Included critic2 python codes and lammps, tensorflow, pytorch and spm…

… tools

Dockerfile

@@ -2,27 +2,64 @@ FROM aiidalab/full-stack:2025.1025
 
 USER root
 
+
 #RUN apt-get update -y && apt-get install -y cp2k && apt-get clean -y
 # Install required system dependencies, including MPI development libraries
 RUN apt-get update -y && apt-get install -y  cp2k libmpich-dev libopenmpi-dev  build-essential  && apt-get clean -y
 
 USER ${NB_USER}
 
+
+
+
 RUN mkdir /home/${NB_USER}/opt
 
-RUN cd /home/${NB_USER}/opt &&  git clone https://github.com/lammps/lammps && cd lammps/src && make lib-pace args="-b" && make yes-molecule && make yes-reaxff && make yes-rigid && make yes-ml-pace && make yes-manybody && make lib-voronoi args="-b" && make yes-voronoi && make mpi
+RUN pip install virtualenv
+
+ENV deepmd_root=/home/${NB_USER}/opt/deepmd-kit
+ENV deepmd_source_dir=/home/${NB_USER}/opt/deepmd-kit
+ENV tensorflow_venv=/home/${NB_USER}/opt/tensorflow_venv
+ENV deepmd_root=/home/${NB_USER}/opt/deepmd-kit
+
+RUN cd /home/${NB_USER}/opt && git clone https://github.com/deepmodeling/deepmd-kit.git deepmd-kit
+
+
+
+RUN virtualenv -p python3 $tensorflow_venv
+
+RUN source $tensorflow_venv/bin/activate
+
+
+RUN pip install --upgrade tensorflow
+
+RUN cd $deepmd_source_dir && pip install .
+
+RUN cd $deepmd_source_dir/source && mkdir build && cd build
+
+RUN cd $deepmd_source_dir/source/build && pwd && pip install -U cmake && cmake -DUSE_TF_PYTHON_LIBS=TRUE -DCMAKE_INSTALL_PREFIX=$deepmd_source_dir .. && make && make install
+
+RUN cd $deepmd_source_dir/source/build && make lammps
+
+
+RUN cd /home/${NB_USER}/opt &&  git clone https://github.com/lammps/lammps && cd lammps/src && cp -r $deepmd_source_dir/source/build/USER-DEEPMD . && make lib-pace args="-b" && make yes-molecule && make yes-reaxff && make yes-rigid && make yes-ml-pace && make yes-manybody && make lib-voronoi args="-b" && make yes-voronoi && make lib-plumed args="-b" CC=gcc CXX=g++ && make yes-plumed && make yes-kspace && make yes-extra-fix && make yes-user-deepmd && make serial
+
+RUN deactivate 
 
 USER root
 
-RUN cp /home/${NB_USER}/opt/lammps/src/lmp_mpi /usr/bin/lmp_mpi
+RUN cp /home/${NB_USER}/opt/lammps/src/lmp_serial /usr/bin/lmp_serial
 
 USER ${NB_USER}
 
 ENV JUPYTER_TERMINAL_IDLE_TIMEOUT=3600
-ENV ASE_LAMMPSRUN_COMMAND="/opt/conda/bin/mpirun --np 2 /usr/bin/lmp_mpi"
+ENV ASE_LAMMPSRUN_COMMAND="/usr/bin/lmp_serial"
 
 RUN rm -rf /home/${NB_USER}/opt/lammps/
 
+RUN pip install nglview
+
+RUN pip install mdtraj
+
 RUN pip install --user skmatter
 
 RUN cd opt && git clone https://github.com/lab-cosmo/librascal.git && cd librascal && pip install --user .
@@ -35,7 +72,8 @@ RUN pip install --user spglib
 
 RUN pip install pythtb
 
-RUN conda install -c conda-forge mpi4py
+#RUN conda install -c conda-forge mpi4py
+RUN pip install cp2k-spm-tools
 
 COPY configs /home/${NB_USER}/configs
 
@@ -44,3 +82,10 @@ COPY before-notebook.d/* /usr/local/bin/before-notebook.d/
 RUN pip install scikit-learn optuna xgboost lightgbm sympy pandas
 
 RUN pip install torch  torchmetrics torchvision
+
+
+RUN cd /home/${NB_USER}/opt && git clone https://github.com/aoterodelaroza/critic2.git
+
+RUN cd /home/${NB_USER}/opt/critic2 && mkdir build && cd build && cmake .. && make 
+
+RUN pip install pymatgen scikit-image

before-notebook.d/70_setup_cp2k.sh

@@ -8,5 +8,5 @@ if verdi code list | grep -q 'cp2k@localhost'; then
     echo "CP2K code found"
 else
     echo "CP2K code not found, creating"
-    verdi code create core.code.installed --config /home/${NB_USER}/configs/cp2k.yaml
+    verdi code create core.code.installed --config /home/${NB_USER}/configs/cp2k.yml
 fi

before-notebook.d/71_setup_stm.sh

@@ -8,5 +8,5 @@ if verdi code list | grep -q 'stm@localhost'; then
     echo "STM code found"
 else
     echo "STM code not found, creating"
-    verdi code create core.code.installed --config /home/${NB_USER}/configs/stm.yaml
+    verdi code create core.code.installed --config /home/${NB_USER}/configs/stm.yml
 fi

before-notebook.d/72_setup_critic2.sh

@@ -0,0 +1,12 @@
+
+#!/bin/bash -e
+
+# Debugging.
+set -x
+
+if verdi code list | grep -q 'critic2@localhost'; then
+    echo "critic2 code found"
+else
+    echo "critic2 code not found, creating"
+    verdi code create core.code.installed --config /home/${NB_USER}/configs/critic2.yml
+fi

before-notebook.d/73_setup_python-py39.sh

@@ -0,0 +1,12 @@
+
+#!/bin/bash -e
+
+# Debugging.
+set -x
+
+if verdi code list | grep -q 'python-py39@localhost'; then
+    echo "python-py39 code found"
+else
+    echo "python-py39 code not found, creating"
+    verdi code create core.code.installed --config /home/${NB_USER}/configs/python.yml
+fi

configs/critic2.yml

@@ -0,0 +1,8 @@
+append_text: ' '
+computer: localhost
+default_calc_job_plugin: critic2
+description: critic2 at daint alps
+filepath_executable: /home/jovyan/opt/critic2/build/src/critic2
+label: critic2
+prepend_text: ''
+use_double_quotes: 'False'

configs/python.yml

@@ -0,0 +1,8 @@
+append_text: ' '
+computer: localhost
+default_calc_job_plugin: pythonjob.pythonjob
+description: python at daint alps
+filepath_executable: /opt/conda/bin/python
+label: python-py39
+prepend_text: ' '
+use_double_quotes: 'False'

configs/stm.yaml → configs/stm.yml

@@ -1,7 +1,7 @@
 label: "stm"
 description: "stm code from https://github.com/nanotech-empa/cp2k-spm-tools.git"
 default_calc_job_plugin: "nanotech_empa.stm"
-filepath_executable: "/home/jovyan/soft/cp2k-spm-tools/stm_sts_from_wfn.py"
+filepath_executable: "/home/jovyan/.local/bin/cp2k-stm-sts-wfn"
 computer: "localhost"
 prepend_text: " "
 append_text: " "