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05fa033
Trivial external engine to create example.
dwhswenson Feb 4, 2015
604cee7
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Mar 19, 2015
8e50086
Little Makefile for the test external engine
dwhswenson Mar 19, 2015
1511664
Start on the external_engine.py
dwhswenson Mar 19, 2015
f25fdfa
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Mar 29, 2015
8d1597e
Skeleton of tests for external engine
dwhswenson Mar 29, 2015
c653573
More organization work on external_engine
dwhswenson Mar 30, 2015
4efb9ba
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Mar 31, 2015
0ddfff2
Engine starts and stops correctly.
dwhswenson Apr 1, 2015
938a89e
Start some docs on external_engine
dwhswenson Apr 2, 2015
1ecbd35
Draft read_frame_from_file
dwhswenson Apr 2, 2015
9ee153d
Working read_file_from_frame and tests
dwhswenson Apr 2, 2015
c975d6c
External engine passes its test suite.
dwhswenson Apr 2, 2015
699086e
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Apr 3, 2015
e5863f9
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Apr 8, 2015
dede53b
More docs on dynamics engine API
dwhswenson Apr 24, 2015
f988b00
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Apr 24, 2015
10de799
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson May 28, 2015
f498d96
returned psutils to reqs
dwhswenson May 28, 2015
e2ff3e2
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Jun 23, 2015
11eba04
Fixes for long-ago changes in other PRs
dwhswenson Jun 23, 2015
59ac806
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Nov 2, 2015
f9d7dc9
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Apr 11, 2016
7cfa0e8
Add psutil to conda recipe
dwhswenson Apr 11, 2016
b8610cc
Move external engine into engines/
dwhswenson Apr 11, 2016
f6ac4cc
Fixes for external engine with new dynamics engine
dwhswenson Apr 11, 2016
86563ed
External toy engine now has velocities & positions
dwhswenson Apr 22, 2016
fab66f8
Implement write_frame_to_file for toy external
dwhswenson Apr 22, 2016
3648deb
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson May 4, 2016
abbb439
Draft of shooting move test
dwhswenson May 4, 2016
d9b6f1a
Shooting-based test of external engine
dwhswenson May 4, 2016
a7796c7
Automatic sleep optimization works beautifully!
dwhswenson May 11, 2016
360f749
Move ext_eng tests to tests/ dir, restructure eng/
dwhswenson May 13, 2016
d165a9e
Remove test comments
dwhswenson May 13, 2016
8376503
Fix test to be not zombie, instead of running
dwhswenson May 13, 2016
d031c57
More docs. Coverage exclusions.
dwhswenson May 13, 2016
2886eff
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Jun 17, 2016
0816b57
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Jul 7, 2016
ec4178c
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Aug 1, 2016
f9e974d
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Aug 2, 2016
7bb4828
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Aug 3, 2016
e66fbce
Seems to fix the problem.... weird
dwhswenson Aug 3, 2016
7d1fab1
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Aug 7, 2016
670ffcd
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Sep 1, 2016
9ab6509
Fix external engine test for removed generate_fwd
dwhswenson Sep 1, 2016
add9d26
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Sep 13, 2016
9ec757f
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Sep 30, 2016
a49a885
Seems to fix local tests
dwhswenson Oct 2, 2016
030d89d
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Oct 3, 2016
f766bfb
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Nov 2, 2016
4bbf62f
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Dec 2, 2016
d7b15de
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Jan 17, 2017
7522a33
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Mar 21, 2017
4fd979b
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson May 11, 2017
44fd122
whitespace cleanup
dwhswenson May 16, 2017
83d7c77
ExternalEngine.prepare(); and some cleanup
dwhswenson May 30, 2017
292fc2d
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson May 30, 2017
d3b9258
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Jul 3, 2017
364cb23
Fix for bad merge decision
dwhswenson Jul 3, 2017
f362f66
Fix import for Py3
dwhswenson Jul 3, 2017
4e393f0
Use test_helpers.assert_items_equal
dwhswenson Jul 3, 2017
76970c3
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Sep 6, 2017
6f7d887
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Oct 2, 2017
c1d5b4e
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Nov 12, 2017
a54ea99
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Dec 9, 2017
ea159d7
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Dec 17, 2017
10759c8
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Jan 1, 2018
2920d95
Update microtest.py for (long-ago) changed API
dwhswenson Jan 18, 2018
4688841
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Mar 13, 2019
a650524
Fix external engine tests for pytest
dwhswenson Mar 20, 2019
694a462
correct name for pytest module-level setup
dwhswenson Mar 20, 2019
0ccbb28
Update (most of) indirect engine API docs
dwhswenson Mar 24, 2019
158e4b5
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson Mar 25, 2019
74c195f
Merge remote-tracking branch 'upstream/master' into external_engine
dwhswenson May 1, 2019
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whitespace cleanup
  • Loading branch information
dwhswenson committed May 16, 2017
commit 44fd12201574e21fde154b10dad3de9e69b3458e
13 changes: 5 additions & 8 deletions openpathsampling/engines/external_engine.py
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@

class ExternalEngine(DynamicsEngine):
"""
Generic object to handle arbitrary external engines.
Generic object to handle arbitrary external engines.

Typically, this will be subclassed for any given engine. As written, it
will work with the trivial `engine.c` developed for testing purposes.
Expand Down Expand Up @@ -79,7 +79,7 @@ def generate_next_frame(self):
else: # pragma: no cover
raise RuntimeError("Strange return value from read_next_frame_from_file")
if self.auto_optimize_sleep and self.n_frames_since_start > 0:
self.sleep_ms = ((now - self.start_time) /
self.sleep_ms = ((now - self.start_time) /
self.n_frames_since_start) * 1000.0
return self.current_snapshot

Expand Down Expand Up @@ -112,15 +112,15 @@ def stop(self, trajectory):
# FROM HERE ARE THE FUNCTIONS TO OVERRIDE IN SUBCLASSES:
def read_frame_from_file(self, filename, frame_num):
"""Reads given frame number from file, and returns snapshot.

If no frame is available, returns None. If the frame appears to be
partially written, returns string "partial".
"""
# under most circumstances, start with linecache.checkcache and
# setting the value of the first line
linecache.checkcache(filename)
first_line = frame_num + 1

# create a snapshot out of lines starting with first_line... if
# nothing exists, linecache returns '', so we return None.
# Otherwise, try to make a snapshot and return "partial" if we fail
Expand Down Expand Up @@ -151,7 +151,7 @@ def write_frame_to_file(self, filename, snapshot, mode="a"):

def who_to_kill(self):
"""Returns psutil.Process object to send kill signal to.

Might override to send kill signal to a process other than the one
directly spawned above (e.g., when launching parallel runs)
"""
Expand All @@ -177,6 +177,3 @@ def engine_command(self):
engine_path = "engine"
return (engine_path + " " + str(self.engine_sleep)
+ " " + str(self.output_file) + " " + str(self.input_file))