「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]

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

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

2023y04m27d_032328394.png

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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Last-modified: 2023-05-08 (月) 02:48:40