Merge branch 'release/0.2.0'

.coveragerc

@@ -0,0 +1,2 @@
+[run]
+parallel = True

CHANGELOG.md

@@ -1,3 +1,8 @@
+## [0.2.0] - 2020-05-05
+
+* add cp2k_bs2csv with support for CP2K v8+ and an API
+* add xyz_restart_cleaner
+
 ## [0.1.4] - 2020-04-03
 
 * updated project urls

README.md

@@ -1,8 +1,12 @@
 # cp2k-output-tools
 
-[![Build Status](https://github.com/cp2k/cp2k-output-tools/workflows/tests/badge.svg)](https://github.com/dev-zero/cp2k-output-tools/actions) [![codecov](https://codecov.io/gh/dev-zero/cp2k-output-tools/branch/develop/graph/badge.svg)](https://codecov.io/gh/dev-zero/cp2k-output-tools) [![PyPI](https://img.shields.io/pypi/pyversions/cp2k-output-tools)](https://pypi.org/project/cp2k-output-tools/)
+[![Build Status](https://github.com/cp2k/cp2k-output-tools/workflows/tests/badge.svg)](https://github.com/cp2k/cp2k-output-tools/actions) [![codecov](https://codecov.io/gh/cp2k/cp2k-output-tools/branch/develop/graph/badge.svg)](https://codecov.io/gh/cp2k/cp2k-output-tools) [![PyPI](https://img.shields.io/pypi/pyversions/cp2k-output-tools)](https://pypi.org/project/cp2k-output-tools/)
 
-Modular CP2K output file parsers, mostly in the form of regular expressions.
+Modular CP2K output file parsers, mostly in the form of regular expressions plus other tools to mangle various CP2K output:
+
+  * `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.
 
 ## Requirements
 
@@ -12,7 +16,7 @@ Modular CP2K output file parsers, mostly in the form of regular expressions.
 For development: https://poetry.eustace.io/ https://pytest.org/
 
 
-## Usage
+## Usage: cp2kparse
 
 There is a simple command-line interface `cp2kparse`:
 
@@ -493,6 +497,14 @@ with open("calc.out", "r") as fhandle:
         print(match.values)
 ```
 
+## Usage: xyz_restart_cleaner
+
+```console
+$ xyz_restart_cleaner orig_trajectory.xyz new_trajectory.xyz
+found restart point @1, dropping 1 frames, flushing 1
+flushing remaining 2 frames
+```
+
 ## Development
 
 ```console

cp2k_output_tools/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.1.4"
+__version__ = "0.2.0"
 
 __all__ = ["builtin_matchers", "parse_iter"]
 

cp2k_output_tools/bandstructure.py

@@ -0,0 +1,192 @@
+"""
+Convert the CP2K band structure output to CSV files
+"""
+
+__all__ = ["SpecialPoint", "Point", "set_gen"]
+
+import re
+import argparse
+from dataclasses import dataclass
+from typing import List, Optional
+import itertools
+
+
+@dataclass
+class SpecialPoint:
+    number: int
+    name: str
+    a: float
+    b: float
+    c: float
+
+
+@dataclass
+class Point:
+    a: float
+    b: float
+    c: float
+    bands: List[float]
+    spin: int
+    weight: Optional[float] = None
+
+
+SET_MATCH = re.compile(
+    r"""
+[ ]*
+  SET: [ ]* (?P<setnr>\d+) [ ]*
+  TOTAL [ ] POINTS: [ ]* (?P<totalpoints>\d+) [ ]*
+  \n
+(?P<content>
+  [\s\S]*?(?=\n.*?[ ] SET|$)  # match everything until next 'SET' or EOL
+)
+""",
+    re.VERBOSE,
+)
+
+SPOINTS_MATCH = re.compile(
+    r"""
+[ ]*
+  POINT [ ]+ (?P<number>\d+) [ ]+ (?P<name>\S+) [ ]+ (?P<a>\S+) [ ]+ (?P<b>\S+) [ ]+ (?P<c>\S+)
+""",
+    re.VERBOSE,
+)
+
+POINTS_MATCH = re.compile(
+    r"""
+[ ]*
+  Nr\. [ ]+ (?P<nr>\d+) [ ]+
+  Spin [ ]+ (?P<spin>\d+) [ ]+
+  K-Point [ ]+ (?P<a>\S+) [ ]+ (?P<b>\S+) [ ]+ (?P<c>\S+) [ ]*
+  \n
+[ ]* (?P<npoints>\d+) [ ]* \n
+(?P<bands>
+  [\s\S]*?(?=\n.*?[ ] Nr|$)  # match everything until next 'Nr.' or EOL
+)
+""",
+    re.VERBOSE,
+)
+
+
+def _specialpoints_gen(content):
+    for match in SPOINTS_MATCH.finditer(content):
+        yield SpecialPoint(int(match["number"]), match["name"], float(match["a"]), float(match["b"]), float(match["c"]))
+
+
+def _points_gen(content):
+    for match in POINTS_MATCH.finditer(content):
+        yield Point(
+            a=float(match["a"]),
+            b=float(match["b"]),
+            c=float(match["c"]),
+            bands=[float(v) for v in match["bands"].split()],
+            spin=int(match["spin"]),
+        )
+
+
+SET_MATCH8 = re.compile(
+    r"""
+\#\ Set\ (?P<setnr>\d+):\ \d+\ special\ points,\ (?P<totalpoints>\d+)\ k-points,\ \d+\ bands \s*
+(?P<content>
+  [\s\S]*?(?=\n.*?\#\ Set|$)  # match everything until next 'SET' or EOL
+)
+""",
+    re.VERBOSE,
+)
+
+
+SPOINTS_MATCH8 = re.compile(
+    r"""
+\#\s+ Special\ point\ (?P<number>\d+) \s+ (?P<a>\S+) \s+ (?P<b>\S+) \s+ (?P<c>\S+) \s+ (?P<name>\S+)
+""",
+    re.VERBOSE,
+)
+
+
+POINTS_MATCH8 = re.compile(
+    r"""
+\#\ \ Point\ (?P<nr>\d+)\s+ Spin\ (?P<spin>\d+): \s+ (?P<a>\S+) \s+ (?P<b>\S+) \s+ (?P<c>\S+) [ ]* ((?P<weight>\S+) [ ]*)? \n
+\#\ \ \ Band \s+ Energy\ \[eV\] \s+ Occupation \s*
+(?P<bands>
+  [\s\S]*?(?=\n.*?\#\ \ Point|$)  # match everything until next '# Point' or EOL
+)
+""",
+    re.VERBOSE,
+)
+
+
+def _points_gen8(content):
+    for match in POINTS_MATCH8.finditer(content):
+        try:
+            weight = float(match["weight"])
+        except TypeError:
+            weight = None
+
+        values = match["bands"].split()
+
+        yield Point(
+            a=float(match["a"]),
+            b=float(match["b"]),
+            c=float(match["c"]),
+            bands=[float(v) for v in values[1::3]],
+            weight=weight,
+            spin=int(match["spin"]),
+        )
+
+
+def _specialpoints_gen8(content):
+    for match in SPOINTS_MATCH8.finditer(content):
+        yield SpecialPoint(int(match["number"]), match["name"], float(match["a"]), float(match["b"]), float(match["c"]))
+
+
+def set_gen(content):
+    # try with the CP2K+8+ regex first
+    matchiter = SET_MATCH8.finditer(content)
+    specialpoints_gen = _specialpoints_gen8
+    points_gen = _points_gen8
+
+    try:
+        peek = next(matchiter)
+        matchiter = itertools.chain([peek], matchiter)
+    except StopIteration:
+        # if nothing could be found, fallback to the older format
+        matchiter = SET_MATCH.finditer(content)
+        specialpoints_gen = _specialpoints_gen
+        points_gen = _points_gen
+
+    for match in matchiter:
+        yield (int(match["setnr"]), int(match["totalpoints"]), specialpoints_gen(match["content"]), points_gen(match["content"]))
+
+
+def cp2k_bs2csv():
+    parser = argparse.ArgumentParser(
+        description="""
+    Convert the input from the given input file handle and write
+    CSV output files based on the given pattern.
+    """,
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+    parser.add_argument(
+        "bsfile", metavar="<bandstructure-file>", type=argparse.FileType("r"), help="the band structure file generated by CP2K"
+    )
+    parser.add_argument(
+        "-p", "--output-pattern", help="The output pattern for the different set files", default="{bsfile.name}.set-{setnr}.csv"
+    )
+    args = parser.parse_args()
+
+    content = args.bsfile.read()
+
+    for setnr, totalpoints, specialpoints, points in set_gen(content):
+        filename = args.output_pattern.format(bsfile=args.bsfile, setnr=setnr)
+
+        with open(filename, "w") as csvout:
+            print(f"writing point set {filename} (total number of k-points: {totalpoints})")
+            print("with the following special points:")
+
+            for point in specialpoints:
+                print(f"  {point.name:>8}: {point.a:10.8f} / {point.b:10.8f} / {point.c:10.8f}")
+
+            for point in points:
+                csvout.write(f"{point.a:10.8f} {point.b:10.8f} {point.c:10.8f}")
+                for value in point.bands:
+                    csvout.write(f" {value:10.8f}")
+                csvout.write("\n")