From ced125c2b4e73e5bcc03b870d4091b623e36a95b Mon Sep 17 00:00:00 2001
From: sjplimp <sjplimp@f3b2605a-c512-4ea7-a41b-209d697bcdaa>
Date: Fri, 5 Dec 2014 22:05:02 +0000
Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12819
 f3b2605a-c512-4ea7-a41b-209d697bcdaa

---
 src/USER-MISC/fix_gle.cpp |  8 +++++++-
 src/USER-MISC/fix_ipi.cpp | 14 ++++++--------
 2 files changed, 13 insertions(+), 9 deletions(-)

diff --git a/src/USER-MISC/fix_gle.cpp b/src/USER-MISC/fix_gle.cpp
index 5f28dea37b..95f868f95f 100644
--- a/src/USER-MISC/fix_gle.cpp
+++ b/src/USER-MISC/fix_gle.cpp
@@ -82,7 +82,13 @@ void StabCholesky(int n, const double* MMt, double* M)
         for (k=0; k<i; ++k) D[i]-=L[midx(n,i,k)]*L[midx(n,i,k)]*D[k];
     }
 
-    for(i=0; i<n; ++i) D[i]=(D[i]>0.?sqrt(D[i]):0.);
+    for(i=0; i<n; ++i) 
+    {
+#ifdef GLE_DEBUG		
+		if (D[i]<0) fprintf(stderr,"GLE Cholesky: Negative diagonal term %le, has been set to zero.\n", D[i]);			
+#endif		
+		D[i]=(D[i]>0.?sqrt(D[i]):0.);
+	}
 
     for(i=0; i<n; ++i) for (j=0; j<n; j++) M[midx(n,i,j)]=L[midx(n,i,j)]*D[j];
 }
diff --git a/src/USER-MISC/fix_ipi.cpp b/src/USER-MISC/fix_ipi.cpp
index 02cfcd9abb..58251a814e 100644
--- a/src/USER-MISC/fix_ipi.cpp
+++ b/src/USER-MISC/fix_ipi.cpp
@@ -319,12 +319,12 @@ void FixIPI::initial_integrate(int vflag)
   double *boxlo = domain->boxlo;
   double posconv;
   posconv=0.52917721*force->angstrom;
-  boxlo[0] = 0;
-  boxlo[1] = 0;
-  boxlo[2] = 0;
-  boxhi[0] = cellh[0]*posconv;
-  boxhi[1] = cellh[4]*posconv;
-  boxhi[2] = cellh[8]*posconv;
+  boxlo[0] = -0.5*cellh[0]*posconv;
+  boxlo[1] = -0.5*cellh[4]*posconv;
+  boxlo[2] = -0.5*cellh[8]*posconv;
+  boxhi[0] = -boxlo[0];
+  boxhi[1] = -boxlo[1];
+  boxhi[2] = -boxlo[2];
   domain->xy = cellh[1]*posconv;
   domain->xz = cellh[2]*posconv;
   domain->yz = cellh[5]*posconv;
@@ -421,7 +421,6 @@ void FixIPI::final_integrate()
       error->one(FLERR, "Got EXIT message from i-PI. Now leaving!");
 
     if (strcmp(header,"GETFORCE    ") == 0 )  {
-
       writebuffer(ipisock,"FORCEREADY  ",MSGLEN, error);
       writebuffer(ipisock,(char*) &pot,8, error);
       writebuffer(ipisock,(char*) &nat,4, error);
@@ -432,7 +431,6 @@ void FixIPI::final_integrate()
     }
     else
       error->one(FLERR, "Wrapper did not ask for forces, I will now die!");
-
   }
 
   hasdata=0;