Commit 202855f7 authored by Nicholas Breen's avatar Nicholas Breen

New upstream release 5.1.1

parent bb7ed95f
gromacs (5.1.1-1) unstable; urgency=medium
* New upstream release.
-- Nicholas Breen <nbreen@debian.org> Mon, 09 Nov 2015 17:24:02 -0800
gromacs (5.1-1) unstable; urgency=low
* New upstream release. This release completes the transition to "gmx"
......
......@@ -11,4 +11,4 @@ Index: /usr/share/doc/gromacs/html/index.html
Files: /usr/share/doc/gromacs/html/*.html /usr/share/doc/gromacs/html/user-guide/*.html
Format: PDF
Files: /usr/share/doc/gromacs/html/manual-5.1.pdf
Files: /usr/share/doc/gromacs/html/manual-5.1.1.pdf
......@@ -3,10 +3,10 @@ Origin: vendor
Last-Update: 2014-06-12
---
This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
Index: gromacs-5.1/src/contrib/mkice.c
Index: gromacs-5.1.1/src/contrib/mkice.c
===================================================================
--- gromacs-5.1.orig/src/contrib/mkice.c
+++ gromacs-5.1/src/contrib/mkice.c
--- gromacs-5.1.1.orig/src/contrib/mkice.c
+++ gromacs-5.1.1/src/contrib/mkice.c
@@ -493,7 +493,7 @@ int main(int argc,char *argv[])
"If an input file is given it is interpreted as a series of oxygen",
"coordinates the distance between which can be scaled by the odist flag.",
......@@ -16,10 +16,10 @@ Index: gromacs-5.1/src/contrib/mkice.c
"build water clusters based on oxygen coordinates only."
};
static int nx=1,ny=1,nz=1;
Index: gromacs-5.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
Index: gromacs-5.1.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
===================================================================
--- gromacs-5.1.orig/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
+++ gromacs-5.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
--- gromacs-5.1.1.orig/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
+++ gromacs-5.1.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
@@ -202,7 +202,7 @@ void
{{
if (ic->ljpme_comb_rule == eljpmeLB)
......@@ -29,10 +29,10 @@ Index: gromacs-5.1/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/n
}}
vdwkt = vdwktLJEWALDCOMBGEOM;
}}
Index: gromacs-5.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
Index: gromacs-5.1.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
===================================================================
--- gromacs-5.1.orig/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
+++ gromacs-5.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
--- gromacs-5.1.1.orig/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
+++ gromacs-5.1.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
@@ -338,7 +338,7 @@ nbnxn_kernel_simd_2xnn(nbnxn_pairlist_se
{
if (ic->ljpme_comb_rule == eljpmeLB)
......@@ -42,10 +42,10 @@ Index: gromacs-5.1/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2
}
vdwkt = vdwktLJEWALDCOMBGEOM;
}
Index: gromacs-5.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
Index: gromacs-5.1.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
===================================================================
--- gromacs-5.1.orig/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
+++ gromacs-5.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
--- gromacs-5.1.1.orig/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
+++ gromacs-5.1.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
@@ -337,7 +337,7 @@ nbnxn_kernel_simd_4xn(nbnxn_pairlist_set
{
if (ic->ljpme_comb_rule == eljpmeLB)
......@@ -55,10 +55,10 @@ Index: gromacs-5.1/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4x
}
vdwkt = vdwktLJEWALDCOMBGEOM;
}
Index: gromacs-5.1/src/programs/mdrun/mdrun.cpp
Index: gromacs-5.1.1/src/programs/mdrun/mdrun.cpp
===================================================================
--- gromacs-5.1.orig/src/programs/mdrun/mdrun.cpp
+++ gromacs-5.1/src/programs/mdrun/mdrun.cpp
--- gromacs-5.1.1.orig/src/programs/mdrun/mdrun.cpp
+++ gromacs-5.1.1/src/programs/mdrun/mdrun.cpp
@@ -214,8 +214,8 @@ int gmx_mdrun(int argc, char *argv[])
"the [TT]mdrun[tt] process that is the parent of the others.",
"[PAR]",
......@@ -70,10 +70,10 @@ Index: gromacs-5.1/src/programs/mdrun/mdrun.cpp
"[TT]mdrun[tt] pauses whenever no IMD client is connected. Pulling from the",
"IMD remote can be turned on by [TT]-imdpull[tt].",
"The port [TT]mdrun[tt] listens to can be altered by [TT]-imdport[tt].The",
Index: gromacs-5.1/src/gromacs/gmxana/gmx_wham.cpp
Index: gromacs-5.1.1/src/gromacs/gmxana/gmx_wham.cpp
===================================================================
--- gromacs-5.1.orig/src/gromacs/gmxana/gmx_wham.cpp
+++ gromacs-5.1/src/gromacs/gmxana/gmx_wham.cpp
--- gromacs-5.1.1.orig/src/gromacs/gmxana/gmx_wham.cpp
+++ gromacs-5.1.1/src/gromacs/gmxana/gmx_wham.cpp
@@ -3427,7 +3427,7 @@ int gmx_wham(int argc, char *argv[])
{ "-ac-trestart", FALSE, etREAL, {&opt.acTrestart},
"When computing autocorrelation functions, restart computing every .. (ps)"},
......@@ -83,11 +83,11 @@ Index: gromacs-5.1/src/gromacs/gmxana/gmx_wham.cpp
"during smoothing"},
{ "-nBootstrap", FALSE, etINT, {&opt.nBootStrap},
"nr of bootstraps to estimate statistical uncertainty (e.g., 200)" },
Index: gromacs-5.1/src/gromacs/gmxana/dlist.c
Index: gromacs-5.1.1/src/gromacs/gmxana/dlist.c
===================================================================
--- gromacs-5.1.orig/src/gromacs/gmxana/dlist.c
+++ gromacs-5.1/src/gromacs/gmxana/dlist.c
@@ -318,7 +318,7 @@ gmx_bool has_dihedral(int Dih, t_dlist *
--- gromacs-5.1.1.orig/src/gromacs/gmxana/dlist.c
+++ gromacs-5.1.1/src/gromacs/gmxana/dlist.c
@@ -328,7 +328,7 @@ gmx_bool has_dihedral(int Dih, t_dlist *
break;
default:
pr_dlist(stdout, 1, dl, 1, 0, TRUE, TRUE, TRUE, TRUE, MAXCHI);
......@@ -96,10 +96,10 @@ Index: gromacs-5.1/src/gromacs/gmxana/dlist.c
Dih, __FILE__, __LINE__);
}
return b;
Index: gromacs-5.1/src/gromacs/pbcutil/mshift.cpp
Index: gromacs-5.1.1/src/gromacs/pbcutil/mshift.cpp
===================================================================
--- gromacs-5.1.orig/src/gromacs/pbcutil/mshift.cpp
+++ gromacs-5.1/src/gromacs/pbcutil/mshift.cpp
--- gromacs-5.1.1.orig/src/gromacs/pbcutil/mshift.cpp
+++ gromacs-5.1.1/src/gromacs/pbcutil/mshift.cpp
@@ -146,7 +146,7 @@ static void mk_igraph(t_graph *g, int ft
gmx_noreturn static void g_error(int line, const char *file)
......@@ -109,10 +109,10 @@ Index: gromacs-5.1/src/gromacs/pbcutil/mshift.cpp
file, line);
}
#define GCHECK(g) if (g == NULL) g_error(__LINE__, __FILE__)
Index: gromacs-5.1/docs/man/gmx-mdrun.1
Index: gromacs-5.1.1/docs/man/gmx-mdrun.1
===================================================================
--- gromacs-5.1.orig/docs/man/gmx-mdrun.1
+++ gromacs-5.1/docs/man/gmx-mdrun.1
--- gromacs-5.1.1.orig/docs/man/gmx-mdrun.1
+++ gromacs-5.1.1/docs/man/gmx-mdrun.1
@@ -200,7 +200,7 @@ is sufficient, this signal should not be
the \fBmdrun\fP process that is the parent of the others.
.sp
......
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