diff --git a/doc/src/manifolds.txt b/doc/src/manifolds.txt
index eb3bd6d486aef0fda13b215010cec47d3b75a590..c9bb1ce57f850242b8940365a4a4cebfff4fa162 100644
--- a/doc/src/manifolds.txt
+++ b/doc/src/manifolds.txt
@@ -24,8 +24,9 @@ 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 @
+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
+gaussian_bump @ A l rc1 rc2 @ if( x < rc1) -z + A * exp( -x^2 / (2 l^2) ); else if( x < rc2 ) -z + a + b*x + c*x^2 + d*x^3; else z @ A Gaussian bump at x = y = 0, smoothly tapered to a flat plane z = 0.
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
diff --git a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
index 4f6b62590d9b71e50d24728417ff225e5953a1d4..67f298d8dfb4e67b8b68c9fe3d6b89142ceab0a1 100644
--- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
+++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
@@ -115,6 +115,13 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg,
error->all(FLERR, "Error creating manifold arg arrays");
}
+ // Check if you have enough args:
+ if( 6 + nvars > narg ){
+ char msg[2048];
+ sprintf(msg, "Not enough args for manifold %s, %d expected but got %d\n",
+ ptr_m->id(), nvars, narg - 6);
+ error->all(FLERR, msg);
+ }
// Loop over manifold args:
for( int i = 0; i < nvars; ++i ){
int len = 0, offset = 0;
diff --git a/src/USER-MANIFOLD/manifold.h b/src/USER-MANIFOLD/manifold.h
index d0ffa214ac4b0bd11fa6334f534c0d4c71377a50..b89e765a6eab068f99194cd492d867fe456fa4f8 100644
--- a/src/USER-MANIFOLD/manifold.h
+++ b/src/USER-MANIFOLD/manifold.h
@@ -24,7 +24,7 @@
testing purposes) and a wave-y plane.
See the README file for more info.
- Stefan Paquay, s.paquay@tue.nl
+ Stefan Paquay, stefanpaquay@gmail.com
Applied Physics/Theory of Polymers and Soft Matter,
Eindhoven University of Technology (TU/e), The Netherlands
diff --git a/src/USER-MANIFOLD/manifold_factory.cpp b/src/USER-MANIFOLD/manifold_factory.cpp
index 57c6e8305f24af3255946f28f5d2c98dd87f34f7..f98180ddb651540aea8b355b62823f4de25ccb2c 100644
--- a/src/USER-MANIFOLD/manifold_factory.cpp
+++ b/src/USER-MANIFOLD/manifold_factory.cpp
@@ -37,6 +37,7 @@
#include "manifold_cylinder_dent.h"
#include "manifold_dumbbell.h"
#include "manifold_ellipsoid.h"
+#include "manifold_gaussian_bump.h"
#include "manifold_plane.h"
#include "manifold_plane_wiggle.h"
#include "manifold_sphere.h"
@@ -58,12 +59,13 @@ manifold* LAMMPS_NS::user_manifold::create_manifold(const char *mname,
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_gaussian_bump> ( &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_two> ( &man, mname, lmp, narg, arg );
+ make_manifold_if<manifold_spine_two> ( &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 );
diff --git a/src/USER-MANIFOLD/manifold_gaussian_bump.cpp b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp
new file mode 100644
index 0000000000000000000000000000000000000000..200edd2fb0874bb20a752ed6b8440b885eff198e
--- /dev/null
+++ b/src/USER-MANIFOLD/manifold_gaussian_bump.cpp
@@ -0,0 +1,138 @@
+#include "manifold_gaussian_bump.h"
+
+using namespace LAMMPS_NS;
+using namespace user_manifold;
+
+// The constraint is z = f(r = sqrt( x^2 + y^2) )
+// f(x) = A*exp( -x^2 / 2 l^2 ) if x < rc1
+// = a + b*x + c*x**2 + d*x**3 if rc1 <= x < rc2
+// = 0 if x >= rc2
+//
+double manifold_gaussian_bump::g( const double *x )
+{
+ double xf[3];
+ xf[0] = x[0];
+ xf[1] = x[1];
+ xf[2] = 0.0;
+
+ double x2 = dot(xf,xf);
+ if( x2 < rc12 ){
+ return x[2] - gaussian_bump_x2( x2 );
+ }else if( x2 < rc22 ){
+ double rr = sqrt(x2);
+ double xi = rr - rc1;
+ xi *= inv_dr;
+ double xi2 = x2 * inv_dr*inv_dr;
+ double xi3 = xi*xi2;
+ return x[2] - ( aa + bb*xi + cc*xi2 + dd*xi3 );
+
+ }else{
+ return x[2];
+ }
+}
+
+void manifold_gaussian_bump::n( const double *x, double *nn )
+{
+ double xf[3];
+ xf[0] = x[0];
+ xf[1] = x[1];
+ xf[2] = 0.0;
+ nn[2] = 1.0;
+
+ double x2 = dot(xf,xf);
+
+ if( x2 < rc12 ){
+ double factor = gaussian_bump_x2(x2);
+ factor /= (ll*ll);
+ nn[0] = factor * x[0];
+ nn[1] = factor * x[1];
+ }else if( x2 < rc22 ){
+ double rr = sqrt(x2);
+ double xi = rr - rc1;
+ xi *= inv_dr;
+ double xi2 = x2 * inv_dr*inv_dr;
+ double der = bb + 2*cc*xi + 3*dd*xi2;
+
+ nn[0] = -der * x[0] / rr;
+ nn[1] = -der * x[1] / rr;
+ }else{
+ nn[0] = nn[1] = 0.0;
+ }
+}
+
+double manifold_gaussian_bump::g_and_n( const double *x, double *nn )
+{
+ double xf[3];
+ xf[0] = x[0];
+ xf[1] = x[1];
+ xf[2] = 0.0;
+ nn[2] = 1.0;
+
+ double x2 = dot(xf,xf);
+ if( x2 < rc12 ){
+ double gb = gaussian_bump_x2(x2);
+ double factor = gb / (ll*ll);
+ nn[0] = factor * x[0];
+ nn[1] = factor * x[1];
+
+ return x[2] - gb;
+ }else if( x2 < rc22 ){
+
+ double rr = sqrt(x2);
+ double xi = rr - rc1;
+ xi *= inv_dr;
+ double xi2 = x2 * inv_dr*inv_dr;
+ double xi3 = xi*xi2;
+
+ double der = bb + 2*cc*xi + 3*dd*xi2;
+
+ nn[0] = -der * x[0] / rr;
+ nn[1] = -der * x[1] / rr;
+
+
+ return x[2] - ( aa + bb*xi + cc*xi2 + dd*xi3 );
+
+ }else{
+ nn[0] = nn[1] = 0.0;
+ return x[2];
+ }
+
+}
+
+
+void manifold_gaussian_bump::post_param_init()
+{
+ // Read in the params:
+ AA = params[0];
+ ll = params[1];
+ rc1 = params[2];
+ rc2 = params[3];
+
+ ll2 = 2.0*ll*ll;
+
+ f_at_rc = gaussian_bump_x2 ( rc12 );
+ fp_at_rc = gaussian_bump_der( rc12 );
+
+ rc12 = rc1*rc1;
+ rc22 = rc2*rc2;
+ dr = rc2 - rc1;
+ inv_dr = 1.0 / dr;
+}
+
+
+double manifold_gaussian_bump::gaussian_bump( double x )
+{
+ double x2 = x*x;
+ return gaussian_bump_x2( x2 );
+}
+
+double manifold_gaussian_bump::gaussian_bump_x2( double x2 )
+{
+ return AA*exp( -x2 / ll2 );
+}
+
+double manifold_gaussian_bump::gaussian_bump_der( double x )
+{
+ double x2 = x*x;
+ return gaussian_bump_x2( x2 )*( -x/(ll*ll) );
+}
diff --git a/src/USER-MANIFOLD/manifold_gaussian_bump.h b/src/USER-MANIFOLD/manifold_gaussian_bump.h
new file mode 100644
index 0000000000000000000000000000000000000000..f3401a4a33d0d1a9082d13a6e9d201ed0f8e05fd
--- /dev/null
+++ b/src/USER-MANIFOLD/manifold_gaussian_bump.h
@@ -0,0 +1,82 @@
+/* ----------------------------------------------------------------------
+ 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, spaquay@brandeis.edu
+ Brandeis University, Waltham, MA, USA.
+
+ This package was mainly developed at
+ 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_GAUSSIAN_BUMP_H
+#define LMP_MANIFOLD_GAUSSIAN_BUMP_H
+
+#include "manifold.h"
+
+namespace LAMMPS_NS {
+
+namespace user_manifold {
+
+ // A Gaussian bump with a smoothed decay to flat 2D.
+ class manifold_gaussian_bump : public manifold {
+ public:
+ enum { NPARAMS = 4 };
+ manifold_gaussian_bump(class LAMMPS*, int, char **) : manifold(lmp) {}
+ virtual ~manifold_gaussian_bump(){}
+
+ virtual double g( const double * );
+ virtual void n( const double *, double * );
+
+ // Variant of g that computes n at the same time.
+ virtual double g_and_n( const double *x, double *nn );
+
+ static const char* type(){ return "gaussian_bump"; }
+ virtual const char *id() { return type(); }
+
+ virtual int nparams(){ return NPARAMS; }
+ virtual void post_param_init();
+ private:
+ // Some private constants:
+ double aa, bb, cc, dd, AA, ll, ll2, f_at_rc, fp_at_rc;
+ double rc1, rc2, rc12, rc22, dr, inv_dr;
+
+ double gaussian_bump ( double );
+ double gaussian_bump_x2 ( double );
+ double gaussian_bump_der( double );
+
+ };
+}
+
+}
+
+
+#endif // LMP_MANIFOLD_GAUSSIAN_BUMP_H