; // Padding to prevent improper look-ups
|
||||
wB = 3.0;
|
||||
LB = 10.0;
|
||||
lB = 3.0;
|
||||
|
||||
wB = params[0];
|
||||
LB = params[1];
|
||||
lB = params[2];
|
||||
|
||||
if( comm->me == 0 ){
|
||||
fprintf(screen,"My params are now: lT = %f, LT = %f, pad = %f, "
|
||||
"wB = %f, LB = %f, lB = %f\n", lT, LT, pad, wB, LB, lB );
|
||||
fprintf(screen,"Calling init_domains() from post_param_init().\n");
|
||||
}
|
||||
init_domains();
|
||||
checkup();
|
||||
}
|
||||
|
||||
void manifold_thylakoid::checkup()
|
||||
{
|
||||
if( comm->me == 0 ){
|
||||
fprintf(screen,"This is checkup of thylakoid %p\n", this);
|
||||
fprintf(screen,"I have %ld parts. They are:\n", parts.size());
|
||||
for( int i = 0; i < parts.size(); ++i ){
|
||||
fprintf(screen, "[%f, %f] x [%f, %f] x [%f, %f]\n",
|
||||
parts[i]->xlo, parts[i]->xhi,
|
||||
parts[i]->ylo, parts[i]->yhi,
|
||||
parts[i]->zlo, parts[i]->zhi );
|
||||
}
|
||||
fprintf(screen,"My params are:\n");
|
||||
for( int i = 0; i < NPARAMS; ++i ){
|
||||
fprintf(screen,"%f\n", params[i]);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
double manifold_thylakoid::g( const double *x )
|
||||
{
|
||||
int err = 0;
|
||||
std::size_t idx;
|
||||
thyla_part *p = get_thyla_part(x,&err,&idx);
|
||||
if(err){
|
||||
char msg[2048];
|
||||
sprintf(msg,"Error getting thyla_part for x = (%f, %f, %f)",x[0],x[1],x[2]);
|
||||
error->one(FLERR,msg);
|
||||
}
|
||||
double con_val = p->g(x);
|
||||
if( isfinite(con_val) ){
|
||||
return con_val;
|
||||
}else{
|
||||
char msg[2048];
|
||||
sprintf(msg,"Error, thyla_part of type %s returned %f as constraint val!",
|
||||
p->type, con_val);
|
||||
error->one(FLERR,msg);
|
||||
return 0;
|
||||
}
|
||||
}
|
||||
|
||||
void manifold_thylakoid::n( const double *x, double *n )
|
||||
{
|
||||
int err = 0;
|
||||
std::size_t idx;
|
||||
thyla_part *p = get_thyla_part(x,&err,&idx);
|
||||
if(err){
|
||||
char msg[2048];
|
||||
sprintf(msg,"Error getting thyla_part for x = (%f, %f, %f)",x[0],x[1],x[2]);
|
||||
error->one(FLERR,msg);
|
||||
}
|
||||
p->n(x,n);
|
||||
if( isfinite(n[0]) && isfinite(n[1]) && isfinite(n[2]) ){
|
||||
return;
|
||||
}else{
|
||||
char msg[2048];
|
||||
sprintf(msg,"Error, thyla_part of type %s returned (%f,%f,%f) as gradient!",
|
||||
p->type, n[0], n[1], n[2]);
|
||||
error->one(FLERR,msg);
|
||||
}
|
||||
}
|
||||
|
||||
thyla_part *manifold_thylakoid::get_thyla_part( const double *x, int *err_flag, std::size_t *idx )
|
||||
{
|
||||
|
||||
for( std::size_t i = 0; i < parts.size(); ++i ){
|
||||
thyla_part *p = parts[i];
|
||||
if( is_in_domain(p,x) ){
|
||||
if( idx != NULL ) *idx = i;
|
||||
return p;
|
||||
}
|
||||
}
|
||||
char msg[2048];
|
||||
sprintf(msg,"Could not find thyla_part for x = (%f,%f,%f)", x[0],x[1],x[2]);
|
||||
error->one(FLERR,msg);
|
||||
return NULL;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
void manifold_thylakoid::init_domains()
|
||||
{
|
||||
if( wB + 2*lB > LT ){
|
||||
char msg[2048];
|
||||
sprintf(msg,"LT = %f not large enough to accomodate bridge with "
|
||||
"wB = %f and lB = %f! %f > %f\n", LT, wB, lB, wB + 2*lB, LT);
|
||||
error->one(FLERR,msg);
|
||||
}
|
||||
|
||||
// Determine some constant coordinates:
|
||||
x0 = -( 0.5*LB + lB + lT + LT + lT + pad);
|
||||
y0 = -( 0.5*LT + lT + pad );
|
||||
z0 = -15;
|
||||
#ifdef MANIFOLD_THYLAKOID_DEBUG
|
||||
if( comm->me == 0 ){
|
||||
fprintf(screen,"x0, y0, z0 = %f, %f, %f\n",x0,y0,z0);
|
||||
}
|
||||
#endif // MANIFOLD_THYLAKOID_DEBUG
|
||||
|
||||
#ifndef USE_PHONY_LAMMPS
|
||||
if( x0 < domain->boxlo[0] ){
|
||||
char msg[2048];
|
||||
sprintf(msg,"Thylakoid expects xlo of at most %f, but found %f",
|
||||
x0, domain->boxlo[0]);
|
||||
error->one(FLERR,msg);
|
||||
}
|
||||
if( y0 < domain->boxlo[1] ){
|
||||
char msg[2048];
|
||||
sprintf(msg,"Thylakoid expects ylo of at most %f, but found %f",
|
||||
y0, domain->boxlo[1]);
|
||||
error->one(FLERR,msg);
|
||||
}
|
||||
#endif
|
||||
|
||||
// Add some padding to prevent improper lookups.
|
||||
z0 -= pad;
|
||||
|
||||
x1 = -x0;
|
||||
y1 = -y0;
|
||||
z1 = -z0;
|
||||
|
||||
Lx = x1 - x0;
|
||||
Ly = y1 - y0;
|
||||
Lz = z1 - z0;
|
||||
|
||||
#ifndef USE_PHONY_LAMMPS
|
||||
char msg[2048];
|
||||
if(x1 > domain->boxhi[0]){
|
||||
sprintf(msg,"Expected xhi larger than current box has: %f > %f",
|
||||
x1, domain->boxhi[0]);
|
||||
error->one(FLERR,msg);
|
||||
}
|
||||
if(y1 > domain->boxhi[1]){
|
||||
sprintf(msg,"Expected yhi larger than current box has: %f > %f",
|
||||
y1, domain->boxhi[1]);
|
||||
error->one(FLERR,msg);
|
||||
}
|
||||
// if(z1 > domain->boxhi[2]){
|
||||
// sprintf(msg,"Expected zhi larger than current box has: %f > %f",
|
||||
// z1, domain->boxhi[2]);
|
||||
// error->one(FLERR,msg);
|
||||
// }
|
||||
#endif
|
||||
|
||||
// Create and add the manifold parts to the array.
|
||||
thyla_part *p;
|
||||
|
||||
|
||||
// Determine coordinates of domain boundaries and centres of "mass":
|
||||
thyla_part_geom cllb, cllt, clrb, clrt; // Left thylakoid cylinder parts
|
||||
thyla_part_geom pll, plb, plt, plr; // Left thylakoid plane parts
|
||||
|
||||
thyla_part_geom crlb, crlt, crrb, crrt; // Right thylakoid cylinder parts
|
||||
thyla_part_geom prl, prb, prt, prr; // Right thylakoid plane parts
|
||||
|
||||
thyla_part_geom bl, br, bc; // Bridge left, right connectors and cylinder.
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
// The bridge is three parts.
|
||||
// 1. A connector between the right face of the left grana and a cylinder
|
||||
// 2. A connector between the left face of the right grana and a cylinder
|
||||
// 3. The aforementioned cylinder.
|
||||
|
||||
// 1.:
|
||||
// Args: pt, X0, R0, R, x0, y0, z0, sign
|
||||
double rB = 0.5*wB;
|
||||
double Reff = rB + lB;
|
||||
double safety_fac = 1.0;
|
||||
bl.pt[0] = -0.5*LB;
|
||||
bl.pt[1] = 0;
|
||||
bl.pt[2] = 0;
|
||||
|
||||
bl.lo[0] = bl.pt[0] - safety_fac*lB;
|
||||
bl.lo[1] = -(1.0 + safety_fac) * Reff;
|
||||
bl.lo[2] = -(1.0 + safety_fac) * Reff;
|
||||
|
||||
bl.hi[0] = bl.pt[0];
|
||||
bl.hi[1] = (1.0 + safety_fac) * Reff;
|
||||
bl.hi[2] = (1.0 + safety_fac) * Reff;
|
||||
|
||||
// double X0, double R0, double R, double s,
|
||||
#ifdef MANIFOLD_THYLAKOID_DEBUG
|
||||
if( comm->me == 0 ){
|
||||
fprintf(screen,"x0, r0, R = %f, %f, %f\n", bl.pt[0], rB, lB);
|
||||
}
|
||||
#endif // MANIFOLD_THYLAKOID_DEBUG
|
||||
p = make_cyl_to_plane_part(bl.pt[0], rB, lB, -1, bl.pt);
|
||||
set_domain(p, bl.lo, bl.hi);
|
||||
parts.push_back(p);
|
||||
|
||||
// 2.:
|
||||
br.pt[0] = 0.5*LB;
|
||||
br.pt[1] = 0;
|
||||
br.pt[2] = 0;
|
||||
|
||||
br.lo[0] = br.pt[0];
|
||||
br.lo[1] = -(1.0 + safety_fac) * Reff;
|
||||
br.lo[2] = -(1.0 + safety_fac) * Reff;
|
||||
|
||||
br.hi[0] = br.pt[0] + safety_fac*lB;
|
||||
br.hi[1] = (1.0 + safety_fac) * Reff;
|
||||
br.hi[2] = (1.0 + safety_fac) * Reff;
|
||||
|
||||
// double X0, double R0, double R, double s,
|
||||
#ifdef MANIFOLD_THYLAKOID_DEBUG
|
||||
if( comm->me == 0 ){
|
||||
fprintf(screen,"x0, r0, R = %f, %f, %f\n", br.pt[0], rB, lB);
|
||||
}
|
||||
#endif // MANIFOLD_THYLAKOID_DEBUG
|
||||
p = make_cyl_to_plane_part(br.pt[0], rB, lB, 1, br.pt);
|
||||
set_domain(p, br.lo, br.hi);
|
||||
parts.push_back(p);
|
||||
|
||||
|
||||
|
||||
// 3.:
|
||||
// Cylinder in between:
|
||||
bc.pt[0] = 0;
|
||||
bc.pt[1] = 0;
|
||||
bc.pt[2] = 0;
|
||||
|
||||
bc.lo[0] = bl.pt[0];
|
||||
bc.lo[1] = -Reff;
|
||||
bc.lo[2] = -Reff;
|
||||
|
||||
bc.hi[0] = br.pt[0];
|
||||
bc.hi[1] = Reff;
|
||||
bc.hi[2] = Reff;
|
||||
|
||||
p = make_cyl_part( 0, 1, 1, bc.pt, rB );
|
||||
set_domain( p, bc.lo, bc.hi );
|
||||
#ifdef MANIFOLD_THYLAKOID_DEBUG
|
||||
if( comm->me == 0 ){
|
||||
fprintf(screen,"Cylinder lives on [ %f x %f ] x [ %f x %f ] x [ %f x %f]\n",
|
||||
bc.lo[0], bc.hi[0], bc.lo[1], bc.hi[1], bc.lo[2], bc.hi[2]);
|
||||
}
|
||||
#endif // MANIFOLD_THYLAKOID_DEBUG
|
||||
|
||||
parts.push_back(p);
|
||||
|
||||
|
||||
// The stack on the left:
|
||||
cllb.lo[0] = x0;
|
||||
cllb.lo[1] = y0;
|
||||
cllb.lo[2] = z0;
|
||||
cllb.pt[0] = x0 + pad + lT;
|
||||
cllb.pt[1] = y0 + pad + lT;
|
||||
cllb.pt[2] = 0;
|
||||
cllb.hi[0] = cllb.pt[0];
|
||||
cllb.hi[1] = cllb.pt[1];
|
||||
cllb.hi[2] = z1;
|
||||
|
||||
p = make_cyl_part(1,1,0,cllb.pt,lT);
|
||||
set_domain(p, cllb.lo, cllb.hi);
|
||||
parts.push_back(p);
|
||||
|
||||
// left left top cylinder
|
||||
cllt = cllb;
|
||||
cllt.lo[1] = y1 - pad - lT;
|
||||
cllt.hi[1] = y1;
|
||||
cllt.pt[1] = cllb.pt[1] + LT;
|
||||
|
||||
p = make_cyl_part(1,1,0,cllt.pt,lT);
|
||||
set_domain(p, cllt.lo, cllt.hi);
|
||||
parts.push_back(p);
|
||||
|
||||
// left right bottom cylinder
|
||||
clrb = cllb;
|
||||
clrb.pt[0] += LT;
|
||||
clrb.lo[0] = clrb.pt[0];
|
||||
clrb.hi[0] = clrb.lo[0] + lT + lB;
|
||||
|
||||
p = make_cyl_part(1,1,0,clrb.pt,lT);
|
||||
set_domain(p, clrb.lo, clrb.hi);
|
||||
parts.push_back(p);
|
||||
|
||||
// left right top cylinder
|
||||
clrt = clrb;
|
||||
clrt.pt[1] += LT;
|
||||
clrt.lo[1] = y1 - pad - lT;
|
||||
clrt.hi[1] = y1;
|
||||
|
||||
p = make_cyl_part(1,1,0,clrt.pt,lT);
|
||||
set_domain(p, clrt.lo, clrt.hi);
|
||||
parts.push_back(p);
|
||||
|
||||
|
||||
// left left plane
|
||||
pll.pt[0] = x0 + pad;
|
||||
pll.pt[1] = 0;
|
||||
pll.pt[2] = 0;
|
||||
pll.lo[0] = x0;
|
||||
pll.lo[1] = cllb.pt[1];
|
||||
pll.lo[2] = z0;
|
||||
pll.hi[0] = pll.lo[0] + pad + lT;
|
||||
pll.hi[1] = pll.lo[1] + LT;
|
||||
pll.hi[2] = z1;
|
||||
|
||||
p = make_plane_part(1,0,0,pll.pt);
|
||||
set_domain(p, pll.lo, pll.hi);
|
||||
parts.push_back(p);
|
||||
|
||||
// left bottom plane
|
||||
plb.pt[0] = x0 + pad + lT + 0.5*LT;
|
||||
plb.pt[1] = y0 + pad;
|
||||
plb.pt[2] = 0;
|
||||
plb.lo[0] = x0 + pad + lT;
|
||||
plb.lo[1] = y0;
|
||||
plb.lo[2] = z0;
|
||||
plb.hi[0] = plb.lo[0] + LT;
|
||||
plb.hi[1] = plb.lo[1] + pad + lT;
|
||||
plb.hi[2] = z1;
|
||||
|
||||
p = make_plane_part(0,1,0,plb.pt);
|
||||
set_domain(p, plb.lo, plb.hi);
|
||||
parts.push_back(p);
|
||||
|
||||
// left top plane
|
||||
plt = plb;
|
||||
plt.lo[1] = cllb.pt[1] + LT;
|
||||
plt.hi[1] = y1;
|
||||
plt.pt[1] = y1 - pad;
|
||||
|
||||
p = make_plane_part(0,1,0,plt.pt);
|
||||
set_domain(p, plt.lo, plt.hi);
|
||||
parts.push_back(p);
|
||||
|
||||
// left right plane
|
||||
plr = pll;
|
||||
plr.lo[0] = bl.lo[0] - 0.5;
|
||||
plr.lo[1] = y0 - pad;
|
||||
plr.hi[0] = bl.lo[0] + 0.5;
|
||||
plr.hi[1] = y1 + pad;
|
||||
plr.pt[0] = bl.pt[0] - lB;
|
||||
plr.pt[1] = 0.0;
|
||||
plr.pt[2] = 0.0;
|
||||
plr.hi[2] = z1 + pad;
|
||||
plr.lo[2] = z0 - pad;
|
||||
|
||||
p = make_plane_part(1,0,0,plr.pt);
|
||||
set_domain(p, plr.lo, plr.hi);
|
||||
parts.push_back(p);
|
||||
|
||||
// Check if this plane lines up with bl:
|
||||
if( fabs(plr.pt[0] - bl.pt[0] + lB) > 1e-8 ){
|
||||
char msg[2048];
|
||||
sprintf(msg,"Origins of plane left right and bridge left misaligned! %f != %f!\n",
|
||||
plr.pt[0], bl.pt[0] - lB );
|
||||
error->one(FLERR,msg);
|
||||
}
|
||||
|
||||
// Now, for the right stack, you can mirror the other...
|
||||
// To mirror them you need to invert lo[0] and hi[0] and flip their sign.
|
||||
|
||||
thyla_part_geom::mirror(thyla_part_geom::DIR_X, &crlb, &cllb);
|
||||
p = make_cyl_part(1,1,0,crlb.pt,lT);
|
||||
set_domain(p, crlb.lo, crlb.hi);
|
||||
parts.push_back(p);
|
||||
|
||||
thyla_part_geom::mirror(thyla_part_geom::DIR_X, &crlt, &cllt);
|
||||
p = make_cyl_part(1,1,0,crlt.pt,lT);
|
||||
set_domain(p, crlt.lo, crlt.hi);
|
||||
parts.push_back(p);
|
||||
|
||||
thyla_part_geom::mirror(thyla_part_geom::DIR_X, &crrb, &clrb);
|
||||
p = make_cyl_part(1,1,0,crrb.pt,lT);
|
||||
set_domain(p, crrb.lo, crrb.hi);
|
||||
parts.push_back(p);
|
||||
|
||||
thyla_part_geom::mirror(thyla_part_geom::DIR_X, &crrt, &clrt);
|
||||
p = make_cyl_part(1,1,0,crrt.pt,lT);
|
||||
set_domain(p, crrt.lo, crrt.hi);
|
||||
parts.push_back(p);
|
||||
|
||||
|
||||
|
||||
thyla_part_geom::mirror(thyla_part_geom::DIR_X, &prl , &pll );
|
||||
p = make_plane_part(1,0,0,prl.pt);
|
||||
set_domain(p, prl.lo, prl.hi);
|
||||
parts.push_back(p);
|
||||
|
||||
thyla_part_geom::mirror(thyla_part_geom::DIR_X, &prb , &plb );
|
||||
p = make_plane_part(0,1,0,prb.pt);
|
||||
set_domain(p, prb.lo, prb.hi);
|
||||
parts.push_back(p);
|
||||
|
||||
thyla_part_geom::mirror(thyla_part_geom::DIR_X, &prt , &plt );
|
||||
p = make_plane_part(0,1,0,prt.pt);
|
||||
set_domain(p, prt.lo, prt.hi);
|
||||
parts.push_back(p);
|
||||
|
||||
// Careful, this one is wrongly named.
|
||||
thyla_part_geom::mirror(thyla_part_geom::DIR_X, &prr, &plr);
|
||||
p = make_plane_part(1,0,0,prr.pt);
|
||||
set_domain(p, prr.lo, prr.hi);
|
||||
parts.push_back(p);
|
||||
|
||||
if( fabs(prr.pt[0] - br.pt[0] - lB) > 1e-8 ){
|
||||
char msg[2048];
|
||||
sprintf(msg,"Origins of plane left right and bridge left misaligned! %f != %f!\n",
|
||||
prr.pt[0], br.pt[0] + lB);
|
||||
error->one(FLERR,msg);
|
||||
}
|
||||
|
||||
// For debugging, print the domains and coms:
|
||||
#ifdef MANIFOLD_THYLAKOID_DEBUG
|
||||
if( comm->me == 0 ){
|
||||
FILE *fp_doms = fopen("test_doms.dat","w");
|
||||
FILE *fp_coms = fopen("test_coms.dat","w");
|
||||
print_part_data(fp_doms, fp_coms);
|
||||
fclose(fp_doms);
|
||||
fclose(fp_coms);
|
||||
}
|
||||
#endif // MANIFOLD_THYLAKOID_DEBUG
|
||||
}
|
||||
|
||||
|
||||
void manifold_thylakoid::set_domain( thyla_part *p, const std::vector<double> &lo,
|
||||
const std::vector<double> &hi )
|
||||
{
|
||||
#ifdef MANIFOLD_THYLAKOID_DEBUG
|
||||
if( comm->me == 0 ){
|
||||
fprintf(screen,"Adding part with domain [%f, %f] x [%f, %f] x [%f, %f]\n",
|
||||
lo[0],hi[0],lo[1],hi[1],lo[2],hi[2] );
|
||||
}
|
||||
#endif // MANIFOLD_THYLAKOID_DEBUG
|
||||
if( lo[0] >= hi[0] ){
|
||||
char msg[2048];
|
||||
sprintf(msg,"xlo >= xhi (%f >= %f)",lo[0],hi[0]);
|
||||
error->one(FLERR,msg);
|
||||
}else if( lo[1] >= hi[1] ){
|
||||
char msg[2048];
|
||||
sprintf(msg,"ylo >= yhi (%f >= %f)",lo[1],hi[1]);
|
||||
error->one(FLERR,msg);
|
||||
}else if( lo[2] >= hi[2] ){
|
||||
char msg[2048];
|
||||
sprintf(msg,"zlo >= zhi (%f >= %f)",lo[2],hi[2]);
|
||||
error->one(FLERR,msg);
|
||||
}
|
||||
p->xlo = lo[0];
|
||||
p->ylo = lo[1];
|
||||
p->zlo = lo[2];
|
||||
|
||||
p->xhi = hi[0];
|
||||
p->yhi = hi[1];
|
||||
p->zhi = hi[2];
|
||||
}
|
||||
|
||||
int manifold_thylakoid::is_in_domain( thyla_part *part, const double *x )
|
||||
{
|
||||
bool domain_ok = (x[0] >= part->xlo) && (x[0] <= part->xhi) &&
|
||||
(x[1] >= part->ylo) && (x[1] <= part->yhi) &&
|
||||
(x[2] >= part->zlo) && (x[2] <= part->zhi);
|
||||
|
||||
if( !domain_ok ) return false;
|
||||
|
||||
// From here on out, domain is ok.
|
||||
|
||||
if( part->type == thyla_part::THYLA_TYPE_CYL_TO_PLANE ){
|
||||
|
||||
double R0 = part->params[1];
|
||||
double R = part->params[2];
|
||||
double X0 = part->params[0];
|
||||
double y = x[1];
|
||||
double z = x[2];
|
||||
double dist2 = y*y + z*z;
|
||||
double RR = R0+R;
|
||||
double RR2 = RR*RR;
|
||||
double s = part->params[6];
|
||||
|
||||
|
||||
|
||||
if( dist2 < RR2 ){
|
||||
return true;
|
||||
}else{
|
||||
// Domain was ok, but radius not.
|
||||
return false;
|
||||
}
|
||||
}else{
|
||||
return true;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
thyla_part *manifold_thylakoid::make_plane_part (double a, double b, double c,
|
||||
const std::vector<double> &pt )
|
||||
{
|
||||
double args[7];
|
||||
args[0] = a;
|
||||
args[1] = b;
|
||||
args[2] = c;
|
||||
args[3] = pt[0];
|
||||
args[4] = pt[1];
|
||||
args[5] = pt[2];
|
||||
thyla_part *p = new thyla_part(thyla_part::THYLA_TYPE_PLANE,args,0,0,0,0,0,0);
|
||||
return p;
|
||||
}
|
||||
|
||||
thyla_part *manifold_thylakoid::make_cyl_part (double a, double b, double c,
|
||||
const std::vector<double> &pt, double R)
|
||||
{
|
||||
double args[7];
|
||||
args[0] = a;
|
||||
args[1] = b;
|
||||
args[2] = c;
|
||||
args[3] = pt[0];
|
||||
args[4] = pt[1];
|
||||
args[5] = pt[2];
|
||||
args[6] = R;
|
||||
thyla_part *p = new thyla_part(thyla_part::THYLA_TYPE_CYL,args,0,0,0,0,0,0);
|
||||
return p;
|
||||
}
|
||||
|
||||
|
||||
thyla_part *manifold_thylakoid::make_sphere_part(const std::vector<double> &pt, double R)
|
||||
{
|
||||
double args[7];
|
||||
args[0] = R;
|
||||
args[1] = pt[0];
|
||||
args[2] = pt[1];
|
||||
args[3] = pt[2];
|
||||
thyla_part *p = new thyla_part(thyla_part::THYLA_TYPE_SPHERE,args,0,0,0,0,0,0);
|
||||
return p;
|
||||
}
|
||||
|
||||
|
||||
thyla_part *manifold_thylakoid::make_cyl_to_plane_part(double X0, double R0, double R,
|
||||
double s, const std::vector<double> &pt )
|
||||
{
|
||||
double args[7];
|
||||
args[0] = X0;
|
||||
args[1] = R0;
|
||||
args[2] = R;
|
||||
args[3] = pt[0];
|
||||
args[4] = pt[1];
|
||||
args[5] = pt[2];
|
||||
args[6] = s;
|
||||
thyla_part *p = new thyla_part(thyla_part::THYLA_TYPE_CYL_TO_PLANE,args,0,0,0,0,0,0);
|
||||
return p;
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
void manifold_thylakoid::print_part_data( FILE *fp_doms, FILE *fp_coms )
|
||||
{
|
||||
for( std::size_t i = 0; i < parts.size(); ++i ){
|
||||
thyla_part *p = parts[i];
|
||||
fprintf(fp_doms, "%f %f\n", p->xlo, p->ylo);
|
||||
fprintf(fp_doms, "%f %f\n", p->xlo, p->yhi);
|
||||
fprintf(fp_doms, "%f %f\n", p->xhi, p->yhi);
|
||||
fprintf(fp_doms, "%f %f\n", p->xhi, p->ylo);
|
||||
fprintf(fp_doms, "%f %f\n\n",p->xlo, p->ylo);
|
||||
fprintf(fp_coms, "%f %f\n", p->x0, p->y0 );
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
101
src/USER-MANIFOLD/manifold_thylakoid.h
Normal file
101
src/USER-MANIFOLD/manifold_thylakoid.h
Normal file
@ -0,0 +1,101 @@
|
||||
#ifndef LMP_MANIFOLD_THYLAKOID_H
|
||||
#define LMP_MANIFOLD_THYLAKOID_H
|
||||
|
||||
#include "manifold.h"
|
||||
|
||||
#include <cassert>
|
||||
#include <vector>
|
||||
|
||||
#include "manifold_thylakoid_shared.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
using LAMMPS_NS::thyla_part;
|
||||
using LAMMPS_NS::thyla_part_geom;
|
||||
|
||||
|
||||
|
||||
class manifold_thylakoid : public manifold, protected Pointers {
|
||||
public:
|
||||
enum { NPARAMS = 3 };
|
||||
manifold_thylakoid( LAMMPS *lmp, int, char ** );
|
||||
virtual ~manifold_thylakoid();
|
||||
|
||||
virtual double g( const double *x );
|
||||
virtual void n( const double *x, double *n );
|
||||
|
||||
static const char* type(){ return "thylakoid"; }
|
||||
virtual const char *id(){ return type(); }
|
||||
static int expected_argc(){ return NPARAMS; }
|
||||
virtual int nparams(){ return NPARAMS; }
|
||||
|
||||
|
||||
virtual void post_param_init();
|
||||
virtual void checkup(); // Some diagnostics...
|
||||
private:
|
||||
void init_domains();
|
||||
|
||||
thyla_part *get_thyla_part( const double *x, int *err_flag, std::size_t *idx = NULL );
|
||||
int is_in_domain( thyla_part *p, const double *x );
|
||||
void check_overlap();
|
||||
std::vector<thyla_part*> parts;
|
||||
|
||||
thyla_part *make_plane_part (double a, double b, double c,
|
||||
const std::vector<double> &pt);
|
||||
thyla_part *make_cyl_part (double a, double b, double c,
|
||||
const std::vector<double> &pt, double R);
|
||||
thyla_part *make_sphere_part(const std::vector<double> &pt, double R);
|
||||
thyla_part *make_cyl_to_plane_part(double X0, double R0, double R, double s,
|
||||
const std::vector<double> &pt );
|
||||
|
||||
|
||||
void set_domain( thyla_part *p, const std::vector<double> &lo,
|
||||
const std::vector<double> &hi );
|
||||
|
||||
void add_part( thyla_part *part, double x0, double y0,
|
||||
double z0, double x1, double y1, double z1 )
|
||||
{
|
||||
int me = -1;
|
||||
MPI_Comm_rank(world, &me);
|
||||
|
||||
std::vector<double> lo(3), hi(3);
|
||||
lo[0] = x0; lo[1] = y0; lo[2] = z0;
|
||||
hi[0] = x1; hi[1] = y1; hi[2] = z1;
|
||||
|
||||
set_domain(part, lo, hi);
|
||||
parts.push_back( part );
|
||||
|
||||
fprintf(my_screen,"This is proc %d: Added part %p of type %d, "
|
||||
"size is now %lu.\n", me, part, part->type, parts.size());
|
||||
fflush(my_screen);
|
||||
}
|
||||
|
||||
|
||||
void print_part_data( FILE *fp_doms, FILE *fp_coms );
|
||||
|
||||
void assert_part_ok( const thyla_part *part ){
|
||||
if( !part ) error->one(FLERR,"Error! Part was NULL!");
|
||||
}
|
||||
|
||||
|
||||
|
||||
// Coefficients for the thylakoid model. At the moment it is just
|
||||
// a cylinder, we slowly expand it.
|
||||
double pad; // Padding to make sure periodic images are mapped back properly.
|
||||
FILE *my_screen;
|
||||
|
||||
|
||||
double LB, lT, lB, wB, LT;
|
||||
|
||||
// Domain size:
|
||||
double x0, y0, z0;
|
||||
double x1, y1, z1;
|
||||
double Lx, Ly, Lz;
|
||||
};
|
||||
|
||||
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
|
||||
#endif // LMP_MANIFOLD_THYLAKOID_H
|
||||
234
src/USER-MANIFOLD/manifold_thylakoid_shared.cpp
Normal file
234
src/USER-MANIFOLD/manifold_thylakoid_shared.cpp
Normal file
@ -0,0 +1,234 @@
|
||||
#include "manifold_thylakoid_shared.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
||||
|
||||
|
||||
thyla_part::thyla_part( int type, double *args, double xlo, double ylo, double zlo,
|
||||
double xhi, double yhi, double zhi )
|
||||
: type(type), xlo(xlo), xhi(xhi),
|
||||
ylo(ylo), yhi(yhi), zlo(zlo), zhi(zhi),
|
||||
x0( (type == THYLA_TYPE_SPHERE) ? params[1] : params[3] ),
|
||||
y0( (type == THYLA_TYPE_SPHERE) ? params[2] : params[4] ),
|
||||
z0( (type == THYLA_TYPE_SPHERE) ? params[3] : params[5] )
|
||||
{
|
||||
switch(type){
|
||||
case THYLA_TYPE_PLANE: // a*(x-x0) + b*(y-y0) + c*(z-z0) = 0
|
||||
params[0] = args[0]; // a
|
||||
params[1] = args[1]; // b
|
||||
params[2] = args[2]; // c
|
||||
params[3] = args[3]; // x0
|
||||
params[4] = args[4]; // y0
|
||||
params[5] = args[5]; // z0
|
||||
break;
|
||||
case THYLA_TYPE_SPHERE: // (x-x0)^2 + (y-y0)^2 + (z-z0)^2 - R^2 = 0
|
||||
params[0] = args[0]; // R
|
||||
params[1] = args[1]; // x0
|
||||
params[2] = args[2]; // y0
|
||||
params[3] = args[3]; // z0
|
||||
break;
|
||||
case THYLA_TYPE_CYL: // a*(x-x0)^2 + b*(y-y0)^2 + c*(z-z0)^2 - R^2 = 0
|
||||
params[0] = args[0]; // a
|
||||
params[1] = args[1]; // b
|
||||
params[2] = args[2]; // c
|
||||
params[3] = args[3]; // x0
|
||||
params[4] = args[4]; // y0
|
||||
params[5] = args[5]; // z0
|
||||
params[6] = args[6]; // R
|
||||
if( (args[0] != 0.0) && (args[1] != 0.0) && (args[2] != 0.0) ){
|
||||
err_flag = -1;
|
||||
return;
|
||||
}
|
||||
// The others should be 1.
|
||||
if( (args[0] != 1.0) && (args[0] != 0.0) &&
|
||||
(args[1] != 1.0) && (args[1] != 0.0) &&
|
||||
(args[2] != 1.0) && (args[2] != 0.0) ){
|
||||
err_flag = -1;
|
||||
}
|
||||
break;
|
||||
case THYLA_TYPE_CYL_TO_PLANE:
|
||||
/*
|
||||
* Funky bit that connects a cylinder to a plane.
|
||||
* It is what you get by rotating the equation
|
||||
* r(x) = R0 + R*( 1 - sqrt( 1 - ( ( X0 - x ) /R )^2 ) ) around the x-axis.
|
||||
* I kid you not.
|
||||
*
|
||||
* The shape is symmetric so you have to set whether it is the "left" or
|
||||
* "right" end by truncating it properly. It is designed to run from
|
||||
* X0 to X0 + R if "right" or X0 - R to X0 if "left".
|
||||
*
|
||||
* As params it takes X0, R0, R, and a sign that determines whether it is
|
||||
* "left" (args[3] < 0) or "right" (args[3] > 0).
|
||||
*
|
||||
* The args are: X0, R0, R, x0, y0, z0, sign.
|
||||
*/
|
||||
params[0] = args[0];
|
||||
params[1] = args[1];
|
||||
params[2] = args[2];
|
||||
params[3] = args[3];
|
||||
params[4] = args[4];
|
||||
params[5] = args[5];
|
||||
params[6] = args[6];
|
||||
break;
|
||||
default:
|
||||
err_flag = -1;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
thyla_part::~thyla_part()
|
||||
{}
|
||||
|
||||
double thyla_part::g(const double *x)
|
||||
{
|
||||
switch(type){
|
||||
case THYLA_TYPE_PLANE:{ // a*(x-x0) + b*(y-y0) + c*(z-z0) = 0
|
||||
double a = params[0];
|
||||
double b = params[1];
|
||||
double c = params[2];
|
||||
double dx = x[0] - params[3];
|
||||
double dy = x[1] - params[4];
|
||||
double dz = x[2] - params[5];
|
||||
return a*dx + b*dy + c*dz;
|
||||
break;
|
||||
}
|
||||
case THYLA_TYPE_SPHERE:{ // (x-x0)^2 + (y-y0)^2 + (z-z0)^2 - R^2 = 0
|
||||
double R2 = params[0]*params[0];
|
||||
double dx = x[0] - params[1];
|
||||
double dy = x[1] - params[2];
|
||||
double dz = x[2] - params[3];
|
||||
return dx*dx + dy*dy + dz*dz - R2;
|
||||
|
||||
break;
|
||||
}
|
||||
case THYLA_TYPE_CYL:{ // a*(x-x0)^2 + b*(y-y0)^2 + c*(z-z0)^2 - R^2 = 0
|
||||
double a = params[0];
|
||||
double b = params[1];
|
||||
double c = params[2];
|
||||
double X0 = params[3];
|
||||
double Y0 = params[4];
|
||||
double Z0 = params[5];
|
||||
double R = params[6];
|
||||
double dx = x[0] - X0;
|
||||
double dy = x[1] - Y0;
|
||||
double dz = x[2] - Z0;
|
||||
|
||||
return a*dx*dx + b*dy*dy + c*dz*dz - R*R;
|
||||
break;
|
||||
}
|
||||
case THYLA_TYPE_CYL_TO_PLANE:{
|
||||
double X0 = params[0];
|
||||
double R0 = params[1];
|
||||
double R = params[2];
|
||||
double s = sign(params[6]);
|
||||
|
||||
// Determine the centre of the sphere.
|
||||
double dx = (x[0] - X0);
|
||||
double dyz = sqrt( x[1]*x[1] + x[2]*x[2] );
|
||||
double rdyz = dyz - (R0 + R);
|
||||
double norm = 1.0 / (2.0*R);
|
||||
// Maybe sign is important here...
|
||||
double g = norm*(dx*dx + rdyz*rdyz - R*R);
|
||||
return g;
|
||||
|
||||
}
|
||||
default:
|
||||
err_flag = -1;
|
||||
return 0; // Mostly to get rid of compiler werrors.
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
void thyla_part::n( const double *x, double *n )
|
||||
{
|
||||
switch(type){
|
||||
case THYLA_TYPE_PLANE:{ // a*(x-x0) + b*(y-y0) + c*(z-z0) = 0
|
||||
double a = params[0];
|
||||
double b = params[1];
|
||||
double c = params[2];
|
||||
n[0] = a;
|
||||
n[1] = b;
|
||||
n[2] = c;
|
||||
break;
|
||||
}
|
||||
case THYLA_TYPE_SPHERE:{ // (x-x0)^2 + (y-y0)^2 + (z-z0)^2 - R^2 = 0
|
||||
double dx = x[0] - params[1];
|
||||
double dy = x[1] - params[2];
|
||||
double dz = x[2] - params[3];
|
||||
n[0] = 2*dx;
|
||||
n[1] = 2*dy;
|
||||
n[2] = 2*dz;
|
||||
break;
|
||||
}
|
||||
case THYLA_TYPE_CYL:{ // a*(x-x0)^2 + b*(y-y0)^2 + c*(z-z0)^2 - R^2 = 0
|
||||
double a = params[0];
|
||||
double b = params[1];
|
||||
double c = params[2];
|
||||
double X0 = params[3];
|
||||
double Y0 = params[4];
|
||||
double Z0 = params[5];
|
||||
double R = params[6];
|
||||
double dx = x[0] - X0;
|
||||
double dy = x[1] - Y0;
|
||||
double dz = x[2] - Z0;
|
||||
|
||||
n[0] = 2*a*dx;
|
||||
n[1] = 2*b*dy;
|
||||
n[2] = 2*c*dz;
|
||||
break;
|
||||
}
|
||||
case THYLA_TYPE_CYL_TO_PLANE:{
|
||||
double X0 = params[0];
|
||||
double R0 = params[1];
|
||||
double R = params[2];
|
||||
double s = sign(params[6]);
|
||||
|
||||
// Determine the centre of the sphere.
|
||||
double dx = s*(x[0] - X0);
|
||||
double ryz = sqrt( x[1]*x[1] + x[2]*x[2] );
|
||||
// Maybe sign is important here...
|
||||
// Normalize g and n so that the normal is continuous:
|
||||
double norm = 1.0 / (2.0 * R);
|
||||
double x0[3];
|
||||
x0[0] = X0-R;
|
||||
x0[1] = 0;
|
||||
x0[2] = R0+R;
|
||||
|
||||
n[0] = s*2*dx*norm;
|
||||
|
||||
double const_part = 1.0 - (R0 + R) / ryz;
|
||||
n[1] = 2*x[1]*const_part*norm;
|
||||
n[2] = 2*x[2]*const_part*norm;
|
||||
break;
|
||||
}
|
||||
default:
|
||||
err_flag = -1;
|
||||
break;
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
void thyla_part_geom::mirror( unsigned int axis, thyla_part_geom *m,
|
||||
const thyla_part_geom *o )
|
||||
{
|
||||
// Since dir is already the index of the array this is really simple:
|
||||
m->lo[0] = o->lo[0];
|
||||
m->lo[1] = o->lo[1];
|
||||
m->lo[2] = o->lo[2];
|
||||
m->pt[0] = o->pt[0];
|
||||
m->pt[1] = o->pt[1];
|
||||
m->pt[2] = o->pt[2];
|
||||
m->hi[0] = o->hi[0];
|
||||
m->hi[1] = o->hi[1];
|
||||
m->hi[2] = o->hi[2];
|
||||
|
||||
m->lo[axis] = -o->hi[axis];
|
||||
m->hi[axis] = -o->lo[axis];
|
||||
m->pt[axis] = -o->pt[axis];
|
||||
}
|
||||
|
||||
|
||||
74
src/USER-MANIFOLD/manifold_thylakoid_shared.h
Normal file
74
src/USER-MANIFOLD/manifold_thylakoid_shared.h
Normal file
@ -0,0 +1,74 @@
|
||||
#ifndef MANIFOLD_THYLAKOID_SHARED_H
|
||||
#define MANIFOLD_THYLAKOID_SHARED_H
|
||||
|
||||
|
||||
#include <vector>
|
||||
#include <cassert>
|
||||
#include "math.h"
|
||||
|
||||
|
||||
#include "pointers.h"
|
||||
#include "error.h"
|
||||
#include "lammps.h"
|
||||
#include "manifold.h"
|
||||
|
||||
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
|
||||
// The thylakoid is composed of many parts
|
||||
struct thyla_part {
|
||||
enum thyla_types {
|
||||
THYLA_TYPE_PLANE,
|
||||
THYLA_TYPE_SPHERE,
|
||||
THYLA_TYPE_CYL,
|
||||
THYLA_TYPE_CYL_TO_PLANE
|
||||
};
|
||||
|
||||
thyla_part( int type, double *args, double xlo, double ylo, double zlo,
|
||||
double xhi, double yhi, double zhi );
|
||||
thyla_part() : type(-1), x0(-1337), y0(-1337), z0(-1337){}
|
||||
~thyla_part();
|
||||
|
||||
double g( const double *x );
|
||||
void n( const double *x, double *n );
|
||||
|
||||
int type;
|
||||
double params[7];
|
||||
double tol;
|
||||
int maxit;
|
||||
|
||||
int err_flag;
|
||||
tagint a_id;
|
||||
|
||||
double xlo, xhi, ylo, yhi, zlo, zhi;
|
||||
double x0, y0, z0;
|
||||
|
||||
}; // struct thyla_part
|
||||
|
||||
|
||||
|
||||
struct thyla_part_geom {
|
||||
thyla_part_geom() : pt(3), lo(3), hi(3){}
|
||||
std::vector<double> pt, lo, hi;
|
||||
|
||||
// Function for mirroring thyla_geoms:
|
||||
enum DIRS { DIR_X, DIR_Y, DIR_Z };
|
||||
static void mirror( unsigned int axis, thyla_part_geom *m,
|
||||
const thyla_part_geom *o );
|
||||
|
||||
}; // struct thyla_part_geom
|
||||
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
|
||||
inline double sign( const double x )
|
||||
{
|
||||
return (x > 0.0) ? 1.0 : -1.0;
|
||||
}
|
||||
|
||||
|
||||
|
||||
#endif // MANIFOLD_THYLAKOID_SHARED_H
|
||||
37
src/USER-MANIFOLD/manifold_torus.cpp
Normal file
37
src/USER-MANIFOLD/manifold_torus.cpp
Normal file
@ -0,0 +1,37 @@
|
||||
#include "manifold_torus.h"
|
||||
#include <math.h>
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
manifold_torus::manifold_torus( LAMMPS *lmp, int argc, char **argv ) : Pointers(lmp)
|
||||
{}
|
||||
|
||||
|
||||
double manifold_torus::g( const double *x )
|
||||
{
|
||||
double R = params[0];
|
||||
double r = params[1];
|
||||
if( R < r ){
|
||||
error->all(FLERR,"Large radius < small radius!");
|
||||
}
|
||||
|
||||
double rad = sqrt(x[0]*x[0] + x[1]*x[1]);
|
||||
double c = R - rad;
|
||||
return c*c + x[2]*x[2] - r*r;
|
||||
}
|
||||
|
||||
void manifold_torus::n( const double *x, double *n )
|
||||
{
|
||||
double R = params[0];
|
||||
double r = params[1];
|
||||
if( R < r ){
|
||||
error->all(FLERR,"Large radius < small radius!");
|
||||
}
|
||||
|
||||
double rad = sqrt(x[0]*x[0] + x[1]*x[1]);
|
||||
double c = R - rad;
|
||||
double fac = c / rad;
|
||||
n[0] = -2.0 * fac * x[0];
|
||||
n[1] = -2.0 * fac * x[1];
|
||||
n[2] = 2.0 * x[2];
|
||||
}
|
||||
25
src/USER-MANIFOLD/manifold_torus.h
Normal file
25
src/USER-MANIFOLD/manifold_torus.h
Normal file
@ -0,0 +1,25 @@
|
||||
#ifndef LMP_MANIFOLD_TORUS_H
|
||||
#define LMP_MANIFOLD_TORUS_H
|
||||
|
||||
#include "manifold.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
class manifold_torus : public manifold, protected Pointers {
|
||||
public:
|
||||
enum {NPARAMS=2};
|
||||
manifold_torus( LAMMPS *, int, char ** );
|
||||
~manifold_torus(){}
|
||||
virtual double g( const double *x );
|
||||
virtual void n( const double *x, double *n );
|
||||
|
||||
static const char *type(){ return "torus"; }
|
||||
virtual const char *id(){ return type(); }
|
||||
static int expected_argc(){ return NPARAMS; }
|
||||
virtual int nparams(){ return NPARAMS; }
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
#endif // LMP_MANIFOLD_TORUS_H
|
||||
102
src/USER-MANIFOLD/sincos_lookup.cpp
Normal file
102
src/USER-MANIFOLD/sincos_lookup.cpp
Normal file
@ -0,0 +1,102 @@
|
||||
#include "sincos_lookup.h"
|
||||
|
||||
#include <cmath>
|
||||
#include <iostream>
|
||||
|
||||
#define SINCOS_LOOKUP_NO_SAFETY
|
||||
|
||||
#if __cplusplus < 201103L
|
||||
#define nullptr NULL
|
||||
#endif // __cplusplus
|
||||
|
||||
|
||||
sincos_lookup::sincos_lookup( int N ) : cos_table(nullptr), size(N)
|
||||
{
|
||||
std::cout << "Constructing table of size " << size
|
||||
<< ", this might take a while... ";
|
||||
make_cos_table();
|
||||
std::cout << "Done!\n";
|
||||
}
|
||||
|
||||
sincos_lookup::~sincos_lookup()
|
||||
{
|
||||
if( cos_table ) delete [] cos_table;
|
||||
}
|
||||
|
||||
double sincos_lookup::sin( double x )
|
||||
{
|
||||
return this->cos( my_pi2 - x );
|
||||
}
|
||||
|
||||
double sincos_lookup::cos( double x )
|
||||
{
|
||||
double x0 = x;
|
||||
|
||||
// Wrap to first quadrant:
|
||||
x = fabs(x);
|
||||
|
||||
const double rounded_n_over_2pi = static_cast<int>(x / my_2pi) * my_2pi;
|
||||
x -= rounded_n_over_2pi;
|
||||
if( x > my_pi ){
|
||||
// make use of cos( x ) = -cos(pi-x)
|
||||
x -= 2.0*( x - my_pi );
|
||||
}
|
||||
// Get index:
|
||||
int idx = static_cast<int>( x / dx_tab );
|
||||
#ifdef SINCOS_LOOKUP_NO_SAFETY
|
||||
// Assume safe:
|
||||
#else
|
||||
if( idx > size || idx < 0 ){
|
||||
std::cerr << "Illegal table lookup for index " << idx << ", x="
|
||||
<< x << ", x0=" << x0 << "!\n";
|
||||
}
|
||||
#endif // SINCOS_LOOKUP_NO_SAFETY
|
||||
|
||||
// static_cast always truncates to left, so lookup with "delta to right":
|
||||
double delta = x - idx*dx_tab;
|
||||
double cos_idx = cos_table[idx];
|
||||
double diff_cos = cos_table[idx+1] - cos_idx;
|
||||
return cos_idx + delta*diff_cos*inv_dx_tab;
|
||||
}
|
||||
|
||||
|
||||
void sincos_lookup::sincos(double x, double *s, double *c)
|
||||
{
|
||||
*s = this->sin(x);
|
||||
*c = this->cos(x);
|
||||
}
|
||||
|
||||
void sincos_lookup::test_lookup( )
|
||||
{
|
||||
double dx = 1e-5;
|
||||
double max_err_c = 0, max_err_s = 0;
|
||||
|
||||
for( double x = 0; x < 2*my_2pi; x += dx ){
|
||||
double c = this->cos(x);
|
||||
double s = this->sin(x);
|
||||
// Compare with math.h:
|
||||
double c_err = c - cos(x);
|
||||
double s_err = s - sin(x);
|
||||
|
||||
if( fabs(max_err_c) < fabs(c_err) ) max_err_c = c_err;
|
||||
if( fabs(max_err_s) < fabs(s_err) ) max_err_s = s_err;
|
||||
}
|
||||
std::cout << "Largest lookup table errors (sin/cos): ( " << max_err_s
|
||||
<< ", " << max_err_c << " ).\n";
|
||||
}
|
||||
|
||||
|
||||
void sincos_lookup::make_cos_table()
|
||||
{
|
||||
cos_table = new double [size+1];
|
||||
if( !cos_table ){
|
||||
// error.
|
||||
}
|
||||
dx_tab = my_pi/static_cast<double>(size-1);
|
||||
inv_dx_tab = 1.0 / dx_tab;
|
||||
|
||||
for( int i = 0; i <= size; ++i ){
|
||||
double f = i*dx_tab;
|
||||
cos_table[i] = std::cos(f);
|
||||
}
|
||||
}
|
||||
35
src/USER-MANIFOLD/sincos_lookup.h
Normal file
35
src/USER-MANIFOLD/sincos_lookup.h
Normal file
@ -0,0 +1,35 @@
|
||||
#ifndef SINCOS_LOOKUP_H
|
||||
#define SINCOS_LOOKUP_H
|
||||
|
||||
class sincos_lookup
|
||||
{
|
||||
public:
|
||||
sincos_lookup( int N );
|
||||
~sincos_lookup();
|
||||
double sin(double x);
|
||||
double cos(double x);
|
||||
void sincos(double x, double *s, double *c);
|
||||
|
||||
void test_lookup();
|
||||
|
||||
#if __cplusplus < 201103L
|
||||
#define my_pi2 1.57079632679489661923
|
||||
#define my_pi 3.14159265358979323846
|
||||
#define my_2pi 6.28318530717958647692
|
||||
#else
|
||||
static constexpr const double my_pi2 = 1.57079632679489661923;
|
||||
static constexpr const double my_pi = 3.14159265358979323846;
|
||||
static constexpr const double my_2pi = 6.28318530717958647692;
|
||||
#endif
|
||||
|
||||
private:
|
||||
double *cos_table;
|
||||
double dx_tab, inv_dx_tab;
|
||||
int size;
|
||||
|
||||
|
||||
|
||||
void make_cos_table();
|
||||
};
|
||||
|
||||
#endif // SINCOS_LOOKUP_H
|
||||
Reference in New Issue
Block a user