Commit b780feda authored by Nicholas Breen's avatar Nicholas Breen

New upstream release 5.0.6

parent 96bf2c26
gromacs (5.0.6-1) unstable; urgency=medium
* New upstream release.
-- Nicholas Breen <nbreen@debian.org> Sun, 26 Jul 2015 13:58:11 -0700
gromacs (5.0.5-1) unstable; urgency=medium
* New upstream release.
......
......@@ -6,11 +6,11 @@ Origin: vendor
Forwarded: not-needed
Last-Update: 2013-05-15
---
Index: gromacs-5.0.5/CMakeLists.txt
Index: gromacs-5.0.6/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")
--- gromacs-5.0.6.orig/CMakeLists.txt
+++ gromacs-5.0.6/CMakeLists.txt
@@ -144,7 +144,7 @@ set(CPACK_PACKAGE_VENDOR "gromacs.org")
set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "Gromacs - a toolkit for high-performance molecular simulation")
set(CPACK_RESOURCE_FILE_WELCOME "${CMAKE_SOURCE_DIR}/admin/InstallWelcome.txt")
# Its GPL/LGPL, so they do not have to agree to a license for mere usage, but some installers require this...
......@@ -19,7 +19,7 @@ Index: gromacs-5.0.5/CMakeLists.txt
set(CPACK_RESOURCE_FILE_README "${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")
@@ -912,7 +912,7 @@ endif()
@@ -921,7 +921,7 @@ endif()
#COPYING file: Only necessary for binary distributions.
#Simpler to always install.
......
This source diff could not be displayed because it is too large. You can view the blob instead.
......@@ -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-5.0.5/src/contrib/mkice.c
Index: gromacs-5.0.6/src/contrib/mkice.c
===================================================================
--- gromacs-5.0.5.orig/src/contrib/mkice.c
+++ gromacs-5.0.5/src/contrib/mkice.c
--- gromacs-5.0.6.orig/src/contrib/mkice.c
+++ gromacs-5.0.6/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-5.0.5/src/contrib/mkice.c
"build water clusters based on oxygen coordinates only."
};
static int nx=1,ny=1,nz=1;
Index: gromacs-5.0.5/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
Index: gromacs-5.0.6/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
--- gromacs-5.0.6.orig/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
+++ gromacs-5.0.6/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-5.0.5/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator
}}
vdwkt = vdwktLJEWALDCOMBGEOM;
}}
Index: gromacs-5.0.5/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
Index: gromacs-5.0.6/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
--- gromacs-5.0.6.orig/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
+++ gromacs-5.0.6/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-5.0.5/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd
}
vdwkt = vdwktLJEWALDCOMBGEOM;
}
Index: gromacs-5.0.5/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
Index: gromacs-5.0.6/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
--- gromacs-5.0.6.orig/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
+++ gromacs-5.0.6/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-5.0.5/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_
}
vdwkt = vdwktLJEWALDCOMBGEOM;
}
Index: gromacs-5.0.5/src/programs/mdrun/mdrun.cpp
Index: gromacs-5.0.6/src/programs/mdrun/mdrun.cpp
===================================================================
--- gromacs-5.0.5.orig/src/programs/mdrun/mdrun.cpp
+++ gromacs-5.0.5/src/programs/mdrun/mdrun.cpp
--- gromacs-5.0.6.orig/src/programs/mdrun/mdrun.cpp
+++ gromacs-5.0.6/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-5.0.5/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-5.0.5/docs/man/man1/gmx-mdrun.1
Index: gromacs-5.0.6/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
--- gromacs-5.0.6.orig/docs/man/man1/gmx-mdrun.1
+++ gromacs-5.0.6/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.
......@@ -83,10 +83,10 @@ Index: gromacs-5.0.5/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
Index: gromacs-5.0.6/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
--- gromacs-5.0.6.orig/src/gromacs/gmxana/gmx_wham.cpp
+++ gromacs-5.0.6/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)"},
......@@ -96,3 +96,24 @@ Index: gromacs-5.0.5/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-5.0.6/docs/man/man1/gmx-dos.1
===================================================================
--- gromacs-5.0.6.orig/docs/man/man1/gmx-dos.1
+++ gromacs-5.0.6/docs/man/man1/gmx-dos.1
@@ -12,7 +12,15 @@ gmx dos [\-f [<.trr/.cpt/...>]] [\-s [<.
[\-beginfit <real>] [\-endfit <real>]
.SH DESCRIPTION
-\fBgmx dos\fR computes the Density of States from a simulations. In order for this to be meaningful the velocities must be saved in the trajecotry with sufficiently high frequency such as to cover all vibrations. For flexible systems that would be around a few fs between saving. Properties based on the DoS are printed on the standard output.Note that the density of states is calculated from the mass\-weighted autocorrelation, and by default only from the square of the real component rather than absolute value. This means the shape can differ substantially from the plain vibrational power spectrum you can calculate with gmx velacc.
+\fBgmx dos\fR computes the Density of States from a simulation. In order for
+this to be meaningful the velocities must be saved in the trajectory with
+sufficiently high frequency such as to cover all vibrations. For flexible
+systems, that would be around a few fs between saving. Properties based on the
+DoS are printed on the standard output. Note that the density of states is
+calculated from the mass\-weighted autocorrelation, and by default only from
+the square of the real component rather than absolute value. This means the
+shape can differ substantially from the plain vibrational power spectrum you
+can calculate with \fBgmx velacc\fR.
.SH OPTIONS
Options to specify input and output files:
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment