git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5992 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/COLLOID/pair_lubricate.cpp

@@ -385,15 +385,15 @@ void PairLubricate::init_style()
 
   int irequest = neighbor->request(this);
 
-  // require that atom radii are identical within each type require
-  // monodisperse system with same radii for all types
+  // require that atom radii are identical within each type
+  // require monodisperse system with same radii for all types
 
   double rad,radtype;
   for (int i = 1; i <= atom->ntypes; i++) {
     if (!atom->radius_consistency(i,radtype))
-      error->all("Pair colloid requires atoms with same type have same radius");
+      error->all("Pair lubricate requires monodisperse particles");
     if (i > 1 && radtype != rad)
-      error->all("Pair colloid requires mono-disperse particles");
+      error->all("Pair lubricate requires monodisperse particles");
     rad = radtype;
   }
 }

src/COLLOID/pair_yukawa_colloid.cpp

@@ -12,7 +12,7 @@
 ------------------------------------------------------------------------- */
 
 /* ----------------------------------------------------------------------
-   Contributing authors: Randy Schunk (SNL)
+   Contributing authors: Randy Schunk (Sandia)
 ------------------------------------------------------------------------- */
 
 #include "math.h"

src/atom_vec_ellipsoid.cpp

@@ -767,7 +767,7 @@ void AtomVecEllipsoid::unpack_border(int n, int first, double *buf)
     type[i] = static_cast<int> (buf[m++]);
     mask[i] = static_cast<int> (buf[m++]);
     ellipsoid[i] = static_cast<int> (buf[m++]);
-    if (ellipsoid[i] < 0) ellipsoid[i] = 0;
+    if (ellipsoid[i] == 0) ellipsoid[i] = -1;
     else {
       j = nlocal_bonus + nghost_bonus;
       if (j == nmax_bonus) grow_bonus();
@@ -805,9 +805,8 @@ void AtomVecEllipsoid::unpack_border_vel(int n, int first, double *buf)
     type[i] = static_cast<int> (buf[m++]);
     mask[i] = static_cast<int> (buf[m++]);
     ellipsoid[i] = static_cast<int> (buf[m++]);
-    if (ellipsoid[i] < 0) ellipsoid[i] = 0;
+    if (ellipsoid[i] == 0) ellipsoid[i] = -1;
     else {
-      j = nlocal_bonus + nghost_bonus;
       if (j == nmax_bonus) grow_bonus();
       shape = bonus[j].shape;
       quat = bonus[j].quat;
@@ -842,7 +841,7 @@ int AtomVecEllipsoid::unpack_border_hybrid(int n, int first, double *buf)
   last = first + n;
   for (i = first; i < last; i++) {
     ellipsoid[i] = static_cast<int> (buf[m++]);
-    if (ellipsoid[i] < 0) ellipsoid[i] = 0;
+    if (ellipsoid[i] == 0) ellipsoid[i] = -1;
     else {
       j = nlocal_bonus + nghost_bonus;
       if (j == nmax_bonus) grow_bonus();
@@ -933,7 +932,8 @@ int AtomVecEllipsoid::unpack_exchange(double *buf)
   angmom[nlocal][2] = buf[m++];
 
   ellipsoid[nlocal] = static_cast<int> (buf[m++]);
-  if (ellipsoid[nlocal]) {
+  if (ellipsoid[nlocal] == 0) ellipsoid[nlocal] = -1;
+  else {
     if (nlocal_bonus == nmax_bonus) grow_bonus();
     double *shape = bonus[nlocal_bonus].shape;
     double *quat = bonus[nlocal_bonus].quat;
@@ -1057,7 +1057,8 @@ int AtomVecEllipsoid::unpack_restart(double *buf)
   angmom[nlocal][2] = buf[m++];
 
   ellipsoid[nlocal] = static_cast<int> (buf[m++]);
-  if (ellipsoid[nlocal]) {
+  if (ellipsoid[nlocal] == 0) ellipsoid[nlocal] = -1;
+  else {
     if (nlocal_bonus == nmax_bonus) grow_bonus();
     double *shape = bonus[nlocal_bonus].shape;
     double *quat = bonus[nlocal_bonus].quat;

src/fix_nh.cpp

@@ -19,6 +19,7 @@
 #include "stdlib.h"
 #include "math.h"
 #include "fix_nh.h"
+#include "math_extra.h"
 #include "atom.h"
 #include "force.h"
 #include "comm.h"
@@ -31,7 +32,6 @@
 #include "domain.h"
 #include "memory.h"
 #include "error.h"
-#include "math_extra.h"
 
 using namespace LAMMPS_NS;
 

src/fix_store_state.cpp

@@ -468,7 +468,7 @@ double FixStoreState::memory_usage()
 
 void FixStoreState::grow_arrays(int nmax)
 {
-  memory->grow(values,nmax,nvalues,"fix_store:values");
+ memory->grow(values,nmax,nvalues,"store/state:values");
   if (nvalues == 1) {
     if (nmax) vector_atom = &values[0][0];
     else vector_atom = NULL;

src/math_extra.cpp

@@ -428,8 +428,8 @@ void quat_to_mat_trans(const double *quat, double mat[3][3])
 
 /* ----------------------------------------------------------------------
    compute space-frame inertia tensor of an ellipsoid
-   quat = orientiation quaternion of ellipsoid
    radii = 3 radii of ellipsoid
+   quat = orientiation quaternion of ellipsoid
    return symmetric inertia tensor as 6-vector in Voigt notation
 ------------------------------------------------------------------------- */
 
@@ -454,6 +454,36 @@ void inertia_ellipsoid(double *radii, double *quat, double mass,
   inertia[5] = tensor[0][1];
 }
 
+/* ----------------------------------------------------------------------
+   compute space-frame inertia tensor of a line segment in 2d
+   length = length of line
+   theta = orientiation of line
+   return symmetric inertia tensor as 6-vector in Voigt notation
+------------------------------------------------------------------------- */
+
+void inertia_line(double length, double theta, double mass, double *inertia)
+{
+  double p[3][3],ptrans[3][3],itemp[3][3],tensor[3][3];
+  double q[4],idiag[3];
+
+  q[0] = cos(0.5*theta);
+  q[1] = q[2] = 0.0;
+  q[3] = sin(0.5*theta);
+  MathExtra::quat_to_mat(q,p);
+  MathExtra::quat_to_mat_trans(q,ptrans);
+  idiag[0] = 0.0;
+  idiag[1] = 1.0/12.0 * mass * length*length;
+  idiag[2] = 1.0/12.0 * mass * length*length;
+  MathExtra::diag_times3(idiag,ptrans,itemp);
+  MathExtra::times3(p,itemp,tensor);
+  inertia[0] = tensor[0][0];
+  inertia[1] = tensor[1][1];
+  inertia[2] = tensor[2][2];
+  inertia[3] = tensor[1][2];
+  inertia[4] = tensor[0][2];
+  inertia[5] = tensor[0][1];
+}
+
 /* ----------------------------------------------------------------------
    compute space-frame inertia tensor of a triangle
    v0,v1,v2 = 3 vertices of triangle

src/math_extra.h

@@ -114,6 +114,8 @@ namespace MathExtra {
 
   void inertia_ellipsoid(double *shape, double *quat, double mass,
 			 double *inertia);
+  void inertia_line(double length, double theta, double mass,
+		    double *inertia);
   void inertia_triangle(double *v0, double *v1, double *v2, 
 			double mass, double *inertia);
 }

src/read_data.cpp

@@ -41,7 +41,7 @@ using namespace LAMMPS_NS;
 #define DELTA 4            // must be 2 or larger
 
                            // customize for new sections
-#define NSECTIONS 23       // change when add to header::section_keywords
+#define NSECTIONS 21       // change when add to header::section_keywords
 
 #define MIN(a,b) ((a) < (b) ? (a) : (b))
 #define MAX(a,b) ((a) > (b) ? (a) : (b))