added mpi4py and stm.yml and cp2k-spm-tools and increased timeout for… (

#21)

* added mpi4py and stm.yml and cp2k-spm-tools and increased timeout for terminal

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Dockerfile

@@ -16,6 +16,8 @@ RUN cp /home/${NB_USER}/opt/lammps/src/lmp_serial /usr/bin/lmp_serial
 
 USER ${NB_USER}
 
+ENV JUPYTER_TERMINAL_IDLE_TIMEOUT=3600
+
 RUN rm -rf /home/${NB_USER}/opt/lammps/
 
 RUN pip install --user skmatter
@@ -28,6 +30,10 @@ RUN pip install --user aiida-cp2k
 
 RUN pip install --user spglib
 
+RUN pip install pythtb
+
+RUN conda install -c conda-forge mpi4py
+
 COPY configs /home/${NB_USER}/configs
 
 COPY before-notebook.d/* /usr/local/bin/before-notebook.d/

before-notebook.d/71_setup_stm.sh

@@ -0,0 +1,12 @@
+
+#!/bin/bash -e
+
+# Debugging.
+set -x
+
+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
+fi

before-notebook.d/72_setup_stm_tools.sh

@@ -0,0 +1,21 @@
+
+#!/bin/bash -e
+
+# Debugging.
+set -x
+
+
+if [ -d "/home/jovyan/soft/" ]; then
+    echo "Directory /home/jovyan/soft/ exists."
+else
+    echo "Directory does not exist. Creating"
+    mkdir /home/jovyan/soft
+    mkdir /home/jovyan/soft/cp2k-spm-tools
+fi
+
+if [ -f "/home/jovyan/soft/cp2k-spm-tools/cube_from_wfn.py" ]; then
+    echo "cp2k-spm-tools found"
+else
+    echo "cp2k-spm-tools not found, installing"
+    git clone https://github.com/nanotech-empa/cp2k-spm-tools.git /home/jovyan/soft/cp2k-spm-tools
+fi

configs/stm.yml

@@ -0,0 +1,8 @@
+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"
+computer: "localhost"
+prepend_text: " "
+append_text: " "
+use_double_quotes: "False"