git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@1119 f3b2605a-c512-4ea7-a41b-209d697bcdaa

2007-11-02 20:25:11 +00:00
parent f12471d507
commit 6de4e59a38
28 changed files with 610 additions and 280 deletions
--- a/src/compute_pe.cpp
+++ b/src/compute_pe.cpp
@ -0,0 +1,102 @@
+/* ----------------------------------------------------------------------
+   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_pe.h"
+#include "atom.h"
+#include "force.h"
+#include "pair.h"
+#include "bond.h"
+#include "angle.h"
+#include "dihedral.h"
+#include "improper.h"
+#include "kspace.h"
+#include "modify.h"
+#include "domain.h"
+#include "error.h"
+
+using namespace LAMMPS_NS;
+
+/* ---------------------------------------------------------------------- */
+
+ComputePE::ComputePE(LAMMPS *lmp, int narg, char **arg) : 
+  Compute(lmp, narg, arg)
+{
+  if (narg < 3) error->all("Illegal compute pe command");
+  if (igroup) error->all("Compute pe must use group all");
+
+  if (narg == 3) {
+    pairflag = 1;
+    bondflag = angleflag = dihedralflag = improperflag = 1;
+    kspaceflag = 1;
+    thermoflag = 1;
+  } else {
+    pairflag = 0;
+    bondflag = angleflag = dihedralflag = improperflag = 0;
+    kspaceflag = 0;
+    thermoflag = 0;
+    int iarg = 3;
+    while (iarg < narg) {
+      if (strcmp(arg[iarg],"pair") == 0) pairflag = 1;
+      else if (strcmp(arg[iarg],"bond") == 0) bondflag = 1;
+      else if (strcmp(arg[iarg],"angle") == 0) angleflag = 1;
+      else if (strcmp(arg[iarg],"dihedral") == 0) dihedralflag = 1;
+      else if (strcmp(arg[iarg],"improper") == 0) improperflag = 1;
+      else if (strcmp(arg[iarg],"kspace") == 0) kspaceflag = 1;
+      else error->all("Illegal compute pe command");
+      iarg++;
+    }
+  }
+
+  // settings
+
+  scalar_flag = 1;
+  extensive = 1;
+  peflag = 1;
+  timeflag = 1;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double ComputePE::compute_scalar()
+{
+  invoked = 1;
+  double one = 0.0;
+
+  if (pairflag) {
+    if (force->pair) one += force->pair->eng_vdwl + force->pair->eng_coul;
+    if (force->bond) one += force->bond->eng_vdwl;
+    if (force->dihedral) 
+      one += force->dihedral->eng_vdwl + force->dihedral->eng_coul;
+  }
+
+  if (atom->molecular) {
+    if (bondflag && force->bond) one += force->bond->energy;
+    if (angleflag && force->angle) one += force->angle->energy;
+    if (dihedralflag && force->dihedral) one += force->dihedral->energy;
+    if (improperflag && force->improper) one += force->improper->energy;
+  }
+
+  MPI_Allreduce(&one,&scalar,1,MPI_DOUBLE,MPI_SUM,world);
+
+  if (kspaceflag && force->kspace) scalar += force->kspace->energy;
+  if (pairflag && force->pair && force->pair->tail_flag) {
+    double volume = domain->xprd * domain->yprd * domain->zprd;
+    scalar += force->pair->etail / volume;
+  }
+
+  if (thermoflag && modify->n_thermo_energy) scalar += modify->thermo_energy();
+
+  return scalar;
+}