Merge pull request #67 from pylada/pwscf_fixes

fixing some bugs

pylada

@@ -0,0 +1 @@
+src/pylada

src/pylada/crystal/read.py

@@ -357,7 +357,8 @@ def icsd_cif_a(filename, make_primitive=True):
     from numpy import array, transpose
     from numpy import pi, sin, cos, sqrt, dot
 
-    lines = open(filename, 'r').readlines()
+#vladan    lines = open(filename, 'r').readlines()
+    lines = open(filename, 'r',encoding= 'unicode_escape').readlines()
     logger.info("crystal/read: icsd_cif_a: %s" % filename)
 
     sym_big = 0

src/pylada/espresso/extract.py

@@ -176,6 +176,8 @@ def __cell(self, structure):
         cards = [u for u in read_cards(self.output_path.open(mode='r'))
                  if u.name == 'cell_parameters']
         structure.cell = [u.split() for u in cards[-1].value.split('\n')]
+        # vladan: transposing so the cell vectors are rows and not columns
+        structure.cell = structure.cell.T
 
     @property
     @make_cached

src/pylada/espresso/functional.py

@@ -266,7 +266,8 @@ def iter(self, structure, outdir=".", comm=None, overwrite=False, restart=None,
         if not overwrite:
             # Check with this instance's Extract, cos it is this calculation we shall
             # do here. Derived instance's Extract might be checking for other stuff.
-            extract = self.Extract(str(outdir))
+#vladan            extract = self.Extract(str(outdir))
+            extract = self.Extract(str(outdir),prefix=self.control.prefix)
             if extract.success:
                 yield extract  # in which case, returns extraction object.
                 return
@@ -296,7 +297,8 @@ def onfinish(process, error):
                              stdin=stdin, stdout=stdout, stderr=stderr,
                              dompi=comm is not None)
         # yields final extraction object.
-        yield self.Extract(str(outdir))
+#vladan        yield self.Extract(str(outdir))
+        yield self.Extract(str(outdir),prefix=self.control.prefix)
 
     def pseudos_do_exist(self, structure, verbose=False):
         """ True if it all pseudos exist
@@ -329,7 +331,8 @@ def _restarting(self, structure, restart, outdir):
             return structure
 
         # normalize: restart could be an Extract object, or a path
-        restart = self.Extract(restart)
+#vladan        restart = self.Extract(restart)
+        restart = self.Extract(str(outdir),prefix=self.control.prefix)
         if not restart.success:
             logger.critical("Cannot restart from unsuccessful calculation")
             raise error.RuntimeError("Cannot restart from unsuccessful calculation")

src/pylada/espresso/pwscf_namelists.py

@@ -180,7 +180,17 @@ class Cell(Namelist):
     cell_factor = Float(allow_none=True, default_value=None, min=0e0,
                         help="Used when constructing pseudopotential tables")
     factor = alias(cell_factor)
-    cell_dofree = CaselessStringEnum(['all', 'x', 'y', 'z', 'xy', 'xz', 'yz', 'shape', 'volume',
-                                      '2Dxy', '2Dshape'], default_value=None, allow_none=True,
+
+    #vladan
+    #cell_dofree = CaselessStringEnum(['all', 'x', 'y', 'z', 'xy', 'xz', 'yz', 'shape', 'volume',
+    #                                  '2Dxy', '2Dshape'], default_value=None, allow_none=True,
+    #                                 help="Degrees of freedom during relaxation")
+
+    cell_dofree = CaselessStringEnum(['all', 'a', 'b', 'c', 'fixa', 'fixb', 'fixc',
+                                      'x', 'y', 'z', 'xy', 'xz', 'yz', 'shape', 'volume',
+                                      '2Dxy', '2Dshape', 'epitaxial_ab', 'epitaxial_ac', 'epitaxial_bc'],
+                                     default_value=None, allow_none=True,
                                      help="Degrees of freedom during relaxation")
+
+
     dofree = alias(cell_dofree)

src/pylada/espresso/structure_handling.py

@@ -223,10 +223,26 @@ def add_structure(structure, f90namelist, cards):
         positions = card_dict['atomic_positions']
     positions.subtitle = 'alat'
     positions.value = ""
-    for atom in structure:
-        positions.value += "%s %18.12e %18.12e %18.12e\n" % (atom.type, atom.pos[0], atom.pos[1],
-                                                             atom.pos[2])
 
+    #vladan
+    #for atom in structure:
+    #    positions.value += "%s %18.12e %18.12e %18.12e\n" % (atom.type, atom.pos[0], atom.pos[1], atom.pos[2])
+
+    # new code for selective dynamics (by Matt Jank.)
+    selective_dynamics = any([len(getattr(atom, 'freeze', '')) != 0 for atom in structure])
+
+    for atom in structure:
+        if not selective_dynamics:
+            positions.value += "%s %18.12e %18.12e %18.12e\n" % (atom.type, atom.pos[0],
+                                                                 atom.pos[1], atom.pos[2])
+        else:
+            positions.value += "%s %18.12e %18.12e %18.12e %i %i %i\n"
+            %(atom.type, atom.pos[0],atom.pos[1], atom.pos[2],
+              'x' not in getattr(atom, 'freeze', ''),
+              'y' not in getattr(atom, 'freeze', ''),
+              'z' not in getattr(atom, 'freeze', '')) 
+    # end selective dynamics modification
+
     __add_forces_to_input(cards, structure)
 
 

src/pylada/ipython/launch/__init__.py

@@ -167,7 +167,8 @@ def mppalloc(job):
             """ Returns number of processes for this job. """
             natom = len(job.structure)  # number of atoms.
             # Round down to a multiple of ppn
-            nnode = max(1, natom / event.ppn)
+#vladan            nnode = max(1, natom / event.ppn)
+            nnode = max(1, natom // event.ppn)
             nproc = nnode * event.ppn
             return nproc
     logger.info("launch/init: mppalloc b: %s" % mppalloc)

src/pylada/ipython/launch/scattered.py

@@ -110,13 +110,23 @@ def pbspaths(directory, jobname, suffix):
             # added by Peter Graf
             # avoid jobfolder which is already in the queue:
             qstuff = qstat(name)
+            # vladan
+            # qstat(name) will return all jobs with names whose first parts
+            # match the name. For example qstat('job.12') will return the
+            # both 'job.12' and 'job.123'. So, Peter's stuff has a bug, if
+            # 'job.123' is in the queue pylada will think 'job.12' is also.
+            # To deal with this one can do:
+            qstuff = [x for x in qstuff if x.split()[-1]==name]
             if (len(qstuff) > 0 and not event.force):
-                status = [x.split()[2] for x in qstuff]
+                #status = [x.split()[2] for x in qstuff]
+                status = qstuff[0].split()[2]
                 # status is a list like ['Q'], ['R'], ['H'], ['C'], ['R', 'C'], etc
                 # 'RHQ' is the status that the job is indeed in the queue, 'C' job completed and
                 # being removed from the queue if needed, a prefix can be used to distinguish two
                 # jobs with the same name
-                if len(set(status) & set('RHQ')) > 0:
+                queue_options=['R','H','Q','PD','C'] # I (vladan) find this to work better
+                #if len(set(status) & set('RHQ')) > 0: # this was before, also has problems
+                if (status in queue_options):
                     print(("Job %s is in the queue, will not be re-queued" % name))
                     continue
 

src/pylada/ipython/magics.py

@@ -153,7 +153,8 @@ def qdel(self, arg):
                 message = "Are you sure you want to cancel"\
                     "the jobs listed above? [y/n] "
         else:
-            message = "Cancel all jobs? [y/n] "
+#vladan            message = "Cancel all jobs? [y/n] "
+            message = "Cancel all %s jobs? [y/n] " %(arg)
             key = ''
             while key not in ['n', 'y']:
                 key = cmdl_input(message)

src/pylada/misc/relativepath.py

@@ -209,7 +209,8 @@ def hook(self):
     @hook.setter
     def hook(self, value):
         from sys import version_info
-        from inspect import ismethod, getargspec, isfunction
+#vladan        from inspect import ismethod, getargspec, isfunction
+        from inspect import ismethod, isfunction
         if version_info[0] == 2:
             from inspect import getargspec
         else: