From 5f65a63c6a8bcb8b92cafacf2e4a052f3fe33d2e Mon Sep 17 00:00:00 2001 From: Shyue Ping Ong Date: Sat, 22 Jul 2023 08:21:13 -0700 Subject: [PATCH] Update dev docs --- custodian/__init__.py | 2 +- docs/_modules/custodian/ansible/actions.html | 4 +- .../custodian/ansible/interpreter.html | 4 +- .../custodian/cli/converge_geometry.html | 4 +- .../custodian/cli/converge_kpoints.html | 4 +- docs/_modules/custodian/cli/cstdn.html | 4 +- docs/_modules/custodian/cli/run_nwchem.html | 4 +- docs/_modules/custodian/cli/run_vasp.html | 4 +- docs/_modules/custodian/cp2k/handlers.html | 4 +- docs/_modules/custodian/cp2k/interpreter.html | 4 +- docs/_modules/custodian/cp2k/jobs.html | 4 +- docs/_modules/custodian/cp2k/utils.html | 4 +- docs/_modules/custodian/cp2k/validators.html | 4 +- docs/_modules/custodian/custodian.html | 26 +++++--- docs/_modules/custodian/feff/handlers.html | 4 +- docs/_modules/custodian/feff/interpreter.html | 4 +- docs/_modules/custodian/feff/jobs.html | 4 +- docs/_modules/custodian/lobster/handlers.html | 4 +- docs/_modules/custodian/lobster/jobs.html | 4 +- docs/_modules/custodian/nwchem/handlers.html | 4 +- docs/_modules/custodian/nwchem/jobs.html | 4 +- docs/_modules/custodian/qchem/utils.html | 4 +- docs/_modules/custodian/utils.html | 4 +- docs/_modules/custodian/vasp/handlers.html | 31 ++++++---- docs/_modules/custodian/vasp/interpreter.html | 4 +- docs/_modules/custodian/vasp/jobs.html | 58 ++++++++++-------- docs/_modules/custodian/vasp/validators.html | 4 +- docs/_modules/index.html | 4 +- docs/_static/documentation_options.js | 2 +- docs/_themes/README.html | 6 +- docs/changelog.html | 15 ++++- docs/custodian.ansible.html | 6 +- docs/custodian.cli.html | 6 +- docs/custodian.cp2k.html | 6 +- docs/custodian.feff.html | 6 +- docs/custodian.html | 6 +- docs/custodian.lobster.html | 6 +- docs/custodian.nwchem.html | 6 +- docs/custodian.qchem.html | 6 +- docs/custodian.vasp.html | 34 +++++----- docs/genindex.html | 4 +- docs/index.html | 6 +- docs/modules.html | 6 +- docs/objects.inv | Bin 2444 -> 2445 bytes docs/py-modindex.html | 4 +- docs/search.html | 4 +- docs/searchindex.js | 2 +- setup.py | 2 +- 48 files changed, 187 insertions(+), 159 deletions(-) diff --git a/custodian/__init__.py b/custodian/__init__.py index 2b52b201..3d5d2987 100644 --- a/custodian/__init__.py +++ b/custodian/__init__.py @@ -4,6 +4,6 @@ """ __author__ = "Shyue Ping Ong, William Davidson Richards, Stephen Dacek, Xiaohui Qu, Matthew Horton, Samuel M. Blau" -__version__ = "2023.6.5" +__version__ = "2023.7.22" from .custodian import Custodian diff --git a/docs/_modules/custodian/ansible/actions.html b/docs/_modules/custodian/ansible/actions.html index 1122caaa..02371ebe 100644 --- a/docs/_modules/custodian/ansible/actions.html +++ b/docs/_modules/custodian/ansible/actions.html @@ -4,7 +4,7 @@ - custodian.ansible.actions — custodian 2023.6.5 documentation + custodian.ansible.actions — custodian 2023.7.22 documentation @@ -34,7 +34,7 @@

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    • diff --git a/docs/_modules/custodian/custodian.html b/docs/_modules/custodian/custodian.html index 05fecd6d..9680eda7 100644 --- a/docs/_modules/custodian/custodian.html +++ b/docs/_modules/custodian/custodian.html @@ -4,7 +4,7 @@ - custodian.custodian — custodian 2023.6.5 documentation + custodian.custodian — custodian 2023.7.22 documentation @@ -34,7 +34,7 @@

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    • @@ -99,7 +99,7 @@

    Source code for custodian.custodian

     if SENTRY_DSN:
     import sentry_sdk
 
-    sentry_sdk.init(dsn=SENTRY_DSN)
+    sentry_sdk.init(dsn=SENTRY_DSN)  # pylint: disable=E0110
 
     with sentry_sdk.configure_scope() as scope:
         from getpass import getuser
@@ -507,6 +507,11 @@ 
    Source code for custodian.custodian
                 has_error = False
             zero_return_code = True
 
+            # Choose the terminate function to run. If a terminate_func exists, this
+            # should take priority, followed by Job.terminate if implemented, and finally
+            # subprocess.Popen.terminate if neither of the former exist.
+            terminate = self.terminate_func or job.terminate or p.terminate
+
             # While the job is running, we use the handlers that are
             # monitors to monitor the job.
             if isinstance(p, subprocess.Popen):
@@ -515,13 +520,18 @@ 
    Source code for custodian.custodian
                         while True:
                         n += 1
                         time.sleep(self.polling_time_step)
+                        # We poll the process p to check if it is still running.
+                        # Note that the process here is not the actual calculation
+                        # but whatever is used to control the execution of the
+                        # calculation executable. For instance; mpirun, srun, and so on.
                         if p.poll() is not None:
                             break
-                        terminate = self.terminate_func or p.terminate
                         if n % self.monitor_freq == 0:
+                            # At every self.polling_time_step * self.monitor_freq seconds,
+                            # we check the job for errors using handlers that are monitors.
+                            # In order to properly kill a running calculation, we use
+                            # the appropriate implementation of terminate.
                             has_error = self._do_check(self.monitors, terminate)
-                        if terminate is not None and terminate != p.terminate:
-                            time.sleep(self.polling_time_step)
                 else:
                     p.wait()
                     if self.terminate_func is not None and self.terminate_func != p.terminate:
@@ -539,10 +549,6 @@ 
    Source code for custodian.custodian
                 else:
                 has_error = self._do_check(self.handlers)
 
-            if has_error:
-                # This makes sure the job is killed cleanly for certain systems.
-                job.terminate()
-
             # If there are no errors detected, perform
             # postprocessing and exit.
             if not has_error:
diff --git a/docs/_modules/custodian/feff/handlers.html b/docs/_modules/custodian/feff/handlers.html
index 559c4768..639dd260 100644
--- a/docs/_modules/custodian/feff/handlers.html
+++ b/docs/_modules/custodian/feff/handlers.html
@@ -4,7 +4,7 @@
   
     
     
-    custodian.feff.handlers — custodian 2023.6.5 documentation
+    custodian.feff.handlers — custodian 2023.7.22 documentation
     
     
     
@@ -34,7 +34,7 @@ 
    Navigation
    
         
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  • custodian 2023.6.5 documentation »
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    •  
       
diff --git a/docs/_modules/custodian/feff/interpreter.html b/docs/_modules/custodian/feff/interpreter.html
index c948c7ea..bc822f56 100644
--- a/docs/_modules/custodian/feff/interpreter.html
+++ b/docs/_modules/custodian/feff/interpreter.html
@@ -4,7 +4,7 @@
   
     
     
-    custodian.feff.interpreter — custodian 2023.6.5 documentation
+    custodian.feff.interpreter — custodian 2023.7.22 documentation
     
     
     
@@ -34,7 +34,7 @@ 
    Navigation
    
         
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-        
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  • custodian.feff.interpreter
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diff --git a/docs/_modules/custodian/feff/jobs.html b/docs/_modules/custodian/feff/jobs.html
index bf91d13d..1c3f9b52 100644
--- a/docs/_modules/custodian/feff/jobs.html
+++ b/docs/_modules/custodian/feff/jobs.html
@@ -4,7 +4,7 @@
   
     
     
-    custodian.feff.jobs — custodian 2023.6.5 documentation
+    custodian.feff.jobs — custodian 2023.7.22 documentation
     
     
     
@@ -34,7 +34,7 @@ 
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diff --git a/docs/_modules/custodian/lobster/handlers.html b/docs/_modules/custodian/lobster/handlers.html
index e6c99456..dc9933d3 100644
--- a/docs/_modules/custodian/lobster/handlers.html
+++ b/docs/_modules/custodian/lobster/handlers.html
@@ -4,7 +4,7 @@
   
     
     
-    custodian.lobster.handlers — custodian 2023.6.5 documentation
+    custodian.lobster.handlers — custodian 2023.7.22 documentation
     
     
     
@@ -34,7 +34,7 @@ 
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diff --git a/docs/_modules/custodian/lobster/jobs.html b/docs/_modules/custodian/lobster/jobs.html
index cd6ce5f3..52842388 100644
--- a/docs/_modules/custodian/lobster/jobs.html
+++ b/docs/_modules/custodian/lobster/jobs.html
@@ -4,7 +4,7 @@
   
     
     
-    custodian.lobster.jobs — custodian 2023.6.5 documentation
+    custodian.lobster.jobs — custodian 2023.7.22 documentation
     
     
     
@@ -34,7 +34,7 @@ 
    Navigation
    
         
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diff --git a/docs/_modules/custodian/nwchem/handlers.html b/docs/_modules/custodian/nwchem/handlers.html
index 5ae1282f..6744c956 100644
--- a/docs/_modules/custodian/nwchem/handlers.html
+++ b/docs/_modules/custodian/nwchem/handlers.html
@@ -4,7 +4,7 @@
   
     
     
-    custodian.nwchem.handlers — custodian 2023.6.5 documentation
+    custodian.nwchem.handlers — custodian 2023.7.22 documentation
     
     
     
@@ -34,7 +34,7 @@ 
    Navigation
    
         
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diff --git a/docs/_modules/custodian/nwchem/jobs.html b/docs/_modules/custodian/nwchem/jobs.html
index 964bb900..b9099f8b 100644
--- a/docs/_modules/custodian/nwchem/jobs.html
+++ b/docs/_modules/custodian/nwchem/jobs.html
@@ -4,7 +4,7 @@
   
     
     
-    custodian.nwchem.jobs — custodian 2023.6.5 documentation
+    custodian.nwchem.jobs — custodian 2023.7.22 documentation
     
     
     
@@ -34,7 +34,7 @@ 
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diff --git a/docs/_modules/custodian/qchem/utils.html b/docs/_modules/custodian/qchem/utils.html
index 3f7e09f3..eeb595c3 100644
--- a/docs/_modules/custodian/qchem/utils.html
+++ b/docs/_modules/custodian/qchem/utils.html
@@ -4,7 +4,7 @@
   
     
     
-    custodian.qchem.utils — custodian 2023.6.5 documentation
+    custodian.qchem.utils — custodian 2023.7.22 documentation
     
     
     
@@ -34,7 +34,7 @@ 
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diff --git a/docs/_modules/custodian/utils.html b/docs/_modules/custodian/utils.html
index 12a4131f..942ec306 100644
--- a/docs/_modules/custodian/utils.html
+++ b/docs/_modules/custodian/utils.html
@@ -4,7 +4,7 @@
   
     
     
-    custodian.utils — custodian 2023.6.5 documentation
+    custodian.utils — custodian 2023.7.22 documentation
     
     
     
@@ -34,7 +34,7 @@ 
    Navigation
    
         
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diff --git a/docs/_modules/custodian/vasp/handlers.html b/docs/_modules/custodian/vasp/handlers.html
index 6f8f2201..f0b2a39e 100644
--- a/docs/_modules/custodian/vasp/handlers.html
+++ b/docs/_modules/custodian/vasp/handlers.html
@@ -4,7 +4,7 @@
   
     
     
-    custodian.vasp.handlers — custodian 2023.6.5 documentation
+    custodian.vasp.handlers — custodian 2023.7.22 documentation
     
     
     
@@ -34,7 +34,7 @@ 
    Navigation
    
         
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+        
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  • custodian.vasp.handlers
    •  
       
@@ -172,21 +172,21 @@ 
    Source code for custodian.vasp.handlers
                     default redirect used by :class:`custodian.vasp.jobs.VaspJob`.
             errors_subset_to_detect (list): A subset of errors to catch. The
                 default is None, which means all supported errors are detected.
-                Use this to only catch only a subset of supported errors.
-                E.g., ["eddrrm", "zheev"] will only catch the eddrmm and zheev
-                errors, and not others. If you wish to only excluded one or
+                Use this to catch only a subset of supported errors.
+                E.g., ["eddrmm", "zheev"] will only catch the eddrmm and zheev
+                errors, and not others. If you wish to only exclude one or
                 two of the errors, you can create this list by the following
                 lines:
-            vtst_fixes (bool): Whether to consider VTST optimizers. Defaults to
-                False for compatibility purposes, but if you have VTST, you
-                would likely benefit from setting this to True.
 
                 ```
-                subset = list(VaspErrorHandler.error_msgs.keys())
-                subset.pop("eddrrm")
+                subset = list(VaspErrorHandler().error_msgs.keys())
+                subset.remove("eddrmm")
 
                 handler = VaspErrorHandler(errors_subset_to_catch=subset)
                 ```
+            vtst_fixes (bool): Whether to consider VTST optimizers. Defaults to
+                False for compatibility purposes, but if you have VTST, you
+                would likely benefit from setting this to True.
         """
         self.output_filename = output_filename
         self.errors = set()
@@ -1299,7 +1299,7 @@ 
    Source code for custodian.vasp.handlers
                 # Can't perform check if Outcar not valid
             return False
 
-        if incar.get("ISMEAR", 0) > 0:
+        if incar.get("ISMEAR", 1) > 0:
             # Read the latest entropy term.
             outcar.read_pattern(
                 {"entropy": r"entropy T\*S.*= *(\D\d*\.\d*)"}, postprocess=float, reverse=True, terminate_on_match=True
@@ -1333,6 +1333,15 @@ 
    Source code for custodian.vasp.handlers
                         "action": {"_set": {"SIGMA": sigma - 0.06}},
                 }
             )
+        else:
+            # https://vasp.at/wiki/index.php/ISMEAR recommends ISMEAR = 0 if you have
+            # no a priori knowledge of your system ("then always use Gaussian smearing"
+            actions.append(
+                {
+                    "dict": "INCAR",
+                    "action": {"_set": {"ISMEAR": 0, "SIGMA": 0.05}},
+                }
+            )
 
         VaspModder(vi=vi).apply_actions(actions)
         return {"errors": ["LargeSigma"], "actions": actions}
    
diff --git a/docs/_modules/custodian/vasp/interpreter.html b/docs/_modules/custodian/vasp/interpreter.html
index d6bf14ee..284dcb6d 100644
--- a/docs/_modules/custodian/vasp/interpreter.html
+++ b/docs/_modules/custodian/vasp/interpreter.html
@@ -4,7 +4,7 @@
   
     
     
-    custodian.vasp.interpreter — custodian 2023.6.5 documentation
+    custodian.vasp.interpreter — custodian 2023.7.22 documentation
     
     
     
@@ -34,7 +34,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • custodian 2023.6.5 documentation »
    • 
+        
  • custodian 2023.7.22 documentation »
    • 
           
  • Module code »
    • 
         
  • custodian.vasp.interpreter
    •  
       
diff --git a/docs/_modules/custodian/vasp/jobs.html b/docs/_modules/custodian/vasp/jobs.html
index 02430177..d3877ec8 100644
--- a/docs/_modules/custodian/vasp/jobs.html
+++ b/docs/_modules/custodian/vasp/jobs.html
@@ -4,7 +4,7 @@
   
     
     
-    custodian.vasp.jobs — custodian 2023.6.5 documentation
+    custodian.vasp.jobs — custodian 2023.7.22 documentation
     
     
     
@@ -34,7 +34,7 @@ 
    Navigation
    
         
  • 
           modules |
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-        
  • custodian 2023.6.5 documentation »
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+        
  • custodian 2023.7.22 documentation »
    • 
           
  • Module code »
    • 
         
  • custodian.vasp.jobs
    •  
       
@@ -187,7 +187,7 @@ 
    Source code for custodian.vasp.jobs
                     wall-time handler which will write a read-only STOPCAR to
                 prevent VASP from deleting it once it finishes
         """
-        self.vasp_cmd = vasp_cmd
+        self.vasp_cmd = tuple(vasp_cmd)
         self.output_file = output_file
         self.stderr_file = stderr_file
         self.final = final
@@ -196,7 +196,7 @@ 
    Source code for custodian.vasp.jobs
             self.settings_override = settings_override
         self.auto_npar = auto_npar
         self.auto_gamma = auto_gamma
-        self.gamma_vasp_cmd = gamma_vasp_cmd
+        self.gamma_vasp_cmd = tuple(gamma_vasp_cmd) if gamma_vasp_cmd else None
         self.copy_magmom = copy_magmom
         self.auto_continue = auto_continue
 
@@ -294,7 +294,7 @@ 
    Source code for custodian.vasp.jobs
                 kpts = vi["KPOINTS"]
             if kpts is not None:
                 if kpts.style == Kpoints.supported_modes.Gamma and tuple(kpts.kpts[0]) == (1, 1, 1):
-                    if self.gamma_vasp_cmd is not None and which(self.gamma_vasp_cmd[-1]):
+                    if self.gamma_vasp_cmd is not None and which(self.gamma_vasp_cmd[-1]):  # pylint: disable=E1136
                         cmd = self.gamma_vasp_cmd
                     elif which(cmd[-1] + ".gamma"):
                         cmd[-1] += ".gamma"
@@ -713,35 +713,39 @@ 
    Source code for custodian.vasp.jobs
     
 
    [docs]    def terminate(self):
         """
-        Kill all vasp processes associated with the current job.
+        Kill all VASP processes associated with the current job.
         This is done by looping over all processes and selecting the ones
-        that contain "vasp" as well as access files (CHGCAR in particular)
+        that contain "vasp" as well as access files (vasprun.xml in particular)
         in the custodian working directory.
-        There is also a safety that kills all vasp processes if non of the
-        processes can be killed (This is bad if more than one vasp runs are
+        There is also a safety that kills all VASP processes if none of the
+        processes can be killed (This is bad if more than one VASP runs are
         simultaneously executed on the same node). However, this should never
         happen.
         """
         workdir = os.getcwd()
-        logger.info(f"kill vasp processes in work dir {workdir}")
-        is_killed = False
+        logger.info(f"Killing VASP processes in workdir {workdir}.")
         for proc in psutil.process_iter():
             try:
                 if "vasp" in proc.name().lower():
-                    for file in proc.open_files():
-                        if workdir + "/CHGCAR" == file.path and psutil.pid_exists(proc.pid):
-                            proc.kill()
-                            is_killed = True
-            except (psutil.NoSuchProcess, psutil.AccessDenied):
+                    open_paths = [file.path for file in proc.open_files()]
+                    vasprun_path = os.path.join(workdir, "vasprun.xml")
+                    if (vasprun_path in open_paths) and psutil.pid_exists(proc.pid):
+                        proc.kill()
+                        return
+            except (psutil.NoSuchProcess, psutil.AccessDenied) as e:
+                logger.warning(f"Exception {e} encountered while killing VASP.")
                 continue
-        if not is_killed:
-            logger.warning(f"killing vasp processes in work dir {workdir} failed. Resorting to 'killall'.")
-            cmds = self.vasp_cmd
-            if self.gamma_vasp_cmd:
-                cmds += self.gamma_vasp_cmd
-                for k in cmds:
-                    if "vasp" in k:
-                        subprocess.run(["killall", f"{k}"])
    
+
+        logger.warning(
+            f"Killing VASP processes in workdir {workdir} failed with subprocess.Popen.terminate(). "
+            "Resorting to 'killall'."
+        )
+        cmds = self.vasp_cmd
+        if self.gamma_vasp_cmd:
+            cmds += self.gamma_vasp_cmd
+        for k in cmds:
+            if "vasp" in k:
+                subprocess.run(["killall", f"{k}"])
    
 
 
 
    [docs]class VaspNEBJob(VaspJob):
@@ -818,7 +822,7 @@ 
    Source code for custodian.vasp.jobs
                           "action": {"_file_copy": {"dest": "POSCAR"}}}]
         """
 
-        self.vasp_cmd = vasp_cmd
+        self.vasp_cmd = tuple(vasp_cmd)
         self.output_file = output_file
         self.stderr_file = stderr_file
         self.final = final
@@ -827,7 +831,7 @@ 
    Source code for custodian.vasp.jobs
             self.auto_npar = auto_npar
         self.half_kpts = half_kpts
         self.auto_gamma = auto_gamma
-        self.gamma_vasp_cmd = gamma_vasp_cmd
+        self.gamma_vasp_cmd = tuple(gamma_vasp_cmd) if gamma_vasp_cmd else None
         self.auto_continue = auto_continue
         self.settings_override = settings_override
         self.neb_dirs = []  # 00, 01, etc.
@@ -912,7 +916,7 @@ 
    Source code for custodian.vasp.jobs
                     1,
                 1,
             ):
-                if self.gamma_vasp_cmd is not None and which(self.gamma_vasp_cmd[-1]):
+                if self.gamma_vasp_cmd is not None and which(self.gamma_vasp_cmd[-1]):  # pylint: disable=E1136
                     cmd = self.gamma_vasp_cmd
                 elif which(cmd[-1] + ".gamma"):
                     cmd[-1] += ".gamma"
diff --git a/docs/_modules/custodian/vasp/validators.html b/docs/_modules/custodian/vasp/validators.html
index 4fadd22b..5ab0e63a 100644
--- a/docs/_modules/custodian/vasp/validators.html
+++ b/docs/_modules/custodian/vasp/validators.html
@@ -4,7 +4,7 @@
   
     
     
-    custodian.vasp.validators — custodian 2023.6.5 documentation
+    custodian.vasp.validators — custodian 2023.7.22 documentation
     
     
     
@@ -34,7 +34,7 @@ 
    Navigation
    
         
  • 
           modules |
    • 
-        
  • custodian 2023.6.5 documentation »
    • 
+        
  • custodian 2023.7.22 documentation »
    • 
           
  • Module code »
    • 
         
  • custodian.vasp.validators
    •  
       
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
index b80690f1..951ff1ca 100644
--- a/docs/_modules/index.html
+++ b/docs/_modules/index.html
@@ -4,7 +4,7 @@
   
     
     
-    Overview: module code — custodian 2023.6.5 documentation
+    Overview: module code — custodian 2023.7.22 documentation
     
     
     
@@ -34,7 +34,7 @@ 
    Navigation
    
         
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           modules |
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-        
  • custodian 2023.6.5 documentation »
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+        
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  • Overview: module code
    •  
       
     
      
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
index fedca7e5..88af4a35 100644
--- a/docs/_static/documentation_options.js
+++ b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '2023.6.5',
+    VERSION: '2023.7.22',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/docs/_themes/README.html b/docs/_themes/README.html
index 2f828bc4..c14eb38c 100644
--- a/docs/_themes/README.html
+++ b/docs/_themes/README.html
@@ -3,9 +3,9 @@
 
   
     
-    
+    
 
-    krTheme Sphinx Style — custodian 2023.6.5 documentation
+    krTheme Sphinx Style — custodian 2023.7.22 documentation
     
     
     
@@ -35,7 +35,7 @@ 
    Navigation
    
         
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           modules |
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-        
  • custodian 2023.6.5 documentation »
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+        
  • custodian 2023.7.22 documentation »
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  • krTheme Sphinx Style
    •  
       
     
      
diff --git a/docs/changelog.html b/docs/changelog.html
index c374d8b1..5b53aeb0 100644
--- a/docs/changelog.html
+++ b/docs/changelog.html
@@ -3,9 +3,9 @@
 
   
     
-    
+    
 
-    Change Log — custodian 2023.6.5 documentation
+    Change Log — custodian 2023.7.22 documentation
     
     
     
@@ -35,7 +35,7 @@ 
    Navigation
    
         
  • 
           modules |
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-        
  • custodian 2023.6.5 documentation »
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+        
  • custodian 2023.7.22 documentation »
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  • Change Log
    •  
       
     
      
@@ -47,6 +47,14 @@ 
    Navigation
    
             
   
    
 
    Change Log
    
+
    
+
    v2023.7.22
    
+
      
+
    • Fix for LargeSigmaHandler. Now defaults to ISMEAR=1 and fallback to ISMEAR=0 if SIGMA has been modified
+three times from 0.2 (@arosen93, @janosh)
      • 
+
    • More robust VASP job termination (@fyalcin)
      • 
+
    
+
    
 
    
 
    v2023.6.5
    
 
      
diff --git a/docs/custodian.cli.html b/docs/custodian.cli.html
index 32c3d4c1..6647a427 100644
--- a/docs/custodian.cli.html
+++ b/docs/custodian.cli.html
@@ -3,9 +3,9 @@
 
   
     
-    
+    
 
-    custodian.cli package — custodian 2023.6.5 documentation
+    custodian.cli package — custodian 2023.7.22 documentation
     
     
     
@@ -35,7 +35,7 @@ 
    Navigation
    
         
  • 
           modules |
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-        
  • custodian 2023.6.5 documentation »
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+        
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  • custodian.cli package
    •  
       
     
      
diff --git a/docs/custodian.cp2k.html b/docs/custodian.cp2k.html
index 6a632c9a..88619f00 100644
--- a/docs/custodian.cp2k.html
+++ b/docs/custodian.cp2k.html
@@ -3,9 +3,9 @@
 
   
     
-    
+    
 
-    custodian.cp2k package — custodian 2023.6.5 documentation
+    custodian.cp2k package — custodian 2023.7.22 documentation
     
     
     
@@ -35,7 +35,7 @@ 
    Navigation
    
         
  • 
           modules |
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-        
  • custodian 2023.6.5 documentation »
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+        
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  • custodian.cp2k package
    •  
       
     
      
diff --git a/docs/custodian.feff.html b/docs/custodian.feff.html
index ad775918..40094e33 100644
--- a/docs/custodian.feff.html
+++ b/docs/custodian.feff.html
@@ -3,9 +3,9 @@
 
   
     
-    
+    
 
-    custodian.feff package — custodian 2023.6.5 documentation
+    custodian.feff package — custodian 2023.7.22 documentation
     
     
     
@@ -35,7 +35,7 @@ 
    Navigation
    
         
  • 
           modules |
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-        
  • custodian 2023.6.5 documentation »
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+        
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  • custodian.feff package
    •  
       
     
      
diff --git a/docs/custodian.html b/docs/custodian.html
index d91a0a47..c0c330f6 100644
--- a/docs/custodian.html
+++ b/docs/custodian.html
@@ -3,9 +3,9 @@
 
   
     
-    
+    
 
-    custodian package — custodian 2023.6.5 documentation
+    custodian package — custodian 2023.7.22 documentation
     
     
     
@@ -35,7 +35,7 @@ 
    Navigation
    
         
  • 
           modules |
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-        
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  • custodian package
    •  
       
     
      
diff --git a/docs/custodian.lobster.html b/docs/custodian.lobster.html
index 2c54a678..1d6f8d5c 100644
--- a/docs/custodian.lobster.html
+++ b/docs/custodian.lobster.html
@@ -3,9 +3,9 @@
 
   
     
-    
+    
 
-    custodian.lobster package — custodian 2023.6.5 documentation
+    custodian.lobster package — custodian 2023.7.22 documentation
     
     
     
@@ -35,7 +35,7 @@ 
    Navigation
    
         
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-        
  • custodian 2023.6.5 documentation »
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    •  
       
     
      
diff --git a/docs/custodian.nwchem.html b/docs/custodian.nwchem.html
index 64b3f716..6c48838b 100644
--- a/docs/custodian.nwchem.html
+++ b/docs/custodian.nwchem.html
@@ -3,9 +3,9 @@
 
   
     
-    
+    
 
-    custodian.nwchem package — custodian 2023.6.5 documentation
+    custodian.nwchem package — custodian 2023.7.22 documentation
     
     
     
@@ -35,7 +35,7 @@ 
    Navigation
    
         
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    •
    diff --git a/docs/custodian.qchem.html b/docs/custodian.qchem.html index 7857182f..9260f5c5 100644 --- a/docs/custodian.qchem.html +++ b/docs/custodian.qchem.html @@ -3,9 +3,9 @@ - + - custodian.qchem package — custodian 2023.6.5 documentation + custodian.qchem package — custodian 2023.7.22 documentation @@ -35,7 +35,7 @@

    Navigation

  • modules |
    • -
  • custodian 2023.6.5 documentation »
    • +
  • custodian 2023.7.22 documentation »
  • custodian.qchem package
    • diff --git a/docs/custodian.vasp.html b/docs/custodian.vasp.html index 9b15aef9..1f763f00 100644 --- a/docs/custodian.vasp.html +++ b/docs/custodian.vasp.html @@ -3,9 +3,9 @@ - + - custodian.vasp package — custodian 2023.6.5 documentation + custodian.vasp package — custodian 2023.7.22 documentation @@ -35,7 +35,7 @@

    Navigation

  • modules |
    • -
  • custodian 2023.6.5 documentation »
    • +
  • custodian 2023.7.22 documentation »
  • custodian.vasp package
    • @@ -724,22 +724,22 @@

    Submodulescustodian.vasp.jobs.VaspJob.

    -

  • errors_subset_to_detect (list) – A subset of errors to catch. The +

  • errors_subset_to_detect (list) –

    A subset of errors to catch. The default is None, which means all supported errors are detected. -Use this to only catch only a subset of supported errors. -E.g., [“eddrrm”, “zheev”] will only catch the eddrmm and zheev -errors, and not others. If you wish to only excluded one or +Use this to catch only a subset of supported errors. +E.g., [“eddrmm”, “zheev”] will only catch the eddrmm and zheev +errors, and not others. If you wish to only exclude one or two of the errors, you can create this list by the following -lines:

    • -

  • vtst_fixes (bool) –

    Whether to consider VTST optimizers. Defaults to -False for compatibility purposes, but if you have VTST, you -would likely benefit from setting this to True.

    +lines:

    ``` -subset = list(VaspErrorHandler.error_msgs.keys()) -subset.pop(“eddrrm”)

    +subset = list(VaspErrorHandler().error_msgs.keys()) +subset.remove(“eddrmm”)

    handler = VaspErrorHandler(errors_subset_to_catch=subset) ```

    • +

  • vtst_fixes (bool) – Whether to consider VTST optimizers. Defaults to +False for compatibility purposes, but if you have VTST, you +would likely benefit from setting this to True.

    • @@ -1152,12 +1152,12 @@

    Submodules
    terminate()[source]
    -

    Kill all vasp processes associated with the current job. +

    Kill all VASP processes associated with the current job. This is done by looping over all processes and selecting the ones -that contain “vasp” as well as access files (CHGCAR in particular) +that contain “vasp” as well as access files (vasprun.xml in particular) in the custodian working directory. -There is also a safety that kills all vasp processes if non of the -processes can be killed (This is bad if more than one vasp runs are +There is also a safety that kills all VASP processes if none of the +processes can be killed (This is bad if more than one VASP runs are simultaneously executed on the same node). However, this should never happen.

    diff --git a/docs/genindex.html b/docs/genindex.html index 57d6744c..17c1be8d 100644 --- a/docs/genindex.html +++ b/docs/genindex.html @@ -4,7 +4,7 @@ - Index — custodian 2023.6.5 documentation + Index — custodian 2023.7.22 documentation @@ -34,7 +34,7 @@

    Navigation

  • modules |
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  • custodian 2023.6.5 documentation »
    • +
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  • Index
    • diff --git a/docs/index.html b/docs/index.html index 0a462c9d..0ed9cd4d 100644 --- a/docs/index.html +++ b/docs/index.html @@ -3,9 +3,9 @@ - + - Custodian — custodian 2023.6.5 documentation + Custodian — custodian 2023.7.22 documentation @@ -35,7 +35,7 @@

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    • diff --git a/docs/modules.html b/docs/modules.html index ef52cbbb..98a40736 100644 --- a/docs/modules.html +++ b/docs/modules.html @@ -3,9 +3,9 @@ - + - custodian — custodian 2023.6.5 documentation + custodian — custodian 2023.7.22 documentation @@ -35,7 +35,7 @@

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    • diff --git a/docs/objects.inv b/docs/objects.inv index e3870e2be08b8e7561ac73be7c9d28e789969462..c3681569f5821acad289606edd1087cee6a12cea 100644 GIT binary patch delta 15 WcmeAX?iHTk#A2>zWVF%Mof7~fj07bB delta 14 VcmeAb?h&5g#B8Q#y3x&@696CT1N8s^ diff --git a/docs/py-modindex.html b/docs/py-modindex.html index 03dcd8b0..20b8b666 100644 --- a/docs/py-modindex.html +++ b/docs/py-modindex.html @@ -4,7 +4,7 @@ - Python Module Index — custodian 2023.6.5 documentation + Python Module Index — custodian 2023.7.22 documentation @@ -37,7 +37,7 @@

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    • diff --git a/docs/search.html b/docs/search.html index d6fafb09..d7b55fe5 100644 --- a/docs/search.html +++ b/docs/search.html @@ -4,7 +4,7 @@ - Search — custodian 2023.6.5 documentation + Search — custodian 2023.7.22 documentation @@ -40,7 +40,7 @@

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method)": [[5, "custodian.cp2k.handlers.AbortHandler.correct"]], "correct() (divergingscferrorhandler method)": [[5, "custodian.cp2k.handlers.DivergingScfErrorHandler.correct"]], "correct() (frozenjoberrorhandler method)": [[5, "custodian.cp2k.handlers.FrozenJobErrorHandler.correct"], [10, "custodian.vasp.handlers.FrozenJobErrorHandler.correct"]], "correct() (numericalprecisionhandler method)": [[5, "custodian.cp2k.handlers.NumericalPrecisionHandler.correct"]], "correct() (stderrhandler method)": [[5, "custodian.cp2k.handlers.StdErrHandler.correct"], [10, "custodian.vasp.handlers.StdErrHandler.correct"]], "correct() (unconvergedrelaxationerrorhandler method)": [[5, "custodian.cp2k.handlers.UnconvergedRelaxationErrorHandler.correct"]], "correct() (unconvergedscferrorhandler method)": [[5, "custodian.cp2k.handlers.UnconvergedScfErrorHandler.correct"]], "correct() (walltimehandler method)": [[5, "custodian.cp2k.handlers.WalltimeHandler.correct"], [10, "custodian.vasp.handlers.WalltimeHandler.correct"]], "custodian.cp2k": [[5, "module-custodian.cp2k"]], "custodian.cp2k.handlers": [[5, "module-custodian.cp2k.handlers"]], "custodian.cp2k.interpreter": [[5, "module-custodian.cp2k.interpreter"]], "custodian.cp2k.jobs": [[5, "module-custodian.cp2k.jobs"]], "custodian.cp2k.utils": [[5, "module-custodian.cp2k.utils"]], "custodian.cp2k.validators": [[5, "module-custodian.cp2k.validators"]], "double_job() (cp2kjob class method)": [[5, "custodian.cp2k.jobs.Cp2kJob.double_job"]], "error_msgs (stderrhandler attribute)": [[5, "custodian.cp2k.handlers.StdErrHandler.error_msgs"], [10, "custodian.vasp.handlers.StdErrHandler.error_msgs"]], "exit (cp2koutputvalidator property)": [[5, "custodian.cp2k.validators.Cp2kOutputValidator.exit"]], "exit (cp2kvalidator property)": [[5, "custodian.cp2k.validators.Cp2kValidator.exit"]], "get_conv() (in module custodian.cp2k.utils)": [[5, "custodian.cp2k.utils.get_conv"]], "gga_static_to_hybrid() (cp2kjob class method)": [[5, "custodian.cp2k.jobs.Cp2kJob.gga_static_to_hybrid"]], "is_monitor (aborthandler attribute)": [[5, "custodian.cp2k.handlers.AbortHandler.is_monitor"]], "is_monitor (divergingscferrorhandler attribute)": [[5, "custodian.cp2k.handlers.DivergingScfErrorHandler.is_monitor"]], "is_monitor (frozenjoberrorhandler attribute)": [[5, "custodian.cp2k.handlers.FrozenJobErrorHandler.is_monitor"], [10, "custodian.vasp.handlers.FrozenJobErrorHandler.is_monitor"]], "is_monitor (numericalprecisionhandler attribute)": [[5, "custodian.cp2k.handlers.NumericalPrecisionHandler.is_monitor"]], "is_monitor (stderrhandler attribute)": [[5, "custodian.cp2k.handlers.StdErrHandler.is_monitor"], [10, "custodian.vasp.handlers.StdErrHandler.is_monitor"]], "is_monitor (unconvergedrelaxationerrorhandler attribute)": [[5, "custodian.cp2k.handlers.UnconvergedRelaxationErrorHandler.is_monitor"]], "is_monitor (unconvergedscferrorhandler attribute)": [[5, "custodian.cp2k.handlers.UnconvergedScfErrorHandler.is_monitor"]], "is_monitor (walltimehandler attribute)": [[5, "custodian.cp2k.handlers.WalltimeHandler.is_monitor"], [10, "custodian.vasp.handlers.WalltimeHandler.is_monitor"]], "is_terminating (aborthandler attribute)": [[5, "custodian.cp2k.handlers.AbortHandler.is_terminating"]], "is_terminating (walltimehandler attribute)": [[5, "custodian.cp2k.handlers.WalltimeHandler.is_terminating"], [10, "custodian.vasp.handlers.WalltimeHandler.is_terminating"]], "kill (cp2koutputvalidator property)": [[5, "custodian.cp2k.validators.Cp2kOutputValidator.kill"]], "kill (cp2kvalidator property)": [[5, "custodian.cp2k.validators.Cp2kValidator.kill"]], "no_children (cp2koutputvalidator property)": [[5, "custodian.cp2k.validators.Cp2kOutputValidator.no_children"]], "no_children (cp2kvalidator property)": [[5, "custodian.cp2k.validators.Cp2kValidator.no_children"]], "postprocess() (cp2kjob method)": [[5, "custodian.cp2k.jobs.Cp2kJob.postprocess"]], "pre_screen_hybrid() (cp2kjob class method)": [[5, "custodian.cp2k.jobs.Cp2kJob.pre_screen_hybrid"]], "raises_runtime_error (stderrhandler attribute)": [[5, "custodian.cp2k.handlers.StdErrHandler.raises_runtime_error"]], "raises_runtime_error (walltimehandler attribute)": [[5, "custodian.cp2k.handlers.WalltimeHandler.raises_runtime_error"], [10, "custodian.vasp.handlers.WalltimeHandler.raises_runtime_error"]], "restart() (in module custodian.cp2k.utils)": [[5, "custodian.cp2k.utils.restart"]], "run() (cp2kjob method)": [[5, "custodian.cp2k.jobs.Cp2kJob.run"]], "setup() (cp2kjob method)": [[5, "custodian.cp2k.jobs.Cp2kJob.setup"]], "tail() (in module custodian.cp2k.utils)": [[5, "custodian.cp2k.utils.tail"]], "terminate() (cp2kjob method)": [[5, "custodian.cp2k.jobs.Cp2kJob.terminate"]], "feffjob (class in custodian.feff.jobs)": [[6, "custodian.feff.jobs.FeffJob"]], "feffmodder (class in custodian.feff.interpreter)": [[6, "custodian.feff.interpreter.FeffModder"]], "unconvergederrorhandler (class in custodian.feff.handlers)": [[6, "custodian.feff.handlers.UnconvergedErrorHandler"]], "apply_actions() (feffmodder method)": [[6, "custodian.feff.interpreter.FeffModder.apply_actions"]], "check() (unconvergederrorhandler method)": [[6, "custodian.feff.handlers.UnconvergedErrorHandler.check"], [10, "custodian.vasp.handlers.UnconvergedErrorHandler.check"]], "correct() (unconvergederrorhandler method)": [[6, "custodian.feff.handlers.UnconvergedErrorHandler.correct"], [10, "custodian.vasp.handlers.UnconvergedErrorHandler.correct"]], "custodian.feff": [[6, "module-custodian.feff"]], "custodian.feff.handlers": [[6, "module-custodian.feff.handlers"]], "custodian.feff.interpreter": [[6, "module-custodian.feff.interpreter"]], "custodian.feff.jobs": [[6, "module-custodian.feff.jobs"]], "is_monitor (unconvergederrorhandler attribute)": [[6, "custodian.feff.handlers.UnconvergedErrorHandler.is_monitor"], [10, "custodian.vasp.handlers.UnconvergedErrorHandler.is_monitor"]], "postprocess() (feffjob method)": [[6, "custodian.feff.jobs.FeffJob.postprocess"]], "run() (feffjob method)": [[6, "custodian.feff.jobs.FeffJob.run"]], "setup() (feffjob method)": [[6, "custodian.feff.jobs.FeffJob.setup"]], "chargespillingvalidator (class in custodian.lobster.handlers)": [[7, "custodian.lobster.handlers.ChargeSpillingValidator"]], "enoughbandsvalidator (class in custodian.lobster.handlers)": [[7, "custodian.lobster.handlers.EnoughBandsValidator"]], "lobsterfilesvalidator (class in custodian.lobster.handlers)": [[7, "custodian.lobster.handlers.LobsterFilesValidator"]], "lobsterjob (class in custodian.lobster.jobs)": [[7, "custodian.lobster.jobs.LobsterJob"]], "check() (chargespillingvalidator method)": [[7, "custodian.lobster.handlers.ChargeSpillingValidator.check"]], "check() (enoughbandsvalidator method)": [[7, "custodian.lobster.handlers.EnoughBandsValidator.check"]], "check() (lobsterfilesvalidator method)": [[7, "custodian.lobster.handlers.LobsterFilesValidator.check"]], "custodian.lobster": [[7, "module-custodian.lobster"]], "custodian.lobster.handlers": [[7, "module-custodian.lobster.handlers"]], "custodian.lobster.jobs": [[7, "module-custodian.lobster.jobs"]], "postprocess() (lobsterjob method)": [[7, "custodian.lobster.jobs.LobsterJob.postprocess"]], "run() (lobsterjob method)": [[7, "custodian.lobster.jobs.LobsterJob.run"]], "setup() (lobsterjob method)": [[7, "custodian.lobster.jobs.LobsterJob.setup"]], "nwchemerrorhandler (class in custodian.nwchem.handlers)": [[8, "custodian.nwchem.handlers.NwchemErrorHandler"]], "nwchemjob (class in custodian.nwchem.jobs)": [[8, "custodian.nwchem.jobs.NwchemJob"]], "check() (nwchemerrorhandler method)": [[8, "custodian.nwchem.handlers.NwchemErrorHandler.check"]], "correct() (nwchemerrorhandler method)": [[8, "custodian.nwchem.handlers.NwchemErrorHandler.correct"]], "custodian.nwchem": [[8, "module-custodian.nwchem"]], "custodian.nwchem.handlers": [[8, "module-custodian.nwchem.handlers"]], "custodian.nwchem.jobs": [[8, "module-custodian.nwchem.jobs"]], "postprocess() (nwchemjob method)": [[8, "custodian.nwchem.jobs.NwchemJob.postprocess"]], "run() (nwchemjob method)": [[8, "custodian.nwchem.jobs.NwchemJob.run"]], "setup() (nwchemjob method)": [[8, "custodian.nwchem.jobs.NwchemJob.setup"]], "custodian.qchem": [[9, "module-custodian.qchem"]], "custodian.qchem.utils": [[9, "module-custodian.qchem.utils"]], "perturb_coordinates() (in module custodian.qchem.utils)": [[9, "custodian.qchem.utils.perturb_coordinates"]], "vector_list_diff() (in module custodian.qchem.utils)": [[9, "custodian.qchem.utils.vector_list_diff"]], "aliasingerrorhandler (class in custodian.vasp.handlers)": [[10, "custodian.vasp.handlers.AliasingErrorHandler"]], "checkpointhandler (class in custodian.vasp.handlers)": [[10, "custodian.vasp.handlers.CheckpointHandler"]], "drifterrorhandler (class in custodian.vasp.handlers)": [[10, "custodian.vasp.handlers.DriftErrorHandler"]], "frozenjoberrorhandler (class in custodian.vasp.handlers)": [[10, "custodian.vasp.handlers.FrozenJobErrorHandler"]], "generatevaspinputjob (class in custodian.vasp.jobs)": [[10, "custodian.vasp.jobs.GenerateVaspInputJob"]], "incorrectsmearinghandler (class in custodian.vasp.handlers)": [[10, "custodian.vasp.handlers.IncorrectSmearingHandler"]], "largesigmahandler (class in custodian.vasp.handlers)": [[10, "custodian.vasp.handlers.LargeSigmaHandler"]], "lrfcommutatorhandler (class in custodian.vasp.handlers)": [[10, "custodian.vasp.handlers.LrfCommutatorHandler"]], "meshsymmetryerrorhandler (class in custodian.vasp.handlers)": [[10, "custodian.vasp.handlers.MeshSymmetryErrorHandler"]], "nonconvergingerrorhandler (class in custodian.vasp.handlers)": [[10, "custodian.vasp.handlers.NonConvergingErrorHandler"]], "positiveenergyerrorhandler (class in custodian.vasp.handlers)": [[10, "custodian.vasp.handlers.PositiveEnergyErrorHandler"]], "potimerrorhandler (class in custodian.vasp.handlers)": [[10, "custodian.vasp.handlers.PotimErrorHandler"]], "scanmetalhandler (class in custodian.vasp.handlers)": [[10, "custodian.vasp.handlers.ScanMetalHandler"]], "stderrhandler (class in custodian.vasp.handlers)": [[10, "custodian.vasp.handlers.StdErrHandler"]], "stoppedrunhandler (class in custodian.vasp.handlers)": [[10, "custodian.vasp.handlers.StoppedRunHandler"]], "unconvergederrorhandler (class in custodian.vasp.handlers)": [[10, "custodian.vasp.handlers.UnconvergedErrorHandler"]], "vaspaeccarvalidator (class in custodian.vasp.validators)": [[10, "custodian.vasp.validators.VaspAECCARValidator"]], "vasperrorhandler (class in custodian.vasp.handlers)": [[10, "custodian.vasp.handlers.VaspErrorHandler"]], "vaspfilesvalidator (class in custodian.vasp.validators)": [[10, "custodian.vasp.validators.VaspFilesValidator"]], "vaspjob (class in custodian.vasp.jobs)": [[10, "custodian.vasp.jobs.VaspJob"]], "vaspmodder (class in custodian.vasp.interpreter)": [[10, "custodian.vasp.interpreter.VaspModder"]], "vaspnebjob (class in custodian.vasp.jobs)": [[10, "custodian.vasp.jobs.VaspNEBJob"]], "vaspnptmdvalidator (class in custodian.vasp.validators)": [[10, "custodian.vasp.validators.VaspNpTMDValidator"]], "vasprunxmlvalidator (class in custodian.vasp.validators)": [[10, "custodian.vasp.validators.VasprunXMLValidator"]], "walltimehandler (class in custodian.vasp.handlers)": [[10, "custodian.vasp.handlers.WalltimeHandler"]], "apply_actions() (vaspmodder method)": [[10, "custodian.vasp.interpreter.VaspModder.apply_actions"]], "check() (aliasingerrorhandler method)": [[10, "custodian.vasp.handlers.AliasingErrorHandler.check"]], "check() (checkpointhandler method)": [[10, "custodian.vasp.handlers.CheckpointHandler.check"]], "check() (drifterrorhandler method)": [[10, "custodian.vasp.handlers.DriftErrorHandler.check"]], "check() (incorrectsmearinghandler method)": [[10, "custodian.vasp.handlers.IncorrectSmearingHandler.check"]], "check() (largesigmahandler method)": [[10, "custodian.vasp.handlers.LargeSigmaHandler.check"]], "check() (lrfcommutatorhandler method)": [[10, "custodian.vasp.handlers.LrfCommutatorHandler.check"]], "check() (meshsymmetryerrorhandler method)": [[10, "custodian.vasp.handlers.MeshSymmetryErrorHandler.check"]], "check() (nonconvergingerrorhandler method)": [[10, "custodian.vasp.handlers.NonConvergingErrorHandler.check"]], "check() (positiveenergyerrorhandler method)": [[10, "custodian.vasp.handlers.PositiveEnergyErrorHandler.check"]], "check() (potimerrorhandler method)": [[10, "custodian.vasp.handlers.PotimErrorHandler.check"]], "check() (scanmetalhandler method)": [[10, "custodian.vasp.handlers.ScanMetalHandler.check"]], "check() (stoppedrunhandler method)": [[10, "custodian.vasp.handlers.StoppedRunHandler.check"]], "check() (vaspaeccarvalidator method)": [[10, "custodian.vasp.validators.VaspAECCARValidator.check"]], "check() (vasperrorhandler method)": [[10, "custodian.vasp.handlers.VaspErrorHandler.check"]], "check() (vaspfilesvalidator method)": [[10, "custodian.vasp.validators.VaspFilesValidator.check"]], "check() (vaspnptmdvalidator method)": [[10, "custodian.vasp.validators.VaspNpTMDValidator.check"]], "check() (vasprunxmlvalidator method)": [[10, "custodian.vasp.validators.VasprunXMLValidator.check"]], "check_broken_chgcar() (in module custodian.vasp.validators)": [[10, "custodian.vasp.validators.check_broken_chgcar"]], "constrained_opt_run() (vaspjob class method)": [[10, "custodian.vasp.jobs.VaspJob.constrained_opt_run"]], "correct() (aliasingerrorhandler method)": [[10, "custodian.vasp.handlers.AliasingErrorHandler.correct"]], "correct() (checkpointhandler method)": [[10, "custodian.vasp.handlers.CheckpointHandler.correct"]], "correct() (drifterrorhandler method)": [[10, "custodian.vasp.handlers.DriftErrorHandler.correct"]], "correct() (incorrectsmearinghandler method)": [[10, "custodian.vasp.handlers.IncorrectSmearingHandler.correct"]], "correct() (largesigmahandler method)": [[10, "custodian.vasp.handlers.LargeSigmaHandler.correct"]], "correct() (lrfcommutatorhandler method)": [[10, "custodian.vasp.handlers.LrfCommutatorHandler.correct"]], "correct() (meshsymmetryerrorhandler method)": [[10, "custodian.vasp.handlers.MeshSymmetryErrorHandler.correct"]], "correct() (nonconvergingerrorhandler method)": [[10, "custodian.vasp.handlers.NonConvergingErrorHandler.correct"]], "correct() (positiveenergyerrorhandler method)": [[10, "custodian.vasp.handlers.PositiveEnergyErrorHandler.correct"]], "correct() (potimerrorhandler method)": [[10, "custodian.vasp.handlers.PotimErrorHandler.correct"]], "correct() (scanmetalhandler method)": [[10, "custodian.vasp.handlers.ScanMetalHandler.correct"]], "correct() (stoppedrunhandler method)": [[10, "custodian.vasp.handlers.StoppedRunHandler.correct"]], "correct() (vasperrorhandler method)": [[10, "custodian.vasp.handlers.VaspErrorHandler.correct"]], "custodian.vasp": [[10, "module-custodian.vasp"]], "custodian.vasp.handlers": [[10, "module-custodian.vasp.handlers"]], "custodian.vasp.interpreter": [[10, "module-custodian.vasp.interpreter"]], "custodian.vasp.jobs": [[10, "module-custodian.vasp.jobs"]], "custodian.vasp.validators": [[10, "module-custodian.vasp.validators"]], "double_relaxation_run() (vaspjob class method)": [[10, "custodian.vasp.jobs.VaspJob.double_relaxation_run"]], "error_msgs (aliasingerrorhandler attribute)": [[10, "custodian.vasp.handlers.AliasingErrorHandler.error_msgs"]], "error_msgs (lrfcommutatorhandler attribute)": [[10, "custodian.vasp.handlers.LrfCommutatorHandler.error_msgs"]], "error_msgs (vasperrorhandler attribute)": [[10, "custodian.vasp.handlers.VaspErrorHandler.error_msgs"]], "from_dict() (nonconvergingerrorhandler class method)": [[10, "custodian.vasp.handlers.NonConvergingErrorHandler.from_dict"]], "full_opt_run() (vaspjob class method)": [[10, "custodian.vasp.jobs.VaspJob.full_opt_run"]], "is_monitor (aliasingerrorhandler attribute)": [[10, "custodian.vasp.handlers.AliasingErrorHandler.is_monitor"]], "is_monitor (checkpointhandler attribute)": [[10, "custodian.vasp.handlers.CheckpointHandler.is_monitor"]], "is_monitor (incorrectsmearinghandler attribute)": [[10, "custodian.vasp.handlers.IncorrectSmearingHandler.is_monitor"]], "is_monitor (largesigmahandler attribute)": [[10, "custodian.vasp.handlers.LargeSigmaHandler.is_monitor"]], "is_monitor (lrfcommutatorhandler attribute)": [[10, "custodian.vasp.handlers.LrfCommutatorHandler.is_monitor"]], "is_monitor (meshsymmetryerrorhandler attribute)": [[10, "custodian.vasp.handlers.MeshSymmetryErrorHandler.is_monitor"]], "is_monitor (nonconvergingerrorhandler attribute)": [[10, "custodian.vasp.handlers.NonConvergingErrorHandler.is_monitor"]], "is_monitor (positiveenergyerrorhandler attribute)": [[10, "custodian.vasp.handlers.PositiveEnergyErrorHandler.is_monitor"]], "is_monitor (potimerrorhandler attribute)": [[10, "custodian.vasp.handlers.PotimErrorHandler.is_monitor"]], "is_monitor (scanmetalhandler attribute)": [[10, "custodian.vasp.handlers.ScanMetalHandler.is_monitor"]], "is_monitor (stoppedrunhandler attribute)": [[10, "custodian.vasp.handlers.StoppedRunHandler.is_monitor"]], "is_monitor (vasperrorhandler attribute)": [[10, "custodian.vasp.handlers.VaspErrorHandler.is_monitor"]], "is_terminating (checkpointhandler attribute)": [[10, "custodian.vasp.handlers.CheckpointHandler.is_terminating"]], "is_terminating (stoppedrunhandler attribute)": [[10, "custodian.vasp.handlers.StoppedRunHandler.is_terminating"]], "metagga_opt_run() (vaspjob class method)": [[10, "custodian.vasp.jobs.VaspJob.metagga_opt_run"]], "postprocess() (generatevaspinputjob method)": [[10, "custodian.vasp.jobs.GenerateVaspInputJob.postprocess"]], "postprocess() (vaspjob method)": [[10, "custodian.vasp.jobs.VaspJob.postprocess"]], "postprocess() (vaspnebjob method)": [[10, "custodian.vasp.jobs.VaspNEBJob.postprocess"]], "run() (generatevaspinputjob method)": [[10, "custodian.vasp.jobs.GenerateVaspInputJob.run"]], "run() (vaspjob method)": [[10, "custodian.vasp.jobs.VaspJob.run"]], "run() (vaspnebjob method)": [[10, "custodian.vasp.jobs.VaspNEBJob.run"]], "setup() (generatevaspinputjob method)": [[10, "custodian.vasp.jobs.GenerateVaspInputJob.setup"]], "setup() (vaspjob method)": [[10, "custodian.vasp.jobs.VaspJob.setup"]], "setup() (vaspnebjob method)": [[10, "custodian.vasp.jobs.VaspNEBJob.setup"]], "terminate() (vaspjob method)": [[10, "custodian.vasp.jobs.VaspJob.terminate"]]}}) \ No newline at end of file diff --git a/setup.py b/setup.py index 83fe8a3f..a7e390de 100644 --- a/setup.py +++ b/setup.py @@ -11,7 +11,7 @@ setup( name="custodian", packages=find_packages(), - version="2023.6.5", + version="2023.7.22", install_requires=["monty>=2.0.6", "ruamel.yaml>=0.15.6", "sentry-sdk>=0.8.0", "psutil"], extras_require={"vasp, nwchem, qchem": ["pymatgen>=2019.8.23"]}, package_data={},