Commit 96bf2c26 authored by Nicholas Breen's avatar Nicholas Breen

New upstream release, patch rebasing

parent 98b186f1
gromacs (5.0.5-1) unstable; urgency=medium
* New upstream release.
-- Nicholas Breen <nbreen@debian.org> Sat, 16 May 2015 11:30:11 -0700
gromacs (5.0.4-2) unstable; urgency=medium
* Post-Jessie upload to unstable, no other changes.
......
......@@ -6,10 +6,10 @@ Origin: vendor
Forwarded: not-needed
Last-Update: 2013-05-15
---
Index: gromacs-5.0.4/CMakeLists.txt
Index: gromacs-5.0.5/CMakeLists.txt
===================================================================
--- gromacs-5.0.4.orig/CMakeLists.txt
+++ gromacs-5.0.4/CMakeLists.txt
--- gromacs-5.0.5.orig/CMakeLists.txt
+++ gromacs-5.0.5/CMakeLists.txt
@@ -141,7 +141,7 @@ set(CPACK_PACKAGE_VENDOR "gromacs.org")
set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Gromacs - a toolkit for high-performance molecular simulation")
set(CPACK_RESOURCE_FILE_WELCOME "${CMAKE_SOURCE_DIR}/admin/InstallWelcome.txt")
......@@ -19,7 +19,7 @@ Index: gromacs-5.0.4/CMakeLists.txt
set(CPACK_RESOURCE_FILE_README "${CMAKE_SOURCE_DIR}/admin/InstallInfo.txt")
set(CPACK_SOURCE_IGNORE_FILES "\\\\.isreposource$;\\\\.git/;\\\\.gitignore$;\\\\.gitattributes;")
set(CPACK_PROJECT_CONFIG_FILE "${CMAKE_SOURCE_DIR}/CPackInit.cmake")
@@ -902,7 +902,7 @@ endif()
@@ -912,7 +912,7 @@ endif()
#COPYING file: Only necessary for binary distributions.
#Simpler to always install.
......
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......@@ -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-5.0.2/src/contrib/mkice.c
Index: gromacs-5.0.5/src/contrib/mkice.c
===================================================================
--- gromacs-5.0.2.orig/src/contrib/mkice.c
+++ gromacs-5.0.2/src/contrib/mkice.c
--- gromacs-5.0.5.orig/src/contrib/mkice.c
+++ gromacs-5.0.5/src/contrib/mkice.c
@@ -494,7 +494,7 @@ 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-5.0.2/src/contrib/mkice.c
"build water clusters based on oxygen coordinates only."
};
static int nx=1,ny=1,nz=1;
Index: gromacs-5.0.2/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
Index: gromacs-5.0.5/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
===================================================================
--- gromacs-5.0.2.orig/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
+++ gromacs-5.0.2/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
--- gromacs-5.0.5.orig/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
+++ gromacs-5.0.5/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
@@ -201,7 +201,7 @@ void
{{
if (ic->ljpme_comb_rule == eljpmeLB)
......@@ -29,10 +29,10 @@ Index: gromacs-5.0.2/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator
}}
vdwkt = vdwktLJEWALDCOMBGEOM;
}}
Index: gromacs-5.0.2/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
Index: gromacs-5.0.5/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
===================================================================
--- gromacs-5.0.2.orig/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
+++ gromacs-5.0.2/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
--- gromacs-5.0.5.orig/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
+++ gromacs-5.0.5/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
@@ -336,7 +336,7 @@ nbnxn_kernel_simd_2xnn(nbnxn_pairlist_se
{
if (ic->ljpme_comb_rule == eljpmeLB)
......@@ -42,10 +42,10 @@ Index: gromacs-5.0.2/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd
}
vdwkt = vdwktLJEWALDCOMBGEOM;
}
Index: gromacs-5.0.2/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
Index: gromacs-5.0.5/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
===================================================================
--- gromacs-5.0.2.orig/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
+++ gromacs-5.0.2/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
--- gromacs-5.0.5.orig/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
+++ gromacs-5.0.5/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
@@ -335,7 +335,7 @@ nbnxn_kernel_simd_4xn(nbnxn_pairlist_set
{
if (ic->ljpme_comb_rule == eljpmeLB)
......@@ -55,10 +55,10 @@ Index: gromacs-5.0.2/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_
}
vdwkt = vdwktLJEWALDCOMBGEOM;
}
Index: gromacs-5.0.2/src/programs/mdrun/mdrun.cpp
Index: gromacs-5.0.5/src/programs/mdrun/mdrun.cpp
===================================================================
--- gromacs-5.0.2.orig/src/programs/mdrun/mdrun.cpp
+++ gromacs-5.0.2/src/programs/mdrun/mdrun.cpp
--- gromacs-5.0.5.orig/src/programs/mdrun/mdrun.cpp
+++ gromacs-5.0.5/src/programs/mdrun/mdrun.cpp
@@ -386,8 +386,8 @@ 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-5.0.2/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-5.0.2/docs/man/man1/gmx-mdrun.1
Index: gromacs-5.0.5/docs/man/man1/gmx-mdrun.1
===================================================================
--- gromacs-5.0.2.orig/docs/man/man1/gmx-mdrun.1
+++ gromacs-5.0.2/docs/man/man1/gmx-mdrun.1
--- gromacs-5.0.5.orig/docs/man/man1/gmx-mdrun.1
+++ gromacs-5.0.5/docs/man/man1/gmx-mdrun.1
@@ -101,7 +101,7 @@ With option \fB\-maxh\fR a simulation is
When \fBmdrun\fR receives a TERM signal, it will set nsteps to the current step plus one. When \fBmdrun\fR receives an INT signal (e.g. when ctrl+C is pressed), it will stop after the next neighbor search step (with nstlist=0 at the next step). In both cases all the usual output will be written to file. When running with MPI, a signal to one of the \fBmdrun\fR ranks is sufficient, this signal should not be sent to mpirun or the \fBmdrun\fR process that is the parent of the others.
......@@ -83,3 +83,16 @@ Index: gromacs-5.0.2/docs/man/man1/gmx-mdrun.1
When \fBmdrun\fR is started with MPI, it does not run niced by default.
Index: gromacs-5.0.5/src/gromacs/gmxana/gmx_wham.cpp
===================================================================
--- gromacs-5.0.5.orig/src/gromacs/gmxana/gmx_wham.cpp
+++ gromacs-5.0.5/src/gromacs/gmxana/gmx_wham.cpp
@@ -3306,7 +3306,7 @@ int gmx_wham(int argc, char *argv[])
{ "-ac-trestart", FALSE, etREAL, {&opt.acTrestart},
"When computing autocorrelation functions, restart computing every .. (ps)"},
{ "-acred", FALSE, etBOOL, {&opt.bAllowReduceIact},
- "HIDDENWhen smoothing the ACTs, allow to reduce ACTs. Otherwise, only increase ACTs "
+ "HIDDENWhen smoothing the ACTs, allows one to reduce ACTs. Otherwise, only increase ACTs "
"during smoothing"},
{ "-nBootstrap", FALSE, etINT, {&opt.nBootStrap},
"nr of bootstraps to estimate statistical uncertainty (e.g., 200)" },
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