git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14740 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/XTC/dump_xtc.cpp

@@ -151,7 +151,7 @@ void DumpXTC::write_header(bigint nbig)
   if (nbig > MAXSMALLINT) error->all(FLERR,"Too many atoms for dump xtc");
   int n = nbig;
   if (update->ntimestep > MAXSMALLINT)
-    error->all(FLERR,"Too big a timestep for dump xtc");
+    error->one(FLERR,"Too big a timestep for dump xtc");
   int ntimestep = update->ntimestep;
 
   // all procs realloc coords if total count grew

src/compute_bond.cpp

@@ -0,0 +1,89 @@
+/* ----------------------------------------------------------------------
+   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 <mpi.h>
+#include <string.h>
+#include "compute_bond.h"
+#include "update.h"
+#include "force.h"
+#include "bond.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputeBond::ComputeBond(LAMMPS *lmp, int narg, char **arg) :
+  Compute(lmp, narg, arg)
+{
+  if (narg < 4 || narg > 5) error->all(FLERR,"Illegal compute bond command");
+  if (igroup) error->all(FLERR,"Compute bond must use group all");
+
+  scalar_flag = 1;
+  extscalar = 1;
+  peflag = 1;
+  timeflag = 1;
+
+  int n = strlen(arg[3]) + 1;
+  if (lmp->suffix) n += strlen(lmp->suffix) + 1;
+  bstyle = new char[n];
+  strcpy(bstyle,arg[3]);
+
+  // check if bond style with and without suffix exists
+
+  bond = force->bond_match(bstyle);
+  if (!bond && lmp->suffix) {
+    strcat(bstyle,"/");
+    strcat(bstyle,lmp->suffix);
+    bond = force->bond_match(bstyle);
+  }
+  if (!bond)
+    error->all(FLERR,"Unrecognized bond style in compute bond command");
+
+  vector = NULL;
+}
+
+/* ---------------------------------------------------------------------- */
+
+ComputeBond::~ComputeBond()
+{
+  delete [] bstyle;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void ComputeBond::init()
+{
+  // recheck for bond style in case it has been deleted
+
+  bond = force->bond_match(bstyle);
+
+  if (!bond)
+    error->all(FLERR,"Unrecognized bond style in compute bond command");
+}
+
+/* ---------------------------------------------------------------------- */
+
+double ComputeBond::compute_scalar()
+{
+  invoked_scalar = update->ntimestep;
+  if (update->eflag_global != invoked_scalar)
+    error->all(FLERR,"Energy was not tallied on needed timestep");
+
+  double eng;
+  eng = bond->energy;
+
+  MPI_Allreduce(&eng,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
+  return scalar;
+}
+

src/compute_bond.h

@@ -0,0 +1,67 @@
+/* -*- 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.
+------------------------------------------------------------------------- */
+
+#ifdef COMPUTE_CLASS
+
+ComputeStyle(bond,ComputeBond)
+
+#else
+
+#ifndef LMP_COMPUTE_BOND_H
+#define LMP_COMPUTE_BOND_H
+
+#include "compute.h"
+
+namespace LAMMPS_NS {
+
+class ComputeBond : public Compute {
+ public:
+  ComputeBond(class LAMMPS *, int, char **);
+  ~ComputeBond();
+  void init();
+  double compute_scalar();
+
+ private:
+  int nbond;
+  char *bstyle;
+  class Bond *bond;
+};
+
+}
+
+#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.
+
+E: Compute bond must use group all
+
+Bond styles accumlate energy on all atoms.
+
+E: Unrecognized bond style in compute bond command
+
+Self-explanatory.
+
+E: Energy was not tallied on needed timestep
+
+You are using a thermo keyword that requires potentials to
+have tallied energy, but they didn't on this timestep.  See the
+variable doc page for ideas on how to make this work.
+
+*/

src/dump_dcd.cpp

@@ -126,7 +126,7 @@ void DumpDCD::write_header(bigint n)
 {
   if (n != natoms) error->all(FLERR,"Dump dcd of non-matching # of atoms");
   if (update->ntimestep > MAXSMALLINT)
-    error->all(FLERR,"Too big a timestep for dump dcd");
+    error->one(FLERR,"Too big a timestep for dump dcd");
 
   // first time, write header for entire file