git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2362 f3b2605a-c512-4ea7-a41b-209d697bcdaa

README

@@ -1,4 +1,4 @@
-This is the LAMMPS (6 Jan 2009) software package.
+This is the LAMMPS (9 Jan 2009) software package.
 
 LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
 Simulator.
@@ -20,7 +20,7 @@ The primary author of the code is Steve Plimpton, who can be emailed
 at sjplimp@sandia.gov.  The LAMMPS WWW Site at lammps.sandia.gov has
 more information about the code and its uses.
 
-The LAMMPS (6 Jan 2009) distribution includes the following files
+The LAMMPS (9 Jan 2009) distribution includes the following files
 and directories:
 
 README			   this file

doc/Section_errors.txt

@@ -1801,14 +1801,26 @@ The time window for pressure relaxation must be > 0 :dd
 
 The time window for temperature or pressure relaxation must be > 0 :dd
 
+{Fix npt/asphere requires atom attributes quat, angmom, torque, shape} :dt
+
+An atom style that specifies these quantities is needed. :dd
+
 {Fix npt/sphere requires atom attribute shape} :dt
 
 An atom style that specifies atom shape is needed. :dd
 
+{Fix npt/sphere requires atom attributes omega, torque} :dt
+
+An atom style that specifies these quantities is needed. :dd
+
 {Fix npt/sphere requires spherical particle shapes} :dt
 
 Self-explanatory. :dd
 
+{Fix nve/asphere requires atom attributes quat, angmom, torque, shape} :dt
+
+An atom style that specifies these quantities is needed. :dd
+
 {Fix nve/sphere requires atom attribute mu} :dt
 
 An atom style with this attribute is needed. :dd
@@ -1833,6 +1845,10 @@ Self-explanatory. :dd
 
 The time window for temperature relaxation must be > 0 :dd
 
+{Fix nvt/asphere requires atom attributes quat, angmom, torque, shape} :dt
+
+An atom style that specifies these quantities is needed. :dd
+
 {Fix nvt/sphere requires atom attribute shape} :dt
 
 An atom style with this attribute is needed. :dd
@@ -3115,6 +3131,10 @@ Style in pair coeff must have been listed in pair_style command. :dd
 One or more pairwise cutoffs are too short to use with the specified
 rRESPA cutoffs. :dd
 
+{Pair dipole/cut requires atom attributes q, mu, torque, dipole} :dt
+
+An atom style that specifies these quantities is needed. :dd
+
 {Pair distance < table inner cutoff} :dt
 
 Two atoms are closer together than the pairwise table allows. :dd
@@ -4039,6 +4059,24 @@ restriction. :dd
 Other fixes may change the position of the center-of-mass, so 
 fix recenter should come last. :dd
 
+{Fix thermal/conductivity comes before fix ave/spatial} :dt
+
+The order of these 2 fixes in your input script is such that fix
+thermal/conductivity comes first.  If you are using fix ave/spatial to
+measure the temperature profile induced by fix viscosity, then this
+may cause a glitch in the profile since you are averaging immediately
+after swaps have occurred.  Flipping the order of the 2 fixes
+typically helps. :dd
+
+{Fix viscosity comes before fix ave/spatial} :dt
+
+The order of these 2 fixes in your input script is such that
+fix viscosity comes first.  If you are using fix ave/spatial
+to measure the velocity profile induced by fix viscosity, then
+this may cause a glitch in the profile since you are averaging
+immediately after swaps have occurred.  Flipping the order
+of the 2 fixes typically helps. :dd
+
 {Group for fix_modify temp != fix group} :dt
 
 The fix_modify command is specifying a temperature computation that

src/fix_npt_sphere.cpp

@@ -36,7 +36,7 @@ FixNPTSphere::FixNPTSphere(LAMMPS *lmp, int narg, char **arg) :
   FixNPT(lmp, narg, arg)
 {
   if (!atom->omega_flag || !atom->torque_flag)
-    error->all("Fix nvt/sphere requires atom attributes omega, torque");
+    error->all("Fix npt/sphere requires atom attributes omega, torque");
 
   dttype = new double[atom->ntypes+1];
 }

src/fix_thermal_conductivity.cpp

@@ -19,6 +19,7 @@
 #include "atom.h"
 #include "force.h"
 #include "domain.h"
+#include "modify.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
@@ -103,6 +104,16 @@ int FixThermalConductivity::setmask()
 
 void FixThermalConductivity::init()
 {
+  // warn if any fix ave/spatial comes after this fix
+  // can cause glitch in averaging since ave will happen after swap
+
+  int foundme = 0;
+  for (int i = 0; i < modify->nfix; i++) {
+    if (modify->fix[i] == this) foundme = 1;
+    if (foundme && strcmp(modify->fix[i]->style,"ave/spatial") == 0 && me == 0)
+      error->warning("Fix thermal/conductivity comes before fix ave/spatial");
+  }
+
   // set bounds of 2 slabs in edim
   // only necessary for static box, else re-computed in end_of_step()
   // lo bin is always bottom bin

src/fix_viscosity.cpp

@@ -18,6 +18,7 @@
 #include "fix_viscosity.h"
 #include "atom.h"
 #include "domain.h"
+#include "modify.h"
 #include "error.h"
 
 using namespace LAMMPS_NS;
@@ -113,6 +114,16 @@ int FixViscosity::setmask()
 
 void FixViscosity::init()
 {
+  // warn if any fix ave/spatial comes after this fix
+  // can cause glitch in averaging since ave will happen after swap
+
+  int foundme = 0;
+  for (int i = 0; i < modify->nfix; i++) {
+    if (modify->fix[i] == this) foundme = 1;
+    if (foundme && strcmp(modify->fix[i]->style,"ave/spatial") == 0 && me == 0)
+      error->warning("Fix viscosity comes before fix ave/spatial");
+  }
+
   // set bounds of 2 slabs in pdim
   // only necessary for static box, else re-computed in end_of_step()
   // lo bin is always bottom bin

src/verlet.cpp

@@ -129,6 +129,13 @@ void Verlet::iterate(int n)
 {
   int nflag,ntimestep;
 
+  int n_post_integrate = modify->n_post_integrate;
+  int n_pre_exchange = modify->n_pre_exchange;
+  int n_pre_neighbor = modify->n_pre_neighbor;
+  int n_pre_force = modify->n_pre_force;
+  int n_post_force = modify->n_post_force;
+  int n_end_of_step = modify->n_end_of_step;
+
   for (int i = 0; i < n; i++) {
 
     ntimestep = ++update->ntimestep;
@@ -137,7 +144,7 @@ void Verlet::iterate(int n)
     // initial time integration
 
     modify->initial_integrate(vflag);
-    if (modify->n_post_integrate) modify->post_integrate();
+    if (n_post_integrate) modify->post_integrate();
 
     // regular communication vs neighbor list rebuild
 
@@ -148,7 +155,7 @@ void Verlet::iterate(int n)
       comm->communicate();
       timer->stamp(TIME_COMM);
     } else {
-      if (modify->n_pre_exchange) modify->pre_exchange();
+      if (n_pre_exchange) modify->pre_exchange();
       if (triclinic) domain->x2lamda(atom->nlocal);
       domain->pbc();
       if (domain->box_change) {
@@ -161,7 +168,7 @@ void Verlet::iterate(int n)
       comm->borders();
       if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
       timer->stamp(TIME_COMM);
-      if (modify->n_pre_neighbor) modify->pre_neighbor();
+      if (n_pre_neighbor) modify->pre_neighbor();
       neighbor->build();
       timer->stamp(TIME_NEIGHBOR);
     }
@@ -169,7 +176,7 @@ void Verlet::iterate(int n)
     // force computations
 
     force_clear();
-    if (modify->n_pre_force) modify->pre_force(vflag);
+    if (n_pre_force) modify->pre_force(vflag);
 
     timer->stamp();
 
@@ -200,9 +207,9 @@ void Verlet::iterate(int n)
 
     // force modifications, final time integration, diagnostics
 
-    if (modify->n_post_force) modify->post_force(vflag);
+    if (n_post_force) modify->post_force(vflag);
     modify->final_integrate();
-    if (modify->n_end_of_step) modify->end_of_step();
+    if (n_end_of_step) modify->end_of_step();
 
     // all output
 

tools/restart2data.cpp

@@ -416,7 +416,7 @@ int main (int argc, char **argv)
 
 void header(FILE *fp, Data &data)
 {
-  char *version = "21 May 2008";
+  char *version = "9 Jan 2009";
 
   data.triclinic = 0;