Re: [Avogadro-devel] Some symmetry operations fail to honor spacegroup setting
Hi Jure,
Thanks for offering to fix up some of the rough edges here, any
contributions are greatly appreciated!
The eigen fix looks reasonable, but surprising that it didn't get inherited
from a higher level directory.
For now, you might be better off basing your work off of master. The
QuantumEspresso patch needs some attention to see if it will work on all
platforms and there hasn't been much activity on it in a while.
Dave
On Tue, Feb 4, 2014 at 5:39 AM, Jure Varlec jure.var...@ki.si wrote:
Also, I had to add an include path for Eigen to fix building, do I
have
to make a separate branch for that single commit?
I'm not sure why that (adding an Eigen include path) would be necessary.
That should be covered by CMake. Why don't you comment on your problems
with Eigen and we'll see if it can be fixed outside of a patch.
Well, CMake finds both Eigen2 and Eigen3, but build fails with 'fatal
error:
Eigen/Core: No such file or directory' unless I patch it with
diff --git a/libavogadro/src/colors/CMakeLists.txt
b/libavogadro/src/colors/CMakeLists.txt
index a967516..c0836a8 100644
--- a/libavogadro/src/colors/CMakeLists.txt
+++ b/libavogadro/src/colors/CMakeLists.txt
@@ -6,7 +6,7 @@ ADD_DEFINITIONS(-DQT_SHARED)
set(DESTINATION_DIR ${Avogadro_PLUGIN_INSTALL_DIR}/colors)
-include_directories(${CMAKE_CURRENT_BINARY_DIR})
+include_directories(${CMAKE_CURRENT_BINARY_DIR} ${EIGEN_INCLUDE_DIR})
set(LINK_LIBS avogadro)
set(PLUGIN_LABEL colors)
---
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Re: [Avogadro-devel] Some symmetry operations fail to honor spacegroup setting
On Tue, Feb 4, 2014 at 5:39 AM, Jure Varlec jure.var...@ki.si wrote:
Also, I had to add an include path for Eigen to fix building, do I have
to make a separate branch for that single commit?
I'm not sure why that (adding an Eigen include path) would be necessary.
That should be covered by CMake. Why don't you comment on your problems
with Eigen and we'll see if it can be fixed outside of a patch.
Well, CMake finds both Eigen2 and Eigen3, but build fails with 'fatal error:
Eigen/Core: No such file or directory' unless I patch it with
diff --git a/libavogadro/src/colors/CMakeLists.txt
b/libavogadro/src/colors/CMakeLists.txt
index a967516..c0836a8 100644
--- a/libavogadro/src/colors/CMakeLists.txt
+++ b/libavogadro/src/colors/CMakeLists.txt
@@ -6,7 +6,7 @@ ADD_DEFINITIONS(-DQT_SHARED)
set(DESTINATION_DIR ${Avogadro_PLUGIN_INSTALL_DIR}/colors)
-include_directories(${CMAKE_CURRENT_BINARY_DIR})
+include_directories(${CMAKE_CURRENT_BINARY_DIR} ${EIGEN_INCLUDE_DIR})
set(LINK_LIBS avogadro)
set(PLUGIN_LABEL colors)
Are you building with Eigen 2 or 3? I just looked at master, and
libavogadro/src/CMakeLists.txt adds it to the include directories, the
same is not true for Eigen 3. There are still a number of rough edges
with the Eigen 3 support, we should take a pass at getting that to
build consistently. A lot of people (myself included) have Eigen
installed and can miss this.
I also don't see anything that defines EIGEN_INCLUDE_DIR, both
variants have the major version number. Hope that helps.
Marcus
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Re: [Avogadro-devel] Some symmetry operations fail to honor spacegroup setting
On Tue, Feb 4, 2014 at 10:45 AM, Jure Varlec jure.var...@ki.si wrote:
On Tuesday 04 of February 2014 09:56:01 Marcus D. Hanwell wrote:
Are you building with Eigen 2 or 3? I just looked at master, and
libavogadro/src/CMakeLists.txt adds it to the include directories, the
same is not true for Eigen 3. There are still a number of rough edges
with the Eigen 3 support, we should take a pass at getting that to
build consistently. A lot of people (myself included) have Eigen
installed and can miss this.
I also don't see anything that defines EIGEN_INCLUDE_DIR, both
variants have the major version number. Hope that helps.
I'm building with both. Although Eigen is a header-only library, I'm running
Gentoo so both versions need to be installed as build-time dependencies of
various packages, they are at /usr/include/eigen{2,3}
Actually, when I touched one of CMakeLists and caused a reconfiguration, the
problem popped out elsewhere, then disappeared later. It seems that, starting
with an empty build directory, I have to run CMake twice, then it builds
successfully. This behaviour seems to be consistent.
It is, I will see if I can reproduce. I don't even see where
EIGEN_INCLUDE_DIR would get defined, and how it would solve any
problem. A git grep for it in the source tree turns up nothing, and we
should consistently choose Eigen 2 or 3 - mixing the two would not end
well.
Thanks for your feedback, I will try to dig a little deeper when I
have some time and see if we can clean things up a little more.
Marcus
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Re: [Avogadro-devel] Some symmetry operations fail to honor spacegroup setting
Hi guys,
I don't have a Windows machine to test the QuantumEspresso patch, but is there
something I can do to help this along?
Jure, the QuantumEspresso patch does change some details about how spglib is
integrated into Avogadro, but I believe I could re-work any changes you need to
make back into the QuantumEspresso patch.
Finally, it might be easier to just prepare QuantumEspresso for Avogadro 2.
There is already some python support for spglib, so it seems reasonable that I
could move the the whole input builder into python fro use in Avogadro 2.
Albert
Message: 8
Date: Tue, 4 Feb 2014 08:56:49 -0500
From: David Lonie david.lo...@kitware.com
Subject: Re: [Avogadro-devel] Some symmetry operations fail to honor
spacegroup setting
To: Jure Varlec jure.var...@ki.si
Cc: Avogadro-devel Devel avogadro-devel@lists.sourceforge.net
Message-ID:
CA+=e1ovv5yTeHD7SU=dgx1ktfj68bjiukvp6_26e33xdacf...@mail.gmail.com
Content-Type: text/plain; charset=iso-8859-1
Hi Jure,
Thanks for offering to fix up some of the rough edges here, any
contributions are greatly appreciated!
The eigen fix looks reasonable, but surprising that it didn't get inherited
from a higher level directory.
For now, you might be better off basing your work off of master. The
QuantumEspresso patch needs some attention to see if it will work on all
platforms and there hasn't been much activity on it in a while.
Dave
On Tue, Feb 4, 2014 at 5:39 AM, Jure Varlec jure.var...@ki.si wrote:
Also, I had to add an include path for Eigen to fix building, do I
have
to make a separate branch for that single commit?
I'm not sure why that (adding an Eigen include path) would be necessary.
That should be covered by CMake. Why don't you comment on your problems
with Eigen and we'll see if it can be fixed outside of a patch.
Well, CMake finds both Eigen2 and Eigen3, but build fails with 'fatal
error:
Eigen/Core: No such file or directory' unless I patch it with
diff --git a/libavogadro/src/colors/CMakeLists.txt
b/libavogadro/src/colors/CMakeLists.txt
index a967516..c0836a8 100644
--- a/libavogadro/src/colors/CMakeLists.txt
+++ b/libavogadro/src/colors/CMakeLists.txt
@@ -6,7 +6,7 @@ ADD_DEFINITIONS(-DQT_SHARED)
set(DESTINATION_DIR ${Avogadro_PLUGIN_INSTALL_DIR}/colors)
-include_directories(${CMAKE_CURRENT_BINARY_DIR})
+include_directories(${CMAKE_CURRENT_BINARY_DIR} ${EIGEN_INCLUDE_DIR})
set(LINK_LIBS avogadro)
set(PLUGIN_LABEL colors)
---
--
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