Merge branch 'master' of github.com:LCPQ/quantum_package

scripts/create_module.sh

@@ -36,6 +36,13 @@ function fail()
 }
 
 
+if [[ -z $QPACKAGE_ROOT ]]
+then
+  echo "Error:"
+  echo "QPACKAGE_ROOT environment variable is not set."
+  echo "source quantum_package.rc"
+  exit 1
+fi
 
 MODULE=$1
 

scripts/follow_output.py

@@ -0,0 +1,68 @@
+#!/usr/bin/env python
+
+import time
+import os
+import sys
+
+"""Follow the output files in standard output"""
+
+class OutputFollower(object):
+
+  def __init__(self,filename):
+    self.filename = filename
+    self.dir = filename+'/output/'
+    self.last_time = {}
+    self.last_line = {}
+    self.data      = {}
+    self.update_file_list()
+    self.running = False
+
+  def update_file_list(self):
+    self.file_list = filter(lambda x: x.endswith('.rst'), os.listdir(self.dir) )
+    for filename in self.file_list:
+      filename = self.dir+'/'+filename
+      statbuf = os.stat(filename)
+      date = statbuf.st_mtime 
+      if filename not in self.last_time:
+        self.last_time[filename] = -1
+        self.last_line[filename] = -1
+        self.data[filename] = []
+      if date > self.last_time[filename]:
+          # Read file
+          file = open(filename,'r')
+          self.data[filename] = file.read().splitlines()
+          file.close()
+          # Print new lines
+          output = self.data[filename]
+          for line in output[self.last_line[filename]+1:]:
+            print line
+          self.last_time[filename] = date
+          self.last_line[filename] = len(output)-1
+
+  def start(self):
+    self.running = True
+    while self.running:
+      time.sleep(1.)
+      self.update_file_list()
+
+
+def main():
+  F = OutputFollower(sys.argv[1])
+
+  # Handle signals
+  import signal
+  def handler(signum,frame):
+    F.running = False
+
+  for i in [2, 15]:
+   try:
+    signal.signal(i, handler)
+   except:
+    pass
+
+  F.start()
+
+if __name__ == '__main__':
+  main()
+
+

scripts/qp_bitmasks.py

@@ -0,0 +1,133 @@
+#! /usr/bin/env python
+
+BIT_KIND_SIZE=64
+
+
+def int_to_string(s):
+    """Transforms any integer to a string representation
+    >>> print int_to_string(10)
+    1010
+    >>> print int_to_string(1024)
+    10000000000
+    >>> print int_to_string(123456789)
+    111010110111100110100010101
+    >>> print int_to_string(12345678912345678910)
+    1010101101010100101010011000111110000001011001010010010000111110
+    >>> print int_to_string(0)
+    0
+    >>> print int_to_string(-128)
+    Traceback (most recent call last):
+      File "<stdin>", line 1, in <module>
+      File "qp_bitmasks.py", line 23, in int_to_string
+        assert s>=0
+    AssertionError
+    """
+    assert type(s) in (int, long)
+    assert s>=0
+    return str(s) if s in (0,1) else int_to_string(s>>1) + str(s&1) 
+
+
+def string_to_bitmask(s,bit_kind_size=BIT_KIND_SIZE):
+    """Transforms a string into an bitmask
+    >>> print string_to_bitmask(10)
+    Traceback (most recent call last):
+      File "<stdin>", line 1, in <module>
+      File "qp_bitmasks.py", line 30, in string_to_bitmask
+        assert type(s) == str
+    AssertionError
+    >>> print string_to_bitmask('10')
+    ['0000000000000000000000000000000000000000000000000000000000000010']
+    >>> print string_to_bitmask('1010'*64)
+    ['1010101010101010101010101010101010101010101010101010101010101010', '1010101010101010101010101010101010101010101010101010101010101010', '1010101010101010101010101010101010101010101010101010101010101010', '1010101010101010101010101010101010101010101010101010101010101010']
+    >>> print string_to_bitmask('1010'*64,4)
+    ['1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010', '1010']
+    """
+    assert type(s) == str
+    assert bit_kind_size > 0
+
+    while len(s) % bit_kind_size != 0:
+        s = '0'+s
+    return [ s[i:i+bit_kind_size] for i in range(0,len(s),bit_kind_size) ]
+
+
+def int_to_bitmask(s,bit_kind_size=BIT_KIND_SIZE):
+    """Transforms a string into an bitmask
+    >>> int_to_bitmask(1)
+    ['0000000000000000000000000000000000000000000000000000000000000001']
+    >>> int_to_bitmask(-1)
+    ['1111111111111111111111111111111111111111111111111111111111111111']
+    >>> int_to_bitmask(10)
+    ['0000000000000000000000000000000000000000000000000000000000001010']
+    >>> int_to_bitmask(-10)
+    ['1111111111111111111111111111111111111111111111111111111111110110']
+    >>> 
+    """
+    assert type(s) in (int, long)
+    if s>=0:
+      s = int_to_string(s)
+      result = string_to_bitmask( s, bit_kind_size )
+    else:
+      s = int_to_string(-s-1)
+      result = string_to_bitmask( s, bit_kind_size )
+      result = [ x.replace('1','.').replace('0','1').replace('.','0') for x in result ]
+    return result
+
+
+
+class BitMask(object):
+
+  """
+  >>> A = BitMask( [ -127,47  ], bit_kind_size=8)
+  >>> print A
+  ['10000001', '00101111']
+  >>> print A[0]
+  -127
+  >>> print A[1]
+  47
+  >>> A[0] = 127
+  >>> print A
+  ['01111111', '00101111']
+  >>> A[1] = '100'
+  >>> print A
+  ['01111111', '00000100']
+  >>> A[1] = '10000001'
+  >>> print A
+  ['01111111', '10000001']
+  >>> print A[1]
+  -127
+  """
+  
+
+  def __init__(self,l=[],bit_kind_size=BIT_KIND_SIZE):
+    self.bit_kind_size = bit_kind_size
+    self._data_int = l
+
+  def get_N_int(self):
+    return len(self._data_int)
+  N_int = property(fget=get_N_int)
+
+  def __getitem__(self,i):
+    return self._data_int[i]
+
+  def __setitem__(self,i,value):
+    if type(value) in (int,long):
+        self._data_int[i] = value
+    elif type(value) == str:
+        s = string_to_bitmask(value,bit_kind_size=self.bit_kind_size)[0]
+        if s[0] == '0':
+          self._data_int[i] = int(s,2)
+        else:
+          s = s.replace('0','.').replace('1','0').replace('.','1')
+          self._data_int[i] = -int(s,2)-1
+
+  def __repr__(self):
+    result = []
+    for i in self._data_int:
+      result += int_to_bitmask(i,bit_kind_size=self.bit_kind_size)
+    return str(result)
+
+
+
+if __name__ == '__main__':
+  import doctest
+  doctest.testmod()

scripts/qpackage

@@ -0,0 +1,127 @@
+#!/bin/bash
+# 
+# Runs the programs.
+# Thu Jun 26 23:40:20 CEST 2014
+
+# Check environment
+###################
+
+if [[ -z $QPACKAGE_ROOT ]]
+then
+   echo "Error:"
+   echo "QPACKAGE_ROOT environment variable is not set."
+   echo "source quantum_package.rc"
+   exit 1
+fi
+
+# List of executables
+#####################
+
+declare -A EXECUTABLES
+for EXE in $(find $QPACKAGE_ROOT/src -type f -executable | grep -e "$QPACKAGE_ROOT/src/[^/]*/[^/]*$") 
+do
+  EXECUTABLES["$(basename "${EXE}")"]="${EXE}"
+done
+
+function print_list()
+{
+  echo
+  echo "Available programs:"
+  echo
+  for EXE in ${!EXECUTABLES[@]}
+  do
+    printf " * %-30s [ %s ]\n" $EXE ${EXECUTABLES[$EXE]}
+  done | sort
+  echo
+}
+
+# Help message
+##############
+
+function print_help()
+{
+  cat << EOF
+
+Usage:
+   qpackage -h | --help
+   qpackage -l | --list
+   qpackage run <program> <EZFIO_input>
+   qpackage reset <EZFIO_input>
+
+Options:
+   -h  --help       Print help message
+   -l  --list       List executables
+
+EOF
+}
+
+ARGS=$(getopt -o "hl" -l "help,list" -n $0 -- "$@")
+
+[[ $? -eq 0 ]] || exit 1
+
+eval set -- "$ARGS"
+
+while true
+do
+  case "$1" in
+    -h|--help)
+      print_help
+      exit 0
+      shift ;;
+
+    -l|--list)
+      print_list
+      exit 0
+      shift ;;
+
+    --)
+      shift
+      break;;
+  esac
+done
+
+# Run commands
+##############
+
+function run()
+{
+  # run $EXE $EZFIO
+  # Starts the executable in one process and
+  # displays the output files in stdout
+  EXE=${EXECUTABLES[$1]}
+  EZFIO=$2
+  date
+  ${QPACKAGE_ROOT}/scripts/follow_output.py ${EZFIO} &
+  ${EXE} ${EZFIO} 
+  kill -2 %1
+  wait
+  date
+}
+
+function reset()
+{
+  # reset $EZFIO
+  rm -rf $1/output/*.rst
+  rm -rf $1/determinants/{n_det,psi_det.gz,psi_coef.gz}
+}
+
+COMMAND=$1
+shift
+
+case "${COMMAND}" in
+  run)
+    run $1 $2
+    ;;
+  reset)
+    reset $1 
+    ;;
+  *)
+    print_help
+    ;;
+esac
+
+
+
+
+
+