From 6fbbb51569ba718fa2e8bfd8101a0b30f4f8a63c Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Thu, 30 Jan 2014 19:47:17 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11395
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/PERI/fix_peri_neigh.cpp | 11 +++++++++++
 src/atom.cpp                |  4 ++++
 src/atom.h                  |  4 ++++
 src/dump_cfg.cpp            | 24 +++++++++---------------
 4 files changed, 28 insertions(+), 15 deletions(-)

diff --git a/src/PERI/fix_peri_neigh.cpp b/src/PERI/fix_peri_neigh.cpp
index cd6e3d5c81..23e0a392af 100644
--- a/src/PERI/fix_peri_neigh.cpp
+++ b/src/PERI/fix_peri_neigh.cpp
@@ -119,6 +119,17 @@ void FixPeriNeigh::init()
   neighbor->requests[irequest]->half = 0;
   neighbor->requests[irequest]->full = 1;
   neighbor->requests[irequest]->occasional = 1;
+
+  // compute PD scale factor, stored in Atom class, used by DumpCFG
+
+  int nlocal = atom->nlocal;
+  double vone = 0.0;
+  for (int i = 0; i < nlocal; i++) vone += atom->vfrac[i];
+  double vave;
+  MPI_Allreduce(&vone,&vave,1,MPI_DOUBLE,MPI_SUM,world);
+  if (atom->natoms) vave /= atom->natoms;
+  if (vave > 0.0) atom->pdscale = 1.44 / pow(vave,1.0/3.0);
+  else atom->pdscale = 1.0;
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/atom.cpp b/src/atom.cpp
index 98d199a013..fb2fa564ea 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -140,6 +140,10 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
   cs_flag = csforce_flag = vforce_flag = ervelforce_flag= etag_flag = 0;
   rho_flag = e_flag = cv_flag = vest_flag = 0;
 
+  // Peridynamic scale factor
+
+  pdscale = 1.0;
+
   // ntype-length arrays
 
   mass = NULL;
diff --git a/src/atom.h b/src/atom.h
index 15ce88f08b..fd48f7620a 100644
--- a/src/atom.h
+++ b/src/atom.h
@@ -114,6 +114,10 @@ class Atom : protected Pointers {
   int cs_flag,csforce_flag,vforce_flag,ervelforce_flag,etag_flag;
   int rho_flag,e_flag,cv_flag,vest_flag;
 
+  // Peridynamics scale factor, used by dump cfg
+
+  double pdscale;
+
   // molecule templates
   // each template can be a set of consecutive molecules
   // each with same ID (stored in molecules)
diff --git a/src/dump_cfg.cpp b/src/dump_cfg.cpp
index 558512ace7..5b74642fe6 100755
--- a/src/dump_cfg.cpp
+++ b/src/dump_cfg.cpp
@@ -130,22 +130,16 @@ void DumpCFG::init_style()
 
 void DumpCFG::write_header(bigint n)
 {
-  // special handling for atom style peri
-  //   use average volume of particles to scale particles to mimic C atoms
-  //   scale box dimension to sc lattice for C with sigma = 1.44 Angstroms
-  // special handling for unwrapped coordinates
+  // set scale factor used by AtomEye for CFG viz
+  // default = 1.0
+  // for peridynamics, set to pre-computed PD scale factor
+  //   so PD particles mimic C atoms
+  // for unwrapped coords, set to UNWRAPEXPAND (10.0)
+  //   so molecules are not split across periodic box boundaries
 
-  double scale;
-  if (atom->peri_flag) {
-    int nlocal = atom->nlocal;
-    double vone = 0.0;
-    for (int i = 0; i < nlocal; i++) vone += atom->vfrac[i];
-    double vave;
-    MPI_Allreduce(&vone,&vave,1,MPI_DOUBLE,MPI_SUM,world);
-    if (atom->natoms) vave /= atom->natoms;
-    if (vave > 0.0) scale = 1.44 / pow(vave,1.0/3.0);
-  } else if (unwrapflag == 1) scale = UNWRAPEXPAND;
-  else scale = 1.0;
+  double scale = 1.0;
+  if (atom->peri_flag) scale = atom->pdscale;
+  else if (unwrapflag == 1) scale = UNWRAPEXPAND;
 
   char str[64];
   sprintf(str,"Number of particles = %s\n",BIGINT_FORMAT);