From 877ac050e37a9cfe7d23e01db90407c27950978e Mon Sep 17 00:00:00 2001 From: zyrd Date: Fri, 8 Jan 2021 10:37:00 -0800 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/custodian.html | 4 +- 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/handlers.html | 4 +- docs/_modules/custodian/qchem/jobs.html | 4 +- docs/_modules/custodian/utils.html | 4 +- docs/_modules/custodian/vasp/handlers.html | 54 +++++++++++++----- docs/_modules/custodian/vasp/interpreter.html | 4 +- docs/_modules/custodian/vasp/jobs.html | 4 +- docs/_modules/custodian/vasp/validators.html | 4 +- docs/_modules/index.html | 4 +- docs/_static/documentation_options.js | 2 +- docs/_themes/README.html | 4 +- docs/changelog.html | 11 +++- docs/custodian.ansible.html | 4 +- docs/custodian.cli.html | 4 +- docs/custodian.feff.html | 4 +- docs/custodian.html | 4 +- docs/custodian.lobster.html | 4 +- docs/custodian.nwchem.html | 4 +- docs/custodian.qchem.html | 4 +- docs/custodian.vasp.html | 6 +- docs/genindex.html | 4 +- docs/index.html | 4 +- docs/modules.html | 4 +- docs/objects.inv | Bin 2115 -> 2115 bytes docs/py-modindex.html | 4 +- docs/search.html | 4 +- docs/searchindex.js | 2 +- setup.py | 2 +- 43 files changed, 125 insertions(+), 94 deletions(-) diff --git a/custodian/__init__.py b/custodian/__init__.py index 852f83f6..ca537733 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__ = "2021.1.7" +__version__ = "2021.1.8" from .custodian import Custodian diff --git a/docs/_modules/custodian/ansible/actions.html b/docs/_modules/custodian/ansible/actions.html index 6da8c1d3..90af5108 100644 --- a/docs/_modules/custodian/ansible/actions.html +++ b/docs/_modules/custodian/ansible/actions.html @@ -5,7 +5,7 @@ - custodian.ansible.actions — custodian 2021.1.7 documentation + custodian.ansible.actions — custodian 2021.1.8 documentation @@ -37,7 +37,7 @@

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    • @@ -117,11 +117,12 @@

    Source code for custodian.vasp.handlers

     
     error_msgs = {
         "tet": [
-            "Tetrahedron method fails for NKPT<4",
+            "Tetrahedron method fails",
             "Fatal error detecting k-mesh",
             "Fatal error: unable to match k-point",
             "Routine TETIRR needs special values",
             "Tetrahedron method fails (number of k-points < 4)",
+            "BZINTS"
         ],
         "inv_rot_mat": [
             "rotation matrix was not found (increase " "SYMPREC)"
@@ -135,7 +136,7 @@ 
    Source code for custodian.vasp.handlers
             "dentet": ["DENTET"],
         "too_few_bands": ["TOO FEW BANDS"],
         "triple_product": ["ERROR: the triple product of the basis vectors"],
-        "rot_matrix": ["Found some non-integer element in rotation matrix"],
+        "rot_matrix": ["Found some non-integer element in rotation matrix", "SGRCON"],
         "brions": ["BRIONS problems: POTIM should be increased"],
         "pricel": ["internal error in subroutine PRICEL"],
         "zpotrf": ["LAPACK: Routine ZPOTRF failed"],
@@ -150,8 +151,9 @@ 
    Source code for custodian.vasp.handlers
             "elf_kpar": ["ELF: KPAR>1 not implemented"],
         "elf_ncl": ["WARNING: ELF not implemented for non collinear case"],
         "rhosyg": ["RHOSYG"],
-        "posmap": ["POSMAP internal error: symmetry equivalent atom not found"],
+        "posmap": ["POSMAP"],
         "point_group": ["group operation missing"],
+        "symprec_noise": ["determination of the symmetry of your systems shows a strong"]
     }
 
     def __init__(
@@ -516,11 +518,29 @@ 
    Source code for custodian.vasp.handlers
                 actions.append({"dict": "INCAR", "action": {"_set": {"SYMPREC": 1e-4}}})
 
         if "posmap" in self.errors:
-            actions.append({"dict": "INCAR", "action": {"_set": {"SYMPREC": 1e-6}}})
+            # VASP advises to decrease or increase SYMPREC by an order of magnitude
+            # the default SYMPREC value is 1e-5
+            if self.error_count["posmap"] == 0:
+                # first, reduce by 10x
+                orig_symprec = vi["INCAR"].get("SYMPREC", 1e-5)
+                actions.append({"dict": "INCAR", "action": {"_set": {"SYMPREC": orig_symprec / 10}}})
+            elif self.error_count["posmap"] == 1:
+                # next, increase by 100x (10x the original)
+                orig_symprec = vi["INCAR"].get("SYMPREC", 1e-6)
+                actions.append({"dict": "INCAR", "action": {"_set": {"SYMPREC": orig_symprec * 100}}})
+            else:
+                # if we have already corrected twice, there's nothing else to do
+                pass
 
         if "point_group" in self.errors:
             actions.append({"dict": "INCAR", "action": {"_set": {"ISYM": 0}}})
 
+        if "symprec_noise" in self.errors:
+            if (vi["INCAR"].get("ISYM", 2) > 0) and (vi["INCAR"].get("SYMPREC", 1e-5) > 1e-6):
+                actions.append({"dict": "INCAR", "action": {"_set": {"SYMPREC": 1e-6}}})
+            else:
+                actions.append({"dict": "INCAR", "action": {"_set": {"ISYM": 0}}})
+
         VaspModder(vi=vi).apply_actions(actions)
         return {"errors": list(self.errors), "actions": actions}
    
 
@@ -1170,16 +1190,20 @@ 
    Source code for custodian.vasp.handlers
             backup(VASP_BACKUP_FILES)
         actions = []
         vi = VaspInput.from_directory(".")
+        sigma = vi["INCAR"].get("SIGMA", 0.2)
 
-        # Reduce SIGMA
-        actions.append(
-                {
-                    "dict": "INCAR",
-                    "action": {
-                        "_set": {"SIGMA": vi["INCAR"].get("SIGMA", 0.2) - 0.04}
-                    },
-                }
-            )
+        # Reduce SIGMA by 0.06 if larger than 0.08
+        # this will reduce SIGMA from the default of 0.2 to the practical
+        # minimum value of 0.02 in 3 steps
+        if sigma > 0.08:
+            actions.append(
+                    {
+                        "dict": "INCAR",
+                        "action": {
+                            "_set": {"SIGMA": sigma - 0.06}
+                        },
+                    }
+                )
 
         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 8a0824c5..92e266c3 100644
--- a/docs/_modules/custodian/vasp/interpreter.html
+++ b/docs/_modules/custodian/vasp/interpreter.html
@@ -5,7 +5,7 @@
   
     
     
-    custodian.vasp.interpreter — custodian 2021.1.7 documentation
+    custodian.vasp.interpreter — custodian 2021.1.8 documentation
     
     
     
@@ -37,7 +37,7 @@ 
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diff --git a/docs/_modules/custodian/vasp/jobs.html b/docs/_modules/custodian/vasp/jobs.html
index cd8d1450..d5fa11be 100644
--- a/docs/_modules/custodian/vasp/jobs.html
+++ b/docs/_modules/custodian/vasp/jobs.html
@@ -5,7 +5,7 @@
   
     
     
-    custodian.vasp.jobs — custodian 2021.1.7 documentation
+    custodian.vasp.jobs — custodian 2021.1.8 documentation
     
     
     
@@ -37,7 +37,7 @@ 
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diff --git a/docs/_modules/custodian/vasp/validators.html b/docs/_modules/custodian/vasp/validators.html
index f7497dd9..d7eaa100 100644
--- a/docs/_modules/custodian/vasp/validators.html
+++ b/docs/_modules/custodian/vasp/validators.html
@@ -5,7 +5,7 @@
   
     
     
-    custodian.vasp.validators — custodian 2021.1.7 documentation
+    custodian.vasp.validators — custodian 2021.1.8 documentation
     
     
     
@@ -37,7 +37,7 @@ 
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diff --git a/docs/_modules/index.html b/docs/_modules/index.html
index fc156a84..d3a0700d 100644
--- a/docs/_modules/index.html
+++ b/docs/_modules/index.html
@@ -5,7 +5,7 @@
   
     
     
-    Overview: module code — custodian 2021.1.7 documentation
+    Overview: module code — custodian 2021.1.8 documentation
     
     
     
@@ -37,7 +37,7 @@ 
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    diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js index 8ab2b387..aad23dc8 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: '2021.1.7', + VERSION: '2021.1.8', LANGUAGE: 'None', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/docs/_themes/README.html b/docs/_themes/README.html index b4ca8e98..56d09d82 100644 --- a/docs/_themes/README.html +++ b/docs/_themes/README.html @@ -5,7 +5,7 @@ - krTheme Sphinx Style — custodian 2021.1.7 documentation + krTheme Sphinx Style — custodian 2021.1.8 documentation @@ -37,7 +37,7 @@

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    • @@ -49,6 +49,12 @@

    Navigation

    Change Log

    +
    +

    v2020.1.8

    +
      +

    • New handlers for VASP6 (@mkhorton, @rkingsbury)

      • +
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    Submodules
    -error_msgs = {'amin': ['One of the lattice vectors is very long (>50 A), but AMIN'], 'brions': ['BRIONS problems: POTIM should be increased'], 'brmix': ['BRMIX: very serious problems'], 'dentet': ['DENTET'], 'edddav': ['Error EDDDAV: Call to ZHEGV failed'], 'eddrmm': ['WARNING in EDDRMM: call to ZHEGV failed'], 'elf_kpar': ['ELF: KPAR>1 not implemented'], 'elf_ncl': ['WARNING: ELF not implemented for non collinear case'], 'grad_not_orth': ['EDWAV: internal error, the gradient is not orthogonal'], 'incorrect_shift': ['Could not get correct shifts'], 'inv_rot_mat': ['rotation matrix was not found (increase SYMPREC)'], 'nicht_konv': ['ERROR: SBESSELITER : nicht konvergent'], 'point_group': ['group operation missing'], 'posmap': ['POSMAP internal error: symmetry equivalent atom not found'], 'pricel': ['internal error in subroutine PRICEL'], 'pssyevx': ['ERROR in subspace rotation PSSYEVX'], 'real_optlay': ['REAL_OPTLAY: internal error', 'REAL_OPT: internal ERROR'], 'rhosyg': ['RHOSYG'], 'rot_matrix': ['Found some non-integer element in rotation matrix'], 'rspher': ['ERROR RSPHER'], 'subspacematrix': ['WARNING: Sub-Space-Matrix is not hermitian in DAV'], 'tet': ['Tetrahedron method fails for NKPT<4', 'Fatal error detecting k-mesh', 'Fatal error: unable to match k-point', 'Routine TETIRR needs special values', 'Tetrahedron method fails (number of k-points < 4)'], 'tetirr': ['Routine TETIRR needs special values'], 'too_few_bands': ['TOO FEW BANDS'], 'triple_product': ['ERROR: the triple product of the basis vectors'], 'zbrent': ['ZBRENT: fatal internal in', 'ZBRENT: fatal error in bracketing'], 'zheev': ['ERROR EDDIAG: Call to routine ZHEEV failed!'], 'zpotrf': ['LAPACK: Routine ZPOTRF failed']}
    +error_msgs = {'amin': ['One of the lattice vectors is very long (>50 A), but AMIN'], 'brions': ['BRIONS problems: POTIM should be increased'], 'brmix': ['BRMIX: very serious problems'], 'dentet': ['DENTET'], 'edddav': ['Error EDDDAV: Call to ZHEGV failed'], 'eddrmm': ['WARNING in EDDRMM: call to ZHEGV failed'], 'elf_kpar': ['ELF: KPAR>1 not implemented'], 'elf_ncl': ['WARNING: ELF not implemented for non collinear case'], 'grad_not_orth': ['EDWAV: internal error, the gradient is not orthogonal'], 'incorrect_shift': ['Could not get correct shifts'], 'inv_rot_mat': ['rotation matrix was not found (increase SYMPREC)'], 'nicht_konv': ['ERROR: SBESSELITER : nicht konvergent'], 'point_group': ['group operation missing'], 'posmap': ['POSMAP'], 'pricel': ['internal error in subroutine PRICEL'], 'pssyevx': ['ERROR in subspace rotation PSSYEVX'], 'real_optlay': ['REAL_OPTLAY: internal error', 'REAL_OPT: internal ERROR'], 'rhosyg': ['RHOSYG'], 'rot_matrix': ['Found some non-integer element in rotation matrix', 'SGRCON'], 'rspher': ['ERROR RSPHER'], 'subspacematrix': ['WARNING: Sub-Space-Matrix is not hermitian in DAV'], 'symprec_noise': ['determination of the symmetry of your systems shows a strong'], 'tet': ['Tetrahedron method fails', 'Fatal error detecting k-mesh', 'Fatal error: unable to match k-point', 'Routine TETIRR needs special values', 'Tetrahedron method fails (number of k-points < 4)', 'BZINTS'], 'tetirr': ['Routine TETIRR needs special values'], 'too_few_bands': ['TOO FEW BANDS'], 'triple_product': ['ERROR: the triple product of the basis vectors'], 'zbrent': ['ZBRENT: fatal internal in', 'ZBRENT: fatal error in bracketing'], 'zheev': ['ERROR EDDIAG: Call to routine ZHEEV failed!'], 'zpotrf': ['LAPACK: Routine ZPOTRF failed']}
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