Contribution to use FDMNES and FDMNES_SPACEGROUP environment variables

README.md

@@ -4,15 +4,15 @@ pyFDMNES
 Python interface to fdmnes simulations. Simplifies and automates data input/output.
 - load cif files
 - Read/Modify/Write FDMNES input files
-- easily perform repeated `Colvolution` on existing DOS calculation
+- easily perform repeated `Convolution` on existing DOS calculation
 - flexibly extract `DAFS`/`XANES` curves from existing calculation
 
-A new FDMNES simulation is represented by the `fdmnes` object which  can be created by loading an existing (manually created) fdmnes input file, a .cif file of by defining space-group or metric and subsequently fill the unit cell with atoms.
+A new FDMNES simulation is represented by the `fdmnes` object which  can be created by loading an existing (manually created) FDMNES input file, a `.cif` file of by defining space-group or metric and subsequently fill the unit cell with atoms.
 
-After loading an existing input file, one can for example change some parameters in the `fdmnes.P` Parameter instance and save/create new inputfiles with WriteInputFile. One can add the saved file to the job queue which can be executed using sim.Run().
+After loading an existing input file, one can for example change some parameters in the `fdmnes.P` Parameter instance and save/create new input files with `WriteInputFile`. One can add the saved file to the job queue which can be executed using sim.Run().
 
 Furthermore, the `fdmnes.P` Parameters Object similar to a python dict but does some consistency check of all given parameters, to a certain extent. Basically it checks if the given parameter has the proper shape (2d, 1d, 0d, or bool, etc..). How the definitions are stored, can be seen in the settings file:
-https://github.com/tinaw/pyFDMNES/blob/master/fdmnes/settings.py The idea is also to identify parameters which are crucial for the computation of the matrix elements and others which are used for post-processing (e.g. Convolution). This would allow to let pyFDMNES decide when a new computation of the matrix elements or electron density is necessary.
+[fdmnes/settings.py](fdmnes/settings.py) The idea is also to identify parameters which are crucial for the computation of the matrix elements and others which are used for post-processing (e.g. Convolution). This would allow to let pyFDMNES decide when a new computation of the matrix elements or electron density is necessary.
 
 
 Certainly, FDMNES evolved and not all parameters are correctly represented in the settings file. Therefore it is not complete yet and updates are needed.
@@ -22,11 +22,11 @@ Certainly, FDMNES evolved and not all parameters are correctly represented in th
 - python 2.7 or 3
 - numpy
 - PyCifRW
-- fdmnes (version > March 28th 2014)
+- fdmnes (version > March 28th 2014) from e.g. https://fdmnes.neel.cnrs.fr/
 
 
 # Installation
-change dir to the downloaded repository (where the setup.py is found) and modify the `setup.cfg`
+Change dir to the downloaded repository (where the setup.py is found) and modify the `setup.cfg`.
 
 ## using pip (recommended)
     pip install . [--user]
@@ -35,4 +35,22 @@ change dir to the downloaded repository (where the setup.py is found) and modify
     python setup.py install [--user]
 
 # Usage
-See `examples` folder
+See `examples` folder.
+
+You may set the `FDMNES` environment variable to specify the FDMNES executable command,
+for instance when using MPI:
+```
+FDMNES='mpirun fdmnes'
+FDMNES='/path/to/fdmnes_linux_serial'
+FDMNES='/path/to/fdmnes_linux_parallel'
+```
+
+For instance you may start:
+```
+cd examples/BaTiO3
+FDMNES="mpirun fdmnes_parallel" python3 BaTiO3_cif_open.py
+```
+The default is to use the executable defined in the `setup.cfg` file of the pyFDMNES package.
+
+You may as well set the `FDMNES_SPACEGROUP` environment variable to specify the `spacegroup.txt` file which defines the space-group operators. The default is to use the file provided by the pyFDMNES package.
+

fdmnes/pyFDMNES.py

@@ -277,6 +277,10 @@ def __init__(self, structure, resonant="", verbose=False,
                             or
                                 - detailed name of space group 
                                   (including setting)
+            The FDMNES environment variable can be set from the FDMNES
+            environment variable. The space-group list can be set from the 
+            FDMNES_SPACEGROUP environment variable, or defaults to the one from
+            the pyFDMNES package.
         """
         self.positions = collections.OrderedDict() # symmetric unit
         self.Defaults = settings.Defaults
@@ -294,33 +298,38 @@ def __init__(self, structure, resonant="", verbose=False,
 
         ### FIND FDMNES ####################################################
         if fdmnes_path==None:
-            if not conf.has_option("global", "fdmnes_path"):
+            if conf.has_option("global", "fdmnes_path"):
+                fdmnes_path = conf.get("global", "fdmnes_path")
+                fdmnes_path = os.path.realpath(fdmnes_path)
+            if 'FDMNES' in os.environ and os.environ['FDMNES']:
+                fdmnes_path = os.environ['FDMNES']
+            if fdmnes_path is None or not fdmnes_path:
                 raise ValueError(
-                    "No entry for ``fdmnes_path'' found in config file:%s%s"\
+                    "No valid FDMNES environment variable nor entry for 'fdmnes_path' found in config file:%s%s"\
                     %(os.linesep, conffile))
-            else:
-                fdmnes_path = conf.get("global", "fdmnes_path")
 
-        fdmnes_path = os.path.realpath(fdmnes_path)
-        print("Using FDMNES at %s"%fdmnes_path)
-        self.fdmnes_dir = os.path.dirname(fdmnes_path)
+        print("Using FDMNES=%s" % fdmnes_path)
+        # self.fdmnes_dir = os.path.dirname(fdmnes_path)
         self.fdmnes_exe = fdmnes_path
-        fdmnes_bin = os.path.basename(fdmnes_path)
-
-        for fname in [fdmnes_bin]:
-            fpath = os.path.join(self.fdmnes_dir, fname)
-            if not os.path.isfile(fpath):
-                raise ValueError(
-                    """
-                        File %s not found in %s
-
-                        Have you entered a valid path in %s?
-                        It must point on the fdmnes executable.
-                    """%(fname, self.fdmnes_dir, conffile))
-
-        fpath = os.path.join(self.fdmnes_dir, "spacegroup.txt")
-        if not os.path.isfile(fpath):
-            fpath = resource_filename("spacegroup.txt")
+        # fdmnes_bin = os.path.basename(fdmnes_path)
+
+#        for fname in [fdmnes_bin]:
+#            fpath = os.path.join(self.fdmnes_dir, fname)
+#            if not os.path.isfile(fpath):
+#                print(
+#                    """WARNING:
+#                        File %s not found in %s
+
+#                        Have you entered a valid path in %s?
+#                        It must point on the fdmnes executable.
+#                    """%(fname, self.fdmnes_dir, conffile))
+
+#        fpath = os.path.join(self.fdmnes_dir, "spacegroup.txt")
+#        if not os.path.isfile(fpath):
+        fpath = resource_filename("spacegroup.txt")
+        if 'FDMNES_SPACEGROUP' in os.environ and os.environ['FDMNES_SPACEGROUP'] and os.path.exists(os.environ['FDMNES_SPACEGROUP']):
+          fpath = os.environ['FDMNES_SPACEGROUP']
+        print("Using FDMNES_SPACEGROUP=%s" % fpath)
 
         with open(fpath, "r") as fh:
             sgcont = filter(lambda s: s.startswith("*"), fh.readlines())

setup.cfg

@@ -1,3 +1,3 @@
 [global]
 ; enter here the path to the fdmnes executable:
-fdmnes_path=/usr/bin/fdmnes_parallel
+fdmnes_path=fdmnes

setup.py

@@ -25,7 +25,7 @@ def fdmnes_path():
     else:
         fdmnes_path = conf.get("global", "fdmnes_path")
     if not os.path.isfile(fdmnes_path):
-        raise IOError("File not found: {}\Please edit file ``setup.cfg''".format(fdmnes_path))
+        raise IOError("File not found: {}\nPlease edit file ``setup.cfg''".format(fdmnes_path))
     return fdmnes_path
 
 def create_ini(fdmnes_path):