Merge branch 'release/0.3.1'

CHANGELOG.md

@@ -1,3 +1,7 @@
+## [0.3.1] - 2020-09-09
+
+* cp2k_pdos: add support for list-of-atoms output
+
 ## [0.3.0] - 2020-09-09
 
 * add cp2k_pdos tool

README.md

@@ -7,6 +7,7 @@ Modular CP2K output file parsers, mostly in the form of regular expressions plus
   * `cp2kparse` ... parse CP2K output files (for restart & input files look at the [cp2k-input-tools](https://github.com/cp2k/cp2k-input-tools) project)
   * `xyz_restart_parser` ... when restarts occur during an MD you may end up with duplicated frames in the trajectory, this tool filters them
   * `cp2k_bs2csv` ... convert a CP2K band structure file to multiple (one-per-set) CSV files for easier plotting. There is also an API available if you need to import bandstructure data into your application.
+  * `cp2k_pdos` ... bring CP2Ks PDOS dump into a more CSV-like form for easier plotting/parsing
 
 ## Requirements
 

cp2k_output_tools/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.3.0"
+__version__ = "0.3.1"
 
 __all__ = ["builtin_matchers", "parse_iter"]
 

cp2k_output_tools/scripts/pdos.py

@@ -1,5 +1,8 @@
 """
 Convert the discrete CP2K PDOS points to a smoothed curve using convoluted gaussians.
+
+If you have separate alpha/beta-spin pdos files (spin-unrestricted calculation),
+pass both files as arguments to get one common grid for both of them.
 """
 
 # Copyright (c) 2020 Tiziano Müller <[email protected]>,
@@ -15,7 +18,8 @@
 
 
 HEADER_MATCH = re.compile(
-    r"\# Projected DOS for atomic kind (?P<element>\w+) at iteration step i = \d+, E\(Fermi\) = [ \t]* (?P<Efermi>[^\t ]+) a\.u\."
+    r"\# Projected DOS for (?:atomic kind \w+|list \d+ of \d+ atoms,)"
+    r" at iteration step i = \d+, E\(Fermi\) = [ \t]* (?P<Efermi>[^\t ]+) a\.u\."
 )
 
 # Column indexes, starting from 0
@@ -45,7 +49,7 @@ def cp2k_pdos():
         metavar="<PDOS-file>",
         type=str,
         nargs="+",
-        help="the PDOS file generated by CP2K, specify two (alpha/beta) files for a common grid",
+        help="the PDOS file generated by CP2K, specify two files (alpha/beta) in a spin-unrestricted case",
     )
     parser.add_argument("--sigma", "-s", type=float, default=0.02, help="sigma for the gaussian distribution (default: 0.02)")
     parser.add_argument("--de", "-d", type=float, default=0.001, help="integration step size (default: 0.001)")
@@ -67,7 +71,7 @@ def cp2k_pdos():
                 print(
                     f"The file '{pdosfilename}' does not look like a CP2K PDOS output.\n"
                     "If it is indeed a correct output file, please report an issue at\n"
-                    "    https://github.com/dev-zero/cp2k-tools/issues"
+                    "    https://github.com/cp2k/cp2k-output-tools/issues"
                 )
                 sys.exit(1)
 

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "cp2k-output-tools"
-version = "0.3.0"
+version = "0.3.1"
 description = "Python tools to handle CP2K output files"
 authors = ["Tiziano Müller <[email protected]>"]
 repository = "https://github.com/cp2k/cp2k-output-tools"

tests/test_pdos.py

@@ -10,3 +10,12 @@ def test_pdos(script_runner):
     assert ret.success
     assert "Nr of lines:                  936" in ret.stderr
     assert "Energy_[eV]" in ret.stdout
+
+
+@pytest.mark.script_launch_mode("subprocess")
+def test_pdos_list_of_atoms(script_runner):
+    ret = script_runner.run("cp2k_pdos", str(TEST_DIR / "inputs" / "list-of-atoms.pdos"))
+
+    assert ret.success
+    assert "Nr of lines:                 6142" in ret.stderr
+    assert "Energy_[eV]" in ret.stdout