「分子エディター」
Avogadro ( https://avogadro.cc/ ) 最新版は Avogadro 1.2.0[2016-06-15リリース]
と
Avogadro2 ( https://two.avogadro.cc/ ) 最新版は Avogadro 1.97.0[2022-07-22リリース]
がある.
Avogadro2はAvogadroの作り直しでスケーリングが向上したそうな 扱える原子数が増えたそうな
ここでは Avogadro2 こと Avogadro 1.97.0 を扱います
git先 https://github.com/OpenChemistry/openchemistry
インストール †
[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.1 (Blue Onyx)
[root@rockylinux9 ~]# cd /apps/src/
[root@rockylinux9 src]# git clone --recursive https://github.com/OpenChemistry/openchemistry
するとAvogadroを含む関連プロジェクトが一緒にダウンロードされます.
[root@rockylinux9 src]# ls -l
total 4
drwxr-xr-x. 12 root root 4096 May 7 00:11 openchemistry
[root@rockylinux9 src]# ls -l openchemistry/
total 48
drwxr-xr-x. 11 root root 4096 May 7 00:11 avogadroapp
drwxr-xr-x. 6 root root 97 May 7 00:11 avogadrodata
drwxr-xr-x. 3 root root 4096 May 7 00:11 avogadrogenerators
drwxr-xr-x. 12 root root 4096 May 7 00:11 avogadrolibs
drwxr-xr-x. 2 root root 4096 May 7 00:11 cmake
-rw-r--r--. 1 root root 4911 May 7 00:11 CMakeLists.txt
-rw-r--r--. 1 root root 896 May 7 00:11 CONTRIBUTING.md
drwxr-xr-x. 24 root root 4096 May 7 00:11 crystals
-rw-r--r--. 1 root root 554 May 7 00:11 CTestConfig.cmake
-rw-r--r--. 1 root root 1509 May 7 00:11 LICENSE
drwxr-xr-x. 30 root root 4096 May 7 00:11 molecules
drwxr-xr-x. 7 root root 191 May 7 00:11 molequeue
-rw-r--r--. 1 root root 2535 May 7 00:11 README.md
drwxr-xr-x. 6 root root 87 May 7 00:11 thirdparty
[root@rockylinux9 src]#
コンパイルの要件は
- C/C++ compiler that supports C++11
- OpenGL
- Qt 5.6+
- CMake 3.3+
- Python
とある. 下準備として開発環境を入れます.
dnf groupinstall "Development Tools" -y
dnf install cmake -y
dnf install qt5-qtbase qt5-qtbase-devel qt5-qtwebkit-devel libxml2-devel qt5-qtsvg-devel -y
dnf install mesa-libGLU-devel -y
っで調理開始. cmakeがRockyLinux標準の3.20.2ではなく、それ以上を要求します. なのでcmakeで最新を入れて於きます.
[root@rockylinux9 src]# mkdir openchemistry-build ; cd openchemistry-build
[root@rockylinux9 openchemistry-build]# pwd
/apps/src/openchemistry-build
[root@rockylinux9 openchemistry-build]# module load cmake
[root@rockylinux9 openchemistry-build]# cmake ../openchemistry -DCMAKE_INSTALL_PREFIX=/apps/avogadro -DCMAKE_BUILD_TYPE=Release
-- The CXX compiler identification is GNU 11.3.1
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Found ZLIB: /usr/lib64/libz.so (found version "1.2.11")
-- Found LibXml2: /usr/lib64/libxml2.so (found version "2.9.13")
-- Configuring done (0.3s)
-- Generating done (0.0s)
-- Build files have been written to: /apps/src/openchemistry-build
[root@rockylinux9 openchemistry-build]# make -j 20
:
:
[root@rockylinux9 openchemistry-build]#
完成品を展開します
[root@rockylinux9 openchemistry-build]# cp -arp ./prefix /apps/avogadro2-1.97.0-132
Environment Modulesですが、
[root@rockylinux9 ~]# mkdir -p /apps/modulefiles/avogadro/
[root@rockylinux9 ~]# vi /apps/modulefiles/avogadro/1.97.0
#%Module
set root /apps/avogadro2-1.97.0-132
prepend-path PATH $root/bin
[root@rockylinux9 ~]#
っで使ってみる
[saber@rockylinux9 ~]$ module use /apps/modulefiles
[saber@rockylinux9 ~]$ module load avogadro
[saber@rockylinux9 ~]$ avogadro2
メモ †
実行時に下記メッセージが表示される
ScriptLoader::queryProgramName: Unable to retrieve program name for "/apps/avogadro2-1.97.0-132/lib64/avogadro2/scripts/charges/antechamber.py" ;
"Error running script '/usr/bin/python3 /apps/avogadro2-1.97.0-132/lib64/avogadro2/scripts/charges/antechamber.py --display-name --lang en_US':
Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n File
\"/apps/avogadro2-1.97.0-132/lib64/avogadro2/scripts/charges/antechamber.py\", line 151, in <module>\n raise RuntimeError(\"antechamber is
unavailable\")\nRuntimeError: antechamber is unavailable\n"
ScriptLoader::queryProgramName: Unable to retrieve program name for "/apps/avogadro2-1.97.0-132/lib64/avogadro2/scripts/charges/xtb.py" ;
"Error running script '/usr/bin/python3 /apps/avogadro2-1.97.0-132/lib64/avogadro2/scripts/charges/xtb.py --display-name --lang en_US':
Abnormal exit status 1 (Unknown error.: Unknown error)\n\nOutput:\nTraceback (most recent call last):\n File
\"/apps/avogadro2-1.97.0-132/lib64/avogadro2/scripts/charges/xtb.py\", line 100, in <module>\n raise RuntimeError(\"xtb is
unavailable\")\nRuntimeError: xtb is unavailable\n"
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