Initial commit

.gitignore

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+quantum_package_static.tar.gz

Dockerfile

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+# For help about how Dockerfiles work, see https://docs.docker.com/engine/reference/builder
+
+# This image is based from Ubuntu LTS
+FROM ubuntu:latest
+LABEL version="0.1" \
+maintainer.name="Mickaël Véril" \
+maintainer.email="" \
+quantum_package.author.name="Anthony Scemama" \
+quantum_package.author.email="" \
+quantum_package.url="https://quantumpackage.github.io/qp2" \
+quantum_package.repo="https://github.com/QuantumPackage/qp2" \
+laboratory.name="Laboratoire de Chimie et Physique Quantique (LCPQ)" \
+laboratory.url="http://www.lcpq.ups-tlse.fr/"
+# Build argument (can be changed at build time see buiild.sh for an example)
+# This argument define the user name
+ARG user=user
+# This argument define timezone for tzdata requierd by qp_run
+ARG tz=Etc/UTC
+# We could add another argument to configure the language of the image
+# enable manpages installation
+RUN sed -i 's,^path-exclude=/usr/share/man/,#path-exclude=/usr/share/man/,' /etc/dpkg/dpkg.cfg.d/excludes
+# Install all requierd packages
+RUN apt-get update && \
+DEBIAN_FRONTEND=noninteractive apt-get install \
+python htop vim emacs screen tmux less wget curl tzdata man manpages-posix lsb-release \
+ -y && \
+apt-get autoremove && apt-get clean
+# Reconfigure tzdata with the good timezone
+RUN echo $tz > /etc/timezone && rm -rf /etc/localtime && echo "set mouse=" > ~/.vimrc
+RUN dpkg-reconfigure -f noninteractive tzdata
+# ADD user and switch to this user
+RUN adduser --disabled-password --gecos '' $user
+USER $user
+# I don't know why but the USER environment variable is not set so I set it because it's requested for ninja
+ENV USER=$user
+# Go to home
+WORKDIR /home/$user
+# untar directly static quantum package and examples
+ADD quantum_package_static.tar.gz .
+COPY examples examples
+# move quantum package
+RUN mv quantum_package_static qp2
+RUN echo "set -g default-command /home/$user/qp2/bin/qpsh" >> .tmux.conf
+RUN echo "shell \"/home/$user/qp2/bin/qpsh\"" >> .screenrc
+# start a qp shell when run
+# I deleted /home/user because it's not necesary and can be a source of big if user arg is diferent to "user"
+CMD ["./qp2/bin/qpsh"]
+
+

Dockerfile.compile

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+# For help about how Dockerfiles work, see https://docs.docker.com/engine/reference/builder
+
+# This image is based from Ubuntu LTS
+FROM ubuntu:latest
+LABEL version="0.1" \
+maintainer.name="Mickaël Véril" \
+maintainer.email="" \
+quantum_package.author.name="Anthony Scemama" \
+quantum_package.author.email="" \
+quantum_package.url="https://quantumpackage.github.io/qp2" \
+quantum_package.repo="https://github.com/QuantumPackage/qp2" \
+laboratory.name="Laboratoire de Chimie et Physique Quantique (LCPQ)" \
+laboratory.url="http://www.lcpq.ups-tlse.fr/"
+# Build argument (can be changed at build time see buiild.sh for an example)
+# This argument define the user name
+ARG user=user
+# This argument define timezone for tzdata requierd by qp_run
+ARG tz=Etc/UTC
+# We could add another argument to configure the language of the image
+# Install all requierd packages
+RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install apt-utils -y
+RUN DEBIAN_FRONTEND=noninteractive apt-get install \
+# Git for download quantum package
+git \
+# All necessary packages to compile and run quantum package
+curl wget python gfortran gcc g++ build-essential unzip liblapack-dev pkg-config autoconf zlib1g zlib1g-dev tzdata libgmp-dev \
+# Other packages for user usage
+htop vim emacs screen tmux less man -y
+# Reconfigure tzdata with the good timezone
+RUN echo $tz > /etc/timezone
+RUN rm -rf /etc/localtime
+RUN dpkg-reconfigure -f noninteractive tzdata
+# ADD user and switch to this user
+RUN adduser --disabled-password --gecos '' $user
+USER $user
+# I don't know why but the USER environment variable is not set so I set it because it's requested for ninja
+ENV USER=$user
+# Go to home
+WORKDIR /home/$user
+# Download quantum package
+RUN git clone https://github.com/QuantumPackage/qp2
+# Go to quantum package
+WORKDIR /home/$user/qp2
+# Configure
+RUN TRAVIS=1 ./configure -i all -c config/gfortran.cfg
+# source don't work with /bin/sh (used by the run command so I use bash)
+# Compile the code
+RUN /bin/bash -c "source quantum_package.rc ; ninja"
+# Run tests
+RUN /bin/bash -c "source quantum_package.rc ; qp_test -a"
+# Return to the user directory
+WORKDIR /home/$user/
+# Add source to bashrc
+RUN echo "source /home/$user/quantum_package/quantum_package.rc" >> ~/.bashrc
+## start a login shell when run
+#CMD ["/bin/bash","--login"]
+# start a qpsh when run
+CMD ["/bin/bash","--login", "-c", "qpsh"]
+
+

Makefile

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+IMAGE = qp2
+NETWORK = demo-net
+
+default:
+	docker build -t $(IMAGE) .
+
+no-cache:
+	docker build -t $(IMAGE) --no-cache .
+
+compile:
+	docker build -t $(IMAGE) -f Dockerfile.compile .
+
+compile-no-cache:
+	docker build -t $(IMAGE) -f Dockerfile.compile --no-cache . .
+
+network:
+	docker network create -o "com.docker.network.bridge.enable_icc"="false" $(NETWORK)
+
+network-clean:
+	docker network rm $(NETWORK)
+
+image-clean:
+	docker image rm $(IMAGE)
+
+clean: network-clean image-clean
+
+test:
+	docker run -h qp-demo --rm -it $(IMAGE)

README.md

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+# qp-demo
+

examples/1_hcn/README

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+Everything is explained in the run.qpsh script.
+Open it with a text editor.

examples/1_hcn/hcn.xyz

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+3
+HCN Geo: Experiment Mult: 1 symmetry: 14
+C    0.0    0.0    0.0
+H    0.0    0.0    1.064
+N    0.0    0.0    -1.156
+
+

examples/1_hcn/run.qpsh

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+#!/usr/bin/env qpsh
+
+# This first tutorial consists in obtaining the FCI energy of the HCN molecule.
+# You can execute the commands interactively or you can execute this script.
+# 
+# In interactive sessions, don't hesitate to use tab-completion with qp
+# commands.
+#
+# To know what a qp command does, you can use qp man, for example:
+#
+# qp man qp_edit
+
+
+
+# 1. Create the EZFIO database, with the STO-6G* basis set:
+
+qp create_ezfio -b sto-6g_star hcn.xyz
+
+# 2. Run the Hartree-Fock calculation:
+
+qp run scf | tee scf.out
+
+# 3. Set the core MOs as frozen:
+
+qp set_frozen_core
+
+# 4. Run the selected Full-CI:
+
+qp run fci | tee fci.out
+
+
+
+# To see all the possible control parameters, you can do
+#
+# qp edit
+#
+# which will open a virtual input file in a text editor.
+# The choice of the editor can be set via the EDITOR environment variable:
+#
+# export EDITOR=vim
+#
+

examples/2_h2o2/README

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+Everything is explained in the run.qpsh script.
+Open it with a text editor.

examples/2_h2o2/h2o2.zmt

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+ o
+ o    1 oo
+ h    1 ho         2 hoo
+ h    2 ho         1 hoo          3 dih
+
+oo          1.475
+ho          0.95
+hoo         94.8
+dih        119.8
+
+

examples/2_h2o2/run.qpsh

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+#!/usr/bin/env qpsh
+
+# This second tutorial consists in obtaining the FCI energy of the
+# H2O2 molecule. The geometry is given here in z-matrix format.
+#
+# To accelerate the convergence, instead of using Hartree-Fock MOs
+# we will use CISD natural orbitals.
+
+# 1. Create the EZFIO database, with the 6-31g basis set:
+
+qp create_ezfio -b sto-6g_star h2o2.zmt
+
+# 2. Run the Hartree-Fock calculation:
+
+qp run scf | tee scf.out
+
+# 3. Set the core MOs as frozen:
+
+qp set_frozen_core
+
+# 4. Run a CISD
+
+qp run cisd | tee cisd.out
+
+# 5. Obtain the natural orbitals of the CISD, and use them from now on
+
+qp run save_natorb
+
+# 6. Run the selected FCI with the CISD natural orbitals
+
+qp run fci | tee fci.out
+
+

examples/3_n2/README

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+Everything is explained in the run.qpsh script.
+Open it with a text editor.

examples/3_n2/n2.zmt

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+n
+n 1 1.0976
+

examples/3_n2/run.qpsh

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+#!/usr/bin/env qpsh
+
+# In this third tutorial, we will compute the ground state and the lowest
+# singly excited of N2.
+
+# 1. Create the EZFIO database, with the def2-svp basis set:
+
+qp create_ezfio -b def2-svp n2.zmt
+
+# 2. Run the Hartree-Fock calculation:
+
+qp run scf | tee scf.out
+
+# 3. Set the core MOs as frozen:
+
+qp set_frozen_core
+
+# 4. Request for two states
+
+qp set determinants n_states 2
+
+# 5. Run a CIS
+
+qp run cis
+
+# 6. Truncate the wave function to the 2 most important determinants : the
+#    Hartree-Fock and one a singly excited determinant (spin symmetry will 
+#    be automatically restored in the next calculation)
+
+qp edit -n 2
+
+# 7. Set the CIS wave function as the starting trial wave function
+
+qp set determinants read_wf True
+
+# 8. To avoid collapsing to the ground state and a doubly excited state,
+#    force to use a state-following algorithm
+
+qp set davidson state_following True
+
+# 9. Terminate when we have 50000 determinants
+
+qp set determinants n_det_max 50*10**3
+
+# 10. Run the selected FCI calculation
+
+qp run fci | tee fci.out
+
+

run.sh

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+#!/bin/bash
+
+# Add a timeout to a existing container
+DockerTimeout() {
+ docker events -f event=start -f type=container -f container=$1 | head -n 0
+ timeout $2 docker wait $1>/dev/null
+ if [ $? -eq 124 ] ; then
+   docker kill $1> /dev/null
+   return 1
+ else
+   return 0
+ fi
+}
+
+# Create an interactive docker container for an image and echo it's ID (use docker start command to start the container)
+DockerCreate() {
+  docker create -h qp-demo -l demo --network=demo-net --rm -it $1
+}
+DockerGetNextID() {
+  docker ps -aq -f ancestor="$1" -f "label=demo" -f status=created --no-trunc | tail -n 1
+}
+
+# Count the number of container for a specific image
+DockerCountCont() {
+  docker ps -f ancestor="$1" -f "label=demo" -q | wc -l
+}
+# Selected image
+image=scemama/qp2
+# Time limit for the container in the format of the timeout command
+timeout=10m
+# Number of container that running at the same time
+contlimit=4
+allocated=false
+printwaitmessage=true
+allowRun=true
+
+cont=$(DockerCreate $image)
+trap "docker rm $cont" EXIT INT TERM
+echo "Your ID is : $cont"
+# Until a container is started
+until $allocated
+do
+  # If the limit is reached
+  if [ $(DockerCountCont $image) -ge $contlimit ] ; then
+    allowRun=false
+    # Get the next container in the queue
+    nextcont=$(DockerGetNextID $image)
+    # print the message only one time
+    if $printwaitmessage ; then
+      echo Maximum number of sessions reached. Please wait for allocation...
+    fi
+    printwaitmessage=false
+    # Wait the die of a container
+    docker events -f event=die -f event=destroy -f type=container -f image=$image -f "label=demo" | head -n 0
+    if [ "$nextcont" == "$cont" ]; then
+      allowRun=true
+    fi
+    # Sleep because is's needed by docker for a good count of containers
+  else
+    if $allowRun ; then
+      allocated=true
+      # If there it's permited by the container number limit allocate a container and get it's ID
+      echo -e "Session allocated."
+      # Count the number of container available
+      aval=$(expr $(expr $contlimit - $(DockerCountCont $image) - 1))
+      [[ "$aval" -lt 0 ]] && aval=0
+      # Show it to the user
+      echo "There are $aval sessions left available"
+      if [ $# -eq 0 ]  || [ "$1" != "unlimited" ] ; then
+        # Apply a timout only if the argument ulimited is not given to the script
+        DockerTimeout $cont $timeout &
+      fi
+      # start the container in interactive mode and attach it to the terminal
+      trap "docker kill $cont" EXIT INT TERM
+      docker start -a -i $cont
+      trap - EXIT INT TERM 
+    fi
+  fi
+done