Added scripts

README.md

@@ -37,15 +37,48 @@ Warnings:
 Requirements
 ------------
 
-* Ninja building system (replacement for GNU make)
+* [Ninja build tool](http://github.com/martine/ninja)
-* EZFIO library generator
+* [Ocaml compiler with Opam and Core library](http://github.com/ocaml)
-* ZeroMQ library
+* [ZeroMQ high performance communication library](http://www.zeromq.org)
-* ZeroMQ Fortran77 binding
+* [F77_ZMQ ZeroMQ Fortran interface](http://github.com/scemama/f77_zmq/)
-* IRPF90 Fortran code generator
+* [IRPF90 Fortran code generator](http://irpf90.ups-tlse.fr)
-* OCaml compiler
+* [EZFIO Easy Fortran I/O library generator](http://github.com/scemama/EZFIO)
-* Fortran compiler (Intel Fortran recommended)
+* GNU C++ Compiler (g++) for ZeroMQ
+* Python >= 2.6 for install scripts
+* Bash
+* Fortran compiler, Intel Fortran recommended
+* Lapack library, Intel MKL recommended
+
+
+Most of the dependencies are open-source will be downloaded automatically.
+The Fortran and C++ compilers, Python and Bash interpreters and the Lapack
+library need to be installed manually by the user.
+
+Installation
+------------
+
+This script will first download the [Ninja](http://github.com/martine/ninja)
+build tool, and will then run Ninja using the ``install/build.ninja`` file.
+The configuration script will work in the ``install`` directory.  It will first
+download into the ``install/Downloads`` directory everything that needs to be
+installed. The building of the dependencies takes place in the ``install/_build``
+directory, and the packages that are being installed can be followed by looking
+at the log files in this directory. When a package was successfully installed,
+a ``*.ok`` file is created and the log file is deleted.
+
+Before using or compiling QMC=Chem, environment variables need to be loaded. The
+environment variables are located in the ``qmcchemrc`` file:
+
+```bash
+$ source qmcchemrc
+```
+
+To compile the program, run
+
+```bash
+$ ninja
+```
 
-All the dependencies will be downloaded automatically
 
 Example of a QMC=Chem calculation
 ---------------------------------

build.ninja

@@ -0,0 +1,91 @@
+rule compile_ezfio
+  command = ./scripts/compile_ezfio.sh
+  description = Compiling the EZFIO library
+  pool = console
+
+rule build_properties_config
+  command = bash -c "source qmcchemrc ; exec python ./scripts/create_properties_ezfio.py"
+  pool = console
+
+rule compile_irpf90
+  command = ./scripts/compile_irpf90.sh
+  description = Compiling IRPF90
+  pool = console
+
+rule compile_src
+  command = ./scripts/compile_src.sh
+  description = Compiling src
+  pool = console
+
+rule create_archive
+  command = git archive --format tar.gz HEAD --prefix "QmcChem/" -7 -o qmcchem.tar.gz
+  description = Creating archive
+  pool = console
+
+rule compile_ocaml_dep
+  command = scripts/compile_ocaml_dep.sh
+  description = Finding dependencies in OCaml files
+  pool = console
+
+rule compile_ocaml
+  command = scripts/compile_ocaml.sh  $target
+  description = Compiling OCaml tools
+  pool = console
+
+rule copy_to_bin
+  command = bash -c "cp $in $out ; touch $out"
+  description = Copying $in into bin/
+  pool = console
+
+rule clean
+  command = ./scripts/clean.sh
+  pool = console
+
+# put all files of PROPERTIES here
+# --------------------------------
+
+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
+
+# EZFIO 
+# -----
+
+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
+
+# Fortran executables
+# -------------------
+
+build always: phony
+
+build src/tags src/irpf90_entities src/irpf90.make src/IRPF90_temp/build.ninja: compile_irpf90 | make.config always
+
+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
+
+# Archive
+# -------
+
+build qmcchem.tar.gz: create_archive
+
+# Ocaml
+# -----
+
+build ocaml/generated.ninja : compile_ocaml_dep | always
+build ocaml/qmcchem : compile_ocaml | ocaml/generated.ninja EZFIO/Ocaml/ezfio.ml 
+  target = qmcchem
+
+
+# Copy binaries in bin
+# --------------------
+
+build bin/qmc: copy_to_bin src/MAIN/qmc
+build bin/qmcchem_info: copy_to_bin src/MAIN/qmcchem_info
+build bin/qmc_create_walkers: copy_to_bin src/MAIN/qmc_create_walkers
+build bin/qmc_nozmq: copy_to_bin src/MAIN/qmc_nozmq
+build bin/qmcchem: copy_to_bin ocaml/qmcchem 
+
+default bin/qmc bin/qmcchem_info bin/qmc_create_walkers bin/qmc_nozmq bin/qmcchem 
+
+# Clean
+# -----
+
+build clean: clean
+

ocaml/compile.sh

@@ -6,7 +6,8 @@ then
   exit -1
 fi
 
-cd ${QMCCHEM_PATH}/ocaml
+cd ${QMCCHEM_PATH}/ocaml || exit -1
+cp ${QMCCHEM_PATH}/EZFIO/Ocaml/ezfio.ml . || exit -1
 
 LSMD5_FILE=${QMCCHEM_PATH}/ocaml/.ls_md5
 FILES="*.ml *.mli"
@@ -19,6 +20,7 @@ then
   REF=$(cat ${LSMD5_FILE})
 fi
 
+
 if [[ ${MD5} != ${REF} ]]
 then
   echo ${MD5} > ${LSMD5_FILE}

scripts/clean.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+# This script is supposed to run in $QMCCHEM_PATH
+
+ninja -C ocaml clean 
+if [[ -d src/IRPF90_temp ]]
+then
+  ninja -C src/IRPF90_temp -t clean 
+fi
+ninja -t clean
+
+rm -f ocaml/qmcchem ocaml/.ls_md5 ocaml/generated.ninja
+rm -f EZFIO/Ocaml/ezfio.ml
+cd src
+ rm -rf tags irpf90_entities irpf90.make IRPF90_temp IRPF90_man .ls_md5
+ cd MAIN
+  rm -f qmc qmcchem_info qmc_create_walkers
+cd ../..
+
+
+
+

scripts/compile_ezfio.sh

@@ -0,0 +1,18 @@
+#!/bin/bash 
+
+if [[ ! -f qmcchemrc ]]
+then
+  echo "Error: qmcchemrc not found"
+  exit -1
+fi
+
+source make.config
+source qmcchemrc
+FCFLAGS="${FCFLAGS} -fPIC"
+export IRPF90 FC FCFLAGS AR RANLIB
+cd EZFIO
+rm -f make.config
+${NINJA} || exit -1
+cp lib/libezfio{,_irp}.a ${QMCCHEM_PATH}/lib/ || exit 1
+
+

scripts/compile_irpf90.sh

@@ -0,0 +1,49 @@
+#!/bin/bash 
+
+if [[ -z ${QMCCHEM_PATH} ]]
+then
+  echo "Error: qmcchemrc not loaded"
+  exit -1
+fi
+
+cd ${QMCCHEM_PATH}/src
+
+LSMD5_FILE=${QMCCHEM_PATH}/src/.ls_md5
+FILES="*.f *.f90 *.F *.py */*.f */*.f90 */*.F */*.py"
+MD5=$(ls -ltr --full-time ${FILES} 2>/dev/null | md5sum | cut -d ' ' -f 1)
+
+REF=0
+
+if [[ -f ${LSMD5_FILE} ]]
+then
+  REF=$(cat ${LSMD5_FILE})
+fi
+
+if [[ ${MD5} != ${REF} ]]
+then
+  echo ${MD5} > ${LSMD5_FILE}
+  echo Running IRPF90
+
+  source ${QMCCHEM_PATH}/make.config
+
+  LIB="${LIB} ${QMCCHEM_PATH}/lib/libezfio_irp.a ${QMCCHEM_PATH}/lib/libf77zmq.a ${QMCCHEM_PATH}/lib/libzmq.a -lstdc++ -lrt"
+  SRC="${SRC} ZMQ/f77_zmq_module.f90" 
+  OBJ="${OBJ} IRPF90_temp/ZMQ/f77_zmq_module.o"
+  INCLUDES="${INCLUDES} -I AO -I SAMPLING -I TOOLS -I JASTROW -I TESTING -I MAIN -I PROPERTIES -I ZMQ"
+  IRPF90_FLAGS="${IRPF90_FLAGS} --ninja"
+
+  # Check IRPF90 version
+  if [[ $( ${IRPF90} -v | python -c "import sys ; print float(sys.stdin.read().rsplit('.',1)[0]) >= 1.6") == False ]]
+  then
+    echo "IRPF90 version >= 1.6 required"
+    exit -1
+  fi
+
+  export IRPF90 IRPF90_FLAGS INCLUDES LIB SRC OBJ 
+
+  exec ${IRPF90} ${IRPF90_FLAGS} ${INCLUDES} || exit -1
+fi
+
+
+
+

scripts/compile_ocaml.sh

@@ -0,0 +1,13 @@
+#!/bin/bash
+
+if [[ -z ${QMCCHEM_PATH} ]]
+then
+  echo "Error: qmcchemrc not loaded"
+  exit -1
+fi
+
+cd ${QMCCHEM_PATH}/ocaml || exit -1
+
+cp ${QMCCHEM_PATH}/EZFIO/Ocaml/ezfio.ml . || exit -1
+
+exec ninja -f generated.ninja ${@}

scripts/compile_ocaml_dep.sh

@@ -0,0 +1,39 @@
+#!/bin/bash
+
+if [[ -z ${QMCCHEM_PATH} ]]
+then
+  echo "Error: qmcchemrc not loaded"
+  exit -1
+fi
+
+cd ${QMCCHEM_PATH}/ocaml || exit -1
+
+LSMD5_FILE=${QMCCHEM_PATH}/ocaml/.ls_md5
+FILES="*.ml *.mli"
+MD5=$(ls -ltr --full-time ${FILES} 2>/dev/null | md5sum | cut -d ' ' -f 1)
+
+REF=0
+
+if [[ -f ${LSMD5_FILE} ]]
+then
+  REF=$(cat ${LSMD5_FILE})
+fi
+
+if [[ ${MD5} != ${REF} ]]
+then
+  echo ${MD5} > ${LSMD5_FILE}
+  echo Finding dependencies in OCaml files
+  python ./ninja_ocaml.py
+  if [[ ! -f qptypes_generator ]]
+  then
+    ninja -f generated.ninja qptypes_generator
+  fi
+  if [[ ! -f Qptypes.ml ]]
+  then
+    ./qptypes_generator
+    python ./ninja_ocaml.py
+  fi
+
+fi
+
+

scripts/compile_src.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+if [[ -z ${QMCCHEM_PATH} ]]
+then
+  echo "Error: qmcchemrc not loaded"
+  exit -1
+fi
+
+cd ${QMCCHEM_PATH}/src/IRPF90_temp || exit -1
+
+exec ninja ${@}

scripts/create_properties_python.py

@@ -0,0 +1,81 @@
+#!/usr/bin/python
+
+import string
+import os
+import sys
+
+root = os.environ['QMCCHEM_PATH']
+
+os.chdir(root+'/src/')
+sys.path.insert(0,'./')
+
+properties = []
+dims = {}
+
+files = filter(lambda x: x.startswith("PROPERTIES") and \
+                         x.endswith("irp.f"), os.listdir(os.getcwd()))
+
+files = map(lambda x: 'PROPERTIES/'+x, filter(lambda x: x.endswith("irp.f"), os.listdir(os.getcwd()+'/PROPERTIES')))
+                         
+
+#files = filter(lambda x: x.endswith("irp.f"), os.listdir(os.getcwd()))
+
+for filename in files:
+  lines = []
+  check_dims = False
+  file = open(filename,'r')
+  lines += file.readlines()
+  file.close()
+  for i,line in enumerate(lines):
+    if line.startswith("! PROPERTIES"):
+      lines = lines[i:]
+      break
+
+  for line in map(lambda x: x.lower(),lines):
+    if line.lstrip().startswith('begin_provider'):
+      check_dims = False
+      buffer = line
+      buffer = buffer.split('[')[1]
+      buffer = buffer.split(']')[0]
+      buffer = buffer.split(',')
+      if (len(buffer) == 2):
+        buffer.append("")
+      else:
+        buffer = [ buffer[0], buffer[1], ','.join(buffer[2:]) ]
+        check_dims = True
+      buffer = map(string.strip,buffer)
+      properties.append(buffer)
+      current_prop = buffer[1]
+    elif check_dims:
+      if 'dimensions :' in line:
+        dims[current_prop] = line.split(':')[1].strip()
+
+
+import numerical_derivatives as deriv
+properties += map(lambda x: ["double precision", "d_var_"+x.lower(), "(size_d_var_"+x.lower()+")"], deriv.vectors)
+properties += map(lambda x: ["double precision", "d_var_"+x.lower(), "(7)"], deriv.scalars)
+
+
+def sq(item):
+  return [item[0], item[1]+"_2", item[2]]
+properties_with_square = properties + map(sq,properties)
+
+for p in [ properties, properties_with_square ]:
+  def c(x,y):
+    if x[1] >  y[1]: return 1
+    if x[1] == y[1]: return 0
+    if x[1] <  y[1]: return -1
+  p.sort(c)
+  
+
+def touch_all():
+  print "TOUCH", 
+  for p in properties:
+    print "calc_"+p[1],
+  print ""
+
+with open(root+'/scripts/properties.py','w') as f:
+  print >>f,'properties = ',properties
+  print >>f,'dims = ',dims
+
+

src/MAIN/qmcchem_info.irp.f

@@ -13,15 +13,12 @@ program qmcchem_info
   endif
   print *,  'Number of determinants                   : ', det_num
   print *,  'Number of unique alpha/beta determinants : ', det_alpha_num, det_beta_num
-!  print *,  'Number of vectors in SVD                 : ', psi_svd_size
   print *,  'Closed-shell MOs                         : ', mo_closed_num
   print *,  'Number of MOs in determinants            : ', num_present_mos
-!  print *,  'do SVD?                                  : ', do_det_svd
+!  print *,  'Det alpha norm:'
-!  print *,  'det_coef matrix is sparse                : ', det_coef_matrix_is_sparse
+!  print *,  det_alpha_norm
-  print *,  'Det alpha norm:'
+!  print *,  'Det beta norm:'
-  print *,  det_alpha_norm
+!  print *,  det_beta_norm
-  print *,  'Det beta norm:'
-  print *,  det_beta_norm
   call step1
   call cpu_time (cpu0)
   call step2(imax)