Merge branch 'develop'

CHANGELOG.md

@@ -14,6 +14,19 @@ The changelog format is inspired by [keep-a-changelog](https://github.com/olivie
 
 ## [Unreleased]
 
+## [1.1] - 2018-04-30
+
+### Fixed
+- Python3 compatibility
+- Bug in decimal place tolerance option
+
+### Added
+- Comma-separated kgrid-series output option
+- CASTEP-like reciprocal spacing cutoff (2 pi factor smaller than KSPACING)
+
+### Changed
+- Make filename a positional argument; -f or --filename no longer needed
+
 ## [1.0] - 2016-10-07
 
 ### Changed
@@ -46,6 +59,7 @@ The changelog format is inspired by [keep-a-changelog](https://github.com/olivie
 - Optparse-based interface
 - GPL
 
-[Unreleased]: https://github.com/wmd-group/kgrid/compare/v1.0...HEAD
+[Unreleased]: https://github.com/wmd-group/kgrid/compare/v1.1...HEAD
+[1.1]: https://github.com/wmd-group/kgrid/compare/v1.0...v1.1
 [1.0]: https://github.com/wmd-group/kgrid/compare/v0.2...v1.0
 [0.2]: https://github.com/wmd-group/kgrid/compare/v0.1...v0.2

README.md

@@ -1,7 +1,7 @@
 kgrid
 =====
 
-Version 1.0: [Change log](./CHANGELOG.md)
+Version 1.1: [Change log](./CHANGELOG.md)
 
 Generates a suitably converged **k**-point grid for solid-state
 quantum chemical calculations.
@@ -37,7 +37,7 @@ Two programs are provided: kgrid and kgrid-series
 Requirements
 ------------
 
-* Developed with Python 2.7; not tested with other versions
+* Developed with Python 2.7 and Python 3.6
 * [Atomic Simulation Environment](https://wiki.fysik.dtu.dk/ase) (ASE)
 * [Numpy](www.numpy.org) (Also a requirement for ASE.)
 
@@ -48,7 +48,7 @@ Usage
 From the command line
 
 ``` bash
-    kgrid -f FILE -t TYPE -c CUTOFF
+    kgrid FILE -t TYPE -c CUTOFF
 ```
 
 will return a suggested set of mesh dimensions. FILE can be any
@@ -86,7 +86,7 @@ functional, using **kgrid** to determine the reciprocal-space sampling.
 ### kgrid-series
 
 ``` bash
-kgrid-series -file FILE -t TYPE --min MIN --max MAX
+kgrid-series FILE -t TYPE --min MIN --max MAX
 ```
 
 Example output:
@@ -121,7 +121,11 @@ Length cutoff  KSPACING    Samples
 
 ```
 
-Installation
+Use the `--castep` option to replace KSPACING with "MP SPACING", which
+corresponds to the *KPOINTS_MP_SPACING* parameter in CASTEP
+(i.e. divide by 2π).
+
+INSTALLATION
 ------------
 
 **kgrid** uses setuptools; from a reasonable healthy Python environment you can use
@@ -133,7 +137,7 @@ with the usual pip caveats:
 - the `--user` flag is highly recommended and avoids the need for administrator privileges, but on a somewhat unhealthy Python installation the user packages location may not be on your paths yet.
 - the `-e` flag creates an "editable" installation which links to this repository and enables easy updates with git.
 
-**kgrid** is not tested on Windows but no problems are anticipated; the Anaconda Python distribution includes pip.
+**kgrid** is not developed on Windows but no problems are anticipated; the Anaconda Python distribution includes pip. We have had good experiences using the Windows subsystem for Linux (WSL), available on Windows 10.
 On Mac OSX, the system Python does not include pip but there are various ways of getting a more complete distribution such as Homebrew or Anaconda.
 
 Disclaimer

kgrid/__init__.py

@@ -51,6 +51,9 @@ def calc_kpt_tuple(atoms, cutoff_length=10, realspace=False, mode='default'):
     elif mode.lower() == 'kspacing':
         cutoff_length = np.pi / cutoff_length
         rounding = 'up'
+    elif mode.lower() == 'castep_mp_spacing':
+        cutoff_length = 1 / (2 * cutoff_length)
+        rounding = 'up'
 
     if realspace:
         return calc_kpt_tuple_naive(atoms, cutoff_length=cutoff_length,

kgrid/cli.py

@@ -46,20 +46,12 @@ def calc_grid(cutoff_length,
 def main():
     parser = ArgumentParser()
     parser.add_argument(
-        "structure",
-        type=str,
-        help="Path to input file",
-        nargs='?',
-        default=None
-        )
-    parser.add_argument(
-        "-f",
-        "--file",
         action="store",
+        nargs="?",
         type=str,
         dest="file",
         default="geometry.in",
-        help="Path to input file [default: ./geometry.in]")    
+        help="Path to input file [default: ./geometry.in]")
     threshold = parser.add_mutually_exclusive_group()
     threshold.add_argument(
         "-c",
@@ -82,7 +74,16 @@ def main():
         action="store",
         type=float,
         dest="kspacing",
-        help="Reciprocal space distance like KSPACING in VASP")
+        help="Reciprocal-space distance like KSPACING in VASP")
+    threshold.add_argument(
+        "--castep",
+        "--castep_spacing",
+        "--castep_mp_spacing",
+        action="store",
+        type=float,
+        dest="castep_mp_spacing",
+        help=("Reciprocal-space distance like KPOINTS_MP_SPACING in CASTEP; "
+              "this differs from Vasp-like KSPACING by factor of 1/(2 pi)."))
     parser.add_argument(
         "-t",
         "--type",
@@ -96,7 +97,7 @@ def main():
         action="store_true",
         help="Use real-space vector lengths instead of "
         "computing reciprocal cell; not recommended!")
-    # Add further options here
+
     args = parser.parse_args()
 
     if args.vasp_auto:
@@ -105,19 +106,17 @@ def main():
     elif args.kspacing:
         mode = 'kspacing'
         cutoff = args.kspacing
+    elif args.castep_mp_spacing:
+        mode = 'castep_mp_spacing'
+        cutoff = args.castep_mp_spacing
     else:
         mode = 'default'
         cutoff = args.cutoff_length
 
-    if args.structure is None:
-        filename = args.file
-    else:
-        filename = args.structure        
-
     calc_grid(
         cutoff,
         mode=mode,
-        filename=filename,
+        filename=args.file,
         filetype=args.type,
         realspace=args.realspace,
         pretty_print=True)

kgrid/series.py

@@ -17,12 +17,13 @@
 #    along with this program.  If not, see <http://www.gnu.org/licenses/>.
 ###############################################################################
 from __future__ import print_function
-from argparse import ArgumentParser
+
 import numpy as np
+from argparse import ArgumentParser
 
 import ase.io
-from kgrid import calc_kpt_tuple
 
+from kgrid import calc_kpt_tuple
 
 def get_increments(lattice_lengths):
     """
@@ -93,18 +94,9 @@ def kspacing_series(atoms, l_min, l_max, decimals=4):
 def main():
     parser = ArgumentParser("Calculate a systematic series of k-point samples")
     parser.add_argument(
-        "structure",
-        type=str,
-        help="Path to input file",
+        'filename',
         nargs='?',
-        default=None
-        )
-    parser.add_argument(
-        "-f",
-        "--file",
-        action="store",
         type=str,
-        dest="file",
         default="geometry.in",
         help="Path to input file [default: ./geometry.in]")    
     parser.add_argument(
@@ -123,32 +115,47 @@ def main():
         type=float,
         default=30,
         help='Maximum real-space cutoff / angstroms')
+    parser.add_argument('--comma_sep', action='store_true',
+                        help='Output as comma-separated list on one line')
+    parser.add_argument('--castep', action='store_true',
+                        help=('Provide CASTEP-like MP spacing instead of '
+                              'vasp-like KSPACING'))
 
     args = parser.parse_args()
 
-    if args.structure is None:
-        filename = args.file
-    else:
-        filename = args.structure        
-
     if args.type:
-        atoms = ase.io.read(filename, format=args.type)
+        atoms = ase.io.read(args.filename, format=args.type)
     else:
-        atoms = ase.io.read(filename)
+        atoms = ase.io.read(args.filename)
 
     cutoffs = cutoff_series(atoms, args.min, args.max)
 
-    kspacing = [np.pi / c for c in cutoffs]
+    if args.castep:
+        kspacing = [0.5 / c for c in cutoffs]
+    else:
+        kspacing = [np.pi / c for c in cutoffs]
 
     samples = [calc_kpt_tuple(
         atoms, cutoff_length=(cutoff - 1e-4)) for cutoff in cutoffs]
 
-    print("Length cutoff  KSPACING    Samples")
-    print("-------------  --------  ------------")
+    if args.comma_sep:
+        def print_sample(sample):
+            return ' '.join((str(x) for x in sample))
+
+        print(','.join((print_sample(sample) for sample in samples)))
 
-    fstring = "{0:12.3f}   {1:7.4f}   {2:3d} {3:3d} {4:3d}"
-    for cutoff, s, sample in zip(cutoffs, kspacing, samples):
-        print(fstring.format(cutoff, s, *sample))
+    else:
+        if args.castep:
+            print("Length cutoff  MP SPACING    Samples")
+            print("-------------  ----------  ------------")
+            fstring = "{0:12.3f}   {1:9.6f}   {2:3d} {3:3d} {4:3d}"
+        else:
+            print("Length cutoff  KSPACING    Samples")
+            print("-------------  --------  ------------")
+            fstring = "{0:12.3f}   {1:7.4f}   {2:3d} {3:3d} {4:3d}"
+
+        for cutoff, s, sample in zip(cutoffs, kspacing, samples):
+            print(fstring.format(cutoff, s, *sample))
 
 
 if __name__ == '__main__':