mirror of https://gitlab.com/scemama/qmcchem.git
Added scripts
This commit is contained in:
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99e4ad9e12
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README.md
49
README.md
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@ -37,15 +37,48 @@ Warnings:
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Requirements
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------------
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* Ninja building system (replacement for GNU make)
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* EZFIO library generator
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* ZeroMQ library
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* ZeroMQ Fortran77 binding
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* IRPF90 Fortran code generator
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* OCaml compiler
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* Fortran compiler (Intel Fortran recommended)
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* [Ninja build tool](http://github.com/martine/ninja)
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* [Ocaml compiler with Opam and Core library](http://github.com/ocaml)
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* [ZeroMQ high performance communication library](http://www.zeromq.org)
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* [F77_ZMQ ZeroMQ Fortran interface](http://github.com/scemama/f77_zmq/)
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* [IRPF90 Fortran code generator](http://irpf90.ups-tlse.fr)
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* [EZFIO Easy Fortran I/O library generator](http://github.com/scemama/EZFIO)
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* GNU C++ Compiler (g++) for ZeroMQ
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* Python >= 2.6 for install scripts
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* Bash
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* Fortran compiler, Intel Fortran recommended
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* Lapack library, Intel MKL recommended
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Most of the dependencies are open-source will be downloaded automatically.
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The Fortran and C++ compilers, Python and Bash interpreters and the Lapack
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library need to be installed manually by the user.
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Installation
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------------
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This script will first download the [Ninja](http://github.com/martine/ninja)
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build tool, and will then run Ninja using the ``install/build.ninja`` file.
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The configuration script will work in the ``install`` directory. It will first
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download into the ``install/Downloads`` directory everything that needs to be
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installed. The building of the dependencies takes place in the ``install/_build``
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directory, and the packages that are being installed can be followed by looking
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at the log files in this directory. When a package was successfully installed,
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a ``*.ok`` file is created and the log file is deleted.
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Before using or compiling QMC=Chem, environment variables need to be loaded. The
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environment variables are located in the ``qmcchemrc`` file:
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```bash
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$ source qmcchemrc
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```
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To compile the program, run
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```bash
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$ ninja
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```
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All the dependencies will be downloaded automatically
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Example of a QMC=Chem calculation
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---------------------------------
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@ -0,0 +1,91 @@
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rule compile_ezfio
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command = ./scripts/compile_ezfio.sh
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description = Compiling the EZFIO library
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pool = console
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rule build_properties_config
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command = bash -c "source qmcchemrc ; exec python ./scripts/create_properties_ezfio.py"
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pool = console
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rule compile_irpf90
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command = ./scripts/compile_irpf90.sh
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description = Compiling IRPF90
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pool = console
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rule compile_src
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command = ./scripts/compile_src.sh
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description = Compiling src
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pool = console
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rule create_archive
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command = git archive --format tar.gz HEAD --prefix "QmcChem/" -7 -o qmcchem.tar.gz
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description = Creating archive
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pool = console
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rule compile_ocaml_dep
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command = scripts/compile_ocaml_dep.sh
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description = Finding dependencies in OCaml files
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pool = console
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rule compile_ocaml
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command = scripts/compile_ocaml.sh $target
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description = Compiling OCaml tools
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pool = console
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rule copy_to_bin
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command = bash -c "cp $in $out ; touch $out"
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description = Copying $in into bin/
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pool = console
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rule clean
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command = ./scripts/clean.sh
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pool = console
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# put all files of PROPERTIES here
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# --------------------------------
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build ezfio_config/properties.config: build_properties_config | src/PROPERTIES/density.irp.f src/PROPERTIES/properties.irp.f src/PROPERTIES/properties_energy.irp.f src/PROPERTIES/voronoi.irp.f src/PROPERTIES/properties_general.irp.f scripts/create_properties_python.py || src/IRPF90_temp/build.ninja
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# EZFIO
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# -----
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build lib/libezfio.a lib/libezfio_irp.a EZFIO/lib/libezfio.a EZFIO/lib/libezfio_irp.a EZFIO/Ocaml/ezfio.ml EZFIO/Python/ezfio.py: compile_ezfio | ezfio_config/qmc.config ezfio_config/properties.config make.config scripts/create_properties_ezfio.py || src/tags src/irpf90_entities src/irpf90.make src/IRPF90_temp/build.ninja
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# Fortran executables
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# -------------------
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build always: phony
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build src/tags src/irpf90_entities src/irpf90.make src/IRPF90_temp/build.ninja: compile_irpf90 | make.config always
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build src/MAIN/qmc src/MAIN/qmc_nozmq src/MAIN/qmc_create_walkers src/MAIN/qmcchem_info: compile_src | lib/libezfio.a lib/libezfio_irp.a src/tags || src/irpf90_entities src/irpf90.make src/IRPF90_temp/build.ninja
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# Archive
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# -------
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build qmcchem.tar.gz: create_archive
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# Ocaml
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# -----
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build ocaml/generated.ninja : compile_ocaml_dep | always
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build ocaml/qmcchem : compile_ocaml | ocaml/generated.ninja EZFIO/Ocaml/ezfio.ml
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target = qmcchem
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# Copy binaries in bin
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# --------------------
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build bin/qmc: copy_to_bin src/MAIN/qmc
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build bin/qmcchem_info: copy_to_bin src/MAIN/qmcchem_info
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build bin/qmc_create_walkers: copy_to_bin src/MAIN/qmc_create_walkers
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build bin/qmc_nozmq: copy_to_bin src/MAIN/qmc_nozmq
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build bin/qmcchem: copy_to_bin ocaml/qmcchem
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default bin/qmc bin/qmcchem_info bin/qmc_create_walkers bin/qmc_nozmq bin/qmcchem
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# Clean
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# -----
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build clean: clean
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@ -6,7 +6,8 @@ then
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exit -1
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fi
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cd ${QMCCHEM_PATH}/ocaml
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cd ${QMCCHEM_PATH}/ocaml || exit -1
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cp ${QMCCHEM_PATH}/EZFIO/Ocaml/ezfio.ml . || exit -1
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LSMD5_FILE=${QMCCHEM_PATH}/ocaml/.ls_md5
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FILES="*.ml *.mli"
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@ -19,6 +20,7 @@ then
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REF=$(cat ${LSMD5_FILE})
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fi
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if [[ ${MD5} != ${REF} ]]
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then
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echo ${MD5} > ${LSMD5_FILE}
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@ -0,0 +1,21 @@
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#!/bin/bash
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# This script is supposed to run in $QMCCHEM_PATH
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ninja -C ocaml clean
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if [[ -d src/IRPF90_temp ]]
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then
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ninja -C src/IRPF90_temp -t clean
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fi
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ninja -t clean
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rm -f ocaml/qmcchem ocaml/.ls_md5 ocaml/generated.ninja
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rm -f EZFIO/Ocaml/ezfio.ml
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cd src
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rm -rf tags irpf90_entities irpf90.make IRPF90_temp IRPF90_man .ls_md5
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cd MAIN
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rm -f qmc qmcchem_info qmc_create_walkers
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cd ../..
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#!/bin/bash
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if [[ ! -f qmcchemrc ]]
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then
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echo "Error: qmcchemrc not found"
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exit -1
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fi
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source make.config
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source qmcchemrc
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FCFLAGS="${FCFLAGS} -fPIC"
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export IRPF90 FC FCFLAGS AR RANLIB
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cd EZFIO
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rm -f make.config
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${NINJA} || exit -1
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cp lib/libezfio{,_irp}.a ${QMCCHEM_PATH}/lib/ || exit 1
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#!/bin/bash
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if [[ -z ${QMCCHEM_PATH} ]]
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then
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echo "Error: qmcchemrc not loaded"
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exit -1
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fi
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cd ${QMCCHEM_PATH}/src
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LSMD5_FILE=${QMCCHEM_PATH}/src/.ls_md5
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FILES="*.f *.f90 *.F *.py */*.f */*.f90 */*.F */*.py"
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MD5=$(ls -ltr --full-time ${FILES} 2>/dev/null | md5sum | cut -d ' ' -f 1)
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REF=0
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if [[ -f ${LSMD5_FILE} ]]
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then
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REF=$(cat ${LSMD5_FILE})
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fi
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if [[ ${MD5} != ${REF} ]]
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then
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echo ${MD5} > ${LSMD5_FILE}
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echo Running IRPF90
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source ${QMCCHEM_PATH}/make.config
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LIB="${LIB} ${QMCCHEM_PATH}/lib/libezfio_irp.a ${QMCCHEM_PATH}/lib/libf77zmq.a ${QMCCHEM_PATH}/lib/libzmq.a -lstdc++ -lrt"
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SRC="${SRC} ZMQ/f77_zmq_module.f90"
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OBJ="${OBJ} IRPF90_temp/ZMQ/f77_zmq_module.o"
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INCLUDES="${INCLUDES} -I AO -I SAMPLING -I TOOLS -I JASTROW -I TESTING -I MAIN -I PROPERTIES -I ZMQ"
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IRPF90_FLAGS="${IRPF90_FLAGS} --ninja"
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# Check IRPF90 version
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if [[ $( ${IRPF90} -v | python -c "import sys ; print float(sys.stdin.read().rsplit('.',1)[0]) >= 1.6") == False ]]
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then
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echo "IRPF90 version >= 1.6 required"
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exit -1
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fi
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export IRPF90 IRPF90_FLAGS INCLUDES LIB SRC OBJ
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exec ${IRPF90} ${IRPF90_FLAGS} ${INCLUDES} || exit -1
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fi
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#!/bin/bash
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if [[ -z ${QMCCHEM_PATH} ]]
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then
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echo "Error: qmcchemrc not loaded"
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exit -1
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fi
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cd ${QMCCHEM_PATH}/ocaml || exit -1
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cp ${QMCCHEM_PATH}/EZFIO/Ocaml/ezfio.ml . || exit -1
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exec ninja -f generated.ninja ${@}
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#!/bin/bash
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if [[ -z ${QMCCHEM_PATH} ]]
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then
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echo "Error: qmcchemrc not loaded"
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exit -1
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fi
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cd ${QMCCHEM_PATH}/ocaml || exit -1
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LSMD5_FILE=${QMCCHEM_PATH}/ocaml/.ls_md5
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FILES="*.ml *.mli"
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MD5=$(ls -ltr --full-time ${FILES} 2>/dev/null | md5sum | cut -d ' ' -f 1)
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REF=0
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if [[ -f ${LSMD5_FILE} ]]
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then
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REF=$(cat ${LSMD5_FILE})
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fi
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if [[ ${MD5} != ${REF} ]]
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then
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echo ${MD5} > ${LSMD5_FILE}
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echo Finding dependencies in OCaml files
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python ./ninja_ocaml.py
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if [[ ! -f qptypes_generator ]]
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then
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ninja -f generated.ninja qptypes_generator
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fi
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if [[ ! -f Qptypes.ml ]]
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then
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./qptypes_generator
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python ./ninja_ocaml.py
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fi
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fi
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#!/bin/bash
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if [[ -z ${QMCCHEM_PATH} ]]
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then
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echo "Error: qmcchemrc not loaded"
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exit -1
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fi
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cd ${QMCCHEM_PATH}/src/IRPF90_temp || exit -1
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exec ninja ${@}
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#!/usr/bin/python
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import string
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import os
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import sys
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root = os.environ['QMCCHEM_PATH']
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os.chdir(root+'/src/')
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sys.path.insert(0,'./')
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properties = []
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dims = {}
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files = filter(lambda x: x.startswith("PROPERTIES") and \
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x.endswith("irp.f"), os.listdir(os.getcwd()))
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files = map(lambda x: 'PROPERTIES/'+x, filter(lambda x: x.endswith("irp.f"), os.listdir(os.getcwd()+'/PROPERTIES')))
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#files = filter(lambda x: x.endswith("irp.f"), os.listdir(os.getcwd()))
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for filename in files:
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lines = []
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check_dims = False
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file = open(filename,'r')
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lines += file.readlines()
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file.close()
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for i,line in enumerate(lines):
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if line.startswith("! PROPERTIES"):
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lines = lines[i:]
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break
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for line in map(lambda x: x.lower(),lines):
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if line.lstrip().startswith('begin_provider'):
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check_dims = False
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buffer = line
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buffer = buffer.split('[')[1]
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buffer = buffer.split(']')[0]
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buffer = buffer.split(',')
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if (len(buffer) == 2):
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buffer.append("")
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else:
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buffer = [ buffer[0], buffer[1], ','.join(buffer[2:]) ]
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check_dims = True
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buffer = map(string.strip,buffer)
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properties.append(buffer)
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current_prop = buffer[1]
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elif check_dims:
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if 'dimensions :' in line:
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dims[current_prop] = line.split(':')[1].strip()
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import numerical_derivatives as deriv
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properties += map(lambda x: ["double precision", "d_var_"+x.lower(), "(size_d_var_"+x.lower()+")"], deriv.vectors)
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properties += map(lambda x: ["double precision", "d_var_"+x.lower(), "(7)"], deriv.scalars)
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def sq(item):
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return [item[0], item[1]+"_2", item[2]]
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properties_with_square = properties + map(sq,properties)
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for p in [ properties, properties_with_square ]:
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def c(x,y):
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if x[1] > y[1]: return 1
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if x[1] == y[1]: return 0
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if x[1] < y[1]: return -1
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p.sort(c)
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def touch_all():
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print "TOUCH",
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for p in properties:
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print "calc_"+p[1],
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print ""
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with open(root+'/scripts/properties.py','w') as f:
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print >>f,'properties = ',properties
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print >>f,'dims = ',dims
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@ -13,15 +13,12 @@ program qmcchem_info
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endif
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print *, 'Number of determinants : ', det_num
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print *, 'Number of unique alpha/beta determinants : ', det_alpha_num, det_beta_num
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! print *, 'Number of vectors in SVD : ', psi_svd_size
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print *, 'Closed-shell MOs : ', mo_closed_num
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print *, 'Number of MOs in determinants : ', num_present_mos
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! print *, 'do SVD? : ', do_det_svd
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! print *, 'det_coef matrix is sparse : ', det_coef_matrix_is_sparse
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print *, 'Det alpha norm:'
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print *, det_alpha_norm
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print *, 'Det beta norm:'
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print *, det_beta_norm
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! print *, 'Det alpha norm:'
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! print *, det_alpha_norm
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! print *, 'Det beta norm:'
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! print *, det_beta_norm
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call step1
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call cpu_time (cpu0)
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call step2(imax)
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