diff --git a/tutorials/GaN_0001.ipynb b/tutorials/GaN_0001.ipynb index 3c243b5..683dbf9 100644 --- a/tutorials/GaN_0001.ipynb +++ b/tutorials/GaN_0001.ipynb @@ -151,157 +151,6 @@ "lammps_surf_calc.set(**calc_settings)" ] }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "environ{'USER': 'dux',\n", - " 'SSH_CLIENT': '10.31.169.98 57197 22',\n", - " 'XDG_SESSION_TYPE': 'tty',\n", - " 'SHLVL': '2',\n", - " 'MOTD_SHOWN': 'pam',\n", - " 'HOME': '/home/dux',\n", - " 'OLDPWD': '/home/dux',\n", - " 'SSL_CERT_FILE': '/usr/lib/ssl/certs/ca-certificates.crt',\n", - " 'DBUS_SESSION_BUS_ADDRESS': 'unix:path=/run/user/1026/bus',\n", - " 'LOGNAME': 'dux',\n", - " '_': '/home/dux/miniforge3/envs/vssr-mc/bin/python',\n", - " 'XDG_SESSION_CLASS': 'user',\n", - " 'VSCODE_CLI_REQUIRE_TOKEN': '61fe5d2b-6e46-4619-bd57-22ab43e398a7',\n", - " 'XDG_SESSION_ID': '40473',\n", - " 'PATH': '/home/dux/miniforge3/envs/vssr-mc/bin:/home/dux/.vscode-server/cli/servers/Stable-ea1445cc7016315d0f5728f8e8b12a45dc0a7286/server/bin/remote-cli:/home/dux/QUIP/build/linux_x86_64_gfortran:/home/dux/miniforge3/envs/vssr-mc/bin:/home/dux/miniconda3/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin',\n", - " 'VSCODE_AGENT_FOLDER': '/home/dux/.vscode-server',\n", - " 'XDG_RUNTIME_DIR': '/run/user/1026',\n", - " 'SSL_CERT_DIR': '/usr/lib/ssl/certs',\n", - " 'LANG': 'en_US.UTF-8',\n", - " 'SSH_AUTH_SOCK': '/tmp/ssh-7DLtPPwgPuO7/agent.3998',\n", - " 'SHELL': '/bin/zsh',\n", - " 'PWD': '/home/dux',\n", - " 'SSH_CONNECTION': '10.31.169.98 57197 10.82.2.145 22',\n", - " 'VSCODE_HANDLES_SIGPIPE': 'true',\n", - " 'ZSH': '/home/dux/.oh-my-zsh',\n", - " 'PAGER': 'cat',\n", - " 'LESS': '-R',\n", - " 'LSCOLORS': 'Gxfxcxdxbxegedabagacad',\n", - " 'LS_COLORS': '',\n", - " 'SSH_AGENT_PID': '4000',\n", - " 'P9K_SSH': '1',\n", - " '_P9K_SSH_TTY': '',\n", - " 'CONDA_EXE': '/home/dux/miniforge3/bin/conda',\n", - " '_CE_M': '',\n", - " '_CE_CONDA': '',\n", - " 'CONDA_PYTHON_EXE': '/home/dux/miniforge3/bin/python',\n", - " 'CONDA_SHLVL': '3',\n", - " 'CONDA_PREFIX': '/home/dux/miniforge3/envs/vssr-mc',\n", - " 'CONDA_DEFAULT_ENV': 'vssr-mc',\n", - " 'CONDA_PROMPT_MODIFIER': '(vssr-mc) ',\n", - " 'DJANGOCHEMDIR': '/home/dux/htvs/djangochem',\n", - " 'HTVSDIR': '/home/dux/htvs',\n", - " 'ADVATTDIR': '/home/dux/Atomistic-Adversarial-Attacks',\n", - " 'PYTHONPATH': '/home/dux/Atomistic-Adversarial-Attacks:/home/dux/htvs:/home/dux/htvs/djangochem:',\n", - " 'LAMMPS_COMMAND': '/home/dux/miniforge3/envs/vssr-mc/bin/lmp',\n", - " 'LAMMPS_POTENTIALS': '/home/dux/surface_sampling/mcmc/potentials',\n", - " 'ASE_LAMMPSRUN_COMMAND': '/home/dux/miniforge3/envs/vssr-mc/bin/lmp',\n", - " 'HOME2': '/mnt/data0/dux',\n", - " 'MP_API_KEY': 'AuU7jLQOeQRjZkLH28ZAgutMdfXbMl46',\n", - " 'CONDA_PREFIX_1': '/home/dux/miniconda3',\n", - " 'XML_CATALOG_FILES': 'file:///home/dux/miniforge3/envs/vssr-mc/etc/xml/catalog file:///etc/xml/catalog',\n", - " 'VSCODE_AMD_ENTRYPOINT': 'vs/workbench/api/node/extensionHostProcess',\n", - " 'VSCODE_HANDLES_UNCAUGHT_ERRORS': 'true',\n", - " 'VSCODE_NLS_CONFIG': '{\"locale\":\"en\",\"osLocale\":\"en\",\"availableLanguages\":{}}',\n", - " 'BROWSER': '/home/dux/.vscode-server/cli/servers/Stable-ea1445cc7016315d0f5728f8e8b12a45dc0a7286/server/bin/helpers/browser.sh',\n", - " 'VSCODE_CWD': '/home/dux',\n", - " 'ELECTRON_RUN_AS_NODE': '1',\n", - " 'VSCODE_IPC_HOOK_CLI': '/run/user/1026/vscode-ipc-0b7ed475-2d4f-41b1-888d-74dc1065d46a.sock',\n", - " 'APPLICATION_INSIGHTS_NO_DIAGNOSTIC_CHANNEL': '1',\n", - " 'VSCODE_L10N_BUNDLE_LOCATION': '',\n", - " 'DEBUG_FFLAGS': '-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/dux/miniforge3/envs/vssr-mc/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -ffunction-sections -pipe',\n", - " 'GCC_RANLIB': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-gcc-ranlib',\n", - " 'PYTHONUNBUFFERED': '1',\n", - " 'build_alias': 'x86_64-conda-linux-gnu',\n", - " 'CMAKE_ARGS': '-DCMAKE_AR=/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-ar -DCMAKE_CXX_COMPILER_AR=/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_C_COMPILER_AR=/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-gcc-ar -DCMAKE_RANLIB=/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-ranlib -DCMAKE_CXX_COMPILER_RANLIB=/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_C_COMPILER_RANLIB=/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-gcc-ranlib -DCMAKE_LINKER=/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-ld -DCMAKE_STRIP=/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-strip -DCMAKE_BUILD_TYPE=Release',\n", - " 'GPROF': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-gprof',\n", - " 'CONDA_TOOLCHAIN_BUILD': 'x86_64-conda-linux-gnu',\n", - " '_CONDA_PYTHON_SYSCONFIGDATA_NAME': '_sysconfigdata_x86_64_conda_cos6_linux_gnu',\n", - " 'STRINGS': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-strings',\n", - " 'CPP': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-cpp',\n", - " 'FFLAGS': '-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/dux/miniforge3/envs/vssr-mc/include',\n", - " 'CONDA_ROOT': '/home/dux/miniforge3',\n", - " 'CXX': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-c++',\n", - " 'CXXFLAGS': '-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/dux/miniforge3/envs/vssr-mc/include',\n", - " 'CONDA_TOOLCHAIN_HOST': 'x86_64-conda-linux-gnu',\n", - " 'DEBUG_CXXFLAGS': '-fvisibility-inlines-hidden -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/dux/miniforge3/envs/vssr-mc/include',\n", - " 'LDFLAGS': '-Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,--gc-sections -Wl,--allow-shlib-undefined -Wl,-rpath,/home/dux/miniforge3/envs/vssr-mc/lib -Wl,-rpath-link,/home/dux/miniforge3/envs/vssr-mc/lib -L/home/dux/miniforge3/envs/vssr-mc/lib',\n", - " 'MESON_ARGS': '--buildtype release',\n", - " 'DEBUG_CFLAGS': '-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fvar-tracking-assignments -ffunction-sections -pipe -isystem /home/dux/miniforge3/envs/vssr-mc/include',\n", - " 'CXX_FOR_BUILD': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-c++',\n", - " 'ELFEDIT': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-elfedit',\n", - " 'CMAKE_PREFIX_PATH': '/home/dux/miniforge3/envs/vssr-mc:/home/dux/miniforge3/envs/vssr-mc/x86_64-conda-linux-gnu/sysroot/usr',\n", - " 'CPPFLAGS': '-DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/dux/miniforge3/envs/vssr-mc/include',\n", - " 'LD': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-ld',\n", - " 'READELF': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-readelf',\n", - " 'GXX': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-g++',\n", - " 'FC_FOR_BUILD': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-gfortran',\n", - " 'GCC_AR': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-gcc-ar',\n", - " 'ADDR2LINE': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-addr2line',\n", - " 'GCC_NM': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-gcc-nm',\n", - " 'SIZE': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-size',\n", - " 'F77': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-gfortran',\n", - " 'HOST': 'x86_64-conda-linux-gnu',\n", - " 'CC_FOR_BUILD': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-cc',\n", - " 'PYTHONIOENCODING': 'utf-8',\n", - " 'AR': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-ar',\n", - " 'AS': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-as',\n", - " 'DEBUG_CPPFLAGS': '-D_DEBUG -D_FORTIFY_SOURCE=2 -Og -isystem /home/dux/miniforge3/envs/vssr-mc/include',\n", - " 'F95': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-f95',\n", - " 'F90': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-gfortran',\n", - " 'host_alias': 'x86_64-conda-linux-gnu',\n", - " 'NM': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-nm',\n", - " 'GCC': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-gcc',\n", - " 'DEBUG_FORTRANFLAGS': '-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/dux/miniforge3/envs/vssr-mc/include -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-all -fno-plt -Og -g -Wall -Wextra -fcheck=all -fbacktrace -fimplicit-none -fvar-tracking-assignments -ffunction-sections -pipe',\n", - " 'FORTRANFLAGS': '-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/dux/miniforge3/envs/vssr-mc/include',\n", - " 'LD_GOLD': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-ld.gold',\n", - " 'GFORTRAN': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-gfortran',\n", - " 'OBJCOPY': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-objcopy',\n", - " 'FC': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-gfortran',\n", - " 'STRIP': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-strip',\n", - " 'OBJDUMP': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-objdump',\n", - " 'CC': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-cc',\n", - " 'CFLAGS': '-march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/dux/miniforge3/envs/vssr-mc/include',\n", - " 'CXXFILT': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-c++filt',\n", - " 'BUILD': 'x86_64-conda-linux-gnu',\n", - " 'CONDA_PREFIX_2': '/home/dux/miniforge3',\n", - " 'RANLIB': '/home/dux/miniforge3/envs/vssr-mc/bin/x86_64-conda-linux-gnu-ranlib',\n", - " 'CONDA_BUILD_SYSROOT': '/home/dux/miniforge3/envs/vssr-mc/x86_64-conda-linux-gnu/sysroot',\n", - " 'PYDEVD_IPYTHON_COMPATIBLE_DEBUGGING': '1',\n", - " 'PYTHON_FROZEN_MODULES': 'on',\n", - " 'PYDEVD_USE_FRAME_EVAL': 'NO',\n", - " 'TERM': 'xterm-color',\n", - " 'CLICOLOR': '1',\n", - " 'FORCE_COLOR': '1',\n", - " 'CLICOLOR_FORCE': '1',\n", - " 'GIT_PAGER': 'cat',\n", - " 'MPLBACKEND': 'module://matplotlib_inline.backend_inline',\n", - " 'RDBASE': '/home/dux/miniforge3/envs/vssr-mc/lib/python3.11/site-packages/rdkit',\n", - " 'KMP_DUPLICATE_LIB_OK': 'True',\n", - " 'KMP_INIT_AT_FORK': 'FALSE'}" - ] - }, - "execution_count": 5, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "import os\n", - "\n", - "os.environ" - ] - }, { "cell_type": "markdown", "metadata": {}, diff --git a/tutorials/Si_111_5x5.ipynb b/tutorials/Si_111_5x5.ipynb index 69923af..4634dff 100644 --- a/tutorials/Si_111_5x5.ipynb +++ b/tutorials/Si_111_5x5.ipynb @@ -33,7 +33,7 @@ "np.set_printoptions(precision=3, suppress=True)\n", "# uncomment and replace with correct path if there are errors with LAMMPS\n", "# os.environ[\"LAMMPS_POTENTIALS\"] = \"/path/to/lammps/potentials/\"\n", - "# os.environ[\"LAMMPS_COMMAND\"] = \"/home/dux/miniforge3/envs/htvs/bin/lmp_serial\"\n", + "# os.environ[\"LAMMPS_COMMAND\"] =\"/path/to/lammps/src/lmp_serial\"\n", "# os.environ[\"ASE_LAMMPSRUN_COMMAND\"] = os.environ[\"LAMMPS_COMMAND\"]" ] },