Collected bugfixes

README.md

@@ -3,9 +3,8 @@ The CASM Python packages
 
 The `casm-python` Python packages provide a Python interface to the CASM libraries, implement wrappers to fitting methods and DFT software, and provide other tools for plotting and analysis.
 
-This version of `casm-python` is compatible with  [CASM](https://prisms-center.github.io/CASMcode_docs/) >=1.2.
-
-A basic online reference is located [here](https://prisms-center.github.io/CASMcode_pydocs/latest/index.html)
+This version of `casm-python` is compatible with [CASM](https://prisms-center.github.io/CASMcode_docs/) >=1.2.
 
+A basic online reference is located [here](https://prisms-center.github.io/CASMcode_pydocs/casm/overview/latest)
 
 For a summary of changes, see [CHANGELOG.md](https://github.com/prisms-center/CASMpython/blob/1.X/CHANGELOG.md).

casm/casm/scripts/vasp_relax_report.py

@@ -5,6 +5,8 @@
 import json
 import sys
 
+import six
+
 from casm.misc import compat, noindent
 import casm.vaspwrapper
 
@@ -26,13 +28,12 @@ def main():
             % configdir))
         raise
 
-    compat.dump(json,
-                output,
-                'properties.calc.json',
-                'w',
-                cls=noindent.NoIndentEncoder,
-                indent=4,
-                sort_keys=True)
+    with open('properties.calc.json', 'w') as f:
+        f.write(six.u(json.dumps(
+            output,
+            cls=noindent.NoIndentEncoder,
+            indent=4,
+            sort_keys=True)))
 
     print("Finish vasp.relax.report\n\n")
 

casm/casm/vasp/error.py

@@ -724,32 +724,34 @@ def fix(err_jobdir, new_jobdir, settings):
 
 def error_check(jobdir, stdoutfile, err_types):
     """ Check vasp stdout for errors """
+    if err_types is None: return None
     err = dict()
     err_objs = {}
+    check_once = ['FreezeError']
     for i_err in _RunError.__subclasses__():
         err_objs[i_err.__name__] = i_err()
-    if err_types is None:
-        possible = [SubSpaceMatrixError()]
-    else:
-        # err_objs = {'IbzkptError' : IbzkptError(), 'SubSpaceMatrixError' : SubSpaceMatrixError(), 'NbandsError' : NbandsError()}
-        for s in err_types:
-            if s not in err_objs.keys():
-                raise VaspError('Invalid err_type: %s' % s)
-        possible = [err_objs[s] for s in err_types]
+    for i_err in _FreezeError.__subclasses__():
+        err_objs[i_err.__name__] = i_err()
+    # err_objs = {'IbzkptError' : IbzkptError(), 'SubSpaceMatrixError' : SubSpaceMatrixError(),
+    #             'NbandsError' : NbandsError(), 'FreezeError' : FreezeError()}
+    for s in err_types:
+        if s not in err_objs.keys():
+            raise VaspError('Invalid err_type: %s' % s)
+    possible = [err_objs[s] for s in err_types]
 
     # Error to check line by line, only look for first of each type
     sout = open(stdoutfile, 'r')
     for line in sout:
         for p in possible:
-            if not p.__class__.__name__ in err:
+            if not p.__class__.__name__ in err and not p.__class__.__name__ in check_once:
                 if p.error(line=line, jobdir=jobdir):
                     err[p.__class__.__name__] = p
 
     # Error to check for once
-    possible = [i_err() for i_err in _FreezeError.__subclasses__()]
     for p in possible:
-        if p.error(line=None, jobdir=jobdir):
-            err[p.__class__.__name__] = p
+        if not p.__class__.__name__ in err and p.__class__.__name__ in check_once:
+            if p.error(line=None, jobdir=jobdir):
+                err[p.__class__.__name__] = p
 
     sout.close()
     if len(err) == 0:

casm/casm/vasp/relax.py

@@ -195,12 +195,17 @@ def complete(self):
     def converged(self):
         """Check if configuration is relaxed.
 
-           This is called when self.rundir[-1] is complete and not a constant volume job.
+           This is called when self.rundir[-1] is complete.
 
            Convergence criteria is: at least 2 relaxation jobs are complete, and:
                                     1) the last job completed with <= 3 ionic steps
                                     or 2) the last two jobs had final E0 differ by less than
                                           self.settings["nrg_convergence"]
+                                    OR
+                                    at least 1 relaxation job is complete, and
+                                    the last job completed with 1 ionic step, and
+                                    the volume is fixed (ISIF = 0, 1, 2)
+                                    (ISIF must be set explicitly in the INCAR)
         """
         if len(self.rundir) >= 2:
             if io.ionic_steps(self.rundir[-1]) <= 3:
@@ -213,13 +218,18 @@ def converged(self):
                     if abs(o1.E[-1] -
                            o2.E[-1]) < self.settings["nrg_convergence"]:
                         return True
+        # note: this will not work if ISIF was not explicitly set in the INCAR
+        elif len(self.rundir) == 1:
+            if io.ionic_steps(self.rundir[-1]) == 1:
+                if io.get_incar_tag("ISIF", self.rundir[-1]) in [0, 1, 2]:
+                    return True
 
         return False
 
     def not_converging(self):
         """Check if configuration is not converging.
 
-           This is called when self.rundir[-1] is complete and not a constant volume job and self.converged() == False.
+           This is called when self.rundir[-1] is complete and self.converged() == False.
 
            Not converging criteria: >= 10 runs without completion
         """
@@ -416,16 +426,6 @@ def status(self):
                     #    io.get_incar_tag("ISMEAR", self.rundir[-1]) == -5:
                     return ("complete", None)
 
-            # elif constant volume run (but not the final one)
-            if io.get_incar_tag("ISIF", self.rundir[-1]) in [0, 1, 2]:
-                if io.get_incar_tag("NSW", self.rundir[-1]) == len(
-                        io.Oszicar(os.path.join(self.rundir[-1],
-                                                "OSZICAR")).E):
-                    return ("incomplete", "relax"
-                            )  # static run hit NSW limit and so isn't "done"
-                else:
-                    return ("incomplete", "constant")
-
             # elif convergence criteria met
             if self.converged():
                 return ("incomplete", "constant")

casm/casm/vaspwrapper/relax.py

@@ -136,8 +136,9 @@ def finalize(self, config_data):
         super(Relax, self).finalize(config_data)
         sys.stdout.flush()
 
-    def properties(self, calcdir, super_poscarfile=None, speciesfile=None):
+    @staticmethod
+    def properties(calcdir, super_poscarfile=None, speciesfile=None):
         """Make properties output as a list of dict of each image properties"""
-        output = super(Relax, self).properties(calcdir, super_poscarfile,
-                                               speciesfile)
+        output = super(Relax, Relax).properties(
+            calcdir, super_poscarfile, speciesfile)
         return output

casm/casm/vaspwrapper/vasp_calculator_base.py

@@ -421,6 +421,9 @@ def submit(self):
                       message=settings["message"],
                       email=settings["email"],
                       priority=settings["priority"],
+                      constraint=settings["constraint"],
+                      exclude=settings["exclude"],
+                      gpus=settings["gpus"],
                       command=cmd,
                       auto=self.auto)
 
@@ -671,7 +674,6 @@ def finalize(self, config_data):
     @staticmethod
     def properties(vaspdir, initial_structurefile=None, speciesfile=None):
         """ return a dict of output form a vasp directory"""
-        structure_info = structure.StructureInfo(initial_structurefile)
         output = dict()
         # load the OSZICAR and OUTCAR
         zcar = vasp.io.Oszicar(os.path.join(vaspdir, "OSZICAR"))
@@ -697,7 +699,7 @@ def properties(vaspdir, initial_structurefile=None, speciesfile=None):
         #   unsorted_dict[sorted_index] == orig_index
         #   For example:
         #     'unsort_dict[0]' returns the index into the unsorted POSCAR of the first atom in the sorted POSCAR
-        output["atom_type"] = initial_structure.atom_type
+        output["atom_type"] = [i.occ_alias for i in initial_structure.basis]
         #output["atoms_per_type"] = initial_structure.num_atoms
         output["coordinate_mode"] = contcar.coordinate_mode
 
@@ -723,32 +725,34 @@ def properties(vaspdir, initial_structurefile=None, speciesfile=None):
         output["global_properties"]["energy"] = {}
         output["global_properties"]["energy"]["value"] = zcar.E[-1]
 
-        if structure_info.atom_properties is not None:
-            if "Cmagspin" in list(structure_info.atom_properties.keys()):
-                output["global_properties"]["Cmagspin"] = {}
-                cmagspin_specific_output = attribute_classes.CmagspinAttr(
-                    structure_info).vasp_output_dictionary(ocar)
-                output["atom_properties"].update(cmagspin_specific_output)
-                #TODO: Need a better way to write global magmom. I don't like what I did here
-                output["global_properties"]["Cmagspin"]["value"] = zcar.mag[-1]
-
-            #TODO: When you don't have Cmagspin but have magnetic calculations. This part can be removed if you runall magnetic calculations as Cmagspin calculations.
-            #TODO: Need a better way of doing this. Some code duplication here.
-            else:
-                if ocar.ispin == 2:
+        if initial_structurefile is not None:
+            structure_info = structure.StructureInfo(initial_structurefile)
+            if structure_info.atom_properties is not None:
+                if "Cmagspin" in list(structure_info.atom_properties.keys()):
                     output["global_properties"]["Cmagspin"] = {}
+                    cmagspin_specific_output = attribute_classes.CmagspinAttr(
+                        structure_info).vasp_output_dictionary(ocar)
+                    output["atom_properties"].update(cmagspin_specific_output)
+                    #TODO: Need a better way to write global magmom. I don't like what I did here
                     output["global_properties"]["Cmagspin"]["value"] = zcar.mag[-1]
-                    if ocar.lorbit in [1, 2, 11, 12]:
-                        output["atom_properties"]["Cmagspin"] = {}
-                        output["atom_properties"]["Cmagspin"]["value"] = [
-                            None for i in range(len(contcar.basis))
-                        ]
-
-                        for i, v in enumerate(contcar.basis):
-                            output["atom_properties"]["Cmagspin"]["value"][
-                                unsort_dict[i]] = [
-                                    noindent.NoIndent(ocar.mag[i])
-                                ]
+
+                    #TODO: When you don't have Cmagspin but have magnetic calculations. This part can be removed if you runall magnetic calculations as Cmagspin calculations.
+                    #TODO: Need a better way of doing this. Some code duplication here.
+                else:
+                    if ocar.ispin == 2:
+                        output["global_properties"]["Cmagspin"] = {}
+                        output["global_properties"]["Cmagspin"]["value"] = zcar.mag[-1]
+                        if ocar.lorbit in [1, 2, 11, 12]:
+                            output["atom_properties"]["Cmagspin"] = {}
+                            output["atom_properties"]["Cmagspin"]["value"] = [
+                                None for i in range(len(contcar.basis))
+                            ]
+
+                            for i, v in enumerate(contcar.basis):
+                                output["atom_properties"]["Cmagspin"]["value"][
+                                    unsort_dict[i]] = [
+                                        noindent.NoIndent(ocar.mag[i])
+                                    ]
 
         #TODO: Code duplication here. If you have a magnetic calculation without dofs, you still need to write magmom values. This can be removed if you run all the magnetic calculations as Cmagspin dof calculations.
         #TODO: If you still want to have this particular functionality, wrap it up in a helper function to avoid code duplication.

casm/casm/vaspwrapper/vaspwrapper.py

@@ -36,6 +36,8 @@ def read_settings(filename):
         "pmem": string for requested memory (default None)
         "priority": requested job priority (default "0")
         "constraint": constraint. ex: ``"haswell"`` (default None)
+        "exclude": nodes to exclude (slurm only). ex: ``"node01,node02,node03"`` (default None)
+        "gpus": how many gpus to request (slurm only). ex: 4 (default None)
         "message": when to send messages about jobs (ex. "abe", default "a")
         "email": where to send messages (ex. "[email protected]", default None)
         "qos": quality of service, 'qos' option (ex. "fluxoe")
@@ -78,7 +80,7 @@ def read_settings(filename):
     select_one = [["nodes", "atom_per_proc", "nodes_per_image"]]
 
     optional = [
-        "account", "pmem", "priority", "constraint", "message", "email", "qos",
+        "account", "pmem", "priority", "constraint", "exclude", "gpus", "message", "email", "qos",
         "npar", "ncore", "kpar", "ncpus", "vasp_cmd", "run_limit",
         "nrg_convergence", "encut", "kpoints", "extra_input_files", "move",
         "copy", "remove", "compress", "backup", "initial", "final",
@@ -88,6 +90,11 @@ def read_settings(filename):
         "endstate_calctype", "initial_deformation"
     ]
 
+    if "gpus" in settings:
+        # user must supply their own run command
+        if not "vasp_cmd" in settings or len(settings["vasp_cmd"]) == 0:
+            raise VaspWrapperError("gpu setting requires you to set vasp_cmd manually")
+
     for key in required:
         if not key in settings:
             raise VaspWrapperError(key + "' missing from: '" + filename + "'")

casm/requirements.txt

@@ -4,5 +4,5 @@ pandas
 prisms-jobs
 scikit-learn
 scipy
-sh
+sh==1.14.2
 six

casm/setup.py

@@ -36,7 +36,7 @@ def script_str(file):
     entry_points={'console_scripts': console_scripts},
     install_requires=[
         'deap', 'mock', 'pandas', 'prisms-jobs', 'scikit-learn',
-        'scipy', 'sh'
+        'scipy', 'sh==1.14.2'
     ],
     classifiers=[
         'Development Status :: 5 - Production/Stable',