Improvements to vasp jobs (re)launching

1. Added correct handling of partial hydrogen atoms (e.g. H.75)
2. Fixed selective dynamics so that the property is retained when launching a vasp job
3. Fixed the infamous float number of nodes error with an integer division

Author: ftherrien

src/pylada/crystal/read.py

@@ -89,12 +89,23 @@ def poscar(path="POSCAR", types=None):
         for i in line:
             if not re.match(r"[A-Z][a-z]?", i):
                 is_vasp_5 = False
-                break
+                break  
         if is_vasp_5:
             text_types = deepcopy(line)
-            if types is not None and not set(text_types).issubset(set(types)):
-                raise error.ValueError("Unknown species in poscar: {0} not in {1}."
-                                       .format(text_types, types))
+
+            if types is not None:
+                # If partial H (e.g. H.75) are specified they will replace H
+                # in the order they were specified
+                for s in types:
+                    if s[0] == "H" and "." in s:
+                        for i,c in enumerate(text_types):
+                            if c == "H":
+                                text_types[i] = s
+                                break
+                            
+                if not set(text_types).issubset(set(types)):
+                    raise error.ValueError("Unknown species in poscar: {0} not in {1}."
+                                           .format(text_types, types))
             types = text_types
             line = poscar.readline().split()
         if types is None:

src/pylada/ipython/launch/__init__.py

@@ -167,7 +167,7 @@ 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)
+            nnode = max(1, natom // event.ppn)
             nproc = nnode * event.ppn
             return nproc
     logger.info("launch/init: mppalloc b: %s" % mppalloc)

src/pylada/vasp/extract/base.py

@@ -269,12 +269,12 @@ def structure(self):
         """ Greps structure and total energy from OUTCAR. """
         if self.nsw == 0 or self.ibrion == -1:
             return self.initial_structure
-
+        
         try:
             result = self._contcar_structure
         except:
             result = self._grep_structure
-
+            
         # tries to find adequate name for structure.
         try:
             name = self.system
@@ -329,6 +329,7 @@ def structure(self):
         else:
             for force, atom in zip(forces, result):
                 atom.force = force
+        
         return result
 
     @property
@@ -447,7 +448,7 @@ def _contcar_structure(self):
         """ Greps structure from CONTCAR. """
         from ...crystal import read
         from quantities import eV
-
+        
         result = read.poscar(self.__contcar__(), self.species)
         result.energy = float(self.total_energy.rescale(eV)) if self.is_dft else 0e0
         return result
@@ -470,8 +471,21 @@ def ions_per_specie(self):
     @property
     @make_cached
     def species(self):
+        import re
         """ Greps species from OUTCAR. """
-        return [ u.group(1) for u in self._search_OUTCAR(r"""VRHFIN\s*=\s*(\S+)\s*:""") ]
+        result = []
+        for u in self._search_OUTCAR(r"""VRHFIN\s*=\s*(.*)$"""):
+            atom = u[1].split(":")[0].strip()
+            match = re.search(r"Z\s*=\s*(\S+)", u[1])
+            if match is None:
+                result.append(atom)
+            else:
+                result.append(atom + ("%3.2f"%(eval(match[1]))).strip(" 0"))
+        
+        # return [ u.group(1) for u in self._search_OUTCAR(r"""VRHFIN\s*=\s*(\S+)\s*:""") ]
+        # return [ u.group(1) for u in self._search_OUTCAR(r"""TITEL\s*=\s*\S*\s*(\S+)""") ]
+
+        return result
 
     @property
     @make_cached

src/pylada/vasp/functional.py

@@ -304,7 +304,7 @@ def __init__(self, copy=None, species=None, kpoints=None, **kwargs):
 
             .. _CONTCAR: http://cms.mpi.univie.ac.at/vasp/guide/node60.html
         """
-        self.isym = ChoiceKeyword(values=list(range(-1, 3)))
+        self.isym = ChoiceKeyword(values=list(range(-1, 4)))
         """ Symmetry scheme.
 
             .. seealso:: ISYM_
@@ -1017,8 +1017,9 @@ def bringup(self, structure, outdir, **kwargs):
             # creates POTCAR file
             logger.debug("vasp/functional bringup: files.POTCAR: %s " % files.POTCAR)
             with open(files.POTCAR, 'w') as potcar:
-                self.write_potcar(potcar, structure)
-
+                for s in specieset(structure):
+                    outLines = self.species[s].read_potcar()
+                    potcar.writelines(outLines)
             # Add is running file marker.
             local_path(outdir).join('.pylada_is_running').ensure(file=True)
             self._copy_additional_files(outdir)
@@ -1114,14 +1115,7 @@ def write_kpoints(self, file, structure, kpoints=None):
                 outLine = "{0[0]} {0[1]} {0[2]} {1}\n".format(
                     kpoint, 1 if len(kpoint) == 3 else kpoint[3])
                 file.write(outLine)
-    
-    def write_potcar(self, file, structure):
-        """ Writes the potcar file """
-        from ..crystal import specieset
-        for s in specieset(structure):
-            outLines = self.species[s].read_potcar()
-            file.writelines(outLines)
-    
+
     def __repr__(self, defaults=True, name=None):
         """ Returns representation of this instance """
         from ..tools.uirepr import uirepr

src/pylada/vasp/keywords.py

@@ -356,7 +356,10 @@ def value(self, value):
         if value is None:
             self._value = None
             return None
-        from pylada import is_vasp_4
+        try:
+            from pylada import is_vasp_4
+        except:
+            is_vasp_4 = False
         if not hasattr(value, 'lower'):
             raise TypeError("ALGO cannot be set with {0}.".format(value))
         lower = value.lower().rstrip().lstrip()
@@ -871,8 +874,7 @@ def output_map(self, **kwargs):
         from ..error import ValueError
         from ..crystal import write, read, specieset
         from . import files
-        from pylada import is_vasp_4
-        
+
         istruc = self._value
         if istruc is None:
             istruc = 0
@@ -886,7 +888,7 @@ def output_map(self, **kwargs):
             has_restart = vasp.restart.success
         if has_restart:
             structure = vasp.restart.structure
-
+            
         # determines which CONTCAR is the latest, if any exist.
         if istruc in [-1, 1]:
             last_contcar = latest_file(join(outdir, files.CONTCAR))
@@ -896,6 +898,7 @@ def output_map(self, **kwargs):
             # specifically, the order of the atoms of a given specie are the same).
             if last_contcar is not None:
                 other = read.poscar(path=last_contcar, types=specieset(structure))
+                
                 if len(other) != len(structure):
                     raise ValueError('CONTCAR and input structure differ in size.')
                 for type in specieset(other):
@@ -908,6 +911,9 @@ def output_map(self, **kwargs):
                         if a.type != type:
                             continue
                         a.pos = b.pos
+                        if len(getattr(b, 'freeze', '')) != 0:
+                            a.freeze = b.freeze
+    
                 structure.cell = other.cell
                 structure.scale = other.scale
                 print("setting cell and scale!")
@@ -920,7 +926,8 @@ def output_map(self, **kwargs):
             raise ValueError('Structure scale is zero')
         if structure.volume < 1e-8:
             raise ValueError('Structure volume is zero')
-        write.poscar(structure, join(outdir, 'POSCAR'), vasp5=not is_vasp_4)
+        
+        write.poscar(structure, join(outdir, 'POSCAR'))
         return None